Index: /issm/branches/trunk-dlcheng-ASE/Makefile.am =================================================================== --- /issm/branches/trunk-dlcheng-ASE/Makefile.am (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/Makefile.am (revision 27955) @@ -0,0 +1,5 @@ +EXTRA_DIST = reconf scripts test m4 examples cron etc doc packages contributors.txt +SUBDIRS = src +bin_SCRIPTS= README.rtf + +ACLOCAL_AMFLAGS = -I m4 Index: /issm/branches/trunk-dlcheng-ASE/README =================================================================== --- /issm/branches/trunk-dlcheng-ASE/README (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/README (revision 27955) @@ -0,0 +1,45 @@ +------------------------------------------------------------------------------ + +ISSM +Ice Sheet System Modeling: a framework for modeling ice flow on ice sheet/ice shelf +systems using Finite Elemenent Analysis, and parallel technologies. + +Email: issm@jpl.nasa.gov +Website: http://issm.jpl.nasa.gov/ + +------------------------------------------------------------------------------ + +License + +ISSM is California Institute of Technology Copyright, Distributed under BSD Three Clause License. + + +Copyright (c) 2002-2018, California Institute of Technology. +All rights reserved. Based on Government Sponsored Research under contracts +NAS7-1407 and/or NAS7-03001. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. +3. Neither the name of the California Institute of Technology (Caltech), + its operating division the Jet Propulsion Laboratory (JPL), the National + Aeronautics and Space Administration (NASA), nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE CALIFORNIA INSTITUTE OF TECHNOLOGY BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +------------------------------------------------------------------------------ Index: /issm/branches/trunk-dlcheng-ASE/configure.ac =================================================================== --- /issm/branches/trunk-dlcheng-ASE/configure.ac (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/configure.ac (revision 27955) @@ -0,0 +1,50 @@ +# Process this file with autoconf to produce a configure script. + +#AUTOCONF +AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[4.23],[https://issm.ess.uci.edu/forum/],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_CONFIG_AUX_DIR([./aux-config]) # Put config files in aux-config +AC_CONFIG_MACRO_DIR([m4]) # m4 macros are located in m4 +m4_include([m4/issm_options.m4]) + +#print header +AC_MSG_NOTICE(============================================================================) +AC_MSG_NOTICE(= AC_PACKAGE_NAME AC_PACKAGE_VERSION configuration =) +AC_MSG_NOTICE(============================================================================) + +#Determine System type and OS +AC_CANONICAL_TARGET + +#Compilers +AC_PROG_CC([icc cl icl gcc]) +AC_PROG_CPP +AC_PROG_CXX([icpc cl icl g++]) +AC_PROG_F77([ifort g77 gfortran]) +AC_PROG_FC([ifort gfortran]) + +#AUTOMAKE +#Initialize automake and declare foreign so that we don't need a ChangeLog, INSTALL, etc +AM_INIT_AUTOMAKE([foreign]) +AC_CONFIG_HEADERS([./config.h]) # Config file must be config.h +AM_SILENT_RULES([yes]) # Reduce compilation and linking output (comment this line out or set value to "no" for verbose output) +AM_PROG_AR + +#Libtool +LT_INIT([win32-dll]) + +#Run issm_options.m4 +ISSM_OPTIONS + +#List all Makefiles +AC_CONFIG_FILES([ + Makefile + src/Makefile + src/c/Makefile + src/wrappers/Makefile + src/wrappers/python/Makefile + src/wrappers/matlab/Makefile + src/wrappers/javascript/Makefile + src/m/Makefile +]) + +#End of configure.ac +AC_OUTPUT Index: /issm/branches/trunk-dlcheng-ASE/etc/environment.csh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/etc/environment.csh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/etc/environment.csh (revision 27955) @@ -0,0 +1,247 @@ +# Modifies path-related envrionment variables based on which external packages +# have been installed. +# +# ISSM_DIR and ISSM_ARCH should have been defined already in your shell +# settings file (i.e. .bashrc, .cshrc). +# +# TODO: +# - Condition all path modifications on existence of external package 'install' +# directory +# + +# Silence `: no match` +set nonomatch=1 + +setenv PATH "{$PATH}:{$ISSM_DIR}/aux-config" +setenv PATH "{$PATH}:{$ISSM_DIR}/scripts" + +set ISSM_EXT_DIR="{$ISSM_DIR}/externalpackages" # Redefine this constant if externalpackages are installed to a different directory + +######################### +# Command-line utilities +######################### +set SSH_ROOT="{$ISSM_EXT_DIR}/ssh" +if ( -d {$SSH_ROOT} ) then + setenv PATH "{$PATH}:{$SSH_ROOT}" +endif + +############################# +# Build systems +############################# +set AUTOTOOLS_ROOT="{$ISSM_EXT_DIR}/autotools/install" +setenv PATH "{$AUTOTOOLS_ROOT}/bin:{$PATH}" + +set CMAKE_ROOT="{$ISSM_EXT_DIR}/cmake/install" +setenv PATH "{$CMAKE_ROOT}/bin:{$PATH}" + +############################# +# Libraries / binaries +############################# +set MPI_ROOT="{$ISSM_EXT_DIR}/mpich/install" +if ( -d {$MPI_ROOT} ) then + setenv MPI_DIR {$MPI_ROOT} + setenv MPI_HOME {$MPI_ROOT} # Used in installation of Dakota + setenv MPI_INC_DIR {$MPI_ROOT}/include + setenv PATH "{$MPI_ROOT}/bin:{$PATH}" + setenv CPATH "{$MPI_ROOT}/include:{$CPATH}" + setenv LD_LIBRARY_PATH "{$LD_LIBRARY_PATH}:{$MPI_ROOT}/lib" +endif + +# NOTE: Check *must* come before PETSc as we prefer packages installed via +# PETSc +# +set ZLIB_ROOT="{$ISSM_EXT_DIR}/zlib/install" +if ( -d {$ZLIB_ROOT} ) then + setenv ZLIB_ROOT {$ZLIB_ROOT} # Used in installation of NetCDF, GDAL, GMT + setenv LD_LIBRARY_PATH "{$LD_LIBRARY_PATH}:{$LD_LIBRARY_PATH}/lib" +endif + +set PETSC_ROOT="{$ISSM_EXT_DIR}/petsc/install" +if ( -d {$PETSC_ROOT} ) then + setenv PETSC_ROOT {$PETSC_ROOT} + setenv LD_LIBRARY_PATH {$PETSC_ROOT}/lib:{$LD_LIBRARY_PATH} + + # In case we have installed certain external packages via PETSc + # + + # BLAS + if ( `find {$PETSC_ROOT}/lib -name libblas.*` != "" || `find {$PETSC_ROOT}/lib -name libfblas.*` != "" ) then + setenv BLAS_ROOT "{$PETSC_ROOT}" # Used in installation of Dakota, GMT + endif + + # HDF5 + if ( `find {$PETSC_ROOT}/lib -name libhdf5.*` != "" ) then + setenv HDF5_ROOT "{$PETSC_ROOT}" # Used in installation of NetCDF, GDAL + setenv CPATH {$CPATH}:{$PETSC_ROOT}/include + setenv LIBRARY_PATH {$LIBRARY_PATH}:{$PETSC_ROOT}/lib + setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:{$PETSC_ROOT}/lib + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$PETSC_ROOT}/lib + endif + + # LAPACK + if ( `find {$PETSC_ROOT}/lib -name liblapack.*` != "" || `find {$PETSC_ROOT}/lib -name libflapack.*` != "" ) then + setenv LAPACK_ROOT "{$PETSC_ROOT}" # Used in installation of Dakota, GMT + endif + + # METIS + if ( `find {$PETSC_ROOT}/lib -name libmetis.*` != "" ) then + setenv METIS_ROOT "{$PETSC_ROOT}" # Used in installation of Gmsh + endif + + # MPICH + if ( -f "{$PETSC_ROOT}/bin/mpiexec" ) then + set MPI_ROOT={$PETSC_ROOT} + setenv MPI_DIR {$MPI_ROOT} + setenv MPI_HOME {$MPI_ROOT} # Used in installation of Dakota + setenv MPI_INC_DIR {$MPI_ROOT}/include + setenv PATH {$MPI_ROOT}/bin:{$PATH} + setenv CPATH {$MPI_ROOT}/include:{$CPATH} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$MPI_ROOT}/lib + endif + + # ZLIB + if ( `find {$PETSC_ROOT}/lib -name libz.*` != "" ) then + setenv ZLIB_ROOT "{$PETSC_ROOT}" # Used in installation of NetCDF, GDAL + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$PETSC_ROOT}/lib + endif +endif + +set SCOTCH_ROOT="{$ISSM_EXT_DIR}/scotch/install" +if ( -d {$SCOTCH_ROOT} ) then + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$SCOTCH_ROOT}/lib +endif + +set SLEPC_ROOT="{$ISSM_EXT_DIR}/slepc/install" +if ( -d {$SLEPC_ROOT} ) then + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$SLEPC_ROOT}/lib +endif + +set TAO_ROOT="{$ISSM_EXT_DIR}/tao/install" +if ( -d {$TAO_ROOT} ) then + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$TAO_ROOT}/lib +endif + +set DAKOTA_ROOT="{$ISSM_EXT_DIR}/dakota/install" +if ( -d {$DAKOTA_ROOT} ) then + setenv PATH {$PATH}:{$DAKOTA_ROOT}/bin + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$DAKOTA_ROOT}/lib + setenv DYLD_LIBRARY_PATH {$DAKOTA_ROOT}/lib:{$DYLD_LIBRARY_PATH} +endif + +set MERCURIAL_ROOT="{$ISSM_EXT_DIR}/mercurial/install" +if ( -d {$MERCURIAL_ROOT} ) then + setenv PYTHONPATH {$PYTHONPATH}:{$MERCURIAL_ROOT}/mercurial/pure + setenv PATH {$PATH}:{$MERCURIAL_ROOT} +endif + +set BOOST_ROOT="{$ISSM_EXT_DIR}/boost/install" +if ( -d {$BOOST_ROOT} ) then + setenv BOOST_ROOT {$BOOST_ROOT} # Used in installation of Dakota + setenv BOOST_DIR {$BOOST_ROOT} + setenv BOOSTROOT {$BOOST_ROOT} + setenv LIBRARY_PATH {$BOOST_ROOT}/lib:{$LIBRARY_PATH} + setenv LD_LIBRARY_PATH {$BOOST_ROOT}/lib:{$LD_LIBRARY_PATH} + setenv DYLD_LIBRARY_PATH {$BOOST_ROOT}/lib:{$DYLD_LIBRARY_PATH} + setenv PATH {$BOOST_ROOT}/bin:{$PATH} +endif + +set GSL_ROOT="{$ISSM_EXT_DIR}/gsl/install" +if ( -d {$GSL_ROOT} ) then + setenv GSL_HOME {$GSL_ROOT} # Used in installation of Dakota + setenv GSL_ROOT {$GSL_ROOT} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GSL_ROOT}/lib + setenv DYLD_LIBRARY_PATH {$GSL_ROOT}/lib:{$DYLD_LIBRARY_PATH} +endif + +set NETCDF_ROOT="{$ISSM_EXT_DIR}/netcdf/install" +if ( -d {$NETCDF_ROOT} ) then + setenv NETCDF_ROOT "{$NETCDF_ROOT}" # Used in installation of GDAL, GMT + setenv PATH {$PATH}:{$NETCDF_ROOT}/bin + setenv CPATH {$CPATH}:{$NETCDF_ROOT}/include + setenv LIBRARY_PATH {$LIBRARY_PATH}:{$NETCDF_ROOT}/lib + setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:{$NETCDF_ROOT}/lib + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$NETCDF_ROOT}/lib +endif + +set CURL_ROOT="{$ISSM_EXT_DIR}/curl/install" +if ( -d {$CURL_ROOT} ) then + setenv CURL_ROOT "{$CURL_ROOT}" # Used in installation of NetCDF, GDAL, GMT + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$CURL_ROOT}/lib + setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:{$CURL_ROOT}/lib + setenv PATH {$PATH}:{$CURL_ROOT}/bin +endif + +set HDF5_ROOT="{$ISSM_EXT_DIR}/hdf5/install" +if ( -d {$HDF5_ROOT} ) then + setenv HDF5_ROOT "{$HDF5_ROOT}" # Used in installation of NetCDF, GDAL + setenv CPATH {$CPATH}:{$HDF5_ROOT}/include + setenv LIBRARY_PATH {$LIBRARY_PATH}:{$HDF5_ROOT}/lib + setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:{$HDF5_ROOT}/lib + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$HDF5_ROOT}/lib +endif + +set SQLITE_ROOT="{$ISSM_EXT_DIR}/sqlite/install" +if ( -d {$SQLITE_ROOT} ) then + setenv PATH {$PATH}:{$SQLITE_ROOT}/bin + setenv LIBRARY_PATH {$LIBRARY_PATH}:{$SQLITE_ROOT}/lib + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$SQLITE_ROOT}/lib +endif + +set PROJ_ROOT="{$ISSM_EXT_DIR}/proj/install" +if ( -d {$PROJ_ROOT} ) then + setenv PROJ_ROOT "${PROJ_ROOT}" # Used in installation of GDAL + setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:{$PROJ_ROOT}/lib + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$PROJ_ROOT}/lib +endif + +set GDAL_ROOT="{$ISSM_EXT_DIR}/gdal/install" +if ( -d {$GDAL_ROOT} ) then + setenv GDAL_ROOT "{$GDAL_ROOT}" # Used in installation of GMT + setenv PATH {$GDAL_ROOT}/bin:{$PATH} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GDAL_ROOT}/lib +endif + +set GSHHG_ROOT="{$ISSM_EXT_DIR}/gshhg/install" +if ( -d {$GSHHG_ROOT} ) then + setenv GSHHG_ROOT "{$GSHHG_ROOT}" # Used in installation of GMT +endif + +set GMT_ROOT="{$ISSM_EXT_DIR}/gmt/install" +if ( -d {$GMT_ROOT} ) then + setenv PATH {$GMT_ROOT}/bin:{$PATH} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GMT_ROOT}/lib + setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:{$GMT_ROOT}/lib +endif + +set GMSH_ROOT="{$ISSM_EXT_DIR}/gmsh/install" +if ( -d {$GMSH_ROOT} ) then + setenv PATH {$GMSH_ROOT}/bin:{$PATH} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GMSH_ROOT}/lib + setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:{$GMSH_ROOT}/lib +endif + +set TRIANGLE_ROOT="{$ISSM_EXT_DIR}/triangle/install" +if ( -d {$TRIANGLE_ROOT} ) then + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$TRIANGLE_ROOT}/lib + setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:{$TRIANGLE_ROOT}/lib +endif + +set YAMS_ROOT="{$ISSM_EXT_DIR}/yams/install" +if ( -d {$YAMS_ROOT} ) then + setenv PATH {$PATH}:{$YAMS_ROOT} +endif + +set VALGRIND_ROOT="{$ISSM_EXT_DIR}/valgrind/install" +if ( -d {$VALGRIND_ROOT} ) then + setenv PATH {$VALGRIND_ROOT}/bin:{$PATH} +endif + +set DOXYGEN_ROOT="{$ISSM_EXT_DIR}/doxygen/install" +if ( -d {$DOXYGEN_ROOT} ) then + setenv PATH {$DOXYGEN_ROOT}/bin:{$PATH} +endif + +set SHELL2JUNIT_ROOT="{$ISSM_EXT_DIR}/shell2junit/install" +if ( -d {$SHELL2JUNIT_ROOT} ) then + setenv PATH {$PATH}:{$SHELL2JUNIT_ROOT}/install +endif Index: /issm/branches/trunk-dlcheng-ASE/etc/environment.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/etc/environment.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/etc/environment.sh (revision 27955) @@ -0,0 +1,688 @@ +# Modifies path-related environment variables based on which external packages +# have been installed. +# +# ISSM_DIR and ISSM_ARCH should have been defined already in your shell +# settings file (i.e. .bashrc, .cshrc). +# +# TODO: +# - Condition all path modifications on existence of external package 'install' +# directory +# + +if [[ -n "$ZSH_VERSION" ]]; then + # Silence `zsh: no matches found: ` + setopt +o nomatch 1> /dev/null 2>&1 +fi + +## Functions +# +c_include_path_append(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${C_INCLUDE_PATH}" ]; then + export C_INCLUDE_PATH="${1}" + elif [[ ":${C_INCLUDE_PATH}:" != *":${1}:"* ]]; then + export C_INCLUDE_PATH="${C_INCLUDE_PATH}:${1}" + fi + fi +} #}}} +c_include_path_prepend(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${C_INCLUDE_PATH}" ]; then + export C_INCLUDE_PATH="${1}" + elif [[ ":${C_INCLUDE_PATH}:" != *":${1}:"* ]]; then + export C_INCLUDE_PATH="${1}:${C_INCLUDE_PATH}" + fi + fi +} #}}} + +cpath_append(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${CPATH}" ]; then + export CPATH="${1}" + elif [[ ":${CPATH}:" != *":${1}:"* ]]; then + export CPATH="${CPATH}:${1}" + fi + fi +} #}}} +cpath_prepend(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${CPATH}" ]; then + export CPATH="${1}" + elif [[ ":${CPATH}:" != *":${1}:"* ]]; then + export CPATH="${1}:${CPATH}" + fi + fi +} #}}} + +cplus_include_path_append(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${CPLUS_INCLUDE_PATH}" ]; then + export CPLUS_INCLUDE_PATH="${1}" + elif [[ ":${CPLUS_INCLUDE_PATH}:" != *":${1}:"* ]]; then + export CPLUS_INCLUDE_PATH="${CPLUS_INCLUDE_PATH}:${1}" + fi + fi +} #}}} +cplus_include_path_prepend(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${CPLUS_INCLUDE_PATH}" ]; then + export CPLUS_INCLUDE_PATH="${1}" + elif [[ ":${CPLUS_INCLUDE_PATH}:" != *":${1}:"* ]]; then + export CPLUS_INCLUDE_PATH="${1}:${CPLUS_INCLUDE_PATH}" + fi + fi +} #}}} + +dyld_library_path_append(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${DYLD_LIBRARY_PATH}" ]; then + export DYLD_LIBRARY_PATH="${1}" + elif [[ ":${DYLD_LIBRARY_PATH}:" != *":${1}:"* ]]; then + export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}:${1}" + fi + if [ -z "${LD_RUN_PATH}" ]; then + export LD_RUN_PATH=$1 + elif [[ ":${LD_RUN_PATH}:" != *":${1}:"* ]]; then + export LD_RUN_PATH="${LD_RUN_PATH}:${1}" + fi + fi +} #}}} +dyld_library_path_prepend(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${DYLD_LIBRARY_PATH}" ]; then + export DYLD_LIBRARY_PATH="${1}" + elif [[ ":${DYLD_LIBRARY_PATH}:" != *":${1}:"* ]]; then + export DYLD_LIBRARY_PATH="${1}:${DYLD_LIBRARY_PATH}" + fi + if [ -z "${LD_RUN_PATH}" ]; then + export LD_RUN_PATH="${1}" + elif [[ ":${LD_RUN_PATH}:" != *":${1}:"* ]]; then + export LD_RUN_PATH="${1}:${LD_RUN_PATH}" + fi + fi +} #}}} + +ld_library_path_append(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${LD_LIBRARY_PATH}" ]; then + export LD_LIBRARY_PATH="${1}" + elif [[ ":${LD_LIBRARY_PATH}:" != *":${1}:"* ]]; then + export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${1}" + fi + if [ -z "${LD_RUN_PATH}" ]; then + export LD_RUN_PATH="${1}" + elif [[ ":${LD_RUN_PATH}:" != *":$1:"* ]]; then + export LD_RUN_PATH="${LD_RUN_PATH}:${1}" + fi + fi +} #}}} +ld_library_path_prepend(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${LD_LIBRARY_PATH}" ]; then + export LD_LIBRARY_PATH="${1}" + elif [[ ":${LD_LIBRARY_PATH}:" != *":${1}:"* ]]; then + export LD_LIBRARY_PATH="${1}:${LD_LIBRARY_PATH}" + fi + if [ -z "${LD_RUN_PATH}" ]; then + export LD_RUN_PATH="${1}" + elif [[ ":${LD_RUN_PATH}:" != *":${1}:"* ]]; then + export LD_RUN_PATH="${1}:${LD_RUN_PATH}" + fi + fi +} #}}} + +library_path_append(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${LIBRARY_PATH}" ]; then + export LIBRARY_PATH="${1}" + elif [[ ":${LIBRARY_PATH}:" != *":$1:"* ]]; then + export LIBRARY_PATH="${LIBRARY_PATH}:${1}" + fi + fi +} #}}} +library_path_prepend(){ #{{{ + if [ -d "${1}" ]; then + if [ -z "${LIBRARY_PATH}" ]; then + export LIBRARY_PATH="${1}" + elif [[ ":${LIBRARY_PATH}:" != *":$1:"* ]]; then + export LIBRARY_PATH="${1}:${LIBRARY_PATH}" + fi + fi +} #}}} + +path_append(){ #{{{ + if [ -d "${1}" ] && [[ ":${PATH}:" != *":${1}:"* ]]; then + PATH_IN="${1}" + if [[ "${ISSM_ARCH}" == "cygwin-intel" ]]; then + PATH_IN=`cygpath -u "${1}"` + fi + export PATH="${PATH}:${PATH_IN}" + fi +} #}}} +path_prepend(){ #{{{ + if [ -d "${1}" ] && [[ ":${PATH}:" != *":${1}:"* ]]; then + PATH_IN="${1}" + if [[ "${ISSM_ARCH}" == "cygwin-intel" ]]; then + PATH_IN=`cygpath -u "${1}"` + fi + export PATH="${PATH_IN}:${PATH}" + fi +} #}}} + +path_append "${ISSM_DIR}/aux-config" +path_append "${ISSM_DIR}/scripts" + +# Default path to external packages. Redefine this constant if they are +# installed to a different directory. Alternatively, export it on the command +# line or in a profile initialization file (that is why we check here if it is +# set already). +# +if [ -z "${ISSM_EXT_DIR+x}" ]; then + export ISSM_EXT_DIR="${ISSM_DIR}/externalpackages" +fi + +####################### +# OS-specific handling +####################### + +MINGW=0 +if [[ $(uname -s) == MINGW* ]]; then + MINGW=1 + MSMPI_ROOT="${ISSM_EXT_DIR}/msmpi/install" + if [ -d "${MSMPI_ROOT}" ]; then + export MSMPI_ROOT # Used in installation of ParMETIS, ScaLAPACK + cpath_prepend "${MSMPI_ROOT}/include" + library_path_prepend "${MSMPI_ROOT}/lib" + fi + + MPIEXEC_DIR=$(cygpath -u $(cygpath -ms "/c/Program Files/Microsoft MPI/Bin")) + if [ -d "${MPIEXEC_DIR}" ]; then + export MPIEXEC_DIR + path_append "${MPIEXEC_DIR}" + fi + + path_prepend "${ISSM_DIR}/bin" # Allows dynamic loader to find DLLs +fi + +# Windows compilers +if [[ "${ISSM_ARCH}" == "cygwin-intel" ]]; then + source ${ISSM_DIR}/externalpackages/windows/windows_environment.sh +fi + +######################### +# Command-line utilities +######################### +SSH_ROOT="${ISSM_EXT_DIR}/ssh" +if [ -d "${SSH_ROOT}" ]; then + path_append "${SSH_ROOT}" +fi + +SVN_ROOT="${ISSM_EXT_DIR}/svn/install" +if [ -d "${SVN_ROOT}" ]; then + path_prepend "${SVN_ROOT}/bin" + ld_library_path_append "${SVN_ROOT}/lib" +fi + +GIT_ROOT="${ISSM_EXT_DIR}/git/install" +if [ -d "${GIT_ROOT}" ]; then + path_prepend "${GIT_ROOT}/bin" +fi + +############################# +# Compilers / runtime / SDKs +############################# +export ANDROID_DIR="${ISSM_EXT_DIR}/android" + +export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install" +path_append "$ANDROID_NDK_DIR/arm-linux-android-install/bin" + +export ANDROID_SDK_ROOT="$ANDROID_DIR/android-sdk/install" +path_append "$ANDROID_SDK_ROOT/" + +EMSCRIPTEN_ROOT="${ISSM_EXT_DIR}/emscripten/install" +if [ -d ${EMSCRIPTEN_ROOT} ]; then + export EMSCRIPTEN_ROOT # Used in JavaScript build in installation of GSL, Triangle +fi + +JVM_ROOT="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/" +ld_library_path_append "${JVM_ROOT}" + +############################# +# IDEs +############################# +ECLIPSE_ROOT="${ISSM_EXT_DIR}/eclipse/install" +path_append "${ECLIPSE_ROOT}" + +############################# +# Build systems +############################# +AUTOTOOLS_ROOT="${ISSM_EXT_DIR}/autotools/install" +path_prepend "${AUTOTOOLS_ROOT}/bin" + +CMAKE_ROOT="${ISSM_EXT_DIR}/cmake/install" +path_prepend "${CMAKE_ROOT}/bin" + +GMAKE_ROOT="${ISSM_EXT_DIR}/gmake/install" +path_prepend "${GMAKE_ROOT}/bin" + +############################# +# Packagers +############################# +PACKAGEMAKER_ROOT="${ISSM_EXT_DIR}/packagemaker/install" +path_append "${PACKAGEMAKER_ROOT}" + +############################# +# Libraries / binaries +############################# +MPI_ROOT_TEMP="${ISSM_EXT_DIR}/mpich/install" +if [ -d "${MPI_ROOT_TEMP}" ]; then + export MPI_DIR=${MPI_ROOT_TEMP} + export MPI_HOME=${MPI_ROOT_TEMP} # Used in installation of Dakota + export MPI_INC_DIR="${MPI_ROOT_TEMP}/include" + path_prepend "${MPI_ROOT_TEMP}/bin" + cpath_prepend "${MPI_ROOT_TEMP}/include" + ld_library_path_append "${MPI_ROOT_TEMP}/lib" +fi + +# NOTE: The following checks *must* come before PETSc as we prefer packages +# installed via PETSc +# +BLAS_ROOT="${ISSM_EXT_DIR}/blas/install" +if [ -d "${BLAS_ROOT}" ]; then + export BLAS_ROOT # Used in installation of LAPACK, ScaLAPACK, PETSc + library_path_append "${BLAS_ROOT}/lib" + ld_library_path_append "${BLAS_ROOT}/lib" + + if [[ ${MINGW} -eq 1 ]]; then + path_append "${BLAS_ROOT}/lib" # Allows dynamic loader to find DLLs + fi +fi + +HDF5_ROOT="${ISSM_EXT_DIR}/hdf5/install" +if [ -d "${HDF5_ROOT}" ]; then + export HDF5_ROOT # Used in installation of NetCDF, GDAL + cpath_append "${HDF5_ROOT}/include" + library_path_append "${HDF5_ROOT}/lib" + dyld_library_path_append "${HDF5_ROOT}/lib" + ld_library_path_append "${HDF5_ROOT}/lib" +fi + +LAPACK_ROOT="${ISSM_EXT_DIR}/lapack/install" +if [ -d "${LAPACK_ROOT}" ]; then + export LAPACK_ROOT # Used in installation of ScaLAPACK, MUMPS, PETSc + library_path_append "${LAPACK_ROOT}/lib" + ld_library_path_append "${LAPACK_ROOT}/lib" + + if [[ ${MINGW} -eq 1 ]]; then + path_append "${LAPACK_ROOT}/lib" # Allows dynamic loader to find DLLs + fi + + if ls ${LAPACK_ROOT}/lib/libblas.* 1> /dev/null 2>&1; then + export BLAS_ROOT="${LAPACK_ROOT}" + fi +fi + +METIS_ROOT="${ISSM_EXT_DIR}/metis/install" +if [ -d "${METIS_ROOT}" ]; then + export METIS_ROOT # Used in installation of ParMETIS, Gmsh, PETSc + library_path_prepend "${METIS_ROOT}/lib" + ld_library_path_prepend "${METIS_ROOT}/lib" + + if [[ ${MINGW} -eq 1 ]]; then + path_append "${METIS_ROOT}/lib" # Allows dynamic loader to find DLLs + fi +fi + +MUMPS_ROOT="${ISSM_EXT_DIR}/mumps/install" +if [ -d "${MUMPS_ROOT}" ]; then + export MUMPS_ROOT # Used in installation of PETSc + library_path_append "${MUMPS_ROOT}/lib" + + if [[ ${MINGW} -eq 1 ]]; then + path_append "${MUMPS_ROOT}/lib" # Allows dynamic loader to find DLLs + fi +fi + +PARMETIS_ROOT="${ISSM_EXT_DIR}/parmetis/install" +if [ -d "${PARMETIS_ROOT}" ]; then + export PARMETIS_ROOT # Used in installation of MUMPS, PETSc + library_path_prepend "${PARMETIS_ROOT}/lib" + ld_library_path_prepend "${PARMETIS_ROOT}/lib" + + if [[ ${MINGW} -eq 1 ]]; then + path_append "${PARMETIS_ROOT}/lib" # Allows dynamic loader to find DLLs + fi +fi + +QD_ROOT="${ISSM_EXT_DIR}/qd/install" +if [ -d "${QD_ROOT}" ]; then + export QD_ROOT # Used in installation of MPLAPACK + library_path_prepend "${QD_ROOT}/lib" + ld_library_path_prepend "${QD_ROOT}/lib" +fi + +SCALAPACK_ROOT="${ISSM_EXT_DIR}/scalapack/install" +if [ -d "${SCALAPACK_ROOT}" ]; then + export SCALAPACK_ROOT # Used in installation of MUMPS, PETSc + library_path_append "${SCALAPACK_ROOT}/lib" + + if [[ ${MINGW} -eq 1 ]]; then + path_append "${SCALAPACK_ROOT}/lib" # Allows dynamic loader to find DLLs + fi +fi + +ZLIB_ROOT="${ISSM_EXT_DIR}/zlib/install" +if [ -d "${ZLIB_ROOT}" ]; then + export ZLIB_ROOT # Used in installation of NetCDF, GDAL, GMT + ld_library_path_append "${ZLIB_ROOT}/lib" +fi + +PETSC_ROOT="${ISSM_EXT_DIR}/petsc/install" +if [ -d "${PETSC_ROOT}" ]; then + export PETSC_ROOT # Used in installation of Gmsh + cpath_prepend "${PETSC_ROOT}/include" + library_path_prepend "${PETSC_ROOT}/lib" + ld_library_path_prepend "${PETSC_ROOT}/lib" + + if [[ ${MINGW} -eq 1 ]]; then + path_append "${PETSC_ROOT}/lib" # Allows dynamic loader to find DLLs + fi + + # In case we have installed certain external packages via PETSc + # + + # BLAS + if ls ${PETSC_ROOT}/lib/libblas.* 1> /dev/null 2>&1 || ls ${PETSC_ROOT}/lib/libfblas.* 1> /dev/null 2>&1; then + export BLAS_ROOT="${PETSC_ROOT}" # Used in installation of Dakota, GMT + fi + + # HDF5 + if ls ${PETSC_ROOT}/lib/libhdf5.* 1> /dev/null 2>&1; then + export HDF5_ROOT="${PETSC_ROOT}" # Used in installation of NetCDF, GDAL + cpath_append "${PETSC_ROOT}/include" + library_path_append "${PETSC_ROOT}/lib" + dyld_library_path_append "${PETSC_ROOT}/lib" + ld_library_path_append "${PETSC_ROOT}/lib" + fi + + # LAPACK + if ls ${PETSC_ROOT}/lib/liblapack.* 1> /dev/null 2>&1 || ls ${PETSC_ROOT}/lib/libflapack.* 1> /dev/null 2>&1; then + export LAPACK_ROOT="${PETSC_ROOT}" # Used in installation of Dakota, GMT + fi + + # METIS + if ls ${PETSC_ROOT}/lib/libmetis.* 1> /dev/null 2>&1; then + export METIS_ROOT="${PETSC_ROOT}" # Used in installation of Gmsh + fi + + # MPICH + if [ -f "${PETSC_ROOT}/bin/mpiexec" ]; then + MPI_ROOT=${PETSC_ROOT} + export MPI_DIR=${MPI_ROOT} + export MPI_HOME=${MPI_ROOT} # Used in installation of Dakota + export MPI_INC_DIR="${MPI_ROOT}/include" + path_prepend "${MPI_ROOT}/bin" + cpath_prepend "${MPI_ROOT}/include" + ld_library_path_append "${MPI_ROOT}/lib" + fi + + # ZLIB + if ls ${PETSC_ROOT}/lib/libz.* 1> /dev/null 2>&1; then + export ZLIB_ROOT="${PETSC_ROOT}" # Used in installation of NetCDF, GDAL + ld_library_path_append "${PETSC_ROOT}/lib" + fi +fi + +MPLAPACK_ROOT="${ISSM_EXT_DIR}/mplapack/install" +if [ -d "${MPLAPACK_ROOT}" ]; then + cplus_include_path_prepend "${MPLAPACK_ROOT}/include" + cplus_include_path_prepend "${MPLAPACK_ROOT}/include/mplapack" + library_path_prepend "${MPLAPACK_ROOT}/lib" + ld_library_path_prepend "${MPLAPACK_ROOT}/lib" +fi + +SCOTCH_ROOT="${ISSM_EXT_DIR}/scotch/install" +ld_library_path_append "${SCOTCH_ROOT}/lib" + +SLEPC_ROOT="${ISSM_EXT_DIR}/slepc/install" +ld_library_path_append "${SLEPC_ROOT}/lib" + +TAO_ROOT="${ISSM_EXT_DIR}/tao/install" +ld_library_path_append "${TAO_ROOT}/lib" + +BOOST_ROOT="${ISSM_EXT_DIR}/boost/install" +if [ -d "${BOOST_ROOT}" ]; then + export BOOST_ROOT # Used in installation of Dakota + export BOOST_DIR=${BOOST_ROOT} + export BOOSTROOT=${BOOST_ROOT} + path_append "${BOOST_ROOT}/bin" + library_path_prepend "${BOOST_ROOT}/lib" + ld_library_path_prepend "${BOOST_ROOT}/lib" + dyld_library_path_prepend "${BOOST_ROOT}/lib" +fi + +DAKOTA_ROOT="${ISSM_EXT_DIR}/dakota/install" +if [ -d "${DAKOTA_ROOT}" ]; then + path_append "${DAKOTA_ROOT}/bin" + ld_library_path_prepend "${DAKOTA_ROOT}/lib" + dyld_library_path_prepend "${DAKOTA_ROOT}/lib" +fi + +NCO_ROOT="${ISSM_EXT_DIR}/nco/install/bin" +path_prepend "${NCO_ROOT}/bin" + +CPPCHECK_ROOT="${ISSM_EXT_DIR}/cppcheck/install" +path_append "${CPPCHECK_ROOT}/bin" + +MERCURIAL_ROOT="${ISSM_EXT_DIR}/mercurial/install" +if [ -d "${MERCURIAL_ROOT}" ]; then + export PYTHONPATH="${PYTHONPATH}:${MERCURIAL_ROOT}/mercurial/pure/" + path_append "${MERCURIAL_ROOT}" +fi + +GSL_ROOT="${ISSM_EXT_DIR}/gsl/install" +if [ -d "${GSL_ROOT}" ]; then + export GSL_HOME="${GSL_ROOT}" # Used in installation of Dakota + cpath_prepend "${GSL_ROOT}/include" + ld_library_path_append "${GSL_ROOT}/lib" +fi + +NETCDF_ROOT="${ISSM_EXT_DIR}/netcdf/install" +if [ -d "${NETCDF_ROOT}" ]; then + export NETCDF_ROOT # Used in installation of GDAL, GMT + path_prepend "${NETCDF_ROOT}/bin" + cpath_prepend "${NETCDF_ROOT}/include" + library_path_prepend "${NETCDF_ROOT}/lib" + dyld_library_path_prepend "${NETCDF_ROOT}/lib" + ld_library_path_prepend "${NETCDF_ROOT}/lib" +fi + +NETCDF_CXX_ROOT="${ISSM_EXT_DIR}/netcdf-cxx/install" +if [ -d "${NETCDF_CXX_ROOT}" ]; then + ld_library_path_append "${NETCDF_CXX_ROOT}/lib" +fi + +NETCDF_PYTHON_ROOT="${ISSM_EXT_DIR}/netcdf-python/install" +if [ -d "${NETCDF_PYTHON_ROOT}" ]; then + if [ -d "${NETCDF_PYTHON_ROOT}/lib/python2.7/site-packages" ]; then + ld_library_path_append "${NETCDF_PYTHON_ROOT}/lib/python2.7/site-packages" + fi +fi + +CURL_ROOT="${ISSM_EXT_DIR}/curl/install" +if [ -d "${CURL_ROOT}" ]; then + export CURL_ROOT # Used in installation of NetCDF, GDAL, GMT + cpath_prepend "${CURL_ROOT}/include" + ld_library_path_prepend "${CURL_ROOT}/lib" + dyld_library_path_prepend "${CURL_ROOT}/lib" + path_append "${CURL_ROOT}/bin" +fi + +SQLITE_ROOT="${ISSM_EXT_DIR}/sqlite/install" +if [ -d "${SQLITE_ROOT}" ]; then + export SQLITE_ROOT # Used in installation of GDAL + path_prepend "${SQLITE_ROOT}/bin" + cpath_prepend "${SQLITE_ROOT}/include" + library_path_prepend "${SQLITE_ROOT}/lib" + ld_library_path_prepend "${SQLITE_ROOT}/lib" +fi + +LIBTIFF_ROOT="${ISSM_EXT_DIR}/libtiff/install" +if [ -d "${LIBTIFF_ROOT}" ]; then + dyld_library_path_append "${LIBTIFF_ROOT}/install/libtiff" + ld_library_path_append "${LIBTIFF_ROOT}/install/libtiff" +fi + +PROJ_ROOT="${ISSM_EXT_DIR}/proj/install" +if [ -d "${PROJ_ROOT}" ]; then + export PROJ_ROOT # Used in installation of GDAL + path_append "${PROJ_ROOT}/bin" + dyld_library_path_append "${PROJ_ROOT}/lib" + ld_library_path_append "${PROJ_ROOT}/lib" +fi + +GDAL_ROOT="${ISSM_EXT_DIR}/gdal/install" +if [ -d "${GDAL_ROOT}" ]; then + export GDAL_ROOT # Used in installation of GMT + path_prepend "${GDAL_ROOT}/bin" + ld_library_path_append "${GDAL_ROOT}/lib" +fi + +GSHHG_ROOT="${ISSM_EXT_DIR}/gshhg/install" +if [ -d "${GSHHG_ROOT}" ]; then + export GSHHG_ROOT # Used in installation of GMT +fi + +GMT_ROOT="${ISSM_EXT_DIR}/gmt/install" +if [ -d "${GMT_ROOT}" ]; then + path_prepend "${GMT_ROOT}/bin" + ld_library_path_append "${GMT_ROOT}/lib" + dyld_library_path_append "${GMT_ROOT}/lib" +fi + +GMSH_ROOT="${ISSM_EXT_DIR}/gmsh/install" +if [ -d "${GMSH_ROOT}" ]; then + path_prepend "${GMSH_ROOT}/bin" + ld_library_path_append "${GMSH_ROOT}/lib" + dyld_library_path_append "${GMSH_ROOT}/lib" +fi + +TRIANGLE_ROOT="${ISSM_EXT_DIR}/triangle/install" +if [ -d "${TRIANGLE_ROOT}" ]; then + ld_library_path_append "${TRIANGLE_ROOT}/lib" + dyld_library_path_append "${TRIANGLE_ROOT}/lib" + + if [[ ${MINGW} -eq 1 ]]; then + path_append "${TRIANGLE_ROOT}/lib" # Allows dynamic loader to find DLLs + fi +fi + +ANGELROOT="${ISSM_EXT_DIR}/angel/angel" +if [ -d "${ANGELROOT}" ]; then + export ANGELROOT +fi + +OPENANALYSISROOT="${ISSM_EXT_DIR}/openanalysis/install" +if [ -d "${OPENANALYSISROOT}" ]; then + export OPENANALYSISROOT + ld_library_path_append "${OPENANALYSISROOT}/lib" +fi + +BBFTP_ROOT="${ISSM_EXT_DIR}/bbftp/install" +path_append "${BBFTP_ROOT}/bin" + +ADIC_ROOT="${ISSM_EXT_DIR}/adic/install" +path_append "${ADIC_ROOT}/bin" +ld_library_path_append "${ADIC_ROOT}/lib" + +COLPACK_ROOT="${ISSM_EXT_DIR}/colpack/install" +ld_library_path_append "${COLPACK_ROOT}/lib" + +APPSCAN_ROOT="${ISSM_EXT_DIR}/appscan/install" +path_append "${APPSCAN_ROOT}/bin" + +RATS_ROOT="${ISSM_EXT_DIR}/rats/install" +path_append "${RATS_ROOT}/bin" + +DYSON_ROOT="${ISSM_EXT_DIR}/dyson/" +path_append "${DYSON_ROOT}" + +SHAPELIB_ROOT="${ISSM_EXT_DIR}/shapelib/install" +path_append "${SHAPELIB_ROOT}/exec" + +CCCL_ROOT="${ISSM_EXT_DIR}/cccl/install" +path_append "${CCCL_ROOT}/bin" + +MODELE_ROOT="${ISSM_EXT_DIR}/modelE/install" +path_append "${MODELE_ROOT}/src/exec" + +NCVIEW_ROOT="${ISSM_EXT_DIR}/ncview/install" +path_append "${NCVIEW_ROOT}" + +TCLX_ROOT="${ISSM_EXT_DIR}/tclx/install/lib/tclx8.4" +ld_library_path_append "${TCLX_ROOT}" + +ASPELL_ROOT="${ISSM_EXT_DIR}/aspell/install" +path_append "${ASPELL_ROOT}/bin" + +ESMF_ROOT="${ISSM_EXT_DIR}/esmf/install" +if [ -d "${ESMF_ROOT}" ]; then + path_prepend "${ESMF_ROOT}/bin" + ld_library_path_append "${ESMF_ROOT}/lib/libO/Linux.gfortran.64.mpich.default/" +fi + +CVS_ROOT="${ISSM_EXT_DIR}/cvs/install" +path_prepend "${CVS_ROOT}/bin" + +APR_ROOT="${ISSM_EXT_DIR}/apr/install" +path_append "${APR_ROOT}/bin" +ld_library_path_append "${APR_ROOT}/lib" + +APR_UTIL_ROOT="${ISSM_EXT_DIR}/apr-util/install" +path_prepend "${APR_UTIL_ROOT}/bin" +ld_library_path_append "${APR_UTIL_ROOT}/lib" + +YAMS_ROOT="${ISSM_EXT_DIR}/yams/install" +path_append "${YAMS_ROOT}" + +SWIG_ROOT="${ISSM_EXT_DIR}/swig/install" +path_append "${SWIG_ROOT}" + +INISHELL_ROOT="${ISSM_EXT_DIR}/inishell/install" +path_append "${INISHELL_ROOT}" + +EXPAT_ROOT="${ISSM_EXT_DIR}/expat/install" +ld_library_path_prepend "${EXPAT_ROOT}" +dyld_library_path_prepend "${EXPAT_ROOT}" + +NEOPZ_ROOT="${ISSM_EXT_DIR}/neopz/install" +if [ -d "${NEOPZ_ROOT}" ]; then + export REFPATTERNDIR="${NEOPZ_ROOT}/include/refpatterns" +fi + +XERCESROOT="${ISSM_EXT_DIR}/xerces/install" +if [ -d "${XERCESROOT}" ]; then + export XERCESROOT + export XERCESCROOT="${ISSM_EXT_DIR}/xerces/src" +fi + +XAIFBOOSTERROOT="${ISSM_EXT_DIR}/xaifbooster" +XAIF_ROOT="${XAIFBOOSTERROOT}/xaifBooster" +if [ -d "${XAIF_ROOT}" ]; then + export XAIFBOOSTERROOT + export XAIF_DIR="${XAIF_ROOT}" + export XAIFBOOSTER_HOME="${XAIF_ROOT}" + export PLATFORM="x86-Linux" +fi + +VALGRIND_ROOT="${ISSM_DIR}/externalpackages/valgrind/install" +if [ -d "${VALGRIND_ROOT="${ISSM_DIR}/valgrind/install" +}" ]; then + path_prepend "${VALGRIND_ROOT}/bin" +fi + +DOXYGEN_ROOT="${ISSM_EXT_DIR}/doxygen/install" +path_prepend "${DOXYGEN_ROOT}/bin" + +SHELL2JUNIT_ROOT="${ISSM_EXT_DIR}/shell2junit/install" +path_append "${SHELL2JUNIT_ROOT}" Index: /issm/branches/trunk-dlcheng-ASE/examples/AMR/domain.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/AMR/domain.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/AMR/domain.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:domainoutline +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +0 0 +800000 0 +800000 50000 +0 50000 +0 0 Index: /issm/branches/trunk-dlcheng-ASE/examples/AMR/front.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/AMR/front.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/AMR/front.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:icefront +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +799900 -100 +800100 -100 +800100 50100 +799900 50100 +799900 -100 Index: /issm/branches/trunk-dlcheng-ASE/examples/AMR/mismip.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/AMR/mismip.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/AMR/mismip.par (revision 27955) @@ -0,0 +1,51 @@ +% creating thickness +md.geometry.bed=-100-abs(md.mesh.x)/1000; +md.geometry.base=-90*ones(md.mesh.numberofvertices,1); +md.geometry.surface=10*ones(md.mesh.numberofvertices,1); +md.geometry.thickness=md.geometry.surface-md.geometry.base; +md.mask.ocean_levelset=-1*ones(md.mesh.numberofvertices,1); + +% creating basal drag +md.friction.coefficient=sqrt(10^7)*ones(md.mesh.numberofvertices,1); %q=1. +md.friction.p=3*ones(md.mesh.numberofelements,1); +md.friction.q=zeros(md.mesh.numberofelements,1); + +% creating flow law paramter +md.materials.rheology_B=1/((10^-25)^(1/3))*ones(md.mesh.numberofvertices,1); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_law='None'; + +% creating boundary conditions +md=SetIceShelfBC(md,'./front.exp'); +md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1); +pos=find((md.mesh.y<50000.1 & md.mesh.y>49999.9) | (md.mesh.y<0.1 & md.mesh.y>-0.1)); +md.stressbalance.spcvy(pos)=0; +pos2=find(md.mesh.x<0.1 & md.mesh.x>-0.1); +md.stressbalance.spcvx(pos2)=0; +md.stressbalance.spcvz(pos)=NaN; +md.stressbalance.spcvz(pos2)=NaN; + +% creating forcing conditions +md.smb.mass_balance=0.5*ones(md.mesh.numberofvertices,1); +md.basalforcings.geothermalflux=0.5*ones(md.mesh.numberofvertices,1); +md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1); +md.groundingline.migration='SubelementMigration'; + +% setting parameters +md.materials.rho_ice=900; +md.materials.rho_water=1000; +md.constants.g=9.8; +md.constants.yts=3600*24*365; +md.transient.isthermal=0; +md.transient.isgroundingline=1; +md.stressbalance.isnewton=0; + +% setting inital condition +md.initialization.vx=ones(md.mesh.numberofvertices,1); +md.initialization.vy=ones(md.mesh.numberofvertices,1); +md.initialization.vz=ones(md.mesh.numberofvertices,1); +md.initialization.vel=sqrt(2)*ones(md.mesh.numberofvertices,1); +md.initialization.pressure=md.constants.g*md.materials.rho_ice*md.geometry.thickness; +md.initialization.temperature=273*ones(md.mesh.numberofvertices,1); Index: /issm/branches/trunk-dlcheng-ASE/examples/AMR/mismip.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/AMR/mismip.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/AMR/mismip.py (revision 27955) @@ -0,0 +1,54 @@ +import numpy as np +from SetIceShelfBC import SetIceShelfBC + +# creating thickness +md.geometry.bed = -100 - np.abs(md.mesh.x) / 1000 +md.geometry.base = -90 * np.ones((md.mesh.numberofvertices)) +md.geometry.surface = 10 * np.ones((md.mesh.numberofvertices)) +md.geometry.thickness = md.geometry.surface - md.geometry.base +md.mask.ocean_levelset = -1 * np.ones((md.mesh.numberofvertices)) + +# creating basal drag +md.friction.coefficient = np.sqrt(10**7) * np.ones((md.mesh.numberofvertices)) #q = 1. +md.friction.p = 3 * np.ones((md.mesh.numberofelements)) +md.friction.q = np.zeros((md.mesh.numberofelements)) + +# creating flow law paramter +md.materials.rheology_B = 1 / ((1e-25)**(1 / 3)) * np.ones((md.mesh.numberofvertices)) +md.materials.rheology_n = 3 * np.ones((md.mesh.numberofelements)) +md.materials.rheology_law = 'None' + +# creating boundary conditions +md = SetIceShelfBC(md, './front.exp') +md.stressbalance.spcvx = np.nan * np.ones((md.mesh.numberofvertices)) +md.stressbalance.spcvy = np.nan * np.ones((md.mesh.numberofvertices)) +md.stressbalance.spcvz = np.nan * np.ones((md.mesh.numberofvertices)) +pos = np.nonzero(np.logical_or((np.abs(md.mesh.y - 50000) < 0.1), np.abs(md.mesh.y) < 0.1)) +md.stressbalance.spcvy[pos] = 0 +pos2 = np.nonzero(np.abs(md.mesh.x) < 0.1) +md.stressbalance.spcvx[pos2] = 0 +md.stressbalance.spcvz[pos] = np.nan +md.stressbalance.spcvz[pos2] = np.nan + +# creating forcing conditions +md.smb.mass_balance = 0.5 * np.ones((md.mesh.numberofvertices)) +md.basalforcings.geothermalflux = 0.5 * np.ones((md.mesh.numberofvertices)) +md.thermal.spctemperature = np.nan * np.ones((md.mesh.numberofvertices)) +md.groundingline.migration = 'SubelementMigration' + +# setting parameters +md.materials.rho_ice = 900 +md.materials.rho_water = 1000 +md.constants.g = 9.8 +md.constants.yts = 3600 * 24 * 365 +md.transient.isthermal = 0 +md.transient.isgroundingline = 1 +md.stressbalance.isnewton = 0 + +# setting inital condition +md.initialization.vx = np.ones((md.mesh.numberofvertices)) +md.initialization.vy = np.ones((md.mesh.numberofvertices)) +md.initialization.vz = np.ones((md.mesh.numberofvertices)) +md.initialization.vel = np.sqrt(2) * np.ones((md.mesh.numberofvertices)) +md.initialization.pressure = md.constants.g * md.materials.rho_ice * md.geometry.thickness +md.initialization.temperature = 273 * np.ones((md.mesh.numberofvertices)) Index: /issm/branches/trunk-dlcheng-ASE/examples/AMR/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/AMR/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/AMR/runme.m (revision 27955) @@ -0,0 +1,69 @@ +% Mismip3D experiment with AMR using BAMG +steps=[1:3]; + +if any(steps==1) + disp(' Step 1: Coarse mesh'); + + %Generate an unstructured coarse mesh on the MISMIP domain with typical element edge length equal to 10,000 m + md=bamg(model,'domain','./domain.exp','hmax',10000,'splitcorners',1); + + save AMRCoarseMesh md +end + +if any(steps==2) + disp(' Step 2: Parameterization'); + + md=loadmodel('AMRCoarseMesh'); + + md=setmask(md,'',''); + + % Run parameterization script to set up geometry, inital velocity, material properties, etc. + md=parameterize(md,'./mismip.par'); + + % Set the AMR properties and the refinement criteria + % Here, we are refining around the grounding line + % We impose the element resolution at grounding equal to 1000 m (1 km) + % The criterion used is the element distance to the grounding line + % The distance used here is 10000 m (10 km), used in both side around the grouding line (upstream and downstream) + md.amr.groundingline_resolution=1000; + md.amr.groundingline_distance=10000; + md.amr.hmin=1000; % the same resolution used around the grounding line + md.amr.hmax=10000; % the same coase resolution used to generate the coarse mesh + md.amr.gradation=1.7; % this controls the ratio between two consecutive edges + md.amr.fieldname='None'; % no field used here + md.amr.keepmetric=0; % no field, no metric + + save AMRParam md +end + +if any(steps==3) + disp(' Step 3: Solve!'); + + md=loadmodel('AMRParam'); + + % Run transient with adaptive mesh refinement + md.timestepping.time_step=1; + md.timestepping.final_time=500; % here, as example, only 500 yr. + md.settings.output_frequency=10;% here, save results every 10 yr + md.stressbalance.maxiter=30; + md.stressbalance.abstol=NaN; + md.stressbalance.restol=1; + md.settings.solver_residue_threshold=1e-2; % relaxing (the first stress balance solver iteration presents values higher than the original threshold. This probably happens because the initial velocity is set to one). + md.verbose=verbose('convergence',false,'solution',true); + + % Specify that you want to run the model on your current (local host) computer + % Change the number of processors according to your machine (here np=2) + md.cluster=generic('np',2); + + % Set the AMR frequency, i.e., can be 1 or larger depending on how often the mesh needs to be updated + md.transient.amr_frequency=1; % here, we are refining the mesh in every time step + + % Set the flow equation (SSA) and run + md=setflowequation(md,'SSA','all'); + md=solve(md,'Transient'); + + % Print the solutions and the mesh in VTK format (needs ParaView: https://www.paraview.org) + AMRexportVTK('./VTK',md); + + save AMRTransient md +end Index: /issm/branches/trunk-dlcheng-ASE/examples/AMR/runme.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/AMR/runme.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/AMR/runme.py (revision 27955) @@ -0,0 +1,78 @@ +# Mismip3D experiment with AMR using BAMG +from bamg import bamg +from model import * +from export_netCDF import export_netCDF +from setmask import setmask +from loadmodel import loadmodel +from parameterize import parameterize +from generic import generic +from exportVTK import exportVTK +from setflowequation import setflowequation +from solve import solve +from plotmodel import plotmodel + + +steps = [4] + +if 1 in steps: + print(' Step 1: Coarse mesh') + + #Generate an unstructured coarse mesh on the MISMIP domain with typical element edge length equal to 10, 000 m + md = bamg(model(), 'domain', './domain.exp', 'hmax', 10000, 'splitcorners', 1) + + export_netCDF(md, 'AMRCoarseMesh.nc') + +if 2 in steps: + print(' Step 2: Parameterization') + + md = loadmodel('AMRCoarseMesh.nc') + + md = setmask(md, '', '') + + # Run parameterization script to set up geometry, inital velocity, material properties, etc. + md = parameterize(md, './mismip.py') + + # Set the AMR properties and the refinement criteria + # Here, we are refining around the grounding line + # We impose the element resolution at grounding equal to 1000 m (1 km) + # The criterion used is the element distance to the grounding line + # The distance used here is 10000 m (10 km), used in both side around the grouding line (upstream and downstream) + md.amr.groundingline_resolution = 1000 + md.amr.groundingline_distance = 10000 + md.amr.hmin = 1000 # the same resolution used around the grounding line + md.amr.hmax = 10000 # the same coase resolution used to generate the coarse mesh + md.amr.gradation = 1.7 # this controls the ratio between two consecutive edges + md.amr.fieldname = 'None' # no field used here + md.amr.keepmetric = 0 # no field, no metric + + export_netCDF(md, 'AMRParam.nc') + +if 3 in steps: + print(' Step 3: Solve!') + + md = loadmodel('AMRParam.nc') + + # Run transient with adaptive mesh refinement + md.timestepping.time_step = 1 + md.timestepping.final_time = 500 # here, as example, only 500 yr. + md.settings.output_frequency = 10 # here, save results every 10 yr + md.stressbalance.maxiter = 30 + md.stressbalance.abstol = np.nan + md.stressbalance.restol = 1 + md.settings.solver_residue_threshold = 1e-2 # relaxing (the first stress balance solver iteration presents values higher than the original threshold. This probably happens because the initial velocity is set to one). + md.verbose = verbose('convergence', False, 'solution', True) + + # Specify that you want to run the model on your current (local host) computer + # Change the number of processors according to your machine (here np = 2) + md.cluster = generic('np', 2) + + # Set the AMR frequency, i.e., can be 1 or larger depending on how often the mesh needs to be updated + md.transient.amr_frequency = 1 # here, we are refining the mesh in every time step + + # Set the flow equation (SSA) and run + md = setflowequation(md, 'SSA', 'all') + md = solve(md, 'Transient') + + # Print the solutions and the mesh in VTK format (needs ParaView: https: / / www.paraview.org) + exportVTK('./VTKpy', md) + export_netCDF(md, 'AMRTransient.nc') Index: /issm/branches/trunk-dlcheng-ASE/examples/AMR/runme_with_neopz.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/AMR/runme_with_neopz.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/AMR/runme_with_neopz.m (revision 27955) @@ -0,0 +1,66 @@ +% Mismip3D experiment with AMR using NeoPZ (requires NeoPZ installation first, see external packages) +steps=[1:3]; + +if any(steps==1) + disp(' Step 1: Coarse mesh'); + + %Generate an unstructured coarse mesh on the MISMIP domain with typical element edge length equal to 10,000 m + md=bamg(model,'domain','./domain.exp','hmax',10000,'splitcorners',1); + + save AMRCoarseMesh md +end + +if any(steps==2) + disp(' Step 2: Parameterization'); + + md=loadmodel('AMRCoarseMesh'); + + md=setmask(md,'',''); + + % Run parameterization script to set up geometry, inital velocity, material properties, etc. + md=parameterize(md,'./mismip.par'); + + % Set the AMR properties and the refinement criteria + % Here, we are refining around the grounding line + % We impose the element resolution at grounding equal to ~1250 m, which corresponds to 3 levels of refinement + % The criterion used is the element distance to the grounding line + % The distance used here is 10000 m (10 km), used in both side around the grouding line (upstream and downstream) + md.amr=amrneopz; + md.amr.level_max=3; % refine 3 times so we have about 1250 m around the grounding line + md.amr.gradation=2; % maximum ratio between two adjacent edges + md.amr.groundingline_distance=10000; + + save AMRParam md +end + +if any(steps==3) + disp(' Step 3: Solve!'); + + md=loadmodel('AMRParam'); + + % Run transient with adaptive mesh refinement + md.timestepping.time_step=1; + md.timestepping.final_time=500; % here, as example, only 500 yr. + md.settings.output_frequency=10;% here, save results every 10 yr + md.stressbalance.maxiter=30; + md.stressbalance.abstol=NaN; + md.stressbalance.restol=1; + md.settings.solver_residue_threshold=1e-2; % relaxing (the first stress balance solver iteration presents values higher than the original threshold. This probably happens because the initial velocity is set to one). + md.verbose=verbose('convergence',false,'solution',true); + + % Specify that you want to run the model on your current (local host) computer + % Change the number of processors according to your machine (here np=2) + md.cluster=generic('np',2); + + % Set the AMR frequency, i.e., can be 1 or larger depending on how often the mesh needs to be updated + md.transient.amr_frequency=1; % here, we are refining the mesh in every time step + + % Set the flow equation (SSA) and run + md=setflowequation(md,'SSA','all'); + md=solve(md,'Transient'); + + % Print the solutions and the mesh in VTK format (needs ParaView: https://www.paraview.org) + AMRexportVTK('./VTK',md); + + save AMRTransient md +end Index: /issm/branches/trunk-dlcheng-ASE/examples/EsaGRACE/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/EsaGRACE/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/EsaGRACE/runme.m (revision 27955) @@ -0,0 +1,143 @@ +clear all; +addpath('../Data','../Functions'); + +steps=[1]; + +if any(steps==1) + disp(' Step 1: Global mesh creation'); + + resolution=300; % [km] + radius = 6.371012*10^3; % [km] + + md=model; + md.mesh=gmshplanet('radius',radius,'resolution',resolution); + + md.mask.ocean_levelset=gmtmask(md.mesh.lat,md.mesh.long); + + save ./Models/EsaGRACE_Mesh md; + + plotmodel (md,'data',md.mask.ocean_levelset,'edgecolor','k'); +end + +if any(steps==2) + disp(' Step 2: Define loads in meters of ice height equivalent'); + md = loadmodel('./Models/EsaGRACE_Mesh'); + + year_month = 2007+15/365; + time_range = [year_month year_month]; + + onvertex = 0; % map data on vertex. If 0, it maps on the elemental centroid. + water_load = grace(md.mesh.elements,md.mesh.lat,md.mesh.long,time_range(1),time_range(2),onvertex); + + md.esa.deltathickness = water_load*md.materials.rho_freshwater/md.materials.rho_ice; % ice height equivalent + + save ./Models/EsaGRACE_Loads md; + + plotmodel (md,'data',md.esa.deltathickness,... + 'view',[90 -90],'caxis',[-.1 .1],... + 'title','Ice height equivalent [m]'); +end + +if any(steps==3) + disp(' Step 3: Parameterization'); + md = loadmodel('./Models/EsaGRACE_Loads'); + + love_numbers = lovenumbers('maxdeg',10000,'referenceframe','CF'); + md.esa.love_h = love_numbers.h; + md.esa.love_l = love_numbers.l; + + md.mask.ocean_levelset = ones(md.mesh.numberofvertices,1); + md.mask.ice_levelset = ones(md.mesh.numberofvertices,1); + pos=find(md.esa.deltathickness~=0); + md.mask.ice_levelset(md.mesh.elements(pos,:))=-1; + %md.mask.land_levelset = 1-md.mask.ocean_levelset; + + di=md.materials.rho_ice/md.materials.rho_water; + md.geometry.thickness=ones(md.mesh.numberofvertices,1); + md.geometry.surface=(1-di)*zeros(md.mesh.numberofvertices,1); + md.geometry.base=md.geometry.surface-md.geometry.thickness; + md.geometry.bed=md.geometry.base; + + md.initialization.temperature=273.25*ones(md.mesh.numberofvertices,1); + md.materials.rheology_B=paterson(md.initialization.temperature); + md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); + + md.miscellaneous.name='EsaGRACE'; + + save ./Models/EsaGRACE_Parameterization md; +end + +if any(steps==4) + disp(' Step 4: Solve Esa solver'); + md = loadmodel('./Models/EsaGRACE_Parameterization'); + + md.esa.requested_outputs = {'EsaUmotion','EsaNmotion','EsaEmotion'}; + + md.cluster=generic('name',oshostname(),'np',3); + md.verbose=verbose('111111111'); + + md=solve(md,'Esa'); + + save ./Models/EsaGRACE_Solution md; +end + +if any(steps==5) + disp(' Step 5: Plot solutions'); + md = loadmodel('./Models/EsaGRACE_Solution'); + + sol1 = md.esa.deltathickness*100; % [cm] + sol2 = md.results.EsaSolution.EsaUmotion*1000; % [mm] + sol3 = md.results.EsaSolution.EsaNmotion*1000; % [mm] + sol4 = md.results.EsaSolution.EsaEmotion*1000; % [mm] + + sol_name={'Change in water equivalent height [cm]', 'Vertical displacement [mm]',... + 'Horizontal (NS) displacement [mm]', 'Horizontal (EW) displacement [mm]'}; + fig_name={'Fig_dH.pdf','Fig_vert.pdf','Fig_horzNS.pdf','Fig_horzEW.pdf'}; + + res = 1.0; % [degree] + + [lat_grid, lon_grid] = meshgrid(linspace(-90,90,180/res), linspace(-180,180,360/res)); + sol_grid = zeros(size(lat_grid)); + + for kk=1:4 + sol=eval(sprintf('sol%d',kk)); + + if length(sol)==md.mesh.numberofelements + for jj=1:md.mesh.numberofelements + ii=(jj-1)*3; + pp(ii+1:ii+3)=md.mesh.elements(jj,:); + end + for jj=1:md.mesh.numberofvertices + pos=ceil(find(pp==jj)/3); + temp(jj)=mean(sol(pos)); + end + sol=temp'; + end + + F = scatteredInterpolant(md.mesh.lat,md.mesh.long,sol); + F.Method = 'linear'; + F.ExtrapolationMethod = 'linear'; + + sol_grid = F(lat_grid, lon_grid); + sol_grid(isnan(sol_grid))=0; + sol_grid(lat_grid>85 & sol_grid==0)=NaN; + + set(0,'DefaultAxesFontSize',18,'DefaultAxesLineWidth',1,'DefaultTextFontSize',18,'DefaultLineMarkerSize',8) + figure1=figure('Position', [100, 100, 1000, 500]); + gcf; load coastlines; cla; + pcolor(lon_grid,lat_grid,sol_grid); shading flat; hold on; + if (kk==1) + geoshow(flipud(coastlat),flipud(coastlon),'DisplayType','polygon','FaceColor','white'); + end + plot(coastlon,coastlat,'k'); hold off; + c1=colorbar; + colormap('haxby'); + caxis([-min(abs(min(sol)),abs(max(sol))) min(abs(min(sol)),abs(max(sol)))]); + xlim([-180 180]); + ylim([-90 90]); + grid on; + title(sol_name(kk)); + set(gcf,'color','w'); + %export_fig(fig_name{kk}); + end +end Index: /issm/branches/trunk-dlcheng-ASE/examples/EsaWahr/RoundDomain.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/EsaWahr/RoundDomain.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/EsaWahr/RoundDomain.exp (revision 27955) @@ -0,0 +1,49 @@ +## Name: +## Icon:0 +# Points Count Value +41 1 +# X pos Y pos +20000 0 +19754 3128.7 +19021 6180.3 +17820 9079.8 +16180 11756 +14142 14142 +11756 16180 +9079.8 17820 +6180.3 19021 +3128.7 19754 +0 20000 +-3128.7 19754 +-6180.3 19021 +-9079.8 17820 +-11756 16180 +-14142 14142 +-16180 11756 +-17820 9079.8 +-19021 6180.3 +-19754 3128.7 +-20000 0 +-19754 -3128.7 +-19021 -6180.3 +-17820 -9079.8 +-16180 -11756 +-14142 -14142 +-11756 -16180 +-9079.8 -17820 +-6180.3 -19021 +-3128.7 -19754 +-0 -20000 +3128.7 -19754 +6180.3 -19021 +9079.8 -17820 +11756 -16180 +14142 -14142 +16180 -11756 +17820 -9079.8 +19021 -6180.3 +19754 -3128.7 +20000 0 + + + Index: /issm/branches/trunk-dlcheng-ASE/examples/EsaWahr/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/EsaWahr/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/EsaWahr/runme.m (revision 27955) @@ -0,0 +1,164 @@ +clear all; +addpath('../Functions'); + +steps=[1]; + +if any(steps==1) + disp(' Step 1: Mesh creation'); + + md=roundmesh(model,100000,10000); % Domain radius and element size [m] + + save ./Models/EsaWahr_Mesh md; + + plotmodel(md,'data','mesh'); +end + +if any(steps==2) + disp(' Step 2: Anisotropic mesh creation'); + + md=roundmesh(model,100000,1000); + + disc_radius=20*1000; + rad_dist=sqrt(md.mesh.x.^2+md.mesh.y.^2); + field = abs(rad_dist-disc_radius); + + md = bamg(md,'field',field,'err',50,'hmax',10000); + + save ./Models/EsaWahr_Mesh md; + + plotmodel (md,'data','mesh'); +end + +if any(steps==3) + disp(' Step 3: Define loads'); + md = loadmodel('./Models/EsaWahr_Mesh'); + + rho_w_i=md.materials.rho_freshwater/md.materials.rho_ice; + + index=md.mesh.elements; + x_cent=mean(md.mesh.x(index),2); + y_cent=mean(md.mesh.y(index),2); + + md.esa.deltathickness = zeros(md.mesh.numberofelements,1); + disc_radius=20; % [km] + rad_dist=sqrt(x_cent.^2+y_cent.^2)/1000; + md.esa.deltathickness(rad_dist<=disc_radius) = -1.0*rho_w_i; + + save ./Models/EsaWahr_Loads md; + + plotmodel (md,'data',md.esa.deltathickness,'title','Ice height equivalent [m]'); +end + +if any(steps==4) + disp(' Step 4: Parameterization'); + md = loadmodel('./Models/EsaWahr_Loads'); + + love_numbers = lovenumbers('maxdeg',10000,'referenceframe','CF'); + md.esa.love_h = love_numbers.h; + md.esa.love_l = love_numbers.l; + + md.mask.ice_levelset = -ones(md.mesh.numberofvertices,1); + md.mask.ocean_levelset = ones(md.mesh.numberofvertices,1); + + di=md.materials.rho_ice/md.materials.rho_water; + md.geometry.thickness=ones(md.mesh.numberofvertices,1); + md.geometry.surface=(1-di)*zeros(md.mesh.numberofvertices,1); + md.geometry.base=md.geometry.surface-md.geometry.thickness; + md.geometry.bed=md.geometry.base; + + md.initialization.temperature=273.25*ones(md.mesh.numberofvertices,1); + md.materials.rheology_B=paterson(md.initialization.temperature); + md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); + + md.miscellaneous.name='EsaWahr'; + + save ./Models/EsaWahr_Parameterization md; +end + +if any(steps==5) + disp(' Step 5: Solve Esa solver'); + md = loadmodel('./Models/EsaWahr_Parameterization'); + + md.esa.requested_outputs = {'EsaUmotion','EsaXmotion','EsaYmotion'}; + + md.cluster=generic('name',oshostname(),'np',3); + md.verbose=verbose('111111111'); + + md=solve(md,'Esa'); + + save ./Models/EsaWahr_Solution md; +end + +if any(steps==6) + disp(' Step 6: Plot solutions'); + md = loadmodel('./Models/EsaWahr_Solution'); + + vert = md.results.EsaSolution.EsaUmotion*1000; % [mm] + horz_n = md.results.EsaSolution.EsaYmotion*1000; % [mm] + horz_e = md.results.EsaSolution.EsaXmotion*1000; % [mm] + horz = sqrt(horz_n.^2+horz_e.^2); % [mm] + + set(0,'DefaultAxesFontSize',24,'DefaultAxesLineWidth',1,'DefaultTextFontSize',24,'DefaultLineMarkerSize',6); + figure('Position', [100, 100, 800, 600]); + plotmodel(md,'data',vert,... + 'xTickLabel#all',[],'yTickLabel#all',[],... + 'colormap#all','jet','colorbarcornerposition#all','south',... + 'expdisp#all','./RoundDomain.exp',... + 'gridded#all',1,... + 'axispos#1',[0.02 0.505 0.47 0.47],... + 'colorbarpos#1',[0.045,0.55,0.18,0.02],'colorbartitle#1','Vertical [mm]',... + 'caxis#1',[0 3.5],... + 'data',horz,... + 'axispos#2',[0.505 0.505 0.47 0.47],... + 'colorbarpos',[0.53,0.55,0.18,0.02],'colorbartitle#2','Horizontal [mm]',... + 'caxis#2',[0 0.5],... + 'data',horz_n,... + 'axispos',[0.02 0.02 0.47 0.47],... + 'colorbarpos',[0.045,0.065,0.18,0.02],'colorbartitle#3','North-south [mm]',... + 'data',horz_e,... + 'caxis#3-4',[-0.5 0.5],... + 'axispos',[0.505 0.02 0.47 0.47],... + 'colorbarpos',[0.53,0.065,0.18,0.02],'colorbartitle#4','East-west [mm]'); + %export_fig('Fig5.pdf'); +end + +if any(steps==7) + disp(' Step 7: Compare results against Wahr semi-analytic solutions'); + md = loadmodel('./Models/EsaWahr_Solution'); + + vert = md.results.EsaSolution.EsaUmotion*1000; % [mm] + horz_n = md.results.EsaSolution.EsaYmotion*1000; % [mm] + horz_e = md.results.EsaSolution.EsaXmotion*1000; % [mm] + horz = sqrt(horz_n.^2+horz_e.^2); % [mm] + + xi=[0:500:100000]; % grid points [m] + yi=zeros(1,length(xi)); + vert_track=griddata(md.mesh.x,md.mesh.y,vert,xi,yi,'linear'); + horz_track=griddata(md.mesh.x,md.mesh.y,horz,xi,yi,'linear'); + + % semi-analytic solution (Wahr et al., 2013, JGR, Figure 1) + disc_radius = 20*1000; % [m] + [vert_wahr, horz_wahr] = wahr(disc_radius,xi,md.esa.love_h,md.esa.love_l); + + set(0,'DefaultAxesFontSize',16,'DefaultAxesLineWidth',1,'DefaultTextFontSize',16,'DefaultLineMarkerSize',6); + figure1=figure('Position', [100, 100, 700, 400]); + ylabel_1={'0',' ','1','','2','','3',''}; + axes1 = axes('Layer','top','Position',[0.1 0.15 0.8 0.8],... + 'XTick',[0:10:100],'xlim',[0 100],... + 'ylim',[0 3.5],'Ytick',[0:0.5:3.5],'yticklabel',ylabel_1); + box(axes1,'on'); hold(axes1,'all'); grid on; + xlabel(axes1,'Radial distance [km]'); + ylabel(axes1,'Displacement [mm]'); + plot([20 20],[0 3.5],'-k','linewidth',2,'parent',axes1); + % analytic soln + h3=plot(xi/1000,vert_wahr,'-r','linewidth',5,'parent',axes1); + h4=plot(xi/1000,horz_wahr,'-m','linewidth',5,'parent',axes1); + % ISSM soln + h1=plot(xi/1000,vert_track*917/1000,'-b','linewidth',3,'parent',axes1); + h2=plot(xi/1000,horz_track*917/1000,'-c','linewidth',3,'parent',axes1); + ag1 = gca; + leg1a = legend(ag1,[h3,h1,h4,h2],'Vertical (Wahr)','Vertical (ISSM)','Horizontal (Wahr)','Horizontal (ISSM)'); + set(leg1a,'location','east','Orientation','Vertical','Box','Off','FontSize',16); + set(gcf,'color','w'); + %export_fig('Fig6.pdf'); +end Index: /issm/branches/trunk-dlcheng-ASE/examples/Functions/domain_mask.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Functions/domain_mask.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Functions/domain_mask.m (revision 27955) @@ -0,0 +1,65 @@ +% mask cryospheric domains: GrIS, AIS, RGI regions +function mask = domain_mask(lat,lon,varargin); + + nv = length(lat); + mask=zeros(nv,1); + + if (strcmp(varargin{:},'Antarctica')==1) + % antarctica + rad=30*pi/180; + phi0=-90*pi/180; lambda0=0*pi/180; + for j=1:nv + phi=lat(j)/180*pi; lambda=lon(j)/180*pi; + delPhi=abs(phi-phi0); delLambda=abs(lambda-lambda0); + dist0(j)=2*asin(sqrt(sin(delPhi/2).^2+cos(phi).*cos(phi0).*sin(delLambda/2).^2)); + end + pos=find(dist01.5 & mask_0<2.5)=1; % that would be GrIS + mask(isnan(mask))=0; % there are not many glaciers there + + elseif (strcmp(varargin{:},'Alaska')==1) + + gla_data=dlmread('rgi_glacier_fraction_0125X0125.txt'); + gla_lat=90-gla_data(:,1); + gla_lon=gla_data(:,2); + gla_lon(gla_lon>180)=gla_lon(gla_lon>180)-360; + mask_reg=gla_data(:,3); % Alaska + mask_reg(mask_reg>0)=1; + mask=griddata(gla_lat,gla_lon,mask_reg,lat,lon); + mask(mask>0)=1; + mask(isnan(mask))=0; % there are not many glaciers there + + elseif (strcmp(varargin{:},'HMA')==1) + + gla_data=dlmread('rgi_glacier_fraction_0125X0125.txt'); + gla_lat=90-gla_data(:,1); + gla_lon=gla_data(:,2); + gla_lon(gla_lon>180)=gla_lon(gla_lon>180)-360; + mask_reg=sum(gla_data(:,15:17),2); % HMA regions 13-15 + mask_reg(mask_reg>0)=1; + mask=griddata(gla_lat,gla_lon,mask_reg,lat,lon); + mask(mask>0)=1; + mask(isnan(mask))=0; % there are not many glaciers there + + elseif (strcmp(varargin{:},'Glaciers')==1) + + gla_data=dlmread('rgi_glacier_fraction_0125X0125.txt'); + gla_lat=90-gla_data(:,1); + gla_lon=gla_data(:,2); + gla_lon(gla_lon>180)=gla_lon(gla_lon>180)-360; + mask_reg=sum(gla_data(:,3:20),2); % all RGI regions excluding AIS peripheral glaciers (#19) + mask_reg(mask_reg>0)=1; + mask=griddata(gla_lat,gla_lon,mask_reg,lat,lon); + mask(mask>0)=1; + mask(isnan(mask))=0; % there are not many glaciers there + + end + Index: /issm/branches/trunk-dlcheng-ASE/examples/Functions/grace.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Functions/grace.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Functions/grace.m (revision 27955) @@ -0,0 +1,138 @@ +% map grace loads in meters [m] of water equivalent height +function water_load = grace(index,lat,lon,tmin,tmax,onvertex); + + %compute centroids using (lat,lon) data {{{ + ne = length(index); % number of elements + nv = length(lat); % number of vertices + % [lat,lon] \in [-90:90,-180,180]; + lat_vertex_0=lat; long_vertex_0=lon; + % lat -> [0,180]; long -> [0,360] to compute centroids + lat=90-lat; + lon(lon<0)=180+(180+lon(lon<0)); + + ax_0=lat(index(:,1)); ay_0=lon(index(:,1)); + bx_0=lat(index(:,2)); by_0=lon(index(:,2)); + cx_0=lat(index(:,3)); cy_0=lon(index(:,3)); + % find whether long is 0 or 360! This is important to compute centroids as well as elemental area + for ii=1:ne + if (min([ay_0(ii),by_0(ii),cy_0(ii)])==0 && max([ay_0(ii),by_0(ii),cy_0(ii)])>180) + if ay_0(ii)==0 + ay_0(ii)=360; + end + if by_0(ii)==0 + by_0(ii)=360; + end + if cy_0(ii)==0 + cy_0(ii)=360; + end + end + end + % correction at the north pole + ay_0(ax_0==0)=(by_0(ax_0==0)+cy_0(ax_0==0))./2; + by_0(bx_0==0)=(cy_0(bx_0==0)+ay_0(bx_0==0))./2; + cy_0(cx_0==0)=(ay_0(cx_0==0)+by_0(cx_0==0))./2; + % correction at the south pole + ay_0(ax_0==180)=(by_0(ax_0==180)+cy_0(ax_0==180))./2; + by_0(bx_0==180)=(cy_0(bx_0==180)+ay_0(bx_0==180))./2; + cy_0(cx_0==180)=(ay_0(cx_0==180)+by_0(cx_0==180))./2; + % + lat_element=(ax_0+bx_0+cx_0)/3; + lon_element=(ay_0+by_0+cy_0)/3; + + % [lat,lon] \in [-90:90,-180,180]; + lat_element_0 = 90-lat_element; lon_element_0 = lon_element; + lon_element_0(lon_element>180) = (lon_element(lon_element>180)-180) - 180; + % }}} + + % Monthly GRACE data + filename=['../Data/GRCTellus.JPL.200204_201701.LND.RL05_1.DSTvSCS1411.nc']; + try + time_0=ncread(filename,'time'); % days since 2002-01-01 00:00:00 UTC + long_0=ncread(filename,'lon'); % longitudes: 0.27-359.75 + lati_0=ncread(filename,'lat'); % latitudes: -89.75:89.75 + rec=ncread(filename,'lwe_thickness');% rec_ensemble_mean [cm] + catch e + disp('If dataset file exists at another location, modify the path in examples/Functions/grace.m') + rethrow(e) + end + + + time_yr = 2002+time_0/365; % [yr] + + [nn_0,mm_0] = size(squeeze(rec(:,:,1))); + for jj=1:mm_0 % chose a latitude + for kk=1:nn_0 + ii=nn_0*(jj-1)+kk; + lat_0(ii)=lati_0(jj); + lon_0(ii)=long_0(kk); + tws_monthly(:,ii) = rec(kk,jj,:); + end + end + % + %% translate variables as grace-related variables -- so I do not need to do too much editing + grace_monthly=tws_monthly; + grace_monthly(grace_monthly<-1344.6016 | grace_monthly>858.5046)=0; + + % detrend over the entire time period + %grace_monthly = detrend(grace_monthly); % 159X64800 => remove trends from each column! + + % fill out the blanks {{{ + + lat_grace=lat_0; + lon_grace=lon_0; + num_org=length(lon_grace); + + qq=1; mm=1; + for jj=2:num_org-1 + if (lat_grace(jj)~=lat_grace(jj+1)) + lat_new(qq)=lat_grace(jj); + lon_new(qq)=lon_grace(jj)+(lon_grace(jj)-lon_grace(jj-1)); + load_new(:,qq)=grace_monthly(:,mm); + lat_new(qq+1)=lat_grace(jj); + lon_new(qq+1)=lon_grace(mm)-(lon_grace(jj)-lon_grace(jj-1)); + load_new(:,qq+1)=grace_monthly(:,jj); + qq=qq+2; + mm=jj+1; % to find out the value for monthly data + end + end + + num_add=length(lat_new); + num_plus=num_org+num_add; + + lat_grace_plus=zeros(num_plus,1); + lon_grace_plus=zeros(num_plus,1); + load_grace_plus=zeros(length(time_0),num_plus); + + lat_grace_plus(1:num_org)=lat_grace; + lat_grace_plus(1+num_org:num_plus)=lat_new; + lon_grace_plus(1:num_org)=lon_grace; + lon_grace_plus(1+num_org:num_plus)=lon_new; + load_grace_plus(:,1:num_org)=grace_monthly; + load_grace_plus(:,1+num_org:num_plus)=load_new; %(:,:); + % }}} + + % choose selected months ONLY + [diff1,pos1] = min(abs(tmin-time_yr)); + [diff2,pos2] = min(abs(tmax-time_yr)); + + time_yr=time_yr(pos1:pos2); + load_grace_plus=load_grace_plus(pos1:pos2,:); + num_yr=length(time_yr); + if onvertex + water_load_0=zeros(nv,num_yr); + else + water_load_0=zeros(ne,num_yr); + end + + for jj=1:num_yr + if onvertex + water_load_0(:,jj) = griddata(lat_grace_plus,lon_grace_plus,load_grace_plus(jj,:),lat_vertex_0,lon); + else + water_load_0(:,jj) = griddata(lat_grace_plus,lon_grace_plus,load_grace_plus(jj,:),lat_element_0,lon_element); + end + disp([num2str(jj),' of ',num2str(num_yr),' months done!']); + end + + water_load=water_load_0/100; % cm -> meters of water + water_load(isnan(water_load))=0; + Index: /issm/branches/trunk-dlcheng-ASE/examples/Greenland/CheatSheet.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Greenland/CheatSheet.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Greenland/CheatSheet.m (revision 27955) @@ -0,0 +1,72 @@ +if any(steps==7) + disp(' Step 7: Historical Relaxation run'); + md = loadmodel('./Models/Greenland.Control_drag'); + + load smbbox + + %convert mesh x,y into the Box projection + [md.mesh.lat,md.mesh.long] = xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + [xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70); + + %Interpolate and set surface mass balance + index = BamgTriangulate(x1(:),y1(:)); + smb_mo = InterpFromMeshToMesh2d(index,x1(:),y1(:),smbmean(:),xi,yi); + smb = smb_mo*12/1000*md.materials.rho_freshwater/md.materials.rho_ice; + md.smb.mass_balance = [smb;1 ]; + + %Set transient options, run for 20 years, saving every 5 timesteps + md.timestepping.time_step=0.2; + md.timestepping.final_time=200; + md.settings.output_frequency=5; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb', ... + 'SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.HistoricTransient_200yr md; +end + +if any(steps==8) + disp(' Step 8: Plotting exercise'); + + %Load historic transient model + md = loadmodel('./Models/Greenland.HistoricTransient_200yr'); + + %Create Line Plots of relaxation run. Create a figure. + figure + + %Save surface mass balance, by looping through 200 years (1000 steps) + % Note, the first output will always contain output from time step 1 + surfmb=[]; for i=2:201; surfmb=[surfmb ... + md.results.TransientSolution(i).SmbMassBalance]; end + + %Plot surface mass balance time series in first subplot + subplot(3,1,1); plot([1:200],mean(surfmb)); + + %Title this plot Mean surface mass balance + title('Mean Surface mass balance'); + + %Save velocity by looping through 200 years + vel=[]; for i=2:201; vel=[vel md.results.TransientSolution(i).Vel]; end + + %Plot velocity time series in second subplot + subplot(3,1,2); plot([1:200],mean(vel)); + + %Title this plot Mean Velocity + title('Mean Velocity'); + + %Save Ice Volume by looping through 200 years + volume=[]; for i=2:201; volume=[volume md.results.TransientSolution(i).IceVolume]; end + + %Plot volume time series in third subplot + subplot(3,1,3); plot([1:200],volume); + + %Title this plot Mean Velocity and add an x label of years + title('Ice Volume'); xlabel('years'); +end Index: /issm/branches/trunk-dlcheng-ASE/examples/Greenland/CheatSheet.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Greenland/CheatSheet.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Greenland/CheatSheet.py (revision 27955) @@ -0,0 +1,89 @@ +if 7 in steps: + # Step 7: Historical Relaxation run {{{ + print(' Step 7: Historical Relaxation run') + md = loadmodel('./Models/Greenland.Control_drag.nc') + + with open('./smbbox.npz', "rb") as smbFile: + SMB = np.load(smbFile) + x1 = np.squeeze(SMB['x1']) + y1 = np.squeeze(SMB['y1']) + smbmean = np.squeeze(SMB['smbmean']) + + #convert mesh x, y into the Box projection + [md.mesh.lat, md.mesh.long] = xy2ll(md.mesh.x, md.mesh.y, + 1, 39, 71) + [xi, yi] = ll2xy(md.mesh.lat, md.mesh.long, + 1, 45, 70) + + #Interpolate and set surface mass balance + x1 = x1.flatten() + y1 = y1.flatten() + smbmean = smbmean.flatten() + index = BamgTriangulate(x1, y1) + smb_mo = InterpFromMeshToMesh2d(index, x1, y1, smbmean, xi, yi) + smb = smb_mo * 12 / 1000 * md.materials.rho_freshwater / md.materials.rho_ice + md.smb.mass_balance = np.append(smb, 1) + + #Set transient options, run for 20 years, saving every timestep + md.timestepping.time_step = 0.2 + md.timestepping.final_time = 200 + md.settings.output_frequency = 5 + + #Additional options + md.inversion.iscontrol = 0 + md.transient.requested_outputs = ['IceVolume', 'TotalSmb', 'SmbMassBalance'] + md.verbose = verbose('solution', True, 'module', True) + + #Go solve + md.cluster = generic('name', gethostname(), 'np', 2) + md = solve(md, 'Transient') + + export_netCDF(md, './Models/Greenland.HistoricTransient_200yr.nc') + # }}} + +if 8 in steps: + # Step 8: Plotting exercise {{{ + print(' Step 8: Plotting exercise') + md = loadmodel('./Models/Greenland.HistoricTransient_200yr.nc') + + #Create Line Plots of relaxation run. Create a figure. + fig = plt.figure(tight_layout=True) + + #Save surface mass balance, by looping through 200 years (1000 steps) + #Note, the first output will always contain output from time step 1 + + Timer = np.arange(0.2, 200.2) + surfmb = [] + for i in range(0, 200): + surfmb.append(md.results.TransientSolution[i].SmbMassBalance) + + #Plot surface mass balance time series in first subplot + ax = fig.add_subplot(311) + ax.plot(Timer, np.nanmean(surfmb, axis=1)) + + #Title this plot Mean surface mass balance + ax.set_title('Mean Surface mass balance') + + #Save velocity by looping through 200 years + vel = [] + for i in range(0, 200): + vel.append(md.results.TransientSolution[i].Vel) + + #Plot velocity time series in second subplot + ay = fig.add_subplot(312) + ay.plot(Timer, np.nanmean(vel, axis=1)) + + #Title this plot Mean Velocity + ay.set_title('Mean Velocity') + + #Save Ice Volume by looping through 200 years + volume = [] + for i in range(0, 200): + volume.append(md.results.TransientSolution[i].IceVolume) + + #Plot volume time series in third subplot + az = fig.add_subplot(313) + az.plot(Timer, volume) + + #Title this plot Mean Velocity and add an x label of years + az.set_title('Ice Volume') + az.set_xlabel('years') + # }}} Index: /issm/branches/trunk-dlcheng-ASE/examples/Greenland/DomainOutline.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Greenland/DomainOutline.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Greenland/DomainOutline.exp (revision 27955) @@ -0,0 +1,733 @@ +## Name:DomainOutline +## Icon:0 +# Points Count Value +727 1.000000 +# X pos Y pos +47662.8073760000 -2621047.2585999998 +39869.9055420000 -2638077.6292949999 +26037.5047870000 -2644088.3483640002 +24868.5695120000 -2659115.1460360000 +25647.8596950000 -2674141.9437079998 +16880.8451320000 -2687666.0616130000 +515.7512810000 -2685662.4885900002 +-7666.7956450000 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+97537.3791130000 -2587111.7405229998 +88380.7194580000 -2573587.6226180000 +74743.1412490000 -2567076.0102940002 +61105.5630390000 -2577093.8754090001 +66950.2394150000 -2594124.2461040001 +57598.7572140000 -2581101.0214539999 +53117.8386600000 -2598131.3921500002 +41818.1310010000 -2586610.8472679998 +30810.6571600000 -2599133.1786610000 +44253.4128240000 -2608650.1505200001 +47662.8073760000 -2621047.2585999998 + Index: /issm/branches/trunk-dlcheng-ASE/examples/Greenland/Greenland.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Greenland/Greenland.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Greenland/Greenland.par (revision 27955) @@ -0,0 +1,77 @@ +%Name and Coordinate system +md.miscellaneous.name='SeaRISEgreenland'; +md.mesh.epsg=3413; + +disp(' Loading SeaRISE data from NetCDF'); +ncdata='../Data/Greenland_5km_dev1.2.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +velx = ncread(ncdata,'surfvelx')'; +vely = ncread(ncdata,'surfvely')'; +temp = ncread(ncdata,'airtemp2m')'; +smb = ncread(ncdata,'smb')'; +gflux = ncread(ncdata,'bheatflx')'; + +disp(' Interpolating surface and bedrock'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); + +disp(' Constructing thickness'); +md.geometry.thickness=md.geometry.surface-md.geometry.base; + +%Set min thickness to 1 meter +pos0=find(md.geometry.thickness<=0); +md.geometry.thickness(pos0)=1; +md.geometry.surface=md.geometry.thickness+md.geometry.base; + +disp(' Interpolating velocities '); +md.inversion.vx_obs = InterpFromGridToMesh(x1,y1,velx,md.mesh.x,md.mesh.y,0); +md.inversion.vy_obs = InterpFromGridToMesh(x1,y1,vely,md.mesh.x,md.mesh.y,0); +md.inversion.vel_obs = sqrt(md.inversion.vx_obs.^2+md.inversion.vy_obs.^2); +md.initialization.vx = md.inversion.vx_obs; +md.initialization.vy = md.inversion.vy_obs; +md.initialization.vz = zeros(md.mesh.numberofvertices,1); +md.initialization.vel= md.inversion.vel_obs; + +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; + +disp(' Interpolating surface mass balance'); +md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; + +disp(' Construct basal friction parameters'); +md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +pos=find(md.mask.ocean_levelset<0); +md.friction.coefficient(pos)=0; %no friction applied on floating ice +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.friction.q=ones(md.mesh.numberofelements,1); +md.friction.p=ones(md.mesh.numberofelements,1); + +disp(' Set other boundary conditions'); +md.mask.ice_levelset(md.mesh.vertexonboundary==1)=0; +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.thermal.spctemperature = [md.initialization.temperature;1]; %impose observed temperature on surface +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux=InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); + +disp(' Set Pressure'); +md.initialization.pressure=md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +disp(' Single point constraints'); +%Initialize single point constraint arrays +md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6); +md.stressbalance.spcvx = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvy = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvz = NaN*ones(md.mesh.numberofvertices,1); + Index: /issm/branches/trunk-dlcheng-ASE/examples/Greenland/Greenland.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Greenland/Greenland.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Greenland/Greenland.py (revision 27955) @@ -0,0 +1,83 @@ +import numpy as np +from paterson import paterson +from netCDF4 import Dataset +from InterpFromGridToMesh import InterpFromGridToMesh + +#Name and Coordinate system +md.miscellaneous.name = 'SeaRISEgreenland' +md.mesh.epsg = 3413 + +print(' Loading SeaRISE data from NetCDF') +ncdata = Dataset('../Data/Greenland_5km_dev1.2.nc', mode='r') +x1 = np.squeeze(ncdata.variables['x1'][:].data) +y1 = np.squeeze(ncdata.variables['y1'][:].data) +usrf = np.squeeze(ncdata.variables['usrf'][:].data) +topg = np.squeeze(ncdata.variables['topg'][:].data) +velx = np.squeeze(ncdata.variables['surfvelx'][:].data) +vely = np.squeeze(ncdata.variables['surfvely'][:].data) +temp = np.squeeze(ncdata.variables['airtemp2m'][:].data) +smb = np.squeeze(ncdata.variables['smb'][:].data) +gflux = np.squeeze(ncdata.variables['bheatflx'][:].data) +ncdata.close() + +print(' Interpolating surface and bedrock') +md.geometry.base = InterpFromGridToMesh(x1, y1, topg, md.mesh.x, md.mesh.y, 0) +md.geometry.surface = InterpFromGridToMesh(x1, y1, usrf, md.mesh.x, md.mesh.y, 0) + +print(' Constructing thickness') +md.geometry.thickness = md.geometry.surface - md.geometry.base + +#Set min thickness to 1 meter +pos0 = np.nonzero(md.geometry.thickness <= 0) +md.geometry.thickness[pos0] = 1 +md.geometry.surface = md.geometry.thickness + md.geometry.base + +print(' Interpolating velocities ') +md.inversion.vx_obs = InterpFromGridToMesh(x1, y1, velx, md.mesh.x, md.mesh.y, 0) +md.inversion.vy_obs = InterpFromGridToMesh(x1, y1, vely, md.mesh.x, md.mesh.y, 0) +md.inversion.vel_obs = np.sqrt(md.inversion.vx_obs**2 + md.inversion.vy_obs**2) +md.initialization.vx = md.inversion.vx_obs +md.initialization.vy = md.inversion.vy_obs +md.initialization.vz = np.zeros((md.mesh.numberofvertices)) +md.initialization.vel = md.inversion.vel_obs + +print(' Interpolating temperatures') +md.initialization.temperature = InterpFromGridToMesh(x1, y1, temp, md.mesh.x, md.mesh.y, 0) + 273.15 + +print(' Interpolating surface mass balance') +md.smb.mass_balance = InterpFromGridToMesh(x1, y1, smb, md.mesh.x, md.mesh.y, 0) +md.smb.mass_balance = md.smb.mass_balance * md.materials.rho_water / md.materials.rho_ice + +print(' Construct basal friction parameters') +md.friction.coefficient = 30 * np.ones((md.mesh.numberofvertices)) +pos = np.nonzero(md.mask.ocean_levelset < 0) +md.friction.coefficient[pos] = 0 #no friction applied on floating ice +md.friction.p = np.ones((md.mesh.numberofelements)) +md.friction.q = np.ones((md.mesh.numberofelements)) + +print(' Construct ice rheological properties') +md.materials.rheology_n = 3 * np.ones((md.mesh.numberofelements)) +md.materials.rheology_B = paterson(md.initialization.temperature) +md.friction.q = np.ones((md.mesh.numberofelements)) +md.friction.p = np.ones((md.mesh.numberofelements)) + +print(' Set other boundary conditions') +md.mask.ice_levelset[np.nonzero(md.mesh.vertexonboundary == 1)] = 0 +md.basalforcings.floatingice_melting_rate = np.zeros((md.mesh.numberofvertices)) +md.basalforcings.groundedice_melting_rate = np.zeros((md.mesh.numberofvertices)) +#impose observed temperature on surface +md.thermal.spctemperature = md.initialization.temperature +md.masstransport.spcthickness = np.nan * np.ones((md.mesh.numberofvertices)) + +print(' Set geothermal heat flux') +md.basalforcings.geothermalflux = InterpFromGridToMesh(x1, y1, gflux, md.mesh.x, md.mesh.y, 0) + +print(' Set Pressure') +md.initialization.pressure = md.materials.rho_ice * md.constants.g * md.geometry.thickness + +print(' Single point constraints') +#Initialize single point constraint arrays +md.stressbalance.referential = np.nan * np.ones((md.mesh.numberofvertices, 6)) +md.stressbalance.spcvx = np.nan * np.ones((md.mesh.numberofvertices)) +md.stressbalance.spcvy = np.nan * np.ones((md.mesh.numberofvertices)) +md.stressbalance.spcvz = np.nan * np.ones((md.mesh.numberofvertices)) Index: /issm/branches/trunk-dlcheng-ASE/examples/Greenland/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Greenland/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Greenland/runme.m (revision 27955) @@ -0,0 +1,315 @@ +clear all; +steps=[1]; + +%Location of SeaRISE dataset +ncdata='../Data/Greenland_5km_dev1.2.nc'; + +if any(steps==1) + disp(' Step 1: Mesh creation'); + + %Generate initial uniform mesh (resolution = 20000 m) + md=triangle(model,'./DomainOutline.exp',20000); + + % Get velocities (Note: You can use ncdisp('file') to see an ncdump) + x1 = ncread(ncdata,'x1'); + y1 = ncread(ncdata,'y1'); + velx = ncread(ncdata,'surfvelx'); + vely = ncread(ncdata,'surfvely'); + vx = InterpFromGridToMesh(x1,y1,velx',md.mesh.x,md.mesh.y,0); + vy = InterpFromGridToMesh(x1,y1,vely',md.mesh.x,md.mesh.y,0); + vel = sqrt(vx.^2+vy.^2); + + %Mesh Greenland + md=bamg(md,'hmax',400000,'hmin',5000,'gradation',1.4,'field',vel,'err',8); + + %convert x,y coordinates (Polar stereo) to lat/lon + [md.mesh.lat,md.mesh.long]=xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + + save ./Models/Greenland.Mesh_generation md; + + plotmodel (md,'data','mesh'); +end + +if any(steps==2) + disp(' Step 2: Parameterization'); + md = loadmodel('./Models/Greenland.Mesh_generation'); + + md = setmask(md,'',''); + md = parameterize(md,'./Greenland.par'); + md = setflowequation(md,'SSA','all'); + + save ./Models/Greenland.Parameterization md; +end + +if any(steps==3) + disp(' Step 3: Control method friction'); + md = loadmodel('./Models/Greenland.Parameterization'); + + %Control general + md.inversion.iscontrol=1; + md.inversion.nsteps=30; + md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); + md.inversion.maxiter_per_step=5*ones(md.inversion.nsteps,1); + + %Cost functions + md.inversion.cost_functions=[101 103 501]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); + md.inversion.cost_functions_coefficients(:,1)=350; + md.inversion.cost_functions_coefficients(:,2)=0.2; + md.inversion.cost_functions_coefficients(:,3)=2e-6; + + %Controls + md.inversion.control_parameters={'FrictionCoefficient'}; + md.inversion.gradient_scaling(1:md.inversion.nsteps)=50; + md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); + + %Additional parameters + md.stressbalance.restol=0.01; md.stressbalance.reltol=0.1; + md.stressbalance.abstol=NaN; + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md.toolkits=toolkits; + md.verbose=verbose('solution',true,'control',true); + md=solve(md,'Stressbalance'); + + %Update model friction fields accordingly + md.friction.coefficient=md.results.StressbalanceSolution.FrictionCoefficient; + + save ./Models/Greenland.Control_drag md; +end + +if any(steps==4) + disp(' Step 4: Transient run'); + md = loadmodel('./Models/Greenland.Control_drag'); + + %Set surface mass balance + x1 = ncread(ncdata,'x1'); + y1 = ncread(ncdata,'y1'); + smb = ncread(ncdata,'smb'); + smb = InterpFromGridToMesh(x1,y1,smb',md.mesh.x,md.mesh.y,0); + smb = smb*md.materials.rho_freshwater/md.materials.rho_ice; + smb = [smb smb smb-1.0]; + md.smb.mass_balance = [smb;1 10 20]; + + %Set transient options, run for 20 years, saving every timestep + md.timestepping.time_step=0.2; + md.timestepping.final_time=20; + md.settings.output_frequency=1; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb','SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true,'convergence',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.Transient md; +end + +if any(steps==5) + disp(' Step 5: Plotting'); + md = loadmodel('./Models/Greenland.Transient'); + + %Planview plots + plotmodel(md,'data',md.results.TransientSolution(end).Vel,'log#1', 10, ... + 'caxis#1', [1e-1 1e4], ... + 'title#1', 'Velocity (m/y)',... + 'data',md.results.TransientSolution(1).SmbMassBalance,... + 'title#2', 'Surface Mass Balance (m/y)',... + 'data',md.results.TransientSolution(end).Thickness,... + 'title', 'Thickness (m)',... + 'data',md.results.TransientSolution(end).Surface,... + 'title', 'Surface (m)'); + + %Line Plots + figure + + %Plot surface mass balance + surfmb=[]; for i=1:100; surfmb=[surfmb ... + md.results.TransientSolution(i).SmbMassBalance]; end + subplot(3,1,1); plot([0.2:0.2:20],mean(surfmb)); title('Mean Surface mass balance'); + + %Plot velocity + vel=[]; for i=1:100; vel=[vel md.results.TransientSolution(i).Vel]; end + subplot(3,1,2); plot([0.2:0.2:20],mean(vel)); title('Mean Velocity'); + + %Plot Volume + volume=[]; for i=1:100; volume=[volume md.results.TransientSolution(i).IceVolume]; end + subplot(3,1,3); plot([0.2:0.2:20],volume); title('Ice Volume'); + xlabel('years') +end + +if any(steps==6) + disp(' Step 6: Extract Box SMB'); + md = loadmodel('./Models/Greenland.Transient'); + + ncbox='../Data/Box_Greenland_SMB_monthly_1840-2012_5km_cal_ver20141007.nc'; + + %Set surface mass balance + lat = ncread(ncbox,'lat'); + lon = ncread(ncbox,'lon'); + smbbox = ncread(ncbox,'MassFlux'); + [x1 y1]=ll2xy(lat,lon,+1,45,70); + + years_of_simulation = 1840:2012; + t = [years_of_simulation(1):1/12:years_of_simulation(end)+11/12]; + + %Area of grid for 5km box + area_of_grid=5000*5000; + totalsmb=reshape(sum(sum(smbbox/1000,1),2),length(t),1)*area_of_grid; + + %save surface mass balance mat dataset + smbmean = mean(mean(smbbox,3),4); + save -v7.3 smbbox smbmean totalsmb smbbox x1 y1 t; + + %plot a time series of total SMB + figure; plot(t,totalsmb/1e9); title('Total Surface mass balance, Gt'); xlabel('year'); ylabel('Gt/yr'); + + clear smbbox +end + +if any(steps==7) + disp(' Step 7: Historical Relaxation run'); + md = loadmodel('./Models/Greenland.Control_drag'); + + load smbbox + + %convert mesh x,y into the Box projection + [md.mesh.lat,md.mesh.long] = xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + [xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70); + + %Interpolate and set surface mass balance + index = BamgTriangulate(x1(:),y1(:)); + smb_mo = InterpFromMeshToMesh2d(index,x1(:),y1(:),smbmean(:),xi,yi); + smb = smb_mo*12/1000*md.materials.rho_freshwater/md.materials.rho_ice; + md.smb.mass_balance = [smb;1 ]; + + %Set transient options, run for 20 years, saving every timestep + md.timestepping.time_step=0.2; + md.timestepping.final_time=20; + md.settings.output_frequency=1; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb','SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.HistoricTransient md; +end % step 7 end + +if any(steps==8) + disp(' Step 8: Plotting exercise'); + + %Load historic transient model + + %Create Line Plots of relaxation run. Create a figure. + + %Save surface mass balance, by looping through 200 years (1000 steps) + %Note, the first output will always contain output from time step 1 + + %Plot surface mass balance time series in first subplot + + %Title this plot Mean surface mass balance + + %Save velocity by looping through 200 years + + %Plot velocity time series in second subplot + + %Title this plot Mean Velocity + + %Save Ice Volume by looping through 200 years + + %Plot volume time series in third subplot + + %Title this plot Mean Velocity and add an x label of years + +end % step 8 end + +if any(steps==9) + disp(' Step 9: Box Transient run'); + md = loadmodel('./Models/Greenland.HistoricTransient_200yr'); + + %load past transient results + md.geometry.base=md.results.TransientSolution(end).Base; + md.geometry.thickness=md.results.TransientSolution(end).Thickness; + md.geometry.surface=md.geometry.base+md.geometry.thickness; + md.initialization.vx=(md.results.TransientSolution(end).Vx); + md.initialization.vy=(md.results.TransientSolution(end).Vy); + md.results=[]; + + %convert mesh x,y into the Box projection + [md.mesh.lat,md.mesh.long] = xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + [xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70); + + %Set surface mass balance + load smbbox + index = BamgTriangulate(x1(:),y1(:)); + + %Set years to run + years_of_simulation = 2003:2012; + + %initialize surface mass balance matrix + smb = nan*ones(md.mesh.numberofvertices,length(years_of_simulation)*12); + + %Interpolate and set surface mass balance + for year=years_of_simulation + for month=1:12 + smb_mo = griddata(double(x1),double(y1),... + double(squeeze(smbbox(:,:,month,year-1839))),xi,yi,'nearest'); + smb(:,(year-years_of_simulation(1))*12+month) = smb_mo; + end + end + md.smb.mass_balance = ... + [smb*12/1000*md.materials.rho_freshwater/md.materials.rho_ice; ... + [1/24:1/12:length(years_of_simulation)]]; + + %Set transient options, monthly timestep, saving every month + md.timestepping.time_step=1/12; + md.timestepping.final_time=length(years_of_simulation); + md.settings.output_frequency=1; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb','SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.BoxTransient md; +end + +if any(steps==10) + disp(' Step 10: Plot Box Transient'); + md = loadmodel('./Models/Greenland.BoxTransient'); + + %Set years run + years_of_simulation = 2003:2012; + t = [years_of_simulation(1):1/12:years_of_simulation(end)+11/12]; + + %Line Plots + figure + + %Plot surface mass balance + surfmb=[]; for i=1:length(t); surfmb=[surfmb ... + md.results.TransientSolution(i).TotalSmb]; end + subplot(3,1,1); plot(t,surfmb); title('Total Surface mass balance'); + + %Plot velocity + vel=[]; for i=1:length(t); vel=[vel md.results.TransientSolution(i).Vel]; end + subplot(3,1,2); plot(t,max(vel)); title('Max Velocity'); + + %Plot Volume + volume=[]; for i=1:length(t); volume=[volume md.results.TransientSolution(i).IceVolume]; end + subplot(3,1,3); plot(t,volume); title('Ice Volume'); + xlabel('years') +end Index: /issm/branches/trunk-dlcheng-ASE/examples/Greenland/runme.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Greenland/runme.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Greenland/runme.py (revision 27955) @@ -0,0 +1,369 @@ +import numpy as np +from triangle import triangle +from model import * +from netCDF4 import Dataset +from InterpFromGridToMesh import InterpFromGridToMesh +from bamg import bamg +from xy2ll import xy2ll +from plotmodel import plotmodel +from export_netCDF import export_netCDF +from loadmodel import loadmodel +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from socket import gethostname +from solve import solve +from ll2xy import ll2xy +from BamgTriangulate import BamgTriangulate +from InterpFromMeshToMesh2d import InterpFromMeshToMesh2d +from scipy.interpolate import griddata + +steps = [1] + +if 1 in steps: + # Step 1: Mesh creation {{{ + print(' Step 1: Mesh creation') + + #Generate initial uniform mesh (resolution = 20000 m) + md = triangle(model(), './DomainOutline.exp', 20000) + + ncdata = Dataset('../Data/Greenland_5km_dev1.2.nc', mode='r') + + # Get velocities (Note: You can use ncprint('file') to see an ncdump) + x1 = np.squeeze(ncdata.variables['x1'][:].data) + y1 = np.squeeze(ncdata.variables['y1'][:].data) + velx = np.squeeze(ncdata.variables['surfvelx'][:].data) + vely = np.squeeze(ncdata.variables['surfvely'][:].data) + ncdata.close() + + vx = InterpFromGridToMesh(x1, y1, velx, md.mesh.x, md.mesh.y, 0) + vy = InterpFromGridToMesh(x1, y1, vely, md.mesh.x, md.mesh.y, 0) + vel = np.sqrt(vx**2 + vy**2) + + #Mesh Greenland + md = bamg(md, 'hmax', 400000, 'hmin', 5000, 'gradation', 1.4, 'field', vel, 'err', 8) + + #convert x, y coordinates (Polar stereo) to lat / lon + [md.mesh.lat, md.mesh.long] = xy2ll(md.mesh.x, md.mesh.y, + 1, 39, 71) + + export_netCDF(md, './Models/Greenland.Mesh_generation.nc') + plotmodel(md, 'data', 'mesh') + # }}} + +if 2 in steps: + # Step 2: Parameterization{{{ + print(' Step 2: Parameterization') + md = loadmodel('./Models/Greenland.Mesh_generation.nc') + + md = setmask(md, '', '') + md = parameterize(md, './Greenland.py') + md = setflowequation(md, 'SSA', 'all') + + export_netCDF(md, "./Models/Greenland.Parameterization.nc") + # }}} + +if 3 in steps: + # Step 3: Control method friction {{{ + print(' Step 3: Control method friction') + md = loadmodel('./Models/Greenland.Parameterization.nc') + #Control general + md.inversion.iscontrol = 1 + md.inversion.nsteps = 30 + md.inversion.step_threshold = 0.99 * np.ones((md.inversion.nsteps)) + md.inversion.maxiter_per_step = 5 * np.ones((md.inversion.nsteps)) + + #Cost functions + md.inversion.cost_functions = [101, 103, 501] + md.inversion.cost_functions_coefficients = np.ones((md.mesh.numberofvertices, 3)) + md.inversion.cost_functions_coefficients[:, 0] = 350 + md.inversion.cost_functions_coefficients[:, 1] = 0.2 + md.inversion.cost_functions_coefficients[:, 2] = 2e-6 + + #Controls + md.inversion.control_parameters = ['FrictionCoefficient'] + md.inversion.gradient_scaling = 50 * np.ones((md.inversion.nsteps, 1)) + md.inversion.min_parameters = 1 * np.ones((md.mesh.numberofvertices, 1)) + md.inversion.max_parameters = 200 * np.ones((md.mesh.numberofvertices, 1)) + + #Additional parameters + md.stressbalance.restol = 0.01 + md.stressbalance.reltol = 0.1 + md.stressbalance.abstol = np.nan + md.stressbalance.loadingforce = np.zeros((md.mesh.numberofvertices, 3)) + + #Go solve + md.cluster = generic('name', gethostname(), 'np', 2) + md.toolkits = toolkits() + md.verbose = verbose('solution', True, 'control', True) + md = solve(md, 'Stressbalance') + + #Update model friction fields accordingly + md.friction.coefficient = md.results.StressbalanceSolution.FrictionCoefficient + + export_netCDF(md, "./Models/Greenland.Control_drag.nc") + # }}} + +if 4 in steps: + # Step 4: Transient run {{{ + print(' Step 4: Transient run') + md = loadmodel('./Models/Greenland.Control_drag.nc') + + #Set surface mass balance + ncdata = Dataset('../Data/Greenland_5km_dev1.2.nc', mode='r') + x1 = np.squeeze(ncdata.variables['x1'][:].data) + y1 = np.squeeze(ncdata.variables['y1'][:].data) + smb = np.squeeze(ncdata.variables['smb'][:].data) + ncdata.close() + + smb = InterpFromGridToMesh(x1, y1, smb, md.mesh.x, md.mesh.y, 0) + smb = smb * md.materials.rho_freshwater / md.materials.rho_ice + smb = np.vstack((smb, smb, smb - 1.0)).T + md.smb.mass_balance = np.vstack((smb, np.asarray([[1, 10, 20]]))) + #Set transient options, run for 20 years, saving every timestep + md.timestepping.time_step = 0.2 + md.timestepping.final_time = 20 + md.settings.output_frequency = 1 + + #Additional options + md.inversion.iscontrol = 0 + md.transient.requested_outputs = ['IceVolume', 'TotalSmb', 'SmbMassBalance'] + md.verbose = verbose('solution', True, 'module', True, 'convergence', True) + + #Go solve + md.cluster = generic('name', gethostname(), 'np', 2) + md = solve(md, 'Transient') + + export_netCDF(md, './Models/Greenland.Transient.nc') + # }}} + +if 5 in steps: + # Step 5: Plotting {{{ + print(' Step 5: Plotting') + md = loadmodel('./Models/Greenland.Transient.nc') + + #Planview plots + plotmodel(md, 'data', md.results.TransientSolution[-1].Vel, 'log#1', 1e-1, + 'caxis#1', [1e-1, 1e4], 'title#1', 'Velocity (m / y)', + 'data', md.results.TransientSolution[1].SmbMassBalance, + 'title#2', 'Surface Mass Balance (m / y)', + 'data', md.results.TransientSolution[-1].Thickness, + 'title', 'Thickness (m)', + 'data', md.results.TransientSolution[-1].Surface, + 'title', 'Surface (m)') + + #Line Plots + figure + + #Plot surface mass balance, velocity and volume + surfmb = [] + vel = [] + volume = [] + for i in range(0, 100): + surfmb.append(md.results.TransientSolution[i].SmbMassBalance) + vel.append(md.results.TransientSolution[i].Vel) + volume.append(md.results.TransientSolution[i].IceVolume) + + layout, ax = plt.subplots(3, 1, sharex=True, sharey=False, figsize=(5, 5)) + ax[0].plot(np.arange(0.2, 20.2, 0.2), np.nanmean(surfmb, axis=1)) + ax[0].set_title('Mean Surface mass balance') + ax[1].plot(np.arange(0.2, 20.2, 0.2), np.nanmean(vel, axis=1)) + ax[1].set_title('Mean Velocity') + ax[2].plot(np.arange(0.2, 20.2, 0.2), volume) + ax[2].set_title('Ice Volume') + ax[2].set_xlabel('years') + # }}} + +if 6 in steps: + # Step 6: Extract Box SMB{{{ + print(' Step 6: Extract Box SMB') + md = loadmodel('./Models/Greenland.Transient.nc') + + #Set surface mass balance + ncbox = Dataset('../Data/Box_Greenland_SMB_monthly_1840-2012_5km_cal_ver20141007.nc', mode='r') + lat = np.squeeze(ncbox.variables['lat'][:].data) + lon = np.squeeze(ncbox.variables['lon'][:].data) + smbbox = np.squeeze(ncbox.variables['MassFlux'][:].data) + ncbox.close() + [x1, y1] = ll2xy(lat, lon, + 1, 45, 70) + + years_of_simulation = np.arange(1840, 2012 + 1) + t = np.arange(years_of_simulation[0], years_of_simulation[-1] + 11 / 12, 1 / 12) + #Area of grid for 5km box + area_of_grid = 5000 * 5000 + totalsmb = reshape(np.nansum(smbbox / 1000, axis=(-2, -1)), (len(t), 1)) * area_of_grid + + #save surface mass balance mat dataset + smbmean = np.nanmean(smbbox, axis=(0, 1)) + SMB = {} + SMB['smbmean'] = smbmean + SMB['totalsmb '] = totalsmb + SMB['smbbox'] = smbbox + SMB['x1'] = x1 + SMB['y1'] = y1 + SMB['t'] = t + + np.savez('./smbbox.npz', **SMB) + + #plot a time series of total SMB + fig = plt.figure(tight_layout=True) + ax = fig.add_subplot(111) + ax.plot(t, totalsmb / 1e9) + ax.set_title('Total Surface mass balance, Gt') + ax.set_xlabel('year') + ax.set_ylabel('Gt/yr') + + del smbbox + # }}} + +if 7 in steps: + # Step 7: Historical Relaxation run {{{ + print(' Step 7: Historical Relaxation run') + md = loadmodel('./Models/Greenland.Control_drag.nc') + + with open('./smbbox.npz', "rb") as smbFile: + SMB = np.load(smbFile) + x1 = np.squeeze(SMB['x1']) + y1 = np.squeeze(SMB['y1']) + smbmean = np.squeeze(SMB['smbmean']) + + #convert mesh x, y into the Box projection + [md.mesh.lat, md.mesh.long] = xy2ll(md.mesh.x, md.mesh.y, + 1, 39, 71) + [xi, yi] = ll2xy(md.mesh.lat, md.mesh.long, + 1, 45, 70) + + #Interpolate and set surface mass balance + x1 = x1.flatten() + y1 = y1.flatten() + smbmean = smbmean.flatten() + index = BamgTriangulate(x1, y1) + smb_mo = InterpFromMeshToMesh2d(index, x1, y1, smbmean, xi, yi) + smb = smb_mo * 12 / 1000 * md.materials.rho_freshwater / md.materials.rho_ice + md.smb.mass_balance = np.append(smb, 1) + + #Set transient options, run for 20 years, saving every timestep + md.timestepping.time_step = 0.2 + md.timestepping.final_time = 20 + md.settings.output_frequency = 1 + + #Additional options + md.inversion.iscontrol = 0 + md.transient.requested_outputs = ['IceVolume', 'TotalSmb', 'SmbMassBalance'] + md.verbose = verbose('solution', True, 'module', True) + + #Go solve + md.cluster = generic('name', gethostname(), 'np', 2) + md = solve(md, 'Transient') + + export_netCDF(md, './Models/Greenland.HistoricTransient.nc') + # }}} + +if 8 in steps: + # Step 8: Plotting exercise {{{ + print(' Step 8: Plotting exercise') + #Load historic transient model + + #Create Line Plots of relaxation run. Create a figure. + + #Save surface mass balance, by looping through 200 years (1000 steps) + #Note, the first output will always contain output from time step 1 + + #Plot surface mass balance time series in first subplot + + #Title this plot Mean surface mass balance + + #Save velocity by looping through 200 years + + #Plot velocity time series in second subplot + + #Title this plot Mean Velocity + + #Save Ice Volume by looping through 200 years + + #Plot volume time series in third subplot + + #Title this plot Mean Velocity and add an x label of years + # }}} + +if 9 in steps: + # Step 9: Box Transient run{{{ + print(' Step 9: Box Transient run') + md = loadmodel('./Models/Greenland.HistoricTransient.nc') + + #load past transient results + md.geometry.base = md.results.TransientSolution[-1].Base + md.geometry.thickness = md.results.TransientSolution[-1].Thickness + md.geometry.surface = md.geometry.base + md.geometry.thickness + md.initialization.vx = md.results.TransientSolution[-1].Vx + md.initialization.vy = md.results.TransientSolution[-1].Vy + md.results = [] + + #convert mesh x, y into the Box projection + [md.mesh.lat, md.mesh.long] = xy2ll(md.mesh.x, md.mesh.y, + 1, 39, 71) + [xi, yi] = ll2xy(md.mesh.lat, md.mesh.long, + 1, 45, 70) + + #Set surface mass balance + with open('./smbbox.npz', "rb") as smbFile: + SMB = np.load(smbFile) + x1 = np.squeeze(SMB['x1']) + y1 = np.squeeze(SMB['y1']) + smbbox = np.squeeze(SMB['smbbox']) + + x1 = x1.flatten() + y1 = y1.flatten() + index = BamgTriangulate(x1, y1) + #Set years to run + years_of_simulation = np.arange(2003, 2012 + 1) + + #initialize surface mass balance matrix + smb = np.nan * np.ones((md.mesh.numberofvertices, len(years_of_simulation) * 12)) + + #Interpolate and set surface mass balance + for year in years_of_simulation: + for month in range(0, 12): + smb_mo = griddata((np.double(x1), np.double(y1)), np.double(smbbox[year - 1840, month, :, :].flatten()), (xi, yi), method='nearest') + smb[:, (year - years_of_simulation[0]) * 12 + month] = smb_mo + smb = smb * 12 / 1000 * md.materials.rho_freshwater / md.materials.rho_ice + timer = np.arange(1 / 24, len(years_of_simulation), 1 / 12) + md.smb.mass_balance = np.vstack((smb, timer)) + + #Set transient options, monthly timestep, saving every month + md.timestepping.time_step = 1 / 12 + md.timestepping.final_time = len(years_of_simulation) + md.settings.output_frequency = 1 + + #Additional options + md.inversion.iscontrol = 0 + md.transient.requested_outputs = ['IceVolume', 'TotalSmb', 'SmbMassBalance'] + md.verbose = verbose('solution', True, 'module', True) + + #Go solve + md.cluster = generic('name', gethostname(), 'np', 2) + md = solve(md, 'Transient') + + export_netCDF(md, './Models/Greenland.BoxTransient.nc') + # }}} + +if 10 in steps: + print(' Step 10: Plot Box Transient') + md = loadmodel('./Models/Greenland.BoxTransient.nc') + + #Set years run + years_of_simulation = np.arange(2003, 2012 + 1) + t = np.arange(years_of_simulation[0], years_of_simulation[-1] + 11 / 12, 1 / 12) + + #Line Plots + layout, ax = plt.subplots(3, 1, sharex=True, sharey=False, figsize=(5, 5)) + #Plot surface mass balance + surfmb = [] + vel = [] + volume = [] + for i in range(0, len(t)): + surfmb.append(md.results.TransientSolution[i].TotalSmb) + vel.append(md.results.TransientSolution[i].Vel) + volume.append(md.results.TransientSolution[i].IceVolume) + ax[0].plot(t, surfmb) + ax[0].set_title('Total Surface mass balance') + ax[1].plot(t, np.nanmax(vel, axis=1)) + ax[1].set_title('Max Velocity') + ax[2].plot(t, volume) + ax[2].set_title('Ice Volume') + ax[2].set_xlabel('years') Index: /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipA.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipA.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipA.par (revision 27955) @@ -0,0 +1,52 @@ +%Parameterization for ISMIP A experiment + +%Set the Simulation generic name #md.miscellaneous +%-> + +%Geometry +disp(' Constructing Geometry'); + +%Define the geometry of the simulation #md.geometry +%surface is [-x*tan(0.5*pi/180)] #md.mesh +%-> + +%base is [surface-1000+500*sin(x*2*pi/L).*sin(y*2*pi/L)] +%L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x) +%-> + +%-> + +%thickness is the difference between surface and base #md.geometry +%-> + +%plot the geometry to check it out +%-> + + +disp(' Defining friction parameters'); + +%These parameters will not be used but need to be fixed #md.friction +%one friciton coefficient per node (md.mesh.numberofvertices,1) +%-> + +%one friciton exponent (p,q) per element +%-> + +%-> + + +disp(' Construct ice rheological properties'); + +%The rheology parameters sit in the material section #md.materials +%B has one value per vertex +%-> + +%n has one value per element +%-> + + +disp(' Set boundary conditions'); + +%Set the default boundary conditions for an ice-sheet +% #help SetIceSheetBC +%-> Index: /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipA.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipA.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipA.py (revision 27955) @@ -0,0 +1,55 @@ +import numpy as np +from plotmodel import plotmodel +from SetIceSheetBC import SetIceSheetBC +#Parameterization for ISMIP A experiment + +#Set the Simulation generic name #md.miscellaneous +#-> + +#Geometry +print(' Constructing Geometry') + +#Define the geometry of the simulation #md.geometry +#surface is [-x*tan(0.5*pi/180)] #md.mesh +#-> + +#base is [surface-1000+500*sin(x*2*pi/L).*sin(y*2*pi/L)] +#L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x) +#-> + +#-> + +#thickness is the difference between surface and base #md.geometry +#-> + +#plot the geometry to check it out +#-> + + +print(' Defining friction parameters') + +#These parameters will not be used but need to be fixed #md.friction +#one friciton coefficient per node (md.mesh.numberofvertices,1) +#-> + +#one friciton exponent (p,q) per element +#-> + +#-> + + +print(' Construct ice rheological properties') + +#The rheology parameters sit in the material section #md.materials +#B has one value per vertex +#-> + +#n has one value per element +#-> + + +print(' Set boundary conditions') + +#Set the default boundary conditions for an ice-sheet +# help SetIceSheetBC +#-> Index: /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipF.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipF.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipF.par (revision 27955) @@ -0,0 +1,64 @@ +%Parameterization for ISMIP F experiment + +%Set the Simulation generic name #md.miscellaneous +%-> + +%Geometry +disp(' Constructing Geometry'); + +%Define the geometry of the simulation #md.geometry +%surface is [-x*tan(3.0*pi/180)] #md.mesh +%-> + +%base is [surface-1000+100*exp(-((x-L/2).^2+(y-L/2).^2)/(10000.^2))] +%L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x) +%-> + +%-> + +%thickness is the difference between surface and base #md.geometry +%-> + +%plot the geometry to check it out +%-> + + +disp(' Defining friction parameters'); + +%These parameters will not be used but need to be fixed #md.friction +%one friciton coefficient per node (md.mesh.numberofvertices,1) +%conversion from year to seconds with #md.constants.yts +%-> + +%one friction exponent (p,q) per element +%-> + +%-> + + +disp(' Construct ice rheological properties'); + +%The rheology parameters sit in the material section #md.materials +%B has one value per vertex +%-> + +%n has one value per element +%-> + + +disp(' Set boundary conditions'); + +%Set the default boundary conditions for an ice-sheet +% #help SetIceSheetBC +%-> + +disp(' Initializing velocity and pressure'); + +%initialize the velocity and pressurefields of #md.initialization +%-> + +%-> + +%-> + +%-> Index: /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipF.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipF.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/IsmipF.py (revision 27955) @@ -0,0 +1,67 @@ +import numpy as np +from plotmodel import plotmodel +from SetIceSheetBC import SetIceSheetBC +#Parameterization for ISMIP F experiment + +#Set the Simulation generic name #md.miscellaneous +#-> + +#Geometry +print(' Constructing Geometry') + +#Define the geometry of the simulation #md.geometry +#surface is [-x*tan(3.0*pi/180)] #md.mesh +#-> + +#base is [surface-1000+100*exp(-((x-L/2).^2+(y-L/2).^2)/(10000.^2))] +#L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x) +#-> + +#-> + +#thickness is the difference between surface and base #md.geometry +#-> + +#plot the geometry to check it out +#-> + + +print(' Defining friction parameters') + +#These parameters will not be used but need to be fixed #md.friction +#one friciton coefficient per node (md.mesh.numberofvertices,1) +#conversion from year to seconds with #md.constants.yts +#-> + +#one friction exponent (p,q) per element +#-> + +#-> + + +print(' Construct ice rheological properties') + +#The rheology parameters sit in the material section #md.materials +#B has one value per vertex +#-> + +#n has one value per element +#-> + + +print(' Set boundary conditions') + +#Set the default boundary conditions for an ice-sheet +# #help SetIceSheetBC +#-> + +print(' Initializing velocity and pressure') + +#initialize the velocity and pressurefields of #md.initialization +#-> + +#-> + +#-> + +#-> Index: /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/runme.m (revision 27955) @@ -0,0 +1,217 @@ +%which steps to perform; steps are from 1 to 8 +%step 7 is specific to ISMIPA +%step 8 is specific to ISMIPF + +steps=[1]; + +% parameter file to be used, choose between IsmipA.par or IsmipF.par +ParamFile='IsmipA.par'; + +%Run Steps + +%Mesh Generation #1 +if any(steps==1) + + %initialize md as a new model #help model + %-> + + % generate a squaremesh #help squaremesh + % Side is 80 km long with 20 points + %-> + + % plot the given mesh #plotdoc + %-> + + % save the given model + %-> + +end + +%Masks #2 +if any(steps==2) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % set the mask #help setmask + % all MISMIP nodes are grounded + %-> + + % plot the given mask #md.mask to locate the field + %-> + + % save the given model + %-> + +end + +%Parameterization #3 +if any(steps==3) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % parametrize the model # help parameterize + % you will need to fil-up the parameter file (given by the + % ParamFile variable) + %-> + + % save the given model + %-> + +end + +%Extrusion #4 +if any(steps==4) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % vertically extrude the preceding mesh #help extrude + % only 5 layers exponent 1 + %-> + + % plot the 3D geometry #plotdoc + %-> + + % save the given model + %-> + +end + +%Set the flow computing method #5 +if any(steps==5) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % set the approximation for the flow computation #help setflowequation + % We will be using the Higher Order Model (HO) + %-> + + % save the given model + %-> + +end + +%Set Boundary Conditions #6 +if any(steps==6) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % dirichlet boundary condition are known as SPCs + % ice frozen to the base, no velocity #md.stressbalance + % SPCs are initialized at NaN one value per vertex + %-> + + %-> + + %-> + + % extract the nodenumbers at the base #md.mesh.vertexonbase + %-> + + % set the sliding to zero on the bed (Vx and Vy) + %-> + + %-> + + % periodic boundaries have to be fixed on the sides + % Find the indices of the sides of the domain, for x and then for y + % for x + % create maxX, list of indices where x is equal to max of x (use >> help find) + %-> + + % create minX, list of indices where x is equal to min of x + %-> + + % for y + % create maxY, list of indices where y is equal to max of y + % but not where x is equal to max or min of x + % (i.e, indices in maxX and minX should be excluded from maxY and minY) + %-> + + % create minY, list of indices where y is equal to max of y + % but not where x is equal to max or min of x + %-> + + % set the node that should be paired together, minX with maxX and minY with maxY + % #md.stressbalance.vertex_pairing + %-> + + if (ParamFile=='IsmipF.par') + % if we are dealing with IsmipF the solution is in masstransport + md.masstransport.vertex_pairing=md.stressbalance.vertex_pairing; + end + % save the given model + %-> + +end + +%Solving #7 +if any(steps==7) + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % Set cluster #md.cluster + % generic parameters #help generic + % set only the name and number of process + %-> + + % Set which control message you want to see #help verbose + %-> + + % Solve #help solve + % we are solving a StressBalanc + %-> + + % save the given model + %-> + + % plot the surface velocities #plotdoc + %-> +end + +%Solving #8 +if any(steps==8) + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % Set cluster #md.cluster + % generic parameters #help generic + % set only the name and number of process + %-> + + % Set which control message you want to see #help verbose + %-> + + % set the transient model to ignore the thermal model + % #md.transient + %-> + + % define the timestepping scheme + % everything here should be provided in years #md.timestepping + % give the length of the time_step (4 years) + %-> + + % give final_time (20*4 years time_steps) + %-> + + % Solve #help solve + % we are solving a TransientSolution + %-> + + % save the given model + %-> + + % plot the surface velocities #plotdoc + %-> +end Index: /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/runme.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/runme.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/ISMIP/runme.py (revision 27955) @@ -0,0 +1,217 @@ +import numpy as np +from model import * +from squaremesh import squaremesh +from plotmodel import plotmodel +from export_netCDF import export_netCDF +from loadmodel import loadmodel +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from socket import gethostname +from solve import solve +#which steps to perform; steps are from 1 to 8 +#step 7 is specific to ISMIPA +#step 8 is specific to ISMIPF + +steps = [1] + +# parameter file to be used, choose between IsmipA.py or IsmipF.py +ParamFile = 'IsmipA.py' + +#Run Steps + +#Mesh Generation #1 +if 1 in steps: + print("Now generating the mesh") + #initialize md as a new model #help(model) + #-> + + # generate a squaremesh #help(squaremesh) + # Side is 80 km long with 20 points + #-> + + # plot the given mesh #plotdoc + #-> + + # save the given model + #-> + +#Masks #2 +if 2 in steps: + print("Setting the masks") + # load the preceding step #help(loadmodel) + # path is given by the organizer with the name of the given step + #-> + + # set the mask #help(setmask) + # all MISMIP nodes are grounded + #-> + + # plot the given mask #md.mask to locate the field + #-> + + # save the given model + #-> + +#Parameterization #3 +if 3 in steps: + print("Parameterizing") + # load the preceding step #help(loadmodel) + # path is given by the organizer with the name of the given step + #-> + + # parametrize the model # help(parameterize) + # you will need to fil-up the parameter file (given by the + # ParamFile variable) + #-> + + # save the given model + #-> + + +#Extrusion #4 +if 4 in steps: + print("Extruding") + # load the preceding step #help(loadmodel) + # path is given by the organizer with the name of the given step + #-> + + # vertically extrude the preceding mesh #help(extrude) + # only 5 layers exponent 1 + #-> + + # plot the 3D geometry #plotdoc + #-> + + # save the given model + #-> + +#Set the flow computing method #5 +if 5 in steps: + print("setting flow approximation") + # load the preceding step #help(loadmodel) + # path is given by the organizer with the name of the given step + #-> + + # set the approximation for the flow computation #help(setflowequation) + # We will be using the Higher Order Model (HO) + #-> + + # save the given model + #-> + +#Set Boundary Conditions #6 +if 6 in steps: + print("setting boundary conditions") + # load the preceding step #help(loadmodel) + # path is given by the organizer with the name of the given step + #-> + + # dirichlet boundary condition are known as SPCs + # ice frozen to the base, no velocity #md.stressbalance + # SPCs are initialized at NaN one value per vertex + #-> + + #-> + + #-> + + # extract the nodenumbers at the base #md.mesh.vertexonbase + #-> + + # set the sliding to zero on the bed (Vx and Vy) + #-> + + #-> + + # periodic boundaries have to be fixed on the sides + # Find the indices of the sides of the domain, for x and then for y + # for x + # create maxX, list of indices where x is equal to max of x + #-> + + # create minX, list of indices where x is equal to min of x + #-> + + # for y + # create maxY, list of indices where y is equal to max of y + # but not where x is equal to max or min of x + # (i.e, indices in maxX and minX should be excluded from maxY and minY) + #-> + + # create minY, list of indices where y is equal to max of y + # but not where x is equal to max or min of x + #-> + + # set the node that should be paired together, minX with maxX and minY with maxY + # #md.stressbalance.vertex_pairing + #-> + + if ParamFile=='IsmipF.py': + # if we are dealing with IsmipF the solution is in masstransport + md.masstransport.vertex_pairing = md.stressbalance.vertex_pairing + + # save the given model + #-> + +#Solving #7 +if 7 in steps: + print("running the solver for the A case") + # load the preceding step #help(loadmodel) + # path is given by the organizer with the name of the given step + #-> + + # Set cluster #md.cluster + # generic parameters #help(generic) + # set only the name and number of process + #-> + + # Set which control message you want to see #help(verbose) + #-> + + # Solve #help(solve) + # we are solving a StressBalanc + #-> + + # save the given model + #-> + + # plot the surface velocities #plotdoc + #-> + +#Solving #8 +if 8 in steps: + print("running the solver for the F case") + # load the preceding step #help(loadmodel) + # path is given by the organizer with the name of the given step + #-> + + # Set cluster #md.cluster + # generic parameters #help(generic) + # set only the name and number of process + #-> + + # Set which control message you want to see #help(verbose) + #-> + + # set the transient model to ignore the thermal model + # #md.transient + #-> + + # define the timestepping scheme + # everything here should be provided in years #md.timestepping + # give the length of the time_step (4 years) + #-> + + # give final_time (20*4 years time_steps) + #-> + + # Solve #help(solve) + # we are solving a TransientSolution + #-> + + # save the given model + #-> + + # plot the surface velocities #plotdoc + #-> Index: /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/DomainOutline.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/DomainOutline.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/DomainOutline.exp (revision 27955) @@ -0,0 +1,733 @@ +## Name:DomainOutline +## Icon:0 +# Points Count Value +727 1.000000 +# X pos Y pos +47662.8073760000 -2621047.2585999998 +39869.9055420000 -2638077.6292949999 +26037.5047870000 -2644088.3483640002 +24868.5695120000 -2659115.1460360000 +25647.8596950000 -2674141.9437079998 +16880.8451320000 -2687666.0616130000 +515.7512810000 -2685662.4885900002 +-7666.7956450000 -2672639.2639410002 +-22083.6640370000 -2677147.3032430001 +-30071.3884170000 -2690170.5278920000 +-44683.0793550000 -2694678.5671930001 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-2577093.8754090001 +66950.2394150000 -2594124.2461040001 +57598.7572140000 -2581101.0214539999 +53117.8386600000 -2598131.3921500002 +41818.1310010000 -2586610.8472679998 +30810.6571600000 -2599133.1786610000 +44253.4128240000 -2608650.1505200001 +47662.8073760000 -2621047.2585999998 + Index: /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Greenland.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Greenland.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Greenland.par (revision 27955) @@ -0,0 +1,99 @@ +%Name and Coordinate system +md.miscellaneous.name='SeaRISEgreenland'; +md.mesh.epsg=3413; + +disp(' Loading SeaRISE data from NetCDF'); +ncdata='../Data/Greenland_5km_dev1.2.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +velx = ncread(ncdata,'surfvelx')'; +vely = ncread(ncdata,'surfvely')'; +temp = ncread(ncdata,'airtemp2m')'; +smb = ncread(ncdata,'smb')'; +gflux = ncread(ncdata,'bheatflx')'; + +disp(' Interpolating surface and bedrock'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); + +disp(' Constructing thickness'); +md.geometry.thickness=md.geometry.surface-md.geometry.base; + +%Set min thickness to 1 meter +pos0=find(md.geometry.thickness<=0); +md.geometry.thickness(pos0)=1; +md.geometry.surface=md.geometry.thickness+md.geometry.base; + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%Reading IceBridge data for Jakobshavn +disp(' reading IceBridge Jakobshavn bedrock'); +fid = fopen('../Data/Jakobshavn_2008_2011_Composite/grids/Jakobshavn_2008_2011_Composite_XYZGrid.txt'); +titles = fgets(fid); +data = fscanf(fid,'%g,%g,%g,%g,%g',[5 266400])'; +fclose(fid); + +[xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70); +bed = flipud(reshape(data(:,5),[360 740])); bed(find(bed==-9999))=NaN; +bedy = flipud(reshape(data(:,1),[360 740])); +bedx = flipud(reshape(data(:,2),[360 740])); + +%Insert Icebridge bed and recalculate thickness +bed_jks=InterpFromGridToMesh(bedx(1,:)',bedy(:,1),bed,xi,yi,NaN); +in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,... + 'Jak_grounded.exp','node',1); +bed_jks(~in)=NaN; +pos=find(~isnan(bed_jks)); +md.geometry.base(pos)=bed_jks(pos); +md.geometry.thickness=md.geometry.surface-md.geometry.base; +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +disp(' Interpolating velocities '); +md.inversion.vx_obs = InterpFromGridToMesh(x1,y1,velx,md.mesh.x,md.mesh.y,0); +md.inversion.vy_obs = InterpFromGridToMesh(x1,y1,vely,md.mesh.x,md.mesh.y,0); +md.inversion.vel_obs = sqrt(md.inversion.vx_obs.^2+md.inversion.vy_obs.^2); +md.initialization.vx = md.inversion.vx_obs; +md.initialization.vy = md.inversion.vy_obs; +md.initialization.vz = zeros(md.mesh.numberofvertices,1); +md.initialization.vel= md.inversion.vel_obs; + +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; + +disp(' Interpolating surface mass balance'); +md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; + +disp(' Construct basal friction parameters'); +md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +pos=find(md.mask.ocean_levelset<0); +md.friction.coefficient(pos)=0; %no friction applied on floating ice +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.friction.q=ones(md.mesh.numberofelements,1); +md.friction.p=ones(md.mesh.numberofelements,1); + +disp(' Set other boundary conditions'); +md.mask.ice_levelset(md.mesh.vertexonboundary==1)=0; +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.thermal.spctemperature = [md.initialization.temperature;1]; %impose observed temperature on surface +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux=InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); + +disp(' Set Pressure'); +md.initialization.pressure=md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +disp(' Single point constraints'); +%Initialize single point constraint arrays +md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6); +md.stressbalance.spcvx = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvy = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvz = NaN*ones(md.mesh.numberofvertices,1); Index: /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Greenland_noOIB.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Greenland_noOIB.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Greenland_noOIB.par (revision 27955) @@ -0,0 +1,82 @@ +%Name and Coordinate system +md.miscellaneous.name='SeaRISEgreenland'; +md.mesh.epsg=3413; + +disp(' Loading SeaRISE data from NetCDF'); +ncdata='../Data/Greenland_5km_dev1.2.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +velx = ncread(ncdata,'surfvelx')'; +vely = ncread(ncdata,'surfvely')'; +temp = ncread(ncdata,'airtemp2m')'; +smb = ncread(ncdata,'smb')'; +gflux = ncread(ncdata,'bheatflx')'; + +disp(' Interpolating surface and bedrock'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); + +disp(' Constructing thickness'); +md.geometry.thickness=md.geometry.surface-md.geometry.base; + +%Set min thickness to 1 meter +pos0=find(md.geometry.thickness<=0); +md.geometry.thickness(pos0)=1; +md.geometry.surface=md.geometry.thickness+md.geometry.base; + +disp(' Interpolating velocities '); +md.inversion.vx_obs = InterpFromGridToMesh(x1,y1,velx,md.mesh.x,md.mesh.y,0); +md.inversion.vy_obs = InterpFromGridToMesh(x1,y1,vely,md.mesh.x,md.mesh.y,0); +md.inversion.vel_obs = sqrt(md.inversion.vx_obs.^2+md.inversion.vy_obs.^2); +md.initialization.vx = md.inversion.vx_obs; +md.initialization.vy = md.inversion.vy_obs; +md.initialization.vz = zeros(md.mesh.numberofvertices,1); +md.initialization.vel= md.inversion.vel_obs; + +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; + +disp(' Interpolating surface mass balance'); +md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; + +disp(' Construct basal friction parameters'); +md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +pos=find(md.mask.ocean_levelset<0); +md.friction.coefficient(pos)=0; %no friction applied on floating ice +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.friction.q=ones(md.mesh.numberofelements,1); +md.friction.p=ones(md.mesh.numberofelements,1); + +disp(' Set other boundary conditions'); +md.mask.ice_levelset(md.mesh.vertexonboundary==1)=0; +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.thermal.spctemperature = [md.initialization.temperature;1]; %impose observed temperature on surface +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux=InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); + +disp(' Set Pressure'); +md.initialization.pressure=md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +disp(' Single point constraint for continental model'); +%Set at least one vertex to velocity 0 so as to not get a singular problem (point on the wet peninsula) +md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6); +md.stressbalance.spcvx = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvy = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvz = NaN*ones(md.mesh.numberofvertices,1); +location = 1.0e+06 *[.32011 -2.2039]; +[dist pos]=min(sqrt((md.mesh.x - location(1)).^2 + (md.mesh.y - location(2)).^2)); +md.stressbalance.spcvx(pos) = 0; +md.stressbalance.spcvy(pos) = 0; +md.stressbalance.spcvz(pos) = 0; + Index: /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Greenland_solution.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Greenland_solution.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Greenland_solution.par (revision 27955) @@ -0,0 +1,103 @@ +%Name and Coordinate system +md.miscellaneous.name='SeaRISEgreenland'; +md.mesh.epsg=3413; + +disp(' Loading SeaRISE data from NetCDF'); +ncdata='../Data/Greenland_5km_dev1.2.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +velx = ncread(ncdata,'surfvelx')'; +vely = ncread(ncdata,'surfvely')'; +temp = ncread(ncdata,'airtemp2m')'; +smb = ncread(ncdata,'smb')'; +gflux = ncread(ncdata,'bheatflx')'; + +disp(' Interpolating surface and bedrock'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); + +disp(' Constructing thickness'); +md.geometry.thickness=md.geometry.surface-md.geometry.base; + +%Set min thickness to 1 meter +pos0=find(md.geometry.thickness<=0); +md.geometry.thickness(pos0)=1; +md.geometry.surface=md.geometry.thickness+md.geometry.base; + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%Reading IceBridge data for Jakobshavn +disp(' reading IceBridge Jakobshavn bedrock'); +fid = fopen('../Data/Jakobshavn_2008_2011_Composite_XYZGrid.txt'); +titles = fgets(fid); +data = fscanf(fid,'%g,%g,%g,%g,%g',[5 266400])'; +fclose(fid); + +[xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70); +bed = flipud(reshape(data(:,5),[360 740])); bed(find(bed==-9999))=NaN; +surf = flipud(reshape(data(:,4),[360 740])); surf(find(surf==-9999))=NaN; +bedy = flipud(reshape(data(:,1),[360 740])); +bedx = flipud(reshape(data(:,2),[360 740])); + +%Insert Icebridge bed and recalculate thickness +bed_jks=InterpFromGridToMesh(bedx(1,:)',bedy(:,1),bed,xi,yi,NaN); +surf_jks=InterpFromGridToMesh(bedx(1,:)',bedy(:,1),surf,xi,yi,NaN); +in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,... + 'Jak_grounded.exp','node',1); +bed_jks(~in)=NaN; +surf_jks(~in)=NaN; +pos=find(~isnan(bed_jks)); +md.geometry.base(pos)=bed_jks(pos); +md.geometry.surface(pos)=surf_jks(pos); +md.geometry.thickness=md.geometry.surface-md.geometry.base; +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +disp(' Interpolating velocities '); +md.inversion.vx_obs = InterpFromGridToMesh(x1,y1,velx,md.mesh.x,md.mesh.y,0); +md.inversion.vy_obs = InterpFromGridToMesh(x1,y1,vely,md.mesh.x,md.mesh.y,0); +md.inversion.vel_obs = sqrt(md.inversion.vx_obs.^2+md.inversion.vy_obs.^2); +md.initialization.vx = md.inversion.vx_obs; +md.initialization.vy = md.inversion.vy_obs; +md.initialization.vz = zeros(md.mesh.numberofvertices,1); +md.initialization.vel= md.inversion.vel_obs; + +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; + +disp(' Interpolating surface mass balance'); +md.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.mass_balance*md.materials.rho_water/md.materials.rho_ice; + +disp(' Construct basal friction parameters'); +md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +pos=find(md.mask.ocean_levelset<0); +md.friction.coefficient(pos)=0; %no friction applied on floating ice +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.friction.q=ones(md.mesh.numberofelements,1); +md.friction.p=ones(md.mesh.numberofelements,1); + +disp(' Set other boundary conditions'); +md.mask.ice_levelset(md.mesh.vertexonboundary==1)=0; +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.thermal.spctemperature = [md.initialization.temperature;1]; %impose observed temperature on surface +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux=InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); + +disp(' Set Pressure'); +md.initialization.pressure=md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +disp(' Single point constraints'); +%Initialize single point constraint arrays +md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6); +md.stressbalance.spcvx = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvy = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvz = NaN*ones(md.mesh.numberofvertices,1); Index: /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Jak_grounded.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Jak_grounded.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Jak_grounded.exp (revision 27955) @@ -0,0 +1,19 @@ +## Name:Jak_grouded +## Icon:0 +# Points Count Value +13 1.000000 +# X pos Y pos +-414397.6663804040 -2243466.6708395295 +-421486.9037621063 -2215731.3059818177 +-342860.8164377716 -2178965.8223332223 +-275835.2993744044 -2209281.2211311869 +-226210.6377024883 -2262816.9253914217 +-228144.0660793162 -2295067.3496445753 +-333193.6745536321 -2328607.7908678548 +-379595.9555975018 -2325382.7484425395 +-422775.8560133249 -2285392.2223686292 +-427287.1888925899 -2265396.9593316740 +-411819.7618779668 -2254431.8150856020 +-413108.7141291854 -2243466.6708395295 +-414397.6663804040 -2243466.6708395295 + Index: /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Jak_outline.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Jak_outline.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/Jak_outline.exp (revision 27955) @@ -0,0 +1,17 @@ +## Name:Jak +## Icon:0 +# Points Count Value +11 1.000000 +# X pos Y pos +-421561.7247949215 -2216716.3488182197 +-386019.6416099078 -2203459.4896082953 +-351446.8879663036 -2185999.2360147359 +-289086.6874689616 -2214129.6445821370 +-255160.1535196303 -2282353.9688088228 +-340138.0433165266 -2317597.8140254519 +-383306.1449952667 -2302506.6581698526 +-416391.9672407377 -2279120.5885137189 +-448056.7322601135 -2246463.4475331730 +-429126.8716234095 -2231167.6696134652 +-421561.7247949215 -2216716.3488182197 + Index: /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/data_gaps.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/data_gaps.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/data_gaps.exp (revision 27955) @@ -0,0 +1,70 @@ +## Name:data_gaps +## Icon:0 +# Points Count Value +13 1.000000 +# X pos Y pos +-183076.0390091268 -1794119.5324780210 +-233886.6983670916 -1838953.5447257366 +-239864.4229974404 -2006333.8571172084 +-299641.6693009282 -2081057.2108634012 +-269753.0461491842 -2116924.4206615738 +-257797.5968884868 -2185669.9061080711 +-278719.6330947075 -2248437.5232548732 +-254808.7345733123 -2266371.1281539593 +-224920.1114215683 -2167736.3012089850 +-198020.3505849990 -2093012.9474627920 +-123298.7927056390 -1967477.7131691882 +-180087.1766939524 -1797108.4666278686 +-183076.0390091268 -1794119.5324780210 + +## Name:data_gaps +## Icon:0 +# Points Count Value +12 1.000000 +# X pos Y pos +-90421.3072387208 -1824008.8739764981 +-117321.0680752902 -1946555.1741202541 +-156176.2781725575 -2075079.3425637058 +-177098.3143787782 -2203603.5110071572 +-174109.4520636038 -2314194.0745515227 +-72488.1333476745 -2293271.5355025884 +-93410.1695538952 -2203603.5110071572 +-30644.0609352330 -2206592.4451570050 +-6733.1624138379 -2081057.2108634012 +44077.4969441269 -1967477.7131691882 +-93410.1695538952 -1824008.8739764981 +-90421.3072387208 -1824008.8739764981 + +## Name:data_gaps +## Icon:0 +# Points Count Value +15 1.000000 +# X pos Y pos +-87432.4449235464 -2365005.9550989335 +-287686.2200402305 -2639987.8968849229 +-284697.3577250564 -2879102.6288727401 +-470006.8212658686 -2983715.3241174100 +-538750.6545148797 -3157073.5048085772 +-356430.0532892416 -3267664.0683529424 +-189053.7636394757 -3270653.0025027902 +-272741.9084643587 -3243752.5951541606 +-218942.3867912197 -3076372.2827626891 +-236875.5606822660 -3019582.5339155826 +-117321.0680752902 -2834268.6166250245 +20166.5984227317 -2669877.2383834003 +-12710.8870441865 -2469618.6503436035 +-87432.4449235464 -2367994.8892487814 +-87432.4449235464 -2365005.9550989335 + +## Name:data_gaps +## Icon:0 +# Points Count Value +6 1.000000 +# X pos Y pos +-186064.9013243013 -1555004.8004902040 +-177098.3143787782 -1695484.7055330465 +-81454.7202931975 -1698473.6396828941 +-36621.7855655816 -1513159.7223923360 +-186064.9013243013 -1552015.8663403564 +-186064.9013243013 -1555004.8004902040 + Index: /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceBridge/runme.m (revision 27955) @@ -0,0 +1,156 @@ +clear all; +steps=[1]; + +%Location of SeaRISE dataset +ncdata='../Data/Greenland_5km_dev1.2.nc'; + +if any(steps==1) + disp(' Step 1: Mesh creation'); + + %Generate initial uniform mesh (resolution = 20000 m) + md=triangle(model,'./DomainOutline.exp',20000); + + % Get velocities (Note: You can use ncdisp('file') to see an ncdump) + x1 = ncread(ncdata,'x1'); + y1 = ncread(ncdata,'y1'); + velx = ncread(ncdata,'surfvelx'); + vely = ncread(ncdata,'surfvely'); + vx = InterpFromGridToMesh(x1,y1,velx',md.mesh.x,md.mesh.y,0); + vy = InterpFromGridToMesh(x1,y1,vely',md.mesh.x,md.mesh.y,0); + vel = sqrt(vx.^2+vy.^2); + + %Mesh greenland without refinement in Jak basin + md=bamg(md,'hmax',400000,'hmin',5000,'gradation',1.7,'field',vel,'err',8); + return; + + %Refine mesh in the region of Jakobshavn (resolution = 3000 m) + hmaxVertices=NaN*ones(md.mesh.numberofvertices,1); + in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,... + 'Jak_outline.exp','node',1); + hmaxVertices(find(in))=3000; + md=bamg(md,'hmax',400000,'hmin',5000,'gradation',1.7,'field',vel,... + 'err',8,'hmaxVertices',hmaxVertices); + + %convert x,y coordinates (Polar stereo) to lat/lon + [md.mesh.lat,md.mesh.long]=xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + + save ./Models/Greenland.Mesh_generation md; +end + +if any(steps==2) + disp(' Step 2: Parameterization'); + md = loadmodel('./Models/Greenland.Mesh_generation'); + + md = setmask(md,'',''); + md = parameterize(md,'./Greenland.par'); + md = setflowequation(md,'SSA','all'); + + save ./Models/Greenland.Parameterization2 md; +end + +if any(steps==3) + disp(' Step 3: Control method friction'); + md = loadmodel('./Models/Greenland.Parameterization2'); + + %Control general + md.inversion.iscontrol=1; + md.inversion.nsteps=30; + md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); + md.inversion.maxiter_per_step=5*ones(md.inversion.nsteps,1); + md.verbose=verbose('solution',true,'control',true); + + %Cost functions + md.inversion.cost_functions=[101 103 501]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); + md.inversion.cost_functions_coefficients(:,1)=350; + md.inversion.cost_functions_coefficients(:,2)=0.6; + md.inversion.cost_functions_coefficients(:,3)=2e-6; + + %Controls + md.inversion.control_parameters={'FrictionCoefficient'}; + md.inversion.gradient_scaling(1:md.inversion.nsteps)=50; + md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); + in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,... + 'data_gaps.exp','node',1); + md.inversion.cost_functions_coefficients(find(in),1)=0.0; + md.inversion.cost_functions_coefficients(find(in),2)=0.0; + + %Additional parameters + md.stressbalance.restol=0.01; + md.stressbalance.reltol=0.1; + md.stressbalance.abstol=NaN; + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + + md.verbose=verbose('solution',true,'control',true); + md=solve(md,'Stressbalance'); + + %Update model friction fields accordingly + md.friction.coefficient=md.results.StressbalanceSolution.FrictionCoefficient; + + save ./Models/Greenland.Control_drag md; +end + +if any(steps==4) + disp(' Step 4: Transient run'); + md = loadmodel('./Models/Greenland.Control_drag'); + + %Set surface mass balance + x1 = ncread(ncdata,'x1'); + y1 = ncread(ncdata,'y1'); + smb = ncread(ncdata,'smb'); + smb = InterpFromGridToMesh(x1,y1,smb',md.mesh.x,md.mesh.y,0)*1000/md.materials.rho_ice; + smb = [smb smb smb-1.0]; + md.smb.mass_balance = [smb;1 10 20]; + + %Set transient options, run for 20 years, saving every year + md.timestepping.time_step=0.2; %This must be reduced for finer resolutions + md.timestepping.final_time=20; + md.settings.output_frequency=1; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb','SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true,'convergence',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.Transient md; +end + +if any(steps==5) + disp(' Step 5: Plotting'); + md = loadmodel('./Models/Greenland.Transient'); + + %Planview plots + plotmodel(md,'data',md.results.TransientSolution(end).Vel,'caxis',[1e-1 6000],... + 'log', 10, 'title', 'Velocity (m/y)','gridded',1, ... + 'data', md.results.TransientSolution(end).SmbMassBalance, ... + 'title', 'Surface mass balance (m/y)','gridded',1, ... + 'data',md.results.TransientSolution(end).Thickness,... + 'title','Thickness (m)','gridded',1, ... + 'data',md.results.TransientSolution(end).Surface, ... + 'title', 'Surface (m)','gridded',1); + + %Line Plots + figure + time_plot=md.results.TransientSolution(1).time:md.timestepping.time_step:md.timestepping.final_time; + + %Plot surface mass balance + surfmb=[]; for i=1:100; surfmb=[surfmb ... + md.results.TransientSolution(i).SmbMassBalance]; end + subplot(3,1,1); plot(time_plot,mean(surfmb)); title('Mean Surface mass balance'); + + %Plot velocity + vel=[]; for i=1:100; vel=[vel md.results.TransientSolution(i).Vel]; end + subplot(3,1,2); plot(time_plot,mean(vel)); title('Mean Velocity'); + + %Plot Volume + volume=[]; for i=1:100; volume=[volume md.results.TransientSolution(i).IceVolume]; end + subplot(3,1,3); plot(time_plot,volume); title('Ice Volume'); + xlabel('years') +end Index: /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/Contour.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/Contour.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/Contour.exp (revision 27955) @@ -0,0 +1,11 @@ +## Name:Contour +## Icon:0 +# Points Count Value +5 1.000000 +# X pos Y pos +260815.7808871837 745919.4159004869 +712422.3484428506 757574.3645213632 +640499.8210173184 195805.8409951325 +342774.0098139530 279721.4710654409 +260815.7808871837 745919.4159004869 + Index: /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/EISMINT.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/EISMINT.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/EISMINT.par (revision 27955) @@ -0,0 +1,53 @@ +disp(' creating thickness'); +hmin=0.01; +hmax=2756.7; +radius=sqrt((md.mesh.x).^2+(md.mesh.y).^2); +radiusmax=max(radius); +radius(find(radius>(1.-10^-9)*radiusmax))=radiusmax; %eliminate roundoff issues in next statement +md.geometry.thickness=hmin*ones(size(md.mesh.x,1),1)+hmax*(4.*((1./2.)^(4./3.)*ones(size(md.mesh.x,1),1)-((radius)./(2.*radiusmax)).^(4./3.))).^(3./8.); +md.geometry.base=0.*md.geometry.thickness; +md.geometry.surface=md.geometry.base+md.geometry.thickness; + +disp(' creating drag'); +md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' creating temperatures'); +tmin=238.15; %K +st=1.67*10^-2/1000.; %k/m +md.initialization.temperature=tmin+st*radius; +md.basalforcings.geothermalflux=4.2*10^-2*ones(md.mesh.numberofvertices,1); + +disp(' creating flow law parameter'); +md.materials.rheology_B=6.81*10^7*ones(md.mesh.numberofvertices,1); %to have the same B as the analytical solution +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); + +disp(' creating surface mass balance'); +smb_max=0.5; %m/yr +sb=10^-2/1000.; %m/yr/m +rel=450.*1000.; %m +md.smb.mass_balance=min(smb_max,sb*(rel-radius)); + +disp(' creating velocities'); +constant=0.3; +md.inversion.vx_obs=constant/2.*md.mesh.x.*(md.geometry.thickness).^-1; +md.inversion.vy_obs=constant/2.*md.mesh.y.*(md.geometry.thickness).^-1; +md.inversion.vel_obs=sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2); +md.initialization.vx=zeros(md.mesh.numberofvertices,1); +md.initialization.vy=zeros(md.mesh.numberofvertices,1); +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); + +%Deal with boundary conditions: +disp(' boundary conditions for stressbalance model:'); +md=SetMarineIceSheetBC(md,'./RoundFront.exp'); + +radius=sqrt((md.mesh.x).^2+(md.mesh.y).^2); +pos=find(radius==min(radius)); +md.mesh.x(pos)=0.; md.mesh.y(pos)=0.; %the closest node to the center is changed to be exactly at the center + +md.stressbalance.spcvx(pos)=0.; +md.stressbalance.spcvy(pos)=0.; +md.stressbalance.spcvz(pos)=0.; Index: /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/RoundFront.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/RoundFront.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/RoundFront.exp (revision 27955) @@ -0,0 +1,47 @@ +## Name: +## Icon:0 +# Points Count Value +41 1 +# X pos Y pos +1000000.000000 0.000000 +987688.340595 156434.465040 +951056.516295 309016.994375 +891006.524188 453990.499740 +809016.994375 587785.252292 +707106.781187 707106.781187 +587785.252292 809016.994375 +453990.499740 891006.524188 +309016.994375 951056.516295 +156434.465040 987688.340595 +0.000000 1000000.000000 +-156434.465040 987688.340595 +-309016.994375 951056.516295 +-453990.499740 891006.524188 +-587785.252292 809016.994375 +-707106.781187 707106.781187 +-809016.994375 587785.252292 +-891006.524188 453990.499740 +-951056.516295 309016.994375 +-987688.340595 156434.465040 +-1000000.000000 0.000000 +-987688.340595 -156434.465040 +-951056.516295 -309016.994375 +-891006.524188 -453990.499740 +-809016.994375 -587785.252292 +-707106.781187 -707106.781187 +-587785.252292 -809016.994375 +-453990.499740 -891006.524188 +-309016.994375 -951056.516295 +-156434.465040 -987688.340595 +-0.000000 -1000000.000000 +156434.465040 -987688.340595 +309016.994375 -951056.516295 +453990.499740 -891006.524188 +587785.252292 -809016.994375 +707106.781187 -707106.781187 +809016.994375 -587785.252292 +891006.524188 -453990.499740 +951056.516295 -309016.994375 +987688.340595 -156434.465040 +1000000.000000 0.000000 + Index: /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/Square.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/Square.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/Square.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:domainoutline +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +0 0 +1000000 0 +1000000 1000000 +0 1000000 +0 0 Index: /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/SquareFront.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/SquareFront.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/SquareFront.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:icefront +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +-1000 900000 +-1000 1100000 +1100000 1100000 +1100000 900000 +-1000 900000 Index: /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/SquareShelf.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/SquareShelf.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/SquareShelf.par (revision 27955) @@ -0,0 +1,54 @@ +%Start defining model parameters here + +%Geometry +hmin=300; +hmax=1000; +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +xmin=min(md.mesh.x); +xmax=max(md.mesh.x); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x-xmin)/(xmax-xmin); +md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.base+md.geometry.thickness; + +%Initial velocity and pressure +x = transpose(ncread('../Data/SquareShelf.nc','x')); +y = transpose(ncread('../Data/SquareShelf.nc','y')); +vx = transpose(ncread('../Data/SquareShelf.nc','vx')); +vy = transpose(ncread('../Data/SquareShelf.nc','vy')); +index = transpose(ncread('../Data/SquareShelf.nc','index')); +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); +clear vx vy x y index; +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); + +%Materials +md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); + +%Friction +md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +%Numerical parameters +md.masstransport.stabilization=1; +md.thermal.stabilization=1; +md.settings.waitonlock=30; +md.verbose=verbose(0); +md.stressbalance.restol=0.10; +md.steadystate.reltol=0.02; +md.stressbalance.reltol=0.02; +md.stressbalance.abstol=NaN; +md.timestepping.time_step=1; +md.timestepping.final_time=3; + +%Boundary conditions: +md=SetIceShelfBC(md,'./SquareFront.exp'); + +%Change name so that no test have the same name +A=dbstack; +if (length(A)>2), md.miscellaneous.name=A(3).file(1:end-2); end Index: /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/eismint.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/eismint.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/eismint.m (revision 27955) @@ -0,0 +1,51 @@ +md=model(); + +%Create mesh with roundmesh +md=roundmesh(md,750000,30000); + +%Set mask +md=setmask(md,'',''); + +%Parameterize model +md=parameterize(md,'EISMINT.par'); + +%We extrude the model to have a 3d model +md=extrude(md,10,1.); + +%Set ice flow approximation +md=setflowequation(md,'SIA','all'); + +%Create boundary conditions: zero velocity on the bed +pos=find(md.mesh.vertexonbase); +md.stressbalance.spcvx(pos)=0; +md.stressbalance.spcvy(pos)=0; +md.stressbalance.spcvz(pos)=0; + +%Go Solve +md.cluster=generic('np',2); +md.verbose.convergence=1; +md=solve(md,'Stressbalance'); +vel=DepthAverage(md,sqrt(md.results.StressbalanceSolution.Vx.^2+md.results.StressbalanceSolution.Vy.^2)); + +%Calculate analytical velocity +constant=0.3; +vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; +vel_obs=sqrt(vx_obs.^2+vy_obs.^2); +vel_obs=project2d(md,vel_obs,1); + +plotmodel(md,... + 'data',vel ,'view',2,'caxis',[0 200],'title','Modelled velocity',... + 'data',vel_obs,'view',2,'caxis',[0 200],'title','Analytical velocity',... + 'data',abs(vel-vel_obs)./(vel_obs+eps)*100,'caxis',[0 30],'view',2,'title','Relative misfit (%)'); + +subplot(2,2,4) +hold on; +plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel,'r.'); +plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); +title('Analytical vs calculated velocity'); +xlabel('distance to the center of the ice sheet (m)'); +ylabel('velocity (m/yr)'); +legend('calculated velocity','exact velocity'); +axis([0 750000 0 200]); +hold off; Index: /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/IceflowModels/runme.m (revision 27955) @@ -0,0 +1,8 @@ +md=triangle(model(),'Square.exp',80000.); +md=setmask(md,'all',''); +md=parameterize(md,'SquareShelf.par'); +md=extrude(md,3,1); +%Set flow equation +md=setflowequation(md,'HO','Contour.exp','fill','SSA','coupling','tiling'); +%Solve +md=solve(md,'Stressbalance'); Index: /issm/branches/trunk-dlcheng-ASE/examples/Inversion/DomainOutline.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Inversion/DomainOutline.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Inversion/DomainOutline.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:DomainOutline +## Icon:0 +# Points Count Value +5 1.000000 +# X pos Y pos +0 0 +1000000 0 +1000000 1000000 +0 1000000 +0 0 Index: /issm/branches/trunk-dlcheng-ASE/examples/Inversion/Front.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Inversion/Front.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Inversion/Front.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:icefront +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +-1000 900000 +-1000 1100000 +1100000 1100000 +1100000 900000 +-1000 900000 Index: /issm/branches/trunk-dlcheng-ASE/examples/Inversion/Square.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Inversion/Square.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Inversion/Square.par (revision 27955) @@ -0,0 +1,24 @@ +%Start defining model parameters here + +disp(' creating thickness'); +hmin = 300; +hmax = 1000; +ymin = min(md.mesh.y); +ymax = max(md.mesh.y); +md.geometry.thickness = hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); +md.geometry.base = -md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface = md.geometry.base+md.geometry.thickness; + +disp(' creating drag'); +md.friction.coefficient=50*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; +md.friction.p = ones(md.mesh.numberofelements,1); +md.friction.q = ones(md.mesh.numberofelements,1); + +disp(' creating flow law paramter'); +md.materials.rheology_B=1.8*10^8*ones(md.mesh.numberofvertices,1); +md.materials.rheology_B(find(md.mesh.x=-18.0e5); +x_pig = x(posx); +posy = find(y<=1.0e5 & y>-4.0e5); +y_pig = flipud(y(posy)); + +vx_pig = flipud(vx(posx,posy)'); +vy_pig = flipud(vy(posx,posy)'); +vel_pig = sqrt(vx_pig.^2+vy_pig.^2); + +imagesc(x_pig,y_pig,log(vel_pig+1)); +axis xy equal tight; Index: /issm/branches/trunk-dlcheng-ASE/examples/Pig/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Pig/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Pig/runme.m (revision 27955) @@ -0,0 +1,182 @@ +steps=[1]; + +if any(steps==1) %Mesh Generation #1 + %Mesh parameters + domain =['./DomainOutline.exp']; + hinit=10000; % element size for the initial mesh + hmax=40000; % maximum element size of the final mesh + hmin=5000; % minimum element size of the final mesh + gradation=1.7; % maximum size ratio between two neighboring elements + err=8; % maximum error between interpolated and control field + + % Generate an initial uniform mesh (resolution = hinit m) + md=bamg(model,'domain',domain,'hmax',hinit); + + % Load Velocities + nsidc_vel='../Data/Antarctica_ice_velocity.nc'; + + % Get necessary data to build up the velocity grid + xmin = ncreadatt(nsidc_vel,'/','xmin'); + ymax = ncreadatt(nsidc_vel,'/','ymax'); + spacing = ncreadatt(nsidc_vel,'/','spacing'); + nx = double(ncreadatt(nsidc_vel,'/','nx')); + ny = double(ncreadatt(nsidc_vel,'/','ny')); + vx = double(ncread(nsidc_vel,'vx')); + vy = double(ncread(nsidc_vel,'vy')); + + % Read coordinates + xmin = strtrim(xmin); + xmin = str2num(xmin(1:end-2)); + ymax = strtrim(ymax); + ymax = str2num(ymax(1:end-2)); + spacing = strtrim(spacing); + spacing = str2num(spacing(1:end-2)); + + % Build the coordinates + x=xmin+(0:1:nx)'*spacing; + y=(ymax-ny*spacing)+(0:1:ny)'*spacing; + + % Interpolate velocities onto coarse mesh + vx_obs=InterpFromGridToMesh(x,y,flipud(vx'),md.mesh.x,md.mesh.y,0); + vy_obs=InterpFromGridToMesh(x,y,flipud(vy'),md.mesh.x,md.mesh.y,0); + vel_obs=sqrt(vx_obs.^2+vy_obs.^2); + clear vx vy x y; + + % Adapt the mesh to minimize error in velocity interpolation + md=bamg(md,'hmax',hmax,'hmin',hmin,'gradation',gradation,'field',vel_obs,'err',err); + + %ploting + plotmodel(md,'data','mesh') + + % Save model + save ./Models/PIG_Mesh_generation md; +end + +if any(steps==2) %Masks #2 + md = loadmodel('./Models/PIG_Mesh_generation'); + + % Load SeaRISe dataset for Antarctica + % http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica + searise='../Data/Antarctica_5km_withshelves_v0.75.nc'; + + %read thickness mask from SeaRISE + x1=double(ncread(searise,'x1')); + y1=double(ncread(searise,'y1')); + thkmask=double(ncread(searise,'thkmask')); + + %interpolate onto our mesh vertices + groundedice=double(InterpFromGridToMesh(x1,y1,thkmask',md.mesh.x,md.mesh.y,0)); + groundedice(groundedice<=0)=-1; + clear thkmask; + + %fill in the md.mask structure + md.mask.ocean_levelset=groundedice; %ice is grounded for mask equal one + md.mask.ice_levelset=-1*ones(md.mesh.numberofvertices,1);%ice is present when negatvie + + %ploting + plotmodel(md,'data',md.mask.ocean_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') + + % Save model + save ./Models/PIG_SetMask md; +end + +if any(steps==3) %Parameterization #3 + md = loadmodel('./Models/PIG_SetMask'); + md = parameterize(md,'./Pig.par'); + + % Use a MacAyeal flow model + md = setflowequation(md,'SSA','all'); + + % Save model + save ./Models/PIG_Parameterization md; +end + +if any(steps==4) %Control Method #4 + md = loadmodel('./Models/PIG_Parameterization'); + + % Control general + md.inversion.iscontrol=1; + md.inversion.maxsteps=20; + md.inversion.maxiter=40; + md.inversion.dxmin=0.1; + md.inversion.gttol=1.0e-4; + md.verbose=verbose('control',true); + + % Cost functions + md.inversion.cost_functions=[101 103 501]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); + md.inversion.cost_functions_coefficients(:,1)=1; + md.inversion.cost_functions_coefficients(:,2)=1; + md.inversion.cost_functions_coefficients(:,3)=8e-15; + + % Controls + md.inversion.control_parameters={'FrictionCoefficient'}; + md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); + + % Additional parameters + md.stressbalance.restol=0.01; + md.stressbalance.reltol=0.1; + md.stressbalance.abstol=NaN; + + % Solve + md.toolkits=toolkits; + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Stressbalance'); + + % Update model friction fields accordingly + md.friction.coefficient=md.results.StressbalanceSolution.FrictionCoefficient; + + plotmodel(md,'data',md.friction.coefficient) + + % Save model + save ./Models/PIG_Control_drag md; +end + +if any(steps==5) %Plot #5 + md = loadmodel('./Models/PIG_Control_drag'); + + plotmodel(md,... + 'data',md.initialization.vel,'title','Observed velocity',... + 'data',md.results.StressbalanceSolution.Vel,'title','Modeled Velocity',... + 'data',md.geometry.base,'title','Bed elevation',... + 'data',md.results.StressbalanceSolution.FrictionCoefficient,'title','Friction Coefficient',... + 'colorbar#all','on','colorbartitle#1-2','(m/yr)',... + 'caxis#1-2',([1.5,4000]),... + 'colorbartitle#3','(m)', 'log#1-2',10); +end + +if any(steps==6) %Higher-Order #6 + % Load Model + + % Disable inversion + + % Extrude Mesh + + % Set Flowequation + + % Solve + + % Save Model + +end % step 6 end + +if any(steps==7) %Plot #7 + mdHO = loadmodel('./Models/PIG_ModelHO'); + mdSSA = loadmodel('./Models/PIG_Control_drag'); + + basal=find(mdHO.mesh.vertexonbase); + surf=find(mdHO.mesh.vertexonsurface); + + plotmodel(mdHO,'nlines',3,'ncols',2,'axis#all','equal',... + 'data',mdHO.initialization.vel,'title','Observed velocity',... + 'data',(mdHO.results.StressbalanceSolution.Vel(surf)-mdHO.initialization.vel(surf)),'title','(HO-observed) velocities',... + 'data',mdSSA.results.StressbalanceSolution.Vel,'title','Modeled SSA Velocity',... + 'data',(mdHO.results.StressbalanceSolution.Vel(surf)-mdSSA.results.StressbalanceSolution.Vel),'title','(HO-SSA) velocities',... + 'data',mdHO.results.StressbalanceSolution.Vel,'title','Modeled HO surface Velocities',... + 'data',(mdHO.results.StressbalanceSolution.Vel(surf)-mdHO.results.StressbalanceSolution.Vel(basal)),'title','(HOsurf-HO base) velocities',... + 'caxis#1',([1.5,4000]),'caxis#3',([1.5,4000]),'caxis#5',([1.5,4000]),... + 'colorbar#all','on','view#all',2,... + 'colorbartitle#all','(m/yr)',... + 'layer#5',1, 'log#1', 10,'log#3', 10,'log#5', 10); +end Index: /issm/branches/trunk-dlcheng-ASE/examples/Pig2/DomainOutline.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Pig2/DomainOutline.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Pig2/DomainOutline.exp (revision 27955) @@ -0,0 +1,101 @@ +## Name: +## Icon:0 +# Points Count Value +95 25000.000000 +# X pos Y pos +-1712113.0179281300 -349656.0205056490 +-1711509.1917759699 -349354.1074295690 +-1709240.6586108401 -349354.1074295690 +-1707080.1508345299 -348922.0058743060 +-1705459.7700022999 -347193.5996532570 +-1703083.2114483600 -345249.1426545770 +-1701138.7544496800 -344168.8887664210 +-1698438.1197292900 -343952.8379887900 +-1698006.0181740201 -341900.3556012940 +-1693793.0280102200 -340279.9747690600 +-1691092.3932898301 -339631.8224361670 +-1688391.7585694401 -339415.7716585360 +-1686447.3015707601 -340063.9239914290 +-1683530.6160727399 -341036.1524907690 +-1682558.3875734000 -343304.6856558960 +-1682134.7209454600 -344182.1487658350 +-1682126.2860181299 -345681.2442098390 +-1681072.0444963200 -345932.4393879640 +-1680634.4718407800 -346682.5639403050 +-1680571.9614614199 -348557.8753211580 +-1677446.4424933300 -348370.3441830730 +-1675508.6207331200 -349495.5310115840 +-1676616.9911885399 -353567.0975933760 +-1672991.8601872099 -353799.6175753630 +-1668839.1631938200 -353999.1991486380 +-1667132.2298986400 -355121.4651541420 +-1666069.5534494901 -357496.8595698890 +-1662944.0344814099 -358309.4945015920 +-1660756.1712037399 -358747.0671571240 +-1657922.9836098100 -361682.8074238540 +-1656579.2228470000 -364003.8487410000 +-1653004.8841628900 -364748.0635758530 +-1653442.4568184200 -361622.5446077650 +-1651129.5727820301 -355684.0585683980 +-1648929.2928810001 -350845.9692010000 +-1646260.7698359799 -347802.2804785470 +-1644571.8968503401 -341785.6704672340 +-1643503.3064999001 -340869.0986596620 +-1643190.7546030900 -336680.9032424240 +-1642690.6715682000 -335243.1645171040 +-1641913.0916588283 -332341.0814454452 +-1640683.9739821283 -330436.6112348017 +-1637816.0327364956 -328532.1410241582 +-1635241.2508976001 -328652.8685499910 +-1631765.4107996500 -327017.1790921330 +-1625934.5618617306 -322342.6128395668 +-1620608.3852626982 -320438.1426289233 +-1616101.6204481323 -320438.1426289233 +-1611594.8556335662 -320914.2601815842 +-1607907.5026034669 -321866.4952869060 +-1602991.0318966676 -324723.2006028712 +-1599713.3847588014 -327579.9059188365 +-1593977.5022675355 -328532.1410241582 +-1590699.8551296694 -334721.6692087495 +-1589259.8391499999 -338300.0840570000 +-1588627.0898328500 -343572.9950327750 +-1588056.6000060199 -345432.3563530700 +-1586993.9235568701 -347432.6884926460 +-1589259.8391499999 -349315.9832070000 +-1585493.6744521901 -352996.1122558430 +-1585118.6121760199 -354496.3613605250 +-1585861.9157163899 -356240.3342513760 +-1586368.8197632500 -358747.0671571240 +-1587889.0972700799 -360996.6006787950 +-1586681.3716600600 -363935.4286441500 +-1585806.2263489999 -365748.2296456410 +-1586743.8820394201 -368373.6655788350 +-1586056.2678664399 -370123.9562009640 +-1585493.6744521901 -371124.1222707520 +-1586243.7990045301 -373562.0270658610 +-1414257.6683934701 -327460.5482541260 +-1412220.4351378100 -325972.8942023180 +-1404515.9240538401 -296165.1737279960 +-1387984.9332285200 -267002.0106682320 +-1360067.9373810000 -107884.1934940000 +-1423274.3497420000 -81217.9259650000 +-1402446.7987670000 -45916.9921070000 +-1478343.8065599999 60338.8188030000 +-1503760.4789370000 36334.1837800000 +-1528509.5619775900 63667.6809196406 +-1623055.4918765700 62841.1506965373 +-1725734.5897359999 -61372.6193030000 +-1719614.6457630000 -69022.5492690000 +-1759088.2843859999 -114004.1374660000 +-1755416.3180020000 -117064.1094530000 +-1761230.2647760001 -126856.0198080000 +-1758170.2927900001 -130527.9861920000 +-1762148.2563720001 -135423.9413700000 +-1764902.2311590000 -131445.9777880000 +-1769798.1863370000 -134199.9525750000 +-1775000.1387139999 -131445.9777880000 +-1794277.9622269999 -153477.7760890000 +-1712576.7101950001 -225081.1205660000 +-1729939.5891459100 -335652.4567604720 +-1712113.0179281300 -349656.0205056490 + Index: /issm/branches/trunk-dlcheng-ASE/examples/Pig2/FrontRetreat.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Pig2/FrontRetreat.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Pig2/FrontRetreat.exp (revision 27955) @@ -0,0 +1,17 @@ +## Name:FrontRetreat +## Icon:0 +# Points Count Value +11 1.000000 +# X pos Y pos +-1626858.6376043619 -327176.4356578548 +-1605190.4936934854 -325911.1425827671 +-1604716.0087903275 -316263.2828852235 +-1607088.4333061168 -312625.5652943464 +-1612465.9288752396 -311676.5954880306 +-1618476.0709819060 -312467.4036599604 +-1624011.7281854146 -313890.8583694341 +-1626858.6376043619 -315788.7979820656 +-1627807.6074106777 -319268.3539385567 +-1628756.5772169936 -322589.7482606619 +-1626858.6376043619 -327176.4356578548 + Index: /issm/branches/trunk-dlcheng-ASE/examples/Pig2/Pig.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Pig2/Pig.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Pig2/Pig.par (revision 27955) @@ -0,0 +1,118 @@ +% Parameters to change/Try +friction_coefficient = 10; % default [10] +Temp_change = 0; % default [0 K] + +%Name and Coordinate system +md.miscellaneous.name='PIG'; +md.mesh.epsg=3031; + +%NetCdf Loading +disp(' Loading SeaRISE data from NetCDF'); +ncdata='../Data/Antarctica_5km_withshelves_v0.75.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +temp = ncread(ncdata,'presartm')'; +smb = ncread(ncdata,'presprcp')'; +gflux = ncread(ncdata,'bheatflx_fox')'; + +%Geometry +disp(' Interpolating surface and ice base'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); +clear usrf, topg; + +disp(' Constructing thickness'); +md.geometry.thickness=md.geometry.surface-md.geometry.base; + +%ensure hydrostatic equilibrium on ice shelf: +di=md.materials.rho_ice/md.materials.rho_water; + +%Get the node numbers of floating nodes +pos=find(md.mask.ocean_levelset<0); + +%apply a flotation criterion on the precedingly defined nodes and +%redefine base and thickness accordingly +md.geometry.thickness(pos)=1/(1-di)*md.geometry.surface(pos); +md.geometry.base(pos)=md.geometry.surface(pos)-md.geometry.thickness(pos); +md.geometry.hydrostatic_ratio=ones(md.mesh.numberofvertices,1); %For Dakota + +%Set min thickness to 1 meter +pos0=find(md.geometry.thickness<=1); +md.geometry.thickness(pos0)=1; +md.geometry.surface=md.geometry.thickness+md.geometry.base; +md.geometry.bed=md.geometry.base; +md.geometry.bed(pos)=md.geometry.base(pos)-1000; + +%Initialization parameters +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15+Temp_change; +clear temp; + +disp(' Loading velocities data from NetCDF'); +nsidc_vel='../Data/Antarctica_ice_velocity.nc'; +xmin = ncreadatt(nsidc_vel,'/','xmin'); +ymax = ncreadatt(nsidc_vel,'/','ymax'); +spacing = ncreadatt(nsidc_vel,'/','spacing'); +nx = double(ncreadatt(nsidc_vel,'/','nx')); +ny = double(ncreadatt(nsidc_vel,'/','ny')); +velx = double(ncread(nsidc_vel,'vx')); +vely = double(ncread(nsidc_vel,'vy')); +% Read coordinates +xmin = strtrim(xmin); +xmin = str2num(xmin(1:end-2)); +ymax = strtrim(ymax); +ymax = str2num(ymax(1:end-2)); +spacing = strtrim(spacing); +spacing = str2num(spacing(1:end-2)); +% Build the coordinates +x2=xmin+(0:1:nx)'*spacing; +y2=(ymax-ny*spacing)+(0:1:ny)'*spacing; + +disp(' Set observed velocities') +md.initialization.vx=InterpFromGridToMesh(x2,y2,flipud(velx'),md.mesh.x,md.mesh.y,0); +md.initialization.vy=InterpFromGridToMesh(x2,y2,flipud(vely'),md.mesh.x,md.mesh.y,0); +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.vel=sqrt(md.initialization.vx.^2+md.initialization.vy.^2); +clear velx vely; + +disp(' Set Pressure'); +md.initialization.pressure=md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); + +%Forcings +disp(' Interpolating surface mass balance'); +mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=mass_balance*md.materials.rho_water/md.materials.rho_ice; +clear smb; + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux=InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); +clear gflux; + +%Friction and inversion set up +disp(' Construct basal friction parameters'); +md.friction.coefficient=friction_coefficient*ones(md.mesh.numberofvertices,1); +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +%no friction applied on floating ice +pos=find(md.mask.ocean_levelset<0); +md.friction.coefficient(pos)=0; +md.groundingline.migration='SubelementMigration'; + +md.inversion=m1qn3inversion(); +md.inversion.vx_obs=md.initialization.vx; +md.inversion.vy_obs=md.initialization.vy; +md.inversion.vel_obs=md.initialization.vel; + +disp(' Set boundary conditions'); +md=SetMarineIceSheetBC(md); +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.thermal.spctemperature = md.initialization.temperature; +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); Index: /issm/branches/trunk-dlcheng-ASE/examples/Pig2/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/Pig2/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/Pig2/runme.m (revision 27955) @@ -0,0 +1,228 @@ +steps=[1]; + +if any(steps==1) %Mesh Generation #1 + + %Mesh parameters + domain =['./DomainOutline.exp']; + hinit=5000; % element size for the initial mesh + hmax=40000; % maximum element size of the final mesh + hmin=4000; % minimum element size of the final mesh + gradation=1.7; % maximum size ratio between two neighboring elements + err=8; % maximum error between interpolated and control field + + % Generate an initial uniform mesh (resolution = hinit m) + md=bamg(model,'domain',domain,'hmax',hinit); + + % Get necessary data to build up the velocity grid + nsidc_vel ='../Data/Antarctica_ice_velocity.nc'; + xmin = strsplit(ncreadatt(nsidc_vel,'/','xmin')); xmin = str2num(xmin{2}); + ymax = strsplit(ncreadatt(nsidc_vel,'/','ymax')); ymax = str2num(ymax{2}); + spacing = strsplit(ncreadatt(nsidc_vel,'/','spacing')); spacing = str2num(spacing{2}); + nx = double(ncreadatt(nsidc_vel,'/','nx')); + ny = double(ncreadatt(nsidc_vel,'/','ny')); + vx = double(ncread(nsidc_vel,'vx')); + vy = double(ncread(nsidc_vel,'vy')); + + % Build the coordinates + x=xmin+(0:1:nx)'*spacing; + y=(ymax-ny*spacing)+(0:1:ny)'*spacing; + + % Interpolate velocities onto coarse mesh + vx_obs=InterpFromGridToMesh(x,y,flipud(vx'),md.mesh.x,md.mesh.y,0); + vy_obs=InterpFromGridToMesh(x,y,flipud(vy'),md.mesh.x,md.mesh.y,0); + vel_obs=sqrt(vx_obs.^2+vy_obs.^2); + clear vx vy x y; + + % Adapt the mesh to minimize error in velocity interpolation + md=bamg(md,'hmax',hmax,'hmin',hmin,'gradation',gradation,'field',vel_obs,'err',err); + + % Plot and save model + plotmodel(md,'data','mesh') + save ./Models/PIG_Mesh_generation md; +end + +if any(steps==2) %Masks #2 + md = loadmodel('./Models/PIG_Mesh_generation'); + + % Load SeaRISe dataset for Antarctica http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica + searise='../Data/Antarctica_5km_withshelves_v0.75.nc'; + + %read thickness mask from SeaRISE + x1=double(ncread(searise,'x1')); + y1=double(ncread(searise,'y1')); + thkmask=double(ncread(searise,'thkmask')); + + %interpolate onto our mesh vertices + groundedice=double(InterpFromGridToMesh(x1,y1,thkmask',md.mesh.x,md.mesh.y,0)); + groundedice(groundedice<=0)=-1; + clear thkmask; + + %fill in the md.mask structure + md.mask.ocean_levelset=groundedice; %ice is grounded for mask equal one + md.mask.ice_levelset=-1*ones(md.mesh.numberofvertices,1);%ice is present when negatvie + + plotmodel(md,'data',md.mask.ocean_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') + + save ./Models/PIG_SetMask md; +end + +if any(steps==3) %Parameterization #3 + md = loadmodel('./Models/PIG_SetMask'); + md = setflowequation(md,'SSA','all'); + md = parameterize(md,'./Pig.par'); + + save ./Models/PIG_Parameterization md; +end + +if any(steps==4) %Rheology B inversion + md = loadmodel('./Models/PIG_Parameterization'); + + % Control general + md.inversion.iscontrol=1; + md.inversion.maxsteps=40; + md.inversion.maxiter=40; + md.inversion.dxmin=0.1; + md.inversion.gttol=1.0e-6; + md.verbose=verbose('control',true); + + % Cost functions + md.inversion.cost_functions=[101 103 502]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); + md.inversion.cost_functions_coefficients(:,1)=1000; + md.inversion.cost_functions_coefficients(:,2)=1; + md.inversion.cost_functions_coefficients(:,3)=1.e-16; + + % Controls + md.inversion.control_parameters={'MaterialsRheologyBbar'}; + md.inversion.min_parameters=md.materials.rheology_B; + md.inversion.max_parameters=md.materials.rheology_B; + pos = find(md.mask.ocean_levelset<0); + md.inversion.min_parameters(pos) = cuffey(273); + md.inversion.max_parameters(pos) = cuffey(200); + + % Additional parameters + md.stressbalance.restol=0.01; + md.stressbalance.reltol=0.1; + md.stressbalance.abstol=NaN; + + % Solve + md.cluster=generic('name',oshostname,'np',2); + mds=extract(md,md.mask.ocean_levelset<0); + mds=solve(mds,'Stressbalance'); + + % Update model rheology_B accordingly + md.materials.rheology_B(mds.mesh.extractedvertices)=mds.results.StressbalanceSolution.MaterialsRheologyBbar; + plotmodel(md,'data',md.materials.rheology_B) + + % Save model + save ./Models/PIG_Control_B md; +end + +if any(steps==5) %drag inversion + md = loadmodel('./Models/PIG_Control_B'); + + % Cost functions + md.inversion.cost_functions=[101 103 501]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); + md.inversion.cost_functions_coefficients(:,1)=2000; + md.inversion.cost_functions_coefficients(:,2)=1; + md.inversion.cost_functions_coefficients(:,3)=8e-7; + + % Controls + md.inversion.control_parameters={'FrictionCoefficient'}; + md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); + + % Solve + md=solve(md,'Stressbalance'); + + % Update model friction fields accordingly + md.friction.coefficient=md.results.StressbalanceSolution.FrictionCoefficient; + + %Plot and save + plotmodel(md,... + 'data',md.initialization.vel,'title','Observed velocity',... + 'data',md.results.StressbalanceSolution.Vel,'title','Modeled Velocity',... + 'data',md.geometry.base,'title','Bed elevation',... + 'data',md.results.StressbalanceSolution.FrictionCoefficient,'title','Friction Coefficient',... + 'colorbar#all','on','colorbartitle#1-2','(m/yr)',... + 'caxis#1-2',([1.5,4000]),... + 'colorbartitle#3','(m)', 'log#1-2',10); + + save ./Models/PIG_Control_drag md; +end + +if any(steps==6) %Transient Run #1 + + md = loadmodel('./Models/PIG_Control_drag'); + + md.inversion.iscontrol=0; + md.transient.ismasstransport=1; + md.transient.isstressbalance=1; + md.transient.isgroundingline=1; + md.transient.ismovingfront=0; + md.transient.isthermal=0; + md.verbose.solution=1; + md.timestepping.time_step=0.1; + md.timestepping.final_time=10; + md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + %Set melt to 25 m/yr under floating ice + md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1); + + + md=solve(md,'Transient'); + time = cell2mat({md.results.TransientSolution(:).time}); + V_control = cell2mat({md.results.TransientSolution(:).IceVolumeAboveFloatation}); + plot(time,V_control); legend({'Control run'}); + + % Save model + save ./Models/PIG_Transient md; +end + +if any(steps==7) %High Melt #2 + md = loadmodel('./Models/PIG_Transient'); + + %Set melt to 60 m/yr under floating ice + md.basalforcings.floatingice_melting_rate=60*ones(md.mesh.numberofvertices,1); + + md=solve(md,'Transient'); + V_melt = cell2mat({md.results.TransientSolution(:).IceVolumeAboveFloatation}); + plot(time,[V_control',V_melt']); legend({'Control run','High melt'}); + + save ./Models/PIG_HighMelt md; +end + +if any(steps==8) %Ice Front retreat + md = loadmodel('./Models/PIG_Transient'); + + pos = find(ContourToNodes(md.mesh.x,md.mesh.y,'FrontRetreat.exp',2)); + md.mask.ice_levelset(pos) = +1; %Deactivate nodes in retreated area + + md=solve(md,'Transient'); + V_retreat = cell2mat({md.results.TransientSolution(:).IceVolumeAboveFloatation}); + plot(time,[V_control',V_melt',V_retreat']); legend({'Control run','High melt','Retreat'}); + + save ./Models/PIG_FrontRetreat md; +end + +if any(steps==9) %High surface mass balance #3 + %Load model from PIG_Transient + %... + + %Change surface mass balance (x2) + %... + + %Solve + %... + + %Get volume time series + %... + + %plot + plot(time,[V_control',V_melt',V_retreat',V_smb']); legend({'Control run','High melt','Retreat','SMB'}); + + %Save model + save ./Models/PIG_SMB md; +end Index: /issm/branches/trunk-dlcheng-ASE/examples/PigSensitivity/FrontRetreat.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/PigSensitivity/FrontRetreat.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/PigSensitivity/FrontRetreat.exp (revision 27955) @@ -0,0 +1,17 @@ +## Name:FrontRetreat +## Icon:0 +# Points Count Value +11 1.000000 +# X pos Y pos +-1626858.6376043619 -327176.4356578548 +-1605190.4936934854 -325911.1425827671 +-1604716.0087903275 -316263.2828852235 +-1607088.4333061168 -312625.5652943464 +-1612465.9288752396 -311676.5954880306 +-1618476.0709819060 -312467.4036599604 +-1624011.7281854146 -313890.8583694341 +-1626858.6376043619 -315788.7979820656 +-1627807.6074106777 -319268.3539385567 +-1628756.5772169936 -322589.7482606619 +-1626858.6376043619 -327176.4356578548 + Index: /issm/branches/trunk-dlcheng-ASE/examples/PigSensitivity/Help.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/PigSensitivity/Help.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/PigSensitivity/Help.m (revision 27955) @@ -0,0 +1,22 @@ +if step==4 + %Load model + md = loadmodel('./Models/PIG_Transient'); + + %Change external forcing basal melting rate and surface mass balance) + md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1); + md.smb.mass_balance=2*md.smb.mass_balance; + + %Define time steps and time span of the simulation + md.timestepping.time_step=0.1; + md.timestepping.final_time=10; + + %Request additional outputs + md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + %Solve + md=solve(md,'Transient'); + + %Save model + save ./Models/PIG_SMB md; +end Index: /issm/branches/trunk-dlcheng-ASE/examples/PigSensitivity/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/PigSensitivity/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/PigSensitivity/runme.m (revision 27955) @@ -0,0 +1,109 @@ +steps=[1]; + +if any(steps==1) %Transient Run #1 + + md = loadmodel('../Pig/Models/PIG_Control_drag'); + + md.inversion.iscontrol=0; + md.transient.ismasstransport=1; + md.transient.isstressbalance=1; + md.transient.isgroundingline=1; + md.transient.ismovingfront=0; + md.transient.isthermal=0; + + pos=find(md.mask.ocean_levelset<0); + md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1); + + md.timestepping.time_step=0.1; + md.timestepping.final_time=10; + md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + md=solve(md,'Transient'); + + plotmodel(md, 'data', md.results.TransientSolution(1).Vel,... + 'title#1', 'Velocity t=0 years (m/yr)',... + 'data', md.results.TransientSolution(end).Vel,... + 'title#2', 'Velocity t=10 years (m/yr)',... + 'data', md.results.TransientSolution(1).MaskOceanLevelset,... + 'title#3', 'Floating ice t=0 years',... + 'data', md.results.TransientSolution(end).MaskOceanLevelset,... + 'title#4', 'Floating ice t=10 years',... + 'caxis#1',([0 4500]),'caxis#2',([0 4500]),... + 'caxis#3',([-1,1]),'caxis#4',([-1,1])); + + % Save model + save ./Models/PIG_Transient md; +end + +if any(steps==2) %High Melt #2 + md = loadmodel('./Models/PIG_Transient'); + + md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.basalforcings.floatingice_melting_rate=60*ones(md.mesh.numberofvertices,1); + + md.timestepping.time_step=0.1; + md.timestepping.final_time=10; + md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + md=solve(md,'Transient'); + + plotmodel(md, 'data', md.results.TransientSolution(1).Vel,... + 'title#1', 'Velocity t=0 years (m/yr)',... + 'data', md.results.TransientSolution(end).Vel,... + 'title#2', 'Velocity t=10 years (m/yr)',... + 'data', md.results.TransientSolution(1).MaskOceanLevelset,... + 'title#3', 'Floating ice t=0 years',... + 'data', md.results.TransientSolution(end).MaskOceanLevelset,... + 'title#4', 'Floating ice t=10 years',... + 'caxis#1',([0 4500]),'caxis#2',([0 4500]),... + 'caxis#3',([-1,1]),'caxis#4',([-1,1])); + + save ./Models/PIG_HighMelt md; +end + +if any(steps==3) %Ice Front retreat + md = loadmodel('./Models/PIG_Transient'); + + md2=extract(md,'~FrontRetreat.exp'); + + md2=SetMarineIceSheetBC(md2); + + md2.basalforcings.groundedice_melting_rate=zeros(md2.mesh.numberofvertices,1); + md2.basalforcings.floatingice_melting_rate=25*ones(md2.mesh.numberofvertices,1); + + md2.timestepping.time_step=0.1; + md2.timestepping.final_time=10; + md2.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + md2=solve(md2,'Transient'); + + plotmodel(md, 'data', md.results.TransientSolution(1).Vel,... + 'title#1', 'Velocity t=0 years (m/yr)',... + 'data', md.results.TransientSolution(end).Vel,... + 'title#2', 'Velocity t=10 years (m/yr)',... + 'data', md.results.TransientSolution(1).MaskOceanLevelset,... + 'title#3', 'Floating ice t=0 years',... + 'data', md.results.TransientSolution(end).MaskOceanLevelset,... + 'title#4', 'Floating ice t=10 years',... + 'caxis#1',([0 4500]),'caxis#2',([0 4500]),... + 'caxis#3',([-1,1]),'caxis#4',([-1,1])); + + save ./Models/PIG_FrontRetreat md2; +end + +if any(steps==4) %High surface mass balance #3 + + %Load model + + %Change external forcing basal melting rate and surface mass balance) + + %Refine time steps and time span of the simulation + + %Request additional outputs + + %Solve + + %Save model + +end % step 4 end Index: /issm/branches/trunk-dlcheng-ASE/examples/README.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/README.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/README.txt (revision 27955) @@ -0,0 +1,10 @@ +To run the following examples, see the accompanying tutorials that can be found within the +documentation tab on the ISSM webpages: https://issm.jpl.nasa.gov/documentation/tutorials/ + +The tutorials were created to be parallel to lectures given, +but the tutorials are up to date on their version of ISSM. If more help is +needed see the User manual also found under the documentation tab +(https://issm.jpl.nasa.gov/documentation/). + +Make sure to download the required datasets +see https://issm.jpl.nasa.gov/documentation/tutorials/datasets/) Index: /issm/branches/trunk-dlcheng-ASE/examples/SlrFarrell/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/SlrFarrell/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/SlrFarrell/runme.m (revision 27955) @@ -0,0 +1,154 @@ +clear all; + +steps=[4]; + +if any(steps==1) + disp(' Step 1: Global mesh creation'); + + numrefine=1; + resolution=150*1e3; % inital resolution [m] + radius = 6.371012*10^6; % mean radius of Earth, m + mindistance_coast=150*1e3; % coastal resolution [m] + mindistance_land=300*1e3; % resolution on the continents [m] + maxdistance=600*1e3; % max element size (on mid-oceans) [m] + + md=model; + md.mesh=gmshplanet('radius',radius*1e-3,'resolution',resolution*1e-3); % attributes in [km] + + for i=1:numrefine, + ocean_mask_levelset=gmtmask(md.mesh.lat,md.mesh.long); + + distance=zeros(md.mesh.numberofvertices,1); + + pos=find(~ocean_mask_levelset); coaste.lat=md.mesh.lat(pos); coaste.long=md.mesh.long(pos); + pos=find(ocean_mask_levelset); coasto.lat=md.mesh.lat(pos); coasto.long=md.mesh.long(pos); + + for j=1:md.mesh.numberofvertices + phi1=md.mesh.lat(j)/180*pi; lambda1=md.mesh.long(j)/180*pi; + if ocean_mask_levelset(j), + phi2=coaste.lat/180*pi; lambda2=coaste.long/180*pi; + deltaphi=abs(phi2-phi1); deltalambda=abs(lambda2-lambda1); + d=radius*2*asin(sqrt(sin(deltaphi/2).^2+cos(phi1).*cos(phi2).*sin(deltalambda/2).^2)); + else + phi2=coasto.lat/180*pi; lambda2=coasto.long/180*pi; + deltaphi=abs(phi2-phi1); deltalambda=abs(lambda2-lambda1); + d=radius*2*asin(sqrt(sin(deltaphi/2).^2+cos(phi1).*cos(phi2).*sin(deltalambda/2).^2)); + end + distance(j)=min(d); + end + pos=find(distancemindistance_land); + distance(pos2)=mindistance_land; + + dist=min(maxdistance,distance); + md.mesh=gmshplanet('radius',radius*1e-3,'resolution',resolution*1e-3,'refine',md.mesh,'refinemetric',dist); + end + + ocean_mask=gmtmask(md.mesh.lat,md.mesh.long); + pos = find(ocean_mask==0); + md.mask.ocean_levelset=-ones(md.mesh.numberofvertices,1); + md.mask.ocean_levelset(pos)=1; + + save ./Models/SlrFarrell_Mesh md; + + plotmodel (md,'data',md.mask.ocean_levelset,'edgecolor','k'); +end + +if any(steps==2) + disp(' Step 2: Define source as in Farrell, 1972, Figure 1'); + md = loadmodel('./Models/SlrFarrell_Mesh'); + + md.solidearth.surfaceload.icethicknesschange=zeros(md.mesh.numberofvertices,1); + md.mask.ice_levelset=ones(md.mesh.numberofvertices,1); + + pos = find(md.mask.ocean_levelset==-1); + md.solidearth.initialsealevel=zeros(md.mesh.numberofvertices,1); + md.solidearth.initialsealevel(pos)=1; % 1 m SLR everywhere + md.dsl.global_average_thermosteric_sea_level_change=[0;0]; + md.dsl.sea_surface_height_change_above_geoid=zeros(md.mesh.numberofvertices+1,1); + md.dsl.sea_water_pressure_change_at_sea_floor=zeros(md.mesh.numberofvertices+1,1); + + save ./Models/SlrFarrell_Loads md; + + plotmodel (md,'data',md.solidearth.initialsealevel,'view',[90 90],'title#all','Initial sea-level [m]'); +end + +if any(steps==3) + disp(' Step 3: Parameterization'); + md = loadmodel('./Models/SlrFarrell_Loads'); + + md.solidearth.lovenumbers=lovenumbers('maxdeg',10000); + + %md.mask.ice_levelset = ones(md.mesh.numberofvertices,1); + %md.mask.ocean_levelset = -ones(md.mesh.numberofvertices,1); + %pos=find(md.mesh.lat <-80); + %md.mask.ice_levelset(pos(1))=-1; % ice yes! + %md.mask.ocean_levelset(pos(1))=1; % ice grounded! + + % arbitary to pass consistency check. + md.geometry.bed=-ones(md.mesh.numberofvertices,1); + md.geometry.surface=ones(md.mesh.numberofvertices,1); + md.geometry.base=md.geometry.bed; + md.geometry.thickness=md.geometry.surface-md.geometry.base; + + md.initialization.temperature=273.25*ones(md.mesh.numberofvertices,1); + md.materials.rheology_B=paterson(md.initialization.temperature); + md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); + + md.miscellaneous.name='SlrFarrell'; + + save ./Models/SlrFarrell_Parameterization md; +end + +if any(steps==4) + disp(' Step 4: Solve Slr solver'); + md = loadmodel('./Models/SlrFarrell_Parameterization'); + + md.cluster=generic('name',oshostname(),'np',3); + md.verbose=verbose('111111111'); + + md.solidearth.settings.reltol = 0.1/100; % percent change in solution + + md=solve(md,'Slr'); + + save ./Models/SlrFarrell_Solution md; +end + +if any(steps==5) + disp(' Step 5: Plot solutions'); + md = loadmodel('./Models/SlrFarrell_Solution'); + + sol = md.results.SealevelriseSolution.Sealevel*100; % per cent normalized by GMSL (which 1 m) + + res = 1; % [degree] + + [lat_grid, lon_grid] = meshgrid(linspace(-90,90,180/res), linspace(-180,180,360/res)); + sol_grid = zeros(size(lat_grid)); + + F = scatteredInterpolant(md.mesh.lat,md.mesh.long,sol); + F.Method = 'linear'; + F.ExtrapolationMethod = 'linear'; + + sol_grid = F(lat_grid, lon_grid); + sol_grid(isnan(sol_grid))=0; + sol_grid(lat_grid>85 & sol_grid==0)=NaN; + + set(0,'DefaultAxesFontSize',18,'DefaultAxesLineWidth',1,'DefaultTextFontSize',18,'DefaultLineMarkerSize',8) + figure1=figure('Position', [100, 100, 1000, 500]); + gcf; load coast; cla; + pcolor(lon_grid,lat_grid,sol_grid); shading flat; hold on; + [C,h]=contour(lon_grid,lat_grid,sol_grid,[96 98 100 102 104 105],'-k','linewidth',2); + clabel(C,h,'FontSize',18,'Color','red','LabelSpacing',500); + geoshow(lat,long,'DisplayType','polygon','FaceColor',[.82 .82 .82]); + plot(long,lat,'k'); hold off; + c1=colorbar; + colormap(flipud(haxby)); + caxis([96 105]); + xlim([-170 170]); + ylim([-85 85]); + grid on; + title('Relative sea-level [% of GMSL]'); + set(gcf,'color','w'); + %export_fig('Fig5.pdf'); +end Index: /issm/branches/trunk-dlcheng-ASE/examples/SlrGRACE/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/SlrGRACE/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/SlrGRACE/runme.m (revision 27955) @@ -0,0 +1,324 @@ +%clear all; +addpath('../Data','../Functions'); + +%steps=[1:7]; + +if any(steps==1) % {{{ + disp(' Step 1: Global mesh creation'); + + numrefine=1; + resolution=150*1e3; % inital resolution [m] + radius = 6.371012*10^6; % mean radius of Earth, m + mindistance_coast=150*1e3; % coastal resolution [m] + mindistance_land=300*1e3; % resolution on the continents [m] + maxdistance=600*1e3; % max element size (on mid-oceans) [m] + + md=model; + md.mesh=gmshplanet('radius',radius*1e-3,'resolution',resolution*1e-3); % attributes in [km] + + for i=1:numrefine, + + ocean_mask=gmtmask(md.mesh.lat,md.mesh.long); + + distance=zeros(md.mesh.numberofvertices,1); + + pos=find(~ocean_mask); coaste.lat=md.mesh.lat(pos); coaste.long=md.mesh.long(pos); pos=find(ocean_mask); coasto.lat=md.mesh.lat(pos); coasto.long=md.mesh.long(pos); + for j=1:md.mesh.numberofvertices + phi1=md.mesh.lat(j)/180*pi; lambda1=md.mesh.long(j)/180*pi; + if ocean_mask(j), + phi2=coaste.lat/180*pi; lambda2=coaste.long/180*pi; + deltaphi=abs(phi2-phi1); deltalambda=abs(lambda2-lambda1); + d=radius*2*asin(sqrt(sin(deltaphi/2).^2+cos(phi1).*cos(phi2).*sin(deltalambda/2).^2)); + else + phi2=coasto.lat/180*pi; lambda2=coasto.long/180*pi; + deltaphi=abs(phi2-phi1); deltalambda=abs(lambda2-lambda1); + d=radius*2*asin(sqrt(sin(deltaphi/2).^2+cos(phi1).*cos(phi2).*sin(deltalambda/2).^2)); + end + distance(j)=min(d); + end + pos=find(distancemindistance_land); + distance(pos2)=mindistance_land; + + dist=min(maxdistance,distance); + md.mesh=gmshplanet('radius',radius*1e-3,'resolution',resolution*1e-3,'refine',md.mesh,'refinemetric',dist); + end + + ocean_mask=gmtmask(md.mesh.lat,md.mesh.long); + pos = find(ocean_mask==0); md.mask.ocean_levelset=-ones(md.mesh.numberofvertices,1); md.mask.ocean_levelset(pos)=1; + save ./Models/SlrGRACE_Mesh md; + + plotmodel (md,'data',md.mask.ocean_levelset,'edgecolor','k','view',[45 45]); + +end % }}} +if any(steps==2) % {{{ + disp(' Step 2: Define loads in meters of ice height equivalent'); + md = loadmodel('./Models/SlrGRACE_Mesh'); + + year_month = 2007+15/365; + time_range = [year_month year_month]; + + onvertex = 1; % map data on vertex. If 0, it maps on the elemental centroid. + water_load = grace(md.mesh.elements,md.mesh.lat,md.mesh.long,time_range(1),time_range(2),onvertex); + rho_water2ice = md.materials.rho_freshwater/md.materials.rho_ice; + ice_load = water_load*rho_water2ice; % ice height equivalent. + + %Geometry for the bed, arbitrary thickness of 100: + md.geometry.bed=zeros(md.mesh.numberofvertices,1); + md.geometry.base=md.geometry.bed; + md.geometry.thickness = 100*ones(md.mesh.numberofvertices,1); + md.geometry.surface=md.geometry.bed+md.geometry.thickness; + + md.masstransport.spcthickness = repmat(md.geometry.thickness,1,2); + md.masstransport.spcthickness(:,end) = md.masstransport.spcthickness(:,end) + ice_load; + md.masstransport.spcthickness(end+1,:) = [0 1]; % dummy time. + + md.smb.mass_balance=zeros(md.mesh.numberofvertices,1); + + save ./Models/SlrGRACE_Loads md; + + plotmodel (md,'data',ice_load,... + 'edgecolor','k','view',[45 45],'caxis',[-.1 .1],... + 'title','Ice height equivalent [m]'); +end % }}} +if any(steps==3) % {{{ + disp(' Step 3: Parameterization'); + md = loadmodel('./Models/SlrGRACE_Loads'); + + md.mask.ice_levelset=-md.mask.ocean_levelset; + + md.solidearth.lovenumbers = lovenumbers('maxdeg',10000); + md.solidearth.settings.reltol=NaN; + md.solidearth.settings.abstol=1e-3; + md.solidearth.settings.sealevelloading=1; + md.solidearth.settings.isgrd=1; + md.solidearth.settings.grdmodel=1; + md.solidearth.settings.maxiter=10; + + %time stepping: + md.timestepping.start_time=0; + md.timestepping.time_step=1; + md.timestepping.final_time=1; + + %masstransport: + md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.basalforcings.floatingice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.initialization.vx=zeros(md.mesh.numberofvertices,1); + md.initialization.vy=zeros(md.mesh.numberofvertices,1); + md.initialization.sealevel=zeros(md.mesh.numberofvertices,1); + md.initialization.str=0; + + md.miscellaneous.name='SlrGRACE'; + + save ./Models/SlrGRACE_Parameterization md; +end % }}} +if any(steps==4) % {{{ + disp(' Step 4: Solve Slr solver'); + md = loadmodel('./Models/SlrGRACE_Parameterization'); + + md.solidearth.settings.viscous=0; + md.solidearth.settings.selfattraction=1; + md.solidearth.settings.elastic=1; + md.solidearth.settings.rotation=1; + + %Physics: + md.transient.issmb=0; + md.transient.isstressbalance=0; + md.transient.isthermal=0; + md.transient.ismasstransport=1; + md.transient.isslc=1; + + md.solidearth.requested_outputs={'Sealevel','Bed'}; + + md.cluster=generic('name',oshostname(),'np',3); + md.verbose=verbose('111111111'); + + md=solve(md,'Transient'); + + save ./Models/SlrGRACE_Solution md; +end % }}} +if any(steps==5) % {{{ + disp(' Step 5: Plot solutions'); + md = loadmodel('./Models/SlrGRACE_Solution'); + + sol1 = (md.masstransport.spcthickness(1:end-1,2)-md.masstransport.spcthickness(1:end-1,1))*100; % [cm] + sol2 = (md.results.TransientSolution.Sealevel-md.results.TransientSolution.Bed)*1000; % [mm] + + sol_name={'Change in water equivalent height [cm]', 'Relative sea level [mm]'}; + fig_name={'Fig_dH.pdf','Fig_slr.pdf'}; + + res = 1.0; + + [lat_grid, lon_grid] = meshgrid(linspace(-90,90,180/res), linspace(-180,180,360/res)); + sol_grid = zeros(size(lat_grid)); + + for kk=1:2 + sol=eval(sprintf('sol%d',kk)); + + if length(sol)==md.mesh.numberofelements + for jj=1:md.mesh.numberofelements + ii=(jj-1)*3; + pp(ii+1:ii+3)=md.mesh.elements(jj,:); + end + for jj=1:md.mesh.numberofvertices + pos=ceil(find(pp==jj)/3); + temp(jj)=mean(sol(pos)); + end + sol=temp'; + end + + F = scatteredInterpolant(md.mesh.lat,md.mesh.long,sol); + F.Method = 'linear'; + F.ExtrapolationMethod = 'linear'; + + sol_grid = F(lat_grid, lon_grid); + sol_grid(isnan(sol_grid))=0; + sol_grid(lat_grid>85 & sol_grid==0) = NaN; + + set(0,'DefaultAxesFontSize',18,'DefaultAxesLineWidth',1,'DefaultTextFontSize',18,'DefaultLineMarkerSize',8) + figure1=figure('Position', [100, 100, 1000, 500]); + gcf; load coastlines; cla; + pcolor(lon_grid,lat_grid,sol_grid); shading flat; hold on; + if (kk==1) + geoshow(flipud(coastlat),flipud(coastlon),'DisplayType','polygon','FaceColor','white'); + else + geoshow(coastlat,coastlon,'DisplayType','polygon','FaceColor','none'); + end + plot(coastlon, coastlat,'k'); hold off; + c1=colorbar; + colormap('haxby'); + caxis([-floor(min(abs(min(sol)),abs(max(sol)))) floor(min(abs(min(sol)),abs(max(sol))))]); + xlim([-180 180]); + ylim([-90 90]); + grid on; + title(sol_name(kk)); + set(gcf,'color','w'); + %export_fig(fig_name{kk}); + end +end % }}} +if any(steps==6) % {{{ + disp(' Step 6: Transient run'); + md = loadmodel('./Models/SlrGRACE_Parameterization'); + + disp('Projecting loads onto the mesh...'); + time_range = 2007 + [15 350]/365; + onvertex = 1; % map data on vertex. If 0, it maps on the elemental centroid. + water_load = grace(md.mesh.elements,md.mesh.lat,md.mesh.long,time_range(1),time_range(2),onvertex); + rho_water2ice = md.materials.rho_freshwater/md.materials.rho_ice; + ice_load = water_load*rho_water2ice; % ice height equivalent. + + % masstransport evalulates diff between the successive times, so we should cumsum. + num_time = size(ice_load,2); + md.masstransport.spcthickness = repmat(md.geometry.thickness,1,num_time+1); + md.masstransport.spcthickness(:,2:end) = md.masstransport.spcthickness(:,2:end) + ice_load; + md.masstransport.spcthickness(end+1,:) = 0:num_time; % dummy time. + + %Physics + md.transient.issmb=0; + md.transient.isstressbalance=0; + md.transient.isthermal=0; + md.transient.ismasstransport=1; + md.transient.isslc=1; + + md.solidearth.settings.viscous=0; + md.solidearth.settings.selfattraction=1; + md.solidearth.settings.elastic=1; + md.solidearth.settings.rotation=1; + + %time stepping: + md.timestepping.start_time=0; + md.timestepping.time_step=1; + md.timestepping.final_time=num_time; + + md.cluster=generic('name',oshostname(),'np',3); + md.verbose=verbose('111111111'); + + md.solidearth.requested_outputs = {'Sealevel','Bed'}; + + md=solve(md,'tr'); + + save ./Models/SlrGRACE_Transient md; +end % }}} +if any(steps==7) % {{{ + disp(' Step 7: Plot transient'); + md = loadmodel('./Models/SlrGRACE_Transient'); + + time = md.masstransport.spcthickness(end,2:end); + + for tt=1:length(time) + gmsl(tt) = md.results.TransientSolution(tt).CumBslc*1000; % [mm] + sol1(:,tt) = (md.masstransport.spcthickness(1:end-1,tt+1)-md.geometry.thickness)*100; % [cm] + sol2(:,tt) = (md.results.TransientSolution(tt).Sealevel-md.results.TransientSolution(tt).Bed)*1000; % [mm] + end + sol_name = {'Change in water equivalent height [cm]', 'Relative sea level [mm]'}; + movie_name = {'Movie_dH','Movie_slr'}; + + res = 1.0; + + [lat_grid, lon_grid] = meshgrid(linspace(-90,90,180/res), linspace(-180,180,360/res)); + sol_grid = zeros(size(lat_grid)); + + for kk=1:2 + sol=eval(sprintf('sol%d',kk)); + + if length(sol)==md.mesh.numberofelements + for jj=1:md.mesh.numberofelements + ii=(jj-1)*3; + pp(ii+1:ii+3)=md.mesh.elements(jj,:); + end + for jj=1:md.mesh.numberofvertices + pos=ceil(find(pp==jj)/3); + temp2(jj,:)=mean(sol(pos,:)); + end + sol=temp2; + end + + vidObj = VideoWriter(movie_name{kk}); + vidObj.FrameRate=2; % frames per second + open(vidObj); + + for jj=1:length(time) + fprintf('creating frame %d...', jj); + F = scatteredInterpolant(md.mesh.lat,md.mesh.long,sol(:,jj)); + F.Method = 'linear'; + F.ExtrapolationMethod = 'linear'; + + sol_grid = F(lat_grid, lon_grid); + sol_grid(isnan(sol_grid))=0; + sol_grid(lat_grid>85 & sol_grid==0) = NaN; + + set(0,'DefaultAxesFontSize',18,'DefaultAxesLineWidth',1,'DefaultTextFontSize',18,'DefaultLineMarkerSize',8) + figure1=figure('Position', [100, 100, 1000, 500]); + gcf; load coastlines; cla; + pcolor(lon_grid,lat_grid,sol_grid); shading flat; hold on; + if (kk==1) + geoshow(flipud(coastlat),flipud(coastlon),'DisplayType','polygon','FaceColor','white'); + else + geoshow(coastlat,coastlon,'DisplayType','polygon','FaceColor','none'); + end + plot(coastlon,coastlat,'k'); hold off; + c1=colorbar; + colormap('haxby'); + %caxis([-floor(min(abs(min(min(sol))),abs(max(max(sol))))) floor(min(abs(min(min(sol))),abs(max(max(sol)))))]); + xlim([-180 180]); + ylim([-90 90]); + grid on; + title(sol_name(kk)); + set(gcf,'color','w'); + writeVideo(vidObj,getframe(gcf)); + close + fprintf('done\n'); + end + disp('closing vidObj...'); + close(vidObj); + end + + % plot GMSL time series + plot(time,gmsl,'-*','linewidth',3); grid on; + xlabel('# month'); + ylabel('GMSL [mm/yr]'); + set(gcf,'color','w'); + %export_fig('Fig7.pdf'); +end % }}} + Index: /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/DomainOutline.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/DomainOutline.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/DomainOutline.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:DomainOutline +## Icon:0 +# Points Count Value +5 1.000000 +# X pos Y pos +0 0 +1000000 0 +1000000 1000000 +0 1000000 +0 0 Index: /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/Front.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/Front.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/Front.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:icefront +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +-1000 999999 +-1000 1100000 +1100000 1100000 +1100000 999999 +-1000 999999 Index: /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/Square.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/Square.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/Square.par (revision 27955) @@ -0,0 +1,30 @@ +%Start defining model parameters here + +disp(' creating thickness'); +hmin=300; +hmax=1000; +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness = hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); +md.geometry.base = -md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface = md.geometry.base+md.geometry.thickness; + +disp(' creating drag'); +md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.ocean_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' initial velocity'); +md.initialization.vx=zeros(md.mesh.numberofvertices,1); +md.initialization.vy=zeros(md.mesh.numberofvertices,1); +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.vel=zeros(md.mesh.numberofvertices,1); + +disp(' creating flow law parameter'); +md.materials.rheology_B=paterson((273-20)*ones(md.mesh.numberofvertices,1)); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.damage.D=zeros(md.mesh.numberofvertices,1); + +disp(' creating boundary conditions'); +md=SetIceShelfBC(md,'Front.exp'); Index: /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/Square.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/Square.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/Square.py (revision 27955) @@ -0,0 +1,32 @@ +import numpy as np +from paterson import paterson +from SetIceShelfBC import SetIceShelfBC +#Start defining model parameters here + +print(' creating thickness') +hmin = 300 +hmax = 1000 +ymin = np.nanmin(md.mesh.y) +ymax = np.nanmax(md.mesh.y) +md.geometry.thickness = hmax + (hmin - hmax) * (md.mesh.y - ymin) / (ymax - ymin) +md.geometry.base = - md.materials.rho_ice / md.materials.rho_water * md.geometry.thickness +md.geometry.surface = md.geometry.base + md.geometry.thickness + +print(' creating drag') +md.friction.coefficient = np.where(md.mask.ocean_levelset < 0., 0, 200) +md.friction.p = np.ones((md.mesh.numberofelements)) +md.friction.q = np.ones((md.mesh.numberofelements)) + +print(' initial velocity') +md.initialization.vx = np.zeros((md.mesh.numberofvertices)) +md.initialization.vy = np.zeros((md.mesh.numberofvertices)) +md.initialization.vz = np.zeros((md.mesh.numberofvertices)) +md.initialization.vel = np.zeros((md.mesh.numberofvertices)) + +print(' creating flow law parameter') +md.materials.rheology_B = paterson((273 - 20) * np.ones((md.mesh.numberofvertices))) +md.materials.rheology_n = 3 * np.ones((md.mesh.numberofelements)) +md.damage.D = np.zeros((md.mesh.numberofvertices)) + +print(' creating boundary conditions') +md = SetIceShelfBC(md, 'Front.exp') Index: /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/runme.m (revision 27955) @@ -0,0 +1,7 @@ +md=model; +md=triangle(md,'DomainOutline.exp',100000); +md=setmask(md,'all',''); +md=parameterize(md,'Square.par'); +md=setflowequation(md,'SSA','all'); +md.cluster=generic('name',oshostname,'np',2); +md=solve(md,'Stressbalance'); Index: /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/runme.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/runme.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/SquareIceShelf/runme.py (revision 27955) @@ -0,0 +1,16 @@ +from model import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from generic import generic +from socket import gethostname +from solve import solve + +md = model() +md = triangle(md, 'DomainOutline.exp', 100000) +md = setmask(md, 'all', '') +md = parameterize(md, 'Square.py') +md = setflowequation(md, 'SSA', 'all') +md.cluster = generic('name', gethostname(), 'np', 2) +md = solve(md, 'Stressbalance') Index: /issm/branches/trunk-dlcheng-ASE/examples/StISSM/DomainOutline.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/StISSM/DomainOutline.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/StISSM/DomainOutline.exp (revision 27955) @@ -0,0 +1,101 @@ +## Name: +## Icon:0 +# Points Count Value +95 25000.000000 +# X pos Y pos +-1712113.0179281300 -349656.0205056490 +-1711509.1917759699 -349354.1074295690 +-1709240.6586108401 -349354.1074295690 +-1707080.1508345299 -348922.0058743060 +-1705459.7700022999 -347193.5996532570 +-1703083.2114483600 -345249.1426545770 +-1701138.7544496800 -344168.8887664210 +-1698438.1197292900 -343952.8379887900 +-1698006.0181740201 -341900.3556012940 +-1693793.0280102200 -340279.9747690600 +-1691092.3932898301 -339631.8224361670 +-1688391.7585694401 -339415.7716585360 +-1686447.3015707601 -340063.9239914290 +-1683530.6160727399 -341036.1524907690 +-1682558.3875734000 -343304.6856558960 +-1682134.7209454600 -344182.1487658350 +-1682126.2860181299 -345681.2442098390 +-1681072.0444963200 -345932.4393879640 +-1680634.4718407800 -346682.5639403050 +-1680571.9614614199 -348557.8753211580 +-1677446.4424933300 -348370.3441830730 +-1675508.6207331200 -349495.5310115840 +-1676616.9911885399 -353567.0975933760 +-1672991.8601872099 -353799.6175753630 +-1668839.1631938200 -353999.1991486380 +-1667132.2298986400 -355121.4651541420 +-1666069.5534494901 -357496.8595698890 +-1662944.0344814099 -358309.4945015920 +-1660756.1712037399 -358747.0671571240 +-1657922.9836098100 -361682.8074238540 +-1656579.2228470000 -364003.8487410000 +-1653004.8841628900 -364748.0635758530 +-1653442.4568184200 -361622.5446077650 +-1651129.5727820301 -355684.0585683980 +-1648929.2928810001 -350845.9692010000 +-1646260.7698359799 -347802.2804785470 +-1644571.8968503401 -341785.6704672340 +-1643503.3064999001 -340869.0986596620 +-1643190.7546030900 -336680.9032424240 +-1642690.6715682000 -335243.1645171040 +-1641913.0916588283 -332341.0814454452 +-1640683.9739821283 -330436.6112348017 +-1637816.0327364956 -328532.1410241582 +-1635241.2508976001 -328652.8685499910 +-1631765.4107996500 -327017.1790921330 +-1625934.5618617306 -322342.6128395668 +-1620608.3852626982 -320438.1426289233 +-1616101.6204481323 -320438.1426289233 +-1611594.8556335662 -320914.2601815842 +-1607907.5026034669 -321866.4952869060 +-1602991.0318966676 -324723.2006028712 +-1599713.3847588014 -327579.9059188365 +-1593977.5022675355 -328532.1410241582 +-1590699.8551296694 -334721.6692087495 +-1589259.8391499999 -338300.0840570000 +-1588627.0898328500 -343572.9950327750 +-1588056.6000060199 -345432.3563530700 +-1586993.9235568701 -347432.6884926460 +-1589259.8391499999 -349315.9832070000 +-1585493.6744521901 -352996.1122558430 +-1585118.6121760199 -354496.3613605250 +-1585861.9157163899 -356240.3342513760 +-1586368.8197632500 -358747.0671571240 +-1587889.0972700799 -360996.6006787950 +-1586681.3716600600 -363935.4286441500 +-1585806.2263489999 -365748.2296456410 +-1586743.8820394201 -368373.6655788350 +-1586056.2678664399 -370123.9562009640 +-1585493.6744521901 -371124.1222707520 +-1586243.7990045301 -373562.0270658610 +-1414257.6683934701 -327460.5482541260 +-1412220.4351378100 -325972.8942023180 +-1404515.9240538401 -296165.1737279960 +-1387984.9332285200 -267002.0106682320 +-1360067.9373810000 -107884.1934940000 +-1423274.3497420000 -81217.9259650000 +-1402446.7987670000 -45916.9921070000 +-1478343.8065599999 60338.8188030000 +-1503760.4789370000 36334.1837800000 +-1528509.5619775900 63667.6809196406 +-1623055.4918765700 62841.1506965373 +-1725734.5897359999 -61372.6193030000 +-1719614.6457630000 -69022.5492690000 +-1759088.2843859999 -114004.1374660000 +-1755416.3180020000 -117064.1094530000 +-1761230.2647760001 -126856.0198080000 +-1758170.2927900001 -130527.9861920000 +-1762148.2563720001 -135423.9413700000 +-1764902.2311590000 -131445.9777880000 +-1769798.1863370000 -134199.9525750000 +-1775000.1387139999 -131445.9777880000 +-1794277.9622269999 -153477.7760890000 +-1712576.7101950001 -225081.1205660000 +-1729939.5891459100 -335652.4567604720 +-1712113.0179281300 -349656.0205056490 + Index: /issm/branches/trunk-dlcheng-ASE/examples/StISSM/PigStISSM.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/StISSM/PigStISSM.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/StISSM/PigStISSM.par (revision 27955) @@ -0,0 +1,117 @@ + +% Name and Coordinate system +md.miscellaneous.name = 'PigStISSM'; +md.mesh.epsg = 3031; + +% NetCdf Loading +disp(' Loading SeaRISE data from NetCDF'); +ncdata ='../Data/Antarctica_5km_withshelves_v0.75.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +temp = ncread(ncdata,'presartm')'; +smb = ncread(ncdata,'presprcp')'; +gflux = ncread(ncdata,'bheatflx_fox')'; + +% Geometry +disp(' Interpolating surface and ice base'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); +clear usrf, topg; + +disp(' Constructing thickness'); +md.geometry.thickness = md.geometry.surface-md.geometry.base; + +% Ensure hydrostatic equilibrium on ice shelf: +di = md.materials.rho_ice/md.materials.rho_water; + +% Get the node numbers of floating nodes +pos = find(md.mask.ocean_levelset<0); + +% Apply a flotation criterion on the precedingly defined nodes and +% redefine base and thickness accordingly +md.geometry.thickness(pos) = 1/(1-di)*md.geometry.surface(pos); +md.geometry.base(pos) = md.geometry.surface(pos)-md.geometry.thickness(pos); +md.geometry.hydrostatic_ratio = ones(md.mesh.numberofvertices,1); %For Dakota + +% Set min thickness to 1 meter +pos0 = find(md.geometry.thickness<=1); +md.geometry.thickness(pos0) = 1; +md.geometry.surface = md.geometry.thickness+md.geometry.base; +md.geometry.bed = md.geometry.base; +md.geometry.bed(pos) = md.geometry.base(pos)-1000; + +% Initialization parameters +disp(' Interpolating temperatures'); +Temp_change = 0; +md.initialization.temperature = InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15+Temp_change; +clear temp; + +disp(' Loading velocities data from NetCDF'); +nsidc_vel = '../Data/Antarctica_ice_velocity.nc'; +xmin = ncreadatt(nsidc_vel,'/','xmin'); +ymax = ncreadatt(nsidc_vel,'/','ymax'); +spacing = ncreadatt(nsidc_vel,'/','spacing'); +nx = double(ncreadatt(nsidc_vel,'/','nx')); +ny = double(ncreadatt(nsidc_vel,'/','ny')); +velx = double(ncread(nsidc_vel,'vx')); +vely = double(ncread(nsidc_vel,'vy')); +% Read coordinates +xmin = strtrim(xmin); +xmin = str2num(xmin(1:end-2)); +ymax = strtrim(ymax); +ymax = str2num(ymax(1:end-2)); +spacing = strtrim(spacing); +spacing = str2num(spacing(1:end-2)); +% Build the coordinates +x2 = xmin+(0:1:nx)'*spacing; +y2 = (ymax-ny*spacing)+(0:1:ny)'*spacing; + +disp(' Set observed velocities') +md.initialization.vx = InterpFromGridToMesh(x2,y2,flipud(velx'),md.mesh.x,md.mesh.y,0); +md.initialization.vy = InterpFromGridToMesh(x2,y2,flipud(vely'),md.mesh.x,md.mesh.y,0); +md.initialization.vz = zeros(md.mesh.numberofvertices,1); +md.initialization.vel = sqrt(md.initialization.vx.^2+md.initialization.vy.^2); +clear velx vely; + +disp(' Set Pressure'); +md.initialization.pressure = md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +disp(' Construct ice rheological properties'); +md.materials.rheology_n = 3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B = paterson(md.initialization.temperature); + +%Forcings +disp(' Interpolating surface mass balance'); +mass_balance = InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance = mass_balance*md.materials.rho_water/md.materials.rho_ice; +clear smb; + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux = InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); +clear gflux; + +% Friction and inversion set up +disp(' Construct basal friction parameters'); +friction_coefficient = 10.0; +md.friction.coefficient = friction_coefficient*ones(md.mesh.numberofvertices,1); +md.friction.p = ones(md.mesh.numberofelements,1); +md.friction.q = ones(md.mesh.numberofelements,1); + +% No friction applied on floating ice +pos = find(md.mask.ocean_levelset<0); +md.friction.coefficient(pos) = 0; +md.groundingline.migration = 'SubelementMigration'; + +md.inversion = m1qn3inversion(); +md.inversion.vx_obs = md.initialization.vx; +md.inversion.vy_obs = md.initialization.vy; +md.inversion.vel_obs = md.initialization.vel; + +disp(' Set boundary conditions'); +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md = SetMarineIceSheetBC(md); +md.thermal.spctemperature = md.initialization.temperature; +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); Index: /issm/branches/trunk-dlcheng-ASE/examples/StISSM/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/StISSM/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/StISSM/runme.m (revision 27955) @@ -0,0 +1,288 @@ + +%%% +% Tutorial for StISSM +%%% + +steps = [1]; + +if any(steps==1) + % Mesh parameters + domain = ['./DomainOutline.exp']; + hinit = 5000; % element size for the initial mesh + hmax = 40000; % maximum element size of the final mesh + hmin = 4000; % minimum element size of the final mesh + gradation = 1.7; % maximum size ratio between two neighboring elements + err = 8; % maximum error between interpolated and control field + + % Generate an initial uniform mesh (resolution = hinit m) + md = bamg(model,'domain',domain,'hmax',hinit); + + % Get necessary data to build up the velocity grid + nsidc_vel = '../Data/Antarctica_ice_velocity.nc'; + xmin = strsplit(ncreadatt(nsidc_vel,'/','xmin')); + xmin = str2num(xmin{2}); + ymax = strsplit(ncreadatt(nsidc_vel,'/','ymax')); + ymax = str2num(ymax{2}); + spacing = strsplit(ncreadatt(nsidc_vel,'/','spacing')); + spacing = str2num(spacing{2}); + nx = double(ncreadatt(nsidc_vel,'/','nx')); + ny = double(ncreadatt(nsidc_vel,'/','ny')); + vx = double(ncread(nsidc_vel,'vx')); + vy = double(ncread(nsidc_vel,'vy')); + + % Build the coordinates + x = xmin+(0:1:nx)'*spacing; + y = (ymax-ny*spacing)+(0:1:ny)'*spacing; + + % Interpolate velocities onto coarse mesh + vx_obs = InterpFromGridToMesh(x,y,flipud(vx'),md.mesh.x,md.mesh.y,0); + vy_obs = InterpFromGridToMesh(x,y,flipud(vy'),md.mesh.x,md.mesh.y,0); + vel_obs = sqrt(vx_obs.^2+vy_obs.^2); + clear vx vy x y; + + % Adapt the mesh to minimize error in velocity interpolation + md = bamg(md,'hmax',hmax,'hmin',hmin,'gradation',gradation,'field',vel_obs,'err',err); + + % Plot and save model + plotmodel(md,'data','mesh') + save ./Models/PIG_StISSM_Mesh_generation md; + +end + +if any(steps==2) %Masks #2 + md = loadmodel('./Models/PIG_StISSM_Mesh_generation'); + + % Load SeaRISe dataset for Antarctica http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica + searise = '../Data/Antarctica_5km_withshelves_v0.75.nc'; + + % Read thickness mask from SeaRISE + x1 = double(ncread(searise,'x1')); + y1 = double(ncread(searise,'y1')); + thkmask = double(ncread(searise,'thkmask')); + + % Interpolate onto our mesh vertices + groundedice = double(InterpFromGridToMesh(x1,y1,thkmask',md.mesh.x,md.mesh.y,0)); + groundedice(groundedice<=0) = -1; + clear thkmask; + + % Fill in the md.mask structure + md.mask.ocean_levelset = groundedice; %ice is grounded for mask equal one + md.mask.ice_levelset = -1*ones(md.mesh.numberofvertices,1); %ice is present when negatvie + + plotmodel(md,'data',md.mask.ocean_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') + + save ./Models/PIG_StISSM_SetMask md; +end + +if any(steps==3) %Parameterization #3 + + md = loadmodel('./Models/PIG_StISSM_SetMask'); + md = setflowequation(md,'SSA','all'); + md = parameterize(md,'./PigStISSM.par'); + + save ./Models/PIG_StISSM_Parameterization md; +end + +if any(steps==4) %Stochastic SMB + md = loadmodel('./Models/PIG_StISSM_Parameterization'); + + % Create the different subdomains for SMB % + ymax = max(md.mesh.y); + ymin = min(md.mesh.y); + xmax = max(md.mesh.x); + xmin = min(md.mesh.x); + idsmb = zeros(md.mesh.numberofelements,1); %subdomain ID is defined for each element + iid1 = find(md.mesh.x>=(xmax-2/3*(xmax-xmin))); %vertices in subdomain 1 + iid2 = find(md.mesh.x<(xmax-2/3*(xmax-xmin))); %vertices in subdomain 2 + for ii=1:md.mesh.numberofelements + for vertex=1:3 + if any(iid1==md.mesh.elements(ii,vertex)) %one vertex in subdomain 1 + idsmb(ii) = 1; + end + end + if idsmb(ii)==0 %no vertex was found in subdomain 1 + idsmb(ii) = 2; + end + end + + % SMBarma implementation + md.smb = SMBarma(); + md.smb.num_basins = 2; %we use two different subdomains + md.smb.basin_id = idsmb; %element subdomain IDs + md.smb.num_breaks = 1; %1 breakpoint in the piecewise polynomial + md.smb.datebreaks = [5;5]; %breakpoint occurs at year 5 in both subdomains + md.smb.num_params = 2; %use a constant and a linear trend for the piecwise polynomial + constsmb = [0.5,0.2;0.3,0.5]; %constant SMB term for subdomains pre- and post-breakpoint [m yr^-1] + trendsmb = [0,0;0.01,0.001]; %trend is SMB for subdomains pre- and post-breakpoint [m yr^-2] + md.smb.polynomialparams = cat(3,constsmb,trendsmb); %concatenating const and trend along a 3rd dimension + md.smb.ar_order = 1; %first-order AR + md.smb.ma_order = 1; %first-order MA + md.smb.arlag_coefs = [0.3;0]; %AR coefficients in each subdomain + md.smb.malag_coefs = zeros(md.smb.num_basins,md.smb.ma_order); %all zeros is equivalent to MA order 0 + md.smb.arma_timestep = 1.0; %yearly ARMA + md.smb.elevationbins = [300,1000;300,1000]; %elevations separating different lapse rate values [m] + md.smb.lapserates = 1e-2*[0.03,0.01,-1e-4;0.02,0.02,-1e-5]; %lapse rate values [m ice eq. m^-1 yr^-1] + md.smb.refelevation = [500,500]; %elevations at which the SMBarma calculated values apply (i.e., before using lapse rates) + + % Set-up the covariance matrix + sdevSMB1 = 0.01; %low standard deviation in subdomain 1 [m ice eq. yr^-1] + sdevSMB2 = 0.2; %higher variability in subdomain 2 [m ice eq. yr^-1] + correlationSMB = [1.0,0.5;0.5,1.0]; %moderate correlation between the subdomains + covarianceSMB = diag([sdevSMB1,sdevSMB2])*correlationSMB*diag([sdevSMB1,sdevSMB2]); %covariance matrix [(m ice eq. yr^-1)^2] + + % Stochasticforcing implementation + md.stochasticforcing.isstochasticforcing = 1; %activate stochasticity + md.stochasticforcing.fields = [{'SMBarma'}]; + md.stochasticforcing.covariance = covarianceSMB; %prescribe the SMB covariance + md.stochasticforcing.stochastictimestep = 1.0; %yearly stochasticity + + save ./Models/PIG_StISSM_StochSMB md; + +end + +if any(steps==5) % Transient Run #1 + + md = loadmodel('./Models/PIG_StISSM_StochSMB'); + + md.inversion.iscontrol = 0; + md.transient.ismasstransport = 1; + md.transient.isstressbalance = 1; + md.transient.isgroundingline = 1; + md.transient.ismovingfront = 0; + md.transient.isthermal = 0; + md.verbose.solution = 1; + md.timestepping.time_step = 0.1; + md.timestepping.final_time = 10; + md.transient.requested_outputs = {'default','SmbMassBalance','MaskIceLevelset'}; + + md = solve(md,'Transient'); + timing = cell2mat({md.results.TransientSolution(:).time}); + fullsmb = cell2mat({md.results.TransientSolution(:).SmbMassBalance}); + timemeansmb = mean(fullsmb,2); + timesdevsmb = std(fullsmb,0,2); + maxsmb = max(fullsmb,[],'all'); + minsmb = min(fullsmb,[],'all'); + + + plotmodel(md,'figure',1,... + 'data',md.results.TransientSolution(1).SmbMassBalance,'title','SMB at timestep 1','caxis#1',[minsmb,maxsmb],... + 'data',md.results.TransientSolution(end).SmbMassBalance,'title','SMB at last timestep','caxis#2',[minsmb,maxsmb]) + plotmodel(md,'figure',2,... + 'data',timemeansmb,'title','SMB mean over simulation',... + 'data',timesdevsmb,'title','SMB standard deviation over simulation') + + seriesSMB1 = fullsmb(1,:); + seriesSMB71 = fullsmb(71,:); + figure(3); + plot(timing,seriesSMB1,'b'); + hold on + plot(timing,seriesSMB71,'r'); + title('SMB at two different vertices'); + hold off + + save ./Models/PIG_StISSM_Transient1 md; + +end + +if any(steps==6) % Set up stochastic calving also + + md = loadmodel('./Models/PIG_StISSM_Transient1'); + + md.calving.calvingrate = 20*ones(md.mesh.numberofvertices,1); + md.frontalforcings.meltingrate = zeros(md.mesh.numberofvertices,1); + md.levelset.spclevelset = NaN(md.mesh.numberofvertices,1); + md.levelset.migration_max = 100.0; %avoid too fast advance/retreat of the front + md.transient.ismovingfront = 1; + + % Parameterize stochastic calving + idbasinsCalving = md.smb.basin_id; %same subdomains as for SMB + sdevClv1 = 0.5; %low standard deviation in subdomain 1 [m yr^-1] + sdevClv2 = 5; %higher variability in subdomain 2 [m yr^-1] + correlationClv = [1.0,0.0;0.0,1.0]; %no correlation between the subdomains + covarianceClv = diag([sdevClv1,sdevClv2])*correlationClv*diag([sdevClv1,sdevClv2]); %covariance matrix [(m yr^-1)^2] + + % Adjust stochastic forcing class + md.stochasticforcing.fields = [{'SMBarma'},{'DefaultCalving'}]; + oldcovarianceSMB = md.stochasticforcing.covariance; + covarianceGlobal = blkdiag(oldcovarianceSMB,covarianceClv); %independence between SMB and calving + md.stochasticforcing.covariance = covarianceGlobal; + md.stochasticforcing.defaultdimension = md.smb.num_basins; %2 basins for stochastic default (used for calving, same as SMB) + md.stochasticforcing.default_id = idbasinsCalving; + + save ./Models/PIG_StISSM_StochCalving md; + +end + +if any(steps==7) % Transient Run #2 + + md = loadmodel('./Models/PIG_StISSM_StochCalving'); + + md.verbose.solution = 1; + md.timestepping.start_time = md.timestepping.final_time; + md.timestepping.time_step = 0.1; + md.timestepping.final_time = md.timestepping.start_time+5; + md.transient.requested_outputs = {'default','SmbMassBalance','CalvingCalvingrate'}; + + % Set up initial conditions from previous transient results + md.geometry.thickness = md.results.TransientSolution(end).Thickness; + md.initialization.vx = md.results.TransientSolution(end).Vx; + md.initialization.vy = md.results.TransientSolution(end).Vy; + md.initialization.vel = md.results.TransientSolution(end).Vel; + md.mask.ocean_levelset = md.results.TransientSolution(end).MaskOceanLevelset; + md.initialization.pressure = md.results.TransientSolution(end).Pressure; + md.geometry.base = md.results.TransientSolution(end).Base; + md.geometry.surface = md.results.TransientSolution(end).Surface; + md.mask.ice_levelset = md.results.TransientSolution(end).MaskIceLevelset; + + md = solve(md,'Transient'); + md = loadresultsfromcluster(md); + timing = cell2mat({md.results.TransientSolution(:).time}); + fullsmb = cell2mat({md.results.TransientSolution(:).SmbMassBalance}); + fullclv = cell2mat({md.results.TransientSolution(:).CalvingCalvingrate}); + + timemeansmb = mean(fullsmb,2); + timesdevsmb = std(fullsmb,0,2); + maxsmb = max(fullsmb,[],'all'); + minsmb = min(fullsmb,[],'all'); + timemeanclv = mean(fullclv,2); + timesdevclv = std(fullclv,0,2); + maxclv = max(fullclv,[],'all'); + minclv = min(fullclv,[],'all'); + + plotmodel(md,'figure',1,... + 'data',md.results.TransientSolution(1).SmbMassBalance,'title','SMB at timestep 1','caxis#1',[minsmb,maxsmb],... + 'data',md.results.TransientSolution(end).SmbMassBalance,'title','SMB at last timestep','caxis#2',[minsmb,maxsmb]) + plotmodel(md,'figure',2,... + 'data',timemeansmb,'title','SMB mean over simulation',... + 'data',timesdevsmb,'title','SMB standard deviation over simulation') + plotmodel(md,'figure',3,... + 'data',timemeanclv,'title','Calving mean over simulation',... + 'data',timesdevclv,'title','Calving standard deviation over simulation') + + seriesSMB1 = fullsmb(1,:); + seriesSMB71 = fullsmb(71,:); + figure(4); + plot(timing,seriesSMB1,'b'); + hold on + plot(timing,seriesSMB71,'r'); + title('SMB at two different vertices'); + hold off + + seriesclv1 = fullclv(1,:); + seriesclv71 = fullclv(71,:); + figure(5); + plot(timing,seriesclv1,'b'); + hold on + plot(timing,seriesclv71,'r'); + title('Calving at two different vertices'); + hold off + +end + + + + + + + + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/ErrorContour.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/ErrorContour.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/ErrorContour.exp (revision 27955) @@ -0,0 +1,24 @@ +## Name:ErrorContour +## Icon:0 +# Points Count Value +18 1.000000 +# X pos Y pos +-1642090.6657102096 -328038.7002928721 +-1665417.0018035804 -319119.8070807009 +-1681882.6508106657 -304712.3641995014 +-1666103.0705122089 -245710.4552574461 +-1632485.7037894099 -232675.1497935036 +-1616020.0547823247 -224442.3252899610 +-1598182.2683579824 -200429.9204879618 +-1596810.1309407253 -181219.9966463624 +-1615333.9860736963 -160637.9353875059 +-1559762.4206747836 -147602.6299235635 +-1527517.1913692418 -188080.6837326479 +-1566623.1077610692 -218953.7756209326 +-1533691.8097468987 -229244.8062503609 +-1523400.7791174706 -309514.8451599012 +-1533691.8097468987 -350678.9676776142 +-1594751.9248148398 -371261.0289364707 +-1636602.1160411814 -349306.8302603571 +-1642090.6657102096 -328038.7002928721 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux1.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux1.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux1.exp (revision 27955) @@ -0,0 +1,22 @@ +## Name:MassFlux1 +## Icon:0 +# Points Count Value +16 1.000000 +# X pos Y pos +-1638344.3538415846 -328022.1178486745 +-1636175.0592654669 -328022.1178486745 +-1634647.1933393457 -327710.7373731936 +-1631836.4701132313 -326087.2311287920 +-1629847.9500851235 -324428.7567974643 +-1626413.2336729371 -321756.7703747695 +-1622074.6445207016 -320098.2960434417 +-1618278.3790124957 -319637.6087291840 +-1614210.9516822749 -319729.7461920356 +-1609601.2007080249 -320466.8458948479 +-1604539.5133637502 -322954.5573918396 +-1602370.2187876324 -324613.0317231673 +-1599206.6641974607 -326824.3308316044 +-1595681.5605112694 -327008.6057573075 +-1593150.7168391321 -327653.5679972683 +-1590710.2604409996 -330786.2417342208 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux10.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux10.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux10.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux11 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1539536.1089629673 -171232.8272031187 +-1540384.1546699132 -200614.0179257037 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux11.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux11.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux11.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux12 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1559431.5986180613 -236969.7272119786 +-1549112.1094185982 -261719.2194756830 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux12.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux12.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux12.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux13 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1572656.1032135738 -292391.9615161452 +-1573651.1418990945 -315407.7936937447 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux13.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux13.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux13.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux14 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1579674.9916810417 -321516.2892665596 +-1587436.3185859676 -337140.9687259690 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux14.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux14.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux14.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux14 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1579674.9916810417 -321516.2892665596 +-1587436.3185859676 -337140.9687259690 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux15.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux15.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux15.exp (revision 27955) @@ -0,0 +1,127 @@ +## Name: +## Icon:0 +# Points Count Value +121 25000.000000 +# X pos Y pos +-1712012.0818103175 -348661.1275967784 +-1711738.9446965172 -348380.8584401013 +-1709339.1962288069 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62751.8076344339 +-1622627.2364271644 61937.4929792271 +-1647011.3496706884 32864.6807476235 +-1637527.3859760596 19912.7371761968 +-1650069.2631712460 30042.0704865309 +-1724734.6043381831 -61378.0233897057 +-1718614.9048978437 -69045.3133313945 +-1758091.3164752426 -113926.3236823874 +-1754430.7541207569 -116894.8054778867 +-1760233.4203404333 -126776.6398906443 +-1757170.3120773330 -130521.7753713153 +-1762186.6328915418 -136423.2047200473 +-1765126.7323215308 -132420.4516091067 +-1769785.4415677825 -135199.8713571306 +-1774818.6171028516 -132429.3647437230 +-1793280.1507095622 -153411.6536596067 +-1711636.5537849038 -224740.3773715630 +-1729008.9305659365 -335286.5679692774 +-1712012.0818103175 -348661.1275967784 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux2.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux2.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux2.exp (revision 27955) @@ -0,0 +1,171 @@ +## Name:MassFlux2 +## Icon:0 +# Points Count Value +165 1.000000 +# X pos Y pos +-1609993.8450579999 -266189.3103270000 +-1609790.4465310001 -265898.8271340000 +-1609587.0480040000 -265608.3439410000 +-1609383.6494770001 -265317.8607480000 +-1609136.7086169999 -265274.3184150000 +-1608933.3100900000 -264983.8352220000 +-1608686.3692300001 -264940.2928890000 +-1608236.0298430000 -264606.2673630000 +-1607989.0889830000 -264562.7250310000 +-1607785.6904559999 -264272.2418380000 +-1607538.7495960000 -264228.6995050000 +-1607291.8087370000 -264185.1571720000 +-1607044.8678770000 -264141.6148390000 +-1606797.9270170000 -264098.0725060000 +-1606304.0452970001 -264010.9878410000 +-1606057.1044369999 -263967.4455080000 +-1605810.1635769999 -263923.9031750000 +-1605563.2227179999 -263880.3608420000 +-1605316.2818580000 -263836.8185100000 +-1605069.3409980000 -263793.2761770000 +-1604778.8578049999 -263996.6747040000 +-1604531.9169449999 -263953.1323710000 +-1604038.0352250000 -263866.0477060000 +-1603791.0943660000 -263822.5053730000 +-1603500.6111730000 -264025.9039000000 +-1603253.6703130000 -263982.3615680000 +-1602963.1871199999 -264185.7600950000 +-1602716.2462599999 -264142.2177620000 +-1602425.7630680001 -264345.6162900000 +-1601888.3390150000 -264505.4724840000 +-1601641.3981550001 -264461.9301510000 +-1601350.9149630000 -264665.3286790000 +-1601060.4317699999 -264868.7272060000 +-1600479.4653840000 -265275.5242610000 +-1600188.9821919999 -265478.9227880000 +-1599898.4989990001 -265682.3213160000 +-1599608.0158060000 -265885.7198430000 +-1599027.0494210001 -266292.5168980000 +-1598736.5662280000 -266495.9154250000 +-1598446.0830349999 -266699.3139520000 +-1598402.5407030000 -266946.2548130000 +-1598605.9392299999 -267236.7380050000 +-1598518.8545639999 -267730.6197260000 +-1598722.2530910000 -268021.1029190000 +-1598678.7107579999 -268268.0437790000 +-1598635.1684250000 -268514.9846390000 +-1598591.6260919999 -268761.9254990000 +-1598795.0246190000 -269052.4086920000 +-1598751.4822869999 -269299.3495520000 +-1598707.9399540001 -269546.2904130000 +-1598620.8552880001 -270040.1721330000 +-1598577.3129550000 -270287.1129930000 +-1598533.7706220001 -270534.0538530000 +-1598737.1691490000 -270824.5370460000 +-1598693.6268170001 -271071.4779060000 +-1598650.0844840000 -271318.4187660000 +-1598606.5421509999 -271565.3596270000 +-1598316.0589580000 -271768.7581540000 +-1598228.9742930001 -272262.6398740000 +-1597938.4911000000 -272466.0384020000 +-1597648.0079069999 -272669.4369290000 +-1597067.0415220000 -273076.2339840000 +-1597023.4991890001 -273323.1748440000 +-1596979.9568560000 -273570.1157040000 +-1596936.4145229999 -273817.0565640000 +-1596892.8721900000 -274063.9974240000 +-1596805.7875250001 -274557.8791450000 +-1596762.2451919999 -274804.8200050000 +-1596718.7028590001 -275051.7608650000 +-1596675.1605260000 -275298.7017250000 +-1596631.6181930001 -275545.6425850000 +-1596341.1350010000 -275749.0411130000 +-1596297.5926679999 -275995.9819730000 +-1595963.5671420000 -276446.3213600000 +-1595920.0248090001 -276693.2622210000 +-1595629.5416170000 -276896.6607480000 +-1595339.0584239999 -277100.0592750000 +-1595048.5752310001 -277303.4578030000 +-1594467.6088459999 -277710.2548570000 +-1594177.1256530001 -277913.6533850000 +-1593886.6424600000 -278117.0519120000 +-1593392.7607410001 -278029.9672470000 +-1593102.2775480000 -278233.3657740000 +-1592898.8790209999 -277942.8825810000 +-1592695.4804940000 -277652.3993880000 +-1592201.5987740001 -277565.3147220000 +-1591998.2002470000 -277274.8315290000 +-1592041.7425800001 -277027.8906690000 +-1591838.3440530000 -276737.4074760000 +-1591881.8863860001 -276490.4666160000 +-1591722.0301910001 -275953.0425630000 +-1591765.5725240000 -275706.1017030000 +-1591562.1739970001 -275415.6185100000 +-1591605.7163300000 -275168.6776500000 +-1591402.3178030001 -274878.1944570000 +-1591198.9192760000 -274587.7112640000 +-1591242.4616090001 -274340.7704040000 +-1591039.0630820000 -274050.2872110000 +-1591082.6054150001 -273803.3463510000 +-1590922.7492209999 -273265.9222970000 +-1590966.2915530000 -273018.9814370000 +-1590762.8930259999 -272728.4982440000 +-1590806.4353590000 -272481.5573840000 +-1590603.0368319999 -272191.0741910000 +-1590399.6383050000 -271900.5909980000 +-1590443.1806379999 -271653.6501380000 +-1590239.7821110000 -271363.1669450000 +-1590036.3835839999 -271072.6837520000 +-1590123.4682499999 -270578.8020320000 +-1589920.0697230001 -270288.3188390000 +-1589716.6711960000 -269997.8356460000 +-1589760.2135280001 -269750.8947860000 +-1589556.8150010000 -269460.4115930000 +-1589600.3573340001 -269213.4707330000 +-1589440.5011400001 -268676.0466800000 +-1589484.0434729999 -268429.1058190000 +-1589280.6449460001 -268138.6226260000 +-1589077.2464190000 -267848.1394340000 +-1588873.8478920001 -267557.6562410000 +-1588423.5085050000 -267223.6307150000 +-1588220.1099779999 -266933.1475220000 +-1587973.1691180000 -266889.6051890000 +-1587726.2282580000 -266846.0628560000 +-1587479.2873980000 -266802.5205230000 +-1586985.4056780001 -266715.4358580000 +-1586738.4648190001 -266671.8935250000 +-1586491.5239589999 -266628.3511920000 +-1586244.5830989999 -266584.8088590000 +-1585997.6422389999 -266541.2665270000 +-1585750.7013790000 -266497.7241940000 +-1585256.8196590000 -266410.6395280000 +-1585009.8787990001 -266367.0971960000 +-1584762.9379400001 -266323.5548630000 +-1584472.4547470000 -266526.9533900000 +-1584428.9124139999 -266773.8942500000 +-1584138.4292210001 -266977.2927780000 +-1583804.4036960001 -267427.6321650000 +-1583760.8613630000 -267674.5730250000 +-1583470.3781699999 -267877.9715530000 +-1583179.8949770001 -268081.3700800000 +-1583136.3526450000 -268328.3109400000 +-1582845.8694519999 -268531.7094680000 +-1582802.3271190000 -268778.6503280000 +-1582468.3015940001 -269228.9897150000 +-1582424.7592610000 -269475.9305750000 +-1582134.2760679999 -269679.3291030000 +-1582090.7337350000 -269926.2699630000 +-1581800.2505419999 -270129.6684900000 +-1581509.7673500001 -270333.0670180000 +-1581219.2841570000 -270536.4655450000 +-1581132.1994910000 -271030.3472650000 +-1580841.7162990000 -271233.7457930000 +-1580551.2331060001 -271437.1443200000 +-1580507.6907730000 -271684.0851800000 +-1580217.2075799999 -271887.4837080000 +-1580173.6652470001 -272134.4245680000 +-1579839.6397220001 -272584.7639550000 +-1579796.0973890000 -272831.7048160000 +-1579505.6141959999 -273035.1033430000 +-1579462.0718640001 -273282.0442030000 +-1579418.5295309999 -273528.9850630000 +-1579128.0463380001 -273732.3835910000 +-1579084.5040050000 -273979.3244510000 +-1578750.4784800000 -274429.6638380000 +-1578706.9361469999 -274676.6046980000 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux3.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux3.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux3.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:MassFlux4 +## Icon:0 +# Points Count Value +4 1.000000 +# X pos Y pos +-1605390.0162510793 -209047.7381093690 +-1592454.5133393104 -208141.0538114636 +-1574086.0992045982 -208918.2117810968 +-1560891.8862345938 -210472.5277203633 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux4.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux4.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux4.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux5 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1660144.8928561222 -319887.0521198768 +-1630434.8468677206 -298387.4931837295 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux5.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux5.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux5.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux6 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1635925.9455644884 -157610.4872330402 +-1625288.0602165582 -120861.2411445094 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux6.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux6.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux6.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux7 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1642052.5574172530 -95522.7999921589 +-1610982.9267521810 -78949.7704229522 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux7.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux7.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux7.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux8 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1605014.5365509845 -81707.1563440522 +-1566756.1417461073 -82763.2940976564 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux8.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux8.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux8.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux9 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1555378.1885604258 -45179.9925785796 +-1550583.9034971579 -68415.0231578706 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux9.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux9.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/MassFluxes/MassFlux9.exp (revision 27955) @@ -0,0 +1,8 @@ +## Name:MassFlux10 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1565010.6613481115 -111795.8673475993 +-1537474.3225972611 -138442.9656094175 + Index: /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/UncertaintyQuantification/runme.m (revision 27955) @@ -0,0 +1,316 @@ +%PIG Uncertainty Quantification Tutorial +steps=[1]; + +if any(steps==1) + disp(' Step 1: plot flux gates'); + + % NOTE: Need to run all steps of ../Pig/runme.m first! + md = loadmodel('../Pig/Models/PIG_Control_drag'); + + texts=cell(1,13); + textpositions=cell(1,13); + + for i=1:13, + contour=expread(['./MassFluxes/MassFlux' num2str(i) '.exp']); + textpositions{i}=[contour.x(end) contour.y(end)]; + end + vel=md.results.StressbalanceSolution.Vel; vel(vel==0)=nan; + plotmodel(md,'data',vel,'log',10,'expdisp',... + {'MassFluxes/MassFlux1.exp','MassFluxes/MassFlux2.exp',... + 'MassFluxes/MassFlux3.exp','MassFluxes/MassFlux4.exp',... + 'MassFluxes/MassFlux5.exp','MassFluxes/MassFlux6.exp',... + 'MassFluxes/MassFlux7.exp','MassFluxes/MassFlux8.exp',... + 'MassFluxes/MassFlux9.exp','MassFluxes/MassFlux10.exp',... + 'MassFluxes/MassFlux11.exp','MassFluxes/MassFlux12.exp',... + 'MassFluxes/MassFlux13.exp'},... + 'expstyle',{'k-','k-','k-','k-','k-','k-','k-',... + 'k-','k-','k-','k-','k-','k-'},'linewidth',2,... + 'text',{'1','2','3','4','5','6','7',... + '8','9','10','11','12','13'},... + 'textposition',textpositions); +end + +if any(steps==2) + disp(' Step 2: compute cross overs from CRESIS'); + + md = loadmodel('../Pig/Models/PIG_Control_drag'); + + %load cross overs: CRESIS McCord Antarctica, 2009 (courtesy of John Paden) + load('../Data/CrossOvers2009.mat'); + + %interpolate cross over errors over our mesh vertices + DeltaHH=InterpFromMeshToMesh2d(index,x,y,dhh,md.mesh.x,md.mesh.y); + + %avoid NaN values + pos=find(isnan(DeltaHH)); DeltaHH(pos)=0; + + %filter out unrealistic error ranges + flags=ContourToNodes(md.mesh.x,md.mesh.y,'ErrorContour.exp',1); + pos=find(~flags); DeltaHH(pos)=0; + + %avoid large unrealistic values + pos=find(DeltaHH>1); DeltaHH(pos)=1; + pos=find(DeltaHH<-1); DeltaHH(pos)=-1; + + %transform into absolute errors and setup a minimum error everywhere. + DeltaHH=abs(DeltaHH); + pos=find(DeltaHH==0); pos2=find(DeltaHH~=0); + DeltaHH(pos)=min(DeltaHH(pos2)); + + save Models/PIG.CrossOvers DeltaHH +end + +if any(steps==3) + disp(' Step 3: sampling analysis'); + + %load model and cross over errors + md = loadmodel('../Pig/Models/PIG_Control_drag'); + load -mat Models/PIG.CrossOvers + + %partition the mesh + npart=50; + [partition,md]=partitioner(md,'package','chaco','npart',npart,'weighting','on'); + partition=partition-1; + + %make DeltaHH into our 3 sigma deviation + DeltaHH=DeltaHH/6; %2 (to transform DeltaHH into a radius) x 3 (for 3 sigma) + DeltaHH_on_partition=AreaAverageOntoPartition(md,DeltaHH,partition); + DeltaHH_on_grids=DeltaHH_on_partition(partition+1); %just to check in case + + md.qmu.variables.thickness=normal_uncertain('descriptor','scaled_Thickness',... + 'mean',ones(npart,1),... + 'stddev',DeltaHH_on_partition,... + 'partition',partition); + + %responses + md.qmu.responses.MassFlux1=response_function('descriptor','indexed_MassFlux_1'); + md.qmu.responses.MassFlux2=response_function('descriptor','indexed_MassFlux_2'); %grounding line + md.qmu.responses.MassFlux3=response_function('descriptor','indexed_MassFlux_3'); + md.qmu.responses.MassFlux4=response_function('descriptor','indexed_MassFlux_4'); + md.qmu.responses.MassFlux5=response_function('descriptor','indexed_MassFlux_5'); + md.qmu.responses.MassFlux6=response_function('descriptor','indexed_MassFlux_6'); + md.qmu.responses.MassFlux7=response_function('descriptor','indexed_MassFlux_7'); + md.qmu.responses.MassFlux8=response_function('descriptor','indexed_MassFlux_8'); + md.qmu.responses.MassFlux9=response_function('descriptor','indexed_MassFlux_9'); + md.qmu.responses.MassFlux10=response_function('descriptor','indexed_MassFlux_10'); + md.qmu.responses.MassFlux11=response_function('descriptor','indexed_MassFlux_11'); + md.qmu.responses.MassFlux12=response_function('descriptor','indexed_MassFlux_12'); + md.qmu.responses.MassFlux13=response_function('descriptor','indexed_MassFlux_13'); + + %mass flux profiles + md.qmu.mass_flux_profiles={... + 'MassFlux1.exp',... + 'MassFlux2.exp',... + 'MassFlux3.exp',... + 'MassFlux4.exp',... + 'MassFlux5.exp',... + 'MassFlux6.exp',... + 'MassFlux7.exp',... + 'MassFlux8.exp',... + 'MassFlux9.exp',... + 'MassFlux10.exp',... + 'MassFlux11.exp',... + 'MassFlux12.exp',... + 'MassFlux13.exp'... + }; + md.qmu.mass_flux_profile_directory='./MassFluxes/'; + + %sampling analysis + md.qmu.method =dakota_method('nond_samp'); + md.qmu.method(end) =dmeth_params_set(... + md.qmu.method(end),... + 'seed',1234,... + 'samples',30,... + 'sample_type','lhs'... + ); %random or lhs + + %a variety of parameters + md.qmu.params.direct=true; + md.qmu.params.analysis_driver=''; + md.qmu.params.analysis_components=''; + md.qmu.params.evaluation_concurrency=1; + md.qmu.params.tabular_graphics_data=true; + + md.stressbalance.restol=10^-5; %tighten tolerances for UQ analyses + + %Turn off verbosity + md.verbose=verbose(0); + + %Here, we choose to run with 4 processors, 3 for Dakota + % while one serves as the master + md.cluster=generic('name',oshostname,'np',4); + + %Dakota runs in parallel with a master/slave configuration. + % At least 2 CPUs are needed to run the UQ + md.qmu.params.evaluation_scheduling='master'; + md.qmu.params.processors_per_evaluation=md.cluster.np-1; + + %Turn dakota on + md.qmu.isdakota=1; md.inversion.iscontrol=0; + md=solve(md,'Stressbalance','overwrite','y'); + + save ./Models/PIG.Sampling md; +end + +if any(steps==4) + disp(' Step 4: plot partition'); + + %load model + md = loadmodel('./Models/PIG.Sampling'); + + plotmodel(md,'data','mesh','partition',partition,... + 'linewidth',2, 'axis#all','image','unit','km','colorbar','off',... + 'title','Partition Edges on ISSM mesh','grid','on'); +end + +if any(steps==5) + disp(' Step 5: sensitivity analysis'); + + %load model + md = loadmodel('../Pig/Models/PIG_Control_drag'); + + %partition the mesh + npart=10; + [partition,md]=partitioner(md,'package','chaco','weighting','on'); + partition=partition-1; %switch partition to c-indexing + + %all types of variables and responses: scaled_Thickness, indexed_MassFlux_i,MaxVel,nodal_DragCoefficient_i. scaled variables are expanded. + + %variables + md.qmu.variables.drag_coefficient=normal_uncertain('descriptor','scaled_FrictionCoefficient',... + 'mean',ones(npart,1),... + 'stddev',0.05*ones(npart,1),... + 'partition',partition); + md.qmu.variables.rheology_B=normal_uncertain('descriptor','scaled_MaterialsRheologyB',... + 'mean',ones(npart,1),... + 'stddev',0.05*ones(npart,1),... + 'partition',partition); + md.qmu.variables.thickness=normal_uncertain('descriptor','scaled_Thickness',... + 'mean',ones(npart,1),... + 'stddev',0.05*ones(npart,1),... + 'partition',partition); + + %responses + md.qmu.responses.MassFlux1=response_function('descriptor','indexed_MassFlux_1'); + md.qmu.responses.MassFlux2=response_function('descriptor','indexed_MassFlux_2'); + md.qmu.responses.MassFlux3=response_function('descriptor','indexed_MassFlux_3'); + md.qmu.responses.MassFlux4=response_function('descriptor','indexed_MassFlux_4'); + md.qmu.responses.MassFlux5=response_function('descriptor','indexed_MassFlux_5'); + md.qmu.responses.MassFlux6=response_function('descriptor','indexed_MassFlux_6'); + md.qmu.responses.MassFlux7=response_function('descriptor','indexed_MassFlux_7'); + md.qmu.responses.MassFlux8=response_function('descriptor','indexed_MassFlux_8'); + md.qmu.responses.MassFlux9=response_function('descriptor','indexed_MassFlux_9'); + md.qmu.responses.MassFlux10=response_function('descriptor','indexed_MassFlux_10'); + md.qmu.responses.MassFlux11=response_function('descriptor','indexed_MassFlux_11'); + md.qmu.responses.MassFlux12=response_function('descriptor','indexed_MassFlux_12'); + md.qmu.responses.MassFlux13=response_function('descriptor','indexed_MassFlux_13'); + + %mass flux profiles + md.qmu.mass_flux_profiles={... + 'MassFlux1.exp',... + 'MassFlux2.exp',... + 'MassFlux3.exp',... + 'MassFlux4.exp',... + 'MassFlux5.exp',... + 'MassFlux6.exp',... + 'MassFlux7.exp',... + 'MassFlux8.exp',... + 'MassFlux9.exp',... + 'MassFlux10.exp',... + 'MassFlux11.exp',... + 'MassFlux12.exp',... + 'MassFlux13.exp'... + }; + md.qmu.mass_flux_profile_directory='./MassFluxes/'; + + %method: local reliability + md.qmu.method =dakota_method('nond_l'); + md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),... + 'output','quiet'); + + %parameters + md.qmu.params.direct=true; + md.qmu.params.analysis_driver=''; + md.qmu.params.analysis_components=''; + md.qmu.params.evaluation_concurrency=1; + md.qmu.params.tabular_graphics_data=false; + + md.stressbalance.restol=10^-5; %tighten for qmu analyses + + %Here, we choose to run with 2 processors, 1 for Dakota + % while one serves as the master + md.cluster=generic('name',oshostname,'np',2); + + %Dakota runs in parallel with a master/slave configuration. + % At least 2 CPUs are needed to run the UQ + md.qmu.params.evaluation_scheduling='master'; + md.qmu.params.processors_per_evaluation=md.cluster.np-1; + + %Clear results and turn dakota on + md.results=[]; + md.qmu.isdakota=1; md.inversion.iscontrol=0; + md.verbose=verbose('qmu',true); + md=solve(md,'Stressbalance','overwrite','y'); + + save ./Models/PIG.Sensitivity md; +end + +if any(steps==6) + disp(' Step 6: plot histogram'); + + %load model + md = loadmodel('./Models/PIG.Sampling'); + + %which profile are we looking at? + index=1; + + %retrieve results for the specific profile, mass flux in m^3 water equiv/s + result=md.results.dakota.dresp_dat(npart+index); + result.sample=result.sample/1e12*60*60*24*365; + + %plot histogram + plot_hist_norm(result,'cdfleg','off','cdfplt','off','nrmplt','off',... + 'xlabelplt','M (Gt/yr)','ylabelplt','F','FontSize',8,'FaceColor',... + 'none','EdgeColor','red'); +end + +if any(steps==7) + disp(' Step 7: plot sensitivity'); + + %load model + md = loadmodel('./Models/PIG.Sensitivity'); + %copy dakota results into model qmu + md.qmu.results=md.results.dakota; + + %which profile are we looking at? + index=1; + + %To plot sensitivities + sa=md.results.dakota.dresp_out(index).sens(1:10); sa=sa(partition+1)/1e12*60*60*24*365; + sb=md.results.dakota.dresp_out(index).sens(11:20); sb=sb(partition+1)/1e12*60*60*24*365; + sh=md.results.dakota.dresp_out(index).sens(21:30); sh=sh(partition+1)/1e12*60*60*24*365; + + plotmodel(md,'data',sh,'data',sa,'data',sb,'expdisp#all',... + ['MassFluxes/MassFlux' num2str(index) '.exp'],... + 'expstyle#all','b-','linewidth#all',2,... + 'nlines',3,'ncols',1, 'axis#all','image',... + 'caxis#1',[0 150],'caxis#2',[-20 0],'caxis#3',[-25 0],... + 'colorbar#all','on','colorbarfontsize#all',10,... + 'colorbartitle#1','S_{H}', 'colorbartitle#2','S_{\alpha}',... + 'colorbartitle#3','S_{B}','unit#all','km','figure',1,... + 'title','Sensitivities: H, \alpha, B'); + + %To plot importance factors + ifa=importancefactors(md,'scaled_FrictionCoefficient',['indexed_MassFlux_' num2str(index)],partition); + ifb=importancefactors(md,'scaled_MaterialsRheologyB',['indexed_MassFlux_' num2str(index)],partition); + ifh=importancefactors(md,'scaled_Thickness',['indexed_MassFlux_' num2str(index)],partition); + + plotmodel(md,'data',ifh,'data',ifa,'data',ifb,'expdisp#all',... + ['MassFluxes/MassFlux' num2str(index) '.exp'],... + 'expstyle#all','b-','linewidth#all',2,'log#all',10,... + 'nlines',3,'ncols',1, 'axis#all','image','caxis#all',[1e-10 1],... + 'colorbar#all','on','colorbarfontsize#all',10,... + 'colorbartitle#1','If_{H}', 'colorbartitle#2','If_{\alpha}',... + 'colorbartitle#3','If_{B}','unit#all','km','figure',2,... + 'title','Importance Factors: H, \alpha, B'); +end Index: /issm/branches/trunk-dlcheng-ASE/examples/shakti/moulin.par =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/shakti/moulin.par (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/shakti/moulin.par (revision 27955) @@ -0,0 +1,44 @@ +%Start defining model parameters here + +% Set up bed topography and ice geometry for a tilted 500m thick slab +md.geometry.base = .02*md.mesh.x; +md.geometry.bed = md.geometry.base; +md.geometry.surface = .02*md.mesh.x + 500; +md.geometry.thickness = md.geometry.surface - md.geometry.bed; + +% Define ice sliding velocity (m/yr) +md.initialization.vx = 10^-6*md.constants.yts*ones(md.mesh.numberofvertices,1); +md.initialization.vy = zeros(md.mesh.numberofvertices,1); +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); + +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); + +% Materials +% Ice flow law parameter (note that the standard parameter A=B^(-3)) +md.materials.rheology_B= (5e-25)^(-1/3)*ones(md.mesh.numberofvertices,1); +md.initialization.temperature=(273)*ones(md.mesh.numberofvertices,1); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); + +%Calving +md.calving.calvingrate=zeros(md.mesh.numberofvertices,1); +%md.calving.spclevelset=NaN(md.mesh.numberofvertices,1); + +% Friction law and coefficient +md.friction=frictionshakti(md.friction); +md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); + +%Numerical parameters +%md.stressbalance.viscosity_overshoot=0.0; +md.masstransport.stabilization=1.; +md.thermal.stabilization=1.; +md.verbose=verbose(0); +md.settings.waitonlock=30; +md.stressbalance.restol=0.05; +md.steadystate.reltol=0.05; +md.stressbalance.reltol=0.05; +md.stressbalance.abstol=NaN; +md.timestepping.time_step=1.; +md.timestepping.final_time=3.; + +%Boundary conditions: +md=SetIceSheetBC(md); Index: /issm/branches/trunk-dlcheng-ASE/examples/shakti/moulin.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/shakti/moulin.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/shakti/moulin.py (revision 27955) @@ -0,0 +1,57 @@ +import numpy as np +from SetIceSheetBC import SetIceSheetBC +from frictionshakti import frictionshakti +from verbose import verbose + +#Start defining model parameters here +# Set up bed topography and ice geometry for a tilted 500m thick slab +md.geometry.base = .02 * md.mesh.x +md.geometry.bed = md.geometry.base +md.geometry.surface = .02 * md.mesh.x + 500 +md.geometry.thickness = md.geometry.surface - md.geometry.bed + +# Define ice sliding velocity (m / yr) +md.initialization.vx = 1.0e-6 * md.constants.yts * np.ones(md.mesh.numberofvertices) +md.initialization.vy = np.zeros(md.mesh.numberofvertices) +md.initialization.pressure = np.zeros(md.mesh.numberofvertices) + +# Materials +# Ice flow law parameter (note that the standard parameter A = B^(- 3)) +md.materials.rheology_B = 5e-25**(-1. / 3.) * np.ones(md.mesh.numberofvertices) +md.initialization.temperature = 273. * np.ones(md.mesh.numberofvertices) +md.materials.rheology_n = 3. * np.ones(md.mesh.numberofelements) + +#Calving +md.calving.calvingrate = np.zeros(md.mesh.numberofvertices) +#md.calving.spclevelset = NaN(md.mesh.numberofvertices, 1) + +# Friction law and coefficient +md.friction = frictionshakti(md) +md.friction.coefficient = 20. * np.ones(md.mesh.numberofvertices) + +#Numerical parameters +#md.stressbalance.viscosity_overshoot = 0.0 +md.masstransport.stabilization = 1. +md.thermal.stabilization = 1. +md.verbose = verbose(0) +md.settings.waitonlock = 30 +md.stressbalance.restol = 0.05 +md.steadystate.reltol = 0.05 +md.stressbalance.reltol = 0.05 +md.stressbalance.abstol = np.nan +md.timestepping.time_step = 1. +md.timestepping.final_time = 3. + +#GIA: +md.gia.lithosphere_thickness = 100. * np.ones(md.mesh.numberofvertices) # in km +md.gia.mantle_viscosity = 1.0e21 * np.ones(md.mesh.numberofvertices) # in Pa.s +md.materials.lithosphere_shear_modulus = 6.7e10 # in Pa +md.materials.lithosphere_density = 3.32 # in g / cm^ - 3 +md.materials.mantle_shear_modulus = 1.45e11 # in Pa +md.materials.mantle_density = 3.34 # in g / cm^ - 3 + +#Boundary conditions: +md = SetIceSheetBC(md) + +#Change name so that no test have the same name +md.private.runtimename = True Index: /issm/branches/trunk-dlcheng-ASE/examples/shakti/outline.exp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/shakti/outline.exp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/shakti/outline.exp (revision 27955) @@ -0,0 +1,10 @@ +## Name:DomainOutline +## Icon:0 +# Points Count Value +5 1.000000 +# X pos Y pos +0 0 +1000 0 +1000 1000 +0 1000 +0 0 Index: /issm/branches/trunk-dlcheng-ASE/examples/shakti/runme.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/shakti/runme.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/shakti/runme.m (revision 27955) @@ -0,0 +1,84 @@ +steps=[1:3]; + +if any(steps==1) + disp(' Step 1: Mesh'); + + %Generate unstructured mesh on 1,000 m square with typical element edge length of 20 m + md=triangle(model,'./outline.exp',20); + + save MoulinMesh md +end + +if any(steps==2) + disp(' Step 2: Parameterization'); + md=loadmodel('MoulinMesh'); + + md=setmask(md,'',''); + + % Run parameterization script to set up geometry, velocity, material properties, etc. + md=parameterize(md,'moulin.par'); + + % HYDROLOGY SPECIFIC PARAMETERIZATION: + % Change hydrology class to Sommers' SHaKTI model + md.hydrology=hydrologyshakti(); + + % Define initial water head such that water pressure is 50% of ice overburden pressure + md.hydrology.head = 0.5*md.materials.rho_ice/md.materials.rho_freshwater*md.geometry.thickness + md.geometry.base; + + % Initial subglacial gap height of 0.01m everywhere + md.hydrology.gap_height = 0.01*ones(md.mesh.numberofelements,1); + + % Typical bed bump bump spacing (2m) + md.hydrology.bump_spacing = 2*ones(md.mesh.numberofelements,1); + + % Typical bed bump height (0.1m) + md.hydrology.bump_height = 0.1*ones(md.mesh.numberofelements,1); + + % Define distributed englacial input to the subglacial system (m/yr) + % Change the value 0.0 to add distributed input + md.hydrology.englacial_input = 0.0*ones(md.mesh.numberofvertices,1); + + % Initial Reynolds number (start at Re=1000 everywhere) + md.hydrology.reynolds= 1000*ones(md.mesh.numberofelements,1); + + % Set up atmospheric pressure Type I boundary condition at left edge of + % domain (outflow, i.e. h=zb at x=xmin) + md.hydrology.spchead = NaN(md.mesh.numberofvertices,1); + pos=find(md.mesh.vertexonboundary & md.mesh.x==min(md.mesh.x)); + md.hydrology.spchead(pos)=md.geometry.base(pos); + + save MoulinParam md; +end + +if any(steps==3) + disp(' Step 3: Solve!'); + md=loadmodel('MoulinParam'); + + md.transient=deactivateall(md.transient); + md.transient.ishydrology=1; + + % Specify that you want to run the model on your current computer + % Change the number of processors according to your machine (here np=4) + md.cluster=generic('np',2); + + % Define the time stepping scheme: run for 90 days with a time step of 1 hr + md.timestepping.time_step=3600/md.constants.yts; % Time step (in years) + md.timestepping.final_time=30/365; + + %Add one moulin with steady input at x=500, y=500 + [a,pos] = min(sqrt((md.mesh.x-500).