Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 27034) +++ /issm/trunk/configure.ac (revision 27035) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([Ice Sheet System Model (ISSM)],[4.19],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[4.20],[issm@jpl.nasa.gov],[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 @@ -9,5 +9,5 @@ #print header AC_MSG_NOTICE(============================================================================) -AC_MSG_NOTICE(= AC_PACKAGE_NAME AC_PACKAGE_VERSION configuration =) +AC_MSG_NOTICE(= AC_PACKAGE_NAME AC_PACKAGE_VERSION configuration =) AC_MSG_NOTICE(============================================================================) Index: /issm/trunk/etc/environment.csh =================================================================== --- /issm/trunk/etc/environment.csh (revision 27034) +++ /issm/trunk/etc/environment.csh (revision 27035) @@ -148,6 +148,8 @@ set GSL_ROOT="{$ISSM_EXT_DIR}/gsl/install" if ( -d {$GSL_ROOT} ) then - setenv GSL_HOME "{$GSL_ROOT}" # Used in installation of Dakota + setenv GSL_HOME {$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 Index: /issm/trunk/etc/environment.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 27034) +++ /issm/trunk/etc/environment.sh (revision 27035) @@ -295,5 +295,5 @@ if [[ ${MINGW} -eq 1 ]]; then - path_append "${BLAS_ROOT}/lib" # Allows dynamic loaded to find DLLs + path_append "${BLAS_ROOT}/lib" # Allows dynamic loader to find DLLs fi fi @@ -306,5 +306,5 @@ if [[ ${MINGW} -eq 1 ]]; then - path_append "${LAPACK_ROOT}/lib" # Allows dynamic loaded to find DLLs + path_append "${LAPACK_ROOT}/lib" # Allows dynamic loader to find DLLs fi fi @@ -317,5 +317,5 @@ if [[ ${MINGW} -eq 1 ]]; then - path_append "${METIS_ROOT}/lib" # Allows dynamic loaded to find DLLs + path_append "${METIS_ROOT}/lib" # Allows dynamic loader to find DLLs fi fi @@ -327,5 +327,5 @@ if [[ ${MINGW} -eq 1 ]]; then - path_append "${MUMPS_ROOT}/lib" # Allows dynamic loaded to find DLLs + path_append "${MUMPS_ROOT}/lib" # Allows dynamic loader to find DLLs fi fi @@ -338,5 +338,5 @@ if [[ ${MINGW} -eq 1 ]]; then - path_append "${PARMETIS_ROOT}/lib" # Allows dynamic loaded to find DLLs + path_append "${PARMETIS_ROOT}/lib" # Allows dynamic loader to find DLLs fi fi @@ -348,5 +348,5 @@ if [[ ${MINGW} -eq 1 ]]; then - path_append "${SCALAPACK_ROOT}/lib" # Allows dynamic loaded to find DLLs + path_append "${SCALAPACK_ROOT}/lib" # Allows dynamic loader to find DLLs fi fi @@ -365,5 +365,5 @@ if [[ ${MINGW} -eq 1 ]]; then - path_append "${PETSC_ROOT}/lib" # Allows dynamic loaded to find DLLs + path_append "${PETSC_ROOT}/lib" # Allows dynamic loader to find DLLs fi @@ -413,4 +413,12 @@ fi +MPLAPACK_ROOT="${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 "${SCOTCH_ROOT}/lib" @@ -499,10 +507,11 @@ SQLITE_ROOT="${ISSM_EXT_DIR}/sqlite/install" if [ -d "${SQLITE_ROOT}" ]; then - path_append "${SQLITE_ROOT}/bin" - library_path_append "${SQLITE_ROOT}/lib" - ld_library_path_append "${SQLITE_ROOT}/lib" -fi - -LIBTIFF_ROOT="${ISSM_EXT_SHARED_DIR}/libtiff/install" + path_prepend "${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" @@ -550,5 +559,5 @@ if [[ ${MINGW} -eq 1 ]]; then - path_append "${TRIANGLE_ROOT}/lib" # Allows dynamic loaded to find DLLs + path_append "${TRIANGLE_ROOT}/lib" # Allows dynamic loader to find DLLs fi fi Index: /issm/trunk/examples/Inversion/Square.par =================================================================== --- /issm/trunk/examples/Inversion/Square.par (revision 27034) +++ /issm/trunk/examples/Inversion/Square.par (revision 27035) @@ -11,5 +11,5 @@ disp(' creating drag'); -md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); +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); Index: /issm/trunk/examples/Inversion/runme.m =================================================================== --- /issm/trunk/examples/Inversion/runme.m (revision 27034) +++ /issm/trunk/examples/Inversion/runme.m (revision 27035) @@ -1,3 +1,3 @@ -steps=[1]; +steps=[4]; if any(steps==1) Index: /issm/trunk/examples/SlrGRACE/runme.m =================================================================== --- /issm/trunk/examples/SlrGRACE/runme.m (revision 27034) +++ /issm/trunk/examples/SlrGRACE/runme.m (revision 27035) @@ -1,11 +1,11 @@ -clear all; +%clear all; addpath('../Data','../Functions'); -steps=[1:7]; +%steps=[1:7]; if any(steps==1) % {{{ disp(' Step 1: Global mesh creation'); - numrefine=5; + numrefine=1; resolution=150*1e3; % inital resolution [m] radius = 6.371012*10^6; % mean radius of Earth, m @@ -50,5 +50,6 @@ save ./Models/SlrGRACE_Mesh md; - plotmodel (md,'data',md.mask.ocean_levelset,'edgecolor','k'); + plotmodel (md,'data',md.mask.ocean_levelset,'edgecolor','k','view',[45 45]); + end % }}} if any(steps==2) % {{{ @@ -70,5 +71,7 @@ md.geometry.surface=md.geometry.bed+md.geometry.thickness; - md.masstransport.spcthickness = [md.geometry.thickness + ice_load; 0]; + 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); @@ -140,5 +143,5 @@ md = loadmodel('./Models/SlrGRACE_Solution'); - sol1 = (md.masstransport.spcthickness(1:end-1)-md.geometry.thickness)*100; % [cm] + 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] @@ -208,6 +211,7 @@ % 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,size(ice_load,2)) + ice_load]; - md.masstransport.spcthickness =[ md.masstransport.spcthickness; 0:num_time-1]; + 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 @@ -241,13 +245,13 @@ md = loadmodel('./Models/SlrGRACE_Transient'); - time = md.masstransport.spcthickness(end,:); + 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)-md.geometry.thickness)*100; % [cm] + 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.mp4','Movie_slr.mp4'}; + movie_name = {'Movie_dH','Movie_slr'}; res = 1.0; @@ -273,5 +277,4 @@ vidObj = VideoWriter(movie_name{kk}); vidObj.FrameRate=2; % frames per second - vifObj.FileFormat='mp4'; open(vidObj); @@ -311,5 +314,4 @@ close(vidObj); end - !open *.mp4; % plot GMSL time series Index: /issm/trunk/externalpackages/autotools/install-linux.sh =================================================================== --- /issm/trunk/externalpackages/autotools/install-linux.sh (revision 27034) +++ /issm/trunk/externalpackages/autotools/install-linux.sh (revision 27035) @@ -7,5 +7,5 @@ AUTOCONF_VER="2.69" AUTOMAKE_VER="1.16.1" -LIBTOOL_VER="2.4.2" +LIBTOOL_VER="2.4.6" M4_VER="1.4.19" Index: /issm/trunk/externalpackages/autotools/install-mac.sh =================================================================== --- /issm/trunk/externalpackages/autotools/install-mac.sh (revision 27034) +++ /issm/trunk/externalpackages/autotools/install-mac.sh (revision 27035) @@ -7,5 +7,5 @@ AUTOCONF_VER="2.69" AUTOMAKE_VER="1.16.1" -LIBTOOL_VER="2.4.2" +LIBTOOL_VER="2.4.6" M4_VER="1.4.19" Index: /issm/trunk/externalpackages/autotools/install-win.sh =================================================================== --- /issm/trunk/externalpackages/autotools/install-win.sh (revision 27034) +++ /issm/trunk/externalpackages/autotools/install-win.sh (revision 27035) @@ -8,5 +8,5 @@ AUTOMAKE_MIN_VER="1.16" AUTOMAKE_VER="${AUTOMAKE_MIN_VER}.1" -LIBTOOL_VER="2.4.2" +LIBTOOL_VER="2.4.6" M4_VER="1.4.19" Index: /issm/trunk/externalpackages/curl/install-7-linux-static.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-7-linux-static.sh (revision 27034) +++ /issm/trunk/externalpackages/curl/install-7-linux-static.sh (revision 27035) @@ -34,5 +34,8 @@ --disable-ldaps \ --with-zlib="${ZLIB_ROOT}" \ - --without-libidn2 + --without-libidn2 \ + --without-nghttp2 \ + --without-brotli \ + --without-librtmp # Compile and install Index: /issm/trunk/externalpackages/curl/install-7-mac-static.sh =================================================================== --- /issm/trunk/externalpackages/curl/install-7-mac-static.sh (revision 27034) +++ /issm/trunk/externalpackages/curl/install-7-mac-static.sh (revision 27035) @@ -39,4 +39,7 @@ --with-zlib="${ZLIB_ROOT}" \ --without-libidn2 \ + --without-nghttp2 \ + --without-brotli \ + --without-librtmp \ --with-secure-transport Index: /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch (revision 27034) +++ /issm/trunk/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch (revision 27035) @@ -1,11 +1,11 @@ -67a68,75 +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) -> set( MPI_INCLUDE_PATH -> "/nasa/hpe/mpt/2.17r13/include" -> CACHE FILEPATH "Use installed MPI headers" FORCE) -> set( MPI_LIBRARY -> "/nasa/hpe/mpt/2.17r13/lib/libmpi.so" -> CACHE FILEPATH "Use installed MPI library" FORCE) 73,77c73,77 < #set(BOOST_ROOT @@ -16,5 +16,5 @@ --- > set(BOOST_ROOT -> "/nasa/pkgsrc/sles12/2018Q3/" +> "$ISSM_DIR/externalpackages/boost/install" > CACHE PATH "Use non-standard Boost install" FORCE) > set( Boost_NO_SYSTEM_PATHS TRUE Index: /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 27034) +++ /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 27035) @@ -3,4 +3,4 @@ --- > # TODO: Can't this be integrated into the following logic? -> set(BLAS_LIBS "-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core") -> set(LAPACK_LIBS "-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core") +> 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/trunk/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.pleiades.cmake =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.pleiades.cmake (revision 27035) +++ /issm/trunk/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.pleiades.cmake (revision 27035) @@ -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/trunk/externalpackages/dakota/install-6.2-discover.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-discover.sh (revision 27034) +++ /issm/trunk/externalpackages/dakota/install-6.2-discover.sh (revision 27035) @@ -37,16 +37,17 @@ cmake -D CMAKE_C_COMPILER=mpicc \ - -D CMAKE_CXX_COMPILER=mpicxx \ - -D CMAKE_Fortran_COMPILER=/usr/bin/gfortran \ - -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 + -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 \ + $DAK_SRC cd .. Index: /issm/trunk/externalpackages/dakota/install-6.2-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-6.2-pleiades.sh (revision 27034) +++ /issm/trunk/externalpackages/dakota/install-6.2-pleiades.sh (revision 27035) @@ -2,43 +2,56 @@ set -eu -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf build -rm -rf install -mkdir src build install -#Download from ISSM server -$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' +## Constants +# +VER="6.2" -#Untar -tar -zxvf dakota-6.2-public-src.tar.gz +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed -#Move Dakota to src directory -mv dakota-6.2.0.src/* src -rm -rf dakota-6.2.0.src +## Environment +# +export BLAS_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64 +export CXXFLAGS='-std=c++11' +export DAK_BUILD=${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 -#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/6.2/BuildDakotaCustom.cmake.pfe.patch -patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch -patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.pfe.patch +# Cleanup +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} -#Apply patches -patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch -patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch -patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" -#Configure dakota -cd $DAK_BUILD +# Unpack source +tar -zxvf dakota-${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=mpif77 \ + -DCMAKE_Fortran_COMPILER=/usr/bin/gfortran \ -DBoost_NO_BOOST_CMAKE=TRUE \ -DHAVE_ACRO=OFF \ @@ -50,10 +63,6 @@ ${DAK_SRC} -cd .. - -#Compile and install dakota -cd $DAK_BUILD -if [ $# -eq 0 ]; -then +# Compile and install +if [ $# -eq 0 ]; then make make install @@ -62,3 +71,8 @@ make -j $1 install fi -cd .. + +cd ${DAK_INSTALL} + +# Comment out definition of HAVE_MPI in Teuchos config header file in order to +# avoid conflict with our definition +sed -i -e "s/#define HAVE_MPI/\/* #define HAVE_MPI *\//g" include/Teuchos_config.h Index: /issm/trunk/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake (revision 27034) +++ /issm/trunk/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake (revision 27035) @@ -39,5 +39,5 @@ # Installation path (usually defaults to /usr/local) [auto]: -set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") +set (CMAKE_INSTALL_PREFIX "$ENV{PREFIX}") # Set install name suffix used for directories and gmt executables Index: /issm/trunk/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake =================================================================== --- /issm/trunk/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake (revision 27034) +++ /issm/trunk/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake (revision 27035) @@ -39,5 +39,5 @@ # Installation path (usually defaults to /usr/local) [auto]: -set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") +set (CMAKE_INSTALL_PREFIX "$ENV{PREFIX}") # Set install name suffix used for directories and gmt executables Index: /issm/trunk/externalpackages/hdf5/install-1-parallel-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1-parallel-with_tests.sh (revision 27035) +++ /issm/trunk/externalpackages/hdf5/install-1-parallel-with_tests.sh (revision 27035) @@ -0,0 +1,47 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="1.10.5" + +PREFIX="${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="${PREFIX}" \ + --enable-parallel \ + --with-zlib="${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 $1 install +fi Index: /issm/trunk/externalpackages/hdf5/install-1-parallel.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1-parallel.sh (revision 27035) +++ /issm/trunk/externalpackages/hdf5/install-1-parallel.sh (revision 27035) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="1.10.5" + +PREFIX="${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="${PREFIX}" \ + --enable-parallel \ + --with-zlib="${ZLIB_ROOT}" \ + --enable-hl + +# Compile and install +# +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/hdf5/install-1-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1-with_tests.sh (revision 27035) +++ /issm/trunk/externalpackages/hdf5/install-1-with_tests.sh (revision 27035) @@ -0,0 +1,42 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="1.10.5" + +PREFIX="${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="${PREFIX}" \ + --with-zlib="${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 $1 install +fi Index: sm/trunk/externalpackages/hdf5/install-1.10-parallel-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1.10-parallel-with_tests.sh (revision 27034) +++ (revision ) @@ -1,49 +1,0 @@ -#!/bin/bash -set -eu - - -# Constants -# -VER="1.10.5" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" - -## 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="${ISSM_DIR}/externalpackages/hdf5/install" \ - --enable-parallel \ - --with-zlib=${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 $1 install -fi - -# Return to initial directory -cd .. Index: sm/trunk/externalpackages/hdf5/install-1.10-parallel.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1.10-parallel.sh (revision 27034) +++ (revision ) @@ -1,47 +1,0 @@ -#!/bin/bash -set -eu - - -# Constants -# -VER="1.10.5" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" - -## 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="${ISSM_DIR}/externalpackages/hdf5/install" \ - --enable-parallel \ - --with-zlib=${ZLIB_ROOT} \ - --enable-hl - -# Compile and install -# -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Return to initial directory -cd .. Index: sm/trunk/externalpackages/hdf5/install-1.10-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1.10-with_tests.sh (revision 27034) +++ (revision ) @@ -1,44 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="1.10.5" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" - -# 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="${ISSM_DIR}/externalpackages/hdf5/install" \ - --with-zlib=${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 $1 install -fi - -# Return to initial directory -cd .. Index: sm/trunk/externalpackages/hdf5/install-1.10.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1.10.sh (revision 27034) +++ (revision ) @@ -1,42 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="1.10.5" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" - -# 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="${ISSM_DIR}/externalpackages/hdf5/install" \ - --with-zlib=${ZLIB_ROOT} \ - --enable-hl - -# Compile and install -# -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi - -# Return to initial directory -cd .. Index: /issm/trunk/externalpackages/hdf5/install-1.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install-1.sh (revision 27035) +++ /issm/trunk/externalpackages/hdf5/install-1.sh (revision 27035) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="1.10.5" + +PREFIX="${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="${PREFIX}" \ + --with-zlib="${ZLIB_ROOT}" \ + --enable-hl + +# Compile and install +# +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: sm/trunk/externalpackages/hdf5/install.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install.sh (revision 27034) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - -VER="1.8.9" - -# Cleanup -rm -rf src install hdf5-${VER} -mkdir src install - -# 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 - -# Move source to src directory -rm -rf src/* -mv hdf5-${VER}/* src/ -rm -rf hdf5-${VER} - -# This project uses C code with C++-style comments. As such, we need to specify -# a C standard that supports them. -export CFLAGS='-std=c99' - -# Configure, compile, and install -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/hdf5/install" - -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: /issm/trunk/externalpackages/mplapack/install-1-linux.sh =================================================================== --- /issm/trunk/externalpackages/mplapack/install-1-linux.sh (revision 27035) +++ /issm/trunk/externalpackages/mplapack/install-1-linux.sh (revision 27035) @@ -0,0 +1,74 @@ +#!/bin/bash +set -eu + +## +# Source code and installation guidelines available at, +# +# https://github.com/nakatamaho/mplapack +# +# Note that original website (for MPACK) at, +# +# http://mplapack.sourceforge.net +# +# is not maintained. +# + +## Constants +# +VER="1.0.1" + +PREFIX="${ISSM_DIR}/externalpackages/mplapack/install" # Set to location where external package should be installed + +## Environment +# +export CC=gcc +export CXX=g++ +export FC=gfortran +export F77=gfortran + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/mplapack-${VER}.tar.gz" "mplapack-${VER}.tar.gz" + +# Unpack source +tar -zxvf mplapack-${VER}.tar.gz + +# Move source to 'src' directory +mv mplapack-${VER}/* src +rm -rf mplapack-${VER} + +# Configure +cd src +pushd mplapack/test/compare +bash gen.Makefile.am.sh +popd +autoreconf --force --install +aclocal +autoconf +automake --add-missing +autoreconf --force --install +./configure \ + --prefix="${PREFIX}" \ + --disable-static \ + --enable-fast-install=yes \ + --disable-dependency-tracking \ + --enable-fortranwrapper=yes \ + --enable-gmp=yes \ + --enable-mpfr=yes \ + --enable-qd=yes \ + --enable-dd=yes \ + --enable-double=yes \ + --enable-_Float128=yes \ + --enable-_Float64x=yes + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/petsc/install-3.14-discover.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-discover.sh (revision 27034) +++ /issm/trunk/externalpackages/petsc/install-3.14-discover.sh (revision 27035) @@ -10,5 +10,5 @@ # Constants -VER="3.14.0" +VER="3.14.6" # Download source Index: /issm/trunk/externalpackages/petsc/install-3.14-linux.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-linux.sh (revision 27034) +++ /issm/trunk/externalpackages/petsc/install-3.14-linux.sh (revision 27035) @@ -5,5 +5,5 @@ ## Constants # -VER="3.14.0" +VER="3.14.6" PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS @@ -11,5 +11,5 @@ # Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" # Unpack source Index: /issm/trunk/externalpackages/petsc/install-3.14-mac-nohdf5.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-mac-nohdf5.sh (revision 27035) +++ /issm/trunk/externalpackages/petsc/install-3.14-mac-nohdf5.sh (revision 27035) @@ -0,0 +1,59 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.14.6" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Configure +# +# NOTE: +# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. +# (may need to remove it for earlier versions not using the C99 standard). +# - Added -fallow-argument-mismatch to FFLAGS in order to clear, +# +# error: The Fortran compiler gfortran will not compile files that call +# the same routine with arguments of different types. +# +# for gfortran 10 or later (may need to remove it for earlier versions). +# +cd ${PETSC_DIR} +./config/configure.py \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --CFLAGS="-Wno-error=implicit-function-declaration" \ + --FFLAGS="-fallow-argument-mismatch" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.14-mac.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-mac.sh (revision 27034) +++ /issm/trunk/externalpackages/petsc/install-3.14-mac.sh (revision 27035) @@ -4,8 +4,12 @@ ## Constants -VER="3.14.0" +# +VER="3.14.6" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed # Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" # Unpack source @@ -13,9 +17,9 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir ${PETSC_DIR} -# Move source to 'src' directory -mv petsc-${VER}/* src/ +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} rm -rf petsc-${VER} @@ -23,4 +27,6 @@ # # NOTE: +# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. +# (may need to remove it for earlier versions not using the C99 standard). # - Added -fallow-argument-mismatch to FFLAGS in order to clear, # @@ -29,11 +35,9 @@ # # for gfortran 10 or later (may need to remove it for earlier versions). -# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. -# (may need to remove it for earlier versions not using the C99 standard). # -cd src +cd ${PETSC_DIR} ./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ --CFLAGS="-Wno-error=implicit-function-declaration" \ --FFLAGS="-fallow-argument-mismatch" \ Index: /issm/trunk/externalpackages/petsc/install-3.14-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-pleiades.sh (revision 27035) +++ /issm/trunk/externalpackages/petsc/install-3.14-pleiades.sh (revision 27035) @@ -0,0 +1,50 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.14.6" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir ${PETSC_DIR} + +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} +rm -rf petsc-${VER} + +# Configure +cd ${PETSC_DIR} +./config/configure.py \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --CFLAGS="-g -O3" \ + --CXXFLAGS="-g -O3" \ + --FFLAGS="-g -O3" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --with-batch=1 \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl" \ + --with-scalapack-include=/nasa/intel/Compiler/2018.3.222/mkl/include \ + --with-scalapack-lib="/nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_scalapack_lp64.so /nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so" \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=0 \ + --download-mumps=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.14-tetralith.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-tetralith.sh (revision 27034) +++ /issm/trunk/externalpackages/petsc/install-3.14-tetralith.sh (revision 27035) @@ -10,5 +10,5 @@ # Constants -VER="3.14.0" +VER="3.14.6" # Download source Index: /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh (revision 27034) +++ /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh (revision 27035) @@ -18,5 +18,5 @@ ## Constants # -VER="3.14.4" +VER="3.14.6" MAKEFILE_GENERATOR='-G "MSYS Makefiles"' Index: /issm/trunk/externalpackages/petsc/install-3.15-discovery.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.15-discovery.sh (revision 27034) +++ /issm/trunk/externalpackages/petsc/install-3.15-discovery.sh (revision 27035) @@ -21,21 +21,23 @@ cd src ./config/configure.py \ - COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \ - --with-make-np=20 \ - --with-blas-lapack-dir=$MKL_ROOT \ - --with-mpi-dir="/optnfs/el7/mpich/3.3-intel19.3/" \ - --known-mpi-shared-libraries=1 \ - --known-mpi-long-double=1 \ - --known-mpi-int64_t=1 \ - --known-mpi-c-double-complex=1 \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 + COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \ + --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ + --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --with-make-np=20 \ + --with-blas-lapack-dir=$MKL_ROOT \ + --with-mpi-dir="/optnfs/el7/mpich/3.3-intel19.3/" \ + --known-mpi-shared-libraries=1 \ + --known-mpi-long-double=1 \ + --known-mpi-int64_t=1 \ + --known-mpi-c-double-complex=1 \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 # Compile and install Index: sm/trunk/externalpackages/petsc/install-3.15-mac-arm.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.15-mac-arm.sh (revision 27034) +++ (revision ) @@ -1,56 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -VER="3.15.2" - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" - -# Unpack source -tar -zxvf petsc-${VER}.tar.gz - -# Cleanup -rm -rf install src -mkdir install src - -# Move source to 'src' directory -mv petsc-${VER}/* src/ -rm -rf petsc-${VER} - -# Configure -# -# NOTE: -# - Added -fallow-argument-mismatch to FFLAGS in order to clear, -# -# error: The Fortran compiler gfortran will not compile files that call -# the same routine with arguments of different types. -# -# for gfortran 10 or later (may need to remove it for earlier versions). -# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. -# (may need to remove it for earlier versions not using the C99 standard). -# -cd src -./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --CFLAGS="-Wno-error=implicit-function-declaration" \ - --FFLAGS="-fallow-argument-mismatch" \ - --LDFLAGS="-Wl,-no_compact_unwind" \ - --with-debugging=0 \ - --with-valgrind=0 \ - --with-x=0 \ - --with-ssl=0 \ - --with-pic=1 \ - --download-fblaslapack=1 \ - --download-mpich=1 \ - --download-metis=1 \ - --download-parmetis=1 \ - --download-scalapack=1 \ - --download-mumps=1 \ - --download-zlib=1 - -# Compile and install -make -make install Index: /issm/trunk/externalpackages/petsc/install-3.15-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.15-pleiades.sh (revision 27034) +++ /issm/trunk/externalpackages/petsc/install-3.15-pleiades.sh (revision 27035) @@ -7,6 +7,9 @@ VER="3.15.0" +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + # Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.15.0.tar.gz' 'petsc-3.15.0.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" # Unpack source @@ -28,10 +31,10 @@ cd src ./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ - --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort\ - -COPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" -CXXOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" -FOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl" \ + --with-scalapack-include=/nasa/intel/Compiler/2018.3.222/mkl/include \ + --with-scalapack-lib="/nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_scalapack_lp64.so /nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so" \ --with-make-np=10 \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/" \ --known-mpi-shared-libraries=1 \ --with-debugging=0 \ @@ -44,5 +47,5 @@ --download-parmetis=1 \ --download-mumps=1 \ - --download-scalapack=1 + --download-scalapack=0 # Compile and install Index: /issm/trunk/externalpackages/petsc/install-3.16-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.16-pleiades.sh (revision 27035) +++ /issm/trunk/externalpackages/petsc/install-3.16-pleiades.sh (revision 27035) @@ -0,0 +1,53 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.16.4" + +PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to $PETSC_DIR +mv petsc-${VER}/* src/ +rm -rf petsc-${VER} + + +# Configure +# +# NOTE: Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables; look for CONFIGURE_OPTIONS +# +cd src +./config/configure.py \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl" \ + --with-scalapack-include=/nasa/intel/Compiler/2018.3.222/mkl/include \ + --with-scalapack-lib="/nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_scalapack_lp64.so /nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so" \ + --with-make-np=10 \ + --known-mpi-shared-libraries=1 \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-batch=1 \ + --with-shared-libraries=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-mumps=1 \ + --download-scalapack=0 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.17-mac-m1.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.17-mac-m1.sh (revision 27035) +++ /issm/trunk/externalpackages/petsc/install-3.17-mac-m1.sh (revision 27035) @@ -0,0 +1,42 @@ +#!/bin/bash +set -eu + + +## Constants +VER="3.17.0" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv petsc-${VER}/* src/ +rm -rf petsc-${VER} + +cd src +./config/configure.py \ + --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ + --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --LDFLAGS="-Wl,-no_compact_unwind" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-pic=1 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 + +# Compile and install +make +make install Index: /issm/trunk/externalpackages/proj/install-6-static.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-6-static.sh (revision 27035) +++ /issm/trunk/externalpackages/proj/install-6-static.sh (revision 27035) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="6.2.1" + +PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed + +## Environment +# +export CC=mpicc +export CXX=mpicxx + +# NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently +# requires, +# +# SQLITE3_LIBS="-lsqlite3". +# +# On Ubuntu Linux, install the SQLite3 binary, libraries and headers with, +# +# apt-get install sqlite3 libsqlite3-dev +# +export SQLITE3_LIBS="-lsqlite3" + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/proj-${VER}.tar.gz" "proj-${VER}.tar.gz" + +# Unpack source +tar -zxvf proj-${VER}.tar.gz + +# Move source into 'src' directory +mv proj-${VER}/* src +rm -rf proj-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-shared \ + --disable-tiff + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/proj/install-6.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-6.sh (revision 27034) +++ /issm/trunk/externalpackages/proj/install-6.sh (revision 27035) @@ -13,13 +13,13 @@ export CC=mpicc export CXX=mpicxx + # NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently -# requires, +# requires, # -# SQLITE3_LIBS="-lsqlite3". +# SQLITE3_LIBS="-lsqlite3". # -# On Ubuntu Linux, install the SQLite3 binary, libraries and headers -# with, +# On Ubuntu Linux, install the SQLite3 binary, libraries and headers with, # -# `apt-get install sqlite3 libsqlite3-dev` +# apt-get install sqlite3 libsqlite3-dev # export SQLITE3_LIBS="-lsqlite3" Index: /issm/trunk/externalpackages/proj/install-8-static-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-8-static-with_tests.sh (revision 27034) +++ /issm/trunk/externalpackages/proj/install-8-static-with_tests.sh (revision 27035) @@ -7,5 +7,5 @@ VER="8.1.0" -PREFIX="${ISSM_EXT_STATIC_DIR}/proj/install" # Set to location where external package should be installed +PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed ## Environment @@ -21,5 +21,5 @@ # On Ubuntu Linux, install the SQLite3 binary, libraries and headers with, # -# `apt-get install sqlite3 libsqlite3-dev` +# apt-get install sqlite3 libsqlite3-dev # export SQLITE3_LIBS="-lsqlite3" Index: /issm/trunk/externalpackages/proj/install-8-static.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-8-static.sh (revision 27034) +++ /issm/trunk/externalpackages/proj/install-8-static.sh (revision 27035) @@ -7,5 +7,5 @@ VER="8.1.0" -PREFIX="${ISSM_EXT_STATIC_DIR}/proj/install" # Set to location where external package should be installed +PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed ## Environment @@ -21,5 +21,5 @@ # On Ubuntu Linux, install the SQLite3 binary, libraries and headers with, # -# `apt-get install sqlite3 libsqlite3-dev` +# apt-get install sqlite3 libsqlite3-dev # export SQLITE3_LIBS="-lsqlite3" Index: /issm/trunk/externalpackages/proj/install-8-with_tests.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-8-with_tests.sh (revision 27034) +++ /issm/trunk/externalpackages/proj/install-8-with_tests.sh (revision 27035) @@ -7,5 +7,5 @@ VER="8.1.0" -PREFIX="${ISSM_EXT_SHARED_DIR}/proj/install" # Set to location where external package should be installed +PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed ## Environment @@ -21,5 +21,5 @@ # On Ubuntu Linux, install the SQLite3 binary, libraries and headers with, # -# `apt-get install sqlite3 libsqlite3-dev` +# apt-get install sqlite3 libsqlite3-dev # export SQLITE3_LIBS="-lsqlite3" Index: /issm/trunk/externalpackages/proj/install-8.sh =================================================================== --- /issm/trunk/externalpackages/proj/install-8.sh (revision 27034) +++ /issm/trunk/externalpackages/proj/install-8.sh (revision 27035) @@ -21,5 +21,5 @@ # On Ubuntu Linux, install the SQLite3 binary, libraries and headers with, # -# `apt-get install sqlite3 libsqlite3-dev` +# apt-get install sqlite3 libsqlite3-dev # export SQLITE3_LIBS="-lsqlite3" Index: /issm/trunk/externalpackages/python/install-2-linux.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2-linux.sh (revision 27035) +++ /issm/trunk/externalpackages/python/install-2-linux.sh (revision 27035) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure python +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/python/install" \ + --enable-shared + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install/include +cp python2.7/* ./ +cd ../lib +ln -s libpython2.7.so.1.0 libpython.so Index: /issm/trunk/externalpackages/python/install-2-mac-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2-mac-snowleopard.sh (revision 27035) +++ /issm/trunk/externalpackages/python/install-2-mac-snowleopard.sh (revision 27035) @@ -0,0 +1,41 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#exports +export MACOSX_DEPLOYMENT_TARGET=10.6 + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure doxygen +cd src +# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory +# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include +./configure --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" \ + LDFLAGS="-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/ -lgfortran " + +#make +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install +ln -s Library/Frameworks/Python.framework/Headers include +ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib + +#Patch pyport.h: +cd include +patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: /issm/trunk/externalpackages/python/install-2-mac.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2-mac.sh (revision 27035) +++ /issm/trunk/externalpackages/python/install-2-mac.sh (revision 27035) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure and compile +cd src +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install + +#get rid of bin, because it's just a copy of +#Library/Frameworks/Python.framework/Versions/2.7/bin, and will not reflect +#new changes being made +rm -rf bin +ln -s Library/Frameworks/Python.framework/Headers include +ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib +ln -s Library/Frameworks/Python.framework/Versions/2.7/bin bin + +#Patch pyport.h: +cd include +patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: sm/trunk/externalpackages/python/install-2.7.3-linux64.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2.7.3-linux64.sh (revision 27034) +++ (revision ) @@ -1,33 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install src -rm -rf Python-2.7.3 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz - -#Untar and move python into install directory -tar -zxvf Python-2.7.3.tgz -mv Python-2.7.3/* src -rm -rf Python-2.7.3 - -#Configure python -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/python/install" \ - --enable-shared - -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install - -cd ../install/include -cp python2.7/* ./ -cd ../lib -ln -s libpython2.7.so.1.0 libpython.so Index: sm/trunk/externalpackages/python/install-2.7.3-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2.7.3-macosx-snowleopard.sh (revision 27034) +++ (revision ) @@ -1,41 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install src -rm -rf Python-2.7.3 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz - -#exports -export MACOSX_DEPLOYMENT_TARGET=10.6 - -#Untar and move python into install directory -tar -zxvf Python-2.7.3.tgz -mv Python-2.7.3/* src -rm -rf Python-2.7.3 - -#Configure doxygen -cd src -# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory -# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include -./configure --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" \ - LDFLAGS="-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/ -lgfortran " - -#make -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install - -cd ../install -ln -s Library/Frameworks/Python.framework/Headers include -ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib - -#Patch pyport.h: -cd include -patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: sm/trunk/externalpackages/python/install-2.7.3-macosx.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2.7.3-macosx.sh (revision 27034) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install src -rm -rf Python-2.7.3 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz - -#Untar and move python into install directory -tar -zxvf Python-2.7.3.tgz -mv Python-2.7.3/* src -rm -rf Python-2.7.3 - -#Configure and compile -cd src -./configure \ - --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install - -cd ../install - -#get rid of bin, because it's just a copy of -#Library/Frameworks/Python.framework/Versions/2.7/bin, and will not reflect -#new changes being made -rm -rf bin -ln -s Library/Frameworks/Python.framework/Headers include -ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib -ln -s Library/Frameworks/Python.framework/Versions/2.7/bin bin - -#Patch pyport.h: -cd include -patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: /issm/trunk/externalpackages/python/install-3-linux.sh =================================================================== --- /issm/trunk/externalpackages/python/install-3-linux.sh (revision 27035) +++ /issm/trunk/externalpackages/python/install-3-linux.sh (revision 27035) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-3.2.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz + +#exports +export CC + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* src +rm -rf Python-3.2.2 + +#Configure python +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/python/install" \ + --enable-shared + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install/bin +ln -s python3.2 python +cd ../ +ln -s Python.framework/Versions/3.2/include/python3.2m include +ln -s Python.framework/Versions/3.2/lib/ lib Index: /issm/trunk/externalpackages/python/install-3-mac-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/python/install-3-mac-snowleopard.sh (revision 27035) +++ /issm/trunk/externalpackages/python/install-3-mac-snowleopard.sh (revision 27035) @@ -0,0 +1,41 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-3.2.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz + +#exports +export CC +export MACOSX_DEPLOYMENT_TARGET=10.6 + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* src +rm -rf Python-3.2.2 + +#Configure doxygen +cd src +# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory +# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" + +#make +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install +cd .. + +cd install/bin +ln -s python3.2 python +cd ../ +ln -s Python.framework/Versions/3.2/include/python3.2m include +ln -s Python.framework/Versions/3.2/lib/ lib Index: /issm/trunk/externalpackages/python/install-3-mac.sh =================================================================== --- /issm/trunk/externalpackages/python/install-3-mac.sh (revision 27035) +++ /issm/trunk/externalpackages/python/install-3-mac.sh (revision 27035) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-3.2.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz + +#exports +export CC + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* src +rm -rf Python-3.2.2 + +#Configure doxygen +cd src +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" + +#obsolete? +#./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" + +#make +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd install/bin +ln -s python3.2 python +cd ../ +ln -s Python.framework/Versions/3.2/include/python3.2m include +ln -s Python.framework/Versions/3.2/lib/ lib Index: sm/trunk/externalpackages/python/install-3.2.2-linux64.sh =================================================================== --- /issm/trunk/externalpackages/python/install-3.2.2-linux64.sh (revision 27034) +++ (revision ) @@ -1,37 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install src -rm -rf Python-3.2.2 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz - -#exports -export CC - -#Untar and move python into install directory -tar -zxvf Python-3.2.2.tgz -mv Python-3.2.2/* src -rm -rf Python-3.2.2 - -#Configure python -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/python/install" \ - --enable-shared - -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install - -cd ../install/bin -ln -s python3.2 python -cd ../ -ln -s Python.framework/Versions/3.2/include/python3.2m include -ln -s Python.framework/Versions/3.2/lib/ lib Index: sm/trunk/externalpackages/python/install-3.2.2-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/python/install-3.2.2-macosx-snowleopard.sh (revision 27034) +++ (revision ) @@ -1,41 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install src -rm -rf Python-3.2.2 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz - -#exports -export CC -export MACOSX_DEPLOYMENT_TARGET=10.6 - -#Untar and move python into install directory -tar -zxvf Python-3.2.2.tgz -mv Python-3.2.2/* src -rm -rf Python-3.2.2 - -#Configure doxygen -cd src -# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory -# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include -./configure \ - --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" - -#make -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install -cd .. - -cd install/bin -ln -s python3.2 python -cd ../ -ln -s Python.framework/Versions/3.2/include/python3.2m include -ln -s Python.framework/Versions/3.2/lib/ lib Index: sm/trunk/externalpackages/python/install-3.2.2-macosx.sh =================================================================== --- /issm/trunk/externalpackages/python/install-3.2.2-macosx.sh (revision 27034) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install src -rm -rf Python-3.2.2 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz - -#exports -export CC - -#Untar and move python into install directory -tar -zxvf Python-3.2.2.tgz -mv Python-3.2.2/* src -rm -rf Python-3.2.2 - -#Configure doxygen -cd src -./configure \ - --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" - -#obsolete? -#./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" - -#make -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install - -cd install/bin -ln -s python3.2 python -cd ../ -ln -s Python.framework/Versions/3.2/include/python3.2m include -ln -s Python.framework/Versions/3.2/lib/ lib Index: /issm/trunk/externalpackages/sqlite/install.sh =================================================================== --- /issm/trunk/externalpackages/sqlite/install.sh (revision 27034) +++ /issm/trunk/externalpackages/sqlite/install.sh (revision 27035) @@ -3,9 +3,13 @@ +# Constants +# VER="3300100" +PREFIX="${ISSM_DIR}/externalpackages/sqlite/install" # Set to location where external package should be installed + # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source @@ -13,14 +17,14 @@ # Unpack source -tar -zxvf sqlite-autoconf-$VER.tar.gz +tar -zxvf sqlite-autoconf-${VER}.tar.gz # Move source into 'src' directory -mv sqlite-autoconf-$VER/* src -rm -rf sqlite-autoconf-$VER +mv sqlite-autoconf-${VER}/* src +rm -rf sqlite-autoconf-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/sqlite/install" + --prefix="${PREFIX}" # Compile and install Index: /issm/trunk/jenkins/aws-amazon_linux-solid_earth =================================================================== --- /issm/trunk/jenkins/aws-amazon_linux-solid_earth (revision 27034) +++ /issm/trunk/jenkins/aws-amazon_linux-solid_earth (revision 27035) @@ -42,5 +42,5 @@ curl install-7-linux.sh netcdf install-4.7-parallel.sh - proj install-8.sh + proj install-6.sh gdal install-3-python.sh gshhg install.sh Index: /issm/trunk/jenkins/jenkins.sh =================================================================== --- /issm/trunk/jenkins/jenkins.sh (revision 27034) +++ /issm/trunk/jenkins/jenkins.sh (revision 27035) @@ -345,8 +345,10 @@ EOF cd $ISSM_DIR/test/NightlyRun + + # NOTE: We redirect all output to logfile in order to catch certain errors. For some reason, this does not work under Windows: the logifle option must be used and process must be run in background if [[ "${OS}" == CYGWIN* || ${MINGW} -eq 1 ]]; then $MATLAB_PATH/bin/matlab -nodesktop -nosplash -nojvm -r "addpath ${ISSM_DIR_WIN}/src/m/dev; devpath; addpath ${ISSM_DIR_WIN}/nightlylog; matlab_run$i" -logfile ${ISSM_DIR_WIN}/nightlylog/matlab_log$i.log & else - $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath ${ISSM_DIR}/src/m/dev; devpath; addpath ${ISSM_DIR}/nightlylog; matlab_run$i" -logfile ${ISSM_DIR}/nightlylog/matlab_log$i.log & + $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath ${ISSM_DIR}/src/m/dev; devpath; addpath ${ISSM_DIR}/nightlylog; matlab_run$i" &> ${ISSM_DIR}/nightlylog/matlab_log$i.log & fi done @@ -377,8 +379,22 @@ echo "pid: ${pid}" echo '-----------------------------' - while [ -n "${pid}" ]; do + + # Time out after $max_time seconds because sometimes multiple MATLAB processes get locked in race condition + timer=0 + max_time=7200 + while [[ $timer -lt $max_time && -n "${pid}" ]]; do pid=$(ps -W | grep MATLAB | awk '{print $1}') + timer=$((timer + 1)) sleep 1; done + + # Check if timer hit $max_time + if [ $timer -eq $max_time ]; then + echo "Testing timed out at ${timer} seconds" + # Kill MATLAB processes + pid=$(ps -W | grep MATLAB | awk '{print $1}') + echo "${pid}" | xargs /bin/kill -f + exit 1 + fi else wait Index: /issm/trunk/jenkins/pine_island-mac-adolc-ampion =================================================================== --- /issm/trunk/jenkins/pine_island-mac-adolc-ampion (revision 27034) +++ /issm/trunk/jenkins/pine_island-mac-adolc-ampion (revision 27035) @@ -18,5 +18,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/10.3.0/lib/gcc/10 -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ Index: /issm/trunk/jenkins/pine_island-mac-basic =================================================================== --- /issm/trunk/jenkins/pine_island-mac-basic (revision 27034) +++ /issm/trunk/jenkins/pine_island-mac-basic (revision 27035) @@ -12,5 +12,5 @@ --with-numthreads=4 \ --with-matlab-dir=${MATLAB_PATH} \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/10.3.0/lib/gcc/10 -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ Index: /issm/trunk/jenkins/pine_island-mac-binaries-matlab =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-matlab (revision 27034) +++ /issm/trunk/jenkins/pine_island-mac-binaries-matlab (revision 27035) @@ -19,5 +19,5 @@ --disable-dependency-tracking \ --with-matlab-dir=${MATLAB_PATH} \ - --with-fortran-lib="/usr/local/Cellar/gcc/10.3.0/lib/gcc/10/libgfortran.a /usr/local/Cellar/gcc/10.3.0/lib/gcc/10/libquadmath.a /usr/local/Cellar/gcc/10.3.0/lib/gcc/10/gcc/x86_64-apple-darwin15/10.3.0/libgcc.a" \ + --with-fortran-lib="/usr/local/Cellar/gcc/11.3.0/lib/gcc/11/libgfortran.a /usr/local/Cellar/gcc/11.3.0/lib/gcc/11/libquadmath.a /usr/local/Cellar/gcc/11.3.0/lib/gcc/11/gcc/x86_64-apple-darwin15/11/libgcc.a" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ @@ -52,5 +52,5 @@ curl install-7-mac-static.sh netcdf install-4.7-parallel-static.sh - proj install-8-static.sh + proj install-6-static.sh gdal install-3-static.sh gshhg install.sh Index: sm/trunk/jenkins/pine_island-mac-binaries-python =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-python (revision 27034) +++ (revision ) @@ -1,89 +1,0 @@ -#--------------------# -# ISSM Configuration # -#--------------------# - -# NOTE: -# - We can disable dependency tracking in the Autotools because the binaries -# should always be a one-time build. -# - -# ISSM CONFIGURATION -ISSM_CONFIG='\ - --prefix=${ISSM_DIR} \ - --enable-standalone-executables \ - --enable-standalone-modules \ - --enable-standalone-libraries \ - --disable-dependency-tracking \ - --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ - --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="/usr/local/Cellar/gcc/10.3.0/lib/gcc/10/libgfortran.a /usr/local/Cellar/gcc/10.3.0/lib/gcc/10/libquadmath.a /usr/local/Cellar/gcc/10.3.0/lib/gcc/10/gcc/x86_64-apple-darwin15/10.3.0/libgcc.a" \ - --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ - --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ - --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ - --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ - --with-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ - --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ -' - -#-------------------# -# External Packages # -#-------------------# - -EXTERNALPACKAGES=" - autotools install-mac.sh - cmake install.sh - petsc install-3.12-mac-static.sh - gsl install-static.sh - boost install-1.7-mac-static.sh - dakota install-6.2-mac-static.sh - curl install-7-mac-static.sh - netcdf install-4.7-parallel-static.sh - proj install-8-static.sh - gdal install-3-python-static.sh - gshhg install.sh - gmt install-6-mac-static.sh - gmsh install-4-static.sh - triangle install-mac-static.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh -" - -#---------# -# Testing # -#---------# - -# Test suites -MATLAB_TEST=0 -PYTHON_TEST=0 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - -# Number of CPUs used in ISSM compilation -# -# NOTE: One is usually safer as some packages are very sensitive to parallel -# compilation -# -NUMCPUS_INSTALL=8 - -# Number of CPUs used in the nightly runs -NUMCPUS_RUN=1 - -# Nightly run options -# -# See documentation in test/NightlyRun/runme.* for more information. -# -PYTHON_NROPTIONS="" -MATLAB_NROPTIONS="" Index: /issm/trunk/jenkins/pine_island-mac-binaries-python-2 =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-python-2 (revision 27035) +++ /issm/trunk/jenkins/pine_island-mac-binaries-python-2 (revision 27035) @@ -0,0 +1,89 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# + +# ISSM CONFIGURATION +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ + --with-fortran-lib="/usr/local/Cellar/gcc/11.3.0/lib/gcc/11/libgfortran.a /usr/local/Cellar/gcc/11.3.0/lib/gcc/11/libquadmath.a /usr/local/Cellar/gcc/11.3.0/lib/gcc/11/gcc/x86_64-apple-darwin15/11/libgcc.a" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-mac.sh + cmake install.sh + petsc install-3.12-mac-static.sh + gsl install-static.sh + boost install-1.7-mac-static.sh + dakota install-6.2-mac-static.sh + curl install-7-mac-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6-static.sh + gdal install-3-python-static.sh + gshhg install.sh + gmt install-6-mac-static.sh + gmsh install-4-static.sh + triangle install-mac-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +PYTHON_NROPTIONS="" +MATLAB_NROPTIONS="" Index: /issm/trunk/jenkins/pine_island-mac-binaries-python-3 =================================================================== --- /issm/trunk/jenkins/pine_island-mac-binaries-python-3 (revision 27035) +++ /issm/trunk/jenkins/pine_island-mac-binaries-python-3 (revision 27035) @@ -0,0 +1,90 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# + +# ISSM CONFIGURATION +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-python-version=3.4 \ + --with-python-dir=/Library/Frameworks/Python.framework/Versions/3.4 \ + --with-python-numpy-dir=/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/numpy \ + --with-fortran-lib="/usr/local/Cellar/gcc/11.3.0/lib/gcc/11/libgfortran.a /usr/local/Cellar/gcc/11.3.0/lib/gcc/11/libquadmath.a /usr/local/Cellar/gcc/11.3.0/lib/gcc/11/gcc/x86_64-apple-darwin15/11/libgcc.a" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-mac.sh + cmake install.sh + petsc install-3.12-mac-static.sh + gsl install-static.sh + boost install-1.7-mac-static.sh + dakota install-6.2-mac-static.sh + curl install-7-mac-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6-static.sh + gdal install-3-python-static.sh + gshhg install.sh + gmt install-6-mac-static.sh + gmsh install-4-static.sh + triangle install-mac-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +PYTHON_NROPTIONS="" +MATLAB_NROPTIONS="" Index: /issm/trunk/jenkins/pine_island-mac-dakota =================================================================== --- /issm/trunk/jenkins/pine_island-mac-dakota (revision 27034) +++ /issm/trunk/jenkins/pine_island-mac-dakota (revision 27035) @@ -18,5 +18,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/10.3.0/lib/gcc/10 -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ Index: /issm/trunk/jenkins/pine_island-mac-examples =================================================================== --- /issm/trunk/jenkins/pine_island-mac-examples (revision 27034) +++ /issm/trunk/jenkins/pine_island-mac-examples (revision 27035) @@ -20,5 +20,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/10.3.0/lib/gcc/10 -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ Index: /issm/trunk/jenkins/pine_island-mac-full =================================================================== --- /issm/trunk/jenkins/pine_island-mac-full (revision 27034) +++ /issm/trunk/jenkins/pine_island-mac-full (revision 27035) @@ -17,5 +17,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/10.3.0/lib/gcc/10 -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ @@ -50,5 +50,5 @@ curl install-7-mac.sh netcdf install-4.7-parallel.sh - proj install-8.sh + proj install-6.sh gdal install-3-python.sh gshhg install.sh Index: /issm/trunk/jenkins/pine_island-mac-full-valgrind =================================================================== --- /issm/trunk/jenkins/pine_island-mac-full-valgrind (revision 27034) +++ /issm/trunk/jenkins/pine_island-mac-full-valgrind (revision 27035) @@ -17,5 +17,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/10.3.0/lib/gcc/10 -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ @@ -50,5 +50,5 @@ curl install-7-mac.sh netcdf install-4.7-parallel.sh - proj install-8.sh + proj install-6.sh gdal install-3-python.sh gshhg install.sh Index: sm/trunk/jenkins/pine_island-mac-python =================================================================== --- /issm/trunk/jenkins/pine_island-mac-python (revision 27034) +++ (revision ) @@ -1,90 +1,0 @@ -#--------------------# -# ISSM Configuration # -#--------------------# - -ISSM_CONFIG='\ - --prefix=${ISSM_DIR} \ - --disable-static \ - --enable-development \ - --enable-debugging \ - --with-numthreads=4 \ - --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ - --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/10.3.0/lib/gcc/10 -lgfortran" \ - --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ - --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ - --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ - --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ - --with-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ - --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ -' - -#-------------------# -# External Packages # -#-------------------# - -# List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES=" - autotools install-mac.sh - cmake install.sh - petsc install-3.12-mac.sh - gsl install.sh - boost install-1.7-mac.sh - dakota install-6.2-mac.sh - curl install-7-mac.sh - netcdf install-4.7-parallel.sh - proj install-8.sh - gdal install-3-python.sh - gshhg install.sh - gmt install-6-mac.sh - gmsh install-4.sh - triangle install-mac.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh -" - -#---------# -# Testing # -#---------# - -# Test suites -MATLAB_TEST=0 -PYTHON_TEST=1 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - -# Number of CPUs used in ISSM compilation -# -# NOTE: One is usually safer as some packages are very sensitive to parallel -# compilation -# -NUMCPUS_INSTALL=4 - -# Number of CPUs used in the nightly runs -NUMCPUS_RUN=2 - -# Nightly run options -# -# See documentation in test/NightlyRun/runme.* for more information. -# -# NOTE: -# - Errors are large for tests 234 418 and 420 under Python -# - See test417.py for why it is excluded -# - Test 444 fails intermittently under Python with "IndexError: list index out of range" -# - Tests 701, 702, and 703 are skipped because they use full Stokes equations -# -MATLAB_NROPTIONS="" -PYTHON_NROPTIONS="--exclude 234 417 418 420 435 444 445 701 702 703" Index: /issm/trunk/jenkins/pine_island-mac-solid_earth =================================================================== --- /issm/trunk/jenkins/pine_island-mac-solid_earth (revision 27034) +++ /issm/trunk/jenkins/pine_island-mac-solid_earth (revision 27035) @@ -18,5 +18,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/10.3.0/lib/gcc/10 -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ @@ -90,5 +90,7 @@ # NOTE: # - Excluding 2006 until it can be debugged (file I/O) +# - Excluding 2012 until it can be looked at by Eric ("FindParam error message: Parameter HydrologyModel not set") +# - Excluding 2091 until it can be debugged (resource starvation) # -MATLAB_NROPTIONS="'benchmark','slc','exclude',[2004 2006 2051 2052 2053 2084 2085 2424 2425]" -PYTHON_NROPTIONS="--benchmark slc --exclude 2004 2006 2051 2052 2053 2084 2085 2424 2425" +MATLAB_NROPTIONS="'benchmark','slc','exclude',[2004 2006 2012 2051 2052 2053 2085 2091 2424 2425]" +PYTHON_NROPTIONS="--benchmark slc --exclude 2004 2006 2012 2051 2052 2053 2085 2091 2424 2425" Index: /issm/trunk/jenkins/pine_island-mac-solid_earth-lambert =================================================================== --- /issm/trunk/jenkins/pine_island-mac-solid_earth-lambert (revision 27034) +++ /issm/trunk/jenkins/pine_island-mac-solid_earth-lambert (revision 27035) @@ -18,5 +18,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/Cellar/gcc/10.3.0/lib/gcc/10 -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ @@ -90,5 +90,6 @@ # NOTE: # - Excluding 2006 until it can be debugged (file I/O) +# - Excluding 2091 until it can be debugged (resource starvation) # -MATLAB_NROPTIONS="'benchmark','slc','exclude',[2006]" -PYTHON_NROPTIONS="--benchmark slc --exclude 2005 2006" +MATLAB_NROPTIONS="'benchmark','slc','exclude',[2006 2091]" +PYTHON_NROPTIONS="--benchmark slc --exclude 2006 2091" Index: /issm/trunk/jenkins/pleiades-dakota =================================================================== --- /issm/trunk/jenkins/pleiades-dakota (revision 27035) +++ /issm/trunk/jenkins/pleiades-dakota (revision 27035) @@ -0,0 +1,67 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=$ISSM_DIR \ + --enable-development \ + --enable-standalone-libraries \ + --with-wrappers=no \ + --with-vendor="intel-pleiades-mpi" \ + --with-cxxoptflags="-O3 " \ + --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \ + --with-boost-dir="${ISSM_DIR}/externalpackages/boost/install" \ + --with-dakota-dir="${ISSM_DIR}/externalpackages/dakota/install" \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-mpi-include=" " \ + --with-mpi-libflags=" -lmpi" \ + --with-mkl-libflags="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \ + --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-scalapack-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-fortran-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin/ -lifcore -lifport -lgfortran" \ +' + +#-------------------# +# External Packages # +#-------------------# + +# NOTE: Python 3 is installed only as a build system for GSL +EXTERNALPACKAGES=" + python install-3-linux.sh + petsc install-3.14-pleiades.sh + gsl install-pleiades.sh + boost install-1.55-pleiades.sh + dakota install-6.2-pleiades.sh + m1qn3 install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/pleiades-solid_earth =================================================================== --- /issm/trunk/jenkins/pleiades-solid_earth (revision 27035) +++ /issm/trunk/jenkins/pleiades-solid_earth (revision 27035) @@ -0,0 +1,83 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +ISSM_CONFIG='\ + --prefix=$ISSM_DIR \ + --enable-development \ + --enable-standalone-libraries \ + --with-wrappers=no \ + --with-vendor="intel-pleiades-mpi" \ + --with-cxxoptflags="-O3 " \ + --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \ + --with-boost-dir="${ISSM_DIR}/externalpackages/boost/install" \ + --with-dakota-dir="${ISSM_DIR}/externalpackages/dakota/install" \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-mpi-include=" " \ + --with-mpi-libflags=" -lmpi" \ + --with-mkl-libflags="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \ + --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-scalapack-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-fortran-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin/ -lifcore -lifport -lgfortran" \ +' + +#-------------------# +# External Packages # +#-------------------# + +# NOTE: +# - Python 3 is installed only as a build system for GSL +# - shell2junit is included to run test suites via jenkins.sh +# +EXTERNALPACKAGES=" + python install-3-linux.sh + petsc install-3.14-pleiades.sh + zlib install-1.sh + hdf5 install-1-parallel.sh + gsl install-pleiades.sh + boost install-1.55-pleiades.sh + dakota install-6.2-pleiades.sh + curl install-7-linux.sh + netcdf install-4.7-parallel.sh + sqlite install.sh + proj install-6.sh + gdal install-3.sh + gshhg install.sh + gmt install-6-linux.sh + gmsh install-4.sh + triangle install-linux.sh + chaco install.sh + m1qn3 install.sh + semic install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-binaries-matlab =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-matlab (revision 27034) +++ /issm/trunk/jenkins/ross-debian_linux-binaries-matlab (revision 27035) @@ -50,5 +50,5 @@ curl install-7-linux-static.sh netcdf install-4.7-parallel-static.sh - proj install-8-static.sh + proj install-6-static.sh gdal install-3-static.sh gshhg install.sh Index: sm/trunk/jenkins/ross-debian_linux-binaries-python =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-python (revision 27034) +++ (revision ) @@ -1,89 +1,0 @@ -#--------------------# -# ISSM Configuration # -#--------------------# - -# NOTE: -# - We can disable dependency tracking in the Autotools because the binaries -# should always be a one-time build. -# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is -# copied by packaging script. -# -ISSM_CONFIG='\ - --prefix=${ISSM_DIR} \ - --enable-standalone-executables \ - --enable-standalone-modules \ - --enable-standalone-libraries \ - --disable-dependency-tracking \ - --with-pic \ - --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ - --with-fortran-lib="-L${ISSM_DIR}/lib -lgfortran" \ - --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ - --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ - --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ - --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ - --with-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ - --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ -' -#-------------------# -# External Packages # -#-------------------# - -EXTERNALPACKAGES=" - autotools install-linux.sh - cmake install.sh - petsc install-3.12-linux-static.sh - gsl install-static.sh - boost install-1.7-linux-static.sh - dakota install-6.2-linux-static.sh - curl install-7-linux-static.sh - netcdf install-4.7-parallel-static.sh - proj install-8-static.sh - gdal install-3-python-static.sh - gshhg install.sh - gmt install-6-linux-static.sh - gmsh install-4-static.sh - triangle install-linux-static.