^2+(md.mesh.y-500).^2)); + time=0:md.timestepping.time_step:md.timestepping.final_time; + md.hydrology.moulin_input = zeros(md.mesh.numberofvertices+1,numel(time)); + md.hydrology.moulin_input(end,:)=time; + md.hydrology.moulin_input(pos,:)=4; + + % Specify no-flux Type 2 boundary conditions on all edges (except + % the Type 1 condition set at the outflow above) + md.hydrology.neumannflux=zeros(md.mesh.numberofelements+1,numel(time)); + md.hydrology.neumannflux(end,:)=time; + + md.verbose.solution=1; + md=solve(md,'Transient'); + + save MoulinTransient md +end Index: /issm/branches/trunk-dlcheng-ASE/examples/shakti/runme.py =================================================================== --- /issm/branches/trunk-dlcheng-ASE/examples/shakti/runme.py (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/examples/shakti/runme.py (revision 27955) @@ -0,0 +1,91 @@ +import numpy as np +from model import * +from solve import solve +from hydrologyshakti import hydrologyshakti +from parameterize import parameterize +from export_netCDF import export_netCDF +from transient import transient +from setmask import setmask +from triangle import triangle + + +steps = [1, 2, 3] + +if 1 in steps: + print(' Step 1: Mesh') + #Generate unstructured mesh on 1, 000 m square with typical element edge length of 20 m + md = triangle(model(), './outline.exp', 20) + export_netCDF(md, 'MoulinMesh.nc') + + +if 2 in steps: + print(' Step 2: Parameterization') + md = loadmodel('MoulinMesh.nc') + md = setmask(md, '', '') + + # Run parameterization script to set up geometry, velocity, material properties, etc. + md = parameterize(md, 'moulin.py') + + # HYDROLOGY SPECIFIC PARAMETERIZATION: + # Change hydrology class to Sommers' SHaKTI model + md.hydrology = hydrologyshakti() + + # Define initial water head such that water pressure is 50% of ice overburden pressure + md.hydrology.head = 0.5 * md.materials.rho_ice / md.materials.rho_freshwater * md.geometry.thickness + md.geometry.base + + # Initial subglacial gap height of 0.01m everywhere + md.hydrology.gap_height = 0.01 * np.ones(md.mesh.numberofelements) + + # Typical bed bump bump spacing (2m) + md.hydrology.bump_spacing = 2 * np.ones(md.mesh.numberofelements) + + # Typical bed bump height (0.1m) + md.hydrology.bump_height = 0.1 * np.ones(md.mesh.numberofelements) + + # Define distributed englacial input to the subglacial system (m / yr) + # Change the value 0.0 to add distributed input + md.hydrology.englacial_input = 0.0 * np.ones(md.mesh.numberofvertices) + + # Initial Reynolds number (start at Re = 1000 everywhere) + md.hydrology.reynolds = 1000. * np.ones(md.mesh.numberofelements) + + # Set up atmospheric pressure Type I boundary condition at left edge of + # domain (outflow, i.e. h = zb at x = xmin) + md.hydrology.spchead = np.nan * np.ones(md.mesh.numberofvertices) + pos = np.where(np.logical_and(md.mesh.vertexonboundary, md.mesh.x == np.nanmin(md.mesh.x))) + md.hydrology.spchead[pos] = md.geometry.base[pos] + + export_netCDF(md, 'MoulinParam.nc') + +if 3 in steps: + print(' Step 3: Solve!') + md = loadmodel('MoulinParam.nc') + + md.transient = transient.deactivateall(md.transient) + md.transient.ishydrology = 1 + + # Specify that you want to run the model on your current computer + # Change the number of processors according to your machine (here np = 4) + md.cluster = generic('np', 2) + + # Define the time stepping scheme: run for 90 days with a time step of 1 hr + md.timestepping.time_step = 3600. / md.constants.yts # Time step (in years) + md.timestepping.final_time = 30. / 365. + + #Add one moulin with steady input at x = 500, y = 500 + DistToCenter = np.sqrt((md.mesh.x - 500)**2 + (md.mesh.y - 500)**2) + loc = np.where(np.nanmin(DistToCenter) == DistToCenter) + time = np.arange(0, md.timestepping.final_time + md.timestepping.time_step, md.timestepping.time_step) + md.hydrology.moulin_input = np.zeros((md.mesh.numberofvertices, len(time))) + md.hydrology.moulin_input = np.vstack((md.hydrology.moulin_input, time)) + md.hydrology.moulin_input[loc, :] = 4 + + # Specify no - flux Type 2 boundary conditions on all edges (except + # the Type 1 condition set at the outflow above) + md.hydrology.neumannflux = np.zeros((md.mesh.numberofelements, len(time))) + md.hydrology.neumannflux = np.vstack((md.hydrology.neumannflux, time)) + + md.verbose.solution = 1 + md = solve(md, 'Transient') + + export_netCDF(md, 'MoulinTransient.nc') Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adic/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adic/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adic/install.sh (revision 27955) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf source build install + +#Download code +hg clone http://mercurial.mcs.anl.gov/ad/ADIC -r 631 source + +#Then update to -r 631 +cd source +hg update -r 631 + +#Configure and Compile +cd source +./autogen.sh +./aclocal +cd .. +mkdir build +cd build +../source/configure \ + --with-rose=$ISSM_DIR/externalpackages/rose/install \ + --with-openanalysis=$ISSM_DIR/externalpackages/openanalysis/openanalysis/x86_64-Linux \ + --with-boost=$ISSM_DIR/externalpackages/boost/install \ + --with-xerces=$ISSM_DIR/externalpackages/xerces/src \ + --with-xaifbooster=$ISSM_DIR/externalpackages/xaifbooster/xaifBooster \ + --with-colpack=$ISSM_DIR/externalpackages/colpack/install\ + --prefix=$ISSM_DIR/externalpackages/adic/install +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adic/tests/notes =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adic/tests/notes (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adic/tests/notes (revision 27955) @@ -0,0 +1,143 @@ +mini1.c is: +7:37 PM +#include + +void mini1(double *y, double *x) +{ + int i; + for (i = 0; i < 2; i=i+1) { + y[i] = x[i] + sin(x[i]*x[i]); + } + } + Eric Larour 7:37 PM + ok + Sri Hari Krishna Narayanan 7:37 PM + If you cat any of mini1_grad_length.ad.c mini1_dense_forward.ad.c mini1_sparse_forward.ad.c + 7:37 PM + You should be able to see the forward mode output + Eric Larour 7:38 PM + ok + Sri Hari Krishna Narayanan 7:38 PM + First the makefile compiles mini1_grad_length.ad.c with a runtime library to estimate the number of columns in the Jacobian. + Eric Larour 7:39 PM + ok, makes sense + Sri Hari Krishna Narayanan 7:39 PM + That generates the output : ADIC_GRADVEC_LENGTH 2 + Eric Larour 7:39 PM + where? + 7:39 PM + ok, sorry, got it + Sri Hari Krishna Narayanan 7:40 PM + The value is also written to : runtime_dense/adic_gradvec_length.h + Eric Larour 7:40 PM + where is the main for this? + 7:40 PM + oh, it creates a .h directly + Sri Hari Krishna Narayanan 7:40 PM + mini1_driver.c + 7:40 PM + yes. + 7:40 PM + The runtime library takes care of that + 7:40 PM + There is alot or #defined compilation going on + Eric Larour 7:41 PM + wraps around mini1_forward_array.exe ? + Sri Hari Krishna Narayanan 7:41 PM + /*intermediary: */ creates mini1_grad_length.exe + Eric Larour 7:41 PM + Isn't that the Makefile? what is the runtime library ? + 7:42 PM + ok, the Makefile launches the runtime library + Sri Hari Krishna Narayanan 7:42 PM + Makefile copies versions of the runtime library (bunch of macros in most cases) + Eric Larour 7:42 PM + what is the name of the runtime library? + Sri Hari Krishna Narayanan 7:43 PM + form $adicsrc/runtime/ + 7:43 PM + There are multiple versions + Eric Larour 7:44 PM + ah, I see the grad_length dir + 7:44 PM + is all that stuff compiled into adic2? + Sri Hari Krishna Narayanan 7:44 PM + The one used to estimate the grad_lengh is : $adicinstall/grad_length + 7:44 PM + yes + Eric Larour 7:44 PM + ok, makes sense + Sri Hari Krishna Narayanan 7:45 PM + For the next step though + 7:45 PM + the 'dense' case + 7:45 PM + the runtime library cannot be precompiled + 7:45 PM + the .h file has been created in the previous step + 7:46 PM + So we copy the runtime/dense to the local directory + Eric Larour 7:46 PM + because we can't guess the size of the gradient right? + Sri Hari Krishna Narayanan 7:46 PM + and copy the .h into it + 7:46 PM + correct + Eric Larour 7:46 PM + nice + Sri Hari Krishna Narayanan 7:46 PM + Then we compile it and create a .la file + 7:46 PM + which is then linked to create mini1_dense_forward.exe + 7:47 PM + When we run this, it also happens to run the analyticla derivates (the driver is built this way) + 7:47 PM + Also diveded differences + 7:47 PM + So you get the output: + 7:47 PM + Analytic result is: [1.968912] + Analytic result is: [1.968912] + DD result is: [1.968997] error {-8.45e-05} + DD result is: [1.968997] error {-8.45e-05} + AD result is: [1.968912] error {0.000000} + AD result is: [1.968912] error {0.000000} + 7:48 PM + The next step is to detect sparsity in the Jacobian and possibly compress it using Colpack (create a seed matrix). + 7:49 PM + The gradient computation takes place on the compressed matrix. + 7:49 PM + The output : ADIC_GRADVEC_LENGTH 1 + 7:49 PM + means that the seed matrix has one column. + 7:50 PM + After the calculation of the elements of the compressed matrix, it is then extracted to form the 'full Jacobian' (sorry if these tems are inexact). + 7:51 PM + The extracted output is then printed out: + 7:51 PM + AD result is: [1.968912] + AD result is: [1.968912] + 7:51 PM + And we are done! + Eric Larour 7:51 PM + This is a lot for me to take in at once I'm going to have to look through the makefile, + 7:51 PM + and your explanations, and figure it out + Sri Hari Krishna Narayanan 7:51 PM + Sure. + Eric Larour 7:52 PM + I'll get back to you as soon as I have injested all of this + Sri Hari Krishna Narayanan 7:52 PM + No problem. + Eric Larour 7:52 PM + I'll probably have a million questions + Sri Hari Krishna Narayanan 7:52 PM + This is an exhaustive test + 7:52 PM + FOr m ost purposes, we wil not need all of this + Eric Larour 7:52 PM + this is really nice, I'm pretty exited ! + Sri Hari Krishna Narayanan 7:52 PM + Jean belives for example the the grad_length version is pointless. I find it interesting though. + 7:53 PM + Okay. There are more interesting examples we can try Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-linux.sh (revision 27955) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + + +# Cleanup +rm -rf install src +mkdir install + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz" "adjoinablempi.tar.gz" + +# Unpack source +tar -zxvf adjoinablempi.tar.gz + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/adjoinablempi/install" \ + --libdir="${ISSM_DIR}/externalpackages/adjoinablempi/install/lib" \ + --with-mpi-root="${ISSM_DIR}/externalpackages/petsc/install" \ + --enable-requestOnTrace + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-mac.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-mac.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-mac.sh (revision 27955) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + + +## Environment +# +#export CPATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc:/usr/include # If path to malloc is not included in shell configuration files, export it here after verifying that the path is correct. +export CFLAGS=-Wno-error=implicit-function-declaration + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz" "adjoinablempi.tar.gz" + +# Unpack source +tar -zxvf adjoinablempi.tar.gz + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/adjoinablempi/install" \ + --libdir="${ISSM_DIR}/externalpackages/adjoinablempi/install/lib" \ + --disable-dependency-tracking \ + --with-mpi-root="${ISSM_DIR}/externalpackages/petsc/install" \ + --enable-requestOnTrace + +# Clean +make clean + +# Compile +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi + +# Install +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-pleaides-gcc.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 27955) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install + +# Keeping this for potential future use +#Mercurial cloning: +#hg clone -r 268 http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz' + +#Untar ADOL-C +tar -zxf adjoinablempi.tar.gz + +#Configure adjoinablempi +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ + --libdir="$ISSM_DIR/externalpackages/adjoinablempi/install/lib" \ + --with-mpi-root="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-requestOnTrace CFLAGS="-g -O0" + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-pleaides.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-pleaides.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adjoinablempi/install-pleaides.sh (revision 27955) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install + +# Keeping this for potential future use +#Mercurial cloning: +#hg clone -r 268 http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz' + +#Untar ADOL-C +tar -zxf adjoinablempi.tar.gz + +#Configure adjoinablempi +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ + --libdir="$ISSM_DIR/externalpackages/adjoinablempi/install/lib" \ + --with-mpi-root="/nasa/sgi/mpt/2.06rp16/" \ + --enable-requestOnTrace + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adjointmpi/install-pleiades.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adjointmpi/install-pleiades.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adjointmpi/install-pleiades.sh (revision 27955) @@ -0,0 +1,25 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +#Almost the same as adjoinable mpi but some adaptations to CoDiPack +svn co https://github.com/michel2323/AdjointMPI.git/branches/doubleFixMaster src +mkdir install + +cd src +autoreconf -fi + ./configure \ + --prefix="$ISSM_DIR/externalpackages/adjointmpi/install" \ + --with-mpi-root="/nasa/sgi/mpt/2.15r20/" \ + CXXFLAGS="-O2 -fPIC" CFLAGS="-O2 -fPIC" + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adjointmpi/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adjointmpi/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adjointmpi/install.sh (revision 27955) @@ -0,0 +1,25 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +#Almost the same as adjoinable mpi but some adaptations to CoDiPack +svn co https://github.com/michel2323/AdjointMPI.git/branches/doubleFixMaster src +mkdir install + +cd src +autoreconf -fi + ./configure \ + --prefix="$ISSM_DIR/externalpackages/adjointmpi/install" \ + --with-mpi-root="$ISSM_DIR/externalpackages/mpich/install" \ + CXXFLAGS="-O2 -fPIC" CFLAGS="-O2 -fPIC" + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-mac-with_ampi.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-mac-with_ampi.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-mac-with_ampi.sh (revision 27955) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + + +## Environment +# +export CFLAGS="-O2 -L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi" +export CXXFLAGS="-O2 -L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz" "ADOL-C.tar.gz" + +# Unpack source +tar -zxvf ADOL-C.tar.gz + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/adolc/install" \ + --libdir="${ISSM_DIR}/externalpackages/adolc/install/lib" \ + --with-mpi-root="${ISSM_DIR}/externalpackages/petsc/install" \ + --enable-ampi \ + --with-ampi="${ISSM_DIR}/externalpackages/adjoinablempi/install" \ + --with-soname=adolc \ + --disable-tapedoc-values + +# Compile and install +if [ $# -eq 0 ]; then + make V=1 + make V=1 install +else + make V=1 -j $1 + make V=1 install -j $1 +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-with_ampi.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-with_ampi.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-with_ampi.sh (revision 27955) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + + +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +## Environment +# +export CFLAGS="-O2 -L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi" +export CXXFLAGS="-O2 -std=c++11 -L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz" "ADOL-C.tar.gz" + +# Unpack source +tar -zxvf ADOL-C.tar.gz + +# Configure +cd src +./configure \ + --prefix=${ISSM_DIR}/externalpackages/adolc/install \ + --libdir=${ISSM_DIR}/externalpackages/adolc/install/lib \ + --with-mpi-root=${ISSM_DIR}/externalpackages/petsc/install \ + --enable-ampi \ + --with-ampi=${ISSM_DIR}/externalpackages/adjoinablempi/install \ + --with-soname=adolc \ + --disable-tapedoc-values + +# Clean +make clean + +# Compile +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi + +# Install +make V=1 install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-withampi-pleiades-gcc.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 27955) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz' 'ADOL-C.tar.gz' + +#Untar ADOL-C +tar -zxf ADOL-C.tar.gz + +#Compile ADOL-C +cd src +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ + --with-mpi-root=$ISSM_DIR/externalpackages/mpich/install \ + --enable-ampi \ + --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ + --with-soname=adolc \ + --disable-tapedoc-values + +make clean +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-withampi-pleiades.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-withampi-pleiades.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install-withampi-pleiades.sh (revision 27955) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz' 'ADOL-C.tar.gz' + +#Untar ADOL-C +tar -zxf ADOL-C.tar.gz + +#Compile ADOL-C +cd src +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ + --with-mpi-root="/nasa/sgi/mpt/2.06rp16/" \ + --enable-ampi \ + --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ + --with-soname=adolc \ + --disable-tapedoc-values + +make clean +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/install.sh (revision 27955) @@ -0,0 +1,26 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C.tar.gz' 'ADOL-C.tar.gz' + +#Untar ADOL-C +tar -zxf ADOL-C.tar.gz + +#Compile ADOL-C +cd src +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib + +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/old/install-2.2.0.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/old/install-2.2.0.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/old/install-2.2.0.sh (revision 27955) @@ -0,0 +1,60 @@ +#!/bin/bash +set -eu + +#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. + +#Some cleanup +rm -rf install ADOL-C-2.2.0 src trunk + +#Create install directories +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' + +#Untar +tar -zxvf ADOL-C-2.2.0.tar.gz + +#Move ADOL-C into install directory +mv ADOL-C-2.2.0/* src +rm -rf ADOL-C-2.2.0 + +#Compile ADOL-C +cd src + +#export CC=gcc +#export CXX=g++ +#export CFLAGS="-arch x86_64" +#export CXXFLAGS="-arch x86_64" + +./configure \ + --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --enable-sparse \ + --enable-docexa \ + --enable-addexa \ + --disable-shave + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + + +#Ok, bug with libtool: replace all LIBTOOL= by LIBTOOL=libtool +#in all Makefiles +for i in `find ./ -name Makefile ` +do + echo $i + cat $i | sed 's/LIBTOOL =/LIBTOOL = libtool/g' > $i.bak + mv $i.bak $i +done + +#remake: +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/old/update.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/old/update.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/old/update.sh (revision 27955) @@ -0,0 +1,14 @@ +#!/bin/bash + +cd adolc_issm +git pull + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/update-existing.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/update-existing.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/adolc/update-existing.sh (revision 27955) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#This script is very specific to the larour larsen nightly using adolc. +#It relies on just an update of adolc, and symlink to an existing adolc +#repo. + +#Some cleanup +rm -rf install src + +#symlink: +ln -s /proj/ice/larour2/issm-uci/trunk-jpl/externalpackages/adolc/adolc_issm ./src + +#update and compile +cd src +git pull origin +git checkout ampi +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-ndk/android_aux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-ndk/android_aux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-ndk/android_aux.sh (revision 27955) @@ -0,0 +1,43 @@ +#!/bin/bash +# +# android_aux.sh serves as an auxiliary script for all installation +# scripts with the Android suffix. +# +# TODO: include M4 macros for generic options. +# + +sdk_rev=22.6.2 +ndk_rev=9 +api_levels="android-14,android-15,android-16" +host_triplet="arm-linux-androideabi" +default_droid="android-4.1" + +step=0; +j=1; + +echo "" +echo "This install script utilizes 'android_aux.sh' to allow for options." +echo "For usage information enter: '--help'" +echo Number of arguments is: $# + +for arg in $* +do + if [[ "$arg" =~ --step=([0-9])* ]]; then + step=${BASH_REMATCH[1]}; + echo "Setting step to: " $step + elif [[ "$arg" == "--help" ]]; then + echo "" + echo "USAGE: $ install.sh [--step=#] [-j#]" + echo "" + echo "Where '#' is some integer." + echo "To check the number of steps check the install script." + echo "" + exit 1; + elif [[ "$arg" =~ -j=([1-9]+[0-9]*) ]]; then + j=${BASH_REMATCH[1]}; + echo "Number of jobs set to: " $j + else + echo "Option not recognized" + exit 1; + fi +done Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-ndk/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-ndk/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-ndk/install.sh (revision 27955) @@ -0,0 +1,31 @@ +#!/bin/bash + +# This installs the Android NDK (Native Development Kit) +# which is needed for the compilation of C/C++ code into the +# native architecture of the Android device. + +# The android-ndk-r8-darwin-x86.tar.bz2 ndk.tar.bz2 file was downloaded +# from the android developer website: +source $ANDROID_DIR/android_aux.sh + +if [[ $step == "1" || $step == "0" ]]; then + # Cleanup the install + rm -rf install + rm -rf $ANDROID_DIR/arm-linux-android-${default_droid} + + # Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/android-ndk-r'${ndk_rev}'-darwin-x86.tar.bz2' 'ndk.tar.bz2' + + # Untar + tar -zxvf ndk.tar.bz2 + rm -rf ndk.tar ndk.tar.bz2 + + # Move to install + mv android-ndk-r${ndk_rev} install +fi + +# Create Standalone Development Directory +# Note: API-14 corresponds to Android 4.0. +if [[ $step == "2" || $step == "0" ]]; then + $ANDROID_DIR/android-ndk/install/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/android-ndk/install/arm-linux-android-install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-ndk/installNDK-linux-x86.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-ndk/installNDK-linux-x86.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-ndk/installNDK-linux-x86.sh (revision 27955) @@ -0,0 +1,39 @@ +#!/bin/bash + +# This installs the Android NDK (Native Development Kit) +# which is needed for the compilation of C/C++ code into the +# native architecture of the Android device. + +# The android-ndk-r8-darwin-x86.tar.bz2 ndk.tar.bz2 file was downloaded +# from the android developer website: +source $ANDROID_DIR/android_aux.sh + +if [[ $step == "1" || $step == "0" ]]; then + # Cleanup the install + rm -rf install + rm -rf $ANDROID_DIR/arm-linux-android-${default_droid} + + # Download from ISSM server +# $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/android-ndk-r'${ndk_rev}'-darwin-x86.tar.bz2' 'ndk.tar.bz2' + # Download from google +# if ["$(uname -m)" = "x86_64"]; then +# wget 'https://dl.google.com/android/ndk/android-ndk-r'${ndk_rev}'d-linux-x86_64.tar.bz2' 'ndk.tar.bz2' +# fi + +# if ["$(uname -m)" = "x86"]; then + wget 'https://dl.google.com/android/ndk/android-ndk-r'${ndk_rev}'d-linux-x86.tar.bz2' + # fi + # Install Android NDK + mv 'android-ndk-r'${ndk_rev}'d-linux-x86.tar.bz2' ndk.tar.bz2 + tar -xvf ndk.tar.bz2 + rm -rf ndk.tar ndk.tar.bz2 + + # Move to install + mv android-ndk-r${ndk_rev}d install +fi + +# Create Standalone Development Directory +# Note: API-14 corresponds to Android 4.0. +if [[ $step == "2" || $step == "0" ]]; then + $ANDROID_DIR/android-ndk/install/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/android-ndk/install/arm-linux-android-install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-sdk/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-sdk/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-sdk/install.sh (revision 27955) @@ -0,0 +1,82 @@ +#!/bin/bash + +# This installs the Android SDK (Software Development Kit) +# which is needed for the compilation of the Java project. + +source $ANDROID_DIR/android_aux.sh + +# Different steps here. +# 0: do all +# 1: install sdk, ant and sdk tools +# 2: install an emulator. +# 3: test the emulator +# 4: cleanup + +present_dir=`pwd`; +sd_card="issm-sdcard" + +if [[ $step == "1" || $step == "0" ]]; then + + # Cleanup the install + rm -rf install + + # Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/android-sdk_r'$sdk_rev'-macosx.zip' 'android-sdk_r'${sdk_rev}'-macosx.zip' + + # Install Android SDK and NDK. + unzip -o android-sdk_r${sdk_rev}-macosx.zip + + # Move to install + mv -f android-sdk-macosx install + + # Post_install configuration: + # We need specific settings for specific platforms, for the SDK to + # function properly + + # For now, we need to install: + # android sdk platform tools + # and a specific android api: API 16, API 15 and API 14 + # Note: API 16, API 15 and 14 correspond to Android 4.1, 4.0.3 and 4.0 respectively. + + cd install/tools/ && source ./android update sdk -t platform-tool,${api_levels},system-image --no-ui + +fi + +if [[ $step == "2" || $step == "0" ]]; then + + # Once this is done, we need to install an emulator. Location will default to ~/.android/avd, + # which we will move to $ISSM_DIR/externalpackages/android-emulators. + # For now, it's called: Android-4.0.3 + + # Here we delete the Android-4.0.3 device if it already exists. + cd $present_dir/install/tools + + if [ -e $ANDROID_DIR/android-emulators/$default_droid ] + then + echo "Deleting previously created device: $default_droid" + ./android delete avd -n $default_droid + fi + + # Android will prompt the user to specify hardware emulation options. For now, default + # default settings will suffice. Press 'enter' to take default settings or enter 'no'. + + ./android create avd -f -n $default_droid -t 1 -p $ANDROID_DIR/android-emulators/$default_droid --abi armeabi-v7a + echo "Creating an SD Card" + ./mksdcard -l $sd_card 2G $ANDROID_DIR/android-emulators/$sd_card.img +fi + +if [[ $step == "3" || $step == "0" ]]; then + # Here we will start up our default emulator to test that it is working properly. + # Once the device has booted we will use the Android Debug Bridge tool to gain + # a terminal in our device. + + cd $present_dir/install/tools + ./emulator -avd $default_droid -sdcard $ANDROID_DIR/android-emulators/$sd_card.img & + + cd ../platform-tools + ./adb wait-for-device shell +fi + +if [[ $step == "4" || $step == "0" ]]; then + rm -rf install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-sdk/installSDK-linux-x86.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-sdk/installSDK-linux-x86.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android-sdk/installSDK-linux-x86.sh (revision 27955) @@ -0,0 +1,85 @@ +#!/bin/bash + +# This installs the Android SDK (Software Development Kit) +# which is needed for the compilation of the Java project. + +source $ANDROID_DIR/android_aux.sh + +# Different steps here. +# 0: do all +# 1: install sdk, ant and sdk tools +# 2: install an emulator. +# 3: test the emulator +# 4: cleanup + +present_dir=`pwd`; +sd_card="issm-sdcard" + +if [[ $step == "1" || $step == "0" ]]; then + + # Cleanup the install + rm -rf install + + # Download from ISSM server +# $ISSM_DIR/scripts/DownloadExternalPackage.sh 'http://developer.android.com/sdk/index.html#download' 'android-sdk-linux.zip' + + #Download from Google server + wget https://dl.google.com/android/android-sdk_r$sdk_rev-linux.tgz + + # Install Android SDK. + tar -zxvf android-sdk_r$sdk_rev-linux.tgz + rm -rf android-sdk_r$sdk_rev-linux.tgz + # Move to install + mv -f android-sdk-linux install + + # Post_install configuration: + # We need specific settings for specific platforms, for the SDK to + # function properly + + # For now, we need to install: + # android sdk platform tools + # and a specific android api: API 16, API 15 and API 14 + # Note: API 16, API 15 and 14 correspond to Android 4.1, 4.0.3 and 4.0 respectively. + + cd install/tools/ && source ./android update sdk -t platform-tool,${api_levels},system-image --no-ui + +fi + +if [[ $step == "2" || $step == "0" ]]; then + + # Once this is done, we need to install an emulator. Location will default to ~/.android/avd, + # which we will move to $ISSM_DIR/externalpackages/android-emulators. + # For now, it's called: Android-4.0.3 + + # Here we delete the Android-4.0.3 device if it already exists. + cd $present_dir/install/tools + + if [ -e $ANDROID_DIR/android-emulators/$default_droid ] + then + echo "Deleting previously created device: $default_droid" + ./android delete avd -n $default_droid + fi + + # Android will prompt the user to specify hardware emulation options. For now, default + # default settings will suffice. Press 'enter' to take default settings or enter 'no'. + + ./android create avd -f -n $default_droid -t 1 -p $ANDROID_DIR/android-emulators/$default_droid --abi armeabi-v7a + echo "Creating an SD Card" + ./mksdcard -l $sd_card 2G $ANDROID_DIR/android-emulators/$sd_card.img +fi + +if [[ $step == "3" || $step == "0" ]]; then + # Here we will start up our default emulator to test that it is working properly. + # Once the device has booted we will use the Android Debug Bridge tool to gain + # a terminal in our device. + + cd $present_dir/install/tools + ./emulator -avd $default_droid -sdcard $ANDROID_DIR/android-emulators/$sd_card.img & + + cd ../platform-tools + ./adb wait-for-device shell +fi + +#if [[ $step == "4" || $step == "0" ]]; then +# rm -rf install +#fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android_aux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android_aux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/android/android_aux.sh (revision 27955) @@ -0,0 +1,43 @@ +#!/bin/bash +# +# android_aux.sh serves as an auxiliary script for all installation +# scripts with the Android suffix. +# +# TODO: include M4 macros for generic options. +# + +sdk_rev=20 +ndk_rev=8 +api_levels="android-14,android-15,android-16" +host_triplet="arm-linux-androideabi" +default_droid="android-4.1" + +step=0; +j=1; + +echo "" +echo "This install script utilizes 'android_aux.sh' to allow for options." +echo "For usage information enter: '--help'" +echo Number of arguments is: $# + +for arg in $* +do + if [[ "$arg" =~ --step=([0-9])* ]]; then + step=${BASH_REMATCH[1]}; + echo "Setting step to: " $step + elif [[ "$arg" == "--help" ]]; then + echo "" + echo "USAGE: $ install.sh [--step=#] [-j#]" + echo "" + echo "Where '#' is some integer." + echo "To check the number of steps check the install script." + echo "" + exit 1; + elif [[ "$arg" =~ -j=([1-9]+[0-9]*) ]]; then + j=${BASH_REMATCH[1]}; + echo "Number of jobs set to: " $j + else + echo "Option not recognized" + exit 1; + fi +done Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/angel/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/angel/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/angel/install.sh (revision 27955) @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf angel + +#download +svn co -r 82 https://angellib.svn.sourceforge.net/svnroot/angellib/trunk angel + +#Compile +cd angel +make Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/appscan/bin/genouncemakePFile.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/appscan/bin/genouncemakePFile.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/appscan/bin/genouncemakePFile.sh (revision 27955) @@ -0,0 +1,593 @@ +#!/bin/bash + +#---------------------------------------------------------------------- +#VARIABLES containing information to generate OunceMake Properties file +#---------------------------------------------------------------------- +XMLHEADER="" +OUNCEHEADER="" +MAKEOPT="-f Makefile" + +COMPILER_TAG="Compiler" +COMPILER_MACRO="macro" + +C_COMPILER_MVALUE="\"CC\"" +CPP_COMPILER_MVALUE="\"CXX\"" + +MAKE_TAG="Make" +MAKE_MACRO="macro" +MAKE_MVALUE="\"MAKE\"" + + +LINKER_TAG="Linker" +LINKER_MACRO="macro" +LINKER_MVALUE="\"LD\"" + + +ARCHIVE_TAG="Executable" +ARCHIVE_MACRO="macro" +ARCHIVE_MVALUE="\"ARCHIVE\"" + +OUNCEOPT="" + +OUNCE_MAIN_TAG="OunceMakeProperties" +OUNCE_COMPILER_GPO_TAG="GlobalProjectOptions" +OUNCE_COMPILER_OPT="compiler_options" +OUNCE_COMPILER_OPT_gpp="\"-g++_linux_i386\"" +OUNCE_COMPILER_OPT_gcc="\"-gcc_linux_i386\"" + +OUNCE_INCLUDE_PATH="include_paths" +OUNCE_MACRO_PATH="macros" + +OUNCE_COMPILER_FO_TAG="FileOptions" +OUNCE_COMPILER_EXT="extensions" + +OUNCE_COMPILER_EXT_CPP="cpp;cxx" +OUNCE_COMPILER_EXT_C="c" + +#Did the search for a particular tool pass/fail +FAIL_FILE="failed.status" + +#--------------------------------- +#COMPILER data extraction function +#--------------------------------- + +function initialize { +#Create Directory for info + echo;echo + echo -e "Initialization....\t\t\t[\c " + echo -e "\E[33mSTARTED\c "; tput sgr0 + echo "]" + search_tool which + FILEPRE=${1} + + case "$1" in + "gcc"|"cc") + TESTFILE="testfoo.c" + ;; + "g++"|"CC") + TESTFILE="testfoo.cpp" + ;; + *) + echo "Error setting prefix" + ;; + esac + + DATAFOLDER="${FILEPRE}results" +#Declare files to generate and store results + RESULTFILE="${DATAFOLDER}/${FILEPRE}libinc.result" + SLIMFILE="${DATAFOLDER}/${FILEPRE}slim.inc" + SLIM2FILE="${DATAFOLDER}/${FILEPRE}slim2.inc" + +#Declare the Tags that enclose the information needed + START_TAG="#include <...> search starts here:" + END_TAG="End of search list." + +#Declare Variable to track Tags + MARK_FOUND=0 + +#For Macros + MACROSDUMPFILE="${DATAFOLDER}/${FILEPRE}macrosd.result" + INTFILE1="${DATAFOLDER}/${FILEPRE}interf1.result" + INTFILE2="${DATAFOLDER}/${FILEPRE}interf2.result" + + +#The file extensions for (both) options +CONFIG_FOLDER="config" +C_EXT="${CONFIG_FOLDER}/cext.data" +CPP_EXT="${CONFIG_FOLDER}/cppext.data" + +if [ -d ${CONFIG_FOLDER} ]; then + echo +else + mkdir ${CONFIG_FOLDER} + echo ${OUNCE_COMPILER_EXT_CPP} > ${C_EXT} + echo ${OUNCE_COMPILER_EXT_C} > ${CPP_EXT} +fi + + echo -e "Initialization....\t\t\t[\c " + echo -e "\E[33mDONE\c "; tput sgr0 + echo "]" +} + +function purgefiles { + echo -e "Purging files....\t\t\t[\c " + echo -e "\E[33mSTARTED\c "; tput sgr0 + echo "]" + if [ -e ${DATAFOLDER} ]; then + rm -R ${DATAFOLDER} + mkdir ${DATAFOLDER} + else + mkdir ${DATAFOLDER} + fi + echo -e "Purging files....\t\t\t[\c " + echo -e "\E[33mDONE\c "; tput sgr0 + echo "]" +} + + +function processGNUInclude { +echo +#Create the dummy file is does not exist +if [ -e ${TESTFILE} ]; then + echo "Will use an existing ${TESTFILE} file" +else + echo -e "int main(){\n return 0;\n}" &> ${TESTFILE} + if [ -e ${TESTFILE} ]; then + echo -e "Generating new test file\t\t[\c " + echo -e "\E[31m${TESTFILE}\c " ; tput sgr0 + echo "]" + else + echo -e "Error generating new test file\t\t[\c " + echo -e "\E[31m${TESTFILE}\c " ; tput sgr0 + echo "]" + #TO DO + #Will the user like to continue or exit? + fi +fi + + + echo + echo -e "Generating information for Compiler\t\t[\c " + echo -e "\E[31m${COMPILER}\c " ; tput sgr0 + echo "]" + +${COMPILER} -v ${TESTFILE} &> ${RESULTFILE} + + +cat ${RESULTFILE} | while read line +do + + if [ "${line}" = "${START_TAG}" ] + then + MARK_FOUND=1 + fi + + + if [ "${line}" = "${END_TAG}" ] + then + MARK_FOUND=0 + fi + + + if [ "${MARK_FOUND}" = 1 ] && [ "${line}" != "${START_TAG}" ] + then + let "inclib += 1" + echo ${line} 1>> ${SLIMFILE} + fi +done + +if [ -e ${SLIMFILE} ]; then + sed -e :a -e N -e 's/\n/; /' -e ta ${SLIMFILE} > ${RESULTFILE} + echo -e "Inc & Lib results are in file...\t\t[\c " + echo -e "\033[1m\E[31m${RESULTFILE}\033[0m\c " ; tput sgr0 + echo "]" +fi + +#String to contatenate the include path +concatpath="include_paths=\"" +#Merge file content +sed -e 's/\n/;/' ${SLIMFILE} > ${SLIM2FILE} + +} + + +function processGNUMacro { +#***************************** +#Generate macros for system +#***************************** + echo + echo -e "Generating Macro data for Compiler\t\t[\c " + echo -e "\E[31m${COMPILER} \c " ; tput sgr0 + echo "]" + + ${COMPILER} -dM -E ${TESTFILE} >> ${MACROSDUMPFILE} + sed 's/#define //' ${MACROSDUMPFILE} > ${INTFILE1} + if [ -e ${INTFILE1} ]; then + sed 's/ /=/' ${INTFILE1} > ${INTFILE2} + else + echo -e "\033[1m Sorry <${INTFILE1}> was not created.. \033[0m" + fi + + if [ -e ${INTFILE2} ]; then + #Remove the Macro's that have no values + sed '/^_.*=$/d' ${INTFILE2} > ${INTFILE1} + #Join the individual line and delimit with a (; ) + sed -e :a -e N -e 's/\n/; /' -e ta ${INTFILE1} > ${MACROSDUMPFILE} + #All done display the results file + echo -e "Macro results are in file...\t\t\t[\c " + echo -e "\033[1m\E[31m${MACROSDUMPFILE}\033[0m\c " ; tput sgr0 + echo "]" + else + echo -e "\033[1m Sorry <${MACROSDUMPFILE}> was not created.. \033[0m" + fi +} + +function processSUNMacro { +#******************************************* +#This function is for the SUN Compilers ONLY +#******************************************* + echo + echo -e "Generating Macro data for Compiler\t\t[\c " + echo -e "\E[31m${COMPILER} \c " ; tput sgr0 + echo "]" + + ${COMPILER} -xdumpmacros ${TESTFILE} &> ${MACROSDUMPFILE} + sed 's/#define //' ${MACROSDUMPFILE} > ${INTFILE1} + if [ -e ${INTFILE1} ]; then + sed 's/ /=/' ${INTFILE1} > ${INTFILE2} + else + echo -e "\033[1m Sorry <${INTFILE1}> was not created.. \033[0m" + fi + + if [ -e ${INTFILE2} ]; then + #Remove the Macro's that have no values + sed '/^_.*=$/d' ${INTFILE2} > ${INTFILE1} + #Join the individual line and delimit with a (; ) + sed -e :a -e N -e 's/\n/; /' -e ta ${INTFILE1} > ${MACROSDUMPFILE} + #All done display the results file + echo -e "Macro results are in file...\t\t\t[\c " + echo -e "\033[1m\E[31m${MACROSDUMPFILE}\033[0m\c " ; tput sgr0 + echo "]" + else + echo -e "\033[1m Sorry <${MACROSDUMPFILE}> was not created.. \033[0m" + fi +} + +#-------------------------- +#DATA Processing variables +#-------------------------- +PROPFILE="ouncemake_properties.xml" +PROBEFILE="probe.results" +ERRORLOG="error.log" + +#--------------------------------------- +#FUNCTION TO CREATE FILE +#-------------------------------------- + +function create_file { +#If a previous copy of file exist, delete it +if [ -e ${PROPFILE} ]; then + rm ${PROPFILE} +fi + +echo;echo +echo "CREATING THE PROPERTIES XML FILE" +#insert file headers +echo ${XMLHEADER} >> ${PROPFILE} +echo ${OUNCEHEADER} >> ${PROPFILE} +echo ${MAKEOPT} >> ${PROPFILE} +case "${1}" in + 'gcc') + search_tool gcc + ;; + 'g++') + search_tool g++ + ;; + 'bothGNU') + search_tool gcc + search_tool g++ + ;; + 'cc') + search_tool cc + ;; + 'CC') + search_tool CC + ;; + 'bothSUN') + search_tool gcc + search_tool g++ + ;; + '*') + ;; +esac +search_tool make +search_tool ld +search_tool ar +echo " ${OUNCEOPT}" >> ${PROPFILE} + +case "${1}" in + 'gcc') + singleGNUC gcc + ;; + 'g++') + singleGNUC g++ + ;; + 'bothGNU') + bothGNUC gcc + bothGNUC g++ + ;; + 'cc') + singleSUNC cc + ;; + 'CC') + singleSUNC CC + ;; + 'bothSUN') + bothSUNC cc + bothSUNC CC + ;; + '*') + ;; +esac + +echo "" >> ${PROPFILE} + +echo +echo -e "Successully created Properties file\t\t[\c " +echo -e "\033[1m\E[31m${PROPFILE}\033[0m\c " ; tput sgr0 +echo "]" +echo +} + +#when the system is unable to locate the tool +#the user is prompted to provide that information +function usersupplypath { + echo "Please provide the path to ${1}." + read TOOLPATH +} + + +function search_tool { +which $1 &> ${PROBEFILE} +#Why this approach? I had to be able to non-interactively +#know if the pattern was successfully found. + +sed -n -e "/.*no[ ]${1}[ ]in[ ].*/w $FAIL_FILE" ${PROBEFILE} + +#If the file is empty, the process PASSED +#else the Fail criteria was found. Process FAILED +if [ -e ${FAIL_FILE} ]; then + exec < ${FAIL_FILE} + read FAILPASS + if [${FAILPASS} = ""]; then + SEARCHTOOL="PASSED" + rm ${FAIL_FILE} + else + SEARCHTOOL="FAILED" + fi +fi + + +if [ ${SEARCHTOOL} == "FAILED" ] ; then + echo "Failed to find ${1} in PATH" >> ${ERRORLOG} + echo -e "check for $1 in ${TLOC}\t\t\t[$SEARCHTOOL]" +elif [ ${SEARCHTOOL} == "PASSED" ]; then + #Redirects stdin to a file so that + exec < ${PROBEFILE} + #I can read line by line + read TLOC + echo -e "check for $1 in ${TLOC}\t\t\t[\c " + echo -e "\E[33m${SEARCHTOOL}\c "; tput sgr0 + echo "]" +else + echo "Unable to process the request" + #exit +fi + +case "$1" in + 'gcc') + #set up the sub strings + TAG_L="<${COMPILER_TAG} ${COMPILER_MACRO}=${C_COMPILER_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'g++') + TAG_L="<${COMPILER_TAG} ${COMPILER_MACRO}=${CPP_COMPILER_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'make') + TAG_L="<${MAKE_TAG} ${MAKE_MACRO}=${MAKE_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'ld') + TAG_L="<${LINKER_TAG} ${LINKER_MACRO}=${LINKER_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'ar') + TAG_L="<${ARCHIVE_TAG} ${ARCHIVE_MACRO}=${ARCHIVE_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + '*') + ;; +esac + +#then concatenate +FULL_STRING="${TAG_L}${MVALUE}${TAG_R}" +#and store in file +echo " $FULL_STRING" >> ${PROPFILE} +} +function singleGNUC { + +echo " <${OUNCE_COMPILER_GPO_TAG}" >> ${PROPFILE} + +case "$1" in + 'gcc') + echo -e "\t ${OUNCE_COMPILER_OPT}=${OUNCE_COMPILER_OPT_gcc}" >> ${PROPFILE} + ;; + 'g++') + echo -e "\t ${OUNCE_COMPILER_OPT}=${OUNCE_COMPILER_OPT_gpp}" >> ${PROPFILE} + ;; + '*') + ;; +esac + +exec < ${RESULTFILE} +read INCLUDE_DATA +echo -e "\t ${OUNCE_INCLUDE_PATH}=\"${INCLUDE_DATA}\"" >> ${PROPFILE} +exec < ${MACROSDUMPFILE} +read MACRO_DATA +#Using single quotes to wrap double quotes in data +echo -e "\t ${OUNCE_MACRO_PATH}='${MACRO_DATA}' />" >> ${PROPFILE} + +} + + +function bothGNUC { + +echo -e "\t<${OUNCE_COMPILER_FO_TAG}" >> ${PROPFILE} + +case "$1" in + 'gcc') + FILEPRE="$1" + exec < ${C_EXT} + read CEXTENSIONS + if [ ${CEXTENSIONS} = "" ]; then + CEXTENSIONS=${OUNCE_COMPILER_EXT_C} + else + OUNCE_COMPILER_EXT_C=${CEXTENSIONS} + fi + echo -e "\t ${OUNCE_COMPILER_EXT}=\"${OUNCE_COMPILER_EXT_C}\"" >> ${PROPFILE} + ;; + 'g++') + FILEPRE="$1" + exec < ${CPP_EXT} + read CPPEXTENSIONS + if [ ${CPPEXTENSIONS} = "" ]; then + CPPEXTENSIONS=${OUNCE_COMPILER_EXT_CPP} + else + OUNCE_COMPILER_EXT_CPP=${CPPEXTENSIONS} + fi + echo -e "\t ${OUNCE_COMPILER_EXT}=\"${OUNCE_COMPILER_EXT_CPP}\"" >> ${PROPFILE} + ;; + '*') + ;; +esac + +#To make sure that the correct folder and file is read +DATAFOLDER="${FILEPRE}results" +#Declare files to generate and store results +RESULTFILE="${DATAFOLDER}/${FILEPRE}libinc.result" + +exec < ${RESULTFILE} +read INCLUDE_DATA +echo -e "\t ${OUNCE_INCLUDE_PATH}=\"${INCLUDE_DATA}\"" >> ${PROPFILE} +exec < ${MACROSDUMPFILE} +read MACRO_DATA +echo -e "\t ${OUNCE_MACRO_PATH}='${MACRO_DATA}'/>" >> ${PROPFILE} + +} + + +clear +echo +echo -e "\t \E[34m\033[1mOUNCEMAKE PROPERTIES FILE GENERATOR (1.0)b\033[0m";tput sgr0 + +#Start of the program +case "$1" in + '-t') + case "$2" in + "gcc") + COMPILER=${2} + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + create_file ${2} + ;; + "g++") + COMPILER=${2} + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + create_file ${2} + ;; + "bothGNU") + COMPILER="gcc" + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + COMPILER="g++" + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + create_file ${2} + ;; + "cc") + COMPILER=${2} + initialize ${2} + purgefiles + processSUNInclude + processSUNMacro + create_file ${2} + ;; + "CC") + COMPILER=${2} + initialize ${2} + purgefiles + # processSUNInclude + processSUNMacro + # create_file ${2} + ;; + "bothSUN") + COMPILER="cc" + initialize cc + purgefiles + processSUNInclude + processSUNMacro + COMPILER="CC" + initialize CC + purgefiles + processSUNInclude + processSUNMacro + create_file both + ;; + '*') + echo "Usage: -t [gcc|g++|bothGNU]" + exit $? + ;; + esac + ;; + '-h') + echo -e "Usage: -t [Options] -v " + echo -e "Options:" + echo -e "\t[gcc]\tC project only"; + echo -e "\t[g++]\tCPP project only" + echo -e "\t[bothGNU]\tMixed C and CPP project" + echo + echo -e "\t-v \tDisplay version information" + exit $? + ;; + '-v') + echo "Version 1.0 beta" + exit $? + ;; + *) + echo -e "Usage: -t [Options] -v " + echo -e "Options:" + echo -e "\t[gcc]\tC project only"; + echo -e "\t[g++]\tCPP project only" + echo -e "\t[both]\tMixed C and CPP project" + echo + echo -e "\t-v \tDisplay version information" + exit $? + ;; +esac +echo "[ P R O C E S S C O M P L E T E !!! ]" +echo Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/appscan/hostname =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/appscan/hostname (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/appscan/hostname (revision 27955) @@ -0,0 +1,1 @@ +jplsec-codescan.jpl.nasa.gov Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/appscan/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/appscan/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/appscan/install.sh (revision 27955) @@ -0,0 +1,10 @@ +#!/bin/bash +set -eu + +#AppScan install directory. Just symlink to your existing AppScan software + +#Erase symlink +rm -rf install + +#Select or create a new simlink +ln -s /opt/IBM/AppScan_Source ./install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/apr-util/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/apr-util/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/apr-util/install.sh (revision 27955) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf apr-util-1.4.1 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/apr-util-1.4.1.tar.gz' 'apr-util-1.4.1.tar.gz' + +#Untar +tar -zxvf apr-util-1.4.1.tar.gz + +#Move apr-util into src directory +mv apr-util-1.4.1/* src +rm -rf apr-util-1.4.1 + +#Configure apr-util +cd src +./configure --prefix="$ISSM_DIR/externalpackages/apr-util/install" --with-apr="$ISSM_DIR/externalpackages/apr/install" + +#Compile and install apr-util +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/apr/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/apr/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/apr/install.sh (revision 27955) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf apr-1.4.6 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/apr-1.4.6.tar.gz' 'apr-1.4.6.tar.gz' + +#Untar +tar -zxvf apr-1.4.6.tar.gz + +#Move apr into src directory +mv apr-1.4.6/* src +rm -rf apr-1.4.6 + +#Configure apr +cd src +./configure --prefix="$ISSM_DIR/externalpackages/apr/install" + +#Compile and install apr +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/aspell/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/aspell/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/aspell/install.sh (revision 27955) @@ -0,0 +1,62 @@ +#!/bin/bash +set -eu + +#0: cleanup +#1: install aspell +#2: install en dictionary +step=2 + + +#Some cleanup +if [[ $step == "0" ]]; then + rm -rf src install dicts + rm -rf aspell-0.50.5 + rm -rf aspell5-en-6.0.0 +fi + +#install aspell +if [[ $step == "1" ]]; then + + mkdir src install dicts + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/aspell-0.50.5.tar.gz' 'aspell-0.50.5.tar.gz' + + #Untar + tar -zxvf aspell-0.50.5.tar.gz + + #Move aspell into src directory + mv aspell-0.50.5/* src + rm -rf aspell-0.50.5 + + #Configure aspell + cd src + ./configure \ + --prefix="$ISSM_DIR/externalpackages/aspell/install" \ + + #Compile and install aspell + if [ -z $1 ]; then + make + else + make -j $1 + fi + make install +fi + +#languages +if [[ $step == "2" ]]; then + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/aspell5-en-6.0.0.tar.gz' 'aspell5-en-6.0.0.tar.gz' + + #Untar + tar -zxvf aspell5-en-6.0.0.tar.gz + + #Move aspell into src directory + mv aspell5-en-6.0.0 dicts + + #install + cd dicts/aspell5-en-6.0.0 + ./configure + make install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/atlas/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/atlas/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/atlas/install.sh (revision 27955) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install ATLAS build +mkdir src install build + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/atlas3.10.0.tar.bz2' 'atlas3.10.0.tar.bz2' + +#Untar +tar -zxvf atlas3.10.0.tar.bz2 + +#Move atlas into src directory +mv ATLAS/* src +rm -rf ATLAS + +#Configure atlas +cd build + +export CFLAGS=" -arch x86_64" + +../src/configure \ + --prefix="$ISSM_DIR/externalpackages/atlas/install" + +#Compile atlas +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/install-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/install-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/install-linux.sh (revision 27955) @@ -0,0 +1,95 @@ +#!/bin/bash +set -eu + + +## Constants +# +AUTOCONF_VER="2.69" +AUTOMAKE_VER="1.16.1" +LIBTOOL_VER="2.4.6" +M4_VER="1.4.19" + +PREFIX="${ISSM_DIR}/externalpackages/autotools/install" # Set to location where external package should be installed + +## Environment +# +export PATH="${PREFIX}/bin:${PATH}" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} + +# Install m4 +echo " === INSTALLING M4 ===" +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m4-${M4_VER}.tar.gz" "m4-${M4_VER}.tar.gz" +tar -zxvf m4-${M4_VER}.tar.gz +mv m4-${M4_VER} src +cd src + +## Fixes required by glibc-2.28 +# +# Source: http://www.linuxfromscratch.org/lfs/view/development/chapter06/m4.html +# +sed -i 's/IO_ftrylockfile/IO_EOF_SEEN/' lib/*.c +echo "#define _IO_IN_BACKUP 0x100" >> lib/stdio-impl.h + +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# Install Autoconf +echo " === INSTALLING AUTOCONF ===" +rm -rf src +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/autoconf-${AUTOCONF_VER}.tar.gz" "autoconf-${AUTOCONF_VER}.tar.gz" +tar -zxvf autoconf-${AUTOCONF_VER}.tar.gz +mv autoconf-${AUTOCONF_VER} src +cd src +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# Install Automake +echo " === INSTALLING AUTOMAKE ===" +rm -rf src +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/automake-${AUTOMAKE_VER}.tar.gz" "automake-${AUTOMAKE_VER}.tar.gz" +tar -zxvf automake-${AUTOMAKE_VER}.tar.gz +mv automake-${AUTOMAKE_VER} src +cd src +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# Install libtool +echo " === INSTALLING LIBTOOL ===" +rm -rf src +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/libtool-${LIBTOOL_VER}.tar.gz" "libtool-${LIBTOOL_VER}.tar.gz" +tar -zxvf libtool-${LIBTOOL_VER}.tar.gz +mv libtool-${LIBTOOL_VER} src +cd src +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/install-mac.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/install-mac.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/install-mac.sh (revision 27955) @@ -0,0 +1,88 @@ +#!/bin/bash +set -eu + + +## Constants +# +AUTOCONF_VER="2.69" +AUTOMAKE_VER="1.16.1" +LIBTOOL_VER="2.4.6" +M4_VER="1.4.19" + +PREFIX="${ISSM_DIR}/externalpackages/autotools/install" # Set to location where external package should be installed + +## Environment +# +export PATH="${PREFIX}/bin:${PATH}" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} + +# Install m4 +echo " === INSTALLING M4 ===" +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m4-${M4_VER}.tar.gz" "m4-${M4_VER}.tar.gz" +tar -zxvf m4-${M4_VER}.tar.gz +mv m4-${M4_VER} src +cd src + +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# Install Autoconf +echo " === INSTALLING AUTOCONF ==" +rm -rf src +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/autoconf-${AUTOCONF_VER}.tar.gz" "autoconf-${AUTOCONF_VER}.tar.gz" +tar -zxvf autoconf-${AUTOCONF_VER}.tar.gz +mv autoconf-${AUTOCONF_VER} src +cd src +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# Install Automake +echo " === INSTALLING AUTOMAKE ===" +rm -rf src +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/automake-${AUTOMAKE_VER}.tar.gz" "automake-${AUTOMAKE_VER}.tar.gz" +tar -zxvf automake-${AUTOMAKE_VER}.tar.gz +mv automake-${AUTOMAKE_VER} src +cd src +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# Install libtool +echo " === INSTALLING LIBTOOL ===" +rm -rf src +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/libtool-${LIBTOOL_VER}.tar.gz" "libtool-${LIBTOOL_VER}.tar.gz" +tar -zxvf libtool-${LIBTOOL_VER}.tar.gz +mv libtool-${LIBTOOL_VER} src +cd src +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/install-win.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/install-win.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/install-win.sh (revision 27955) @@ -0,0 +1,103 @@ +#!/bin/bash +set -eu + + +## Constants +# +AUTOCONF_VER="2.69" +AUTOMAKE_MIN_VER="1.16" +AUTOMAKE_VER="${AUTOMAKE_MIN_VER}.1" +LIBTOOL_VER="2.4.6" +M4_VER="1.4.19" + +PREFIX="${ISSM_DIR}/externalpackages/autotools/install" # Set to location where external package should be installed + +## Environment +# +export PATH="${PREFIX}/bin:${PATH}" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} + +# Install m4 +echo " === INSTALLING M4 ===" +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m4-${M4_VER}.tar.gz" "m4-${M4_VER}.tar.gz" +tar -zxvf m4-${M4_VER}.tar.gz +mv m4-${M4_VER} src +cd src + +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# Install Autoconf +echo " === INSTALLING AUTOCONF ==" +rm -rf src +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/autoconf-${AUTOCONF_VER}.tar.gz" "autoconf-${AUTOCONF_VER}.tar.gz" +tar -zxvf autoconf-${AUTOCONF_VER}.tar.gz +mv autoconf-${AUTOCONF_VER} src +cd src +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# Install Automake +echo " === INSTALLING AUTOMAKE ===" +rm -rf src +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/automake-${AUTOMAKE_VER}.tar.gz" "automake-${AUTOMAKE_VER}.tar.gz" +tar -zxvf automake-${AUTOMAKE_VER}.tar.gz +mv automake-${AUTOMAKE_VER} src +cd src +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# Install libtool +echo " === INSTALLING LIBTOOL ===" +rm -rf src +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/libtool-${LIBTOOL_VER}.tar.gz" "libtool-${LIBTOOL_VER}.tar.gz" +tar -zxvf libtool-${LIBTOOL_VER}.tar.gz +mv libtool-${LIBTOOL_VER} src +cd src +./configure --prefix="${PREFIX}" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +# This patch takes care of removing options passed to the linker that causes +# the build to fail, as well as changing some flags to match up to Microsoft +# compilers. +patch ./install/share/aclocal/libtool.m4 < ./patches/libtool.m4.patch + +# Small change to Automake in order to get the right flags for Microsoft's +# compiler. +patch ./install/bin/automake < ./patches/automake.patch + +# This patch is for ar-lib, and removes carriage return characters that cause +# commands to overwrite themselves and be misinterpreted during linking on +# Cygwin Windows. +patch ./install/share/automake-${AUTOMAKE_MIN_VER}/ar-lib < ./patches/ar-lib.patch Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/patches/ar-lib.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/patches/ar-lib.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/patches/ar-lib.patch (revision 27955) @@ -0,0 +1,11 @@ +--- ar-lib 2017-08-30 21:58:06.863512300 -0700 ++++ /home/Daniel/issm/trunk/aux-config/ar-lib 2017-08-30 21:58:01.291710300 -0700 +@@ -226,7 +226,7 @@ + else + $AR -NOLOGO -LIST "$archive" | sed -e 's/\\/\\\\/g' | while read member + do +- $AR -NOLOGO -EXTRACT:"$member" "$archive" || exit $? ++ $AR -NOLOGO -EXTRACT:"$(echo $member | tr -d '\r')" "$archive" || exit $? + done + fi + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/patches/automake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/patches/automake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/patches/automake.patch (revision 27955) @@ -0,0 +1,13 @@ +--- ./externalpackages/autotools/install/bin/automake 2015-09-24 19:26:11.796659200 -0700 ++++ /home/daeden/tmp/automake 2015-09-25 11:32:53.557609300 -0700 +@@ -702,8 +702,8 @@ + 'compile' => "\$(CXX) @cpplike_flags \$(AM_CXXFLAGS) \$(CXXFLAGS)", + 'ccer' => 'CXX', + 'compiler' => 'CXXCOMPILE', +- 'compile_flag' => '-c', +- 'output_flag' => '-o', ++ 'compile_flag' => '/c', ++ 'output_flag' => '/Fo:', + 'libtool_tag' => 'CXX', + 'lder' => 'CXXLD', + 'ld' => '$(CXX)', Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/patches/libtool.m4.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/patches/libtool.m4.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/autotools/patches/libtool.m4.patch (revision 27955) @@ -0,0 +1,74 @@ +--- ./install/share/aclocal/libtool.m4 2015-09-25 15:51:40.870862200 -0700 ++++ /home/daeden/tmp/libtool.m4 2015-09-25 15:42:15.385935100 -0700 +@@ -2382,7 +2382,7 @@ + # Native MSVC + libname_spec='$name' + soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}' +- library_names_spec='${libname}.dll.lib' ++ library_names_spec='${libname}${shrext_cmds}' + + case $build_os in + mingw*) +@@ -3142,7 +3142,7 @@ + case $host_os in + cygwin* | mingw* | pw32* | cegcc*) + if test "$GCC" != yes; then +- reload_cmds=false ++ reload_cmds='lib /OUT:$output$reload_objs' + fi + ;; + darwin*) +@@ -4752,7 +4752,7 @@ + _LT_TAGVAR(exclude_expsyms, $1)=['[_]+GLOBAL_OFFSET_TABLE_|[_]+GLOBAL__[FID]_.*|[_]+head_[A-Za-z0-9_]+_dll|[A-Za-z0-9_]+_dll_iname'] + + if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then +- _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' ++ _LT_TAGVAR(archive_cmds, $1)='$CC /LD $libobjs $deplibs $compiler_flags /OUT:$output_objdir/$soname ' + # If the export-symbols file already is a .def file (1st line + # is EXPORTS), use it as is; otherwise, prepend... + _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then +@@ -4761,7 +4761,7 @@ + echo EXPORTS > $output_objdir/$soname.def; + cat $export_symbols >> $output_objdir/$soname.def; + fi~ +- $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' ++ $CC /LD $output_objdir/$soname.def $libobjs $deplibs $compiler_flags /OUT:$output_objdir/$soname ' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi +@@ -5136,7 +5136,7 @@ + else + sed -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; + fi~ +- $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ ++ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs~ + linknames=' + # The linker will not automatically build a static lib if we build a DLL. + # _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' +@@ -6135,7 +6135,7 @@ + else + $SED -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; + fi~ +- $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ ++ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs~ + linknames=' + # The linker will not automatically build a static lib if we build a DLL. + # _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' +@@ -6168,7 +6168,7 @@ + _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes + + if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then +- _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' ++ _LT_TAGVAR(archive_cmds, $1)='$CC /LD -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags /OUT:$output_objdir/$soname ' + # If the export-symbols file already is a .def file (1st line + # is EXPORTS), use it as is; otherwise, prepend... + _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then +@@ -6177,7 +6177,7 @@ + echo EXPORTS > $output_objdir/$soname.def; + cat $export_symbols >> $output_objdir/$soname.def; + fi~ +- $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' ++ $CC /LD -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags /OUT:$output_objdir/$soname ' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/bbftp/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/bbftp/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/bbftp/install.sh (revision 27955) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install bbftp-client-3.2.0 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/bbftp-client-3.2.0.tar.gz' 'bbftp-client-3.2.0.tar.gz' + +#Create install directories +mkdir install src + +#Untar +tar -zxvf bbftp-client-3.2.0.tar.gz + +#Move bbftp-client into install directory +mv bbftp-client-3.2.0/* src +rm -rf bbftp-client-3.2.0 + +#Apply patches +cd src + +#Configure and compile +cd bbftpc +./configure --prefix=$ISSM_DIR/externalpackages/bbftp/install +make +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/gcc/Makefile =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/gcc/Makefile (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/gcc/Makefile (revision 27955) @@ -0,0 +1,172 @@ +include make.inc + +####################################################################### +# This is the makefile to create a library for the BLAS. +# The files are grouped as follows: +# +# SBLAS1 -- Single precision real BLAS routines +# CBLAS1 -- Single precision complex BLAS routines +# DBLAS1 -- Double precision real BLAS routines +# ZBLAS1 -- Double precision complex BLAS routines +# +# CB1AUX -- Real BLAS routines called by complex routines +# ZB1AUX -- D.P. real BLAS routines called by d.p. complex +# routines +# +# ALLBLAS -- Auxiliary routines for Level 2 and 3 BLAS +# +# SBLAS2 -- Single precision real BLAS2 routines +# CBLAS2 -- Single precision complex BLAS2 routines +# DBLAS2 -- Double precision real BLAS2 routines +# ZBLAS2 -- Double precision complex BLAS2 routines +# +# SBLAS3 -- Single precision real BLAS3 routines +# CBLAS3 -- Single precision complex BLAS3 routines +# DBLAS3 -- Double precision real BLAS3 routines +# ZBLAS3 -- Double precision complex BLAS3 routines +# +# The library can be set up to include routines for any combination +# of the four precisions. To create or add to the library, enter make +# followed by one or more of the precisions desired. Some examples: +# make single +# make single complex +# make single double complex complex16 +# Note that these commands are not safe for parallel builds. +# +# Alternatively, the commands +# make all +# or +# make +# without any arguments creates a library of all four precisions. +# The name of the library is held in BLASLIB, which is set in the +# make.inc +# +# To remove the object files after the library is created, enter +# make clean +# To force the source files to be recompiled, enter, for example, +# make single FRC=FRC +# +#--------------------------------------------------------------------- +# +# Edward Anderson, University of Tennessee +# March 26, 1990 +# Susan Ostrouchov, September 30, 1994 +# Julie Langou, March 2007 +# +####################################################################### + +all: $(BLASLIB) + +#--------------------------------------------------------- +# Comment out the next 6 definitions if you already have +# the Level 1 BLAS. +#--------------------------------------------------------- +SBLAS1 = isamax.o sasum.o saxpy.o scopy.o sdot.o snrm2.o \ + srot.o srotg.o sscal.o sswap.o sdsdot.o srotmg.o srotm.o +$(SBLAS1): $(FRC) + +CBLAS1 = scabs1.o scasum.o scnrm2.o icamax.o caxpy.o ccopy.o \ + cdotc.o cdotu.o csscal.o crotg.o cscal.o cswap.o csrot.o +$(CBLAS1): $(FRC) + +DBLAS1 = idamax.o dasum.o daxpy.o dcopy.o ddot.o dnrm2.o \ + drot.o drotg.o dscal.o dsdot.o dswap.o drotmg.o drotm.o +$(DBLAS1): $(FRC) + +ZBLAS1 = dcabs1.o dzasum.o dznrm2.o izamax.o zaxpy.o zcopy.o \ + zdotc.o zdotu.o zdscal.o zrotg.o zscal.o zswap.o zdrot.o +$(ZBLAS1): $(FRC) + +CB1AUX = isamax.o sasum.o saxpy.o scopy.o snrm2.o sscal.o +$(CB1AUX): $(FRC) + +ZB1AUX = idamax.o dasum.o daxpy.o dcopy.o dnrm2.o dscal.o +$(ZB1AUX): $(FRC) + +#--------------------------------------------------------------------- +# The following line defines auxiliary routines needed by both the +# Level 2 and Level 3 BLAS. Comment it out only if you already have +# both the Level 2 and 3 BLAS. +#--------------------------------------------------------------------- +ALLBLAS = lsame.o xerbla.o +$(ALLBLAS) : $(FRC) + +#--------------------------------------------------------- +# Comment out the next 4 definitions if you already have +# the Level 2 BLAS. +#--------------------------------------------------------- +SBLAS2 = sgemv.o sgbmv.o ssymv.o ssbmv.o sspmv.o \ + strmv.o stbmv.o stpmv.o strsv.o stbsv.o stpsv.o \ + sger.o ssyr.o sspr.o ssyr2.o sspr2.o +$(SBLAS2): $(FRC) + +CBLAS2 = cgemv.o cgbmv.o chemv.o chbmv.o chpmv.o \ + ctrmv.o ctbmv.o ctpmv.o ctrsv.o ctbsv.o ctpsv.o \ + cgerc.o cgeru.o cher.o chpr.o cher2.o chpr2.o +$(CBLAS2): $(FRC) + +DBLAS2 = dgemv.o dgbmv.o dsymv.o dsbmv.o dspmv.o \ + dtrmv.o dtbmv.o dtpmv.o dtrsv.o dtbsv.o dtpsv.o \ + dger.o dsyr.o dspr.o dsyr2.o dspr2.o +$(DBLAS2): $(FRC) + +ZBLAS2 = zgemv.o zgbmv.o zhemv.o zhbmv.o zhpmv.o \ + ztrmv.o ztbmv.o ztpmv.o ztrsv.o ztbsv.o ztpsv.o \ + zgerc.o zgeru.o zher.o zhpr.o zher2.o zhpr2.o +$(ZBLAS2): $(FRC) + +#--------------------------------------------------------- +# Comment out the next 4 definitions if you already have +# the Level 3 BLAS. +#--------------------------------------------------------- +SBLAS3 = sgemm.o ssymm.o ssyrk.o ssyr2k.o strmm.o strsm.o +$(SBLAS3): $(FRC) + +CBLAS3 = cgemm.o csymm.o csyrk.o csyr2k.o ctrmm.o ctrsm.o \ + chemm.o cherk.o cher2k.o +$(CBLAS3): $(FRC) + +DBLAS3 = dgemm.o dsymm.o dsyrk.o dsyr2k.o dtrmm.o dtrsm.o +$(DBLAS3): $(FRC) + +ZBLAS3 = zgemm.o zsymm.o zsyrk.o zsyr2k.o ztrmm.o ztrsm.o \ + zhemm.o zherk.o zher2k.o +$(ZBLAS3): $(FRC) + +ALLOBJ=$(SBLAS1) $(SBLAS2) $(SBLAS3) $(DBLAS1) $(DBLAS2) $(DBLAS3) \ + $(CBLAS1) $(CBLAS2) $(CBLAS3) $(ZBLAS1) \ + $(ZBLAS2) $(ZBLAS3) $(ALLBLAS) + +$(BLASLIB): $(ALLOBJ) + $(FORTRAN) -shared -o $@ \ + $(ALLOBJ) \ + -Wl,--out-implib=$(IMP_LIB_NAME) + +single: $(SBLAS1) $(ALLBLAS) $(SBLAS2) $(SBLAS3) + $(ARCH) $(ARCHFLAGS) $(BLASLIB) $(SBLAS1) $(ALLBLAS) \ + $(SBLAS2) $(SBLAS3) + $(RANLIB) $(BLASLIB) + +double: $(DBLAS1) $(ALLBLAS) $(DBLAS2) $(DBLAS3) + $(ARCH) $(ARCHFLAGS) $(BLASLIB) $(DBLAS1) $(ALLBLAS) \ + $(DBLAS2) $(DBLAS3) + $(RANLIB) $(BLASLIB) + +complex: $(CBLAS1) $(CB1AUX) $(ALLBLAS) $(CBLAS2) $(CBLAS3) + $(ARCH) $(ARCHFLAGS) $(BLASLIB) $(CBLAS1) $(CB1AUX) \ + $(ALLBLAS) $(CBLAS2) $(CBLAS3) + $(RANLIB) $(BLASLIB) + +complex16: $(ZBLAS1) $(ZB1AUX) $(ALLBLAS) $(ZBLAS2) $(ZBLAS3) + $(ARCH) $(ARCHFLAGS) $(BLASLIB) $(ZBLAS1) $(ZB1AUX) \ + $(ALLBLAS) $(ZBLAS2) $(ZBLAS3) + $(RANLIB) $(BLASLIB) + +FRC: + @FRC=$(FRC) + +clean: + rm -f *.o + +.f.o: + $(FORTRAN) $(OPTS) -c $< -o $@ Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/gcc/make.inc =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/gcc/make.inc (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/gcc/make.inc (revision 27955) @@ -0,0 +1,38 @@ +#################################################################### +# BLAS make include file. # +# March 2007 # +#################################################################### +# +SHELL = /usr/bin/bash +# +# The machine (platform) identifier to append to the library names +# +PLAT = +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -O2 -fPIC +DRVOPTS = $(OPTS) +NOOPT = -O0 -fPIC +LOADER = gfortran +LOADOPTS = +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib + +MODULE = blas +IMP_LIB_NAME = lib$(MODULE).dll.a +LIB_NAME = msys-$(MODULE).dll +# +# The location and name of the Reference BLAS library. +# +BLASLIB = $(LIB_NAME) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/mingw64/Makefile =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/mingw64/Makefile (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/mingw64/Makefile (revision 27955) @@ -0,0 +1,172 @@ +include make.inc + +####################################################################### +# This is the makefile to create a library for the BLAS. +# The files are grouped as follows: +# +# SBLAS1 -- Single precision real BLAS routines +# CBLAS1 -- Single precision complex BLAS routines +# DBLAS1 -- Double precision real BLAS routines +# ZBLAS1 -- Double precision complex BLAS routines +# +# CB1AUX -- Real BLAS routines called by complex routines +# ZB1AUX -- D.P. real BLAS routines called by d.p. complex +# routines +# +# ALLBLAS -- Auxiliary routines for Level 2 and 3 BLAS +# +# SBLAS2 -- Single precision real BLAS2 routines +# CBLAS2 -- Single precision complex BLAS2 routines +# DBLAS2 -- Double precision real BLAS2 routines +# ZBLAS2 -- Double precision complex BLAS2 routines +# +# SBLAS3 -- Single precision real BLAS3 routines +# CBLAS3 -- Single precision complex BLAS3 routines +# DBLAS3 -- Double precision real BLAS3 routines +# ZBLAS3 -- Double precision complex BLAS3 routines +# +# The library can be set up to include routines for any combination +# of the four precisions. To create or add to the library, enter make +# followed by one or more of the precisions desired. Some examples: +# make single +# make single complex +# make single double complex complex16 +# Note that these commands are not safe for parallel builds. +# +# Alternatively, the commands +# make all +# or +# make +# without any arguments creates a library of all four precisions. +# The name of the library is held in BLASLIB, which is set in the +# make.inc +# +# To remove the object files after the library is created, enter +# make clean +# To force the source files to be recompiled, enter, for example, +# make single FRC=FRC +# +#--------------------------------------------------------------------- +# +# Edward Anderson, University of Tennessee +# March 26, 1990 +# Susan Ostrouchov, September 30, 1994 +# Julie Langou, March 2007 +# +####################################################################### + +all: $(BLASLIB) + +#--------------------------------------------------------- +# Comment out the next 6 definitions if you already have +# the Level 1 BLAS. +#--------------------------------------------------------- +SBLAS1 = isamax.o sasum.o saxpy.o scopy.o sdot.o snrm2.o \ + srot.o srotg.o sscal.o sswap.o sdsdot.o srotmg.o srotm.o +$(SBLAS1): $(FRC) + +CBLAS1 = scabs1.o scasum.o scnrm2.o icamax.o caxpy.o ccopy.o \ + cdotc.o cdotu.o csscal.o crotg.o cscal.o cswap.o csrot.o +$(CBLAS1): $(FRC) + +DBLAS1 = idamax.o dasum.o daxpy.o dcopy.o ddot.o dnrm2.o \ + drot.o drotg.o dscal.o dsdot.o dswap.o drotmg.o drotm.o +$(DBLAS1): $(FRC) + +ZBLAS1 = dcabs1.o dzasum.o dznrm2.o izamax.o zaxpy.o zcopy.o \ + zdotc.o zdotu.o zdscal.o zrotg.o zscal.o zswap.o zdrot.o +$(ZBLAS1): $(FRC) + +CB1AUX = isamax.o sasum.o saxpy.o scopy.o snrm2.o sscal.o +$(CB1AUX): $(FRC) + +ZB1AUX = idamax.o dasum.o daxpy.o dcopy.o dnrm2.o dscal.o +$(ZB1AUX): $(FRC) + +#--------------------------------------------------------------------- +# The following line defines auxiliary routines needed by both the +# Level 2 and Level 3 BLAS. Comment it out only if you already have +# both the Level 2 and 3 BLAS. +#--------------------------------------------------------------------- +ALLBLAS = lsame.o xerbla.o +$(ALLBLAS) : $(FRC) + +#--------------------------------------------------------- +# Comment out the next 4 definitions if you already have +# the Level 2 BLAS. +#--------------------------------------------------------- +SBLAS2 = sgemv.o sgbmv.o ssymv.o ssbmv.o sspmv.o \ + strmv.o stbmv.o stpmv.o strsv.o stbsv.o stpsv.o \ + sger.o ssyr.o sspr.o ssyr2.o sspr2.o +$(SBLAS2): $(FRC) + +CBLAS2 = cgemv.o cgbmv.o chemv.o chbmv.o chpmv.o \ + ctrmv.o ctbmv.o ctpmv.o ctrsv.o ctbsv.o ctpsv.o \ + cgerc.o cgeru.o cher.o chpr.o cher2.o chpr2.o +$(CBLAS2): $(FRC) + +DBLAS2 = dgemv.o dgbmv.o dsymv.o dsbmv.o dspmv.o \ + dtrmv.o dtbmv.o dtpmv.o dtrsv.o dtbsv.o dtpsv.o \ + dger.o dsyr.o dspr.o dsyr2.o dspr2.o +$(DBLAS2): $(FRC) + +ZBLAS2 = zgemv.o zgbmv.o zhemv.o zhbmv.o zhpmv.o \ + ztrmv.o ztbmv.o ztpmv.o ztrsv.o ztbsv.o ztpsv.o \ + zgerc.o zgeru.o zher.o zhpr.o zher2.o zhpr2.o +$(ZBLAS2): $(FRC) + +#--------------------------------------------------------- +# Comment out the next 4 definitions if you already have +# the Level 3 BLAS. +#--------------------------------------------------------- +SBLAS3 = sgemm.o ssymm.o ssyrk.o ssyr2k.o strmm.o strsm.o +$(SBLAS3): $(FRC) + +CBLAS3 = cgemm.o csymm.o csyrk.o csyr2k.o ctrmm.o ctrsm.o \ + chemm.o cherk.o cher2k.o +$(CBLAS3): $(FRC) + +DBLAS3 = dgemm.o dsymm.o dsyrk.o dsyr2k.o dtrmm.o dtrsm.o +$(DBLAS3): $(FRC) + +ZBLAS3 = zgemm.o zsymm.o zsyrk.o zsyr2k.o ztrmm.o ztrsm.o \ + zhemm.o zherk.o zher2k.o +$(ZBLAS3): $(FRC) + +ALLOBJ=$(SBLAS1) $(SBLAS2) $(SBLAS3) $(DBLAS1) $(DBLAS2) $(DBLAS3) \ + $(CBLAS1) $(CBLAS2) $(CBLAS3) $(ZBLAS1) \ + $(ZBLAS2) $(ZBLAS3) $(ALLBLAS) + +$(BLASLIB): $(ALLOBJ) + $(FORTRAN) -shared -o $@ \ + $(ALLOBJ) \ + -Wl,--out-implib=$(IMP_LIB_NAME) + +single: $(SBLAS1) $(ALLBLAS) $(SBLAS2) $(SBLAS3) + $(ARCH) $(ARCHFLAGS) $(BLASLIB) $(SBLAS1) $(ALLBLAS) \ + $(SBLAS2) $(SBLAS3) + $(RANLIB) $(BLASLIB) + +double: $(DBLAS1) $(ALLBLAS) $(DBLAS2) $(DBLAS3) + $(ARCH) $(ARCHFLAGS) $(BLASLIB) $(DBLAS1) $(ALLBLAS) \ + $(DBLAS2) $(DBLAS3) + $(RANLIB) $(BLASLIB) + +complex: $(CBLAS1) $(CB1AUX) $(ALLBLAS) $(CBLAS2) $(CBLAS3) + $(ARCH) $(ARCHFLAGS) $(BLASLIB) $(CBLAS1) $(CB1AUX) \ + $(ALLBLAS) $(CBLAS2) $(CBLAS3) + $(RANLIB) $(BLASLIB) + +complex16: $(ZBLAS1) $(ZB1AUX) $(ALLBLAS) $(ZBLAS2) $(ZBLAS3) + $(ARCH) $(ARCHFLAGS) $(BLASLIB) $(ZBLAS1) $(ZB1AUX) \ + $(ALLBLAS) $(ZBLAS2) $(ZBLAS3) + $(RANLIB) $(BLASLIB) + +FRC: + @FRC=$(FRC) + +clean: + rm -f *.o + +.f.o: + $(FORTRAN) $(OPTS) -c $< -o $@ Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/mingw64/make.inc =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/mingw64/make.inc (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/3.8/win/msys2/mingw64/make.inc (revision 27955) @@ -0,0 +1,38 @@ +#################################################################### +# BLAS make include file. # +# March 2007 # +#################################################################### +# +SHELL = /usr/bin/bash +# +# The machine (platform) identifier to append to the library names +# +PLAT = +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -O2 -fPIC +DRVOPTS = $(OPTS) +NOOPT = -O0 -fPIC +LOADER = gfortran +LOADOPTS = +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib + +MODULE = blas +IMP_LIB_NAME = lib$(MODULE).dll.a +LIB_NAME = msys-$(MODULE).dll +# +# The location and name of the Reference BLAS library. +# +BLASLIB = $(LIB_NAME) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/linux64/make.inc =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/linux64/make.inc (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/linux64/make.inc (revision 27955) @@ -0,0 +1,34 @@ +#################################################################### +# BLAS make include file. # +# March 2007 # +#################################################################### +# +SHELL = /bin/sh +# +# The machine (platform) identifier to append to the library names +# +PLAT = _LINUX +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O3 +DRVOPTS = $(OPTS) +NOOPT = +LOADER = gfortran +LOADOPTS = +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# The location and name of the Reference BLAS library. +# +BLASLIB = blas$(PLAT).a Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/macosx64/make.inc =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/macosx64/make.inc (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/configs/macosx64/make.inc (revision 27955) @@ -0,0 +1,34 @@ +#################################################################### +# BLAS make include file. # +# March 2007 # +#################################################################### +# +SHELL = /bin/sh +# +# The machine (platform) identifier to append to the library names +# +PLAT = _LINUX +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O3 +DRVOPTS = $(OPTS) +NOOPT = +LOADER = gfortran +LOADOPTS = +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# The location and name of the Reference BLAS library. +# +BLASLIB = blas$(PLAT).a Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-3-win-msys2-gcc.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-3-win-msys2-gcc.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-3-win-msys2-gcc.sh (revision 27955) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER=3.8.0 + +PREFIX="${ISSM_DIR}/externalpackages/blas/install" + +MODULE="blas" +IMP_LIB_NAME="lib${MODULE}.dll.a" +LIB_NAME="msys-${MODULE}.dll" + +# Cleanup +rm -rf ${PREFIX} src +mkdir ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/blas-${VER}.tgz" "blas-${VER}.tgz" + +# Unpack source +tar -zxvf blas-${VER}.tgz + +# Move source into 'src' directory +mv BLAS-${VER}/* src +rm -rf BLAS-${VER} + +# Copy customized source and configuration files to 'src' directory +cp configs/3.8/win/msys2/gcc/make.inc src +cp configs/3.8/win/msys2/gcc/Makefile src + +# Compile +cd src +make + +# Install +mkdir ${PREFIX}/lib +cp ${IMP_LIB_NAME} ${PREFIX}/lib +cp ${LIB_NAME} ${PREFIX}/lib + +# Create link to shared version of library so that libtool can find it +cd ${PREFIX}/lib +ln -s ./${LIB_NAME} ./libblas.dll Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-3-win-msys2-mingw.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-3-win-msys2-mingw.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-3-win-msys2-mingw.sh (revision 27955) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER=3.8.0 + +PREFIX="${ISSM_DIR}/externalpackages/blas/install" + +MODULE="blas" +IMP_LIB_NAME="lib${MODULE}.dll.a" +LIB_NAME="msys-${MODULE}.dll" + +# Cleanup +rm -rf ${PREFIX} src +mkdir ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/blas-${VER}.tgz" "blas-${VER}.tgz" + +# Unpack source +tar -zxvf blas-${VER}.tgz + +# Move source into 'src' directory +mv BLAS-${VER}/* src +rm -rf BLAS-${VER} + +# Copy customized source and configuration files to 'src' directory +cp configs/3.8/win/msys2/mingw/make.inc src +cp configs/3.8/win/msys2/mingw/Makefile src + +# Compile +cd src +make + +# Install +mkdir ${PREFIX}/lib +cp ${IMP_LIB_NAME} ${PREFIX}/lib +cp ${LIB_NAME} ${PREFIX}/lib + +# Create link to shared version of library so that libtool can find it +cd ${PREFIX}/lib +ln -s ./${LIB_NAME} ./libblas.dll Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-linux64.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-linux64.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-linux64.sh (revision 27955) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install BLAS blas.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/blas.tgz' 'blas.tgz' + +#Untar +tar -zxvf blas.tgz + +#Move blas into install directory +mv BLAS/* src +rm -rf BLAS + +#install +cd src +cp ../configs/linux64/make.inc ./ +make + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/*.a . +ln -s blas_LINUX.a blas.a +ln -s blas_LINUX.a libblas.a Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-macosx64.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-macosx64.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/blas/install-macosx64.sh (revision 27955) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install BLAS blas.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/blas.tgz' 'blas.tgz' + +#Untar +tar -zxvf blas.tgz + +#Move blas into install directory +mv BLAS/* src +rm -rf BLAS + +#install +cd src +cp ../configs/macosx64/make.inc ./ +make + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/*.a . +ln -s blas_LINUX.a blas.a +ln -s blas_LINUX.a libblas.a Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/adl.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/adl.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/adl.hpp.patch (revision 27955) @@ -0,0 +1,7 @@ +33,34c33,35 +< || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +< ) +--- +> ) +> // || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +> // ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/boost/multi_index/ordered_index.hpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/boost/multi_index/ordered_index.hpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/boost/multi_index/ordered_index.hpp (revision 27955) @@ -0,0 +1,1529 @@ +/* Copyright 2003-2013 Joaquin M Lopez Munoz. + * Distributed under the Boost Software License, Version 1.0. + * (See accompanying file LICENSE_1_0.txt or copy at + * http://www.boost.org/LICENSE_1_0.txt) + * + * See http://www.boost.org/libs/multi_index for library home page. + * + * The internal implementation of red-black trees is based on that of SGI STL + * stl_tree.h file: + * + * Copyright (c) 1996,1997 + * Silicon Graphics Computer Systems, Inc. + * + * Permission to use, copy, modify, distribute and sell this software + * and its documentation for any purpose is hereby granted without fee, + * provided that the above copyright notice appear in all copies and + * that both that copyright notice and this permission notice appear + * in supporting documentation. Silicon Graphics makes no + * representations about the suitability of this software for any + * purpose. It is provided "as is" without express or implied warranty. + * + * + * Copyright (c) 1994 + * Hewlett-Packard Company + * + * Permission to use, copy, modify, distribute and sell this software + * and its documentation for any purpose is hereby granted without fee, + * provided that the above copyright notice appear in all copies and + * that both that copyright notice and this permission notice appear + * in supporting documentation. Hewlett-Packard Company makes no + * representations about the suitability of this software for any + * purpose. It is provided "as is" without express or implied warranty. + * + */ + +#ifndef BOOST_MULTI_INDEX_ORDERED_INDEX_HPP +#define BOOST_MULTI_INDEX_ORDERED_INDEX_HPP + +#if defined(_MSC_VER)&&(_MSC_VER>=1200) +#pragma once +#endif + +#include /* keep it first to prevent nasty warns in MSVC */ +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#if !defined(BOOST_NO_CXX11_HDR_INITIALIZER_LIST) +#include +#endif + +#if !defined(BOOST_MULTI_INDEX_DISABLE_SERIALIZATION) +#include +#include +#include +#include +#endif + +#if defined(BOOST_MULTI_INDEX_ENABLE_INVARIANT_CHECKING) +#define BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT_OF(x) \ + detail::scope_guard BOOST_JOIN(check_invariant_,__LINE__)= \ + detail::make_obj_guard(x,&ordered_index::check_invariant_); \ + BOOST_JOIN(check_invariant_,__LINE__).touch(); +#define BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT \ + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT_OF(*this) +#else +#define BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT_OF(x) +#define BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT +#endif + +namespace boost{ + +namespace multi_index{ + +namespace detail{ + +/* ordered_index adds a layer of ordered indexing to a given Super */ + +/* Most of the implementation of unique and non-unique indices is + * shared. We tell from one another on instantiation time by using + * these tags. + */ + +struct ordered_unique_tag{}; +struct ordered_non_unique_tag{}; + +template< + typename KeyFromValue,typename Compare, + typename SuperMeta,typename TagList,typename Category +> +class ordered_index: + BOOST_MULTI_INDEX_PROTECTED_IF_MEMBER_TEMPLATE_FRIENDS SuperMeta::type + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) +#if BOOST_WORKAROUND(BOOST_MSVC,<1300) + ,public safe_ctr_proxy_impl< + bidir_node_iterator< + ordered_index_node >, + ordered_index > +#else + ,public safe_mode::safe_container< + ordered_index > +#endif +#endif + +{ +#if defined(BOOST_MULTI_INDEX_ENABLE_INVARIANT_CHECKING)&&\ + BOOST_WORKAROUND(__MWERKS__,<=0x3003) +/* The "ISO C++ Template Parser" option in CW8.3 has a problem with the + * lifetime of const references bound to temporaries --precisely what + * scopeguards are. + */ + +#pragma parse_mfunc_templ off +#endif + + typedef typename SuperMeta::type super; + +protected: + typedef ordered_index_node< + typename super::node_type> node_type; + +private: + typedef typename node_type::impl_type node_impl_type; + typedef typename node_impl_type::pointer node_impl_pointer; + +public: + /* types */ + + typedef typename KeyFromValue::result_type key_type; + typedef typename node_type::value_type value_type; + typedef KeyFromValue key_from_value; + typedef Compare key_compare; + typedef value_comparison< + value_type,KeyFromValue,Compare> value_compare; + typedef tuple ctor_args; + typedef typename super::final_allocator_type allocator_type; + typedef typename allocator_type::reference reference; + typedef typename allocator_type::const_reference const_reference; + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) +#if BOOST_WORKAROUND(BOOST_MSVC,<1300) + typedef safe_mode::safe_iterator< + bidir_node_iterator, + safe_ctr_proxy< + bidir_node_iterator > > iterator; +#else + typedef safe_mode::safe_iterator< + bidir_node_iterator, + ordered_index> iterator; +#endif +#else + typedef bidir_node_iterator iterator; +#endif + + typedef iterator const_iterator; + + typedef std::size_t size_type; + typedef std::ptrdiff_t difference_type; + typedef typename allocator_type::pointer pointer; + typedef typename allocator_type::const_pointer const_pointer; + typedef typename + boost::reverse_iterator reverse_iterator; + typedef typename + boost::reverse_iterator const_reverse_iterator; + typedef TagList tag_list; + +protected: + typedef typename super::final_node_type final_node_type; + typedef tuples::cons< + ctor_args, + typename super::ctor_args_list> ctor_args_list; + typedef typename mpl::push_front< + typename super::index_type_list, + ordered_index>::type index_type_list; + typedef typename mpl::push_front< + typename super::iterator_type_list, + iterator>::type iterator_type_list; + typedef typename mpl::push_front< + typename super::const_iterator_type_list, + const_iterator>::type const_iterator_type_list; + typedef typename super::copy_map_type copy_map_type; + +#if !defined(BOOST_MULTI_INDEX_DISABLE_SERIALIZATION) + typedef typename super::index_saver_type index_saver_type; + typedef typename super::index_loader_type index_loader_type; +#endif + +private: +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) +#if BOOST_WORKAROUND(BOOST_MSVC,<1300) + typedef safe_ctr_proxy_impl< + bidir_node_iterator, + ordered_index> safe_super; +#else + typedef safe_mode::safe_container safe_super; +#endif +#endif + + typedef typename call_traits< + value_type>::param_type value_param_type; + typedef typename call_traits< + key_type>::param_type key_param_type; + + /* Needed to avoid commas in BOOST_MULTI_INDEX_OVERLOADS_TO_VARTEMPL + * expansion. + */ + + typedef std::pair emplace_return_type; + +public: + + /* construct/copy/destroy + * Default and copy ctors are in the protected section as indices are + * not supposed to be created on their own. No range ctor either. + */ + + ordered_index& operator=( + const ordered_index& x) + { + this->final()=x.final(); + return *this; + } + +#if !defined(BOOST_NO_CXX11_HDR_INITIALIZER_LIST) + ordered_index& operator=( + std::initializer_list list) + { + this->final()=list; + return *this; + } +#endif + + allocator_type get_allocator()const + { + return this->final().get_allocator(); + } + + /* iterators */ + + iterator begin(){return make_iterator(leftmost());} + const_iterator begin()const{return make_iterator(leftmost());} + iterator end(){return make_iterator(header());} + const_iterator end()const{return make_iterator(header());} + reverse_iterator rbegin(){return boost::make_reverse_iterator(end());} + const_reverse_iterator rbegin()const{return make_reverse_iterator(end());} + reverse_iterator rend(){return make_reverse_iterator(begin());} + const_reverse_iterator rend()const{return make_reverse_iterator(begin());} + const_iterator cbegin()const{return begin();} + const_iterator cend()const{return end();} + const_reverse_iterator crbegin()const{return rbegin();} + const_reverse_iterator crend()const{return rend();} + + iterator iterator_to(const value_type& x) + { + return make_iterator(node_from_value(&x)); + } + + const_iterator iterator_to(const value_type& x)const + { + return make_iterator(node_from_value(&x)); + } + + /* capacity */ + + bool empty()const{return this->final_empty_();} + size_type size()const{return this->final_size_();} + size_type max_size()const{return this->final_max_size_();} + + /* modifiers */ + + BOOST_MULTI_INDEX_OVERLOADS_TO_VARTEMPL( + emplace_return_type,emplace,emplace_impl) + + BOOST_MULTI_INDEX_OVERLOADS_TO_VARTEMPL_EXTRA_ARG( + iterator,emplace_hint,emplace_hint_impl,iterator,position) + + std::pair insert(const value_type& x) + { + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + std::pair p=this->final_insert_(x); + return std::pair(make_iterator(p.first),p.second); + } + + std::pair insert(BOOST_RV_REF(value_type) x) + { + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + std::pair p=this->final_insert_rv_(x); + return std::pair(make_iterator(p.first),p.second); + } + + iterator insert(iterator position,const value_type& x) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + std::pair p=this->final_insert_( + x,static_cast(position.get_node())); + return make_iterator(p.first); + } + + iterator insert(iterator position,BOOST_RV_REF(value_type) x) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + std::pair p=this->final_insert_rv_( + x,static_cast(position.get_node())); + return make_iterator(p.first); + } + + template + void insert(InputIterator first,InputIterator last) + { + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + node_type* hint=header(); /* end() */ + for(;first!=last;++first){ + hint=this->final_insert_ref_( + *first,static_cast(hint)).first; + node_type::increment(hint); + } + } + +#if !defined(BOOST_NO_CXX11_HDR_INITIALIZER_LIST) + void insert(std::initializer_list list) + { + insert(list.begin(),list.end()); + } +#endif + + iterator erase(iterator position) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_DEREFERENCEABLE_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + this->final_erase_(static_cast(position++.get_node())); + return position; + } + + size_type erase(key_param_type x) + { + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + std::pair p=equal_range(x); + size_type s=0; + while(p.first!=p.second){ + p.first=erase(p.first); + ++s; + } + return s; + } + + iterator erase(iterator first,iterator last) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(first); + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(last); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(first,*this); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(last,*this); + BOOST_MULTI_INDEX_CHECK_VALID_RANGE(first,last); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + while(first!=last){ + first=erase(first); + } + return first; + } + + bool replace(iterator position,const value_type& x) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_DEREFERENCEABLE_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + return this->final_replace_( + x,static_cast(position.get_node())); + } + + bool replace(iterator position,BOOST_RV_REF(value_type) x) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_DEREFERENCEABLE_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + return this->final_replace_rv_( + x,static_cast(position.get_node())); + } + + template + bool modify(iterator position,Modifier mod) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_DEREFERENCEABLE_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + /* MSVC++ 6.0 optimizer on safe mode code chokes if this + * this is not added. Left it for all compilers as it does no + * harm. + */ + + position.detach(); +#endif + + return this->final_modify_( + mod,static_cast(position.get_node())); + } + + template + bool modify(iterator position,Modifier mod,Rollback back) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_DEREFERENCEABLE_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + /* MSVC++ 6.0 optimizer on safe mode code chokes if this + * this is not added. Left it for all compilers as it does no + * harm. + */ + + position.detach(); +#endif + + return this->final_modify_( + mod,back,static_cast(position.get_node())); + } + + template + bool modify_key(iterator position,Modifier mod) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_DEREFERENCEABLE_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + return modify( + position,modify_key_adaptor(mod,key)); + } + + template + bool modify_key(iterator position,Modifier mod,Rollback back) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_DEREFERENCEABLE_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + return modify( + position, + modify_key_adaptor(mod,key), + modify_key_adaptor(back,key)); + } + + void swap(ordered_index& x) + { + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT_OF(x); + this->final_swap_(x.final()); + } + + void clear() + { + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + this->final_clear_(); + } + + /* observers */ + + key_from_value key_extractor()const{return key;} + key_compare key_comp()const{return comp_;} + value_compare value_comp()const{return value_compare(key,comp_);} + + /* set operations */ + + /* Internally, these ops rely on const_iterator being the same + * type as iterator. + */ + + template + iterator find(const CompatibleKey& x)const + { + return make_iterator(ordered_index_find(root(),header(),key,x,comp_)); + } + + template + iterator find( + const CompatibleKey& x,const CompatibleCompare& comp)const + { + return make_iterator(ordered_index_find(root(),header(),key,x,comp)); + } + + template + size_type count(const CompatibleKey& x)const + { + return count(x,comp_); + } + + template + size_type count(const CompatibleKey& x,const CompatibleCompare& comp)const + { + std::pair p=equal_range(x,comp); + size_type n=std::distance(p.first,p.second); + return n; + } + + template + iterator lower_bound(const CompatibleKey& x)const + { + return make_iterator( + ordered_index_lower_bound(root(),header(),key,x,comp_)); + } + + template + iterator lower_bound( + const CompatibleKey& x,const CompatibleCompare& comp)const + { + return make_iterator( + ordered_index_lower_bound(root(),header(),key,x,comp)); + } + + template + iterator upper_bound(const CompatibleKey& x)const + { + return make_iterator( + ordered_index_upper_bound(root(),header(),key,x,comp_)); + } + + template + iterator upper_bound( + const CompatibleKey& x,const CompatibleCompare& comp)const + { + return make_iterator( + ordered_index_upper_bound(root(),header(),key,x,comp)); + } + + template + std::pair equal_range( + const CompatibleKey& x)const + { + std::pair p= + ordered_index_equal_range(root(),header(),key,x,comp_); + return std::pair( + make_iterator(p.first),make_iterator(p.second)); + } + + template + std::pair equal_range( + const CompatibleKey& x,const CompatibleCompare& comp)const + { + std::pair p= + ordered_index_equal_range(root(),header(),key,x,comp); + return std::pair( + make_iterator(p.first),make_iterator(p.second)); + } + + /* range */ + + template + std::pair + range(LowerBounder lower,UpperBounder upper)const + { + typedef typename mpl::if_< + is_same, + BOOST_DEDUCED_TYPENAME mpl::if_< + is_same, + both_unbounded_tag, + lower_unbounded_tag + >::type, + BOOST_DEDUCED_TYPENAME mpl::if_< + is_same, + upper_unbounded_tag, + none_unbounded_tag + >::type + >::type dispatch; + + return range(lower,upper,dispatch()); + } + +BOOST_MULTI_INDEX_PROTECTED_IF_MEMBER_TEMPLATE_FRIENDS: + ordered_index(const ctor_args_list& args_list,const allocator_type& al): + super(args_list.get_tail(),al), + key(tuples::get<0>(args_list.get_head())), + comp_(tuples::get<1>(args_list.get_head())) + { + empty_initialize(); + } + + ordered_index( + const ordered_index& x): + super(x), + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + safe_super(), +#endif + + key(x.key), + comp_(x.comp_) + { + /* Copy ctor just takes the key and compare objects from x. The rest is + * done in a subsequent call to copy_(). + */ + } + + ordered_index( + const ordered_index& x, + do_not_copy_elements_tag): + super(x,do_not_copy_elements_tag()), + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + safe_super(), +#endif + + key(x.key), + comp_(x.comp_) + { + empty_initialize(); + } + + ~ordered_index() + { + /* the container is guaranteed to be empty by now */ + } + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + iterator make_iterator(node_type* node){return iterator(node,this);} + const_iterator make_iterator(node_type* node)const + {return const_iterator(node,const_cast(this));} +#else + iterator make_iterator(node_type* node){return iterator(node);} + const_iterator make_iterator(node_type* node)const + {return const_iterator(node);} +#endif + + void copy_( + const ordered_index& x, + const copy_map_type& map) + { + if(!x.root()){ + empty_initialize(); + } + else{ + header()->color()=x.header()->color(); + + node_type* root_cpy=map.find(static_cast(x.root())); + header()->parent()=root_cpy->impl(); + + node_type* leftmost_cpy=map.find( + static_cast(x.leftmost())); + header()->left()=leftmost_cpy->impl(); + + node_type* rightmost_cpy=map.find( + static_cast(x.rightmost())); + header()->right()=rightmost_cpy->impl(); + + typedef typename copy_map_type::const_iterator copy_map_iterator; + for(copy_map_iterator it=map.begin(),it_end=map.end();it!=it_end;++it){ + node_type* org=it->first; + node_type* cpy=it->second; + + cpy->color()=org->color(); + + node_impl_pointer parent_org=org->parent(); + if(parent_org==node_impl_pointer(0))cpy->parent()=node_impl_pointer(0); + else{ + node_type* parent_cpy=map.find( + static_cast(node_type::from_impl(parent_org))); + cpy->parent()=parent_cpy->impl(); + if(parent_org->left()==org->impl()){ + parent_cpy->left()=cpy->impl(); + } + else if(parent_org->right()==org->impl()){ + /* header() does not satisfy this nor the previous check */ + parent_cpy->right()=cpy->impl(); + } + } + + if(org->left()==node_impl_pointer(0)) + cpy->left()=node_impl_pointer(0); + if(org->right()==node_impl_pointer(0)) + cpy->right()=node_impl_pointer(0); + } + } + + super::copy_(x,map); + } + + template + node_type* insert_(value_param_type v,node_type* x,Variant variant) + { + link_info inf; + if(!link_point(key(v),inf,Category())){ + return node_type::from_impl(inf.pos); + } + + node_type* res=static_cast(super::insert_(v,x,variant)); + if(res==x){ + node_impl_type::link(x->impl(),inf.side,inf.pos,header()->impl()); + } + return res; + } + + template + node_type* insert_( + value_param_type v,node_type* position,node_type* x,Variant variant) + { + link_info inf; + if(!hinted_link_point(key(v),position,inf,Category())){ + return node_type::from_impl(inf.pos); + } + + node_type* res=static_cast(super::insert_(v,position,x,variant)); + if(res==x){ + node_impl_type::link(x->impl(),inf.side,inf.pos,header()->impl()); + } + return res; + } + + void erase_(node_type* x) + { + node_impl_type::rebalance_for_erase( + x->impl(),header()->parent(),header()->left(),header()->right()); + super::erase_(x); + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + detach_iterators(x); +#endif + } + + void delete_all_nodes_() + { + delete_all_nodes(root()); + } + + void clear_() + { + super::clear_(); + empty_initialize(); + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + safe_super::detach_dereferenceable_iterators(); +#endif + } + + void swap_(ordered_index& x) + { + std::swap(key,x.key); + std::swap(comp_,x.comp_); + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + safe_super::swap(x); +#endif + + super::swap_(x); + } + + void swap_elements_( + ordered_index& x) + { +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + safe_super::swap(x); +#endif + + super::swap_elements_(x); + } + + template + bool replace_(value_param_type v,node_type* x,Variant variant) + { + if(in_place(v,x,Category())){ + return super::replace_(v,x,variant); + } + + node_type* next=x; + node_type::increment(next); + + node_impl_type::rebalance_for_erase( + x->impl(),header()->parent(),header()->left(),header()->right()); + + BOOST_TRY{ + link_info inf; + if(link_point(key(v),inf,Category())&&super::replace_(v,x,variant)){ + node_impl_type::link(x->impl(),inf.side,inf.pos,header()->impl()); + return true; + } + node_impl_type::restore(x->impl(),next->impl(),header()->impl()); + return false; + } + BOOST_CATCH(...){ + node_impl_type::restore(x->impl(),next->impl(),header()->impl()); + BOOST_RETHROW; + } + BOOST_CATCH_END + } + + bool modify_(node_type* x) + { + bool b; + BOOST_TRY{ + b=in_place(x->value(),x,Category()); + } + BOOST_CATCH(...){ + erase_(x); + BOOST_RETHROW; + } + BOOST_CATCH_END + if(!b){ + node_impl_type::rebalance_for_erase( + x->impl(),header()->parent(),header()->left(),header()->right()); + BOOST_TRY{ + link_info inf; + if(!link_point(key(x->value()),inf,Category())){ + super::erase_(x); + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + detach_iterators(x); +#endif + return false; + } + node_impl_type::link(x->impl(),inf.side,inf.pos,header()->impl()); + } + BOOST_CATCH(...){ + super::erase_(x); + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + detach_iterators(x); +#endif + + BOOST_RETHROW; + } + BOOST_CATCH_END + } + + BOOST_TRY{ + if(!super::modify_(x)){ + node_impl_type::rebalance_for_erase( + x->impl(),header()->parent(),header()->left(),header()->right()); + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + detach_iterators(x); +#endif + + return false; + } + else return true; + } + BOOST_CATCH(...){ + node_impl_type::rebalance_for_erase( + x->impl(),header()->parent(),header()->left(),header()->right()); + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + detach_iterators(x); +#endif + + BOOST_RETHROW; + } + BOOST_CATCH_END + } + + bool modify_rollback_(node_type* x) + { + if(in_place(x->value(),x,Category())){ + return super::modify_rollback_(x); + } + + node_type* next=x; + node_type::increment(next); + + node_impl_type::rebalance_for_erase( + x->impl(),header()->parent(),header()->left(),header()->right()); + + BOOST_TRY{ + link_info inf; + if(link_point(key(x->value()),inf,Category())&& + super::modify_rollback_(x)){ + node_impl_type::link(x->impl(),inf.side,inf.pos,header()->impl()); + return true; + } + node_impl_type::restore(x->impl(),next->impl(),header()->impl()); + return false; + } + BOOST_CATCH(...){ + node_impl_type::restore(x->impl(),next->impl(),header()->impl()); + BOOST_RETHROW; + } + BOOST_CATCH_END + } + +#if !defined(BOOST_MULTI_INDEX_DISABLE_SERIALIZATION) + /* serialization */ + + template + void save_( + Archive& ar,const unsigned int version,const index_saver_type& sm)const + { + save_(ar,version,sm,Category()); + } + + template + void load_(Archive& ar,const unsigned int version,const index_loader_type& lm) + { + load_(ar,version,lm,Category()); + } +#endif + +#if defined(BOOST_MULTI_INDEX_ENABLE_INVARIANT_CHECKING) + /* invariant stuff */ + + bool invariant_()const + { + if(size()==0||begin()==end()){ + if(size()!=0||begin()!=end()|| + header()->left()!=header()->impl()|| + header()->right()!=header()->impl())return false; + } + else{ + if((size_type)std::distance(begin(),end())!=size())return false; + + std::size_t len=node_impl_type::black_count( + leftmost()->impl(),root()->impl()); + for(const_iterator it=begin(),it_end=end();it!=it_end;++it){ + node_type* x=it.get_node(); + node_type* left_x=node_type::from_impl(x->left()); + node_type* right_x=node_type::from_impl(x->right()); + + if(x->color()==red){ + if((left_x&&left_x->color()==red)|| + (right_x&&right_x->color()==red))return false; + } + if(left_x&&comp_(key(x->value()),key(left_x->value())))return false; + if(right_x&&comp_(key(right_x->value()),key(x->value())))return false; + if(!left_x&&!right_x&& + node_impl_type::black_count(x->impl(),root()->impl())!=len) + return false; + } + + if(leftmost()->impl()!=node_impl_type::minimum(root()->impl())) + return false; + if(rightmost()->impl()!=node_impl_type::maximum(root()->impl())) + return false; + } + + return super::invariant_(); + } + + + /* This forwarding function eases things for the boost::mem_fn construct + * in BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT. Actually, + * final_check_invariant is already an inherited member function of + * ordered_index. + */ + void check_invariant_()const{this->final_check_invariant_();} +#endif + +private: + node_type* header()const{return this->final_header();} + node_type* root()const{return node_type::from_impl(header()->parent());} + node_type* leftmost()const{return node_type::from_impl(header()->left());} + node_type* rightmost()const{return node_type::from_impl(header()->right());} + + void empty_initialize() + { + header()->color()=red; + /* used to distinguish header() from root, in iterator.operator++ */ + + header()->parent()=node_impl_pointer(0); + header()->left()=header()->impl(); + header()->right()=header()->impl(); + } + + struct link_info + { + link_info():side(to_left){} + + ordered_index_side side; + node_impl_pointer pos; + }; + + bool link_point(key_param_type k,link_info& inf,ordered_unique_tag) + { + node_type* y=header(); + node_type* x=root(); + bool c=true; + while(x){ + y=x; + c=comp_(k,key(x->value())); + x=node_type::from_impl(c?x->left():x->right()); + } + node_type* yy=y; + if(c){ + if(yy==leftmost()){ + inf.side=to_left; + inf.pos=y->impl(); + return true; + } + else node_type::decrement(yy); + } + + if(comp_(key(yy->value()),k)){ + inf.side=c?to_left:to_right; + inf.pos=y->impl(); + return true; + } + else{ + inf.pos=yy->impl(); + return false; + } + } + + bool link_point(key_param_type k,link_info& inf,ordered_non_unique_tag) + { + node_type* y=header(); + node_type* x=root(); + bool c=true; + while (x){ + y=x; + c=comp_(k,key(x->value())); + x=node_type::from_impl(c?x->left():x->right()); + } + inf.side=c?to_left:to_right; + inf.pos=y->impl(); + return true; + } + + bool lower_link_point(key_param_type k,link_info& inf,ordered_non_unique_tag) + { + node_type* y=header(); + node_type* x=root(); + bool c=false; + while (x){ + y=x; + c=comp_(key(x->value()),k); + x=node_type::from_impl(c?x->right():x->left()); + } + inf.side=c?to_right:to_left; + inf.pos=y->impl(); + return true; + } + + bool hinted_link_point( + key_param_type k,node_type* position,link_info& inf,ordered_unique_tag) + { + if(position->impl()==header()->left()){ + if(size()>0&&comp_(k,key(position->value()))){ + inf.side=to_left; + inf.pos=position->impl(); + return true; + } + else return link_point(k,inf,ordered_unique_tag()); + } + else if(position==header()){ + if(comp_(key(rightmost()->value()),k)){ + inf.side=to_right; + inf.pos=rightmost()->impl(); + return true; + } + else return link_point(k,inf,ordered_unique_tag()); + } + else{ + node_type* before=position; + node_type::decrement(before); + if(comp_(key(before->value()),k)&&comp_(k,key(position->value()))){ + if(before->right()==node_impl_pointer(0)){ + inf.side=to_right; + inf.pos=before->impl(); + return true; + } + else{ + inf.side=to_left; + inf.pos=position->impl(); + return true; + } + } + else return link_point(k,inf,ordered_unique_tag()); + } + } + + bool hinted_link_point( + key_param_type k,node_type* position,link_info& inf,ordered_non_unique_tag) + { + if(position->impl()==header()->left()){ + if(size()>0&&!comp_(key(position->value()),k)){ + inf.side=to_left; + inf.pos=position->impl(); + return true; + } + else return lower_link_point(k,inf,ordered_non_unique_tag()); + } + else if(position==header()){ + if(!comp_(k,key(rightmost()->value()))){ + inf.side=to_right; + inf.pos=rightmost()->impl(); + return true; + } + else return link_point(k,inf,ordered_non_unique_tag()); + } + else{ + node_type* before=position; + node_type::decrement(before); + if(!comp_(k,key(before->value()))){ + if(!comp_(key(position->value()),k)){ + if(before->right()==node_impl_pointer(0)){ + inf.side=to_right; + inf.pos=before->impl(); + return true; + } + else{ + inf.side=to_left; + inf.pos=position->impl(); + return true; + } + } + else return lower_link_point(k,inf,ordered_non_unique_tag()); + } + else return link_point(k,inf,ordered_non_unique_tag()); + } + } + + void delete_all_nodes(node_type* x) + { + if(!x)return; + + delete_all_nodes(node_type::from_impl(x->left())); + delete_all_nodes(node_type::from_impl(x->right())); + this->final_delete_node_(static_cast(x)); + } + + bool in_place(value_param_type v,node_type* x,ordered_unique_tag) + { + node_type* y; + if(x!=leftmost()){ + y=x; + node_type::decrement(y); + if(!comp_(key(y->value()),key(v)))return false; + } + + y=x; + node_type::increment(y); + return y==header()||comp_(key(v),key(y->value())); + } + + bool in_place(value_param_type v,node_type* x,ordered_non_unique_tag) + { + node_type* y; + if(x!=leftmost()){ + y=x; + node_type::decrement(y); + if(comp_(key(v),key(y->value())))return false; + } + + y=x; + node_type::increment(y); + return y==header()||!comp_(key(y->value()),key(v)); + } + +#if defined(BOOST_MULTI_INDEX_ENABLE_SAFE_MODE) + void detach_iterators(node_type* x) + { + iterator it=make_iterator(x); + safe_mode::detach_equivalent_iterators(it); + } +#endif + + template + std::pair emplace_impl(BOOST_MULTI_INDEX_FUNCTION_PARAM_PACK) + { + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + std::pairp= + this->final_emplace_(BOOST_MULTI_INDEX_FORWARD_PARAM_PACK); + return std::pair(make_iterator(p.first),p.second); + } + + template + iterator emplace_hint_impl( + iterator position,BOOST_MULTI_INDEX_FUNCTION_PARAM_PACK) + { + BOOST_MULTI_INDEX_CHECK_VALID_ITERATOR(position); + BOOST_MULTI_INDEX_CHECK_IS_OWNER(position,*this); + BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT; + std::pairp= + this->final_emplace_hint_( + static_cast(position.get_node()), + BOOST_MULTI_INDEX_FORWARD_PARAM_PACK); + return make_iterator(p.first); + } + + template + std::pair + range(LowerBounder lower,UpperBounder upper,none_unbounded_tag)const + { + node_type* y=header(); + node_type* z=root(); + + while(z){ + if(!lower(key(z->value()))){ + z=node_type::from_impl(z->right()); + } + else if(!upper(key(z->value()))){ + y=z; + z=node_type::from_impl(z->left()); + } + else{ + return std::pair( + make_iterator( + lower_range(node_type::from_impl(z->left()),z,lower)), + make_iterator( + upper_range(node_type::from_impl(z->right()),y,upper))); + } + } + + return std::pair(make_iterator(y),make_iterator(y)); + } + + template + std::pair + range(LowerBounder,UpperBounder upper,lower_unbounded_tag)const + { + return std::pair( + begin(), + make_iterator(upper_range(root(),header(),upper))); + } + + template + std::pair + range(LowerBounder lower,UpperBounder,upper_unbounded_tag)const + { + return std::pair( + make_iterator(lower_range(root(),header(),lower)), + end()); + } + + template + std::pair + range(LowerBounder,UpperBounder,both_unbounded_tag)const + { + return std::pair(begin(),end()); + } + + template + node_type * lower_range(node_type* top,node_type* y,LowerBounder lower)const + { + while(top){ + if(lower(key(top->value()))){ + y=top; + top=node_type::from_impl(top->left()); + } + else top=node_type::from_impl(top->right()); + } + + return y; + } + + template + node_type * upper_range(node_type* top,node_type* y,UpperBounder upper)const + { + while(top){ + if(!upper(key(top->value()))){ + y=top; + top=node_type::from_impl(top->left()); + } + else top=node_type::from_impl(top->right()); + } + + return y; + } + +#if !defined(BOOST_MULTI_INDEX_DISABLE_SERIALIZATION) + template + void save_( + Archive& ar,const unsigned int version,const index_saver_type& sm, + ordered_unique_tag)const + { + super::save_(ar,version,sm); + } + + template + void load_( + Archive& ar,const unsigned int version,const index_loader_type& lm, + ordered_unique_tag) + { + super::load_(ar,version,lm); + } + + template + void save_( + Archive& ar,const unsigned int version,const index_saver_type& sm, + ordered_non_unique_tag)const + { + typedef duplicates_iterator dup_iterator; + + sm.save( + dup_iterator(begin().get_node(),end().get_node(),value_comp()), + dup_iterator(end().get_node(),value_comp()), + ar,version); + super::save_(ar,version,sm); + } + + template + void load_( + Archive& ar,const unsigned int version,const index_loader_type& lm, + ordered_non_unique_tag) + { + lm.load( + ::boost::bind(&ordered_index::rearranger,this,_1,_2), + ar,version); + super::load_(ar,version,lm); + } + + void rearranger(node_type* position,node_type *x) + { + if(!position||comp_(key(position->value()),key(x->value()))){ + position=lower_bound(key(x->value())).get_node(); + } + else if(comp_(key(x->value()),key(position->value()))){ + /* inconsistent rearrangement */ + throw_exception( + archive::archive_exception( + archive::archive_exception::other_exception)); + } + else node_type::increment(position); + + if(position!=x){ + node_impl_type::rebalance_for_erase( + x->impl(),header()->parent(),header()->left(),header()->right()); + node_impl_type::restore( + x->impl(),position->impl(),header()->impl()); + } + } +#endif /* serialization */ + + key_from_value key; + key_compare comp_; + +#if defined(BOOST_MULTI_INDEX_ENABLE_INVARIANT_CHECKING)&&\ + BOOST_WORKAROUND(__MWERKS__,<=0x3003) +#pragma parse_mfunc_templ reset +#endif +}; + +/* comparison */ + +template< + typename KeyFromValue1,typename Compare1, + typename SuperMeta1,typename TagList1,typename Category1, + typename KeyFromValue2,typename Compare2, + typename SuperMeta2,typename TagList2,typename Category2 +> +bool operator==( + const ordered_index& x, + const ordered_index& y) +{ + return x.size()==y.size()&&std::equal(x.begin(),x.end(),y.begin()); +} + +template< + typename KeyFromValue1,typename Compare1, + typename SuperMeta1,typename TagList1,typename Category1, + typename KeyFromValue2,typename Compare2, + typename SuperMeta2,typename TagList2,typename Category2 +> +bool operator<( + const ordered_index& x, + const ordered_index& y) +{ + return std::lexicographical_compare(x.begin(),x.end(),y.begin(),y.end()); +} + +template< + typename KeyFromValue1,typename Compare1, + typename SuperMeta1,typename TagList1,typename Category1, + typename KeyFromValue2,typename Compare2, + typename SuperMeta2,typename TagList2,typename Category2 +> +bool operator!=( + const ordered_index& x, + const ordered_index& y) +{ + return !(x==y); +} + +template< + typename KeyFromValue1,typename Compare1, + typename SuperMeta1,typename TagList1,typename Category1, + typename KeyFromValue2,typename Compare2, + typename SuperMeta2,typename TagList2,typename Category2 +> +bool operator>( + const ordered_index& x, + const ordered_index& y) +{ + return y +bool operator>=( + const ordered_index& x, + const ordered_index& y) +{ + return !(x +bool operator<=( + const ordered_index& x, + const ordered_index& y) +{ + return !(x>y); +} + +/* specialized algorithms */ + +template< + typename KeyFromValue,typename Compare, + typename SuperMeta,typename TagList,typename Category +> +void swap( + ordered_index& x, + ordered_index& y) +{ + x.swap(y); +} + +} /* namespace multi_index::detail */ + +/* ordered_index specifiers */ + +template +struct ordered_unique +{ + typedef typename detail::ordered_index_args< + Arg1,Arg2,Arg3> index_args; + typedef typename index_args::tag_list_type::type tag_list_type; + typedef typename index_args::key_from_value_type key_from_value_type; + typedef typename index_args::compare_type compare_type; + + template + struct node_class + { + typedef detail::ordered_index_node type; + }; + + template + struct index_class + { + typedef detail::ordered_index< + key_from_value_type,compare_type, + SuperMeta,tag_list_type,detail::ordered_unique_tag> type; + }; +}; + +template +struct ordered_non_unique +{ + typedef detail::ordered_index_args< + Arg1,Arg2,Arg3> index_args; + typedef typename index_args::tag_list_type::type tag_list_type; + typedef typename index_args::key_from_value_type key_from_value_type; + typedef typename index_args::compare_type compare_type; + + template + struct node_class + { + typedef detail::ordered_index_node type; + }; + + template + struct index_class + { + typedef detail::ordered_index< + key_from_value_type,compare_type, + SuperMeta,tag_list_type,detail::ordered_non_unique_tag> type; + }; +}; + +} /* namespace multi_index */ + +} /* namespace boost */ + +/* Boost.Foreach compatibility */ + +template< + typename KeyFromValue,typename Compare, + typename SuperMeta,typename TagList,typename Category +> +inline boost::mpl::true_* boost_foreach_is_noncopyable( + boost::multi_index::detail::ordered_index< + KeyFromValue,Compare,SuperMeta,TagList,Category>*&, + boost::foreach::tag) +{ + return 0; +} + +#undef BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT +#undef BOOST_MULTI_INDEX_ORD_INDEX_CHECK_INVARIANT_OF + +#endif Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/cas128strong.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/cas128strong.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/cas128strong.hpp.patch (revision 27955) @@ -0,0 +1,17 @@ +199c199 +< explicit base_atomic(value_type const& v) BOOST_NOEXCEPT : v_(0) +--- +> explicit base_atomic(value_type const& v) BOOST_NOEXCEPT +200a201 +> memset(&v_, 0, sizeof(v_)); +207c208,209 +< storage_type value_s = 0; +--- +> storage_type value_s; +> memset(&value_s, 0, sizeof(value_s)); +250c252,254 +< storage_type expected_s = 0, desired_s = 0; +--- +> storage_type expected_s, desired_s; +> memset(&expected_s, 0, sizeof(expected_s)); +> memset(&desired_s, 0, sizeof(desired_s)); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/darwin.jam.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/darwin.jam.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/darwin.jam.patch (revision 27955) @@ -0,0 +1,4 @@ +587c587 +< "$(.LIBTOOL)" -static -o "$(<:T)" $(ARFLAGS) "$(>:T)" +--- +> /usr/bin/libtool -static -o "$(<:T)" $(ARFLAGS) "$(>:T)" Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/darwin.py.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/darwin.py.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/darwin.py.patch (revision 27955) @@ -0,0 +1,4 @@ +40c40 +< toolset.flags ('darwin.compile', 'OPTIONS', None, ['-Wno-long-double', '-no-cpp-precomp']) +--- +> toolset.flags ('darwin.compile', 'OPTIONS', None, ['-Wno-long-double']) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/gcc-atomic.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/gcc-atomic.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/gcc-atomic.hpp.patch (revision 27955) @@ -0,0 +1,28 @@ +961c961 +< explicit base_atomic(value_type const& v) BOOST_NOEXCEPT : v_(0) +--- +> explicit base_atomic(value_type const& v) BOOST_NOEXCEPT +962a963 +> memset(&v_, 0, sizeof(v_)); +968c969,970 +< storage_type tmp = 0; +--- +> storage_type tmp; +> memset(&tmp, 0, sizeof(tmp)); +983c985,986 +< storage_type tmp = 0; +--- +> storage_type tmp; +> memset(&tmp, 0, sizeof(tmp)); +997c1000,1002 +< storage_type expected_s = 0, desired_s = 0; +--- +> storage_type expected_s, desired_s; +> memset(&expected_s, 0, sizeof(expected_s)); +> memset(&desired_s, 0, sizeof(desired_s)); +1013c1018,1020 +< storage_type expected_s = 0, desired_s = 0; +--- +> storage_type expected_s, desired_s; +> memset(&expected_s, 0, sizeof(expected_s)); +> memset(&desired_s, 0, sizeof(desired_s)); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/ordered_index.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/ordered_index.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/ordered_index.hpp.patch (revision 27955) @@ -0,0 +1,4 @@ +270c270 +< reverse_iterator rbegin(){return make_reverse_iterator(end());} +--- +> reverse_iterator rbegin(){return boost::make_reverse_iterator(end());} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/reverse_iterator.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/reverse_iterator.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/reverse_iterator.hpp.patch (revision 27955) @@ -0,0 +1,4 @@ +64c64 +< return reverse_iterator(x); +--- +> return boost::reverse_iterator(x); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/user-config.jam.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/user-config.jam.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.55/user-config.jam.patch (revision 27955) @@ -0,0 +1,4 @@ +42c42 +< # using gcc ; +--- +> using darwin : std0x : "/usr/local/gfortran/bin/x86_64-apple-darwin10-g++" : -std=gnu++0x; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.73/boost/math/tools/user.hpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.73/boost/math/tools/user.hpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/configs/1.73/boost/math/tools/user.hpp (revision 27955) @@ -0,0 +1,105 @@ +// Copyright John Maddock 2007. +// Copyright Paul A. Bristow 2007. + +// Use, modification and distribution are subject to the +// Boost Software License, Version 1.0. +// (See accompanying file LICENSE_1_0.txt +// or copy at http://www.boost.org/LICENSE_1_0.txt) + +#ifndef BOOST_MATH_TOOLS_USER_HPP +#define BOOST_MATH_TOOLS_USER_HPP + +#ifdef _MSC_VER +#pragma once +#endif + +// This file can be modified by the user to change the default policies. +// See "Changing the Policy Defaults" in documentation. + +// define this if the platform has no long double functions, +// or if the long double versions have only double precision: +// +// #define BOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS +// +// Performance tuning options: +// +// #define BOOST_MATH_POLY_METHOD 3 +// #define BOOST_MATH_RATIONAL_METHOD 3 +// +// The maximum order of polynomial that will be evaluated +// via an unrolled specialisation: +// +// #define BOOST_MATH_MAX_POLY_ORDER 17 +// +// decide whether to store constants as integers or reals: +// +// #define BOOST_MATH_INT_TABLE_TYPE(RT, IT) IT + +// +// Default policies follow: +// +// Domain errors: +// +// #define BOOST_MATH_DOMAIN_ERROR_POLICY throw_on_error +// +// Pole errors: +// +// #define BOOST_MATH_POLE_ERROR_POLICY throw_on_error +// +// Overflow Errors: +// +// #define BOOST_MATH_OVERFLOW_ERROR_POLICY throw_on_error +// +// Internal Evaluation Errors: +// +// #define BOOST_MATH_EVALUATION_ERROR_POLICY throw_on_error +// +// Underflow: +// +// #define BOOST_MATH_UNDERFLOW_ERROR_POLICY ignore_error +// +// Denorms: +// +// #define BOOST_MATH_DENORM_ERROR_POLICY ignore_error +// +// Max digits to use for internal calculations: +// +// #define BOOST_MATH_DIGITS10_POLICY 0 +// +// Promote floats to doubles internally? +// +// #define BOOST_MATH_PROMOTE_FLOAT_POLICY true +// +// Promote doubles to long double internally: +// +#define BOOST_MATH_PROMOTE_DOUBLE_POLICY false +// +// What do discrete quantiles return? +// +// #define BOOST_MATH_DISCRETE_QUANTILE_POLICY integer_round_outwards +// +// If a function is mathematically undefined +// (for example the Cauchy distribution has no mean), +// then do we stop the code from compiling? +// +// #define BOOST_MATH_ASSERT_UNDEFINED_POLICY true +// +// Maximum series iterations permitted: +// +// #define BOOST_MATH_MAX_SERIES_ITERATION_POLICY 1000000 +// +// Maximum root finding steps permitted: +// +// define BOOST_MATH_MAX_ROOT_ITERATION_POLICY 200 +// +// Enable use of __float128 in numeric constants: +// +// #define BOOST_MATH_USE_FLOAT128 +// +// Disable use of __float128 in numeric_constants even if the compiler looks to support it: +// +// #define BOOST_MATH_DISABLE_FLOAT128 + +#endif // BOOST_MATH_TOOLS_USER_HPP + + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.49-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.49-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.49-linux.sh (revision 27955) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_49_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz' + +#Untar +tar -zxvf boost_1_49_0.tar.gz + +#Move boost into install directory +mv boost_1_49_0/* src +rm -rf boost_1_49_0 +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.49-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.49-macosx-snowleopard.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.49-macosx-snowleopard.sh (revision 27955) @@ -0,0 +1,35 @@ +#!/bin/bash + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_49_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz' + +#Untar +tar -zxvf boost_1_49_0.tar.gz + +#Move boost into install directory +mv boost_1_49_0/* src +rm -rf boost_1_49_0 +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +#./b2 address-model=32 architecture=x86 cxxflags="-arch i386" variant=release threading=multi install +./b2 toolset=darwin address-model=32 architecture=x86 variant=release threading=multi install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-discover.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-discover.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-discover.sh (revision 27955) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-linux-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-linux-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-linux-static.sh (revision 27955) @@ -0,0 +1,45 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_55_0" + +## Environment +# +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source into 'src' directory +mv boost_${VER}/* src/ +rm -rf boost_${VER} + +# Copy customized source and configuration files to 'src' directory +cp configs/1.55/boost/multi_index/ordered_index.hpp src/boost/multi_index + +# Configure +cd src +./bootstrap.sh \ + --prefix=${BOOST_ROOT}/install \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./bjam link=static install + +# Copy binary to install directory +mkdir ${BOOST_ROOT}/install/bin +cp bjam ${BOOST_ROOT}/install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-linux.sh (revision 27955) @@ -0,0 +1,45 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_55_0" + +## Environment +# +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source into 'src' directory +mv boost_${VER}/* src/ +rm -rf boost_${VER} + +# Copy customized source and configuration files to 'src' directory +cp configs/1.55/boost/multi_index/ordered_index.hpp src/boost/multi_index + +# Configure +cd src +./bootstrap.sh \ + --prefix=${BOOST_ROOT}/install \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./bjam install + +# Copy binary to install directory +mkdir ${BOOST_ROOT}/install/bin +cp bjam ${BOOST_ROOT}/install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-lonestar.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-lonestar.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-lonestar.sh (revision 27955) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch +patch src/boost/iterator/reverse_iterator.hpp ./configs/1.55/reverse_iterator.hpp.patch +patch src/boost/multi_index/ordered_index.hpp ./configs/1.55/ordered_index.hpp.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin + +cd ../ + +patch install/include/boost/multi_index/ordered_index.hpp ./configs/1.55/ordered_index.hpp.patch Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-mac-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-mac-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-mac-static.sh (revision 27955) @@ -0,0 +1,45 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_55_0" + +## Environment +# +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source into 'src' directory +mv boost_${VER}/* src/ +rm -rf boost_${VER} + +# Copy customized source and configuration files to 'src' directory +cp configs/1.55/boost/multi_index/ordered_index.hpp src/boost/multi_index + +# Configure +cd src +./bootstrap.sh \ + --prefix=${BOOST_ROOT}/install \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./bjam link=static install + +# Copy binary to install directory +mkdir ${BOOST_ROOT}/install/bin +cp bjam ${BOOST_ROOT}/install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-mac.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-mac.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-mac.sh (revision 27955) @@ -0,0 +1,57 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_55_0" + +## Environment +# +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source into 'src' directory +mv boost_${VER}/* src/ +rm -rf boost_${VER} + +# Copy customized source and configuration files to 'src' directory +cp configs/1.55/boost/multi_index/ordered_index.hpp src/boost/multi_index + +# Configure +cd src +./bootstrap.sh \ + --prefix=${BOOST_ROOT}/install \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./bjam install + +# Copy binary to install directory +mkdir ${BOOST_ROOT}/install/bin +cp bjam ${BOOST_ROOT}/install/bin + +# Set install_name for all shared libraries +cd ${BOOST_ROOT}/install/lib +for name in *.dylib; do + install_name_tool -id ${BOOST_ROOT}/install/lib/${name} ${name} +done + +## Patch install names for certain libraries +# +# TODO: Figure out how to reconfigure source to apply these install names at compile time +# +install_name_tool -change libboost_system.dylib ${BOOST_ROOT}/install/lib/libboost_system.dylib libboost_filesystem.dylib Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh (revision 27955) @@ -0,0 +1,47 @@ +#!/bin/bash +set -eu + +# NOTE: Stop after boostrap phase, and run +# +# bjam --debug-configuration +# +# to figure out which paths boost is using to include python. Make sure everyone +# of these paths is covered by python. If not, just make symlinks in +# externalpackages/python to what boost is expecting. There is NO WAY to get the +# boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +# export CC=/usr/local/gfortan/bin/gcc +# export CXX=/usr/local/gfortran/bin/g++ +./bjam toolset=darwin link=static runtime-link=static install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-el_capitan.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-el_capitan.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-el_capitan.sh (revision 27955) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +# export CC=/usr/local/gfortan/bin/gcc +# export CXX=/usr/local/gfortran/bin/g++ +./bjam toolset=darwin link=static install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-mavericks.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-mavericks.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-mavericks.sh (revision 27955) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +./bjam toolset=darwin-std0x link=static install + +#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-snowleopard.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-snowleopard.sh (revision 27955) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +./bjam toolset=darwin-std0x link=static install + +#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-yosemite.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-yosemite.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-macosx-yosemite.sh (revision 27955) @@ -0,0 +1,46 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +#./bjam toolset=darwin-std0x link=static install + +export CC=/usr/local/gfortan/bin/gcc +export CXX=/usr/local/gfortran/bin/g++ +./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 architecture=x86 variant=release link=static threading=multi install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-pleiades.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-pleiades.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-pleiades.sh (revision 27955) @@ -0,0 +1,43 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +export CXXFLAGS="-D_INTEL_LINUX_ -std=c++11" +export CFLAGS="-D_INTEL_LINUX_" + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch +# Copy customized source and configuration files to 'src' directory +cp configs/1.55/boost/multi_index/ordered_index.hpp src/boost/multi_index + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix=${BOOST_ROOT}/install \ + --with-python=python2.7 + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-stallo.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-stallo.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.55-stallo.sh (revision 27955) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch + +#Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost +#export PATH="/usr/bin":$PATH +export CXXFLAGS='-std=c++98' +export CC=mpicc +export CXX=mpicxx + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 + +#Compile boost +#./bjam install +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-linux-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-linux-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-linux-static.sh (revision 27955) @@ -0,0 +1,41 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source into 'src' directory +mv boost_${VER}/* src +rm -rf boost_${VER} + +# Configure +cd src +./bootstrap.sh \ + --prefix=${PREFIX} \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=static runtime-link=static + +# Remove any dynamic libraries that may have been compiled +# +# TODO: Reconfigure so that dynamic libraries are not compiled at all +# +rm -f $(find ${PREFIX}/lib -name *.so*) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-linux-valgrind.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 27955) @@ -0,0 +1,38 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source into 'src' directory +mv boost_${VER}/* src +rm -rf boost_${VER} + +# Copy customized source and configuration files to 'src' directory +cp ./configs/1.73/boost/math/tools/user.hpp ./src/boost/math/tools + +# Configure +cd src +./bootstrap.sh \ + --prefix=${PREFIX} \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=shared runtime-link=shared Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-linux.sh (revision 27955) @@ -0,0 +1,35 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source into 'src' directory +mv boost_${VER}/* src +rm -rf boost_${VER} + +# Configure +cd src +./bootstrap.sh \ + --prefix=${PREFIX} \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=shared runtime-link=shared Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-mac-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-mac-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-mac-static.sh (revision 27955) @@ -0,0 +1,45 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + +## Environment +# +export LDFLAGS="-Wl,-headerpad_max_install_names" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source into 'src' directory +mv boost_${VER}/* src +rm -rf boost_${VER} + +# Configure +cd src +./bootstrap.sh \ + --prefix=${PREFIX} \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=static runtime-link=static + +# Remove any dynamic libraries that may have been compiled +# +# TODO: Reconfigure so that dynamic libraries are not compiled at all +# +rm -f $(find ${PREFIX}/lib -name *.dylib) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-mac-valgrind.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-mac-valgrind.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-mac-valgrind.sh (revision 27955) @@ -0,0 +1,66 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + +## Environment +# +export LDFLAGS="-Wl,-headerpad_max_install_names" + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source into 'src' directory +mv boost_${VER}/* src +rm -rf boost_${VER} + +# Copy customized source and configuration files to 'src' directory +cp ./configs/1.73/boost/math/tools/user.hpp ./src/boost/math/tools + +# Configure +cd src +./bootstrap.sh \ + --prefix=${PREFIX} \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=shared runtime-link=shared + +# Set install_name for all shared libraries +# +# NOTE: The install_name_tool prints an error message on some installations, +# but this is not a shell error, and it does not seem to affect the +# Boost libraries called by ISSM. For now, we are simply redirecting the +# error to null. +# +# TODO: +# - Modify the source to apply absolute paths to the library ids so that +# patching it after the fact with install_name_tool is not necessary. +# +cd ${PREFIX}/lib +for name in *.dylib; do + install_name_tool -id ${PREFIX}/lib/${name} ${name} 2>/dev/null +done + +if [ "${VER}" == "1_79_0" ]; then + ## Patch install names for certain libraries + # + # TODO: Figure out how to reconfigure source to apply these install names at compile time + # + install_name_tool -change @rpath/libboost_atomic.dylib ${PREFIX}/lib/libboost_atomic.dylib libboost_filesystem.dylib +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-mac.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-mac.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/boost/install-1.7-mac.sh (revision 27955) @@ -0,0 +1,63 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + +## Environment +# +export LDFLAGS="-Wl,-headerpad_max_install_names" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source into 'src' directory +mv boost_${VER}/* src +rm -rf boost_${VER} + +# Configure +cd src +./bootstrap.sh \ + --prefix=${PREFIX} \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=shared runtime-link=shared + +# Set install_name for all shared libraries +# +# NOTE: The install_name_tool prints an error message on some installations, +# but this is not a shell error, and it does not seem to affect the +# Boost libraries called by ISSM. For now, we are simply redirecting the +# error to null. +# +# TODO: +# - Modify the source to apply absolute paths to the library ids so that +# patching it after the fact with install_name_tool is not necessary. +# +cd ${PREFIX}/lib +for name in *.dylib; do + install_name_tool -id ${PREFIX}/lib/${name} ${name} 2>/dev/null +done + +if [ "${VER}" == "1_79_0" ]; then + ## Patch install names for certain libraries + # + # TODO: Figure out how to reconfigure source to apply these install names at compile time + # + install_name_tool -change @rpath/libboost_atomic.dylib ${PREFIX}/lib/libboost_atomic.dylib libboost_filesystem.dylib +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/bsdtar/install-win7.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/bsdtar/install-win7.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/bsdtar/install-win7.sh (revision 27955) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src libarchive-3.0.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/libarchive-3.0.3.tar.gz' 'libarchive-3.0.3.tar.gz' + +#Untar +tar -zxvf libarchive-3.0.3.tar.gz + +#Move libarchive into src directory +mv libarchive-3.0.3/* src +rm -rf libarchive-3.0.3 + +cd src +./configure --prefix="$ISSM_DIR/externalpackages/bsdtar/install" +make +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/InterX.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/InterX.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/InterX.m (revision 27955) @@ -0,0 +1,82 @@ +function P = InterX(L1,varargin) +%INTERX Intersection of curves +% P = INTERX(L1,L2) returns the intersection points of two curves L1 +% and L2. The curves L1,L2 can be either closed or open and are described +% by two-row-matrices, where each row contains its x- and y- coordinates. +% The intersection of groups of curves (e.g. contour lines, multiply +% connected regions etc) can also be computed by separating them with a +% column of NaNs as for example +% +% L = [x11 x12 x13 ... NaN x21 x22 x23 ...; +% y11 y12 y13 ... NaN y21 y22 y23 ...] +% +% P has the same structure as L1 and L2, and its rows correspond to the +% x- and y- coordinates of the intersection points of L1 and L2. If no +% intersections are found, the returned P is empty. +% +% P = INTERX(L1) returns the self-intersection points of L1. To keep +% the code simple, the points at which the curve is tangent to itself are +% not included. P = INTERX(L1,L1) returns all the points of the curve +% together with any self-intersection points. +% +% Example: +% t = linspace(0,2*pi); +% r1 = sin(4*t)+2; x1 = r1.*cos(t); y1 = r1.*sin(t); +% r2 = sin(8*t)+2; x2 = r2.*cos(t); y2 = r2.*sin(t); +% P = InterX([x1;y1],[x2;y2]); +% plot(x1,y1,x2,y2,P(1,:),P(2,:),'ro') + +% Author : NS +% Version: 3.0, 21 Sept. 2010 + +% Two words about the algorithm: Most of the code is self-explanatory. +% The only trick lies in the calculation of C1 and C2. To be brief, this +% is essentially the two-dimensional analog of the condition that needs +% to be satisfied by a function F(x) that has a zero in the interval +% [a,b], namely +% F(a)*F(b) <= 0 +% C1 and C2 exactly do this for each segment of curves 1 and 2 +% respectively. If this condition is satisfied simultaneously for two +% segments then we know that they will cross at some point. +% Each factor of the 'C' arrays is essentially a matrix containing +% the numerators of the signed distances between points of one curve +% and line segments of the other. + + %...Argument checks and assignment of L2 + error(nargchk(1,2,nargin)); + if nargin == 1, + L2 = L1; hF = @lt; %...Avoid the inclusion of common points + else + L2 = varargin{1}; hF = @le; + end + + %...Preliminary stuff + x1 = L1(1,:)'; x2 = L2(1,:); + y1 = L1(2,:)'; y2 = L2(2,:); + dx1 = diff(x1); dy1 = diff(y1); + dx2 = diff(x2); dy2 = diff(y2); + + %...Determine 'signed distances' + S1 = dx1.*y1(1:end-1) - dy1.*x1(1:end-1); + S2 = dx2.*y2(1:end-1) - dy2.*x2(1:end-1); + + C1 = feval(hF,D(bsxfun(@times,dx1,y2)-bsxfun(@times,dy1,x2),S1),0); + C2 = feval(hF,D((bsxfun(@times,y1,dx2)-bsxfun(@times,x1,dy2))',S2'),0)'; + + %...Obtain the segments where an intersection is expected + [i,j] = find(C1 & C2); + if isempty(i),P = zeros(2,0);return; end; + + %...Transpose and prepare for output + i=i'; dx2=dx2'; dy2=dy2'; S2 = S2'; + L = dy2(j).*dx1(i) - dy1(i).*dx2(j); + i = i(L~=0); j=j(L~=0); L=L(L~=0); %...Avoid divisions by 0 + + %...Solve system of eqs to get the common points + P = unique([dx2(j).*S1(i) - dx1(i).*S2(j), ... + dy2(j).*S1(i) - dy1(i).*S2(j)]./[L L],'rows')'; + + function u = D(x,y) + u = bsxfun(@minus,x(:,1:end-1),y).*bsxfun(@minus,x(:,2:end),y); + end +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/license.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/license.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/license.txt (revision 27955) @@ -0,0 +1,25 @@ +Copyright (c) 2006, Antoni J. Canós +Copyright (c) 2008, Douglas M. Schwarz +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/licenseNS.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/licenseNS.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/licenseNS.txt (revision 27955) @@ -0,0 +1,24 @@ +Copyright (c) 2009, NS +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/selfintersect.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/selfintersect.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/canos/selfintersect.m (revision 27955) @@ -0,0 +1,174 @@ +function [x0,y0,segments]=selfintersect(x,y) + +%SELFINTERSECT Self-intersections of a curve. +% +% [X0,Y0,SEGMENTS] = SELFINTERSECT(X,Y) computes the locations where +% a curve self-intersects in a fast and robust way. +% The curve can be broken with NaNs or have vertical segments. +% Segments of the curve involved in each of the self-interesections are +% also provided. +% +% Vectors X and Y are equal-length vectors of at least four points defining +% the curve. +% X0 and Y0 are column vectors with the x- and y- coordinates, respectively +% of the N self-intersections. +% SEGMENTS is an N x 2 matrix containing the pairs of segments involved in +% each self-intersection. +% +% This program uses the theory of operation of the file "Fast and Robust Curve +% Intersections" submitted by Douglas M. Schwartz (intersections.m, F.Id: 11837). +% +% Example of use +% N=201; +% th=linspace(-3*pi,4*pi,N); +% R=1; +% x=R*cos(th)+linspace(0,6,N); +% y=R*sin(th)+linspace(0,1,N); +% t0=clock; +% [x0,y0,segments]=selfintersect(x,y) +% etime(clock,t0) +% plot(x,y,'b',x0,y0,'.r'); +% axis ('equal'); grid + +% +% See also INTERSECTIONS. +% +%Version: 1.0, December 11, 2006 +%Tested under MATLAB 6.5.0. R13. +% +% (c) Antoni J. Canos. +% ITACA. Techincal University of Valencia (Spain) +% Email: ancama2@dcom.upv.es + + +% Input checks. +error(nargchk(2,2,nargin)) +% x and y must be vectors with same number of points (at least 4 for self-intersection). +if sum(size(x) > 3) ~= 1 || sum(size(y) > 3) ~= 1 || ... + length(x) ~= length(y) + error('X and Y must be equal-length vectors of at least 4 points.') +end + +x0=[]; +y0=[]; +segments=[]; + +% Two similar curves are firstly created. +x1=x; x2=x; +y1=y; y2=y; + +x1 = x1(:); +y1 = y1(:); +x2 = x2(:); +y2 = y2(:); + +% Compute number of line segments in each curve and some differences we'll +% need later. +n1 = length(x1) - 1; +n2 = length(x2) - 1; + +dxy1 = diff([x1 y1]); +dxy2 = diff([x2 y2]); + +% Determine the combinations of i and j where the rectangle enclosing the +% i'th line segment of curve 1 overlaps with the rectangle enclosing the +% j'th line segment of curve 2. +[i,j] = find(repmat(min(x1(1:end-1),x1(2:end)),1,n2) <= ... + repmat(max(x2(1:end-1),x2(2:end)).',n1,1) & ... + repmat(max(x1(1:end-1),x1(2:end)),1,n2) >= ... + repmat(min(x2(1:end-1),x2(2:end)).',n1,1) & ... + repmat(min(y1(1:end-1),y1(2:end)),1,n2) <= ... + repmat(max(y2(1:end-1),y2(2:end)).',n1,1) & ... + repmat(max(y1(1:end-1),y1(2:end)),1,n2) >= ... + repmat(min(y2(1:end-1),y2(2:end)).',n1,1)); + +% Removing coincident and adjacent segments. +remove=find(abs(i-j)<2); +i(remove)=[]; +j(remove)=[]; + +% Removing duplicate combinations of segments. +remove=[]; +for ii=1:size(i,1) + ind=find((i(ii)==j(ii:end))&(j(ii)==i(ii:end))); + remove=[remove;ii-1+ind]; +end +i(remove)=[]; +j(remove)=[]; + +% Find segments pairs which have at least one vertex = NaN and remove them. +% This line is a fast way of finding such segment pairs. We take +% advantage of the fact that NaNs propagate through calculations, in +% particular subtraction (in the calculation of dxy1 and dxy2, which we +% need anyway) and addition. +remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2)); +i(remove) = []; +j(remove) = []; + +% Find segments pairs which have at least one vertex = NaN and remove them. +% This line is a fast way of finding such segment pairs. We take +% advantage of the fact that NaNs propagate through calculations, in +% particular subtraction (in the calculation of dxy1 and dxy2, which we +% need anyway) and addition. +remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2)); +i(remove) = []; +j(remove) = []; + +% Initialize matrices. We'll put the T's and B's in matrices and use them +% one column at a time. For some reason, the \ operation below is faster +% on my machine when A is sparse so we'll initialize a sparse matrix with +% the fixed values and then assign the changing values in the loop. +n = length(i); +T = zeros(4,n); +A = sparse([1 2 3 4],[3 3 4 4],-1,4,4,8); +B = -[x1(i) x2(j) y1(i) y2(j)].'; +index_dxy1 = [1 3]; % A(1) = A(1,1), A(3) = A(3,1) +index_dxy2 = [6 8]; % A(6) = A(2,2), A(8) = A(4,2) + +% Loop through possibilities. Set warning not to trigger for anomalous +% results (i.e., when A is singular). +warning_state = warning('off','MATLAB:singularMatrix'); +try + for k = 1:n + A(index_dxy1) = dxy1(i(k),:); + A(index_dxy2) = dxy2(j(k),:); + T(:,k) = A\B(:,k); + end + warning(warning_state) +catch + warning(warning_state) + rethrow(lasterror) +end + +% Find where t1 and t2 are between 0 and 1 and return the corresponding x0 +% and y0 values. Anomalous segment pairs can be segment pairs that are +% colinear (overlap) or the result of segments that are degenerate (end +% points the same). The algorithm will return an intersection point that +% is at the center of the overlapping region. Because of the finite +% precision of floating point arithmetic it is difficult to predict when +% two line segments will be considered to overlap exactly or even intersect +% at an end point. For this algorithm, an anomaly is detected when any +% element of the solution (a single column of T) is a NaN. + +in_range = T(1,:) >= 0 & T(2,:) >= 0 & T(1,:) < 1 & T(2,:) < 1; +anomalous = any(isnan(T)); +if any(anomalous) + ia = i(anomalous); + ja = j(anomalous); + % set x0 and y0 to middle of overlapping region. + T(3,anomalous) = (max(min(x1(ia),x1(ia+1)),min(x2(ja),x2(ja+1))) + ... + min(max(x1(ia),x1(ia+1)),max(x2(ja),x2(ja+1))))/2; + T(4,anomalous) = (max(min(y1(ia),y1(ia+1)),min(y2(ja),y2(ja+1))) + ... + min(max(y1(ia),y1(ia+1)),max(y2(ja),y2(ja+1))))/2; + x0 = T(3,in_range | anomalous).'; + y0 = T(4,in_range | anomalous).'; + i=i(in_range | anomalous); + j=j(in_range | anomalous); +else + x0 = T(3,in_range).'; + y0 = T(4,in_range).'; + i=i(in_range); + j=j(in_range); +end + +segments=sort([i,j],2); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cccl/install-win7.orig.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cccl/install-win7.orig.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cccl/install-win7.orig.sh (revision 27955) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install cccl-0.03 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/cccl-0.03.tar.gz' 'cccl-0.03.tar.gz' + +#Untar +tar -zxvf cccl-0.03.tar.gz + +#Move cccl into install directory +mv cccl-0.03/* src +rm -rf cccl-0.03 + +cd src + +#Compile +./configure --prefix="$ISSM_DIR/externalpackages/cccl/install" + +make +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cccl/install-win7.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cccl/install-win7.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cccl/install-win7.sh (revision 27955) @@ -0,0 +1,11 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src cccl-0.03 +mkdir install +mkdir install/bin + +#Move cccl into install directory +cp issm/cccl install/bin +chmod 755 install/bin/cccl Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cccl/issm/cccl =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cccl/issm/cccl (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cccl/issm/cccl (revision 27955) @@ -0,0 +1,113 @@ +#!/bin/sh + +# cccl +# Wrapper around MS's cl.exe and link.exe to make them act more like +# Unix cc and ld +# +# Copyright (C) 2000-2003 Geoffrey Wossum (gwossum@acm.org) +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your optsion) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. +# + +usage() +{ + cat < hypercube, d => d-dimensional mesh */ + int ndims_tot, /* total number of cube dimensions to divide */ + int mesh_dims[3], /* dimensions of mesh of processors */ + double *goal, /* desired set sizes for each set */ + int global_method, /* global partitioning algorithm */ + int local_method, /* local partitioning algorithm */ + int rqi_flag, /* should I use RQI/Symmlq eigensolver? */ + int vmax, /* how many vertices to coarsen down to? */ + int ndims, /* number of eigenvectors (2^d sets) */ + double eigtol, /* tolerance on eigenvectors */ + long seed); /* for random graph mutations */ + +extern "C" void read_params(FILE* pfile); /* file with new user parameters */ +extern "C" void smalloc_stats(void); +extern "C" double* smalloc(unsigned int n); /* number of bytes to be allocated */ + +#endif //ifndef _CHACO_INCLUDES_H_ + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco.patch (revision 27955) @@ -0,0 +1,572 @@ +Only in src/code/assign: assign.o +diff -rc src/code/assign/assign_out.c old/code/assign/assign_out.c +*** src/code/assign/assign_out.c 2010-07-16 16:28:47.352242454 -0700 +--- old/code/assign/assign_out.c 1995-08-08 14:32:10.000000000 -0700 +*************** +*** 3,9 **** + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include +- #include "defs.h" + + static void assign_out_normal(), assign_out_inv(); + +--- 3,8 ---- +Only in src/code/assign: assign_out.o +Only in src/code/assign: mapper.o +Only in src/code/assign: median.o +Only in src/code/assign: merge_assign.o +Only in src/code/assign: rec_median.o +Only in src/code/assign: rotate.o +Only in src/code/assign: y2x.o +Only in src/code/bpmatch: checkbp.o +Only in src/code/bpmatch: genvals2d.o +Only in src/code/bpmatch: genvals3d.o +Only in src/code/bpmatch: inits2d.o +Only in src/code/bpmatch: inits3d.o +Only in src/code/bpmatch: map2d.o +Only in src/code/bpmatch: map3d.o +Only in src/code/bpmatch: movevtxs.o +Only in src/code/bpmatch: sorts2d.o +Only in src/code/bpmatch: sorts3d.o +Only in src/code: chacominusblas.a +Only in src/code/coarsen: coarsen1.o +Only in src/code/coarsen: coarsen.o +Only in src/code/coarsen: interpolate.o +Only in src/code/coarsen: makeccoords.o +Only in src/code/coarsen: makefgraph.o +Only in src/code/coarsen: makev2cv.o +Only in src/code/coarsen: maxmatch1.o +Only in src/code/coarsen: maxmatch2.o +Only in src/code/coarsen: maxmatch3.o +Only in src/code/coarsen: maxmatch4.o +Only in src/code/coarsen: maxmatch5.o +Only in src/code/coarsen: maxmatch.o +Only in src/code/connect: add_edges.o +Only in src/code/connect: connected.o +Only in src/code/connect: find_edges.o +Only in src/code/eigen: bidir.o +Only in src/code/eigen: bisect.o +Only in src/code/eigen: checkeig_ext.o +Only in src/code/eigen: checkeig.o +Only in src/code/eigen: checkorth.o +Only in src/code/eigen: cksturmcnt.o +Only in src/code/eigen: eigensolve.o +diff -rc src/code/eigen/get_extval.c old/code/eigen/get_extval.c +*** src/code/eigen/get_extval.c 2010-07-16 16:28:47.353242463 -0700 +--- old/code/eigen/get_extval.c 1995-08-08 14:32:20.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Finds first extended eigenpair of system corresponding to + tridiagonal T using using Rafael's bisection technique. */ +--- 4,9 ---- +Only in src/code/eigen: get_extval.o +Only in src/code/eigen: get_ritzvals.o +Only in src/code/eigen: lanc_seconds.o +Only in src/code/eigen: lanczos_ext_float.o +Only in src/code/eigen: lanczos_ext.o +Only in src/code/eigen: lanczos_FO.o +Only in src/code/eigen: lanczos_SO_float.o +Only in src/code/eigen: lanczos_SO.o +Only in src/code/eigen: lanpause.o +Only in src/code/eigen: makeorthlnk.o +Only in src/code/eigen: mkeigvecs.o +Only in src/code/eigen: mkscanlist.o +Only in src/code/eigen: orthog1.o +Only in src/code/eigen: orthogonalize.o +Only in src/code/eigen: orthogvec.o +Only in src/code/eigen: ql.o +Only in src/code/eigen: rqi_ext.o +Only in src/code/eigen: rqi.o +Only in src/code/eigen: scale_diag.o +Only in src/code/eigen: scanmax.o +Only in src/code/eigen: scanmin.o +Only in src/code/eigen: solistout.o +Only in src/code/eigen: sorthog.o +Only in src/code/eigen: splarax.o +Only in src/code/eigen: sturmcnt.o +Only in src/code/eigen: Tevec.o +Only in src/code/eigen: tri_solve.o +Only in src/code/eigen: warnings.o +Only in src/code/graph: check_graph.o +Only in src/code/graph: free_graph.o +Only in src/code/graph: graph_out.o +Only in src/code/graph: reformat.o +Only in src/code/graph: subgraph.o +Only in src/code/inertial: eigenvec2.o +Only in src/code/inertial: eigenvec3.o +Only in src/code/inertial: inertial1d.o +Only in src/code/inertial: inertial2d.o +Only in src/code/inertial: inertial3d.o +Only in src/code/inertial: inertial.o +Only in src/code/inertial: make_subgeom.o +Only in src/code/input: check_input.o +Only in src/code/input: input_assign.o +Only in src/code/input: input_geom.o +Only in src/code/input: input_graph.o +Only in src/code/input: input.o +Only in src/code/input: read_params.o +Only in src/code/input: read_val.o +Only in src/code/input: reflect_input.o +Only in src/code/internal: check_internal.o +Only in src/code/internal: force_internal.o +Only in src/code/internal: improve_internal.o +Only in src/code/klspiff: bilistops.o +Only in src/code/klspiff: buckets1.o +Only in src/code/klspiff: buckets_bi.o +Only in src/code/klspiff: buckets.o +Only in src/code/klspiff: coarsen_kl.o +Only in src/code/klspiff: compress_ewgts.o +Only in src/code/klspiff: count_weights.o +Only in src/code/klspiff: kl_init.o +Only in src/code/klspiff: kl_output.o +Only in src/code/klspiff: klspiff.o +Only in src/code/klspiff: make_bndy_list.o +Only in src/code/klspiff: make_kl_list.o +Only in src/code/klspiff: nway_kl.o +Only in src/code/klvspiff: bpm_improve.o +Only in src/code/klvspiff: bucketsv.o +Only in src/code/klvspiff: clear_dvals.o +Only in src/code/klvspiff: coarsen_klv.o +Only in src/code/klvspiff: countup_vtx_sep.o +Only in src/code/klvspiff: find_bndy.o +Only in src/code/klvspiff: flatten.o +Only in src/code/klvspiff: flow.o +Only in src/code/klvspiff: klv_init.o +Only in src/code/klvspiff: klvspiff.o +Only in src/code/klvspiff: make_bpgraph.o +Only in src/code/klvspiff: make_sep_list.o +diff -rc src/code/klvspiff/matching.c old/code/klvspiff/matching.c +*** src/code/klvspiff/matching.c 2010-07-16 16:28:47.356242493 -0700 +--- old/code/klvspiff/matching.c 1996-03-11 10:24:25.000000000 -0800 +*************** +*** 6,12 **** + code provided by Ed Rothberg at SGI. */ + + #include +- #include "defs.h" + + #define TRUE 1 + #define FALSE 0 +--- 6,11 ---- +Only in src/code/klvspiff: matching.o +Only in src/code/klvspiff: nway_klv.o +diff -rc src/code/main/defs.h old/code/main/defs.h +*** src/code/main/defs.h 2010-07-16 16:28:47.359242522 -0700 +--- old/code/main/defs.h 1995-08-08 14:32:41.000000000 -0700 +*************** +*** 1,39 **** +! #ifndef _CHACO_DEFS_H_ +! #define _CHACO_DEFS_H_ +! + #define TRUE 1 + #define FALSE 0 + +! #ifndef _HAVE_CHACO_ //protect ISSM compilation. This symbol is defined when we compile ISSM +! +! #define max(A, B) ((A) > (B) ? (A) : (B)) +! #define min(A, B) ((A) < (B) ? (A) : (B)) +! #define sign(A) ((A) < 0 ? -1 : 1) +! #define absval(A) ((A) < 0 ? -(A): (A)) +! +! /* Define constants that are needed in various places */ +! #define PI 3.141592653589793 +! #define TWOPI 6.283185307179586 +! #define HALFPI 1.570796326794896 +! +! #define check_graph chaco_check_graph +! +! +! #ifdef MATLAB +! #include "mat.h" +! #include "mex.h" +! #include "matrix.h" +! +! #define printf mexPrintf +! #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +! #define malloc mxMalloc +! #define calloc mxCalloc +! #define realloc mxRealloc +! #define free mxFree +! #define exit(status) mexErrMsgTxt("exit=" #status) +! +! #endif +! +! #endif //#ifndef _HAVE_CHACO_ +! +! #endif //ifndef _CHACO_DEFS_H_ +--- 1,11 ---- +! #define max(A, B) ((A) > (B) ? (A) : (B)) +! #define min(A, B) ((A) < (B) ? (A) : (B)) +! #define sign(A) ((A) < 0 ? -1 : 1) +! #define absval(A) ((A) < 0 ? -(A): (A)) + #define TRUE 1 + #define FALSE 0 + +! /* Define constants that are needed in various places */ +! #define PI 3.141592653589793 +! #define TWOPI 6.283185307179586 +! #define HALFPI 1.570796326794896 +Only in src/code/main: interface.o +Only in src/code/main: main.o +diff -rc src/code/main/params.h old/code/main/params.h +*** src/code/main/params.h 2010-07-16 16:28:47.361242541 -0700 +--- old/code/main/params.h 1995-08-08 14:32:43.000000000 -0700 +*************** +*** 1,12 **** +- #ifndef _CHACO_PARAMS_H_ +- #define _CHACO_PARAMS_H_ +- +- + #define NAME_LENGTH 80 /* Maximum length of file name */ + #define LINE_LENGTH 200 /* Length of input files read at once */ + + #define MAXDIMS 3 /* Most cuts allowed at one time */ + #define MAXSETS 8 /* 2^MAXDIMS */ +- +- +- #endif //ifndef _CHACO_PARAMS_H_ +--- 1,5 ---- +Only in src/code/main: user_params.o +diff -rc src/code/Makefile old/code/Makefile +*** src/code/Makefile 2010-07-21 18:22:19.909939194 -0700 +--- old/code/Makefile 1997-10-02 10:23:22.000000000 -0700 +*************** +*** 2,18 **** + DEST= ${DEST_DIR}/chaco + CC = gcc + IFLAG = -Imain +! #IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include +! #CFLAGS = -O2 +! #OFLAGS = -O2 +! #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +! CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g +! #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +! OFLAGS = -O2 +! #AR = /usr/ccs/bin/ar rcv # for solaris 2 +! AR = /usr/bin/ar rcv +! #RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +! RANLIB = /usr/bin/ranlib + + FILES.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ +--- 2,9 ---- + DEST= ${DEST_DIR}/chaco + CC = gcc + IFLAG = -Imain +! CFLAGS = -O2 +! OFLAGS = -O2 + + FILES.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ +*************** +*** 96,196 **** + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + +- +- FILESMINUSBLAS.c= main/user_params.c main/interface.c main/main.c \ +- submain/balance.c submain/divide.c submain/submain.c \ +- input/input_assign.c \ +- input/check_input.c input/input.c input/input_geom.c \ +- input/input_graph.c input/read_params.c input/reflect_input.c \ +- input/read_val.c \ +- graph/check_graph.c graph/free_graph.c \ +- graph/reformat.c graph/subgraph.c graph/graph_out.c \ +- inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \ +- inertial/inertial1d.c inertial/inertial2d.c \ +- inertial/inertial3d.c inertial/make_subgeom.c \ +- klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \ +- klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \ +- klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \ +- klspiff/klspiff.c klspiff/make_bndy_list.c \ +- klspiff/make_kl_list.c klspiff/nway_kl.c \ +- klvspiff/bpm_improve.c klvspiff/bucketsv.c \ +- klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \ +- klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \ +- klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \ +- klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \ +- klvspiff/flatten.c \ +- coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \ +- coarsen/makeccoords.c \ +- coarsen/coarsen1.c coarsen/makev2cv.c \ +- coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \ +- coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \ +- connect/add_edges.c connect/connected.c connect/find_edges.c \ +- eigen/bidir.c eigen/bisect.c eigen/checkeig.c \ +- eigen/checkeig_ext.c \ +- eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\ +- eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \ +- eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \ +- eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\ +- eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \ +- eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \ +- eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \ +- eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \ +- eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \ +- eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \ +- symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \ +- symmlq/symmlq.c \ +- tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \ +- optimize/determinant.c optimize/func2d.c \ +- optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \ +- assign/assign.c assign/assign_out.c assign/mapper.c \ +- assign/median.c assign/merge_assign.c \ +- assign/rec_median.c assign/rotate.c assign/y2x.c \ +- bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \ +- bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \ +- bpmatch/map3d.c bpmatch/movevtxs.c \ +- bpmatch/sorts2d.c bpmatch/sorts3d.c \ +- refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \ +- refine_map/refine_cube.c refine_map/update_cube_edata.c \ +- refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \ +- refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \ +- refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \ +- refine_map/init_mesh_edata.c refine_map/refine_mesh.c \ +- refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \ +- refine_map/refine_map.c refine_map/make_comm_graph.c \ +- refine_part/refine_part.c refine_part/kl_refine.c \ +- refine_part/make_maps_ref.c refine_part/make_terms_ref.c \ +- internal/force_internal.c internal/improve_internal.c \ +- internal/check_internal.c \ +- misc/define_subcubes.c misc/define_submeshes.c \ +- misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \ +- misc/count.c misc/countup.c misc/countup_cube.c \ +- misc/countup_mesh.c misc/make_subgoal.c \ +- misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \ +- misc/sequence.c misc/perturb.c misc/simple_part.c \ +- misc/time_kernels.c misc/timing.c \ +- util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \ +- util/checkpnt.c util/cpvec.c util/dot.c \ +- util/doubleout.c util/input_int.c util/gray.c \ +- util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \ +- util/normalize.c util/mergesort.c \ +- util/randomize.c util/smalloc.c util/bail.c \ +- util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \ +- util/strout.c util/tri_prod.c util/true_or_false.c \ +- util/update.c util/vecout.c util/vecran.c \ +- util/vecscale.c +- + FILES.o= $(FILES.c:.c=.o) +- FILESMINUSBLAS.o= $(FILESMINUSBLAS.c:.c=.o) +- +- +- ${DEST}: ${FILES.c} chaco.a Makefile +- ${CC} ${OFLAGS} chaco.a -lm -o ${DEST} + +- chaco.a: ${FILES.o} +- ${AR} chaco.a ${FILES.o} ; ${RANLIB} chaco.a + +! chacominusblas.a: ${FILESMINUSBLAS.o} +! ${AR} chacominusblas.a ${FILESMINUSBLAS.o} ; ${RANLIB} chacominusblas.a + + lint: + lint ${IFLAG} ${FILES.c} -lm +--- 87,97 ---- + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + + FILES.o= $(FILES.c:.c=.o) + + +! ${DEST}: ${FILES.o} Makefile +! ${CC} ${OFLAGS} ${FILES.o} -lm -o ${DEST} + + lint: + lint ${IFLAG} ${FILES.c} -lm +Only in src/code/misc: count.o +Only in src/code/misc: countup_cube.o +Only in src/code/misc: countup_mesh.o +Only in src/code/misc: countup.o +Only in src/code/misc: define_subcubes.o +Only in src/code/misc: define_submeshes.o +Only in src/code/misc: divide_procs.o +Only in src/code/misc: find_maxdeg.o +Only in src/code/misc: make_maps.o +Only in src/code/misc: make_setlists.o +Only in src/code/misc: make_subgoal.o +Only in src/code/misc: make_term_props.o +Only in src/code/misc: merge_goals.o +Only in src/code/misc: perturb.o +Only in src/code/misc: sequence.o +Only in src/code/misc: simple_part.o +Only in src/code/misc: time_kernels.o +diff -rc src/code/misc/timing.c old/code/misc/timing.c +*** src/code/misc/timing.c 2010-07-16 16:28:47.366242590 -0700 +--- old/code/misc/timing.c 1997-01-03 09:10:52.000000000 -0800 +*************** +*** 3,9 **** + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include +- #include "defs.h" + + /* Timing parameters. */ + +--- 3,8 ---- +Only in src/code/misc: timing.o +Only in src/code/optimize: determinant.o +Only in src/code/optimize: func2d.o +Only in src/code/optimize: func3d.o +Only in src/code/optimize: opt2d.o +Only in src/code/optimize: opt3d.o +Only in src/code/refine_map: compute_cube_edata.o +Only in src/code/refine_map: compute_cube_vdata.o +Only in src/code/refine_map: compute_mesh_edata.o +Only in src/code/refine_map: compute_mesh_vdata.o +Only in src/code/refine_map: find_edge_cube.o +Only in src/code/refine_map: find_edge_mesh.o +Only in src/code/refine_map: init_cube_edata.o +Only in src/code/refine_map: init_mesh_edata.o +Only in src/code/refine_map: make_comm_graph.o +Only in src/code/refine_map: refine_cube.o +Only in src/code/refine_map: refine_map.o +Only in src/code/refine_map: refine_mesh.o +Only in src/code/refine_map: update_cube_edata.o +Only in src/code/refine_map: update_cube_vdata.o +Only in src/code/refine_map: update_mesh_edata.o +Only in src/code/refine_map: update_mesh_vdata.o +Only in src/code/refine_part: kl_refine.o +Only in src/code/refine_part: make_maps_ref.o +Only in src/code/refine_part: make_terms_ref.o +Only in src/code/refine_part: refine_part.o +Only in src/code/submain: balance.o +Only in src/code/submain: divide.o +Only in src/code/submain: submain.o +Only in src/code/symmlq: aprod.o +Only in src/code/symmlq: msolve.o +Only in src/code/symmlq: pow_dd.o +diff -rc src/code/symmlq/symmlqblas.f old/code/symmlq/symmlqblas.f +*** src/code/symmlq/symmlqblas.f 2010-07-21 18:09:10.370123273 -0700 +--- old/code/symmlq/symmlqblas.f 2010-07-21 14:02:09.633743650 -0700 +*************** +*** 16,22 **** + c uses unrolled loops for increments equal to one. + c jack dongarra, linpack, 3/11/78. + c +! double precision dx(1),dy(1),da + integer i,incx,incy,ix,iy,m,mp1,n + c + if(n.le.0)return +--- 16,22 ---- + c uses unrolled loops for increments equal to one. + c jack dongarra, linpack, 3/11/78. + c +! double precision dx(*),dy(*),da + integer i,incx,incy,ix,iy,m,mp1,n + c + if(n.le.0)return +Only in src/code/symmlq: symmlqblas.o +Only in src/code/symmlq: symmlq.o +Only in src/code/tinvit: epslon.o +Only in src/code/tinvit: pythag.o +Only in src/code/tinvit: tinvit.o +Only in src/code/util: affirm.o +Only in src/code/util: array_alloc_2D.o +diff -rc src/code/util/bail.c old/code/util/bail.c +*** src/code/util/bail.c 2010-07-16 16:28:47.368242609 -0700 +--- old/code/util/bail.c 1995-08-08 14:33:01.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Wrapper for exit() - print message and exit with status code. Exit code + of 0 indicates normal termination. Exit code of 1 indicates early +--- 4,9 ---- +*************** +*** 15,20 **** +--- 14,20 ---- + int status; + { + extern FILE *Output_File; /* Output file or NULL */ ++ void exit(); + + if (msg != NULL && (int) strlen(msg) > 0) { + printf("%s\n", msg); +Only in src/code/util: bail.o +Only in src/code/util: bit_reverse.o +diff -rc src/code/util/checkpnt.c old/code/util/checkpnt.c +*** src/code/util/checkpnt.c 2010-07-16 16:28:47.370242629 -0700 +--- old/code/util/checkpnt.c 1995-08-08 14:33:01.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Debug break point. */ + void checkpnt(tag) +--- 4,9 ---- +Only in src/code/util: checkpnt.o +Only in src/code/util: cpvec.o +Only in src/code/util: dot.o +diff -rc src/code/util/doubleout.c old/code/util/doubleout.c +*** src/code/util/doubleout.c 2010-07-16 16:28:47.372242648 -0700 +--- old/code/util/doubleout.c 1995-08-08 14:33:02.000000000 -0700 +*************** +*** 3,9 **** + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include +- #include "defs.h" + + /* Print a double precision number with filtering format to screen. */ + void doubleout(number, mode) +--- 3,8 ---- +Only in src/code/util: doubleout.o +Only in src/code/util: gray.o +Only in src/code/util: input_int.o +Only in src/code/util: machine_params.o +Only in src/code/util: makevwsqrt.o +Only in src/code/util: mergesort.o +Only in src/code/util: mkvec.o +Only in src/code/util: normalize.o +Only in src/code/util: norm.o +Only in src/code/util: randomize.o +Only in src/code/util: scadd.o +Only in src/code/util: seconds.o +Only in src/code/util: setvec.o +Only in src/code/util: shell_sort.o +diff -rc src/code/util/smalloc.c old/code/util/smalloc.c +*** src/code/util/smalloc.c 2010-07-16 16:28:47.375242677 -0700 +--- old/code/util/smalloc.c 1996-03-11 10:44:07.000000000 -0800 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + static int nmalloc = 0; /* number of calls to malloc */ + static int nfree = 0; /* number of calls to free */ +--- 4,9 ---- +Only in src/code/util: smalloc.o +diff -rc src/code/util/strout.c old/code/util/strout.c +*** src/code/util/strout.c 2010-07-16 16:28:47.377242697 -0700 +--- old/code/util/strout.c 1995-08-08 14:33:05.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Wrapper for a printf statement with a string as only arg. + Prints to screen and to output file if there is one. */ +--- 4,9 ---- +Only in src/code/util: strout.o +Only in src/code/util: tri_prod.o +Only in src/code/util: true_or_false.o +Only in src/code/util: update.o +Only in src/code/util: vecout.o +Only in src/code/util: vecran.o +Only in src/code/util: vecscale.o Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco_README.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco_README.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco_README.txt (revision 27955) @@ -0,0 +1,55 @@ +Chaco-2.2.tar (5/03/00? -- 2.0 was 2/95) +http://www.sandia.gov/~bahendr/chaco.html + + +Note that meshpart pulls the object files from here, compiled with +the MATLAB flag for use in the mlchaco mex function, and assembles +them into a library in its own directory. This means that any +objects compiled for the mlchaco mex function and left here should +not be used for the stand-alone chaco executable, and vice versa. + + +[jschierm@astrid main]$ diff defs_old.h defs.h +11a12,27 [for running as a matlab mex function] +> +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> +> #define check_graph chaco_check_graph +> #endif +> + + +added #include "defs.h" to the following: +assign/assign_out.c +eigen/get_extval.c +klvspiff/matching.c +misc/timing.c +util/bail.c +util/checkpnt.c +util/doubleout.c +util/smalloc.c +util/strout.c + + +[jschierm@astrid code]$ diff Makefile_old Makefile +4,5c4,9 [fPIC required, CFLAGS and OFLAGS copied from Cielo gccopts_v75.sh for glnxa64] +< IFLAG = -Imain +< CFLAGS = -O2 +--- +> IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include +> #CFLAGS = -O2 +> #OFLAGS = -O2 +> #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +> CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +> #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco_jes_notes.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco_jes_notes.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco_jes_notes.txt (revision 27955) @@ -0,0 +1,86 @@ +7/13/09: + +[jschierm@astrid Chaco-2.2]$ diff ../chaco/code/Makefile code +5,6c5,8 [fPIC required, CFLAGS and OFLAGS copied from Cielo gccopts_v75.sh for glnxa64] +< CFLAGS = -O2 +< OFLAGS = -O2 +--- +> #CFLAGS = -O2 +> #OFLAGS = -O2 +> CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +> OFLAGS = -O -DNDEBUG +34a37,38 [added for meshpart chaco.a library, specified by its makefile] +> coarsen/makecgraph.c \ +> coarsen/countcedges.c \ + +7/30/09: + +[jschierm@astrid main]$ diff defs_old.h defs.h +11a12,26 [for running as a matlab mex function] +> +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> +> #define check_graph chaco_check_graph +> #endif +> + +added #include "defs.h" to the following: +assign/assign_out.c +eigen/get_extval.c +klvspiff/matching.c +misc/timing.c +util/bail.c +util/checkpnt.c +util/doubleout.c +util/smalloc.c +util/strout.c + +[jschierm@astrid code]$ diff Makefile_old Makefile | more +4,5c4,9 +< IFLAG = -Imain +< CFLAGS = -O2 +--- +> IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include +> #CFLAGS = -O2 +> #OFLAGS = -O2 +> #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread +> -fexceptions +> CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +> #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions + +8/25/09: + +added macro for fprintf to capture missing output: +[jschierm@astrid main]$ diff defs_old.h defs.h +11a12,27 +> +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> +> #define check_graph chaco_check_graph +> #endif +> + +6/15/10: + +- moved check_graph rename outside of MATLAB compiler directive. +- created library chaco.a (without MATLAB compiler directive) for Chaco x-layer to link and implemented it in chaco stand-alone link. + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco_njs_notes.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco_njs_notes.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/chaco_njs_notes.txt (revision 27955) @@ -0,0 +1,8 @@ +chaco build must be able to see malloc.h +sudo ln -s /usr/include/malloc/malloc.h /usr/include/malloc.h +or else make sure you include the malloc directory in path + +if on sierra, you must download a version of malloc.h - +one can be found here: http://web.mit.edu/jhawk/mnt/spo/phone-project/include/malloc.h +place this file in /usr/local/include/, and run the sierra install script + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/mac/code/util/smalloc.c.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/mac/code/util/smalloc.c.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/mac/code/util/smalloc.c.patch (revision 27955) @@ -0,0 +1,4 @@ +6c6 +< #include +--- +> #include Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/Makefile =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/Makefile (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/Makefile (revision 27955) @@ -0,0 +1,202 @@ +DEST_DIR = ../exec +DEST= ${DEST_DIR}/chaco +CC = gcc +IFLAG = -Imain -I/mingw64/x86_64-w64-mingw32/include +CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -Wno-implicit-function-declaration -D_MSYS2_ +OFLAGS = -O2 +#AR = /usr/ccs/bin/ar rcv # for solaris 2 +#AR = /usr/bin/ar rcv +AR = ar cr +#RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +#RANLIB = /usr/bin/ranlib +RANLIB = ranlib + +FILES.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ + input/input_assign.c \ + input/check_input.c input/input.c input/input_geom.c \ + input/input_graph.c input/read_params.c input/reflect_input.c \ + input/read_val.c \ + graph/check_graph.c graph/free_graph.c \ + graph/reformat.c graph/subgraph.c graph/graph_out.c \ + inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \ + inertial/inertial1d.c inertial/inertial2d.c \ + inertial/inertial3d.c inertial/make_subgeom.c \ + klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \ + klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \ + klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \ + klspiff/klspiff.c klspiff/make_bndy_list.c \ + klspiff/make_kl_list.c klspiff/nway_kl.c \ + klvspiff/bpm_improve.c klvspiff/bucketsv.c \ + klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \ + klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \ + klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \ + klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \ + klvspiff/flatten.c \ + coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \ + coarsen/makeccoords.c \ + coarsen/coarsen1.c coarsen/makev2cv.c \ + coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \ + coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \ + connect/add_edges.c connect/connected.c connect/find_edges.c \ + eigen/bidir.c eigen/bisect.c eigen/checkeig.c \ + eigen/checkeig_ext.c \ + eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\ + eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \ + eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \ + eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\ + eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \ + eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \ + eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \ + eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \ + eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \ + eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \ + symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \ + symmlq/symmlq.c symmlq/symmlqblas.c \ + tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \ + optimize/determinant.c optimize/func2d.c \ + optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \ + assign/assign.c assign/assign_out.c assign/mapper.c \ + assign/median.c assign/merge_assign.c \ + assign/rec_median.c assign/rotate.c assign/y2x.c \ + bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \ + bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \ + bpmatch/map3d.c bpmatch/movevtxs.c \ + bpmatch/sorts2d.c bpmatch/sorts3d.c \ + refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \ + refine_map/refine_cube.c refine_map/update_cube_edata.c \ + refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \ + refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \ + refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \ + refine_map/init_mesh_edata.c refine_map/refine_mesh.c \ + refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \ + refine_map/refine_map.c refine_map/make_comm_graph.c \ + refine_part/refine_part.c refine_part/kl_refine.c \ + refine_part/make_maps_ref.c refine_part/make_terms_ref.c \ + internal/force_internal.c internal/improve_internal.c \ + internal/check_internal.c \ + misc/define_subcubes.c misc/define_submeshes.c \ + misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \ + misc/count.c misc/countup.c misc/countup_cube.c \ + misc/countup_mesh.c misc/make_subgoal.c \ + misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \ + misc/sequence.c misc/perturb.c misc/simple_part.c \ + misc/time_kernels.c misc/timing.c \ + util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \ + util/checkpnt.c util/cpvec.c util/dot.c \ + util/doubleout.c util/input_int.c util/gray.c \ + util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \ + util/normalize.c util/mergesort.c \ + util/randomize.c util/smalloc.c util/bail.c \ + util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \ + util/strout.c util/tri_prod.c util/true_or_false.c \ + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + + +FILESMINUSBLAS.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ + input/input_assign.c \ + input/check_input.c input/input.c input/input_geom.c \ + input/input_graph.c input/read_params.c input/reflect_input.c \ + input/read_val.c \ + graph/check_graph.c graph/free_graph.c \ + graph/reformat.c graph/subgraph.c graph/graph_out.c \ + inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \ + inertial/inertial1d.c inertial/inertial2d.c \ + inertial/inertial3d.c inertial/make_subgeom.c \ + klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \ + klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \ + klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \ + klspiff/klspiff.c klspiff/make_bndy_list.c \ + klspiff/make_kl_list.c klspiff/nway_kl.c \ + klvspiff/bpm_improve.c klvspiff/bucketsv.c \ + klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \ + klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \ + klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \ + klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \ + klvspiff/flatten.c \ + coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \ + coarsen/makeccoords.c \ + coarsen/coarsen1.c coarsen/makev2cv.c \ + coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \ + coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \ + connect/add_edges.c connect/connected.c connect/find_edges.c \ + eigen/bidir.c eigen/bisect.c eigen/checkeig.c \ + eigen/checkeig_ext.c \ + eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\ + eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \ + eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \ + eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\ + eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \ + eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \ + eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \ + eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \ + eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \ + eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \ + symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \ + symmlq/symmlq.c \ + tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \ + optimize/determinant.c optimize/func2d.c \ + optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \ + assign/assign.c assign/assign_out.c assign/mapper.c \ + assign/median.c assign/merge_assign.c \ + assign/rec_median.c assign/rotate.c assign/y2x.c \ + bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \ + bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \ + bpmatch/map3d.c bpmatch/movevtxs.c \ + bpmatch/sorts2d.c bpmatch/sorts3d.c \ + refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \ + refine_map/refine_cube.c refine_map/update_cube_edata.c \ + refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \ + refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \ + refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \ + refine_map/init_mesh_edata.c refine_map/refine_mesh.c \ + refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \ + refine_map/refine_map.c refine_map/make_comm_graph.c \ + refine_part/refine_part.c refine_part/kl_refine.c \ + refine_part/make_maps_ref.c refine_part/make_terms_ref.c \ + internal/force_internal.c internal/improve_internal.c \ + internal/check_internal.c \ + misc/define_subcubes.c misc/define_submeshes.c \ + misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \ + misc/count.c misc/countup.c misc/countup_cube.c \ + misc/countup_mesh.c misc/make_subgoal.c \ + misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \ + misc/sequence.c misc/perturb.c misc/simple_part.c \ + misc/time_kernels.c misc/timing.c \ + util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \ + util/checkpnt.c util/cpvec.c util/dot.c \ + util/doubleout.c util/input_int.c util/gray.c \ + util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \ + util/normalize.c util/mergesort.c \ + util/randomize.c util/smalloc.c util/bail.c \ + util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \ + util/strout.c util/tri_prod.c util/true_or_false.c \ + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + +FILES.o= $(FILES.c:.c=.o) +FILESMINUSBLAS.o= $(FILESMINUSBLAS.c:.c=.o) + + +${DEST}: ${FILES.c} chaco.a Makefile + ${CC} ${OFLAGS} chaco.a -lm -o ${DEST} + +chaco.a: ${FILES.o} + ${AR} $@ ${FILES.o} ; ${RANLIB} $@ + +chacominusblas.a: ${FILESMINUSBLAS.o} + ${AR} $@ ${FILESMINUSBLAS.o} ; ${RANLIB} $@ + +lint: + lint ${IFLAG} ${FILES.c} -lm + +alint: + alint ${IFLAG} ${FILES.c} -lm + +clean: + rm -f */*.o ${DEST_DIR}/core + +.c.o: + ${CC} -c ${IFLAG} ${CFLAGS} -o $*.o $*.c Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/main/interface.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/main/interface.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/main/interface.c (revision 27955) @@ -0,0 +1,234 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#include +#include "defs.h" +#include "structs.h" + +int Using_Main = FALSE; /* Is main routine being called? */ + +int interface(nvtxs, start, adjacency, vwgts, ewgts, x, y, z, + outassignname, outfilename, + assignment, + architecture, ndims_tot, mesh_dims, goal, + global_method, local_method, rqi_flag, vmax, ndims, + eigtol, seed) +int nvtxs; /* number of vertices in full graph */ +int *start; /* start of edge list for each vertex */ +int *adjacency; /* edge list data */ +int *vwgts; /* weights for all vertices */ +float *ewgts; /* weights for all edges */ +float *x, *y, *z; /* coordinates for inertial method */ +char *outassignname; /* name of assignment output file */ +char *outfilename; /* output file name */ +short *assignment; /* set number of each vtx (length n) */ +int architecture; /* 0 => hypercube, d => d-dimensional mesh */ +int ndims_tot; /* total number of cube dimensions to divide */ +int mesh_dims[3]; /* dimensions of mesh of processors */ +double *goal; /* desired set sizes for each set */ +int global_method; /* global partitioning algorithm */ +int local_method; /* local partitioning algorithm */ +int rqi_flag; /* should I use RQI/Symmlq eigensolver? */ +int vmax; /* how many vertices to coarsen down to? */ +int ndims; /* number of eigenvectors (2^d sets) */ +double eigtol; /* tolerance on eigenvectors */ +long seed; /* for random graph mutations */ +{ + extern char *PARAMS_FILENAME; /* name of file with parameter updates */ + extern int MAKE_VWGTS; /* make vertex weights equal to degrees? */ + extern int MATCH_TYPE; /* matching routine to use */ + extern int FREE_GRAPH; /* free graph data structure after reformat? */ + extern int DEBUG_PARAMS; /* debug flag for reading parameters */ + extern int DEBUG_TRACE; /* trace main execution path */ + extern double start_time; /* time routine is entered */ + extern double reformat_time;/* time spent reformatting graph */ + FILE *params_file; /* file for reading new parameters */ + struct vtx_data **graph; /* graph data structure */ + double vwgt_sum; /* sum of vertex weights */ + double time; /* timing variable */ + float **coords; /* coordinates for vertices if used */ + int *vptr; /* loops through vertex weights */ + int flag; /* return code from balance */ + int nedges; /* number of edges in graph */ + int using_vwgts; /* are vertex weights being used? */ + int using_ewgts; /* are edge weights being used? */ + int nsets_tot; /* total number of sets being created */ + int igeom; /* geometric dimension for inertial method */ + int default_goal; /* using default goals? */ + int i; /* loop counter */ + double seconds(); + double *smalloc_ret(); + int sfree(), submain(), reformat(); + void free_graph(), read_params(), strout(); + + if (DEBUG_TRACE > 0) { + printf("\n"); + } + + flag = 0; + graph = NULL; + coords = NULL; + + if (!Using_Main) { /* If not using main, need to read parameters file. */ + start_time = seconds(); + params_file = fopen(PARAMS_FILENAME, "r"); + if (params_file == NULL && DEBUG_PARAMS > 1) { + printf("Parameter file `%s' not found; using default parameters.\n", + PARAMS_FILENAME); + } + read_params(params_file); + } + + if (goal == NULL) { /* If not passed in, default goals have equal set sizes. */ + default_goal = TRUE; + if (architecture == 0) + nsets_tot = 1 << ndims_tot; + else if (architecture == 1) + nsets_tot = mesh_dims[0]; + else if (architecture == 2) + nsets_tot = mesh_dims[0] * mesh_dims[1]; + else if (architecture > 2) + nsets_tot = mesh_dims[0] * mesh_dims[1] * mesh_dims[2]; + + if (MAKE_VWGTS && start != NULL) { + vwgt_sum = start[nvtxs] - start[0] + nvtxs; + } + else if (vwgts == NULL) { + vwgt_sum = nvtxs; + } + else { + vwgt_sum = 0; + vptr = vwgts; + for (i = nvtxs; i; i--) + vwgt_sum += *(vptr++); + } + + vwgt_sum /= nsets_tot; + goal = (double *) smalloc_ret((unsigned) nsets_tot * sizeof(double)); + if (goal == NULL) { + strout("\nERROR: No room to make goals.\n"); + flag = 1; + goto skip; + } + for (i = 0; i < nsets_tot; i++) + goal[i] = vwgt_sum; + } + else { + default_goal = FALSE; + } + + if (MAKE_VWGTS) { + /* Generate vertex weights equal to degree of node. */ + if (vwgts != NULL) { + strout("WARNING: Vertex weights being overwritten by vertex degrees."); + } + vwgts = (int *) smalloc_ret((unsigned) nvtxs * sizeof(int)); + if (vwgts == NULL) { + strout("\nERROR: No room to make vertex weights.\n"); + flag = 1; + goto skip; + } + if (start != NULL) { + for (i = 0; i < nvtxs; i++) + vwgts[i] = 1 + start[i + 1] - start[i]; + } + else { + for (i = 0; i < nvtxs; i++) + vwgts[i] = 1; + } + } + + using_vwgts = (vwgts != NULL); + using_ewgts = (ewgts != NULL); + + if (start != NULL || vwgts != NULL) { /* Reformat into our data structure. */ + time = seconds(); + flag = reformat(start, adjacency, nvtxs, &nedges, vwgts, ewgts, &graph); + + if (flag) { + strout("\nERROR: No room to reformat graph.\n"); + goto skip; + } + + reformat_time += seconds() - time; + } + else { + nedges = 0; + } + + if (FREE_GRAPH) { /* Free old graph data structures. */ + sfree((char *) start); + sfree((char *) adjacency); + if (vwgts != NULL) + sfree((char *) vwgts); + if (ewgts != NULL) + sfree((char *) ewgts); + start = NULL; + adjacency = NULL; + vwgts = NULL; + ewgts = NULL; + } + + + if (global_method == 3 || + (MATCH_TYPE == 5 && (global_method == 1 || + (global_method == 2 && rqi_flag)))) { + if (x == NULL) { + igeom = 0; + } + else { /* Set up coordinate data structure. */ + coords = (float **) smalloc_ret((unsigned) 3 * sizeof(float *)); + if (coords == NULL) { + strout("\nERROR: No room to make coordinate array.\n"); + flag = 1; + goto skip; + } + /* Minus 1's are to allow remainder of program to index with 1. */ + coords[0] = x - 1; + igeom = 1; + if (y != NULL) { + coords[1] = y - 1; + igeom = 2; + if (z != NULL) { + coords[2] = z - 1; + igeom = 3; + } + } + } + } + else { + igeom = 0; + } + + /* Subtract from assignment to allow code to index from 1. */ + assignment = assignment - 1; + flag = submain(graph, nvtxs, nedges, using_vwgts, using_ewgts, igeom, coords, + outassignname, outfilename, + assignment, goal, + architecture, ndims_tot, mesh_dims, + global_method, local_method, rqi_flag, vmax, ndims, + eigtol, seed); + +skip: + if (coords != NULL) + sfree((char *) coords); + + if (default_goal) + sfree((char *) goal); + + if (graph != NULL) + free_graph(graph); + + if (flag && FREE_GRAPH) { + sfree((char *) start); + sfree((char *) adjacency); + sfree((char *) vwgts); + sfree((char *) ewgts); + } + + if (!Using_Main && params_file != NULL) + fclose(params_file); + + return (flag); +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/util/bail.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/util/bail.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/util/bail.c (revision 27955) @@ -0,0 +1,27 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#include +#include +#include +#include "defs.h" + +/* Wrapper for exit() - print message and exit with status code. Exit code + of 0 indicates normal termination. Exit code of 1 indicates early + termination following detection of some problem. Call with bail(NULL,status) + to suppress message. */ +void bail(msg, status) +char *msg; +int status; +{ + extern FILE *Output_File; /* Output file or NULL */ + + if (msg != NULL && (int) strlen(msg) > 0) { + printf("%s\n", msg); + if (Output_File != NULL) { + fprintf(Output_File, "%s\n", msg); + } + } + exit(status); +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/util/seconds.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/util/seconds.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/configs/win/msys2/mingw64/code/util/seconds.c (revision 27955) @@ -0,0 +1,35 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#if defined(_INTEL_WIN_) || defined(_MSYS2_) +#include +#else +#include +#include +#endif + +double seconds() +{ + double curtime; + +#ifdef RUSAGE_SELF + +/* This timer is faster and more robust (if it exists). */ + struct rusage rusage; + int getrusage(); + + getrusage(RUSAGE_SELF, &rusage); + curtime = ((rusage.ru_utime.tv_sec + rusage.ru_stime.tv_sec) + + 1.0e-6 * (rusage.ru_utime.tv_usec + rusage.ru_stime.tv_usec)); + +#else + +/* ANSI timer, but lower resolution & wraps around after ~36 minutes. */ + + curtime = clock()/((double) CLOCKS_PER_SEC); + +#endif + + return (curtime); +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/install-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/install-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/install-linux.sh (revision 27955) @@ -0,0 +1,60 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER=2.2 + +PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed + +## Environment +# +export CFLAGS="-Wno-error=implicit-function-declaration" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf" + +# Unpack source +tar -xvzf Chaco-${VER}.tar.gz + +# Move source to 'src' directory +mv Chaco-${VER}/* src +rm -rf Chaco-${VER} + +# Apply patches +patch -R -p0 < chaco.patch # Written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch +patch src/code/Makefile < patches/Makefile.patch + +# Compile +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Install +cp -p src/exec/README ${PREFIX} +cp -p src/exec/User_Params ${PREFIX} +cp -p src/exec/*.coords ${PREFIX} +cp -p src/exec/*.graph ${PREFIX} +mkdir ${PREFIX}/include +cp -p src/code/main/defs.h ${PREFIX}/include/defs.h +cp -p src/code/main/params.h ${PREFIX}/include/params.h +cp -p chaco.h ${PREFIX}/include/chaco.h +mkdir ${PREFIX}/lib +mv src/code/chaco.a ${PREFIX}/lib/libchaco.a +mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a +mkdir ${PREFIX}/exec +mv src/exec/chaco ${PREFIX}/exec Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/install-mac.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/install-mac.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/install-mac.sh (revision 27955) @@ -0,0 +1,61 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER=2.2 + +PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed + +## Environment +# +export CFLAGS="-Wno-error=implicit-function-declaration" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf" + +# Unpack source +tar -xvzf Chaco-${VER}.tar.gz + +# Move source to 'src' directory +mv Chaco-${VER}/* src +rm -rf Chaco-${VER} + +# Apply patches +patch -R -p0 < chaco.patch # Written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch +patch src/code/Makefile < patches/Makefile.patch +patch src/code/util/smalloc.c < configs/mac/code/util/smalloc.c.patch + +# Compile +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Install +cp -p src/exec/README ${PREFIX} +cp -p src/exec/User_Params ${PREFIX} +cp -p src/exec/*.coords ${PREFIX} +cp -p src/exec/*.graph ${PREFIX} +mkdir ${PREFIX}/include +cp -p src/code/main/defs.h ${PREFIX}/include/defs.h +cp -p src/code/main/params.h ${PREFIX}/include/params.h +cp -p chaco.h ${PREFIX}/include/chaco.h +mkdir ${PREFIX}/lib +mv src/code/chaco.a ${PREFIX}/lib/libchaco.a +mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a +mkdir ${PREFIX}/exec +mv src/exec/chaco ${PREFIX}/exec Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/install-win-msys2-mingw.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/install-win-msys2-mingw.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/install-win-msys2-mingw.sh (revision 27955) @@ -0,0 +1,61 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER=2.2 + +PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/docs/chaco_guide.pdf" "chaco_guide.pdf" + +# Unpack source +tar -xvzf Chaco-${VER}.tar.gz + +# Move source to 'src' directory +mv Chaco-${VER}/* src +rm -rf Chaco-${VER} + +# Apply patches +patch -R -p0 < chaco.patch # Written by diff -rc src ~/Libs/Chaco-${VER} > chaco.patch + +# Copy customized source and configuration files to 'src' directory +cp configs/win/msys2/mingw64/code/Makefile src/code +cp configs/win/msys2/mingw64/code/main/interface.c src/code/main +cp configs/win/msys2/mingw64/code/util/bail.c src/code/util +cp configs/win/msys2/mingw64/code/util/seconds.c src/code/util + +# Compile +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Install +cp -p src/exec/README ${PREFIX} +cp -p src/exec/User_Params ${PREFIX} +cp -p src/exec/*.coords ${PREFIX} +cp -p src/exec/*.graph ${PREFIX} +mkdir ${PREFIX}/include +cp -p src/code/main/defs.h ${PREFIX}/include/defs.h +cp -p src/code/main/params.h ${PREFIX}/include/params.h +cp -p chaco.h ${PREFIX}/include/chaco.h +mkdir ${PREFIX}/lib +mv src/code/chaco.a ${PREFIX}/lib/libchaco.a +mv src/code/chacominusblas.a ${PREFIX}/lib/libchacominusblas.a +mkdir ${PREFIX}/exec +mv src/exec/chaco ${PREFIX}/exec Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Chaco.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Chaco.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Chaco.c (revision 27955) @@ -0,0 +1,244 @@ + +#include +#include /* strcasecmp */ +#include /* clock,time,difftime */ +#include "mex.h" + + +#define THISFUNCTION "Chaco" + +/* Input Arguments */ + +#define A_IN prhs[0] +#define VWGTS_IN prhs[1] +#define EWGTS_IN prhs[2] +#define XYZ_IN prhs[3] +#define OPTNS_IN prhs[4] +#define NPARTS_IN prhs[5] +#define GOAL_IN prhs[6] + +/* Output Arguments */ + +#define ASSGN_OUT plhs[0] + + +void ChacoUsage( void ); + +int Chacox( + int nvtxs, /* number of vertices in graph */ + int *start, /* start of edge list for each vertex */ + int *adjacency, /* edge list data */ + int *vwgts, /* weights for all vertices */ + float *ewgts, /* weights for all edges */ + float *x, + float *y, + float *z, /* coordinates for inertial method */ + short *assignment, /* set number of each vtx (length nvtxs+1) */ + double options[10], /* architecture and partitioning options */ + int *nparts, /* number of parts options */ + double *goal /* desired set sizes */ +); + + +void mexFunction( + int nlhs, /* number of outputs */ + mxArray *plhs[], /* array of pointers to output arguments */ + int nrhs, /* number of inputs */ + const mxArray *prhs[] /* array of pointers to input arguments */ +) +{ + int nvtxs; /* number of vertices in graph */ + int *start; /* start of edge list for each vertex */ + int *adjacency; /* edge list data */ + int *vwgts=NULL; /* weights for all vertices */ + float *ewgts=NULL; /* weights for all edges */ + float *x=NULL; + float *y=NULL; + float *z=NULL; /* coordinates for inertial method */ + short *assignment=NULL; /* set number of each vtx (length nvtxs+1) */ + double options[10]={1,1,0,0,1,1,50,0,.001,7654321}; + /* architecture and partitioning options */ + int *nparts=NULL; /* number of parts options */ + double *goal=NULL; /* desired set sizes */ + + int i, nedges, nterms, ncols, ierr=0; + double *p; + mwIndex *mwstart, *mwadjacency; + + clock_t clock0,clock1; + time_t time0, time1; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + ChacoUsage(); + return; + } + else if (nrhs < 1 || nlhs > 1) { + ChacoUsage(); + mexErrMsgTxt(" "); + } + + clock0=clock(); + time0 =time(NULL); + mexPrintf("\nChaco Module -- %s",ctime(&time0)); + + /* Assign pointers to the various parameters */ + /* and convert to the appropriate format for Chaco */ + + if (!mxIsEmpty(A_IN) && mxIsNumeric(A_IN) && mxIsSparse(A_IN)) { + nvtxs = mxGetN(A_IN); + mwstart = mxGetJc(A_IN); + start = mxMalloc((mxGetN(A_IN)+1)*sizeof(int)); + for (i=0; i<(mxGetN(A_IN)+1); i++) + start[i]= (int)mwstart[i]; + nedges = start[nvtxs]; + mwadjacency = mxGetIr(A_IN); + adjacency = mxMalloc(mxGetNzmax(A_IN)*sizeof(int)); + for (i=0; i= 2 && !mxIsEmpty(VWGTS_IN)) { + if (mxIsNumeric(VWGTS_IN) && !mxIsSparse(VWGTS_IN) && + (nterms=mxGetM(VWGTS_IN)*mxGetN(VWGTS_IN)) == nvtxs) { + vwgts = (int *) mxCalloc(nvtxs, sizeof(int)); + p = mxGetPr(VWGTS_IN); + for (i = 0; i < nvtxs; vwgts[i++] = (int) *p++); + } + else { + mexPrintf("%s -- Vertex weight vector must be numeric, full, and length=%d.\n", + THISFUNCTION,nvtxs); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 3 && !mxIsEmpty(EWGTS_IN)) { + if (mxIsNumeric(EWGTS_IN) && mxIsSparse(EWGTS_IN) && + (nterms=mxGetNzmax(EWGTS_IN)) == nedges) { + ewgts = (float *) mxCalloc(nedges, sizeof(float)); + p = mxGetPr(A_IN); + for (i = 0; i < nedges; ewgts[i++] = (float) *p++); + } + else { + mexPrintf("%s -- Edge weight matrix must be numeric, sparse, and nonzeroes=%d.\n", + THISFUNCTION,nedges); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 4 && (ncols = mxGetN(XYZ_IN)) >= 1) { + if (mxIsNumeric(XYZ_IN) && !mxIsSparse(XYZ_IN) && + mxGetM(XYZ_IN) == nvtxs) { + x = (float *) mxCalloc(nvtxs, sizeof(float)); + p = mxGetPr(XYZ_IN); + for (i = 0; i < nvtxs; x[i++] = (float) *p++); + } + else { + mexPrintf("%s -- XYZ coordinate matrix must be numeric, full, and length=%d.\n", + THISFUNCTION,nvtxs); + mexErrMsgTxt(" "); + } + if ((ncols ) >= 2) { + y = (float *) mxCalloc(nvtxs, sizeof(float)); + for (i = 0; i < nvtxs; y[i++] = (float) *p++); + if ((ncols ) >= 3) { + z = (float *) mxCalloc(nvtxs, sizeof(float)); + for (i = 0; i < nvtxs; z[i++] = (float) *p++); + } + } + } + + if (nrhs >= 5 && !mxIsEmpty(OPTNS_IN)) { + if (mxIsNumeric(OPTNS_IN) && !mxIsSparse(OPTNS_IN) && + (nterms=mxGetM(OPTNS_IN)*mxGetN(OPTNS_IN))) { + p = mxGetPr(OPTNS_IN); + for (i = 0; i < (nterms<10 ? nterms : 10); options[i++] = *p++); + } + else { + mexPrintf("%s -- Options vector must be numeric and full.\n", + THISFUNCTION); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 6 && !mxIsEmpty(NPARTS_IN)) { + if (mxIsNumeric(NPARTS_IN) && !mxIsSparse(NPARTS_IN) && + (nterms=mxGetM(NPARTS_IN)*mxGetN(NPARTS_IN))) { + nparts = (int *) mxCalloc(nterms, sizeof(int)); + p = mxGetPr(NPARTS_IN); + for (i = 0; i < nterms; nparts[i++] = (int) *p++); + } + else { + mexPrintf("%s -- Parts vector must be numeric and full.\n", + THISFUNCTION); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 7 && !mxIsEmpty(GOAL_IN)) { + if (mxIsNumeric(GOAL_IN) && !mxIsSparse(GOAL_IN) && + (nterms=mxGetM(GOAL_IN)*mxGetN(GOAL_IN))) { + goal = (double *) mxCalloc(nterms, sizeof(double)); + p = mxGetPr(GOAL_IN); + for (i = 0; i < nterms; goal[i++] = *p++); + } + else { + mexPrintf("%s -- Goal vector must be numeric and full.\n", + THISFUNCTION); + mexErrMsgTxt(" "); + } + } + + assignment = (short *) mxCalloc(nvtxs, sizeof(short)); + + /* Do the actual computations in a subroutine */ + + ierr = Chacox(nvtxs, start, adjacency, vwgts, ewgts, x, y, z, + assignment, options, nparts, goal); + + /* Create matrices for the return arguments */ + + if (!ierr) { + ASSGN_OUT = mxCreateDoubleMatrix(1,nvtxs,mxREAL); + p = mxGetPr(ASSGN_OUT); + for (i = 0; i < nvtxs; *p++ = (double) assignment[i++]); + } + else + ASSGN_OUT = mxCreateDoubleMatrix(0,0,mxREAL); + + /* Free what we allocated */ + + if (!assignment) mxFree((void *) assignment); + if (!goal) mxFree((void *) goal); + if (!nparts) mxFree((void *) nparts); + if (!z) mxFree((void *) z); + if (!y) mxFree((void *) y); + if (!x) mxFree((void *) x); + if (!ewgts) mxFree((void *) ewgts); + if (!vwgts) mxFree((void *) vwgts); + if (!adjacency) mxFree((void *) adjacency); + if (!start) mxFree((void *) start); + + clock1=clock(); + time1 =time(NULL); + mexPrintf("Chaco Module -- %f CPU seconds; %f elapsed seconds.\n\n", + ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0)); + + return; +} + +void ChacoUsage( void ) +{ + mexPrintf("\n"); + mexPrintf("Usage: [assgn] = Chaco(A,vwgts,ewgts,xyz,options,nparts,goal);\n"); + mexPrintf("\n"); + + return; +} + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Chaco_m.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Chaco_m.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Chaco_m.m (revision 27955) @@ -0,0 +1,217 @@ +function [part1,part2,chaco_time] = chaco(A,xy,method,nparts,goal) +% CHACO : Hendrickson/Leland's graph partitioner. +% +% [part1,part2,chaco_time] = chaco(A) returns a 50/50 vertex partition of the mesh +% whose symmetric adjacency matrix is A. +% +% Optional arguments: +% map = chaco(A, xy, method, nparts, goal); +% map = chaco(A, xy, method, inmap, goal); +% +% A: Depending on "method", A may contain vertex and edge weights. +% +% xy: Each row of xy is the coordinates of a vertex. +% If xy is non-null and there is no output, draw a picture. +% +% method: Scalar or vector describing the desired method. +% Default is multilevel Kernighan-Lin; other possibilities below. +% +% nparts Number of parts to divide into. Default is 2. If nparts is +% or present, the output is a "map vector", see below. (If method(5) +% inmap: is specified, nparts is interpreted differently; see below. In +% any case, the default is to divide into two parts.) +% If method(1) = 7 (see below), this argument is a map vector +% specifying an initial 2-way partition, and Chaco refines it. +% +% goal: Optionally, a vector of desired sizes (or total vertex weights) +% for each of the nparts parts. Default is all sizes equal. +% +% map: If nparts and inmap are not present, the output is a vector of +% the n/2 vertex numbers in one part of the 2-way partition, for +% compatibility with geopart and specpart. +% If nparts or imap is present, the output is a vector of the +% n part numbers, from 0 to nparts-1, assigned to the vertices. +% +% This is a Matlab interface to the graph partitioning software described +% in B. Hendrickson and R. Leland, "The Chaco User's Guide (Version 2.0)", +% Sandia National Laboratories report SAND94-2692, October 1994. +% This interface was written by John Gilbert, Xerox PARC, and is +% Copyright (c) 1994-1996 by Xerox Corporation. All rights reserved. +% HELP COPYRIGHT for complete copyright and licensing notice. +% +% Modified by Tim Davis, for Matlab 5.1. July 6, 1998. +% 05/28/10 jes Reorganization into Matlab-layer and x-layer. +% +% See also GEOPART, SPECPART. +% +% "method" is a vector of flags as follows. Not all combinations are supported. +% See Section 6.10 of the Chaco manual for more details on all the arguments. +% If "method" is shorter than 10, we use the defaults for unspecified entries. +% +% method(1): Global partitioning method ("global_method" in the Chaco manual). +% 1 Multilevel Kernighan-Lin (default) +% 2 Spectral +% 3 Inertial +% 4 Linear +% 5 Random +% 6 Scattered +% 7 Use "inmap" as the global (2-way) partition +% +% method(2): Local refinement method ("local_method" in the Chaco manual). +% 1 Kernighan-Lin (default) +% 2 None +% +% method(3): Vertex weighting. +% 0 No weights (default) +% 1 Use diag(A) as (positive integer) vertex weights +% +% method(4): Edge weighting. +% 0 No weights (default) +% 1 Use off-diagonals of A as (positive integer) edge weights +% +% method(5): Target architecture ("architecture" in the Chaco manual). +% If method(5) = 0, the target is a hypercube, "nparts" is the +% number of dimensions, and the partition is into 2^nparts parts. +% If method(5) = 1, 2, or 3, the target is a 1-, 2-, or 3-D grid, +% "nparts" is a vector of the sizes of the grid in each dimension, +% and the partition is into prod(nparts) parts. +% Default is method(5) = 1, so nparts is the number of parts. +% +% method(6): Partitioning dimension ("ndims" in the Chaco manual). +% 1 Bisection (default) +% 2 Quadrisection +% 3 Octasection +% +% method(7): Number of vertices to coarsen to ("vmax" in the Chaco manual). +% Default is 50. +% +% method(8): Eigensolver ("rqi_flag" in the Chaco manual). +% 0 RQI/Symmlq (default) +% 1 Lanczos +% +% method(9): Eigensolver convergence tolerance ("eigtol" in the Chaco manual). +% Default is .001 +% +% method(10): Seed for random number generator ("seed" in the Chaco manual). +% Default is 7654321. +% +% Many esoteric details of Chaco's behavior can be changed by placing a file +% called "User_Params" in the same directory as the executable mlchaco.mex. +% As always, see the manual for details. + +DefaultMethod = [1 1 0 0 1 1 50 0 .001 7654321]; + +% Fill in default arguments. +if nargin < 2, xy = []; end; +if nargin < 3, method = DefaultMethod; end; +if nargin < 4, nparts = []; end; +if nargin < 5, goal = []; end; +if length(method) < length(DefaultMethod) + method = [method DefaultMethod(length(method)+1 : length(DefaultMethod))]; +end; + +% Decide on output and graphics. +if (isempty (nparts)) + mapvector = 0; +else + mapvector = 1; +end; +picture = (nargout == 0) & (size(xy,2) >= 2); + +% Chaco numbers vertices from 1 and the Matlab sparse data structure +% numbers rows from 0, so we add an empty first row to make things line up. +% This code also makes sure the arg to Chaco will be sparse. +[n,n] = size(A); +Adiag = diag(diag(A)); +%Aout = [sparse(1,n) ; A-Adiag]; +Aout = sparse(A-Adiag); + +% Make sure all args except the adj matrix are full; +if issparse(xy) + xy = full(xy); +end; +if issparse(method) + method = full(method); +end; +if issparse(nparts) + nparts = full(nparts); +end; +if issparse(goal) + goal = full(goal); +end; + +% Decode "method" to get the actual args to Chaco. +% Note that "nparts" may correspond to any of several Chaco +% parameters, depending on the method. + +if method(3) + vwgts = full(diag(A)); + totalvwgt = sum(vwgts); +else + vwgts = []; + totalvwgt = size(A,2); +end; +if method(4) + ewgts = Aout; +else + ewgts = []; +end; +if method(1) == 7 + % Refine an input partition: "nparts" is the input partition. + % This seems to work only for hypercube architecture, + % so we force a 1-D hypercube with 2-way partitioning. + nsets = 2; +elseif method(5) == 0 + % Partition for hypercube: "nparts" is # of dimensions (default 1). + if (isempty (nparts)) + nsets = 2^1; + else + nsets = 2^nparts; + end; +else + % Partition for mesh: "nparts" is vector of mesh sizes in each + % dimension, default [2 1 ... 1] with "architecture" dimensions. + if (isempty (nparts)) + nsets = prod(2); + else + nsets = prod(nparts); + end; +end; +if length(goal) ~= nsets + goal = totalvwgt/nsets * ones(1,nsets); +end; + +[map,chaco_time]=Chaco(Aout, vwgts, ewgts, xy, method, nparts, goal); + +% Draw the picture. +if picture + if size(xy,2) >= 3 && unique(xy(:,3)) == 0 + xy=xy(:,1:2); + end + if length(unique(map)) == 2 + gplotpart(A,xy,find(map==0)); + else + gplotmap(A,xy,map); + end; + if method(1)==1, heading = 'Multilevel Kernighan-Lin'; + elseif method(1)==2, heading = 'Spectral'; + elseif method(1)==3, heading = 'Inertial'; + elseif method(1)==4, heading = 'Linear'; + elseif method(1)==5, heading = 'Random'; + elseif method(1)==6, heading = 'Scattered'; + elseif method(1)==7, heading = 'Input'; + end; + heading = [heading ' Partition']; + if method(2)==1 & method(1) ~= 1 + heading =[heading ' Refined by KL']; + end; + title(heading); +end; + +% Put output in the right form. +if mapvector + part1 = map; +else + part1 = find(map==0); + part2 = find(map==1); +end; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Chacox.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Chacox.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Chacox.c (revision 27955) @@ -0,0 +1,471 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#include +#include +#include "defs.h" +#include "params.h" + +#define THISFUNCTION "Chacox" + +#define OPT_GLOBAL 0 +#define OPT_LOCAL 1 +#define OPT_VWGTS 2 +#define OPT_EWGTS 3 +#define OPT_ARCH 4 +#define OPT_NDIMS 5 +#define OPT_VMAX 6 +#define OPT_RQI 7 +#define OPT_EIGTOL 8 +#define OPT_SEED 9 + +int input_parse( + char *outassignname, /* name of assignment output file */ + char *outfilename, /* name of file for outputing run results */ + int *architecture, /* 0=> hypercube, d=> d-dimensional mesh */ + int *ndims_tot, /* target number of hypercube dimensions */ + int mesh_dims[3], /* mesh dimensions */ + int *global_method, /* what global partitioning strategy to use? */ + int *local_method, /* what local refinement strategy to use? */ + int *rqi_flag, /* should I use multilevel eigensolver? */ + int *vmax, /* if so, how far should I coarsen? */ + int *ndims, /* number of divisions at each stage */ + int *nprocs, /* number of processors being divided into */ + double options[10], /* architecture and partitioning options */ + int *nparts /* number of parts options */ +); + + +int Chacox( + int nvtxs, /* number of vertices in graph */ + int *start, /* start of edge list for each vertex */ + int *adjacency, /* edge list data */ + int *vwgts, /* weights for all vertices */ + float *ewgts, /* weights for all edges */ + float *x, + float *y, + float *z, /* coordinates for inertial method */ + short *assignment, /* set number of each vtx (length nvtxs+1) */ + double options[10], /* architecture and partitioning options */ + int *nparts, /* number of parts options */ + double *goal /* desired set sizes */ +) +{ + extern int Using_Main; /* is main routine being called? */ + extern char *PARAMS_FILENAME; /* name of file with parameter updates */ + extern double EIGEN_TOLERANCE; /* tolerance for eigen calculations */ + extern int OUTPUT_ASSIGN; /* whether to write assignment to file */ + extern int DEBUG_MEMORY; /* debug memory allocation and freeing? */ + extern int DEBUG_TRACE; /* trace main execution path */ + extern int DEBUG_PARAMS; /* debug flag for reading parameters */ + extern long RANDOM_SEED; /* seed for random number generators */ + extern int ECHO; /* controls amount of output */ + extern int PROMPT; /* prompt for input or not? */ + extern int PRINT_HEADERS; /* print lines for output sections? */ + extern int MATCH_TYPE; /* matching routine to call */ + extern double input_time; /* times data file input */ + extern double start_time; /* time partitioning starts */ + FILE *params_file; /* file with parameter value updates */ + int global_method; /* global partitioning method */ + int local_method; /* local partitioning method */ + double eigtol; /* tolerance in eigenvector calculation */ + int ndims; /* dimension of recursive partitioning */ + int architecture; /* 0 => hypercube, d => d-dimensional mesh */ + int ndims_tot; /* total number of cube dimensions to divide */ + int mesh_dims[3]; /* dimensions of mesh of processors */ + long seed; /* for random graph mutations */ + int rqi_flag; /* use RQI/Symmlq eigensolver? */ + int vmax; /* if so, how many vertices to coarsen down to? */ + char outassignname[NAME_LENGTH]; /* assignment output file name */ + char outfilename[NAME_LENGTH]; /* name of output file */ + char *outassignptr; /* name or null pointer for output assignment */ + char *outfileptr; /* name or null pointer for output file */ + int nprocs; /* number of processors being divided into */ + double time; /* timing marker */ + int flag; /* return code from input routines */ + double *smalloc(); /* safe version of malloc */ + double seconds(); /* returns elapsed time in seconds */ + int sfree(), interface(), affirm(); + void input_queries(), smalloc_stats(), read_params(), clear_timing(); + + int i,tvwgt; + double tgoal; + + if (DEBUG_TRACE > 0) { + printf("\n"); + } + + if (PRINT_HEADERS) { + printf("\n Chaco 2.0\n"); + printf(" Sandia National Laboratories\n\n"); + } + + Using_Main = TRUE; + params_file = fopen(PARAMS_FILENAME, "r"); + if (params_file == NULL && DEBUG_PARAMS > 1) { + printf("Parameter file `%s' not found; using default parameters.\n", + PARAMS_FILENAME); + } + + start_time = time = seconds(); + + read_params(params_file); + + flag = input_parse(outassignname, outfilename, + &architecture, &ndims_tot, mesh_dims, + &global_method, &local_method, &rqi_flag, &vmax, &ndims, &nprocs, + options, nparts); + if (flag) + return(flag); + + if (OUTPUT_ASSIGN > 0) + outassignptr = outassignname; + else + outassignptr = NULL; + + if (ECHO < 0) + outfileptr = outfilename; + else + outfileptr = NULL; + + if ((int)options[OPT_VWGTS] && vwgts) { + printf("%s -- Applying weights for %d vertices.\n", + THISFUNCTION,nvtxs); + tvwgt = 0.; + for (i=0; i 0) + eigtol = options[OPT_EIGTOL]; + else + eigtol = EIGEN_TOLERANCE; + if ((int)options[OPT_SEED] > 0) + seed = (int)options[OPT_SEED]; + else + seed = RANDOM_SEED; + +/* Chaco numbers vertices from 1 and the Matlab sparse data structure + numbers rows from 0, so increment the row indices for each column. */ + + for (i=0; i 0) { + printf("\n"); + smalloc_stats(); + } + + if (params_file != NULL) + fclose(params_file); + + if (DEBUG_TRACE > 1) { + printf("\n"); + } + + return(0); +} + + +int input_parse( + char *outassignname, /* name of assignment output file */ + char *outfilename, /* name of file for outputing run results */ + int *architecture, /* 0=> hypercube, d=> d-dimensional mesh */ + int *ndims_tot, /* target number of hypercube dimensions */ + int mesh_dims[3], /* mesh dimensions */ + int *global_method, /* what global partitioning strategy to use? */ + int *local_method, /* what local refinement strategy to use? */ + int *rqi_flag, /* should I use multilevel eigensolver? */ + int *vmax, /* if so, how far should I coarsen? */ + int *ndims, /* number of divisions at each stage */ + int *nprocs, /* number of processors being divided into */ + double options[10], /* architecture and partitioning options */ + int *nparts /* number of parts options */ +) +{ + extern int SEQUENCE; /* sequence instead of partition graph? */ + extern int ARCHITECTURE; /* 0=> hypercube, d=> d-dimensional mesh */ + extern int OUTPUT_ASSIGN; /* write assignments to file? */ + extern int ECHO; /* copy input to screen? results to file? */ + extern int DEBUG_TRACE; /* trace main execution path */ + extern int PROMPT; /* prompt for input? */ + extern int MATCH_TYPE; /* max-matching routine to call */ + int eigensolver; /* which kind of eigensolver to use */ + + if (DEBUG_TRACE > 0) { + printf("\n"); + } + + if (PROMPT) { + printf("Parallel machine architecture:\n"); + printf(" (0) Hypercube\n"); + printf(" (1) One-dimensional mesh\n"); + printf(" (2) Two-dimensional mesh\n"); + printf(" (3) Three-dimensional mesh\n"); + } + *architecture = (int)options[OPT_ARCH]; + if (*architecture < 0 || *architecture > 3) { + printf("%s -- Architecture %d must be between 0 and 3.\n", + THISFUNCTION,options[OPT_ARCH]); + return(-1); + } + + /* Name output assignment file. */ + if (PROMPT) + printf("Assignment output file: "); + outassignname = NULL; + + /* Name output results file. */ + if (PROMPT) + printf("File name for saving run results: "); + outfilename = NULL; + + /* Initialize the method flags */ + *rqi_flag = 0; + *global_method = 0; + + /* Get global method, if any. */ + if (SEQUENCE) { + *global_method = 2; + } + else { + if (PROMPT) { + printf("Global partitioning method:\n"); + printf(" (1) Multilevel-KL\n"); + printf(" (2) Spectral\n"); + printf(" (3) Inertial\n"); + printf(" (4) Linear\n"); + printf(" (5) Random\n"); + printf(" (6) Scattered\n"); + printf(" (7) Read-from-file\n"); + } + *global_method = (int)options[OPT_GLOBAL]; + if (*global_method < 1 || *global_method > 7) { + printf("%s -- Global method %d must be between 1 and 7.\n", + THISFUNCTION,options[OPT_GLOBAL]); + return(-1); + } + } + + if (*global_method == 7) { /* Name and open input assignment file. */ + if (PROMPT) + printf("Assignment input file: "); + } + + else if (*global_method == 3) { + if (PROMPT) + printf("Geometry input file name: "); + } + + else if (*global_method == 2) { + if (PROMPT) { + printf("Eigensolver:\n"); + printf(" (1) Multilevel RQI/Symmlq\n"); + printf(" (2) Lanczos\n"); + } + eigensolver = (int)options[OPT_RQI]; + if (eigensolver < 0 || eigensolver > 2) { + printf("%s -- RQI/Symmlq flag %d must be between 0 and 2.\n", + THISFUNCTION,options[OPT_RQI]); + return(-1); + } + if (eigensolver == 1) { + if (MATCH_TYPE == 5) { /* geometric matching */ + if (PROMPT) + printf("Geometry input file name: "); + } + *rqi_flag = 1; + if (PROMPT) + printf("Number of vertices to coarsen down to: "); + *vmax = (int)options[OPT_VMAX]; + if (*vmax <= 0) { + printf("%s -- Vmax %d must be greater then 0.\n", + THISFUNCTION,options[OPT_VMAX]); + return(-1); + } + } + else if (eigensolver == 0 || eigensolver == 2) { + *rqi_flag = 0; + } + } + + else if (*global_method == 1) { + if (MATCH_TYPE == 5) { /* geometric matching */ + if (PROMPT) + printf("Geometry input file name: "); + } + if (PROMPT) + printf("Number of vertices to coarsen down to: "); + *vmax = (int)options[OPT_VMAX]; + if (*vmax <= 0) { + printf("%s -- Vmax %d must be greater then 0.\n", + THISFUNCTION,options[OPT_VMAX]); + return(-1); + } + } + + if (SEQUENCE) { + *local_method = 2; + if (*architecture == 0) { + *ndims_tot = 1; + } + else if (*architecture > 0) { + mesh_dims[0] = 2; + mesh_dims[1] = mesh_dims[2] = 1; + } + *ndims = 1; + goto End_Label; + } + + /* Get local method, if any */ + *local_method = 0; + if (*global_method == 1) + *local_method = 1; + else { + if (PROMPT) { + printf("Local refinement method:\n"); + printf(" (1) Kernighan-Lin\n"); + printf(" (2) None\n"); + } + *local_method = (int)options[OPT_LOCAL]; + if (*local_method < 1 || *local_method > 2) { + printf("%s -- Local method %d must be 1 and 2.\n", + THISFUNCTION,options[OPT_LOCAL]); + return(-1); + } + } + + /* Now learn about the parallel architecture. */ + if (*architecture == 0) { + /* Get total number of hypercube dimensions in which to partition. */ + *ndims_tot = 0; + if (PROMPT) + printf("Total number of target hypercube dimensions: "); + *ndims_tot = nparts[0]; + if (*ndims_tot < 1) { + printf(" Number of divisions must be at least 1\n"); + printf("%s -- Number of divisions %d must be at least 1.\n", + THISFUNCTION,nparts[0]); + return(-1); + } + *nprocs = 1 << (*ndims_tot); + } + + else { /* Get dimensions of mesh. */ + mesh_dims[1] = mesh_dims[2] = 1; + if (*architecture == 2) { + if (PROMPT) + printf("X and Y extent of of 2-D mesh: "); + mesh_dims[0] = nparts[0]; + mesh_dims[1] = nparts[1]; + } + else if (*architecture == 3) { + if (PROMPT) + printf("X, Y and Z extent of 3-D mesh: "); + mesh_dims[0] = nparts[0]; + mesh_dims[1] = nparts[1]; + mesh_dims[2] = nparts[2]; + } + else { /* Anything else => 1-D mesh */ + if (PROMPT) + printf("Size of 1-D mesh: "); + mesh_dims[0] = nparts[0]; + *architecture = 1; + } + *nprocs = mesh_dims[0] * mesh_dims[1] * mesh_dims[2]; + } + + /* Get number of dimensions in which to partition at each level. */ + *ndims = 0; + if (*nprocs <= 3) { + *ndims = 1; + } + else if (*nprocs <= 7) { + if (PROMPT) { + printf("Partitioning dimension: \n"); + printf(" (1) Bisection\n"); + printf(" (2) Quadrisection\n"); + } + *ndims = (int)options[OPT_NDIMS]; + if (*ndims < 1 || *ndims > 2) { + printf("%s -- Ndims %d must be 1 or 2 for %d processors.\n", + THISFUNCTION,options[OPT_NDIMS],*nprocs); + return(-1); + } + } + else { + if (PROMPT) { + printf("Partitioning dimension: \n"); + printf(" (1) Bisection\n"); + printf(" (2) Quadrisection\n"); + printf(" (3) Octasection\n"); + } + *ndims = (int)options[OPT_NDIMS]; + if (*ndims < 1 || *ndims > 3) { + printf("%s -- Ndims %d must be between 1 and 3 for %d processors.\n", + THISFUNCTION,options[OPT_NDIMS],*nprocs); + return(-1); + } + } +End_Label: + + if (*global_method == 1 || *rqi_flag) { + if (*vmax < 2 * (1 << *ndims)) { + *vmax = 2 * (1 << *ndims); + } + } + + return(0); +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Makefile =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Makefile (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/Makefile (revision 27955) @@ -0,0 +1,293 @@ +# This is the Makefile for the mex-file version of Chaco, to be dynamically +# linked with Matlab using the interface in the "meshpart" toolbox. +# See file "README" for more information. +# +# You may need to change the following variables: +# +# MATLAB Matlab's top-level directory, often "/usr/matlab" or similar. +# CHACO Chaco's source directory, normally the "code" subdirectory +# of the Chaco distribution. +# MLCHACO Directory with Chaco files modified for Matlab, normally +# the directory containing this Makefile. +# DEST_DIR Directory for the executable mlchaco.mex, normally the +# "meshpart" directory, which is normally the parent of the +# directory containing this Makefile. +# CC Choice of C compiler. gcc seems to work best for Matlab for me. +# IFLAGS, CFLAGS, OFLAGS Flags to go with the compiler and linker. +# +# This Makefile works under Solaris 2. To use it with a different Unix, +# you may need to change the references to "ar" and/or "ranlib" and +# possibly other things. +# +# John Gilbert, 1996. +# Copyright (c) 1990-1996 by Xerox Corporation. All rights reserved. +# See file ../copyright.m for complete copyright and licensing notice. + +#MATLAB = /import/matlab +#MATLAB = /usr/local/libexec/matlab +#MATLAB = /usr/local/pkgs/matlab-7.6 +MATLAB = ${MATLAB_DIR} + +#CHACO = /project/sparse/chaco/version2/code +#CHACO = ../../Chaco-2.0/code +#CHACO = ../../Chaco-2.2/code +#CHACO = ../../../chaco/src/code +CHACO = ${CHACO_DIR}/../src/code + +MLCHACO = . +DEST_DIR = .. +CC = gcc +#CC = cc +IFLAGS = -I${MATLAB}/extern/include -I${CHACO}/main +#CFLAGS = -Xa -G -xO4 -xcg92 +#CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions +#OFLAGS = -xO4 -xcg92 +OFLAGS = -O2 +#AR = /usr/ccs/bin/ar rcv # for solaris 2 +AR = /usr/bin/ar rcv # for solaris 2 +#RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +RANLIB = /usr/bin/ranlib # for solaris 2 + + +MLFILES.c= ${MLCHACO}/Chacox.c \ + ${MLCHACO}/user_params.c +# ${MLCHACO}/bail.c \ # redefined original with -DMATLAB +# ${MLCHACO}/chaco_check_graph.c \ # redefined original with -DMATLAB +# ${MLCHACO}/check_input.c \ # redefined original with -DMATLAB +# ${MLCHACO}/smalloc.c \ # redefined original with -DMATLAB + +CHFILES.c= ${CHACO}/main/interface.c \ + ${CHACO}/main/main.c \ + ${CHACO}/submain/balance.c \ + ${CHACO}/submain/divide.c \ + ${CHACO}/submain/submain.c \ + ${CHACO}/input/input_assign.c \ + ${CHACO}/input/check_input.c \ + ${CHACO}/input/input.c \ + ${CHACO}/input/input_geom.c \ + ${CHACO}/input/input_graph.c \ + ${CHACO}/input/read_params.c \ + ${CHACO}/input/reflect_input.c \ + ${CHACO}/input/read_val.c \ + ${CHACO}/graph/check_graph.c \ + ${CHACO}/graph/free_graph.c \ + ${CHACO}/graph/reformat.c \ + ${CHACO}/graph/subgraph.c \ + ${CHACO}/graph/graph_out.c \ + ${CHACO}/inertial/eigenvec2.c \ + ${CHACO}/inertial/eigenvec3.c \ + ${CHACO}/inertial/inertial.c \ + ${CHACO}/inertial/inertial1d.c \ + ${CHACO}/inertial/inertial2d.c \ + ${CHACO}/inertial/inertial3d.c \ + ${CHACO}/inertial/make_subgeom.c \ + ${CHACO}/klspiff/buckets.c \ + ${CHACO}/klspiff/buckets_bi.c \ + ${CHACO}/klspiff/buckets1.c \ + ${CHACO}/klspiff/bilistops.c \ + ${CHACO}/klspiff/coarsen_kl.c \ + ${CHACO}/klspiff/count_weights.c \ + ${CHACO}/klspiff/compress_ewgts.c \ + ${CHACO}/klspiff/kl_init.c \ + ${CHACO}/klspiff/kl_output.c \ + ${CHACO}/klspiff/klspiff.c \ + ${CHACO}/klspiff/make_bndy_list.c \ + ${CHACO}/klspiff/make_kl_list.c \ + ${CHACO}/klspiff/nway_kl.c \ + ${CHACO}/klvspiff/bpm_improve.c \ + ${CHACO}/klvspiff/bucketsv.c \ + ${CHACO}/klvspiff/clear_dvals.c \ + ${CHACO}/klvspiff/coarsen_klv.c \ + ${CHACO}/klvspiff/countup_vtx_sep.c \ + ${CHACO}/klvspiff/find_bndy.c \ + ${CHACO}/klvspiff/flow.c \ + ${CHACO}/klvspiff/klv_init.c \ + ${CHACO}/klvspiff/klvspiff.c \ + ${CHACO}/klvspiff/make_bpgraph.c \ + ${CHACO}/klvspiff/make_sep_list.c \ + ${CHACO}/klvspiff/matching.c \ + ${CHACO}/klvspiff/nway_klv.c \ + ${CHACO}/klvspiff/flatten.c \ + ${CHACO}/coarsen/coarsen.c \ + ${CHACO}/coarsen/interpolate.c \ + ${CHACO}/coarsen/makefgraph.c \ + ${CHACO}/coarsen/makeccoords.c \ + ${CHACO}/coarsen/coarsen1.c \ + ${CHACO}/coarsen/makev2cv.c \ + ${CHACO}/coarsen/maxmatch.c \ + ${CHACO}/coarsen/maxmatch1.c \ + ${CHACO}/coarsen/maxmatch2.c \ + ${CHACO}/coarsen/maxmatch3.c \ + ${CHACO}/coarsen/maxmatch4.c \ + ${CHACO}/coarsen/maxmatch5.c \ + ${CHACO}/connect/add_edges.c \ + ${CHACO}/connect/connected.c \ + ${CHACO}/connect/find_edges.c \ + ${CHACO}/eigen/bidir.c \ + ${CHACO}/eigen/bisect.c \ + ${CHACO}/eigen/checkeig.c \ + ${CHACO}/eigen/checkeig_ext.c \ + ${CHACO}/eigen/checkorth.c \ + ${CHACO}/eigen/cksturmcnt.c \ + ${CHACO}/eigen/mkeigvecs.c\ + ${CHACO}/eigen/eigensolve.c \ + ${CHACO}/eigen/get_extval.c \ + ${CHACO}/eigen/get_ritzvals.c \ + ${CHACO}/eigen/lanczos_FO.c \ + ${CHACO}/eigen/lanczos_SO.c \ + ${CHACO}/eigen/lanczos_SO_float.c \ + ${CHACO}/eigen/lanczos_ext.c \ + ${CHACO}/eigen/lanczos_ext_float.c \ + ${CHACO}/eigen/lanc_seconds.c\ + ${CHACO}/eigen/lanpause.c \ + ${CHACO}/eigen/makeorthlnk.c \ + ${CHACO}/eigen/mkscanlist.c \ + ${CHACO}/eigen/orthog1.c \ + ${CHACO}/eigen/orthogonalize.c \ + ${CHACO}/eigen/orthogvec.c \ + ${CHACO}/eigen/ql.c \ + ${CHACO}/eigen/rqi.c \ + ${CHACO}/eigen/rqi_ext.c \ + ${CHACO}/eigen/scale_diag.c \ + ${CHACO}/eigen/scanmax.c \ + ${CHACO}/eigen/scanmin.c \ + ${CHACO}/eigen/solistout.c \ + ${CHACO}/eigen/sorthog.c \ + ${CHACO}/eigen/splarax.c \ + ${CHACO}/eigen/sturmcnt.c \ + ${CHACO}/eigen/Tevec.c \ + ${CHACO}/eigen/tri_solve.c \ + ${CHACO}/eigen/warnings.c \ + ${CHACO}/symmlq/aprod.c \ + ${CHACO}/symmlq/msolve.c \ + ${CHACO}/symmlq/pow_dd.c \ + ${CHACO}/symmlq/symmlq.c \ + ${CHACO}/symmlq/symmlqblas.c \ + ${CHACO}/tinvit/tinvit.c \ + ${CHACO}/tinvit/pythag.c \ + ${CHACO}/tinvit/epslon.c \ + ${CHACO}/optimize/determinant.c \ + ${CHACO}/optimize/func2d.c \ + ${CHACO}/optimize/func3d.c \ + ${CHACO}/optimize/opt2d.c \ + ${CHACO}/optimize/opt3d.c \ + ${CHACO}/assign/assign.c \ + ${CHACO}/assign/assign_out.c \ + ${CHACO}/assign/mapper.c \ + ${CHACO}/assign/median.c \ + ${CHACO}/assign/merge_assign.c \ + ${CHACO}/assign/rec_median.c \ + ${CHACO}/assign/rotate.c \ + ${CHACO}/assign/y2x.c \ + ${CHACO}/bpmatch/checkbp.c \ + ${CHACO}/bpmatch/inits2d.c \ + ${CHACO}/bpmatch/inits3d.c \ + ${CHACO}/bpmatch/genvals2d.c \ + ${CHACO}/bpmatch/genvals3d.c \ + ${CHACO}/bpmatch/map2d.c \ + ${CHACO}/bpmatch/map3d.c \ + ${CHACO}/bpmatch/movevtxs.c \ + ${CHACO}/bpmatch/sorts2d.c \ + ${CHACO}/bpmatch/sorts3d.c \ + ${CHACO}/refine_map/compute_cube_edata.c \ + ${CHACO}/refine_map/compute_cube_vdata.c \ + ${CHACO}/refine_map/refine_cube.c \ + ${CHACO}/refine_map/update_cube_edata.c \ + ${CHACO}/refine_map/update_cube_vdata.c \ + ${CHACO}/refine_map/find_edge_cube.c \ + ${CHACO}/refine_map/init_cube_edata.c \ + ${CHACO}/refine_map/compute_mesh_edata.c \ + ${CHACO}/refine_map/compute_mesh_vdata.c \ + ${CHACO}/refine_map/find_edge_mesh.c \ + ${CHACO}/refine_map/init_mesh_edata.c \ + ${CHACO}/refine_map/refine_mesh.c \ + ${CHACO}/refine_map/update_mesh_edata.c \ + ${CHACO}/refine_map/update_mesh_vdata.c \ + ${CHACO}/refine_map/refine_map.c \ + ${CHACO}/refine_map/make_comm_graph.c \ + ${CHACO}/refine_part/refine_part.c \ + ${CHACO}/refine_part/kl_refine.c \ + ${CHACO}/refine_part/make_maps_ref.c \ + ${CHACO}/refine_part/make_terms_ref.c \ + ${CHACO}/internal/force_internal.c \ + ${CHACO}/internal/improve_internal.c \ + ${CHACO}/internal/check_internal.c \ + ${CHACO}/misc/define_subcubes.c \ + ${CHACO}/misc/define_submeshes.c \ + ${CHACO}/misc/divide_procs.c \ + ${CHACO}/misc/merge_goals.c \ + ${CHACO}/misc/make_term_props.c \ + ${CHACO}/misc/count.c \ + ${CHACO}/misc/countup.c \ + ${CHACO}/misc/countup_cube.c \ + ${CHACO}/misc/countup_mesh.c \ + ${CHACO}/misc/make_subgoal.c \ + ${CHACO}/misc/find_maxdeg.c \ + ${CHACO}/misc/make_maps.c \ + ${CHACO}/misc/make_setlists.c \ + ${CHACO}/misc/sequence.c \ + ${CHACO}/misc/perturb.c \ + ${CHACO}/misc/simple_part.c \ + ${CHACO}/misc/time_kernels.c \ + ${CHACO}/misc/timing.c \ + ${CHACO}/util/affirm.c \ + ${CHACO}/util/array_alloc_2D.c \ + ${CHACO}/util/bit_reverse.c \ + ${CHACO}/util/checkpnt.c \ + ${CHACO}/util/cpvec.c \ + ${CHACO}/util/dot.c \ + ${CHACO}/util/doubleout.c \ + ${CHACO}/util/input_int.c \ + ${CHACO}/util/gray.c \ + ${CHACO}/util/machine_params.c \ + ${CHACO}/util/makevwsqrt.c \ + ${CHACO}/util/mkvec.c \ + ${CHACO}/util/norm.c \ + ${CHACO}/util/normalize.c \ + ${CHACO}/util/mergesort.c \ + ${CHACO}/util/randomize.c \ + ${CHACO}/util/smalloc.c \ + ${CHACO}/util/bail.c \ + ${CHACO}/util/scadd.c \ + ${CHACO}/util/seconds.c \ + ${CHACO}/util/setvec.c \ + ${CHACO}/util/shell_sort.c \ + ${CHACO}/util/strout.c \ + ${CHACO}/util/tri_prod.c \ + ${CHACO}/util/true_or_false.c \ + ${CHACO}/util/update.c \ + ${CHACO}/util/vecout.c \ + ${CHACO}/util/vecran.c \ + ${CHACO}/util/vecscale.c +# ${CHACO}/main/user_params.c \ + +MLFILES.o= $(MLFILES.c:.c=.o) + +CHFILES.o= $(CHFILES.c:.c=.o) + +#mlchaco: ${MLFILES.o} chaco.a Makefile +# ${MATLAB}/bin/cmex CC='gcc -G' -lm ${OFLAGS} ${MLFILES.o} chaco.a; \ +# mv mlchaco.mex* ${DEST_DIR} + +#mlchaco: ${MLFILES.c} chaco.a Makefile +# mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +# mv mlchaco.mex* ${DEST_DIR} + +#mlchaco: ${MLFILES.c} ${CHFILES.c} ${CHACO}/chaco.a Makefile +# ${MATLAB}/bin/mex mlchaco.c -largeArrayDims -DMATLAB ${MLFILES.c} ${CHACO}/chaco.a -I${CHACO}/main +# mv mlchaco.mex* ${DEST_DIR} + +Chaco: ${MLFILES.c} ${CHFILES.c} ${CHACO}/chaco.a Makefile + ${MATLAB}/bin/mex Chaco.c -largeArrayDims ${MLFILES.c} ${CHACO}/chaco.a -I${CHACO}/main +# mv Chaco.mex* ${DEST_DIR} + +chaco.a: ${CHFILES.o} + ${AR} ${CHACO}/chaco.a ${CHFILES.o} ; ${RANLIB} ${CHACO}/chaco.a + +clean: + rm -f ${CHACO}/*/*.o chaco.a ${MLCHACO}/*.o ${DEST_DIR}/core + +.c.o: + ${CC} -c ${IFLAGS} ${CFLAGS} -o $*.o $*.c + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/User_Params.debug =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/User_Params.debug (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/User_Params.debug (revision 27955) @@ -0,0 +1,27 @@ +% This file, User_Params, is read at runtime to modify Chaco's defaults. +% The purpose of this version is to turn on some debugging stuff that +% the Matlab version will normally have off. + +ECHO = 2 +OUTPUT_METRICS = 2 +OUTPUT_TIME = 2 +PRINT_HEADERS = 1 + +DEBUG_EVECS = 1 +DEBUG_KL = 1 +DEBUG_INERTIAL = 1 +DEBUG_CONNECTED = 1 +DEBUG_PERTURB = 1 +DEBUG_ASSIGN = 1 +DEBUG_OPTIMIZE = 1 +DEBUG_BPMATCH = 1 +DEBUG_COARSEN = 1 +DEBUG_MEMORY = 1 +DEBUG_INPUT = 0 +DEBUG_PARAMS = 1 +DEBUG_INTERNAL = 1 +DEBUG_REFINE_PART = 1 +DEBUG_REFINE_MAP = 1 +DEBUG_SIMULATOR = 1 +DEBUG_TRACE = 1 +DEBUG_MACH_PARAMS = 1 Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/User_Params.verbose =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/User_Params.verbose (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/User_Params.verbose (revision 27955) @@ -0,0 +1,8 @@ +% This file, User_Params, is read at runtime to modify Chaco's defaults. +% The purpose of this version is to turn on some verbose output that +% the Matlab version will normally have off. + +ECHO = 1 +OUTPUT_METRICS = 1 +OUTPUT_TIME = 1 +PRINT_HEADERS = 1 Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/user_params.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/user_params.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mex/user_params.c (revision 27955) @@ -0,0 +1,142 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +/* Modified by John Gilbert 25 Aug 1995 for Matlab mex-file interface */ +/* Modified by Tim Davis, July 6, 1998, for Matlab 5.1 interface, and */ +/* a more picky compiler (cc) that complains about duplicate global */ +/* declarations. */ + +#include "params.h" + +#define TRUE 1 +#define FALSE 0 + + +/* Input and ouput control parameters */ + +int CHECK_INPUT = TRUE; /* Check input for consistency? (TRUE/FALSE) */ +int ECHO = 0; /* Print input/param options? to file? (-2..2) */ +int OUTPUT_METRICS = 0; /* Controls displaying of results (-2..2) */ +int OUTPUT_TIME = 0; /* At what level to display timings (0..2) */ +int OUTPUT_ASSIGN = FALSE; /* Write assignments to file? (TRUE/FALSE) */ +int OUT_ASSIGN_INV = FALSE;/* If so, use inverse form? (TRUE/FALSE) */ +int IN_ASSIGN_INV = FALSE; /* Input file in inverse form? (TRUE/FALSE) */ +int PROMPT = FALSE; /* Prompt for input? (TRUE/FALSE) */ +int PRINT_HEADERS = FALSE; /* Print pretty output headers (TRUE/FALSE) */ + + +/* Eigenvector calculation parameters */ + +int LANCZOS_TYPE = 3; /* type of Lanczos to use */ + /* 1 => full orthog, 2 => full inverse operator */ + /* 3 => selective orthogonalization */ +double EIGEN_TOLERANCE = 1e-3; /* Numerical eigen-tolerance */ +double SRESTOL = -1.; /* Rel resid tol on T evec; autoset if <= 0 */ +int LANCZOS_SO_INTERVAL = 10; /* Itns. between SO orthog checks; set >= 2 */ +int LANCZOS_MAXITNS = -1; /* Max Lanczos its; autoset if <= 0 */ +double BISECTION_SAFETY = 10; /* Divides Lanczos bisection tol */ +int LANCZOS_CONVERGENCE_MODE = 0; /* Lanczos convergence test type: */ + /* 0=> residual, 1=> partition */ +int RQI_CONVERGENCE_MODE = 1; /* RQI convergence test type: */ + /* 0=> residual, 1=> partition */ +int LANCZOS_SO_PRECISION = 2; /* 2 => double Lanczos, 1 => float */ +int WARNING_EVECS = 2; /* Warnings in eigenvector generation (0..3) */ +double WARNING_ORTHTOL = 2; /* Warning if Ares and bjitol have this ratio */ +double WARNING_MISTOL = 100; /* Warning if Ares and bjitol have this ratio */ +int LANCZOS_TIME = FALSE; /* Detailed Lanczos times? (TRUE/FALSE) */ +int TIME_KERNELS = FALSE; /* Time numerical kernels? (TRUE/FALSE) */ + + +/* Other parameters for spectral methods */ + +int MAKE_CONNECTED = TRUE;/* Connect graph if using spectral method? */ +int PERTURB = TRUE; /* Randomly perturb matrix in spectral method? */ +int NPERTURB = 2; /* If so, how many edges to modify? */ +double PERTURB_MAX = 3.0e-3; /* Largest value for perturbation */ +int MAPPING_TYPE = 1; /* How to map from eigenvectors to partition */ + /* 0 => cut at origin, 1 => min-cost assign */ +int COARSE_NLEVEL_RQI = 2;/* # levels between RQI calls in uncoarsening */ +int OPT3D_NTRIES = 5; /* # local opts to look for global min in opt3d */ + + +/* Kernighan--Lin/Fiduccia--Mattheyses parameters */ + +int KL_METRIC = 2; /* KL interset cost: 1=>cuts, 2=>hops */ +int KL_RANDOM = TRUE; /* Use randomness in Kernighan-Lin? (TRUE/FALSE)*/ +int KL_BAD_MOVES = 20; /* Number of unhelpful moves in a row allowed */ +int KL_NTRIES_BAD = 1; /* # unhelpful passes before quitting KL */ +int KL_UNDO_LIST = TRUE; /* Only resort changed vtxs? (TRUE/FALSE) */ +double KL_IMBALANCE = 0.0; /* Fractional imbalance allowed by KL */ + + +/* Coarsening parameters */ + +double COARSEN_RATIO_MIN = .7; /* Min vtx reduction each coarsen stage */ +int COARSE_NLEVEL_KL = 2; /* # levels between KL calls in uncoarsening */ +int MATCH_TYPE = 1; /* Type of contraction matching (1..4) */ +int HEAVY_MATCH = FALSE; /* Encourage heavy match edges? (TRUE/FALSE) */ +int COARSE_KL_BOTTOM = TRUE; /* Force KL at lowest level (TRUE/FALSE) */ +int COARSEN_VWGTS = TRUE; /* Sum vtx weights in coarsening? (TRUE/FALSE) */ +int COARSEN_EWGTS = TRUE; /* Sum edge weights in coarsening? (TRUE/FALSE) */ +int KL_ONLY_BNDY = TRUE; /* Start moving vtxs on boundary? (TRUE/FALSE) */ + + +/* Parameters for post-processing options */ + +int REFINE_PARTITION = FALSE; /* Postprocess to improve cuts? */ +int INTERNAL_VERTICES = FALSE; /* ... to up internal vtxs? (TRUE/FALSE) */ +int REFINE_MAP = FALSE; /* ... to reduce hops? (TRUE/FALSE) */ + + +/* Architecture and simulator parameters */ + +int ARCHITECTURE = 0; /* 0=> hypercube, d=> d-dimensional mesh (0..3)*/ + +/* Modified by Tim Davis: remove duplicate definitions */ +#ifdef DUPLICATE_DEFINITIONS_REMOVED +int SIMULATOR = 0; /* Run simulator? In what mode? */ +int SIMULATION_ITNS = 1; /* # iterations simulator is to imitate. */ +int PERCENTAGE_OUTPUT = FALSE; /* Output in percent? (TRUE/FALSE) */ +double CUT_COST = 0.0; /* Communication cost of a cut-edge. */ +double HOP_COST = 0.0; /* Communication cost of a hop. */ +double BDY_COST = 0.0; /* Cost associated with boundary vertices. */ +double BDY_HOP_COST = 0.0; /* Cost associated with boundary hops. */ +double STARTUP_COST = 0.0; /* Communication cost of a message startup. */ + /* Note: nCUBE2 startup: 112e-6, per byte: 4.6e-6, buffering 5.6e-6 */ + /* Intel Paragon startup: 70e-6, per byte: 5.3e-8 */ +#endif + +/* Miscellaneous parameters */ + +int TERM_PROP = FALSE; /* Invoke terminal propagation? (TRUE/FALSE) */ +double CUT_TO_HOP_COST = 1; /* ..if so, relative importance of cuts/hops */ +int SEQUENCE = FALSE; /* Only do spectral ordering? (TRUE/FALSE) */ +char SEQ_FILENAME[NAME_LENGTH] = "Sequence.out"; /* If so, file name */ +long RANDOM_SEED = 7654321L; /* Seed for random number generator */ +int NSQRTS = 1000; /* # square roots to precompute if coarsening */ +int MAKE_VWGTS = FALSE; /* Make vtx weights degrees+1? (TRUE/FALSE) */ +int FREE_GRAPH = FALSE; /* Free input graph data? (TRUE/FALSE) */ +char *PARAMS_FILENAME = "User_Params"; /* File of parameter changes */ + + +/* Parameters that control debugging output */ + +int DEBUG_EVECS = 0; /* Debug flag for eigenvector generation (0..5) */ +int DEBUG_KL = 0; /* Debug flag for Kernighan-Lin (0..3) */ +int DEBUG_INERTIAL = 0; /* Debug flag for inertial method (0..1) */ +int DEBUG_CONNECTED = 0; /* Debug flag for connected components (0..1) */ +int DEBUG_PERTURB = 0; /* Debug flag for matrix perturbation (0..1) */ +int DEBUG_ASSIGN = 0; /* Debug flag for assignment to sets (0..1) */ +int DEBUG_OPTIMIZE = 0; /* Debug flag for optimization/rotation (0..2) */ +int DEBUG_BPMATCH = 0; /* Debug flag for bipartite matching code (0..2) */ +int DEBUG_COARSEN = 0; /* Debug flag for coarsening/uncoarsening (0..1) */ +int DEBUG_MEMORY = 0; /* Debug flag for smalloc/sfree (0..3) */ +int DEBUG_INPUT = 0; /* Debug flag for having read input files (0..1) */ +int DEBUG_PARAMS = 1; /* Debug flag for reading parameter file (0..2) */ +int DEBUG_INTERNAL = 0; /* Debug flag for internal vertices (0..2) */ +int DEBUG_REFINE_PART = 0;/* Debug flag for refine partition (0..1) */ +int DEBUG_REFINE_MAP = 0; /* Debug flag for refining mapping (0..1) */ +int DEBUG_SIMULATOR = 0; /* Debug flag for comm simulator (0..2) */ +int DEBUG_TRACE = 0; /* Trace main execution path (0..2) */ +int DEBUG_MACH_PARAMS = 0;/* Print computed machine params? (0..1) */ Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mlchaco_README.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mlchaco_README.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mlchaco_README.txt (revision 27955) @@ -0,0 +1,136 @@ +mlchaco (from meshpartdist.tar, 2/08/02) +http://www.cerfacs.fr/algor/Softs/MESHPART/ + + +[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c +34a35 [CLK_TCK undefined, so use CLOCKS_PER_SEC] +> #include /* CLOCKS_PER_SEC */ +56,61c57,62 [update for current Matlab] +< void mexFunction( +< int nlhs, /* number of expected outputs */ +< Matrix *plhs[], /* matrix pointer array returning outputs */ +< int nrhs, /* number of inputs */ +< Matrix *prhs[] /* matrix pointer array for inputs */ +< ) +--- +> void mexFunction( +> int nlhs, /* number of expected outputs */ +> mxArray *plhs[], /* array of pointers to output arguments +> */ +> int nrhs, /* number of inputs */ +> const mxArray *prhs[] /* array of pointers to input arguments */ +> ) +87a89 [update for current Matlab] +> mwIndex *mwstart,*mwadjacency; +104c106,110 [update for current Matlab] +< start = mxGetJc(A_in); +--- +> /* start = mxGetJc(A_in);*/ +> mwstart = mxGetJc(A_in); +> start = mxMalloc((mxGetN(A_in)+1)*sizeof(int)); +> for (i=0; i<(mxGetN(A_in)+1); i++) +> start[i]= (int)mwstart[i]; +106c112,116 [update for current Matlab] +< adjacency = mxGetIr(A_in); +--- +> /* adjacency = mxGetIr(A_in);*/ +> mwadjacency = mxGetIr(A_in); +> adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int)); +> for (i=0; i adjacency[i]= (int)mwadjacency[i]; +131,132c141,144 [provide default filenames, since no way to input] +< outassignname = NULL; +< outfilename = NULL; +--- +> /* outassignname = NULL; +> outfilename = NULL;*/ +> outassignname = "chaco_assign.txt"; +> outfilename = "chaco_out.txt"; +169c181 [update for current Matlab] +< plhs [1] = mxCreateFull (1, 1, REAL) ; +--- +> plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ; +173c185 [CLK_TCK undefined, so use CLOCKS_PER_SEC] +< ((double) CLK_TCK) ; +--- +> ((double) CLOCKS_PER_SEC) ; +179c191 [update for current Matlab] +< map_out = mxCreateFull(1,nvtxs,REAL); +--- +> map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL); +185a198,199 [update for current Matlab] +> if (start != NULL) mxFree((char *) start); +> if (adjacency != NULL) mxFree((char *) adjacency); + + +[jschierm@astrid chaco]$ diff Makefile_old Makefile +27c27,28 [current Matlab location] +< MATLAB = /usr/local/libexec/matlab +--- +> #MATLAB = /usr/local/libexec/matlab +> MATLAB = /usr/local/pkgs/matlab-7.6 +30c31,32 [current Chaco 2.2 location] +< CHACO = ../../Chaco-2.0/code +--- +> #CHACO = ../../Chaco-2.0/code +> CHACO = ../../Chaco-2.2/code +34,35c36,37 [use gcc instead of cc] +< #CC = gcc +< CC = cc +--- +> CC = gcc +> #CC = cc +37c39,40 [add MATLAB flag to compile for mex-function] +< CFLAGS = -Xa -G -xO4 -xcg92 +--- +> #CFLAGS = -Xa -G -xO4 -xcg92 +> CFLAGS = -Xa -G -xO4 -xcg92 -DMATLAB +39,40c42,45 [current function locations] +< AR = /usr/ccs/bin/ar rcv # for solaris 2 +< RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +--- +> #AR = /usr/ccs/bin/ar rcv # for solaris 2 +> AR = /usr/bin/ar rcv # for solaris 2 +> #RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +> RANLIB = /usr/bin/ranlib # for solaris 2 +45,47d49 [use Chaco versions with MATLAB switch rather than local versions] +< ${MLCHACO}/chaco_check_graph.c \ +< ${MLCHACO}/check_input.c \ +< ${MLCHACO}/smalloc.c \ +48a51,53 +> # ${MLCHACO}/chaco_check_graph.c \ +> # ${MLCHACO}/check_input.c \ +> # ${MLCHACO}/smalloc.c \ +55a61 [update CHLIST to match Chaco 2.2] +> ${CHACO}/input/check_input.c \ +61a68 [update CHLIST to match Chaco 2.2] +> ${CHACO}/graph/check_graph.c \ +91a99 [update CHLIST to match Chaco 2.2] +> ${CHACO}/klvspiff/flow.c \ +97a106 [update CHLIST to match Chaco 2.2] +> ${CHACO}/klvspiff/flatten.c \ +100c109,110 [update CHLIST to match Chaco 2.2] +< ${CHACO}/coarsen/makecgraph.c \ +--- +> ${CHACO}/coarsen/makefgraph.c \ +> ${CHACO}/coarsen/makeccoords.c \ +102d111 [update CHLIST to match Chaco 2.2] +< ${CHACO}/coarsen/countcedges.c \ +108a118 [update CHLIST to match Chaco 2.2] +> ${CHACO}/coarsen/maxmatch5.c \ +234a245 [update CHLIST to match Chaco 2.2] +> ${CHACO}/util/smalloc.c \ +245a257,258 [use local versions rather than Chaco versions (added for clarity)] +> # ${CHACO}/main/user_params.c \ +> # ${CHACO}/util/bail.c \ +254a268,271 [update for current mex] +> #mlchaco: ${MLFILES.c} chaco.a Makefile +> # mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +> # mv mlchaco.mex* ${DEST_DIR} +> +256c273 [update for current mex] +< mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +--- +> mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c} +> chaco.a -I${CHACO}/main + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mlchaco_jes_notes.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mlchaco_jes_notes.