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - shell2junit install.sh -" - -#---------# -# Testing # -#---------# - -# Test suites -MATLAB_TEST=0 -PYTHON_TEST=0 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - -# Number of CPUs used in ISSM compilation -# -# NOTE: One is usually safer as some packages are very sensitive to parallel -# compilation. -# -NUMCPUS_INSTALL=8 - -# Number of CPUs used in the nightly runs -NUMCPUS_RUN=1 - -# Nightly run options -# -# See documentation in test/NightlyRun/runme.* for more information. -# -MATLAB_NROPTIONS="" -PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-binaries-python-2 =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-python-2 (revision 27035) +++ /issm/trunk/jenkins/ross-debian_linux-binaries-python-2 (revision 27035) @@ -0,0 +1,89 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is +# copied by packaging script. +# +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-pic \ + --with-python-dir=/usr \ + --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-fortran-lib="-L${ISSM_DIR}/lib -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-linux.sh + cmake install.sh + petsc install-3.12-linux-static.sh + gsl install-static.sh + boost install-1.7-linux-static.sh + dakota install-6.2-linux-static.sh + curl install-7-linux-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6-static.sh + gdal install-3-python-static.sh + gshhg install.sh + gmt install-6-linux-static.sh + gmsh install-4-static.sh + triangle install-linux-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-binaries-python-3 =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-binaries-python-3 (revision 27035) +++ /issm/trunk/jenkins/ross-debian_linux-binaries-python-3 (revision 27035) @@ -0,0 +1,90 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is +# copied by packaging script. +# +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-pic \ + --with-python-dir=/usr \ + --with-python-version=3.7 \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ + --with-fortran-lib="-L${ISSM_DIR}/lib -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ + --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ + --with-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ + --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ + --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ +' +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-linux.sh + cmake install.sh + petsc install-3.12-linux-static.sh + gsl install-static.sh + boost install-1.7-linux-static.sh + dakota install-6.2-linux-static.sh + curl install-7-linux-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6-static.sh + gdal install-3-python-static.sh + gshhg install.sh + gmt install-6-linux-static.sh + gmsh install-4-static.sh + triangle install-linux-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-codipack =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-codipack (revision 27034) +++ /issm/trunk/jenkins/ross-debian_linux-codipack (revision 27035) @@ -74,4 +74,4 @@ # See documentation in test/NightlyRun/runme.* for more information. # -MATLAB_NROPTIONS="'benchmark','all','id',[3015,3119,3480,3201,3202]" +MATLAB_NROPTIONS="'benchmark','all','id',[3015,3119,3480,3201:3205]" PYTHON_NROPTIONS="--benchmark='all' -i 3015 3119 3480" Index: /issm/trunk/jenkins/ross-debian_linux-dakota =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-dakota (revision 27034) +++ /issm/trunk/jenkins/ross-debian_linux-dakota (revision 27035) @@ -49,5 +49,5 @@ curl install-7-linux.sh netcdf install-4.7-parallel.sh - proj install-8.sh + proj install-6.sh gdal install-3-python.sh gshhg install.sh Index: /issm/trunk/jenkins/ross-debian_linux-full =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-full (revision 27034) +++ /issm/trunk/jenkins/ross-debian_linux-full (revision 27035) @@ -18,21 +18,21 @@ --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ - --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ - --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ - --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \ - --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ - --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \ - --with-proj-dir=${ISSM_DIR}/externalpackages/proj/install \ - --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ + --with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-hdf5-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-gsl-dir="${ISSM_DIR}/externalpackages/gsl/install" \ + --with-boost-dir="${ISSM_DIR}/externalpackages/boost/install" \ + --with-dakota-dir="${ISSM_DIR}/externalpackages/dakota/install" \ + --with-proj-dir="${ISSM_DIR}/externalpackages/proj/install" \ + --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \ + --with-chaco-dir="${ISSM_DIR}/externalpackages/chaco/install" \ + --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \ + --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \ ' @@ -50,5 +50,5 @@ curl install-7-linux.sh netcdf install-4.7-parallel.sh - proj install-8.sh + proj install-6.sh gdal install-3-python.sh gshhg install.sh Index: /issm/trunk/jenkins/ross-debian_linux-full-mplapack =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-full-mplapack (revision 27035) +++ /issm/trunk/jenkins/ross-debian_linux-full-mplapack (revision 27035) @@ -0,0 +1,89 @@ +# NOTE: This configuration adds solid earth and Dakota capabilities to the +# basic build. + +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/usr/local/MATLAB/R2019b" + +ISSM_CONFIG='\ + --prefix=${ISSM_DIR} \ + --disable-static \ + --enable-development \ + --enable-debugging \ + --with-cxxoptflags="-g -O2 -fPIC -std=gnu++11" \ + --with-numthreads=4 \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-dir=/usr \ + --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ + --with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-hdf5-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-mplapack-dir="${ISSM_DIR}/externalpackages/mplapack/install" \ + --with-gsl-dir="${ISSM_DIR}/externalpackages/gsl/install" \ + --with-boost-dir="${ISSM_DIR}/externalpackages/boost/install" \ + --with-dakota-dir="${ISSM_DIR}/externalpackages/dakota/install" \ + --with-proj-dir="${ISSM_DIR}/externalpackages/proj/install" \ + --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \ + --with-chaco-dir="${ISSM_DIR}/externalpackages/chaco/install" \ + --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \ + --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-linux.sh + cmake install.sh + petsc install-3.12-linux.sh + mplapack install-1-linux.sh + gsl install.sh + boost install-1.7-linux.sh + dakota install-6.2-linux.sh + curl install-7-linux.sh + netcdf install-4.7-parallel.sh + proj install-6.sh + gdal install-3-python.sh + gshhg install.sh + gmt install-6-linux.sh + gmsh install-4.sh + triangle install-linux.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk/jenkins/ross-debian_linux-full-valgrind =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-full-valgrind (revision 27034) +++ /issm/trunk/jenkins/ross-debian_linux-full-valgrind (revision 27035) @@ -50,5 +50,5 @@ curl install-7-linux.sh netcdf install-4.7-parallel.sh - proj install-8.sh + proj install-6.sh gdal install-3-python.sh gshhg install.sh Index: /issm/trunk/jenkins/ross-debian_linux-python =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-python (revision 27034) +++ /issm/trunk/jenkins/ross-debian_linux-python (revision 27035) @@ -10,5 +10,6 @@ --with-numthreads=4 \ --with-python-dir=/usr \ - --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-python-version=3.7 \ + --with-python-numpy-dir=/usr/local/lib/python3.7/dist-packages/numpy \ --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ @@ -44,5 +45,5 @@ curl install-7-linux.sh netcdf install-4.7-parallel.sh - proj install-8.sh + proj install-6.sh gdal install-3-python.sh gshhg install.sh Index: /issm/trunk/jenkins/ross-debian_linux-solid_earth =================================================================== --- /issm/trunk/jenkins/ross-debian_linux-solid_earth (revision 27034) +++ /issm/trunk/jenkins/ross-debian_linux-solid_earth (revision 27035) @@ -47,5 +47,5 @@ curl install-7-linux.sh netcdf install-4.7-parallel.sh - proj install-8.sh + proj install-6.sh gdal install-3-python.sh gshhg install.sh @@ -88,8 +88,6 @@ # NOTE: # - Excluding 2006 until it can be debugged (PETSc crash) -# - Tests 2002, 2003, 2005, 2008, 2010, 2011, 2021, 2090, and 2101, are -# excluded as Gmsh produces different meshes on macOS and Linux for (archives -# are generated on macOS). +# - Excluding 2012 until it can be looked at by Eric ("FindParam error message: Parameter HydrologyModel not set") # -MATLAB_NROPTIONS="'benchmark','slc','exclude',[2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425]" -PYTHON_NROPTIONS="--benchmark slc --exclude 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425" +MATLAB_NROPTIONS="'benchmark','slc','exclude',[2004 2006 2012 2021 2051 2052 2053 2085 2090 2101 2424 2425]" +PYTHON_NROPTIONS="--benchmark slc --exclude 2004 2006 2012 2021 2051 2052 2053 2085 2090 2101 2424 2425" Index: /issm/trunk/jenkins/ross-win-msys2-mingw-msmpi-basic =================================================================== --- /issm/trunk/jenkins/ross-win-msys2-mingw-msmpi-basic (revision 27034) +++ /issm/trunk/jenkins/ross-win-msys2-mingw-msmpi-basic (revision 27035) @@ -7,5 +7,5 @@ --with-numthreads=4 \ --with-vendor="win-msys2" \ - --with-matlab-dir=${MATLAB_PATH} \ + --with-matlab-dir="${MATLAB_PATH}" \ --with-mpi-include="${MSMPI_ROOT}/include" \ --with-mpi-libdir="${MSMPI_ROOT}/lib" \ @@ -15,11 +15,11 @@ --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \ --with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \ + --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \ --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \ --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \ - --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \ - --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \ - --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \ + --with-chaco-dir="${ISSM_DIR}/externalpackages/chaco/install" \ + --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \ + --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \ ' Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 27034) +++ /issm/trunk/m4/issm_options.m4 (revision 27035) @@ -205,10 +205,11 @@ AC_MSG_RESULT([${IS_MAC}]) - dnl If macOS, check if system copy of libc has fmemopen (if it is not + dnl If macOS, check if system copy of libc has fmemopen (if it is not dnl macOS, we do not check, but still must set SYSTEM_HAS_FMEMOPEN) AC_MSG_CHECKING([if system copy of libc has fmemopen]) SYSTEM_FMEMOPEN=1 if test "${IS_MAC}" == "yes"; then - if [[ $(system_profiler SPSoftwareDataType | grep "System Version:" | sed -e "s/[[:space:]]*System Version: macOS //" | cut -d "." -f 2) -lt 13 ]]; then + sys_ver=$(sw_vers -productVersion) + if test $(echo ${sys_ver} | cut -d "." -f 1) -eq 10 && test $(echo ${sys_ver} | cut -d "." -f 2) -lt 13; then SYSTEM_FMEMOPEN=0 fi @@ -291,6 +292,6 @@ export CFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK" elif test "${VENDOR}" == "intel-discover"; then - export CC=mpicc - export CXX=mpicxx + export CC=mpicc + export CXX=mpicxx export CXXFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK -std=c++11" export CFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK" @@ -313,5 +314,5 @@ export CC=mpicc export CXX=mpicxx - export CXXFLAGS="-O3 -march=corei7-avx -std=c++11" + export CXXFLAGS="-O3 -march=corei7-avx -std=c++11 -lirc -lsvml -limf" export CFLAGS="-O3 -march=corei7-avx" elif test "${VENDOR}" == "intel-pleiades-icpc"; then @@ -603,9 +604,9 @@ AC_MSG_CHECKING(for Dakota version) dnl TODO: - dnl - Check if this method applies to all other versions of Dakota (it - dnl should as long as the Dakota binaries have been compiled). If so, + dnl - Check if this method applies to all other versions of Dakota (it + dnl should as long as the Dakota binaries have been compiled). If so, dnl we can remove the other methods of getting the version. - dnl - Modify src/wrappers/IssmConfig/IssmConfig.cpp so that strlen is - dnl not called with _DAKOTA_VERSION_ as an argument so that we can + dnl - Modify src/wrappers/IssmConfig/IssmConfig.cpp so that strlen is + dnl not called with _DAKOTA_VERSION_ as an argument so that we can dnl do, dnl @@ -817,4 +818,6 @@ fi AC_MSG_RESULT([found]) + + AC_MSG_CHECKING([for Python library libpython]) if ls ${PYTHON_ROOT}/lib/x86_64-linux-gnu/libpython${PYTHON_VERSION}m.* 1> /dev/null 2>&1; then PYTHONLIB="-L${PYTHON_ROOT}/lib/x86_64-linux-gnu -lpython${PYTHON_VERSION}m" @@ -823,7 +826,13 @@ elif ls ${PYTHON_ROOT}/lib/libpython${PYTHON_VERSION}m.* 1> /dev/null 2>&1; then PYTHONLIB="-L${PYTHON_ROOT}/lib -lpython${PYTHON_VERSION}m" + elif ls ${PYTHON_ROOT}/lib64/libpython${PYTHON_VERSION}m.* 1> /dev/null 2>&1; then + PYTHONLIB="-L${PYTHON_ROOT}/lib64 -lpython${PYTHON_VERSION}m" + elif ls ${PYTHON_ROOT}/lib/libpython${PYTHON_VERSION}.* 1> /dev/null 2>&1; then + PYTHONLIB="-L${PYTHON_ROOT}/lib -lpython${PYTHON_VERSION}" else - PYTHONLIB="-L${PYTHON_ROOT}/lib -lpython${PYTHON_VERSION}" - fi + AC_MSG_ERROR([libpython not found! Please locate this file and contact ISSM developers via forum or email.]); + fi + AC_MSG_RESULT([found]) + PYTHONEXT=.so case "${host_os}" in @@ -1774,5 +1783,9 @@ if test "x${HAVE_SHAPELIB}" == "xyes"; then SHAPELIBINCL="-I${SHAPELIB_ROOT}/include" - SHAPELIBLIB="-L${SHAPELIB_ROOT}/lib -lshape" + if test -f "${SHAPELIB_ROOT}/lib/libshp.a"; then + SHAPELIBLIB="-L${SHAPELIB_ROOT}/lib -lshp" + else + SHAPELIBLIB="-L${SHAPELIB_ROOT}/lib -lshape" + fi AC_DEFINE([_HAVE_SHAPELIB_], [1], [with shapelib in ISSM src]) AC_SUBST([SHAPELIBINCL]) @@ -1974,4 +1987,32 @@ fi AC_MSG_RESULT([${HAVE_PLAPACK}]) + dnl }}} + dnl MPLAPACK{{{ + AC_MSG_CHECKING([for MPLAPACK]) + AC_ARG_WITH( + [mplapack-dir], + AS_HELP_STRING([--with-mplapack-dir=DIR], [MPLAPACK root directory]), + [MPLAPACK_ROOT=${withval}], + [MPLAPACK_ROOT="no"] + ) + if test "x${MPLAPACK_ROOT}" == "xno"; then + HAVE_MPLAPACK=no + else + HAVE_MPLAPACK=yes + if ! test -d "${MPLAPACK_ROOT}"; then + AC_MSG_ERROR([MPLAPACK directory provided (${MPLAPACK_ROOT}) does not exist!]); + fi + fi + AC_MSG_RESULT([${HAVE_MPLAPACK}]) + + dnl MPLAPACK libraries and header files + if test "x${HAVE_MPLAPACK}" == "xyes"; then + MPLAPACKINCL="-I${MPLAPACK_ROOT}/include/mplapack -I${MPLAPACK_ROOT}/include" + MPLAPACKLIB="-L${MPLAPACK_ROOT}/lib -lmpblas__Float128 -lmplapack__Float128 -lgomp -lquadmath" + AC_DEFINE([_HAVE_MPLAPACK_], [1], [with MPLAPACK in ISSM src]) + AC_SUBST([MPLAPACKINCL]) + AC_SUBST([MPLAPACKLIB]) + fi + AM_CONDITIONAL([MPLAPACK], [test "x${HAVE_MPLAPACK}" == "xyes"]) dnl }}} dnl MUMPS{{{ @@ -2567,5 +2608,5 @@ AC_MSG_RESULT([${GMSH_VERSION_MAJOR}]) AC_DEFINE_UNQUOTED([_GMSH_VERSION_MAJOR_], ${GMSH_VERSION_MAJOR}, [Gmsh major version]) - fi + fi dnl }}} dnl Capabilities @@ -2721,5 +2762,5 @@ ) dnl Check that supplied value is an integer - if [[ "${NUMTHREADS_VALUE}" != "${NUMTHREADS_VALUE}" 2> /dev/null ]]; then + if test "${NUMTHREADS_VALUE}" != "${NUMTHREADS_VALUE}"; then AC_MSG_ERROR([Number of threads provided (${NUMTHREADS_VALUE}) is not an integer!]); elif test "${NUMTHREADS_VALUE}" == "0"; then Index: /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-2.sh (revision 27035) +++ /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-2.sh (revision 27035) @@ -0,0 +1,94 @@ +#!/bin/bash + +################################################################################ +# Wrapper script to build, package, and transfer to ISSM Web site ISSM +# distributable package for Linux with Python 2 API. +# +# Normally, we would put this directly into the project configuration under +# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a +# good idea to version it. +# +# When no failures/errors occur, performs the following: +# - Builds ISSM according to configuration. +# - Packages executables and libraries. +# - Runs test suite against package. +# - Transmits package to ISSM Web site for distribution. +# +# Options: +# -b/--skipbuild Skip ISSM compilation. +# -s/--skiptests Skip ISSM compilation and testing during packaging +# step. Use if packaging fails for some reason but build +# is valid. +# -t/--transferonly Transfer package to ISSM Web site only. Use if transfer +# fails for some reason to skip building, packaging, and +# signing. +# +# NOTE: +# - Use only *one* of the above options at a time, and make sure it is removed +# again after a single run. +# - Builds will fail when any of the above options are used on a clean +# workspace. For example, if 'Source Code Management' -> 'Check-out Strategy' +# select menu is set to "Always check out a fresh copy". +################################################################################ + +## Constants +# +PKG="ISSM-Linux-Python-2" # Name of directory to copy distributable files to + +COMPRESSED_PKG="${PKG}.tar.gz" + +## Environment +# +export COMPRESSED_PKG +export PKG + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +# NOTE: We could do this with binary switching (i.e. 0011 to sign and transfer, +# but the following is self-documenting). +# +build=1 +package=1 +transfer=1 + +if [ $# -eq 1 ]; then + case $1 in + -b|--skipbuild) build=0; shift ;; + -s|--skiptests) build=0; ;; + -t|--transferonly) build=0; package=0; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# Build +if [ ${build} -eq 1 ]; then + ./jenkins/jenkins.sh ./jenkins/ross-debian_linux-binaries-python-2 + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Package +if [ ${package} -eq 1 ]; then + ./packagers/linux/package-issm-linux-binaries-python-2.sh $1 + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Transfer distributable package to ISSM Web site +if [ ${transfer} -eq 1 ]; then + ./packagers/linux/transfer-issm-linux-binaries.sh + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + Index: /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-3.sh (revision 27035) +++ /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-3.sh (revision 27035) @@ -0,0 +1,94 @@ +#!/bin/bash + +################################################################################ +# Wrapper script to build, package, and transfer to ISSM Web site ISSM +# distributable package for Linux with Python 3 API. +# +# Normally, we would put this directly into the project configuration under +# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a +# good idea to version it. +# +# When no failures/errors occur, performs the following: +# - Builds ISSM according to configuration. +# - Packages executables and libraries. +# - Runs test suite against package. +# - Transmits package to ISSM Web site for distribution. +# +# Options: +# -b/--skipbuild Skip ISSM compilation. +# -s/--skiptests Skip ISSM compilation and testing during packaging +# step. Use if packaging fails for some reason but build +# is valid. +# -t/--transferonly Transfer package to ISSM Web site only. Use if transfer +# fails for some reason to skip building, packaging, and +# signing. +# +# NOTE: +# - Use only *one* of the above options at a time, and make sure it is removed +# again after a single run. +# - Builds will fail when any of the above options are used on a clean +# workspace. For example, if 'Source Code Management' -> 'Check-out Strategy' +# select menu is set to "Always check out a fresh copy". +################################################################################ + +## Constants +# +PKG="ISSM-Linux-Python-3" # Name of directory to copy distributable files to + +COMPRESSED_PKG="${PKG}.tar.gz" + +## Environment +# +export COMPRESSED_PKG +export PKG + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +# NOTE: We could do this with binary switching (i.e. 0011 to sign and transfer, +# but the following is self-documenting). +# +build=1 +package=1 +transfer=1 + +if [ $# -eq 1 ]; then + case $1 in + -b|--skipbuild) build=0; shift ;; + -s|--skiptests) build=0; ;; + -t|--transferonly) build=0; package=0; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# Build +if [ ${build} -eq 1 ]; then + ./jenkins/jenkins.sh ./jenkins/ross-debian_linux-binaries-python-3 + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Package +if [ ${package} -eq 1 ]; then + ./packagers/linux/package-issm-linux-binaries-python-3.sh $1 + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Transfer distributable package to ISSM Web site +if [ ${transfer} -eq 1 ]; then + ./packagers/linux/transfer-issm-linux-binaries.sh + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + Index: sm/trunk/packagers/linux/complete-issm-linux-binaries-python.sh =================================================================== --- /issm/trunk/packagers/linux/complete-issm-linux-binaries-python.sh (revision 27034) +++ (revision ) @@ -1,94 +1,0 @@ -#!/bin/bash - -################################################################################ -# Wrapper script to build, package, and transfer to ISSM Web site ISSM -# distributable package for Linux with Python API. -# -# Normally, we would put this directly into the project configuration under -# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a -# good idea to version it. -# -# When no failures/errors occur, performs the following: -# - Builds ISSM according to configuration. -# - Packages executables and libraries. -# - Runs test suite against package. -# - Transmits package to ISSM Web site for distribution. -# -# Options: -# -b/--skipbuild Skip ISSM compilation. -# -s/--skiptests Skip ISSM compilation and testing during packaging -# step. Use if packaging fails for some reason but build -# is valid. -# -t/--transferonly Transfer package to ISSM Web site only. Use if transfer -# fails for some reason to skip building, packaging, and -# signing. -# -# NOTE: -# - Use only *one* of the above options at a time, and make sure it is removed -# again after a single run. -# - Builds will fail when any of the above options are used on a clean -# workspace. For example, if 'Source Code Management' -> 'Check-out Strategy' -# select menu is set to "Always check out a fresh copy". -################################################################################ - -## Constants -# -PKG="ISSM-Linux-Python" # Name of directory to copy distributable files to - -COMPRESSED_PKG="${PKG}.tar.gz" - -## Environment -# -export COMPRESSED_PKG -export PKG - -## Parse options -# -if [ $# -gt 1 ]; then - echo "Can use only one option at a time" - exit 1 -fi - -# NOTE: We could do this with binary switching (i.e. 0011 to sign and transfer, -# but the following is self-documenting). -# -build=1 -package=1 -transfer=1 - -if [ $# -eq 1 ]; then - case $1 in - -b|--skipbuild) build=0; shift ;; - -s|--skiptests) build=0; ;; - -t|--transferonly) build=0; package=0; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -# Build -if [ ${build} -eq 1 ]; then - ./jenkins/jenkins.sh ./jenkins/ross-debian_linux-binaries-python - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - -# Package -if [ ${package} -eq 1 ]; then - ./packagers/linux/package-issm-linux-binaries-python.sh $1 - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - -# Transfer distributable package to ISSM Web site -if [ ${transfer} -eq 1 ]; then - ./packagers/linux/transfer-issm-linux-binaries.sh - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh (revision 27034) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh (revision 27035) @@ -119,11 +119,10 @@ # Run tests, redirecting output to logfile and suppressing output to console - ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null + ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -nojvm -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" &> matlab.log # Check that MATLAB did not exit in error - matlabExitCode=`echo $?` - matlabExitedInError=`grep -E "Activation cannot proceed|Error in matlab_run" matlab.log | wc -l` + matlabExitedInError=`grep -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword" matlab.log | wc -l` - if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then + if [ ${matlabExitedInError} -ne 0 ]; then echo "----------MATLAB exited in error!----------" cat matlab.log @@ -139,5 +138,5 @@ numTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"` - if [[ ${numTestsFailed} -ne 0 ]]; then + if [ ${numTestsFailed} -ne 0 ]; then echo "One or more tests FAILED" exit 1 Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-python-2.sh (revision 27035) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries-python-2.sh (revision 27035) @@ -0,0 +1,166 @@ +#!/bin/bash + +################################################################################ +# Packages and tests ISSM distributable package for Linux with Python 2 API. +# +# Options: +# -s/--skiptests Skip testing during packaging Use if packaging fails +# for some reason but build is valid. +# +# NOTE: +# - Assumes that the following constants are defined, +# +# COMPRESSED_PKG +# ISSM_DIR +# PKG +# +# See also: +# - packagers/linux/complete-issm-linux-binaries-python-2.sh +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +## Override certain aliases +# +alias grep=$(which grep) + +## Constants +# +LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself +LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +skip_tests=0 + +if [ $# -eq 1 ]; then + case $1 in + -s|--skiptests) skip_tests=1; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd ${ISSM_DIR} +rm -rf ${PKG} ${COMPRESSED_PKG} +mkdir ${PKG} + +# Add required binaries and libraries to package and modify them where needed +cd ${ISSM_DIR}/bin + +echo "Modify generic" +cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py + +echo "Moving MPICH binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . +elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "MPICH not found" + exit 1 +fi + +echo "Moving GDAL binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . +else + echo "GDAL not found" + exit 1 +fi + +echo "Moving GMT binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . +else + echo "GMT not found" + exit 1 +fi + +echo "Moving Gmsh binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then + cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . +else + echo "Gmsh not found" + exit 1 +fi + +echo "Moving libgfortran to lib/" +cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null + + +# Run tests +if [ ${skip_tests} -eq 0 ]; then + echo "Running tests" + cd ${ISSM_DIR}/test/NightlyRun + rm python.log 2> /dev/null + + # Set Python environment + export PYTHONPATH="${ISSM_DIR}/src/m/dev" + export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" + export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + + # Run tests, redirecting output to logfile and suppressing output to console + ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + + # Check that Python did not exit in error + pythonExitCode=`echo $?` + pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l` + + if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 + fi + + # Check that all tests passed + numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + + if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 + else + echo "All tests PASSED" + fi +else + echo "Skipping tests" +fi + +# Create package +cd ${ISSM_DIR} +svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) +echo "Copying assets to package: ${PKG}" +cp -rf bin examples lib scripts test ${PKG} +mkdir ${PKG}/execution +${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files +echo "Cleaning up unneeded/unwanted files" +rm -f ${PKG}/bin/*.py # Remove all Python scripts +rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes +rm -f ${PKG}/lib/*.a # Remove static libraries from package +rm -f ${PKG}/lib/*.la # Remove libtool libraries from package +rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package + +# Compress package +echo "Compressing package" +tar -czf ${COMPRESSED_PKG} ${PKG} Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-python-3.sh (revision 27035) +++ /issm/trunk/packagers/linux/package-issm-linux-binaries-python-3.sh (revision 27035) @@ -0,0 +1,169 @@ +#!/bin/bash + +################################################################################ +# Packages and tests ISSM distributable package for Linux with Python 3 API. +# +# Options: +# -s/--skiptests Skip testing during packaging Use if packaging fails +# for some reason but build is valid. +# +# NOTE: +# - Assumes that the following constants are defined, +# +# COMPRESSED_PKG +# ISSM_DIR +# PKG +# +# See also: +# - packagers/linux/complete-issm-linux-binaries-python-3.sh +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +## Override certain aliases +# +alias grep=$(which grep) + +## Constants +# +LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself +LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +skip_tests=0 + +if [ $# -eq 1 ]; then + case $1 in + -s|--skiptests) skip_tests=1; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd ${ISSM_DIR} +rm -rf ${PKG} ${COMPRESSED_PKG} +mkdir ${PKG} + +# Add required binaries and libraries to package and modify them where needed +cd ${ISSM_DIR}/bin + +echo "Modify generic" +cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py + +echo "Moving MPICH binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . +elif [ -f ${ISSM_DIR}/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "MPICH not found" + exit 1 +fi + +echo "Moving GDAL binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . +else + echo "GDAL not found" + exit 1 +fi + +echo "Moving GMT binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . +else + echo "GMT not found" + exit 1 +fi + +echo "Moving Gmsh binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then + cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . +else + echo "Gmsh not found" + exit 1 +fi + +echo "Moving libgfortran to lib/" +cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null + + +# Run tests +if [ ${skip_tests} -eq 0 ]; then + echo "Running tests" + cd ${ISSM_DIR}/test/NightlyRun + rm python.log 2> /dev/null + + # Set Python environment + export PYTHONPATH="${ISSM_DIR}/src/m/dev" + export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" + export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + + # Ensure that runme.py uses Python 3 interpreter + sed -i "s|/usr/bin/env python|/usr/bin/python3|g" ./runme.py + + # Run tests, redirecting output to logfile and suppressing output to console + ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + + # Check that Python did not exit in error + pythonExitCode=`echo $?` + pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l` + + if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 + fi + + # Check that all tests passed + numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + + if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 + else + echo "All tests PASSED" + fi +else + echo "Skipping tests" +fi + +# Create package +cd ${ISSM_DIR} +svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) +echo "Copying assets to package: ${PKG}" +cp -rf bin examples lib scripts test ${PKG} +mkdir ${PKG}/execution +${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files +echo "Cleaning up unneeded/unwanted files" +rm -f ${PKG}/bin/*.py # Remove all Python scripts +rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes +rm -f ${PKG}/lib/*.a # Remove static libraries from package +rm -f ${PKG}/lib/*.la # Remove libtool libraries from package +rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package + +# Compress package +echo "Compressing package" +tar -czf ${COMPRESSED_PKG} ${PKG} Index: sm/trunk/packagers/linux/package-issm-linux-binaries-python.sh =================================================================== --- /issm/trunk/packagers/linux/package-issm-linux-binaries-python.sh (revision 27034) +++ (revision ) @@ -1,166 +1,0 @@ -#!/bin/bash - -################################################################################ -# Packages and tests ISSM distributable package for Linux with Python API. -# -# Options: -# -s/--skiptests Skip testing during packaging Use if packaging fails -# for some reason but build is valid. -# -# NOTE: -# - Assumes that the following constants are defined, -# -# COMPRESSED_PKG -# ISSM_DIR -# PKG -# -# See also: -# - packagers/linux/complete-issm-linux-binaries-python.sh -################################################################################ - -# Expand aliases within the context of this script -shopt -s expand_aliases - -## Override certain aliases -# -alias grep=$(which grep) - -## Constants -# -LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself -LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it -PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded - -## Environment -# -export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' - -## Parse options -# -if [ $# -gt 1 ]; then - echo "Can use only one option at a time" - exit 1 -fi - -skip_tests=0 - -if [ $# -eq 1 ]; then - case $1 in - -s|--skiptests) skip_tests=1; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -# Clean up from previous packaging -echo "Cleaning up existing assets" -cd ${ISSM_DIR} -rm -rf ${PKG} ${COMPRESSED_PKG} -mkdir ${PKG} - -# Add required binaries and libraries to package and modify them where needed -cd ${ISSM_DIR}/bin - -echo "Modify generic" -cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py - -echo "Moving MPICH binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then - cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . - cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . -elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then - cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . - cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . -else - echo "MPICH not found" - exit 1 -fi - -echo "Moving GDAL binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then - cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . - cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . -else - echo "GDAL not found" - exit 1 -fi - -echo "Moving GMT binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then - cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . - cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . -else - echo "GMT not found" - exit 1 -fi - -echo "Moving Gmsh binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then - cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . -else - echo "Gmsh not found" - exit 1 -fi - -echo "Moving libgfortran to lib/" -cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null - - -# Run tests -if [ ${skip_tests} -eq 0 ]; then - echo "Running tests" - cd ${ISSM_DIR}/test/NightlyRun - rm python.log 2> /dev/null - - # Set Python environment - export PYTHONPATH="${ISSM_DIR}/src/m/dev" - export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" - export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured - - # Run tests, redirecting output to logfile and suppressing output to console - ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 - - # Check that Python did not exit in error - pythonExitCode=`echo $?` - pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l` - - if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then - echo "----------Python exited in error!----------" - cat python.log - echo "-----------End of python.log-----------" - - # Clean up execution directory - rm -rf ${ISSM_DIR}/execution/* - - exit 1 - fi - - # Check that all tests passed - numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` - - if [[ ${numTestsFailed} -ne 0 ]]; then - echo "One or more tests FAILED" - exit 1 - else - echo "All tests PASSED" - fi -else - echo "Skipping tests" -fi - -# Create package -cd ${ISSM_DIR} -svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) -echo "Copying assets to package: ${PKG}" -cp -rf bin examples lib scripts test ${PKG} -mkdir ${PKG}/execution -${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files -echo "Cleaning up unneeded/unwanted files" -rm -f ${PKG}/bin/*.py # Remove all Python scripts -rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes -rm -f ${PKG}/lib/*.a # Remove static libraries from package -rm -f ${PKG}/lib/*.la # Remove libtool libraries from package -rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package - -# Compress package -echo "Compressing package" -tar -czf ${COMPRESSED_PKG} ${PKG} Index: /issm/trunk/packagers/linux/transfer-issm-linux-binaries.sh =================================================================== --- /issm/trunk/packagers/linux/transfer-issm-linux-binaries.sh (revision 27034) +++ /issm/trunk/packagers/linux/transfer-issm-linux-binaries.sh (revision 27035) @@ -2,6 +2,5 @@ ################################################################################ -# Transfers ISSM distributable package for Linux with MATLAB API to ISSM Web -# site. +# Transfers ISSM distributable package for Linux to ISSM website. # # NOTE: @@ -12,5 +11,6 @@ # See also: # - packagers/linux/complete-issm-linux-binaries-matlab.sh -# - packagers/linux/complete-issm-linux-binaries-python.sh +# - packagers/linux/complete-issm-linux-binaries-python-2.sh +# - packagers/linux/complete-issm-linux-binaries-python-3.sh ################################################################################ Index: /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh (revision 27034) +++ /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh (revision 27035) @@ -50,5 +50,5 @@ # NOTE: May be able to remove this after updating macOS. # -alias svn='/usr/local/bin/svn' +#alias svn='/usr/local/bin/svn' ## Override certain other aliases @@ -242,2 +242,7 @@ fi done + +if [ ! -f ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} ]; then + echo "Signing timed out!" + exit 1 +fi Index: /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh (revision 27035) +++ /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh (revision 27035) @@ -0,0 +1,248 @@ +#!/bin/bash + +################################################################################ +# Commits ISSM distributable package for macOS with Python 2 API to repository +# for signing. This repository is polled by a project running on a JPL +# Cybersecurity Jenkins server and performs the actual signing and +# notarization. +# +# Options: +# -r/--resign Skip ISSM compilation and packaging. Use to retrigger +# signing/notarization if it fails but build and package +# are valid. +# -u/--unlock Remove lock file from signed package repository. Use if +# build is aborted to allow for subsequent fresh build. +# +# NOTE: +# - Assumes that the following constants are defined, +# +# COMPRESSED_PKG +# ISSM_BINARIES_REPO_PASS +# ISSM_BINARIES_REPO_USER +# SIGNED_REPO_COPY +# SIGNED_REPO_URL +# +# See also: +# - packagers/mac/complete-issm-mac-binaries-python-2.sh +# - packagers/mac/sign-issm-mac-binaries-python-2.sh +# +# TODO: +# - Generalize checkout_*_repo_copy and validate_*_repo_copy functions (e.g. +# pass 'signed' or 'unsigned' as argument) +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +# NOTE: May be able to remove this after updating macOS. +# +#alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias cp=$(which cp) +alias grep=$(which grep) + +## Constants +# +MAX_SIGNING_CHECK_ATTEMPTS=30 +NOTARIZATION_LOGFILE="notarization.log" +RETRIGGER_SIGNING_FILE="retrigger.txt" +SIGNING_CHECK_PERIOD=60 # in seconds +SIGNING_LOCK_FILE="signing.lock" +UNSIGNED_REPO_COPY="./unsigned" +UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/2/unsigned" + +## Functions +# +checkout_signed_repo_copy(){ + echo "Checking out copy of repository for signed packages" + + # NOTE: Get empty copy because we do not want to have to check out package + # from previous signing. + # + svn checkout \ + --trust-server-cert \ + --non-interactive \ + --depth empty \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 +} +checkout_unsigned_repo_copy(){ + echo "Checking out copy of repository for unsigned packages" + svn checkout \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${UNSIGNED_REPO_URL} \ + ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 +} +validate_signed_repo_copy(){ + # Validate copy of repository for signed binaries (e.g. + # 'Check-out Strategy' was set to 'Use 'svn update' as much as possible'; + # initial checkout failed) + if [[ ! -d ${SIGNED_REPO_COPY} || ! -d ${SIGNED_REPO_COPY}/.svn ]]; then + rm -rf ${SIGNED_REPO_COPY} + checkout_signed_repo_copy + fi +} +validate_unsigned_repo_copy(){ + # Validate copy of repository for unsigned binaries (e.g. + # 'Check-out Strategy' was set to 'Use 'svn update' as much as possible'; + # initial checkout failed) + if [[ ! -d ${UNSIGNED_REPO_COPY} || ! -d ${UNSIGNED_REPO_COPY}/.svn ]]; then + rm -rf ${UNSIGNED_REPO_COPY} + checkout_unsigned_repo_copy + fi +} + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +retrigger_signing=0 +unlock=0 + +if [ $# -eq 1 ]; then + case $1 in + -r|--resign) retrigger_signing=1; ;; + -u|--unlock) unlock=1; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +validate_signed_repo_copy + +if [ ${unlock} -eq 1 ]; then + # Remove signing lock file from signed package repository so that a new + # build can run + echo "Removing lock file from repository for signed packages" + svn update \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + --message "DEL: Removing lock file after failed build" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + svn cleanup ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + echo "Remove -u/--unlock option from configuration and run again" + exit 1 +fi + +# If lock file exists, a signing build is still in process by JPL Cybersecurity +svn update \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + +if [ -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]; then + echo "Previous signing job still in process by JPL Cybersecurity. Please try again later." + exit 1 +fi + +# Commit lock file to repository for signed packages +echo "Committing lock file to repository for signed packages" +touch ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} +svn add ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 +svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + --message "ADD: New lock file" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + +# Check out copy of repository for unsigned packages +validate_unsigned_repo_copy + +if [ ${retrigger_signing} -eq 0 ]; then + # Commit new compressed package to repository for unsigned binaries + echo "Committing package to repository for unsigned packages" + cp ${COMPRESSED_PKG} ${UNSIGNED_REPO_COPY} + svn add ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + --message "CHG: New unsigned package" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 +else + # NOTE: If notarize_only == 1, we commit a dummy file as we do not want to + # have to commit the entire compressed package again simply to + # retrigger the signing build on the remote JPL Cybersecurity Jenkins + # server. + # + echo "Attempting to sign existing package again" + echo $(date +'%Y-%m-%d-%H-%M-%S') > ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} # Write datetime stamp to file to ensure modification is made + svn add ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} > /dev/null 2>&1 + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + --message "ADD: Retriggering signing with same package (previous attempt failed)" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 +fi + +# Check status of signing +echo "Checking progress of signing..." +SIGNING_CHECK_ATTEMPT=0 +while [ ${SIGNING_CHECK_ATTEMPT} -lt ${MAX_SIGNING_CHECK_ATTEMPTS} ]; do + echo "...in progress still; checking again in ${SIGNING_CHECK_PERIOD} seconds" + sleep ${SIGNING_CHECK_PERIOD} + svn update \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + if [ ! -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]; then + # Retrieve notarization lock file + svn update \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} + + # Check status + STATUS=$(grep 'Status:' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') + if [[ "${STATUS}" == "success" ]]; then + echo "Notarization successful!" + break + else + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" + + exit 1 + fi + else + ((++SIGNING_CHECK_ATTEMPT)) + fi +done + +if [ ! -f ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} ]; then + echo "Signing timed out!" + exit 1 +fi Index: /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh (revision 27035) +++ /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh (revision 27035) @@ -0,0 +1,248 @@ +#!/bin/bash + +################################################################################ +# Commits ISSM distributable package for macOS with Python 3 API to repository +# for signing. This repository is polled by a project running on a JPL +# Cybersecurity Jenkins server and performs the actual signing and +# notarization. +# +# Options: +# -r/--resign Skip ISSM compilation and packaging. Use to retrigger +# signing/notarization if it fails but build and package +# are valid. +# -u/--unlock Remove lock file from signed package repository. Use if +# build is aborted to allow for subsequent fresh build. +# +# NOTE: +# - Assumes that the following constants are defined, +# +# COMPRESSED_PKG +# ISSM_BINARIES_REPO_PASS +# ISSM_BINARIES_REPO_USER +# SIGNED_REPO_COPY +# SIGNED_REPO_URL +# +# See also: +# - packagers/mac/complete-issm-mac-binaries-python-3.sh +# - packagers/mac/sign-issm-mac-binaries-python-3.sh +# +# TODO: +# - Generalize checkout_*_repo_copy and validate_*_repo_copy functions (e.g. +# pass 'signed' or 'unsigned' as argument) +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +# NOTE: May be able to remove this after updating macOS. +# +#alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias cp=$(which cp) +alias grep=$(which grep) + +## Constants +# +MAX_SIGNING_CHECK_ATTEMPTS=30 +NOTARIZATION_LOGFILE="notarization.log" +RETRIGGER_SIGNING_FILE="retrigger.txt" +SIGNING_CHECK_PERIOD=60 # in seconds +SIGNING_LOCK_FILE="signing.lock" +UNSIGNED_REPO_COPY="./unsigned" +UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/3/unsigned" + +## Functions +# +checkout_signed_repo_copy(){ + echo "Checking out copy of repository for signed packages" + + # NOTE: Get empty copy because we do not want to have to check out package + # from previous signing. + # + svn checkout \ + --trust-server-cert \ + --non-interactive \ + --depth empty \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 +} +checkout_unsigned_repo_copy(){ + echo "Checking out copy of repository for unsigned packages" + svn checkout \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${UNSIGNED_REPO_URL} \ + ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 +} +validate_signed_repo_copy(){ + # Validate copy of repository for signed binaries (e.g. + # 'Check-out Strategy' was set to 'Use 'svn update' as much as possible'; + # initial checkout failed) + if [[ ! -d ${SIGNED_REPO_COPY} || ! -d ${SIGNED_REPO_COPY}/.svn ]]; then + rm -rf ${SIGNED_REPO_COPY} + checkout_signed_repo_copy + fi +} +validate_unsigned_repo_copy(){ + # Validate copy of repository for unsigned binaries (e.g. + # 'Check-out Strategy' was set to 'Use 'svn update' as much as possible'; + # initial checkout failed) + if [[ ! -d ${UNSIGNED_REPO_COPY} || ! -d ${UNSIGNED_REPO_COPY}/.svn ]]; then + rm -rf ${UNSIGNED_REPO_COPY} + checkout_unsigned_repo_copy + fi +} + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +retrigger_signing=0 +unlock=0 + +if [ $# -eq 1 ]; then + case $1 in + -r|--resign) retrigger_signing=1; ;; + -u|--unlock) unlock=1; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +validate_signed_repo_copy + +if [ ${unlock} -eq 1 ]; then + # Remove signing lock file from signed package repository so that a new + # build can run + echo "Removing lock file from repository for signed packages" + svn update \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + --message "DEL: Removing lock file after failed build" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + svn cleanup ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + echo "Remove -u/--unlock option from configuration and run again" + exit 1 +fi + +# If lock file exists, a signing build is still in process by JPL Cybersecurity +svn update \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 + +if [ -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]; then + echo "Previous signing job still in process by JPL Cybersecurity. Please try again later." + exit 1 +fi + +# Commit lock file to repository for signed packages +echo "Committing lock file to repository for signed packages" +touch ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} +svn add ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 +svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + --message "ADD: New lock file" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + +# Check out copy of repository for unsigned packages +validate_unsigned_repo_copy + +if [ ${retrigger_signing} -eq 0 ]; then + # Commit new compressed package to repository for unsigned binaries + echo "Committing package to repository for unsigned packages" + cp ${COMPRESSED_PKG} ${UNSIGNED_REPO_COPY} + svn add ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + --message "CHG: New unsigned package" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 +else + # NOTE: If notarize_only == 1, we commit a dummy file as we do not want to + # have to commit the entire compressed package again simply to + # retrigger the signing build on the remote JPL Cybersecurity Jenkins + # server. + # + echo "Attempting to sign existing package again" + echo $(date +'%Y-%m-%d-%H-%M-%S') > ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} # Write datetime stamp to file to ensure modification is made + svn add ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} > /dev/null 2>&1 + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + --message "ADD: Retriggering signing with same package (previous attempt failed)" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 +fi + +# Check status of signing +echo "Checking progress of signing..." +SIGNING_CHECK_ATTEMPT=0 +while [ ${SIGNING_CHECK_ATTEMPT} -lt ${MAX_SIGNING_CHECK_ATTEMPTS} ]; do + echo "...in progress still; checking again in ${SIGNING_CHECK_PERIOD} seconds" + sleep ${SIGNING_CHECK_PERIOD} + svn update \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + + if [ ! -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]; then + # Retrieve notarization lock file + svn update \ + --username ${ISSM_BINARIES_REPO_USER} \ + --password ${ISSM_BINARIES_REPO_PASS} \ + ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} + + # Check status + STATUS=$(grep 'Status:' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') + if [[ "${STATUS}" == "success" ]]; then + echo "Notarization successful!" + break + else + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" + + exit 1 + fi + else + ((++SIGNING_CHECK_ATTEMPT)) + fi +done + +if [ ! -f ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} ]; then + echo "Signing timed out!" + exit 1 +fi Index: sm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python.sh =================================================================== --- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python.sh (revision 27034) +++ (revision ) @@ -1,243 +1,0 @@ -#!/bin/bash - -################################################################################ -# Commits ISSM distributable package for macOS with Python API to repository -# for signing. This repository is polled by a project running on a JPL -# Cybersecurity Jenkins server and performs the actual signing and -# notarization. -# -# Options: -# -r/--resign Skip ISSM compilation and packaging. Use to retrigger -# signing/notarization if it fails but build and package -# are valid. -# -u/--unlock Remove lock file from signed package repository. Use if -# build is aborted to allow for subsequent fresh build. -# -# NOTE: -# - Assumes that the following constants are defined, -# -# COMPRESSED_PKG -# ISSM_BINARIES_REPO_PASS -# ISSM_BINARIES_REPO_USER -# SIGNED_REPO_COPY -# SIGNED_REPO_URL -# -# See also: -# - packagers/mac/complete-issm-mac-binaries-python.sh -# - packagers/mac/sign-issm-mac-binaries-python.sh -# -# TODO: -# - Generalize checkout_*_repo_copy and validate_*_repo_copy functions (e.g. -# pass 'signed' or 'unsigned' as argument) -################################################################################ - -# Expand aliases within the context of this script -shopt -s expand_aliases - -# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, -# -# Command line tool support for Subversion — including svn, git-svn, and -# related commands — is no longer provided by Xcode. (50266910) -# -# which results in, -# -# svn: error: The subversion command line tools are no longer provided by -# Xcode. -# -# when calling svn, even when subversion is installed via Homebrew and its path -# is available in PATH. -# -# NOTE: May be able to remove this after updating macOS. -# -alias svn='/usr/local/bin/svn' - -## Override certain other aliases -# -alias cp=$(which cp) -alias grep=$(which grep) - -## Constants -# -MAX_SIGNING_CHECK_ATTEMPTS=30 -NOTARIZATION_LOGFILE="notarization.log" -RETRIGGER_SIGNING_FILE="retrigger.txt" -SIGNING_CHECK_PERIOD=60 # in seconds -SIGNING_LOCK_FILE="signing.lock" -UNSIGNED_REPO_COPY="./unsigned" -UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/unsigned" - -## Functions -# -checkout_signed_repo_copy(){ - echo "Checking out copy of repository for signed packages" - - # NOTE: Get empty copy because we do not want to have to check out package - # from previous signing. - # - svn checkout \ - --trust-server-cert \ - --non-interactive \ - --depth empty \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_URL} \ - ${SIGNED_REPO_COPY} > /dev/null 2>&1 -} -checkout_unsigned_repo_copy(){ - echo "Checking out copy of repository for unsigned packages" - svn checkout \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${UNSIGNED_REPO_URL} \ - ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 -} -validate_signed_repo_copy(){ - # Validate copy of repository for signed binaries (e.g. - # 'Check-out Strategy' was set to 'Use 'svn update' as much as possible'; - # initial checkout failed) - if [[ ! -d ${SIGNED_REPO_COPY} || ! -d ${SIGNED_REPO_COPY}/.svn ]]; then - rm -rf ${SIGNED_REPO_COPY} - checkout_signed_repo_copy - fi -} -validate_unsigned_repo_copy(){ - # Validate copy of repository for unsigned binaries (e.g. - # 'Check-out Strategy' was set to 'Use 'svn update' as much as possible'; - # initial checkout failed) - if [[ ! -d ${UNSIGNED_REPO_COPY} || ! -d ${UNSIGNED_REPO_COPY}/.svn ]]; then - rm -rf ${UNSIGNED_REPO_COPY} - checkout_unsigned_repo_copy - fi -} - -## Parse options -# -if [ $# -gt 1 ]; then - echo "Can use only one option at a time" - exit 1 -fi - -retrigger_signing=0 -unlock=0 - -if [ $# -eq 1 ]; then - case $1 in - -r|--resign) retrigger_signing=1; ;; - -u|--unlock) unlock=1; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -validate_signed_repo_copy - -if [ ${unlock} -eq 1 ]; then - # Remove signing lock file from signed package repository so that a new - # build can run - echo "Removing lock file from repository for signed packages" - svn update \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 - svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 - svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - --message "DEL: Removing lock file after failed build" ${SIGNED_REPO_COPY} > /dev/null 2>&1 - svn cleanup ${SIGNED_REPO_COPY} > /dev/null 2>&1 - - echo "Remove -u/--unlock option from configuration and run again" - exit 1 -fi - -# If lock file exists, a signing build is still in process by JPL Cybersecurity -svn update \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 - -if [ -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]; then - echo "Previous signing job still in process by JPL Cybersecurity. Please try again later." - exit 1 -fi - -# Commit lock file to repository for signed packages -echo "Committing lock file to repository for signed packages" -touch ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} -svn add ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} > /dev/null 2>&1 -svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - --message "ADD: New lock file" ${SIGNED_REPO_COPY} > /dev/null 2>&1 - -# Check out copy of repository for unsigned packages -validate_unsigned_repo_copy - -if [ ${retrigger_signing} -eq 0 ]; then - # Commit new compressed package to repository for unsigned binaries - echo "Committing package to repository for unsigned packages" - cp ${COMPRESSED_PKG} ${UNSIGNED_REPO_COPY} - svn add ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 - svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - --message "CHG: New unsigned package" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 -else - # NOTE: If notarize_only == 1, we commit a dummy file as we do not want to - # have to commit the entire compressed package again simply to - # retrigger the signing build on the remote JPL Cybersecurity Jenkins - # server. - # - echo "Attempting to sign existing package again" - echo $(date +'%Y-%m-%d-%H-%M-%S') > ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} # Write datetime stamp to file to ensure modification is made - svn add ${UNSIGNED_REPO_COPY}/${RETRIGGER_SIGNING_FILE} > /dev/null 2>&1 - svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - --message "ADD: Retriggering signing with same package (previous attempt failed)" ${UNSIGNED_REPO_COPY} > /dev/null 2>&1 -fi - -# Check status of signing -echo "Checking progress of signing..." -SIGNING_CHECK_ATTEMPT=0 -while [ ${SIGNING_CHECK_ATTEMPT} -lt ${MAX_SIGNING_CHECK_ATTEMPTS} ]; do - echo "...in progress still; checking again in ${SIGNING_CHECK_PERIOD} seconds" - sleep ${SIGNING_CHECK_PERIOD} - svn update \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_COPY} > /dev/null 2>&1 - - if [ ! -f ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} ]; then - # Retrieve notarization lock file - svn update \ - --username ${ISSM_BINARIES_REPO_USER} \ - --password ${ISSM_BINARIES_REPO_PASS} \ - ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} - - # Check status - STATUS=$(grep 'Status:' ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') - if [[ "${STATUS}" == "success" ]]; then - echo "Notarization successful!" - break - else - echo "Notarization failed!" - echo "----------------------- Contents of notarization logfile -----------------------" - cat ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} - echo "--------------------------------------------------------------------------------" - - exit 1 - fi - else - ((++SIGNING_CHECK_ATTEMPT)) - fi -done Index: /issm/trunk/packagers/mac/complete-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/complete-issm-mac-binaries-matlab.sh (revision 27034) +++ /issm/trunk/packagers/mac/complete-issm-mac-binaries-matlab.sh (revision 27035) @@ -99,5 +99,6 @@ ./jenkins/jenkins.sh ./jenkins/pine_island-mac-binaries-matlab - if [ $? -ne 0 ]; then + if [ $? -ne 0 ]; then + echo "Failure while compiling" exit 1 fi @@ -107,9 +108,11 @@ if [ ${package} -eq 1 ]; then ./packagers/mac/package-issm-mac-binaries-matlab.sh $1 - shift # Clear $1 so that it is not passed to commit_for_signing script - if [ $? -ne 0 ]; then + if [ $? -ne 0 ]; then + echo "Failure during packaging" exit 1 fi + + shift # Clear $1 so that it is not passed to commit_for_signing script fi @@ -118,5 +121,6 @@ ./packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh $1 - if [ $? -ne 0 ]; then + if [ $? -ne 0 ]; then + echo "Failure while committing package for signing" exit 1 fi @@ -127,5 +131,6 @@ ./packagers/mac/transfer-issm-mac-binaries.sh - if [ $? -ne 0 ]; then + if [ $? -ne 0 ]; then + echo "Failure while transferring package to ISSM server" exit 1 fi Index: /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-2.sh (revision 27035) +++ /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-2.sh (revision 27035) @@ -0,0 +1,134 @@ +#!