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/mlchaco_jes_notes.txt (revision 27955) @@ -0,0 +1,182 @@ +7/15/09: + +[jschierm@astrid chaco]$ diff Makefile_old Makefile +27c27,28 +< MATLAB = /usr/local/libexec/matlab +--- +> #MATLAB = /usr/local/libexec/matlab +> MATLAB = /usr/local/matlab780 +30c31,32 +< CHACO = ../../Chaco-2.0/code +--- +> #CHACO = ../../Chaco-2.0/code +> CHACO = ../../Chaco-2.2/code +34,35c36,37 +< #CC = gcc +< CC = cc +--- +> CC = gcc +> #CC = cc +39,40c41,44 +< AR = /usr/ccs/bin/ar rcv # for solaris 2 +< RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +--- +> #AR = /usr/ccs/bin/ar rcv # for solaris 2 +> AR = /usr/bin/ar rcv # for solaris 2 +> #RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +> RANLIB = /usr/bin/ranlib # for solaris 2 +91a96,97 [missing symbols] +> ${CHACO}/klvspiff/flatten.c \ +> ${CHACO}/klvspiff/flow.c \ +99a106 [missing symbols] +> ${CHACO}/coarsen/makeccoords.c \ +102a110 [missing symbols] +> ${CHACO}/coarsen/makefgraph.c \ +108a117 [missing symbols] +> ${CHACO}/coarsen/maxmatch5.c \ +254a264,267 +> #mlchaco: ${MLFILES.c} chaco.a Makefile +> # mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +> # mv mlchaco.mex* ${DEST_DIR} +> +256c269 +< mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +--- +> mex -output mlchaco -largeArrayDims ${MLFILES.c} chaco.a -I${CHACO}/main + +[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c +34a35 +> #include /* CLOCKS_PER_SEC */ +56,61c57,62 +< void mexFunction( +< int nlhs, /* number of expected outputs */ +< Matrix *plhs[], /* matrix pointer array returning outputs */ +< int nrhs, /* number of inputs */ +< Matrix *prhs[] /* matrix pointer array for inputs */ +< ) +--- +> void mexFunction( +> int nlhs, /* number of expected outputs */ +> mxArray *plhs[], /* array of pointers to output arguments +> */ +> int nrhs, /* number of inputs */ +> const mxArray *prhs[] /* array of pointers to input arguments */ +> ) +87a89 +> mwIndex *mwstart,*mwadjacency; +104c106,110 +< start = mxGetJc(A_in); +--- +> /* start = mxGetJc(A_in);*/ +> mwstart = mxGetJc(A_in); +> start = mxMalloc((mxGetN(A_in)+1)*sizeof(int)); +> for (i=0; i<(mxGetN(A_in)+1); i++) +> start[i]= (int)mwstart[i]; +106c112,116 +< adjacency = mxGetIr(A_in); +--- +> /* adjacency = mxGetIr(A_in);*/ +> mwadjacency = mxGetIr(A_in); +> adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int)); +> for (i=0; i adjacency[i]= (int)mwadjacency[i]; +169c181 +< plhs [1] = mxCreateFull (1, 1, REAL) ; +--- +> plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ; +173c185 +< ((double) CLK_TCK) ; +--- +> ((double) CLOCKS_PER_SEC) ; +179c191 +< map_out = mxCreateFull(1,nvtxs,REAL); +--- +> map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL); +185a198,199 +> if (start != NULL) mxFree((char *) start); +> if (adjacency != NULL) mxFree((char *) adjacency); + + +7/29/09: + +[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c +131,132c141,144 +< outassignname = NULL; +< outfilename = NULL; +--- +> /* outassignname = NULL; +> outfilename = NULL;*/ +> outassignname = "chaco_assign.txt"; +> outfilename = "chaco_out.txt"; + +7/30/09: + +[jschierm@astrid chaco]$ diff Makefile_old Makefile +27c27,28 +< MATLAB = /usr/local/libexec/matlab +--- +> #MATLAB = /usr/local/libexec/matlab +> MATLAB = /usr/local/pkgs/matlab-7.6 +37c39,40 +< CFLAGS = -Xa -G -xO4 -xcg92 +--- +> #CFLAGS = -Xa -G -xO4 -xcg92 +> CFLAGS = -Xa -G -xO4 -xcg92 -DMATLAB +45,47d49 [using Chaco versions with MATLAB switch] +< ${MLCHACO}/chaco_check_graph.c \ +< ${MLCHACO}/check_input.c \ +< ${MLCHACO}/smalloc.c \ +48a51,53 +> # ${MLCHACO}/chaco_check_graph.c \ +> # ${MLCHACO}/check_input.c \ +> # ${MLCHACO}/smalloc.c \ +55a61 +> ${CHACO}/input/check_input.c \ +61a68 +> ${CHACO}/graph/check_graph.c \ +91a99 [compared CHFILES with Chaco Makefile CHFILES] +> ${CHACO}/klvspiff/flow.c \ +97a106 [compared CHFILES with Chaco Makefile CHFILES] +> ${CHACO}/klvspiff/flatten.c \ +100c109,110 [compared CHFILES with Chaco Makefile CHFILES] +< ${CHACO}/coarsen/makecgraph.c \ +--- +> ${CHACO}/coarsen/makefgraph.c \ +> ${CHACO}/coarsen/makeccoords.c \ +102d111 [compared CHFILES with Chaco Makefile CHFILES] +< ${CHACO}/coarsen/countcedges.c \ +108a118 [compared CHFILES with Chaco Makefile CHFILES] +> ${CHACO}/coarsen/maxmatch5.c \ +234a245 +> ${CHACO}/util/smalloc.c \ +245a257,258 +> # ${CHACO}/main/user_params.c \ +> # ${CHACO}/util/bail.c \ +254a268,271 +> #mlchaco: ${MLFILES.c} chaco.a Makefile +> # mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +> # mv mlchaco.mex* ${DEST_DIR} +> +256c273 +< mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +--- +> mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c} +> chaco.a -I${CHACO}/main + +5/25/10: + +- reorganized chaco.m and mlchaco.c drivers into Chaco.c matlab-layer (independent of chaco) and Chacox.c x-layer (independent of matlab). + +5/26/10: + +- added mexchaco target to Makefile (and related changes). + +5/27/10 + +- added define for exit(status) to ${CHACO}/main/defs.h so that local bail.c is + unnecessary. + +6/15/10: + +- separated chaco x-layer from meshpart build. + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/patches/Makefile.mac-sierra.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/patches/Makefile.mac-sierra.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/patches/Makefile.mac-sierra.patch (revision 27955) @@ -0,0 +1,11 @@ +--- ./src/code/Makefile 2016-02-16 19:39:30.000000000 -0800 ++++ ./Makefile 2016-02-16 19:37:49.000000000 -0800 +@@ -6,7 +6,7 @@ + #CFLAGS = -O2 + #OFLAGS = -O2 + #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +-CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g ++CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/local/include/ -Wno-implicit-function-declaration + #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB + OFLAGS = -O2 + #AR = /usr/ccs/bin/ar rcv # for solaris 2 Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/patches/Makefile.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/patches/Makefile.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/chaco/patches/Makefile.patch (revision 27955) @@ -0,0 +1,11 @@ +--- ./src/code/Makefile 2016-02-16 19:39:30.000000000 -0800 ++++ ./Makefile 2016-02-16 19:37:49.000000000 -0800 +@@ -6,7 +6,7 @@ + #CFLAGS = -O2 + #OFLAGS = -O2 + #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +-CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g ++CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/include/malloc -Wno-implicit-function-declaration + #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB + OFLAGS = -O2 + #AR = /usr/ccs/bin/ar rcv # for solaris 2 Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/configs/MacOS/High_Sierra/Source/CPack/cmCPackDragNDropGenerator.cxx.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/configs/MacOS/High_Sierra/Source/CPack/cmCPackDragNDropGenerator.cxx.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/configs/MacOS/High_Sierra/Source/CPack/cmCPackDragNDropGenerator.cxx.patch (revision 27955) @@ -0,0 +1,9 @@ +--- Source/CPack/cmCPackDragNDropGenerator.cxx_orig 2017-08-29 08:45:50.000000000 +0200 ++++ Source/CPack/cmCPackDragNDropGenerator.cxx 2017-08-29 08:46:04.000000000 +0200 +@@ -12,6 +12,7 @@ + #include + #include + #include ++#include + + #include Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/configs/MacOS/High_Sierra/Utilities/cmcurl/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/configs/MacOS/High_Sierra/Utilities/cmcurl/CMakeLists.txt.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/configs/MacOS/High_Sierra/Utilities/cmcurl/CMakeLists.txt.patch (revision 27955) @@ -0,0 +1,11 @@ +--- Utilities/cmcurl/CMakeLists.txt_orig 2017-08-29 08:37:31.000000000 +0200 ++++ Utilities/cmcurl/CMakeLists.txt 2017-08-29 08:37:55.000000000 +0200 +@@ -50,7 +50,7 @@ + ) + endif() + if(NOT OSX_VERSION VERSION_LESS 10.6 AND +- CMAKE_C_COMPILER_ID MATCHES "GNU|Clang|AppleClang") ++ CMAKE_C_COMPILER_ID MATCHES "Clang|AppleClang") + set(CMAKE_USE_DARWINSSL ON CACHE INTERNAL "enable Apple OS native SSL/TLS") + else() + set(CMAKE_USE_DARWINSSL OFF CACHE INTERNAL "enable Apple OS native SSL/TLS") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/install-macosx64-highsierra.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/install-macosx64-highsierra.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/install-macosx64-highsierra.sh (revision 27955) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu +VER="3.14.5" + +#Some cleanup +rm -rf install cmake-$VER.tar.gz +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/cmake-$VER.tar.gz" "cmake-$VER.tar.gz" + +#Untar +tar -zxvf cmake-$VER.tar.gz + +#Move cmake into install directory +mv cmake-$VER/* install +rm -rf cmake-$VER + +#Compile cmake +cd install +./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install + +if [ $# -eq 0 ]; then + make +else + make -j $1; +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/install-macosx64-snowleopard.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/install-macosx64-snowleopard.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/install-macosx64-snowleopard.sh (revision 27955) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu +VER="2.8.11.2" + +#Some cleanup +rm -rf install cmake-$VER +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/cmake-$VER.tar.gz" "cmake-$VER.tar.gz" + +#Untar +tar -zxvf cmake-$VER.tar.gz + +#Move cmake into install directory +mv cmake-$VER/* install +rm -rf cmake-$VER + +LDFLAGS="-L/usr/lib/ -lstdc++ -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/ -lgfortran" +F77="/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran" + +#Compile cmake +cd install +./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install +if [ $# -eq 0 ]; then + make +else + make -j $1; +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cmake/install.sh (revision 27955) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.19.3" + +PREFIX="${ISSM_DIR}/externalpackages/cmake/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/cmake-${VER}.tar.gz" "cmake-${VER}.tar.gz" + +# Unpack source +tar -zxvf cmake-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} + +# Move source into 'src' directory +mv cmake-${VER} src + +# Configure +cd src +#./bootstrap \ +# --prefix=${PREFIX} # Breaks on ronne +./configure \ + --prefix="${PREFIX}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make install -j $1 +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/codipack/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/codipack/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/codipack/install.sh (revision 27955) @@ -0,0 +1,20 @@ +#!/bin/bash +set -eu + +VER=1.8 + +# Cleanup from previous installation +rm -rf install CoDiPack-$VER.tar.gz + +#Download development version +git clone https://github.com/SciCompKL/CoDiPack.git install + +## Download source +#$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/CoDiPack-${VER}.tar.gz" "CoDiPack-${VER}.tar.gz" +# +## Untar +#tar -zxvf CoDiPack-$VER.tar.gz +# +## Move source into install directory +#mv CoDiPack-$VER install +#rm -rf CoDiPack-$VER/ Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/colpack/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/colpack/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/colpack/install.sh (revision 27955) @@ -0,0 +1,26 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src ColPack + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ColPack-1.0.3.tar.gz' 'ColPack-1.0.3.tar.gz' + +#install directory +mkdir src +tar -zxvf ColPack-1.0.3.tar.gz +mv ColPack/* src +rm -rf ColPack + +#compile +cd src +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +cd .. + +#install +ln -s src/build ./install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cppcheck/install-dev.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cppcheck/install-dev.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cppcheck/install-dev.sh (revision 27955) @@ -0,0 +1,18 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src + +#Download +git clone git://github.com/danmar/cppcheck.git src + +#compile +cd src +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install PREFIX=$ISSM_DIR/externalpackages/cppcheck/install +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cppcheck/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cppcheck/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cppcheck/install.sh (revision 27955) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src cppcheck-1.48 +mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/cppcheck-1.48.tar' 'cppcheck-1.48.tar' +tar -xvf cppcheck-1.48.tar + +mv cppcheck-1.48/* src +rm -rf cppcheck-1.48 + +#compile +cd src +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install PREFIX=$ISSM_DIR/externalpackages/cppcheck/install +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-linux-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-linux-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-linux-static.sh (revision 27955) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source to 'src' directory +mv curl-${VER}/* src +rm -rf curl-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-shared \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose \ + --disable-ldap \ + --disable-ldaps \ + --with-zlib="${ZLIB_ROOT}" \ + --without-zstd \ + --without-libidn2 \ + --without-nghttp2 \ + --without-brotli \ + --without-librtmp + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-linux-with_tests.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-linux-with_tests.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-linux-with_tests.sh (revision 27955) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source to 'src' directory +mv curl-${VER}/* src +rm -rf curl-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-static \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose \ + --with-zlib="${ZLIB_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make test + make install +else + make -j $1 + make -j $1 test + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-linux.sh (revision 27955) @@ -0,0 +1,42 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source to 'src' directory +mv curl-${VER}/* src +rm -rf curl-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-static \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose \ + --with-zlib="${ZLIB_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-mac-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-mac-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-mac-static.sh (revision 27955) @@ -0,0 +1,54 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed + +## Environment +# +export MACOSX_DEPLOYMENT_TARGET="10.5" # Allows fall back to older API (source: https://curl.se/docs/install.html) + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source to 'src' directory +mv curl-${VER}/* src +rm -rf curl-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-shared \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose \ + --disable-ldap \ + --disable-ldaps \ + --with-zlib="${ZLIB_ROOT}" \ + --without-zstd \ + --without-libidn2 \ + --without-nghttp2 \ + --without-brotli \ + --without-librtmp \ + --with-secure-transport + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-mac.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-mac.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/curl/install-7-mac.sh (revision 27955) @@ -0,0 +1,47 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.73.0" + +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed + +## Environment +# +export MACOSX_DEPLOYMENT_TARGET="10.5" # Allows fall back to older API (source: https://curl.se/docs/install.html) + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source to 'src' directory +mv curl-${VER}/* src +rm -rf curl-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-static \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose \ + --with-zlib="${ZLIB_ROOT}" \ + --with-secure-transport + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cvs/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cvs/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cvs/install.sh (revision 27955) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf cvs-1.11.23 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/cvs-1.11.23.tar.gz' 'cvs-1.11.23.tar.gz' + +#Untar +tar -zxvf cvs-1.11.23.tar.gz + +#Move subversion into src directory +mv cvs-1.11.23/* src +rm -rf cvs-1.11.23 + +#Patch getline +cd src +cat lib/getline.c | sed -e "s/getline /get_line /" > BACK && mv BACK lib/getline.c +cat lib/getline.h | sed -e "s/getline /get_line /" > BACK && mv BACK lib/getline.h + +#Configure +./configure --prefix="$ISSM_DIR/externalpackages/cvs/install" + +#Compile and install subversion +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-18.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-18.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-18.sh (revision 27955) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.18 + +#download numpy first +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Cython-0.18.tar.gz' 'cython.tar.gz' + +#install numpy +tar -zxvf cython.tar.gz +cd Cython-0.18 +python setup.py install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-19.2.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-19.2.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-19.2.sh (revision 27955) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.19.2 + +#download numpy first +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Cython-0.19.2.tar.gz' 'cython.tar.gz' + +#install numpy +tar -zxvf cython.tar.gz +cd Cython-0.19.2 +python setup.py install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-22.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-22.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-22.sh (revision 27955) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.22 + +#download numpy first +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Cython-0.22.tar.gz' 'cython.tar.gz' + +#install numpy +tar -zxvf cython.tar.gz +cd Cython-0.22 +python setup.py install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-26.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-26.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install-26.sh (revision 27955) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.26 + +#download numpy first +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Cython-0.26.tar.gz' 'cython.tar.gz' + +#install numpy +tar -zxvf cython.tar.gz +cd Cython-0.26 +python setup.py install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/cython/install.sh (revision 27955) @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf cython + +#download cython first +git clone https://github.com/cython/cython.git + +#install cython +cd cython +python setup.py install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch (revision 27955) @@ -0,0 +1,8 @@ +766c766 +< /*char output_string[32], message_string[32], title_string[32], +--- +> char output_string[32], message_string[32], title_string[32], +802c802 +< check_error(err_code, "lhs_files");*/ +--- +> check_error(err_code, "lhs_files"); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch (revision 27955) @@ -0,0 +1,4 @@ +95a96,98 +> +> //close the input file +> fclose(nidrin); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch (revision 27955) @@ -0,0 +1,7 @@ +2276a2277 +> // add sensitivity output to importance factors (jes, 8/06/10) +2280c2281,2282 +< << impFactor[i][j] << '\n'; +--- +> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) +> << fnGradsMeanX(i, j) << '\n'; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NonDSampling.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NonDSampling.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NonDSampling.C.patch (revision 27955) @@ -0,0 +1,15 @@ +656a657,658 +> +> +659a662,663 +> +> return; //don't compute for now, too expensive. +705c709 +< //calculate simple rank correlation coeff +--- +> //calculate simple correlation coeff +710a715 +> +1071a1077,1078 +> +> return; //don't output for now. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch (revision 27955) @@ -0,0 +1,10 @@ +1052,1053c1052,1057 +< s << " Importance Factor for variable " << setw(11) +< << uv_labels[j].data() << " = " << impFactor[i][j] << '\n'; +--- +> // add sensitivity output to importance factors (jes, 8/06/10) +> s << " Importance Factor for variable " << setiosflags(ios::left) +> << setw(11) << uv_labels[j].data() << " = " +> << resetiosflags(ios::adjustfield) << setw(write_precision+7) +> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) +> << fnGradsMeanX(i, j) << '\n'; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch (revision 27955) @@ -0,0 +1,34 @@ +134a135 +> initialized=0; //we run serially all the time! +165a167,197 +> /** This constructor is provided for the Issm software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dryRunFlag(false), dummyFlag(false), +> stdOutputFlag(false), stdErrorFlag(false), startClock(0), +> stdOutputFilename(NULL), stdErrorFilename(NULL), readRestartFilename(NULL), +> writeRestartFilename(NULL), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> startClock = clock(); +> #ifdef DAKOTA_UTILIB +> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); +> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp +> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp +> #endif // DAKOTA_UTILIB +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota in serial mode on CPU 0, inside an MPI ring."; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota in serial mode.\n"; +> #endif // HAVE_MPI +> +> parallelLevels.insert(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch (revision 27955) @@ -0,0 +1,3 @@ +346a347,348 +> /// library mode constructor, serial mode +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch (revision 27955) @@ -0,0 +1,5 @@ +109a110,113 +> +> //close the input file +> fclose(nidrin); +> Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch (revision 27955) @@ -0,0 +1,9 @@ +2218a2219 +> // add sensitivity output to importance factors (jes, 8/06/10) +2223c2224,2227 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NonDSampling.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NonDSampling.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NonDSampling.C.patch (revision 27955) @@ -0,0 +1,14 @@ +438,439c438,440 +< if (!subIteratorFlag) +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +894,895c895,897 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +--- +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch (revision 27955) @@ -0,0 +1,7 @@ +1046a1047 +> // add sensitivity output to importance factors (jes, 8/06/10) +1048c1049,1050 +< << uv_labels[j].data() << " = " << impFactor[i][j] << '\n'; +--- +> << uv_labels[j].data() << " = " << impFactor[i][j] +> << " Sensitivity = " << fnGradsMeanX(i,j) << '\n'; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch (revision 27955) @@ -0,0 +1,36 @@ +178a179 +> initialized=0; //we run serially all the time! +214a216,248 +> /** This constructor is provided for the Issm software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dummyFlag(false), +> stdOutputToFile(false), stdErrorToFile(false), checkFlag(false), +> preRunFlag(true), runFlag(true), postRunFlag(true), userModesFlag(false), +> startClock(0), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> startClock = clock(); +> #ifdef DAKOTA_UTILIB +> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); +> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp +> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp +> #endif // DAKOTA_UTILIB +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.2 MPI executable in serial mode on CPU 0 for ISSM."; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.2 serial executable in serial mode for ISSM.\n"; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> +> Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch (revision 27955) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the Issm software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/Teuchos_ConfigDefs.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/Teuchos_ConfigDefs.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/Teuchos_ConfigDefs.hpp.patch (revision 27955) @@ -0,0 +1,2 @@ +87a88 +> #include Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch (revision 27955) @@ -0,0 +1,4 @@ +24a25 +> #ifndef PI +25a27 +> #endif Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch (revision 27955) @@ -0,0 +1,14 @@ +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch (revision 27955) @@ -0,0 +1,26 @@ +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch (revision 27955) @@ -0,0 +1,26 @@ +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "/nasa/boost/1.50.0" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.patch (revision 27955) @@ -0,0 +1,4 @@ +47a48,50 +> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE) +> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE) +> Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm") +> set(LAPACK_LIBS "-L/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch (revision 27955) @@ -0,0 +1,16 @@ +4,8c4,8 +< set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +< "Enable DAKOTA specification maintenance mode?") +< set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +--- +> #set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +> # "Enable DAKOTA specification maintenance mode?") +> #set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +14c14 +< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) +--- +> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch (revision 27955) @@ -0,0 +1,9 @@ +2587a2588 +> // add sensitivity output to importance factors (jes, 8/06/10) +2592c2593,2596 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch (revision 27955) @@ -0,0 +1,25 @@ +703,709c703,710 +< if (!subIteratorFlag) { +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +< // archive the correlations to the results DB +< nonDSampCorr.archive_correlations(run_identifier(), resultsDB, +< cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +< } +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) { +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +> // // archive the correlations to the results DB +> // nonDSampCorr.archive_correlations(run_identifier(), resultsDB, +> // cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1196,1197c1197,1200 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch (revision 27955) @@ -0,0 +1,35 @@ +107a108 +> initialized=0; //we run serially all the time! +133a135 +> initialized=0; //we run serially all the time! +141a144,171 +> /** This constructor is provided for the ISSM software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> dakotaMPIComm(MPI_COMM_WORLD), worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dummyFlag(false), +> stdOutputToFile(false), stdErrorToFile(false), checkFlag(false), +> preRunFlag(true), runFlag(true), postRunFlag(true), userModesFlag(false), +> outputTimings(true), startClock(0), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> initialize_timers(); +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.3.1 MPI executable in serial mode on CPU 0 for ISSM." << std::endl; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.3.1 serial executable in serial mode for ISSM." << std::endl; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> +> +1536a1567 +> initialized=0; //we run serially all the time! Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch (revision 27955) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the ISSM software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch (revision 27955) @@ -0,0 +1,4 @@ +25a26 +> #ifndef PI +26a28 +> #endif Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/BuildDakotaCustom.cmake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/BuildDakotaCustom.cmake.patch (revision 27955) @@ -0,0 +1,40 @@ +41,46c41,46 +< #set( BLAS_LIBS +< # "/usr/lib64" +< # CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +< #set( LAPACK_LIBS +< # "/usr/lib64" +< # CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +--- +> set( BLAS_LIBS +> "/usr/lib64/libblas.so.3.0.3" +> CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +> set( LAPACK_LIBS +> "/usr/lib64/liblapack.so.3.0.3" +> CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/DakotaDev.cmake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/DakotaDev.cmake.patch (revision 27955) @@ -0,0 +1,14 @@ +4,7c4,7 +< set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +< "Enable DAKOTA specification maintenance mode?") +--- +> #set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +> # "Enable DAKOTA specification maintenance mode?") +13c13 +< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) +--- +> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/NonDLocalReliability.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/NonDLocalReliability.cpp.patch (revision 27955) @@ -0,0 +1,9 @@ +2579a2580 +> // add sensitivity output to importance factors (jes, 8/06/10) +2584c2585,2588 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/NonDSampling.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/NonDSampling.cpp.patch (revision 27955) @@ -0,0 +1,25 @@ +703,709c703,710 +< if (!subIteratorFlag) { +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +< // archive the correlations to the results DB +< nonDSampCorr.archive_correlations(run_identifier(), resultsDB, +< cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +< } +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) { +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +> // // archive the correlations to the results DB +> // nonDSampCorr.archive_correlations(run_identifier(), resultsDB, +> // cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1196,1197c1197,1200 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch (revision 27955) @@ -0,0 +1,40 @@ +103a104 +> initialized=0; //we run serially all the time! +129a131 +> initialized=0; //we run serially all the time! +137a140,172 +> /** This constructor is provided for the ISSM software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dummyFlag(false), +> stdOutputToFile(false), stdErrorToFile(false), checkFlag(false), +> preRunFlag(true), runFlag(true), postRunFlag(true), userModesFlag(false), +> startClock(0), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> startClock = clock(); +> #ifdef DAKOTA_UTILIB +> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); +> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp +> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp +> #endif // DAKOTA_UTILIB +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.3 MPI executable in serial mode on CPU 0 for ISSM."; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.3 serial executable in serial mode for ISSM.\n"; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> +> +1517a1553 +> initialized=0; //we run serially all the time! Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch (revision 27955) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the ISSM software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/pecos_global_defs.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/pecos_global_defs.hpp.patch (revision 27955) @@ -0,0 +1,4 @@ +25a26 +> #ifndef PI +26a28 +> #endif Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/utilibExpat_patch.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/utilibExpat_patch.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/5.3/utilibExpat_patch.txt (revision 27955) @@ -0,0 +1,58 @@ +Index: CMakeLists.txt +=================================================================== +--- CMakeLists.txt (revision 1968) ++++ CMakeLists.txt (working copy) +@@ -30,6 +30,17 @@ + if(UTILIB_YES_MEMDEBUG) + add_definitions(-DUTILIB_YES_MEMDEBUG=1) + endif() ++option(UTILIB_HAVE_EXPAT "Enable expat in utilib" OFF) ++if (UTILIB_HAVE_EXPAT) ++ find_package(EXPAT) ++ if (EXPAT_FOUND) ++ # Use the same definition as autotools build ++ add_definitions("-DUTILIB_HAVE_EXPAT_H") ++ # TODO: add include path (EXPAT_INCLUDE_DIRS) in relevant subdirs? ++ else() ++ message(WARNING "expat requested, but not found") ++ endif() ++endif() + + #inspect the system so that we can generate utilib_config.h + include(CheckFunctionExists) +@@ -47,7 +58,6 @@ + CHECK_INCLUDE_FILES("windows.h;dbghelp.h" UTILIB_HAVE_DBGHELP_H) + CHECK_INCLUDE_FILE(err.h UTILIB_HAVE_ERR_H) + CHECK_INCLUDE_FILE(execinfo.h UTILIB_HAVE_EXECINFO_H) +-CHECK_INCLUDE_FILE(expat.h UTILIB_HAVE_EXPAT_H) + CHECK_INCLUDE_FILE(float.h UTILIB_HAVE_FLOAT_H) + CHECK_INCLUDE_FILE(limits.h UTILIB_HAVE_LIMITS_H) + CHECK_INCLUDE_FILE(strings.h UTILIB_HAVE_STRINGS_H) +@@ -57,9 +67,7 @@ + CHECK_INCLUDE_FILE(values.h UTILIB_HAVE_VALUES_H) + CHECK_INCLUDE_FILE(windows.h UTILIB_HAVE_WINDOWS_H) + +-find_library(EXPAT_LIB expat) + +- + # Use common HAVE_BOOST to indicate usage of Boost across packages + # Ultimately need to #define UTILIB_HAVE_BOOST if used + set(HAVE_BOOST OFF CACHE BOOL "Should Utilib use BOOST?") + + +Index: CMakeLists.txt +=================================================================== +--- src/libs/CMakeLists.txt 2013/03/25 19:19:06 1970 ++++ src/libs/CMakeLists.txt 2013/03/25 19:51:47 1971 +@@ -77,8 +77,9 @@ + list(APPEND libs ${MPI_LIBRARY}) + endif() + +-if(UTILIB_HAVE_EXPAT_H AND EXPAT_LIB) +- list(APPEND libs ${EXPAT_LIB}) ++if(UTILIB_HAVE_EXPAT AND EXPAT_FOUND) ++ include_directories(${EXPAT_INCLUDE_DIRS}) ++ list(APPEND libs ${EXPAT_LIBRARIES}) + endif() + if(MSVC) + list(APPEND libs dbghelp) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.mac.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.mac.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.mac.patch (revision 27955) @@ -0,0 +1,14 @@ +64,65c64,65 +< #set( DAKOTA_HAVE_MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE_MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.patch (revision 27955) @@ -0,0 +1,26 @@ +64,65c64,65 +< #set( DAKOTA_HAVE_MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE_MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/CMakeLists.txt.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/CMakeLists.txt.patch (revision 27955) @@ -0,0 +1,4 @@ +47a48,50 +> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE) +> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE) +> Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/CMakeLists.txt.pfe.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/CMakeLists.txt.pfe.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/CMakeLists.txt.pfe.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") +> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/DakotaDev.cmake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/DakotaDev.cmake.patch (revision 27955) @@ -0,0 +1,16 @@ +4,8c4,8 +< set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +< "Enable DAKOTA specification maintenance mode?") +< set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +--- +> #set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +> # "Enable DAKOTA specification maintenance mode?") +> #set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +14c14 +< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) +--- +> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/NonDLocalReliability.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/NonDLocalReliability.cpp.patch (revision 27955) @@ -0,0 +1,9 @@ +2645a2646 +> // add sensitivity output to importance factors (jes, 8/06/10) +2651c2652,2655 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/NonDSampling.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/NonDSampling.cpp.patch (revision 27955) @@ -0,0 +1,25 @@ +780,786c780,787 +< if (!subIteratorFlag) { +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +< // archive the correlations to the results DB +< nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels, +< div_labels, dsv_labels, drv_labels, +< iteratedModel.response_labels()); +< } +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) { +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +> // // archive the correlations to the results DB +> // nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels, +> // div_labels, dsv_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1277,1278c1278,1281 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +< drv_labels,iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +> // drv_labels,iteratedModel.response_labels()); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/ParallelLibrary.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/ParallelLibrary.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/ParallelLibrary.cpp.patch (revision 27955) @@ -0,0 +1,24 @@ +51a54,76 +> /** This constructor is provided for the ISSM software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> mpiManager(dummy_mpi_mgr), programOptions(dummy_prg_opt), +> outputManager(dummy_out_mgr), dummyFlag(true), outputTimings(false) +> { +> initialize_timers(); +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 6.1 MPI executable in serial mode on CPU 0 for ISSM." << std::endl; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 6.1 serial executable in serial mode for ISSM." << std::endl; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> increment_parallel_configuration(); +> } +> +> Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/ParallelLibrary.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/ParallelLibrary.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/ParallelLibrary.hpp.patch (revision 27955) @@ -0,0 +1,3 @@ +475a476,477 +> /// library mode constructor, serial mode (for the ISSM software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/pecos_global_defs.hpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.1/pecos_global_defs.hpp.patch (revision 27955) @@ -0,0 +1,4 @@ +25a26 +> #ifndef PI +26a28 +> #endif Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.aurora.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.aurora.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.aurora.patch (revision 27955) @@ -0,0 +1,38 @@ +54,55c54,55 +< #set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} " +< # CACHE STRING "CXX Flags for my platform" ) +--- +> set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK" +> CACHE STRING "CXX Flags for my platform" ) +67a68,78 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +> set( MPI_EXTRA_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use MPI extra libraries" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch (revision 27955) @@ -0,0 +1,35 @@ +54,55c54,55 +< #set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} " +< # CACHE STRING "CXX Flags for my platform" ) +--- +> set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK" +> CACHE STRING "CXX Flags for my platform" ) +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover20.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover20.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover20.patch (revision 27955) @@ -0,0 +1,35 @@ +54,55c54,55 +< #set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} " +< # CACHE STRING "CXX Flags for my platform" ) +--- +> set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK" +> CACHE STRING "CXX Flags for my platform" ) +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.mac.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.mac.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.mac.patch (revision 27955) @@ -0,0 +1,8 @@ +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.patch (revision 27955) @@ -0,0 +1,32 @@ +67a68,78 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +> set( MPI_EXTRA_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use MPI extra libraries" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch (revision 27955) @@ -0,0 +1,29 @@ +54,55c54,55 +< #set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} " +< # CACHE STRING "CXX Flags for my platform" ) +--- +> set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK" +> CACHE STRING "CXX Flags for my platform" ) +67a68,69 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ISSM_DIR/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.stallo.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.stallo.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.stallo.patch (revision 27955) @@ -0,0 +1,42 @@ +52,55c52,55 +< #set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} " +< # CACHE STRING "C Flags my platform" ) +< #set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} " +< # CACHE STRING "CXX Flags for my platform" ) +--- +> set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -L/lib64/libc.so.6 -L/lib64/ -lpthread -ldl -lm" +> CACHE STRING "C Flags my platform" ) +> set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -L/lib64/libc.so.6 -L/lib64/ -lpthread -ldl -lm" +> CACHE STRING "CXX Flags for my platform" ) +67a68,78 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/include64/" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/lib64/libmpi.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +> set( MPI_EXTRA_LIBRARY +> "/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/lib64/libmpi.so" +> CACHE FILEPATH "Use MPI extra libraries" FORCE) +73,77c84,88 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c102,104 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.yosemite.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.yosemite.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.yosemite.patch (revision 27955) @@ -0,0 +1,29 @@ +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.a" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.aurora.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.aurora.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.aurora.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/usr/local/intel/Composer/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/usr/local/intel/Composer/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover16.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover16.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover16.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/usr/local/intel/2016/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/usr/local/intel/2016/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover20.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover20.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover20.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/usr/local/intel/2020/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/usr/local/intel/2020/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.libvars.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.libvars.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.libvars.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS $ENV{BLAS_LIBS}) +> set(LAPACK_LIBS $ENV{LAPACK_LIBS}) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.lonestar.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.lonestar.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.lonestar.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L$TACC_MKL_LIB -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm") +> set(LAPACK_LIBS "-L$TACC_MKL_LIB -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.patch (revision 27955) @@ -0,0 +1,4 @@ +47a48,50 +> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE) +> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE) +> Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.petsclibs.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.petsclibs.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.petsclibs.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran") +> set(LAPACK_LIBS "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 27955) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core") +> set(LAPACK_LIBS "-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.stallo.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.stallo.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/CMakeLists.txt.stallo.patch (revision 27955) @@ -0,0 +1,9 @@ +229c229,231 +< option(BUILD_SHARED_LIBS "Build shared libraries?" ON) +--- +> option(BUILD_SHARED_LIBS "Build shared libraries?" ON) +> find_package(Threads) +> +237a240,241 +> set(BLAS_LIBS "-Wl,--no-as-needed -L/global/hds/software/cpu/eb3/imkl/11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/lib64/libc.so.6 -L/lib64/ -lpthread -lm -ldl") +> set(LAPACK_LIBS "-Wl,--no-as-needed -L/global/hds/software/cpu/eb3/imkl/11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/lib64/libc.so.6 -L/lib64/ -lpthread -lm -ldl") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/DakotaDev.cmake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/DakotaDev.cmake.patch (revision 27955) @@ -0,0 +1,14 @@ +5,8c5,8 +< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +< "Enable DAKOTA specification maintenance mode?") +< set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +--- +> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +> # "Enable DAKOTA specification maintenance mode?") +> #set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +14c14 +< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) +--- +> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/DakotaInterface.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/DakotaInterface.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/DakotaInterface.patch (revision 27955) @@ -0,0 +1,16 @@ +112c112 +< Cerr << "\nError: failure opening " << ampl_col << std::endl; +--- +> Cerr << "\nError: failure opening " << col.c_str() << std::endl; +121c121 +< Cerr << "\nError: failure reading AMPL col file " << ampl_col +--- +> Cerr << "\nError: failure reading AMPL col file " << col.c_str() +129c129 +< Cerr << "\nError: failure opening " << ampl_row << std::endl; +--- +> Cerr << "\nError: failure opening " << row.c_str() << std::endl; +142c142 +< Cerr << "\nError: failure reading AMPL row file " << ampl_row +--- +> Cerr << "\nError: failure reading AMPL row file " << row.c_str() Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/InstallDarwinDylibs.cmake.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/InstallDarwinDylibs.cmake.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/InstallDarwinDylibs.cmake.patch (revision 27955) @@ -0,0 +1,7 @@ +22,23c22,24 +< +< if ( DAKOTA_JENKINS_BUILD OR DEFINED ENV{WORKSPACE} ) +--- +> if ( DEFINED ENV{DAK_BUILD} ) +> set ( CMAKE_CURRENT_BINARY_DIR $ENV{DAK_BUILD} ) +> elseif ( DAKOTA_JENKINS_BUILD OR DEFINED ENV{WORKSPACE} ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/MainEffectsExcelOutput.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/MainEffectsExcelOutput.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/MainEffectsExcelOutput.patch (revision 27955) @@ -0,0 +1,4 @@ +276c276 +< std::cout << ss << std::endl; +--- +> std::cout << ss.str() << std::endl; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/NKM_KrigingModel.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/NKM_KrigingModel.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/NKM_KrigingModel.patch (revision 27955) @@ -0,0 +1,6 @@ +9d8 +< +86c85 +< << "has not been implemented." << std::cerr; +--- +> << "has not been implemented." << std::endl; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/NonDLocalReliability.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/NonDLocalReliability.cpp.patch (revision 27955) @@ -0,0 +1,9 @@ +2645a2646 +> // add sensitivity output to importance factors (jes, 8/06/10) +2651c2652,2655 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/NonDSampling.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/NonDSampling.cpp.patch (revision 27955) @@ -0,0 +1,25 @@ +780,786c780,787 +< if (!subIteratorFlag) { +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +< // archive the correlations to the results DB +< nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels, +< div_labels, dsv_labels, drv_labels, +< iteratedModel.response_labels()); +< } +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) { +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +> // // archive the correlations to the results DB +> // nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels, +> // div_labels, dsv_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1277,1278c1278,1281 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +< drv_labels,iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +> // drv_labels,iteratedModel.response_labels()); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.cmake (revision 27955) @@ -0,0 +1,97 @@ +############################################################################## +# +# Template CMake Configuration File. +# +############################################################################## +# The following CMake variables represent the minimum set of variables +# that are required to allow Dakota to +# * find all prerequisite third party libraries (TPLs) +# * configure compiler and MPI options +# * set Dakota install path +# +# Instructions: +# 1. Read Dakota/INSTALL - Source Quick Start to use this template file. +# +# 2. Uncomment CMake variables below ONLY for values you need to change for +# your platform. Edit variables as needed. +# +# For example, if you are using a custom install of Boost, installed in +# /home/me/usr/boost, uncomment both CMake Boost variables and edit +# paths: +# set(BOOST_ROOT +# "/home/me/usr/boost" +# CACHE PATH "Use non-standard Boost install" FORCE) +# set( Boost_NO_SYSTEM_PATHS TRUE +# CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +# +# Save file and exit. +# +# 6. Run CMake with script file. At terminal window, type: +# $ cmake -C BuildCustom.cmake $DAK_SRC +# +# If you have not followed instructions in INSTALL -Source Quick Start, +# you will need to replace BuildCustom.cmake with the actual filename of +# this file and $DAK_SRC with the actual path to Dakota source. +# +############################################################################## + +############################################################################## +# Set BLAS, LAPACK library paths ONLY if in non-standard locations +############################################################################## +set( BLAS_LIBS + "$ENV{BLAS_LIBS}" + CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +set( LAPACK_LIBS + "$ENV{LAPACK_LIBS}" + CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) + +############################################################################## +# Set additional compiler options +# Uncomment and replace with actual compiler flag, e.g. -xxe4.2 +############################################################################## +set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS}" + CACHE STRING "C Flags my platform" ) +set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}" + CACHE STRING "CXX Flags for my platform" ) +set( CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}" + CACHE STRING "Fortran Flags for my platform" ) + +############################################################################## +# Set MPI options +# Recommended practice is to set DAKOTA_HAVE_MPI and set MPI_CXX_COMPILER +# to a compiler wrapper. +############################################################################## +set( DAKOTA_HAVE_MPI ON + CACHE BOOL "Build with MPI enabled" FORCE) +set( MPI_INCLUDE_PATH "$ENV{MPI_INSTALL}/include" + CACHE FILEPATH "Use MPI headers" FORCE) +set( MPI_LIBRARY "-L$ENV{MPI_INSTALL}/lib -lmpich" + CACHE FILEPATH "Use MPI library" FORCE) +set( MPI_EXTRA_LIBRARY "-L$ENV{MPI_INSTALL}/lib -lmpich" + CACHE FILEPATH "Use MPI extra libraries" FORCE) + +############################################################################## +# Set Boost path if CMake cannot find your installed version of Boost or +# if you have a custom Boost install location. +############################################################################## +set(BOOST_ROOT + $ENV{BOOST_ROOT} + CACHE PATH "Use non-standard Boost install" FORCE) +set( Boost_NO_SYSTEM_PATHS TRUE + CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) + +############################################################################## +# Set Trilinos path if you want have a custom Trilinos install location. If +# not set, the Trilinos package, teuchos, will be build during the Dakota +# build. +############################################################################## +#set( Trilinos_DIR +# "path/to/Trilinos/install" +# CACHE PATH "Path to installed Trilinos" FORCE ) + +############################################################################## +# Customize DAKOTA +############################################################################## +set( CMAKE_INSTALL_PREFIX + $ENV{DAK_INSTALL} + CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.pleiades.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.pleiades.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.pleiades.cmake (revision 27955) @@ -0,0 +1,93 @@ +############################################################################## +# +# Template CMake Configuration File. +# +############################################################################## +# The following CMake variables represent the minimum set of variables +# that are required to allow Dakota to +# * find all prerequisite third party libraries (TPLs) +# * configure compiler and MPI options +# * set Dakota install path +# +# Instructions: +# 1. Read Dakota/INSTALL - Source Quick Start to use this template file. +# +# 2. Uncomment CMake variables below ONLY for values you need to change for +# your platform. Edit variables as needed. +# +# For example, if you are using a custom install of Boost, installed in +# /home/me/usr/boost, uncomment both CMake Boost variables and edit +# paths: +# set(BOOST_ROOT +# "/home/me/usr/boost" +# CACHE PATH "Use non-standard Boost install" FORCE) +# set( Boost_NO_SYSTEM_PATHS TRUE +# CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +# +# Save file and exit. +# +# 6. Run CMake with script file. At terminal window, type: +# $ cmake -C BuildCustom.cmake $DAK_SRC +# +# If you have not followed instructions in INSTALL -Source Quick Start, +# you will need to replace BuildCustom.cmake with the actual filename of +# this file and $DAK_SRC with the actual path to Dakota source. +# +############################################################################## + +############################################################################## +# Set BLAS, LAPACK library paths ONLY if in non-standard locations +############################################################################## +set( BLAS_LIBS + "$ENV{BLAS_LIBS}" + CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +set( LAPACK_LIBS + "$ENV{LAPACK_LIBS}" + CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) + +############################################################################## +# Set additional compiler options +# Uncomment and replace with actual compiler flag, e.g. -xxe4.2 +############################################################################## +#set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} " +# CACHE STRING "C Flags my platform" ) +set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK" + CACHE STRING "CXX Flags for my platform" ) +#set( CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} " +# CACHE STRING "Fortran Flags for my platform" ) + +############################################################################## +# Set MPI options +# Recommended practice is to set DAKOTA_HAVE_MPI and set MPI_CXX_COMPILER +# to a compiler wrapper. +############################################################################## +set( DAKOTA_HAVE_MPI ON + CACHE BOOL "Build with MPI enabled" FORCE) +#set( MPI_CXX_COMPILER "path/to/mpicxx" +# CACHE FILEPATH "Use MPI compiler wrapper" FORCE) + +############################################################################## +# Set Boost path if CMake cannot find your installed version of Boost or +# if you have a custom Boost install location. +############################################################################## +set(BOOST_ROOT + $ENV{BOOST_ROOT} + CACHE PATH "Use non-standard Boost install" FORCE) +set( Boost_NO_SYSTEM_PATHS TRUE + CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) + +############################################################################## +# Set Trilinos path if you want have a custom Trilinos install location. If +# not set, the Trilinos package, teuchos, will be build during the Dakota +# build. +############################################################################## +#set( Trilinos_DIR +# "path/to/Trilinos/install" +# CACHE PATH "Path to installed Trilinos" FORCE ) + +############################################################################## +# Customize DAKOTA +############################################################################## +set( CMAKE_INSTALL_PREFIX + $ENV{DAK_INSTALL} + CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/cmake/DakotaDev.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/cmake/DakotaDev.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/cmake/DakotaDev.cmake (revision 27955) @@ -0,0 +1,18 @@ +# CMake options for DAKOTA developer builds + +# Developer options +#set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +set(ENABLE_DAKOTA_DOCS FALSE CACHE BOOL "Enable DAKOTA documentation build") +set(ENABLE_SPEC_MAINT FALSE CACHE BOOL + "Enable DAKOTA specification maintenance mode?") +set(PECOS_ENABLE_TESTS FALSE CACHE BOOL "Enable Pecos-specific tests?") + +# Not included from Mike's configs, but may help some + +# Disable optional X graphics +#-DHAVE_X_GRAPHICS:BOOL=FALSE +set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) + +# CMake 2.8.6 has problems with RHEL6/Boost -- the following is a workaround +#-DBoost_NO_BOOST_CMAKE=ON +#set(Boost_NO_BOOST_CMAKE ON CACHE BOOL "Obtain desired behavior on RHEL6" FORCE) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/packages/pecos/src/pecos_global_defs.hpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/packages/pecos/src/pecos_global_defs.hpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/linux/packages/pecos/src/pecos_global_defs.hpp (revision 27955) @@ -0,0 +1,190 @@ +/* _______________________________________________________________________ + + PECOS: Parallel Environment for Creation Of Stochastics + Copyright (c) 2011, Sandia National Laboratories. + This software is distributed under the GNU Lesser General Public License. + For more information, see the README file in the top Pecos directory. + _______________________________________________________________________ */ + +#ifndef PECOS_GLOBAL_DEFS_H +#define PECOS_GLOBAL_DEFS_H + +#include +#include // for DBL_MIN, DBL_MAX +#include +#include + +#include + +namespace Pecos { + +// -------------- +// Special values +// -------------- +/// the value for PI used in various numerical routines +#ifndef PI +const double PI = boost::math::constants::pi(); +#endif + +/// special value returned by index() when entry not found +const size_t _NPOS = ~(size_t)0; // one's complement + +/// used in ostream data output functions +const int WRITE_PRECISION = 10; + +/// small value used for protecting division by zero, etc.; an alternative +/// to DBL_MIN that is less likely to cause underflow/overflow when numbers +/// larger than it are used in calculations +const double SMALL_NUMBER = 1.e-25; +/// large value used as a surrogate for infinity in error traps; an alternative +/// to DBL_MAX or inf that is less likely to cause underflow/overflow when used +/// in subsequent calculations +const double LARGE_NUMBER = 1.e+50; + +// define special values for vector/matrix data copying modes +enum { DEFAULT_COPY=0, SHALLOW_COPY, DEEP_COPY }; + +// define special values for ExpansionConfigOptions::outputLevel +enum { SILENT_OUTPUT, QUIET_OUTPUT, NORMAL_OUTPUT, VERBOSE_OUTPUT, + DEBUG_OUTPUT }; + +// define special values for ranVarTypesX/U +enum { NO_TYPE=0, CONTINUOUS_DESIGN, STD_NORMAL, NORMAL, BOUNDED_NORMAL, + LOGNORMAL, BOUNDED_LOGNORMAL, STD_UNIFORM, UNIFORM, LOGUNIFORM, + TRIANGULAR, STD_EXPONENTIAL, EXPONENTIAL, STD_BETA, BETA, STD_GAMMA, + GAMMA, GUMBEL, FRECHET, WEIBULL, HISTOGRAM_BIN, CONTINUOUS_INTERVAL, + CONTINUOUS_STATE, STOCHASTIC_EXPANSION }; + +// define special values for secondaryACVarMapTargets/secondaryADVarMapTargets +enum { NO_TARGET=0, CDV_LWR_BND, CDV_UPR_BND, DDRIV_LWR_BND, DDRIV_UPR_BND, + N_MEAN, N_STD_DEV, N_LWR_BND, N_UPR_BND, N_LOCATION, N_SCALE, LN_MEAN, + LN_STD_DEV, LN_LAMBDA, LN_ZETA, LN_ERR_FACT, LN_LWR_BND, LN_UPR_BND, + U_LWR_BND, U_UPR_BND, U_LOCATION, U_SCALE, LU_LWR_BND, LU_UPR_BND, + T_MODE, T_LWR_BND, T_UPR_BND, T_LOCATION, T_SCALE, E_BETA, + BE_ALPHA, BE_BETA, BE_LWR_BND, BE_UPR_BND, GA_ALPHA, GA_BETA, + GU_ALPHA, GU_BETA, F_ALPHA, F_BETA, W_ALPHA, W_BETA, + P_LAMBDA, BI_P_PER_TRIAL, BI_TRIALS, NBI_P_PER_TRIAL, NBI_TRIALS, + GE_P_PER_TRIAL, HGE_TOT_POP, HGE_SEL_POP, HGE_FAILED, + CSV_LWR_BND, CSV_UPR_BND, DSRIV_LWR_BND, DSRIV_UPR_BND }; + +/// derived basis approximation types +enum { NO_BASIS=0, //FOURIER_BASIS, EIGEN_BASIS, + GLOBAL_NODAL_INTERPOLATION_POLYNOMIAL, + PIECEWISE_NODAL_INTERPOLATION_POLYNOMIAL, + GLOBAL_HIERARCHICAL_INTERPOLATION_POLYNOMIAL, + PIECEWISE_HIERARCHICAL_INTERPOLATION_POLYNOMIAL, + GLOBAL_REGRESSION_ORTHOGONAL_POLYNOMIAL, + GLOBAL_PROJECTION_ORTHOGONAL_POLYNOMIAL, + GLOBAL_ORTHOGONAL_POLYNOMIAL }; + //PIECEWISE_REGRESSION_ORTHOGONAL_POLYNOMIAL, + //PIECEWISE_PROJECTION_ORTHOGONAL_POLYNOMIAL, + //PIECEWISE_ORTHOGONAL_POLYNOMIAL }; + +/// derived basis polynomial types (orthogonal polynomial order follows +/// uncertain variable spec order of normal, uniform, exponential, beta, gamma) +enum { NO_POLY=0, HERMITE_ORTHOG, LEGENDRE_ORTHOG, LAGUERRE_ORTHOG, + JACOBI_ORTHOG, GEN_LAGUERRE_ORTHOG, CHEBYSHEV_ORTHOG, NUM_GEN_ORTHOG, + LAGRANGE_INTERP, HERMITE_INTERP, PIECEWISE_LINEAR_INTERP, + PIECEWISE_QUADRATIC_INTERP, PIECEWISE_CUBIC_INTERP }; + +/// integration rules within VPISparseGrid (1-12: CC through User-closed) +/// and beyond (GOLUB_WELSCH, NEWTON_COTES) +enum { NO_RULE=0, CLENSHAW_CURTIS, FEJER2, GAUSS_PATTERSON, GAUSS_LEGENDRE, + GAUSS_HERMITE, GEN_GAUSS_HERMITE, GAUSS_LAGUERRE, GEN_GAUSS_LAGUERRE, + GAUSS_JACOBI, GENZ_KEISTER, /*USER_OPEN, USER_CLOSED,*/ GOLUB_WELSCH, + NEWTON_COTES }; + +// growth rules within VPISparseGrid +//enum { DEFAULT_GROWTH=0, SLOW_LINEAR, SLOW_LINEAR_ODD, MODERATE_LINEAR, +// SLOW_EXPONENTIAL, MODERATE_EXPONENTIAL, FULL_EXPONENTIAL }; + +/// options for synchronizing linear and exponential growth rule settings +/// (consistent with slow/moderate/full growth for new level_to_growth_* +/// functions in sandia_rules.cpp) +enum { SLOW_RESTRICTED_GROWTH, MODERATE_RESTRICTED_GROWTH, + UNRESTRICTED_GROWTH }; + +/// solution approaches for calculating the polynomial basis coefficients +/// (options for ExpansionConfigOptions::expCoeffsSolnApproach) +enum { QUADRATURE, CUBATURE, LIGHTWEIGHT_SPARSE_GRID, COMBINED_SPARSE_GRID, + HIERARCHICAL_SPARSE_GRID, SAMPLING, DEFAULT_REGRESSION, + DEFAULT_LEAST_SQ_REGRESSION, SVD_LEAST_SQ_REGRESSION, + EQ_CON_LEAST_SQ_REGRESSION, BASIS_PURSUIT, BASIS_PURSUIT_DENOISING, + ORTHOG_MATCH_PURSUIT, LASSO_REGRESSION, LEAST_ANGLE_REGRESSION, + ORTHOG_LEAST_INTERPOLATION }; +/// options for BasisConfigOptions::nestingOverride (inactive) +enum { NO_NESTING_OVERRIDE=0, NESTED, NON_NESTED }; +/// options for overriding the default growth restriction policy +enum { NO_GROWTH_OVERRIDE=0, RESTRICTED, UNRESTRICTED }; +/// options for ExpansionConfigOptions::refinementType (inactive) +enum { NO_REFINEMENT=0, P_REFINEMENT, H_REFINEMENT }; +/// options for ExpansionConfigOptions::refinementControl +enum { NO_CONTROL=0, UNIFORM_CONTROL, LOCAL_ADAPTIVE_CONTROL, + DIMENSION_ADAPTIVE_CONTROL_SOBOL, DIMENSION_ADAPTIVE_CONTROL_DECAY, + DIMENSION_ADAPTIVE_CONTROL_GENERALIZED }; + +/// options for expansion basis type +enum { DEFAULT_BASIS=0, TENSOR_PRODUCT_BASIS, TOTAL_ORDER_BASIS, + ADAPTED_BASIS_GENERALIZED, ADAPTED_BASIS_EXPANDING_FRONT, + NODAL_INTERPOLANT, HIERARCHICAL_INTERPOLANT }; + +/// mode of integration driver: integration versus interpolation +enum { DEFAULT_MODE=0, INTEGRATION_MODE, INTERPOLATION_MODE }; + +/// options for local basis functions within PiecewiseInterpPolynomial +enum { LINEAR_EQUIDISTANT, LINEAR, QUADRATIC_EQUIDISTANT, QUADRATIC, + CUBIC_EQUIDISTANT, CUBIC }; + +/// special values for nodal interpolation of variance and variance gradient +enum { INTERPOLATION_OF_PRODUCTS, REINTERPOLATION_OF_PRODUCTS, + PRODUCT_OF_INTERPOLANTS_FAST, PRODUCT_OF_INTERPOLANTS_FULL }; + +/// special values for polynomial expansion combination +enum { NO_COMBINE=0, ADD_COMBINE, MULT_COMBINE, ADD_MULT_COMBINE }; + + +// ---------------- +// Standard streams +// ---------------- +#define PCout std::cout +#define PCerr std::cerr + + +// -------------- +// Global objects +// -------------- +/// Dummy struct for overloading letter-envelope constructors. +/** BaseConstructor is used to overload the constructor for the base class + portion of letter objects. It avoids infinite recursion (Coplien p.139) + in the letter-envelope idiom by preventing the letter from instantiating + another envelope. Putting this struct here avoids circular dependencies. */ +struct BaseConstructor { + BaseConstructor(int = 0) {} ///< C++ structs can have constructors +}; + + +// ---------------- +// Global functions +// ---------------- + +/// global function which handles serial or parallel aborts +void abort_handler(int code); + + +inline void abort_handler(int code) +{ std::exit(code); } // for now, prior to use of MPI + + +/** Templatized abort_handler_t method that allows for convenient return from + methods that otherwise have no sensible return from error clauses. Usage: + MyType& method() { return abort_handler(-1); } */ +template +T abort_handler_t(int code) +{ + abort_handler(code); + throw code; +} + +} // namespace Pecos + +#endif // PECOS_GLOBAL_DEFS_H Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/cmake/BuildDakotaCustom.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/cmake/BuildDakotaCustom.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/cmake/BuildDakotaCustom.cmake (revision 27955) @@ -0,0 +1,95 @@ +############################################################################## +# +# Template CMake Configuration File. +# +############################################################################## +# The following CMake variables represent the minimum set of variables +# that are required to allow Dakota to +# * find all prerequisite third party libraries (TPLs) +# * configure compiler and MPI options +# * set Dakota install path +# +# Instructions: +# 1. Read Dakota/INSTALL - Source Quick Start to use this template file. +# +# 2. Uncomment CMake variables below ONLY for values you need to change for +# your platform. Edit variables as needed. +# +# For example, if you are using a custom install of Boost, installed in +# /home/me/usr/boost, uncomment both CMake Boost variables and edit +# paths: +# set(BOOST_ROOT +# "/home/me/usr/boost" +# CACHE PATH "Use non-standard Boost install" FORCE) +# set( Boost_NO_SYSTEM_PATHS TRUE +# CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +# +# Save file and exit. +# +# 6. Run CMake with script file. At terminal window, type: +# $ cmake -C BuildCustom.cmake $DAK_SRC +# +# If you have not followed instructions in INSTALL -Source Quick Start, +# you will need to replace BuildCustom.cmake with the actual filename of +# this file and $DAK_SRC with the actual path to Dakota source. +# +############################################################################## + +############################################################################## +# Set BLAS, LAPACK library paths ONLY if in non-standard locations +############################################################################## +set( BLAS_LIBS + "$ENV{BLAS_LIBS}" + CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +set( LAPACK_LIBS + "$ENV{LAPACK_LIBS}" + CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) + +############################################################################## +# Set additional compiler options +# Uncomment and replace with actual compiler flag, e.g. -xxe4.2 +############################################################################## +set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS}" + CACHE STRING "C Flags my platform" ) +set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}" + CACHE STRING "CXX Flags for my platform" ) +set( CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}" + CACHE STRING "Fortran Flags for my platform" ) + +############################################################################## +# Set MPI options +# Recommended practice is to set DAKOTA_HAVE_MPI and set MPI_CXX_COMPILER +# to a compiler wrapper. +############################################################################## +set( DAKOTA_HAVE_MPI ON + CACHE BOOL "Build with MPI enabled" FORCE) +set( MPI_INCLUDE_PATH "$ENV{MPI_INSTALL}/include" + CACHE FILEPATH "Use MPI headers" FORCE) +set( MPI_LIBRARY "-L$ENV{MPI_INSTALL}/lib -lmpich" + CACHE FILEPATH "Use MPI library" FORCE) + +############################################################################## +# Set Boost path if CMake cannot find your installed version of Boost or +# if you have a custom Boost install location. +############################################################################## +set(BOOST_ROOT + $ENV{BOOST_ROOT} + CACHE PATH "Use non-standard Boost install" FORCE) +set( Boost_NO_SYSTEM_PATHS TRUE + CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) + +############################################################################## +# Set Trilinos path if you want have a custom Trilinos install location. If +# not set, the Trilinos package, teuchos, will be build during the Dakota +# build. +############################################################################## +#set( Trilinos_DIR +# "path/to/Trilinos/install" +# CACHE PATH "Path to installed Trilinos" FORCE ) + +############################################################################## +# Customize DAKOTA +############################################################################## +set( CMAKE_INSTALL_PREFIX + $ENV{DAK_INSTALL} + CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/cmake/DakotaDev.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/cmake/DakotaDev.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/cmake/DakotaDev.cmake (revision 27955) @@ -0,0 +1,18 @@ +# CMake options for DAKOTA developer builds + +# Developer options +#set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +set(ENABLE_DAKOTA_DOCS FALSE CACHE BOOL "Enable DAKOTA documentation build") +set(ENABLE_SPEC_MAINT FALSE CACHE BOOL + "Enable DAKOTA specification maintenance mode?") +set(PECOS_ENABLE_TESTS FALSE CACHE BOOL "Enable Pecos-specific tests?") + +# Not included from Mike's configs, but may help some + +# Disable optional X graphics +#-DHAVE_X_GRAPHICS:BOOL=FALSE +set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) + +# CMake 2.8.6 has problems with RHEL6/Boost -- the following is a workaround +#-DBoost_NO_BOOST_CMAKE=ON +#set(Boost_NO_BOOST_CMAKE ON CACHE BOOL "Obtain desired behavior on RHEL6" FORCE) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/cmake/InstallDarwinDylibs.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/cmake/InstallDarwinDylibs.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/cmake/InstallDarwinDylibs.cmake (revision 27955) @@ -0,0 +1,132 @@ +# Find the Darwin dylib dependencies of dakota, excluding system libraries, +# and install to ${CMAKE_INSTALL_PREFIX}/bin + +# NOTE: This script will only work for make install from top of build tree +# TODO: Review string quoting conventions and test with spaces in filename + +# Function to install a single Dakota dll dependency +# (used by multiple platforms) +function(dakota_install_dll dakota_dll) + if (EXISTS "${dakota_dll}") + get_filename_component(dll_filename "${dakota_dll}" NAME) + message("-- Installing: ${CMAKE_INSTALL_PREFIX}/bin/${dll_filename}") + execute_process( + COMMAND + ${CMAKE_COMMAND} -E copy "${dakota_dll}" "${CMAKE_INSTALL_PREFIX}/bin" + ) + else() + message(WARNING "Install couldn't find dynamic dependency ${dakota_dll}") + endif() +endfunction() + +if ( DEFINED ENV{DAK_BUILD} ) + set ( CMAKE_CURRENT_BINARY_DIR $ENV{DAK_BUILD} ) +elseif ( DAKOTA_JENKINS_BUILD OR DEFINED ENV{WORKSPACE} ) + # By convention, all Dakota, jenkins-driven build jobs use a 'build' + # subdir for clear separation of source and build trees in the WORKSPACE + set( CMAKE_CURRENT_BINARY_DIR $ENV{WORKSPACE}/build ) +elseif ( NOT CMAKE_CURRENT_BINARY_DIR ) + set( CMAKE_CURRENT_BINARY_DIR $ENV{PWD} ) +endif() + +message( "CMAKE_SHARED_LIBRARY_SUFFIX: ${CMAKE_SHARED_LIBRARY_SUFFIX}" ) +#message( "... If NOT .dylib, then CMake cache is not respected" ) + +# otool may resolve symlinks, do the same for the build tree location +get_filename_component(resolved_build_dir ${CMAKE_CURRENT_BINARY_DIR} REALPATH) + +# Get the dylibs excluding system libraries as a semicolon-separated list +execute_process( + COMMAND otool -L "${CMAKE_CURRENT_BINARY_DIR}/src/dakota" + # Omit the header and get the library only + COMMAND awk "FNR > 1 {print $1}" + # Omit system libraries + COMMAND egrep -v "(^/System|^/usr/lib|^/usr/X11)" + COMMAND tr "\\n" ";" + OUTPUT_VARIABLE dakota_darwin_dylibs + ) + +# Probe the CMakeCache.txt for location of the known Boost dynlib dependency + +file( STRINGS ${CMAKE_CURRENT_BINARY_DIR}/CMakeCache.txt + Boost_LIBRARY_DIRS_PAIR REGEX "^Boost_LIBRARY_DIRS:FILEPATH=(.*)$" ) +string( REGEX REPLACE "^Boost_LIBRARY_DIRS:FILEPATH=(.*)$" "\\1" + Cached_Boost_LIBRARY_DIRS "${Boost_LIBRARY_DIRS_PAIR}" ) + +#message("Boost rpath=${Cached_Boost_LIBRARY_DIRS}") + +# Modify dakota_darwin_dylibs for "special case" of Boost +# otool DOES NOT return absolute path to Boost libs, so workaround the issue + +set(dakota_boost_dylibs "") + +# Ignore empty list elements: +cmake_policy(PUSH) +cmake_policy(SET CMP0007 OLD) + +foreach(pri_lib ${dakota_darwin_dylibs}) + string(REGEX REPLACE "^libboost_(.*)$" + "${Cached_Boost_LIBRARY_DIRS}/libboost_\\1" + boost_dylib_fullpath "${pri_lib}") + + if( ${pri_lib} MATCHES libboost_ ) + # REMOVE boost entries if NOT absolute path + list(REMOVE_ITEM dakota_darwin_dylibs ${pri_lib}) + list(APPEND dakota_boost_dylibs ${boost_dylib_fullpath}) + endif() +endforeach() + +# Get the secondary dylibs of the dylibs +foreach(pri_lib ${dakota_darwin_dylibs}) + execute_process( + COMMAND otool -L "${pri_lib}" + COMMAND awk "FNR > 1 {print $1}" + # Omit system libraries + COMMAND egrep -v "(^/System|^/usr/lib|^/usr/X11)" + COMMAND tr "\\n" ";" + OUTPUT_VARIABLE dakota_secondary_dylibs + ) + list(APPEND dakota_darwin_dylibs ${dakota_secondary_dylibs}) +endforeach() + +# Make a second pass over the list to prepend paths to boost libs that were +# discovered while looking for dakota_secondary_dylibs. Any duplicates +# will be removed below. +foreach(pri_lib ${dakota_darwin_dylibs}) + string(REGEX REPLACE "^libboost_(.*)$" + "${Cached_Boost_LIBRARY_DIRS}/libboost_\\1" + boost_dylib_fullpath "${pri_lib}") + + if( ${pri_lib} MATCHES libboost_ ) + # REMOVE boost entries if NOT absolute path + list(REMOVE_ITEM dakota_darwin_dylibs ${pri_lib}) + list(APPEND dakota_boost_dylibs ${boost_dylib_fullpath}) + endif() +endforeach() + +# otool finished proccessing dylibs - +# OK to "re-insert" Boost dylibs into the list (ABSOLUTE PATH!) + +#message("Boost dylibs=${dakota_boost_dylibs}") +list(APPEND dakota_darwin_dylibs ${dakota_boost_dylibs}) + +list(REMOVE_DUPLICATES dakota_darwin_dylibs) +cmake_policy(POP) + +# Process each DLL and install, excluding anything in the build tree +foreach(dakota_dll ${dakota_darwin_dylibs}) + string(REGEX REPLACE "^${CMAKE_CURRENT_BINARY_DIR}(.*)$" + "dak_omit/\\1" omit_btree_dll "${dakota_dll}") + string(REGEX REPLACE "^${resolved_build_dir}(.*)$" + "dak_omit/\\1" omit_resolved_btree_dll "${dakota_dll}") + + if( ${omit_btree_dll} MATCHES dak_omit ) + #message("-- EXCLUDE: ${omit_btree_dll} - OK, already installed in lib") + message("-- EXCLUDE: ${dakota_dll} - OK, already installed in lib") + elseif( ${omit_resolved_btree_dll} MATCHES dak_omit ) + message("-- EXCLUDE: ${dakota_dll} - OK, already installed in lib") + else() + dakota_install_dll("${dakota_dll}") + endif() +endforeach() + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/include/xtndispatch.h =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/include/xtndispatch.h (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/include/xtndispatch.h (revision 27955) @@ -0,0 +1,147 @@ +/* This code was computer generated */ + +/* + + These programs construct and manipulate orthogonal +arrays. They were prepared by + + Art Owen + Department of Statistics + Sequoia Hall + Stanford CA 94305 + + They may be freely used and shared. This code comes +with no warranty of any kind. Use it at your own +risk. + + I thank the Semiconductor Research Corporation and +the National Science Foundation for supporting this +work. + +*/ + +/* Fix for C99 */ +extern int ipow(int a, int b); /* primes.c */ + +if( q== ipow(2,2) )xtn = xtn2t2; +if( q== ipow(2,3) )xtn = xtn2t3; +if( q== ipow(2,4) )xtn = xtn2t4; +if( q== ipow(2,5) )xtn = xtn2t5; +if( q== ipow(2,6) )xtn = xtn2t6; +if( q== ipow(2,7) )xtn = xtn2t7; +if( q== ipow(2,8) )xtn = xtn2t8; +if( q== ipow(2,9) )xtn = xtn2t9; +if( q== ipow(2,10) )xtn = xtn2t10; +if( q== ipow(2,11) )xtn = xtn2t11; +if( q== ipow(2,12) )xtn = xtn2t12; +if( q== ipow(2,13) )xtn = xtn2t13; +if( q== ipow(2,14) )xtn = xtn2t14; +if( q== ipow(2,15) )xtn = xtn2t15; +if( q== ipow(2,16) )xtn = xtn2t16; +if( q== ipow(2,17) )xtn = xtn2t17; +if( q== ipow(2,18) )xtn = xtn2t18; +if( q== ipow(2,19) )xtn = xtn2t19; +if( q== ipow(2,20) )xtn = xtn2t20; +if( q== ipow(2,21) )xtn = xtn2t21; +if( q== ipow(2,22) )xtn = xtn2t22; +if( q== ipow(2,23) )xtn = xtn2t23; +if( q== ipow(2,24) )xtn = xtn2t24; +if( q== ipow(2,25) )xtn = xtn2t25; +if( q== ipow(2,26) )xtn = xtn2t26; +if( q== ipow(2,27) )xtn = xtn2t27; +if( q== ipow(2,28) )xtn = xtn2t28; +if( q== ipow(2,29) )xtn = xtn2t29; +if( q== ipow(3,2) )xtn = xtn3t2; +if( q== ipow(3,3) )xtn = xtn3t3; +if( q== ipow(3,4) )xtn = xtn3t4; +if( q== ipow(3,5) )xtn = xtn3t5; +if( q== ipow(3,6) )xtn = xtn3t6; +if( q== ipow(3,7) )xtn = xtn3t7; +if( q== ipow(3,8) )xtn = xtn3t8; +if( q== ipow(3,9) )xtn = xtn3t9; +if( q== ipow(3,10) )xtn = xtn3t10; +if( q== ipow(3,11) )xtn = xtn3t11; +if( q== ipow(3,12) )xtn = xtn3t12; +if( q== ipow(3,13) )xtn = xtn3t13; +if( q== ipow(3,14) )xtn = xtn3t14; +if( q== ipow(3,15) )xtn = xtn3t15; +if( q== ipow(3,16) )xtn = xtn3t16; +if( q== ipow(3,17) )xtn = xtn3t17; +if( q== ipow(3,18) )xtn = xtn3t18; +if( q== ipow(5,2) )xtn = xtn5t2; +if( q== ipow(5,3) )xtn = xtn5t3; +if( q== ipow(5,4) )xtn = xtn5t4; +if( q== ipow(5,5) )xtn = xtn5t5; +if( q== ipow(5,6) )xtn = xtn5t6; +if( q== ipow(5,7) )xtn = xtn5t7; +if( q== ipow(5,8) )xtn = xtn5t8; +if( q== ipow(5,9) )xtn = xtn5t9; +if( q== ipow(5,10) )xtn = xtn5t10; +if( q== ipow(5,11) )xtn = xtn5t11; +if( q== ipow(5,12) )xtn = xtn5t12; +if( q== ipow(7,2) )xtn = xtn7t2; +if( q== ipow(7,3) )xtn = xtn7t3; +if( q== ipow(7,4) )xtn = xtn7t4; +if( q== ipow(7,5) )xtn = xtn7t5; +if( q== ipow(7,6) )xtn = xtn7t6; +if( q== ipow(7,7) )xtn = xtn7t7; +if( q== ipow(7,8) )xtn = xtn7t8; +if( q== ipow(7,9) )xtn = xtn7t9; +if( q== ipow(7,10) )xtn = xtn7t10; +if( q== ipow(11,2) )xtn = xtn11t2; +if( q== ipow(11,3) )xtn = xtn11t3; +if( q== ipow(11,4) )xtn = xtn11t4; +if( q== ipow(11,5) )xtn = xtn11t5; +if( q== ipow(11,6) )xtn = xtn11t6; +if( q== ipow(11,7) )xtn = xtn11t7; +if( q== ipow(11,8) )xtn = xtn11t8; +if( q== ipow(13,2) )xtn = xtn13t2; +if( q== ipow(13,3) )xtn = xtn13t3; +if( q== ipow(13,4) )xtn = xtn13t4; +if( q== ipow(13,5) )xtn = xtn13t5; +if( q== ipow(13,6) )xtn = xtn13t6; +if( q== ipow(13,7) )xtn = xtn13t7; +if( q== ipow(13,8) )xtn = xtn13t8; +if( q== ipow(17,2) )xtn = xtn17t2; +if( q== ipow(17,3) )xtn = xtn17t3; +if( q== ipow(17,4) )xtn = xtn17t4; +if( q== ipow(17,5) )xtn = xtn17t5; +if( q== ipow(17,6) )xtn = xtn17t6; +if( q== ipow(17,7) )xtn = xtn17t7; +if( q== ipow(19,2) )xtn = xtn19t2; +if( q== ipow(19,3) )xtn = xtn19t3; +if( q== ipow(19,4) )xtn = xtn19t4; +if( q== ipow(19,5) )xtn = xtn19t5; +if( q== ipow(19,6) )xtn = xtn19t6; +if( q== ipow(19,7) )xtn = xtn19t7; +if( q== ipow(23,2) )xtn = xtn23t2; +if( q== ipow(23,3) )xtn = xtn23t3; +if( q== ipow(23,4) )xtn = xtn23t4; +if( q== ipow(23,5) )xtn = xtn23t5; +if( q== ipow(23,6) )xtn = xtn23t6; +if( q== ipow(29,2) )xtn = xtn29t2; +if( q== ipow(29,3) )xtn = xtn29t3; +if( q== ipow(29,4) )xtn = xtn29t4; +if( q== ipow(29,5) )xtn = xtn29t5; +if( q== ipow(29,6) )xtn = xtn29t6; +if( q== ipow(31,2) )xtn = xtn31t2; +if( q== ipow(31,3) )xtn = xtn31t3; +if( q== ipow(31,4) )xtn = xtn31t4; +if( q== ipow(31,5) )xtn = xtn31t5; +if( q== ipow(31,6) )xtn = xtn31t6; +if( q== ipow(37,2) )xtn = xtn37t2; +if( q== ipow(37,3) )xtn = xtn37t3; +if( q== ipow(37,4) )xtn = xtn37t4; +if( q== ipow(37,5) )xtn = xtn37t5; +if( q== ipow(41,2) )xtn = xtn41t2; +if( q== ipow(41,3) )xtn = xtn41t3; +if( q== ipow(41,4) )xtn = xtn41t4; +if( q== ipow(41,5) )xtn = xtn41t5; +if( q== ipow(43,2) )xtn = xtn43t2; +if( q== ipow(43,3) )xtn = xtn43t3; +if( q== ipow(43,4) )xtn = xtn43t4; +if( q== ipow(43,5) )xtn = xtn43t5; +if( q== ipow(47,2) )xtn = xtn47t2; +if( q== ipow(47,3) )xtn = xtn47t3; +if( q== ipow(47,4) )xtn = xtn47t4; +if( q== ipow(47,5) )xtn = xtn47t5; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/boselink.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/boselink.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/boselink.c (revision 27955) @@ -0,0 +1,150 @@ +#if defined(HAVE_CONFIG_H) && !defined(DISABLE_DAKOTA_CONFIG_H) + #include "ddace_config.h" +#endif +#include +#include +#include "galois.h" + +/* Fix for C99*/ +extern int bose(struct GF *gf, int **A, int ncol); /* construct.c */ +extern int bush(struct GF *gf, int **A, int str, int ncol); /* construct.c */ +extern void GF_free(struct GF *gf); /* galois.c */ +extern int GF_getfield(int q, struct GF *gf); /* gfields.c */ + +int bose_link( int n, int ninputs, int str, int ***AA ) +{ + int i, nsym, nsamples, **A; + double dtemp, dpower; + struct GF gf; + + if ( n <= 0 ) return -1; + + /* only one method for strength of 3 */ + + if ( str == 3 ) + { + dtemp = (double) n; + dtemp = pow(dtemp, 0.333333334); + nsym = (int) dtemp; + if( ninputs > (nsym+1) ){ + fprintf(stderr,"Only q+1 = %d cols given in Bush design.\n",nsym+1); + fprintf(stderr,"Columns requested was %d.\n",ninputs); + return -1; + } + if( !GF_getfield(nsym, &gf) ) { + fprintf(stderr,"Could not construct the Galois field needed\n"); + fprintf(stderr,"for the strength 3 Bush design.\n"); + GF_free( &gf ); + return -1; + } + nsamples = nsym * nsym * nsym; + A = imatrix( 0, nsamples, 0, ninputs-1 ); + if( !A ) + { + fprintf(stderr,"Could not allocate array for Bush design.\n"); + GF_free( &gf ); + return -1; + } + if( ! bush( &gf, A, 3, ninputs ) ) + { + fprintf(stderr,"Unable to construct the strength 3 "); + fprintf(stderr,"Bush design nsym=%d, ninputs=%d.\n", nsym,ninputs); + GF_free( &gf ); + return -1; + } + else + { + (*AA) = A; + return nsamples; + } + } + + /* only one method for strength greater than 3 */ + + if ( str > 3 ) + { + dtemp = (double) n; + dpower = 1.0 / (double) str + 0.00000001; + dtemp = pow(dtemp, dpower); + nsym = (int) dtemp; + if( ninputs > (nsym+1) ){ + fprintf(stderr,"Only q+1 = %d cols given in Bush design.\n",nsym+1); + fprintf(stderr,"Columns requested was %d.\n",ninputs); + return -1; + } + nsamples = nsym; + for ( i = 1; i < str; i++ ) nsamples = nsamples * nsym; + if( !GF_getfield(nsym, &gf) ){ + fprintf(stderr,"Could not construct the Galois field needed\n"); + fprintf(stderr,"for the strength %d Bush design\n",str); + fprintf(stderr,"on %d levels.\n", nsym); + GF_free( &gf ); + return -1; + } + A = imatrix( 0, nsamples-1, 0, ninputs-1 ); + if( !A ) + { + fprintf(stderr,"Could not allocate array for Bush design.\n"); + GF_free( &gf ); + return -1; + } + if( ! bush( &gf, A, str, ninputs ) ) + { + fprintf(stderr,"Unable to construct the strength %d \n", str); + fprintf(stderr,"Bush design nsym=%d, ninputs=%d.\n", nsym,ninputs); + GF_free( &gf ); + return -1; + } + else + { + (*AA) = A; + GF_free( &gf ); + return nsamples; + } + } + + /* for the cases when strength = 2 */ + + if ( str == 2 ) + { + dtemp = (double) n; + dtemp = pow(dtemp, 0.500001); + nsym = (int) dtemp; + + if ( ninputs > ( nsym + 1 ) ) + { + fprintf(stderr,"Number of samples too small to construct OA.\n"); + fprintf(stderr,"Need at least %d. \n", (ninputs-1)*(ninputs-1)); + return -1; + } + if( !GF_getfield( nsym, &gf) ) + { + fprintf(stderr,"Could not construct Galois field needed\n"); + fprintf(stderr,"for Bose design.\n"); + GF_free( &gf ); + return -1; + } + nsamples = nsym * nsym; + A = imatrix( 0, nsamples-1, 0, ninputs-1 ); + if( !A ) + { + fprintf(stderr,"Could not allocate array for Bose design.\n"); + GF_free( &gf ); + return -1; + } + if( ! bose( &gf, A, ninputs ) ) + { + fprintf(stderr,"Unable to construct Bose design q=%d,",nsym); + fprintf(stderr," ninputs=%d.\n", ninputs); + GF_free( &gf ); + return -1; + } + else + { + (*AA) = A; + GF_free( &gf ); + return nsamples; + } + } +} + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/construct.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/construct.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/construct.c (revision 27955) @@ -0,0 +1,410 @@ +#if defined(HAVE_CONFIG_H) && !defined(DISABLE_DAKOTA_CONFIG_H) + #include "ddace_config.h" +#endif +/* + + These programs construct and manipulate orthogonal +arrays. They were prepared by + + Art Owen + Department of Statistics + Sequoia Hall + Stanford CA 94305 + + They may be freely used and shared. This code comes +with no warranty of any kind. Use it at your own +risk. + + I thank the Semiconductor Research Corporation and +the National Science Foundation for supporting this +work. + +*/ + + +/* Constructions for designs using Galois fields */ + +#include +#include + +#include "galois.h" + +/* Fix for C99 */ +extern int ipow(int a, int b); /* primes.c */ +extern int isprime(int p); /* primes.c */ +extern void free_ivector(int *v, int nl, int nh); /* memory.c */ +extern void free_imatrix(int **m, int nrl, int nrh, int ncl, int nch); /* memory.c */ +extern int akodd(struct GF *gf, int *kay, int *b, int *c, int *k); /* akconst.c */ +extern int akeven(struct GF *gf, int *kay, int *b, int *c, int *k); /* akconst.c */ + +/* Glossary: + + bose: OA( q^2, q+1, q, 2 ) + R.C. Bose (1938) Sankhya Vol 3 pp 323-338 + bosecheck: test input to bose + + bosebush: OA( 2q^2, 2q+1, q, 2 ), only implemented for q=2^n + bosebushcheck: test input to bosebush + + polyeval: evaluate a polynomial with coefficients, argument + and result in a Galois field + +*/ + + +bosecheck( q,ncol ) +int q, ncol; +{ +if( ncol > q+1 ){ + fprintf(stderr,"Bose's design must have ncol <= q+1.\n"); + fprintf(stderr,"Had q=%d and ncol=%d.\n",q,ncol); + return 0; +} +if( ncol <= 0 ){ + fprintf(stderr,"Nonpositive number of columns requested for Bose's design\n"); + return 0; +} +return 1; +} + + +bose( gf, A, ncol ) +struct GF *gf; +int **A, ncol; +{ +int i,j, icol, q=gf->q, irow; + +if( !bosecheck(q,ncol) )return 0; + +irow = 0; +for( i=0; i 1 )A[ irow ][ icol++ ] = j; + for( icol=2; icolplus[j][gf->times[i][icol-1]]; + irow++; +} + + +return 1; +} + +itopoly( n,q,d,coef ) +int n,q,d,*coef; +{ +int i; + +for( i=0; i<=d; i++ ){ + coef[i] = n % q; + n = n/q; +} +} + + +polyeval( gf, d, poly, arg, value ) +/* find value = poly(arg) where poly is a polynomial of degree d + and all the arithmetic takes place in the given Galois field.*/ + +struct GF *gf; +int d, *poly, arg, *value; +{ +int i,ans; + +ans = 0; +for( i= d; i>=0; i-- ) /* Horner's rule */ + ans = gf->plus[ gf->times[ans][arg] ][ poly[i] ]; + +*value = ans; +} + +bushcheck(q,str,ncol) +int q,str,ncol; +{ +if( ncol > q+1 ){ + fprintf(stderr,"Bush designs require ncol <= q+1.\n"); + fprintf(stderr,"Cannot have q = %d and ncol = %d.\n",q,ncol); + return 0; +} +if( str > ncol ){ + fprintf(stderr,"It doesn't make sense to have an array of strength\n"); + fprintf(stderr,"%d with only %d columns.\n",str,ncol); + return 0; +} +if( str >= q+1 ){ + fprintf(stderr,"Bush's (1952) theorem has a condition tq; +if( !bushcheck(q,str,ncol) )return 0; + +coef = ivector( 0,str-1 ); +if( !coef ){ /* Very unlikely */ + fprintf(stderr,"Could not allocate memory for Bush design.\n"); + return 0; +} + +for( i=0; i4 ){ + fprintf(stderr,"This Addelman-Kempthorne OA(2q^2,ncol,q,2) is only\n"); + fprintf(stderr,"available for odd prime powers q and for even prime\n"); + fprintf(stderr,"powers q<=4. q=%d is not available, but a Bose Bush\n",q); + fprintf(stderr,"construction exists for that design.\n"); + return 0; +} + +if( ncol > 2*q+1 ){ + fprintf(stderr,"The Addelman-Kempthorne construction needs ncol <= 2q+1.\n"); + fprintf(stderr,"Can't have ncol = %d with q = %d,\n",ncol,q); + return 0; +} + +if( ncol == 2*q+1 ){ + fprintf(stderr,"\nWarning: The Addelman-Kempthorne construction with ncol = 2q+1\n"); + fprintf(stderr,"has a defect. While it is still an OA(2q^2,2q+1,q,2),\n"); + fprintf(stderr,"there exist some pairs of rows that agree in three columns.\n"); + fprintf(stderr,"The final column in the array is involved in all of these\n"); + fprintf(stderr,"triple coincidences.\n\n\n"); +} +return 1; +} + + +addelkemp( gf, A, ncol ) +/* Implement Addelman and Kempthorne's 1961 A.M.S. method with n=2 */ +struct GF *gf; +int ncol, **A; +{ +int i,j,m,p,q; +int kay,*b,*c,*k; /* A&K notation */ +int row, col, square, ksquare, temp; + +p=gf->p, q=gf->q; + +if( !addelkempcheck( q,p,ncol ) )return 0; + +b = ivector( 0,q-1 ); +c = ivector( 0,q-1 ); +k = ivector( 0,q-1 ); + +for( i=0; itimes[i][i]; + for( j=0; jplus[i][gf->times[m][j]]; + for( m=0; mplus[j][gf->times[m][i]]; + A[row][col++] = gf->plus[temp][square]; /* Rgt cols */ + } + if( coltimes[i][i]; + ksquare = gf->times[kay][square]; + for( j=0; jplus[A[row-q*q][col]][b[m]]; + if( colplus[ksquare][j]; /* q+1 */ + for( m=1; mtimes[i][k[m]]; + temp = gf->plus[ksquare][temp]; + temp = gf->plus[j][temp]; + A[row][col++] = gf->plus[temp][c[m]]; + } + if( col 2*q+1 ){ + fprintf(stderr,"The Bose-Bush construction needs ncol <= 2q+1.\n"); + fprintf(stderr,"Can't have ncol = %d with q = %d,\n",ncol,q); + return 0; +} + +if( ncol == 2*q+1 ){ + fprintf(stderr,"\nWarning: The Bose-Bush construction with ncol = 2q+1\n"); + fprintf(stderr,"has a defect. While it is still an OA(2q^2,2q+1,q,2),\n"); + fprintf(stderr,"there exist some pairs of rows that agree in three columns.\n\n\n"); +} +return 1; +} + +bosebush( gf, B, ncol ) +/* Implement Bose and Bush's 1952 A.M.S. method with p=2, u=1 */ +struct GF *gf; +int **B; +{ +int p,q,s,irow; +int i,j,k,mul; +int **A; + +p=gf->p, /* GF(q) used to generate design with q/2 levels */ +q=gf->q; +s=q/2; /* number of levels in design */ + +if( !bosebushcheck( s,p,ncol ) ) + return 0; + +A = imatrix(0,s-1,0,q-1); +if( !A ){ + fprintf(stderr,"Unable to allocate scratch space for Bose-Bush array.\n"); + return 0; +} + +irow = 0; +for( i=0; itimes[i][j]; + mul = mul % s; + for( k=0; kplus[mul][k];*/ + A[k][j] = gf->plus[mul][k]; + } + for( k=0; k lam*s+1 ){ + fprintf(stderr,"The Bose-Bush construction needs ncol <= lambda*q+1.\n"); + fprintf(stderr,"Can't have ncol = %d with lam = %d and q = %d,\n",ncol,lam,s); + return 0; +} + +if( ncol == lam*s+1 ){ + fprintf(stderr,"\nWarning: The Bose-Bush construction with ncol = lambda*q+1\n"); + fprintf(stderr,"has a defect. While it is still an OA(lambda*q^2,lambda*q+1,q,2),\n"); + fprintf(stderr,"it may have worse coincidence properties than\n"); + fprintf(stderr,"OA(lambda*q^2,lambda*q+1,q,2).\n"); +} +return 1; +} + +bosebushl( gf, lam, B, ncol ) +/* Implement Bose and Bush's 1952 A.M.S. method with given lambda */ +struct GF *gf; +int **B, lam; +{ +int p,q,s,irow; +int i,j,k,mul; +int **A; + +p=gf->p, /* GF(q) used to generate design with q/lam levels */ +q=gf->q; +s=q/lam; /* number of levels in design */ + +if( !bosebushlcheck( s,p,lam,ncol ) ) + return 0; + +A = imatrix(0,s-1,0,q-1); +if( !A ){ + fprintf(stderr,"Unable to allocate scratch space for Bose-Bush array.\n"); + return 0; +} + +irow = 0; +for( i=0; itimes[i][j]; + mul = mul % s; + for( k=0; kplus[mul][k];*/ + A[k][j] = gf->plus[mul][k]; + } + for( k=0; k +#include + +#include "galois.h" + +/* Fix for C99 */ +extern void free_ivector(int v, int nl, int nh); /* memory.c */ +extern void free_imatrix(int m, int nrl, int nrh, int ncl, int nch); /* memory.c */ + +/* Glossary: + + GF_poly_sum Addition in polynomial representation + GF_poly_prod Multiplication in polynomial representation + GF_poly2int Convert polynomial to integer in 0..q-1 + GF_ready Prepare (+,*,^-1) lookup tables + GF_print Print Galois field + GF_free Free storage + +*/ + + +/*---------------------------------------------------------------*/ + +GF_poly_sum( p,n,p1,p2,sum ) +int n,p,*p1,*p2,*sum; +{ +int i; + +for( i=0; in-1; i-- ) +for( j=0; j0; i-- ) + ans = (ans+poly[i])*p; +ans += poly[0]; + +return ans; +} + +/*---------------------------------------------------------------*/ + +#define GFPUNT {fprintf(stderr,"Unable to allocate space for Galois field on %d elements.\n",q);return 0;} + +GF_ready( gf,p,n,xton ) +/* + Make ready the Galois Field +*/ +struct GF *gf; +int n,p,*xton; +{ +int i,j,q,click,*poly; + +poly = ivector(0,n-1); + +gf->n = n; +gf->p = p; +q = 1; +for( i=0; iq = q; +gf->xton = ivector(0,n-1); if( !gf->xton )GFPUNT; +for( i=0; ixton[i] = xton[i]; +gf->plus = imatrix(0,q-1,0,q-1); if( !gf->plus )GFPUNT; +gf->times= imatrix(0,q-1,0,q-1); if( !gf->times )GFPUNT; +gf->inv = ivector(0,q-1); if( !gf->inv )GFPUNT; +gf->neg = ivector(0,q-1); if( !gf->neg )GFPUNT; +gf->root = ivector(0,q-1); if( !gf->root )GFPUNT; +gf->poly = imatrix(0,q-1,0,n-1); if( !gf->poly )GFPUNT; + +for( i=0; ipoly[0][i] = 0; + +for( i=1; ipoly[i-1][click]==(p-1); click++ ) + gf->poly[i][click] = 0; + gf->poly[i][click] = gf->poly[i-1][click]+1; + for( j=click+1; jpoly[i][j] = gf->poly[i-1][j]; +} + +for( i=0; ipoly[i],gf->poly[j],poly ); + gf->plus[i][j] = GF_poly2int( p,n,poly ); + GF_poly_prod( p,n,xton,gf->poly[i],gf->poly[j],poly ); + gf->times[i][j] = GF_poly2int( p,n,poly ); +} + +for( i=0; iinv[i] = -1; + for( j=0; jtimes[i][j]==1 ) + gf->inv[i] = j; + if( i>0 && gf->inv[i] <= 0 ){ + fprintf(stderr,"There is something wrong with the Galois field\n"); + fprintf(stderr,"used for q=%d. Element %d has no reciprocal.\n",q,i); + return 0; + } +} + +for( i=0; ineg[i] = -1; + for( j=0; jplus[i][j]==0 ) + gf->neg[i] = j; + if( i>0 && gf->neg[i] <= 0 ){ + fprintf(stderr,"There is something wrong with the Galois field\n"); + fprintf(stderr,"used for q=%d. Element %d has no negative.\n",q,i); + return 0; + } +} + +for( i=0; iroot[i] = -1; + for( j=0; jtimes[j][j]==i ) + gf->root[i] = j; +} + +/*printf("%d %d %d\n",q,p,n);*/ + +/* Added by J Cramp 07.02.04 to fix memory leak. */ +free_ivector(poly,0,n-1); + +return 1; +} + +/*---------------------------------------------------------------*/ + +GF_print( gf ) + +struct GF *gf; +{ +int i,j,n,p,q; + +n=gf->n, p=gf->p, q=gf->q; + +if( q>999 )fprintf(stderr,"Warning q=%d will overflow print field.\n",q); + +printf("\nFor GF(%d) p=%d n=%d\n",q,p,n); +printf("x**n = ("); +for( i=0; ixton[i]); +printf("%d)\n",gf->xton[n-1]); +printf("\n\nGF(%d) Polynomial coefficients:\n",q); +for( i=0; ipoly[i][j]); + printf("\n"); +} +printf("\n\nGF(%d) Addition Table\n",q); +for( i=0; iplus[i][j]); + printf("\n"); +} +printf("\n\nGF(%d) Multiplication table\n",q); +for( i=0; itimes[i][j]); + printf("\n"); +} +printf("\n\nGF(%d) Reciprocals\n",q); +for( i=1; iinv[i]); + +printf("\n\nGF(%d) Negatives\n",q); +for( i=0; ineg[i]); + +printf("\n\nGF(%d) Square roots\n",q); +for( i=0; iroot[i]); +} + +/*---------------------------------------------------------------*/ + +GF_free( gf ) +/* + Deallocate the Galois Field +*/ +struct GF *gf; +{ +/*int q,p,n; +q = gf->q, p=gf->p, n=gf->n;*/ + +int q,n; +q = gf->q, n=gf->n; /* Shuts lint up */ + +free_imatrix(gf->poly,0,q-1,0,n-1); +free_ivector(gf->root,0,q-1); +free_ivector(gf->neg,0,q-1); +free_ivector(gf->inv,0,q-1); +free_imatrix(gf->times,0,q-1,0,q-1); +free_imatrix(gf->plus,0,q-1,0,q-1); +free_ivector(gf->xton,0,n-1); +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/gfields.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/gfields.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/gfields.c (revision 27955) @@ -0,0 +1,120 @@ +#if defined(HAVE_CONFIG_H) && !defined(DISABLE_DAKOTA_CONFIG_H) + #include "ddace_config.h" +#endif +/* + + These programs construct and manipulate orthogonal +arrays. They were prepared by + + Art Owen + Department of Statistics + Sequoia Hall + Stanford CA 94305 + + They may be freely used and shared. This code comes +with no warranty of any kind. Use it at your own +risk. + + I thank the Semiconductor Research Corporation and +the National Science Foundation for supporting this +work. + +*/ + + +/* Construction of specific Galois fields. See galois.c + for manipulation of generic Galois fields. + + To add a new Galois field GF(q)=GF(p^n) it is necessary + to find the polynomial representation of x^n, and use it to + include another *xtn--- vector like those used below. + +*/ + +#include +#include + +#include "galois.h" + +/* Fix for C99 */ +extern int isprime(int p); /* primes.c */ +extern void primepow(int q, int *p, int *n, int *isit); /* primes.c */ +extern int GF_ready(struct GF *gf, int p, int n, int *xton); /* galois.c */ + +/* Glossary: + + xtn2t2 Polynomial representation of x^2 in gf2t2 + xtn2t3 Polynomial representation of x^3 in gf2t3 + . . . Polynomial representation of p^n in gfptn + xtn13t2 Polynomial representation of x^2 in gf13t2 + + GF_set_fields Initialize polynomial representations + GF_fields_are_set Indicates initialization done + GF_getfield Construct and return GF(q) if possible +*/ + +#include "xtndeclare.h" +int *xtnpt1; + +int GF_fields_are_set = 0; + +GF_set_fields() +{ +/* Brute force set up of defining vectors, from Carmichael */ + +/* Declare x-to-the-power-n vectors, for GFs p-to-the-n */ + +if( GF_fields_are_set ) + fprintf(stderr,"Warning: Fields being re-initialized. Possible memory waste.\n"); + + +#include "xtnset.h" + +xtnpt1 = ivector(0,0); +xtnpt1[0] = 0; +GF_fields_are_set = 1; +} + + +GF_getfield( q, gf ) +int q; +struct GF *gf; +{ +int *xtn; +int p,n,ispp; + +if( !GF_fields_are_set ) + GF_set_fields(); + +if( q<1 ){ /* Impossible argument */ + fprintf(stderr,"Field must have positive number of elements.\n"); + return 0; } +if( q==1 ){ /* Pointless argument */ + fprintf(stderr,"Field with 1 element was requested.\n"); + return 0; } + +primepow( q,&p,&n,&ispp ); +if( !ispp ){ + fprintf(stderr,"q=%d is not a prime power.\n",q); + return 0; } + +xtn = NULL; + +#include "xtndispatch.h" + +if( isprime(q) )xtn = xtnpt1; /* Could have tested p=q, or n=1 */ + +if( xtn ){ + if( GF_ready( gf,p,n,xtn ) ) + return 1; + else{ + fprintf(stderr,"Construction failed for GF(%d).\n",q); + return 0; + } +} +else { + fprintf(stderr,"GF(%d) = GF(%d^%d) is not included in this program.\n",q,p,n); + fprintf(stderr,"To add it, consider modifying gfields.c.\n"); + return 0; +} +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/oa.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/oa.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/DDACE/src/Bose/oa.c (revision 27955) @@ -0,0 +1,664 @@ +#if defined(HAVE_CONFIG_H) && !defined(DISABLE_DAKOTA_CONFIG_H) + #include "ddace_config.h" +#endif +/** + + These programs construct and manipulate orthogonal +arrays. They were prepared by + + Art Owen + Department of Statistics + Sequoia Hall + Stanford CA 94305 + + They may be freely used and shared. This code comes +with no warranty of any kind. Use it at your own +risk. + + I thank the Semiconductor Research Corporation and +the National Science Foundation for supporting this +work. + +*/ + + +#include +/* for exit: */ +#include + +#include "oa.h" + +int **imatrix(), *ivector(); + +/* Fix for C99 */ +extern int grow_imatrix_byrows(int ***imat, int oldrowsize, int newrowsize, int colsize); /* memory.c */ +extern void free_ivector(int *v, int nl, int nh); /* memory.c */ +extern int ipow(int a, int b); /* primes.c */ + +/** + + Glossary: + + OA_put write OA to standard output + OA_fput write OA to stream + OA_get get OA from standard input + OA_fget get OA from stream + + OA_parsein read arguments q,nrow,ncol to OA "filter programs" + OA_strworkcheck warn about large work loads in strength checking programs + +*/ + + +/* OUTPUT OUTPUT OUTPUT OUTPUT OUTPUT OUTPUT OUTPUT */ + +OA_fput( stream,A,n,k,q ) +FILE *stream; +int **A, n, k, q; +{ +int i,j; +char* format; + +format = "%d%s"; +if( q < 1000 )format = "%3d%s"; +if( q < 100 )format = "%2d%s"; +if( q < 10 )format = "%1d%s"; +if( q < 0 )format = "%d%s"; + +for( i=0; i= q ){ + fprintf(stderr,"Invalid array element %d. All elements should be\n", + A[i][j]); + fprintf(stderr,"strictly less than q = %d.\n",q); + return 0; + }else if( A[i][j] <0 ){ + fprintf(stderr,"Invalid array element %d, should be >= 0.\n",A[i][j]); + return 0; + } + +if( eof_assert && fscanf(stream,"%d",&eof_assert) != EOF ){ + fprintf(stderr,"Input has more integers than expected.\n"); + fprintf(stderr,"Perhaps the number of rows and/or columns is incorrect.\n"); + return 0; + } +return 1; +} + +OA_get( A,n,k,q, eof_assert ) +int **A, n, k, q, eof_assert; +{ +return OA_fget( stdin,A,n,k,q,eof_assert ); +} + +/* READ READ READ READ READ READ READ READ READ */ + +/* Read array and determine dimensions. Inspired by approach +taken in Xgobi. */ + +#define MAXK 5000 +#define ROWINC 1000 +int line0[ MAXK ]; + +OA_fread( stream,A,n,k,q ) +FILE *stream; +int ***A, *n, *k, *q; +{ +int i, j; +char c; + +*k = 0; + +while( (c = getc(stream)) != '\n' ){ + if( c=='\t' || c==' ' ) + ; + else{ + ungetc(c,stream); + if( *k >= MAXK ){ + fprintf(stderr,"Error: Input appears to have more than %d columns.\n",*k); + fprintf(stderr,"If such large input is desired, increase MAXK in oa.c\n"); + fprintf(stderr,"and re-install the software.\n"); + return 0; + } + if( fscanf(stream,"%d",&line0[(*k)++]) <= 0 ){ + fprintf(stderr,"Error: no newline character found. Could be empty\n"); + fprintf(stderr,"input or matrix all on one line.\n"); + return 0; + } + } +} + +*A = imatrix( 0,ROWINC-1, 0,*k-1 ); +if( !(*A) ){ + fprintf(stderr,"Unable to allocate memory to read the array.\n"); + return 0; +} + +*n = 0; +for( j=0; j<*k; j++ ) + A[0][*n][j] = line0[j]; + +while( 1 ){ + (*n)++; + if( (*n % ROWINC)==0 ) + if( !grow_imatrix_byrows( A, (*n), (*n)+ROWINC, *k ) ){ + fprintf(stderr,"Unable to allocate extra memory for row %d of the array.\n" + ,*n); + return 0; + } + + if( fscanf(stream,"%d",&(A[0][*n][0])) == EOF ) + break; + + for( j=1; j<*k; j++ ) + if( fscanf(stream,"%d",&(A[0][*n][j])) == EOF ){ + fprintf(stderr,"Unexpected end of input encountered. Row %d only has\n",*n); + fprintf(stderr,"%d elements of %d expected.\n",j,*k); + return 0; + } +} +*q = 0; /* Assume that q = max(A)+1 */ + +for( i=0; i<*n; i++ ) +for( j=0; j<*k; j++ ) + if( A[0][i][j] > *q ) + *q = A[0][i][j]; +*q = *q +1; + +return 1; +} + +OA_read( A,n,k,q ) +int ***A, *n, *k, *q; +{ +return OA_fread( stdin,A,n,k,q ); +} + +/* PARSE PARSE PARSE PARSE PARSE PARSE PARSE PARSE */ + +OA_parsein( argc,argv, q,nrow,ncol, A ) +int argc; +char *argv[]; +int *q, *nrow, *ncol, ***A; +{ +if( argc<=1 ){ + if( !OA_read( A,nrow,ncol,q ) ){ + fprintf(stderr,"Fatal error while reading the array.\n"); + exit(1); + } +} +else if( argc==2 ){ + sscanf(argv[1],"%d",q); + scanf("%d %d",nrow,ncol); +}else if( argc==3 ){ + sscanf(argv[1],"%d",q); + sscanf(argv[2],"%d",nrow); + scanf("%d",ncol); +}else{ + sscanf(argv[1],"%d",q); + sscanf(argv[2],"%d",nrow); + sscanf(argv[3],"%d",ncol); +} + +if( *q<1 ){ + fprintf(stderr,"Array has only %d symbol(s). At least one\n",*q); + fprintf(stderr,"symbol is necessary in an orthogonal array.\n"); + exit(1); +} + +if( *ncol<1 ){ + fprintf(stderr,"Array has only %d column(s). At least one\n",*ncol); + fprintf(stderr,"column is necessary in an orthogonal array.\n"); + exit(1); +} + +if( *nrow<1 ){ + fprintf(stderr,"Array has only %d rows. At least one\n",*nrow); + fprintf(stderr,"row is necessary in an orthogonal array.\n"); + exit(1); +} + + +if( argc >1 ){ + *A = imatrix( 0,*nrow-1,0,*ncol-1 ); + if( !(*A) ){ + fprintf(stderr,"The array is too large (%d by %d) to fit in memory.\n",nrow,ncol); + exit(1); + } + + if( !OA_get( *A,*nrow,*ncol,*q, 1 ) ){/* Read 'em all */ + fprintf(stderr,"Read error getting the orthogonal array.\n"); + exit(1); + } +} +} + + +/* WORK WORK WORK WORK WORK WORK WORK WORK WORK */ + +OA_strworkcheck( work,str ) +double work; +int str; +{ +if( work > BIGWORK ){ + fprintf(stderr,"If the array has strength %d, %g comparisons will\n", + str, work); + fprintf(stderr,"be required to prove it. This might take a long time.\n"); + fprintf(stderr,"This warning is triggered when more than %d comparisons\n", + BIGWORK); + fprintf(stderr,"are required. To avoid this warning increase BIGWORK in\n"); + fprintf(stderr,"oa.h. Intermediate results will be printed.\n\n"); + fflush(stderr); +}else if( work > MEDWORK ){ + fprintf(stderr,"Since more than %d comparisons may be required to\n",MEDWORK); + fprintf(stderr,"to check whether the array has strength %d, intermediate\n", + str); + fprintf(stderr,"results will be printed. To avoid this warning increase\n"); + fprintf(stderr,"MEDWORK in oa.h\n\n"); + fflush(stderr); +} +} + + +/* STRENGTH STRENGTH STRENGTH STRENGTH STRENGTH */ + +/* Check strength 0 */ +OA_str0( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1; + +for( j1=0; j1= q ){ + if( verbose >= 2 ){ + printf("Array is not even of strength 0, that is there are elements\n"); + // BMA 20141204; added q-1 as argument to silence compiler warning + //printf("other than integers 0 through %d inclusive in it.\n"); + printf("other than integers 0 through %d inclusive in it.\n", (q-1)); + printf("The first exception is A[%d][%d] = %d.\n",i,j1,A[i][j1]); + } + return 0; + } +if( verbose >=2 ) + printf("The array has strength (at least) 0.\n"); +return 1; +} + + +/* Check strength 1 */ +OA_str1( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1, q1; +int lambda, count; +double work; + +if( nrow%q ){ + if( verbose >= 2 ){ + printf("The array cannot have strength 1, because the number\n"); + printf("of rows %d is not a multiple of q = %d.\n",nrow,q); + } + return 0; +} + +lambda = nrow/q; +work = nrow * ncol * q * 1.0; +OA_strworkcheck( work,1 ); +for( j1=0; j1= 2 ){ + printf("Array is not of strength 1. The first violation arises for\n"); + printf("the number of times A[,%d] = %d.\n", + j1, q1); + printf("This happened in %d rows, it should have happened in %d rows.\n", + count, lambda); + } + return 0; + } + } +if( work > MEDWORK && verbose > 0 ) + fprintf(stderr,"No violation of strength 1 involves column %d.\n",j1); +} +if( verbose >=2 ) + printf("The array has strength (at least) 1.\n"); +return 1; +} + +/* Check strength 2 */ +OA_str2( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1,j2, q1,q2; +int lambda, count; +double work; + +if( ncol<2 ){ + if( verbose > 0 ){ + fprintf(stderr,"Array has only %d column(s). At least two\n",ncol); + fprintf(stderr,"columns are necessary for strength 2 to make sense.\n"); + } + return 0; +} +if( nrow % (q*q) ){ + if( verbose > 0 ){ + fprintf(stderr,"The array cannot have strength 2, because the number\n"); + fprintf(stderr,"of rows %d is not a multiple of q^2 = %d^2 = %d.\n",nrow,q,q*q); + } + return 0; +} + +lambda = nrow/(q*q); +work = nrow*ncol*(ncol-1.0)*q*q/2.0; +OA_strworkcheck( work,2 ); + +for( j1=0; j1= 2 ){ + printf("Array is not of strength 2. The first violation arises for\n"); + printf("the number of times (A[,%d],A[,%d]) = (%d,%d).\n", + j1,j2, q1,q2 ); + printf("This happened in %d rows, it should have happened in %d rows.\n", + count, lambda); + } + return 0; + } + } +} +if( work > MEDWORK && verbose > 0 ) + fprintf(stderr,"No violation of strength 2 involves column %d.\n",j1); +} + +if( verbose >=2 ) + printf("The array has strength (at least) 2.\n"); +return 1; +} + + + +/* Check strength 3 */ +OA_str3( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1,j2,j3, q1,q2,q3; +int lambda, count; +double work; + +if( ncol<3 ){ + if( verbose > 0 ){ + fprintf(stderr,"Array has only %d column(s). At least three\n",ncol); + fprintf(stderr,"columns are necessary for strength 3 to make sense.\n"); + } + return 0; +} +if( nrow % (q*q*q) ){ + if( verbose > 0 ){ + fprintf(stderr,"The array cannot have strength 3, because the number\n"); + fprintf(stderr,"of rows %d is not a multiple of q^3 = %d^3 = %d.\n",nrow,q,q*q*q); + } + return 0; +} + +lambda = nrow/(q*q*q); +work = nrow*ncol*(ncol-1.0)*(ncol-2.0)*q*q*q/6.0; +OA_strworkcheck( work,3 ); + +for( j1=0; j1= 2 ){ + printf("Array is not of strength 3. The first violation arises for\n"); + printf("the number of times (A[,%d],A[,%d],A[,%d]) = (%d,%d,%d).\n", + j1,j2,j3, q1,q2,q3 ); + printf("This happened in %d rows, it should have happened in %d rows.\n", + count, lambda); + } + return 0; + } + } +} +if( work > MEDWORK && verbose > 0 ) + fprintf(stderr,"No violation of strength 3 involves column %d.\n",j1); +} +if( verbose >=2 ) + printf("The array has strength (at least) 3.\n"); +return 1; +} + + +/* Check strength 4 */ +OA_str4( q,nrow,ncol,A,verbose ) +int q,nrow,ncol,**A, verbose; +{ +int i, j1,j2,j3,j4, q1,q2,q3,q4; +int lambda, count; +double work; + +if( ncol<4 ){ + if( verbose > 0 ){ + fprintf(stderr,"Array has only %d column(s). At least four\n",ncol); + fprintf(stderr,"columns are necessary for strength 4 to make sense.\n"); + } + return 0; +} +if( nrow % (q*q*q*q) ){ + if( verbose > 0 ){ + fprintf(stderr,"The array cannot have strength 4, because the number\n"); + fprintf(stderr,"of rows %d is not a multiple of q^4 = %d^4 = %d.\n",nrow,q,q*q*q*q); + } + return 0; +} + +lambda = nrow/(q*q*q*q); +work = nrow*ncol*(ncol-1.0)*(ncol-2.0)*(ncol-3.0)*q*q*q*q/24.0; +OA_strworkcheck( work,4 ); + +for( j1=0; j1= 2 ){ + printf("Array is not of strength 4. The first violation arises for\n"); + printf("the number of times (A[,%d],A[,%d],A[,%d],A[,%d]) = (%d,%d,%d,%d).\n", + j1,j2,j3,j4, q1,q2,q3,q4 ); + printf("This happened in %d rows, it should have happened in %d rows.\n", + count, lambda); + } + return 0; + } + } + } +} +if( work > MEDWORK && verbose > 0 ) + fprintf(stderr,"No violation of strength 4 involves column %d.\n",j1); + +if( verbose >=2 ) + printf("The array has strength (at least) 4.\n"); +return 1; +} + + +/* Check strength t */ +OA_strt( q,nrow,ncol,A,t,verbose ) +int q,nrow,ncol,**A,t,verbose; +{ +int row, i, ic, iq, *clist, *qlist, ctuples, qtuples; +int lambda, count, match; +double work; + +if( t<0 ){ + if( verbose > 0 ){ + fprintf(stderr,"Don't know how to verify strength %d. It doesn't\n",t); + fprintf(stderr,"make sense.\n"); + } + return 0; +} +if( ncol 0 ){ + fprintf(stderr,"Array has only %d column(s). At least %d\n",ncol,t); + fprintf(stderr,"columns are necessary for strength %d to make sense.\n",t); + } + return 0; +} +if( t==0 ) + return OA_str0( q,nrow,ncol,A,verbose ); +if( nrow % ipow(q,t) ){ + if( verbose > 0 ){ + fprintf(stderr,"The array cannot have strength %d, because the number\n",t); + fprintf(stderr,"of rows %d is not a multiple of q^%d = %d^%d = %d.\n", + nrow,t,q,t,ipow(q,t)); + } + return 0; +} + +lambda = nrow/ipow(q,t); +work = nrow*ipow(q,t); +ctuples = 1; + +clist = ivector( 0,t-1 ); +qlist = ivector( 0,t-1 ); + +for( i=0; i= 2 ){ + printf("Array is not of strength %d. The first violation arises for\n",t); + printf("the number of times ("); + for( i=0; i=0; i-- ){ + qlist[i] = (qlist[i]+1) % q; + if( qlist[i] )break; + } + } + + for( i= t-1; i>=0; i-- ){ + clist[i] = (clist[i]+1) % (ncol+i-t+1); + if( clist[i] )break; + } + + if( work > MEDWORK && verbose > 0 && (t==1||t>1 && clist[1]==0) ) + fprintf(stderr,"No violation of strength %d involves column %d.\n", + t,(clist[0]+ncol-1)%ncol); + + for( i=1; i< t; i++ ) + if( clist[i] <= clist[i-1] ) + clist[i] = clist[i-1]+1; +} + +if( verbose >=2 ) + printf("The array has strength (at least) %d.\n",t); + +/* Added by J Cramp on 07.02.04 to + * fix memory leak problems. */ +free_ivector(clist,0,t-1); +free_ivector(qlist,0,t-1); + +return 1; +} + +void OA_strength( q,nrow,ncol,A,str,verbose ) +int q,nrow,ncol,**A,*str, verbose; +/* + Calculate and return the strength of the array A. + +verbose = 0 => No printed output +verbose = 1 => Only stderr output +verbose = 2 => Output to both stdout and stderr + +*/ +{ +*str = -1; + +if( OA_str0( q,nrow,ncol,A,verbose) ) + *str = 0; +else + return; +if( OA_str1( q,nrow,ncol,A,verbose) ) + *str = 1; +else + return; +while( OA_strt( q,nrow,ncol,A,*str+1,verbose ) ) + (*str)++; +return; +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr-scanner.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr-scanner.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr-scanner.c (revision 27955) @@ -0,0 +1,2063 @@ +/* A lexical scanner generated by flex*/ + +/* Scanner skeleton version: + * $Header: /home/daffy/u0/vern/flex/RCS/flex.skl,v 2.91 96/09/10 16:58:48 vern Exp $ + */ + +#define FLEX_SCANNER +#define YY_FLEX_MAJOR_VERSION 2 +#define YY_FLEX_MINOR_VERSION 5 + +#include + + +/* cfront 1.2 defines "c_plusplus" instead of "__cplusplus" */ +#ifdef c_plusplus +#ifndef __cplusplus +#define __cplusplus +#endif +#endif + + +#ifdef __cplusplus + +#include + +/* Use prototypes in function declarations. */ +#define YY_USE_PROTOS + +/* The "const" storage-class-modifier is valid. */ +#define YY_USE_CONST + +#else /* ! __cplusplus */ + +#if __STDC__ + +#define YY_USE_PROTOS +#define YY_USE_CONST + +#endif /* __STDC__ */ +#endif /* ! __cplusplus */ + +#ifdef __TURBOC__ + #pragma warn -rch + #pragma warn -use +#include +#include +#define YY_USE_CONST +#define YY_USE_PROTOS +#endif + +#ifdef YY_USE_CONST +#define nidrconst const +#else +#define nidrconst +#endif + + +#ifdef YY_USE_PROTOS +#define YY_PROTO(proto) proto +#else +#define YY_PROTO(proto) () +#endif + +/* Returned upon end-of-file. */ +#define YY_NULL 0 + +/* Promotes a possibly negative, possibly signed char to an unsigned + * integer for use as an array index. If the signed char is negative, + * we want to instead treat it as an 8-bit unsigned char, hence the + * double cast. + */ +#define YY_SC_TO_UI(c) ((unsigned int) (unsigned char) c) + +/* Enter a start condition. This macro really ought to take a parameter, + * but we do it the disgusting crufty way forced on us by the ()-less + * definition of BEGIN. + */ +#define BEGIN nidr_start = 1 + 2 * + +/* Translate the current start state into a value that can be later handed + * to BEGIN to return to the state. The YYSTATE alias is for lex + * compatibility. + */ +#define YY_START ((nidr_start - 1) / 2) +#define YYSTATE YY_START + +/* Action number for EOF rule of a given start state. */ +#define YY_STATE_EOF(state) (YY_END_OF_BUFFER + state + 1) + +/* Special action meaning "start processing a new file". */ +#define YY_NEW_FILE nidrrestart( nidrin ) + +#define YY_END_OF_BUFFER_CHAR 0 + +/* Size of default input buffer. */ +#define YY_BUF_SIZE 16384 + +typedef struct nidr_buffer_state *YY_BUFFER_STATE; + +extern int nidrleng; +extern FILE *nidrin, *nidrout; + +#define EOB_ACT_CONTINUE_SCAN 0 +#define EOB_ACT_END_OF_FILE 1 +#define EOB_ACT_LAST_MATCH 2 + +/* The funky do-while in the following #define is used to turn the definition + * int a single C statement (which needs a semi-colon terminator). This + * avoids problems with code like: + * + * if ( condition_holds ) + * nidrless( 5 ); + * else + * do_something_else(); + * + * Prior to using the do-while the compiler would get upset at the + * "else" because it interpreted the "if" statement as being all + * done when it reached the ';' after the nidrless() call. + */ + +/* Return all but the first 'n' matched characters back to the input stream. */ + +#define nidrless(n) \ + do \ + { \ + /* Undo effects of setting up nidrtext. */ \ + *nidr_cp = nidr_hold_char; \ + YY_RESTORE_YY_MORE_OFFSET \ + nidr_c_buf_p = nidr_cp = nidr_bp + n - YY_MORE_ADJ; \ + YY_DO_BEFORE_ACTION; /* set up nidrtext again */ \ + } \ + while ( 0 ) + +#define unput(c) nidrunput( c, nidrtext_ptr ) + +/* Some routines like nidr_flex_realloc() are emitted as static but are + not called by all lexers. This generates warnings in some compilers, + notably GCC. Arrange to suppress these. */ +#ifdef __GNUC__ +#define YY_MAY_BE_UNUSED __attribute__((unused)) +#else +#define YY_MAY_BE_UNUSED +#endif + +/* The following is because we cannot portably get our hands on size_t + * (without autoconf's help, which isn't available because we want + * flex-generated scanners to compile on their own). + */ +typedef unsigned int nidr_size_t; + + +struct nidr_buffer_state + { + FILE *nidr_input_file; + + char *nidr_ch_buf; /* input buffer */ + char *nidr_buf_pos; /* current position in input buffer */ + + /* Size of input buffer in bytes, not including room for EOB + * characters. + */ + nidr_size_t nidr_buf_size; + + /* Number of characters read into nidr_ch_buf, not including EOB + * characters. + */ + int nidr_n_chars; + + /* Whether we "own" the buffer - i.e., we know we created it, + * and can realloc() it to grow it, and should free() it to + * delete it. + */ + int nidr_is_our_buffer; + + /* Whether this is an "interactive" input source; if so, and + * if we're using stdio for input, then we want to use getc() + * instead of fread(), to make sure we stop fetching input after + * each newline. + */ + int nidr_is_interactive; + + /* Whether we're considered to be at the beginning of a line. + * If so, '^' rules will be active on the next match, otherwise + * not. + */ + int nidr_at_bol; + + /* Whether to try to fill the input buffer when we reach the + * end of it. + */ + int nidr_fill_buffer; + + int nidr_buffer_status; +#define YY_BUFFER_NEW 0 +#define YY_BUFFER_NORMAL 1 + /* When an EOF's been seen but there's still some text to process + * then we mark the buffer as YY_EOF_PENDING, to indicate that we + * shouldn't try reading from the input source any more. We might + * still have a bunch of tokens to match, though, because of + * possible backing-up. + * + * When we actually see the EOF, we change the status to "new" + * (via nidrrestart()), so that the user can continue scanning by + * just pointing nidrin at a new input file. + */ +#define YY_BUFFER_EOF_PENDING 2 + }; + +static YY_BUFFER_STATE nidr_current_buffer = 0; + +/* We provide macros for accessing buffer states in case in the + * future we want to put the buffer states in a more general + * "scanner state". + */ +#define YY_CURRENT_BUFFER nidr_current_buffer + + +/* nidr_hold_char holds the character lost when nidrtext is formed. */ +static char nidr_hold_char; + +static int nidr_n_chars; /* number of characters read into nidr_ch_buf */ + + +int nidrleng; + +/* Points to current character in buffer. */ +static char *nidr_c_buf_p = (char *) 0; +static int nidr_init = 1; /* whether we need to initialize */ +static int nidr_start = 0; /* start state number */ + +/* Flag which is used to allow nidrwrap()'s to do buffer switches + * instead of setting up a fresh nidrin. A bit of a hack ... + */ +static int nidr_did_buffer_switch_on_eof; + +void nidrrestart YY_PROTO(( FILE *input_file )); + +void nidr_switch_to_buffer YY_PROTO(( YY_BUFFER_STATE new_buffer )); +void nidr_load_buffer_state YY_PROTO(( void )); +YY_BUFFER_STATE nidr_create_buffer YY_PROTO(( FILE *file, int size )); +void nidr_delete_buffer YY_PROTO(( YY_BUFFER_STATE b )); +void nidr_init_buffer YY_PROTO(( YY_BUFFER_STATE b, FILE *file )); +void nidr_flush_buffer YY_PROTO(( YY_BUFFER_STATE b )); +#define YY_FLUSH_BUFFER nidr_flush_buffer( nidr_current_buffer ) + +YY_BUFFER_STATE nidr_scan_buffer YY_PROTO(( char *base, nidr_size_t size )); +YY_BUFFER_STATE nidr_scan_string YY_PROTO(( nidrconst char *nidr_str )); +YY_BUFFER_STATE nidr_scan_bytes YY_PROTO(( nidrconst char *bytes, int len )); + +static void *nidr_flex_alloc YY_PROTO(( nidr_size_t )); +static void *nidr_flex_realloc YY_PROTO(( void *, nidr_size_t )) YY_MAY_BE_UNUSED; +static void nidr_flex_free YY_PROTO(( void * )); + +#define nidr_new_buffer nidr_create_buffer + +#define nidr_set_interactive(is_interactive) \ + { \ + if ( ! nidr_current_buffer ) \ + nidr_current_buffer = nidr_create_buffer( nidrin, YY_BUF_SIZE ); \ + nidr_current_buffer->nidr_is_interactive = is_interactive; \ + } + +#define nidr_set_bol(at_bol) \ + { \ + if ( ! nidr_current_buffer ) \ + nidr_current_buffer = nidr_create_buffer( nidrin, YY_BUF_SIZE ); \ + nidr_current_buffer->nidr_at_bol = at_bol; \ + } + +#define YY_AT_BOL() (nidr_current_buffer->nidr_at_bol) + +typedef unsigned char YY_CHAR; +FILE *nidrin = (FILE *) 0, *nidrout = (FILE *) 0; +typedef int nidr_state_type; +extern char *nidrtext; +#define nidrtext_ptr nidrtext + +static nidr_state_type nidr_get_previous_state YY_PROTO(( void )); +static nidr_state_type nidr_try_NUL_trans YY_PROTO(( nidr_state_type current_state )); +static int nidr_get_next_buffer YY_PROTO(( void )); +static void nidr_fatal_error YY_PROTO(( nidrconst char msg[] )); + +/* Done after the current pattern has been matched and before the + * corresponding action - sets up nidrtext. + */ +#define YY_DO_BEFORE_ACTION \ + nidrtext_ptr = nidr_bp; \ + nidrtext_ptr -= nidr_more_len; \ + nidrleng = (int) (nidr_cp - nidrtext_ptr); \ + nidr_hold_char = *nidr_cp; \ + *nidr_cp = '\0'; \ + nidr_c_buf_p = nidr_cp; + +#define YY_NUM_RULES 27 +#define YY_END_OF_BUFFER 28 +static nidrconst short int nidr_accept[125] = + { 0, + 0, 0, 0, 0, 21, 21, 18, 18, 28, 6, + 5, 2, 25, 4, 3, 3, 6, 16, 12, 2, + 15, 25, 13, 26, 16, 8, 16, 9, 14, 7, + 11, 11, 11, 16, 21, 21, 22, 22, 21, 21, + 18, 18, 19, 18, 19, 18, 5, 25, 0, 25, + 25, 4, 24, 3, 3, 0, 23, 12, 8, 7, + 0, 9, 0, 0, 10, 9, 9, 9, 7, 11, + 11, 11, 21, 21, 21, 21, 20, 21, 21, 21, + 18, 18, 18, 18, 18, 18, 17, 18, 24, 3, + 0, 0, 10, 10, 9, 10, 9, 9, 10, 10, + + 10, 21, 18, 1, 10, 10, 10, 10, 10, 9, + 10, 11, 0, 10, 10, 11, 0, 11, 0, 11, + 0, 10, 10, 0 + } ; + +static nidrconst int nidr_ec[256] = + { 0, + 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 2, 1, 4, 5, 1, 1, 1, 6, 1, + 1, 7, 8, 9, 10, 11, 1, 12, 12, 12, + 12, 12, 12, 12, 12, 12, 12, 7, 13, 1, + 14, 1, 1, 15, 16, 17, 17, 17, 18, 19, + 17, 17, 20, 17, 17, 17, 17, 21, 17, 17, + 17, 17, 17, 22, 17, 17, 17, 23, 24, 17, + 1, 25, 1, 1, 26, 1, 16, 17, 17, 17, + + 18, 19, 17, 17, 20, 17, 17, 17, 17, 21, + 17, 17, 17, 17, 17, 22, 17, 17, 17, 23, + 24, 17, 1, 1, 1, 15, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1 + } ; + +static nidrconst int nidr_meta[27] = + { 0, + 1, 1, 2, 3, 1, 4, 1, 5, 1, 6, + 6, 6, 1, 1, 7, 6, 6, 6, 6, 6, + 6, 6, 6, 6, 1, 6 + } ; + +static nidrconst short int nidr_base[137] = + { 0, + 0, 0, 26, 0, 51, 75, 99, 123, 263, 264, + 56, 264, 57, 264, 0, 239, 57, 264, 147, 264, + 264, 236, 264, 264, 162, 264, 248, 53, 264, 257, + 0, 237, 241, 64, 0, 67, 264, 252, 59, 71, + 0, 81, 264, 62, 249, 86, 88, 229, 92, 228, + 86, 227, 249, 0, 230, 94, 264, 0, 264, 247, + 236, 96, 226, 230, 91, 233, 98, 107, 242, 0, + 224, 212, 0, 116, 108, 120, 264, 126, 226, 129, + 0, 132, 114, 133, 121, 224, 264, 140, 217, 191, + 193, 178, 169, 150, 168, 126, 155, 167, 166, 157, + + 0, 174, 173, 0, 151, 264, 158, 157, 156, 147, + 143, 133, 132, 138, 135, 125, 120, 76, 63, 51, + 33, 0, 264, 264, 183, 190, 197, 199, 202, 203, + 210, 217, 224, 231, 234, 236 + } ; + +static nidrconst short int nidr_def[137] = + { 0, + 124, 1, 124, 3, 125, 125, 126, 126, 124, 124, + 124, 124, 127, 124, 128, 128, 124, 124, 124, 124, + 124, 127, 124, 124, 124, 124, 124, 129, 124, 124, + 130, 130, 130, 124, 131, 131, 124, 124, 132, 131, + 133, 133, 124, 134, 124, 133, 124, 127, 124, 127, + 127, 127, 124, 128, 128, 124, 124, 19, 124, 124, + 124, 129, 124, 124, 135, 129, 136, 129, 124, 130, + 130, 130, 131, 131, 132, 131, 124, 132, 131, 131, + 133, 133, 134, 133, 134, 133, 124, 133, 124, 128, + 124, 124, 135, 135, 136, 135, 136, 129, 135, 130, + + 130, 131, 133, 128, 124, 124, 135, 135, 135, 136, + 135, 130, 124, 135, 135, 130, 124, 130, 124, 130, + 124, 130, 124, 0, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124 + } ; + +static nidrconst short int nidr_nxt[291] = + { 0, + 10, 11, 12, 10, 13, 10, 10, 10, 10, 10, + 10, 10, 14, 10, 10, 15, 15, 16, 15, 15, + 15, 15, 15, 15, 17, 10, 18, 19, 20, 21, + 22, 23, 24, 25, 26, 25, 27, 28, 29, 30, + 18, 31, 31, 31, 31, 32, 33, 31, 31, 31, + 34, 18, 36, 37, 38, 39, 123, 47, 56, 57, + 48, 51, 50, 67, 62, 56, 57, 50, 74, 52, + 68, 75, 80, 57, 122, 40, 36, 37, 38, 39, + 49, 53, 82, 79, 121, 83, 86, 88, 57, 47, + 51, 76, 48, 56, 57, 56, 57, 120, 52, 40, + + 42, 43, 65, 44, 45, 84, 67, 62, 94, 96, + 53, 50, 49, 68, 98, 97, 98, 74, 99, 50, + 75, 80, 57, 46, 42, 43, 50, 44, 45, 50, + 80, 57, 79, 82, 88, 57, 83, 96, 86, 119, + 76, 88, 57, 109, 118, 86, 115, 46, 58, 115, + 79, 48, 117, 116, 111, 59, 84, 107, 111, 107, + 60, 108, 110, 114, 110, 114, 111, 115, 108, 108, + 113, 49, 61, 62, 103, 102, 112, 99, 99, 124, + 124, 63, 64, 35, 35, 35, 35, 35, 35, 35, + 41, 41, 41, 41, 41, 41, 41, 50, 106, 50, + + 50, 50, 50, 50, 54, 54, 66, 66, 70, 70, + 73, 105, 104, 73, 73, 73, 73, 78, 89, 78, + 78, 78, 78, 78, 81, 103, 81, 102, 81, 81, + 81, 85, 101, 85, 85, 85, 85, 85, 93, 93, + 95, 95, 100, 69, 124, 92, 91, 65, 69, 90, + 89, 53, 53, 53, 87, 77, 72, 71, 69, 65, + 53, 55, 124, 9, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124, 124, 124, 124, 124 + } ; + +static nidrconst short int nidr_chk[291] = + { 0, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, + 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, + 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, + 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, + 3, 3, 5, 5, 5, 5, 121, 11, 17, 17, + 11, 13, 39, 28, 28, 34, 34, 44, 36, 13, + 28, 36, 40, 40, 120, 5, 6, 6, 6, 6, + 11, 13, 42, 39, 119, 42, 44, 46, 46, 47, + 51, 36, 47, 49, 49, 56, 56, 118, 51, 6, + + 7, 7, 65, 7, 7, 42, 62, 62, 65, 67, + 51, 75, 47, 62, 68, 67, 68, 74, 68, 83, + 74, 76, 76, 7, 8, 8, 85, 8, 8, 78, + 80, 80, 75, 82, 84, 84, 82, 96, 83, 117, + 74, 88, 88, 96, 116, 85, 115, 8, 19, 114, + 78, 19, 113, 112, 111, 19, 82, 94, 110, 94, + 19, 94, 97, 109, 97, 109, 97, 109, 108, 107, + 105, 19, 25, 25, 103, 102, 100, 99, 98, 95, + 93, 25, 25, 125, 125, 125, 125, 125, 125, 125, + 126, 126, 126, 126, 126, 126, 126, 127, 92, 127, + + 127, 127, 127, 127, 128, 128, 129, 129, 130, 130, + 131, 91, 90, 131, 131, 131, 131, 132, 89, 132, + 132, 132, 132, 132, 133, 86, 133, 79, 133, 133, + 133, 134, 72, 134, 134, 134, 134, 134, 135, 135, + 136, 136, 71, 69, 66, 64, 63, 61, 60, 55, + 53, 52, 50, 48, 45, 38, 33, 32, 30, 27, + 22, 16, 9, 124, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, + 124, 124, 124, 124, 124, 124, 124, 124, 124, 124 + } ; + +static nidr_state_type nidr_last_accepting_state; +static char *nidr_last_accepting_cpos; + +/* The intent behind this definition is that it'll catch + * any uses of REJECT which flex missed. + */ +#define REJECT reject_used_but_not_detected +static int nidr_more_flag = 0; +static int nidr_more_len = 0; +#define nidrmore() (nidr_more_flag = 1) +#define YY_MORE_ADJ nidr_more_len +#define YY_RESTORE_YY_MORE_OFFSET +char *nidrtext; +/* #line 1 "nidrscan.l" */ +#define INITIAL 0 +/* #line 2 "nidrscan.l" */ +/********************************************************************* +Copyright 2008, 2010 Sandia Corporation. Under the terms of Contract +DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government +retains certain rights in this software. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: + +* Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright +notice, this list of conditions and the following disclaimer in the +documentation and/or other materials provided with the distribution. + +* Neither the name of Sandia Corporation nor the names of its +contributors may be used to endorse or promote products derived from +this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +***********************************************************************/ + +#ifndef NIDR_H +#include "nidr.h" +#endif +#ifndef NIDR_PARSER_H +#include "nidr-parser.h" +#endif +#include /* possibly redundant, but necessary for strtod on some systems */ + +static int my_nidr_input(char*, int); +extern char *nidr_KWscopy(const char*); + +#ifdef IDR_DEBUG +static void print_token( char*, char*, char* ); +#else +#define print_token(a,b,c) /*nothing*/ +#endif + + +#define YY_INPUT(buf,result,maxsize) result = my_nidr_input(buf,maxsize) + +int nidrLineNumber = 1; + +extern void nidr_abort(void); +extern void (*nidr_comment)(const char*); +extern KeyWord *(*nidr_identifier)(const char*); +extern KeyWord *nidr_keyword(const char*); +extern const char *nidr_keyword_name(void); +/* Hardwire the now rarely used help text. It truly is something the + application should provide, not NIDR, but had trouble with the + declaration/definition w.r.t. MSVS when building DAKOTA source. + Ultimately would want to pass it into nidr_parse(...) +extern char nidr_please_refer[]; +*/ +char nidr_please_refer[] = + "Please refer to the input specification reference for this application."; +extern void nidr_tolower(char*); +static void bad_number(const char*); +static void unput_string(char *, int); +#define DATA 1 + +#define DQ_STRING 2 + +#define Q_STRING 3 + +/* #line 545 "nidr-scanner.c" */ + +/* Macros after this point can all be overridden by user definitions in + * section 1. + */ + +#ifndef YY_SKIP_YYWRAP +#ifdef __cplusplus +extern "C" int nidrwrap YY_PROTO(( void )); +#else +extern int nidrwrap YY_PROTO(( void )); +#endif +#endif + +#ifndef YY_NO_UNPUT +static void nidrunput YY_PROTO(( int c, char *buf_ptr )); +#endif + +#ifndef nidrtext_ptr +static void nidr_flex_strncpy YY_PROTO(( char *, nidrconst char *, int )); +#endif + +#ifdef YY_NEED_STRLEN +static int nidr_flex_strlen YY_PROTO(( nidrconst char * )); +#endif + +#ifndef YY_NO_INPUT +#ifdef __cplusplus +static int nidrinput YY_PROTO(( void )); +#else +static int input YY_PROTO(( void )); +#endif +#endif + +#if YY_STACK_USED +static int nidr_start_stack_ptr = 0; +static int nidr_start_stack_depth = 0; +static int *nidr_start_stack = 0; +#ifndef YY_NO_PUSH_STATE +static void nidr_push_state YY_PROTO(( int new_state )); +#endif +#ifndef YY_NO_POP_STATE +static void nidr_pop_state YY_PROTO(( void )); +#endif +#ifndef YY_NO_TOP_STATE +static int nidr_top_state YY_PROTO(( void )); +#endif + +#else +#define YY_NO_PUSH_STATE 1 +#define YY_NO_POP_STATE 1 +#define YY_NO_TOP_STATE 1 +#endif + +#ifdef YY_MALLOC_DECL +YY_MALLOC_DECL +#else +#if __STDC__ +#ifndef __cplusplus +#include +#endif +#else +/* Just try to get by without declaring the routines. This will fail + * miserably on non-ANSI systems for which sizeof(size_t) != sizeof(int) + * or sizeof(void*) != sizeof(int). + */ +#endif +#endif + +/* Amount of stuff to slurp up with each read. */ +#ifndef YY_READ_BUF_SIZE +#define YY_READ_BUF_SIZE 8192 +#endif + +/* Copy whatever the last rule matched to the standard output. */ + +#ifndef ECHO +/* This used to be an fputs(), but since the string might contain NUL's, + * we now use fwrite(). + */ +#define ECHO (void) fwrite( nidrtext, nidrleng, 1, nidrout ) +#endif + +/* Gets input and stuffs it into "buf". number of characters read, or YY_NULL, + * is returned in "result". + */ +#ifndef YY_INPUT +#define YY_INPUT(buf,result,max_size) \ + if ( nidr_current_buffer->nidr_is_interactive ) \ + { \ + int c = '*', n; \ + for ( n = 0; n < max_size && \ + (c = getc( nidrin )) != EOF && c != '\n'; ++n ) \ + buf[n] = (char) c; \ + if ( c == '\n' ) \ + buf[n++] = (char) c; \ + if ( c == EOF && ferror( nidrin ) ) \ + YY_FATAL_ERROR( "input in flex scanner failed" ); \ + result = n; \ + } \ + else if ( ((result = fread( buf, 1, max_size, nidrin )) == 0) \ + && ferror( nidrin ) ) \ + YY_FATAL_ERROR( "input in flex scanner failed" ); +#endif + +/* No semi-colon after return; correct usage is to write "nidrterminate();" - + * we don't want an extra ';' after the "return" because that will cause + * some compilers to complain about unreachable statements. + */ +#ifndef nidrterminate +#define nidrterminate() return YY_NULL +#endif + +/* Number of entries by which start-condition stack grows. */ +#ifndef YY_START_STACK_INCR +#define YY_START_STACK_INCR 25 +#endif + +/* Report a fatal error. */ +#ifndef YY_FATAL_ERROR +#define YY_FATAL_ERROR(msg) nidr_fatal_error( msg ) +#endif + +/* Default declaration of generated scanner - a define so the user can + * easily add parameters. + */ +#ifndef YY_DECL +#define YY_DECL int nidrlex YY_PROTO(( void )) +#endif + +/* Code executed at the beginning of each rule, after nidrtext and nidrleng + * have been set up. + */ +#ifndef YY_USER_ACTION +#define YY_USER_ACTION +#endif + +/* Code executed at the end of each rule. */ +#ifndef YY_BREAK +#define YY_BREAK break; +#endif + +#define YY_RULE_SETUP \ + YY_USER_ACTION + +YY_DECL + { + register nidr_state_type nidr_current_state; + register char *nidr_cp = NULL, *nidr_bp = NULL; + register int nidr_act; + +/* #line 85 "nidrscan.l" */ + + + + KeyWord *identifier, *keyword; + char *se; + + +/* #line 704 "nidr-scanner.c" */ + + if ( nidr_init ) + { + nidr_init = 0; + +#ifdef YY_USER_INIT + YY_USER_INIT; +#endif + + if ( ! nidr_start ) + nidr_start = 1; /* first start state */ + + if ( ! nidrin ) + nidrin = stdin; + + if ( ! nidrout ) + nidrout = stdout; + + if ( ! nidr_current_buffer ) + nidr_current_buffer = + nidr_create_buffer( nidrin, YY_BUF_SIZE ); + + nidr_load_buffer_state(); + } + + while ( 1 ) /* loops until end-of-file is reached */ + { + nidr_more_len = 0; + if ( nidr_more_flag ) + { + nidr_more_len = nidr_c_buf_p - nidrtext_ptr; + nidr_more_flag = 0; + } + nidr_cp = nidr_c_buf_p; + + /* Support of nidrtext. */ + *nidr_cp = nidr_hold_char; + + /* nidr_bp points to the position in nidr_ch_buf of the start of + * the current run. + */ + nidr_bp = nidr_cp; + + nidr_current_state = nidr_start; +nidr_match: + do + { + register YY_CHAR nidr_c = nidr_ec[YY_SC_TO_UI(*nidr_cp)]; + if ( nidr_accept[nidr_current_state] ) + { + nidr_last_accepting_state = nidr_current_state; + nidr_last_accepting_cpos = nidr_cp; + } + while ( nidr_chk[nidr_base[nidr_current_state] + nidr_c] != nidr_current_state ) + { + nidr_current_state = (int) nidr_def[nidr_current_state]; + if ( nidr_current_state >= 125 ) + nidr_c = nidr_meta[(unsigned int) nidr_c]; + } + nidr_current_state = nidr_nxt[nidr_base[nidr_current_state] + (unsigned int) nidr_c]; + ++nidr_cp; + } + while ( nidr_base[nidr_current_state] != 264 ); + +nidr_find_action: + nidr_act = nidr_accept[nidr_current_state]; + if ( nidr_act == 0 ) + { /* have to back up */ + nidr_cp = nidr_last_accepting_cpos; + nidr_current_state = nidr_last_accepting_state; + nidr_act = nidr_accept[nidr_current_state]; + } + + YY_DO_BEFORE_ACTION; + + +do_action: /* This label is used only to access EOF actions. */ + + + switch ( nidr_act ) + { /* beginning of action switch */ + case 0: /* must back up */ + /* undo the effects of YY_DO_BEFORE_ACTION */ + *nidr_cp = nidr_hold_char; + nidr_cp = nidr_last_accepting_cpos; + nidr_current_state = nidr_last_accepting_state; + goto nidr_find_action; + +case 1: +YY_RULE_SETUP +/* #line 92 "nidrscan.l" */ +{ + print_token("exit", NULL, "" ); + return 0; + } + YY_BREAK +case 2: +YY_RULE_SETUP +/* #line 97 "nidrscan.l" */ +{ + if (nidr_comment) + nidr_comment(nidrtext); + nidrLineNumber++; + } + YY_BREAK +case 3: +YY_RULE_SETUP +/* #line 103 "nidrscan.l" */ +{ + nidr_tolower(nidrtext); + keyword = nidr_keyword(nidrtext); + + if (keyword) { + print_token( "keyword", (char*) nidrtext, "" ); + if (keyword->kind & KWKind_Dynmult) + return END; + nidrlval.keyword = keyword; + BEGIN DATA; + return KEY_WORD; + } + print_token( "error", (char*) nidrtext, "" ); + nidrlval.string = nidrtext; + return KEYWORDERROR; + } + YY_BREAK +case 4: +YY_RULE_SETUP +/* #line 120 "nidrscan.l" */ +{ + if (*nidrtext == '#') { + if (nidr_comment) + nidr_comment(nidrtext); + } + else { + print_token( "end", NULL, "" ); + return END; + } + } + YY_BREAK +case 5: +YY_RULE_SETUP +/* #line 131 "nidrscan.l" */ +{ print_token( "whitespace", (char*) nidrtext, "" ); } + YY_BREAK +case 6: +YY_RULE_SETUP +/* #line 133 "nidrscan.l" */ +{ + print_token( "word", (char*) nidrtext, "" ); + nidrlval.string = nidr_KWscopy(nidrtext); + return STRING; + } + YY_BREAK +case 7: +YY_RULE_SETUP +/* #line 138 "nidrscan.l" */ +{ + print_token( "equals", NULL, "" ); + return EQUALS; + } + YY_BREAK +case 8: +YY_RULE_SETUP +/* #line 142 "nidrscan.l" */ +{ + print_token( "separator", NULL, "" ); + return SEPARATOR; + } + YY_BREAK +case 9: +YY_RULE_SETUP +/* #line 146 "nidrscan.l" */ +{ + print_token( "integer", (char*) nidrtext, "" ); + /* The following, old way has trouble with */ + /* big floating-point numbers written without */ + /* a decimal point */ + /* nidrlval.integer = (int) atoi( (char*) nidrtext ); */ + /* return INTEGER; */ + nidrlval.real = strtod(nidrtext,&se); + if (*se) + bad_number(nidrtext); + return REAL; + } + YY_BREAK +case 10: +YY_RULE_SETUP +/* #line 158 "nidrscan.l" */ +{ + print_token( "real", (char*) nidrtext, "" ); + nidrlval.real = strtod(nidrtext,&se); + if (*se) + bad_number(nidrtext); + return REAL; + } + YY_BREAK +case 11: +YY_RULE_SETUP +/* #line 165 "nidrscan.l" */ +{ + nidr_tolower(nidrtext); + if (nidr_keyword(nidrtext)) { + unput_string(nidrtext, nidrleng); + BEGIN INITIAL; + return END; + } + identifier = nidr_identifier(nidrtext); + + if (identifier) { + print_token( "identifier", (char*) nidrtext, ""); + + nidrlval.identifier = identifier; + return IDENTIFIER; + } + else { + print_token( "word", (char*) nidrtext, "" ); + fprintf(stderr,"\n\tunrecognized identifier '%s'\n", nidrtext); + fprintf(stderr,"\tinput line %d, within %s keyword.\n", + nidrLineNumber, nidr_keyword_name()); + fprintf(stderr, "%s\n", nidr_please_refer); + nidr_abort(); + nidrlval.string = nidr_KWscopy(nidrtext); + return STRING; + } + } + YY_BREAK +case 12: +YY_RULE_SETUP +/* #line 192 "nidrscan.l" */ +{ print_token( "whitespace", (char*) nidrtext, "" ); } + YY_BREAK +case 13: +YY_RULE_SETUP +/* #line 194 "nidrscan.l" */ +{ + print_token( "opening quote", NULL, "" ); + BEGIN Q_STRING; + } + YY_BREAK +case 14: +YY_RULE_SETUP +/* #line 198 "nidrscan.l" */ +{ + print_token( "end", NULL, "" ); + BEGIN INITIAL; + return END; + } + YY_BREAK +case 15: +YY_RULE_SETUP +/* #line 203 "nidrscan.l" */ +{ + print_token( "double quote", NULL, "" ); + BEGIN DQ_STRING; + } + YY_BREAK +case 16: +YY_RULE_SETUP +/* #line 207 "nidrscan.l" */ +{ + print_token( "word", (char*) nidrtext, "" ); + fprintf(stderr, "Input line %d: '%s' unexpected.\n", + nidrLineNumber, nidrtext); + nidr_abort(); + nidrlval.string = nidr_KWscopy(nidrtext); + return STRING; + } + YY_BREAK +case 17: +YY_RULE_SETUP +/* #line 215 "nidrscan.l" */ +{ + print_token( "q:repeated quote", NULL, "" ); + nidrtext[--nidrleng] = 0; + nidrmore(); + } + YY_BREAK +case 18: +YY_RULE_SETUP +/* #line 220 "nidrscan.l" */ +{ + nidrmore(); + print_token( "q:text", (char*) nidrtext, "" ); + } + YY_BREAK +case 19: +YY_RULE_SETUP +/* #line 224 "nidrscan.l" */ +{ + print_token( "closing quote", NULL, "" ); + if (nidrtext[--nidrleng] == '\n') + unput('\n'); + nidrtext[nidrleng] = 0; + print_token( "quoted string", (char*) nidrtext, "" ); + nidrlval.qstring = nidr_KWscopy(nidrtext); + BEGIN DATA; + return QUOTED_STRING; + } + YY_BREAK +case 20: +YY_RULE_SETUP +/* #line 234 "nidrscan.l" */ +{ + print_token( "q:repeated double quote", NULL, "" ); + nidrtext[--nidrleng] = 0; + nidrmore(); + } + YY_BREAK +case 21: +YY_RULE_SETUP +/* #line 239 "nidrscan.l" */ +{ + nidrmore(); + print_token( "q:text", (char*) nidrtext, "" ); + } + YY_BREAK +case 22: +YY_RULE_SETUP +/* #line 243 "nidrscan.l" */ +{ + print_token( "closing double quote", NULL, "" ); + if (nidrtext[--nidrleng] == '\n') + unput('\n'); + nidrtext[nidrleng] = 0; + print_token( "quoted string", (char*) nidrtext, "" ); + nidrlval.qstring = nidr_KWscopy(nidrtext); + BEGIN DATA; + return QUOTED_STRING; + } + YY_BREAK +case 23: +YY_RULE_SETUP +/* #line 253 "nidrscan.l" */ +{ + print_token( "newline", NULL, NULL ); + if (nidr_comment) + nidr_comment(nidrtext); + nidrLineNumber++; + } + YY_BREAK +case 24: +YY_RULE_SETUP +/* #line 259 "nidrscan.l" */ +{ + if (nidr_comment) + nidr_comment(nidrtext); + print_token( "comment - escaped newline", (char*) nidrtext, "" ); + unput( '\\' ); + } + YY_BREAK +case 25: +YY_RULE_SETUP +/* #line 265 "nidrscan.l" */ +{ + if (nidr_comment) + nidr_comment(nidrtext); + print_token( "comment", (char*) nidrtext, "" ); + } + YY_BREAK +case 26: +YY_RULE_SETUP +/* #line 270 "nidrscan.l" */ +{ return nidrtext[0]; } + YY_BREAK +case 27: +YY_RULE_SETUP +/* #line 272 "nidrscan.l" */ +ECHO; + YY_BREAK +/* #line 1074 "nidr-scanner.c" */ +case YY_STATE_EOF(INITIAL): +case YY_STATE_EOF(DATA): +case YY_STATE_EOF(DQ_STRING): +case YY_STATE_EOF(Q_STRING): + nidrterminate(); + + case YY_END_OF_BUFFER: + { + /* Amount of text matched not including the EOB char. */ + int nidr_amount_of_matched_text = (int) (nidr_cp - nidrtext_ptr) - 1; + + /* Undo the effects of YY_DO_BEFORE_ACTION. */ + *nidr_cp = nidr_hold_char; + YY_RESTORE_YY_MORE_OFFSET + + if ( nidr_current_buffer->nidr_buffer_status == YY_BUFFER_NEW ) + { + /* We're scanning a new file or input source. It's + * possible that this happened because the user + * just pointed nidrin at a new source and called + * nidrlex(). If so, then we have to assure + * consistency between nidr_current_buffer and our + * globals. Here is the right place to do so, because + * this is the first action (other than possibly a + * back-up) that will match for the new input source. + */ + nidr_n_chars = nidr_current_buffer->nidr_n_chars; + nidr_current_buffer->nidr_input_file = nidrin; + nidr_current_buffer->nidr_buffer_status = YY_BUFFER_NORMAL; + } + + /* Note that here we test for nidr_c_buf_p "<=" to the position + * of the first EOB in the buffer, since nidr_c_buf_p will + * already have been incremented past the NUL character + * (since all states make transitions on EOB to the + * end-of-buffer state). Contrast this with the test + * in input(). + */ + if ( nidr_c_buf_p <= &nidr_current_buffer->nidr_ch_buf[nidr_n_chars] ) + { /* This was really a NUL. */ + nidr_state_type nidr_next_state; + + nidr_c_buf_p = nidrtext_ptr + nidr_amount_of_matched_text; + + nidr_current_state = nidr_get_previous_state(); + + /* Okay, we're now positioned to make the NUL + * transition. We couldn't have + * nidr_get_previous_state() go ahead and do it + * for us because it doesn't know how to deal + * with the possibility of jamming (and we don't + * want to build jamming into it because then it + * will run more slowly). + */ + + nidr_next_state = nidr_try_NUL_trans( nidr_current_state ); + + nidr_bp = nidrtext_ptr + YY_MORE_ADJ; + + if ( nidr_next_state ) + { + /* Consume the NUL. */ + nidr_cp = ++nidr_c_buf_p; + nidr_current_state = nidr_next_state; + goto nidr_match; + } + + else + { + nidr_cp = nidr_c_buf_p; + goto nidr_find_action; + } + } + + else switch ( nidr_get_next_buffer() ) + { + case EOB_ACT_END_OF_FILE: + { + nidr_did_buffer_switch_on_eof = 0; + + if ( nidrwrap() ) + { + /* Note: because we've taken care in + * nidr_get_next_buffer() to have set up + * nidrtext, we can now set up + * nidr_c_buf_p so that if some total + * hoser (like flex itself) wants to + * call the scanner after we return the + * YY_NULL, it'll still work - another + * YY_NULL will get returned. + */ + nidr_c_buf_p = nidrtext_ptr + YY_MORE_ADJ; + + nidr_act = YY_STATE_EOF(YY_START); + goto do_action; + } + + else + { + if ( ! nidr_did_buffer_switch_on_eof ) + YY_NEW_FILE; + } + break; + } + + case EOB_ACT_CONTINUE_SCAN: + nidr_c_buf_p = + nidrtext_ptr + nidr_amount_of_matched_text; + + nidr_current_state = nidr_get_previous_state(); + + nidr_cp = nidr_c_buf_p; + nidr_bp = nidrtext_ptr + YY_MORE_ADJ; + goto nidr_match; + + case EOB_ACT_LAST_MATCH: + nidr_c_buf_p = + &nidr_current_buffer->nidr_ch_buf[nidr_n_chars]; + + nidr_current_state = nidr_get_previous_state(); + + nidr_cp = nidr_c_buf_p; + nidr_bp = nidrtext_ptr + YY_MORE_ADJ; + goto nidr_find_action; + } + break; + } + + default: + YY_FATAL_ERROR( + "fatal flex scanner internal error--no action found" ); + } /* end of action switch */ + } /* end of scanning one token */ + } /* end of nidrlex */ + + +/* nidr_get_next_buffer - try to read in a new buffer + * + * Returns a code representing an action: + * EOB_ACT_LAST_MATCH - + * EOB_ACT_CONTINUE_SCAN - continue scanning from current position + * EOB_ACT_END_OF_FILE - end of file + */ + +static int nidr_get_next_buffer() + { + register char *dest = nidr_current_buffer->nidr_ch_buf; + register char *source = nidrtext_ptr; + register int number_to_move, i; + int ret_val; + + if ( nidr_c_buf_p > &nidr_current_buffer->nidr_ch_buf[nidr_n_chars + 1] ) + YY_FATAL_ERROR( + "fatal flex scanner internal error--end of buffer missed" ); + + if ( nidr_current_buffer->nidr_fill_buffer == 0 ) + { /* Don't try to fill the buffer, so this is an EOF. */ + if ( nidr_c_buf_p - nidrtext_ptr - YY_MORE_ADJ == 1 ) + { + /* We matched a single character, the EOB, so + * treat this as a final EOF. + */ + return EOB_ACT_END_OF_FILE; + } + + else + { + /* We matched some text prior to the EOB, first + * process it. + */ + return EOB_ACT_LAST_MATCH; + } + } + + /* Try to read more data. */ + + /* First move last chars to start of buffer. */ + number_to_move = (int) (nidr_c_buf_p - nidrtext_ptr) - 1; + + for ( i = 0; i < number_to_move; ++i ) + *(dest++) = *(source++); + + if ( nidr_current_buffer->nidr_buffer_status == YY_BUFFER_EOF_PENDING ) + /* don't do the read, it's not guaranteed to return an EOF, + * just force an EOF + */ + nidr_current_buffer->nidr_n_chars = nidr_n_chars = 0; + + else + { + int num_to_read = + nidr_current_buffer->nidr_buf_size - number_to_move - 1; + + while ( num_to_read <= 0 ) + { /* Not enough room in the buffer - grow it. */ +#ifdef YY_USES_REJECT + YY_FATAL_ERROR( +"input buffer overflow, can't enlarge buffer because scanner uses REJECT" ); +#else + + /* just a shorter name for the current buffer */ + YY_BUFFER_STATE b = nidr_current_buffer; + + int nidr_c_buf_p_offset = + (int) (nidr_c_buf_p - b->nidr_ch_buf); + + if ( b->nidr_is_our_buffer ) + { + int new_size = b->nidr_buf_size * 2; + + if ( new_size <= 0 ) + b->nidr_buf_size += b->nidr_buf_size / 8; + else + b->nidr_buf_size *= 2; + + b->nidr_ch_buf = (char *) + /* Include room in for 2 EOB chars. */ + nidr_flex_realloc( (void *) b->nidr_ch_buf, + b->nidr_buf_size + 2 ); + } + else + /* Can't grow it, we don't own it. */ + b->nidr_ch_buf = 0; + + if ( ! b->nidr_ch_buf ) + YY_FATAL_ERROR( + "fatal error - scanner input buffer overflow" ); + + nidr_c_buf_p = &b->nidr_ch_buf[nidr_c_buf_p_offset]; + + num_to_read = nidr_current_buffer->nidr_buf_size - + number_to_move - 1; +#endif + } + + if ( num_to_read > YY_READ_BUF_SIZE ) + num_to_read = YY_READ_BUF_SIZE; + + /* Read in more data. */ + YY_INPUT( (&nidr_current_buffer->nidr_ch_buf[number_to_move]), + nidr_n_chars, num_to_read ); + + nidr_current_buffer->nidr_n_chars = nidr_n_chars; + } + + if ( nidr_n_chars == 0 ) + { + if ( number_to_move == YY_MORE_ADJ ) + { + ret_val = EOB_ACT_END_OF_FILE; + nidrrestart( nidrin ); + } + + else + { + ret_val = EOB_ACT_LAST_MATCH; + nidr_current_buffer->nidr_buffer_status = + YY_BUFFER_EOF_PENDING; + } + } + + else + ret_val = EOB_ACT_CONTINUE_SCAN; + + nidr_n_chars += number_to_move; + nidr_current_buffer->nidr_ch_buf[nidr_n_chars] = YY_END_OF_BUFFER_CHAR; + nidr_current_buffer->nidr_ch_buf[nidr_n_chars + 1] = YY_END_OF_BUFFER_CHAR; + + nidrtext_ptr = &nidr_current_buffer->nidr_ch_buf[0]; + + return ret_val; + } + + +/* nidr_get_previous_state - get the state just before the EOB char was reached */ + +static nidr_state_type nidr_get_previous_state() + { + register nidr_state_type nidr_current_state; + register char *nidr_cp; + + nidr_current_state = nidr_start; + + for ( nidr_cp = nidrtext_ptr + YY_MORE_ADJ; nidr_cp < nidr_c_buf_p; ++nidr_cp ) + { + register YY_CHAR nidr_c = (*nidr_cp ? nidr_ec[YY_SC_TO_UI(*nidr_cp)] : 1); + if ( nidr_accept[nidr_current_state] ) + { + nidr_last_accepting_state = nidr_current_state; + nidr_last_accepting_cpos = nidr_cp; + } + while ( nidr_chk[nidr_base[nidr_current_state] + nidr_c] != nidr_current_state ) + { + nidr_current_state = (int) nidr_def[nidr_current_state]; + if ( nidr_current_state >= 125 ) + nidr_c = nidr_meta[(unsigned int) nidr_c]; + } + nidr_current_state = nidr_nxt[nidr_base[nidr_current_state] + (unsigned int) nidr_c]; + } + + return nidr_current_state; + } + + +/* nidr_try_NUL_trans - try to make a transition on the NUL character + * + * synopsis + * next_state = nidr_try_NUL_trans( current_state ); + */ + +#ifdef YY_USE_PROTOS +static nidr_state_type nidr_try_NUL_trans( nidr_state_type nidr_current_state ) +#else +static nidr_state_type nidr_try_NUL_trans( nidr_current_state ) +nidr_state_type nidr_current_state; +#endif + { + register int nidr_is_jam; + register char *nidr_cp = nidr_c_buf_p; + + register YY_CHAR nidr_c = 1; + if ( nidr_accept[nidr_current_state] ) + { + nidr_last_accepting_state = nidr_current_state; + nidr_last_accepting_cpos = nidr_cp; + } + while ( nidr_chk[nidr_base[nidr_current_state] + nidr_c] != nidr_current_state ) + { + nidr_current_state = (int) nidr_def[nidr_current_state]; + if ( nidr_current_state >= 125 ) + nidr_c = nidr_meta[(unsigned int) nidr_c]; + } + nidr_current_state = nidr_nxt[nidr_base[nidr_current_state] + (unsigned int) nidr_c]; + nidr_is_jam = (nidr_current_state == 124); + + return nidr_is_jam ? 0 : nidr_current_state; + } + + +#ifndef YY_NO_UNPUT +#ifdef YY_USE_PROTOS +static void nidrunput( int c, register char *nidr_bp ) +#else +static void nidrunput( c, nidr_bp ) +int c; +register char *nidr_bp; +#endif + { + register char *nidr_cp = nidr_c_buf_p; + + /* undo effects of setting up nidrtext */ + *nidr_cp = nidr_hold_char; + + if ( nidr_cp < nidr_current_buffer->nidr_ch_buf + 2 ) + { /* need to shift things up to make room */ + /* +2 for EOB chars. */ + register int number_to_move = nidr_n_chars + 2; + register char *dest = &nidr_current_buffer->nidr_ch_buf[ + nidr_current_buffer->nidr_buf_size + 2]; + register char *source = + &nidr_current_buffer->nidr_ch_buf[number_to_move]; + + while ( source > nidr_current_buffer->nidr_ch_buf ) + *--dest = *--source; + + nidr_cp += (int) (dest - source); + nidr_bp += (int) (dest - source); + nidr_current_buffer->nidr_n_chars = + nidr_n_chars = nidr_current_buffer->nidr_buf_size; + + if ( nidr_cp < nidr_current_buffer->nidr_ch_buf + 2 ) + YY_FATAL_ERROR( "flex scanner push-back overflow" ); + } + + *--nidr_cp = (char) c; + + + nidrtext_ptr = nidr_bp; + nidr_hold_char = *nidr_cp; + nidr_c_buf_p = nidr_cp; + } +#endif /* ifndef YY_NO_UNPUT */ + + +#ifndef YY_NO_INPUT +#ifdef __cplusplus +static int nidrinput() +#else +static int input() +#endif + { + int c; + + *nidr_c_buf_p = nidr_hold_char; + + if ( *nidr_c_buf_p == YY_END_OF_BUFFER_CHAR ) + { + /* nidr_c_buf_p now points to the character we want to return. + * If this occurs *before* the EOB characters, then it's a + * valid NUL; if not, then we've hit the end of the buffer. + */ + if ( nidr_c_buf_p < &nidr_current_buffer->nidr_ch_buf[nidr_n_chars] ) + /* This was really a NUL. */ + *nidr_c_buf_p = '\0'; + + else + { /* need more input */ + int offset = nidr_c_buf_p - nidrtext_ptr; + ++nidr_c_buf_p; + + switch ( nidr_get_next_buffer() ) + { + case EOB_ACT_LAST_MATCH: + /* This happens because nidr_g_n_b() + * sees that we've accumulated a + * token and flags that we need to + * try matching the token before + * proceeding. But for input(), + * there's no matching to consider. + * So convert the EOB_ACT_LAST_MATCH + * to EOB_ACT_END_OF_FILE. + */ + + /* Reset buffer status. */ + nidrrestart( nidrin ); + + /* fall through */ + + case EOB_ACT_END_OF_FILE: + { + if ( nidrwrap() ) + return EOF; + + if ( ! nidr_did_buffer_switch_on_eof ) + YY_NEW_FILE; +#ifdef __cplusplus + return nidrinput(); +#else + return input(); +#endif + } + + case EOB_ACT_CONTINUE_SCAN: + nidr_c_buf_p = nidrtext_ptr + offset; + break; + } + } + } + + c = *(unsigned char *) nidr_c_buf_p; /* cast for 8-bit char's */ + *nidr_c_buf_p = '\0'; /* preserve nidrtext */ + nidr_hold_char = *++nidr_c_buf_p; + + + return c; + } +#endif /* YY_NO_INPUT */ + +#ifdef YY_USE_PROTOS +void nidrrestart( FILE *input_file ) +#else +void nidrrestart( input_file ) +FILE *input_file; +#endif + { + if ( ! nidr_current_buffer ) + nidr_current_buffer = nidr_create_buffer( nidrin, YY_BUF_SIZE ); + + nidr_init_buffer( nidr_current_buffer, input_file ); + nidr_load_buffer_state(); + } + + +#ifdef YY_USE_PROTOS +void nidr_switch_to_buffer( YY_BUFFER_STATE new_buffer ) +#else +void nidr_switch_to_buffer( new_buffer ) +YY_BUFFER_STATE new_buffer; +#endif + { + if ( nidr_current_buffer == new_buffer ) + return; + + if ( nidr_current_buffer ) + { + /* Flush out information for old buffer. */ + *nidr_c_buf_p = nidr_hold_char; + nidr_current_buffer->nidr_buf_pos = nidr_c_buf_p; + nidr_current_buffer->nidr_n_chars = nidr_n_chars; + } + + nidr_current_buffer = new_buffer; + nidr_load_buffer_state(); + + /* We don't actually know whether we did this switch during + * EOF (nidrwrap()) processing, but the only time this flag + * is looked at is after nidrwrap() is called, so it's safe + * to go ahead and always set it. + */ + nidr_did_buffer_switch_on_eof = 1; + } + + +#ifdef YY_USE_PROTOS +void nidr_load_buffer_state( void ) +#else +void nidr_load_buffer_state() +#endif + { + nidr_n_chars = nidr_current_buffer->nidr_n_chars; + nidrtext_ptr = nidr_c_buf_p = nidr_current_buffer->nidr_buf_pos; + nidrin = nidr_current_buffer->nidr_input_file; + nidr_hold_char = *nidr_c_buf_p; + } + + +#ifdef YY_USE_PROTOS +YY_BUFFER_STATE nidr_create_buffer( FILE *file, int size ) +#else +YY_BUFFER_STATE nidr_create_buffer( file, size ) +FILE *file; +int size; +#endif + { + YY_BUFFER_STATE b; + + b = (YY_BUFFER_STATE) nidr_flex_alloc( sizeof( struct nidr_buffer_state ) ); + if ( ! b ) + YY_FATAL_ERROR( "out of dynamic memory in nidr_create_buffer()" ); + + b->nidr_buf_size = size; + + /* nidr_ch_buf has to be 2 characters longer than the size given because + * we need to put in 2 end-of-buffer characters. + */ + b->nidr_ch_buf = (char *) nidr_flex_alloc( b->nidr_buf_size + 2 ); + if ( ! b->nidr_ch_buf ) + YY_FATAL_ERROR( "out of dynamic memory in nidr_create_buffer()" ); + + b->nidr_is_our_buffer = 1; + + nidr_init_buffer( b, file ); + + return b; + } + + +#ifdef YY_USE_PROTOS +void nidr_delete_buffer( YY_BUFFER_STATE b ) +#else +void nidr_delete_buffer( b ) +YY_BUFFER_STATE b; +#endif + { + if ( ! b ) + return; + + if ( b == nidr_current_buffer ) + nidr_current_buffer = (YY_BUFFER_STATE) 0; + + if ( b->nidr_is_our_buffer ) + nidr_flex_free( (void *) b->nidr_ch_buf ); + + nidr_flex_free( (void *) b ); + } + +/* Fix for C99 */ +#ifndef __cplusplus +extern int isatty(int); +#endif /* __cplusplus */ + +#ifdef YY_USE_PROTOS +void nidr_init_buffer( YY_BUFFER_STATE b, FILE *file ) +#else +void nidr_init_buffer( b, file ) +YY_BUFFER_STATE b; +FILE *file; +#endif + + + { + nidr_flush_buffer( b ); + + b->nidr_input_file = file; + b->nidr_fill_buffer = 1; + +#if YY_ALWAYS_INTERACTIVE + b->nidr_is_interactive = 1; +#else +#if YY_NEVER_INTERACTIVE + b->nidr_is_interactive = 0; +#else + b->nidr_is_interactive = file ? (isatty( fileno(file) ) > 0) : 0; +#endif +#endif + } + + +#ifdef YY_USE_PROTOS +void nidr_flush_buffer( YY_BUFFER_STATE b ) +#else +void nidr_flush_buffer( b ) +YY_BUFFER_STATE b; +#endif + + { + if ( ! b ) + return; + + b->nidr_n_chars = 0; + + /* We always need two end-of-buffer characters. The first causes + * a transition to the end-of-buffer state. The second causes + * a jam in that state. + */ + b->nidr_ch_buf[0] = YY_END_OF_BUFFER_CHAR; + b->nidr_ch_buf[1] = YY_END_OF_BUFFER_CHAR; + + b->nidr_buf_pos = &b->nidr_ch_buf[0]; + + b->nidr_at_bol = 1; + b->nidr_buffer_status = YY_BUFFER_NEW; + + if ( b == nidr_current_buffer ) + nidr_load_buffer_state(); + } + + +#ifndef YY_NO_SCAN_BUFFER +#ifdef YY_USE_PROTOS +YY_BUFFER_STATE nidr_scan_buffer( char *base, nidr_size_t size ) +#else +YY_BUFFER_STATE nidr_scan_buffer( base, size ) +char *base; +nidr_size_t size; +#endif + { + YY_BUFFER_STATE b; + + if ( size < 2 || + base[size-2] != YY_END_OF_BUFFER_CHAR || + base[size-1] != YY_END_OF_BUFFER_CHAR ) + /* They forgot to leave room for the EOB's. */ + return 0; + + b = (YY_BUFFER_STATE) nidr_flex_alloc( sizeof( struct nidr_buffer_state ) ); + if ( ! b ) + YY_FATAL_ERROR( "out of dynamic memory in nidr_scan_buffer()" ); + + b->nidr_buf_size = size - 2; /* "- 2" to take care of EOB's */ + b->nidr_buf_pos = b->nidr_ch_buf = base; + b->nidr_is_our_buffer = 0; + b->nidr_input_file = 0; + b->nidr_n_chars = b->nidr_buf_size; + b->nidr_is_interactive = 0; + b->nidr_at_bol = 1; + b->nidr_fill_buffer = 0; + b->nidr_buffer_status = YY_BUFFER_NEW; + + nidr_switch_to_buffer( b ); + + return b; + } +#endif + + +#ifndef YY_NO_SCAN_STRING +#ifdef YY_USE_PROTOS +YY_BUFFER_STATE nidr_scan_string( nidrconst char *nidr_str ) +#else +YY_BUFFER_STATE nidr_scan_string( nidr_str ) +nidrconst char *nidr_str; +#endif + { + int len; + for ( len = 0; nidr_str[len]; ++len ) + ; + + return nidr_scan_bytes( nidr_str, len ); + } +#endif + + +#ifndef YY_NO_SCAN_BYTES +#ifdef YY_USE_PROTOS +YY_BUFFER_STATE nidr_scan_bytes( nidrconst char *bytes, int len ) +#else +YY_BUFFER_STATE nidr_scan_bytes( bytes, len ) +nidrconst char *bytes; +int len; +#endif + { + YY_BUFFER_STATE b; + char *buf; + nidr_size_t n; + int i; + + /* Get memory for full buffer, including space for trailing EOB's. */ + n = len + 2; + buf = (char *) nidr_flex_alloc( n ); + if ( ! buf ) + YY_FATAL_ERROR( "out of dynamic memory in nidr_scan_bytes()" ); + + for ( i = 0; i < len; ++i ) + buf[i] = bytes[i]; + + buf[len] = buf[len+1] = YY_END_OF_BUFFER_CHAR; + + b = nidr_scan_buffer( buf, n ); + if ( ! b ) + YY_FATAL_ERROR( "bad buffer in nidr_scan_bytes()" ); + + /* It's okay to grow etc. this buffer, and we should throw it + * away when we're done. + */ + b->nidr_is_our_buffer = 1; + + return b; + } +#endif + + +#ifndef YY_NO_PUSH_STATE +#ifdef YY_USE_PROTOS +static void nidr_push_state( int new_state ) +#else +static void nidr_push_state( new_state ) +int new_state; +#endif + { + if ( nidr_start_stack_ptr >= nidr_start_stack_depth ) + { + nidr_size_t new_size; + + nidr_start_stack_depth += YY_START_STACK_INCR; + new_size = nidr_start_stack_depth * sizeof( int ); + + if ( ! nidr_start_stack ) + nidr_start_stack = (int *) nidr_flex_alloc( new_size ); + + else + nidr_start_stack = (int *) nidr_flex_realloc( + (void *) nidr_start_stack, new_size ); + + if ( ! nidr_start_stack ) + YY_FATAL_ERROR( + "out of memory expanding start-condition stack" ); + } + + nidr_start_stack[nidr_start_stack_ptr++] = YY_START; + + BEGIN(new_state); + } +#endif + + +#ifndef YY_NO_POP_STATE +static void nidr_pop_state() + { + if ( --nidr_start_stack_ptr < 0 ) + YY_FATAL_ERROR( "start-condition stack underflow" ); + + BEGIN(nidr_start_stack[nidr_start_stack_ptr]); + } +#endif + + +#ifndef YY_NO_TOP_STATE +static int nidr_top_state() + { + return nidr_start_stack[nidr_start_stack_ptr - 1]; + } +#endif + +#ifndef YY_EXIT_FAILURE +#define YY_EXIT_FAILURE 2 +#endif + +#ifdef YY_USE_PROTOS +static void nidr_fatal_error( nidrconst char msg[] ) +#else +static void nidr_fatal_error( msg ) +char msg[]; +#endif + { + (void) fprintf( stderr, "%s\n", msg ); + exit( YY_EXIT_FAILURE ); + } + + + +/* Redefine nidrless() so it works in section 3 code. */ + +#undef nidrless +#define nidrless(n) \ + do \ + { \ + /* Undo effects of setting up nidrtext. */ \ + nidrtext[nidrleng] = nidr_hold_char; \ + nidr_c_buf_p = nidrtext + n; \ + nidr_hold_char = *nidr_c_buf_p; \ + *nidr_c_buf_p = '\0'; \ + nidrleng = n; \ + } \ + while ( 0 ) + + +/* Internal utility routines. */ + +#ifndef nidrtext_ptr +#ifdef YY_USE_PROTOS +static void nidr_flex_strncpy( char *s1, nidrconst char *s2, int n ) +#else +static void nidr_flex_strncpy( s1, s2, n ) +char *s1; +nidrconst char *s2; +int n; +#endif + { + register int i; + for ( i = 0; i < n; ++i ) + s1[i] = s2[i]; + } +#endif + +#ifdef YY_NEED_STRLEN +#ifdef YY_USE_PROTOS +static int nidr_flex_strlen( nidrconst char *s ) +#else +static int nidr_flex_strlen( s ) +nidrconst char *s; +#endif + { + register int n; + for ( n = 0; s[n]; ++n ) + ; + + return n; + } +#endif + + +#ifdef YY_USE_PROTOS +static void *nidr_flex_alloc( nidr_size_t size ) +#else +static void *nidr_flex_alloc( size ) +nidr_size_t size; +#endif + { + return (void *) malloc( size ); + } + +#ifdef YY_USE_PROTOS +static void *nidr_flex_realloc( void *ptr, nidr_size_t size ) +#else +static void *nidr_flex_realloc( ptr, size ) +void *ptr; +nidr_size_t size; +#endif + { + /* The cast to (char *) in the following accommodates both + * implementations that use char* generic pointers, and those + * that use void* generic pointers. It works with the latter + * because both ANSI C and C++ allow castless assignment from + * any pointer type to void*, and deal with argument conversions + * as though doing an assignment. + */ + return (void *) realloc( (char *) ptr, size ); + } + +#ifdef YY_USE_PROTOS +static void nidr_flex_free( void *ptr ) +#else +static void nidr_flex_free( ptr ) +void *ptr; +#endif + { + free( ptr ); + } + +#if YY_MAIN +int main() + { + nidrlex(); + return 0; + } +#endif +/* #line 272 "nidrscan.l" */ + + + static int nidr_ateof = 0; + static const char *nidr_instring = 0; + + void +bad_number(const char *s) +{ + fprintf(stderr, "\n*** Invalid number \"%s\" on input line %d within " + "%s keyword.\n", s, nidrLineNumber, nidr_keyword_name()); + nidr_abort(); + } + + void +nidr_set_input_string(const char *s) +{ + nidr_instring = s; + } + + static int +my_nidr_input(char *buf, int bmax) +{ + int c, n; + + if (nidr_ateof) + return 0; + n = 0; + if (nidr_instring) { + while(n < bmax && (c = *nidr_instring)) { + ++nidr_instring; + if (c != '\r') + buf[n++] = c; + if (c == '\n') + break; + } + } + else if (nidr_current_buffer->nidr_is_interactive) + while(n < bmax) { + if ((c = getc(nidrin)) == EOF) + break; + if (c != '\r') + buf[n++] = c; + if (c == '\n') + break; + } + else + while(n < bmax) { + if ((c = getc(nidrin)) == EOF) + break; + if (c != '\r') + buf[n++] = c; + } + if (n <= 0) { + nidr_ateof = n = 1; + if (c == EOF) { + fclose(nidrin); + nidrin = NULL; + } + buf[0] = ';'; + } + return n; + } + + void +reset_nidrlex_state(void) +{ + BEGIN INITIAL; + nidr_abort(); + } + + void +unput_string(char *s, int len) +{ + while(--len >= 0) + unput(s[len]); + } + + void +nidr_reinit(void) +{ + nidr_init = 1; + nidr_ateof = 0; + if (nidr_current_buffer) { + free(nidr_current_buffer->nidr_ch_buf); + free(nidr_current_buffer); + nidr_current_buffer = 0; + } + } + + int +nidrwrap(void) +{ return 1; } Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr.c =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr.c (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/mac/static/packages/nidr/nidr.c (revision 27955) @@ -0,0 +1,2427 @@ +/********************************************************************* +Copyright 2008, 2010 Sandia Corporation. Under the terms of Contract +DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government +retains certain rights in this software. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: + +* Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright +notice, this list of conditions and the following disclaimer in the +documentation and/or other materials provided with the distribution. + +* Neither the name of Sandia Corporation nor the names of its +contributors may be used to endorse or promote products derived from +this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +***********************************************************************/ + +/* nidr.c */ + +#ifndef NIDR_H /* for $DAKOTA/src/nidr.c */ +#include "nidr.h" +#endif +#include +#include +#include +#include +#include +#include +#include +#include "avltree.h" + +#ifndef NIDR_SQUAWKMAX +#define NIDR_SQUAWKMAX 10 +#endif + +#ifndef NO_NIDR_DYNLIB /*{*/ +typedef KeyWord *(*KW_ADD)(void); +static KeyWord *kwfind(const char *, KeyWord *, int, int *); +static KeyWord *toomany(const char *, KeyWord *, int); +#ifdef _WIN32 /*{{*/ +#include +#define dlopen(x,y) LoadLibrary(x) +#define find_dlsym(a,b,c) (a = (KW_ADD)GetProcAddress((HINSTANCE)(b),c)) +#define dlclose(x) FreeLibrary((HMODULE)x) +#define NO_DLERROR +#else /*}{*/ +#include +#include +#define find_dlsym(a,b,c) (a = (KW_ADD)dlsym(b,c)) +#undef NO_DLERROR +#endif /*}}*/ +#endif /*}*/ + + extern KeyWord Dakota_Keyword_Top; + extern int nidrLineNumber; + static KeyWord* Keyword_Top = &Dakota_Keyword_Top; + static void *KW_g; + void (*nidr_comment)(const char*); + static void nidr_keyword_finish(void); + static Comment *OutsideComment; + static void kw_finish2(void), kw_finish3(void); + static void kw_setup1(KeyWord *); + static FILE *dumpfile; + static KeyWord **ToClear, **ToClear0, **ToClearEnd; + static int dumplev, nsquawk, nparse_errors, primary, strict; + + int NIDR_disallow_missing_start = 1; + + enum {n_KWStack0 = 64}; + + static KWinfo KWStack0[n_KWStack0]; + + static Uint n_KWStack = n_KWStack0; + + static KeyWord *curid, *curkw; + static KWinfo *KWStack = KWStack0, + *KWStackBot = KWStack0, + *KWStackEnd = KWStack0 + n_KWStack0; + + static Values KWval, KWvalmax; + static Real *KWvalbuf; + static Uint nKWvalbuf; + + typedef struct Sbuf Sbuf; + enum { n_KWsbuf = 8192 }; + struct Sbuf { + char buf[n_KWsbuf]; + Sbuf *next; + }; + + typedef struct KWseen KWseen; + + struct +KWseen { + const char *name; + KeyWord *kw; + KWseen *mnext, *mprev; /* for identifiers so far unrequited when kw == 0 */ + /* kw != 0 ==> mprev = first child, and mnext = next sibling */ + KWseen *parent; + KWseen **lcn; /* &mprev field of last child; lcn == 0 when this */ + /* keyword was entered into the AVL tree because */ + /* its parent was seen. */ + Comment *comment; + char **svals; + Real *rvals; + size_t nvals; + }; + + static KWseen *KW_cur; + NIDR_KWlib *NIDR_Libs; + + void +nidr_lib_cleanup(void) +{ + KeyWord *kw; + NIDR_KWlib *L, *L1; + + L1 = NIDR_Libs; + NIDR_Libs = 0; + while((L = L1)) { + if (L->oldtop) + Keyword_Top = L->oldtop; + if ((kw = L->kw0)) { + kw->f.vs = 0; + kw->kind &= ~KWKind_Loaded; + } +#ifndef NO_NIDR_DYNLIB /*{{*/ + dlclose(L->h); +#else /*}{*/ + /* botch("dlclose is NOT SUPPORTED for current configuration"); */ + fprintf(stderr, "\ndlclose is NOT SUPPORTED for current configuration"); +#endif /*}}*/ + L1 = L->next; + free(L); + } + } + + static Sbuf KWsbuf0, *KWsbuf = &KWsbuf0; + static char *KWsbuf1 = KWsbuf0.buf, *KWsbufe = KWsbuf0.buf + n_KWsbuf; + static KWseen *curkws; + static const char *valkind[3] = {"integer","numeric","string"}; + + int +nidr_parse_error(void) +{ + int n; + if ((n = nsquawk - NIDR_SQUAWKMAX) > 0) + fprintf(stderr, "\n%d error message%s suppressed.\n", + n, "s" + (n == 1)); + return nsquawk + nparse_errors; + } + + void +nidr_signal_parse_error(void) +{ ++nparse_errors; } + + void +nidr_tolower(char *s) +{ + for(; *s; ++s) + *s = tolower(*s); + } + + static void +botch(const char *fmt, ...) +{ + va_list ap; + va_start(ap, fmt); + fprintf(stderr, "\nBotch: "); + vfprintf(stderr, fmt, ap); + fputs(".\n", stderr); + va_end(ap); + exit(1); + } + + static void +squawk(const char *fmt, ...) +{ + va_list ap; + if (++nsquawk <= NIDR_SQUAWKMAX) { + fprintf(stderr, "Input line %d: ", nidrLineNumber); + va_start(ap, fmt); + vfprintf(stderr, fmt, ap); + fputs(".\n", stderr); + va_end(ap); + } + } + +#ifdef NIDR_MALLOC_DEBUG + typedef struct MallocDebug MallocDebug; + struct MallocDebug +{ + MallocDebug *next, *prev; + char *where; + int nalloc; + }; + + static MallocDebug MDtop = {&MDtop, &MDtop, 0, 0}; + int MallocDebugCount, MallocDebugCount1; + + static void* +Alloc(const char *where, size_t len) +{ + MallocDebug *md = malloc(len + sizeof(MallocDebug)); + if (!md) { + fprintf(stderr, "malloc(%lu) failure in %s\n", (unsigned long)len, where); + exit(1); + } + (md->next = MDtop.next)->prev = md; + (md->prev = &MDtop)->next = md; + md->where = where; + if ((md->nalloc = ++MallocDebugCount) == MallocDebugCount1) + printf("Hit %d\n", md->nalloc); + return (void*)(md + 1); + } + + static void +MallocDebugFree(void *v) +{ + MallocDebug *md = (MallocDebug *)v - 1; + md->next->prev = md->prev; + md->prev->next = md->next; + free(md); + } +#define free MallocDebugFree + +#else //!NIDR_MALLOC_DEBUG + static void* +Alloc(const char *where, size_t len) +{ + void *rv = malloc(len); + if (!rv) { + fprintf(stderr, "malloc(%lu) failure in %s\n", (unsigned long)len, where); + exit(1); + } + return rv; + } +#endif //NIDR_MALLOC_DEBUG + + const char * +nidr_basename(const char *p) +{ + const char *b; + +#ifdef _WIN32 + if (p[0] && p[1] == ':') + p += 2; + else if (p[0] == '\\' && p[1] == '\\') + for(p += 2; *p; ) + switch(*p++) { + case '/': + case '\\': + goto break2; + } + break2: +#endif + b = p; + while(*p) + switch(*p++) { + case '/': +#ifdef _WIN32 + case '\\': +#endif + b = p; + } + return b; + } + + const char *nidr_exedir; + int nidr_exedir_len = -1; /* allow resetting to -1 for debugging */ + +#ifndef _WIN32 + static int +Is_executable(uid_t myuid, gid_t mygid, struct stat *sb) +{ + if (sb->st_uid == myuid) { + if (sb->st_mode & S_IXUSR) + return 1; + } + else if (sb->st_gid == mygid) { + if (sb->st_mode & S_IXGRP) + return 1; + } + else if (sb->st_mode & S_IXOTH) + return 1; + return 0; + } +#endif + + int +nidr_save_exedir(const char *argv0, int pathadj) +{ + /* pathadj & 1 ==> add exedir to $PATH */ + /* pathadj & 2 ==> add . to $PATH */ + /* (in both cases if not already there) */ + + /* These conditionals don't seem to work (perhaps expected) for Cygwin + binaries run from Windows command prompt as the compile-time is + unix-style, but runtime the path is windows-like. For now comment + out warning when on Cygwin build */ +#ifdef _WIN32 +#define Pathname "Path" +#define Sep ';' +#define Slash '\\' +#define Executable(x) !stat(x,&sb) +#else +#define Pathname "PATH" +#define Sep ':' +#define Slash '/' +#define Executable(x) !stat(x,&sb) && Is_executable(myuid, mygid, &sb) +#endif + char *buf, buf0[4096], *s; + const char *av0, *p, *p0, *p1, *p2; + int dotseen, finaldot, rc; + size_t buflen, L, L1, L2, L3; + struct stat sb; + static const char dotslash[3] = { '.', Slash, 0 }; +#ifdef _WIN32 + int c; + pathadj &= 1; /* . is implicitly in $PATH under _WIN32 */ +#else + gid_t mygid; + uid_t myuid; +#endif + if (nidr_exedir_len != -1) { + fprintf(stderr, "\nIgnoring extra call on nidr_save_argv0()\n"); + return 1; + } + nidr_exedir_len = 0; + if (!(av0 = argv0)) + return 2; + if (!(p = getenv(Pathname))) { + fprintf(stderr, "\nnidr_save_exedir: no $%s\n", Pathname); + return 3; + } + dotseen = finaldot = rc = 0; + buf = buf0; + buflen = sizeof(buf0); + p0 = p2 = p; + p1 = nidr_basename(av0); + if ((L = p1 - av0) > 0) { + memcpy(s = (char*)Alloc("nidr_save_argv0", L+1), av0, L); + s[L] = 0; + nidr_exedir = s; + nidr_exedir_len = (int)L; +#ifdef _WIN32 + for(L1 = 0; L1 < L; ++L1) + if (s[L1] == '/') + s[L1] = '\\'; +#endif + if (!pathadj) + return 0; + if (*p == Sep) + dotseen = 1; + while(*p) { + if (*p == Sep && (p[1] == Sep || p[1] == 0)) { + dotseen = 1; + break; + } + ++p; + } + if (s[0] == '.' && s[1] == Slash && L == 2) { +#ifdef _WIN32 + return 0; +#else + if (!dotseen) + goto dot_add; +#endif + } + L1 = L - 1; + for(p = p0;;) { + while(*p == Sep) + ++p; + if (!*p) + break; + if (!strncmp(p, s, L1)) { +#ifdef _WIN32 + return 0; +#else + if (!(pathadj &= ~1) || *p0 == Sep) + return 0; + for(p = p0;;) { + if (*p == Sep || (*p == '.' && p[1] == Sep)) + return 0; + while(*p != Sep) { + if (!*p) + goto dot_add; + ++p; + } + if (!*++p) + return 0; + } +#endif + } + while(*++p != Sep) + if (!*p) + goto break2; + if (!*++p) { +#ifdef _WIN32 + finaldot = 1; /* leave at 0 for !_WIN32 */ +#endif + break; + } + } + break2: + L1 = strlen(Pathname); + L2 = strlen(p0); + if (!pathadj & 2) + dotseen = 1; + L3 = L1 + L2 + L + 3; + s = (char*)Alloc("nidr_save_argv0", L3); + memcpy(s, Pathname, L1); + s[L1++] = '='; + memcpy(s+L1, p0, L2); + L1 += L2; + if (!finaldot) + s[L1++] = Sep; + memcpy(s+L1, nidr_exedir, --L); + L1 += L; + if (!dotseen) + s[L1++] = Sep; + s[L1] = 0; /* omit final slash */ + putenv(s); + return 0; + } + L = strlen(av0); +#ifdef _WIN32 + if (L < 5 || av0[L-4] != '.' + || ((c = av0[L-3]) != 'e' && c != 'E') + || ((c = av0[L-2]) != 'x' && c != 'X') + || ((c = av0[L-1]) != 'e' && c != 'E')) { + memcpy(s = (char*)Alloc("nidr_save_argv0", L + 5), av0, L); + strcpy(s+L, ".exe"); + L += 4; + av0 = s; + } + if (Executable(av0)) { + /* handle implicit . */ + dotseen = 1; + nidr_exedir = dotslash; + } + else /* do for loop */ +#else + +/* Fix for C99 */ +#ifndef __cplusplus +extern uid_t geteuid(void); +extern uid_t getegid(void); +#endif /* __cplusplus */ + + myuid = geteuid(); + mygid = getegid(); +#endif + for(; *p; p = p2) { + for(p1 = p;; ++p1) { + if (*p1 == Sep) { + p2 = p1 + 1; + if (!*p2) + finaldot = 1; + break; + } + if (!*p1) { + p2 = p1; + break; + } + } + if (p1 == p || (*p == '.' && p1 == p + 1)) { + if (!dotseen) { + dotseen = 1; + if (Executable(av0)) { + nidr_exedir = dotslash; + break; + } + } + } + else { + L1 = p1 - p; + L2 = L + L1 + 2; + if (L2 > buflen) { + if (buf != buf0) + free(buf); + buf = (char*)Alloc("nidr_save_argv0", L2); + buflen = L2; + } + memcpy(buf, p, L1); + buf[L1++] = Slash; + strcpy(buf+L1, av0); + if (Executable(buf)) { + s = (char*)Alloc("nidr_save_argv0", L1+1); + memcpy(s, buf, L1); + s[L1] = 0; + nidr_exedir = s; + nidr_exedir_len = (int)L1; + pathadj &= ~1; + break; + } + } + } + if (dotseen) + pathadj &= ~2; + if (!finaldot && *p2) { + while(p2[1]) + ++p2; + if (*p2 == Sep) + finaldot = 1; + } + if (finaldot && !dotseen && !nidr_exedir) { + dotseen = 1; + if (Executable(av0)) + nidr_exedir = dotslash; + } + if (nidr_exedir == dotslash) + nidr_exedir_len = 2; + else { + if (pathadj & 2 && !finaldot) { +#ifndef _WIN32 + dot_add: +#endif + L = strlen(p0); + L1 = strlen(Pathname); + L2 = L + L1 + 3; + s = (char*)Alloc("nidr_save_argv0", L2); + memcpy(s, Pathname, L1); + s[L1++] = '='; + memcpy(s+L1, p0, L); + s[L += L1] = Sep; + s[L+1] = 0; + putenv(s); + } + if (!nidr_exedir) { +/* Suppress warning for Cygwin and Windows, where path isn't resolved correctly above */ +#if !defined(__CYGWIN__) && !defined(_MSC_VER) + fprintf(stderr, "\nnidr_save_exedir: could not find \"%s\" in $%s\n", + av0, Pathname); +#endif + rc = 4; + } + } + if (buf != buf0) + free(buf); + return rc; + } + + void * +nidr_dlopen(const char *libname) +{ +#ifdef NO_NIDR_DYNLIB /*{{*/ + botch("dlopen for \"%s\" is NOT SUPPORTED", libname); + return (void*)libname; +#else /*}{*/ + char buf0[4096], *buf; + const char *b; + size_t buflen, L, L1; + void *h; + + b = nidr_basename(libname); + if (b > libname) + return dlopen(libname, RTLD_NOW); + buf = buf0; + buflen = sizeof(buf0); + L = strlen(libname); + if (nidr_exedir) { + L1 = L + nidr_exedir_len + 1; + if (L1 > buflen) { + buf = (char*)Alloc("nidr_dlopen", L1); + buflen = L1; + } + memcpy(buf, nidr_exedir, nidr_exedir_len); + strcpy(buf + nidr_exedir_len, libname); + if ((h = dlopen(buf, RTLD_NOW))) + goto ret; + } + if (!(h = dlopen(libname, RTLD_NOW))) { + L1 = L + 3; + if (L1 > buflen) { + buf = (char*)Alloc("nidr_dlopen", L1); + buflen = L1; + } + buf[0] = '.'; + buf[1] = Slash; + strcpy(buf+2, libname); + if (!(h = dlopen(buf, RTLD_NOW))) + h = dlopen(libname, RTLD_NOW); /* for dlerror */ + } + ret: + if (buf != buf0) + free(buf); + return h; +#endif /*}}*/ + } + +#undef Executable +#undef Slash +#undef Sep +#undef Pathname + + + struct +Comment { + int k; /* subscript for comfree */ + size_t avail; /* bytes left (from tnext) */ + char *text; /* text of comment */ + char *tnext; /* null byte at end of comment */ + Comment *fnext; /* next free Comment */ + }; + + enum { Comment_kmax = 7 }; + + static Comment *comfree[Comment_kmax+1]; + static size_t Comment_maxlen[Comment_kmax+1]; + + static void +comment_free(Comment *c) +{ + int k = c->k; + + if (k > Comment_kmax) + free(c); + else { + c->fnext = comfree[k]; + comfree[k] = c; + } + } + + static Comment* +alloc_comment(int k, size_t L) +{ + Comment *c; + + for(; k <= Comment_kmax; ++k) { + if (L <= Comment_maxlen[k]) { + L = Comment_maxlen[k]; + if ((c = comfree[k])) { + comfree[k] = c->fnext; + goto have_c; + } + break; + } + } + c = (Comment*)Alloc("save_comment", L + sizeof(Comment) + 1); + c->k = k; + c->text = (char*)(c+1); + have_c: + c->avail = L; + c->tnext = c->text; + return c; + } + + static void +save_comment(const char *s) +{ + Comment *c, *c1, **cp; + size_t L, L1; + + L = strlen(s); + cp = curid ? &curid->comment : curkws ? &curkws->comment : &OutsideComment; + if ((c = *cp)) { + if (c->avail >= L) + goto cupdate; + L1 = c->tnext - c->text; + c1 = alloc_comment(c->k + 1, L + L1); + memcpy(c1->text, c->text, L1); + c1->tnext = c1->text + L1; + c1->avail -= L1; + comment_free(c); + c = c1; + } + else + c = alloc_comment(0, L); + cupdate: + memcpy(c->tnext, s, L+1); + c->tnext += L; + c->avail -= L; + *cp = c; + } + + static void +comment_setup(void) +{ + int i; + size_t L; + nidr_comment = save_comment; + /* "- 1" to allow for terminating '\0' */ + for(L = 64; L <= sizeof(Comment) - 1; L <<= 1); + for(i = 0; i <= Comment_kmax; ++i, L <<= 1) + Comment_maxlen[i] = L - sizeof(Comment) - 1; + } + + static void +comment_reset(void) +{ + Comment *c, *c1; + int i; + + for(i = 0; i <= Comment_kmax; ++i) { + c1 = comfree[i]; + comfree[i] = 0; + while((c = c1)) { + c1 = c->fnext; + free(c); + } + } + nidr_comment = 0; + } + + static void +dumpcomment(Comment **cp) +{ + Comment *c = *cp; + *cp = 0; + fprintf(dumpfile, "%s", c->text); + comment_free(c); + } + + static void +dumpname(int hasval, KeyWord *kw) +{ + const char *fmt[2] = { "%s", "%s =" }; + int i; + if (OutsideComment) + dumpcomment(&OutsideComment); + if (primary) + kw += kw->paoff; + for(i = 0; i < dumplev; ++i) + putc(' ', dumpfile); + fprintf(dumpfile,fmt[hasval],kw->name); + if (!hasval) { + if (kw->comment) + dumpcomment(&kw->comment); + else if (kw != curkw) + putc('\n', dumpfile); + } + } + + static void +dumpstring(const char *s0) +{ + const char *s; + int c, n1, n2, q; + + n1 = n2 = 0; + for(s = s0;;) + switch(*s++) { + case 0: goto break2; + case '\'': + ++n1; + break; + case '"': + ++n2; + } + break2: + q = '\''; + if (n1 > n2) + q = '"'; + putc(' ', dumpfile); + putc(q, dumpfile); + s = s0; + while((c = *s++)) { + if (c == q) + putc(q, dumpfile); + putc(c, dumpfile); + } + putc(q, dumpfile); + } + + static void +dumpvals0(KeyWord *kw) +{ + Real *r; + const char **sp; + int i, *ip, indent, j, n; + + ip = 0; /* shut up warning of possible use without initialization */ + sp = 0; /* ditto */ + if (!(r = KWval.r) && !(ip = KWval.i) && !(sp = KWval.s)) + return; + n = KWval.n; + putc((indent = n > 1) ? '\n' : ' ', dumpfile); + for(i = 0;;) { + if (indent) { + putc('\t', dumpfile); + for(j = 0; j < dumplev; ++j) + putc(' ', dumpfile); + } + if (r) + fprintf(dumpfile, "%.15g", r[i]); + else if (ip) + fprintf(dumpfile, "%d", ip[i]); + else + dumpstring(sp[i]); + if (++i >= n) + break; + indent = 1; + putc('\n', dumpfile); + } + if (kw->comment) + dumpcomment(&kw->comment); + else + putc('\n', dumpfile); + } + + static void (*dumpvals)(KeyWord *kw) = dumpvals0; + + static void +dumpvals1(KeyWord *kw) +{ + Real *r; + const char **sp; + int i, *ip, n; + + ip = 0; /* shut up warning of possible use without initialization */ + sp = 0; /* ditto */ + if ((r = KWval.r) || (ip = KWval.i) || (sp = KWval.s)) { + n = KWval.n; + for(i = 0; i < n; ++i) { + if (r) + fprintf(dumpfile, " %.15g", r[i]); + else if (ip) + fprintf(dumpfile, " %d", ip[i]); + else + dumpstring(sp[i]); + } + } + if (kw->comment) + dumpcomment(&kw->comment); + else + putc('\n', dumpfile); + } + + char * +nidr_KWscopy(const char *s) +{ + Sbuf *sb; + char *rv; + + size_t L = strlen(s) + 1; + if (L >= n_KWsbuf) + botch("String too long in KWscopy"); + if (KWsbufe - KWsbuf1 < L) { + if (!KWsbuf->next) { + KWsbuf->next = sb = (Sbuf*)Alloc("KWscopy", sizeof(Sbuf)); + sb->next = 0; + } + KWsbuf = KWsbuf->next; + KWsbuf1 = KWsbuf->buf; + KWsbufe = KWsbuf1 + n_KWsbuf; + } + strcpy(KWsbuf1, s); + rv = KWsbuf1; + KWsbuf1 += L; + return rv; + } + + static void +KWvalbuf_inc(void) +{ + Real *r; + Uint n; + + n = nKWvalbuf << 1; + r = (Real*)Alloc("KWvalbuf", n*sizeof(Real)); + memcpy(r, KWvalbuf, nKWvalbuf*sizeof(Real)); + free(KWvalbuf); + KWvalbuf = r; + nKWvalbuf = n; + KWvalmax.n <<= 1; + if (KWval.r) { + KWval.r = r; + KWvalmax.r = r + n; + } + else if (KWval.i) { + KWval.i = (int*) r; + KWvalmax.i = (int*)(r + n); + } + else if (KWval.s) { + KWval.s = (const char**)r; + KWvalmax.s = (const char**)(r + n); + } + else + botch("Unexpected case in KWvalbuf_inc"); + } + +/* KWval.rstate values... + * value form seen + * 0 v + * 1 L:u + * 2 L:s:u + * 3 n*v + * 4 n*L:u + * 5 n*L:s:u + */ + + static void +finish_rexpand(void) +{ + int i, k, n, os; + Real sgn, st, u, v, x; + + os = KWval.rstate; + KWval.rstate = 0; + n = KWval.n; + k = 1; + if (os >= 3) { + KWval.n = n -= os-1; + k = KWval.r[n]; + if (k != KWval.r[n]) { + squawk("Noninteger replication factor %.17g", KWval.r[n]); + return; + } + else if (k < 1) { + squawk("Nonpositive replication factor %d", k); + return; + } + ++n; + os -= 3; + } + else + KWval.n = n -= os + 1; + v = KWval.r[n++]; + u = st = 0.; /* Shut up warning of not being initialized. */ + /* Both will be assigned before being used. */ + switch(os) { + case 0: + n = KWval.n; + for(i = 0; i < k; ++i) { + if (n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.r[n++] = v; + } + KWval.n = n; + return; + case 1: + st = 1; + u = KWval.r[n]; + break; + case 2: + st = KWval.r[n]; + if (st == 0.) { + squawk("Invalid stride == zero."); + return; + } + u = KWval.r[n+1]; + } + sgn = 1.; + if (st < 0.) + sgn = -1.; + if (sgn*(u - v) < 0.) { + squawk("Empty sequence."); + return; + } + n = KWval.n; + do { + for(i = 0; sgn*(u - (x = v + i*st)) >= 0.; ++i) { + if (n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.r[n++] = x; + } + } + while(--k > 0); + KWval.n = n; + } + + static void +rexpand(int state) +{ + int os; + + os = KWval.rstate; + KWval.rstate = 0; + switch(state) { + case 1: /* just saw *v */ + if (os == 0) + KWval.rstate = 3; + else + squawk("Unexpected '*'"); + break; + case 2: /* just saw :v */ + if (os == 2 || os == 5) + squawk("Unexpected ':'"); + else + KWval.rstate = os + 1; + break; + } + } + + static void +nidr_bufr_strict(Real r, int state) +{ + int k, n; + + if (KWval.s) { + squawk("expected a quoted string, but found a number"); + return; + } + if (KWval.rstate && !state) + finish_rexpand(); + if (!KWval.r && !KWval.i) { + squawk("No values may be specified for %s", KWStack->kw->name); + return; + } + if ((n = KWval.n) >= KWvalmax.n) + KWvalbuf_inc(); + if (KWval.r) + KWval.r[n] = r; + else { + k = (int)r; + if (k != r) + squawk("truncating %.17g to %d", r, k); + KWval.i[n] = k; + } + ++KWval.n; + if (state | KWval.rstate) + rexpand(state); + } + + static void +nidr_bufs_strict(const char *s) +{ + if (!KWval.s) { + if (KWval.r) + squawk("Expected a number, but found a quoted string"); + else + squawk("Misplaced quoted string"); + return; + } + if (KWval.n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.s[KWval.n++] = s; + } + + void +nidr_reset(void) +{ + /* Originally did this in case KWKind_Str of kw_setup(), */ + /* but this leads to confusion with erroneous input. */ + if (curkw) + nidr_keyword_finish(); + KWsbuf = &KWsbuf0; + KWsbuf1 = KWsbuf0.buf; + KWsbufe = KWsbuf0.buf + n_KWsbuf; + } + + NIDR_KWlib * +nidr_lib_record(void *h, const char *libname) +{ + NIDR_KWlib *Lib; + size_t L; + + L = strlen(libname) + 1; + Lib = (NIDR_KWlib*)Alloc("NIDR_lib_record", sizeof(NIDR_KWlib) + L); + memset(Lib, 0, sizeof(NIDR_KWlib)); + memcpy(Lib->libname = (char*)(Lib+1), libname, L); + if (!(Lib->next = NIDR_Libs)) + atexit(nidr_lib_cleanup); + NIDR_Libs = Lib; + Lib->h = h; + return Lib; + } + + static KeyWord* +kw_insert(KeyWord *kw, int *tryagain) +{ +#ifdef NO_NIDR_DYNLIB /*{{*/ + botch("Loading library \"%s\" for %s is disallowed", + kw->f.vf, kw->name); +#else /*}{*/ + KW_ADD kwa; + KeyWord *kw0, *kw1, *kw2; + NIDR_KWlib *Lib; + Uint u1, ui; + const char *lname, *s; + int newtop, nmatch; + void *h; + + if (tryagain) + *tryagain = 0; + if (kw->kind & KWKind_Loaded) + return (KeyWord*)kw->f.vs; + h = nidr_dlopen(lname = (const char*)kw->f.vf); + if (!h) { +#ifndef NO_DLERROR + if ((s = dlerror())) + botch("Cannot open library \"%s\" for %s:\n\t%s", + lname, kw->name, s); + else +#endif + botch("Cannot open library \"%s\" for %s", + lname, kw->name); + } + if (!find_dlsym(kwa, h, "keyword_add")) + botch("dlsym(\"keyword_add\") failed for %s", lname); + kw1 = (*kwa)(); + if (!(s = kw1->name)) { + s = ""; + goto namebotch; + } + newtop = 0; + if (strcmp(s, kw->name)) { + if (!KW_cur && !strcmp(s,"KeywordTop") && kw1->kind & KWKind_Dynmult) + newtop = 1; + else if (tryagain && kw1->nkw > 0 + && (kw2 = kwfind(kw->name, kw1->kw, kw1->nkw, &nmatch))) { + if (nmatch > 1) { + toomany(kw->name, kw1, nmatch); + botch("Too many matches in library %s", lname); + } + *tryagain = 1; + } + else + namebotch: + botch("Library %s: expected top keyword to be %s but got %s", + lname, kw->name, s); + } + ui = kw->kind & (KWKind_Mask|KWKind_List); + u1 = kw1->kind & (KWKind_Mask|KWKind_List); + if (ui != u1) + botch("Library %s: expected kind %u for %s, but got %u", + lname, ui, s, u1); + Lib = nidr_lib_record(h, lname); + Lib->kw0 = kw0 = kw; + memcpy(&Lib->kw, kw, sizeof(KeyWord)); + kw = &Lib->kw; + kw->kw = kw1->kw; + kw->nkw = kw1->nkw; + kw->f = kw1->f; + kw0->f.vs = (void*)kw; + kw0->kind |= KWKind_Loaded; + if (newtop) { + Lib->oldtop = Keyword_Top; + Keyword_Top = kw; + kw->kind |= KWKind_Dynmult; + } +#endif /*}}*/ + return kw; + } + + static void +kwnext_setup(KeyWord *kw, Uint n) +{ + KeyWord *kwe; + + if (kw->kwnext || (n <= 1 && kw->name)) + return; +#ifndef NO_NIDR_DYNLIB /*{*/ + if (kw->kind & KWKind_Extended) { + KeyWordx *kx1, *kxe; + for(kx1 = (KeyWordx*)kw; !kx1->kw.name; ++kx1) + kx1->kw.kwnext = (KeyWord*)(kx1 + 1); + for(kxe = kx1 + n - 1; kx1 < kxe; ++kx1) + kx1->kw.kwnext = (KeyWord*)(kx1 + 1); + return; + } +#endif + for(; !kw->name; ++kw) + kw->kwnext = kw + 1; + for(kwe = kw + n - 1; kw < kwe; ++kw) + kw->kwnext = kw + 1; + } + + static void +KWStack_inc(void) +{ + KWinfo *kwi; + Uint nn; + size_t len; + + nn = n_KWStack << 1; + kwi = (KWinfo*)Alloc("kw_setup", len = nn*sizeof(KWinfo)); + memcpy(kwi, KWStackBot, len >> 1); + if (KWStackBot != KWStack0) + free(KWStackBot); + KWStackBot = kwi; + KWStackEnd = kwi + nn; + KWStack = kwi + n_KWStack; + n_KWStack = nn; + } + + static KeyWord* +kw_setup(KeyWord *kw, void *g, const char *name) +{ + KWinfo *kwi; + KeyWord **alt, *kw1, **req; + + Uint k, nalt, nn, nreq; + int *altct, deferred; + size_t len; + + deferred = 0; + if (kw->kind & KWKind_Dynlib) { + if (kw->kw) + deferred = 1; + else + kw = kw_insert(kw, 0); + } + top: + if ((kw1 = kw->kw)) { + kwnext_setup(kw1, kw->nkw); + if (kw->kind & KWKind_Dynmult) + return kw; + while(!kw1->name) { + if (!(kw1->kind & KWKind_Stacked)) { + kw1->kind |= KWKind_Stacked; + kw_setup(kw1, g, name); + } + kw1 = kw1->kwnext; + } + } + if (!curkw) { + KWStack = KWStackBot = KWStack0; + KWStackEnd = KWStack0 + n_KWStack0; + curkw = kw; + } + else if (++KWStack >= KWStackEnd) + KWStack_inc(); + kwi = KWStack; + kwi->name = name; + kwi->kw = kw; + kwi->kw1 = kw1; + nalt = nreq = 0; + if (kw1) + for(; kw1; kw1 = kw1->kwnext) { + if (nalt < kw1->alt) + nalt = kw1->alt; + if (nreq < kw1->req) + nreq = kw1->req; + } + kwi->nalt = nalt; + kwi->nreq = nreq; + alt = req = 0; + altct = 0; + if ((nn = nalt + nreq) > 0) { + nn += 2; + alt = (KeyWord**)Alloc("kw_setup(alt)", + len = nn*sizeof(KeyWord*) + (nalt+1)*sizeof(int)); + memset(alt, 0, len); + req = alt + nalt + 1; + altct = (int*)(req + nreq + 1); + /* altct[0], alt[0] and req[0] = "don't care" slots */ + } + kwi->alt = alt; + kwi->req = req; + kwi->altct = altct; + if (nreq) + for(kw1 = kwi->kw1; kw1; kw1 = kw1->kwnext) + req[kw1->req] = kw1; + if (nalt) + for(kw1 = kwi->kw1; kw1; kw1 = kw1->kwnext) + if (kw1->kind & KWKind_primary) + ++altct[kw1->alt]; + kwi->g = g; + KWval.n = 0; + KWval.i = 0; + KWval.r = 0; + KWval.s = 0; + if ((k = kw->kind & KWKind_Mask)) { + if (!KWvalmax.r) + KWvalbuf = (Real *)Alloc("kw_setup(KWvalbuf)", + (nKWvalbuf = 128)*sizeof(Real)); + switch(k) { + + case KWKind_Int: + KWval.i = (int*)KWvalbuf; + KWvalmax.n = (nKWvalbuf*sizeof(Real))/sizeof(int); + KWvalmax.i = KWval.i + KWvalmax.n; + break; + + case KWKind_Real: + KWval.r = KWvalbuf; + KWvalmax.r = KWvalbuf + (KWvalmax.n = nKWvalbuf); + break; + + case KWKind_Str: + KWval.s = (const char**)KWvalbuf; + KWvalmax.n = (nKWvalbuf*sizeof(Real))/sizeof(char*); + KWvalmax.s = KWval.s + KWvalmax.n; + } + } + if (deferred) { + kw = kw_insert(kw, 0); + deferred = 0; + goto top; + } + if (!(kwi->needstart = kw->kind & KWKind_Mask)) { + if (kw->name) { + if (dumpfile) + dumpname(0, kw); + ++dumplev; + } + if (kw->f.start) + (*kw->f.start)(kw->name, 0, &KWStack->g, kw->f.vs); + } + else if (!kw->f.start && NIDR_disallow_missing_start) + botch("No start routine for %s", kw->name); + return kw; + } + + static KeyWord * +kwfind(const char *name, KeyWord *keywds, int n, int *nmatch) +{ + KeyWord *kn, *kn1; + int k, n0, n1, n2, nn; + size_t L; + + *nmatch = 0; + if (n <= 0) + return 0; + L = strlen(name); + n0 = 0; + nn = n; +#ifndef NO_NIDR_DYNLIB /*{*/ + if (n > 0 && keywds->kind & KWKind_Extended) { + while(n > 0) { + n1 = n >> 1; + kn = (KeyWord*)((KeyWordx*)keywds + n1); + k = strncmp(name, kn->name, L); + if (k < 0) + n = n1; + else if (k > 0) { + n -= ++n1; + n0 += n1; + keywds = (KeyWord*)((KeyWordx*)kn + 1); + } + else { + /* Found -- check for range of matches. */ + /* Here we use linear search, as we expect */ + /* the range to be small. */ + n = n1 + n0; + n2 = n + 1; + if (kn->name[L]) { + for(kn1 = kn; n2 < nn; ++n2) { + kn1 = (KeyWord*)((KeyWordx*)kn1 + 1); + if (strncmp(name, kn1->name, L)) + break; + if (!kn1->name[L]) + goto found1; + } + kn1 = kn; + while(n > 0) { + kn1 = (KeyWord*)((KeyWordx*)kn1 - 1); + if (strncmp(name, kn1->name, L)) + break; + if (!kn1->name[L]) + goto found1; + --n; + kn = kn1; + } + } + *nmatch = n2 - n; + return kn; + } + } + } + else +#endif /*}*/ + while(n > 0) { + n1 = n >> 1; + kn = keywds + n1; + k = strncmp(name, kn->name, L); + if (k < 0) + n = n1; + else if (k > 0) { + n -= ++n1; + n0 += n1; + keywds = kn + 1; + } + else { + /* Found -- check for range of matches. */ + /* Here we use linear search, as we expect */ + /* the range to be small. */ + n = n1 + n0; + n2 = n + 1; + if (kn->name[L]) { + for(kn1 = kn; n2 < nn; ++n2) { + ++kn1; + if (strncmp(name, kn1->name, L)) + break; + if (!kn1->name[L]) + goto found1; + } + kn1 = kn; + while(n > 0) { + --kn1; + if (strncmp(name, kn1->name, L)) + break; + if (!kn1->name[L]) { + found1: + *nmatch = 1; + return kn1; + } + --n; + kn = kn1; + } + } + *nmatch = n2 - n; + return kn; + } + } + return 0; /* not found */ + } + + static KeyWord * +toomany(const char *name, KeyWord *kw, int nmatch) +{ + int i; + squawk("\"%s\" is ambiguous; possible matches..", name); + if (nsquawk <= NIDR_SQUAWKMAX) + for(i = 0; i < nmatch; i++, kw++) + fprintf(stderr, "\t%s\n", kw->name); + return 0; + } + + KeyWord * +nidr_keyword(const char *name) +{ + int nmatch; + KeyWord *kw, *kw1; + + kw = kwfind(name, Keyword_Top->kw, Keyword_Top->nkw, &nmatch); + if (nmatch > 1) + return toomany(name, kw, nmatch); + else if (kw) { + if (!(kw1 = curkw)) { + kw = kw_setup(kw, KW_g, name); + if (kw->kind & KWKind_Dynmult) + return kw; + } + if (!strict) { + if (kw1) + nidr_keyword_finish(); + kw_setup1(kw); + } + } + return kw; + } + + static void +valcheck(KeyWord *kw) +{ + Real *r; + int *z; + int i, k, n; + + n = KWval.n; + switch(k = kw->kind & KWKind_Mask) { + case KWKind_Int: + z = KWval.i; + if (kw->kind & KWKind_strictLb) { + for(i = 0; i < n; ++i) + if (z[i] <= kw->Lb) { + squawk("%s must be > %.0f", kw->name, kw->Lb); + break; + } + } + else if (kw->kind & KWKind_caneqLb) { + for(i = 0; i < n; ++i) + if (z[i] < kw->Lb) { + squawk("%s must be >= %.0f", kw->name, kw->Lb); + break; + } + } + if (kw->kind & KWKind_strictUb) { + for(i = 0; i < n; ++i) + if (z[i] >= kw->Ub) { + squawk("%s must be < %.0f", kw->name, kw->Ub); + break; + } + } + else if (kw->kind & KWKind_caneqUb) { + for(i = 0; i < n; ++i) + if (z[i] > kw->Ub) { + squawk("%s must be >= %.0f", kw->name, kw->Ub); + break; + } + } + break; + case KWKind_Real: + r = KWval.r; + if (kw->kind & KWKind_strictLb) { + for(i = 0; i < n; ++i) + if (r[i] <= kw->Lb) { + squawk("%s must be > %g", kw->name, kw->Lb); + break; + } + } + else if (kw->kind & KWKind_caneqLb) { + for(i = 0; i < n; ++i) + if (r[i] < kw->Lb) { + squawk("%s must be >= %g", kw->name, kw->Lb); + break; + } + } + if (kw->kind & KWKind_strictUb) { + for(i = 0; i < n; ++i) + if (r[i] >= kw->Ub) { + squawk("%s must be < %g", kw->name, kw->Ub); + break; + } + } + else if (kw->kind & KWKind_caneqUb) { + for(i = 0; i < n; ++i) + if (r[i] > kw->Ub) { + squawk("%s must be >= %g", kw->name, kw->Ub); + break; + } + } + break; + default: + botch("Bug: unexpected (kw->kind & KWKind_Mask) = %d in valcheck",n); + } + } + + static void +read_lib(const char *libname, KeyWord *kw) +{ +#ifdef NO_NIDR_DYNLIB /*{{*/ + botch("LIBNAME is disallowed: cannot read \"%s\"", libname); +#else /*}{*/ + KeyWord *kw1; + KW_ADD kwa; + NIDR_KWlib *Lib; + void *h; + + h = nidr_dlopen(libname); + if (!h) { +#ifndef NO_DLERROR + const char *s; + if ((s = dlerror())) + botch("Cannot open library \"%s\":\n\t%s", libname, s); + else +#endif + botch("Cannot open library \"%s\"", libname); + } + if (!find_dlsym(kwa, h, "keyword_add")) + botch("dlsym(\"keyword_add\") failed for %s", libname); + kw1 = (*kwa)(); + Lib = nidr_lib_record(h, libname); + kw->nkw = kw1->nkw; + kw->kw = kw1->kw; + kw->f = kw1->f; + kw->kind |= KWKind_Loaded; +#endif /*}}*/ + } + + static void +nidr_id_strict_finish(KWinfo *kwi, KeyWord *kw, const char *name) +{ + KeyWord *kw1; + int n; + + if (kw->alt) { + if ((kw1 = kwi->alt[n = kw->alt])) { + if (strcmp(kw1->name, name)) + squawk("%s and %s are mutually exclusive", + kw1->name, name); + else + squawk("%s was already specified", name); + } + else + kwi->alt[n] = kw; + } + if (kw->req) { + if (kwi->req[n = kw->req]) + kwi->req[n] = 0; + else if (!kw->alt) + squawk("%s specified more than once", name); + } + } + + static KWinfo * +dispatch_val(KWinfo *kwi) +{ + KeyWord *kw = kwi->kw; + + kwi->needstart = 0; + if (KWval.n) { + if (KWval.rstate) + finish_rexpand(); + if (dumpfile) { + dumpname(1, kw); + dumpvals(kw); + } + if (kw->kind & (KWKind_Lb|KWKind_Ub)) + valcheck(kw); + if (kw->f.start) + (*kw->f.start)(kw->name, &KWval, &kwi->g, kw->f.vs); + else if ((kw->kind & (KWKind_Libname | KWKind_Loaded)) == KWKind_Libname) { + read_lib(KWval.s[0], kw); + kw = kw_setup(kw, kwi->g, kw->name); + if (kw->f.start) + (*kw->f.start)(kw->name, &KWval, &kwi->g, kw->f.vs); + if (kw == kwi->kw) { + *kwi = *KWStack; + --KWStack; + } + else + kwi = KWStack; + } + KWval.n = 0; + } + else if ((kw->kind & (KWKind_Libname|KWKind_Loaded)) + != (KWKind_Libname|KWKind_Loaded)) + squawk("expected %sone %s value for %s", + kw->kind & KWKind_List ? "at least " : "", + valkind[(kw->kind & KWKind_Mask)-1], kw->name); + ++dumplev; + return kwi; + } + + static void +oneof(KeyWord *kw, int alt, int n) +{ + KeyWord *kw1; + + squawk("One of the following %d entities\nmust be specified for %s..", + n, kw->name); + for(kw1 = kw->kw; !kw1->name; kw1 = kw1->kwnext); + for(; kw1; kw1 = kw1->kwnext) + if (kw1->alt == alt && kw1->kind & KWKind_primary) + fprintf(stderr, "\t%s\n", kw1->name); + } + + static void +missing_chk(KeyWord *kw1, KWinfo *kwi) +{ + KeyWord *kw0, *kw2, **req; + Uint a; + char seen0[1024], *seen; + const char *kwname; + int n; + size_t nreq; + + /* only issue one error message per missing keyword */ + + nreq = 0; + for(kw0 = kw1; kw1; kw1 = kw1->kwnext) + if (nreq < kw1->req) + nreq = kw1->req; + seen = seen0; + if (++nreq > sizeof(seen0)) + seen = (char*)Alloc("missing_chk", nreq); + memset(seen, 0, nreq); + req = kwi->req; + for(kw1 = kw0; kw1; kw1 = kw1->kwnext) { + if (kw1->req && req[kw1->req] && !seen[kw1->req] && kw1->kind & KWKind_primary) { + seen[kw1->req] = 1; + a = -1; + if (!kw1->alt || (n = kwi->altct[a = kw1->alt]) <= 1) { + if (!(kwname = kwi->name)) + kwname = ""; + for(kw2 = kw1;;) { + if (kw2->alt == a && kw2->kind & KWKind_primary) + break; + if (!(kw2 = kw2->kwnext)) + botch("Bug in missing_chk"); + } + squawk("%s must be specified for %s", + kw2->name, kwname); + } + else + oneof(kwi->kw, kw1->alt, n); + } + } + if (seen != seen0) + free(seen); + } + + static void +finalize(KWinfo *kwi) +{ + KeyWord *kw, *kw1, **req; + + kw = kwi->kw; + kw->kind &= ~KWKind_Stacked; + if (kwi->needstart) + kwi = dispatch_val(kwi); + if (kw->name) + --dumplev; + if (kw->f.final) + (*kw->f.final)(kw->name, 0, &kwi->g, kw->f.vf); + if (kwi->alt) { + if (kwi->nreq) { + req = kwi->req; + for(kw1 = kwi->kw1; kw1; kw1 = kw1->kwnext) + if (kw1->req && req[kw1->req]) { + missing_chk(kw1, kwi); + break; + } + } + free(kwi->alt); + } + } + + static KeyWord * +nidr_identifier_strict(const char *name) +{ + KWinfo *kwi, *kwi1; + KeyWord *kw, *kw1; + int nmatch; + size_t height; + + if (!curkw) + botch("curkw = 0 in nidr_identifier"); + kwi = KWStack; + if (kwi->needstart) + kwi = dispatch_val(kwi); + for(kwi1 = kwi;;) { + kw1 = kwi->kw; + if ((kw = kwfind(name, kwi->kw1, kw1->nkw, &nmatch))) + break; + if (kwi == KWStackBot) + return 0; + if ((--kwi)->kw->name && !(kwi->kw->kind & KWKind_Loaded)) + kwi1 = kwi; + } + if (nmatch > 1) + return toomany(name, kw, nmatch); + while(KWStack > kwi1) + finalize(KWStack--); + if ((kw->kind & (KWKind_Libname | KWKind_Loaded)) == KWKind_Libname) { + nidr_id_strict_finish(kwi, kw, name); + if (!KWvalmax.r) + KWvalbuf = (Real *)Alloc("nidr_identifier_strict", + (nKWvalbuf = 128)*sizeof(Real)); + if (++KWStack >= KWStackEnd) + KWStack_inc(); + kwi = KWStack; + kwi->kw = kw; + kwi->needstart = 1; + KWval.s = (const char**)KWvalbuf; + KWvalmax.n = (nKWvalbuf*sizeof(Real))/sizeof(char*); + KWvalmax.s = KWval.s + KWvalmax.n; + } + else { + height = kwi - KWStackBot; + kw = kw_setup(kw, kwi->g, name); + kwi = KWStackBot + height; /* in case kw_setup reallocated KWStack */ + nidr_id_strict_finish(kwi, kw, name); + } + return kw; + } + + static void +nidr_keyword_finish(void) +{ + if (!strict) + kw_finish2(); + for(;;--KWStack) { + finalize(KWStack); + if (KWStack == KWStackBot) + break; + } + if (!strict) + kw_finish3(); + curid = curkw = 0; + } + + const char* +nidr_keyword_name(void) +{ return curkw ? curkw->name : ""; } + +/* Some of the above assumes strict nesting according to dakota.input.nspec. */ +/* Code here is meant to relax this assumption, allowing more flexibility in */ +/* the order of identifiers within a DAKOTA "keyword". */ + + typedef struct KWpair KWpair; + typedef struct KWmblk KWmblk; + + struct +KWmblk { + KWmblk *next; + size_t len; + /* memory of length len immediately follows */ + }; + + struct +KWpair { + KeyWord *kw; + KWseen *kws; + }; + + enum{ KWmblk_gulp = 32000 }; + + static AVL_Tree *AVLT, *AVLKWP; + static KWseen **KW_p, **KW_pe, KWmissing, *KWs0; + static KWmblk *KWmblk0, *KWmblk1; + static const char *KWmem0, *KWmem1; + + typedef struct +AVLCmpInfo { + KWseen **found[2]; + int nfound; + int inexact; + } AVLCmpInfo; + + static int +avlcmp(void *v, KWseen **a, KWseen **b) +{ + AVLCmpInfo *AI = (AVLCmpInfo*)v; + KWseen *ksa, *ksb; + const char *s, *t; + + s = (ksa = *a)->name; + t = (ksb = *b)->name; + for(; *s == *t; ++s, ++t) + if (!*s) + return 0; + if ((!*s && !ksa->kw && ksb->kw) + ||(!*t && !ksb->kw && ksa->kw)) { + /* inexact match */ + if (AI->nfound == 0 + || (AI->nfound == 1 && AI->found[0] != b)) + AI->found[AI->nfound++] = b; + return AI->inexact; + } + return *s - *t; + } + + static int +kwpcmp(void *v, KWpair *a, KWpair *b) +{ + if (a->kw == b->kw) + return 0; + return a->kw > b->kw ? 1 : -1; + } + + static void +KWmeminit(void) +{ + KWmblk0 = KWmblk1 = (KWmblk*)Alloc("KWmeminit", + sizeof(KWmblk) + KWmblk_gulp); + KWmem0 = (char*)(KWmblk0 + 1); + KWmem1 = KWmem0 + KWmblk_gulp; + KWmblk0->len = KWmblk_gulp; + KWmblk0->next = 0; + KWmissing.mnext = KWmissing.mprev = &KWmissing; + KW_cur = 0; + memset(&KWval, 0, sizeof(KWval)); + KWvalbuf = (Real *)Alloc("kw_setup(KWValbuf)", (nKWvalbuf = 128)*sizeof(Real)); + ToClear = ToClear0 = (KeyWord**)Alloc("kw_setup(ToClear)", 256*sizeof(KeyWord*)); + ToClearEnd = ToClear0 + 256; + } + + static void +KWmembump(size_t L) +{ + KWmblk *mb, *mb1; + size_t L1; + + for(L1 = KWmblk_gulp; L1 < L; L1 <<= 1); + if ((mb = mb1 = KWmblk1->next) && L1 <= mb->len) + L1 = mb->len; + else { + KWmblk1->next = mb = (KWmblk*)Alloc("KWmembump", L1 + sizeof(KWmblk)); + mb->len = L1; + mb->next = mb1; + } + KWmblk1 = mb; + KWmem0 = (char*)(mb+1); + KWmem1 = KWmem0 + L1; + } + + static void * +KWgetmem(size_t L) /* for aligned memory */ +{ + void *rv; + + L = (L + sizeof(Real) - 1) & ~(sizeof(Real) - 1); + if (KWmem1 - KWmem0 < L) + KWmembump(L); + rv = (void*)KWmem0; + KWmem0 += L; + return rv; + } + + static KWseen ** +KWhash(const char *s, KeyWord *kw) +{ + AVLCmpInfo AI; + KWseen KW0, *KW0p, *kws, **kwsp; + char **ps; + const char *sa, *sb; + + AI.nfound = 0; + AI.inexact = -1; + AVL_setv(AVLT, &AI); + KW0.name = s; + KW0.kw = kw; + KW0p = &KW0; + curkws = 0; + if ((kwsp = (KWseen**)AVL_find((const Element*)&KW0p, AVLT))) + return kwsp; + if (AI.nfound) { + if (AI.nfound == 1) { + AI.inexact = 1; + AVL_find((const Element*)&KW0p, AVLT); + if (AI.nfound == 1) { + if (kw && (kw->kind & (KWKind_Libname | KWKind_Loaded)) + == KWKind_Libname + && (ps = (*AI.found[0])->svals)) + read_lib(ps[0], kw); + return AI.found[0]; + } + } + sa = (*AI.found[0])->name; + sb = (*AI.found[1])->name; + if (kw) + squawk("Both '%s' and '%s' match '%s'", + sa, sb, s); + else + squawk("'%s' is ambiguous:\n\tit matches both '%s' and '%s'", + s, sa, sb); + return AI.found[0]; + } + kws = (KWseen*)KWgetmem(sizeof(KWseen)); + memset(kws, 0, sizeof(KWseen)); + if ((kws->kw = kw)) + s = kw->name; + else { + curkws = kws; + kws->mnext = &KWmissing; + KWmissing.mprev = (kws->mprev = KWmissing.mprev)->mnext = kws; + s = nidr_KWscopy(s); + } + kws->name = s; + if (KW_p >= KW_pe) { + KW_p = (KWseen**)KWgetmem(32*sizeof(KWseen*)); + KW_pe = KW_p + 32; + } + *(kwsp = KW_p++) = kws; + AVL_insert((const Element*)kwsp, AVLT); + return kwsp; + } + + static void +mixed_squawk(void) +{ + squawk("values for %s cannot be both strings and numbers", + KW_cur->name); + } + + static void +nidr_bufr_relaxed(Real r, int state) +{ + int n; + + if (KWval.rstate && !state) + finish_rexpand(); + if (!(n = KWval.n)) { + KWval.r = KWvalbuf; + KWvalmax.r = KWvalbuf + (KWvalmax.n = nKWvalbuf); + } + else if (KWval.s) { + mixed_squawk(); + return; + } + if (n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.r[KWval.n++] = r; + if (state | KWval.rstate) + rexpand(state); + } + + static void +nidr_bufs_relaxed(const char *s) +{ + int n; + + if (!(n = KWval.n)) { + KWval.s = (const char**)KWvalbuf; + KWvalmax.n = (nKWvalbuf*sizeof(Real))/sizeof(char*); + KWvalmax.s = KWval.s + KWvalmax.n; + } + else if (KWval.r) { + mixed_squawk(); + return; + } + if (n >= KWvalmax.n) + KWvalbuf_inc(); + KWval.s[KWval.n++] = s; + } + + static void kw_setup2(KWseen*); + + static void +kw_finish1(KWseen *kws) +{ + KeyWord *kw; + int n; + size_t L; + + if (KWval.rstate) + finish_rexpand(); + kws->nvals = n = KWval.n; + KWval.n = 0; + if (KWval.r) { + L = n*sizeof(Real); + memcpy(kws->rvals = (Real*)KWgetmem(L), KWval.r, L); + KWval.r = 0; + } + else if (KWval.s) { + L = n*sizeof(char*); + memcpy(kws->svals = (char**)KWgetmem(L), KWval.s, L); + if ((kw = kws->kw) && kw->kind & KWKind_Libname) { + read_lib(KWval.s[0], kw); + if (kw->kw) + kw_setup2(kws); + } + KWval.s = 0; + } + } + + static void* +Alloc1(size_t len) +{ + void *rv = malloc(len); + if (!rv) { + fprintf(stderr, "malloc(%lu) failure in Alloc1\n", (unsigned long)len); + exit(1); + } + return rv; + } + + static void +AVL_Clear(void) +{ + while(ToClear > ToClear0) + (*--ToClear)->kind &= ~KWKind_Hashed; + AVL_Tree_free(&AVLT); + if (AVLKWP) + AVL_Tree_free(&AVLKWP); + } + + static void +kw_setup1(KeyWord *kw) +{ + KWseen *kws, *kws1; + KeyWord *kw1; + + if ((kw1 = kw->kw)) + kwnext_setup(kw1, kw->nkw); + if (!KWmblk0) + KWmeminit(); + if (AVLT) + AVL_Clear(); + AVLT = AVL_Tree_alloc(0, (AVL_Elcomp)avlcmp, Alloc1); + KW_cur = KWs0 = kws = (KWseen*)KWgetmem(sizeof(KWseen)); + memset(kws, 0, sizeof(KWseen)); + kws->name = kw->name; + kws->kw = kw; + kws->lcn = &kws->mprev; + if (kw1) { + while(!kw1->name) + kw1 = kw1->kwnext; + for(; kw1; kw1 = kw1->kwnext) { + kws1 = *KWhash(kw1->name, kw1); + kws1->parent = kws; + } + } + } + + static KWseen** +kw_setup3(KWseen **kwtodo1, KWseen *kws, KeyWord *kw) +{ + KWseen *kws1, **kwsp; + + for(; kw; kw = kw->kwnext) { + kwsp = KWhash(kw->name, kw); + kws1 = *kwsp; + if (kws1->comment) { + kw->comment = kws1->comment; + kws1->comment = 0; + } + if (kws1->parent) { + kws1 = (KWseen*)KWgetmem(sizeof(KWseen)); + memset(kws1, 0, sizeof(KWseen)); + kws1->kw = kw; + kws1->name = kw->name; + *kwsp = kws1; + } + kws1->parent = kws; + if (!kws1->kw) { + kws1->mprev->mnext = kws1->mnext; + kws1->mnext->mprev = kws1->mprev; + *kwtodo1 = kws1; + kwtodo1 = kws1->lcn = &kws1->mprev; + *kws->lcn = kws1; + kws->lcn = &kws1->mnext; + } + kws1->kw = kw; + } + return kwtodo1; + } + + static void +bumpToClear(void) +{ + KeyWord **ntc; + size_t L, L1; + + L = ToClearEnd - ToClear0; + L1 = L << 1; + ntc = (KeyWord**)Alloc("bumpToClear", L1*sizeof(KeyWord*)); + memcpy(ntc, ToClear0, L*sizeof(KeyWord*)); + free(ToClear0); + ToClear0 = ntc; + ToClear = ntc + L; + ToClearEnd = ntc + L1; + } + + static void +kw_setup2(KWseen *kws) +{ + KWpair kwp, *pkwp; + KWseen *kws1, *kws2, *kws3, *kwtodo, **kwtodo1, **pkws; + KeyWord *kw, *kw1; + + kwtodo1 = &kwtodo; + for(;;) { + kw = kws->kw; + if ((kw1 = kw->kw)) { + kwnext_setup(kw1, kw->nkw); + kws2 = kws; + while(!kw1->name) { + if (!AVLKWP) + AVLKWP = AVL_Tree_alloc(0, (AVL_Elcomp)kwpcmp, Alloc1); + if (kw1->kind & KWKind_Hashed) { + kwp.kw = kw1->kw; + kwp.kws = 0; + pkwp = (KWpair*)AVL_find((const Element*)&kwp, AVLKWP); + kws2 = pkwp->kws; + } + else { + if (ToClear >= ToClearEnd) + bumpToClear(); + *ToClear++ = kw1; + kw1->kind |= KWKind_Hashed; + pkwp = (KWpair*)KWgetmem(sizeof(KWpair) + sizeof(KWseen)); + kws1 = (KWseen*)(pkwp + 1); + pkwp->kw = kw1->kw; + pkwp->kws = kws1; + memset(kws1, 0, sizeof(KWseen)); + kws1->kw = kw1; + kws1->name = kws->name; + kws1->lcn = &kws1->mprev; + kws1->parent = kws2; + *kws2->lcn = 0; + for(pkws = &kws2->mprev; + (kws3 = *pkws) && !kws3->name; + pkws = &kws3->mnext); + kws1->mnext = *pkws; + if (pkws == kws2->lcn) + kws2->lcn = &kws1->mnext; + kws2 = *pkws = kws1; + kwnext_setup(kw1->kw, kw1->nkw); + kwtodo1 = kw_setup3(kwtodo1, kws1, kw1->kw); + AVL_insert((const Element*)pkwp, AVLKWP); + } + kw1 = kw1->kwnext; + } + if (kw->nkw) + kwtodo1 = kw_setup3(kwtodo1, kws2, kw1); + } + *kwtodo1 = 0; + if (!kwtodo) + break; + kws = kwtodo; + kw = kws->kw; + if (!(kwtodo = kwtodo->mprev)) + kwtodo1 = &kwtodo; + } + } + + static KeyWord * +nidr_identifier_relaxed(const char *name) +{ + KWseen *kws, *kws1; + KeyWord *kw; + int tryagain; + + kw_finish1(KW_cur); + top: + KW_cur = kws = *KWhash(name, 0); + if ((kw = kws->kw)) { + curid = kw; + if (kws->lcn) + squawk("'%s' already seen", kw->name); + else { + if (kws->comment) { + kw->comment = kws->comment; + kws->comment = 0; + } + kws->lcn = &kws->mprev; + kws1 = kws->parent; + *kws1->lcn = kws; + kws1->lcn = &kws->mnext; + if (kw->kw) + kw_setup2(kws); + if (kw->kind & KWKind_Dynlib) { + kw = kw_insert(kw, &tryagain); + if (kw->kw) { + kws->kw = kw; + kw_setup2(kws); + } + if (tryagain) + goto top; + } + } + } + return (KeyWord*)kws; /* just needs to be nonzero; won't be dereferenced */ + } + + static void +num_expected(KeyWord *kw, int n) +{ + squawk("expected numerical value%s for %s, not quoted strings", + "s" + (n == 1), kw->name); + } + + static void +kw_process(KWseen *kws) +{ + KWseen *kws1; + KeyWord *kw; + Real *r; + Uint k; + int i, n; + + kw = kws->kw; + if (kw->name) { + if (kws != KWs0 && !nidr_identifier_strict(kw->name)) + botch("nidr_identifier_strict did not find \"%s\"", kw->name); + if ((n = KWval.n = kws->nvals)) { + KWval.i = 0; + KWval.r = 0; + KWval.s = 0; + KWval.rstate = 0; + switch(k = kw->kind & KWKind_Mask) { + case 0: + squawk("No values may be specified for %s", kw->name); + break; + + case KWKind_Int: + if (!(r = kws->rvals)) { + num_expected(kw,n); + break; + } + KWval.i = (int*)KWvalbuf; + for(i = 0; i < n; i++) + KWval.i[i] = (int)r[i]; + break; + + case KWKind_Real: + if (!(r = kws->rvals)) { + num_expected(kw,n); + break; + } + KWval.r = r; + break; + + case KWKind_Str: + if (!(KWval.s = (const char **)kws->svals)) + squawk("expected string value%s for %s", + "s" + (n == 1), kw->name); + } + } + } + *kws->lcn = 0; + for(kws1 = kws->mprev; kws1; kws1 = kws1->mnext) + kw_process(kws1); + } + + static void +kw_finish2(void) +{ + KWseen *kws, *kwe; + + kw_finish1(KW_cur); + kwe = &KWmissing; + for(kws = KWmissing.mnext; kws != kwe; kws = kws->mnext) { + squawk("unrecognized identifier '%s'", kws->name); + } + KWmissing.mnext = KWmissing.mprev = &KWmissing; + kw_process(KWs0); + KWs0 = 0; + AVL_Clear(); + } + + static void +kw_finish3(void) +{ + KWmblk1 = KWmblk0; + KWmem0 = (char*)(KWmblk0 + 1); + KWmem1 = KWmem0 + KWmblk_gulp; + KW_p = KW_pe = 0; + } + + void (*nidr_bufr)(Real,int) = nidr_bufr_relaxed; + void (*nidr_bufs)(const char*) = nidr_bufs_relaxed; + KeyWord *(*nidr_identifier)(const char*) = nidr_identifier_relaxed; + + void +nidr_set_strict(int n) +{ + if ((strict = n)) { + nidr_bufr = nidr_bufr_strict; + nidr_bufs = nidr_bufs_strict; + nidr_identifier = nidr_identifier_strict; + } + else { + nidr_bufr = nidr_bufr_relaxed; + nidr_bufs = nidr_bufs_relaxed; + nidr_identifier = nidr_identifier_relaxed; + } + } + + int +nidr_cleanup(void) +{ + KWmblk *mb, *mb1; + Sbuf *sb, *sb1; + + if (curkw) + nidr_keyword_finish(); + if (dumpfile) { + if (OutsideComment) + dumpcomment(&OutsideComment); + if (dumpfile != stdout) { + fclose(dumpfile); + dumpfile = 0; + } + if (nidr_comment) + comment_reset(); + } + if (ToClear0) { + free(ToClear0); + ToClear = ToClear0 = 0; + } + if ((mb1 = KWmblk0)) { + KWmblk0 = 0; + do { + mb = mb1; + mb1 = mb->next; + free(mb); + } while(mb1); + } + if (KWvalbuf) { + free(KWvalbuf); + KWvalbuf = 0; + } + if ((sb1 = KWsbuf0.next)) { + KWsbuf0.next = 0; + do { + sb = sb1; + sb1 = sb->next; + free(sb); + } while(sb1); + } + if (AVLT) + AVL_Clear(); + return nidr_parse_error(); + } + + void +nidr_setup(const char *parser, FILE *df) +{ + const char *s; + int comkeep, oneline; + + if (!(s = parser)) + return; + if (!strncmp(s,"nidr",4)) + s += 4; + if (!strncmp(parser,"strict",6)) { + nidr_set_strict(1); + s += 6; + } + comkeep = oneline = 0; + if (*s == '-') for(;;) { + switch(*++s) { + case '1': + ++oneline; + continue; + case 'p': + ++primary; + continue; + case 'c': + ++comkeep; + continue; + } + break; + } + if (df) + dumpfile = df; + else if (s[0] == ':' && s[1]) { + if (s[1] == '-' && !s[2]) + dumpfile = df = stdout; + else { + dumpfile = df = fopen(++s,"w"); + if (!dumpfile) { + fprintf(stderr, "Cannot open \"%s\"\n", s); + exit(1); + } + } + } + if (df) { + if (oneline) + dumpvals = dumpvals1; + if (comkeep) + comment_setup(); + } + } Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp (revision 27955) @@ -0,0 +1,284 @@ +#include "MainEffectsExcelOutput.h" + + std::ostringstream ss; + + MainEffectsExcelOutput::MainEffectsExcelOutput(){;} + + MainEffectsExcelOutput::~MainEffectsExcelOutput(){;} + + std::string MainEffectsExcelOutput::outputColumnHeaders + (int numInputs, int numOutputs) { + + std::ostringstream ss; + + /* input variables */ + for (int i=0; i responses = response.responses_; + ss << response.getSumPop(); + } + + /* average of all Observation */ + ss << ","; + if (indexOfInputValue==0) { + DDaceMainEffects::Response response = factor.getResponse(); + ss << response.getAveragePop(); + } + + /* sum of squares for Observation */ + ss << ","; + if (indexOfInputValue==0) { + DDaceMainEffects::Response response = factor.getResponse(); + ss << response.getSumOfSquaresPop(); + } + + /* degrees of freedom for all Observation*/ + ss << ","; + if (indexOfInputValue==0) { + int dTotal = factor.getNumberOfObservations() - 1; + ss << dTotal; + } + + /* variance for all Observations */ + ss << ","; + if (indexOfInputValue==0) { + DDaceMainEffects::Response response = factor.getResponse(); + ss << response.getVariancePop(); + } + + /* sum */ + ss << "," << factor.getLevelSum(indexOfInputValue); + + /* average */ + ss << "," << factor.getLevelAverage(indexOfInputValue); + + /* sum of squares */ + ss << "," << factor.getLevelSumOfSquares(indexOfInputValue); + + /* variance */ + ss << "," << factor.getLevelVariance(indexOfInputValue); + + /* sum of squares between groups */ + ss << ","; + if (indexOfInputValue==0) { + ss << factor.sumOfSquaresBetweenGroups(); + } + + /* degrees of freedom between groups */ + ss << ","; + if (indexOfInputValue==0) { + ss << factor.doFBetween(); + } + + /* variance between groups */ + ss << ","; + if (indexOfInputValue==0) { + ss << factor.varianceBetweenGroups(); + } + + /* sum of squares within groups */ + ss << ","; + if (indexOfInputValue==0) { + ss << factor.sumOfSquaresWithinGroups(); + } + + /* degrees of freedom within groups */ + ss << ","; + if (indexOfInputValue==0) { + ss << factor.doFWithin(); + } + + /* variance within groups */ + ss << ","; + if (indexOfInputValue==0) { + ss << factor.varianceWithinGroups(); + } + + /* F */ + ss << ","; + if (indexOfInputValue==0) { + ss << factor.Fdata(); + } + + + ss << "\n"; + + return(ss.str()); + } + + std::string MainEffectsExcelOutput::computeExcelOutput + (std::vector > vectorInputData, + std::vector > vectorOutputData){ + + std::ostringstream ss; + + /* error check */ + if (vectorInputData.size() == 0) return(""); + if (vectorOutputData.size() == 0) return(""); + + + MainEffectsConverter converter; + + /* Replace every INPUT data value with a counting number */ + VectorCountingNumbersAndCount vectorCountingNumbersAndCount = + converter.convertAllDoublesToCountingNumbers(vectorInputData); + std::vector > vectorInputIndicies = + vectorCountingNumbersAndCount.vectorCountingNumbers; + int numberOfCountingNumbers = vectorCountingNumbersAndCount.count; + + /* How many columns are in the input table? */ + int numInputs = vectorInputData[0].size(); + + /* How many columns are in the output table? */ + int numOutputs = vectorOutputData[0].size(); + + /* output the column headers */ + ss << outputColumnHeaders (numInputs, numOutputs); + + /* pair input column 1 with output column 1 */ + /* pair input column 1 with output column 2 */ + /* pair input column 1 with output column 3 */ + /* etc. */ + /* pair input column 2 with output column 1 */ + /* pair input column 2 with output column 2 */ + /* pair input column 2 with output column 3 */ + /* etc. */ + for (int indexInput=0; indexInput +# include +# include +# include +# include + +namespace webbur +{ +//****************************************************************************80 + +void binary_vector_next ( int n, int bvec[] ) + +//****************************************************************************80 +// +// Purpose: +// +// BINARY_VECTOR_NEXT generates the next binary vector. +// +// Discussion: +// +// A binary vector is a vector whose entries are 0 or 1. +// +// The user inputs an initial zero vector to start. The program returns +// the "next" vector. +// +// The vectors are produced in the order: +// +// ( 0, 0, 0, ..., 0 ) +// ( 1, 0, 0, ..., 0 ) +// ( 0, 1, 0, ..., 0 ) +// ( 1, 1, 0, ..., 0 ) +// ( 0, 0, 1, ..., 0 ) +// ( 1, 0, 1, ..., 0 ) +// ... +// ( 1, 1, 1, ..., 1) +// +// and the "next" vector after (1,1,...,1) is (0,0,...,0). That is, +// we allow wrap around. +// +// Example: +// +// N = 3 +// +// Input Output +// ----- ------ +// 0 0 0 => 1 0 0 +// 1 0 0 => 0 1 0 +// 0 1 0 => 1 1 0 +// 1 1 0 => 0 0 1 +// 0 0 1 => 1 0 1 +// 1 0 1 => 0 1 1 +// 0 1 1 => 1 1 1 +// 1 1 1 => 0 0 0 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 04 September 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the dimension of the vectors. +// +// Input/output, int BVEC[N], on output, the successor +// to the input vector. +// +{ + int i; + + for ( i = 0; i < n; i++ ) + { + if ( bvec[i] == 1 ) + { + bvec[i] = 0; + } + else + { + bvec[i] = 1; + break; + } + } + return; +} +//****************************************************************************80 + +void ccn_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CCN_COMPUTE computes a nested Clenshaw Curtis quadrature rule. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::ccn_compute_points ( n, x ); + webbur::ccn_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void ccn_compute_np ( int n, int np, double p[], double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CCN_COMPUTE_NP computes a nested Clenshaw Curtis quadrature rule. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::ccn_compute_points ( n, x ); + webbur::ccn_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void ccn_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CCN_COMPUTE_POINTS: compute nested Clenshaw Curtis points. +// +// Discussion: +// +// We want to compute the following sequence: +// +// 1/2, +// 0, 1 +// 1/4, 3/4 +// 1/8, 3/8, 5/8, 7/8, +// 1/16, 3/16, 5/16, 7/16, 9/16, 11/16, 13/16, 15/16, and so on. +// +// But we would prefer that the numbers in each row be regrouped in pairs +// that are symmetric about 1/2, with the number above 1/2 coming first. +// Thus, the last row might become: +// (9/16, 7/16), (11/16, 5/16), ..., (15/16, 1/16). +// +// Once we have our sequence, we apply the Chebyshev transformation +// which maps [0,1] to [-1,+1]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 06 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of elements to compute. +// +// Output, double X[N], the elements of the sequence. +// +{ + int d; + int i; + int k; + int m; + double pi = 3.141592653589793; + int td; + int tu; +// +// Handle first three entries specially. +// + if ( 1 <= n ) + { + x[0] = 0.5; + } + + if ( 2 <= n ) + { + x[1] = 1.0; + } + + if ( 3 <= n ) + { + x[2] = 0.0; + } + + m = 3; + d = 2; + + while ( m < n ) + { + tu = d + 1; + td = d - 1; + + k = webbur::i4_min ( d, n - m ); + + for ( i = 1; i <= k; i++ ) + { + if ( ( i % 2 ) == 1 ) + { + x[m+i-1] = tu / 2.0 / ( double ) ( k ); + tu = tu + 2; + } + else + { + x[m+i-1] = td / 2.0 / ( double ) ( k ); + td = td - 2; + } + } + m = m + k; + d = d * 2; + } +// +// Apply the Chebyshev transformation. +// + for ( i = 0; i < n; i++ ) + { + x[i] = std::cos ( x[i] * pi ); + } + x[0] = 0.0; + + if ( 2 <= n ) + { + x[1] = -1.0; + } + + if ( 3 <= n ) + { + x[2] = +1.0; + } + + return; +} +//****************************************************************************80 + +void ccn_compute_points_np ( int n, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CCN_COMPUTE_POINTS_NP: nested Clenshaw Curtis quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + webbur::ccn_compute_points ( n, x ); + + return; +} +//****************************************************************************80 + +void ccn_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CCN_COMPUTE_WEIGHTS: weights for nested Clenshaw Curtis rule. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order of the rule. +// +// Output, double W[N], the weights. +// +{ + double *x; + double x_max; + double x_min; + + x = new double[n]; + + webbur::ccn_compute_points ( n, x ); +// +// Get the weights. +// + x_min = -1.0; + x_max = +1.0; + + webbur::nc_compute ( n, x_min, x_max, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void ccn_compute_weights_np ( int n, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CCN_COMPUTE_WEIGHTS_NP: nested Clenshaw Curtis quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + webbur::ccn_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void chebyshev1_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV1_COMPUTE computes a Chebyshev type 1 quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) F(X) / sqrt ( 1 - x^2 ) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= N ) W(I) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + int i; + double pi = 3.141592653589793; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "CHEBYSHEV1_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::exit ( 1 ); + } + + for ( i = 0; i < n; i++ ) + { + w[i] = pi / ( double ) ( n ); + } + for ( i = 0; i < n; i++ ) + { + x[i] = std::cos ( pi * ( double ) ( 2 * n - 1 - 2 * i ) + / ( double ) ( 2 * n ) ); + } + if ( ( n % 2 ) == 1 ) + { + x[(n-1)/2] = 0.0; + } + + return; +} +//****************************************************************************80 + +void chebyshev1_compute_np ( int n, int np, double p[], double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV1_COMPUTE_NP computes a Chebyshev type 1 quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) F(X) / sqrt ( 1 - x^2 ) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= N ) W(I) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::chebyshev1_compute ( n, x, w ); + + return; +} +//****************************************************************************80 + +void chebyshev1_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV1_COMPUTE_POINTS computes Chebyshev type 1 quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +{ + int i; + double pi = 3.141592653589793; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "CHEBYSHEV1_COMPUTE_POINTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::exit ( 1 ); + } + + for ( i = 0; i < n; i++ ) + { + x[i] = std::cos ( pi * ( double ) ( 2 * n - 1 - 2 * i ) + / ( double ) ( 2 * n ) ); + } + if ( ( n % 2 ) == 1 ) + { + x[(n-1)/2] = 0.0; + } + + return; +} +//****************************************************************************80 + +void chebyshev1_compute_points_np ( int n, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV1_COMPUTE_POINTS_NP computes Chebyshev type 1 quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + webbur::chebyshev1_compute_points ( n, x ); + + return; +} +//****************************************************************************80 + +void chebyshev1_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV1_COMPUTE_WEIGHTS computes Chebyshev type 1 quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double W[N], the weights. +// +{ + int i; + double pi = 3.141592653589793; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "CHEBYSHEV1_COMPUTE_WEIGHTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::exit ( 1 ); + } + + for ( i = 0; i < n; i++ ) + { + w[i] = pi / ( double ) ( n ); + } + + return; +} +//****************************************************************************80 + +void chebyshev1_compute_weights_np ( int n, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV1_COMPUTE_WEIGHTS_NP: Chebyshev type 1 quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + webbur::chebyshev1_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +double chebyshev1_integral ( int expon ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV1_INTEGRAL evaluates a monomial Chebyshev type 1 integral. +// +// Discussion: +// +// The integral: +// +// integral ( -1 <= x <= +1 ) x^n / sqrt ( 1 - x^2 ) dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 26 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int EXPON, the exponent. +// +// Output, double CHEBYSHEV1_INTEGRAL, the value of the exact integral. +// +{ + double bot; + double exact; + int i; + double pi = 3.141592653589793; + double top; +// +// Get the exact value of the integral. +// + if ( ( expon % 2 ) == 0 ) + { + top = 1; + bot = 1; + for ( i = 2; i <= expon; i = i + 2 ) + { + top = top * ( i - 1 ); + bot = bot * i; + } + + exact = pi * ( double ) ( top ) / ( double ) ( bot ); + } + else + { + exact = 0.0; + } + + return exact; +} +//****************************************************************************80 + +void chebyshev2_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV2_COMPUTE computes a Chebyshev type 2 quadrature rule. +// +// Discussion: +// +// The integral: +// +// integral ( -1 <= x <= 1 ) f(x) sqrt ( 1 - x^2 ) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double angle; + int i; + double pi = 3.141592653589793; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "CHEBYSHEV2_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::exit ( 1 ); + } + + for ( i = 0; i < n; i++ ) + { + angle = pi * ( double ) ( n - i ) / ( double ) ( n + 1 ); + w[i] = pi / ( double ) ( n + 1 ) * std::pow ( std::sin ( angle ), 2 ); + x[i] = std::cos ( angle ); + } + + if ( ( n % 2 ) == 1 ) + { + x[(n-1)/2] = 0.0; + } + + return; +} +//****************************************************************************80 + +void chebyshev2_compute_np ( int n, int np, double p[], double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV2_COMPUTE_NP computes a Chebyshev type 2 quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) F(X) sqrt ( 1 - x^2 ) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= N ) W(I) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::chebyshev2_compute ( n, x, w ); + + return; +} +//****************************************************************************80 + +void chebyshev2_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV2_COMPUTE_POINTS computes Chebyshev type 2 quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +{ + double angle; + int i; + double pi = 3.141592653589793; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "CHEBYSHEV2_COMPUTE_POINTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::exit ( 1 ); + } + + for ( i = 0; i < n; i++ ) + { + angle = pi * ( double ) ( n - i ) / ( double ) ( n + 1 ); + x[i] = std::cos ( angle ); + } + + if ( ( n % 2 ) == 1 ) + { + x[(n-1)/2] = 0.0; + } + + return; +} +//****************************************************************************80 + +void chebyshev2_compute_points_np ( int n, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV2_COMPUTE_POINTS_NP computes Chebyshev type 2 quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 03 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + webbur::chebyshev2_compute_points ( n, x ); + + return; +} +//****************************************************************************80 + +void chebyshev2_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV2_COMPUTE_WEIGHTS computes Chebyshev type 2 quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double W[N], the weights. +// +{ + double angle; + int i; + double pi = 3.141592653589793; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "CHEBYSHEV2_COMPUTE_WEIGHTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::exit ( 1 ); + } + + for ( i = 0; i < n; i++ ) + { + angle = pi * ( double ) ( n - i ) / ( double ) ( n + 1 ); + w[i] = pi / ( double ) ( n + 1 ) * std::pow ( std::sin ( angle ), 2 ); + } + + return; +} +//****************************************************************************80 + +void chebyshev2_compute_weights_np ( int n, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV2_COMPUTE_WEIGHTS_NP: Chebyshev type 2 quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + webbur::chebyshev2_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +double chebyshev2_integral ( int expon ) + +//****************************************************************************80 +// +// Purpose: +// +// CHEBYSHEV2_INTEGRAL evaluates a monomial Chebyshev type 2 integral. +// +// Discussion: +// +// The integral: +// +// integral ( -1 <= x <= +1 ) x^n * sqrt ( 1 - x^2 ) dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 26 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int EXPON, the exponent. +// +// Output, double CHEBYSHEV2_INTEGRAL, the value of the exact integral. +// +{ + double bot; + double exact; + int i; + double pi = 3.141592653589793; + double top; +// +// Get the exact value of the integral. +// + if ( ( expon % 2 ) == 0 ) + { + top = 1; + bot = 1; + for ( i = 2; i <= expon; i = i + 2 ) + { + top = top * ( i - 1 ); + bot = bot * i; + } + + bot = bot * ( double ) ( expon + 2 ); + + exact = pi * ( double ) ( top ) / ( double ) ( bot ); + } + else + { + exact = 0.0; + } + return exact; +} +//****************************************************************************80 + +void clenshaw_curtis_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CLENSHAW_CURTIS_COMPUTE computes a Clenshaw Curtis quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= N ) W(I) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 March 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double b; + int i; + int j; + double pi = 3.141592653589793; + double theta; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "CLENSHAW_CURTIS_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::exit ( 1 ); + } + else if ( n == 1 ) + { + x[0] = 0.0; + w[0] = 2.0; + } + else + { + for ( i = 0; i < n; i++ ) + { + x[i] = std::cos ( ( double ) ( n - 1 - i ) * pi + / ( double ) ( n - 1 ) ); + } + x[0] = -1.0; + if ( ( n % 2 ) == 1 ) + { + x[(n-1)/2] = 0.0; + } + x[n-1] = +1.0; + + for ( i = 0; i < n; i++ ) + { + theta = ( double ) ( i ) * pi / ( double ) ( n - 1 ); + + w[i] = 1.0; + + for ( j = 1; j <= ( n - 1 ) / 2; j++ ) + { + if ( 2 * j == ( n - 1 ) ) + { + b = 1.0; + } + else + { + b = 2.0; + } + + w[i] = w[i] - b * std::cos ( 2.0 * ( double ) ( j ) * theta ) + / ( double ) ( 4 * j * j - 1 ); + } + } + + w[0] = w[0] / ( double ) ( n - 1 ); + for ( i = 1; i < n - 1; i++ ) + { + w[i] = 2.0 * w[i] / ( double ) ( n - 1 ); + } + w[n-1] = w[n-1] / ( double ) ( n - 1 ); + } + + return; +} +//****************************************************************************80 + +void clenshaw_curtis_compute_np ( int n, int np, double p[], double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CLENSHAW_CURTIS_COMPUTE_NP computes a Clenshaw Curtis quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= N ) W(I) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::clenshaw_curtis_compute ( n, x, w ); + + return; +} +//****************************************************************************80 + +void clenshaw_curtis_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CLENSHAW_CURTIS_COMPUTE_POINTS computes Clenshaw Curtis quadrature points. +// +// Discussion: +// +// Our convention is that the abscissas are numbered from left to right. +// +// This rule is defined on [-1,1]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double X[N], the abscissas. +// +{ + int index; + double pi = 3.141592653589793; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "CLENSHAW_CURTIS_COMPUTE_POINTS - Fatal error!\n"; + std::cerr << " N < 1.\n"; + std::exit ( 1 ); + } + else if ( n == 1 ) + { + x[0] = 0.0; + } + else + { + for ( index = 1; index <= n; index++ ) + { + x[index-1] = std::cos ( ( double ) ( n - index ) * pi + / ( double ) ( n - 1 ) ); + } + x[0] = -1.0; + if ( ( n % 2 ) == 1 ) + { + x[(n-1)/2] = 0.0; + } + x[n-1] = +1.0; + } + return; +} +//****************************************************************************80 + +void clenshaw_curtis_compute_points_np ( int n, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CLENSHAW_CURTIS_COMPUTE_POINTS_NP: Clenshaw Curtis quadrature points. +// +// Discussion: +// +// Our convention is that the abscissas are numbered from left to right. +// +// This rule is defined on [-1,1]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + webbur::clenshaw_curtis_compute_points ( n, x ); + + return; +} +//****************************************************************************80 + +void clenshaw_curtis_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CLENSHAW_CURTIS_COMPUTE_WEIGHTS computes Clenshaw Curtis quadrature weights. +// +// Discussion: +// +// The user must preallocate space for the output array W. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Charles Clenshaw, Alan Curtis, +// A Method for Numerical Integration on an Automatic Computer, +// Numerische Mathematik, +// Volume 2, Number 1, December 1960, pages 197-205. +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double W[N], the weights. +// +{ + double b; + int i; + int j; + double pi = 3.141592653589793; + double theta; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "CLENSHAW_CURTIS_COMPUTE_WEIGHTS - Fatal error!\n"; + std::cerr << " N < 1.\n"; + std::exit ( 1 ); + } + else if ( n == 1 ) + { + w[0] = 2.0; + return; + } + + for ( i = 1; i <= n; i++ ) + { + theta = ( double ) ( i - 1 ) * pi / ( double ) ( n - 1 ); + + w[i-1] = 1.0; + + for ( j = 1; j <= ( n - 1 ) / 2; j++ ) + { + if ( 2 * j == ( n - 1 ) ) + { + b = 1.0; + } + else + { + b = 2.0; + } + + w[i-1] = w[i-1] - b * std::cos ( 2.0 * ( double ) ( j ) * theta ) + / ( double ) ( 4 * j * j - 1 ); + } + } + + w[0] = w[0] / ( double ) ( n - 1 ); + for ( i = 1; i < n - 1; i++ ) + { + w[i] = 2.0 * w[i] / ( double ) ( n - 1 ); + } + w[n-1] = w[n-1] / ( double ) ( n - 1 ); + + return; +} +//****************************************************************************80 + +void clenshaw_curtis_compute_weights_np ( int n, int np, double p[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// CLENSHAW_CURTIS_COMPUTE_WEIGHTS_NP: Clenshaw Curtis quadrature weights. +// +// Discussion: +// +// The user must preallocate space for the output array W. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Charles Clenshaw, Alan Curtis, +// A Method for Numerical Integration on an Automatic Computer, +// Numerische Mathematik, +// Volume 2, Number 1, December 1960, pages 197-205. +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + webbur::clenshaw_curtis_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void comp_next ( int n, int k, int a[], bool *more, int *h, int *t ) + +//****************************************************************************80 +// +// Purpose: +// +// COMP_NEXT computes the compositions of the integer N into K parts. +// +// Discussion: +// +// A composition of the integer N into K parts is an ordered sequence +// of K nonnegative integers which sum to N. The compositions (1,2,1) +// and (1,1,2) are considered to be distinct. +// +// The routine computes one composition on each call until there are no more. +// For instance, one composition of 6 into 3 parts is +// 3+2+1, another would be 6+0+0. +// +// On the first call to this routine, set MORE = FALSE. The routine +// will compute the first element in the sequence of compositions, and +// return it, as well as setting MORE = TRUE. If more compositions +// are desired, call again, and again. Each time, the routine will +// return with a new composition. +// +// However, when the LAST composition in the sequence is computed +// and returned, the routine will reset MORE to FALSE, signaling that +// the end of the sequence has been reached. +// +// This routine originally used a SAVE statement to maintain the +// variables H and T. I have decided that it is safer +// to pass these variables as arguments, even though the user should +// never alter them. This allows this routine to safely shuffle +// between several ongoing calculations. +// +// +// There are 28 compositions of 6 into three parts. This routine will +// produce those compositions in the following order: +// +// I A +// - --------- +// 1 6 0 0 +// 2 5 1 0 +// 3 4 2 0 +// 4 3 3 0 +// 5 2 4 0 +// 6 1 5 0 +// 7 0 6 0 +// 8 5 0 1 +// 9 4 1 1 +// 10 3 2 1 +// 11 2 3 1 +// 12 1 4 1 +// 13 0 5 1 +// 14 4 0 2 +// 15 3 1 2 +// 16 2 2 2 +// 17 1 3 2 +// 18 0 4 2 +// 19 3 0 3 +// 20 2 1 3 +// 21 1 2 3 +// 22 0 3 3 +// 23 2 0 4 +// 24 1 1 4 +// 25 0 2 4 +// 26 1 0 5 +// 27 0 1 5 +// 28 0 0 6 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 02 July 2008 +// +// Author: +// +// Original FORTRAN77 version by Albert Nijenhuis, Herbert Wilf. +// C++ version by John Burkardt. +// +// Reference: +// +// Albert Nijenhuis, Herbert Wilf, +// Combinatorial Algorithms for Computers and Calculators, +// Second Edition, +// Academic Press, 1978, +// ISBN: 0-12-519260-6, +// LC: QA164.N54. +// +// Parameters: +// +// Input, int N, the integer whose compositions are desired. +// +// Input, int K, the number of parts in the composition. +// +// Input/output, int A[K], the parts of the composition. +// +// Input/output, bool *MORE. +// Set MORE = FALSE on first call. It will be reset to TRUE on return +// with a new composition. Each new call returns another composition until +// MORE is set to FALSE when the last composition has been computed +// and returned. +// +// Input/output, int *H, *T, two internal parameters needed for the +// computation. The user should allocate space for these in the calling +// program, include them in the calling sequence, but never alter them! +// +{ + int i; + + if ( !( *more ) ) + { + *t = n; + *h = 0; + a[0] = n; + for ( i = 1; i < k; i++ ) + { + a[i] = 0; + } + } + else + { + if ( 1 < *t ) + { + *h = 0; + } + *h = *h + 1; + *t = a[*h-1]; + a[*h-1] = 0; + a[0] = *t - 1; + a[*h] = a[*h] + 1; + } + + *more = ( a[k-1] != n ); + + return; +} +//****************************************************************************80 + +double cpu_time ( ) + +//****************************************************************************80 +// +// Purpose: +// +// CPU_TIME reports the elapsed CPU time. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 26 July 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Output, double CPU_TIME, the current total elapsed CPU time in second. +// +{ + double value; + + value = ( double ) std::clock ( ) / ( double ) CLOCKS_PER_SEC; + + return value; +} +//****************************************************************************80 + +void dif_deriv ( int nd, double xd[], double yd[], int *ndp, double xdp[], + double ydp[] ) + +//****************************************************************************80 +// +// Purpose: +// +// DIF_DERIV computes the derivative of a polynomial in divided difference form. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 June 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Carl deBoor, +// A Practical Guide to Splines, +// Springer, 2001, +// ISBN: 0387953663, +// LC: QA1.A647.v27. +// +// Parameters: +// +// Input, int ND, the size of the input table. +// +// Input, double XD[ND], the abscissas for the divided +// difference table. +// +// Input, double YD[ND], the divided difference table. +// +// Output, int *NDP, the size of the output table, which is ND-1. +// +// Input, double XDP[NP], the abscissas for the divided +// difference table for the derivative. +// +// Output, double YDP[NDP], the divided difference +// table for the derivative. +// +{ + int i; + double *xd_temp; + double *yd_temp; +// +// Using a temporary copy of the difference table, shift the +// abscissas to zero. +// + xd_temp = new double[nd]; + yd_temp = new double[nd]; + + for ( i = 0; i < nd; i++ ) + { + xd_temp[i] = xd[i]; + } + for ( i = 0; i < nd; i++ ) + { + yd_temp[i] = yd[i]; + } + + webbur::dif_shift_zero ( nd, xd_temp, yd_temp ); +// +// Construct the derivative. +// + *ndp = nd - 1; + + for ( i = 0; i < *ndp; i++ ) + { + xdp[i] = 0.0; + } + + for ( i = 0; i < *ndp; i++ ) + { + ydp[i] = ( double ) ( i + 1 ) * yd_temp[i+1]; + } + + delete [] xd_temp; + delete [] yd_temp; + + return; +} +//****************************************************************************80 + +void dif_shift_x ( int nd, double xd[], double yd[], double xv ) + +//****************************************************************************80 +// +// Purpose: +// +// DIF_SHIFT_X replaces one abscissa of a divided difference table with a new one. +// +// Discussion: +// +// This routine shifts the representation of a divided difference polynomial by +// dropping the last X value in XD, and adding a new X value to the +// beginning of the Xd array, suitably modifying the coefficients stored +// in YD. +// +// The representation of the polynomial is changed, but the polynomial itself +// should be identical. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 June 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Carl deBoor, +// A Practical Guide to Splines, +// Springer, 2001, +// ISBN: 0387953663, +// LC: QA1.A647.v27. +// +// Parameters: +// +// Input, int ND, the number of divided difference coefficients, and +// the number of entries in XD. +// +// Input/output, double XD[ND], the X values used in the representation of +// the divided difference polynomial. After a call to this routine, the +// last entry of XD has been dropped, the other +// entries have shifted up one index, and XV has been inserted at the +// beginning of the array. +// +// Input/output, double YD[ND], the divided difference coefficients +// corresponding to the XD array. On output, this array has been +// adjusted. +// +// Input, double XV, a new X value which is to be used in the representation +// of the polynomial. On output, XD[0] equals XV and the representation +// of the polynomial has been suitably changed. +// Note that XV does not have to be distinct from any of the original XD +// values. +// +{ + int i; +// +// Recompute the divided difference coefficients. +// + for ( i = nd - 2; 0 <= i; i-- ) + { + yd[i] = yd[i] + ( xv - xd[i] ) * yd[i+1]; + } +// +// Shift the X values up one position and insert XV. +// + for ( i = nd - 1; 0 < i; i-- ) + { + xd[i] = xd[i-1]; + } + + xd[0] = xv; + + return; +} +//****************************************************************************80 + +void dif_shift_zero ( int nd, double xd[], double yd[] ) + +//****************************************************************************80 +// +// Purpose: +// +// DIF_SHIFT_ZERO shifts a divided difference table so that all abscissas are zero. +// +// Discussion: +// +// When the abscissas are changed, the coefficients naturally +// must also be changed. +// +// The resulting pair (XD, YD) still represents the +// same polynomial, but the entries in YD are now the +// standard polynomial coefficients. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 June 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Carl deBoor, +// A Practical Guide to Splines, +// Springer, 2001, +// ISBN: 0387953663, +// LC: QA1.A647.v27. +// +// Parameters: +// +// Input, int ND, the length of the XD and YD arrays. +// +// Input/output, double XD[ND], the X values that correspond to the +// divided difference table. On output, XD contains only zeroes. +// +// Input/output, double YD[ND], the divided difference table +// for the polynomial. On output, YD is also +// the coefficient array for the standard representation +// of the polynomial. +// +{ + int i; + double xv; + + xv = 0.0; + + for ( i = 1; i <= nd; i++ ) + { + webbur::dif_shift_x ( nd, xd, yd, xv ); + } + + return; +} +//****************************************************************************80 + +void dif_to_r8poly ( int nd, double xd[], double yd[], double c[] ) + +//****************************************************************************80 +// +// Purpose: +// +// DIF_TO_R8POLY converts a divided difference table to a standard polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 21 February 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Carl deBoor, +// A Practical Guide to Splines, +// Springer, 2001, +// ISBN: 0387953663, +// LC: QA1.A647.v27. +// +// Parameters: +// +// Input, int ND, the number of coefficients, and abscissas. +// +// Input, double XD[ND], the X values used in the divided difference +// representation of the polynomial. +// +// Input, double YD[ND], the divided difference table. +// +// Output, double C[ND], the standard form polyomial coefficients. +// C[0] is the constant term, and C[ND-1] is the coefficient +// of X^(ND-1). +// +{ + int i; + int j; + + for ( i = 0; i < nd; i++ ) + { + c[i] = yd[i]; + } +// +// Recompute the divided difference coefficients. +// + for ( j = 1; j <= nd - 1; j++ ) + { + for ( i = 1; i <= nd - j; i++ ) + { + c[nd-i-1] = c[nd-i-1] - xd[nd-i-j] * c[nd-i]; + } + } + + return; +} +//****************************************************************************80 + +void fejer2_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// FEJER2_COMPUTE computes a Fejer type 2 rule. +// +// Discussion: +// +// Our convention is that the abscissas are numbered from left to right. +// +// The rule is defined on [-1,1]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + int i; + int j; + double p; + double pi = 3.141592653589793; + double theta; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "FEJER2_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::exit ( 1 ); + } + else if ( n == 1 ) + { + x[0] = 0.0; + w[0] = 2.0; + return; + } + + for ( i = 0; i < n; i++ ) + { + x[i] = std::cos ( ( double ) ( n - i ) * pi + / ( double ) ( n + 1 ) ); + } + if ( ( n % 2 ) == 1 ) + { + x[(n-1)/2] = 0.0; + } + + if ( n == 2 ) + { + w[0] = 1.0; + w[1] = 1.0; + } + else + { + for ( i = 0; i < n; i++ ) + { + theta = ( double ) ( n - i ) * pi + / ( double ) ( n + 1 ); + + w[i] = 1.0; + + for ( j = 1; j <= ( ( n - 1 ) / 2 ); j++ ) + { + w[i] = w[i] - 2.0 * std::cos ( 2.0 * ( double ) ( j ) * theta ) + / ( double ) ( 4 * j * j - 1 ); + } + p = 2.0 * ( double ) ( ( ( n + 1 ) / 2 ) ) - 1.0; + w[i] = w[i] - std::cos ( ( p + 1.0 ) * theta ) / p; + } + for ( i = 0; i < n; i++ ) + { + w[i] = 2.0 * w[i] / ( double ) ( n + 1 ); + } + } + return; +} +//****************************************************************************80 + +void fejer2_compute_np ( int n, int np, double p[], double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// FEJER2_COMPUTE_NP computes a Fejer type 2 rule. +// +// Discussion: +// +// Our convention is that the abscissas are numbered from left to right. +// +// The rule is defined on [-1,1]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::fejer2_compute ( n, x, w ); + + return; +} +//****************************************************************************80 + +void fejer2_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// FEJER2_COMPUTE_POINTS computes Fejer type 2 quadrature points. +// +// Discussion: +// +// Our convention is that the abscissas are numbered from left to right. +// +// The rule is defined on [-1,1]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +{ + int i; + double pi = 3.141592653589793; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "FEJER2_COMPUTE_POINTS - Fatal error!\n"; + std::cerr << " N < 1.\n"; + std::exit ( 1 ); + } + else if ( n == 1 ) + { + x[0] = 0.0; + } + else + { + for ( i = 1; i <= n; i++ ) + { + x[i-1] = std::cos ( ( double ) ( n + 1 - i ) * pi + / ( double ) ( n + 1 ) ); + } + if ( ( n % 2 ) == 1 ) + { + x[(n-1)/2] = 0.0; + } + } + return; +} +//****************************************************************************80 + +void fejer2_compute_points_np ( int n, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// FEJER2_COMPUTE_POINTS_NP computes Fejer type 2 quadrature points. +// +// Discussion: +// +// Our convention is that the abscissas are numbered from left to right. +// +// The rule is defined on [-1,1]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + webbur::fejer2_compute_points ( n, x ); + + return; +} +//****************************************************************************80 + +void fejer2_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// FEJER2_COMPUTE_WEIGHTS computes Fejer type 2 quadrature weights. +// +// Discussion: +// +// The user must preallocate space for the output array W. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Walter Gautschi, +// Numerical Quadrature in the Presence of a Singularity, +// SIAM Journal on Numerical Analysis, +// Volume 4, Number 3, 1967, pages 357-362. +// +// Joerg Waldvogel, +// Fast Construction of the Fejer and Clenshaw-Curtis Quadrature Rules, +// BIT Numerical Mathematics, +// Volume 43, Number 1, 2003, pages 1-18. +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double W[N], the weights. +// +{ + int i; + int j; + double p; + double pi = 3.141592653589793; + double theta; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "FEJER2_COMPUTE_WEIGHTS - Fatal error!\n"; + std::cerr << " N < 1.\n"; + std::exit ( 1 ); + } + else if ( n == 1 ) + { + w[0] = 2.0; + } + else if ( n == 2 ) + { + w[0] = 1.0; + w[1] = 1.0; + } + else + { + for ( i = 1; i <= n; i++ ) + { + theta = ( double ) ( n + 1 - i ) * pi + / ( double ) ( n + 1 ); + + w[i-1] = 1.0; + + for ( j = 1; j <= ( ( n - 1 ) / 2 ); j++ ) + { + w[i-1] = w[i-1] - 2.0 * std::cos ( 2.0 * ( double ) ( j ) * theta ) + / ( double ) ( 4 * j * j - 1 ); + } + p = 2.0 * ( double ) ( ( ( n + 1 ) / 2 ) ) - 1.0; + w[i-1] = w[i-1] - std::cos ( ( p + 1.0 ) * theta ) / p; + } + for ( i = 0; i < n; i++ ) + { + w[i] = 2.0 * w[i] / ( double ) ( n + 1 ); + } + } + return; +} +//****************************************************************************80 + +void fejer2_compute_weights_np ( int n, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// FEJER2_COMPUTE_WEIGHTS_NP computes Fejer type 2 quadrature weights. +// +// Discussion: +// +// The user must preallocate space for the output array W. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Walter Gautschi, +// Numerical Quadrature in the Presence of a Singularity, +// SIAM Journal on Numerical Analysis, +// Volume 4, Number 3, 1967, pages 357-362. +// +// Joerg Waldvogel, +// Fast Construction of the Fejer and Clenshaw-Curtis Quadrature Rules, +// BIT Numerical Mathematics, +// Volume 43, Number 1, 2003, pages 1-18. +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + webbur::fejer2_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void gegenbauer_compute ( int order, double alpha, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEGENBAUER_COMPUTE computes a Gegenbauer quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) (1-X^2)^ALPHA * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// Thanks to Janiki Raman for pointing out a problem in an earlier +// version of the code that occurred when ALPHA was -0.5. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, double ALPHA, the exponent of (1-X^2). -1.0 < ALPHA is required. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double an; + double *c; + double cc; + double delta; + double dp2; + int i; + double p1; + double prod; + double r1; + double r2; + double r3; + double temp; + double x0; +// +// Check ORDER. +// + if ( order < 1 ) + { + std::cerr << "\n"; + std::cerr << "GEGENBAUER_COMPUTE - Fatal error!\n"; + std::cerr << " 1 <= ORDER is required.\n"; + std::exit ( 1 ); + } + c = new double[order]; +// +// Check ALPHA. +// + if ( alpha <= -1.0 ) + { + std::cerr << "\n"; + std::cerr << "GEGENBAUER_COMPUTE - Fatal error!