/bin/bash + +################################################################################ +# Wrapper script to build, package, send for signing, and transfer to ISSM Web +# site ISSM distributable package for macOS with Python 2 API. +# +# Normally, we would put this directly into the project configuration under +# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a +# good idea to version it. +# +# When no failures/errors occur, performs the following: +# - Builds ISSM according to configuration. +# - Packages executables and libraries. +# - Runs test suite against package. +# - Commits compressed package to repository to be signed by JPL Cybersecurity. +# - Retrieves signed package and transmits it to ISSM Web site for +# distribution. +# +# Options: +# -b/--skipbuild Skip ISSM compilation. +# -r/--resign Skip ISSM compilation and packaging. Use to retrigger +# signing/notarization if it fails but build and package +# are valid. +# -s/--skiptests Skip ISSM compilation and testing during packaging +# step. Use if packaging fails for some reason but build +# is valid. +# -t/--transferonly Transfer package to ISSM Web site only. Use if transfer +# fails for some reason to skip building, packaging, and +# signing. +# -u/--unlock Remove lock file from signed package repository. Use if +# build is aborted to allow for subsequent fresh build. +# +# Debugging: +# - Relies on a very tight handshake with project on remote JPL Cybersecurity +# Jenkins server. Debugging may be perfomed locally by running, +# +# packagers/mac/sign-issm-mac-binaries-python-2.sh +# +# with "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" hardcoded to Apple +# Developer credentials. +# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can +# help debug potential SVN issues. +# +# NOTE: +# - Use only *one* of the above options at a time, and make sure it is removed +# again after a single run. +# - Builds will fail when any of the above options are used on a clean +# workspace. For example, if 'Source Code Management' -> 'Check-out Strategy' +# select menu is set to "Always check out a fresh copy". +# - Assumes that "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" are set up in +# the 'Bindings' section under a 'Username and password (separated)' binding +# (requires 'Credentials Binding Plugin') with 'Credentials' select menu set +# to "jenkins/****** (SVN repository for ISSM binaries)". +################################################################################ + +## Constants +# +PKG="ISSM-macOS-Python-2" # Name of directory to copy distributable files to +SIGNED_REPO_COPY="./signed" +SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/2/signed" + +COMPRESSED_PKG="${PKG}.zip" + +## Environment +# +export COMPRESSED_PKG +export PKG +export SIGNED_REPO_COPY +export SIGNED_REPO_URL + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +# NOTE: We could do this with binary switching (i.e. 0011 to sign and transfer, +# but the following is self-documenting). +# +build=1 +package=1 +sign=1 +transfer=1 + +if [ $# -eq 1 ]; then + case $1 in + -b|--skipbuild) build=0; shift ;; + -r|--resign) build=0; package=0; ;; + -s|--skiptests) build=0; ;; + -t|--transferonly) build=0; package=0; sign=0; ;; + -u|--unlock) build=0; package=0; transfer=0; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# Build +if [ ${build} -eq 1 ]; then + ./jenkins/jenkins.sh ./jenkins/pine_island-mac-binaries-python-2 + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Package +if [ ${package} -eq 1 ]; then + ./packagers/mac/package-issm-mac-binaries-python-2.sh $1 + + if [ $? -ne 0 ]; then + exit 1 + fi + + shift # Clear $1 so that it is not passed to commit_for_signing script +fi + +# Commit for signing +if [ ${sign} -eq 1 ]; then + ./packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh $1 + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Transfer distributable package to ISSM Web site +if [ ${transfer} -eq 1 ]; then + ./packagers/mac/transfer-issm-mac-binaries.sh + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + Index: /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-3.sh (revision 27035) +++ /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-3.sh (revision 27035) @@ -0,0 +1,134 @@ +#!/bin/bash + +################################################################################ +# Wrapper script to build, package, send for signing, and transfer to ISSM Web +# site ISSM distributable package for macOS with Python 3 API. +# +# Normally, we would put this directly into the project configuration under +# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a +# good idea to version it. +# +# When no failures/errors occur, performs the following: +# - Builds ISSM according to configuration. +# - Packages executables and libraries. +# - Runs test suite against package. +# - Commits compressed package to repository to be signed by JPL Cybersecurity. +# - Retrieves signed package and transmits it to ISSM Web site for +# distribution. +# +# Options: +# -b/--skipbuild Skip ISSM compilation. +# -r/--resign Skip ISSM compilation and packaging. Use to retrigger +# signing/notarization if it fails but build and package +# are valid. +# -s/--skiptests Skip ISSM compilation and testing during packaging +# step. Use if packaging fails for some reason but build +# is valid. +# -t/--transferonly Transfer package to ISSM Web site only. Use if transfer +# fails for some reason to skip building, packaging, and +# signing. +# -u/--unlock Remove lock file from signed package repository. Use if +# build is aborted to allow for subsequent fresh build. +# +# Debugging: +# - Relies on a very tight handshake with project on remote JPL Cybersecurity +# Jenkins server. Debugging may be perfomed locally by running, +# +# packagers/mac/sign-issm-mac-binaries-python-3.sh +# +# with "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" hardcoded to Apple +# Developer credentials. +# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can +# help debug potential SVN issues. +# +# NOTE: +# - Use only *one* of the above options at a time, and make sure it is removed +# again after a single run. +# - Builds will fail when any of the above options are used on a clean +# workspace. For example, if 'Source Code Management' -> 'Check-out Strategy' +# select menu is set to "Always check out a fresh copy". +# - Assumes that "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" are set up in +# the 'Bindings' section under a 'Username and password (separated)' binding +# (requires 'Credentials Binding Plugin') with 'Credentials' select menu set +# to "jenkins/****** (SVN repository for ISSM binaries)". +################################################################################ + +## Constants +# +PKG="ISSM-macOS-Python-3" # Name of directory to copy distributable files to +SIGNED_REPO_COPY="./signed" +SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/3/signed" + +COMPRESSED_PKG="${PKG}.zip" + +## Environment +# +export COMPRESSED_PKG +export PKG +export SIGNED_REPO_COPY +export SIGNED_REPO_URL + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +# NOTE: We could do this with binary switching (i.e. 0011 to sign and transfer, +# but the following is self-documenting). +# +build=1 +package=1 +sign=1 +transfer=1 + +if [ $# -eq 1 ]; then + case $1 in + -b|--skipbuild) build=0; shift ;; + -r|--resign) build=0; package=0; ;; + -s|--skiptests) build=0; ;; + -t|--transferonly) build=0; package=0; sign=0; ;; + -u|--unlock) build=0; package=0; transfer=0; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# Build +if [ ${build} -eq 1 ]; then + ./jenkins/jenkins.sh ./jenkins/pine_island-mac-binaries-python-3 + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Package +if [ ${package} -eq 1 ]; then + ./packagers/mac/package-issm-mac-binaries-python-3.sh $1 + + if [ $? -ne 0 ]; then + exit 1 + fi + + shift # Clear $1 so that it is not passed to commit_for_signing script +fi + +# Commit for signing +if [ ${sign} -eq 1 ]; then + ./packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh $1 + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + +# Transfer distributable package to ISSM Web site +if [ ${transfer} -eq 1 ]; then + ./packagers/mac/transfer-issm-mac-binaries.sh + + if [ $? -ne 0 ]; then + exit 1 + fi +fi + Index: sm/trunk/packagers/mac/complete-issm-mac-binaries-python.sh =================================================================== --- /issm/trunk/packagers/mac/complete-issm-mac-binaries-python.sh (revision 27034) +++ (revision ) @@ -1,133 +1,0 @@ -#!/bin/bash - -################################################################################ -# Wrapper script to build, package, send for signing, and transfer to ISSM Web -# site ISSM distributable package for macOS with Python API. -# -# Normally, we would put this directly into the project configuration under -# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a -# good idea to version it. -# -# When no failures/errors occur, performs the following: -# - Builds ISSM according to configuration. -# - Packages executables and libraries. -# - Runs test suite against package. -# - Commits compressed package to repository to be signed by JPL Cybersecurity. -# - Retrieves signed package and transmits it to ISSM Web site for -# distribution. -# -# Options: -# -b/--skipbuild Skip ISSM compilation. -# -r/--resign Skip ISSM compilation and packaging. Use to retrigger -# signing/notarization if it fails but build and package -# are valid. -# -s/--skiptests Skip ISSM compilation and testing during packaging -# step. Use if packaging fails for some reason but build -# is valid. -# -t/--transferonly Transfer package to ISSM Web site only. Use if transfer -# fails for some reason to skip building, packaging, and -# signing. -# -u/--unlock Remove lock file from signed package repository. Use if -# build is aborted to allow for subsequent fresh build. -# -# Debugging: -# - Relies on a very tight handshake with project on remote JPL Cybersecurity -# Jenkins server. Debugging may be perfomed locally by running, -# -# packagers/mac/sign-issm-mac-binaries-python.sh -# -# with "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" hardcoded to Apple -# Developer credentials. -# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can -# help debug potential SVN issues. -# -# NOTE: -# - Use only *one* of the above options at a time, and make sure it is removed -# again after a single run. -# - Builds will fail when any of the above options are used on a clean -# workspace. For example, if 'Source Code Management' -> 'Check-out Strategy' -# select menu is set to "Always check out a fresh copy". -# - Assumes that "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" are set up in -# the 'Bindings' section under a 'Username and password (separated)' binding -# (requires 'Credentials Binding Plugin') with 'Credentials' select menu set -# to "jenkins/****** (SVN repository for ISSM binaries)". -################################################################################ - -## Constants -# -PKG="ISSM-macOS-Python" # Name of directory to copy distributable files to -SIGNED_REPO_COPY="./signed" -SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/signed" - -COMPRESSED_PKG="${PKG}.zip" - -## Environment -# -export COMPRESSED_PKG -export PKG -export SIGNED_REPO_COPY -export SIGNED_REPO_URL - -## Parse options -# -if [ $# -gt 1 ]; then - echo "Can use only one option at a time" - exit 1 -fi - -# NOTE: We could do this with binary switching (i.e. 0011 to sign and transfer, -# but the following is self-documenting). -# -build=1 -package=1 -sign=1 -transfer=1 - -if [ $# -eq 1 ]; then - case $1 in - -b|--skipbuild) build=0; shift ;; - -r|--resign) build=0; package=0; ;; - -s|--skiptests) build=0; ;; - -t|--transferonly) build=0; package=0; sign=0; ;; - -u|--unlock) build=0; package=0; transfer=0; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -# Build -if [ ${build} -eq 1 ]; then - ./jenkins/jenkins.sh ./jenkins/pine_island-mac-binaries-python - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - -# Package -if [ ${package} -eq 1 ]; then - ./packagers/mac/package-issm-mac-binaries-python.sh $1 - shift # Clear $1 so that it is not passed to commit_for_signing script - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - -# Commit for signing -if [ ${sign} -eq 1 ]; then - ./packagers/mac/commit_for_signing-issm-mac-binaries-python.sh $1 - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - -# Transfer distributable package to ISSM Web site -if [ ${transfer} -eq 1 ]; then - ./packagers/mac/transfer-issm-mac-binaries.sh - - if [ $? -ne 0 ]; then - exit 1 - fi -fi - Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh (revision 27034) +++ /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh (revision 27035) @@ -38,5 +38,5 @@ # NOTE: May be able to remove this after updating macOS. # -alias svn='/usr/local/bin/svn' +#alias svn='/usr/local/bin/svn' ## Override certain other aliases @@ -47,5 +47,5 @@ ## Constants # -MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2006,2020,2021,2051,2052,2053,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded +MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded MATLAB_PATH="/Applications/MATLAB_R2018a.app" @@ -133,11 +133,10 @@ # Run tests, redirecting output to logfile and suppressing output to console - ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null + ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -nojvm -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" &> matlab.log # Check that MATLAB did not exit in error - matlabExitCode=`echo $?` - matlabExitedInError=`grep -E "Activation cannot proceed|Error in matlab_run" matlab.log | wc -l` + matlabExitedInError=`grep -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword" matlab.log | wc -l` - if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then + if [ ${matlabExitedInError} -ne 0 ]; then echo "----------MATLAB exited in error!----------" cat matlab.log Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-python-2.sh (revision 27035) +++ /issm/trunk/packagers/mac/package-issm-mac-binaries-python-2.sh (revision 27035) @@ -0,0 +1,179 @@ +#!/bin/bash + +################################################################################ +# Packages and tests ISSM distributable package for macOS with Python 2 API. +# +# Options: +# -s/--skiptests Skip testing during packaging Use if packaging fails +# for some reason but build is valid. +# +# NOTE: +# - Assumes that the following constants are defined, +# +# COMPRESSED_PKG +# ISSM_DIR +# PKG +# +# See also: +# - packagers/mac/complete-issm-mac-binaries-python-2.sh +# - packagers/mac/sign-issm-mac-binaries-python-2.sh +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +# NOTE: May be able to remove this after updating macOS. +# +#alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias grep=$(which grep) + +## Constants +# +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +skip_tests=0 + +if [ $# -eq 1 ]; then + case $1 in + -s|--skiptests) skip_tests=1; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd ${ISSM_DIR} +rm -rf ${PKG} ${COMPRESSED_PKG} +mkdir ${PKG} + +# Add required binaries and libraries to package and modify them where needed +cd ${ISSM_DIR}/bin + +echo "Modify generic" +cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py + +echo "Moving MPICH binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . +elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "MPICH not found" + exit 1 +fi + +echo "Moving GDAL binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . +else + echo "GDAL not found" + exit 1 +fi + +echo "Moving GMT binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . +else + echo "GMT not found" + exit 1 +fi + +echo "Moving Gmsh binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then + cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . +else + echo "Gmsh not found" + exit 1 +fi + +# Run tests +if [ ${skip_tests} -eq 0 ]; then + echo "Running tests" + cd ${ISSM_DIR}/test/NightlyRun + rm python.log 2> /dev/null + + # Set Python environment + export PYTHONPATH="${ISSM_DIR}/src/m/dev" + export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" + export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + + # Run tests, redirecting output to logfile and suppressing output to console + ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + + # Check that Python did not exit in error + pythonExitCode=`echo $?` + pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l` + + if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 + fi + + # Check that all tests passed + numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + + if [ ${numTestsFailed} -ne 0 ]; then + echo "One or more tests FAILED" + exit 1 + else + echo "All tests PASSED" + fi +else + echo "Skipping tests" +fi + +# Create package +cd ${ISSM_DIR} +svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) +echo "Copying assets to package: ${PKG}" +cp -rf bin examples lib scripts test ${PKG} +mkdir ${PKG}/execution +cp packagers/mac/issm-executable_entitlements.plist ${PKG}/bin/entitlements.plist +${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files +echo "Cleaning up unneeded/unwanted files" +rm -f ${PKG}/bin/*.py # Remove all Python scripts +rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes +rm -f ${PKG}/lib/*.a # Remove static libraries from package +rm -f ${PKG}/lib/*.la # Remove libtool libraries from package +rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package + +# Compress package +echo "Compressing package" +ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-python-3.sh (revision 27035) +++ /issm/trunk/packagers/mac/package-issm-mac-binaries-python-3.sh (revision 27035) @@ -0,0 +1,182 @@ +#!/bin/bash + +################################################################################ +# Packages and tests ISSM distributable package for macOS with Python 3 API. +# +# Options: +# -s/--skiptests Skip testing during packaging Use if packaging fails +# for some reason but build is valid. +# +# NOTE: +# - Assumes that the following constants are defined, +# +# COMPRESSED_PKG +# ISSM_DIR +# PKG +# +# See also: +# - packagers/mac/complete-issm-mac-binaries-python-3.sh +# - packagers/mac/sign-issm-mac-binaries-python-3.sh +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +# NOTE: May be able to remove this after updating macOS. +# +#alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias grep=$(which grep) + +## Constants +# +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded + +## Environment +# +export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' + +## Parse options +# +if [ $# -gt 1 ]; then + echo "Can use only one option at a time" + exit 1 +fi + +skip_tests=0 + +if [ $# -eq 1 ]; then + case $1 in + -s|--skiptests) skip_tests=1; ;; + *) echo "Unknown parameter passed: $1"; exit 1 ;; + esac +fi + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd ${ISSM_DIR} +rm -rf ${PKG} ${COMPRESSED_PKG} +mkdir ${PKG} + +# Add required binaries and libraries to package and modify them where needed +cd ${ISSM_DIR}/bin + +echo "Modify generic" +cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py + +echo "Moving MPICH binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . +elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "MPICH not found" + exit 1 +fi + +echo "Moving GDAL binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . + cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . +else + echo "GDAL not found" + exit 1 +fi + +echo "Moving GMT binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . + cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . +else + echo "GMT not found" + exit 1 +fi + +echo "Moving Gmsh binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then + cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . +else + echo "Gmsh not found" + exit 1 +fi + +# Run tests +if [ ${skip_tests} -eq 0 ]; then + echo "Running tests" + cd ${ISSM_DIR}/test/NightlyRun + rm python.log 2> /dev/null + + # Set Python environment + export PYTHONPATH="${ISSM_DIR}/src/m/dev" + export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" + export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + + # Ensure that runme.py uses Python 3 interpreter + sed -i '' "s|/usr/bin/env python|/usr/local/bin/python3|g" ./runme.py + + # Run tests, redirecting output to logfile and suppressing output to console + ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + + # Check that Python did not exit in error + pythonExitCode=`echo $?` + pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l` + + if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 + fi + + # Check that all tests passed + numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + + if [ ${numTestsFailed} -ne 0 ]; then + echo "One or more tests FAILED" + exit 1 + else + echo "All tests PASSED" + fi +else + echo "Skipping tests" +fi + +# Create package +cd ${ISSM_DIR} +svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) +echo "Copying assets to package: ${PKG}" +cp -rf bin examples lib scripts test ${PKG} +mkdir ${PKG}/execution +cp packagers/mac/issm-executable_entitlements.plist ${PKG}/bin/entitlements.plist +${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files +echo "Cleaning up unneeded/unwanted files" +rm -f ${PKG}/bin/*.py # Remove all Python scripts +rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes +rm -f ${PKG}/lib/*.a # Remove static libraries from package +rm -f ${PKG}/lib/*.la # Remove libtool libraries from package +rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package + +# Compress package +echo "Compressing package" +ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} Index: sm/trunk/packagers/mac/package-issm-mac-binaries-python.sh =================================================================== --- /issm/trunk/packagers/mac/package-issm-mac-binaries-python.sh (revision 27034) +++ (revision ) @@ -1,179 +1,0 @@ -#!/bin/bash - -################################################################################ -# Packages and tests ISSM distributable package for macOS with Python API. -# -# Options: -# -s/--skiptests Skip testing during packaging Use if packaging fails -# for some reason but build is valid. -# -# NOTE: -# - Assumes that the following constants are defined, -# -# COMPRESSED_PKG -# ISSM_DIR -# PKG -# -# See also: -# - packagers/mac/complete-issm-mac-binaries-python.sh -# - packagers/mac/sign-issm-mac-binaries-python.sh -################################################################################ - -# Expand aliases within the context of this script -shopt -s expand_aliases - -# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, -# -# Command line tool support for Subversion — including svn, git-svn, and -# related commands — is no longer provided by Xcode. (50266910) -# -# which results in, -# -# svn: error: The subversion command line tools are no longer provided by -# Xcode. -# -# when calling svn, even when subversion is installed via Homebrew and its path -# is available in PATH. -# -# NOTE: May be able to remove this after updating macOS. -# -alias svn='/usr/local/bin/svn' - -## Override certain other aliases -# -alias grep=$(which grep) - -## Constants -# -PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2006 2020 2021 2051 2052 2053 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded - -## Environment -# -export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages' - -## Parse options -# -if [ $# -gt 1 ]; then - echo "Can use only one option at a time" - exit 1 -fi - -skip_tests=0 - -if [ $# -eq 1 ]; then - case $1 in - -s|--skiptests) skip_tests=1; ;; - *) echo "Unknown parameter passed: $1"; exit 1 ;; - esac -fi - -# Clean up from previous packaging -echo "Cleaning up existing assets" -cd ${ISSM_DIR} -rm -rf ${PKG} ${COMPRESSED_PKG} -mkdir ${PKG} - -# Add required binaries and libraries to package and modify them where needed -cd ${ISSM_DIR}/bin - -echo "Modify generic" -cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py - -echo "Moving MPICH binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then - cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . - cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . -elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then - cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . - cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . -else - echo "MPICH not found" - exit 1 -fi - -echo "Moving GDAL binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then - cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo . - cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform . -else - echo "GDAL not found" - exit 1 -fi - -echo "Moving GMT binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then - cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt . - cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect . -else - echo "GMT not found" - exit 1 -fi - -echo "Moving Gmsh binaries to bin/" -if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then - cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh . -else - echo "Gmsh not found" - exit 1 -fi - -# Run tests -if [ ${skip_tests} -eq 0 ]; then - echo "Running tests" - cd ${ISSM_DIR}/test/NightlyRun - rm python.log 2> /dev/null - - # Set Python environment - export PYTHONPATH="${ISSM_DIR}/src/m/dev" - export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" - export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured - - # Run tests, redirecting output to logfile and suppressing output to console - ./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 - - # Check that Python did not exit in error - pythonExitCode=`echo $?` - pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l` - - if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then - echo "----------Python exited in error!----------" - cat python.log - echo "-----------End of python.log-----------" - - # Clean up execution directory - rm -rf ${ISSM_DIR}/execution/* - - exit 1 - fi - - # Check that all tests passed - numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` - - if [ ${numTestsFailed} -ne 0 ]; then - echo "One or more tests FAILED" - exit 1 - else - echo "All tests PASSED" - fi -else - echo "Skipping tests" -fi - -# Create package -cd ${ISSM_DIR} -svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) -echo "Copying assets to package: ${PKG}" -cp -rf bin examples lib scripts test ${PKG} -mkdir ${PKG}/execution -cp packagers/mac/issm-executable_entitlements.plist ${PKG}/bin/entitlements.plist -${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files -echo "Cleaning up unneeded/unwanted files" -rm -f ${PKG}/bin/*.py # Remove all Python scripts -rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes -rm -f ${PKG}/lib/*.a # Remove static libraries from package -rm -f ${PKG}/lib/*.la # Remove libtool libraries from package -rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package - -# Compress package -echo "Compressing package" -ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh (revision 27034) +++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh (revision 27035) @@ -67,5 +67,5 @@ # NOTE: May be able to remove this after updating macOS. # -alias svn='/usr/local/bin/svn' +#alias svn='/usr/local/bin/svn' ## Override certain other aliases Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-2.sh (revision 27035) +++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-2.sh (revision 27035) @@ -0,0 +1,348 @@ +#!/bin/bash + +################################################################################ +# Intended to be run in the context of a Jenkins project on a JPL +# Cybersecurity server for signing macOS applications. Polls SCM of the +# Subversion repository hosted at +# https://issm.ess.uci.edu/svn/issm-binaries/mac/python/2/unsigned to trigger +# new builds. +# +# In order to replicate the requried Jenkins project configuration: +# - First, navigate to 'Manage Jenkins' -> 'Manage Plugins' and install the +# 'Credentials Bindings Plugin' if it is not already installed. +# - Contact one of the members of the ISSM development team for crendentials +# for the ISSM binaries repository (mention that the credentials are stored +# in ISSM-Infrastructure.pdf). +# - Navigate to 'Manage Jenkins' -> 'Manage Credentials' -> -> +# 'Add Credentials' and enter the crendentials from above. +# - From the 'Dashboard', select 'New Item' -> 'Freestyle project'. +# - Under 'Source Code Management', select 'Subversion'. +# - The 'Repository URL' text field should be set to +# "https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned". +# - The 'Credentials' select menu should be set to the new credentials +# created previously. +# - The 'Local module directory' text field should be set to the same +# value as the constant UNSIGNED_REPO_COPY (set below to './unsigned'). +# - Under 'Build Trigggers', check the box for 'Poll SCM' and set the +# 'Schedule' text area to "H/5 * * * *". +# - Under 'Build Environment', check the box for 'Use secret text(s) or +# file(s)', then under 'Bindings' click the 'Add...' button and select +# 'Username and password (separated)'. +# - Set 'Username Variable' to "ISSM_BINARIES_USER". +# - Set 'Password Variable' to "ISSM_BINARIES_PASS". +# - Under 'Credentials', select the same, new credentials that created +# previously. +# - The contents of this script can be copied/pasted directly into the ‘Build' +# -> 'Execute Shell' -> ‘Command' textarea of the project configuration (or +# you can simply store the script on disk and call it from there). +# - Make sure to click the 'Save' button. +# +# Current point of contact at JPL Cybersecurity: +# Alex Coward, alexander.g.coward@jpl.nasa.gov +# +# NOTE: +# - Assumes that "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" are set up in +# the 'Bindings' section under a 'Username and password (separated)' binding +# (requires 'Credentials Binding Plugin'). +# - For local debugging, the aformentioned credentials can be hardcoded into +# the 'USERNAME' and 'PASSWORD' constants below. +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +# NOTE: May be able to remove this after updating macOS. +# +#alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias cp=$(which cp) +alias grep=$(which grep) + +## Constants +# +AD_IDENTITY="**********" # Apple Developer identity +AD_USERNAME="**********" # Apple Developer username +ALTOOL_PASSWORD="@keychain:**********" # altool password (assumed to be stored in keychain) +ASC_PROVIDER="**********" +MAX_SVN_ATTEMPTS=10 +NOTARIZATION_CHECK_ATTEMPTS=20 +NOTARIZATION_CHECK_PERIOD=60 +NOTARIZATION_LOGFILE="notarization.log" +NOTARIZATION_LOGFILE_PATH="." +PASSWORD=${ISSM_BINARIES_PASS} +PKG="ISSM-macOS-Python-2" +PRIMARY_BUNDLE_ID="gov.nasa.jpl.issm.python" +SIGNED_REPO_COPY="./signed" +SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/2/signed" +SIGNING_LOCK_FILE="signing.lock" +SUCCESS_LOGFILE="${SIGNED_REPO_COPY}/success.log" +UNSIGNED_REPO_COPY="./unsigned" +UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/2/unsigned" +USERNAME=${ISSM_BINARIES_USER} + +COMPRESSED_PKG="${PKG}.zip" +EXE_ENTITLEMENTS_PLIST="${PKG}/bin/entitlements.plist" + +# NOTE: Uncomment the following for local testing (Jenkins checks out copy of +# repository for unsigned packages to working directory) +# + +# # Clean up from previous packaging (not necessary for single builds on Jenkins, +# # but useful when testing packaging locally) +# echo "Cleaning up existing assets" +# rm -rf ${COMPRESSED_PKG} ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${UNSIGNED_REPO_COPY} + +# # Check out copy of repository for unsigned packages +# echo "Checking out copy of respository for unsigned packages" +# svn checkout \ +# --trust-server-cert \ +# --non-interactive \ +# --username ${USERNAME} \ +# --password ${PASSWORD} \ +# ${UNSIGNED_REPO_URL} \ +# ${UNSIGNED_REPO_COPY} + +rm -rf ${PKG} ${SIGNED_REPO_COPY} + + +# Extract package contents +echo "Extracting package contents" +ditto -xk ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} . + +# Clear extended attributes on all files +xattr -cr ${PKG} + +# Build list of ISSM executables +ISSM_BINS=$(\ + find ${PKG}/bin -type f -name *.exe; \ + find ${PKG}/bin -type f -name *.pyc; \ +) + +# Build list of third party executables +THIRD_PARTY_BINS=$(\ + echo ${PKG}/bin/mpiexec; \ + echo ${PKG}/bin/hydra_pmi_proxy; \ + echo ${PKG}/bin/gdalsrsinfo; \ + echo ${PKG}/bin/gdaltransform; \ + echo ${PKG}/bin/gmt; \ + echo ${PKG}/bin/gmtselect; \ + echo ${PKG}/bin/gmsh; \ +) + +# Sign all executables in package +echo "Signing all executables in package" +codesign -s ${AD_IDENTITY} --timestamp --options=runtime --entitlements ${EXE_ENTITLEMENTS_PLIST} ${ISSM_BINS} +codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${THIRD_PARTY_BINS} + +# Build list of ISSM libraries +ISSM_LIBS=$(\ + find ${PKG}/lib -type f -name *.so; \ +) + +# Sign all libraries in package +echo "Signing all libraries in package" +codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${ISSM_LIBS} + +# NOTE: Skipping signature validation because this is not a true package nor app + +# Compress signed package +echo "Compressing signed package" +ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + +# Submit compressed package for notarization +echo "Submitting signed package to Apple for notarization" +xcrun altool --notarize-app --primary-bundle-id ${PRIMARY_BUNDLE_ID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} --asc-provider ${ASC_PROVIDER} --file ${COMPRESSED_PKG} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + +# Sleep until notarization request response is received +echo "Waiting for notarizaion request response" +while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do + sleep 30 +done + +echo "Notarizaion request response received" + +# Check if UUID exists in response +HAS_UUID=$(grep 'RequestUUID = ' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) # NOTE: Checking for "RequestUUID = " because "RequestUUID" shows up in some error messages +if [ -z "${HAS_UUID}" ]; then + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" + + # Clean up + rm -rf ${PKG} ${COMPRESSED_PKG} + + exit 1 +fi + +# Get UUID from notarization request response +UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*RequestUUID = //') +echo "UUID: ${UUID}" + +# Check notarization status +# +# NOTE: Currently, this checks if notarization was successful, but we are not +# able to staple notarization as this is not a true package nor app and, +# at the very least, MATLAB Mex files cannot be stapled. As such, clients +# will not be able to clear Gatekeeper if they are offline. +# +echo "Checking notarization status" +SUCCESS=0 +for ATTEMPT in $(seq 1 ${NOTARIZATION_CHECK_ATTEMPTS}); do + echo " Attempt #${ATTEMPT}..." + xcrun altool --notarization-info ${UUID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + if [[ -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} && -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; then + + # First, check if there is an error + ERROR_CHECK=$(grep 'Error' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) + if [ ! -z "${ERROR_CHECK}" ]; then + break + fi + + # No error, so check status + STATUS=$(grep 'Status:' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') + if [[ "${STATUS}" == "success" ]]; then + # Staple notarization to all elements of package that were previously signed + #xcrun stapler staple ${THIRD_PARTY_BINS} # NOTE: Fails with "Stapler is incapable of working with MATLAB Mex files." + + # Validate stapling of notarization + #xcrun stapler validation ${THIRD_PARTY_BINS} # NOTE: Skipping notarization stapling validation because this is not a true package nor app + + # Compress signed and notarized package + ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + + # Set flag indicating notarization was successful + SUCCESS=1 + + break + elif [[ "${STATUS}" == "in progress" ]]; then + echo " ...in progress still; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds." + sleep ${NOTARIZATION_CHECK_PERIOD} + elif [[ "${STATUS}" == "invalid" ]]; then + break + fi + else + if [ ${ATTEMPT} -lt ${NOTARIZATION_CHECK_ATTEMPTS} ]; then + echo " ...not ready yet; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds" + sleep ${NOTARIZATION_CHECK_PERIOD} + else + echo " ...maximum attempts reached, but no response, or something else went wrong" + echo " If contents of notarization status check logfile appear to be valid, increase NOTARIZATION_CHECK_ATTEMPTS and run again" + break + fi + fi +done + +if [ ${SUCCESS} -eq 1 ]; then + echo "Notarization successful!" +else + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" +fi + +# Check out copy of repository for signed packages +echo "Checking out copy of respository for signed packages" +SVN_ATTEMPT=0 +SVN_SUCCESS=0 +while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do + rm -rf ${SIGNED_REPO_COPY} + svn checkout \ + --trust-server-cert \ + --non-interactive \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + if [ $? -eq 0 ]; then + SVN_SUCCESS=1 + break + else + ((++SVN_ATTEMPT)) + sleep 5 + fi +done + +if [ ${SVN_SUCCESS} -eq 0 ]; then + echo "Checkout of respository for signed packages failed" + exit 1 +fi + +# Copy notarization file to repository for signed packages +cp ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${SIGNED_REPO_COPY} +svn add ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} > /dev/null 2>&1 + +# Remove lock file from repository for signed packages +svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} + +SVN_ATTEMPT=0 +SVN_SUCCESS=0 +if [ ${SUCCESS} -eq 1 ]; then + # Copy signed package to repository for signed packages + cp ${COMPRESSED_PKG} ${SIGNED_REPO_COPY} + svn add ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + + # Commit changes + echo "Committing changes to repository for signed packages" + while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + --message "CHG: New signed package (success)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + if [ $? -eq 0 ]; then + SVN_SUCCESS=1 + break + else + ((++SVN_ATTEMPT)) + sleep 5 + fi + done + + if [ ${SVN_SUCCESS} -eq 0 ]; then + echo "Commit to respository for signed packages failed" + exit 1 + fi +else + # Commit changes + echo "Committing changes to repository for signed packages" + while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + --message "CHG: New signed package (failure)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + if [ $? -eq 0 ]; then + SVN_SUCCESS=1 + break + else + ((++SVN_ATTEMPT)) + sleep 5 + fi + done + + if [ ${SVN_SUCCESS} -eq 0 ]; then + echo "Commit to respository for signed packages failed" + exit 1 + fi + + exit 1 +fi Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-3.sh (revision 27035) +++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-3.sh (revision 27035) @@ -0,0 +1,348 @@ +#!/bin/bash + +################################################################################ +# Intended to be run in the context of a Jenkins project on a JPL +# Cybersecurity server for signing macOS applications. Polls SCM of the +# Subversion repository hosted at +# https://issm.ess.uci.edu/svn/issm-binaries/mac/python/3/unsigned to trigger +# new builds. +# +# In order to replicate the requried Jenkins project configuration: +# - First, navigate to 'Manage Jenkins' -> 'Manage Plugins' and install the +# 'Credentials Bindings Plugin' if it is not already installed. +# - Contact one of the members of the ISSM development team for crendentials +# for the ISSM binaries repository (mention that the credentials are stored +# in ISSM-Infrastructure.pdf). +# - Navigate to 'Manage Jenkins' -> 'Manage Credentials' -> -> +# 'Add Credentials' and enter the crendentials from above. +# - From the 'Dashboard', select 'New Item' -> 'Freestyle project'. +# - Under 'Source Code Management', select 'Subversion'. +# - The 'Repository URL' text field should be set to +# "https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned". +# - The 'Credentials' select menu should be set to the new credentials +# created previously. +# - The 'Local module directory' text field should be set to the same +# value as the constant UNSIGNED_REPO_COPY (set below to './unsigned'). +# - Under 'Build Trigggers', check the box for 'Poll SCM' and set the +# 'Schedule' text area to "H/5 * * * *". +# - Under 'Build Environment', check the box for 'Use secret text(s) or +# file(s)', then under 'Bindings' click the 'Add...' button and select +# 'Username and password (separated)'. +# - Set 'Username Variable' to "ISSM_BINARIES_USER". +# - Set 'Password Variable' to "ISSM_BINARIES_PASS". +# - Under 'Credentials', select the same, new credentials that created +# previously. +# - The contents of this script can be copied/pasted directly into the ‘Build' +# -> 'Execute Shell' -> ‘Command' textarea of the project configuration (or +# you can simply store the script on disk and call it from there). +# - Make sure to click the 'Save' button. +# +# Current point of contact at JPL Cybersecurity: +# Alex Coward, alexander.g.coward@jpl.nasa.gov +# +# NOTE: +# - Assumes that "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" are set up in +# the 'Bindings' section under a 'Username and password (separated)' binding +# (requires 'Credentials Binding Plugin'). +# - For local debugging, the aformentioned credentials can be hardcoded into +# the 'USERNAME' and 'PASSWORD' constants below. +################################################################################ + +# Expand aliases within the context of this script +shopt -s expand_aliases + +# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, +# +# Command line tool support for Subversion — including svn, git-svn, and +# related commands — is no longer provided by Xcode. (50266910) +# +# which results in, +# +# svn: error: The subversion command line tools are no longer provided by +# Xcode. +# +# when calling svn, even when subversion is installed via Homebrew and its path +# is available in PATH. +# +# NOTE: May be able to remove this after updating macOS. +# +#alias svn='/usr/local/bin/svn' + +## Override certain other aliases +# +alias cp=$(which cp) +alias grep=$(which grep) + +## Constants +# +AD_IDENTITY="**********" # Apple Developer identity +AD_USERNAME="**********" # Apple Developer username +ALTOOL_PASSWORD="@keychain:**********" # altool password (assumed to be stored in keychain) +ASC_PROVIDER="**********" +MAX_SVN_ATTEMPTS=10 +NOTARIZATION_CHECK_ATTEMPTS=20 +NOTARIZATION_CHECK_PERIOD=60 +NOTARIZATION_LOGFILE="notarization.log" +NOTARIZATION_LOGFILE_PATH="." +PASSWORD=${ISSM_BINARIES_PASS} +PKG="ISSM-macOS-Python-3" +PRIMARY_BUNDLE_ID="gov.nasa.jpl.issm.python" +SIGNED_REPO_COPY="./signed" +SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/3/signed" +SIGNING_LOCK_FILE="signing.lock" +SUCCESS_LOGFILE="${SIGNED_REPO_COPY}/success.log" +UNSIGNED_REPO_COPY="./unsigned" +UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/3/unsigned" +USERNAME=${ISSM_BINARIES_USER} + +COMPRESSED_PKG="${PKG}.zip" +EXE_ENTITLEMENTS_PLIST="${PKG}/bin/entitlements.plist" + +# NOTE: Uncomment the following for local testing (Jenkins checks out copy of +# repository for unsigned packages to working directory) +# + +# # Clean up from previous packaging (not necessary for single builds on Jenkins, +# # but useful when testing packaging locally) +# echo "Cleaning up existing assets" +# rm -rf ${COMPRESSED_PKG} ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${UNSIGNED_REPO_COPY} + +# # Check out copy of repository for unsigned packages +# echo "Checking out copy of respository for unsigned packages" +# svn checkout \ +# --trust-server-cert \ +# --non-interactive \ +# --username ${USERNAME} \ +# --password ${PASSWORD} \ +# ${UNSIGNED_REPO_URL} \ +# ${UNSIGNED_REPO_COPY} + +rm -rf ${PKG} ${SIGNED_REPO_COPY} + + +# Extract package contents +echo "Extracting package contents" +ditto -xk ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} . + +# Clear extended attributes on all files +xattr -cr ${PKG} + +# Build list of ISSM executables +ISSM_BINS=$(\ + find ${PKG}/bin -type f -name *.exe; \ + find ${PKG}/bin -type f -name *.pyc; \ +) + +# Build list of third party executables +THIRD_PARTY_BINS=$(\ + echo ${PKG}/bin/mpiexec; \ + echo ${PKG}/bin/hydra_pmi_proxy; \ + echo ${PKG}/bin/gdalsrsinfo; \ + echo ${PKG}/bin/gdaltransform; \ + echo ${PKG}/bin/gmt; \ + echo ${PKG}/bin/gmtselect; \ + echo ${PKG}/bin/gmsh; \ +) + +# Sign all executables in package +echo "Signing all executables in package" +codesign -s ${AD_IDENTITY} --timestamp --options=runtime --entitlements ${EXE_ENTITLEMENTS_PLIST} ${ISSM_BINS} +codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${THIRD_PARTY_BINS} + +# Build list of ISSM libraries +ISSM_LIBS=$(\ + find ${PKG}/lib -type f -name *.so; \ +) + +# Sign all libraries in package +echo "Signing all libraries in package" +codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${ISSM_LIBS} + +# NOTE: Skipping signature validation because this is not a true package nor app + +# Compress signed package +echo "Compressing signed package" +ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + +# Submit compressed package for notarization +echo "Submitting signed package to Apple for notarization" +xcrun altool --notarize-app --primary-bundle-id ${PRIMARY_BUNDLE_ID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} --asc-provider ${ASC_PROVIDER} --file ${COMPRESSED_PKG} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + +# Sleep until notarization request response is received +echo "Waiting for notarizaion request response" +while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do + sleep 30 +done + +echo "Notarizaion request response received" + +# Check if UUID exists in response +HAS_UUID=$(grep 'RequestUUID = ' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) # NOTE: Checking for "RequestUUID = " because "RequestUUID" shows up in some error messages +if [ -z "${HAS_UUID}" ]; then + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" + + # Clean up + rm -rf ${PKG} ${COMPRESSED_PKG} + + exit 1 +fi + +# Get UUID from notarization request response +UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*RequestUUID = //') +echo "UUID: ${UUID}" + +# Check notarization status +# +# NOTE: Currently, this checks if notarization was successful, but we are not +# able to staple notarization as this is not a true package nor app and, +# at the very least, MATLAB Mex files cannot be stapled. As such, clients +# will not be able to clear Gatekeeper if they are offline. +# +echo "Checking notarization status" +SUCCESS=0 +for ATTEMPT in $(seq 1 ${NOTARIZATION_CHECK_ATTEMPTS}); do + echo " Attempt #${ATTEMPT}..." + xcrun altool --notarization-info ${UUID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + if [[ -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} && -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; then + + # First, check if there is an error + ERROR_CHECK=$(grep 'Error' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) + if [ ! -z "${ERROR_CHECK}" ]; then + break + fi + + # No error, so check status + STATUS=$(grep 'Status:' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') + if [[ "${STATUS}" == "success" ]]; then + # Staple notarization to all elements of package that were previously signed + #xcrun stapler staple ${THIRD_PARTY_BINS} # NOTE: Fails with "Stapler is incapable of working with MATLAB Mex files." + + # Validate stapling of notarization + #xcrun stapler validation ${THIRD_PARTY_BINS} # NOTE: Skipping notarization stapling validation because this is not a true package nor app + + # Compress signed and notarized package + ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} + + # Set flag indicating notarization was successful + SUCCESS=1 + + break + elif [[ "${STATUS}" == "in progress" ]]; then + echo " ...in progress still; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds." + sleep ${NOTARIZATION_CHECK_PERIOD} + elif [[ "${STATUS}" == "invalid" ]]; then + break + fi + else + if [ ${ATTEMPT} -lt ${NOTARIZATION_CHECK_ATTEMPTS} ]; then + echo " ...not ready yet; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds" + sleep ${NOTARIZATION_CHECK_PERIOD} + else + echo " ...maximum attempts reached, but no response, or something else went wrong" + echo " If contents of notarization status check logfile appear to be valid, increase NOTARIZATION_CHECK_ATTEMPTS and run again" + break + fi + fi +done + +if [ ${SUCCESS} -eq 1 ]; then + echo "Notarization successful!" +else + echo "Notarization failed!" + echo "----------------------- Contents of notarization logfile -----------------------" + cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} + echo "--------------------------------------------------------------------------------" +fi + +# Check out copy of repository for signed packages +echo "Checking out copy of respository for signed packages" +SVN_ATTEMPT=0 +SVN_SUCCESS=0 +while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do + rm -rf ${SIGNED_REPO_COPY} + svn checkout \ + --trust-server-cert \ + --non-interactive \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + ${SIGNED_REPO_URL} \ + ${SIGNED_REPO_COPY} > /dev/null 2>&1 + if [ $? -eq 0 ]; then + SVN_SUCCESS=1 + break + else + ((++SVN_ATTEMPT)) + sleep 5 + fi +done + +if [ ${SVN_SUCCESS} -eq 0 ]; then + echo "Checkout of respository for signed packages failed" + exit 1 +fi + +# Copy notarization file to repository for signed packages +cp ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${SIGNED_REPO_COPY} +svn add ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} > /dev/null 2>&1 + +# Remove lock file from repository for signed packages +svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} + +SVN_ATTEMPT=0 +SVN_SUCCESS=0 +if [ ${SUCCESS} -eq 1 ]; then + # Copy signed package to repository for signed packages + cp ${COMPRESSED_PKG} ${SIGNED_REPO_COPY} + svn add ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 + + # Commit changes + echo "Committing changes to repository for signed packages" + while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + --message "CHG: New signed package (success)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + if [ $? -eq 0 ]; then + SVN_SUCCESS=1 + break + else + ((++SVN_ATTEMPT)) + sleep 5 + fi + done + + if [ ${SVN_SUCCESS} -eq 0 ]; then + echo "Commit to respository for signed packages failed" + exit 1 + fi +else + # Commit changes + echo "Committing changes to repository for signed packages" + while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do + svn commit \ + --trust-server-cert \ + --non-interactive \ + --username ${USERNAME} \ + --password ${PASSWORD} \ + --message "CHG: New signed package (failure)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 + if [ $? -eq 0 ]; then + SVN_SUCCESS=1 + break + else + ((++SVN_ATTEMPT)) + sleep 5 + fi + done + + if [ ${SVN_SUCCESS} -eq 0 ]; then + echo "Commit to respository for signed packages failed" + exit 1 + fi + + exit 1 +fi Index: sm/trunk/packagers/mac/sign-issm-mac-binaries-python.sh =================================================================== --- /issm/trunk/packagers/mac/sign-issm-mac-binaries-python.sh (revision 27034) +++ (revision ) @@ -1,348 +1,0 @@ -#!/bin/bash - -################################################################################ -# Intended to be run in the context of a Jenkins project on a JPL -# Cybersecurity server for signing macOS applications. Polls SCM of the -# Subversion repository hosted at -# https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned to trigger new -# builds. -# -# In order to replicate the requried Jenkins project configuration: -# - First, navigate to 'Manage Jenkins' -> 'Manage Plugins' and install the -# 'Credentials Bindings Plugin' if it is not already installed. -# - Contact one of the members of the ISSM development team for crendentials -# for the ISSM binaries repository (mention that the credentials are stored -# in ISSM-Infrastructure.pdf). -# - Navigate to 'Manage Jenkins' -> 'Manage Credentials' -> -> -# 'Add Credentials' and enter the crendentials from above. -# - From the 'Dashboard', select 'New Item' -> 'Freestyle project'. -# - Under 'Source Code Management', select 'Subversion'. -# - The 'Repository URL' text field should be set to -# "https://issm.ess.uci.edu/svn/issm-binaries/mac/matlab/unsigned". -# - The 'Credentials' select menu should be set to the new credentials -# created previously. -# - The 'Local module directory' text field should be set to the same -# value as the constant UNSIGNED_REPO_COPY (set below to './unsigned'). -# - Under 'Build Trigggers', check the box for 'Poll SCM' and set the -# 'Schedule' text area to "H/5 * * * *". -# - Under 'Build Environment', check the box for 'Use secret text(s) or -# file(s)', then under 'Bindings' click the 'Add...' button and select -# 'Username and password (separated)'. -# - Set 'Username Variable' to "ISSM_BINARIES_USER". -# - Set 'Password Variable' to "ISSM_BINARIES_PASS". -# - Under 'Credentials', select the same, new credentials that created -# previously. -# - The contents of this script can be copied/pasted directly into the ‘Build' -# -> 'Execute Shell' -> ‘Command' textarea of the project configuration (or -# you can simply store the script on disk and call it from there). -# - Make sure to click the 'Save' button. -# -# Current point of contact at JPL Cybersecurity: -# Alex Coward, alexander.g.coward@jpl.nasa.gov -# -# NOTE: -# - Assumes that "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" are set up in -# the 'Bindings' section under a 'Username and password (separated)' binding -# (requires 'Credentials Binding Plugin'). -# - For local debugging, the aformentioned credentials can be hardcoded into -# the 'USERNAME' and 'PASSWORD' constants below. -################################################################################ - -# Expand aliases within the context of this script -shopt -s expand_aliases - -# From https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes, -# -# Command line tool support for Subversion — including svn, git-svn, and -# related commands — is no longer provided by Xcode. (50266910) -# -# which results in, -# -# svn: error: The subversion command line tools are no longer provided by -# Xcode. -# -# when calling svn, even when subversion is installed via Homebrew and its path -# is available in PATH. -# -# NOTE: May be able to remove this after updating macOS. -# -alias svn='/usr/local/bin/svn' - -## Override certain other aliases -# -alias cp=$(which cp) -alias grep=$(which grep) - -## Constants -# -AD_IDENTITY="**********" # Apple Developer identity -AD_USERNAME="**********" # Apple Developer username -ALTOOL_PASSWORD="@keychain:**********" # altool password (assumed to be stored in keychain) -ASC_PROVIDER="**********" -MAX_SVN_ATTEMPTS=10 -NOTARIZATION_CHECK_ATTEMPTS=20 -NOTARIZATION_CHECK_PERIOD=60 -NOTARIZATION_LOGFILE="notarization.log" -NOTARIZATION_LOGFILE_PATH="." -PASSWORD=${ISSM_BINARIES_PASS} -PKG="ISSM-macOS-Python" -PRIMARY_BUNDLE_ID="gov.nasa.jpl.issm.python" -SIGNED_REPO_COPY="./signed" -SIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/signed" -SIGNING_LOCK_FILE="signing.lock" -SUCCESS_LOGFILE="${SIGNED_REPO_COPY}/success.log" -UNSIGNED_REPO_COPY="./unsigned" -UNSIGNED_REPO_URL="https://issm.ess.uci.edu/svn/issm-binaries/mac/python/unsigned" -USERNAME=${ISSM_BINARIES_USER} - -COMPRESSED_PKG="${PKG}.zip" -EXE_ENTITLEMENTS_PLIST="${PKG}/bin/entitlements.plist" - -# NOTE: Uncomment the following for local testing (Jenkins checks out copy of -# repository for unsigned packages to working directory) -# - -# # Clean up from previous packaging (not necessary for single builds on Jenkins, -# # but useful when testing packaging locally) -# echo "Cleaning up existing assets" -# rm -rf ${COMPRESSED_PKG} ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${UNSIGNED_REPO_COPY} - -# # Check out copy of repository for unsigned packages -# echo "Checking out copy of respository for unsigned packages" -# svn checkout \ -# --trust-server-cert \ -# --non-interactive \ -# --username ${USERNAME} \ -# --password ${PASSWORD} \ -# ${UNSIGNED_REPO_URL} \ -# ${UNSIGNED_REPO_COPY} - -rm -rf ${PKG} ${SIGNED_REPO_COPY} - - -# Extract package contents -echo "Extracting package contents" -ditto -xk ${UNSIGNED_REPO_COPY}/${COMPRESSED_PKG} . - -# Clear extended attributes on all files -xattr -cr ${PKG} - -# Build list of ISSM executables -ISSM_BINS=$(\ - find ${PKG}/bin -type f -name *.exe; \ - find ${PKG}/bin -type f -name *.pyc; \ -) - -# Build list of third party executables -THIRD_PARTY_BINS=$(\ - echo ${PKG}/bin/mpiexec; \ - echo ${PKG}/bin/hydra_pmi_proxy; \ - echo ${PKG}/bin/gdalsrsinfo; \ - echo ${PKG}/bin/gdaltransform; \ - echo ${PKG}/bin/gmt; \ - echo ${PKG}/bin/gmtselect; \ - echo ${PKG}/bin/gmsh; \ -) - -# Sign all executables in package -echo "Signing all executables in package" -codesign -s ${AD_IDENTITY} --timestamp --options=runtime --entitlements ${EXE_ENTITLEMENTS_PLIST} ${ISSM_BINS} -codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${THIRD_PARTY_BINS} - -# Build list of ISSM libraries -ISSM_LIBS=$(\ - find ${PKG}/lib -type f -name *.so; \ -) - -# Sign all libraries in package -echo "Signing all libraries in package" -codesign -s ${AD_IDENTITY} --timestamp --options=runtime ${ISSM_LIBS} - -# NOTE: Skipping signature validation because this is not a true package nor app - -# Compress signed package -echo "Compressing signed package" -ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} - -# Submit compressed package for notarization -echo "Submitting signed package to Apple for notarization" -xcrun altool --notarize-app --primary-bundle-id ${PRIMARY_BUNDLE_ID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} --asc-provider ${ASC_PROVIDER} --file ${COMPRESSED_PKG} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} - -# Sleep until notarization request response is received -echo "Waiting for notarizaion request response" -while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do - sleep 30 -done - -echo "Notarizaion request response received" - -# Check if UUID exists in response -HAS_UUID=$(grep 'RequestUUID = ' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) # NOTE: Checking for "RequestUUID = " because "RequestUUID" shows up in some error messages -if [ -z "${HAS_UUID}" ]; then - echo "Notarization failed!" - echo "----------------------- Contents of notarization logfile -----------------------" - cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} - echo "--------------------------------------------------------------------------------" - - # Clean up - rm -rf ${PKG} ${COMPRESSED_PKG} - - exit 1 -fi - -# Get UUID from notarization request response -UUID=$(echo ${HAS_UUID} | sed 's/[[:space:]]*RequestUUID = //') -echo "UUID: ${UUID}" - -# Check notarization status -# -# NOTE: Currently, this checks if notarization was successful, but we are not -# able to staple notarization as this is not a true package nor app and, -# at the very least, MATLAB Mex files cannot be stapled. As such, clients -# will not be able to clear Gatekeeper if they are offline. -# -echo "Checking notarization status" -SUCCESS=0 -for ATTEMPT in $(seq 1 ${NOTARIZATION_CHECK_ATTEMPTS}); do - echo " Attempt #${ATTEMPT}..." - xcrun altool --notarization-info ${UUID} --username ${AD_USERNAME} --password ${ALTOOL_PASSWORD} &> ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} - if [[ -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} && -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; then - - # First, check if there is an error - ERROR_CHECK=$(grep 'Error' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE}) - if [ ! -z "${ERROR_CHECK}" ]; then - break - fi - - # No error, so check status - STATUS=$(grep 'Status:' ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} | sed -e 's/[[:space:]]*Status: //') - if [[ "${STATUS}" == "success" ]]; then - # Staple notarization to all elements of package that were previously signed - #xcrun stapler staple ${THIRD_PARTY_BINS} # NOTE: Fails with "Stapler is incapable of working with MATLAB Mex files." - - # Validate stapling of notarization - #xcrun stapler validation ${THIRD_PARTY_BINS} # NOTE: Skipping notarization stapling validation because this is not a true package nor app - - # Compress signed and notarized package - ditto -ck --sequesterRsrc --keepParent ${PKG} ${COMPRESSED_PKG} - - # Set flag indicating notarization was successful - SUCCESS=1 - - break - elif [[ "${STATUS}" == "in progress" ]]; then - echo " ...in progress still; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds." - sleep ${NOTARIZATION_CHECK_PERIOD} - elif [[ "${STATUS}" == "invalid" ]]; then - break - fi - else - if [ ${ATTEMPT} -lt ${NOTARIZATION_CHECK_ATTEMPTS} ]; then - echo " ...not ready yet; checking again in ${NOTARIZATION_CHECK_PERIOD} seconds" - sleep ${NOTARIZATION_CHECK_PERIOD} - else - echo " ...maximum attempts reached, but no response, or something else went wrong" - echo " If contents of notarization status check logfile appear to be valid, increase NOTARIZATION_CHECK_ATTEMPTS and run again" - break - fi - fi -done - -if [ ${SUCCESS} -eq 1 ]; then - echo "Notarization successful!" -else - echo "Notarization failed!" - echo "----------------------- Contents of notarization logfile -----------------------" - cat ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} - echo "--------------------------------------------------------------------------------" -fi - -# Check out copy of repository for signed packages -echo "Checking out copy of respository for signed packages" -SVN_ATTEMPT=0 -SVN_SUCCESS=0 -while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do - rm -rf ${SIGNED_REPO_COPY} - svn checkout \ - --trust-server-cert \ - --non-interactive \ - --username ${USERNAME} \ - --password ${PASSWORD} \ - ${SIGNED_REPO_URL} \ - ${SIGNED_REPO_COPY} > /dev/null 2>&1 - if [ $? -eq 0 ]; then - SVN_SUCCESS=1 - break - else - ((++SVN_ATTEMPT)) - sleep 5 - fi -done - -if [ ${SVN_SUCCESS} -eq 0 ]; then - echo "Checkout of respository for signed packages failed" - exit 1 -fi - -# Copy notarization file to repository for signed packages -cp ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} ${SIGNED_REPO_COPY} -svn add ${SIGNED_REPO_COPY}/${NOTARIZATION_LOGFILE} > /dev/null 2>&1 - -# Remove lock file from repository for signed packages -svn delete ${SIGNED_REPO_COPY}/${SIGNING_LOCK_FILE} - -SVN_ATTEMPT=0 -SVN_SUCCESS=0 -if [ ${SUCCESS} -eq 1 ]; then - # Copy signed package to repository for signed packages - cp ${COMPRESSED_PKG} ${SIGNED_REPO_COPY} - svn add ${SIGNED_REPO_COPY}/${COMPRESSED_PKG} > /dev/null 2>&1 - - # Commit changes - echo "Committing changes to repository for signed packages" - while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do - svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${USERNAME} \ - --password ${PASSWORD} \ - --message "CHG: New signed package (success)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 - if [ $? -eq 0 ]; then - SVN_SUCCESS=1 - break - else - ((++SVN_ATTEMPT)) - sleep 5 - fi - done - - if [ ${SVN_SUCCESS} -eq 0 ]; then - echo "Commit to respository for signed packages failed" - exit 1 - fi -else - # Commit changes - echo "Committing changes to repository for signed packages" - while [[ ${SVN_ATTEMPT} -lt ${MAX_SVN_ATTEMPTS} && ${SVN_SUCCESS} -eq 0 ]]; do - svn commit \ - --trust-server-cert \ - --non-interactive \ - --username ${USERNAME} \ - --password ${PASSWORD} \ - --message "CHG: New signed package (failure)" ${SIGNED_REPO_COPY} > /dev/null 2>&1 - if [ $? -eq 0 ]; then - SVN_SUCCESS=1 - break - else - ((++SVN_ATTEMPT)) - sleep 5 - fi - done - - if [ ${SVN_SUCCESS} -eq 0 ]; then - echo "Commit to respository for signed packages failed" - exit 1 - fi - - exit 1 -fi Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh =================================================================== --- /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh (revision 27034) +++ /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh (revision 27035) @@ -11,5 +11,5 @@ # INSTALL_DIR=. -MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2004,2006,2051,2052,2053,2084,2085,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded +MATLAB_NROPTIONS="'benchmark','all','exclude',[125,126,234,235,418,420,435,444,445,701,702,703,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1201,1202,1203,1204,1205,1206,1207,1208,1301,1302,1303,1304,1401,1402,1601,1602,2002,2003,2004,2006,2007,2008,2010,2011,2021,2051,2052,2053,2084,2085,2090,2101,2424,2425,3001:3200,3201,3202,3300,3480,3481,4001,4002,4003]" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded MATLAB_PATH="/Applications/MATLAB_R2018a.app" PKG="ISSM-macOS-MATLAB" Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-python-2.sh =================================================================== --- /issm/trunk/packagers/mac/test-issm-mac-binaries-python-2.sh (revision 27035) +++ /issm/trunk/packagers/mac/test-issm-mac-binaries-python-2.sh (revision 27035) @@ -0,0 +1,53 @@ +#!/bin/bash + +################################################################################ +# This script is intended to test ISSM macOS Python 2 binaries on an end-user +# machine after successful packaging and signing. +# +# NOTE: Tarball must already exist in INSTALL_DIR +################################################################################ + +## Constants +# +INSTALL_DIR=. +PKG="ISSM-macOS-Python-2" +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded + +COMPRESSED_PKG="${PKG}.zip" + +export ISSM_DIR="${INSTALL_DIR}/${PKG}" +export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" +export PYTHONPATH="${ISSM_DIR}/scripts" +export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" +export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + +cd ${INSTALL_DIR} +rm -rf ${PKG} +ditto -xk ${COMPRESSED_PKG} . +cd ${PKG}/test/NightlyRun + +# Run tests, redirecting output to logfile and suppressing output to console +echo "Running tests" +rm python.log 2> /dev/null +./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + +# Check that Python did not exit in error +pythonExitCode=`echo $?` +pythonExitedInError=`grep -E "runme.py: error" python.log | wc -l` + +if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + exit 1 +fi + +# Check that all tests passed +numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 +else + echo "All tests PASSED" +fi Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-python-3.sh =================================================================== --- /issm/trunk/packagers/mac/test-issm-mac-binaries-python-3.sh (revision 27035) +++ /issm/trunk/packagers/mac/test-issm-mac-binaries-python-3.sh (revision 27035) @@ -0,0 +1,53 @@ +#!/bin/bash + +################################################################################ +# This script is intended to test ISSM macOS Python 3 binaries on an end-user +# machine after successful packaging and signing. +# +# NOTE: Tarball must already exist in INSTALL_DIR +################################################################################ + +## Constants +# +INSTALL_DIR=. +PKG="ISSM-macOS-Python-3" +PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2004 2005 2006 2007 2008 2010 2011 2021 2051 2052 2053 2084 2085 2090 2101 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded + +COMPRESSED_PKG="${PKG}.zip" + +export ISSM_DIR="${INSTALL_DIR}/${PKG}" +export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" +export PYTHONPATH="${ISSM_DIR}/scripts" +export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" +export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + +cd ${INSTALL_DIR} +rm -rf ${PKG} +ditto -xk ${COMPRESSED_PKG} . +cd ${PKG}/test/NightlyRun + +# Run tests, redirecting output to logfile and suppressing output to console +echo "Running tests" +rm python.log 2> /dev/null +./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + +# Check that Python did not exit in error +pythonExitCode=`echo $?` +pythonExitedInError=`grep -E "runme.py: error" python.log | wc -l` + +if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + exit 1 +fi + +# Check that all tests passed +numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numTestsFailed} -ne 0 ]]; then + echo "One or more tests FAILED" + exit 1 +else + echo "All tests PASSED" +fi Index: sm/trunk/packagers/mac/test-issm-mac-binaries-python.sh =================================================================== --- /issm/trunk/packagers/mac/test-issm-mac-binaries-python.sh (revision 27034) +++ (revision ) @@ -1,53 +1,0 @@ -#!/bin/bash - -################################################################################ -# This script is intended to test ISSM macOS MATLAB binaries on an end-user -# machine after successful packaging and signing. -# -# NOTE: Tarball must already exist in INSTALL_DIR -################################################################################ - -## Constants -# -INSTALL_DIR=. -PKG="ISSM-macOS-Python" -PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2004 2006 2007 2051 2052 2053 2084 2085 2424 2425 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded - -COMPRESSED_PKG="${PKG}.zip" - -export ISSM_DIR="${INSTALL_DIR}/${PKG}" -export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" -export PYTHONPATH="${ISSM_DIR}/scripts" -export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" -export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured - -cd ${INSTALL_DIR} -rm -rf ${PKG} -ditto -xk ${COMPRESSED_PKG} . -cd ${PKG}/test/NightlyRun - -# Run tests, redirecting output to logfile and suppressing output to console -echo "Running tests" -rm python.log 2> /dev/null -./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 - -# Check that Python did not exit in error -pythonExitCode=`echo $?` -pythonExitedInError=`grep -E "runme.py: error" python.log | wc -l` - -if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then - echo "----------Python exited in error!----------" - cat python.log - echo "-----------End of python.log-----------" - exit 1 -fi - -# Check that all tests passed -numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` - -if [[ ${numTestsFailed} -ne 0 ]]; then - echo "One or more tests FAILED" - exit 1 -else - echo "All tests PASSED" -fi Index: /issm/trunk/packagers/mac/transfer-issm-mac-binaries.sh =================================================================== --- /issm/trunk/packagers/mac/transfer-issm-mac-binaries.sh (revision 27034) +++ /issm/trunk/packagers/mac/transfer-issm-mac-binaries.sh (revision 27035) @@ -2,6 +2,5 @@ ################################################################################ -# Transfers ISSM distributable package for macOS with MATLAB API to ISSM Web -# site. +# Transfers ISSM distributable package for macOS to ISSM website. # # NOTE: @@ -16,5 +15,6 @@ # See also: # - packagers/mac/complete-issm-mac-binaries-matlab.sh -# - packagers/mac/complete-issm-mac-binaries-python.sh +# - packagers/mac/complete-issm-mac-binaries-python-2.sh +# - packagers/mac/complete-issm-mac-binaries-python-3.sh ################################################################################ @@ -37,5 +37,5 @@ # NOTE: May be able to remove this after updating macOS. # -alias svn='/usr/local/bin/svn' +#alias svn='/usr/local/bin/svn' ## Override certain other aliases Index: /issm/trunk/scripts/DownloadExternalPackage.sh =================================================================== --- /issm/trunk/scripts/DownloadExternalPackage.sh (revision 27034) +++ /issm/trunk/scripts/DownloadExternalPackage.sh (revision 27035) @@ -42,15 +42,25 @@ ## Download file +# +if [ ! -z `which curl` ]; then + curl --silent $URL -o $OUT_FILE -if [ ! -z `which curl` ] -then - curl --silent $URL -o $OUT_FILE -elif [ ! -z `which wget` ] -then + # Try wget if curl exists but fails + if [ $? -ne 0 ]; then + if [ ! -z `which wget` ]; then + wget --quiet -O $OUT_FILE $URL + + if [ $? -ne 0 ]; then + echo "Error: both curl and wget failed. To debug, download package manually using curl without '--silent' option and/or wget without '--quiet' option." + exit 0 + fi + else + echo $MSG_ERR_NO_GET_CMD + exit 0 + fi + fi +elif [ ! -z `which wget` ]; then wget --quiet -O $OUT_FILE $URL else echo $MSG_ERR_NO_GET_CMD - exit 0 fi - -exit 0 Index: /issm/trunk/src/c/Makefile.am =================================================================== --- /issm/trunk/src/c/Makefile.am (revision 27034) +++ /issm/trunk/src/c/Makefile.am (revision 27035) @@ -1,3 +1,3 @@ -AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @TRIANGLEINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @PARMETISINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJINCL@ @ESMFINCL@ @PROJINCL@ +AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @TRIANGLEINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @PARMETISINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJINCL@ @ESMFINCL@ @PROJINCL@ @MPLAPACKINCL@ AM_FCFLAGS = @SEMICINCL@ @@ -273,4 +273,5 @@ ./classes/RiftStruct.cpp \ ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp \ + ./modules/ModelProcessorx/Transient/UpdateParametersTransient.cpp \ ./cores/transient_core.cpp \ ./cores/steadystate_core.cpp \ @@ -714,5 +715,5 @@ if !WINDOWS if !STANDALONE_LIBRARIES -libISSMCore_la_LIBADD = $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(OSLIBS) +libISSMCore_la_LIBADD = $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(OSLIBS) if FORTRAN libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB) @@ -830,5 +831,5 @@ # External packages -LDADD += $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS) +LDADD += $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS) if FORTRAN Index: /issm/trunk/src/c/analyses/AdjointHorizAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/AdjointHorizAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/AdjointHorizAnalysis.cpp (revision 27035) @@ -52,8 +52,8 @@ case FSApproximationEnum: return CreateKMatrixFS(element); - case MLHOApproximationEnum: + case MOLHOApproximationEnum: // a more accurate option, but integrate in the vertical direction numerically. - // return CreateKMatrixMLHOVerticalIntergrated(element); - return CreateKMatrixMLHO(element); + // return CreateKMatrixMOLHOVerticalIntergrated(element); + return CreateKMatrixMOLHO(element); case NoneApproximationEnum: return NULL; @@ -220,5 +220,5 @@ return Ke; }/*}}}*/ -ElementMatrix* AdjointHorizAnalysis::CreateKMatrixMLHO(Element* element){/*{{{*/ +ElementMatrix* AdjointHorizAnalysis::CreateKMatrixMOLHO(Element* element){/*{{{*/ /* Check if ice in element */ @@ -226,5 +226,4 @@ /*Intermediaries */ - bool incomplete_adjoint; IssmDouble Jdet,mu_prime,n,thickness,mu,effmu; IssmDouble *xyz_list = NULL; @@ -238,5 +237,137 @@ IssmDouble vxshear, vyshear; - Element* basalelement; + /*Get basal element*/ + Element* basalelement = NULL; + element->FindParam(&domaintype,DomainTypeEnum); + switch(domaintype){ + case Domain2DhorizontalEnum: + basalelement = element; + break; + case Domain3DEnum: case Domain2DverticalEnum: + _error_("mesh "<FindParam(&incomplete_adjoint,InversionIncompleteAdjointEnum); + StressbalanceAnalysis* analysis = new StressbalanceAnalysis(); + ElementMatrix* Ke=analysis->CreateKMatrix(basalelement); + delete analysis; + if(incomplete_adjoint) return Ke; + + /*Second part of the Gateau derivative if requested*/ + + /*Fetch number of nodes and dof for this finite element*/ + int numnodes = basalelement->GetNumberOfNodes(); + IssmDouble* dbasis = xNew(2*numnodes); // like SSA + IssmDouble* basis = xNew(numnodes); // like SSA + + /*Retrieve all inputs and parameters*/ + element->GetVerticesCoordinates(&xyz_list); + Input* vx_input = element->GetInput(VxEnum); _assert_(vx_input); //vertically integrated vx + Input* vy_input = element->GetInput(VyEnum); _assert_(vy_input); //vertically integrated vy + Input* vxbase_input = element->GetInput(VxBaseEnum); _assert_(vxbase_input); + Input* vybase_input = element->GetInput(VyBaseEnum); _assert_(vybase_input); + Input* vxshear_input = element->GetInput(VxShearEnum); _assert_(vxshear_input); + Input* vyshear_input = element->GetInput(VyShearEnum); _assert_(vyshear_input); + Input* thickness_input= element->GetInput(ThicknessEnum); _assert_(thickness_input); + Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + + /* Start looping on the number of gaussian points: */ + Gauss* gauss = element->NewGauss(5); + Gauss* gauss_base = basalelement->NewGauss(); + while(gauss->next()){ + gauss->SynchronizeGaussBase(gauss_base); + + element->JacobianDeterminant(&Jdet,xyz_list,gauss_base); + basalelement->NodalFunctionsDerivatives(dbasis,xyz_list,gauss_base); + basalelement->NodalFunctions(basis, gauss_base); + + thickness_input->GetInputValue(&thickness, gauss); + n_input->GetInputValue(&n,gauss); + + vxshear_input->GetInputValue(&vxshear,gauss); + vyshear_input->GetInputValue(&vyshear,gauss); + + element->material->ViscosityMOLHOAdjoint(&viscosity[0],dim,xyz_list,gauss,vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input); + + effmu = 2.0*(1-n)/2.0/n; + + element->StrainRateHO(&epsilonbase[0],xyz_list,gauss,vxbase_input, vybase_input); + element->StrainRateHO(&epsilonshear[0],xyz_list,gauss,vxshear_input, vyshear_input); + + e1b[0] = 2*epsilonbase[0]+epsilonbase[1]; e1b[1] = epsilonbase[2]; + e2b[1] = epsilonbase[0]+2*epsilonbase[1]; e2b[0] = epsilonbase[2]; + + e1sh[0] = 2*epsilonshear[0]+epsilonshear[1]; e1sh[1] = epsilonshear[2]; + e2sh[1] = epsilonshear[0]+2*epsilonshear[1]; e2sh[0] = epsilonshear[2]; + + for(int i=0;ivalues[4*numnodes*(4*i+0)+4*j+0]+=gauss->weight*Jdet*effmu*(viscosity[0]*eb1j*eb1i+viscosity[1]*(esh1j*eb1i+eb1j*esh1i)+viscosity[2]*esh1j*esh1i); + Ke->values[4*numnodes*(4*i+1)+4*j+0]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb1j*eb1i+viscosity[2]*(esh1j*eb1i+eb1j*esh1i)+viscosity[4]*esh1j*esh1i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*eb1j*basis[i]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*esh1j*basis[i]); + Ke->values[4*numnodes*(4*i+2)+4*j+0]+=gauss->weight*Jdet*effmu*(viscosity[0]*eb1j*eb2i+viscosity[1]*(esh1j*eb2i+eb1j*esh2i)+viscosity[2]*esh1j*esh2i); + Ke->values[4*numnodes*(4*i+3)+4*j+0]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb1j*eb2i+viscosity[2]*(esh1j*eb2i+eb1j*esh2i)+viscosity[4]*esh1j*esh2i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*eb1j*basis[i]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*esh1j*basis[i]); + + Ke->values[4*numnodes*(4*i+0)+4*j+1]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb1j*eb1i+viscosity[2]*(esh1j*eb1i+eb1j*esh1i)+viscosity[4]*esh1j*esh1i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*eb1i*basis[j]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*esh1i*basis[j]); + Ke->values[4*numnodes*(4*i+1)+4*j+1]+=gauss->weight*Jdet*effmu*(viscosity[2]*eb1j*eb1i+viscosity[4]*(esh1j*eb1i+eb1j*esh1i)+viscosity[5]*esh1j*esh1i+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*(eb1i*basis[j]+eb1j*basis[i])+viscosity[7]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*(esh1i*basis[j]+esh1j*basis[i])+viscosity[8]*(n+1)*(n+1)*(n+1)*(n+1)/4.0/thickness/thickness/thickness/thickness*vxshear*vxshear*basis[j]*basis[i]); + Ke->values[4*numnodes*(4*i+2)+4*j+1]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb1j*eb2i+viscosity[2]*(esh1j*eb2i+eb1j*esh2i)+viscosity[4]*esh1j*esh2i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*eb2i*basis[j]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*esh2i*basis[j]); + Ke->values[4*numnodes*(4*i+3)+4*j+1]+=gauss->weight*Jdet*effmu*(viscosity[2]*eb1j*eb2i+viscosity[4]*(esh1j*eb2i+eb1j*esh2i)+viscosity[5]*esh1j*esh2i+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*(vxshear*eb2i*basis[j]+vyshear*eb1j*basis[i])+viscosity[7]*(n+1)*(n+1)/2.0/thickness/thickness*(vxshear*esh2i*basis[j]+vyshear*esh1j*basis[i])+viscosity[8]*(n+1)*(n+1)*(n+1)*(n+1)/4.0/thickness/thickness/thickness/thickness*vxshear*vyshear*basis[j]*basis[i]); + + + Ke->values[4*numnodes*(4*i+0)+4*j+2]+=gauss->weight*Jdet*effmu*(viscosity[0]*eb2j*eb1i+viscosity[1]*(esh2j*eb1i+eb2j*esh1i)+viscosity[2]*esh2j*esh1i); + Ke->values[4*numnodes*(4*i+1)+4*j+2]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb2j*eb1i+viscosity[2]*(esh2j*eb1i+eb2j*esh1i)+viscosity[4]*esh2j*esh1i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*eb2j*basis[i]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*esh2j*basis[i]); + Ke->values[4*numnodes*(4*i+2)+4*j+2]+=gauss->weight*Jdet*effmu*(viscosity[0]*eb2j*eb2i+viscosity[1]*(esh2j*eb2i+eb2j*esh2i)+viscosity[2]*esh2j*esh2i); + Ke->values[4*numnodes*(4*i+3)+4*j+2]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb2j*eb2i+viscosity[2]*(esh2j*eb2i+eb2j*esh2i)+viscosity[4]*esh2j*esh2i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*eb2j*basis[i]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*esh2j*basis[i]); + + + Ke->values[4*numnodes*(4*i+0)+4*j+3]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb2j*eb1i+viscosity[2]*(esh2j*eb1i+eb2j*esh1i)+viscosity[4]*esh2j*esh1i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*eb1i*basis[j]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*esh1i*basis[j]); + Ke->values[4*numnodes*(4*i+1)+4*j+3]+=gauss->weight*Jdet*effmu*(viscosity[2]*eb2j*eb1i+viscosity[4]*(esh2j*eb1i+eb2j*esh1i)+viscosity[5]*esh2j*esh1i+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*(vyshear*eb1i*basis[j]+vxshear*eb2j*basis[i])+viscosity[7]*(n+1)*(n+1)/2.0/thickness/thickness*(vxshear*esh2j*basis[i]+vyshear*esh1i*basis[j])+viscosity[8]*(n+1)*(n+1)*(n+1)*(n+1)/4.0/thickness/thickness/thickness/thickness*vxshear*vxshear*basis[j]*basis[i]); + Ke->values[4*numnodes*(4*i+2)+4*j+3]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb2j*eb2i+viscosity[2]*(esh2j*eb2i+eb2j*esh2i)+viscosity[4]*esh2j*esh2i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*eb2i*basis[j]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*esh2i*basis[j]); + Ke->values[4*numnodes*(4*i+3)+4*j+3]+=gauss->weight*Jdet*effmu*(viscosity[2]*eb2j*eb2i+viscosity[4]*(esh2j*eb2i+eb2j*esh2i)+viscosity[5]*esh2j*esh2i+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*(eb2i*basis[j]+eb1j*basis[i])+viscosity[7]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*(esh2i*basis[j]+esh1j*basis[i])+viscosity[8]*(n+1)*(n+1)*(n+1)*(n+1)/4.0/thickness/thickness/thickness/thickness*vyshear*vyshear*basis[j]*basis[i]); + } + } + } + + /*Transform Coordinate System*/ + /*element->TransformStiffnessMatrixCoord(Ke,XYEnum);*/ + + /*Clean up and return*/ + delete gauss; + delete gauss_base; + if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; + xDelete(xyz_list); + xDelete(dbasis); + xDelete(basis); + return Ke; +}/*}}}*/ +ElementMatrix* AdjointHorizAnalysis::CreateKMatrixMOLHOVerticalIntergrated(Element* element){/*{{{*/ + + /* Check if ice in element */ + if(!element->IsIceInElement()) return NULL; + + /*Intermediaries */ + IssmDouble Jdet,mu_prime,n,thickness,mu,effmu; + IssmDouble *xyz_list = NULL; + IssmDouble zeta, epsilon_eff; + int domaintype; + int dim=2; + + IssmDouble e1phi1i, e1phi1j, e2phi1i, e2phi1j, e1phi2i, e1phi2j, e2phi2i, e2phi2j; + IssmDouble epsilon[5];/* epsilon=[exx,eyy,exy,exz,eyz];*/ + IssmDouble e1[3],e2[3]; + + Element* basalelement = NULL; /*Get basal element*/ @@ -251,10 +382,7 @@ default: _error_("mesh "<GetNumberOfNodes(); - IssmDouble* dbasis = xNew(2*numnodes); // like SSA - IssmDouble* basis = xNew(numnodes); // like SSA /*Initialize Jacobian with regular HO (first part of the Gateau derivative)*/ + bool incomplete_adjoint; element->FindParam(&incomplete_adjoint,InversionIncompleteAdjointEnum); StressbalanceAnalysis* analysis = new StressbalanceAnalysis(); @@ -263,133 +391,11 @@ if(incomplete_adjoint) return Ke; - /*Retrieve all inputs and parameters*/ - element->GetVerticesCoordinates(&xyz_list); - Input* vx_input = element->GetInput(VxEnum); _assert_(vx_input); //vertically integrated vx - Input* vy_input = element->GetInput(VyEnum); _assert_(vy_input); //vertically integrated vy - Input* vxbase_input = element->GetInput(VxBaseEnum); _assert_(vxbase_input); - Input* vybase_input = element->GetInput(VyBaseEnum); _assert_(vybase_input); - Input* vxshear_input = element->GetInput(VxShearEnum); _assert_(vxshear_input); - Input* vyshear_input = element->GetInput(VyShearEnum); _assert_(vyshear_input); - Input* thickness_input= element->GetInput(ThicknessEnum); _assert_(thickness_input); - Input* n_input = element->GetInput(MaterialsRheologyNEnum); _assert_(n_input); - - /* Start looping on the number of gaussian points: */ - Gauss* gauss = element->NewGauss(5); - Gauss* gauss_base = basalelement->NewGauss(); - while(gauss->next()){ - gauss->SynchronizeGaussBase(gauss_base); - - element->JacobianDeterminant(&Jdet,xyz_list,gauss_base); - basalelement->NodalFunctionsDerivatives(dbasis,xyz_list,gauss_base); - basalelement->NodalFunctions(basis, gauss_base); - - thickness_input->GetInputValue(&thickness, gauss); - n_input->GetInputValue(&n,gauss); - - vxshear_input->GetInputValue(&vxshear,gauss); - vyshear_input->GetInputValue(&vyshear,gauss); - - element->material->ViscosityMLHOAdjoint(&viscosity[0],dim,xyz_list,gauss,vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input); - - effmu = 2.0*(1-n)/2.0/n; - - element->StrainRateHO(&epsilonbase[0],xyz_list,gauss,vxbase_input, vybase_input); - element->StrainRateHO(&epsilonshear[0],xyz_list,gauss,vxshear_input, vyshear_input); - - e1b[0] = 2*epsilonbase[0]+epsilonbase[1]; e1b[1] = epsilonbase[2]; - e2b[1] = epsilonbase[0]+2*epsilonbase[1]; e2b[0] = epsilonbase[2]; - - e1sh[0] = 2*epsilonshear[0]+epsilonshear[1]; e1sh[1] = epsilonshear[2]; - e2sh[1] = epsilonshear[0]+2*epsilonshear[1]; e2sh[0] = epsilonshear[2]; - - for(int i=0;ivalues[4*numnodes*(4*i+0)+4*j+0]+=gauss->weight*Jdet*effmu*(viscosity[0]*eb1j*eb1i+viscosity[1]*(esh1j*eb1i+eb1j*esh1i)+viscosity[2]*esh1j*esh1i); - Ke->values[4*numnodes*(4*i+1)+4*j+0]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb1j*eb1i+viscosity[2]*(esh1j*eb1i+eb1j*esh1i)+viscosity[4]*esh1j*esh1i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*eb1j*basis[i]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*esh1j*basis[i]); - Ke->values[4*numnodes*(4*i+2)+4*j+0]+=gauss->weight*Jdet*effmu*(viscosity[0]*eb1j*eb2i+viscosity[1]*(esh1j*eb2i+eb1j*esh2i)+viscosity[2]*esh1j*esh2i); - Ke->values[4*numnodes*(4*i+3)+4*j+0]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb1j*eb2i+viscosity[2]*(esh1j*eb2i+eb1j*esh2i)+viscosity[4]*esh1j*esh2i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*eb1j*basis[i]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*esh1j*basis[i]); - - Ke->values[4*numnodes*(4*i+0)+4*j+1]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb1j*eb1i+viscosity[2]*(esh1j*eb1i+eb1j*esh1i)+viscosity[4]*esh1j*esh1i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*eb1i*basis[j]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*esh1i*basis[j]); - Ke->values[4*numnodes*(4*i+1)+4*j+1]+=gauss->weight*Jdet*effmu*(viscosity[2]*eb1j*eb1i+viscosity[4]*(esh1j*eb1i+eb1j*esh1i)+viscosity[5]*esh1j*esh1i+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*(eb1i*basis[j]+eb1j*basis[i])+viscosity[7]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*(esh1i*basis[j]+esh1j*basis[i])+viscosity[8]*(n+1)*(n+1)*(n+1)*(n+1)/4.0/thickness/thickness/thickness/thickness*vxshear*vxshear*basis[j]*basis[i]); - Ke->values[4*numnodes*(4*i+2)+4*j+1]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb1j*eb2i+viscosity[2]*(esh1j*eb2i+eb1j*esh2i)+viscosity[4]*esh1j*esh2i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*eb2i*basis[j]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*esh2i*basis[j]); - Ke->values[4*numnodes*(4*i+3)+4*j+1]+=gauss->weight*Jdet*effmu*(viscosity[2]*eb1j*eb2i+viscosity[4]*(esh1j*eb2i+eb1j*esh2i)+viscosity[5]*esh1j*esh2i+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*(vxshear*eb2i*basis[j]+vyshear*eb1j*basis[i])+viscosity[7]*(n+1)*(n+1)/2.0/thickness/thickness*(vxshear*esh2i*basis[j]+vyshear*esh1j*basis[i])+viscosity[8]*(n+1)*(n+1)*(n+1)*(n+1)/4.0/thickness/thickness/thickness/thickness*vxshear*vyshear*basis[j]*basis[i]); - - - Ke->values[4*numnodes*(4*i+0)+4*j+2]+=gauss->weight*Jdet*effmu*(viscosity[0]*eb2j*eb1i+viscosity[1]*(esh2j*eb1i+eb2j*esh1i)+viscosity[2]*esh2j*esh1i); - Ke->values[4*numnodes*(4*i+1)+4*j+2]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb2j*eb1i+viscosity[2]*(esh2j*eb1i+eb2j*esh1i)+viscosity[4]*esh2j*esh1i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*eb2j*basis[i]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vxshear*esh2j*basis[i]); - Ke->values[4*numnodes*(4*i+2)+4*j+2]+=gauss->weight*Jdet*effmu*(viscosity[0]*eb2j*eb2i+viscosity[1]*(esh2j*eb2i+eb2j*esh2i)+viscosity[2]*esh2j*esh2i); - Ke->values[4*numnodes*(4*i+3)+4*j+2]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb2j*eb2i+viscosity[2]*(esh2j*eb2i+eb2j*esh2i)+viscosity[4]*esh2j*esh2i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*eb2j*basis[i]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*esh2j*basis[i]); - - - Ke->values[4*numnodes*(4*i+0)+4*j+3]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb2j*eb1i+viscosity[2]*(esh2j*eb1i+eb2j*esh1i)+viscosity[4]*esh2j*esh1i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*eb1i*basis[j]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*esh1i*basis[j]); - Ke->values[4*numnodes*(4*i+1)+4*j+3]+=gauss->weight*Jdet*effmu*(viscosity[2]*eb2j*eb1i+viscosity[4]*(esh2j*eb1i+eb2j*esh1i)+viscosity[5]*esh2j*esh1i+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*(vyshear*eb1i*basis[j]+vxshear*eb2j*basis[i])+viscosity[7]*(n+1)*(n+1)/2.0/thickness/thickness*(vxshear*esh2j*basis[i]+vyshear*esh1i*basis[j])+viscosity[8]*(n+1)*(n+1)*(n+1)*(n+1)/4.0/thickness/thickness/thickness/thickness*vxshear*vxshear*basis[j]*basis[i]); - Ke->values[4*numnodes*(4*i+2)+4*j+3]+=gauss->weight*Jdet*effmu*(viscosity[1]*eb2j*eb2i+viscosity[2]*(esh2j*eb2i+eb2j*esh2i)+viscosity[4]*esh2j*esh2i+viscosity[3]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*eb2i*basis[j]+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*esh2i*basis[j]); - Ke->values[4*numnodes*(4*i+3)+4*j+3]+=gauss->weight*Jdet*effmu*(viscosity[2]*eb2j*eb2i+viscosity[4]*(esh2j*eb2i+eb2j*esh2i)+viscosity[5]*esh2j*esh2i+viscosity[6]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*(eb2i*basis[j]+eb1j*basis[i])+viscosity[7]*(n+1)*(n+1)/2.0/thickness/thickness*vyshear*(esh2i*basis[j]+esh1j*basis[i])+viscosity[8]*(n+1)*(n+1)*(n+1)*(n+1)/4.0/thickness/thickness/thickness/thickness*vyshear*vyshear*basis[j]*basis[i]); - } - } - } - - /*Transform Coordinate System*/ - /*element->TransformStiffnessMatrixCoord(Ke,XYEnum);*/ - - /*Clean up and return*/ - delete gauss; - delete gauss_base; - if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; - xDelete(xyz_list); - xDelete(dbasis); - xDelete(basis); - return Ke; -}/*}}}*/ -ElementMatrix* AdjointHorizAnalysis::CreateKMatrixMLHOVerticalIntergrated(Element* element){/*{{{*/ - - /* Check if ice in element */ - if(!element->IsIceInElement()) return NULL; - - /*Intermediaries */ - bool incomplete_adjoint; - IssmDouble Jdet,mu_prime,n,thickness,mu,effmu; - IssmDouble *xyz_list = NULL; - IssmDouble zeta, epsilon_eff; - int domaintype; - int dim=2; - - IssmDouble e1phi1i, e1phi1j, e2phi1i, e2phi1j, e1phi2i, e1phi2j, e2phi2i, e2phi2j; - IssmDouble epsilon[5];/* epsilon=[exx,eyy,exy,exz,eyz];*/ - IssmDouble e1[3],e2[3]; - - Element* basalelement; - - /*Get basal element*/ - element->FindParam(&domaintype,DomainTypeEnum); - switch(domaintype){ - case Domain2DhorizontalEnum: - basalelement = element; - break; - case Domain3DEnum: case Domain2DverticalEnum: - _error_("mesh "<GetNumberOfNodes(); IssmDouble* dbasis = xNew(2*numnodes); // like SSA IssmDouble* basis = xNew(numnodes); // like SSA - - /*Initialize Jacobian with regular HO (first part of the Gateau derivative)*/ - element->FindParam(&incomplete_adjoint,InversionIncompleteAdjointEnum); - StressbalanceAnalysis* analysis = new StressbalanceAnalysis(); - ElementMatrix* Ke=analysis->CreateKMatrix(basalelement); - delete analysis; - if(incomplete_adjoint) return Ke; /*Retrieve all inputs and parameters*/ @@ -427,5 +433,5 @@ /* eps_eff^2 = exx^2 + eyy^2 + exy^2 + exz^2 + eyz^2 + exx*eyy (for a given zeta)*/ - element->StrainRateMLHO(&epsilon[0],xyz_list,gauss, + element->StrainRateMOLHO(&epsilon[0],xyz_list,gauss, vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input,zeta); epsilon_eff=sqrt(epsilon[0]*epsilon[0] + epsilon[1]*epsilon[1] + epsilon[2]*epsilon[2] @@ -612,6 +618,6 @@ case FSApproximationEnum: return CreatePVectorFS(element); - case MLHOApproximationEnum: - return CreatePVectorMLHO(element); + case MOLHOApproximationEnum: + return CreatePVectorMOLHO(element); case NoneApproximationEnum: return NULL; @@ -1099,5 +1105,5 @@ }/*}}}*/ -ElementVector* AdjointHorizAnalysis::CreatePVectorMLHO(Element* element){/*{{{*/ +ElementVector* AdjointHorizAnalysis::CreatePVectorMOLHO(Element* element){/*{{{*/ /*Intermediaries*/ @@ -1137,5 +1143,5 @@ /*Initialize Element vector and vectors*/ - ElementVector* pe = basalelement->NewElementVector(MLHOApproximationEnum); + ElementVector* pe = basalelement->NewElementVector(MOLHOApproximationEnum); IssmDouble* basis = xNew(numnodes); @@ -1206,5 +1212,5 @@ } else { - _error_("2D vertical is not implemented for MLHO"); + _error_("2D vertical is not implemented for MOLHO"); } } @@ -1234,5 +1240,5 @@ } else{ - _error_("2D vertical is not implemented for MLHO"); + _error_("2D vertical is not implemented for MOLHO"); } } @@ -1263,5 +1269,5 @@ } else{ - _error_("2D vertical is not implemented for MLHO"); + _error_("2D vertical is not implemented for MOLHO"); } } @@ -1289,5 +1295,5 @@ } else{ - _error_("2D vertical is not implemented for MLHO"); + _error_("2D vertical is not implemented for MOLHO"); } } @@ -1313,5 +1319,5 @@ } else{ - _error_("2D vertical is not implemented for MLHO"); + _error_("2D vertical is not implemented for MOLHO"); } } @@ -1663,5 +1669,5 @@ case L1L2ApproximationEnum:GradientJDragL1L2(element,gradient,control_interp,control_index); break; case HOApproximationEnum: GradientJDragHO( element,gradient,control_interp,control_index); break; - case MLHOApproximationEnum: GradientJDragMLHO( element,gradient,control_interp,control_index); break; + case MOLHOApproximationEnum: GradientJDragMOLHO( element,gradient,control_interp,control_index); break; case FSApproximationEnum: GradientJDragFS( element,gradient,control_interp,control_index); break; case NoneApproximationEnum: /*Gradient is 0*/ break; @@ -1684,5 +1690,5 @@ case L1L2ApproximationEnum:GradientJBbarL1L2(element,gradient,control_interp,control_index); break; case HOApproximationEnum: GradientJBbarHO( element,gradient,control_interp,control_index); break; - case MLHOApproximationEnum: GradientJBbarMLHO( element,gradient,control_interp,control_index); break; + case MOLHOApproximationEnum: GradientJBbarMOLHO( element,gradient,control_interp,control_index); break; case FSApproximationEnum: GradientJBbarFS( element,gradient,control_interp,control_index); break; case NoneApproximationEnum: /*Gradient is 0*/ break; @@ -1694,5 +1700,5 @@ case SSAApproximationEnum: GradientJBSSA(element,gradient,control_interp,control_index); break; case HOApproximationEnum: GradientJBHO( element,gradient,control_interp,control_index); break; - // case MLHOApproximationEnum: GradientJBMLHO( element,gradient,control_interp,control_index); break; + // case MOLHOApproximationEnum: GradientJBMOLHO( element,gradient,control_interp,control_index); break; case FSApproximationEnum: GradientJBFS( element,gradient,control_interp,control_index); break; case NoneApproximationEnum: /*Gradient is 0*/ break; @@ -1804,5 +1810,5 @@ this->GradientJBbarSSA(element,gradient,control_interp,control_index); }/*}}}*/ -void AdjointHorizAnalysis::GradientJBbarMLHO(Element* element,Vector* gradient,int control_interp,int control_index){/*{{{*/ +void AdjointHorizAnalysis::GradientJBbarMOLHO(Element* element,Vector* gradient,int control_interp,int control_index){/*{{{*/ if(control_interp!=P1Enum) _error_("not implemented yet..."); @@ -1887,8 +1893,8 @@ zeta=0.5*(gauss_seg->coord1+1); - basalelement->StrainRateMLHO(&epsilon[0],xyz_list,gauss, + basalelement->StrainRateMOLHO(&epsilon[0],xyz_list,gauss, vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input,zeta); - basalelement->dViscositydBMLHO(&dmudB,dim,xyz_list,gauss,vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input,zeta); + basalelement->dViscositydBMOLHO(&dmudB,dim,xyz_list,gauss,vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input,zeta); e1[0] = 2.0*epsilon[0]+epsilon[1]; @@ -2245,5 +2251,5 @@ delete gauss; }/*}}}*/ -void AdjointHorizAnalysis::GradientJBMLHO(Element* element,Vector* gradient,int control_interp,int control_index){/*{{{*/ +void AdjointHorizAnalysis::GradientJBMOLHO(Element* element,Vector* gradient,int control_interp,int control_index){/*{{{*/ _error_("not implemented yet..."); }/*}}}*/ @@ -2645,5 +2651,5 @@ delete friction; }/*}}}*/ -void AdjointHorizAnalysis::GradientJDragMLHO(Element* element,Vector* gradient,int control_interp,int control_index){/*{{{*/ +void AdjointHorizAnalysis::GradientJDragMOLHO(Element* element,Vector* gradient,int control_interp,int control_index){/*{{{*/ /*return if floating (gradient is 0)*/ @@ -3266,6 +3272,6 @@ InputUpdateFromSolutionFS(solution,element); } - else if (approximation==MLHOApproximationEnum) { - InputUpdateFromSolutionMLHO(solution, element); + else if (approximation==MOLHOApproximationEnum) { + InputUpdateFromSolutionMOLHO(solution, element); } else{ @@ -3414,5 +3420,5 @@ xDelete(doflist); }/*}}}*/ -void AdjointHorizAnalysis::InputUpdateFromSolutionMLHO(IssmDouble* solution,Element* element){/*{{{*/ +void AdjointHorizAnalysis::InputUpdateFromSolutionMOLHO(IssmDouble* solution,Element* element){/*{{{*/ int i; int* doflist=NULL; @@ -3427,13 +3433,13 @@ /*Fetch dof list and allocate solution vectors*/ - element->GetDofListLocal(&doflist,MLHOApproximationEnum,GsetEnum); - IssmDouble* values = xNew(numdof); - IssmDouble* lambdax = xNew(numnodes); - IssmDouble* lambday = xNew(numnodes); - IssmDouble* lambdabx = xNew(numnodes); - IssmDouble* lambdaby = xNew(numnodes); + element->GetDofListLocal(&doflist,MOLHOApproximationEnum,GsetEnum); + IssmDouble* values = xNew(numdof); + IssmDouble* lambdax = xNew(numnodes); + IssmDouble* lambday = xNew(numnodes); + IssmDouble* lambdabx = xNew(numnodes); + IssmDouble* lambdaby = xNew(numnodes); IssmDouble* lambdashx = xNew(numnodes); IssmDouble* lambdashy = xNew(numnodes); - IssmDouble* n = xNew(numnodes); + IssmDouble* n = xNew(numnodes); /*Use the dof list to index into the solution vector: */ @@ -3485,4 +3491,5 @@ xDelete(lambdashx); xDelete(lambdashy); + xDelete(n); xDelete(doflist); }/*}}}*/ Index: /issm/trunk/src/c/analyses/AdjointHorizAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/AdjointHorizAnalysis.h (revision 27034) +++ /issm/trunk/src/c/analyses/AdjointHorizAnalysis.h (revision 27035) @@ -28,6 +28,6 @@ ElementMatrix* CreateKMatrixFS(Element* element); ElementMatrix* CreateKMatrixHO(Element* element); - ElementMatrix* CreateKMatrixMLHO(Element* element); - ElementMatrix* CreateKMatrixMLHOVerticalIntergrated(Element* element); + ElementMatrix* CreateKMatrixMOLHO(Element* element); + ElementMatrix* CreateKMatrixMOLHOVerticalIntergrated(Element* element); ElementMatrix* CreateKMatrixL1L2(Element* element); ElementMatrix* CreateKMatrixSSA(Element* element); @@ -36,5 +36,5 @@ ElementVector* CreatePVectorL1L2(Element* element); ElementVector* CreatePVectorHO(Element* element); - ElementVector* CreatePVectorMLHO(Element* element); + ElementVector* CreatePVectorMOLHO(Element* element); ElementVector* CreatePVectorSSA(Element* element); void GetSolutionFromInputs(Vector* solution,Element* element); @@ -45,10 +45,10 @@ void GradientJBbarL1L2(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJBbarHO(Element* element,Vector* gradient,int control_interp,int control_index); - void GradientJBbarMLHO(Element* element,Vector* gradient,int control_interp,int control_index); + void GradientJBbarMOLHO(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJBbarSSA(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJBFS(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJBGradient(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJBHO(Element* element,Vector* gradient,int control_interp,int control_index); - void GradientJBMLHO(Element* element,Vector* gradient,int control_interp,int control_index); + void GradientJBMOLHO(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJBSSA(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJDragFS(Element* element,Vector* gradient,int control_interp,int control_index); @@ -56,5 +56,5 @@ void GradientJDragL1L2(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJDragHO(Element* element,Vector* gradient,int control_interp,int control_index); - void GradientJDragMLHO(Element* element,Vector* gradient,int control_interp,int control_index); + void GradientJDragMOLHO(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJDragSSA(Element* element,Vector* gradient,int control_interp,int control_index); void GradientJDragHydroFS(Element* element,Vector* gradient,int control_interp,int control_index); @@ -66,5 +66,5 @@ void InputUpdateFromSolutionFS(IssmDouble* solution,Element* element); void InputUpdateFromSolutionHoriz(IssmDouble* solution,Element* element); - void InputUpdateFromSolutionMLHO(IssmDouble* solution,Element* element); + void InputUpdateFromSolutionMOLHO(IssmDouble* solution,Element* element); void UpdateConstraints(FemModel* femmodel); }; Index: /issm/trunk/src/c/analyses/BalancethicknessAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/BalancethicknessAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/BalancethicknessAnalysis.cpp (revision 27035) @@ -552,5 +552,4 @@ }/*}}}*/ void BalancethicknessAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ - /*Default, do nothing*/ - return; -}/*}}}*/ + SetActiveNodesLSMx(femmodel); +}/*}}}*/ Index: /issm/trunk/src/c/analyses/FreeSurfaceBaseAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/FreeSurfaceBaseAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/FreeSurfaceBaseAnalysis.cpp (revision 27035) @@ -73,5 +73,5 @@ } - iomodel->FetchDataToInput(inputs,elements,"md.geometry.surface",SurfaceEnum); + iomodel->FetchDataToInput(inputs,elements,"md.geometry.base",BaseEnum); iomodel->FetchDataToInput(inputs,elements,"md.initialization.sealevel",SealevelEnum,0); iomodel->FetchDataToInput(inputs,elements,"md.mask.ice_levelset",MaskIceLevelsetEnum); @@ -96,7 +96,7 @@ iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); if(isstochastic){ - iomodel->FetchDataToInput(inputs,elements,"md.stochasticforcing.default_id",StochasticForcingDefaultIdEnum); - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.floatingice_melting_rate",BaselineBasalforcingsFloatingiceMeltingRateEnum); - } + iomodel->FetchDataToInput(inputs,elements,"md.stochasticforcing.default_id",StochasticForcingDefaultIdEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.floatingice_melting_rate",BaselineBasalforcingsFloatingiceMeltingRateEnum); + } break; case LinearFloatingMeltRateEnum: @@ -108,7 +108,12 @@ break; case SpatialLinearFloatingMeltRateEnum: - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsSpatialDeepwaterMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_elevation",BasalforcingsSpatialDeepwaterElevationEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_melting_rate",BasalforcingsSpatialUpperwaterMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_elevation",BasalforcingsSpatialUpperwaterElevationEnum); + if(isstochastic){ + iomodel->FetchDataToInput(inputs,elements,"md.stochasticforcing.default_id",StochasticForcingDefaultIdEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum); + } break; case BasalforcingsPicoEnum: @@ -143,5 +148,5 @@ }/*}}}*/ ElementMatrix* FreeSurfaceBaseAnalysis::CreateJacobianMatrix(Element* element){/*{{{*/ -_error_("Not implemented"); + _error_("Not implemented"); }/*}}}*/ ElementMatrix* FreeSurfaceBaseAnalysis::CreateKMatrix(Element* element){/*{{{*/ @@ -152,5 +157,5 @@ IssmDouble *xyz_list = NULL; IssmDouble Jdet,D_scalar,dt,h; - IssmDouble vel,vx,vy; + IssmDouble vel,vx,vy,tau; /*Get basal element*/ @@ -225,19 +230,5 @@ } - if(stabilization==2){ - /*Streamline upwinding*/ - if(dim==1){ - vel=fabs(vx)+1.e-8; - D[0] = h/(2.*vel)*vx*vx; - } - else{ - vel=sqrt(vx*vx+vy*vy)+1.e-8; - D[0*dim+0]=h/(2*vel)*vx*vx; - D[1*dim+0]=h/(2*vel)*vy*vx; - D[0*dim+1]=h/(2*vel)*vx*vy; - D[1*dim+1]=h/(2*vel)*vy*vy; - } - } - else if(stabilization==1){ + if(stabilization==1){ /*SSA*/ if(dim==1){ @@ -250,4 +241,31 @@ D[0*dim+0]=h/2.0*fabs(vx); D[1*dim+1]=h/2.0*fabs(vy); + } + } + else if(stabilization==2){ + /*Streamline upwinding*/ + if(dim==1){ + vel=fabs(vx)+1.e-8; + D[0] = h/(2.*vel)*vx*vx; + } + else{ + vel=sqrt(vx*vx+vy*vy)+1.e-8; + D[0*dim+0]=h/(2*vel)*vx*vx; + D[1*dim+0]=h/(2*vel)*vy*vx; + D[0*dim+1]=h/(2*vel)*vx*vy; + D[1*dim+1]=h/(2*vel)*vy*vy; + } + + } + else if(stabilization==5){ + /*SUPG*/ + if(dim==1){ + vx_input->GetInputAverage(&vx); + tau=h/(2.*fabs(vx)+1e-10); + } + else{ + vx_input->GetInputAverage(&vx); + vy_input->GetInputAverage(&vy); + tau=1*h/(2.*pow(vx*vx+vy*vy,0.5)+1e-10); } } @@ -258,7 +276,7 @@ for(int j=0;jvalues[i*numnodes+j] += ( - dbasis[0*numnodes+i] *(D[0*dim+0]*dbasis[0*numnodes+j] + D[0*dim+1]*dbasis[1*numnodes+j]) + - dbasis[1*numnodes+i] *(D[1*dim+0]*dbasis[0*numnodes+j] + D[1*dim+1]*dbasis[1*numnodes+j]) - ); + dbasis[0*numnodes+i] *(D[0*dim+0]*dbasis[0*numnodes+j] + D[0*dim+1]*dbasis[1*numnodes+j]) + + dbasis[1*numnodes+i] *(D[1*dim+0]*dbasis[0*numnodes+j] + D[1*dim+1]*dbasis[1*numnodes+j]) + ); } } @@ -266,4 +284,19 @@ else{ for(int i=0;ivalues[i*numnodes+j] += dbasis[0*numnodes+i]*D[0]*dbasis[0*numnodes+j]; + } + } + else if(stabilization==5){ + D_scalar=gauss->weight*Jdet*dt; + if(dim==2){ + for(int i=0;ivalues[i*numnodes+j]+=tau*D_scalar* + (vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i])* + (vx*dbasis[0*numnodes+j]+vy*dbasis[1*numnodes+j]); + } + } + } + else{ + for(int i=0;ivalues[i*numnodes+j]+=tau*D_scalar*(vx*dbasis[0*numnodes+i])*(vx*dbasis[0*numnodes+j]); } } @@ -280,8 +313,9 @@ }/*}}}*/ ElementVector* FreeSurfaceBaseAnalysis::CreatePVector(Element* element){/*{{{*/ + /*Intermediaries*/ - int domaintype,dim; + int domaintype,dim,stabilization; IssmDouble Jdet,dt; - IssmDouble gmb,fmb,mb,bed,phi,vz; + IssmDouble gmb,fmb,mb,bed,vx,vy,vz,tau; Element* basalelement = NULL; IssmDouble *xyz_list = NULL; @@ -309,25 +343,52 @@ /*Fetch number of nodes and dof for this finite element*/ int numnodes = basalelement->GetNumberOfNodes(); + int melt_style,point1; + IssmDouble fraction1,fraction2; + bool mainlyfloating; /*Initialize Element vector and other vectors*/ ElementVector* pe = basalelement->NewElementVector(); IssmDouble* basis = xNew(numnodes); + IssmDouble* dbasis = xNew(dim*numnodes); + IssmDouble gllevelset,phi=1.; /*Retrieve all inputs and parameters*/ - basalelement->GetVerticesCoordinates(&xyz_list); basalelement->FindParam(&dt,TimesteppingTimeStepEnum); + basalelement->FindParam(&melt_style,GroundinglineMeltInterpolationEnum); Input* groundedice_input = basalelement->GetInput(MaskOceanLevelsetEnum); _assert_(groundedice_input); Input* gmb_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(gmb_input); Input* fmb_input = basalelement->GetInput(BasalforcingsFloatingiceMeltingRateEnum); _assert_(fmb_input); Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); - Input* vz_input = NULL; + Input* gllevelset_input = basalelement->GetInput(MaskOceanLevelsetEnum); _assert_(gllevelset_input); + Input* vz_input = NULL; + Input* vx_input = NULL; + Input* vy_input = NULL; switch(dim){ - case 1: vz_input = basalelement->GetInput(VyEnum); _assert_(vz_input); break; - case 2: vz_input = basalelement->GetInput(VzEnum); _assert_(vz_input); break; + case 1: + vx_input=basalelement->GetInput(VxEnum); _assert_(vx_input); + vz_input=basalelement->GetInput(VyEnum) ; _assert_(vz_input); + break; + case 2: + vx_input=basalelement->GetInput(VxEnum); _assert_(vx_input); + vy_input=basalelement->GetInput(VyEnum); _assert_(vy_input); + vz_input=basalelement->GetInput(VzEnum); _assert_(vz_input); + break; default: _error_("not implemented"); } + IssmDouble h = basalelement->CharacteristicLength(); + + /*Recover portion of element that is grounded*/ + basalelement->GetVerticesCoordinates(&xyz_list); + phi=basalelement->GetGroundedPortion(xyz_list); + Gauss* gauss = NULL; + if(melt_style==SubelementMelt2Enum){ + basalelement->GetGroundedPart(&point1,&fraction1,&fraction2,&mainlyfloating); + gauss = basalelement->NewGauss(point1,fraction1,fraction2,3); + } + else{ + gauss = basalelement->NewGauss(3); + } /* Start looping on the number of gaussian points: */ - Gauss* gauss=basalelement->NewGauss(2); while(gauss->next()){ @@ -335,13 +396,48 @@ basalelement->NodalFunctions(basis,gauss); - vz_input->GetInputValue(&vz,gauss); + + vz_input->GetInputValue(&vz,gauss); gmb_input->GetInputValue(&gmb,gauss); fmb_input->GetInputValue(&fmb,gauss); base_input->GetInputValue(&bed,gauss); groundedice_input->GetInputValue(&phi,gauss); - if(phi>0) mb=gmb; - else mb=fmb; + gllevelset_input->GetInputValue(&gllevelset,gauss); + if(melt_style==SubelementMelt1Enum){ + //if (phi>0.999999999) mb=gmb; + //else mb=(1-phi)*fmb+phi*gmb; // phi is the fraction of grounded ice so (1-phi) is floating + if(phi>0) mb=gmb; + else mb=fmb; + } + else if(melt_style==SubelementMelt2Enum){ + if(gllevelset>0.) mb=gmb; + else mb=fmb; + } + else if(melt_style==NoMeltOnPartiallyFloatingEnum){ + if (phi<0.00000001) mb=fmb; + else mb=gmb; + } + else if(melt_style==FullMeltOnPartiallyFloatingEnum){ + if (phi<0.99999999) mb=fmb; + else mb=gmb; + } + else _error_("melt interpolation "<values[i]+=Jdet*gauss->weight*(bed+dt*(mb) + dt*vz)*basis[i]; + + if(stabilization==5){ + /*SUPG*/ + basalelement->NodalFunctionsDerivatives(dbasis,xyz_list,gauss); + if(dim==1){ + vx_input->GetInputAverage(&vx); + tau=h/(2.*fabs(vx)+1e-10); + for(int i=0;ivalues[i]+=Jdet*gauss->weight*(dt*mb+dt*vz)*tau*(vx*dbasis[0*numnodes+i]); + } + else{ + vx_input->GetInputAverage(&vx); + vy_input->GetInputAverage(&vy); + tau=1*h/(2.*pow(vx*vx+vy*vy,0.5)+1e-10); + for(int i=0;ivalues[i]+=Jdet*gauss->weight*(bed*0.+dt*mb+dt*vz)*tau*(vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i]); + } + } } @@ -349,4 +445,5 @@ xDelete(xyz_list); xDelete(basis); + xDelete(dbasis); delete gauss; if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; @@ -355,5 +452,5 @@ }/*}}}*/ void FreeSurfaceBaseAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/ - _error_("not implemented yet"); + _error_("not implemented yet"); }/*}}}*/ void FreeSurfaceBaseAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_interp,int control_index){/*{{{*/ Index: /issm/trunk/src/c/analyses/FreeSurfaceTopAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/FreeSurfaceTopAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/FreeSurfaceTopAnalysis.cpp (revision 27035) @@ -80,4 +80,5 @@ iomodel->FetchDataToInput(inputs,elements,"md.mask.ice_levelset",MaskIceLevelsetEnum); iomodel->FetchDataToInput(inputs,elements,"md.initialization.vx",VxEnum); + iomodel->FetchDataToInput(inputs,elements,"md.initialization.vy",VyEnum); if(iomodel->domaintype!=Domain2DhorizontalEnum){ iomodel->FetchDataToInput(inputs,elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); @@ -111,5 +112,5 @@ }/*}}}*/ ElementMatrix* FreeSurfaceTopAnalysis::CreateJacobianMatrix(Element* element){/*{{{*/ -_error_("Not implemented"); + _error_("Not implemented"); }/*}}}*/ ElementMatrix* FreeSurfaceTopAnalysis::CreateKMatrix(Element* element){/*{{{*/ @@ -120,5 +121,5 @@ IssmDouble *xyz_list = NULL; IssmDouble Jdet,D_scalar,dt,h; - IssmDouble vel,vx,vy; + IssmDouble vel,vx,vy,tau; /*Get top element*/ @@ -195,5 +196,19 @@ } - if(stabilization==2){ + if(stabilization==1){ + /*artifical diffusion*/ + if(dim==1){ + vx_input->GetInputAverage(&vx); + D[0]=h/2.*fabs(vx); + } + else{ + vx_input->GetInputAverage(&vx); + vy_input->GetInputAverage(&vy); + + D[0*dim+0]=h/2.0*fabs(vx); + D[1*dim+1]=h/2.0*fabs(vy); + } + } + else if(stabilization==2){ /*Streamline upwinding*/ if(dim==1){ @@ -209,16 +224,14 @@ } } - else if(stabilization==1){ - /*SSA*/ + else if(stabilization==5){ + /*SUPG*/ if(dim==1){ vx_input->GetInputAverage(&vx); - D[0]=h/2.*fabs(vx); + tau=h/(2.*fabs(vx)+1e-10); } else{ vx_input->GetInputAverage(&vx); vy_input->GetInputAverage(&vy); - - D[0*dim+0]=h/2.0*fabs(vx); - D[1*dim+1]=h/2.0*fabs(vy); + tau=1*h/(2.*pow(vx*vx+vy*vy,0.5)+1e-10); } } @@ -229,7 +242,7 @@ for(int j=0;jvalues[i*numnodes+j] += ( - dbasis[0*numnodes+i] *(D[0*dim+0]*dbasis[0*numnodes+j] + D[0*dim+1]*dbasis[1*numnodes+j]) + - dbasis[1*numnodes+i] *(D[1*dim+0]*dbasis[0*numnodes+j] + D[1*dim+1]*dbasis[1*numnodes+j]) - ); + dbasis[0*numnodes+i] *(D[0*dim+0]*dbasis[0*numnodes+j] + D[0*dim+1]*dbasis[1*numnodes+j]) + + dbasis[1*numnodes+i] *(D[1*dim+0]*dbasis[0*numnodes+j] + D[1*dim+1]*dbasis[1*numnodes+j]) + ); } } @@ -237,4 +250,19 @@ else{ for(int i=0;ivalues[i*numnodes+j] += dbasis[0*numnodes+i]*D[0]*dbasis[0*numnodes+j]; + } + } + else if(stabilization==5){ + D_scalar=gauss->weight*Jdet*dt; + if(dim==2){ + for(int i=0;ivalues[i*numnodes+j]+=tau*D_scalar* + (vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i])* + (vx*dbasis[0*numnodes+j]+vy*dbasis[1*numnodes+j]); + } + } + } + else{ + for(int i=0;ivalues[i*numnodes+j]+=tau*D_scalar*(vx*dbasis[0*numnodes+i])*(vx*dbasis[0*numnodes+j]); } } @@ -251,8 +279,9 @@ }/*}}}*/ ElementVector* FreeSurfaceTopAnalysis::CreatePVector(Element* element){/*{{{*/ + /*Intermediaries*/ - int domaintype,dim; + int domaintype,dim,stabilization; IssmDouble Jdet,dt; - IssmDouble ms,surface,vz; + IssmDouble ms,surface,vx,vy,vz,tau; Element* topelement = NULL; IssmDouble *xyz_list = NULL; @@ -284,16 +313,27 @@ ElementVector* pe = topelement->NewElementVector(); IssmDouble* basis = xNew(numnodes); + IssmDouble* dbasis = xNew(dim*numnodes); /*Retrieve all inputs and parameters*/ topelement->GetVerticesCoordinates(&xyz_list); topelement->FindParam(&dt,TimesteppingTimeStepEnum); - Input* ms_input = topelement->GetInput(SmbMassBalanceEnum); _assert_(ms_input); - Input* surface_input = topelement->GetInput(SurfaceEnum); _assert_(surface_input); - Input* vz_input = NULL; + Input *ms_input = topelement->GetInput(SmbMassBalanceEnum); _assert_(ms_input); + Input *surface_input = topelement->GetInput(SurfaceEnum); _assert_(surface_input); + Input *vz_input = NULL; + Input *vx_input = NULL; + Input *vy_input = NULL; switch(dim){ - case 1: vz_input = topelement->GetInput(VyEnum); _assert_(vz_input); break; - case 2: vz_input = topelement->GetInput(VzEnum); _assert_(vz_input); break; + case 1: + vx_input=topelement->GetInput(VxEnum); _assert_(vx_input); + vz_input = topelement->GetInput(VyEnum) ; _assert_(vz_input); + break; + case 2: + vx_input=topelement->GetInput(VxEnum); _assert_(vx_input); + vy_input = topelement->GetInput(VyEnum); _assert_(vy_input); + vz_input = topelement->GetInput(VzEnum); _assert_(vz_input); + break; default: _error_("not implemented"); } + IssmDouble h = topelement->CharacteristicLength(); /*Initialize mb_correction to 0, do not forget!:*/ @@ -312,7 +352,24 @@ } + if(stabilization==5){ + /*SUPG*/ + topelement->NodalFunctionsDerivatives(dbasis,xyz_list,gauss); + if(dim==1){ + vx_input->GetInputAverage(&vx); + tau=h/(2.*fabs(vx)+1e-10); + for(int i=0;ivalues[i]+=Jdet*gauss->weight*(dt*ms+dt*vz)*tau*(vx*dbasis[0*numnodes+i]); + } + else{ + vx_input->GetInputAverage(&vx); + vy_input->GetInputAverage(&vy); + tau=h/(2.*pow(vx*vx+vy*vy,0.5)+1e-10); + for(int i=0;ivalues[i]+=Jdet*gauss->weight*(dt*ms+dt*vz)*tau*(vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i]); + } + } + /*Clean up and return*/ xDelete(xyz_list); xDelete(basis); + xDelete(dbasis); delete gauss; if(topelement->IsSpawnedElement()){topelement->DeleteMaterials(); delete topelement;}; @@ -321,5 +378,5 @@ }/*}}}*/ void FreeSurfaceTopAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/ - _error_("not implemented yet"); + _error_("not implemented yet"); }/*}}}*/ void FreeSurfaceTopAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_interp,int control_index){/*{{{*/ @@ -329,4 +386,71 @@ element->InputUpdateFromSolutionOneDof(solution,SurfaceEnum); + + /*Now, we need to do some "processing"*/ + int numvertices = element->GetNumberOfVertices(); + int migration_style; + + IssmDouble* surface = xNew(numvertices); + IssmDouble* newsurface = xNew(numvertices); + IssmDouble* thickness = xNew(numvertices); + IssmDouble* base = xNew(numvertices); + IssmDouble* bed = xNew(numvertices); + IssmDouble* phi = xNew(numvertices); + IssmDouble* sealevel = xNew(numvertices); + + IssmDouble minthickness = element->FindParam(MasstransportMinThicknessEnum); + IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); + IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum); + + bool isgroundingline; + element->FindParam(&isgroundingline,TransientIsgroundinglineEnum); + element->FindParam(&migration_style,GroundinglineMigrationEnum); + if(isgroundingline) element->GetInputListOnVertices(&bed[0],BedEnum); + + element->GetInputListOnVertices(&base[0],BaseEnum); + element->GetInputListOnVertices(&surface[0],SurfaceEnum); + element->GetInputListOnVertices(&phi[0],MaskOceanLevelsetEnum); + element->GetInputListOnVertices(&sealevel[0],SealevelEnum); + + for(int i=0;i(thickness[i])) _error_("NaN found in solution vector"); + if(xIsInf(thickness[i])) _error_("Inf found in solution vector"); + + /* check for thickness0.){ + if(base[i]<=bed[i]) base[i] = bed[i]; + newsurface[i] = base[i]+minthickness; + }else{ + // assume floatation condition + newsurface[i] = (1.