\n"; + std::cerr << " -1.0 < ALPHA is required.\n"; + std::exit ( 1 ); + } +// +// Set the recursion coefficients. +// + c[0] = 0.0; + if ( 2 <= order ) + { + c[1] = 1.0 / ( 2.0 * alpha + 3.0 ); + } + + for ( i = 3; i <= order; i++ ) + { + c[i-1] = ( double ) ( i - 1 ) + * ( alpha + alpha + ( double ) ( i - 1 ) ) / + ( ( alpha + alpha + ( double ) ( 2 * i - 1 ) ) + * ( alpha + alpha + ( double ) ( 2 * i - 3 ) ) ); + } + + delta = webbur::r8_gamma ( alpha + 1.0 ) + * webbur::r8_gamma ( alpha + 1.0 ) + / webbur::r8_gamma ( alpha + alpha + 2.0 ); + + prod = 1.0; + for ( i = 2; i <= order; i++ ) + { + prod = prod * c[i-1]; + } + cc = delta * std::pow ( 2.0, alpha + alpha + 1.0 ) * prod; + + for ( i = 1; i <= order; i++ ) + { + if ( i == 1 ) + { + an = alpha / ( double ) ( order ); + + r1 = ( 1.0 + alpha ) + * ( 2.78 / ( 4.0 + ( double ) ( order * order ) ) + + 0.768 * an / ( double ) ( order ) ); + + r2 = 1.0 + 2.44 * an + 1.282 * an * an; + + x0 = ( r2 - r1 ) / r2; + } + else if ( i == 2 ) + { + r1 = ( 4.1 + alpha ) / + ( ( 1.0 + alpha ) * ( 1.0 + 0.156 * alpha ) ); + + r2 = 1.0 + 0.06 * ( ( double ) ( order ) - 8.0 ) * + ( 1.0 + 0.12 * alpha ) / ( double ) ( order ); + + r3 = 1.0 + 0.012 * alpha * + ( 1.0 + 0.25 * r8_abs ( alpha ) ) / ( double ) ( order ); + + x0 = x0 - r1 * r2 * r3 * ( 1.0 - x0 ); + } + else if ( i == 3 ) + { + r1 = ( 1.67 + 0.28 * alpha ) / ( 1.0 + 0.37 * alpha ); + + r2 = 1.0 + 0.22 * ( ( double ) ( order ) - 8.0 ) + / ( double ) ( order ); + + r3 = 1.0 + 8.0 * alpha / + ( ( 6.28 + alpha ) * ( double ) ( order * order ) ); + + x0 = x0 - r1 * r2 * r3 * ( x[0] - x0 ); + } + else if ( i < order - 1 ) + { + x0 = 3.0 * x[i-2] - 3.0 * x[i-3] + x[i-4]; + } + else if ( i == order - 1 ) + { + r1 = ( 1.0 + 0.235 * alpha ) / ( 0.766 + 0.119 * alpha ); + + r2 = 1.0 / ( 1.0 + 0.639 + * ( ( double ) ( order ) - 4.0 ) + / ( 1.0 + 0.71 * ( ( double ) ( order ) - 4.0 ) ) ); + + r3 = 1.0 / ( 1.0 + 20.0 * alpha / ( ( 7.5 + alpha ) * + ( double ) ( order * order ) ) ); + + x0 = x0 + r1 * r2 * r3 * ( x0 - x[i-3] ); + } + else if ( i == order ) + { + r1 = ( 1.0 + 0.37 * alpha ) / ( 1.67 + 0.28 * alpha ); + + r2 = 1.0 / + ( 1.0 + 0.22 * ( ( double ) ( order ) - 8.0 ) + / ( double ) ( order ) ); + + r3 = 1.0 / ( 1.0 + 8.0 * alpha / + ( ( 6.28 + alpha ) * ( double ) ( order * order ) ) ); + + x0 = x0 + r1 * r2 * r3 * ( x0 - x[i-3] ); + } + + webbur::gegenbauer_root ( &x0, order, alpha, &dp2, &p1, c ); + + x[i-1] = x0; + w[i-1] = cc / ( dp2 * p1 ); + } +// +// Reverse the order of the values. +// + for ( i = 1; i <= order/2; i++ ) + { + temp = x[i-1]; + x[i-1] = x[order-i]; + x[order-i] = temp; + } + + for ( i = 1; i <=order/2; i++ ) + { + temp = w[i-1]; + w[i-1] = w[order-i]; + w[order-i] = temp; + } + + delete [] c; + + return; +} +//****************************************************************************80 + +void gegenbauer_compute_np ( int order, int np, double p[], double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEGENBAUER_COMPUTE_NP computes a Gegenbauer quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) (1-X^2)^ALPHA * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// Thanks to Janiki Raman for pointing out a problem in an earlier +// version of the code that occurred when ALPHA was -0.5. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], contains parameters. +// P[0] = ALPHA = the exponent of (1-X^2). -1.0 < ALPHA is required. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double alpha; + + alpha = p[0]; + + webbur::gegenbauer_compute ( order, alpha, x, w ); + + return; +} +//****************************************************************************80 + +void gegenbauer_compute_points ( int order, double alpha, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEGENBAUER_COMPUTE_POINTS computes Gegenbauer quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, double ALPHA, the exponent of (1-X^2). -1.0 < ALPHA is required. +// +// Output, double X[ORDER], the abscissas. +// +{ + double *w; + + w = new double[order]; + + webbur::gegenbauer_compute ( order, alpha, x, w ); + + delete [] w; + + return; +} +//****************************************************************************80 + +void gegenbauer_compute_points_np ( int order, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEGENBAUER_COMPUTE_POINTS_NP computes Gegenbauer quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], contains parameters. +// P[0] = ALPHA = the exponent of (1-X^2). -1.0 < ALPHA is required. +// +// Output, double X[ORDER], the abscissas. +// +{ + double alpha; + + alpha = p[0]; + + webbur::gegenbauer_compute_points ( order, alpha, x ); + + return; +} +//****************************************************************************80 + +void gegenbauer_compute_weights ( int order, double alpha, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEGENBAUER_COMPUTE_WEIGHTS computes Gegenbauer quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, double ALPHA, the exponent of (1-X^2). -1.0 < ALPHA is required. +// +// Output, double W[ORDER], the weights. +// +{ + double *x; + + x = new double[order]; + + webbur::gegenbauer_compute ( order, alpha, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void gegenbauer_compute_weights_np ( int order, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEGENBAUER_COMPUTE_WEIGHTS_NP computes Gegenbauer quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, double P[1], contains parameters. +// P[0] = ALPHA = the exponent of (1-X^2). -1.0 < ALPHA is required. +// +// Output, double W[ORDER], the weights. +// +{ + double alpha; + + alpha = p[0]; + + webbur::gegenbauer_compute_weights ( order, alpha, w ); + + return; +} +//****************************************************************************80 + +double gegenbauer_integral ( int expon, double alpha ) + +//****************************************************************************80 +// +// Purpose: +// +// GEGENBAUER_INTEGRAL integrates a monomial with Gegenbauer weight. +// +// Discussion: +// +// VALUE = Integral ( -1 <= X <= +1 ) x^EXPON (1-x^2)^ALPHA dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 26 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int EXPON, the exponent. +// +// Input, double ALPHA, the exponent of (1-X^2) in the weight factor. +// +// Output, double GEGENBAUER_INTEGRAL, the value of the integral. +// +{ + double arg1; + double arg2; + double arg3; + double arg4; + double c; + double value; + double value1; + + if ( ( expon % 2 ) == 1 ) + { + value = 0.0; + return value; + } + + c = ( double ) ( expon ); + + arg1 = - alpha; + arg2 = 1.0 + c; + arg3 = 2.0 + alpha + c; + arg4 = - 1.0; + + value1 = webbur::r8_hyper_2f1 ( arg1, arg2, arg3, arg4 ); + + value = webbur::r8_gamma ( 1.0 + c ) * 2.0 + * webbur::r8_gamma ( 1.0 + alpha ) * value1 + / webbur::r8_gamma ( 2.0 + alpha + c ); + + return value; +} +//****************************************************************************80 + +void gegenbauer_recur ( double *p2, double *dp2, double *p1, double x, + int order, double alpha, double c[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEGENBAUER_RECUR evaluates a Gegenbauer polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 26 February 2008 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Output, double *P2, the value of J(ORDER)(X). +// +// Output, double *DP2, the value of J'(ORDER)(X). +// +// Output, double *P1, the value of J(ORDER-1)(X). +// +// Input, double X, the point at which polynomials are evaluated. +// +// Input, int ORDER, the order of the polynomial. +// +// Input, double ALPHA, the exponents of (1-X^2). +// +// Input, double C[ORDER], the recursion coefficients. +// +{ + double dp0; + double dp1; + int i; + double p0; + + *p1 = 1.0; + dp1 = 0.0; + + *p2 = x; + *dp2 = 1.0; + + for ( i = 2; i <= order; i++ ) + { + p0 = *p1; + dp0 = dp1; + + *p1 = *p2; + dp1 = *dp2; + + *p2 = x * ( *p1 ) - c[i-1] * p0; + *dp2 = x * dp1 + ( *p1 ) - c[i-1] * dp0; + } + return; +} +//****************************************************************************80 + +void gegenbauer_root ( double *x, int order, double alpha, double *dp2, + double *p1, double c[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEGENBAUER_ROOT improves an approximate root of a Gegenbauer polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 26 February 2008 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input/output, double *X, the approximate root, which +// should be improved on output. +// +// Input, int ORDER, the order of the polynomial. +// +// Input, double ALPHA, the exponents of (1-X^2). +// +// Output, double *DP2, the value of J'(ORDER)(X). +// +// Output, double *P1, the value of J(ORDER-1)(X). +// +// Input, double C[ORDER], the recursion coefficients. +// +{ + double d; + double eps; + double p2; + int step; + int step_max = 10; + + eps = webbur::r8_epsilon ( ); + + for ( step = 1; step <= step_max; step++ ) + { + webbur::gegenbauer_recur ( &p2, dp2, p1, *x, order, alpha, c ); + + d = p2 / ( *dp2 ); + *x = *x - d; + + if ( webbur::r8_abs ( d ) <= eps * ( webbur::r8_abs ( *x ) + 1.0 ) ) + { + return; + } + } + return; +} +//****************************************************************************80 + +void gen_hermite_compute ( int n, double alpha, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_HERMITE_COMPUTE computes a generalized Gauss-Hermite quadrature rule. +// +// Discussion: +// +// The code uses an algorithm by Elhay and Kautsky. +// +// The integral: +// +// integral ( -oo < x < +oo ) |x|^alpha exp(-x^2) f(x) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 30 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Sylvan Elhay, Jaroslav Kautsky. +// C++ version by John Burkardt. +// +// Reference: +// +// Sylvan Elhay, Jaroslav Kautsky, +// Algorithm 655: IQPACK, FORTRAN Subroutines for the Weights of +// Interpolatory Quadrature, +// ACM Transactions on Mathematical Software, +// Volume 13, Number 4, December 1987, pages 399-415. +// +// Parameters: +// +// Input, int N, the number of abscissas. +// +// Input, double ALPHA, the parameter. +// -1.0 < ALPHA. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double *bj; + int i; + double i_r8; + double zemu; +// +// Define the zero-th moment. +// + zemu = webbur::r8_gamma ( ( alpha + 1.0 ) / 2.0 ); +// +// Define the Jacobi matrix. +// + bj = new double[n]; + + for ( i = 0; i < n; i++ ) + { + i_r8 = ( double ) ( i + 1 ); + if ( ( i % 2 ) == 0 ) + { + bj[i] = ( i_r8 + alpha ) / 2.0; + } + else + { + bj[i] = i_r8 / 2.0; + } + } + + for ( i = 0; i < n; i++ ) + { + bj[i] = std::sqrt ( bj[i] ); + } + + for ( i = 0; i < n; i++ ) + { + x[i] = 0.0; + } + + w[0] = std::sqrt ( zemu ); + for ( i = 1; i < n; i++ ) + { + w[i] = 0.0; + } +// +// Diagonalize the Jacobi matrix. +// + webbur::imtqlx ( n, x, bj, w ); + + for ( i = 0; i < n; i++ ) + { + w[i] = w[i] * w[i]; + } + + delete [] bj; + + return; +} +//****************************************************************************80 + +void gen_hermite_compute_np ( int order, int np, double p[], double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_HERMITE_COMPUTE_NP computes a Generalized Hermite quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -oo < x < +oo ) |x|^ALPHA exp(-x^2) f(x) dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], contains parameters. +// P[0] = ALPHA, the exponent of the X factor. -1.0 < ALPHA. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double alpha; + + alpha = p[0]; + + webbur::gen_hermite_compute ( order, alpha, x, w ); + + return; +} +//****************************************************************************80 + +void gen_hermite_compute_points ( int order, double alpha, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_HERMITE_COMPUTE_POINTS computes Generalized Hermite quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, double ALPHA, the exponent of the X factor. +// -1.0 < ALPHA. +// +// Output, double X[ORDER], the abscissas. +// +{ + double *w; + + w = new double[order]; + + webbur::gen_hermite_compute ( order, alpha, x, w ); + + delete [] w; + + return; +} +//****************************************************************************80 + +void gen_hermite_compute_points_np ( int order, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_HERMITE_COMPUTE_POINTS_NP: Generalized Hermite quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], contains parameters. +// P[0] = ALPHA, the exponent of the X factor. -1.0 < ALPHA. +// +// Output, double X[ORDER], the abscissas. +// +{ + double alpha; + + alpha = p[0]; + + webbur::gen_hermite_compute_points ( order, alpha, x ); + + return; +} +//****************************************************************************80 + +void gen_hermite_compute_weights ( int order, double alpha, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_HERMITE_COMPUTE_WEIGHTS computes Generalized Hermite quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, double ALPHA, the exponent of the X factor. +// -1.0 < ALPHA. +// +// Output, double W[ORDER], the weights. +// +{ + double *x; + + x = new double[order]; + + webbur::gen_hermite_compute ( order, alpha, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void gen_hermite_compute_weights_np ( int order, int np, double p[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_HERMITE_COMPUTE_WEIGHTS_NP: Generalized Hermite quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], contains parameters. +// P[0] = ALPHA, the exponent of the X factor. -1.0 < ALPHA. +// +// Output, double W[ORDER], the weights. +// +{ + double alpha; + + alpha = p[0]; + + webbur::gen_hermite_compute_weights ( order, alpha, w ); + + return; +} +//****************************************************************************80 + +void gen_hermite_dr_compute ( int order, double alpha, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_HERMITE_DR_COMPUTE computes a Generalized Hermite quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -oo < x < +oo ) |x|^ALPHA exp(-x^2) f(x) dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, double ALPHA, the exponent of the X factor. +// -1.0 < ALPHA. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double alpha_laguerre; + double arg; + int i; + int order_laguerre; + double *w_laguerre; + double *x_laguerre; + + if ( order < 1 ) + { + std::cerr << "\n"; + std::cerr << "GEN_HERMITE_DR_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of ORDER = " << order << "\n"; + std::exit ( 1 ); + } + + if ( order == 1 ) + { + arg = ( alpha + 1.0 ) / 2.0; + x[0] = 0.0; + w[0] = webbur::r8_gamma ( arg ); + return; + } + + if ( ( order % 2 ) == 0 ) + { + order_laguerre = order / 2; + alpha_laguerre = ( alpha - 1.0 ) / 2.0; + } + else + { + order_laguerre = ( order - 1 ) / 2; + alpha_laguerre = ( alpha + 1.0 ) / 2.0; + } + + w_laguerre = new double[order_laguerre]; + x_laguerre = new double[order_laguerre]; + + webbur::gen_laguerre_ss_compute ( order_laguerre, alpha_laguerre, x_laguerre, + w_laguerre ); + + if ( ( order % 2 ) == 0 ) + { + for ( i = 0; i < order_laguerre; i++ ) + { + x[i] = - std::sqrt ( x_laguerre[order_laguerre-1-i] ); + } + for ( i = 0; i < order_laguerre; i++ ) + { + x[order_laguerre+i] = std::sqrt ( x_laguerre[i] ); + } + for ( i = 0; i < order_laguerre; i++ ) + { + w[i] = 0.5 * w_laguerre[order_laguerre-1-i]; + } + for ( i = 0; i < order_laguerre; i++ ) + { + w[order_laguerre+i] = 0.5 * w_laguerre[i]; + } + } + else if ( ( order % 2 ) == 1 ) + { + for ( i = 0; i < order_laguerre; i++ ) + { + x[i] = - std::sqrt ( x_laguerre[order_laguerre-1-i] ); + } + x[order_laguerre] = 0.0; + for ( i = 0; i < order_laguerre; i++ ) + { + x[order_laguerre+1+i] = std::sqrt ( x_laguerre[i] ); + } + for ( i = 0; i < order_laguerre; i++ ) + { + w[i] = 0.5 * w_laguerre[order_laguerre-1-i] / x_laguerre[order_laguerre-1-i]; + } + + arg = ( alpha + 1.0 ) / 2.0; + w[order_laguerre] = webbur::r8_gamma ( arg ); + for ( i = 0; i < order_laguerre; i++ ) + { + w[order_laguerre] = w[order_laguerre] - w_laguerre[i] / x_laguerre[i]; + } + + for ( i = 0; i < order_laguerre; i++ ) + { + w[order_laguerre+1+i] = 0.5 * w_laguerre[i] / x_laguerre[i]; + } + } + delete [] w_laguerre; + delete [] x_laguerre; + + return; +} +//****************************************************************************80 + +double gen_hermite_integral ( int expon, double alpha ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_HERMITE_INTEGRAL evaluates a monomial Generalized Hermite integral. +// +// Discussion: +// +// H(n,alpha) = Integral ( -oo < x < +oo ) x^n |x|^alpha exp(-x^2) dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int EXPON, the exponent of the monomial. +// 0 <= EXPON. +// +// Input, double ALPHA, the exponent of |X| in the weight function. +// -1.0 < ALPHA. +// +// Output, double GEN_HERMITE_INTEGRAL, the value of the integral. +// +{ + double a; + double arg; + double value; + + if ( ( expon % 2 ) == 1 ) + { + value = 0.0; + } + else + { + a = alpha + ( double ) ( expon ); + if ( a <= - 1.0 ) + { + value = - webbur::r8_huge ( ); + } + else + { + arg = ( a + 1.0 ) / 2.0; + value = webbur::r8_gamma ( arg ); + } + } + return value; +} +//****************************************************************************80 + +void gen_laguerre_compute ( int n, double alpha, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_COMPUTE: generalized Gauss-Laguerre quadrature rule. +// +// Discussion: +// +// The integral: +// +// integral ( 0 <= x < +oo ) exp ( - x ) * x^alpha * f(x) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// The integral: +// +// integral ( 0 <= x < +oo ) x^alpha * f(x) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * exp ( x(i) ) * f ( x(i) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Sylvan Elhay, Jaroslav Kautsky. +// C++ version by John Burkardt. +// +// Reference: +// +// Sylvan Elhay, Jaroslav Kautsky, +// Algorithm 655: IQPACK, FORTRAN Subroutines for the Weights of +// Interpolatory Quadrature, +// ACM Transactions on Mathematical Software, +// Volume 13, Number 4, December 1987, pages 399-415. +// +// Parameters: +// +// Input, int N, the order. +// +// Input, double ALPHA, the exponent of the X factor. +// ALPHA must be nonnegative. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double *bj; + int i; + double i_r8; + double zemu; +// +// Define the zero-th moment. +// + zemu = webbur::r8_gamma ( alpha + 1.0 ); +// +// Define the Jacobi matrix. +// + bj = new double[n]; + + for ( i = 0; i < n; i++ ) + { + i_r8 = ( double ) ( i + 1 ); + bj[i] = std::sqrt ( i_r8 * ( i_r8 + alpha ) ); + } + + for ( i = 0; i < n; i++ ) + { + i_r8 = ( double ) ( i + 1 ); + x[i] = 2.0 * i_r8 - 1.0 + alpha; + } + + w[0] = std::sqrt ( zemu ); + + for ( i = 1; i < n; i++ ) + { + w[i] = 0.0; + } +// +// Diagonalize the Jacobi matrix. +// + imtqlx ( n, x, bj, w ); + + for ( i = 0; i < n; i++ ) + { + w[i] = w[i] * w[i]; + } + + delete [] bj; + + return; +} +//****************************************************************************80 + +void gen_laguerre_compute_np ( int order, int np, double p[], double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_COMPUTE_NP computes a Generalized Laguerre quadrature rule. +// +// Discussion: +// +// In the simplest case, ALPHA is 0, and we are approximating the +// integral from 0 to +oo of exp(-X) * F(X). When this is so, +// it is easy to modify the rule to approximate the integral from +// A to +oo as well. +// +// If ALPHA is nonzero, then there is no simple way to extend the +// rule to approximate the integral from A to +oo. The simplest +// procedures would be to approximate the integral from 0 to A. +// +// If the integral to approximate is: +// +// Integral ( A <= X < +oo ) exp ( - X ) * F(X) dX +// or +// Integral ( 0 <= X < +oo ) exp ( - X ) * X^ALPHA * F(X) dX +// +// then the quadrature rule is: +// +// exp ( - A ) * Sum ( 1 <= I <= ORDER ) W(I) * F ( A+X(I) ) +// or +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// +// If the integral to approximate is: +// +// Integral ( A <= X < +oo ) F(X) dX +// or +// Integral ( 0 <= X < +oo ) X^ALPHA * F(X) dX +// +// then the quadrature rule is: +// +// exp ( - A ) * Sum ( 1 <= I <= ORDER ) +// W(I) * exp(A+X(I)) * F ( A+X(I) ) +// or +// Sum ( 1 <= I <= ORDER ) W(I) * exp(X(I)) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, double P[1], contains parameters. +// P[0] = ALPHA, the exponent of the X factor. +// Set ALPHA = 0.0 for the simplest rule. +// ALPHA must be nonnegative. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double alpha; + + alpha = p[0]; + + webbur::gen_laguerre_compute ( order, alpha, x, w ); + + return; +} +//****************************************************************************80 + +void gen_laguerre_compute_points ( int order, double alpha, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_COMPUTE_POINTS: Generalized Laguerre quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 March 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, double ALPHA, the exponent of the X factor. +// Set ALPHA = 0.0 for the simplest rule. +// ALPHA must be nonnegative. +// +// Output, double X[ORDER], the abscissas. +// +{ + double *w; + + w = new double[order]; + + webbur::gen_laguerre_compute ( order, alpha, x, w ); + + delete [] w; + + return; +} +//****************************************************************************80 + +void gen_laguerre_compute_points_np ( int order, int np, double p[], + double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_COMPUTE_POINTS_NP: Generalized Laguerre quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], contains parameters. +// P[0] = ALPHA, the exponent of the X factor. +// Set ALPHA = 0.0 for the simplest rule. +// ALPHA must be nonnegative. +// +// Output, double X[ORDER], the abscissas. +// +{ + double alpha; + + alpha = p[0]; + + webbur::gen_laguerre_compute_points ( order, alpha, x ); + + return; +} +//****************************************************************************80 + +void gen_laguerre_compute_weights ( int order, double alpha, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_COMPUTE_WEIGHTS: Generalized Laguerre quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, double ALPHA, the exponent of the X factor. +// Set ALPHA = 0.0 for the simplest rule. +// ALPHA must be nonnegative. +// +// Output, double W[ORDER], the weights. +// +{ + double *x; + + x = new double[order]; + + webbur::gen_laguerre_compute ( order, alpha, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void gen_laguerre_compute_weights_np ( int order, int np, double p[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_COMPUTE_WEIGHTS_NP: Generalized Laguerre quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], contains parameters. +// P[0] = ALPHA, the exponent of the X factor. +// Set ALPHA = 0.0 for the simplest rule. +// ALPHA must be nonnegative. +// +// Output, double W[ORDER], the weights. +// +{ + double alpha; + + alpha = p[0]; + + webbur::gen_laguerre_compute_weights ( order, alpha, w ); + + return; +} +//****************************************************************************80 + +double gen_laguerre_integral ( int expon, double alpha ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_INTEGRAL evaluates a monomial Generalized Laguerre integral. +// +// Discussion: +// +// L(n,alpha) = Integral ( 0 <= x < +oo ) x^n * x^alpha exp(-x) dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 20 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int EXPON, the exponent of the monomial. +// 0 <= EXPON. +// +// Input, double ALPHA, the exponent of X in the weight function. +// -1.0 < ALPHA. +// +// Output, double GEN_LAGUERRE_INTEGRAL, the value of the integral. +// +{ + double arg; + double value; + + arg = alpha + ( double ) ( expon + 1.0 ); + value = webbur::r8_gamma ( arg ); + + return value; +} +//****************************************************************************80 + +void gen_laguerre_ss_compute ( int order, double alpha, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_SS_COMPUTE computes a Generalized Laguerre quadrature rule. +// +// Discussion: +// +// In the simplest case, ALPHA is 0, and we are approximating the +// integral from 0 to +oo of exp(-X) * F(X). When this is so, +// it is easy to modify the rule to approximate the integral from +// A to +oo as well. +// +// If ALPHA is nonzero, then there is no simple way to extend the +// rule to approximate the integral from A to +oo. The simplest +// procedures would be to approximate the integral from 0 to A. +// +// If the integral to approximate is: +// +// Integral ( A <= X < +oo ) exp ( - X ) * F(X) dX +// or +// Integral ( 0 <= X < +oo ) exp ( - X ) * X^ALPHA * F(X) dX +// +// then the quadrature rule is: +// +// exp ( - A ) * Sum ( 1 <= I <= ORDER ) W(I) * F ( A+X(I) ) +// or +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// +// If the integral to approximate is: +// +// Integral ( A <= X < +oo ) F(X) dX +// or +// Integral ( 0 <= X < +oo ) X^ALPHA * F(X) dX +// +// then the quadrature rule is: +// +// exp ( - A ) * Sum ( 1 <= I <= ORDER ) +// W(I) * exp(A+X(I)) * F ( A+X(I) ) +// or +// Sum ( 1 <= I <= ORDER ) W(I) * exp(X(I)) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, double ALPHA, the exponent of the X factor. +// Set ALPHA = 0.0 for the simplest rule. +// ALPHA must be nonnegative. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double *b; + double *c; + double cc; + double dp2; + int i; + double p1; + double prod; + double r1; + double r2; + double ratio; + double x0; + + if ( order < 1 ) + { + std::cerr << "\n"; + std::cerr << "GEN_LAGUERRE_SS_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of ORDER = " << order << "\n"; + std::exit ( 1 ); + } + + b = new double[order]; + c = new double[order]; +// +// Set the recursion coefficients. +// + for ( i = 0; i < order; i++ ) + { + b[i] = ( alpha + ( double ) ( 2 * i + 1 ) ); + } + + for ( i = 0; i < order; i++ ) + { + c[i] = ( double ) ( i ) * ( alpha + ( double ) ( i ) ); + } + prod = 1.0; + for ( i = 1; i < order; i++ ) + { + prod = prod * c[i]; + } + cc = webbur::r8_gamma ( alpha + 1.0 ) * prod; + + for ( i = 0; i < order; i++ ) + { +// +// Compute an estimate for the root. +// + if ( i == 0 ) + { + x0 = ( 1.0 + alpha ) * ( 3.0+ 0.92 * alpha ) / + ( 1.0 + 2.4 * ( double ) ( order ) + 1.8 * alpha ); + } + else if ( i == 1 ) + { + x0 = x0 + ( 15.0 + 6.25 * alpha ) / + ( 1.0 + 0.9 * alpha + 2.5 * ( double ) ( order ) ); + } + else + { + r1 = ( 1.0 + 2.55 * ( double ) ( i - 1 ) ) + / ( 1.9 * ( double ) ( i - 1 ) ); + + r2 = 1.26 * ( double ) ( i - 1 ) * alpha / + ( 1.0 + 3.5 * ( double ) ( i - 1 ) ); + + ratio = ( r1 + r2 ) / ( 1.0 + 0.3 * alpha ); + + x0 = x0 + ratio * ( x0 - x[i-2] ); + } +// +// Use iteration to find the root. +// + webbur::gen_laguerre_ss_root ( &x0, order, alpha, &dp2, &p1, b, c ); +// +// Set the abscissa and weight. +// + x[i] = x0; + w[i] = ( cc / dp2 ) / p1; + } + + delete [] b; + delete [] c; + + return; +} +//****************************************************************************80 + +void gen_laguerre_ss_recur ( double *p2, double *dp2, double *p1, double x, + int order, double alpha, double b[], double c[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_SS_RECUR evaluates a Generalized Laguerre polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 February 2008 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Output, double *P2, the value of L(ORDER)(X). +// +// Output, double *DP2, the value of L'(ORDER)(X). +// +// Output, double *P1, the value of L(ORDER-1)(X). +// +// Input, double X, the point at which polynomials are evaluated. +// +// Input, int ORDER, the order of the polynomial. +// +// Input, double ALPHA, the exponent of the X factor in the +// integrand. +// +// Input, double B[ORDER], C[ORDER], the recursion coefficients. +// +{ + double dp0; + double dp1; + int i; + double p0; + + *p1 = 1.0; + dp1 = 0.0; + + *p2 = x - alpha - 1.0; + *dp2 = 1.0; + + for ( i = 1; i < order; i++ ) + { + p0 = *p1; + dp0 = dp1; + + *p1 = *p2; + dp1 = *dp2; + + *p2 = ( x - b[i] ) * ( *p1 ) - c[i] * p0; + *dp2 = ( x - b[i] ) * dp1 + ( *p1 ) - c[i] * dp0; + } + + return; +} +//****************************************************************************80 + +void gen_laguerre_ss_root ( double *x, int order, double alpha, double *dp2, + double *p1, double b[], double c[] ) + +//****************************************************************************80 +// +// Purpose: +// +// GEN_LAGUERRE_SS_ROOT improves a root of a Generalized Laguerre polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 February 2008 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input/output, double *X, the approximate root, which +// should be improved on output. +// +// Input, int ORDER, the order of the polynomial. +// +// Input, double ALPHA, the exponent of the X factor. +// +// Output, double *DP2, the value of L'(ORDER)(X). +// +// Output, double *P1, the value of L(ORDER-1)(X). +// +// Input, double B[ORDER], C[ORDER], the recursion coefficients. +// +{ + double d; + double eps; + double p2; + int step; + int step_max = 10; + + eps = webbur::r8_epsilon ( ); + + for ( step = 1; step <= step_max; step++ ) + { + webbur::gen_laguerre_ss_recur ( &p2, dp2, p1, *x, order, alpha, b, c ); + + d = p2 / ( *dp2 ); + *x = *x - d; + + if ( webbur::r8_abs ( d ) <= eps * ( webbur::r8_abs ( *x ) + 1.0 ) ) + { + break; + } + } + return; +} +//****************************************************************************80 + +void hc_compute_weights_from_points ( int nhalf, double xhalf[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HC_COMPUTE_WEIGHTS_FROM_POINTS: Hermite-Cubic weights, user-supplied points. +// +// Discussion: +// +// An interval [A,B] has been divided by NHALF points X; at each +// point both function and derivative information is available. +// +// The piecewise cubic Hermite interpolant is constructed for this data. +// +// A quadrature rule is determined for the interpolant. +// +// There will be N=2*NHALF weights. If the quadrature rule is to be written +// out, one would normally list each point twice, so that the number of points +// and weights are equal. The listing of the same point value twice is an +// implicit indication that both function and derivative values should be +// used. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 28 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int NHALF, the number of points, not counting repetitions. +// +// Input, double XHALF[NHALF], the points, without repetition. +// +// Output, double W[2*NHALF], the weights. The first two weights are +// associated with the first point, and so on. +// +{ + int j; + + w[0+0*2] = 0.5 * ( xhalf[1] - xhalf[0] ); + w[1+0*2] = std::pow ( xhalf[1] - xhalf[0], 2 ) / 12.0; + + for ( j = 1; j < nhalf - 1; j++ ) + { + w[0+j*2] = 0.5 * ( xhalf[j+1] - xhalf[j-1] ); + w[1+j*2] = ( xhalf[j+1] - xhalf[j-1] ) + * ( xhalf[j+1] - 2.0 * xhalf[j] + xhalf[j-1] ) / 12.0; + } + + w[0+(nhalf-1)*2] = 0.5 * ( xhalf[nhalf-1] - xhalf[nhalf-2] ); + w[1+(nhalf-1)*2] = - std::pow ( xhalf[nhalf-2] - xhalf[nhalf-1], 2 ) / 12.0; + + return; +} +//****************************************************************************80 + +void hcc_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCC_COMPUTE computes a Hermite-Cubic-Chebyshev-Spacing quadrature rule. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into Chebyshev-spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 24 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + int nhalf; + double *xhalf; + + nhalf = n / 2; + xhalf = new double[nhalf]; + + webbur::clenshaw_curtis_compute_points ( nhalf, xhalf ); + webbur::r8vec_stutter ( nhalf, xhalf, 2, x ); + webbur::hc_compute_weights_from_points ( nhalf, xhalf, w ); + + delete [] xhalf; + + return; +} +//****************************************************************************80 + +void hcc_compute_np ( int n, int np, double p[], double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCC_COMPUTE_NP computes a Hermite-Cubic-Chebyshev-Spacing quadrature rule. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into Chebyshev-spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::hcc_compute ( n, x, w ); + + return; +} +//****************************************************************************80 + +void hcc_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCC_COMPUTE_POINTS computes Hermite-Cubic-Chebyshev-Spacing quadrature points. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into Chebyshev-spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 24 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double X[N], the abscissas. +// +{ + int nhalf; + double *xhalf; + + if ( ( n % 2 ) != 0 ) + { + std::cerr << "\n"; + std::cerr << "HCC_COMPUTE_POINTS - Fatal error!\n"; + std::cerr << " Order of rule N is not even.\n"; + std::exit ( 1 ); + } + + nhalf = n / 2; + xhalf = new double[nhalf]; + + webbur::clenshaw_curtis_compute_points ( nhalf, xhalf ); + webbur::r8vec_stutter ( nhalf, xhalf, 2, x ); + + delete [] xhalf; + + return; +} +//****************************************************************************80 + +void hcc_compute_points_np ( int n, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCC_COMPUTE_POINTS_NP: Hermite-Cubic-Chebyshev-Spacing quadrature points. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into Chebyshev-spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + webbur::hcc_compute_points ( n, x ); + + return; +} +//****************************************************************************80 + +void hcc_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCC_COMPUTE_WEIGHTS: Hermite-Cubic-Chebyshev-Spacing quadrature weights. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into Chebyshev-spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 24 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double W[N], the weights. +// +{ + int nhalf; + double *xhalf; + + if ( ( n % 2 ) != 0 ) + { + std::cerr << "\n"; + std::cerr << "HCC_COMPUTE_WEIGHTS - Fatal error!\n"; + std::cerr << " Order of rule N is not even.\n"; + std::exit ( 1 ); + } + + nhalf = n / 2; + xhalf = new double[nhalf]; + + webbur::hc_compute_weights_from_points ( nhalf, xhalf, w ); + + delete [] xhalf; + + return; +} +//****************************************************************************80 + +void hcc_compute_weights_np ( int n, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCC_COMPUTE_WEIGHTS_NP: Hermite-Cubic-Chebyshev-Spacing quadrature weights. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into Chebyshev-spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + webbur::hcc_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void hce_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCE_COMPUTE computes a Hermite-Cubic-Equal-Spacing quadrature rule. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into equally spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 28 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double a_high = 1.0; + double a_low = 0.0; + int nhalf; + double *xhalf; + + a_low = 0.0; + a_high = 1.0; + + nhalf = n / 2; + + xhalf = webbur::r8vec_linspace_new ( nhalf, a_low, a_high ); + webbur::r8vec_stutter ( nhalf, xhalf, 2, x ); + webbur::hc_compute_weights_from_points ( nhalf, xhalf, w ); + + delete [] xhalf; + + return; +} +//****************************************************************************80 + +void hce_compute_np ( int n, int np, double p[], double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCE_COMPUTE_NP computes a Hermite-Cubic-Equal-Spacing quadrature rule. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into equally spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::hce_compute ( n, x, w ); + + return; +} +//****************************************************************************80 + +void hce_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCE_COMPUTE_POINTS computes Hermite-Cubic-Equal-Spacing quadrature points. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into equally spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double X[N], the abscissas. +// +{ + int i; + int j; + int m; + double x_value; + + if ( ( n % 2 ) != 0 ) + { + std::cerr << "\n"; + std::cerr << "HCE_COMPUTE_POINTS - Fatal error!\n"; + std::cerr << " Order of rule N is not even.\n"; + std::exit ( 1 ); + } + m = n / 2; + + for ( j = 0; j < m; j++ ) + { + x_value = ( double ) ( 2 * j + 1 - m ) / ( double ) ( m - 1 ); + for ( i = 0; i < 2; i++ ) + { + x[i+j*2] = x_value; + } + } + return; +} +//****************************************************************************80 + +void hce_compute_points_np ( int n, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCE_COMPUTE_POINTS_NP: Hermite-Cubic-Equal-Spacing quadrature points. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into equally spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + webbur::hce_compute_points ( n, x ); + + return; +} +//****************************************************************************80 + +void hce_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCE_COMPUTE_WEIGHTS: Hermite-Cubic-Equal-Spacing quadrature weights. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into equally spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 24 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double W[N], the weights. +// +{ + int nhalf; + double *xhalf; + + if ( ( n % 2 ) != 0 ) + { + std::cerr << "\n"; + std::cerr << "HCE_COMPUTE_WEIGHTS - Fatal error!\n"; + std::cerr << " Order of rule N is not even.\n"; + std::exit ( 1 ); + } + + nhalf = n / 2; + xhalf = new double[nhalf]; + + webbur::hc_compute_weights_from_points ( nhalf, xhalf, w ); + + delete [] xhalf; + + return; +} +//****************************************************************************80 + +void hce_compute_weights_np ( int n, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HCE_COMPUTE_WEIGHTS_NP: Hermite-Cubic-Equal-Spacing quadrature weights. +// +// Discussion: +// +// For the HCE rule, we assume that an interval has been divided by +// M nodes X into equally spaced subintervals, and that at each +// abscissa both function and derivative information is available. +// The piecewise cubic Hermite interpolant is constructed for this data. +// The quadrature rule uses N = 2 * M abscissas, where each node is +// listed twice, and the weights occur in pairs, with the first multiplying +// the function value and the second the derivative. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + webbur::hce_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void hermite_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_COMPUTE computes a Gauss-Hermite quadrature rule. +// +// Discussion: +// +// The code uses an algorithm by Elhay and Kautsky. +// +// The abscissas are the zeros of the N-th order Hermite polynomial. +// +// The integral: +// +// integral ( -oo < x < +oo ) exp ( - x * x ) * f(x) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Sylvan Elhay, Jaroslav Kautsky. +// C++ version by John Burkardt. +// +// Reference: +// +// Sylvan Elhay, Jaroslav Kautsky, +// Algorithm 655: IQPACK, FORTRAN Subroutines for the Weights of +// Interpolatory Quadrature, +// ACM Transactions on Mathematical Software, +// Volume 13, Number 4, December 1987, pages 399-415. +// +// Parameters: +// +// Input, int N, the number of abscissas. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double arg; + double *bj; + int i; + double zemu; +// +// Define the zero-th moment. +// + arg = 0.5; + zemu = webbur::r8_gamma ( arg ); +// +// Define the Jacobi matrix. +// + bj = new double[n]; + + for ( i = 0; i < n; i++ ) + { + bj[i] = std::sqrt ( ( double ) ( i + 1 ) / 2.0 ); + } + + for ( i = 0; i < n; i++ ) + { + x[i] = 0.0; + } + + w[0] = std::sqrt ( zemu ); + for ( i = 1; i < n; i++ ) + { + w[i] = 0.0; + } +// +// Diagonalize the Jacobi matrix. +// + webbur::imtqlx ( n, x, bj, w ); + + for ( i = 0; i < n; i++ ) + { + w[i] = w[i] * w[i]; + } + + delete [] bj; + + return; +} +//****************************************************************************80 + +void hermite_compute_np ( int order, int np, double p[], double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_COMPUTE_NP computes a Hermite quadrature rule. +// +// Discussion: +// +// The abscissas are the zeros of the N-th order Hermite polynomial. +// +// The integral: +// +// Integral ( -oo < X < +oo ) exp ( - X * X ) * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + webbur::hermite_compute ( order, x, w ); + + return; +} +//****************************************************************************80 + +void hermite_compute_points ( int order, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_COMPUTE_POINTS computes Hermite quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Output, double X[ORDER], the abscissas. +// +{ + double *w; + + w = new double[order]; + + webbur::hermite_compute ( order, x, w ); + + delete [] w; + + return; +} +//****************************************************************************80 + +void hermite_compute_points_np ( int order, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_COMPUTE_POINTS_NP computes Hermite quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[ORDER], the abscissas. +// +{ + webbur::hermite_compute_points ( order, x ); + + return; +} +//****************************************************************************80 + +void hermite_compute_weights ( int order, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_COMPUTE_WEIGHTS computes Hermite quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Output, double W[ORDER], the weights. +// +{ + double *x; + + x = new double[order]; + + webbur::hermite_compute ( order, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void hermite_compute_weights_np ( int order, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_COMPUTE_WEIGHTS_NP computes Hermite quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[ORDER], the weights. +// +{ + webbur::hermite_compute_weights ( order, w ); + + return; +} +//****************************************************************************80 + +void hermite_genz_keister_lookup ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_GENZ_KEISTER_LOOKUP looks up a Genz-Keister Hermite rule. +// +// Discussion: +// +// The integral: +// +// integral ( -oo <= x <= +oo ) f(x) exp ( - x * x ) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// A nested family of rules for the Hermite integration problem +// was produced by Genz and Keister. The structure of the nested +// family was denoted by 1+2+6+10+16, that is, it comprised rules +// of successive orders O = 1, 3, 9, 19, and 35. +// +// The precisions of these rules are P = 1, 5, 15, 29, and 51. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 June 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Alan Genz, Bradley Keister, +// Fully symmetric interpolatory rules for multiple integrals +// over infinite regions with Gaussian weight, +// Journal of Computational and Applied Mathematics, +// Volume 71, 1996, pages 299-309 +// +// Florian Heiss, Viktor Winschel, +// Likelihood approximation by numerical integration on sparse grids, +// Journal of Econometrics, +// Volume 144, 2008, pages 62-80. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// N must be 1, 3, 9, 19, 35, 37, 41 or 43. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::hermite_genz_keister_lookup_points ( n, x ); + webbur::hermite_genz_keister_lookup_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void hermite_genz_keister_lookup_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_GENZ_KEISTER_LOOKUP_POINTS looks up Genz-Keister Hermite abscissas. +// +// Discussion: +// +// The integral: +// +// integral ( -oo <= x <= +oo ) f(x) exp ( - x * x ) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// A nested family of rules for the Hermite integration problem +// was produced by Genz and Keister. The structure of the nested +// family was denoted by 1+2+6+10+?, that is, it comprised rules +// of successive orders O = 1, 3, 9, 19, and a final rule of order +// 35, 37, 41 or 43. +// +// The precisions of these rules are P = 1, 5, 15, 29, +// with the final rule of precision 51, 55, 63 or 67. +// +// Three related families begin the same way, but end with a different final +// rule. As a convenience, this function includes these final rules as well: +// +// Designation Orders Precisions +// +// 1+2+6+10+16, 1,3,9,19,35 1,5,15,29,51 +// 1+2+6+10+18 1,3,9,19,37 1,5,15,29,55 +// 1+2+6+10+22 1,3,9,19,41 1,5,15,29,63 +// 1+2+6+10+24 1,3,9,19,43 1,5,15,29,67 +// +// Some of the data in this function was kindly supplied directly by +// Alan Genz on 24 April 2011. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 04 October 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Alan Genz, Bradley Keister, +// Fully symmetric interpolatory rules for multiple integrals +// over infinite regions with Gaussian weight, +// Journal of Computational and Applied Mathematics, +// Volume 71, 1996, pages 299-309 +// +// Florian Heiss, Viktor Winschel, +// Likelihood approximation by numerical integration on sparse grids, +// Journal of Econometrics, +// Volume 144, 2008, pages 62-80. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// N must be 1, 3, 9, 19, 35, 37, 41, or 43. +// +// Output, double X[N], the abscissas. +// +{ + if ( n == 1 ) + { + x[ 0] = 0.0000000000000000E+00; + } + else if ( n == 3 ) + { + x[ 0] = -1.2247448713915889E+00; + x[ 1] = 0.0000000000000000E+00; + x[ 2] = 1.2247448713915889E+00; + } + else if ( n == 9 ) + { + x[ 0] = -2.9592107790638380E+00; + x[ 1] = -2.0232301911005157E+00; + x[ 2] = -1.2247448713915889E+00; + x[ 3] = -5.2403354748695763E-01; + x[ 4] = 0.0000000000000000E+00; + x[ 5] = 5.2403354748695763E-01; + x[ 6] = 1.2247448713915889E+00; + x[ 7] = 2.0232301911005157E+00; + x[ 8] = 2.9592107790638380E+00; + } + else if ( n == 19 ) + { + x[ 0] = -4.4995993983103881E+00; + x[ 1] = -3.6677742159463378E+00; + x[ 2] = -2.9592107790638380E+00; + x[ 3] = -2.2665132620567876E+00; + x[ 4] = -2.0232301911005157E+00; + x[ 5] = -1.8357079751751868E+00; + x[ 6] = -1.2247448713915889E+00; + x[ 7] = -8.7004089535290285E-01; + x[ 8] = -5.2403354748695763E-01; + x[ 9] = 0.0000000000000000E+00; + x[10] = 5.2403354748695763E-01; + x[11] = 8.7004089535290285E-01; + x[12] = 1.2247448713915889E+00; + x[13] = 1.8357079751751868E+00; + x[14] = 2.0232301911005157E+00; + x[15] = 2.2665132620567876E+00; + x[16] = 2.9592107790638380E+00; + x[17] = 3.6677742159463378E+00; + x[18] = 4.4995993983103881E+00; + } + else if ( n == 35 ) + { + x[ 0] = -6.3759392709822356E+00; + x[ 1] = -5.6432578578857449E+00; + x[ 2] = -5.0360899444730940E+00; + x[ 3] = -4.4995993983103881E+00; + x[ 4] = -4.0292201405043713E+00; + x[ 5] = -3.6677742159463378E+00; + x[ 6] = -3.3491639537131945E+00; + x[ 7] = -2.9592107790638380E+00; + x[ 8] = -2.5705583765842968E+00; + x[ 9] = -2.2665132620567876E+00; + x[10] = -2.0232301911005157E+00; + x[11] = -1.8357079751751868E+00; + x[12] = -1.5794121348467671E+00; + x[13] = -1.2247448713915889E+00; + x[14] = -8.7004089535290285E-01; + x[15] = -5.2403354748695763E-01; + x[16] = -1.7606414208200893E-01; + x[17] = 0.0000000000000000E+00; + x[18] = 1.7606414208200893E-01; + x[19] = 5.2403354748695763E-01; + x[20] = 8.7004089535290285E-01; + x[21] = 1.2247448713915889E+00; + x[22] = 1.5794121348467671E+00; + x[23] = 1.8357079751751868E+00; + x[24] = 2.0232301911005157E+00; + x[25] = 2.2665132620567876E+00; + x[26] = 2.5705583765842968E+00; + x[27] = 2.9592107790638380E+00; + x[28] = 3.3491639537131945E+00; + x[29] = 3.6677742159463378E+00; + x[30] = 4.0292201405043713E+00; + x[31] = 4.4995993983103881E+00; + x[32] = 5.0360899444730940E+00; + x[33] = 5.6432578578857449E+00; + x[34] = 6.3759392709822356E+00; + } + else if ( n == 37 ) + { + x[ 0] = -6.853200069757519; + x[ 1] = -6.124527854622158; + x[ 2] = -5.521865209868350; + x[ 3] = -4.986551454150765; + x[ 4] = -4.499599398310388; + x[ 5] = -4.057956316089741; + x[ 6] = -3.667774215946338; + x[ 7] = -3.315584617593290; + x[ 8] = -2.959210779063838; + x[ 9] = -2.597288631188366; + x[10] = -2.266513262056788; + x[11] = -2.023230191100516; + x[12] = -1.835707975175187; + x[13] = -1.561553427651873; + x[14] = -1.224744871391589; + x[15] = -0.870040895352903; + x[16] = -0.524033547486958; + x[17] = -0.214618180588171; + x[18] = 0.000000000000000; + x[19] = 0.214618180588171; + x[20] = 0.524033547486958; + x[21] = 0.870040895352903; + x[22] = 1.224744871391589; + x[23] = 1.561553427651873; + x[24] = 1.835707975175187; + x[25] = 2.023230191100516; + x[26] = 2.266513262056788; + x[27] = 2.597288631188366; + x[28] = 2.959210779063838; + x[29] = 3.315584617593290; + x[30] = 3.667774215946338; + x[31] = 4.057956316089741; + x[32] = 4.499599398310388; + x[33] = 4.986551454150765; + x[34] = 5.521865209868350; + x[35] = 6.124527854622158; + x[36] = 6.853200069757519; + } + else if ( n == 41 ) + { + x[ 0] = -7.251792998192644; + x[ 1] = -6.547083258397540; + x[ 2] = -5.961461043404500; + x[ 3] = -5.437443360177798; + x[ 4] = -4.953574342912980; + x[ 5] = -4.4995993983103881; + x[ 6] = -4.070919267883068; + x[ 7] = -3.6677742159463378; + x[ 8] = -3.296114596212218; + x[ 9] = -2.9592107790638380; + x[10] = -2.630415236459871; + x[11] = -2.2665132620567876; + x[12] = -2.043834754429505; + x[13] = -2.0232301911005157; + x[14] = -1.8357079751751868; + x[15] = -1.585873011819188; + x[16] = -1.2247448713915889; + x[17] = -0.87004089535290285; + x[18] = -0.52403354748695763; + x[19] = -0.195324784415805; + x[20] = 0.0000000000000000; + x[21] = 0.195324784415805; + x[22] = 0.52403354748695763; + x[23] = 0.87004089535290285; + x[24] = 1.2247448713915889; + x[25] = 1.585873011819188; + x[26] = 1.8357079751751868; + x[27] = 2.0232301911005157; + x[28] = 2.043834754429505; + x[29] = 2.2665132620567876; + x[30] = 2.630415236459871; + x[31] = 2.9592107790638380; + x[32] = 3.296114596212218; + x[33] = 3.6677742159463378; + x[34] = 4.070919267883068; + x[35] = 4.4995993983103881; + x[36] = 4.953574342912980; + x[37] = 5.437443360177798; + x[38] = 5.961461043404500; + x[39] = 6.547083258397540; + x[40] = 7.251792998192644; + } + else if ( n == 43 ) + { + x[ 0] = -10.167574994881873; + x[ 1] = -7.231746029072501; + x[ 2] = -6.535398426382995; + x[ 3] = -5.954781975039809; + x[ 4] = -5.434053000365068; + x[ 5] = -4.952329763008589; + x[ 6] = -4.4995993983103881; + x[ 7] = -4.071335874253583; + x[ 8] = -3.6677742159463378; + x[ 9] = -3.295265921534226; + x[10] = -2.9592107790638380; + x[11] = -2.633356763661946; + x[12] = -2.2665132620567876; + x[13] = -2.089340389294661; + x[14] = -2.0232301911005157; + x[15] = -1.8357079751751868; + x[16] = -1.583643465293944; + x[17] = -1.2247448713915889; + x[18] = -0.87004089535290285; + x[19] = -0.52403354748695763; + x[20] = -0.196029453662011; + x[21] = 0.0000000000000000; + x[22] = 0.196029453662011; + x[23] = 0.52403354748695763; + x[24] = 0.87004089535290285; + x[25] = 1.2247448713915889; + x[26] = 1.583643465293944; + x[27] = 1.8357079751751868; + x[28] = 2.0232301911005157; + x[29] = 2.089340389294661; + x[30] = 2.2665132620567876; + x[31] = 2.633356763661946; + x[32] = 2.9592107790638380; + x[33] = 3.295265921534226; + x[34] = 3.6677742159463378; + x[35] = 4.071335874253583; + x[36] = 4.4995993983103881; + x[37] = 4.952329763008589; + x[38] = 5.434053000365068; + x[39] = 5.954781975039809; + x[40] = 6.535398426382995; + x[41] = 7.231746029072501; + x[42] = 10.167574994881873; + } + else + { + std::cerr << "\n"; + std::cerr << "HERMITE_GENZ_KEISTER_LOOKUP_POINTS - Fatal error!\n"; + std::cerr << " Illegal input value of N.\n"; + std::cerr << " N must be 1, 3, 9, 19, 35, 37, 41 or 43.\n"; + std::exit ( 1 ); + } + return; +} +//****************************************************************************80 + +void hermite_genz_keister_lookup_points_np ( int n, int np, double p[], + double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_GENZ_KEISTER_LOOKUP_POINTS_NP looks up Genz-Keister Hermite abscissas. +// +// Discussion: +// +// The integral: +// +// integral ( -oo <= x <= +oo ) f(x) exp ( - x * x ) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// A nested family of rules for the Hermite integration problem +// was produced by Genz and Keister. The structure of the nested +// family was denoted by 1+2+6+10+?, that is, it comprised rules +// of successive orders O = 1, 3, 9, 19, and a final rule of order +// 35, 37, 41 or 43. +// +// The precisions of these rules are P = 1, 5, 15, 29, +// with the final rule of precision 51, 55, 63 or 67. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 04 October 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Alan Genz, Bradley Keister, +// Fully symmetric interpolatory rules for multiple integrals +// over infinite regions with Gaussian weight, +// Journal of Computational and Applied Mathematics, +// Volume 71, 1996, pages 299-309 +// +// Florian Heiss, Viktor Winschel, +// Likelihood approximation by numerical integration on sparse grids, +// Journal of Econometrics, +// Volume 144, 2008, pages 62-80. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// N must be 1, 3, 9, 19, 35, 37, 41 or 43. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + webbur::hermite_genz_keister_lookup_points ( n, x ); + + return; +} +//****************************************************************************80 + +void hermite_genz_keister_lookup_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_GENZ_KEISTER_LOOKUP_WEIGHTS looks up Genz-Keister Hermite weights. +// +// Discussion: +// +// The integral: +// +// integral ( -oo <= x <= +oo ) f(x) exp ( - x * x ) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// A nested family of rules for the Hermite integration problem +// was produced by Genz and Keister. The structure of the nested +// family was denoted by 1+2+6+10+?, that is, it comprised rules +// of successive orders O = 1, 3, 9, 19, and a final rule of order +// 35, 37, 41 or 43. +// +// The precisions of these rules are P = 1, 5, 15, 29, +// with the final rule of precision 51, 55, 63 or 67. +// +// Three related families begin the same way, but end with a different final +// rule. As a convenience, this function includes these final rules as well: +// +// Designation Orders Precisions +// +// 1+2+6+10+16, 1,3,9,19,35 1,5,15,29,51 +// 1+2+6+10+18 1,3,9,19,37 1,5,15,29,55 +// 1+2+6+10+22 1,3,9,19,41 1,5,15,29,63 +// 1+2+6+10+24 1,3,9,19,43 1,5,15,29,67 +// +// Some of the data in this function was kindly supplied directly by +// Alan Genz on 24 April 2011. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 04 October 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Alan Genz, Bradley Keister, +// Fully symmetric interpolatory rules for multiple integrals +// over infinite regions with Gaussian weight, +// Journal of Computational and Applied Mathematics, +// Volume 71, 1996, pages 299-309 +// +// Florian Heiss, Viktor Winschel, +// Likelihood approximation by numerical integration on sparse grids, +// Journal of Econometrics, +// Volume 144, 2008, pages 62-80. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// N must be 1, 3, 9, 19, 35, 37, 41, or 43. +// +// Output, double W[N], the weights. +// +{ + static double sqrtpi = 1.7724538509055159; + + if ( n == 1 ) + { + w[ 0] = 1.7724538509055159E+00; + } + else if ( n == 3 ) + { + w[ 0] = 2.9540897515091930E-01; + w[ 1] = 1.1816359006036772E+00; + w[ 2] = 2.9540897515091930E-01; + } + else if ( n == 9 ) + { + w[ 0] = 1.6708826306882348E-04; + w[ 1] = 1.4173117873979098E-02; + w[ 2] = 1.6811892894767771E-01; + w[ 3] = 4.7869428549114124E-01; + w[ 4] = 4.5014700975378197E-01; + w[ 5] = 4.7869428549114124E-01; + w[ 6] = 1.6811892894767771E-01; + w[ 7] = 1.4173117873979098E-02; + w[ 8] = 1.6708826306882348E-04; + } + else if ( n == 19 ) + { + w[ 0] = 1.5295717705322357E-09; + w[ 1] = 1.0802767206624762E-06; + w[ 2] = 1.0656589772852267E-04; + w[ 3] = 5.1133174390883855E-03; + w[ 4] = -1.1232438489069229E-02; + w[ 5] = 3.2055243099445879E-02; + w[ 6] = 1.1360729895748269E-01; + w[ 7] = 1.0838861955003017E-01; + w[ 8] = 3.6924643368920851E-01; + w[ 9] = 5.3788160700510168E-01; + w[10] = 3.6924643368920851E-01; + w[11] = 1.0838861955003017E-01; + w[12] = 1.1360729895748269E-01; + w[13] = 3.2055243099445879E-02; + w[14] = -1.1232438489069229E-02; + w[15] = 5.1133174390883855E-03; + w[16] = 1.0656589772852267E-04; + w[17] = 1.0802767206624762E-06; + w[18] = 1.5295717705322357E-09; + } + else if ( n == 35 ) + { + w[ 0] = 1.8684014894510604E-18; + w[ 1] = 9.6599466278563243E-15; + w[ 2] = 5.4896836948499462E-12; + w[ 3] = 8.1553721816916897E-10; + w[ 4] = 3.7920222392319532E-08; + w[ 5] = 4.3737818040926989E-07; + w[ 6] = 4.8462799737020461E-06; + w[ 7] = 6.3328620805617891E-05; + w[ 8] = 4.8785399304443770E-04; + w[ 9] = 1.4515580425155904E-03; + w[10] = 4.0967527720344047E-03; + w[11] = 5.5928828911469180E-03; + w[12] = 2.7780508908535097E-02; + w[13] = 8.0245518147390893E-02; + w[14] = 1.6371221555735804E-01; + w[15] = 2.6244871488784277E-01; + w[16] = 3.3988595585585218E-01; + w[17] = 9.1262675363737921E-04; + w[18] = 3.3988595585585218E-01; + w[19] = 2.6244871488784277E-01; + w[20] = 1.6371221555735804E-01; + w[21] = 8.0245518147390893E-02; + w[22] = 2.7780508908535097E-02; + w[23] = 5.5928828911469180E-03; + w[24] = 4.0967527720344047E-03; + w[25] = 1.4515580425155904E-03; + w[26] = 4.8785399304443770E-04; + w[27] = 6.3328620805617891E-05; + w[28] = 4.8462799737020461E-06; + w[29] = 4.3737818040926989E-07; + w[30] = 3.7920222392319532E-08; + w[31] = 8.1553721816916897E-10; + w[32] = 5.4896836948499462E-12; + w[33] = 9.6599466278563243E-15; + w[34] = 1.8684014894510604E-18; + } + else if ( n == 37 ) + { + w[ 0] = 0.337304188079177058E-20; + w[ 1] = 0.332834739632930463E-16; + w[ 2] = 0.323016866782871498E-13; + w[ 3] = 0.809333688669950037E-11; + w[ 4] = 0.748907559239519284E-09; + w[ 5] = 0.294146671497083432E-07; + w[ 6] = 0.524482423744884136E-06; + w[ 7] = 0.586639457073896277E-05; + w[ 8] = 0.571885531470621903E-04; + w[ 9] = 0.41642095727577091E-03; + w[10] = 0.174733389581099482E-02; + w[11] = 0.313373786000304381E-02; + w[12] = 0.768092665770660459E-02; + w[13] = 0.274962713372148476E-01; + w[14] = 0.783630990508037449E-01; + w[15] = 0.16611584261479281E+00; + w[16] = 0.253636910481387185E+00; + w[17] = 0.261712932511430884E+00; + w[18] = 0.171719680968980257E+00; + w[19] = 0.261712932511430884E+00; + w[20] = 0.253636910481387185E+00; + w[21] = 0.16611584261479281E+00; + w[22] = 0.783630990508037449E-01; + w[23] = 0.274962713372148476E-01; + w[24] = 0.768092665770660459E-02; + w[25] = 0.313373786000304381E-02; + w[26] = 0.174733389581099482E-02; + w[27] = 0.41642095727577091E-03; + w[28] = 0.571885531470621903E-04; + w[29] = 0.586639457073896277E-05; + w[30] = 0.524482423744884136E-06; + w[31] = 0.294146671497083432E-07; + w[32] = 0.748907559239519284E-09; + w[33] = 0.809333688669950037E-11; + w[34] = 0.323016866782871498E-13; + w[35] = 0.332834739632930463E-16; + w[36] = 0.337304188079177058E-20; + } + else if ( n == 41 ) + { + w[ 0] = 0.117725656974405367E-22; + w[ 1] = 0.152506745534300636E-18; + w[ 2] = 0.202183949965101288E-15; + w[ 3] = 0.724614869051195508E-13; + w[ 4] = 0.103121966469463034E-10; + w[ 5] = 0.710371395169350952E-09; + w[ 6] = 0.264376044449260516E-07; + w[ 7] = 0.558982787078644997E-06; + w[ 8] = 0.675628907134744976E-05; + w[ 9] = 0.512198007019776873E-04; + w[10] = 0.335013114947200879E-03; + w[11] = 0.249379691096933139E-02; + w[12] = - 0.25616995850607458E-01; + w[13] = 0.317007878644325588E-01; + w[14] = 0.125041498584003435E-02; + w[15] = 0.293244560924894295E-01; + w[16] = 0.799536390803302298E-01; + w[17] = 0.164543666806555251E+00; + w[18] = 0.258718519718241095E+00; + w[19] = 0.293588795735908566E+00; + w[20] = 0.997525375254611951E-01; + w[21] = 0.293588795735908566E+00; + w[22] = 0.258718519718241095E+00; + w[23] = 0.164543666806555251E+00; + w[24] = 0.799536390803302298E-01; + w[25] = 0.293244560924894295E-01; + w[26] = 0.125041498584003435E-02; + w[27] = 0.317007878644325588E-01; + w[28] = - 0.25616995850607458E-01; + w[29] = 0.249379691096933139E-02; + w[30] = 0.335013114947200879E-03; + w[31] = 0.512198007019776873E-04; + w[32] = 0.675628907134744976E-05; + w[33] = 0.558982787078644997E-06; + w[34] = 0.264376044449260516E-07; + w[35] = 0.710371395169350952E-09; + w[36] = 0.103121966469463034E-10; + w[37] = 0.724614869051195508E-13; + w[38] = 0.202183949965101288E-15; + w[39] = 0.152506745534300636E-18; + w[40] = 0.117725656974405367E-22; + } + else if ( n == 43 ) + { + w[ 0] = 0.968100020641528185E-37; + w[ 1] = 0.15516931262860431E-22; + w[ 2] = 0.175937309107750992E-18; + w[ 3] = 0.217337608710893738E-15; + w[ 4] = 0.747837010380540069E-13; + w[ 5] = 0.104028132097205732E-10; + w[ 6] = 0.70903573389336778E-09; + w[ 7] = 0.263481722999966618E-07; + w[ 8] = 0.560127964848432175E-06; + w[ 9] = 0.680410934802210232E-05; + w[10] = 0.508343873102544037E-04; + w[11] = 0.32753080006610181E-03; + w[12] = 0.267479828788552937E-02; + w[13] = - 0.687704270963253854E-02; + w[14] = 0.119383201790913588E-01; + w[15] = 0.248083722871002796E-02; + w[16] = 0.29000335749726387E-01; + w[17] = 0.798689557875757008E-01; + w[18] = 0.164609842422580606E+00; + w[19] = 0.258535954731607738E+00; + w[20] = 0.292243810406117141E+00; + w[21] = 0.102730713753441829E+00; + w[22] = 0.292243810406117141E+00; + w[23] = 0.258535954731607738E+00; + w[24] = 0.164609842422580606E+00; + w[25] = 0.798689557875757008E-01; + w[26] = 0.29000335749726387E-01; + w[27] = 0.248083722871002796E-02; + w[28] = 0.119383201790913588E-01; + w[29] = - 0.687704270963253854E-02; + w[30] = 0.267479828788552937E-02; + w[31] = 0.32753080006610181E-03; + w[32] = 0.508343873102544037E-04; + w[33] = 0.680410934802210232E-05; + w[34] = 0.560127964848432175E-06; + w[35] = 0.263481722999966618E-07; + w[36] = 0.70903573389336778E-09; + w[37] = 0.104028132097205732E-10; + w[38] = 0.747837010380540069E-13; + w[39] = 0.217337608710893738E-15; + w[40] = 0.175937309107750992E-18; + w[41] = 0.15516931262860431E-22; + w[42] = 0.968100020641528185E-37; + } + else + { + std::cerr << "\n"; + std::cerr << "HERMITE_GENZ_KEISTER_LOOKUP_WEIGHTS - Fatal error!\n"; + std::cerr << " Illegal input value of N.\n"; + std::cerr << " N must be 1, 3, 9, 19, 35, 37, 41 or 43.\n"; + std::exit ( 1 ); + } + return; +} +//****************************************************************************80 + +void hermite_genz_keister_lookup_weights_np ( int n, int np, double p[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_GENZ_KEISTER_LOOKUP_WEIGHTS_NP looks up Genz-Keister Hermite weights. +// +// Discussion: +// +// The integral: +// +// integral ( -oo <= x <= +oo ) f(x) exp ( - x * x ) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// A nested family of rules for the Hermite integration problem +// was produced by Genz and Keister. The structure of the nested +// family was denoted by 1+2+6+10+?, that is, it comprised rules +// of successive orders O = 1, 3, 9, 19, and a final rule of order +// 35, 37, 41 or 43. +// +// The precisions of these rules are P = 1, 5, 15, 29, +// with the final rule of precision 51, 55, 63 or 67. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 04 October 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Alan Genz, Bradley Keister, +// Fully symmetric interpolatory rules for multiple integrals +// over infinite regions with Gaussian weight, +// Journal of Computational and Applied Mathematics, +// Volume 71, 1996, pages 299-309 +// +// Florian Heiss, Viktor Winschel, +// Likelihood approximation by numerical integration on sparse grids, +// Journal of Econometrics, +// Volume 144, 2008, pages 62-80. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// N must be 1, 3, 9, 19, 35, 37, 41 or 43. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + webbur::hermite_genz_keister_lookup_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void hermite_gk18_lookup_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_GK18_LOOKUP_POINTS: abscissas of a Hermite Genz-Keister 18 rule. +// +// Discussion: +// +// The integral: +// +// integral ( -oo <= x <= +oo ) f(x) exp ( - x * x ) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// A nested family of rules for the Hermite integration problem +// was produced by Genz and Keister. The structure of the nested +// family was denoted by 1+2+6+10+18, that is, it comprised rules +// of successive orders O = 1, 3, 9, 19, and 37. +// +// The precisions of these rules are P = 1, 5, 15, 29, and 55. +// +// Some of the data in this function was kindly supplied directly by +// Alan Genz on 24 April 2011. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 30 April 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Alan Genz, Bradley Keister, +// Fully symmetric interpolatory rules for multiple integrals +// over infinite regions with Gaussian weight, +// Journal of Computational and Applied Mathematics, +// Volume 71, 1996, pages 299-309 +// +// Florian Heiss, Viktor Winschel, +// Likelihood approximation by numerical integration on sparse grids, +// Journal of Econometrics, +// Volume 144, 2008, pages 62-80. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// N must be 1, 3, 9, 19, or 37. +// +// Output, double X[N], the abscissas. +// +{ + if ( n == 1 ) + { + x[ 0] = 0.0000000000000000E+00; + } + else if ( n == 3 ) + { + x[ 0] = -1.2247448713915889E+00; + x[ 1] = 0.0000000000000000E+00; + x[ 2] = 1.2247448713915889E+00; + } + else if ( n == 9 ) + { + x[ 0] = -2.9592107790638380E+00; + x[ 1] = -2.0232301911005157E+00; + x[ 2] = -1.2247448713915889E+00; + x[ 3] = -5.2403354748695763E-01; + x[ 4] = 0.0000000000000000E+00; + x[ 5] = 5.2403354748695763E-01; + x[ 6] = 1.2247448713915889E+00; + x[ 7] = 2.0232301911005157E+00; + x[ 8] = 2.9592107790638380E+00; + } + else if ( n == 19 ) + { + x[ 0] = -4.4995993983103881E+00; + x[ 1] = -3.6677742159463378E+00; + x[ 2] = -2.9592107790638380E+00; + x[ 3] = -2.2665132620567876E+00; + x[ 4] = -2.0232301911005157E+00; + x[ 5] = -1.8357079751751868E+00; + x[ 6] = -1.2247448713915889E+00; + x[ 7] = -8.7004089535290285E-01; + x[ 8] = -5.2403354748695763E-01; + x[ 9] = 0.0000000000000000E+00; + x[10] = 5.2403354748695763E-01; + x[11] = 8.7004089535290285E-01; + x[12] = 1.2247448713915889E+00; + x[13] = 1.8357079751751868E+00; + x[14] = 2.0232301911005157E+00; + x[15] = 2.2665132620567876E+00; + x[16] = 2.9592107790638380E+00; + x[17] = 3.6677742159463378E+00; + x[18] = 4.4995993983103881E+00; + } + else if ( n == 35 ) + { + x[ 0] = -6.853200069757519; + x[ 1] = -6.124527854622158; + x[ 2] = -5.521865209868350; + x[ 3] = -4.986551454150765; + x[ 4] = -4.499599398310388; + x[ 5] = -4.057956316089741; + x[ 6] = -3.667774215946338; + x[ 7] = -3.315584617593290; + x[ 8] = -2.959210779063838; + x[ 9] = -2.597288631188366; + x[10] = -2.266513262056788; + x[11] = -2.023230191100516; + x[12] = -1.835707975175187; + x[13] = -1.561553427651873; + x[14] = -1.224744871391589; + x[15] = -0.870040895352903; + x[16] = -0.524033547486958; + x[17] = -0.214618180588171; + x[18] = 0.000000000000000; + x[19] = 0.214618180588171; + x[20] = 0.524033547486958; + x[21] = 0.870040895352903; + x[22] = 1.224744871391589; + x[23] = 1.561553427651873; + x[24] = 1.835707975175187; + x[25] = 2.023230191100516; + x[26] = 2.266513262056788; + x[27] = 2.597288631188366; + x[28] = 2.959210779063838; + x[29] = 3.315584617593290; + x[30] = 3.667774215946338; + x[31] = 4.057956316089741; + x[32] = 4.499599398310388; + x[33] = 4.986551454150765; + x[34] = 5.521865209868350; + x[35] = 6.124527854622158; + x[36] = 6.853200069757519; + } + else + { + std::cerr << "\n"; + std::cerr << "HERMITE_GK18_LOOKUP_POINTS - Fatal error!\n"; + std::cerr << " Illegal input value of N.\n"; + std::cerr << " N must be 1, 3, 9, 19, or 37.\n"; + std::exit ( 1 ); + } + return; +} +//****************************************************************************80 + +void hermite_gk22_lookup_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_GK22_LOOKUP_POINTS looks up Hermite Genz-Keister 22 points. +// +// Discussion: +// +// The integral: +// +// integral ( -oo <= x <= +oo ) f(x) exp ( - x * x ) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// A nested family of rules for the Hermite integration problem +// was produced by Genz and Keister. The structure of the nested +// family was denoted by 1+2+6+10+16, that is, it comprised rules +// of successive orders O = 1, 3, 9, 19, and 41. +// +// The precisions of these rules are P = 1, 5, 15, 29, and 63. +// +// Some of the data in this function was kindly supplied directly by +// Alan Genz on 24 April 2011. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 26 April 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Alan Genz, Bradley Keister, +// Fully symmetric interpolatory rules for multiple integrals +// over infinite regions with Gaussian weight, +// Journal of Computational and Applied Mathematics, +// Volume 71, 1996, pages 299-309 +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// N must be 1, 3, 9, 19, or 41. +// +// Output, double X[N], the abscissas. +// +{ + if ( n == 1 ) + { + x[ 0] = 0.0000000000000000E+00; + } + else if ( n == 3 ) + { + x[ 0] = -1.2247448713915889E+00; + x[ 1] = 0.0000000000000000E+00; + x[ 2] = 1.2247448713915889E+00; + } + else if ( n == 9 ) + { + x[ 0] = -2.9592107790638380E+00; + x[ 1] = -2.0232301911005157E+00; + x[ 2] = -1.2247448713915889E+00; + x[ 3] = -5.2403354748695763E-01; + x[ 4] = 0.0000000000000000E+00; + x[ 5] = 5.2403354748695763E-01; + x[ 6] = 1.2247448713915889E+00; + x[ 7] = 2.0232301911005157E+00; + x[ 8] = 2.9592107790638380E+00; + } + else if ( n == 19 ) + { + x[ 0] = -4.4995993983103881E+00; + x[ 1] = -3.6677742159463378E+00; + x[ 2] = -2.9592107790638380E+00; + x[ 3] = -2.2665132620567876E+00; + x[ 4] = -2.0232301911005157E+00; + x[ 5] = -1.8357079751751868E+00; + x[ 6] = -1.2247448713915889E+00; + x[ 7] = -8.7004089535290285E-01; + x[ 8] = -5.2403354748695763E-01; + x[ 9] = 0.0000000000000000E+00; + x[10] = 5.2403354748695763E-01; + x[11] = 8.7004089535290285E-01; + x[12] = 1.2247448713915889E+00; + x[13] = 1.8357079751751868E+00; + x[14] = 2.0232301911005157E+00; + x[15] = 2.2665132620567876E+00; + x[16] = 2.9592107790638380E+00; + x[17] = 3.6677742159463378E+00; + x[18] = 4.4995993983103881E+00; + } + else if ( n == 41 ) + { + x[ 0] = -7.251792998192644; + x[ 1] = -6.547083258397540; + x[ 2] = -5.961461043404500; + x[ 3] = -5.437443360177798; + x[ 4] = -4.953574342912980; + x[ 5] = -4.4995993983103881; + x[ 6] = -4.070919267883068; + x[ 7] = -3.6677742159463378; + x[ 8] = -3.296114596212218; + x[ 9] = -2.9592107790638380; + x[10] = -2.630415236459871; + x[11] = -2.2665132620567876; + x[12] = -2.043834754429505; + x[13] = -2.0232301911005157; + x[14] = -1.8357079751751868; + x[15] = -1.585873011819188; + x[16] = -1.2247448713915889; + x[17] = -0.87004089535290285; + x[18] = -0.52403354748695763; + x[19] = -0.195324784415805; + x[20] = 0.0000000000000000; + x[21] = 0.195324784415805; + x[22] = 0.52403354748695763; + x[23] = 0.87004089535290285; + x[24] = 1.2247448713915889; + x[25] = 1.585873011819188; + x[26] = 1.8357079751751868; + x[27] = 2.0232301911005157; + x[28] = 2.043834754429505; + x[29] = 2.2665132620567876; + x[30] = 2.630415236459871; + x[31] = 2.9592107790638380; + x[32] = 3.296114596212218; + x[33] = 3.6677742159463378; + x[34] = 4.070919267883068; + x[35] = 4.4995993983103881; + x[36] = 4.953574342912980; + x[37] = 5.437443360177798; + x[38] = 5.961461043404500; + x[39] = 6.547083258397540; + x[40] = 7.251792998192644; + } + else + { + std::cerr << "\n"; + std::cerr << "HERMITE_GK22_LOOKUP_POINTS - Fatal error!\n"; + std::cerr << " Illegal input value of N.\n"; + std::cerr << " N must be 1, 3, 9, 19, or 41.\n"; + std::exit ( 1 ); + } + return; +} +//****************************************************************************80 + +void hermite_gk24_lookup_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_GK24_LOOKUP_POINTS looks up Hermite Genz-Keister 24 points. +// +// Discussion: +// +// The integral: +// +// integral ( -oo <= x <= +oo ) f(x) exp ( - x * x ) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ) +// +// A nested family of rules for the Hermite integration problem +// was produced by Genz and Keister. The structure of the nested +// family was denoted by 1+2+6+10+16, that is, it comprised rules +// of successive orders O = 1, 3, 9, 19, and 43. +// +// The precisions of these rules are P = 1, 5, 15, 29, and 67. +// +// Some of the data in this function was kindly supplied directly by +// Alan Genz on 24 April 2011. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 26 April 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Alan Genz, Bradley Keister, +// Fully symmetric interpolatory rules for multiple integrals +// over infinite regions with Gaussian weight, +// Journal of Computational and Applied Mathematics, +// Volume 71, 1996, pages 299-309 +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// N must be 1, 3, 9 19, or 43. +// +// Output, double X[N], the abscissas. +// +{ + if ( n == 1 ) + { + x[ 0] = 0.0000000000000000E+00; + } + else if ( n == 3 ) + { + x[ 0] = -1.2247448713915889E+00; + x[ 1] = 0.0000000000000000E+00; + x[ 2] = 1.2247448713915889E+00; + } + else if ( n == 9 ) + { + x[ 0] = -2.9592107790638380E+00; + x[ 1] = -2.0232301911005157E+00; + x[ 2] = -1.2247448713915889E+00; + x[ 3] = -5.2403354748695763E-01; + x[ 4] = 0.0000000000000000E+00; + x[ 5] = 5.2403354748695763E-01; + x[ 6] = 1.2247448713915889E+00; + x[ 7] = 2.0232301911005157E+00; + x[ 8] = 2.9592107790638380E+00; + } + else if ( n == 19 ) + { + x[ 0] = -4.4995993983103881E+00; + x[ 1] = -3.6677742159463378E+00; + x[ 2] = -2.9592107790638380E+00; + x[ 3] = -2.2665132620567876E+00; + x[ 4] = -2.0232301911005157E+00; + x[ 5] = -1.8357079751751868E+00; + x[ 6] = -1.2247448713915889E+00; + x[ 7] = -8.7004089535290285E-01; + x[ 8] = -5.2403354748695763E-01; + x[ 9] = 0.0000000000000000E+00; + x[10] = 5.2403354748695763E-01; + x[11] = 8.7004089535290285E-01; + x[12] = 1.2247448713915889E+00; + x[13] = 1.8357079751751868E+00; + x[14] = 2.0232301911005157E+00; + x[15] = 2.2665132620567876E+00; + x[16] = 2.9592107790638380E+00; + x[17] = 3.6677742159463378E+00; + x[18] = 4.4995993983103881E+00; + } + else if ( n == 43 ) + { + x[ 0] = -10.167574994881873; + x[ 1] = -7.231746029072501; + x[ 2] = -6.535398426382995; + x[ 3] = -5.954781975039809; + x[ 4] = -5.434053000365068; + x[ 5] = -4.952329763008589; + x[ 6] = -4.4995993983103881; + x[ 7] = -4.071335874253583; + x[ 8] = -3.6677742159463378; + x[ 9] = -3.295265921534226; + x[10] = -2.9592107790638380; + x[11] = -2.633356763661946; + x[12] = -2.2665132620567876; + x[13] = -2.089340389294661; + x[14] = -2.0232301911005157; + x[15] = -1.8357079751751868; + x[16] = -1.583643465293944; + x[17] = -1.2247448713915889; + x[18] = -0.87004089535290285; + x[19] = -0.52403354748695763; + x[20] = -0.196029453662011; + x[21] = 0.0000000000000000; + x[22] = 0.196029453662011; + x[23] = 0.52403354748695763; + x[24] = 0.87004089535290285; + x[25] = 1.2247448713915889; + x[26] = 1.583643465293944; + x[27] = 1.8357079751751868; + x[28] = 2.0232301911005157; + x[29] = 2.089340389294661; + x[30] = 2.2665132620567876; + x[31] = 2.633356763661946; + x[32] = 2.9592107790638380; + x[33] = 3.295265921534226; + x[34] = 3.6677742159463378; + x[35] = 4.071335874253583; + x[36] = 4.4995993983103881; + x[37] = 4.952329763008589; + x[38] = 5.434053000365068; + x[39] = 5.954781975039809; + x[40] = 6.535398426382995; + x[41] = 7.231746029072501; + x[42] = 10.167574994881873; + } + else + { + std::cerr << "\n"; + std::cerr << "HERMITE_GK24_LOOKUP_POINTS - Fatal error!\n"; + std::cerr << " Illegal input value of N.\n"; + std::cerr << " N must be 1, 3, 9, 19, or 43.\n"; + std::exit ( 1 ); + } + return; +} +//****************************************************************************80 + +double hermite_integral ( int n ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_INTEGRAL evaluates a monomial Hermite integral. +// +// Discussion: +// +// H(n) = Integral ( -oo < x < +oo ) x^n exp(-x^2) dx +// +// H(n) is 0 for n odd. +// +// H(n) = (n-1)!! * sqrt(pi) / 2^(n/2) for n even. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order of the integral. +// 0 <= N. +// +// Output, double VALUE, the value of the integral. +// +{ + double pi = 3.141592653589793; + double value; + + if ( n < 0 ) + { + value = - webbur::r8_huge ( ); + } + else if ( ( n % 2 ) == 1 ) + { + value = 0.0; + } + else + { + value = webbur::r8_factorial2 ( n - 1 ) * std::sqrt ( pi ) + / std::pow ( 2.0, n / 2 ); + } + + return value; +} +//****************************************************************************80 + +void hermite_interpolant ( int n, double x[], double y[], double yp[], + double xd[], double yd[], double xdp[], double ydp[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_INTERPOLANT sets up a divided difference table from Hermite data. +// +// Discussion: +// +// The polynomial represented by the divided difference table can be +// evaluated by calling DIF_VALS. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 October 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Carl deBoor, +// A Practical Guide to Splines, +// Springer, 2001, +// ISBN: 0387953663, +// LC: QA1.A647.v27. +// +// Parameters: +// +// Input, int N, of items of data +// ( X(I), Y(I), YP(I) ). +// +// Input, double X[N], the abscissas. +// These values must be distinct. +// +// Input, double Y[N], YP[N], the function and derivative values. +// +// Output, double XD[2*N], YD[2*N], the divided difference table +// for the interpolant value. +// +// Output, double XDP[2*N-1], YDP[2*N-1], the divided difference +// table for the interpolant derivative. +// +{ + int i; + int j; + int nd; + int ndp; +// +// Copy the data. +// + nd = 2 * n; + + for ( i = 0; i < n; i++ ) + { + xd[0+i*2] = x[i]; + xd[1+i*2] = x[i]; + } +// +// Carry out the first step of differencing. +// + yd[0] = y[0]; + for ( i = 1; i < n; i++ ) + { + yd[0+2*i] = ( y[i] - y[i-1] ) / ( x[i] - x[i-1] ); + } + for ( i = 0; i < n; i++ ) + { + yd[1+2*i] = yp[i]; + } +// +// Carry out the remaining steps in the usual way. +// + for ( i = 2; i < nd; i++ ) + { + for ( j = nd - 1; i <= j; j-- ) + { + yd[j] = ( yd[j] - yd[j-1] ) / ( xd[j] - xd[j-i] ); + } + } +// +// Compute the difference table for the derivative. +// + webbur::dif_deriv ( nd, xd, yd, &ndp, xdp, ydp ); + + return; +} +//****************************************************************************80 + +void hermite_interpolant_rule ( int n, double a, double b, double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_INTERPOLANT_RULE: quadrature rule for a Hermite interpolant. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 October 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of abscissas. +// +// Input, double A, B, the integration limits. +// +// Input, double X[N], the abscissas. +// +// Output, double W[2*N], the quadrature +// coefficients, given as pairs for function and derivative values +// at each abscissa. +// +{ + double a_value; + double b_value; + double *c; + int i; + int j; + int k; + int nd; + int ndp; + double *xd; + double *xdp; + double *y; + double *yd; + double *ydp; + double *yp; + + y = new double[n]; + yp = new double[n]; + + nd = 2 * n; + c = new double[nd]; + xd = new double[nd]; + yd = new double[nd]; + + ndp = 2 * n - 1; + xdp = new double[ndp]; + ydp = new double[ndp]; + + for ( i = 0; i < n; i++ ) + { + y[i] = 0.0; + yp[i] = 0.0; + } + + k = 0; + + for ( i = 0; i < n; i++ ) + { + y[i] = 1.0; + webbur::hermite_interpolant ( n, x, y, yp, xd, yd, xdp, ydp ); + webbur::dif_to_r8poly ( nd, xd, yd, c ); + a_value = webbur::r8poly_ant_val ( n, c, a ); + b_value = webbur::r8poly_ant_val ( n, c, b ); + w[k] = b_value - a_value; + y[i] = 0.0; + k = k + 1; + + yp[i] = 1.0; + webbur::hermite_interpolant ( n, x, y, yp, xd, yd, xdp, ydp ); + webbur::dif_to_r8poly ( nd, xd, yd, c ); + a_value = webbur::r8poly_ant_val ( n, c, a ); + b_value = webbur::r8poly_ant_val ( n, c, b ); + w[k] = b_value - a_value; + yp[i] = 0.0; + k = k + 1; + } + + delete [] c; + delete [] xd; + delete [] xdp; + delete [] y; + delete [] yd; + delete [] ydp; + delete [] yp; + + return; +} +//****************************************************************************80 + +void hermite_interpolant_value ( int nd, double xd[], double yd[], double xdp[], + double ydp[], int nv, double xv[], double yv[], double yvp[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_INTERPOLANT_VALUE evaluates the Hermite interpolant polynomial. +// +// Discussion: +// +// In fact, this function will evaluate an arbitrary polynomial that is +// represented by a difference table. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 October 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Carl deBoor, +// A Practical Guide to Splines, +// Springer, 2001, +// ISBN: 0387953663, +// LC: QA1.A647.v27. +// +// Parameters: +// +// Input, int ND, the order of the difference table. +// +// Input, double XD[ND], YD[ND], the difference table for the +// interpolant value. +// +// Input, double XDP[ND-1], YDP[ND-1], the difference table for +// the interpolant derivative. +// +// Input, int NV, the number of evaluation points. +// +// Input, double XV[NV], the evaluation points. +// +// Output, double YV[NV], YVP[NV], the value of the interpolant and +// its derivative at the evaluation points. +// +{ + int i; + int j; + int ndp; + + ndp = nd - 1; + + for ( j = 0; j < nv; j++ ) + { + yv[j] = yd[nd-1]; + for ( i = nd - 2; 0 <= i; i-- ) + { + yv[j] = yd[i] + ( xv[j] - xd[i] ) * yv[j]; + } + + yvp[j] = ydp[ndp-1]; + for ( i = ndp - 2; 0 <= i; i-- ) + { + yvp[j] = ydp[i] + ( xv[j] - xdp[i] ) * yvp[j]; + } + } + return; +} +//****************************************************************************80 + +void hermite_lookup ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_LOOKUP looks up abscissas and weights for Gauss-Hermite quadrature. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 April 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Vladimir Krylov, +// Approximate Calculation of Integrals, +// Dover, 2006, +// ISBN: 0486445798. +// LC: QA311.K713. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Stephen Wolfram, +// The Mathematica Book, +// Fourth Edition, +// Cambridge University Press, 1999, +// ISBN: 0-521-64314-7, +// LC: QA76.95.W65. +// +// Daniel Zwillinger, editor, +// CRC Standard Mathematical Tables and Formulae, +// 30th Edition, +// CRC Press, 1996, +// ISBN: 0-8493-2479-3, +// LC: QA47.M315. +// +// Parameters: +// +// Input, int N, the order. +// N must be between 1 and 20. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::hermite_lookup_points ( n, x ); + + webbur::hermite_lookup_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void hermite_lookup_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_LOOKUP_POINTS looks up abscissas for Hermite quadrature. +// +// Discussion: +// +// The integral: +// +// integral ( -oo < x < +oo ) exp ( - x * x ) * f(x) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ). +// +// Mathematica can numerically estimate the abscissas +// of order N to P digits by the command: +// +// NSolve [ HermiteH [ n, x ] == 0, x, p ] +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 April 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Vladimir Krylov, +// Approximate Calculation of Integrals, +// Dover, 2006, +// ISBN: 0486445798, +// LC: QA311.K713. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Stephen Wolfram, +// The Mathematica Book, +// Fourth Edition, +// Cambridge University Press, 1999, +// ISBN: 0-521-64314-7, +// LC: QA76.95.W65. +// +// Daniel Zwillinger, editor, +// CRC Standard Mathematical Tables and Formulae, +// 30th Edition, +// CRC Press, 1996, +// ISBN: 0-8493-2479-3, +// LC: QA47.M315. +// +// Parameters: +// +// Input, int N, the order. +// N must be between 1 and 20. +// +// Output, double X[N], the abscissas. +// +{ + if ( n == 1 ) + { + x[0] = 0.0; + } + else if ( n == 2 ) + { + x[0] = - 0.707106781186547524400844362105E+00; + x[1] = 0.707106781186547524400844362105E+00; + } + else if ( n == 3 ) + { + x[0] = - 0.122474487139158904909864203735E+01; + x[1] = 0.0E+00; + x[2] = 0.122474487139158904909864203735E+01; + } + else if ( n == 4 ) + { + x[0] = - 0.165068012388578455588334111112E+01; + x[1] = - 0.524647623275290317884060253835E+00; + x[2] = 0.524647623275290317884060253835E+00; + x[3] = 0.165068012388578455588334111112E+01; + } + else if ( n == 5 ) + { + x[0] = - 0.202018287045608563292872408814E+01; + x[1] = - 0.958572464613818507112770593893E+00; + x[2] = 0.0E+00; + x[3] = 0.958572464613818507112770593893E+00; + x[4] = 0.202018287045608563292872408814E+01; + } + else if ( n == 6 ) + { + x[0] = - 0.235060497367449222283392198706E+01; + x[1] = - 0.133584907401369694971489528297E+01; + x[2] = - 0.436077411927616508679215948251E+00; + x[3] = 0.436077411927616508679215948251E+00; + x[4] = 0.133584907401369694971489528297E+01; + x[5] = 0.235060497367449222283392198706E+01; + } + else if ( n == 7 ) + { + x[0] = - 0.265196135683523349244708200652E+01; + x[1] = - 0.167355162876747144503180139830E+01; + x[2] = - 0.816287882858964663038710959027E+00; + x[3] = 0.0E+00; + x[4] = 0.816287882858964663038710959027E+00; + x[5] = 0.167355162876747144503180139830E+01; + x[6] = 0.265196135683523349244708200652E+01; + } + else if ( n == 8 ) + { + x[0] = - 0.293063742025724401922350270524E+01; + x[1] = - 0.198165675669584292585463063977E+01; + x[2] = - 0.115719371244678019472076577906E+01; + x[3] = - 0.381186990207322116854718885584E+00; + x[4] = 0.381186990207322116854718885584E+00; + x[5] = 0.115719371244678019472076577906E+01; + x[6] = 0.198165675669584292585463063977E+01; + x[7] = 0.293063742025724401922350270524E+01; + } + else if ( n == 9 ) + { + x[0] = - 0.319099320178152760723004779538E+01; + x[1] = - 0.226658058453184311180209693284E+01; + x[2] = - 0.146855328921666793166701573925E+01; + x[3] = - 0.723551018752837573322639864579E+00; + x[4] = 0.0E+00; + x[5] = 0.723551018752837573322639864579E+00; + x[6] = 0.146855328921666793166701573925E+01; + x[7] = 0.226658058453184311180209693284E+01; + x[8] = 0.319099320178152760723004779538E+01; + } + else if ( n == 10 ) + { + x[0] = - 0.343615911883773760332672549432E+01; + x[1] = - 0.253273167423278979640896079775E+01; + x[2] = - 0.175668364929988177345140122011E+01; + x[3] = - 0.103661082978951365417749191676E+01; + x[4] = - 0.342901327223704608789165025557E+00; + x[5] = 0.342901327223704608789165025557E+00; + x[6] = 0.103661082978951365417749191676E+01; + x[7] = 0.175668364929988177345140122011E+01; + x[8] = 0.253273167423278979640896079775E+01; + x[9] = 0.343615911883773760332672549432E+01; + } + else if ( n == 11 ) + { + x[0] = - 0.366847084655958251845837146485E+01; + x[1] = - 0.278329009978165177083671870152E+01; + x[2] = - 0.202594801582575533516591283121E+01; + x[3] = - 0.132655708449493285594973473558E+01; + x[4] = - 0.656809566882099765024611575383E+00; + x[5] = 0.0E+00; + x[6] = 0.656809566882099765024611575383E+00; + x[7] = 0.132655708449493285594973473558E+01; + x[8] = 0.202594801582575533516591283121E+01; + x[9] = 0.278329009978165177083671870152E+01; + x[10] = 0.366847084655958251845837146485E+01; + } + else if ( n == 12 ) + { + x[0] = - 0.388972489786978191927164274724E+01; + x[1] = - 0.302063702512088977171067937518E+01; + x[2] = - 0.227950708050105990018772856942E+01; + x[3] = - 0.159768263515260479670966277090E+01; + x[4] = - 0.947788391240163743704578131060E+00; + x[5] = - 0.314240376254359111276611634095E+00; + x[6] = 0.314240376254359111276611634095E+00; + x[7] = 0.947788391240163743704578131060E+00; + x[8] = 0.159768263515260479670966277090E+01; + x[9] = 0.227950708050105990018772856942E+01; + x[10] = 0.302063702512088977171067937518E+01; + x[11] = 0.388972489786978191927164274724E+01; + } + else if ( n == 13 ) + { + x[0] = - 0.410133759617863964117891508007E+01; + x[1] = - 0.324660897837240998812205115236E+01; + x[2] = - 0.251973568567823788343040913628E+01; + x[3] = - 0.185310765160151214200350644316E+01; + x[4] = - 0.122005503659074842622205526637E+01; + x[5] = - 0.605763879171060113080537108602E+00; + x[6] = 0.0E+00; + x[7] = 0.605763879171060113080537108602E+00; + x[8] = 0.122005503659074842622205526637E+01; + x[9] = 0.185310765160151214200350644316E+01; + x[10] = 0.251973568567823788343040913628E+01; + x[11] = 0.324660897837240998812205115236E+01; + x[12] = 0.410133759617863964117891508007E+01; + } + else if ( n == 14 ) + { + x[0] = - 0.430444857047363181262129810037E+01; + x[1] = - 0.346265693360227055020891736115E+01; + x[2] = - 0.274847072498540256862499852415E+01; + x[3] = - 0.209518325850771681573497272630E+01; + x[4] = - 0.147668273114114087058350654421E+01; + x[5] = - 0.878713787329399416114679311861E+00; + x[6] = - 0.291745510672562078446113075799E+00; + x[7] = 0.291745510672562078446113075799E+00; + x[8] = 0.878713787329399416114679311861E+00; + x[9] = 0.147668273114114087058350654421E+01; + x[10] = 0.209518325850771681573497272630E+01; + x[11] = 0.274847072498540256862499852415E+01; + x[12] = 0.346265693360227055020891736115E+01; + x[13] = 0.430444857047363181262129810037E+01; + } + else if ( n == 15 ) + { + x[0] = - 0.449999070730939155366438053053E+01; + x[1] = - 0.366995037340445253472922383312E+01; + x[2] = - 0.296716692790560324848896036355E+01; + x[3] = - 0.232573248617385774545404479449E+01; + x[4] = - 0.171999257518648893241583152515E+01; + x[5] = - 0.113611558521092066631913490556E+01; + x[6] = - 0.565069583255575748526020337198E+00; + x[7] = 0.0E+00; + x[8] = 0.565069583255575748526020337198E+00; + x[9] = 0.113611558521092066631913490556E+01; + x[10] = 0.171999257518648893241583152515E+01; + x[11] = 0.232573248617385774545404479449E+01; + x[12] = 0.296716692790560324848896036355E+01; + x[13] = 0.366995037340445253472922383312E+01; + x[14] = 0.449999070730939155366438053053E+01; + } + else if ( n == 16 ) + { + x[0] = - 0.468873893930581836468849864875E+01; + x[1] = - 0.386944790486012269871942409801E+01; + x[2] = - 0.317699916197995602681399455926E+01; + x[3] = - 0.254620215784748136215932870545E+01; + x[4] = - 0.195178799091625397743465541496E+01; + x[5] = - 0.138025853919888079637208966969E+01; + x[6] = - 0.822951449144655892582454496734E+00; + x[7] = - 0.273481046138152452158280401965E+00; + x[8] = 0.273481046138152452158280401965E+00; + x[9] = 0.822951449144655892582454496734E+00; + x[10] = 0.138025853919888079637208966969E+01; + x[11] = 0.195178799091625397743465541496E+01; + x[12] = 0.254620215784748136215932870545E+01; + x[13] = 0.317699916197995602681399455926E+01; + x[14] = 0.386944790486012269871942409801E+01; + x[15] = 0.468873893930581836468849864875E+01; + } + else if ( n == 17 ) + { + x[0] = - 0.487134519367440308834927655662E+01; + x[1] = - 0.406194667587547430689245559698E+01; + x[2] = - 0.337893209114149408338327069289E+01; + x[3] = - 0.275776291570388873092640349574E+01; + x[4] = - 0.217350282666662081927537907149E+01; + x[5] = - 0.161292431422123133311288254454E+01; + x[6] = - 0.106764872574345055363045773799E+01; + x[7] = - 0.531633001342654731349086553718E+00; + x[8] = 0.0E+00; + x[9] = 0.531633001342654731349086553718E+00; + x[10] = 0.106764872574345055363045773799E+01; + x[11] = 0.161292431422123133311288254454E+01; + x[12] = 0.217350282666662081927537907149E+01; + x[13] = 0.275776291570388873092640349574E+01; + x[14] = 0.337893209114149408338327069289E+01; + x[15] = 0.406194667587547430689245559698E+01; + x[16] = 0.487134519367440308834927655662E+01; + } + else if ( n == 18 ) + { + x[0] = - 0.504836400887446676837203757885E+01; + x[1] = - 0.424811787356812646302342016090E+01; + x[2] = - 0.357376906848626607950067599377E+01; + x[3] = - 0.296137750553160684477863254906E+01; + x[4] = - 0.238629908916668600026459301424E+01; + x[5] = - 0.183553160426162889225383944409E+01; + x[6] = - 0.130092085838961736566626555439E+01; + x[7] = - 0.776682919267411661316659462284E+00; + x[8] = - 0.258267750519096759258116098711E+00; + x[9] = 0.258267750519096759258116098711E+00; + x[10] = 0.776682919267411661316659462284E+00; + x[11] = 0.130092085838961736566626555439E+01; + x[12] = 0.183553160426162889225383944409E+01; + x[13] = 0.238629908916668600026459301424E+01; + x[14] = 0.296137750553160684477863254906E+01; + x[15] = 0.357376906848626607950067599377E+01; + x[16] = 0.424811787356812646302342016090E+01; + x[17] = 0.504836400887446676837203757885E+01; + } + else if ( n == 19 ) + { + x[0] = - 0.522027169053748216460967142500E+01; + x[1] = - 0.442853280660377943723498532226E+01; + x[2] = - 0.376218735196402009751489394104E+01; + x[3] = - 0.315784881834760228184318034120E+01; + x[4] = - 0.259113378979454256492128084112E+01; + x[5] = - 0.204923170985061937575050838669E+01; + x[6] = - 0.152417061939353303183354859367E+01; + x[7] = - 0.101036838713431135136859873726E+01; + x[8] = - 0.503520163423888209373811765050E+00; + x[9] = 0.0E+00; + x[10] = 0.503520163423888209373811765050E+00; + x[11] = 0.101036838713431135136859873726E+01; + x[12] = 0.152417061939353303183354859367E+01; + x[13] = 0.204923170985061937575050838669E+01; + x[14] = 0.259113378979454256492128084112E+01; + x[15] = 0.315784881834760228184318034120E+01; + x[16] = 0.376218735196402009751489394104E+01; + x[17] = 0.442853280660377943723498532226E+01; + x[18] = 0.522027169053748216460967142500E+01; + } + else if ( n == 20 ) + { + x[0] = - 0.538748089001123286201690041068E+01; + x[1] = - 0.460368244955074427307767524898E+01; + x[2] = - 0.394476404011562521037562880052E+01; + x[3] = - 0.334785456738321632691492452300E+01; + x[4] = - 0.278880605842813048052503375640E+01; + x[5] = - 0.225497400208927552308233334473E+01; + x[6] = - 0.173853771211658620678086566214E+01; + x[7] = - 0.123407621539532300788581834696E+01; + x[8] = - 0.737473728545394358705605144252E+00; + x[9] = - 0.245340708300901249903836530634E+00; + x[10] = 0.245340708300901249903836530634E+00; + x[11] = 0.737473728545394358705605144252E+00; + x[12] = 0.123407621539532300788581834696E+01; + x[13] = 0.173853771211658620678086566214E+01; + x[14] = 0.225497400208927552308233334473E+01; + x[15] = 0.278880605842813048052503375640E+01; + x[16] = 0.334785456738321632691492452300E+01; + x[17] = 0.394476404011562521037562880052E+01; + x[18] = 0.460368244955074427307767524898E+01; + x[19] = 0.538748089001123286201690041068E+01; + } + else + { + std::cerr << "\n"; + std::cerr << "HERMITE_LOOKUP_POINTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::cerr << " Legal values are 1 through 20.\n"; + std::exit ( 1 ); + } + + return; +} +//****************************************************************************80 + +void hermite_lookup_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_LOOKUP_WEIGHTS looks up weights for Hermite quadrature. +// +// Discussion: +// +// The integral: +// +// integral ( -oo < x < +oo ) exp ( - x * x ) * f(x) dx +// +// The quadrature rule: +// +// sum ( 1 <= i <= n ) w(i) * f ( x(i) ). +// +// Mathematica can numerically estimate the abscissas +// of order N to P digits by the command: +// +// NSolve [ HermiteH [ n, x ] == 0, x, p ] +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 April 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Vladimir Krylov, +// Approximate Calculation of Integrals, +// Dover, 2006, +// ISBN: 0486445798, +// LC: QA311.K713. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Stephen Wolfram, +// The Mathematica Book, +// Fourth Edition, +// Cambridge University Press, 1999, +// ISBN: 0-521-64314-7, +// LC: QA76.95.W65. +// +// Daniel Zwillinger, editor, +// CRC Standard Mathematical Tables and Formulae, +// 30th Edition, +// CRC Press, 1996, +// ISBN: 0-8493-2479-3, +// LC: QA47.M315. +// +// Parameters: +// +// Input, int N, the order. +// N must be between 1 and 20. +// +// Output, double W[N], the weights. +// +{ + if ( n == 1 ) + { + w[0] = 1.77245385090551602729816748334; + } + else if ( n == 2 ) + { + w[0] = 0.886226925452758013649083741671E+00; + w[1] = 0.886226925452758013649083741671E+00; + } + else if ( n == 3 ) + { + w[0] = 0.295408975150919337883027913890E+00; + w[1] = 0.118163590060367735153211165556E+01; + w[2] = 0.295408975150919337883027913890E+00; + } + else if ( n == 4 ) + { + w[0] = 0.813128354472451771430345571899E-01; + w[1] = 0.804914090005512836506049184481E+00; + w[2] = 0.804914090005512836506049184481E+00; + w[3] = 0.813128354472451771430345571899E-01; + } + else if ( n == 5 ) + { + w[0] = 0.199532420590459132077434585942E-01; + w[1] = 0.393619323152241159828495620852E+00; + w[2] = 0.945308720482941881225689324449E+00; + w[3] = 0.393619323152241159828495620852E+00; + w[4] = 0.199532420590459132077434585942E-01; + } + else if ( n == 6 ) + { + w[0] = 0.453000990550884564085747256463E-02; + w[1] = 0.157067320322856643916311563508E+00; + w[2] = 0.724629595224392524091914705598E+00; + w[3] = 0.724629595224392524091914705598E+00; + w[4] = 0.157067320322856643916311563508E+00; + w[5] = 0.453000990550884564085747256463E-02; + } + else if ( n == 7 ) + { + w[0] = 0.971781245099519154149424255939E-03; + w[1] = 0.545155828191270305921785688417E-01; + w[2] = 0.425607252610127800520317466666E+00; + w[3] = 0.810264617556807326764876563813E+00; + w[4] = 0.425607252610127800520317466666E+00; + w[5] = 0.545155828191270305921785688417E-01; + w[6] = 0.971781245099519154149424255939E-03; + } + else if ( n == 8 ) + { + w[0] = 0.199604072211367619206090452544E-03; + w[1] = 0.170779830074134754562030564364E-01; + w[2] = 0.207802325814891879543258620286E+00; + w[3] = 0.661147012558241291030415974496E+00; + w[4] = 0.661147012558241291030415974496E+00; + w[5] = 0.207802325814891879543258620286E+00; + w[6] = 0.170779830074134754562030564364E-01; + w[7] = 0.199604072211367619206090452544E-03; + } + else if ( n == 9 ) + { + w[0] = 0.396069772632643819045862946425E-04; + w[1] = 0.494362427553694721722456597763E-02; + w[2] = 0.884745273943765732879751147476E-01; + w[3] = 0.432651559002555750199812112956E+00; + w[4] = 0.720235215606050957124334723389E+00; + w[5] = 0.432651559002555750199812112956E+00; + w[6] = 0.884745273943765732879751147476E-01; + w[7] = 0.494362427553694721722456597763E-02; + w[8] = 0.396069772632643819045862946425E-04; + } + else if ( n == 10 ) + { + w[0] = 0.764043285523262062915936785960E-05; + w[1] = 0.134364574678123269220156558585E-02; + w[2] = 0.338743944554810631361647312776E-01; + w[3] = 0.240138611082314686416523295006E+00; + w[4] = 0.610862633735325798783564990433E+00; + w[5] = 0.610862633735325798783564990433E+00; + w[6] = 0.240138611082314686416523295006E+00; + w[7] = 0.338743944554810631361647312776E-01; + w[8] = 0.134364574678123269220156558585E-02; + w[9] = 0.764043285523262062915936785960E-05; + } + else if ( n == 11 ) + { + w[0] = 0.143956039371425822033088366032E-05; + w[1] = 0.346819466323345510643413772940E-03; + w[2] = 0.119113954449115324503874202916E-01; + w[3] = 0.117227875167708503381788649308E+00; + w[4] = 0.429359752356125028446073598601E+00; + w[5] = 0.654759286914591779203940657627E+00; + w[6] = 0.429359752356125028446073598601E+00; + w[7] = 0.117227875167708503381788649308E+00; + w[8] = 0.119113954449115324503874202916E-01; + w[9] = 0.346819466323345510643413772940E-03; + w[10] = 0.143956039371425822033088366032E-05; + } + else if ( n == 12 ) + { + w[0] = 0.265855168435630160602311400877E-06; + w[1] = 0.857368704358785865456906323153E-04; + w[2] = 0.390539058462906185999438432620E-02; + w[3] = 0.516079856158839299918734423606E-01; + w[4] = 0.260492310264161129233396139765E+00; + w[5] = 0.570135236262479578347113482275E+00; + w[6] = 0.570135236262479578347113482275E+00; + w[7] = 0.260492310264161129233396139765E+00; + w[8] = 0.516079856158839299918734423606E-01; + w[9] = 0.390539058462906185999438432620E-02; + w[10] = 0.857368704358785865456906323153E-04; + w[11] = 0.265855168435630160602311400877E-06; + } + else if ( n == 13 ) + { + w[0] = 0.482573185007313108834997332342E-07; + w[1] = 0.204303604027070731248669432937E-04; + w[2] = 0.120745999271938594730924899224E-02; + w[3] = 0.208627752961699392166033805050E-01; + w[4] = 0.140323320687023437762792268873E+00; + w[5] = 0.421616296898543221746893558568E+00; + w[6] = 0.604393187921161642342099068579E+00; + w[7] = 0.421616296898543221746893558568E+00; + w[8] = 0.140323320687023437762792268873E+00; + w[9] = 0.208627752961699392166033805050E-01; + w[10] = 0.120745999271938594730924899224E-02; + w[11] = 0.204303604027070731248669432937E-04; + w[12] = 0.482573185007313108834997332342E-07; + } + else if ( n == 14 ) + { + w[0] = 0.862859116812515794532041783429E-08; + w[1] = 0.471648435501891674887688950105E-05; + w[2] = 0.355092613551923610483661076691E-03; + w[3] = 0.785005472645794431048644334608E-02; + w[4] = 0.685055342234652055387163312367E-01; + w[5] = 0.273105609064246603352569187026E+00; + w[6] = 0.536405909712090149794921296776E+00; + w[7] = 0.536405909712090149794921296776E+00; + w[8] = 0.273105609064246603352569187026E+00; + w[9] = 0.685055342234652055387163312367E-01; + w[10] = 0.785005472645794431048644334608E-02; + w[11] = 0.355092613551923610483661076691E-03; + w[12] = 0.471648435501891674887688950105E-05; + w[13] = 0.862859116812515794532041783429E-08; + } + else if ( n == 15 ) + { + w[0] = 0.152247580425351702016062666965E-08; + w[1] = 0.105911554771106663577520791055E-05; + w[2] = 0.100004441232499868127296736177E-03; + w[3] = 0.277806884291277589607887049229E-02; + w[4] = 0.307800338725460822286814158758E-01; + w[5] = 0.158488915795935746883839384960E+00; + w[6] = 0.412028687498898627025891079568E+00; + w[7] = 0.564100308726417532852625797340E+00; + w[8] = 0.412028687498898627025891079568E+00; + w[9] = 0.158488915795935746883839384960E+00; + w[10] = 0.307800338725460822286814158758E-01; + w[11] = 0.277806884291277589607887049229E-02; + w[12] = 0.100004441232499868127296736177E-03; + w[13] = 0.105911554771106663577520791055E-05; + w[14] = 0.152247580425351702016062666965E-08; + } + else if ( n == 16 ) + { + w[0] = 0.265480747401118224470926366050E-09; + w[1] = 0.232098084486521065338749423185E-06; + w[2] = 0.271186009253788151201891432244E-04; + w[3] = 0.932284008624180529914277305537E-03; + w[4] = 0.128803115355099736834642999312E-01; + w[5] = 0.838100413989858294154207349001E-01; + w[6] = 0.280647458528533675369463335380E+00; + w[7] = 0.507929479016613741913517341791E+00; + w[8] = 0.507929479016613741913517341791E+00; + w[9] = 0.280647458528533675369463335380E+00; + w[10] = 0.838100413989858294154207349001E-01; + w[11] = 0.128803115355099736834642999312E-01; + w[12] = 0.932284008624180529914277305537E-03; + w[13] = 0.271186009253788151201891432244E-04; + w[14] = 0.232098084486521065338749423185E-06; + w[15] = 0.265480747401118224470926366050E-09; + } + else if ( n == 17 ) + { + w[0] = 0.458057893079863330580889281222E-10; + w[1] = 0.497707898163079405227863353715E-07; + w[2] = 0.711228914002130958353327376218E-05; + w[3] = 0.298643286697753041151336643059E-03; + w[4] = 0.506734995762753791170069495879E-02; + w[5] = 0.409200341495762798094994877854E-01; + w[6] = 0.172648297670097079217645196219E+00; + w[7] = 0.401826469470411956577635085257E+00; + w[8] = 0.530917937624863560331883103379E+00; + w[9] = 0.401826469470411956577635085257E+00; + w[10] = 0.172648297670097079217645196219E+00; + w[11] = 0.409200341495762798094994877854E-01; + w[12] = 0.506734995762753791170069495879E-02; + w[13] = 0.298643286697753041151336643059E-03; + w[14] = 0.711228914002130958353327376218E-05; + w[15] = 0.497707898163079405227863353715E-07; + w[16] = 0.458057893079863330580889281222E-10; + } + else if ( n == 18 ) + { + w[0] = 0.782819977211589102925147471012E-11; + w[1] = 0.104672057957920824443559608435E-07; + w[2] = 0.181065448109343040959702385911E-05; + w[3] = 0.918112686792940352914675407371E-04; + w[4] = 0.188852263026841789438175325426E-02; + w[5] = 0.186400423875446519219315221973E-01; + w[6] = 0.973017476413154293308537234155E-01; + w[7] = 0.284807285669979578595606820713E+00; + w[8] = 0.483495694725455552876410522141E+00; + w[9] = 0.483495694725455552876410522141E+00; + w[10] = 0.284807285669979578595606820713E+00; + w[11] = 0.973017476413154293308537234155E-01; + w[12] = 0.186400423875446519219315221973E-01; + w[13] = 0.188852263026841789438175325426E-02; + w[14] = 0.918112686792940352914675407371E-04; + w[15] = 0.181065448109343040959702385911E-05; + w[16] = 0.104672057957920824443559608435E-07; + w[17] = 0.782819977211589102925147471012E-11; + } + else if ( n == 19 ) + { + w[0] = 0.132629709449851575185289154385E-11; + w[1] = 0.216305100986355475019693077221E-08; + w[2] = 0.448824314722312295179447915594E-06; + w[3] = 0.272091977631616257711941025214E-04; + w[4] = 0.670877521407181106194696282100E-03; + w[5] = 0.798886677772299020922211491861E-02; + w[6] = 0.508103869090520673569908110358E-01; + w[7] = 0.183632701306997074156148485766E+00; + w[8] = 0.391608988613030244504042313621E+00; + w[9] = 0.502974888276186530840731361096E+00; + w[10] = 0.391608988613030244504042313621E+00; + w[11] = 0.183632701306997074156148485766E+00; + w[12] = 0.508103869090520673569908110358E-01; + w[13] = 0.798886677772299020922211491861E-02; + w[14] = 0.670877521407181106194696282100E-03; + w[15] = 0.272091977631616257711941025214E-04; + w[16] = 0.448824314722312295179447915594E-06; + w[17] = 0.216305100986355475019693077221E-08; + w[18] = 0.132629709449851575185289154385E-11; + } + else if ( n == 20 ) + { + w[0] = 0.222939364553415129252250061603E-12; + w[1] = 0.439934099227318055362885145547E-09; + w[2] = 0.108606937076928169399952456345E-06; + w[3] = 0.780255647853206369414599199965E-05; + w[4] = 0.228338636016353967257145917963E-03; + w[5] = 0.324377334223786183218324713235E-02; + w[6] = 0.248105208874636108821649525589E-01; + w[7] = 0.109017206020023320013755033535E+00; + w[8] = 0.286675505362834129719659706228E+00; + w[9] = 0.462243669600610089650328639861E+00; + w[10] = 0.462243669600610089650328639861E+00; + w[11] = 0.286675505362834129719659706228E+00; + w[12] = 0.109017206020023320013755033535E+00; + w[13] = 0.248105208874636108821649525589E-01; + w[14] = 0.324377334223786183218324713235E-02; + w[15] = 0.228338636016353967257145917963E-03; + w[16] = 0.780255647853206369414599199965E-05; + w[17] = 0.108606937076928169399952456345E-06; + w[18] = 0.439934099227318055362885145547E-09; + w[19] = 0.222939364553415129252250061603E-12; + } + else + { + std::cerr << "\n"; + std::cerr << "HERMITE_LOOKUP_WEIGHTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::cerr << " Legal values are 1 through 20.\n"; + std::exit ( 1 ); + } + + return; +} +//****************************************************************************80 + +void hermite_ss_compute ( int order, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_SS_COMPUTE computes a Hermite quadrature rule. +// +// Discussion: +// +// The abscissas are the zeros of the N-th order Hermite polynomial. +// +// The integral: +// +// Integral ( -oo < X < +oo ) exp ( - X * X ) * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double cc; + double dp2; + int i; + double p1; + double s; + double temp; + double x0; + + if ( order < 1 ) + { + std::cerr << "\n"; + std::cerr << "HERMITE_SS_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of ORDER = " << order << "\n"; + std::exit ( 1 ); + } + + cc = 1.7724538509 * webbur::r8_gamma ( ( double ) ( order ) ) + / std::pow ( 2.0, order - 1 ); + + s = std::pow ( 2.0 * ( double ) ( order ) + 1.0, 1.0 / 6.0 ); + + for ( i = 0; i < ( order + 1 ) / 2; i++ ) + { + if ( i == 0 ) + { + x0 = s * s * s - 1.85575 / s; + } + else if ( i == 1 ) + { + x0 = x0 - 1.14 * std::pow ( ( double ) ( order ), 0.426 ) / x0; + } + else if ( i == 2 ) + { + x0 = 1.86 * x0 - 0.86 * x[0]; + } + else if ( i == 3 ) + { + x0 = 1.91 * x0 - 0.91 * x[1]; + } + else + { + x0 = 2.0 * x0 - x[i-2]; + } + + webbur::hermite_ss_root ( &x0, order, &dp2, &p1 ); + + x[i] = x0; + w[i] = ( cc / dp2 ) / p1; + + x[order-i-1] = -x0; + w[order-i-1] = w[i]; + } +// +// Reverse the order of the abscissas. +// + for ( i = 1; i <= order/2; i++ ) + { + temp = x[i-1]; + x[i-1] = x[order-i]; + x[order-i] = temp; + } + + if ( ( order % 2 ) == 1 ) + { + x[(order-1)/2] = 0.0; + } + + return; +} +//****************************************************************************80 + +void hermite_ss_recur ( double *p2, double *dp2, double *p1, double x, int order ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_SS_RECUR finds the value and derivative of a Hermite polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Output, double *P2, the value of H(ORDER)(X). +// +// Output, double *DP2, the value of H'(ORDER)(X). +// +// Output, double *P1, the value of H(ORDER-1)(X). +// +// Input, double X, the point at which polynomials are evaluated. +// +// Input, int ORDER, the order of the polynomial. +// +{ + int i; + double dq0; + double dq1; + double dq2; + double q0; + double q1; + double q2; + + q1 = 1.0; + dq1 = 0.0; + + q2 = x; + dq2 = 1.0; + + for ( i = 2; i <= order; i++ ) + { + q0 = q1; + dq0 = dq1; + + q1 = q2; + dq1 = dq2; + + q2 = x * q1 - 0.5 * ( ( double ) ( i ) - 1.0 ) * q0; + dq2 = x * dq1 + q1 - 0.5 * ( ( double ) ( i ) - 1.0 ) * dq0; + } + + *p2 = q2; + *dp2 = dq2; + *p1 = q1; + + return; +} +//****************************************************************************80 + +void hermite_ss_root ( double *x, int order, double *dp2, double *p1 ) + +//****************************************************************************80 +// +// Purpose: +// +// HERMITE_SS_ROOT improves an approximate root of a Hermite polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input/output, double *X, the approximate root, which +// should be improved on output. +// +// Input, int ORDER, the order of the Hermite polynomial. +// +// Output, double *DP2, the value of H'(ORDER)(X). +// +// Output, double *P1, the value of H(ORDER-1)(X). +// +{ + double d; + double eps; + double p2; + int step; + int step_max = 10; + + eps = webbur::r8_epsilon ( ); + + for ( step = 1; step <= step_max; step++ ) + { + webbur::hermite_ss_recur ( &p2, dp2, p1, *x, order ); + + d = p2 / ( *dp2 ); + *x = *x - d; + + if ( webbur::r8_abs ( d ) <= eps * ( webbur::r8_abs ( *x ) + 1.0 ) ) + { + return; + } + } + return; +} +//****************************************************************************80 + +int i4_choose ( int n, int k ) + +//****************************************************************************80 +// +// Purpose: +// +// I4_CHOOSE computes the binomial coefficient C(N,K). +// +// Discussion: +// +// The value is calculated in such a way as to avoid overflow and +// roundoff. The calculation is done in integer arithmetic. +// +// The formula used is: +// +// C(N,K) = N! / ( K! * (N-K)! ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 09 November 2007 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// ML Wolfson, HV Wright, +// Algorithm 160: +// Combinatorial of M Things Taken N at a Time, +// Communications of the ACM, +// Volume 6, Number 4, April 1963, page 161. +// +// Parameters: +// +// Input, int N, K, the values of N and K. +// +// Output, int I4_CHOOSE, the number of combinations of N +// things taken K at a time. +// +{ + int i; + int mn; + int mx; + int value; + + mn = i4_min ( k, n - k ); + + if ( mn < 0 ) + { + value = 0; + } + else if ( mn == 0 ) + { + value = 1; + } + else + { + mx = i4_max ( k, n - k ); + value = mx + 1; + + for ( i = 2; i <= mn; i++ ) + { + value = ( value * ( mx + i ) ) / i; + } + } + + return value; +} +//****************************************************************************80 + +int i4_log_2 ( int i ) + +//****************************************************************************80 +// +// Purpose: +// +// I4_LOG_2 returns the integer part of the logarithm base 2 of an I4. +// +// Example: +// +// I I4_LOG_10 +// ----- -------- +// 0 0 +// 1 0 +// 2 1 +// 3 1 +// 4 2 +// 5 2 +// 7 2 +// 8 3 +// 9 3 +// 1000 9 +// 1024 10 +// +// Discussion: +// +// I4_LOG_2 ( I ) + 1 is the number of binary digits in I. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 04 January 2004 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int I, the number whose logarithm base 2 is desired. +// +// Output, int I4_LOG_2, the integer part of the logarithm base 2 of +// the absolute value of X. +// +{ + int i_abs; + int two_pow; + int value; + + if ( i == 0 ) + { + value = 0; + } + else + { + value = 0; + two_pow = 2; + + i_abs = std::abs ( i ); + + while ( two_pow <= i_abs ) + { + value = value + 1; + two_pow = two_pow * 2; + } + } + + return value; +} +//****************************************************************************80 + +int i4_max ( int i1, int i2 ) + +//****************************************************************************80 +// +// Purpose: +// +// I4_MAX returns the maximum of two I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 October 1998 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int I1, I2, are two integers to be compared. +// +// Output, int I4_MAX, the larger of I1 and I2. +// +{ + int value; + + if ( i2 < i1 ) + { + value = i1; + } + else + { + value = i2; + } + return value; +} +//****************************************************************************80 + +int i4_min ( int i1, int i2 ) + +//****************************************************************************80 +// +// Purpose: +// +// I4_MIN returns the minimum of two I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 October 1998 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int I1, I2, two integers to be compared. +// +// Output, int I4_MIN, the smaller of I1 and I2. +// +{ + int value; + + if ( i1 < i2 ) + { + value = i1; + } + else + { + value = i2; + } + return value; +} +//****************************************************************************80 + +int i4_power ( int i, int j ) + +//****************************************************************************80 +// +// Purpose: +// +// I4_POWER returns the value of I^J. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 01 April 2004 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int I, J, the base and the power. J should be nonnegative. +// +// Output, int I4_POWER, the value of I^J. +// +{ + int k; + int value; + + if ( j < 0 ) + { + if ( i == 1 ) + { + value = 1; + } + else if ( i == 0 ) + { + std::cerr << "\n"; + std::cerr << "I4_POWER - Fatal error!\n"; + std::cerr << " I^J requested, with I = 0 and J negative.\n"; + std::exit ( 1 ); + } + else + { + value = 0; + } + } + else if ( j == 0 ) + { + if ( i == 0 ) + { + std::cerr << "\n"; + std::cerr << "I4_POWER - Fatal error!\n"; + std::cerr << " I^J requested, with I = 0 and J = 0.\n"; + std::exit ( 1 ); + } + else + { + value = 1; + } + } + else if ( j == 1 ) + { + value = i; + } + else + { + value = 1; + for ( k = 1; k <= j; k++ ) + { + value = value * i; + } + } + return value; +} +//****************************************************************************80 + +void i4mat_copy ( int m, int n, int a1[], int a2[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4MAT_COPY copies one I4MAT to another. +// +// Discussion: +// +// An I4MAT is an MxN array of I4's, stored by (I,J) -> [I+J*M]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 August 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns. +// +// Input, int A1[M*N], the matrix to be copied. +// +// Output, int A2[M*N], the copy of A1. +// +{ + int i; + int j; + + for ( j = 0; j < n; j++ ) + { + for ( i = 0; i < m; i++ ) + { + a2[i+j*m] = a1[i+j*m]; + } + } + return; +} +//****************************************************************************80 + +int *i4mat_copy_new ( int m, int n, int a1[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4MAT_COPY_NEW copies an I4MAT to a "new" I4MAT. +// +// Discussion: +// +// An I4MAT is an MxN array of I4's, stored by (I,J) -> [I+J*M]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 August 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns. +// +// Input, int A1[M*N], the matrix to be copied. +// +// Output, int I4MAT_COPY_NEW[M*N], the copy of A1. +// +{ + int *a2; + int i; + int j; + + a2 = new int[m*n]; + + for ( j = 0; j < n; j++ ) + { + for ( i = 0; i < m; i++ ) + { + a2[i+j*m] = a1[i+j*m]; + } + } + return a2; +} +//****************************************************************************80 + +void i4mat_transpose_print ( int m, int n, int a[], std::string title ) + +//****************************************************************************80 +// +// Purpose: +// +// I4MAT_TRANSPOSE_PRINT prints an I4MAT, transposed. +// +// Discussion: +// +// An I4MAT is an MxN array of I4's, stored by (I,J) -> [I+J*M]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 January 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows in A. +// +// Input, int N, the number of columns in A. +// +// Input, int A[M*N], the M by N matrix. +// +// Input, string TITLE, a title. +// +{ + i4mat_transpose_print_some ( m, n, a, 1, 1, m, n, title ); + + return; +} +//****************************************************************************80 + +void i4mat_transpose_print_some ( int m, int n, int a[], int ilo, int jlo, + int ihi, int jhi, std::string title ) + +//****************************************************************************80 +// +// Purpose: +// +// I4MAT_TRANSPOSE_PRINT_SOME prints some of an I4MAT, transposed. +// +// Discussion: +// +// An I4MAT is an MxN array of I4's, stored by (I,J) -> [I+J*M]. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 14 June 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows of the matrix. +// M must be positive. +// +// Input, int N, the number of columns of the matrix. +// N must be positive. +// +// Input, int A[M*N], the matrix. +// +// Input, int ILO, JLO, IHI, JHI, designate the first row and +// column, and the last row and column to be printed. +// +// Input, string TITLE, a title. +// +{ +# define INCX 10 + + int i; + int i2hi; + int i2lo; + int j; + int j2hi; + int j2lo; + + std::cout << "\n"; + std::cout << title << "\n"; +// +// Print the columns of the matrix, in strips of INCX. +// + for ( i2lo = ilo; i2lo <= ihi; i2lo = i2lo + INCX ) + { + i2hi = i2lo + INCX - 1; + i2hi = webbur::i4_min ( i2hi, m ); + i2hi = webbur::i4_min ( i2hi, ihi ); + + std::cout << "\n"; +// +// For each row I in the current range... +// +// Write the header. +// + std::cout << " Row: "; + for ( i = i2lo; i <= i2hi; i++ ) + { + std::cout << std::setw(6) << i - 1 << " "; + } + std::cout << "\n"; + std::cout << " Col\n"; + std::cout << "\n"; +// +// Determine the range of the rows in this strip. +// + j2lo = webbur::i4_max ( jlo, 1 ); + j2hi = webbur::i4_min ( jhi, n ); + + for ( j = j2lo; j <= j2hi; j++ ) + { +// +// Print out (up to INCX) entries in column J, that lie in the current strip. +// + std::cout << std::setw(5) << j - 1 << ":"; + for ( i = i2lo; i <= i2hi; i++ ) + { + std::cout << std::setw(6) << a[i-1+(j-1)*m] << " "; + } + std::cout << "\n"; + } + } + + return; +# undef INCX +} +//****************************************************************************80 + +void i4mat_write ( std::string output_filename, int m, int n, int table[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4MAT_WRITE writes an I4MAT file. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 01 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, string OUTPUT_FILENAME, the output filename. +// +// Input, int M, the spatial dimension. +// +// Input, int N, the number of points. +// +// Input, int TABLE[M*N], the table data. +// +{ + int i; + int j; + std::ofstream output; +// +// Open the file. +// + output.open ( output_filename.c_str ( ) ); + + if ( !output ) + { + std::cerr << "\n"; + std::cerr << "I4MAT_WRITE - Fatal error!\n"; + std::cerr << " Could not open the output file.\n"; + return; + } +// +// Write the data. +// + for ( j = 0; j < n; j++ ) + { + for ( i = 0; i < m; i++ ) + { + output << std::setw(10) << table[i+j*m] << " "; + } + output << "\n"; + } +// +// Close the file. +// + output.close ( ); + + return; +} +//****************************************************************************80 + +int *i4vec_add_new ( int n, int a[], int b[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_ADD_NEW computes C = A + B for I4VEC's. +// +// Discussion: +// +// An I4VEC is a vector of I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 28 April 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries. +// +// Input, int A[N], the first vector. +// +// Input, int B[N], the second vector. +// +// Output, int I4VEC_ADD_NEW[N], the sum of the vectors. +// +{ + int *c; + int i; + + c = new int[n]; + + for ( i = 0; i < n; i++ ) + { + c[i] = a[i] + b[i]; + } + return c; +} +//****************************************************************************80 + +bool i4vec_any_lt ( int n, int a[], int b[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_ANY_LT: ( any ( A < B ) ) for I4VEC's. +// +// Discussion: +// +// An I4VEC is a vector of I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 28 April 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries. +// +// Input, int A[N], the first vector. +// +// Input, int B[N], the second vector. +// +// Output, bool I4VEC_ANY_LT is TRUE if any entry +// of A is less than the corresponding entry of B. +// +{ + int i; + bool value; + + for ( i = 0; i < n; i++ ) + { + if ( a[i] < b[i] ) + { + value = true; + return value; + } + } + value = false; + + return value; +} +//****************************************************************************80 + +void i4vec_copy ( int n, int a1[], int a2[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_COPY copies an I4VEC. +// +// Discussion: +// +// An I4VEC is a vector of I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 25 April 2007 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vectors. +// +// Input, int A1[N], the vector to be copied. +// +// Output, int A2[N], the copy of A1. +// +{ + int i; + + for ( i = 0; i < n; i++ ) + { + a2[i] = a1[i]; + } + return; +} +//****************************************************************************80 + +int *i4vec_copy_new ( int n, int a1[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_COPY_NEW copies an I4VEC to a "new" I4VEC. +// +// Discussion: +// +// An I4VEC is a vector of I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 04 July 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vectors. +// +// Input, int A1[N], the vector to be copied. +// +// Output, int I4VEC_COPY_NEW[N], the copy of A1. +// +{ + int *a2; + int i; + + a2 = new int[n]; + + for ( i = 0; i < n; i++ ) + { + a2[i] = a1[i]; + } + return a2; +} +//****************************************************************************80 + +void i4vec_min_mv ( int m, int n, int u[], int v[], int w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_MIN_MV determines U(1:N) /\ V for vectors U and a single vector V. +// +// Discussion: +// +// For two vectors U and V, each of length M, we define +// +// ( U /\ V ) (I) = min ( U(I), V(I) ). +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 12 January 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the dimension of the vectors. +// +// Input, int N, the number of vectors in U. +// +// Input, int U[M*N], N vectors, each of length M. +// +// Input, int V[M], a vector of length M. +// +// Output, int W[M*N], the value of U /\ W. +// +{ + int i; + int j; + + for ( j = 0; j < n; j++ ) + { + for ( i = 0; i < m; i++ ) + { + w[i+j*m] = i4_min ( u[i+j*m], v[i] ); + } + } + return; +} +//****************************************************************************80 + +void i4vec_print ( int n, int a[], std::string title ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_PRINT prints an I4VEC. +// +// Discussion: +// +// An I4VEC is a vector of I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 14 November 2003 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of components of the vector. +// +// Input, int A[N], the vector to be printed. +// +// Input, string TITLE, a title. +// +{ + int i; + + std::cout << "\n"; + std::cout << title << "\n"; + std::cout << "\n"; + for ( i = 0; i < n; i++ ) + { + std::cout << " " << std::setw(8) << i + << ": " << std::setw(8) << a[i] << "\n"; + } + return; +} +//****************************************************************************80 + +int i4vec_product ( int n, int a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_PRODUCT multiplies the entries of an I4VEC. +// +// Discussion: +// +// An I4VEC is a vector of integer values. +// +// Example: +// +// Input: +// +// A = ( 1, 2, 3, 4 ) +// +// Output: +// +// I4VEC_PRODUCT = 24 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 May 2003 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Input, int A[N], the vector +// +// Output, int I4VEC_PRODUCT, the product of the entries of A. +// +{ + int i; + int product; + + product = 1; + for ( i = 0; i < n; i++ ) + { + product = product * a[i]; + } + + return product; +} +//****************************************************************************80 + +int i4vec_sum ( int n, int a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_SUM sums the entries of an I4VEC. +// +// Discussion: +// +// An I4VEC is a vector of I4's. +// +// Example: +// +// Input: +// +// A = ( 1, 2, 3, 4 ) +// +// Output: +// +// I4VEC_SUM = 10 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 04 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Input, int A[N], the vector to be summed. +// +// Output, int I4VEC_SUM, the sum of the entries of A. +// +{ + int i; + int sum; + + sum = 0; + for ( i = 0; i < n; i++ ) + { + sum = sum + a[i]; + } + + return sum; +} +//****************************************************************************80 + +void i4vec_zero ( int n, int a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_ZERO zeroes an I4VEC. +// +// Discussion: +// +// An I4VEC is a vector of I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 01 August 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Output, int A[N], a vector of zeroes. +// +{ + int i; + + for ( i = 0; i < n; i++ ) + { + a[i] = 0; + } + return; +} +//****************************************************************************80 + +int *i4vec_zero_new ( int n ) + +//****************************************************************************80 +// +// Purpose: +// +// I4VEC_ZERO_NEW creates and zeroes an I4VEC. +// +// Discussion: +// +// An I4VEC is a vector of I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 11 July 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Output, int I4VEC_ZERO_NEW[N], a vector of zeroes. +// +{ + int *a; + int i; + + a = new int[n]; + + for ( i = 0; i < n; i++ ) + { + a[i] = 0; + } + return a; +} +//****************************************************************************80 + +void imtqlx ( int n, double d[], double e[], double z[] ) + +//****************************************************************************80 +// +// Purpose: +// +// IMTQLX diagonalizes a symmetric tridiagonal matrix. +// +// Discussion: +// +// This routine is a slightly modified version of the EISPACK routine to +// perform the implicit QL algorithm on a symmetric tridiagonal matrix. +// +// The authors thank the authors of EISPACK for permission to use this +// routine. +// +// It has been modified to produce the product Q' * Z, where Z is an input +// vector and Q is the orthogonal matrix diagonalizing the input matrix. +// The changes consist (essentially) of applying the orthogonal transformations +// directly to Z as they are generated. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 08 January 2010 +// +// Author: +// +// Original FORTRAN77 version by Sylvan Elhay, Jaroslav Kautsky. +// C++ version by John Burkardt. +// +// Reference: +// +// Sylvan Elhay, Jaroslav Kautsky, +// Algorithm 655: IQPACK, FORTRAN Subroutines for the Weights of +// Interpolatory Quadrature, +// ACM Transactions on Mathematical Software, +// Volume 13, Number 4, December 1987, pages 399-415. +// +// Roger Martin, James Wilkinson, +// The Implicit QL Algorithm, +// Numerische Mathematik, +// Volume 12, Number 5, December 1968, pages 377-383. +// +// Parameters: +// +// Input, int N, the order of the matrix. +// +// Input/output, double D(N), the diagonal entries of the matrix. +// On output, the information in D has been overwritten. +// +// Input/output, double E(N), the subdiagonal entries of the +// matrix, in entries E(1) through E(N-1). On output, the information in +// E has been overwritten. +// +// Input/output, double Z(N). On input, a vector. On output, +// the value of Q' * Z, where Q is the matrix that diagonalizes the +// input symmetric tridiagonal matrix. +// +{ + double b; + double c; + double f; + double g; + int i; + int ii; + int itn = 30; + int j; + int k; + int l; + int m; + int mml; + double p; + double prec; + double r; + double s; + + prec = webbur::r8_epsilon ( ); + + if ( n == 1 ) + { + return; + } + + e[n-1] = 0.0; + + for ( l = 1; l <= n; l++ ) + { + j = 0; + for ( ; ; ) + { + for ( m = l; m <= n; m++ ) + { + if ( m == n ) + { + break; + } + + if ( webbur::r8_abs ( e[m-1] ) <= + prec * ( webbur::r8_abs ( d[m-1] ) + webbur::r8_abs ( d[m] ) ) ) + { + break; + } + } + p = d[l-1]; + if ( m == l ) + { + break; + } + if ( itn <= j ) + { + std::cerr << "\n"; + std::cerr << "IMTQLX - Fatal error!\n"; + std::cerr << " Iteration limit exceeded\n"; + std::exit ( 1 ); + } + j = j + 1; + g = ( d[l] - p ) / ( 2.0 * e[l-1] ); + r = std::sqrt ( g * g + 1.0 ); + g = d[m-1] - p + e[l-1] / ( g + webbur::r8_abs ( r ) * webbur::r8_sign ( g ) ); + s = 1.0; + c = 1.0; + p = 0.0; + mml = m - l; + + for ( ii = 1; ii <= mml; ii++ ) + { + i = m - ii; + f = s * e[i-1]; + b = c * e[i-1]; + + if ( webbur::r8_abs ( g ) <= webbur::r8_abs ( f ) ) + { + c = g / f; + r = std::sqrt ( c * c + 1.0 ); + e[i] = f * r; + s = 1.0 / r; + c = c * s; + } + else + { + s = f / g; + r = std::sqrt ( s * s + 1.0 ); + e[i] = g * r; + c = 1.0 / r; + s = s * c; + } + g = d[i] - p; + r = ( d[i-1] - g ) * s + 2.0 * c * b; + p = s * r; + d[i] = g + p; + g = c * r - b; + f = z[i]; + z[i] = s * z[i-1] + c * f; + z[i-1] = c * z[i-1] - s * f; + } + d[l-1] = d[l-1] - p; + e[l-1] = g; + e[m-1] = 0.0; + } + } +// +// Sorting. +// + for ( ii = 2; ii <= m; ii++ ) + { + i = ii - 1; + k = i; + p = d[i-1]; + + for ( j = ii; j <= n; j++ ) + { + if ( d[j-1] < p ) + { + k = j; + p = d[j-1]; + } + } + + if ( k != i ) + { + d[k-1] = d[i-1]; + d[i-1] = p; + p = z[i-1]; + z[i-1] = z[k-1]; + z[k-1] = p; + } + } + return; +} +//****************************************************************************80 + +void jacobi_compute ( int n, double alpha, double beta, double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_COMPUTE: Elhay-Kautsky method for Gauss-Jacobi quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) (1-X)**ALPHA * (1+X)**BETA * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) WEIGHT(I) * F ( XTAB(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 30 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Sylvan Elhay, Jaroslav Kautsky. +// C++ version by John Burkardt. +// +// Reference: +// +// Sylvan Elhay, Jaroslav Kautsky, +// Algorithm 655: IQPACK, FORTRAN Subroutines for the Weights of +// Interpolatory Quadrature, +// ACM Transactions on Mathematical Software, +// Volume 13, Number 4, December 1987, pages 399-415. +// +// Parameters: +// +// Input, int N, the order. +// +// Input, double ALPHA, BETA, the exponents of (1-X) and +// (1+X) in the quadrature rule. For simple Gauss-Legendre quadrature, +// set ALPHA = BETA = 0.0. -1.0 < ALPHA and -1.0 < BETA are required. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double abi; + double *bj; + int i; + double i_r8; + double zemu; +// +// Define the zero-th moment. +// + zemu = std::pow ( 2.0, alpha + beta + 1.0 ) + * webbur::r8_gamma ( alpha + 1.0 ) + * webbur::r8_gamma ( beta + 1.0 ) + / webbur::r8_gamma ( 2.0 + alpha + beta ); +// +// Define the Jacobi matrix. +// + bj = new double[n]; + + x[0] = ( beta - alpha ) / ( 2.0 + alpha + beta ); + + bj[0] = 4.0 * ( 1.0 + alpha ) * ( 1.0 + beta ) + / ( ( 3.0 + alpha + beta ) + * ( 2.0 + alpha + beta ) * ( 2.0 + alpha + beta ) ); + + for ( i = 1; i < n; i++ ) + { + i_r8 = ( double ) ( i + 1 ); + abi = 2.0 * i_r8 + alpha + beta; + x[i] = ( beta + alpha ) * ( beta - alpha ) / ( ( abi - 2.0 ) * abi ); + bj[i] = 4.0 * i_r8 * ( i_r8 + alpha ) * ( i_r8 + beta ) + * ( i_r8 + alpha + beta ) + / ( ( abi - 1.0 ) * ( abi + 1.0 ) * abi * abi ); + } + + for ( i = 0; i < n; i++ ) + { + bj[i] = std::sqrt ( bj[i] ); + } + + w[0] = std::sqrt ( zemu ); + + for ( i = 1; i < n; i++ ) + { + w[i] = 0.0; + } +// +// Diagonalize the Jacobi matrix. +// + webbur::imtqlx ( n, x, bj, w ); + + for ( i = 0; i < n; i++ ) + { + w[i] = w[i] * w[i]; + } + + delete [] bj; + + return; +} +//****************************************************************************80 + +void jacobi_compute_np ( int order, int np, double p[], double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_COMPUTE_NP computes a Jacobi quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) (1-X)^ALPHA * (1+X)^BETA * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// Thanks to Xu Xiang of Fudan University for pointing out that +// an earlier implementation of this routine was incorrect! +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameter values. +// P[0] = ALPHA, the exponent of (1-X) +// P[1] = BETA, the exponent of (1+X). +// -1.0 < ALPHA and -1.0 < BETA are required. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double alpha; + double beta; + + alpha = p[0]; + beta = p[1]; + + webbur::jacobi_compute ( order, alpha, beta, x, w ); + + return; +} +//****************************************************************************80 + +void jacobi_compute_points ( int order, double alpha, double beta, + double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_COMPUTE_POINTS computes Jacobi quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 14 October 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, double ALPHA, BETA, the exponents of the (1-X) and (1+X) factors. +// +// Output, double X[ORDER], the abscissas. +// +{ + double *w; + + w = new double[order]; + + webbur::jacobi_compute ( order, alpha, beta, x, w ); + + delete [] w; + + return; +} +//****************************************************************************80 + +void jacobi_compute_points_np ( int order, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_COMPUTE_POINTS_NP computes Jacobi quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameter values. +// P[0] = ALPHA, the exponent of (1-X) +// P[1] = BETA, the exponent of (1+X). +// -1.0 < ALPHA and -1.0 < BETA are required. +// +// Output, double X[ORDER], the abscissas. +// +{ + double alpha; + double beta; + + alpha = p[0]; + beta = p[1]; + + webbur::jacobi_compute_points ( order, alpha, beta, x ); + + return; +} +//****************************************************************************80 + +void jacobi_compute_weights ( int order, double alpha, double beta, + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_COMPUTE_WEIGHTS computes Jacobi quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 14 October 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, double ALPHA, BETA, the exponents of the (1-X) and (1+X) factors. +// +// Output, double W[ORDER], the weights. +// +{ + double *x; + + x = new double[order]; + + webbur::jacobi_compute ( order, alpha, beta, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void jacobi_compute_weights_np ( int order, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_COMPUTE_WEIGHTS_NP computes Jacobi quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameter values. +// P[0] = ALPHA, the exponent of (1-X) +// P[1] = BETA, the exponent of (1+X). +// -1.0 < ALPHA and -1.0 < BETA are required. +// +// Output, double W[ORDER], the weights. +// +{ + double alpha; + double beta; + + alpha = p[0]; + beta = p[1]; + + webbur::jacobi_compute_weights ( order, alpha, beta, w ); + + return; +} +//****************************************************************************80 + +double jacobi_integral ( int expon, double alpha, double beta ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_INTEGRAL integrates a monomial with Jacobi weight. +// +// Discussion: +// +// VALUE = Integral ( -1 <= X <= +1 ) x^EXPON (1-x)^ALPHA (1+x)^BETA dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 08 September 2007 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int EXPON, the exponent. +// +// Input, double ALPHA, the exponent of (1-X) in the weight factor. +// +// Input, double BETA, the exponent of (1+X) in the weight factor. +// +// Output, double JACOBI_INTEGRAL, the value of the integral. +// +{ + double arg1; + double arg2; + double arg3; + double arg4; + double c; + double s; + double value; + double value1; + double value2; + + c = ( double ) ( expon ); + + if ( ( expon % 2 ) == 0 ) + { + s = +1.0; + } + else + { + s = -1.0; + } + + arg1 = - alpha; + arg2 = 1.0 + c; + arg3 = 2.0 + beta + c; + arg4 = - 1.0; + + value1 = webbur::r8_hyper_2f1 ( arg1, arg2, arg3, arg4 ); + + arg1 = - beta; + arg2 = 1.0 + c; + arg3 = 2.0 + alpha + c; + arg4 = - 1.0; + + value2 = webbur::r8_hyper_2f1 ( arg1, arg2, arg3, arg4 ); + + value = webbur::r8_gamma ( 1.0 + c ) * ( + s * webbur::r8_gamma ( 1.0 + beta ) * value1 + / webbur::r8_gamma ( 2.0 + beta + c ) + + webbur::r8_gamma ( 1.0 + alpha ) * value2 + / webbur::r8_gamma ( 2.0 + alpha + c ) ); + + return value; +} +//****************************************************************************80 + +void jacobi_ss_compute ( int order, double alpha, double beta, double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_SS_COMPUTE computes a Jacobi quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) (1-X)^ALPHA * (1+X)^BETA * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// Thanks to Xu Xiang of Fudan University for pointing out that +// an earlier implementation of this routine was incorrect! +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 February 2008 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, double ALPHA, BETA, the exponents of (1-X) and +// (1+X) in the quadrature rule. For simple Legendre quadrature, +// set ALPHA = BETA = 0.0. -1.0 < ALPHA and -1.0 < BETA are required. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double an; + double *b; + double bn; + double *c; + double cc; + double delta; + double dp2; + int i; + double p1; + double prod; + double r1; + double r2; + double r3; + double temp; + double x0; + + if ( order < 1 ) + { + std::cerr << "\n"; + std::cerr << "JACOBI_SS_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of ORDER = " << order << "\n"; + std::exit ( 1 ); + } + + b = new double[order]; + c = new double[order]; +// +// Check ALPHA and BETA. +// + if ( alpha <= -1.0 ) + { + std::cerr << "\n"; + std::cerr << "JACOBI_SS_COMPUTE - Fatal error!\n"; + std::cerr << " -1.0 < ALPHA is required.\n"; + std::exit ( 1 ); + } + + if ( beta <= -1.0 ) + { + std::cerr << "\n"; + std::cerr << "JACOBI_SS_COMPUTE - Fatal error!\n"; + std::cerr << " -1.0 < BETA is required.\n"; + std::exit ( 1 ); + } +// +// Set the recursion coefficients. +// + for ( i = 1; i <= order; i++ ) + { + if ( alpha + beta == 0.0 || beta - alpha == 0.0 ) + { + b[i-1] = 0.0; + } + else + { + b[i-1] = ( alpha + beta ) * ( beta - alpha ) / + ( ( alpha + beta + ( double ) ( 2 * i ) ) + * ( alpha + beta + ( double ) ( 2 * i - 2 ) ) ); + } + + if ( i == 1 ) + { + c[i-1] = 0.0; + } + else + { + c[i-1] = 4.0 * ( double ) ( i - 1 ) + * ( alpha + ( double ) ( i - 1 ) ) + * ( beta + ( double ) ( i - 1 ) ) + * ( alpha + beta + ( double ) ( i - 1 ) ) / + ( ( alpha + beta + ( double ) ( 2 * i - 1 ) ) + * std::pow ( alpha + beta + ( double ) ( 2 * i - 2 ), 2 ) + * ( alpha + beta + ( double ) ( 2 * i - 3 ) ) ); + } + } + + delta = webbur::r8_gamma ( alpha + 1.0 ) + * webbur::r8_gamma ( beta + 1.0 ) + / webbur::r8_gamma ( alpha + beta + 2.0 ); + + prod = 1.0; + for ( i = 2; i <= order; i++ ) + { + prod = prod * c[i-1]; + } + cc = delta * std::pow ( 2.0, alpha + beta + 1.0 ) * prod; + + for ( i = 1; i <= order; i++ ) + { + if ( i == 1 ) + { + an = alpha / ( double ) ( order ); + bn = beta / ( double ) ( order ); + + r1 = ( 1.0 + alpha ) + * ( 2.78 / ( 4.0 + ( double ) ( order * order ) ) + + 0.768 * an / ( double ) ( order ) ); + + r2 = 1.0 + 1.48 * an + 0.96 * bn + + 0.452 * an * an + 0.83 * an * bn; + + x0 = ( r2 - r1 ) / r2; + } + else if ( i == 2 ) + { + r1 = ( 4.1 + alpha ) / + ( ( 1.0 + alpha ) * ( 1.0 + 0.156 * alpha ) ); + + r2 = 1.0 + 0.06 * ( ( double ) ( order ) - 8.0 ) * + ( 1.0 + 0.12 * alpha ) / ( double ) ( order ); + + r3 = 1.0 + 0.012 * beta * + ( 1.0 + 0.25 * r8_abs ( alpha ) ) / ( double ) ( order ); + + x0 = x0 - r1 * r2 * r3 * ( 1.0 - x0 ); + } + else if ( i == 3 ) + { + r1 = ( 1.67 + 0.28 * alpha ) / ( 1.0 + 0.37 * alpha ); + + r2 = 1.0 + 0.22 * ( ( double ) ( order ) - 8.0 ) + / ( double ) ( order ); + + r3 = 1.0 + 8.0 * beta / + ( ( 6.28 + beta ) * ( double ) ( order * order ) ); + + x0 = x0 - r1 * r2 * r3 * ( x[0] - x0 ); + } + else if ( i < order - 1 ) + { + x0 = 3.0 * x[i-2] - 3.0 * x[i-3] + x[i-4]; + } + else if ( i == order - 1 ) + { + r1 = ( 1.0 + 0.235 * beta ) / ( 0.766 + 0.119 * beta ); + + r2 = 1.0 / ( 1.0 + 0.639 + * ( ( double ) ( order ) - 4.0 ) + / ( 1.0 + 0.71 * ( ( double ) ( order ) - 4.0 ) ) ); + + r3 = 1.0 / ( 1.0 + 20.0 * alpha / ( ( 7.5 + alpha ) * + ( double ) ( order * order ) ) ); + + x0 = x0 + r1 * r2 * r3 * ( x0 - x[i-3] ); + } + else if ( i == order ) + { + r1 = ( 1.0 + 0.37 * beta ) / ( 1.67 + 0.28 * beta ); + + r2 = 1.0 / + ( 1.0 + 0.22 * ( ( double ) ( order ) - 8.0 ) + / ( double ) ( order ) ); + + r3 = 1.0 / ( 1.0 + 8.0 * alpha / + ( ( 6.28 + alpha ) * ( double ) ( order * order ) ) ); + + x0 = x0 + r1 * r2 * r3 * ( x0 - x[i-3] ); + } + + webbur::jacobi_ss_root ( &x0, order, alpha, beta, &dp2, &p1, b, c ); + + x[i-1] = x0; + w[i-1] = cc / ( dp2 * p1 ); + } +// +// Reverse the order of the values. +// + for ( i = 1; i <= order/2; i++ ) + { + temp = x[i-1]; + x[i-1] = x[order-i]; + x[order-i] = temp; + } + + for ( i = 1; i <=order/2; i++ ) + { + temp = w[i-1]; + w[i-1] = w[order-i]; + w[order-i] = temp; + } + + delete [] b; + delete [] c; + + return; +} +//****************************************************************************80 + +void jacobi_ss_recur ( double *p2, double *dp2, double *p1, double x, int order, + double alpha, double beta, double b[], double c[] ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_SS_RECUR evaluates a Jacobi polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 February 2008 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Output, double *P2, the value of J(ORDER)(X). +// +// Output, double *DP2, the value of J'(ORDER)(X). +// +// Output, double *P1, the value of J(ORDER-1)(X). +// +// Input, double X, the point at which polynomials are evaluated. +// +// Input, int ORDER, the order of the polynomial. +// +// Input, double ALPHA, BETA, the exponents of (1-X) and +// (1+X) in the quadrature rule. +// +// Input, double B[ORDER], C[ORDER], the recursion coefficients. +// +{ + double dp0; + double dp1; + int i; + double p0; + + *p1 = 1.0; + dp1 = 0.0; + + *p2 = x + ( alpha - beta ) / ( alpha + beta + 2.0 ); + *dp2 = 1.0; + + for ( i = 2; i <= order; i++ ) + { + p0 = *p1; + dp0 = dp1; + + *p1 = *p2; + dp1 = *dp2; + + *p2 = ( x - b[i-1] ) * ( *p1 ) - c[i-1] * p0; + *dp2 = ( x - b[i-1] ) * dp1 + ( *p1 ) - c[i-1] * dp0; + } + return; +} +//****************************************************************************80 + +void jacobi_ss_root ( double *x, int order, double alpha, double beta, + double *dp2, double *p1, double b[], double c[] ) + +//****************************************************************************80 +// +// Purpose: +// +// JACOBI_SS_ROOT improves an approximate root of a Jacobi polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 February 2008 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input/output, double *X, the approximate root, which +// should be improved on output. +// +// Input, int ORDER, the order of the polynomial. +// +// Input, double ALPHA, BETA, the exponents of (1-X) and +// (1+X) in the quadrature rule. +// +// Output, double *DP2, the value of J'(ORDER)(X). +// +// Output, double *P1, the value of J(ORDER-1)(X). +// +// Input, double B[ORDER], C[ORDER], the recursion coefficients. +// +{ + double d; + double eps; + double p2; + int step; + int step_max = 10; + + eps = webbur::r8_epsilon ( ); + + for ( step = 1; step <= step_max; step++ ) + { + webbur::jacobi_ss_recur ( &p2, dp2, p1, *x, order, alpha, beta, b, c ); + + d = p2 / ( *dp2 ); + *x = *x - d; + + if ( webbur::r8_abs ( d ) <= eps * ( webbur::r8_abs ( *x ) + 1.0 ) ) + { + return; + } + } + return; +} +//****************************************************************************80 + +void laguerre_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_COMPUTE: Laguerre quadrature rule by the Elhay-Kautsky method. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Sylvan Elhay, Jaroslav Kautsky. +// C++ version by John Burkardt. +// +// Reference: +// +// Sylvan Elhay, Jaroslav Kautsky, +// Algorithm 655: IQPACK, FORTRAN Subroutines for the Weights of +// Interpolatory Quadrature, +// ACM Transactions on Mathematical Software, +// Volume 13, Number 4, December 1987, pages 399-415. +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double *bj; + int i; + double zemu; +// +// Define the zero-th moment. +// + zemu = 1.0; +// +// Define the Jacobi matrix. +// + bj = new double[n]; + + for ( i = 0; i < n; i++ ) + { + bj[i] = ( double ) ( i + 1 ); + } + + for ( i = 0; i < n; i++ ) + { + x[i] = ( double ) ( 2 * i + 1 ); + } + + w[0] = std::sqrt ( zemu ); + + for ( i = 1; i < n; i++ ) + { + w[i] = 0.0; + } +// +// Diagonalize the Jacobi matrix. +// + webbur::imtqlx ( n, x, bj, w ); + + for ( i = 0; i < n; i++ ) + { + w[i] = w[i] * w[i]; + } + + delete [] bj; + + return; +} +//****************************************************************************80 + +void laguerre_compute_np ( int order, int np, double p[], double x[], + double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_COMPUTE_NP computes a Laguerre quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( 0 <= X < +oo ) exp ( - X ) * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// The integral: +// +// Integral ( A <= X < +oo ) F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * exp ( X(I) ) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + webbur::laguerre_compute ( order, x, w ); + + return; +} +//****************************************************************************80 + +void laguerre_compute_points ( int order, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_COMPUTE_POINTS computes Laguerre quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Output, double X[ORDER], the abscissas. +// +{ + double *w; + + w = new double[order]; + + webbur::laguerre_compute ( order, x, w ); + + delete [] w; + + return; +} +//****************************************************************************80 + +void laguerre_compute_points_np ( int order, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_COMPUTE_POINTS_NP computes Laguerre quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[ORDER], the abscissas. +// +{ + webbur::laguerre_compute_points ( order, x ); + + return; +} +//****************************************************************************80 + +void laguerre_compute_weights ( int order, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_COMPUTE_WEIGHTS computes Laguerre quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Output, double W[ORDER], the weights. +// +{ + double *x; + + x = new double[order]; + + webbur::laguerre_compute ( order, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void laguerre_compute_weights_np ( int order, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_COMPUTE_WEIGHTS_NP computes Laguerre quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int ORDER, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[ORDER], the weights. +// +{ + webbur::laguerre_compute_weights ( order, w ); + + return; +} +//****************************************************************************80 + +double laguerre_integral ( int expon ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_INTEGRAL evaluates a monomial Laguerre integral. +// +// Discussion: +// +// The integral: +// +// integral ( 0 <= x < +oo ) x^n * exp ( -x ) dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int EXPON, the exponent. +// 0 <= EXPON. +// +// Output, double EXACT, the value of the integral. +// +{ + double exact; + + exact = webbur::r8_factorial ( expon ); + + return exact; +} +//****************************************************************************80 + +void laguerre_lookup ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_LOOKUP looks up abscissas and weights for Laguerre quadrature. +// +// Discussion: +// +// The abscissas are the zeroes of the Laguerre polynomial L(N)(X). +// +// The integral: +// +// Integral ( 0 <= X < +oo ) exp ( -X ) * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= N ) W(I) * f ( X(I) ) +// +// The integral: +// +// Integral ( 0 <= X < +oo ) F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= N ) W(I) * exp ( X(I) ) * f ( X(I) ) +// +// Mathematica can numerically estimate the abscissas for the +// n-th order polynomial to p digits of precision by the command: +// +// NSolve [ LaguerreL[n,x] == 0, x, p ] +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 April 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Vladimir Krylov, +// Approximate Calculation of Integrals, +// Dover, 2006, +// ISBN: 0486445798, +// LC: QA311.K713. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Stephen Wolfram, +// The Mathematica Book, +// Fourth Edition, +// Cambridge University Press, 1999, +// ISBN: 0-521-64314-7, +// LC: QA76.95.W65. +// +// Daniel Zwillinger, editor, +// CRC Standard Mathematical Tables and Formulae, +// 30th Edition, +// CRC Press, 1996, +// ISBN: 0-8493-2479-3. +// +// Parameters: +// +// Input, int N, the order. +// N must be between 1 and 20. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::laguerre_lookup_points ( n, x ); + + webbur::laguerre_lookup_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void laguerre_lookup_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_LOOKUP_POINTS looks up abscissas for Laguerre quadrature. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 April 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Vladimir Krylov, +// Approximate Calculation of Integrals, +// Dover, 2006, +// ISBN: 0486445798, +// LC: QA311.K713. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Stephen Wolfram, +// The Mathematica Book, +// Fourth Edition, +// Cambridge University Press, 1999, +// ISBN: 0-521-64314-7, +// LC: QA76.95.W65. +// +// Daniel Zwillinger, editor, +// CRC Standard Mathematical Tables and Formulae, +// 30th Edition, +// CRC Press, 1996, +// ISBN: 0-8493-2479-3. +// +// Parameters: +// +// Input, int N, the order. +// N must be between 1 and 20. +// +// Output, double X[N], the abscissas. +// +{ + if ( n == 1 ) + { + x[0] = 1.00000000000000000000000000000E+00; + } + else if ( n == 2 ) + { + x[0] = 0.585786437626904951198311275790E+00; + x[1] = 3.41421356237309504880168872421E+00; + } + else if ( n == 3 ) + { + x[0] = 0.415774556783479083311533873128E+00; + x[1] = 2.29428036027904171982205036136E+00; + x[2] = 6.28994508293747919686641576551E+00; + } + else if ( n == 4 ) + { + x[0] = 0.322547689619392311800361459104E+00; + x[1] = 1.74576110115834657568681671252E+00; + x[2] = 4.53662029692112798327928538496E+00; + x[3] = 9.39507091230113312923353644342E+00; + } + else if ( n == 5 ) + { + x[0] = 0.263560319718140910203061943361E+00; + x[1] = 1.41340305910651679221840798019E+00; + x[2] = 3.59642577104072208122318658878E+00; + x[3] = 7.08581000585883755692212418111E+00; + x[4] = 12.6408008442757826594332193066E+00; + } + else if ( n == 6 ) + { + x[0] = 0.222846604179260689464354826787E+00; + x[1] = 1.18893210167262303074315092194E+00; + x[2] = 2.99273632605931407769132528451E+00; + x[3] = 5.77514356910451050183983036943E+00; + x[4] = 9.83746741838258991771554702994E+00; + x[5] = 15.9828739806017017825457915674E+00; + } + else if ( n == 7 ) + { + x[0] = 0.193043676560362413838247885004E+00; + x[1] = 1.02666489533919195034519944317E+00; + x[2] = 2.56787674495074620690778622666E+00; + x[3] = 4.90035308452648456810171437810E+00; + x[4] = 8.18215344456286079108182755123E+00; + x[5] = 12.7341802917978137580126424582E+00; + x[6] = 19.3957278622625403117125820576E+00; + } + else if ( n == 8 ) + { + x[0] = 0.170279632305100999788861856608E+00; + x[1] = 0.903701776799379912186020223555E+00; + x[2] = 2.25108662986613068930711836697E+00; + x[3] = 4.26670017028765879364942182690E+00; + x[4] = 7.04590540239346569727932548212E+00; + x[5] = 10.7585160101809952240599567880E+00; + x[6] = 15.7406786412780045780287611584E+00; + x[7] = 22.8631317368892641057005342974E+00; + } + else if ( n == 9 ) + { + x[0] = 0.152322227731808247428107073127E+00; + x[1] = 0.807220022742255847741419210952E+00; + x[2] = 2.00513515561934712298303324701E+00; + x[3] = 3.78347397333123299167540609364E+00; + x[4] = 6.20495677787661260697353521006E+00; + x[5] = 9.37298525168757620180971073215E+00; + x[6] = 13.4662369110920935710978818397E+00; + x[7] = 18.8335977889916966141498992996E+00; + x[8] = 26.3740718909273767961410072937E+00; + } + else if ( n == 10 ) + { + x[0] = 0.137793470540492430830772505653E+00; + x[1] = 0.729454549503170498160373121676E+00; + x[2] = 1.80834290174031604823292007575E+00; + x[3] = 3.40143369785489951448253222141E+00; + x[4] = 5.55249614006380363241755848687E+00; + x[5] = 8.33015274676449670023876719727E+00; + x[6] = 11.8437858379000655649185389191E+00; + x[7] = 16.2792578313781020995326539358E+00; + x[8] = 21.9965858119807619512770901956E+00; + x[9] = 29.9206970122738915599087933408E+00; + } + else if ( n == 11 ) + { + x[0] = 0.125796442187967522675794577516E+00; + x[1] = 0.665418255839227841678127839420E+00; + x[2] = 1.64715054587216930958700321365E+00; + x[3] = 3.09113814303525495330195934259E+00; + x[4] = 5.02928440157983321236999508366E+00; + x[5] = 7.50988786380661681941099714450E+00; + x[6] = 10.6059509995469677805559216457E+00; + x[7] = 14.4316137580641855353200450349E+00; + x[8] = 19.1788574032146786478174853989E+00; + x[9] = 25.2177093396775611040909447797E+00; + x[10] = 33.4971928471755372731917259395E+00; + } + else if ( n == 12 ) + { + x[0] = 0.115722117358020675267196428240E+00; + x[1] = 0.611757484515130665391630053042E+00; + x[2] = 1.51261026977641878678173792687E+00; + x[3] = 2.83375133774350722862747177657E+00; + x[4] = 4.59922763941834848460572922485E+00; + x[5] = 6.84452545311517734775433041849E+00; + x[6] = 9.62131684245686704391238234923E+00; + x[7] = 13.0060549933063477203460524294E+00; + x[8] = 17.1168551874622557281840528008E+00; + x[9] = 22.1510903793970056699218950837E+00; + x[10] = 28.4879672509840003125686072325E+00; + x[11] = 37.0991210444669203366389142764E+00; + } + else if ( n == 13 ) + { + x[0] = 0.107142388472252310648493376977E+00; + x[1] = 0.566131899040401853406036347177E+00; + x[2] = 1.39856433645101971792750259921E+00; + x[3] = 2.61659710840641129808364008472E+00; + x[4] = 4.23884592901703327937303389926E+00; + x[5] = 6.29225627114007378039376523025E+00; + x[6] = 8.81500194118697804733348868036E+00; + x[7] = 11.8614035888112425762212021880E+00; + x[8] = 15.5107620377037527818478532958E+00; + x[9] = 19.8846356638802283332036594634E+00; + x[10] = 25.1852638646777580842970297823E+00; + x[11] = 31.8003863019472683713663283526E+00; + x[12] = 40.7230086692655795658979667001E+00; + } + else if ( n == 14 ) + { + x[0] = 0.0997475070325975745736829452514E+00; + x[1] = 0.526857648851902896404583451502E+00; + x[2] = 1.30062912125149648170842022116E+00; + x[3] = 2.43080107873084463616999751038E+00; + x[4] = 3.93210282229321888213134366778E+00; + x[5] = 5.82553621830170841933899983898E+00; + x[6] = 8.14024014156514503005978046052E+00; + x[7] = 10.9164995073660188408130510904E+00; + x[8] = 14.2108050111612886831059780825E+00; + x[9] = 18.1048922202180984125546272083E+00; + x[10] = 22.7233816282696248232280886985E+00; + x[11] = 28.2729817232482056954158923218E+00; + x[12] = 35.1494436605924265828643121364E+00; + x[13] = 44.3660817111174230416312423666E+00; + } + else if ( n == 15 ) + { + x[0] = 0.0933078120172818047629030383672E+00; + x[1] = 0.492691740301883908960101791412E+00; + x[2] = 1.21559541207094946372992716488E+00; + x[3] = 2.26994952620374320247421741375E+00; + x[4] = 3.66762272175143727724905959436E+00; + x[5] = 5.42533662741355316534358132596E+00; + x[6] = 7.56591622661306786049739555812E+00; + x[7] = 10.1202285680191127347927394568E+00; + x[8] = 13.1302824821757235640991204176E+00; + x[9] = 16.6544077083299578225202408430E+00; + x[10] = 20.7764788994487667729157175676E+00; + x[11] = 25.6238942267287801445868285977E+00; + x[12] = 31.4075191697539385152432196202E+00; + x[13] = 38.5306833064860094162515167595E+00; + x[14] = 48.0260855726857943465734308508E+00; + } + else if ( n == 16 ) + { + x[0] = 0.0876494104789278403601980973401E+00; + x[1] = 0.462696328915080831880838260664E+00; + x[2] = 1.14105777483122685687794501811E+00; + x[3] = 2.12928364509838061632615907066E+00; + x[4] = 3.43708663389320664523510701675E+00; + x[5] = 5.07801861454976791292305830814E+00; + x[6] = 7.07033853504823413039598947080E+00; + x[7] = 9.43831433639193878394724672911E+00; + x[8] = 12.2142233688661587369391246088E+00; + x[9] = 15.4415273687816170767647741622E+00; + x[10] = 19.1801568567531348546631409497E+00; + x[11] = 23.5159056939919085318231872752E+00; + x[12] = 28.5787297428821403675206137099E+00; + x[13] = 34.5833987022866258145276871778E+00; + x[14] = 41.9404526476883326354722330252E+00; + x[15] = 51.7011603395433183643426971197E+00; + } + else if ( n == 17 ) + { + x[0] = 0.0826382147089476690543986151980E+00; + x[1] = 0.436150323558710436375959029847E+00; + x[2] = 1.07517657751142857732980316755E+00; + x[3] = 2.00519353164923224070293371933E+00; + x[4] = 3.23425612404744376157380120696E+00; + x[5] = 4.77351351370019726480932076262E+00; + x[6] = 6.63782920536495266541643929703E+00; + x[7] = 8.84668551116980005369470571184E+00; + x[8] = 11.4255293193733525869726151469E+00; + x[9] = 14.4078230374813180021982874959E+00; + x[10] = 17.8382847307011409290658752412E+00; + x[11] = 21.7782682577222653261749080522E+00; + x[12] = 26.3153178112487997766149598369E+00; + x[13] = 31.5817716804567331343908517497E+00; + x[14] = 37.7960938374771007286092846663E+00; + x[15] = 45.3757165339889661829258363215E+00; + x[16] = 55.3897517898396106640900199790E+00; + } + else if ( n == 18 ) + { + x[0] = 0.0781691666697054712986747615334E+00; + x[1] = 0.412490085259129291039101536536E+00; + x[2] = 1.01652017962353968919093686187E+00; + x[3] = 1.89488850996976091426727831954E+00; + x[4] = 3.05435311320265975115241130719E+00; + x[5] = 4.50420553888989282633795571455E+00; + x[6] = 6.25672507394911145274209116326E+00; + x[7] = 8.32782515660563002170470261564E+00; + x[8] = 10.7379900477576093352179033397E+00; + x[9] = 13.5136562075550898190863812108E+00; + x[10] = 16.6893062819301059378183984163E+00; + x[11] = 20.3107676262677428561313764553E+00; + x[12] = 24.4406813592837027656442257980E+00; + x[13] = 29.1682086625796161312980677805E+00; + x[14] = 34.6279270656601721454012429438E+00; + x[15] = 41.0418167728087581392948614284E+00; + x[16] = 48.8339227160865227486586093290E+00; + x[17] = 59.0905464359012507037157810181E+00; + } + else if ( n == 19 ) + { + x[0] = 0.0741587837572050877131369916024E+00; + x[1] = 0.391268613319994607337648350299E+00; + x[2] = 0.963957343997958058624878377130E+00; + x[3] = 1.79617558206832812557725825252E+00; + x[4] = 2.89365138187378399116494713237E+00; + x[5] = 4.26421553962776647436040018167E+00; + x[6] = 5.91814156164404855815360191408E+00; + x[7] = 7.86861891533473373105668358176E+00; + x[8] = 10.1324237168152659251627415800E+00; + x[9] = 12.7308814638423980045092979656E+00; + x[10] = 15.6912783398358885454136069861E+00; + x[11] = 19.0489932098235501532136429732E+00; + x[12] = 22.8508497608294829323930586693E+00; + x[13] = 27.1606693274114488789963947149E+00; + x[14] = 32.0691222518622423224362865906E+00; + x[15] = 37.7129058012196494770647508283E+00; + x[16] = 44.3173627958314961196067736013E+00; + x[17] = 52.3129024574043831658644222420E+00; + x[18] = 62.8024231535003758413504690673E+00; + } + else if ( n == 20 ) + { + x[0] = 0.0705398896919887533666890045842E+00; + x[1] = 0.372126818001611443794241388761E+00; + x[2] = 0.916582102483273564667716277074E+00; + x[3] = 1.70730653102834388068768966741E+00; + x[4] = 2.74919925530943212964503046049E+00; + x[5] = 4.04892531385088692237495336913E+00; + x[6] = 5.61517497086161651410453988565E+00; + x[7] = 7.45901745367106330976886021837E+00; + x[8] = 9.59439286958109677247367273428E+00; + x[9] = 12.0388025469643163096234092989E+00; + x[10] = 14.8142934426307399785126797100E+00; + x[11] = 17.9488955205193760173657909926E+00; + x[12] = 21.4787882402850109757351703696E+00; + x[13] = 25.4517027931869055035186774846E+00; + x[14] = 29.9325546317006120067136561352E+00; + x[15] = 35.0134342404790000062849359067E+00; + x[16] = 40.8330570567285710620295677078E+00; + x[17] = 47.6199940473465021399416271529E+00; + x[18] = 55.8107957500638988907507734445E+00; + x[19] = 66.5244165256157538186403187915E+00; + } + else + { + std::cerr << "\n"; + std::cerr << "LAGUERRE_LOOKUP_POINTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::cerr << " Legal values are 1 through 20.\n"; + std::exit ( 1 ); + } + + return; +} +//****************************************************************************80 + +void laguerre_lookup_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_LOOKUP_WEIGHTS looks up weights for Laguerre quadrature. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 April 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Vladimir Krylov, +// Approximate Calculation of Integrals, +// Dover, 2006, +// ISBN: 0486445798, +// LC: QA311.K713. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Stephen Wolfram, +// The Mathematica Book, +// Fourth Edition, +// Cambridge University Press, 1999, +// ISBN: 0-521-64314-7, +// LC: QA76.95.W65. +// +// Daniel Zwillinger, editor, +// CRC Standard Mathematical Tables and Formulae, +// 30th Edition, +// CRC Press, 1996, +// ISBN: 0-8493-2479-3. +// +// Parameters: +// +// Input, int N, the order. +// N must be between 1 and 20. +// +// Output, double W[N], the weights. +// +{ + if ( n == 1 ) + { + w[0] = 1.00000000000000000000000000000E+00; + } + else if ( n == 2 ) + { + w[0] = 0.85355339059327376220042218105E+00; + w[1] = 0.146446609406726237799577818948E+00; + } + else if ( n == 3 ) + { + w[0] = 0.71109300992917301544959019114E+00; + w[1] = 0.27851773356924084880144488846E+00; + w[2] = 0.010389256501586135748964920401E+00; + } + else if ( n == 4 ) + { + w[0] = 0.60315410434163360163596602382E+00; + w[1] = 0.35741869243779968664149201746E+00; + w[2] = 0.03888790851500538427243816816E+00; + w[3] = 0.0005392947055613274501037905676E+00; + } + else if ( n == 5 ) + { + w[0] = 0.52175561058280865247586092879E+00; + w[1] = 0.3986668110831759274541333481E+00; + w[2] = 0.0759424496817075953876533114E+00; + w[3] = 0.00361175867992204845446126257E+00; + w[4] = 0.00002336997238577622789114908455E+00; + } + else if ( n == 6 ) + { + w[0] = 0.45896467394996359356828487771E+00; + w[1] = 0.4170008307721209941133775662E+00; + w[2] = 0.1133733820740449757387061851E+00; + w[3] = 0.01039919745314907489891330285E+00; + w[4] = 0.000261017202814932059479242860E+00; + w[5] = 8.98547906429621238825292053E-07; + } + else if ( n == 7 ) + { + w[0] = 0.40931895170127390213043288002E+00; + w[1] = 0.4218312778617197799292810054E+00; + w[2] = 0.1471263486575052783953741846E+00; + w[3] = 0.0206335144687169398657056150E+00; + w[4] = 0.00107401014328074552213195963E+00; + w[5] = 0.0000158654643485642012687326223E+00; + w[6] = 3.17031547899558056227132215E-08; + } + else if ( n == 8 ) + { + w[0] = 0.36918858934163752992058283938E+00; + w[1] = 0.4187867808143429560769785813E+00; + w[2] = 0.175794986637171805699659867E+00; + w[3] = 0.033343492261215651522132535E+00; + w[4] = 0.0027945362352256725249389241E+00; + w[5] = 0.00009076508773358213104238501E+00; + w[6] = 8.4857467162725315448680183E-07; + w[7] = 1.04800117487151038161508854E-09; + } + else if ( n == 9 ) + { + w[0] = 0.336126421797962519673467717606E+00; + w[1] = 0.411213980423984387309146942793E+00; + w[2] = 0.199287525370885580860575607212E+00; + w[3] = 0.0474605627656515992621163600479E+00; + w[4] = 0.00559962661079458317700419900556E+00; + w[5] = 0.000305249767093210566305412824291E+00; + w[6] = 6.59212302607535239225572284875E-06; + w[7] = 4.1107693303495484429024104033E-08; + w[8] = 3.29087403035070757646681380323E-11; + } + else if ( n == 10 ) + { + w[0] = 0.30844111576502014154747083468E+00; + w[1] = 0.4011199291552735515157803099E+00; + w[2] = 0.218068287611809421588648523E+00; + w[3] = 0.062087456098677747392902129E+00; + w[4] = 0.009501516975181100553839072E+00; + w[5] = 0.0007530083885875387754559644E+00; + w[6] = 0.00002825923349599565567422564E+00; + w[7] = 4.249313984962686372586577E-07; + w[8] = 1.839564823979630780921535E-09; + w[9] = 9.911827219609008558377547E-13; + } + else if ( n == 11 ) + { + w[0] = 0.28493321289420060505605102472E+00; + w[1] = 0.3897208895278493779375535080E+00; + w[2] = 0.232781831848991333940223796E+00; + w[3] = 0.076564453546196686400854179E+00; + w[4] = 0.014393282767350695091863919E+00; + w[5] = 0.001518880846484873069847776E+00; + w[6] = 0.0000851312243547192259720424E+00; + w[7] = 2.29240387957450407857683E-06; + w[8] = 2.48635370276779587373391E-08; + w[9] = 7.71262693369132047028153E-11; + w[10] = 2.883775868323623861597778E-14; + } + else if ( n == 12 ) + { + w[0] = 0.26473137105544319034973889206E+00; + w[1] = 0.3777592758731379820244905567E+00; + w[2] = 0.244082011319877564254870818E+00; + w[3] = 0.09044922221168093072750549E+00; + w[4] = 0.02010238115463409652266129E+00; + w[5] = 0.002663973541865315881054158E+00; + w[6] = 0.000203231592662999392121433E+00; + w[7] = 8.3650558568197987453363E-06; + w[8] = 1.66849387654091026116990E-07; + w[9] = 1.34239103051500414552392E-09; + w[10] = 3.06160163503502078142408E-12; + w[11] = 8.148077467426241682473119E-16; + } + else if ( n == 13 ) + { + w[0] = 0.24718870842996262134624918596E+00; + w[1] = 0.3656888229005219453067175309E+00; + w[2] = 0.252562420057658502356824289E+00; + w[3] = 0.10347075802418370511421863E+00; + w[4] = 0.02643275441556161577815877E+00; + w[5] = 0.00422039604025475276555209E+00; + w[6] = 0.000411881770472734774892473E+00; + w[7] = 0.0000235154739815532386882897E+00; + w[8] = 7.3173116202490991040105E-07; + w[9] = 1.10884162570398067979151E-08; + w[10] = 6.7708266922058988406462E-11; + w[11] = 1.15997995990507606094507E-13; + w[12] = 2.245093203892758415991872E-17; + } + else if ( n == 14 ) + { + w[0] = 0.23181557714486497784077486110E+00; + w[1] = 0.3537846915975431518023313013E+00; + w[2] = 0.258734610245428085987320561E+00; + w[3] = 0.11548289355692321008730499E+00; + w[4] = 0.03319209215933736003874996E+00; + w[5] = 0.00619286943700661021678786E+00; + w[6] = 0.00073989037786738594242589E+00; + w[7] = 0.000054907194668416983785733E+00; + w[8] = 2.4095857640853774967578E-06; + w[9] = 5.801543981676495180886E-08; + w[10] = 6.819314692484974119616E-10; + w[11] = 3.2212077518948479398089E-12; + w[12] = 4.2213524405165873515980E-15; + w[13] = 6.05237502228918880839871E-19; + } + else if ( n == 15 ) + { + w[0] = 0.21823488594008688985641323645E+00; + w[1] = 0.3422101779228833296389489568E+00; + w[2] = 0.263027577941680097414812275E+00; + w[3] = 0.12642581810593053584303055E+00; + w[4] = 0.04020686492100091484158548E+00; + w[5] = 0.00856387780361183836391576E+00; + w[6] = 0.00121243614721425207621921E+00; + w[7] = 0.00011167439234425194199258E+00; + w[8] = 6.459926762022900924653E-06; + w[9] = 2.226316907096272630332E-07; + w[10] = 4.227430384979365007351E-09; + w[11] = 3.921897267041089290385E-11; + w[12] = 1.4565152640731264063327E-13; + w[13] = 1.4830270511133013354616E-16; + w[14] = 1.60059490621113323104998E-20; + } + else if ( n == 16 ) + { + w[0] = 0.20615171495780099433427363674E+00; + w[1] = 0.3310578549508841659929830987E+00; + w[2] = 0.265795777644214152599502021E+00; + w[3] = 0.13629693429637753997554751E+00; + w[4] = 0.0473289286941252189780623E+00; + w[5] = 0.0112999000803394532312490E+00; + w[6] = 0.0018490709435263108642918E+00; + w[7] = 0.00020427191530827846012602E+00; + w[8] = 0.00001484458687398129877135E+00; + w[9] = 6.828319330871199564396E-07; + w[10] = 1.881024841079673213882E-08; + w[11] = 2.862350242973881619631E-10; + w[12] = 2.127079033224102967390E-12; + w[13] = 6.297967002517867787174E-15; + w[14] = 5.050473700035512820402E-18; + w[15] = 4.1614623703728551904265E-22; + } + else if ( n == 17 ) + { + w[0] = 0.19533220525177083214592729770E+00; + w[1] = 0.3203753572745402813366256320E+00; + w[2] = 0.267329726357171097238809604E+00; + w[3] = 0.14512985435875862540742645E+00; + w[4] = 0.0544369432453384577793806E+00; + w[5] = 0.0143572977660618672917767E+00; + w[6] = 0.0026628247355727725684324E+00; + w[7] = 0.0003436797271562999206118E+00; + w[8] = 0.00003027551783782870109437E+00; + w[9] = 1.768515053231676895381E-06; + w[10] = 6.57627288681043332199E-08; + w[11] = 1.469730932159546790344E-09; + w[12] = 1.81691036255544979555E-11; + w[13] = 1.095401388928687402976E-13; + w[14] = 2.617373882223370421551E-16; + w[15] = 1.6729356931461546908502E-19; + w[16] = 1.06562631627404278815253E-23; + } + else if ( n == 18 ) + { + w[0] = 0.18558860314691880562333775228E+00; + w[1] = 0.3101817663702252936495975957E+00; + w[2] = 0.267866567148536354820854395E+00; + w[3] = 0.15297974746807490655384308E+00; + w[4] = 0.0614349178609616527076780E+00; + w[5] = 0.0176872130807729312772600E+00; + w[6] = 0.0036601797677599177980266E+00; + w[7] = 0.0005406227870077353231284E+00; + w[8] = 0.0000561696505121423113818E+00; + w[9] = 4.01530788370115755859E-06; + w[10] = 1.91466985667567497969E-07; + w[11] = 5.8360952686315941292E-09; + w[12] = 1.07171126695539012773E-10; + w[13] = 1.08909871388883385562E-12; + w[14] = 5.38666474837830887608E-15; + w[15] = 1.049865978035703408779E-17; + w[16] = 5.405398451631053643566E-21; + w[17] = 2.6916532692010286270838E-25; + } + else if ( n == 19 ) + { + w[0] = 0.17676847491591250225103547981E+00; + w[1] = 0.3004781436072543794821568077E+00; + w[2] = 0.267599547038175030772695441E+00; + w[3] = 0.15991337213558021678551215E+00; + w[4] = 0.0682493799761491134552355E+00; + w[5] = 0.0212393076065443249244062E+00; + w[6] = 0.0048416273511483959672501E+00; + w[7] = 0.0008049127473813667665946E+00; + w[8] = 0.0000965247209315350170843E+00; + w[9] = 8.20730525805103054409E-06; + w[10] = 4.8305667247307725394E-07; + w[11] = 1.90499136112328569994E-08; + w[12] = 4.8166846309280615577E-10; + w[13] = 7.3482588395511443768E-12; + w[14] = 6.2022753875726163989E-14; + w[15] = 2.54143084301542272372E-16; + w[16] = 4.07886129682571235007E-19; + w[17] = 1.707750187593837061004E-22; + w[18] = 6.715064649908189959990E-27; + } + else if ( n == 20 ) + { + w[0] = 0.168746801851113862149223899689E+00; + w[1] = 0.291254362006068281716795323812E+00; + w[2] = 0.266686102867001288549520868998E+00; + w[3] = 0.166002453269506840031469127816E+00; + w[4] = 0.0748260646687923705400624639615E+00; + w[5] = 0.0249644173092832210728227383234E+00; + w[6] = 0.00620255084457223684744754785395E+00; + w[7] = 0.00114496238647690824203955356969E+00; + w[8] = 0.000155741773027811974779809513214E+00; + w[9] = 0.0000154014408652249156893806714048E+00; + w[10] = 1.08648636651798235147970004439E-06; + w[11] = 5.33012090955671475092780244305E-08; + w[12] = 1.7579811790505820035778763784E-09; + w[13] = 3.72550240251232087262924585338E-11; + w[14] = 4.76752925157819052449488071613E-13; + w[15] = 3.37284424336243841236506064991E-15; + w[16] = 1.15501433950039883096396247181E-17; + w[17] = 1.53952214058234355346383319667E-20; + w[18] = 5.28644272556915782880273587683E-24; + w[19] = 1.65645661249902329590781908529E-28; + } + else + { + std::cerr << "\n"; + std::cerr << "LAGUERRE_LOOKUP_WEIGHTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::cerr << " Legal values are 1 through 20.\n"; + std::exit ( 1 ); + } + + return; +} +//****************************************************************************80 + +void laguerre_ss_compute ( int order, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_SS_COMPUTE computes a Laguerre quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( 0 <= X < +oo ) exp ( - X ) * F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * F ( X(I) ) +// +// The integral: +// +// Integral ( A <= X < +oo ) F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= ORDER ) W(I) * exp ( X(I) ) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int ORDER, the order. +// 1 <= ORDER. +// +// Output, double X[ORDER], the abscissas. +// +// Output, double W[ORDER], the weights. +// +{ + double *b; + double *c; + double cc; + double dp2; + int i; + int j; + double p1; + double prod; + double r1; + double x0; + + if ( order < 1 ) + { + std::cerr << "\n"; + std::cerr << "LAGUERRE_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of ORDER = " << order << "\n"; + std::exit ( 1 ); + } + + b = new double[order]; + c = new double[order]; +// +// Set the recursion coefficients. +// + for ( i = 0; i < order; i++ ) + { + b[i] = ( double ) ( 2 * i + 1 ); + } + + for ( i = 0; i < order; i++ ) + { + c[i] = ( double ) ( i * i ); + } + prod = 1.0; + for ( i = 1; i < order; i++ ) + { + prod = prod * c[i]; + } + cc = prod; + + for ( i = 0; i < order; i++ ) + { +// +// Compute an estimate for the root. +// + if ( i == 0 ) + { + x0 = 3.0 / ( 1.0 + 2.4 * ( double ) ( order ) ); + } + else if ( i == 1 ) + { + x0 = x0 + 15.0 / ( 1.0 + 2.5 * ( double ) ( order ) ); + } + else + { + r1 = ( 1.0 + 2.55 * ( double ) ( i - 1 ) ) + / ( 1.9 * ( double ) ( i - 1 ) ); + + x0 = x0 + r1 * ( x0 - x[i-2] ); + } +// +// Use iteration to find the root. +// + webbur::laguerre_ss_root ( &x0, order, &dp2, &p1, b, c ); +// +// Set the abscissa and weight. +// + x[i] = x0; +// +// Because of the huge values involved, this calculation breaks down +// for ORDER = 127. +// +// It was originally w[i] = ( cc / dp2 ) / p1, which breaks down sooner. +// + w[i] = ( 1.0 / dp2 ); + for ( j = 2; j <= order; j++ ) + { + w[i] = w[i] * ( double ) ( j - 1 ); + } + w[i] = w[i] / p1; + for ( j = 2; j <= order; j++ ) + { + w[i] = w[i] * ( double ) ( j - 1 ); + } + +// w[i] = ( cc / dp2 ) / p1; + } + + delete [] b; + delete [] c; + + return; +} +//****************************************************************************80 + +void laguerre_ss_recur ( double *p2, double *dp2, double *p1, double x, + int order, double b[], double c[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_SS_RECUR evaluates a Laguerre polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Output, double *P2, the value of L(ORDER)(X). +// +// Output, double *DP2, the value of L'(ORDER)(X). +// +// Output, double *P1, the value of L(ORDER-1)(X). +// +// Input, double X, the point at which polynomials are evaluated. +// +// Input, int ORDER, the order of the polynomial. +// +// Input, double B[ORDER], C[ORDER], the recursion coefficients. +// +{ + double dp0; + double dp1; + int i; + double p0; + + *p1 = 1.0; + dp1 = 0.0; + + *p2 = x - 1.0; + *dp2 = 1.0; + + for ( i = 1; i < order; i++ ) + { + p0 = *p1; + dp0 = dp1; + + *p1 = *p2; + dp1 = *dp2; + + *p2 = ( x - b[i] ) * ( *p1 ) - c[i] * p0; + *dp2 = ( x - b[i] ) * dp1 + ( *p1 ) - c[i] * dp0; + } + + return; +} +//****************************************************************************80 + +void laguerre_ss_root ( double *x, int order, double *dp2, double *p1, + double b[], double c[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LAGUERRE_SS_ROOT improves a root of a Laguerre polynomial. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Arthur Stroud, Don Secrest. +// C++ version by John Burkardt. +// +// Reference: +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input/output, double *X, the approximate root, which +// should be improved on output. +// +// Input, int ORDER, the order of the polynomial. +// +// Output, double *DP2, the value of L'(ORDER)(X). +// +// Output, double *P1, the value of L(ORDER-1)(X). +// +// Input, double B[ORDER], C[ORDER], the recursion coefficients. +// +{ + double d; + double eps; + double p2; + int step; + int step_max = 10; + + eps = webbur::r8_epsilon ( ); + + for ( step = 1; step <= step_max; step++ ) + { + webbur::laguerre_ss_recur ( &p2, dp2, p1, *x, order, b, c ); + + d = p2 / ( *dp2 ); + *x = *x - d; + + if ( webbur::r8_abs ( d ) <= eps * ( webbur::r8_abs ( *x ) + 1.0 ) ) + { + break; + } + } + + return; +} +//****************************************************************************80 + +void legendre_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_COMPUTE: Legendre quadrature rule by the Elhay-Kautsky method. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 April 2011 +// +// Author: +// +// Original FORTRAN77 version by Sylvan Elhay, Jaroslav Kautsky. +// C++ version by John Burkardt. +// +// Reference: +// +// Sylvan Elhay, Jaroslav Kautsky, +// Algorithm 655: IQPACK, FORTRAN Subroutines for the Weights of +// Interpolatory Quadrature, +// ACM Transactions on Mathematical Software, +// Volume 13, Number 4, December 1987, pages 399-415. +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double *bj; + int i; + double zemu; +// +// Define the zero-th moment. +// + zemu = 2.0; +// +// Define the Jacobi matrix. +// + bj = new double[n]; + + for ( i = 0; i < n; i++ ) + { + bj[i] = ( double ) ( ( i + 1 ) * ( i + 1 ) ) + / ( double ) ( 4 * ( i + 1 ) * ( i + 1 ) - 1 ); + bj[i] = std::sqrt ( bj[i] ); + } + + for ( i = 0; i < n; i++ ) + { + x[i] = 0.0; + } + + w[0] = std::sqrt ( zemu ); + + for ( i = 1; i < n; i++ ) + { + w[i] = 0.0; + } +// +// Diagonalize the Jacobi matrix. +// + webbur::imtqlx ( n, x, bj, w ); + + for ( i = 0; i < n; i++ ) + { + w[i] = w[i] * w[i]; + } + + delete [] bj; + + return; +} +//****************************************************************************80 + +void legendre_compute_np ( int n, int np, double p[], double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_COMPUTE_NP computes a Legendre quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= N ) W(I) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// Original FORTRAN77 version by Philip Davis, Philip Rabinowitz. +// C++ version by John Burkardt. +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + webbur::legendre_compute ( n, x, w ); + + return; +} +//****************************************************************************80 + +void legendre_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_COMPUTE_POINTS computes Legendre quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double X[N], the abscissas. +// +{ + double *w; + + w= new double[n]; + + webbur::legendre_compute ( n, x, w ); + + delete [] w; + + return; +} +//****************************************************************************80 + +void legendre_compute_points_np ( int n, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_COMPUTE_POINTS_NP computes Legendre quadrature points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + webbur::legendre_compute_points ( n, x ); + + return; +} +//****************************************************************************80 + +void legendre_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_COMPUTE_WEIGHTS computes Legendre quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double W[N], the weights. +// +{ + double *x; + + x = new double[n]; + + webbur::legendre_compute ( n, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void legendre_compute_weights_np ( int n, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_COMPUTE_WEIGHTS_NP computes Legendre quadrature weights. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + webbur::legendre_compute_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void legendre_dr_compute ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_DR_COMPUTE computes a Legendre quadrature rule. +// +// Discussion: +// +// The integral: +// +// Integral ( -1 <= X <= 1 ) F(X) dX +// +// The quadrature rule: +// +// Sum ( 1 <= I <= N ) W(I) * F ( X(I) ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 June 2009 +// +// Author: +// +// Original FORTRAN77 version by Philip Davis, Philip Rabinowitz. +// C++ version by John Burkardt. +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int N, the order. +// 1 <= N. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double d1; + double d2pn; + double d3pn; + double d4pn; + double dp; + double dpn; + double e1; + double fx; + double h; + int i; + int iback; + int k; + int m; + int mp1mi; + int ncopy; + int nmove; + double p; + double pi = 3.141592653589793; + double pk; + double pkm1; + double pkp1; + double t; + double u; + double v; + double x0; + double xtemp; + + if ( n < 1 ) + { + std::cerr << "\n"; + std::cerr << "LEGENDRE_DR_COMPUTE - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::exit ( 1 ); + } + + e1 = ( double ) ( n * ( n + 1 ) ); + + m = ( n + 1 ) / 2; + + for ( i = 1; i <= m; i++ ) + { + mp1mi = m + 1 - i; + + t = ( double ) ( 4 * i - 1 ) * pi / ( double ) ( 4 * n + 2 ); + + x0 = std::cos ( t ) * ( 1.0 - ( 1.0 - 1.0 / ( double ) ( n ) ) + / ( double ) ( 8 * n * n ) ); + + pkm1 = 1.0; + pk = x0; + + for ( k = 2; k <= n; k++ ) + { + pkp1 = 2.0 * x0 * pk - pkm1 - ( x0 * pk - pkm1 ) / ( double ) ( k ); + pkm1 = pk; + pk = pkp1; + } + + d1 = ( double ) ( n ) * ( pkm1 - x0 * pk ); + + dpn = d1 / ( 1.0 - x0 * x0 ); + + d2pn = ( 2.0 * x0 * dpn - e1 * pk ) / ( 1.0 - x0 * x0 ); + + d3pn = ( 4.0 * x0 * d2pn + ( 2.0 - e1 ) * dpn ) / ( 1.0 - x0 * x0 ); + + d4pn = ( 6.0 * x0 * d3pn + ( 6.0 - e1 ) * d2pn ) / ( 1.0 - x0 * x0 ); + + u = pk / dpn; + v = d2pn / dpn; +// +// Initial approximation H: +// + h = -u * ( 1.0 + 0.5 * u * ( v + u * ( v * v - d3pn / ( 3.0 * dpn ) ) ) ); +// +// Refine H using one step of Newton's method: +// + p = pk + h * ( dpn + 0.5 * h * ( d2pn + h / 3.0 + * ( d3pn + 0.25 * h * d4pn ) ) ); + + dp = dpn + h * ( d2pn + 0.5 * h * ( d3pn + h * d4pn / 3.0 ) ); + + h = h - p / dp; + + xtemp = x0 + h; + + x[mp1mi-1] = xtemp; + + fx = d1 - h * e1 * ( pk + 0.5 * h * ( dpn + h / 3.0 + * ( d2pn + 0.25 * h * ( d3pn + 0.2 * h * d4pn ) ) ) ); + + w[mp1mi-1] = 2.0 * ( 1.0 - xtemp * xtemp ) / ( fx * fx ); + } + + if ( ( n % 2 ) == 1 ) + { + x[0] = 0.0; + } +// +// Shift the data up. +// + nmove = ( n + 1 ) / 2; + ncopy = n - nmove; + + for ( i = 1; i <= nmove; i++ ) + { + iback = n + 1 - i; + x[iback-1] = x[iback-ncopy-1]; + w[iback-1] = w[iback-ncopy-1]; + } +// +// Reflect values for the negative abscissas. +// + for ( i = 1; i <= n - nmove; i++ ) + { + x[i-1] = - x[n-i]; + w[i-1] = w[n-i]; + } + + return; +} +//****************************************************************************80 + +double legendre_integral ( int expon ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_INTEGRAL evaluates a monomial Legendre integral. +// +// Discussion: +// +// The integral: +// +// integral ( -1 <= x <= +1 ) x^n dx +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int EXPON, the exponent. +// +// Output, double LEGENDRE_INTEGRAL, the value of the exact integral. +// +{ + double exact; +// +// Get the exact value of the integral. +// + if ( ( expon % 2 ) == 0 ) + { + exact = 2.0 / ( double ) ( expon + 1 ); + } + else + { + exact = 0.0; + } + + return exact; +} +//****************************************************************************80 + +void legendre_lookup ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_LOOKUP looks up abscissas and weights for Gauss-Legendre quadrature. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 April 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Vladimir Krylov, +// Approximate Calculation of Integrals, +// Dover, 2006, +// ISBN: 0486445798. +// LC: QA311.K713. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Stephen Wolfram, +// The Mathematica Book, +// Fourth Edition, +// Cambridge University Press, 1999, +// ISBN: 0-521-64314-7, +// LC: QA76.95.W65. +// +// Daniel Zwillinger, editor, +// CRC Standard Mathematical Tables and Formulae, +// 30th Edition, +// CRC Press, 1996, +// ISBN: 0-8493-2479-3, +// LC: QA47.M315. +// +// Parameters: +// +// Input, int N, the order. +// N must be between 1 and 33. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the abscissas. +// +{ + webbur::legendre_lookup_points ( n, x ); + + webbur::legendre_lookup_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void legendre_lookup_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_LOOKUP_POINTS looks up abscissas for Gauss-Legendre quadrature. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 April 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Vladimir Krylov, +// Approximate Calculation of Integrals, +// Dover, 2006, +// ISBN: 0486445798. +// LC: QA311.K713. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Stephen Wolfram, +// The Mathematica Book, +// Fourth Edition, +// Cambridge University Press, 1999, +// ISBN: 0-521-64314-7, +// LC: QA76.95.W65. +// +// Daniel Zwillinger, editor, +// CRC Standard Mathematical Tables and Formulae, +// 30th Edition, +// CRC Press, 1996, +// ISBN: 0-8493-2479-3, +// LC: QA47.M315. +// +// Parameters: +// +// Input, int N, the order. +// N must be between 1 and 33. +// +// Output, double X[N], the abscissas. +// +{ + if ( n == 1 ) + { + x[0] = 0.000000000000000000000000000000; + } + else if ( n == 2 ) + { + x[0] = -0.577350269189625764509148780502; + x[1] = 0.577350269189625764509148780502; + } + else if ( n == 3 ) + { + x[0] = -0.774596669241483377035853079956; + x[1] = 0.000000000000000000000000000000; + x[2] = 0.774596669241483377035853079956; + } + else if ( n == 4 ) + { + x[0] = -0.861136311594052575223946488893; + x[1] = -0.339981043584856264802665759103; + x[2] = 0.339981043584856264802665759103; + x[3] = 0.861136311594052575223946488893; + } + else if ( n == 5 ) + { + x[0] = -0.906179845938663992797626878299; + x[1] = -0.538469310105683091036314420700; + x[2] = 0.000000000000000000000000000000; + x[3] = 0.538469310105683091036314420700; + x[4] = 0.906179845938663992797626878299; + } + else if ( n == 6 ) + { + x[0] = -0.932469514203152027812301554494; + x[1] = -0.661209386466264513661399595020; + x[2] = -0.238619186083196908630501721681; + x[3] = 0.238619186083196908630501721681; + x[4] = 0.661209386466264513661399595020; + x[5] = 0.932469514203152027812301554494; + } + else if ( n == 7 ) + { + x[0] = -0.949107912342758524526189684048; + x[1] = -0.741531185599394439863864773281; + x[2] = -0.405845151377397166906606412077; + x[3] = 0.000000000000000000000000000000; + x[4] = 0.405845151377397166906606412077; + x[5] = 0.741531185599394439863864773281; + x[6] = 0.949107912342758524526189684048; + } + else if ( n == 8 ) + { + x[0] = -0.960289856497536231683560868569; + x[1] = -0.796666477413626739591553936476; + x[2] = -0.525532409916328985817739049189; + x[3] = -0.183434642495649804939476142360; + x[4] = 0.183434642495649804939476142360; + x[5] = 0.525532409916328985817739049189; + x[6] = 0.796666477413626739591553936476; + x[7] = 0.960289856497536231683560868569; + } + else if ( n == 9 ) + { + x[0] = -0.968160239507626089835576203; + x[1] = -0.836031107326635794299429788; + x[2] = -0.613371432700590397308702039; + x[3] = -0.324253423403808929038538015; + x[4] = 0.000000000000000000000000000; + x[5] = 0.324253423403808929038538015; + x[6] = 0.613371432700590397308702039; + x[7] = 0.836031107326635794299429788; + x[8] = 0.968160239507626089835576203; + } + else if ( n == 10 ) + { + x[0] = -0.973906528517171720077964012; + x[1] = -0.865063366688984510732096688; + x[2] = -0.679409568299024406234327365; + x[3] = -0.433395394129247190799265943; + x[4] = -0.148874338981631210884826001; + x[5] = 0.148874338981631210884826001; + x[6] = 0.433395394129247190799265943; + x[7] = 0.679409568299024406234327365; + x[8] = 0.865063366688984510732096688; + x[9] = 0.973906528517171720077964012; + } + else if ( n == 11 ) + { + x[0] = -0.978228658146056992803938001; + x[1] = -0.887062599768095299075157769; + x[2] = -0.730152005574049324093416252; + x[3] = -0.519096129206811815925725669; + x[4] = -0.269543155952344972331531985; + x[5] = 0.000000000000000000000000000; + x[6] = 0.269543155952344972331531985; + x[7] = 0.519096129206811815925725669; + x[8] = 0.730152005574049324093416252; + x[9] = 0.887062599768095299075157769; + x[10] = 0.978228658146056992803938001; + } + else if ( n == 12 ) + { + x[0] = -0.981560634246719250690549090; + x[1] = -0.904117256370474856678465866; + x[2] = -0.769902674194304687036893833; + x[3] = -0.587317954286617447296702419; + x[4] = -0.367831498998180193752691537; + x[5] = -0.125233408511468915472441369; + x[6] = 0.125233408511468915472441369; + x[7] = 0.367831498998180193752691537; + x[8] = 0.587317954286617447296702419; + x[9] = 0.769902674194304687036893833; + x[10] = 0.904117256370474856678465866; + x[11] = 0.981560634246719250690549090; + } + else if ( n == 13 ) + { + x[0] = -0.984183054718588149472829449; + x[1] = -0.917598399222977965206547837; + x[2] = -0.801578090733309912794206490; + x[3] = -0.642349339440340220643984607; + x[4] = -0.448492751036446852877912852; + x[5] = -0.230458315955134794065528121; + x[6] = 0.000000000000000000000000000; + x[7] = 0.230458315955134794065528121; + x[8] = 0.448492751036446852877912852; + x[9] = 0.642349339440340220643984607; + x[10] = 0.80157809073330991279420649; + x[11] = 0.91759839922297796520654784; + x[12] = 0.98418305471858814947282945; + } + else if ( n == 14 ) + { + x[0] = -0.986283808696812338841597267; + x[1] = -0.928434883663573517336391139; + x[2] = -0.827201315069764993189794743; + x[3] = -0.687292904811685470148019803; + x[4] = -0.515248636358154091965290719; + x[5] = -0.319112368927889760435671824; + x[6] = -0.108054948707343662066244650; + x[7] = 0.108054948707343662066244650; + x[8] = 0.31911236892788976043567182; + x[9] = 0.51524863635815409196529072; + x[10] = 0.68729290481168547014801980; + x[11] = 0.82720131506976499318979474; + x[12] = 0.92843488366357351733639114; + x[13] = 0.98628380869681233884159727; + } + else if ( n == 15 ) + { + x[0] = -0.987992518020485428489565719; + x[1] = -0.937273392400705904307758948; + x[2] = -0.848206583410427216200648321; + x[3] = -0.724417731360170047416186055; + x[4] = -0.570972172608538847537226737; + x[5] = -0.394151347077563369897207371; + x[6] = -0.201194093997434522300628303; + x[7] = 0.00000000000000000000000000; + x[8] = 0.20119409399743452230062830; + x[9] = 0.39415134707756336989720737; + x[10] = 0.57097217260853884753722674; + x[11] = 0.72441773136017004741618605; + x[12] = 0.84820658341042721620064832; + x[13] = 0.93727339240070590430775895; + x[14] = 0.98799251802048542848956572; + } + else if ( n == 16 ) + { + x[0] = -0.989400934991649932596154173; + x[1] = -0.944575023073232576077988416; + x[2] = -0.865631202387831743880467898; + x[3] = -0.755404408355003033895101195; + x[4] = -0.617876244402643748446671764; + x[5] = -0.458016777657227386342419443; + x[6] = -0.281603550779258913230460501; + x[7] = -0.09501250983763744018531934; + x[8] = 0.09501250983763744018531934; + x[9] = 0.28160355077925891323046050; + x[10] = 0.45801677765722738634241944; + x[11] = 0.61787624440264374844667176; + x[12] = 0.75540440835500303389510119; + x[13] = 0.86563120238783174388046790; + x[14] = 0.94457502307323257607798842; + x[15] = 0.98940093499164993259615417; + } + else if ( n == 17 ) + { + x[0] = -0.990575475314417335675434020; + x[1] = -0.950675521768767761222716958; + x[2] = -0.880239153726985902122955694; + x[3] = -0.781514003896801406925230056; + x[4] = -0.657671159216690765850302217; + x[5] = -0.512690537086476967886246569; + x[6] = -0.35123176345387631529718552; + x[7] = -0.17848418149584785585067749; + x[8] = 0.00000000000000000000000000; + x[9] = 0.17848418149584785585067749; + x[10] = 0.35123176345387631529718552; + x[11] = 0.51269053708647696788624657; + x[12] = 0.65767115921669076585030222; + x[13] = 0.78151400389680140692523006; + x[14] = 0.88023915372698590212295569; + x[15] = 0.95067552176876776122271696; + x[16] = 0.99057547531441733567543402; + } + else if ( n == 18 ) + { + x[0] = -0.991565168420930946730016005; + x[1] = -0.955823949571397755181195893; + x[2] = -0.892602466497555739206060591; + x[3] = -0.803704958972523115682417455; + x[4] = -0.691687043060353207874891081; + x[5] = -0.55977083107394753460787155; + x[6] = -0.41175116146284264603593179; + x[7] = -0.25188622569150550958897285; + x[8] = -0.08477501304173530124226185; + x[9] = 0.08477501304173530124226185; + x[10] = 0.25188622569150550958897285; + x[11] = 0.41175116146284264603593179; + x[12] = 0.55977083107394753460787155; + x[13] = 0.69168704306035320787489108; + x[14] = 0.80370495897252311568241746; + x[15] = 0.89260246649755573920606059; + x[16] = 0.95582394957139775518119589; + x[17] = 0.99156516842093094673001600; + } + else if ( n == 19 ) + { + x[0] = -0.992406843843584403189017670; + x[1] = -0.960208152134830030852778841; + x[2] = -0.903155903614817901642660929; + x[3] = -0.822714656537142824978922487; + x[4] = -0.72096617733522937861709586; + x[5] = -0.60054530466168102346963816; + x[6] = -0.46457074137596094571726715; + x[7] = -0.31656409996362983199011733; + x[8] = -0.16035864564022537586809612; + x[9] = 0.00000000000000000000000000; + x[10] = 0.16035864564022537586809612; + x[11] = 0.31656409996362983199011733; + x[12] = 0.46457074137596094571726715; + x[13] = 0.60054530466168102346963816; + x[14] = 0.72096617733522937861709586; + x[15] = 0.82271465653714282497892249; + x[16] = 0.90315590361481790164266093; + x[17] = 0.96020815213483003085277884; + x[18] = 0.99240684384358440318901767; + } + else if ( n == 20 ) + { + x[0] = -0.993128599185094924786122388; + x[1] = -0.963971927277913791267666131; + x[2] = -0.912234428251325905867752441; + x[3] = -0.83911697182221882339452906; + x[4] = -0.74633190646015079261430507; + x[5] = -0.63605368072651502545283670; + x[6] = -0.51086700195082709800436405; + x[7] = -0.37370608871541956067254818; + x[8] = -0.22778585114164507808049620; + x[9] = -0.07652652113349733375464041; + x[10] = 0.07652652113349733375464041; + x[11] = 0.22778585114164507808049620; + x[12] = 0.37370608871541956067254818; + x[13] = 0.51086700195082709800436405; + x[14] = 0.63605368072651502545283670; + x[15] = 0.74633190646015079261430507; + x[16] = 0.83911697182221882339452906; + x[17] = 0.91223442825132590586775244; + x[18] = 0.96397192727791379126766613; + x[19] = 0.99312859918509492478612239; + } + else if ( n == 21 ) + { + x[ 0] = -0.99375217062038950026024204; + x[ 1] = -0.96722683856630629431662221; + x[ 2] = -0.92009933415040082879018713; + x[ 3] = -0.85336336458331728364725064; + x[ 4] = -0.76843996347567790861587785; + x[ 5] = -0.66713880419741231930596667; + x[ 6] = -0.55161883588721980705901880; + x[ 7] = -0.42434212020743878357366889; + x[ 8] = -0.28802131680240109660079252; + x[9] = -0.14556185416089509093703098; + x[10] = 0.00000000000000000000000000; + x[11] = +0.14556185416089509093703098; + x[12] = +0.28802131680240109660079252; + x[13] = +0.42434212020743878357366889; + x[14] = +0.55161883588721980705901880; + x[15] = +0.66713880419741231930596667; + x[16] = +0.76843996347567790861587785; + x[17] = +0.85336336458331728364725064; + x[18] = +0.92009933415040082879018713; + x[19] = +0.96722683856630629431662221; + x[20] = +0.99375217062038950026024204; + } + else if ( n == 22 ) + { + x[0] = -0.99429458548239929207303142; + x[1] = -0.97006049783542872712395099; + x[2] = -0.92695677218717400052069294; + x[3] = -0.86581257772030013653642564; + x[4] = -0.78781680597920816200427796; + x[5] = -0.69448726318668278005068984; + x[6] = -0.58764040350691159295887693; + x[7] = -0.46935583798675702640633071; + x[8] = -0.34193582089208422515814742; + x[9] = -0.20786042668822128547884653; + x[10] = -0.06973927331972222121384180; + x[11] = 0.06973927331972222121384180; + x[12] = 0.20786042668822128547884653; + x[13] = 0.34193582089208422515814742; + x[14] = 0.46935583798675702640633071; + x[15] = 0.58764040350691159295887693; + x[16] = 0.69448726318668278005068984; + x[17] = 0.78781680597920816200427796; + x[18] = 0.86581257772030013653642564; + x[19] = 0.92695677218717400052069294; + x[20] = 0.97006049783542872712395099; + x[21] = 0.99429458548239929207303142; + } + else if ( n == 23 ) + { + x[0] = -0.99476933499755212352392572; + x[1] = -0.97254247121811523195602408; + x[2] = -0.93297108682601610234919699; + x[3] = -0.87675235827044166737815689; + x[4] = -0.80488840161883989215111841; + x[5] = -0.71866136313195019446162448; + x[6] = -0.61960987576364615638509731; + x[7] = -0.50950147784600754968979305; + x[8] = -0.39030103803029083142148887; + x[9] = -0.26413568097034493053386954; + x[10] = -0.13325682429846611093174268; + x[11] = 0.00000000000000000000000000; + x[12] = 0.13325682429846611093174268; + x[13] = 0.26413568097034493053386954; + x[14] = 0.39030103803029083142148887; + x[15] = 0.50950147784600754968979305; + x[16] = 0.61960987576364615638509731; + x[17] = 0.71866136313195019446162448; + x[18] = 0.80488840161883989215111841; + x[19] = 0.87675235827044166737815689; + x[20] = 0.93297108682601610234919699; + x[21] = 0.97254247121811523195602408; + x[22] = 0.99476933499755212352392572; + } + else if ( n == 24 ) + { + x[0] = -0.99518721999702136017999741; + x[1] = -0.97472855597130949819839199; + x[2] = -0.93827455200273275852364900; + x[3] = -0.88641552700440103421315434; + x[4] = -0.82000198597390292195394987; + x[5] = -0.74012419157855436424382810; + x[6] = -0.64809365193697556925249579; + x[7] = -0.54542147138883953565837562; + x[8] = -0.43379350762604513848708423; + x[9] = -0.31504267969616337438679329; + x[10] = -0.19111886747361630915863982; + x[11] = -0.06405689286260562608504308; + x[12] = 0.06405689286260562608504308; + x[13] = 0.19111886747361630915863982; + x[14] = 0.31504267969616337438679329; + x[15] = 0.43379350762604513848708423; + x[16] = 0.54542147138883953565837562; + x[17] = 0.64809365193697556925249579; + x[18] = 0.74012419157855436424382810; + x[19] = 0.82000198597390292195394987; + x[20] = 0.88641552700440103421315434; + x[21] = 0.93827455200273275852364900; + x[22] = 0.97472855597130949819839199; + x[23] = 0.99518721999702136017999741; + } + else if ( n == 25 ) + { + x[0] = -0.99555696979049809790878495; + x[1] = -0.97666392145951751149831539; + x[2] = -0.94297457122897433941401117; + x[3] = -0.89499199787827536885104201; + x[4] = -0.83344262876083400142102111; + x[5] = -0.75925926303735763057728287; + x[6] = -0.67356636847346836448512063; + x[7] = -0.57766293024122296772368984; + x[8] = -0.47300273144571496052218212; + x[9] = -0.36117230580938783773582173; + x[10] = -0.24386688372098843204519036; + x[11] = -0.12286469261071039638735982; + x[12] = 0.00000000000000000000000000; + x[13] = 0.12286469261071039638735982; + x[14] = 0.24386688372098843204519036; + x[15] = 0.36117230580938783773582173; + x[16] = 0.47300273144571496052218212; + x[17] = 0.57766293024122296772368984; + x[18] = 0.67356636847346836448512063; + x[19] = 0.75925926303735763057728287; + x[20] = 0.83344262876083400142102111; + x[21] = 0.89499199787827536885104201; + x[22] = 0.94297457122897433941401117; + x[23] = 0.97666392145951751149831539; + x[24] = 0.99555696979049809790878495; + } + else if ( n == 26 ) + { + x[0] = -0.99588570114561692900321696; + x[1] = -0.97838544595647099110058035; + x[2] = -0.94715906666171425013591528; + x[3] = -0.90263786198430707421766560; + x[4] = -0.84544594278849801879750706; + x[5] = -0.77638594882067885619296725; + x[6] = -0.69642726041995726486381391; + x[7] = -0.60669229301761806323197875; + x[8] = -0.50844071482450571769570306; + x[9] = -0.40305175512348630648107738; + x[10] = -0.29200483948595689514283538; + x[11] = -0.17685882035689018396905775; + x[12] = -0.05923009342931320709371858; + x[13] = 0.05923009342931320709371858; + x[14] = 0.17685882035689018396905775; + x[15] = 0.29200483948595689514283538; + x[16] = 0.40305175512348630648107738; + x[17] = 0.50844071482450571769570306; + x[18] = 0.60669229301761806323197875; + x[19] = 0.69642726041995726486381391; + x[20] = 0.77638594882067885619296725; + x[21] = 0.84544594278849801879750706; + x[22] = 0.90263786198430707421766560; + x[23] = 0.94715906666171425013591528; + x[24] = 0.97838544595647099110058035; + x[25] = 0.99588570114561692900321696; + } + else if ( n == 27 ) + { + x[0] = -0.99617926288898856693888721; + x[1] = -0.97992347596150122285587336; + x[2] = -0.95090055781470500685190803; + x[3] = -0.90948232067749110430064502; + x[4] = -0.85620790801829449030273722; + x[5] = -0.79177163907050822714439734; + x[6] = -0.71701347373942369929481621; + x[7] = -0.63290797194649514092773464; + x[8] = -0.54055156457945689490030094; + x[9] = -0.44114825175002688058597416; + x[10] = -0.33599390363850889973031903; + x[11] = -0.22645936543953685885723911; + x[12] = -0.11397258560952996693289498; + x[13] = 0.00000000000000000000000000; + x[14] = 0.11397258560952996693289498; + x[15] = 0.22645936543953685885723911; + x[16] = 0.33599390363850889973031903; + x[17] = 0.44114825175002688058597416; + x[18] = 0.54055156457945689490030094; + x[19] = 0.63290797194649514092773464; + x[20] = 0.71701347373942369929481621; + x[21] = 0.79177163907050822714439734; + x[22] = 0.85620790801829449030273722; + x[23] = 0.90948232067749110430064502; + x[24] = 0.95090055781470500685190803; + x[25] = 0.97992347596150122285587336; + x[26] = 0.99617926288898856693888721; + } + else if ( n == 28 ) + { + x[0] = -0.99644249757395444995043639; + x[1] = -0.98130316537087275369455995; + x[2] = -0.95425928062893819725410184; + x[3] = -0.91563302639213207386968942; + x[4] = -0.86589252257439504894225457; + x[5] = -0.80564137091717917144788596; + x[6] = -0.73561087801363177202814451; + x[7] = -0.65665109403886496121989818; + x[8] = -0.56972047181140171930800328; + x[9] = -0.47587422495511826103441185; + x[10] = -0.37625151608907871022135721; + x[11] = -0.27206162763517807767682636; + x[12] = -0.16456928213338077128147178; + x[13] = -0.05507928988403427042651653; + x[14] = 0.05507928988403427042651653; + x[15] = 0.16456928213338077128147178; + x[16] = 0.27206162763517807767682636; + x[17] = 0.37625151608907871022135721; + x[18] = 0.47587422495511826103441185; + x[19] = 0.56972047181140171930800328; + x[20] = 0.65665109403886496121989818; + x[21] = 0.73561087801363177202814451; + x[22] = 0.80564137091717917144788596; + x[23] = 0.86589252257439504894225457; + x[24] = 0.91563302639213207386968942; + x[25] = 0.95425928062893819725410184; + x[26] = 0.98130316537087275369455995; + x[27] = 0.99644249757395444995043639; + } + else if ( n == 29 ) + { + x[0] = -0.99667944226059658616319153; + x[1] = -0.98254550526141317487092602; + x[2] = -0.95728559577808772579820804; + x[3] = -0.92118023295305878509375344; + x[4] = -0.87463780492010279041779342; + x[5] = -0.81818548761525244498957221; + x[6] = -0.75246285173447713391261008; + x[7] = -0.67821453760268651515618501; + x[8] = -0.59628179713822782037958621; + x[9] = -0.50759295512422764210262792; + x[10] = -0.41315288817400866389070659; + x[11] = -0.31403163786763993494819592; + x[12] = -0.21135228616600107450637573; + x[13] = -0.10627823013267923017098239; + x[14] = 0.00000000000000000000000000; + x[15] = 0.10627823013267923017098239; + x[16] = 0.21135228616600107450637573; + x[17] = 0.31403163786763993494819592; + x[18] = 0.41315288817400866389070659; + x[19] = 0.50759295512422764210262792; + x[20] = 0.59628179713822782037958621; + x[21] = 0.67821453760268651515618501; + x[22] = 0.75246285173447713391261008; + x[23] = 0.81818548761525244498957221; + x[24] = 0.87463780492010279041779342; + x[25] = 0.92118023295305878509375344; + x[26] = 0.95728559577808772579820804; + x[27] = 0.98254550526141317487092602; + x[28] = 0.99667944226059658616319153; + } + else if ( n == 30 ) + { + x[0] = -0.99689348407464954027163005; + x[1] = -0.98366812327974720997003258; + x[2] = -0.96002186496830751221687103; + x[3] = -0.92620004742927432587932428; + x[4] = -0.88256053579205268154311646; + x[5] = -0.82956576238276839744289812; + x[6] = -0.76777743210482619491797734; + x[7] = -0.69785049479331579693229239; + x[8] = -0.62052618298924286114047756; + x[9] = -0.53662414814201989926416979; + x[10] = -0.44703376953808917678060990; + x[11] = -0.35270472553087811347103721; + x[12] = -0.25463692616788984643980513; + x[13] = -0.15386991360858354696379467; + x[14] = -0.05147184255531769583302521; + x[15] = 0.05147184255531769583302521; + x[16] = 0.15386991360858354696379467; + x[17] = 0.25463692616788984643980513; + x[18] = 0.35270472553087811347103721; + x[19] = 0.44703376953808917678060990; + x[20] = 0.53662414814201989926416979; + x[21] = 0.62052618298924286114047756; + x[22] = 0.69785049479331579693229239; + x[23] = 0.76777743210482619491797734; + x[24] = 0.82956576238276839744289812; + x[25] = 0.88256053579205268154311646; + x[26] = 0.92620004742927432587932428; + x[27] = 0.96002186496830751221687103; + x[28] = 0.98366812327974720997003258; + x[29] = 0.99689348407464954027163005; + } + else if ( n == 31 ) + { + x[0] = -0.99708748181947707405562655; + x[1] = -0.98468590966515248400246517; + x[2] = -0.96250392509294966178905240; + x[3] = -0.93075699789664816495694576; + x[4] = -0.88976002994827104337419201; + x[5] = -0.83992032014626734008690454; + x[6] = -0.78173314841662494040636002; + x[7] = -0.71577678458685328390597087; + x[8] = -0.64270672292426034618441820; + x[9] = -0.56324916140714926272094492; + x[10] = -0.47819378204490248044059404; + x[11] = -0.38838590160823294306135146; + x[12] = -0.29471806998170161661790390; + x[13] = -0.19812119933557062877241300; + x[14] = -0.09955531215234152032517479; + x[15] = 0.00000000000000000000000000; + x[16] = 0.09955531215234152032517479; + x[17] = 0.19812119933557062877241300; + x[18] = 0.29471806998170161661790390; + x[19] = 0.38838590160823294306135146; + x[20] = 0.47819378204490248044059404; + x[21] = 0.56324916140714926272094492; + x[22] = 0.64270672292426034618441820; + x[23] = 0.71577678458685328390597087; + x[24] = 0.78173314841662494040636002; + x[25] = 0.83992032014626734008690454; + x[26] = 0.88976002994827104337419201; + x[27] = 0.93075699789664816495694576; + x[28] = 0.96250392509294966178905240; + x[29] = 0.98468590966515248400246517; + x[30] = 0.99708748181947707405562655; + } + else if ( n == 32 ) + { + x[0] = -0.99726386184948156354498113; + x[1] = -0.98561151154526833540017504; + x[2] = -0.96476225558750643077381193; + x[3] = -0.93490607593773968917091913; + x[4] = -0.89632115576605212396530724; + x[5] = -0.84936761373256997013369300; + x[6] = -0.79448379596794240696309730; + x[7] = -0.73218211874028968038742667; + x[8] = -0.66304426693021520097511517; + x[9] = -0.58771575724076232904074548; + x[10] = -0.50689990893222939002374747; + x[11] = -0.42135127613063534536411944; + x[12] = -0.33186860228212764977991681; + x[13] = -0.23928736225213707454460321; + x[14] = -0.14447196158279649348518637; + x[15] = -0.04830766568773831623481257; + x[16] = 0.04830766568773831623481257; + x[17] = 0.14447196158279649348518637; + x[18] = 0.23928736225213707454460321; + x[19] = 0.33186860228212764977991681; + x[20] = 0.42135127613063534536411944; + x[21] = 0.50689990893222939002374747; + x[22] = 0.58771575724076232904074548; + x[23] = 0.66304426693021520097511517; + x[24] = 0.73218211874028968038742667; + x[25] = 0.79448379596794240696309730; + x[26] = 0.84936761373256997013369300; + x[27] = 0.89632115576605212396530724; + x[28] = 0.93490607593773968917091913; + x[29] = 0.96476225558750643077381193; + x[30] = 0.98561151154526833540017504; + x[31] = 0.99726386184948156354498113; + } + else if ( n == 33 ) + { + x[0] = -0.99742469424645521726616802; + x[1] = -0.98645572623064248811037570; + x[2] = -0.96682290968999276892837771; + x[3] = -0.93869437261116835035583512; + x[4] = -0.90231676774343358304053133; + x[5] = -0.85800965267650406464306148; + x[6] = -0.80616235627416658979620087; + x[7] = -0.74723049644956215785905512; + x[8] = -0.68173195996974278626821595; + x[9] = -0.61024234583637902730728751; + x[10] = -0.53338990478634764354889426; + x[11] = -0.45185001727245069572599328; + x[12] = -0.36633925774807334107022062; + x[13] = -0.27760909715249702940324807; + x[14] = -0.18643929882799157233579876; + x[15] = -0.09363106585473338567074292; + x[16] = 0.00000000000000000000000000; + x[17] = 0.09363106585473338567074292; + x[18] = 0.18643929882799157233579876; + x[19] = 0.27760909715249702940324807; + x[20] = 0.36633925774807334107022062; + x[21] = 0.45185001727245069572599328; + x[22] = 0.53338990478634764354889426; + x[23] = 0.61024234583637902730728751; + x[24] = 0.68173195996974278626821595; + x[25] = 0.74723049644956215785905512; + x[26] = 0.80616235627416658979620087; + x[27] = 0.85800965267650406464306148; + x[28] = 0.90231676774343358304053133; + x[29] = 0.93869437261116835035583512; + x[30] = 0.96682290968999276892837771; + x[31] = 0.98645572623064248811037570; + x[32] = 0.99742469424645521726616802; + } + else + { + std::cerr << "\n"; + std::cerr << "LEGENDRE_LOOKUP_POINTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::cerr << " Legal values are 1 through 33.\n"; + std::exit ( 1 ); + } + return; +} +//****************************************************************************80 + +void legendre_lookup_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_LOOKUP_WEIGHTS looks up weights for Gauss-Legendre quadrature. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 April 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Vladimir Krylov, +// Approximate Calculation of Integrals, +// Dover, 2006, +// ISBN: 0486445798. +// LC: QA311.K713. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Stephen Wolfram, +// The Mathematica Book, +// Fourth Edition, +// Cambridge University Press, 1999, +// ISBN: 0-521-64314-7, +// LC: QA76.95.W65. +// +// Daniel Zwillinger, editor, +// CRC Standard Mathematical Tables and Formulae, +// 30th Edition, +// CRC Press, 1996, +// ISBN: 0-8493-2479-3, +// LC: QA47.M315. +// +// Parameters: +// +// Input, int N, the order. +// N must be between 1 and 33. +// +// Output, double W[N], the weights. +// +{ + if ( n == 1 ) + { + w[0] = 2.000000000000000000000000000000; + } + else if ( n == 2 ) + { + w[0] = 1.000000000000000000000000000000; + w[1] = 1.000000000000000000000000000000; + } + else if ( n == 3 ) + { + w[0] = 0.555555555555555555555555555556; + w[1] = 0.888888888888888888888888888889; + w[2] = 0.555555555555555555555555555556; + } + else if ( n == 4 ) + { + w[0] = 0.347854845137453857373063949222; + w[1] = 0.652145154862546142626936050778; + w[2] = 0.652145154862546142626936050778; + w[3] = 0.347854845137453857373063949222; + } + else if ( n == 5 ) + { + w[0] = 0.236926885056189087514264040720; + w[1] = 0.478628670499366468041291514836; + w[2] = 0.568888888888888888888888888889; + w[3] = 0.478628670499366468041291514836; + w[4] = 0.236926885056189087514264040720; + } + else if ( n == 6 ) + { + w[0] = 0.171324492379170345040296142173; + w[1] = 0.360761573048138607569833513838; + w[2] = 0.467913934572691047389870343990; + w[3] = 0.467913934572691047389870343990; + w[4] = 0.360761573048138607569833513838; + w[5] = 0.171324492379170345040296142173; + } + else if ( n == 7 ) + { + w[0] = 0.129484966168869693270611432679; + w[1] = 0.279705391489276667901467771424; + w[2] = 0.381830050505118944950369775489; + w[3] = 0.417959183673469387755102040816; + w[4] = 0.381830050505118944950369775489; + w[5] = 0.279705391489276667901467771424; + w[6] = 0.129484966168869693270611432679; + } + else if ( n == 8 ) + { + w[0] = 0.101228536290376259152531354310; + w[1] = 0.222381034453374470544355994426; + w[2] = 0.313706645877887287337962201987; + w[3] = 0.362683783378361982965150449277; + w[4] = 0.362683783378361982965150449277; + w[5] = 0.313706645877887287337962201987; + w[6] = 0.222381034453374470544355994426; + w[7] = 0.101228536290376259152531354310; + } + else if ( n == 9 ) + { + w[0] = 0.081274388361574411971892158111; + w[1] = 0.18064816069485740405847203124; + w[2] = 0.26061069640293546231874286942; + w[3] = 0.31234707704000284006863040658; + w[4] = 0.33023935500125976316452506929; + w[5] = 0.31234707704000284006863040658; + w[6] = 0.26061069640293546231874286942; + w[7] = 0.18064816069485740405847203124; + w[8] = 0.081274388361574411971892158111; + } + else if ( n == 10 ) + { + w[0] = 0.066671344308688137593568809893; + w[1] = 0.14945134915058059314577633966; + w[2] = 0.21908636251598204399553493423; + w[3] = 0.26926671930999635509122692157; + w[4] = 0.29552422471475287017389299465; + w[5] = 0.29552422471475287017389299465; + w[6] = 0.26926671930999635509122692157; + w[7] = 0.21908636251598204399553493423; + w[8] = 0.14945134915058059314577633966; + w[9] = 0.066671344308688137593568809893; + } + else if ( n == 11 ) + { + w[0] = 0.055668567116173666482753720443; + w[1] = 0.12558036946490462463469429922; + w[2] = 0.18629021092773425142609764143; + w[3] = 0.23319376459199047991852370484; + w[4] = 0.26280454451024666218068886989; + w[5] = 0.27292508677790063071448352834; + w[6] = 0.26280454451024666218068886989; + w[7] = 0.23319376459199047991852370484; + w[8] = 0.18629021092773425142609764143; + w[9] = 0.12558036946490462463469429922; + w[10] = 0.055668567116173666482753720443; + } + else if ( n == 12 ) + { + w[0] = 0.047175336386511827194615961485; + w[1] = 0.10693932599531843096025471819; + w[2] = 0.16007832854334622633465252954; + w[3] = 0.20316742672306592174906445581; + w[4] = 0.23349253653835480876084989892; + w[5] = 0.24914704581340278500056243604; + w[6] = 0.24914704581340278500056243604; + w[7] = 0.23349253653835480876084989892; + w[8] = 0.20316742672306592174906445581; + w[9] = 0.16007832854334622633465252954; + w[10] = 0.10693932599531843096025471819; + w[11] = 0.047175336386511827194615961485; + } + else if ( n == 13 ) + { + w[0] = 0.040484004765315879520021592201; + w[1] = 0.092121499837728447914421775954; + w[2] = 0.13887351021978723846360177687; + w[3] = 0.17814598076194573828004669200; + w[4] = 0.20781604753688850231252321931; + w[5] = 0.22628318026289723841209018604; + w[6] = 0.23255155323087391019458951527; + w[7] = 0.22628318026289723841209018604; + w[8] = 0.20781604753688850231252321931; + w[9] = 0.17814598076194573828004669200; + w[10] = 0.13887351021978723846360177687; + w[11] = 0.092121499837728447914421775954; + w[12] = 0.040484004765315879520021592201; + } + else if ( n == 14 ) + { + w[0] = 0.035119460331751863031832876138; + w[1] = 0.08015808715976020980563327706; + w[2] = 0.12151857068790318468941480907; + w[3] = 0.15720316715819353456960193862; + w[4] = 0.18553839747793781374171659013; + w[5] = 0.20519846372129560396592406566; + w[6] = 0.21526385346315779019587644332; + w[7] = 0.21526385346315779019587644332; + w[8] = 0.20519846372129560396592406566; + w[9] = 0.18553839747793781374171659013; + w[10] = 0.15720316715819353456960193862; + w[11] = 0.12151857068790318468941480907; + w[12] = 0.08015808715976020980563327706; + w[13] = 0.035119460331751863031832876138; + } + else if ( n == 15 ) + { + w[0] = 0.030753241996117268354628393577; + w[1] = 0.070366047488108124709267416451; + w[2] = 0.107159220467171935011869546686; + w[3] = 0.13957067792615431444780479451; + w[4] = 0.16626920581699393355320086048; + w[5] = 0.18616100001556221102680056187; + w[6] = 0.19843148532711157645611832644; + w[7] = 0.20257824192556127288062019997; + w[8] = 0.19843148532711157645611832644; + w[9] = 0.18616100001556221102680056187; + w[10] = 0.16626920581699393355320086048; + w[11] = 0.13957067792615431444780479451; + w[12] = 0.107159220467171935011869546686; + w[13] = 0.070366047488108124709267416451; + w[14] = 0.030753241996117268354628393577; + } + else if ( n == 16 ) + { + w[0] = 0.027152459411754094851780572456; + w[1] = 0.062253523938647892862843836994; + w[2] = 0.09515851168249278480992510760; + w[3] = 0.12462897125553387205247628219; + w[4] = 0.14959598881657673208150173055; + w[5] = 0.16915651939500253818931207903; + w[6] = 0.18260341504492358886676366797; + w[7] = 0.18945061045506849628539672321; + w[8] = 0.18945061045506849628539672321; + w[9] = 0.18260341504492358886676366797; + w[10] = 0.16915651939500253818931207903; + w[11] = 0.14959598881657673208150173055; + w[12] = 0.12462897125553387205247628219; + w[13] = 0.09515851168249278480992510760; + w[14] = 0.062253523938647892862843836994; + w[15] = 0.027152459411754094851780572456; + } + else if ( n == 17 ) + { + w[0] = 0.024148302868547931960110026288; + w[1] = 0.055459529373987201129440165359; + w[2] = 0.085036148317179180883535370191; + w[3] = 0.111883847193403971094788385626; + w[4] = 0.13513636846852547328631998170; + w[5] = 0.15404576107681028808143159480; + w[6] = 0.16800410215645004450997066379; + w[7] = 0.17656270536699264632527099011; + w[8] = 0.17944647035620652545826564426; + w[9] = 0.17656270536699264632527099011; + w[10] = 0.16800410215645004450997066379; + w[11] = 0.15404576107681028808143159480; + w[12] = 0.13513636846852547328631998170; + w[13] = 0.111883847193403971094788385626; + w[14] = 0.085036148317179180883535370191; + w[15] = 0.055459529373987201129440165359; + w[16] = 0.024148302868547931960110026288; + } + else if ( n == 18 ) + { + w[0] = 0.021616013526483310313342710266; + w[1] = 0.049714548894969796453334946203; + w[2] = 0.07642573025488905652912967762; + w[3] = 0.10094204410628716556281398492; + w[4] = 0.12255520671147846018451912680; + w[5] = 0.14064291467065065120473130375; + w[6] = 0.15468467512626524492541800384; + w[7] = 0.16427648374583272298605377647; + w[8] = 0.16914238296314359184065647013; + w[9] = 0.16914238296314359184065647013; + w[10] = 0.16427648374583272298605377647; + w[11] = 0.15468467512626524492541800384; + w[12] = 0.14064291467065065120473130375; + w[13] = 0.12255520671147846018451912680; + w[14] = 0.10094204410628716556281398492; + w[15] = 0.07642573025488905652912967762; + w[16] = 0.049714548894969796453334946203; + w[17] = 0.021616013526483310313342710266; + } + else if ( n == 19 ) + { + w[0] = 0.019461788229726477036312041464; + w[1] = 0.044814226765699600332838157402; + w[2] = 0.069044542737641226580708258006; + w[3] = 0.091490021622449999464462094124; + w[4] = 0.111566645547333994716023901682; + w[5] = 0.12875396253933622767551578486; + w[6] = 0.14260670217360661177574610944; + w[7] = 0.15276604206585966677885540090; + w[8] = 0.15896884339395434764995643946; + w[9] = 0.16105444984878369597916362532; + w[10] = 0.15896884339395434764995643946; + w[11] = 0.15276604206585966677885540090; + w[12] = 0.14260670217360661177574610944; + w[13] = 0.12875396253933622767551578486; + w[14] = 0.111566645547333994716023901682; + w[15] = 0.091490021622449999464462094124; + w[16] = 0.069044542737641226580708258006; + w[17] = 0.044814226765699600332838157402; + w[18] = 0.019461788229726477036312041464; + } + else if ( n == 20 ) + { + w[0] = 0.017614007139152118311861962352; + w[1] = 0.040601429800386941331039952275; + w[2] = 0.062672048334109063569506535187; + w[3] = 0.08327674157670474872475814322; + w[4] = 0.10193011981724043503675013548; + w[5] = 0.11819453196151841731237737771; + w[6] = 0.13168863844917662689849449975; + w[7] = 0.14209610931838205132929832507; + w[8] = 0.14917298647260374678782873700; + w[9] = 0.15275338713072585069808433195; + w[10] = 0.15275338713072585069808433195; + w[11] = 0.14917298647260374678782873700; + w[12] = 0.14209610931838205132929832507; + w[13] = 0.13168863844917662689849449975; + w[14] = 0.11819453196151841731237737771; + w[15] = 0.10193011981724043503675013548; + w[16] = 0.08327674157670474872475814322; + w[17] = 0.062672048334109063569506535187; + w[18] = 0.040601429800386941331039952275; + w[19] = 0.017614007139152118311861962352; + } + else if ( n == 21 ) + { + w[ 0] = 0.016017228257774333324224616858; + w[ 1] = 0.036953789770852493799950668299; + w[ 2] = 0.057134425426857208283635826472; + w[ 3] = 0.076100113628379302017051653300; + w[ 4] = 0.093444423456033861553289741114; + w[ 5] = 0.108797299167148377663474578070; + w[ 6] = 0.12183141605372853419536717713; + w[ 7] = 0.13226893863333746178105257450; + w[ 8] = 0.13988739479107315472213342387; + w[9] = 0.14452440398997005906382716655; + w[10] = 0.14608113364969042719198514768; + w[11] = 0.14452440398997005906382716655; + w[12] = 0.13988739479107315472213342387; + w[13] = 0.13226893863333746178105257450; + w[14] = 0.12183141605372853419536717713; + w[15] = 0.108797299167148377663474578070; + w[16] = 0.093444423456033861553289741114; + w[17] = 0.076100113628379302017051653300; + w[18] = 0.057134425426857208283635826472; + w[19] = 0.036953789770852493799950668299; + w[20] = 0.016017228257774333324224616858; + } + else if ( n == 22 ) + { + w[0] = 0.014627995298272200684991098047; + w[1] = 0.033774901584814154793302246866; + w[2] = 0.052293335152683285940312051273; + w[3] = 0.06979646842452048809496141893; + w[4] = 0.08594160621706772741444368137; + w[5] = 0.10041414444288096493207883783; + w[6] = 0.11293229608053921839340060742; + w[7] = 0.12325237681051242428556098615; + w[8] = 0.13117350478706237073296499253; + w[9] = 0.13654149834601517135257383123; + w[10] = 0.13925187285563199337541024834; + w[11] = 0.13925187285563199337541024834; + w[12] = 0.13654149834601517135257383123; + w[13] = 0.13117350478706237073296499253; + w[14] = 0.12325237681051242428556098615; + w[15] = 0.11293229608053921839340060742; + w[16] = 0.10041414444288096493207883783; + w[17] = 0.08594160621706772741444368137; + w[18] = 0.06979646842452048809496141893; + w[19] = 0.052293335152683285940312051273; + w[20] = 0.033774901584814154793302246866; + w[21] = 0.014627995298272200684991098047; + } + else if ( n == 23 ) + { + w[0] = 0.013411859487141772081309493459; + w[1] = 0.030988005856979444310694219642; + w[2] = 0.048037671731084668571641071632; + w[3] = 0.064232421408525852127169615159; + w[4] = 0.079281411776718954922892524742; + w[5] = 0.092915766060035147477018617370; + w[6] = 0.104892091464541410074086185015; + w[7] = 0.11499664022241136494164351293; + w[8] = 0.12304908430672953046757840067; + w[9] = 0.12890572218808214997859533940; + w[10] = 0.13246203940469661737164246470; + w[11] = 0.13365457218610617535145711055; + w[12] = 0.13246203940469661737164246470; + w[13] = 0.12890572218808214997859533940; + w[14] = 0.12304908430672953046757840067; + w[15] = 0.11499664022241136494164351293; + w[16] = 0.104892091464541410074086185015; + w[17] = 0.092915766060035147477018617370; + w[18] = 0.079281411776718954922892524742; + w[19] = 0.064232421408525852127169615159; + w[20] = 0.048037671731084668571641071632; + w[21] = 0.030988005856979444310694219642; + w[22] = 0.013411859487141772081309493459; + } + else if ( n == 24 ) + { + w[0] = 0.012341229799987199546805667070; + w[1] = 0.028531388628933663181307815952; + w[2] = 0.044277438817419806168602748211; + w[3] = 0.059298584915436780746367758500; + w[4] = 0.07334648141108030573403361525; + w[5] = 0.08619016153195327591718520298; + w[6] = 0.09761865210411388826988066446; + w[7] = 0.10744427011596563478257734245; + w[8] = 0.11550566805372560135334448391; + w[9] = 0.12167047292780339120446315348; + w[10] = 0.12583745634682829612137538251; + w[11] = 0.12793819534675215697405616522; + w[12] = 0.12793819534675215697405616522; + w[13] = 0.12583745634682829612137538251; + w[14] = 0.12167047292780339120446315348; + w[15] = 0.11550566805372560135334448391; + w[16] = 0.10744427011596563478257734245; + w[17] = 0.09761865210411388826988066446; + w[18] = 0.08619016153195327591718520298; + w[19] = 0.07334648141108030573403361525; + w[20] = 0.059298584915436780746367758500; + w[21] = 0.044277438817419806168602748211; + w[22] = 0.028531388628933663181307815952; + w[23] = 0.012341229799987199546805667070; + } + else if ( n == 25 ) + { + w[0] = 0.0113937985010262879479029641132; + w[1] = 0.026354986615032137261901815295; + w[2] = 0.040939156701306312655623487712; + w[3] = 0.054904695975835191925936891541; + w[4] = 0.068038333812356917207187185657; + w[5] = 0.080140700335001018013234959669; + w[6] = 0.091028261982963649811497220703; + w[7] = 0.100535949067050644202206890393; + w[8] = 0.108519624474263653116093957050; + w[9] = 0.11485825914571164833932554587; + w[10] = 0.11945576353578477222817812651; + w[11] = 0.12224244299031004168895951895; + w[12] = 0.12317605372671545120390287308; + w[13] = 0.12224244299031004168895951895; + w[14] = 0.11945576353578477222817812651; + w[15] = 0.11485825914571164833932554587; + w[16] = 0.108519624474263653116093957050; + w[17] = 0.100535949067050644202206890393; + w[18] = 0.091028261982963649811497220703; + w[19] = 0.080140700335001018013234959669; + w[20] = 0.068038333812356917207187185657; + w[21] = 0.054904695975835191925936891541; + w[22] = 0.040939156701306312655623487712; + w[23] = 0.026354986615032137261901815295; + w[24] = 0.0113937985010262879479029641132; + } + else if ( n == 26 ) + { + w[0] = 0.010551372617343007155651187685; + w[1] = 0.024417851092631908789615827520; + w[2] = 0.037962383294362763950303141249; + w[3] = 0.050975825297147811998319900724; + w[4] = 0.063274046329574835539453689907; + w[5] = 0.07468414976565974588707579610; + w[6] = 0.08504589431348523921044776508; + w[7] = 0.09421380035591414846366488307; + w[8] = 0.10205916109442542323841407025; + w[9] = 0.10847184052857659065657942673; + w[10] = 0.11336181654631966654944071844; + w[11] = 0.11666044348529658204466250754; + w[12] = 0.11832141527926227651637108570; + w[13] = 0.11832141527926227651637108570; + w[14] = 0.11666044348529658204466250754; + w[15] = 0.11336181654631966654944071844; + w[16] = 0.10847184052857659065657942673; + w[17] = 0.10205916109442542323841407025; + w[18] = 0.09421380035591414846366488307; + w[19] = 0.08504589431348523921044776508; + w[20] = 0.07468414976565974588707579610; + w[21] = 0.063274046329574835539453689907; + w[22] = 0.050975825297147811998319900724; + w[23] = 0.037962383294362763950303141249; + w[24] = 0.024417851092631908789615827520; + w[25] = 0.010551372617343007155651187685; + } + else if ( n == 27 ) + { + w[0] = 0.0097989960512943602611500550912; + w[1] = 0.022686231596180623196034206447; + w[2] = 0.035297053757419711022578289305; + w[3] = 0.047449412520615062704096710114; + w[4] = 0.058983536859833599110300833720; + w[5] = 0.069748823766245592984322888357; + w[6] = 0.079604867773057771263074959010; + w[7] = 0.088423158543756950194322802854; + w[8] = 0.096088727370028507565652646558; + w[9] = 0.102501637817745798671247711533; + w[10] = 0.107578285788533187212162984427; + w[11] = 0.111252488356845192672163096043; + w[12] = 0.113476346108965148620369948092; + w[13] = 0.11422086737895698904504573690; + w[14] = 0.113476346108965148620369948092; + w[15] = 0.111252488356845192672163096043; + w[16] = 0.107578285788533187212162984427; + w[17] = 0.102501637817745798671247711533; + w[18] = 0.096088727370028507565652646558; + w[19] = 0.088423158543756950194322802854; + w[20] = 0.079604867773057771263074959010; + w[21] = 0.069748823766245592984322888357; + w[22] = 0.058983536859833599110300833720; + w[23] = 0.047449412520615062704096710114; + w[24] = 0.035297053757419711022578289305; + w[25] = 0.022686231596180623196034206447; + w[26] = 0.0097989960512943602611500550912; + } + else if ( n == 28 ) + { + w[0] = 0.009124282593094517738816153923; + w[1] = 0.021132112592771259751500380993; + w[2] = 0.032901427782304379977630819171; + w[3] = 0.044272934759004227839587877653; + w[4] = 0.055107345675716745431482918227; + w[5] = 0.06527292396699959579339756678; + w[6] = 0.07464621423456877902393188717; + w[7] = 0.08311341722890121839039649824; + w[8] = 0.09057174439303284094218603134; + w[9] = 0.09693065799792991585048900610; + w[10] = 0.10211296757806076981421663851; + w[11] = 0.10605576592284641791041643700; + w[12] = 0.10871119225829413525357151930; + w[13] = 0.11004701301647519628237626560; + w[14] = 0.11004701301647519628237626560; + w[15] = 0.10871119225829413525357151930; + w[16] = 0.10605576592284641791041643700; + w[17] = 0.10211296757806076981421663851; + w[18] = 0.09693065799792991585048900610; + w[19] = 0.09057174439303284094218603134; + w[20] = 0.08311341722890121839039649824; + w[21] = 0.07464621423456877902393188717; + w[22] = 0.06527292396699959579339756678; + w[23] = 0.055107345675716745431482918227; + w[24] = 0.044272934759004227839587877653; + w[25] = 0.032901427782304379977630819171; + w[26] = 0.021132112592771259751500380993; + w[27] = 0.009124282593094517738816153923; + } + else if ( n == 29 ) + { + w[0] = 0.0085169038787464096542638133022; + w[1] = 0.019732085056122705983859801640; + w[2] = 0.030740492202093622644408525375; + w[3] = 0.041402062518682836104830010114; + w[4] = 0.051594826902497923912594381180; + w[5] = 0.061203090657079138542109848024; + w[6] = 0.070117933255051278569581486949; + w[7] = 0.078238327135763783828144888660; + w[8] = 0.085472257366172527545344849297; + w[9] = 0.091737757139258763347966411077; + w[10] = 0.096963834094408606301900074883; + w[11] = 0.101091273759914966121820546907; + w[12] = 0.104073310077729373913328471285; + w[13] = 0.105876155097320941406591327852; + w[14] = 0.10647938171831424424651112691; + w[15] = 0.105876155097320941406591327852; + w[16] = 0.104073310077729373913328471285; + w[17] = 0.101091273759914966121820546907; + w[18] = 0.096963834094408606301900074883; + w[19] = 0.091737757139258763347966411077; + w[20] = 0.085472257366172527545344849297; + w[21] = 0.078238327135763783828144888660; + w[22] = 0.070117933255051278569581486949; + w[23] = 0.061203090657079138542109848024; + w[24] = 0.051594826902497923912594381180; + w[25] = 0.041402062518682836104830010114; + w[26] = 0.030740492202093622644408525375; + w[27] = 0.019732085056122705983859801640; + w[28] = 0.0085169038787464096542638133022; + } + else if ( n == 30 ) + { + w[0] = 0.007968192496166605615465883475; + w[1] = 0.018466468311090959142302131912; + w[2] = 0.028784707883323369349719179611; + w[3] = 0.038799192569627049596801936446; + w[4] = 0.048402672830594052902938140423; + w[5] = 0.057493156217619066481721689402; + w[6] = 0.06597422988218049512812851512; + w[7] = 0.07375597473770520626824385002; + w[8] = 0.08075589522942021535469493846; + w[9] = 0.08689978720108297980238753072; + w[10] = 0.09212252223778612871763270709; + w[11] = 0.09636873717464425963946862635; + w[12] = 0.09959342058679526706278028210; + w[13] = 0.10176238974840550459642895217; + w[14] = 0.10285265289355884034128563671; + w[15] = 0.10285265289355884034128563671; + w[16] = 0.10176238974840550459642895217; + w[17] = 0.09959342058679526706278028210; + w[18] = 0.09636873717464425963946862635; + w[19] = 0.09212252223778612871763270709; + w[20] = 0.08689978720108297980238753072; + w[21] = 0.08075589522942021535469493846; + w[22] = 0.07375597473770520626824385002; + w[23] = 0.06597422988218049512812851512; + w[24] = 0.057493156217619066481721689402; + w[25] = 0.048402672830594052902938140423; + w[26] = 0.038799192569627049596801936446; + w[27] = 0.028784707883323369349719179611; + w[28] = 0.018466468311090959142302131912; + w[29] = 0.007968192496166605615465883475; + } + else if ( n == 31 ) + { + w[0] = 0.0074708315792487758586968750322; + w[1] = 0.017318620790310582463157996087; + w[2] = 0.027009019184979421800608708092; + w[3] = 0.036432273912385464024392010468; + w[4] = 0.045493707527201102902315857895; + w[5] = 0.054103082424916853711666259087; + w[6] = 0.062174786561028426910343543687; + w[7] = 0.069628583235410366167756126255; + w[8] = 0.076390386598776616426357674901; + w[9] = 0.082392991761589263903823367432; + w[10] = 0.087576740608477876126198069695; + w[11] = 0.091890113893641478215362871607; + w[12] = 0.095290242912319512807204197488; + w[13] = 0.097743335386328725093474010979; + w[14] = 0.099225011226672307874875514429; + w[15] = 0.09972054479342645142753383373; + w[16] = 0.099225011226672307874875514429; + w[17] = 0.097743335386328725093474010979; + w[18] = 0.095290242912319512807204197488; + w[19] = 0.091890113893641478215362871607; + w[20] = 0.087576740608477876126198069695; + w[21] = 0.082392991761589263903823367432; + w[22] = 0.076390386598776616426357674901; + w[23] = 0.069628583235410366167756126255; + w[24] = 0.062174786561028426910343543687; + w[25] = 0.054103082424916853711666259087; + w[26] = 0.045493707527201102902315857895; + w[27] = 0.036432273912385464024392010468; + w[28] = 0.027009019184979421800608708092; + w[29] = 0.017318620790310582463157996087; + w[30] = 0.0074708315792487758586968750322; + } + else if ( n == 32 ) + { + w[0] = 0.007018610009470096600407063739; + w[1] = 0.016274394730905670605170562206; + w[2] = 0.025392065309262059455752589789; + w[3] = 0.034273862913021433102687732252; + w[4] = 0.042835898022226680656878646606; + w[5] = 0.050998059262376176196163244690; + w[6] = 0.058684093478535547145283637300; + w[7] = 0.06582222277636184683765006371; + w[8] = 0.07234579410884850622539935648; + w[9] = 0.07819389578707030647174091883; + w[10] = 0.08331192422694675522219907460; + w[11] = 0.08765209300440381114277146275; + w[12] = 0.09117387869576388471286857711; + w[13] = 0.09384439908080456563918023767; + w[14] = 0.09563872007927485941908200220; + w[15] = 0.09654008851472780056676483006; + w[16] = 0.09654008851472780056676483006; + w[17] = 0.09563872007927485941908200220; + w[18] = 0.09384439908080456563918023767; + w[19] = 0.09117387869576388471286857711; + w[20] = 0.08765209300440381114277146275; + w[21] = 0.08331192422694675522219907460; + w[22] = 0.07819389578707030647174091883; + w[23] = 0.07234579410884850622539935648; + w[24] = 0.06582222277636184683765006371; + w[25] = 0.058684093478535547145283637300; + w[26] = 0.050998059262376176196163244690; + w[27] = 0.042835898022226680656878646606; + w[28] = 0.034273862913021433102687732252; + w[29] = 0.025392065309262059455752589789; + w[30] = 0.016274394730905670605170562206; + w[31] = 0.007018610009470096600407063739; + } + else if ( n == 33 ) + { + w[0] = 0.0066062278475873780586492352085; + w[1] = 0.015321701512934676127945768534; + w[2] = 0.023915548101749480350533257529; + w[3] = 0.032300358632328953281561447250; + w[4] = 0.040401541331669591563409790527; + w[5] = 0.048147742818711695670146880138; + w[6] = 0.055470846631663561284944495439; + w[7] = 0.062306482530317480031627725771; + w[8] = 0.068594572818656712805955073015; + w[9] = 0.074279854843954149342472175919; + w[10] = 0.079312364794886738363908384942; + w[11] = 0.083647876067038707613928014518; + w[12] = 0.087248287618844337607281670945; + w[13] = 0.090081958660638577239743705500; + w[14] = 0.092123986643316846213240977717; + w[15] = 0.093356426065596116160999126274; + w[16] = 0.09376844616020999656730454155; + w[17] = 0.093356426065596116160999126274; + w[18] = 0.092123986643316846213240977717; + w[19] = 0.090081958660638577239743705500; + w[20] = 0.087248287618844337607281670945; + w[21] = 0.083647876067038707613928014518; + w[22] = 0.079312364794886738363908384942; + w[23] = 0.074279854843954149342472175919; + w[24] = 0.068594572818656712805955073015; + w[25] = 0.062306482530317480031627725771; + w[26] = 0.055470846631663561284944495439; + w[27] = 0.048147742818711695670146880138; + w[28] = 0.040401541331669591563409790527; + w[29] = 0.032300358632328953281561447250; + w[30] = 0.023915548101749480350533257529; + w[31] = 0.015321701512934676127945768534; + w[32] = 0.0066062278475873780586492352085; + } + else + { + std::cerr << "\n"; + std::cerr << "LEGENDRE_LOOKUP_WEIGHTS - Fatal error!\n"; + std::cerr << " Illegal value of N = " << n << "\n"; + std::cerr << " Legal values are 1 through 33.\n"; + std::exit ( 1 ); + } + return; +} +//****************************************************************************80 + +double *legendre_zeros ( int order ) + +//****************************************************************************80 +// +// Purpose: +// +// LEGENDRE_ZEROS returns the zeros of the Legendre polynomial of degree N. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 June 2011 +// +// Author: +// +// Original FORTRAN77 version by Philip Davis, Philip Rabinowitz. +// C++ version by John Burkardt. +// +// Reference: +// +// Philip Davis, Philip Rabinowitz, +// Methods of Numerical Integration, +// Second Edition, +// Dover, 2007, +// ISBN: 0486453391, +// LC: QA299.3.D28. +// +// Parameters: +// +// Input, int ORDER, the order. +// ORDER must be greater than 0. +// +// Output, double LEGENDRE_ZEROS[ORDER], the zeros. +// +{ + double d1; + double d2pn; + double d3pn; + double d4pn; + double dp; + double dpn; + double e1; + double fx; + double h; + int i; + int iback; + int k; + int m; + int mp1mi; + int ncopy; + int nmove; + double p; + double pi = 3.141592653589793; + double pk; + double pkm1; + double pkp1; + double t; + double u; + double v; + double x0; + double *xtab; + double xtemp; + + xtab = new double[order]; + + e1 = ( double ) ( order * ( order + 1 ) ); + + m = ( order + 1 ) / 2; + + for ( i = 1; i <= m; i++ ) + { + mp1mi = m + 1 - i; + + t = ( double ) ( 4 * i - 1 ) * pi / ( double ) ( 4 * order + 2 ); + + x0 = std::cos ( t ) * ( 1.0 - ( 1.0 - 1.0 / ( double ) ( order ) ) + / ( double ) ( 8 * order * order ) ); + + pkm1 = 1.0; + pk = x0; + + for ( k = 2; k <= order; k++ ) + { + pkp1 = 2.0 * x0 * pk - pkm1 - ( x0 * pk - pkm1 ) / ( double ) ( k ); + pkm1 = pk; + pk = pkp1; + } + + d1 = ( double ) ( order ) * ( pkm1 - x0 * pk ); + + dpn = d1 / ( 1.0 - x0 * x0 ); + + d2pn = ( 2.0 * x0 * dpn - e1 * pk ) / ( 1.0 - x0 * x0 ); + + d3pn = ( 4.0 * x0 * d2pn + ( 2.0 - e1 ) * dpn ) / ( 1.0 - x0 * x0 ); + + d4pn = ( 6.0 * x0 * d3pn + ( 6.0 - e1 ) * d2pn ) / ( 1.0 - x0 * x0 ); + + u = pk / dpn; + v = d2pn / dpn; +// +// Initial approximation H: +// + h = - u * ( 1.0 + 0.5 * u * ( v + u * ( v * v - d3pn / ( 3.0 * dpn ) ) ) ); +// +// Refine H using one step of Newton's method: +// + p = pk + h * ( dpn + 0.5 * h * ( d2pn + h / 3.0 + * ( d3pn + 0.25 * h * d4pn ) ) ); + + dp = dpn + h * ( d2pn + 0.5 * h * ( d3pn + h * d4pn / 3.0 ) ); + + h = h - p / dp; + + xtemp = x0 + h; + + xtab[mp1mi-1] = xtemp; + + fx = d1 - h * e1 * ( pk + 0.5 * h * ( dpn + h / 3.0 + * ( d2pn + 0.25 * h * ( d3pn + 0.2 * h * d4pn ) ) ) ); + } + + if ( ( order % 2 ) == 1 ) + { + xtab[0] = 0.0; + } +// +// Shift the data up. +// + nmove = ( order + 1 ) / 2; + ncopy = order - nmove; + + for ( i = 1; i <= nmove; i++ ) + { + iback = order + 1 - i; + xtab[iback-1] = xtab[iback-ncopy-1]; + } +// +// Reflect values for the negative abscissas. +// + for ( i = 1; i <= order - nmove; i++ ) + { + xtab[i-1] = - xtab[order-i]; + } + + return xtab; +} +//****************************************************************************80 + +void level_growth_to_order ( int dim_num, int level[], int rule[], + int growth[], int order[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_GROWTH_TO_ORDER: convert Level and Growth to Order. +// +// Discussion: +// +// This function is given level, rule, and growth information +// for each dimension of a quadrature rule, and determines the +// corresponding order of the rule in each dimension. +// +// This is a revised version of LEVEL_GROWTH_TO_ORDER. +// +// In particular, it revises the interpretation of the RULE vector as +// far as the values 10, 11, and 12 are concerned. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 16 October 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int DIM_NUM, the spatial dimension. +// +// Input, int LEVEL[DIM_NUM], the 1D levels. +// +// Input, int RULE[DIM_NUM], the rule in each dimension. +// 1, "CC", Clenshaw Curtis, Closed Fully Nested. +// 2, "F2", Fejer Type 2, Open Fully Nested. +// 3, "GP", Gauss Patterson, Open Fully Nested. +// 4, "GL", Gauss Legendre, Open Weakly Nested. +// 5, "GH", Gauss Hermite, Open Weakly Nested. +// 6, "GGH", Generalized Gauss Hermite, Open Weakly Nested. +// 7, "LG", Gauss Laguerre, Open Non Nested. +// 8, "GLG", Generalized Gauss Laguerre, Open Non Nested. +// 9, "GJ", Gauss Jacobi, Open Non Nested. +// 10, "HGK", Hermite Genz-Keister, Open Fully Nested. +// 11, "UO", User supplied Open, presumably Non Nested. +// 12, "UC", User supplied Closed, presumably Non Nested. +// +// Input, int GROWTH[DIM_NUM], the desired growth in each dimension. +// 0, "DF", default growth associated with this quadrature rule; +// 1, "SL", slow linear, L+1; +// 2 "SO", slow linear odd, O=1+2((L+1)/2) +// 3, "ML", moderate linear, 2L+1; +// 4, "SE", slow exponential; +// 5, "ME", moderate exponential; +// 6, "FE", full exponential. +// +// Output, int ORDER[DIM_NUM], the 1D orders (number of points). +// +{ + int dim; + int l; + int o; + static int o_hgk[6] = { 1, 3, 9, 19, 35, 43 }; + int p; + static int p_hgk[6] = { 1, 5, 15, 29, 51, 67 }; +// +// Check the input. +// + for ( dim = 0; dim < dim_num; dim++ ) + { + if ( level[dim] < 0 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Negative value of LEVEL[DIM]!\n"; + std::cerr << " LEVEL[" << dim << "] = " << level[dim] << "\n"; + std::exit ( 1 ); + } + + if ( rule[dim] < 1 || 12 < rule[dim] ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Illegal value of RULE[DIM]!\n"; + std::cerr << " RULE[" << dim << "] = " << rule[dim] << "\n"; + std::exit ( 1 ); + } + + if ( growth[dim] < 0 || 6 < growth[dim] ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Illegal value of GROWTH[DIM]!\n"; + std::cerr << " GROWTH[" << dim << "] = " << growth[dim] << "\n"; + std::exit ( 1 ); + } + } +// +// Compute the order vector. +// + for ( dim = 0; dim < dim_num; dim++ ) + { +// +// CC +// Default is Moderate Exponential Growth. +// + if ( rule[dim] == 1 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + o = 2; + while ( o < 2 * level[dim] + 1 ) + { + o = 2 * ( o - 1 ) + 1; + } + } + } + else if ( growth[dim] == 5 || growth[dim] == 0 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + o = 2; + while ( o < 4 * level[dim] + 1 ) + { + o = 2 * ( o - 1 ) + 1; + } + } + } + else if ( growth[dim] == 6 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + o = webbur::i4_power ( 2, level[dim] ) + 1; + } + } + } +// +// F2 +// Default is Moderate Exponential Growth. +// + else if ( rule[dim] == 2 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + o = 1; + while ( o < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 5 || growth[dim] == 0 ) + { + o = 1; + while ( o < 4 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 6 ) + { + o = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + } +// +// GP +// Default is Moderate Exponential Growth. +// + else if ( rule[dim] == 3 ) + { + if ( growth[dim] == 1 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Growth rate 1 for rule 3 not available!\n"; + std::exit ( 1 ); + } + else if ( growth[dim] == 2 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Growth rate 2 for rule 3 not available!\n"; + std::exit ( 1 ); + } + else if ( growth[dim] == 3 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Growth rate 3 for rule 3 not available!\n"; + std::exit ( 1 ); + } + else if ( growth[dim] == 4 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + p = 5; + o = 3; + while ( p < 2 * level[dim] + 1 ) + { + p = 2 * p + 1; + o = 2 * o + 1; + } + } + } + else if ( growth[dim] == 5 || growth[dim] == 0 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + p = 5; + o = 3; + while ( p < 4 * level[dim] + 1 ) + { + p = 2 * p + 1; + o = 2 * o + 1; + } + } + } + else if ( growth[dim] == 6 ) + { + o = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + } +// +// GL +// Default is Moderate Linear Growth. +// + else if ( rule[dim] == 4 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 || growth[dim] == 0 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + o = 1; + while ( 2 * o - 1 < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 5 ) + { + o = 1; + while ( 2 * o - 1 < 4 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 6 ) + { + o = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + } +// +// GH +// Default is Moderate Linear Growth. +// + else if ( rule[dim] == 5 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 || growth[dim] == 0 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + o = 1; + while ( 2 * o - 1 < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 5 ) + { + o = 1; + while ( 2 * o - 1 < 4 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 6 ) + { + o = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + } +// +// GGH +// Default is Moderate Linear Growth. +// + else if ( rule[dim] == 6 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 || growth[dim] == 0 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + o = 1; + while ( 2 * o - 1 < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 5 ) + { + o = 1; + while ( 2 * o - 1 < 4 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 6 ) + { + o = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + } +// +// LG +// Default is Moderate Linear Growth. +// + else if ( rule[dim] == 7 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 || growth[dim] == 0 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + o = 1; + while ( 2 * o - 1 < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 5 ) + { + o = 1; + while ( 2 * o - 1 < 4 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 6 ) + { + o = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + } +// +// GLG +// Default is Moderate Linear Growth. +// + else if ( rule[dim] == 8 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 || growth[dim] == 0 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + o = 1; + while ( 2 * o - 1 < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 5 ) + { + o = 1; + while ( 2 * o - 1 < 4 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 6 ) + { + o = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + } +// +// GJ +// Default is Moderate Linear Growth. +// + else if ( rule[dim] == 9 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 || growth[dim] == 0 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + o = 1; + while ( 2 * o - 1 < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 5 ) + { + o = 1; + while ( 2 * o - 1 < 4 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 6 ) + { + o = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + } +// +// HGK +// Default is Moderate Exponential Growth. +// Exponential growth is interpreted to mean simply take successive rules. +// + else if ( rule[dim] == 10 ) + { + if ( growth[dim] == 1 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Growth rate 1 for rule 10 not available!\n"; + std::exit ( 1 ); + } + else if ( growth[dim] == 2 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Growth rate 2 for rule 10 not available!\n"; + std::exit ( 1 ); + } + else if ( growth[dim] == 3 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Growth rate 3 for rule 10 not available!\n"; + std::exit ( 1 ); + } + else if ( growth[dim] == 4 ) + { + l = 0; + p = p_hgk[l]; + o = o_hgk[l]; + while ( p < 2 * level[dim] + 1 ) + { + l = l + 1; + if ( 5 < l ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Hermite Genz-Keister maximum level exceeded.\n"; + std::exit ( 1 ); + } + p = p_hgk[l]; + o = o_hgk[l]; + } + } + else if ( growth[dim] == 5 || growth[dim] == 0 ) + { + l = 0; + p = p_hgk[l]; + o = o_hgk[l]; + while ( p < 4 * level[dim] + 1 ) + { + l = l + 1; + if ( 5 < l ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Hermite Genz-Keister maximum level exceeded.\n"; + std::exit ( 1 ); + } + p = p_hgk[l]; + o = o_hgk[l]; + } + } + else if ( growth[dim] == 6 ) + { + l = level[dim]; + l = webbur::i4_max ( l, 0 ); + if ( 5 < l ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_GROWTH_TO_ORDER - Fatal error!\n"; + std::cerr << " Hermite Genz-Keister maximum level exceeded.\n"; + std::exit ( 1 ); + } + o = o_hgk[l]; + } + } +// +// UO +// Default is Moderate Linear Growth. +// We assume the rule is of OPEN type and that it +// has a precision typical of Gauss rules. +// + else if ( rule[dim] == 11 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 || growth[dim] == 0 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + o = 1; + while ( 2 * o - 1 < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 5 ) + { + o = 1; + while ( 2 * o - 1 < 4 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + else if ( growth[dim] == 6 ) + { + o = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + } +// +// UC +// Default is Moderate Linear Growth. +// We assume the rule is of CLOSED type and that it +// has a precision typical of Clenshaw-Curtis rules. +// + else if ( rule[dim] == 12 ) + { + if ( growth[dim] == 1 ) + { + o = level[dim] + 1; + } + else if ( growth[dim] == 2 ) + { + o = 2 * ( ( level[dim] + 1 ) / 2 ) + 1; + } + else if ( growth[dim] == 3 || growth[dim] == 0 ) + { + o = 2 * level[dim] + 1; + } + else if ( growth[dim] == 4 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + o = 2; + while ( o < 2 * level[dim] + 1 ) + { + o = 2 * ( o - 1 ) + 1; + } + } + } + else if ( growth[dim] == 5 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + o = 2; + while ( o < 4 * level[dim] + 1 ) + { + o = 2 * ( o - 1 ) + 1; + } + } + } + else if ( growth[dim] == 6 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + o = webbur::i4_power ( 2, level[dim] ) + 1; + } + } + } + order[dim] = o; + } + return; +} +//****************************************************************************80 + +void level_to_order_default ( int dim_num, int level[], int rule[], + int order[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_DEFAULT: default growth. +// +// Discussion: +// +// This function uses: +// +// * exponential growth rates for fully nested quadrature rules, +// ( "CC", "F2", "GP"); +// +// * linear growth rates for other rules. +// ( "GL", "GH", "GGH", "LG", "GLG", "GJ", "GW" ). +// +// * slow exponential growth alternative for fully nested rules: +// ("CC_SE", "F2_SE", "GP_SE"). +// +// * moderate exponential growth alternative for fully nested rules: +// ("CC_ME", "F2_ME", "GP_ME"). +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int DIM_NUM, the spatial dimension. +// +// Input, int LEVEL[DIM_NUM], the 1D levels. +// +// Input, int RULE[DIM_NUM], the rule in each dimension. +// 1, "CC", Clenshaw Curtis, Closed Fully Nested rule. +// 2, "F2", Fejer Type 2, Open Fully Nested rule. +// 3, "GP", Gauss Patterson, Open Fully Nested rule. +// 4, "GL", Gauss Legendre, Open Weakly Nested rule. +// 5, "GH", Gauss Hermite, Open Weakly Nested rule. +// 6, "GGH", Generalized Gauss Hermite, Open Weakly Nested rule. +// 7, "LG", Gauss Laguerre, Open Non Nested rule. +// 8, "GLG", Generalized Gauss Laguerre, Open Non Nested rule. +// 9, "GJ", Gauss Jacobi, Open Non Nested rule. +// 10, "GW", Golub Welsch, (presumed) Open Non Nested rule. +// 11, "CC_SE", Clenshaw Curtis Slow Exponential, Closed Fully Nested rule. +// 12, "F2_SE", Fejer Type 2 Slow Exponential, Open Fully Nested rule. +// 13, "GP_SE", Gauss Patterson Slow Exponential, Open Fully Nested rule. +// 14, "CC_ME", Clenshaw Curtis Moderate Exponential, Closed Fully Nested rule. +// 15, "F2_ME", Fejer Type 2 Moderate Exponential, Open Fully Nested rule. +// 16, "GP_ME", Gauss Patterson Moderate Exponential, Open Fully Nested rule. +// 17, "CCN", Clenshaw Curtis Nested, Linear, Closed Fully Nested rule. +// +// Output, int ORDER[DIM_NUM], the 1D orders (number of points). +// +{ + int dim; + int o; + int p; + + for ( dim = 0; dim < dim_num; dim++ ) + { + if ( level[dim] < 0 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_DEFAULT - Fatal error!