-rho_ice/rho_water)*minthickness; + base[i] = -rho_ice/rho_water*minthickness; + } + } + + /* update thickness */ + thickness[i]=newsurface[i]-base[i]; + /* some checks */ + if(thickness[i]<0.) _error_("thickness<0"); + if(newsurface[i]AddInput(BaseEnum,base,element->GetElementType()); + element->AddInput(SurfaceEnum,newsurface,element->GetElementType()); + element->AddInput(ThicknessEnum,thickness,element->GetElementType()); + + /* Free resources */ + xDelete(newsurface); + xDelete(surface); + xDelete(thickness); + xDelete(base); + xDelete(bed); + xDelete(phi); + xDelete(sealevel); }/*}}}*/ void FreeSurfaceTopAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ Index: /issm/trunk/src/c/analyses/HydrologyGlaDSAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyGlaDSAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/HydrologyGlaDSAnalysis.cpp (revision 27035) @@ -472,5 +472,5 @@ /*Skip if water or ice shelf element*/ - if(element->IsAllFloating()) return; + //if(element->IsAllFloating()) return; /*Intermediaries */ @@ -543,4 +543,9 @@ if(h_new[iv]IsAllFloating()){ + for(int iv=0;ivAddInput(HydrologySheetThicknessEnum,h_new,P1Enum); @@ -561,5 +566,5 @@ /*Skip if water or ice shelf element*/ - if(element->IsAllFloating()) return; + //if(element->IsAllFloating()) return; /*Intermediary*/ @@ -604,6 +609,11 @@ } + /*Force floating ice to have zero effective pressure*/ + if(element->IsAllFloating()){ + for(int iv=0;ivAddInput(EffectivePressureEnum,N,element->FiniteElement()); - + /*Clean up and return*/ delete gauss; Index: /issm/trunk/src/c/analyses/HydrologyShaktiAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyShaktiAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/HydrologyShaktiAnalysis.cpp (revision 27035) @@ -286,5 +286,5 @@ IssmDouble lr,br,vx,vy,beta,lc; IssmDouble alpha2,frictionheat; - IssmDouble PMPheat,dpressure_water[2],dbed[2]; + IssmDouble PMPheat,dissipation,dpressure_water[2],dbed[2]; IssmDouble* xyz_list = NULL; // IssmDouble dgapxx; /***/ @@ -381,8 +381,8 @@ dpressure_water[0] = rho_water*g*(dh[0] - dbed[0]); dpressure_water[1] = rho_water*g*(dh[1] - dbed[1]); - PMPheat=-CT*CW*conductivity*(dh[0]*dpressure_water[0]+dh[1]*dpressure_water[1]); + PMPheat=CT*CW*conductivity*rho_water*(dh[0]*dpressure_water[0]+dh[1]*dpressure_water[1]); + PMPheat=0; /*** TEST no PMPheat***/ meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1])-PMPheat); - _assert_(meltrate>0.); for(int i=0;ivalues[i]+=Jdet*gauss->weight* @@ -549,5 +549,5 @@ IssmDouble alpha2,frictionheat; IssmDouble* xyz_list = NULL; - IssmDouble dpressure_water[2],dbed[2],PMPheat; + IssmDouble dpressure_water[2],dbed[2],PMPheat,dissipation; IssmDouble q = 0.; IssmDouble channelization = 0.; @@ -629,8 +629,15 @@ dpressure_water[0] = rho_water*g*(dh[0] - dbed[0]); dpressure_water[1] = rho_water*g*(dh[1] - dbed[1]); - PMPheat=-CT*CW*conductivity*(dh[0]*dpressure_water[0]+dh[1]*dpressure_water[1]); + PMPheat=CT*CW*conductivity*rho_water*(dh[0]*dpressure_water[0]+dh[1]*dpressure_water[1]); +PMPheat=0; /*** TEST no PMPheat***/ + dissipation=rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1]); meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1])-PMPheat); - _assert_(meltrate>0.); + + element->AddInput(DummyEnum,&meltrate,P0Enum); + element->AddInput(EsaEmotionEnum,&frictionheat,P0Enum); + element->AddInput(EsaNmotionEnum,&dissipation,P0Enum); + element->AddInput(EsaUmotionEnum,&PMPheat,P0Enum); + newgap += gauss->weight*Jdet*(gap+dt*( @@ -664,6 +671,8 @@ /*Limit gap height to grow to surface*/ - if(newgap>thickness) - newgap = thickness; +// if(newgap>thickness) +// newgap = thickness; + if(newgap>1) + newgap = 1; /*Add new gap as an input*/ Index: /issm/trunk/src/c/analyses/HydrologyTwsAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyTwsAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/HydrologyTwsAnalysis.cpp (revision 27035) @@ -44,4 +44,21 @@ }/*}}}*/ void HydrologyTwsAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ + + /*retrieve some parameters: */ + int hydrology_model; + int numoutputs; + char** requestedoutputs = NULL; + iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); + + /*Now, do we really want Tws?*/ + if(hydrology_model!=HydrologyTwsEnum) return; + + parameters->AddObject(new IntParam(HydrologyModelEnum,hydrology_model)); + + /*Requested outputs*/ + iomodel->FindConstant(&requestedoutputs,&numoutputs,"md.hydrology.requested_outputs"); + parameters->AddObject(new IntParam(HydrologyNumRequestedOutputsEnum,numoutputs)); + if(numoutputs)parameters->AddObject(new StringArrayParam(HydrologyRequestedOutputsEnum,requestedoutputs,numoutputs)); + iomodel->DeleteData(&requestedoutputs,numoutputs,"md.hydrology.requested_outputs"); }/*}}}*/ Index: /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 27035) @@ -10,4 +10,5 @@ #include "../modules/modules.h" #include "../solutionsequences/solutionsequences.h" +#include void LevelsetAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/ @@ -79,4 +80,5 @@ iomodel->FetchDataToInput(inputs,elements,"md.mask.ice_levelset",MaskIceLevelsetEnum); + iomodel->FetchDataToInput(inputs,elements,"md.mask.ocean_levelset",MaskOceanLevelsetEnum); iomodel->FetchDataToInput(inputs,elements,"md.initialization.vx",VxEnum); iomodel->FetchDataToInput(inputs,elements,"md.initialization.vy",VyEnum); @@ -88,4 +90,6 @@ iomodel->FindConstant(&isstochastic,"md.stochasticforcing.isstochasticforcing"); switch(calvinglaw){ + + /*"Continuous" calving laws*/ case DefaultCalvingEnum: iomodel->FetchDataToInput(inputs,elements,"md.calving.calvingrate",CalvingCalvingrateEnum); @@ -103,17 +107,33 @@ iomodel->FetchDataToInput(inputs,elements,"md.geometry.bed",BedEnum); break; - case CalvingMinthicknessEnum: - iomodel->FetchDataToInput(inputs,elements,"md.geometry.bed",BedEnum); - break; - case CalvingHabEnum: - iomodel->FetchDataToInput(inputs,elements,"md.calving.flotation_fraction",CalvingHabFractionEnum); - break; - case CalvingCrevasseDepthEnum: - iomodel->FetchDataToInput(inputs,elements,"md.calving.water_height",WaterheightEnum); - break; case CalvingDev2Enum: iomodel->FetchDataToInput(inputs,elements,"md.calving.stress_threshold_groundedice",CalvingStressThresholdGroundediceEnum); iomodel->FetchDataToInput(inputs,elements,"md.calving.stress_threshold_floatingice",CalvingStressThresholdFloatingiceEnum); break; + case CalvingTestEnum: + break; + case CalvingParameterizationEnum: + iomodel->FetchDataToInput(inputs,elements,"md.calving.stress_threshold_groundedice",CalvingStressThresholdGroundediceEnum); + iomodel->FetchDataToInput(inputs,elements,"md.calving.stress_threshold_floatingice",CalvingStressThresholdFloatingiceEnum); + iomodel->FetchDataToInput(inputs,elements,"md.geometry.bed",BedEnum); + break; + + /*"Discrete" calving laws (need to specify rate as 0 so that we can still solve the level set equation)*/ + case CalvingMinthicknessEnum: + iomodel->FetchDataToInput(inputs,elements,"md.geometry.bed",BedEnum); + iomodel->ConstantToInput(inputs,elements,0.,CalvingratexEnum,P1Enum); + iomodel->ConstantToInput(inputs,elements,0.,CalvingrateyEnum,P1Enum); + break; + case CalvingHabEnum: + iomodel->FetchDataToInput(inputs,elements,"md.calving.flotation_fraction",CalvingHabFractionEnum); + iomodel->ConstantToInput(inputs,elements,0.,CalvingratexEnum,P1Enum); + iomodel->ConstantToInput(inputs,elements,0.,CalvingrateyEnum,P1Enum); + break; + case CalvingCrevasseDepthEnum: + iomodel->FetchDataToInput(inputs,elements,"md.calving.water_height",WaterheightEnum); + iomodel->ConstantToInput(inputs,elements,0.,CalvingratexEnum,P1Enum); + iomodel->ConstantToInput(inputs,elements,0.,CalvingrateyEnum,P1Enum); + break; + default: _error_("Calving law "<FetchDataToInput(inputs,elements,"md.frontalforcings.meltingrate",CalvingMeltingrateEnum); + if (calvinglaw == CalvingParameterizationEnum) { + iomodel->FetchDataToInput(inputs,elements,"md.frontalforcings.ablationrate",CalvingAblationrateEnum); + } break; case FrontalForcingsRignotEnum: @@ -148,4 +171,9 @@ int calvinglaw; + IssmDouble *transparam = NULL; + IssmDouble yts; + int N,M; + bool interp,cycle; + iomodel->FindConstant(&calvinglaw,"md.calving.law"); switch(calvinglaw){ @@ -168,4 +196,36 @@ parameters->AddObject(iomodel->CopyConstantObject("md.calving.height_above_floatation",CalvingHeightAboveFloatationEnum)); break; + case CalvingTestEnum: + iomodel->FindConstant(&interp,"md.timestepping.interp_forcing"); + iomodel->FindConstant(&cycle,"md.timestepping.cycle_forcing"); + iomodel->FetchData(&transparam,&N,&M,"md.calving.speedfactor"); + if(N==1){ + _assert_(M==1); + parameters->AddObject(new DoubleParam(CalvingTestSpeedfactorEnum,transparam[0])); + } + else{ + _assert_(N==2); + parameters->AddObject(new TransientParam(CalvingTestSpeedfactorEnum,&transparam[0],&transparam[M],interp,cycle,M)); + } + xDelete(transparam); + iomodel->FetchData(&transparam,&N,&M,"md.calving.independentrate"); + if(N==1){ + _assert_(M==1); + parameters->AddObject(new DoubleParam(CalvingTestIndependentRateEnum,transparam[0])); + } + else{ + _assert_(N==2); + parameters->AddObject(new TransientParam(CalvingTestIndependentRateEnum,&transparam[0],&transparam[M],interp,cycle,M)); + } + xDelete(transparam); + break; + case CalvingParameterizationEnum: + parameters->AddObject(iomodel->CopyConstantObject("md.calving.min_thickness",CalvingMinthicknessEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.calving.use_param",CalvingUseParamEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.calving.scale_theta",CalvingScaleThetaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.calving.amp_alpha",CalvingAmpAlphaEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.calving.midp",CalvingMidpointEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.calving.nonlinearlaw",CalvingNonlinearLawEnum)); + break; default: _error_("Calving law "<FindConstant(&melt_parameterization,"md.frontalforcings.parameterization"); - int M,N; - IssmDouble* transparam = NULL; switch(melt_parameterization){ case FrontalForcingsDefaultEnum: @@ -209,6 +267,4 @@ /*parameters: */ int stabilization; - bool save_results; - femmodel->parameters->FindParam(&save_results,SaveResultsEnum); femmodel->parameters->FindParam(&stabilization,LevelsetStabilizationEnum); @@ -222,9 +278,4 @@ else{ solutionsequence_linear(femmodel); - } - - if(save_results){ - int outputs[1] = {MaskIceLevelsetEnum}; - femmodel->RequestedOutputsx(&femmodel->results,&outputs[0],1); } }/*}}}*/ @@ -400,4 +451,71 @@ break; } + case 6:{ + /*SUPG*/ + IssmDouble vx,vy; + mf_vx_input->GetInputAverage(&vx); + mf_vy_input->GetInputAverage(&vy); + vel=sqrt(vx*vx+vy*vy)+1.e-8; + IssmDouble ECN, K; + ECN = vel *dt /h; + K = 1./tanh(ECN) - 1./ECN; +// if (ECN<1e-6) K = ECN /3.0; + + /*According to Hilmar, xi=K is too large*/ + IssmDouble xi=0.1*K; + + IssmDouble tau=xi*h/(2*vel); + Input* levelset_input = NULL; + + + IssmDouble kappa; + IssmDouble p=4, q=4; + IssmDouble phi[3]; + + levelset_input=basalelement->GetInput(MaskIceLevelsetEnum); _assert_(levelset_input); + levelset_input->GetInputValue(&phi[0], gauss); + + IssmDouble dphidx=0., dphidy=0.; + IssmDouble nphi; + + for(int i=0;i= 1) { + kappa = 1 - 1.0/nphi; + } + else { + kappa = 0.5/M_PI *sin(2*M_PI*nphi)/nphi; + } + + kappa = kappa * vel / h; + + /*Mass matrix - part 2*/ + for(int i=0;ivalues[i*numnodes+j]+=gauss->weight*Jdet*tau*basis[j]*(vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i]); + } + } + + /*Advection matrix - part 2, A*/ + for(int i=0;ivalues[i*numnodes+j]+=dt*gauss->weight*Jdet*tau*(vx*dbasis[0*numnodes+j]+vy*dbasis[1*numnodes+j])*(vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i]); + } + } + /*Add the pertubation term \nabla\cdot(\kappa*\nabla\phi)*/ + for(int i=0;ivalues[i*numnodes+j]+= dt*gauss->weight*Jdet*kappa*dbasis[k*numnodes+j]*dbasis[k*numnodes+i]; + } + } + } + + break; + } default: _error_("unknown type of stabilization in LevelsetAnalysis.cpp"); @@ -435,5 +553,5 @@ IssmDouble* basis = xNew(numnodes); IssmDouble* dbasis = NULL; - if(stabilization==5) dbasis= xNew(2*numnodes); + if((stabilization==5) |(stabilization == 6)) dbasis= xNew(2*numnodes); /*Retrieve all inputs and parameters*/ @@ -456,5 +574,5 @@ if(stabilization==5){ /*SUPG*/ - IssmDouble vx,vy,vel; + IssmDouble vx,vy,vel; basalelement->NodalFunctionsDerivatives(dbasis,xyz_list,gauss); mf_vx_input->GetInputAverage(&vx); @@ -469,4 +587,26 @@ } } + else if (stabilization ==6) { + IssmDouble vx,vy,vel; + basalelement->NodalFunctionsDerivatives(dbasis,xyz_list,gauss); + mf_vx_input->GetInputAverage(&vx); + mf_vy_input->GetInputAverage(&vy); + vel=sqrt(vx*vx+vy*vy)+1.e-8; + + IssmDouble ECN, K; + ECN = vel *dt /h; + K = 1./tanh(ECN) - 1./ECN; + // if (ECN<1e-6) K = ECN /3.0; + + /*According to Hilmar, xi=K is too large*/ + IssmDouble xi=0.1*K; + + IssmDouble tau=xi*h/(2*vel); + + /*Force vector - part 2*/ + for(int i=0;ivalues[i]+=Jdet*gauss->weight*lsf*tau*(vx*dbasis[0*numnodes+i]+vy*dbasis[1*numnodes+i]); + } + } } @@ -474,5 +614,5 @@ xDelete(xyz_list); xDelete(basis); - xDelete(dbasis); + xDelete(dbasis); basalelement->FindParam(&domaintype,DomainTypeEnum); if(basalelement->IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; @@ -525,4 +665,66 @@ } }/*}}}*/ +void LevelsetAnalysis::PostProcess(FemModel* femmodel){/*{{{*/ + + /*This function is only used by "discrete calving laws" for which we change + * the value of the levelset after the advection step (level set equation + * solve) based on the law*/ + + /*Intermediaries*/ + int calvinglaw; + IssmDouble newlevelset[6]; + femmodel->parameters->FindParam(&calvinglaw,CalvingLawEnum); + + /*Apply minimum thickness criterion*/ + if(calvinglaw==CalvingMinthicknessEnum || calvinglaw==CalvingVonmisesEnum || calvinglaw==CalvingParameterizationEnum){ + + IssmDouble mig_max = femmodel->parameters->FindParam(MigrationMaxEnum); + IssmDouble dt = femmodel->parameters->FindParam(TimesteppingTimeStepEnum); + + /*Get current distance to terminus*/ + InputDuplicatex(femmodel,MaskIceLevelsetEnum,DistanceToCalvingfrontEnum); + femmodel->DistanceToFieldValue(MaskIceLevelsetEnum,0,DistanceToCalvingfrontEnum); + + /*Intermediaries*/ + IssmDouble thickness,bed,sealevel,distance,levelset; + IssmDouble min_thickness = femmodel->parameters->FindParam(CalvingMinthicknessEnum); + + /*Loop over all elements of this partition*/ + for(Object* & object : femmodel->elements->objects){ + Element* element = xDynamicCast(object); + + /*no need to postprocess an ice free element*/ + if(!element->IsIceInElement()) continue; + + int numnodes = element->GetNumberOfNodes(); _assert_(numnodes<7); + Gauss* gauss = element->NewGauss(); + Input *H_input = element->GetInput(ThicknessEnum); _assert_(H_input); + Input *b_input = element->GetInput(BedEnum); _assert_(b_input); + Input *sl_input = element->GetInput(SealevelEnum); _assert_(sl_input); + Input *dis_input = element->GetInput(DistanceToCalvingfrontEnum); _assert_(dis_input); + Input *levelset_input = element->GetInput(MaskIceLevelsetEnum); _assert_(levelset_input); + + /*Potentially constrain nodes of this element*/ + for(int in=0;inGaussNode(element->GetElementType(),in); + + levelset_input->GetInputValue(&levelset,gauss); + H_input->GetInputValue(&thickness,gauss); + b_input->GetInputValue(&bed,gauss); + sl_input->GetInputValue(&sealevel,gauss); + dis_input->GetInputValue(&distance,gauss); + + if(thickness 0 number (i.e. deactivate this node) + } + else{ + newlevelset[in] = levelset; + } + } + element->AddInput(MaskIceLevelsetEnum,&newlevelset[0],element->GetElementType()); + delete gauss; + } + } +}/*}}}*/ void LevelsetAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ @@ -530,10 +732,15 @@ int calvinglaw; femmodel->parameters->FindParam(&calvinglaw,CalvingLawEnum); - - if(calvinglaw==CalvingMinthicknessEnum || calvinglaw==CalvingVonmisesEnum){ + IssmDouble mig_max = femmodel->parameters->FindParam(MigrationMaxEnum); + IssmDouble dt = femmodel->parameters->FindParam(TimesteppingTimeStepEnum); + + /*Get current distance to terminus*/ + InputDuplicatex(femmodel,MaskIceLevelsetEnum,DistanceToCalvingfrontEnum); + femmodel->DistanceToFieldValue(MaskIceLevelsetEnum,0,DistanceToCalvingfrontEnum); + + if(calvinglaw==CalvingHabEnum){ /*Intermediaries*/ - IssmDouble thickness,bed,sealevel; - IssmDouble min_thickness = femmodel->parameters->FindParam(CalvingMinthicknessEnum); + IssmDouble thickness,water_depth,distance,hab_fraction; /*Loop over all elements of this partition*/ @@ -541,9 +748,13 @@ Element* element = xDynamicCast(object); - int numnodes = element->GetNumberOfNodes(); - Gauss* gauss = element->NewGauss(); - Input* H_input = element->GetInput(ThicknessEnum); _assert_(H_input); - Input* b_input = element->GetInput(BedEnum); _assert_(b_input); - Input* sl_input = element->GetInput(SealevelEnum); _assert_(sl_input); + IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); + IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum); + + int numnodes = element->GetNumberOfNodes(); + Gauss* gauss = element->NewGauss(); + Input* H_input = element->GetInput(ThicknessEnum); _assert_(H_input); + Input* bed_input = element->GetInput(BedEnum); _assert_(bed_input); + Input* hab_fraction_input = element->GetInput(CalvingHabFractionEnum); _assert_(hab_fraction_input); + Input* dis_input = element->GetInput(DistanceToCalvingfrontEnum); _assert_(dis_input); /*Potentially constrain nodes of this element*/ @@ -554,52 +765,9 @@ H_input->GetInputValue(&thickness,gauss); - b_input->GetInputValue(&bed,gauss); - sl_input->GetInputValue(&sealevel,gauss); - if(thicknessApplyConstraint(0,+1.); - } - else { - /* no ice, set no spc */ - node->DofInFSet(0); - } - } - delete gauss; - } - } - else if(calvinglaw==CalvingHabEnum){ - - /*Intermediaries*/ - IssmDouble thickness,water_depth,levelset,hab_fraction; - - /*Get the fraction of the flotation thickness at the terminus*/ - InputDuplicatex(femmodel,MaskIceLevelsetEnum,DistanceToCalvingfrontEnum); - femmodel->DistanceToFieldValue(MaskIceLevelsetEnum,0,DistanceToCalvingfrontEnum); - - /*Loop over all elements of this partition*/ - for(Object* & object : femmodel->elements->objects){ - Element* element = xDynamicCast(object); - - IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum); - IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum); - - int numnodes = element->GetNumberOfNodes(); - Gauss* gauss = element->NewGauss(); - Input* H_input = element->GetInput(ThicknessEnum); _assert_(H_input); - Input* bed_input = element->GetInput(BedEnum); _assert_(bed_input); - Input* hab_fraction_input = element->GetInput(CalvingHabFractionEnum); _assert_(hab_fraction_input); - Input* ls_input = element->GetInput(DistanceToCalvingfrontEnum); _assert_(ls_input); - - /*Potentially constrain nodes of this element*/ - for(int in=0;inGaussNode(element->GetElementType(),in); - Node* node=element->GetNode(in); - if(!node->IsActive()) continue; - - H_input->GetInputValue(&thickness,gauss); bed_input->GetInputValue(&water_depth,gauss); - ls_input->GetInputValue(&levelset,gauss); + dis_input->GetInputValue(&distance,gauss); hab_fraction_input->GetInputValue(&hab_fraction,gauss); - if(thickness<((rho_water/rho_ice)*(1+hab_fraction)*-water_depth) && levelset>-300. && levelset<0.){ + if(thickness<((rho_water/rho_ice)*(1+hab_fraction)*-water_depth) && fabs(distance)ApplyConstraint(0,+1.); } @@ -628,6 +796,5 @@ IssmDouble crevasse_threshold = femmodel->parameters->FindParam(CalvingCrevasseThresholdEnum); - IssmDouble mig_max = femmodel->parameters->FindParam(MigrationMaxEnum); - IssmDouble dt = femmodel->parameters->FindParam(TimesteppingTimeStepEnum); + for(Object* & object : femmodel->elements->objects){ @@ -704,4 +871,5 @@ surface_input->GetInputValue(&surface,gauss); + /*FIXME: not sure about levelset<0. && fabs(levelset)>-mig_max*dt! SHould maybe be distancesurface || crevassedepth>crevasse_threshold*thickness) && bed<0. && levelset<0. && levelset>-mig_max*dt && constraint_nodes[node->Lid()]==0.){ local_nflipped++; Index: /issm/trunk/src/c/analyses/LevelsetAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/LevelsetAnalysis.h (revision 27034) +++ /issm/trunk/src/c/analyses/LevelsetAnalysis.h (revision 27035) @@ -32,4 +32,7 @@ void InputUpdateFromSolution(IssmDouble* solution,Element* element); void UpdateConstraints(FemModel* femmodel); + + /*Specific methods to LevelsetAnalysis*/ + void PostProcess(FemModel* femmodel); }; #endif Index: /issm/trunk/src/c/analyses/LoveAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/LoveAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/LoveAnalysis.cpp (revision 27035) @@ -33,6 +33,8 @@ parameters->AddObject(iomodel->CopyConstantObject("md.love.mu0",LoveMu0Enum)); parameters->AddObject(iomodel->CopyConstantObject("md.love.Gravitational_Constant",LoveGravitationalConstantEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.love.chandler_wobble",LoveChandlerWobbleEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.love.allow_layer_deletion",LoveAllowLayerDeletionEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.love.underflow_tol",LoveUnderflowTolEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.love.pw_threshold",LovePostWidderThresholdEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.love.integration_steps_per_layer",LoveIntStepsPerLayerEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.love.istemporal",LoveIsTemporalEnum)); @@ -43,4 +45,8 @@ parameters->AddObject(iomodel->CopyConstantObject("md.love.core_mantle_boundary",LoveCoreMantleBoundaryEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.love.complex_computation",LoveComplexComputationEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.rotational.equatorialmoi",RotationalEquatorialMoiEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.rotational.polarmoi",RotationalPolarMoiEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.rotational.angularvelocity",RotationalAngularVelocityEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.lovenumbers.tk2secular",TidalLoveK2SecularEnum)); }/*}}}*/ void LoveAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ Index: /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 27035) @@ -182,7 +182,13 @@ break; case SpatialLinearFloatingMeltRateEnum: - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsSpatialDeepwaterMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_elevation",BasalforcingsSpatialDeepwaterElevationEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_melting_rate",BasalforcingsSpatialUpperwaterMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_elevation",BasalforcingsSpatialUpperwaterElevationEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.perturbation_melting_rate",BasalforcingsPerturbationMeltingRateEnum,0.); + if(isstochastic){ + iomodel->FetchDataToInput(inputs,elements,"md.stochasticforcing.default_id",StochasticForcingDefaultIdEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum); + } break; case BasalforcingsPicoEnum: @@ -212,4 +218,8 @@ iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.ocean_salinity",BasalforcingsOceanSalinityEnum); iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.ocean_temp",BasalforcingsOceanTempEnum); + break; + case AutoregressionLinearFloatingMeltRateEnum: + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.basin_id",BasalforcingsLinearBasinIdEnum); + if(isstochastic) iomodel->FetchDataToInput(inputs,elements,"md.stochasticforcing.default_id",StochasticForcingDefaultIdEnum); break; default: Index: /issm/trunk/src/c/analyses/SamplingAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/SamplingAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/SamplingAnalysis.cpp (revision 27035) @@ -76,5 +76,8 @@ iomodel->FetchDataToInput(inputs,elements,"md.sampling.kappa",SamplingKappaEnum); iomodel->FetchDataToInput(inputs,elements,"md.sampling.beta",SamplingBetaEnum,0.); + iomodel->FetchDataToInput(inputs,elements,"md.sampling.tau",SamplingTauEnum); iomodel->FetchDataToInput(inputs,elements,"md.initialization.sample",SampleEnum,0.); + iomodel->FetchDataToInput(inputs,elements,"md.initialization.sample",SampleNoiseEnum,0.); + if(iomodel->solution_enum==TransientSolutionEnum) iomodel->FetchDataToInput(inputs,elements,"md.sampling.phi",SamplingPhiEnum,0.); }/*}}}*/ @@ -84,8 +87,6 @@ char** requestedoutputs = NULL; - parameters->AddObject(iomodel->CopyConstantObject("md.sampling.tau",SamplingTauEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.sampling.alpha",SamplingAlphaEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.sampling.robin",SamplingRobinEnum)); - if(solution_enum==TransientSolutionEnum) parameters->AddObject(iomodel->CopyConstantObject("md.sampling.phi",SamplingPhiEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.sampling.seed",SamplingSeedEnum)); @@ -273,8 +274,11 @@ element->GetDofListLocal(&doflist,NoneApproximationEnum,GsetEnum); IssmDouble* newsample = xNew(numnodes); + IssmDouble* tau = xNew(numnodes); + element->GetInputListOnNodes(&tau[0],SamplingTauEnum); /*Use the dof list to index into the solution vector: */ for(int i=0;i(newsample[i])) _error_("NaN found in solution vector"); @@ -287,4 +291,5 @@ /*Free ressources:*/ xDelete(newsample); + xDelete(tau); xDelete(doflist); }/*}}}*/ @@ -418,2 +423,48 @@ *pMff=Mff; }/*}}}*/ +void SamplingAnalysis::UpdateTransientSample(FemModel * femmodel){ + + for(int j=0;jelements->Size();j++){ + Element* element=(Element*)femmodel->elements->GetObjectByOffset(j); + UpdateTransientSample(element); + } + +} +void SamplingAnalysis::UpdateTransientSample(Element * element){ + + /*Intermediaries */ + IssmDouble phi, sample, noise; + + /*Fetch number vertices for this element*/ + int numvertices = element->GetNumberOfVertices(); + + /*Initialize new sample*/ + IssmDouble* sample_new = xNew(numvertices); + + /*Retrieve all inputs and parameters*/ + Input* sample_input=element->GetInput(SampleOldEnum); _assert_(sample_input); + Input* noise_input=element->GetInput(SampleNoiseEnum); _assert_(noise_input); + Input* phi_input=element->GetInput(SamplingPhiEnum); _assert_(phi_input); + + /* Start looping on the number of gaussian points: */ + Gauss* gauss=element->NewGauss(); + for(int iv=0;ivGaussVertex(iv); + + /*Get input values at gauss points*/ + sample_input->GetInputValue(&sample,gauss); + noise_input->GetInputValue(&noise,gauss); + phi_input->GetInputValue(&phi,gauss); + + /*Get new sample*/ + sample_new[iv] = phi*sample + noise; + + } + + element->AddInput(SampleEnum,sample_new,element->GetElementType()); + + /*Clean up and return*/ + xDelete(sample_new); + delete gauss; + +} Index: /issm/trunk/src/c/analyses/SamplingAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/SamplingAnalysis.h (revision 27034) +++ /issm/trunk/src/c/analyses/SamplingAnalysis.h (revision 27035) @@ -40,4 +40,7 @@ void MassMatrix(Matrix** pMff,FemModel* femmodel); + void UpdateTransientSample(FemModel* femmodel); + void UpdateTransientSample(Element * element); + }; #endif Index: /issm/trunk/src/c/analyses/SealevelchangeAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/SealevelchangeAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/SealevelchangeAnalysis.cpp (revision 27035) @@ -85,4 +85,6 @@ IssmDouble* love_tk=NULL; IssmDouble* love_tl=NULL; + IssmDouble* love_pmtf_colinear=NULL; + IssmDouble* love_pmtf_ortho=NULL; IssmDouble* love_timefreq=NULL; bool love_istime=true; @@ -101,4 +103,11 @@ IssmDouble* H_viscoelastic_interpolated= NULL; IssmDouble* H_viscoelastic_local = NULL; + IssmDouble* Pmtf_col_interpolated = NULL; + IssmDouble* Pmtf_ortho_interpolated = NULL; + IssmDouble* Pmtf_z_interpolated = NULL; + IssmDouble* Love_th2_interpolated = NULL; + IssmDouble* Love_tk2_interpolated = NULL; + IssmDouble* Love_tl2_interpolated = NULL; + int M,m,lower_row,upper_row; IssmDouble degacc=.01; @@ -166,5 +175,5 @@ /*compute planet area and plug into parameters:*/ iomodel->FetchData(&planetradius,"md.solidearth.planetradius"); - planetarea=4*PI*planetradius*planetradius; + planetarea=4*M_PI*planetradius*planetradius; parameters->AddObject(new DoubleParam(SolidearthPlanetAreaEnum,planetarea)); @@ -253,7 +262,4 @@ iomodel->FetchData(&love_k,&ndeg,&precomputednt,"md.solidearth.lovenumbers.k"); iomodel->FetchData(&love_l,&ndeg,&precomputednt,"md.solidearth.lovenumbers.l"); - iomodel->FetchData(&love_th,&ndeg,&precomputednt,"md.solidearth.lovenumbers.th"); - iomodel->FetchData(&love_tk,&ndeg,&precomputednt,"md.solidearth.lovenumbers.tk"); - iomodel->FetchData(&love_tl,&ndeg,&precomputednt,"md.solidearth.lovenumbers.tl"); parameters->AddObject(new DoubleParam(SolidearthSettingsTimeAccEnum,timeacc)); @@ -261,7 +267,19 @@ parameters->AddObject(new DoubleMatParam(LoadLoveKEnum,love_k,ndeg,precomputednt)); parameters->AddObject(new DoubleMatParam(LoadLoveLEnum,love_l,ndeg,precomputednt)); - parameters->AddObject(new DoubleMatParam(TidalLoveHEnum,love_th,ndeg,precomputednt)); - parameters->AddObject(new DoubleMatParam(TidalLoveKEnum,love_tk,ndeg,precomputednt)); - parameters->AddObject(new DoubleMatParam(TidalLoveLEnum,love_tl,ndeg,precomputednt)); + + if (rotation){ + iomodel->FetchData(&love_th,&ndeg,&precomputednt,"md.solidearth.lovenumbers.th"); + iomodel->FetchData(&love_tk,&ndeg,&precomputednt,"md.solidearth.lovenumbers.tk"); + iomodel->FetchData(&love_tl,&ndeg,&precomputednt,"md.solidearth.lovenumbers.tl"); + iomodel->FetchData(&love_pmtf_colinear,&dummy,&precomputednt,"md.solidearth.lovenumbers.pmtf_colinear"); + iomodel->FetchData(&love_pmtf_ortho,&dummy,&precomputednt,"md.solidearth.lovenumbers.pmtf_ortho"); + + parameters->AddObject(new DoubleMatParam(LovePolarMotionTransferFunctionColinearEnum,love_pmtf_colinear,1,precomputednt)); + parameters->AddObject(new DoubleMatParam(LovePolarMotionTransferFunctionOrthogonalEnum,love_pmtf_ortho,1,precomputednt)); + parameters->AddObject(new DoubleMatParam(TidalLoveHEnum,love_th,ndeg,precomputednt)); + parameters->AddObject(new DoubleMatParam(TidalLoveKEnum,love_tk,ndeg,precomputednt)); + parameters->AddObject(new DoubleMatParam(TidalLoveLEnum,love_tl,ndeg,precomputednt)); + } + parameters->AddObject(new DoubleMatParam(LoveTimeFreqEnum,love_timefreq,precomputednt,1)); parameters->AddObject(new BoolParam(LoveIsTimeEnum,love_istime)); @@ -283,4 +301,10 @@ parameters->AddObject(new IntParam(SealevelchangeViscousIndexEnum,0)); xDelete(viscoustimes); + if (rotation){ + IssmDouble* viscouspolarmotion=NULL; + viscouspolarmotion=xNewZeroInit(3*nt); + parameters->AddObject(new DoubleMatParam(SealevelchangeViscousPolarMotionEnum,viscouspolarmotion,3,nt)); + xDelete(viscouspolarmotion); + } } else { @@ -307,9 +331,8 @@ } - if(rotation)parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.lovenumbers.tk2secular",TidalLoveK2SecularEnum)); - + if(rotation) parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.lovenumbers.tk2secular",TidalLoveK2SecularEnum)); if(selfattraction){ - /*compute combined legendre + love number (elastic green function:*/ + /*compute combined legendre + love number (elastic green function):*/ m=DetermineLocalSize(M,IssmComm::GetComm()); GetOwnershipBoundariesFromRange(&lower_row,&upper_row,m,IssmComm::GetComm()); @@ -441,8 +464,24 @@ U_viscoelastic_interpolated=xNew(M*nt,"t"); if(horiz)H_viscoelastic_interpolated=xNew(M*nt,"t"); + if(rotation){ + Pmtf_col_interpolated=xNew(nt,"t"); + Pmtf_ortho_interpolated=xNew(nt,"t"); + Pmtf_z_interpolated=xNew(nt,"t"); + Love_tk2_interpolated=xNew(nt,"t"); + Love_th2_interpolated=xNew(nt,"t"); + if (horiz) Love_tl2_interpolated=xNew(nt,"t"); + } #else G_viscoelastic_interpolated=xNew(M*nt); U_viscoelastic_interpolated=xNew(M*nt); if(horiz)H_viscoelastic_interpolated=xNew(M*nt); + if(rotation){ + Pmtf_col_interpolated=xNew(nt); + Pmtf_ortho_interpolated=xNew(nt); + Pmtf_z_interpolated=xNew(nt); + Love_tk2_interpolated=xNew(nt); + Love_th2_interpolated=xNew(nt); + if (horiz) Love_tl2_interpolated=xNew(nt); + } #endif @@ -477,4 +516,14 @@ if(horiz)H_viscoelastic_interpolated[timeindex]=(1-lincoeff)*H_viscoelastic[timepreindex]+lincoeff*H_viscoelastic[timepreindex+1]; } + + if(rotation){ + int timepreindex= 2*precomputednt+timeindex2; + Pmtf_col_interpolated[t]=(1.0-lincoeff)*love_pmtf_colinear[timeindex2]+lincoeff*love_pmtf_colinear[timeindex2+1]; + Pmtf_ortho_interpolated[t]=(1.0-lincoeff)*love_pmtf_ortho[timeindex2]+lincoeff*love_pmtf_ortho[timeindex2+1]; + Pmtf_z_interpolated[t]=1.0+(1.0-lincoeff)*love_k[timepreindex]+lincoeff*love_k[timepreindex+1]; + Love_tk2_interpolated[t]=(1.0-lincoeff)*love_tk[timepreindex]+lincoeff*love_tk[timepreindex+1]; + Love_th2_interpolated[t]=(1.0-lincoeff)*love_th[timepreindex]+lincoeff*love_th[timepreindex+1]; + if (horiz) Love_tl2_interpolated[t]=(1.0-lincoeff)*love_tl[timepreindex]+lincoeff*love_tl[timepreindex+1]; + } } @@ -491,4 +540,29 @@ if(horiz)H_viscoelastic_interpolated=H_viscoelastic; #endif + + if(rotation){ //if this cpu handles degree 2 +#ifdef _HAVE_AD_ + Pmtf_col_interpolated=xNew(1,"t"); + Pmtf_ortho_interpolated=xNew(1,"t"); + Pmtf_z_interpolated=xNew(1,"t"); + Love_tk2_interpolated=xNew(1,"t"); + Love_th2_interpolated=xNew(1,"t"); + if (horiz) Love_tl2_interpolated=xNew(1,"t"); +#else + Pmtf_col_interpolated=xNew(1); + Pmtf_ortho_interpolated=xNew(1); + Pmtf_z_interpolated=xNew(1); + Love_tk2_interpolated=xNew(1); + Love_th2_interpolated=xNew(1); + if (horiz) Love_tl2_interpolated=xNew(1); +#endif + + Pmtf_col_interpolated=love_pmtf_colinear; + Pmtf_ortho_interpolated=love_pmtf_ortho; + Pmtf_z_interpolated[0]=1.0+love_k[2]; + Love_tk2_interpolated[0]=love_tk[2]; + Love_th2_interpolated[0]=love_th[2]; + if (horiz) Love_tl2_interpolated[0]=love_tl[2]; + } } @@ -499,4 +573,12 @@ parameters->AddObject(new DoubleVecParam(SealevelchangeUViscoElasticEnum,U_viscoelastic_interpolated,M*nt)); if(horiz)parameters->AddObject(new DoubleVecParam(SealevelchangeHViscoElasticEnum,H_viscoelastic_interpolated,M*nt)); + if(rotation){ + parameters->AddObject(new DoubleVecParam(SealevelchangePolarMotionTransferFunctionColinearEnum,Pmtf_col_interpolated,nt)); + parameters->AddObject(new DoubleVecParam(SealevelchangePolarMotionTransferFunctionOrthogonalEnum,Pmtf_ortho_interpolated,nt)); + parameters->AddObject(new DoubleVecParam(SealevelchangePolarMotionTransferFunctionZEnum,Pmtf_z_interpolated,nt)); + parameters->AddObject(new DoubleVecParam(SealevelchangeTidalH2Enum,Love_th2_interpolated,nt)); + parameters->AddObject(new DoubleVecParam(SealevelchangeTidalK2Enum,Love_tk2_interpolated,nt)); + if (horiz) parameters->AddObject(new DoubleVecParam(SealevelchangeTidalL2Enum,Love_tl2_interpolated,nt)); + } } @@ -519,4 +601,9 @@ xDelete(H_viscoelastic_local); } + if(rotation){ + xDelete(love_pmtf_colinear); + xDelete(love_pmtf_ortho); + + } } } /*}}}*/ @@ -545,5 +632,4 @@ iomodel->DeleteData(&requestedoutputs,numoutputs,"md.solidearth.requested_outputs"); /*}}}*/ - }/*}}}*/ Index: /issm/trunk/src/c/analyses/SmbAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 27035) @@ -24,5 +24,5 @@ int smb_model; - bool isdelta18o,ismungsm,isd18opd,issetpddfac,isprecipscaled,istemperaturescaled,isfirnwarming; + bool isdelta18o,ismungsm,isd18opd,issetpddfac,isprecipscaled,istemperaturescaled,isfirnwarming,isstochastic; /*Update elements: */ @@ -38,7 +38,12 @@ /*Figure out smb model: */ iomodel->FindConstant(&smb_model,"md.smb.model"); + iomodel->FindConstant(&isstochastic,"md.stochasticforcing.isstochasticforcing"); switch(smb_model){ case SMBforcingEnum: iomodel->FetchDataToInput(inputs,elements,"md.smb.mass_balance",SmbMassBalanceEnum,0.); + if(isstochastic){ + iomodel->FetchDataToInput(inputs,elements,"md.stochasticforcing.default_id",StochasticForcingDefaultIdEnum); + iomodel->FetchDataToInput(inputs,elements,"md.smb.mass_balance",BaselineSmbMassBalanceEnum,0.); + } break; case SMBgembEnum: Index: /issm/trunk/src/c/analyses/StressbalanceAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/StressbalanceAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/StressbalanceAnalysis.cpp (revision 27035) @@ -31,5 +31,5 @@ IssmDouble rho_ice; IssmDouble FSreconditioning; - bool isSIA,isSSA,isL1L2,isMLHO,isHO,isFS,iscoupling; + bool isSIA,isSSA,isL1L2,isMOLHO,isHO,isFS,iscoupling; bool spcpresent = false; int Mx,Nx; @@ -59,13 +59,13 @@ iomodel->FindConstant(&isSSA,"md.flowequation.isSSA"); iomodel->FindConstant(&isL1L2,"md.flowequation.isL1L2"); - iomodel->FindConstant(&isMLHO,"md.flowequation.isMLHO"); + iomodel->FindConstant(&isMOLHO,"md.flowequation.isMOLHO"); iomodel->FindConstant(&isHO,"md.flowequation.isHO"); iomodel->FindConstant(&isFS,"md.flowequation.isFS"); /*Is this model only SIA??*/ - if(!isSSA && !isHO && !isFS && !isL1L2 && !isMLHO) return; + if(!isSSA && !isHO && !isFS && !isL1L2 && !isMOLHO) return; /*Do we have coupling*/ - if((isSIA?1.:0.) + (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) + if((isSIA?1.:0.) + (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMOLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) iscoupling = true; else @@ -78,5 +78,5 @@ if(isSSA) iomodel->FindConstant(&finiteelement,"md.flowequation.fe_SSA"); else if(isL1L2) finiteelement = P1Enum; - else if(isMLHO) finiteelement = P1Enum; + else if(isMOLHO) finiteelement = P1Enum; else if(isHO) iomodel->FindConstant(&finiteelement,"md.flowequation.fe_HO"); else if(isFS){ iomodel->FindConstant(&finiteelement,"md.flowequation.fe_FS"); @@ -188,5 +188,5 @@ } else{ - if(!isMLHO){ + if(!isMOLHO){ IoModelToConstraintsx(constraints,iomodel,"md.stressbalance.spcvx",StressbalanceAnalysisEnum,finiteelement,0); if(iomodel->domaintype!=Domain2DverticalEnum){ @@ -194,5 +194,5 @@ } } - else{//MLHO + else{//MOLHO IoModelToConstraintsx(constraints,iomodel,"md.stressbalance.spcvx_base",StressbalanceAnalysisEnum,finiteelement,0); IoModelToConstraintsx(constraints,iomodel,"md.stressbalance.spcvx_shear",StressbalanceAnalysisEnum,finiteelement,1); @@ -462,5 +462,5 @@ int count; int penpair_ids[2]; - bool isSSA,isL1L2,isMLHO,isHO,isFS; + bool isSSA,isL1L2,isMOLHO,isHO,isFS; int numpenalties,numrifts,numriftsegments; IssmDouble *riftinfo = NULL; @@ -470,5 +470,5 @@ /*Fetch parameters: */ iomodel->FindConstant(&isL1L2,"md.flowequation.isL1L2"); - iomodel->FindConstant(&isMLHO,"md.flowequation.isMLHO"); + iomodel->FindConstant(&isMOLHO,"md.flowequation.isMOLHO"); iomodel->FindConstant(&isFS,"md.flowequation.isFS"); iomodel->FindConstant(&isSSA,"md.flowequation.isSSA"); @@ -477,5 +477,5 @@ /*Is this SIA only?*/ - if(!isSSA && !isHO && !isFS && !isL1L2 && !isMLHO) return; + if(!isSSA && !isHO && !isFS && !isL1L2 && !isMOLHO) return; /*Initialize counter: */ @@ -522,5 +522,5 @@ /*Intermediary*/ - bool isSSA,isL1L2,isMLHO,isHO,isFS,iscoupling; + bool isSSA,isL1L2,isMOLHO,isHO,isFS,iscoupling; int finiteelement=-1,approximation=-1; @@ -528,13 +528,13 @@ iomodel->FindConstant(&isSSA,"md.flowequation.isSSA"); iomodel->FindConstant(&isL1L2,"md.flowequation.isL1L2"); - iomodel->FindConstant(&isMLHO,"md.flowequation.isMLHO"); + iomodel->FindConstant(&isMOLHO,"md.flowequation.isMOLHO"); iomodel->FindConstant(&isHO,"md.flowequation.isHO"); iomodel->FindConstant(&isFS,"md.flowequation.isFS"); /*Now, check that we have non SIA elements */ - if(!isSSA && !isL1L2 && !isMLHO && !isHO && !isFS) return; + if(!isSSA && !isL1L2 && !isMOLHO && !isHO && !isFS) return; /*Do we have coupling*/ - if( (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) + if( (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMOLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) iscoupling = true; else @@ -553,6 +553,6 @@ finiteelement = P1Enum; } - else if(isMLHO){ - approximation = MLHOApproximationEnum; + else if(isMOLHO){ + approximation = MOLHOApproximationEnum; finiteelement = P1Enum; } @@ -630,5 +630,5 @@ break; case L1L2ApproximationEnum: numdofs = 2; break; - case MLHOApproximationEnum: numdofs = 4; break; + case MOLHOApproximationEnum: numdofs = 4; break; case HOApproximationEnum: switch(domaintype){ @@ -695,5 +695,5 @@ int FrictionCoupling; int* finiteelement_list=NULL; - bool isSSA,isL1L2,isMLHO,isHO,isFS,iscoupling; + bool isSSA,isL1L2,isMOLHO,isHO,isFS,iscoupling; bool control_analysis; bool dakota_analysis; @@ -703,5 +703,5 @@ iomodel->FindConstant(&isSSA,"md.flowequation.isSSA"); iomodel->FindConstant(&isL1L2,"md.flowequation.isL1L2"); - iomodel->FindConstant(&isMLHO,"md.flowequation.isMLHO"); + iomodel->FindConstant(&isMOLHO,"md.flowequation.isMOLHO"); iomodel->FindConstant(&isHO,"md.flowequation.isHO"); iomodel->FindConstant(&isFS,"md.flowequation.isFS"); @@ -713,5 +713,5 @@ /*return if no processing required*/ - if(!isSSA && !isL1L2 && !isMLHO && !isHO && !isFS) return; + if(!isSSA && !isL1L2 && !isMOLHO && !isHO && !isFS) return; /*Fetch data needed and allocate vectors: */ @@ -720,5 +720,5 @@ /*Do we have coupling*/ - if( (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) + if( (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMOLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) iscoupling = true; else @@ -729,5 +729,5 @@ if(isSSA) iomodel->FindConstant(&finiteelement,"md.flowequation.fe_SSA"); else if(isL1L2) finiteelement = P1Enum; - else if(isMLHO) finiteelement = P1Enum; + else if(isMOLHO) finiteelement = P1Enum; else if(isHO) iomodel->FindConstant(&finiteelement,"md.flowequation.fe_HO"); else if(isFS) iomodel->FindConstant(&finiteelement,"md.flowequation.fe_FS"); @@ -781,9 +781,9 @@ iomodel->FetchDataToInput(inputs,elements,"md.initialization.vx",VxEnum,0.); iomodel->FetchDataToInput(inputs,elements,"md.initialization.vy",VyEnum,0.); - /*MLHO*/ - if(isMLHO){ + /*MOLHO*/ + if(isMOLHO){ iomodel->FetchDataToInput(inputs,elements,"md.initialization.vx",VxShearEnum,0.); iomodel->FetchDataToInput(inputs,elements,"md.initialization.vy",VyShearEnum,0.); - /*3D MLHO also need to have VxBase and VyBase for reconstruting Vx and Vy*/ + /*3D MOLHO also need to have VxBase and VyBase for reconstruting Vx and Vy*/ if (iomodel->domaintype==Domain3DEnum) { iomodel->FetchDataToInput(inputs,elements,"md.initialization.vx",VxBaseEnum,0.); @@ -836,7 +836,12 @@ break; case SpatialLinearFloatingMeltRateEnum: - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsSpatialDeepwaterMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_elevation",BasalforcingsSpatialDeepwaterElevationEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_melting_rate",BasalforcingsSpatialUpperwaterMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_elevation",BasalforcingsSpatialUpperwaterElevationEnum); + if(isstochastic){ + iomodel->FetchDataToInput(inputs,elements,"md.stochasticforcing.default_id",StochasticForcingDefaultIdEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum); + } break; case BasalforcingsPicoEnum: @@ -985,5 +990,5 @@ parameters->AddObject(iomodel->CopyConstantObject("md.flowequation.isSSA",FlowequationIsSSAEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.flowequation.isL1L2",FlowequationIsL1L2Enum)); - parameters->AddObject(iomodel->CopyConstantObject("md.flowequation.isMLHO",FlowequationIsMLHOEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.flowequation.isMOLHO",FlowequationIsMOLHOEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.flowequation.isHO",FlowequationIsHOEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.flowequation.isFS",FlowequationIsFSEnum)); @@ -1088,5 +1093,5 @@ /*Intermediaries*/ - bool isSSA,isL1L2,isMLHO,isHO,isFS; + bool isSSA,isL1L2,isMOLHO,isHO,isFS; bool conserve_loads = true; int newton,domaintype,fe_FS; @@ -1095,5 +1100,5 @@ femmodel->parameters->FindParam(&isSSA,FlowequationIsSSAEnum); femmodel->parameters->FindParam(&isL1L2,FlowequationIsL1L2Enum); - femmodel->parameters->FindParam(&isMLHO,FlowequationIsMLHOEnum); + femmodel->parameters->FindParam(&isMOLHO,FlowequationIsMOLHOEnum); femmodel->parameters->FindParam(&isHO,FlowequationIsHOEnum); femmodel->parameters->FindParam(&isFS,FlowequationIsFSEnum); @@ -1102,5 +1107,5 @@ femmodel->parameters->FindParam(&newton,StressbalanceIsnewtonEnum); - if(isFS && !(isSSA || isHO || isL1L2 || isMLHO)){ + if(isFS && !(isSSA || isHO || isL1L2 || isMOLHO)){ femmodel->SetCurrentConfiguration(StressbalanceAnalysisEnum); @@ -1124,5 +1129,5 @@ solutionsequence_nonlinear(femmodel,conserve_loads); } - else if(!isFS && (isSSA || isHO || isL1L2 || isMLHO)){ + else if(!isFS && (isSSA || isHO || isL1L2 || isMOLHO)){ femmodel->SetCurrentConfiguration(StressbalanceAnalysisEnum); if(newton>0) @@ -1138,5 +1143,5 @@ } } - else if ((isSSA || isL1L2 || isMLHO || isHO) && isFS){ + else if ((isSSA || isL1L2 || isMOLHO || isHO) && isFS){ if(VerboseSolution()) _printf0_(" computing coupling between lower order models and FS\n"); solutionsequence_FScoupling_nonlinear(femmodel,conserve_loads); @@ -1190,6 +1195,6 @@ case L1L2ApproximationEnum: return CreateKMatrixL1L2(element); - case MLHOApproximationEnum: - return CreateKMatrixMLHO(element); + case MOLHOApproximationEnum: + return CreateKMatrixMOLHO(element); case HOApproximationEnum: return CreateKMatrixHO(element); @@ -1219,6 +1224,6 @@ case L1L2ApproximationEnum: return CreatePVectorL1L2(element); - case MLHOApproximationEnum: - return CreatePVectorMLHO(element); + case MOLHOApproximationEnum: + return CreatePVectorMOLHO(element); case HOApproximationEnum: return CreatePVectorHO(element); @@ -1248,6 +1253,6 @@ GetSolutionFromInputsHoriz(solution,element); return; - case MLHOApproximationEnum: - GetSolutionFromInputsMLHO(solution,element); + case MOLHOApproximationEnum: + GetSolutionFromInputsMOLHO(solution,element); return; case SSAHOApproximationEnum: case HOFSApproximationEnum: case SSAFSApproximationEnum: @@ -1330,6 +1335,6 @@ InputUpdateFromSolutionL1L2(solution,element); return; - case MLHOApproximationEnum: - InputUpdateFromSolutionMLHO(solution,element); + case MOLHOApproximationEnum: + InputUpdateFromSolutionMOLHO(solution,element); return; case SSAHOApproximationEnum: @@ -2755,6 +2760,6 @@ }/*}}}*/ -/*MLHO*/ -ElementMatrix* StressbalanceAnalysis::CreateKMatrixMLHO(Element* element){/*{{{*/ +/*MOLHO*/ +ElementMatrix* StressbalanceAnalysis::CreateKMatrixMOLHO(Element* element){/*{{{*/ /* Check if ice in element */ @@ -2779,6 +2784,6 @@ /*compute all stiffness matrices for this element*/ - ElementMatrix* Ke1=CreateKMatrixMLHOViscous(basalelement); - ElementMatrix* Ke2=CreateKMatrixMLHOFriction(basalelement); + ElementMatrix* Ke1=CreateKMatrixMOLHOViscous(basalelement); + ElementMatrix* Ke2=CreateKMatrixMOLHOFriction(basalelement); ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2); @@ -2789,5 +2794,5 @@ return Ke; }/*}}}*/ -ElementMatrix* StressbalanceAnalysis::CreateKMatrixMLHOFriction(Element* element){/*{{{*/ +ElementMatrix* StressbalanceAnalysis::CreateKMatrixMOLHOFriction(Element* element){/*{{{*/ if(element->IsAllFloating()) return NULL; @@ -2816,5 +2821,5 @@ /*Initialize Element matrix and vectors*/ - ElementMatrix* Ke = element->NewElementMatrix(MLHOApproximationEnum); + ElementMatrix* Ke = element->NewElementMatrix(MOLHOApproximationEnum); IssmDouble* basis = xNew(numnodes); @@ -2871,5 +2876,5 @@ return Ke; }/*}}}*/ -ElementMatrix* StressbalanceAnalysis::CreateKMatrixMLHOViscous(Element* element){/*{{{*/ +ElementMatrix* StressbalanceAnalysis::CreateKMatrixMOLHOViscous(Element* element){/*{{{*/ /* Check if ice in element */ @@ -2886,5 +2891,5 @@ /*Initialize Element matrix and vectors*/ - ElementMatrix* Ke = element->NewElementMatrix(MLHOApproximationEnum); + ElementMatrix* Ke = element->NewElementMatrix(MOLHOApproximationEnum); IssmDouble* dbasis = xNew(2*numnodes); // like SSA IssmDouble* basis = xNew(numnodes); // like SSA @@ -2910,5 +2915,5 @@ thickness_input->GetInputValue(&thickness, gauss); n_input->GetInputValue(&n,gauss); - element->material->ViscosityMLHO(&viscosity[0],dim,xyz_list,gauss,vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input); + element->material->ViscosityMOLHO(&viscosity[0],dim,xyz_list,gauss,vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input); for(int i=0;iTransformStiffnessMatrixCoord(Ke,XYMLHOEnum); + //basalelement->TransformStiffnessMatrixCoord(Ke,XYMOLHOEnum); /*Clean up and return*/ @@ -2985,5 +2990,5 @@ return Ke; }/*}}}*/ -ElementVector* StressbalanceAnalysis::CreatePVectorMLHO(Element* element){/*{{{*/ +ElementVector* StressbalanceAnalysis::CreatePVectorMOLHO(Element* element){/*{{{*/ /* Check if ice in element */ @@ -3008,6 +3013,6 @@ /*compute all load vectors for this element*/ - ElementVector* pe1=CreatePVectorMLHODrivingStress(basalelement); - ElementVector* pe2=CreatePVectorMLHOFront(basalelement); + ElementVector* pe1=CreatePVectorMOLHODrivingStress(basalelement); + ElementVector* pe2=CreatePVectorMOLHOFront(basalelement); ElementVector* pe =new ElementVector(pe1,pe2); @@ -3018,5 +3023,5 @@ return pe; }/*}}}*/ -ElementVector* StressbalanceAnalysis::CreatePVectorMLHODrivingStress(Element* element){/*{{{*/ +ElementVector* StressbalanceAnalysis::CreatePVectorMOLHODrivingStress(Element* element){/*{{{*/ /*Intermediaries */ @@ -3028,5 +3033,5 @@ /*Initialize Element vector and vectors*/ - ElementVector* pe = element->NewElementVector(MLHOApproximationEnum); + ElementVector* pe = element->NewElementVector(MOLHOApproximationEnum); IssmDouble* basis = xNew(numnodes); @@ -3057,5 +3062,5 @@ /*Transform coordinate system*/ - //element->TransformLoadVectorCoord(pe,XYMLHOEnum); + //element->TransformLoadVectorCoord(pe,XYMOLHOEnum); /*Clean up and return*/ @@ -3065,5 +3070,5 @@ return pe; }/*}}}*/ -ElementVector* StressbalanceAnalysis::CreatePVectorMLHOFront(Element* element){/*{{{*/ +ElementVector* StressbalanceAnalysis::CreatePVectorMOLHOFront(Element* element){/*{{{*/ /*If no front, return NULL*/ @@ -3081,5 +3086,5 @@ /*Initialize Element vector and other vectors*/ - ElementVector* pe = element->NewElementVector(MLHOApproximationEnum); + ElementVector* pe = element->NewElementVector(MOLHOApproximationEnum); IssmDouble* basis = xNew(numnodes); @@ -3130,5 +3135,5 @@ /*Transform coordinate system*/ - //element->TransformLoadVectorCoord(pe,XYMLHOEnum); + //element->TransformLoadVectorCoord(pe,XYMOLHOEnum); /*Clean up and return*/ @@ -3139,5 +3144,5 @@ return pe; }/*}}}*/ -void StressbalanceAnalysis::InputUpdateFromSolutionMLHO(IssmDouble* solution,Element* element){/*{{{*/ +void StressbalanceAnalysis::InputUpdateFromSolutionMOLHO(IssmDouble* solution,Element* element){/*{{{*/ int i,dim,domaintype; @@ -3192,5 +3197,5 @@ /*Fetch dof list and allocate solution vectors*/ - basalelement->GetDofListLocal(&doflist,MLHOApproximationEnum,GsetEnum); + basalelement->GetDofListLocal(&doflist,MOLHOApproximationEnum,GsetEnum); IssmDouble* values = xNew(numdof); IssmDouble* vbx = xNew(numnodes); @@ -3215,5 +3220,5 @@ /*Ok, we have vx and vy in values, fill in vx and vy arrays: */ - for(i=0;iGetInputListOnNodes(&H[0],ThicknessEnum,0.); basalelement->GetInputListOnNodes(&s[0],SurfaceEnum,0.); - element->Recover3DMLHOInput(VxEnum, numnodes, vbx, vshx, n, H, s); - element->Recover3DMLHOInput(VyEnum, numnodes, vby, vshy, n, H, s); + element->Recover3DMOLHOInput(VxEnum, numnodes, vbx, vshx, n, H, s); + element->Recover3DMOLHOInput(VyEnum, numnodes, vby, vshy, n, H, s); break; default: _error_("mesh "<IsSpawnedElement()){basalelement->DeleteMaterials(); delete basalelement;}; }/*}}}*/ -void StressbalanceAnalysis::GetSolutionFromInputsMLHO(Vector* solution,Element* element){/*{{{*/ +void StressbalanceAnalysis::GetSolutionFromInputsMOLHO(Vector* solution,Element* element){/*{{{*/ IssmDouble vbx,vby,vshx,vshy; @@ -3308,5 +3313,5 @@ int numdof = numnodes*dofpernode; element->GetInputValue(&approximation,ApproximationEnum); - if(approximation!=MLHOApproximationEnum) _error_("mesh "<* solution,Element* element); + /*MOLHO*/ + ElementMatrix* CreateKMatrixMOLHO(Element* element); + ElementMatrix* CreateKMatrixMOLHOFriction(Element* element); + ElementMatrix* CreateKMatrixMOLHOViscous(Element* element); + ElementVector* CreatePVectorMOLHO(Element* element); + ElementVector* CreatePVectorMOLHOFront(Element* element); + ElementVector* CreatePVectorMOLHODrivingStress(Element* element); + void InputUpdateFromSolutionMOLHO(IssmDouble* solution,Element* element); + void GetSolutionFromInputsMOLHO(Vector* solution,Element* element); /*HO*/ ElementMatrix* CreateJacobianMatrixHO(Element* element); Index: /issm/trunk/src/c/analyses/StressbalanceSIAAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/StressbalanceSIAAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/StressbalanceSIAAnalysis.cpp (revision 27035) @@ -10,5 +10,5 @@ /*Intermediaries*/ - bool isSIA,isSSA,isL1L2,isMLHO,isHO,isFS,iscoupling; + bool isSIA,isSSA,isL1L2,isMOLHO,isHO,isFS,iscoupling; /*Fetch parameters: */ @@ -16,5 +16,5 @@ iomodel->FindConstant(&isSSA,"md.flowequation.isSSA"); iomodel->FindConstant(&isL1L2,"md.flowequation.isL1L2"); - iomodel->FindConstant(&isMLHO,"md.flowequation.isMLHO"); + iomodel->FindConstant(&isMOLHO,"md.flowequation.isMOLHO"); iomodel->FindConstant(&isHO,"md.flowequation.isHO"); iomodel->FindConstant(&isFS,"md.flowequation.isFS"); @@ -24,5 +24,5 @@ /*Do we have coupling*/ - if((isSIA?1.:0.) + (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) + if((isSIA?1.:0.) + (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMOLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) iscoupling = true; else Index: /issm/trunk/src/c/analyses/StressbalanceVerticalAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 27034) +++ /issm/trunk/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 27035) @@ -12,5 +12,5 @@ /*Intermediary*/ - bool isSIA,isSSA,isL1L2,isMLHO,isHO,isFS,iscoupling; + bool isSIA,isSSA,isL1L2,isMOLHO,isHO,isFS,iscoupling; int Mz,Nz; IssmDouble *spcvz = NULL; @@ -23,10 +23,10 @@ iomodel->FindConstant(&isSSA,"md.flowequation.isSSA"); iomodel->FindConstant(&isL1L2,"md.flowequation.isL1L2"); - iomodel->FindConstant(&isMLHO,"md.flowequation.isMLHO"); + iomodel->FindConstant(&isMOLHO,"md.flowequation.isMOLHO"); iomodel->FindConstant(&isHO,"md.flowequation.isHO"); iomodel->FindConstant(&isFS,"md.flowequation.isFS"); /*Do we have coupling*/ - if((isSIA?1.:0.) + (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) + if((isSIA?1.:0.) + (isSSA?1.:0.) + (isL1L2?1.:0.) + (isMOLHO?1.:0.) + (isHO?1.:0.) + (isFS?1.:0.) >1.) iscoupling = true; else @@ -139,7 +139,12 @@ break; case SpatialLinearFloatingMeltRateEnum: - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); - iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsSpatialDeepwaterMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_elevation",BasalforcingsSpatialDeepwaterElevationEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_melting_rate",BasalforcingsSpatialUpperwaterMeltingRateEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.upperwater_elevation",BasalforcingsSpatialUpperwaterElevationEnum); + if(isstochastic){ + iomodel->FetchDataToInput(inputs,elements,"md.stochasticforcing.default_id",StochasticForcingDefaultIdEnum); + iomodel->FetchDataToInput(inputs,elements,"md.basalforcings.deepwater_melting_rate",BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum); + } break; case BasalforcingsPicoEnum: Index: /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.cpp (revision 27035) @@ -30,5 +30,4 @@ this->name = NULL; this->weights_enum = UNDEF; - this->misfit=0; this->timepassedflag = false; } @@ -43,11 +42,8 @@ this->weights_enum=in_weights_enum; this->timepassedflag=in_timepassedflag; - - this->misfit=0; } /*}}}*/ Cfdragcoeffabsgrad::~Cfdragcoeffabsgrad(){/*{{{*/ if(this->name)xDelete(this->name); - this->misfit=0; } /*}}}*/ @@ -55,5 +51,4 @@ Object* Cfdragcoeffabsgrad::copy() {/*{{{*/ Cfdragcoeffabsgrad* mf = new Cfdragcoeffabsgrad(this->name,this->definitionenum, this->weights_enum,this->timepassedflag); - mf->misfit=this->misfit; return (Object*) mf; } @@ -115,5 +110,5 @@ int domaintype,numcomponents; IssmDouble Jelem=0.; - IssmDouble misfit,Jdet; + IssmDouble Jdet; IssmDouble dp[2],weight; IssmDouble* xyz_list = NULL; Index: /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.h =================================================================== --- /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.h (revision 27034) +++ /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.h (revision 27035) @@ -11,5 +11,4 @@ IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); -void GetVectorFromInputsx( IssmDouble** pvector, int* pvector_size, FemModel* femmodel,int name); class Cfdragcoeffabsgrad: public Object, public Definition{ @@ -21,6 +20,4 @@ int weights_enum; bool timepassedflag; - - IssmDouble misfit; //value carried over in time. /*Cfdragcoeffabsgrad constructors, destructors :*/ Index: /issm/trunk/src/c/classes/Cflevelsetmisfit.cpp =================================================================== --- /issm/trunk/src/c/classes/Cflevelsetmisfit.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Cflevelsetmisfit.cpp (revision 27035) @@ -32,5 +32,4 @@ this->observation_enum = UNDEF; this->weights_enum = UNDEF; - this->misfit=0; this->datatime=0.; this->timepassedflag = false; @@ -49,11 +48,8 @@ this->datatime=in_datatime; this->timepassedflag=in_timepassedflag; - - this->misfit=0; } /*}}}*/ Cflevelsetmisfit::~Cflevelsetmisfit(){/*{{{*/ if(this->name)xDelete(this->name); - this->misfit=0; } /*}}}*/ @@ -61,5 +57,4 @@ Object* Cflevelsetmisfit::copy() {/*{{{*/ Cflevelsetmisfit* mf = new Cflevelsetmisfit(this->name,this->definitionenum, this->model_enum,this->observation_enum,this->weights_enum,this->datatime,this->timepassedflag); - mf->misfit=this->misfit; return (Object*) mf; } @@ -95,5 +90,4 @@ marshallhandle->call(this->datatime); marshallhandle->call(this->timepassedflag); - marshallhandle->call(this->misfit); } /*}}}*/ Index: /issm/trunk/src/c/classes/Cflevelsetmisfit.h =================================================================== --- /issm/trunk/src/c/classes/Cflevelsetmisfit.h (revision 27034) +++ /issm/trunk/src/c/classes/Cflevelsetmisfit.h (revision 27035) @@ -11,5 +11,4 @@ IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); -void GetVectorFromInputsx( IssmDouble** pvector, int* pvector_size, FemModel* femmodel,int name); class Cflevelsetmisfit: public Object, public Definition{ @@ -24,6 +23,4 @@ IssmDouble datatime; bool timepassedflag; - - IssmDouble misfit; //value carried over in time. /*Cflevelsetmisfit constructors, destructors :*/ Index: /issm/trunk/src/c/classes/Cfsurfacelogvel.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacelogvel.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Cfsurfacelogvel.cpp (revision 27035) @@ -29,5 +29,4 @@ this->definitionenum = -1; this->name = NULL; - this->misfit=0; this->datatime=0.; this->timepassedflag = false; @@ -45,10 +44,8 @@ this->timepassedflag=in_timepassedflag; - this->misfit=0; } /*}}}*/ Cfsurfacelogvel::~Cfsurfacelogvel(){/*{{{*/ if(this->name)xDelete(this->name); - this->misfit=0; } /*}}}*/ @@ -56,5 +53,4 @@ Object* Cfsurfacelogvel::copy() {/*{{{*/ Cfsurfacelogvel* mf = new Cfsurfacelogvel(this->name,this->definitionenum,this->datatime,this->timepassedflag); - mf->misfit=this->misfit; return (Object*) mf; } @@ -75,5 +71,11 @@ /*}}}*/ void Cfsurfacelogvel::Marshall(MarshallHandle* marshallhandle){/*{{{*/ - _error_("not implemented yet!"); + int object_enum=CfsurfacelogvelEnum; + marshallhandle->call(object_enum); + + marshallhandle->call(this->definitionenum); + marshallhandle->call(this->name); + marshallhandle->call(this->datatime); + marshallhandle->call(this->timepassedflag); } /*}}}*/ @@ -100,7 +102,9 @@ femmodel->parameters->FindParam(&time,TimeEnum); - IssmDouble J=0.; - IssmDouble J_sum=0.; - if(this->datatime<=time && !timepassedflag){ + if(this->datatime<=time && !this->timepassedflag){ + + IssmDouble J=0.; + IssmDouble J_sum=0.; + for(Object* & object : femmodel->elements->objects){ Element* element=xDynamicCast(object); @@ -113,6 +117,9 @@ this->timepassedflag = true; - } - return J; + return J_sum; + } + else{ + return 0.; + } }/*}}}*/ IssmDouble Cfsurfacelogvel::Cfsurfacelogvel_Calculation(Element* element, int definitionenum){/*{{{*/ Index: /issm/trunk/src/c/classes/Cfsurfacelogvel.h =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacelogvel.h (revision 27034) +++ /issm/trunk/src/c/classes/Cfsurfacelogvel.h (revision 27035) @@ -11,5 +11,4 @@ IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); -void GetVectorFromInputsx( IssmDouble** pvector, int* pvector_size, FemModel* femmodel,int name); class Cfsurfacelogvel: public Object, public Definition{ @@ -21,6 +20,4 @@ IssmDouble datatime; bool timepassedflag; - - IssmDouble misfit; //value carried over in time. /*Cfsurfacelogvel constructors, destructors :*/ Index: /issm/trunk/src/c/classes/Cfsurfacesquare.cpp =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacesquare.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Cfsurfacesquare.cpp (revision 27035) @@ -6,5 +6,5 @@ /*{{{*/ #ifdef HAVE_CONFIG_H - #include +#include #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" @@ -27,12 +27,11 @@ Cfsurfacesquare::Cfsurfacesquare(){/*{{{*/ - this->definitionenum = -1; - this->name = NULL; - this->model_enum = UNDEF; + this->definitionenum = -1; + this->name = NULL; + this->model_enum = UNDEF; this->observation_enum = UNDEF; - this->weights_enum = UNDEF; - this->misfit=0; - this->datatime=0.; - this->timepassedflag = false; + this->weights_enum = UNDEF; + this->datatime = 0.; + this->timepassedflag = false; } /*}}}*/ @@ -49,17 +48,14 @@ this->datatime=in_datatime; this->timepassedflag=in_timepassedflag; - - this->misfit=0; } /*}}}*/ Cfsurfacesquare::~Cfsurfacesquare(){/*{{{*/ if(this->name)xDelete(this->name); - this->misfit=0; -} -/*}}}*/ +} +/*}}}*/ + /*Object virtual function resolutoin: */ Object* Cfsurfacesquare::copy() {/*{{{*/ Cfsurfacesquare* mf = new Cfsurfacesquare(this->name,this->definitionenum, this->model_enum,this->observation_enum,this->weights_enum,this->datatime,this->timepassedflag); - mf->misfit=this->misfit; return (Object*) mf; } @@ -95,5 +91,4 @@ marshallhandle->call(this->datatime); marshallhandle->call(this->timepassedflag); - marshallhandle->call(this->misfit); } /*}}}*/ @@ -102,4 +97,5 @@ } /*}}}*/ + /*Definition virtual function resolutoin: */ int Cfsurfacesquare::DefinitionEnum(){/*{{{*/ @@ -115,29 +111,31 @@ /*}}}*/ IssmDouble Cfsurfacesquare::Response(FemModel* femmodel){/*{{{*/ - /*diverse: */ - IssmDouble time; - - /*recover time parameters: */ - femmodel->parameters->FindParam(&time,TimeEnum); - - IssmDouble J=0.; - IssmDouble J_sum=0.; - - if(datatime<=time && !timepassedflag){ - for(Object* & object : femmodel->elements->objects){ - Element* element=xDynamicCast(object); - J+=this->Cfsurfacesquare_Calculation(element,model_enum,observation_enum,weights_enum); - } - - ISSM_MPI_Allreduce ( (void*)&J,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); - ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); - J=J_sum; - - timepassedflag = true; - return J; - } - else return J; - } - /*}}}*/ + + /*recover time parameters: */ + IssmDouble time; + femmodel->parameters->FindParam(&time,TimeEnum); + + /*Do the calculation only if this is the first time we are passed datatime*/ + if(this->datatime<=time && !this->timepassedflag){ + + IssmDouble J=0.; + IssmDouble J_sum=0.; + + for(Object* & object : femmodel->elements->objects){ + Element* element=xDynamicCast(object); + J+=this->Cfsurfacesquare_Calculation(element,model_enum,observation_enum,weights_enum); + } + + ISSM_MPI_Allreduce ( (void*)&J,(void*)&J_sum,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + ISSM_MPI_Bcast(&J_sum,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + + this->timepassedflag = true; + return J_sum; + } + else{ + return 0.; + } +} +/*}}}*/ IssmDouble Cfsurfacesquare::Cfsurfacesquare_Calculation(Element* element, int model_enum, int observation_enum, int weights_enum){/*{{{*/ Index: /issm/trunk/src/c/classes/Cfsurfacesquare.h =================================================================== --- /issm/trunk/src/c/classes/Cfsurfacesquare.h (revision 27034) +++ /issm/trunk/src/c/classes/Cfsurfacesquare.h (revision 27035) @@ -11,5 +11,4 @@ IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); -void GetVectorFromInputsx( IssmDouble** pvector, int* pvector_size, FemModel* femmodel,int name); class Cfsurfacesquare: public Object, public Definition{ @@ -25,6 +24,4 @@ IssmDouble datatime; bool timepassedflag; - - IssmDouble misfit; //value carried over in time. /*Cfsurfacesquare constructors, destructors :*/ Index: /issm/trunk/src/c/classes/Elements/Element.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Element.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Elements/Element.cpp (revision 27035) @@ -69,6 +69,7 @@ /*Get Basin ID and Basin coefficients*/ - if(enum_type==SMBautoregressionEnum) this->GetInputValue(&basinid,SmbBasinsIdEnum); - if(enum_type==FrontalForcingsRignotAutoregressionEnum) this->GetInputValue(&basinid,FrontalForcingsBasinIdEnum); + if(enum_type==SMBautoregressionEnum) this->GetInputValue(&basinid,SmbBasinsIdEnum); + if(enum_type==FrontalForcingsRignotAutoregressionEnum) this->GetInputValue(&basinid,FrontalForcingsBasinIdEnum); + if(enum_type==BasalforcingsDeepwaterMeltingRateAutoregressionEnum) this->GetInputValue(&basinid,BasalforcingsLinearBasinIdEnum); for(int i=0;i(oldvarspin); } - if(enum_type==SMBautoregressionEnum) this->inputs->SetArrayInput(SmbValuesAutoregressionEnum,this->lid,varspin,numvertices*arorder); - if(enum_type==FrontalForcingsRignotAutoregressionEnum) this->inputs->SetArrayInput(ThermalforcingValuesAutoregressionEnum,this->lid,varspin,numvertices*arorder); + if(enum_type==SMBautoregressionEnum) this->inputs->SetArrayInput(SmbValuesAutoregressionEnum,this->lid,varspin,numvertices*arorder); + if(enum_type==FrontalForcingsRignotAutoregressionEnum) this->inputs->SetArrayInput(ThermalforcingValuesAutoregressionEnum,this->lid,varspin,numvertices*arorder); + if(enum_type==BasalforcingsDeepwaterMeltingRateAutoregressionEnum) this->inputs->SetArrayInput(BasalforcingsDeepwaterMeltingRateValuesAutoregressionEnum,this->lid,varspin,numvertices*arorder); /*Cleanup and return*/ @@ -123,4 +125,10 @@ outenum_type = FrontalForcingsThermalForcingEnum; break; + case(BasalforcingsDeepwaterMeltingRateAutoregressionEnum): + arenum_type = BasalforcingsDeepwaterMeltingRateValuesAutoregressionEnum; + basinenum_type = BasalforcingsLinearBasinIdEnum; + noiseenum_type = BasalforcingsDeepwaterMeltingRateNoiseEnum; + outenum_type = BasalforcingsSpatialDeepwaterMeltingRateEnum; + break; } @@ -172,4 +180,108 @@ xDelete(varlist); xDelete(valuesautoregression); +}/*}}}*/ +void Element::BasinLinearFloatingiceMeltingRate(IssmDouble* deepwaterel,IssmDouble* upperwatermelt,IssmDouble* upperwaterel,IssmDouble* perturbation){/*{{{*/ + + const int NUM_VERTICES = this->GetNumberOfVertices(); + + int basinid; + IssmDouble alpha; + IssmDouble base[MAXVERTICES]; + IssmDouble values[MAXVERTICES]; + IssmDouble deepwatermelt[MAXVERTICES]; + + /*Get element-specific values*/ + this->GetInputValue(&basinid,BasalforcingsLinearBasinIdEnum); + this->GetInputListOnVertices(&base[0],BaseEnum); + this->GetInputListOnVertices(&deepwatermelt[0],BasalforcingsSpatialDeepwaterMeltingRateEnum); + + /*Compute melt rate at vertices according to basin-specific values of input arguments*/ + for(int i=0;i=upperwaterel[basinid]){ + values[i]=upperwatermelt[basinid]; + } + else if (base[i]AddInput(BasalforcingsFloatingiceMeltingRateEnum,&values[0],P1Enum); +}/*}}}*/ +void Element::CalvingFromRate(){/*{{{*/ + + /*We are provided a calving rate, figure out the x/y components*/ + int dim,domaintype; + IssmDouble vx,vy,vel,dphidx,dphidy,dphi,c; + IssmDouble calvingratex[MAXVERTICES]; + IssmDouble calvingratey[MAXVERTICES]; + + /*Get problem dimension and whether there is moving front or not*/ + this->FindParam(&domaintype,DomainTypeEnum); + + switch(domaintype){ + case Domain2DverticalEnum: dim = 1; break; + case Domain2DhorizontalEnum: dim = 2; break; + case Domain3DEnum: dim = 2; break; + default: _error_("mesh "<GetInput(CalvingCalvingrateEnum); _assert_(calvingrate_input); + Input *vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input *vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input *lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); + Input *lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); + + /*Allocate arrays*/ + const int NUM_VERTICES = this->GetNumberOfVertices(); + + /* Start looping on the number of vertices: */ + Gauss* gauss=this->NewGauss(); + for (int iv=0;ivGaussVertex(iv); + + calvingrate_input->GetInputValue(&c,gauss); + vx_input->GetInputValue(&vx,gauss); + vy_input->GetInputValue(&vy,gauss); + lsf_slopex_input->GetInputValue(&dphidx,gauss); + lsf_slopey_input->GetInputValue(&dphidy,gauss); + + vel=sqrt(vx*vx + vy*vy) + 1e-14; + dphi=sqrt(dphidx*dphidx+dphidy*dphidy)+ 1e-14; + + if(false){ + /*Velocity direction*/ + calvingratex[iv] = c*vx/vel; + calvingratey[iv] = c*vy/vel; + } + else{ + /*Lelvelset gradient (perpendicular to ice front)*/ + calvingratex[iv] = c*dphidx/dphi; + calvingratey[iv] = c*dphidy/dphi; + } + } + + + /*Add to inputs*/ + this->AddInput(CalvingratexEnum,&calvingratex[0],P1DGEnum); + this->AddInput(CalvingrateyEnum,&calvingratey[0],P1DGEnum); + //this->AddInput(CalvingCalvingrateEnum,&calvingrate[0],P1DGEnum); /*Do not change calving rate, that's our input!*/ + + /*Clean up and return*/ + delete gauss; +}/*}}}*/ +void Element::CalvingSetZeroRate(){/*{{{*/ + + /*Set calving rate as 0, this is probably because we are dealing with discrete calving laws*/ + IssmDouble calvingratex[MAXVERTICES] = {0.}; + IssmDouble calvingratey[MAXVERTICES] = {0.}; + IssmDouble calvingrate[MAXVERTICES] = {0.}; + this->AddInput(CalvingratexEnum,&calvingratex[0],P1DGEnum); + this->AddInput(CalvingrateyEnum,&calvingratey[0],P1DGEnum); + this->AddInput(CalvingCalvingrateEnum,&calvingrate[0],P1DGEnum); }/*}}}*/ void Element::ComputeLambdaS(){/*{{{*/ @@ -929,5 +1041,5 @@ } /*}}}*/ -void Element::dViscositydBMLHO(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vxbase_input,Input* vybase_input, Input* vxshear_input ,Input* vyshear_input,Input* thickness_input,Input* n_input, IssmDouble zeta){/*{{{*/ +void Element::dViscositydBMOLHO(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vxbase_input,Input* vybase_input, Input* vxshear_input ,Input* vyshear_input,Input* thickness_input,Input* n_input, IssmDouble zeta){/*{{{*/ /*Intermediaries*/ @@ -939,5 +1051,5 @@ /* eps_eff^2 = exx^2 + eyy^2 + exy^2 + exz^2 + eyz^2 + exx*eyy */ - this->StrainRateMLHO(&epsilon[0],xyz_list,gauss, + this->StrainRateMOLHO(&epsilon[0],xyz_list,gauss, vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input,zeta); eps_eff=sqrt(epsilon[0]*epsilon[0] + epsilon[1]*epsilon[1] + epsilon[2]*epsilon[2] @@ -2158,4 +2270,14 @@ return shelf; }/*}}}*/ +bool Element::IsAllGrounded(){/*{{{*/ + + Input* input=this->GetInput(MaskOceanLevelsetEnum); _assert_(input); + if(input->GetInputMin() < 0.){ + return false; + } + else{ + return true; + } +}/*}}}*/ bool Element::IsGrounded(){/*{{{*/ @@ -2257,4 +2379,70 @@ }/*}}}*/ +void Element::LapseRateBasinSMB(int numelevbins, IssmDouble* lapserates, IssmDouble* elevbins,IssmDouble* refelevation){/*{{{*/ + + /*Variable declaration*/ + const int numvertices = this->GetNumberOfVertices(); + bool isadjustsmb = false; + int basinid,bb1,bb2; + IssmDouble ela,refelevation_b; + IssmDouble* surfacelist = xNew(numvertices); + IssmDouble* smblist = xNew(numvertices); + /* numelevbins values of lapse rates */ + IssmDouble* lapserates_b = xNew(numelevbins); + /* (numelevbins-1) limits between elevation bins (be cautious with indexing) */ + IssmDouble* elevbins_b = xNew(numelevbins-1); + + /*Retrieve SMB values non-adjusted for SMB lapse rate*/ + this->GetInputListOnVertices(smblist,SmbMassBalanceEnum); + /*Get surface elevation on vertices*/ + this->GetInputListOnVertices(surfacelist,SurfaceEnum); + /*Get basin-specific parameters of the element*/ + this->GetInputValue(&basinid,SmbBasinsIdEnum); + refelevation_b = refelevation[basinid]; + for(int ii=0;ii<(numelevbins-1);ii++) elevbins_b[ii] = elevbins[basinid*(numelevbins-1)+ii]; + for(int ii=0;iielevbins_b[numelevbins-1-1]) bb1 = numelevbins-1; + if(refelevation_b>elevbins_b[numelevbins-1-1]) bb2 = numelevbins-1; + /*Vertex and Reference elevation in same elevation bin*/ + if(bb1==bb2){ + smblist[v] = smblist[v]+(surfacelist[v]-refelevation_b)*lapserates_b[bb2]; + } + /*Vertex in lower elevation bin than Reference elevation*/ + if(bb1bb1;ii--) smblist[v] = smblist[v]+(elevbins_b[ii-1]-elevbins_b[ii])*lapserates_b[ii]; + smblist[v] = smblist[v]+(surfacelist[v]-elevbins_b[bb1])*lapserates_b[bb1]; + } + /*Vertex in higher elevation bin than Reference elevation*/ + if(bb1>bb2){ + smblist[v] = smblist[v]+(elevbins_b[bb2]-refelevation_b)*lapserates_b[bb2]; + for(int ii=bb2+1;iiAddInput(SmbMassBalanceEnum,smblist,P1Enum); + + /*Cleanup*/ + xDelete(lapserates_b); + xDelete(elevbins_b); + xDelete(surfacelist); + xDelete(smblist); +}/*}}}*/ void Element::LinearFloatingiceMeltingRate(){/*{{{*/ @@ -2264,5 +2452,4 @@ IssmDouble base[MAXVERTICES]; IssmDouble values[MAXVERTICES]; - IssmDouble perturbation[MAXVERTICES]; IssmDouble time; @@ -2275,5 +2462,4 @@ this->GetInputListOnVertices(&base[0],BaseEnum); - this->GetInputListOnVertices(&perturbation[0],BasalforcingsPerturbationMeltingRateEnum); for(int i=0;i=upperwaterel){ @@ -2287,6 +2473,4 @@ values[i]=deepwatermelt*alpha+(1.-alpha)*upperwatermelt; } - - values[i]+=perturbation[i]; } @@ -2298,19 +2482,32 @@ const int NUM_VERTICES = this->GetNumberOfVertices(); + IssmDouble alpha; IssmDouble deepwatermelt[MAXVERTICES]; - IssmDouble deepwaterel[MAXVERTICES];; + IssmDouble deepwaterel[MAXVERTICES]; + IssmDouble upperwatermelt[MAXVERTICES]; IssmDouble upperwaterel[MAXVERTICES]; + IssmDouble perturbation[MAXVERTICES]; IssmDouble base[MAXVERTICES]; IssmDouble values[MAXVERTICES]; this->GetInputListOnVertices(&base[0],BaseEnum); - this->GetInputListOnVertices(&deepwatermelt[0],BasalforcingsDeepwaterMeltingRateEnum); - this->GetInputListOnVertices(&deepwaterel[0],BasalforcingsDeepwaterElevationEnum); - this->GetInputListOnVertices(&upperwaterel[0],BasalforcingsUpperwaterElevationEnum); + this->GetInputListOnVertices(&deepwatermelt[0],BasalforcingsSpatialDeepwaterMeltingRateEnum); + this->GetInputListOnVertices(&deepwaterel[0],BasalforcingsSpatialDeepwaterElevationEnum); + this->GetInputListOnVertices(&upperwatermelt[0],BasalforcingsSpatialUpperwaterMeltingRateEnum); + this->GetInputListOnVertices(&upperwaterel[0],BasalforcingsSpatialUpperwaterElevationEnum); + this->GetInputListOnVertices(&perturbation[0],BasalforcingsPerturbationMeltingRateEnum); for(int i=0;iupperwaterel[i]) values[i]=0; - else if (base[i]=upperwaterel[i]){ + values[i]=upperwatermelt[i]; + } + else if (base[i]element_values[3] = yearlytemperatures[3]; temp_input->element_values[4] = yearlytemperatures[4]; @@ -3074,4 +3272,5 @@ case P1xP3Enum: case P1xP4Enum: + case P1DGEnum: ThermalToEnthalpy(&enth_input->element_values[3],yearlytemperatures[3],0.,0.); ThermalToEnthalpy(&enth_input->element_values[4],yearlytemperatures[4],0.,0.); @@ -3355,4 +3554,10 @@ this->CalvingCrevasseDepth(); break; + case CalvingParameterizationEnum: + this->CalvingRateParameterization(); + break; + case CalvingTestEnum: + this->CalvingRateTest(); + break; default: _error_("Calving law "<StrainRateperpendicular(); break; case SurfaceCrevasseEnum: this->CalvingCrevasseDepth(); break; - case SigmaVMEnum: this->CalvingRateVonmises(); break; + case SigmaVMEnum: this->ComputeSigmaVM(); break; case PartitioningEnum: this->inputs->SetInput(PartitioningEnum,this->lid,IssmComm::GetRank()); break; } @@ -4414,6 +4619,6 @@ }/*}}}*/ -void Element::StrainRateMLHO(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vxbase_input,Input* vybase_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input,IssmDouble zeta){/*{{{*/ - /*Compute the 2d Blatter/MLHO Strain Rate (5 components) for a given vertical coordinate (zeta): +void Element::StrainRateMOLHO(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vxbase_input,Input* vybase_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input,IssmDouble zeta){/*{{{*/ + /*Compute the 2d Blatter/MOLHO Strain Rate (5 components) for a given vertical coordinate (zeta): * * epsilon=[exx eyy exy exz eyz] Index: /issm/trunk/src/c/classes/Elements/Element.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Element.h (revision 27034) +++ /issm/trunk/src/c/classes/Elements/Element.h (revision 27035) @@ -70,4 +70,7 @@ void AutoregressionInit(int numbasins,int arorder,int nspin,IssmDouble starttime,IssmDouble tstep_ar,IssmDouble tinit_ar,IssmDouble* beta0,IssmDouble* beta1,IssmDouble* phi,int enum_type); void Autoregression(bool isstepforar,int arorder,IssmDouble telapsed_ar,IssmDouble* beta0,IssmDouble* beta1,IssmDouble* phi,bool isfieldstochastic,int enum_type); + void BasinLinearFloatingiceMeltingRate(IssmDouble* deepwaterel,IssmDouble* upperwatermelt,IssmDouble* upperwaterel,IssmDouble* perturbation); + void CalvingSetZeroRate(void); + void CalvingFromRate(void); void ComputeLambdaS(void); void ComputeNewDamage(); @@ -83,5 +86,5 @@ void dViscositydBHO(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); void dViscositydBSSA(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); - void dViscositydBMLHO(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vxbase_input,Input* vybase_input, Input* vxshear_input ,Input* vyshear_input,Input* thickness_input,Input* n_input, IssmDouble zeta); + void dViscositydBMOLHO(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vxbase_input,Input* vybase_input, Input* vxshear_input ,Input* vyshear_input,Input* thickness_input,Input* n_input, IssmDouble zeta); void dViscositydDSSA(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); void Echo(); @@ -144,4 +147,5 @@ bool IsAllFloating(); + bool IsAllGrounded(); bool IsGrounded(); bool IsOnBase(); @@ -153,4 +157,5 @@ bool IsLandInElement(); void Ismip6FloatingiceMeltingRate(); + void LapseRateBasinSMB(int numelevbins, IssmDouble* lapserates, IssmDouble* elevbins,IssmDouble* refelevation); void LinearFloatingiceMeltingRate(); void SpatialLinearFloatingiceMeltingRate(); @@ -185,5 +190,5 @@ void StrainRateHO(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); void StrainRateHO2dvertical(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); - void StrainRateMLHO(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input,IssmDouble zeta); + void StrainRateMOLHO(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input,IssmDouble zeta); void StrainRateSSA(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); void StrainRateSSA1d(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input); @@ -227,5 +232,7 @@ virtual void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part)=0; virtual void BasalNodeIndices(int* pnumindices,int** pindices,int finiteelement){_error_("not implemented yet");}; + virtual void CalvingRateParameterization(void){_error_("not implemented yet");}; virtual void CalvingRateVonmises(void){_error_("not implemented yet");}; + virtual void CalvingRateTest(void){_error_("not implemented yet");}; virtual void CalvingCrevasseDepth(void){_error_("not implemented yet");}; virtual void CalvingRateLevermann(void)=0; @@ -236,4 +243,5 @@ virtual void ComputeDeviatoricStressTensor(void)=0; virtual void ComputeSigmaNN(void)=0; + virtual void ComputeSigmaVM(void){_error_("not implemented yet");}; virtual void ComputeStressTensor(void)=0; virtual void ComputeEsaStrainAndVorticity(void)=0; @@ -343,5 +351,5 @@ virtual void PotentialUngrounding(Vector* potential_sheet_ungrounding)=0; virtual int PressureInterpolation()=0; - virtual void Recover3DMLHOInput(int targetVel_enum, int numnodes, IssmDouble* vb, IssmDouble* vsh, IssmDouble* n, IssmDouble* H, IssmDouble* s){_error_("not implemented yet");}; + virtual void Recover3DMOLHOInput(int targetVel_enum, int numnodes, IssmDouble* vb, IssmDouble* vsh, IssmDouble* n, IssmDouble* H, IssmDouble* s){_error_("not implemented yet");}; virtual void ReduceMatrices(ElementMatrix* Ke,ElementVector* pe)=0; virtual void ResetFSBasalBoundaryCondition()=0; @@ -395,5 +403,4 @@ virtual void SealevelchangeGeometrySubElementKernel(SealevelGeometry* slgeom)=0; - virtual void SealevelchangeMomentOfInertiaCentroid(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom)=0; virtual void SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom)=0; virtual void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae)=0; @@ -404,6 +411,5 @@ virtual void SealevelchangeOceanAverage(GrdLoads* loads, Vector* oceanareas, Vector* subelementoceanareas, IssmDouble* sealevelpercpu, SealevelGeometry* slgeom)=0; virtual void SealevelchangeDeformationConvolution(IssmDouble* sealevelpercpu, GrdLoads* loads, IssmDouble* rotationvector,SealevelGeometry* slgeom)=0; - virtual void SealevelchangeMomentOfInertiaSubElement(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom)=0; - virtual void SealevelchangeUpdateViscousFields()=0; + virtual void SealevelchangeUpdateViscousFields(IssmDouble lincoeff, int newindex, int offset)=0; #endif Index: /issm/trunk/src/c/classes/Elements/Penta.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Penta.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Elements/Penta.cpp (revision 27035) @@ -271,20 +271,12 @@ if(!this->IsOnBase()) return; - - IssmDouble xyz_list[NUMVERTICES][3]; - IssmDouble epsilon[3]; /* epsilon=[exx,eyy,exy];*/ - IssmDouble calvingratex[NUMVERTICES]; - IssmDouble calvingratey[NUMVERTICES]; + this->ComputeSigmaVM(); + IssmDouble calvingrate[NUMVERTICES]; - IssmDouble lambda1,lambda2,ex,ey,vx,vy,vel; - IssmDouble B,sigma_max,sigma_max_floating,sigma_max_grounded,n; - IssmDouble epse_2,groundedice,bed,sealevel; - IssmDouble sigma_vm[NUMVERTICES]; - - /* Get node coordinates and dof list: */ - ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + IssmDouble vx,vy; + IssmDouble sigma_vm,sigma_max,sigma_max_floating,sigma_max_grounded; + IssmDouble groundedice,bed,sealevel; /*Depth average B for stress calculation*/ - this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum); this->InputDepthAverageAtBase(VxEnum,VxAverageEnum); this->InputDepthAverageAtBase(VyEnum,VyAverageEnum); @@ -295,9 +287,8 @@ Input* gr_input = this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); Input* bs_input = this->GetInput(BaseEnum); _assert_(bs_input); - Input* B_input = this->GetInput(MaterialsRheologyBbarEnum); _assert_(B_input); - Input* n_input = this->GetInput(MaterialsRheologyNEnum); _assert_(n_input); Input* smax_fl_input = this->GetInput(CalvingStressThresholdFloatingiceEnum); _assert_(smax_fl_input); Input* smax_gr_input = this->GetInput(CalvingStressThresholdGroundediceEnum); _assert_(smax_gr_input); Input* sl_input = this->GetInput(SealevelEnum); _assert_(sl_input); + Input* sigma_vm_input = this->GetInput(SigmaVMEnum); _assert_(sigma_vm_input); /* Start looping on the number of vertices: */ @@ -307,30 +298,12 @@ /*Get velocity components and thickness*/ - B_input->GetInputValue(&B,&gauss); - n_input->GetInputValue(&n,&gauss); vx_input->GetInputValue(&vx,&gauss); vy_input->GetInputValue(&vy,&gauss); + sigma_vm_input->GetInputValue(&sigma_vm,&gauss); gr_input->GetInputValue(&groundedice,&gauss); bs_input->GetInputValue(&bed,&gauss); smax_fl_input->GetInputValue(&sigma_max_floating,&gauss); smax_gr_input->GetInputValue(&sigma_max_grounded,&gauss); - vel=sqrt(vx*vx+vy*vy)+1.e-14; sl_input->GetInputValue(&sealevel,&gauss); - - /*Compute strain rate and viscosity: */ - this->StrainRateSSA(&epsilon[0],&xyz_list[0][0],&gauss,vx_input,vy_input); - - /*Get Eigen values*/ - Matrix2x2Eigen(&lambda1,&lambda2,&ex,&ey,epsilon[0],epsilon[2],epsilon[1]); - _assert_(!xIsNan(lambda1)); - _assert_(!xIsNan(lambda2)); - - /*Process Eigen values (only account for extension)*/ - lambda1 = max(lambda1,0.); - lambda2 = max(lambda2,0.); - - /*Calculate sigma_vm*/ - epse_2 = 1./2. *(lambda1*lambda1 + lambda2*lambda2); - sigma_vm[iv] = sqrt(3.) * B * pow(epse_2,1./(2.*n)); /*Tensile stress threshold*/ @@ -342,24 +315,19 @@ /*Assign values*/ if(bed>sealevel){ - calvingratex[iv]=0.; - calvingratey[iv]=0.; + calvingrate[iv] = 0.; } else{ - calvingratex[iv]=vx*sigma_vm[iv]/sigma_max; - calvingratey[iv]=vy*sigma_vm[iv]/sigma_max; - } - calvingrate[iv] =sqrt(calvingratex[iv]*calvingratex[iv] + calvingratey[iv]*calvingratey[iv]); + calvingrate[iv] = sqrt(vx*vx+vy*vy)*sigma_vm/sigma_max; + } } /*Add input*/ - this->AddBasalInput(CalvingratexEnum,&calvingratex[0],P1DGEnum); - this->AddBasalInput(CalvingrateyEnum,&calvingratey[0],P1DGEnum); this->AddBasalInput(CalvingCalvingrateEnum,&calvingrate[0],P1DGEnum); - this->AddBasalInput(SigmaVMEnum,&sigma_vm[0],P1DGEnum); - + this->CalvingFromRate(); + + /*Extrude*/ + this->InputExtrude(CalvingCalvingrateEnum,-1); this->InputExtrude(CalvingratexEnum,-1); this->InputExtrude(CalvingrateyEnum,-1); - this->InputExtrude(CalvingCalvingrateEnum,-1); - this->InputExtrude(SigmaVMEnum,-1); } /*}}}*/ @@ -847,4 +815,62 @@ this->AddInput(StressTensoryzEnum,&sigma_yz[0],P1DGEnum); this->AddInput(StressTensorzzEnum,&sigma_zz[0],P1DGEnum); +} +/*}}}*/ +void Penta::ComputeSigmaVM(){/*{{{*/ + + if(!this->IsOnBase()) return; + + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble epsilon[3]; /* epsilon=[exx,eyy,exy];*/ + IssmDouble lambda1,lambda2,ex,ey,vx,vy,vel; + IssmDouble B,n; + IssmDouble sigma_vm[NUMVERTICES]; + + /* Get node coordinates and dof list: */ + ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + + /*Depth average B for stress calculation*/ + this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum); + this->InputDepthAverageAtBase(VxEnum,VxAverageEnum); + this->InputDepthAverageAtBase(VyEnum,VyAverageEnum); + + /*Retrieve all inputs and parameters we will need*/ + Input* vx_input = this->GetInput(VxAverageEnum); _assert_(vx_input); + Input* vy_input = this->GetInput(VyAverageEnum); _assert_(vy_input); + Input* B_input = this->GetInput(MaterialsRheologyBbarEnum); _assert_(B_input); + Input* n_input = this->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + + /* Start looping on the number of vertices: */ + GaussPenta gauss; + for(int iv=0;iv<3;iv++){ + gauss.GaussVertex(iv); + + /*Get velocity components and thickness*/ + B_input->GetInputValue(&B,&gauss); + n_input->GetInputValue(&n,&gauss); + vx_input->GetInputValue(&vx,&gauss); + vy_input->GetInputValue(&vy,&gauss); + vel=sqrt(vx*vx+vy*vy)+1.e-14; + + /*Compute strain rate and viscosity: */ + this->StrainRateSSA(&epsilon[0],&xyz_list[0][0],&gauss,vx_input,vy_input); + + /*Get Eigen values*/ + Matrix2x2Eigen(&lambda1,&lambda2,&ex,&ey,epsilon[0],epsilon[2],epsilon[1]); + _assert_(!xIsNan(lambda1)); + _assert_(!xIsNan(lambda2)); + + /*Process Eigen values (only account for extension)*/ + lambda1 = max(lambda1,0.); + lambda2 = max(lambda2,0.); + + /*Calculate sigma_vm*/ + IssmDouble epse_2 = 1./2. *(lambda1*lambda1 + lambda2*lambda2); + sigma_vm[iv] = sqrt(3.) * B * pow(epse_2,1./(2.*n)); + } + + /*Add input*/ + this->AddBasalInput(SigmaVMEnum,&sigma_vm[0],P1DGEnum); + this->InputExtrude(SigmaVMEnum,-1); } /*}}}*/ @@ -2840,100 +2866,48 @@ } /*}}}*/ -void Penta::MovingFrontalVelocity(void){/*{{{*/ +void Penta::MovingFrontalVelocity(void){/*{{{*/ + if(!this->IsOnBase()) return; - int dim, domaintype, calvinglaw, i; + int domaintype, calvinglaw, i; IssmDouble v[3],w[3],c[3],m[3],dlsf[3]; IssmDouble norm_dlsf, norm_calving, calvingrate, meltingrate, groundedice; IssmDouble migrationmax, calvinghaf, heaviside, haf_eps; - IssmDouble xyz_list[NUMVERTICES][3]; - IssmDouble movingfrontvx[NUMVERTICES]; - IssmDouble movingfrontvy[NUMVERTICES]; - IssmDouble vel; + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble movingfrontvx[NUMVERTICES]; + IssmDouble movingfrontvy[NUMVERTICES]; + IssmDouble vel; + int dim=2; /* Get node coordinates and dof list: */ ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); - - Input* vx_input = NULL; - Input* vy_input = NULL; Input* calvingratex_input = NULL; Input* calvingratey_input = NULL; - Input* lsf_slopex_input = NULL; - Input* lsf_slopey_input = NULL; Input* calvingrate_input = NULL; Input* meltingrate_input = NULL; - Input* gr_input = NULL; + + /*Load levelset function gradients*/ + Input *lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); + Input *lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); + Input *vx_input = this->GetInput(VxAverageEnum); _assert_(vx_input); + Input *vy_input = this->GetInput(VyAverageEnum); _assert_(vy_input); + Input *gr_input = this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); /*Get problem dimension and whether there is moving front or not*/ - this->FindParam(&domaintype,DomainTypeEnum); this->FindParam(&calvinglaw,CalvingLawEnum); - - switch(domaintype){ - case Domain2DverticalEnum: dim = 1; break; - case Domain2DhorizontalEnum: dim = 2; break; - case Domain3DEnum: dim = 2; break; - default: _error_("mesh "<GetInput(VxEnum); _assert_(vx_input); - break; - case Domain2DhorizontalEnum: - vx_input=this->GetInput(VxEnum); _assert_(vx_input); - vy_input=this->GetInput(VyEnum); _assert_(vy_input); - gr_input=this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); - break; - case Domain3DEnum: - vx_input=this->GetInput(VxAverageEnum); _assert_(vx_input); - vy_input=this->GetInput(VyAverageEnum); _assert_(vy_input); - gr_input=this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); - break; - default: _error_("mesh "<GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); - calvingrate_input = this->GetInput(CalvingCalvingrateEnum); _assert_(calvingrate_input); - meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); - break; case CalvingLevermannEnum: - switch(domaintype){ - case Domain2DverticalEnum: - calvingratex_input=this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); - break; - case Domain2DhorizontalEnum: - calvingratex_input=this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); - break; - case Domain3DEnum: - calvingratex_input=this->GetInput(CalvingratexAverageEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyAverageEnum); _assert_(calvingratey_input); - break; - default: _error_("mesh "<GetInput(CalvingratexEnum); _assert_(calvingratex_input); + calvingratey_input=this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); break; case CalvingMinthicknessEnum: - lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); - meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); - break; case CalvingHabEnum: - lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); - meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); - break; case CalvingCrevasseDepthEnum: - lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); break; case CalvingDev2Enum: this->FindParam(&calvinghaf,CalvingHeightAboveFloatationEnum); - lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); calvingrate_input = this->GetInput(CalvingCalvingrateEnum); _assert_(calvingrate_input); meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); @@ -2952,4 +2926,7 @@ vy_input->GetInputValue(&v[1],&gauss); gr_input->GetInputValue(&groundedice,&gauss); + lsf_slopex_input->GetInputValue(&dlsf[0],&gauss); + lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); + norm_dlsf=sqrt(dlsf[0]*dlsf[0] + dlsf[1]*dlsf[1]); /*Get calving speed*/ @@ -2957,43 +2934,18 @@ case DefaultCalvingEnum: case CalvingVonmisesEnum: - lsf_slopex_input->GetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); - calvingrate_input->GetInputValue(&calvingrate,&gauss); - meltingrate_input->GetInputValue(&meltingrate,&gauss); - - if(groundedice<0) meltingrate = 0.; - - norm_dlsf=0.; - for(i=0;i1.e-10) - for(i=0;iGetInputValue(&c[0],&gauss); - if(dim==2) calvingratey_input->GetInputValue(&c[1],&gauss); + calvingratey_input->GetInputValue(&c[1],&gauss); meltingrate_input->GetInputValue(&meltingrate,&gauss); - norm_calving=0.; - for(i=0;iGetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); + case CalvingHabEnum: + case CalvingCrevasseDepthEnum: meltingrate_input->GetInputValue(&meltingrate,&gauss); - - norm_dlsf=0.; - for(i=0;i1.e-10) @@ -3009,52 +2961,6 @@ break; - case CalvingHabEnum: - lsf_slopex_input->GetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); - meltingrate_input->GetInputValue(&meltingrate,&gauss); - - norm_dlsf=0.; - for(i=0;i1.e-10) - for(i=0;iGetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); - meltingrate_input->GetInputValue(&meltingrate,&gauss); - - if(groundedice<0) meltingrate = 0.; - - norm_dlsf=0.; - for(i=0;i1.e-10) - for(i=0;iGetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); calvingrate_input->GetInputValue(&calvingrate,&gauss); meltingrate_input->GetInputValue(&meltingrate,&gauss); @@ -3081,8 +2987,4 @@ } - norm_dlsf=0.; - for(i=0;i1.e-10) for(i=0;iAddInput(MovingFrontalVxEnum,&movingfrontvx[0],P1DGEnum); this->AddInput(MovingFrontalVyEnum,&movingfrontvy[0],P1DGEnum); - this->InputExtrude(MovingFrontalVxEnum,-1); this->InputExtrude(MovingFrontalVyEnum,-1); @@ -3296,5 +3197,5 @@ norm=sqrt(normal[0]*normal[0]+normal[1]*normal[1]+normal[2]*normal[2]); - for(int i=0;i<3;i++) normal[i]=normal[i]/norm; + for(int i=0;i<3;i++) normal[i]=normal[i]/(norm+1e-10); } /*}}}*/ @@ -3381,5 +3282,5 @@ } /*}}}*/ -void Penta::Recover3DMLHOInput(int targetVel_enum, int numnodes, IssmDouble* vb, IssmDouble* vsh, IssmDouble* n, IssmDouble* H, IssmDouble* s){/*{{{*/ +void Penta::Recover3DMOLHOInput(int targetVel_enum, int numnodes, IssmDouble* vb, IssmDouble* vsh, IssmDouble* n, IssmDouble* H, IssmDouble* s){/*{{{*/ /* Recover the velocity acording to v=vb+(1-\zeta^{n+1})vsh, where \zeta=(s-z)/H * The variables vb, vsh, n, H and s are all from the 2D horizontal mesh(Tria), with "numnodes" DOFs Index: /issm/trunk/src/c/classes/Elements/Penta.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Penta.h (revision 27034) +++ /issm/trunk/src/c/classes/Elements/Penta.h (revision 27035) @@ -49,4 +49,5 @@ void AddControlInput(int input_enum,Inputs* inputs,IoModel* iomodel,IssmDouble* values,IssmDouble* values_min,IssmDouble* values_max, int interpolation_enum,int id); void ControlInputExtrude(int enum_type,int start); + void ComputeSigmaVM(void); void DatasetInputExtrude(int enum_type,int start); void DatasetInputCreate(IssmDouble* array,int M,int N,int* individual_enums,int num_inputs,Inputs* inputs,IoModel* iomodel,int input_enum); @@ -169,5 +170,5 @@ void PotentialUngrounding(Vector* potential_sheet_ungrounding); int PressureInterpolation(); - void Recover3DMLHOInput(int targetVel_enum, int numnodes, IssmDouble* vb, IssmDouble* vsh, IssmDouble* n, IssmDouble* H, IssmDouble* s); + void Recover3DMOLHOInput(int targetVel_enum, int numnodes, IssmDouble* vb, IssmDouble* vsh, IssmDouble* n, IssmDouble* H, IssmDouble* s); void ReduceMatrices(ElementMatrix* Ke,ElementVector* pe); void ResetFSBasalBoundaryCondition(void); @@ -225,5 +226,4 @@ void GiaDeflection(Vector* wg,Vector* dwgdt,Matlitho* litho, IssmDouble* x,IssmDouble* y){_error_("not implemented yet");}; void SealevelchangeGeometrySubElementKernel(SealevelGeometry* slgeom){_error_("not implemented yet");}; - void SealevelchangeMomentOfInertiaCentroid(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom){_error_("not implemented yet");}; void SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom){_error_("not implemented yet");}; void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){_error_("not implemented yet");}; @@ -234,6 +234,5 @@ void SealevelchangeOceanAverage(GrdLoads* loads, Vector* oceanareas, Vector* subelementoceanareas, IssmDouble* sealevelpercpu, SealevelGeometry* slgeom){_error_("not implemented yet");}; void SealevelchangeDeformationConvolution(IssmDouble* sealevelpercpu, GrdLoads* loads, IssmDouble* rotationvector,SealevelGeometry* slgeom){_error_("not implemented yet");}; - void SealevelchangeMomentOfInertiaSubElement(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom){_error_("not implemented yet");}; - void SealevelchangeUpdateViscousFields(){_error_("not implemented yet");}; + void SealevelchangeUpdateViscousFields(IssmDouble lincoeff, int newindex, int offset){_error_("not implemented yet");}; #endif Index: /issm/trunk/src/c/classes/Elements/Seg.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Seg.h (revision 27034) +++ /issm/trunk/src/c/classes/Elements/Seg.h (revision 27035) @@ -179,5 +179,4 @@ void GiaDeflection(Vector* wg,Vector* dwgdt,Matlitho* litho, IssmDouble* x,IssmDouble* y){_error_("not implemented yet");}; void SealevelchangeGeometrySubElementKernel(SealevelGeometry* slgeom){_error_("not implemented yet");}; - void SealevelchangeMomentOfInertiaCentroid(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom){_error_("not implemented yet");}; void SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom){_error_("not implemented yet");}; void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){_error_("not implemented yet");}; @@ -188,6 +187,5 @@ void SealevelchangeOceanAverage(GrdLoads* loads, Vector* oceanareas, Vector* subelementoceanareas, IssmDouble* sealevelpercpu, SealevelGeometry* slgeom){_error_("not implemented yet");}; void SealevelchangeDeformationConvolution(IssmDouble* sealevelpercpu, GrdLoads* loads, IssmDouble* rotationvector,SealevelGeometry* slgeom){_error_("not implemented yet");}; - void SealevelchangeMomentOfInertiaSubElement(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom){_error_("not implemented yet");}; - void SealevelchangeUpdateViscousFields(){_error_("not implemented yet");}; + void SealevelchangeUpdateViscousFields(IssmDouble lincoeff, int newindex, int offset){_error_("not implemented yet");}; #endif Index: /issm/trunk/src/c/classes/Elements/Tetra.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Tetra.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Elements/Tetra.cpp (revision 27035) @@ -605,5 +605,5 @@ norm=sqrt(normal[0]*normal[0]+normal[1]*normal[1]+normal[2]*normal[2]); - for(int i=0;i<3;i++) normal[i]=normal[i]/norm; + for(int i=0;i<3;i++) normal[i]=normal[i]/(norm+1e-10); } /*}}}*/ Index: /issm/trunk/src/c/classes/Elements/Tetra.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Tetra.h (revision 27034) +++ /issm/trunk/src/c/classes/Elements/Tetra.h (revision 27035) @@ -186,5 +186,4 @@ void GiaDeflection(Vector* wg,Vector* dwgdt, Matlitho* litho, IssmDouble* x,IssmDouble* y){_error_("not implemented yet");}; void SealevelchangeGeometrySubElementKernel(SealevelGeometry* slgeom){_error_("not implemented yet");}; - void SealevelchangeMomentOfInertiaCentroid(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom){_error_("not implemented yet");}; void SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom){_error_("not implemented yet");}; void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){_error_("not implemented yet");}; @@ -195,6 +194,5 @@ void SealevelchangeOceanAverage(GrdLoads* loads, Vector* oceanareas, Vector* subelementoceanareas, IssmDouble* sealevelpercpu, SealevelGeometry* slgeom){_error_("not implemented yet");}; void SealevelchangeDeformationConvolution(IssmDouble* sealevelpercpu, GrdLoads* loads, IssmDouble* rotationvector,SealevelGeometry* slgeom){_error_("not implemented yet");}; - void SealevelchangeMomentOfInertiaSubElement(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom){_error_("not implemented yet");}; - void SealevelchangeUpdateViscousFields(){_error_("not implemented yet");}; + void SealevelchangeUpdateViscousFields(IssmDouble lincoeff, int newindex, int offset){_error_("not implemented yet");}; #endif Index: /issm/trunk/src/c/classes/Elements/Tria.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Tria.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Elements/Tria.cpp (revision 27035) @@ -29,5 +29,5 @@ #define NUMVERTICES 3 #define NUMVERTICES1D 2 -//#define ISMICI 1 +//#define MICI 1 //1 = DeConto & Pollard, 2 = DOMINOS /*Constructors/destructor/copy*/ @@ -313,27 +313,22 @@ void Tria::CalvingRateVonmises(){/*{{{*/ - IssmDouble xyz_list[NUMVERTICES][3]; - IssmDouble epsilon[3]; /* epsilon=[exx,eyy,exy];*/ - IssmDouble calvingratex[NUMVERTICES]; - IssmDouble calvingratey[NUMVERTICES]; + /*First, compute Von Mises Stress*/ + this->ComputeSigmaVM(); + + /*Now compute calving rate*/ IssmDouble calvingrate[NUMVERTICES]; - IssmDouble lambda1,lambda2,ex,ey,vx,vy,vel; - IssmDouble sigma_vm[NUMVERTICES]; - IssmDouble B,sigma_max,sigma_max_floating,sigma_max_grounded,n; - IssmDouble epse_2,groundedice,bed,sealevel; // added sealevel - - /* Get node coordinates and dof list: */ - ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + IssmDouble sigma_vm,vx,vy; + IssmDouble sigma_max,sigma_max_floating,sigma_max_grounded,n; + IssmDouble groundedice,bed,sealevel; /*Retrieve all inputs and parameters we will need*/ - Input* vx_input = this->GetInput(VxEnum); _assert_(vx_input); - Input* vy_input = this->GetInput(VyEnum); _assert_(vy_input); - Input* B_input = this->GetInput(MaterialsRheologyBbarEnum); _assert_(B_input); - Input* gr_input = this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); - Input* bs_input = this->GetInput(BaseEnum); _assert_(bs_input); - Input* smax_fl_input = this->GetInput(CalvingStressThresholdFloatingiceEnum); _assert_(smax_fl_input); - Input* smax_gr_input = this->GetInput(CalvingStressThresholdGroundediceEnum); _assert_(smax_gr_input); - Input* n_input = this->GetInput(MaterialsRheologyNEnum); _assert_(n_input); - Input* sl_input = this->GetInput(SealevelEnum); _assert_(sl_input); + Input* vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input* gr_input = this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); + Input* bs_input = this->GetInput(BaseEnum); _assert_(bs_input); + Input* smax_fl_input = this->GetInput(CalvingStressThresholdFloatingiceEnum); _assert_(smax_fl_input); + Input* smax_gr_input = this->GetInput(CalvingStressThresholdGroundediceEnum); _assert_(smax_gr_input); + Input* sl_input = this->GetInput(SealevelEnum); _assert_(sl_input); + Input* sigma_vm_input = this->GetInput(SigmaVMEnum); _assert_(sigma_vm_input); /* Start looping on the number of vertices: */ @@ -343,6 +338,5 @@ /*Get velocity components and thickness*/ - B_input->GetInputValue(&B,&gauss); - n_input->GetInputValue(&n,&gauss); + sigma_vm_input->GetInputValue(&sigma_vm,&gauss); vx_input->GetInputValue(&vx,&gauss); vy_input->GetInputValue(&vy,&gauss); @@ -351,27 +345,5 @@ smax_fl_input->GetInputValue(&sigma_max_floating,&gauss); smax_gr_input->GetInputValue(&sigma_max_grounded,&gauss); - vel=sqrt(vx*vx+vy*vy)+1.e-14; sl_input->GetInputValue(&sealevel,&gauss); - - /*Compute strain rate and viscosity: */ - this->StrainRateSSA(&epsilon[0],&xyz_list[0][0],&gauss,vx_input,vy_input); - - /*Get Eigen values*/ - Matrix2x2Eigen(&lambda1,&lambda2,&ex,&ey,epsilon[0],epsilon[2],epsilon[1]); - _assert_(!xIsNan(lambda1)); - _assert_(!xIsNan(lambda2)); - - /*Process Eigen values (only account for extension)*/ - lambda1 = max(lambda1,0.); - lambda2 = max(lambda2,0.); - - /*Calculate sigma_vm*/ - epse_2 = 1./2. *(lambda1*lambda1 + lambda2*lambda2); - sigma_vm[iv] = sqrt(3.) * B * pow(epse_2,1./(2.*n)); - - /*OLD (keep for a little bit)*/ - //sigma_max = 800.e+3; //IUGG previous test - //sigma_max = 1000.e+3; //GRL - //if(groundedice<0) sigma_max=150.e+3; /*Tensile stress threshold*/ @@ -380,15 +352,57 @@ else sigma_max = sigma_max_grounded; + /*Assign values*/ - if(bed>sealevel){ // Changed 0. to sealevel - calvingratex[iv]=0.; - calvingratey[iv]=0.; + if(bed>sealevel){ + calvingrate[iv] = 0.; } else{ - calvingratex[iv]=vx*sigma_vm[iv]/sigma_max; - calvingratey[iv]=vy*sigma_vm[iv]/sigma_max; - } - calvingrate[iv] =sqrt(calvingratex[iv]*calvingratex[iv] + calvingratey[iv]*calvingratey[iv]); - + calvingrate[iv] = sqrt(vx*vx+vy*vy)*sigma_vm/sigma_max; + } + } + + /*Add input*/ + this->AddInput(CalvingCalvingrateEnum,&calvingrate[0],P1DGEnum); + this->CalvingFromRate(); +} +/*}}}*/ +void Tria::CalvingRateTest(){/*{{{*/ + + IssmDouble calvingratex[NUMVERTICES]; + IssmDouble calvingratey[NUMVERTICES]; + IssmDouble calvingrate[NUMVERTICES]; + IssmDouble vx,vy,vel; + IssmDouble dphidx, dphidy, dphi; + IssmDouble time; + IssmDouble coeff, indrate; + + /*Retrieve all inputs and parameters we will need*/ + parameters->FindParam(&time,TimeEnum); + parameters->FindParam(&coeff,CalvingTestSpeedfactorEnum,time); + parameters->FindParam(&indrate,CalvingTestIndependentRateEnum,time); + + Input* vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input *lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); + Input *lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); + + /* Start looping on the number of vertices: */ + GaussTria gauss; + for(int iv=0;ivGetInputValue(&vx,&gauss); + vy_input->GetInputValue(&vy,&gauss); + + lsf_slopex_input->GetInputValue(&dphidx,&gauss); + lsf_slopey_input->GetInputValue(&dphidy,&gauss); + + vel=sqrt(vx*vx + vy*vy) + 1e-14; + dphi=sqrt(dphidx*dphidx+dphidy*dphidy)+ 1e-14; + + calvingratex[iv]= coeff*vx + indrate*dphidx/dphi; + calvingratey[iv]= coeff*vy + indrate*dphidy/dphi; + calvingrate[iv] = sqrt(calvingratex[iv]*calvingratex[iv] + calvingratey[iv]*calvingratey[iv]); } @@ -397,5 +411,4 @@ this->AddInput(CalvingrateyEnum,&calvingratey[0],P1DGEnum); this->AddInput(CalvingCalvingrateEnum,&calvingrate[0],P1DGEnum); - this->AddInput(SigmaVMEnum,&sigma_vm[0],P1DGEnum); } /*}}}*/ @@ -655,15 +668,7 @@ IssmDouble calvingratex,calvingratey,thickness,Jdet,flux_per_area; IssmDouble rho_ice=FindParam(MaterialsRhoIceEnum); - Input* thickness_input=this->GetInput(ThicknessEnum); _assert_(thickness_input); - Input* calvingratex_input=NULL; - Input* calvingratey_input=NULL; - if(domaintype==Domain2DhorizontalEnum){ - calvingratex_input=this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); - } - else{ - calvingratex_input=this->GetInput(CalvingratexAverageEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyAverageEnum); _assert_(calvingratey_input); - } + Input* thickness_input = this->GetInput(ThicknessEnum); _assert_(thickness_input); + Input* calvingratex_input = this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); + Input* calvingratey_input = this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); /*Start looping on Gaussian points*/ @@ -789,21 +794,10 @@ IssmDouble calvingratex,calvingratey,vx,vy,vel,meltingrate,meltingratex,meltingratey,thickness,Jdet,flux_per_area; IssmDouble rho_ice=FindParam(MaterialsRhoIceEnum); - Input* thickness_input=this->GetInput(ThicknessEnum); _assert_(thickness_input); - Input* calvingratex_input=NULL; - Input* calvingratey_input=NULL; - Input* vx_input=NULL; - Input* vy_input=NULL; - Input* meltingrate_input=NULL; - if(domaintype==Domain2DhorizontalEnum){ - calvingratex_input=this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); - vx_input=this->GetInput(VxEnum); _assert_(vx_input); - vy_input=this->GetInput(VyEnum); _assert_(vy_input); - meltingrate_input=this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); - } - else{ - calvingratex_input=this->GetInput(CalvingratexAverageEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyAverageEnum); _assert_(calvingratey_input); - } + Input* thickness_input = this->GetInput(ThicknessEnum); _assert_(thickness_input); + Input* calvingratex_input = this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); + Input* calvingratey_input = this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); + Input* vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input* meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); /*Start looping on Gaussian points*/ @@ -832,4 +826,148 @@ delete gauss; } +} +/*}}}*/ +void Tria::CalvingRateParameterization(){/*{{{*/ + + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble epsilon[3]; /* epsilon=[exx,eyy,exy];*/ + IssmDouble calvingrate[NUMVERTICES]; + IssmDouble lambda1,lambda2,ex,ey,vx,vy,vel; + IssmDouble sigma_vm[NUMVERTICES]; + IssmDouble B,sigma_max,sigma_max_floating,sigma_max_grounded,n; + IssmDouble epse_2,groundedice,bed,sealevel; + IssmDouble arate, rho_ice, rho_water, thickness, paramX, Hab; + int use_parameter=0; + int nonlinear_law=0; + IssmDouble theta, alpha, midp, gamma; + + /* Get node coordinates and dof list: */ + ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + + /*Retrieve all inputs and parameters we will need*/ + Input *vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input *vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input *B_input = this->GetInput(MaterialsRheologyBbarEnum); _assert_(B_input); + Input *gr_input = this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); + Input *bs_input = this->GetInput(BedEnum); _assert_(bs_input); + Input *H_input = this->GetInput(ThicknessEnum); _assert_(H_input); + Input *smax_fl_input = this->GetInput(CalvingStressThresholdFloatingiceEnum); _assert_(smax_fl_input); + Input *smax_gr_input = this->GetInput(CalvingStressThresholdGroundediceEnum); _assert_(smax_gr_input); + Input *n_input = this->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + Input *sl_input = this->GetInput(SealevelEnum); _assert_(sl_input); + Input *arate_input = this->GetInput(CalvingAblationrateEnum); _assert_(arate_input); + + /* Ice and sea water density */ + this->FindParam(&rho_ice,MaterialsRhoIceEnum); + this->FindParam(&rho_water,MaterialsRhoSeawaterEnum); + + /* Use which parameter */ + this->FindParam(&use_parameter, CalvingUseParamEnum); + this->FindParam(&theta, CalvingScaleThetaEnum); + this->FindParam(&alpha, CalvingAmpAlphaEnum); + this->FindParam(&midp, CalvingMidpointEnum); + this->FindParam(&nonlinear_law, CalvingNonlinearLawEnum); + + /* Start looping on the number of vertices: */ + GaussTria* gauss=new GaussTria(); + for(int iv=0;ivGaussVertex(iv); + + /*Get velocity components and thickness*/ + B_input->GetInputValue(&B,gauss); + n_input->GetInputValue(&n,gauss); + vx_input->GetInputValue(&vx,gauss); + vy_input->GetInputValue(&vy,gauss); + gr_input->GetInputValue(&groundedice,gauss); + bs_input->GetInputValue(&bed,gauss); + H_input->GetInputValue(&thickness,gauss); + smax_fl_input->GetInputValue(&sigma_max_floating,gauss); + smax_gr_input->GetInputValue(&sigma_max_grounded,gauss); + vel=sqrt(vx*vx+vy*vy)+1.e-14; + sl_input->GetInputValue(&sealevel,gauss); + arate_input->GetInputValue(&arate,gauss); + + /*Compute strain rate and viscosity: */ + this->StrainRateSSA(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input); + + /*Get Eigen values*/ + Matrix2x2Eigen(&lambda1,&lambda2,&ex,&ey,epsilon[0],epsilon[2],epsilon[1]); + _assert_(!xIsNan(lambda1)); + _assert_(!xIsNan(lambda2)); + + /*Process Eigen values (only account for extension)*/ + lambda1 = max(lambda1,0.); + lambda2 = max(lambda2,0.); + + /*Calculate sigma_vm*/ + epse_2 = 1./2. *(lambda1*lambda1 + lambda2*lambda2); + sigma_vm[iv] = sqrt(3.) * B * pow(epse_2,1./(2.*n)); + + /*Tensile stress threshold*/ + if(groundedice<0) + sigma_max = sigma_max_floating; + else + sigma_max = sigma_max_grounded; + + switch (use_parameter) { + case 0: + /* bed elevation */ + paramX = bed; + break; + case 1: + /* Height above floatation */ + if (bed>sealevel) paramX = 0.0; + else paramX = thickness - (rho_water/rho_ice) * (sealevel-bed); + break; + case 2: + /* Thicknese */ + paramX = thickness; + break; + case 4: + /* bed elevation+linear curve fitting */ + paramX = bed; + break; + case -1: + /* use nothing, just the arate*/ + break; + default: + _error_("The parameter is not supported yet!"); + } + + /* Compute the hyperbolic tangent function */ + if ((use_parameter>-0.5) & (use_parameter<3)) { + gamma = 0.5*theta*(1.0-tanh((paramX+midp)/alpha))+(1.0-theta); + if (gamma<0.0) gamma =0.0; + } + else if (use_parameter>=3) { + gamma = alpha*paramX + theta; + if (gamma > 1.0) gamma = 1.0; + if (gamma < 0.0) gamma = 0.0; + } + else gamma = 1; + + /*-------------------------------------------*/ + if (nonlinear_law) { + /*This von Mises type has too strong positive feedback with vel included + * calvingrate[iv] = (arate+sigma_vm[iv]*vel/sigma_max)*gamma; + */ + Hab = thickness - (rho_water/rho_ice) * (sealevel-bed); + if (Hab < 0.) Hab = 0.; + if (bed > sealevel) Hab = 0.; + + calvingrate[iv] = (arate+Hab/sigma_max)*gamma; + } + else { + calvingrate[iv] = arate*gamma; + } + } + + /*Add input*/ + this->AddInput(CalvingCalvingrateEnum,&calvingrate[0],P1DGEnum); + this->AddInput(SigmaVMEnum,&sigma_vm[0],P1DGEnum); + this->CalvingFromRate(); + + /*Clean up and return*/ + delete gauss; } /*}}}*/ @@ -914,5 +1052,5 @@ } /*}}}*/ -void Tria::ComputeEsaStrainAndVorticity(){ /*{{{*/ +void Tria::ComputeEsaStrainAndVorticity(){ /*{{{*/ IssmDouble xyz_list[NUMVERTICES][3]; @@ -1010,4 +1148,54 @@ delete gauss; } +} +/*}}}*/ +void Tria::ComputeSigmaVM(){/*{{{*/ + + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble epsilon[3]; /* epsilon=[exx,eyy,exy];*/ + IssmDouble lambda1,lambda2,ex,ey,vx,vy,vel; + IssmDouble sigma_vm[NUMVERTICES]; + IssmDouble B,n; + + /* Get node coordinates and dof list: */ + ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + + /*Retrieve all inputs and parameters we will need*/ + Input* vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input* B_input = this->GetInput(MaterialsRheologyBbarEnum); _assert_(B_input); + Input* n_input = this->GetInput(MaterialsRheologyNEnum); _assert_(n_input); + + /* Start looping on the number of vertices: */ + GaussTria gauss; + for(int iv=0;ivGetInputValue(&B,&gauss); + n_input->GetInputValue(&n,&gauss); + vx_input->GetInputValue(&vx,&gauss); + vy_input->GetInputValue(&vy,&gauss); + vel=sqrt(vx*vx+vy*vy)+1.e-14; + + /*Compute strain rate and viscosity: */ + this->StrainRateSSA(&epsilon[0],&xyz_list[0][0],&gauss,vx_input,vy_input); + + /*Get Eigen values*/ + Matrix2x2Eigen(&lambda1,&lambda2,&ex,&ey,epsilon[0],epsilon[2],epsilon[1]); + _assert_(!xIsNan(lambda1)); + _assert_(!xIsNan(lambda2)); + + /*Process Eigen values (only account for extension)*/ + lambda1 = max(lambda1,0.); + lambda2 = max(lambda2,0.); + + /*Calculate sigma_vm*/ + IssmDouble epse_2 = 1./2. *(lambda1*lambda1 + lambda2*lambda2); + sigma_vm[iv] = sqrt(3.) * B * pow(epse_2,1./(2.*n)); + } + + /*Add input*/ + this->AddInput(SigmaVMEnum,&sigma_vm[0],P1DGEnum); } /*}}}*/ @@ -1937,5 +2125,5 @@ //compute sea level load weights this->GetFractionGeometry(loadweights,&phi,&point1,&fraction1,&fraction2,&istrapeze1,levelset); - + for (int i=0;iGetBarycenterFromLevelset(platbar,plongbar, phi, fraction1, fraction2, late, longe, point1,istrapeze1,planetradius); @@ -2028,4 +2216,5 @@ this->GetFractionGeometry(loadweights,&phi2,&point2,&f,&g,&istrapeze2,levelset2); this->GetBarycenterFromLevelset(platbar,plongbar, phi2, f, g, late, longe, point2,istrapeze2,planetradius); + for (int i=0;iGetFractionGeometry(loadweights,&phi1,&point1,&d,&e,&istrapeze1,levelset1); this->GetBarycenterFromLevelset(platbar,plongbar, phi1, d, e, late, longe, point1,istrapeze1,planetradius); + for (int i=0;iGetBarycenterFromLevelset(platbar,plongbar, phi1, d, e, late, longe, point1,istrapeze1,planetradius); *ploadarea=area*phi1; - for (int i=0;iServe(numindices,&indices[0]); break; + case P1xP2Enum: + case P1xP3Enum: case P1xP4Enum: case P1DGEnum: @@ -3596,5 +3788,4 @@ } - /*Cleanup & return: */ xDelete(indices); @@ -4101,21 +4292,16 @@ IssmDouble norm_dlsf, norm_calving, calvingrate, meltingrate, groundedice; IssmDouble migrationmax, calvinghaf, heaviside, haf_eps; - IssmDouble xyz_list[NUMVERTICES][3]; - IssmDouble movingfrontvx[NUMVERTICES]; - IssmDouble movingfrontvy[NUMVERTICES]; - IssmDouble vel; + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble movingfrontvx[NUMVERTICES]; + IssmDouble movingfrontvy[NUMVERTICES]; + IssmDouble vel; /* Get node coordinates and dof list: */ ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); - Input* vx_input = NULL; - Input* vy_input = NULL; Input* calvingratex_input = NULL; Input* calvingratey_input = NULL; - Input* lsf_slopex_input = NULL; - Input* lsf_slopey_input = NULL; Input* calvingrate_input = NULL; Input* meltingrate_input = NULL; - Input* gr_input = NULL; /*Get problem dimension and whether there is moving front or not*/ @@ -4129,66 +4315,29 @@ default: _error_("mesh "<GetInput(VxEnum); _assert_(vx_input); - break; - case Domain2DhorizontalEnum: - vx_input=this->GetInput(VxEnum); _assert_(vx_input); - vy_input=this->GetInput(VyEnum); _assert_(vy_input); - gr_input=this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); - break; - case Domain3DEnum: - vx_input=this->GetInput(VxAverageEnum); _assert_(vx_input); - vy_input=this->GetInput(VyAverageEnum); _assert_(vy_input); - gr_input=this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); - break; - default: _error_("mesh "<GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); + Input *lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); + Input *lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); + Input *vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input *vy_input = this->GetInput(VyEnum); _assert_(vy_input); switch(calvinglaw){ case DefaultCalvingEnum: case CalvingVonmisesEnum: - lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); - calvingrate_input = this->GetInput(CalvingCalvingrateEnum); _assert_(calvingrate_input); - meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); - break; case CalvingLevermannEnum: - switch(domaintype){ - case Domain2DverticalEnum: - calvingratex_input=this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); - break; - case Domain2DhorizontalEnum: - calvingratex_input=this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); - break; - case Domain3DEnum: - calvingratex_input=this->GetInput(CalvingratexAverageEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyAverageEnum); _assert_(calvingratey_input); - break; - default: _error_("mesh "<GetInput(CalvingratexEnum); _assert_(calvingratex_input); + calvingratey_input=this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); break; case CalvingMinthicknessEnum: - lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); - meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); - break; case CalvingHabEnum: - lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); - meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); - break; case CalvingCrevasseDepthEnum: - lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); break; case CalvingDev2Enum: this->FindParam(&calvinghaf,CalvingHeightAboveFloatationEnum); - lsf_slopex_input = this->GetInput(LevelsetfunctionSlopeXEnum); _assert_(lsf_slopex_input); - if(dim==2) lsf_slopey_input = this->GetInput(LevelsetfunctionSlopeYEnum); _assert_(lsf_slopey_input); calvingrate_input = this->GetInput(CalvingCalvingrateEnum); _assert_(calvingrate_input); meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); @@ -4207,4 +4356,10 @@ vy_input->GetInputValue(&v[1],&gauss); gr_input->GetInputValue(&groundedice,&gauss); + lsf_slopex_input->GetInputValue(&dlsf[0],&gauss); + if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); + + norm_dlsf=0.; + for(i=0;iGetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); - calvingrate_input->GetInputValue(&calvingrate,&gauss); + case CalvingTestEnum: + case CalvingParameterizationEnum: + calvingratex_input->GetInputValue(&c[0],&gauss); + calvingratey_input->GetInputValue(&c[1],&gauss); meltingrate_input->GetInputValue(&meltingrate,&gauss); if(groundedice<0) meltingrate = 0.; - - norm_dlsf=0.; - for(i=0;i1.e-10) - for(i=0;iGetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); + case CalvingHabEnum: + case CalvingCrevasseDepthEnum: meltingrate_input->GetInputValue(&meltingrate,&gauss); - - norm_dlsf=0.; - for(i=0;i1.e-10) @@ -4263,52 +4410,6 @@ break; - case CalvingHabEnum: - lsf_slopex_input->GetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); - meltingrate_input->GetInputValue(&meltingrate,&gauss); - - norm_dlsf=0.; - for(i=0;i1.e-10) - for(i=0;iGetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); - meltingrate_input->GetInputValue(&meltingrate,&gauss); - - if(groundedice<0) meltingrate = 0.; - - norm_dlsf=0.; - for(i=0;i1.e-10) - for(i=0;iGetInputValue(&dlsf[0],&gauss); - if(dim==2) lsf_slopey_input->GetInputValue(&dlsf[1],&gauss); calvingrate_input->GetInputValue(&calvingrate,&gauss); meltingrate_input->GetInputValue(&meltingrate,&gauss); @@ -4335,8 +4436,4 @@ } - norm_dlsf=0.; - for(i=0;i1.e-10) for(i=0;iGetInputValue(&c[0],&gauss); + if(dim==2) calvingratey_input->GetInputValue(&c[1],&gauss); + for(i=0;iGetInputValue(&ls,&gauss); - /*Do we assume that the calving front does not move?*/ - //movingfrontvx[iv] = 0.; - //movingfrontvy[iv] = 0.; - - //if(Hc>80. && bed<0. && fabs(ls)<100.e3){ //Pollard & De Conto - if(Hc>135. && bed<0. && fabs(ls)<100.e3){ // Crawford et all - - lsf_slopex_input->GetInputValue(&dlsf[0],&gauss); - norm_dlsf=0.; - for(i=0;iGetInputValue(&v[0],&gauss); - vy_input->GetInputValue(&v[1],&gauss); - vel=sqrt(v[0]*v[0] + v[1]*v[1]); - norm_dlsf = max(vel,1.e-10); - dlsf[0] = v[0]; - dlsf[1] = v[1]; + /*use vel direction instead of LSF*/ + vx_input->GetInputValue(&v[0],&gauss); + vy_input->GetInputValue(&v[1],&gauss); + vel=sqrt(v[0]*v[0] + v[1]*v[1]); + norm_dlsf = max(vel,1.e-10); + dlsf[0] = v[0]; + dlsf[1] = v[1]; + + /*Do we assume that the calving front does not move if MICI is not engaged?*/ + movingfrontvx[iv] = 0.; + movingfrontvy[iv] = 0.; + //movingfrontvx[iv] = -2000./(365*24*3600.)*dlsf[0]/norm_dlsf; + //movingfrontvy[iv] = -2000./(365*24*3600.)*dlsf[1]/norm_dlsf; + + if(MICI==1 && Hc>80. && bed<0. && fabs(ls)<100.e3){ //Pollard & De Conto + IssmDouble C = (min(max(Hc,80.),100.) - 80.)/20. * 10./(24*3600.); /*Original MICI! convert from m/day to m/s*/ + + /*Front motion = ice speed (v) - calving rate*/ + movingfrontvx[iv] = v[0]-C*dlsf[0]/norm_dlsf; + movingfrontvy[iv] = v[1]-C*dlsf[1]/norm_dlsf; + } + else if (MICI==2 && Hc>135. && bed<0. && fabs(ls)<100.e3){ // Crawford et all /*5C Bn (worst case scenario)*/ @@ -4405,7 +4509,8 @@ IssmDouble alpha = 7.3; IssmDouble C = min(2000.,I*pow(Hc,alpha))/(24*3600.); /*convert from m/day to m/s*/ - //IssmDouble C = (min(max(Hc,80.),100.) - 80.)