\n"; + std::cerr << " Negative value of LEVEL[DIM]!\n"; + std::cerr << " LEVEL[" << dim << "] = " << level[dim] << "\n"; + std::exit ( 1 ); + } + else if ( rule[dim] == 1 ) + { + if ( level[dim] == 0 ) + { + order[dim] = 1; + } + else + { + order[dim] = webbur::i4_power ( 2, level[dim] ) + 1; + } + } + else if ( rule[dim] == 2 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 3 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 4 ) + { + order[dim] = 2 * level[dim] + 1; + } + else if ( rule[dim] == 5 ) + { + order[dim] = 2 * level[dim] + 1; + } + else if ( rule[dim] == 6 ) + { + order[dim] = 2 * level[dim] + 1; + } + else if ( rule[dim] == 7 ) + { + order[dim] = 2 * level[dim] + 1; + } + else if ( rule[dim] == 8 ) + { + order[dim] = 2 * level[dim] + 1; + } + else if ( rule[dim] == 9 ) + { + order[dim] = 2 * level[dim] + 1; + } + else if ( rule[dim] == 10 ) + { + order[dim] = 2 * level[dim] + 1; + } + else if ( rule[dim] == 11 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + o = 2; + while ( o < 2 * level[dim] + 1 ) + { + o = 2 * ( o - 1 ) + 1; + } + } + order[dim] = o; + } + else if ( rule[dim] == 12 ) + { + o = 1; + while ( o < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + order[dim] = o; + } + else if ( rule[dim] == 13 ) + { + if ( level[dim] == 0 ) + { + order[dim] = 1; + } + else + { + p = 5; + o = 3; + while ( p < 2 * level[dim] + 1 ) + { + p = 2 * p + 1; + o = 2 * o + 1; + } + order[dim] = o; + } + } + else if ( rule[dim] == 14 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + o = 2; + while ( o < 4 * level[dim] + 1 ) + { + o = 2 * ( o - 1 ) + 1; + } + } + order[dim] = o; + } + else if ( rule[dim] == 15 ) + { + o = 1; + while ( o < 4 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + order[dim] = o; + } + else if ( rule[dim] == 16 ) + { + if ( level[dim] == 0 ) + { + order[dim] = 1; + } + else + { + p = 5; + o = 3; + while ( p < 4 * level[dim] + 1 ) + { + p = 2 * p + 1; + o = 2 * o + 1; + } + order[dim] = o; + } + } + else if ( rule[dim] == 17 ) + { + order[dim] = 2 * level[dim] + 1; + } + else + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_DEFAULT - Fatal error!\n"; + std::cerr << " Unexpected value of RULE[" + << dim << "] = " << rule[dim] << ".\n"; + std::exit ( 1 ); + } + } + return; +} +//****************************************************************************80 + +void level_to_order_exponential ( int dim_num, int level[], int rule[], + int order[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_EXPONENTIAL: exponential growth. +// +// Discussion: +// +// The user must preallocate space for the output array ORDER. +// +// Closed rules: +// +// O(0) = 1 +// O(L) = 2^L + 1; +// +// O = 1, 3, 5, 9, 17, 33, ... +// +// Open rules: +// +// O(L) = 2^(L+1) - 1; +// +// O = 1, 3, 7, 15, 31, 63, ... +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int DIM_NUM, the spatial dimension. +// +// Input, int LEVEL[DIM_NUM], the 1D levels. +// +// Input, int RULE[DIM_NUM], the rule in each dimension. +// 1, "CC", Clenshaw Curtis, Closed Fully Nested rule. +// 2, "F2", Fejer Type 2, Open Fully Nested rule. +// 3, "GP", Gauss Patterson, Open Fully Nested rule. +// 4, "GL", Gauss Legendre, Open Weakly Nested rule. +// 5, "GH", Gauss Hermite, Open Weakly Nested rule. +// 6, "GGH", Generalized Gauss Hermite, Open Weakly Nested rule. +// 7, "LG", Gauss Laguerre, Open Non Nested rule. +// 8, "GLG", Generalized Gauss Laguerre, Open Non Nested rule. +// 9, "GJ", Gauss Jacobi, Open Non Nested rule. +// 10, "GW", Golub Welsch, (presumed) Open Non Nested rule. +// 11, "CC_SE", Clenshaw Curtis Slow Exponential, Closed Fully Nested rule. +// 12, "F2_SE", Fejer Type 2 Slow Exponential, Open Fully Nested rule. +// 13, "GP_SE", Gauss Patterson Slow Exponential, Open Fully Nested rule. +// 14, "CC_ME", Clenshaw Curtis Moderate Exponential, Closed Fully Nested rule. +// 15, "F2_ME", Fejer Type 2 Moderate Exponential, Open Fully Nested rule. +// 16, "GP_ME", Gauss Patterson Moderate Exponential, Open Fully Nested rule. +// 17, "CCN", Clenshaw Curtis Nested, Linear, Closed Fully Nested rule. +// +// Output, int ORDER[DIM_NUM], the 1D orders (number of points). +// +{ + int dim; + + for ( dim = 0; dim < dim_num; dim++ ) + { + if ( level[dim] < 0 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXPONENTIAL - Fatal error!\n"; + std::cerr << " Negative value of LEVEL[DIM]!\n"; + std::cerr << " LEVEL[" << dim << "] = " << level[dim] << "\n"; + std::exit ( 1 ); + } + else if ( rule[dim] == 1 ) + { + if ( level[dim] == 0 ) + { + order[dim] = 1; + } + else + { + order[dim] = webbur::i4_power ( 2, level[dim] ) + 1; + } + } + else if ( rule[dim] == 2 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 3 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 4 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 5 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 6 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 7 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 8 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 9 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 10 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 11 ) + { + if ( level[dim] == 0 ) + { + order[dim] = 1; + } + else + { + order[dim] = webbur::i4_power ( 2, level[dim] ) + 1; + } + } + else if ( rule[dim] == 12 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 13 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 14 ) + { + if ( level[dim] == 0 ) + { + order[dim] = 1; + } + else + { + order[dim] = webbur::i4_power ( 2, level[dim] ) + 1; + } + } + else if ( rule[dim] == 15 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 16 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ) - 1; + } + else if ( rule[dim] == 17 ) + { + order[dim] = webbur::i4_power ( 2, level[dim] + 1 ); + } + else + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXPONENTIAL - Fatal error!\n"; + std::cerr << " Unexpected value of RULE[" + << dim << "] = " << rule[dim] << ".\n"; + std::exit ( 1 ); + } + } + return; +} +//****************************************************************************80 + +void level_to_order_exponential_slow ( int dim_num, int level[], int rule[], + int order[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_EXPONENTIAL_SLOW: slow exponential growth; +// +// Discussion: +// +// We seek a sequence of quadrature rules with two opposing constraints: +// * a measured rise in polynomial precision with increasing level; +// * a control on the increase in (new) points per level; +// +// Essentially, we are trying to keep some of the advantages of nesting, +// while moderating the cost of the explosive growth in order that occurs +// due to the repeated order doubling of nesting. +// +// We wish the number of points at a given level L to be "about" 2 * L + 1, +// but we also wish the rules to be completely nested. +// +// One way to do this is to start with a nested family of rules, whose +// order will tend to grow exponentially (doubling from one to the next), +// but simply to REPEAT each rule as many times as possible. We move to +// the next rule only when the desired precision 2 * L + 1 exceeds the +// precision of the current rule. +// +// For both the Clenshaw Curtis and Fejer Type 2 rules, the order and +// precision are the same if the order is odd. That is, an 11 point rule +// will integrate exactly all polynomials up to and including degree 11. +// +// For Gauss Patterson rules, the relationship between order and precision +// is somewhat more complicated. For that rule, we take the philosophy +// that at each level L, we wish to choose the rule of smallest order +// so that the precision of 2 * L + 1 is guaranteed. +// +// L 2*L+1 CC Order F2 Order GP Order/Precision +// +// 0 1 1 1 1/1 +// 1 3 3 3 3/5 +// 2 5 5 7 3/5 +// 3 7 9 7 7/11 +// 4 9 9 15 7/11 +// 5 11 17 15 7/11 +// 6 13 17 15 15/23 +// 7 15 17 15 15/23 +// 8 17 17 31 15/23 +// 9 19 33 31 15/23 +// 10 21 33 31 15/23 +// 11 23 33 31 15/23 +// 12 25 33 31 31/47 +// 13 27 33 31 31/47 +// 14 29 33 31 31/47 +// 15 31 33 31 31/47 +// 16 33 33 63 31/47 +// 17 35 65 63 31/47 +// 18 37 65 63 31/47 +// 19 39 65 63 31/47 +// 20 41 65 63 31/47 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Knut Petras, +// Smolyak Cubature of Given Polynomial Degree with Few Nodes +// for Increasing Dimension, +// Numerische Mathematik, +// Volume 93, Number 4, February 2003, pages 729-753. +// +// Parameters: +// +// Input, int DIM_NUM, the spatial dimension. +// +// Input, int LEVEL[DIM_NUM], the 1D levels. +// +// Input, int RULE[DIM_NUM], the rule in each dimension. +// 1, "CC", Clenshaw Curtis, Closed Fully Nested rule. +// 2, "F2", Fejer Type 2, Open Fully Nested rule. +// 3, "GP", Gauss Patterson, Open Fully Nested rule. +// 4, "GL", Gauss Legendre, Open Weakly Nested rule. +// 5, "GH", Gauss Hermite, Open Weakly Nested rule. +// 6, "GGH", Generalized Gauss Hermite, Open Weakly Nested rule. +// 7, "LG", Gauss Laguerre, Open Non Nested rule. +// 8, "GLG", Generalized Gauss Laguerre, Open Non Nested rule. +// 9, "GJ", Gauss Jacobi, Open Non Nested rule. +// 10, "GW", Golub Welsch, (presumed) Open Non Nested rule. +// 11, "CC_SE", Clenshaw Curtis Slow Exponential, Closed Fully Nested rule. +// 12, "F2_SE", Fejer Type 2 Slow Exponential, Open Fully Nested rule. +// 13, "GP_SE", Gauss Patterson Slow Exponential, Open Fully Nested rule. +// 14, "CC_ME", Clenshaw Curtis Moderate Exponential, Closed Fully Nested rule. +// 15, "F2_ME", Fejer Type 2 Moderate Exponential, Open Fully Nested rule. +// 16, "GP_ME", Gauss Patterson Moderate Exponential, Open Fully Nested rule. +// 17, "CCN", Clenshaw Curtis Nested, Linear, Closed Fully Nested rule. +// +// Output, int ORDER[DIM_NUM], the 1D orders (number of points). +// +{ + int dim; + int o; + int p; + + for ( dim = 0; dim < dim_num; dim++ ) + { + if ( level[dim] < 0 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXPONENTIAL_SLOW - Fatal error!\n"; + std::cerr << " Negative value of LEVEL[DIM]!\n"; + std::cerr << " LEVEL[" << dim << "] = " << level[dim] << "\n"; + std::exit ( 1 ); + } + } + + for ( dim = 0; dim < dim_num; dim++ ) + { + if ( rule[dim] == 1 || rule[dim] == 11 || rule[dim] == 14 || rule[dim] == 17 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + o = 2; + while ( o < 2 * level[dim] + 1 ) + { + o = 2 * ( o - 1 ) + 1; + } + } + } + else if ( rule[dim] == 3 || rule[dim] == 13 || rule[dim] == 16 ) + { + if ( level[dim] == 0 ) + { + o = 1; + } + else + { + p = 5; + o = 3; + while ( p < 2 * level[dim] + 1 ) + { + p = 2 * p + 1; + o = 2 * o + 1; + } + } + } + else + { + o = 1; + while ( o < 2 * level[dim] + 1 ) + { + o = 2 * o + 1; + } + } + order[dim] = o; + } + + return; +} +//****************************************************************************80 + +void level_to_order_linear ( int dim_num, int level[], int rule[], + int order[] ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_LINEAR: linear growth. +// +// Discussion: +// +// The user must preallocate space for the output array ORDER. +// +// O(L) = 2 * L + 1; +// +// O = 1, 3, 5, 7, 9, ... +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 07 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int DIM_NUM, the spatial dimension. +// +// Input, int LEVEL[DIM_NUM], the 1D levels. +// +// Input, int RULE[DIM_NUM], the rule in each dimension. +// 1, "CC", Clenshaw Curtis, Closed Fully Nested rule. +// 2, "F2", Fejer Type 2, Open Fully Nested rule. +// 3, "GP", Gauss Patterson, Open Fully Nested rule. +// 4, "GL", Gauss Legendre, Open Weakly Nested rule. +// 5, "GH", Gauss Hermite, Open Weakly Nested rule. +// 6, "GGH", Generalized Gauss Hermite, Open Weakly Nested rule. +// 7, "LG", Gauss Laguerre, Open Non Nested rule. +// 8, "GLG", Generalized Gauss Laguerre, Open Non Nested rule. +// 9, "GJ", Gauss Jacobi, Open Non Nested rule. +// 10, "GW", Golub Welsch, (presumed) Open Non Nested rule. +// 11, "CC_SE", Clenshaw Curtis Slow Exponential, Closed Fully Nested rule. +// 12, "F2_SE", Fejer Type 2 Slow Exponential, Open Fully Nested rule. +// 13, "GP_SE", Gauss Patterson Slow Exponential, Open Fully Nested rule. +// 14, "CC_ME", Clenshaw Curtis Moderate Exponential, Closed Fully Nested rule. +// 15, "F2_ME", Fejer Type 2 Moderate Exponential, Open Fully Nested rule. +// 16, "GP_ME", Gauss Patterson Moderate Exponential, Open Fully Nested rule. +// 17, "CCN", Clenshaw Curtis Nested, Linear, Closed Fully Nested rule. +// +// Output, int ORDER[DIM_NUM], the 1D orders (number of points). +// +{ + int dim; + + for ( dim = 0; dim < dim_num; dim++ ) + { + if ( level[dim] < 0 ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_LINEAR - Fatal error!\n"; + std::cerr << " Negative value of LEVEL[DIM]!\n"; + std::cerr << " LEVEL[" << dim << "] = " << level[dim] << "\n"; + std::exit ( 1 ); + } + } + + for ( dim = 0; dim < dim_num; dim++ ) + { + order[dim] = 2 * level[dim] + 1; + } + + return; +} +//****************************************************************************80 + +int level_to_order_exp_cc ( int level, int growth ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_EXP_CC is used for Clenshaw-Curtis type rules. +// +// Discussion: +// +// Rules of this type are assumed to be closed (including both endpoints +// except for the level 0 rule) and having a precision +// behavior typical of Clenshaw Curtis rules, namely, the ORDER-point +// rule is exact for polynomials of degree less than ORDER, and if +// ORDER is odd, then the exactness includes polynomials of degree ORDER +// as well. +// +// LEVEL ORDER ORDER ORDER +// G = 0 G = 1 G = 2 +// ----- ----- ----- ----- +// 0 1 1 1 +// 1 3 5 3 +// 2 5 9 5 +// 3 9 17 9 +// 4 9 17 17 +// 5 17 33 33 +// 6 17 33 65 +// 7 17 33 129 +// 8 17 33 257 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 December 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int LEVEL, the level of the rule. +// +// Input, int GROWTH, the growth policy: +// 0, slow growth; +// 1, moderate growth; +// 2, full growth. +// +// Output, int LEVEL_TO_ORDER_EXP_CC, the order of the rule. +// +{ + int o; +// +// Slow exponential growth. +// + if ( growth == 0 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = 2; + while ( o < 2 * level + 1 ) + { + o = 2 * ( o - 1 ) + 1; + } + } + } +// +// Moderate Exponential Growth. +// + else if ( growth == 1 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = 2; + while ( o < 4 * level + 1 ) + { + o = 2 * ( o - 1 ) + 1; + } + } + } +// +// Full Exponential Growth. +// + else if ( growth == 2 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = webbur::i4_power ( 2, level ) + 1; + } + } + else + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_CC - Fatal error!\n"; + std::cerr << " Illegal value of GROWTH = " << growth << "\n"; + std::exit ( 1 ); + } + return o; +} +//****************************************************************************80 + +int level_to_order_exp_f2 ( int level, int growth ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_EXP_F2 is used for Fejer 2 type rules. +// +// Discussion: +// +// Rules of this type are assumed to be open (not including either endpoint) +// and having a precision behavior typical of Fejer Type 2 +// rules, namely, the ORDER-point rule is exact for polynomials of degree +// less than ORDER, and if ORDER is odd, then the exactness includes +// polynomials of degree ORDER as well. +// +// LEVEL ORDER ORDER ORDER +// G = 0 G = 1 G = 2 +// +// 0 1 1 1 +// 1 3 7 3 +// 2 7 15 7 +// 3 7 15 15 +// 4 15 31 31 +// 5 15 31 63 +// 6 15 31 127 +// 7 15 31 255 +// 8 31 63 511 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 December 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int LEVEL, the level of the rule. +// +// Input, int GROWTH, the growth policy: +// 0, slow growth; +// 1, moderate growth; +// 2, full growth. +// +// Output, int LEVEL_TO_ORDER_EXP_F2, the order of the rule. +// +{ + int o; +// +// Slow exponential growth. +// + if ( growth == 0 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = 1; + while ( o < 2 * level + 1 ) + { + o = 2 * o + 1; + } + } + } +// +// Moderate Exponential Growth. +// + else if ( growth == 1 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = 1; + while ( o < 4 * level + 1 ) + { + o = 2 * o + 1; + } + } + } +// +// Full Exponential Growth. +// + else if ( growth == 2 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = webbur::i4_power ( 2, level + 1 ) - 1; + } + } + else + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_F2 - Fatal error!\n"; + std::cerr << " Illegal value of GROWTH = " << growth << "\n"; + std::exit ( 1 ); + } + return o; +} +//****************************************************************************80 + +int level_to_order_exp_gauss ( int level, int growth ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_EXP_GAUSS is used for Gauss type rules. +// +// Discussion: +// +// Rules of this type are assumed to be open (not including either endpoint), +// and having a precision behavior typical of Gauss rules, namely, the +// ORDER-point rule is exact for polynomials of degree less than 2 * ORDER. +// +// LEVEL ORDER ORDER ORDER +// G = 0 G = 1 G = 2 +// +// 0 1 1 1 +// 1 3 3 3 +// 2 3 7 7 +// 3 7 7 15 +// 4 7 15 31 +// 5 7 15 63 +// 6 7 15 127 +// 7 15 15 255 +// 8 15 31 511 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 December 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int LEVEL, the level of the rule. +// +// Input, int GROWTH, the growth policy: +// 0, slow growth; +// 1, moderate growth; +// 2, full growth. +// +// Output, int LEVEL_TO_ORDER_EXP_GAUSS, the order of the rule. +// +{ + int o; +// +// Slow exponential growth. +// + if ( growth == 0 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = 1; + while ( 2 * o - 1 < 2 * level + 1 ) + { + o = 2 * o + 1; + } + } + } +// +// Moderate Exponential Growth. +// + else if ( growth == 1 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = 1; + while ( 2 * o - 1 < 4 * level + 1 ) + { + o = 2 * o + 1; + } + } + } +// +// Full Exponential Growth. +// + else if ( growth == 2 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = webbur::i4_power ( 2, level + 1 ) - 1; + } + } + else + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_GAUSS - Fatal error!\n"; + std::cerr << " Illegal value of GROWTH = " << growth << "\n"; + std::exit ( 1 ); + } + + return o; +} +//****************************************************************************80 + +int level_to_order_exp_gp ( int level, int growth ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_EXP_GP is used for Gauss-Patterson type rules. +// +// Discussion: +// +// Rules of this type are assumed to be open (not including either endpoint) +// and having a precision behavior typical of Gauss Patterson rules. +// +// Note that there are onlly 9 rules in the family, and so it is possible to +// specify input for which the function will fail. +// +// LEVEL ORDER ORDER ORDER +// G = 0 G = 1 G = 2 +// +// 0 1 1 1 +// 1 3 3 3 +// 2 3 7 7 +// 3 7 15 15 +// 4 7 15 31 +// 5 7 15 63 +// 6 15 31 127 +// 7 15 31 255 +// 8 15 31 511 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 December 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int LEVEL, the level of the rule. +// +// Input, int GROWTH, the growth policy: +// 0, slow growth; +// 1, moderate growth; +// 2, full growth. +// +// Output, int LEVEL_TO_ORDER_EXP_GP, the order of the rule. +// +{ + int o; + int p; +// +// Slow exponential growth. +// + if ( growth == 0 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + p = 5; + o = 3; + while ( p < 2 * level + 1 ) + { + p = 2 * p + 1; + o = 2 * o + 1; + if ( 511 < o ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_GP - Fatal error!\n"; + std::cerr << " Request for unavailable Patterson rule.\n"; + std::exit ( 1 ); + } + } + } + } +// +// Moderate Exponential Growth. +// + else if ( growth == 1 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + p = 5; + o = 3; + while ( p < 4 * level + 1 ) + { + p = 2 * p + 1; + o = 2 * o + 1; + if ( 511 < o ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_GP - Fatal error!\n"; + std::cerr << " Request for unavailable Patterson rule.\n"; + std::exit ( 1 ); + } + } + } + } +// +// Full Exponential Growth. +// + else if ( growth == 2 ) + { + if ( level == 0 ) + { + o = 1; + } + else + { + o = webbur::i4_power ( 2, level + 1 ) - 1; + if ( 511 < o ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_GP - Fatal error!\n"; + std::cerr << " Request for unavailable Patterson rule.\n"; + std::exit ( 1 ); + } + } + } + else + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_GP - Fatal error!\n"; + std::cerr << " Illegal value of GROWTH = " << growth << "\n"; + std::exit ( 1 ); + } + + return o; +} +//****************************************************************************80 + +int level_to_order_exp_hgk ( int level, int growth ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_EXP_HGK is used for Hermite Genz-Keister type rules. +// +// Discussion: +// +// Rules of this type are assumed to be open (not including either endpoint) +// and having a precision behavior typical of Hermite Genz-Keister rules. +// +// Note that there are only 6 rules in the family, and so it is possible to +// specify input for which the function will fail. +// +// LEVEL ORDER ORDER ORDER +// G = 0 G = 1 G = 2 +// +// 0 1 1 1 +// 1 3 3 3 +// 2 3 9 9 +// 3 9 9 19 +// 4 9 19 35 +// 5 9 19 43 +// 6 9 19 -- +// 7 9 19 -- +// 8 19 35 -- +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 December 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int LEVEL, the level of the rule. +// +// Input, int GROWTH, the growth policy: +// 0, slow growth; +// 1, moderate growth; +// 2, full growth. +// +// Output, int LEVEL_TO_ORDER_EXP_HGK, the order of the rule. +// +{ + int l; + int o; + static int o_hgk[6] = { 1, 3, 9, 19, 35, 43 }; + int p; + static int p_hgk[6] = { 1, 5, 15, 29, 51, 67 }; +// +// Slow exponential growth. +// + if ( growth == 0 ) + { + l = 0; + p = p_hgk[l]; + o = o_hgk[l]; + while ( p < 2 * level + 1 ) + { + l = l + 1; + if ( 5 < l ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_HGK - Fatal error!\n"; + std::cerr << " Hermite Genz-Keister maximum level exceeded.\n"; + std::exit ( 1 ); + } + p = p_hgk[l]; + o = o_hgk[l]; + } + } + else if ( growth == 1 ) + { + l = 0; + p = p_hgk[l]; + o = o_hgk[l]; + while ( p < 4 * level + 1 ) + { + l = l + 1; + if ( 5 < l ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_HGK - Fatal error!\n"; + std::cerr << " Hermite Genz-Keister maximum level exceeded.\n"; + std::exit ( 1 ); + } + p = p_hgk[l]; + o = o_hgk[l]; + } + } + else if ( growth == 2 ) + { + l = level; + l = webbur::i4_max ( l, 0 ); + if ( 5 < l ) + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_HGK - Fatal error!\n"; + std::cerr << " Hermite Genz-Keister maximum level exceeded.\n"; + std::exit ( 1 ); + } + o = o_hgk[l]; + } + else + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_EXP_HGK - Fatal error!\n"; + std::cerr << " Illegal value of GROWTH = " << growth << "\n"; + std::exit ( 1 ); + } + + return o; +} +//****************************************************************************80 + +int level_to_order_linear_nn ( int level, int growth ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_LINEAR_NN is used for non-nested Gauss type rules. +// +// Discussion: +// +// Rules of this type are assumed to be open (not including either endpoint), +// non-nested, and having a precision behavior typical of Gauss rules. +// +// LEVEL ORDER ORDER +// G = 0 G = 1 +// +// 0 1 1 +// 1 2 3 +// 2 3 5 +// 3 4 7 +// 4 5 9 +// 5 6 11 +// 6 7 13 +// 7 8 15 +// 8 9 17 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 December 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int LEVEL, the level of the rule. +// +// Input, int GROWTH, the growth policy: +// 0, slow growth; +// 1, moderate growth; +// +// Output, int LEVEL_TO_ORDER_LINEAR_NN, the order of the rule. +// +{ + int o; +// +// Slow linear growth. +// + if ( growth == 0 ) + { + o = level + 1; + } +// +// Moderate linear growth. +// + else if ( growth == 1 ) + { + o = 2 * level + 1; + } + else if ( growth == 2 ) + { + o = 2 * level + 1; + } + else + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_LINEAR_NN - Fatal error!\n"; + std::cerr << " Illegal value of GROWTH = " << growth << "\n"; + std::exit ( 1 ); + } + return o; +} +//****************************************************************************80 + +int level_to_order_linear_wn ( int level, int growth ) + +//****************************************************************************80 +// +// Purpose: +// +// LEVEL_TO_ORDER_LINEAR_WN is used for weakly-nested Gauss type rules. +// +// Discussion: +// +// Rules of this type are assumed to be open (not including either endpoint), +// nested, and having a precision behavior typical of Gauss rules. +// +// We assume the rules are to be generated with an odd number of points, +// and that all the rules will share a single point, namely 0. +// +// Note that the "moderate growth" option for this function results in the +// same values as the moderate growth option for LEVEL_TO_ORDER_LINEAR_NN. +// +// LEVEL ORDER ORDER +// G = 0 G = 1 +// +// 0 1 1 +// 1 3 3 +// 2 3 5 +// 3 5 7 +// 4 5 9 +// 5 7 11 +// 6 7 13 +// 7 9 15 +// 8 9 17 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 December 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int LEVEL, the level of the rule. +// +// Input, int GROWTH, the growth policy: +// 0, slow growth; +// 1, moderate growth; +// +// Output, int LEVEL_TO_ORDER_LINEAR_WN, the order of the rule. +// +{ + int o; +// +// Slow growth. +// + if ( growth == 0 ) + { + o = 2 * ( ( level + 1 ) / 2 ) + 1; + } + else if ( growth == 1 ) + { + o = 2 * level + 1; + } + else if ( growth == 2 ) + { + o = 2 * level + 1; + } + else + { + std::cerr << "\n"; + std::cerr << "LEVEL_TO_ORDER_LINEAR_WN - Fatal error!\n"; + std::cerr << " Illegal value of GROWTH = " << growth << "\n"; + std::exit ( 1 ); + } + return o; +} +//****************************************************************************80 + +void nc_compute ( int n, double x_min, double x_max, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// NC_COMPUTE computes a Newton-Cotes quadrature rule. +// +// Discussion: +// +// For the interval [X_MIN,X_MAX], the Newton-Cotes quadrature rule +// estimates +// +// Integral ( X_MIN <= X <= X_MAX ) F(X) dX +// +// using N abscissas X and weights W: +// +// Sum ( 1 <= I <= N ) W(I) * F ( X(I) ). +// +// For the CLOSED rule, the abscissas include the end points. +// For the OPEN rule, the abscissas do not include the end points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 November 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, double X_MIN, X_MAX, the endpoints of the interval. +// +// Input, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + double *d; + int i; + int j; + int k; + double yvala; + double yvalb; + + d = new double[n]; + + for ( i = 0; i < n; i++ ) + { +// +// Compute the Lagrange basis polynomial which is 1 at XTAB(I), +// and zero at the other nodes. +// + for ( j = 0; j < n; j++ ) + { + d[j] = 0.0; + } + d[i] = 1.0; + + for ( j = 2; j <= n; j++ ) + { + for ( k = j; k <= n; k++ ) + { + d[n+j-k-1] = ( d[n+j-k-1-1] - d[n+j-k-1] ) / ( x[n+1-k-1] - x[n+j-k-1] ); + } + } + + for ( j = 1; j <= n - 1; j++ ) + { + for ( k = 1; k <= n - j; k++ ) + { + d[n-k-1] = d[n-k-1] - x[n-k-j] * d[n-k]; + } + } +// +// Evaluate the antiderivative of the polynomial at the left and +// right endpoints. +// + yvala = d[n-1] / ( double ) ( n ); + for ( j = n - 2; 0 <= j; j-- ) + { + yvala = yvala * x_min + d[j] / ( double ) ( j + 1 ); + } + yvala = yvala * x_min; + + yvalb = d[n-1] / ( double ) ( n ); + for ( j = n - 2; 0 <= j; j-- ) + { + yvalb = yvalb * x_max + d[j] / ( double ) ( j + 1 ); + } + yvalb = yvalb * x_max; + + w[i] = yvalb - yvala; + } + + delete [] d; + + return; +} +//****************************************************************************80 + +double *nc_compute_new ( int n, double x_min, double x_max, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// NC_COMPUTE_NEW computes a Newton-Cotes quadrature rule. +// +// Discussion: +// +// For the interval [X_MIN,X_MAX], the Newton-Cotes quadrature rule +// estimates +// +// Integral ( X_MIN <= X <= X_MAX ) F(X) dX +// +// using N abscissas X and weights W: +// +// Sum ( 1 <= I <= N ) W(I) * F ( X(I) ). +// +// For the CLOSED rule, the abscissas include the end points. +// For the OPEN rule, the abscissas do not include the end points. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 November 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Input, double X_MIN, X_MAX, the endpoints of the interval. +// +// Input, double X[N], the abscissas. +// +// Output, double NC_COMPUTE_NEW[N], the weights. +// +{ + double *d; + int i; + int j; + int k; + double *w; + double yvala; + double yvalb; + + d = new double[n]; + w = new double[n]; + + for ( i = 0; i < n; i++ ) + { +// +// Compute the Lagrange basis polynomial which is 1 at XTAB(I), +// and zero at the other nodes. +// + for ( j = 0; j < n; j++ ) + { + d[j] = 0.0; + } + d[i] = 1.0; + + for ( j = 2; j <= n; j++ ) + { + for ( k = j; k <= n; k++ ) + { + d[n+j-k-1] = ( d[n+j-k-1-1] - d[n+j-k-1] ) / ( x[n+1-k-1] - x[n+j-k-1] ); + } + } + + for ( j = 1; j <= n - 1; j++ ) + { + for ( k = 1; k <= n - j; k++ ) + { + d[n-k-1] = d[n-k-1] - x[n-k-j] * d[n-k]; + } + } +// +// Evaluate the antiderivative of the polynomial at the left and +// right endpoints. +// + yvala = d[n-1] / ( double ) ( n ); + for ( j = n - 2; 0 <= j; j-- ) + { + yvala = yvala * x_min + d[j] / ( double ) ( j + 1 ); + } + yvala = yvala * x_min; + + yvalb = d[n-1] / ( double ) ( n ); + for ( j = n - 2; 0 <= j; j-- ) + { + yvalb = yvalb * x_max + d[j] / ( double ) ( j + 1 ); + } + yvalb = yvalb * x_max; + + w[i] = yvalb - yvala; + } + + delete [] d; + + return w; +} +//****************************************************************************80 + +void ncc_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// NCC_COMPUTE_POINTS: points of a Newton-Cotes Closed quadrature rule. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 16 November 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double X[N], the abscissas. +// +{ + int i; + double x_max = 1.0; + double x_min = -1.0; + + if ( n == 1 ) + { + x[0] = ( x_max + x_min ) / 2.0; + } + else + { + for ( i = 0; i < n; i++ ) + { + x[i] = ( ( double ) ( n - i - 1 ) * x_min + + ( double ) ( i ) * x_max ) + / ( double ) ( n - 1 ); + } + } + return; +} +//****************************************************************************80 + +void ncc_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// NCC_COMPUTE_WEIGHTS: weights of a Newton-Cotes Closed quadrature rule. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 16 November 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double W[N], the weights. +// +{ + int i; + double *x; + double x_max = 1.0; + double x_min = -1.0; + + if ( n == 1 ) + { + w[0] = x_max - x_min; + } + else + { + x = new double[n]; + + for ( i = 0; i < n; i++ ) + { + x[i] = ( ( double ) ( n - i - 1 ) * x_min + + ( double ) ( i ) * x_max ) + / ( double ) ( n - 1 ); + } + webbur::nc_compute ( n, x_min, x_max, x, w ); + + delete [] x; + } + return; +} +//****************************************************************************80 + +void nco_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// NCO_COMPUTE_POINTS: points for a Newton-Cotes Open quadrature rule. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 November 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double X[N], the abscissas. +// +{ + int i; + double x_max = 1.0; + double x_min = -1.0; + + for ( i = 0; i < n; i++ ) + { + x[i] = ( ( double ) ( n - i ) * x_min + + ( double ) ( + i + 1 ) * x_max ) + / ( double ) ( n + 1 ); + } + + return; +} +//****************************************************************************80 + +void nco_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// NCO_COMPUTE_WEIGHTS: weights for a Newton-Cotes Open quadrature rule. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 November 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double W[N], the weights. +// +{ + int i; + double *x; + double x_max = 1.0; + double x_min = -1.0; + + x = new double[n]; + + webbur::nco_compute_points ( n, x ); + + webbur::nc_compute ( n, x_min, x_max, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void ncoh_compute_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// NCOH_COMPUTE_POINTS computes points for a Newton-Cotes "open half" quadrature rule. +// +// Discussion: +// +// The input value N is used to define N equal subintervals of [-1,+1]. +// The I-th abscissa is the center of the I-th subinterval. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 03 July 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double X[N], the abscissas. +// +{ + int i; + const double x_max = 1.0; + const double x_min = -1.0; + + for ( i = 0; i < n; i++ ) + { + x[i] = ( ( double ) ( 2 * n - 2 * i - 1 ) * x_min + + ( double ) ( 2 * i + 1 ) * x_max ) + / ( double ) ( 2 * n ); + } + + return; +} +//****************************************************************************80 + +void ncoh_compute_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// NCOH_COMPUTE_WEIGHTS computes weights for a Newton-Cotes "open half" quadrature rule. +// +// Discussion: +// +// The input value N is used to define N equal subintervals of [-1,+1]. +// The I-th abscissa is the center of the I-th subinterval. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 03 July 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order. +// +// Output, double W[N], the weights. +// +{ + int i; + double *x; + const double x_max = 1.0; + const double x_min = -1.0; + + x = new double[n]; + + webbur::ncoh_compute_points ( n, x ); + + webbur::nc_compute ( n, x_min, x_max, x, w ); + + delete [] x; + + return; +} +//****************************************************************************80 + +void patterson_lookup ( int n, double x[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// PATTERSON_LOOKUP looks up Patterson quadrature points and weights. +// +// Discussion: +// +// Our convention is that the abscissas are numbered from left to right. +// +// The rule is defined on [-1,1], +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 11 February 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Prem Kythe, Michael Schaeferkotter, +// Handbook of Computational Methods for Integration, +// Chapman and Hall, 2004, +// ISBN: 1-58488-428-2, +// LC: QA299.3.K98. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// Legal values are 1, 3, 7, 15, 31, 63, 127, 255 and 511. +// +// Output, double X[N], the abscissas. +// +// Output, double W[N], the weights. +// +{ + patterson_lookup_points ( n, x ); + patterson_lookup_weights ( n, w ); + + return; +} +//****************************************************************************80 + +void patterson_lookup_points ( int n, double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// PATTERSON_LOOKUP_POINTS looks up Patterson quadrature points. +// +// Discussion: +// +// Our convention is that the abscissas are numbered from left to right. +// +// The rule is defined on [-1,1], +// +// These rules constitute a nested family. The rules can integrate exactly +// any polynomial of degree 1, 5, 11, 23, 47, 95, 191, 383 or 767, +// respectively. +// +// The data for N = 511 was supplied by Dirk Laurie, and is derived +// from a NAG Library function d01arf. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 14 September 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Prem Kythe, Michael Schaeferkotter, +// Handbook of Computational Methods for Integration, +// Chapman and Hall, 2004, +// ISBN: 1-58488-428-2, +// LC: QA299.3.K98. +// +// NAG Library Documentation, +// D01ARF, +// The Numerical Algorithms Group. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// Legal values are 1, 3, 7, 15, 31, 63, 127, 255 and 511. +// +// Output, double X[N], the abscissas. +// +{ + static double x_001[1] = + { + 0.0 + }; + static double x_003[3] = + { + -0.77459666924148337704, + 0.0, + 0.77459666924148337704 + }; + static double x_007[7] = + { + -0.96049126870802028342, + -0.77459666924148337704, + -0.43424374934680255800, + 0.0, + 0.43424374934680255800, + 0.77459666924148337704, + 0.96049126870802028342 + }; + static double x_015[15] = + { + -0.99383196321275502221, + -0.96049126870802028342, + -0.88845923287225699889, + -0.77459666924148337704, + -0.62110294673722640294, + -0.43424374934680255800, + -0.22338668642896688163, + 0.0, + 0.22338668642896688163, + 0.43424374934680255800, + 0.62110294673722640294, + 0.77459666924148337704, + 0.88845923287225699889, + 0.96049126870802028342, + 0.99383196321275502221 + }; + static double x_031[31] = + { + -0.99909812496766759766, + -0.99383196321275502221, + -0.98153114955374010687, + -0.96049126870802028342, + -0.92965485742974005667, + -0.88845923287225699889, + -0.83672593816886873550, + -0.77459666924148337704, + -0.70249620649152707861, + -0.62110294673722640294, + -0.53131974364437562397, + -0.43424374934680255800, + -0.33113539325797683309, + -0.22338668642896688163, + -0.11248894313318662575, + 0.0, + 0.11248894313318662575, + 0.22338668642896688163, + 0.33113539325797683309, + 0.43424374934680255800, + 0.53131974364437562397, + 0.62110294673722640294, + 0.70249620649152707861, + 0.77459666924148337704, + 0.83672593816886873550, + 0.88845923287225699889, + 0.92965485742974005667, + 0.96049126870802028342, + 0.98153114955374010687, + 0.99383196321275502221, + 0.99909812496766759766 + }; + static double x_063[63] = + { + -0.99987288812035761194, + -0.99909812496766759766, + -0.99720625937222195908, + -0.99383196321275502221, + -0.98868475754742947994, + -0.98153114955374010687, + -0.97218287474858179658, + -0.96049126870802028342, + -0.94634285837340290515, + -0.92965485742974005667, + -0.91037115695700429250, + -0.88845923287225699889, + -0.86390793819369047715, + -0.83672593816886873550, + -0.80694053195021761186, + -0.77459666924148337704, + -0.73975604435269475868, + -0.70249620649152707861, + -0.66290966002478059546, + -0.62110294673722640294, + -0.57719571005204581484, + -0.53131974364437562397, + -0.48361802694584102756, + -0.43424374934680255800, + -0.38335932419873034692, + -0.33113539325797683309, + -0.27774982202182431507, + -0.22338668642896688163, + -0.16823525155220746498, + -0.11248894313318662575, + -0.056344313046592789972, + 0.0, + 0.056344313046592789972, + 0.11248894313318662575, + 0.16823525155220746498, + 0.22338668642896688163, + 0.27774982202182431507, + 0.33113539325797683309, + 0.38335932419873034692, + 0.43424374934680255800, + 0.48361802694584102756, + 0.53131974364437562397, + 0.57719571005204581484, + 0.62110294673722640294, + 0.66290966002478059546, + 0.70249620649152707861, + 0.73975604435269475868, + 0.77459666924148337704, + 0.80694053195021761186, + 0.83672593816886873550, + 0.86390793819369047715, + 0.88845923287225699889, + 0.91037115695700429250, + 0.92965485742974005667, + 0.94634285837340290515, + 0.96049126870802028342, + 0.97218287474858179658, + 0.98153114955374010687, + 0.98868475754742947994, + 0.99383196321275502221, + 0.99720625937222195908, + 0.99909812496766759766, + 0.99987288812035761194 + }; + static double x_127[127] = + { + -0.99998243035489159858, + -0.99987288812035761194, + -0.99959879967191068325, + -0.99909812496766759766, + -0.99831663531840739253, + -0.99720625937222195908, + -0.99572410469840718851, + -0.99383196321275502221, + -0.99149572117810613240, + -0.98868475754742947994, + -0.98537149959852037111, + -0.98153114955374010687, + -0.97714151463970571416, + -0.97218287474858179658, + -0.96663785155841656709, + -0.96049126870802028342, + -0.95373000642576113641, + -0.94634285837340290515, + -0.93832039777959288365, + -0.92965485742974005667, + -0.92034002547001242073, + -0.91037115695700429250, + -0.89974489977694003664, + -0.88845923287225699889, + -0.87651341448470526974, + -0.86390793819369047715, + -0.85064449476835027976, + -0.83672593816886873550, + -0.82215625436498040737, + -0.80694053195021761186, + -0.79108493379984836143, + -0.77459666924148337704, + -0.75748396638051363793, + -0.73975604435269475868, + -0.72142308537009891548, + -0.70249620649152707861, + -0.68298743109107922809, + -0.66290966002478059546, + -0.64227664250975951377, + -0.62110294673722640294, + -0.59940393024224289297, + -0.57719571005204581484, + -0.55449513263193254887, + -0.53131974364437562397, + -0.50768775753371660215, + -0.48361802694584102756, + -0.45913001198983233287, + -0.43424374934680255800, + -0.40897982122988867241, + -0.38335932419873034692, + -0.35740383783153215238, + -0.33113539325797683309, + -0.30457644155671404334, + -0.27774982202182431507, + -0.25067873030348317661, + -0.22338668642896688163, + -0.19589750271110015392, + -0.16823525155220746498, + -0.14042423315256017459, + -0.11248894313318662575, + -0.084454040083710883710, + -0.056344313046592789972, + -0.028184648949745694339, + 0.0, + 0.028184648949745694339, + 0.056344313046592789972, + 0.084454040083710883710, + 0.11248894313318662575, + 0.14042423315256017459, + 0.16823525155220746498, + 0.19589750271110015392, + 0.22338668642896688163, + 0.25067873030348317661, + 0.27774982202182431507, + 0.30457644155671404334, + 0.33113539325797683309, + 0.35740383783153215238, + 0.38335932419873034692, + 0.40897982122988867241, + 0.43424374934680255800, + 0.45913001198983233287, + 0.48361802694584102756, + 0.50768775753371660215, + 0.53131974364437562397, + 0.55449513263193254887, + 0.57719571005204581484, + 0.59940393024224289297, + 0.62110294673722640294, + 0.64227664250975951377, + 0.66290966002478059546, + 0.68298743109107922809, + 0.70249620649152707861, + 0.72142308537009891548, + 0.73975604435269475868, + 0.75748396638051363793, + 0.77459666924148337704, + 0.79108493379984836143, + 0.80694053195021761186, + 0.82215625436498040737, + 0.83672593816886873550, + 0.85064449476835027976, + 0.86390793819369047715, + 0.87651341448470526974, + 0.88845923287225699889, + 0.89974489977694003664, + 0.91037115695700429250, + 0.92034002547001242073, + 0.92965485742974005667, + 0.93832039777959288365, + 0.94634285837340290515, + 0.95373000642576113641, + 0.96049126870802028342, + 0.96663785155841656709, + 0.97218287474858179658, + 0.97714151463970571416, + 0.98153114955374010687, + 0.98537149959852037111, + 0.98868475754742947994, + 0.99149572117810613240, + 0.99383196321275502221, + 0.99572410469840718851, + 0.99720625937222195908, + 0.99831663531840739253, + 0.99909812496766759766, + 0.99959879967191068325, + 0.99987288812035761194, + 0.99998243035489159858 + }; + static double x_255[255] = + { + -0.99999759637974846462, + -0.99998243035489159858, + -0.99994399620705437576, + -0.99987288812035761194, + -0.99976049092443204733, + -0.99959879967191068325, + -0.99938033802502358193, + -0.99909812496766759766, + -0.99874561446809511470, + -0.99831663531840739253, + -0.99780535449595727456, + -0.99720625937222195908, + -0.99651414591489027385, + -0.99572410469840718851, + -0.99483150280062100052, + -0.99383196321275502221, + -0.99272134428278861533, + -0.99149572117810613240, + -0.99015137040077015918, + -0.98868475754742947994, + -0.98709252795403406719, + -0.98537149959852037111, + -0.98351865757863272876, + -0.98153114955374010687, + -0.97940628167086268381, + -0.97714151463970571416, + -0.97473445975240266776, + -0.97218287474858179658, + -0.96948465950245923177, + -0.96663785155841656709, + -0.96364062156981213252, + -0.96049126870802028342, + -0.95718821610986096274, + -0.95373000642576113641, + -0.95011529752129487656, + -0.94634285837340290515, + -0.94241156519108305981, + -0.93832039777959288365, + -0.93406843615772578800, + -0.92965485742974005667, + -0.92507893290707565236, + -0.92034002547001242073, + -0.91543758715576504064, + -0.91037115695700429250, + -0.90514035881326159519, + -0.89974489977694003664, + -0.89418456833555902286, + -0.88845923287225699889, + -0.88256884024734190684, + -0.87651341448470526974, + -0.87029305554811390585, + -0.86390793819369047715, + -0.85735831088623215653, + -0.85064449476835027976, + -0.84376688267270860104, + -0.83672593816886873550, + -0.82952219463740140018, + -0.82215625436498040737, + -0.81462878765513741344, + -0.80694053195021761186, + -0.79909229096084140180, + -0.79108493379984836143, + -0.78291939411828301639, + -0.77459666924148337704, + -0.76611781930376009072, + -0.75748396638051363793, + -0.74869629361693660282, + -0.73975604435269475868, + -0.73066452124218126133, + -0.72142308537009891548, + -0.71203315536225203459, + -0.70249620649152707861, + -0.69281376977911470289, + -0.68298743109107922809, + -0.67301883023041847920, + -0.66290966002478059546, + -0.65266166541001749610, + -0.64227664250975951377, + -0.63175643771119423041, + -0.62110294673722640294, + -0.61031811371518640016, + -0.59940393024224289297, + -0.58836243444766254143, + -0.57719571005204581484, + -0.56590588542365442262, + -0.55449513263193254887, + -0.54296566649831149049, + -0.53131974364437562397, + -0.51955966153745702199, + -0.50768775753371660215, + -0.49570640791876146017, + -0.48361802694584102756, + -0.47142506587165887693, + -0.45913001198983233287, + -0.44673538766202847374, + -0.43424374934680255800, + -0.42165768662616330006, + -0.40897982122988867241, + -0.39621280605761593918, + -0.38335932419873034692, + -0.37042208795007823014, + -0.35740383783153215238, + -0.34430734159943802278, + -0.33113539325797683309, + -0.31789081206847668318, + -0.30457644155671404334, + -0.29119514851824668196, + -0.27774982202182431507, + -0.26424337241092676194, + -0.25067873030348317661, + -0.23705884558982972721, + -0.22338668642896688163, + -0.20966523824318119477, + -0.19589750271110015392, + -0.18208649675925219825, + -0.16823525155220746498, + -0.15434681148137810869, + -0.14042423315256017459, + -0.12647058437230196685, + -0.11248894313318662575, + -0.098482396598119202090, + -0.084454040083710883710, + -0.070406976042855179063, + -0.056344313046592789972, + -0.042269164765363603212, + -0.028184648949745694339, + -0.014093886410782462614, + 0.0, + 0.014093886410782462614, + 0.028184648949745694339, + 0.042269164765363603212, + 0.056344313046592789972, + 0.070406976042855179063, + 0.084454040083710883710, + 0.098482396598119202090, + 0.11248894313318662575, + 0.12647058437230196685, + 0.14042423315256017459, + 0.15434681148137810869, + 0.16823525155220746498, + 0.18208649675925219825, + 0.19589750271110015392, + 0.20966523824318119477, + 0.22338668642896688163, + 0.23705884558982972721, + 0.25067873030348317661, + 0.26424337241092676194, + 0.27774982202182431507, + 0.29119514851824668196, + 0.30457644155671404334, + 0.31789081206847668318, + 0.33113539325797683309, + 0.34430734159943802278, + 0.35740383783153215238, + 0.37042208795007823014, + 0.38335932419873034692, + 0.39621280605761593918, + 0.40897982122988867241, + 0.42165768662616330006, + 0.43424374934680255800, + 0.44673538766202847374, + 0.45913001198983233287, + 0.47142506587165887693, + 0.48361802694584102756, + 0.49570640791876146017, + 0.50768775753371660215, + 0.51955966153745702199, + 0.53131974364437562397, + 0.54296566649831149049, + 0.55449513263193254887, + 0.56590588542365442262, + 0.57719571005204581484, + 0.58836243444766254143, + 0.59940393024224289297, + 0.61031811371518640016, + 0.62110294673722640294, + 0.63175643771119423041, + 0.64227664250975951377, + 0.65266166541001749610, + 0.66290966002478059546, + 0.67301883023041847920, + 0.68298743109107922809, + 0.69281376977911470289, + 0.70249620649152707861, + 0.71203315536225203459, + 0.72142308537009891548, + 0.73066452124218126133, + 0.73975604435269475868, + 0.74869629361693660282, + 0.75748396638051363793, + 0.76611781930376009072, + 0.77459666924148337704, + 0.78291939411828301639, + 0.79108493379984836143, + 0.79909229096084140180, + 0.80694053195021761186, + 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+0.999822363679787739196, + +0.999872888120357611938, + +0.999913081144678282800, + +0.999943996207054375764, + +0.999966730098486276883, + +0.999982430354891598580, + +0.999992298136257588028, + +0.999997596379748464620, + +0.999999672956734384381 + }; + + if ( n == 1 ) + { + webbur::r8vec_copy ( n, x_001, x ); + } + else if ( n == 3 ) + { + webbur::r8vec_copy ( n, x_003, x ); + } + else if ( n == 7 ) + { + webbur::r8vec_copy ( n, x_007, x ); + } + else if ( n == 15 ) + { + webbur::r8vec_copy ( n, x_015, x ); + } + else if ( n == 31 ) + { + webbur::r8vec_copy ( n, x_031, x ); + } + else if ( n == 63 ) + { + webbur::r8vec_copy ( n, x_063, x ); + } + else if ( n == 127 ) + { + webbur::r8vec_copy ( n, x_127, x ); + } + else if ( n == 255 ) + { + webbur::r8vec_copy ( n, x_255, x ); + } + else if ( n == 511 ) + { + webbur::r8vec_copy ( n, x_511, x ); + } + else + { + std::cerr << "\n"; + std::cerr << "PATTERSON_LOOKUP_POINTS - Fatal error!\n"; + std::cerr << " Unexpected value of N = " << n << "\n"; + std::exit ( 1 ); + } + return; +} +//****************************************************************************80 + +void patterson_lookup_points_np ( int n, int np, double p[], double x[] ) + +//****************************************************************************80 +// +// Purpose: +// +// PATTERSON_LOOKUP_POINTS_NP looks up Patterson quadrature points. +// +// Discussion: +// +// Our convention is that the abscissas are numbered from left to right. +// +// The rule is defined on [-1,1], +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 December 2009 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Prem Kythe, Michael Schaeferkotter, +// Handbook of Computational Methods for Integration, +// Chapman and Hall, 2004, +// ISBN: 1-58488-428-2, +// LC: QA299.3.K98. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// Legal values are 1, 3, 7, 15, 31, 63, 127, 255 and 511. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double X[N], the abscissas. +// +{ + patterson_lookup_points ( n, x ); + + return; +} +//****************************************************************************80 + +void patterson_lookup_weights ( int n, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// PATTERSON_LOOKUP_WEIGHTS looks up Patterson quadrature weights. +// +// Discussion: +// +// The allowed orders are 1, 3, 7, 15, 31, 63, 127, 255 and 511. +// +// The weights are positive, symmetric and should sum to 2. +// +// The user must preallocate space for the output array W. +// +// These rules constitute a nested family. The rules can integrate exactly +// any polynomial of degree 1, 5, 11, 23, 47, 95, 191, 383 or 767, +// respectively. +// +// The data for N = 511 was supplied by Dirk Laurie, and is derived +// from a NAG Library function d01arf. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 14 September 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Prem Kythe, Michael Schaeferkotter, +// Handbook of Computational Methods for Integration, +// Chapman and Hall, 2004, +// ISBN: 1-58488-428-2, +// LC: QA299.3.K98. +// +// NAG Library Documentation, +// D01ARF, +// The Numerical Algorithms Group. +// +// Thomas Patterson, +// The Optimal Addition of Points to Quadrature Formulae, +// Mathematics of Computation, +// Volume 22, Number 104, October 1968, pages 847-856. +// +// Parameters: +// +// Input, int N, the order. +// Legal values are 1, 3, 7, 15, 31, 63, 127, 255 or 511. +// +// Output, double W[N], the weights. +// +{ + static double w_001[1] = + { + 2.0 + }; + static double w_003[3] = + { + 0.555555555555555555556, + 0.888888888888888888889, + 0.555555555555555555556 + }; + static double w_007[7] = + { + 0.104656226026467265194, + 0.268488089868333440729, + 0.401397414775962222905, + 0.450916538658474142345, + 0.401397414775962222905, + 0.268488089868333440729, + 0.104656226026467265194 + }; + static double w_015[15] = + { + 0.0170017196299402603390, + 0.0516032829970797396969, + 0.0929271953151245376859, + 0.134415255243784220360, + 0.171511909136391380787, + 0.200628529376989021034, + 0.219156858401587496404, + 0.225510499798206687386, + 0.219156858401587496404, + 0.200628529376989021034, + 0.171511909136391380787, + 0.134415255243784220360, + 0.0929271953151245376859, + 0.0516032829970797396969, + 0.0170017196299402603390 + }; + static double w_031[31] = + { + 0.00254478079156187441540, + 0.00843456573932110624631, + 0.0164460498543878109338, + 0.0258075980961766535646, + 0.0359571033071293220968, + 0.0464628932617579865414, + 0.0569795094941233574122, + 0.0672077542959907035404, + 0.0768796204990035310427, + 0.0857559200499903511542, + 0.0936271099812644736167, + 0.100314278611795578771, + 0.105669893580234809744, + 0.109578421055924638237, + 0.111956873020953456880, + 0.112755256720768691607, + 0.111956873020953456880, + 0.109578421055924638237, + 0.105669893580234809744, + 0.100314278611795578771, + 0.0936271099812644736167, + 0.0857559200499903511542, + 0.0768796204990035310427, + 0.0672077542959907035404, + 0.0569795094941233574122, + 0.0464628932617579865414, + 0.0359571033071293220968, + 0.0258075980961766535646, + 0.0164460498543878109338, + 0.00843456573932110624631, + 0.00254478079156187441540 + }; + static double w_063[63] = + { + 0.000363221481845530659694, + 0.00126515655623006801137, + 0.00257904979468568827243, + 0.00421763044155885483908, + 0.00611550682211724633968, + 0.00822300795723592966926, + 0.0104982469096213218983, + 0.0129038001003512656260, + 0.0154067504665594978021, + 0.0179785515681282703329, + 0.0205942339159127111492, + 0.0232314466399102694433, + 0.0258696793272147469108, + 0.0284897547458335486125, + 0.0310735511116879648799, + 0.0336038771482077305417, + 0.0360644327807825726401, + 0.0384398102494555320386, + 0.0407155101169443189339, + 0.0428779600250077344929, + 0.0449145316536321974143, + 0.0468135549906280124026, + 0.0485643304066731987159, + 0.0501571393058995374137, + 0.0515832539520484587768, + 0.0528349467901165198621, + 0.0539054993352660639269, + 0.0547892105279628650322, + 0.0554814043565593639878, + 0.0559784365104763194076, + 0.0562776998312543012726, + 0.0563776283603847173877, + 0.0562776998312543012726, + 0.0559784365104763194076, + 0.0554814043565593639878, + 0.0547892105279628650322, + 0.0539054993352660639269, + 0.0528349467901165198621, + 0.0515832539520484587768, + 0.0501571393058995374137, + 0.0485643304066731987159, + 0.0468135549906280124026, + 0.0449145316536321974143, + 0.0428779600250077344929, + 0.0407155101169443189339, + 0.0384398102494555320386, + 0.0360644327807825726401, + 0.0336038771482077305417, + 0.0310735511116879648799, + 0.0284897547458335486125, + 0.0258696793272147469108, + 0.0232314466399102694433, + 0.0205942339159127111492, + 0.0179785515681282703329, + 0.0154067504665594978021, + 0.0129038001003512656260, + 0.0104982469096213218983, + 0.00822300795723592966926, + 0.00611550682211724633968, + 0.00421763044155885483908, + 0.00257904979468568827243, + 0.00126515655623006801137, + 0.000363221481845530659694 + }; + static double w_127[127] = + { + 0.0000505360952078625176247, + 0.000180739564445388357820, + 0.000377746646326984660274, + 0.000632607319362633544219, + 0.000938369848542381500794, + 0.00128952408261041739210, + 0.00168114286542146990631, + 0.00210881524572663287933, + 0.00256876494379402037313, + 0.00305775341017553113613, + 0.00357289278351729964938, + 0.00411150397865469304717, + 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0.345456507169149134898E-05, + 0.945715933950007048827E-06, + }; + + if ( n == 1 ) + { + webbur::r8vec_copy ( n, w_001, w ); + } + else if ( n == 3 ) + { + webbur::r8vec_copy ( n, w_003, w ); + } + else if ( n == 7 ) + { + webbur::r8vec_copy ( n, w_007, w ); + } + else if ( n == 15 ) + { + webbur::r8vec_copy ( n, w_015, w ); + } + else if ( n == 31 ) + { + webbur::r8vec_copy ( n, w_031, w ); + } + else if ( n == 63 ) + { + webbur::r8vec_copy ( n, w_063, w ); + } + else if ( n == 127 ) + { + webbur::r8vec_copy ( n, w_127, w ); + } + else if ( n == 255 ) + { + webbur::r8vec_copy ( n, w_255, w ); + } + else if ( n == 511 ) + { + webbur::r8vec_copy ( n, w_511, w ); + } + else + { + std::cerr << "\n"; + std::cerr << "PATTERSON_LOOKUP_WEIGHTS - Fatal error!\n"; + std::cerr << " Unexpected value of N = " << n << ".\n"; + std::exit ( 1 ); + } + return; +} +//****************************************************************************80 + +void patterson_lookup_weights_np ( int n, int np, double p[], double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// PATTERSON_LOOKUP_WEIGHTS_NP looks up Patterson quadrature weights. +// +// Discussion: +// +// The allowed orders are 1, 3, 7, 15, 31, 63, 127, 255 and 511. +// +// The weights are positive, symmetric and should sum to 2. +// +// The user must preallocate space for the output array W. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 25 April 2011 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Milton Abramowitz, Irene Stegun, +// Handbook of Mathematical Functions, +// National Bureau of Standards, 1964, +// ISBN: 0-486-61272-4, +// LC: QA47.A34. +// +// Arthur Stroud, Don Secrest, +// Gaussian Quadrature Formulas, +// Prentice Hall, 1966, +// LC: QA299.4G3S7. +// +// Parameters: +// +// Input, int N, the order. +// Legal values are 1, 3, 7, 15, 31, 63, 127, 255 or 511. +// +// Input, int NP, the number of parameters. +// +// Input, double P[NP], parameters which are not needed by this function. +// +// Output, double W[N], the weights. +// +{ + patterson_lookup_weights ( n, w ); + + return; +} +//****************************************************************************80 + +int point_radial_tol_unique_count ( int m, int n, double a[], double tol, + int *seed ) + +//****************************************************************************80 +// +// Purpose: +// +// POINT_RADIAL_TOL_UNIQUE_COUNT counts the tolerably unique points. +// +// Discussion: +// +// The input data is an M x N array A, representing the M-dimensional +// coordinates of N points. +// +// The output is the number of tolerably unique points in the list. +// +// This program performs the same task as POINT_TOL_UNIQUE_COUNT. +// But that program is guaranteed to use N^2 comparisons. +// +// It is hoped that this function, on the other hand, will tend +// to use O(N) comparisons after an O(NLog(N)) sort. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 24 July 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows. +// +// Input, int N, the number of columns. +// +// Input, double A[M*N], the array of N columns of data. +// +// Input, double TOL, a tolerance for equality. +// +// Input/output, int *SEED, a seed for the random +// number generator. +// +// Output, int POINT_RADIAL_TOL_UNIQUE_COUNT, the number of tolerably +// unique points. +// +{ + double dist; + int hi; + int i; + int *indx; + int j; + int k; + double *r; + bool *unique; + int unique_num; + double *w; + double w_sum; + double *z; + + if ( n <= 0 ) + { + unique_num = 0; + return unique_num; + } +// +// Assign a base point Z randomly in the convex hull. +// + w = webbur::r8vec_uniform_01_new ( n, seed ); + w_sum = webbur::r8vec_sum ( n, w ); + for ( j = 0; j < n; j++ ) + { + w[j] = w[j] / w_sum; + } + + z = new double[m]; + for ( i = 0; i < m; i++ ) + { + z[i] = 0.0; + for ( j = 0; j < n; j++ ) + { + z[i] = z[i] + a[i+j*m] * w[j]; + } + } +// +// Compute the radial distance R of each point to Z. +// + r = new double[n]; + + for ( j = 0; j < n; j++ ) + { + r[j] = 0.0; + for ( i = 0; i < m; i++ ) + { + r[j] = r[j] + std::pow ( a[i+j*m] - z[i], 2 ); + } + r[j] = std::sqrt ( r[j] ); + } +// +// Implicitly sort the R array. +// + indx = webbur::r8vec_sort_heap_index_a_new ( n, r ); +// +// To determine if a point I is tolerably unique, we only have to check +// whether it is distinct from all points J such that R(I) <= R(J) <= R(J)+TOL. +// + unique_num = 0; + + unique = new bool[n]; + for ( i = 0; i < n; i++ ) + { + unique[i] = true; + } + + for ( i = 0; i < n; i++ ) + { + if ( unique[indx[i]] ) + { +// +// Point INDX(I) is unique, in that no earlier point is near it. +// + unique_num = unique_num + 1; +// +// Look for later points which are close to point INDX(I) +// in terms of R. +// + hi = i; + + while ( hi < n - 1 ) + { + if ( r[indx[i]] + tol < r[indx[hi+1]] ) + { + break; + } + hi = hi + 1; + } +// +// Points INDX(I+1) through INDX(HI) have an R value close to +// point INDX(I). Are they truly close to point INDEX(I)? +// + for ( j = i + 1; j <= hi; j++ ) + { + if ( unique[indx[j]] ) + { + dist = 0.0; + for ( k = 0; k < m; k++ ) + { + dist = dist + std::pow ( a[k+indx[i]*m] - a[k+indx[j]*m], 2 ); + } + dist = std::sqrt ( dist ); + + if ( dist <= tol ) + { + unique[indx[j]] = false; + } + } + } + } + } + + delete [] indx; + delete [] r; + delete [] unique; + delete [] w; + delete [] z; + + return unique_num; +} +//****************************************************************************80 + +void point_radial_tol_unique_count_inc1 ( int m, int n1, double a1[], + double tol, int *seed, double z[], double r1[], int indx1[], bool unique1[], + int *unique_num1 ) + +//****************************************************************************80 +// +// Purpose: +// +// POINT_RADIAL_TOL_UNIQUE_COUNT_INC1 counts the tolerably unique points. +// +// Discussion: +// +// The input data includes an M x N1 array A1 of a set of N1 +// "permanent" points and N2 "temporary" points. +// +// This is a two step version of POINT_RADIAL_TOL_UNIQUE_COUNT_INC. +// +// This means that we want to identify the tolerably unique points +// among the permanent points before processing the temporary points. +// +// If many sets of temporary data are considered, this function will +// do a lot of unnecessary work resorting the permanent data; it would +// be possible to avoid repetitions of that work at the expense of saving +// various work vectors. This function accepts the overhead of the +// repeated calculations for the benefit of only having to "remember" +// the number of unique points discovered. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 01 October 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows. +// +// Input, int N1, the number of permanent points. +// +// Input, double A1[M*N1], the permanent points. +// +// Input, double TOL, a tolerance for equality. +// +// Input/output, int *SEED, a seed for the random +// number generator. +// +// Output, double Z[M], a random base vector used to +// linearly sort the data. +// +// Output, double R1[N1], the scalar values assigned to +// the data for sorting. +// +// Output, int INDX1[N1], the ascending sort index +// for A1. +// +// Output, bool UNIQUE1[N1], is TRUE for each unique permanent point. +// +// Output, int *UNIQUE_NUM1, the number of tolerably +// unique permanent points. +// +{ + double dist; + int hi; + int i; + int j; + int j1; + int k1; + double *w; + double w_sum; +// +// Assign a base point Z randomly in the convex hull of the permanent points. +// + w = webbur::r8vec_uniform_01_new ( n1, seed ); + w_sum = webbur::r8vec_sum ( n1, w ); + for ( j1 = 0; j1 < n1; j1++ ) + { + w[j1] = w[j1] / w_sum; + } + for ( i = 0; i < m; i++ ) + { + z[i] = 0.0; + for ( j1 = 0; j1 < n1; j1++ ) + { + z[i] = z[i] + a1[i+j1*m] * w[j1]; + } + } +// +// Initialize the permanent point data. +// + for ( j1 = 0; j1 < n1; j1++ ) + { + r1[j1] = 0.0; + for ( i = 0; i < m; i++ ) + { + r1[j1] = r1[j1] + std::pow ( a1[i+j1*m] - z[i], 2 ); + } + r1[j1] = std::sqrt ( r1[j1] ); + } + webbur::r8vec_sort_heap_index_a ( n1, r1, indx1 ); + + *unique_num1 = 0; + for ( j1 = 0; j1 < n1; j1++ ) + { + unique1[j1] = true; + } +// +// STEP 1: +// Compare PERMANENT POINTS to PERMANENT POINTS. +// + for ( j1 = 0; j1 < n1; j1++ ) + { + if ( unique1[indx1[j1]] ) + { + *unique_num1 = *unique_num1 + 1; + + hi = j1; + + while ( hi < n1 - 1 ) + { + if ( r1[indx1[j1]] + tol < r1[indx1[hi+1]] ) + { + break; + } + hi = hi + 1; + } + + for ( k1 = j1 + 1; k1 <= hi; k1++ ) + { + if ( unique1[indx1[k1]] ) + { + dist = 0.0; + for ( i = 0; i < m; i++ ) + { + dist = dist + std::pow ( a1[i+indx1[j1]*m] - a1[i+indx1[k1]*m], 2 ); + } + dist = std::sqrt ( dist ); + + if ( dist <= tol ) + { + unique1[indx1[k1]] = false; + } + } + } + } + } + + delete [] w; + + return; +} +//****************************************************************************80 + +void point_radial_tol_unique_count_inc2 ( int m, int n1, double a1[], int n2, + double a2[], double tol, double z[], double r1[], int indx1[], bool unique1[], + int *unique_num2 ) + +//****************************************************************************80 +// +// Purpose: +// +// POINT_RADIAL_TOL_UNIQUE_COUNT_INC2 counts the tolerably unique points. +// +// Discussion: +// +// The input data includes an M x N1 array A1 and an M x N2 array A2, +// representing the M-dimensional coordinates of a set of N1 +// "permanent" points and N2 "temporary" points. +// +// This is an "incremental" version of POINT_RADIAL_TOL_UNIQUE_COUNT. +// +// This means that we want to identify the tolerably unique points +// among the permanent points before processing the temporary points. +// +// If many sets of temporary data are considered, this function will +// do a lot of unnecessary work resorting the permanent data; it would +// be possible to avoid repetitions of that work at the expense of saving +// various work vectors. This function accepts the overhead of the +// repeated calculations for the benefit of only having to "remember" +// the number of unique points discovered. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 01 October 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows. +// +// Input, int N1, the number of permanent points. +// +// Input, double A1[M*N1], the permanent points. +// +// Input, int N2, the number of temporary points. +// +// Input, double A2[M*N2], the temporary points. +// +// Input, double TOL, a tolerance for equality. +// +// Input, double Z[M], a random base vector used to +// linearly sort the data. +// +// Input, double R1[N1], the scalar values assigned to +// the data for sorting. +// +// Input, int INDX1[N1], the ascending sort index +// for A1. +// +// Input, bool UNIQUE1[N1], is TRUE for each unique permanent point. +// +// Output, int *UNIQUE_NUM2, the number of additional +// tolerably unique points if the temporary points are included. +// +{ + double dist; + int hi; + int i; + int *indx2; + int j; + int j1; + int j2; + int j2_hi; + int j2_lo; + int k1; + int k2; + double r_hi; + double r_lo; + double *r2; + bool *unique2; +// +// Initialize the temporary point data. +// + r2 = new double[n2]; + for ( j2 = 0; j2 < n2; j2++ ) + { + r2[j2] = 0.0; + for ( i = 0; i < m; i++ ) + { + r2[j2] = r2[j2] + std::pow ( a2[i+j2*m] - z[i], 2 ); + } + r2[j2] = std::sqrt ( r2[j2] ); + } + + indx2 = new int[n2]; + webbur::r8vec_sort_heap_index_a ( n2, r2, indx2 ); + + unique2 = new bool[n2]; + for ( j2 = 0; j2 < n2; j2++ ) + { + unique2[j2] = true; + } + + *unique_num2 = 0; +// +// STEP 2: +// Use PERMANENT points to eliminate TEMPORARY points. +// + for ( j1 = 0; j1 < n1; j1++ ) + { + if ( unique1[indx1[j1]] ) + { + r_lo = r1[indx1[j1]] - tol; + r_hi = r1[indx1[j1]] + tol; + + webbur::r8vec_index_sorted_range ( n2, r2, indx2, r_lo, r_hi, + &j2_lo, &j2_hi ); + + for ( j2 = j2_lo; j2 <= j2_hi; j2++ ) + { + if ( unique2[indx2[j2]] ) + { + dist = 0.0; + for ( i = 0; i < m; i++ ) + { + dist = dist + std::pow ( a1[i+indx1[j1]*m] + - a2[i+indx2[j2]*m], 2 ); + } + dist = std::sqrt ( dist ); + if ( dist <= tol ) + { + unique2[indx2[j2]] = false; + } + } + } + } + } +// +// STEP 3: +// Use TEMPORARY points to eliminate TEMPORARY points. +// + for ( j2 = 0; j2 < n2; j2++ ) + { + if ( unique2[indx2[j2]] ) + { + *unique_num2 = *unique_num2 + 1; + + hi = j2; + + while ( hi < n2 - 1 ) + { + if ( r2[indx2[j2]] + tol < r2[indx2[hi+1]] ) + { + break; + } + hi = hi + 1; + } + + for ( k2 = j2 + 1; k2 <= hi; k2++ ) + { + if ( unique2[indx2[k2]] ) + { + dist = 0.0; + for ( i = 0; i < m; i++ ) + { + dist = dist + std::pow ( a2[i+indx2[j2]*m] - a2[i+indx2[k2]*m], 2 ); + } + dist = std::sqrt ( dist ); + + if ( dist <= tol ) + { + unique2[indx2[k2]] = false; + } + } + } + } + } + delete [] indx2; + delete [] r2; + delete [] unique2; + + return; +} +//****************************************************************************80 + +int point_radial_tol_unique_index ( int m, int n, double a[], double tol, + int *seed, int undx[], int xdnu[] ) + +//****************************************************************************80 +// +// Purpose: +// +// POINT_RADIAL_TOL_UNIQUE_INDEX indexes the tolerably unique points. +// +// Discussion: +// +// The input data is an M x N array A, representing the M-dimensional +// coordinates of N points. +// +// The output is: +// * the number of tolerably unique points in the list; +// * the index, in the list of unique items, of the representatives +// of each point; +// * the index, in A, of the tolerably unique representatives. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 28 July 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows. +// +// Input, int N, the number of columns. +// +// Input, double A[M*N], the array of N columns of data. +// +// Input, double TOL, a tolerance for equality. +// +// Input/output, int SEED, a seed for the random +// number generator. +// +// Output, int UNDX[UNIQUE_NUM], the index, in A, of the +// tolerably unique points. +// +// Output, int XDNU[N], the index, in UNDX, of the +// tolerably unique point that "represents" this point. +// +// Output, int POINT_RADIAL_TOL_UNIQUE_INDEX, the number of tolerably +// unique points. +// +{ + double dist; + int hi; + int i; + int *indx; + int j; + int k; + double *r; + bool *unique; + int unique_num; + double *w; + double w_sum; + double *z; + + if ( n <= 0 ) + { + unique_num = 0; + return unique_num; + } +// +// Assign a base point Z randomly in the convex hull. +// + w = webbur::r8vec_uniform_01_new ( n, seed ); + w_sum = webbur::r8vec_sum ( n, w ); + for ( j = 0; j < n; j++ ) + { + w[j] = w[j] / w_sum; + } + + z = new double[m]; + for ( i = 0; i < m; i++ ) + { + z[i] = 0.0; + for ( j = 0; j < n; j++ ) + { + z[i] = z[i] + a[i+j*m] * w[j]; + } + } +// +// Compute the radial distance R of each point to Z. +// + r = new double[n]; + + for ( j = 0; j < n; j++ ) + { + r[j] = 0.0; + for ( i = 0; i < m; i++ ) + { + r[j] = r[j] + std::pow ( a[i+j*m] - z[i], 2 ); + } + r[j] = std::sqrt ( r[j] ); + } +// +// Implicitly sort the R array. +// + indx = webbur::r8vec_sort_heap_index_a_new ( n, r ); +// +// To determine if a point I is tolerably unique, we only have to check +// whether it is distinct from all points J such that R(I) <= R(J) <= R(J)+TOL. +// + unique_num = 0; + + unique = new bool[n]; + for ( i = 0; i < n; i++ ) + { + unique[i] = true; + } + + for ( i = 0; i < n; i++ ) + { + if ( unique[indx[i]] ) + { +// +// Point INDX(I) is unique, in that no earlier point is near it. +// + xdnu[indx[i]] = unique_num; + undx[unique_num] = indx[i]; + unique_num = unique_num + 1; +// +// Look for later points which are close to point INDX(I) +// in terms of R. +// + hi = i; + + while ( hi < n - 1 ) + { + if ( r[indx[i]] + tol < r[indx[hi+1]] ) + { + break; + } + hi = hi + 1; + } +// +// Points INDX(I+1) through INDX(HI) have an R value close to +// point INDX(I). Are they truly close to point INDEX(I)? +// + for ( j = i + 1; j <= hi; j++ ) + { + if ( unique[indx[j]] ) + { + dist = 0.0; + for ( k = 0; k < m; k++ ) + { + dist = dist + std::pow ( a[k+indx[i]*m] - a[k+indx[j]*m], 2 ); + } + dist = std::sqrt ( dist ); + + if ( dist <= tol ) + { + unique[indx[j]] = false; + xdnu[indx[j]] = xdnu[indx[i]]; + } + } + } + } + } + + delete [] indx; + delete [] r; + delete [] unique; + delete [] w; + delete [] z; + + return unique_num; +} +//****************************************************************************80 + +void point_radial_tol_unique_index_inc1 ( int m, int n1, double a1[], + double tol, int *seed, double z[], double r1[], int indx1[], bool unique1[], + int *unique_num1, int undx1[], int xdnu1[] ) + +//****************************************************************************80 +// +// Purpose: +// +// POINT_RADIAL_TOL_UNIQUE_INDEX_INC1 indexes the tolerably unique points. +// +// Discussion: +// +// The input data includes an M x N1 array A1 of +// "permanent" points. +// +// This is a two step version of POINT_RADIAL_TOL_UNIQUE_INDEX_INC. +// +// The output is: +// * the number of tolerably unique points in the list; +// * the index, in the list of unique items, of the representatives +// of each point; +// * the index, in A1, of the tolerably unique representatives. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 02 October 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows. +// +// Input, int N1, the number of permanent points. +// +// Input, double A1[M*N1], the permanent points. +// +// Input, double TOL, a tolerance for equality. +// +// Input/output, int *SEED, a seed for the random +// number generator. +// +// Output, double Z[M], a random base vector used to +// linearly sort the data. +// +// Output, double R1[N1], the scalar values assigned to +// the data for sorting. +// +// Output, int INDX1[N1], the ascending sort index for A1. +// +// Output, bool UNIQUE1[N1], is TRUE for unique permanent points. +// +// Output, int *UNIQUE_NUM1, the number of tolerably unique points +// with just the permanent points. +// +// Output, int UNDX1[UNIQUE_NUM1], the index, in A1, of the tolerably +// unique points. +// +// Output, int XDNU1[N1], the index, in UNDX1, of the tolerably unique +// point that "represents" this point. +// +{ + double dist; + int hi; + int i; + int j; + int j1; + int k1; + double *w; + double w_sum; +// +// Assign a base point Z randomly in the convex hull of the permanent points. +// + w = webbur::r8vec_uniform_01_new ( n1, seed ); + w_sum = webbur::r8vec_sum ( n1, w ); + for ( j1 = 0; j1 < n1; j1++ ) + { + w[j1] = w[j1] / w_sum; + } + + for ( i = 0; i < m; i++ ) + { + z[i] = 0.0; + for ( j1 = 0; j1 < n1; j1++ ) + { + z[i] = z[i] + a1[i+j1*m] * w[j1]; + } + } +// +// Initialize the permanent point data. +// + for ( j1 = 0; j1 < n1; j1++ ) + { + r1[j1] = 0.0; + for ( i = 0; i < m; i++ ) + { + r1[j1] = r1[j1] + std::pow ( a1[i+j1*m] - z[i], 2 ); + } + r1[j1] = std::sqrt ( r1[j1] ); + } + webbur::r8vec_sort_heap_index_a ( n1, r1, indx1 ); + + *unique_num1 = 0; + for ( j1 = 0; j1 < n1; j1++ ) + { + unique1[j1] = true; + } +// +// STEP 1: +// Compare PERMANENT POINTS to PERMANENT POINTS. +// + for ( j1 = 0; j1 < n1; j1++ ) + { + if ( unique1[indx1[j1]] ) + { + xdnu1[indx1[j1]] = *unique_num1; + undx1[*unique_num1] = indx1[j1]; + *unique_num1 = *unique_num1 + 1; + + hi = j1; + + while ( hi < n1 - 1 ) + { + if ( r1[indx1[j1]] + tol < r1[indx1[hi+1]] ) + { + break; + } + hi = hi + 1; + } + + for ( k1 = j1 + 1; k1 <= hi; k1++ ) + { + if ( unique1[indx1[k1]] ) + { + dist = 0.0; + for ( i = 0; i < m; i++ ) + { + dist = dist + std::pow ( a1[i+indx1[j1]*m] - a1[i+indx1[k1]*m], 2 ); + } + dist = std::sqrt ( dist ); + + if ( dist <= tol ) + { + unique1[indx1[k1]] = false; + xdnu1[indx1[k1]] = xdnu1[indx1[j1]]; + } + } + } + } + } + + delete [] w; + + return; +} +//****************************************************************************80 + +void point_radial_tol_unique_index_inc2 ( int m, int n1, double a1[], int n2, + double a2[], double tol, double z[], double r1[], int indx1[], bool unique1[], + int unique_num1, int undx1[], int xdnu1[], double r2[], + int indx2[], bool unique2[], int *unique_num2, int undx2[], int xdnu2[] ) + +//****************************************************************************80 +// +// Purpose: +// +// POINT_RADIAL_TOL_UNIQUE_INDEX_INC2 indexes unique temporary points. +// +// Discussion: +// +// The input data includes an M x N1 array A1 and an M x N2 array A2, +// representing the M-dimensional coordinates of a set of N1 +// "permanent" points and N2 "temporary" points. +// +// For notation, we use "A" to describe the M x (N1+N2) array that would be +// formed by starting with A1 and appending A2. +// +// The output is: +// * the number of tolerably unique points in the list; +// * the index, in the list of unique items, of the representatives +// of each point; +// * the index, in A, of the tolerably unique representatives. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 08 October 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows. +// +// Input, int N1, the number of permanent points. +// +// Input, double A1[M*N1], the permanent points. +// +// Input, int N2, the number of temporary points. +// +// Input, double A2[M*N2], the temporary points. +// +// Input, double TOL, a tolerance for equality. +// +// Input, double Z[M], a random base vector used to +// linearly sort the data. +// +// Input, double R1[N1], the scalar values assigned to +// A1 for sorting. +// +// Input, int INDX1[N1], the ascending sort index for A1. +// +// Input, bool UNIQUE1[N1], is TRUE for unique permanent points. +// +// Input, int UNIQUE_NUM1, the number of tolerably unique permanent points. +// +// Input, int UNDX1[UNIQUE_NUM1], +// the index in A1 of the tolerably unique permanent points. +// +// Input, int XDNU1[N1], the index in UNDX1 +// of the tolerably unique permanent point that "represents" this point. +// +// Output, double R2[N2], the scalar values assigned to +// A2 for sorting. +// +// Output, int INDX2[N2], the ascending sort index for A2. +// +// Output, bool UNIQUE2[N2], is TRUE for unique temporary points. +// +// Output, int *UNIQUE_NUM2, the number +// of tolerably unique temporary points. +// +// Output, int UNDX2[UNIQUE_NUM2], +// the index in A2 of the tolerably unique points, incremented by N1. +// +// Output, int XDNU2[N2], the index, in UNDX1 +// or UNDX2, of the tolerably unique point that "represents" this +// temporary point. If the value represents an index in UNDX2, this +// can be inferred by the fact that its value is greater than or +// equal to UNIQUE_NUM1. To reference UNDX2, the value should then be +// decremented by UNIQUE_NUM1. +// +{ + double dist; + int hi; + int i; + int j; + int j1; + int j2; + int j2_hi; + int j2_lo; + int k1; + int k2; + double r_hi; + double r_lo; +// +// Initialize the temporary point data. +// + for ( j2 = 0; j2 < n2; j2++ ) + { + r2[j2] = 0.0; + for ( i = 0; i < m; i++ ) + { + r2[j2] = r2[j2] + std::pow ( a2[i+j2*m] - z[i], 2 ); + } + r2[j2] = std::sqrt ( r2[j2] ); + } + + webbur::r8vec_sort_heap_index_a ( n2, r2, indx2 ); + + for ( j2 = 0; j2 < n2; j2++ ) + { + unique2[j2] = true; + } + + *unique_num2 = 0; +// +// STEP 2: +// Use PERMANENT points to eliminate TEMPORARY points. +// + for ( j1 = 0; j1 < n1; j1++ ) + { + if ( unique1[indx1[j1]] ) + { + r_lo = r1[indx1[j1]] - tol; + r_hi = r1[indx1[j1]] + tol; + + webbur::r8vec_index_sorted_range ( n2, r2, indx2, r_lo, r_hi, + &j2_lo, &j2_hi ); + + for ( j2 = j2_lo; j2 <= j2_hi; j2++ ) + { + if ( unique2[indx2[j2]] ) + { + dist = 0.0; + for ( i = 0; i < m; i++ ) + { + dist = dist + std::pow ( a1[i+indx1[j1]*m] + - a2[i+indx2[j2]*m], 2 ); + } + dist = std::sqrt ( dist ); + if ( dist <= tol ) + { + unique2[indx2[j2]] = false; + xdnu2[indx2[j2]] = xdnu1[indx1[j1]]; + } + } + } + } + } +// +// STEP 3: +// Use TEMPORARY points to eliminate TEMPORARY points. +// + for ( j2 = 0; j2 < n2; j2++ ) + { + if ( unique2[indx2[j2]] ) + { + xdnu2[indx2[j2]] = unique_num1 + *unique_num2; + undx2[*unique_num2] = indx2[j2] + n1; + *unique_num2 = *unique_num2 + 1; + + hi = j2; + + while ( hi < n2 - 1 ) + { + if ( r2[indx2[j2]] + tol < r2[indx2[hi+1]] ) + { + break; + } + hi = hi + 1; + } + + for ( k2 = j2 + 1; k2 <= hi; k2++ ) + { + if ( unique2[indx2[k2]] ) + { + dist = 0.0; + for ( i = 0; i < m; i++ ) + { + dist = dist + std::pow ( a2[i+indx2[j2]*m] - a2[i+indx2[k2]*m], 2 ); + } + dist = std::sqrt ( dist ); + + if ( dist <= tol ) + { + unique2[indx2[k2]] = false; + xdnu2[indx2[k2]] = xdnu2[indx2[j2]]; + } + } + } + } + } + + return; +} +//****************************************************************************80 + +void point_radial_tol_unique_index_inc3 ( int m, int n1, double a1[], + double r1[], int indx1[], bool unique1[], int unique_num1, int undx1[], + int xdnu1[], int n2, double a2[], double r2[], int indx2[], bool unique2[], + int unique_num2, int undx2[], int xdnu2[], int *n3, double a3[], double r3[], + int indx3[], bool unique3[], int *unique_num3, int undx3[], int xdnu3[] ) + +//****************************************************************************80 +// +// Purpose: +// +// POINT_RADIAL_TOL_UNIQUE_INDEX_INC3 merges index data. +// +// Discussion: +// +// This function may be called after *INDEX_INC1 has created index +// information for the permanent data, and *INDEX_INC2 has created +// augmenting information for a set of temporary data which now is +// to be merged with the permanent data. +// +// The function merges the data and index information to create a +// new "permanent" data set. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 08 October 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows. +// +// Input, int N1, the number of permanent points. +// +// Input, double A1[M*N1], the permanent points. +// +// Input, double R1[N1], the scalar values assigned to +// the data for sorting. +// +// Input, int INDX1[N1], the ascending sort index +// for A1. +// +// Input, bool UNIQUE1[N1], is TRUE for each unique permanent point. +// +// Input, int UNIQUE_NUM1, the number +// of tolerably unique points with just the permanent points. +// +// Input, int UNDX1[UNIQUE_NUM1], +// the index in A1 of the tolerably unique points. +// +// Input, int XDNU1[N1], the index in UNDX1 +// of the tolerably unique point that "represents" this point. +// +// Input, int N2, the number of temporary points. +// +// Input, double A2[M,N2], the temporary points. +// +// Input, double R2[N2], the scalar values assigned to +// the data for sorting. +// +// Input, int INDX2[N2], the ascending sort index +// for A2. +// +// Input, bool UNIQUE2[N2], is TRUE for each unique temporary point. +// +// Input, int UNIQUE_NUM2, the number +// of tolerably unique temporary points. +// +// Input, int UNDX2[UNIQUE_NUM2], +// the index in A2 of the tolerably unique points, incremented by UNIQUE_NUM1. +// +// Input, int XDNU2[N2], the index in UNDX1 or UNDX2 +// of the tolerably unique point that "represents" this point. +// +// Output, int *N3, the number of permanent points. +// +// Output, double A3[M,N3], the permanent points. +// +// Output, double R3[N3], the scalar values assigned to +// the data for sorting. +// +// Output, int INDX3[N3], the ascending sort index +// for A3. +// +// Output, bool UNIQUE3[N3], is TRUE for each unique permanent point. +// +// Output, int *UNIQUE_NUM3, the number +// of tolerably unique points. +// +// Output, int UNDX3[UNIQUE_NUM3], +// the index in A3 of the tolerably unique points. +// +// Output, int XDNU3[N3], the index in UNDX3 +// of the tolerably unique point that "represents" this point. +// +{ + int i; + int i1; + int i2; + int i3; + double v1; + double v2; + + *n3 = n1 + n2; + + for ( i1 = 0; i1 < n1; i1++ ) + { + for ( i = 0; i < m; i++ ) + { + a3[i+i1*m] = a1[i+i1*m]; + } + } + for ( i2 = 0; i2 < n2; i2++ ) + { + i3 = n1 + i2; + for ( i = 0; i < m; i++ ) + { + a3[i+i3*m] = a2[i+i2*m]; + } + } + for ( i1 = 0; i1 < n1; i1++ ) + { + r3[i1]= r1[i1]; + } + for ( i2 = 0; i2 < n2; i2++ ) + { + i3 = n1 + i2; + r3[i3] = r2[i2]; + } +// +// Interleave the two INDX arrays so that INDX3 presents the entries +// of A3 in ascending R3 order. +// + i1 = 0; + i2 = 0; + + for ( i3 = 0; i3 < *n3; i3++ ) + { + if ( i1 < n1 ) + { + v1 = r1[indx1[i1]]; + } + else + { + v1 = r8_huge ( ); + } + + if ( i2 < n2 ) + { + v2 = r2[indx2[i2]]; + } + else + { + v2 = r8_huge ( ); + } + + if ( v1 <= v2 ) + { + indx3[i3] = indx1[i1]; + i1 = i1 + 1; + } + else + { + indx3[i3] = indx2[i2] + n1; + i2 = i2 + 1; + } + } + + *unique_num3 = unique_num1 + unique_num2; + + for ( i1 = 0; i1 < n1; i1++ ) + { + unique3[i1] = unique1[i1]; + } + for ( i2 = 0; i2 < n2; i2++ ) + { + i3 = n1 + i2; + unique3[i3] = unique2[i2]; + } +// +// The entries in UNDX2 were already incremented by N2 if they pointed +// to an entry of A2, so all entries in UNDX2 correctly index A3. +// + for ( i1 = 0; i1 < unique_num1; i1++ ) + { + undx3[i1] = undx1[i1]; + } + for ( i2 = 0; i2 < unique_num2; i2++ ) + { + i3 = unique_num1 + i2; + undx3[i3] = undx2[i2]; + } +// +// Note that the entries of XDNU2 were already incremented by N2 +// so that they correctly index A3, not A2. +// + for ( i1 = 0; i1 < n1; i1++ ) + { + xdnu3[i1] = xdnu1[i1]; + } + for ( i2 = 0; i2 < n2; i2++ ) + { + i3 = n1 + i2; + xdnu3[i3] = xdnu2[i2]; + } + + return; +} +//****************************************************************************80 + +void point_unique_index ( int m, int n, double a[], int unique_num, int undx[], + int xdnu[] ) + +//****************************************************************************80 +// +// Purpose: +// +// POINT_UNIQUE_INDEX indexes unique points. +// +// Discussion: +// +// An R8COL is an M by N array of R8's, regarded as an array of N columns, +// each of length M. +// +// The goal of this routine is to determine a vector UNDX, +// which points to the unique elements of A, in sorted order, +// and a vector XDNU, which identifies, for each entry of A, the index of +// the unique sorted element of A. +// +// This is all done with index vectors, so that the elements of +// A are never moved. +// +// The first step of the algorithm requires the indexed sorting +// of A, which creates arrays INDX and XDNI. (If all the entries +// of A are unique, then these arrays are the same as UNDX and XDNU.) +// +// We then use INDX to examine the entries of A in sorted order, +// noting the unique entries, creating the entries of XDNU and +// UNDX as we go. +// +// Once this process has been completed, the vector A could be +// replaced by a compressed vector XU, containing the unique entries +// of A in sorted order, using the formula +// +// XU(*) = A(UNDX(*)). +// +// We could then, if we wished, reconstruct the entire vector A, or +// any element of it, by index, as follows: +// +// A(I) = XU(XDNU(I)). +// +// We could then replace A by the combination of XU and XDNU. +// +// Later, when we need the I-th entry of A, we can locate it as +// the XDNU(I)-th entry of XU. +// +// Here is an example of a vector A, the sort and inverse sort +// index vectors, and the unique sort and inverse unique sort vectors +// and the compressed unique sorted vector. +// +// I A Indx Xdni XU Undx Xdnu +// ----+-----+-----+-----+--------+-----+-----+ +// 0 | 11. 0 0 | 11. 0 0 +// 1 | 22. 2 4 | 22. 1 1 +// 2 | 11. 5 1 | 33. 3 0 +// 3 | 33. 8 7 | 55. 4 2 +// 4 | 55. 1 8 | 3 +// 5 | 11. 6 2 | 0 +// 6 | 22. 7 5 | 1 +// 7 | 22. 3 6 | 1 +// 8 | 11. 4 3 | 0 +// +// INDX(2) = 3 means that sorted item(2) is A(3). +// XDNI(2) = 5 means that A(2) is sorted item(5). +// +// UNDX(3) = 4 means that unique sorted item(3) is at A(4). +// XDNU(8) = 2 means that A(8) is at unique sorted item(2). +// +// XU(XDNU(I))) = A(I). +// XU(I) = A(UNDX(I)). +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 July 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the dimension of the data values. +// +// Input, int N, the number of data values, +// +// Input, double A[M*N], the data values. +// +// Input, int UNIQUE_NUM, the number of unique values in A. +// This value is only required for languages in which the size of +// UNDX must be known in advance. +// +// Output, int UNDX[UNIQUE_NUM], the UNDX vector. +// +// Output, int XDNU[N], the XDNU vector. +// +{ + double diff; + int i; + int *indx; + int j; + int k; +// +// Implicitly sort the array. +// + indx = webbur::r8col_sort_heap_index_a ( m, n, a ); +// +// Walk through the implicitly sorted array. +// + i = 0; + + j = 0; + undx[j] = indx[i]; + + xdnu[indx[i]] = j; + + for ( i = 1; i < n; i++ ) + { + diff = 0.0; + for ( k = 0; k < m; k++ ) + { + diff = webbur::r8_max ( diff, + webbur::r8_abs ( a[k+indx[i]*m] - a[k+undx[j]*m] ) ); + } + if ( 0.0 < diff ) + { + j = j + 1; + undx[j] = indx[i]; + } + xdnu[indx[i]] = j; + } + delete [] indx; + + return; +} +//****************************************************************************80 + +void product_mixed_weight ( int dim_num, int order_1d[], int order_nd, + int rule[], double alpha[], double beta[], double weight_nd[] ) + +//****************************************************************************80 +// +// Purpose: +// +// PRODUCT_MIXED_WEIGHT computes the weights of a mixed product rule. +// +// Discussion: +// +// This routine computes the weights for a quadrature rule which is +// a product of 1D rules of varying order and kind. +// +// The user must preallocate space for the output array WEIGHT_ND. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 11 February 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int DIM_NUM, the spatial dimension. +// +// Input, int ORDER_1D[DIM_NUM], the order of the 1D rules. +// +// Input, int ORDER_ND, the order of the product rule. +// +// Input, int RULE[DIM_NUM], the rule in each dimension. +// 1, "CC", Clenshaw Curtis, Closed Fully Nested rule. +// 2, "F2", Fejer Type 2, Open Fully Nested rule. +// 3, "GP", Gauss Patterson, Open Fully Nested rule. +// 4, "GL", Gauss Legendre, Open Weakly Nested rule. +// 5, "GH", Gauss Hermite, Open Weakly Nested rule. +// 6, "GGH", Generalized Gauss Hermite, Open Weakly Nested rule. +// 7, "LG", Gauss Laguerre, Open Non Nested rule. +// 8, "GLG", Generalized Gauss Laguerre, Open Non Nested rule. +// 9, "GJ", Gauss Jacobi, Open Non Nested rule. +// 10, "GW", Golub Welsch, (presumed) Open Non Nested rule. +// 11, "CC_SE", Clenshaw Curtis Slow Exponential, Closed Fully Nested rule. +// 12, "F2_SE", Fejer Type 2 Slow Exponential, Open Fully Nested rule. +// 13, "GP_SE", Gauss Patterson Slow Exponential, Open Fully Nested rule. +// 14, "CC_ME", Clenshaw Curtis Moderate Exponential, Closed Fully Nested rule. +// 15, "F2_ME", Fejer Type 2 Moderate Exponential, Open Fully Nested rule. +// 16, "GP_ME", Gauss Patterson Moderate Exponential, Open Fully Nested rule. +// 17, "CCN", Clenshaw Curtis Nested, Linear, Closed Fully Nested rule. +// +// Input, double ALPHA[DIM_NUM], BETA[DIM_NUM], parameters used for +// Generalized Gauss Hermite, Generalized Gauss Laguerre, +// and Gauss Jacobi rules. +// +// Output, double WEIGHT_ND[ORDER_ND], the product rule weights. +// +{ + int dim; + int i; + double *weight_1d; + + for ( i = 0; i < order_nd; i++ ) + { + weight_nd[i] = 1.0; + } + + for ( dim = 0; dim < dim_num; dim++ ) + { + weight_1d = new double[order_1d[dim]]; + + if ( rule[dim] == 1 ) + { + webbur::clenshaw_curtis_compute_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 2 ) + { + webbur::fejer2_compute_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 3 ) + { + webbur::patterson_lookup_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 4 ) + { + webbur::legendre_compute_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 5 ) + { + webbur::hermite_compute_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 6 ) + { + webbur::gen_hermite_compute_weights ( order_1d[dim], alpha[dim], weight_1d ); + } + else if ( rule[dim] == 7 ) + { + webbur::laguerre_compute_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 8 ) + { + webbur::gen_laguerre_compute_weights ( order_1d[dim], alpha[dim], weight_1d ); + } + else if ( rule[dim] == 9 ) + { + webbur::jacobi_compute_weights ( order_1d[dim], alpha[dim], beta[dim], weight_1d ); + } + else if ( rule[dim] == 10 ) + { + std::cerr << "\n"; + std::cerr << "PRODUCT_MIXED_WEIGHT - Fatal error!\n"; + std::cerr << " Do not know how to set weights for rule 10.\n"; + std::exit ( 1 ); + } + else if ( rule[dim] == 11 ) + { + webbur::clenshaw_curtis_compute_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 12 ) + { + webbur::fejer2_compute_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 13 ) + { + webbur::patterson_lookup_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 14 ) + { + webbur::clenshaw_curtis_compute_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 15 ) + { + webbur::fejer2_compute_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 16 ) + { + webbur::patterson_lookup_weights ( order_1d[dim], weight_1d ); + } + else if ( rule[dim] == 17 ) + { + webbur::ccn_compute_weights ( order_1d[dim], weight_1d ); + } + else + { + std::cerr << "\n"; + std::cerr << "PRODUCT_MIXED_WEIGHT - Fatal error!\n"; + std::cerr << " Unexpected value of RULE[" << dim << "] = " + << rule[dim] << ".\n"; + std::exit ( 1 ); + } + + webbur::r8vec_direct_product2 ( dim, order_1d[dim], weight_1d, + dim_num, order_nd, weight_nd ); + + delete [] weight_1d; + } + return; +} +//****************************************************************************80 + +double r8_abs ( double x ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_ABS returns the absolute value of an R8. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, double X, the quantity whose absolute value is desired. +// +// Output, double R8_ABS, the absolute value of X. +// +{ + double value; + + if ( 0.0 <= x ) + { + value = x; + } + else + { + value = -x; + } + return value; +} +//****************************************************************************80 + +double r8_ceiling ( double x ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_CEILING rounds an R8 "up" (towards +oo) to the next integer. +// +// Example: +// +// X R8_CEILING(X) +// +// -1.1 -1.0 +// -1.0 -1.0 +// -0.9 0.0 +// -0.1 0.0 +// 0.0 0.0 +// 0.1 1.0 +// 0.9 1.0 +// 1.0 1.0 +// 1.1 2.0 +// 2.9 3.0 +// 3.0 3.0 +// 3.14159 4.0 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 01 April 2004 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, double X, the number whose ceiling is desired. +// +// Output, double R8_CEILING, the ceiling of X. +// +{ + double value; + + value = ( int ) x; + + if ( value < x ) + { + value = value + 1.0; + } + + return value; +} +//****************************************************************************80 + +double r8_choose ( int n, int k ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_CHOOSE computes the binomial coefficient C(N,K) as an R8. +// +// Discussion: +// +// The value is calculated in such a way as to avoid overflow and +// roundoff. The calculation is done in R8 arithmetic. +// +// The formula used is: +// +// C(N,K) = N! / ( K! * (N-K)! ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 24 March 2008 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// ML Wolfson, HV Wright, +// Algorithm 160: +// Combinatorial of M Things Taken N at a Time, +// Communications of the ACM, +// Volume 6, Number 4, April 1963, page 161. +// +// Parameters: +// +// Input, int N, K, the values of N and K. +// +// Output, double R8_CHOOSE, the number of combinations of N +// things taken K at a time. +// +{ + int i; + int mn; + int mx; + int value; + + mn = webbur::i4_min ( k, n - k ); + + if ( mn < 0 ) + { + value = 0.0; + } + else if ( mn == 0 ) + { + value = 1.0; + } + else + { + mx = webbur::i4_max ( k, n - k ); + value = ( double ) ( mx + 1 ); + + for ( i = 2; i <= mn; i++ ) + { + value = ( value * ( double ) ( mx + i ) ) / ( double ) i; + } + } + return value; +} +//****************************************************************************80 + +double r8_epsilon ( ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_EPSILON returns the R8 roundoff unit. +// +// Discussion: +// +// The roundoff unit is a number R which is a power of 2 with the +// property that, to the precision of the computer's arithmetic, +// 1 < 1 + R +// but +// 1 = ( 1 + R / 2 ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 February 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Output, double R8_EPSILON, the R8 round-off unit. +// +{ + double value; + + value = 1.0; + + while ( 1.0 < ( double ) ( 1.0 + value ) ) + { + value = value / 2.0; + } + + value = 2.0 * value; + + return value; +} +//****************************************************************************80 + +double r8_factorial ( int n ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_FACTORIAL computes the factorial of N. +// +// Discussion: +// +// factorial ( N ) = product ( 1 <= I <= N ) I +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 16 January 1999 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the argument of the factorial function. +// If N is less than 1, the function value is returned as 1. +// +// Output, double R8_FACTORIAL, the factorial function. +// +{ + int i; + double value; + + value = 1.0; + + for ( i = 1; i <= n; i++ ) + { + value = value * ( double ) ( i ); + } + + return value; +} +//****************************************************************************80 + +double r8_factorial2 ( int n ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_FACTORIAL2 computes the double factorial function. +// +// Discussion: +// +// FACTORIAL2( N ) = Product ( N * (N-2) * (N-4) * ... * 2 ) (N even) +// = Product ( N * (N-2) * (N-4) * ... * 1 ) (N odd) +// +// Example: +// +// N FACTORIAL2(N) +// +// 0 1 +// 1 1 +// 2 2 +// 3 3 +// 4 8 +// 5 15 +// 6 48 +// 7 105 +// 8 384 +// 9 945 +// 10 3840 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 January 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the argument of the double factorial +// function. If N is less than 1, R8_FACTORIAL2 is returned as 1.0. +// +// Output, double R8_FACTORIAL2, the double factorial function. +// +{ + int n_copy; + double value; + + value = 1.0; + + if ( n < 1 ) + { + return value; + } + + n_copy = n; + + while ( 1 < n_copy ) + { + value = value * ( double ) n_copy; + n_copy = n_copy - 2; + } + + return value; +} +//****************************************************************************80 + +double r8_floor ( double x ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_FLOOR rounds an R8 "down" (towards -infinity) to the next integer. +// +// Example: +// +// X R8_FLOOR(X) +// +// -1.1 -2.0 +// -1.0 -1.0 +// -0.9 -1.0 +// -0.1 -1.0 +// 0.0 0.0 +// 0.1 0.0 +// 0.9 0.0 +// 1.0 1.0 +// 1.1 1.0 +// 2.9 2.0 +// 3.0 3.0 +// 3.14159 3.0 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 15 April 2007 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, double X, the number whose floor is desired. +// +// Output, double R8_FLOOR, the floor of X. +// +{ + double value; + + value = ( int ) x; + + if ( x < value ) + { + value = value - 1.0; + } + + return value; +} +//****************************************************************************80 + +double r8_gamma ( double x ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_GAMMA evaluates Gamma(X) for a real argument. +// +// Discussion: +// +// This routine calculates the gamma function for a real argument X. +// +// Computation is based on an algorithm outlined in reference 1. +// The program uses rational functions that approximate the gamma +// function to at least 20 significant decimal digits. Coefficients +// for the approximation over the interval (1,2) are unpublished. +// Those for the approximation for 12 <= X are from reference 2. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 January 2008 +// +// Author: +// +// Original FORTRAN77 version by William Cody, Laura Stoltz. +// C++ version by John Burkardt. +// +// Reference: +// +// William Cody, +// An Overview of Software Development for Special Functions, +// in Numerical Analysis Dundee, 1975, +// edited by GA Watson, +// Lecture Notes in Mathematics 506, +// Springer, 1976. +// +// John Hart, Ward Cheney, Charles Lawson, Hans Maehly, +// Charles Mesztenyi, John Rice, Henry Thatcher, +// Christoph Witzgall, +// Computer Approximations, +// Wiley, 1968, +// LC: QA297.C64. +// +// Parameters: +// +// Input, double X, the argument of the function. +// +// Output, double R8_GAMMA, the value of the function. +// +{ +// +// Coefficients for minimax approximation over (12, INF). +// + double c[7] = { + -1.910444077728E-03, + 8.4171387781295E-04, + -5.952379913043012E-04, + 7.93650793500350248E-04, + -2.777777777777681622553E-03, + 8.333333333333333331554247E-02, + 5.7083835261E-03 }; + double eps = 2.22E-16; + double fact; + int i; + int n; + double one = 1.0; + double p[8] = { + -1.71618513886549492533811E+00, + 2.47656508055759199108314E+01, + -3.79804256470945635097577E+02, + 6.29331155312818442661052E+02, + 8.66966202790413211295064E+02, + -3.14512729688483675254357E+04, + -3.61444134186911729807069E+04, + 6.64561438202405440627855E+04 }; + bool parity; + double pi = 3.1415926535897932384626434; + double q[8] = { + -3.08402300119738975254353E+01, + 3.15350626979604161529144E+02, + -1.01515636749021914166146E+03, + -3.10777167157231109440444E+03, + 2.25381184209801510330112E+04, + 4.75584627752788110767815E+03, + -1.34659959864969306392456E+05, + -1.15132259675553483497211E+05 }; + double res; + double sqrtpi = 0.9189385332046727417803297; + double sum; + double twelve = 12.0; + double two = 2.0; + double value; + double xbig = 171.624; + double xden; + double xinf = 1.79E+308; + double xminin = 2.23E-308; + double xnum; + double y; + double y1; + double ysq; + double z; + + parity = false; + fact = one; + n = 0; + y = x; +// +// Argument is negative. +// + if ( y <= 0.0 ) + { + y = - x; + y1 = ( double ) ( int ) ( y ); + res = y - y1; + + if ( res != 0.0 ) + { + if ( y1 != ( double ) ( int ) ( y1 * 0.5 ) * two ) + { + parity = true; + } + + fact = - pi / std::sin ( pi * res ); + y = y + one; + } + else + { + res = xinf; + value = res; + return value; + } + } +// +// Argument is positive. +// + if ( y < eps ) + { +// +// Argument < EPS. +// + if ( xminin <= y ) + { + res = one / y; + } + else + { + res = xinf; + value = res; + return value; + } + } + else if ( y < twelve ) + { + y1 = y; +// +// 0.0 < argument < 1.0. +// + if ( y < one ) + { + z = y; + y = y + one; + } +// +// 1.0 < argument < 12.0. +// Reduce argument if necessary. +// + else + { + n = ( int ) ( y ) - 1; + y = y - ( double ) ( n ); + z = y - one; + } +// +// Evaluate approximation for 1.0 < argument < 2.0. +// + xnum = 0.0; + xden = one; + for ( i = 0; i < 8; i++ ) + { + xnum = ( xnum + p[i] ) * z; + xden = xden * z + q[i]; + } + res = xnum / xden + one; +// +// Adjust result for case 0.0 < argument < 1.0. +// + if ( y1 < y ) + { + res = res / y1; + } +// +// Adjust result for case 2.0 < argument < 12.0. +// + else if ( y < y1 ) + { + for ( i = 1; i <= n; i++ ) + { + res = res * y; + y = y + one; + } + } + } + else + { +// +// Evaluate for 12.0 <= argument. +// + if ( y <= xbig ) + { + ysq = y * y; + sum = c[6]; + for ( i = 0; i < 6; i++ ) + { + sum = sum / ysq + c[i]; + } + sum = sum / y - y + sqrtpi; + sum = sum + ( y - 0.5 ) * std::log ( y ); + res = std::exp ( sum ); + } + else + { + res = xinf; + value = res; + return value; + } + } +// +// Final adjustments and return. +// + if ( parity ) + { + res = - res; + } + + if ( fact != one ) + { + res = fact / res; + } + + value = res; + + return value; +} +//****************************************************************************80 + +double r8_huge ( ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_HUGE returns a "huge" R8. +// +// Discussion: +// +// The value returned by this function is NOT required to be the +// maximum representable R8. This value varies from machine to machine, +// from compiler to compiler, and may cause problems when being printed. +// We simply want a "very large" but non-infinite number. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 06 October 2007 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Output, double R8_HUGE, a "huge" R8 value. +// +{ + double value; + + value = 1.0E+30; + + return value; +} +//****************************************************************************80 + +double r8_hyper_2f1 ( double a, double b, double c, double x ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_HYPER_2F1 evaluates the hypergeometric function 2F1(A,B,C,X). +// +// Discussion: +// +// A bug was corrected. A line which read +// c1 = - ( - 1.0, m ) * gc / ( gam * gbm * rm ); +// was corrected to read +// c1 = - std::pow ( - 1.0, m ) * gc / ( gam * gbm * rm ); +// JVB, 05 July 2009. +// +// A minor bug was corrected. The HW variable, used in several places as +// the "old" value of a quantity being iteratively improved, was not +// being initialized. JVB, 11 February 2008. +// +// The FORTRAN77 original version of this routine is copyrighted by +// Shanjie Zhang and Jianming Jin. However, they give permission to +// incorporate this routine into a user program provided that the copyright +// is acknowledged. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 05 July 2009 +// +// Author: +// +// Original FORTRAN77 version by Shanjie Zhang, Jianming Jin. +// C++ version by John Burkardt. +// +// Reference: +// +// Shanjie Zhang, Jianming Jin, +// Computation of Special Functions, +// Wiley, 1996, +// ISBN: 0-471-11963-6, +// LC: QA351.C45 +// +// Parameters: +// +// Input, double A, B, C, X, the arguments of the function. +// C must not be equal to a nonpositive integer. +// X < 1. +// +// Output, double R8_HYPER_2F1, the value of the function. +// +{ + double a0; + double aa; + double bb; + double c0; + double c1; + double el = 0.5772156649015329; + double eps; + double f0; + double f1; + double g0; + double g1; + double g2; + double g3; + double ga; + double gabc; + double gam; + double gb; + double gbm; + double gc; + double gca; + double gcab; + double gcb; + double gm; + double hf; + double hw; + int j; + int k; + bool l0; + bool l1; + bool l2; + bool l3; + bool l4; + bool l5; + int m; + int nm; + double pa; + double pb; + double pi = 3.141592653589793; + double r; + double r0; + double r1; + double rm; + double rp; + double sm; + double sp; + double sp0; + double x1; + + l0 = ( c == ( int ) ( c ) ) && ( c < 0.0 ); + l1 = ( 1.0 - x < 1.0E-15 ) && ( c - a - b <= 0.0 ); + l2 = ( a == ( int ) ( a ) ) && ( a < 0.0 ); + l3 = ( b == ( int ) ( b ) ) && ( b < 0.0 ); + l4 = ( c - a == ( int ) ( c - a ) ) && ( c - a <= 0.0 ); + l5 = ( c - b == ( int ) ( c - b ) ) && ( c - b <= 0.0 ); + + if ( l0 ) + { + std::cerr << "\n"; + std::cerr << "R8_HYPER_2F1 - Fatal error!\n"; + std::cerr << " The hypergeometric series is divergent.\n"; + std::cerr << " C is integral and negative.\n"; + std::cerr << " C = " << c << "\n"; + std::exit ( 1 ); + } + + if ( l1 ) + { + std::cerr << "\n"; + std::cerr << "R8_HYPER_2F1 - Fatal error!\n"; + std::cerr << " The hypergeometric series is divergent.\n"; + std::cerr << " 1 - X < 0, C - A - B <= 0\n"; + std::cerr << " A = " << a << "\n"; + std::cerr << " B = " << b << "\n"; + std::cerr << " C = " << c << "\n"; + std::cerr << " X = " << x << "\n"; + std::exit ( 1 ); + } + + if ( 0.95 < x ) + { + eps = 1.0E-08; + } + else + { + eps = 1.0E-15; + } + + if ( x == 0.0 || a == 0.0 || b == 0.0 ) + { + hf = 1.0; + return hf; + } + else if ( 1.0 - x == eps && 0.0 < c - a - b ) + { + gc = webbur::r8_gamma ( c ); + gcab = webbur::r8_gamma ( c - a - b ); + gca = webbur::r8_gamma ( c - a ); + gcb = webbur::r8_gamma ( c - b ); + hf = gc * gcab / ( gca * gcb ); + return hf; + } + else if ( 1.0 + x <= eps && r8_abs ( c - a + b - 1.0 ) <= eps ) + { + g0 = std::sqrt ( pi ) * std::pow ( 2.0, - a ); + g1 = webbur::r8_gamma ( c ); + g2 = webbur::r8_gamma ( 1.0 + a / 2.0 - b ); + g3 = webbur::r8_gamma ( 0.5 + 0.5 * a ); + hf = g0 * g1 / ( g2 * g3 ); + return hf; + } + else if ( l2 || l3 ) + { + if ( l2 ) + { + nm = ( int ) ( webbur::r8_abs ( a ) ); + } + + if ( l3 ) + { + nm = ( int ) ( webbur::r8_abs ( b ) ); + } + + hf = 1.0; + r = 1.0; + + for ( k = 1; k <= nm; k++ ) + { + r = r * ( a + k - 1.0 ) * ( b + k - 1.0 ) + / ( k * ( c + k - 1.0 ) ) * x; + hf = hf + r; + } + + return hf; + } + else if ( l4 || l5 ) + { + if ( l4 ) + { + nm = ( int ) ( webbur::r8_abs ( c - a ) ); + } + + if ( l5 ) + { + nm = ( int ) ( webbur::r8_abs ( c - b ) ); + } + + hf = 1.0; + r = 1.0; + for ( k = 1; k <= nm; k++ ) + { + r = r * ( c - a + k - 1.0 ) * ( c - b + k - 1.0 ) + / ( k * ( c + k - 1.0 ) ) * x; + hf = hf + r; + } + hf = std::pow ( 1.0 - x, c - a - b ) * hf; + return hf; + } + + aa = a; + bb = b; + x1 = x; + + if ( x < 0.0 ) + { + x = x / ( x - 1.0 ); + if ( a < c && b < a && 0.0 < b ) + { + a = bb; + b = aa; + } + b = c - b; + } + + if ( 0.75 <= x ) + { + gm = 0.0; + + if ( webbur::r8_abs ( c - a - b - ( int ) ( c - a - b ) ) < 1.0E-15 ) + { + m = ( int ) ( c - a - b ); + ga = webbur::r8_gamma ( a ); + gb = webbur::r8_gamma ( b ); + gc = webbur::r8_gamma ( c ); + gam = webbur::r8_gamma ( a + m ); + gbm = webbur::r8_gamma ( b + m ); + + pa = webbur::r8_psi ( a ); + pb = webbur::r8_psi ( b ); + + if ( m != 0 ) + { + gm = 1.0; + } + + for ( j = 1; j <= std::abs ( m ) - 1; j++ ) + { + gm = gm * j; + } + + rm = 1.0; + for ( j = 1; j <= std::abs ( m ); j++ ) + { + rm = rm * j; + } + + f0 = 1.0; + r0 = 1.0;; + r1 = 1.0; + sp0 = 0.0;; + sp = 0.0; + + if ( 0 <= m ) + { + c0 = gm * gc / ( gam * gbm ); + c1 = - gc * std::pow ( x - 1.0, m ) / ( ga * gb * rm ); + + for ( k = 1; k <= m - 1; k++ ) + { + r0 = r0 * ( a + k - 1.0 ) * ( b + k - 1.0 ) + / ( k * ( k - m ) ) * ( 1.0 - x ); + f0 = f0 + r0; + } + + for ( k = 1; k <= m; k++ ) + { + sp0 = sp0 + 1.0 / ( a + k - 1.0 ) + 1.0 / ( b + k - 1.0 ) + - 1.0 / ( double ) ( k ); + } + + f1 = pa + pb + sp0 + 2.0 * el + std::log ( 1.0 - x ); + hw = f1; + + for ( k = 1; k <= 250; k++ ) + { + sp = sp + ( 1.0 - a ) / ( k * ( a + k - 1.0 ) ) + + ( 1.0 - b ) / ( k * ( b + k - 1.0 ) ); + + sm = 0.0; + for ( j = 1; j <= m; j++ ) + { + sm = sm + ( 1.0 - a ) + / ( ( j + k ) * ( a + j + k - 1.0 ) ) + + 1.0 / ( b + j + k - 1.0 ); + } + + rp = pa + pb + 2.0 * el + sp + sm + std::log ( 1.0 - x ); + + r1 = r1 * ( a + m + k - 1.0 ) * ( b + m + k - 1.0 ) + / ( k * ( m + k ) ) * ( 1.0 - x ); + + f1 = f1 + r1 * rp; + + if ( r8_abs ( f1 - hw ) < r8_abs ( f1 ) * eps ) + { + break; + } + hw = f1; + } + hf = f0 * c0 + f1 * c1; + } + else if ( m < 0 ) + { + m = - m; + c0 = gm * gc / ( ga * gb * std::pow ( 1.0 - x, m ) ); + c1 = - std::pow ( - 1.0, m ) * gc / ( gam * gbm * rm ); + + for ( k = 1; k <= m - 1; k++ ) + { + r0 = r0 * ( a - m + k - 1.0 ) * ( b - m + k - 1.0 ) + / ( k * ( k - m ) ) * ( 1.0 - x ); + f0 = f0 + r0; + } + + for ( k = 1; k <= m; k++ ) + { + sp0 = sp0 + 1.0 / ( double ) ( k ); + } + + f1 = pa + pb - sp0 + 2.0 * el + std::log ( 1.0 - x ); + hw = f1; + + for ( k = 1; k <= 250; k++ ) + { + sp = sp + ( 1.0 - a ) + / ( k * ( a + k - 1.0 ) ) + + ( 1.0 - b ) / ( k * ( b + k - 1.0 ) ); + + sm = 0.0; + for ( j = 1; j <= m; j++ ) + { + sm = sm + 1.0 / ( double ) ( j + k ); + } + + rp = pa + pb + 2.0 * el + sp - sm + std::log ( 1.0 - x ); + + r1 = r1 * ( a + k - 1.0 ) * ( b + k - 1.0 ) + / ( k * ( m + k ) ) * ( 1.0 - x ); + + f1 = f1 + r1 * rp; + + if ( webbur::r8_abs ( f1 - hw ) < webbur::r8_abs ( f1 ) * eps ) + { + break; + } + + hw = f1; + } + + hf = f0 * c0 + f1 * c1; + } + } + else + { + ga = webbur::r8_gamma ( a ); + gb = webbur::r8_gamma ( b ); + gc = webbur::r8_gamma ( c ); + gca = webbur::r8_gamma ( c - a ); + gcb = webbur::r8_gamma ( c - b ); + gcab = webbur::r8_gamma ( c - a - b ); + gabc = webbur::r8_gamma ( a + b - c ); + c0 = gc * gcab / ( gca * gcb ); + c1 = gc * gabc / ( ga * gb ) * std::pow ( 1.0 - x, c - a - b ); + hf = 0.0; + hw = hf; + r0 = c0; + r1 = c1; + + for ( k = 1; k <= 250; k++ ) + { + r0 = r0 * ( a + k - 1.0 ) * ( b + k - 1.0 ) + / ( k * ( a + b - c + k ) ) * ( 1.0 - x ); + + r1 = r1 * ( c - a + k - 1.0 ) * ( c - b + k - 1.0 ) + / ( k * ( c - a - b + k ) ) * ( 1.0 - x ); + + hf = hf + r0 + r1; + + if ( webbur::r8_abs ( hf - hw ) < webbur::r8_abs ( hf ) * eps ) + { + break; + } + hw = hf; + } + hf = hf + c0 + c1; + } + } + else + { + a0 = 1.0; + + if ( a < c && c < 2.0 * a && b < c && c < 2.0 * b ) + { + a0 = std::pow ( 1.0 - x, c - a - b ); + a = c - a; + b = c - b; + } + + hf = 1.0; + hw = hf; + r = 1.0; + + for ( k = 1; k <= 250; k++ ) + { + r = r * ( a + k - 1.0 ) * ( b + k - 1.0 ) + / ( k * ( c + k - 1.0 ) ) * x; + + hf = hf + r; + + if ( webbur::r8_abs ( hf - hw ) <= webbur::r8_abs ( hf ) * eps ) + { + break; + } + + hw = hf; + } + hf = a0 * hf; + } + + if ( x1 < 0.0 ) + { + x = x1; + c0 = 1.0 / std::pow ( 1.0 - x, aa ); + hf = c0 * hf; + } + + a = aa; + b = bb; + + if ( 120 < k ) + { + std::cerr << "\n"; + std::cerr << "R8_HYPER_2F1 - Warning!\n"; + std::cerr << " A large number of iterations were needed.\n"; + std::cerr << " The accuracy of the results should be checked.\n"; + } + + return hf; +} +//****************************************************************************80 + +double r8_max ( double x, double y ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_MAX returns the maximum of two R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 August 2004 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, double X, Y, the quantities to compare. +// +// Output, double R8_MAX, the maximum of X and Y. +// +{ + double value; + + if ( y < x ) + { + value = x; + } + else + { + value = y; + } + return value; +} +//****************************************************************************80 + +double r8_min ( double x, double y ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_MIN returns the minimum of two R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 31 August 2004 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, double X, Y, the quantities to compare. +// +// Output, double R8_MIN, the minimum of X and Y. +// +{ + double value; + + if ( y < x ) + { + value = y; + } + else + { + value = x; + } + return value; +} +//****************************************************************************80 + +double r8_mop ( int i ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_MOP returns the I-th power of -1 as an R8 value. +// +// Discussion: +// +// An R8 is an double value. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 16 November 2007 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int I, the power of -1. +// +// Output, double R8_MOP, the I-th power of -1. +// +{ + double value; + + if ( ( i % 2 ) == 0 ) + { + value = 1.0; + } + else + { + value = -1.0; + } + + return value; +} +//****************************************************************************80 + +double r8_psi ( double xx ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_PSI evaluates the function Psi(X). +// +// Discussion: +// +// This routine evaluates the logarithmic derivative of the +// Gamma function, +// +// PSI(X) = d/dX ( GAMMA(X) ) / GAMMA(X) +// = d/dX LN ( GAMMA(X) ) +// +// for real X, where either +// +// - XMAX1 < X < - XMIN, and X is not a negative integer, +// +// or +// +// XMIN < X. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 09 February 2008 +// +// Author: +// +// Original FORTRAN77 version by William Cody. +// C++ version by John Burkardt. +// +// Reference: +// +// William Cody, Anthony Strecok, Henry Thacher, +// Chebyshev Approximations for the Psi Function, +// Mathematics of Computation, +// Volume 27, Number 121, January 1973, pages 123-127. +// +// Parameters: +// +// Input, double XX, the argument of the function. +// +// Output, double R8_PSI, the value of the function. +// +{ + double aug; + double den; + int i; + int n; + int nq; + double one = 1.0; + double p1[9] = { + 4.5104681245762934160E-03, + 5.4932855833000385356, + 3.7646693175929276856E+02, + 7.9525490849151998065E+03, + 7.1451595818951933210E+04, + 3.0655976301987365674E+05, + 6.3606997788964458797E+05, + 5.8041312783537569993E+05, + 1.6585695029761022321E+05 }; + double p2[7] = { + -2.7103228277757834192, + -1.5166271776896121383E+01, + -1.9784554148719218667E+01, + -8.8100958828312219821, + -1.4479614616899842986, + -7.3689600332394549911E-02, + -6.5135387732718171306E-21 }; + double piov4 = 0.78539816339744830962; + double q1[8] = { + 9.6141654774222358525E+01, + 2.6287715790581193330E+03, + 2.9862497022250277920E+04, + 1.6206566091533671639E+05, + 4.3487880712768329037E+05, + 5.4256384537269993733E+05, + 2.4242185002017985252E+05, + 6.4155223783576225996E-08 }; + double q2[6] = { + 4.4992760373789365846E+01, + 2.0240955312679931159E+02, + 2.4736979003315290057E+02, + 1.0742543875702278326E+02, + 1.7463965060678569906E+01, + 8.8427520398873480342E-01 }; + double sgn; + double three = 3.0; + double upper; + double value; + double w; + double x; + double x01 = 187.0; + double x01d = 128.0; + double x02 = 6.9464496836234126266E-04; + double xinf = 1.70E+38; + double xlarge = 2.04E+15; + double xmax1 = 3.60E+16; + double xmin1 = 5.89E-39; + double xsmall = 2.05E-09; + double z; + + x = xx; + w = webbur::r8_abs ( x ); + aug = 0.0; +// +// Check for valid arguments, then branch to appropriate algorithm. +// + if ( xmax1 <= - x || w < xmin1 ) + { + if ( 0.0 < x ) + { + value = - xinf; + } + else + { + value = xinf; + } + return value; + } + + if ( x < 0.5 ) + { +// +// X < 0.5, use reflection formula: psi(1-x) = psi(x) + pi * cot(pi*x) +// Use 1/X for PI*COTAN(PI*X) when XMIN1 < |X| <= XSMALL. +// + if ( w <= xsmall ) + { + aug = - one / x; + } +// +// Argument reduction for cotangent. +// + else + { + if ( x < 0.0 ) + { + sgn = piov4; + } + else + { + sgn = - piov4; + } + + w = w - ( double ) ( ( int ) ( w ) ); + nq = ( int ) ( w * 4.0 ); + w = 4.0 * ( w - ( double ) ( nq ) * 0.25 ); +// +// W is now related to the fractional part of 4.0 * X. +// Adjust argument to correspond to values in the first +// quadrant and determine the sign. +// + n = nq / 2; + + if ( n + n != nq ) + { + w = one - w; + } + + z = piov4 * w; + + if ( ( n % 2 ) != 0 ) + { + sgn = - sgn; + } +// +// Determine the final value for -pi * cotan(pi*x). +// + n = ( nq + 1 ) / 2; + if ( ( n % 2 ) == 0 ) + { +// +// Check for singularity. +// + if ( z == 0.0 ) + { + if ( 0.0 < x ) + { + value = -xinf; + } + else + { + value = xinf; + } + return value; + } + aug = sgn * ( 4.0 / std::tan ( z ) ); + } + else + { + aug = sgn * ( 4.0 * std::tan ( z ) ); + } + } + x = one - x; + } +// +// 0.5 <= X <= 3.0. +// + if ( x <= three ) + { + den = x; + upper = p1[0] * x; + for ( i = 1; i <= 7; i++ ) + { + den = ( den + q1[i-1] ) * x; + upper = ( upper + p1[i]) * x; + } + den = ( upper + p1[8] ) / ( den + q1[7] ); + x = ( x - x01 / x01d ) - x02; + value = den * x + aug; + return value; + } +// +// 3.0 < X. +// + if ( x < xlarge ) + { + w = one / ( x * x ); + den = w; + upper = p2[0] * w; + for ( i = 1; i <= 5; i++ ) + { + den = ( den + q2[i-1] ) * w; + upper = ( upper + p2[i] ) * w; + } + aug = ( upper + p2[6] ) / ( den + q2[5] ) - 0.5 / x + aug; + } + + value = aug + std::log ( x ); + + return value; +} +//****************************************************************************80 + +double r8_sign ( double x ) + +//****************************************************************************80 +// +// Purpose: +// +// R8_SIGN returns the sign of an R8. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 October 2004 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, double X, the number whose sign is desired. +// +// Output, double R8_SIGN, the sign of X. +// +{ + double value; + + if ( x < 0.0 ) + { + value = -1.0; + } + else + { + value = 1.0; + } + return value; +} +//****************************************************************************80 + +int r8col_compare ( int m, int n, double a[], int i, int j ) + +//****************************************************************************80 +// +// Purpose: +// +// R8COL_COMPARE compares two columns in an R8COL. +// +// Discussion: +// +// An R8COL is an M by N array of R8's, regarded as an array of N columns, +// each of length M. +// +// Example: +// +// Input: +// +// M = 3, N = 4, I = 2, J = 4 +// +// A = ( +// 1. 2. 3. 4. +// 5. 6. 7. 8. +// 9. 10. 11. 12. ) +// +// Output: +// +// R8COL_COMPARE = -1 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 13 September 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns. +// +// Input, double A[M*N], the M by N array. +// +// Input, int I, J, the columns to be compared. +// I and J must be between 1 and N. +// +// Output, int R8COL_COMPARE, the results of the comparison: +// -1, column I < column J, +// 0, column I = column J, +// +1, column J < column I. +// +{ + int k; + int value; +// +// Check. +// + if ( i < 1 || n < i ) + { + std::cerr << "\n"; + std::cerr << "R8COL_COMPARE - Fatal error!\n"; + std::cerr << " Column index I is out of bounds.\n"; + std::cerr << " I = " << i << "\n"; + std::exit ( 1 ); + } + + if ( j < 1 || n < j ) + { + std::cerr << "\n"; + std::cerr << "R8COL_COMPARE - Fatal error!\n"; + std::cerr << " Column index J is out of bounds.\n"; + std::cerr << " J = " << j << "\n"; + std::exit ( 1 ); + } + + value = 0; + + if ( i == j ) + { + return value; + } + + k = 0; + + while ( k < m ) + { + if ( a[k+(i-1)*m] < a[k+(j-1)*m] ) + { + value = -1; + return value; + } + else if ( a[k+(j-1)*m] < a[k+(i-1)*m] ) + { + value = +1; + return value; + } + k = k + 1; + } + + return value; +} +//****************************************************************************80 + +void r8col_sort_heap_a ( int m, int n, double a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8COL_SORT_HEAP_A ascending heapsorts an R8COL. +// +// Discussion: +// +// An R8COL is an M by N array of R8's, regarded as an array of N columns, +// each of length M. +// +// In lexicographic order, the statement "X < Y", applied to two real +// vectors X and Y of length M, means that there is some index I, with +// 1 <= I <= M, with the property that +// +// X(J) = Y(J) for J < I, +// and +// X(I) < Y(I). +// +// In other words, the first time they differ, X is smaller. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 15 September 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns. +// +// Input/output, double A[M*N]. +// On input, the array of N columns of M-vectors. +// On output, the columns of A have been sorted in lexicographic order. +// +{ + int i; + int indx; + int isgn; + int j; + + if ( m <= 0 ) + { + return; + } + + if ( n <= 1 ) + { + return; + } +// +// Initialize. +// + i = 0; + indx = 0; + isgn = 0; + j = 0; +// +// Call the external heap sorter. +// + for ( ; ; ) + { + webbur::sort_heap_external ( n, &indx, &i, &j, isgn ); +// +// Interchange the I and J objects. +// + if ( 0 < indx ) + { + webbur::r8col_swap ( m, n, a, i, j ); + } +// +// Compare the I and J objects. +// + else if ( indx < 0 ) + { + isgn = webbur::r8col_compare ( m, n, a, i, j ); + } + else if ( indx == 0 ) + { + break; + } + } + + return; +} +//****************************************************************************80 + +int *r8col_sort_heap_index_a ( int m, int n, double a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8COL_SORT_HEAP_INDEX_A does an indexed heap ascending sort of an R8COL. +// +// Discussion: +// +// An R8COL is an M by N array of R8's, regarded as an array of N columns, +// each of length M. +// +// The sorting is not actually carried out. Rather an index array is +// created which defines the sorting. This array may be used to sort +// or index the array, or to sort or index related arrays keyed on the +// original array. +// +// A(*,J1) < A(*,J2) if the first nonzero entry of A(*,J1)-A(*,J2) +// is negative. +// +// Once the index array is computed, the sorting can be carried out +// "implicitly: +// +// A(*,INDX(*)) is sorted, +// +// Note that the index vector is 0-based. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 01 November 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the number of rows in each column of A. +// +// Input, int N, the number of columns in A. +// +// Input, double A[M*N], the array. +// +// Output, int R8COL_SORT_HEAP_INDEX_A[N], contains the sort index. The +// I-th column of the sorted array is A(*,INDX(I)). +// +{ + double *column; + int i; + int *indx; + int indxt; + int ir; + int isgn; + int j; + int k; + int l; + + if ( n < 1 ) + { + return NULL; + } + + indx = new int[n]; + + for ( i = 0; i < n; i++ ) + { + indx[i] = i; + } + + if ( n == 1 ) + { + return indx; + } + + column = new double[m]; + + l = n / 2 + 1; + ir = n; + + for ( ; ; ) + { + if ( 1 < l ) + { + l = l - 1; + indxt = indx[l-1]; + for ( k = 0; k < m; k++ ) + { + column[k] = a[k+indxt*m]; + } + } + else + { + indxt = indx[ir-1]; + for ( k = 0; k < m; k++ ) + { + column[k] = a[k+indxt*m]; + } + indx[ir-1] = indx[0]; + ir = ir - 1; + + if ( ir == 1 ) + { + indx[0] = indxt; + break; + } + } + + i = l; + j = l + l; + + while ( j <= ir ) + { + if ( j < ir ) + { + isgn = webbur::r8vec_compare ( m, a+indx[j-1]*m, a+indx[j]*m ); + + if ( isgn < 0 ) + { + j = j + 1; + } + } + + isgn = webbur::r8vec_compare ( m, column, a+indx[j-1]*m ); + + if ( isgn < 0 ) + { + indx[i-1] = indx[j-1]; + i = j; + j = j + j; + } + else + { + j = ir + 1; + } + } + indx[i-1] = indxt; + } + delete [] column; + + return indx; +} +//****************************************************************************80 + +int r8col_sorted_unique_count ( int m, int n, double a[], double tol ) + +//****************************************************************************80 +// +// Purpose: +// +// R8COL_SORTED_UNIQUE_COUNT counts unique elements in a sorted R8COL. +// +// Discussion: +// +// An R8COL is an M by N array of R8's, regarded as an array of N columns, +// each of length M. +// +// The columns of the array may be ascending or descending sorted. +// +// If the tolerance is large enough, then the concept of uniqueness +// can become ambiguous. If we have a tolerance of 1.5, then in the +// list ( 1, 2, 3, 4, 5, 6, 7, 8, 9 ) is it fair to say we have only +// one unique entry? That would be because 1 may be regarded as unique, +// and then 2 is too close to 1 to be unique, and 3 is too close to 2 to +// be unique and so on. +// +// This seems wrongheaded. So I prefer the idea that an item is not +// unique under a tolerance only if it is close to something that IS unique. +// Thus, the unique items are guaranteed to cover the space if we include +// a disk of radius TOL around each one. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 01 November 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns. +// +// Input, double A[M*N], a sorted array, containing +// N columns of data. +// +// Input, double TOL, a tolerance for equality. +// +// Output, int R8COL_SORTED_UNIQUE_COUNT, the number of unique columns. +// +{ + double diff; + int i; + int j1; + int j2; + int unique_num; + + unique_num = 0; + + if ( n <= 0 ) + { + return unique_num; + } + + unique_num = 1; + j1 = 0; + + for ( j2 = 1; j2 < n; j2++ ) + { + diff = 0.0; + for ( i = 0; i < m; i++ ) + { + diff = webbur::r8_max ( diff, webbur::r8_abs ( a[i+j1*m] - a[i+j2*m] ) ); + } + if ( tol < diff ) + { + unique_num = unique_num + 1; + j1 = j2; + } + } + + return unique_num; +} +//****************************************************************************80 + +void r8col_swap ( int m, int n, double a[], int j1, int j2 ) + +//****************************************************************************80 +// +// Purpose: +// +// R8COL_SWAP swaps columns J1 and J2 of an R8COL. +// +// Discussion: +// +// An R8COL is an M by N array of R8's, regarded as an array of N columns, +// each of length M. +// +// Example: +// +// Input: +// +// M = 3, N = 4, J1 = 2, J2 = 4 +// +// A = ( +// 1. 2. 3. 4. +// 5. 6. 7. 8. +// 9. 10. 11. 12. ) +// +// Output: +// +// A = ( +// 1. 4. 3. 2. +// 5. 8. 7. 6. +// 9. 12. 11. 10. ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 October 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns. +// +// Input/output, double A[M*N], the M by N array. +// +// Input, int J1, J2, the columns to be swapped. +// These columns are 1-based. +// +{ + int i; + double temp; + + if ( j1 < 1 || n < j1 || j2 < 1 || n < j2 ) + { + std::cerr << "\n"; + std::cerr << "R8COL_SWAP - Fatal error!\n"; + std::cerr << " J1 or J2 is out of bounds.\n"; + std::cerr << " J1 = " << j1 << "\n"; + std::cerr << " J2 = " << j2 << "\n"; + std::cerr << " NCOL = " << n << "\n"; + std::exit ( 1 ); + } + + if ( j1 == j2 ) + { + return; + } + + for ( i = 0; i < m; i++ ) + { + temp = a[i+(j1-1)*m]; + a[i+(j1-1)*m] = a[i+(j2-1)*m]; + a[i+(j2-1)*m] = temp; + } + + return; +} +//****************************************************************************80 + +void r8col_tol_undex ( int m, int n, double a[], int unique_num, double tol, + int undx[], int xdnu[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8COL_TOL_UNDEX indexes tolerably unique entries of an R8COL. +// +// Discussion: +// +// An R8COL is an M by N array of R8's, regarded as an array of N columns, +// each of length M. +// +// The goal of this routine is to determine a vector UNDX, +// which points to the unique elements of A, in sorted order, +// and a vector XDNU, which identifies, for each entry of A, the index of +// the unique sorted element of A. +// +// This is all done with index vectors, so that the elements of +// A are never moved. +// +// The first step of the algorithm requires the indexed sorting +// of A, which creates arrays INDX and XDNI. (If all the entries +// of A are unique, then these arrays are the same as UNDX and XDNU.) +// +// We then use INDX to examine the entries of A in sorted order, +// noting the unique entries, creating the entries of XDNU and +// UNDX as we go. +// +// Once this process has been completed, the vector A could be +// replaced by a compressed vector XU, containing the unique entries +// of A in sorted order, using the formula +// +// XU(*) = A(UNDX(*)). +// +// We could then, if we wished, reconstruct the entire vector A, or +// any element of it, by index, as follows: +// +// A(I) = XU(XDNU(I)). +// +// We could then replace A by the combination of XU and XDNU. +// +// Later, when we need the I-th entry of A, we can locate it as +// the XDNU(I)-th entry of XU. +// +// Here is an example of a vector A, the sort and inverse sort +// index vectors, and the unique sort and inverse unique sort vectors +// and the compressed unique sorted vector. +// +// I A Indx Xdni XU Undx Xdnu +// ----+-----+-----+-----+--------+-----+-----+ +// 0 | 11. 0 0 | 11. 0 0 +// 1 | 22. 2 4 | 22. 1 1 +// 2 | 11. 5 1 | 33. 3 0 +// 3 | 33. 8 7 | 55. 4 2 +// 4 | 55. 1 8 | 3 +// 5 | 11. 6 2 | 0 +// 6 | 22. 7 5 | 1 +// 7 | 22. 3 6 | 1 +// 8 | 11. 4 3 | 0 +// +// INDX(2) = 3 means that sorted item(2) is A(3). +// XDNI(2) = 5 means that A(2) is sorted item(5). +// +// UNDX(3) = 4 means that unique sorted item(3) is at A(4). +// XDNU(8) = 2 means that A(8) is at unique sorted item(2). +// +// XU(XDNU(I))) = X(I). +// XU(I) = X(UNDX(I)). +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 July 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, the dimension of the data values. +// +// Input, int N, the number of data values, +// +// Input, double A[M*N], the data values. +// +// Input, int UNIQUE_NUM, the number of unique values in A. +// This value is only required for languages in which the size of +// UNDX must be known in advance. +// +// Input, double TOL, a tolerance for equality. +// +// Output, int UNDX[UNIQUE_NUM], the UNDX vector. +// +// Output, int XDNU[N], the XDNU vector. +// +{ + double diff; + int i; + int i2; + int *indx; + int j; + int k; + bool unique; +// +// Implicitly sort the array. +// + indx = webbur::r8col_sort_heap_index_a ( m, n, a ); +// +// Consider entry I = 0. +// It is unique, so set the number of unique items to K. +// Set the K-th unique item to I. +// Set the representative of item I to the K-th unique item. +// + i = 0; + k = 0; + undx[k] = indx[i]; + xdnu[indx[i]] = k; +// +// Consider entry I. +// +// If it is unique, increase the unique count K, set the +// K-th unique item to I, and set the representative of I to K. +// +// If it is not unique, set the representative of item I to a +// previously determined unique item that is close to it. +// + for ( i = 1; i < n; i++ ) + { + unique = true; + for ( j = 0; j <= k; j++ ) + { + diff = 0.0; + for ( i2 = 0; i2 < m; i2++ ) + { + diff = webbur::r8_max ( diff, + webbur::r8_abs ( a[i2+indx[i]*m] - a[i2+undx[j]*m] ) ); + } + if ( diff <= tol ) + { + unique = false; + xdnu[indx[i]] = j; + break; + } + } + if ( unique ) + { + k = k + 1; + undx[k] = indx[i]; + xdnu[indx[i]] = k; + } + } + delete [] indx; + + return; +} +//****************************************************************************80 + +int r8col_tol_unique_count ( int m, int n, double a[], double tol ) + +//****************************************************************************80 +// +// Purpose: +// +// R8COL_TOL_UNIQUE_COUNT counts tolerably unique entries in an R8COL. +// +// Discussion: +// +// An R8COL is an M by N array of R8's, regarded as an array of N columns, +// each of length M. +// +// The columns of the array may be ascending or descending sorted. +// +// If the tolerance is large enough, then the concept of uniqueness +// can become ambiguous. If we have a tolerance of 1.5, then in the +// list ( 1, 2, 3, 4, 5, 6, 7, 8, 9 ) is it fair to say we have only +// one unique entry? That would be because 1 may be regarded as unique, +// and then 2 is too close to 1 to be unique, and 3 is too close to 2 to +// be unique and so on. +// +// This seems wrongheaded. So I prefer the idea that an item is not +// unique under a tolerance only if it is close to something that IS unique. +// Thus, the unique items are guaranteed to cover the space if we include +// a disk of radius TOL around each one. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 July 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns. +// +// Input, double A[M*N], the array of N columns of data. +// +// Input, double TOL, a tolerance for equality. +// +// Output, int R8COL_TOL_UNIQUE_COUNT, the number of unique columns. +// +{ + double diff; + int i; + int i2; + int *indx; + int j; + int k; + bool unique; + int *undx; + + undx = new int[n]; +// +// Implicitly sort the array. +// + indx = webbur::r8col_sort_heap_index_a ( m, n, a ); +// +// Consider entry I = 0. +// It is unique, so set the number of unique items to K. +// Set the K-th unique item to I. +// Set the representative of item I to the K-th unique item. +// + i = 0; + k = 0; + undx[k] = indx[i]; +// +// Consider entry I. +// +// If it is unique, increase the unique count K, set the +// K-th unique item to I, and set the representative of I to K. +// +// If it is not unique, set the representative of item I to a +// previously determined unique item that is close to it. +// + for ( i = 1; i < n; i++ ) + { + unique = true; + for ( j = 0; j <= k; j++ ) + { + diff = 0.0; + for ( i2 = 0; i2 < m; i2++ ) + { + diff = webbur::r8_max ( diff, + webbur::r8_abs ( a[i2+indx[i]*m] - a[i2+undx[j]*m] ) ); + } + if ( diff <= tol ) + { + unique = false; + break; + } + } + if ( unique ) + { + k = k + 1; + undx[k] = indx[i]; + } + } + delete [] indx; + delete [] undx; + + k = k + 1; + + return k; +} +//****************************************************************************80 + +void r8col_undex ( int x_dim, int x_num, double x_val[], int x_unique_num, + double tol, int undx[], int xdnu[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8COL_UNDEX returns unique sorted indexes for an R8COL. +// +// Discussion: +// +// An R8COL is an M by N array of R8's, regarded as an array of N columns, +// each of length M. +// +// The goal of this routine is to determine a vector UNDX, +// which points to the unique elements of X, in sorted order, +// and a vector XDNU, which identifies, for each entry of X, the index of +// the unique sorted element of X. +// +// This is all done with index vectors, so that the elements of +// X are never moved. +// +// The first step of the algorithm requires the indexed sorting +// of X, which creates arrays INDX and XDNI. (If all the entries +// of X are unique, then these arrays are the same as UNDX and XDNU.) +// +// We then use INDX to examine the entries of X in sorted order, +// noting the unique entries, creating the entries of XDNU and +// UNDX as we go. +// +// Once this process has been completed, the vector X could be +// replaced by a compressed vector XU, containing the unique entries +// of X in sorted order, using the formula +// +// XU(*) = X(UNDX(*)). +// +// We could then, if we wished, reconstruct the entire vector X, or +// any element of it, by index, as follows: +// +// X(I) = XU(XDNU(I)). +// +// We could then replace X by the combination of XU and XDNU. +// +// Later, when we need the I-th entry of X, we can locate it as +// the XDNU(I)-th entry of XU. +// +// Here is an example of a vector X, the sort and inverse sort +// index vectors, and the unique sort and inverse unique sort vectors +// and the compressed unique sorted vector. +// +// I X Indx Xdni XU Undx Xdnu +// ----+-----+-----+-----+--------+-----+-----+ +// 0 | 11. 0 0 | 11. 0 0 +// 1 | 22. 2 4 | 22. 1 1 +// 2 | 11. 5 1 | 33. 3 0 +// 3 | 33. 8 7 | 55. 4 2 +// 4 | 55. 1 8 | 3 +// 5 | 11. 6 2 | 0 +// 6 | 22. 7 5 | 1 +// 7 | 22. 3 6 | 1 +// 8 | 11. 4 3 | 0 +// +// INDX(2) = 3 means that sorted item(2) is X(3). +// XDNI(2) = 5 means that X(2) is sorted item(5). +// +// UNDX(3) = 4 means that unique sorted item(3) is at X(4). +// XDNU(8) = 2 means that X(8) is at unique sorted item(2). +// +// XU(XDNU(I))) = X(I). +// XU(I) = X(UNDX(I)). +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 02 November 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int X_DIM, the dimension of the data values. +// (the number of rows in the R8COL). +// +// Input, int X_NUM, the number of data values, +// (the number of columns in the R8COL). +// +// Input, double X_VAL[X_DIM*X_NUM], the data values. +// +// Input, int X_UNIQUE_NUM, the number of unique values in X_VAL. +// This value is only required for languages in which the size of +// UNDX must be known in advance. +// +// Input, double TOL, a tolerance for equality. +// +// Output, int UNDX[X_UNIQUE_NUM], the UNDX vector. +// +// Output, int XDNU[X_NUM], the XDNU vector. +// +{ + double diff; + int i; + int *indx; + int j; + int k; +// +// Implicitly sort the array. +// + indx = webbur::r8col_sort_heap_index_a ( x_dim, x_num, x_val ); +// +// Walk through the implicitly sorted array X. +// + i = 0; + + j = 0; + undx[j] = indx[i]; + + xdnu[indx[i]] = j; + + for ( i = 1; i < x_num; i++ ) + { + diff = 0.0; + for ( k = 0; k < x_dim; k++ ) + { + diff = r8_max ( diff, + webbur::r8_abs ( x_val[k+indx[i]*x_dim] - x_val[k+undx[j]*x_dim] ) ); + } + if ( tol < diff ) + { + j = j + 1; + undx[j] = indx[i]; + } + xdnu[indx[i]] = j; + } + delete [] indx; + + return; +} +//****************************************************************************80 + +void r8col_unique_index ( int m, int n, double a[], double tol, + int unique_index[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8COL_UNIQUE_INDEX indexes the first occurrence of values in an R8COL. +// +// Discussion: +// +// An R8COL is an M by N array of R8 values. +// It is regarded as an array of N columns of length M. +// +// For element A(1:M,J) of the matrix, UNIQUE_INDEX(J) is the uniqueness +// index of A(1:M,J). That is, if A_UNIQUE contains the unique elements +// of A, gathered in order, then +// +// A_UNIQUE ( 1:M, UNIQUE_INDEX(J) ) = A(1:M,J) +// +// The user must preallocate space for the output array UNIQUE_INDEX. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 24 November 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns of A. +// The length of an "element" of A, and the number of "elements". +// +// Input, double A[M*N], the array. +// +// Input, double TOL, a tolerance for equality. +// +// Output, int UNIQUE_INDEX[N], the unique index. +// +{ + double diff; + int i; + int j1; + int j2; + int unique_num; + + for ( j1 = 0; j1 < n; j1++ ) + { + unique_index[j1] = -1; + } + unique_num = 0; + + for ( j1 = 0; j1 < n; j1++ ) + { + if ( unique_index[j1] == -1 ) + { + unique_index[j1] = unique_num; + + for ( j2 = j1 + 1; j2 < n; j2++ ) + { + diff = 0.0; + for ( i = 0; i < m; i++ ) + { + diff = webbur::r8_max ( diff, + webbur::r8_abs ( a[i+j1*m] - a[i+j2*m] ) ); + } + if ( diff <= tol ) + { + unique_index[j2] = unique_num; + } + } + unique_num = unique_num + 1; + } + } + return; +} +//****************************************************************************80 + +void r8mat_transpose_print ( int m, int n, double a[], std::string title ) + +//****************************************************************************80 +// +// Purpose: +// +// R8MAT_TRANSPOSE_PRINT prints an R8MAT, transposed. +// +// Discussion: +// +// An R8MAT is a doubly dimensioned array of R8 values, stored as a vector +// in column-major order. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 10 September 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns. +// +// Input, double A[M*N], an M by N matrix to be printed. +// +// Input, string TITLE, a title. +// +{ + r8mat_transpose_print_some ( m, n, a, 1, 1, m, n, title ); + + return; +} +//****************************************************************************80 + +void r8mat_transpose_print_some ( int m, int n, double a[], int ilo, int jlo, + int ihi, int jhi, std::string title ) + +//****************************************************************************80 +// +// Purpose: +// +// R8MAT_TRANSPOSE_PRINT_SOME prints some of an R8MAT, transposed. +// +// Discussion: +// +// An R8MAT is a doubly dimensioned array of R8 values, stored as a vector +// in column-major order. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 10 September 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int M, N, the number of rows and columns. +// +// Input, double A[M*N], an M by N matrix to be printed. +// +// Input, int ILO, JLO, the first row and column to print. +// +// Input, int IHI, JHI, the last row and column to print. +// +// Input, string TITLE, a title. +// +{ +# define INCX 5 + + int i; + int i2; + int i2hi; + int i2lo; + int inc; + int j; + int j2hi; + int j2lo; + + std::cout << "\n"; + std::cout << title << "\n"; + + for ( i2lo = i4_max ( ilo, 1 ); i2lo <= i4_min ( ihi, m ); i2lo = i2lo + INCX ) + { + i2hi = i2lo + INCX - 1; + i2hi = i4_min ( i2hi, m ); + i2hi = i4_min ( i2hi, ihi ); + + inc = i2hi + 1 - i2lo; + + std::cout << "\n"; + std::cout << " Row: "; + for ( i = i2lo; i <= i2hi; i++ ) + { + std::cout << std::setw(7) << i - 1 << " "; + } + std::cout << "\n"; + std::cout << " Col\n"; + std::cout << "\n"; + + j2lo = i4_max ( jlo, 1 ); + j2hi = i4_min ( jhi, n ); + + for ( j = j2lo; j <= j2hi; j++ ) + { + std::cout << std::setw(5) << j - 1 << ":"; + for ( i2 = 1; i2 <= inc; i2++ ) + { + i = i2lo - 1 + i2; + std::cout << std::setw(14) << a[(i-1)+(j-1)*m]; + } + std::cout << "\n"; + } + } + + return; +# undef INCX +} +//****************************************************************************80 + +void r8mat_write ( std::string output_filename, int m, int n, double table[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8MAT_WRITE writes an R8MAT file. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 11 August 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, string OUTPUT_FILENAME, the output filename. +// +// Input, int M, the spatial dimension. +// +// Input, int N, the number of points. +// +// Input, double TABLE[M*N], the table data. +// +{ + int i; + int j; + std::ofstream output; +// +// Open the file. +// + output.open ( output_filename.c_str ( ) ); + + if ( !output ) + { + std::cerr << "\n"; + std::cerr << "R8MAT_WRITE - Fatal error!\n"; + std::cerr << " Could not open the output file.\n"; + return; + } +// +// Write the data. +// + for ( j = 0; j < n; j++ ) + { + for ( i = 0; i < m; i++ ) + { + output << " " << std::setw(24) << std::setprecision(16) << table[i+j*m]; + } + output << "\n"; + } +// +// Close the file. +// + output.close ( ); + + return; +} +//****************************************************************************80 + +double r8poly_ant_val ( int n, double poly_cof[], double xval ) + +//****************************************************************************80 +// +// Purpose: +// +// R8POLY_ANT_VAL evaluates the antiderivative of an R8POLY in standard form. +// +// Discussion: +// +// The constant term of the antiderivative is taken to be zero. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 June 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the order of the polynomial. +// +// Input, double POLY_COF[N], the polynomial coefficients. POLY_COF[0] +// is the constant term, and POLY_COF[N-1] is the coefficient of X**(N-1). +// +// Input, double XVAL, the point where the antiderivative is to be +// evaluated. +// +// Output, double R8POLY_ANT_VAL, the value of the antiderivative of the polynomial +// at XVAL. +// +{ + int i; + double value; + + value = 0.0; + + for ( i = n - 1; 0 <= i; i-- ) + { + value = ( value + poly_cof[i] / ( double ) ( i + 1 ) ) * xval; + } + + return value; +} +//****************************************************************************80 + +double *r8vec_chebyshev_new ( int n, double a_first, double a_last ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_CHEBYSHEV_NEW creates a vector of Chebyshev spaced values. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 08 June 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Input, double A_FIRST, A_LAST, the first and last entries. +// +// Output, double R8VEC_CHEBYSHEV_NEW[N], a vector of Chebyshev spaced data. +// +{ + double *a; + double c; + int i; + double pi = 3.141592653589793; + double theta; + + a = new double[n]; + + if ( n == 1 ) + { + a[0] = ( a_first + a_last ) / 2.0; + } + else + { + for ( i = 0; i < n; i++ ) + { + theta = ( double ) ( n - i - 1 ) * pi / ( double ) ( n - 1 ); + + c = std::cos ( theta ); + + if ( ( n % 2 ) == 1 ) + { + if ( 2 * i + 1 == n ) + { + c = 0.0; + } + } + + a[i] = ( ( 1.0 - c ) * a_first + + ( 1.0 + c ) * a_last ) + / 2.0; + } + } + return a; +} +//****************************************************************************80 + +int r8vec_compare ( int n, double a[], double b[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_COMPARE compares two R8VEC's. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// The lexicographic ordering is used. +// +// Example: +// +// Input: +// +// A1 = ( 2.0, 6.0, 2.0 ) +// A2 = ( 2.0, 8.0, 12.0 ) +// +// Output: +// +// ISGN = -1 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 23 September 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vectors. +// +// Input, double A[N], B[N], the vectors to be compared. +// +// Output, int R8VEC_COMPARE, the results of the comparison: +// -1, A is lexicographically less than B, +// 0, A is equal to B, +// +1, A is lexicographically greater than B. +// +{ + int isgn; + int k; + + isgn = 0; + + for ( k = 0; k < n; k++ ) + { + if ( a[k] < b[k] ) + { + isgn = -1; + return isgn; + } + else if ( b[k] < a[k] ) + { + isgn = +1; + return isgn; + } + } + return isgn; +} +//****************************************************************************80 + +void r8vec_copy ( int n, double a1[], double a2[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_COPY copies an R8VEC. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 03 July 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vectors. +// +// Input, double A1[N], the vector to be copied. +// +// Output, double A2[N], the copy of A1. +// +{ + int i; + + for ( i = 0; i < n; i++ ) + { + a2[i] = a1[i]; + } + return; +} +//****************************************************************************80 + +double *r8vec_copy_new ( int n, double a1[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_COPY_NEW copies an R8VEC to a "new" R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 03 July 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vectors. +// +// Input, double A1[N], the vector to be copied. +// +// Output, double R8VEC_COPY_NEW[N], the copy of A1. +// +{ + double *a2; + int i; + + a2 = new double[n]; + + for ( i = 0; i < n; i++ ) + { + a2[i] = a1[i]; + } + return a2; +} +//****************************************************************************80 + +double r8vec_diff_norm_li ( int n, double a[], double b[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_DIFF_NORM_LI returns the L-oo norm of the difference of R8VEC's. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// The vector L-oo norm is defined as: +// +// R8VEC_NORM_LI = max ( 1 <= I <= N ) abs ( A(I) ). +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 02 April 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in A. +// +// Input, double A[N], B[N], the vectors. +// +// Output, double R8VEC_DIFF_NORM_LI, the L-oo norm of A - B. +// +{ + int i; + double value; + + value = 0.0; + + for ( i = 0; i < n; i++ ) + { + value = webbur::r8_max ( value, webbur::r8_abs ( a[i] - b[i] ) ); + } + return value; +} +//****************************************************************************80 + +void r8vec_direct_product2 ( int factor_index, int factor_order, + double factor_value[], int factor_num, int point_num, double w[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_DIRECT_PRODUCT2 creates a direct product of R8VEC's. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// To explain what is going on here, suppose we had to construct +// a multidimensional quadrature rule as the product of K rules +// for 1D quadrature. +// +// The product rule will be represented as a list of points and weights. +// +// The J-th item in the product rule will be associated with +// item J1 of 1D rule 1, +// item J2 of 1D rule 2, +// ..., +// item JK of 1D rule K. +// +// In particular, +// X(J) = ( X(1,J1), X(2,J2), ..., X(K,JK)) +// and +// W(J) = W(1,J1) * W(2,J2) * ... * W(K,JK) +// +// So we can construct the quadrature rule if we can properly +// distribute the information in the 1D quadrature rules. +// +// This routine carries out that task for the weights W. +// +// Another way to do this would be to compute, one by one, the +// set of all possible indices (J1,J2,...,JK), and then index +// the appropriate information. An advantage of the method shown +// here is that you can process the K-th set of information and +// then discard it. +// +// Example: +// +// Rule 1: +// Order = 4 +// W(1:4) = ( 2, 3, 5, 7 ) +// +// Rule 2: +// Order = 3 +// W(1:3) = ( 11, 13, 17 ) +// +// Rule 3: +// Order = 2 +// W(1:2) = ( 19, 23 ) +// +// Product Rule: +// Order = 24 +// W(1:24) = +// ( 2 * 11 * 19 ) +// ( 3 * 11 * 19 ) +// ( 4 * 11 * 19 ) +// ( 7 * 11 * 19 ) +// ( 2 * 13 * 19 ) +// ( 3 * 13 * 19 ) +// ( 5 * 13 * 19 ) +// ( 7 * 13 * 19 ) +// ( 2 * 17 * 19 ) +// ( 3 * 17 * 19 ) +// ( 5 * 17 * 19 ) +// ( 7 * 17 * 19 ) +// ( 2 * 11 * 23 ) +// ( 3 * 11 * 23 ) +// ( 5 * 11 * 23 ) +// ( 7 * 11 * 23 ) +// ( 2 * 13 * 23 ) +// ( 3 * 13 * 23 ) +// ( 5 * 13 * 23 ) +// ( 7 * 13 * 23 ) +// ( 2 * 17 * 23 ) +// ( 3 * 17 * 23 ) +// ( 5 * 17 * 23 ) +// ( 7 * 17 * 23 ) +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 April 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int FACTOR_INDEX, the index of the factor being processed. +// The first factor processed must be factor 0. +// +// Input, int FACTOR_ORDER, the order of the factor. +// +// Input, double FACTOR_VALUE[FACTOR_ORDER], the factor values for +// factor FACTOR_INDEX. +// +// Input, int FACTOR_NUM, the number of factors. +// +// Input, int POINT_NUM, the number of elements in the direct product. +// +// Input/output, double W[POINT_NUM], the elements of the +// direct product, which are built up gradually. +// +// Local Parameters: +// +// Local, integer START, the first location of a block of values to set. +// +// Local, integer CONTIG, the number of consecutive values to set. +// +// Local, integer SKIP, the distance from the current value of START +// to the next location of a block of values to set. +// +// Local, integer REP, the number of blocks of values to set. +// +{ + static int contig = 0; + int i; + int j; + int k; + static int rep = 0; + static int skip = 0; + int start; + + if ( factor_index == 0 ) + { + contig = 1; + skip = 1; + rep = point_num; + for ( i = 0; i < point_num; i++ ) + { + w[i] = 1.0; + } + } + + rep = rep / factor_order; + skip = skip * factor_order; + + for ( j = 0; j < factor_order; j++ ) + { + start = 0 + j * contig; + + for ( k = 1; k <= rep; k++ ) + { + for ( i = start; i < start + contig; i++ ) + { + w[i] = w[i] * factor_value[j]; + } + start = start + skip; + } + } + + contig = contig * factor_order; + + return; +} +//****************************************************************************80 + +double r8vec_dot_product ( int n, double a1[], double a2[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_DOT_PRODUCT computes the dot product of a pair of R8VEC's. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 03 July 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vectors. +// +// Input, double A1[N], A2[N], the two vectors to be considered. +// +// Output, double R8VEC_DOT_PRODUCT, the dot product of the vectors. +// +{ + int i; + double value; + + value = 0.0; + for ( i = 0; i < n; i++ ) + { + value = value + a1[i] * a2[i]; + } + return value; +} +//****************************************************************************80 + +double r8vec_i4vec_dot_product ( int n, double r8vec[], int i4vec[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_I4VEC_DOT_PRODUCT computes the dot product of an R8VEC and an I4VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// An I4VEC is a vector of I4's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 30 June 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vectors. +// +// Input, double R8VEC[N], the first vector. +// +// Input, int I4VEC[N], the second vector. +// +// Output, double R8VEC_I4VEC_DOT_PRODUCT, the dot product of the vectors. +// +{ + int i; + double value; + + value = 0.0; + for ( i = 0; i < n; i++ ) + { + value = value + r8vec[i] * ( double ) ( i4vec[i] ); + } + return value; +} +//****************************************************************************80 + +void r8vec_index_sorted_range ( int n, double r[], int indx[], double r_lo, + double r_hi, int *i_lo, int *i_hi ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_INDEX_SORTED_RANGE: search index sorted vector for elements in a range. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 27 September 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of items in the vector. +// +// Input, double R[N], the index sorted vector. +// +// Input, int INDX[N], the vector used to sort R. +// The vector R[INDX[*]] is sorted. +// +// Input, double R_LO, R_HI, the limits of the range. +// +// Output, int *I_LO, *I_HI, the range of indices +// so that I_LO <= I <= I_HI => R_LO <= R[INDX[I]] <= R_HI. If no +// values in R lie in the range, then I_HI < I_LO will be returned. +// +{ + int i1; + int i2; + int j1; + int j2; +// +// Cases we can handle immediately. +// + if ( r[indx[n-1]] < r_lo ) + { + *i_lo = n; + *i_hi = n - 1; + return; + } + + if ( r_hi < r[indx[0]] ) + { + *i_lo = 0; + *i_hi = -1; + return; + } +// +// Are there are least two intervals? +// + if ( n == 1 ) + { + if ( r_lo <= r[indx[0]] && r[indx[0]] <= r_hi ) + { + *i_lo = 0; + *i_hi = 0; + } + else + { + *i_lo = -1; + *i_hi = -2; + } + return; + } +// +// Bracket R_LO. +// + if ( r_lo <= r[indx[0]] ) + { + *i_lo = 0; + } + else + { +// +// R_LO is in one of the intervals spanned by R(INDX(J1)) to R(INDX(J2)). +// Examine the intermediate interval [R(INDX(I1)), R(INDX(I1+1))]. +// Does R_LO lie here, or below or above? +// + j1 = 0; + j2 = n - 1; + i1 = ( j1 + j2 - 1 ) / 2; + i2 = i1 + 1; + + for ( ; ; ) + { + if ( r_lo < r[indx[i1]] ) + { + j2 = i1; + i1 = ( j1 + j2 - 1 ) / 2; + i2 = i1 + 1; + } + else if ( r[indx[i2]] < r_lo ) + { + j1 = i2; + i1 = ( j1 + j2 - 1 ) / 2; + i2 = i1 + 1; + } + else + { + *i_lo = i1; + break; + } + } + } +// +// Bracket R_HI. +// + if ( r[indx[n-1]] <= r_hi ) + { + *i_hi = n - 1; + } + else + { + j1 = *i_lo; + j2 = n - 1; + i1 = ( j1 + j2 - 1 ) / 2; + i2 = i1 + 1; + + for ( ; ; ) + { + if ( r_hi < r[indx[i1]] ) + { + j2 = i1; + i1 = ( j1 + j2 - 1 ) / 2; + i2 = i1 + 1; + } + else if ( r[indx[i2]] < r_hi ) + { + j1 = i2; + i1 = ( j1 + j2 - 1 ) / 2; + i2 = i1 + 1; + } + else + { + *i_hi = i2; + break; + } + } + } +// +// We expect to have computed the largest I_LO and smallest I_HI such that +// R(INDX(I_LO)) <= R_LO <= R_HI <= R(INDX(I_HI)) +// but what we want is actually +// R_LO <= R(INDX(I_LO)) <= R(INDX(I_HI)) <= R_HI +// which we can usually get simply by incrementing I_LO and decrementing I_HI. +// + if ( r[indx[*i_lo]] < r_lo ) + { + *i_lo = *i_lo + 1; + if ( n - 1 < *i_lo ) + { + *i_hi = *i_lo - 1; + } + } + + if ( r_hi < r[indx[*i_hi]] ) + { + *i_hi = *i_hi - 1; + if ( *i_hi < 0 ) + { + *i_lo = *i_hi + 1; + } + } + + return; +} +//****************************************************************************80 + +void r8vec_indexed_heap_d ( int n, double a[], int indx[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_INDEXED_HEAP_D creates a descending heap from an indexed R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// An indexed R8VEC is an R8VEC of data values, and an R8VEC of N indices, +// each referencing an entry of the data vector. +// +// The function adjusts the index vector INDX so that, for 1 <= J <= N/2, +// we have: +// A[INDX[2*J+1]] <= A[INDX[J]] +// and +// A[INDX[2*J+2]] <= A[INDX[J]] +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 August 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Albert Nijenhuis, Herbert Wilf, +// Combinatorial Algorithms for Computers and Calculators, +// Academic Press, 1978, +// ISBN: 0-12-519260-6, +// LC: QA164.N54. +// +// Parameters: +// +// Input, int N, the size of the index array. +// +// Input, double A[*], the data vector. +// +// Input/output, int INDX[N], the index array. +// Each entry of INDX must be a valid index for the array A. +// On output, the indices have been reordered into a descending heap. +// +{ + int i; + int ifree; + int key; + int m; +// +// Only nodes N/2 - 1 down to 0 can be "parent" nodes. +// + for ( i = ( n / 2 ) - 1; 0 <= i; i-- ) + { +// +// Copy the value out of the parent node. +// Position IFREE is now "open". +// + key = indx[i]; + ifree = i; + + for ( ; ; ) + { +// +// Positions 2*IFREE+1 and 2*IFREE+2 are the descendants of position +// IFREE. (One or both may not exist because they exceed N-1.) +// + m = 2 * ifree + 1; +// +// Does the first position exist? +// + if ( n - 1 < m ) + { + break; + } +// +// Does the second position exist? +// + if ( m + 1 <= n - 1 ) + { +// +// If both positions exist, take the larger of the two values, +// and update M if necessary. +// + if ( a[indx[m]] < a[indx[m+1]] ) + { + m = m + 1; + } + } +// +// If the large descendant is larger than KEY, move it up, +// and update IFREE, the location of the free position, and +// consider the descendants of THIS position. +// + if ( a[indx[m]] <= a[key] ) + { + break; + } + + indx[ifree] = indx[m]; + ifree = m; + } +// +// Once there is no more shifting to do, KEY moves into the free spot IFREE. +// + indx[ifree] = key; + } + + return; +} +//****************************************************************************80 + +int r8vec_indexed_heap_d_extract ( int *n, double a[], int indx[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_INDEXED_HEAP_D_EXTRACT: extract from heap descending indexed R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// An indexed R8VEC is an R8VEC of data values, and an R8VEC of N indices, +// each referencing an entry of the data vector. +// +// The routine finds the maximum value in the heap, returns that value to the +// user, deletes that value from the heap, and restores the heap to its +// proper form. +// +// Note that the argument N must be a variable, which will be decremented +// before return, and that INDX will hold one less value on output than it +// held on input. +// +// This is one of three functions needed to model a priority queue. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 August 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Thomas Cormen, Charles Leiserson, Ronald Rivest, +// Introduction to Algorithms, +// MIT Press, 2001, +// ISBN: 0262032937, +// LC: QA76.C662. +// +// Parameters: +// +// Input/output, int *N, the number of items in the index vector. +// +// Input, double A[*], the data vector. +// +// Input/output, int INDX[N], the index vector. +// +// Output, int R8VEC_INDEXED_HEAP_D_EXTRACT, the index in A of the item of +// maximum value, which has now been removed from the heap. +// +{ + int indx_extract; + + if ( *n < 1 ) + { + std::cerr << "\n"; + std::cerr << "R8VEC_INDEXED_HEAP_D_EXTRACT - Fatal error!\n"; + std::cerr << " The heap is empty.\n"; + std::exit ( 1 ); + } +// +// Get the index of the maximum value. +// + indx_extract = indx[0]; + + if ( *n == 1 ) + { + *n = 0; + return indx_extract; + } +// +// Shift the last index down. +// + indx[0] = indx[*n-1]; +// +// Restore the heap structure. +// + *n = *n - 1; + webbur::r8vec_indexed_heap_d ( *n, a, indx ); + + return indx_extract; +} +//****************************************************************************80 + +void r8vec_indexed_heap_d_insert ( int *n, double a[], int indx[], + int indx_insert ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_INDEXED_HEAP_D_INSERT: insert value into heap descending indexed R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// An indexed R8VEC is an R8VEC of data values, and an R8VEC of N indices, +// each referencing an entry of the data vector. +// +// Note that the argument N must be a variable, and will be incremented before +// return, and that INDX must be able to hold one more entry on output than +// it held on input. +// +// This is one of three functions needed to model a priority queue. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 August 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Thomas Cormen, Charles Leiserson, Ronald Rivest, +// Introduction to Algorithms, +// MIT Press, 2001, +// ISBN: 0262032937, +// LC: QA76.C662. +// +// Parameters: +// +// Input/output, int *N, the number of items in the index vector. +// +// Input, double A[*], the data vector. +// +// Input/output, int INDX[N], the index vector. +// +// Input, int INDX_INSERT, the index in A of the value +// to be inserted into the heap. +// +{ + int i; + int parent; + + *n = *n + 1; + i = *n - 1; + + while ( 0 < i ) + { + parent = ( i - 1 ) / 2; + + if ( a[indx_insert] <= a[indx[parent]] ) + { + break; + } + + indx[i] = indx[parent]; + i = parent; + } + + indx[i] = indx_insert; + + return; +} +//****************************************************************************80 + +int r8vec_indexed_heap_d_max ( int n, double a[], int indx[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_INDEXED_HEAP_D_MAX: maximum value in heap descending indexed R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// An indexed R8VEC is an R8VEC of data values, and an R8VEC of N indices, +// each referencing an entry of the data vector. +// +// This is one of three functions needed to model a priority queue. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 18 August 2010 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Thomas Cormen, Charles Leiserson, Ronald Rivest, +// Introduction to Algorithms, +// MIT Press, 2001, +// ISBN: 0262032937, +// LC: QA76.C662. +// +// Parameters: +// +// Input, int N, the number of items in the index vector. +// +// Input, double A[*], the data vector. +// +// Input, int INDX[N], the index vector. +// +// Output, int R8VEC_INDEXED_HEAP_D_MAX, the index in A of the maximum value +// in the heap. +// +{ + int indx_max; + + indx_max = indx[0]; + + return indx_max; +} +//****************************************************************************80 + +double *r8vec_legendre_new ( int n, double a_first, double a_last ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_LEGENDRE_NEW creates a vector of Chebyshev spaced values. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 17 June 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Input, double A_FIRST, A_LAST, the first and last entries. +// +// Output, double R8VEC_LEGENDRE_NEW[N], a vector of Legendre spaced data. +// +{ + double *a; + int i; + + a = webbur::legendre_zeros ( n ); + + for ( i = 0; i < n; i++ ) + { + a[i] = ( ( 1.0 - a[i] ) * a_first + + ( 1.0 + a[i] ) * a_last ) + / 2.0; + } + return a; +} +//****************************************************************************80 + +double *r8vec_linspace_new ( int n, double a_first, double a_last ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_LINSPACE_NEW creates a vector of linearly spaced values. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 14 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Input, double A_FIRST, A_LAST, the first and last entries. +// +// Output, double R8VEC_LINSPACE_NEW[N], a vector of linearly spaced data. +// +{ + double *a; + int i; + + a = new double[n]; + + if ( n == 1 ) + { + a[0] = ( a_first + a_last ) / 2.0; + } + else + { + for ( i = 0; i < n; i++ ) + { + a[i] = ( ( double ) ( n - 1 - i ) * a_first + + ( double ) ( i ) * a_last ) + / ( double ) ( n - 1 ); + } + } + return a; +} +//****************************************************************************80 + +double r8vec_min ( int n, double r8vec[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_MIN returns the value of the minimum element in an R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 02 July 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the array. +// +// Input, double R8VEC[N], the array to be checked. +// +// Output, double R8VEC_MIN, the value of the minimum element. +// +{ + int i; + double value; + + value = r8vec[0]; + + for ( i = 1; i < n; i++ ) + { + if ( r8vec[i] < value ) + { + value = r8vec[i]; + } + } + return value; +} +//****************************************************************************80 + +double r8vec_min_pos ( int n, double a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_MIN_POS returns the minimum positive value of an R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 08 November 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries. +// +// Input, double A[N], the array. +// +// Output, double R8VEC_MIN_POS, the smallest positive entry, +// or R8_HUGE if no entry is positive. +// +{ + int i; + double r8_huge = 1.0E+30; + double value; + + value = r8_huge; + + for ( i = 0; i < n; i++ ) + { + if ( 0.0 < a[i] ) + { + if ( a[i] < value ) + { + value = a[i]; + } + } + } + return value; +} +//****************************************************************************80 + +void r8vec_print ( int n, double a[], std::string title ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_PRINT prints an R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 16 August 2004 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of components of the vector. +// +// Input, double A[N], the vector to be printed. +// +// Input, string TITLE, a title. +// +{ + int i; + + std::cout << "\n"; + std::cout << title << "\n"; + std::cout << "\n"; + for ( i = 0; i < n; i++ ) + { + std::cout << " " << std::setw(8) << i + << ": " << std::setw(14) << a[i] << "\n"; + } + + return; +} +//****************************************************************************80 + +void r8vec_scale ( double s, int n, double a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_SCALE multiples an R8VEC by a scale factor. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 22 September 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, double S, the scale factor. +// +// Input, int N, the number of entries in the vectors. +// +// Input/output, double A[N], the vector to be scaled. +// On output, A[] = S * A[]. +// +{ + int i; + + for ( i = 0; i < n; i++ ) + { + a[i] = s * a[i]; + } + return; +} +//****************************************************************************80 + +void r8vec_sort_heap_index_a ( int n, double a[], int indx[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_SORT_HEAP_INDEX_A does an indexed heap ascending sort of an R8VEC +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// The sorting is not actually carried out. Rather an index array is +// created which defines the sorting. This array may be used to sort +// or index the array, or to sort or index related arrays keyed on the +// original array. +// +// Once the index array is computed, the sorting can be carried out +// "implicitly: +// +// a(indx(*)) +// +// or explicitly, by the call +// +// r8vec_permute ( n, indx, 0, a ) +// +// after which a(*) is sorted. +// +// Note that the index vector is 0-based. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 02 October 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the array. +// +// Input, double A[N], an array to be index-sorted. +// +// Output, int INDX[N], contains the sort index. The +// I-th element of the sorted array is A(INDX(I)). +// +{ + double aval; + int i; + int indxt; + int ir; + int j; + int l; + + if ( n < 1 ) + { + return; + } + + for ( i = 0; i < n; i++ ) + { + indx[i] = i; + } + + if ( n == 1 ) + { + return; + } + + l = n / 2 + 1; + ir = n; + + for ( ; ; ) + { + if ( 1 < l ) + { + l = l - 1; + indxt = indx[l-1]; + aval = a[indxt]; + } + else + { + indxt = indx[ir-1]; + aval = a[indxt]; + indx[ir-1] = indx[0]; + ir = ir - 1; + + if ( ir == 1 ) + { + indx[0] = indxt; + break; + } + } + + i = l; + j = l + l; + + while ( j <= ir ) + { + if ( j < ir ) + { + if ( a[indx[j-1]] < a[indx[j]] ) + { + j = j + 1; + } + } + + if ( aval < a[indx[j-1]] ) + { + indx[i-1] = indx[j-1]; + i = j; + j = j + j; + } + else + { + j = ir + 1; + } + } + indx[i-1] = indxt; + } + + return; +} +//****************************************************************************80 + +int *r8vec_sort_heap_index_a_new ( int n, double a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_SORT_HEAP_INDEX_A_NEW does an indexed heap ascending sort of an R8VEC +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// The sorting is not actually carried out. Rather an index array is +// created which defines the sorting. This array may be used to sort +// or index the array, or to sort or index related arrays keyed on the +// original array. +// +// Once the index array is computed, the sorting can be carried out +// "implicitly: +// +// a(indx(*)) +// +// or explicitly, by the call +// +// r8vec_permute ( n, indx, 0, a ) +// +// after which a(*) is sorted. +// +// Note that the index vector is 0-based. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 02 October 2010 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the array. +// +// Input, double A[N], an array to be index-sorted. +// +// Output, int R8VEC_SORT_HEAP_INDEX_A_NEW[N], contains the sort index. The +// I-th element of the sorted array is A(INDX(I)). +// +{ + double aval; + int i; + int *indx; + int indxt; + int ir; + int j; + int l; + + if ( n < 1 ) + { + return NULL; + } + + indx = new int[n]; + + for ( i = 0; i < n; i++ ) + { + indx[i] = i; + } + + if ( n == 1 ) + { + return indx; + } + + l = n / 2 + 1; + ir = n; + + for ( ; ; ) + { + if ( 1 < l ) + { + l = l - 1; + indxt = indx[l-1]; + aval = a[indxt]; + } + else + { + indxt = indx[ir-1]; + aval = a[indxt]; + indx[ir-1] = indx[0]; + ir = ir - 1; + + if ( ir == 1 ) + { + indx[0] = indxt; + break; + } + } + + i = l; + j = l + l; + + while ( j <= ir ) + { + if ( j < ir ) + { + if ( a[indx[j-1]] < a[indx[j]] ) + { + j = j + 1; + } + } + + if ( aval < a[indx[j-1]] ) + { + indx[i-1] = indx[j-1]; + i = j; + j = j + j; + } + else + { + j = ir + 1; + } + } + indx[i-1] = indxt; + } + + return indx; +} +//****************************************************************************80 + +void r8vec_stutter ( int n, double a[], int m, double am[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_STUTTER makes a "stuttering" copy of an R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Applying a stuttering factor M of 3, the vector A = ( 1, 5, 8 ) becomes +// AM = ( 1, 1, 1, 5, 5, 5, 8, 8, 8 ). +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 28 March 2011 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the size of the input vector. +// +// Input, double A[N], the vector. +// +// Input, int M, the "stuttering factor". +// +// Output, double AM[M*N], the stuttering vector. +// +{ + int i; + int j; + int k; + + k = 0; + for ( i = 0; i < n; i++ ) + { + for ( j = 0; j < m; j++ ) + { + am[k] = a[i]; + k = k + 1; + } + } + return; +} +//****************************************************************************80 + +double r8vec_sum ( int n, double a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_SUM returns the sum of an R8VEC. +// +// Discussion: +// +// An R8VEC is a double precision vector. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 15 October 2004 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Input, double A[N], the vector. +// +// Output, double R8VEC_SUM, the sum of the vector. +// +{ + int i; + double value; + + value = 0.0; + for ( i = 0; i < n; i++ ) + { + value = value + a[i]; + } + + return value; +} +//****************************************************************************80 + +void r8vec_uniform_01 ( int n, int *seed, double r[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_UNIFORM_01 returns a unit pseudorandom R8VEC. +// +// Discussion: +// +// This routine implements the recursion +// +// seed = ( 16807 * seed ) mod ( 2^31 - 1 ) +// u = seed / ( 2^31 - 1 ) +// +// The integer arithmetic never requires more than 32 bits, +// including a sign bit. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 August 2004 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Paul Bratley, Bennett Fox, Linus Schrage, +// A Guide to Simulation, +// Second Edition, +// Springer, 1987, +// ISBN: 0387964673, +// LC: QA76.9.C65.B73. +// +// Bennett Fox, +// Algorithm 647: +// Implementation and Relative Efficiency of Quasirandom +// Sequence Generators, +// ACM Transactions on Mathematical Software, +// Volume 12, Number 4, December 1986, pages 362-376. +// +// Pierre L'Ecuyer, +// Random Number Generation, +// in Handbook of Simulation, +// edited by Jerry Banks, +// Wiley, 1998, +// ISBN: 0471134031, +// LC: T57.62.H37. +// +// Peter Lewis, Allen Goodman, James Miller, +// A Pseudo-Random Number Generator for the System/360, +// IBM Systems Journal, +// Volume 8, Number 2, 1969, pages 136-143. +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Input/output, int *SEED, a seed for the random number generator. +// +// Output, double R[N], the vector of pseudorandom values. +// +{ + int i; + int i4_huge = 2147483647; + int k; + + if ( *seed == 0 ) + { + std::cerr << "\n"; + std::cerr << "R8VEC_UNIFORM_01 - Fatal error!\n"; + std::cerr << " Input value of SEED = 0.\n"; + std::exit ( 1 ); + } + + for ( i = 0; i < n; i++ ) + { + k = *seed / 127773; + + *seed = 16807 * ( *seed - k * 127773 ) - k * 2836; + + if ( *seed < 0 ) + { + *seed = *seed + i4_huge; + } + + r[i] = ( double ) ( *seed ) * 4.656612875E-10; + } + + return; +} +//****************************************************************************80 + +double *r8vec_uniform_01_new ( int n, int *seed ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_UNIFORM_01_NEW returns a new unit pseudorandom R8VEC. +// +// Discussion: +// +// This routine implements the recursion +// +// seed = ( 16807 * seed ) mod ( 2^31 - 1 ) +// u = seed / ( 2^31 - 1 ) +// +// The integer arithmetic never requires more than 32 bits, +// including a sign bit. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 August 2004 +// +// Author: +// +// John Burkardt +// +// Reference: +// +// Paul Bratley, Bennett Fox, Linus Schrage, +// A Guide to Simulation, +// Second Edition, +// Springer, 1987, +// ISBN: 0387964673, +// LC: QA76.9.C65.B73. +// +// Bennett Fox, +// Algorithm 647: +// Implementation and Relative Efficiency of Quasirandom +// Sequence Generators, +// ACM Transactions on Mathematical Software, +// Volume 12, Number 4, December 1986, pages 362-376. +// +// Pierre L'Ecuyer, +// Random Number Generation, +// in Handbook of Simulation, +// edited by Jerry Banks, +// Wiley, 1998, +// ISBN: 0471134031, +// LC: T57.62.H37. +// +// Peter Lewis, Allen Goodman, James Miller, +// A Pseudo-Random Number Generator for the System/360, +// IBM Systems Journal, +// Volume 8, Number 2, 1969, pages 136-143. +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Input/output, int *SEED, a seed for the random number generator. +// +// Output, double R8VEC_UNIFORM_01_NEW[N], the vector of pseudorandom values. +// +{ + int i; + int i4_huge = 2147483647; + int k; + double *r; + + if ( *seed == 0 ) + { + std::cerr << "\n"; + std::cerr << "R8VEC_UNIFORM_01_NEW - Fatal error!\n"; + std::cerr << " Input value of SEED = 0.\n"; + std::exit ( 1 ); + } + + r = new double[n]; + + for ( i = 0; i < n; i++ ) + { + k = *seed / 127773; + + *seed = 16807 * ( *seed - k * 127773 ) - k * 2836; + + if ( *seed < 0 ) + { + *seed = *seed + i4_huge; + } + + r[i] = ( double ) ( *seed ) * 4.656612875E-10; + } + + return r; +} +//****************************************************************************80 + +void r8vec_zero ( int n, double a[] ) + +//****************************************************************************80 +// +// Purpose: +// +// R8VEC_ZERO zeroes an R8VEC. +// +// Discussion: +// +// An R8VEC is a vector of R8's. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 03 July 2005 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int N, the number of entries in the vector. +// +// Output, double A[N], a vector of zeroes. +// +{ + int i; + + for ( i = 0; i < n; i++ ) + { + a[i] = 0.0; + } + return; +} +//****************************************************************************80 + +void sort_heap_external ( int n, int *indx, int *i, int *j, int isgn ) + +//****************************************************************************80 +// +// Purpose: +// +// SORT_HEAP_EXTERNAL externally sorts a list of items into ascending order. +// +// Discussion: +// +// The actual list is not passed to the routine. Hence it may +// consist of integers, reals, numbers, names, etc. The user, +// after each return from the routine, will be asked to compare or +// interchange two items. +// +// The current version of this code mimics the FORTRAN version, +// so the values of I and J, in particular, are FORTRAN indices. +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 05 February 2004 +// +// Author: +// +// Original FORTRAN77 version by Albert Nijenhuis, Herbert Wilf. +// C++ version by John Burkardt +// +// Reference: +// +// Albert Nijenhuis, Herbert Wilf, +// Combinatorial Algorithms, +// Academic Press, 1978, second edition, +// ISBN 0-12-519260-6. +// +// Parameters: +// +// Input, int N, the length of the input list. +// +// Input/output, int *INDX. +// The user must set INDX to 0 before the first call. +// On return, +// if INDX is greater than 0, the user must interchange +// items I and J and recall the routine. +// If INDX is less than 0, the user is to compare items I +// and J and return in ISGN a negative value if I is to +// precede J, and a positive value otherwise. +// If INDX is 0, the sorting is done. +// +// Output, int *I, *J. On return with INDX positive, +// elements I and J of the user's list should be +// interchanged. On return with INDX negative, elements I +// and J are to be compared by the user. +// +// Input, int ISGN. On return with INDX negative, the +// user should compare elements I and J of the list. If +// item I is to precede item J, set ISGN negative, +// otherwise set ISGN positive. +// +{ + static int i_save = 0; + static int j_save = 0; + static int k = 0; + static int k1 = 0; + static int n1 = 0; +// +// INDX = 0: This is the first call. +// + if ( *indx == 0 ) + { + + i_save = 0; + j_save = 0; + k = n / 2; + k1 = k; + n1 = n; + } +// +// INDX < 0: The user is returning the results of a comparison. +// + else if ( *indx < 0 ) + { + if ( *indx == -2 ) + { + if ( isgn < 0 ) + { + i_save = i_save + 1; + } + j_save = k1; + k1 = i_save; + *indx = -1; + *i = i_save; + *j = j_save; + return; + } + + if ( 0 < isgn ) + { + *indx = 2; + *i = i_save; + *j = j_save; + return; + } + + if ( k <= 1 ) + { + if ( n1 == 1 ) + { + i_save = 0; + j_save = 0; + *indx = 0; + } + else + { + i_save = n1; + j_save = 1; + n1 = n1 - 1; + *indx = 1; + } + *i = i_save; + *j = j_save; + return; + } + k = k - 1; + k1 = k; + } +// +// 0 < INDX: the user was asked to make an interchange. +// + else if ( *indx == 1 ) + { + k1 = k; + } + + for ( ; ; ) + { + + i_save = 2 * k1; + + if ( i_save == n1 ) + { + j_save = k1; + k1 = i_save; + *indx = -1; + *i = i_save; + *j = j_save; + return; + } + else if ( i_save <= n1 ) + { + j_save = i_save + 1; + *indx = -2; + *i = i_save; + *j = j_save; + return; + } + + if ( k <= 1 ) + { + break; + } + + k = k - 1; + k1 = k; + } + + if ( n1 == 1 ) + { + i_save = 0; + j_save = 0; + *indx = 0; + *i = i_save; + *j = j_save; + } + else + { + i_save = n1; + j_save = 1; + n1 = n1 - 1; + *indx = 1; + *i = i_save; + *j = j_save; + } + + return; +} +//****************************************************************************80 + +void timestamp ( ) + +//****************************************************************************80 +// +// Purpose: +// +// TIMESTAMP prints the current YMDHMS date as a time stamp. +// +// Example: +// +// 31 May 2001 09:45:54 AM +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 08 July 2009 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// None +// +{ +# define TIME_SIZE 40 + + static char time_buffer[TIME_SIZE]; + const struct std::tm *tm_ptr; + size_t len; + std::time_t now; + + now = std::time ( NULL ); + tm_ptr = std::localtime ( &now ); + + len = std::strftime ( time_buffer, TIME_SIZE, "%d %B %Y %I:%M:%S %p", tm_ptr ); + + std::cout << time_buffer << "\n"; + + return; +# undef TIME_SIZE +} +//****************************************************************************80 + +void vec_colex_next3 ( int dim_num, int base[], int a[], bool *more ) + +//****************************************************************************80 +// +// Purpose: +// +// VEC_COLEX_NEXT3 generates vectors in colex order. +// +// Discussion: +// +// The vectors are produced in colexical order, starting with +// +// (1, 1, ...,1), +// (2, 1, ...,1), +// ... +// (BASE(1), 1, ...,1) +// +// (1, 2, ...,1) +// (2, 2, ...,1) +// ... +// (BASE(1), 2, ...,1) +// +// (1, 3, ...,1) +// (2, 3, ...,1) +// ... +// (BASE(1), BASE(2), ...,BASE(DIM_NUM)). +// +// Example: +// +// DIM_NUM = 2, +// BASE = { 3, 3 } +// +// 1 1 +// 2 1 +// 3 1 +// 1 2 +// 2 2 +// 3 2 +// 1 3 +// 2 3 +// 3 3 +// +// Licensing: +// +// This code is distributed under the GNU LGPL license. +// +// Modified: +// +// 19 August 2008 +// +// Author: +// +// John Burkardt +// +// Parameters: +// +// Input, int DIM_NUM, the spatial dimension. +// +// Input, int BASE[DIM_NUM], the bases to be used in each dimension. +// In dimension I, entries will range from 1 to BASE[I]. +// +// Output, int A[DIM_NUM], the next vector. +// +// Input/output, bool *MORE. Set this variable false before +// the first call. On return, MORE is TRUE if another vector has +// been computed. If MORE is returned FALSE, ignore the output +// vector and stop calling the routine. +// +{ + int i; + + if ( !( *more ) ) + { + for ( i = 0; i < dim_num; i++ ) + { + a[i] = 1; + } + *more = true; + } + else + { + for ( i = 0; i < dim_num; i++ ) + { + a[i] = a[i] + 1; + + if ( a[i] <= base[i] ) + { + return; + } + a[i] = 1; + } + *more = false; + } + + return; +} + + +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/packages/queso/src/misc/src/1DQuadrature.C =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/packages/queso/src/misc/src/1DQuadrature.C (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/packages/queso/src/misc/src/1DQuadrature.C (revision 27955) @@ -0,0 +1,755 @@ +//-----------------------------------------------------------------------bl- +//-------------------------------------------------------------------------- +// +// QUESO - a library to support the Quantification of Uncertainty +// for Estimation, Simulation and Optimization +// +// Copyright (C) 2008-2015 The PECOS Development Team +// +// This library is free software; you can redistribute it and/or +// modify it under the terms of the Version 2.1 GNU Lesser General +// Public License as published by the Free Software Foundation. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// Lesser General Public License for more details. +// +// You should have received a copy of the GNU Lesser General Public +// License along with this library; if not, write to the Free Software +// Foundation, Inc. 51 Franklin Street, Fifth Floor, +// Boston, MA 02110-1301 USA +// +//-----------------------------------------------------------------------el- + +#include + +namespace QUESO { + +//***************************************************** +// Base 1D quadrature class +//***************************************************** +Base1DQuadrature::Base1DQuadrature( + double minDomainValue, + double maxDomainValue, + unsigned int order) + : + m_minDomainValue(minDomainValue), + m_maxDomainValue(maxDomainValue), + m_order (order), + m_positions (0), + m_weights (0) +{ + UQ_FATAL_TEST_MACRO(m_minDomainValue >= m_maxDomainValue, + UQ_UNAVAILABLE_RANK, + "Base1DQuadrature::constructor()", + "min >= max"); + //UQ_FATAL_TEST_MACRO(order == 0, // eep2011 + // UQ_UNAVAILABLE_RANK, + // "Base1DQuadrature::constructor()", + // "order = 0"); +} + +Base1DQuadrature::~Base1DQuadrature() +{ +} + +double +Base1DQuadrature::minDomainValue() const +{ + return m_minDomainValue; +} + +double +Base1DQuadrature::maxDomainValue() const +{ + return m_maxDomainValue; +} + +unsigned int +Base1DQuadrature::order() const +{ + return m_order; +} + +const std::vector& +Base1DQuadrature::positions() const +{ + UQ_FATAL_TEST_MACRO(m_positions.size() == 0, + UQ_UNAVAILABLE_RANK, + "Base1DQuadrature::positions()", + "size = 0"); + return m_positions; +} + +const std::vector& +Base1DQuadrature::weights() const +{ + UQ_FATAL_TEST_MACRO(m_weights.size() == 0, + UQ_UNAVAILABLE_RANK, + "Base1DQuadrature::weights()", + "size = 0"); + return m_weights; +} + +//***************************************************** +// Generic 1D quadrature class +//***************************************************** +Generic1DQuadrature::Generic1DQuadrature( + double minDomainValue, + double maxDomainValue, + const std::vector& positions, + const std::vector& weights) + : + Base1DQuadrature(minDomainValue,maxDomainValue,positions.size()-1) +{ + m_positions = positions; + m_weights = weights; + + UQ_FATAL_TEST_MACRO(m_positions.size() == 0, + UQ_UNAVAILABLE_RANK, + "Generic1DQuadrature::constructor()", + "invalid positions"); + + UQ_FATAL_TEST_MACRO(m_positions.size() != m_weights.size(), + UQ_UNAVAILABLE_RANK, + "Generic1DQuadrature::constructor()", + "inconsistent positions and weight"); +} + +Generic1DQuadrature::~Generic1DQuadrature() +{ +} + +void +Generic1DQuadrature::dumbRoutine() const +{ + return; +} + +//***************************************************** +// UniformLegendre 1D quadrature class +//***************************************************** +UniformLegendre1DQuadrature::UniformLegendre1DQuadrature( + double minDomainValue, + double maxDomainValue, + unsigned int order, + bool densityIsNormalized) + : + Base1DQuadrature(minDomainValue,maxDomainValue,order) +{ + m_positions.resize(m_order+1,0.); // Yes, '+1' + m_weights.resize (m_order+1,0.); // Yes, '+1' + + // http://www.holoborodko.com/pavel/?page_id=679 + switch (m_order) { // eep2011 + case 1: + m_weights [0] = 1.; + m_weights [1] = 1.; + + m_positions[0] = -1./sqrt(3.); + m_positions[1] = 1./sqrt(3.); + break; + + case 2: + m_weights [0] = 5./9.; + m_weights [1] = 8./9.; + m_weights [2] = 5./9.; + + m_positions[0] = -sqrt(.6); + m_positions[1] = 0.; + m_positions[2] = sqrt(.6); + break; + + case 3: + m_weights [0] = 0.5 - sqrt(30.)/36.; + m_weights [1] = 0.5 + sqrt(30.)/36.; + m_weights [2] = 0.5 + sqrt(30.)/36.; + m_weights [3] = 0.5 - sqrt(30.)/36.; + + m_positions[0] = -sqrt(3.+2.*sqrt(1.2))/sqrt(7.); + m_positions[1] = -sqrt(3.-2.*sqrt(1.2))/sqrt(7.); + m_positions[2] = sqrt(3.-2.*sqrt(1.2))/sqrt(7.); + m_positions[3] = sqrt(3.+2.*sqrt(1.2))/sqrt(7.); + break; + + case 4: + m_weights [0] = (322.-13.*sqrt(70.))/900.; // 0.236926885 + m_weights [1] = (322.+13.*sqrt(70.))/900.; // 0.478628670 + m_weights [2] = 128./225.; // 0.568888889 + m_weights [3] = (322.+13.*sqrt(70.))/900.; + m_weights [4] = (322.-13.*sqrt(70.))/900.; + + m_positions[0] = -sqrt(5.+2.*sqrt(10./7.))/3.; + m_positions[1] = -sqrt(5.-2.*sqrt(10./7.))/3.; + m_positions[2] = 0.; + m_positions[3] = sqrt(5.-2.*sqrt(10./7.))/3.; + m_positions[4] = sqrt(5.+2.*sqrt(10./7.))/3.; + break; + + case 5: + m_weights [0] = 0.1713244923791703450402961; + m_weights [1] = 0.3607615730481386075698335; + m_weights [2] = 0.4679139345726910473898703; + m_weights [3] = 0.4679139345726910473898703; + m_weights [4] = 0.3607615730481386075698335; + m_weights [5] = 0.1713244923791703450402961; + + m_positions[0] = -0.9324695142031520278123016; + m_positions[1] = -0.6612093864662645136613996; + m_positions[2] = -0.2386191860831969086305017; + m_positions[3] = 0.2386191860831969086305017; + m_positions[4] = 0.6612093864662645136613996; + m_positions[5] = 0.9324695142031520278123016; + break; + + case 6: + m_weights [0] = 0.1294849661688696932706114; + m_weights [1] = 0.2797053914892766679014678; + m_weights [2] = 0.3818300505051189449503698; + m_weights [3] = 0.4179591836734693877551020; + m_weights [4] = 0.3818300505051189449503698; + m_weights [5] = 0.2797053914892766679014678; + m_weights [6] = 0.1294849661688696932706114; + + m_positions[0] = -0.9491079123427585245261897; + m_positions[1] = -0.7415311855993944398638648; + m_positions[2] = -0.4058451513773971669066064; + m_positions[3] = 0.; + m_positions[4] = 0.4058451513773971669066064; + m_positions[5] = 0.7415311855993944398638648; + m_positions[6] = 0.9491079123427585245261897; + break; + + case 7: + m_weights [0] = 0.10122854; + m_weights [1] = 0.22238103; + m_weights [2] = 0.31370665; + m_weights [3] = 0.36268378; + m_weights [4] = 0.36268378; + m_weights [5] = 0.31370665; + m_weights [6] = 0.22238103; + m_weights [7] = 0.10122854; + + m_positions[0] = -0.96028986; + m_positions[1] = -0.79666648; + m_positions[2] = -0.52553241; + m_positions[3] = -0.18343464; + m_positions[4] = 0.18343464; + m_positions[5] = 0.52553241; + m_positions[6] = 0.79666648; + m_positions[7] = 0.96028986; + break; + + case 10: + m_weights [ 0] = 0.0556685671161736664827537; + m_weights [ 1] = 0.1255803694649046246346943; + m_weights [ 2] = 0.1862902109277342514260976; + m_weights [ 3] = 0.2331937645919904799185237; + m_weights [ 4] = 0.2628045445102466621806889; + m_weights [ 5] = 0.2729250867779006307144835; + m_weights [ 6] = 0.2628045445102466621806889; + m_weights [ 7] = 0.2331937645919904799185237; + m_weights [ 8] = 0.1862902109277342514260976; + m_weights [ 9] = 0.1255803694649046246346943; + m_weights [10] = 0.0556685671161736664827537; + + m_positions[ 0] = -0.9782286581460569928039380; + m_positions[ 1] = -0.8870625997680952990751578; + m_positions[ 2] = -0.7301520055740493240934163; + m_positions[ 3] = -0.5190961292068118159257257; + m_positions[ 4] = -0.2695431559523449723315320; + m_positions[ 5] = 0.; + m_positions[ 6] = 0.2695431559523449723315320; + m_positions[ 7] = 0.5190961292068118159257257; + m_positions[ 8] = 0.7301520055740493240934163; + m_positions[ 9] = 0.8870625997680952990751578; + m_positions[10] = 0.9782286581460569928039380; + break; + + case 11: + m_weights [ 0] = 0.0471753363865118271946160; + m_weights [ 1] = 0.1069393259953184309602547; + m_weights [ 2] = 0.1600783285433462263346525; + m_weights [ 3] = 0.2031674267230659217490645; + m_weights [ 4] = 0.2334925365383548087608499; + m_weights [ 5] = 0.2491470458134027850005624; + m_weights [ 6] = 0.2491470458134027850005624; + m_weights [ 7] = 0.2334925365383548087608499; + m_weights [ 8] = 0.2031674267230659217490645; + m_weights [ 9] = 0.1600783285433462263346525; + m_weights [10] = 0.1069393259953184309602547; + m_weights [11] = 0.0471753363865118271946160; + + m_positions[ 0] = -0.9815606342467192506905491; + m_positions[ 1] = -0.9041172563704748566784659; + m_positions[ 2] = -0.7699026741943046870368938; + m_positions[ 3] = -0.5873179542866174472967024; + m_positions[ 4] = -0.3678314989981801937526915; + m_positions[ 5] = -0.1252334085114689154724414; + m_positions[ 6] = 0.1252334085114689154724414; + m_positions[ 7] = 0.3678314989981801937526915; + m_positions[ 8] = 0.5873179542866174472967024; + m_positions[ 9] = 0.7699026741943046870368938; + m_positions[10] = 0.9041172563704748566784659; + m_positions[11] = 0.9815606342467192506905491; + break; + + case 12: + m_weights [ 0] = 0.0404840047653158795200216; + m_weights [ 1] = 0.0921214998377284479144218; + m_weights [ 2] = 0.1388735102197872384636018; + m_weights [ 3] = 0.1781459807619457382800467; + m_weights [ 4] = 0.2078160475368885023125232; + m_weights [ 5] = 0.2262831802628972384120902; + m_weights [ 6] = 0.2325515532308739101945895; + m_weights [ 7] = 0.2262831802628972384120902; + m_weights [ 8] = 0.2078160475368885023125232; + m_weights [ 9] = 0.1781459807619457382800467; + m_weights [10] = 0.1388735102197872384636018; + m_weights [11] = 0.0921214998377284479144218; + m_weights [12] = 0.0404840047653158795200216; + + m_positions[ 0] = -0.9841830547185881494728294; + m_positions[ 1] = -0.9175983992229779652065478; + m_positions[ 2] = -0.8015780907333099127942065; + m_positions[ 3] = -0.6423493394403402206439846; + m_positions[ 4] = -0.4484927510364468528779129; + m_positions[ 5] = -0.2304583159551347940655281; + m_positions[ 6] = 0.; + m_positions[ 7] = 0.2304583159551347940655281; + m_positions[ 8] = 0.4484927510364468528779129; + m_positions[ 9] = 0.6423493394403402206439846; + m_positions[10] = 0.8015780907333099127942065; + m_positions[11] = 0.9175983992229779652065478; + m_positions[12] = 0.9841830547185881494728294; + break; +#if 0 + case 13: + m_weights [ 0] = ; + m_weights [ 1] = ; + m_weights [ 2] = ; + m_weights [ 3] = ; + m_weights [ 4] = ; + m_weights [ 5] = ; + m_weights [ 6] = ; + m_weights [ 7] = ; + m_weights [ 8] = ; + m_weights [ 9] = ; + m_weights [10] = ; + m_weights [11] = ; + m_weights [12] = ; + m_weights [13] = ; + + m_positions[ 0] = -; + m_positions[ 1] = -; + m_positions[ 2] = -; + m_positions[ 3] = -; + m_positions[ 4] = -; + m_positions[ 5] = -; + m_positions[ 6] = -; + m_positions[ 7] = ; + m_positions[ 8] = ; + m_positions[ 9] = ; + m_positions[10] = ; + m_positions[11] = ; + m_positions[12] = ; + m_positions[13] = ; + break; +#endif +/* + 14 ±0.1080549487073436620662447 0.2152638534631577901958764 + ±0.3191123689278897604356718 0.2051984637212956039659241 + ±0.5152486363581540919652907 0.1855383974779378137417166 + ±0.6872929048116854701480198 0.1572031671581935345696019 + ±0.8272013150697649931897947 0.1215185706879031846894148 + ±0.9284348836635735173363911 0.0801580871597602098056333 + ±0.9862838086968123388415973 0.0351194603317518630318329 +*/ + + case 16: + m_weights [ 0] = 0.0241483028685479319601100; + m_weights [ 1] = 0.0554595293739872011294402; + m_weights [ 2] = 0.0850361483171791808835354; + m_weights [ 3] = 0.1118838471934039710947884; + m_weights [ 4] = 0.1351363684685254732863200; + m_weights [ 5] = 0.1540457610768102880814316; + m_weights [ 6] = 0.1680041021564500445099707; + m_weights [ 7] = 0.1765627053669926463252710; + m_weights [ 8] = 0.1794464703562065254582656; + m_weights [ 9] = 0.1765627053669926463252710; + m_weights [10] = 0.1680041021564500445099707; + m_weights [11] = 0.1540457610768102880814316; + m_weights [12] = 0.1351363684685254732863200; + m_weights [13] = 0.1118838471934039710947884; + m_weights [14] = 0.0850361483171791808835354; + m_weights [15] = 0.0554595293739872011294402; + m_weights [16] = 0.0241483028685479319601100; + + m_positions[ 0] = -0.9905754753144173356754340; + m_positions[ 1] = -0.9506755217687677612227170; + m_positions[ 2] = -0.8802391537269859021229557; + m_positions[ 3] = -0.7815140038968014069252301; + m_positions[ 4] = -0.6576711592166907658503022; + m_positions[ 5] = -0.5126905370864769678862466; + m_positions[ 6] = -0.3512317634538763152971855; + m_positions[ 7] = -0.1784841814958478558506775; + m_positions[ 8] = 0.; + m_positions[ 9] = 0.1784841814958478558506775; + m_positions[10] = 0.3512317634538763152971855; + m_positions[11] = 0.5126905370864769678862466; + m_positions[12] = 0.6576711592166907658503022; + m_positions[13] = 0.7815140038968014069252301; + m_positions[14] = 0.8802391537269859021229557; + m_positions[15] = 0.9506755217687677612227170; + m_positions[16] = 0.9905754753144173356754340; + break; + + default: + std::cerr << "In UniformLegendre1DQuadrature::constructor()" + << ": m_order = " << m_order + << std::endl; + UQ_FATAL_TEST_MACRO(true, + UQ_UNAVAILABLE_RANK, + "UniformLegendre1DQuadrature::constructor()", + "order not supported"); + break; + } + + // Scale positions from the interval [-1, 1] to the interval [min,max] + for (unsigned int j = 0; j < m_positions.size(); ++j) { + m_positions[j] = .5*(m_maxDomainValue - m_minDomainValue)*m_positions[j] + .5*(m_maxDomainValue + m_minDomainValue); + if (densityIsNormalized) { + // Since \rho is "1/\Delta", we just multiply by ".5" + m_weights[j] *= .5; + } + else { + // Since \rho is "1", we multiply by ".5 * \Delta" + m_weights[j] *= .5*(m_maxDomainValue - m_minDomainValue); + } + } +} + +UniformLegendre1DQuadrature::~UniformLegendre1DQuadrature() +{ +} + +void +UniformLegendre1DQuadrature::dumbRoutine() const +{ + return; +} + +//***************************************************** +// GaussianHermite 1D quadrature class +//***************************************************** +GaussianHermite1DQuadrature::GaussianHermite1DQuadrature( + double mean, + double stddev, + unsigned int order) + : + Base1DQuadrature(-INFINITY,INFINITY,order), + m_mean (mean), + m_stddev(stddev) +{ + // FIX ME: prepare code for mean != 0 and stddev != 1 + m_positions.resize(m_order+1,0.); // Yes, '+1' + m_weights.resize (m_order+1,0.); // Yes, '+1' + + // http://www.efunda.com/math/num_integration/findgausshermite.cfm + switch (m_order) { // eep2011 + case 1: + m_weights [0] = sqrt(M_PI)/2.; + m_weights [1] = sqrt(M_PI)/2.; + + m_positions[0] = -1./sqrt(2.); + m_positions[1] = 1./sqrt(2.); + break; + + case 2: + m_weights [0] = sqrt(M_PI)/6.; + m_weights [1] = 2.*sqrt(M_PI)/3.; + m_weights [2] = sqrt(M_PI)/6.; + + m_positions[0] = -sqrt(1.5); + m_positions[1] = 0.; + m_positions[2] = sqrt(1.5); + break; + + case 3: + m_weights [0] = sqrt(M_PI)/4./(3.-sqrt(6.)); + m_weights [1] = sqrt(M_PI)/4./(3.+sqrt(6.)); + m_weights [2] = sqrt(M_PI)/4./(3.+sqrt(6.)); + m_weights [3] = sqrt(M_PI)/4./(3.-sqrt(6.)); + + m_positions[0] = -sqrt(1.5+sqrt(1.5)); + m_positions[1] = -sqrt(1.5-sqrt(1.5)); + m_positions[2] = sqrt(1.5-sqrt(1.5)); + m_positions[3] = sqrt(1.5+sqrt(1.5)); + break; + + case 4: + m_weights [0] = 0.019953242049; + m_weights [1] = 0.393619323152; + m_weights [2] = 0.945308720483; + m_weights [3] = 0.393619323152; + m_weights [4] = 0.019953242059; + + m_positions[0] = -sqrt(2.5+sqrt(2.5)); + m_positions[1] = -sqrt(2.5-sqrt(2.5)); + m_positions[2] = 0.; + m_positions[3] = sqrt(2.5-sqrt(2.5)); + m_positions[4] = sqrt(2.5+sqrt(2.5)); + break; + + case 5: + m_weights [0] = 0.00453000990551; + m_weights [1] = 0.157067320323; + m_weights [2] = 0.724629595224; + m_weights [3] = 0.724629595224; + m_weights [4] = 0.157067320323; + m_weights [5] = 0.00453000990551; + + m_positions [0] = -2.35060497367; + m_positions [1] = -1.33584907401; + m_positions [2] = -0.436077411928; + m_positions [3] = 0.436077411928; + m_positions [4] = 1.33584907401; + m_positions [5] = 2.35060497367; + break; + + case 6: + m_weights [0] = 0.0009717812451; + m_weights [1] = 0.0545155828191; + m_weights [2] = 0.42560725261; + m_weights [3] = 0.810264617557; + m_weights [4] = 0.42560725261; + m_weights [5] = 0.0545155828191; + m_weights [6] = 0.0009717812451; + + m_positions [0] = -2.65196135684; + m_positions [1] = -1.67355162877; + m_positions [2] = -0.816287882859; + m_positions [3] = 0.; + m_positions [4] = 0.816287882859; + m_positions [5] = 1.67355162877; + m_positions [6] = 2.65196135684; + break; + + case 7: + m_weights [0] = 0.000199604072211; + m_weights [1] = 0.0170779830074; + m_weights [2] = 0.207802325815; + m_weights [3] = 0.661147012558; + m_weights [4] = 0.661147012558; + m_weights [5] = 0.207802325815; + m_weights [6] = 0.0170779830074; + m_weights [7] = 0.000199604072211; + + m_positions [0] = -2.93063742026; + m_positions [1] = -1.9816567567; + m_positions [2] = -1.15719371245; + m_positions [3] = -0.381186990207; + m_positions [4] = 0.381186990207; + m_positions [5] = 1.15719371245; + m_positions [6] = 1.9816567567; + m_positions [7] = 2.93063742026; + break; + + case 8: + m_weights [0] = 3.96069772633e-5; + m_weights [1] = 0.00494362427554; + m_weights [2] = 0.0884745273944; + m_weights [3] = 0.432651559003; + m_weights [4] = 0.720235215606; + m_weights [5] = 0.432651559003; + m_weights [6] = 0.0884745273944; + m_weights [7] = 0.00494362427554; + m_weights [8] = 3.96069772633e-5; + + m_positions [0] = -3.19099320178; + m_positions [1] = -2.26658058453; + m_positions [2] = -1.46855328922; + m_positions [3] = -0.723551018753; + m_positions [4] = 0.; + m_positions [5] = 0.723551018753; + m_positions [6] = 1.46855328922; + m_positions [7] = 2.26658058453; + m_positions [8] = 3.19099320178; + break; + + case 9: + m_weights [0] = 7.64043285523e-6; + m_weights [1] = 0.00134364574678; + m_weights [2] = 0.0338743944555; + m_weights [3] = 0.240138611082; + m_weights [4] = 0.610862633735; + m_weights [5] = 0.610862633735; + m_weights [6] = 0.240138611082; + m_weights [7] = 0.0338743944555; + m_weights [8] = 0.00134364574678; + m_weights [9] = 7.64043285523e-6; + + m_positions [0] = -3.43615911884; + m_positions [1] = -2.53273167423; + m_positions [2] = -1.7566836493; + m_positions [3] = -1.03661082979; + m_positions [4] = -0.342901327224; + m_positions [5] = 0.342901327224; + m_positions [6] = 1.03661082979; + m_positions [7] = 1.7566836493; + m_positions [8] = 2.53273167423; + m_positions [9] = 3.43615911884; + break; + + case 19: + m_weights [0] = 2.22939364554e-13; + m_weights [1] = 4.39934099226e-10; + m_weights [2] = 1.08606937077e-7; + m_weights [3] = 7.8025564785e-6; + m_weights [4] = 0.000228338636017; + m_weights [5] = 0.00324377334224; + m_weights [6] = 0.0248105208875; + m_weights [7] = 0.10901720602; + m_weights [8] = 0.286675505363; + m_weights [9] = 0.462243669601; + m_weights [10] = 0.462243669601; + m_weights [11] = 0.286675505363; + m_weights [12] = 0.10901720602; + m_weights [13] = 0.0248105208875; + m_weights [14] = 0.00324377334224; + m_weights [15] = 0.000228338636017; + m_weights [16] = 7.8025564785e-6; + m_weights [17] = 1.08606937077e-7; + m_weights [18] = 4.39934099226e-10; + m_weights [19] = 2.22939364554e-13; + + m_positions [0] = -5.38748089001; + m_positions [1] = -4.60368244955; + m_positions [2] = -3.94476404012; + m_positions [3] = -3.34785456738; + m_positions [4] = -2.78880605843; + m_positions [5] = -2.25497400209; + m_positions [6] = -1.73853771212; + m_positions [7] = -1.2340762154; + m_positions [8] = -0.737473728545; + m_positions [9] = -0.245340708301; + m_positions[10] = 0.245340708301; + m_positions[11] = 0.737473728545; + m_positions[12] = 1.2340762154; + m_positions[13] = 1.73853771212; + m_positions[14] = 2.25497400209; + m_positions[15] = 2.78880605843; + m_positions[16] = 3.34785456738; + m_positions[17] = 3.94476404012; + m_positions[18] = 4.60368244955; + m_positions[19] = 5.38748089001; + break; + + default: + std::cerr << "In GaussianHermite1DQuadrature::constructor()" + << ": m_order = " << m_order + << std::endl; + UQ_FATAL_TEST_MACRO(true, + UQ_UNAVAILABLE_RANK, + "GaussianHermite1DQuadrature::constructor()", + "order not supported"); + break; + } + for (unsigned int j = 0; j < (m_order+1); ++j) { + m_weights [j] *= sqrt(2.); + m_positions[j] *= sqrt(2.); + } +} + +GaussianHermite1DQuadrature::~GaussianHermite1DQuadrature() +{ +} + +void +GaussianHermite1DQuadrature::dumbRoutine() const +{ + return; +} + +//***************************************************** +// WignerInverseChebyshev1st 1D quadrature class +//***************************************************** +WignerInverseChebyshev1st1DQuadrature::WignerInverseChebyshev1st1DQuadrature( + double minDomainValue, + double maxDomainValue, + unsigned int order) + : + Base1DQuadrature(minDomainValue,maxDomainValue,order) +{ + m_positions.resize(m_order+1,0.); // Yes, '+1' + m_weights.resize (m_order+1,0.); // Yes, '+1' + + // http://en.wikipedia.org/wiki/Chebyshev-Gauss_quadrature + switch (m_order) { + default: + UQ_FATAL_TEST_MACRO(true, + UQ_UNAVAILABLE_RANK, + "WignerInverseChebyshev1st1DQuadrature::constructor()", + "order not supported"); + break; + } + + // Scale positions from the interval [-1, 1] to the interval [min,max] + for (unsigned int j = 0; j < m_positions.size(); ++j) { + m_positions[j] = .5*(m_maxDomainValue - m_minDomainValue)*m_positions[j] + .5*(m_maxDomainValue + m_minDomainValue); + m_weights[j] *= .5*(m_maxDomainValue - m_minDomainValue); + } +} + +WignerInverseChebyshev1st1DQuadrature::~WignerInverseChebyshev1st1DQuadrature() +{ +} + +void +WignerInverseChebyshev1st1DQuadrature::dumbRoutine() const +{ + return; +} + +//***************************************************** +// WignerChebyshev2nd 1D quadrature class +//***************************************************** +WignerChebyshev2nd1DQuadrature::WignerChebyshev2nd1DQuadrature( + double minDomainValue, + double maxDomainValue, + unsigned int order) + : + Base1DQuadrature(minDomainValue,maxDomainValue,order) +{ + m_positions.resize(m_order+1,0.); // Yes, '+1' + m_weights.resize (m_order+1,0.); // Yes, '+1' + + // http://en.wikipedia.org/wiki/Chebyshev-Gauss_quadrature + unsigned int n = m_order+1; + for (unsigned int i = 0; i < n; ++i) { + double angle = M_PI*((double)(i+1))/((double)(n+1)); + double cosValue = cos(angle); + double sinValue = sin(angle); + m_positions[i] = cosValue; + m_weights[i] = ( M_PI/((double)(n+1)) )*sinValue*sinValue; + } + + // Scale positions from the interval [-1, 1] to the interval [min,max] + for (unsigned int j = 0; j < m_positions.size(); ++j) { + m_positions[j] = .5*(m_maxDomainValue - m_minDomainValue)*m_positions[j] + .5*(m_maxDomainValue + m_minDomainValue); + m_weights[j] *= .5*(m_maxDomainValue - m_minDomainValue); + } +} + +WignerChebyshev2nd1DQuadrature::~WignerChebyshev2nd1DQuadrature() +{ +} + +void +WignerChebyshev2nd1DQuadrature::dumbRoutine() const +{ + return; +} + +} // End namespace QUESO Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp (revision 27955) @@ -0,0 +1,4681 @@ +#include "NKM_SurfPack.hpp" +#include "NKM_KrigingModel.hpp" +//#include "Accel.hpp" +//#include "NKM_LinearRegressionModel.hpp" +#include +#include +#include + + +#ifdef SURFPACK_HAVE_BOOST_SERIALIZATION +BOOST_CLASS_EXPORT(nkm::KrigingModel) +#endif + + +namespace nkm { + +using std::cout; +using std::cerr; +using std::endl; +using std::ostringstream; + + +//#define __KRIG_ERR_CHECK__ +#define __NKM_UNBIASED_LIKE__ + + + +// typical constructor +KrigingModel::KrigingModel(const SurfData& sd, const ParamMap& params) + : SurfPackModel(sd,sd.getIOut()), numVarsr(sd.getNVarsr()), + numTheta(numVarsr), numPoints(sdBuild.getNPts()), XR(sdBuild.xr) +{ + //printf("calling the right KrigingModel constructor\n"); fflush(stdout); + + //if the SurfDataScaler class does what it's supposed to (the only private content in sdBuild that a Model can access are the scaling bits and then only through SurfDataScaler, and only the model can see inside the scaler) the next line will cause an error when you try to compile with it uncommented, that is intentional + //printf("scaler->mySd.iout=%d\n",scaler.mySd.iout); + + // OPTIONS PARSING + ParamMap::const_iterator param_it; + + // ************************************************************* + // control verbosity outputLevel + // ************************************************************* + param_it = params.find("verbosity"); + if (param_it != params.end() && param_it->second.size() > 0) + outputLevel=static_cast(std::atoi(param_it->second.c_str())); + // outputLevel is a member of nkm::SurfPackModel which nkm::KrigingModel + // is derived from + + // ******************************************************************** + // does the user want to use derivative information to build the + // Kriging model (e.g. Gradient Enhanced Kriging) + // ******************************************************************** + + buildDerOrder=0; //default is regular Kriging (i.e. not GEK) + param_it = params.find("derivative_order"); + if(param_it != params.end() && param_it->second.size() > 0) + buildDerOrder = std::atoi(param_it->second.c_str()); + if(buildDerOrder==0) {//Kriging + numEqnAvail=numPoints; + nDer=1; + Der.newSize(numVarsr,nDer); Der.zero(); + } else if(buildDerOrder==1) { //Gradient Enhanced Kriging (GEK) + numEqnAvail=(1+numVarsr)*numPoints; + multi_dim_poly_power(Der, numVarsr, 1); //use all mixed partial + //derivatives, up to first order, of the basis functions + nDer=Der.getNCols(); //for GradKrigingModel nDer=(1+numVarsr); + //printf("nDer=%d\n",nDer); + int data_der_order=sdBuild.getDerOrder(); + if(data_der_order<1) { + std::cerr << "the order of derivative information available in the " + << "build data is " << data_der_order << "\n" + << "You need to supply gradients of the output in order to " + << "construct a\nGradient Enhanced Kriging (GEK) Model." + << std::endl; + assert(false); + } + } + else{ + std::cerr << "derivative_order=" << buildDerOrder + << " in the nkm::KrigingModel constructor.\n" + << "For Kriging you must use derivative_order=0.\n" + << "For Gradient Enhanced Kriging (GEK) you must use " + << "derivative_order=1.\nHigher order derivative " + << "enhanced Kriging (e.g. Hessian Enhanced Kriging)\n" + << "has not been implemented." << std::endl; + assert(false); + } + + // ************************************************************* + // detect an anchor point if present this is the one point that + // we make sure that the equationSelectingCholR does not discard + // ************************************************************* + iAnchorPoint=0; + ifHaveAnchorPoint=false; + param_it = params.find("anchor_index"); + if (param_it != params.end() && param_it->second.size() > 0) { + ifHaveAnchorPoint=true; + //printf("nkm::KrigingModel() sees an anchor point\n"); + //fflush(stdout); + iAnchorPoint=std::atoi(param_it->second.c_str()); + //printf("iAnchorPoint=%d\n",iAnchorPoint); + //fflush(stdout); + if(!((0<=iAnchorPoint)&&(iAnchorPointsecond.size() > 0) { + if_user_specified_lower_bounds=true; + if(min_max_xr.putCols(param_it->second,0)) { + std::cerr << "You didn't enter the right number of lower bounds" + << std::endl; + assert(false); + } + } + + bool if_user_specified_upper_bounds=false; + param_it = params.find("upper_bounds"); + if (param_it != params.end() && param_it->second.size() > 0) { + if_user_specified_upper_bounds=true; + if(min_max_xr.putCols(param_it->second,1)) { + std::cerr << "You didn't enter the right number of upper bounds" + << std::endl; + assert(false); + } + } + + if(!(if_user_specified_lower_bounds==if_user_specified_upper_bounds)) { + std::cerr << "Your options are to\n(A) specify both the upper and lower, or\n(B) specify neither the upper nor lower,\nbounds of the domain of the Kriging Model\n"; + assert(false); + } + + if(if_user_specified_lower_bounds==true) { + for(int ixr=0; ixrsecond.size() > 0) { + MtxInt dim_groups(numVarsr,1); + if(dim_groups.putCols(param_it->second,0)) { + std::cerr << "If you specify dimension_groups for any dimensions, " + << "you must specify groups\nfor all dimensions. If you " + << "don't want some of the dimensions to be grouped\n" + << "with other dimensions during scaling, give each of " + << "them their own group." << std::endl; + assert(false); + } + sdBuild.setDimGroups(dim_groups); + } + + scaler.scaleToDefault(); //scale outputs to -0.5<=Y<=0.5 and scale + //real inputs to volume 1 hyper-rectangle centered at 0 if real + //input dimensions are locked or the unit hypercube centered at 0 if + //no dimensions are locked. The scaling is done to let us define + //the feasible region simply (region is defined in create); + + if(buildDerOrder==0) { + sdBuild.getY(Yall); + Yall.reshape(numPoints,1); + } + else if(buildDerOrder==1) { + sdBuild.getUpToDerY(Yall,1); + Yall.reshape(numEqnAvail,1); + //Yall is now a column vector that contains + //[y0, dy_0/dxr_0, ..., dy_0/dxr_{numVarsr-1}, y1, dy_1/dxr_0, ..., y2, ... + // y_{numPoints-1}, dy_{numPoints-1}/dxr_0, ..., + // dy_{numPoints-1}/dx_{numVarsr-1}]^T + } + + // ************************************************************* + // this starts the input section about optimizing or directly + // specifying correlation lengths, it must come after the + // scaling section + // ************************************************************* + + // current options are none (fixed correl) | sampling (guess) | local | + // global | global_local + optimizationMethod = "global"; //the default + //optimizationMethod = "none"; //the default + param_it = params.find("optimization_method"); + if (param_it != params.end() && param_it->second.size() > 0) + optimizationMethod = param_it->second; + + if(optimizationMethod.compare("none")==0) + maxTrials=1; + else if(optimizationMethod.compare("local")==0) + maxTrials=20; + else if(optimizationMethod.compare("sampling")==0) + maxTrials=2*numVarsr+1; + else if(optimizationMethod.compare("global")==0) + maxTrials = 10000; + else if(optimizationMethod.compare("global_local")==0) { + maxTrials = 10000; //ensure it has non-zero as a fail safe but this + //shouldn't be used + maxTrialsGlobal = 500; + maxTrialsLocal = 20; + } + else{ //error checking the input + std::cerr << "KrigingModel() unknown optimization_method [" << optimizationMethod << "] aborting\n"; + assert(false); + } + + //std::cout << "optimization_method=\"" << optimizationMethod << "\"\n"; + + //numStarts is the number of starting locations in a multi-start local search + numStarts=1; //default is a single starting location + param_it = params.find("num_starts"); + if (param_it != params.end() && param_it->second.size() > 0) { + numStarts = std::atoi(param_it->second.c_str()); + if(numStarts<1) { + std::cerr << "You can't specify fewer than one starting location " + << "for the optimization\nof correlation lenghts" + << std::endl; + assert(false); + } + } + + if(!((numStarts==1)||(optimizationMethod.compare("local")==0))) { + std::cerr << "Local optimization is the only optimization method for Kriging that uses the \"num_starts\" key word. Check your input file for errors.\n"; + assert(false); + } + + //std::cout << "num_starts=" << numStarts << "\n"; + + + // does the user want to specify correlation lengths directly? + ifUserSpecifiedCorrLengths=false; //the default is no + param_it = params.find("correlation_lengths"); + if (param_it != params.end() && param_it->second.size() > 0) { + ifUserSpecifiedCorrLengths=true; + //printf("User specifying correlation lengths\n"); fflush(stdout); + + // make sure that the user didn't + // * say they want to global optimize __AND__ + // * specify correlation lengths + if(optimizationMethod.compare("global")==0) { + std::cerr << "You can't both \n (A) use the global optimization method to choose, and \n (B) directly specify \n correlation lengths for the Kriging model.\n"; + assert(false); + } + else if(optimizationMethod.compare("global_local")==0) { + //they can't coarse global followed by local either + std::cerr << "You can't both \n (A) use the coarse global polished by local optimization method to choose, and \n (B) directly specify \n correlation lengths for the Kriging model.\n"; + assert(false); + } + else if(optimizationMethod.compare("sampling")==0) { + // this is only the default number of samples/maxTrials; the user can + // still overide this below + maxTrials+=1; + } + + natLogCorrLen.newSize(numVarsr,1); //allocate space + + //read the correlation lengths in from the string + if(natLogCorrLen.putCols(param_it->second,0)) { + std::cerr << "The specified correlation lengths had the wrong " + << "number of input dimensions." << std::endl; + assert(false); + } + // "natLogCorrLen" currently holds the unscaled correlation LENGTHS, not + // the natural log of the scaled correlation length, we need to fix that + // but first we need to check the input for errors + for(int ixr=0; ixr0.0)) { + std::cerr << "For the Kriging Model, correlation lengths must be strictly positive\n."; + assert(false); + } + + //printf("unscaled corr lens = [%12.6g",natLogCorrLen(0,0)); + //for(int ixr=1; ixrsecond.size() > 0) { + maxTrials = std::atoi(param_it->second.c_str()); + } + + if(!(maxTrials > 0)) { + std::cerr << "You can't specify a maximum number of trials that is " + << "less than or equal\nto zero." << std::endl; + assert(false); + } + + //printf("maxTrials=%d\n",maxTrials); + + + // ************************************************************* + // this starts the input section about the trend function + // ************************************************************* + polyOrderRequested = 2; + ifReducedPoly=false; + param_it = params.find("order"); + if (param_it != params.end() && param_it->second.size() > 0) { + polyOrderRequested = std::atoi(param_it->second.c_str()); + //ssstd::cerr << "polyOrderRequested=" << polyOrderRequested << std::endl; + if(!(polyOrderRequested >= 0)) { + std::cerr << "You can't use a trend function with a polynomial " + << "order less than zero." << std::endl; + assert(false); + } + } + else{ + //if they don't specify a polynomial order use a main effects + //polynomial with order 2 for the trend function, (if they do + //specify a polynomial order assume they mean a full polynomial + //order unless they specify that it's a reduced_polynomial) + ifReducedPoly=true; + } + numTrend.newSize(polyOrderRequested+1,1); + + //cout << "order=" << polyOrder << "\n"; + + //polyOrder = 2; //for debug + //main_effects_poly_power(Poly, numVarsr, polyOrder); //for debug + //commented out for debug + + param_it = params.find("reduced_polynomial"); + if (param_it != params.end() && param_it->second.size() > 0) + if((std::atoi(param_it->second.c_str()))!=0) + ifReducedPoly=true; + + //cout << "ifReducedPoly=" << ifReducedPoly << "\n"; + + if(ifReducedPoly) { + for(polyOrder=0; polyOrder<=polyOrderRequested; ++polyOrder) + numTrend(polyOrder,0)=polyOrder*numVarsr+1; + main_effects_poly_power(Poly, numVarsr, polyOrderRequested); + } + else{ + for(polyOrder=0; polyOrder<=polyOrderRequested; ++polyOrder) + numTrend(polyOrder,0)=num_multi_dim_poly_coef(numVarsr, polyOrder); + multi_dim_poly_power(Poly, numVarsr, polyOrderRequested); + } + + + // ******************************************************************** + // this starts the section about the choice of correlation functions + // need to do build derivative order before this + // ******************************************************************** + corrFunc=DEFAULT_CORR_FUNC; + + //POW_EXP_CORR_FUNC + powExpCorrFuncPow=0.0; //only 1.0<=powExpCorrFunc<=2.0 are allowed + //later if corrFunc==POW_EXP_CORR_FUNC and powExpCorrFuncPow==0.0 we know + //we have an error + param_it = params.find("powered_exponential"); + if(param_it != params.end() && param_it->second.size() > 0) { + if(corrFunc!=DEFAULT_CORR_FUNC) { + std::cerr << "You can only specify one correlation function\n"; + assert(false); + } + corrFunc=POW_EXP_CORR_FUNC; + powExpCorrFuncPow=std::atof(param_it->second.c_str()); + if(!((1.0<=powExpCorrFuncPow)&&(powExpCorrFuncPow<=2.0))){ + std::cerr << "The powered exponential correlation function must have 1.0<=power<=2.0\n"; + assert(false); + } + //need to require 1second.size() > 0) { + if(corrFunc!=DEFAULT_CORR_FUNC) { + std::cerr << "You can only specify one correlation function\n"; + assert(false); + } + if(param_it->second.compare("infinity")==0) { + corrFunc=GAUSSIAN_CORR_FUNC; + //matern nu=infinty is the Gaussian correlation function + } + else{ + corrFunc=MATERN_CORR_FUNC; + maternCorrFuncNu=std::atof(param_it->second.c_str()); + if(!((maternCorrFuncNu==0.5)||(maternCorrFuncNu==1.5)|| + (maternCorrFuncNu==2.5))) { + //could allow more later if 3rd+ order derivatives are enabled later + std::cerr << "For the Matern correlation function the only allowed values for nu are 0.5, 1.5, 2.5, and infinity\n"; + assert(false); + } + if(maternCorrFuncNu==0.5) { + corrFunc=EXP_CORR_FUNC; //matern nu=0.5 is the exponential correlation function + //need to disallow maternCorrFuncNu=0.5 if gradients or higher order derivatives are used to construct the Kriging model + } + //need to disallow maternCorrFuncNu=1.5 it hessians or higher order derivatives are used to construct the Kriging model + } + } + + if(corrFunc==DEFAULT_CORR_FUNC) + corrFunc=GAUSSIAN_CORR_FUNC; + + // ************************************************************* + // this starts the input section HOW to bound the condition + // number, this determines which derivatives of the constraint + // function can be computed analytically so handle that here too + // ************************************************************* + //constraintType="rcond"; //rcond is now the only option for type of + //constraint against ill conditioning + numConFunc=1; + + //convert to the Dakota bitflag convention for derivative orders + int num_analytic_obj_ders_in=0; //analytical derivatives have been removed + int num_analytic_con_ders_in=0; //analytical derivatives have been removed + maxObjDerMode=(static_cast(std::pow(2.0,num_analytic_obj_ders_in+1)))-1; //analytical gradients of objective function + maxConDerMode=(static_cast (std::pow(2.0,num_analytic_con_ders_in+1)))-1; //analytical gradients of constraint function(s) + + maxCondNum=std::pow(1024.0,4); + + // ************************************************************* + // this starts the input section about the nugget which can be + // used to smooth the data and also decrease the condition + // number + // ************************************************************* + + ifChooseNug = false; + //ifChooseNug = true; + ifAssumeRcondZero=false; + param_it = params.find("find_nugget"); + if (param_it != params.end() && param_it->second.size() > 0) { + ifChooseNug = true; + int zero_or_one = std::atoi(param_it->second.c_str()); + if(zero_or_one==0) + ifAssumeRcondZero=true; + } + //ifChooseNug = true ; std::cout << "ifChooseNug=" << ifChooseNug << "\n"; + + // fixed value for now + nug = 0.0; //default + ifPrescribedNug=false; + param_it = params.find("nugget"); + if (param_it != params.end() && param_it->second.size() > 0) { + if(!(ifChooseNug==false)) { + std::cerr << "You can do at most 1 of the following (A) auto-select " + << "the nugget\n(approximately the minimum needed to " + << "satisfy the condition number bound)\n(B) directly " + << "specify a nugget. The default is not to use a nugget " + << "at all\n(i.e. use a nugget of zero)." << std::endl; + assert(false); + } + nug = std::atof(param_it->second.c_str()); + if(!(nug >= 0.0)) { + std::cerr << "The nugget must be greater than or equal to zero." + << std::endl; + assert(false); + } + ifPrescribedNug=true; + } + + // ************************************************************* + // this ends the input parsing now finish up the prep work + // ************************************************************* + preAllocateMaxMemory(); //so we don't have to constantly dynamically + //allocate, the SurfMat class can use a subset of the allocated memory + //without using dynamic reallocation + + // precompute and store the trend function for all build points + if(buildDerOrder==0) //for Kriging + eval_trend_fn(Gall, XR); + else if(buildDerOrder>=1) { //for GEK + //actually this is generic to higher order derivative enhanced Kriging + //(e.g. Hessian Enhanced Kriging) provided that Der is appropriately + //defined + eval_der_trend_fn(Gall, Der, XR); + } else{ + std::cerr << "bogus buildDerOrder=" << buildDerOrder + << " in the constructor when evaluating Gall" << std::endl; + assert(false); + } + + if((ifChooseNug==true)||(ifPrescribedNug==true)) { + //if we're using a nugget then we aren't using pivoted cholesky to + //select an optimal subset of points, that means that the order of + //points aren't going to change so we'll set Y and Gtran to what + //we know they need to be + iPtsKeep.newSize(numPoints,1); + for(int ipt=0; ipt= NORMAL_OUTPUT) { + std::cout << model_summary_string(); + //std::cout << std::endl; + } + + + //variables whose values needed to be retained between sequential call to masterObjectiveAndConstraints for precompute and store strategy to work + prevObjDerMode=prevConDerMode=0; + + //deallocate matrices we no longer need after emulator has been created + //these were made member variables (instead of local variables) to avoid + //the cost of dynamic allocation and deallocation each cycle of the + //optimization of the correlation parameters + scaleRChol.clear(); //matrix + sumAbsColR.clear(); //vector + oneNormR.clear(); //vector + lapackRcondR.clear(); //vector + rcondDblWork.clear(); //vector + rcondIntWork.clear(); //vector + Yall.clear(); //vector + Gall.clear(); //matrix + Gtran.clear(); //matrix + iTrendKeep.clear(); //vector + Z.clear(); //matrix + Ztran_theta.clear(); //vector + deltaXR.clear(); //matrix + R.clear(); //matrix + G_Rinv_Gtran.clear(); //matrix + G_Rinv_Gtran_Chol_Scale.clear(); //vector + G_Rinv_Gtran_Chol_DblWork.clear(); //vector + G_Rinv_Gtran_Chol_IntWork.clear(); //vector + G_Rinv_Y.clear(); //vector + eps.clear(); //vector + prevTheta.clear(); //vector + con.clear(); //vector +} + +std::string KrigingModel::get_corr_func() const { + std::ostringstream oss; + + switch(corrFunc) { + case GAUSSIAN_CORR_FUNC: + oss << "Gaussian"; + break; + case EXP_CORR_FUNC: + oss << "exponential"; + break; + case POW_EXP_CORR_FUNC: + oss << "powered exponential with power=" << powExpCorrFuncPow; + break; + case MATERN_CORR_FUNC: + oss << "Matern " << static_cast(maternCorrFuncNu*2.0) << "/2"; + break; + default: + std::cerr << "unknown correlation function enumerated as " << corrFunc + << std::endl; + assert(false); + } + return (oss.str()); +} + + +std::string KrigingModel::model_summary_string() const { + MtxDbl temp_out_corr_lengths(numVarsr,1); + get_corr_len_from_theta(temp_out_corr_lengths,correlations); + scaler.unScaleXrDist(temp_out_corr_lengths); + + //printf("numPoints=%d numTrend=%d numPointsKeep=%d numWholePointsKeep=%d numExtraDerKeep=%d\n",numPoints,numTrend(polyOrder,0),numPointsKeep,numWholePointsKeep,numExtraDerKeep); + + std::ostringstream oss; + oss << "--- Surfpack Kriging Diagnostics ---\n"; + if(buildDerOrder==0) + oss << "KM: #real inputs=" << numVarsr << "; #pts=" << numPoints + << "; used " << numPointsKeep << "/" << numPoints << " pts;\n"; + else if(buildDerOrder==1) + oss << "GEK: #real inputs=" << numVarsr << "; #pts=" << numPoints + << "; #eqns=" << numEqnAvail << "; used " + << numRowsR << "/" << numEqnAvail << " eqns;\n"; + else{ + oss << "error std::string KrigingModel::model_summary_string() const\n" + << "buildDerOrder=" << buildDerOrder << "; it should be 0 for Kriging" + << " or 1 for Gradient Enhanced Kriging (GEK);" + << " the model_summary_string() function will need to be modified " + << "to handle other build derivative orders.\n"; + } + oss << "using the "; + if(corrFunc==GAUSSIAN_CORR_FUNC) + oss << "Gaussian"; + else if(corrFunc==EXP_CORR_FUNC) + oss << "exponential"; + else if(corrFunc==POW_EXP_CORR_FUNC) + oss << "powered exponential (with power = " << powExpCorrFuncPow << ")"; + else if(corrFunc==MATERN_CORR_FUNC) + oss << "Matern " << maternCorrFuncNu; + else{ + std::cerr << "unknown corr func in model_summary_string()" << std::endl; + assert(false); + } + oss << " correlation function with (unscaled)\n" + << "Correlation lengths=[" << temp_out_corr_lengths(0,0); + for(int ixr=1; ixr1) { + if(ifReducedPoly==true) + oss << "reduced_"; + else oss <<"full "; + } + oss << "polynomial\nof order " << polyOrderRequested << " (with " + << numTrend(polyOrderRequested,0) << " terms) was requested " + << "for the trend function; the build\ndata was "; + if(nTrend1) + oss << "^" << Poly(ixr,itrend); + } + if(itrend=0.0) + oss << "+ "; + if(nterm_on_this_line==3) { + oss << "...\n "; + nterm_on_this_line=0; + } + } + } + oss << "\n------------------------------------\n"; + return (oss.str()); +} + +void KrigingModel::preAllocateMaxMemory() { + //this preallocates the maximum sizce of arrays whose size depends on how many equations were discarded by pivoted Cholesky and they could possibly be allocated to a different size than their maximum the first time they are allocated. + + nTrend=numTrend(polyOrderRequested,0); + Y.newSize(numEqnAvail,1); + Gtran.newSize(numEqnAvail,nTrend); + Rinv_Gtran.newSize(numEqnAvail,nTrend); + G_Rinv_Gtran.newSize(nTrend,nTrend); + G_Rinv_Gtran_Chol.newSize(nTrend,nTrend); + rhs.newSize(numEqnAvail,1); + betaHat.newSize(nTrend,1); + G_Rinv_Y.newSize(nTrend,1); + eps.newSize(numEqnAvail,1); + iPtsKeep.newSize(numPoints,1); + RChol.newSize(numEqnAvail,numEqnAvail); + int nrows = nTrend; + if((ifChooseNug==false)&&(ifPrescribedNug==false)&&(numEqnAvail>nTrend)) + nrows=numEqnAvail; + scaleRChol.newSize(nrows,3); + lapackRcondR.newSize(nrows,1); + + return; +} + +// BMA TODO: combine these two functions? + +/// evaluate (y) the Kriging Model at a single point (xr) +double KrigingModel::evaluate(const MtxDbl& xr) +{ + if(buildDerOrder==0) { + //you wouldn't want to do this for Gradient Enhanced Kriging + //i.e. if gradients of y were used as inputs + double singular_y; + if(scaler.isYSingular(0,singular_y)) + return singular_y; + } + + //assert( (numVarsr == xr.getNCols()) && (xr.getNRows() == 1) ); + MtxDbl g(nTrend,1), r(numRowsR,1); + + /* + printf("double evaluate()\n"); + printf("xr=[%20.14g", xr(0,0)); + for(int ixr=1; ixr y = betaHat^T*g + matrix_mult(y, betaHat, g, 0.0, 1.0,'T','N'); + + //y=1.0*y+1.0*r*rhs where rhs=R^-1*(Y-G(XR)^T*betaHat), initial y=betaHat^T*g => y=betaHat^T*g+rhs^T*r + matrix_mult(y, rhs , r, 1.0, 1.0,'T','N'); + + scaler.unScaleYOther(y); + + //printf("y is correct for ValidateMain because it isn't being unscaled\n"); + + return y; +} + +MtxDbl& KrigingModel::evaluate_d1y(MtxDbl& d1y, const MtxDbl& xr) +{ + int nptsxr=xr.getNCols(); +#ifdef __KRIG_ERR_CHECK__ + assert((numVarsr == xr.getNRows())&&(00) + break; + //printf("ixr=%d ",ixr); +#ifdef __KRIG_ERR_CHECK__ + assert(ixr==ider); +#endif + + double d1y_unscale_factor=scaler.unScaleFactorDerY(ixr); + //printf("d1y_usf=%g\n",d1y_unscale_factor); + + dcorrelation_matrix_dxI(d1r, r, xr_scaled, ixr); + matrix_mult(temp_vec,rhs,d1r,0.0,1.0,'T'); + + for(int ipt=0; ipt0.0)) { + //printf("adj_var=%g unscaled_unadj_var=%g rcondR=%g\n",adj_var,unscaled_unadj_var,rcondR); + //fflush(stdout); + //} + adj_var=std::fabs(adj_var); //hack to handle "negative zero" variance (numerical precision round off error) + if(adj_var<0.0) { + printf("NKM setting adj_var to zero adj_var=%g unadj_var=%g rcondR=%g\n",adj_var,unscaled_unadj_var,rcondR); + adj_var=0.0; + } + else if(adj_var==0.0) + printf("NKM adj_var is zero =%g\n",adj_var); + else if(!(adj_var>=0.0)) + printf("double NKM_KrigingModel::eval_variance(...) adj_var=nan rcondR=%g\n",rcondR); + + return adj_var; +} + +/** Evaluate the adjusted variance for a collection of points using matrix + ops (i.e. BLAS and LAPACK) as much as possible) + adj_var=unadjvar* + (1-r^T*R^-1*r+(g-G*R^-1*r)^T*(G*R^-1*G^T)^-1*(g-G*R^-1*r)) + on a point by point basis */ +MtxDbl& KrigingModel:: eval_variance(MtxDbl& adj_var, const MtxDbl& xr) +{ +#ifdef __KRIG_ERR_CHECK__ + assert(numVarsr==xr.getNRows()); +#endif + int nptsxr=xr.getNCols(); + adj_var.newSize(1,nptsxr); + MtxDbl g_minus_G_Rinv_r(nTrend,nptsxr), r(numRowsR,nptsxr); + + double unscaled_unadj_var=estVarianceMLE; + if(scaler.isUnScaled()) { + eval_trend_fn(g_minus_G_Rinv_r, xr); + correlation_matrix(r, xr); + } + else{ + unscaled_unadj_var*=scaler.unScaleFactorVarY(); + MtxDbl xr_scaled(xr); + scaler.scaleXrOther(xr_scaled); + eval_trend_fn(g_minus_G_Rinv_r, xr_scaled); + correlation_matrix(r, xr_scaled); + } + //right now g_minus_G_Rinv_r actually holds g + + MtxDbl Rinv_r(numRowsR,nptsxr); + MtxDbl G_Rinv_Gtran_inv_g_minus_G_Rinv_r(nTrend,nptsxr); + + solve_after_Chol_fact(Rinv_r,RChol,r); + matrix_mult(g_minus_G_Rinv_r,Rinv_Gtran,r,1.0,-1.0,'T','N'); + //g_minus_G_Rinv_r now holds g-G*R^-1*r (i.e. it's name is correct) + + solve_after_Chol_fact(G_Rinv_Gtran_inv_g_minus_G_Rinv_r, + G_Rinv_Gtran_Chol,g_minus_G_Rinv_r); + + for(int ipt=0; ipt=0.0)) + printf("MtxDbl& NKM_KrigingModel::eval_variance(...) adj_var(%d)=nan rcondR=%g\n",ipt,rcondR); + } + + return adj_var; +} + +/** set R=(R+nug*I), where the original R is the correlation matrix for the + data that the model is built from. For GEK this generalizes to + R(i,i)=R(i,i)*(1+nug); Modifying the correlation matrix by the inclusion + of a nugget causes the KrigingModel to smooth the data, i.e. approximate + it rather than interpolate it (which is good if you know how big your + measurement noise is), it can also be used to fix an ill conditioned + correlation matrix. The convention is that capital matrices are for + data the model is built from, lower case matrices are for arbitrary + points to evaluate the model at */ +void KrigingModel::apply_nugget_build() { + if(!(nug>0.0)) return; + //printf("applying nugget=%22.16g\n",nug); + + int nrowsR=R.getNRows(); +#ifdef __KRIG_ERR_CHECK__ + assert(nrowsR==R.getNCols()); +#endif + + double one_plus_nug=1.0+nug; + for(int i=0; inumWholePointsKeep) { + //since there's part of another point left and we know that + //there is only one derivative it means that were missing that + //derivative and only have the function value +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)&& + (i==numRowsR-1)); +#endif + deltax=(xr(0,j)-XRreorder(0,ipt)); + r(i,j)=std::exp(-theta*deltax*deltax); + } + } + } else{ //there is more than 1 dimensions and more than one + //evaluation point + for(j=0; jnumWholePointsKeep) { + //the last XR point isn't a "whole point" we dropped some derivatives + //out of its gradient to meet the bound on rcond, numExtraDerKeep + //is the number of derivatives kept for the last point. The + //derivatives of the last point have NOT been reordered, they appear + //in the same order as the input variables +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + //printf("deltax=xr(0,%d)-XRreorder(0,%d);\n",j,ipt); + deltax=xr(0,j)-XRreorder(0,ipt); + krig_r=-correlations(0,0)*deltax*deltax; //=- is correct + for(k=1; knumWholePointsKeep) { + //since there's part of another point left and we know that + //there is only one derivative it means that were missing that + //derivative and only have the function value +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)&& + (i==numRowsR-1)); +#endif + theta_abs_dx=theta*std::fabs(xr(0,j)-XRreorder(0,ipt)); + r(i,j)=(1.0+theta_abs_dx)*std::exp(-theta_abs_dx); //1D correlation + //function + } + } + } + else{ //there is more than 1 dimension + double matern_coef, matern_coef_prod, sum_neg_theta_abs_dx; + for(j=0; jnumWholePointsKeep) { + //the last XR point isn't a "whole point" we dropped some derivatives + //out of its gradient to meet the bound on rcond, numExtraDerKeep + //is the number of derivatives kept for the last point. The + //derivatives of the last point have NOT been reordered, they appear + //in the same order as the input variables +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + theta_abs_dx=correlations(0,0)*std::fabs(xr(0,j)-XRreorder(0,ipt)); + matern_coef_prod=1.0+theta_abs_dx; + sum_neg_theta_abs_dx=-theta_abs_dx; //=- is correct + for(k=1; knumWholePointsKeep) { + //since there's part of another point left and we know that + //there is only one derivative it means that were missing that + //derivative and only have the function value +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)&& + (i==numRowsR-1)); +#endif + theta_abs_dx=theta*std::fabs(xr(0,j)-XRreorder(0,ipt)); + r(i ,j)=(1.0+theta_abs_dx+theta_abs_dx*theta_abs_dx*one_third)* + std::exp(-theta_abs_dx); //1D correlation function + } + } + } + else{ //there is more than 1 dimension + double matern_coef, matern_coef_prod, sum_neg_theta_abs_dx; + for(j=0; jnumWholePointsKeep) { + //the last XR point isn't a "whole point" we dropped some derivatives + //out of its gradient to meet the bound on rcond, numExtraDerKeep + //is the number of derivatives kept for the last point. The + //derivatives of the last point have NOT been reordered, they appear + //in the same order as the input variables +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + theta_abs_dx=correlations(0,0)*std::fabs(xr(0,j)-XRreorder(0,ipt)); + matern_coef_prod=1.0+theta_abs_dx+theta_abs_dx*theta_abs_dx*one_third; + sum_neg_theta_abs_dx=-theta_abs_dx; //=- is correct + for(k=1; knumWholePointsKeep) { + //ipt and i should be what we need them to be +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + neg_two_theta_dx=two_theta*(XRreorder(Ider,ipt)-xr(Ider,j)); + dr(i,j)=r(i,j)*neg_two_theta_dx; + for(k=0; knumWholePointsKeep) { + //ipt and i should be what we need them to be +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + deltax=(xr(Ider,j)-XRreorder(Ider,ipt)); + matern_coef=1.0+theta*std::fabs(deltax); + matern_d1_mult_r=neg_theta_squared*deltax/matern_coef; + dr(i ,j)=r(i,j)*matern_d1_mult_r; + for(k=0; knumWholePointsKeep) { + //ipt and i should be what we need them to be +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + deltax=xr(Ider,j)-XRreorder(Ider,ipt); + theta_abs_dx=theta*std::fabs(deltax); + theta_squared_div_3_matern_coef=theta_squared/ + (3.0*(1.0+theta_abs_dx)+theta_abs_dx*theta_abs_dx); + matern_d1_mult_r=-theta_squared_div_3_matern_coef* + deltax*(1.0+theta_abs_dx); + dr(i ,j)=r(i,j)*matern_d1_mult_r; + for(k=0; knumWholePointsKeep) { + //ipt and i should already have the values we need them to +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + deltax=xr(Jder,j)-XRreorder(Jder,ipt); + thetaJ_abs_dx=thetaJ*std::fabs(deltax); + matern_coef=(1.0+thetaJ_abs_dx); + d2_mult_r=thetaJ_squared*(thetaJ_abs_dx-1.0)/matern_coef; + d2r(i,j)=r(i,j)*d2_mult_r; + for(k=0; knumWholePointsKeep) { + //ipt and i should already have the values we need them to +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + deltax=xr(Jder,j)-XRreorder(Jder,ipt); + thetaJ_abs_dx=thetaJ*std::fabs(deltax); + matern_coef=1.0+thetaJ_abs_dx; + d1_mult_r=-thetaJ_squared*deltax/matern_coef; + d2r(i,j)=drI(i,j)*d1_mult_r; + for(k=0; knumWholePointsKeep) { + //ipt and i should already have the values we need them to +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + deltax=xr(Jder,j)-XRreorder(Jder,ipt); + thetaJ_abs_dx=thetaJ*std::fabs(deltax); + neg_thetaJ_squared_div_3_matern_coef=-thetaJ_squared/ + (3.0*(1.0+thetaJ_abs_dx)+thetaJ_abs_dx*thetaJ_abs_dx); + d2_mult_r=neg_thetaJ_squared_div_3_matern_coef* + (1.0+thetaJ_abs_dx-thetaJ_abs_dx*thetaJ_abs_dx); + d2r(i,j)=r(i,j)*d2_mult_r; + for(k=0; knumWholePointsKeep) { + //ipt and i should already have the values we need them to +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (ipt==numPointsKeep-1)&& + (i==neqn_per_pt*numWholePointsKeep)); +#endif + deltax=xr(Jder,j)-XRreorder(Jder,ipt); + thetaJ_abs_dx=thetaJ*std::fabs(deltax); + thetaJ_squared_div_3_matern_coef=thetaJ_squared/ + (3.0*(1.0+thetaJ_abs_dx)+thetaJ_abs_dx*thetaJ_abs_dx); + d1_mult_r=-thetaJ_squared_div_3_matern_coef* + deltax*(1.0+thetaJ_abs_dx); + d2r(i,j)=drI(i,j)*d1_mult_r; + for(k=0; k0) { + //Gaussian Matern1.5 and Matern2.5 are valid correlation functions for + //Gradient Enhanced Kriging + double temp_double; + int zij, j; + + + if(corrFunc==GAUSSIAN_CORR_FUNC) { + //now handle the first order derivative submatrices, indiviually the first + //order derivative SUBmatrices are anti-symmetric but the whole matrix is + //symmetric + int Ii, Ij, Jj, Ji; //first letter identifies index OF derivative submatrix + //second letter identifies index INTO derivative SUBmatrix + for(int Ider=0; Ider0) { + //deltaXR is only needed for GEK + deltaXR.newSize(ncolsZ,numVarsr); //this ordering (transpose of Z) + //is useful for constructing the GEK R matrix + } + + int ij=0; + if(corrFunc==GAUSSIAN_CORR_FUNC) { + // **************************************************************** + // The Gausssian Correlation Function + // can be used for Gradient Enhanced Kriging (GEK) + // (or more generally, for derivative enhanced Kriging) because + // it is C infinity continuous. + // It uses Z(k,ij) = -(XR(k,i)-XR(k,j))^2 + // if GEK is used we will also compute and store + // deltaXR(ij,k) = XR(k,i)-XR(k,j), the order of indexes is correct + // this transposed ordering is useful for efficient computation of + // the GEK R matrix (using the SUBmatrix construction process) + // **************************************************************** + double dXR; //a temporary variable to make squaring easier + if(buildDerOrder>0) + for(int j=0; j0) { + if(corrFunc==EXP_CORR_FUNC) { + std::cerr << "the exponential correlation function is not a valid choice for Gradient Enhanced Kriging\n"; + assert(!((corrFunc==EXP_CORR_FUNC)&&(buildDerOrder>0))); + } + for(int j=0; j0) { + std::cerr << "the powered exponential correlation function is not a valid choice for Gradient Enhanced Kriging\n"; + assert(!((corrFunc==POW_EXP_CORR_FUNC)&&(buildDerOrder>0))); + } + for(int j=0; j(numEqnAvail); + double sqrt_num_eqn=std::sqrt(dbl_num_eqn); + min_allowed_rcond*=sqrt_num_eqn; //one norm is within a factor of N^0.5 + //of 2 norm + rcondR/=sqrt_num_eqn; //one norm is within a factor of N^0.5 of 2 norm + double min_eig_worst=(rcondR*dbl_num_eqn)/(1.0+(dbl_num_eqn-1.0)*rcondR); + double max_eig_worst=dbl_num_eqn-(dbl_num_eqn-1.0)*min_eig_worst; + nug=(min_allowed_rcond*max_eig_worst-min_eig_worst)/ + (1.0-min_allowed_rcond); + //this nugget will make the worst case scenario meet (with an ==) + //the maxCondNum constraint, I (KRD) don't expect this to + //ever == fail because I don't expect rcond to be *N^-0.5 without + //nugget and be *N^0.5 with nugget while the maximum eigen value + //of R (without nugget) is N-(N-1)*min_eigval (that comes from + //assumming all eigenvalues except the largest are the smallest + //possible for the given rcond) note that rcond is the LAPACK + //ESTIMATE of the 1 norm condition number so there are no 100% + //guarantees. + apply_nugget_build(); //multiply the diagonal elements by (1.0+nug) + reorderCopyRtoRChol(); + + Chol_fact_workspace(RChol,scaleRChol,rcondDblWork,rcondIntWork, + chol_info,rcondR); + } + return; +} + + +/* use Pivoted Cholesky to efficiently select an optimal subset + of available build points from which to construct the Gaussian + Process. Here "optimal" means that, given the current set of + assumed correlation parameters, this subset maximizes the + amount of unique information content in R, note that this is + equivalent to a "best spaced" (for the chosen correlation + function and its parameters) set of points and the output at + those points does is not considered. Thus if you have 2 points + that are very close together but on opposite sides of a + discontinutity it is highly likely that at least one of them + will get discarded */ +void KrigingModel::equationSelectingCholR(){ + if(!((buildDerOrder==0)||(buildDerOrder==1))) { + std::cerr << "buildDerOrder=" << buildDerOrder + << " in void KrigingModel::equationSelectingCholR(). " + << "For Kriging buildDerOrder must equal 0. " + << "For Gradient Enhanced Kriging (GEK) buildDerOrder " + << "must equal 1. Higher order derivative enhanced " + << "Kriging (e.g. Hessian Enhanced Kriging) has not " + << "been implemented." << std::endl; + assert(false); + } + + //polyOrder=polyOrderRequested; + nTrend=numTrend(polyOrderRequested,0); + Rinv_Gtran.newSize(numEqnAvail,nTrend); + + + //printf("Entered equationSelectingCholR()\n"); + double min_allowed_rcond=1.0/maxCondNum; + //printf("min_allowed_rcond=%g\n",min_allowed_rcond); + //exit(0); + //double min_allowed_pivot_est_rcond=256.0/maxCondNum; + + int ld_RChol=RChol.getNRowsAct(); + //printf("ld_RChol=%d\n",ld_RChol); + int chol_info; + RChol.newSize(numPoints,numPoints); + scaleRChol.newSize(numEqnAvail,3); //maximum space needed + rcondDblWork.newSize(3*ld_RChol,1); + rcondIntWork.newSize(ld_RChol,1); + ld_RChol=RChol.getNRowsAct(); + + iPtsKeep.newSize(numPoints,1); + //assign the default order to points + for(int ipt=0; ipt + (inext_lapack_rcondR-iprev_lapack_rcondR)) + /std::log(2.0)); + while((lapackRcondR(inext_lapack_rcondR,0)<=min_allowed_rcond)&& + (inext_lapack_rcondR>iprev_lapack_rcondR)) { + //printf("inWhile\n"); + ++rcond_iter; + icurr_lapack_rcondR=(iprev_lapack_rcondR+inext_lapack_rcondR)/2; + num_eqn_keep=icurr_lapack_rcondR+1; + + //the LAPACK rcond function + DPOCON_F77(&uplo,&num_eqn_keep,RChol.ptr(0,0),&ld_RChol, + oneNormR.ptr(icurr_lapack_rcondR,0), + &rcondR,rcondDblWork.ptr(0,0),rcondIntWork.ptr(0,0), + &info); + lapackRcondR(icurr_lapack_rcondR,0)=rcondR; + //printf("rcond_iter=%d icurr_lapack_rcondR=%d rcondR=%g\n", + //rcond_iter,icurr_lapack_rcondR,rcondR); + + if(rcondR=10) { + printf("RChol(1:10,1:10)=\n"); + for(int i=0; i<10; ++i) { + for(int j=0; j<10; ++j) + printf("%12.6g ",RChol(i,j)); + printf("\n"); + } + printf("\n\n"); + } + */ + + //polyOrder=polyOrderRequested; //redundant but for clarity + + //the following while loop was commented out when adaptive selection of + //the trend basis functions via pivote cholesky factorization of G*R^-1*G^T + //was implemented + //while((numRowsR<=numTrend(polyOrder,0))&&(polyOrder>0)) + //--polyOrder; + + //nTrend=numTrend(polyOrder,0); //commented out because we now select a subset of Poly based using a Pivoted Cholesky factorization of G*R^-1*G^T which happens when trendSelectingPivotedCholesy is called by materObjectiveAndConstraints() (we no longer select SOLELY on polynomial order and number of points + + nTrend=numTrend(polyOrderRequested,0); + + //printf("num_eqn_keep=%d numRowsR=%d polyOrder=%d nTrend=%d rcondR=%g lapackRcondR(num_eqn_keep-1,0)=%g\n",num_eqn_keep,numRowsR,polyOrder,nTrend,rcondR,lapackRcondR(num_eqn_keep-1,0)); + + //we need to downsize Gtran now but we only need to downsize Poly at + //the end of create() + Gtran.newSize(num_eqn_keep,nTrend); //newSize() because we don't care + //about the current contents of Gtran + + Y.newSize(num_eqn_keep,1); //newSize() because we don't care about + //the current contents of Y + + if(buildDerOrder==0) { + // keep only the useful parts for Kriging + numWholePointsKeep=numPointsKeep=num_eqn_keep; + numExtraDerKeep=0; + + /* + if(numPointsKeep>10) { + + MtxDbl RCholDEBUG(numPointsKeep,numPointsKeep); + for(int jpt=0; jpt(std::ceil(static_cast(num_eqn_keep)/ + static_cast(1+numVarsr))); + + if(numPointsKeep==numWholePointsKeep) { + //perhaps a better name would be numLastDerKeep... this is the number + //of derivatives retained for the last point. + numExtraDerKeep==numVarsr; + } else + numExtraDerKeep=num_eqn_keep-(1+numWholePointsKeep*(1+numVarsr)); + + //we need to undo the equilibration of RChol, recall that scaleRChol + //is already in the pivoted Cholesky order + for(int j=0; jnumWholePointsKeep) { +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (i==(numWholePointsKeep*(1+numVarsr)))&& + (numWholePointsKeep+1==numPointsKeep)); +#endif + int isrc=iPtsKeep(ipt,0)*(1+numVarsr); + Gtran(i,itrend)=Gall(itrend,isrc); + ++i; + ++isrc; + for(int k=0; knumWholePointsKeep) { +#ifdef __KRIG_ERR_CHECK__ + assert((ipt==numWholePointsKeep)&& + (i==(numWholePointsKeep*(1+numVarsr)))&& + (numWholePointsKeep+1==numPointsKeep)); +#endif + int isrc=iPtsKeep(ipt,0)*(1+numVarsr); + Y(i,0)=Yall(isrc,0); + ++i; + ++isrc; + for(int k=0; k + (inext_lapack_rcond-iprev_lapack_rcond)) + /std::log(2.0)); + while((lapackRcondR(inext_lapack_rcond,0)<=min_allowed_rcond)&& + (inext_lapack_rcond>iprev_lapack_rcond)) { + //printf("inWhile\n"); + ++rcond_iter; + icurr_lapack_rcond=(iprev_lapack_rcond+inext_lapack_rcond)/2; + num_trend_keep=icurr_lapack_rcond+1; + + //the LAPACK rcond function + DPOCON_F77(&uplo,&num_trend_keep,G_Rinv_Gtran_Chol.ptr(0,0), + &ld_G_Rinv_Gtran_Chol,oneNormR.ptr(icurr_lapack_rcond,0), + &rcond_G_Rinv_Gtran,rcondDblWork.ptr(0,0), + rcondIntWork.ptr(0,0),&info); + lapackRcondR(icurr_lapack_rcond,0)=rcond_G_Rinv_Gtran; + //printf("rcond_iter=%d icurr_lapack_rcondR=%d rcondR=%g\n", + //rcond_iter,icurr_lapack_rcondR,rcondR); + + if(rcond_G_Rinv_Gtran 0th derivative) calculate objective function + // if(con_der_mode=1) (1=2^0=> 0th derivative) calculate the constraint + //functions + // ERROR if(con_der_mode>=2) (2=2^1 = 1st derivative) this function does not + // support analytical derivatives of the objective + // function + // ERROR if(con_der_mode>=2) (2=2^1 = 1st derivative) this function does not + // support analytical derivatives of the constraint + // function + + //printf("maxConDerMode=%d con_der_mode=%d maxObjDerMode=%d obj_der_mode=%d\n", + //maxConDerMode,con_der_mode,maxObjDerMode,obj_der_mode); + + //might want to replace this with a thrown exception + assert((maxObjDerMode<=1)&&(maxConDerMode<=1)&& + (0<=obj_der_mode)&&(obj_der_mode<=maxObjDerMode)&& + (0<=con_der_mode)&&(con_der_mode<=maxConDerMode)&& + ((1<=obj_der_mode)||(1<=con_der_mode))); + + //if theta was the same as the last time we called this function than we can reuse some of the things we calculated last time + + if(prevTheta.getNElems()!