/20. * 10./(24*3600.); /*Original MICI! convert from m/day to m/s*/ - movingfrontvx[iv] = -C*dlsf[0]/norm_dlsf; - movingfrontvy[iv] = -C*dlsf[1]/norm_dlsf; + + /*Front motion = ice speed (v) - calving rate*/ + movingfrontvx[iv] = v[0] -C*dlsf[0]/norm_dlsf; + movingfrontvy[iv] = v[1] -C*dlsf[1]/norm_dlsf; } } @@ -4587,6 +4692,6 @@ norm=sqrt(vector[0]*vector[0] + vector[1]*vector[1]); - normal[0]= + vector[1]/norm; - normal[1]= - vector[0]/norm; + normal[0]= + vector[1]/(norm+1e-10); + normal[1]= - vector[0]/(norm+1e-10); } /*}}}*/ @@ -5214,15 +5319,7 @@ IssmDouble calvingratex,calvingratey,thickness,Jdet; IssmDouble rho_ice=FindParam(MaterialsRhoIceEnum); - Input* thickness_input=this->GetInput(ThicknessEnum); _assert_(thickness_input); - Input* calvingratex_input=NULL; - Input* calvingratey_input=NULL; - if(domaintype==Domain2DhorizontalEnum){ - calvingratex_input=this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); - } - else{ - calvingratex_input=this->GetInput(CalvingratexAverageEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyAverageEnum); _assert_(calvingratey_input); - } + Input* thickness_input = this->GetInput(ThicknessEnum); _assert_(thickness_input); + Input* calvingratex_input = this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); + Input* calvingratey_input = this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); /*Start looping on Gaussian points*/ @@ -5340,23 +5437,13 @@ /*Get inputs*/ IssmDouble flux = 0.; - IssmDouble calvingratex,calvingratey,vx,vy,vel,meltingrate,meltingratex,meltingratey,thickness,Jdet; + IssmDouble calvingratex,calvingratey,vx,vy,vel,meltingrate,meltingratex,meltingratey,thickness,Jdet,groundedice; IssmDouble rho_ice=FindParam(MaterialsRhoIceEnum); - Input* thickness_input=this->GetInput(ThicknessEnum); _assert_(thickness_input); - Input* calvingratex_input=NULL; - Input* calvingratey_input=NULL; - Input* vx_input=NULL; - Input* vy_input=NULL; - Input* meltingrate_input=NULL; - if(domaintype==Domain2DhorizontalEnum){ - calvingratex_input=this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); - vx_input=this->GetInput(VxEnum); _assert_(vx_input); - vy_input=this->GetInput(VyEnum); _assert_(vy_input); - meltingrate_input=this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); - } - else{ - calvingratex_input=this->GetInput(CalvingratexAverageEnum); _assert_(calvingratex_input); - calvingratey_input=this->GetInput(CalvingrateyAverageEnum); _assert_(calvingratey_input); - } + Input* thickness_input = this->GetInput(ThicknessEnum); _assert_(thickness_input); + Input *gr_input = this->GetInput(MaskOceanLevelsetEnum); _assert_(gr_input); + Input* calvingratex_input = this->GetInput(CalvingratexEnum); _assert_(calvingratex_input); + Input* calvingratey_input = this->GetInput(CalvingrateyEnum); _assert_(calvingratey_input); + Input* vx_input = this->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input = this->GetInput(VyEnum); _assert_(vy_input); + Input* meltingrate_input = this->GetInput(CalvingMeltingrateEnum); _assert_(meltingrate_input); /*Start looping on Gaussian points*/ @@ -5366,8 +5453,10 @@ calvingratex_input->GetInputValue(&calvingratex,gauss); calvingratey_input->GetInputValue(&calvingratey,gauss); + gr_input->GetInputValue(&groundedice,gauss); vx_input->GetInputValue(&vx,gauss); vy_input->GetInputValue(&vy,gauss); vel=vx*vx+vy*vy; meltingrate_input->GetInputValue(&meltingrate,gauss); + if(groundedice<0) meltingrate = 0.; meltingratex=meltingrate*vx/(sqrt(vel)+1.e-14); meltingratey=meltingrate*vy/(sqrt(vel)+1.e-14); @@ -6237,8 +6326,7 @@ IssmDouble area,planetarea,planetradius; IssmDouble constant,ratioe; - IssmDouble I; //change in ice thickness or water level(Farrel and Clarke, Equ. 4) IssmDouble rho_earth; IssmDouble NewtonG; - IssmDouble g; + IssmDouble g, cent_scaling; IssmDouble lati,longi; IssmDouble latitude[NUMVERTICES]; @@ -6291,15 +6379,32 @@ /*Rotational:*/ + #ifdef _HAVE_RESTRICT_ + IssmDouble* __restrict__ tide_love_h = NULL; + IssmDouble* __restrict__ tide_love_k = NULL; + IssmDouble* __restrict__ tide_love_l = NULL; + IssmDouble* __restrict__ LoveRotRSL = NULL; + IssmDouble* __restrict__ LoveRotU = NULL; + IssmDouble* __restrict__ LoveRothoriz = NULL; + IssmDouble* __restrict__ Grot = NULL; + IssmDouble* __restrict__ GUrot = NULL; + IssmDouble* __restrict__ GNrot = NULL; + IssmDouble* __restrict__ GErot = NULL; + #else IssmDouble* tide_love_h = NULL; IssmDouble* tide_love_k = NULL; IssmDouble* tide_love_l = NULL; + IssmDouble* LoveRotRSL = NULL; + IssmDouble* LoveRotU = NULL; + IssmDouble* LoveRothoriz = NULL; + IssmDouble* Grot = NULL; + IssmDouble* GUrot = NULL; + IssmDouble* GNrot = NULL; + IssmDouble* GErot = NULL; + #endif + IssmDouble moi_e, moi_p, omega; - IssmDouble Grotm1[3],GUrotm1[3],GNrotm1[3],GErotm1[3]; - IssmDouble Grotm2[3],GUrotm2[3],GNrotm2[3],GErotm2[3]; - IssmDouble Grotm3[3],GUrotm3[3],GNrotm3[3],GErotm3[3]; IssmDouble Y21cos , Y21sin , Y20; IssmDouble dY21cos_dlat,dY21sin_dlat,dY20_dlat; IssmDouble dY21cos_dlon,dY21sin_dlon; - IssmDouble LoveRotRSL,LoveRotU,LoveRothoriz; IssmDouble polenudge; /*}}}*/ @@ -6324,10 +6429,10 @@ if(computerotation){ - parameters->FindParam(&tide_love_h,NULL,NULL,TidalLoveHEnum); - parameters->FindParam(&tide_love_k,NULL,NULL,TidalLoveKEnum); - parameters->FindParam(&tide_love_l,NULL,NULL,TidalLoveLEnum); parameters->FindParam(&moi_e,RotationalEquatorialMoiEnum); parameters->FindParam(&moi_p,RotationalPolarMoiEnum); parameters->FindParam(&omega,RotationalAngularVelocityEnum); + //parameters->FindParam(&tide_love_h,NULL,NULL,SealevelchangeTidalH2Enum); + //parameters->FindParam(&tide_love_k,NULL,NULL,SealevelchangeTidalK2Enum); + //if(horiz) parameters->FindParam(&tide_love_l,NULL,NULL,SealevelchangeTidalL2Enum); } /*}}}*/ @@ -6347,4 +6452,17 @@ parameter = static_cast(this->parameters->FindParamObject(SealevelchangeHViscoElasticEnum)); _assert_(parameter); parameter->GetParameterValueByPointer((IssmDouble**)&H_viscoelastic_precomputed,NULL); + } + + if(computerotation){ + parameter = static_cast(this->parameters->FindParamObject(SealevelchangeTidalH2Enum)); _assert_(parameter); + parameter->GetParameterValueByPointer((IssmDouble**)&tide_love_h,NULL); + + parameter = static_cast(this->parameters->FindParamObject(SealevelchangeTidalK2Enum)); _assert_(parameter); + parameter->GetParameterValueByPointer((IssmDouble**)&tide_love_k,NULL); + + if (horiz) { + parameter = static_cast(this->parameters->FindParamObject(SealevelchangeTidalL2Enum)); _assert_(parameter); + parameter->GetParameterValueByPointer((IssmDouble**)&tide_love_l,NULL); + } } } @@ -6387,5 +6505,5 @@ IssmDouble alpha; IssmDouble delPhi,delLambda; - /*recover info for this element and vertex:*/ + /*recovers info for this element and vertex:*/ IssmDouble late= asin(zze[e]/sqrt( pow(xxe[e],2.0)+ pow(yye[e],2.0)+ pow(zze[e],2.0))); IssmDouble longe= atan2(yye[e],xxe[e]); @@ -6394,5 +6512,5 @@ longi=longitude[i]; - /*Compute alpha angle between centroid and current vertex and index into precomputed tables: */ + /*Computes alpha angle between centroid and current vertex, and indexes alpha in precomputed tables: */ delPhi=fabs(lati-late); delLambda=fabs(longi-longe); if (delLambda>M_PI)delLambda=2*M_PI-delLambda; alpha=2.*asin(sqrt(pow(sin(delPhi/2),2)+cos(lati)*cos(late)*pow(sin(delLambda/2),2))); @@ -6462,13 +6580,26 @@ /*Compute rotation kernel:{{{*/ if(computerotation){ + //initialization + LoveRotRSL = xNewZeroInit(nt); + LoveRotU = xNewZeroInit(nt); + LoveRothoriz= xNewZeroInit(nt); + Grot = xNewZeroInit(3*3*nt); //3 polar motion components * 3 vertices * number of time steps + GUrot = xNewZeroInit(3*3*nt); + + if (horiz){ + GErot=xNewZeroInit(3*3*nt); + GNrot=xNewZeroInit(3*3*nt); + } /*What is the gravity at planet's surface: */ g=4.0/3.0*M_PI*rho_earth*NewtonG*planetradius; - - //Amplitude of the rotational feedback - LoveRotRSL=((1.0+tide_love_k[2]-tide_love_h[2])/g)*pow(omega*planetradius,2.0); - LoveRotU=(tide_love_h[2]/g)*pow(omega*planetradius,2.0); - LoveRothoriz=(tide_love_l[2]/g)*pow(omega*planetradius,2.0); - + cent_scaling=pow(omega*planetradius,2.0); //centrifugal potential dimensioning constant + for(int t=0;tAddInput(SealevelGrotm1Enum,&Grotm1[0],P1Enum); - this->AddInput(SealevelGrotm2Enum,&Grotm2[0],P1Enum); - this->AddInput(SealevelGrotm3Enum,&Grotm3[0],P1Enum); + this->inputs->SetArrayInput(SealevelchangeGrotEnum,this->lid,Grot,3*3*nt); if (computeelastic){ - this->AddInput(SealevelGUrotm1Enum,&GUrotm1[0],P1Enum); - this->AddInput(SealevelGUrotm2Enum,&GUrotm2[0],P1Enum); - this->AddInput(SealevelGUrotm3Enum,&GUrotm3[0],P1Enum); + this->inputs->SetArrayInput(SealevelchangeGUrotEnum,this->lid,GUrot,3*3*nt); if(horiz){ - this->AddInput(SealevelGNrotm1Enum,&GNrotm1[0],P1Enum); - this->AddInput(SealevelGNrotm2Enum,&GNrotm2[0],P1Enum); - this->AddInput(SealevelGNrotm3Enum,&GNrotm3[0],P1Enum); - this->AddInput(SealevelGErotm1Enum,&GErotm1[0],P1Enum); - this->AddInput(SealevelGErotm2Enum,&GErotm2[0],P1Enum); - this->AddInput(SealevelGErotm3Enum,&GErotm3[0],P1Enum); + this->inputs->SetArrayInput(SealevelchangeGNrotEnum,this->lid,GNrot,3*3*nt); + this->inputs->SetArrayInput(SealevelchangeGErotEnum,this->lid,GErot,3*3*nt); } } @@ -6551,6 +6682,6 @@ viscousN=xNewZeroInit(3*nt); viscousE=xNewZeroInit(3*nt); - this->inputs->SetArrayInput(SealevelchangeViscousNEnum,this->lid,viscousRSL,3*nt); - this->inputs->SetArrayInput(SealevelchangeViscousEEnum,this->lid,viscousU,3*nt); + this->inputs->SetArrayInput(SealevelchangeViscousNEnum,this->lid,viscousN,3*nt); + this->inputs->SetArrayInput(SealevelchangeViscousEEnum,this->lid,viscousE,3*nt); } } @@ -6566,4 +6697,12 @@ delete GE; } + if(computerotation){ + delete Grot; + delete GUrot; + if (horiz){ + delete GNrot; + delete GErot; + } + } } #else @@ -6574,4 +6713,12 @@ xDelete(GN); xDelete(GE); + } + if(computerotation){ + xDelete(Grot); + xDelete(GUrot); + if (horiz){ + xDelete(GNrot); + xDelete(GErot); + } } } @@ -7127,5 +7274,5 @@ } /*}}}*/ -void Tria::SealevelchangeUpdateViscousFields(){ /*{{{*/ +void Tria::SealevelchangeUpdateViscousFields(IssmDouble lincoeff, int newindex, int offset){ /*{{{*/ /*Inputs:*/ @@ -7134,13 +7281,8 @@ IssmDouble* viscousN=NULL; IssmDouble* viscousE=NULL; - IssmDouble* viscoustimes=NULL; int viscousnumsteps; - int viscousindex=0; - int newindex=0; int dummy; bool viscous=false; - IssmDouble currenttime; - IssmDouble lincoeff=0; - int horiz; + int horiz=0; this->parameters->FindParam(&viscous,SolidearthSettingsViscousEnum); @@ -7148,9 +7290,5 @@ if(viscous){ this->parameters->FindParam(&horiz,SolidearthSettingsHorizEnum); - this->parameters->FindParam(&viscousnumsteps,SealevelchangeViscousNumStepsEnum); - this->parameters->FindParam(&viscoustimes,NULL,SealevelchangeViscousTimesEnum); - this->parameters->FindParam(&viscousindex,SealevelchangeViscousIndexEnum); - this->parameters->FindParam(¤ttime,TimeEnum); this->inputs->GetArrayPtr(SealevelchangeViscousRSLEnum,this->lid,&viscousRSL,&dummy); @@ -7161,21 +7299,4 @@ } - bool foundtime=false; - int offset=1; - lincoeff=0; - newindex=viscousnumsteps-2; - - for(int t=viscousindex;tcurrenttime){ - newindex=t-1; - lincoeff=(currenttime-viscoustimes[newindex])/(viscoustimes[t]-viscoustimes[newindex]); - foundtime=true; - offset=0; - break; - } - } - - if(!foundtime) lincoeff=1; - viscoustimes[newindex]=currenttime; for(int i=0;iparameters->SetParam(viscousindex,SealevelchangeViscousIndexEnum); - this->parameters->SetParam(viscoustimes,viscousnumsteps,SealevelchangeViscousTimesEnum); - - /*free allocations:*/ - xDelete(viscoustimes); + } @@ -7198,4 +7313,6 @@ /*}}}*/ void Tria::SealevelchangeBarystaticLoads(GrdLoads* loads, BarystaticContributions* barycontrib, SealevelGeometry* slgeom){ /*{{{*/ + + int nel; /*Inputs:*/ @@ -7203,4 +7320,5 @@ IssmDouble W[NUMVERTICES]; IssmDouble BP[NUMVERTICES]; + IssmDouble* areae=NULL; /*output: */ @@ -7219,4 +7337,5 @@ this->parameters->FindParam(&rho_water,MaterialsRhoSeawaterEnum); this->parameters->FindParam(&rho_freshwater,MaterialsRhoFreshwaterEnum); + this->parameters->FindParam(&areae,&nel,AreaeEnum); /*Retrieve inputs:*/ @@ -7243,4 +7362,5 @@ /*Compute barystatic component in kg:*/ + // Note: Iavg, etc, already include partial area factor phi for subelement loading bslcice = -slgeom->LoadArea[SLGEOM_ICE][this->lid]*Iavg; bslchydro = -slgeom->LoadArea[SLGEOM_WATER][this->lid]*Wavg; @@ -7267,5 +7387,5 @@ BPavg=0; } - /*Plug remaining values into centroi load vector:*/ + /*Plug remaining values into centroid load vector:*/ loads->vloads->SetValue(this->sid,Iavg+Wavg+BPavg,INS_VAL); @@ -7279,4 +7399,5 @@ /*sal green function:*/ IssmDouble* G=NULL; + IssmDouble* Grot=NULL; IssmDouble* Gsub[SLGEOM_NUMLOADS]; bool computefuture=false; @@ -7288,7 +7409,5 @@ int size; int nel,nbar; - IssmDouble Grotm1[3]; - IssmDouble Grotm2[3]; - IssmDouble Grotm3[3]; + this->parameters->FindParam(&sal,SolidearthSettingsSelfAttractionEnum); @@ -7302,24 +7421,13 @@ this->inputs->GetArrayPtr(SealevelchangeGsubelHydroEnum,this->lid,&Gsub[SLGEOM_WATER],&size); this->inputs->GetArrayPtr(SealevelchangeGsubelOceanEnum,this->lid,&Gsub[SLGEOM_OCEAN],&size); - - this->SealevelchangeGxL(sealevelpercpu, G, Gsub, loads, slgeom, nel,percpu=true,SealevelchangeViscousRSLEnum,computefuture=false); - } - - if(rotation){ - Element::GetInputListOnVertices(&Grotm1[0],SealevelGrotm1Enum); - Element::GetInputListOnVertices(&Grotm2[0],SealevelGrotm2Enum); - Element::GetInputListOnVertices(&Grotm3[0],SealevelGrotm3Enum); - - for(int i=0;ilids[this->vertices[i]->lid]==this->lid){ - sealevelpercpu[this->vertices[i]->lid]+=Grotm1[i]*polarmotionvector[0]+Grotm2[i]*polarmotionvector[1]+Grotm3[i]*polarmotionvector[2]; - } - } - } + if (rotation) this->inputs->GetArrayPtr(SealevelchangeGrotEnum,this->lid,&Grot,&size); + + this->SealevelchangeGxL(sealevelpercpu, G, Gsub, Grot, loads, polarmotionvector, slgeom, nel,percpu=true,SealevelchangeViscousRSLEnum,computefuture=false); + } + return; } /*}}}*/ void Tria::SealevelchangeOceanAverage(GrdLoads* loads, Vector* oceanareas, Vector* subelementoceanareas, IssmDouble* sealevelpercpu, SealevelGeometry* slgeom){ /*{{{*/ - /*sal green function:*/ IssmDouble oceanaverage=0; IssmDouble oceanarea=0; @@ -7369,4 +7477,8 @@ IssmDouble* GE=NULL; IssmDouble* GN=NULL; + IssmDouble* Grot=NULL; + IssmDouble* GUrot=NULL; + IssmDouble* GNrot=NULL; + IssmDouble* GErot=NULL; IssmDouble* Gsub[SLGEOM_NUMLOADS]; IssmDouble* GUsub[SLGEOM_NUMLOADS]; @@ -7377,16 +7489,5 @@ int horiz; int size; - IssmDouble Grotm1[3]; - IssmDouble Grotm2[3]; - IssmDouble Grotm3[3]; - IssmDouble GUrotm1[3]; - IssmDouble GUrotm2[3]; - IssmDouble GUrotm3[3]; - IssmDouble GNrotm1[3]; - IssmDouble GNrotm2[3]; - IssmDouble GNrotm3[3]; - IssmDouble GErotm1[3]; - IssmDouble GErotm2[3]; - IssmDouble GErotm3[3]; + bool rotation= false; bool elastic=false; @@ -7424,51 +7525,20 @@ this->inputs->GetArrayPtr(SealevelchangeGEsubelOceanEnum,this->lid,&GEsub[SLGEOM_OCEAN],&size); } - } - this->SealevelchangeGxL(&RSLGrd[0],G, Gsub, loads, slgeom, nel,percpu=false,SealevelchangeViscousRSLEnum,computefuture=true); + if (rotation) { + this->inputs->GetArrayPtr(SealevelchangeGrotEnum,this->lid,&Grot,&size); + this->inputs->GetArrayPtr(SealevelchangeGUrotEnum,this->lid,&GUrot,&size); + if (horiz){ + this->inputs->GetArrayPtr(SealevelchangeGErotEnum,this->lid,&GErot,&size); + this->inputs->GetArrayPtr(SealevelchangeGNrotEnum,this->lid,&GNrot,&size); + } + } + } + this->SealevelchangeGxL(&RSLGrd[0],G, Gsub, Grot, loads, polarmotionvector, slgeom, nel,percpu=false,SealevelchangeViscousRSLEnum,computefuture=true); if(elastic){ - this->SealevelchangeGxL(&UGrd[0],GU, GUsub, loads, slgeom, nel,percpu=false,SealevelchangeViscousUEnum,computefuture=true); - if(horiz ){ - this->SealevelchangeGxL(&NGrd[0],GN, GNsub, loads, slgeom, nel,percpu=false,SealevelchangeViscousNEnum,computefuture=true); - this->SealevelchangeGxL(&EGrd[0],GE, GEsub, loads, slgeom, nel,percpu=false,SealevelchangeViscousEEnum,computefuture=true); - } - } - } - - if(rotation){ - Element::GetInputListOnVertices(&Grotm1[0],SealevelGrotm1Enum); - Element::GetInputListOnVertices(&Grotm2[0],SealevelGrotm2Enum); - Element::GetInputListOnVertices(&Grotm3[0],SealevelGrotm3Enum); - - for(int i=0;ilids[this->vertices[i]->lid]==this->lid){ - RSLGrd[i]+=Grotm1[i]*polarmotionvector[0]+Grotm2[i]*polarmotionvector[1]+Grotm3[i]*polarmotionvector[2]; - } - } - - if (elastic){ - Element::GetInputListOnVertices(&GUrotm1[0],SealevelGUrotm1Enum); - Element::GetInputListOnVertices(&GUrotm2[0],SealevelGUrotm2Enum); - Element::GetInputListOnVertices(&GUrotm3[0],SealevelGUrotm3Enum); - - for(int i=0;ilids[this->vertices[i]->lid]==this->lid){ - UGrd[i]+=GUrotm1[i]*polarmotionvector[0]+GUrotm2[i]*polarmotionvector[1]+GUrotm3[i]*polarmotionvector[2]; - } - } - if (horiz){ - Element::GetInputListOnVertices(&GNrotm1[0],SealevelGNrotm1Enum); - Element::GetInputListOnVertices(&GNrotm2[0],SealevelGNrotm2Enum); - Element::GetInputListOnVertices(&GNrotm3[0],SealevelGNrotm3Enum); - Element::GetInputListOnVertices(&GErotm1[0],SealevelGErotm1Enum); - Element::GetInputListOnVertices(&GErotm2[0],SealevelGErotm2Enum); - Element::GetInputListOnVertices(&GErotm3[0],SealevelGErotm3Enum); - - for(int i=0;ilids[this->vertices[i]->lid]==this->lid){ - NGrd[i]+=GNrotm1[i]*polarmotionvector[0]+GNrotm2[i]*polarmotionvector[1]+GNrotm3[i]*polarmotionvector[2]; - EGrd[i]+=GErotm1[i]*polarmotionvector[0]+GErotm2[i]*polarmotionvector[1]+GErotm3[i]*polarmotionvector[2]; - } - } + this->SealevelchangeGxL(&UGrd[0],GU, GUsub, GUrot, loads, polarmotionvector, slgeom, nel,percpu=false,SealevelchangeViscousUEnum,computefuture=true); + if(horiz){ + this->SealevelchangeGxL(&NGrd[0],GN, GNsub, GNrot, loads, polarmotionvector, slgeom, nel,percpu=false,SealevelchangeViscousNEnum,computefuture=true); + this->SealevelchangeGxL(&EGrd[0],GE, GEsub, GErot, loads, polarmotionvector, slgeom, nel,percpu=false,SealevelchangeViscousEEnum,computefuture=true); } } @@ -7495,27 +7565,46 @@ } /*}}}*/ -void Tria::SealevelchangeGxL(IssmDouble* grdfieldout, IssmDouble* G, IssmDouble** Gsub, GrdLoads* loads, SealevelGeometry* slgeom, int nel, bool percpu, int viscousenum, bool computefuture) { /*{{{*/ +void Tria::SealevelchangeGxL(IssmDouble* grdfieldout, IssmDouble* G, IssmDouble** Gsub, IssmDouble* Grot, GrdLoads* loads, IssmDouble* polarmotionvector, SealevelGeometry* slgeom, int nel, bool percpu, int viscousenum, bool computefuture) { /*{{{*/ + + //This function performs the actual convolution between Green functions and surface Loads for a particular grd field IssmDouble* grdfield=NULL; int i,e,l,t,nbar; bool computeviscous=false; + bool rotation=false; IssmDouble* viscousfield=NULL; - int nt=1; //important + int nt=1; //important, ensures there is a defined value if computeviscous is false int viscousindex=0; //important int viscousnumsteps=1; //important this->parameters->FindParam(&computeviscous,SolidearthSettingsViscousEnum); + this->parameters->FindParam(&rotation,SolidearthSettingsRotationEnum); if(computeviscous){ this->parameters->FindParam(&viscousnumsteps,SealevelchangeViscousNumStepsEnum); - if(computefuture) nt=viscousnumsteps; + this->parameters->FindParam(&viscousindex,SealevelchangeViscousIndexEnum); + if(computefuture) { + nt=viscousnumsteps-viscousindex+2; //number of time steps remaining to reach final_time, +1 is sufficient with no adaptative time stepping, +2 necessary otherwise; we assume the safe choice here for the sake of simplicity + if (nt>viscousnumsteps) nt=viscousnumsteps; + } else nt=1; - - //allocate - grdfield=xNewZeroInit(3*nt); - } - else grdfield=xNewZeroInit(3*nt); - - if(loads->sealevelloads){ - + } + //allocate + grdfield=xNewZeroInit(3*nt); + + if(rotation){ //add rotational feedback + for(int i=0;ilids[this->vertices[i]->lid]==this->lid){ + for (int m=0;m<3;m++){ //polar motion components + for(t=0;tsealevelloads){ // general case: loads + sealevel loads for(i=0;ilids[this->vertices[i]->lid]!=this->lid)continue; @@ -7546,5 +7635,4 @@ } else{ //this is the initial convolution where only loads are provided - for(i=0;ilids[this->vertices[i]->lid]!=this->lid)continue; @@ -7567,5 +7655,10 @@ } - if(computeviscous){ + if(computeviscous){ /*{{{*/ + // we need to do up to 3 things (* = only if computefuture) + // 1*: add new grdfield contribution to the viscous stack for future time steps + // 2: collect viscous grdfield from past loads due at present-day and add it to grdfield[current_time] + // 3*: subtract from viscous stack the grdfield that has already been accounted for so we don't add it again at the next time step + IssmDouble* grdfieldinterp=NULL; IssmDouble* viscoustimes=NULL; @@ -7574,25 +7667,23 @@ IssmDouble timeacc; - this->parameters->FindParam(&viscousindex,SealevelchangeViscousIndexEnum); this->parameters->FindParam(&viscoustimes,NULL,SealevelchangeViscousTimesEnum); this->parameters->FindParam(&final_time,TimesteppingFinalTimeEnum); this->parameters->FindParam(&timeacc,SolidearthSettingsTimeAccEnum); this->inputs->GetArrayPtr(viscousenum,this->lid,&viscousfield,NULL); + /* Map new grdfield generated by present-day loads onto viscous time vector*/ if(computefuture){ - grdfieldinterp=xNew(3*nt); + grdfieldinterp=xNewZeroInit(3*viscousnumsteps); + //viscousindex time and first time step of grdfield coincide, so just copy that value + for(int i=0;ilids[this->vertices[i]->lid]!=this->lid)continue; + grdfieldinterp[i*viscousnumsteps+viscousindex]= grdfield[i*nt+0]; + } if(viscoustimes[viscousindex]lids[this->vertices[i]->lid]!=this->lid)continue; - grdfieldinterp[i*nt+t]= grdfield[i*nt+0]; - } - } - else{ - for(int i=0;ilids[this->vertices[i]->lid]!=this->lid)continue; - grdfieldinterp[i*nt+t]= (1-lincoeff)*grdfield[i*nt+(t-viscousindex-1)]+lincoeff*grdfield[i*nt+(t-viscousindex)]; - } + for(int t=viscousindex+1;tlids[this->vertices[i]->lid]!=this->lid)continue; + grdfieldinterp[i*viscousnumsteps+t]= (1-lincoeff)*grdfield[i*nt+(t-viscousindex-1)]+lincoeff*grdfield[i*nt+(t-viscousindex)]; } } @@ -7606,14 +7697,14 @@ } - if(computefuture){ /*update viscous stack with future deformation from present load: */ - - for(int t=nt-1;t>=viscousindex;t--){ + /*update viscous stack with future deformation from present load: */ + if(computefuture){ + for(int t=viscousnumsteps-1;t>=viscousindex;t--){ for(int i=0;ilids[this->vertices[i]->lid]!=this->lid)continue; //offset viscousfield to remove all deformation that has already been added - viscousfield[i*viscousnumsteps+t]+=grdfieldinterp[i*nt+t]-grdfieldinterp[i*nt+viscousindex]-viscousfield[i*viscousnumsteps+viscousindex]; + viscousfield[i*viscousnumsteps+t]+=grdfieldinterp[i*viscousnumsteps+t]-grdfieldinterp[i*viscousnumsteps+viscousindex]-viscousfield[i*viscousnumsteps+viscousindex]; } } - /*Re-add viscous stack now that we updated:*/ + /*Save viscous stack now that we updated the values:*/ this->inputs->SetArrayInput(viscousenum,this->lid,viscousfield,3*viscousnumsteps); } @@ -7621,5 +7712,6 @@ /*Free allocatoins:*/ xDelete(viscoustimes); - } + } + /*}}}*/ /*store values computed on vertices, but don't repeat the computation if another element already computed it!:*/ @@ -7636,77 +7728,5 @@ } /*}}}*/ -void Tria::SealevelchangeMomentOfInertiaCentroid(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom){/*{{{*/ - - IssmDouble S=0; - - /*Compute area of element:*/ - IssmDouble area,planetarea,re; - IssmDouble late,longe; - this->Element::GetInputValue(&area,AreaEnum); - - /*recover parameters: */ - this->parameters->FindParam(&planetarea,SolidearthPlanetAreaEnum); - this->parameters->FindParam(&re,SolidearthPlanetRadiusEnum); - late=slgeom->late[this->lid]/180*M_PI; - longe=slgeom->longe[this->lid]/180*M_PI; - - /*recover total load: */ - if(loads->loads) S+=loads->loads[this->Sid()]; - if(loads->sealevelloads) S+=loads->sealevelloads[this->Sid()]; - - /* Perturbation terms for moment of inertia (moi_list): - * computed analytically (see Wu & Peltier, eqs 10 & 32) - * also consistent with my GMD formulation! - * ALL in geographic coordinates - * */ - dI_list[0] = -4*M_PI*(S*area)*pow(re,4)*(sin(late)*cos(late)*cos(longe))/planetarea; - dI_list[1] = -4*M_PI*(S*area)*pow(re,4)*(sin(late)*cos(late)*sin(longe))/planetarea; - dI_list[2] = +4*M_PI*(S*area)*pow(re,4)*(1-pow(sin(late),2))/planetarea; - return; -}/*}}}*/ -void Tria::SealevelchangeMomentOfInertiaSubElement(IssmDouble* dI_list, GrdLoads* grdloads, SealevelGeometry* slgeom){/*{{{*/ - - IssmDouble SA=0; - IssmDouble* loads=NULL; - IssmDouble* sealevelloads=NULL; - IssmDouble late,longe,re; - int intj; - IssmDouble area; - IssmDouble planetarea; - - /*recover parameters: */ - this->parameters->FindParam(&planetarea,SolidearthPlanetAreaEnum); - this->parameters->FindParam(&re,SolidearthPlanetRadiusEnum); - - /*Initalize:*/ - for(int i=0;i<3;i++)dI_list[i]=0; - - /*Go through our loads:*/ - for(int i=0;iissubelement[i][this->lid]){ - loads=grdloads->subloads[i]; - if(i==SLGEOM_OCEAN) sealevelloads=grdloads->subsealevelloads; - intj=slgeom->subelementmapping[i][this->lid]; - late=slgeom->latbarycentre[i][intj]/180*M_PI; - longe=slgeom->longbarycentre[i][intj]/180*M_PI; - area=slgeom->area_subel[i][intj]; - - /*recover total load: */ - if(loads) SA+=loads[intj]*area; - if(sealevelloads) SA+=sealevelloads[intj]*area; - } - } - - /* Perturbation terms for moment of inertia (moi_list): - * computed analytically (see Wu & Peltier, eqs 10 & 32) - * also consistent with my GMD formulation! - * ALL in geographic coordinates - * */ - dI_list[0] += -4*M_PI*(SA)*pow(re,4)*(sin(late)*cos(late)*cos(longe))/planetarea; - dI_list[1] += -4*M_PI*(SA)*pow(re,4)*(sin(late)*cos(late)*sin(longe))/planetarea; - dI_list[2] += +4*M_PI*(SA)*pow(re,4)*(1-pow(sin(late),2))/planetarea; - - return; -}/*}}}*/ + void Tria::SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom){ /*{{{*/ Index: /issm/trunk/src/c/classes/Elements/Tria.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Tria.h (revision 27034) +++ /issm/trunk/src/c/classes/Elements/Tria.h (revision 27035) @@ -55,8 +55,10 @@ void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part); void CalvingRateVonmises(); + void CalvingRateTest(); void CalvingCrevasseDepth(); void CalvingRateLevermann(); void CalvingFluxLevelset(); void CalvingMeltingFluxLevelset(); + void CalvingRateParameterization(); IssmDouble CharacteristicLength(void); void ComputeBasalStress(void); @@ -64,4 +66,5 @@ void ComputeEsaStrainAndVorticity(); void ComputeSigmaNN(); + void ComputeSigmaVM(); void ComputeStressTensor(); void ComputeSurfaceNormalVelocity(); @@ -177,7 +180,5 @@ void SealevelchangeDeformationConvolution(IssmDouble* sealevelpercpu, GrdLoads* loads, IssmDouble* rotationvector,SealevelGeometry* slgeom); void SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom); - void SealevelchangeMomentOfInertiaCentroid(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom); - void SealevelchangeMomentOfInertiaSubElement(IssmDouble* dI_list, GrdLoads* loads, SealevelGeometry* slgeom); - void SealevelchangeUpdateViscousFields(); + void SealevelchangeUpdateViscousFields(IssmDouble lincoeff, int newindex, int offset); #endif /*}}}*/ @@ -243,5 +244,5 @@ void UpdateConstraintsExtrudeFromBase(void); void UpdateConstraintsExtrudeFromTop(void); - void SealevelchangeGxL(IssmDouble* sealevel, IssmDouble* G, IssmDouble** Gsub, GrdLoads* loads, SealevelGeometry* slgeom, int nel, bool percpu,int stackenum,bool computefuture); + void SealevelchangeGxL(IssmDouble* sealevel, IssmDouble* G, IssmDouble** Gsub, IssmDouble* Grot, GrdLoads* loads, IssmDouble* polarmotionvector,SealevelGeometry* slgeom, int nel, bool percpu,int stackenum,bool computefuture); /*}}}*/ Index: /issm/trunk/src/c/classes/ExternalResults/GenericExternalResult.h =================================================================== --- /issm/trunk/src/c/classes/ExternalResults/GenericExternalResult.h (revision 27034) +++ /issm/trunk/src/c/classes/ExternalResults/GenericExternalResult.h (revision 27035) @@ -227,5 +227,4 @@ } /*}}}*/ template <> inline void GenericExternalResult::Marshall(MarshallHandle* marshallhandle){/*{{{*/ - printf("-------------- file: GenericExternalResult.h line: %i\n",__LINE__); this->GenericMarshall(marshallhandle); @@ -331,5 +330,4 @@ } /*}}}*/ template <> inline void GenericExternalResult::Marshall(MarshallHandle* marshallhandle){/*{{{*/ - printf("-------------- file: GenericExternalResult.h line: %i\n",__LINE__); marshallhandle->call(this->id); marshallhandle->call(this->result_name); @@ -456,5 +454,4 @@ } /*}}}*/ template <> inline void GenericExternalResult::Marshall(MarshallHandle* marshallhandle){/*{{{*/ - printf("-------------- file: GenericExternalResult.h line: %i\n",__LINE__); int object_enum = this->ObjectEnum(); @@ -590,5 +587,4 @@ } /*}}}*/ template <> inline void GenericExternalResult::Marshall(MarshallHandle* marshallhandle){/*{{{*/ - printf("-------------- file: GenericExternalResult.h line: %i\n",__LINE__); int object_enum = this->ObjectEnum(); Index: /issm/trunk/src/c/classes/FemModel.cpp =================================================================== --- /issm/trunk/src/c/classes/FemModel.cpp (revision 27034) +++ /issm/trunk/src/c/classes/FemModel.cpp (revision 27035) @@ -576,12 +576,12 @@ } /*}}}*/ -void FemModel::Restart(){ /*{{{*/ - - FILE* restartfid=NULL; - char* restartfilename = NULL; - int femmodel_size=0; - int fread_return=0; - char* femmodel_buffer=NULL; - char* femmodel_buffer_ini=NULL; +void FemModel::Restart(int verboselevel){ /*{{{*/ + + FILE *restartfid = NULL; + char *restartfilename = NULL; + int femmodel_size = 0; + int fread_return = 0; + char *femmodel_buffer = NULL; + char *femmodel_buffer_ini = NULL; /*First, recover the name of the restart file: */ @@ -597,9 +597,17 @@ /*Print banner*/ - _printf0_(" \n"); - _printf0_("====================================================================\n"); - _printf0_(" RESTART DETECTED: "<1){ + _printf0_(" \n"); + _printf0_("====================================================================\n"); + _printf0_(" RESTART DETECTED: "<Restart(); + this->Restart(1); /*Clean up and return*/ @@ -3097,5 +3105,5 @@ void FemModel::UpdateConstraintsx(void){ /*{{{*/ - IssmDouble time; + IssmDouble time,yts; int analysis_type,config_type; @@ -3104,4 +3112,5 @@ parameters->FindParam(&config_type,ConfigurationTypeEnum); parameters->FindParam(&time,TimeEnum); + parameters->FindParam(&yts,ConstantsYtsEnum); int index=AnalysisIndex(config_type); @@ -3109,5 +3118,5 @@ /*start module: */ - if(VerboseModule()) _printf0_(" Updating constraints and active domain of analysis " << EnumToStringx(analysis_type) << " for time: " << time << "\n"); + if(VerboseModule()) _printf0_(" Updating constraints and active domain of analysis " << EnumToStringx(analysis_type) << " for time: " << time/yts << "\n"); Analysis* analysis= EnumToAnalysis(analysis_type); @@ -3121,6 +3130,5 @@ NodesDofx(nodes,parameters); -} -/*}}}*/ +}/*}}}*/ int FemModel::UpdateVertexPositionsx(void){ /*{{{*/ @@ -3211,5 +3219,5 @@ this->parameters->FindParam(&temp,FlowequationIsSSAEnum); iomodel->AddConstant(new IoConstant(temp,"md.flowequation.isSSA")); this->parameters->FindParam(&temp,FlowequationIsL1L2Enum); iomodel->AddConstant(new IoConstant(temp,"md.flowequation.isL1L2")); - this->parameters->FindParam(&temp,FlowequationIsMLHOEnum); iomodel->AddConstant(new IoConstant(temp,"md.flowequation.isMLHO")); + this->parameters->FindParam(&temp,FlowequationIsMOLHOEnum); iomodel->AddConstant(new IoConstant(temp,"md.flowequation.isMOLHO")); this->parameters->FindParam(&temp,FlowequationIsHOEnum); iomodel->AddConstant(new IoConstant(temp,"md.flowequation.isHO")); this->parameters->FindParam(&temp,FlowequationIsFSEnum); iomodel->AddConstant(new IoConstant(temp,"md.flowequation.isFS")); Index: /issm/trunk/src/c/classes/FemModel.h =================================================================== --- /issm/trunk/src/c/classes/FemModel.h (revision 27034) +++ /issm/trunk/src/c/classes/FemModel.h (revision 27035) @@ -83,5 +83,5 @@ void InitFromFids(char* rootpath, FILE* IOMODEL, FILE* toolkitsoptionsfid, int in_solution_type, bool trace, IssmPDouble* X=NULL); void Marshall(MarshallHandle* marshallhandle); - void Restart(void); + void Restart(int verboselevel=2); void RestartAD(int step); void SetCurrentConfiguration(int configuration_type); Index: /issm/trunk/src/c/classes/GrdLoads.cpp =================================================================== --- /issm/trunk/src/c/classes/GrdLoads.cpp (revision 27034) +++ /issm/trunk/src/c/classes/GrdLoads.cpp (revision 27035) @@ -68,2 +68,54 @@ } /*}}}*/ +void GrdLoads::SHDegree2Coefficients(IssmDouble* deg2coeff, FemModel* femmodel, SealevelGeometry* slgeom){ + + IssmDouble area,re, S; + int ylmindex, intj; + IssmDouble deg2coeff_local[5]; + + femmodel->parameters->FindParam(&re,SolidearthPlanetRadiusEnum); + + for (int c=0;c<5;c++) deg2coeff_local[c]=0; + + for(Object* & object : femmodel->elements->objects){ + Element* element = xDynamicCast(object); + //first, loads on centroids + S=0; + S+=loads[element->Sid()]; + + if(sealevelloads) S+=sealevelloads[element->Sid()]; + if(S!=0){ + element->Element::GetInputValue(&area,AreaEnum); + + for (int c=0;c<5;c++){ //degree l=2 has 2*l+1=5 coefficients: 2,0; 2,1cos; 2,1sin; 2,2cos; 2,2sin + ylmindex=(4+c)*slgeom->localnel+element->lid; // starting at index=l^2 + deg2coeff_local[c] += S*area/re/re*slgeom->Ylm[ylmindex]; + } + } + //add loads on subelement barycenters + for (int i=0;iissubelement[i][element->lid]){ + intj=slgeom->subelementmapping[i][element->lid]; + S=0; + S+=subloads[i][intj]; + if(i==SLGEOM_OCEAN && sealevelloads) S+=subsealevelloads[intj]; + if(S!=0){ + area=slgeom->area_subel[i][intj]; + for (int c=0;c<5;c++){ //degree l=2 has 2*l+1=5 coefficients + ylmindex=(4+c)*slgeom->localnel+element->lid; // starting at index=l^2 + deg2coeff_local[c] += S*area/re/re*slgeom->Ylm_subel[i][ylmindex]; + } + } + } + } + } + + //sum each degree 2 coefficient across all cpus to get global total + ISSM_MPI_Reduce (°2coeff_local[0],°2coeff[0],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); + ISSM_MPI_Bcast(°2coeff[0],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + ISSM_MPI_Reduce (°2coeff_local[1],°2coeff[1],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); + ISSM_MPI_Bcast(°2coeff[1],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + ISSM_MPI_Reduce (°2coeff_local[2],°2coeff[2],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); + ISSM_MPI_Bcast(°2coeff[2],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + +} Index: /issm/trunk/src/c/classes/GrdLoads.h =================================================================== --- /issm/trunk/src/c/classes/GrdLoads.h (revision 27034) +++ /issm/trunk/src/c/classes/GrdLoads.h (revision 27035) @@ -29,4 +29,5 @@ void BroadcastLoads(void); void BroadcastSealevelLoads(void); + void SHDegree2Coefficients(IssmDouble* deg2coeff, FemModel* femmodel, SealevelGeometry* slgeom); }; #endif /* _SEALEVELGRDLOADS_H_ */ Index: /issm/trunk/src/c/classes/Inputs/TransientInput.cpp =================================================================== --- /issm/trunk/src/c/classes/Inputs/TransientInput.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Inputs/TransientInput.cpp (revision 27035) @@ -125,4 +125,6 @@ void TransientInput::Marshall(MarshallHandle* marshallhandle){ /*{{{*/ + bool isnull; + int object_enum = TransientInputEnum; marshallhandle->call(object_enum); @@ -149,26 +151,36 @@ if(marshallhandle->OperationNumber()!=MARSHALLING_LOAD){ for(int i=0;inumtimesteps;i++){ - _assert_(this->inputs[i]); - object_enum = this->inputs[i]->ObjectEnum(); - marshallhandle->call(object_enum); - this->inputs[i]->Marshall(marshallhandle); + + //_assert_(this->inputs[i]); + isnull = false; + if(!this->inputs[i]) isnull = true; + marshallhandle->call(isnull); + + if(!isnull){ + object_enum = this->inputs[i]->ObjectEnum(); + marshallhandle->call(object_enum); + this->inputs[i]->Marshall(marshallhandle); + } } } else{ for(int i=0;inumtimesteps;i++){ - marshallhandle->call(object_enum); - - if(object_enum==TriaInputEnum){ - TriaInput* triainput2=new TriaInput(); - triainput2->Marshall(marshallhandle); - this->inputs[i]=triainput2; - } - else if(object_enum==PentaInputEnum){ - PentaInput* pentainput2=new PentaInput(); - pentainput2->Marshall(marshallhandle); - this->inputs[i]=pentainput2; - } - else{ - _error_("input "<call(isnull); + if(!isnull){ + marshallhandle->call(object_enum); + + if(object_enum==TriaInputEnum){ + TriaInput* triainput2=new TriaInput(); + triainput2->Marshall(marshallhandle); + this->inputs[i]=triainput2; + } + else if(object_enum==PentaInputEnum){ + PentaInput* pentainput2=new PentaInput(); + pentainput2->Marshall(marshallhandle); + this->inputs[i]=pentainput2; + } + else{ + _error_("input "<IsIceInElement() || this->boundary){ + if(!tria->IsIceInElement() || tria->IsAllFloating() || this->boundary){ this->S = 0.; return; Index: /issm/trunk/src/c/classes/Loads/Penpair.cpp =================================================================== --- /issm/trunk/src/c/classes/Loads/Penpair.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Loads/Penpair.cpp (revision 27035) @@ -355,7 +355,7 @@ default: _error_("Approximation "<StrainRateMLHO(&epsilon[0],xyz_list,gauss, + element->StrainRateMOLHO(&epsilon[0],xyz_list,gauss, vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input,zeta); epsilon_eff=sqrt(epsilon[0]*epsilon[0] + epsilon[1]*epsilon[1] + epsilon[2]*epsilon[2] @@ -797,5 +795,5 @@ delete gauss_seg; }/*}}}*/ -void Matice::ViscosityMLHOAdjoint(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vxbase_input,Input* vybase_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input){/*{{{*/ +void Matice::ViscosityMOLHOAdjoint(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vxbase_input,Input* vybase_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input){/*{{{*/ /* To compute the additional 5 terms in the viscosity appear in the adjoint equation*/ @@ -819,5 +817,5 @@ /* eps_eff^2 = exx^2 + eyy^2 + exy^2 + exz^2 + eyz^2 + exx*eyy (for a given zeta)*/ - element->StrainRateMLHO(&epsilon[0],xyz_list,gauss, + element->StrainRateMOLHO(&epsilon[0],xyz_list,gauss, vxbase_input,vybase_input,vxshear_input,vyshear_input,thickness_input,n_input,zeta); epsilon_eff=sqrt(epsilon[0]*epsilon[0] + epsilon[1]*epsilon[1] + epsilon[2]*epsilon[2] Index: /issm/trunk/src/c/classes/Materials/Matice.h =================================================================== --- /issm/trunk/src/c/classes/Materials/Matice.h (revision 27034) +++ /issm/trunk/src/c/classes/Materials/Matice.h (revision 27035) @@ -78,6 +78,6 @@ void ViscosityFS(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input); void ViscosityHO(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); - void ViscosityMLHO(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input); - void ViscosityMLHOAdjoint(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input); + void ViscosityMOLHO(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input); + void ViscosityMOLHOAdjoint(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input); void ViscosityL1L2(IssmDouble* pviscosity,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* surf); void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); Index: /issm/trunk/src/c/classes/Materials/Matlitho.h =================================================================== --- /issm/trunk/src/c/classes/Materials/Matlitho.h (revision 27034) +++ /issm/trunk/src/c/classes/Materials/Matlitho.h (revision 27035) @@ -72,6 +72,6 @@ void ViscosityFS(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){_error_("not supported");}; void ViscosityHO(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; - void ViscosityMLHO(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input){_error_("not supported");}; - void ViscosityMLHOAdjoint(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input){_error_("not supported");}; + void ViscosityMOLHO(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input){_error_("not supported");}; + void ViscosityMOLHOAdjoint(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vxshear_input,Input* vyshear_input,Input* thickness_input,Input* n_input){_error_("not supported");}; void ViscosityL1L2(IssmDouble* pviscosity,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* surf){_error_("not supported");}; void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; Index: /issm/trunk/src/c/classes/Node.cpp =================================================================== --- /issm/trunk/src/c/classes/Node.cpp (revision 27034) +++ /issm/trunk/src/c/classes/Node.cpp (revision 27035) @@ -118,5 +118,5 @@ this->HardDeactivate(); } - if(in_approximation==MLHOApproximationEnum && !reCast(iomodel->Data("md.mesh.vertexonbase")[io_index])){ + if(in_approximation==MOLHOApproximationEnum && !reCast(iomodel->Data("md.mesh.vertexonbase")[io_index])){ this->HardDeactivate(); } Index: /issm/trunk/src/c/classes/Radar.h =================================================================== --- /issm/trunk/src/c/classes/Radar.h (revision 27034) +++ /issm/trunk/src/c/classes/Radar.h (revision 27035) @@ -11,5 +11,4 @@ IssmDouble OutputDefinitionsResponsex(FemModel* femmodel,int output_enum); -void GetVectorFromInputsx( IssmDouble** pvector, int* pvector_size, FemModel* femmodel,int name); class Radar: public Object, public Definition{ Index: /issm/trunk/src/c/classes/SealevelGeometry.cpp =================================================================== --- /issm/trunk/src/c/classes/SealevelGeometry.cpp (revision 27034) +++ /issm/trunk/src/c/classes/SealevelGeometry.cpp (revision 27035) @@ -35,4 +35,5 @@ nsubel[i]=0; nbar[i]=0; + Ylm_subel[i]= xNewZeroInit(localnel*9); } late=xNew(localnel); @@ -40,4 +41,5 @@ isoceanin=xNew(localnel); lids=xNew(localnodsin); + Ylm=xNewZeroInit(localnel*9); // (degmax+1)^2 terms, degmax=2 }; /*}}}*/ @@ -56,5 +58,7 @@ xDelete(longbarycentre[i]); xDelete(area_subel[i]); - } + xDelete(Ylm_subel[i]); + } + xDelete(Ylm); xDelete(late); xDelete(longe); @@ -71,5 +75,9 @@ for (int i=0;i(localnel); + #ifdef _HAVE_PETSC_ GetOwnershipBoundariesFromRange(&lower_row,&dummy,nsubel[i],IssmComm::GetComm()); + #else + _error_("not supported without PETSc compiled"); + #endif int count=0; @@ -155,2 +163,62 @@ } /*}}}*/ +void SealevelGeometry::BuildSphericalHarmonics(){ /*{{{*/ + //builds spherical harmonics functions for degrees 0, 1, 2 on centroids/barycenters + //0: used for global average + //1: used for geocenter motion + //2: used for rotational feedback + int intj, count; + + IssmDouble YlmNorm[9]; + + //YlmNormalization: N^2=(2*l+1)/4/pi * factorial(l-m)/factorial(l+m) if m==0 + // : 2*N^2 if m>0 + // such that integral(Ylm * Ylm *YlmNorm dS) = 1 on the unit sphere. + YlmNorm[0]=(0.25/M_PI); //Y00 + YlmNorm[1]=(0.75/M_PI); //Y10 + YlmNorm[2]=(0.75/M_PI); //Y11c + YlmNorm[3]=YlmNorm[2]; //Y11s + YlmNorm[4]=(1.25/M_PI); //Y20 + YlmNorm[5]=(1.25/3./M_PI); //Y21c + YlmNorm[6]=YlmNorm[5]; //Y21s + YlmNorm[7]=(1.25/12./M_PI); //Y22c + YlmNorm[8]=YlmNorm[7]; //Y22s + + for (int e=0;enrows;i++) if(this->fglobaldoflist[i] == dof) return true; + } + else if(set==GsetEnum){ + for(int i=0;inrows;i++) if(this->gglobaldoflist[i] == dof) return true; + } + else if(set==SsetEnum){ + for(int i=0;inrows;i++) if(this->sglobaldoflist[i] == dof) return true; + } + else{ + _error_("not supported yet"); + } + + return false; } /*}}}*/ Index: /issm/trunk/src/c/classes/matrix/ElementMatrix.h =================================================================== --- /issm/trunk/src/c/classes/matrix/ElementMatrix.h (revision 27034) +++ /issm/trunk/src/c/classes/matrix/ElementMatrix.h (revision 27035) @@ -46,4 +46,5 @@ void StaticCondensation(int numindices,int* indices); void Transpose(void); + bool HasDof(int dof,int set); }; #endif //#ifndef _ELEMENT_MATRIX_H_ Index: /issm/trunk/src/c/cores/ProcessArguments.cpp =================================================================== --- /issm/trunk/src/c/cores/ProcessArguments.cpp (revision 27034) +++ /issm/trunk/src/c/cores/ProcessArguments.cpp (revision 27035) @@ -29,10 +29,11 @@ /*Create all file paths*/ - char* binfilename = xNew(strlen(rootpath)+strlen(modelname)+strlen(".bin") +1); sprintf(binfilename, "%s%s%s",rootpath,modelname,".bin"); - char* outbinfilename = xNew(strlen(rootpath)+strlen(modelname)+strlen(".outbin") +1); sprintf(outbinfilename,"%s%s%s",rootpath,modelname,".outbin"); - char* toolkitsfilename = xNew(strlen(rootpath)+strlen(modelname)+strlen(".toolkits") +1); sprintf(toolkitsfilename,"%s%s%s",rootpath,modelname,".toolkits"); - char* lockfilename = xNew(strlen(rootpath)+strlen(modelname)+strlen(".lock") +1); sprintf(lockfilename, "%s%s%s",rootpath,modelname,".lock"); - char* restartfilename = xNew(strlen(rootpath)+strlen(modelname)+strlen(".rst.")+rank_length+1); - sprintf(restartfilename,"%s%s%s%i",rootpath,modelname,".rst.",my_rank); + int base_length = strlen(rootpath)+strlen(modelname); + char* binfilename = xNew(base_length+strlen(".bin") +1); sprintf(binfilename, "%s%s%s",rootpath,modelname,".bin"); + char* outbinfilename = xNew(base_length+strlen(".outbin") +1); sprintf(outbinfilename,"%s%s%s",rootpath,modelname,".outbin"); + char* toolkitsfilename = xNew(base_length+strlen(".toolkits")+1); sprintf(toolkitsfilename,"%s%s%s",rootpath,modelname,".toolkits"); + char* lockfilename = xNew(base_length+strlen(".lock") +1); sprintf(lockfilename, "%s%s%s",rootpath,modelname,".lock"); + char* restartfilename = xNew(base_length+strlen("_rank")+rank_length+strlen(".rst")+1); + sprintf(restartfilename,"%s%s%s%i%s",rootpath,modelname,"_rank",my_rank,".rst"); /*Clean up and assign output pointer*/ @@ -44,4 +45,3 @@ *prootpath=rootpath; *pmodelname=modelname; - } Index: /issm/trunk/src/c/cores/bmb_core.cpp =================================================================== --- /issm/trunk/src/c/cores/bmb_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/bmb_core.cpp (revision 27035) @@ -36,6 +36,8 @@ FloatingiceMeltingRatex(femmodel); - /*Extrude basal melt*/ - femmodel->parameters->SetParam(BasalforcingsFloatingiceMeltingRateEnum,InputToExtrudeEnum); - extrudefrombase_core(femmodel); + /*Extrude basal melt if not default melting rate (which may be a transient input that can't be extruded)*/ + if(basalforcing_model!=FloatingMeltRateEnum){ + femmodel->parameters->SetParam(BasalforcingsFloatingiceMeltingRateEnum,InputToExtrudeEnum); + extrudefrombase_core(femmodel); + } } Index: /issm/trunk/src/c/cores/controladm1qn3_core.cpp =================================================================== --- /issm/trunk/src/c/cores/controladm1qn3_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/controladm1qn3_core.cpp (revision 27035) @@ -15,5 +15,5 @@ #include // for output of the CoDiPack tape #include -void transient_ad(FemModel* femmodel); +double transient_ad(FemModel* femmodel, double* G,double* Jlist); #endif @@ -222,4 +222,5 @@ int *N = NULL; int *control_enum = NULL; + int checkpoint_frequency; femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); femmodel->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); @@ -228,4 +229,5 @@ femmodel->parameters->FindParam(&M,NULL,ControlInputSizeMEnum); femmodel->parameters->FindParam(&control_enum,NULL,InversionControlParametersEnum); + femmodel->parameters->FindParam(&checkpoint_frequency,SettingsCheckpointFrequencyEnum); /*Constrain input vector and update controls*/ @@ -236,5 +238,5 @@ int offset = 0; - for (int c=0;c(intn,"t"); + IssmDouble* aX=xNew(intn,"t"); #else - IssmDouble* aX=xNew(intn); + IssmDouble* aX=xNew(intn); #endif - #if defined(_HAVE_ADOLC_) - if(my_rank==0){ - for(int i=0;i(aX); - - /*Compute solution (forward)*/ - void (*solutioncore)(FemModel*)=NULL; - CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); - solutioncore(femmodel); - - /*Get Dependents*/ - IssmDouble output_value; - int num_dependents; - IssmPDouble *dependents; - IssmDouble J = 0.; - DataSet *dependent_objects = ((DataSetParam*)femmodel->parameters->FindParamObject(AutodiffDependentObjectsEnum))->value; - femmodel->parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); - - /*Go through our dependent variables, and compute the response:*/ - dependents=xNew(num_dependents); - #if defined(_HAVE_CODIPACK_) - codi_global.output_indices.clear(); - #endif - int i=-1; - for(Object* & object:dependent_objects->objects){ - i++; - DependentObject* dep=xDynamicCast(object); - if(solution_type==TransientSolutionEnum) output_value = dep->GetValue(); - if(solution_type!=TransientSolutionEnum) dep->Responsex(&output_value,femmodel); - if(my_rank==0) { + #if defined(_HAVE_ADOLC_) + if(my_rank==0){ + for(int i=0;i(aX); + + /*Compute solution (forward)*/ + void (*solutioncore)(FemModel*)=NULL; + CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + solutioncore(femmodel); + + /*Get Dependents*/ + IssmDouble output_value; + int num_dependents; + IssmPDouble *dependents; + IssmDouble J = 0.; + DataSet *dependent_objects = ((DataSetParam*)femmodel->parameters->FindParamObject(AutodiffDependentObjectsEnum))->value; + femmodel->parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); + + /*Go through our dependent variables, and compute the response:*/ + dependents=xNew(num_dependents); + #if defined(_HAVE_CODIPACK_) + codi_global.output_indices.clear(); + #endif + int i=-1; + for(Object* & object:dependent_objects->objects){ + i++; + DependentObject* dep=xDynamicCast(object); + if(solution_type==TransientSolutionEnum) output_value = dep->GetValue(); + if(solution_type!=TransientSolutionEnum) dep->Responsex(&output_value,femmodel); #if defined(_HAVE_CODIPACK_) @@ -340,141 +351,145 @@ J+=output_value; } - } - - /*Turning off trace tape*/ - simul_stoptrace(); - - /*intermediary: */ - int num_independents=intn; - IssmPDouble *aWeightVector=NULL; - IssmPDouble *weightVectorTimesJac=NULL; - IssmPDouble *totalgradient=xNewZeroInit(num_independents); - - /*if no dependents, no point in running a driver: */ - if(!(num_dependents*num_independents)) _error_("this is not allowed"); - - /*for adolc to run in parallel, we 0 out on rank~=0. But we still keep track of num_dependents:*/ - int num_dependents_old = num_dependents; - int num_independents_old = num_independents; - - #if defined(_HAVE_ADOLC_) - /*Get gradient for ADOLC {{{*/ - if(my_rank!=0){ - num_dependents = 0; - num_independents = 0; - } - - /*get the EDF pointer:*/ - ext_diff_fct *anEDF_for_solverx_p=xDynamicCast * >(femmodel->parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p; - - /* these are always needed regardless of the interpreter */ - anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); - anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); - - /* Ok, now we are going to call the fos_reverse in a loop on the index, from 0 to num_dependents, so - * as to generate num_dependents gradients: */ - for(int aDepIndex=0;aDepIndex(num_dependents); - if (my_rank==0) aWeightVector[aDepIndex]=1.; - - /*initialize output gradient: */ - weightVectorTimesJac=xNew(num_independents); - - /*set the forward method function pointer: */ - #ifdef _HAVE_GSL_ - anEDF_for_solverx_p->fos_reverse=EDF_fos_reverse_for_solverx; - #endif - #ifdef _HAVE_MUMPS_ - anEDF_for_solverx_p->fos_reverse_iArr=fos_reverse_mumpsSolveEDF; - #endif - - anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); - anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); - - /*call driver: */ - fos_reverse(my_rank,num_dependents,num_independents, aWeightVector, weightVectorTimesJac ); - - /*Add to totalgradient: */ - if(my_rank==0) for(int i=0;i=num_dependents || codi_global.output_indices.size() <= dep_index){ - _error_("index value for dependent index should be in [0,num_dependents-1]"); + + /*Turning off trace tape*/ + simul_stoptrace(); + + /*intermediary: */ + int num_independents=intn; + IssmPDouble *aWeightVector=NULL; + IssmPDouble *weightVectorTimesJac=NULL; + IssmPDouble *totalgradient=xNewZeroInit(num_independents); + + /*if no dependents, no point in running a driver: */ + if(!(num_dependents*num_independents)) _error_("this is not allowed"); + + /*for adolc to run in parallel, we 0 out on rank~=0. But we still keep track of num_dependents:*/ + int num_dependents_old = num_dependents; + int num_independents_old = num_independents; + + #if defined(_HAVE_ADOLC_) + /*Get gradient for ADOLC {{{*/ + if(my_rank!=0){ + num_dependents = 0; + num_independents = 0; + } + + /*get the EDF pointer:*/ + ext_diff_fct *anEDF_for_solverx_p=xDynamicCast * >(femmodel->parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p; + + /* these are always needed regardless of the interpreter */ + anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); + anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); + + /* Ok, now we are going to call the fos_reverse in a loop on the index, from 0 to num_dependents, so + * as to generate num_dependents gradients: */ + for(int aDepIndex=0;aDepIndex(num_dependents); + if (my_rank==0) aWeightVector[aDepIndex]=1.; + + /*initialize output gradient: */ + weightVectorTimesJac=xNew(num_independents); + + /*set the forward method function pointer: */ + #ifdef _HAVE_GSL_ + anEDF_for_solverx_p->fos_reverse=EDF_fos_reverse_for_solverx; + #endif + #ifdef _HAVE_MUMPS_ + anEDF_for_solverx_p->fos_reverse_iArr=fos_reverse_mumpsSolveEDF; + #endif + + anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); + + /*call driver: */ + fos_reverse(my_rank,num_dependents,num_independents, aWeightVector, weightVectorTimesJac ); + + /*Add to totalgradient: */ + if(my_rank==0) for(int i=0;i(num_independents); - auto in_size = codi_global.input_indices.size(); - for(size_t i = 0; i < in_size; ++i){ - _assert_(i(J); - ISSM_MPI_Bcast(pf,1,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); - _printf0_("f(x) = "<(J); - - if(*indic==0){ - /*dry run, no gradient required*/ - - /*Retrieve objective functions independently*/ - _printf0_(" N/A |\n"); - for(int i=0;i(XU); - xDelete(XL); - return; - } - - /*Compute gradient*/ - for(long i=0;i=num_dependents || codi_global.output_indices.size() <= dep_index){ + _error_("index value for dependent index should be in [0,num_dependents-1]"); + } + tape_codi.setGradient(codi_global.output_indices[dep_index],1.0); + } + //feclearexcept(FE_ALL_EXCEPT); + //feenableexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW); + tape_codi.evaluate(); + + /*Get gradient for this dependent */ + weightVectorTimesJac=xNew(num_independents); + auto in_size = codi_global.input_indices.size(); + for(size_t i = 0; i < in_size; ++i){ + _assert_(i(J); + ISSM_MPI_Bcast(pf,1,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + + /*Record cost function values and delete Jtemp*/ + for(int i=0;i(J); + + if(*indic==0){ + /*dry run, no gradient required*/ + + /*Retrieve objective functions independently*/ + _printf0_("f(x) = "<(XU); + xDelete(XL); + return; + } + + /*Compute gradient*/ + for(long i=0;i(dependents); + xDelete(totalgradient); + } /*====????*/ /*Constrain Gradient*/ @@ -496,4 +511,5 @@ /*Print info*/ + _printf0_("f(x) = "<(N); xDelete(scaling_factors); - xDelete(dependents); - xDelete(totalgradient); }/*}}}*/ void controladm1qn3_core(FemModel* femmodel){/*{{{*/ - int checkpoint_frequency; - femmodel->parameters->FindParam(&checkpoint_frequency,SettingsCheckpointFrequencyEnum); - if(checkpoint_frequency){ - #ifdef _HAVE_CODIPACK_ - transient_ad(femmodel); - femmodel->OutputControlsx(&femmodel->results); - printf("No optimization implemented yet, skipping\n"); - return; - #else - _error_("checkpointing not implemented for ADOLC"); - #endif - } /*Intermediaries*/ Index: /issm/trunk/src/c/cores/controltao_core.cpp =================================================================== --- /issm/trunk/src/c/cores/controltao_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/controltao_core.cpp (revision 27035) @@ -95,5 +95,10 @@ GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + #if PETSC_VERSION_LT(3,17,0) TaoSetInitialVector(tao,X->pvector->vector); + #else + //TaoSetSolution(tao,X->pvector->vector); + _error_("not implemented yet"); + #endif TaoSetVariableBounds(tao,XL->pvector->vector,XU->pvector->vector); delete XL; @@ -110,7 +115,16 @@ /*Save results*/ + #if PETSC_VERSION_LT(3,17,0) TaoGetSolutionVector(tao,&X->pvector->vector); + #else + TaoGetSolution(tao,&X->pvector->vector); + #endif G=new Vector(0); VecFree(&G->pvector->vector); + #if PETSC_VERSION_LT(3,17,0) TaoGetGradientVector(tao,&G->pvector->vector); + #else + //TaoGetGradient(tao,&G->pvector->vector); + _error_("not implemented yet"); + #endif SetControlInputsFromVectorx(femmodel,X); ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,G); Index: /issm/trunk/src/c/cores/groundingline_core.cpp =================================================================== --- /issm/trunk/src/c/cores/groundingline_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/groundingline_core.cpp (revision 27035) @@ -16,8 +16,12 @@ /* intermediaries */ + int numoutputs; bool save_results; + char** requested_outputs = NULL; /* recover parameters */ femmodel->parameters->FindParam(&save_results,SaveResultsEnum); + femmodel->parameters->FindParam(&numoutputs,GroundinglineNumRequestedOutputsEnum); + if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,GroundinglineRequestedOutputsEnum); /*Move grounding line*/ @@ -33,8 +37,9 @@ extrudefrombase_core(femmodel); - if(save_results){ - int outputs[3] = {SurfaceEnum,BaseEnum,MaskOceanLevelsetEnum}; - femmodel->RequestedOutputsx(&femmodel->results,&outputs[0],3); - } + /*Save results*/ + if(save_results) femmodel->RequestedOutputsx(&femmodel->results,requested_outputs,numoutputs); + + /*Free ressources:*/ + if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} /*Stop profiler*/ Index: /issm/trunk/src/c/cores/love_core.cpp =================================================================== --- /issm/trunk/src/c/cores/love_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/love_core.cpp (revision 27035) @@ -10,4 +10,13 @@ #include "../solutionsequences/solutionsequences.h" #include "petscblaslapack.h" +#ifdef _HAVE_MPLAPACK_ +#include +#include "mpblas__Float128.h" +#include "mplapack__Float128.h" +#endif + +#ifdef _HAVE_MPLAPACK_ +_Float128 a = 0.2345234534512079875620048770134538q; +#endif /*local definitions:*/ @@ -20,4 +29,5 @@ int nyi; int starting_layer; + int* deg_layer_delete; LoveVariables(){ /*{{{*/ @@ -27,6 +37,7 @@ nyi=0; starting_layer=0; + deg_layer_delete=NULL; } /*}}}*/ - LoveVariables(IssmDouble* EarthMassin,IssmDouble g0in,IssmDouble r0in,int nyiin,int starting_layerin){ /*{{{*/ + LoveVariables(IssmDouble* EarthMassin,IssmDouble g0in,IssmDouble r0in,int nyiin,int starting_layerin, int* deg_layer_deletein){ /*{{{*/ EarthMass=EarthMassin; g0=g0in; @@ -34,6 +45,87 @@ nyi=nyiin; starting_layer=starting_layerin; + deg_layer_delete=deg_layer_deletein; } /*}}}*/ ~LoveVariables(){}; +}; /*}}}*/ + +template class LoveNumbers{ /*{{{*/ + + public: + doubletype* H; + doubletype* K; + doubletype* L; + doubletype* Kernels; + int sh_nmin, sh_nmax, nfreq, nkernels; + + LoveNumbers(){ /*{{{*/ + H=NULL; + K=NULL; + L=NULL; + Kernels=NULL; + sh_nmin=0; + sh_nmax=0; + nfreq=0; + nkernels=0; + } /*}}}*/ + LoveNumbers(int sh_nminin, int sh_nmaxin, int nfreqin, Matlitho* matlitho){ /*{{{*/ + sh_nmax=sh_nmaxin; + sh_nmin=sh_nminin; + nfreq=nfreqin; + nkernels=(sh_nmax+1)*(matlitho->numlayers+1)*6; + H=xNewZeroInit(nfreq*(sh_nmax+1)); + K=xNewZeroInit(nfreq*(sh_nmax+1)); + L=xNewZeroInit(nfreq*(sh_nmax+1)); + Kernels=xNewZeroInit(nfreq*nkernels); + } /*}}}*/ + void DownCastToDouble(LoveNumbers* LoveDouble){ + for(int i=0;i<(sh_nmax+1)*nfreq;i++){ + LoveDouble->H[i]=std::real(H[i]); + LoveDouble->K[i]=std::real(K[i]); + LoveDouble->L[i]=std::real(L[i]); + } + } + void LoveMPI_Gather(LoveNumbers* Love_local, int lower_row){ + int* recvcounts=xNew(IssmComm::GetSize()); + int* displs=xNew(IssmComm::GetSize()); + int rc; + int offset; + int nf_local = Love_local->nfreq; + + /*Deal H, K, L first, as they share the same size*/ + rc=(sh_nmax+1)*nf_local; + offset=(sh_nmax+1)*lower_row; + ISSM_MPI_Allgather(&rc,1,ISSM_MPI_INT,recvcounts,1,ISSM_MPI_INT,IssmComm::GetComm()); + ISSM_MPI_Allgather(&offset,1,ISSM_MPI_INT,displs,1,ISSM_MPI_INT,IssmComm::GetComm()); + ISSM_MPI_Allgatherv(Love_local->H, rc, ISSM_MPI_DOUBLE, H, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm()); + ISSM_MPI_Allgatherv(Love_local->K, rc, ISSM_MPI_DOUBLE, K, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm()); + ISSM_MPI_Allgatherv(Love_local->L, rc, ISSM_MPI_DOUBLE, L, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm()); + + /* deal with love kernels now */ + rc=nf_local*nkernels; + offset=lower_row*nkernels; + ISSM_MPI_Allgather(&rc,1,ISSM_MPI_INT,recvcounts,1,ISSM_MPI_INT,IssmComm::GetComm()); + ISSM_MPI_Allgather(&offset,1,ISSM_MPI_INT,displs,1,ISSM_MPI_INT,IssmComm::GetComm()); + ISSM_MPI_Allgatherv(Love_local->Kernels, rc, ISSM_MPI_DOUBLE, Kernels, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm()); + + xDelete(recvcounts); + xDelete(displs); + } + void Copy(LoveNumbers* LoveDup){ + for(int i=0;i<(sh_nmax+1)*nfreq;i++){ + H[i]=LoveDup->H[i]; + K[i]=LoveDup->K[i]; + L[i]=LoveDup->L[i]; + } + for(int i=0;iKernels[i]; + } + } + ~LoveNumbers(){ + xDelete(H); + xDelete(K); + xDelete(L); + xDelete(Kernels); + }; }; /*}}}*/ @@ -123,13 +215,29 @@ return xi; }/*}}}*/ -template void postwidder_transform(doubletype* Lovet, doubletype* Lovef,int d, int t, int NTit, doubletype* xi, FemModel* femmodel){ /*{{{*/ +template void postwidder_transform(doubletype* Lovet, doubletype* Lovef,int d, int t, int sh_nmax,int NTit, doubletype* xi, FemModel* femmodel){ /*{{{*/ //Computes Lovet for time step t and degree d from the PW coefficients xi and the corresponding 2*NTit frequency samples in Lovef - int nfreq, indxi, indf; - femmodel->parameters->FindParam(&nfreq,LoveNfreqEnum); - int nt=nfreq/2/NTit; - - indf=d*nfreq+t*2*NTit; + int indxi, indf; + IssmDouble PW_test; + IssmDouble PW_threshold; + femmodel->parameters->FindParam(&PW_threshold,LovePostWidderThresholdEnum); + + indf=(t*2*NTit)*(sh_nmax+1)+d; doubletype* LoveM = xNew(NTit); + + + // test variation across frequencies tested, something with little frequency dependence is not worth going through PW tranform + // that transform would also be numerically unstable + PW_test = abs((Lovef[indf+(2*NTit-1)*(sh_nmax+1)]-Lovef[indf])/Lovef[indf]); + + //if (PW_test < PW_threshold){ //elastic or fluid response: Love(t) = Love(s), we can do an early return + // Lovet[t*(sh_nmax+1)+d]=Lovef[indf]; + // return; + //} + + if (PW_test==0){ //elastic or fluid response: Love(t) = Love(s), we can do an early return + Lovet[t*(sh_nmax+1)+d]=Lovef[indf]; + return; + } for (int M=1;M abs(LoveM[M-2]-LoveM[M-3]) && abs(LoveM[M-2]-LoveM[M-3]) > abs(LoveM[M-3]-LoveM[M-4]) ){ - Lovet[d*nt+t]=LoveM[M-3]; + Lovet[t*(sh_nmax+1)+d]=LoveM[M-3]; return; } } } - Lovet[d*nt+t]=LoveM[NTit-1]; + Lovet[t*(sh_nmax+1)+d]=LoveM[NTit-1]; }/*}}}*/ template void GetEarthRheology(doubletype* pla, doubletype* pmu, int layer_index, doubletype omega, Matlitho* matlitho){ /*{{{*/ @@ -726,8 +834,8 @@ }/*}}}*/ -template void yi_boundary_conditions(doubletype* yi_righthandside, int deg, FemModel* femmodel, Matlitho* matlitho,LoveVariables* vars){ /*{{{*/ +template void yi_boundary_conditions(doubletype* yi_righthandside, int deg, FemModel* femmodel, Matlitho* matlitho,LoveVariables* vars, int forcing_type){ /*{{{*/ IssmDouble g0,r0,mu0,ra,rb,rc; - int nyi, forcing_type,icb,cmb,starting_layer; + int nyi,icb,cmb,starting_layer; IssmDouble* EarthMass; @@ -739,5 +847,4 @@ femmodel->parameters->FindParam(&mu0,LoveMu0Enum); - femmodel->parameters->FindParam(&forcing_type,LoveForcingTypeEnum); femmodel->parameters->FindParam(&icb,LoveInnerCoreBoundaryEnum); femmodel->parameters->FindParam(&cmb,LoveCoreMantleBoundaryEnum); @@ -810,8 +917,8 @@ } }/*}}}*/ -template void solve_yi_system(doubletype* loveh, doubletype* lovel, doubletype* lovek, int deg, doubletype omega, doubletype* yi, doubletype* rhs, FemModel* femmodel, Matlitho* matlitho, LoveVariables* vars){ /*{{{*/ +template void solve_yi_system(doubletype* loveh, doubletype* lovel, doubletype* lovek, int deg, doubletype omega, IssmDouble* frequencies, doubletype* yi, doubletype* rhs, FemModel* femmodel, Matlitho* matlitho, LoveVariables* vars, bool verbosecpu){ /*{{{*/ IssmDouble g0,r0,mu0,loveratio,underflow_tol; - IssmDouble* frequencies; + //IssmDouble* frequencies; int nyi,starting_layer, dummy; bool allow_layer_deletion; @@ -827,8 +934,9 @@ femmodel->parameters->FindParam(&allow_layer_deletion,LoveAllowLayerDeletionEnum); femmodel->parameters->FindParam(&underflow_tol,LoveUnderflowTolEnum); - femmodel->parameters->FindParam(&frequencies,&dummy,LoveFrequenciesEnum); + //femmodel->parameters->FindParam(&frequencies,&dummy,LoveFrequenciesEnum); IssmDouble ra=matlitho->radius[matlitho->numlayers]; bool exit=false; int lda,ldb; + for(;!exit;){ //cycles of: attempt to solve the yi system, then delete a layer if necessary @@ -854,6 +962,17 @@ xDelete(ipiv); - if(VerboseModule() && info!