=numTheta) { + //different number of elements means we can't reuse + prevTheta.newSize(numTheta,1); + prevObjDerMode=prevConDerMode=0; + } + else + for(int k=0; k=DBL_MAX) + //printf("[estVarianceMLE=%g determinant_R=%g]",estVarianceMLE,determinant_R); + + //the objective function being MINIMIZED is the negative of the log + //likelihood (on a per equation basis so numbers will be comparable + //regardless of how many equations there are) + obj=-likelihood; + //printf("[obj=%g]",obj); + + prevObjDerMode=1; //increase prevObjDerMode to the current value + if((obj_der_mode==1)&&(con_der_mode<=prevConDerMode)) { + //we have everything we need so exit early + return; + } + } + + if((prevConDerMode==0)&&(1<=con_der_mode)) { + //calculate the constraint on reciprocal condition number that ensures + //that the correlation matrix is well conditioned. + con.newSize(numConFunc,1); + + if(!(1<=prevObjDerMode)) + std::cerr << "We need to have already calculated rcondR (during the " + << "calculation of the\nobjective function) in order to " + << "calculate the constraint (on rcondR)\nfunction (where " + << "rcondR is the reciprocal of the condition number of R,\n" + << "and R is the ''correlation matrix'')." << std::endl; + else if(!(numConFunc==1)) + std::cerr << "The calling function is asking us for more than one " + << "constraint function\nbut we only have one constraint " + << "function; only rcondR (the reciprocal of\nthe " + << "condition number of the ''correlation matrix'', R) is " + << "constrained." << std::endl; + assert((1<=prevObjDerMode)&&(numConFunc==1)); + + //the matrix is considered "ill-conditioned" if the following constraint + //equation is greater than zero + con(0,0)=1.0-rcondR*maxCondNum; + + prevConDerMode=1; //increase prevConDerMode to current value + if((con_der_mode==1)&&(obj_der_mode<=prevObjDerMode)) { + //we have everything we need so exit early + return; + } + } + + return; +} + + +void KrigingModel::getRandGuess(MtxDbl& guess) const +{ + int mymod = 1048576; //2^20 instead of 10^6 to be kind to the computer + guess.newSize(numVarsr,1); + for(int k=0; k #ifndef PI +25a27 +> #endif Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/sandia_rules.cpp.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/sandia_rules.cpp.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/sandia_rules.cpp.patch (revision 27955) @@ -0,0 +1,4 @@ +24145c24145 +< if ( i_hi < 0 ) +--- +> if ( *i_hi < 0 ) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/src/DakotaInterface.cpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/src/DakotaInterface.cpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/src/DakotaInterface.cpp (revision 27955) @@ -0,0 +1,1358 @@ +/* _______________________________________________________________________ + + DAKOTA: Design Analysis Kit for Optimization and Terascale Applications + Copyright 2014 Sandia Corporation. + This software is distributed under the GNU Lesser General Public License. + For more information, see the README file in the top Dakota directory. + _______________________________________________________________________ */ + +//- Class: Interface +//- Description: Class implementation for abstract interface base class +//- Owner: Michael Eldred + +#include "DakotaInterface.hpp" +#include "ProblemDescDB.hpp" +#include "DakotaVariables.hpp" + +#include "SysCallApplicInterface.hpp" + +#if defined(HAVE_SYS_WAIT_H) && defined(HAVE_UNISTD_H) +#include "ForkApplicInterface.hpp" +#elif defined(_WIN32) // or _MSC_VER (native MSVS compilers) +#include "SpawnApplicInterface.hpp" +#endif // HAVE_SYS_WAIT_H, HAVE_UNISTD_H + +// Direct interfaces +#ifdef DAKOTA_GRID +#include "GridApplicInterface.hpp" +#endif // DAKOTA_GRID +#ifdef DAKOTA_MATLAB +#include "MatlabInterface.hpp" +#endif // DAKOTA_MATLAB +#ifdef DAKOTA_PYTHON +#include "PythonInterface.hpp" +#endif // DAKOTA_PYTHON +#ifdef DAKOTA_SCILAB +#include "ScilabInterface.hpp" +#endif // DAKOTA_SCILAB +#include "TestDriverInterface.hpp" + +#include "ApproximationInterface.hpp" + +#ifdef HAVE_AMPL +#undef NO // avoid name collision from UTILIB +#include "ampl/asl.h" +#endif // HAVE_AMPL + +//#define DEBUG +//#define REFCOUNT_DEBUG + +namespace Dakota { + + +/** This constructor is the one which must build the base class data for all + inherited interfaces. get_interface() instantiates a derived class letter + and the derived constructor selects this base class constructor in its + initialization list (to avoid the recursion of the base class constructor + calling get_interface() again). Since this is the letter and the letter + IS the representation, interfaceRep is set to NULL (an uninitialized + pointer causes problems in ~Interface). */ +Interface::Interface(BaseConstructor, const ProblemDescDB& problem_db): + interfaceType(problem_db.get_ushort("interface.type")), + interfaceId(problem_db.get_string("interface.id")), algebraicMappings(false), + coreMappings(true), outputLevel(problem_db.get_short("method.output")), + currEvalId(0), fineGrainEvalCounters(outputLevel > NORMAL_OUTPUT), + evalIdCntr(0), newEvalIdCntr(0), evalIdRefPt(0), newEvalIdRefPt(0), + multiProcEvalFlag(false), ieDedMasterFlag(false), + // See base constructor in DakotaIterator.cpp for full discussion of output + // verbosity. Interfaces support the full granularity in verbosity. + appendIfaceId(true), interfaceRep(NULL), referenceCount(1), asl(NULL) +{ +#ifdef DEBUG + outputLevel = DEBUG_OUTPUT; +#endif // DEBUG + + // Process the algebraic_mappings file (an AMPL .nl file) to get the number + // of variables/responses (currently, the tags are converted to index arrays + // at evaluation time, using the passed vars and response). + // TO DO: parallel bcast of data or very proc reads file? + const String& ampl_file_name + = problem_db.get_string("interface.algebraic_mappings"); + if (!ampl_file_name.empty()) { +#ifdef HAVE_AMPL + algebraicMappings = true; + bool hess_flag + = (problem_db.get_string("responses.hessian_type") == "analytic"); + asl = (hess_flag) ? ASL_alloc(ASL_read_pfgh) : ASL_alloc(ASL_read_fg); + // allow user input of either stub or stub.nl + String stub = (strends(ampl_file_name, ".nl")) ? + String(ampl_file_name, 0, ampl_file_name.size() - 3) : ampl_file_name; + //std::ifstream ampl_nl(ampl_file_name); + fint stub_str_len = stub.size(); + // BMA NOTE: casting away the constness as done historically in DakotaString + char* nonconst_stub = (char*) stub.c_str(); + FILE* ampl_nl = jac0dim(nonconst_stub, stub_str_len); + if (!ampl_nl) { + Cerr << "\nError: failure opening " << ampl_file_name << std::endl; + abort_handler(IO_ERROR); + } + int rtn = (hess_flag) ? pfgh_read(ampl_nl, ASL_return_read_err) + : fg_read(ampl_nl, ASL_return_read_err); + if (rtn) { + Cerr << "\nError: AMPL processing problem with " << ampl_file_name + << std::endl; + abort_handler(IO_ERROR); + } + + // extract input/output tag lists + String row = stub + ".row", col = stub + ".col", ampl_tag; + + std::ifstream ampl_col(col.c_str()); + if (!ampl_col) { + Cerr << "\nError: failure opening " << col.c_str() << std::endl; + abort_handler(IO_ERROR); + } + algebraicVarTags.resize(n_var); + for (size_t i=0; i>>>> algebraicVarTags =\n" << algebraicVarTags + << "\n>>>>> algebraicFnTags =\n" << algebraicFnTags + << "\n>>>>> algebraicFnTypes =\n" << algebraicFnTypes << std::endl; +#endif + +#else + Cerr << "\nError: algebraic_mappings not supported without the AMPL solver " + << "library provided with the Acro package." << std::endl; + abort_handler(-1); +#endif // HAVE_AMPL + } + +#ifdef REFCOUNT_DEBUG + Cout << "Interface::Interface(BaseConstructor, ProblemDescDB&) called to " + << "build base class data for letter object." << std::endl; +#endif +} + + +Interface::Interface(NoDBBaseConstructor, size_t num_fns, short output_level): + interfaceId("NO_SPECIFICATION"), algebraicMappings(false), coreMappings(true), + outputLevel(output_level), currEvalId(0), + fineGrainEvalCounters(outputLevel > NORMAL_OUTPUT), evalIdCntr(0), + newEvalIdCntr(0), evalIdRefPt(0), newEvalIdRefPt(0), multiProcEvalFlag(false), + ieDedMasterFlag(false), appendIfaceId(true), interfaceRep(NULL), + referenceCount(1) +{ +#ifdef DEBUG + outputLevel = DEBUG_OUTPUT; +#endif // DEBUG + +#ifdef REFCOUNT_DEBUG + Cout << "Interface::Interface(NoDBBaseConstructor) called to build base " + << "class data for letter object." << std::endl; +#endif +} + + +/** used in Model envelope class instantiations */ +Interface::Interface(): interfaceRep(NULL), referenceCount(1) +{ } + + +/** Used in Model instantiation to build the envelope. This constructor + only needs to extract enough data to properly execute get_interface, since + Interface::Interface(BaseConstructor, problem_db) builds the + actual base class data inherited by the derived interfaces. */ +Interface::Interface(ProblemDescDB& problem_db): referenceCount(1) +{ +#ifdef REFCOUNT_DEBUG + Cout << "Interface::Interface(ProblemDescDB&) called to instantiate envelope." + << std::endl; +#endif + + // Set the rep pointer to the appropriate interface type + interfaceRep = get_interface(problem_db); + if (!interfaceRep) // bad type or insufficient memory + abort_handler(-1); +} + + +/** used only by the envelope constructor to initialize interfaceRep + to the appropriate derived type. */ +Interface* Interface::get_interface(ProblemDescDB& problem_db) +{ + const unsigned short interface_type = problem_db.get_ushort("interface.type"); +#ifdef REFCOUNT_DEBUG + Cout << "Envelope instantiating letter: Getting interface " + << interface_enum_to_string(interface_type) << std::endl; +#endif + + // In the case where a derived interface type has been selected for managing + // analysis_drivers, then this determines the letter instantiation and any + // algebraic mappings are overlayed by ApplicationInterface. + const String& algebraic_map_file + = problem_db.get_string("interface.algebraic_mappings"); + if (interface_type == SYSTEM_INTERFACE) + return new SysCallApplicInterface(problem_db); + + else if (interface_type == FORK_INTERFACE) { +#if defined(HAVE_SYS_WAIT_H) && defined(HAVE_UNISTD_H) // includes CYGWIN/MINGW + return new ForkApplicInterface(problem_db); +#elif defined(_WIN32) // or _MSC_VER (native MSVS compilers) + return new SpawnApplicInterface(problem_db); +#else + Cerr << "Fork interface requested, but not enabled in this DAKOTA " + << "executable." << std::endl; + return NULL; +#endif + } + + else if (interface_type == TEST_INTERFACE) + return new TestDriverInterface(problem_db); + // Note: in the case of a plug-in direct interface, this object gets replaced + // using Interface::assign_rep(). Error checking in DirectApplicInterface:: + // derived_map_ac() should catch if this replacement fails to occur properly. + +#ifdef DAKOTA_GRID + else if (interface_type == GRID_INTERFACE) + return new GridApplicInterface(problem_db); +#endif + + else if (interface_type == MATLAB_INTERFACE) { +#ifdef DAKOTA_MATLAB + return new MatlabInterface(problem_db); +#else + Cerr << "Direct Matlab interface requested, but not enabled in this " + << "DAKOTA executable." << std::endl; + return NULL; +#endif + } + + else if (interface_type == PYTHON_INTERFACE) { +#ifdef DAKOTA_PYTHON + return new PythonInterface(problem_db); +#else + Cerr << "Direct Python interface requested, but not enabled in this " + << "DAKOTA executable." << std::endl; + return NULL; +#endif + } + + else if (interface_type == SCILAB_INTERFACE) { +#ifdef DAKOTA_SCILAB + return new ScilabInterface(problem_db); +#else + Cerr << "Direct Scilab interface requested, but not enabled in this " + << "DAKOTA executable." << std::endl; + return NULL; +#endif + } + + // Should not be needed since ApproximationInterface is plugged-in from + // DataFitSurrModel using Interface::assign_rep(). + //else if (interface_type == APPROX_INTERFACE) + // return new ApproximationInterface(problem_db, num_acv, num_fns); + + // In the case where only algebraic mappings are used, then no derived map + // functionality is needed and ApplicationInterface is used for the letter. + else if (!algebraic_map_file.empty()) { +#ifdef DEBUG + Cout << ">>>>> new ApplicationInterface: " << algebraic_map_file + << std::endl; +#endif // DEBUG + return new ApplicationInterface(problem_db); + } + + // If the interface type is empty (e.g., from default DataInterface creation + // in ProblemDescDB::check_input()), then ApplicationInterface is the letter. + else if (interface_type == DEFAULT_INTERFACE) { + Cerr << "Warning: empty interface type in Interface::get_interface()." + << std::endl; + return new ApplicationInterface(problem_db); + } + + else { + Cerr << "Invalid interface: " << interface_enum_to_string(interface_type) + << std::endl; + return NULL; + } +} + + +/** Copy constructor manages sharing of interfaceRep and incrementing + of referenceCount. */ +Interface::Interface(const Interface& interface_in) +{ + // Increment new (no old to decrement) + interfaceRep = interface_in.interfaceRep; + if (interfaceRep) // Check for an assignment of NULL + ++interfaceRep->referenceCount; + +#ifdef REFCOUNT_DEBUG + Cout << "Interface::Interface(Interface&)" << std::endl; + if (interfaceRep) + Cout << "interfaceRep referenceCount = " << interfaceRep->referenceCount + << std::endl; +#endif +} + + +/** Assignment operator decrements referenceCount for old interfaceRep, assigns + new interfaceRep, and increments referenceCount for new interfaceRep. */ +Interface Interface::operator=(const Interface& interface_in) +{ + if (interfaceRep != interface_in.interfaceRep) { // normal case: old != new + // Decrement old + if (interfaceRep) // Check for NULL + if ( --interfaceRep->referenceCount == 0 ) + delete interfaceRep; + // Assign and increment new + interfaceRep = interface_in.interfaceRep; + if (interfaceRep) // Check for NULL + ++interfaceRep->referenceCount; + } + // else if assigning same rep, then do nothing since referenceCount + // should already be correct + +#ifdef REFCOUNT_DEBUG + Cout << "Interface::operator=(Interface&)" << std::endl; + if (interfaceRep) + Cout << "interfaceRep referenceCount = " << interfaceRep->referenceCount + << std::endl; +#endif + + return *this; // calls copy constructor since returned by value +} + + +/** Destructor decrements referenceCount and only deletes interfaceRep + if referenceCount is zero. */ +Interface::~Interface() +{ + // Check for NULL pointer + if (interfaceRep) { + --interfaceRep->referenceCount; +#ifdef REFCOUNT_DEBUG + Cout << "interfaceRep referenceCount decremented to " + << interfaceRep->referenceCount << std::endl; +#endif + if (interfaceRep->referenceCount == 0) { +#ifdef REFCOUNT_DEBUG + Cout << "deleting interfaceRep" << std::endl; +#endif + delete interfaceRep; + } + } +} + + +/** Similar to the assignment operator, the assign_rep() function + decrements referenceCount for the old interfaceRep and assigns the + new interfaceRep. It is different in that it is used for + publishing derived class letters to existing envelopes, as opposed + to sharing representations among multiple envelopes (in particular, + assign_rep is passed a letter object and operator= is passed an + envelope object). Letter assignment supports two models as + governed by ref_count_incr: + + \li ref_count_incr = true (default): the incoming letter belongs to + another envelope. In this case, increment the reference count in the + normal manner so that deallocation of the letter is handled properly. + + \li ref_count_incr = false: the incoming letter is instantiated on the + fly and has no envelope. This case is modeled after get_interface(): + a letter is dynamically allocated using new and passed into assign_rep, + the letter's reference count is not incremented, and the letter is not + remotely deleted (its memory management is passed over to the envelope). */ +void Interface::assign_rep(Interface* interface_rep, bool ref_count_incr) +{ + if (interfaceRep == interface_rep) { + // if ref_count_incr = true (rep from another envelope), do nothing as + // referenceCount should already be correct (see also operator= logic). + // if ref_count_incr = false (rep from on the fly), then this is an error. + if (!ref_count_incr) { + Cerr << "Error: duplicated interface_rep pointer assignment without " + << "reference count increment in Interface::assign_rep()." + << std::endl; + abort_handler(-1); + } + } + else { // normal case: old != new + // Decrement old + if (interfaceRep) // Check for NULL + if ( --interfaceRep->referenceCount == 0 ) + delete interfaceRep; + // Assign new + interfaceRep = interface_rep; + // Increment new + if (interfaceRep && ref_count_incr) // Check for NULL & honor ref_count_incr + interfaceRep->referenceCount++; + } + +#ifdef REFCOUNT_DEBUG + Cout << "Interface::assign_rep(Interface*)" << std::endl; + if (interfaceRep) + Cout << "interfaceRep referenceCount = " << interfaceRep->referenceCount + << std::endl; +#endif +} + + +void Interface::fine_grained_evaluation_counters(size_t num_fns) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->fine_grained_evaluation_counters(num_fns); + else if (!fineGrainEvalCounters) { // letter (not virtual) + init_evaluation_counters(num_fns); + fineGrainEvalCounters = true; + } +} + + +void Interface::init_evaluation_counters(size_t num_fns) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->init_evaluation_counters(num_fns); + else { // letter (not virtual) + //if (fnLabels.empty()) { + // fnLabels.resize(num_fns); + // build_labels(fnLabels, "response_fn_"); // generic resp fn labels + //} + if (fnValCounter.size() != num_fns) { + fnValCounter.assign(num_fns, 0); fnGradCounter.assign(num_fns, 0); + fnHessCounter.assign(num_fns, 0); newFnValCounter.assign(num_fns, 0); + newFnGradCounter.assign(num_fns, 0); newFnHessCounter.assign(num_fns, 0); + fnValRefPt.assign(num_fns, 0); fnGradRefPt.assign(num_fns, 0); + fnHessRefPt.assign(num_fns, 0); newFnValRefPt.assign(num_fns, 0); + newFnGradRefPt.assign(num_fns, 0); newFnHessRefPt.assign(num_fns, 0); + } + } +} + + +void Interface::set_evaluation_reference() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->set_evaluation_reference(); + else { // letter (not virtual) + + evalIdRefPt = evalIdCntr; + newEvalIdRefPt = newEvalIdCntr; + + if (fineGrainEvalCounters) { + size_t i, num_fns = fnValCounter.size(); + for (i=0; iprint_evaluation_summary(s, minimal_header, relative_count); + else { // letter (not virtual) + + // standard evaluation summary + if (minimal_header) { + if (interfaceId.empty()) + s << " Interface evaluations"; + else + s << " " << interfaceId << " evaluations"; + } + else { + s << "<<<<< Function evaluation summary"; + if (!interfaceId.empty()) + s << " (" << interfaceId << ')'; + } + int fn_evals = (relative_count) ? evalIdCntr - evalIdRefPt + : evalIdCntr; + int new_fn_evals = (relative_count) ? newEvalIdCntr - newEvalIdRefPt + : newEvalIdCntr; + s << ": " << fn_evals << " total (" << new_fn_evals << " new, " + << fn_evals - new_fn_evals << " duplicate)\n"; + + // detailed evaluation summary + if (fineGrainEvalCounters) { + size_t i, num_fns = std::min(fnValCounter.size(), fnLabels.size()); + for (i=0; ieval_tag_prefix(eval_id_str, append_iface_id); + else { + evalTagPrefix = eval_id_str; + appendIfaceId = append_iface_id; + } +} + + +void Interface::map(const Variables& vars, const ActiveSet& set, + Response& response, bool asynch_flag) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->map(vars, set, response, asynch_flag); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual map function.\n" + << "No default map defined at Interface base class." << std::endl; + abort_handler(-1); + } +} + + +void Interface:: +init_algebraic_mappings(const Variables& vars, const Response& response) +{ + size_t i, num_alg_vars = algebraicVarTags.size(), + num_alg_fns = algebraicFnTags.size(); + + algebraicACVIndices.resize(num_alg_vars); + algebraicACVIds.resize(num_alg_vars); + StringMultiArrayConstView acv_labels = vars.all_continuous_variable_labels(); + SizetMultiArrayConstView acv_ids = vars.all_continuous_variable_ids(); + for (i=0; i nl_vars (reduced AMPL space) + const RealVector& dak_a_c_vars = vars.all_continuous_variables(); + //IntVector dak_a_d_vars = vars.all_discrete_variables(); + Real* nl_vars = new Real [num_alg_vars]; + for (i=0; i algebraic_response + algebraic_response.reset_inactive(); // zero inactive data + Real fn_val; RealVector fn_grad; RealSymMatrix fn_hess; + fint err = 0; + for (i=0; i response fns via AMPL + if (algebraic_asv[i] & 1) { + if (algebraicFnTypes[i] > 0) + fn_val = objval(algebraicFnTypes[i]-1, nl_vars, &err); + else + fn_val = conival(-1-algebraicFnTypes[i], nl_vars, &err); + if (err) { + Cerr << "\nError: AMPL processing failure in objval().\n" << std::endl; + abort_handler(INTERFACE_ERROR); + } + algebraic_response.function_value(fn_val, i); + } + // nl_vars -> response grads via AMPL + if (algebraic_asv[i] & 6) { // need grad for Hessian + fn_grad = algebraic_response.function_gradient_view(i); + if (algebraicFnTypes[i] > 0) + objgrd(algebraicFnTypes[i]-1, nl_vars, fn_grad.values(), &err); + else + congrd(-1-algebraicFnTypes[i], nl_vars, fn_grad.values(), &err); + if (err) { + Cerr << "\nError: AMPL processing failure in objgrad().\n" << std::endl; + abort_handler(INTERFACE_ERROR); + } + } + // nl_vars -> response Hessians via AMPL + if (algebraic_asv[i] & 4) { + fn_hess = algebraic_response.function_hessian_view(i); + // the fullhess calls must follow corresp call to objgrad/congrad + if (algebraicFnTypes[i] > 0) + fullhes(fn_hess.values(), num_alg_vars, algebraicFnTypes[i]-1, + NULL, NULL); + else { + algebraicConstraintWeights.assign(algebraicConstraintWeights.size(), 0); + algebraicConstraintWeights[-1-algebraicFnTypes[i]] = 1; + fullhes(fn_hess.values(), num_alg_vars, num_alg_vars, NULL, + &algebraicConstraintWeights[0]); + } + } + } + delete [] nl_vars; + algebraic_response.function_labels(algebraicFnTags); +#ifdef DEBUG + Cout << ">>>>> algebraic_response.fn_labels\n" + << algebraic_response.function_labels() << std::endl; +#endif // DEBUG + + if (outputLevel > NORMAL_OUTPUT) + Cout << "Algebraic mapping applied.\n"; +#endif // HAVE_AMPL +} + + +/** This function will get invoked even when only algebraic mappings are + active (no core mappings from derived_map), since the AMPL + algebraic_response may be ordered differently from the total_response. + In this case, the core_response object is unused. */ +void Interface:: +response_mapping(const Response& algebraic_response, + const Response& core_response, Response& total_response) +{ + const ShortArray& total_asv = total_response.active_set_request_vector(); + const SizetArray& total_dvv = total_response.active_set_derivative_vector(); + size_t i, j, k, num_total_fns = total_asv.size(), + num_total_vars = total_dvv.size(); + bool grad_flag = false, hess_flag = false; + for (i=0; i num_total_fns) { + Cerr << "Error: response size mismatch in Interface::response_mapping()." + << std::endl; + abort_handler(-1); + } + if ( (grad_flag || hess_flag) && num_alg_vars > num_total_vars) { + Cerr << "Error: derivative variables size mismatch in Interface::" + << "response_mapping()." << std::endl; + abort_handler(-1); + } + SizetArray algebraic_dvv_indices; + if (grad_flag || hess_flag) { + algebraic_dvv_indices.resize(num_alg_vars); + using Pecos::find_index; + for (i=0; ifinal_eval_id_tag(iface_eval_id); + + if (appendIfaceId) + return evalTagPrefix + "." + boost::lexical_cast(iface_eval_id); + return evalTagPrefix; +} + + +int Interface::algebraic_function_type(String functionTag) +{ +#ifdef HAVE_AMPL + int i; + for (i=0; isynch(); +} + + +const IntResponseMap& Interface::synch_nowait() +{ + if (!interfaceRep) { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual synch_nowait " + << "function.\nNo default synch_nowait defined at Interface base " + << "class." << std::endl; + abort_handler(-1); + } + + return interfaceRep->synch_nowait(); +} + + +void Interface::serve_evaluations() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->serve_evaluations(); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual serve_evaluations " + << "function.\nNo default serve_evaluations defined at Interface" + << " base class." << std::endl; + abort_handler(-1); + } +} + + +void Interface::stop_evaluation_servers() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->stop_evaluation_servers(); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual stop_evaluation_" + << "servers fn.\nNo default stop_evaluation_servers defined at " + << "Interface base class." << std::endl; + abort_handler(-1); + } +} + + +void Interface::init_communicators(const IntArray& message_lengths, + int max_eval_concurrency) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->init_communicators(message_lengths, max_eval_concurrency); + else { // letter lacking redefinition of virtual fn. + // ApproximationInterfaces: do nothing + } +} + + +void Interface::set_communicators(const IntArray& message_lengths, + int max_eval_concurrency) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->set_communicators(message_lengths, max_eval_concurrency); + else { // letter lacking redefinition of virtual fn. + // ApproximationInterfaces: do nothing + } +} + + +/* +void Interface::free_communicators() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->free_communicators(); + else { // letter lacking redefinition of virtual fn. + // default is no-op + } +} +*/ + + +void Interface::init_serial() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->init_serial(); + else { // letter lacking redefinition of virtual fn. + // ApproximationInterfaces: do nothing + } +} + + +int Interface::asynch_local_evaluation_concurrency() const +{ + if (interfaceRep) // envelope fwd to letter + return interfaceRep->asynch_local_evaluation_concurrency(); + else // letter lacking redefinition of virtual fn. + return 0; // default (redefined only for ApplicationInterfaces) +} + + +short Interface::interface_synchronization() const +{ + if (interfaceRep) // envelope fwd to letter + return interfaceRep->interface_synchronization(); // ApplicationInterfaces + else // letter lacking redefinition of virtual fn. + return SYNCHRONOUS_INTERFACE; // default (ApproximationInterfaces) +} + + +int Interface::minimum_points(bool constraint_flag) const +{ + if (interfaceRep) // envelope fwd to letter + return interfaceRep->minimum_points(constraint_flag); + else // letter lacking redefinition of virtual fn. + return 0; // default (currently redefined only for ApproximationInterfaces) +} + + +int Interface::recommended_points(bool constraint_flag) const +{ + if (interfaceRep) // envelope fwd to letter + return interfaceRep->recommended_points(constraint_flag); + else // letter lacking redefinition of virtual fn. + return 0; // default (currently redefined only for ApproximationInterfaces) +} + + +void Interface::approximation_function_indices(const IntSet& approx_fn_indices) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->approximation_function_indices(approx_fn_indices); + // else: default implementation is no-op +} + + +void Interface:: +update_approximation(const Variables& vars, const IntResponsePair& response_pr) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->update_approximation(vars, response_pr); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual update_approximation" + << "(Variables, IntResponsePair) function.\n This interface " + << "does not support approximation updating." << std::endl; + abort_handler(-1); + } +} + + +void Interface:: +update_approximation(const RealMatrix& samples, const IntResponseMap& resp_map) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->update_approximation(samples, resp_map); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual update_approximation" + << "(RealMatrix, IntResponseMap) function.\n This interface " + << "does not support approximation updating." << std::endl; + abort_handler(-1); + } +} + + +void Interface:: +update_approximation(const VariablesArray& vars_array, + const IntResponseMap& resp_map) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->update_approximation(vars_array, resp_map); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual update_approximation" + << "(VariablesArray, IntResponseMap) function.\n This interface " + << "does not support approximation updating." << std::endl; + abort_handler(-1); + } +} + + +void Interface:: +append_approximation(const Variables& vars, const IntResponsePair& response_pr) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->append_approximation(vars, response_pr); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual append_approximation" + << "(Variables, IntResponsePair) function.\n This interface " + << "does not support approximation appending." << std::endl; + abort_handler(-1); + } +} + + +void Interface:: +append_approximation(const RealMatrix& samples, const IntResponseMap& resp_map) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->append_approximation(samples, resp_map); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual append_approximation" + << "(RealMatrix, IntResponseMap) function.\n This interface " + << "does not support approximation appending." << std::endl; + abort_handler(-1); + } +} + + +void Interface:: +append_approximation(const VariablesArray& vars_array, + const IntResponseMap& resp_map) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->append_approximation(vars_array, resp_map); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual append_approximation" + << "(VariablesArray, IntResponseMap) function.\n This interface " + << "does not support approximation appending." << std::endl; + abort_handler(-1); + } +} + + +void Interface:: +build_approximation(const RealVector& c_l_bnds, const RealVector& c_u_bnds, + const IntVector& di_l_bnds, const IntVector& di_u_bnds, + const RealVector& dr_l_bnds, const RealVector& dr_u_bnds) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->build_approximation(c_l_bnds, c_u_bnds, di_l_bnds, di_u_bnds, + dr_l_bnds, dr_u_bnds); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual build_approximation" + << "() function.\n This interface does not support " + << "approximations." << std::endl; + abort_handler(-1); + } +} + + +void Interface:: +rebuild_approximation(const BoolDeque& rebuild_deque) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->rebuild_approximation(rebuild_deque); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual rebuild_" + << "approximation() function.\n This interface does not " + << "support approximations." << std::endl; + abort_handler(-1); + } +} + + +void Interface::pop_approximation(bool save_surr_data) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->pop_approximation(save_surr_data); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual pop_approximation" + << "(bool)\n function. This interface does not support " + << "approximation\n data removal." << std::endl; + abort_handler(-1); + } +} + + +void Interface::restore_approximation() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->restore_approximation(); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual restore_" + << "approximation() function.\n This interface does not " + << "support approximation restoration." << std::endl; + abort_handler(-1); + } +} + + +bool Interface::restore_available() +{ + if (!interfaceRep) { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual restore_" + << "available() function.\n This interface does not " + << "support approximation restoration queries." << std::endl; + abort_handler(-1); + } + return interfaceRep->restore_available(); +} + + +void Interface::finalize_approximation() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->finalize_approximation(); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual finalize_" + << "approximation() function.\n This interface does not " + << "support approximation finalization." << std::endl; + abort_handler(-1); + } +} + + +void Interface::store_approximation() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->store_approximation(); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual store_" + << "approximation() function.\n This interface does not " + << "support approximation storage." << std::endl; + abort_handler(-1); + } +} + + +void Interface::combine_approximation(short corr_type) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->combine_approximation(corr_type); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual combine_" + << "approximation() function.\n This interface does not " + << "support approximation combination." << std::endl; + abort_handler(-1); + } +} + + +void Interface::clear_current() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->clear_current(); + else { // letter lacking redefinition of virtual fn. + // ApplicationInterfaces: do nothing + } +} + + +void Interface::clear_all() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->clear_all(); + else { // letter lacking redefinition of virtual fn. + // ApplicationInterfaces: do nothing + } +} + + +void Interface::clear_saved() +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->clear_saved(); + else { // letter lacking redefinition of virtual fn. + // ApplicationInterfaces: do nothing + } +} + + +SharedApproxData& Interface::shared_approximation() +{ + if (!interfaceRep) { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual shared_approximation" + << "() function.\nThis interface does not support approximations." + << std::endl; + abort_handler(-1); + } + + // envelope fwd to letter + return interfaceRep->shared_approximation(); +} + + +std::vector& Interface::approximations() +{ + if (!interfaceRep) { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual approximations() " + << "function.\n This interface does not support approximations." + << std::endl; + abort_handler(-1); + } + + // envelope fwd to letter + return interfaceRep->approximations(); +} + + +const Pecos::SurrogateData& Interface::approximation_data(size_t index) +{ + if (!interfaceRep) { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual approximation_data " + << "function.\n This interface does not support approximations." + << std::endl; + abort_handler(-1); + } + + // envelope fwd to letter + return interfaceRep->approximation_data(index); +} + + +const RealVectorArray& Interface::approximation_coefficients(bool normalized) +{ + if (!interfaceRep) { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual approximation_" + << "coefficients function.\n This interface does not support " + << "approximations." << std::endl; + abort_handler(-1); + } + + // envelope fwd to letter + return interfaceRep->approximation_coefficients(normalized); +} + + +void Interface:: +approximation_coefficients(const RealVectorArray& approx_coeffs, + bool normalized) +{ + if (interfaceRep) // envelope fwd to letter + interfaceRep->approximation_coefficients(approx_coeffs, normalized); + else { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual approximation_" + << "coefficients function.\n This interface does not support " + << "approximations." << std::endl; + abort_handler(-1); + } +} + + +const RealVector& Interface::approximation_variances(const Variables& vars) +{ + if (!interfaceRep) { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual approximation_" + << "variances function.\n This interface does not support " + << "approximations." << std::endl; + abort_handler(-1); + } + + // envelope fwd to letter + return interfaceRep->approximation_variances(vars); +} + + +const StringArray& Interface::analysis_drivers() const +{ + if (!interfaceRep) { // letter lacking redefinition of virtual fn. + Cerr << "Error: Letter lacking redefinition of virtual analysis_drivers " + << "function." << std::endl; + abort_handler(-1); + } + + // envelope fwd to letter + return interfaceRep->analysis_drivers(); +} + + +bool Interface::evaluation_cache() const +{ + if (interfaceRep) + return interfaceRep->evaluation_cache(); + else // letter lacking redefinition of virtual fn. + return false; // default +} + + +void Interface::file_cleanup() const +{ + if (interfaceRep) + interfaceRep->file_cleanup(); + // else no-op +} + +} // namespace Dakota Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/src/NonDLocalReliability.cpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/src/NonDLocalReliability.cpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/configs/6.2/src/NonDLocalReliability.cpp (revision 27955) @@ -0,0 +1,2704 @@ +/* _______________________________________________________________________ + + DAKOTA: Design Analysis Kit for Optimization and Terascale Applications + Copyright 2014 Sandia Corporation. + This software is distributed under the GNU Lesser General Public License. + For more information, see the README file in the top Dakota directory. + _______________________________________________________________________ */ + +//- Class: NonDLocalReliability +//- Description: Implementation code for NonDLocalReliability class +//- Owner: Mike Eldred +//- Checked by: +//- Version: + +#include "dakota_system_defs.hpp" +#include "DakotaResponse.hpp" +#include "ParamResponsePair.hpp" +#include "PRPMultiIndex.hpp" +#include "ProblemDescDB.hpp" +#include "DakotaGraphics.hpp" +#include "NonDLocalReliability.hpp" +#include "NonDAdaptImpSampling.hpp" +#ifdef HAVE_NPSOL +#include "NPSOLOptimizer.hpp" +#endif +#ifdef HAVE_OPTPP +#include "SNLLOptimizer.hpp" +using OPTPP::NLPFunction; +using OPTPP::NLPGradient; +#endif +#include "RecastModel.hpp" +#include "DataFitSurrModel.hpp" +#include "NestedModel.hpp" +#include "Teuchos_LAPACK.hpp" +#include "Teuchos_SerialDenseHelpers.hpp" +#include +#include "dakota_data_io.hpp" + +//#define MPP_CONVERGE_RATE +//#define DEBUG + +static const char rcsId[] = "@(#) $Id: NonDLocalReliability.cpp 4058 2006-10-25 01:39:40Z mseldre $"; + +namespace Dakota { +extern PRPCache data_pairs; // global container + + +// define special values for componentParallelMode +//#define SURROGATE_MODEL 1 +#define TRUTH_MODEL 2 + + +// initialization of statics +NonDLocalReliability* NonDLocalReliability::nondLocRelInstance(NULL); + + +NonDLocalReliability:: +NonDLocalReliability(ProblemDescDB& problem_db, Model& model): + NonDReliability(problem_db, model), + initialPtUserSpec( + probDescDB.get_bool("variables.uncertain.initial_point_flag")), + warmStartFlag(true), nipModeOverrideFlag(true), + curvatureDataAvailable(false), kappaUpdated(false), + secondOrderIntType(HOHENRACK), curvatureThresh(1.e-10), warningBits(0) +{ + // check for suitable gradient and variables specifications + if (iteratedModel.gradient_type() == "none") { + Cerr << "\nError: local_reliability requires a gradient specification." + << std::endl; + abort_handler(-1); + } + if (numEpistemicUncVars) { + Cerr << "Error: epistemic variables are not supported in local " + << "reliability methods." << std::endl; + abort_handler(-1); + } + + if (mppSearchType) { // default is MV = 0 + + // Map MPP search NIP/SQP algorithm specification into an NPSOL/OPT++ + // selection based on configuration availability. +#if !defined(HAVE_NPSOL) && !defined(HAVE_OPTPP) + Cerr << "Error: this executable not configured with NPSOL or OPT++.\n" + << " NonDLocalReliability cannot perform MPP search." + << std::endl; + abort_handler(-1); +#endif + unsigned short mpp_optimizer = probDescDB.get_ushort("method.sub_method"); + if (mpp_optimizer == SUBMETHOD_SQP) { +#ifdef HAVE_NPSOL + npsolFlag = true; +#else + Cerr << "\nError: this executable not configured with NPSOL SQP.\n" + << " Please select OPT++ NIP within local_reliability." + << std::endl; + abort_handler(-1); +#endif + } + else if (mpp_optimizer == SUBMETHOD_NIP) { +#ifdef HAVE_OPTPP + npsolFlag = false; +#else + Cerr << "\nError: this executable not configured with OPT++ NIP.\n" + << " please select NPSOL SQP within local_reliability." + << std::endl; + abort_handler(-1); +#endif + } + else if (mpp_optimizer == SUBMETHOD_DEFAULT) { +#ifdef HAVE_NPSOL + npsolFlag = true; +#elif HAVE_OPTPP + npsolFlag = false; +#endif + } + + // Error check for a specification of at least 1 level for MPP methods + if (!totalLevelRequests) { + Cerr << "\nError: An MPP search method requires the specification of at " + << "least one response, probability, or reliability level." + << std::endl; + abort_handler(-1); + } + } + + // Prevent nesting of an instance of a Fortran iterator within another + // instance of the same iterator (which would result in data clashes since + // Fortran does not support object independence). Recurse through all + // sub-models and test each sub-iterator for SOL presence. + // Note 1: This check is performed for DOT, CONMIN, and SOLBase, but not + // for LHS since it is only active in pre-processing. + // Note 2: NPSOL/NLSSOL on the outer loop with NonDLocalReliability on the + // inner loop precludes all NPSOL-based MPP searches; + // NonDLocalReliability on the outer loop with NPSOL/NLSSOL on an + // inner loop is only a problem for the no_approx MPP search (since + // iteratedModel is not invoked w/i an approx-based MPP search). + if (mppSearchType == NO_APPROX && npsolFlag) { + Iterator sub_iterator = iteratedModel.subordinate_iterator(); + if (!sub_iterator.is_null() && + ( sub_iterator.method_name() == NPSOL_SQP || + sub_iterator.method_name() == NLSSOL_SQP || + sub_iterator.uses_method() == NPSOL_SQP || + sub_iterator.uses_method() == NLSSOL_SQP ) ) + sub_iterator.method_recourse(); + ModelList& sub_models = iteratedModel.subordinate_models(); + for (ModelLIter ml_iter = sub_models.begin(); + ml_iter != sub_models.end(); ml_iter++) { + sub_iterator = ml_iter->subordinate_iterator(); + if (!sub_iterator.is_null() && + ( sub_iterator.method_name() == NPSOL_SQP || + sub_iterator.method_name() == NLSSOL_SQP || + sub_iterator.uses_method() == NPSOL_SQP || + sub_iterator.uses_method() == NLSSOL_SQP ) ) + sub_iterator.method_recourse(); + } + } + + // Map response Hessian specification into taylorOrder for use by MV/AMV/AMV+ + // variants. Note that taylorOrder and integrationOrder are independent + // (although the Hessian specification required for 2nd-order integration + // means that taylorOrder = 2 will be used for MV/AMV/AMV+; taylorOrder = 2 + // may however be used with 1st-order integration). + const String& hess_type = iteratedModel.hessian_type(); + taylorOrder = (hess_type != "none" && mppSearchType <= AMV_PLUS_U) ? 2 : 1; + + // assign iterator-specific defaults for approximation-based MPP searches + if (maxIterations < 0 && // DataMethod default = -1 + mppSearchType >= AMV_PLUS_X && mppSearchType < NO_APPROX) // approx-based + maxIterations = 25; + + // The model of the limit state in u-space (uSpaceModel) is constructed here + // one time. The RecastModel for the RIA/PMA formulations varies with the + // level requests and is constructed for each level within mpp_search(). + + // Instantiate the Nataf Recast and any DataFit model recursions. Recast is + // bounded to 10 std devs in u space. This is particularly important for PMA + // since an SQP-based optimizer will not enforce the constraint immediately + // and min +/-g has been observed to have significant excursions early on + // prior to the u'u = beta^2 constraint enforcement bringing it back. A + // large excursion can cause overflow; a medium excursion can cause poor + // performance since far-field info is introduced into the BFGS Hessian. + if (mppSearchType == AMV_X || mppSearchType == AMV_PLUS_X || + mppSearchType == TANA_X) { // Recast( DataFit( iteratedModel ) ) + + // Construct g-hat(x) using a local/multipoint approximation over the + // uncertain variables (using the same view as iteratedModel). + Model g_hat_x_model; + String sample_reuse, approx_type = (mppSearchType == TANA_X) ? + "multipoint_tana" : "local_taylor"; + UShortArray approx_order(1, taylorOrder); + short corr_order = -1, corr_type = NO_CORRECTION, + data_order = (taylorOrder == 2) ? 7 : 3; + int samples = 0, seed = 0; + Iterator dace_iterator; + //const Variables& curr_vars = iteratedModel.current_variables(); + ActiveSet surr_set = iteratedModel.current_response().active_set(); // copy + surr_set.request_values(3); // surrogate gradient evals + g_hat_x_model.assign_rep(new DataFitSurrModel(dace_iterator, iteratedModel, + surr_set, approx_type, approx_order, corr_type, corr_order, data_order, + outputLevel, sample_reuse), false); + + // transform g_hat_x_model from x-space to u-space + transform_model(g_hat_x_model, uSpaceModel, true); // globally bounded + } + else if (mppSearchType == AMV_U || mppSearchType == AMV_PLUS_U || + mppSearchType == TANA_U) { // DataFit( Recast( iteratedModel ) ) + + // Recast g(x) to G(u) + Model g_u_model; + transform_model(iteratedModel, g_u_model, true); // globally bounded + + // Construct G-hat(u) using a local/multipoint approximation over the + // uncertain variables (using the same view as iteratedModel/g_u_model). + String sample_reuse, approx_type = (mppSearchType == TANA_U) ? + "multipoint_tana" : "local_taylor"; + UShortArray approx_order(1, taylorOrder); + short corr_order = -1, corr_type = NO_CORRECTION, + data_order = (taylorOrder == 2) ? 7 : 3; + int samples = 0, seed = 0; + Iterator dace_iterator; + //const Variables& g_u_vars = g_u_model.current_variables(); + ActiveSet surr_set = g_u_model.current_response().active_set(); // copy + surr_set.request_values(3); // surrogate gradient evals + uSpaceModel.assign_rep(new DataFitSurrModel(dace_iterator, g_u_model, + surr_set, approx_type, approx_order, corr_type, corr_order, data_order, + outputLevel, sample_reuse), false); + } + else if (mppSearchType == NO_APPROX) // Recast( iteratedModel ) + // Recast g(x) to G(u) + transform_model(iteratedModel, uSpaceModel, true); // globally bounded + + // configure a RecastModel with one objective and one equality constraint + // using the alternate minimalist constructor + if (mppSearchType) { + SizetArray recast_vars_comps_total; // default: empty; no change in size + BitArray all_relax_di, all_relax_dr; // default: empty; no discrete relax + mppModel.assign_rep( + new RecastModel(uSpaceModel, recast_vars_comps_total, + all_relax_di, all_relax_dr, 1, 1, 0), false); + RealVector nln_eq_targets(1, false); nln_eq_targets = 0.; + mppModel.nonlinear_eq_constraint_targets(nln_eq_targets); + + // Use NPSOL/OPT++ in "user_functions" mode to perform the MPP search + if (npsolFlag) { + // NPSOL deriv level: 1 = supplied grads of objective fn, 2 = supplied + // grads of constraints, 3 = supplied grads of both. Always use the + // supplied grads of u'u (deriv level = 1 for RIA, deriv level = 2 for + // PMA). In addition, use supplied gradients of G(u) in most cases. + // Exception: deriv level = 3 results in a gradient-based line search, + // which could be too expensive for FORM with numerical grads unless + // seeking parallel load balance. + //int npsol_deriv_level; + //if ( mppSearchType == NO_APPROX && !iteratedModel.asynch_flag() + // && iteratedModel.gradient_type() != "analytic" ) + // npsol_deriv_level = (ria_flag) ? 1 : 2; + //else + // npsol_deriv_level = 3; + //Cout << "Derivative level = " << npsol_deriv_level << '\n'; + + // The gradient-based line search (deriv. level = 3) appears to be + // outperforming the value-based line search in PMA testing. In + // addition, the RIA warm start needs fnGradU so deriv. level = 3 has + // superior performance there as well. Therefore, deriv level = 3 can + // be used for all cases. + int npsol_deriv_level = 3; + + // run a tighter tolerance on approximation-based MPP searches + //Real conv_tol = (mppSearchType == NO_APPROX) ? 1.e-4 : 1.e-6; + Real conv_tol = -1.; // use NPSOL default + +#ifdef HAVE_NPSOL + mppOptimizer.assign_rep(new NPSOLOptimizer(mppModel, npsol_deriv_level, + conv_tol), false); +#endif + } +#ifdef HAVE_OPTPP + else + mppOptimizer.assign_rep(new SNLLOptimizer("optpp_q_newton", mppModel), + false); +#endif + } + + // Map integration specification into integrationOrder. Second-order + // integration requires an MPP search in u-space, and is not warranted for + // unconverged MPP's (AMV variants). In addition, AMV variants only compute + // verification function values at u* (no Hessians). For an AMV-like + // approach with 2nd-order integration, use AMV+ with max_iterations = 1. + const String& integration_method + = probDescDB.get_string("method.nond.reliability_integration"); + if (integration_method.empty() || integration_method == "first_order") + integrationOrder = 1; + else if (integration_method == "second_order") { + if (hess_type == "none") { + Cerr << "\nError: second-order integration requires Hessian " + << "specification." << std::endl; + abort_handler(-1); + } + else if (mppSearchType <= AMV_U) { + Cerr << "\nError: second-order integration only supported for fully " + << "converged MPP methods." << std::endl; + abort_handler(-1); + } + else + integrationOrder = 2; + } + else { + Cerr << "Error: bad integration selection in NonDLocalReliability." + << std::endl; + abort_handler(-1); + } + + if (integrationRefinement) { + for (size_t i=0; i Pecos::SMALL_NUMBER) { + const Pecos::RealVector& x_std_devs = natafTransform.x_std_deviations(); + for (i=0; iz. + size_t rl_len = requestedRespLevels[respFnCount].length(), + pl_len = requestedProbLevels[respFnCount].length(), + bl_len = requestedRelLevels[respFnCount].length(), + gl_len = requestedGenRelLevels[respFnCount].length(); + for (levelCount=0; levelCount Pecos::SMALL_NUMBER) { + Real ratio = (mean - z)/std_dev; + beta = computedRelLevels[respFnCount][levelCount] + = computedGenRelLevels[respFnCount][levelCount] + = (cdfFlag) ? ratio : -ratio; + p = computedProbLevels[respFnCount][levelCount] = probability(beta); + } + else { + if ( ( cdfFlag && mean <= z) || + (!cdfFlag && mean > z) ) { + beta = computedRelLevels[respFnCount][levelCount] + = computedGenRelLevels[respFnCount][levelCount] + = -Pecos::LARGE_NUMBER; + p = computedProbLevels[respFnCount][levelCount] = 1.; + } + else { + beta = computedRelLevels[respFnCount][levelCount] + = computedGenRelLevels[respFnCount][levelCount] + = Pecos::LARGE_NUMBER; + p = computedProbLevels[respFnCount][levelCount] = 0.; + } + } + switch (respLevelTarget) { + case PROBABILITIES: + finalStatistics.function_value(p, statCount); break; + case RELIABILITIES: case GEN_RELIABILITIES: + finalStatistics.function_value(beta, statCount); break; + } + if (final_asv[statCount] & 2) { + Cerr << "Error: response probability/reliability/gen_reliability level " + << "sensitivity not supported for Mean Value." << std::endl; + abort_handler(-1); + } + statCount++; + // Update specialty graphics + if (!subIteratorFlag) + dakota_graphics.add_datapoint(respFnCount, z, p); + } + for (i=0; i= rl_len + pl_len + bl_len ) ); + if (ria_flag) { + requestedTargetLevel = requestedRespLevels[respFnCount][levelCount]; + Cout << "\n>>>>> Reliability Index Approach (RIA) for response level " + << levelCount+1 << " = " << requestedTargetLevel << '\n'; + } + else if (levelCount < rl_len + pl_len) { + index = levelCount - rl_len; + Real p = requestedProbLevels[respFnCount][index]; + Cout << "\n>>>>> Performance Measure Approach (PMA) for probability " + << "level " << index + 1 << " = " << p << '\n'; + // gen beta target for 2nd-order PMA; beta target for 1st-order PMA: + requestedTargetLevel = reliability(p); + + // CDF probability < 0.5 --> CDF beta > 0 --> minimize g + // CDF probability > 0.5 --> CDF beta < 0 --> maximize g + // CDF probability = 0.5 --> CDF beta = 0 --> compute g + // Note: "compute g" means that min/max is irrelevant since there is + // a single G(u) value when the radius beta collapses to the origin + Real p_cdf = (cdfFlag) ? p : 1. - p; + pmaMaximizeG = (p_cdf > 0.5); // updated in update_pma_maximize() + } + else if (levelCount < rl_len + pl_len + bl_len) { + index = levelCount - rl_len - pl_len; + requestedTargetLevel = requestedRelLevels[respFnCount][index]; + Cout << "\n>>>>> Performance Measure Approach (PMA) for reliability " + << "level " << index + 1 << " = " << requestedTargetLevel << '\n'; + Real beta_cdf = (cdfFlag) ? + requestedTargetLevel : -requestedTargetLevel; + pmaMaximizeG = (beta_cdf < 0.); + } + else { + index = levelCount - rl_len - pl_len - bl_len; + requestedTargetLevel = requestedGenRelLevels[respFnCount][index]; + Cout << "\n>>>>> Performance Measure Approach (PMA) for generalized " + << "reliability level " << index + 1 << " = " + << requestedTargetLevel << '\n'; + Real gen_beta_cdf = (cdfFlag) ? + requestedTargetLevel : -requestedTargetLevel; + pmaMaximizeG = (gen_beta_cdf < 0.); // updated in update_pma_maximize() + } + + // Assign cold/warm-start values for initialPtU, mostProbPointX/U, + // computedRespLevel, fnGradX/U, and fnHessX/U. + if (levelCount) + initialize_mpp_search_data(); + +#ifdef DERIV_DEBUG + // numerical verification of analytic Jacobian/Hessian routines + if (mppSearchType == NO_APPROX && levelCount == 0) + mostProbPointU = ranVarMeansU;//mostProbPointX = ranVarMeansX; + //natafTransform.verify_trans_jacobian_hessian(mostProbPointU); + //natafTransform.verify_trans_jacobian_hessian(mostProbPointX); + natafTransform.verify_design_jacobian(mostProbPointU); +#endif // DERIV_DEBUG + + // For AMV+/TANA approximations, iterate until current expansion point + // converges to the MPP. + approxIters = 0; + approxConverged = false; + while (!approxConverged) { + + Sizet2DArray vars_map, primary_resp_map, secondary_resp_map; + BoolDequeArray nonlinear_resp_map(2); + RecastModel* mpp_model_rep = (RecastModel*)mppModel.model_rep(); + if (ria_flag) { // RIA: g is in constraint + primary_resp_map.resize(1); // one objective, no contributors + secondary_resp_map.resize(1); // one constraint, one contributor + secondary_resp_map[0].resize(1); + secondary_resp_map[0][0] = respFnCount; + nonlinear_resp_map[1] = BoolDeque(1, false); + mpp_model_rep->initialize(vars_map, false, NULL, NULL, + primary_resp_map, secondary_resp_map, nonlinear_resp_map, + RIA_objective_eval, RIA_constraint_eval); + } + else { // PMA: g is in objective + primary_resp_map.resize(1); // one objective, one contributor + primary_resp_map[0].resize(1); + primary_resp_map[0][0] = respFnCount; + secondary_resp_map.resize(1); // one constraint, no contributors + nonlinear_resp_map[0] = BoolDeque(1, false); + // If 2nd-order PMA with p-level or generalized beta-level, use + // PMA2_set_mapping() & PMA2_constraint_eval(). For approx-based + // 2nd-order PMA, we utilize curvature of the surrogate (if any) + // to update beta* + if (pma2_flag) + mpp_model_rep->initialize(vars_map, false, NULL, PMA2_set_mapping, + primary_resp_map, secondary_resp_map, nonlinear_resp_map, + PMA_objective_eval, PMA2_constraint_eval); + else + mpp_model_rep->initialize(vars_map, false, NULL, NULL, + primary_resp_map, secondary_resp_map, nonlinear_resp_map, + PMA_objective_eval, PMA_constraint_eval); + } + mppModel.continuous_variables(initialPtU); + + // Execute MPP search and retrieve u-space results + Cout << "\n>>>>> Initiating search for most probable point (MPP)\n"; + ParLevLIter pl_iter + = methodPCIter->mi_parallel_level_iterator(miPLIndex); + mppOptimizer.run(pl_iter); + const Variables& vars_star = mppOptimizer.variables_results(); + const Response& resp_star = mppOptimizer.response_results(); + const RealVector& fns_star = resp_star.function_values(); + Cout << "\nResults of MPP optimization:\nInitial point (u-space) =\n" + << initialPtU << "Final point (u-space) =\n"; + write_data(Cout, vars_star.continuous_variables()); + if (ria_flag) + Cout << "RIA optimum =\n " + << std::setw(write_precision+7) << fns_star[0] << " [u'u]\n" + << " " << std::setw(write_precision+7) + << fns_star[1] << " [G(u) - z]\n"; + else { + Cout << "PMA optimum =\n " + << std::setw(write_precision+7) << fns_star[0] << " ["; + if (pmaMaximizeG) Cout << '-'; + Cout << "G(u)]\n " << std::setw(write_precision+7) + << fns_star[1]; + if (pma2_flag) Cout << " [B* - bar-B*]\n"; + else Cout << " [u'u - B^2]\n"; + } + + // Update MPP search data + update_mpp_search_data(vars_star, resp_star); + + } // end AMV+ while loop + + // Update response/probability/reliability level data + update_level_data(); + + statCount++; + } // end loop over levels + } // end loop over response fns + + // Update warm-start data + if (warmStartFlag && subIteratorFlag) // view->copy + copy_data(iteratedModel.inactive_continuous_variables(), prevICVars); + + // This function manages either component or system reliability metrics + // via post-processing of computed{Resp,Prob,Rel,GenRel}Levels + update_final_statistics(); + + // restore in case of recursion + nondLocRelInstance = prev_instance; +} + + +/** An initial first- or second-order Taylor-series approximation is + required for MV/AMV/AMV+/TANA or for the case where momentStats + (from MV) are required within finalStatistics for subIterator + usage of NonDLocalReliability. */ +void NonDLocalReliability::initial_taylor_series() +{ + bool init_ts_flag = (mppSearchType < NO_APPROX); // updated below + const String& hess_type = iteratedModel.hessian_type(); + size_t i, j, k; + ShortArray asrv(numFunctions, 0); + short mode = 3; + if (taylorOrder == 2 && hess_type != "quasi") // no data yet in quasiHess + mode |= 4; + + const ShortArray& final_asv = finalStatistics.active_set_request_vector(); + switch (mppSearchType) { + case MV: + asrv.assign(numFunctions, mode); + break; + case AMV_X: case AMV_U: + case AMV_PLUS_X: case AMV_PLUS_U: + case TANA_X: case TANA_U: + for (i=0; i>>>> Evaluating response at mean values\n"; + if (mppSearchType && mppSearchType < NO_APPROX) + uSpaceModel.component_parallel_mode(TRUTH_MODEL); + iteratedModel.continuous_variables(natafTransform.x_means()); + activeSet.request_vector(asrv); + iteratedModel.compute_response(activeSet); + const Response& curr_resp = iteratedModel.current_response(); + fnValsMeanX = curr_resp.function_values(); + fnGradsMeanX = curr_resp.function_gradients(); + if (mode & 4) + fnHessiansMeanX = curr_resp.function_hessians(); + + // compute the covariance matrix from the correlation matrix + RealSymMatrix covariance; + const Pecos::RealVector& x_std_devs = natafTransform.x_std_deviations(); + if (correlation_flag) { + covariance.shapeUninitialized(numUncertainVars); + const Pecos::RealSymMatrix& x_corr_mat + = natafTransform.x_correlation_matrix(); + for (i=0; i bad for MV CDF estimates. + bool t2nq = (taylorOrder == 2 && hess_type != "quasi"); // 2nd-order mean + for (i=0; i>>>> Evaluating response at median values\n"; + if (mppSearchType && mppSearchType < NO_APPROX) + uSpaceModel.component_parallel_mode(TRUTH_MODEL); + RealVector ep_median_u(numUncertainVars), // inits vals to 0 + ep_median_x(numUncertainVars, false); + natafTransform.trans_U_to_X(ep_median_u, ep_median_x); + iteratedModel.continuous_variables(ep_median_x); + activeSet.request_values(0); // initialize + for (size_t i=0; iinitialize_random_variables(natafTransform); + } +} + + +/** For a particular response function prior to the first z/p/beta level, + initialize/warm-start optimizer initial guess (initialPtU), + expansion point (mostProbPointX/U), and associated response + data (computedRespLevel, fnGradX/U, and fnHessX/U). */ +void NonDLocalReliability::initialize_level_data() +{ + // All reliability methods need initialization of initialPtU; AMV/AMV+/TANA + // methods additionally need initialization of fnGradX/U; and AMV+/TANA + // methods additionally need initialization of mostProbPointX/U and + // computedRespLevel. + + // If warm-starting across multiple NonDLocalReliability invocations (e.g., + // for modified design parameters in RBDO), warm-start using the level 0 final + // results for the corresponding response fn. For all subsequent levels, + // the warm-start procedure is self-contained (i.e., no data from the + // previous NonDLocalReliability invocation is used). + + // For AMV+ across multiple NonDLocalReliability invocations, the previous + // level 0 converged MPP provides the basis for the initial expansion point. + // If inactive variable design sensitivities are available, a projection + // from the previous MPP is used. In either case, re-evaluation of response + // data is required to capture the effect of inactive variable changes + // (design variables in RBDO). Since the mean expansion at the new d + // has already been computed, one could also use this since it may predict + // an MPP estimate (after one opt cycle, prior to the expense of the second + // expansion evaluation) as good as the converged/projected MPP at the + // old d. However, the former approach has been observed to be preferable + // in practice (even without projection). + + if (warmStartFlag && subIteratorFlag && numRelAnalyses) { + // level 0 of each response fn in subsequent UQ analysis: initial + // optimizer guess and initial expansion point are the converged + // MPP from the previous UQ analysis, for which the computedRespLevel + // and fnGradX/U must be re-evaluated due to design variable changes. + + // simplest approach + initialPtU = prevMPPULev0[respFnCount]; // AMV/AMV+/FORM + + // If inactive var sensitivities are available, then apply a correction + // to initialPtU using a design sensitivity projection (Burton & Hajela). + // Note 1: only valid for RIA. + // Note 2: when the top level RBDO optimizer is performing a value-based + // line search, it is possible for prevFnGradDLev0 to be older than + // prevICVars/prevMPPULev0/prevFnGradULev0. In testing, this appears to + // be OK and preferable to bypassing the projection when prevFnGradDLev0 + // is out of date (which is why the previous ASV test is cumulative: if + // prevFnGradDLev0 has been populated, use it whether or not it was from + // the last analysis). + bool inactive_grads = (prevCumASVLev0[respFnCount] & 2) ? true : false; + bool lev0_ria = (requestedRespLevels[respFnCount].empty()) ? false : true; + if (inactive_grads && lev0_ria) { + RealVector fn_grad_d = Teuchos::getCol(Teuchos::View, prevFnGradDLev0, + respFnCount); + RealVector fn_grad_u = Teuchos::getCol(Teuchos::View, prevFnGradULev0, + respFnCount); + const RealVector& d_k_plus_1 + = iteratedModel.inactive_continuous_variables(); // view + Real grad_d_delta_d = 0., norm_grad_u_sq = 0.; + size_t i, num_icv = d_k_plus_1.length(); + for (i=0; i>>>> Evaluating new response at projected MPP\n"; + else + Cout << "\n>>>>> Evaluating new response at previous MPP\n"; + uSpaceModel.component_parallel_mode(TRUTH_MODEL); + // set active/uncertain vars augmenting inactive design vars + iteratedModel.continuous_variables(mostProbPointX); + short mode = (taylorOrder == 2) ? 7 : 3; + activeSet.request_values(0); activeSet.request_value(mode, respFnCount); + + iteratedModel.compute_response(activeSet); + const Response& curr_resp = iteratedModel.current_response(); + computedRespLevel = curr_resp.function_value(respFnCount); + fnGradX = curr_resp.function_gradient_copy(respFnCount); + + SizetMultiArrayConstView cv_ids = iteratedModel.continuous_variable_ids(); + SizetArray x_dvv; copy_data(cv_ids, x_dvv); + natafTransform.trans_grad_X_to_U(fnGradX, fnGradU, mostProbPointX, + x_dvv, cv_ids); + if (mode & 4) { + fnHessX = curr_resp.function_hessian(respFnCount); + natafTransform.trans_hess_X_to_U(fnHessX, fnHessU, mostProbPointX, + fnGradX, x_dvv, cv_ids); + curvatureDataAvailable = true; kappaUpdated = false; + } + } + } + else { // level 0 of each response fn in first or only UQ analysis + + // initial fnGradX/U for AMV/AMV+ = grads at mean x values, initial + // expansion point for AMV+ = mean x values. + if (mppSearchType < NO_APPROX) { // AMV/AMV+/TANA + // update mostProbPointX/U, computedRespLevel, fnGradX/U, fnHessX/U + assign_mean_data(); +#ifdef MPP_CONVERGE_RATE + if (mppSearchType >= AMV_PLUS_X) + Cout << "u'u = " << mostProbPointU.dot(mostProbPointU) + << " G(u) = " << computedRespLevel << '\n'; +#endif // MPP_CONVERGE_RATE + } + + // initial optimizer guess in u-space (initialPtU) + initialPtU = initialPtUSpec; // initialPtUSpec set in ctor + + /* + // fall back if projection is unavailable (or numerics don't work out). + initialPtU = (ria_flag) ? initialPtUSpec : + std::fabs(requestedCDFRelLevel)/std::sqrt((Real)numUncertainVars); + + // if fnValsMeanX/fnGradU are available, then warm start initialPtU using + // a projection from the means. + if (warmStartFlag && mv_flag) { + Real alpha, norm_grad_u_sq = fnGradU.dot(fnGradU); + if (ria_flag) { + // use same projection idea as for a z level change, + // but project from means + if ( norm_grad_u_sq > 1.e-10 ) { + alpha = (requestedRespLevel - fnValsMeanX[respFnCount]) + / norm_grad_u_sq; + for (i=0; i= 0. && norm_grad_u_sq > 1.e-10) { + Real alpha1 = (-b + std::sqrt(b2m4ac))/2./norm_grad_u_sq, + alpha2 = (-b - std::sqrt(b2m4ac))/2./norm_grad_u_sq, + g_est1 = fnValsMeanX[respFnCount] + alpha1*norm_grad_u_sq; + // Select the correct root based on sign convention involving beta + // and relationship of projected G to G(0): + if (requestedCDFRelLevel >= 0.) + // if beta_cdf >= 0, then projected G should be <= G(0) + alpha = (g_est1 <= medianFnVals[respFnCount]) ? alpha1 : alpha2; + else + // if beta_cdf < 0, then projected G should be > G(0) + alpha = (g_est1 > medianFnVals[respFnCount]) ? alpha1 : alpha2; + for (i=0; i 1.e-10 ) { // also handles NPSOL numerical case + Real alpha = (requestedTargetLevel - + requestedRespLevels[respFnCount][levelCount-1])/norm_grad_u_sq; + for (size_t i=0; i= rl_len + pl_len + bl_len ) ) ? + computedGenRelLevels[respFnCount][levelCount-1] : + computedRelLevels[respFnCount][levelCount-1]; + // Note: scaling is applied to mppU, so we want best est of new beta. + // Don't allow excessive init pt scaling if secant Hessian updating. + Real high_tol = 1.e+3, + low_tol = ( ( taylorOrder == 2 || integrationOrder == 2 ) && + iteratedModel.hessian_type() == "quasi" ) ? 1.e-3 : 1.e-10; + if ( std::abs(prev_bl) > low_tol && std::abs(prev_bl) < high_tol && + std::abs(requestedTargetLevel) > low_tol && + std::abs(requestedTargetLevel) < high_tol ) { + // CDF or CCDF does not matter for scale_factor so long as it is + // consistent (CDF/CDF or CCDF/CCDF). + Real scale_factor = requestedTargetLevel / prev_bl; +#ifdef DEBUG + Cout << "PMA warm start: previous = " << prev_bl + << " current = " << requestedTargetLevel + << " scale_factor = " << scale_factor << std::endl; +#endif // DEBUG + for (size_t i=0; i copy + natafTransform.trans_U_to_X(mostProbPointU, mostProbPointX); + + // Set computedRespLevel to the current g(x) value by either performing + // a validation function evaluation (AMV/AMV+) or retrieving data from + // resp_star (FORM). Also update approximations and convergence tols. + SizetMultiArrayConstView cv_ids = iteratedModel.continuous_variable_ids(); + SizetArray x_dvv; copy_data(cv_ids, x_dvv); + switch (mppSearchType) { + case AMV_X: case AMV_U: { + approxConverged = true; // break out of while loop + uSpaceModel.component_parallel_mode(TRUTH_MODEL); + activeSet.request_values(0); activeSet.request_value(1, respFnCount); + iteratedModel.continuous_variables(mostProbPointX); + iteratedModel.compute_response(activeSet); + computedRespLevel + = iteratedModel.current_response().function_value(respFnCount); + break; + } + case AMV_PLUS_X: case AMV_PLUS_U: case TANA_X: case TANA_U: { + // Assess AMV+/TANA iteration convergence. ||del_u|| is not a perfect + // metric since cycling between MPP estimates can occur. Therefore, + // a maximum number of iterations is also enforced. + //conv_metric = std::fabs(fn_vals[respFnCount] - requestedRespLevel); + ++approxIters; + if (conv_metric < convergenceTol) + approxConverged = true; + else if (approxIters >= maxIterations) { + Cerr << "\nWarning: maximum number of limit state approximation cycles " + << "exceeded.\n"; + warningBits |= 1; // first warning in output summary + approxConverged = true; + } + // Update response data for local/multipoint MPP approximation + short mode = 1; + if (approxConverged) { + Cout << "\n>>>>> Approximate MPP iterations converged. " + << "Evaluating final response.\n"; + // fnGradX/U needed for warm starting by projection, final_stat_grad, + // and/or 2nd-order integration. + const ShortArray& final_asv = finalStatistics.active_set_request_vector(); + if ( warmStartFlag || ( final_asv[statCount] & 2 ) ) + mode |= 2; + if (integrationOrder == 2) { + mode |= 4; + if (numUncertainVars != numNormalVars) + mode |= 2; // fnGradX needed to transform fnHessX to fnHessU + } + } + else { // not converged + Cout << "\n>>>>> Updating approximation for MPP iteration " + << approxIters+1 << "\n"; + mode |= 2; // update AMV+/TANA approximation + if (taylorOrder == 2) // update AMV^2+ approximation + mode |= 4; + if (warmStartFlag) // warm start initialPtU for next AMV+ iteration + initialPtU = mostProbPointU; + } + // evaluate new expansion point + uSpaceModel.component_parallel_mode(TRUTH_MODEL); + activeSet.request_values(0); + activeSet.request_value(mode, respFnCount); + iteratedModel.continuous_variables(mostProbPointX); + iteratedModel.compute_response(activeSet); + const Response& curr_resp = iteratedModel.current_response(); + computedRespLevel = curr_resp.function_value(respFnCount); +#ifdef MPP_CONVERGE_RATE + Cout << "u'u = " << mostProbPointU.dot(mostProbPointU) + << " G(u) = " << computedRespLevel << '\n'; +#endif // MPP_CONVERGE_RATE + if (mode & 2) { + fnGradX = curr_resp.function_gradient_copy(respFnCount); + natafTransform.trans_grad_X_to_U(fnGradX, fnGradU, mostProbPointX, + x_dvv, cv_ids); + } + if (mode & 4) { + fnHessX = curr_resp.function_hessian(respFnCount); + natafTransform.trans_hess_X_to_U(fnHessX, fnHessU, mostProbPointX, + fnGradX, x_dvv, cv_ids); + curvatureDataAvailable = true; kappaUpdated = false; + } + + // Update the limit state surrogate model + update_limit_state_surrogate(); + + // Update pmaMaximizeG if 2nd-order PMA for specified p / beta* level + if ( !approxConverged && !ria_flag && integrationOrder == 2 ) + update_pma_maximize(mostProbPointU, fnGradU, fnHessU); + + break; + } + case NO_APPROX: { // FORM/SORM + + // direct optimization converges to MPP: no new approximation to compute + approxConverged = true; // break out of while loop + if (ria_flag) // RIA computed response = eq_con_star + response target + computedRespLevel = fns_star[1] + requestedTargetLevel; + else // PMA computed response = +/- obj_fn_star + computedRespLevel = (pmaMaximizeG) ? -fns_star[0] : fns_star[0]; + + // fnGradX/U needed for warm starting by projection, final_stat_grad, and/or + // 2nd-order integration (for nonlinear transformations), and should be + // retrievable from previous evals. If second-order integration for RIA, + // fnHessX/U also needed, but not retrievable. If second-order PMA with + // specified p-level, Hessian should be retrievable since it was computed + // during the update of requestedCDFRelLevel from requestedCDFProbLevel. + // When data should be retrievable, we cannot in general assume that the + // last grad/Hessian eval corresponds to the converged MPP; therefore, we + // use a DB search. If the DB search fails (e.g., the eval cache is + // deactivated), then we resort to reevaluation. + short mode = 0, found_mode = 0; // computedRespLevel already retrieved + const ShortArray& final_asv = finalStatistics.active_set_request_vector(); + if ( warmStartFlag || ( final_asv[statCount] & 2 ) ) + mode |= 2; + if ( integrationOrder == 2 ) {// apply 2nd-order integr in all RIA/PMA cases + mode |= 4; + if (numUncertainVars != numNormalVars) + mode |= 2; // fnGradX needed to transform fnHessX to fnHessU + } + + // retrieve previously evaluated gradient information, if possible + if (mode & 2) { // avail in all RIA/PMA cases (exception: numerical grads) + // query data_pairs to retrieve the fn gradient at the MPP + Variables search_vars = iteratedModel.current_variables().copy(); + search_vars.continuous_variables(mostProbPointX); + ActiveSet search_set = resp_star.active_set(); + ShortArray search_asv(numFunctions, 0); + search_asv[respFnCount] = 2; + search_set.request_vector(search_asv); + PRPCacheHIter cache_it = lookup_by_val(data_pairs, + iteratedModel.interface_id(), search_vars, search_set); + if (cache_it != data_pairs.get().end()) { + fnGradX = cache_it->response().function_gradient_copy(respFnCount); + found_mode |= 2; + } + } + // retrieve previously evaluated Hessian information, if possible + // > RIA and std PMA beta-level: Hessian not avail since not yet evaluated + // > PMA p-level and generalized beta-level: Hessian should be available + if ( ( mode & 4 ) && !ria_flag && + ( levelCount < rl_len + pl_len || + levelCount >= rl_len + pl_len + bl_len ) ) { + // query data_pairs to retrieve the fn Hessian at the MPP + Variables search_vars = iteratedModel.current_variables().copy(); + search_vars.continuous_variables(mostProbPointX); + ActiveSet search_set = resp_star.active_set(); + ShortArray search_asv(numFunctions, 0); + search_asv[respFnCount] = 4; + search_set.request_vector(search_asv); + PRPCacheHIter cache_it = lookup_by_val(data_pairs, + iteratedModel.interface_id(), search_vars, search_set); + if (cache_it != data_pairs.get().end()) { + fnHessX = cache_it->response().function_hessian(respFnCount); + found_mode |= 4; + } + } + // evaluate any remaining required data which could not be retrieved + short remaining_mode = mode - found_mode; + if (remaining_mode) { + Cout << "\n>>>>> Evaluating limit state derivatives at MPP\n"; + iteratedModel.continuous_variables(mostProbPointX); + activeSet.request_values(0); + activeSet.request_value(remaining_mode, respFnCount); + iteratedModel.compute_response(activeSet); + const Response& curr_resp = iteratedModel.current_response(); + if (remaining_mode & 2) + fnGradX = curr_resp.function_gradient_copy(respFnCount); + if (remaining_mode & 4) + fnHessX = curr_resp.function_hessian(respFnCount); + } + if (mode & 2) + natafTransform.trans_grad_X_to_U(fnGradX, fnGradU, mostProbPointX, + x_dvv, cv_ids); + if (mode & 4) { + natafTransform.trans_hess_X_to_U(fnHessX, fnHessU, mostProbPointX, + fnGradX, x_dvv, cv_ids); + curvatureDataAvailable = true; kappaUpdated = false; + } + break; + } + } + + // set computedRelLevel using u'u from fns_star; must follow fnGradU update + if (ria_flag) + computedRelLevel = signed_norm(std::sqrt(fns_star[0])); + else if (integrationOrder == 2) { // second-order PMA + // no op: computed{Rel,GenRel}Level updated in PMA2_constraint_eval() + } + else { // first-order PMA + Real norm_u_sq = fns_star[1] + std::pow(requestedTargetLevel, 2); + computedRelLevel = signed_norm(std::sqrt(norm_u_sq)); + } +} + + +/** Updates computedRespLevels/computedProbLevels/computedRelLevels, + finalStatistics, warm start, and graphics data. */ +void NonDLocalReliability::update_level_data() +{ + // local reliability data aren't output to tabular, so send directly + // to graphics window only + Graphics& dakota_graphics = parallelLib.output_manager().graphics(); + + bool ria_flag = (levelCount < requestedRespLevels[respFnCount].length()); + + // Update computed Resp/Prob/Rel/GenRel levels arrays. finalStatistics + // is updated within update_final_statistics() for all resp fns & levels. + computedRespLevels[respFnCount][levelCount] = computedRespLevel; + computedRelLevels[respFnCount][levelCount] = computedRelLevel; + Real computed_prob_level; + if (!ria_flag && integrationOrder == 2) { + computedGenRelLevels[respFnCount][levelCount] = computedGenRelLevel; + computedProbLevels[respFnCount][levelCount] = computed_prob_level = + probability(computedGenRelLevel); + } + else { + computedProbLevels[respFnCount][levelCount] = computed_prob_level = + probability(computedRelLevel, cdfFlag, mostProbPointU, fnGradU, fnHessU); + computedGenRelLevels[respFnCount][levelCount] = computedGenRelLevel = + reliability(computed_prob_level); + } + + // Final statistic gradients are dz/ds, dbeta/ds, or dp/ds + const ShortArray& final_asv = finalStatistics.active_set_request_vector(); + bool system_grad_contrib = false; + if (respLevelTargetReduce && + levelCount < requestedRespLevels[respFnCount].length()) { + size_t sys_stat_count = 2*numFunctions + totalLevelRequests + levelCount; + if (final_asv[sys_stat_count] & 2) + system_grad_contrib = true; + } + if ( (final_asv[statCount] & 2) || system_grad_contrib ) { + + // evaluate dg/ds at the MPP and store in final_stat_grad + RealVector final_stat_grad; + dg_ds_eval(mostProbPointX, fnGradX, final_stat_grad); + + // for warm-starting next run + if (warmStartFlag && subIteratorFlag && levelCount == 0) + Teuchos::setCol(final_stat_grad, respFnCount, prevFnGradDLev0); + + // RIA: sensitivity of beta/p/beta* w.r.t. inactive variables + // dbeta/ds = 1/norm_grad_u * dg/ds (first-order) + // dp/ds = -phi(-beta) * dbeta/ds (first-order) + // dp_2/ds = [Phi(-beta_corr)*sum - phi(-beta_corr)*prod] * dbeta/ds + // (second-order) + // dbeta*/ds = -1/phi(-beta*) * dp_2/ds (second-order) + // PMA: sensitivity of g function w.r.t. inactive variables + // dz/ds = dg/ds + if (ria_flag) { + // beta_cdf = -beta_ccdf, p_cdf = 1. - p_ccdf + // -->> dbeta_cdf/ds = -dbeta_ccdf/ds, dp_cdf/ds = -dp_ccdf/ds + Real norm_grad_u = fnGradU.normFrobenius(); + // factor for first-order dbeta/ds: + Real factor = (cdfFlag) ? 1./norm_grad_u : -1./norm_grad_u; + if (integrationOrder == 2 && respLevelTarget != RELIABILITIES) { + factor *= dp2_dbeta_factor(computedRelLevel, cdfFlag); + // factor for second-order dbeta*/ds + if (respLevelTarget == GEN_RELIABILITIES) + factor *= -1. / Pecos::phi(-computedGenRelLevel); + } + else if (respLevelTarget == PROBABILITIES) // factor for first-order dp/ds + factor *= -Pecos::phi(-computedRelLevel); + + // apply factor: + size_t i, num_final_grad_vars + = finalStatistics.active_set_derivative_vector().size(); + for (i=0; i 1 && respFnCount < numFunctions-1 && + levelCount == requestedRespLevels[respFnCount].length() + + requestedProbLevels[respFnCount].length() + + requestedRelLevels[respFnCount].length() + + requestedGenRelLevels[respFnCount].length() - 1) + dakota_graphics.new_dataset(numFunctions+i); + } + } +} + + +void NonDLocalReliability::update_limit_state_surrogate() +{ + bool x_space = (mppSearchType == AMV_X || mppSearchType == AMV_PLUS_X || + mppSearchType == TANA_X); + + // construct local Variables object + Variables mpp_vars(iteratedModel.current_variables().shared_data()); + if (x_space) mpp_vars.continuous_variables(mostProbPointX); + else mpp_vars.continuous_variables(mostProbPointU); + + // construct Response object + ShortArray asv(numFunctions, 0); + asv[respFnCount] = (taylorOrder == 2) ? 7 : 3; + ActiveSet set;//(numFunctions, numUncertainVars); + set.request_vector(asv); + set.derivative_vector(iteratedModel.continuous_variable_ids()); + Response response(SIMULATION_RESPONSE, set); + response.function_value(computedRespLevel, respFnCount); + if (x_space) { + response.function_gradient(fnGradX, respFnCount); + if (taylorOrder == 2) + response.function_hessian(fnHessX, respFnCount); + } + else { + response.function_gradient(fnGradU, respFnCount); + if (taylorOrder == 2) + response.function_hessian(fnHessU, respFnCount); + } + IntResponsePair response_pr(0, response); // dummy eval id + + // After a design variable change, history data (e.g., TANA) needs + // to be cleared (build_approximation() only calls clear_current()) + if (numRelAnalyses && levelCount == 0) + uSpaceModel.approximations()[respFnCount].clear_all(); + // build the new local/multipoint approximation + uSpaceModel.build_approximation(mpp_vars, response_pr); +} + + +void NonDLocalReliability:: +update_pma_maximize(const RealVector& mpp_u, const RealVector& fn_grad_u, + const RealSymMatrix& fn_hess_u) +{ + Real p_cdf; bool update = false; + size_t rl_len = requestedRespLevels[respFnCount].length(), + rl_pl_len = rl_len + requestedProbLevels[respFnCount].length(), + rl_pl_bl_len = rl_pl_len + requestedRelLevels[respFnCount].length(); + if (levelCount < rl_pl_len) { + Real p = requestedProbLevels[respFnCount][levelCount-rl_len]; + p_cdf = (cdfFlag) ? p : 1. - p; + update = true; + } + else if (levelCount >= rl_pl_bl_len) { + Real gen_beta = requestedGenRelLevels[respFnCount][levelCount-rl_pl_bl_len]; + Real gen_beta_cdf = (cdfFlag) ? gen_beta : -gen_beta; + p_cdf = probability(gen_beta_cdf); + update = true; + } + if (update) { + Real beta_cdf = reliability(p_cdf, true, mpp_u, fn_grad_u, fn_hess_u); + pmaMaximizeG = (beta_cdf < 0.); + } +} + + +void NonDLocalReliability::assign_mean_data() +{ + const Pecos::RealVector& x_means = natafTransform.x_means(); + mostProbPointX = x_means; + mostProbPointU = ranVarMeansU; + computedRespLevel = fnValsMeanX(respFnCount); + for (size_t i=0; i 0.) + // grad_f[i] = u[i]/sqrt_sum_sq; + //else // gradient undefined at origin, use 0. to keep optimizer happy + // grad_f[i] = 0.; +} + + +/** This function recasts a G(u) response set (already transformed and + approximated in other recursions) into an RIA equality constraint. */ +void NonDLocalReliability:: +RIA_constraint_eval(const Variables& sub_model_vars, + const Variables& recast_vars, + const Response& sub_model_response, + Response& recast_response) +{ + // -------------------------------------------------------- + // The RIA equality constraint is G(u) - response level = 0 + // -------------------------------------------------------- + + short asv_val = recast_response.active_set_request_vector()[1]; + int resp_fn = nondLocRelInstance->respFnCount; + if (asv_val & 1) { + const Real& sub_model_fn = sub_model_response.function_value(resp_fn); + recast_response.function_value( + sub_model_fn - nondLocRelInstance->requestedTargetLevel, 1); + } + if (asv_val & 2) // dG/du: no additional transformation needed + recast_response.function_gradient( + sub_model_response.function_gradient_view(resp_fn), 1); + if (asv_val & 4) // d^2G/du^2: no additional transformation needed + recast_response.function_hessian( + sub_model_response.function_hessian(resp_fn), 1); +} + + +/** This function recasts a G(u) response set (already transformed and + approximated in other recursions) into an PMA objective function. */ +void NonDLocalReliability:: +PMA_objective_eval(const Variables& sub_model_vars, + const Variables& recast_vars, + const Response& sub_model_response, + Response& recast_response) +{ + // ---------------------------------- + // The PMA objective function is G(u) + // ---------------------------------- + + int resp_fn = nondLocRelInstance->respFnCount; + short sm_asv_val = sub_model_response.active_set_request_vector()[resp_fn]; + Real fn; RealVector fn_grad_u; RealSymMatrix fn_hess_u; + if (sm_asv_val & 2) + fn_grad_u = sub_model_response.function_gradient_view(resp_fn); + if (sm_asv_val & 4) + fn_hess_u = sub_model_response.function_hessian_view(resp_fn); + + // Due to RecastModel, objective_eval always called before constraint_eval, + // so perform NO_APPROX updates here. + if (nondLocRelInstance->mppSearchType == NO_APPROX && + nondLocRelInstance->integrationOrder == 2) { + nondLocRelInstance->curvatureDataAvailable = true; + nondLocRelInstance->kappaUpdated = false; // new fn_{grad,hess}_u data + nondLocRelInstance->update_pma_maximize(recast_vars.continuous_variables(), + fn_grad_u, fn_hess_u); + } + + short asv_val = recast_response.active_set_request_vector()[0]; + bool pma_max = nondLocRelInstance->pmaMaximizeG; + if (asv_val & 1) { + fn = sub_model_response.function_value(resp_fn); + if (pma_max) recast_response.function_value(-fn, 0); + else recast_response.function_value( fn, 0); + } + if (asv_val & 2) { // dG/du: no additional transformation needed + if (pma_max) { + RealVector recast_grad = recast_response.function_gradient_view(0); + size_t i, num_vars = fn_grad_u.length(); + for (i=0; irequestedTargetLevel, 2); + recast_response.function_value(c, 1); + } + if (asv_val & 2) { + RealVector grad_f = recast_response.function_gradient_view(1); + for (i=0; irespFnCount; + short sm_asv_val = sub_model_response.active_set_request_vector()[resp_fn]; + bool cdf = nondLocRelInstance->cdfFlag; + + // Calculate beta --> p --> beta*. Use up-to-date mpp/grad/Hessian info, + // including surrogate-based data, within signed_norm(), but disallow + // surrogate-based curvature corrections due to their sensitivity. The + // presence of fn_grad_u/fn_hess_u data is enforced in PMA2_set_mapping(). + RealVector fn_grad_u = sub_model_response.function_gradient_view(resp_fn); + Real comp_rel = nondLocRelInstance->computedRelLevel = + nondLocRelInstance->signed_norm(u, fn_grad_u, cdf); + // Don't update curvature correction when nonlinear transformation + // induces additional curvature on top of a low-order approximation. + // Note: if linear transformation or u-space AMV^2+, then Hessian is + // consistent with the previous truth and is constant over the surrogate. + Real computed_prob_level = (nondLocRelInstance->mppSearchType == NO_APPROX) ? + nondLocRelInstance->probability(comp_rel, cdf, u, fn_grad_u, + sub_model_response.function_hessian(resp_fn)) : + nondLocRelInstance->probability(comp_rel, cdf, + nondLocRelInstance->mostProbPointU, nondLocRelInstance->fnGradU, + nondLocRelInstance->fnHessU); + Real comp_gen_rel = nondLocRelInstance->computedGenRelLevel = + nondLocRelInstance->reliability(computed_prob_level); + + if (asv_val & 1) { // calculate the equality constraint: beta* - bar-beta* + Real c = comp_gen_rel - nondLocRelInstance->requestedTargetLevel; +#ifdef DEBUG + Cout << "In PMA2_constraint_eval, beta* = " << comp_gen_rel + << " bar-beta* = " << nondLocRelInstance->requestedTargetLevel + << " eq constr = " << c << std::endl; +#endif + recast_response.function_value(c, 1); + } + if (asv_val & 2) { + // Note: for second-order integrations, beta* is a function of p and + // kappa(u). dbeta*/du involves dkappa/du, but these terms are neglected + // as in dbeta*/ds (design sensitivities). + // dbeta/du_i = u_i/beta (in factor below) + // dp_2/du_i = [Phi(-beta_corr)*sum - phi(-beta_corr)*prod] * dbeta/du_i + // (term in brackets computed in dp2_dbeta_factor()) + // dbeta*/du_i = -1/phi(-beta*) * dp_2/du (in factor below) + Real factor = -nondLocRelInstance->dp2_dbeta_factor(comp_rel, cdf) + / comp_rel / Pecos::phi(-comp_gen_rel); + size_t i, num_vars = u.length(); + RealVector grad_f = recast_response.function_gradient_view(1); + for (i=0; ip-->beta* calcs + int sm_index = nondLocRelInstance->respFnCount; + short sub_model_request = sub_model_set.request_value(sm_index); + + // all cases require latest fn_grad_u (either truth-based or approx-based) + sub_model_request |= 2; + // PMA SORM requires latest fn_hess_u (truth-based) + if (nondLocRelInstance->mppSearchType == NO_APPROX) + sub_model_request |= 4; + // else value/grad request utilizes most recent truth fnGradU/fnHessU + + sub_model_set.request_value(sub_model_request, sm_index); + } +} + + +/** Computes dg/ds where s = design variables. Supports potentially + overlapping cases of design variable augmentation and insertion. */ +void NonDLocalReliability:: +dg_ds_eval(const RealVector& x_vars, const RealVector& fn_grad_x, + RealVector& final_stat_grad) +{ + const SizetArray& final_dvv = finalStatistics.active_set_derivative_vector(); + size_t i, num_final_grad_vars = final_dvv.size(); + if (final_stat_grad.empty()) + final_stat_grad.resize(num_final_grad_vars); + + // For design vars that are distribution parameters of the uncertain vars, + // dg/ds = dg/dx * dx/ds where dx/ds is the design Jacobian. Since dg/dx is + // already available (passed in as fn_grad_x), these sensitivities do not + // require additional response evaluations. + bool dist_param_deriv = false; + size_t num_outer_cv = secondaryACVarMapTargets.size(); + for (i=0; i>>>> Evaluating sensitivity with respect to augmented inactive " + << "variables\n"; + if (mppSearchType && mppSearchType < NO_APPROX) + uSpaceModel.component_parallel_mode(TRUTH_MODEL); + iteratedModel.continuous_variables(x_vars); + ActiveSet inactive_grad_set = activeSet; + inactive_grad_set.request_values(0); + inactive_grad_set.request_value(2, respFnCount); + // final_dvv is mapped from the top-level DVV in NestedModel::set_mapping() + // and includes augmented and inserted variable ids. Since we only want the + // augmented ids in this case, the UQ-level inactive ids are sufficient. + SizetMultiArrayConstView icv_ids + = iteratedModel.inactive_continuous_variable_ids(); + inactive_grad_set.derivative_vector(icv_ids); + /* More rigorous with reqd deriv vars, but equivalent in practice: + // Filter final_dvv to contain only inactive continuous variable ids: + SizetArray filtered_final_dvv; + for (i=0; imedian: CDF p(g<=z)>0.5, CDF beta<0, CCDF p(g>z)<0.5, CCDF beta>0 + // z0, CCDF p(g>z)>0.5, CCDF beta<0 + // z=median: CDF p(g<=z) = CCDF p(g>z) = 0.5, CDF beta = CCDF beta = 0 + //Real beta_cdf = (computedRespLevel > medianFnVals[respFnCount]) + // ? -std::sqrt(norm_u_sq) : std::sqrt(norm_u_sq); + + // This approach avoids the need to evaluate medianFnVals. Thanks to + // Barron Bichon for suggesting it. + // if > 0, then G is increasing along u and G(u*) > G(0) + // if < 0, then G is decreasing along u and G(u*) < G(0) + Real beta_cdf = (mpp_u.dot(fn_grad_u) > 0.) ? -norm_mpp_u : norm_mpp_u; +#ifdef DEBUG + Cout << "\nSign of is "; + if (mpp_u.dot(fn_grad_u) > 0.) Cout << " 1.\n\n"; + else Cout << "-1.\n\n"; +#endif + return (cdf_flag) ? beta_cdf : -beta_cdf; +} + + +/** Converts beta into a probability using either first-order (FORM) or + second-order (SORM) integration. The SORM calculation first calculates + the principal curvatures at the MPP (using the approach in Ch. 8 of + Haldar & Mahadevan), and then applies correction formulations from the + literature (Breitung, Hohenbichler-Rackwitz, or Hong). */ +Real NonDLocalReliability:: +probability(Real beta, bool cdf_flag, const RealVector& mpp_u, + const RealVector& fn_grad_u, const RealSymMatrix& fn_hess_u) +{ + Real p = probability(beta); // FORM approximation + int wpp7; + if (outputLevel > NORMAL_OUTPUT) { + wpp7 = write_precision+7; + Cout << "Probability:"// << " beta = " << beta + << " first-order = " << std::setw(wpp7) << p; + } + + if (integrationOrder == 2 && curvatureDataAvailable) { + + if (!kappaUpdated) { + principal_curvatures(mpp_u, fn_grad_u, fn_hess_u, kappaU); + kappaUpdated = true; + } + + // The correction to p is applied for beta >= 0 (FORM p <= 0.5). + // For beta < 0, apply correction to complementary problem (Tvedt 1990). + // > beta changes sign + // > p becomes complement + // > principal curvature sign convention defined for CDF beta > 0 + // (negate for CDF beta < 0 or CCDF beta > 0, OK for CCDF beta < 0) + Real beta_corr = std::abs(beta); + Real p_corr = (beta >= 0.) ? p : 1. - p; + RealVector kappa; scale_curvature(beta, cdf_flag, kappaU, kappa); + + // Test for numerical exceptions in sqrt. Problematic kappa are large and + // negative (kterm is always positive). Skipping individual kappa means + // neglecting a primary curvature and including secondary curvatures, which + // may be counter-productive (potentially less accurate than FORM). + // Therefore, the entire correction is skipped if any curvature is + // problematic. A consistent approach must be used in reliability(). + bool apply_correction = true; + Real psi_m_beta; + if (secondOrderIntType != BREITUNG) + psi_m_beta = Pecos::phi(-beta_corr) / Pecos::Phi(-beta_corr); + Real kterm = (secondOrderIntType == BREITUNG) ? beta_corr : psi_m_beta; + int i, num_kappa = numUncertainVars - 1; + for (i=0; i + initialize(mpp_u, x_data_flag, respFnCount, p, requestedTargetLevel); + ParLevLIter pl_iter = methodPCIter->mi_parallel_level_iterator(miPLIndex); + importanceSampler.run(pl_iter); + p = importance_sampler_rep->final_probability(); + if (outputLevel > NORMAL_OUTPUT) + Cout << " refined = " << std::setw(wpp7) << p; + } + if (outputLevel > NORMAL_OUTPUT) + Cout << '\n'; +#ifdef DEBUG + if (integrationOrder == 2 && curvatureDataAvailable) + { Cout << "In probability(), kappaU:\n"; write_data(Cout, kappaU); } +#endif + + return p; +} + + +/** Compute sensitivity of second-order probability w.r.t. beta for use + in derivatives of p_2 or beta* w.r.t. auxilliary parameters s (design, + epistemic) or derivatives of beta* w.r.t. u in PMA2_constraint_eval(). */ +Real NonDLocalReliability::dp2_dbeta_factor(Real beta, bool cdf_flag) +{ + // dp/ds = -phi(-beta) * dbeta/ds + // (fall back to first-order, if needed) + // dp_2/ds = [Phi(-beta_corr)*sum - phi(-beta_corr)*prod] * dbeta/ds + // (this function computes term in brackets) + // dbeta*/ds = -1/phi(-beta*) * dp_2/ds (second-order) + + // For beta < 0, beta_corr = -beta and p_corr = 1 - p: + // dp/ds = -dp_corr/ds = -(dp_corr/dbeta_corr * dbeta_corr/ds) + // = -(dp_corr/dbeta_corr * -dbeta/ds) + // = dp_corr/dbeta_corr * dbeta/ds + + bool apply_correction; size_t i, j, num_kappa; + Real kterm, dpsi_m_beta_dbeta, beta_corr; RealVector kappa; + if (curvatureDataAvailable) { + + //if (!kappaUpdated) { // should already be up to date + // principal_curvatures(mpp_u, fn_grad_u, fn_hess_u, kappaU); + // kappaUpdated = true; + //} + + scale_curvature(beta, cdf_flag, kappaU, kappa); + beta_corr = (beta >= 0.) ? beta : -beta; + + switch (secondOrderIntType) { + case HONG: // addtnl complexity not warranted + Cerr << "\nError: final statistic gradients not implemented for Hong." + << std::endl; + abort_handler(-1); break; + case BREITUNG: + kterm = beta_corr; break; + case HOHENRACK: + // Psi(beta) = phi(beta) / Phi(beta) + // dPsi/dbeta = (Phi dphi/dbeta - phi^2)/Phi^2 + // where dphi/dbeta = -beta phi + // dPsi/dbeta = -phi (beta Phi + phi) / Phi^2 + // = -Psi (beta + Psi) + // --> dPsi/dbeta(-beta_corr) + // = -Psi(-beta_corr) (-beta_corr + Psi(-beta_corr) ) + // = Psi(-beta_corr) ( beta_corr - Psi(-beta_corr) ) + kterm = Pecos::phi(-beta_corr) / Pecos::Phi(-beta_corr); // psi_m_beta + dpsi_m_beta_dbeta = kterm*(beta_corr - kterm); // orig (kterm + beta_corr) + break; + } + + num_kappa = numUncertainVars - 1; + apply_correction = true; + for (i=0; i= 0. && p2_corr <= 1.) // factor for second-order dp/ds: + return p1_corr * sum - Pecos::phi(-beta_corr) * prod2; + } + + // if not returned, then there was an exception + Cerr << "\nWarning: second-order probability sensitivity bypassed.\n"; + warningBits |= 2; // second warning in output summary + } + + return -Pecos::phi(-beta); +} + + +// Converts a probability into a reliability using the inverse of the +// first-order or second-order integrations implemented in +// NonDLocalReliability::probability(). +Real NonDLocalReliability:: +reliability(Real p, bool cdf_flag, const RealVector& mpp_u, + const RealVector& fn_grad_u, const RealSymMatrix& fn_hess_u) +{ + Real beta = reliability(p); // FORM approximation + + if (integrationOrder == 2 && curvatureDataAvailable) { + + if (!kappaUpdated) { + principal_curvatures(mpp_u, fn_grad_u, fn_hess_u, kappaU); + kappaUpdated = true; + } + + // NOTE: these conversions are currently done once. It may be necessary + // to redo them for each beta estimate (when inverting near beta = zero). + Real beta_corr = (beta >= 0.) ? beta : -beta; + Real p_corr = (beta >= 0.) ? p : 1. - p; + RealVector kappa; scale_curvature(beta, cdf_flag, kappaU, kappa); + + // SORM correction to FORM: direct inversion of the SORM formulas is + // infeasible due to the multiple instances of beta on the RHS, even for + // the simplest case (Breitung). Therefore, use Newton's method to solve + // for beta(p) using Phi_inverse() as an initial guess. + // > Newton's method uses reliability_residual() to compute the residual f + // and reliability_residual_derivative() to compute df/dbeta. + // > Newton step is then beta -= f(beta)/[df/dbeta(beta)]. + // > Other options include using an inexact df/dbeta = phi(-beta) from + // FORM or using a quasi-Newton (Broyden update) or FD Newton approach. + + // evaluate residual + Real res; + bool terminate = reliability_residual(p_corr, beta_corr, kappa, res); + + size_t newton_iters = 0, max_iters = 20; // usually converges in ~3 iters + bool converged = false; + while (!terminate && !converged) { + + // evaluate derivative of residual w.r.t. beta + Real dres_dbeta + = reliability_residual_derivative(p_corr, beta_corr, kappa); + + // compute Newton step + Real delta_beta; + if (std::fabs(dres_dbeta) > DBL_MIN) { + delta_beta = -res/dres_dbeta; // full Newton step + // assess convergence using delta_beta, rather than residual, + // since this should be better scaled. + if (std::fabs(delta_beta) < convergenceTol) + converged = true; // but go ahead and take the step, if beneficial + } + else + terminate = true; + + // Simple backtracking line search globalization + bool reduction = false; + size_t backtrack_iters = 0; + while (!reduction && !terminate) { // enter loop even if converged + Real beta_step = beta_corr + delta_beta; + + // verify that new beta_step doesn't violate safeguards. If not, + // evaluate residual res_step at beta_step. + Real res_step; + terminate = reliability_residual(p_corr, beta_step, kappa, res_step); + + if (!terminate) { + if ( std::fabs(res_step) < std::fabs(res) ) { // accept step + reduction = true; + beta_corr = beta_step; + res = res_step; + //Cout << "residual = " << res << " delta = " << delta_beta + // << " beta = " << beta_corr <<'\n'; + } + else if (converged) + terminate = true; // kick out of inner while + else { // backtrack + //Cout << "Backtracking\n"; + delta_beta /= 2.; // halve the step + if (backtrack_iters++ >= max_iters) {// backtrack iter must complete + Cerr << "\nWarning: maximum back-tracking iterations exceeded in " + << "second-order reliability inversion.\n"; + warningBits |= 4; // third warning in output summary + terminate = true; + } + } + } + } + if (++newton_iters >= max_iters && !converged) { // Newton iter completed + Cerr << "\nWarning: maximum Newton iterations exceeded in second-order " + << "reliability inversion.\n"; + warningBits |= 8; // fourth warning in output summary + terminate = true; + } + } + return (beta >= 0.) ? beta_corr : -beta_corr; + } + return beta; +} + + +bool NonDLocalReliability:: +reliability_residual(const Real& p, const Real& beta, + const RealVector& kappa, Real& res) +{ + int i, num_kappa = numUncertainVars - 1; + + // Test for numerical exceptions in sqrt. Problematic kappa are large and + // negative (kterm is always positive). Skipping individual kappa means + // neglecting a primary curvature and including secondary curvatures, which + // may be counter-productive (potentially less accurate than FORM). Since + // the Newton solve can be problematic on its own, skip the entire solve in + // this case. + Real psi_m_beta; + if (secondOrderIntType != BREITUNG) + psi_m_beta = Pecos::phi(-beta) / Pecos::Phi(-beta); + Real kterm = (secondOrderIntType == BREITUNG) ? beta : psi_m_beta; + for (i=0; i DBL_MIN) + for (i=0; i DBL_MIN) { + // Can match the sign of fn_grad_u[i]/norm_grad_u in PMA case (align for + // max G, oppose for min G), but can't in general in RIA case (vectors + // may align or oppose). Fortunately, the R0 sign does not appear to + // matter since R is applied twice in R fn_hess_u R^T. + bool pma_max = (levelCount >= requestedRespLevels[respFnCount].length() && + pmaMaximizeG) ? true : false; + for (i=0; i=0; i--) { // update the ith row vector + for (j=i+1; j principal curvatures + Teuchos::LAPACK la; + int info, lwork = 3*num_kappa - 1; + double* work = new double [lwork]; + // LAPACK eigenvalue solution for real, symmetric A + if (kappa_u.length() != num_kappa) + kappa_u.sizeUninitialized(num_kappa); + la.SYEV('N', A.UPLO(), num_kappa, A.values(), A.stride(), kappa_u.values(), + work, lwork, &info); + delete [] work; + if (info) { + Cerr << "\nError: internal error in LAPACK eigenvalue routine." + << std::endl; + abort_handler(-1); + } + //Cout << "\nkappa_u:" << kappa_u; +} + + +void NonDLocalReliability::print_results(std::ostream& s) +{ + size_t i, j, width = write_precision+7; + StringMultiArrayConstView uv_labels + = iteratedModel.continuous_variable_labels(); + const StringArray& fn_labels = iteratedModel.response_labels(); + s << "-----------------------------------------------------------------\n"; + + if (warningBits) { + s << "Warnings accumulated during solution for one or more levels:\n"; + if (warningBits & 1) + s << " Maximum number of limit state approximation cycles exceeded.\n"; + if (warningBits & 2) + s << " Second-order probability integration bypassed due to numerical " + << "issues.\n"; + if (warningBits & 4) + s << " Maximum back-tracking iterations exceeded in second-order " + << "reliability inversion.\n"; + if (warningBits & 8) + s << " Maximum Newton iterations exceeded in second-order reliability " + << "inversion.\n"; + s << "Please interpret results with care.\n"; + s << "-----------------------------------------------------------------\n"; + } + + for (i=0; i + +#include + +static const char rcsId[]="@(#) $Id: NonDSampling.cpp 7036 2010-10-22 23:20:24Z mseldre $"; + + +namespace Dakota { + + +/** This constructor is called for a standard letter-envelope iterator + instantiation. In this case, set_db_list_nodes has been called and + probDescDB can be queried for settings from the method specification. */ +NonDSampling::NonDSampling(ProblemDescDB& problem_db, Model& model): + NonD(problem_db, model), seedSpec(probDescDB.get_int("method.random_seed")), + randomSeed(seedSpec), samplesSpec(probDescDB.get_int("method.samples")), + samplesRef(samplesSpec), numSamples(samplesSpec), + rngName(probDescDB.get_string("method.random_number_generator")), + sampleType(probDescDB.get_ushort("method.sample_type")), + statsFlag(true), allDataFlag(false), samplingVarsMode(ACTIVE), + sampleRanksMode(IGNORE_RANKS), + varyPattern(!probDescDB.get_bool("method.fixed_seed")), + backfillFlag(probDescDB.get_bool("method.backfill")), + numLHSRuns(0) +{ + if (epistemicStats && totalLevelRequests) { + Cerr << "\nError: sampling does not support level requests for " + << "analyses containing epistemic uncertainties." << std::endl; + abort_handler(-1); + } + + // Since the sampleType is shared with other iterators for other purposes, + // its default in DataMethod.cpp is SUBMETHOD_DEFAULT (0). Enforce an LHS + // default here. + if (!sampleType) + sampleType = SUBMETHOD_LHS; + + // initialize finalStatistics using the default statistics set + initialize_final_statistics(); + + // update concurrency + if (numSamples) // samples is optional (default = 0) + maxEvalConcurrency *= numSamples; +} + + +/** This alternate constructor is used for generation and evaluation + of on-the-fly sample sets. */ +NonDSampling:: +NonDSampling(unsigned short method_name, Model& model, + unsigned short sample_type, int samples, int seed, + const String& rng, bool vary_pattern, short sampling_vars_mode): + NonD(method_name, model), seedSpec(seed), randomSeed(seed), + samplesSpec(samples), samplesRef(samples), numSamples(samples), rngName(rng), + sampleType(sample_type), statsFlag(false), allDataFlag(true), + samplingVarsMode(sampling_vars_mode), sampleRanksMode(IGNORE_RANKS), + varyPattern(vary_pattern), backfillFlag(false), numLHSRuns(0) +{ + subIteratorFlag = true; // suppress some output + + // override default epistemicStats setting from NonD ctor + bool aleatory_mode = (samplingVarsMode == ALEATORY_UNCERTAIN || + samplingVarsMode == ALEATORY_UNCERTAIN_UNIFORM); + epistemicStats = (numEpistemicUncVars && !aleatory_mode); + + // enforce LHS as default sample type + if (!sampleType) + sampleType = SUBMETHOD_LHS; + + // not used but included for completeness + if (numSamples) // samples is optional (default = 0) + maxEvalConcurrency *= numSamples; +} + + +/** This alternate constructor is used by ConcurrentStrategy for + generation of uniform, uncorrelated sample sets. */ +NonDSampling:: +NonDSampling(unsigned short sample_type, int samples, int seed, + const String& rng, const RealVector& lower_bnds, + const RealVector& upper_bnds): + NonD(RANDOM_SAMPLING, lower_bnds, upper_bnds), seedSpec(seed), + randomSeed(seed), samplesSpec(samples), samplesRef(samples), + numSamples(samples), rngName(rng), sampleType(sample_type), statsFlag(false), + allDataFlag(true), samplingVarsMode(ACTIVE_UNIFORM), + sampleRanksMode(IGNORE_RANKS), varyPattern(true), backfillFlag(false), + numLHSRuns(0) +{ + subIteratorFlag = true; // suppress some output + + // enforce LHS as default sample type + if (!sampleType) + sampleType = SUBMETHOD_LHS; + + // not used but included for completeness + if (numSamples) // samples is optional (default = 0) + maxEvalConcurrency *= numSamples; +} + + +NonDSampling::~NonDSampling() +{ } + + +/** This version of get_parameter_sets() extracts data from the + user-defined model in any of the four sampling modes. */ +void NonDSampling::get_parameter_sets(Model& model) +{ + initialize_lhs(true); + + short model_view = model.current_variables().view().first; + switch (samplingVarsMode) { + case ACTIVE_UNIFORM: case ALL_UNIFORM: case UNCERTAIN_UNIFORM: + case ALEATORY_UNCERTAIN_UNIFORM: case EPISTEMIC_UNCERTAIN_UNIFORM: + // Use LHSDriver::generate_uniform_samples() between lower/upper bounds + if ( samplingVarsMode == ACTIVE_UNIFORM || + ( samplingVarsMode == ALL_UNIFORM && + ( model_view == RELAXED_ALL || model_view == MIXED_ALL ) ) || + ( samplingVarsMode == UNCERTAIN_UNIFORM && + ( model_view == RELAXED_UNCERTAIN || + model_view == MIXED_UNCERTAIN ) ) || + ( samplingVarsMode == ALEATORY_UNCERTAIN_UNIFORM && + ( model_view == RELAXED_ALEATORY_UNCERTAIN || + model_view == MIXED_ALEATORY_UNCERTAIN ) ) || + ( samplingVarsMode == EPISTEMIC_UNCERTAIN_UNIFORM && + ( model_view == RELAXED_EPISTEMIC_UNCERTAIN || + model_view == MIXED_EPISTEMIC_UNCERTAIN ) ) ) { + // sample uniformly from ACTIVE lower/upper bounds (regardless of model + // view), from UNCERTAIN lower/upper bounds (with model in DISTINCT view), + // or from ALL lower/upper bounds (with model in ALL view). + // loss of sampleRanks control is OK since NonDIncremLHS uses ACTIVE mode. + // TO DO: add support for uniform discrete + lhsDriver.generate_uniform_samples(model.continuous_lower_bounds(), + model.continuous_upper_bounds(), + numSamples, allSamples, backfillFlag); + } + else if (samplingVarsMode == ALL_UNIFORM) { + // sample uniformly from ALL lower/upper bnds with model in distinct view. + // loss of sampleRanks control is OK since NonDIncremLHS uses ACTIVE mode. + // TO DO: add support for uniform discrete + lhsDriver.generate_uniform_samples(model.all_continuous_lower_bounds(), + model.all_continuous_upper_bounds(), + numSamples, allSamples, backfillFlag); + } + else { // A, E, A+E UNCERTAIN + // sample uniformly from {A,E,A+E} UNCERTAIN lower/upper bounds + // with model using a non-corresponding view (corresponding views + // handled in first case above) + size_t start_acv, num_acv, dummy; + mode_counts(model, start_acv, num_acv, dummy, dummy, dummy, dummy, + dummy, dummy); + if (!num_acv) { + Cerr << "Error: no active continuous variables for sampling in " + << "uniform mode" << std::endl; + abort_handler(-1); + } + const RealVector& all_c_l_bnds = model.all_continuous_lower_bounds(); + const RealVector& all_c_u_bnds = model.all_continuous_upper_bounds(); + RealVector uncertain_c_l_bnds(Teuchos::View, + const_cast(&all_c_l_bnds[start_acv]), num_acv); + RealVector uncertain_c_u_bnds(Teuchos::View, + const_cast(&all_c_u_bnds[start_acv]), num_acv); + // loss of sampleRanks control is OK since NonDIncremLHS uses ACTIVE mode + // TO DO: add support for uniform discrete + lhsDriver.generate_uniform_samples(uncertain_c_l_bnds, + uncertain_c_u_bnds, + numSamples, allSamples, backfillFlag); + } + break; + case ALEATORY_UNCERTAIN: + { + lhsDriver.generate_samples(model.aleatory_distribution_parameters(), + numSamples, allSamples, backfillFlag); + break; + } + case EPISTEMIC_UNCERTAIN: + { + lhsDriver.generate_samples(model.epistemic_distribution_parameters(), + numSamples, allSamples, backfillFlag); + break; + } + case UNCERTAIN: + { + lhsDriver.generate_samples(model.aleatory_distribution_parameters(), + model.epistemic_distribution_parameters(), + numSamples, allSamples, backfillFlag); + break; + } + case ACTIVE: case ALL: { + // extract design and state bounds + RealVector cdv_l_bnds, cdv_u_bnds, csv_l_bnds, csv_u_bnds; + IntVector ddriv_l_bnds, ddriv_u_bnds, dsriv_l_bnds, dsriv_u_bnds; + const RealVector& all_c_l_bnds = model.all_continuous_lower_bounds(); + const RealVector& all_c_u_bnds = model.all_continuous_upper_bounds(); + if (numContDesVars) { + cdv_l_bnds + = RealVector(Teuchos::View, all_c_l_bnds.values(), numContDesVars); + cdv_u_bnds + = RealVector(Teuchos::View, all_c_u_bnds.values(), numContDesVars); + } + if (numContStateVars) { + size_t cv_start = model.acv() - numContStateVars; + csv_l_bnds = RealVector(Teuchos::View, + const_cast(&all_c_l_bnds[cv_start]), numContStateVars); + csv_u_bnds = RealVector(Teuchos::View, + const_cast(&all_c_u_bnds[cv_start]), numContStateVars); + } + const IntVector& all_di_l_bnds = model.all_discrete_int_lower_bounds(); + const IntVector& all_di_u_bnds = model.all_discrete_int_upper_bounds(); + size_t num_ddriv = (numDiscIntDesVars) ? + numDiscIntDesVars - model.discrete_design_set_int_values().size() : 0; + if (num_ddriv) { + ddriv_l_bnds = IntVector(Teuchos::View, all_di_l_bnds.values(),num_ddriv); + ddriv_u_bnds = IntVector(Teuchos::View, all_di_u_bnds.values(),num_ddriv); + } + size_t num_dsriv = (numDiscIntStateVars) ? + numDiscIntStateVars - model.discrete_state_set_int_values().size() : 0; + if (num_dsriv) { + size_t di_start = model.adiv() - numDiscIntStateVars; + dsriv_l_bnds = IntVector(Teuchos::View, + const_cast(&all_di_l_bnds[di_start]), num_dsriv); + dsriv_u_bnds = IntVector(Teuchos::View, + const_cast(&all_di_u_bnds[di_start]), num_dsriv); + } + IntSetArray empty_isa; StringSetArray empty_ssa; RealSetArray empty_rsa; + const IntSetArray& di_design_sets = (numDiscIntDesVars) ? + model.discrete_design_set_int_values() : empty_isa; + const StringSetArray& ds_design_sets = (numDiscStringDesVars) ? + model.discrete_design_set_string_values() : empty_ssa; + const RealSetArray& dr_design_sets = (numDiscRealDesVars) ? + model.discrete_design_set_real_values() : empty_rsa; + const IntSetArray& di_state_sets = (numDiscIntStateVars) ? + model.discrete_state_set_int_values() : empty_isa; + const StringSetArray& ds_state_sets = (numDiscStringStateVars) ? + model.discrete_state_set_string_values() : empty_ssa; + const RealSetArray& dr_state_sets = (numDiscRealStateVars) ? + model.discrete_state_set_real_values() : empty_rsa; + + // Call LHS to generate the specified samples within the specified + // distributions. Use model distribution parameters unless ACTIVE + // excludes {aleatory,epistemic,both} uncertain variables. + if ( samplingVarsMode == ACTIVE && + ( model_view == RELAXED_DESIGN || model_view == RELAXED_STATE || + model_view == MIXED_DESIGN || model_view == MIXED_STATE ) ) { + Pecos::AleatoryDistParams empty_adp; Pecos::EpistemicDistParams empty_edp; + if ( !backfillFlag ) + lhsDriver.generate_samples(cdv_l_bnds, cdv_u_bnds, ddriv_l_bnds, + ddriv_u_bnds, di_design_sets, ds_design_sets, dr_design_sets, + csv_l_bnds, csv_u_bnds, dsriv_l_bnds, dsriv_u_bnds, di_state_sets, + ds_state_sets, dr_state_sets, empty_adp, empty_edp, numSamples, + allSamples, sampleRanks); + else + lhsDriver.generate_unique_samples(cdv_l_bnds, cdv_u_bnds, ddriv_l_bnds, + ddriv_u_bnds, di_design_sets, ds_design_sets, dr_design_sets, + csv_l_bnds, csv_u_bnds, dsriv_l_bnds, dsriv_u_bnds, di_state_sets, + ds_state_sets, dr_state_sets, empty_adp, empty_edp, numSamples, + allSamples, sampleRanks); + } + else if ( samplingVarsMode == ACTIVE && + ( model_view == RELAXED_ALEATORY_UNCERTAIN || + model_view == MIXED_ALEATORY_UNCERTAIN ) ) { + Pecos::EpistemicDistParams empty_edp; + if ( !backfillFlag ) + lhsDriver.generate_samples(cdv_l_bnds, cdv_u_bnds, ddriv_l_bnds, + ddriv_u_bnds, di_design_sets, ds_design_sets, dr_design_sets, + csv_l_bnds, csv_u_bnds, dsriv_l_bnds, dsriv_u_bnds, di_state_sets, + ds_state_sets, dr_state_sets, model.aleatory_distribution_parameters(), + empty_edp, numSamples, allSamples, sampleRanks); + else + lhsDriver.generate_unique_samples(cdv_l_bnds, cdv_u_bnds, ddriv_l_bnds, + ddriv_u_bnds, di_design_sets, ds_design_sets, dr_design_sets, + csv_l_bnds, csv_u_bnds, dsriv_l_bnds, dsriv_u_bnds, di_state_sets, + ds_state_sets, dr_state_sets, model.aleatory_distribution_parameters(), + empty_edp, numSamples, allSamples, sampleRanks); + } + else if ( samplingVarsMode == ACTIVE && + ( model_view == RELAXED_EPISTEMIC_UNCERTAIN || + model_view == MIXED_EPISTEMIC_UNCERTAIN ) ) { + Pecos::AleatoryDistParams empty_adp; + if ( !backfillFlag ) + lhsDriver.generate_samples(cdv_l_bnds, cdv_u_bnds, ddriv_l_bnds, + ddriv_u_bnds, di_design_sets, ds_design_sets, dr_design_sets, + csv_l_bnds, csv_u_bnds, dsriv_l_bnds, dsriv_u_bnds, di_state_sets, + ds_state_sets, dr_state_sets, empty_adp, + model.epistemic_distribution_parameters(), numSamples, allSamples, + sampleRanks); + else + lhsDriver.generate_unique_samples(cdv_l_bnds, cdv_u_bnds, ddriv_l_bnds, + ddriv_u_bnds, di_design_sets, ds_design_sets, dr_design_sets, + csv_l_bnds, csv_u_bnds, dsriv_l_bnds, dsriv_u_bnds, di_state_sets, + ds_state_sets, dr_state_sets, empty_adp, + model.epistemic_distribution_parameters(), numSamples, allSamples, + sampleRanks); + } + else + { + if ( !backfillFlag ) + lhsDriver.generate_samples(cdv_l_bnds, cdv_u_bnds, ddriv_l_bnds, + ddriv_u_bnds, di_design_sets, ds_design_sets, dr_design_sets, + csv_l_bnds, csv_u_bnds, dsriv_l_bnds, dsriv_u_bnds, di_state_sets, + ds_state_sets, dr_state_sets, model.aleatory_distribution_parameters(), + model.epistemic_distribution_parameters(), numSamples, allSamples, + sampleRanks); + else + lhsDriver.generate_unique_samples(cdv_l_bnds, cdv_u_bnds, ddriv_l_bnds, + ddriv_u_bnds, di_design_sets, ds_design_sets, dr_design_sets, + csv_l_bnds, csv_u_bnds, dsriv_l_bnds, dsriv_u_bnds, di_state_sets, + ds_state_sets, dr_state_sets, model.aleatory_distribution_parameters(), + model.epistemic_distribution_parameters(), numSamples, allSamples, + sampleRanks); + // warning sampleRanks will empty. + // See comment in lhs_driver.cpp generate_unique_samples() + } + break; + } + } +} + + +/** This version of get_parameter_sets() does not extract data from the + user-defined model, but instead relies on the incoming bounded region + definition. It only support a UNIFORM sampling mode, where the + distinction of ACTIVE_UNIFORM vs. ALL_UNIFORM is handled elsewhere. */ +void NonDSampling:: +get_parameter_sets(const RealVector& lower_bnds, + const RealVector& upper_bnds) +{ + initialize_lhs(true); + lhsDriver.generate_uniform_samples(lower_bnds, upper_bnds, + numSamples, allSamples); +} + + +void NonDSampling:: +update_model_from_sample(Model& model, const Real* sample_vars) +{ + size_t i, cntr = 0, cv_start, num_cv, div_start, num_div, dsv_start, num_dsv, + drv_start, num_drv; + mode_counts(model, cv_start, num_cv, div_start, num_div, dsv_start, num_dsv, + drv_start, num_drv); + + // sampled continuous vars (by value) + size_t end = cv_start + num_cv; + for (i=cv_start; i= RELAXED_DESIGN && active_view <= RELAXED_STATE ) ); + short all_view = (relax) ? RELAXED_ALL : MIXED_ALL; + const StringSetArray& all_dss_values + = model.discrete_set_string_values(all_view); + end = dsv_start + num_dsv; + for (i=dsv_start; i= RELAXED_DESIGN && active_view <= RELAXED_STATE ) ); + short all_view = (relax) ? RELAXED_ALL : MIXED_ALL; + const StringSetArray& all_dss_values + = iteratedModel.discrete_set_string_values(all_view); + end = dsv_start + num_dsv; + for (i=dsv_start; i= RELAXED_DESIGN && active_view <= RELAXED_STATE ) ); + short all_view = (relax) ? RELAXED_ALL : MIXED_ALL; + const StringSetArray& all_dss_values + = iteratedModel.discrete_set_string_values(all_view); + + // is care needed to manage active vs. all string variables? + + StringMultiArrayConstView ds_vars = vars.discrete_string_variables(); + for (size_t j=0; j nonrepeatable behavior + randomSeed = generate_system_seed(); + lhsDriver.seed(randomSeed); + } + else if (varyPattern) // define sequence of seed values for numLHSRuns > 1 + lhsDriver.advance_seed_sequence(); + else // fixed_seed + lhsDriver.seed(randomSeed); // reset original/machine-generated seed + + // Needed a way to turn this off when LHS sampling is being used in + // NonDAdaptImpSampling because it gets written a _LOT_ + String sample_string = submethod_enum_to_string(sampleType); + if (write_message) { + Cout << "\nNonD " << sample_string << " Samples = " << numSamples; + if (numLHSRuns == 1 || !varyPattern) { + if (seedSpec) Cout << " Seed (user-specified) = "; + else Cout << " Seed (system-generated) = "; + Cout << randomSeed << '\n'; + } + else if (rngName == "rnum2") { + if (seedSpec) Cout << " Seed (sequence from user-specified) = "; + else Cout << " Seed (sequence from system-generated) = "; + Cout << lhsDriver.seed() << '\n'; + } + else // default Boost Mersenne twister + Cout << " Seed not reset from previous LHS execution\n"; + } + + lhsDriver.initialize(sample_string, sampleRanksMode, !subIteratorFlag); +} + + +void NonDSampling:: +compute_statistics(const RealMatrix& vars_samples, + const IntResponseMap& resp_samples) +{ + StringMultiArrayConstView + acv_labels = iteratedModel.all_continuous_variable_labels(), + adiv_labels = iteratedModel.all_discrete_int_variable_labels(), + adsv_labels = iteratedModel.all_discrete_string_variable_labels(), + adrv_labels = iteratedModel.all_discrete_real_variable_labels(); + size_t cv_start, num_cv, div_start, num_div, dsv_start, num_dsv, + drv_start, num_drv; + mode_counts(iteratedModel, cv_start, num_cv, div_start, num_div, + dsv_start, num_dsv, drv_start, num_drv); + StringMultiArrayConstView + cv_labels = + acv_labels[boost::indices[idx_range(cv_start, cv_start+num_cv)]], + div_labels = + adiv_labels[boost::indices[idx_range(div_start, div_start+num_div)]], + dsv_labels = + adsv_labels[boost::indices[idx_range(dsv_start, dsv_start+num_dsv)]], + drv_labels = + adrv_labels[boost::indices[idx_range(drv_start, drv_start+num_drv)]]; + + // archive the active variables with the results + if (resultsDB.active()) { + if (num_cv) + resultsDB.insert(run_identifier(), resultsNames.cv_labels, cv_labels); + if (num_div) + resultsDB.insert(run_identifier(), resultsNames.div_labels, div_labels); + if (num_dsv) + resultsDB.insert(run_identifier(), resultsNames.dsv_labels, dsv_labels); + if (num_drv) + resultsDB.insert(run_identifier(), resultsNames.drv_labels, drv_labels); + resultsDB.insert(run_identifier(), resultsNames.fn_labels, + iteratedModel.response_labels()); + } + + if (epistemicStats) // Epistemic/mixed + compute_intervals(resp_samples); // compute min/max response intervals + else { // Aleatory + // compute means and std deviations with confidence intervals + compute_moments(resp_samples); + // compute CDF/CCDF mappings of z to p/beta and p/beta to z + if (totalLevelRequests) + compute_distribution_mappings(resp_samples); + } + + // Don't compute for now: too expensive + // if (!subIteratorFlag) { + // nonDSampCorr.compute_correlations(vars_samples, resp_samples); + // // archive the correlations to the results DB + // nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels, + // div_labels, dsv_labels, drv_labels, + // iteratedModel.response_labels()); + // } + if (!finalStatistics.is_null()) + update_final_statistics(); +} + + +void NonDSampling::compute_intervals(const IntResponseMap& samples) +{ + // For the samples array, calculate min/max response intervals + + using boost::math::isfinite; + size_t i, j, num_obs = samples.size(), num_samp; + const StringArray& resp_labels = iteratedModel.response_labels(); + + if (extremeValues.empty()) extremeValues.shapeUninitialized(2, numFunctions); + IntRespMCIter it; + for (i=0; isecond.function_value(i); + if (isfinite(sample)) { // neither NaN nor +/-Inf + if (sample < min) min = sample; + if (sample > max) max = sample; + ++num_samp; + } + } + extremeValues(0, i) = min; + extremeValues(1, i) = max; + if (num_samp != num_obs) + Cerr << "Warning: sampling statistics for " << resp_labels[i] << " omit " + << num_obs-num_samp << " failed evaluations out of " << num_obs + << " samples.\n"; + } + + if (resultsDB.active()) { + MetaDataType md; + md["Row Labels"] = make_metadatavalue("Min", "Max"); + md["Column Labels"] = make_metadatavalue(resp_labels); + resultsDB.insert(run_identifier(), resultsNames.extreme_values, + extremeValues, md); + } +} + + +void NonDSampling::compute_moments(const IntResponseMap& samples) +{ + // For the samples array, calculate means and standard deviations + // with confidence intervals + + using boost::math::isfinite; + size_t i, j, num_obs = samples.size(), num_samp; + Real sum, var, skew, kurt; + const StringArray& resp_labels = iteratedModel.response_labels(); + + if (momentStats.empty()) momentStats.shapeUninitialized(4, numFunctions); + if (momentCIs.empty()) momentCIs.shapeUninitialized(4, numFunctions); + + IntRespMCIter it; + for (i=0; isecond.function_value(i); + if (isfinite(sample)) { // neither NaN nor +/-Inf + sum += sample; + ++num_samp; + } + } + + if (num_samp != num_obs) + Cerr << "Warning: sampling statistics for " << resp_labels[i] << " omit " + << num_obs-num_samp << " failed evaluations out of " << num_obs + << " samples.\n"; + if (!num_samp) { + Cerr << "Error: Number of samples for " << resp_labels[i] + << " must be nonzero for moment calculation in NonDSampling::" + << "compute_statistics()." << std::endl; + abort_handler(-1); + } + + Real* moments_i = momentStats[i]; + Real& mean = moments_i[0]; + mean = sum/((Real)num_samp); + + // accumulate variance, skewness, and kurtosis + Real centered_fn, pow_fn; + for (it=samples.begin(); it!=samples.end(); ++it) { + const Real& sample = it->second.function_value(i); + if (isfinite(sample)) { // neither NaN nor +/-Inf + pow_fn = centered_fn = sample - mean; + pow_fn *= centered_fn; var += pow_fn; + pow_fn *= centered_fn; skew += pow_fn; + pow_fn *= centered_fn; kurt += pow_fn; + } + } + + // sample std deviation + Real& std_dev = moments_i[1]; + std_dev = (num_samp > 1) ? std::sqrt(var/(Real)(num_samp-1)) : 0.; + + // skewness + moments_i[2] = (num_samp > 2 && var > 0.) ? + // sample skewness + skew/(Real)num_samp/std::pow(var/(Real)num_samp,1.5) * + // population skewness + std::sqrt((Real)(num_samp*(num_samp-1)))/(Real)(num_samp-2) : + // for no variation, central moment is zero + 0.; + + // kurtosis + moments_i[3] = (num_samp > 3 && var > 0.) ? + // sample kurtosis + (Real)((num_samp+1)*num_samp*(num_samp-1))*kurt/ + (Real)((num_samp-2)*(num_samp-3)*var*var) - + // population kurtosis + 3.*std::pow((Real)(num_samp-1),2)/(Real)((num_samp-2)*(num_samp-3)) : + // for no variation, central moment is zero minus excess kurtosis + -3.; + + if (num_samp > 1) { + // 95% confidence intervals (2-sided interval, not 1-sided limit) + Real dof = num_samp - 1; +//#ifdef HAVE_BOOST + // mean: the better formula does not assume known variance but requires + // a function for the Student's t-distr. with (num_samp-1) degrees of + // freedom (Haldar & Mahadevan, p. 127). + Pecos::students_t_dist t_dist(dof); + Real mean_ci_delta = + std_dev*bmth::quantile(t_dist,0.975)/std::sqrt((Real)num_samp); + momentCIs(0,i) = mean - mean_ci_delta; + momentCIs(1,i) = mean + mean_ci_delta; + // std dev: chi-square distribution with (num_samp-1) degrees of freedom + // (Haldar & Mahadevan, p. 132). + Pecos::chi_squared_dist chisq(dof); + momentCIs(2,i) = std_dev*std::sqrt(dof/bmth::quantile(chisq, 0.975)); + momentCIs(3,i) = std_dev*std::sqrt(dof/bmth::quantile(chisq, 0.025)); +/* +#elif HAVE_GSL + // mean: the better formula does not assume known variance but requires + // a function for the Student's t-distr. with (num_samp-1) degrees of + // freedom (Haldar & Mahadevan, p. 127). + mean95CIDeltas[i] + = std_dev*gsl_cdf_tdist_Pinv(0.975,dof)/std::sqrt((Real)num_samp); + // std dev: chi-square distribution with (num_samp-1) degrees of freedom + // (Haldar & Mahadevan, p. 132). + stdDev95CILowerBnds[i] + = std_dev*std::sqrt(dof/gsl_cdf_chisq_Pinv(0.975, dof)); + stdDev95CIUpperBnds[i] + = std_dev*std::sqrt(dof/gsl_cdf_chisq_Pinv(0.025, dof)); +#else + // mean: k_(alpha/2) = Phi^(-1)(0.975) = 1.96 (Haldar & Mahadevan, + // p. 123). This simple formula assumes a known variance, which + // requires a sample of sufficient size (i.e., greater than 10). + mean95CIDeltas[i] = 1.96*std_dev/std::sqrt((Real)num_samp); +#endif // HAVE_BOOST +*/ + } + else + momentCIs(0,i) = momentCIs(1,i) = momentCIs(2,i) = momentCIs(3,i) = 0.0; + } + + if (resultsDB.active()) { + // archive the moments to results DB + MetaDataType md_moments; + md_moments["Row Labels"] = + make_metadatavalue("Mean", "Standard Deviation", "Skewness", "Kurtosis"); + md_moments["Column Labels"] = make_metadatavalue(resp_labels); + resultsDB.insert(run_identifier(), resultsNames.moments_std, + momentStats, md_moments); + // archive the confidence intervals to results DB + MetaDataType md; + md["Row Labels"] = + make_metadatavalue("LowerCI_Mean", "UpperCI_Mean", "LowerCI_StdDev", + "UpperCI_StdDev"); + md["Column Labels"] = make_metadatavalue(resp_labels); + resultsDB.insert(run_identifier(), resultsNames.moment_cis, momentCIs, md); + } +} + + +void NonDSampling::compute_distribution_mappings(const IntResponseMap& samples) +{ + // Size the output arrays here instead of in the ctor in order to support + // alternate sampling ctors. + initialize_distribution_mappings(); + archive_allocate_mappings(); + if (pdfOutput) { + computedPDFAbscissas.resize(numFunctions); + computedPDFOrdinates.resize(numFunctions); + archive_allocate_pdf(); + } + + // For the samples array, calculate the following statistics: + // > CDF/CCDF mappings of response levels to probability/reliability levels + // > CDF/CCDF mappings of probability/reliability levels to response levels + using boost::math::isfinite; + size_t i, j, k, num_obs = samples.size(), num_samp, bin_accumulator; + const StringArray& resp_labels = iteratedModel.response_labels(); + RealArray sorted_samples; // STL-based array for sorting + SizetArray bins; Real min, max; + + // check if moments are required, and if so, compute them now + if (momentStats.empty()) { + bool need_moments = false; + for (i=0; i p/beta/beta* and p/beta/beta* -> z + size_t rl_len = requestedRespLevels[i].length(), + pl_len = requestedProbLevels[i].length(), + bl_len = requestedRelLevels[i].length(), + gl_len = requestedGenRelLevels[i].length(); + + // ---------------------------------------------------------------------- + // Preliminaries: define finite subset, sort (if needed), and bin samples + // ---------------------------------------------------------------------- + num_samp = 0; + if (pl_len || gl_len) { // sort samples array for p/beta* -> z mappings + sorted_samples.clear(); sorted_samples.reserve(num_obs); + for (it=samples.begin(); it!=samples.end(); ++it) { + const Real& sample = it->second.function_value(i); + if (isfinite(sample)) + { ++num_samp; sorted_samples.push_back(sample); } + } + // sort in ascending order + std::sort(sorted_samples.begin(), sorted_samples.end()); + if (pdfOutput) + { min = sorted_samples[0]; max = sorted_samples[num_samp-1]; } + // in case of rl_len mixed with pl_len/gl_len, bin using sorted array. + // Note: all bins open on right end due to use of less than. + if (rl_len && respLevelTarget != RELIABILITIES) { + const RealVector& req_rl_i = requestedRespLevels[i]; + bins.assign(rl_len+1, 0); size_t samp_cntr = 0; + for (j=0; j samp_cntr) + bins[rl_len] += num_samp - samp_cntr; + } + } + else if (rl_len && respLevelTarget != RELIABILITIES) { + // in case of rl_len without pl_len/gl_len, bin from original sample set + const RealVector& req_rl_i = requestedRespLevels[i]; + bins.assign(rl_len+1, 0); min = DBL_MAX; max = -DBL_MAX; + for (it=samples.begin(); it!=samples.end(); ++it) { + const Real& sample = it->second.function_value(i); + if (isfinite(sample)) { + ++num_samp; + if (pdfOutput) { + if (sample < min) min = sample; + if (sample > max) max = sample; + } + // 1st PDF bin from -inf to 1st resp lev; last PDF bin from last resp + // lev to +inf. Note: all bins open on right end due to use of <. + bool found = false; + for (k=0; k p/beta* (based on binning) + bin_accumulator = 0; + for (j=0; j beta (based on moment projection) + Real& mean = momentStats(0,i); Real& std_dev = momentStats(1,i); + for (j=0; j Pecos::SMALL_NUMBER) { + Real ratio = (mean - z)/std_dev; + computedRelLevels[i][j] = (cdfFlag) ? ratio : -ratio; + } + else + computedRelLevels[i][j] + = ( (cdfFlag && mean <= z) || (!cdfFlag && mean > z) ) + ? -Pecos::LARGE_NUMBER : Pecos::LARGE_NUMBER; + } + break; + } + } + } + for (j=0; j z + Real p = (j .9) + ? std::pow(10., ceil(std::log10(cdf_p_x_obs))) : 0.; + int index = (int)std::floor(cdf_p_x_obs - order*DBL_EPSILON); + // clip at array ends due to possible roundoff effects + if (index < 0) index = 0; + if (index >= num_samp) index = num_samp - 1; + if (j z + const Real& beta = requestedRelLevels[i][j]; + computedRespLevels[i][j+pl_len] = (cdfFlag) ? + mean - beta * std_dev : mean + beta * std_dev; + } + } + + // archive the mappings from response levels + archive_from_resp(i); + // archive the mappings to response levels + archive_to_resp(i); + + // --------------------------------------------------------------------- + // Post-process for PDF incorporating all requested/computed resp levels + // --------------------------------------------------------------------- + if (pdfOutput) { + size_t req_comp_rl_len = pl_len + gl_len; + if (respLevelTarget != RELIABILITIES) req_comp_rl_len += rl_len; + if (req_comp_rl_len) { + RealVector pdf_all_rlevs; + if (pl_len || gl_len) { + // merge all requested & computed rlevs into pdf rlevs and sort + pdf_all_rlevs.sizeUninitialized(req_comp_rl_len); + // merge requested/computed --> pdf_all_rlevs + int offset = 0; + if (rl_len && respLevelTarget != RELIABILITIES) { + copy_data_partial(requestedRespLevels[i], pdf_all_rlevs, 0); + offset += rl_len; + } + if (pl_len) { + copy_data_partial(computedRespLevels[i], 0, (int)pl_len, + pdf_all_rlevs, offset); + offset += pl_len; + } + if (gl_len) + copy_data_partial(computedRespLevels[i], (int)(pl_len+bl_len), + (int)gl_len, pdf_all_rlevs, offset); + // sort combined array; retain unique entries; update req_comp_rl_len + Real* start = pdf_all_rlevs.values(); + std::sort(start, start+req_comp_rl_len); + req_comp_rl_len = std::distance(start, + std::unique(start, start+req_comp_rl_len)); + // (re)compute bins from sorted_samples. Note that these bins are + // open on right end due to use of strictly less than. + bins.assign(req_comp_rl_len+1, 0); size_t samp_cntr = 0; + for (j=0; j samp_cntr) + bins[req_comp_rl_len] += num_samp - samp_cntr; + } + RealVector& pdf_rlevs = (pl_len || gl_len) ? + pdf_all_rlevs : requestedRespLevels[i]; + size_t last_rl_index = req_comp_rl_len-1; + const Real& lev_0 = pdf_rlevs[0]; + const Real& lev_last = pdf_rlevs[last_rl_index]; + // to properly sum to 1, final PDF bin must be closed on right end. + // --> where the max sample value defines the last response level, + // move any max samples on right boundary inside last PDF bin. + if (max <= lev_last && bins[req_comp_rl_len]) { + bins[req_comp_rl_len-1] += bins[req_comp_rl_len]; + bins[req_comp_rl_len] = 0; + } + + // compute computedPDF{Abscissas,Ordinates} from bin counts and widths + size_t pdf_size = last_rl_index; + if (min < lev_0) ++pdf_size; + if (max > lev_last) ++pdf_size; + RealVector& abs_i = computedPDFAbscissas[i]; abs_i.resize(pdf_size+1); + RealVector& ord_i = computedPDFOrdinates[i]; ord_i.resize(pdf_size); + size_t offset = 0; + if (min < lev_0) { + abs_i[0] = min; + ord_i[0] = (Real)bins[0]/(Real)num_samp/(lev_0 - min); + offset = 1; + } + for (j=0; j lev_last) { + abs_i[pdf_size-1] = pdf_rlevs[last_rl_index]; + abs_i[pdf_size] = max; + ord_i[pdf_size-1] + = (Real)bins[req_comp_rl_len]/(Real)num_samp/(max - lev_last); + } + else + abs_i[pdf_size] = pdf_rlevs[last_rl_index]; + } + archive_pdf(i); + } + } +} + + +void NonDSampling::update_final_statistics() +{ + //if (finalStatistics.is_null()) + // initialize_final_statistics(); + + if (epistemicStats) { + size_t i, cntr = 0; + for (i=0; i 1) { + // output 95% confidence intervals as (,) interval + s << "\n95% confidence intervals for each response function:\n" + << std::setw(width+15) << "LowerCI_Mean" << std::setw(width+1) + << "UpperCI_Mean" << std::setw(width+1) << "LowerCI_StdDev" + << std::setw(width+2) << "UpperCI_StdDev\n"; + for (i=0; i + (run_identifier(), resultsNames.pdf_histograms, numFunctions, md); +} + + +void NonDSampling::archive_pdf(size_t i) // const +{ + if (!resultsDB.active()) return; + + size_t pdf_len = computedPDFOrdinates[i].length(); + RealMatrix pdf(3, pdf_len); + for (size_t j=0; j + (run_identifier(), resultsNames.pdf_histograms, i, pdf); +} + +} // namespace Dakota + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-altix64-cosmos.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-altix64-cosmos.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-altix64-cosmos.sh (revision 27955) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/opt/intel/mkl/9.1.023/lib/64/libmkl.so \ + --with-lapack=/opt/intel/mkl/9.1.023/lib/64/libmkl_lapack.so +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-discover.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-discover.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-discover.sh (revision 27955) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" \ +--with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-linux64-cloud.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-linux64-cloud.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-linux64-cloud.sh (revision 27955) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/usr/lib/libblas.so \ + --with-lapack=/usr/lib/liblapack.so +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-linux64-murdo.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-linux64-murdo.sh (revision 27955) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/usr/lib64/libblas.so.3.1.1 \ + --with-lapack=/usr/lib64/liblapack.so.3.1.1 +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-macosx64.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-macosx64.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-4.2-macosx64.sh (revision 27955) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ + --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2 -D_NONSTD_SOURCE/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-discover.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-discover.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-discover.sh (revision 27955) @@ -0,0 +1,52 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +#patch src/src/NIDRProblemDescDB.C configs/5.2/NIDRProblemDescDB.C.patch # causes segfault in 5.2 +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-plugin \ +--with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" \ +--with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" + +cd .. + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-linux64-caladan.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-linux64-caladan.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-linux64-caladan.sh (revision 27955) @@ -0,0 +1,48 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch +patch src/packages/teuchos/src/Teuchos_ConfigDefs.hpp configs/5.2/Teuchos_ConfigDefs.hpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas="$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a" \ + --with-lapack="$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a" + +#Compile and install dakota +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-linux64-larsen.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-linux64-larsen.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-linux64-larsen.sh (revision 27955) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch +patch src/packages/teuchos/src/Teuchos_ConfigDefs.hpp configs/5.2/Teuchos_ConfigDefs.hpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-plugin \ + --with-blas="$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a" \ + --with-lapack="$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a" + +#Compile and install dakota +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-macosx64.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-macosx64.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.2-macosx64.sh (revision 27955) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +#patch src/src/NIDRProblemDescDB.C configs/5.2/NIDRProblemDescDB.C.patch # causes segfault in 5.2 +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-plugin \ + --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ + --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " +cd .. + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-linux64-caladan.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-linux64-caladan.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-linux64-caladan.sh (revision 27955) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +#patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC -DBLAS_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a -DLAPACK_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-linux64.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-linux64.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-linux64.sh (revision 27955) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +#patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-lonestar.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-lonestar.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-lonestar.sh (revision 27955) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.lonestar.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh (revision 27955) @@ -0,0 +1,62 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.mac.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install + +#Configure dakota +# Set your local gcc compiler here +cd $DAK_BUILD +cmake -DBoost_NO_BOOST_CMAKE=TRUE \ + -DBoost_NO_SYSTEM_PATHS=TRUE \ + -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ + -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \ + -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CC_COMPILER=/usr/bin/gcc \ + -DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC + +#-DCMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran + +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-macosx64-yosemite.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-macosx64-yosemite.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-macosx64-yosemite.sh (revision 27955) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -D CMAKE_C_COMPILER=/usr/local/gfortran/bin/gcc -D CMAKE_CXX_COMPILER=/usr/local/gfortran/bin/g++ -D CMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/gfortran -D LDFLAGS="-std=gnu++0x" -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-macosx64.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-macosx64.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-5.3.1-macosx64.sh (revision 27955) @@ -0,0 +1,62 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.mac.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install + +#Configure dakota +# Set your local gcc compiler here +cd $DAK_BUILD +cmake -DBoost_NO_BOOST_CMAKE=TRUE \ + -DBoost_NO_SYSTEM_PATHS=TRUE \ + -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ + -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \ + -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CC_COMPILER=gcc \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC + +#-DCMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran + +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-discover.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-discover.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-discover.sh (revision 27955) @@ -0,0 +1,64 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.discover.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.discover20.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=mpicc \ + -D CMAKE_CXX_COMPILER=mpicxx \ + -D CMAKE_Fortran_COMPILER=/usr/bin/gfortran \ + -DCMAKE_CXX_FLAGS="-lstdc++ -lirc -lsvml -limf" \ + -DBUILD_SHARED_LIBS=ON \ + -DBUILD_STATIC_LIBS=OFF \ + -DBoost_NO_BOOST_CMAKE=TRUE \ + -DHAVE_ACRO=OFF \ + -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-linux-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-linux-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-linux-static.sh (revision 27955) @@ -0,0 +1,94 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed + +# Find libgfortran and libgcc so we do not have to hardcode them +# +# TODO: +# - Move this to etc/environment.sh +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1) + +## Environment +# +export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L/usr/lib/x86_64-linux-gnu ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it + +# Cleanup +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" + +# Unpack source +tar -zxvf dakota-${VER}-public-src.tar.gz + +# Move source to 'src' directory +mv dakota-${VER}.0.src/* ${DAK_SRC} +rm -rf dakota-${VER}.0.src + +# Copy customized source and configuration files to 'src' directory +cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer +cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src +cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm +cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src +cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src + +# Copy customized source and configuration files specific to Linux to 'src' directory +cp configs/${VER}/linux/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake +cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake + +# Disable requirement of Python 2 for TriBITS +sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake + +# Configure +cd ${DAK_BUILD} +cmake \ + -DBUILD_SHARED_LIBS=OFF \ + -DBUILD_STATIC_LIBS=ON \ + -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \ + -DCMAKE_C_FLAGS="-fPIC -Wno-error=implicit-function-declaration" \ + -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \ + -DCMAKE_CXX_FLAGS="-fPIC" \ + -DCMAKE_CXX_STANDARD="11" \ + -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \ + -DBoost_NO_BOOST_CMAKE=TRUE \ + -DHAVE_ACRO=OFF \ + -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ + -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ + -C${DAK_SRC}/cmake/DakotaDev.cmake \ + ${DAK_SRC} + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +cd ${DAK_INSTALL} + +# Comment out definition of HAVE_MPI in Teuchos config header file in order to +# avoid conflict with our definition +sed -i -e "s/#define HAVE_MPI/\/* #define HAVE_MPI *\//g" include/Teuchos_config.h Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-linux.sh (revision 27955) @@ -0,0 +1,90 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed + +# Find libgfortran so that we do not have to hardcode it. +# +# TODO: +# - Move this to etc/environment.sh +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} + +## Environment +# +export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it + +# Cleanup +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" + +# Unpack source +tar -zxvf dakota-${VER}-public-src.tar.gz + +# Move source to 'src' directory +mv dakota-${VER}.0.src/* ${DAK_SRC} +rm -rf dakota-${VER}.0.src + +# Copy customized source and configuration files to 'src' directory +cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer +cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src +cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm +cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src +cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src + +# Copy customized source and configuration files specific to Linux to 'src' directory +cp configs/${VER}/linux/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake +cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake + +# Disable requirement of Python 2 for TriBITS +sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake + +# Configure +cd ${DAK_BUILD} +cmake \ + -DBUILD_SHARED_LIBS=ON \ + -DBUILD_STATIC_LIBS=OFF \ + -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \ + -DCMAKE_C_FLAGS="-Wno-error=implicit-function-declaration" \ + -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \ + -DCMAKE_CXX_STANDARD="11" \ + -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \ + -DBoost_NO_BOOST_CMAKE=TRUE \ + -DHAVE_ACRO=OFF \ + -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ + -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ + -C${DAK_SRC}/cmake/DakotaDev.cmake \ + ${DAK_SRC} + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +cd ${DAK_INSTALL} + +# Comment out definition of HAVE_MPI in Teuchos config header file in order to +# avoid conflict with our definition +sed -i -e "s/#define HAVE_MPI/\/* #define HAVE_MPI *\//g" include/Teuchos_config.h Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-lonestar.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-lonestar.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-lonestar.sh (revision 27955) @@ -0,0 +1,63 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=/opt/cray/pe/mpt/7.7.3/gni/mpich-intel/16.0/ + +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.lonestar.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch +patch src/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp configs/6.2/NKM_KrigingModel.patch +patch src/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp configs/6.2/MainEffectsExcelOutput.patch +patch src/src/DakotaInterface.cpp configs/6.2/DakotaInterface.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=mpicc \ + -D CMAKE_CXX_COMPILER=mpicxx \ + -D CMAKE_Fortran_COMPILER=mpif77 \ + -D MPIEXEC_EXECUTABLE=/opt/apps/tacc/bin/ibrun \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-mac-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-mac-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-mac-static.sh (revision 27955) @@ -0,0 +1,115 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed + +# Find libgfortran and libgcc so we do not have to hardcode them +# +# TODO: +# - Move this to etc/environment.sh +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) + +## Environment +# +export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export LDFLAGS="-framework CoreFoundation" + +# Cleanup +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" + +# Unpack source +tar -zxvf dakota-${VER}-public-src.tar.gz + +# Move source to 'src' directory +mv dakota-${VER}.0.src/* ${DAK_SRC} +rm -rf dakota-${VER}.0.src + +# Copy customized source and configuration files to 'src' directory +cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer +cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src +cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm +cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src +cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src + +# Copy customized source and configuration files specific to Mac to 'src' directory +cp configs/${VER}/mac/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake +cp configs/${VER}/mac/cmake/DakotaDev.cmake ${DAK_SRC}/cmake +cp configs/${VER}/mac/cmake/InstallDarwinDylibs.cmake ${DAK_SRC}/cmake + +# Uncomment to copy the following customized source files if using C99 or later +# standard. If uncommented, adding -Wno-error=implicit-function-declaration +# option to CFLAGS is not needed. +# cp configs/${VER}/mac/static/packages/DDACE/include/xtndispatch.h ${DAK_SRC}/packages/DDACE/include +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/Boselink.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/construct.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/galois.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/gfields.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/DDACE/src/Bose/oa.c ${DAK_SRC}/packages/DDACE/src/Bose +# cp configs/${VER}/mac/static/packages/nidr/nidr.c ${DAK_SRC}/packages/nidr +# cp configs/${VER}/mac/static/packages/nidr/nidr-scanner.c ${DAK_SRC}/packages/nidr + +# Disable requirement of Python 2 for TriBITS +sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake + +# Configure +# +# NOTE: +# - The -w option has been added to CMAKE_C_FLAGS, CMAKE_CXX_FLAGS, and +# CMAKE_Fortran_FLAGS. This should be removed for more recent versions of +# Dakota. +# +cd ${DAK_BUILD} +cmake \ + -DBUILD_SHARED_LIBS=OFF \ + -DBUILD_STATIC_LIBS=ON \ + -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \ + -DCMAKE_C_FLAGS="-fPIC -Wno-error=implicit-function-declaration -w" \ + -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \ + -DCMAKE_CXX_FLAGS="-fPIC -fdelayed-template-parsing -w" \ + -DCMAKE_CXX_STANDARD="11" \ + -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \ + -DCMAKE_Fortran_FLAGS="-fPIC -fallow-argument-mismatch -w" \ + -DBoost_NO_BOOST_CMAKE=TRUE \ + -DHAVE_ACRO=OFF \ + -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ + -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ + -C${DAK_SRC}/cmake/DakotaDev.cmake \ + ${DAK_SRC} + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +cd ${DAK_INSTALL} + +# Comment out definition of HAVE_MPI in Teuchos config header file in order to +# avoid conflict with our definition +sed -i -e "s/#define HAVE_MPI/\/* #define HAVE_MPI *\//g" include/Teuchos_config.h Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-mac.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-mac.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-mac.sh (revision 27955) @@ -0,0 +1,141 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed + +# Find libgfortran so that we do not have to hardcode it. +# +# TODO: +# - Move this to etc/environment.sh +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} + +## Environment +# +export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export LDFLAGS="-framework CoreFoundation" + +# Cleanup +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" + +# Unpack source +tar -zxvf dakota-${VER}-public-src.tar.gz + +# Move source to 'src' directory +mv dakota-${VER}.0.src/* ${DAK_SRC} +rm -rf dakota-${VER}.0.src + +# Copy customized source and configuration files to 'src' directory +cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer +cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src +cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm +cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src +cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src + +# Copy customized source and configuration files specific to Mac to 'src' directory +cp configs/${VER}/mac/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake +cp configs/${VER}/mac/cmake/DakotaDev.cmake ${DAK_SRC}/cmake +cp configs/${VER}/mac/cmake/InstallDarwinDylibs.cmake ${DAK_SRC}/cmake + +# Disable requirement of Python 2 for TriBITS +sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake + +echo "Debug:" +echo "GSL_HOME : ${GSL_HOME}" +echo "CPATH : ${CPATH}" + +# Configure +# +# NOTE: +# - The -w option has been added to CMAKE_C_FLAGS, CMAKE_CXX_FLAGS, and +# CMAKE_Fortran_FLAGS. This should be removed for more recent versions of +# Dakota. +# +cd ${DAK_BUILD} +cmake \ + -DBUILD_SHARED_LIBS=ON \ + -DBUILD_STATIC_LIBS=OFF \ + -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \ + -DCMAKE_C_FLAGS="-w" \ + -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \ + -DCMAKE_CXX_FLAGS="-fdelayed-template-parsing -w" \ + -DCMAKE_CXX_STANDARD="11" \ + -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \ + -DBoost_NO_BOOST_CMAKE=TRUE \ + -DHAVE_ACRO=OFF \ + -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ + -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ + -C${DAK_SRC}/cmake/DakotaDev.cmake \ + ${DAK_SRC} + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +cd ${DAK_INSTALL} + +# Comment out definition of HAVE_MPI in Teuchos config header file in order to +# avoid conflict with our definition +sed -i -e "s/#define HAVE_MPI/\/* #define HAVE_MPI *\//g" include/Teuchos_config.h + +# Set install_name for all shared libraries +cd ${DAK_INSTALL}/lib +for name in *.dylib; do + install_name_tool -id ${DAK_INSTALL}/lib/${name} ${name} +done + +## Patch install names for certain libraries +# +# TODO: Figure out how to reconfigure source to apply these install names at +# compile time +# +install_name_tool -change libdakota_src_fortran.dylib ${DAK_INSTALL}/lib/libdakota_src_fortran.dylib libdakota_src.dylib +install_name_tool -change liblhs_mod.dylib ${DAK_INSTALL}/lib/liblhs_mod.dylib liblhs.dylib +install_name_tool -change liblhs_mods.dylib ${DAK_INSTALL}/lib/liblhs_mods.dylib liblhs.dylib +install_name_tool -change liblhs_mod.dylib ${DAK_INSTALL}/lib/liblhs_mod.dylib liblhs_mods.dylib +install_name_tool -change libteuchos.dylib ${DAK_INSTALL}/lib/libteuchos.dylib liboptpp.dylib +install_name_tool -change libdfftpack.dylib ${DAK_INSTALL}/lib/libdfftpack.dylib libpecos.dylib +install_name_tool -change liblhs.dylib ${DAK_INSTALL}/lib/liblhs.dylib libpecos.dylib +install_name_tool -change liblhs_mod.dylib ${DAK_INSTALL}/lib/liblhs_mod.dylib libpecos.dylib +install_name_tool -change liblhs_mods.dylib ${DAK_INSTALL}/lib/liblhs_mods.dylib libpecos.dylib +install_name_tool -change libpecos_src.dylib ${DAK_INSTALL}/lib/libpecos_src.dylib libpecos.dylib +install_name_tool -change libteuchos.dylib ${DAK_INSTALL}/lib/libteuchos.dylib libpecos.dylib +install_name_tool -change libdfftpack.dylib ${DAK_INSTALL}/lib/libdfftpack.dylib libpecos_src.dylib +install_name_tool -change liblhs.dylib ${DAK_INSTALL}/lib/liblhs.dylib libpecos_src.dylib +install_name_tool -change liblhs_mod.dylib ${DAK_INSTALL}/lib/liblhs_mod.dylib libpecos_src.dylib +install_name_tool -change liblhs_mods.dylib ${DAK_INSTALL}/lib/liblhs_mods.dylib libpecos_src.dylib +install_name_tool -change libteuchos.dylib ${DAK_INSTALL}/lib/libteuchos.dylib libpecos_src.dylib +install_name_tool -change libsurfpack_fortran.dylib ${DAK_INSTALL}/lib/libsurfpack_fortran.dylib libsurfpack.dylib + +## Add LIBGFORTRAN_ROOT to rpath for libraries that need it +# +# TODO: Figure out how to reconfigure source to add to rpath at compile time +# +install_name_tool -add_rpath ${LIBGFORTRAN_ROOT} libpecos.dylib +install_name_tool -add_rpath ${LIBGFORTRAN_ROOT} libteuchos.dylib +install_name_tool -add_rpath ${LIBGFORTRAN_ROOT} liboptpp.dylib + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-pleiades.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-pleiades.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-pleiades.sh (revision 27955) @@ -0,0 +1,78 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed + +## Environment +# +export BLAS_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64 +export CXXFLAGS='-std=c++11' +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64 + +# Cleanup +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" + +# Unpack source +tar -zxvf dakota-${VER}-public-src.tar.gz + +# Move source to 'src' directory +mv dakota-${VER}.0.src/* ${DAK_SRC} +rm -rf dakota-${VER}.0.src + +# Copy customized source and configuration files to 'src' directory +cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer +cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src +cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm +cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src +cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src + +# Copy customized source and configuration files specific to Linux to 'src' directory +cp configs/${VER}/linux/cmake/BuildDakotaCustom.pleiades.cmake ${DAK_SRC}/cmake/BuildDakotaCustom.cmake +cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake + +# Configure +cd ${DAK_BUILD} +cmake \ + -DBUILD_SHARED_LIBS=ON \ + -DBUILD_STATIC_LIBS=OFF \ + -DCMAKE_C_COMPILER=mpicc \ + -DCMAKE_C_FLAGS="-Wno-error=implicit-function-declaration" \ + -DCMAKE_CXX_COMPILER=mpicxx \ + -DCMAKE_Fortran_COMPILER=/usr/bin/gfortran \ + -DBoost_NO_BOOST_CMAKE=TRUE \ + -DHAVE_ACRO=OFF \ + -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ + -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ + -C${DAK_SRC}/cmake/DakotaDev.cmake \ + ${DAK_SRC} + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +cd ${DAK_INSTALL} + +# Comment out definition of HAVE_MPI in Teuchos config header file in order to +# avoid conflict with our definition +sed -i -e "s/#define HAVE_MPI/\/* #define HAVE_MPI *\//g" include/Teuchos_config.h Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-pleiades_toss4.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-pleiades_toss4.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-pleiades_toss4.sh (revision 27955) @@ -0,0 +1,78 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed + +## Environment +# +export BLAS_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64 +export CXXFLAGS='-std=c++98' +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64 + +# Cleanup +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" + +# Unpack source +tar -zxvf dakota-${VER}-public-src.tar.gz + +# Move source to 'src' directory +mv dakota-${VER}.0.src/* ${DAK_SRC} +rm -rf dakota-${VER}.0.src + +# Copy customized source and configuration files to 'src' directory +cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer +cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src +cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm +cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src +cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src +cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src + +# Copy customized source and configuration files specific to Linux to 'src' directory +cp configs/${VER}/linux/cmake/BuildDakotaCustom.pleiades.cmake ${DAK_SRC}/cmake/BuildDakotaCustom.cmake +cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake + +# Configure +cd ${DAK_BUILD} +cmake \ + -DBUILD_SHARED_LIBS=ON \ + -DBUILD_STATIC_LIBS=OFF \ + -DCMAKE_C_COMPILER=mpicc \ + -DCMAKE_C_FLAGS="-Wno-error=implicit-function-declaration" \ + -DCMAKE_CXX_COMPILER=mpicxx \ + -DCMAKE_Fortran_COMPILER=gfortran \ + -DBoost_NO_BOOST_CMAKE=TRUE \ + -DHAVE_ACRO=OFF \ + -DHAVE_JEGA=OFF \ + -DHAVE_QUESO=ON \ + -DDAKOTA_HAVE_GSL=ON \ + -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \ + -C${DAK_SRC}/cmake/DakotaDev.cmake \ + ${DAK_SRC} + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +cd ${DAK_INSTALL} + +# Comment out definition of HAVE_MPI in Teuchos config header file in order to +# avoid conflict with our definition +sed -i -e "s/#define HAVE_MPI/\/* #define HAVE_MPI *\//g" include/Teuchos_config.h Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-stallo.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-stallo.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/install-6.2-stallo.sh (revision 27955) @@ -0,0 +1,63 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +#export PATH="/usr/bin":$PATH +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/ + +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.stallo.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.stallo.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch +patch src/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp configs/6.2/NKM_KrigingModel.patch +patch src/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp configs/6.2/MainEffectsExcelOutput.patch +patch src/src/DakotaInterface.cpp configs/6.2/DakotaInterface.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/bin64/mpicc \ + -D CMAKE_CXX_COMPILER=/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/bin64/mpicxx \ + -D CMAKE_Fortran_COMPILER=gfortran \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/tests/test.in =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/tests/test.in (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/tests/test.in (revision 27955) @@ -0,0 +1,36 @@ +method, + nond_sampling + seed = 1234 + rng rnum2 + samples = 2000 + sample_type lhs + distribution cumulative + num_probability_levels = 9 + probability_levels = + 0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 + 0.9999 + +model, + single + +variables, + normal_uncertain = 2 + nuv_means = + 1 1 + nuv_std_deviations = + 0.1 0.1 + nuv_descriptors = + 'x1' 'x2' + +interface, + direct + analysis_driver = 'plugin_text_book' + evaluation_scheduling master + processors_per_evaluation = 3 + +responses, + num_response_functions = 1 + response_descriptors = + 'MaxVel' + no_gradients + no_hessians Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/tests/test2.in =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/tests/test2.in (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dakota/tests/test2.in (revision 27955) @@ -0,0 +1,36 @@ +method, + nond_sampling + seed = 1234 + rng rnum2 + samples = 3 + sample_type lhs + distribution cumulative + num_probability_levels = 9 + probability_levels = + 0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 + 0.9999 + +model, + single + +variables, + normal_uncertain = 2 + nuv_means = + 1 1 + nuv_std_deviations = + 0.1 0.1 + nuv_descriptors = + 'x1' 'x2' + +interface, + direct + analysis_driver = 'plugin_text_book' + evaluation_scheduling master + processors_per_evaluation = 1 + +responses, + num_response_functions = 1 + response_descriptors = + 'MaxVel' + no_gradients + no_hessians Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/dem.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/dem.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/dem.m (revision 27955) @@ -0,0 +1,1081 @@ +function varargout=dem(x,y,z,varargin) +%DEM Shaded relief image plot +% +% DEM(X,Y,Z) plots the Digital Elevation Model defined by X and Y +% coordinate vectors and elevation matrix Z, as a lighted image using +% specific "landcolor" and "seacolor" colormaps. DEM uses IMAGESC +% function which is much faster than SURFL when dealing with large +% high-resolution DEM. It produces also high-quality and moderate-size +% Postscript image adapted for publication. +% +% DEM(X,Y,Z,'Param1',Value1,'Param2',Value2,...) specifies options or +% parameter/value couple (case insensitive): +% +% [H,I] = DEM(...); returns graphic handle H and optional illuminated +% image as I, a MxNx3 matrix (if Z is MxN and DECIM is 1). +% +% I = DEM(...,'noplot') returns a structure I containing fields x, y, z, +% and illuminated image .rgb without producing a graph on current figure. +% +% +% --- Lighting options --- +% +% 'Azimuth',A +% Light azimuth in degrees clockwise relative to North. Default is +% A = -45 for a natural northwestern illumination. +% +% 'Contrast',C +% Light contrast, as the exponent of the gradient value: +% C = 1 for linear contrast (default), +% C = 0 to remove lighting, +% C = 0.5 for moderate lighting, +% C = 2 or more for strong contrast. +% +% 'LCut',LC +% Lighting scale saturation cut with a median-style filter in % of +% elements, such as LC% of maximum gradient values are ignored: +% LC = 0.2 is default, +% LC = 0 for full scale gradient. +% +% 'km' +% Stands that X and Y coordinates are in km instead of m (default). +% This allows correct lighting. Ignored if LATLON option is used. +% +% +% --- Elevation colorscale options --- +% +% 'ZLim',[ZMIN,ZMAX] +% Fixes min and max elevation values for colormap. Use NaN to keep +% real min and/or max data values. +% +% 'ZCut',ZC +% Median-style filter to cut extremes values of Z (in % of elements), +% such that ZC% of most min/max elevation values are ignored in the +% colormap application: +% ZC = 0.5 is default, +% ZC = 0 for full scale. +% +% +% --- "No Value" elevation options --- +% +% 'NoValue',NOVALUE +% Defines the values that will be replaced by NaN. Note that values +% equal to minimum of Z class are automatically detected as NaN +% (e.g., -32768 for int16 class). +% +% 'NaNColor',[R,G,B] +% Sets the RGB color for NaN/NoValue pixels (default is a dark gray). +% Note that your must specify a valid 3-scalar vector (between 0 and +% 1); color characters like 'w' or 'k' are not allowed, use [1,1,1] +% or [0,0,0] instead. +% +% 'Interp' +% Interpolates linearly all NaN values (fills the gaps using linear +% triangulation), using an optimized algorithm. +% +% +% --- Colormap options --- +% +% 'LandColor',LMAP +% Uses LMAP colormap instead of default (landcolor, if exists or +% jet) for Z > 0 elevations. +% +% 'SeaColor',SMAP +% Sets the colormap used for Z <= 0 elevations. Default is seacolor +% (if exists) or single color [0.7,0.9,1] (a light cyan) to simulate +% sea color. +% +% 'ColorMap',CMAP +% Uses CMAP colormap for full range of elevations, instead of default +% land/sea. This option overwrites LANDCOLOR/SEACOLOR options. +% +% 'Lake' +% Detects automaticaly flat areas different from sea level (non-zero +% elevations) and colors them as lake surfaces. +% +% 'Watermark',N +% Makes the whole image lighter by a factor of N. +% +% +% --- Basemap and scale options --- +% +% 'Legend' +% Adds legends to the right of graph: elevation scale (colorbar) +% and a distance scale (in km). +% +% 'Cartesian' +% Plots classic basemap-style axis, considering coordinates X and Y +% as cartesian in meters. Use parameter "km' for X/Y in km. +% +% 'LatLon' +% Plots geographic basemap-style axis in deg/min/sec, considering +% coordinates X as longitude and Y as latitude. Axis aspect ratio +% will be adjusted to approximatively preserve distances (this is +% not a real projection!). This overwrites ZRatio option. +% +% 'AxisEqual', 'auto' (default) | 'manual' | 'off' +% When 'Cartesian' or 'LatLon' option is used, automatic axes scaling +% is applied to respect data aspect ratio. Default mode is 'auto' and +% uses AXIS EQUAL and DASPECT functions. The 'manual' mode modifies +% axes width or height with respect to the paper size in order to +% produce correct data scaling at print (but not necessarily at +% screen). The 'off' mode disables any scaling. +% +% Additionnal options for basemap CARTESIAN or LATLON: +% +% 'BorderWidth',BW +% Border width of the basemap axis, in % of axis height. Default is +% BW = 1%. +% +% 'XTick',DX +% 'YTick',DY +% X and Y Tick length (same unit as X and Y). Default is automatic. +% Tick labels are every 2 ticks. +% +% 'FontSize',FS +% Font size for X and Y tick labels. Default is FS = 10. +% +% 'FontBold' +% Font weight bold for tick labels. +% +% 'Position',P +% Position of the tick labels: 'southwest' (default), 'southeast', +% 'northwest','northeast' +% +% +% --- Decimation options --- +% +% For optimization purpose, DEM will automatically decimate data to limit +% to a total of 1500x1500 pixels images. To avoid this, use following +% options, but be aware that large grids may require huge computer +% ressources or induce disk swap or memory errors. +% +% 'Decim',N +% Decimates matrix Z at 1/N times of the original sampling. +% +% 'NoDecim' +% Forces full resolution of Z, no decimation. +% +% +% +% --- Informations --- +% +% Colormaps are Mx3 RGB matrix so it is easy to modify saturation +% (CMAP.^N), set darker (CMAP/N), lighter (1 - 1/N + CMAP/N), inverse +% it (flipud(CMAP)), etc... +% +% To get free worldwide topographic data (SRTM), see READHGT function. +% +% For backward compatibility, the former syntax is still accepted: +% DEM(X,Y,Z,OPT,CMAP,NOVALUE,SEACOLOR) where OPT = [A,C,LC,ZMIN,ZMAX,ZC], +% also option aliases DEC, DMS and SCALE, but there is no argument +% checking. Please prefer the param/value syntax. +% +% Author: François Beauducel +% Created: 2007-05-17 in Guadeloupe, French West Indies +% Updated: 2016-01-31 + +% History: +% [2016-04-19] v2.3 +% - major update (thanks to mas Wiwit) +% [2016-01-31] v2.2 +% - adds option 'Position' for tick labels +% [2015-08-22] v2.1 +% - minor fix (former versions of Matlab compatibility) +% [2015-08-19] v2.0 +% - image is now 100% true color (including the legend colorbar), +% thus completely independent from the figure colormap +% [2014-10-14] +% - 'decim' option allows oversampling (negative value) +% [2014-06-06] +% - improves backward compatibility (adds strjoin subfunction) +% [2014-03-18] +% - adds new axisequal option +% [2013-03-11] +% - new options: 'km', 'watermark', 'fontsize', 'bordersize' +% - improve legend colorbar +% - all options now passed as param/value +% [2013-01-14] +% - improved light rendering (using surface normals instead of gradient) +% - improved 'lake' detection algorithm +% - new 'nancolor' option to set NaN color +% - adds a length scale with 'dec' option +% - minor code improvements +% [2013-01-07] +% - adds 'interp' option (fill the gaps) +% - adds 'seacolor' colormap for negative elevations (bathymetry) +% [2013-01-02] +% - adds a 'lake' option +% - minor bug correction +% [2012-09-26] +% - now accepts row/column vectors for X and/or Y. +% [2012-05-29] +% - adds basemap-style axis in decimal or lat/lon modes +% - adds elevation and distance scales +% [2012-05-18] +% - new landcolor.m colormap function +% - new arguments to control colormap scaling +% - median-style filters for light and colormap +% [2012-04-26] +% - Optimizations: adds a decimation for large DEM grids. + +% +% Copyright (c) 2016, François Beauducel, covered by BSD License. +% All rights reserved. +% +% Redistribution and use in source and binary forms, with or without +% modification, are permitted provided that the following conditions are +% met: +% +% * Redistributions of source code must retain the above copyright +% notice, this list of conditions and the following disclaimer. +% * Redistributions in binary form must reproduce the above copyright +% notice, this list of conditions and the following disclaimer in +% the documentation and/or other materials provided with the distribution +% +% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +% POSSIBILITY OF SUCH DAMAGE. + +if nargin < 3 + error('Not enough input arguments.'); +end + +holdon = ishold; + +degkm = 6378*pi/180; % one latitude degree in km +sea_color = [.7,.9,1]; % default sea color (light cyan) +grey = 0.2*[1,1,1]; % a dark gray + + +% ------------------------------------------------------------------------- +% --- Manage input arguments + +% number of arguments param/value +nargs = 0; + +if ~isnumeric(x) || ~isnumeric(y) || ~isnumeric(z) + error('X,Y and Z must be numeric.') +end + +if all(size(x) ~= 1) || all(size(y) ~= 1) + error('X and Y must be vectors, not matrix.') +end + +if length(x) ~= size(z,2) || length(y) ~= size(z,1) + error('If Z has a size of [M,N], X must have a length of N, and Y a length of M.') +end + +% OPTIONS and PARAM/VALUE arguments + +% AZIMUTH param/value +[s,az] = checkparam(varargin,'azimuth',@isscalar); +nargs = nargs + 2; +if s==0 + az = -45; % default +end + +% ELEVATION param/value +[s,el] = checkparam(varargin,'elevation',@isscalar); +nargs = nargs + 2; +if s==0 + el = 0; % default +end + +% CONTRAST param/value +[s,ct] = checkparam(varargin,'contrast',@isscalar); +nargs = nargs + 2; +if s + ct = abs(ct); +else + ct = 1; % default +end + +% LCUT param/value +[s,lcut] = checkparam(varargin,'lcut',@isperc); +nargs = nargs + 2; +if s==0 + lcut = .2; % default +end + +% NOVALUE param/value +[s,novalue] = checkparam(varargin,'novalue',@isscalar); +nargs = nargs + 2; +if s==0 + % default: min value for integer class / NaN for float + S = whos('z'); + if strfind(S.class,'int') + novalue = intmin(S.class); + else + novalue = NaN; + end +end + +% NANCOLOR param/value +[s,novalue_color] = checkparam(varargin,'nancolor',@isrgb); +nargs = nargs + 2; +if s==0 + novalue_color = grey; % default +end + +% LANDCOLOR param/value +[s,cland] = checkparam(varargin,'landcolor',@isrgb); +nargs = nargs + 2; +if s==0 + % default: landcolor or jet + if exist('landcolor','file') + cland = landcolor.^1.3; + else + cland = jet(256); + end +end + +% SEACOLOR param/value +[s,csea] = checkparam(varargin,'seacolor',@isrgb); +nargs = nargs + 2; +if s==0 + % default: seacolor or single color + if exist('seacolor','file') + csea = seacolor; + else + csea = sea_color; + end +end + +% COLORMAP param/value +[s,cmap] = checkparam(varargin,'colormap',@isrgb); +nargs = nargs + 2; +if s + cland = []; + csea = []; +else + % default + cmap = cland; +end + +% ZLIM param/value +[s,zmm] = checkparam(varargin,'zlim',@isvec); +nargs = nargs + 2; +if s + zmin = min(zmm); + zmax = max(zmm); +else + zmin = NaN; % default + zmax = NaN; % default +end + +% ZCUT param/value +[s,zcut] = checkparam(varargin,'zcut',@isperc); +nargs = nargs + 2; +if s==0 + zcut = .5; % default +end + +% ZRATIO param/value +[s,zratio] = checkparam(varargin,'zratio',@isscalar); +nargs = nargs + 2; +if s==0 + zratio = 1; % default +end + +% WATERMARK param/value +[s,wmark] = checkparam(varargin,'watermark',@isscalar); +nargs = nargs + 2; +if s + wmark = abs(wmark); +else + wmark = 0; % default +end + +% DECIM param/value and NODECIM option +[s,decim] = checkparam(varargin,'decim',@isscalar); +if s + decim = round(decim); + nargs = nargs + 2; +else + decim = any(strcmpi(varargin,'nodecim')); % default + nargs = nargs + 1; +end + +% FONTSIZE param/value +[s,fs] = checkparam(varargin,'fontsize',@isscalar); +nargs = nargs + 2; +if s==0 + fs = 10; % default +end + +% BORDERWIDTH param/value +[s,bw] = checkparam(varargin,'borderwidth',@isperc); +nargs = nargs + 2; +if s==0 + bw = 1; % default +end + +% XTICK param/value +[s,ddx] = checkparam(varargin,'xtick',@isscalar); +nargs = nargs + 2; +if s==0 + ddx = 0; % default (automatic) +end + +% YTICK param/value +[s,ddy] = checkparam(varargin,'ytick',@isscalar); +nargs = nargs + 2; +if s==0 + ddy = 0; % default (automatic) +end + +% POSITION param/value +[s,tpos] = checkparam(varargin,'position',@ischar,{'southwest','southeast','northwest','northeast'}); +nargs = nargs + 2; +if s==0 + tpos = 'southwest'; % default +end + +% AXISEQUAL param/value +[s,axeq] = checkparam(varargin,'axisequal',@ischar,{'auto','manual','off'}); +nargs = nargs + 2; +if s==0 || ~any(strcmpi(axeq,{'manual','off'})) + axeq = 'auto'; % default (automatic) +end + +% CROP param/value +[s,crop] = checkparam(varargin,'crop',@isvec,4); +nargs = nargs + 2; + +% options without argument value +km = any(strcmpi(varargin,'km')); +dec = any(strcmpi(varargin,'cartesian') | strcmpi(varargin,'dec')); +dms = any(strcmpi(varargin,'latlon') | strcmpi(varargin,'dms')); +scale = any(strcmpi(varargin,'legend') | strcmpi(varargin,'scale')); +inter = any(strcmpi(varargin,'interp')); +lake = any(strcmpi(varargin,'lake')); +fbold = any(strcmpi(varargin,'fontbold')); +noplot = any(strcmpi(varargin,'noplot')); + + +% for backward compatibility (former syntax)... +nargs = nargs + dec + dms + scale + lake + inter + km + fbold + noplot; + +if (nargin - nargs) > 3 && ~isempty(varargin{1}) + opt = varargin{1}; + if ~isnumeric(opt) + error('OPT = [A,C,S,ZMIN,ZMAX,ZCUT] argument must be numeric.'); + end + if ~isempty(opt) + az = opt(1); + end + if length(opt) > 1 + ct = opt(2); + end + if length(opt) > 2 + lcut = opt(3); + end + if length(opt) > 4 + zmin = opt(4); + zmax = opt(5); + end + if length(opt) > 5 + zcut = opt(6); + end +end + +if (nargin - nargs) > 4 && ~isempty(varargin{2}) + cmap = varargin{2}; + csea = []; +end + +if (nargin - nargs) > 5 && ~isempty(varargin{3}) + novalue = varargin{3}; +end + +if (nargin - nargs) > 6 && ~isempty(varargin{4}) + csea = varargin{4}; +end + + +% further test of input arguments +if dms && any(abs(y) > 91) + error('With LATLON option Y must be in valid latitudes interval (decimal degrees).') +end + +if km + zratio = 1000; +end + + +% ------------------------------------------------------------------------- +% --- Pre-process DEM data + +% crops data if needed +if numel(crop)==4 + fprintf('DEM: crops original data from [%g,%g,%g,%g] to [%g,%g,%g,%g]...\n', ... + min(x(:)),max(x(:)),min(y(:)),max(y(:)),crop); + kx = find(x >= crop(1) & x <= crop(2)); + ky = find(y >= crop(3) & y <= crop(4)); + x = x(kx); + y = y(ky); + z = z(ky,kx); +end + +% decimates data to avoid disk swap/out of memory... +nmax = 1500; +if decim + n = decim; +else + n = ceil(sqrt(numel(z))/nmax); +end +if n > 1 + x = x(1:n:end); + y = y(1:n:end); + z = z(1:n:end,1:n:end); + fprintf('DEM: data has been decimated by a factor of %d...\n',n); +end + +z = double(z); % necessary for most of the following calculations... +z(z==novalue) = NaN; + +if isempty(csea) + k = (z~=0 & ~isnan(z)); +else + k = ~isnan(z); +end + +if isnan(zmin) + zmin = nmedian(z(k),zcut/100); +end +if isnan(zmax) + zmax = nmedian(z(k),1 - zcut/100); +end +dz = zmax - zmin; + +if decim & n < 0 + xi = linspace(x(1),x(end),-n*length(x)); + yi = linspace(y(1),y(end),-n*length(y))'; + [xx,yy] = meshgrid(xi,yi); + z = interp2(x,y,z,xx,yy,'*cubic'); + x = xi; + y = yi; + fprintf('DEM: data has been oversampled by a factor of %d...\n',-n); +end + +if inter + z = fillgap(x,y,z); +end + +% ------------------------------------------------------------------------- +% --- Process lighting + +if dz > 0 + % builds the colormap: concatenates seacolor and landcolor around 0 + if ~isempty(csea) + l = size(csea,1); + if zmin < 0 && zmax > 0 + r = size(cland,1)*abs(zmin)/zmax/l; + cmap = cat(1,interp1(1:l,csea,linspace(1,l,ceil(l*r)),'*linear'),cland); + elseif zmax <=0 + cmap = csea; + end + end + + % normalisation of Z using CMAP and convertion to RGB + I = ind2rgb(uint16(round((z - zmin)*(size(cmap,1) - 1)/dz) + 1),cmap); + + if ct > 0 + % computes lighting from elevation gradient + %[fx,fy] = gradient(z,x,y); + if dms + ryz = degkm*1000; + rxz = degkm*1000*cosd(mean(y)); + else + rxz = zratio; + ryz = zratio; + end + [xx,yy] = meshgrid(x*rxz,y*ryz); + [fx,fy,fz] = surfnorm(xx,yy,z); + [ux,uy,uz] = sph2cart((90-az)*pi/180,el*pi/180,1); + fxy = fx*ux + fy*uy + fz*uz; + clear xx yy fx fy fz % free some memory... + + fxy(isnan(fxy)) = 0; + + % computes maximum absolute gradient (median-style), normalizes, + % saturates and duplicates in 3-D matrix + li = 1 - abs(sind(el)); % light amplitude (experimental) + r = repmat(max(min(li*fxy/nmedian(abs(fxy),1 - lcut/100),1),-1),[1,1,3]); + rp = (1 - abs(r)).^ct; + + % applies contrast using exponent + I = I.*rp; + + % lighter for positive gradient + I(r>0) = I(r>0) + (1 - rp(r>0)); + + end + + % set novalues / NaN to nancolor + [i,j] = find(isnan(z)); + if ~isempty(i) + I(sub2ind(size(I),repmat(i,1,3),repmat(j,1,3),repmat(1:3,size(i,1),1))) = repmat(novalue_color,size(i,1),1); + end + + % lake option + if lake + klake = islake(z); + else + klake = 0; + end + + % set the seacolor for 0 values + if ~isempty(csea) + [i,j] = find(z==0 | klake); + if ~isempty(i) + I(sub2ind(size(I),repmat(i,1,3),repmat(j,1,3),repmat(1:3,size(i,1),1))) = repmat(csea(end,:),size(i,1),1); + end + end + + if wmark + I = watermark(I,wmark); + end + txt = ''; + +else + + I = repmat(shiftdim(sea_color,-1),size(z)); + cmap = repmat(sea_color,[256,1]); + txt = 'Mak Byur!'; % Splash ! +end + +% ------------------------------------------------------------------------- +% --- ends the function when 'noplot' option is on +if noplot + varargout{1} = struct('x',x,'y',y,'z',z,'rgb',I); + return +end + +% ------------------------------------------------------------------------- +% --- plots the RGB image +hh = imagesc(x,y,I); + +if ~isempty(txt) + text(mean(x),mean(y),txt,'Color',sea_color/4, ... + 'FontWeight','bold','HorizontalAlignment','center') +end + +orient tall; axis xy +if strcmpi(axeq,'auto') + axis equal +end +axis tight +xlim = [min(x),max(x)]; +ylim = [min(y),max(y)]; +zlim = [min([z(z(:) ~= novalue);zmin]),max([z(z(:) ~= novalue);zmax])]; + +if dms + % approximates X-Y aspect ratio for this latitude (< 20-m precision for 1x1° grid) + xyr = cos(mean(y)*pi/180); +else + xyr = 1; +end + +bw0 = max(diff(xlim)*xyr,diff(ylim))/100; +bwy = bw*bw0; % Y border width = 1% +bwx = bwy/xyr; % border width (in degree of longitude) + + +% ------------------------------------------------------------------------- +% --- Axis basemap style +if dec || dms + axis off + + if strcmpi(axeq,'manual') + ppos = get(gcf,'PaperPosition'); + apos = get(gca,'Position'); + xyf = (xyr*diff(xlim)/apos(3)/ppos(3))/(diff(ylim)/apos(4)/ppos(4)); + if xyf >= 1 + set(gca,'Position',[apos(1),apos(2),apos(3),apos(4)/xyf]); + else + set(gca,'Position',[apos(1),apos(2),apos(3)*xyf,apos(4)]); + end + end + if strcmpi(axeq,'auto') + if diff(xlim)*xyr <= diff(ylim) + set(gca,'DataAspectRatio',[1,xyr,1]) + else + set(gca,'DataAspectRatio',[1/xyr,1,1]) + end + end + + if bw > 0 + % transparent borders + patch([xlim(1)-bwx,xlim(2)+bwx,xlim(2)+bwx,xlim(1)-bwx],ylim(1) - bwy*[0,0,1,1],'k','FaceColor','none','clipping','off') + patch([xlim(1)-bwx,xlim(2)+bwx,xlim(2)+bwx,xlim(1)-bwx],ylim(2) + bwy*[0,0,1,1],'k','FaceColor','none','clipping','off') + patch(xlim(1) - bwx*[0,0,1,1],[ylim(1)-bwy,ylim(2)+bwy,ylim(2)+bwy,ylim(1)-bwy],'k','FaceColor','none','clipping','off') + patch(xlim(2) + bwx*[0,0,1,1],[ylim(1)-bwy,ylim(2)+bwy,ylim(2)+bwy,ylim(1)-bwy],'k','FaceColor','none','clipping','off') + end + dlon = {'E','W'}; + dlat = {'N','S'}; + if fbold + fw = 'bold'; + else + fw = 'normal'; + end + + if ddx == 0 + ddx = dtick(diff(xlim),dms); + end + if ddy == 0 + ddy = dtick(diff(ylim),dms); + end + xtick = (ddx*ceil(xlim(1)/ddx)):ddx:xlim(2); + for xt = xtick(1:2:end) + dt = ddx - max(0,xt + ddx - xlim(2)); + patch(repmat(xt + dt*[0,1,1,0]',[1,2]),[ylim(1) - bwy*[0,0,1,1];ylim(2) + bwy*[0,0,1,1]]','k','clipping','off') + if fs > 0 + if ~isempty(regexp(tpos,'north','once')) + text(xt,ylim(2) + 1.2*bwy,deg2dms(xt,dlon,dec),'FontSize',fs,'FontWeight',fw, ... + 'HorizontalAlignment','center','VerticalAlignment','bottom'); + else + text(xt,ylim(1) - 1.2*bwy,deg2dms(xt,dlon,dec),'FontSize',fs,'FontWeight',fw, ... + 'HorizontalAlignment','center','VerticalAlignment','top'); + end + end + end + + ytick = (ddy*ceil(ylim(1)/ddy)):ddy:ylim(2); + for yt = ytick(1:2:end) + dt = ddy - max(0,yt + ddy - ylim(2)); + patch([xlim(1) - bwx*[0,0,1,1];xlim(2) + bwx*[0,0,1,1]]',repmat(yt + dt*[0,1,1,0]',[1,2]),'k','clipping','off') + if fs > 0 + if ~isempty(regexp(tpos,'east','once')) + text(xlim(2) + 1.2*bwx,yt,deg2dms(yt,dlat,dec),'FontSize',fs,'FontWeight',fw, ... + 'HorizontalAlignment','center','VerticalAlignment','top','rotation',90); + else + text(xlim(1) - 1.2*bwx,yt,deg2dms(yt,dlat,dec),'FontSize',fs,'FontWeight',fw, ... + 'HorizontalAlignment','center','VerticalAlignment','bottom','rotation',90); + end + end + end +end + +% ------------------------------------------------------------------------- +% --- Scales legend +if scale + %wsc = diff(xlim)*0.01; + wsc = bw0; + xsc = xlim(2) + wsc*2 + bwx; + + if wmark + cmap = watermark(cmap,wmark); + end + + % -- elevation scale (colorbar) + zscale = linspace(zmin,zmax,length(cmap))'; + yscale = linspace(0,diff(ylim)/2,length(cmap)); + ddz = dtick(dz*max(0.5*xyr*diff(xlim)/yscale(end),1)); + ztick = (ddz*ceil(zscale(1)/ddz)):ddz:zscale(end); + rgbscale = ind2rgb(uint16(round((zscale - zmin)*(size(cmap,1) - 1)/dz) + 1),cmap); + ysc = ylim(1); + hold on + imagesc(xsc + wsc*[-1,1]/2,ysc + yscale,repmat(rgbscale,1,2),'clipping','off'); + patch(xsc + wsc*[-1,1,1,-1],ysc + yscale(end)*[0,0,1,1],'k','FaceColor','none','Clipping','off') + text(xsc + 2*wsc + zeros(size(ztick)),ysc + (ztick - zscale(1))*0.5*diff(ylim)/diff(zscale([1,end])),num2str(ztick'), ... + 'HorizontalAlignment','left','VerticalAlignment','middle','FontSize',6) + % indicates min and max Z values + text(xsc,ysc - bwy/2,sprintf('%g m',roundsd(zlim(1),3)),'FontWeight','bold', ... + 'HorizontalAlignment','left','VerticalAlignment','top','FontSize',6) + text(xsc,ysc + .5*diff(ylim) + bwy/2,sprintf('%g m',roundsd(zlim(2),3)),'FontWeight','bold', ... + 'HorizontalAlignment','left','VerticalAlignment','bottom','FontSize',6) + + % frees axes only if not hold on + if ~holdon + hold off + end + + % -- distance scale (in km) + if dms + fsc = degkm; + else + fsc = zratio/1e3; + end + dkm = dtick(diff(ylim)*fsc); + ysc = ylim(2) - 0.5*dkm/fsc; + patch(xsc + wsc*[-1,-1,0,0],ysc + dkm*0.5*[-1,1,1,-1]/fsc,'k','FaceColor',grey,'clipping','off') + if dkm > 1 + skm = sprintf('%g km',dkm); + else + skm = sprintf('%g m',dkm*1000); + end + text(xsc,ysc,skm,'rotation',-90,'HorizontalAlignment','center','VerticalAlignment','bottom', ... + 'Color',grey,'FontWeight','bold','FontSize',6) +end + + +if nargout > 0 + varargout{1} = hh; +end +if nargout > 1 + varargout{2} = I; +end +if nargout > 2 + varargout{3} = z; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function y = nmedian(x,n) +%NMEDIAN Generalized median filter +% NMEDIAN(X,N) sorts elemets of X and returns N-th value (N normalized). +% So: +% N = 0 is minimum value +% N = 0.5 is median value +% N = 1 is maximum value + +if nargin < 2 + n = 0.5; +end +y = sort(x(:)); +y = interp1(sort(y),n*(length(y)-1) + 1); + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function dd = dtick(dlim,deg) +%DTICK Tick intervals + +if nargin < 2 + deg = 0; +end + +if deg && dlim <= 2/60 + % less than 2 minutes: base 36 + m = 10^floor(log10(dlim*36))/36; +elseif deg && dlim <= 2 + % less than 2 degrees: base 6 + m = 10^floor(log10(dlim*6))/6; +else + % more than few degrees or not degrees: decimal rules + m = 10^floor(log10(dlim)); +end +p = ceil(dlim/m); +if p <= 1 + dd = .1*m; +elseif p == 2 + dd = .2*m; +elseif p <= 5 + dd = .5*m; +else + dd = m; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function s = deg2dms(x,ll,dec) +%DEG2DMS Degree/minute/second display + +if dec + s = sprintf('%7.7g',x); +else + xa = abs(x) + 1/360000; + %sd = sprintf('%d%c',floor(xa),176); % ASCII char 176 is the degree sign + sd = sprintf('%d°',floor(xa)); + sm = ''; + ss = ''; + if mod(x,1) + sm = sprintf('%02d''',floor(mod(60*xa,60))); + sa = floor(mod(3600*xa,60)); + if sa + ss = sprintf('%02d"',sa); + else + if strcmp(sm,'00''') + sm = ''; + end + end + end + s = [sd,sm,ss,ll{1+int8(x<0)}]; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function z = fillgap(x,y,z) +% GRIDDATA is not efficient for large arrays, but has great advantage to be +% included in Matlab's core functions! To optimize interpolation, we +% reduce the amount of relevant data by building a mask of all surrounding +% pixels of novalue areas... playing with linear index! + +sz = size(z); +k = find(isnan(z)); +k(k == 1 | k == numel(z)) = []; % removes first and last index (if exist) +if ~isempty(k) + [xx,yy] = meshgrid(x,y); + mask = zeros(sz,'int8'); + k2 = ind90(sz,k); % k2 is linear index in the row order + % sets to 1 every previous and next index, both in column and row order + mask([k-1;k+1;ind90(fliplr(sz),[k2-1;k2+1])]) = 1; + mask(k) = 0; % removes the novalue index + kb = find(mask); % keeps only border values + z(k) = griddata(xx(kb),yy(kb),z(kb),xx(k),yy(k)); +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function k2 = ind90(sz,k) + +[i,j] = ind2sub(sz,k); +k2 = sub2ind(fliplr(sz),j,i); % switched i and j: k2 is linear index in row order + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function k = islake(z) +% ISLAKE mask of zero gradient on 3x3 tiles +% We use diff matrix in row and column directions, and shift it to build +% a single vectorized test of surrounding pixels. To do this we must +% concatenate unit vectors in different combinations... + +dx = diff(z,1,2); % differences in X direction +dy = diff(z,1,1); % differences in Y direction +u1 = ones(size(z,1),1); % row unit vector +u2 = ones(1,size(z,2)); % column unit vector +u2r = u2(2:end); + +% index of the tiles center pixel +k = ( ... + [u2;dy] == 0 & [dy;u2] == 0 & ... + [u1,dx] == 0 & [dx,u1] == 0 & ... + [u1,[dx(2:end,:);u2r]] == 0 & [[dx(2:end,:);u2r],u1] == 0 & ... + [u1,[u2r;dx(1:end-1,:)]] == 0 & [[u2r;dx(1:end-1,:)],u1] == 0 ... +); + +% now extends it to surrounding pixels +k(1:end-1,:) = (k(1:end-1,:) | k(2:end,:)); +k(2:end,:) = (k(2:end,:) | k(1:end-1,:)); +k(:,1:end-1) = (k(:,1:end-1) | k(:,2:end)); +k(:,2:end) = (k(:,2:end) | k(:,1:end-1)); + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function s = isrgb(x,n) + +if nargin < 2 + n = 0; +end +if isnumeric(x) && (n == 1 && all(size(x) == [1,3]) || n == 0 && size(x,2) == 3) ... + && all(x(:) >= 0 & x(:) <= 1) + s = 1; +else + s = 0; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function s = isperc(x) + +if isnumeric(x) && isscalar(x) && x >= 0 && x <= 100 + s = 1; +else + s = 0; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function s = isvec(x,n) + +if nargin < 2 + n = 2; +end +if isnumeric(x) && numel(x) == n + s = 1; +else + s = 0; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function y=roundsd(x,n) + +og = 10.^(floor(log10(abs(x)) - n + 1)); +y = round(x./og).*og; +y(x==0) = 0; + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function y = watermark(x,n) + +if nargin < 2 + n = 2; +end + +if n == 0 + y = x; +else + y = (x/n + 1 - 1/n); +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function [s,v] = checkparam(arg,nam,func,val) + +switch func2str(func) + case 'isscalar' + num = 1; + mes = 'scalar value'; + case 'isperc' + num = 1; + mes = 'percentage scalar value'; + case 'isvec' + num = 1; + if nargin < 4 + val = 2; + end + mes = sprintf('%d-element vector',val); + case 'isrgb' + num = 1; + mes = '[R,G,B] vector with 0.0 to 1.0 values'; + case 'ischar' + num = 0; + mes = 'string'; + if nargin > 3 + mes = sprintf('%s (%s)',mes,strjoin(val,' or ')); + end + otherwise + num = 1; + mes = 'value'; +end + +s = 0; +v = []; +k = find(strcmpi(arg,nam)); +if ~isempty(k) + if (k + 1) <= length(arg) ... + && (~num || isnumeric(arg{k+1})) ... + && (nargin < 4 && func(arg{k+1}) ... + || (nargin > 3 && (strcmp(func2str(func),'ischar') && ismember(arg{k+1},val)) ... + || strcmp(func2str(func),'isvec') && func(arg{k+1},val))) + v = arg{k+1}; + s = 1; + else + error('%s option must be followed by a valid %s.',upper(nam),mes) + end +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function s=strjoin(c,d) +%STRJOIN Join cell array of strings +%(this is for Matlab versions < 2013a backward compatibility) + +if nargin < 2 + d = ''; +end +n = numel(c); +ss = cell(2,n); +ss(1,:) = reshape(c,1,n); +ss(2,1:n-1) = {d}; +s = [ss{:}]; Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/landcolor.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/landcolor.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/landcolor.m (revision 27955) @@ -0,0 +1,78 @@ +function y = landcolor(n) +%LANDCOLOR Land colormap +% +% Author: Francois Beauducel +% $Revision: 1.0.0 $ $Date: 2012/05/17 11:22:44 $ + +J = [ ... +0.095678 0.53427 0.21682 +0.15785 0.5979 0.23274 +0.21286 0.64673 0.2514 +0.26411 0.68789 0.27268 +0.32959 0.72416 0.31308 +0.39794 0.75695 0.36038 +0.46153 0.7871 0.40624 +0.52108 0.81516 0.45135 +0.57702 0.84152 0.49547 +0.62973 0.86645 0.53891 +0.67946 0.89016 0.58187 +0.72647 0.91282 0.62427 +0.77095 0.93455 0.66619 +0.81306 0.95546 0.70772 +0.85292 0.97563 0.7489 +0.89066 0.99514 0.78976 +0.88379 0.98595 0.77038 +0.86389 0.96758 0.73236 +0.84615 0.94972 0.69623 +0.8303 0.93233 0.66186 +0.81612 0.91536 0.6291 +0.80341 0.8988 0.59784 +0.79201 0.8826 0.56795 +0.78191 0.86676 0.53946 +0.7729 0.85123 0.51224 +0.76479 0.83602 0.48615 +0.75747 0.8211 0.46111 +0.75084 0.80645 0.43704 +0.74506 0.79206 0.41414 +0.73981 0.77792 0.39211 +0.73501 0.76401 0.37089 +0.73068 0.75033 0.35052 +0.72683 0.73685 0.33106 +0.72042 0.72074 0.31228 +0.71032 0.70085 0.29417 +0.69761 0.67821 0.27694 +0.68489 0.65558 0.26026 +0.67235 0.63313 0.24418 +0.65997 0.61082 0.22889 +0.64775 0.58874 0.21406 +0.63568 0.56689 0.19983 +0.62376 0.54527 0.18622 +0.61197 0.52391 0.17299 +0.60033 0.50283 0.16046 +0.58881 0.48203 0.14832 +0.57742 0.46151 0.13667 +0.56616 0.44133 0.12555 +0.55502 0.4214 0.11472 +0.54398 0.4019 0.10456 +0.53306 0.38266 0.094633 +0.52226 0.36382 0.085242 +0.51155 0.3453 0.076179 +0.50095 0.32714 0.067515 +0.49045 0.30938 0.059259 +0.48005 0.29193 0.051294 +0.46973 0.27495 0.043796 +0.45951 0.25823 0.0365 +0.44938 0.24206 0.029715 +0.43934 0.22609 0.023063 +0.42938 0.21074 0.016949 +0.41951 0.19556 0.010917 +0.40971 0.18105 0.0054326 +0.4 0.16667 0 +]; + +l = length(J); +if nargin < 1 + n = 256; +end +y = interp1(1:l,J,linspace(1,l,n),'*linear'); + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/license.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/license.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/license.txt (revision 27955) @@ -0,0 +1,24 @@ +Copyright (c) 2016, François Beauducel +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/seacolor.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/seacolor.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dem/seacolor.m (revision 27955) @@ -0,0 +1,58 @@ +function y = seacolor(n) +%SEACOLOR Sea colormap adapted from NGDC ETOPO1 +% +% Author: Francois Beauducel + +J = [ ... + 0.0392 0 0.4745 + 0.1020 0 0.5373 + 0.1020 0 0.5373 + 0.1490 0 0.5961 + 0.1490 0 0.5961 + 0.1059 0.0118 0.6510 + 0.1059 0.0118 0.6510 + 0.0627 0.0235 0.7059 + 0.0627 0.0235 0.7059 + 0.0196 0.0353 0.7569 + 0.0196 0.0353 0.7569 + 0 0.0549 0.7961 + 0 0.0549 0.7961 + 0 0.0863 0.8235 + 0 0.0863 0.8235 + 0 0.1176 0.8471 + 0 0.1176 0.8471 + 0 0.1529 0.8745 + 0 0.1529 0.8745 + 0.0471 0.2667 0.9059 + 0.0471 0.2667 0.9059 + 0.1020 0.4000 0.9412 + 0.1020 0.4000 0.9412 + 0.0745 0.4588 0.9569 + 0.0745 0.4588 0.9569 + 0.0549 0.5216 0.9765 + 0.0549 0.5216 0.9765 + 0.0824 0.6196 0.9882 + 0.0824 0.6196 0.9882 + 0.1176 0.6980 1.0000 + 0.1176 0.6980 1.0000 + 0.1686 0.7294 1.0000 + 0.1686 0.7294 1.0000 + 0.2157 0.7569 1.0000 + 0.2157 0.7569 1.0000 + 0.2549 0.7843 1.0000 + 0.2549 0.7843 1.0000 + 0.3098 0.8235 1.0000 + 0.3098 0.8235 1.0000 + 0.3686 0.8745 1.0000 + 0.3686 0.8745 1.0000 + 0.5412 0.8902 1.0000 + 0.5412 0.8902 1.0000 + 0.7373 0.9020 1.0000 +]; + +l = length(J); +if nargin < 1 + n = 256; +end +y = interp1(1:l,J,linspace(1,l,n),'*linear'); + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/distribute/README =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/distribute/README (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/distribute/README (revision 27955) @@ -0,0 +1,9 @@ +At: https://pypi.python.org/pypi/setuptools + +Installation Instructions + +The recommended way to bootstrap setuptools on any system is to download ez_setup.py and run it using the target Python environment. Different operating systems have different recommended techniques to accomplish this basic routine, so below are some examples to get you started. + +Setuptools requires Python 2.6 or later. To install setuptools on Python 2.4 or Python 2.5, use the bootstrap script for Setuptools 1.x. + +The link provided to ez_setup.py is a bookmark to bootstrap script for the latest known stable release. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/distribute/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/distribute/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/distribute/install.sh (revision 27955) @@ -0,0 +1,6 @@ +#!/bin/bash +set -eu + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'http://python-distribute.org/distribute_setup.py' 'distribute_setup.py' +python distribute_setup.py Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/doxygen/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/doxygen/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/doxygen/install.sh (revision 27955) @@ -0,0 +1,22 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +mkdir install + +#Download latest version +git clone https://github.com/doxygen/doxygen.git install + +#Configure doxygen +cd install +mkdir build +cd build +cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/doxygen/install" .. +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi + +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dyson/ldap.pl =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dyson/ldap.pl (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dyson/ldap.pl (revision 27955) @@ -0,0 +1,25 @@ +#!/usr/bin/perl +# +# LDAP.PL - Acquire JPL LDAP data and pare down to user IDs - 2011-08-01 +# +$cat="/bin/cat"; $srt="/bin/sort"; $ldb="/usr/bin/ldapsearch"; # Binary locations (change as needed) +$lds="ldap.jpl.nasa.gov"; $ou="ou=personnel,dc=dir,dc=jpl,dc=nasa,dc=gov"; # Define LDAP server & organization +$bn="jplbadgenumber"; $txt="$bn".".txt"; $db="jplusers.db"; # Initialize values +# +system(`$ldb -x -h $lds -b $ou uid=* uid > $txt`); # Execute LDAPsearch, write to file +# +open(I,"<$txt"); # Open input file handle + open(O,">badges.tmp"); # Open output file handle + while () { chomp($_); # Spool through input file + if ($_ =~ "^uid: ") { # If line begins with UID value, + $_=~s/uid: //; $_=~s/,(.*)$//; $_=~s/\n//; # strip line of extraneous data + if (!($_=~/^\d\d\d\d\d\d/)) { print O "$_\n"; } # If UID is non-numeric, print output + } # Close condition + } # Close spool + close(O); # Close output file handle +close(I); # Close input file handle +# +system(`$cat badges.tmp |$srt -u > $db 2>/dev/null`); # Sort output +unlink("badges.tmp"); unlink("$txt"); # Unlink temp files +# +# EOF - 2011-08-01 - Jay Dyson Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dyson/readme.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dyson/readme.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dyson/readme.txt (revision 27955) @@ -0,0 +1,38 @@ +-- ARCHIVE MANIFEST ------------------------------------------ 2011-08-19 -- + + Filename Description + -------------- ---------------------------------------------------------- + readme.txt This file: describes script functions. + ldap.pl PERL script for acquiring JPL user IDs via cron job. + source_seek.sh Code-scanning script. Surveys scripts for hard-coded IP + addresses, password callouts, and user IDs. + +-- SCRIPT INFORMATION ------------------------------------------------------ + + LDAP.PL (requires PERL, UNIX ldapsearch, and related utilities) + -------------------------------------------------------------------------- + The LDAP.PL script is intended solely for twice-daily invocation via cron. + This script should be run once at noon, once at midnight. This script + generates the jplusers.db file on which the SOURCE_SEEK.SH shell script + relies for its scanning of source files. + + SOURCE_SEEK.SH (requires UNIX shell and related utilities) + -------------------------------------------------------------------------- + The SOURCE_SEEK.SH shell script is intended for regular cron invocation, + but may be run at system administrator discretion. This script uses UNIX + 'find' and 'grep' utilities to scan code files for hard-coded JPL Internet + Protocol (IP) addresses, password callouts, and JPL user IDs. This script + accepts the path where source code files reside as a command line + argument (e.g., ./source_seek.sh /path/to/sourcecode/files). + +-- AUTHOR CONTACT INFO ----------------------------------------------------- + + Please direct questions regarding these files to the developer. + + Name : Jay Dyson, CISSP + Role : IT Security Engineer + Group : JPL IT Security + E-mail : jdyson@jpl.nasa.gov + Phone : 818-397-4960 + +------------------------------------------------ LAST UPDATED: 2011-08-19 -- Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/dyson/source_seek.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/dyson/source_seek.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/dyson/source_seek.sh (revision 27955) @@ -0,0 +1,26 @@ +#!/bin/sh +# +# SOURCE_SEEK.SH - Look for IP addresses and mention of 'password' in source files - 2009-10-05 +# +if [ -n "${1}" ]; then + clear + echo "Checking for IP addresses" + echo "--------------------------------------------" + find $1 -name "*" -exec grep -il "128\.149\." {} \; + find $1 -name "*" -exec grep -il "137\.78\." {} \; + find $1 -name "*" -exec grep -il "137\.79\." {} \; + find $1 -name "*" -exec grep -il "137\.228\." {} \; + echo "--------------------------------------------" + echo "\nChecking for 'password'" + echo "--------------------------------------------" + find $1 -name "*" -exec grep -il "password" {} \; + echo "--------------------------------------------" + echo "\nChecking for JPL user IDs" + echo "--------------------------------------------" + find $1 -name "*" -exec grep -ilf jplusers.db {} \; + echo "--------------------------------------------" +else + echo -e "\nUSE: $0 \n"; +fi +# +# EOF - 2011-08-05 - Jay Dyson Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/ec2ami/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/ec2ami/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/ec2ami/install.sh (revision 27955) @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf ec2-api-tools.zip +rm -rf ec2-api-tools-1.4.0.7 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ec2-api-tools.zip' 'ec2-api-tools.zip' + +#Untar +unzip ec2-api-tools.zip Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/ec2api/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/ec2api/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/ec2api/install.sh (revision 27955) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf ec2-api-tools.zip +rm -rf ec2-api-tools-1.6.3.1 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ec2-api-tools.zip' 'ec2-api-tools.zip' +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/docs/ec2-ug.pdf' 'ec2-ug.pdf' + +#Untar +unzip ec2-api-tools.zip Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/emscripten/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/emscripten/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/emscripten/install.sh (revision 27955) @@ -0,0 +1,42 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Introduce build step to $ISSM_DIR/jenkins/jenkins.sh to compile Fortran code in $ISSM_DIR/src/c/modules/GiaDefelectionCorex/ to C with f2c +# - Then, revert $ISSM_DIR/externalpackages/emscripten/install.sh to r24306 and test clean build +# - When builtin support for Fortran is available, remove build step +# + +## Constants +# +VER="latest" # Set this to "latest", or last tag that works in case of failure + +## Environment +# +PREFIX="${ISSM_DIR}/externalpackages/emscripten/install" + +# Cleanup +rm -rf ${PREFIX} + +# Get the emsdk repo +git clone https://github.com/emscripten-core/emsdk.git + +# Create $PREFIX directory +mkdir -p ${PREFIX} + +# Move source to $PREFIX directory +mv emsdk/* ${PREFIX} +rm -rf emsdk + +cd ${PREFIX} + +# Download and install the latest SDK tools. +./emsdk install ${VER} + +# Make the "latest" SDK "active" for the current user. (writes ~/.emscripten +# file) +./emsdk activate ${VER} + +# Activate PATH and other environment variables in the current terminal +source ./emsdk_env.sh Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/esmf/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/esmf/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/esmf/install.sh (revision 27955) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#DOC: https://earthsystemmodeling.org/docs/nightly/develop/ESMC_crefdoc/node5.html#SECTION05063000000000000000 +# https://cpp.hotexamples.com/examples/-/-/ESMC_MeshAddNodes/cpp-esmc_meshaddnodes-function-examples.html + +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/ESMF_8_0_1.tar.gz" "ESMF_8_0_1.tar.gz" +tar -zxvf ESMF_8_0_1.tar.gz +mv ESMF_8_0_1 esmf +export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf +export ESMF_INSTALL_PREFIX=$ISSM_DIR/externalpackages/esmf/install + +#Compile and install esmf +cd esmf +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/ImageSelection.java =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/ImageSelection.java (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/ImageSelection.java (revision 27955) @@ -0,0 +1,38 @@ +/* + * Based on code snippet from + * http://java.sun.com/developer/technicalArticles/releases/data/ + * + * Copyright © 2008, 2010 Oracle and/or its affiliates. All rights reserved. Use is subject to license terms. + */ + +import java.awt.image.BufferedImage; +import java.awt.datatransfer.*; + +public class ImageSelection implements Transferable { + + private static final DataFlavor flavors[] = + {DataFlavor.imageFlavor}; + + private BufferedImage image; + + public ImageSelection(BufferedImage image) { + this.image = image; + } + + // Transferable + public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException { + if (flavor.equals(flavors[0]) == false) { + throw new UnsupportedFlavorException(flavor); + } + return image; + } + + public DataFlavor[] getTransferDataFlavors() { + return flavors; + } + + public boolean isDataFlavorSupported(DataFlavor + flavor) { + return flavor.equals(flavors[0]); + } +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/LICENSE =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/LICENSE (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/LICENSE (revision 27955) @@ -0,0 +1,27 @@ +Copyright (c) 2014, Oliver J. Woodford, Yair M. Altman +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +* Neither the name of the {organization} nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/README.md =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/README.md (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/README.md (revision 27955) @@ -0,0 +1,272 @@ +export_fig +========== + +A toolbox for exporting figures from MATLAB to standard image and document formats nicely. + +### Overview +Exporting a figure from MATLAB the way you want it (hopefully the way it looks on screen), can be a real headache for the unitiated, thanks to all the settings that are required, and also due to some eccentricities (a.k.a. features and bugs) of functions such as `print`. The first goal of export_fig is to make transferring a plot from screen to document, just the way you expect (again, assuming that's as it appears on screen), a doddle. + +The second goal is to make the output media suitable for publication, allowing you to publish your results in the full glory that you originally intended. This includes embedding fonts, setting image compression levels (including lossless), anti-aliasing, cropping, setting the colourspace, alpha-blending and getting the right resolution. + +Perhaps the best way to demonstrate what export_fig can do is with some examples. + +*Note: `export_fig` currently supports only figures created with the `figure` function, or GUIDE. Figures created using `uifigure` or AppDesigner are only partially supported. See issues [#287](https://github.com/altmany/export_fig/issues/287), [#261](https://github.com/altmany/export_fig/issues/261) for details.* + +### Examples +**Visual accuracy** - MATLAB's exporting functions, namely `saveas` and `print`, change many visual properties of a figure, such as size, axes limits and ticks, and background colour, in unexpected and unintended ways. Export_fig aims to faithfully reproduce the figure as it appears on screen. For example: +```Matlab +plot(cos(linspace(0, 7, 1000))); +set(gcf, 'Position', [100 100 150 150]); +saveas(gcf, 'test.png'); +export_fig test2.png +``` +generates the following: + +| Figure: | test.png: | test2.png: | +|:-------:|:---------:|:----------:| +|![](https://farm6.staticflickr.com/5616/15589249291_16e485c29a_o_d.png)|![](https://farm4.staticflickr.com/3944/15406302850_4d2e1c7afa_o_d.png)|![](https://farm6.staticflickr.com/5607/15568225476_8ce9bd5f6b_o_d.png)| + +Note that the size and background colour of test2.png (the output of export_fig) are the same as those of the on screen figure, in contrast to test.png. Of course, if you want the figure background to be white (or any other colour) in the exported file then you can set this prior to exporting using: +```Matlab +set(gcf, 'Color', 'w'); +``` + +Notice also that export_fig crops and anti-aliases (smooths, for bitmaps only) the output by default. However, these options can be disabled; see the Tips section below for details. + +**Resolution** - by default, export_fig exports bitmaps at screen resolution. However, you may wish to save them at a different resolution. You can do this using either of two options: `-m`, where is a positive real number, magnifies the figure by the factor for export, e.g. `-m2` produces an image double the size (in pixels) of the on screen figure; `-r`, again where is a positive real number, specifies the output bitmap to have pixels per inch, the dimensions of the figure (in inches) being those of the on screen figure. For example, using: +```Matlab +export_fig test.png -m2.5 +``` +on the figure from the example above generates: + +![](https://farm4.staticflickr.com/3937/15591910915_dc7040c477_o_d.png) + +Sometimes you might have a figure with an image in. For example: +```Matlab +imshow(imread('cameraman.tif')) +hold on +plot(0:255, sin(linspace(0, 10, 256))*127+128); +set(gcf, 'Position', [100 100 150 150]); +``` +generates this figure: + +![](https://farm4.staticflickr.com/3942/15589249581_ff87a56a3f_o_d.png) + +Here the image is displayed in the figure at resolution lower than its native resolution. However, you might want to export the figure at a resolution such that the image is output at its native (i.e. original) size (in pixels). Ordinarily this would require some non-trivial computation to work out what that resolution should be, but export_fig has an option to do this for you. Using: +```Matlab +export_fig test.png -native +``` +produces: + +![](https://farm6.staticflickr.com/5604/15589249591_da2b2652e4_o_d.png) + +with the image being the size (in pixels) of the original image. Note that if you want an image to be a particular size, in pixels, in the output (other than its original size) then you can resize it to this size and use the `-native` option to achieve this. + +All resolution options (`-m`, `-q` and `-native`) correctly set the resolution information in PNG and TIFF files, as if the image were the dimensions of the on screen figure. + +**Shrinking dots & dashes** - when exporting figures with dashed or dotted lines using either the ZBuffer or OpenGL (default for bitmaps) renderers, the dots and dashes can appear much shorter, even non-existent, in the output file, especially if the lines are thick and/or the resolution is high. For example: +```Matlab +plot(sin(linspace(0, 10, 1000)), 'b:', 'LineWidth', 4); +hold on +plot(cos(linspace(0, 7, 1000)), 'r--', 'LineWidth', 3); +grid on +export_fig test.png +``` +generates: + +![](https://farm4.staticflickr.com/3956/15592747732_f943d4aa0a_o_d.png) + +This problem can be overcome by using the painters renderer. For example: +```Matlab +export_fig test.png -painters +``` +used on the same figure generates: + +![](https://farm4.staticflickr.com/3945/14971168504_77692f11f5_o_d.png) + +Note that not only are the plot lines correct, but the grid lines are too. + +**Transparency** - sometimes you might want a figure and axes' backgrounds to be transparent, so that you can see through them to a document (for example a presentation slide, with coloured or textured background) that the exported figure is placed in. To achieve this, first (optionally) set the axes' colour to 'none' prior to exporting, using: +```Matlab +set(gca, 'Color', 'none'); % Sets axes background +``` + +then use export_fig's `-transparent` option when exporting: +```Matlab +export_fig test.png -transparent +``` + +This will make the background transparent in PDF, EPS and PNG outputs. You can additionally save fully alpha-blended semi-transparent patch objects to the PNG format. For example: + +```Matlab +logo; +alpha(0.5); +``` + +generates a figure like this: + +![](https://farm4.staticflickr.com/3933/15405290339_b08de33528_o_d.png) + +If you then export this to PNG using the `-transparent` option you can then put the resulting image into, for example, a presentation slide with fancy, textured background, like so: + +![](https://farm6.staticflickr.com/5599/15406302920_59beaefff1_o_d.png) + +and the image blends seamlessly with the background. + +**Image quality** - when publishing images of your results, you want them to look as good as possible. By default, when outputting to lossy file formats (PDF, EPS and JPEG), export_fig uses a high quality setting, i.e. low compression, for images, so little information is lost. This is in contrast to MATLAB's print and saveas functions, whose default quality settings are poor. For example: +```Matlab +A = im2double(imread('peppers.png')); +B = randn(ceil(size(A, 1)/6), ceil(size(A, 2)/6), 3) * 0.1; +B = cat(3, kron(B(:,:,1), ones(6)), kron(B(:,:,2), ones(6)), kron(B(:,:,3), ones(6))); +B = A + B(1:size(A, 1),1:size(A, 2),:); +imshow(B); +print -dpdf test.pdf +``` +generates a PDF file, a sub-window of which looks (when zoomed in) like this: + +![](https://farm6.staticflickr.com/5613/15405290309_881b2774d6_o_d.png) + +while the command + +```Matlab +export_fig test.pdf +``` +on the same figure produces this: + +![](https://farm4.staticflickr.com/3947/14971168174_687473133f_o_d.png) + +While much better, the image still contains some compression artifacts (see the low level noise around the edge of the pepper). You may prefer to export with no artifacts at all, i.e. lossless compression. Alternatively, you might need a smaller file, and be willing to accept more compression. Either way, export_fig has an option that can suit your needs: `-q`, where is a number from 0-100, will set the level of lossy image compression (again in PDF, EPS and JPEG outputs only; other formats are lossless), from high compression (0) to low compression/high quality (100). If you want lossless compression in any of those formats then specify a greater than 100. For example: +```Matlab +export_fig test.pdf -q101 +``` +again on the same figure, produces this: + +![](https://farm6.staticflickr.com/5608/15405803908_934512c1fe_o_d.png) + +Notice that all the noise has gone. + +### Tips +**Anti-aliasing** - the anti-aliasing which export_fig applies to bitmap outputs by default makes the images look nice, but it can also blur images and increase exporting time and memory requirements, so you might not always want it. You can set the level of anti-aliasing by using the `-a` option, where is 1 (no anti-aliasing), 2, 3 (default) or 4 (maximum anti-aliasing). + +**Cropping** - by default, export_fig crops its output to minimize the amount of empty space around the figure. If you'd prefer the figure to be uncropped, and instead have the same appearance (in terms of border width) as the on screen figure, then use the `-nocrop` option. + +**Colourspace** - by default, export_fig generates files in the RGB [colourspace](https://en.wikipedia.org/wiki/Color_space). However, you can also export in greyscale or the CMYK colourspace, using the `-grey` (or `-gray`) and `-cmyk` options respectively. The CMYK option is useful for publishers who require documents in this colourspace, but the option is only supported for PDF, EPS and TIFF files. + +**Specifying a target directory** - you can get export_fig to save output files to any directory (for which you have write permission), simply by specifying the full or relative path in the filename. For example: +```Matlab +export_fig ../subdir/fig.png; +export_fig('C:/Users/Me/Documents/figures/myfig', '-pdf', '-png'); +``` + +**Variable file names** - often you might want to save a series of figures in a for loop, each with a different name. For this you can use the functional form of input arguments, i.e. `export_fig(arg1, arg2)`, and construct the filename string in a variable. Here's an example of this: +```Matlab +for a = 1:5 + plot(rand(5, 2)); + export_fig(sprintf('plot%d.png', a)); +end +``` +When using the functional form like this, be sure to put string variables in quotes: +```Matlab +export_fig(sprintf('plot%d', a), '-a1', '-pdf', '-png'); +``` + +**Specifying the figure/axes** - if you have multiple figures open you can specify which figure to export using its handle: +```Matlab +export_fig(figure_handle, filename); +``` +Equally, if your figure contains several subplots then you can export just one of them by giving export_fig the handle to the relevant axes: +```Matlab +export_fig(axes_handle, filename); +``` + +**Multiple formats** - save time by exporting to multiple formats simultaneously. E.g.: +```Matlab +export_fig filename -pdf -eps -png -jpg -tiff +``` + +**Other file formats** - if you'd like to save your figure to a bitmap format that is not supported by export_fig, e.g. animated GIF, PPM file or a frame in a movie, then you can use export_fig to output the image, and optionally an alpha-matte, to the workspace. E.g.: +```Matlab +frame = export_fig; +``` +or +```Matlab +[frame, alpha] = export_fig; +``` +These variables can then be saved to other image formats using other functions, such as imwrite. + +**Appending to a file** - you can use the `-append` option to append the figure to the end of an image/document, if it already exists. This is supported for PDF and TIFF files only. Note that if you wish to append a lot of figures consecutively to a PDF, it can be more efficient to save all the figures to PDF separately then append them all in one go at the end (e.g. using [append_pdfs](http://www.mathworks.com/matlabcentral/fileexchange/31215-appendpdfs)). + +**Output to clipboard** - you can use the `-clipboard` option to copy the specified figure or axes to the system clipboard, for easy paste into other documents (e.g., Word or PowerPoint). Note that the image is copied in bitmap (not vector) format. + +**Font size** - if you want to place an exported figure in a document with the font a particular size then you need to set the font to that size in the figure, and not resize the output of export_fig in the document. To avoid resizing, simply make sure that the on screen figure is the size you want the output to be in the document before exporting. + +**Renderers** - MATLAB has three renderers for displaying and exporting figures: painters, OpenGL and ZBuffer. The different renderers have different [features](http://www.mathworks.com/access/helpdesk/help/techdoc/creating_plots/f3-84337.html#f3-102410), so if you aren't happy with the result from one renderer try another. By default, vector formats (i.e. PDF and EPS outputs) use the painters renderer, while other formats use the OpenGL renderer. Non-default renderers can be selected by using one of these three export_fig input options: `-painters`, `-opengl`, `-zbuffer`: +```Matlab +export_fig test.png -painters +``` + +**Artifacts** - sometimes the output that you get from export_fig is not what you expected. If an output file contains artifacts that aren't in the on screen figure then make sure that the renderer used for rendering the figure on screen is the same as that used for exporting. To set the renderer used to display the figure, use: +```Matlab +set(figure_handle, 'Renderer', 'opengl'); +``` +After matching the two renderers, if the artifact appears in the on screen figure then you'll need to fix that before exporting. Alternatively you can try changing the renderer used by export_fig. Finally check that it isn't one of the known issues mentioned in the section below. + +**Smoothed/interpolated images in output PDF** - if you produce a PDF using export_fig and images in the PDF look overly smoothed or interpolated, this is because the software you are using to view the PDF is smoothing or interpolating the image data. The image is not smoothed in the PDF file itself. If the software has an option to disable this feature, you should select it. Alternatively, use another PDF viewer that doesn't exhibit this problem. + +**Locating Ghostscript/pdftops** - You may find a dialogue box appears when using export_fig, asking you to locate either [Ghostscript](http://www.ghostscript.com) or [pdftops (part of the Xpdf package)](http://www.xpdfreader.com). These are separate applications which export_fig requires to perform certain functions. If such a dialogue appears it is because export_fig can't find the application automatically. This is because you either haven't installed it, or it isn't in the normal place. Make sure you install the applications correctly first. They can be downloaded from the following places: + 1. Ghostscript: [www.ghostscript.com](http://www.ghostscript.com) + 2. pdftops (install the Xpdf package): [www.xpdfreader.com](http://www.xpdfreader.com) + +If you choose to install them in a non-default location then point export_fig +to this location using the dialogue box. + +**Undefined function errors** - If you download and run export_fig and get an error similar to this: +``` +??? Undefined function or method 'print2array' for input arguments of type 'double'. +``` +then you are missing one or more of the files that come in the export_fig package. Make sure that you click the "Get from GitHub" button at the top-right of the download [page](http://www.mathworks.co.uk/matlabcentral/fileexchange/23629-exportfig), then extract all the files in the zip file to the same directory. You should then have all the necessary files. + +### Known issues +There are lots of problems with MATLAB's exporting functions, especially `print`. Export_fig is simply a glorified wrapper for MATLAB's `print` function, and doesn't solve all of its bugs (yet?). Some of the problems I know about are: + +**Fonts** - when using the painters renderer, MATLAB can only export a small number of fonts, details of which can be found [here](http://www.mathworks.com/help/releases/R2014a/matlab/creating_plots/choosing-a-printer-driver.html#f3-96545). Export_fig attempts to correct font names in the resulting EPS file (up to a maximum of 11 different fonts in one figure), but this is not always guaranteed to work. In particular, the text positions will be affected. It also does not work for text blocks where the 'Interpreter' property is set to 'latex'. + +Also, when using the painters renderer, ghostscript will sometimes throw an error such as `Error: /undefined in /findfont`. This suggests that ghostscript could not find a definition file for one of your fonts. One possible fix for this is to make sure the file `EXPORT_FIG_PATH/.ignore/gs_font_path.txt` exists and contains a list of paths to the folder(s) containing the necessary font definitions (make sure that they are TrueType definitions!), separated by a semicolon. + +**RGB color data not yet supported in Painter's mode** - you will see this as a warning if you try to export a figure which contains patch objects whose face or vertex colors are specified as an RGB colour, rather than an index into the colormap, using the painters renderer (the default renderer for vector output). This problem can arise if you use `pcolor`, for example. This is a problem with MATLAB's painters renderer, which also affects `print`; there is currently no fix available in export_fig (other than to export to bitmap). The suggested workaround is to avoid colouring patches using RGB. First, try to use colours in the figure's colourmap (instructions [here](http://www.mathworks.co.uk/support/solutions/en/data/1-6OTPQE/)) - change the colourmap, if necessary. If you are using `pcolor`, try using [uimagesc](http://www.mathworks.com/matlabcentral/fileexchange/11368) (on the file exchange) instead. + +**Dashed contour lines appear solid** - when using the painters renderer, MATLAB cannot generate dashed lines using the `contour` function (either on screen or in exported PDF and EPS files). Details can be found [here](http://www.mathworks.com/support/solutions/en/data/1-14PPHB/?solution=1-14PPHB). + +**Text size** - when using the OpenGL or ZBuffer renderers, large text can be resized relative to the figure when exporting at non-screen-resolution (including using anti-alising at screen resolution). This is a feature of MATLAB's `print `function. In this case, try using the `-painters` option. + +**Lighting and transparency** - when using the painters renderer, transparency and lighting effects are not supported. Sorry, but this is an inherent feature of MATLAB's painters renderer. To find out more about the capabilities of each rendering method, see [here](http://www.mathworks.com/access/helpdesk/help/techdoc/creating_plots/f3-84337.html#f3-102410). You can still export transparent objects to vector format (SVG) using the excellent [plot2svg](http://www.mathworks.com/matlabcentral/fileexchange/7401) package, then convert this to PDF, for example using [Inkscape](http://inkscape.org/). However, it can't handle lighting. + +**Lines in patch objects** - when exporting patch objects to PDF using the painters renderer (default), sometimes the output can appear to have lines across the middle of rectangular patches; these lines are the colour of the background, as if there is a crack in the patch, allowing you to see through. This appears to be due to bugs in MATLAB's internal vector rendering code. These lines can often be removed from the PDF using software such as [InkScape](https://inkscape.org). Sometimes disabling anti-aliasing in the PDF-reader software can get rid of the lines ([discussion](https://github.com/altmany/export_fig/issues/44)). + +**Out of memory** - if you run into memory issues when using export_fig, some ways to get round this are: + 1. Reduce the level of anti-aliasing. + 2. Reduce the size of the figure. + 3. Reduce the export resolution (dpi). + 4. Change the renderer to painters or ZBuffer. + +**Errors** - the other common type of errors people get with export_fig are OpenGL errors. This isn't a fault of export_fig, but either a bug in MATLAB's `print`, or your graphics driver getting itself into a state. Always make sure your graphics driver is up-to-date. If it still doesn't work, try using the ZBuffer renderer. + +### Raising issues +If you think you have found a genuine error or issue with export_fig **that is not listed above**, first ensure that the figure looks correct on screen when rendered using the renderer that export_fig is set to use (e.g. if exporting to PDF or EPS, does the figure look correct on screen using the painters renderer, or if exporting to bitmap, does the figure look correct on screen using the OpenGL renderer?). If it looks wrong then the problem is there, and I cannot help (other than to suggest you try exporting using a different renderer). + +Secondly, if exporting to bitmap, do try all the renderers (i.e. try the options `-opengl`, `-zbuffer` and `-painters` separately), to see if one of them does produce an acceptable output, and if so, use that. + +If this still does not help, then ensure that you are using the latest version of export_fig, which is available [here](https://github.com/altmany/export_fig/archive/master.zip). + +If the figure looks correct on screen, but an error exists in the exported output (which cannot be solved using a different renderer) then please feel free to raise an [issue](https://github.com/altmany/export_fig/issues). Please be sure to include the .fig file, the export_fig command you use, the output you get, and a description of what you expected. I can't promise anything, but if it's easy to fix I may indeed do it. Often I will find that the error is due to a bug in MATLAB's `print` function, in which case I will suggest you submit it as a bug to TheMathWorks, and inform me of any fix they suggest. Also, if there's a feature you'd like that isn't supported please tell me what it is and I'll consider implementing it. + +### And finally... + +![](https://farm4.staticflickr.com/3956/15591911455_b9008bd77e_o_d.jpg) + +If you've ever wondered what's going on in the logo on the export_fig download page (reproduced here), then this explanantion is for you. The logo is designed to demonstrate as many of export_fig's features as possible: + +Given a figure containing a translucent mesh (top right), export_fig can export to pdf (bottom centre), which allows the figure to be zoomed-in without losing quality (because it's a vector graphic), but isn't able to reproduce the translucency. Also, depending on the PDF viewer program, small gaps appear between the patches, which are seen here as thin white lines. + +By contrast, when exporting to png (top left), translucency is preserved (see how the graphic below shows through), and the figure is anti-aliased. However, zooming-in does not reveal more detail since png is a bitmap format. Also, lines appear less sharp than in the pdf output. + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/append_pdfs.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/append_pdfs.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/append_pdfs.m (revision 27955) @@ -0,0 +1,124 @@ +%APPEND_PDFS Appends/concatenates multiple PDF files +% +% Example: +% append_pdfs(output, input1, input2, ...) +% append_pdfs(output, input_list{:}) +% append_pdfs test.pdf temp1.pdf temp2.pdf +% +% This function appends multiple PDF files to an existing PDF file, or +% concatenates them into a PDF file if the output file doesn't yet exist. +% +% This function requires that you have ghostscript installed on your +% system. Ghostscript can be downloaded from: http://www.ghostscript.com +% +% IN: +% output - string of output file name (including the extension, .pdf). +% If it exists it is appended to; if not, it is created. +% input1 - string of an input file name (including the extension, .pdf). +% All input files are appended in order. +% input_list - cell array list of input file name strings. All input +% files are appended in order. + +% Copyright: Oliver Woodford, 2011 + +% Thanks to Reinhard Knoll for pointing out that appending multiple pdfs in +% one go is much faster than appending them one at a time. + +% Thanks to Michael Teo for reporting the issue of a too long command line. +% Issue resolved on 5/5/2011, by passing gs a command file. + +% Thanks to Martin Wittmann for pointing out the quality issue when +% appending multiple bitmaps. +% Issue resolved (to best of my ability) 1/6/2011, using the prepress +% setting + +% 26/02/15: If temp dir is not writable, use the output folder for temp +% files when appending (Javier Paredes); sanity check of inputs +% 24/01/18: Fixed error in case of existing output file (append mode) +% 24/01/18: Fixed issue #213: non-ASCII characters in folder names on Windows +% 06/12/18: Avoid an "invalid escape-char" warning upon error + +function append_pdfs(varargin) + + if nargin < 2, return; end % sanity check + + % Are we appending or creating a new file + append = exist(varargin{1}, 'file') == 2; + output = [tempname '.pdf']; + try + % Ensure that the temp dir is writable (Javier Paredes 26/2/15) + fid = fopen(output,'w'); + fwrite(fid,1); + fclose(fid); + delete(output); + isTempDirOk = true; + catch + % Temp dir is not writable, so use the output folder + [dummy,fname,fext] = fileparts(output); %#ok + fpath = fileparts(varargin{1}); + output = fullfile(fpath,[fname fext]); + isTempDirOk = false; + end + if ~append + output = varargin{1}; + varargin = varargin(2:end); + end + + % Create the command file + if isTempDirOk + cmdfile = [tempname '.txt']; + else + cmdfile = fullfile(fpath,[fname '.txt']); + end + prepareCmdFile(cmdfile, output, varargin{:}); + + % Call ghostscript + [status, errMsg] = ghostscript(['@"' cmdfile '"']); + + % Check for ghostscript execution errors + if status && ~isempty(strfind(errMsg,'undefinedfile')) && ispc %#ok + % Fix issue #213: non-ASCII characters in folder names on Windows + for fileIdx = 2 : numel(varargin) + [fpath,fname,fext] = fileparts(varargin{fileIdx}); + varargin{fileIdx} = fullfile(normalizePath(fpath),[fname fext]); + end + % Rerun ghostscript with the normalized folder names + prepareCmdFile(cmdfile, output, varargin{:}); + [status, errMsg] = ghostscript(['@"' cmdfile '"']); + end + + % Delete the command file + delete(cmdfile); + + % Check for ghostscript execution errors + if status + errMsg = strrep(errMsg,'\','\\'); % Avoid an "invalid escape-char" warning + error('YMA:export_fig:append_pdf',errMsg); + end + + % Rename the file if needed + if append + movefile(output, varargin{1}, 'f'); + end +end + +% Prepare a text file with ghostscript directives +function prepareCmdFile(cmdfile, output, varargin) + fh = fopen(cmdfile, 'w'); + fprintf(fh, '-q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile="%s" -f', output); + fprintf(fh, ' "%s"', varargin{:}); + fclose(fh); +end + +% Convert long/non-ASCII folder names into their short ASCII equivalents +function pathStr = normalizePath(pathStr) + [fpath,fname,fext] = fileparts(pathStr); + if isempty(fpath) || strcmpi(fpath,pathStr), return, end + dirOutput = evalc(['system(''dir /X /AD "' pathStr '*"'')']); + shortName = strtrim(regexprep(dirOutput,{'.*> *',[fname fext '.*']},'')); + if isempty(shortName) + shortName = [fname fext]; + end + fpath = normalizePath(fpath); %recursive until entire fpath is processed + pathStr = fullfile(fpath, shortName); +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/copyfig.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/copyfig.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/copyfig.m (revision 27955) @@ -0,0 +1,59 @@ +function fh = copyfig(fh) +%COPYFIG Create a copy of a figure, without changing the figure +% +% Examples: +% fh_new = copyfig(fh_old) +% +% This function will create a copy of a figure, but not change the figure, +% as copyobj sometimes does, e.g. by changing legends. +% +% IN: +% fh_old - The handle of the figure to be copied. Default: gcf. +% +% OUT: +% fh_new - The handle of the created figure. + +% Copyright (C) Oliver Woodford 2012, Yair Altman 2015 + +% 26/02/15: If temp dir is not writable, use the dest folder for temp +% destination files (Javier Paredes) +% 15/04/15: Suppress warnings during copyobj (Dun Kirk comment on FEX page 2013-10-02) +% 09/09/18: Fix issue #252: Workaround for cases where copyobj() fails for any reason + + % Set the default + if nargin == 0 + fh = gcf; + end + % Is there a legend? + useCopyobj = isempty(findall(fh, 'Type', 'axes', 'Tag', 'legend')); + if useCopyobj + % Safe to copy using copyobj + oldWarn = warning('off'); %Suppress warnings during copyobj (Dun Kirk comment on FEX page 2013-10-02) + try + fh = copyobj(fh, 0); + catch + % Fix issue #252: Workaround for cases where copyobj() fails for any reason + useCopyobj = false; % if copyobj() croaks, use file save/load below + end + warning(oldWarn); + end + if ~useCopyobj + % copyobj will change the figure, so save and then load it instead + tmp_nam = [tempname '.fig']; + try + % Ensure that the temp dir is writable (Javier Paredes 26/2/15) + fid = fopen(tmp_nam,'w'); + fwrite(fid,1); + fclose(fid); + delete(tmp_nam); % cleanup + catch + % Temp dir is not writable, so use the current folder + [dummy,fname,fext] = fileparts(tmp_nam); %#ok + fpath = pwd; + tmp_nam = fullfile(fpath,[fname fext]); + end + hgsave(fh, tmp_nam); + fh = hgload(tmp_nam); + delete(tmp_nam); + end +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/crop_borders.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/crop_borders.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/crop_borders.m (revision 27955) @@ -0,0 +1,157 @@ +function [A, vA, vB, bb_rel] = crop_borders(A, bcol, padding, crop_amounts) +%CROP_BORDERS Crop the borders of an image or stack of images +% +% [B, vA, vB, bb_rel] = crop_borders(A, bcol, [padding]) +% +%IN: +% A - HxWxCxN stack of images. +% bcol - Cx1 background colour vector. +% padding - scalar indicating how much padding to have in relation to +% the cropped-image-size (0<=padding<=1). Default: 0 +% crop_amounts - 4-element vector of crop amounts: [top,right,bottom,left] +% where NaN/Inf indicate auto-cropping, 0 means no cropping, +% and any other value mean cropping in pixel amounts. +% +%OUT: +% B - JxKxCxN cropped stack of images. +% vA - coordinates in A that contain the cropped image +% vB - coordinates in B where the cropped version of A is placed +% bb_rel - relative bounding box (used for eps-cropping) + +%{ +% 06/03/15: Improved image cropping thanks to Oscar Hartogensis +% 08/06/15: Fixed issue #76: case of transparent figure bgcolor +% 21/02/16: Enabled specifying non-automated crop amounts +% 04/04/16: Fix per Luiz Carvalho for old Matlab releases +% 23/10/16: Fixed issue #175: there used to be a 1px minimal padding in case of crop, now removed +%} + + if nargin < 3 + padding = 0; + end + if nargin < 4 + crop_amounts = nan(1,4); % =auto-cropping + end + crop_amounts(end+1:4) = NaN; % fill missing values with NaN + + [h, w, c, n] = size(A); + if isempty(bcol) % case of transparent bgcolor + bcol = A(ceil(end/2),1,:,1); + end + if isscalar(bcol) + bcol = bcol(ones(c, 1)); + end + + % Crop margin from left + if ~isfinite(crop_amounts(4)) + bail = false; + for l = 1:w + for a = 1:c + if ~all(col(A(:,l,a,:)) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end + end + else + l = 1 + abs(crop_amounts(4)); + end + + % Crop margin from right + if ~isfinite(crop_amounts(2)) + bcol = A(ceil(end/2),w,:,1); + bail = false; + for r = w:-1:l + for a = 1:c + if ~all(col(A(:,r,a,:)) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end + end + else + r = w - abs(crop_amounts(2)); + end + + % Crop margin from top + if ~isfinite(crop_amounts(1)) + bcol = A(1,ceil(end/2),:,1); + bail = false; + for t = 1:h + for a = 1:c + if ~all(col(A(t,:,a,:)) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end + end + else + t = 1 + abs(crop_amounts(1)); + end + + % Crop margin from bottom + bcol = A(h,ceil(end/2),:,1); + if ~isfinite(crop_amounts(3)) + bail = false; + for b = h:-1:t + for a = 1:c + if ~all(col(A(b,:,a,:)) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end + end + else + b = h - abs(crop_amounts(3)); + end + + if padding == 0 % no padding + % Issue #175: there used to be a 1px minimal padding in case of crop, now removed + %{ + if ~isequal([t b l r], [1 h 1 w]) % Check if we're actually croppping + padding = 1; % Leave one boundary pixel to avoid bleeding on resize + bcol(:) = nan; % make the 1px padding transparent + end + %} + elseif abs(padding) < 1 % pad value is a relative fraction of image size + padding = sign(padding)*round(mean([b-t r-l])*abs(padding)); % ADJUST PADDING + else % pad value is in units of 1/72" points + padding = round(padding); % fix cases of non-integer pad value + end + + if padding > 0 % extra padding + % Create an empty image, containing the background color, that has the + % cropped image size plus the padded border + B = repmat(bcol,[(b-t)+1+padding*2,(r-l)+1+padding*2,1,n]); % Fix per Luiz Carvalho + % vA - coordinates in A that contain the cropped image + vA = [t b l r]; + % vB - coordinates in B where the cropped version of A will be placed + vB = [padding+1, (b-t)+1+padding, padding+1, (r-l)+1+padding]; + % Place the original image in the empty image + B(vB(1):vB(2), vB(3):vB(4), :, :) = A(vA(1):vA(2), vA(3):vA(4), :, :); + A = B; + else % extra cropping + vA = [t-padding b+padding l-padding r+padding]; + A = A(vA(1):vA(2), vA(3):vA(4), :, :); + vB = [NaN NaN NaN NaN]; + end + + % For EPS cropping, determine the relative BoundingBox - bb_rel + bb_rel = [l-1 h-b-1 r+1 h-t+1]./[w h w h]; +end + +function A = col(A) + A = A(:); +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/eps2pdf.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/eps2pdf.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/eps2pdf.m (revision 27955) @@ -0,0 +1,223 @@ +function eps2pdf(source, dest, crop, append, gray, quality, gs_options) +%EPS2PDF Convert an eps file to pdf format using ghostscript +% +% Examples: +% eps2pdf source dest +% eps2pdf(source, dest, crop) +% eps2pdf(source, dest, crop, append) +% eps2pdf(source, dest, crop, append, gray) +% eps2pdf(source, dest, crop, append, gray, quality) +% eps2pdf(source, dest, crop, append, gray, quality, gs_options) +% +% This function converts an eps file to pdf format. The output can be +% optionally cropped and also converted to grayscale. If the output pdf +% file already exists then the eps file can optionally be appended as a new +% page on the end of the eps file. The level of bitmap compression can also +% optionally be set. +% +% This function requires that you have ghostscript installed on your +% system. Ghostscript can be downloaded from: http://www.ghostscript.com +% +% Inputs: +% source - filename of the source eps file to convert. The filename is +% assumed to already have the extension ".eps". +% dest - filename of the destination pdf file. The filename is assumed +% to already have the extension ".pdf". +% crop - boolean indicating whether to crop the borders off the pdf. +% Default: true. +% append - boolean indicating whether the eps should be appended to the +% end of the pdf as a new page (if the pdf exists already). +% Default: false. +% gray - boolean indicating whether the output pdf should be grayscale +% or not. Default: false. +% quality - scalar indicating the level of image bitmap quality to +% output. A larger value gives a higher quality. quality > 100 +% gives lossless output. Default: ghostscript prepress default. +% gs_options - optional ghostscript options (e.g.: '-dNoOutputFonts'). If +% multiple options are needed, enclose in call array: {'-a','-b'} + +% Copyright (C) Oliver Woodford 2009-2014, Yair Altman 2015- + +% Suggestion of appending pdf files provided by Matt C at: +% http://www.mathworks.com/matlabcentral/fileexchange/23629 + +% Thank you Fabio Viola for pointing out compression artifacts, leading to the quality setting. +% Thank you Scott for pointing out the subsampling of very small images, which was fixed for lossless compression settings. + +% 09/12/11: Pass font path to ghostscript +% 26/02/15: If temp dir is not writable, use the dest folder for temp destination files (Javier Paredes) +% 28/02/15: Enable users to specify optional ghostscript options (issue #36) +% 01/03/15: Upon GS error, retry without the -sFONTPATH= option (this might solve +% some /findfont errors according to James Rankin, FEX Comment 23/01/15) +% 23/06/15: Added extra debug info in case of ghostscript error; code indentation +% 04/10/15: Suggest a workaround for issue #41 (missing font path; thanks Mariia Fedotenkova) +% 22/02/16: Bug fix from latest release of this file (workaround for issue #41) +% 20/03/17: Added informational message in case of GS croak (issue #186) +% 16/01/18: Improved appending of multiple EPS files into single PDF (issue #233; thanks @shartjen) +% 18/10/19: Workaround for GS 9.51+ .setpdfwrite removal problem (issue #285) +% 18/10/19: Warn when ignoring GS fontpath or quality options; clarified error messages + + % Intialise the options string for ghostscript + options = ['-q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile="' dest '"']; + + % Set crop option + if nargin < 3 || crop + options = [options ' -dEPSCrop']; + end + + % Set the font path + fp = font_path(); + if ~isempty(fp) + options = [options ' -sFONTPATH="' fp '"']; + end + + % Set the grayscale option + if nargin > 4 && gray + options = [options ' -sColorConversionStrategy=Gray -dProcessColorModel=/DeviceGray']; + end + + % Set the bitmap quality + qualityOptions = ''; + if nargin > 5 && ~isempty(quality) + qualityOptions = ' -dAutoFilterColorImages=false -dAutoFilterGrayImages=false'; + if quality > 100 + qualityOptions = [qualityOptions ' -dColorImageFilter=/FlateEncode -dGrayImageFilter=/FlateEncode']; + qualityOptions = [qualityOptions ' -c ".setpdfwrite << /ColorImageDownsampleThreshold 10 /GrayImageDownsampleThreshold 10 >> setdistillerparams"']; + else + qualityOptions = [qualityOptions ' -dColorImageFilter=/DCTEncode -dGrayImageFilter=/DCTEncode']; + v = 1 + (quality < 80); + quality = 1 - quality / 100; + s = sprintf('<< /QFactor %.2f /Blend 1 /HSample [%d 1 1 %d] /VSample [%d 1 1 %d] >>', quality, v, v, v, v); + qualityOptions = [qualityOptions ' -c ".setpdfwrite << /ColorImageDict ' s ' /GrayImageDict ' s ' >> setdistillerparams"']; + end + options = [options qualityOptions]; + end + + % Enable users to specify optional ghostscript options (issue #36) + if nargin > 6 && ~isempty(gs_options) + if iscell(gs_options) + gs_options = sprintf(' %s',gs_options{:}); + elseif ~ischar(gs_options) + error('gs_options input argument must be a string or cell-array of strings'); + else + gs_options = [' ' gs_options]; + end + options = [options gs_options]; + end + + % Check if the output file exists + if nargin > 3 && append && exist(dest, 'file') == 2 + % File exists - append current figure to the end + tmp_nam = [tempname '.pdf']; + [fpath,fname,fext] = fileparts(tmp_nam); + try + % Ensure that the temp dir is writable (Javier Paredes 26/2/15) + fid = fopen(tmp_nam,'w'); + fwrite(fid,1); + fclose(fid); + delete(tmp_nam); + catch + % Temp dir is not writable, so use the dest folder + fpath = fileparts(dest); + tmp_nam = fullfile(fpath,[fname fext]); + end + % Copy the existing (dest) pdf file to temporary folder + copyfile(dest, tmp_nam); + % Produce an interim pdf of the source eps, rather than adding the eps directly (issue #233) + ghostscript([options ' -f "' source '"']); + [~,fname] = fileparts(tempname); + tmp_nam2 = fullfile(fpath,[fname fext]); % ensure using a writable folder (not necessarily tempdir) + copyfile(dest, tmp_nam2); + % Add the existing pdf and interim pdf as inputs to ghostscript + %options = [options ' -f "' tmp_nam '" "' source '"']; % append the source eps to dest pdf + options = [options ' -f "' tmp_nam '" "' tmp_nam2 '"']; % append the interim pdf to dest pdf + try + % Convert to pdf using ghostscript + [status, message] = ghostscript(options); + catch me + % Delete the intermediate files and rethrow the error + delete(tmp_nam); + delete(tmp_nam2); + rethrow(me); + end + % Delete the intermediate (temporary) files + delete(tmp_nam); + delete(tmp_nam2); + else + % File doesn't exist or should be over-written + % Add the source eps file as input to ghostscript + options = [options ' -f "' source '"']; + % Convert to pdf using ghostscript + [status, message] = ghostscript(options); + end + + % Check for error + if status + % Retry without the -sFONTPATH= option (this might solve some GS + % /findfont errors according to James Rankin, FEX Comment 23/01/15) + orig_options = options; + if ~isempty(fp) + options = regexprep(options, ' -sFONTPATH=[^ ]+ ',' '); + status = ghostscript(options); + if ~status % hurray! (no error) + warning('export_fig:GS:fontpath','Export_fig font option is ignored - not supported by your Ghostscript version') + return + end + end + + % Retry without quality options (may solve problems with GS 9.51+, issue #285) + if ~isempty(qualityOptions) + options = strrep(orig_options, qualityOptions, ''); + [status, message] = ghostscript(options); + if ~status % hurray! (no error) + warning('export_fig:GS:quality','Export_fig quality option is ignored - not supported by your Ghostscript version') + return + end + end + + % Report error + if isempty(message) + error('Unable to generate pdf. Ensure that the destination folder is writable.'); + elseif ~isempty(strfind(message,'/typecheck in /findfont')) %#ok + % Suggest a workaround for issue #41 (missing font path) + font_name = strtrim(regexprep(message,'.*Operand stack:\s*(.*)\s*Execution.*','$1')); + fprintf(2, 'Ghostscript error: could not find the following font(s): %s\n', font_name); + fpath = fileparts(mfilename('fullpath')); + gs_fonts_file = fullfile(fpath, '.ignore', 'gs_font_path.txt'); + fprintf(2, ' try to add the font''s folder to your %s file\n\n', gs_fonts_file); + error('export_fig error'); + else + fprintf(2, '\nGhostscript error: perhaps %s is open by another application\n', dest); + if ~isempty(gs_options) + fprintf(2, ' or maybe your Ghostscript version does not accept the extra "%s" option(s) that you requested\n', gs_options); + end + fprintf(2, ' or maybe you have another gs executable in your system''s path\n'); + fprintf(2, 'Ghostscript options: %s\n\n', orig_options); + error(message); + end + end +end + +% Function to return (and create, where necessary) the font path +function fp = font_path() + fp = user_string('gs_font_path'); + if ~isempty(fp) + return + end + % Create the path + % Start with the default path + fp = getenv('GS_FONTPATH'); + % Add on the typical directories for a given OS + if ispc + if ~isempty(fp) + fp = [fp ';']; + end + fp = [fp getenv('WINDIR') filesep 'Fonts']; + else + if ~isempty(fp) + fp = [fp ':']; + end + fp = [fp '/usr/share/fonts:/usr/local/share/fonts:/usr/share/fonts/X11:/usr/local/share/fonts/X11:/usr/share/fonts/truetype:/usr/local/share/fonts/truetype']; + end + user_string('gs_font_path', fp); +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/export_fig.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/export_fig.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/export_fig.m (revision 27955) @@ -0,0 +1,1645 @@ +function [imageData, alpha] = export_fig(varargin) %#ok<*STRCL1> +%EXPORT_FIG Exports figures in a publication-quality format +% +% Examples: +% imageData = export_fig +% [imageData, alpha] = export_fig +% export_fig filename +% export_fig filename -format1 -format2 +% export_fig ... -nocrop +% export_fig ... -c[,,,] +% export_fig ... -transparent +% export_fig ... -native +% export_fig ... -m +% export_fig ... -r +% export_fig ... -a +% export_fig ... -q +% export_fig ... -p +% export_fig ... -d +% export_fig ... -depsc +% export_fig ... - +% export_fig ... - +% export_fig ... -append +% export_fig ... -bookmark +% export_fig ... -clipboard +% export_fig ... -update +% export_fig ... -nofontswap +% export_fig ... -font_space +% export_fig ... -linecaps +% export_fig ... -noinvert +% export_fig ... -preserve_size +% export_fig ... -options +% export_fig(..., handle) +% +% This function saves a figure or single axes to one or more vector and/or +% bitmap file formats, and/or outputs a rasterized version to the workspace, +% with the following properties: +% - Figure/axes reproduced as it appears on screen +% - Cropped borders (optional) +% - Embedded fonts (vector formats) +% - Improved line and grid line styles +% - Anti-aliased graphics (bitmap formats) +% - Render images at native resolution (optional for bitmap formats) +% - Transparent background supported (pdf, eps, png, tif) +% - Semi-transparent patch objects supported (png, tif) +% - RGB, CMYK or grayscale output (CMYK only with pdf, eps, tif) +% - Variable image compression, including lossless (pdf, eps, jpg) +% - Optional rounded line-caps (pdf, eps) +% - Optionally append to file (pdf, tif) +% - Vector formats: pdf, eps, svg +% - Bitmap formats: png, tif, jpg, bmp, export to workspace +% +% This function is especially suited to exporting figures for use in +% publications and presentations, because of the high quality and +% portability of media produced. +% +% Note that the background color and figure dimensions are reproduced +% (the latter approximately, and ignoring cropping & magnification) in the +% output file. For transparent background (and semi-transparent patch +% objects), use the -transparent option or set the figure 'Color' property +% to 'none'. To make axes transparent set the axes 'Color' property to +% 'none'. PDF, EPS, TIF & PNG are the only formats that support a transparent +% background; only TIF & PNG formats support transparency of patch objects. +% +% The choice of renderer (opengl/zbuffer/painters) has a large impact on the +% output quality. The default value (opengl for bitmaps, painters for vector +% formats) generally gives good results, but if you aren't satisfied +% then try another renderer. Notes: +% 1) For vector formats (EPS,PDF), only painters generates vector graphics +% 2) For bitmap formats, only opengl correctly renders transparent patches +% 3) For bitmap formats, only painters correctly scales line dash and dot +% lengths when magnifying or anti-aliasing +% 4) Fonts may be substitued with Courier when using painters +% +% When exporting to vector format (PDF & EPS) and bitmap format using the +% painters renderer, this function requires that ghostscript is installed +% on your system. You can download this from: +% http://www.ghostscript.com +% When exporting to EPS it additionally requires pdftops, from the Xpdf +% suite of functions. You can download this from: http://xpdfreader.com +% +% SVG output uses the fig2svg (https://github.com/kupiqu/fig2svg) or plot2svg +% (https://github.com/jschwizer99/plot2svg) utilities, or Matlab's built-in +% SVG export if neither of these utilities are available on Matlab's path. +% Note: cropping/padding are not supported in export_fig's SVG output. +% +% Inputs: +% filename - string containing the name (optionally including full or +% relative path) of the file the figure is to be saved as. If +% a path is not specified, the figure is saved in the current +% directory. If no name and no output arguments are specified, +% the default name, 'export_fig_out', is used. If neither a +% file extension nor a format are specified, a ".png" is added +% and the figure saved in that format. +% - - string(s) containing the output file extension(s). Options: +% '-pdf', '-eps', '-svg', '-png', '-tif', '-jpg' and '-bmp'. +% Multiple formats can be specified, without restriction. +% For example: export_fig('-jpg', '-pdf', '-png', ...) +% Either '-tif','-tiff' can be specified, and either '-jpg','-jpeg'. +% -nocrop - option indicating that empty margins should not be cropped. +% -c[,,,] - option indicating crop amounts. Must be +% a 4-element vector of numeric values: [top,right,bottom,left] +% where NaN/Inf indicate auto-cropping, 0 means no cropping, +% and any other value mean cropping in pixel amounts. +% -transparent - option indicating that the figure background is to be made +% transparent (PNG,PDF,TIF,EPS formats only). Implies -noinvert. +% -m - option where val indicates the factor to magnify the +% on-screen figure pixel dimensions by when generating bitmap +% outputs (does not affect vector formats). Default: '-m1'. +% -r - option val indicates the resolution (in pixels per inch) to +% export bitmap and vector outputs at, keeping the dimensions +% of the on-screen figure. Default: '-r864' (for vector output +% only). Note that the -m option overides the -r option for +% bitmap outputs only. +% -native - option indicating that the output resolution (when outputting +% a bitmap format) should be such that the vertical resolution +% of the first suitable image found in the figure is at the +% native resolution of that image. To specify a particular +% image to use, give it the tag 'export_fig_native'. Notes: +% This overrides any value set with the -m and -r options. It +% also assumes that the image is displayed front-to-parallel +% with the screen. The output resolution is approximate and +% should not be relied upon. Anti-aliasing can have adverse +% effects on image quality (disable with the -a1 option). +% -a1, -a2, -a3, -a4 - option indicating the amount of anti-aliasing to +% use for bitmap outputs. '-a1' means no anti-aliasing; +% '-a4' is the maximum amount (default). +% - - option to force a particular renderer (painters, opengl or +% zbuffer). Default value: opengl for bitmap formats or +% figures with patches and/or transparent annotations; +% painters for vector formats without patches/transparencies. +% - - option indicating which colorspace color figures should +% be saved in: RGB (default), CMYK or gray. Usage example: '-gray'. +% Note: CMYK is only supported in PDF, EPS and TIF formats. +% -q - option to vary bitmap image quality (PDF, EPS, JPG formats only). +% A larger val, in the range 0-100, produces higher quality and +% lower compression. val > 100 results in lossless compression. +% Default: '-q95' for JPG, ghostscript prepress default for PDF,EPS. +% Note: lossless compression can sometimes give a smaller file size +% than the default lossy compression, depending on the image type. +% -p - option to pad a border of width val to exported files, where +% val is either a relative size with respect to cropped image +% size (i.e. p=0.01 adds a 1% border). For EPS & PDF formats, +% val can also be integer in units of 1/72" points (abs(val)>1). +% val can be positive (padding) or negative (extra cropping). +% If used, the -nocrop flag will be ignored, i.e. the image will +% always be cropped and then padded. Default: 0 (i.e. no padding). +% -append - option indicating that if the file already exists the figure is to +% be appended as a new page, instead of being overwritten (default). +% PDF & TIF output formats only. +% -bookmark - option to indicate that a bookmark with the name of the +% figure is to be created in the output file (PDF format only). +% -clipboard - option to save output as an image on the system clipboard. +% Note: background transparency is not preserved in clipboard +% -d - option to indicate a ghostscript setting. For example, +% -dMaxBitmap=0 or -dNoOutputFonts (Ghostscript 9.15+). +% -depsc - option to use EPS level-3 rather than the default level-2 print +% device. This solves some bugs with Matlab's default -depsc2 device +% such as discolored subplot lines on images (vector formats only). +% -update - option to download and install the latest version of export_fig +% -nofontswap - option to avoid font swapping. Font swapping is automatically +% done in vector formats (only): 11 standard Matlab fonts are +% replaced by the original figure fonts. This option prevents this. +% -font_space - option to set a spacer character for font-names that +% contain spaces, used by EPS/PDF. Default: '' +% -linecaps - option to create rounded line-caps (vector formats only). +% -noinvert - option to avoid setting figure's InvertHardcopy property to +% 'off' during output (this solves some problems of empty outputs). +% -preserve_size - option to preserve the figure's PaperSize property in output +% file (PDF/EPS formats only; default is to not preserve it). +% -options - format-specific parameters as defined in Matlab's +% documentation of the imwrite function, contained in a struct under +% the format name. For example to specify the JPG Comment parameter, +% pass a struct such as this: options.JPG.Comment='abc'. Similarly, +% options.PNG.BitDepth=4. Valid only for PNG,TIF,JPG output formats. +% handle - The handle of the figure, axes or uipanels (can be an array of +% handles, but the objects must be in the same figure) which is +% to be saved. Default: gcf (handle of current figure). +% +% Outputs: +% imageData - MxNxC uint8 image array of the exported image. +% alpha - MxN single array of alphamatte values in the range [0,1], +% for the case when the background is transparent. +% +% Some helpful examples and tips can be found at: +% https://github.com/altmany/export_fig +% +% See also PRINT, SAVEAS, ScreenCapture (on the Matlab File Exchange) + +%{ +% Copyright (C) Oliver Woodford 2008-2014, Yair Altman 2015- + +% The idea of using ghostscript is inspired by Peder Axensten's SAVEFIG +% (fex id: 10889) which is itself inspired by EPS2PDF (fex id: 5782). +% The idea for using pdftops came from the MATLAB newsgroup (id: 168171). +% The idea of editing the EPS file to change line styles comes from Jiro +% Doke's FIXPSLINESTYLE (fex id: 17928). +% The idea of changing dash length with line width came from comments on +% fex id: 5743, but the implementation is mine :) +% The idea of anti-aliasing bitmaps came from Anders Brun's MYAA (fex id: +% 20979). +% The idea of appending figures in pdfs came from Matt C in comments on the +% FEX (id: 23629) + +% Thanks to Roland Martin for pointing out the colour MATLAB +% bug/feature with colorbar axes and transparent backgrounds. +% Thanks also to Andrew Matthews for describing a bug to do with the figure +% size changing in -nodisplay mode. I couldn't reproduce it, but included a +% fix anyway. +% Thanks to Tammy Threadgill for reporting a bug where an axes is not +% isolated from gui objects. +%} +%{ +% 23/02/12: Ensure that axes limits don't change during printing +% 14/03/12: Fix bug in fixing the axes limits (thanks to Tobias Lamour for reporting it). +% 02/05/12: Incorporate patch of Petr Nechaev (many thanks), enabling bookmarking of figures in pdf files. +% 09/05/12: Incorporate patch of Arcelia Arrieta (many thanks), to keep tick marks fixed. +% 12/12/12: Add support for isolating uipanels. Thanks to michael for suggesting it. +% 25/09/13: Add support for changing resolution in vector formats. Thanks to Jan Jaap Meijer for suggesting it. +% 07/05/14: Add support for '~' at start of path. Thanks to Sally Warner for suggesting it. +% 24/02/15: Fix Matlab R2014b bug (issue #34): plot markers are not displayed when ZLimMode='manual' +% 25/02/15: Fix issue #4 (using HG2 on R2014a and earlier) +% 25/02/15: Fix issue #21 (bold TeX axes labels/titles in R2014b) +% 26/02/15: If temp dir is not writable, use the user-specified folder for temporary EPS/PDF files (Javier Paredes) +% 27/02/15: Modified repository URL from github.com/ojwoodford to /altmany +% Indented main function +% Added top-level try-catch block to display useful workarounds +% 28/02/15: Enable users to specify optional ghostscript options (issue #36) +% 06/03/15: Improved image padding & cropping thanks to Oscar Hartogensis +% 26/03/15: Fixed issue #49 (bug with transparent grayscale images); fixed out-of-memory issue +% 26/03/15: Fixed issue #42: non-normalized annotations on HG1 +% 26/03/15: Fixed issue #46: Ghostscript crash if figure units <> pixels +% 27/03/15: Fixed issue #39: bad export of transparent annotations/patches +% 28/03/15: Fixed issue #50: error on some Matlab versions with the fix for issue #42 +% 29/03/15: Fixed issue #33: bugs in Matlab's print() function with -cmyk +% 29/03/15: Improved processing of input args (accept space between param name & value, related to issue #51) +% 30/03/15: When exporting *.fig files, then saveas *.fig if figure is open, otherwise export the specified fig file +% 30/03/15: Fixed edge case bug introduced yesterday (commit #ae1755bd2e11dc4e99b95a7681f6e211b3fa9358) +% 09/04/15: Consolidated header comment sections; initialize output vars only if requested (nargout>0) +% 14/04/15: Workaround for issue #45: lines in image subplots are exported in invalid color +% 15/04/15: Fixed edge-case in parsing input parameters; fixed help section to show the -depsc option (issue #45) +% 21/04/15: Bug fix: Ghostscript croaks on % chars in output PDF file (reported by Sven on FEX page, 15-Jul-2014) +% 22/04/15: Bug fix: Pdftops croaks on relative paths (reported by Tintin Milou on FEX page, 19-Jan-2015) +% 04/05/15: Merged fix #63 (Kevin Mattheus Moerman): prevent tick-label changes during export +% 07/05/15: Partial fix for issue #65: PDF export used painters rather than opengl renderer (thanks Nguyenr) +% 08/05/15: Fixed issue #65: bad PDF append since commit #e9f3cdf 21/04/15 (thanks Robert Nguyen) +% 12/05/15: Fixed issue #67: exponent labels cropped in export, since fix #63 (04/05/15) +% 28/05/15: Fixed issue #69: set non-bold label font only if the string contains symbols (\beta etc.), followup to issue #21 +% 29/05/15: Added informative error message in case user requested SVG output (issue #72) +% 09/06/15: Fixed issue #58: -transparent removed anti-aliasing when exporting to PNG +% 19/06/15: Added -update option to download and install the latest version of export_fig +% 07/07/15: Added -nofontswap option to avoid font-swapping in EPS/PDF +% 16/07/15: Fixed problem with anti-aliasing on old Matlab releases +% 11/09/15: Fixed issue #103: magnification must never become negative; also fixed reported error msg in parsing input params +% 26/09/15: Alert if trying to export transparent patches/areas to non-PNG outputs (issue #108) +% 04/10/15: Do not suggest workarounds for certain errors that have already been handled previously +% 01/11/15: Fixed issue #112: use same renderer in print2eps as export_fig (thanks to Jesús Pestana Puerta) +% 10/11/15: Custom GS installation webpage for MacOS. Thanks to Andy Hueni via FEX +% 19/11/15: Fixed clipboard export in R2015b (thanks to Dan K via FEX) +% 21/02/16: Added -c option for indicating specific crop amounts (idea by Cedric Noordam on FEX) +% 08/05/16: Added message about possible error reason when groot.Units~=pixels (issue #149) +% 17/05/16: Fixed case of image YData containing more than 2 elements (issue #151) +% 08/08/16: Enabled exporting transparency to TIF, in addition to PNG/PDF (issue #168) +% 11/12/16: Added alert in case of error creating output PDF/EPS file (issue #179) +% 13/12/16: Minor fix to the commit for issue #179 from 2 days ago +% 22/03/17: Fixed issue #187: only set manual ticks when no exponent is present +% 09/04/17: Added -linecaps option (idea by Baron Finer, issue #192) +% 15/09/17: Fixed issue #205: incorrect tick-labels when Ticks number don't match the TickLabels number +% 15/09/17: Fixed issue #210: initialize alpha map to ones instead of zeros when -transparent is not used +% 18/09/17: Added -font_space option to replace font-name spaces in EPS/PDF (workaround for issue #194) +% 18/09/17: Added -noinvert option to solve some export problems with some graphic cards (workaround for issue #197) +% 08/11/17: Fixed issue #220: axes exponent is removed in HG1 when TickMode is 'manual' (internal Matlab bug) +% 08/11/17: Fixed issue #221: alert if the requested folder does not exist +% 19/11/17: Workaround for issue #207: alert when trying to use transparent bgcolor with -opengl +% 29/11/17: Workaround for issue #206: warn if exporting PDF/EPS for a figure that contains an image +% 11/12/17: Fixed issue #230: use OpenGL renderer when exported image contains transparency (also see issue #206) +% 30/01/18: Updated SVG message to point to https://github.com/kupiqu/plot2svg and display user-selected filename if available +% 27/02/18: Fixed issue #236: axes exponent cropped from output if on right-hand axes +% 29/05/18: Fixed issue #245: process "string" inputs just like 'char' inputs +% 13/08/18: Fixed issue #249: correct black axes color to off-black to avoid extra cropping with -transparent +% 27/08/18: Added a possible file-open reason in EPS/PDF write-error message (suggested by "craq" on FEX page) +% 22/09/18: Xpdf website changed to xpdfreader.com +% 23/09/18: Fixed issue #243: only set non-bold font (workaround for issue #69) in R2015b or earlier; warn if changing font +% 23/09/18: Workaround for issue #241: don't use -r864 in EPS/PDF outputs when -native is requested (solves black lines problem) +% 18/11/18: Issue #261: Added informative alert when trying to export a uifigure (which is not currently supported) +% 13/12/18: Issue #261: Fixed last commit for cases of specifying axes/panel handle as input, rather than a figure handle +% 13/01/19: Issue #72: Added basic SVG output support +% 04/02/19: Workaround for issues #207 and #267: -transparent implies -noinvert +% 08/03/19: Issue #269: Added ability to specify format-specific options for PNG,TIF,JPG outputs; fixed help section +% 21/03/19: Fixed the workaround for issues #207 and #267 from 4/2/19 (-transparent now does *NOT* imply -noinvert; -transparent output should now be ok in all formats) +% 12/06/19: Issue #277: Enabled preservation of figure's PaperSize in output PDF/EPS file +% 06/08/19: Remove warning message about obsolete JavaFrame in R2019b +% 30/10/19: Fixed issue #261: added support for exporting uifigures and uiaxes (thanks to idea by @MarvinILA) +%} + + if nargout + [imageData, alpha] = deal([]); + end + hadError = false; + displaySuggestedWorkarounds = true; + + % Ensure the figure is rendered correctly _now_ so that properties like axes limits are up-to-date + drawnow; + pause(0.05); % this solves timing issues with Java Swing's EDT (http://undocumentedmatlab.com/blog/solving-a-matlab-hang-problem) + + % Parse the input arguments + fig = get(0, 'CurrentFigure'); + [fig, options] = parse_args(nargout, fig, varargin{:}); + + % Ensure that we have a figure handle + if isequal(fig,-1) + return % silent bail-out + elseif isempty(fig) + error('No figure found'); + else + oldWarn = warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame'); + warning off MATLAB:ui:javaframe:PropertyToBeRemoved + uifig = handle(ancestor(fig,'figure')); + try jf = get(uifig,'JavaFrame'); catch, jf=1; end + warning(oldWarn); + if isempty(jf) % this is a uifigure + %error('Figures created using the uifigure command or App Designer are not supported by export_fig. See issue #261 for details.'); + if numel(fig) > 1 + error('export_fig:uifigure:multipleHandles', 'export_fig only supports exporting a single uifigure handle at a time; array of handles is not currently supported.') + elseif ~any(strcmpi(fig.Type,{'figure','axes'})) + error('export_fig:uifigure:notFigureOrAxes', 'export_fig only supports exporting a uifigure or uiaxes handle; other handles of a uifigure are not currently supported.') + end + % fig is either a uifigure or uiaxes handle + isUiaxes = strcmpi(fig.Type,'axes'); + if isUiaxes + % Label the specified axes so that we can find it in the legacy figure + oldUserData = fig.UserData; + tempStr = tempname; + fig.UserData = tempStr; + end + try + % Create an invisible legacy figure at the same position/size as the uifigure + hNewFig = figure('Units',uifig.Units, 'Position',uifig.Position, 'MenuBar','none', 'ToolBar','none', 'Visible','off'); + % Copy the uifigure contents onto the new invisible legacy figure + try + hChildren = allchild(uifig); %=uifig.Children; + copyobj(hChildren,hNewFig); + catch + warning('export_fig:uifigure:controls', 'Some uifigure controls cannot be exported by export_fig and will not appear in the generated output.'); + end + try fig.UserData = oldUserData; catch, end % restore axes UserData, if modified above + % Replace the uihandle in the input args with the legacy handle + if isUiaxes % uiaxes + % Locate the corresponding axes handle in the new legacy figure + hAxes = findall(hNewFig,'type','axes','UserData',tempStr); + if isempty(hAxes) % should never happen, check just in case + hNewHandle = hNewFig; % export the figure instead of the axes + else + hNewHandle = hAxes; % new axes handle found: use it instead of the uiaxes + end + else % uifigure + hNewHandle = hNewFig; + end + varargin(cellfun(@(c)isequal(c,fig),varargin)) = {hNewHandle}; + % Rerun export_fig on the legacy figure (with the replaced handle) + [imageData, alpha] = export_fig(varargin{:}); + % Delete the temp legacy figure and bail out + try delete(hNewFig); catch, end + return + catch err + % Clean up the temp legacy figure and report the error + try delete(hNewFig); catch, end + rethrow(err) + end + end + end + + % Isolate the subplot, if it is one + cls = all(ismember(get(fig, 'Type'), {'axes', 'uipanel'})); + if cls + % Given handles of one or more axes, so isolate them from the rest + fig = isolate_axes(fig); + else + % Check we have a figure + if ~isequal(get(fig, 'Type'), 'figure') + error('Handle must be that of a figure, axes or uipanel'); + end + % Get the old InvertHardcopy mode + old_mode = get(fig, 'InvertHardcopy'); + end + + % Hack the font units where necessary (due to a font rendering bug in print?). + % This may not work perfectly in all cases. + % Also it can change the figure layout if reverted, so use a copy. + magnify = options.magnify * options.aa_factor; + if isbitmap(options) && magnify ~= 1 + fontu = findall(fig, 'FontUnits', 'normalized'); + if ~isempty(fontu) + % Some normalized font units found + if ~cls + fig = copyfig(fig); + set(fig, 'Visible', 'off'); + fontu = findall(fig, 'FontUnits', 'normalized'); + cls = true; + end + set(fontu, 'FontUnits', 'points'); + end + end + + try + % MATLAB "feature": axes limits and tick marks can change when printing + Hlims = findall(fig, 'Type', 'axes'); + if ~cls + % Record the old axes limit and tick modes + Xlims = make_cell(get(Hlims, 'XLimMode')); + Ylims = make_cell(get(Hlims, 'YLimMode')); + Zlims = make_cell(get(Hlims, 'ZLimMode')); + Xtick = make_cell(get(Hlims, 'XTickMode')); + Ytick = make_cell(get(Hlims, 'YTickMode')); + Ztick = make_cell(get(Hlims, 'ZTickMode')); + Xlabel = make_cell(get(Hlims, 'XTickLabelMode')); + Ylabel = make_cell(get(Hlims, 'YTickLabelMode')); + Zlabel = make_cell(get(Hlims, 'ZTickLabelMode')); + end + + % Set all axes limit and tick modes to manual, so the limits and ticks can't change + % Fix Matlab R2014b bug (issue #34): plot markers are not displayed when ZLimMode='manual' + set(Hlims, 'XLimMode', 'manual', 'YLimMode', 'manual'); + set_tick_mode(Hlims, 'X'); + set_tick_mode(Hlims, 'Y'); + if ~using_hg2(fig) + set(Hlims,'ZLimMode', 'manual'); + set_tick_mode(Hlims, 'Z'); + end + catch + % ignore - fix issue #4 (using HG2 on R2014a and earlier) + end + + % Fix issue #21 (bold TeX axes labels/titles in R2014b when exporting to EPS/PDF) + try + if using_hg2(fig) && isvector(options) + % Set the FontWeight of axes labels/titles to 'normal' + % Fix issue #69: set non-bold font only if the string contains symbols (\beta etc.) + % Issue #243: only set non-bold font (workaround for issue #69) in R2015b or earlier + try isPreR2016a = verLessThan('matlab','8.7'); catch, isPreR2016a = true; end + if isPreR2016a + texLabels = findall(fig, 'type','text', 'FontWeight','bold'); + symbolIdx = ~cellfun('isempty',strfind({texLabels.String},'\')); + if ~isempty(symbolIdx) + set(texLabels(symbolIdx), 'FontWeight','normal'); + warning('export_fig:BoldTexLabels', 'Bold labels with Tex symbols converted into non-bold in export_fig (fix for issue #69)'); + end + end + end + catch + % ignore + end + + % Fix issue #42: non-normalized annotations on HG1 (internal Matlab bug) + annotationHandles = []; + try + if ~using_hg2(fig) + annotationHandles = findall(fig,'Type','hggroup','-and','-property','Units','-and','-not','Units','norm'); + try % suggested by Jesús Pestana Puerta (jespestana) 30/9/2015 + originalUnits = get(annotationHandles,'Units'); + set(annotationHandles,'Units','norm'); + catch + end + end + catch + % should never happen, but ignore in any case - issue #50 + end + + % Fix issue #46: Ghostscript crash if figure units <> pixels + oldFigUnits = get(fig,'Units'); + set(fig,'Units','pixels'); + + % Set to print exactly what is there + if options.invert_hardcopy + try set(fig, 'InvertHardcopy', 'off'); catch, end % fail silently in uifigures + end + + % Set the renderer + switch options.renderer + case 1 + renderer = '-opengl'; + case 2 + renderer = '-zbuffer'; + case 3 + renderer = '-painters'; + otherwise + renderer = '-opengl'; % Default for bitmaps + end + + hImages = findall(fig,'type','image'); + + % Handle transparent patches + hasTransparency = ~isempty(findall(fig,'-property','FaceAlpha','-and','-not','FaceAlpha',1)); + hasPatches = ~isempty(findall(fig,'type','patch')); + if hasTransparency + % Alert if trying to export transparent patches/areas to non-supported outputs (issue #108) + % http://www.mathworks.com/matlabcentral/answers/265265-can-export_fig-or-else-draw-vector-graphics-with-transparent-surfaces + % TODO - use transparency when exporting to PDF by not passing via print2eps + msg = 'export_fig currently supports transparent patches/areas only in PNG output. '; + if options.pdf + warning('export_fig:transparency', '%s\nTo export transparent patches/areas to PDF, use the print command:\n print(gcf, ''-dpdf'', ''%s.pdf'');', msg, options.name); + elseif ~options.png && ~options.tif % issue #168 + warning('export_fig:transparency', '%s\nTo export the transparency correctly, try using the ScreenCapture utility on the Matlab File Exchange: http://bit.ly/1QFrBip', msg); + end + elseif ~isempty(hImages) + % Fix for issue #230: use OpenGL renderer when exported image contains transparency + for idx = 1 : numel(hImages) + cdata = get(hImages(idx),'CData'); + if any(isnan(cdata(:))) + hasTransparency = true; + break + end + end + end + + try + % Do the bitmap formats first + if isbitmap(options) + if abs(options.bb_padding) > 1 + displaySuggestedWorkarounds = false; + error('For bitmap output (png,jpg,tif,bmp) the padding value (-p) must be between -1 100 + imwrite(A, [options.name '.jpg'], 'Mode','lossless', format_options{:}); + else + imwrite(A, [options.name '.jpg'], 'Quality',quality, format_options{:}); + end + end + % Save tif images in cmyk if wanted (and possible) + if options.tif + if options.colourspace == 1 && size(A, 3) == 3 + A = double(255 - A); + K = min(A, [], 3); + K_ = 255 ./ max(255 - K, 1); + C = (A(:,:,1) - K) .* K_; + M = (A(:,:,2) - K) .* K_; + Y = (A(:,:,3) - K) .* K_; + A = uint8(cat(3, C, M, Y, K)); + clear C M Y K K_ + end + append_mode = {'overwrite', 'append'}; + format_options = getFormatOptions(options, 'tif'); %Issue #269 + imwrite(A, [options.name '.tif'], 'Resolution',options.magnify*get(0,'ScreenPixelsPerInch'), 'WriteMode',append_mode{options.append+1}, format_options{:}); + end + end + + % Now do the vector formats + if isvector(options) + % Set the default renderer to painters + if ~options.renderer + if hasTransparency || hasPatches + % This is *MUCH* slower, but more accurate for patches and transparent annotations (issue #39) + renderer = '-opengl'; + else + renderer = '-painters'; + end + end + options.rendererStr = renderer; % fix for issue #112 + % Generate some filenames + tmp_nam = [tempname '.eps']; + try + % Ensure that the temp dir is writable (Javier Paredes 30/1/15) + fid = fopen(tmp_nam,'w'); + fwrite(fid,1); + fclose(fid); + delete(tmp_nam); + isTempDirOk = true; + catch + % Temp dir is not writable, so use the user-specified folder + [dummy,fname,fext] = fileparts(tmp_nam); %#ok + fpath = fileparts(options.name); + tmp_nam = fullfile(fpath,[fname fext]); + isTempDirOk = false; + end + if isTempDirOk + pdf_nam_tmp = [tempname '.pdf']; + else + pdf_nam_tmp = fullfile(fpath,[fname '.pdf']); + end + if options.pdf + pdf_nam = [options.name '.pdf']; + try copyfile(pdf_nam, pdf_nam_tmp, 'f'); catch, end % fix for issue #65 + else + pdf_nam = pdf_nam_tmp; + end + % Generate the options for print + printArgs = {renderer}; + if ~isempty(options.resolution) % issue #241 + printArgs{end+1} = sprintf('-r%d', options.resolution); + end + if options.colourspace == 1 % CMYK + % Issue #33: due to internal bugs in Matlab's print() function, we can't use its -cmyk option + %printArgs{end+1} = '-cmyk'; + end + if ~options.crop + % Issue #56: due to internal bugs in Matlab's print() function, we can't use its internal cropping mechanism, + % therefore we always use '-loose' (in print2eps.m) and do our own cropping (in crop_borders) + %printArgs{end+1} = '-loose'; + end + if any(strcmpi(varargin,'-depsc')) + % Issue #45: lines in image subplots are exported in invalid color. + % The workaround is to use the -depsc parameter instead of the default -depsc2 + printArgs{end+1} = '-depsc'; + end + try + % Remove background if requested (issue #207) + originalBgColor = get(fig, 'Color'); + [hXs, hYs, hZs] = deal([]); + if options.transparent %&& ~isequal(get(fig, 'Color'), 'none') + if options.renderer == 1 % OpenGL + warning('export_fig:openglTransparentBG', '-opengl sometimes fails to produce transparent backgrounds; in such a case, try to use -painters instead'); + end + + % Fix for issue #207, #267 (corrected) + set(fig,'Color','none'); + + % Correct black axes color to off-black (issue #249) + hAxes = findall(fig, 'Type','axes'); + hXs = fixBlackAxle(hAxes, 'XColor'); + hYs = fixBlackAxle(hAxes, 'YColor'); + hZs = fixBlackAxle(hAxes, 'ZColor'); + end + % Generate an eps + print2eps(tmp_nam, fig, options, printArgs{:}); + % { + % Remove the background, if desired + if options.transparent %&& ~isequal(get(fig, 'Color'), 'none') + eps_remove_background(tmp_nam, 1 + using_hg2(fig)); + + % Revert the black axes colors + set(hXs, 'XColor', [0,0,0]); + set(hYs, 'YColor', [0,0,0]); + set(hZs, 'ZColor', [0,0,0]); + end + %} + % Restore the figure's previous background color (if modified) + try set(fig,'Color',originalBgColor); drawnow; catch, end + % Fix colorspace to CMYK, if requested (workaround for issue #33) + if options.colourspace == 1 % CMYK + % Issue #33: due to internal bugs in Matlab's print() function, we can't use its -cmyk option + change_rgb_to_cmyk(tmp_nam); + end + % Add a bookmark to the PDF if desired + if options.bookmark + fig_nam = get(fig, 'Name'); + if isempty(fig_nam) + warning('export_fig:EmptyBookmark', 'Bookmark requested for figure with no name. Bookmark will be empty.'); + end + add_bookmark(tmp_nam, fig_nam); + end + % Generate a pdf + eps2pdf(tmp_nam, pdf_nam_tmp, 1, options.append, options.colourspace==2, options.quality, options.gs_options); + % Ghostscript croaks on % chars in the output PDF file, so use tempname and then rename the file + try + % Rename the file (except if it is already the same) + % Abbie K's comment on the commit for issue #179 (#commitcomment-20173476) + if ~isequal(pdf_nam_tmp, pdf_nam) + movefile(pdf_nam_tmp, pdf_nam, 'f'); + end + catch + % Alert in case of error creating output PDF/EPS file (issue #179) + if exist(pdf_nam_tmp, 'file') + errMsg = ['Could not create ' pdf_nam ' - perhaps the folder does not exist, or you do not have write permissions, or the file is open in another application']; + error(errMsg); + else + error('Could not generate the intermediary EPS file.'); + end + end + catch ex + % Restore the figure's previous background color (in case it was not already restored) + try set(fig,'Color',originalBgColor); drawnow; catch, end + % Delete the eps + delete(tmp_nam); + % Rethrow the EPS/PDF-generation error + rethrow(ex); + end + % Delete the eps + delete(tmp_nam); + if options.eps || options.linecaps + try + % Generate an eps from the pdf + % since pdftops can't handle relative paths (e.g., '..\'), use a temp file + eps_nam_tmp = strrep(pdf_nam_tmp,'.pdf','.eps'); + pdf2eps(pdf_nam, eps_nam_tmp); + + % Issue #192: enable rounded line-caps + if options.linecaps + fstrm = read_write_entire_textfile(eps_nam_tmp); + fstrm = regexprep(fstrm, '[02] J', '1 J'); + read_write_entire_textfile(eps_nam_tmp, fstrm); + if options.pdf + eps2pdf(eps_nam_tmp, pdf_nam, 1, options.append, options.colourspace==2, options.quality, options.gs_options); + end + end + + if options.eps + movefile(eps_nam_tmp, [options.name '.eps'], 'f'); + else % if options.pdf + try delete(eps_nam_tmp); catch, end + end + catch ex + if ~options.pdf + % Delete the pdf + delete(pdf_nam); + end + try delete(eps_nam_tmp); catch, end + rethrow(ex); + end + if ~options.pdf + % Delete the pdf + delete(pdf_nam); + end + end + % Issue #206: warn if the figure contains an image + if ~isempty(hImages) && strcmpi(renderer,'-opengl') % see addendum to issue #206 + warnMsg = ['exporting images to PDF/EPS may result in blurry images on some viewers. ' ... + 'If so, try to change viewer, or increase the image''s CData resolution, or use -opengl renderer, or export via the print function. ' ... + 'See issue #206 for details.']; + warning('export_fig:pdf_eps:blurry_image', warnMsg); + end + end + + % SVG format + if options.svg + oldUnits = get(fig,'Units'); + filename = [options.name '.svg']; + % Adapted from Dan Joshea's https://github.com/djoshea/matlab-save-figure : + try %if verLessThan('matlab', '8.4') + % Try using the fig2svg/plot2svg utilities + try + fig2svg(filename, fig); %https://github.com/kupiqu/fig2svg + catch + plot2svg(filename, fig); %https://github.com/jschwizer99/plot2svg + warning('export_fig:SVG:plot2svg', 'export_fig used the plot2svg utility for SVG output. Better results may be gotten via the fig2svg utility (https://github.com/kupiqu/fig2svg).'); + end + catch %else % (neither fig2svg nor plot2svg are available) + % Try Matlab's built-in svg engine (from Batik Graphics2D for java) + try + set(fig,'Units','pixels'); % All data in the svg-file is saved in pixels + printArgs = {renderer}; + if ~isempty(options.resolution) + printArgs{end+1} = sprintf('-r%d', options.resolution); + end + print(fig, '-dsvg', printArgs{:}, filename); + warning('export_fig:SVG:print', 'export_fig used Matlab''s built-in SVG output engine. Better results may be gotten via the fig2svg utility (https://github.com/kupiqu/fig2svg).'); + catch err % built-in print() failed - maybe an old Matlab release (no -dsvg) + set(fig,'Units',oldUnits); + filename = strrep(filename,'export_fig_out','filename'); + msg = ['SVG output is not supported for your figure: ' err.message '\n' ... + 'Try one of the following alternatives:\n' ... + ' 1. saveas(gcf,''' filename ''')\n' ... + ' 2. fig2svg utility: https://github.com/kupiqu/fig2svg\n' ... % Note: replaced defunct https://github.com/jschwizer99/plot2svg with up-to-date fork on https://github.com/kupiqu/fig2svg + ' 3. export_fig to EPS/PDF, then convert to SVG using non-Matlab tools\n']; + error(sprintf(msg)); %#ok + end + end + % SVG output was successful if we reached this point + % Restore original figure units + set(fig,'Units',oldUnits); + % Add warning about unsupported export_fig options with SVG output + if any(~isnan(options.crop_amounts)) || any(options.bb_padding) + warning('export_fig:SVG:options', 'export_fig''s SVG output does not [currently] support cropping/padding.'); + end + end + + % Revert the figure or close it (if requested) + if cls || options.closeFig + % Close the created figure + close(fig); + else + % Reset the hardcopy mode + try set(fig, 'InvertHardcopy', old_mode); catch, end % fail silently in uifigures + % Reset the axes limit and tick modes + for a = 1:numel(Hlims) + try + set(Hlims(a), 'XLimMode', Xlims{a}, 'YLimMode', Ylims{a}, 'ZLimMode', Zlims{a},... + 'XTickMode', Xtick{a}, 'YTickMode', Ytick{a}, 'ZTickMode', Ztick{a},... + 'XTickLabelMode', Xlabel{a}, 'YTickLabelMode', Ylabel{a}, 'ZTickLabelMode', Zlabel{a}); + catch + % ignore - fix issue #4 (using HG2 on R2014a and earlier) + end + end + % Revert the tex-labels font weights + try set(texLabels, 'FontWeight','bold'); catch, end + % Revert annotation units + for handleIdx = 1 : numel(annotationHandles) + try + oldUnits = originalUnits{handleIdx}; + catch + oldUnits = originalUnits; + end + try set(annotationHandles(handleIdx),'Units',oldUnits); catch, end + end + % Revert figure units + set(fig,'Units',oldFigUnits); + end + + % Output to clipboard (if requested) + if options.clipboard + % Delete the output file if unchanged from the default name ('export_fig_out.png') + if strcmpi(options.name,'export_fig_out') + try + fileInfo = dir('export_fig_out.png'); + if ~isempty(fileInfo) + timediff = now - fileInfo.datenum; + ONE_SEC = 1/24/60/60; + if timediff < ONE_SEC + delete('export_fig_out.png'); + end + end + catch + % never mind... + end + end + + % Save the image in the system clipboard + % credit: Jiro Doke's IMCLIPBOARD: http://www.mathworks.com/matlabcentral/fileexchange/28708-imclipboard + try + error(javachk('awt', 'export_fig -clipboard output')); + catch + warning('export_fig:clipboardJava', 'export_fig -clipboard output failed: requires Java to work'); + return; + end + try + % Import necessary Java classes + import java.awt.Toolkit + import java.awt.image.BufferedImage + import java.awt.datatransfer.DataFlavor + + % Get System Clipboard object (java.awt.Toolkit) + cb = Toolkit.getDefaultToolkit.getSystemClipboard(); + + % Add java class (ImageSelection) to the path + if ~exist('ImageSelection', 'class') + javaaddpath(fileparts(which(mfilename)), '-end'); + end + + % Get image size + ht = size(imageData, 1); + wd = size(imageData, 2); + + % Convert to Blue-Green-Red format + try + imageData2 = imageData(:, :, [3 2 1]); + catch + % Probably gray-scaled image (2D, without the 3rd [RGB] dimension) + imageData2 = imageData(:, :, [1 1 1]); + end + + % Convert to 3xWxH format + imageData2 = permute(imageData2, [3, 2, 1]); + + % Append Alpha data (unused - transparency is not supported in clipboard copy) + alphaData2 = uint8(permute(255*alpha,[3,2,1])); %=255*ones(1,wd,ht,'uint8') + imageData2 = cat(1, imageData2, alphaData2); + + % Create image buffer + imBuffer = BufferedImage(wd, ht, BufferedImage.TYPE_INT_RGB); + imBuffer.setRGB(0, 0, wd, ht, typecast(imageData2(:), 'int32'), 0, wd); + + % Create ImageSelection object from the image buffer + imSelection = ImageSelection(imBuffer); + + % Set clipboard content to the image + cb.setContents(imSelection, []); + catch + warning('export_fig:clipboardFailed', 'export_fig -clipboard output failed: %s', lasterr); %#ok + end + end + + % Don't output the data to console unless requested + if ~nargout + clear imageData alpha + end + catch err + % Display possible workarounds before the error message + if displaySuggestedWorkarounds && ~strcmpi(err.message,'export_fig error') + if ~hadError, fprintf(2, 'export_fig error. '); end + fprintf(2, 'Please ensure:\n'); + fprintf(2, ' that you are using the latest version of export_fig\n'); + if isvector(options) + if ismac + fprintf(2, ' and that you have Ghostscript installed\n'); + else + fprintf(2, ' and that you have Ghostscript installed\n'); + end + end + try + if options.eps + fprintf(2, ' and that you have pdftops installed\n'); + end + catch + % ignore - probably an error in parse_args + end + fprintf(2, ' and that you do not have multiple versions of export_fig installed by mistake\n'); + fprintf(2, ' and that you did not made a mistake in the expected input arguments\n'); + try + % Alert per issue #149 + if ~strncmpi(get(0,'Units'),'pixel',5) + fprintf(2, ' or try to set groot''s Units property back to its default value of ''pixels'' (details)\n'); + end + catch + % ignore - maybe an old MAtlab release + end + fprintf(2, '\nIf the problem persists, then please report a new issue.\n\n'); + end + rethrow(err) + end +end + +function options = default_options() + % Default options used by export_fig + options = struct(... + 'name', 'export_fig_out', ... + 'crop', true, ... + 'crop_amounts', nan(1,4), ... % auto-crop all 4 image sides + 'transparent', false, ... + 'renderer', 0, ... % 0: default, 1: OpenGL, 2: ZBuffer, 3: Painters + 'pdf', false, ... + 'eps', false, ... + 'svg', false, ... + 'png', false, ... + 'tif', false, ... + 'jpg', false, ... + 'bmp', false, ... + 'clipboard', false, ... + 'colourspace', 0, ... % 0: RGB/gray, 1: CMYK, 2: gray + 'append', false, ... + 'im', false, ... + 'alpha', false, ... + 'aa_factor', 0, ... + 'bb_padding', 0, ... + 'magnify', [], ... + 'resolution', [], ... + 'bookmark', false, ... + 'closeFig', false, ... + 'quality', [], ... + 'update', false, ... + 'fontswap', true, ... + 'font_space', '', ... + 'linecaps', false, ... + 'invert_hardcopy', true, ... + 'format_options', struct, ... + 'preserve_size', false, ... + 'gs_options', {{}}); +end + +function [fig, options] = parse_args(nout, fig, varargin) + % Parse the input arguments + + % Convert strings => chars + varargin = cellfun(@str2char,varargin,'un',false); + + % Set the defaults + native = false; % Set resolution to native of an image + options = default_options(); + options.im = (nout == 1); % user requested imageData output + options.alpha = (nout == 2); % user requested alpha output + + % Go through the other arguments + skipNext = false; + for a = 1:nargin-2 + if skipNext + skipNext = false; + continue; + end + if all(ishandle(varargin{a})) + fig = varargin{a}; + elseif ischar(varargin{a}) && ~isempty(varargin{a}) + if varargin{a}(1) == '-' + switch lower(varargin{a}(2:end)) + case 'nocrop' + options.crop = false; + options.crop_amounts = [0,0,0,0]; + case {'trans', 'transparent'} + options.transparent = true; + case 'opengl' + options.renderer = 1; + case 'zbuffer' + options.renderer = 2; + case 'painters' + options.renderer = 3; + case 'pdf' + options.pdf = true; + case 'eps' + options.eps = true; + case 'svg' + options.svg = true; + case 'png' + options.png = true; + case {'tif', 'tiff'} + options.tif = true; + case {'jpg', 'jpeg'} + options.jpg = true; + case 'bmp' + options.bmp = true; + case 'rgb' + options.colourspace = 0; + case 'cmyk' + options.colourspace = 1; + case {'gray', 'grey'} + options.colourspace = 2; + case {'a1', 'a2', 'a3', 'a4'} + options.aa_factor = str2double(varargin{a}(3)); + case 'append' + options.append = true; + case 'bookmark' + options.bookmark = true; + case 'native' + native = true; + case 'clipboard' + options.clipboard = true; + options.im = true; + options.alpha = true; + case 'update' + % Download the latest version of export_fig into the export_fig folder + try + zipFileName = 'https://github.com/altmany/export_fig/archive/master.zip'; + folderName = fileparts(which(mfilename('fullpath'))); + targetFileName = fullfile(folderName, datestr(now,'yyyy-mm-dd.zip')); + urlwrite(zipFileName,targetFileName); %#ok + catch + error('Could not download %s into %s\n',zipFileName,targetFileName); + end + + % Unzip the downloaded zip file in the export_fig folder + try + unzip(targetFileName,folderName); + catch + error('Could not unzip %s\n',targetFileName); + end + case 'nofontswap' + options.fontswap = false; + case 'font_space' + options.font_space = varargin{a+1}; + skipNext = true; + case 'linecaps' + options.linecaps = true; + case 'noinvert' + options.invert_hardcopy = false; + case 'preserve_size' + options.preserve_size = true; + case 'options' + % Issue #269: format-specific options + inputOptions = varargin{a+1}; + %options.format_options = inputOptions; + if isempty(inputOptions), continue, end + formats = fieldnames(inputOptions(1)); + for idx = 1 : numel(formats) + optionsStruct = inputOptions.(formats{idx}); + %optionsCells = [fieldnames(optionsStruct) struct2cell(optionsStruct)]'; + formatName = regexprep(lower(formats{idx}),{'tiff','jpeg'},{'tif','jpg'}); + options.format_options.(formatName) = optionsStruct; %=optionsCells(:)'; + end + skipNext = true; + otherwise + try + wasError = false; + if strcmpi(varargin{a}(1:2),'-d') + varargin{a}(2) = 'd'; % ensure lowercase 'd' + options.gs_options{end+1} = varargin{a}; + elseif strcmpi(varargin{a}(1:2),'-c') + if numel(varargin{a})==2 + skipNext = true; + vals = str2num(varargin{a+1}); %#ok + else + vals = str2num(varargin{a}(3:end)); %#ok + end + if numel(vals)~=4 + wasError = true; + error('option -c cannot be parsed: must be a 4-element numeric vector'); + end + options.crop_amounts = vals; + options.crop = true; + else % scalar parameter value + val = str2double(regexp(varargin{a}, '(?<=-(m|M|r|R|q|Q|p|P))-?\d*.?\d+', 'match')); + if isempty(val) || isnan(val) + % Issue #51: improved processing of input args (accept space between param name & value) + val = str2double(varargin{a+1}); + if isscalar(val) && ~isnan(val) + skipNext = true; + end + end + if ~isscalar(val) || isnan(val) + wasError = true; + error('option %s is not recognised or cannot be parsed', varargin{a}); + end + switch lower(varargin{a}(2)) + case 'm' + % Magnification may never be negative + if val <= 0 + wasError = true; + error('Bad magnification value: %g (must be positive)', val); + end + options.magnify = val; + case 'r' + options.resolution = val; + case 'q' + options.quality = max(val, 0); + case 'p' + options.bb_padding = val; + end + end + catch err + % We might have reached here by raising an intentional error + if wasError % intentional raise + rethrow(err) + else % unintentional + error(['Unrecognized export_fig input option: ''' varargin{a} '''']); + end + end + end + else + [p, options.name, ext] = fileparts(varargin{a}); + if ~isempty(p) + % Issue #221: alert if the requested folder does not exist + if ~exist(p,'dir'), error(['Folder ' p ' does not exist!']); end + options.name = [p filesep options.name]; + end + switch lower(ext) + case {'.tif', '.tiff'} + options.tif = true; + case {'.jpg', '.jpeg'} + options.jpg = true; + case '.png' + options.png = true; + case '.bmp' + options.bmp = true; + case '.eps' + options.eps = true; + case '.pdf' + options.pdf = true; + case '.fig' + % If no open figure, then load the specified .fig file and continue + if isempty(fig) + fig = openfig(varargin{a},'invisible'); + varargin{a} = fig; + options.closeFig = true; + else + % save the current figure as the specified .fig file and exit + saveas(fig(1),varargin{a}); + fig = -1; + return + end + case '.svg' + options.svg = true; + otherwise + options.name = varargin{a}; + end + end + end + end + + % Quick bail-out if no figure found + if isempty(fig), return; end + + % Do border padding with repsect to a cropped image + if options.bb_padding + options.crop = true; + end + + % Set default anti-aliasing now we know the renderer + if options.aa_factor == 0 + try isAA = strcmp(get(ancestor(fig, 'figure'), 'GraphicsSmoothing'), 'on'); catch, isAA = false; end + options.aa_factor = 1 + 2 * (~(using_hg2(fig) && isAA) | (options.renderer == 3)); + end + + % Convert user dir '~' to full path + if numel(options.name) > 2 && options.name(1) == '~' && (options.name(2) == '/' || options.name(2) == '\') + options.name = fullfile(char(java.lang.System.getProperty('user.home')), options.name(2:end)); + end + + % Compute the magnification and resolution + if isempty(options.magnify) + if isempty(options.resolution) + options.magnify = 1; + options.resolution = 864; + else + options.magnify = options.resolution ./ get(0, 'ScreenPixelsPerInch'); + end + elseif isempty(options.resolution) + options.resolution = 864; + end + + % Set the default format + if ~isvector(options) && ~isbitmap(options) + options.png = true; + end + + % Check whether transparent background is wanted (old way) + if isequal(get(ancestor(fig(1), 'figure'), 'Color'), 'none') + options.transparent = true; + end + + % If requested, set the resolution to the native vertical resolution of the + % first suitable image found + if native + if isbitmap(options) + % Find a suitable image + list = findall(fig, 'Type','image', 'Tag','export_fig_native'); + if isempty(list) + list = findall(fig, 'Type','image', 'Visible','on'); + end + for hIm = list(:)' + % Check height is >= 2 + height = size(get(hIm, 'CData'), 1); + if height < 2 + continue + end + % Account for the image filling only part of the axes, or vice versa + yl = get(hIm, 'YData'); + if isscalar(yl) + yl = [yl(1)-0.5 yl(1)+height+0.5]; + else + yl = [min(yl), max(yl)]; % fix issue #151 (case of yl containing more than 2 elements) + if ~diff(yl) + continue + end + yl = yl + [-0.5 0.5] * (diff(yl) / (height - 1)); + end + hAx = get(hIm, 'Parent'); + yl2 = get(hAx, 'YLim'); + % Find the pixel height of the axes + oldUnits = get(hAx, 'Units'); + set(hAx, 'Units', 'pixels'); + pos = get(hAx, 'Position'); + set(hAx, 'Units', oldUnits); + if ~pos(4) + continue + end + % Found a suitable image + % Account for stretch-to-fill being disabled + pbar = get(hAx, 'PlotBoxAspectRatio'); + pos = min(pos(4), pbar(2)*pos(3)/pbar(1)); + % Set the magnification to give native resolution + options.magnify = abs((height * diff(yl2)) / (pos * diff(yl))); % magnification must never be negative: issue #103 + break + end + elseif options.resolution == 864 % don't use -r864 in vector mode if user asked for -native + options.resolution = []; % issue #241 (internal Matlab bug produces black lines with -r864) + end + end +end + +% Convert a possible string => char (issue #245) +function value = str2char(value) + if isa(value,'string') + value = char(value); + end +end + +function A = downsize(A, factor) + % Downsample an image + if factor == 1 + % Nothing to do + return + end + try + % Faster, but requires image processing toolbox + A = imresize(A, 1/factor, 'bilinear'); + catch + % No image processing toolbox - resize manually + % Lowpass filter - use Gaussian as is separable, so faster + % Compute the 1d Gaussian filter + filt = (-factor-1:factor+1) / (factor * 0.6); + filt = exp(-filt .* filt); + % Normalize the filter + filt = single(filt / sum(filt)); + % Filter the image + padding = floor(numel(filt) / 2); + for a = 1:size(A, 3) + A(:,:,a) = conv2(filt, filt', single(A([ones(1, padding) 1:end repmat(end, 1, padding)],[ones(1, padding) 1:end repmat(end, 1, padding)],a)), 'valid'); + end + % Subsample + A = A(1+floor(mod(end-1, factor)/2):factor:end,1+floor(mod(end-1, factor)/2):factor:end,:); + end +end + +function A = rgb2grey(A) + A = cast(reshape(reshape(single(A), [], 3) * single([0.299; 0.587; 0.114]), size(A, 1), size(A, 2)), class(A)); % #ok +end + +function A = check_greyscale(A) + % Check if the image is greyscale + if size(A, 3) == 3 && ... + all(reshape(A(:,:,1) == A(:,:,2), [], 1)) && ... + all(reshape(A(:,:,2) == A(:,:,3), [], 1)) + A = A(:,:,1); % Save only one channel for 8-bit output + end +end + +function eps_remove_background(fname, count) + % Remove the background of an eps file + % Open the file + fh = fopen(fname, 'r+'); + if fh == -1 + error('Not able to open file %s.', fname); + end + % Read the file line by line + while count + % Get the next line + l = fgets(fh); + if isequal(l, -1) + break; % Quit, no rectangle found + end + % Check if the line contains the background rectangle + if isequal(regexp(l, ' *0 +0 +\d+ +\d+ +r[fe] *[\n\r]+', 'start'), 1) + % Set the line to whitespace and quit + l(1:regexp(l, '[\n\r]', 'start', 'once')-1) = ' '; + fseek(fh, -numel(l), 0); + fprintf(fh, l); + % Reduce the count + count = count - 1; + end + end + % Close the file + fclose(fh); +end + +function b = isvector(options) + b = options.pdf || options.eps; +end + +function b = isbitmap(options) + b = options.png || options.tif || options.jpg || options.bmp || options.im || options.alpha; +end + +% Helper function +function A = make_cell(A) + if ~iscell(A) + A = {A}; + end +end + +function add_bookmark(fname, bookmark_text) + % Adds a bookmark to the temporary EPS file after %%EndPageSetup + % Read in the file + fh = fopen(fname, 'r'); + if fh == -1 + error('File %s not found.', fname); + end + try + fstrm = fread(fh, '*char')'; + catch ex + fclose(fh); + rethrow(ex); + end + fclose(fh); + + % Include standard pdfmark prolog to maximize compatibility + fstrm = strrep(fstrm, '%%BeginProlog', sprintf('%%%%BeginProlog\n/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse')); + % Add page bookmark + fstrm = strrep(fstrm, '%%EndPageSetup', sprintf('%%%%EndPageSetup\n[ /Title (%s) /OUT pdfmark',bookmark_text)); + + % Write out the updated file + fh = fopen(fname, 'w'); + if fh == -1 + error('Unable to open %s for writing.', fname); + end + try + fwrite(fh, fstrm, 'char*1'); + catch ex + fclose(fh); + rethrow(ex); + end + fclose(fh); +end + +function set_tick_mode(Hlims, ax) + % Set the tick mode of linear axes to manual + % Leave log axes alone as these are tricky + M = get(Hlims, [ax 'Scale']); + if ~iscell(M) + M = {M}; + end + %idx = cellfun(@(c) strcmp(c, 'linear'), M); + idx = find(strcmp(M,'linear')); + %set(Hlims(idx), [ax 'TickMode'], 'manual'); % issue #187 + %set(Hlims(idx), [ax 'TickLabelMode'], 'manual'); % this hides exponent label in HG2! + for idx2 = 1 : numel(idx) + try + % Fix for issue #187 - only set manual ticks when no exponent is present + hAxes = Hlims(idx(idx2)); + props = {[ax 'TickMode'],'manual', [ax 'TickLabelMode'],'manual'}; + tickVals = get(hAxes,[ax 'Tick']); + tickStrs = get(hAxes,[ax 'TickLabel']); + try % Fix issue #236 + exponents = [hAxes.([ax 'Axis']).SecondaryLabel]; + catch + exponents = [hAxes.([ax 'Ruler']).SecondaryLabel]; + end + if isempty([exponents.String]) + % Fix for issue #205 - only set manual ticks when the Ticks number match the TickLabels number + if numel(tickVals) == numel(tickStrs) + set(hAxes, props{:}); % no exponent and matching ticks, so update both ticks and tick labels to manual + end + end + catch % probably HG1 + % Fix for issue #220 - exponent is removed in HG1 when TickMode is 'manual' (internal Matlab bug) + if isequal(tickVals, str2num(tickStrs)') %#ok + set(hAxes, props{:}); % revert back to old behavior + end + end + end +end + +function change_rgb_to_cmyk(fname) % convert RGB => CMYK within an EPS file + % Do post-processing on the eps file + try + % Read the EPS file into memory + fstrm = read_write_entire_textfile(fname); + + % Replace all gray-scale colors + fstrm = regexprep(fstrm, '\n([\d.]+) +GC\n', '\n0 0 0 ${num2str(1-str2num($1))} CC\n'); + + % Replace all RGB colors + fstrm = regexprep(fstrm, '\n[0.]+ +[0.]+ +[0.]+ +RC\n', '\n0 0 0 1 CC\n'); % pure black + fstrm = regexprep(fstrm, '\n([\d.]+) +([\d.]+) +([\d.]+) +RC\n', '\n${sprintf(''%.4g '',[1-[str2num($1),str2num($2),str2num($3)]/max([str2num($1),str2num($2),str2num($3)]),1-max([str2num($1),str2num($2),str2num($3)])])} CC\n'); + + % Overwrite the file with the modified contents + read_write_entire_textfile(fname, fstrm); + catch + % never mind - leave as is... + end +end + +function hBlackAxles = fixBlackAxle(hAxes, axleName) + hBlackAxles = []; + for idx = 1 : numel(hAxes) + ax = hAxes(idx); + axleColor = get(ax, axleName); + if isequal(axleColor,[0,0,0]) || isequal(axleColor,'k') + hBlackAxles(end+1) = ax; %#ok + end + end + set(hBlackAxles, axleName, [0,0,0.01]); % off-black +end + +% Issue #269: format-specific options +function [optionsCells, bitDepth] = getFormatOptions(options, formatName) + bitDepth = []; + try + optionsStruct = options.format_options.(lower(formatName)); + catch + % User did not specify any extra parameters for this format + optionsCells = {}; + return + end + optionNames = fieldnames(optionsStruct); + optionVals = struct2cell(optionsStruct); + optionsCells = [optionNames, optionVals]'; + if nargout < 2, return, end % bail out if BitDepth is not required + try + idx = find(strcmpi(optionNames,'BitDepth'), 1, 'last'); + if ~isempty(idx) + bitDepth = optionVals{idx}; + end + catch + % never mind - ignore + end +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/fix_lines.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/fix_lines.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/fix_lines.m (revision 27955) @@ -0,0 +1,151 @@ +%FIX_LINES Improves the line style of eps files generated by print +% +% Examples: +% fix_lines fname +% fix_lines fname fname2 +% fstrm_out = fixlines(fstrm_in) +% +% This function improves the style of lines in eps files generated by +% MATLAB's print function, making them more similar to those seen on +% screen. Grid lines are also changed from a dashed style to a dotted +% style, for greater differentiation from dashed lines. +% +% The function also places embedded fonts after the postscript header, in +% versions of MATLAB which place the fonts first (R2006b and earlier), in +% order to allow programs such as Ghostscript to find the bounding box +% information. +% +%IN: +% fname - Name or path of source eps file. +% fname2 - Name or path of destination eps file. Default: same as fname. +% fstrm_in - File contents of a MATLAB-generated eps file. +% +%OUT: +% fstrm_out - Contents of the eps file with line styles fixed. + +% Copyright: (C) Oliver Woodford, 2008-2014 + +% The idea of editing the EPS file to change line styles comes from Jiro +% Doke's FIXPSLINESTYLE (fex id: 17928) +% The idea of changing dash length with line width came from comments on +% fex id: 5743, but the implementation is mine :) + +% Thank you to Sylvain Favrot for bringing the embedded font/bounding box +% interaction in older versions of MATLAB to my attention. +% Thank you to D Ko for bringing an error with eps files with tiff previews +% to my attention. +% Thank you to Laurence K for suggesting the check to see if the file was +% opened. + +% 01/03/15: Issue #20: warn users if using this function in HG2 (R2014b+) +% 27/03/15: Fixed out of memory issue with enormous EPS files (generated by print() with OpenGL renderer), related to issue #39 + +function fstrm = fix_lines(fstrm, fname2) + +% Issue #20: warn users if using this function in HG2 (R2014b+) +if using_hg2 + warning('export_fig:hg2','The fix_lines function should not be used in this Matlab version.'); +end + +if nargout == 0 || nargin > 1 + if nargin < 2 + % Overwrite the input file + fname2 = fstrm; + end + % Read in the file + fstrm = read_write_entire_textfile(fstrm); +end + +% Move any embedded fonts after the postscript header +if strcmp(fstrm(1:15), '%!PS-AdobeFont-') + % Find the start and end of the header + ind = regexp(fstrm, '[\n\r]%!PS-Adobe-'); + [ind2, ind2] = regexp(fstrm, '[\n\r]%%EndComments[\n\r]+'); + % Put the header first + if ~isempty(ind) && ~isempty(ind2) && ind(1) < ind2(1) + fstrm = fstrm([ind(1)+1:ind2(1) 1:ind(1) ind2(1)+1:end]); + end +end + +% Make sure all line width commands come before the line style definitions, +% so that dash lengths can be based on the correct widths +% Find all line style sections +ind = [regexp(fstrm, '[\n\r]SO[\n\r]'),... % This needs to be here even though it doesn't have dots/dashes! + regexp(fstrm, '[\n\r]DO[\n\r]'),... + regexp(fstrm, '[\n\r]DA[\n\r]'),... + regexp(fstrm, '[\n\r]DD[\n\r]')]; +ind = sort(ind); +% Find line width commands +[ind2, ind3] = regexp(fstrm, '[\n\r]\d* w[\n\r]'); +% Go through each line style section and swap with any line width commands +% near by +b = 1; +m = numel(ind); +n = numel(ind2); +for a = 1:m + % Go forwards width commands until we pass the current line style + while b <= n && ind2(b) < ind(a) + b = b + 1; + end + if b > n + % No more width commands + break; + end + % Check we haven't gone past another line style (including SO!) + if a < m && ind2(b) > ind(a+1) + continue; + end + % Are the commands close enough to be confident we can swap them? + if (ind2(b) - ind(a)) > 8 + continue; + end + % Move the line style command below the line width command + fstrm(ind(a)+1:ind3(b)) = [fstrm(ind(a)+4:ind3(b)) fstrm(ind(a)+1:ind(a)+3)]; + b = b + 1; +end + +% Find any grid line definitions and change to GR format +% Find the DO sections again as they may have moved +ind = int32(regexp(fstrm, '[\n\r]DO[\n\r]')); +if ~isempty(ind) + % Find all occurrences of what are believed to be axes and grid lines + ind2 = int32(regexp(fstrm, '[\n\r] *\d* *\d* *mt *\d* *\d* *L[\n\r]')); + if ~isempty(ind2) + % Now see which DO sections come just before axes and grid lines + ind2 = repmat(ind2', [1 numel(ind)]) - repmat(ind, [numel(ind2) 1]); + ind2 = any(ind2 > 0 & ind2 < 12); % 12 chars seems about right + ind = ind(ind2); + % Change any regions we believe to be grid lines to GR + fstrm(ind+1) = 'G'; + fstrm(ind+2) = 'R'; + end +end + +% Define the new styles, including the new GR format +% Dot and dash lengths have two parts: a constant amount plus a line width +% variable amount. The constant amount comes after dpi2point, and the +% variable amount comes after currentlinewidth. If you want to change +% dot/dash lengths for a one particular line style only, edit the numbers +% in the /DO (dotted lines), /DA (dashed lines), /DD (dot dash lines) and +% /GR (grid lines) lines for the style you want to change. +new_style = {'/dom { dpi2point 1 currentlinewidth 0.08 mul add mul mul } bdef',... % Dot length macro based on line width + '/dam { dpi2point 2 currentlinewidth 0.04 mul add mul mul } bdef',... % Dash length macro based on line width + '/SO { [] 0 setdash 0 setlinecap } bdef',... % Solid lines + '/DO { [1 dom 1.2 dom] 0 setdash 0 setlinecap } bdef',... % Dotted lines + '/DA { [4 dam 1.5 dam] 0 setdash 0 setlinecap } bdef',... % Dashed lines + '/DD { [1 dom 1.2 dom 4 dam 1.2 dom] 0 setdash 0 setlinecap } bdef',... % Dot dash lines + '/GR { [0 dpi2point mul 4 dpi2point mul] 0 setdash 1 setlinecap } bdef'}; % Grid lines - dot spacing remains constant + +% Construct the output +% This is the original (memory-intensive) code: +%first_sec = strfind(fstrm, '% line types:'); % Isolate line style definition section +%[second_sec, remaining] = strtok(fstrm(first_sec+1:end), '/'); +%[remaining, remaining] = strtok(remaining, '%'); +%fstrm = [fstrm(1:first_sec) second_sec sprintf('%s\r', new_style{:}) remaining]; +fstrm = regexprep(fstrm,'(% line types:.+?)/.+?%',['$1',sprintf('%s\r',new_style{:}),'%']); + +% Write the output file +if nargout == 0 || nargin > 1 + read_write_entire_textfile(fname2, fstrm); +end +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/ghostscript.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/ghostscript.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/ghostscript.m (revision 27955) @@ -0,0 +1,196 @@ +function varargout = ghostscript(cmd) +%GHOSTSCRIPT Calls a local GhostScript executable with the input command +% +% Example: +% [status result] = ghostscript(cmd) +% +% Attempts to locate a ghostscript executable, finally asking the user to +% specify the directory ghostcript was installed into. The resulting path +% is stored for future reference. +% +% Once found, the executable is called with the input command string. +% +% This function requires that you have Ghostscript installed on your +% system. You can download this from: http://www.ghostscript.com +% +% IN: +% cmd - Command string to be passed into ghostscript. +% +% OUT: +% status - 0 iff command ran without problem. +% result - Output from ghostscript. + +% Copyright: Oliver Woodford, 2009-2015, Yair Altman 2015- +%{ +% Thanks to Jonas Dorn for the fix for the title of the uigetdir window on Mac OS. +% Thanks to Nathan Childress for the fix to default location on 64-bit Windows systems. +% 27/04/11 - Find 64-bit Ghostscript on Windows. Thanks to Paul Durack and +% Shaun Kline for pointing out the issue +% 04/05/11 - Thanks to David Chorlian for pointing out an alternative +% location for gs on linux. +% 12/12/12 - Add extra executable name on Windows. Thanks to Ratish +% Punnoose for highlighting the issue. +% 28/06/13 - Fix error using GS 9.07 in Linux. Many thanks to Jannick +% Steinbring for proposing the fix. +% 24/10/13 - Fix error using GS 9.07 in Linux. Many thanks to Johannes +% for the fix. +% 23/01/14 - Add full path to ghostscript.txt in warning. Thanks to Koen +% Vermeer for raising the issue. +% 27/02/15 - If Ghostscript croaks, display suggested workarounds +% 30/03/15 - Improved performance by caching status of GS path check, if ok +% 14/05/15 - Clarified warning message in case GS path could not be saved +% 29/05/15 - Avoid cryptic error in case the ghostscipt path cannot be saved (issue #74) +% 10/11/15 - Custom GS installation webpage for MacOS. Thanks to Andy Hueni via FEX +%} + + try + % Call ghostscript + [varargout{1:nargout}] = system([gs_command(gs_path()) cmd]); + catch err + % Display possible workarounds for Ghostscript croaks + url1 = 'https://github.com/altmany/export_fig/issues/12#issuecomment-61467998'; % issue #12 + url2 = 'https://github.com/altmany/export_fig/issues/20#issuecomment-63826270'; % issue #20 + hg2_str = ''; if using_hg2, hg2_str = ' or Matlab R2014a'; end + fprintf(2, 'Ghostscript error. Rolling back to GS 9.10%s may possibly solve this:\n * %s ',hg2_str,url1,url1); + if using_hg2 + fprintf(2, '(GS 9.10)\n * %s (R2014a)',url2,url2); + end + fprintf('\n\n'); + if ismac || isunix + url3 = 'https://github.com/altmany/export_fig/issues/27'; % issue #27 + fprintf(2, 'Alternatively, this may possibly be due to a font path issue:\n * %s\n\n',url3,url3); + % issue #20 + fpath = which(mfilename); + if isempty(fpath), fpath = [mfilename('fullpath') '.m']; end + fprintf(2, 'Alternatively, if you are using csh, modify shell_cmd from "export..." to "setenv ..."\nat the bottom of %s\n\n',fpath,fpath); + end + rethrow(err); + end +end + +function path_ = gs_path + % Return a valid path + % Start with the currently set path + path_ = user_string('ghostscript'); + % Check the path works + if check_gs_path(path_) + return + end + % Check whether the binary is on the path + if ispc + bin = {'gswin32c.exe', 'gswin64c.exe', 'gs'}; + else + bin = {'gs'}; + end + for a = 1:numel(bin) + path_ = bin{a}; + if check_store_gs_path(path_) + return + end + end + % Search the obvious places + if ispc + default_location = 'C:\Program Files\gs\'; + dir_list = dir(default_location); + if isempty(dir_list) + default_location = 'C:\Program Files (x86)\gs\'; % Possible location on 64-bit systems + dir_list = dir(default_location); + end + executable = {'\bin\gswin32c.exe', '\bin\gswin64c.exe'}; + ver_num = 0; + % If there are multiple versions, use the newest + for a = 1:numel(dir_list) + ver_num2 = sscanf(dir_list(a).name, 'gs%g'); + if ~isempty(ver_num2) && ver_num2 > ver_num + for b = 1:numel(executable) + path2 = [default_location dir_list(a).name executable{b}]; + if exist(path2, 'file') == 2 + path_ = path2; + ver_num = ver_num2; + end + end + end + end + if check_store_gs_path(path_) + return + end + else + executable = {'/usr/bin/gs', '/usr/local/bin/gs'}; + for a = 1:numel(executable) + path_ = executable{a}; + if check_store_gs_path(path_) + return + end + end + end + % Ask the user to enter the path + while true + if strncmp(computer, 'MAC', 3) % Is a Mac + % Give separate warning as the uigetdir dialogue box doesn't have a + % title + uiwait(warndlg('Ghostscript not found. Please locate the program.')) + end + base = uigetdir('/', 'Ghostcript not found. Please locate the program.'); + if isequal(base, 0) + % User hit cancel or closed window + break; + end + base = [base filesep]; %#ok + bin_dir = {'', ['bin' filesep], ['lib' filesep]}; + for a = 1:numel(bin_dir) + for b = 1:numel(bin) + path_ = [base bin_dir{a} bin{b}]; + if exist(path_, 'file') == 2 + if check_store_gs_path(path_) + return + end + end + end + end + end + if ismac + error('Ghostscript not found. Have you installed it (http://pages.uoregon.edu/koch)?'); + else + error('Ghostscript not found. Have you installed it from www.ghostscript.com?'); + end +end + +function good = check_store_gs_path(path_) + % Check the path is valid + good = check_gs_path(path_); + if ~good + return + end + % Update the current default path to the path found + if ~user_string('ghostscript', path_) + filename = fullfile(fileparts(which('user_string.m')), '.ignore', 'ghostscript.txt'); + warning('Path to ghostscript installation could not be saved in %s (perhaps a permissions issue). You can manually create this file and set its contents to %s, to improve performance in future invocations (this warning is safe to ignore).', filename, path_); + return + end +end + +function good = check_gs_path(path_) + persistent isOk + if isempty(path_) + isOk = false; + elseif ~isequal(isOk,true) + % Check whether the path is valid + [status, message] = system([gs_command(path_) '-h']); %#ok + isOk = status == 0; + end + good = isOk; +end + +function cmd = gs_command(path_) + % Initialize any required system calls before calling ghostscript + % TODO: in Unix/Mac, find a way to determine whether to use "export" (bash) or "setenv" (csh/tcsh) + shell_cmd = ''; + if isunix + shell_cmd = 'export LD_LIBRARY_PATH=""; '; % Avoids an error on Linux with GS 9.07 + end + if ismac + shell_cmd = 'export DYLD_LIBRARY_PATH=""; '; % Avoids an error on Mac with GS 9.07 + end + % Construct the command string + cmd = sprintf('%s"%s" ', shell_cmd, path_); +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/im2gif.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/im2gif.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/im2gif.m (revision 27955) @@ -0,0 +1,205 @@ +%IM2GIF Convert a multiframe image to an animated GIF file +% +% Examples: +% im2gif infile +% im2gif infile outfile +% im2gif(A, outfile) +% im2gif(..., '-nocrop') +% im2gif(..., '-nodither') +% im2gif(..., '-ncolors', n) +% im2gif(..., '-loops', n) +% im2gif(..., '-delay', n) +% +% This function converts a multiframe image to an animated GIF. +% +% To create an animation from a series of figures, export to a multiframe +% TIFF file using export_fig, then convert to a GIF, as follows: +% +% for a = 2 .^ (3:6) +% peaks(a); +% export_fig test.tif -nocrop -append +% end +% im2gif('test.tif', '-delay', 0.5); +% +%IN: +% infile - string containing the name of the input image. +% outfile - string containing the name of the output image (must have the +% .gif extension). Default: infile, with .gif extension. +% A - HxWxCxN array of input images, stacked along fourth dimension, to +% be converted to gif. +% -nocrop - option indicating that the borders of the output are not to +% be cropped. +% -nodither - option indicating that dithering is not to be used when +% converting the image. +% -ncolors - option pair, the value of which indicates the maximum number +% of colors the GIF can have. This can also be a quantization +% tolerance, between 0 and 1. Default/maximum: 256. +% -loops - option pair, the value of which gives the number of times the +% animation is to be looped. Default: 65535. +% -delay - option pair, the value of which gives the time, in seconds, +% between frames. Default: 1/15. + +% Copyright (C) Oliver Woodford 2011 + +%{ +% 14/02/18: Merged issue #235: reduced memory usage, improved performance (thanks to @numb7rs) +% 30/11/19: Merged issue #288: Fix im2gif.m for greyscale TIFF images (thanks @Blackbelt1221) +%} + +function im2gif(A, varargin) + + % Parse the input arguments + [A, options] = parse_args(A, varargin{:}); + + if options.crop ~= 0 + % Crop + A = crop_borders(A, A(ceil(end/2),1,:,1)); + end + + % Convert to indexed image + [h, w, c, n] = size(A); + + % Issue #235: Using unique(A,'rows') on the whole image stack at once causes + % massive memory usage when dealing with large images (at least on Matlab 2017b). + % Running unique(...) on individual frames, then again on the results drastically + % reduces the memory usage & slightly improves the execution time (@numb7rs). + uns = cell(1,size(A,4)); + for nn=1:size(A,4) + uns{nn}=unique(reshape(A(:,:,:,nn), h*w, c),'rows'); + end + map=unique(cell2mat(uns'),'rows'); + + A = reshape(permute(A, [1 2 4 3]), h, w*n, c); + + if size(map, 1) > 256 + dither_str = {'dither', 'nodither'}; + dither_str = dither_str{1+(options.dither==0)}; + if options.ncolors <= 1 + [B, map] = rgb2ind(A, options.ncolors, dither_str); + if size(map, 1) > 256 + [B, map] = rgb2ind(A, 256, dither_str); + end + else + [B, map] = rgb2ind(A, min(round(options.ncolors), 256), dither_str); + end + else + if max(map(:)) > 1 + map = double(map) / 255; + A = double(A) / 255; + end + B = rgb2ind(im2double(A), map); + end + B = reshape(B, h, w, 1, n); + + % Bug fix to rgb2ind + map(B(1)+1,:) = im2double(A(1,1,:)); + + % Save as a gif + imwrite(B, map, options.outfile, 'LoopCount', round(options.loops(1)), 'DelayTime', options.delay); +end + +%% Parse the input arguments +function [A, options] = parse_args(A, varargin) + % Set the defaults + options = struct('outfile', '', ... + 'dither', true, ... + 'crop', true, ... + 'ncolors', 256, ... + 'loops', 65535, ... + 'delay', 1/15); + + % Go through the arguments + a = 0; + n = numel(varargin); + while a < n + a = a + 1; + if ischar(varargin{a}) && ~isempty(varargin{a}) + if varargin{a}(1) == '-' + opt = lower(varargin{a}(2:end)); + switch opt + case 'nocrop' + options.crop = false; + case 'nodither' + options.dither = false; + otherwise + if ~isfield(options, opt) + error('Option %s not recognized', varargin{a}); + end + a = a + 1; + if ischar(varargin{a}) && ~ischar(options.(opt)) + options.(opt) = str2double(varargin{a}); + else + options.(opt) = varargin{a}; + end + end + else + options.outfile = varargin{a}; + end + end + end + + if isempty(options.outfile) + if ~ischar(A) + error('No output filename given.'); + end + % Generate the output filename from the input filename + [path, outfile] = fileparts(A); + options.outfile = fullfile(path, [outfile '.gif']); + end + + if ischar(A) + % Read in the image + A = imread_rgb(A); + end +end + +%% Read image to uint8 rgb array +function [A, alpha] = imread_rgb(name) + % Get file info + info = imfinfo(name); + % Special case formats + switch lower(info(1).Format) + case 'gif' + [A, map] = imread(name, 'frames', 'all'); + if ~isempty(map) + map = uint8(map * 256 - 0.5); % Convert to uint8 for storage + A = reshape(map(uint32(A)+1,:), [size(A) size(map, 2)]); % Assume indexed from 0 + A = permute(A, [1 2 5 4 3]); + end + case {'tif', 'tiff'} + A = cell(numel(info), 1); + for a = 1:numel(A) + [A{a}, map] = imread(name, 'Index', a, 'Info', info); + if ~isempty(map) + map = uint8(map * 256 - 0.5); % Convert to uint8 for storage + A{a} = reshape(map(uint32(A{a})+1,:), [size(A) size(map, 2)]); % Assume indexed from 0 + end + if size(A{a}, 3) == 4 + % TIFF in CMYK colourspace - convert to RGB + if isfloat(A{a}) + A{a} = A{a} * 255; + else + A{a} = single(A{a}); + end + A{a} = 255 - A{a}; + A{a}(:,:,4) = A{a}(:,:,4) / 255; + A{a} = uint8(A(:,:,1:3) .* A{a}(:,:,[4 4 4])); + elseif size(A{a}, 3) < 3 %Check whether TIFF has been read in as greyscale + %Convert from greyscale to RGB colorspace (issue #288) + A{a} = cat(3, A{a}, A{a}, A{a}); + end + end + A = cat(4, A{:}); + otherwise + [A, map, alpha] = imread(name); + A = A(:,:,:,1); % Keep only first frame of multi-frame files + if ~isempty(map) + map = uint8(map * 256 - 0.5); % Convert to uint8 for storage + A = reshape(map(uint32(A)+1,:), [size(A) size(map, 2)]); % Assume indexed from 0 + elseif size(A, 3) == 4 + % Assume 4th channel is an alpha matte + alpha = A(:,:,4); + A = A(:,:,1:3); + end + end +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/isolate_axes.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/isolate_axes.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/isolate_axes.m (revision 27955) @@ -0,0 +1,130 @@ +function fh = isolate_axes(ah, vis) +%ISOLATE_AXES Isolate the specified axes in a figure on their own +% +% Examples: +% fh = isolate_axes(ah) +% fh = isolate_axes(ah, vis) +% +% This function will create a new figure containing the axes/uipanels +% specified, and also their associated legends and colorbars. The objects +% specified must all be in the same figure, but they will generally only be +% a subset of the objects in the figure. +% +% IN: +% ah - An array of axes and uipanel handles, which must come from the +% same figure. +% vis - A boolean indicating whether the new figure should be visible. +% Default: false. +% +% OUT: +% fh - The handle of the created figure. + +% Copyright (C) Oliver Woodford 2011-2013 + +% Thank you to Rosella Blatt for reporting a bug to do with axes in GUIs +% 16/03/12: Moved copyfig to its own function. Thanks to Bob Fratantonio +% for pointing out that the function is also used in export_fig.m +% 12/12/12: Add support for isolating uipanels. Thanks to michael for suggesting it +% 08/10/13: Bug fix to allchildren suggested by Will Grant (many thanks!) +% 05/12/13: Bug fix to axes having different units. Thanks to Remington Reid for reporting +% 21/04/15: Bug fix for exporting uipanels with legend/colorbar on HG1 (reported by Alvaro +% on FEX page as a comment on 24-Apr-2014); standardized indentation & help section +% 22/04/15: Bug fix: legends and colorbars were not exported when exporting axes handle in HG2 + + % Make sure we have an array of handles + if ~all(ishandle(ah)) + error('ah must be an array of handles'); + end + % Check that the handles are all for axes or uipanels, and are all in the same figure + fh = ancestor(ah(1), 'figure'); + nAx = numel(ah); + for a = 1:nAx + if ~ismember(get(ah(a), 'Type'), {'axes', 'uipanel'}) + error('All handles must be axes or uipanel handles.'); + end + if ~isequal(ancestor(ah(a), 'figure'), fh) + error('Axes must all come from the same figure.'); + end + end + % Tag the objects so we can find them in the copy + old_tag = get(ah, 'Tag'); + if nAx == 1 + old_tag = {old_tag}; + end + set(ah, 'Tag', 'ObjectToCopy'); + % Create a new figure exactly the same as the old one + fh = copyfig(fh); %copyobj(fh, 0); + if nargin < 2 || ~vis + set(fh, 'Visible', 'off'); + end + % Reset the object tags + for a = 1:nAx + set(ah(a), 'Tag', old_tag{a}); + end + % Find the objects to save + ah = findall(fh, 'Tag', 'ObjectToCopy'); + if numel(ah) ~= nAx + close(fh); + error('Incorrect number of objects found.'); + end + % Set the axes tags to what they should be + for a = 1:nAx + set(ah(a), 'Tag', old_tag{a}); + end + % Keep any legends and colorbars which overlap the subplots + % Note: in HG1 these are axes objects; in HG2 they are separate objects, therefore we + % don't test for the type, only the tag (hopefully nobody but Matlab uses them!) + lh = findall(fh, 'Tag', 'legend', '-or', 'Tag', 'Colorbar'); + nLeg = numel(lh); + if nLeg > 0 + set([ah(:); lh(:)], 'Units', 'normalized'); + try + ax_pos = get(ah, 'OuterPosition'); % axes and figures have the OuterPosition property + catch + ax_pos = get(ah, 'Position'); % uipanels only have Position, not OuterPosition + end + if nAx > 1 + ax_pos = cell2mat(ax_pos(:)); + end + ax_pos(:,3:4) = ax_pos(:,3:4) + ax_pos(:,1:2); + try + leg_pos = get(lh, 'OuterPosition'); + catch + leg_pos = get(lh, 'Position'); % No OuterPosition in HG2, only in HG1 + end + if nLeg > 1; + leg_pos = cell2mat(leg_pos); + end + leg_pos(:,3:4) = leg_pos(:,3:4) + leg_pos(:,1:2); + ax_pos = shiftdim(ax_pos, -1); + % Overlap test + M = bsxfun(@lt, leg_pos(:,1), ax_pos(:,:,3)) & ... + bsxfun(@lt, leg_pos(:,2), ax_pos(:,:,4)) & ... + bsxfun(@gt, leg_pos(:,3), ax_pos(:,:,1)) & ... + bsxfun(@gt, leg_pos(:,4), ax_pos(:,:,2)); + ah = [ah; lh(any(M, 2))]; + end + % Get all the objects in the figure + axs = findall(fh); + % Delete everything except for the input objects and associated items + delete(axs(~ismember(axs, [ah; allchildren(ah); allancestors(ah)]))); +end + +function ah = allchildren(ah) + ah = findall(ah); + if iscell(ah) + ah = cell2mat(ah); + end + ah = ah(:); +end + +function ph = allancestors(ah) + ph = []; + for a = 1:numel(ah) + h = get(ah(a), 'parent'); + while h ~= 0 + ph = [ph; h]; + h = get(h, 'parent'); + end + end +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/pdf2eps.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/pdf2eps.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/pdf2eps.m (revision 27955) @@ -0,0 +1,55 @@ +%PDF2EPS Convert a pdf file to eps format using pdftops +% +% Examples: +% pdf2eps source dest +% +% This function converts a pdf file to eps format. +% +% This function requires that you have pdftops, from the Xpdf suite of +% functions, installed on your system. This can be downloaded from: +% http://xpdfreader.com +% +% Inputs: +% source - filename of the source pdf file to convert. The filename is +% assumed to already have the extension ".pdf". +% dest - filename of the destination eps file. The filename is assumed to +% already have the extension ".eps". + +% Copyright (C) Oliver Woodford 2009-2010, Yair Altman 2015- + +% Thanks to Aldebaro Klautau for reporting a bug when saving to +% non-existant directories. + +% 22/09/2018 - Xpdf website changed to xpdfreader.com + +function pdf2eps(source, dest) + % Construct the options string for pdftops + options = ['-q -paper match -eps -level2 "' source '" "' dest '"']; + + % Convert to eps using pdftops + [status, message] = pdftops(options); + + % Check for error + if status + % Report error + if isempty(message) + error('Unable to generate eps. Check destination directory is writable.'); + else + error(message); + end + end + + % Fix the DSC error created by pdftops + fid = fopen(dest, 'r+'); + if fid == -1 + % Cannot open the file + return + end + fgetl(fid); % Get the first line + str = fgetl(fid); % Get the second line + if strcmp(str(1:min(13, end)), '% Produced by') + fseek(fid, -numel(str)-1, 'cof'); + fwrite(fid, '%'); % Turn ' ' into '%' + end + fclose(fid); +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/pdftops.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/pdftops.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/pdftops.m (revision 27955) @@ -0,0 +1,170 @@ +function varargout = pdftops(cmd) +%PDFTOPS Calls a local pdftops executable with the input command +% +% Example: +% [status result] = pdftops(cmd) +% +% Attempts to locate a pdftops executable, finally asking the user to +% specify the directory pdftops was installed into. The resulting path is +% stored for future reference. +% +% Once found, the executable is called with the input command string. +% +% This function requires that you have pdftops (from the Xpdf package) +% installed on your system. You can download this from: http://xpdfreader.com +% +% IN: +% cmd - Command string to be passed into pdftops (e.g. '-help'). +% +% OUT: +% status - 0 iff command ran without problem. +% result - Output from pdftops. + +% Copyright: Oliver Woodford, 2009-2010 + +% Thanks to Jonas Dorn for the fix for the title of the uigetdir window on Mac OS. +% Thanks to Christoph Hertel for pointing out a bug in check_xpdf_path under linux. +% 23/01/2014 - Add full path to pdftops.txt in warning. +% 27/05/2015 - Fixed alert in case of missing pdftops; fixed code indentation +% 02/05/2016 - Added possible error explanation suggested by Michael Pacer (issue #137) +% 02/05/2016 - Search additional possible paths suggested by Jonas Stein (issue #147) +% 03/05/2016 - Display the specific error message if pdftops fails for some reason (issue #148) +% 22/09/2018 - Xpdf website changed to xpdfreader.com; improved popup logic +% 03/02/2019 - Fixed one-off 'pdftops not found' error after install (Mac/Linux) (issue #266) + + % Call pdftops + [varargout{1:nargout}] = system([xpdf_command(xpdf_path()) cmd]); +end + +function path_ = xpdf_path + % Return a valid path + % Start with the currently set path + path_ = user_string('pdftops'); + % Check the path works + if check_xpdf_path(path_) + return + end + % Check whether the binary is on the path + if ispc + bin = 'pdftops.exe'; + else + bin = 'pdftops'; + end + if check_store_xpdf_path(bin) + path_ = bin; + return + end + % Search the obvious places + if ispc + paths = {'C:\Program Files\xpdf\pdftops.exe', 'C:\Program Files (x86)\xpdf\pdftops.exe'}; + else + paths = {'/usr/bin/pdftops', '/usr/local/bin/pdftops'}; + end + for a = 1:numel(paths) + path_ = paths{a}; + if check_store_xpdf_path(path_) + return + end + end + + % Ask the user to enter the path + errMsg1 = 'Pdftops not found. Please locate the program, or install xpdf-tools from '; + url1 = 'http://xpdfreader.com/download.html'; %='http://foolabs.com/xpdf'; + fprintf(2, '%s\n', [errMsg1 '' url1 '']); + errMsg1 = [errMsg1 url1]; + %if strncmp(computer,'MAC',3) % Is a Mac + % % Give separate warning as the MacOS uigetdir dialogue box doesn't have a title + % uiwait(warndlg(errMsg1)) + %end + + % Provide an alternative possible explanation as per issue #137 + errMsg2 = 'If you have pdftops installed, perhaps Matlab is shaddowing it as described in '; + url2 = 'https://github.com/altmany/export_fig/issues/137'; + fprintf(2, '%s\n', [errMsg2 'issue #137']); + errMsg2 = [errMsg2 url1]; + + state = 1; + while 1 + if state + option1 = 'Install pdftops'; + else + option1 = 'Issue #137'; + end + answer = questdlg({errMsg1,'',errMsg2},'Pdftops error',option1,'Locate pdftops','Cancel','Cancel'); + drawnow; % prevent a Matlab hang: http://undocumentedmatlab.com/blog/solving-a-matlab-hang-problem + switch answer + case 'Install pdftops' + web('-browser',url1); + state = 0; + case 'Issue #137' + web('-browser',url2); + state = 1; + case 'Locate pdftops' + base = uigetdir('/', errMsg1); + if isequal(base, 0) + % User hit cancel or closed window + break + end + base = [base filesep]; %#ok + bin_dir = {'', ['bin' filesep], ['lib' filesep]}; + for a = 1:numel(bin_dir) + path_ = [base bin_dir{a} bin]; + if exist(path_, 'file') == 2 + break + end + end + if check_store_xpdf_path(path_) + return + end + + otherwise % User hit Cancel or closed window + break + end + end + error('pdftops executable not found.'); +end + +function good = check_store_xpdf_path(path_) + % Check the path is valid + good = check_xpdf_path(path_); + if ~good + return + end + % Update the current default path to the path found + if ~user_string('pdftops', path_) + warning('Path to pdftops executable could not be saved. Enter it manually in %s.', fullfile(fileparts(which('user_string.m')), '.ignore', 'pdftops.txt')); + return + end +end + +function good = check_xpdf_path(path_) + % Check the path is valid + [good, message] = system([xpdf_command(path_) '-h']); %#ok + % system returns good = 1 even when the command runs + % Look for something distinct in the help text + good = ~isempty(strfind(message, 'PostScript')); %#ok + + % Display the error message if the pdftops executable exists but fails for some reason + % Note: on Mac/Linux, exist('pdftops','file') will always return 2 due to pdftops.m => check for '/','.' (issue #266) + if ~good && exist(path_,'file') && ~isempty(regexp(path_,'[/.]')) %#ok % file exists but generates an error + fprintf('Error running %s:\n', path_); + fprintf(2,'%s\n\n',message); + end +end + +function cmd = xpdf_command(path_) + % Initialize any required system calls before calling ghostscript + % TODO: in Unix/Mac, find a way to determine whether to use "export" (bash) or "setenv" (csh/tcsh) + shell_cmd = ''; + if isunix + % Avoids an error on Linux with outdated MATLAB lib files + % R20XXa/bin/glnxa64/libtiff.so.X + % R20XXa/sys/os/glnxa64/libstdc++.so.X + shell_cmd = 'export LD_LIBRARY_PATH=""; '; + end + if ismac + shell_cmd = 'export DYLD_LIBRARY_PATH=""; '; + end + % Construct the command string + cmd = sprintf('%s"%s" ', shell_cmd, path_); +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/print2array.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/print2array.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/print2array.m (revision 27955) @@ -0,0 +1,261 @@ +function [A, bcol] = print2array(fig, res, renderer, gs_options) +%PRINT2ARRAY Exports a figure to an image array +% +% Examples: +% A = print2array +% A = print2array(figure_handle) +% A = print2array(figure_handle, resolution) +% A = print2array(figure_handle, resolution, renderer) +% A = print2array(figure_handle, resolution, renderer, gs_options) +% [A bcol] = print2array(...) +% +% This function outputs a bitmap image of the given figure, at the desired +% resolution. +% +% If renderer is '-painters' then ghostcript needs to be installed. This +% can be downloaded from: http://www.ghostscript.com +% +% IN: +% figure_handle - The handle of the figure to be exported. Default: gcf. +% resolution - Resolution of the output, as a factor of screen +% resolution. Default: 1. +% renderer - string containing the renderer paramater to be passed to +% print. Default: '-opengl'. +% gs_options - optional ghostscript options (e.g.: '-dNoOutputFonts'). If +% multiple options are needed, enclose in call array: {'-a','-b'} +% +% OUT: +% A - MxNx3 uint8 image of the figure. +% bcol - 1x3 uint8 vector of the background color + +% Copyright (C) Oliver Woodford 2008-2014, Yair Altman 2015- +%{ +% 05/09/11: Set EraseModes to normal when using opengl or zbuffer +% renderers. Thanks to Pawel Kocieniewski for reporting the issue. +% 21/09/11: Bug fix: unit8 -> uint8! Thanks to Tobias Lamour for reporting it. +% 14/11/11: Bug fix: stop using hardcopy(), as it interfered with figure size +% and erasemode settings. Makes it a bit slower, but more reliable. +% Thanks to Phil Trinh and Meelis Lootus for reporting the issues. +% 09/12/11: Pass font path to ghostscript. +% 27/01/12: Bug fix affecting painters rendering tall figures. Thanks to +% Ken Campbell for reporting it. +% 03/04/12: Bug fix to median input. Thanks to Andy Matthews for reporting it. +% 26/10/12: Set PaperOrientation to portrait. Thanks to Michael Watts for +% reporting the issue. +% 26/02/15: If temp dir is not writable, use the current folder for temp +% EPS/TIF files (Javier Paredes) +% 27/02/15: Display suggested workarounds to internal print() error (issue #16) +% 28/02/15: Enable users to specify optional ghostscript options (issue #36) +% 10/03/15: Fixed minor warning reported by Paul Soderlind; fixed code indentation +% 28/05/15: Fixed issue #69: patches with LineWidth==0.75 appear wide (internal bug in Matlab's print() func) +% 07/07/15: Fixed issue #83: use numeric handles in HG1 +% 11/12/16: Fixed cropping issue reported by Harry D. +% 29/09/18: Fixed issue #254: error in print2array>read_tif_img +%} + + % Generate default input arguments, if needed + if nargin < 2 + res = 1; + if nargin < 1 + fig = gcf; + end + end + % Warn if output is large + old_mode = get(fig, 'Units'); + set(fig, 'Units', 'pixels'); + px = get(fig, 'Position'); + set(fig, 'Units', old_mode); + npx = prod(px(3:4)*res)/1e6; + if npx > 30 + % 30M pixels or larger! + warning('MATLAB:LargeImage', 'print2array generating a %.1fM pixel image. This could be slow and might also cause memory problems.', npx); + end + % Retrieve the background colour + bcol = get(fig, 'Color'); + % Set the resolution parameter + res_str = ['-r' num2str(ceil(get(0, 'ScreenPixelsPerInch')*res))]; + % Generate temporary file name + tmp_nam = [tempname '.tif']; + try + % Ensure that the temp dir is writable (Javier Paredes 26/2/15) + fid = fopen(tmp_nam,'w'); + fwrite(fid,1); + fclose(fid); + delete(tmp_nam); % cleanup + isTempDirOk = true; + catch + % Temp dir is not writable, so use the current folder + [dummy,fname,fext] = fileparts(tmp_nam); %#ok + fpath = pwd; + tmp_nam = fullfile(fpath,[fname fext]); + isTempDirOk = false; + end + % Enable users to specify optional ghostscript options (issue #36) + if nargin > 3 && ~isempty(gs_options) + if iscell(gs_options) + gs_options = sprintf(' %s',gs_options{:}); + elseif ~ischar(gs_options) + error('gs_options input argument must be a string or cell-array of strings'); + else + gs_options = [' ' gs_options]; + end + else + gs_options = ''; + end + if nargin > 2 && strcmp(renderer, '-painters') + % First try to print directly to tif file + try + % Print the file into a temporary TIF file and read it into array A + [A, err, ex] = read_tif_img(fig, res_str, renderer, tmp_nam); + if err, rethrow(ex); end + catch % error - try to print to EPS and then using Ghostscript to TIF + % Print to eps file + if isTempDirOk + tmp_eps = [tempname '.eps']; + else + tmp_eps = fullfile(fpath,[fname '.eps']); + end + print2eps(tmp_eps, fig, 0, renderer, '-loose'); + try + % Initialize the command to export to tiff using ghostscript + cmd_str = ['-dEPSCrop -q -dNOPAUSE -dBATCH ' res_str ' -sDEVICE=tiff24nc']; + % Set the font path + fp = font_path(); + if ~isempty(fp) + cmd_str = [cmd_str ' -sFONTPATH="' fp '"']; + end + % Add the filenames + cmd_str = [cmd_str ' -sOutputFile="' tmp_nam '" "' tmp_eps '"' gs_options]; + % Execute the ghostscript command + ghostscript(cmd_str); + catch me + % Delete the intermediate file + delete(tmp_eps); + rethrow(me); + end + % Delete the intermediate file + delete(tmp_eps); + % Read in the generated bitmap + A = imread(tmp_nam); + % Delete the temporary bitmap file + delete(tmp_nam); + end + % Set border pixels to the correct colour + if isequal(bcol, 'none') + bcol = []; + elseif isequal(bcol, [1 1 1]) + bcol = uint8([255 255 255]); + else + for l = 1:size(A, 2) + if ~all(reshape(A(:,l,:) == 255, [], 1)) + break; + end + end + for r = size(A, 2):-1:l + if ~all(reshape(A(:,r,:) == 255, [], 1)) + break; + end + end + for t = 1:size(A, 1) + if ~all(reshape(A(t,:,:) == 255, [], 1)) + break; + end + end + for b = size(A, 1):-1:t + if ~all(reshape(A(b,:,:) == 255, [], 1)) + break; + end + end + bcol = uint8(median(single([reshape(A(:,[l r],:), [], size(A, 3)); reshape(A([t b],:,:), [], size(A, 3))]), 1)); + for c = 1:size(A, 3) + A(:,[1:l-1, r+1:end],c) = bcol(c); + A([1:t-1, b+1:end],:,c) = bcol(c); + end + end + else + if nargin < 3 + renderer = '-opengl'; + end + % Print the file into a temporary TIF file and read it into array A + [A, err, ex] = read_tif_img(fig, res_str, renderer, tmp_nam); + % Throw any error that occurred + if err + % Display suggested workarounds to internal print() error (issue #16) + fprintf(2, 'An error occured with Matlab''s builtin print function.\nTry setting the figure Renderer to ''painters'' or use opengl(''software'').\n\n'); + rethrow(ex); + end + % Set the background color + if isequal(bcol, 'none') + bcol = []; + else + bcol = bcol * 255; + if isequal(bcol, round(bcol)) + bcol = uint8(bcol); + else + bcol = squeeze(A(1,1,:)); + end + end + end + % Check the output size is correct + if isequal(res, round(res)) + px = round([px([4 3])*res 3]); % round() to avoid an indexing warning below + if ~isequal(size(A), px) + % Correct the output size + A = A(1:min(end,px(1)),1:min(end,px(2)),:); + end + end +end + +% Function to create a TIF image of the figure and read it into an array +function [A, err, ex] = read_tif_img(fig, res_str, renderer, tmp_nam) + A = []; % fix for issue #254 + err = false; + ex = []; + % Temporarily set the paper size + old_pos_mode = get(fig, 'PaperPositionMode'); + old_orientation = get(fig, 'PaperOrientation'); + set(fig, 'PaperPositionMode','auto', 'PaperOrientation','portrait'); + try + % Workaround for issue #69: patches with LineWidth==0.75 appear wide (internal bug in Matlab's print() function) + fp = []; % in case we get an error below + fp = findall(fig, 'Type','patch', 'LineWidth',0.75); + set(fp, 'LineWidth',0.5); + % Fix issue #83: use numeric handles in HG1 + if ~using_hg2(fig), fig = double(fig); end + % Print to tiff file + print(fig, renderer, res_str, '-dtiff', tmp_nam); + % Read in the printed file + A = imread(tmp_nam); + % Delete the temporary file + delete(tmp_nam); + catch ex + err = true; + end + set(fp, 'LineWidth',0.75); % restore original figure appearance + % Reset the paper size + set(fig, 'PaperPositionMode',old_pos_mode, 'PaperOrientation',old_orientation); +end + +% Function to return (and create, where necessary) the font path +function fp = font_path() + fp = user_string('gs_font_path'); + if ~isempty(fp) + return + end + % Create the path + % Start with the default path + fp = getenv('GS_FONTPATH'); + % Add on the typical directories for a given OS + if ispc + if ~isempty(fp) + fp = [fp ';']; + end + fp = [fp getenv('WINDIR') filesep 'Fonts']; + else + if ~isempty(fp) + fp = [fp ':']; + end + fp = [fp '/usr/share/fonts:/usr/local/share/fonts:/usr/share/fonts/X11:/usr/local/share/fonts/X11:/usr/share/fonts/truetype:/usr/local/share/fonts/truetype']; + end + user_string('gs_font_path', fp); +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/print2eps.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/print2eps.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/print2eps.m (revision 27955) @@ -0,0 +1,638 @@ +function print2eps(name, fig, export_options, varargin) +%PRINT2EPS Prints figures to eps with improved line styles +% +% Examples: +% print2eps filename +% print2eps(filename, fig_handle) +% print2eps(filename, fig_handle, export_options) +% print2eps(filename, fig_handle, export_options, print_options) +% +% This function saves a figure as an eps file, with two improvements over +% MATLAB's print command. First, it improves the line style, making dashed +% lines more like those on screen and giving grid lines a dotted line style. +% Secondly, it substitutes original font names back into the eps file, +% where these have been changed by MATLAB, for up to 11 different fonts. +% +% Inputs: +% filename - string containing the name (optionally including full or +% relative path) of the file the figure is to be saved as. A +% ".eps" extension is added if not there already. If a path is +% not specified, the figure is saved in the current directory. +% fig_handle - The handle of the figure to be saved. Default: gcf(). +% export_options - array or struct of optional scalar values: +% bb_padding - Scalar value of amount of padding to add to border around +% the cropped image, in points (if >1) or percent (if <1). +% Can be negative as well as positive; Default: 0 +% crop - Cropping flag. Deafult: 0 +% fontswap - Whether to swap non-default fonts in figure. Default: true +% preserve_size - Whether to preserve the figure's PaperSize. Default: false +% font_space - Character used to separate font-name terms in the EPS output +% e.g. "Courier New" => "Courier-New". Default: '' +% (available only via the struct alternative) +% renderer - Renderer used to generate bounding-box. Default: 'opengl' +% (available only via the struct alternative) +% crop_amounts - 4-element vector of crop amounts: [top,right,bottom,left] +% (available only via the struct alternative) +% print_options - Additional parameter strings to be passed to the print command + +%{ +% Copyright (C) Oliver Woodford 2008-2014, Yair Altman 2015- + +% The idea of editing the EPS file to change line styles comes from Jiro +% Doke's FIXPSLINESTYLE (fex id: 17928) +% The idea of changing dash length with line width came from comments on +% fex id: 5743, but the implementation is mine :) +%} +%{ +% 14/11/11: Fix a MATLAB bug rendering black or white text incorrectly. +% Thanks to Mathieu Morlighem for reporting the issue and +% obtaining a fix from TMW. +% 08/12/11: Added ability to correct fonts. Several people have requested +% this at one time or another, and also pointed me to printeps +% (fex id: 7501), so thank you to them. My implementation (which +% was not inspired by printeps - I'd already had the idea for my +% approach) goes slightly further in that it allows multiple +% fonts to be swapped. +% 14/12/11: Fix bug affecting font names containing spaces. Thanks to David +% Szwer for reporting the issue. +% 25/01/12: Add a font not to be swapped. Thanks to Anna Rafferty and Adam +% Jackson for reporting the issue. Also fix a bug whereby using a +% font alias can lead to another font being swapped in. +% 10/04/12: Make the font swapping case insensitive. +% 26/10/12: Set PaperOrientation to portrait. Thanks to Michael Watts for +% reporting the issue. +% 26/10/12: Fix issue to do with swapping fonts changing other fonts and +% sizes we don't want, due to listeners. Thanks to Malcolm Hudson +% for reporting the issue. +% 22/03/13: Extend font swapping to axes labels. Thanks to Rasmus Ischebeck +% for reporting the issue. +% 23/07/13: Bug fix to font swapping. Thanks to George for reporting the +% issue. +% 13/08/13: Fix MATLAB feature of not exporting white lines correctly. +% Thanks to Sebastian Hesslinger for reporting it. +% 24/02/15: Fix for Matlab R2014b bug (issue #31): LineWidths<0.75 are not +% set in the EPS (default line width is used) +% 25/02/15: Fixed issue #32: BoundingBox problem caused uncropped EPS/PDF files +% 05/03/15: Fixed issue #43: Inability to perform EPS file post-processing +% 06/03/15: Improved image padding & cropping thanks to Oscar Hartogensis +% 21/03/15: Fixed edge-case of missing handles having a 'FontName' property +% 26/03/15: Attempt to fix issue #45: white lines in subplots do not print correctly +% 27/03/15: Attempt to fix issue #44: white artifact lines appearing in patch exports +% 30/03/15: Fixed issue #52: improved performance on HG2 (R2014b+) +% 09/04/15: Comment blocks consolidation and minor code cleanup (no real code change) +% 12/04/15: Fixed issue #56: bad cropping +% 14/04/15: Workaround for issue #45: lines in image subplots are exported in invalid color +% 07/07/15: Added option to avoid font-swapping in EPS/PDF +% 07/07/15: Fixed issue #83: use numeric handles in HG1 +% 22/07/15: Fixed issue #91 (thanks to Carlos Moffat) +% 28/09/15: Fixed issue #108 (thanks to JacobD10) +% 01/11/15: Fixed issue #112: optional renderer for bounding-box computation (thanks to Jesús Pestana Puerta) +% 21/02/16: Enabled specifying non-automated crop amounts +% 22/02/16: Better support + backward compatibility for transparency (issue #108) +% 10/06/16: Fixed issue #159: text handles get cleared by Matlab in the print() command +% 12/06/16: Improved the fix for issue #159 (in the previous commit) +% 12/06/16: Fixed issue #158: transparent patch color in PDF/EPS +% 18/09/17: Fixed issue #194: incorrect fonts in EPS/PDF output +% 18/09/17: Fixed issue #195: relaxed too-tight cropping in EPS/PDF +% 14/11/17: Workaround for issue #211: dashed/dotted lines in 3D axes appear solid +% 15/11/17: Updated issue #211: only set SortMethod='ChildOrder' in HG2, and when it looks the same onscreen; support multiple figure axes +% 18/11/17: Fixed issue #225: transparent/translucent dashed/dotted lines appear solid in EPS/PDF +% 24/03/18: Fixed issue #239: black title meshes with temporary black background figure bgcolor, causing bad cropping +% 21/03/19: Improvement for issue #258: missing fonts in output EPS/PDF (still *NOT* fully solved) +% 21/03/19: Fixed issues #166,#251: Arial font is no longer replaced with Helvetica but rather treated as a non-standard user font +% 14/05/19: Made Helvetica the top default font-swap, replacing Courier +% 12/06/19: Issue #277: Enabled preservation of figure's PaperSize in output PDF/EPS file +% 06/08/19: Issue #281: only fix patch/textbox color if it's not opaque +%} + + options = {'-loose'}; + if nargin > 3 + options = [options varargin]; + elseif nargin < 3 + export_options = 0; + if nargin < 2 + fig = gcf(); + end + end + + % Retrieve padding, crop & font-swap values + crop_amounts = nan(1,4); % auto-crop all 4 sides by default + if isstruct(export_options) + try preserve_size = export_options.preserve_size; catch, preserve_size = false; end + try fontswap = export_options.fontswap; catch, fontswap = true; end + try font_space = export_options.font_space; catch, font_space = ''; end + font_space(2:end) = ''; + try bb_crop = export_options.crop; catch, bb_crop = 0; end + try crop_amounts = export_options.crop_amounts; catch, end + try bb_padding = export_options.bb_padding; catch, bb_padding = 0; end + try renderer = export_options.rendererStr; catch, renderer = 'opengl'; end % fix for issue #110 + if renderer(1)~='-', renderer = ['-' renderer]; end + else + if numel(export_options) > 3 % preserve_size + preserve_size = export_options(4); + else + preserve_size = false; + end + if numel(export_options) > 2 % font-swapping + fontswap = export_options(3); + else + fontswap = true; + end + if numel(export_options) > 1 % cropping + bb_crop = export_options(2); + else + bb_crop = 0; % scalar value, so use default bb_crop value of 0 + end + if numel(export_options) > 0 % padding + bb_padding = export_options(1); + else + bb_padding = 0; + end + renderer = '-opengl'; + font_space = ''; + end + + % Construct the filename + if numel(name) < 5 || ~strcmpi(name(end-3:end), '.eps') + name = [name '.eps']; % Add the missing extension + end + + % Set paper size + old_pos_mode = get(fig, 'PaperPositionMode'); + old_orientation = get(fig, 'PaperOrientation'); + old_paper_units = get(fig, 'PaperUnits'); + set(fig, 'PaperPositionMode','auto', 'PaperOrientation','portrait', 'PaperUnits','points'); + + % Find all the used fonts in the figure + font_handles = findall(fig, '-property', 'FontName'); + fonts = get(font_handles, 'FontName'); + if isempty(fonts) + fonts = {}; + elseif ~iscell(fonts) + fonts = {fonts}; + end + + % Map supported font aliases onto the correct name + fontsl = lower(fonts); + for a = 1:numel(fonts) + f = fontsl{a}; + f(f==' ') = []; + switch f + case {'times', 'timesnewroman', 'times-roman'} + fontsl{a} = 'times'; + %case {'arial', 'helvetica'} % issues #166, #251 + % fontsl{a} = 'helvetica'; + case {'newcenturyschoolbook', 'newcenturyschlbk'} + fontsl{a} = 'newcenturyschlbk'; + otherwise + end + end + fontslu = unique(fontsl); + + % Determine the font swap table + if fontswap + % Issue #258: Rearrange standard fonts list based on decending "problematicness" + % The issue is still *NOT* fully solved because I cannot figure out how to force + % the EPS postscript engine to look for the user's font on disk + % Also see: https://stat.ethz.ch/pipermail/r-help/2005-January/064374.html + matlab_fonts = {'Helvetica', 'Times', 'Courier', 'Symbol', 'ZapfDingbats', ... + 'Palatino', 'Bookman', 'ZapfChancery', 'AvantGarde', ... + 'NewCenturySchlbk', 'Helvetica-Narrow'}; + matlab_fontsl = lower(matlab_fonts); + require_swap = find(~ismember(fontslu, matlab_fontsl)); + unused_fonts = find(~ismember(matlab_fontsl, fontslu)); + font_swap = cell(3, min(numel(require_swap), numel(unused_fonts))); + fonts_new = fonts; + for a = 1:size(font_swap, 2) + font_swap{1,a} = find(strcmp(fontslu{require_swap(a)}, fontsl)); + font_swap{2,a} = matlab_fonts{unused_fonts(a)}; + font_swap{3,a} = fonts{font_swap{1,a}(1)}; + fonts_new(font_swap{1,a}) = font_swap(2,a); + end + else + font_swap = []; + end + + % Swap the fonts + if ~isempty(font_swap) + fonts_size = get(font_handles, 'FontSize'); + if iscell(fonts_size) + fonts_size = cell2mat(fonts_size); + end + M = false(size(font_handles)); + + % Loop because some changes may not stick first time, due to listeners + c = 0; + update = zeros(1000, 1); + for b = 1:10 % Limit number of loops to avoid infinite loop case + for a = 1:numel(M) + M(a) = ~isequal(get(font_handles(a), 'FontName'), fonts_new{a}) || ~isequal(get(font_handles(a), 'FontSize'), fonts_size(a)); + if M(a) + set(font_handles(a), 'FontName', fonts_new{a}, 'FontSize', fonts_size(a)); + c = c + 1; + update(c) = a; + end + end + if ~any(M) + break; + end + end + + % Compute the order to revert fonts later, without the need of a loop + [update, M] = unique(update(1:c)); + [dummy, M] = sort(M); %#ok + update = reshape(update(M), 1, []); + end + + % MATLAB bug fix - black and white text can come out inverted sometimes + % Find the white and black text + black_text_handles = findall(fig, 'Type', 'text', 'Color', [0 0 0]); + white_text_handles = findall(fig, 'Type', 'text', 'Color', [1 1 1]); + % Set the font colors slightly off their correct values + set(black_text_handles, 'Color', [0 0 0] + eps); + set(white_text_handles, 'Color', [1 1 1] - eps); + + % MATLAB bug fix - white lines can come out funny sometimes + % Find the white lines + white_line_handles = findall(fig, 'Type', 'line', 'Color', [1 1 1]); + % Set the line color slightly off white + set(white_line_handles, 'Color', [1 1 1] - 0.00001); + + % MATLAB bug fix (issue #211): dashed/dotted lines in 3D axes appear solid + % Note: this "may limit other functionality in plotting such as hidden line/surface removal" + % reference: Technical Support Case #02838114, https://mail.google.com/mail/u/0/#inbox/15fb7659f70e7bd8 + hAxes = findall(fig, 'Type', 'axes'); + if using_hg2 && ~isempty(hAxes) % issue #211 presumably happens only in HG2, not HG1 + try + % If there are any axes using SortMethod~='ChildOrder' + oldSortMethods = get(hAxes,{'SortMethod'}); % use {'SortMethod'} to ensure we get a cell array, even for single axes + if any(~strcmpi('ChildOrder',oldSortMethods)) % i.e., any oldSortMethods=='depth' + % Check if the axes look visually different onscreen when SortMethod='ChildOrder' + imgBefore = print2array(fig); + set(hAxes,'SortMethod','ChildOrder'); + imgAfter = print2array(fig); + if isequal(imgBefore, imgAfter) + % They look the same, so use SortMethod='ChildOrder' when generating the EPS + else + % They look different, so revert SortMethod and issue a warning message + warning('YMA:export_fig:issue211', ... + ['You seem to be using axes that have overlapping/hidden graphic elements. ' 10 ... + 'Setting axes.SortMethod=''ChildOrder'' may solve potential problems in EPS/PDF export. ' 10 ... + 'Additional info: https://github.com/altmany/export_fig/issues/211']) + set(hAxes,{'SortMethod'},oldSortMethods); + end + end + catch err + % ignore + a=err; %#ok % debug breakpoint + end + end + + % Workaround for issue #45: lines in image subplots are exported in invalid color + % In this case the -depsc driver solves the problem, but then all the other workarounds + % below (for all the other issues) will fail, so it's better to let the user decide by + % just issuing a warning and accepting the '-depsc' input parameter + epsLevel2 = ~any(strcmpi(options,'-depsc')); + if epsLevel2 + % Use -depsc2 (EPS color level-2) if -depsc (EPS color level-3) was not specifically requested + options{end+1} = '-depsc2'; + % Issue a warning if multiple images & lines were found in the figure, and HG1 with painters renderer is used + isPainters = any(strcmpi(options,'-painters')); + if isPainters && ~using_hg2 && numel(findall(fig,'Type','image'))>1 && ~isempty(findall(fig,'Type','line')) + warning('YMA:export_fig:issue45', ... + ['Multiple images & lines detected. In such cases, the lines might \n' ... + 'appear with an invalid color due to an internal MATLAB bug (fixed in R2014b). \n' ... + 'Possible workaround: add a ''-depsc'' or ''-opengl'' parameter to the export_fig command.']); + end + end + + % Fix issue #83: use numeric handles in HG1 + if ~using_hg2(fig), fig = double(fig); end + + % Workaround for when transparency is lost through conversion fig>EPS>PDF (issue #108) + % Replace transparent patch RGB values with an ID value (rare chance that ID color is being used already) + if using_hg2 + origAlphaColors = eps_maintainAlpha(fig); + end + + % Print to eps file + print(fig, options{:}, name); + + % Restore the original axes SortMethods (if updated) + try set(hAxes,{'SortMethod'},oldSortMethods); catch, end + + % Do post-processing on the eps file + try + % Read the EPS file into memory + fstrm = read_write_entire_textfile(name); + catch + fstrm = ''; + end + + % Restore colors for transparent patches/lines and apply the + % setopacityalpha setting in the EPS file (issue #108) + if using_hg2 + [~,fstrm,foundFlags] = eps_maintainAlpha(fig, fstrm, origAlphaColors); + + % If some of the transparencies were not found in the EPS file, then rerun the + % export with only the found transparencies modified (backward compatibility) + if ~isempty(fstrm) && ~all(foundFlags) + foundIdx = find(foundFlags); + for objIdx = 1 : sum(foundFlags) + colorsIdx = foundIdx(objIdx); + colorsData = origAlphaColors{colorsIdx}; + hObj = colorsData{1}; + propName = colorsData{2}; + newColor = colorsData{4}; + hObj.(propName).ColorData = newColor; + end + delete(name); + print(fig, options{:}, name); + fstrm = read_write_entire_textfile(name); + [~,fstrm] = eps_maintainAlpha(fig, fstrm, origAlphaColors(foundFlags)); + end + end + + % Bail out if EPS post-processing is not possible + if isempty(fstrm) + warning('Loading EPS file failed, so unable to perform post-processing. This is usually because the figure contains a large number of patch objects. Consider exporting to a bitmap format in this case.'); + return + end + + % Fix for Matlab R2014b bug (issue #31): LineWidths<0.75 are not set in the EPS (default line width is used) + try + if using_hg2(fig) + % Convert miter joins to line joins + %fstrm = regexprep(fstrm, '\n10.0 ML\n', '\n1 LJ\n'); + % This is faster (the original regexprep could take many seconds when the axes contains many lines): + fstrm = strrep(fstrm, sprintf('\n10.0 ML\n'), sprintf('\n1 LJ\n')); + + % In HG2, grid lines and axes Ruler Axles have a default LineWidth of 0.5 => replace en-bulk (assume that 1.0 LineWidth = 1.333 LW) + % hAxes=gca; hAxes.YGridHandle.LineWidth, hAxes.YRuler.Axle.LineWidth + %fstrm = regexprep(fstrm, '(GC\n2 setlinecap\n1 LJ)\nN', '$1\n0.667 LW\nN'); + % This is faster: + fstrm = strrep(fstrm, sprintf('GC\n2 setlinecap\n1 LJ\nN'), sprintf('GC\n2 setlinecap\n1 LJ\n0.667 LW\nN')); + + % This is more accurate but *MUCH* slower (issue #52) + %{ + % Modify all thin lines in the figure to have 10x LineWidths + hLines = findall(fig,'Type','line'); + hThinLines = []; + for lineIdx = 1 : numel(hLines) + thisLine = hLines(lineIdx); + if thisLine.LineWidth < 0.75 && strcmpi(thisLine.Visible,'on') + hThinLines(end+1) = thisLine; %#ok + thisLine.LineWidth = thisLine.LineWidth * 10; + end + end + + % If any thin lines were found + if ~isempty(hThinLines) + % Prepare an EPS with large-enough line widths + print(fig, options{:}, name); + % Restore the original LineWidths in the figure + for lineIdx = 1 : numel(hThinLines) + thisLine = handle(hThinLines(lineIdx)); + thisLine.LineWidth = thisLine.LineWidth / 10; + end + + % Compare the original and the new EPS files and correct the original stream's LineWidths + fstrm_new = read_write_entire_textfile(name); + idx = 500; % skip heading with its possibly-different timestamp + markerStr = sprintf('10.0 ML\nN'); + markerLen = length(markerStr); + while ~isempty(idx) && idx < length(fstrm) + lastIdx = min(length(fstrm), length(fstrm_new)); + delta = fstrm(idx+1:lastIdx) - fstrm_new(idx+1:lastIdx); + idx = idx + find(delta,1); + if ~isempty(idx) && ... + isequal(fstrm(idx-markerLen+1:idx), markerStr) && ... + ~isempty(regexp(fstrm_new(idx-markerLen+1:idx+12),'10.0 ML\n[\d\.]+ LW\nN')) %#ok + value = str2double(regexprep(fstrm_new(idx:idx+12),' .*','')); + if isnan(value), break; end % something's wrong... - bail out + newStr = sprintf('%0.3f LW\n',value/10); + fstrm = [fstrm(1:idx-1) newStr fstrm(idx:end)]; + idx = idx + 12; + else + break; + end + end + end + %} + + % This is much faster although less accurate: fix all non-gray lines to have a LineWidth of 0.75 (=1 LW) + % Note: This will give incorrect LineWidth of 075 for lines having LineWidth<0.75, as well as for non-gray grid-lines (if present) + % However, in practice these edge-cases are very rare indeed, and the difference in LineWidth should not be noticeable + %fstrm = regexprep(fstrm, '([CR]C\n2 setlinecap\n1 LJ)\nN', '$1\n1 LW\nN'); + % This is faster (the original regexprep could take many seconds when the axes contains many lines): + fstrm = strrep(fstrm, sprintf('\n2 setlinecap\n1 LJ\nN'), sprintf('\n2 setlinecap\n1 LJ\n1 LW\nN')); + end + catch err + fprintf(2, 'Error fixing LineWidths in EPS file: %s\n at %s:%d\n', err.message, err.stack(1).file, err.stack(1).line); + end + + % Reset the font and line colors + try + set(black_text_handles, 'Color', [0 0 0]); + set(white_text_handles, 'Color', [1 1 1]); + catch + % Fix issue #159: redo findall() '*text_handles' + black_text_handles = findall(fig, 'Type', 'text', 'Color', [0 0 0]+eps); + white_text_handles = findall(fig, 'Type', 'text', 'Color', [1 1 1]-eps); + set(black_text_handles, 'Color', [0 0 0]); + set(white_text_handles, 'Color', [1 1 1]); + end + set(white_line_handles, 'Color', [1 1 1]); + + % Preserve the figure's PaperSize in the output file, if requested (issue #277) + if preserve_size + % https://stackoverflow.com/questions/19646329/postscript-document-size + paper_size = get(fig, 'PaperSize'); % in [points] + fstrm = sprintf('<< /PageSize [%d %d] >> setpagedevice\n%s', paper_size, fstrm); + end + + % Reset paper size + set(fig, 'PaperPositionMode',old_pos_mode, 'PaperOrientation',old_orientation, 'PaperUnits',old_paper_units); + + % Reset the font names in the figure + if ~isempty(font_swap) + for a = update + set(font_handles(a), 'FontName', fonts{a}, 'FontSize', fonts_size(a)); + end + end + + % Replace the font names + if ~isempty(font_swap) + for a = 1:size(font_swap, 2) + fontName = font_swap{3,a}; + %fontName = fontName(~isspace(font_swap{3,a})); + if length(fontName) > 29 + warning('YMA:export_fig:font_name','Font name ''%s'' is longer than 29 characters. This might cause problems in some EPS/PDF readers. Consider using a different font.',fontName); + end + if isempty(font_space) + fontName(fontName==' ') = ''; + else + fontName(fontName==' ') = char(font_space); + end + + % Replace all instances of the standard Matlab fonts with the original user's font names + %fstrm = regexprep(fstrm, [font_swap{1,a} '-?[a-zA-Z]*\>'], fontName); + %fstrm = regexprep(fstrm, [font_swap{2,a} '([ \n])'], [fontName '$1']); + %fstrm = regexprep(fstrm, font_swap{2,a}, fontName); % also replace -Bold, -Italic, -BoldItalic + + % Times-Roman's Bold/Italic fontnames don't include '-Roman' + fstrm = regexprep(fstrm, [font_swap{2,a} '(\-Roman)?'], fontName); + end + end + + % Move the bounding box to the top of the file (HG2 only), or fix the line styles (HG1 only) + if using_hg2(fig) + % Move the bounding box to the top of the file (HG2 only) + [s, e] = regexp(fstrm, '%%BoundingBox: [^%]*%%'); + if numel(s) == 2 + fstrm = fstrm([1:s(1)-1 s(2):e(2)-2 e(1)-1:s(2)-1 e(2)-1:end]); + end + else + % Fix the line styles (HG1 only) + fstrm = fix_lines(fstrm); + end + + % Apply the bounding box padding & cropping, replacing Matlab's print()'s bounding box + if bb_crop + % Calculate a new bounding box based on a bitmap print using crop_border.m + % 1. Determine the Matlab BoundingBox and PageBoundingBox + [s,e] = regexp(fstrm, '%%BoundingBox: [^%]*%%'); % location BB in eps file + if numel(s)==2, s=s(2); e=e(2); end + aa = fstrm(s+15:e-3); % dimensions bb - STEP1 + bb_matlab = cell2mat(textscan(aa,'%f32%f32%f32%f32')); % dimensions bb - STEP2 + + [s,e] = regexp(fstrm, '%%PageBoundingBox: [^%]*%%'); % location bb in eps file + if numel(s)==2, s=s(2); e=e(2); end + aa = fstrm(s+19:e-3); % dimensions bb - STEP1 + pagebb_matlab = cell2mat(textscan(aa,'%f32%f32%f32%f32')); % dimensions bb - STEP2 + + % 1b. Fix issue #239: black title meshes with temporary black background figure bgcolor, causing bad cropping + hTitles = []; + if isequal(get(fig,'Color'),'none') + hAxes = findall(fig,'type','axes'); + for idx = 1 : numel(hAxes) + hAx = hAxes(idx); + try + hTitle = hAx.Title; + oldColor = hTitle.Color; + if all(oldColor < 5*eps) || (ischar(oldColor) && lower(oldColor(1))=='k') + hTitles(end+1) = hTitle; %#ok + hTitle.Color = [0,0,.01]; + end + catch + end + end + end + + % 2. Create a bitmap image and use crop_borders to create the relative + % bb with respect to the PageBoundingBox + [A, bcol] = print2array(fig, 1, renderer); + [aa, aa, aa, bb_rel] = crop_borders(A, bcol, bb_padding, crop_amounts); %#ok + + try set(hTitles,'Color','k'); catch, end + + % 3. Calculate the new Bounding Box + pagew = pagebb_matlab(3)-pagebb_matlab(1); + pageh = pagebb_matlab(4)-pagebb_matlab(2); + %bb_new = [pagebb_matlab(1)+pagew*bb_rel(1) pagebb_matlab(2)+pageh*bb_rel(2) ... + % pagebb_matlab(1)+pagew*bb_rel(3) pagebb_matlab(2)+pageh*bb_rel(4)]; + bb_new = pagebb_matlab([1,2,1,2]) + [pagew,pageh,pagew,pageh].*bb_rel; % clearer + bb_offset = (bb_new-bb_matlab) + [-2,-2,2,2]; % 2px margin so that cropping is not TOO tight (issue #195) + + % Apply the bounding box padding + if bb_padding + if abs(bb_padding)<1 + bb_padding = round((mean([bb_new(3)-bb_new(1) bb_new(4)-bb_new(2)])*bb_padding)/0.5)*0.5; % ADJUST BB_PADDING + end + add_padding = @(n1, n2, n3, n4) sprintf(' %.0f', str2double({n1, n2, n3, n4}) + bb_offset + bb_padding*[-1,-1,1,1]); %#ok + else + add_padding = @(n1, n2, n3, n4) sprintf(' %.0f', str2double({n1, n2, n3, n4}) + bb_offset); %#ok % fix small but noticeable bounding box shift + end + fstrm = regexprep(fstrm, '%%BoundingBox:[ ]+([-]?\d+)[ ]+([-]?\d+)[ ]+([-]?\d+)[ ]+([-]?\d+)', '%%BoundingBox:${add_padding($1, $2, $3, $4)}'); + end + + % Fix issue #44: white artifact lines appearing in patch exports + % Note: the problem is due to the fact that Matlab's print() function exports patches + % as a combination of filled triangles, and a white line appears where the triangles touch + % In the workaround below, we will modify such dual-triangles into a filled rectangle. + % We are careful to only modify regexps that exactly match specific patterns - it's better to not + % correct some white-line artifacts than to change the geometry of a patch, or to corrupt the EPS. + % e.g.: '0 -450 937 0 0 450 3 MP PP 937 0 0 -450 0 450 3 MP PP' => '0 -450 937 0 0 450 0 0 4 MP' + fstrm = regexprep(fstrm, '\n([-\d.]+ [-\d.]+) ([-\d.]+ [-\d.]+) ([-\d.]+ [-\d.]+) 3 MP\nPP\n\2 \1 \3 3 MP\nPP\n','\n$1 $2 $3 0 0 4 MP\nPP\n'); + fstrm = regexprep(fstrm, '\n([-\d.]+ [-\d.]+) ([-\d.]+ [-\d.]+) ([-\d.]+ [-\d.]+) 3 MP\nPP\n\2 \3 \1 3 MP\nPP\n','\n$1 $2 $3 0 0 4 MP\nPP\n'); + fstrm = regexprep(fstrm, '\n([-\d.]+ [-\d.]+) ([-\d.]+ [-\d.]+) ([-\d.]+ [-\d.]+) 3 MP\nPP\n\3 \1 \2 3 MP\nPP\n','\n$1 $2 $3 0 0 4 MP\nPP\n'); + fstrm = regexprep(fstrm, '\n([-\d.]+ [-\d.]+) ([-\d.]+ [-\d.]+) ([-\d.]+ [-\d.]+) 3 MP\nPP\n\3 \2 \1 3 MP\nPP\n','\n$1 $2 $3 0 0 4 MP\nPP\n'); + + % Write out the fixed eps file + read_write_entire_textfile(name, fstrm); +end + +function [StoredColors, fstrm, foundFlags] = eps_maintainAlpha(fig, fstrm, StoredColors) + if nargin == 1 % in: convert transparency in Matlab figure into unique RGB colors + hObjs = findall(fig); %findobj(fig,'Type','Area'); + StoredColors = {}; + propNames = {'Face','Edge'}; + for objIdx = 1:length(hObjs) + hObj = hObjs(objIdx); + for propIdx = 1 : numel(propNames) + try + propName = propNames{propIdx}; + if strcmp(hObj.(propName).ColorType, 'truecoloralpha') + oldColor = hObj.(propName).ColorData; + if numel(oldColor)>3 && oldColor(4)~=255 % issue #281: only fix patch/textbox color if it's not opaque + nColors = length(StoredColors); + newColor = uint8([101; 102+floor(nColors/255); mod(nColors,255); 255]); + StoredColors{end+1} = {hObj, propName, oldColor, newColor}; %#ok + hObj.(propName).ColorData = newColor; + end + end + catch + % Never mind - ignore (either doesn't have the property or cannot change it) + end + end + end + else % restore transparency in Matlab figure by converting back from the unique RGBs + %Find the transparent patches + wasError = false; + nColors = length(StoredColors); + foundFlags = false(1,nColors); + for objIdx = 1 : nColors + colorsData = StoredColors{objIdx}; + hObj = colorsData{1}; + propName = colorsData{2}; + origColor = colorsData{3}; + newColor = colorsData{4}; + try + %Restore the EPS files patch color + colorID = num2str(round(double(newColor(1:3)') /255,3),'%.3g %.3g %.3g'); %ID for searching + origRGB = num2str(round(double(origColor(1:3)')/255,3),'%.3g %.3g %.3g'); %Replace with original color + origAlpha = num2str(round(double(origColor(end)) /255,3),'%.3g'); %Convert alpha value for EPS + + %Find and replace the RGBA values within the EPS text fstrm + if strcmpi(propName,'Face') + oldStr = sprintf(['\n' colorID ' RC\n']); % ...N\n (removed to fix issue #225) + newStr = sprintf(['\n' origRGB ' RC\n' origAlpha ' .setopacityalpha true\n']); % ...N\n + else %'Edge' + oldStr = sprintf(['\n' colorID ' RC\n']); % ...1 LJ\n (removed to fix issue #225) + newStr = sprintf(['\n' origRGB ' RC\n' origAlpha ' .setopacityalpha true\n']); + end + foundFlags(objIdx) = ~isempty(strfind(fstrm, oldStr)); %#ok + fstrm = strrep(fstrm, oldStr, newStr); + + %Restore the figure object's original color + hObj.(propName).ColorData = origColor; + catch err + % something is wrong - cannot restore transparent color... + if ~wasError + fprintf(2, 'Error maintaining transparency in EPS file: %s\n at %s:%d\n', err.message, err.stack(1).file, err.stack(1).line); + wasError = true; + end + end + end + end +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/read_write_entire_textfile.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/read_write_entire_textfile.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/read_write_entire_textfile.m (revision 27955) @@ -0,0 +1,37 @@ +%READ_WRITE_ENTIRE_TEXTFILE Read or write a whole text file to/from memory +% +% Read or write an entire text file to/from memory, without leaving the +% file open if an error occurs. +% +% Reading: +% fstrm = read_write_entire_textfile(fname) +% Writing: +% read_write_entire_textfile(fname, fstrm) +% +%IN: +% fname - Pathname of text file to be read in. +% fstrm - String to be written to the file, including carriage returns. +% +%OUT: +% fstrm - String read from the file. If an fstrm input is given the +% output is the same as that input. + +function fstrm = read_write_entire_textfile(fname, fstrm) +modes = {'rt', 'wt'}; +writing = nargin > 1; +fh = fopen(fname, modes{1+writing}); +if fh == -1 + error('Unable to open file %s.', fname); +end +try + if writing + fwrite(fh, fstrm, 'char*1'); + else + fstrm = fread(fh, '*char')'; + end +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/user_string.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/user_string.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/user_string.m (revision 27955) @@ -0,0 +1,111 @@ +function string = user_string(string_name, string) +%USER_STRING Get/set a user specific string +% +% Examples: +% string = user_string(string_name) +% isSaved = user_string(string_name, new_string) +% +% Function to get and set a string in a system or user specific file. This +% enables, for example, system specific paths to binaries to be saved. +% +% The specified string will be saved in a file named .txt, +% either in a subfolder named .ignore under this file's folder, or in the +% user's prefdir folder (in case this file's folder is non-writable). +% +% IN: +% string_name - String containing the name of the string required, which +% sets the filename storing the string: .txt +% new_string - The new string to be saved in the .txt file +% +% OUT: +% string - The currently saved string. Default: '' +% isSaved - Boolean indicating whether the save was succesful + +% Copyright (C) Oliver Woodford 2011-2014, Yair Altman 2015- + +% This method of saving paths avoids changing .m files which might be in a +% version control system. Instead it saves the user dependent paths in +% separate files with a .txt extension, which need not be checked in to +% the version control system. Thank you to Jonas Dorn for suggesting this +% approach. + +% 10/01/2013 - Access files in text, not binary mode, as latter can cause +% errors. Thanks to Christian for pointing this out. +% 29/05/2015 - Save file in prefdir if current folder is non-writable (issue #74) +% 09/01/2018 - Fix issue #232: if the string looks like a file/folder path, ensure it actually exists + + if ~ischar(string_name) + error('string_name must be a string.'); + end + % Create the full filename + fname = [string_name '.txt']; + dname = fullfile(fileparts(mfilename('fullpath')), '.ignore'); + file_name = fullfile(dname, fname); + if nargin > 1 + % Set string + if ~ischar(string) + error('new_string must be a string.'); + end + % Make sure the save directory exists + %dname = fileparts(file_name); + if ~exist(dname, 'dir') + % Create the directory + try + if ~mkdir(dname) + string = false; + return + end + catch + string = false; + return + end + % Make it hidden + try + fileattrib(dname, '+h'); + catch + end + end + % Write the file + fid = fopen(file_name, 'wt'); + if fid == -1 + % file cannot be created/updated - use prefdir if file does not already exist + % (if file exists but is simply not writable, don't create a duplicate in prefdir) + if ~exist(file_name,'file') + file_name = fullfile(prefdir, fname); + fid = fopen(file_name, 'wt'); + end + if fid == -1 + string = false; + return; + end + end + try + fprintf(fid, '%s', string); + catch + fclose(fid); + string = false; + return + end + fclose(fid); + string = true; + else + % Get string + fid = fopen(file_name, 'rt'); + if fid == -1 + % file cannot be read, try to read the file in prefdir + file_name = fullfile(prefdir, fname); + fid = fopen(file_name, 'rt'); + if fid == -1 + string = ''; + return + end + end + string = fgetl(fid); + fclose(fid); + + % Fix issue #232: if the string looks like a file/folder path, ensure it actually exists + if ~isempty(string) && any(string=='\' | string=='/') && ~exist(string) %#ok + string = ''; + end + end +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/using_hg2.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/using_hg2.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/export_fig/using_hg2.m (revision 27955) @@ -0,0 +1,36 @@ +%USING_HG2 Determine if the HG2 graphics engine is used +% +% tf = using_hg2(fig) +% +%IN: +% fig - handle to the figure in question. +% +%OUT: +% tf - boolean indicating whether the HG2 graphics engine is being used +% (true) or not (false). + +% 19/06/2015 - Suppress warning in R2015b; cache result for improved performance +% 06/06/2016 - Fixed issue #156 (bad return value in R2016b) + +function tf = using_hg2(fig) + persistent tf_cached + if isempty(tf_cached) + try + if nargin < 1, fig = figure('visible','off'); end + oldWarn = warning('off','MATLAB:graphicsversion:GraphicsVersionRemoval'); + try + % This generates a [supressed] warning in R2015b: + tf = ~graphicsversion(fig, 'handlegraphics'); + catch + tf = ~verLessThan('matlab','8.4'); % =R2014b + end + warning(oldWarn); + catch + tf = false; + end + if nargin < 1, delete(fig); end + tf_cached = tf; + else + tf = tf_cached; + end +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/ffmpeg/install-macosx64.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/ffmpeg/install-macosx64.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/ffmpeg/install-macosx64.sh (revision 27955) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install ffmpeg-1.1.2 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ffmpeg-1.1.2.tar.gz' 'ffmpeg-1.1.2.tar.gz' + +#Untar +tar -zxvf ffmpeg-1.1.2.tar.gz + +#Move ffmpeg into src directory +mv ffmpeg-1.1.2/* src +rm -rf ffmpeg-1.1.2 + +#Configure ffmpeg +cd src + +export CFLAGS=" -arch x86_64" + +./configure --prefix="$ISSM_DIR/externalpackages/ffmpeg/install" --disable-yasm + +#Compile ffmpeg +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/findbugs/README =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/findbugs/README (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/findbugs/README (revision 27955) @@ -0,0 +1,2 @@ +Fingbugs for Java programs. +Downloaded from http://findbugs.sourceforge.net/downloads.html Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/findbugs/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/findbugs/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/findbugs/install.sh (revision 27955) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install findbugs-1.3.9 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/findbugs-1.3.9.tar.gz' 'findbugs-1.3.9.tar.gz' +tar -zxvf findbugs-1.3.9.tar.gz + +mv findbugs-1.3.9/* install +rm -rf findbugs-1.3.9 Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/fisoc/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/fisoc/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/fisoc/install.sh (revision 27955) @@ -0,0 +1,3 @@ +#!/bin/bash + +git clone https://github.com/RupertGladstone/FISOC.git Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/flaim/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/flaim/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/flaim/install.sh (revision 27955) @@ -0,0 +1,8 @@ +#!/bin/bash +set -eu + +#Erase symlink +rm -rf install + +#symlink to flaim directory +ln -s /home/jschierm/flaim/svn/trunk ./install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/freetype/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/freetype/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/freetype/install.sh (revision 27955) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf freetype-2.5.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/freetype-2.5.0.tar.gz' 'freetype-2.5.0.tar.gz' + +#Untar +tar -zxvf freetype-2.5.0.tar.gz + +#Move freetype into src directory +mv freetype-2.5.0/* src +rm -rf freetype-2.5.0 + +#Configure freetype +cd src +sudo ./configure + +#Compile and install freetype +if [ $# -eq 0 ]; then + sudo make +else + sudo make -j $1 +fi +sudo make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/fti/Makefile =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/fti/Makefile (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/fti/Makefile (revision 27955) @@ -0,0 +1,90 @@ +## * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * +##* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * +##======================================================================= +##Copyright (C) 2010-2013 Leonardo A. BAUTISTA GOMEZ +##This program is free software; you can redistribute it and/or modify +##it under the terms of the GNU General Public License (GPL) as published +##of the License, or (at your option) any later version. +## +##This program is distributed in the hope that it will be useful, +##but WITHOUT ANY WARRANTY; without even the implied warranty of +##MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +##GNU General Public License for more details. +## +##To read the license please visit http://www.gnu.org/copyleft/gpl.html +##======================================================================= + +##======================================================================= +## PLEASE SET THESE VARIABLES BEFORE COMPILING +##======================================================================= + +FTIPATH = $(ISSM_DIR)/externalpackages/fti/install +MPIPATH = $(ISSM_DIR)/externalpackages/mpich/install + +##======================================================================= +## DIRECTORY TREE +##======================================================================= + +LIB = lib +OBJ = obj +SRC = src +DOC = doc +INC = include + +##======================================================================= +## COMPILERS +##======================================================================= + +CC = gcc +MPICC = mpicc + +##======================================================================= +## FLAGS +##======================================================================= + +FTIFLAGS = -fPIC -g -Iinclude/ -c +MPIFLAGS = -I$(MPIPATH)/include -L$(MPIPATH)/lib -lmpich -lpmpich + +##======================================================================= +## TARGETS +##======================================================================= + + +OBJS = $(OBJ)/galois.o $(OBJ)/jerasure.o $(OBJ)/dictionary.o $(OBJ)/iniparser.o \ + $(OBJ)/recover.o $(OBJ)/tools.o $(OBJ)/checkpoint.o $(OBJ)/topo.o \ + $(OBJ)/api.o + +SHARED = libfti.so +STATIC = libfti.a + +all: $(SHARED) $(STATIC) + +doc: + doxygen $(DOC)/Doxyfile + +$(OBJ)/%.o: $(SRC)/%.c + $(MPICC) $(FTIFLAGS) $< -o $@ + +$(SHARED): $(OBJS) + $(CC) $(MPIFLAGS) -shared -o $(LIB)/$(SHARED) $(OBJS) -lc + +$(STATIC): $(OBJS) + $(AR) -cvq $(LIB)/$(STATIC) $(OBJS) +install: + if [ ! -d "$(FTIPATH)/FTI" ]; then mkdir $(FTIPATH)/FTI; fi + if [ ! -d "$(FTIPATH)/FTI/$(LIB)" ]; then mkdir $(FTIPATH)/FTI/$(LIB); fi + if [ ! -d "$(FTIPATH)/FTI/$(INC)" ]; then mkdir $(FTIPATH)/FTI/$(INC); fi + rm -f $(FTIPATH)/FTI/$(LIB)/* $(FTIPATH)/FTI/$(INC)/* + cp $(INC)/* $(FTIPATH)/FTI/$(INC)/ + cp $(LIB)/* $(FTIPATH)/FTI/$(LIB)/ + +uninstall: + rm -f $(FTIPATH)/FTI/$(LIB)/* $(FTIPATH)/FTI/$(INC)/* + if [ -d "$(FTIPATH)/FTI/$(LIB)" ]; then rmdir $(FTIPATH)/FTI/$(LIB); fi + if [ -d "$(FTIPATH)/FTI/$(INC)" ]; then rmdir $(FTIPATH)/FTI/$(INC); fi + if [ -d "$(FTIPATH)/FTI" ]; then rmdir $(FTIPATH)/FTI; fi + +clean: + rm -f $(OBJ)/* $(LIB)/* + +.PHONY: $(SHARED) $(STATIC) doc install uninstall clean Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/fti/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/fti/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/fti/install.sh (revision 27955) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install fti-0.9.2 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/fti-0.9.2.tgz' 'fti-0.9.2.tgz' + +#Untar +tar -zxvf fti-0.9.2.tgz + +#Move mpich into src directory +mv fti/* install +rm -rf fti + +#Configure mpich +cd install +cp ../Makefile . + +#Compile mpich (this new version supports parallel make) +make +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/1.10/linux/debian/frmts/wms/dataset.cpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/1.10/linux/debian/frmts/wms/dataset.cpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/1.10/linux/debian/frmts/wms/dataset.cpp (revision 27955) @@ -0,0 +1,676 @@ +/****************************************************************************** + * $Id: dataset.cpp 25776 2013-03-20 20:46:48Z rouault $ + * + * Project: WMS Client Driver + * Purpose: Implementation of Dataset and RasterBand classes for WMS + * and other similar services. + * Author: Adam Nowacki, nowak@xpam.de + * + ****************************************************************************** + * Copyright (c) 2007, Adam Nowacki + * + * Permission is hereby granted, free of charge, to any person obtaining a + * copy of this software and associated documentation files (the "Software"), + * to deal in the Software without restriction, including without limitation + * the rights to use, copy, modify, merge, publish, distribute, sublicense, + * and/or sell copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included + * in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS + * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL + * THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + * DEALINGS IN THE SOFTWARE. + **************************************************************************** + * + * dataset.cpp: + * Initialization of the GDALWMSdriver, parsing the XML configuration file, + * instantiation of the minidrivers and accessors used by minidrivers + * + ***************************************************************************/ + + +#include "stdinc.h" + +GDALWMSDataset::GDALWMSDataset() { + m_mini_driver = 0; + m_cache = 0; + m_hint.m_valid = false; + m_data_type = GDT_Byte; + m_clamp_requests = true; + m_unsafeSsl = false; + m_data_window.m_sx = -1; + nBands = 0; + m_default_block_size_x = 1024; + m_default_block_size_y = 1024; + m_bNeedsDataWindow = TRUE; + m_default_tile_count_x = 1; + m_default_tile_count_y = 1; + m_default_overview_count = -1; + m_zeroblock_on_serverexceptions = 0; + m_poColorTable = NULL; +} + +GDALWMSDataset::~GDALWMSDataset() { + if (m_mini_driver) delete m_mini_driver; + if (m_cache) delete m_cache; + if (m_poColorTable) delete m_poColorTable; +} + +CPLErr GDALWMSDataset::Initialize(CPLXMLNode *config) { + CPLErr ret = CE_None; + + char* pszXML = CPLSerializeXMLTree( config ); + if (pszXML) + { + m_osXML = pszXML; + CPLFree(pszXML); + } + + // Initialize the minidriver, which can set parameters for the dataset using member functions + CPLXMLNode *service_node = CPLGetXMLNode(config, "Service"); + if (service_node != NULL) + { + const CPLString service_name = CPLGetXMLValue(service_node, "name", ""); + if (!service_name.empty()) + { + GDALWMSMiniDriverManager *const mdm = GetGDALWMSMiniDriverManager(); + GDALWMSMiniDriverFactory *const mdf = mdm->Find(service_name); + if (mdf != NULL) + { + m_mini_driver = mdf->New(); + m_mini_driver->m_parent_dataset = this; + if (m_mini_driver->Initialize(service_node) == CE_None) + { + m_mini_driver_caps.m_capabilities_version = -1; + m_mini_driver->GetCapabilities(&m_mini_driver_caps); + if (m_mini_driver_caps.m_capabilities_version == -1) + { + CPLError(CE_Failure, CPLE_AppDefined, "GDALWMS: Internal error, mini-driver capabilities version not set."); + ret = CE_Failure; + } + } + else + { + delete m_mini_driver; + m_mini_driver = NULL; + + CPLError(CE_Failure, CPLE_AppDefined, "GDALWMS: Failed to initialize minidriver."); + ret = CE_Failure; + } + } + else + { + CPLError(CE_Failure, CPLE_AppDefined, + "GDALWMS: No mini-driver registered for '%s'.", service_name.c_str()); + ret = CE_Failure; + } + } + else + { + CPLError(CE_Failure, CPLE_AppDefined, "GDALWMS: No Service specified."); + ret = CE_Failure; + } + } + else + { + CPLError(CE_Failure, CPLE_AppDefined, "GDALWMS: No Service specified."); + ret = CE_Failure; + } + + + /* + Parameters that could be set by minidriver already, based on server side information. + If the size is set, minidriver has done this already + A "server" side minidriver needs to set at least: + - Blocksize (x and y) + - Clamp flag (defaults to true) + - DataWindow + - Band Count + - Data Type + It should also initialize and register the bands and overviews. + */ + + if (m_data_window.m_sx<1) + { + int nOverviews = 0; + + if (ret == CE_None) + { + m_block_size_x = atoi(CPLGetXMLValue(config, "BlockSizeX", CPLString().Printf("%d", m_default_block_size_x))); + m_block_size_y = atoi(CPLGetXMLValue(config, "BlockSizeY", CPLString().Printf("%d", m_default_block_size_y))); + if (m_block_size_x <= 0 || m_block_size_y <= 0) + { + CPLError( CE_Failure, CPLE_AppDefined, "GDALWMS: Invalid value in BlockSizeX or BlockSizeY" ); + ret = CE_Failure; + } + } + + if (ret == CE_None) + { + m_clamp_requests = StrToBool(CPLGetXMLValue(config, "ClampRequests", "true")); + if (m_clamp_requests<0) + { + CPLError(CE_Failure, CPLE_AppDefined, "GDALWMS: Invalid value of ClampRequests, true/false expected."); + ret = CE_Failure; + } + } + + if (ret == CE_None) + { + CPLXMLNode *data_window_node = CPLGetXMLNode(config, "DataWindow"); + if (data_window_node == NULL && m_bNeedsDataWindow) + { + CPLError(CE_Failure, CPLE_AppDefined, "GDALWMS: DataWindow missing."); + ret = CE_Failure; + } + else + { + CPLString osDefaultX0, osDefaultX1, osDefaultY0, osDefaultY1; + CPLString osDefaultTileCountX, osDefaultTileCountY, osDefaultTileLevel; + CPLString osDefaultOverviewCount; + osDefaultX0.Printf("%.8f", m_default_data_window.m_x0); + osDefaultX1.Printf("%.8f", m_default_data_window.m_x1); + osDefaultY0.Printf("%.8f", m_default_data_window.m_y0); + osDefaultY1.Printf("%.8f", m_default_data_window.m_y1); + osDefaultTileCountX.Printf("%d", m_default_tile_count_x); + osDefaultTileCountY.Printf("%d", m_default_tile_count_y); + if (m_default_data_window.m_tlevel >= 0) + osDefaultTileLevel.Printf("%d", m_default_data_window.m_tlevel); + if (m_default_overview_count >= 0) + osDefaultOverviewCount.Printf("%d", m_default_overview_count); + const char *overview_count = CPLGetXMLValue(config, "OverviewCount", osDefaultOverviewCount); + const char *ulx = CPLGetXMLValue(data_window_node, "UpperLeftX", osDefaultX0); + const char *uly = CPLGetXMLValue(data_window_node, "UpperLeftY", osDefaultY0); + const char *lrx = CPLGetXMLValue(data_window_node, "LowerRightX", osDefaultX1); + const char *lry = CPLGetXMLValue(data_window_node, "LowerRightY", osDefaultY1); + const char *sx = CPLGetXMLValue(data_window_node, "SizeX", ""); + const char *sy = CPLGetXMLValue(data_window_node, "SizeY", ""); + const char *tx = CPLGetXMLValue(data_window_node, "TileX", "0"); + const char *ty = CPLGetXMLValue(data_window_node, "TileY", "0"); + const char *tlevel = CPLGetXMLValue(data_window_node, "TileLevel", osDefaultTileLevel); + const char *str_tile_count_x = CPLGetXMLValue(data_window_node, "TileCountX", osDefaultTileCountX); + const char *str_tile_count_y = CPLGetXMLValue(data_window_node, "TileCountY", osDefaultTileCountY); + const char *y_origin = CPLGetXMLValue(data_window_node, "YOrigin", "default"); + + if (ret == CE_None) + { + if ((ulx[0] != '\0') && (uly[0] != '\0') && (lrx[0] != '\0') && (lry[0] != '\0')) + { + m_data_window.m_x0 = atof(ulx); + m_data_window.m_y0 = atof(uly); + m_data_window.m_x1 = atof(lrx); + m_data_window.m_y1 = atof(lry); + } + else + { + CPLError(CE_Failure, CPLE_AppDefined, + "GDALWMS: Mandatory elements of DataWindow missing: UpperLeftX, UpperLeftY, LowerRightX, LowerRightY."); + ret = CE_Failure; + } + } + + m_data_window.m_tlevel = atoi(tlevel); + + if (ret == CE_None) + { + if ((sx[0] != '\0') && (sy[0] != '\0')) + { + m_data_window.m_sx = atoi(sx); + m_data_window.m_sy = atoi(sy); + } + else if ((tlevel[0] != '\0') && (str_tile_count_x[0] != '\0') && (str_tile_count_y[0] != '\0')) + { + int tile_count_x = atoi(str_tile_count_x); + int tile_count_y = atoi(str_tile_count_y); + m_data_window.m_sx = tile_count_x * m_block_size_x * (1 << m_data_window.m_tlevel); + m_data_window.m_sy = tile_count_y * m_block_size_y * (1 << m_data_window.m_tlevel); + } + else + { + CPLError(CE_Failure, CPLE_AppDefined, + "GDALWMS: Mandatory elements of DataWindow missing: SizeX, SizeY."); + ret = CE_Failure; + } + } + if (ret == CE_None) + { + if ((tx[0] != '\0') && (ty[0] != '\0')) + { + m_data_window.m_tx = atoi(tx); + m_data_window.m_ty = atoi(ty); + } + else + { + CPLError(CE_Failure, CPLE_AppDefined, + "GDALWMS: Mandatory elements of DataWindow missing: TileX, TileY."); + ret = CE_Failure; + } + } + + if (ret == CE_None) + { + if (overview_count[0] != '\0') + { + nOverviews = atoi(overview_count); + } + else if (tlevel[0] != '\0') + { + nOverviews = m_data_window.m_tlevel; + } + else + { + const int min_overview_size = MAX(32, MIN(m_block_size_x, m_block_size_y)); + double a = log(static_cast(MIN(m_data_window.m_sx, m_data_window.m_sy))) / log(2.0) + - log(static_cast(min_overview_size)) / log(2.0); + nOverviews = MAX(0, MIN(static_cast(ceil(a)), 32)); + } + } + if (ret == CE_None) + { + CPLString y_origin_str = y_origin; + if (y_origin_str == "top") { + m_data_window.m_y_origin = GDALWMSDataWindow::TOP; + } else if (y_origin_str == "bottom") { + m_data_window.m_y_origin = GDALWMSDataWindow::BOTTOM; + } else if (y_origin_str == "default") { + m_data_window.m_y_origin = GDALWMSDataWindow::DEFAULT; + } else { + CPLError(CE_Failure, CPLE_AppDefined, "GDALWMS: DataWindow YOrigin must be set to " + "one of 'default', 'top', or 'bottom', not '%s'.", y_origin_str.c_str()); + ret = CE_Failure; + } + } + } + } + + if (ret == CE_None) + { + if (nBands<1) + nBands=atoi(CPLGetXMLValue(config,"BandsCount","3")); + if (nBands<1) + { + CPLError(CE_Failure, CPLE_AppDefined, + "GDALWMS: Bad number of bands."); + ret = CE_Failure; + } + } + + if (ret == CE_None) + { + const char *data_type = CPLGetXMLValue(config, "DataType", "Byte"); + m_data_type = GDALGetDataTypeByName( data_type ); + if ( m_data_type == GDT_Unknown || m_data_type >= GDT_TypeCount ) + { + CPLError( CE_Failure, CPLE_AppDefined, + "GDALWMS: Invalid value in DataType. Data type \"%s\" is not supported.", data_type ); + ret = CE_Failure; + } + } + + // Initialize the bands and the overviews. Assumes overviews are powers of two + if (ret == CE_None) + { + nRasterXSize = m_data_window.m_sx; + nRasterYSize = m_data_window.m_sy; + + if (!GDALCheckDatasetDimensions(nRasterXSize, nRasterYSize) || + !GDALCheckBandCount(nBands, TRUE)) + { + return CE_Failure; + } + + GDALColorInterp default_color_interp[4][4] = { + { GCI_GrayIndex, GCI_Undefined, GCI_Undefined, GCI_Undefined }, + { GCI_GrayIndex, GCI_AlphaBand, GCI_Undefined, GCI_Undefined }, + { GCI_RedBand, GCI_GreenBand, GCI_BlueBand, GCI_Undefined }, + { GCI_RedBand, GCI_GreenBand, GCI_BlueBand, GCI_AlphaBand } + }; + for (int i = 0; i < nBands; ++i) + { + GDALColorInterp color_interp = (nBands <= 4 && i <= 3 ? default_color_interp[nBands - 1][i] : GCI_Undefined); + GDALWMSRasterBand *band = new GDALWMSRasterBand(this, i, 1.0); + band->m_color_interp = color_interp; + SetBand(i + 1, band); + double scale = 0.5; + for (int j = 0; j < nOverviews; ++j) + { + band->AddOverview(scale); + band->m_color_interp = color_interp; + scale *= 0.5; + } + } + } + } + + // UserPwd + const char *pszUserPwd = CPLGetXMLValue(config, "UserPwd", ""); + if (pszUserPwd[0] != '\0') + m_osUserPwd = pszUserPwd; + + const char *pszUserAgent = CPLGetXMLValue(config, "UserAgent", ""); + if (pszUserAgent[0] != '\0') + m_osUserAgent = pszUserAgent; + + const char *pszReferer = CPLGetXMLValue(config, "Referer", ""); + if (pszReferer[0] != '\0') + m_osReferer = pszReferer; + + if (ret == CE_None) { + const char *pszHttpZeroBlockCodes = CPLGetXMLValue(config, "ZeroBlockHttpCodes", ""); + if(pszHttpZeroBlockCodes[0] == '\0') { + m_http_zeroblock_codes.push_back(204); + } else { + char **kv = CSLTokenizeString2(pszHttpZeroBlockCodes,",",CSLT_HONOURSTRINGS); + int nCount = CSLCount(kv); + for(int i=0; iInitialize(cache_node) != CE_None) { + delete m_cache; + m_cache = NULL; + CPLError(CE_Failure, CPLE_AppDefined, "GDALWMS: Failed to initialize cache."); + ret = CE_Failure; + } + } + } + + if (ret == CE_None) { + const int v = StrToBool(CPLGetXMLValue(config, "UnsafeSSL", "false")); + if (v == -1) { + CPLError(CE_Failure, CPLE_AppDefined, "GDALWMS: Invalid value of UnsafeSSL: true or false expected."); + ret = CE_Failure; + } else { + m_unsafeSsl = v; + } + } + + if (ret == CE_None) { + /* If we dont have projection already set ask mini-driver. */ + if (!m_projection.size()) { + const char *proj = m_mini_driver->GetProjectionInWKT(); + if (proj != NULL) { + m_projection = proj; + } + } + } + + return ret; +} + +CPLErr GDALWMSDataset::IRasterIO(GDALRWFlag rw, int x0, int y0, int sx, int sy, void *buffer, int bsx, int bsy, GDALDataType bdt, int band_count, int *band_map, int pixel_space, int line_space, int band_space) { + CPLErr ret; + + if (rw != GF_Read) return CE_Failure; + if (buffer == NULL) return CE_Failure; + if ((sx == 0) || (sy == 0) || (bsx == 0) || (bsy == 0) || (band_count == 0)) return CE_None; + + m_hint.m_x0 = x0; + m_hint.m_y0 = y0; + m_hint.m_sx = sx; + m_hint.m_sy = sy; + m_hint.m_overview = -1; + m_hint.m_valid = true; + // printf("[%p] GDALWMSDataset::IRasterIO(x0: %d, y0: %d, sx: %d, sy: %d, bsx: %d, bsy: %d, band_count: %d, band_map: %p)\n", this, x0, y0, sx, sy, bsx, bsy, band_count, band_map); + ret = GDALDataset::IRasterIO(rw, x0, y0, sx, sy, buffer, bsx, bsy, bdt, band_count, band_map, pixel_space, line_space, band_space); + m_hint.m_valid = false; + + return ret; +} + +const char *GDALWMSDataset::GetProjectionRef() { + return m_projection.c_str(); +} + +CPLErr GDALWMSDataset::SetProjection(const char *proj) { + return CE_Failure; +} + +CPLErr GDALWMSDataset::GetGeoTransform(double *gt) { + gt[0] = m_data_window.m_x0; + gt[1] = (m_data_window.m_x1 - m_data_window.m_x0) / static_cast(m_data_window.m_sx); + gt[2] = 0.0; + gt[3] = m_data_window.m_y0; + gt[4] = 0.0; + gt[5] = (m_data_window.m_y1 - m_data_window.m_y0) / static_cast(m_data_window.m_sy); + return CE_None; +} + +CPLErr GDALWMSDataset::SetGeoTransform(double *gt) { + return CE_Failure; +} + +const GDALWMSDataWindow *GDALWMSDataset::WMSGetDataWindow() const { + return &m_data_window; +} + +void GDALWMSDataset::WMSSetBlockSize(int x, int y) { + m_block_size_x=x; + m_block_size_y=y; +} + +void GDALWMSDataset::WMSSetRasterSize(int x, int y) { + nRasterXSize=x; + nRasterYSize=y; +} + +void GDALWMSDataset::WMSSetBandsCount(int count) { + nBands=count; +} + +void GDALWMSDataset::WMSSetClamp(bool flag=true) { + m_clamp_requests=flag; +} + +void GDALWMSDataset::WMSSetDataType(GDALDataType type) { + m_data_type=type; +} + +void GDALWMSDataset::WMSSetDataWindow(GDALWMSDataWindow &window) { + m_data_window=window; +} + +void GDALWMSDataset::WMSSetDefaultBlockSize(int x, int y) { + m_default_block_size_x=x; + m_default_block_size_y=y; +} + +void GDALWMSDataset::WMSSetDefaultDataWindowCoordinates(double x0, double y0, double x1, double y1) +{ + m_default_data_window.m_x0 = x0; + m_default_data_window.m_y0 = y0; + m_default_data_window.m_x1 = x1; + m_default_data_window.m_y1 = y1; +} + +void GDALWMSDataset::WMSSetDefaultTileCount(int tilecountx, int tilecounty) +{ + m_default_tile_count_x = tilecountx; + m_default_tile_count_y = tilecounty; +} + +void GDALWMSDataset::WMSSetDefaultTileLevel(int tlevel) +{ + m_default_data_window.m_tlevel = tlevel; +} + +void GDALWMSDataset::WMSSetDefaultOverviewCount(int overview_count) +{ + m_default_overview_count = overview_count; +} + +void GDALWMSDataset::WMSSetNeedsDataWindow(int flag) +{ + m_bNeedsDataWindow = flag; +} + +static void list2vec(std::vector &v,const char *pszList) +{ + if ((pszList==NULL)||(pszList[0]==0)) return; + char **papszTokens=CSLTokenizeString2(pszList," \t\n\r", + CSLT_STRIPLEADSPACES|CSLT_STRIPENDSPACES); + v.clear(); + for (int i=0;iAdviseRead(x0, y0, sx, sy, bsx, bsy, bdt, options); +} + +const char *GDALWMSDataset::GetMetadataItem( const char * pszName, + const char * pszDomain ) +{ + if( pszName != NULL && EQUAL(pszName, "XML") && + pszDomain != NULL && EQUAL(pszDomain, "WMS") ) + { + return (m_osXML.size()) ? m_osXML.c_str() : NULL; + } + + return GDALPamDataset::GetMetadataItem(pszName, pszDomain); +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/1.10/linux/debian/ogr/ogrsf_frmts/vfk/vfkfeature.cpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/1.10/linux/debian/ogr/ogrsf_frmts/vfk/vfkfeature.cpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/1.10/linux/debian/ogr/ogrsf_frmts/vfk/vfkfeature.cpp (revision 27955) @@ -0,0 +1,560 @@ +/****************************************************************************** + * $Id: vfkfeature.cpp 25702 2013-03-07 17:17:54Z martinl $ + * + * Project: VFK Reader - Feature definition + * Purpose: Implements IVFKFeature/VFKFeature class. + * Author: Martin Landa, landa.martin gmail.com + * + ****************************************************************************** + * Copyright (c) 2009-2010, 2012-2013, Martin Landa + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, copy, + * modify, merge, publish, distribute, sublicense, and/or sell copies + * of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + * SOFTWARE. + ****************************************************************************/ + +#include "vfkreader.h" +#include "vfkreaderp.h" + +#include "cpl_conv.h" +#include "cpl_error.h" + +/*! + \brief IVFKFeature constructor + + \param poDataBlock pointer to VFKDataBlock instance +*/ +IVFKFeature::IVFKFeature(IVFKDataBlock *poDataBlock) +{ + CPLAssert(NULL != poDataBlock); + m_poDataBlock = poDataBlock; + + m_nFID = -1; + m_nGeometryType = poDataBlock->GetGeometryType(); + m_bGeometry = FALSE; + m_bValid = FALSE; + m_paGeom = NULL; +} + +/*! + \brief IVFKFeature destructor +*/ +IVFKFeature::~IVFKFeature() +{ + if (m_paGeom) + delete m_paGeom; + + m_poDataBlock = NULL; +} + +/*! + \brief Set feature geometry type +*/ +void IVFKFeature::SetGeometryType(OGRwkbGeometryType nGeomType) +{ + m_nGeometryType = nGeomType; +} + +/*! + \brief Set feature id + + FID: 0 for next, -1 for same + + \param nFID feature id +*/ +void IVFKFeature::SetFID(long nFID) +{ + if (m_nFID > 0) { + m_nFID = nFID; + } + else { + m_nFID = m_poDataBlock->GetFeatureCount() + 1; + } +} + +/*! + \brief Set feature geometry + + Also checks if given geometry is valid + + \param poGeom pointer to OGRGeometry + + \return TRUE on valid feature or otherwise FALSE +*/ +bool IVFKFeature::SetGeometry(OGRGeometry *poGeom) +{ + m_bGeometry = TRUE; + + delete m_paGeom; + m_paGeom = NULL; + m_bValid = TRUE; + + if (!poGeom) { + return m_bValid; + } + + /* check empty geometries */ + if (m_nGeometryType == wkbNone && poGeom->IsEmpty()) { + CPLDebug("OGR-VFK", "%s: empty geometry fid = %ld", + m_poDataBlock->GetName(), m_nFID); + m_bValid = FALSE; + } + + /* check coordinates */ + if (m_nGeometryType == wkbPoint) { + double x, y; + x = ((OGRPoint *) poGeom)->getX(); + y = ((OGRPoint *) poGeom)->getY(); + if (x > -430000 || x < -910000 || + y > -930000 || y < -1230000) { + CPLDebug("OGR-VFK", "%s: invalid point fid = %ld", + m_poDataBlock->GetName(), m_nFID); + m_bValid = FALSE; + } + } + + /* check degenerated linestrings */ + if (m_nGeometryType == wkbLineString && + ((OGRLineString *) poGeom)->getNumPoints() < 2) { + CPLDebug("OGR-VFK", "%s: invalid linestring fid = %ld", + m_poDataBlock->GetName(), m_nFID); + m_bValid = FALSE; + } + + /* check degenerated polygons */ + if (m_nGeometryType == wkbPolygon) { + OGRLinearRing *poRing; + poRing = ((OGRPolygon *) poGeom)->getExteriorRing(); + if (!poRing || poRing->getNumPoints() < 3) { + CPLDebug("OGR-VFK", "%s: invalid polygon fid = %ld", + m_poDataBlock->GetName(), m_nFID); + m_bValid = FALSE; + } + } + + if (m_bValid) + m_paGeom = (OGRGeometry *) poGeom->clone(); /* make copy */ + + return m_bValid; +} + +/*! + \brief Get feature geometry + + \return pointer to OGRGeometry or NULL on error +*/ +OGRGeometry *IVFKFeature::GetGeometry() +{ + if (m_nGeometryType != wkbNone && !m_bGeometry) + LoadGeometry(); + + return m_paGeom; +} + + +/*! + \brief Load geometry + + \return TRUE on success or FALSE on failure +*/ +bool IVFKFeature::LoadGeometry() +{ + const char *pszName; + CPLString osSQL; + + if (m_bGeometry) + return TRUE; + + pszName = m_poDataBlock->GetName(); + + if (EQUAL (pszName, "SOBR") || + EQUAL (pszName, "OBBP") || + EQUAL (pszName, "SPOL") || + EQUAL (pszName, "OB") || + EQUAL (pszName, "OP") || + EQUAL (pszName, "OBPEJ")) { + /* -> wkbPoint */ + + return LoadGeometryPoint(); + } + else if (EQUAL (pszName, "SBP")) { + /* -> wkbLineString */ + return LoadGeometryLineStringSBP(); + } + else if (EQUAL (pszName, "HP") || + EQUAL (pszName, "DPM")) { + /* -> wkbLineString */ + return LoadGeometryLineStringHP(); + } + else if (EQUAL (pszName, "PAR") || + EQUAL (pszName, "BUD")) { + /* -> wkbPolygon */ + return LoadGeometryPolygon(); + } + + return FALSE; +} + +/*! + \brief VFKFeature constructor + + \param poDataBlock pointer to VFKDataBlock instance +*/ +VFKFeature::VFKFeature(IVFKDataBlock *poDataBlock, long iFID) : IVFKFeature(poDataBlock) +{ + m_nFID = iFID; + m_propertyList.assign(poDataBlock->GetPropertyCount(), VFKProperty()); + CPLAssert(size_t (poDataBlock->GetPropertyCount()) == m_propertyList.size()); +} + +/*! + \brief Set feature properties + + \param pszLine pointer to line containing feature definition + + \return TRUE on success or FALSE on failure +*/ +bool VFKFeature::SetProperties(const char *pszLine) +{ + unsigned int iIndex, nLength; + const char *poChar, *poProp; + char* pszProp; + bool inString; + + std::vector oPropList; + + pszProp = NULL; + + for (poChar = pszLine; *poChar != '\0' && *poChar != ';'; poChar++) + /* skip data block name */ + ; + if( *poChar == '\0' ) + return FALSE; /* nothing to read */ + + poChar++; /* skip ';' after data block name*/ + + /* read properties into the list */ + poProp = poChar; + iIndex = nLength = 0; + inString = FALSE; + while(*poChar != '\0') { + if (*poChar == '"' && + (*(poChar-1) == ';' || *(poChar+1) == ';' || *(poChar+1) == '\0')) { + poChar++; /* skip '"' */ + inString = inString ? FALSE : TRUE; + if (inString) { + poProp = poChar; + if (*poChar == '"') { + poChar++; + inString = FALSE; + } + } + if (*poChar == '\0') + break; + } + if (*poChar == ';' && !inString) { + pszProp = (char *) CPLRealloc(pszProp, nLength + 1); + if (nLength > 0) + strncpy(pszProp, poProp, nLength); + pszProp[nLength] = '\0'; + oPropList.push_back(pszProp); + iIndex++; + poProp = ++poChar; + nLength = 0; + } + else { + poChar++; + nLength++; + } + } + /* append last property */ + if (inString) { + nLength--; /* ignore '"' */ + } + pszProp = (char *) CPLRealloc(pszProp, nLength + 1); + if (nLength > 0) + strncpy(pszProp, poProp, nLength); + pszProp[nLength] = '\0'; + oPropList.push_back(pszProp); + + /* set properties from the list */ + if (oPropList.size() != (size_t) m_poDataBlock->GetPropertyCount()) { + /* try to read also invalid records */ + CPLDebug("OGR-VFK", "%s: invalid number of properties %d should be %d", + m_poDataBlock->GetName(), + (int) oPropList.size(), m_poDataBlock->GetPropertyCount()); + return FALSE; + } + iIndex = 0; + for (std::vector::iterator ip = oPropList.begin(); + ip != oPropList.end(); ++ip) { + SetProperty(iIndex++, (*ip).c_str()); + } + + /* set fid + if (EQUAL(m_poDataBlock->GetName(), "SBP")) { + GUIntBig id; + const VFKProperty *poVfkProperty; + + poVfkProperty = GetProperty("PORADOVE_CISLO_BODU"); + if (poVfkProperty) + { + id = strtoul(poVfkProperty->GetValueS(), NULL, 0); + if (id == 1) + SetFID(0); + else + SetFID(-1); + } + } + else { + SetFID(0); + } + */ + CPLFree(pszProp); + + return TRUE; +} + +/*! + \brief Set feature property + + \param iIndex property index + \param pszValue property value + + \return TRUE on success + \return FALSE on failure +*/ +bool VFKFeature::SetProperty(int iIndex, const char *pszValue) +{ + if (iIndex < 0 || iIndex >= m_poDataBlock->GetPropertyCount() || + size_t(iIndex) >= m_propertyList.size()) + return FALSE; + + if (strlen(pszValue) < 1) + m_propertyList[iIndex] = VFKProperty(); + else { + OGRFieldType fType; + + const char *pszEncoding; + char *pszValueEnc; + + fType = m_poDataBlock->GetProperty(iIndex)->GetType(); + switch (fType) { + case OFTInteger: + m_propertyList[iIndex] = VFKProperty(atoi(pszValue)); + break; + case OFTReal: + m_propertyList[iIndex] = VFKProperty(CPLAtof(pszValue)); + break; + default: + pszEncoding = m_poDataBlock->GetProperty(iIndex)->GetEncoding(); + if (pszEncoding) { + pszValueEnc = CPLRecode(pszValue, pszEncoding, + CPL_ENC_UTF8); + m_propertyList[iIndex] = VFKProperty(pszValueEnc); + CPLFree(pszValueEnc); + } + else { + m_propertyList[iIndex] = VFKProperty(pszValue); + } + break; + } + } + return TRUE; +} + +/*! + \brief Get property value by index + + \param iIndex property index + + \return property value + \return NULL on error +*/ +const VFKProperty *VFKFeature::GetProperty(int iIndex) const +{ + if (iIndex < 0 || iIndex >= m_poDataBlock->GetPropertyCount() || + size_t(iIndex) >= m_propertyList.size()) + return NULL; + + const VFKProperty* poProperty = &m_propertyList[iIndex]; + return poProperty; +} + +/*! + \brief Get property value by name + + \param pszName property name + + \return property value + \return NULL on error +*/ +const VFKProperty *VFKFeature::GetProperty(const char *pszName) const +{ + return GetProperty(m_poDataBlock->GetPropertyIndex(pszName)); +} + +/*! + \brief Load geometry (point layers) + + \todo Really needed? + + \return TRUE on success + \return FALSE on failure +*/ +bool VFKFeature::LoadGeometryPoint() +{ + double x, y; + int i_idxX, i_idxY; + + i_idxY = m_poDataBlock->GetPropertyIndex("SOURADNICE_Y"); + i_idxX = m_poDataBlock->GetPropertyIndex("SOURADNICE_X"); + if (i_idxY < 0 || i_idxX < 0) + return FALSE; + + x = -1.0 * GetProperty(i_idxY)->GetValueD(); + y = -1.0 * GetProperty(i_idxX)->GetValueD(); + OGRPoint pt(x, y); + SetGeometry(&pt); + + return TRUE; +} + +/*! + \brief Load geometry (linestring SBP layer) + + \todo Really needed? + + \return TRUE on success or FALSE on failure +*/ +bool VFKFeature::LoadGeometryLineStringSBP() +{ + int id, idxId, idxBp_Id, idxPCB, ipcb; + + VFKDataBlock *poDataBlockPoints; + VFKFeature *poPoint, *poLine; + + OGRLineString OGRLine; + + poDataBlockPoints = (VFKDataBlock *) m_poDataBlock->GetReader()->GetDataBlock("SOBR"); + if (!poDataBlockPoints) + return FALSE; + + idxId = poDataBlockPoints->GetPropertyIndex("ID"); + idxBp_Id = m_poDataBlock->GetPropertyIndex("BP_ID"); + idxPCB = m_poDataBlock->GetPropertyIndex("PORADOVE_CISLO_BODU"); + if (idxId < 0 || idxBp_Id < 0 || idxPCB < 0) + return false; + + poLine = this; + while (TRUE) + { + id = poLine->GetProperty(idxBp_Id)->GetValueI(); + ipcb = poLine->GetProperty(idxPCB)->GetValueI(); + if (OGRLine.getNumPoints() > 0 && ipcb == 1) + { + m_poDataBlock->GetPreviousFeature(); /* push back */ + break; + } + + poPoint = poDataBlockPoints->GetFeature(idxId, id); + if (!poPoint) + { + continue; + } + OGRPoint *pt = (OGRPoint *) poPoint->GetGeometry(); + OGRLine.addPoint(pt); + + poLine = (VFKFeature *) m_poDataBlock->GetNextFeature(); + if (!poLine) + break; + }; + + OGRLine.setCoordinateDimension(2); /* force 2D */ + SetGeometry(&OGRLine); + + /* reset reading */ + poDataBlockPoints->ResetReading(); + + return TRUE; +} + +/*! + \brief Load geometry (linestring HP/DPM layer) + + \todo Really needed? + + \return TRUE on success or FALSE on failure +*/ +bool VFKFeature::LoadGeometryLineStringHP() +{ + int id, idxId, idxHp_Id; + VFKDataBlock *poDataBlockLines; + VFKFeature *poLine; + + poDataBlockLines = (VFKDataBlock *) m_poDataBlock->GetReader()->GetDataBlock("SBP"); + if (!poDataBlockLines) + return FALSE; + + idxId = m_poDataBlock->GetPropertyIndex("ID"); + idxHp_Id = poDataBlockLines->GetPropertyIndex("HP_ID"); + if (idxId < 0 || idxHp_Id < 0) + return FALSE; + + id = GetProperty(idxId)->GetValueI(); + poLine = poDataBlockLines->GetFeature(idxHp_Id, id); + if (!poLine || !poLine->GetGeometry()) + return FALSE; + + SetGeometry(poLine->GetGeometry()); + poDataBlockLines->ResetReading(); + + return TRUE; +} + +/*! + \brief Load geometry (polygon BUD/PAR layers) + + \todo Implement (really needed?) + + \return TRUE on success or FALSE on failure +*/ +bool VFKFeature::LoadGeometryPolygon() +{ + return FALSE; +} +OGRErr VFKFeature::LoadProperties(OGRFeature *poFeature) +{ + for (int iField = 0; iField < m_poDataBlock->GetPropertyCount(); iField++) { + if (GetProperty(iField)->IsNull()) + continue; + OGRFieldType fType = poFeature->GetDefnRef()->GetFieldDefn(iField)->GetType(); + if (fType == OFTInteger) + poFeature->SetField(iField, + GetProperty(iField)->GetValueI()); + else if (fType == OFTReal) + poFeature->SetField(iField, + GetProperty(iField)->GetValueD()); + else + poFeature->SetField(iField, + GetProperty(iField)->GetValueS()); + } + + return OGRERR_NONE; +} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/1.10/linux/debian/port/cplkeywordparser.cpp =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/1.10/linux/debian/port/cplkeywordparser.cpp (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/1.10/linux/debian/port/cplkeywordparser.cpp (revision 27955) @@ -0,0 +1,368 @@ +/****************************************************************************** + * $Id: cplkeywordparser.cpp 20996 2010-10-28 18:38:15Z rouault $ + * + * Project: Common Portability Library + * Purpose: Implementation of CPLKeywordParser - a class for parsing + * the keyword format used for files like QuickBird .RPB files. + * This is a slight variation on the NASAKeywordParser used for + * the PDS/ISIS2/ISIS3 formats. + * Author: Frank Warmerdam + * + * Permission is hereby granted, free of charge, to any person obtaining a + * copy of this software and associated documentation files (the "Software"), + * to deal in the Software without restriction, including without limitation + * the rights to use, copy, modify, merge, publish, distribute, sublicense, + * and/or sell copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included + * in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS + * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL + * THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + * DEALINGS IN THE SOFTWARE. + ****************************************************************************/ + +#include "cpl_string.h" +#include "cplkeywordparser.h" + +CPL_CVSID("$Id"); + +/************************************************************************/ +/* ==================================================================== */ +/* CPLKeywordParser */ +/* ==================================================================== */ +/************************************************************************/ + +/************************************************************************/ +/* CPLKeywordParser() */ +/************************************************************************/ + +CPLKeywordParser::CPLKeywordParser() + +{ + papszKeywordList = NULL; +} + +/************************************************************************/ +/* ~CPLKeywordParser() */ +/************************************************************************/ + +CPLKeywordParser::~CPLKeywordParser() + +{ + CSLDestroy( papszKeywordList ); + papszKeywordList = NULL; +} + +/************************************************************************/ +/* Ingest() */ +/************************************************************************/ + +int CPLKeywordParser::Ingest( VSILFILE *fp ) + +{ +/* -------------------------------------------------------------------- */ +/* Read in buffer till we find END all on it's own line. */ +/* -------------------------------------------------------------------- */ + for( ; TRUE; ) + { + const char *pszCheck; + char szChunk[513]; + + int nBytesRead = VSIFReadL( szChunk, 1, 512, fp ); + + szChunk[nBytesRead] = '\0'; + osHeaderText += szChunk; + + if( nBytesRead < 512 ) + break; + + if( osHeaderText.size() > 520 ) + pszCheck = osHeaderText.c_str() + (osHeaderText.size() - 520); + else + pszCheck = szChunk; + + if( strstr(pszCheck,"\r\nEND;\r\n") != NULL + || strstr(pszCheck,"\nEND;\n") != NULL ) + break; + } + + pszHeaderNext = osHeaderText.c_str(); + +/* -------------------------------------------------------------------- */ +/* Process name/value pairs, keeping track of a "path stack". */ +/* -------------------------------------------------------------------- */ + return ReadGroup( "" ); +} + +/************************************************************************/ +/* ReadGroup() */ +/************************************************************************/ + +int CPLKeywordParser::ReadGroup( const char *pszPathPrefix ) + +{ + CPLString osName, osValue; + + for( ; TRUE; ) + { + if( !ReadPair( osName, osValue ) ) + return FALSE; + + if( EQUAL(osName,"BEGIN_GROUP") ) + { + if( !ReadGroup( (CPLString(pszPathPrefix) + osValue + ".").c_str() ) ) + return FALSE; + } + else if( EQUALN(osName,"END",3) ) + { + return TRUE; + } + else + { + osName = pszPathPrefix + osName; + papszKeywordList = CSLSetNameValue( papszKeywordList, + osName, osValue ); + } + } +} + +/************************************************************************/ +/* ReadPair() */ +/* */ +/* Read a name/value pair from the input stream. Strip off */ +/* white space, ignore comments, split on '='. */ +/************************************************************************/ + +int CPLKeywordParser::ReadPair( CPLString &osName, CPLString &osValue ) + +{ + osName = ""; + osValue = ""; + + if( !ReadWord( osName ) ) + return FALSE; + + SkipWhite(); + + if( EQUAL(osName,"END") ) + return TRUE; + + if( *pszHeaderNext != '=' ) + { + // ISIS3 does not have anything after the end group/object keyword. + if( EQUAL(osName,"End_Group") || EQUAL(osName,"End_Object") ) + return TRUE; + else + return FALSE; + } + + pszHeaderNext++; + + SkipWhite(); + + osValue = ""; + + // Handle value lists like: Name = (Red, Red) + // or list of lists like : TLCList = ( (0, 0.000000), (8299, 4.811014) ); + if( *pszHeaderNext == '(' ) + { + CPLString osWord; + int nDepth = 0; + const char* pszLastPos = pszHeaderNext; + + while( ReadWord( osWord ) && pszLastPos != pszHeaderNext) + { + SkipWhite(); + pszLastPos = pszHeaderNext; + + osValue += osWord; + const char* pszIter = osWord.c_str(); + int bInQuote = FALSE; + while(*pszIter != '\0') + { + if (*pszIter == '"') + bInQuote = !bInQuote; + else if (!bInQuote) + { + if (*pszIter == '(') + nDepth ++; + else if (*pszIter == ')') + { + nDepth --; + if (nDepth == 0) + break; + } + } + pszIter ++; + } + if (*pszIter == ')' && nDepth == 0) + break; + } + } + + else // Handle more normal "single word" values. + { + if( !ReadWord( osValue ) ) + return FALSE; + + } + + SkipWhite(); + + // No units keyword? + if( *pszHeaderNext != '<' ) + return TRUE; + + // Append units keyword. For lines that like like this: + // MAP_RESOLUTION = 4.0 + + CPLString osWord; + + osValue += " "; + + while( ReadWord( osWord ) ) + { + SkipWhite(); + + osValue += osWord; + if( osWord[strlen(osWord)-1] == '>' ) + break; + } + + return TRUE; +} + +/************************************************************************/ +/* ReadWord() */ +/************************************************************************/ + +int CPLKeywordParser::ReadWord( CPLString &osWord ) + +{ + osWord = ""; + + SkipWhite(); + + if( *pszHeaderNext == '\0' || *pszHeaderNext == '=' ) + return FALSE; + + while( *pszHeaderNext != '\0' + && *pszHeaderNext != '=' + && *pszHeaderNext != ';' + && !isspace((unsigned char)*pszHeaderNext) ) + { + if( *pszHeaderNext == '"' ) + { + osWord += *(pszHeaderNext++); + while( *pszHeaderNext != '"' ) + { + if( *pszHeaderNext == '\0' ) + return FALSE; + + osWord += *(pszHeaderNext++); + } + osWord += *(pszHeaderNext++); + } + else if( *pszHeaderNext == '\'' ) + { + osWord += *(pszHeaderNext++); + while( *pszHeaderNext != '\'' ) + { + if( *pszHeaderNext == '\0' ) + return FALSE; + + osWord += *(pszHeaderNext++); + } + osWord += *(pszHeaderNext++); + } + else + { + osWord += *pszHeaderNext; + pszHeaderNext++; + } + } + + if( *pszHeaderNext == ';' ) + pszHeaderNext++; + + return TRUE; +} + +/************************************************************************/ +/* SkipWhite() */ +/************************************************************************/ + +void CPLKeywordParser::SkipWhite() + +{ + for( ; TRUE; ) + { + // Skip white space (newline, space, tab, etc ) + if( isspace( (unsigned char)*pszHeaderNext ) ) + { + pszHeaderNext++; + continue; + } + + // Skip C style comments + if( *pszHeaderNext == '/' && pszHeaderNext[1] == '*' ) + { + pszHeaderNext += 2; + + while( *pszHeaderNext != '\0' + && (*pszHeaderNext != '*' + || pszHeaderNext[1] != '/' ) ) + { + pszHeaderNext++; + } + + pszHeaderNext += 2; + continue; + } + + // Skip # style comments + if( *pszHeaderNext == '#' ) + { + pszHeaderNext += 1; + + // consume till end of line. + while( *pszHeaderNext != '\0' + && *pszHeaderNext != 10 + && *pszHeaderNext != 13 ) + { + pszHeaderNext++; + } + continue; + } + + // not white space, return. + return; + } +} + +/************************************************************************/ +/* GetKeyword() */ +/************************************************************************/ + +const char *CPLKeywordParser::GetKeyword( const char *pszPath, + const char *pszDefault ) + +{ + const char *pszResult; + + pszResult = CSLFetchNameValue( papszKeywordList, pszPath ); + if( pszResult == NULL ) + return pszDefault; + else + return pszResult; +} + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/GDALmake.opt.patch.murdo =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/GDALmake.opt.patch.murdo (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/configs/GDALmake.opt.patch.murdo (revision 27955) @@ -0,0 +1,8 @@ +31c31 +< LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +--- +> LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib64 -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +225c225 +< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz +--- +> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3-python-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3-python-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3-python-static.sh (revision 27955) @@ -0,0 +1,63 @@ +#!/bin/bash +set -eu + + +## TODO +# - May want to supply path to Python instead of, effectively, using result of `which python` +# + +## Constants +# +VER="3.5.3" + +## Environment +# +export CC=mpicc +export CXXFLAGS="-std=c++11" +export CXX=mpicxx +export LIBS="-lsqlite3 -lhdf5_hl -lhdf5" +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-${VER}.tar.gz + +# Move source into 'src' directory +mv gdal-${VER}/* src +rm -rf gdal-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --disable-shared \ + --without-ld-shared \ + --enable-static \ + --with-pic \ + --with-python="python3" \ + --with-curl="${CURL_ROOT}/bin/curl-config" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-jpeg=internal \ + --with-libz="${ZLIB_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-pcre=no \ + --with-pg=no \ + --with-png=internal \ + --with-proj="${PROJ_ROOT}" \ + --with-zstd=no + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3-python.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3-python.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3-python.sh (revision 27955) @@ -0,0 +1,50 @@ +#!/bin/bash +set -eu + + +## TODO +# - May want to supply path to Python instead of, effectively, using result of `which python` +# + +## Constants +# +VER="3.5.3" + +## Environment +# +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # NOTE: Need to export this to properly set destination root for Python libraries on macOS (should not affect Linux build). Set to location where external package should be installed. + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-${VER}.tar.gz + +# Move source into 'src' directory +mv gdal-${VER}/* src +rm -rf gdal-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --with-python="python3" \ + --with-curl="${CURL_ROOT}/bin/curl-config" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-libz="${ZLIB_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-proj="${PROJ_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3-static.sh (revision 27955) @@ -0,0 +1,62 @@ +#!/bin/bash +set -eu + + +## TODO +# - May want to supply path to Python instead of, effectively, using result of `which python` +# + +## Constants +# +VER="3.5.3" + +## Environment +# +export CC=mpicc +export CXXFLAGS="-std=c++11" +export CXX=mpicxx +export LIBS="-lsqlite3 -lhdf5_hl -lhdf5" +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # NOTE: Need to export this to properly set destination root for Python libraries on macOS (should not affect Linux build). Set to location where external package should be installed. + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-${VER}.tar.gz + +# Move source into 'src' directory +mv gdal-${VER}/* src +rm -rf gdal-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --disable-shared \ + --without-ld-shared \ + --enable-static \ + --with-pic \ + --with-curl="${CURL_ROOT}/bin/curl-config" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-jpeg=internal \ + --with-libz="${ZLIB_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-pcre=no \ + --with-pg=no \ + --with-png=internal \ + --with-proj="${PROJ_ROOT}" \ + --with-zstd=no + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gdal/install-3.sh (revision 27955) @@ -0,0 +1,43 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.5.3" + +## Environment +# +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # NOTE: Need to export this to properly set destination root for Python libraries on macOS (should not affect Linux build). Set to location where external package should be installed. + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-${VER}.tar.gz + +# Move source into 'src' directory +mv gdal-${VER}/* src +rm -rf gdal-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --with-libz="${ZLIB_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-proj="${PROJ_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/geocode/geoCode.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/geocode/geoCode.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/geocode/geoCode.m (revision 27955) @@ -0,0 +1,180 @@ +function [c] = geoCode(address, service, key) +%GEOCODE look up the latitude and longitude of a an address +% +% COORDS = GEOCODE( ADDRESS ) returns the geocoded latitude and longitude +% of the input address. +% +% COORDS = GEOCODE( ADDRESS, SERVICE) performs the look up using the +% specified SERVICE. Valid services are +% google - Google Maps (default service) +% osm - OpenStreetMap +% yahoo - Yahoo! Place Finder +% +% COORDS = GEOCODE( ..., SERVICE, APIKEY) allows the specifcation of an AppId +% API key if needed. + +% Copyright(c) 2012, Stuart P. Layton +% http://stuartlayton.com +% +% Revision History +% 2012/08/20 - Initial Release +% 2012/08/20 - Simplified XML parsing code + + +% Validate the input arguments + +% Check to see if address is a valid string +if isempty(address) || ~ischar(address) || ~isvector(address) + error('Invalid address provided, must be a string'); +end + +% if no service is specified or an empty service is specified use google +if nargin<2 || isempty(service) + service = 'google'; +end + +% if no key is specified then set it to empty, also check to see if char array +if nargin<3 + key = []; +end + +%replace white spaces in the address with '+' +address = regexprep(address, ' ', '+'); + +% Switch on the specified service, construct the Query URL, and specify the +% function that will be used to parse the resulting XML +switch lower(service) + case('google') + SERVER_URL = 'http://maps.google.com'; + queryUrl = sprintf('%s/maps/geo?output=xml&q=%s',SERVER_URL, address); + parseFcn = @parseGoogleMapsXML; + + case('yahoo') + + SERVER_URL = 'http://where.yahooapis.com/geocode'; + queryUrl = sprintf('%s?location=%s',SERVER_URL, address); + +% The Yahoo docs say that an AppID is required although +% it appears that responses are given without a valid appid +% If an AppId is provided include it in the URL + if ~isempty(key) + queryUrl = sprintf('%s&appid=%s', queryUrl, key); + end + + parseFcn = @parseYahooLocalXML; + + + case {'osm', 'openstreetmaps', 'open street maps'} + + SERVER_URL = 'https://nominatim.openstreetmap.org/search'; + queryUrl = sprintf('%s?format=xml&q=%s', SERVER_URL, address); + parseFcn = @parseOpenStreetMapXML; + + otherwise + error('Invalid geocoding service specified:%s', service); +end + + try + docNode = xmlread(queryUrl); + catch %#ok + error('Error, could not reach %s, is it a valid URL?', SERVER_URL); + end + + c = parseFcn(docNode); +end + +% Function to parse the XML response from Google Maps +function [c] = parseGoogleMapsXML(docNode) + + %check the response code to see if we got a valid response + codeEl = docNode.getElementsByTagName('code'); + errCode = str2double( char( codeEl.item(0).getTextContent ) ); + % code 200 is associated with a valid geocode xml file + if errCode~=200 + fprintf('No data received from server! Received code:%d\n', errCode) + c = nan(2,1); + return; + end + + %get the 'coordinates' element from the document + cordEl = docNode.getElementsByTagName('coordinates'); + + %make sure the xml actually included a coordinates tag + if cordEl.length<1 + c = nan(2,1); + warning('No coordinates returned for the specified address'); + return; + end + + % get the coordinates from the first node, convert them to numbers + coords = cellfun(@str2double, regexp( char( cordEl.item(0).getTextContent), ',', 'split')); + + c = coords([2, 1]); % return the latitude and longitude +end + +% Function to parse the XML response from Yahoo Local +function [c] = parseYahooLocalXML(docNode) + + %check the response code to see if we got a valid response + codeEl = docNode.getElementsByTagName('Error'); + errCode = str2double( char( codeEl.item(0).getTextContent ) ); + + % code 0 is associated with a valid geocode xml file + if errCode~=0 + fprintf('No data received from server! Received code:%d\n', errCode) + c = nan(2,1); + return; + end + + %check to see if a location was actually found + foundEl = docNode.getElementsByTagName('Found'); + found = str2double( char( foundEl.item(0).getTextContent) ); + % + if found<1 + disp('A location with that address was not found!'); + c = nan(2,1); + return; + end + + + latEl = docNode.getElementsByTagName('latitude'); + lonEl = docNode.getElementsByTagName('longitude'); + + %make sure the xml actually included latitude and longitude tags + if latEl.length==0 || lonEl.length==0 + c = nan(2,1); + disp('No coordinates were found for that address'); + return; + end + + c(1) = str2double( char( latEl.item(0).getTextContent) ); + c(2) = str2double( char( lonEl.item(0).getTextContent) ); + +end + +% Function to parse the XML response from OpenStreetMap +function [c] = parseOpenStreetMapXML(docNode) + + serverResponse = docNode.getElementsByTagName('searchresults').item(0); + placeTag = serverResponse.getElementsByTagName('place').item(0); + + if isempty(placeTag) + disp('OpenStreeMap returned no data for that address');%#ok + c = nan(2,1); + return; + end + + c(1) = str2double( char( placeTag.getAttribute('lat') ) ); + c(2) = str2double( char( placeTag.getAttribute('lon') ) ); + +end + + +function elementText = GetElementText(resultNode,elementName) +% GETELEMENTTEXT given a result node and an element name +% returns the text within that node as a Matlab CHAR array + +elementText = ... + char( resultNode.getElementsByTagName(elementName).item(0).getTextContent ); + +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/geocode/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/geocode/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/geocode/install.sh (revision 27955) @@ -0,0 +1,2 @@ +#/bin/bash +unzip geoCode.zip Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/geocode/license.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/geocode/license.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/geocode/license.txt (revision 27955) @@ -0,0 +1,24 @@ +Copyright (c) 2012, Stuart Layton +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/geos5/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/geos5/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/geos5/install.sh (revision 27955) @@ -0,0 +1,7 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf GEOSagcm +#svn download +svn --username eric.larour@jpl.nasa.gov checkout http://geos5.org/svn/branches/Fortuna-2_5_p1 GEOSagcm Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/git/install-macosx64-sierra.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/git/install-macosx64-sierra.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/git/install-macosx64-sierra.sh (revision 27955) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install git-1.7.10.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/git-1.7.10.2.tar.gz' 'git-1.7.10.2.tar.gz' + +#Untar +tar -zxvf git-1.7.10.2.tar.gz + +#Move git into install directory +mv git-1.7.10.2/* src +rm -rf git-1.7.10.2 + +#install +cd src +./configure CFLAGS="-I/usr/local/include" --prefix="$ISSM_DIR/externalpackages/git/install" +# --with-python="$ISSM_DIR/externalpackages/python/install/bin/python" #Do we really need this line? + +#Compile +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/git/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/git/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/git/install.sh (revision 27955) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install git-1.7.10.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/git-1.7.10.2.tar.gz' 'git-1.7.10.2.tar.gz' + +#Untar +tar -zxvf git-1.7.10.2.tar.gz + +#Move git into install directory +mv git-1.7.10.2/* src +rm -rf git-1.7.10.2 + +#install +cd src +./configure --prefix="$ISSM_DIR/externalpackages/git/install" +#--with-python="$ISSM_DIR/externalpackages/python/install/bin/python" #Do we really need this line? + +#Compile +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmake/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmake/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmake/install.sh (revision 27955) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src make-3.82 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/make-3.82.tar.gz' 'make-3.82.tar.gz' + +#Untar +tar -zxvf make-3.82.tar.gz + +#Move make into install directory +mv make-3.82/* src +rm -rf make-3.82 + +#Apply patches +cd src + +#Configure and compile: +./configure --prefix=$ISSM_DIR/externalpackages/gmake/install + +if [ $# -eq 0 ]; then + make + make install +else + make -j $1; + make -j $1 install; +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmp/install-linux64.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmp/install-linux64.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmp/install-linux64.sh (revision 27955) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gmp-5.0.5 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gmp-5.0.5.tar.bz2' 'gmp-5.0.5.tar.bz2' + +#Untar +bunzip2 gmp-5.0.5.tar.bz2 +tar -xvf gmp-5.0.5.tar + +#Move gmp into install directory +mv gmp-5.0.5/* src +rm -rf gmp-5.0.5 + +#install +cd src +./configure --prefix="$ISSM_DIR/externalpackages/gmp/install" + +#Compile and install gmp +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.10.5/mac/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.10.5/mac/CMakeLists.txt.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.10.5/mac/CMakeLists.txt.patch (revision 27955) @@ -0,0 +1,4 @@ +284c284 +< set(CMAKE_INSTALL_RPATH "@executable_path/../lib") +--- +> set(CMAKE_INSTALL_RPATH "@executable_path/../lib;${LIBGFORTRAN_ROOT}") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.10.5/static/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.10.5/static/CMakeLists.txt.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.10.5/static/CMakeLists.txt.patch (revision 27955) @@ -0,0 +1,9 @@ +858,861c860,862 +< find_library(METIS_LIB metis PATH_SUFFIXES lib) +< find_path(METIS_INC "metis.h" PATH_SUFFIXES include) +< if(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC) +< message(STATUS "Using system version of METIS") +--- +> if(METIS_ROOT) +> find_library(METIS_LIB metis PATHS ${METIS_ROOT} PATH_SUFFIXES lib) +> find_path(METIS_INC "metis.h" PATHS ${METIS_ROOT} PATH_SUFFIXES include) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.10.5/static/mac/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.10.5/static/mac/CMakeLists.txt.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.10.5/static/mac/CMakeLists.txt.patch (revision 27955) @@ -0,0 +1,4 @@ +207a208 +> set(CMAKE_FIND_LIBRARY_SUFFIXES ".a" ".so") +226a228 +> set(CMAKE_FIND_LIBRARY_SUFFIXES ".a" ".so") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.5.6/static/CMakeLists.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.5.6/static/CMakeLists.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.5.6/static/CMakeLists.txt (revision 27955) @@ -0,0 +1,2141 @@ +# Gmsh - Copyright (C) 1997-2020 C. Geuzaine, J.-F. Remacle +# +# See the LICENSE.txt file for license information. Please report all +# issues on https://gitlab.onelab.info/gmsh/gmsh/issues. + +cmake_minimum_required(VERSION 2.8 FATAL_ERROR) + +# do not warn about non-definition of WIN32 on Cygwin +set(CMAKE_LEGACY_CYGWIN_WIN32 0) + +# if CMAKE_BUILD_TYPE is specified use it; otherwise set the default +# build type to "RelWithDebInfo" ("-O2 -g" with gcc) prior to calling +# project() +if(DEFINED CMAKE_BUILD_TYPE) + set(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Choose build type") +else() + set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose build type") +endif() + +project(gmsh CXX C) + +# this variable controls the default value of the options which are normally set +# to ON (useful if you want to configure a minimal version of Gmsh: e.g. "cmake +# -DDEFAULT=0 -DENABLE_POST=1 -DENABLE_PARSER=1") +set(DEFAULT ON CACHE INTERNAL "Default value for enabled-by-default options") + +macro(opt OPTION HELP VALUE) + option(ENABLE_${OPTION} ${HELP} ${VALUE}) + set(OPT_TEXI "${OPT_TEXI}\n@item ENABLE_${OPTION}\n${HELP} (default: ${VALUE})") +endmacro() + +opt(3M "Enable proprietary 3M extension" OFF) +opt(ACIS "Enable ACIS geometrical models (experimental)" ${DEFAULT}) +opt(ALGLIB "Enable ALGLIB (used by some mesh optimizers)" ${DEFAULT}) +opt(ANN "Enable ANN (used for fast point search in mesh/post)" ${DEFAULT}) +opt(BAMG "Enable Bamg 2D anisotropic mesh generator" ${DEFAULT}) +opt(BLAS_LAPACK "Enable BLAS/Lapack for linear algebra (required for meshing)" ON) +opt(BLOSSOM "Enable Blossom algorithm (needed for full quad meshing)" ${DEFAULT}) +opt(BUILD_LIB "Enable 'lib' target for building static Gmsh library" OFF) +opt(BUILD_SHARED "Enable 'shared' target for building shared Gmsh library" OFF) +opt(BUILD_DYNAMIC "Enable dynamic Gmsh executable (linked with shared library)" OFF) +opt(BUILD_ANDROID "Enable Android NDK library target (experimental)" OFF) +opt(BUILD_IOS "Enable iOS library target (experimental)" OFF) +opt(CGNS "Enable CGNS import/export (experimental)" ${DEFAULT}) +opt(CGNS_CPEX0045 "Enable high-order CGNS import/export following CPEX0045 (experimental)" OFF) +opt(CAIRO "Enable Cairo to render fonts (experimental)" ${DEFAULT}) +opt(CXX11 "Enable C++11" ON) +opt(C99 "Enable C99" ON) +opt(PROFILE "Enable profiling compiler flags" OFF) +opt(DINTEGRATION "Enable discrete integration (needed for levelsets)" ${DEFAULT}) +opt(DOMHEX "Enable experimental DOMHEX code" ${DEFAULT}) +opt(FLTK "Enable FLTK graphical user interface (requires mesh/post)" ${DEFAULT}) +opt(GETDP "Enable GetDP solver (linked as a library, experimental)" ${DEFAULT}) +opt(GMM "Enable GMM linear solvers (simple alternative to PETSc)" ${DEFAULT}) +opt(GMP "Enable GMP for Kbipack (advanced)" ON) +opt(GRAPHICS "Enable building graphics lib even without GUI (advanced)" OFF) +opt(HXT "Enable HXT library (for reparametrization and meshing)" ${DEFAULT}) +opt(KBIPACK "Enable Kbipack (neeeded by homology solver)" ${DEFAULT}) +opt(MATHEX "Enable Mathex expression parser (used by plugins and options)" ${DEFAULT}) +opt(MED "Enable MED mesh and post file formats" ${DEFAULT}) +opt(MESH "Enable mesh module (required by GUI)" ${DEFAULT}) +opt(METIS "Enable Metis mesh partitioner" ${DEFAULT}) +opt(MMG3D "Enable MMG3D 3D anisotropic mesh refinement" ${DEFAULT}) +opt(MPEG_ENCODE "Enable built-in MPEG movie encoder" ${DEFAULT}) +opt(MPI "Enable MPI (experimental, not used for meshing)" OFF) +opt(MSVC_STATIC_RUNTIME "Enable static Visual C++ runtime" OFF) +opt(MUMPS "Enable MUMPS sparse direct linear solver" OFF) +opt(NETGEN "Enable Netgen 3D frontal mesh generator" ${DEFAULT}) +opt(NUMPY "Enable fullMatrix and numpy array conversion for private API" OFF) +opt(PETSC4PY "Enable petsc4py wrappers for petsc matrices for private API" OFF) +opt(OCC "Enable OpenCASCADE CAD kernel" ${DEFAULT}) +opt(OCC_CAF "Enable OpenCASCADE CAF module (for STEP/IGES attributes)" ${DEFAULT}) +opt(OCC_STATIC "Link OpenCASCADE static instead of dynamic libraries (requires ENABLE_OCC)" OFF) +opt(OCC_TBB "Add TBB libraries in list of OCC libraries" OFF) +opt(ONELAB "Enable ONELAB solver interface" ${DEFAULT}) +opt(ONELAB_METAMODEL "Enable ONELAB metamodels (experimental)" ${DEFAULT}) +opt(OPENACC "Enable OpenACC" OFF) +opt(OPENMP "Enable OpenMP" OFF) +opt(OPTHOM "Enable high-order mesh optimization tools" ${DEFAULT}) +opt(OS_SPECIFIC_INSTALL "Enable OS-specific (e.g. app bundle) installation" OFF) +opt(OSMESA "Enable OSMesa for offscreen rendering (experimental)" OFF) +opt(P4EST "Enable p4est for enabling automatic mesh size firld (experimental)" OFF) +opt(PACKAGE_STRIP "Strip symbols in install packages to reduce install size" ON) +opt(PARSER "Enable GEO file parser (required for .geo/.pos files)" ${DEFAULT}) +opt(PETSC "Enable PETSc linear solvers (required for SLEPc)" OFF) +opt(PLUGINS "Enable post-processing plugins" ${DEFAULT}) +opt(POST "Enable post-processing module (required by GUI)" ${DEFAULT}) +opt(POPPLER "Enable Poppler for displaying PDF documents (experimental)" OFF) +opt(PRIVATE_API "Enable private API" OFF) +opt(QUADTRI "Enable QuadTri structured meshing extensions" ${DEFAULT}) +opt(REVOROPT "Enable Revoropt (used for CVT remeshing)" OFF) +opt(SLEPC "Enable SLEPc eigensolvers" OFF) +opt(SOLVER "Enable built-in finite element solvers (required for compounds)" ${DEFAULT}) +opt(SYSTEM_CONTRIB "Use system versions of contrib libraries, when possible" OFF) +opt(TCMALLOC "Enable libtcmalloc (fast malloc that does not release memory)" OFF) +opt(TOUCHBAR "Enable Apple Touch bar" ${DEFAULT}) +opt(VISUDEV "Enable additional visualization capabilities for development purposes" OFF) +opt(VOROPP "Enable voro++ (for hex meshing, experimental)" ${DEFAULT}) +opt(WRAP_JAVA "Enable generation of Java wrappers for private API" OFF) +opt(WRAP_PYTHON "Enable generation of Python wrappers for private API" OFF) +opt(ZIPPER "Enable Zip file compression/decompression" OFF) + +set(GMSH_MAJOR_VERSION 4) +set(GMSH_MINOR_VERSION 5) +set(GMSH_PATCH_VERSION 6) +set(GMSH_EXTRA_VERSION "") +set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION}") + +if(NOT GMSH_RELEASE) + find_package(Git) + if(GIT_FOUND) + execute_process(COMMAND ${GIT_EXECUTABLE} log -1 --format=%h + WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} ERROR_QUIET + OUTPUT_VARIABLE GIT_COMMIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE) + endif() + if(GIT_COMMIT_HASH) + set(GMSH_EXTRA_VERSION "${GMSH_EXTRA_VERSION}-git-${GIT_COMMIT_HASH}") + endif() + set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION_TEXI} (development version)") +endif() + +set(GMSH_VERSION "${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}") +set(GMSH_VERSION "${GMSH_VERSION}.${GMSH_PATCH_VERSION}${GMSH_EXTRA_VERSION}") +set(GMSH_SHORT_LICENSE "GNU General Public License") + +set(GMSH_API api/gmsh.h api/gmshc.h api/gmsh.h_cwrap) + +if(ENABLE_PRIVATE_API) + message(WARNING "The private API is unsupported and undocumented. It is meant " + "for expert Gmsh developers, not for regular Gmsh users, who should rely " + "on the stable public API (gmsh/api) instead. If you are repackaging Gmsh, " + "e.g. for a Linux distribution, please DO NOT distribute the private API " + "(i.e. all the internal headers) and ship the stable public API instead " + "(i.e. only the headers and modules in gmsh/api).") + file(GLOB_RECURSE HEADERS Common/*.h Numeric/*.h Geo/*.h Mesh/*.h Solver/*.h + Post/*.h Graphics/*.h contrib/kbipack/*.h contrib/DiscreteIntegration/*.h + contrib/HighOrderMeshOptimizer/*.h contrib/MeshOptimizer/*.h + contrib/MeshQualityOptimizer/*.h) + set(GMSH_PRIVATE_API ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h ${HEADERS}) + get_property(IAMCHILD DIRECTORY PROPERTY PARENT_DIRECTORY) + if(IAMCHILD) + set(GMSH_PRIVATE_API ${GMSH_PRIVATE_API} PARENT_SCOPE) + endif() +endif() + +set(ONELAB_PY contrib/onelab/python/onelab.py) +set(GMSH_PY api/gmsh.py) +set(GMSH_JL api/gmsh.jl) + +if(${CMAKE_MAJOR_VERSION} GREATER 2) + string(TIMESTAMP DATE "%Y%m%d") +else() + execute_process(COMMAND date "+%Y%m%d" OUTPUT_VARIABLE DATE + OUTPUT_STRIP_TRAILING_WHITESPACE) +endif() + +if(NOT DATE) + set(DATE "unknown") +endif() +set(GMSH_DATE "${DATE}") + +if(NOT GMSH_HOST) + execute_process(COMMAND hostname OUTPUT_VARIABLE HOSTNAME + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT HOSTNAME) + set(HOSTNAME "unknown") + endif() + set(GMSH_HOST "${HOSTNAME}") +endif() + +if(NOT GMSH_PACKAGER) + execute_process(COMMAND whoami OUTPUT_VARIABLE PACKAGER + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT PACKAGER) + set(PACKAGER "unknown") + endif() + string(REPLACE "\\" " " PACKAGER ${PACKAGER}) + set(GMSH_PACKAGER "${PACKAGER}") +endif() + +if(APPLE) + set(GMSH_OS "MacOSX") +elseif(CYGWIN OR MSYS) + # detect if we use the MinGW compilers on Cygwin - if we do, handle the build + # as a pure Windows build + if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpmachine + OUTPUT_VARIABLE CXX_COMPILER_MACHINE + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(CXX_COMPILER_MACHINE MATCHES "mingw") + set(GMSH_OS "Windows") + set(WIN32 1) + add_definitions(-DWIN32) + endif() + endif() +else() + set(GMSH_OS "${CMAKE_SYSTEM_NAME}") +endif() + +include(CheckTypeSize) +include(CheckFunctionExists) +include(CheckIncludeFile) +include(CheckCXXCompilerFlag) +include(CheckCCompilerFlag) + +macro(set_config_option VARNAME STRING) + set(${VARNAME} TRUE) + list(APPEND CONFIG_OPTIONS ${STRING}) + message(STATUS "Found " ${STRING}) +endmacro() + +# check if the machine is 64 bits (this is more reliable than using +# CMAKE_SIZEOF_VOID_P, which does not seem to work e.g. on some Suse +# machines) +check_type_size("void*" SIZEOF_VOID_P) +if(SIZEOF_VOID_P EQUAL 8) + set_config_option(HAVE_64BIT_SIZE_T "64Bit") +endif() + +# append 32/64 to the build name on Linux and Windows +if(NOT APPLE) + if(HAVE_64BIT_SIZE_T) + set(GMSH_OS "${GMSH_OS}64") + else() + set(GMSH_OS "${GMSH_OS}32") + endif() +endif() + +if(NOT ENABLE_BUILD_SHARED) + if(ENABLE_WRAP_PYTHON OR ENABLE_WRAP_JAVA) + set(ENABLE_BUILD_DYNAMIC ON) + endif() +endif() + +if(ENABLE_BUILD_DYNAMIC) + set(GMSH_OS "${GMSH_OS}-sdk") +endif() + +if(APPLE) + # FIXME: change this once we understand rpaths - the options below do not work + set(CMAKE_MACOSX_RPATH 0) +else() + # make sure that dynamic libraries can be found when installing/ displacing the + # binaries: from https://gitlab.kitware.com/cmake/community/wikis/doc/cmake/ + # RPATH-handling: + + # use, i.e. don't skip the full RPATH for the build tree + set(CMAKE_SKIP_BUILD_RPATH FALSE) + + # when building, don't use the install RPATH already (but later on when + # installing) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") + + # add the automatically determined parts of the RPATH which point to + # directories outside the build tree to the install RPATH + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + + # the RPATH to be used when installing, but only if it's not a system directory + list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" + isSystemDir) + if("${isSystemDir}" STREQUAL "-1") + set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../lib") + endif() +endif() + +if(MSVC) + # remove annoying warning about bool/int cast performance + set(GMSH_CONFIG_PRAGMAS "#pragma warning(disable:4800 4244 4267)") + foreach(VAR + CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE + CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO + CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE + CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO) + if(ENABLE_MSVC_STATIC_RUNTIME AND ${VAR} MATCHES "/MD") + string(REGEX REPLACE "/MD" "/MT" ${VAR} "${${VAR}}") + endif() + if(NOT ${VAR} MATCHES "/MP") # enable parallel compilation + set(${VAR} "${${VAR}} /MP") + endif() + endforeach() + if(ENABLE_PRIVATE_API) + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + # automatically export .def file with all symbols (requires CMake 3.4); + # depending on the compiling options this might lead to more than 64k export + # symbols; just trim the .def file to keep the ones you need + set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + endif() + endif() +endif() + +if(ENABLE_OPENMP) + find_package(OpenMP) + if(OpenMP_FOUND) + set_config_option(HAVE_OPENMP "OpenMP") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + elseif(APPLE AND EXISTS "/opt/local/lib/libomp") + # just for testing the official Apple compiler with macports' libomp + set_config_option(HAVE_OPENMP "OpenMP[MacPorts]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + list(APPEND EXTERNAL_LIBRARIES "-L/opt/local/lib/libomp -lomp") + elseif(APPLE AND EXISTS "/usr/local/lib/libomp.dylib") + set_config_option(HAVE_OPENMP "OpenMP[usr/local]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp") + list(APPEND EXTERNAL_LIBRARIES "-lomp") + endif() +endif() + +if(ENABLE_OPENACC) + find_package(OpenACC) + if(OpenACC_C_FOUND AND OpenACC_CXX_FOUND) + set_config_option(HAVE_OPENACC "OpenACC") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenACC_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenACC_CXX_FLAGS}") + endif() +endif() + +if(ENABLE_CXX11) + # in recent cmake versions we could do e.g. set(CMAKE_CXX_STANDARD 11) + check_cxx_compiler_flag("-std=c++11" STDCXX11) + if(STDCXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() +endif() + +if(ENABLE_C99) + # in recent cmake versions we could do e.g. set(CMAKE_C_STANDARD 99) + check_c_compiler_flag("-std=c99" STDC99) + if(STDC99) + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99") + endif() +endif() + +if(ENABLE_PROFILE) + # Using the perf set of profiling tools doesn't work without the frame + # pointer and a common optimisation is to remove it + check_cxx_compiler_flag("-fno-omit-frame-pointer" FNOFP) + if(FNOFP) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer") + endif() +endif() + +macro(append_gmsh_src DIRNAME FILES) + foreach(FILE ${FILES}) + list(APPEND LIST ${DIRNAME}/${FILE}) + endforeach() + set(GMSH_SRC ${GMSH_SRC};${LIST} PARENT_SCOPE) + set(GMSH_DIRS ${GMSH_DIRS};${DIRNAME} PARENT_SCOPE) +endmacro() + +macro(find_all_libraries VARNAME LISTNAME PATH SUFFIX) + set(${VARNAME}) + list(LENGTH ${LISTNAME} NUM_LIST) + foreach(LIB ${${LISTNAME}}) + if("${PATH}" STREQUAL "") + find_library(FOUND_LIB ${LIB} PATH_SUFFIXES ${SUFFIX}) + else() + find_library(FOUND_LIB ${LIB} PATHS ${PATH} NO_DEFAULT_PATH) + endif() + if(FOUND_LIB) + list(APPEND ${VARNAME} ${FOUND_LIB}) + endif() + unset(FOUND_LIB CACHE) + endforeach() + list(LENGTH ${VARNAME} NUM_FOUND_LIBRARIES) + if(NUM_FOUND_LIBRARIES LESS NUM_LIST) + set(${VARNAME}) + endif() +endmacro() + +macro(set_compile_flags LISTNAME FLAGS) + foreach(FILE ${${LISTNAME}}) + get_source_file_property(PROP ${FILE} COMPILE_FLAGS) + if(PROP) + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${PROP} ${FLAGS}") + else() + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${FLAGS}") + endif() + endforeach() +endmacro() + +if(ENABLE_BLAS_LAPACK) + if(BLAS_LAPACK_LIBRARIES) + # use libs as specified in the BLAS_LAPACK_LIBRARIES variable + set_config_option(HAVE_BLAS "Blas[custom]") + set_config_option(HAVE_LAPACK "Lapack[custom]") + set(LAPACK_LIBRARIES ${BLAS_LAPACK_LIBRARIES}) + else() + if(MSVC) + # on Windows with Visual C++ try really hard to find blas/lapack *without* + # requiring a Fortran compiler: 1) try to find the Intel MKL libs using + # the standard search path; if not found 2) try to get the reference + # blas/lapack libs (useful for users with no Fortran compiler and no MKL + # license, who can just download our precompiled "gmsh-dep" package) + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH em64t/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_lp64 mkl_intel_thread mkl_core) + else() + set(MKL_PATH ia32/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_c mkl_intel_thread mkl_core) + endif() + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + set(REFLAPACK_LIBS_REQUIRED lapack blas g2c gcc) + find_all_libraries(LAPACK_LIBRARIES REFLAPACK_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[ref]") + set_config_option(HAVE_LAPACK "Lapack[ref]") + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + # on Linux try to find the Intel MKL without a Fortran compiler + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH lib/em64t) + else() + set(MKL_PATH lib/32) + endif() + set(MKL_LIBS_REQUIRED mkl_gf_lp64 iomp5 mkl_gnu_thread mkl_core guide pthread) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(NOT LAPACK_LIBRARIES) + # match lapack 9.0 on 64bit + set(MKL_LIBS_REQUIRED mkl_lapack mkl_em64t guide) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + endif() + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + # on Linux also try to find ATLAS without a Fortran compiler, because + # cmake ships with a buggy FindBLAS e.g. on Ubuntu Lucid Lynx + set(ATLAS_LIBS_REQUIRED lapack f77blas cblas atlas) + find_all_libraries(LAPACK_LIBRARIES ATLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[atlas]") + set_config_option(HAVE_LAPACK "Lapack[atlas]") + else() + # try with generic names + set(GENERIC_LIBS_REQUIRED lapack blas pthread) + find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[generic]") + set_config_option(HAVE_LAPACK "Lapack[generic]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "SunOS") + # on SunOS we know blas and lapack are available in sunperf + set(LAPACK_LIBRARIES -library=sunperf) + set_config_option(HAVE_BLAS "Blas[sunperf]") + set_config_option(HAVE_LAPACK "Lapack[sunperf]") + elseif(APPLE) + # on Mac we also know that blas and lapack are available + set(LAPACK_LIBRARIES "-llapack -lblas") + set_config_option(HAVE_BLAS "Blas[veclib]") + set_config_option(HAVE_LAPACK "Lapack[veclib]") + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we haven't found blas and lapack check for OpenBlas + set(OPENBLAS_LIBS_REQUIRED openblas) + find_all_libraries(LAPACK_LIBRARIES OPENBLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[openblas]") + set_config_option(HAVE_LAPACK "Lapack[openblas]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we still haven't found blas and lapack, use the standard cmake tests, + # which require a working Fortran compiler + enable_language(Fortran) + find_package(BLAS) + if(BLAS_FOUND) + set_config_option(HAVE_BLAS "Blas") + find_package(LAPACK) + if(LAPACK_FOUND) + set_config_option(HAVE_LAPACK "Lapack") + else() + set(LAPACK_LIBRARIES ${BLAS_LIBRARIES}) + endif() + if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU") + if(CMAKE_Fortran_COMPILER MATCHES "gfortran") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "f95") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "g77") + list(APPEND LAPACK_LIBRARIES g2c) + endif() + elseif(CMAKE_Fortran_COMPILER MATCHES "pgi") + list(APPEND LAPACK_LIBRARIES -pgf77libs) + endif() + endif() + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + message(WARNING "Could not find Blas or Lapack: most meshing algorithms " + "will not be functional") + endif() + + endif() +endif() + +if(ENABLE_TCMALLOC) + find_library(TCMALLOC tcmalloc) + if(TCMALLOC) + set_config_option(HAVE_TCMALLOC "TCMalloc") + list(APPEND EXTERNAL_LIBRARIES ${TCMALLOC}) + endif() +endif() + +add_subdirectory(Common) +add_subdirectory(Numeric) +add_subdirectory(Geo) + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh AND ENABLE_MESH) + add_subdirectory(Mesh) + set_config_option(HAVE_MESH "Mesh") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Solver AND ENABLE_SOLVER) + add_subdirectory(Solver) + set_config_option(HAVE_SOLVER "Solver") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Post AND ENABLE_POST) + add_subdirectory(Post) + set_config_option(HAVE_POST "Post") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Plugin AND ENABLE_PLUGINS) + add_subdirectory(Plugin) + set_config_option(HAVE_PLUGINS "Plugins") + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Parser AND ENABLE_PARSER) + add_subdirectory(Parser) + set_config_option(HAVE_PARSER "Parser") +endif() + +if(ENABLE_VISUDEV) + set_config_option(HAVE_VISUDEV "VisuDev") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Fltk AND ENABLE_FLTK) + # first, try to use fltk-config for fltk >= 1.3 (FindFLTK is buggy on Unix, + # where e.g. xft and xinerama options are not dealt with) + find_program(FLTK_CONFIG_SCRIPT fltk-config) + if(FLTK_CONFIG_SCRIPT) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --api-version + OUTPUT_VARIABLE FLTK_VERSION) + string(STRIP "${FLTK_VERSION}" FLTK_VERSION) + if(FLTK_VERSION VERSION_GREATER 1.1) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + message(STATUS "Using fltk-config script for Fltk " ${FLTK_VERSION}) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --includedir + OUTPUT_VARIABLE FLTK_INCLUDE_DIR) + string(STRIP ${FLTK_INCLUDE_DIR} FLTK_INCLUDE_DIR) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # On linux (at least OpenSuSE) the following directories are + # not existing (everything is in /usr/include). To avoid warnings + # check existance of these directories before adding them + if(EXISTS ${FLTK_INCLUDE_DIR}/FL/images) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/FL/images) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/jpeg) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/jpeg) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/zlib) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/zlib) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/png) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/png) + endif() + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --ldflags + OUTPUT_VARIABLE FLTK_LIBRARIES) + string(STRIP ${FLTK_LIBRARIES} FLTK_LIBRARIES) + string(REGEX MATCH "fltk[_ ]jpeg" FLTK_JPEG ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]z" FLTK_Z ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]png" FLTK_PNG ${FLTK_LIBRARIES}) + endif() + endif() + # then try the built-in FindFLTK module + if(NOT HAVE_FLTK) + set(FLTK_SKIP_FORMS TRUE) + set(FLTK_SKIP_FLUID TRUE) + find_package(FLTK) + if(FLTK_FOUND) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # find fltk jpeg + find_library(FLTK_JPEG NAMES fltk_jpeg fltkjpeg) + if(FLTK_JPEG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_JPEG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/jpeg) + endforeach() + endif() + # find fltk zlib + find_library(FLTK_Z NAMES fltk_z fltkz) + if(FLTK_Z) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_Z}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/zlib) + endforeach() + endif() + # find fltk png + find_library(FLTK_PNG NAMES fltk_png fltkpng) + if(FLTK_PNG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_PNG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/png) + endforeach() + endif() + endif() + endif() + # workaround for Fedora/Suse messing up fltk-config (see issue #417) + if(HAVE_FLTK AND ${CMAKE_SYSTEM_NAME} MATCHES "Linux") + string(REGEX MATCH "X11" FLTK_X11 ${FLTK_LIBRARIES}) + if(NOT FLTK_X11) + find_package(X11) + if(X11_FOUND) + list(APPEND EXTERNAL_INCLUDES ${X11_INCLUDE_DIR}) + list(APPEND EXTERNAL_LIBRARIES ${X11_LIBRARIES}) + endif() + endif() + endif() +endif() + +if(APPLE AND HAVE_FLTK AND ENABLE_TOUCHBAR) + if(CMAKE_OSX_DEPLOYMENT_TARGET) + if(${CMAKE_OSX_DEPLOYMENT_TARGET} VERSION_GREATER 10.11) + set(GMSH_SRC ${GMSH_SRC};Fltk/touchBar.mm) + set_config_option(HAVE_TOUCHBAR "TouchBar") + endif() + endif() +endif() + +if(ENABLE_ONELAB) + set_config_option(HAVE_ONELAB "ONELAB") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/onelab) + if(ENABLE_ONELAB_METAMODEL) + add_subdirectory(contrib/onelab) + include_directories(contrib/onelab) + set_config_option(HAVE_ONELAB_METAMODEL "ONELABMetamodel") + endif() + file(COPY ${ONELAB_PY} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + endif() +endif() + +if(ENABLE_BUILD_IOS) + find_file(CMAKE_TOOLCHAIN_FILE "ios.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for iOS without a toolchain") + endif() + add_definitions(-DBUILD_IOS) +endif() + +if(HAVE_FLTK OR ENABLE_GRAPHICS) + if(NOT HAVE_MESH OR NOT HAVE_POST OR NOT HAVE_PLUGINS OR NOT HAVE_ONELAB) + message(SEND_ERROR "Cannot compile GUI without Mesh, Post, Plugin and ONELAB") + endif() + + if(FLTK_JPEG) + set_config_option(HAVE_LIBJPEG "Jpeg[fltk]") + else() + find_package(JPEG) + if(JPEG_FOUND) + set_config_option(HAVE_LIBJPEG "Jpeg") + list(APPEND EXTERNAL_LIBRARIES ${JPEG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${JPEG_INCLUDE_DIR}) + endif() + endif() + + if(FLTK_Z) + set_config_option(HAVE_LIBZ "Zlib[fltk]") + else() + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + + if(HAVE_LIBZ) + if(FLTK_PNG) + set_config_option(HAVE_LIBPNG "Png[fltk]") + else() + find_package(PNG) + if(PNG_FOUND) + set_config_option(HAVE_LIBPNG "Png") + list(APPEND EXTERNAL_LIBRARIES ${PNG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${PNG_INCLUDE_DIR}) + endif() + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/mpeg_encode AND + ENABLE_MPEG_ENCODE) + add_subdirectory(contrib/mpeg_encode) + include_directories(contrib/mpeg_encode/headers) + set_config_option(HAVE_MPEG_ENCODE "Mpeg") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/3M AND ENABLE_3M) + add_subdirectory(contrib/3M) + include_directories(contrib/3M) + set_config_option(HAVE_3M "3M") + endif() + + if(ENABLE_OSMESA) + find_library(OSMESA_LIB OSMesa) + if(OSMESA_LIB) + set_config_option(HAVE_OSMESA "OSMesa") + list(APPEND EXTERNAL_LIBRARIES ${OSMESA_LIB}) + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Graphics) + set(OpenGL_GL_PREFERENCE "LEGACY") + find_package(OpenGL REQUIRED) + if(OPENGL_GLU_FOUND AND OPENGL_FOUND) + add_subdirectory(Graphics) + set_config_option(HAVE_OPENGL "OpenGL") + else() + message(SEND_ERROR "Could not find GLU: disabling OpenGL support") + endif() + endif() +endif() + +if(ENABLE_ANN) + find_library(ANN_LIB ANN PATH_SUFFIXES lib) + find_path(ANN_INC "ANN.h" PATH_SUFFIXES src include ANN) + if(ENABLE_SYSTEM_CONTRIB AND ANN_LIB AND ANN_INC) + message(STATUS "Using system version of ANN") + list(APPEND EXTERNAL_LIBRARIES ${ANN_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ANN_INC}) + set_config_option(HAVE_ANN "Ann[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ANN) + add_subdirectory(contrib/ANN) + include_directories(contrib/ANN/include) + set_config_option(HAVE_ANN "Ann") + endif() +endif() + +if(ENABLE_ALGLIB) + find_library(ALGLIB_LIB alglib PATH_SUFFIXES lib) + find_path(ALGLIB_INC "stdafx.h" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND ALGLIB_LIB AND ALGLIB_INC) + list(APPEND EXTERNAL_LIBRARIES ${ALGLIB_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ALGLIB_INC}) + set_config_option(HAVE_ALGLIB "ALGLIB[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ALGLIB) + add_subdirectory(contrib/ALGLIB) + include_directories(contrib/ALGLIB) + set_config_option(HAVE_ALGLIB "ALGLIB") + endif() +endif() + +if(HAVE_FLTK AND ENABLE_CAIRO) + find_library(CAIRO_LIB cairo) + find_path(CAIRO_INC "cairo/cairo.h" PATH_SUFFIXES include) + if(CAIRO_INC AND CAIRO_LIB) + set_config_option(HAVE_CAIRO "Cairo") + list(APPEND EXTERNAL_LIBRARIES ${CAIRO_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CAIRO_INC}) + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/DiscreteIntegration AND + ENABLE_DINTEGRATION) + add_subdirectory(contrib/DiscreteIntegration) + include_directories(contrib/DiscreteIntegration) + set_config_option(HAVE_DINTEGRATION "DIntegration") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/HighOrderMeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshQualityOptimizer AND + ENABLE_OPTHOM AND HAVE_MESH) + add_subdirectory(contrib/HighOrderMeshOptimizer) + include_directories(contrib/HighOrderMeshOptimizer) + add_subdirectory(contrib/MeshOptimizer) + include_directories(contrib/MeshOptimizer) + include_directories(${CMAKE_CURRENT_BINARY_DIR}/contrib/MeshOptimizer) + add_subdirectory(contrib/MeshQualityOptimizer) + include_directories(contrib/MeshQualityOptimizer) + set_config_option(HAVE_OPTHOM "OptHom") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/domhex AND + ENABLE_DOMHEX AND HAVE_MESH) + add_subdirectory(contrib/domhex) + include_directories(contrib/domhex) + set_config_option(HAVE_DOMHEX "DomHex") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/QuadTri AND + ENABLE_QUADTRI AND HAVE_MESH) + add_subdirectory(contrib/QuadTri) + include_directories(contrib/QuadTri) + set_config_option(HAVE_QUADTRI "QuadTri") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/kbipack AND ENABLE_KBIPACK) + set_config_option(HAVE_KBIPACK "Kbipack") + add_subdirectory(contrib/kbipack) + include_directories(contrib/kbipack) + if(ENABLE_GMP) + find_library(GMP_LIB libgmp.a) + find_path(GMP_INC "gmp.h" PATH_SUFFIXES src include) + endif() + if(GMP_LIB AND GMP_INC) + set_config_option(HAVE_GMP "GMP") + list(APPEND EXTERNAL_LIBRARIES ${GMP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GMP_INC}) + else() + message(STATUS "GMP not found: Kbipack uses long int") + endif() +endif() + +if(ENABLE_MATHEX) + find_library(MATHEX_LIB mathex PATH_SUFFIXES lib) + find_path(MATHEX_INC "mathex.h" PATH_SUFFIXES src include) + if(ENABLE_SYSTEM_CONTRIB AND MATHEX_LIB AND MATHEX_INC) + list(APPEND EXTERNAL_LIBRARIES ${MATHEX_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MATHEX_INC}) + set_config_option(HAVE_MATHEX "MathEx[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MathEx) + add_subdirectory(contrib/MathEx) + include_directories(contrib/MathEx) + set_config_option(HAVE_MATHEX "MathEx") + endif() +endif() + +if(ENABLE_MPI) + find_package(MPI) + if(MPI_FOUND) + set_config_option(HAVE_MPI "MPI") + list(APPEND EXTERNAL_INCLUDES ${MPI_CXX_INCLUDE_PATH}) + list(APPEND EXTERNAL_LIBRARIES ${MPI_CXX_LIBRARIES}) + set(CMAKE_C_COMPILER ${MPI_C_COMPILER}) + set(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER}) + set(CMAKE_Fortran_COMPILER ${MPI_Fortran_COMPILER}) + endif() +endif() + +if(ENABLE_POPPLER) + find_library(POPPLER_LIB poppler) + find_library(POPPLER_CPP_LIB poppler-cpp) + find_path(POPPLER_INC "poppler/cpp/poppler-document.h" PATH_SUFFIXES src include) + if(POPPLER_LIB AND POPPLER_INC) + set_config_option(HAVE_POPPLER "Poppler") + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_LIB}) + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_CPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${POPPLER_INC}) + endif() +endif() + +if(ENABLE_P4EST) + find_library(P4EST_LIB p4est) + find_path(P4EST_INC "p4est.h" PATH_SUFFIXES src) + find_library(SC_LIB sc) + if(P4EST_LIB AND P4EST_INC AND SC_LIB) + set_config_option(HAVE_P4EST "P4est") + list(APPEND EXTERNAL_LIBRARIES ${P4EST_LIB} ${SC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${P4EST_INC}) + endif() +endif() + +if(HAVE_MESH OR HAVE_SOLVER) + if(ENABLE_METIS) + if(METIS_ROOT) + find_library(METIS_LIB metis PATHS ${METIS_ROOT} PATH_SUFFIXES lib) + find_path(METIS_INC "metis.h" PATHS ${METIS_ROOT} PATH_SUFFIXES include) + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis") + else() + find_library(METIS_LIB metis PATH_SUFFIXES lib) + find_path(METIS_INC "metis.h" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC) + message(STATUS "Using system version of METIS") + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/metis) + add_definitions(-DUSE_GKREGEX) + add_subdirectory(contrib/metis) + include_directories(contrib/metis/include contrib/metis/libmetis + contrib/metis/GKlib) + set_config_option(HAVE_METIS "Metis") + endif() + endif() + endif() +endif() + +if(HAVE_MESH) + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh/tetgenBR.cxx) + set_config_option(HAVE_TETGENBR "TetGen/BR") + endif() + + if(ENABLE_VOROPP) + find_library(VOROPP_LIB voro++ PATH_SUFFIXES lib) + find_path(VOROPP_INC "voro++.hh" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND VOROPP_LIB AND VOROPP_INC) + message(STATUS "Using system version of voro++") + list(APPEND EXTERNAL_LIBRARIES ${VOROPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${VOROPP_INC}) + set_config_option(HAVE_VOROPP "Voro++[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++) + add_subdirectory(contrib/voro++) + include_directories(contrib/voro++/src) + set_config_option(HAVE_VOROPP "Voro++") + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/blossom AND ENABLE_BLOSSOM) + add_subdirectory(contrib/blossom) + include_directories(contrib/blossom/MATCH contrib/blossom/concorde97 + contrib/blossom/concorde97/INCLUDE) + set_config_option(HAVE_BLOSSOM "Blossom") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/Netgen AND ENABLE_NETGEN) + add_subdirectory(contrib/Netgen) + include_directories(contrib/Netgen contrib/Netgen/libsrc/include + contrib/Netgen/nglib) + set_config_option(HAVE_NETGEN "Netgen") + add_definitions(-DNO_PARALLEL_THREADS -DNOTCL) + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/bamg AND ENABLE_BAMG) + add_subdirectory(contrib/bamg) + include_directories(contrib/bamg contrib/bamg/bamglib) + set_config_option(HAVE_BAMG "Bamg") + endif() + + if(ENABLE_MMG3D) + find_library(MMG3D_LIB mmg3d PATH_SUFFIXES lib) + find_path(MMG3D_INC "libmmg3d.h" PATH_SUFFIXES src include) + if(ENABLE_SYSTEM_CONTRIB AND MMG3D_LIB AND MMG3D_INC) + list(APPEND EXTERNAL_LIBRARIES ${MMG3D_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MMG3D_INC}) + set_config_option(HAVE_MMG3D "Mmg3d[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/mmg3d) + add_subdirectory(contrib/mmg3d) + include_directories(contrib/mmg3d/build/sources) + set_config_option(HAVE_MMG3D "Mmg3d") + endif() + endif() +endif() + +if(ENABLE_MED OR ENABLE_CGNS) + find_package(HDF5) + if(HDF5_FOUND) + set(HDF5_LIB "${HDF5_C_LIBRARIES}") + list(APPEND EXTERNAL_INCLUDES ${HDF5_INCLUDE_DIRS}) + if(ENABLE_MED) + find_library(MED_LIB medC) + if(MED_LIB) + set_config_option(HAVE_MED "Med") + list(APPEND EXTERNAL_LIBRARIES ${MED_LIB}) + endif() + endif() + if(ENABLE_CGNS) + find_library(CGNS_LIB cgns HINTS ENV CGNS_ROOT PATH_SUFFIXES lib) + find_path(CGNS_INC "cgnslib.h" HINTS ENV CGNS_ROOT PATH_SUFFIXES include) + if(CGNS_LIB AND CGNS_INC) + set_config_option(HAVE_LIBCGNS "Cgns") + list(APPEND EXTERNAL_LIBRARIES ${CGNS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CGNS_INC}) + if(ENABLE_CGNS_CPEX0045) + set_config_option(HAVE_LIBCGNS_CPEX0045 "Cgns_CPEX0045") + endif() + endif() + endif() + if(MED_LIB OR CGNS_LIB) + list(APPEND EXTERNAL_LIBRARIES ${HDF5_LIB}) + find_library(SZ_LIB NAMES szlib sz) + if(SZ_LIB) + list(APPEND EXTERNAL_LIBRARIES ${SZ_LIB}) + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + endif() + endif() + endif() + else() + message(STATUS "HDF5 not found") + endif() +endif() + +if(HAVE_SOLVER) + if(ENABLE_GMM) + find_path(GMM_INC "gmm.h" PATH_SUFFIXES src include include/gmm) + if(ENABLE_SYSTEM_CONTRIB AND GMM_INC) + message(STATUS "Using system version of GMM") + list(APPEND EXTERNAL_INCLUDES ${GMM_INC}) + set_config_option(HAVE_GMM "Gmm[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/gmm) + include_directories(contrib/gmm) + set_config_option(HAVE_GMM "Gmm") + endif() + endif() + + if(ENABLE_PETSC) + if(PETSC_DIR) + set(ENV_PETSC_DIR ${PETSC_DIR}) + else() + set(ENV_PETSC_DIR $ENV{PETSC_DIR}) + endif() + if(PETSC_ARCH) + set(ENV_PETSC_ARCH ${PETSC_ARCH}) + else() + set(ENV_PETSC_ARCH $ENV{PETSC_ARCH}) + endif() + set(PETSC_POSSIBLE_CONF_FILES + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc-conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc/conf/petscvariables) + foreach(FILE ${PETSC_POSSIBLE_CONF_FILES}) + if(EXISTS ${FILE}) + # old-style PETSc installations (using PETSC_DIR and PETSC_ARCH) + message(STATUS "Using PETSc dir: ${ENV_PETSC_DIR}") + message(STATUS "Using PETSc arch: ${ENV_PETSC_ARCH}") + # find includes by parsing the petscvariables file + file(STRINGS ${FILE} PETSC_VARIABLES NEWLINE_CONSUME) + endif() + endforeach() + if(PETSC_VARIABLES) + # try to find PETSC_CC_INCLUDES for PETSc >= 3.4 + string(REGEX MATCH "PETSC_CC_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "PETSC_CC_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + else() + # try to find PETSC_PACKAGES_INCLUDES in older versions + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/include) + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/include) + string(REGEX MATCH "PACKAGES_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + string(REPLACE "PACKAGES_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + endif() + if(PETSC_PACKAGES_INCLUDES) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "-I" "" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + string(REPLACE " " ";" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + foreach(VAR ${PETSC_PACKAGES_INCLUDES}) + # seem to include unexisting directories (/usr/include/lib64) + # check to avoid warnings + if(EXISTS ${VAR}) + list(APPEND EXTERNAL_INCLUDES ${VAR}) + endif() + endforeach() + endif() + endif() + # find libraries (<= 3.0) + set(PETSC_LIBS_REQUIRED petscksp petscdm petscmat petscvec petsc) + find_all_libraries(PETSC_LIBS PETSC_LIBS_REQUIRED + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib "") + # petsc 3.1 creates only one library (libpetsc) + if(NOT PETSC_LIBS) + find_library(PETSC_LIBS petsc PATHS ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + endif() + if(PETSC_LIBS) + set_config_option(HAVE_PETSC "PETSc") + if(NOT HAVE_BLAS) + set_config_option(HAVE_BLAS "Blas[petsc]") + endif() + if(NOT HAVE_LAPACK) + set_config_option(HAVE_LAPACK "Lapack[petsc]") + endif() + endif() + # find slepc (needs to be linked in before petsc) + if(ENABLE_SLEPC) + if(SLEPC_DIR) + set(ENV_SLEPC_DIR ${SLEPC_DIR}) + else() + set(ENV_SLEPC_DIR $ENV{SLEPC_DIR}) + endif() + find_library(SLEPC_LIB slepc PATHS ${ENV_SLEPC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + if(SLEPC_LIB) + find_path(SLEPC_INC "slepc.h" PATHS ${ENV_SLEPC_DIR} PATH_SUFFIXES include + ${ENV_PETSC_ARCH}/include include/slepc NO_DEFAULT_PATH) + if(SLEPC_INC) + message(STATUS "Using SLEPc dir: ${ENV_SLEPC_DIR}") + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + find_path(SLEPC_INC2 "slepcconf.h" PATHS ${ENV_SLEPC_DIR} + PATH_SUFFIXES ${ENV_PETSC_ARCH}/include NO_DEFAULT_PATH) + if(SLEPC_INC2) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC2}) + endif() + endif() + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + # find additional libraries to link with + string(REGEX MATCH "PACKAGES_LIBS = [^\n\r]*" PLIBS ${PETSC_VARIABLES}) + if(PLIBS) + string(REPLACE "PACKAGES_LIBS = " "" PLIBS ${PLIBS}) + string(STRIP ${PLIBS} PLIBS) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS}") + endif() + string(REGEX MATCH "PETSC_EXTERNAL_LIB_BASIC = [^\n\r]*" PLIBS_BASIC ${PETSC_VARIABLES}) + if(PLIBS_BASIC) + string(REPLACE "PETSC_EXTERNAL_LIB_BASIC = " "" PLIBS_BASIC ${PLIBS_BASIC}) + string(STRIP ${PLIBS_BASIC} PLIBS_BASIC) + separate_arguments(PLIBS_BASIC) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS_BASIC}") + endif() + string(REGEX MATCH "PCC_LINKER_LIBS = [^\n\r]*" LLIBS ${PETSC_VARIABLES}) + if(LLIBS) + string(REPLACE "PCC_LINKER_LIBS = " "" LLIBS ${LLIBS}) + string(STRIP ${LLIBS} LLIBS) + list(APPEND EXTERNAL_LIBRARIES "${LLIBS}") + endif() + else() + # new-style PETSc installations (in standard system directories) + find_library(PETSC_LIBS petsc) + find_path(PETSC_INC "petsc.h" PATH_SUFFIXES include/petsc) + if(PETSC_LIBS AND PETSC_INC) + set_config_option(HAVE_PETSC "PETSc") + if(ENABLE_SLEPC) + find_library(SLEPC_LIB slepc) + find_path(SLEPC_INC "slepc.h" PATH_SUFFIXES include/slepc) + if(SLEPC_LIB AND SLEPC_INC) + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${PETSC_INC}) + endif() + endif() + endif() + + if(ENABLE_MUMPS AND HAVE_BLAS AND HAVE_LAPACK) + set(MUMPS_LIBS_REQUIRED smumps dmumps cmumps zmumps mumps_common pord) + if(NOT ENABLE_MPI) + list(APPEND MUMPS_LIBS_REQUIRED mpiseq) + endif() + find_all_libraries(MUMPS_LIBRARIES MUMPS_LIBS_REQUIRED "" "lib") + find_path(SMUMPS_INC "smumps_c.h" PATH_SUFFIXES src include) + find_path(DMUMPS_INC "dmumps_c.h" PATH_SUFFIXES src include) + find_path(CMUMPS_INC "cmumps_c.h" PATH_SUFFIXES src include) + find_path(ZMUMPS_INC "zmumps_c.h" PATH_SUFFIXES src include) + if(MUMPS_LIBRARIES AND SMUMPS_INC AND DMUMPS_INC AND CMUMPS_INC AND ZMUMPS_INC) + set_config_option(HAVE_MUMPS "MUMPS") + list(APPEND EXTERNAL_LIBRARIES ${MUMPS_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${SMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${DMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${CMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${ZMUMPS_INC}) + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND EXTERNAL_LIBRARIES ${GFORTRAN_LIB}) + endif() + if(ENABLE_GMM) # use GMM/MUMPS interface + add_definitions(-DGMM_USES_MUMPS) + endif() + endif() + endif() + + if(ENABLE_GETDP) + find_library(GETDP_LIB GetDP) + find_path(GETDP_INC "GetDP.h" PATH_SUFFIXES getdp) + if(GETDP_LIB AND GETDP_INC) + set_config_option(HAVE_GETDP "GetDP") + list(APPEND EXTERNAL_LIBRARIES ${GETDP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GETDP_INC}) + endif() + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt AND + ENABLE_HXT AND HAVE_METIS) + set_config_option(HAVE_HXT "Hxt") + add_subdirectory(contrib/hxt) + include_directories(BEFORE contrib/hxt) + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/hxt_tetDelaunay.c) + set_config_option(HAVE_HXT3D "Hxt3D") + endif() + if(MSVC) + # Visual C++ does not support C99 - force compilation as C++ code + file(GLOB_RECURSE HXT_SRC contrib/hxt/*.c) + set_compile_flags(HXT_SRC "/TP") + endif() + check_include_file("immintrin.h" HAVE_IMMINTRIN_H) + if(NOT HAVE_IMMINTRIN_H) + add_definitions(-DHAVE_NO_IMMINTRIN_H) + endif() + if(HAVE_PETSC) + add_definitions(-DHXT_HAVE_PETSC) + endif() + if(CMAKE_C_COMPILER MATCHES "pgi") + add_definitions(-DHAVE_NO_OPENMP_SIMD) + endif() +endif() + +if(ENABLE_OCC) + set(OCC_MINIMAL_VERSION "6.9.1") + if(WIN32) + if(HAVE_64BIT_SIZE_T) + set(OCC_SYS_NAME win64) + else() + set(OCC_SYS_NAME win32) + endif() + else() + set(OCC_SYS_NAME ${CMAKE_SYSTEM_NAME}) + endif() + find_path(OCC_INC "Standard_Version.hxx" HINTS ENV CASROOT PATH_SUFFIXES + inc include include/oce opencascade include/opencascade + occt include/occt) + if(OCC_INC) + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAJOR REGEX "#define OCC_VERSION_MAJOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MINOR REGEX "#define OCC_VERSION_MINOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAINT REGEX "#define OCC_VERSION_MAINTENANCE.*") + if(OCC_MAJOR AND OCC_MINOR AND OCC_MAINT) + string(REGEX MATCH "[0-9]+" OCC_MAJOR "${OCC_MAJOR}") + string(REGEX MATCH "[0-9]+" OCC_MINOR "${OCC_MINOR}") + string(REGEX MATCH "[0-9]+" OCC_MAINT "${OCC_MAINT}") + set(OCC_VERSION "${OCC_MAJOR}.${OCC_MINOR}.${OCC_MAINT}") + message(STATUS "Found OpenCASCADE version ${OCC_VERSION} in ${OCC_INC}") + endif() + endif() + if(OCC_VERSION AND OCC_VERSION STRLESS ${OCC_MINIMAL_VERSION}) + message(WARNING "Gmsh requires OpenCASCADE >= ${OCC_MINIMAL_VERSION}. " + "Use CMAKE_PREFIX_PATH or the CASROOT environment variable " + "to explicitely specify the installation path of OpenCASCADE") + elseif(OCC_INC) + set(OCC_LIBS_REQUIRED + # subset of DataExchange + TKSTEP TKSTEP209 TKSTEPAttr TKSTEPBase TKIGES TKXSBase + # ModelingAlgorithms + TKOffset TKFeat TKFillet TKBool TKMesh TKHLR TKBO TKPrim TKShHealing + TKTopAlgo TKGeomAlgo + # ModelingData + TKBRep TKGeomBase TKG3d TKG2d + # FoundationClasses + TKMath TKernel) + if(ENABLE_OCC_TBB) + list(APPEND OCC_LIBS_REQUIRED tbb tbbmalloc) + endif() + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS_REQUIRED) + if(OCC_LIBS) + message(STATUS "OCC libraries specified explicitly: " ${OCC_LIBS}) + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS) + else() + set(OCC_LIBS) + foreach(OCC ${OCC_LIBS_REQUIRED}) + if(ENABLE_OCC_STATIC) + set(LIBNAME lib${OCC}.a) + else() + set(LIBNAME ${OCC}) + endif() + find_library(OCC_LIB ${LIBNAME} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib) + if(OCC_LIB) + list(APPEND OCC_LIBS ${OCC_LIB}) + else() + message(STATUS "OCC lib " ${LIBNAME} " not Found") + endif() + unset(OCC_LIB CACHE) + endforeach() + list(LENGTH OCC_LIBS NUM_OCC_LIBS) + endif() + endif() + + # additional OCC libraries to handle reading of STEP/IGES attributes. Oh my... + if(ENABLE_OCC_CAF) + find_package(Freetype) + if(FREETYPE_FOUND) + set(OCC_CAF_LIBS_REQUIRED + TKXDESTEP TKXDEIGES TKXCAF TKLCAF TKVCAF TKCAF TKV3d TKService TKCDF) + list(LENGTH OCC_CAF_LIBS_REQUIRED NUM_OCC_CAF_LIBS_REQUIRED) + set(OCC_CAF_LIBS) + foreach(OCC ${OCC_CAF_LIBS_REQUIRED}) + find_library(OCC_CAF_LIB ${OCC} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib) + if(OCC_CAF_LIB) + list(APPEND OCC_CAF_LIBS ${OCC_CAF_LIB}) + else() + message(STATUS "OCC CAF lib " ${OCC} " not Found") + endif() + unset(OCC_CAF_LIB CACHE) + endforeach() + list(LENGTH OCC_CAF_LIBS NUM_OCC_CAF_LIBS) + endif() + endif() + + # append OCC CAF libraries first... + if(NUM_OCC_CAF_LIBS EQUAL NUM_OCC_CAF_LIBS_REQUIRED) + set_config_option(HAVE_OCC_CAF "OpenCASCADE-CAF") + list(APPEND EXTERNAL_LIBRARIES ${OCC_CAF_LIBS} ${FREETYPE_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${FREETYPE_INCLUDE_DIRS}) + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "windowscodecs") + list(APPEND EXTERNAL_LIBRARIES "ole32") + endif() + endif() + + # then append OCC libraries + if(NUM_OCC_LIBS EQUAL NUM_OCC_LIBS_REQUIRED) + set_config_option(HAVE_OCC "OpenCASCADE") + list(APPEND EXTERNAL_LIBRARIES ${OCC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${OCC_INC}) + if(HAVE_64BIT_SIZE_T) + add_definitions(-D_OCC64) + endif() + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "winspool") + add_definitions(-DOCC_CONVERT_SIGNALS) + elseif(MSVC) + add_definitions(-DWNT) + endif() + endif() +endif() + +if(ENABLE_ACIS) + find_library(ACIS_LIB SpaACIS PATH_SUFFIXES bin/maci386) + if(ACIS_LIB) + find_path(ACIS_INC "kernapi.hxx" PATH_SUFFIXES include) + if(ACIS_INC) + set_config_option(HAVE_ACIS "Acis") + list(APPEND EXTERNAL_LIBRARIES ${ACIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ACIS_INC}) + endif() + endif() +endif() + +if(ENABLE_ZIPPER) + if(ENABLE_BUILD_IOS) + set_config_option(HAVE_LIBZ "Zlib") + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/zipper AND HAVE_LIBZ) + add_subdirectory(contrib/zipper) + include_directories(contrib/zipper) + set_config_option(HAVE_ZIPPER "Zipper") + endif() +endif() + +if(ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON) + find_package(SWIG REQUIRED) + include(${SWIG_USE_FILE}) + find_package(PythonLibs) + if(SWIG_FOUND AND PYTHONLIBS_FOUND) + message(STATUS "Found SWIG version " ${SWIG_VERSION}) + find_package(PythonInterp) + string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION) + if(SWIG_MAJOR_VERSION EQUAL 1) + message(WARNING "Python bindings require SWIG >= 2: disabling Python") + else() + set_config_option(HAVE_PYTHON "Python") + mark_as_advanced(CLEAR PYTHON_LIBRARY PYTHON_INCLUDE_DIR) + if(ENABLE_NUMPY) + if (NOT NUMPY_INC) + EXEC_PROGRAM (${PYTHON_EXECUTABLE} + ARGS "-c \"import numpy; print(numpy.get_include())\"" + OUTPUT_VARIABLE NUMPY_INC + RETURN_VALUE NUMPY_NOT_FOUND) + endif() + if(NUMPY_INC) + list(APPEND EXTERNAL_INCLUDES ${NUMPY_INC}) + set_config_option(HAVE_NUMPY "Numpy") + endif() + endif() + if(HAVE_PETSC) + if(ENABLE_PETSC4PY) + EXECUTE_PROCESS( + COMMAND ${PYTHON_EXECUTABLE} -c "import petsc4py; print(petsc4py.get_include())" + OUTPUT_VARIABLE PETSC4PY_INC + RESULT_VARIABLE PETSC4PY_NOT_FOUND + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(PETSC4PY_INC) + list(APPEND EXTERNAL_INCLUDES ${PETSC4PY_INC}) + set_config_option(HAVE_PETSC4PY "PETSc4py") + endif() + endif() + endif() + endif() + endif() +endif() + +check_function_exists(vsnprintf HAVE_VSNPRINTF) +if(NOT HAVE_VSNPRINTF AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_VSNPRINTF "NoVsnprintf") +endif() + +check_include_file(sys/socket.h HAVE_SYS_SOCKET_H) +if(HAVE_SYS_SOCKET_H) + set(CMAKE_EXTRA_INCLUDE_FILES sys/socket.h) +endif() +check_type_size(socklen_t SOCKLEN_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT SOCKLEN_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_SOCKLEN_T "NoSocklenT") +endif() + +check_include_file(stdint.h HAVE_STDINT_H) +if(HAVE_STDINT_H) + set(CMAKE_EXTRA_INCLUDE_FILES stdint.h) +else() + set_config_option(HAVE_NO_STDINT_H "NoStdintH") +endif() +check_type_size(intptr_t INTPTR_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT INTPTR_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_INTPTR_T "NoIntptrT") +endif() + +check_include_file(dlfcn.h DLFCN_H) +if(DLFCN_H) + set_config_option(HAVE_DLOPEN "Dlopen") + list(APPEND EXTERNAL_LIBRARIES ${CMAKE_DL_LIBS}) +endif() + +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + check_include_file(linux/joystick.h LINUX_JOYSTICK_H) + if(LINUX_JOYSTICK_H) + set_config_option(HAVE_LINUX_JOYSTICK "LinuxJoystick") + endif() +endif() + +if(WIN32) + add_definitions(-D_USE_MATH_DEFINES) + list(APPEND EXTERNAL_LIBRARIES winmm wsock32 ws2_32 psapi) +endif() + +if(MSVC) + add_definitions(-DNOMINMAX -D_CRT_SECURE_NO_DEPRECATE -D_SCL_SECURE_NO_DEPRECATE) +endif() + +# add C functions API +set(GMSH_SRC ${GMSH_SRC};api/gmshc.cpp) + +# force full warnings to encourage everybody to write clean(er) code +check_cxx_compiler_flag("-Wall" WALL) +if(WALL AND NOT MSVC) + file(GLOB_RECURSE WALL_SRC Common/*.cpp Fltk/*.cpp FunctionSpace/*.cpp + Geo/*.cpp Graphics/*.cpp Mesh/*.cpp Numeric/*.cpp Parser/*.cpp + Plugin/*.cpp Post/*.cpp Solver/*.cpp) + set(WF "-Wall") + check_cxx_compiler_flag("-Wint-to-void-pointer-cast" WCAST) + if(WCAST) + set(WF "${WF} -Wno-int-to-void-pointer-cast") + endif() + check_cxx_compiler_flag("-Wdeprecated-declarations" WDEPREC) + if(WDEPREC) + # FIXME: remove this when we have fixed the deprecated GLU code for OpenGL3 + set(WF "${WF} -Wno-deprecated-declarations") + endif() + check_cxx_compiler_flag("-Wmisleading-indentation" WIND) + if(WIND) + set(WF "${WF} -Wno-misleading-indentation") + endif() + set_compile_flags(WALL_SRC ${WF}) +endif() + +# don't issue warnings for contributed libraries +check_cxx_compiler_flag("-w" NOWARN) +if(NOWARN) + file(GLOB_RECURSE NOWARN_SRC contrib/*.cpp contrib/*.cc contrib/*.cxx contrib/*.c) + set_compile_flags(NOWARN_SRC "-w") +endif() + +# disable compile optimization on some known problematic files +check_cxx_compiler_flag("-O0" NOOPT) +if(NOOPT OR ENABLE_BUILD_IOS) + if(ENABLE_BUILD_IOS) # optimized iOS 10 64 bits screws somewhere in Geo + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Geo/G*.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* Mesh/Background*) + else() + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* contrib/bamg/* Mesh/Background*) + endif() + set_compile_flags(NOOPT_SRC "-O0") +endif() + +# do not use arithmetic contraction in predicates.cpp +# if("${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "/fp:strict") +# elseif(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fno-unsafe-math-optimizations -ffp-contract=off") +# elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fp-model strict") +# endif() + +# enable Revoropt and set compile flags for the corresponding plugin +if(ENABLE_REVOROPT) + find_path(EIGEN3_INC "eigen3/Eigen/Dense") + if(EIGEN3_INC AND HAVE_MESH AND HAVE_PLUGINS AND HAVE_ANN AND HAVE_ALGLIB) + list(APPEND EXTERNAL_INCLUDES ${EIGEN3_INC} contrib/Revoropt/include) + message(STATUS "using contrib/Revoropt") + set_config_option(HAVE_REVOROPT "Revoropt") + add_definitions(-DUSE_ANN) + get_source_file_property(PROP Plugin/CVTRemesh.cpp COMPILE_FLAGS) + if(PROP) + set_source_files_properties(Plugin/CVTRemesh.cpp PROPERTIES + COMPILE_FLAGS "${PROP} -std=c++11") + else() + set_source_files_properties(Plugin/CVTRemesh.cpp PROPERTIES + COMPILE_FLAGS "-std=c++11") + endif() + else() + message(WARNING "Revoropt requires Eigen3, Mesh, Plugins, ANN and ALGLIB") + endif() +endif() + +list(SORT CONFIG_OPTIONS) +set(GMSH_CONFIG_OPTIONS "") +foreach(OPT ${CONFIG_OPTIONS}) + set(GMSH_CONFIG_OPTIONS "${GMSH_CONFIG_OPTIONS} ${OPT}") +endforeach() + +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshConfig.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshVersion.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h) + +# the texi version file is modified in the source directory (not ideal, but +# since git tracks the contents of the file this is acceptable as it will only +# change when the actual version is changed - not for each git hash) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi.in + ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi) + +file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/version.txt + ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION}) + +# process cmake environment variables so we can append them to the -I include +# commands. This is not recommended (we should only use the cache variables) but +# it is very convenient: otherwise we have to remember providing the +# -D... options to cmake for each new build. +set(ENV_CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH}) +set(ENV_CMAKE_INCLUDE_PATH $ENV{CMAKE_INCLUDE_PATH}) +if(UNIX) + if(ENV_CMAKE_PREFIX_PATH) + string(REPLACE ":" ";" ENV_CMAKE_PREFIX_PATH ${ENV_CMAKE_PREFIX_PATH}) + endif() + if(ENV_CMAKE_INCLUDE_PATH) + string(REPLACE ":" ";" ENV_CMAKE_INCLUDE_PATH ${ENV_CMAKE_INCLUDE_PATH}) + endif() +endif() +list(APPEND EXTERNAL_INCLUDES ${CMAKE_INCLUDE_PATH} ${ENV_CMAKE_INCLUDE_PATH}) +list(APPEND EXTERNAL_INCLUDES ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) +foreach(DIR ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/include) +endforeach() + +if(EXTERNAL_INCLUDES) + list(REMOVE_DUPLICATES EXTERNAL_INCLUDES) +endif() + +if(HAVE_FLTK) + set(LINK_LIBRARIES ${FLTK_LIBRARIES} ${EXTERNAL_LIBRARIES} + ${OPENGL_LIBRARIES} ${LAPACK_LIBRARIES}) +elseif(HAVE_OPENGL) + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${OPENGL_LIBRARIES} + ${LAPACK_LIBRARIES}) +else() + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) +endif() + +# try to use static gfortran on static builds (cannot do this on dynamic builds +# as e.g. Debian compiles libgfortran.a without -fPIC: sigh...) +if(NOT ENABLE_BUILD_DYNAMIC AND NOT ENABLE_BUILD_SHARED) + find_library(GFORTRAN_STATIC libgfortran.a) + if(GFORTRAN_STATIC) + set(CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES) + message(STATUS "Using static libgfortran") + foreach(STR ${LINK_LIBRARIES}) + string(REPLACE "-lgfortran" ${GFORTRAN_STATIC} STR2 ${STR}) + list(APPEND LINK_LIBRARIES2 ${STR2}) + endforeach() + set(LINK_LIBRARIES ${LINK_LIBRARIES2}) + endif() +endif() + +# Linux-specific linking +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + if(HAVE_OCC) + find_library(RT_LIB rt) + if(RT_LIB) + list(APPEND LINK_LIBRARIES ${RT_LIB}) + endif() + endif() + if(CMAKE_C_COMPILER_ID MATCHES "GNU" OR CMAKE_C_COMPILER_ID MATCHES "Intel") + add_definitions(-fPIC) + endif() +endif() + +# we could specify include dirs more selectively, but this is simpler +include_directories(Common Fltk Geo Graphics Mesh Solver Numeric Parser + Plugin Post api ${EXTERNAL_INCLUDES} ${CMAKE_CURRENT_BINARY_DIR}/Common) + +# set this for external codes that might include this CMakeList file +set(GMSH_EXTERNAL_INCLUDE_DIRS ${EXTERNAL_INCLUDES} CACHE + STRING "External include directories" FORCE) +set(GMSH_EXTERNAL_LIBRARIES ${LINK_LIBRARIES} CACHE + STRING "External libraries" FORCE) + +# group sources for easier navigation in IDEs +foreach(DIR ${GMSH_DIRS}) + string(REGEX REPLACE "\\+" "\\\\+" DIR ${DIR}) + source_group(${DIR} REGULAR_EXPRESSION ${DIR}/.*) +endforeach() + +# static library target +if(ENABLE_BUILD_LIB) + add_library(lib STATIC ${GMSH_SRC}) + set_target_properties(lib PROPERTIES OUTPUT_NAME gmsh) + if(MSVC) + set_target_properties(lib PROPERTIES DEBUG_POSTFIX d) + if(ENABLE_MSVC_STATIC_RUNTIME) + set_target_properties(lib PROPERTIES LINK_FLAGS_RELEASE "/nodefaultlib:LIBCMT") + endif() + endif() +endif() + +# shared library target +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + add_library(shared SHARED ${GMSH_SRC}) + set_target_properties(shared PROPERTIES OUTPUT_NAME gmsh + VERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION} + SOVERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}) + if(WIN32) + set_target_properties(shared PROPERTIES PREFIX "" IMPORT_PREFIX "" + IMPORT_SUFFIX ".lib" COMPILE_FLAGS "-DGMSH_DLL -DGMSH_DLL_EXPORT") + endif() + target_link_libraries(shared ${LINK_LIBRARIES}) + if(MSVC AND ENABLE_MSVC_STATIC_RUNTIME) + message(STATUS "Note: By enabling ENABLE_MSVC_STATIC_RUNTIME, shared library " + "won't link. In MSVC change /MT to /MD in the shared project properties") + endif() +endif() + +# binary targets +if(HAVE_FLTK) + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh WIN32 Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh WIN32 Common/Main.cpp ${GMSH_SRC}) + endif() + # we could add this to create a minimal app bundle even without install + # if(APPLE AND NOT ENABLE_OS_SPECIFIC_INSTALL) + # set_target_properties(gmsh PROPERTIES MACOSX_BUNDLE ON + # MACOSX_BUNDLE_INFO_PLIST ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_dev.plist) + # endif() +else() + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh Common/Main.cpp ${GMSH_SRC}) + endif() +endif() +target_link_libraries(gmsh ${LINK_LIBRARIES}) + +# Windows specific linker options +if(WIN32 AND NOT MSVC) + set(FLAGS "-Wl,--stack,16777216 -mwindows") + if(HAVE_64BIT_SIZE_T) + set(FLAGS "${FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win64Icon.res") + else() + set(FLAGS "${FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win32Icon.res") + endif() + set_target_properties(gmsh PROPERTIES LINK_FLAGS "${FLAGS} -static") + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + set_target_properties(shared PROPERTIES LINK_FLAGS -static) + endif() + # remove -Wl,-Bdynamic flags + set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) + set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS) +elseif(MSVC) + set_target_properties(gmsh PROPERTIES LINK_FLAGS "/STACK:16777216 /SAFESEH:NO") +endif() + +# android target +if(ENABLE_BUILD_ANDROID) + find_file(CMAKE_TOOLCHAIN_FILE "android.toolchain.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for android without android-cmake") + endif() + add_definitions(-D_GLIBCXX_USE_C99_MATH=1) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + set(CMAKE_BUILD_TYPE Release) + set(LIBRARY_OUTPUT_PATH_ROOT ${CMAKE_CURRENT_BINARY_DIR}) + set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_BINARY_DIR}/libs/) + add_definitions(-DBUILD_ANDROID) + add_definitions(-DPICOJSON_USE_LOCALE=0) + add_library(androidGmsh SHARED ${GMSH_SRC}) + set_target_properties(androidGmsh PROPERTIES OUTPUT_NAME gmsh) + target_link_libraries(androidGmsh ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) + add_custom_command(TARGET androidGmsh POST_BUILD COMMAND + ${CMAKE_STRIP} ${LIBRARY_OUTPUT_PATH}/libgmsh.so) +endif() + +# parser target +find_program(BISON bison) +find_program(FLEX flex) +if(BISON AND FLEX) + add_custom_target(parser + COMMAND ${BISON} -p gmsh_yy --output Gmsh.tab.cpp -d Gmsh.y + COMMAND ${FLEX} -P gmsh_yy -o Gmsh.yy.cpp Gmsh.l + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Parser) +endif() + +if(UNIX) + # cannot use cmake's file search functions here (they would only find files + # existing at configuration time) + add_custom_target(purge + COMMAND rm -f `find . -name *~ -o -name *~~` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + add_custom_target(etags + COMMAND etags `find . -name *.cpp -o -name *.h -o -name *.y` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion + OUTPUT_VARIABLE CXX_COMPILER_VERSION + OUTPUT_STRIP_TRAILING_WHITESPACE) +else() + set(CXX_COMPILER_VERSION "Unknown") +endif() + +set(WELCOME_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/WELCOME.txt) +set(SDK_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/SDK.txt) +set(LICENSE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE.txt) +set(CREDITS_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CREDITS.txt) +set(CHANGELOG_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.txt) +file(GLOB TUTORIAL_GEO_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/?*.*) +file(GLOB TUTORIAL_CPP_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c++/?*.*) +file(GLOB TUTORIAL_C_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c/?*.*) +file(GLOB TUTORIAL_PY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/python/?*.*) +file(GLOB TUTORIAL_JL_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/julia/?*.*) +file(GLOB DEMOS ${CMAKE_CURRENT_SOURCE_DIR}/demos/*) +foreach(SUBDIR ${DEMOS}) + if(IS_DIRECTORY ${SUBDIR}) + list(APPEND DEMOS_DIRS ${SUBDIR}) + endif() +endforeach() +set(TEX_DIR ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo) +file(GLOB TEX_SRC ${TEX_DIR}/*.texi) +set(TEX_OBJ ${TEX_DIR}/gmsh.aux ${TEX_DIR}/gmsh.cp ${TEX_DIR}/gmsh.cps + ${TEX_DIR}/gmsh.fn ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.ky + ${TEX_DIR}/gmsh.log ${TEX_DIR}/gmsh.pdf ${TEX_DIR}/gmsh.pg ${TEX_DIR}/gmsh.toc + ${TEX_DIR}/gmsh.tp ${TEX_DIR}/gmsh.tps ${TEX_DIR}/gmsh.txt ${TEX_DIR}/gmsh.vr) + +macro(unix2dos VARNAME) + file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/unix2dos) + set(UNIX2DOS_FILES) + foreach(FILE ${${VARNAME}}) + file(READ ${FILE} F0) + get_filename_component(N ${FILE} NAME) + if(CYGWIN) + string(REGEX REPLACE "\n" "\r\n" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F1}") + else() # if not in Cygwin, cmake adds '\r's automatically + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F0}") + endif() + list(APPEND UNIX2DOS_FILES ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N}) + endforeach() + set(${VARNAME} ${UNIX2DOS_FILES}) +endmacro() + +if(WIN32) + if(ENABLE_OS_SPECIFIC_INSTALL) + set(GMSH_BIN .) + set(GMSH_LIB .) + set(GMSH_DOC .) + set(GMSH_MAN .) + set(GMSH_INC .) + else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) + endif() + if(CYGWIN) + unix2dos(GMSH_API) + if(ENABLE_PRIVATE_API) + unix2dos(GMSH_PRIVATE_API) + endif() + unix2dos(WELCOME_FILE) + unix2dos(SDK_FILE) + unix2dos(LICENSE_FILE) + unix2dos(CREDITS_FILE) + unix2dos(CHANGELOG_FILE) + unix2dos(TUTORIAL_GEO_FILES) + unix2dos(TUTORIAL_CPP_FILES) + unix2dos(TUTORIAL_C_FILES) + unix2dos(TUTORIAL_PY_FILES) + unix2dos(TUTORIAL_JL_FILES) + foreach(DIR ${DEMOS_DIRS}) + file(GLOB DEMO_FILES ${DIR}/?*.*) + unix2dos(DEMO_FILES) + endforeach() + endif() +elseif(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + # set these so that the files get installed nicely in the MacOSX + # .app bundle + set(GMSH_BIN ../MacOS) + set(GMSH_LIB ../MacOS) + set(GMSH_DOC ../../..) + set(GMSH_MAN ../../..) + set(GMSH_INC ../MacOS) +else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) +endif() + +# FIXME: change this once we understand rpaths +if(APPLE) + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + set_target_properties(shared PROPERTIES INSTALL_NAME_DIR + ${CMAKE_INSTALL_PREFIX}/${GMSH_LIB}) + endif() +endif() + +# mark targets as optional so we can install them separately if needed +# (e.g. "make lib" or "make shared" followed by "make install/fast") +install(TARGETS gmsh DESTINATION ${GMSH_BIN} OPTIONAL) +if(ENABLE_BUILD_LIB) + install(TARGETS lib DESTINATION ${GMSH_LIB} OPTIONAL) +endif() +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(TARGETS shared DESTINATION ${GMSH_LIB} OPTIONAL) +endif() + +if(ENABLE_ONELAB) + install(FILES ${ONELAB_PY} DESTINATION ${GMSH_BIN}) +endif() +if(ENABLE_BUILD_LIB OR ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(FILES ${GMSH_API} DESTINATION ${GMSH_INC}) + install(FILES ${GMSH_PY} DESTINATION ${GMSH_LIB}) + install(FILES ${GMSH_JL} DESTINATION ${GMSH_LIB}) + if(ENABLE_PRIVATE_API) + install(FILES ${GMSH_PRIVATE_API} DESTINATION ${GMSH_INC}/gmsh) + endif() +endif() +if(INSTALL_SDK_README) + configure_file(${SDK_FILE} ${CMAKE_CURRENT_BINARY_DIR}/README.txt) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/README.txt DESTINATION .) +endif() +install(FILES ${WELCOME_FILE} DESTINATION ${GMSH_DOC} RENAME README.txt) +install(FILES ${LICENSE_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CREDITS_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CHANGELOG_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${TUTORIAL_GEO_FILES} DESTINATION ${GMSH_DOC}/tutorial) +install(FILES ${TUTORIAL_CPP_FILES} DESTINATION ${GMSH_DOC}/tutorial/c++) +install(FILES ${TUTORIAL_C_FILES} DESTINATION ${GMSH_DOC}/tutorial/c) +install(FILES ${TUTORIAL_PY_FILES} DESTINATION ${GMSH_DOC}/tutorial/python) +install(FILES ${TUTORIAL_JL_FILES} DESTINATION ${GMSH_DOC}/tutorial/julia) +foreach(DIR ${DEMOS_DIRS}) + get_filename_component(DEMOS_DIR_NAME ${DIR} NAME) + file(GLOB DEMO_FILES ${DIR}/?*.*) + install(FILES ${DEMO_FILES} DESTINATION ${GMSH_DOC}/demos/${DEMOS_DIR_NAME}) +endforeach() +if(UNIX AND NOT CYGWIN) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/doc/gmsh.1 DESTINATION ${GMSH_MAN}) +endif() + +add_custom_target(get_headers + COMMAND ${CMAKE_COMMAND} -E make_directory Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +foreach(FILE ${GMSH_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endforeach() +if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/gmsh/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() +endif() + +find_program(MAKEINFO makeinfo) +if(MAKEINFO) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.info DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --split-size 1000000 + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(info DEPENDS ${TEX_DIR}/gmsh.info) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.txt DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --plaintext -o gmsh.txt + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(txt DEPENDS ${TEX_DIR}/gmsh.txt) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.html DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --html --css-ref=http://gmsh.info/gmsh.css + --no-split --set-customization-variable + EXTRA_HEAD='' + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(html DEPENDS ${TEX_DIR}/gmsh.html) + install(FILES ${TEX_DIR}/gmsh.html DESTINATION ${GMSH_DOC} OPTIONAL) +else() + add_custom_target(html COMMAND ${CMAKE_COMMAND} -E touch ${TEX_DIR}/gmsh.html) +endif() + +find_program(TEXI2PDF texi2pdf) +if(TEXI2PDF) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.pdf DEPENDS ${TEX_SRC} + COMMAND ${TEXI2PDF} ARGS gmsh.texi + WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(pdf DEPENDS ${TEX_DIR}/gmsh.pdf) + install(FILES ${TEX_DIR}/gmsh.pdf DESTINATION ${GMSH_DOC} OPTIONAL) +endif() + +execute_process(COMMAND ${CMAKE_COMMAND} -E echo + "@c This file was generated by cmake: do not edit manually!\n${OPT_TEXI}" + OUTPUT_FILE cmake_options.texi) + +if(MAKEINFO AND TEXI2PDF) + add_custom_target(doc COMMAND ${CMAKE_COMMAND} -E tar zcf + ${CMAKE_CURRENT_BINARY_DIR}/gmsh-${GMSH_VERSION}-doc.tgz + CREDITS.txt LICENSE.txt CHANGELOG.txt + doc/gmsh.1 doc/texinfo/gmsh.html doc/texinfo/gmsh.info + doc/texinfo/gmsh.pdf doc/texinfo/gmsh.txt + COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ} + DEPENDS ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.txt + ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.pdf + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(MAKEINFO OR TEXI2PDF) + add_custom_target(clean_doc COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ}) +endif() + +if(APPLE AND ENABLE_BUILD_LIB) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_framework.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info_framework.plist "${F1}") + get_target_property(LIBNAME lib LOCATION) # depracated + #set(LIBNAME $) # FIXME: use this in the future + add_custom_target(framework DEPENDS lib + COMMAND ${CMAKE_COMMAND} -E remove_directory gmsh.framework + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Headers + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Resources + COMMAND ${CMAKE_COMMAND} -E copy ${LIBNAME} gmsh.framework/gmsh + COMMAND ${CMAKE_COMMAND} -E copy Info_framework.plist + gmsh.framework/Resources/Info.plist + COMMAND ${CMAKE_COMMAND} -E create_symlink . gmsh.framework/Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + foreach(FILE ${GMSH_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + endif() +endif() + +set(CPACK_PACKAGE_VENDOR "Christophe Geuzaine and Jean-Francois Remacle") +set(CPACK_PACKAGE_VERSION_MAJOR ${GMSH_MAJOR_VERSION}) +set(CPACK_PACKAGE_VERSION_MINOR ${GMSH_MINOR_VERSION}) +set(CPACK_PACKAGE_VERSION_PATCH ${GMSH_PATCH_VERSION}) +set(CPACK_PACKAGE_DESCRIPTION_FILE ${WELCOME_FILE}) +set(CPACK_PACKAGE_DESCRIPTION_SUMMARY + "3D finite element mesh generator with built-in CAD engine and post-processor") +if(GMSH_EXTRA_VERSION MATCHES "-git.*") # so that we'll overwrite the archives + set(CPACK_PACKAGE_FILE_NAME gmsh-git-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh-git-source) +else() + set(CPACK_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-source) +endif() +set(CPACK_PACKAGE_INSTALL_DIRECTORY "gmsh") +set(CPACK_RESOURCE_FILE_LICENSE ${LICENSE_FILE}) +set(CPACK_RESOURCE_FILE_README ${WELCOME_FILE}) +set(CPACK_RESOURCE_FILE_WELCOME ${WELCOME_FILE}) +set(CPACK_PACKAGE_EXECUTABLE "gmsh") +if(ENABLE_PACKAGE_STRIP) + set(CPACK_STRIP_FILES TRUE) +else() + set(CPACK_STRIP_FILES FALSE) +endif() +set(CPACK_SOURCE_GENERATOR TGZ) +set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR}" "/CVS/" "/.svn" "/.git" + "~$" "DS_Store$" "GmshConfig.h$" "GmshVersion.h$" "/benchmarks/" "/tmp/" + "/bin/" "/lib/" "/nightly/" "GPATH" "GRTAGS" "GSYMS" "GTAGS" "/HTML/" + "/contrib/3M/" "/contrib/Parasolid/") + +if(UNIX) + # make sure we remove previous installs before doing the next one (on Mac for + # example "make package; make package_source" would lead to huge file lists + # getting generated due to the 'Applications' symlink in the bundle) + set(CPACK_INSTALL_COMMANDS "rm -rf ${CMAKE_CURRENT_BINARY_DIR}/_CPack_Packages") +endif() + +if(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + set(CPACK_GENERATOR Bundle) + set(CPACK_BUNDLE_NAME Gmsh) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_app.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info.plist "${F1}") + set(CPACK_BUNDLE_PLIST ${CMAKE_CURRENT_BINARY_DIR}/Info.plist) + set(CPACK_BUNDLE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) + if(PACKAGER STREQUAL "geuzaine - removed: we sign on a separate machine") + # codesigning requires CMake >= 3.2 + set(CPACK_BUNDLE_APPLE_CERT_APP "Developer ID Application: Christophe Geuzaine") + endif() + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsGeo.icns DESTINATION . + RENAME GmshGeo.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsMsh.icns DESTINATION . + RENAME GmshMsh.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsSol.icns DESTINATION . + RENAME GmshSol.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsPos.icns DESTINATION . + RENAME GmshPos.icns) + set(CPACK_PACKAGE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) +elseif(WIN32) + set(CPACK_GENERATOR ZIP) +else() + set(CPACK_GENERATOR TGZ) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/gmshpy AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON AND HAVE_PYTHON) + add_subdirectory(utils/wrappers/gmshpy) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/java AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_JAVA) + add_subdirectory(utils/wrappers/java) +endif() + +include(CPack) + +if(NOT DISABLE_GMSH_TESTS) + # disabling tests is useful when including this CMakeLists in an external project + include(CTest) + file(GLOB_RECURSE TESTFILES + tutorial/*.geo demos/*.geo benchmarks/?d/*.geo benchmarks/extrude/*.geo + benchmarks/occ/*.geo) + # disable this test for now on our Linux32 machine - the current config + # crashes on the OCC STL generation + if(${GMSH_OS} MATCHES "Linux32") + list(REMOVE_ITEM TESTFILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/t18.geo) + endif() + foreach(TESTFILE ${TESTFILES}) + # use relative path for Cygwin/MinGW (the pure win exe built with the MinGW + # compilers does not understand a full Cygwin-style path) + FILE(RELATIVE_PATH TEST ${CMAKE_CURRENT_BINARY_DIR} ${TESTFILE}) + if(HAVE_OCC OR NOT ${TEST} MATCHES "boolean" OR NOT ${TEST} MATCHES "occ") + add_test(${TEST} ./gmsh ${TEST} -3 -nopopup -o ./tmp.msh) + endif() + endforeach() + # test c++ api tutorials with dynamic builds (except on 32 bit windows for + # now: our win32 setup does not currently handle exceptions) + if(ENABLE_BUILD_DYNAMIC AND NOT ${GMSH_OS} MATCHES "Windows32") + file(GLOB_RECURSE TESTFILES tutorial/c++/*.cpp) + foreach(TESTFILE ${TESTFILES}) + get_filename_component(TEST ${TESTFILE} NAME_WE) + add_executable(${TEST} WIN32 ${TESTFILE}) + target_link_libraries(${TEST} shared) + if(WIN32 AND NOT MSVC) + set_target_properties(${TEST} PROPERTIES LINK_FLAGS "-mwindows -static") + endif() + add_test(${TEST}_cpp ${TEST}) + endforeach() + endif() +endif() + +message(STATUS "") +message(STATUS "Gmsh ${GMSH_VERSION} has been configured for ${GMSH_OS}") +message(STATUS "") +message(STATUS " * Build options:" ${GMSH_CONFIG_OPTIONS}) +message(STATUS " * Build type: " ${CMAKE_BUILD_TYPE}) +message(STATUS " * C compiler: " ${CMAKE_C_COMPILER}) +message(STATUS " * C++ compiler: " ${CMAKE_CXX_COMPILER}) +message(STATUS " * Install prefix: " ${CMAKE_INSTALL_PREFIX}) +message(STATUS "") + +mark_as_advanced(GMSH_EXTRA_VERSION + ACIS_LIB ANN_INC ANN_LIB CAIRO_LIB CAIRO_INC CGNS_INC GMM_INC + GMP_INC GMP_LIB MMG3D_INC MMG3D_LIB HDF5_LIB + MED_LIB OCC_INC SZ_LIB + PETSC_LIBS SLEPC_INC SLEPC_INC2 SLEPC_LIB + BISON FLEX MAKEINFO TEXI2PDF FLTK_CONFIG_SCRIPT + GMSH_EXTERNAL_INCLUDE_DIRS GMSH_EXTERNAL_LIBRARIES) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.7.0/static/CMakeLists.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.7.0/static/CMakeLists.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/configs/4.7.0/static/CMakeLists.txt (revision 27955) @@ -0,0 +1,2191 @@ +# Gmsh - Copyright (C) 1997-2020 C. Geuzaine, J.-F. Remacle +# +# See the LICENSE.txt file for license information. Please report all +# issues on https://gitlab.onelab.info/gmsh/gmsh/issues. + +cmake_minimum_required(VERSION 3.1 FATAL_ERROR) + +# if CMAKE_BUILD_TYPE is specified use it; otherwise set the default +# build type to "RelWithDebInfo" ("-O2 -g" with gcc) prior to calling +# project() +if(DEFINED CMAKE_BUILD_TYPE) + set(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Choose build type") +else() + set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose build type") +endif() + +project(gmsh CXX C) + +# require C++11 and request C99 +set(CMAKE_CXX_STANDARD 11) +set(CMAKE_CXX_STANDARD_REQUIRED ON) +set(CMAKE_C_STANDARD 99) + +# this variable controls the default value of the options which are normally set +# to ON (useful if you want to configure a minimal version of Gmsh: e.g. "cmake +# -DDEFAULT=0 -DENABLE_POST=1 -DENABLE_PARSER=1") +set(DEFAULT ON CACHE INTERNAL "Default value for enabled-by-default options") + +macro(opt OPTION HELP VALUE) + option(ENABLE_${OPTION} ${HELP} ${VALUE}) + set(OPT_TEXI "${OPT_TEXI}\n@item ENABLE_${OPTION}\n${HELP} (default: ${VALUE})") +endmacro() + +opt(3M "Enable proprietary 3M extension" OFF) +opt(ALGLIB "Enable ALGLIB (used by some mesh optimizers)" ${DEFAULT}) +opt(ANN "Enable ANN (used for fast point search in mesh/post)" ${DEFAULT}) +opt(BAMG "Enable Bamg 2D anisotropic mesh generator" ${DEFAULT}) +opt(BLAS_LAPACK "Enable BLAS/Lapack for linear algebra (if Eigen if disabled)" OFF) +opt(BLOSSOM "Enable Blossom algorithm (needed for full quad meshing)" ${DEFAULT}) +opt(BUILD_LIB "Enable 'lib' target for building static Gmsh library" OFF) +opt(BUILD_SHARED "Enable 'shared' target for building shared Gmsh library" OFF) +opt(BUILD_DYNAMIC "Enable dynamic Gmsh executable (linked with shared library)" OFF) +opt(BUILD_ANDROID "Enable Android NDK library target (experimental)" OFF) +opt(BUILD_IOS "Enable iOS library target (experimental)" OFF) +opt(CGNS "Enable CGNS import/export (experimental)" ${DEFAULT}) +opt(CGNS_CPEX0045 "Enable high-order CGNS import/export following CPEX0045 (experimental)" OFF) +opt(CAIRO "Enable Cairo to render fonts (experimental)" ${DEFAULT}) +opt(PROFILE "Enable profiling compiler flags" OFF) +opt(DINTEGRATION "Enable discrete integration (needed for levelsets)" ${DEFAULT}) +opt(DOMHEX "Enable experimental DOMHEX code" ${DEFAULT}) +opt(EIGEN "Enable Eigen for linear algebra (instead of Blas/Lapack)" ON) +opt(FLTK "Enable FLTK graphical user interface (requires mesh/post)" ${DEFAULT}) +opt(GETDP "Enable GetDP solver (linked as a library, experimental)" ${DEFAULT}) +opt(GMM "Enable GMM linear solvers (simple alternative to PETSc)" ${DEFAULT}) +opt(GMP "Enable GMP for Kbipack (advanced)" ON) +opt(GRAPHICS "Enable building graphics lib even without GUI (advanced)" OFF) +opt(HXT "Enable HXT library (for reparametrization and meshing)" ${DEFAULT}) +opt(KBIPACK "Enable Kbipack (neeeded by homology solver)" ${DEFAULT}) +opt(MATHEX "Enable Mathex expression parser (used by plugins and options)" ${DEFAULT}) +opt(MED "Enable MED mesh and post file formats" ${DEFAULT}) +opt(MESH "Enable mesh module (required by GUI)" ${DEFAULT}) +opt(METIS "Enable Metis mesh partitioner" ${DEFAULT}) +opt(MMG "Enable Mmg mesh adaptation interface" ${DEFAULT}) +opt(MPEG_ENCODE "Enable built-in MPEG movie encoder" ${DEFAULT}) +opt(MPI "Enable MPI (experimental, not used for meshing)" OFF) +opt(MSVC_STATIC_RUNTIME "Enable static Visual C++ runtime" OFF) +opt(MUMPS "Enable MUMPS sparse direct linear solver" OFF) +opt(NETGEN "Enable Netgen 3D frontal mesh generator" ${DEFAULT}) +opt(NUMPY "Enable fullMatrix and numpy array conversion for private API" OFF) +opt(PETSC4PY "Enable petsc4py wrappers for petsc matrices for private API" OFF) +opt(OCC "Enable OpenCASCADE CAD kernel" ${DEFAULT}) +opt(OCC_CAF "Enable OpenCASCADE CAF module (for STEP/IGES attributes)" ${DEFAULT}) +opt(OCC_STATIC "Link OpenCASCADE static instead of dynamic libraries (requires ENABLE_OCC)" OFF) +opt(OCC_TBB "Add TBB libraries in list of OCC libraries" OFF) +opt(ONELAB "Enable ONELAB solver interface" ${DEFAULT}) +opt(ONELAB_METAMODEL "Enable ONELAB metamodels (experimental)" ${DEFAULT}) +opt(OPENACC "Enable OpenACC" OFF) +opt(OPENMP "Enable OpenMP" OFF) +opt(OPTHOM "Enable high-order mesh optimization tools" ${DEFAULT}) +opt(OS_SPECIFIC_INSTALL "Enable OS-specific (e.g. app bundle) installation" OFF) +opt(OSMESA "Enable OSMesa for offscreen rendering (experimental)" OFF) +opt(P4EST "Enable p4est for enabling automatic mesh size field (experimental)" OFF) +opt(PACKAGE_STRIP "Strip symbols in install packages to reduce install size" ON) +opt(PARSER "Enable GEO file parser (required for .geo/.pos scripts)" ${DEFAULT}) +opt(PETSC "Enable PETSc linear solvers (required for SLEPc)" OFF) +opt(PLUGINS "Enable post-processing plugins" ${DEFAULT}) +opt(POST "Enable post-processing module (required by GUI)" ${DEFAULT}) +opt(POPPLER "Enable Poppler for displaying PDF documents (experimental)" OFF) +opt(PRIVATE_API "Enable private API" OFF) +opt(PRO "Enable PRO extensions" ${DEFAULT}) +opt(QUADTRI "Enable QuadTri structured meshing extensions" ${DEFAULT}) +opt(REVOROPT "Enable Revoropt (used for CVT remeshing)" OFF) +opt(RPATH "Use RPATH in dynamically linked targets" ON) +opt(SLEPC "Enable SLEPc eigensolvers" OFF) +opt(SOLVER "Enable built-in finite element solvers (required for reparametrization)" ${DEFAULT}) +opt(SYSTEM_CONTRIB "Use system versions of contrib libraries, when possible" OFF) +opt(TCMALLOC "Enable libtcmalloc (fast malloc that does not release memory)" OFF) +opt(TOUCHBAR "Enable Apple Touch bar" ${DEFAULT}) +opt(VISUDEV "Enable additional visualization capabilities for development purposes" OFF) +opt(VOROPP "Enable voro++ (for hex meshing, experimental)" ${DEFAULT}) +opt(WRAP_JAVA "Generate SWIG Java wrappers for private API" OFF) +opt(WRAP_PYTHON "Generate SWIG Python wrappers for private API (not used by public API)" OFF) +opt(ZIPPER "Enable Zip file compression/decompression" OFF) + +set(GMSH_MAJOR_VERSION 4) +set(GMSH_MINOR_VERSION 7) +set(GMSH_PATCH_VERSION 0) +if(NOT GMSH_EXTRA_VERSION) + set(GMSH_EXTRA_VERSION "") +endif() +set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION}") +set(GMSH_EXTRA_VERSION_ORIG ${GMSH_EXTRA_VERSION}) + +if(NOT GMSH_RELEASE) + find_package(Git) + if(GIT_FOUND) + execute_process(COMMAND ${GIT_EXECUTABLE} log -1 --format=%h + WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} ERROR_QUIET + OUTPUT_VARIABLE GIT_COMMIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE) + endif() + if(GIT_COMMIT_HASH) + set(GMSH_EXTRA_VERSION "${GMSH_EXTRA_VERSION}-git-${GIT_COMMIT_HASH}") + endif() + set(GMSH_EXTRA_VERSION_TEXI "${GMSH_EXTRA_VERSION_TEXI} (development version)") +endif() + +set(GMSH_SHORT_VERSION + "${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION}") +set(GMSH_VERSION "${GMSH_SHORT_VERSION}${GMSH_EXTRA_VERSION}") +set(GMSH_SHORT_LICENSE "GNU General Public License") + +set(GMSH_GITLAB_PREFIX "https://gitlab.onelab.info/gmsh/gmsh") +if(GMSH_RELEASE) + set(GMSH_GITLAB_PREFIX "${GMSH_GITLAB_PREFIX}/blob/gmsh_${GMSH_SHORT_VERSION}") +else() + set(GMSH_GITLAB_PREFIX "${GMSH_GITLAB_PREFIX}/blob/master") +endif() + +set(GMSH_API api/gmsh.h api/gmshc.h api/gmsh.h_cwrap) + +if(ENABLE_PRIVATE_API) + message(WARNING "The private API is unsupported and undocumented. It is meant " + "for expert Gmsh developers, not for regular Gmsh users, who should rely " + "on the stable public API (gmsh/api) instead.") + file(GLOB_RECURSE HEADERS Common/*.h Numeric/*.h Geo/*.h Mesh/*.h Solver/*.h + Post/*.h Plugin/*.h Graphics/*.h contrib/kbipack/*.h + contrib/DiscreteIntegration/*.h contrib/HighOrderMeshOptimizer/*.h + contrib/MeshOptimizer/*.h contrib/MeshQualityOptimizer/*.h) + set(GMSH_PRIVATE_API ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h ${HEADERS}) + get_property(IAMCHILD DIRECTORY PROPERTY PARENT_DIRECTORY) + if(IAMCHILD) + set(GMSH_PRIVATE_API ${GMSH_PRIVATE_API} PARENT_SCOPE) + endif() + if(ENABLE_WRAP_PYTHON OR ENABLE_WRAP_JAVA) + set(ENABLE_BUILD_DYNAMIC ON) + message(WARNING "SWIG wrappers for the private API are unsupported and " + "undocumented. The stable public Python API does not required SWIG.") + endif() +endif() + +set(ONELAB_PY contrib/onelab/python/onelab.py) +set(GMSH_PY api/gmsh.py) +set(GMSH_JL api/gmsh.jl) + +if(${CMAKE_MAJOR_VERSION} GREATER 2) + string(TIMESTAMP DATE "%Y%m%d") +else() + execute_process(COMMAND date "+%Y%m%d" OUTPUT_VARIABLE DATE + OUTPUT_STRIP_TRAILING_WHITESPACE) +endif() + +if(NOT DATE) + set(DATE "unknown") +endif() +set(GMSH_DATE "${DATE}") + +if(NOT GMSH_HOST) + execute_process(COMMAND hostname OUTPUT_VARIABLE HOST + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT HOST) + set(HOST "unknown") + endif() + set(GMSH_HOST "${HOST}") +endif() + +if(NOT GMSH_PACKAGER) + execute_process(COMMAND whoami OUTPUT_VARIABLE PACKAGER + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(NOT PACKAGER) + set(PACKAGER "unknown") + endif() + string(REPLACE "\\" " " PACKAGER ${PACKAGER}) + set(GMSH_PACKAGER "${PACKAGER}") +endif() + +if(APPLE) + set(GMSH_OS "MacOSX") +elseif(CYGWIN OR MSYS) + # detect if we use the MinGW compilers on Cygwin - if we do, handle the build + # as a pure Windows build and make cmake find pure Windows import libraries + # (.lib) + if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpmachine + OUTPUT_VARIABLE CXX_COMPILER_MACHINE + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(CXX_COMPILER_MACHINE MATCHES "mingw") + set(GMSH_OS "Windows") + set(WIN32 1) + add_definitions(-DWIN32) + set(CMAKE_FIND_LIBRARY_PREFIXES "lib" "") + set(CMAKE_FIND_LIBRARY_SUFFIXES ".a" ".so" ".lib" ".LIB" ".dll" ".DLL" ".dll.a") + endif() + endif() +else() + set(GMSH_OS "${CMAKE_SYSTEM_NAME}") +endif() + +include(CheckTypeSize) +include(CheckFunctionExists) +include(CheckIncludeFile) +include(CheckCXXCompilerFlag) +include(CheckCCompilerFlag) + +macro(set_config_option VARNAME STRING) + set(${VARNAME} TRUE) + list(APPEND CONFIG_OPTIONS ${STRING}) + message(STATUS "Found " ${STRING}) +endmacro() + +# check the size of size_t +check_type_size("size_t" SIZEOF_SIZE_T) +if(SIZEOF_SIZE_T EQUAL 8) + set_config_option(HAVE_64BIT_SIZE_T "64Bit") +endif() + +# append 32/64 to the build name on Linux and Windows +if(NOT APPLE) + if(HAVE_64BIT_SIZE_T) + set(GMSH_OS "${GMSH_OS}64") + else() + set(GMSH_OS "${GMSH_OS}32") + endif() +endif() + +if(ENABLE_BUILD_DYNAMIC) + set(GMSH_OS "${GMSH_OS}-sdk") +endif() + +if(ENABLE_RPATH) + set(CMAKE_MACOSX_RPATH 1) + + # make sure that dynamic libraries can be found when installing/ displacing + # the binaries: from https://gitlab.kitware.com/cmake/community/wikis/doc/ + # cmake/RPATH-handling: + + # use, i.e. don't skip the full RPATH for the build tree + set(CMAKE_SKIP_BUILD_RPATH FALSE) + + # when building, don't use the install RPATH already (but later on when + # installing) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") + + # add the automatically determined parts of the RPATH which point to + # directories outside the build tree to the install RPATH + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + + # the RPATH to be used when installing, but only if it's not a system directory + list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" + isSystemDir) + if("${isSystemDir}" STREQUAL "-1") + if(APPLE) + set(CMAKE_INSTALL_RPATH "@executable_path/../lib") + else() + set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../lib") + endif() + endif() +else() + set(CMAKE_MACOSX_RPATH 0) + set(CMAKE_SKIP_BUILD_RPATH TRUE) +endif() + +if(MSVC) + # remove annoying warning about bool/int cast performance + set(GMSH_CONFIG_PRAGMAS "#pragma warning(disable:4800 4244 4267)") + foreach(VAR + CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE + CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO + CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE + CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO) + if(ENABLE_MSVC_STATIC_RUNTIME AND ${VAR} MATCHES "/MD") + string(REGEX REPLACE "/MD" "/MT" ${VAR} "${${VAR}}") + endif() + if(NOT ${VAR} MATCHES "/MP") # enable parallel compilation + set(${VAR} "${${VAR}} /MP") + endif() + endforeach() + if(ENABLE_PRIVATE_API) + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + # automatically export .def file with all symbols (requires CMake 3.4); + # depending on the compiling options this might lead to more than 64k export + # symbols; just trim the .def file to keep the ones you need + set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + endif() + endif() +endif() + +# reduce memory usage of GCC on 32 bit systems +if(NOT HAVE_64BIT_SIZE_T AND CMAKE_CXX_COMPILER_ID MATCHES "GNU") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} --param ggc-min-expand=1 --param ggc-min-heapsize=512000") +endif() + +if(ENABLE_OPENMP) + find_package(OpenMP) + if(OpenMP_FOUND OR OPENMP_FOUND) + set_config_option(HAVE_OPENMP "OpenMP") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + elseif(APPLE AND EXISTS "/opt/local/lib/libomp") + # official Apple compiler with macports' libomp + set_config_option(HAVE_OPENMP "OpenMP[MacPorts]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp -I/opt/local/include/libomp") + list(APPEND EXTERNAL_LIBRARIES "-L/opt/local/lib/libomp -lomp") + elseif(APPLE AND EXISTS "/usr/local/lib/libomp.dylib") + # official Apple compiler with homebrew's libomp + set_config_option(HAVE_OPENMP "OpenMP[Homebrew]") + set(CMAKE_C_FLAGS + "${CMAKE_C_FLAGS} -Xpreprocessor -fopenmp") + set(CMAKE_CXX_FLAGS + "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp") + list(APPEND EXTERNAL_LIBRARIES "-L/usr/local/lib -lomp") + endif() +endif() + +if(ENABLE_OPENACC) + find_package(OpenACC) + if(OpenACC_C_FOUND AND OpenACC_CXX_FOUND) + set_config_option(HAVE_OPENACC "OpenACC") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenACC_C_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenACC_CXX_FLAGS}") + endif() +endif() + +if(ENABLE_PROFILE) + # Using the perf set of profiling tools doesn't work without the frame + # pointer and a common optimisation is to remove it + check_cxx_compiler_flag("-fno-omit-frame-pointer" FNOFP) + if(FNOFP) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer") + endif() +endif() + +macro(append_gmsh_src DIRNAME FILES) + foreach(FILE ${FILES}) + list(APPEND LIST ${DIRNAME}/${FILE}) + endforeach() + set(GMSH_SRC ${GMSH_SRC};${LIST} PARENT_SCOPE) + set(GMSH_DIRS ${GMSH_DIRS};${DIRNAME} PARENT_SCOPE) +endmacro() + +macro(find_all_libraries VARNAME LISTNAME PATH SUFFIX) + set(${VARNAME}) + list(LENGTH ${LISTNAME} NUM_LIST) + foreach(LIB ${${LISTNAME}}) + if("${PATH}" STREQUAL "") + find_library(FOUND_LIB ${LIB} PATH_SUFFIXES ${SUFFIX}) + else() + find_library(FOUND_LIB ${LIB} PATHS ${PATH} NO_DEFAULT_PATH) + endif() + if(FOUND_LIB) + list(APPEND ${VARNAME} ${FOUND_LIB}) + endif() + unset(FOUND_LIB CACHE) + endforeach() + list(LENGTH ${VARNAME} NUM_FOUND_LIBRARIES) + if(NUM_FOUND_LIBRARIES LESS NUM_LIST) + set(${VARNAME}) + endif() +endmacro() + +macro(set_compile_flags LISTNAME FLAGS) + foreach(FILE ${${LISTNAME}}) + get_source_file_property(PROP ${FILE} COMPILE_FLAGS) + if(PROP) + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${PROP} ${FLAGS}") + else() + set_source_files_properties(${FILE} PROPERTIES COMPILE_FLAGS "${FLAGS}") + endif() + endforeach() +endmacro() + +if(ENABLE_EIGEN) + if(ENABLE_SYSTEM_CONTRIB) + find_path(EIGEN_INC "Eigen/Dense" HINTS eigen3) + if(EIGEN_INC) + include_directories(${EIGEN_INC}) + set_config_option(HAVE_EIGEN "Eigen[system]") + endif() + endif() + if(NOT HAVE_EIGEN) + include_directories(contrib/eigen) + set_config_option(HAVE_EIGEN "Eigen") + endif() + # We could also add an option to use BLAS with Eigen + # add_definitions(-DEIGEN_USE_BLAS) +elseif(ENABLE_BLAS_LAPACK) + if(BLAS_LAPACK_LIBRARIES) + # use libs as specified in the BLAS_LAPACK_LIBRARIES variable + set_config_option(HAVE_BLAS "Blas[custom]") + set_config_option(HAVE_LAPACK "Lapack[custom]") + set(LAPACK_LIBRARIES ${BLAS_LAPACK_LIBRARIES}) + else() + if(MSVC) + # on Windows with Visual C++ try really hard to find blas/lapack *without* + # requiring a Fortran compiler: 1) try to find the Intel MKL libs using + # the standard search path; if not found 2) try to get the reference + # blas/lapack libs (useful for users with no Fortran compiler and no MKL + # license, who can just download our precompiled "gmsh-dep" package) + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH em64t/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_lp64 mkl_intel_thread mkl_core) + else() + set(MKL_PATH ia32/lib) + set(MKL_LIBS_REQUIRED libguide40 mkl_intel_c mkl_intel_thread mkl_core) + endif() + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + set(REFLAPACK_LIBS_REQUIRED lapack blas g2c gcc) + find_all_libraries(LAPACK_LIBRARIES REFLAPACK_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[ref]") + set_config_option(HAVE_LAPACK "Lapack[ref]") + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + # on Linux try to find the Intel MKL without a Fortran compiler + if(HAVE_64BIT_SIZE_T) + set(MKL_PATH lib/em64t) + else() + set(MKL_PATH lib/32) + endif() + set(MKL_LIBS_REQUIRED mkl_gf_lp64 iomp5 mkl_gnu_thread mkl_core guide pthread) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + if(NOT LAPACK_LIBRARIES) + # match lapack 9.0 on 64bit + set(MKL_LIBS_REQUIRED mkl_lapack mkl_em64t guide) + find_all_libraries(LAPACK_LIBRARIES MKL_LIBS_REQUIRED "" ${MKL_PATH}) + endif() + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[mkl]") + set_config_option(HAVE_LAPACK "Lapack[mkl]") + else() + # on Linux also try to find ATLAS without a Fortran compiler, because + # cmake ships with a buggy FindBLAS e.g. on Ubuntu Lucid Lynx + set(ATLAS_LIBS_REQUIRED lapack f77blas cblas atlas) + find_all_libraries(LAPACK_LIBRARIES ATLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[atlas]") + set_config_option(HAVE_LAPACK "Lapack[atlas]") + else() + # try with generic names + set(GENERIC_LIBS_REQUIRED lapack blas pthread) + find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[generic]") + set_config_option(HAVE_LAPACK "Lapack[generic]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + endif() + elseif(${CMAKE_SYSTEM_NAME} MATCHES "SunOS") + # on SunOS we know blas and lapack are available in sunperf + set(LAPACK_LIBRARIES -library=sunperf) + set_config_option(HAVE_BLAS "Blas[sunperf]") + set_config_option(HAVE_LAPACK "Lapack[sunperf]") + elseif(APPLE) + # on Mac we also know that blas and lapack are available + set(LAPACK_LIBRARIES "-llapack -lblas") + set_config_option(HAVE_BLAS "Blas[veclib]") + set_config_option(HAVE_LAPACK "Lapack[veclib]") + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we haven't found blas and lapack check for OpenBlas + set(OPENBLAS_LIBS_REQUIRED openblas) + find_all_libraries(LAPACK_LIBRARIES OPENBLAS_LIBS_REQUIRED "" "") + if(LAPACK_LIBRARIES) + set_config_option(HAVE_BLAS "Blas[openblas]") + set_config_option(HAVE_LAPACK "Lapack[openblas]") + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB}) + endif() + endif() + endif() + + if(NOT HAVE_BLAS OR NOT HAVE_LAPACK) + # if we still haven't found blas and lapack, use the standard cmake tests, + # which require a working Fortran compiler + enable_language(Fortran) + find_package(BLAS) + if(BLAS_FOUND) + set_config_option(HAVE_BLAS "Blas") + find_package(LAPACK) + if(LAPACK_FOUND) + set_config_option(HAVE_LAPACK "Lapack") + else() + set(LAPACK_LIBRARIES ${BLAS_LIBRARIES}) + endif() + if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU") + if(CMAKE_Fortran_COMPILER MATCHES "gfortran") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "f95") + list(APPEND LAPACK_LIBRARIES gfortran) + elseif(CMAKE_Fortran_COMPILER MATCHES "g77") + list(APPEND LAPACK_LIBRARIES g2c) + endif() + elseif(CMAKE_Fortran_COMPILER MATCHES "pgi") + list(APPEND LAPACK_LIBRARIES -pgf77libs) + endif() + endif() + endif() + endif() +endif() + +if(ENABLE_TCMALLOC) + find_library(TCMALLOC tcmalloc) + if(TCMALLOC) + set_config_option(HAVE_TCMALLOC "TCMalloc") + list(APPEND EXTERNAL_LIBRARIES ${TCMALLOC}) + endif() +endif() + +add_subdirectory(Common) +add_subdirectory(Numeric) +add_subdirectory(Geo) + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh AND ENABLE_MESH) + add_subdirectory(Mesh) + set_config_option(HAVE_MESH "Mesh") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Solver AND ENABLE_SOLVER) + add_subdirectory(Solver) + set_config_option(HAVE_SOLVER "Solver") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Post AND ENABLE_POST) + add_subdirectory(Post) + set_config_option(HAVE_POST "Post") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Plugin AND ENABLE_PLUGINS) + add_subdirectory(Plugin) + set_config_option(HAVE_PLUGINS "Plugins") + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Parser AND ENABLE_PARSER) + add_subdirectory(Parser) + set_config_option(HAVE_PARSER "Parser") +endif() + +if(ENABLE_VISUDEV) + set_config_option(HAVE_VISUDEV "VisuDev") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Fltk AND ENABLE_FLTK) + # first, try to use fltk-config for fltk >= 1.3 (FindFLTK is buggy on Unix, + # where e.g. xft and xinerama options are not dealt with) + find_program(FLTK_CONFIG_SCRIPT fltk-config) + if(FLTK_CONFIG_SCRIPT) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --api-version + OUTPUT_VARIABLE FLTK_VERSION) + string(STRIP "${FLTK_VERSION}" FLTK_VERSION) + if(FLTK_VERSION VERSION_GREATER 1.1) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + message(STATUS "Using fltk-config script for Fltk " ${FLTK_VERSION}) + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --includedir + OUTPUT_VARIABLE FLTK_INCLUDE_DIR) + string(STRIP ${FLTK_INCLUDE_DIR} FLTK_INCLUDE_DIR) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # On linux (at least OpenSuSE) the following directories are + # not existing (everything is in /usr/include). To avoid warnings + # check existance of these directories before adding them + if(EXISTS ${FLTK_INCLUDE_DIR}/FL/images) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/FL/images) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/jpeg) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/jpeg) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/zlib) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/zlib) + endif() + if(EXISTS ${FLTK_INCLUDE_DIR}/png) + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}/png) + endif() + execute_process(COMMAND ${FLTK_CONFIG_SCRIPT} --use-gl --use-images --ldflags + OUTPUT_VARIABLE FLTK_LIBRARIES) + string(STRIP ${FLTK_LIBRARIES} FLTK_LIBRARIES) + string(REGEX MATCH "fltk[_ ]jpeg" FLTK_JPEG ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]z" FLTK_Z ${FLTK_LIBRARIES}) + string(REGEX MATCH "fltk[_ ]png" FLTK_PNG ${FLTK_LIBRARIES}) + endif() + endif() + # then try the built-in FindFLTK module + if(NOT HAVE_FLTK) + set(FLTK_SKIP_FORMS TRUE) + set(FLTK_SKIP_FLUID TRUE) + find_package(FLTK) + if(FLTK_FOUND) + add_subdirectory(Fltk) + set_config_option(HAVE_FLTK "Fltk") + list(APPEND EXTERNAL_INCLUDES ${FLTK_INCLUDE_DIR}) + # find fltk jpeg + find_library(FLTK_JPEG NAMES fltk_jpeg fltkjpeg) + if(FLTK_JPEG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_JPEG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/jpeg) + endforeach() + endif() + # find fltk zlib + find_library(FLTK_Z NAMES fltk_z fltkz) + if(FLTK_Z) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_Z}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/zlib) + endforeach() + endif() + # find fltk png + find_library(FLTK_PNG NAMES fltk_png fltkpng) + if(FLTK_PNG) + list(APPEND EXTERNAL_LIBRARIES ${FLTK_PNG}) + foreach(DIR ${FLTK_INCLUDE_DIR}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/FL/images ${DIR}/png) + endforeach() + endif() + endif() + endif() + # workaround for Fedora/Suse messing up fltk-config (see issue #417) + if(HAVE_FLTK AND ${CMAKE_SYSTEM_NAME} MATCHES "Linux") + string(REGEX MATCH "X11" FLTK_X11 ${FLTK_LIBRARIES}) + if(NOT FLTK_X11) + find_package(X11) + if(X11_FOUND) + list(APPEND EXTERNAL_INCLUDES ${X11_INCLUDE_DIR}) + list(APPEND EXTERNAL_LIBRARIES ${X11_LIBRARIES}) + endif() + endif() + endif() +endif() + +if(APPLE AND HAVE_FLTK AND ENABLE_TOUCHBAR) + STRING(REGEX MATCH "([0-9]+.[0-9]+)" OSX_SDK_VERSION "${CMAKE_OSX_SYSROOT}") + if(OSX_SDK_VERSION) + if(${OSX_SDK_VERSION} VERSION_GREATER 10.11) + set(GMSH_SRC ${GMSH_SRC};Fltk/touchBar.mm) + set_config_option(HAVE_TOUCHBAR "TouchBar") + endif() + endif() +endif() + +if(ENABLE_ONELAB) + set_config_option(HAVE_ONELAB "ONELAB") + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/onelab) + if(ENABLE_ONELAB_METAMODEL) + add_subdirectory(contrib/onelab) + include_directories(contrib/onelab) + set_config_option(HAVE_ONELAB_METAMODEL "ONELABMetamodel") + endif() + file(COPY ${ONELAB_PY} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + endif() +endif() + +if(ENABLE_BUILD_IOS) + find_file(CMAKE_TOOLCHAIN_FILE "ios.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for iOS without a toolchain") + endif() + add_definitions(-DBUILD_IOS) +endif() + +if(HAVE_FLTK OR ENABLE_GRAPHICS) + if(NOT HAVE_MESH OR NOT HAVE_POST OR NOT HAVE_PLUGINS OR NOT HAVE_ONELAB) + message(SEND_ERROR "Cannot compile GUI without Mesh, Post, Plugin and ONELAB") + endif() + + if(FLTK_JPEG) + set_config_option(HAVE_LIBJPEG "Jpeg[fltk]") + else() + find_package(JPEG) + if(JPEG_FOUND) + set_config_option(HAVE_LIBJPEG "Jpeg") + list(APPEND EXTERNAL_LIBRARIES ${JPEG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${JPEG_INCLUDE_DIR}) + endif() + endif() + + if(FLTK_Z) + set_config_option(HAVE_LIBZ "Zlib[fltk]") + else() + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + + if(HAVE_LIBZ) + if(FLTK_PNG) + set_config_option(HAVE_LIBPNG "Png[fltk]") + else() + find_package(PNG) + if(PNG_FOUND) + set_config_option(HAVE_LIBPNG "Png") + list(APPEND EXTERNAL_LIBRARIES ${PNG_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${PNG_INCLUDE_DIR}) + endif() + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/mpeg_encode AND + ENABLE_MPEG_ENCODE) + add_subdirectory(contrib/mpeg_encode) + include_directories(contrib/mpeg_encode/headers) + set_config_option(HAVE_MPEG_ENCODE "Mpeg") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/3M AND ENABLE_3M) + add_subdirectory(contrib/3M) + include_directories(contrib/3M) + set_config_option(HAVE_3M "3M") + endif() + + if(ENABLE_OSMESA) + find_library(OSMESA_LIB OSMesa) + if(OSMESA_LIB) + set_config_option(HAVE_OSMESA "OSMesa") + list(APPEND EXTERNAL_LIBRARIES ${OSMESA_LIB}) + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Graphics) + set(OpenGL_GL_PREFERENCE "LEGACY") + find_package(OpenGL REQUIRED) + if(OPENGL_GLU_FOUND AND OPENGL_FOUND) + add_subdirectory(Graphics) + set_config_option(HAVE_OPENGL "OpenGL") + else() + message(SEND_ERROR "Could not find GLU: disabling OpenGL support") + endif() + endif() +endif() + +if(ENABLE_ANN) + find_library(ANN_LIB ANN PATH_SUFFIXES lib) + find_path(ANN_INC "ANN.h" PATH_SUFFIXES src include ANN) + if(ENABLE_SYSTEM_CONTRIB AND ANN_LIB AND ANN_INC) + message(STATUS "Using system version of ANN") + list(APPEND EXTERNAL_LIBRARIES ${ANN_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ANN_INC}) + set_config_option(HAVE_ANN "ANN[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ANN) + add_subdirectory(contrib/ANN) + include_directories(contrib/ANN/include) + set_config_option(HAVE_ANN "ANN") + endif() +endif() + +if(ENABLE_ALGLIB) + find_library(ALGLIB_LIB alglib) + find_path(ALGLIB_INC "stdafx.h" PATH_SUFFIXES libalglib) + if(ENABLE_SYSTEM_CONTRIB AND ALGLIB_LIB AND ALGLIB_INC) + list(APPEND EXTERNAL_LIBRARIES ${ALGLIB_LIB}) + list(APPEND EXTERNAL_INCLUDES ${ALGLIB_INC}) + set_config_option(HAVE_ALGLIB "ALGLIB[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/ALGLIB) + add_subdirectory(contrib/ALGLIB) + include_directories(contrib/ALGLIB) + set_config_option(HAVE_ALGLIB "ALGLIB") + endif() +endif() + +if(HAVE_FLTK AND ENABLE_CAIRO) + find_library(CAIRO_LIB cairo) + find_path(CAIRO_INC "cairo/cairo.h" PATH_SUFFIXES include) + if(CAIRO_INC AND CAIRO_LIB) + set_config_option(HAVE_CAIRO "Cairo") + list(APPEND EXTERNAL_LIBRARIES ${CAIRO_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CAIRO_INC}) + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/DiscreteIntegration AND + ENABLE_DINTEGRATION) + add_subdirectory(contrib/DiscreteIntegration) + include_directories(contrib/DiscreteIntegration) + set_config_option(HAVE_DINTEGRATION "DIntegration") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/HighOrderMeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshOptimizer AND + EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MeshQualityOptimizer AND + ENABLE_OPTHOM AND HAVE_MESH) + add_subdirectory(contrib/HighOrderMeshOptimizer) + include_directories(contrib/HighOrderMeshOptimizer) + add_subdirectory(contrib/MeshOptimizer) + include_directories(contrib/MeshOptimizer) + include_directories(${CMAKE_CURRENT_BINARY_DIR}/contrib/MeshOptimizer) + add_subdirectory(contrib/MeshQualityOptimizer) + include_directories(contrib/MeshQualityOptimizer) + set_config_option(HAVE_OPTHOM "OptHom") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/domhex AND + ENABLE_DOMHEX AND HAVE_MESH) + add_subdirectory(contrib/domhex) + include_directories(contrib/domhex) + set_config_option(HAVE_DOMHEX "DomHex") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/QuadTri AND + ENABLE_QUADTRI AND HAVE_MESH) + add_subdirectory(contrib/QuadTri) + include_directories(contrib/QuadTri) + set_config_option(HAVE_QUADTRI "QuadTri") +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/kbipack AND ENABLE_KBIPACK) + set_config_option(HAVE_KBIPACK "Kbipack") + add_subdirectory(contrib/kbipack) + include_directories(contrib/kbipack) + if(ENABLE_GMP) + find_library(GMP_LIB libgmp.a) + find_path(GMP_INC "gmp.h" PATH_SUFFIXES src include) + endif() + if(GMP_LIB AND GMP_INC) + set_config_option(HAVE_GMP "GMP") + list(APPEND EXTERNAL_LIBRARIES ${GMP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GMP_INC}) + else() + message(STATUS "GMP not found: Kbipack uses long int") + endif() +endif() + +if(ENABLE_MATHEX) + find_library(MATHEX_LIB mathex PATH_SUFFIXES lib) + find_path(MATHEX_INC "mathex.h" PATH_SUFFIXES src include) + if(ENABLE_SYSTEM_CONTRIB AND MATHEX_LIB AND MATHEX_INC) + list(APPEND EXTERNAL_LIBRARIES ${MATHEX_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MATHEX_INC}) + set_config_option(HAVE_MATHEX "MathEx[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/MathEx) + add_subdirectory(contrib/MathEx) + include_directories(contrib/MathEx) + set_config_option(HAVE_MATHEX "MathEx") + endif() +endif() + +if(ENABLE_MPI) + find_package(MPI) + if(MPI_FOUND) + set_config_option(HAVE_MPI "MPI") + list(APPEND EXTERNAL_INCLUDES ${MPI_CXX_INCLUDE_PATH}) + list(APPEND EXTERNAL_LIBRARIES ${MPI_CXX_LIBRARIES}) + set(CMAKE_C_COMPILER ${MPI_C_COMPILER}) + set(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER}) + set(CMAKE_Fortran_COMPILER ${MPI_Fortran_COMPILER}) + endif() +endif() + +if(ENABLE_POPPLER) + find_library(POPPLER_LIB poppler) + find_library(POPPLER_CPP_LIB poppler-cpp) + find_path(POPPLER_INC "poppler/cpp/poppler-document.h" PATH_SUFFIXES src include) + if(POPPLER_LIB AND POPPLER_INC) + set_config_option(HAVE_POPPLER "Poppler") + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_LIB}) + list(APPEND EXTERNAL_LIBRARIES ${POPPLER_CPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${POPPLER_INC}) + endif() +endif() + +if(ENABLE_P4EST) + find_library(P4EST_LIB p4est) + find_path(P4EST_INC "p4est.h" PATH_SUFFIXES src) + find_library(SC_LIB sc) + if(P4EST_LIB AND P4EST_INC AND SC_LIB) + set_config_option(HAVE_P4EST "P4est") + list(APPEND EXTERNAL_LIBRARIES ${P4EST_LIB} ${SC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${P4EST_INC}) + endif() +endif() + +if(HAVE_MESH OR HAVE_SOLVER) + if(ENABLE_METIS) + if(METIS_LIB AND METIS_INC) + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis") + else() + find_library(METIS_LIB metis PATH_SUFFIXES lib) + find_path(METIS_INC "metis.h" PATH_SUFFIXES include) + if(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC) + message(STATUS "Using system version of METIS") + list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${METIS_INC}) + set_config_option(HAVE_METIS "Metis[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/metis) + add_definitions(-DUSE_GKREGEX) + add_subdirectory(contrib/metis) + include_directories(contrib/metis/include contrib/metis/libmetis + contrib/metis/GKlib) + set_config_option(HAVE_METIS "Metis") + endif() + endif() + endif() +endif() + +if(HAVE_MESH) + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Mesh/tetgenBR.cxx) + set_config_option(HAVE_TETGENBR "TetGen/BR") + endif() + + if(ENABLE_VOROPP) + find_library(VOROPP_LIB voro++) + find_path(VOROPP_INC "voro++.hh" PATH_SUFFIXES voro++) + if(ENABLE_SYSTEM_CONTRIB AND VOROPP_LIB AND VOROPP_INC) + message(STATUS "Using system version of voro++") + list(APPEND EXTERNAL_LIBRARIES ${VOROPP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${VOROPP_INC}) + set_config_option(HAVE_VOROPP "Voro++[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++) + add_subdirectory(contrib/voro++) + include_directories(contrib/voro++/src) + set_config_option(HAVE_VOROPP "Voro++") + endif() + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/blossom AND ENABLE_BLOSSOM) + add_subdirectory(contrib/blossom) + include_directories(contrib/blossom/MATCH contrib/blossom/concorde97 + contrib/blossom/concorde97/INCLUDE) + set_config_option(HAVE_BLOSSOM "Blossom") + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/Netgen AND ENABLE_NETGEN) + add_subdirectory(contrib/Netgen) + include_directories(contrib/Netgen contrib/Netgen/libsrc/include + contrib/Netgen/nglib) + set_config_option(HAVE_NETGEN "Netgen") + add_definitions(-DNO_PARALLEL_THREADS -DNOTCL) + endif() + + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/bamg AND ENABLE_BAMG) + add_subdirectory(contrib/bamg) + include_directories(contrib/bamg contrib/bamg/bamglib) + set_config_option(HAVE_BAMG "Bamg") + endif() + + if(ENABLE_MMG) + find_library(MMG_LIB NAMES Mmg mmg) + find_path(MMG_INC "libmmg.h" PATH_SUFFIXES mmg) + if(MMG_LIB AND MMG_INC) + list(APPEND EXTERNAL_LIBRARIES ${MMG_LIB}) + list(APPEND EXTERNAL_INCLUDES ${MMG_INC}) + set_config_option(HAVE_MMG "Mmg") + endif() + endif() +endif() + +if(ENABLE_MED OR ENABLE_CGNS) + find_package(HDF5) + if(HDF5_FOUND) + set(HDF5_LIB "${HDF5_C_LIBRARIES}") + list(APPEND EXTERNAL_INCLUDES ${HDF5_INCLUDE_DIRS}) + if(ENABLE_MED) + find_library(MED_LIB medC) + if(MED_LIB) + set_config_option(HAVE_MED "Med") + list(APPEND EXTERNAL_LIBRARIES ${MED_LIB}) + endif() + endif() + if(ENABLE_CGNS) + find_library(CGNS_LIB cgns HINTS ENV CGNS_ROOT PATH_SUFFIXES lib) + find_path(CGNS_INC "cgnslib.h" HINTS ENV CGNS_ROOT PATH_SUFFIXES include) + if(CGNS_LIB AND CGNS_INC) + set_config_option(HAVE_LIBCGNS "Cgns") + list(APPEND EXTERNAL_LIBRARIES ${CGNS_LIB}) + list(APPEND EXTERNAL_INCLUDES ${CGNS_INC}) + if(ENABLE_CGNS_CPEX0045) + set_config_option(HAVE_LIBCGNS_CPEX0045 "Cgns_CPEX0045") + endif() + endif() + endif() + if(MED_LIB OR CGNS_LIB) + list(APPEND EXTERNAL_LIBRARIES ${HDF5_LIB}) + find_library(SZ_LIB NAMES szlib sz) + if(SZ_LIB) + list(APPEND EXTERNAL_LIBRARIES ${SZ_LIB}) + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + endif() + endif() + endif() + else() + message(STATUS "HDF5 not found") + endif() +endif() + +if(HAVE_SOLVER) + if(ENABLE_GMM) + find_path(GMM_INC "gmm.h" PATH_SUFFIXES src include include/gmm) + if(ENABLE_SYSTEM_CONTRIB AND GMM_INC) + message(STATUS "Using system version of GMM") + list(APPEND EXTERNAL_INCLUDES ${GMM_INC}) + set_config_option(HAVE_GMM "Gmm[system]") + elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/gmm) + include_directories(contrib/gmm) + set_config_option(HAVE_GMM "Gmm") + endif() + endif() + + if(ENABLE_PETSC) + if(PETSC_DIR) + set(ENV_PETSC_DIR ${PETSC_DIR}) + else() + set(ENV_PETSC_DIR $ENV{PETSC_DIR}) + endif() + if(PETSC_ARCH) + set(ENV_PETSC_ARCH ${PETSC_ARCH}) + else() + set(ENV_PETSC_ARCH $ENV{PETSC_ARCH}) + endif() + set(PETSC_POSSIBLE_CONF_FILES + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc-conf/petscvariables + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib/petsc/conf/petscvariables) + foreach(FILE ${PETSC_POSSIBLE_CONF_FILES}) + if(EXISTS ${FILE}) + # old-style PETSc installations (using PETSC_DIR and PETSC_ARCH) + message(STATUS "Using PETSc dir: ${ENV_PETSC_DIR}") + message(STATUS "Using PETSc arch: ${ENV_PETSC_ARCH}") + # find includes by parsing the petscvariables file + file(STRINGS ${FILE} PETSC_VARIABLES NEWLINE_CONSUME) + endif() + endforeach() + if(PETSC_VARIABLES) + # try to find PETSC_CC_INCLUDES for PETSc >= 3.4 + string(REGEX MATCH "PETSC_CC_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "PETSC_CC_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + else() + # try to find PETSC_PACKAGES_INCLUDES in older versions + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/include) + list(APPEND EXTERNAL_INCLUDES ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/include) + string(REGEX MATCH "PACKAGES_INCLUDES = [^\n\r]*" PETSC_PACKAGES_INCLUDES + ${PETSC_VARIABLES}) + string(REPLACE "PACKAGES_INCLUDES = " "" PETSC_PACKAGES_INCLUDES + ${PETSC_PACKAGES_INCLUDES}) + endif() + if(PETSC_PACKAGES_INCLUDES) + if(PETSC_PACKAGES_INCLUDES) + string(REPLACE "-I" "" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + string(REPLACE " " ";" PETSC_PACKAGES_INCLUDES ${PETSC_PACKAGES_INCLUDES}) + foreach(VAR ${PETSC_PACKAGES_INCLUDES}) + # seem to include unexisting directories (/usr/include/lib64) + # check to avoid warnings + if(EXISTS ${VAR}) + list(APPEND EXTERNAL_INCLUDES ${VAR}) + endif() + endforeach() + endif() + endif() + # find libraries (<= 3.0) + set(PETSC_LIBS_REQUIRED petscksp petscdm petscmat petscvec petsc) + find_all_libraries(PETSC_LIBS PETSC_LIBS_REQUIRED + ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib "") + # petsc 3.1 creates only one library (libpetsc) + if(NOT PETSC_LIBS) + find_library(PETSC_LIBS petsc PATHS ${ENV_PETSC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + endif() + if(PETSC_LIBS) + set_config_option(HAVE_PETSC "PETSc") + if(NOT HAVE_BLAS) + set_config_option(HAVE_BLAS "Blas[petsc]") + endif() + if(NOT HAVE_LAPACK) + set_config_option(HAVE_LAPACK "Lapack[petsc]") + endif() + endif() + # find slepc (needs to be linked in before petsc) + if(ENABLE_SLEPC) + if(SLEPC_DIR) + set(ENV_SLEPC_DIR ${SLEPC_DIR}) + else() + set(ENV_SLEPC_DIR $ENV{SLEPC_DIR}) + endif() + find_library(SLEPC_LIB slepc PATHS ${ENV_SLEPC_DIR}/${ENV_PETSC_ARCH}/lib + NO_DEFAULT_PATH) + if(SLEPC_LIB) + find_path(SLEPC_INC "slepc.h" PATHS ${ENV_SLEPC_DIR} PATH_SUFFIXES include + ${ENV_PETSC_ARCH}/include include/slepc NO_DEFAULT_PATH) + if(SLEPC_INC) + message(STATUS "Using SLEPc dir: ${ENV_SLEPC_DIR}") + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + find_path(SLEPC_INC2 "slepcconf.h" PATHS ${ENV_SLEPC_DIR} + PATH_SUFFIXES ${ENV_PETSC_ARCH}/include NO_DEFAULT_PATH) + if(SLEPC_INC2) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC2}) + endif() + endif() + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + # find additional libraries to link with + string(REGEX MATCH "PACKAGES_LIBS = [^\n\r]*" PLIBS ${PETSC_VARIABLES}) + if(PLIBS) + string(REPLACE "PACKAGES_LIBS = " "" PLIBS ${PLIBS}) + string(STRIP ${PLIBS} PLIBS) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS}") + endif() + string(REGEX MATCH "PETSC_EXTERNAL_LIB_BASIC = [^\n\r]*" PLIBS_BASIC ${PETSC_VARIABLES}) + if(PLIBS_BASIC) + string(REPLACE "PETSC_EXTERNAL_LIB_BASIC = " "" PLIBS_BASIC ${PLIBS_BASIC}) + string(STRIP ${PLIBS_BASIC} PLIBS_BASIC) + separate_arguments(PLIBS_BASIC) + list(APPEND EXTERNAL_LIBRARIES "${PLIBS_BASIC}") + endif() + string(REGEX MATCH "PCC_LINKER_LIBS = [^\n\r]*" LLIBS ${PETSC_VARIABLES}) + if(LLIBS) + string(REPLACE "PCC_LINKER_LIBS = " "" LLIBS ${LLIBS}) + string(STRIP ${LLIBS} LLIBS) + list(APPEND EXTERNAL_LIBRARIES "${LLIBS}") + endif() + else() + # new-style PETSc installations (in standard system directories) + find_library(PETSC_LIBS petsc) + find_path(PETSC_INC "petsc.h" PATH_SUFFIXES include/petsc) + if(PETSC_LIBS AND PETSC_INC) + set_config_option(HAVE_PETSC "PETSc") + if(ENABLE_SLEPC) + find_library(SLEPC_LIB slepc) + find_path(SLEPC_INC "slepc.h" PATH_SUFFIXES include/slepc) + if(SLEPC_LIB AND SLEPC_INC) + set_config_option(HAVE_SLEPC "SLEPc") + list(APPEND EXTERNAL_LIBRARIES ${SLEPC_LIB}) + list(APPEND EXTERNAL_INCLUDES ${SLEPC_INC}) + endif() + endif() + list(APPEND EXTERNAL_LIBRARIES ${PETSC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${PETSC_INC}) + endif() + endif() + endif() + + if(ENABLE_MUMPS AND HAVE_BLAS AND HAVE_LAPACK) + set(MUMPS_LIBS_REQUIRED smumps dmumps cmumps zmumps mumps_common pord) + if(NOT ENABLE_MPI) + list(APPEND MUMPS_LIBS_REQUIRED mpiseq) + endif() + find_all_libraries(MUMPS_LIBRARIES MUMPS_LIBS_REQUIRED "" "lib") + find_path(SMUMPS_INC "smumps_c.h" PATH_SUFFIXES src include) + find_path(DMUMPS_INC "dmumps_c.h" PATH_SUFFIXES src include) + find_path(CMUMPS_INC "cmumps_c.h" PATH_SUFFIXES src include) + find_path(ZMUMPS_INC "zmumps_c.h" PATH_SUFFIXES src include) + if(MUMPS_LIBRARIES AND SMUMPS_INC AND DMUMPS_INC AND CMUMPS_INC AND ZMUMPS_INC) + set_config_option(HAVE_MUMPS "MUMPS") + list(APPEND EXTERNAL_LIBRARIES ${MUMPS_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${SMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${DMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${CMUMPS_INC}) + list(APPEND EXTERNAL_INCLUDES ${ZMUMPS_INC}) + find_library(GFORTRAN_LIB gfortran) + if(GFORTRAN_LIB) + list(APPEND EXTERNAL_LIBRARIES ${GFORTRAN_LIB}) + endif() + if(ENABLE_GMM) # use GMM/MUMPS interface + add_definitions(-DGMM_USES_MUMPS) + endif() + endif() + endif() + + if(ENABLE_GETDP) + find_library(GETDP_LIB GetDP) + find_path(GETDP_INC "GetDP.h" PATH_SUFFIXES getdp) + if(GETDP_LIB AND GETDP_INC) + set_config_option(HAVE_GETDP "GetDP") + list(APPEND EXTERNAL_LIBRARIES ${GETDP_LIB}) + list(APPEND EXTERNAL_INCLUDES ${GETDP_INC}) + endif() + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt AND ENABLE_HXT) + add_subdirectory(contrib/hxt) + include_directories(BEFORE ${HXT_INC_DIRS}) + set_config_option(HAVE_HXT "Hxt") + # do not use arithmetic contraction in predicates.c + if(MSVC OR (CMAKE_C_COMPILER_ID STREQUAL "Intel" AND WIN32)) + set_source_files_properties( + "${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/predicates/src/predicates.c" + PROPERTIES COMPILE_FLAGS "/fp:strict") + elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel") + set_source_files_properties( + "${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/predicates/src/predicates.c" + PROPERTIES COMPILE_FLAGS "-fp-model strict") + elseif(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang") + set_source_files_properties( + "${CMAKE_CURRENT_SOURCE_DIR}/contrib/hxt/predicates/src/predicates.c" + PROPERTIES COMPILE_FLAGS "-fno-unsafe-math-optimizations -ffp-contract=off") + else() + message(WARNING + "Unsupported compiler ! + Make sure compiled functions from predicates.c + do NOT use extended double precision and follow IEEE754 standard. + It is crucial for the robustness of geometric predicates.") + endif() +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/pro AND ENABLE_PRO) + add_subdirectory(pro) +endif() + +if(ENABLE_OCC) + set(OCC_MINIMAL_VERSION "6.9.1") + if(WIN32) + if(HAVE_64BIT_SIZE_T) + set(OCC_SYS_NAME win64) + else() + set(OCC_SYS_NAME win32) + endif() + else() + set(OCC_SYS_NAME ${CMAKE_SYSTEM_NAME}) + endif() + find_path(OCC_INC "Standard_Version.hxx" HINTS ENV CASROOT PATH_SUFFIXES + inc include include/oce opencascade include/opencascade + occt include/occt) + if(OCC_INC) + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAJOR REGEX "#define OCC_VERSION_MAJOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MINOR REGEX "#define OCC_VERSION_MINOR.*") + file(STRINGS ${OCC_INC}/Standard_Version.hxx + OCC_MAINT REGEX "#define OCC_VERSION_MAINTENANCE.*") + if(OCC_MAJOR AND OCC_MINOR AND OCC_MAINT) + string(REGEX MATCH "[0-9]+" OCC_MAJOR "${OCC_MAJOR}") + string(REGEX MATCH "[0-9]+" OCC_MINOR "${OCC_MINOR}") + string(REGEX MATCH "[0-9]+" OCC_MAINT "${OCC_MAINT}") + set(OCC_VERSION "${OCC_MAJOR}.${OCC_MINOR}.${OCC_MAINT}") + message(STATUS "Found OpenCASCADE version ${OCC_VERSION} in ${OCC_INC}") + endif() + endif() + if(OCC_VERSION AND OCC_VERSION STRLESS ${OCC_MINIMAL_VERSION}) + message(WARNING "Gmsh requires OpenCASCADE >= ${OCC_MINIMAL_VERSION}. " + "Use CMAKE_PREFIX_PATH or the CASROOT environment variable " + "to explicitely specify the installation path of OpenCASCADE") + elseif(OCC_INC) + set(OCC_LIBS_REQUIRED + # subset of DataExchange + TKSTEP TKSTEP209 TKSTEPAttr TKSTEPBase TKIGES TKXSBase + # ModelingAlgorithms + TKOffset TKFeat TKFillet TKBool TKMesh TKHLR TKBO TKPrim TKShHealing + TKTopAlgo TKGeomAlgo + # ModelingData + TKBRep TKGeomBase TKG3d TKG2d + # FoundationClasses + TKMath TKernel) + if(ENABLE_OCC_TBB) + list(APPEND OCC_LIBS_REQUIRED tbb tbbmalloc) + endif() + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS_REQUIRED) + if(OCC_LIBS) + message(STATUS "OCC libraries specified explicitly: " ${OCC_LIBS}) + list(LENGTH OCC_LIBS_REQUIRED NUM_OCC_LIBS) + else() + set(OCC_LIBS) + foreach(OCC ${OCC_LIBS_REQUIRED}) + find_library(OCC_LIB ${OCC} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib + ${OCC_SYS_NAME}/gcc/lib ${OCC_SYS_NAME}/gcc/bin) + if(OCC_LIB) + list(APPEND OCC_LIBS ${OCC_LIB}) + else() + message(STATUS "OCC lib " ${OCC} " not Found") + endif() + unset(OCC_LIB CACHE) + endforeach() + list(LENGTH OCC_LIBS NUM_OCC_LIBS) + endif() + endif() + + # additional OCC libraries to handle reading of STEP/IGES attributes. Oh my... + if(ENABLE_OCC_CAF) + find_package(Freetype) + if(FREETYPE_FOUND) + set(OCC_CAF_LIBS_REQUIRED + TKXDESTEP TKXDEIGES TKXCAF TKLCAF TKVCAF TKCAF TKV3d TKService TKCDF) + list(LENGTH OCC_CAF_LIBS_REQUIRED NUM_OCC_CAF_LIBS_REQUIRED) + set(OCC_CAF_LIBS) + foreach(OCC ${OCC_CAF_LIBS_REQUIRED}) + find_library(OCC_CAF_LIB ${OCC} HINTS ENV CASROOT PATH_SUFFIXES + lib ${OCC_SYS_NAME}/lib ${OCC_SYS_NAME}/vc8/lib + ${OCC_SYS_NAME}/gcc/lib ${OCC_SYS_NAME}/gcc/bin) + if(OCC_CAF_LIB) + list(APPEND OCC_CAF_LIBS ${OCC_CAF_LIB}) + else() + message(STATUS "OCC CAF lib " ${OCC} " not Found") + endif() + unset(OCC_CAF_LIB CACHE) + endforeach() + list(LENGTH OCC_CAF_LIBS NUM_OCC_CAF_LIBS) + endif() + endif() + + if(NUM_OCC_LIBS EQUAL NUM_OCC_LIBS_REQUIRED) + # append OCC CAF libraries first... + if(NUM_OCC_CAF_LIBS EQUAL NUM_OCC_CAF_LIBS_REQUIRED) + set_config_option(HAVE_OCC_CAF "OpenCASCADE-CAF") + list(APPEND EXTERNAL_LIBRARIES ${OCC_CAF_LIBS} ${FREETYPE_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${FREETYPE_INCLUDE_DIRS}) + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "windowscodecs") + list(APPEND EXTERNAL_LIBRARIES "ole32") + endif() + endif() + # then append OCC libraries + set_config_option(HAVE_OCC "OpenCASCADE") + list(APPEND EXTERNAL_LIBRARIES ${OCC_LIBS}) + list(APPEND EXTERNAL_INCLUDES ${OCC_INC}) + if(HAVE_64BIT_SIZE_T) + add_definitions(-D_OCC64) + endif() + if(WIN32) + list(APPEND EXTERNAL_LIBRARIES "winspool") + add_definitions(-DOCC_CONVERT_SIGNALS) + elseif(MSVC) + add_definitions(-DWNT) + endif() + endif() +endif() + +if(ENABLE_ZIPPER) + if(ENABLE_BUILD_IOS) + set_config_option(HAVE_LIBZ "Zlib") + endif() + if(NOT HAVE_LIBZ) # necessary for non-GUI builds + find_package(ZLIB) + if(ZLIB_FOUND) + set_config_option(HAVE_LIBZ "Zlib") + list(APPEND EXTERNAL_LIBRARIES ${ZLIB_LIBRARIES}) + list(APPEND EXTERNAL_INCLUDES ${ZLIB_INCLUDE_DIR}) + endif() + endif() + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/contrib/zipper AND HAVE_LIBZ) + add_subdirectory(contrib/zipper) + include_directories(contrib/zipper) + set_config_option(HAVE_ZIPPER "Zipper") + endif() +endif() + +if(ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON) + find_package(SWIG REQUIRED) + include(${SWIG_USE_FILE}) + find_package(PythonLibs) + if(SWIG_FOUND AND PYTHONLIBS_FOUND) + message(STATUS "Found SWIG version " ${SWIG_VERSION}) + find_package(PythonInterp) + string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION) + if(SWIG_MAJOR_VERSION EQUAL 1) + message(WARNING "Python bindings require SWIG >= 2: disabling Python") + else() + set_config_option(HAVE_PYTHON "Python") + mark_as_advanced(CLEAR PYTHON_LIBRARY PYTHON_INCLUDE_DIR) + if(ENABLE_NUMPY) + if (NOT NUMPY_INC) + EXEC_PROGRAM (${PYTHON_EXECUTABLE} + ARGS "-c \"import numpy; print(numpy.get_include())\"" + OUTPUT_VARIABLE NUMPY_INC + RETURN_VALUE NUMPY_NOT_FOUND) + endif() + if(NUMPY_INC) + list(APPEND EXTERNAL_INCLUDES ${NUMPY_INC}) + set_config_option(HAVE_NUMPY "Numpy") + endif() + endif() + if(HAVE_PETSC) + if(ENABLE_PETSC4PY) + EXECUTE_PROCESS( + COMMAND ${PYTHON_EXECUTABLE} -c "import petsc4py; print(petsc4py.get_include())" + OUTPUT_VARIABLE PETSC4PY_INC + RESULT_VARIABLE PETSC4PY_NOT_FOUND + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + if(PETSC4PY_INC) + list(APPEND EXTERNAL_INCLUDES ${PETSC4PY_INC}) + set_config_option(HAVE_PETSC4PY "PETSc4py") + endif() + endif() + endif() + endif() + endif() +endif() + +check_function_exists(vsnprintf HAVE_VSNPRINTF) +if(NOT HAVE_VSNPRINTF AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_VSNPRINTF "NoVsnprintf") +endif() + +check_include_file(sys/socket.h HAVE_SYS_SOCKET_H) +if(HAVE_SYS_SOCKET_H) + set(CMAKE_EXTRA_INCLUDE_FILES sys/socket.h) +endif() +check_type_size(socklen_t SOCKLEN_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT SOCKLEN_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_SOCKLEN_T "NoSocklenT") +endif() + +check_include_file(stdint.h HAVE_STDINT_H) +if(HAVE_STDINT_H) + set(CMAKE_EXTRA_INCLUDE_FILES stdint.h) +else() + set_config_option(HAVE_NO_STDINT_H "NoStdintH") +endif() +check_type_size(intptr_t INTPTR_T_SIZE) +set(CMAKE_EXTRA_INCLUDE_FILES) +if(NOT INTPTR_T_SIZE AND NOT ENABLE_BUILD_IOS AND NOT ENABLE_BUILD_ANDROID) + set_config_option(HAVE_NO_INTPTR_T "NoIntptrT") +endif() + +check_include_file(dlfcn.h DLFCN_H) +if(DLFCN_H) + set_config_option(HAVE_DLOPEN "Dlopen") + list(APPEND EXTERNAL_LIBRARIES ${CMAKE_DL_LIBS}) +endif() + +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + check_include_file(linux/joystick.h LINUX_JOYSTICK_H) + if(LINUX_JOYSTICK_H) + set_config_option(HAVE_LINUX_JOYSTICK "LinuxJoystick") + endif() +endif() + +if(WIN32) + add_definitions(-D_USE_MATH_DEFINES) + list(APPEND EXTERNAL_LIBRARIES winmm wsock32 ws2_32 psapi) +endif() + +if(MSVC) + add_definitions(-DNOMINMAX -D_CRT_SECURE_NO_DEPRECATE -D_SCL_SECURE_NO_DEPRECATE) +endif() + +# add C functions API +set(GMSH_SRC ${GMSH_SRC};api/gmshc.cpp) + +# force full warnings to encourage everybody to write clean(er) code +check_cxx_compiler_flag("-Wall" WALL) +if(WALL AND NOT MSVC) + file(GLOB_RECURSE WALL_SRC Common/*.cpp Fltk/*.cpp FunctionSpace/*.cpp + Geo/*.cpp Graphics/*.cpp Mesh/*.cpp Numeric/*.cpp Parser/*.cpp + Plugin/*.cpp Post/*.cpp Solver/*.cpp) + set(WF "-Wall") + check_cxx_compiler_flag("-Wint-to-void-pointer-cast" WCAST) + if(WCAST) + set(WF "${WF} -Wno-int-to-void-pointer-cast") + endif() + check_cxx_compiler_flag("-Wdeprecated-declarations" WDEPREC) + if(WDEPREC) + # FIXME: remove this when we have fixed the deprecated GLU code for OpenGL3 + set(WF "${WF} -Wno-deprecated-declarations") + endif() + check_cxx_compiler_flag("-Wmisleading-indentation" WIND) + if(WIND) + set(WF "${WF} -Wno-misleading-indentation") + endif() + check_cxx_compiler_flag("-Wno-attributes" WATTR) + if(WATTR) + # FIXME: remove this when GCC behaves more intelligently + set(WF "${WF} -Wno-attributes") + endif() + set_compile_flags(WALL_SRC ${WF}) +endif() + +# don't issue warnings for contributed libraries +check_cxx_compiler_flag("-w" NOWARN) +if(NOWARN) + file(GLOB_RECURSE NOWARN_SRC contrib/*.cpp contrib/*.cc contrib/*.cxx contrib/*.c) + set_compile_flags(NOWARN_SRC "-w") +endif() + +# disable compile optimization on some known problematic files +check_cxx_compiler_flag("-O0" NOOPT) +if(NOOPT OR ENABLE_BUILD_IOS) + if(ENABLE_BUILD_IOS) # optimized iOS 10 64 bits screws somewhere in Geo + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Geo/G*.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* Mesh/Background*) + else() + file(GLOB_RECURSE NOOPT_SRC Numeric/robustPredicates.cpp Mesh/BDS.cpp + Parser/Gmsh.tab.cpp contrib/blossom/* contrib/bamg/* Mesh/Background*) + endif() + set_compile_flags(NOOPT_SRC "-O0") +endif() + +# do not use arithmetic contraction in predicates.cpp +# if("${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "/fp:strict") +# elseif(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fno-unsafe-math-optimizations -ffp-contract=off") +# elseif(CMAKE_C_COMPILER_ID STREQUAL "Intel") +# set_source_files_properties(Numeric/robustPredicates.cpp PROPERTIES +# COMPILE_FLAGS "-fp-model strict") +# endif() + +# enable Revoropt and set compile flags for the corresponding plugin +if(ENABLE_REVOROPT) + if(HAVE_EIGEN AND HAVE_MESH AND HAVE_PLUGINS AND HAVE_ANN AND HAVE_ALGLIB) + list(APPEND EXTERNAL_INCLUDES contrib/Revoropt/include) + set_config_option(HAVE_REVOROPT "Revoropt") + add_definitions(-DUSE_ANN) + else() + message(WARNING "Revoropt requires Eigen, Mesh, Plugins, ANN and ALGLIB") + endif() +endif() + +if(HAVE_MESH AND NOT HAVE_EIGEN AND NOT HAVE_LAPACK) + message(WARNING "Most meshing algorithms will not be functional without " + "Eigen or Lapack") +endif() + +list(SORT CONFIG_OPTIONS) +set(GMSH_CONFIG_OPTIONS "") +foreach(OPT ${CONFIG_OPTIONS}) + set(GMSH_CONFIG_OPTIONS "${GMSH_CONFIG_OPTIONS} ${OPT}") +endforeach() + +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshConfig.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshConfig.h) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Common/GmshVersion.h.in + ${CMAKE_CURRENT_BINARY_DIR}/Common/GmshVersion.h) + +# the texi and pypi version files are modified in the source directory (not +# ideal for version.texi, but since git tracks the contents of the file this is +# acceptable as it will only change when the actual version is changed - not for +# each git hash; setup.py is not under version control) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi.in + ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo/version.texi) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh/setup.py.in + ${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh/setup.py) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh-dev/setup.py.in + ${CMAKE_CURRENT_SOURCE_DIR}/utils/pypi/gmsh-dev/setup.py) + +file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/version.txt ${GMSH_SHORT_VERSION}) + +# process cmake environment variables so we can append them to the -I include +# commands. This is not recommended (we should only use the cache variables) but +# it is very convenient: otherwise we have to remember providing the +# -D... options to cmake for each new build. +set(ENV_CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH}) +set(ENV_CMAKE_INCLUDE_PATH $ENV{CMAKE_INCLUDE_PATH}) +if(UNIX) + if(ENV_CMAKE_PREFIX_PATH) + string(REPLACE ":" ";" ENV_CMAKE_PREFIX_PATH ${ENV_CMAKE_PREFIX_PATH}) + endif() + if(ENV_CMAKE_INCLUDE_PATH) + string(REPLACE ":" ";" ENV_CMAKE_INCLUDE_PATH ${ENV_CMAKE_INCLUDE_PATH}) + endif() +endif() +list(APPEND EXTERNAL_INCLUDES ${CMAKE_INCLUDE_PATH} ${ENV_CMAKE_INCLUDE_PATH}) +list(APPEND EXTERNAL_INCLUDES ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) +foreach(DIR ${CMAKE_PREFIX_PATH} ${ENV_CMAKE_PREFIX_PATH}) + list(APPEND EXTERNAL_INCLUDES ${DIR}/include) +endforeach() + +if(EXTERNAL_INCLUDES) + list(REMOVE_DUPLICATES EXTERNAL_INCLUDES) +endif() + +if(HAVE_FLTK) + set(LINK_LIBRARIES ${FLTK_LIBRARIES} ${EXTERNAL_LIBRARIES} + ${OPENGL_LIBRARIES} ${LAPACK_LIBRARIES}) +elseif(HAVE_OPENGL) + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${OPENGL_LIBRARIES} + ${LAPACK_LIBRARIES}) +else() + set(LINK_LIBRARIES ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) +endif() + +# try to use static gfortran on static builds (cannot do this on dynamic builds +# as e.g. Debian compiles libgfortran.a without -fPIC: sigh...) +if(NOT ENABLE_BUILD_DYNAMIC AND NOT ENABLE_BUILD_SHARED) + find_library(GFORTRAN_STATIC libgfortran.a) + if(GFORTRAN_STATIC) + set(CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES) + message(STATUS "Using static libgfortran") + foreach(STR ${LINK_LIBRARIES}) + string(REPLACE "-lgfortran" ${GFORTRAN_STATIC} STR2 ${STR}) + list(APPEND LINK_LIBRARIES2 ${STR2}) + endforeach() + set(LINK_LIBRARIES ${LINK_LIBRARIES2}) + endif() +endif() + +# Linux-specific linker options +if(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + if(HAVE_OCC) + find_library(RT_LIB rt) + if(RT_LIB) + list(APPEND LINK_LIBRARIES ${RT_LIB}) + endif() + endif() + if(CMAKE_C_COMPILER_ID MATCHES "GNU" OR CMAKE_C_COMPILER_ID MATCHES "Intel") + add_definitions(-fPIC) + endif() +endif() + +# we could specify include dirs more selectively, but this is simpler +include_directories(Common Fltk Geo Graphics Mesh Solver Numeric Parser + Plugin Post api ${EXTERNAL_INCLUDES} ${CMAKE_CURRENT_BINARY_DIR}/Common) + +# set this for external codes that might include this CMakeList file +set(GMSH_EXTERNAL_INCLUDE_DIRS ${EXTERNAL_INCLUDES} CACHE + STRING "External include directories" FORCE) +set(GMSH_EXTERNAL_LIBRARIES ${LINK_LIBRARIES} CACHE + STRING "External libraries" FORCE) + +# group sources for easier navigation in IDEs +foreach(DIR ${GMSH_DIRS}) + string(REGEX REPLACE "\\+" "\\\\+" DIR ${DIR}) + source_group(${DIR} REGULAR_EXPRESSION ${DIR}/.*) +endforeach() + +# static library target +if(ENABLE_BUILD_LIB) + add_library(lib STATIC ${GMSH_SRC}) + set_target_properties(lib PROPERTIES OUTPUT_NAME gmsh) + if(MSVC) + set_target_properties(lib PROPERTIES DEBUG_POSTFIX d) + if(ENABLE_MSVC_STATIC_RUNTIME) + set_target_properties(lib PROPERTIES LINK_FLAGS_RELEASE "/nodefaultlib:LIBCMT") + endif() + endif() +endif() + +# shared library target +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + add_library(shared SHARED ${GMSH_SRC}) + set_target_properties(shared PROPERTIES OUTPUT_NAME gmsh + VERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}.${GMSH_PATCH_VERSION} + SOVERSION ${GMSH_MAJOR_VERSION}.${GMSH_MINOR_VERSION}) + if(WIN32) + set_target_properties(shared PROPERTIES PREFIX "" IMPORT_PREFIX "" + IMPORT_SUFFIX ".lib" COMPILE_FLAGS "-DGMSH_DLL -DGMSH_DLL_EXPORT") + endif() + target_link_libraries(shared ${LINK_LIBRARIES}) + # don't define LC_RPATH in dylib for development, to not get endless warnings + # about code signing + if(APPLE AND NOT GMSH_RELEASE) + set_target_properties(shared PROPERTIES INSTALL_RPATH "") + endif() + if(MSVC AND ENABLE_MSVC_STATIC_RUNTIME) + message(STATUS "Note: By enabling ENABLE_MSVC_STATIC_RUNTIME, shared library " + "won't link. In MSVC change /MT to /MD in the shared project properties") + endif() +endif() + +# binary targets +if(HAVE_FLTK) + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh WIN32 Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh WIN32 Common/Main.cpp ${GMSH_SRC}) + endif() + # we could add this to create a minimal app bundle even without install + # if(APPLE AND NOT ENABLE_OS_SPECIFIC_INSTALL) + # set_target_properties(gmsh PROPERTIES MACOSX_BUNDLE ON + # MACOSX_BUNDLE_INFO_PLIST ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_dev.plist) + # endif() +else() + if(ENABLE_BUILD_DYNAMIC) + add_executable(gmsh Common/Main.cpp) + target_link_libraries(gmsh shared) + else() + add_executable(gmsh Common/Main.cpp ${GMSH_SRC}) + endif() +endif() +target_link_libraries(gmsh ${LINK_LIBRARIES}) + +# Windows specific linker options +if(WIN32 AND NOT MSVC) + set(FLAGS "-Wl,--stack,16777216 -static -municode") + if(HAVE_FLTK) + set(FLAGS "${FLAGS} -mwindows") + else() + set(FLAGS "${FLAGS} -mconsole") + endif() + if(HAVE_64BIT_SIZE_T) + set(FLAGS "${FLAGS} \"${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win64Icon.res\"") + else() + set(FLAGS "${FLAGS} \"${CMAKE_CURRENT_SOURCE_DIR}/Fltk/Win32Icon.res\"") + endif() + set_target_properties(gmsh PROPERTIES LINK_FLAGS "${FLAGS}") + if(ENABLE_BUILD_DYNAMIC OR ENABLE_BUILD_SHARED) + set_target_properties(shared PROPERTIES LINK_FLAGS -static) + endif() + # remove -Wl,-Bdynamic flags + set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) + set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS) +elseif(MSVC) + set_target_properties(gmsh PROPERTIES LINK_FLAGS "/STACK:16777216 /SAFESEH:NO") +endif() + +# android target +if(ENABLE_BUILD_ANDROID) + find_file(CMAKE_TOOLCHAIN_FILE "android.toolchain.cmake") + if(NOT CMAKE_TOOLCHAIN_FILE) + message(FATAL_ERROR "Cannot compile Gmsh for android without android-cmake") + endif() + add_definitions(-D_GLIBCXX_USE_C99_MATH=1) + set(CMAKE_BUILD_TYPE Release) + set(LIBRARY_OUTPUT_PATH_ROOT ${CMAKE_CURRENT_BINARY_DIR}) + set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_BINARY_DIR}/libs/) + add_definitions(-DBUILD_ANDROID) + add_definitions(-DPICOJSON_USE_LOCALE=0) + add_library(androidGmsh SHARED ${GMSH_SRC}) + set_target_properties(androidGmsh PROPERTIES OUTPUT_NAME gmsh) + target_link_libraries(androidGmsh ${EXTERNAL_LIBRARIES} ${LAPACK_LIBRARIES}) + add_custom_command(TARGET androidGmsh POST_BUILD COMMAND + ${CMAKE_STRIP} ${LIBRARY_OUTPUT_PATH}/libgmsh.so) +endif() + +# parser target +find_program(BISON bison) +find_program(FLEX flex) +if(BISON AND FLEX) + add_custom_target(parser + COMMAND ${BISON} -p gmsh_yy --output Gmsh.tab.cpp -d Gmsh.y + COMMAND ${FLEX} -P gmsh_yy -o Gmsh.yy.cpp Gmsh.l + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Parser) +endif() + +if(UNIX) + # cannot use cmake's file search functions here (they would only find files + # existing at configuration time) + add_custom_target(purge + COMMAND rm -f `find . -name *~ -o -name *~~` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + add_custom_target(etags + COMMAND etags `find . -name *.cpp -o -name *.h -o -name *.y` + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR + CMAKE_CXX_COMPILER_ID MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion + OUTPUT_VARIABLE CXX_COMPILER_VERSION + OUTPUT_STRIP_TRAILING_WHITESPACE) +else() + set(CXX_COMPILER_VERSION "Unknown") +endif() + +set(WELCOME_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/WELCOME.txt) +set(SDK_FILE ${CMAKE_CURRENT_SOURCE_DIR}/doc/SDK.txt) +set(LICENSE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE.txt) +set(CREDITS_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CREDITS.txt) +set(CHANGELOG_FILE ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.txt) +file(GLOB TUTORIAL_GEO_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/?*.*) +file(GLOB TUTORIAL_CPP_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c++/?*.*) +file(GLOB TUTORIAL_C_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/c/?*.*) +file(GLOB TUTORIAL_PY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/python/?*.*) +file(GLOB TUTORIAL_JL_FILES ${CMAKE_CURRENT_SOURCE_DIR}/tutorial/julia/?*.*) +file(GLOB DEMOS ${CMAKE_CURRENT_SOURCE_DIR}/demos/*) +foreach(SUBDIR ${DEMOS}) + if(IS_DIRECTORY ${SUBDIR}) + list(APPEND DEMOS_DIRS ${SUBDIR}) + endif() +endforeach() +set(TEX_DIR ${CMAKE_CURRENT_SOURCE_DIR}/doc/texinfo) +file(GLOB TEX_SRC ${TEX_DIR}/*.texi) +set(TEX_OBJ ${TEX_DIR}/gmsh.aux ${TEX_DIR}/gmsh.cp ${TEX_DIR}/gmsh.cps + ${TEX_DIR}/gmsh.fn ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.ky + ${TEX_DIR}/gmsh.log ${TEX_DIR}/gmsh.pdf ${TEX_DIR}/gmsh.pg ${TEX_DIR}/gmsh.toc + ${TEX_DIR}/gmsh.tp ${TEX_DIR}/gmsh.tps ${TEX_DIR}/gmsh.txt ${TEX_DIR}/gmsh.vr) + +macro(unix2dos VARNAME) + file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/unix2dos) + set(UNIX2DOS_FILES) + foreach(FILE ${${VARNAME}}) + file(READ ${FILE} F0) + get_filename_component(N ${FILE} NAME) + if(CYGWIN) + string(REGEX REPLACE "\n" "\r\n" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F1}") + else() # if not in Cygwin, cmake adds '\r's automatically + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N} "${F0}") + endif() + list(APPEND UNIX2DOS_FILES ${CMAKE_CURRENT_BINARY_DIR}/unix2dos/${N}) + endforeach() + set(${VARNAME} ${UNIX2DOS_FILES}) +endmacro() + +if(WIN32) + if(ENABLE_OS_SPECIFIC_INSTALL) + set(GMSH_BIN .) + set(GMSH_LIB .) + set(GMSH_DOC .) + set(GMSH_MAN .) + set(GMSH_INC .) + else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) + endif() + if(CYGWIN) + unix2dos(GMSH_API) + if(ENABLE_PRIVATE_API) + unix2dos(GMSH_PRIVATE_API) + endif() + unix2dos(WELCOME_FILE) + unix2dos(SDK_FILE) + unix2dos(LICENSE_FILE) + unix2dos(CREDITS_FILE) + unix2dos(CHANGELOG_FILE) + unix2dos(TUTORIAL_GEO_FILES) + unix2dos(TUTORIAL_CPP_FILES) + unix2dos(TUTORIAL_C_FILES) + unix2dos(TUTORIAL_PY_FILES) + unix2dos(TUTORIAL_JL_FILES) + foreach(DIR ${DEMOS_DIRS}) + file(GLOB DEMO_FILES ${DIR}/?*.*) + unix2dos(DEMO_FILES) + endforeach() + endif() +elseif(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + # set these so that the files get installed nicely in the MacOSX + # .app bundle + set(GMSH_BIN ../MacOS) + set(GMSH_LIB ../MacOS) + set(GMSH_DOC ../../..) + set(GMSH_MAN ../../..) + set(GMSH_INC ../MacOS) +else() + include(GNUInstallDirs) + set(GMSH_BIN ${CMAKE_INSTALL_BINDIR}) + set(GMSH_LIB ${CMAKE_INSTALL_LIBDIR}) + set(GMSH_DOC ${CMAKE_INSTALL_DOCDIR}) + set(GMSH_MAN ${CMAKE_INSTALL_MANDIR}/man1) + set(GMSH_INC ${CMAKE_INSTALL_INCLUDEDIR}) +endif() + +# mark targets as optional so we can install them separately if needed +# (e.g. "make lib" or "make shared" followed by "make install/fast") +install(TARGETS gmsh DESTINATION ${GMSH_BIN} OPTIONAL) +if(ENABLE_BUILD_LIB) + install(TARGETS lib DESTINATION ${GMSH_LIB} OPTIONAL) +endif() +if(ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(TARGETS shared DESTINATION ${GMSH_LIB} OPTIONAL) +endif() + +if(ENABLE_ONELAB) + install(FILES ${ONELAB_PY} DESTINATION ${GMSH_BIN}) +endif() +if(ENABLE_BUILD_LIB OR ENABLE_BUILD_SHARED OR ENABLE_BUILD_DYNAMIC) + install(FILES ${GMSH_API} DESTINATION ${GMSH_INC}) + install(FILES ${GMSH_PY} DESTINATION ${GMSH_LIB}) + install(FILES ${GMSH_JL} DESTINATION ${GMSH_LIB}) + if(ENABLE_PRIVATE_API) + install(FILES ${GMSH_PRIVATE_API} DESTINATION ${GMSH_INC}/gmsh) + endif() +endif() +if(INSTALL_SDK_README) + configure_file(${SDK_FILE} ${CMAKE_CURRENT_BINARY_DIR}/README.txt) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/README.txt DESTINATION .) +endif() +install(FILES ${WELCOME_FILE} DESTINATION ${GMSH_DOC} RENAME README.txt) +install(FILES ${LICENSE_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CREDITS_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${CHANGELOG_FILE} DESTINATION ${GMSH_DOC}) +install(FILES ${TUTORIAL_GEO_FILES} DESTINATION ${GMSH_DOC}/tutorial) +install(FILES ${TUTORIAL_CPP_FILES} DESTINATION ${GMSH_DOC}/tutorial/c++) +install(FILES ${TUTORIAL_C_FILES} DESTINATION ${GMSH_DOC}/tutorial/c) +install(FILES ${TUTORIAL_PY_FILES} DESTINATION ${GMSH_DOC}/tutorial/python) +install(FILES ${TUTORIAL_JL_FILES} DESTINATION ${GMSH_DOC}/tutorial/julia) +foreach(DIR ${DEMOS_DIRS}) + get_filename_component(DEMOS_DIR_NAME ${DIR} NAME) + file(GLOB DEMO_FILES ${DIR}/?*.*) + install(FILES ${DEMO_FILES} DESTINATION ${GMSH_DOC}/demos/${DEMOS_DIR_NAME}) +endforeach() +if(UNIX AND NOT CYGWIN) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/doc/gmsh.1 DESTINATION ${GMSH_MAN}) +endif() + +add_custom_target(get_headers + COMMAND ${CMAKE_COMMAND} -E make_directory Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +foreach(FILE ${GMSH_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endforeach() +if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET get_headers POST_BUILD COMMAND ${CMAKE_COMMAND} + -E copy_if_different ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/Headers/gmsh/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() +endif() + +find_program(MAKEINFO makeinfo) +if(MAKEINFO) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.info DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --split-size 1000000 + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(info DEPENDS ${TEX_DIR}/gmsh.info) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.txt DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --plaintext -o gmsh.txt + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(txt DEPENDS ${TEX_DIR}/gmsh.txt) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.html DEPENDS ${TEX_SRC} + COMMAND ${MAKEINFO} --html --css-ref=/gmsh.css + --no-split --set-customization-variable + EXTRA_HEAD='' + ARGS ${TEX_DIR}/gmsh.texi WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(html DEPENDS ${TEX_DIR}/gmsh.html) + install(FILES ${TEX_DIR}/gmsh.html DESTINATION ${GMSH_DOC} OPTIONAL) +else() + add_custom_target(html COMMAND ${CMAKE_COMMAND} -E touch ${TEX_DIR}/gmsh.html) +endif() + +find_program(TEXI2PDF texi2pdf) +if(TEXI2PDF) + add_custom_command(OUTPUT ${TEX_DIR}/gmsh.pdf DEPENDS ${TEX_SRC} + COMMAND ${TEXI2PDF} ARGS gmsh.texi + WORKING_DIRECTORY ${TEX_DIR}) + add_custom_target(pdf DEPENDS ${TEX_DIR}/gmsh.pdf) + install(FILES ${TEX_DIR}/gmsh.pdf DESTINATION ${GMSH_DOC} OPTIONAL) +endif() + +execute_process(COMMAND ${CMAKE_COMMAND} -E echo + "@c This file was generated by cmake: do not edit manually!\n${OPT_TEXI}" + OUTPUT_FILE cmake_options.texi) + +if(MAKEINFO AND TEXI2PDF) + add_custom_target(doc COMMAND ${CMAKE_COMMAND} -E tar zcf + ${CMAKE_CURRENT_BINARY_DIR}/gmsh-${GMSH_VERSION}-doc.tgz + CREDITS.txt LICENSE.txt CHANGELOG.txt + doc/gmsh.1 doc/texinfo/gmsh.html doc/texinfo/gmsh.info + doc/texinfo/gmsh.pdf doc/texinfo/gmsh.txt + COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ} + DEPENDS ${TEX_DIR}/gmsh.info ${TEX_DIR}/gmsh.txt + ${TEX_DIR}/gmsh.html ${TEX_DIR}/gmsh.pdf + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +endif() + +if(MAKEINFO OR TEXI2PDF) + add_custom_target(clean_doc COMMAND ${CMAKE_COMMAND} -E remove ${TEX_OBJ}) +endif() + +if(APPLE AND ENABLE_BUILD_LIB) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_framework.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info_framework.plist "${F1}") + set(LIBNAME $) + add_custom_target(framework DEPENDS lib + COMMAND ${CMAKE_COMMAND} -E remove_directory gmsh.framework + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Headers + COMMAND ${CMAKE_COMMAND} -E make_directory gmsh.framework/Resources + COMMAND ${CMAKE_COMMAND} -E copy ${LIBNAME} gmsh.framework/gmsh + COMMAND ${CMAKE_COMMAND} -E copy Info_framework.plist + gmsh.framework/Resources/Info.plist + COMMAND ${CMAKE_COMMAND} -E create_symlink . gmsh.framework/Headers/gmsh + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + foreach(FILE ${GMSH_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + if(ENABLE_PRIVATE_API) + foreach(FILE ${GMSH_PRIVATE_API}) + add_custom_command(TARGET framework POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy + ${FILE} ${CMAKE_CURRENT_BINARY_DIR}/gmsh.framework/Headers/ + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) + endforeach() + endif() +endif() + +set(CPACK_PACKAGE_VENDOR "Christophe Geuzaine and Jean-Francois Remacle") +set(CPACK_PACKAGE_VERSION_MAJOR ${GMSH_MAJOR_VERSION}) +set(CPACK_PACKAGE_VERSION_MINOR ${GMSH_MINOR_VERSION}) +set(CPACK_PACKAGE_VERSION_PATCH ${GMSH_PATCH_VERSION}) +set(CPACK_PACKAGE_DESCRIPTION_FILE ${WELCOME_FILE}) +set(CPACK_PACKAGE_DESCRIPTION_SUMMARY + "3D finite element mesh generator with built-in CAD engine and post-processor") +if(GMSH_EXTRA_VERSION MATCHES "-git.*") # so that we'll overwrite the archives + set(CPACK_PACKAGE_FILE_NAME gmsh${GMSH_EXTRA_VERSION_ORIG}-git-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh${GMSH_EXTRA_VERSION_ORIG}-git-source) +else() + set(CPACK_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-${GMSH_OS}) + set(CPACK_SOURCE_PACKAGE_FILE_NAME gmsh-${GMSH_VERSION}-source) +endif() +set(CPACK_PACKAGE_INSTALL_DIRECTORY "gmsh") +set(CPACK_RESOURCE_FILE_LICENSE ${LICENSE_FILE}) +set(CPACK_RESOURCE_FILE_README ${WELCOME_FILE}) +set(CPACK_RESOURCE_FILE_WELCOME ${WELCOME_FILE}) +set(CPACK_PACKAGE_EXECUTABLE "gmsh") +if(ENABLE_PACKAGE_STRIP) + set(CPACK_STRIP_FILES TRUE) +else() + set(CPACK_STRIP_FILES FALSE) +endif() +set(CPACK_SOURCE_GENERATOR TGZ) +set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR}" "/CVS/" "/.svn" "/.git" + "~$" "DS_Store$" "GmshConfig.h$" "GmshVersion.h$" "/benchmarks/" "/tmp/" + "/bin/" "/lib/" "/nightly/" "GPATH" "GRTAGS" "GSYMS" "GTAGS" "/HTML/" + "/contrib/3M/" "/contrib/Parasolid/") + +if(UNIX) + # make sure we remove previous installs before doing the next one (on Mac for + # example "make package; make package_source" would lead to huge file lists + # getting generated due to the 'Applications' symlink in the bundle) + set(CPACK_INSTALL_COMMANDS "rm -rf ${CMAKE_CURRENT_BINARY_DIR}/_CPack_Packages") +endif() + +if(APPLE AND ENABLE_OS_SPECIFIC_INSTALL) + set(CPACK_GENERATOR Bundle) + set(CPACK_BUNDLE_NAME Gmsh) + file(READ ${CMAKE_CURRENT_SOURCE_DIR}/utils/misc/gmsh_app.plist F0) + string(REPLACE GMSH_VERSION "${GMSH_VERSION}" F1 "${F0}") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/Info.plist "${F1}") + set(CPACK_BUNDLE_PLIST ${CMAKE_CURRENT_BINARY_DIR}/Info.plist) + set(CPACK_BUNDLE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) + if(PACKAGER STREQUAL "geuzaine - removed: we sign on a separate machine") + # codesigning requires CMake >= 3.2 + set(CPACK_BUNDLE_APPLE_CERT_APP "Developer ID Application: Christophe Geuzaine") + endif() + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsGeo.icns DESTINATION . + RENAME GmshGeo.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsMsh.icns DESTINATION . + RENAME GmshMsh.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsSol.icns DESTINATION . + RENAME GmshSol.icns) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIconsPos.icns DESTINATION . + RENAME GmshPos.icns) + set(CPACK_PACKAGE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/Fltk/MacIcons.icns) +elseif(WIN32) + set(CPACK_GENERATOR ZIP) +else() + set(CPACK_GENERATOR TGZ) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/gmshpy AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_PYTHON AND HAVE_PYTHON) + add_subdirectory(utils/wrappers/gmshpy) +endif() + +if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/utils/wrappers/java AND + ENABLE_PRIVATE_API AND ENABLE_WRAP_JAVA) + add_subdirectory(utils/wrappers/java) +endif() + +include(CPack) + +macro(filter_tests IN OUT) + unset(${OUT}) + foreach(FILE ${IN}) + unset(BAD1) + unset(BAD2) + unset(BAD3) + # OS-specific + if(${GMSH_OS} MATCHES "Linux32") + # OCC STL generation crashes on our Linux32 docker + string(REGEX MATCH "t18" BAD1 ${FILE}) + endif() + # OpenCASCADE + if(NOT HAVE_OCC AND NOT BAD1 AND NOT BAD2 AND NOT BAD3) + file(STRINGS ${FILE} BAD1 REGEX "^SetFactory.*OpenCASCADE.*") + file(STRINGS ${FILE} BAD2 REGEX ".*occ\\.synchronize.*") + file(STRINGS ${FILE} BAD3 REGEX ".*occ::synchronize.*") + endif() + # Metis + if(NOT HAVE_METIS AND NOT BAD1 AND NOT BAD2 AND NOT BAD3) + file(STRINGS ${FILE} BAD1 REGEX ".*PartitionMesh.*") + file(STRINGS ${FILE} BAD2 REGEX ".*mesh\\.partition.*") + file(STRINGS ${FILE} BAD3 REGEX ".*mesh::partition.*") + endif() + if(BAD1 OR BAD2 OR BAD3) + message("Skipping test " ${FILE}) + else() + list(APPEND ${OUT} ${FILE}) + endif() + endforeach() +endmacro() + +if(NOT DISABLE_GMSH_TESTS) + # disabling tests is useful when including this CMakeLists in an external project + include(CTest) + file(GLOB_RECURSE ALLFILES + tutorial/*.geo demos/*.geo benchmarks/?d/*.geo benchmarks/extrude/*.geo + benchmarks/occ/*.geo) + filter_tests("${ALLFILES}" TESTFILES) + foreach(TESTFILE ${TESTFILES}) + # use relative path for Cygwin/MinGW (the pure win exe built with the MinGW + # compilers does not understand a full Cygwin-style path) + FILE(RELATIVE_PATH TEST ${CMAKE_CURRENT_BINARY_DIR} ${TESTFILE}) + add_test(${TEST} ./gmsh ${TEST} -3 -nopopup -o ./tmp.msh) + endforeach() + # test c++ api tutorials with dynamic builds (except on 32 bit windows for + # now: our win32 setup does not currently handle exceptions) + if(ENABLE_BUILD_DYNAMIC AND NOT ${GMSH_OS} MATCHES "Windows32") + file(GLOB_RECURSE ALLFILES tutorial/c++/*.cpp) + filter_tests("${ALLFILES}" TESTFILES) + foreach(TESTFILE ${TESTFILES}) + get_filename_component(TEST ${TESTFILE} NAME_WE) + add_executable(${TEST} WIN32 ${TESTFILE}) + target_link_libraries(${TEST} shared) + if(WIN32 AND NOT MSVC) + set(FLAGS "-static") + if(HAVE_FLTK) + set(FLAGS "${FLAGS} -mwindows") + else() + set(FLAGS "${FLAGS} -mconsole") + endif() + set_target_properties(${TEST} PROPERTIES LINK_FLAGS "${FLAGS}") + endif() + add_test(${TEST}_cpp ${TEST} -nopopup) + endforeach() + endif() + # enable this once we have worked out the path issues on the build machines + if(0 AND ENABLE_BUILD_DYNAMIC) + find_package(PythonInterp) + if(PYTHONINTERP_FOUND) + file(GLOB_RECURSE ALLFILES tutorial/python/*.py demos/api/*.py) + filter_tests("${ALLFILES}" TESTFILES) + foreach(TESTFILE ${TESTFILES}) + get_filename_component(TEST ${TESTFILE} NAME_WE) + add_test(NAME ${TEST}_py COMMAND ${PYTHON_EXECUTABLE} ${TESTFILE} -nopopup) + set_property(TEST ${TEST}_py APPEND PROPERTY ENVIRONMENT + "PYTHONPATH=${CMAKE_SOURCE_DIR}/api") + set_property(TEST ${TEST}_py APPEND PROPERTY ENVIRONMENT + "LD_LIBRARY_PATH=${CMAKE_CURRENT_BINARY_DIR}") + endforeach() + endif() + endif() +endif() + +message(STATUS "") +message(STATUS "Gmsh ${GMSH_VERSION} has been configured for ${GMSH_OS}") +message(STATUS "") +message(STATUS " * Build options:" ${GMSH_CONFIG_OPTIONS}) +message(STATUS " * Build type: " ${CMAKE_BUILD_TYPE}) +message(STATUS " * C compiler: " ${CMAKE_C_COMPILER}) +message(STATUS " * C++ compiler: " ${CMAKE_CXX_COMPILER}) +message(STATUS " * Install prefix: " ${CMAKE_INSTALL_PREFIX}) +message(STATUS "") + +mark_as_advanced(ANN_INC ANN_LIB CAIRO_LIB CAIRO_INC CGNS_INC GMM_INC + GMP_INC GMP_LIB MMG_INC MMG_LIB HDF5_LIB + MED_LIB OCC_INC SZ_LIB + PETSC_LIBS SLEPC_INC SLEPC_INC2 SLEPC_LIB + BISON FLEX MAKEINFO TEXI2PDF FLTK_CONFIG_SCRIPT + GMSH_EXTERNAL_INCLUDE_DIRS GMSH_EXTERNAL_LIBRARIES) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-3.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-3.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-3.sh (revision 27955) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.0.5" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Configure +cd install +cmake ../src \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_MPI=1 \ + -DENABLE_BUILD_DYNAMIC=1 \ + -DENABLE_BUILD_SHARED=1 + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Make necessary link on RHEL +if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then + cd ${PREFIX} + ln -s ./lib64 ./lib +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-linux-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-linux-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-linux-static.sh (revision 27955) @@ -0,0 +1,88 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Add support for, +# - MUMPS +# - PETSc +# +# See Also: +# - configs/4/static/CMakeLists.txt +# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code +# + +## Constants +# +VER="4.10.5" + +PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed + +# Find libgfortran and libgcc so we do not have to hardcode them +# +# TODO: +# - Move this to etc/environment.sh +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1) + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Unpack source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Apply patches +patch src/CMakeLists.txt < configs/${VER}/static/CMakeLists.txt.patch + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we +# do not need to support Apple Touch bar (does not affect compilation on +# Linux). +# +cd src +cmake \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release \ + -DENABLE_BUILD_LIB=1 \ + -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \ + -DENABLE_BLAS_LAPACK=1 \ + -DENABLE_EIGEN=0 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DENABLE_TOUCHBAR=0 \ + -DMETIS_ROOT="${METIS_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Make necessary link on RHEL +if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then + cd ${PREFIX} + ln -s ./lib64 ./lib +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-linux.sh (revision 27955) @@ -0,0 +1,86 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Add support for, +# - MUMPS +# - PETSc +# +# See Also: +# - configs/4/static/CMakeLists.txt +# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code +# + +## Constants +# +VER="4.10.5" + +PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed + +# Find libgfortran so that we do not have to hardcode it. +# +# TODO: +# - Move this to etc/environment.sh +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Unpack source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we +# do not need to support Apple Touch bar (does not affect compilation on +# Linux). +# +cd src +cmake \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_INSTALL_RPATH="${PREFIX}/lib" \ + -DCMAKE_BUILD_TYPE=Release \ + -DENABLE_BUILD_DYNAMIC=1 \ + -DENABLE_BUILD_SHARED=1 \ + -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" \ + -DENABLE_BLAS_LAPACK=1 \ + -DENABLE_EIGEN=0 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DENABLE_TOUCHBAR=0 \ + -DMETIS_ROOT="${METIS_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Make necessary link on RHEL +if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then + cd ${PREFIX} + ln -s ./lib64 ./lib +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-mac-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-mac-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-mac-static.sh (revision 27955) @@ -0,0 +1,85 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Add support for, +# - MUMPS +# - PETSc +# +# See Also: +# - configs/4/static/CMakeLists.txt +# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code +# + +## Constants +# +VER="4.10.5" + +PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed + +# Find libgfortran and libgcc so we do not have to hardcode them +# +# TODO: +# - Move this to etc/environment.sh +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Unpack source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Apply patches +patch src/CMakeLists.txt < configs/${VER}/static/CMakeLists.txt.patch +patch src/CMakeLists.txt < configs/${VER}/static/mac/CMakeLists.txt.patch + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we +# do not need to support Apple Touch bar (does not affect compilation on +# Linux). +# +cd src +cmake \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release \ + -DENABLE_BUILD_LIB=1 \ + -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \ + -DENABLE_BLAS_LAPACK=1 \ + -DENABLE_EIGEN=0 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DENABLE_TOUCHBAR=0 \ + -DMETIS_ROOT="${METIS_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-mac.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-mac.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmsh/install-4-mac.sh (revision 27955) @@ -0,0 +1,85 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Add support for, +# - MUMPS +# - PETSc +# +# See Also: +# - configs/4/static/CMakeLists.txt +# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code +# + +## Constants +# +VER="4.10.5" + +PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed + +# Find libgfortran so that we do not have to hardcode it. +# +# TODO: +# - Move this to etc/environment.sh +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Unpack source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Apply patches +patch src/CMakeLists.txt < configs/${VER}/mac/CMakeLists.txt.patch + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we +# do not need to support Apple Touch bar (does not affect compilation on +# Linux). +# +cd src +cmake \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_MACOSX_RPATH=ON \ + -DCMAKE_INSTALL_RPATH="${PREFIX}/lib" \ + -DCMAKE_BUILD_TYPE=Release \ + -DENABLE_BUILD_DYNAMIC=1 \ + -DENABLE_BUILD_SHARED=1 \ + -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" \ + -DLIBGFORTRAN_ROOT="${LIBGFORTRAN_ROOT}" \ + -DENABLE_BLAS_LAPACK=1 \ + -DENABLE_EIGEN=0 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DENABLE_TOUCHBAR=0 \ + -DMETIS_ROOT="${METIS_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/linux/cmake/ConfigUser.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/linux/cmake/ConfigUser.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/linux/cmake/ConfigUser.cmake (revision 27955) @@ -0,0 +1,308 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License +# for more details. +# +# Contact info: www.generic-mapping-tools.org +# ---------------------------------------------------------------------------- + +# Use this file to override variables in 'ConfigDefault.cmake' on a per-user +# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then +# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled +# (currently listed in .gitignore). +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## Section 1: Installation paths +## + +# ============================================================================ +# Basic setup begins here. All settings are optional. In most cases, setting +# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with +# reasonable defaults enabled. Note: If you need to specify directory names +# with spaces (e.g., on Windows) then you must put them in quotes. +# ============================================================================ + +# Installation path (usually defaults to /usr/local) [auto]: +set (CMAKE_INSTALL_PREFIX "$ENV{PREFIX}") + +# Set install name suffix used for directories and gmt executables +# [undefined]: +#set (GMT_INSTALL_NAME_SUFFIX "suffix") + +# Install into traditional directory structure. Disable to install a +# distribution type directory structure (doc and share separated) [on]: +#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) + +# Install convenience links for GMT modules. Disable to install only the main +# gmt program and access modules as "gmt modulename options" [TRUE]: +#set (GMT_INSTALL_MODULE_LINKS FALSE) + +# Make executables relocatable on supported platforms (relative RPATH) [FALSE]: +set (GMT_INSTALL_RELOCATABLE TRUE) + +# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE] +#set (GMT_EXCLUDE_GDAL TRUE) +#set (GMT_EXCLUDE_PCRE TRUE) +#set (GMT_EXCLUDE_PCRE2 TRUE) +#set (GMT_EXCLUDE_FFTW3 TRUE) +#set (GMT_EXCLUDE_LAPACK TRUE) +#set (GMT_EXCLUDE_BLAS TRUE) +#set (GMT_EXCLUDE_ZLIB TRUE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set URL to GMT Data server [auto]: +#set (GMT_DATA_SERVER "data_server_url") + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{GSHHG_ROOT}") + +# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]: +#set (COPY_GSHHG TRUE) + +# Set path to DCW Digital Chart of the World for GMT [auto]: +#set (DCW_ROOT "dcw-gmt_path") + +# Copy DCW files to ${GMT_DATADIR}/dcw [FALSE]: +#set (COPY_DCW TRUE) + +# Copy GDAL's 'data' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (GDAL_DATA_PATH C:/programs/compa_libs/gdal_GIT/compileds/VC14_64/data) + +# Copy PROJ4's 'share' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (PROJ_DATA_PATH C:/programs/compa_libs/proj5_GIT/compileds/VC14_64/share/proj) + +# FOR WINDOWS ONLY +# Set path to location of Ghostscript binaries (optional install) +#set (GHOST_DATA_PATH C:/programs/compa_libs/ghostscript/bin) + +# FOR WINDOWS ONLY +# Set path to location where the gmtmex is located. +#set (GMTMEX_PATH "C:/progs_cygw/GMTdev/gmtmex/${GMTver}") + +# Set location of NetCDF (can be root directory, path to header file or path +# to nc-config) [auto]: +set (NETCDF_ROOT "$ENV{NETCDF_ROOT}") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{GDAL_ROOT}") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") +# Alternatively, set location of PCRE2 (can be root directory, path to header file or path to +# pcre2-config) [auto]: +#set (PCRE2_ROOT "pcre2_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +set (ZLIB_ROOT "$ENV{ZLIB_ROOT}") + +# Set location of CURL (can be root directory or path to header file) [auto]: +#set (CURL_ROOT "curl_install_prefix") + +# Set location of GLIB component gthread [auto]. This is an optional (and +# experimental) option which you need to enable: +#set (GMT_USE_THREADS TRUE) +# If pkg-config is not installed (e.g. on Windows) you need to specify these: +#set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0) +#set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib) + +# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically +set (LAPACK_LIBRARY "-L$ENV{LAPACK_ROOT} -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran") +set (BLAS_LIBRARY "-L$ENV{BLAS_ROOT} -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Allow building of OpenMP if compiler supports it +# set (GMT_ENABLE_OPENMP TRUE) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# Enable building of shared libraries [TRUE] (disable to use static libraries; +# not recommended; on non-x86 architectures uncomment the next option as well): +#set (BUILD_SHARED_LIBS FALSE) + +# Create position independent code on all targets [auto] (needed for static +# build on non-x86): +#set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) + +# Build GMT shared lib with supplemental modules [TRUE]: +#set (BUILD_SUPPLEMENTS FALSE) + +# Build/Install GMT Developer include files [TRUE]: +# This installs the extra include files and configured files needed by 3rd-party +# developers. Until we build a separate gmt-devel we include them in the main +# Distribution. +#set (BUILD_DEVELOPER FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#set (DO_EXAMPLES TRUE) +#set (DO_TESTS TRUE) +#set (DO_ANIMATIONS TRUE) +# Number of parallel test jobs with "make check": +#set (N_TEST_JOBS 4) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmt-custom project). +#set (EXTRA_BUILD_DIRS apidemo) +# Uncomment the following line to enable running low-level C tests of the API +#set (DO_API_TESTS ON) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel +# [Release]: +#set (CMAKE_BUILD_TYPE Debug) + +# Extra debugging for developers: +#if ( CMAKE_GENERATOR STREQUAL "Xcode" ) +## So Xcode can find the supplemental plug-ins during debug sessions +# add_definitions(-DXCODER) +# add_definitions(-DDEBUG_MODERN) # To set PPID == 0 during Xcode test +# message("Add Xcode definition for GMT") +#endif() +#add_definitions(-DDEBUG) +#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info +#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies +if (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions") # check uninitialized variables +else (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +endif (HAVE_OPENMP) + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +#set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +# WARNING: if using this option it is mandatory that the suffix starts with an underscore. +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/mac/cmake/ConfigUser.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/mac/cmake/ConfigUser.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/mac/cmake/ConfigUser.cmake (revision 27955) @@ -0,0 +1,308 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License +# for more details. +# +# Contact info: www.generic-mapping-tools.org +# ---------------------------------------------------------------------------- + +# Use this file to override variables in 'ConfigDefault.cmake' on a per-user +# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then +# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled +# (currently listed in .gitignore). +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## Section 1: Installation paths +## + +# ============================================================================ +# Basic setup begins here. All settings are optional. In most cases, setting +# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with +# reasonable defaults enabled. Note: If you need to specify directory names +# with spaces (e.g., on Windows) then you must put them in quotes. +# ============================================================================ + +# Installation path (usually defaults to /usr/local) [auto]: +set (CMAKE_INSTALL_PREFIX "$ENV{PREFIX}") + +# Set install name suffix used for directories and gmt executables +# [undefined]: +#set (GMT_INSTALL_NAME_SUFFIX "suffix") + +# Install into traditional directory structure. Disable to install a +# distribution type directory structure (doc and share separated) [on]: +#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) + +# Install convenience links for GMT modules. Disable to install only the main +# gmt program and access modules as "gmt modulename options" [TRUE]: +#set (GMT_INSTALL_MODULE_LINKS FALSE) + +# Make executables relocatable on supported platforms (relative RPATH) [FALSE]: +set (GMT_INSTALL_RELOCATABLE TRUE) + +# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE] +#set (GMT_EXCLUDE_GDAL TRUE) +#set (GMT_EXCLUDE_PCRE TRUE) +#set (GMT_EXCLUDE_PCRE2 TRUE) +#set (GMT_EXCLUDE_FFTW3 TRUE) +#set (GMT_EXCLUDE_LAPACK TRUE) +#set (GMT_EXCLUDE_BLAS TRUE) +#set (GMT_EXCLUDE_ZLIB TRUE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set URL to GMT Data server [auto]: +#set (GMT_DATA_SERVER "data_server_url") + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{GSHHG_ROOT}") + +# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]: +#set (COPY_GSHHG TRUE) + +# Set path to DCW Digital Chart of the World for GMT [auto]: +#set (DCW_ROOT "dcw-gmt_path") + +# Copy DCW files to ${GMT_DATADIR}/dcw [FALSE]: +#set (COPY_DCW TRUE) + +# Copy GDAL's 'data' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (GDAL_DATA_PATH C:/programs/compa_libs/gdal_GIT/compileds/VC14_64/data) + +# Copy PROJ4's 'share' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (PROJ_DATA_PATH C:/programs/compa_libs/proj5_GIT/compileds/VC14_64/share/proj) + +# FOR WINDOWS ONLY +# Set path to location of Ghostscript binaries (optional install) +#set (GHOST_DATA_PATH C:/programs/compa_libs/ghostscript/bin) + +# FOR WINDOWS ONLY +# Set path to location where the gmtmex is located. +#set (GMTMEX_PATH "C:/progs_cygw/GMTdev/gmtmex/${GMTver}") + +# Set location of NetCDF (can be root directory, path to header file or path +# to nc-config) [auto]: +set (NETCDF_ROOT "$ENV{NETCDF_ROOT}") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{GDAL_ROOT}") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") +# Alternatively, set location of PCRE2 (can be root directory, path to header file or path to +# pcre2-config) [auto]: +#set (PCRE2_ROOT "pcre2_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +set (ZLIB_ROOT "$ENV{ZLIB_ROOT}") + +# Set location of CURL (can be root directory or path to header file) [auto]: +#set (CURL_ROOT "curl_install_prefix") + +# Set location of GLIB component gthread [auto]. This is an optional (and +# experimental) option which you need to enable: +#set (GMT_USE_THREADS TRUE) +# If pkg-config is not installed (e.g. on Windows) you need to specify these: +#set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0) +#set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib) + +# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically +set (LAPACK_LIBRARY "-L$ENV{LAPACK_ROOT} -lflapack") +set (BLAS_LIBRARY "-L$ENV{BLAS_ROOT} -lfblas") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Allow building of OpenMP if compiler supports it +# set (GMT_ENABLE_OPENMP TRUE) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# Enable building of shared libraries [TRUE] (disable to use static libraries; +# not recommended; on non-x86 architectures uncomment the next option as well): +#set (BUILD_SHARED_LIBS FALSE) + +# Create position independent code on all targets [auto] (needed for static +# build on non-x86): +#set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) + +# Build GMT shared lib with supplemental modules [TRUE]: +#set (BUILD_SUPPLEMENTS FALSE) + +# Build/Install GMT Developer include files [TRUE]: +# This installs the extra include files and configured files needed by 3rd-party +# developers. Until we build a separate gmt-devel we include them in the main +# Distribution. +#set (BUILD_DEVELOPER FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#set (DO_EXAMPLES TRUE) +#set (DO_TESTS TRUE) +#set (DO_ANIMATIONS TRUE) +# Number of parallel test jobs with "make check": +#set (N_TEST_JOBS 4) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmt-custom project). +#set (EXTRA_BUILD_DIRS apidemo) +# Uncomment the following line to enable running low-level C tests of the API +#set (DO_API_TESTS ON) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel +# [Release]: +#set (CMAKE_BUILD_TYPE Debug) + +# Extra debugging for developers: +#if ( CMAKE_GENERATOR STREQUAL "Xcode" ) +## So Xcode can find the supplemental plug-ins during debug sessions +# add_definitions(-DXCODER) +# add_definitions(-DDEBUG_MODERN) # To set PPID == 0 during Xcode test +# message("Add Xcode definition for GMT") +#endif() +#add_definitions(-DDEBUG) +#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info +#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies +if (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions") # check uninitialized variables +else (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +endif (HAVE_OPENMP) + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +#set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +# WARNING: if using this option it is mandatory that the suffix starts with an underscore. +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/mac/cmake/modules/ConfigCMake.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/mac/cmake/modules/ConfigCMake.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/mac/cmake/modules/ConfigCMake.cmake (revision 27955) @@ -0,0 +1,250 @@ +# +# +# Useful CMake variables. +# +# There are five configuration files: +# +# 1) "ConfigDefault.cmake" - is version controlled and used to add new default +# variables and set defaults for everyone. +# 2) "ConfigUser.cmake" in the source tree - is not version controlled +# (currently listed in .gitignore) and used to override basic default settings on +# a per-user basis. +# 3) "ConfigUser.cmake" in the build tree - is used to override +# "ConfigUser.cmake" in the source tree. +# 4) "ConfigUserAdvanced.cmake" in the source tree - is not version controlled +# (currently listed in .gitignore) and used to override advanced default settings on +# a per-user basis. +# 5) "ConfigUserAdvanced.cmake" in the build tree - is used to override +# "ConfigUserAdvanced.cmake" in the source tree. +# +# NOTE: If you want to change CMake behaviour just for yourself, +# copy "ConfigUserTemplate.cmake" to "ConfigUser.cmake" and then edit +# "ConfigUser.cmake" for basic settings. For advanced settings, +# copy "ConfigUserAdvancedTemplate.cmake" to "ConfigUserAdvanced.cmake" and edit it. +# DO NOT EDIT "ConfigDefault.cmake" or the CMake template files. +# +include ("${CMAKE_SOURCE_DIR}/cmake/ConfigDefault.cmake") + +# A "ConfigUser.cmake" in the source tree overrides the advanced defaults. +if (EXISTS "${CMAKE_SOURCE_DIR}/cmake/ConfigUser.cmake") + include ("${CMAKE_SOURCE_DIR}/cmake/ConfigUser.cmake") +endif (EXISTS "${CMAKE_SOURCE_DIR}/cmake/ConfigUser.cmake") + +# If you've got a 'ConfigUser.cmake' in the build tree then that overrides the +# one in the source tree. +if (EXISTS "${CMAKE_BINARY_DIR}/cmake/ConfigUser.cmake") + include ("${CMAKE_BINARY_DIR}/cmake/ConfigUser.cmake") +endif (EXISTS "${CMAKE_BINARY_DIR}/cmake/ConfigUser.cmake") + +# A "ConfigUserAdvanced.cmake" in the source tree overrides the advanced defaults. +if (EXISTS "${CMAKE_SOURCE_DIR}/cmake/ConfigUserAdvanced.cmake") + include ("${CMAKE_SOURCE_DIR}/cmake/ConfigUserAdvanced.cmake") +endif (EXISTS "${CMAKE_SOURCE_DIR}/cmake/ConfigUserAdvanced.cmake") + +# If you've got a 'ConfigUserAdvanced.cmake' in the build tree then that overrides the +# one in the source tree. +if (EXISTS "${CMAKE_BINARY_DIR}/cmake/ConfigUserAdvanced.cmake") + include ("${CMAKE_BINARY_DIR}/cmake/ConfigUserAdvanced.cmake") +endif (EXISTS "${CMAKE_BINARY_DIR}/cmake/ConfigUserAdvanced.cmake") + +########################################################### +# Do any needed processing of the configuration variables # +########################################################### + +# Set default build type to 'Release' +if (NOT CMAKE_BUILD_TYPE) + set (CMAKE_BUILD_TYPE Release) +endif (NOT CMAKE_BUILD_TYPE) + +# Here we change it to add the git commit hash for non-public releases +set (GMT_PACKAGE_VERSION_WITH_GIT_REVISION ${GMT_PACKAGE_VERSION}) + +# Check if it's a git repository or not +if (EXISTS ${GMT_SOURCE_DIR}/.git) + set (HAVE_GIT_VERSION TRUE) +endif (EXISTS ${GMT_SOURCE_DIR}/.git) + +# Add the last git commit hash and date to the package version if this is a non-public release. +# A non-public release has a FALSE 'GMT_PUBLIC_RELEASE' variable in 'ConfigDefault.cmake'. +if (GIT_FOUND AND HAVE_GIT_VERSION AND NOT GMT_PUBLIC_RELEASE) + # Get the last git commit hash + execute_process ( + COMMAND ${GIT_EXECUTABLE} describe --abbrev=7 --always --dirty + WORKING_DIRECTORY ${GMT_SOURCE_DIR} + RESULT_VARIABLE GIT_RETURN_CODE + OUTPUT_VARIABLE GIT_COMMIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE) + + if (GIT_RETURN_CODE) + message (STATUS "Unable to determine git commit hash for non-public release - ignoring.") + else (GIT_RETURN_CODE) + if (GIT_COMMIT_HASH) + # For non-public release, add the last git commit hash and date + execute_process ( + COMMAND ${GIT_EXECUTABLE} log -1 --date=short --pretty=format:%cd + WORKING_DIRECTORY ${GMT_SOURCE_DIR} + RESULT_VARIABLE GIT_DATE_RETURN_CODE + OUTPUT_VARIABLE GIT_COMMIT_DATE + OUTPUT_STRIP_TRAILING_WHITESPACE) + string(REPLACE "-" "." GIT_COMMIT_DATE "${GIT_COMMIT_DATE}") + set (GMT_PACKAGE_VERSION_WITH_GIT_REVISION "${GMT_PACKAGE_VERSION}_${GIT_COMMIT_HASH}_${GIT_COMMIT_DATE}") + endif (GIT_COMMIT_HASH) + endif (GIT_RETURN_CODE) +endif (GIT_FOUND AND HAVE_GIT_VERSION AND NOT GMT_PUBLIC_RELEASE) + +# apply license restrictions +if (LICENSE_RESTRICTED) # on + if (LICENSE_RESTRICTED STREQUAL GPL) + # restrict to GPL + elseif (LICENSE_RESTRICTED STREQUAL LGPL) + # restrict to LGPL + else (LICENSE_RESTRICTED STREQUAL GPL) + # unknown license + message (WARNING "unknown license: ${LICENSE_RESTRICTED}") + endif (LICENSE_RESTRICTED STREQUAL GPL) + # restrictions that apply to any of the above licenses +else (LICENSE_RESTRICTED) # off + # no restrictions at all +endif (LICENSE_RESTRICTED) + +# reset list of extra license files +set (GMT_EXTRA_LICENSE_FILES) + +# location of GNU license files +set (COPYING_GPL ${GMT_SOURCE_DIR}/COPYINGv3) +set (COPYING_LGPL ${GMT_SOURCE_DIR}/COPYING.LESSERv3) + +# GMT paths used in the code +if (NOT GMT_DATADIR) + # do not reset user setting + if (GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_DATADIR "share") + else(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_DATADIR "share/gmt${GMT_INSTALL_NAME_SUFFIX}") + endif(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) +endif (NOT GMT_DATADIR) + +# Install path GMT_DOCDIR +if (NOT GMT_DOCDIR) + # do not reset user setting + if (GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_DOCDIR "${GMT_DATADIR}/doc") + else(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_DOCDIR "share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}") + endif(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) +endif (NOT GMT_DOCDIR) + +# Install path GMT_MANDIR +if (NOT GMT_MANDIR) + # do not reset user setting + if (GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_MANDIR "${GMT_DATADIR}/man") + else(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) + set (GMT_MANDIR "${GMT_DOCDIR}/man") + endif(GMT_INSTALL_TRADITIONAL_FOLDERNAMES) +endif (NOT GMT_MANDIR) + +# Install path for GMT binaries, headers and libraries +include (GNUInstallDirs) # defines CMAKE_INSTALL_LIBDIR (lib/lib64) +if (NOT GMT_LIBDIR) + set (GMT_LIBDIR ${CMAKE_INSTALL_LIBDIR}) +endif(NOT GMT_LIBDIR) + +if (NOT GMT_BINDIR) + set (GMT_BINDIR bin) +endif(NOT GMT_BINDIR) + +if (NOT GMT_INCLUDEDIR) + set (GMT_INCLUDEDIR include/gmt${GMT_INSTALL_NAME_SUFFIX}) +endif(NOT GMT_INCLUDEDIR) + +if (GMT_DATA_URL) # Backwards compatibility with old ConfigUser.cmake files + message (WARNING "CMake variable GMT_DATA_URL is deprecated and will be removed in the future releases. Use GMT_DATA_SERVER instead.") + set (GMT_DATA_SERVER ${GMT_DATA_URL}) +endif (GMT_DATA_URL) + +# use, i.e. don't skip the full RPATH for the build tree +set (CMAKE_SKIP_BUILD_RPATH FALSE) + +# when building, don't use the install RPATH already +# (but later on when installing) +set (CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + +# set the RPATH to be used when installing +if (NOT DEFINED GMT_INSTALL_RELOCATABLE) + set (GMT_INSTALL_RELOCATABLE FALSE) +endif (NOT DEFINED GMT_INSTALL_RELOCATABLE) +if (GMT_INSTALL_RELOCATABLE) + # make executables relocatable on supported platforms (relative RPATH) + if (UNIX AND NOT CYGWIN) + # find relative libdir from executable dir + file (RELATIVE_PATH _rpath /${GMT_BINDIR} /${GMT_LIBDIR}) + # remove trailing / + string (REGEX REPLACE "/$" "" _rpath "${_rpath}") + if (APPLE) + # relative RPATH on osx + # CMP0042: CMake 3.0: MACOSX_RPATH is enabled by default + set (CMAKE_MACOSX_RPATH ON) + set (CMAKE_INSTALL_NAME_DIR @rpath) + set (CMAKE_INSTALL_RPATH "@rpath;@executable_path/${_rpath};${LIBGFORTRAN_ROOT}") + else (APPLE) + # relative RPATH on Linux, Solaris, etc. + set (CMAKE_INSTALL_RPATH "\$ORIGIN/${_rpath}") + endif (APPLE) + endif (UNIX AND NOT CYGWIN) +else (GMT_INSTALL_RELOCATABLE) + # set absolute RPATH + if (APPLE) + # CMP0042: CMake 3.0: MACOSX_RPATH is enabled by default + set (CMAKE_MACOSX_RPATH OFF) + set (CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${GMT_LIBDIR}") + else (APPLE) + # the RPATH to be used when installing, but only if it's not a + # system directory + list (FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES + "${CMAKE_INSTALL_PREFIX}/${GMT_LIBDIR}" isSystemDir) + if ("${isSystemDir}" STREQUAL "-1") + set (CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${GMT_LIBDIR}") + endif ("${isSystemDir}" STREQUAL "-1") + endif (APPLE) +endif (GMT_INSTALL_RELOCATABLE) + +# add the automatically determined parts of the RPATH +# which point to directories outside the build tree to the install RPATH +set (CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + +# When running examples/tests with CTest (out-of-source) we need support for +# running GMT programs from within ${GMT_BINARY_DIR}: +if (DO_EXAMPLES OR DO_TESTS AND NOT SUPPORT_EXEC_IN_BINARY_DIR) + message (WARNING "Enabling SUPPORT_EXEC_IN_BINARY_DIR (required for " + "testing). Please disable testing on release builds.") + set (SUPPORT_EXEC_IN_BINARY_DIR ON) +endif (DO_EXAMPLES OR DO_TESTS AND NOT SUPPORT_EXEC_IN_BINARY_DIR) + +# Some tests are known to fail, and can be excluded from the test by adding +# the comment "# GMT_KNOWN_FAILURE". +if (NOT DEFINED GMT_ENABLE_KNOWN2FAIL) + set (GMT_ENABLE_KNOWN2FAIL ON) +endif (NOT DEFINED GMT_ENABLE_KNOWN2FAIL) + +# Make GNU, Intel, Clang and AppleClang compilers default to C99 +if (CMAKE_C_COMPILER_ID MATCHES "(GNU|Intel|Clang)" AND NOT CMAKE_C_FLAGS MATCHES "-std=") + set (CMAKE_C_FLAGS "-std=gnu99 ${CMAKE_C_FLAGS}") +endif () + +# Suppress MSVC deprecation and security warnings +if (MSVC) + set (CMAKE_C_FLAGS "/D_CRT_SECURE_NO_WARNINGS /D_CRT_SECURE_NO_DEPRECATE ${CMAKE_C_FLAGS}") + set (CMAKE_C_FLAGS "/D_CRT_NONSTDC_NO_DEPRECATE /D_SCL_SECURE_NO_DEPRECATE ${CMAKE_C_FLAGS}") +endif (MSVC) + +# Handle the special developer option GMT_DOCS_DEPEND_ON_GMT +# Normally this is ON. +if (NOT DEFINED GMT_DOCS_DEPEND_ON_GMT) + set (GMT_DOCS_DEPEND_ON_GMT TRUE) +endif (NOT DEFINED GMT_DOCS_DEPEND_ON_GMT) +if (GMT_DOCS_DEPEND_ON_GMT) + add_custom_target (gmt_for_img_convert DEPENDS gmt) +else (GMT_DOCS_DEPEND_ON_GMT) + add_custom_target (gmt_for_img_convert) +endif (GMT_DOCS_DEPEND_ON_GMT) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake (revision 27955) @@ -0,0 +1,189 @@ +# +# +# Locate gdal +# +# This module accepts the following environment variables: +# +# GDAL_DIR or GDAL_ROOT - Specify the location of GDAL +# +# This module defines the following CMake variables: +# +# GDAL_FOUND - True if libgdal is found +# GDAL_LIBRARY - A variable pointing to the GDAL library +# GDAL_INCLUDE_DIR - Where to find the headers + +#============================================================================= +# Copyright 2007-2009 Kitware, Inc. +# +# Distributed under the OSI-approved BSD License (the "License"); +# see accompanying file Copyright.txt for details. +# +# This software is distributed WITHOUT ANY WARRANTY; without even the +# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See COPYING-CMAKE-SCRIPTS for more information. +#============================================================================= +# Note: this file is not an exact copy of the original file from Kitware. +# It has been modified for the needs of GMT. + +# +# $GDAL_DIR is an environment variable that would +# correspond to the ./configure --prefix=$GDAL_DIR +# used in building gdal. +# +# Created by Eric Wing. I'm not a gdal user, but OpenSceneGraph uses it +# for osgTerrain so I whipped this module together for completeness. +# I actually don't know the conventions or where files are typically +# placed in distros. +# Any real gdal users are encouraged to correct this (but please don't +# break the OS X framework stuff when doing so which is what usually seems +# to happen). + +# This makes the presumption that you are include gdal.h like +# +#include "gdal.h" + +if (DEFINED GDAL_ROOT AND NOT GDAL_ROOT) + set (GDAL_LIBRARY "" CACHE INTERNAL "") + set (GDAL_INCLUDE_DIR "" CACHE INTERNAL "") + return() +endif (DEFINED GDAL_ROOT AND NOT GDAL_ROOT) + +if (UNIX AND NOT GDAL_FOUND) + # Use gdal-config to obtain the library version (this should hopefully + # allow us to -lgdal1.x.y where x.y are correct version) + # For some reason, libgdal development packages do not contain + # libgdal.so... + find_program (GDAL_CONFIG gdal-config + HINTS + ${GDAL_DIR} + ${GDAL_ROOT} + $ENV{GDAL_DIR} + $ENV{GDAL_ROOT} + PATH_SUFFIXES bin + PATHS + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local + ) + + if (GDAL_CONFIG) + execute_process (COMMAND ${GDAL_CONFIG} --cflags + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE GDAL_CONFIG_CFLAGS) + if (GDAL_CONFIG_CFLAGS) + string (REGEX MATCHALL "-I[^ ]+" _gdal_dashI ${GDAL_CONFIG_CFLAGS}) + string (REGEX REPLACE "-I" "" _gdal_includepath "${_gdal_dashI}") + string (REGEX REPLACE "-I[^ ]+" "" _gdal_cflags_other ${GDAL_CONFIG_CFLAGS}) + endif (GDAL_CONFIG_CFLAGS) + execute_process (COMMAND ${GDAL_CONFIG} --libs + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE GDAL_CONFIG_LIBS) + if (GDAL_CONFIG_LIBS) + string (REGEX MATCHALL "-l[^ ]+" _gdal_dashl ${GDAL_CONFIG_LIBS}) + string (REGEX REPLACE "-l" "" _gdal_lib "${_gdal_dashl}") + string (REGEX MATCHALL "-L[^ ]+" _gdal_dashL ${GDAL_CONFIG_LIBS}) + string (REGEX REPLACE "-L" "" _gdal_libpath "${_gdal_dashL}") + endif (GDAL_CONFIG_LIBS) + execute_process (COMMAND ${GDAL_CONFIG} --dep-libs + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE GDAL_CONFIG_DEP_LIBS) + if (GDAL_CONFIG_DEP_LIBS) + string (REGEX MATCHALL "-l[^ ]+" _gdal_dashl ${GDAL_CONFIG_DEP_LIBS}) + string (REGEX REPLACE "-l" "" _gdal_dep_lib "${_gdal_dashl}") + string (REGEX MATCHALL "-L[^ ]+" _gdal_dashL ${GDAL_CONFIG_DEP_LIBS}) + string (REGEX REPLACE "-L" "" _gdal_dep_libpath "${_gdal_dashL}") + endif (GDAL_CONFIG_DEP_LIBS) + endif (GDAL_CONFIG) + if (_gdal_dep_lib) + list (REMOVE_DUPLICATES _gdal_dep_lib) + list (REMOVE_ITEM _gdal_dep_lib gdal) + endif (_gdal_dep_lib) +endif (UNIX AND NOT GDAL_FOUND) + +find_path (GDAL_INCLUDE_DIR gdal.h + HINTS + ${_gdal_includepath} + ${GDAL_DIR} + ${GDAL_ROOT} + $ENV{GDAL_DIR} + $ENV{GDAL_ROOT} + PATH_SUFFIXES + include/gdal + include/GDAL + include + PATHS + ~/Library/Frameworks/gdal.framework/Headers + /Library/Frameworks/gdal.framework/Headers + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local +) + +find_library (GDAL_LIBRARY + NAMES ${_gdal_lib} gdal gdal_i gdal1.5.0 gdal1.4.0 gdal1.3.2 GDAL + HINTS + ${GDAL_DIR} + ${GDAL_ROOT} + $ENV{GDAL_DIR} + $ENV{GDAL_ROOT} + ${_gdal_libpath} + PATH_SUFFIXES lib + PATHS + ~/Library/Frameworks/gdal.framework + /Library/Frameworks/gdal.framework + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local +) + +# find all libs that gdal-config --dep-libs reports +foreach (_extralib ${_gdal_dep_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + HINTS + ${HDF5_ROOT} + $ENV{HDF5_ROOT} + ${NETCDF_ROOT} + $ENV{NETCDF_ROOT} + ${ZLIB_ROOT} + $ENV{ZLIB_ROOT} + ${CURL_ROOT} + $ENV{CURL_ROOT} + PATH_SUFFIXES lib + PATHS + ${_gdal_dep_libpath} + ) + list (APPEND GDAL_LIBRARY ${_found_lib_${_extralib}}) +endforeach (_extralib) + +# append manually-supplied libs +# find all manually-supplied libs +if (GDAL_EXTRA_LIBS) + # Ensure -l is preceded by whitespace to not match + # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' + string (REGEX MATCHALL "(^| )-l[^ ]+" _gdal_extra_lib_dashl ${GDAL_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-l" "" _gdal_extra_lib "${_gdal_extra_lib_dashl}") + string (REGEX MATCHALL "(^| )-L[^ ]+" _gdal_extra_lib_dashL ${GDAL_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-L" "" _gdal_extra_libpath "${_gdal_extra_lib_dashL}") + foreach (_extralib ${_gdal_extra_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + PATH_SUFFIXES lib + PATHS + ${_gdal_extra_libpath} + ) + list (APPEND GDAL_LIBRARY ${_found_lib_${_extralib}}) + endforeach (_extralib) +endif (GDAL_EXTRA_LIBS) + +include (FindPackageHandleStandardArgs) +find_package_handle_standard_args (GDAL DEFAULT_MSG GDAL_LIBRARY GDAL_INCLUDE_DIR) + +set (GDAL_LIBRARIES ${GDAL_LIBRARY}) +set (GDAL_INCLUDE_DIRS ${GDAL_INCLUDE_DIR}) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/cmake/modules/FindGSHHG.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/cmake/modules/FindGSHHG.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/cmake/modules/FindGSHHG.cmake (revision 27955) @@ -0,0 +1,95 @@ +# +# +# Locate GSHHG shorelines +# +# This module accepts the following environment variables: +# +# GSHHG_ROOT, GSHHGDIR - Specify the location of GSHHG +# +# This module defines the following CMake variables: +# +# GSHHG_FOUND - True if GSHHG is found +# GSHHG_PATH - A variable pointing to the GSHHG path +# GSHHG_VERSION - String of the GSHHG version found +# GSHHG_MIN_REQUIRED_VERSION_{MAJOR, MINOR, PATCH} +# - Major, minor, and patch version required + +# get GSHHG path +find_path (GSHHG_PATH + NAMES binned_GSHHS_c.nc + HINTS ${GSHHG_ROOT} $ENV{GSHHG_ROOT} $ENV{GSHHGDIR} + PATH_SUFFIXES + gmt-gshhg + gshhg + gshhg-gmt + gshhg-gmt-nc4 + share/gmt/gshhg + share/gmt-gshhg + share/gshhg + share/gshhg-gmt + share/gshhg-gmt-nc4 + PATHS + ${CMAKE_SOURCE_DIR} + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local + DOC "Global Self-consistent Hierarchical High-resolution Geography" +) + +# get GSHHG file +if (GSHHG_PATH) + find_file (_GSHHG_FILE + NAMES binned_GSHHS_c.nc + HINTS ${GSHHG_PATH}) +endif (GSHHG_PATH) + +# The minimum required GSHHG version +set (GSHHG_MIN_REQUIRED_VERSION_MAJOR 2 CACHE INTERNAL "GSHHG required version major") +set (GSHHG_MIN_REQUIRED_VERSION_MINOR 2 CACHE INTERNAL "GSHHG required version minor") +set (GSHHG_MIN_REQUIRED_VERSION_PATCH 0 CACHE INTERNAL "GSHHG required version patch") +set (GSHHG_MIN_REQUIRED_VERSION + "${GSHHG_MIN_REQUIRED_VERSION_MAJOR}.${GSHHG_MIN_REQUIRED_VERSION_MINOR}.${GSHHG_MIN_REQUIRED_VERSION_PATCH}") + +# Temporary hack to bypass failure of compilation of code to find GSHHG +set (GSHHG_FOUND TRUE) +set (GSHHG_VERSION "2.3.4" CACHE INTERNAL "GSHHG version") + +# check GSHHG version +if (_GSHHG_FILE AND NOT GSHHG_FOUND) + try_run (_EXIT_GSHHG_VERSION _COMPILED_GSHHG_VERSION + ${CMAKE_BINARY_DIR}/CMakeTmp + ${CMAKE_CURRENT_SOURCE_DIR}/gshhg_version.c + CMAKE_FLAGS + -DINCLUDE_DIRECTORIES=${NETCDF_INCLUDE_DIR} + -DLINK_LIBRARIES=${NETCDF_LIBRARIES} + COMPILE_DEFINITIONS -DSTANDALONE + COMPILE_OUTPUT_VARIABLE _GSHHG_VERSION_COMPILE_OUT + RUN_OUTPUT_VARIABLE _GSHHG_VERSION_STRING + ARGS \"${_GSHHG_FILE}\" ${GSHHG_MIN_REQUIRED_VERSION}) + + if (NOT _COMPILED_GSHHG_VERSION OR _EXIT_GSHHG_VERSION STREQUAL FAILED_TO_RUN) + message(FATAL_ERROR "Cannot determine GSHHG version:\n + ${_GSHHG_VERSION_COMPILE_OUT}\n + ${_GSHHG_VERSION_STRING}") + endif () + + # check version string + if (_COMPILED_GSHHG_VERSION) + # strip whitespace + string (STRIP ${_GSHHG_VERSION_STRING} GSHHG_VERSION) + if (_EXIT_GSHHG_VERSION EQUAL 0) + # found GSHHG of required version or higher + set (GSHHG_VERSION ${GSHHG_VERSION} CACHE INTERNAL "GSHHG version") + elseif (_EXIT_GSHHG_VERSION EQUAL -1) + # found GSHHG but version is too old + message (WARNING "GSHHG found but it is too old (${GSHHG_VERSION}). " + "Need at least ${GSHHG_MIN_REQUIRED_VERSION}.") + endif (_EXIT_GSHHG_VERSION EQUAL 0) + endif (_COMPILED_GSHHG_VERSION) +endif (_GSHHG_FILE AND NOT GSHHG_FOUND) + +include (FindPackageHandleStandardArgs) +find_package_handle_standard_args (GSHHG DEFAULT_MSG + GSHHG_PATH GSHHG_VERSION) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake (revision 27955) @@ -0,0 +1,181 @@ +# +# +# Locate netcdf +# +# This module accepts the following environment variables: +# +# NETCDF_DIR or NETCDF_ROOT - Specify the location of NetCDF +# +# This module defines the following CMake variables: +# +# NETCDF_FOUND - True if libnetcdf is found +# NETCDF_LIBRARY - A variable pointing to the NetCDF library +# NETCDF_INCLUDE_DIR - Where to find the headers +# NETCDF_INCLUDE_DIRS - Where to find the headers +# NETCDF_DEFINITIONS - Extra compiler flags + +#============================================================================= +# Inspired by FindGDAL +# +# Distributed under the OSI-approved bsd license (the "License") +# +# This software is distributed WITHOUT ANY WARRANTY; without even the +# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See COPYING-CMAKE-SCRIPTS for more information. +#============================================================================= + +# This makes the presumption that you are include netcdf.h like +# +#include "netcdf.h" + +if (UNIX AND NOT NETCDF_FOUND) + # Use nc-config to obtain the libraries + find_program (NETCDF_CONFIG nc-config + HINTS + ${NETCDF_DIR} + ${NETCDF_ROOT} + $ENV{NETCDF_DIR} + $ENV{NETCDF_ROOT} + PATH_SUFFIXES bin + PATHS + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local + ) + + if (NETCDF_CONFIG) + execute_process (COMMAND ${NETCDF_CONFIG} --cflags + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE NETCDF_CONFIG_CFLAGS) + if (NETCDF_CONFIG_CFLAGS) + string (REGEX MATCHALL "(^| )-I[^ ]+" _netcdf_dashI ${NETCDF_CONFIG_CFLAGS}) + string (REGEX REPLACE "(^| )-I" "" _netcdf_includepath "${_netcdf_dashI}") + string (REGEX REPLACE "(^| )-I[^ ]+" "" _netcdf_cflags_other ${NETCDF_CONFIG_CFLAGS}) + endif (NETCDF_CONFIG_CFLAGS) + execute_process (COMMAND ${NETCDF_CONFIG} --libs + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE NETCDF_CONFIG_LIBS) + if (NETCDF_CONFIG_LIBS) + # Ensure -l is preceded by whitespace to not match + # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' + string (REGEX MATCHALL "(^| )-l[^ ]+" _netcdf_dashl ${NETCDF_CONFIG_LIBS}) + string (REGEX REPLACE "(^| )-l" "" _netcdf_lib "${_netcdf_dashl}") + string (REGEX MATCHALL "(^| )-L[^ ]+" _netcdf_dashL ${NETCDF_CONFIG_LIBS}) + string (REGEX REPLACE "(^| )-L" "" _netcdf_libpath "${_netcdf_dashL}") + endif (NETCDF_CONFIG_LIBS) + endif (NETCDF_CONFIG) + if (_netcdf_lib) + list (REMOVE_DUPLICATES _netcdf_lib) + list (REMOVE_ITEM _netcdf_lib netcdf) + endif (_netcdf_lib) +endif (UNIX AND NOT NETCDF_FOUND) + +find_path (NETCDF_INCLUDE_DIR netcdf.h + HINTS + ${_netcdf_includepath} + ${NETCDF_DIR} + ${NETCDF_ROOT} + $ENV{NETCDF_DIR} + $ENV{NETCDF_ROOT} + PATH_SUFFIXES + include/netcdf + include/netcdf-4 + include/netcdf-3 + include + PATHS + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local +) + +find_library (NETCDF_LIBRARY + NAMES netcdf + HINTS + ${_netcdf_libpath} + ${NETCDF_DIR} + ${NETCDF_ROOT} + $ENV{NETCDF_DIR} + $ENV{NETCDF_ROOT} + PATH_SUFFIXES lib + PATHS + /sw + /opt/local + /opt/csw + /opt + /usr/local +) + +# find all libs that nc-config reports +foreach (_extralib ${_netcdf_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + HINTS + ${HDF5_ROOT} + $ENV{HDF5_ROOT} + ${ZLIB_ROOT} + $ENV{ZLIB_ROOT} + ${CURL_ROOT} + $ENV{CURL_ROOT} + PATH_SUFFIXES lib + PATHS + ${_netcdf_libpath} + ) + list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) +endforeach (_extralib) + +# find all manually-supplied libs +if (NETCDF_EXTRA_LIBS) + # Ensure -l is preceded by whitespace to not match + # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' + string (REGEX MATCHALL "(^| )-l[^ ]+" _netcdf_extra_lib_dashl ${NETCDF_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-l" "" _netcdf_extra_shared_lib "${_netcdf_extra_lib_dashl}") + string (REGEX MATCHALL "(^| )-L[^ ]+" _netcdf_extra_lib_dashL ${NETCDF_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-L" "" _netcdf_extra_libpath "${_netcdf_extra_lib_dashL}") + foreach (_extralib ${_netcdf_extra_shared_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + PATH_SUFFIXES lib + PATHS + ${_netcdf_extra_libpath} + ) + list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) + endforeach (_extralib) + # Retrieve static library names + string(REGEX MATCHALL "[a-zA-Z0-9]+\\.a" _netcdf_extra_static_lib "${NETCDF_EXTRA_LIBS}") + foreach (_extralib ${_netcdf_extra_static_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + PATH_SUFFIXES lib + PATHS + ${_netcdf_extra_libpath} + ) + list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) + endforeach (_extralib) +endif (NETCDF_EXTRA_LIBS) + +if (NETCDF_LIBRARY AND NETCDF_INCLUDE_DIR AND NOT HAVE_NETCDF4) + # Ensure that NetCDF with version 4 extensions is installed + include (CMakePushCheckState) + include (CheckSymbolExists) + cmake_push_check_state() # save state of CMAKE_REQUIRED_* + set (CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${NETCDF_INCLUDE_DIR}) + set (CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES} ${NETCDF_LIBRARY}) + set (HAVE_NETCDF4 HAVE_NETCDF4) # to force check_symbol_exists again + check_symbol_exists (nc_def_var_deflate netcdf.h HAVE_NETCDF4) + cmake_pop_check_state() # restore state of CMAKE_REQUIRED_* + if (NOT HAVE_NETCDF4) + message (SEND_ERROR "Library found but netCDF-4/HDF5 format unsupported. Do not configure netCDF-4 with --disable-netcdf-4.") + endif (NOT HAVE_NETCDF4) +endif (NETCDF_LIBRARY AND NETCDF_INCLUDE_DIR AND NOT HAVE_NETCDF4) + +include (FindPackageHandleStandardArgs) +find_package_handle_standard_args (NETCDF + DEFAULT_MSG NETCDF_LIBRARY NETCDF_INCLUDE_DIR HAVE_NETCDF4) + +set (NETCDF_LIBRARIES ${NETCDF_LIBRARY}) +set (NETCDF_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR}) +string (REPLACE "-DNDEBUG" "" NETCDF_DEFINITIONS "${_netcdf_cflags_other}") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake (revision 27955) @@ -0,0 +1,308 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License +# for more details. +# +# Contact info: www.generic-mapping-tools.org +# ---------------------------------------------------------------------------- + +# Use this file to override variables in 'ConfigDefault.cmake' on a per-user +# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then +# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled +# (currently listed in .gitignore). +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## Section 1: Installation paths +## + +# ============================================================================ +# Basic setup begins here. All settings are optional. In most cases, setting +# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with +# reasonable defaults enabled. Note: If you need to specify directory names +# with spaces (e.g., on Windows) then you must put them in quotes. +# ============================================================================ + +# Installation path (usually defaults to /usr/local) [auto]: +set (CMAKE_INSTALL_PREFIX "$ENV{PREFIX}") + +# Set install name suffix used for directories and gmt executables +# [undefined]: +#set (GMT_INSTALL_NAME_SUFFIX "suffix") + +# Install into traditional directory structure. Disable to install a +# distribution type directory structure (doc and share separated) [on]: +#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) + +# Install convenience links for GMT modules. Disable to install only the main +# gmt program and access modules as "gmt modulename options" [TRUE]: +#set (GMT_INSTALL_MODULE_LINKS FALSE) + +# Make executables relocatable on supported platforms (relative RPATH) [FALSE]: +set (GMT_INSTALL_RELOCATABLE TRUE) + +# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE] +#set (GMT_EXCLUDE_GDAL TRUE) +set (GMT_EXCLUDE_PCRE TRUE) +set (GMT_EXCLUDE_PCRE2 TRUE) +#set (GMT_EXCLUDE_FFTW3 TRUE) +#set (GMT_EXCLUDE_LAPACK TRUE) +#set (GMT_EXCLUDE_BLAS TRUE) +#set (GMT_EXCLUDE_ZLIB TRUE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set URL to GMT Data server [auto]: +#set (GMT_DATA_SERVER "data_server_url") + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{GSHHG_ROOT}") + +# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]: +set (COPY_GSHHG TRUE) + +# Set path to DCW Digital Chart of the World for GMT [auto]: +#set (DCW_ROOT "dcw-gmt_path") + +# Copy DCW files to ${GMT_DATADIR}/dcw [FALSE]: +#set (COPY_DCW TRUE) + +# Copy GDAL's 'data' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (GDAL_DATA_PATH C:/programs/compa_libs/gdal_GIT/compileds/VC14_64/data) + +# Copy PROJ4's 'share' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (PROJ_DATA_PATH C:/programs/compa_libs/proj5_GIT/compileds/VC14_64/share/proj) + +# FOR WINDOWS ONLY +# Set path to location of Ghostscript binaries (optional install) +#set (GHOST_DATA_PATH C:/programs/compa_libs/ghostscript/bin) + +# FOR WINDOWS ONLY +# Set path to location where the gmtmex is located. +#set (GMTMEX_PATH "C:/progs_cygw/GMTdev/gmtmex/${GMTver}") + +# Set location of NetCDF (can be root directory, path to header file or path +# to nc-config) [auto]: +set (NETCDF_ROOT "$ENV{NETCDF_ROOT}") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{GDAL_ROOT}") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") +# Alternatively, set location of PCRE2 (can be root directory, path to header file or path to +# pcre2-config) [auto]: +#set (PCRE2_ROOT "pcre2_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +set (ZLIB_ROOT "$ENV{ZLIB_ROOT}") + +# Set location of CURL (can be root directory or path to header file) [auto]: +#set (CURL_ROOT "curl_install_prefix") + +# Set location of GLIB component gthread [auto]. This is an optional (and +# experimental) option which you need to enable: +#set (GMT_USE_THREADS TRUE) +# If pkg-config is not installed (e.g. on Windows) you need to specify these: +#set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0) +#set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib) + +# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically +set (LAPACK_LIBRARY "-L$ENV{LAPACK_ROOT} -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran") +set (BLAS_LIBRARY "-L$ENV{BLAS_ROOT} -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Allow building of OpenMP if compiler supports it +# set (GMT_ENABLE_OPENMP TRUE) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# Enable building of shared libraries [TRUE] (disable to use static libraries; +# not recommended; on non-x86 architectures uncomment the next option as well): +set (BUILD_SHARED_LIBS FALSE) + +# Create position independent code on all targets [auto] (needed for static +# build on non-x86): +#set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) + +# Build GMT shared lib with supplemental modules [TRUE]: +set (BUILD_SUPPLEMENTS FALSE) + +# Build/Install GMT Developer include files [TRUE]: +# This installs the extra include files and configured files needed by 3rd-party +# developers. Until we build a separate gmt-devel we include them in the main +# Distribution. +#set (BUILD_DEVELOPER FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#set (DO_EXAMPLES TRUE) +#set (DO_TESTS TRUE) +#set (DO_ANIMATIONS TRUE) +# Number of parallel test jobs with "make check": +#set (N_TEST_JOBS 4) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmt-custom project). +#set (EXTRA_BUILD_DIRS apidemo) +# Uncomment the following line to enable running low-level C tests of the API +#set (DO_API_TESTS ON) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel +# [Release]: +#set (CMAKE_BUILD_TYPE Debug) + +# Extra debugging for developers: +#if ( CMAKE_GENERATOR STREQUAL "Xcode" ) +## So Xcode can find the supplemental plug-ins during debug sessions +# add_definitions(-DXCODER) +# add_definitions(-DDEBUG_MODERN) # To set PPID == 0 during Xcode test +# message("Add Xcode definition for GMT") +#endif() +#add_definitions(-DDEBUG) +#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info +#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies +if (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions") # check uninitialized variables +else (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +endif (HAVE_OPENMP) + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +# WARNING: if using this option it is mandatory that the suffix starts with an underscore. +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake (revision 27955) @@ -0,0 +1,308 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License +# for more details. +# +# Contact info: www.generic-mapping-tools.org +# ---------------------------------------------------------------------------- + +# Use this file to override variables in 'ConfigDefault.cmake' on a per-user +# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then +# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled +# (currently listed in .gitignore). +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## Section 1: Installation paths +## + +# ============================================================================ +# Basic setup begins here. All settings are optional. In most cases, setting +# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with +# reasonable defaults enabled. Note: If you need to specify directory names +# with spaces (e.g., on Windows) then you must put them in quotes. +# ============================================================================ + +# Installation path (usually defaults to /usr/local) [auto]: +set (CMAKE_INSTALL_PREFIX "$ENV{PREFIX}") + +# Set install name suffix used for directories and gmt executables +# [undefined]: +#set (GMT_INSTALL_NAME_SUFFIX "suffix") + +# Install into traditional directory structure. Disable to install a +# distribution type directory structure (doc and share separated) [on]: +#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) + +# Install convenience links for GMT modules. Disable to install only the main +# gmt program and access modules as "gmt modulename options" [TRUE]: +#set (GMT_INSTALL_MODULE_LINKS FALSE) + +# Make executables relocatable on supported platforms (relative RPATH) [FALSE]: +set (GMT_INSTALL_RELOCATABLE TRUE) + +# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE] +#set (GMT_EXCLUDE_GDAL TRUE) +set (GMT_EXCLUDE_PCRE TRUE) +set (GMT_EXCLUDE_PCRE2 TRUE) +#set (GMT_EXCLUDE_FFTW3 TRUE) +#set (GMT_EXCLUDE_LAPACK TRUE) +#set (GMT_EXCLUDE_BLAS TRUE) +#set (GMT_EXCLUDE_ZLIB TRUE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set URL to GMT Data server [auto]: +#set (GMT_DATA_SERVER "data_server_url") + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{GSHHG_ROOT}") + +# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]: +set (COPY_GSHHG TRUE) + +# Set path to DCW Digital Chart of the World for GMT [auto]: +#set (DCW_ROOT "dcw-gmt_path") + +# Copy DCW files to ${GMT_DATADIR}/dcw [FALSE]: +#set (COPY_DCW TRUE) + +# Copy GDAL's 'data' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (GDAL_DATA_PATH C:/programs/compa_libs/gdal_GIT/compileds/VC14_64/data) + +# Copy PROJ4's 'share' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]: +#set (PROJ_DATA_PATH C:/programs/compa_libs/proj5_GIT/compileds/VC14_64/share/proj) + +# FOR WINDOWS ONLY +# Set path to location of Ghostscript binaries (optional install) +#set (GHOST_DATA_PATH C:/programs/compa_libs/ghostscript/bin) + +# FOR WINDOWS ONLY +# Set path to location where the gmtmex is located. +#set (GMTMEX_PATH "C:/progs_cygw/GMTdev/gmtmex/${GMTver}") + +# Set location of NetCDF (can be root directory, path to header file or path +# to nc-config) [auto]: +set (NETCDF_ROOT "$ENV{NETCDF_ROOT}") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{GDAL_ROOT}") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") +# Alternatively, set location of PCRE2 (can be root directory, path to header file or path to +# pcre2-config) [auto]: +#set (PCRE2_ROOT "pcre2_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +set (ZLIB_ROOT "$ENV{ZLIB_ROOT}") + +# Set location of CURL (can be root directory or path to header file) [auto]: +#set (CURL_ROOT "curl_install_prefix") + +# Set location of GLIB component gthread [auto]. This is an optional (and +# experimental) option which you need to enable: +#set (GMT_USE_THREADS TRUE) +# If pkg-config is not installed (e.g. on Windows) you need to specify these: +#set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0) +#set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib) + +# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically +#set (LAPACK_LIBRARY "-L$ENV{LAPACK_ROOT} -lflapack") +#set (BLAS_LIBRARY "-L$ENV{BLAS_ROOT} -lfblas") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Allow building of OpenMP if compiler supports it +# set (GMT_ENABLE_OPENMP TRUE) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# Enable building of shared libraries [TRUE] (disable to use static libraries; +# not recommended; on non-x86 architectures uncomment the next option as well): +set (BUILD_SHARED_LIBS FALSE) + +# Create position independent code on all targets [auto] (needed for static +# build on non-x86): +#set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) + +# Build GMT shared lib with supplemental modules [TRUE]: +set (BUILD_SUPPLEMENTS FALSE) + +# Build/Install GMT Developer include files [TRUE]: +# This installs the extra include files and configured files needed by 3rd-party +# developers. Until we build a separate gmt-devel we include them in the main +# Distribution. +#set (BUILD_DEVELOPER FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#set (DO_EXAMPLES TRUE) +#set (DO_TESTS TRUE) +#set (DO_ANIMATIONS TRUE) +# Number of parallel test jobs with "make check": +#set (N_TEST_JOBS 4) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmt-custom project). +#set (EXTRA_BUILD_DIRS apidemo) +# Uncomment the following line to enable running low-level C tests of the API +#set (DO_API_TESTS ON) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel +# [Release]: +#set (CMAKE_BUILD_TYPE Debug) + +# Extra debugging for developers: +#if ( CMAKE_GENERATOR STREQUAL "Xcode" ) +## So Xcode can find the supplemental plug-ins during debug sessions +# add_definitions(-DXCODER) +# add_definitions(-DDEBUG_MODERN) # To set PPID == 0 during Xcode test +# message("Add Xcode definition for GMT") +#endif() +#add_definitions(-DDEBUG) +#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info +#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies +if (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions") # check uninitialized variables +else (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +endif (HAVE_OPENMP) + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +# WARNING: if using this option it is mandatory that the suffix starts with an underscore. +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/src/CMakeLists.txt =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/src/CMakeLists.txt (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/configs/6/static/src/CMakeLists.txt (revision 27955) @@ -0,0 +1,730 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# Contact info: www.generic-mapping-tools.org +#------------------------------------------------------------------------------- +# +# To modify the cmake process: Edit your cmake/ConfigUser.cmake file +# +# src/CMakeLists.txt +# + +include (ManageString) +include (GmtHelperMacros) + +if (UNIX AND NOT APPLE) + set (LINUX TRUE) +else (UNIX AND NOT APPLE) + set (LINUX FALSE) +endif (UNIX AND NOT APPLE) + +# On Windows do not prefix the DLLs with the 'lib' prefix +if (WIN32) + set(LIB_PREFIX "") +else (WIN32) + set(LIB_PREFIX "lib") +endif (WIN32) + +# Include CREATE_DEBUG_SYM macro and set DEBUG_BUILD +include (CreateDebugSym) + +# Find executable needed by gmt +find_program (OGR2OGR ogr2ogr) +if (NOT OGR2OGR) + message (WARNING "Cannot find program ogr2ogr - gmt will be unable to convert Shapefiles to GMT/OGR format") + set (GMT_CONFIG_OGR2OGR_MESSAGE "no" CACHE INTERNAL "OGR2OGR config message") +else (NOT OGR2OGR) + execute_process(COMMAND ogr2ogr --version OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + string (REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" answer "${answer}") + set (GMT_CONFIG_OGR2OGR_MESSAGE "yes (${answer})" CACHE INTERNAL "OGR2OGR config message") +endif (NOT OGR2OGR) + +# Find executable needed by psconvert +find_program (GDAL_TRANSLATE gdal_translate) +if (NOT GDAL_TRANSLATE) + message (WARNING "Cannot find program gdal_translate - psconvert will be unable to convert TIFF to GeoTIFF") + set (GMT_CONFIG_GDAL_TRANSLATE_MESSAGE "no" CACHE INTERNAL "GDAL_TRANSLATE config message") +else (NOT GDAL_TRANSLATE) + execute_process(COMMAND gdal_translate --version OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + string (REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" answer "${answer}") + set (GMT_CONFIG_GDAL_TRANSLATE_MESSAGE "yes (${answer})" CACHE INTERNAL "GDAL_TRANSLATE config message") +endif (NOT GDAL_TRANSLATE) + +# Find executables needed by movie +find_program (GM gm) +if (NOT GM) + message (WARNING "Cannot find GraphicsMagick program gm - gmt movie will be unable to make animated GIFs") + set (GMT_CONFIG_GM_MESSAGE "no" CACHE INTERNAL "GM config message") +else (NOT GM) + execute_process(COMMAND gm help OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + string (REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" answer "${answer}") + set (GMT_CONFIG_GM_MESSAGE "yes (${answer})" CACHE INTERNAL "GM config message") +endif (NOT GM) + +find_program (FFMPEG ffmpeg) +if (NOT FFMPEG) + message (WARNING "Cannot find ffmpeg - gmt movie will be unable to make movies from frames") + set (GMT_CONFIG_FFMPEG_MESSAGE "no" CACHE INTERNAL "FFMPEG config message") +else (NOT FFMPEG) + execute_process(COMMAND ffmpeg -version OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + string (REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" answer "${answer}") + set (GMT_CONFIG_FFMPEG_MESSAGE "yes (${answer})" CACHE INTERNAL "FFMPEG config message") +endif (NOT FFMPEG) + +# Find executable needed by docs +if (LINUX) + find_program (XDGOPEN xdg-open) + if (NOT XDGOPEN) + message (WARNING "Cannot find program xdg-open - gmt docs will be unable to open the documentation") + set (GMT_CONFIG_OPEN_MESSAGE "no" CACHE INTERNAL "OPEN config message") + else (NOT XDGOPEN) + set (GMT_CONFIG_OPEN_MESSAGE "yes" CACHE INTERNAL "OPEN config message") + endif (NOT XDGOPEN) +else (LINUX) + set (GMT_CONFIG_OPEN_MESSAGE "yes" CACHE INTERNAL "OPEN config message") +endif (LINUX) + +# Find executable needed by psconvert +if (WIN32) + set (GMT_CONFIG_GS_MESSAGE "yes" CACHE INTERNAL "GS config message") +else (WIN32) + find_program (GS gs) + if (NOT GS) + message (WARNING "Cannot find ghostscript program gs - gmt psconvert will be unable to convert PostScript to other formats") + set (GMT_CONFIG_GS_MESSAGE "no" CACHE INTERNAL "GS config message") + else (NOT GS) + execute_process(COMMAND gs --version OUTPUT_VARIABLE answer OUTPUT_STRIP_TRAILING_WHITESPACE) + set (GMT_CONFIG_GS_MESSAGE "yes (${answer})" CACHE INTERNAL "GS config message") + endif (NOT GS) +endif (WIN32) + +# Find libraries +message (STATUS "Searching dependent libraries. This may take a few minutes...") +# NetCDF is required +find_package (NETCDF REQUIRED) +include_directories (${NETCDF_INCLUDE_DIR}) + +# libcurl is required since 5.4 +include_directories ($ENV{CURL_INCLUDE_DIRS}) +list (APPEND GMT_OPTIONAL_LIBRARIES $ENV{CURL_LIBRARIES}) + +if (NOT DEFINED GMT_EXCLUDE_GDAL) + find_package (GDAL) +endif (NOT DEFINED GMT_EXCLUDE_GDAL) +if (GDAL_FOUND) + set (HAVE_GDAL TRUE CACHE INTERNAL "System has GDAL") + include_directories (${GDAL_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${GDAL_LIBRARIES}) +endif (GDAL_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_PCRE) + find_package (PCRE) +endif (NOT DEFINED GMT_EXCLUDE_PCRE) +if (NOT PCRE_FOUND AND NOT DEFINED GMT_EXCLUDE_PCRE2) + find_package (PCRE2) +endif (NOT PCRE_FOUND AND NOT DEFINED GMT_EXCLUDE_PCRE2) +if (PCRE_FOUND) + set (HAVE_PCRE TRUE CACHE INTERNAL "System has PCRE") + set (GMT_CONFIG_REGEX_MESSAGE "PCRE (${PCRE_LIBRARIES})" + CACHE INTERNAL "Regex config message") + include_directories (${PCRE_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${PCRE_LIBRARIES}) +elseif (PCRE2_FOUND) + set (HAVE_PCRE2 TRUE CACHE INTERNAL "System has PCRE2") + set (GMT_CONFIG_REGEX_MESSAGE "PCRE2 (${PCRE2_LIBRARIES})" + CACHE INTERNAL "Regex config message") + include_directories (${PCRE2_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${PCRE2_LIBRARIES}) +else (PCRE_FOUND) + find_package (REGEX) + if (REGEX_FOUND) + set (HAVE_POSIX_ERE TRUE CACHE INTERNAL "System has regex.h") + set (GMT_CONFIG_REGEX_MESSAGE "POSIX Regex (${REGEX_INCLUDE_DIR}/regex.h)" + CACHE INTERNAL "Regex config message") + include_directories (${REGEX_INCLUDE_DIR}) + # I don't think its needed but just in case: + list (APPEND GMT_OPTIONAL_LIBRARIES ${REGEX_LIBRARIES}) + else (REGEX_FOUND) + set (GMT_CONFIG_REGEX_MESSAGE "unsupported" + CACHE INTERNAL "Regex config message") + endif (REGEX_FOUND) +endif (PCRE_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_FFTW3) + find_package (FFTW3) +endif (NOT DEFINED GMT_EXCLUDE_FFTW3) +if (FFTW3_FOUND) + set (HAVE_FFTW3F TRUE CACHE INTERNAL "System has single precision FFTW") + if (FFTW3F_THREADS_LIBRARY) + set (HAVE_FFTW3F_THREADS TRUE CACHE INTERNAL "System has single precision threaded FFTW") + endif (FFTW3F_THREADS_LIBRARY) + include_directories (${FFTW3_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${FFTW3F_LIBRARIES}) +endif (FFTW3_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_LAPACK) + find_package (LAPACK) +endif (NOT DEFINED GMT_EXCLUDE_LAPACK) +if (LAPACK_FOUND) + set (HAVE_LAPACK TRUE CACHE INTERNAL "System has LAPACK") + set (GMT_CONFIG_LAPACK_MESSAGE "yes" CACHE INTERNAL "LAPACK config message") + include_directories (${LAPACK_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${LAPACK_LIBRARIES}) +else (LAPACK_FOUND) + if (LAPACK_LIBRARY) + # Set in ConfigUser.cmake + set (HAVE_LAPACK TRUE CACHE INTERNAL "System has LAPACK") + set (GMT_CONFIG_LAPACK_MESSAGE "yes" CACHE INTERNAL "LAPACK config message") + list (APPEND GMT_OPTIONAL_LIBRARIES ${LAPACK_LIBRARY}) + else (LAPACK_LIBRARY) + set (GMT_CONFIG_LAPACK_MESSAGE "no" CACHE INTERNAL "LAPACK config message") + endif (LAPACK_LIBRARY) +endif (LAPACK_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_BLAS) + find_package (BLAS) +endif (NOT DEFINED GMT_EXCLUDE_BLAS) +if (BLAS_FOUND) + set (HAVE_BLAS TRUE CACHE INTERNAL "System has BLAS") + set (GMT_CONFIG_BLAS_MESSAGE "yes" CACHE INTERNAL "BLAS config message") + include_directories (${BLAS_INCLUDE_DIR}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${BLAS_LIBRARIES}) +else (BLAS_FOUND) + if (BLAS_LIBRARY) + # Set in ConfigUser.cmake + set (HAVE_BLAS TRUE CACHE INTERNAL "System has BLAS") + set (GMT_CONFIG_BLAS_MESSAGE "yes" CACHE INTERNAL "BLAS config message") + list (APPEND GMT_OPTIONAL_LIBRARIES ${BLAS_LIBRARY}) + else (BLAS_LIBRARY) + set (GMT_CONFIG_BLAS_MESSAGE "no" CACHE INTERNAL "BLAS config message") + endif (BLAS_LIBRARY) +endif (BLAS_FOUND) + +if (NOT DEFINED GMT_EXCLUDE_ZLIB) + find_package (ZLIB) +endif (NOT DEFINED GMT_EXCLUDE_ZLIB) +if (ZLIB_FOUND) + set (HAVE_ZLIB TRUE CACHE INTERNAL "System has ZLIB") + include_directories (${ZLIB_INCLUDE_DIRS}) +endif (ZLIB_FOUND) + + +if (APPLE) + # Accelerate framework + find_library (ACCELERATE_FRAMEWORK Accelerate) + mark_as_advanced (ACCELERATE_FRAMEWORK) + list (APPEND GMT_OPTIONAL_LIBRARIES ${ACCELERATE_FRAMEWORK}) +endif (APPLE) + +if (DEFINED GMT_ENABLE_OPENMP) + set (GMT_OPENMP TRUE CACHE INTERNAL "Turn on GMT OpenMP") +endif (DEFINED GMT_ENABLE_OPENMP) +find_package (OpenMP) +if (OPENMP_FOUND AND GMT_OPENMP) + set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}") + set (CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS}") + set (HAVE_OPENMP TRUE CACHE INTERNAL "OpenMP enabled." FORCE) + set (GMT_CONFIG_OPENMP_MESSAGE "enabled" + CACHE INTERNAL "OPENMP config message") + if (WIN32 AND OMP_DLL_LOC) + # UGLY AND RISKY PATCH FOR THE CPACK BUG OF NOT COPYING THE OMP DLL. THIS PATCH RELIES + # ON THE SETTING OF THE OMP_DLL_LOC VARIABLE IN ConfigUser.cmake. MINE HAS: + # set (OMP_DLL_LOC "C:/Program Files (x86)/Microsoft Visual Studio 12.0/VC/redist/x64/Microsoft.VC120.OPENMP/vcomp120.dll") + install(FILES ${OMP_DLL_LOC} DESTINATION bin COMPONENT Libraries) + endif (WIN32 AND OMP_DLL_LOC) +else (OPENMP_FOUND AND GMT_OPENMP) + set (HAVE_OPENMP FALSE CACHE INTERNAL "OpenMP disabled." FORCE) + set (GMT_CONFIG_OPENMP_MESSAGE "disabled" + CACHE INTERNAL "OPENMP config message") +endif (OPENMP_FOUND AND GMT_OPENMP) +if (OPENMP_FOUND AND NOT GMT_OPENMP) + message (STATUS "User variable GMT_OPENMP not set: disabling OpenMP.") + set (GMT_CONFIG_OPENMP_MESSAGE "disabled (GMT_OPENMP not set)" + CACHE INTERNAL "OPENMP config message") +endif (OPENMP_FOUND AND NOT GMT_OPENMP) + +find_package(GLIB COMPONENTS gthread) +if (GLIB_FOUND AND GMT_USE_THREADS) + set (HAVE_GLIB_GTHREAD TRUE CACHE INTERNAL "System has GLIB component gthread") + include_directories (${GLIB_INCLUDE_DIRS}) + list (APPEND GMT_OPTIONAL_LIBRARIES ${GLIB_LIBRARIES}) + set (GMT_CONFIG_GTHREAD_MESSAGE "enabled" + CACHE INTERNAL "GTHREAD config message") +endif (GLIB_FOUND AND GMT_USE_THREADS) +if (GLIB_FOUND AND NOT GMT_USE_THREADS) + set (HAVE_GLIB_GTHREAD FALSE CACHE INTERNAL "User disabled threads") + message (STATUS "User variable GMT_USE_THREADS not set: disabling GThread.") + set (GMT_CONFIG_GTHREAD_MESSAGE "disabled" + CACHE INTERNAL "GTHREAD config message") +endif (GLIB_FOUND AND NOT GMT_USE_THREADS) +if (GMT_USE_THREADS AND NOT GLIB_FOUND) + message (FATAL_ERROR "User variable GMT_USE_THREADS set but GLIB component gthread not found.") + set (GMT_CONFIG_GTHREAD_MESSAGE "unavailable" + CACHE INTERNAL "GTHREAD config message") +endif (GMT_USE_THREADS AND NOT GLIB_FOUND) + +# check for math and POSIX functions +include(ConfigureChecks) + +include_directories (${GMT_SOURCE_DIR}/src) +include_directories (${CMAKE_CURRENT_BINARY_DIR}) +set(CMAKE_INCLUDE_CURRENT_DIR TRUE) + +# Examples and tests depend on Shorelines +find_package (GSHHG) +if (DO_EXAMPLES OR DO_TESTS AND NOT GSHHG_FOUND) + message (FATAL_ERROR "Cannot proceed without GSHHG Shorelines. " + "Need to either set GSHHG_ROOT or disable tests.") +endif (DO_EXAMPLES OR DO_TESTS AND NOT GSHHG_FOUND) + +# Examples and tests depend on DCW +find_package (DCW) +if (DO_EXAMPLES OR DO_TESTS AND NOT DCW_FOUND) + message (FATAL_ERROR "Cannot proceed without DCW polygons. " + "Need to either set DCW_ROOT or disable tests." + "Obtain dcw-gmt-.tar.gz or dcw-gmt-.zip from ftp://ftp.soest.hawaii.edu/gmt and make DCW_ROOT variable point to the directory where you unarchived the files") +endif (DO_EXAMPLES OR DO_TESTS AND NOT DCW_FOUND) + +if (DO_API_TESTS) + # These lines are temporarily here for the beta release - comment to avoid in the build + set (GMT_DEMOS_SRCS testapi.c testpsl.c testgmt.c testgmtshell.c testgmtio.c testgrdio.c testio.c + testapiconv.c example1.c testapi_matrix.c testapi_matrix_plot.c testapi_vector.c test_JL.c testapi_mixmatrix.c + test_walter.c testapi_usergrid.c testapi_userdataset.c testapi_uservectors.c) +endif (DO_API_TESTS) + +if (NOT LICENSE_RESTRICTED) # off + # enable Shewchuk's triangle routine + set (GMT_TRIANGULATE "Shewchuk" PARENT_SCOPE) + set (GMT_TRIANGLE_SRCS triangle.c triangle.h) + list (APPEND GMT_EXTRA_LICENSE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.TRIANGLE) + set (GMT_EXTRA_LICENSE_FILES ${GMT_EXTRA_LICENSE_FILES} PARENT_SCOPE) +else (NOT LICENSE_RESTRICTED) # on + # disable Shewchuk's triangle routine + set (GMT_TRIANGULATE "Watson" PARENT_SCOPE) +endif (NOT LICENSE_RESTRICTED) + +# Note: Developers can set EXTRA_MODULES in ConfigUser.cmake to test new modules +set (GMT_PROGS_SRCS blockmean.c blockmedian.c blockmode.c docs.c dimfilter.c filter1d.c grd2kml.c + fitcircle.c gmt2kml.c gmtconvert.c gmtlogo.c gmtmath.c gmtselect.c gmtsimplify.c + gmtspatial.c gmtconnect.c gmtregress.c gmtvector.c gmtwhich.c grd2cpt.c + grd2xyz.c grdblend.c grdclip.c grdcut.c grdedit.c grdfft.c grdfill.c grdfilter.c + grdgradient.c grdhisteq.c grdinfo.c grdlandmask.c grdmask.c grdmath.c + grdpaste.c grdproject.c grdsample.c grdconvert.c grdtrack.c movie.c + grdtrend.c grdvolume.c greenspline.c kml2gmt.c makecpt.c mapproject.c + gmtinfo.c nearneighbor.c project.c psconvert.c sample1d.c spectrum1d.c + sph2grd.c sphdistance.c sphinterpolate.c sphtriangulate.c splitxyz.c + surface.c trend1d.c trend2d.c triangulate.c xyz2grd.c gmtdefaults.c gmtget.c + gmtset.c grdcontour.c grdimage.c grdvector.c grdview.c psbasemap.c psclip.c + pscoast.c pscontour.c psevents.c pshistogram.c psimage.c psmask.c psrose.c psscale.c + pssolar.c psternary.c pstext.c pswiggle.c psxy.c psxyz.c pslegend.c ${EXTRA_MODULES}) + +# Legacy modules for which to install compatibility links via +# install_module_symlink +set (GMT_COMPAT_MODULES minmax gmt2rgb gmtstitch gmtdp grdreformat ps2raster) + +# libpslib +set (GMT_PSL_SRCS postscriptlight.c declspec.h psl_config.h PSL_Standard+.h + PSL_Standard.h PSL_ISOLatin1+.h PSL_ISOLatin1.h PSL_ISO-8859-1.h + PSL_ISO-8859-2.h PSL_ISO-8859-3.h PSL_ISO-8859-4.h PSL_ISO-8859-5.h + PSL_ISO-8859-6.h PSL_ISO-8859-7.h PSL_ISO-8859-8.h PSL_ISO-8859-9.h + PSL_ISO-8859-10.h PSL_ISO-8859-13.h PSL_ISO-8859-14.h PSL_ISO-8859-15.h + PSL_strings.h PSL_patterns.h) + +set (GMT_MBSYSTEM_SRCS gmt_mbsystem_module.c gmt_mbsystem_module.h) + +# libgmt +set (GMT_LIB_SRCS block_subs.h common_byteswap.h common_math.h + common_runpath.h common_sighandler.c common_string.h clear.c begin.c + gmt_color_rgb.h gmt_colornames.h + gmt_modern.c end.c declspec.h gmt_hidden.h gmt_remote.h gmt_remote.c + figure.c gmt_dev.h gmt_common.h gmt_constants.h compat/qsort.h + gmt_contour.h gmt_customio.h gmt_datums.h gmt_dcw.h gmt_decorate.h gmt_defaults.h + gmt_ellipsoids.h gmt_error.h gmt_gdalread.h gmt_glib.h gmt_grd.h gmt_grdio.h gmt_hash.h + gmt_internals.h gmt_io.h gmt_macros.h gmt_media_name.h gmt_modern.h + gmt_media_size.h gmt_mgg_header2.h gmt_sharedlibs.h gmt_memory.h gmt_mb.h + gmt_core_module.h gmt_nan.h gmt_notposix.h gmt_pennames.h gmt_enum_dict.h + gmt_plot.h gmt_project.h gmt_prototypes.h gmt_psl.h gmt_shore.h gmt_gsformats.h + gmt_symbol.h gmt_synopsis.h gmt_texture.h gmt_time.h gmt_cpt_masters.h + gmt_types.h gmt_unique.h gmt_version.h gshhg_version.h postscriptlight.h + s_rint.h triangle.h gmt.h gmt_resources.h gmt_private.h subplot.c + gmt_error_codes.h gmt_api.c gmt_bcr.c gmt_calclock.c gmt_cdf.c gmt_compat.c + gmt_customio.c gmt_dcw.c gmt_error.c gmt_fft.c gmt_grdio.c gmt_io.c + gmt_memory.c gmt_nc.c gmt_notposix.c gmt_proj.c gmt_shore.c gmt_sph.c + gmt_stat.c gmt_support.c gmt_regexp.c gmt_vector.c gmt_parse.c inset.c + gmt_error_codes.c gshhg_version.c gmtread.c gmtwrite.c common_math.c + common_runpath.c common_sighandler.c common_string.c compat/qsort.c + gmt_sharedlibs.c gmt_core_module.c gmt_init.c gmt_map.c gmt_plot.c + kiss_fft/_kiss_fft_guts.h kiss_fft/kiss_fft.c kiss_fft/kiss_fft.h + kiss_fft/kiss_fftnd.c kiss_fft/kiss_fftnd.h + ${GMT_TRIANGLE_SRCS} ${GMT_MBSYSTEM_SRCS}) + +if (BUILD_SUPPLEMENTS) + # Needed in supplib, + supplements themselves + set (GMT_SUPPL_SRCS gmt_modern.c gmt_supplements_module.h gmt_supplements_module.c) +endif (BUILD_SUPPLEMENTS) + +# dependencies on generated files +set (GMT_GEN_HDRS gmt_keycases.h + gmt_keywords.h gmt_config.h + gmt_dimensions.h + CACHE INTERNAL "Autogenerated GMT headers") + +# Add commands to create header files + +add_custom_command (OUTPUT gmt_keycases.h gmt_keywords.h + COMMAND ${CMAKE_COMMAND} + -D GENERATE_COMMAND=gen_gmt_keywords_h + -D CMAKE_MODULE_PATH=${CMAKE_MODULE_PATH} + -D GMT_SRC=${GMT_SOURCE_DIR} + -P ${CMAKE_MODULE_PATH}/GmtGenExtraHeaders.cmake + DEPENDS gmt_keywords.txt gmt_keywords.d) + +add_custom_command (OUTPUT gmt_dimensions.h + COMMAND ${CMAKE_COMMAND} + -D GENERATE_COMMAND=gen_gmt_dimensions_h + -D CMAKE_MODULE_PATH=${CMAKE_MODULE_PATH} + -D GMT_SRC=${GMT_SOURCE_DIR} + -P ${CMAKE_MODULE_PATH}/GmtGenExtraHeaders.cmake + DEPENDS gmt_media_name.h gmt_pennames.h gmt_unique.h gmt_cpt_masters.h + gmt_keycases.h) + # depends on cached line numbers from these generated files: + +# autogenerated files target +add_custom_target (gen_gmt_headers DEPENDS ${GMT_GEN_HDRS}) + +# Configure header files to pass some of the CMake settings to the source code +configure_file (gmt_config.h.in gmt_config.h) +configure_file (psl_config.h.in psl_config.h) +configure_file (gmt_version.h.in gmt_version.h) +configure_file (isogmt.in isogmt${GMT_INSTALL_NAME_SUFFIX} @ONLY) +configure_file (gmt-config.in gmt-config${GMT_INSTALL_NAME_SUFFIX} @ONLY) + +# gmtprogram +set (GMT_PROGRAM ${GMT_SOURCE_DIR}/src/gmtprogram.c) + +# extra ugly definitions for triangle +set_source_files_properties (triangle.c + PROPERTIES + COMPILE_DEFINITIONS "NO_TIMER;TRILIBRARY;REDUCED;CDT_ONLY;ANSI_DECLARATORS") + +# libpslib +add_library (pslib + ${GMT_GEN_HDRS} + ${GMT_PSL_SRCS}) + +add_dependencies (pslib gen_gmt_headers) # make pslib after gen_gmt_headers + +if (HAVE_M_LIBRARY) + # link the math library + target_link_libraries (pslib m) +endif (HAVE_M_LIBRARY) + +if (HAVE_ZLIB) + # for DEFLATE encoding + target_link_libraries (pslib ${ZLIB_LIBRARIES}) +endif (HAVE_ZLIB) + +# set the build version (VERSION) and the API version (SOVERSION) +set_target_properties (pslib + PROPERTIES + OUTPUT_NAME postscriptlight + PREFIX "${LIB_PREFIX}" + IMPORT_PREFIX "${LIB_PREFIX}" + VERSION ${GMT_LIB_VERSION} + SOVERSION ${GMT_LIB_SOVERSION} + DEFINE_SYMBOL "LIBRARY_EXPORTS") + +# If a renaming of the gmtpslpsl dll has been set in ConfigUser.cmake +if (WIN32 AND PSL_DLL_RENAME) + set_target_properties (pslib PROPERTIES RUNTIME_OUTPUT_NAME ${PSL_DLL_RENAME}) +endif (WIN32 AND PSL_DLL_RENAME) + +if (BUILD_SUPPLEMENTS) + # supplement directories (only those, which are to be included in gmtlib) + # EXTRA_BUILD_DIRS are for testing new supplements that are not yet in + # subversion. See cmake/ConfigUserTemplate.cmake for setting this parameter. + set (GMT_SUPPL_DIRS geodesy gshhg img mgd77 potential segy seis + spotter x2sys ${EXTRA_BUILD_DIRS}) +endif (BUILD_SUPPLEMENTS) + +# path to all binary dirs (used to set PATH in test scripts) +set (GMT_BINARY_DIR_PATH "${CMAKE_CURRENT_BINARY_DIR}/\${CMAKE_CONFIG_TYPE:-.}") + +if (BUILD_SUPPLEMENTS) + # process supplement directories + if (UNIX) + set (CMAKE_SHARED_MODULE_SUFFIX .so) + endif (UNIX) + foreach (_dir ${GMT_SUPPL_DIRS}) + add_subdirectory (${_dir}) + list (APPEND GMT_BINARY_DIR_PATH + "${CMAKE_CURRENT_BINARY_DIR}/${_dir}/\${CMAKE_CONFIG_TYPE:-.}") + endforeach (_dir) + # supplement library files + get_subdir_var_files (GMT_SUPPL_LIB_SRCS LIB_SRCS ${GMT_SUPPL_DIRS}) + + # include supplement directories + foreach (_dir ${GMT_SUPPL_DIRS}) + include_directories (${CMAKE_CURRENT_BINARY_DIR}/${_dir}) + endforeach (_dir) + # libgmtsuppl + if (WIN32) + add_library (supplib + ${GMT_GEN_HDRS} + ${GMT_SUPPL_SRCS} + ${GMT_SUPPL_LIB_SRCS}) + else (WIN32) + add_library (supplib MODULE + ${GMT_GEN_HDRS} + ${GMT_SUPPL_SRCS} + ${GMT_SUPPL_LIB_SRCS}) + endif (WIN32) + + add_dependencies (supplib gen_gmt_headers) # make supplib after gen_gmt_headers + add_dependencies (supplib pslib) # make supplib after pslib + add_dependencies (supplib gmtlib) # make supplib after pslib + + # No SOVERSION & VERSION for a MODULE, only for SHARED libs + target_link_libraries (supplib + gmtlib + pslib) + + # Include any extra files that are listed in EXTRA_INCLUDE_GMTSUPPL defined in ConfigUser.cmake + # This include(s) will add new modules to the official GMT supplements + if (EXTRA_INCLUDE_GMTSUPPL) + foreach (_f ${EXTRA_INCLUDE_GMTSUPPL}) + include (${_f}) + endforeach(_f) + endif (EXTRA_INCLUDE_GMTSUPPL) + + set_target_properties (supplib + PROPERTIES + OUTPUT_NAME supplements + RUNTIME_OUTPUT_NAME supplements + LIBRARY_OUTPUT_DIRECTORY plugins + RUNTIME_OUTPUT_DIRECTORY plugins + PREFIX "" + LINK_FLAGS "${USER_GMTLIB_LINK_FLAGS}" + DEFINE_SYMBOL "LIBRARY_EXPORTS") + + if (WIN32 AND SUPP_DLL_RENAME) + set_target_properties (supplib PROPERTIES RUNTIME_OUTPUT_NAME ${SUPP_DLL_RENAME}) + endif (WIN32 AND SUPP_DLL_RENAME) + + if (HAVE_DLADDR AND HAVE_LIBDL) + # link the dynamic linking loader library + target_link_libraries (supplib dl) + endif (HAVE_DLADDR AND HAVE_LIBDL) + + if (HAVE_M_LIBRARY) + # link the math library + target_link_libraries (supplib m) + endif (HAVE_M_LIBRARY) + + # install target + install (TARGETS supplib + LIBRARY DESTINATION ${GMT_LIBDIR}/gmt${GMT_INSTALL_NAME_SUFFIX}/plugins # UNIX + COMPONENT Runtime + RUNTIME DESTINATION ${GMT_BINDIR}/gmt_plugins # Windows + COMPONENT Runtime) +endif (BUILD_SUPPLEMENTS) + +# Include any extra files that are listed in EXTRA_INCLUDE_NEWSUPPL defined in ConfigUser.cmake +# This include(s) will create new pluggins +if (EXTRA_INCLUDE_NEWSUPPL) + foreach (_f ${EXTRA_INCLUDE_NEWSUPPL}) + include (${_f}) + endforeach(_f) +endif (EXTRA_INCLUDE_NEWSUPPL) + + +# make UNIX PATH variable +string (REPLACE ";" ":" GMT_BINARY_DIR_PATH "${GMT_BINARY_DIR_PATH}") +set (GMT_BINARY_DIR_PATH ${GMT_BINARY_DIR_PATH} CACHE INTERNAL + "UNIX PATH to all binary dirs") + +# libgmt +add_library (gmtlib + ${GMT_GEN_HDRS} + ${GMT_LIB_SRCS} + ${GMT_PROGS_SRCS}) + +add_dependencies (gmtlib gen_gmt_headers) # make gmtlib after gen_gmt_headers +add_dependencies (gmtlib pslib) # make gmtlib after pslib + +target_link_libraries (gmtlib + ${NETCDF_LIBRARIES} + ${GMT_OPTIONAL_LIBRARIES} + pslib) + +if (HAVE_M_LIBRARY) + # link the math library + target_link_libraries (gmtlib m) +endif (HAVE_M_LIBRARY) + +# set the build version (VERSION) and the API version (SOVERSION) +set_target_properties (gmtlib + PROPERTIES + OUTPUT_NAME gmt + PREFIX "${LIB_PREFIX}" + IMPORT_PREFIX "${LIB_PREFIX}" + VERSION ${GMT_LIB_VERSION} + SOVERSION ${GMT_LIB_SOVERSION} + LINK_FLAGS "${USER_GMTLIB_LINK_FLAGS}" + DEFINE_SYMBOL "LIBRARY_EXPORTS") + +# If a renaming of the gmt dll has been set in ConfigUser.cmake +if (WIN32 AND GMT_DLL_RENAME) + set_target_properties (gmtlib PROPERTIES RUNTIME_OUTPUT_NAME ${GMT_DLL_RENAME}) +endif (WIN32 AND GMT_DLL_RENAME) + +if (HAVE_DLADDR AND HAVE_LIBDL) + # link the dynamic linking loader library + target_link_libraries (pslib dl) + target_link_libraries (gmtlib dl) +endif (HAVE_DLADDR AND HAVE_LIBDL) + +if (MSVC AND FFTW3_FOUND) + target_link_libraries (gmtlib ws2_32) +endif (MSVC AND FFTW3_FOUND) + +# build targets for standalone gmt target and demos +string (REPLACE ".c" "" _gmt_progs "gmt.c;${GMT_DEMOS_SRCS}") +foreach (_gmt_prog ${_gmt_progs}) + add_executable (${_gmt_prog} ${_gmt_prog}.c) + target_link_libraries (${_gmt_prog} gmtlib) +endforeach (_gmt_prog) + +add_executable (psldemo psldemo.h psldemo.c) +target_link_libraries (psldemo pslib) + +# Rename gmt target to prevent version clash +set_target_properties (gmt PROPERTIES OUTPUT_NAME gmt${GMT_INSTALL_NAME_SUFFIX}) + +# generate and install Mac/Windows debugging symbols +create_debug_sym (${GMT_BINDIR} gmt) +if (WIN32) + create_debug_sym (${GMT_BINDIR} gmtlib pslib) + create_debug_sym (${GMT_BINDIR}/gmt_plugins supplib) +else (WIN32) + create_debug_sym (${GMT_LIBDIR} gmtlib pslib) + create_debug_sym (${GMT_LIBDIR}/gmt${GMT_INSTALL_NAME_SUFFIX}/plugins supplib) +endif (WIN32) + +# gshhg_version +add_executable (gshhg_version gshhg_version.h gshhg_version.c) +set_target_properties (gshhg_version + PROPERTIES COMPILE_DEFINITIONS "STANDALONE") +target_link_libraries (gshhg_version ${NETCDF_LIBRARIES}) + +# script2verbatim for removing svn keywords, comments etc. from example scripts +add_executable (script2verbatim script2verbatim.c) + +if (BUILD_SUPPLEMENTS) + # Tests depend on GMT progs and supplements: + add_dependencies (check ${_gmt_progs} psldemo supplib) +else (BUILD_SUPPLEMENTS) + # Tests depend on GMT progs and supplements: + add_dependencies (check ${_gmt_progs} psldemo) +endif (BUILD_SUPPLEMENTS) + +if (MSVC) + # Disable automatic manifest generation + string(REGEX REPLACE "/MANIFEST[^ ]*( |$)" "" + CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}") + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /MANIFEST:NO") + + # To expand the command line arguments in Windows, see: + # http://msdn.microsoft.com/en-us/library/8bch7bkk.aspx + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} setargv.obj") +endif (MSVC) + +# add the install targets +install (TARGETS gmtlib pslib gmt + ARCHIVE DESTINATION ${GMT_LIBDIR} + COMPONENT Runtime + LIBRARY DESTINATION ${GMT_LIBDIR} + COMPONENT Runtime + RUNTIME DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) + +string (REPLACE ".c" "" _gmt_modules "${GMT_PROGS_SRCS}") +install_module_symlink (${_gmt_modules} ${GMT_COMPAT_MODULES}) + +# Install public headers +install (FILES gmt.h gmt_resources.h declspec.h + DESTINATION ${GMT_INCLUDEDIR} + COMPONENT Runtime) + +if (BUILD_DEVELOPER) + # Install Developer headers [These are clean and have no #define HAVE_* configuration] + install (FILES postscriptlight.h common_math.h common_string.h gmt_common.h gmt_constants.h gmt_contour.h + gmt_dcw.h gmt_decorate.h gmt_defaults.h gmt_error.h gmt_error_codes.h gmt_fft.h gmt_gdalread.h gmt_grd.h + gmt_grdio.h gmt_hash.h gmt_io.h gmt_macros.h gmt_memory.h gmt_modern.h gmt_nan.h gmt_notposix.h gmt_plot.h + gmt_private.h gmt_project.h gmt_prototypes.h gmt_psl.h gmt_shore.h gmt_symbol.h gmt_synopsis.h + gmt_texture.h gmt_time.h gmt_types.h gmt_dev.h gmt_customio.h gmt_hidden.h gmt_mb.h + gmt_core_module.h gmt_supplements_module.h compat/qsort.h + DESTINATION ${GMT_INCLUDEDIR} + COMPONENT Runtime) + install (FILES compat/qsort.h + DESTINATION ${GMT_INCLUDEDIR}/compat + COMPONENT Runtime) + # Install Configured Developer headers [These are produced by cmake from *.h.in files] + install (FILES ${PROJECT_BINARY_DIR}/src/config.h ${PROJECT_BINARY_DIR}/src/gmt_config.h + ${PROJECT_BINARY_DIR}/src/gmt_dimensions.h ${PROJECT_BINARY_DIR}/src/gmt_version.h + ${PROJECT_BINARY_DIR}/src/psl_config.h + DESTINATION ${GMT_INCLUDEDIR} + COMPONENT Runtime) +endif (BUILD_DEVELOPER) + +# symlink to gmt-wrapper in bindir and libdir: +if (UNIX AND GMT_INSTALL_NAME_SUFFIX) + get_target_property(_gmt_wrapper_name gmt OUTPUT_NAME) + install (CODE " + execute_process ( + COMMAND ${CMAKE_COMMAND} -E create_symlink + \"${_gmt_wrapper_name}\" \"\$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/${GMT_BINDIR}/gmt\") + ") +endif (UNIX AND GMT_INSTALL_NAME_SUFFIX) + +# install extra files +install (PROGRAMS + ${CMAKE_CURRENT_BINARY_DIR}/isogmt${GMT_INSTALL_NAME_SUFFIX} + ${CMAKE_CURRENT_BINARY_DIR}/gmt-config${GMT_INSTALL_NAME_SUFFIX} + DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) + +install (PROGRAMS gmtswitch + RENAME gmtswitch${GMT_INSTALL_NAME_SUFFIX} + DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) + +install (PROGRAMS gmt_shell_functions.sh + RENAME gmt_shell_functions${GMT_INSTALL_NAME_SUFFIX}.sh + DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) + +if (WIN32) + install (PROGRAMS + gmtswitch.bat + DESTINATION ${GMT_BINDIR} + COMPONENT Runtime) +endif (WIN32) + +# this prints out the final version of the compiler/linker flags +string (TOUPPER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_UPPER) +string(REGEX REPLACE "[ ]+" " " _using_cflags ${CMAKE_C_FLAGS} " " + ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE_UPPER}}) +message (STATUS "Using CFLAGS = '${_using_cflags}'") Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-linux-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-linux-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-linux-static.sh (revision 27955) @@ -0,0 +1,86 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.0.0" + +# Find libgfortran and libgcc so we do not have to hardcode them +# +# TODO: +# - Move this to etc/environment.sh +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1) + +GDAL_EXTRA_LIBS="-lstdc++" # Determined by running `$GDAL_ROOT/bin/gdal-config --dep-libs` then removing duplicate libs +NETCDF_EXTRA_LIBS="-lm -ldl -lz" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6.0/static/cmake/modules/FindNETCDF.cmake) + +# Environment +# +export CC=mpicc +export CURL_INCLUDE_DIRS="${CURL_ROOT}/include" +export CURL_LIBRARIES="${CURL_ROOT}/lib/libcurl.a;/usr/lib/x86_64-linux-gnu/libssl.a;/usr/lib/x86_64-linux-gnu/libcrypto.a" +export PREFIX="${ISSM_DIR}/externalpackages/gmt/install" # NOTE: Need to export this to be picked up by customized ConfigUser.cmake (see below). Set to location where external package should be installed. + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gmt-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source to 'src' directory +mv gmt-${VER}/* src +rm -rf gmt-${VER} + +# Copy custom configuration files +cp ./configs/6/static/linux/cmake/ConfigUser.static.cmake ./src/cmake/ConfigUser.cmake +cp ./configs/6/static/cmake/modules/FindGDAL.cmake ./src/cmake/modules +cp ./configs/6/static/cmake/modules/FindGSHHG.cmake ./src/cmake/modules +cp ./configs/6/static/cmake/modules/FindNETCDF.cmake ./src/cmake/modules +cp ./configs/6/static/src/CMakeLists.txt ./src/src + +# Configure +cd src +mkdir build +cd build + +# NOTE: +# - The CMake modules used to find and probe the BLAS and LAPACK libraries do +# not seem to handle the situation where BLAS_LIBRARY and LAPACK_LIBRARY are +# set but we are working with static libraries +# (see customized ConfigUser.static.cmake). Using BLAS_LIBRARIES and +# LAPACK_LIBRARIES is a workaround. +# +cmake \ + -DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \ + -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a" \ + -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \ + -DLAPACK_LIBRARIES="${LAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Make necessary link on RHEL +if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then + cd ${PREFIX} + ln -s ./lib64 ./lib +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-linux.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-linux.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-linux.sh (revision 27955) @@ -0,0 +1,72 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.4.0" + +# Find libgfortran so that we do not have to hardcode it. +# +# TODO: +# - Move this to etc/environment.sh +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} + +# Environment +# +export CC=mpicc +export PREFIX="${ISSM_DIR}/externalpackages/gmt/install" # NOTE: Need to export this to be picked up by customized ConfigUser.cmake (see below). Set to location where external package should be installed. + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gmt-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source to 'src' directory +mv gmt-${VER}/* src +rm -rf gmt-${VER} + +# Copy custom configuration files +cp ./configs/6/linux/cmake/ConfigUser.cmake ./src/cmake + +# Configure +cd src +mkdir build +cd build + +# NOTE: +# - There is a CMake variable named CURL_ROOT in src/cmake/ConfigUser.cmake +# that, ostensibly, allows for supplying the path to curl when it is in a +# non-standard location. That said, newer versions of CMake will ignore said +# variable and instead try to find curl itself. Passing in the two options +# below overrides this behavior. +# +cmake \ + -DBLAS_LIBRARIES="-L${BLAS_ROOT}/lib;-lfblas;-L${LIBGFORTRAN_ROOT};-lgfortran" \ + -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \ + -DCURL_LIBRARY="-L${CURL_ROOT}/lib;-lcurl" \ + -DLAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib;-lflapack;-L${LIBGFORTRAN_ROOT};-lgfortran" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Make necessary link on RHEL +if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then + cd ${PREFIX} + ln -s ./lib64 ./lib +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-mac-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-mac-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-mac-static.sh (revision 27955) @@ -0,0 +1,80 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.0.0" + +# Find libgfortran and libgcc so we do not have to hardcode them +# +# TODO: +# - Move this to etc/environment.sh +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) + +GDAL_EXTRA_LIBS="-lc++" # `$GDAL_ROOT/bin/gdal-config --dep-libs` does not report need to link to libc++ (see also customized configuration file ./configs/6/static/cmake/modules/FindGDAL.cmake) +NETCDF_EXTRA_LIBS="-lpthread -ldl -liconv" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6/static/cmake/modules/FindNETCDF.cmake) + +# Environment +# +export CC=mpicc +export CURL_INCLUDE_DIRS="${CURL_ROOT}/include" +export CURL_LIBRARIES="${CURL_ROOT}/lib/libcurl.a;${ZLIB_ROOT}/lib/libz.a" +export LDFLAGS="-lsqlite3 -framework CoreFoundation -framework Security" +export PREFIX="${ISSM_DIR}/externalpackages/gmt/install" # NOTE: Need to export this to be picked up by customized ConfigUser.cmake (see below). Set to location where external package should be installed. + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gmt-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source to 'src' directory +mv gmt-${VER}/* src +rm -rf gmt-${VER} + +# Copy custom configuration files +cp ./configs/6/static/mac/cmake/ConfigUser.static.cmake ./src/cmake/ConfigUser.cmake +cp ./configs/6/static/cmake/modules/FindGDAL.cmake ./src/cmake/modules +cp ./configs/6/static/cmake/modules/FindGSHHG.cmake ./src/cmake/modules +cp ./configs/6/static/cmake/modules/FindNETCDF.cmake ./src/cmake/modules + +# Configure +cd src +mkdir build +cd build + +# NOTE: +# - The CMake modules used to find and probe the BLAS and LAPACK libraries do +# not seem to handle the situation where BLAS_LIBRARY and LAPACK_LIBRARY are +# set but we are working with static libraries +# (see customized ConfigUser.static.cmake). Using BLAS_LIBRARIES and +# LAPACK_LIBRARIES is a workaround. +# +cmake \ + -DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \ + -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a" \ + -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \ + -DLAPACK_LIBRARIES="${LAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-mac.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-mac.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gmt/install-6-mac.sh (revision 27955) @@ -0,0 +1,68 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.4.0" + +# Find libgfortran so that we do not have to hardcode it. +# +# TODO: +# - Move this to etc/environment.sh +# +echo "Finding libgfortran..." +LIBGFORTRAN=$(find /usr /opt -name libgfortran* 2>/dev/null | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} + +# Environment +# +export CC=mpicc +export PREFIX="${ISSM_DIR}/externalpackages/gmt/install" # NOTE: Need to export this to be picked up by customized ConfigUser.cmake (see below). Set to location where external package should be installed. + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gmt-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source to 'src' directory +mv gmt-${VER}/* src +rm -rf gmt-${VER} + +# Copy custom configuration files +cp ./configs/6/mac/cmake/ConfigUser.cmake ./src/cmake +cp ./configs/6/mac/cmake/modules/ConfigCMake.cmake ./src/cmake/modules + +# Configure +cd src +mkdir build +cd build + +# NOTE: +# - There is a CMake variable named CURL_ROOT in src/cmake/ConfigUser.cmake +# that, ostensibly, allows for supplying the path to curl when it is in a +# non-standard location. That said, newer versions of CMake will ignore said +# variable and instead try to find curl itself. Passing in the two options +# below overrides this behavior. +# +cmake \ + -DBLAS_LIBRARIES="-L${BLAS_ROOT}/lib;-lfblas;-L${LIBGFORTRAN_ROOT};-lgfortran" \ + -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \ + -DCURL_LIBRARY="-L${CURL_ROOT}/lib;-lcurl" \ + -DLAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib;-lflapack;-L${LIBGFORTRAN_ROOT};-lgfortran" \ + -DLIBGFORTRAN_ROOT="${LIBGFORTRAN_ROOT}" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/googleearthtoolbox/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/googleearthtoolbox/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/googleearthtoolbox/install.sh (revision 27955) @@ -0,0 +1,8 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install + +#Download code: +svn checkout http://googleearthtoolbox.googlecode.com/svn/trunk/ install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gshhg/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gshhg/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gshhg/install.sh (revision 27955) @@ -0,0 +1,22 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="2.3.4" + +PREFIX="${ISSM_DIR}/externalpackages/gshhg/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} +mkdir -p ${PREFIX} + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gshhg-gmt-${VER}.tar.gz" "gshhg-gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gshhg-gmt-${VER}.tar.gz + +# Install +mv gshhg-gmt-${VER}/* ${PREFIX} Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/Makefile.am.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/Makefile.am.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/Makefile.am.patch (revision 27955) @@ -0,0 +1,27 @@ +--- Makefile.am 2011-04-14 08:13:48.000000000 -0700 ++++ Makefile.am_tmp 2012-11-12 14:54:02.000000000 -0800 +@@ -24,10 +24,22 @@ + noinst_HEADERS = templates_on.h templates_off.h build.h + + MINGW32_HOST = @MINGW32_HOST@ +-if MINGW32_HOST ++ ++# Origional 'Makefile.am' sets 'libgslcblas.la' as a requirement for ++#'libgsl.ls' only if the host system is detected to be MingW32. This ++# is unfortunate as 'libgsl.la' has undefined 'cblas' symbols the ++# result is linking errors at run time. This patch sets the 'cblas' ++# library as a requirement for linking 'libgsl'. ++# ++# Origional script: ++# ++# if MINGW32_HOST ++# libgsl_la_LIBADD += cblas/libgslcblas.la ++# libgsl_la_LDFLAGS += -no-undefined ++# endif ++ + libgsl_la_LIBADD += cblas/libgslcblas.la + libgsl_la_LDFLAGS += -no-undefined +-endif + + m4datadir = $(datadir)/aclocal + m4data_DATA = gsl.m4 Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/README =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/README (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/README (revision 27955) @@ -0,0 +1,1 @@ +GNU Scientfic Library, obtained from: http://www.gnu.org/software/gsl/ Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/finite.patch =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/finite.patch (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/finite.patch (revision 27955) @@ -0,0 +1,354 @@ +diff -ruN src/gsl_math.h src-mod/gsl_math.h +--- src/gsl_math.h 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/gsl_math.h 2014-05-27 18:47:26.000000000 -0700 +@@ -116,7 +116,7 @@ + #define GSL_SIGN(x) ((x) >= 0.0 ? 1 : -1) + + /* Return nonzero if x is a real number, i.e. non NaN or infinite. */ +-#define GSL_IS_REAL(x) (gsl_finite(x)) ++#define GSL_IS_REAL(x) (isfinite(x)) + + /* Definition of an arbitrary function with parameters */ + +diff -ruN src/integration/cquad.c src-mod/integration/cquad.c +--- src/integration/cquad.c 2011-05-01 11:46:28.000000000 -0700 ++++ src-mod/integration/cquad.c 2014-05-27 18:47:26.000000000 -0700 +@@ -235,7 +235,7 @@ + { + iv->fx[i] = GSL_FN_EVAL (f, m + xi[i] * h); + neval++; +- if (!finite (iv->fx[i])) ++ if (!isfinite (iv->fx[i])) + { + nans[nnans++] = i; + iv->fx[i] = 0.0; +@@ -319,7 +319,7 @@ + nnans = 0; + for (i = 0; i <= 32; i += skip[d]) + { +- if (!finite (iv->fx[i])) ++ if (!isfinite (iv->fx[i])) + { + nans[nnans++] = i; + iv->fx[i] = 0.0; +@@ -444,7 +444,7 @@ + nnans = 0; + for (i = 0; i <= 32; i += skip[0]) + { +- if (!finite (ivl->fx[i])) ++ if (!isfinite (ivl->fx[i])) + { + nans[nnans++] = i; + ivl->fx[i] = 0.0; +@@ -510,7 +510,7 @@ + nnans = 0; + for (i = 0; i <= 32; i += skip[0]) + { +- if (!finite (ivr->fx[i])) ++ if (!isfinite (ivr->fx[i])) + { + nans[nnans++] = i; + ivr->fx[i] = 0.0; +diff -ruN src/linalg/balance.c src-mod/linalg/balance.c +--- src/linalg/balance.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/linalg/balance.c 2014-05-27 18:47:27.000000000 -0700 +@@ -54,7 +54,7 @@ + + double f = 1.0; + +- if (s == 0.0 || !gsl_finite(s)) ++ if (s == 0.0 || !isfinite(s)) + { + gsl_vector_set (D, j, f); + continue; +diff -ruN src/min/min.h src-mod/min/min.h +--- src/min/min.h 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/min/min.h 2014-05-27 18:47:27.000000000 -0700 +@@ -20,6 +20,6 @@ + #define SAFE_FUNC_CALL(f, x, yp) \ + do { \ + *yp = GSL_FN_EVAL(f,x); \ +- if (!gsl_finite(*yp)) \ ++ if (!isfinite(*yp)) \ + GSL_ERROR("computed function value is infinite or NaN", GSL_EBADFUNC); \ + } while (0) +diff -ruN src/multimin/simplex.c src-mod/multimin/simplex.c +--- src/multimin/simplex.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/multimin/simplex.c 2014-05-27 18:47:27.000000000 -0700 +@@ -122,7 +122,7 @@ + we finish the contraction (and do not abort) to allow the user + to handle the situation */ + +- if(!gsl_finite(newval)) ++ if(!isfinite(newval)) + { + status = GSL_EBADFUNC; + } +@@ -260,7 +260,7 @@ + + val = GSL_MULTIMIN_FN_EVAL (f, x); + +- if (!gsl_finite(val)) ++ if (!isfinite(val)) + { + GSL_ERROR("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -283,7 +283,7 @@ + gsl_vector_set (xtemp, i, val); + val = GSL_MULTIMIN_FN_EVAL (f, xtemp); + +- if (!gsl_finite(val)) ++ if (!isfinite(val)) + { + GSL_ERROR("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -374,14 +374,14 @@ + + val = nmsimplex_move_corner (-1.0, state, hi, xc, f); + +- if (gsl_finite(val) && val < gsl_vector_get (y1, lo)) ++ if (isfinite(val) && val < gsl_vector_get (y1, lo)) + { + + /* reflected point becomes lowest point, try expansion */ + + val2 = nmsimplex_move_corner (-2.0, state, hi, xc2, f); + +- if (gsl_finite(val2) && val2 < gsl_vector_get (y1, lo)) ++ if (isfinite(val2) && val2 < gsl_vector_get (y1, lo)) + { + gsl_matrix_set_row (x1, hi, xc2); + gsl_vector_set (y1, hi, val2); +@@ -397,9 +397,9 @@ + or + we got a non-finite (illegal) function value */ + +- else if (!gsl_finite(val) || val > gsl_vector_get (y1, s_hi)) ++ else if (!isfinite(val) || val > gsl_vector_get (y1, s_hi)) + { +- if (gsl_finite(val) && val <= gsl_vector_get (y1, hi)) ++ if (isfinite(val) && val <= gsl_vector_get (y1, hi)) + { + + /* if trial point is better than highest point, replace +@@ -413,7 +413,7 @@ + + val2 = nmsimplex_move_corner (0.5, state, hi, xc2, f); + +- if (gsl_finite(val2) && val2 <= gsl_vector_get (y1, hi)) ++ if (isfinite(val2) && val2 <= gsl_vector_get (y1, hi)) + { + gsl_matrix_set_row (state->x1, hi, xc2); + gsl_vector_set (y1, hi, val2); +diff -ruN src/multimin/simplex2.c src-mod/multimin/simplex2.c +--- src/multimin/simplex2.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/multimin/simplex2.c 2014-05-27 18:47:27.000000000 -0700 +@@ -171,7 +171,7 @@ + we finish the contraction (and do not abort) to allow the user + to handle the situation */ + +- if (!gsl_finite (newval)) ++ if (!isfinite (newval)) + { + status = GSL_EBADFUNC; + } +@@ -367,7 +367,7 @@ + + val = GSL_MULTIMIN_FN_EVAL (f, x); + +- if (!gsl_finite (val)) ++ if (!isfinite (val)) + { + GSL_ERROR ("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -394,7 +394,7 @@ + val = GSL_MULTIMIN_FN_EVAL (f, xtemp); + } + +- if (!gsl_finite (val)) ++ if (!isfinite (val)) + { + GSL_ERROR ("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -477,13 +477,13 @@ + + val = try_corner_move (-1.0, state, hi, xc, f); + +- if (gsl_finite (val) && val < gsl_vector_get (y1, lo)) ++ if (isfinite (val) && val < gsl_vector_get (y1, lo)) + { + /* reflected point is lowest, try expansion */ + + val2 = try_corner_move (-2.0, state, hi, xc2, f); + +- if (gsl_finite (val2) && val2 < gsl_vector_get (y1, lo)) ++ if (isfinite (val2) && val2 < gsl_vector_get (y1, lo)) + { + update_point (state, hi, xc2, val2); + } +@@ -492,12 +492,12 @@ + update_point (state, hi, xc, val); + } + } +- else if (!gsl_finite (val) || val > gsl_vector_get (y1, s_hi)) ++ else if (!isfinite (val) || val > gsl_vector_get (y1, s_hi)) + { + /* reflection does not improve things enough, or we got a + non-finite function value */ + +- if (gsl_finite (val) && val <= gsl_vector_get (y1, hi)) ++ if (isfinite (val) && val <= gsl_vector_get (y1, hi)) + { + /* if trial point is better than highest point, replace + highest point */ +@@ -509,7 +509,7 @@ + + val2 = try_corner_move (0.5, state, hi, xc2, f); + +- if (gsl_finite (val2) && val2 <= gsl_vector_get (y1, hi)) ++ if (isfinite (val2) && val2 <= gsl_vector_get (y1, hi)) + { + update_point (state, hi, xc2, val2); + } +@@ -605,7 +605,7 @@ + + val = GSL_MULTIMIN_FN_EVAL (f, x); + +- if (!gsl_finite (val)) ++ if (!isfinite (val)) + { + GSL_ERROR ("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -669,7 +669,7 @@ + + val = GSL_MULTIMIN_FN_EVAL (f, &r_i.vector); + +- if (!gsl_finite (val)) ++ if (!isfinite (val)) + { + GSL_ERROR ("non-finite function value encountered", GSL_EBADFUNC); + } +diff -ruN src/roots/newton.c src-mod/roots/newton.c +--- src/roots/newton.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/roots/newton.c 2014-05-27 18:47:27.000000000 -0700 +@@ -83,12 +83,12 @@ + state->f = f_new ; + state->df = df_new ; + +- if (!gsl_finite(f_new)) ++ if (!isfinite(f_new)) + { + GSL_ERROR ("function value is not finite", GSL_EBADFUNC); + } + +- if (!gsl_finite (df_new)) ++ if (!isfinite (df_new)) + { + GSL_ERROR ("derivative value is not finite", GSL_EBADFUNC); + } +diff -ruN src/roots/roots.h src-mod/roots/roots.h +--- src/roots/roots.h 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/roots/roots.h 2014-05-27 18:47:27.000000000 -0700 +@@ -28,7 +28,7 @@ + #define SAFE_FUNC_CALL(f, x, yp) \ + do { \ + *yp = GSL_FN_EVAL(f,x); \ +- if (!gsl_finite(*yp)) \ ++ if (!isfinite(*yp)) \ + GSL_ERROR("function value is not finite", GSL_EBADFUNC); \ + } while (0) + +diff -ruN src/roots/secant.c src-mod/roots/secant.c +--- src/roots/secant.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/roots/secant.c 2014-05-27 18:47:27.000000000 -0700 +@@ -94,12 +94,12 @@ + state->f = f_new ; + state->df = df_new ; + +- if (!gsl_finite (f_new)) ++ if (!isfinite (f_new)) + { + GSL_ERROR ("function value is not finite", GSL_EBADFUNC); + } + +- if (!gsl_finite (df_new)) ++ if (!isfinite (df_new)) + { + GSL_ERROR ("derivative value is not finite", GSL_EBADFUNC); + } +diff -ruN src/roots/steffenson.c src-mod/roots/steffenson.c +--- src/roots/steffenson.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/roots/steffenson.c 2014-05-27 18:47:27.000000000 -0700 +@@ -105,7 +105,7 @@ + state->f = f_new ; + state->df = df_new ; + +- if (!gsl_finite (f_new)) ++ if (!isfinite (f_new)) + { + GSL_ERROR ("function value is not finite", GSL_EBADFUNC); + } +@@ -126,7 +126,7 @@ + *root = x_1 - u * u / v ; /* accelerated value */ + } + +- if (!gsl_finite (df_new)) ++ if (!isfinite (df_new)) + { + GSL_ERROR ("derivative value is not finite", GSL_EBADFUNC); + } +diff -ruN src/specfunc/hyperg_U.c src-mod/specfunc/hyperg_U.c +--- src/specfunc/hyperg_U.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/specfunc/hyperg_U.c 2014-05-27 18:47:28.000000000 -0700 +@@ -524,7 +524,7 @@ + t_err = a0_err + b0_err; + dchu_val += t_val; + dchu_err += t_err; +- if(!finite(t_val) || fabs(t_val) < EPS*fabs(dchu_val)) break; ++ if(!isfinite(t_val) || fabs(t_val) < EPS*fabs(dchu_val)) break; + } + + result->val = dchu_val; +diff -ruN src/sys/ldfrexp.c src-mod/sys/ldfrexp.c +--- src/sys/ldfrexp.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/sys/ldfrexp.c 2014-05-27 18:47:28.000000000 -0700 +@@ -60,7 +60,7 @@ + *e = 0; + return 0.0; + } +- else if (!finite (x)) ++ else if (!isfinite (x)) + { + *e = 0; + return x; +@@ -85,7 +85,7 @@ + + f = x * pow (2.0, -ei); + +- if (!finite (f)) ++ if (!isfinite (f)) + { + /* This should not happen */ + *e = 0; +diff -ruN src/test/results.c src-mod/test/results.c +--- src/test/results.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/test/results.c 2014-05-27 18:47:28.000000000 -0700 +@@ -24,7 +24,10 @@ + #include + #include + #include ++#include ++#define STDC_HEADERS + ++/* + #if HAVE_VPRINTF + #ifdef STDC_HEADERS + #include +@@ -32,6 +35,7 @@ + #include + #endif + #endif ++*/ + + #include + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-android.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-android.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-android.sh (revision 27955) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + +source $ANDROID_DIR/android_aux.sh + +if [[ $step == "1" || $step == "0" ]]; then + + #Some cleanup + rm -rf src install gsl-1.15 + mkdir src install + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gsl-1.' 'gsl-1.15.tar.gz' + + #Untar + tar -zxvf gsl-1.15.tar.gz + + #Move gsl into src directory + mv gsl-1.15/* src + rm -rf gsl-1.15 +fi + +#Configure gsl +if [[ $step == "2" || $step == "0" ]]; then + cd src + + patch Makefile.am < ./../Makefile.am.patch + + autoreconf -if + + ./configure \ + --build="i386-apple-darwin10.8.0" \ + --host=$host_triplet \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" +fi + +#Compile gsl +if [[ $step == "3" || $step == "0" ]]; then + cd $ISSM_DIR/externalpackages/gsl/src + + if [ $# -eq 0 ]; then + make + else + make -j $j + fi + + make install +fi + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-greenplanet.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-greenplanet.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-greenplanet.sh (revision 27955) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-ios.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-ios.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-ios.sh (revision 27955) @@ -0,0 +1,63 @@ +#!/bin/bash +set -eu + +source $ANDROID_DIR/android_aux.sh +export DEVROOT="/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/" +export SDKROOT="$DEVROOT/SDKs/iPhoneOS6.0.sdk/" +export CC="$DEVROOT/usr/bin/gcc -arch armv7" +export CFLAGS="-O -arch armv7 -isysroot $SDKROOT" +export CXXFLAGS="-O -arch armv7 -isysroot $SDKROOT" +export CPP=$DEVROOT/usr/bin/cpp +export CXX=$DEVROOT/usr/bin/g++ +export AR=$DEVROOT/usr/bin/ar +export AS=$DEVROOT/usr/bin/as +export LIBTOOL=$DEVROOT/usr/bin/libtool +export LDFLAGS="-lstdc++ -arch armv7 -isysroot $SDKROOT" +export STRIP=$DEVROOT/usr/bin/strip +export RANLIB=$DEVROOT/usr/bin/ranlib + + +if [[ $step == "1" || $step == "0" ]]; then + + #Some cleanup + rm -rf src install gsl-1.15 + mkdir src install + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gsl-1.' 'gsl-1.15.tar.gz' + + #Untar + tar -zxvf gsl-1.15.tar.gz + + #Move gsl into src directory + mv gsl-1.15/* src + rm -rf gsl-1.15 +fi + +#Configure gsl +if [[ $step == "2" || $step == "0" ]]; then + cd src + + patch Makefile.am < ./../Makefile.am.patch + + autoreconf -if + + ./configure \ + --build="i386-apple-darwin10.8.0" \ + --host="arm-apple-darwin10" \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" +fi + +#Compile gsl +if [[ $step == "3" || $step == "0" ]]; then + cd $ISSM_DIR/externalpackages/gsl/src + + if [ $# -eq 0 ]; then + make + else + make -j $j + fi + + make install +fi + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-javascript.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-javascript.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-javascript.sh (revision 27955) @@ -0,0 +1,52 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="2.7" + +PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed + +## Environment +# +export CC=emcc +export CXX=em++ +export AR=emar +export RANLIB=emranlib +#export EMCC_DEBUG=1 # Uncomment to enable debugging + +# Source Emscripten environment +source ${EMSCRIPTEN_ROOT}/emsdk_env.sh + +# Issue with variadic function signatures. +#export CFLAGS=-DSTDC_HEADERS + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gsl-${VER}.tar.gz" "gsl-${VER}.tar.gz" + +# Unpack source +tar -zxvf gsl-${VER}.tar.gz + +# Move source to 'src' directory +mv gsl-${VER}/* src +rm -rf gsl-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-shared \ + +#Compile gsl +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-pleiades.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-pleiades.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-pleiades.sh (revision 27955) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-static.sh (revision 27955) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="2.7" + +PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gsl-${VER}.tar.gz" "gsl-${VER}.tar.gz" + +# Unpack source +tar -zxvf gsl-${VER}.tar.gz + +# Move source to 'src' directory +mv gsl-${VER}/* src +rm -rf gsl-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-shared \ + --with-pic + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-walgreen.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-walgreen.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install-walgreen.sh (revision 27955) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +export CC=icc +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gsl/install.sh (revision 27955) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="2.7" + +PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gsl-${VER}.tar.gz" "gsl-${VER}.tar.gz" + +# Unpack source +tar -zxvf gsl-${VER}.tar.gz + +# Move source to 'src' directory +mv gsl-${VER}/* src +rm -rf gsl-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-static + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/gslib/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/gslib/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/gslib/install.sh (revision 27955) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gslib90_ls.tar.gz' 'gslib90_ls.tar.gz' + +#Untar +tar -zxvf gslib90_ls.tar.gz + +#Move gslib into install directory +mv gslib90/* install +rm -rf gslib90 + +#Change compiler to gfortran +cd install +cat Makefile | sed -e "s/FC=g95/FC=gfortran/g" > Makefile.bak +mv Makefile.bak Makefile +cat gslib/Makefile | sed -e "s/FC=g95/FC=gfortran/g" > Makefile.bak +mv Makefile.bak gslib/Makefile +make Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/h5py/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/h5py/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/h5py/install.sh (revision 27955) @@ -0,0 +1,25 @@ +#!/bin/bash +set -eu + +#needed further along +export HDF5_DIR=$ISSM_DIR/externalpackages/hdf5/install + +#Some cleanup +rm -rf install h5py-2.0.1 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/h5py-2.0.1.tar.gz' 'h5py-2.0.1.tar.gz' + +#Untar +tar -zxvf h5py-2.0.1.tar.gz + +#Move h5py to install directory +rm -rf install/* +mv h5py-2.0.1/* install/ +rm -rf h5py-2.0.1 + +#Configure and compile +cd install +python setup.py build –hdf5=$ISSM_DIR/externalpackages/hdf5/install +python setup.py install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-parallel-static.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-parallel-static.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-parallel-static.sh (revision 27955) @@ -0,0 +1,47 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="1.8.23" + +PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed + +## Environnment +# +export CC=mpicc + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/hdf5-${VER}.tar.gz" "hdf5-${VER}.tar.gz" + +# Untar source +tar -zxvf hdf5-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv hdf5-${VER}/* src/ +rm -rf hdf5-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-shared \ + --enable-parallel \ + --with-zlib="${ZLIB_ROOT}" \ + --enable-hl + +# Compile and install +# +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-parallel-with_tests.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-parallel-with_tests.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-parallel-with_tests.sh (revision 27955) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="1.8.23" + +PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed + +## Environnment +# +export CC=mpicc + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/hdf5-${VER}.tar.gz" "hdf5-${VER}.tar.gz" + +# Untar source +tar -zxvf hdf5-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv hdf5-${VER}/* src/ +rm -rf hdf5-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-static \ + --enable-parallel \ + --with-zlib="${ZLIB_ROOT}" \ + --enable-hl + +# Compile, test, and install +# +if [ $# -eq 0 ]; then + make + make check + make install +else + make -j $1 + make -j $1 check + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-parallel.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-parallel.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-parallel.sh (revision 27955) @@ -0,0 +1,47 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="1.8.23" + +PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed + +## Environnment +# +export CC=mpicc + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/hdf5-${VER}.tar.gz" "hdf5-${VER}.tar.gz" + +# Untar source +tar -zxvf hdf5-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv hdf5-${VER}/* src/ +rm -rf hdf5-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-static \ + --enable-parallel \ + --with-zlib="${ZLIB_ROOT}" \ + --enable-hl + +# Compile and install +# +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-with_tests.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-with_tests.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1-with_tests.sh (revision 27955) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="1.8.23" + +PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/hdf5-${VER}.tar.gz" "hdf5-${VER}.tar.gz" + +# Untar source +tar -zxvf hdf5-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv hdf5-${VER}/* src/ +rm -rf hdf5-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-static \ + --with-zlib="${ZLIB_ROOT}" \ + --enable-hl + +# Compile, test, and install +# +if [ $# -eq 0 ]; then + make + make check + make install +else + make -j $1 + make -j $1 check + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/hdf5/install-1.sh (revision 27955) @@ -0,0 +1,42 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="1.8.23" + +PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/hdf5-${VER}.tar.gz" "hdf5-${VER}.tar.gz" + +# Untar source +tar -zxvf hdf5-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv hdf5-${VER}/* src/ +rm -rf hdf5-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --disable-static \ + --with-zlib="${ZLIB_ROOT}" \ + --enable-hl + +# Compile and install +# +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/howatmask/enviread.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/howatmask/enviread.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/howatmask/enviread.m (revision 27955) @@ -0,0 +1,323 @@ +function I=enviread(varargin) +%enviread: Read binary image files using ENVI header information +% +%I=enviread('filename') where the header file is named filename.hdr +%and exists in the same directory. Otherwise use +% +%I=enviread('filename','hdrfilename') +% +%The output structure I contains fields I.x, I.y, I.z and I.info +%containing the x-coordinate vector, y-coordinate vector, +%images data and header info, respectively. I.z will be in whatever +%number format (double, int, etc.) as in the envi file. +% +%Original version by Ian Howat, Ohio State Universtiy, ihowat@gmail.com +%Thanks to Yushin Ahn and Ray Jung +% +%% Current version 3 - adding subsetting feature to read only parts of +%% files. + +file=varargin{1}; +hdrfile=[deblank(file),'.hdr']; +info=read_envihdr(hdrfile); +sub = [1, info.samples, 1, info.lines]; +if nargin==2 + if varargin{2}=='date' + [pathstr, name, ext, versn] = fileparts(file); + info.hdrname=hdrfile; + info.ipath=pathstr; + info.iname=name; + info.ipname=file; + info.year =name(1:4); + info.month=name(5:6); + info.day =name(7:8); + info.date =name(1:8); + info.sfname=name(1:14); + info.datenum=datenum(str2double(info.year),... + str2double(info.month),str2double(info.day)); + end +end + +% subset +if nargin == 3; + if strcmp(varargin{2},'pixel_subset'); + sub = varargin{3}; + elseif strcmp(varargin{2},'map_subset'); + sub = varargin{3}; + subx = (sub(1:2)-info.map_info.mapx)./info.map_info.dx; + suby = (info.map_info.mapy - sub(3:4))./info.map_info.dy; + subx = round(subx); + suby = round(suby); + + subx(subx < 1) = 1; + suby(suby < 1) = 1; + subx(subx > info.samples) = info.samples; + suby(suby > info.lines) = info.lines; + + sub = [subx,suby]; + end +end + +sub(1:2) = sort(sub(1:2)); +sub(3:4) = sort(sub(3:4)); + + +%% Make geo-location vectors +if isfield(info.map_info,'mapx') && isfield(info.map_info,'mapy') + xi = info.map_info.image_coords(1); + yi = info.map_info.image_coords(2); + xm = info.map_info.mapx; + ym = info.map_info.mapy; + %adjust points to corner (1.5,1.5) + if yi > 1.5 + ym = ym + ((yi*info.map_info.dy)-info.map_info.dy); + end + if xi > 1.5 + xm = xm - ((xi*info.map_info.dy)-info.map_info.dx); + end + + I.x = xm + ((0:info.samples-1).*info.map_info.dx); + I.y = ym - ((0:info.lines-1).* info.map_info.dy); + %I.x = xm + (subE(1):subE(2)-1).*info.map_info.dx; + %I.y = ym - (subE(3):subE(4)-1).*info.map_info.dy; +end + + +I.x = I.x(sub(1):sub(2)); +I.y = I.y(sub(3):sub(4)); + + +%% Set binary format parameters +switch info.byte_order + case {0} + machine = 'ieee-le'; + case {1} + machine = 'ieee-be'; + otherwise + machine = 'n'; +end +switch info.data_type + case {1} + format = 'uint8'; + case {2} + format= 'int16'; + case{3} + format= 'int32'; + case {4} + format= 'single'; + case {5} + format= 'double'; + case {6} + disp('>> Sorry, Complex (2x32 bits)data currently not supported'); + disp('>> Importing as double-precision instead'); + format= 'double'; + case {9} + error('Sorry, double-precision complex (2x64 bits) data currently not supported'); + case {12} + format= 'uint16'; + case {13} + format= 'uint32'; + case {14} + format= 'int64'; + case {15} + format= 'uint64'; + otherwise + error(['File type number: ',num2str(dtype),' not supported']); +end + +%% file read +% Version 2 code by Yushin Ahn - replaces resize calls with loops (except +% for BIP formats) to work on big arrays. + + %tmp=zeros(info.lines, info.samples,info.bands,format); + tmp=zeros(sub(4)-sub(3)+1,sub(2)-sub(1)+1,info.bands,format); + fid=fopen(file,'r'); + +switch lower(info.interleave) + + case {'bsq'} + % Format: + % [Band 1] + % R1: C1, C2, C3, ... + % R2: C1, C2, C3, ... + % ... + % RN: C1, C2, C3, ... + % + % [Band 2] + % ... + % [Band N] + +%% Old Script w/out subsetting +% for b=1:info.bands +% for i=1:info.lines +% t=fread(fid,info.samples,format); +% tmp(i,:,b)=t; +% end +% end + +%% New Subsetting script - IMH + offset1=(sub(3)-1)*info.samples; + fseek(fid,offset1,'bof'); + for b=1:info.bands + for i=sub(3):sub(4) + t=fread(fid,info.samples,format); + %if i >= sub(3) && i <= sub(4) + tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2)); + %end + end + offset2 = info.samples*info.lines*b+offset1; + fseek(fid,offset2,'bof'); + end + + case {'bil'} + % Format: + % [Row 1] + % B1: C1, C2, C3, ... + % B2: C1, C2, C3, ... + % + % ... + % [Row N] + +% for i=1:info.lines +% for b=1:info.bands +% t=fread(fid,info.samples,format); +% tmp(i,:,b)=t; +% end +% end + +%% New Subsetting script - IMH + for i=1:sub(4) + for b=1:info.bands + t=fread(fid,info.samples,format); + if i >= sub(3) && i <= sub(4) + tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2)); + end + end + end + + + + case {'bip'} + + % Row 1 + % C1: B1 B2 B3, ... + % C2: B1 B2 B3, ... + % ... + % Row N + %This section authored by Ray Jung, APL-Johns Hopkins + Z = fread(fid,info.samples*info.lines*info.bands,format,0,machine); + Z = reshape(Z, [info.bands, info.samples, info.lines]); + + for k=1:info.bands + tmp(:,:,k) = squeeze(Z(k,:,:))'; + end +end +fclose(fid); + +% tmp2=zeros(subE(4)-subE(3)+1,subE(2)-subE(1)+1,info.bands,format); +% [a,b]=size(tmp); +% for i=1:info.bands +% tmp2(xoff+1:a,yoff+1:b,1)=tmp(1:a,1:b,1); +% end +I.z=tmp; +I.info =info; + + + +%% sub function +function info = read_envihdr(hdrfile) +% READ_ENVIHDR read and return ENVI image file header information. +% INFO = READ_ENVIHDR('HDR_FILE') reads the ASCII ENVI-generated image +% header file and returns all the information in a structure of +% parameters. +% +% Example: +% >> info = read_envihdr('my_envi_image.hdr') +% info = +% description: [1x101 char] +% samples: 658 +% lines: 749 +% bands: 3 +% header_offset: 0 +% file_type: 'ENVI Standard' +% data_type: 4 +% interleave: 'bsq' +% sensor_type: 'Unknown' +% byte_order: 0 +% map_info: [1x1 struct] +% projection_info: [1x102 char] +% wavelength_units: 'Unknown' +% pixel_size: [1x1 struct] +% band_names: [1x154 char] +% +% NOTE: This function is used by ENVIREAD to import data. +% Ian M. Howat, Applied Physics Lab, University of Washington +% ihowat@apl.washington.edu +% Version 1: 19-Jul-2007 00:50:57 +fid = fopen(hdrfile); +while fid; + line = fgetl(fid); + if line == -1 + break + else + eqsn = findstr(line,'='); + if ~isempty(eqsn) + param = strtrim(line(1:eqsn-1)); + param(findstr(param,' ')) = '_'; + value = strtrim(line(eqsn+1:end)); + if isempty(str2num(value)) + if ~isempty(findstr(value,'{')) && isempty(findstr(value,'}')) + while isempty(findstr(value,'}')) + line = fgetl(fid); + value = [value,strtrim(line)]; + end + end + eval(['info.',param,' = ''',value,''';']) + else + eval(['info.',param,' = ',value,';']) + end + end + end +end +fclose(fid); + +if isfield(info,'map_info') + line = info.map_info; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.map_info = []; + info.map_info.projection = line{1}; + info.map_info.image_coords = [str2num(line{2}),str2num(line{3})]; + info.map_info.mapx = str2num(line{4}); + info.map_info.mapy = str2num(line{5}); + info.map_info.dx = str2num(line{6}); + info.map_info.dy = str2num(line{7}); + if length(line) == 9 + info.map_info.datum = line{8}; + info.map_info.units = line{9}(7:end); + elseif length(line) == 11 + info.map_info.zone = str2num(line{8}); + info.map_info.hemi = line{9}; + info.map_info.datum = line{10}; + info.map_info.units = line{11}(7:end); + end +end + +if isfield(info,'pixel_size') + line = info.pixel_size; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.pixel_size = []; + info.pixel_size.x = str2num(line{1}); + info.pixel_size.y = str2num(line{2}); + info.pixel_size.units = line{3}(7:end); +end + +%% +function A = split(s,d) +%This function by Gerald Dalley (dalleyg@mit.edu), 2004 +A = {}; +while (length(s) > 0) + [t,s] = strtok(s,d); + A = {A{:}, t}; +end Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/howatmask/subsetGimpIceMask.m =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/howatmask/subsetGimpIceMask.m (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/howatmask/subsetGimpIceMask.m (revision 27955) @@ -0,0 +1,282 @@ +function [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1) +% subsetGimpIceMask samples mask tiles for a given coordinate range +% +% [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1) returns the mask in array M +% with map vectors Mx and My within the bounding box specified by +% coordinate ranges x0 < x1 and y0 < y1. The function finds tiles +% overlappimg the box, samples the tiles and mosaics the samples into one +% array. +% +% Example: Specify the following coordinate range and map the result. +% >> x0 = 260000; x1 = 377900; y0 = -2609400; y1 = -2543000; +% >> [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1); +% >> imagesc(Mx,My,M); axis equal xy; colormap gray; +% +% Ian Howat, Ohio State University, ihowat@gmail.com +% The Greenland Ice Mapping Project is funded by NASA. +% $Revision: 0 $ $Date: 09-Nov-2011 14:48:24$ +% + +%make coordinate index +nt = 6; +ps = 15; +xn0 = -640000 ; %xn1 = 857550; +yn0 = -3313350; %yn1 = -665450; + +c = 16640; +r = 29420; + +x = xn0:ps:xn0 + c.*ps.*nt; +y = yn0:ps:yn0 + r.*ps.*nt; + +X = cell(1,nt); +Y = cell(nt,1); +i=1; +for i=1:nt; + + X{i} = [x((i-1)*c+1),x(i*c)]; + Y{i} = [y((i-1)*r+1),y(i*r)]; + +end + +X = repmat(X,[nt,1]); +Y = repmat(Y,[1,nt]); +N = cell(size(X)); + + +i=1; +for i=1:numel(X) + N{i} = [[X{i}(1),Y{i}(2)];... + [X{i}(2),Y{i}(2)];... + [X{i}(2),Y{i}(1)];... + [X{i}(1),Y{i}(1)]]; +end + + +%% find overlapping tiles +p = [[x0,y1];[x1,y1];[x1,y0];[x0,y0]]; + +n = zeros(size(N)); + +i=1; +for i=1:numel(N) + n(i) = any(inpolygon(p(:,1),p(:,2),N{i}(:,1),N{i}(:,2))); +end +i=1; +for i=1:size(n,1) + n(i,find(n(i,:),1,'first'):find(n(i,:),1,'last')) = 1; +end +i=1; +for i=1:size(n,2) + n(find(n(:,i),1,'first'):find(n(:,i),1,'last'),i) = 1; +end + +[i,j] = find(n); +row = (min(i):max(i))'; +col = min(j):max(j); +col = repmat(col,[length(row),1])-1; +row = repmat(row,[1,size(col,2)])-1; + +% make output cells +M = cell(size(row)); +Mx = M; +My = M; + +% read each overlapping file and populate output cell +j=1; +for j=1:size(col,2) + i=1; + for i=1:size(row,1); + m = enviread(['GimpIceMask_15m_tile',num2str(col(i,j)),'_',... + num2str(row(i,j))],'map_subset',[x0 x1 y0 y1]); + M{end-i+1,j} = m.z; + Mx{end-i+1,j} = m.x; + My{end-i+1,j} = m.y'; + + + end +end + +% put together cells +M = cell2mat(M); +Mx =cell2mat(Mx(1,:)); +My =cell2mat(My(:,1)); + + +function I=enviread(varargin) + +file=varargin{1}; +hdrfile=[deblank(file),'.hdr']; +info=read_envihdr(hdrfile); +sub = [1, info.samples, 1, info.lines]; + +sub = varargin{3}; +subx = (sub(1:2)-info.map_info.mapx)./info.map_info.dx; +suby = (info.map_info.mapy - sub(3:4))./info.map_info.dy; +subx = round(subx); +suby = round(suby); + +subx(subx < 1) = 1; +suby(suby < 1) = 1; +subx(subx > info.samples) = info.samples; +suby(suby > info.lines) = info.lines; + +sub = [subx,suby]; + +sub(1:2) = sort(sub(1:2)); +sub(3:4) = sort(sub(3:4)); + +%% Make geo-location vectors +if isfield(info.map_info,'mapx') && isfield(info.map_info,'mapy') + xi = info.map_info.image_coords(1); + yi = info.map_info.image_coords(2); + xm = info.map_info.mapx; + ym = info.map_info.mapy; + %adjust points to corner (1.5,1.5) + if yi > 1.5 + ym = ym + ((yi*info.map_info.dy)-info.map_info.dy); + end + if xi > 1.5 + xm = xm - ((xi*info.map_info.dy)-info.map_info.dx); + end + + I.x = xm + ((0:info.samples-1).*info.map_info.dx); + I.y = ym - ((0:info.lines-1).* info.map_info.dy); + +end + +I.x = I.x(sub(1):sub(2)); +I.y = I.y(sub(3):sub(4)); + +%% Set binary format parameters +switch info.byte_order + case {0} + machine = 'ieee-le'; + case {1} + machine = 'ieee-be'; + otherwise + machine = 'n'; +end + +format = 'uint8'; + +tmp=zeros(sub(4)-sub(3)+1,sub(2)-sub(1)+1,info.bands,format); +fid=fopen(file,'r'); + +offset1=(sub(3)-1)*info.samples; +fseek(fid,offset1,'bof'); +for b=1:info.bands + for i=sub(3):sub(4) + t=fread(fid,info.samples,format); + tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2)); + end + offset2 = info.samples*info.lines*b+offset1; + fseek(fid,offset2,'bof'); +end + +fclose(fid); + +I.z=tmp; +I.info =info; + +%% sub function +function info = read_envihdr(hdrfile) +% READ_ENVIHDR read and return ENVI image file header information. +% INFO = READ_ENVIHDR('HDR_FILE') reads the ASCII ENVI-generated image +% header file and returns all the information in a structure of +% parameters. +% +% Example: +% >> info = read_envihdr('my_envi_image.hdr') +% info = +% description: [1x101 char] +% samples: 658 +% lines: 749 +% bands: 3 +% header_offset: 0 +% file_type: 'ENVI Standard' +% data_type: 4 +% interleave: 'bsq' +% sensor_type: 'Unknown' +% byte_order: 0 +% map_info: [1x1 struct] +% projection_info: [1x102 char] +% wavelength_units: 'Unknown' +% pixel_size: [1x1 struct] +% band_names: [1x154 char] +% +% NOTE: This function is used by ENVIREAD to import data. +% Ian M. Howat, Applied Physics Lab, University of Washington +% ihowat@apl.washington.edu +% Version 1: 19-Jul-2007 00:50:57 +fid = fopen(hdrfile); +while fid; + line = fgetl(fid); + if line == -1 + break + else + eqsn = findstr(line,'='); + if ~isempty(eqsn) + param = strtrim(line(1:eqsn-1)); + param(findstr(param,' ')) = '_'; + value = strtrim(line(eqsn+1:end)); + if isempty(str2num(value)) + if ~isempty(findstr(value,'{')) && isempty(findstr(value,'}')) + while isempty(findstr(value,'}')) + line = fgetl(fid); + value = [value,strtrim(line)]; + end + end + eval(['info.',param,' = ''',value,''';']) + else + eval(['info.',param,' = ',value,';']) + end + end + end +end +fclose(fid); + +if isfield(info,'map_info') + line = info.map_info; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.map_info = []; + info.map_info.projection = line{1}; + info.map_info.image_coords = [str2num(line{2}),str2num(line{3})]; + info.map_info.mapx = str2num(line{4}); + info.map_info.mapy = str2num(line{5}); + info.map_info.dx = str2num(line{6}); + info.map_info.dy = str2num(line{7}); + if length(line) == 9 + info.map_info.datum = line{8}; + info.map_info.units = line{9}(7:end); + elseif length(line) == 11 + info.map_info.zone = str2num(line{8}); + info.map_info.hemi = line{9}; + info.map_info.datum = line{10}; + info.map_info.units = line{11}(7:end); + end +end + +if isfield(info,'pixel_size') + line = info.pixel_size; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.pixel_size = []; + info.pixel_size.x = str2num(line{1}); + info.pixel_size.y = str2num(line{2}); + info.pixel_size.units = line{3}(7:end); +end + +%% +function A = split(s,d) +%This function by Gerald Dalley (dalleyg@mit.edu), 2004 +A = {}; +while (length(s) > 0) + [t,s] = strtok(s,d); + A = {A{:}, t}; +end + + + + Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/inishell/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/inishell/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/inishell/install.sh (revision 27955) @@ -0,0 +1,40 @@ +#!/bin/bash +#inishell install package: this package is not distributed by ISSM. Please request access to the code by +#contacting Mathias Bavay () or logging onto http://models.slf.ch/ and registering. Once you have a tarball +#of the code, please use this script to install. + +#we assume you have a inishell-src-*.tgz tarball +set -eu + +#Do some inquiry about the names of the tar balls: +source_tar=`ls inishell-src-*.tgz` +source_version=`echo $source_tar | sed 's/inishell-src-//g' | sed 's/.tgz//g'` + +if [[ $source_tar == "" ]]; then + echo "Could not identify a tar ball for the source code, name should be inishell-src-*.tgz" + exit 1 +fi +if [[ $source_version == "" ]]; then + echo "Could not identify a tar ball version for the source code" + exit 1 +fi + + +#Some cleanup +rm -rf src install inishell-$source_version +mkdir install + +#First deal with source code +tar -zxvf $source_tar +mv inishell-$source_version src +rm -rf inishell-$source_version + +#Build inishell +cd src && ant snowpack + +#Put the .jar in the install directory +cp dist/inishell.jar ../install + +#Install script to launch inishell jar file directly +cd .. +cp scripts/inishell install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/inishell/scripts/inishell =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/inishell/scripts/inishell (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/inishell/scripts/inishell (revision 27955) @@ -0,0 +1,3 @@ +#/bin/bash + +java -jar $ISSM_DIR/externalpackages/inishell/install/inishell.jar Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/ipython/install.sh =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/ipython/install.sh (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/ipython/install.sh (revision 27955) @@ -0,0 +1,22 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf ipython-1.0.0 +mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/ipython-1.0.0.tar.gz' 'ipython-1.0.0.tar.gz' + +#Untar +tar -zxvf ipython-1.0.0.tar.gz + +#Move ipython into src directory +mv ipython-1.0.0/* src +rm -rf ipython-1.0.0 + +#install ipython +cd src +python setup.py build +python setup.py install Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/javascript/README =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/javascript/README (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/javascript/README (revision 27955) @@ -0,0 +1,3 @@ +This directory contains, at the time of this writing, JavaScript modules used +on the VESL Web site. Arguably, they should just be kept in that project's SVN +repository if no one is pulling them from here. Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/javascript/gauge.min.js =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/javascript/gauge.min.js (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/javascript/gauge.min.js (revision 27955) @@ -0,0 +1,1 @@ +(function(){var a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q={}.hasOwnProperty,r=function(a,b){function c(){this.constructor=a}for(var d in b)q.call(b,d)&&(a[d]=b[d]);return c.prototype=b.prototype,a.prototype=new c,a.__super__=b.prototype,a};!function(){var a,b,c,d,e,f,g;for(g=["ms","moz","webkit","o"],c=0,e=g.length;e>c&&(f=g[c],!window.requestAnimationFrame);c++)window.requestAnimationFrame=window[f+"RequestAnimationFrame"],window.cancelAnimationFrame=window[f+"CancelAnimationFrame"]||window[f+"CancelRequestAnimationFrame"];return a=null,d=0,b={},requestAnimationFrame?window.cancelAnimationFrame?void 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a?cancelAnimationFrame(AnimationUpdater.animId):AnimationUpdater.animId=requestAnimationFrame(AnimationUpdater.run)}},"function"==typeof window.define&&null!=window.define.amd?define(function(){return{Gauge:g,Donut:f,BaseDonut:d,TextRenderer:i}}):"undefined"!=typeof module&&null!=module.exports?module.exports={Gauge:g,Donut:f,BaseDonut:d,TextRenderer:i}:(window.Gauge=g,window.Donut=f,window.BaseDonut=d,window.TextRenderer=i)}).call(this); Index: /issm/branches/trunk-dlcheng-ASE/externalpackages/javascript/gl-matrix-min.js =================================================================== --- /issm/branches/trunk-dlcheng-ASE/externalpackages/javascript/gl-matrix-min.js (revision 27955) +++ /issm/branches/trunk-dlcheng-ASE/externalpackages/javascript/gl-matrix-min.js (revision 27955) @@ -0,0 +1,29 @@ +/** + * @fileoverview gl-matrix - High performance matrix and vector operations + * @author Brandon Jones + * @author Colin MacKenzie IV + * @version 2.3.2 + */ + +/* Copyright (c) 2015, Brandon Jones, Colin MacKenzie IV. + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. */ + +!function(t,a){if("object"==typeof exports&&"object"==typeof module)module.exports=a();else if("function"==typeof define&&define.amd)define(a);else{var n=a();for(var r in n)("object"==typeof exports?exports:t)[r]=n[r]}}(this,function(){return function(t){function a(r){if(n[r])return n[r].exports;var o=n[r]={exports:{},id:r,loaded:!1};return t[r].call(o.exports,o,o.exports,a),o.loaded=!0,o.exports}var n={};return a.m=t,a.c=n,a.p="",a(0)}([function(t,a,n){a.glMatrix=n(1),a.mat2=n(2),a.mat2d=n(3),a.mat3=n(4),a.mat4=n(5),a.quat=n(6),a.vec2=n(9),a.vec3=n(7),a.vec4=n(8)},function(t,a){var n={};n.EPSILON=1e-6,n.ARRAY_TYPE="undefined"!=typeof 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t[0]*t[3]-t[2]*t[1]},o.multiply=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=n[0],M=n[1],i=n[2],s=n[3];return t[0]=r*e+l*M,t[1]=o*e+u*M,t[2]=r*i+l*s,t[3]=o*i+u*s,t},o.mul=o.multiply,o.rotate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=Math.sin(n),M=Math.cos(n);return t[0]=r*M+l*e,t[1]=o*M+u*e,t[2]=r*-e+l*M,t[3]=o*-e+u*M,t},o.scale=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=n[0],M=n[1];return t[0]=r*e,t[1]=o*e,t[2]=l*M,t[3]=u*M,t},o.fromRotation=function(t,a){var n=Math.sin(a),r=Math.cos(a);return t[0]=r,t[1]=n,t[2]=-n,t[3]=r,t},o.fromScaling=function(t,a){return t[0]=a[0],t[1]=0,t[2]=0,t[3]=a[1],t},o.str=function(t){return"mat2("+t[0]+", "+t[1]+", "+t[2]+", "+t[3]+")"},o.frob=function(t){return Math.sqrt(Math.pow(t[0],2)+Math.pow(t[1],2)+Math.pow(t[2],2)+Math.pow(t[3],2))},o.LDU=function(t,a,n,r){return t[2]=r[2]/r[0],n[0]=r[0],n[1]=r[1],n[3]=r[3]-t[2]*n[1],[t,a,n]},t.exports=o},function(t,a,n){var r=n(1),o={};o.create=function(){var t=new r.ARRAY_TYPE(6);return 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r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=n[0],s=n[1];return t[0]=r*i,t[1]=o*i,t[2]=l*s,t[3]=u*s,t[4]=e,t[5]=M,t},o.translate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=n[0],s=n[1];return t[0]=r,t[1]=o,t[2]=l,t[3]=u,t[4]=r*i+l*s+e,t[5]=o*i+u*s+M,t},o.fromRotation=function(t,a){var n=Math.sin(a),r=Math.cos(a);return t[0]=r,t[1]=n,t[2]=-n,t[3]=r,t[4]=0,t[5]=0,t},o.fromScaling=function(t,a){return t[0]=a[0],t[1]=0,t[2]=0,t[3]=a[1],t[4]=0,t[5]=0,t},o.fromTranslation=function(t,a){return t[0]=1,t[1]=0,t[2]=0,t[3]=1,t[4]=a[0],t[5]=a[1],t},o.str=function(t){return"mat2d("+t[0]+", "+t[1]+", "+t[2]+", "+t[3]+", "+t[4]+", "+t[5]+")"},o.frob=function(t){return Math.sqrt(Math.pow(t[0],2)+Math.pow(t[1],2)+Math.pow(t[2],2)+Math.pow(t[3],2)+Math.pow(t[4],2)+Math.pow(t[5],2)+1)},t.exports=o},function(t,a,n){var r=n(1),o={};o.create=function(){var t=new r.ARRAY_TYPE(9);return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=1,t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.fromMat4=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[4],t[4]=a[5],t[5]=a[6],t[6]=a[8],t[7]=a[9],t[8]=a[10],t},o.clone=function(t){var a=new r.ARRAY_TYPE(9);return a[0]=t[0],a[1]=t[1],a[2]=t[2],a[3]=t[3],a[4]=t[4],a[5]=t[5],a[6]=t[6],a[7]=t[7],a[8]=t[8],a},o.copy=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t},o.identity=function(t){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=1,t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.transpose=function(t,a){if(t===a){var n=a[1],r=a[2],o=a[5];t[1]=a[3],t[2]=a[6],t[3]=n,t[5]=a[7],t[6]=r,t[7]=o}else t[0]=a[0],t[1]=a[3],t[2]=a[6],t[3]=a[1],t[4]=a[4],t[5]=a[7],t[6]=a[2],t[7]=a[5],t[8]=a[8];return t},o.invert=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=s*u-e*i,D=-s*l+e*M,S=i*l-u*M,I=n*c+r*D+o*S;return I?(I=1/I,t[0]=c*I,t[1]=(-s*r+o*i)*I,t[2]=(e*r-o*u)*I,t[3]=D*I,t[4]=(s*n-o*M)*I,t[5]=(-e*n+o*l)*I,t[6]=S*I,t[7]=(-i*n+r*M)*I,t[8]=(u*n-r*l)*I,t):null},o.adjoint=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8];return t[0]=u*s-e*i,t[1]=o*i-r*s,t[2]=r*e-o*u,t[3]=e*M-l*s,t[4]=n*s-o*M,t[5]=o*l-n*e,t[6]=l*i-u*M,t[7]=r*M-n*i,t[8]=n*u-r*l,t},o.determinant=function(t){var a=t[0],n=t[1],r=t[2],o=t[3],l=t[4],u=t[5],e=t[6],M=t[7],i=t[8];return a*(i*l-u*M)+n*(-i*o+u*e)+r*(M*o-l*e)},o.multiply=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=n[0],S=n[1],I=n[2],x=n[3],f=n[4],F=n[5],m=n[6],h=n[7],d=n[8];return t[0]=D*r+S*u+I*i,t[1]=D*o+S*e+I*s,t[2]=D*l+S*M+I*c,t[3]=x*r+f*u+F*i,t[4]=x*o+f*e+F*s,t[5]=x*l+f*M+F*c,t[6]=m*r+h*u+d*i,t[7]=m*o+h*e+d*s,t[8]=m*l+h*M+d*c,t},o.mul=o.multiply,o.translate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=n[0],S=n[1];return t[0]=r,t[1]=o,t[2]=l,t[3]=u,t[4]=e,t[5]=M,t[6]=D*r+S*u+i,t[7]=D*o+S*e+s,t[8]=D*l+S*M+c,t},o.rotate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=Math.sin(n),S=Math.cos(n);return t[0]=S*r+D*u,t[1]=S*o+D*e,t[2]=S*l+D*M,t[3]=S*u-D*r,t[4]=S*e-D*o,t[5]=S*M-D*l,t[6]=i,t[7]=s,t[8]=c,t},o.scale=function(t,a,n){var r=n[0],o=n[1];return t[0]=r*a[0],t[1]=r*a[1],t[2]=r*a[2],t[3]=o*a[3],t[4]=o*a[4],t[5]=o*a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t},o.fromTranslation=function(t,a){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=1,t[5]=0,t[6]=a[0],t[7]=a[1],t[8]=1,t},o.fromRotation=function(t,a){var n=Math.sin(a),r=Math.cos(a);return t[0]=r,t[1]=n,t[2]=0,t[3]=-n,t[4]=r,t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.fromScaling=function(t,a){return t[0]=a[0],t[1]=0,t[2]=0,t[3]=0,t[4]=a[1],t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.fromMat2d=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=0,t[3]=a[2],t[4]=a[3],t[5]=0,t[6]=a[4],t[7]=a[5],t[8]=1,t},o.fromQuat=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=n+n,e=r+r,M=o+o,i=n*u,s=r*u,c=r*e,D=o*u,S=o*e,I=o*M,x=l*u,f=l*e,F=l*M;return t[0]=1-c-I,t[3]=s-F,t[6]=D+f,t[1]=s+F,t[4]=1-i-I,t[7]=S-x,t[2]=D-f,t[5]=S+x,t[8]=1-i-c,t},o.normalFromMat4=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15],m=n*e-r*u,h=n*M-o*u,d=n*i-l*u,v=r*M-o*e,z=r*i-l*e,p=o*i-l*M,w=s*x-c*I,A=s*f-D*I,R=s*F-S*I,b=c*f-D*x,Y=c*F-S*x,q=D*F-S*f,y=m*q-h*Y+d*b+v*R-z*A+p*w;return y?(y=1/y,t[0]=(e*q-M*Y+i*b)*y,t[1]=(M*R-u*q-i*A)*y,t[2]=(u*Y-e*R+i*w)*y,t[3]=(o*Y-r*q-l*b)*y,t[4]=(n*q-o*R+l*A)*y,t[5]=(r*R-n*Y-l*w)*y,t[6]=(x*p-f*z+F*v)*y,t[7]=(f*d-I*p-F*h)*y,t[8]=(I*z-x*d+F*m)*y,t):null},o.str=function(t){return"mat3("+t[0]+", "+t[1]+", "+t[2]+", "+t[3]+", "+t[4]+", "+t[5]+", "+t[6]+", "+t[7]+", "+t[8]+")"},o.frob=function(t){return Math.sqrt(Math.pow(t[0],2)+Math.pow(t[1],2)+Math.pow(t[2],2)+Math.pow(t[3],2)+Math.pow(t[4],2)+Math.pow(t[5],2)+Math.pow(t[6],2)+Math.pow(t[7],2)+Math.pow(t[8],2))},t.exports=o},function(t,a,n){var r=n(1),o={scalar:{},SIMD:{}};o.create=function(){var t=new r.ARRAY_TYPE(16);return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=1,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=1,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},o.clone=function(t){var a=new r.ARRAY_TYPE(16);return a[0]=t[0],a[1]=t[1],a[2]=t[2],a[3]=t[3],a[4]=t[4],a[5]=t[5],a[6]=t[6],a[7]=t[7],a[8]=t[8],a[9]=t[9],a[10]=t[10],a[11]=t[11],a[12]=t[12],a[13]=t[13],a[14]=t[14],a[15]=t[15],a},o.copy=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t[9]=a[9],t[10]=a[10],t[11]=a[11],t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.identity=function(t){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=1,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=1,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},o.scalar.transpose=function(t,a){if(t===a){var n=a[1],r=a[2],o=a[3],l=a[6],u=a[7],e=a[11];t[1]=a[4],t[2]=a[8],t[3]=a[12],t[4]=n,t[6]=a[9],t[7]=a[13],t[8]=r,t[9]=l,t[11]=a[14],t[12]=o,t[13]=u,t[14]=e}else t[0]=a[0],t[1]=a[4],t[2]=a[8],t[3]=a[12],t[4]=a[1],t[5]=a[5],t[6]=a[9],t[7]=a[13],t[8]=a[2],t[9]=a[6],t[10]=a[10],t[11]=a[14],t[12]=a[3],t[13]=a[7],t[14]=a[11],t[15]=a[15];return t},o.SIMD.transpose=function(t,a){var n,r,o,l,u,e,M,i,s,c;return n=SIMD.Float32x4.load(a,0),r=SIMD.Float32x4.load(a,4),o=SIMD.Float32x4.load(a,8),l=SIMD.Float32x4.load(a,12),u=SIMD.Float32x4.shuffle(n,r,0,1,4,5),e=SIMD.Float32x4.shuffle(o,l,0,1,4,5),M=SIMD.Float32x4.shuffle(u,e,0,2,4,6),i=SIMD.Float32x4.shuffle(u,e,1,3,5,7),SIMD.Float32x4.store(t,0,M),SIMD.Float32x4.store(t,4,i),u=SIMD.Float32x4.shuffle(n,r,2,3,6,7),e=SIMD.Float32x4.shuffle(o,l,2,3,6,7),s=SIMD.Float32x4.shuffle(u,e,0,2,4,6),c=SIMD.Float32x4.shuffle(u,e,1,3,5,7),SIMD.Float32x4.store(t,8,s),SIMD.Float32x4.store(t,12,c),t},o.transpose=r.USE_SIMD?o.SIMD.transpose:o.scalar.transpose,o.scalar.invert=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15],m=n*e-r*u,h=n*M-o*u,d=n*i-l*u,v=r*M-o*e,z=r*i-l*e,p=o*i-l*M,w=s*x-c*I,A=s*f-D*I,R=s*F-S*I,b=c*f-D*x,Y=c*F-S*x,q=D*F-S*f,y=m*q-h*Y+d*b+v*R-z*A+p*w;return y?(y=1/y,t[0]=(e*q-M*Y+i*b)*y,t[1]=(o*Y-r*q-l*b)*y,t[2]=(x*p-f*z+F*v)*y,t[3]=(D*z-c*p-S*v)*y,t[4]=(M*R-u*q-i*A)*y,t[5]=(n*q-o*R+l*A)*y,t[6]=(f*d-I*p-F*h)*y,t[7]=(s*p-D*d+S*h)*y,t[8]=(u*Y-e*R+i*w)*y,t[9]=(r*R-n*Y-l*w)*y,t[10]=(I*z-x*d+F*m)*y,t[11]=(c*d-s*z-S*m)*y,t[12]=(e*A-u*b-M*w)*y,t[13]=(n*b-r*A+o*w)*y,t[14]=(x*h-I*v-f*m)*y,t[15]=(s*v-c*h+D*m)*y,t):null},o.SIMD.invert=function(t,a){var n,r,o,l,u,e,M,i,s,c,D=SIMD.Float32x4.load(a,0),S=SIMD.Float32x4.load(a,4),I=SIMD.Float32x4.load(a,8),x=SIMD.Float32x4.load(a,12);return u=SIMD.Float32x4.shuffle(D,S,0,1,4,5),r=SIMD.Float32x4.shuffle(I,x,0,1,4,5),n=SIMD.Float32x4.shuffle(u,r,0,2,4,6),r=SIMD.Float32x4.shuffle(r,u,1,3,5,7),u=SIMD.Float32x4.shuffle(D,S,2,3,6,7),l=SIMD.Float32x4.shuffle(I,x,2,3,6,7),o=SIMD.Float32x4.shuffle(u,l,0,2,4,6),l=SIMD.Float32x4.shuffle(l,u,1,3,5,7),u=SIMD.Float32x4.mul(o,l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),e=SIMD.Float32x4.mul(r,u),M=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(SIMD.Float32x4.mul(r,u),e),M=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),M),M=SIMD.Float32x4.swizzle(M,2,3,0,1),u=SIMD.Float32x4.mul(r,o),u=SIMD.Float32x4.swizzle(u,1,0,3,2),e=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),e),s=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(e,SIMD.Float32x4.mul(l,u)),s=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),u=SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(r,2,3,0,1),l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),o=SIMD.Float32x4.swizzle(o,2,3,0,1),e=SIMD.Float32x4.add(SIMD.Float32x4.mul(o,u),e),i=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(e,SIMD.Float32x4.mul(o,u)),i=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),i),i=SIMD.Float32x4.swizzle(i,2,3,0,1),u=SIMD.Float32x4.mul(n,r),u=SIMD.Float32x4.swizzle(u,1,0,3,2),i=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),i),s=SIMD.Float32x4.sub(SIMD.Float32x4.mul(o,u),s),u=SIMD.Float32x4.swizzle(u,2,3,0,1),i=SIMD.Float32x4.sub(SIMD.Float32x4.mul(l,u),i),s=SIMD.Float32x4.sub(s,SIMD.Float32x4.mul(o,u)),u=SIMD.Float32x4.mul(n,l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),M=SIMD.Float32x4.sub(M,SIMD.Float32x4.mul(o,u)),i=SIMD.Float32x4.add(SIMD.Float32x4.mul(r,u),i),u=SIMD.Float32x4.swizzle(u,2,3,0,1),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(o,u),M),i=SIMD.Float32x4.sub(i,SIMD.Float32x4.mul(r,u)),u=SIMD.Float32x4.mul(n,o),u=SIMD.Float32x4.swizzle(u,1,0,3,2),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),M),s=SIMD.Float32x4.sub(s,SIMD.Float32x4.mul(r,u)),u=SIMD.Float32x4.swizzle(u,2,3,0,1),M=SIMD.Float32x4.sub(M,SIMD.Float32x4.mul(l,u)),s=SIMD.Float32x4.add(SIMD.Float32x4.mul(r,u),s),c=SIMD.Float32x4.mul(n,e),c=SIMD.Float32x4.add(SIMD.Float32x4.swizzle(c,2,3,0,1),c),c=SIMD.Float32x4.add(SIMD.Float32x4.swizzle(c,1,0,3,2),c),u=SIMD.Float32x4.reciprocalApproximation(c),c=SIMD.Float32x4.sub(SIMD.Float32x4.add(u,u),SIMD.Float32x4.mul(c,SIMD.Float32x4.mul(u,u))),(c=SIMD.Float32x4.swizzle(c,0,0,0,0))?(SIMD.Float32x4.store(t,0,SIMD.Float32x4.mul(c,e)),SIMD.Float32x4.store(t,4,SIMD.Float32x4.mul(c,M)),SIMD.Float32x4.store(t,8,SIMD.Float32x4.mul(c,i)),SIMD.Float32x4.store(t,12,SIMD.Float32x4.mul(c,s)),t):null},o.invert=r.USE_SIMD?o.SIMD.invert:o.scalar.invert,o.scalar.adjoint=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15];return t[0]=e*(D*F-S*f)-c*(M*F-i*f)+x*(M*S-i*D),t[1]=-(r*(D*F-S*f)-c*(o*F-l*f)+x*(o*S-l*D)),t[2]=r*(M*F-i*f)-e*(o*F-l*f)+x*(o*i-l*M),t[3]=-(r*(M*S-i*D)-e*(o*S-l*D)+c*(o*i-l*M)),t[4]=-(u*(D*F-S*f)-s*(M*F-i*f)+I*(M*S-i*D)),t[5]=n*(D*F-S*f)-s*(o*F-l*f)+I*(o*S-l*D),t[6]=-(n*(M*F-i*f)-u*(o*F-l*f)+I*(o*i-l*M)),t[7]=n*(M*S-i*D)-u*(o*S-l*D)+s*(o*i-l*M),t[8]=u*(c*F-S*x)-s*(e*F-i*x)+I*(e*S-i*c),t[9]=-(n*(c*F-S*x)-s*(r*F-l*x)+I*(r*S-l*c)),t[10]=n*(e*F-i*x)-u*(r*F-l*x)+I*(r*i-l*e),t[11]=-(n*(e*S-i*c)-u*(r*S-l*c)+s*(r*i-l*e)),t[12]=-(u*(c*f-D*x)-s*(e*f-M*x)+I*(e*D-M*c)),t[13]=n*(c*f-D*x)-s*(r*f-o*x)+I*(r*D-o*c),t[14]=-(n*(e*f-M*x)-u*(r*f-o*x)+I*(r*M-o*e)),t[15]=n*(e*D-M*c)-u*(r*D-o*c)+s*(r*M-o*e),t},o.SIMD.adjoint=function(t,a){var n,r,o,l,u,e,M,i,s,c,D,S,I,n=SIMD.Float32x4.load(a,0),r=SIMD.Float32x4.load(a,4),o=SIMD.Float32x4.load(a,8),l=SIMD.Float32x4.load(a,12);return s=SIMD.Float32x4.shuffle(n,r,0,1,4,5),e=SIMD.Float32x4.shuffle(o,l,0,1,4,5),u=SIMD.Float32x4.shuffle(s,e,0,2,4,6),e=SIMD.Float32x4.shuffle(e,s,1,3,5,7),s=SIMD.Float32x4.shuffle(n,r,2,3,6,7),i=SIMD.Float32x4.shuffle(o,l,2,3,6,7),M=SIMD.Float32x4.shuffle(s,i,0,2,4,6),i=SIMD.Float32x4.shuffle(i,s,1,3,5,7),s=SIMD.Float32x4.mul(M,i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),c=SIMD.Float32x4.mul(e,s),D=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(SIMD.Float32x4.mul(e,s),c),D=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),D),D=SIMD.Float32x4.swizzle(D,2,3,0,1),s=SIMD.Float32x4.mul(e,M),s=SIMD.Float32x4.swizzle(s,1,0,3,2),c=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),c),I=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(c,SIMD.Float32x4.mul(i,s)),I=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),I),I=SIMD.Float32x4.swizzle(I,2,3,0,1),s=SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,2,3,0,1),i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),M=SIMD.Float32x4.swizzle(M,2,3,0,1),c=SIMD.Float32x4.add(SIMD.Float32x4.mul(M,s),c),S=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(c,SIMD.Float32x4.mul(M,s)),S=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),S),S=SIMD.Float32x4.swizzle(S,2,3,0,1),s=SIMD.Float32x4.mul(u,e),s=SIMD.Float32x4.swizzle(s,1,0,3,2),S=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),S),I=SIMD.Float32x4.sub(SIMD.Float32x4.mul(M,s),I),s=SIMD.Float32x4.swizzle(s,2,3,0,1),S=SIMD.Float32x4.sub(SIMD.Float32x4.mul(i,s),S),I=SIMD.Float32x4.sub(I,SIMD.Float32x4.mul(M,s)),s=SIMD.Float32x4.mul(u,i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),D=SIMD.Float32x4.sub(D,SIMD.Float32x4.mul(M,s)),S=SIMD.Float32x4.add(SIMD.Float32x4.mul(e,s),S),s=SIMD.Float32x4.swizzle(s,2,3,0,1),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(M,s),D),S=SIMD.Float32x4.sub(S,SIMD.Float32x4.mul(e,s)),s=SIMD.Float32x4.mul(u,M),s=SIMD.Float32x4.swizzle(s,1,0,3,2),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),D),I=SIMD.Float32x4.sub(I,SIMD.Float32x4.mul(e,s)),s=SIMD.Float32x4.swizzle(s,2,3,0,1),D=SIMD.Float32x4.sub(D,SIMD.Float32x4.mul(i,s)),I=SIMD.Float32x4.add(SIMD.Float32x4.mul(e,s),I),SIMD.Float32x4.store(t,0,c),SIMD.Float32x4.store(t,4,D),SIMD.Float32x4.store(t,8,S),SIMD.Float32x4.store(t,12,I),t},o.adjoint=r.USE_SIMD?o.SIMD.adjoint:o.scalar.adjoint,o.determinant=function(t){var a=t[0],n=t[1],r=t[2],o=t[3],l=t[4],u=t[5],e=t[6],M=t[7],i=t[8],s=t[9],c=t[10],D=t[11],S=t[12],I=t[13],x=t[14],f=t[15],F=a*u-n*l,m=a*e-r*l,h=a*M-o*l,d=n*e-r*u,v=n*M-o*u,z=r*M-o*e,p=i*I-s*S,w=i*x-c*S,A=i*f-D*S,R=s*x-c*I,b=s*f-D*I,Y=c*f-D*x;return F*Y-m*b+h*R+d*A-v*w+z*p},o.SIMD.multiply=function(t,a,n){var r=SIMD.Float32x4.load(a,0),o=SIMD.Float32x4.load(a,4),l=SIMD.Float32x4.load(a,8),u=SIMD.Float32x4.load(a,12),e=SIMD.Float32x4.load(n,0),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,3,3,3,3),u))));SIMD.Float32x4.store(t,0,M);var i=SIMD.Float32x4.load(n,4),s=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,3,3,3,3),u))));SIMD.Float32x4.store(t,4,s);var c=SIMD.Float32x4.load(n,8),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,3,3,3,3),u))));SIMD.Float32x4.store(t,8,D);var S=SIMD.Float32x4.load(n,12),I=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,3,3,3,3),u))));return SIMD.Float32x4.store(t,12,I),t},o.scalar.multiply=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=a[9],S=a[10],I=a[11],x=a[12],f=a[13],F=a[14],m=a[15],h=n[0],d=n[1],v=n[2],z=n[3];return t[0]=h*r+d*e+v*c+z*x,t[1]=h*o+d*M+v*D+z*f,t[2]=h*l+d*i+v*S+z*F,t[3]=h*u+d*s+v*I+z*m,h=n[4],d=n[5],v=n[6],z=n[7],t[4]=h*r+d*e+v*c+z*x,t[5]=h*o+d*M+v*D+z*f,t[6]=h*l+d*i+v*S+z*F,t[7]=h*u+d*s+v*I+z*m,h=n[8],d=n[9],v=n[10],z=n[11],t[8]=h*r+d*e+v*c+z*x,t[9]=h*o+d*M+v*D+z*f,t[10]=h*l+d*i+v*S+z*F,t[11]=h*u+d*s+v*I+z*m,h=n[12],d=n[13],v=n[14],z=n[15],t[12]=h*r+d*e+v*c+z*x,t[13]=h*o+d*M+v*D+z*f,t[14]=h*l+d*i+v*S+z*F,t[15]=h*u+d*s+v*I+z*m,t},o.multiply=r.USE_SIMD?o.SIMD.multiply:o.scalar.multiply,o.mul=o.multiply,o.scalar.translate=function(t,a,n){var r,o,l,u,e,M,i,s,c,D,S,I,x=n[0],f=n[1],F=n[2];return a===t?(t[12]=a[0]*x+a[4]*f+a[8]*F+a[12],t[13]=a[1]*x+a[5]*f+a[9]*F+a[13],t[14]=a[2]*x+a[6]*f+a[10]*F+a[14],t[15]=a[3]*x+a[7]*f+a[11]*F+a[15]):(r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=a[9],S=a[10],I=a[11],t[0]=r,t[1]=o,t[2]=l,t[3]=u,t[4]=e,t[5]=M,t[6]=i,t[7]=s,t[8]=c,t[9]=D,t[10]=S,t[11]=I,t[12]=r*x+e*f+c*F+a[12],t[13]=o*x+M*f+D*F+a[13],t[14]=l*x+i*f+S*F+a[14],t[15]=u*x+s*f+I*F+a[15]),t},o.SIMD.translate=function(t,a,n){var r=SIMD.Float32x4.load(a,0),o=SIMD.Float32x4.load(a,4),l=SIMD.Float32x4.load(a,8),u=SIMD.Float32x4.load(a,12),e=SIMD.Float32x4(n[0],n[1],n[2],0);a!==t&&(t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t[9]=a[9],t[10]=a[10],t[11]=a[11]),r=SIMD.Float32x4.mul(r,SIMD.Float32x4.swizzle(e,0,0,0,0)),o=SIMD.Float32x4.mul(o,SIMD.Float32x4.swizzle(e,1,1,1,1)),l=SIMD.Float32x4.mul(l,SIMD.Float32x4.swizzle(e,2,2,2,2));var M=SIMD.Float32x4.add(r,SIMD.Float32x4.add(o,SIMD.Float32x4.add(l,u)));return SIMD.Float32x4.store(t,12,M),t},o.translate=r.USE_SIMD?o.SIMD.translate:o.scalar.translate,o.scalar.scale=function(t,a,n){var r=n[0],o=n[1],l=n[2];return t[0]=a[0]*r,t[1]=a[1]*r,t[2]=a[2]*r,t[3]=a[3]*r,t[4]=a[4]*o,t[5]=a[5]*o,t[6]=a[6]*o,t[7]=a[7]*o,t[8]=a[8]*l,t[9]=a[9]*l,t[10]=a[10]*l,t[11]=a[11]*l,t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.SIMD.scale=function(t,a,n){var r,o,l,u=SIMD.Float32x4(n[0],n[1],n[2],0);return r=SIMD.Float32x4.load(a,0),SIMD.Float32x4.store(t,0,SIMD.Float32x4.mul(r,SIMD.Float32x4.swizzle(u,0,0,0,0))),o=SIMD.Float32x4.load(a,4),SIMD.Float32x4.store(t,4,SIMD.Float32x4.mul(o,SIMD.Float32x4.swizzle(u,1,1,1,1))),l=SIMD.Float32x4.load(a,8),SIMD.Float32x4.store(t,8,SIMD.Float32x4.mul(l,SIMD.Float32x4.swizzle(u,2,2,2,2))),t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.scale=r.USE_SIMD?o.SIMD.scale:o.scalar.scale,o.rotate=function(t,a,n,o){var l,u,e,M,i,s,c,D,S,I,x,f,F,m,h,d,v,z,p,w,A,R,b,Y,q=o[0],y=o[1],E=o[2],g=Math.sqrt(q*q+y*y+E*E);return 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