=0){ - _printf0_("love core warning in DGESV : LAPACK linear equation solver couldn't resolve the system"); + /*_printf_("i j yi[i+nyi*j] rhs[i]"); + for (int i=0;i(frequencies[0])){ + + + if (!allow_layer_deletion || nyi<=12 || omega!=angular_frequency(frequencies[0]) || deg==0){ goto save_results; /*We are not allowed to delete layers, or there is only one layer left. We also don't want to delete @@ -887,10 +1009,18 @@ } - if (loveratio<=underflow_tol || xIsNan(loveratio) || xIsInf(loveratio)){//We need to delete a layer and try again if the ratio between deepest love number to surface love number is too low (risk of underflow) or garbage - if(VerboseSolution()){ - _printf_("\n Degree: " << deg <<", surface/Depth Love number ratio small: "<deg_layer_delete[starting_layer]=deg; + if(VerboseSolution() && verbosecpu){ + _printf_("\n Degree: " << deg <<", surface/Depth Love number ratio small: "<deg_layer_delete[starting_layer]){ // if we are at the degree where we should delete the current layer, proceed to delete the bottom layer + if (omega!=0 && VerboseSolution() && verbosecpu) _printf_(", deleting layer " << starting_layer << "\n"); nyi-=6; starting_layer+=1; @@ -934,27 +1064,173 @@ xDelete(rhslocal); } - xDelete(frequencies); + //xDelete(frequencies); }/*}}}*/ -template void love_freq_to_temporal(doubletype* LoveHt,doubletype* LoveLt,doubletype* LoveKt,doubletype* LoveHf,doubletype* LoveLf,doubletype* LoveKf, FemModel* femmodel){ /*{{{*/ +template void love_freq_to_temporal(LoveNumbers* Lovet, LoveNumbers* Tidalt, doubletype* pmtf_colineart, doubletype* pmtf_orthot, LoveNumbers* Lovef,LoveNumbers* Tidalf, IssmDouble* frequencies, FemModel* femmodel, bool verbosecpu){ /*{{{*/ //Transforms all frequency-dependent love numbers into time-dependent love numbers - int nfreq,sh_nmax,sh_nmin,indxi,indf, NTit; - - femmodel->parameters->FindParam(&nfreq,LoveNfreqEnum); - femmodel->parameters->FindParam(&sh_nmax,LoveShNmaxEnum); - femmodel->parameters->FindParam(&sh_nmin,LoveShNminEnum); + int nfreq,sh_nmax,sh_nmin,indxi,indf, NTit, forcing_type, nt; + IssmDouble kf,Omega,moi_e,moi_p,alpha; + doubletype* pmtf_colinearf=NULL; + doubletype* pmtf_orthof=NULL; + bool chandler_wobble=false; + + nfreq=Lovef->nfreq; + sh_nmin=Lovef->sh_nmin; + sh_nmax=Lovef->sh_nmax; + femmodel->parameters->FindParam(&NTit,LoveNTemporalIterationsEnum); - int nt=nfreq/2/NTit; + //Parameters for the rotationnal feedback + femmodel->parameters->FindParam(&chandler_wobble,LoveChandlerWobbleEnum); + femmodel->parameters->FindParam(&forcing_type,LoveForcingTypeEnum); + femmodel->parameters->FindParam(&kf,TidalLoveK2SecularEnum); + femmodel->parameters->FindParam(&Omega,RotationalAngularVelocityEnum); + femmodel->parameters->FindParam(&moi_e,RotationalEquatorialMoiEnum); + femmodel->parameters->FindParam(&moi_p,RotationalPolarMoiEnum); + + nt=Lovet->nfreq; doubletype* xi=postwidder_coef(NTit); + + if(VerboseSolution() && verbosecpu) _printf_(" Inverse Laplace Transform... "); for (int d=sh_nmin;d(LoveHt,LoveHf,d,t,NTit,xi,femmodel); - postwidder_transform(LoveLt,LoveLf,d,t,NTit,xi,femmodel); - postwidder_transform(LoveKt,LoveKf,d,t,NTit,xi,femmodel); - } - } + postwidder_transform(Lovet->H,Lovef->H,d,t,sh_nmax,NTit,xi,femmodel); + postwidder_transform(Lovet->K,Lovef->K,d,t,sh_nmax,NTit,xi,femmodel); + postwidder_transform(Lovet->L,Lovef->L,d,t,sh_nmax,NTit,xi,femmodel); + } + } + + if(VerboseSolution() && verbosecpu) _printf_("done!\n"); + + if (forcing_type==11){ //Let's retrieve the functions necessary for the rotational_feedback + if(VerboseSolution() && verbosecpu) _printf_(" Transforming PMTF and tidal love numbers... "); + pmtf_colinearf = xNewZeroInit(3*nfreq); + pmtf_orthof = xNewZeroInit(3*nfreq); + int d=2; + doubletype s,R1,R2; + alpha=(moi_p-moi_e)/moi_e; //Earth flattening + + if (chandler_wobble){ //Chandler Wobble is untested yet + for (int fr=0;fr(frequencies[fr]); + R1=alpha*Omega*(1.0-Tidalf->K[fr*3+d]/kf); + R2=1.0+alpha*Tidalf->K[fr*3+d]/kf; + pmtf_colinearf[fr*3+d]=alpha*(1.0+Lovef->K[fr*(sh_nmax+1)+d])*(Omega*R1-pow(s,2)*R2)/(pow(R1,2.0)+pow(s*R2,2.0)); + pmtf_orthof[fr*3+d]=alpha*(1.0+Lovef->K[fr*(sh_nmax+1)+d])*s*Omega*(1.0+alpha)/(pow(R1,2.0)+pow(s*R2,2.0)); + } + } + else { + for (int fr=0;frK[fr*(sh_nmax+1)+d])/(1.0-Tidalf->K[fr*3+d]/kf); + pmtf_orthof[fr*3+d]=0.0; + } + } + for (int t=0;t(Tidalt->H,Tidalf->H,2,t,2,NTit,xi,femmodel); + postwidder_transform(Tidalt->K,Tidalf->K,2,t,2,NTit,xi,femmodel); + postwidder_transform(Tidalt->L,Tidalf->L,2,t,2,NTit,xi,femmodel); + postwidder_transform(pmtf_colineart,pmtf_colinearf,2,t,2,NTit,xi,femmodel); + postwidder_transform(pmtf_orthot,pmtf_orthof,2,t,2,NTit,xi,femmodel); + } + if(VerboseSolution() && verbosecpu) _printf_("done!\n"); + } + xDelete(xi); + xDelete(pmtf_colinearf); + xDelete(pmtf_orthof); +}/*}}}*/ + +template void compute_love_numbers(LoveNumbers* Lovef, LoveNumbers* Elastic, int forcing_type, int sh_cutoff, IssmDouble* frequencies, FemModel* femmodel, Matlitho* matlitho, LoveVariables* vars, bool verbosecpu){ + + int nstep, kernel_index,kernel_indexe,deleted_layer_offset, deg, sh_nmin, sh_nmax, nfreq; + doubletype lovek, loveh, lovel, loveratio; + doubletype omega; + doubletype* yi_prefactor=NULL; + doubletype* yi_righthandside=NULL; + doubletype* yi=NULL; + IssmDouble underflow_tol; + bool freq_skip, istemporal; + + femmodel->parameters->FindParam(&nstep,LoveIntStepsPerLayerEnum); + femmodel->parameters->FindParam(&istemporal,LoveIsTemporalEnum); + + nfreq=Lovef->nfreq; + sh_nmin=Lovef->sh_nmin; + sh_nmax=Lovef->sh_nmax; + if (Elastic==NULL) sh_cutoff=sh_nmax; + + // reset deleted layers in case we have called this function before; + vars->starting_layer=0; + vars->nyi=6*(matlitho->numlayers+1); + + yi_prefactor=xNewZeroInit(6*6*nstep*matlitho->numlayers); + yi_righthandside=xNewZeroInit(vars->nyi); + yi=xNewZeroInit(vars->nyi*vars->nyi); + + //precalculate yi coefficients that do not depend on degree or frequency + fill_yi_prefactor(yi_prefactor, NULL, NULL,femmodel, matlitho,vars); + + if (VerboseSolution() && Elastic && verbosecpu) _printf_("\n"); + + for(int deg=0;deg<2;deg++){ // calculation is in the center of mass reference frame, neutralize degree 0 and 1 mass changes + for (int fr=0;frK[fr*(sh_nmax+1)+deg]=-1.0; + } + } + + for(int deg=sh_nmin;deg(yi_prefactor, °, NULL,femmodel, matlitho,vars); + + for (int fr=0;fr(frequencies[fr]); + + //precalculate yi coefficients that depend on degree and frequency + fill_yi_prefactor(yi_prefactor, °,&omega,femmodel, matlitho,vars); + + //solve the system + yi_boundary_conditions(yi_righthandside,deg,femmodel,matlitho,vars,forcing_type); + build_yi_system(yi,deg,omega,yi_prefactor,femmodel,matlitho,vars); + solve_yi_system(&loveh,&lovel,&lovek, deg, omega, frequencies, yi, yi_righthandside,femmodel, matlitho,vars,verbosecpu); + Lovef->H[fr*(sh_nmax+1)+deg]=loveh; + Lovef->K[fr*(sh_nmax+1)+deg]=lovek-1.0; + Lovef->L[fr*(sh_nmax+1)+deg]=lovel; + deleted_layer_offset=(matlitho->numlayers+1)*6-vars->nyi;// =6 per deleted layer + kernel_index=fr*(sh_nmax+1)*(matlitho->numlayers+1)*6 + deg*(matlitho->numlayers+1)*6 + deleted_layer_offset; + for (int i=0;inyi;i++){ + Lovef->Kernels[kernel_index+i]=yi_righthandside[i]; + } + } + } + + if (Elastic) { // if elastic values were provided, we copy elastic love numbers above the cutoff degree instead of calculating them + for(int deg=sh_cutoff+1;degsh_nmax << " "); + } + for (int fr=0;frH[fr*(sh_nmax+1)+deg]=Elastic->H[deg]; + Lovef->K[fr*(sh_nmax+1)+deg]=Elastic->K[deg]; + Lovef->L[fr*(sh_nmax+1)+deg]=Elastic->L[deg]; + deleted_layer_offset=(matlitho->numlayers+1)*6-vars->nyi;// =6 per deleted layer + kernel_index=fr*(sh_nmax+1)*(matlitho->numlayers+1)*6 + deg*(matlitho->numlayers+1)*6 + deleted_layer_offset; + kernel_indexe=deg*(matlitho->numlayers+1)*6 + deleted_layer_offset; + for (int i=0;inyi;i++){ + Lovef->Kernels[kernel_index+i]=Elastic->Kernels[kernel_indexe+i]; + } + } + } + } + + if (VerboseSolution() && Elastic && verbosecpu) _printf_("\n"); + xDelete(yi); + xDelete(yi_righthandside); + xDelete(yi_prefactor); }/*}}}*/ @@ -973,7 +1249,9 @@ IssmDouble g0,r0; int nyi,starting_layer; + int* deg_layer_delete; femmodel->parameters->FindParam(&GG,LoveGravitationalConstantEnum); EarthMass=xNewZeroInit(numlayers+1); + deg_layer_delete=xNewZeroInit(numlayers); for (int i=0;i* Lovef=NULL; + LoveNumbers* Tidalf=NULL; + + /* parallel computing */ + LoveNumbers* Lovef_local=NULL; + LoveNumbers* Tidalf_local=NULL; + + /*elastic & fluid love numbers*/ + LoveNumbers* Elastic=NULL; + IssmDouble* frequencies_elastic=NULL; + LoveNumbers* Fluid=NULL; + IssmDouble* frequencies_fluid=NULL; + LoveVariables* vars=NULL; - doubletype* yi_prefactor=NULL; - doubletype* yi_righthandside=NULL; - doubletype* yi=NULL; - - if(VerboseSolution()) _printf0_(" computing LOVE numbers\n"); /*recover materials parameters: there is only one Matlitho, chase it down the hard way:*/ @@ -1039,159 +1327,260 @@ femmodel->parameters->FindParam(&sh_nmax,LoveShNmaxEnum); femmodel->parameters->FindParam(&sh_nmin,LoveShNminEnum); - femmodel->parameters->FindParam(&mu0,LoveMu0Enum); femmodel->parameters->FindParam(&allow_layer_deletion,LoveAllowLayerDeletionEnum); femmodel->parameters->FindParam(&love_kernels,LoveKernelsEnum); femmodel->parameters->FindParam(&forcing_type,LoveForcingTypeEnum); femmodel->parameters->FindParam(&istemporal,LoveIsTemporalEnum); - femmodel->parameters->FindParam(&nstep,LoveIntStepsPerLayerEnum); femmodel->parameters->FindParam(&complex_computation,LoveComplexComputationEnum); - - /*Initialize three love matrices: geoid, vertical and horizontal displacement (real and imaginary parts) */ - LoveKf = xNewZeroInit(nfreq*(sh_nmax+1)); - LoveHf = xNewZeroInit(nfreq*(sh_nmax+1)); - LoveLf = xNewZeroInit(nfreq*(sh_nmax+1)); + femmodel->parameters->FindParam(&pw_threshold,LovePostWidderThresholdEnum); + if (istemporal) femmodel->parameters->FindParam(&NTit,LoveNTemporalIterationsEnum); + + /*Initialize three love matrices: geoid, vertical and horizontal displacement*/ + Lovef= new LoveNumbers(sh_nmin,sh_nmax,nfreq, matlitho); + Tidalf= new LoveNumbers(2,2,nfreq, matlitho); + Elastic= new LoveNumbers(sh_nmin,sh_nmax,1,matlitho); + Fluid= new LoveNumbers(sh_nmin,sh_nmax,1,matlitho); /*Initialize love kernels (real and imaginary parts): */ - LoveKernels= xNewZeroInit(nfreq*(sh_nmax+1)*(matlitho->numlayers+1)*6); - vars=love_init(femmodel,matlitho); - yi_prefactor=xNewZeroInit(6*6*nstep*matlitho->numlayers); - yi_righthandside=xNewZeroInit(vars->nyi); - yi=xNewZeroInit(vars->nyi*vars->nyi); - - //precalculate yi coefficients that do not depend on degree or frequency - fill_yi_prefactor(yi_prefactor, NULL, NULL,femmodel, matlitho,vars); - for(int deg=sh_nmin;deg(yi_prefactor, °, NULL,femmodel, matlitho,vars); - - for (int fr=0;fr(frequencies[fr]); - - //precalculate yi coefficients that depend on degree and frequency - fill_yi_prefactor(yi_prefactor, °,&omega,femmodel, matlitho,vars); - - yi_boundary_conditions(yi_righthandside,deg,femmodel,matlitho,vars); - - build_yi_system(yi,deg,omega,yi_prefactor,femmodel,matlitho,vars); - - solve_yi_system(&loveh,&lovel,&lovek, deg, omega, yi, yi_righthandside,femmodel, matlitho,vars); - - LoveHf[deg*nfreq+fr]=loveh; - LoveKf[deg*nfreq+fr]=lovek-1.0; - LoveLf[deg*nfreq+fr]=lovel; - - deleted_layer_offset=(matlitho->numlayers+1)*6-vars->nyi;// =6 per deleted layer - kernel_index=deg*nfreq*(matlitho->numlayers+1)*6 + fr*(matlitho->numlayers+1)*6 + deleted_layer_offset; - for (int i=0;inyi;i++){ - LoveKernels[kernel_index+i]=yi_righthandside[i]; - } - } - } - - xDelete(yi); - xDelete(yi_righthandside); + //distribute frequencies for parallel computation /*{{{*/ + int nt_local, nf_local, lower_row, upper_row; + if (istemporal){ + //temporal love numbers are obtained via blocks of 2*NTit frequencies samples + //here we are making sure no block is split between different cpus, which would make the inverse laplace transform impossible + nt=nfreq/2/NTit; + nt_local=DetermineLocalSize(nt,IssmComm::GetComm()); + nf_local=nt_local*2*NTit; // number of local frequencies + GetOwnershipBoundariesFromRange(&lower_row,&upper_row,nt_local,IssmComm::GetComm()); + lower_row*=2*NTit; + upper_row*=2*NTit; + } + else{ + //in this case frequency samples are completely independent so we can split them evenly across cpus + nf_local=DetermineLocalSize(nfreq,IssmComm::GetComm()); + GetOwnershipBoundariesFromRange(&lower_row,&upper_row,nf_local,IssmComm::GetComm()); + } + + if (lower_row==0) verbosecpu=true; //let only cpu1 be verbose + if(VerboseSolution() && verbosecpu) _printf0_(" computing LOVE numbers\n"); + + frequencies_local=xNewZeroInit(nf_local); + for (int fr=0;fr(sh_nmin,sh_nmax,nf_local, matlitho); + Tidalf_local= new LoveNumbers(2,2,nf_local, matlitho); + + /*}}}*/ + frequencies_elastic=xNewZeroInit(1); + frequencies_fluid=xNewZeroInit(1); + for (int fr=0;frfrequencies[fr]) frequencies_fluid[0]=frequencies[fr]; + } + + // run elastic and fluid love numbers + if(VerboseSolution() && verbosecpu) _printf_(" elastic\n"); + compute_love_numbers(Elastic, NULL, forcing_type, sh_nmax,frequencies_elastic, femmodel, matlitho, vars,verbosecpu); + + if (nfreq>1){ + compute_love_numbers(Fluid, NULL, forcing_type, sh_nmax,frequencies_fluid, femmodel, matlitho, vars,verbosecpu); + sh_cutoff=sh_nmax; + for (int deg=100;degH[deg]-Elastic->H[deg])/Elastic->H[deg]); + pw_test_k=abs((Fluid->K[deg]-Elastic->K[deg])/Elastic->K[deg]); + pw_test_l=abs((Fluid->L[deg]-Elastic->L[deg])/Elastic->L[deg]); + if (pw_test_h=2){ // if forcing is surface loading and we have degree 2 + if(VerboseSolution() && verbosecpu) _printf_(" tidal\n"); + int tidal_forcing_type=9; + compute_love_numbers(Tidalf_local, NULL,tidal_forcing_type=9, 2,frequencies_local, femmodel, matlitho, vars,verbosecpu); + } + /*}}}*/ + + //Resume requested forcing_type + if (nfreq>1){ // if we are not running just elastic love numbers + if(VerboseSolution() && verbosecpu){ + if (forcing_type==11) _printf_(" loading\n"); + else if(forcing_type==9) _printf_(" tidal\n"); + else _printf_(" love\n"); + } + compute_love_numbers(Lovef_local, Elastic, forcing_type, sh_cutoff, frequencies_local, femmodel, matlitho, vars,verbosecpu); + } + else{ + Lovef_local->Copy(Elastic); + } + /*}}}*/ + //Temporal love numbers if (istemporal && !complex_computation){ - - IssmDouble* LoveHtDouble=NULL; - IssmDouble* LoveKtDouble=NULL; - IssmDouble* LoveLtDouble=NULL; - doubletype* LoveHt=NULL; - doubletype* LoveLt=NULL; - doubletype* LoveKt=NULL; - - int NTit; - femmodel->parameters->FindParam(&NTit,LoveNTemporalIterationsEnum); - int nt = nfreq/2/NTit; - - LoveHt=xNewZeroInit((sh_nmax+1)*nt); - LoveLt=xNewZeroInit((sh_nmax+1)*nt); - LoveKt=xNewZeroInit((sh_nmax+1)*nt); - - love_freq_to_temporal(LoveHt,LoveLt,LoveKt,LoveHf,LoveLf,LoveKf,femmodel); - - /*Downcast and add into parameters:*/ - LoveHtDouble=xNew((sh_nmax+1)*nt); - LoveLtDouble=xNew((sh_nmax+1)*nt); - LoveKtDouble=xNew((sh_nmax+1)*nt); - for(int i=0;i<(sh_nmax+1)*nt;i++){ - LoveHtDouble[i]=std::real(LoveHt[i]); - LoveLtDouble[i]=std::real(LoveLt[i]); - LoveKtDouble[i]=std::real(LoveKt[i]); - } + /*Initialize*/ + doubletype* pmtf_colineart=NULL; + doubletype* pmtf_orthot=NULL; + LoveNumbers* Lovet=NULL; + LoveNumbers* Tidalt=NULL; + /*Downcast arrays to be exported in parameters*/ + LoveNumbers* LovetDouble=NULL; + LoveNumbers* TidaltDouble=NULL; + IssmDouble* pmtf_colineartDouble=NULL; + IssmDouble* pmtf_orthotDouble=NULL; + /* parallel computing */ + doubletype* pmtf_colineart_local=NULL; + doubletype* pmtf_orthot_local=NULL; + LoveNumbers* Lovet_local=NULL; + LoveNumbers* Tidalt_local=NULL; + + Lovet= new LoveNumbers(sh_nmin,sh_nmax,nt,matlitho); + Tidalt= new LoveNumbers(2,2,nt,matlitho); + pmtf_colineart=xNewZeroInit(3*nt); + pmtf_orthot=xNewZeroInit(3*nt); + + Lovet_local= new LoveNumbers(sh_nmin,sh_nmax,nt_local,matlitho); + Tidalt_local= new LoveNumbers(2,2,nt_local,matlitho); + pmtf_colineart_local=xNewZeroInit(3*nt_local); + pmtf_orthot_local=xNewZeroInit(3*nt_local); + + love_freq_to_temporal(Lovet_local,Tidalt_local,pmtf_colineart_local,pmtf_orthot_local,Lovef_local,Tidalf_local,frequencies_local,femmodel,verbosecpu); + + /* MPI Gather */ /*{{{*/ + Lovef->LoveMPI_Gather(Lovef_local, lower_row); + if (forcing_type==11 && sh_nmin<=2 && sh_nmax>=2){ + Tidalf->LoveMPI_Gather(Tidalf_local, lower_row); + } + Lovet->LoveMPI_Gather(Lovet_local, lower_row/2/NTit); + Tidalt->LoveMPI_Gather(Tidalt_local, lower_row/2/NTit); + //pmtf: + int* recvcounts=xNew(IssmComm::GetSize()); + int* displs=xNew(IssmComm::GetSize()); + int rc; + int offset; + rc=3*nt_local; + offset=3*lower_row/2/NTit; + ISSM_MPI_Allgather(&rc,1,ISSM_MPI_INT,recvcounts,1,ISSM_MPI_INT,IssmComm::GetComm()); + ISSM_MPI_Allgather(&offset,1,ISSM_MPI_INT,displs,1,ISSM_MPI_INT,IssmComm::GetComm()); + ISSM_MPI_Allgatherv(pmtf_colineart_local, rc, ISSM_MPI_DOUBLE, pmtf_colineart, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm()); + ISSM_MPI_Allgatherv(pmtf_orthot_local, rc, ISSM_MPI_DOUBLE, pmtf_orthot, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm()); + xDelete(recvcounts); + xDelete(displs); + /*}}}*/ + + /*Downcast and add into parameters:*/ /*{{{*/ + LovetDouble= new LoveNumbers(sh_nmin,sh_nmax,nt,matlitho); + TidaltDouble= new LoveNumbers(2,2,nt,matlitho); + + pmtf_colineartDouble=xNew(nt); + pmtf_orthotDouble=xNew(nt); + + Lovet->DownCastToDouble(LovetDouble); + Tidalt->DownCastToDouble(TidaltDouble); + for(int i=0;iparameters->AddObject(new DoubleMatParam(TidalLoveHEnum,LoveHtDouble,(sh_nmax+1)*nt,1)); - femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveKEnum,LoveKtDouble,(sh_nmax+1)*nt,1)); - femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveLEnum,LoveLtDouble,(sh_nmax+1)*nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveHEnum,LovetDouble->H,(sh_nmax+1)*nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveKEnum,LovetDouble->K,(sh_nmax+1)*nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveLEnum,LovetDouble->L,(sh_nmax+1)*nt,1)); } else if(forcing_type==11){ //surface loading - femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveHEnum,LoveHtDouble,(sh_nmax+1)*nt,1)); - femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveKEnum,LoveKtDouble,(sh_nmax+1)*nt,1)); - femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveLEnum,LoveLtDouble,(sh_nmax+1)*nt,1)); - } - xDelete(LoveHtDouble); - xDelete(LoveKtDouble); - xDelete(LoveLtDouble); - + femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveHEnum,LovetDouble->H,(sh_nmax+1)*nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveKEnum,LovetDouble->K,(sh_nmax+1)*nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveLEnum,LovetDouble->L,(sh_nmax+1)*nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveHEnum,TidaltDouble->H,3*nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveKEnum,TidaltDouble->K,3*nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveLEnum,TidaltDouble->L,3*nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(LovePolarMotionTransferFunctionColinearEnum,pmtf_colineartDouble,nt,1)); + femmodel->parameters->AddObject(new DoubleMatParam(LovePolarMotionTransferFunctionOrthogonalEnum,pmtf_orthotDouble,nt,1)); + } + + xDelete(pmtf_colineartDouble); + xDelete(pmtf_orthotDouble); + /*}}}*/ + /*Add into external results, no need to downcast, we can handle complexes/quad precision: */ - femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKrEnum,LoveKt,sh_nmax+1,nt,0,0)); - femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveHrEnum,LoveHt,sh_nmax+1,nt,0,0)); - femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveLrEnum,LoveLt,sh_nmax+1,nt,0,0)); - - xDelete(LoveHt); - xDelete(LoveLt); - xDelete(LoveKt); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKtEnum,Lovet->K,nt,sh_nmax+1,0,0)); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveHtEnum,Lovet->H,nt,sh_nmax+1,0,0)); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveLtEnum,Lovet->L,nt,sh_nmax+1,0,0)); + + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveTidalKtEnum,Tidalt->K,nt,3,0,0)); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveTidalHtEnum,Tidalt->H,nt,3,0,0)); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveTidalLtEnum,Tidalt->L,nt,3,0,0)); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LovePMTF1tEnum,pmtf_colineart,nt,3,0,0)); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LovePMTF2tEnum,pmtf_orthot,nt,3,0,0)); + + delete Lovet; + delete Tidalt; + delete Lovet_local; + delete Tidalt_local; + delete LovetDouble; + delete TidaltDouble; + + xDelete(pmtf_colineart); + xDelete(pmtf_orthot); } else{ - - IssmDouble* LoveHfDouble=NULL; - IssmDouble* LoveKfDouble=NULL; - IssmDouble* LoveLfDouble=NULL; + LoveNumbers* LovefDouble=NULL; + LovefDouble= new LoveNumbers(sh_nmin,sh_nmax,nfreq,matlitho); + + /*MPI_Gather*/ + if (nfreq>1){ + Lovef->LoveMPI_Gather(Lovef_local, lower_row); + if (forcing_type==11 && sh_nmin<=2 && sh_nmax>=2){ + Tidalf->LoveMPI_Gather(Tidalf_local, lower_row); + } + } + else{ + Lovef->Copy(Elastic); + Tidalf->Copy(Tidalf_local); + } /*Add into parameters:*/ - LoveHfDouble=xNew((sh_nmax+1)*nfreq); - LoveLfDouble=xNew((sh_nmax+1)*nfreq); - LoveKfDouble=xNew((sh_nmax+1)*nfreq); - for(int i=0;i<(sh_nmax+1)*nfreq;i++){ - LoveHfDouble[i]=std::real(LoveHf[i]); - LoveLfDouble[i]=std::real(LoveLf[i]); - LoveKfDouble[i]=std::real(LoveKf[i]); - } + Lovef->DownCastToDouble(LovefDouble); if(forcing_type==9){ //tidal loading - femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveHEnum,LoveHfDouble,(sh_nmax+1)*nfreq,1)); - femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveKEnum,LoveKfDouble,(sh_nmax+1)*nfreq,1)); - femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveLEnum,LoveLfDouble,(sh_nmax+1)*nfreq,1)); + femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveHEnum,LovefDouble->H,(sh_nmax+1)*nfreq,1)); + femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveKEnum,LovefDouble->K,(sh_nmax+1)*nfreq,1)); + femmodel->parameters->AddObject(new DoubleMatParam(TidalLoveLEnum,LovefDouble->L,(sh_nmax+1)*nfreq,1)); } else if(forcing_type==11){ //surface loading - femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveHEnum,LoveHfDouble,(sh_nmax+1)*nfreq,1)); - femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveKEnum,LoveKfDouble,(sh_nmax+1)*nfreq,1)); - femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveLEnum,LoveLfDouble,(sh_nmax+1)*nfreq,1)); - } - xDelete(LoveHfDouble); - xDelete(LoveKfDouble); - xDelete(LoveLfDouble); + femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveHEnum,LovefDouble->H,(sh_nmax+1)*nfreq,1)); + femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveKEnum,LovefDouble->K,(sh_nmax+1)*nfreq,1)); + femmodel->parameters->AddObject(new DoubleMatParam(LoadLoveLEnum,LovefDouble->L,(sh_nmax+1)*nfreq,1)); + } + delete LovefDouble; } /*Add into external results:*/ - femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKiEnum,LoveKf,sh_nmax+1,nfreq,0,0)); - femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveHiEnum,LoveHf,sh_nmax+1,nfreq,0,0)); - femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveLiEnum,LoveLf,sh_nmax+1,nfreq,0,0)); - + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKfEnum,Lovef->K,nfreq,sh_nmax+1,0,0)); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveHfEnum,Lovef->H,nfreq,sh_nmax+1,0,0)); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveLfEnum,Lovef->L,nfreq,sh_nmax+1,0,0)); /*Only when love_kernels is on*/ if (love_kernels==1) { - femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKernelsEnum,LoveKernels,(sh_nmax+1)*(matlitho->numlayers+1)*6,nfreq,0,0)); - } - + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKernelsEnum,Lovef->Kernels,nfreq,(sh_nmax+1)*(matlitho->numlayers+1)*6,0,0)); + } /*Free resources:*/ xDelete(frequencies); - xDelete(LoveKf); - xDelete(LoveHf); - xDelete(LoveLf); - xDelete(LoveKernels); - + xDelete(frequencies_local); + xDelete(frequencies_elastic); + delete Lovef; + delete Lovef_local; + delete Tidalf; + delete Tidalf_local; + delete Elastic; /* Legacy for fortran core, to be removed after complete validation */ @@ -1225,10 +1614,10 @@ /*Add love matrices to results:*/ - //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKrEnum,LoveKr,sh_nmax+1,nfreq,0,0)); - //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveHrEnum,LoveHr,sh_nmax+1,nfreq,0,0)); - //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveLrEnum,LoveLr,sh_nmax+1,nfreq,0,0)); - //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKiEnum,LoveKi,sh_nmax+1,nfreq,0,0)); - //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveHiEnum,LoveHi,sh_nmax+1,nfreq,0,0)); - //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveLiEnum,LoveLi,sh_nmax+1,nfreq,0,0)); + //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKtEnum,LoveKr,sh_nmax+1,nfreq,0,0)); + //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveHtEnum,LoveHr,sh_nmax+1,nfreq,0,0)); + //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveLtEnum,LoveLr,sh_nmax+1,nfreq,0,0)); + //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveKfEnum,LoveKi,sh_nmax+1,nfreq,0,0)); + //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveHfEnum,LoveHi,sh_nmax+1,nfreq,0,0)); + //femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,LoveLfEnum,LoveLi,sh_nmax+1,nfreq,0,0)); //xDelete(LoveKr); @@ -1251,6 +1640,6 @@ template void GetEarthRheology(IssmDouble* pla, IssmDouble* pmu, int layer_index, IssmDouble omega, Matlitho* matlitho); template void GetEarthRheology(IssmComplex* pla, IssmComplex* pmu, int layer_index, IssmComplex omega, Matlitho* matlitho); -template void yi_boundary_conditions(IssmDouble* yi_righthandside, int deg, FemModel* femmodel, Matlitho* matlitho,LoveVariables* vars); -template void yi_boundary_conditions(IssmComplex* yi_righthandside, int deg, FemModel* femmodel, Matlitho* matlitho,LoveVariables* vars); +template void yi_boundary_conditions(IssmDouble* yi_righthandside, int deg, FemModel* femmodel, Matlitho* matlitho,LoveVariables* vars, int forcing_type); +template void yi_boundary_conditions(IssmComplex* yi_righthandside, int deg, FemModel* femmodel, Matlitho* matlitho,LoveVariables* vars, int forcing_type); template void yi_derivatives(IssmDouble* dydx, IssmDouble* y, int layer_index, int n, IssmDouble* yi_prefactor, FemModel* femmodel, Matlitho* matlitho); template void yi_derivatives(IssmComplex* dydx, IssmComplex* y, int layer_index, int n, IssmComplex* yi_prefactor, FemModel* femmodel, Matlitho* matlitho); @@ -1263,10 +1652,12 @@ template void build_yi_system(IssmDouble* yi, int deg, IssmDouble omega, IssmDouble* yi_prefactor, FemModel* femmodel, Matlitho* matlitho,LoveVariables* vars); template void build_yi_system(IssmComplex* yi, int deg, IssmComplex omega, IssmComplex* yi_prefactor, FemModel* femmodel, Matlitho* matlitho,LoveVariables* vars); -template void solve_yi_system(IssmDouble* loveh, IssmDouble* lovel, IssmDouble* lovek, int deg, IssmDouble omega, IssmDouble* yi, IssmDouble* rhs, FemModel* femmodel, Matlitho* matlitho, LoveVariables* vars); -template void solve_yi_system(IssmComplex* loveh, IssmComplex* lovel, IssmComplex* lovek, int deg, IssmComplex omega, IssmComplex* yi, IssmComplex* rhs, FemModel* femmodel, Matlitho* matlitho, LoveVariables* vars); +template void solve_yi_system(IssmDouble* loveh, IssmDouble* lovel, IssmDouble* lovek, int deg, IssmDouble omega, IssmDouble* frequencies, IssmDouble* yi, IssmDouble* rhs, FemModel* femmodel, Matlitho* matlitho, LoveVariables* vars,bool verbosecpu); +template void solve_yi_system(IssmComplex* loveh, IssmComplex* lovel, IssmComplex* lovek, int deg, IssmComplex omega, IssmDouble* frequencies, IssmComplex* yi, IssmComplex* rhs, FemModel* femmodel, Matlitho* matlitho, LoveVariables* vars,bool verbosecpu); +template void compute_love_numbers(LoveNumbers* Lovef, LoveNumbers* Elastic, int forcing_type, int sh_cutoff,IssmDouble* frequencies, FemModel* femmodel, Matlitho* matlitho, LoveVariables* vars, bool verbosecpu); +template void compute_love_numbers(LoveNumbers* Lovef, LoveNumbers* Elastic, int forcing_type, int sh_cutoff, IssmDouble* frequencies, FemModel* femmodel, Matlitho* matlitho, LoveVariables* vars, bool verbosecpu); template IssmDouble factorial(int n); template IssmDouble* postwidder_coef(int NTit); template IssmDouble n_C_r(int n, int r); -template void postwidder_transform(IssmDouble* Lovet, IssmDouble* Lovef,int d, int t, int NTit, IssmDouble* xi, FemModel* femmodel); +template void postwidder_transform(IssmDouble* Lovet, IssmDouble* Lovef,int d, int t, int sh_nmax,int NTit, IssmDouble* xi, FemModel* femmodel); /*}}}*/ Index: /issm/trunk/src/c/cores/masstransport_core.cpp =================================================================== --- /issm/trunk/src/c/cores/masstransport_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/masstransport_core.cpp (revision 27035) @@ -49,4 +49,8 @@ solutionsequence_linear(femmodel); femmodel->parameters->SetParam(SurfaceEnum,InputToExtrudeEnum); + extrudefromtop_core(femmodel); + femmodel->parameters->SetParam(ThicknessEnum,InputToExtrudeEnum); + extrudefromtop_core(femmodel); + femmodel->parameters->SetParam(BaseEnum,InputToExtrudeEnum); extrudefromtop_core(femmodel); } Index: /issm/trunk/src/c/cores/movingfront_core.cpp =================================================================== --- /issm/trunk/src/c/cores/movingfront_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/movingfront_core.cpp (revision 27035) @@ -48,4 +48,7 @@ } + /* smoothen slope of lsf for computation of normal on ice domain*/ + levelsetfunctionslope_core(femmodel); + /* start the work from here */ if(VerboseSolution()) _printf0_(" computing calving and undercutting\n"); @@ -53,7 +56,4 @@ FrontalForcingsx(femmodel); if(VerboseSolution()) _printf0_(" computing new ice front position\n"); - - /* smoothen slope of lsf for computation of normal on ice domain*/ - levelsetfunctionslope_core(femmodel); /* determine variables for extrapolation */ @@ -114,12 +114,23 @@ /* solve level set equation */ - analysis = new LevelsetAnalysis(); - analysis->Core(femmodel); - delete analysis; + LevelsetAnalysis lsanalysis; + lsanalysis.Core(femmodel); + lsanalysis.PostProcess(femmodel); /*Kill ice berg to avoid free body motion*/ if(killicebergs){ + int killberg = 0; if(VerboseSolution()) _printf0_(" looking for icebergs to kill\n"); - KillIcebergsx(femmodel); + killberg = KillIcebergsx(femmodel); + /*wait for all cores*/ + int totalkill; + ISSM_MPI_Reduce(&killberg,&totalkill,1,ISSM_MPI_INT,ISSM_MPI_SUM,0,IssmComm::GetComm()); + ISSM_MPI_Bcast(&totalkill,1,ISSM_MPI_INT,0,IssmComm::GetComm()); + + if (totalkill > 0) { + if(VerboseSolution()) _printf0_(" reinitializing level set after killing " << totalkill << " icebergs\n"); + femmodel->ResetLevelset(); + ResetBoundaryConditions(femmodel,LevelsetAnalysisEnum); + } } @@ -128,4 +139,5 @@ if(VerboseSolution()) _printf0_(" reinitializing level set\n"); femmodel->ResetLevelset(); + ResetBoundaryConditions(femmodel,LevelsetAnalysisEnum); } @@ -133,4 +145,10 @@ GetMaskOfIceVerticesLSMx(femmodel); + /*Save results*/ + if(save_results){ + int outputs[1] = {MaskIceLevelsetEnum}; + femmodel->RequestedOutputsx(&femmodel->results,&outputs[0],1); + } + /*End profiler*/ femmodel->profiler->Stop(MOVINGFRONTCORE); Index: /issm/trunk/src/c/cores/sampling_core.cpp =================================================================== --- /issm/trunk/src/c/cores/sampling_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/sampling_core.cpp (revision 27035) @@ -5,4 +5,6 @@ #include "../classes/classes.h" #include "../solutionsequences/solutionsequences.h" +#include "../analyses/analyses.h" // new +#include "../modules/modules.h" void sampling_core(FemModel* femmodel){ @@ -30,6 +32,32 @@ /*Generate random sample*/ if(VerboseSolution()) _printf0_(" call computational core\n"); + SamplingAnalysis* analysis = new SamplingAnalysis(); femmodel->SetCurrentConfiguration(SamplingAnalysisEnum); + + if(solution_type==TransientSolutionEnum){ + InputDuplicatex(femmodel,SampleEnum,SampleOldEnum); + + int seed; + femmodel->parameters->FindParam(&seed,SamplingSeedEnum); + if(seed>=0){ + int step; + femmodel->parameters->FindParam(&step,StepEnum); + seed = seed + 13923272*step; // change default seed for transient simulations (by considering an arbitrary shift based on the step number) + femmodel->parameters->SetParam(seed,SamplingSeedEnum); + } + + } + solutionsequence_sampling(femmodel); + + if(solution_type==TransientSolutionEnum){ + + InputDuplicatex(femmodel,SampleEnum,SampleNoiseEnum); + + analysis->UpdateTransientSample(femmodel); + + } + + delete analysis; if(save_results){ @@ -46,3 +74,5 @@ /*profiler*/ femmodel->profiler->Stop(SAMPLINGCORE); + + } Index: /issm/trunk/src/c/cores/sealevelchange_core.cpp =================================================================== --- /issm/trunk/src/c/cores/sealevelchange_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/sealevelchange_core.cpp (revision 27035) @@ -24,5 +24,6 @@ bool slcconvergence(Vector* RSLg,Vector* RSLg_old,IssmDouble eps_rel,IssmDouble eps_abs); IssmDouble SealevelloadsOceanAverage(GrdLoads* loads, Vector* oceanareas, Vector* subelementoceanareas, IssmDouble totaloceanarea); -void PolarMotion(IssmDouble* m, FemModel* femmodel,GrdLoads* loads, SealevelGeometry* slgeom); +void PolarMotion(IssmDouble* m, FemModel* femmodel,GrdLoads* loads, SealevelGeometry* slgeom, bool computefuture); +void SealevelchangeUpdateViscousTimeSeries(FemModel* femmodel); void ConserveOceanMass(FemModel* femmodel,GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom); void ivins_deformation_core(FemModel* femmodel); @@ -247,4 +248,5 @@ bool rotation=false; bool planethasocean=false; + bool computefuture=false; IssmDouble* sealevelpercpu=NULL; @@ -304,9 +306,6 @@ if(VerboseSolution()) _printf0_(" starting GRD convolutions\n"); - /*update viscous RSL:*/ - for(Object* & object : femmodel->elements->objects){ - Element* element = xDynamicCast(object); - element->SealevelchangeUpdateViscousFields(); - } + /*update viscous time series to keep up with time stepping:*/ + SealevelchangeUpdateViscousTimeSeries(femmodel); /*buildup loads: */ @@ -319,12 +318,9 @@ loads->BroadcastLoads(); - //compute polar motion: - PolarMotion(&polarmotionvector[0],femmodel,loads,slgeom); - /*skip computation of sea level equation if requested, which means sea level loads should be zeroed */ if(!sealevelloading){ loads->sealevelloads=xNewZeroInit(nel); loads->subsealevelloads=xNewZeroInit(slgeom->nbar[SLGEOM_OCEAN]); - + PolarMotion(&polarmotionvector[0],femmodel,loads, slgeom, computefuture=true); goto deformation; } @@ -332,4 +328,7 @@ if(VerboseSolution()) _printf0_(" converging GRD convolutions\n"); for(;;){ + + //compute polar motion: + PolarMotion(&polarmotionvector[0],femmodel,loads,slgeom,computefuture=false); oldsealevelloads=loads->vsealevelloads->Duplicate(); loads->vsealevelloads->Copy(oldsealevelloads); @@ -338,5 +337,5 @@ for(Object* & object : femmodel->elements->objects){ Element* element = xDynamicCast(object); - element->SealevelchangeConvolution(sealevelpercpu, loads , polarmotionvector,slgeom); + element->SealevelchangeConvolution(sealevelpercpu, loads, polarmotionvector,slgeom); } @@ -364,7 +363,4 @@ loads->BroadcastSealevelLoads(); - //compute polar motion: - PolarMotion(&polarmotionvector[0],femmodel,loads, slgeom); - //convergence? if(slcconvergence(loads->vsealevelloads,oldsealevelloads,eps_rel,eps_abs))break; @@ -374,4 +370,7 @@ iterations++; } + + //recompute polar motion one final time, this time updating viscous stacks for future time steps + if (viscous) PolarMotion(&polarmotionvector[0],femmodel,loads, slgeom, computefuture=true); deformation: @@ -418,7 +417,7 @@ if (rotation) { - femmodel->results->AddResult(new GenericExternalResult(femmodel->results->Size()+1,SealevelInertiaTensorXZEnum,polarmotionvector[0],step,time)); - femmodel->results->AddResult(new GenericExternalResult(femmodel->results->Size()+1,SealevelInertiaTensorYZEnum,polarmotionvector[1],step,time)); - femmodel->results->AddResult(new GenericExternalResult(femmodel->results->Size()+1,SealevelInertiaTensorZZEnum,polarmotionvector[2],step,time)); + femmodel->results->AddResult(new GenericExternalResult(femmodel->results->Size()+1,SealevelchangePolarMotionXEnum,polarmotionvector[0],step,time)); + femmodel->results->AddResult(new GenericExternalResult(femmodel->results->Size()+1,SealevelchangePolarMotionYEnum,polarmotionvector[1],step,time)); + femmodel->results->AddResult(new GenericExternalResult(femmodel->results->Size()+1,SealevelchangePolarMotionZEnum,polarmotionvector[2],step,time)); } @@ -666,4 +665,7 @@ } + /*Compute spherical harmonic functions for spatial integrations of the loads*/ + slgeom->BuildSphericalHarmonics(); + femmodel->parameters->AddObject(new DoubleVecParam(XxeEnum,xxe,nel)); femmodel->parameters->AddObject(new DoubleVecParam(YyeEnum,yye,nel)); @@ -731,5 +733,5 @@ vsealevelloadsvolume->PointwiseMult(loads->vsealevelloads,oceanareas); - vsubsealevelloadsvolume->PointwiseMult(loads->vsubsealevelloads,suboceanareas); + vsubsealevelloadsvolume->PointwiseMult(loads->vsubsealevelloads,suboceanareas); vsealevelloadsvolume->Sum(&sealevelloadsaverage); @@ -740,16 +742,29 @@ return (sealevelloadsaverage+subsealevelloadsaverage)/totaloceanarea; } /*}}}*/ -void PolarMotion(IssmDouble* polarmotionvector, FemModel* femmodel,GrdLoads* loads, SealevelGeometry* slgeom){ /*{{{*/ - - IssmDouble moi_list[3]={0,0,0}; - IssmDouble moi_list_sub[3]={0,0,0}; - IssmDouble moi_list_cpu[3]={0,0,0}; - IssmDouble* tide_love_h = NULL; - IssmDouble* tide_love_k = NULL; - IssmDouble* load_love_k = NULL; - IssmDouble tide_love_k2secular; - IssmDouble moi_e, moi_p; - IssmDouble m1, m2, m3; +void PolarMotion(IssmDouble* polarmotionvector, FemModel* femmodel,GrdLoads* loads, SealevelGeometry* slgeom, bool computefuture){ /*{{{*/ + //The purpose of this routine is to get the polar motion vector m=(m1, m2, m3) induced by the GrdLoads + IssmDouble S2coef[3]; + IssmDouble* pmtf_col= NULL; + IssmDouble* pmtf_ortho = NULL; + IssmDouble* pmtf_z = NULL; + IssmDouble* m1=NULL; + IssmDouble* m2=NULL; + IssmDouble* m3=NULL; + IssmDouble* m1interp=NULL; + IssmDouble* m2interp=NULL; + IssmDouble* m3interp=NULL; + + IssmDouble moi_e, moi_p, re; + IssmDouble mhprefactor, mzprefactor; bool rotation=false; + bool viscous=false; + int nt=1; + + IssmDouble* viscoustimes=NULL; + IssmDouble* viscouspolarmotion=NULL; + int viscousnumsteps; + int viscousindex=0; + int dummy; + IssmDouble currenttime, final_time, lincoeff, timeacc; /*early return?:*/ @@ -758,43 +773,170 @@ /*retrieve parameters: */ - femmodel->parameters->FindParam(&load_love_k,NULL,NULL,LoadLoveKEnum); - femmodel->parameters->FindParam(&tide_love_h,NULL,NULL,TidalLoveHEnum); - femmodel->parameters->FindParam(&tide_love_k,NULL,NULL,TidalLoveKEnum); - femmodel->parameters->FindParam(&tide_love_k2secular,TidalLoveK2SecularEnum); + femmodel->parameters->FindParam(&viscous,SolidearthSettingsViscousEnum); femmodel->parameters->FindParam(&moi_e,RotationalEquatorialMoiEnum); femmodel->parameters->FindParam(&moi_p,RotationalPolarMoiEnum); - - for(Object* & object : femmodel->elements->objects){ - Element* element = xDynamicCast(object); - - element->SealevelchangeMomentOfInertiaCentroid(&moi_list[0],loads,slgeom); - element->SealevelchangeMomentOfInertiaSubElement(&moi_list_sub[0],loads, slgeom); - - moi_list_cpu[0] += moi_list[0]+moi_list_sub[0]; - moi_list_cpu[1] += moi_list[1]+moi_list_sub[1]; - moi_list_cpu[2] += moi_list[2]+moi_list_sub[2]; - } - - for (int i=0;i<3;i++) moi_list[i]=0; - - ISSM_MPI_Reduce (&moi_list_cpu[0],&moi_list[0],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); - ISSM_MPI_Bcast(&moi_list[0],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); - - ISSM_MPI_Reduce (&moi_list_cpu[1],&moi_list[1],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); - ISSM_MPI_Bcast(&moi_list[1],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); - - ISSM_MPI_Reduce (&moi_list_cpu[2],&moi_list[2],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); - ISSM_MPI_Bcast(&moi_list[2],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); - - /*compute perturbation terms for angular velocity vector: */ - m1 = 1/(1-tide_love_k[2]/tide_love_k2secular) * (1+load_love_k[2])/(moi_p-moi_e) * moi_list[0]; - m2 = 1/(1-tide_love_k[2]/tide_love_k2secular) * (1+load_love_k[2])/(moi_p-moi_e) * moi_list[1]; - m3 = -(1+load_love_k[2])/moi_p * moi_list[2]; // term associated with fluid number (3-order-of-magnitude smaller) is negelected + femmodel->parameters->FindParam(&pmtf_col,NULL,SealevelchangePolarMotionTransferFunctionColinearEnum); + femmodel->parameters->FindParam(&pmtf_ortho,NULL,SealevelchangePolarMotionTransferFunctionOrthogonalEnum); + femmodel->parameters->FindParam(&pmtf_z,NULL,SealevelchangePolarMotionTransferFunctionZEnum); + femmodel->parameters->FindParam(&re,SolidearthPlanetRadiusEnum); + + if (viscous){ + femmodel->parameters->FindParam(&final_time,TimesteppingFinalTimeEnum); + femmodel->parameters->FindParam(&timeacc,SolidearthSettingsTimeAccEnum); + femmodel->parameters->FindParam(&viscousnumsteps,SealevelchangeViscousNumStepsEnum); + femmodel->parameters->FindParam(&viscoustimes,NULL,SealevelchangeViscousTimesEnum); + femmodel->parameters->FindParam(&viscousindex,SealevelchangeViscousIndexEnum); + femmodel->parameters->FindParam(¤ttime,TimeEnum); + femmodel->parameters->FindParam(&viscouspolarmotion,NULL,NULL,SealevelchangeViscousPolarMotionEnum); + + if (computefuture){ + nt = viscousnumsteps; + m1interp=xNewZeroInit(nt); + m2interp=xNewZeroInit(nt); + m3interp=xNewZeroInit(nt); + } + } + + m1=xNewZeroInit(nt); + m2=xNewZeroInit(nt); + m3=xNewZeroInit(nt); + + //Isolate degree 2 load coefficients + for (int i=0;i<3;i++) S2coef[i]=0; + loads->SHDegree2Coefficients(&S2coef[0],femmodel,slgeom); + + //compute present (& future) polar motion from present loads + mhprefactor=-4.*M_PI/5.*pow(re,4.)/(moi_p-moi_e); + mzprefactor=8.*M_PI/15.*pow(re,4.)/moi_p; + for (int tprime=0;tprime beginning of the simulation + if(t==viscousindex){ + m1interp[t]= m1[0]; + m2interp[t]= m2[0]; + m3interp[t]= m3[0]; + } + else{ //we reinterpolate PM on viscoustimes, so we can handle the case where we are running with adaptative/uneven time steps + int tprime=t-viscousindex-1; + m1interp[t]= (1.0-lincoeff)*m1[tprime]+lincoeff*m1[tprime+1]; + m2interp[t]= (1.0-lincoeff)*m2[tprime]+lincoeff*m2[tprime+1]; + m3interp[t]= (1.0-lincoeff)*m3[tprime]+lincoeff*m3[tprime+1]; + } + } + } + } + /*update PM at present time using viscous stack at present time: */ + m1[0]+=viscouspolarmotion[0*nt+viscousindex]; + m2[0]+=viscouspolarmotion[1*nt+viscousindex]; + m3[0]+=viscouspolarmotion[2*nt+viscousindex]; + if(computefuture){ /*update viscous stack with future deformation from present load: */ + for(int t=nt-1;t>=viscousindex;t--){ + //offset viscous PM to remove all deformation that has already been added + viscouspolarmotion[0*nt+t]+=m1interp[t]-m1interp[viscousindex]-viscouspolarmotion[0*nt+viscousindex]; + viscouspolarmotion[1*nt+t]+=m2interp[t]-m2interp[viscousindex]-viscouspolarmotion[1*nt+viscousindex]; + viscouspolarmotion[2*nt+t]+=m3interp[t]-m3interp[viscousindex]-viscouspolarmotion[2*nt+viscousindex]; + } + // save updated viscous PM + femmodel->parameters->SetParam(viscouspolarmotion,viscousnumsteps,3,SealevelchangeViscousPolarMotionEnum); + } + } + /*Assign output pointers:*/ - polarmotionvector[0]=m1; - polarmotionvector[1]=m2; - polarmotionvector[2]=m3; + polarmotionvector[0]=m1[0]; + polarmotionvector[1]=m2[0]; + polarmotionvector[2]=m3[0]; + + /*Free allocations:*/ + xDelete(m1); + xDelete(m2); + xDelete(m3); + if (viscous){ + if (computefuture){ + xDelete(m1interp); + xDelete(m2interp); + xDelete(m3interp); + } + } + } /*}}}*/ +void SealevelchangeUpdateViscousTimeSeries(FemModel* femmodel){ /*{{{*/ + + IssmDouble* viscouspolarmotion=NULL; + IssmDouble* viscoustimes=NULL; + int viscousnumsteps; + int viscousindex=0; + int newindex=0; + int dummy; + bool viscous=false; + bool rotation=false; + IssmDouble currenttime; + IssmDouble lincoeff=0; + + femmodel->parameters->FindParam(&viscous,SolidearthSettingsViscousEnum); + femmodel->parameters->FindParam(&rotation,SolidearthSettingsRotationEnum); + + if(viscous){ + femmodel->parameters->FindParam(&viscousnumsteps,SealevelchangeViscousNumStepsEnum); + femmodel->parameters->FindParam(&viscoustimes,NULL,SealevelchangeViscousTimesEnum); + femmodel->parameters->FindParam(&viscousindex,SealevelchangeViscousIndexEnum); + femmodel->parameters->FindParam(¤ttime,TimeEnum); + if (rotation) femmodel->parameters->FindParam(&viscouspolarmotion,NULL,NULL,SealevelchangeViscousPolarMotionEnum); + + bool foundtime=false; + int offset=1; //handles the egde case where time found = max time in viscoustimes + lincoeff=0; + newindex=viscousnumsteps-2; + + for(int t=viscousindex;t=currenttime){ + newindex=t-1; + foundtime=true; + lincoeff=(currenttime-viscoustimes[newindex])/(viscoustimes[t]-viscoustimes[newindex]); + offset=0; + break; + } + } + + if(rotation){ + int index=0; + for (int i=0;i<3;i++){ + index=i*viscousnumsteps+newindex; + viscouspolarmotion[index+offset]=(1-lincoeff)*viscouspolarmotion[index]+lincoeff*viscouspolarmotion[index+1]; + } + femmodel->parameters->SetParam(viscouspolarmotion,viscousnumsteps,3,SealevelchangeViscousPolarMotionEnum); + } + + + /*update viscous inputs:*/ + for(Object* & object : femmodel->elements->objects){ + Element* element = xDynamicCast(object); + element->SealevelchangeUpdateViscousFields(lincoeff,newindex,offset); + } + + viscoustimes[newindex]=currenttime; + viscousindex=newindex+offset; + + femmodel->parameters->SetParam(viscousindex,SealevelchangeViscousIndexEnum); + femmodel->parameters->SetParam(viscoustimes,viscousnumsteps,SealevelchangeViscousTimesEnum); + + /*free allocations:*/ + xDelete(viscoustimes); + } + + +} void ConserveOceanMass(FemModel* femmodel,GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom){ /*{{{*/ @@ -809,4 +951,5 @@ IssmDouble* CombineLoads(IssmDouble* load,IssmDouble* subload,FemModel* femmodel, SealevelGeometry* slgeom,int loadtype,int nel){ /*{{{*/ + //merges loads on centroids and subelements onto a single variable loadcopy int* indices=xNew(nel); for(int i=0;iparameters->FindParam(&isSSA,FlowequationIsSSAEnum); femmodel->parameters->FindParam(&isL1L2,FlowequationIsL1L2Enum); - femmodel->parameters->FindParam(&isMLHO,FlowequationIsMLHOEnum); + femmodel->parameters->FindParam(&isMOLHO,FlowequationIsMOLHOEnum); femmodel->parameters->FindParam(&isHO,FlowequationIsHOEnum); femmodel->parameters->FindParam(&isFS,FlowequationIsFSEnum); @@ -75,5 +75,5 @@ /*Compute stressbalance for SSA L1L2 HO and FS*/ - if(isSSA || isL1L2 || isMLHO || isHO || isFS){ + if(isSSA || isL1L2 || isMOLHO || isHO || isFS){ analysis = new StressbalanceAnalysis(); analysis->Core(femmodel); @@ -82,5 +82,5 @@ /*Compute vertical velocities*/ - if (domaintype==Domain3DEnum && (isSIA || isSSA || isL1L2 || isMLHO || isHO)){ + if (domaintype==Domain3DEnum && (isSIA || isSSA || isL1L2 || isMOLHO || isHO)){ /*We need basal melt rates for vertical velocity*/ Index: /issm/trunk/src/c/cores/transient_core.cpp =================================================================== --- /issm/trunk/src/c/cores/transient_core.cpp (revision 27034) +++ /issm/trunk/src/c/cores/transient_core.cpp (revision 27035) @@ -16,4 +16,8 @@ #include "../modules/modules.h" #include "../solutionsequences/solutionsequences.h" + +#ifdef _HAVE_CODIPACK_ +extern CoDi_global codi_global; +#endif /*Prototypes*/ @@ -74,5 +78,5 @@ if(VerboseSolution()){ _printf0_("iteration " << step << "/" << ceil((finaltime-time)/dt)+step << \ - " time [yr]: " << setprecision(4) << time/yts << " (time step: " << dt/yts << ")\n"); + " time [yr]: " <parameters->FindParam(&issampling,TransientIssamplingEnum); femmodel->parameters->FindParam(&numoutputs,TransientNumRequestedOutputsEnum); - femmodel->parameters->FindParam(&isstochasticforcing,StochasticForcingIsStochasticForcingEnum); + femmodel->parameters->FindParam(&isstochasticforcing,StochasticForcingIsStochasticForcingEnum); #if defined(_HAVE_OCEAN_ ) @@ -275,5 +279,5 @@ #ifdef _HAVE_CODIPACK_ -void transient_ad(FemModel* femmodel){/*{{{*/ +double transient_ad(FemModel* femmodel, double* G, double* Jlist){/*{{{*/ /*parameters: */ @@ -282,5 +286,5 @@ bool isoceancoupling; int step,timestepping; - int checkpoint_frequency; + int checkpoint_frequency,num_responses; /*Get rank*/ @@ -293,4 +297,5 @@ femmodel->parameters->FindParam(&yts,ConstantsYtsEnum); femmodel->parameters->FindParam(×tepping,TimesteppingTypeEnum); + femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); femmodel->parameters->FindParam(&checkpoint_frequency,SettingsCheckpointFrequencyEnum); _assert_(checkpoint_frequency>0); @@ -343,11 +348,9 @@ /*Go through our dependent variables, and compute the response:*/ - if(finaltime==time){ - DataSet* dependent_objects=((DataSetParam*)femmodel->parameters->FindParamObject(AutodiffDependentObjectsEnum))->value; - for(Object* & object:dependent_objects->objects){ - DependentObject* dep=(DependentObject*)object; - dep->Responsex(&output_value,femmodel); - dep->AddValue(output_value); - } + DataSet* dependent_objects=((DataSetParam*)femmodel->parameters->FindParamObject(AutodiffDependentObjectsEnum))->value; + for(Object* & object:dependent_objects->objects){ + DependentObject* dep=(DependentObject*)object; + dep->Responsex(&output_value,femmodel); + dep->AddValue(output_value); } @@ -395,15 +398,37 @@ SetControlInputsFromVectorx(femmodel,X); - IssmDouble J = 0.; + IssmDouble J = 0.; + int count = 0; DataSet* dependent_objects=((DataSetParam*)femmodel->parameters->FindParamObject(AutodiffDependentObjectsEnum))->value; for(Object* & object:dependent_objects->objects){ DependentObject* dep=(DependentObject*)object; - J += dep->GetValue(); - } - tape_codi.registerOutput(J); + IssmDouble output_value = dep->GetValue(); + + + J += output_value; + + tape_codi.registerOutput(J); + #if _CODIPACK_MAJOR_==2 + codi_global.output_indices.push_back(J.getIdentifier()); + #elif _CODIPACK_MAJOR_==1 + codi_global.output_indices.push_back(J.getGradientData()); + #else + #error "_CODIPACK_MAJOR_ not supported" + #endif + + /*Keep track of output for printing*/ + Jlist[count] = output_value.getValue(); + count++; + } + Jlist[count] = J.getValue(); + _assert_(count == num_responses); tape_codi.setPassive(); - if(IssmComm::GetRank()==0) J.gradient() = 1.0; - tape_codi.evaluate(); + + if(VerboseAutodiff())_printf0_(" CoDiPack fos_reverse\n"); + for(int i=0;iparameters->SetParam(thisstep,StepEnum); femmodel->parameters->SetParam(thisdt,TimesteppingTimeStepEnum); - _printf0_("step "<parameters->FindParamObject(AutodiffDependentObjectsEnum))->value; - for(Object* & object:dependent_objects->objects){ - DependentObject* dep=(DependentObject*)object; - dep->Responsex(&output_value,femmodel); - dep->AddValue(output_value); - } + DataSet* dependent_objects=((DataSetParam*)femmodel->parameters->FindParamObject(AutodiffDependentObjectsEnum))->value; + for(Object* & object:dependent_objects->objects){ + DependentObject* dep=(DependentObject*)object; + dep->Responsex(&output_value,femmodel); + dep->AddValue(output_value); } @@ -484,22 +511,17 @@ for(int i=0; i(Xsize); - ISSM_MPI_Allreduce(Xb,gradient,Xsize,ISSM_MPI_PDOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); - - /*Now set final gradient*/ - IssmDouble* aG=xNew(Xsize); - for(int i=0;i(gradient[i]); - xDelete(gradient); - ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,aG); - xDelete(aG); - + ISSM_MPI_Allreduce(Xb,G,Xsize,ISSM_MPI_PDOUBLE,ISSM_MPI_SUM,IssmComm::GetComm()); + + /*Cleanup and return misfit*/ xDelete(X); xDelete(Xb); xDelete(Yb); xDelete(Yin); + return J.getValue(); }/*}}}*/ #endif Index: /issm/trunk/src/c/datastructures/DataSet.cpp =================================================================== --- /issm/trunk/src/c/datastructures/DataSet.cpp (revision 27034) +++ /issm/trunk/src/c/datastructures/DataSet.cpp (revision 27035) @@ -261,4 +261,9 @@ this->AddObject(cfsurf); } + else if(obj_enum==CfsurfacelogvelEnum){ + Cfsurfacelogvel* cfsurf=new Cfsurfacelogvel(); + cfsurf->Marshall(marshallhandle); + this->AddObject(cfsurf); + } else if(obj_enum==MassfluxatgateEnum){ Massfluxatgate* massfluxgate=new Massfluxatgate(); Index: /issm/trunk/src/c/modules/Calvingx/Calvingx.cpp =================================================================== --- /issm/trunk/src/c/modules/Calvingx/Calvingx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/Calvingx/Calvingx.cpp (revision 27035) @@ -15,9 +15,14 @@ /*Calculate calving rate*/ switch(calvinglaw){ - case DefaultCalvingEnum: case CalvingMinthicknessEnum: case CalvingHabEnum: + femmodel->ElementOperationx(&Element::CalvingSetZeroRate); + break; + case DefaultCalvingEnum: + femmodel->ElementOperationx(&Element::CalvingFromRate); break; case CalvingCrevasseDepthEnum: + femmodel->ElementOperationx(&Element::CalvingSetZeroRate); + /*rate is 0 but we need to calculate a few things to determine where it will calve*/ femmodel->StrainRateparallelx(); femmodel->StrainRateeffectivex(); @@ -35,4 +40,10 @@ femmodel->ElementOperationx(&Element::CalvingRateVonmises); break; + case CalvingTestEnum: + femmodel->ElementOperationx(&Element::CalvingRateTest); + break; + case CalvingParameterizationEnum: + femmodel->ElementOperationx(&Element::CalvingRateParameterization); + break; default: _error_("Caving law "<parameters->FindParam(&numbasins,BasalforcingsLinearNumBasinsEnum); + femmodel->parameters->FindParam(&arorder,BasalforcingsAutoregressiveOrderEnum); + IssmDouble* beta0 = NULL; + IssmDouble* beta1 = NULL; + IssmDouble* phi = NULL; + femmodel->parameters->FindParam(&starttime,TimesteppingStartTimeEnum); + femmodel->parameters->FindParam(&tstep_ar,BasalforcingsAutoregressionTimestepEnum); + femmodel->parameters->FindParam(&tinit_ar,BasalforcingsAutoregressionInitialTimeEnum); + femmodel->parameters->FindParam(&beta0,&M,BasalforcingsBeta0Enum); _assert_(M==numbasins); + femmodel->parameters->FindParam(&beta1,&M,BasalforcingsBeta1Enum); _assert_(M==numbasins); + femmodel->parameters->FindParam(&phi,&M,&Nphi,BasalforcingsPhiEnum); _assert_(M==numbasins); _assert_(Nphi==arorder); + + /*AR model spin-up with 0 noise to initialize BasalforcingsDeepwaterMeltingRateValuesAutoregressionEnum (688 = log(0.001)/log(0.99): decaying time of inluence of phi[0]=0.99 to 0.001 of beta_0*/ + int nspin = 688; + for(Object* &object:femmodel->elements->objects){ + Element* element = xDynamicCast(object); //generate element object + element->AutoregressionInit(numbasins,arorder,nspin,starttime,tstep_ar,tinit_ar,beta0,beta1,phi,BasalforcingsDeepwaterMeltingRateAutoregressionEnum); + } + /*Cleanup*/ + xDelete(beta0); + xDelete(beta1); + xDelete(phi); +}/*}}}*/ +void AutoregressionLinearFloatingiceMeltingRatex(FemModel* femmodel){/*{{{*/ + + /*Get time parameters*/ + IssmDouble time,dt,starttime,tstep_ar; + femmodel->parameters->FindParam(&time,TimeEnum); + femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + femmodel->parameters->FindParam(&starttime,TimesteppingStartTimeEnum); + femmodel->parameters->FindParam(&tstep_ar,BasalforcingsAutoregressionTimestepEnum); + + /*Initialize module at first time step*/ + if(time<=starttime+dt){AutoregressionLinearFloatingiceMeltingRateInitx(femmodel);} + /*Determine if this is a time step for the AR model*/ + bool isstepforar = false; + + #ifndef _HAVE_AD_ + if((fmod(time,tstep_ar)parameters->FindParam(&numbasins,BasalforcingsLinearNumBasinsEnum); + femmodel->parameters->FindParam(&arorder,BasalforcingsAutoregressiveOrderEnum); + IssmDouble tinit_ar; + IssmDouble* beta0 = NULL; + IssmDouble* beta1 = NULL; + IssmDouble* phi = NULL; + IssmDouble* deepwaterel = NULL; + IssmDouble* upperwaterel = NULL; + IssmDouble* upperwatermelt = NULL; + IssmDouble* perturbation = NULL; + + /*Get autoregressive parameters*/ + femmodel->parameters->FindParam(&tinit_ar,BasalforcingsAutoregressionInitialTimeEnum); + femmodel->parameters->FindParam(&beta0,&M,BasalforcingsBeta0Enum); _assert_(M==numbasins); + femmodel->parameters->FindParam(&beta1,&M,BasalforcingsBeta1Enum); _assert_(M==numbasins); + femmodel->parameters->FindParam(&phi,&M,&Nphi,BasalforcingsPhiEnum); _assert_(M==numbasins); _assert_(Nphi==arorder); + + /*Get basin-specific parameters*/ + femmodel->parameters->FindParam(&deepwaterel,&M,BasalforcingsDeepwaterElevationEnum); _assert_(M==numbasins); + femmodel->parameters->FindParam(&upperwaterel,&M,BasalforcingsUpperwaterElevationEnum); _assert_(M==numbasins); + femmodel->parameters->FindParam(&upperwatermelt,&M,BasalforcingsUpperwaterMeltingRateEnum); _assert_(M==numbasins); + + /*Evaluate whether stochasticity on DeepwaterMeltingRate is requested*/ + femmodel->parameters->FindParam(&isstochastic,StochasticForcingIsStochasticForcingEnum); + if(isstochastic){ + int numstochasticfields; + int* stochasticfields; + femmodel->parameters->FindParam(&numstochasticfields,StochasticForcingNumFieldsEnum); + femmodel->parameters->FindParam(&stochasticfields,&N,StochasticForcingFieldsEnum); _assert_(N==numstochasticfields); + for(int i=0;i(stochasticfields); + } + /*Time elapsed with respect to AR model initial time*/ + IssmDouble telapsed_ar = time-tinit_ar; + + /*Loop over each element to compute FloatingiceMeltingRate at vertices*/ + for(Object* &object:femmodel->elements->objects){ + Element* element = xDynamicCast(object); + /*Compute autoregression*/ + element->Autoregression(isstepforar,arorder,telapsed_ar,beta0,beta1,phi,isdeepmeltingstochastic,BasalforcingsDeepwaterMeltingRateAutoregressionEnum); + element->BasinLinearFloatingiceMeltingRate(deepwaterel,upperwatermelt,upperwaterel,perturbation); + } + + /*Cleanup*/ + xDelete(beta0); + xDelete(beta1); + xDelete(phi); + xDelete(deepwaterel); + xDelete(upperwaterel); + xDelete(upperwatermelt); + xDelete(perturbation); +}/*}}}*/ Index: /issm/trunk/src/c/modules/FloatingiceMeltingRatex/FloatingiceMeltingRatex.h =================================================================== --- /issm/trunk/src/c/modules/FloatingiceMeltingRatex/FloatingiceMeltingRatex.h (revision 27034) +++ /issm/trunk/src/c/modules/FloatingiceMeltingRatex/FloatingiceMeltingRatex.h (revision 27035) @@ -16,4 +16,6 @@ void FloatingiceMeltingRateIsmip6x(FemModel* femmodel); void BeckmannGoosseFloatingiceMeltingRatex(FemModel* femmodel); +void AutoregressionLinearFloatingiceMeltingRateInitx(FemModel* femmodel); +void AutoregressionLinearFloatingiceMeltingRatex(FemModel* femmodel); #endif /* _FloatingiceMeltingRatex_H*/ Index: /issm/trunk/src/c/modules/FrontalForcingsx/FrontalForcingsx.cpp =================================================================== --- /issm/trunk/src/c/modules/FrontalForcingsx/FrontalForcingsx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/FrontalForcingsx/FrontalForcingsx.cpp (revision 27035) @@ -46,6 +46,6 @@ femmodel->parameters->FindParam(&phi,&M,&Nphi,FrontalForcingsPhiEnum); _assert_(M==numbasins); _assert_(Nphi==arorder); - /*AR model spin-up with 0 noise to initialize ThermalforcingValuesAutoregressionEnum*/ - int nspin{2*arorder+5}; + /*AR model spin-up with 0 noise to initialize ThermalforcingValuesAutoregressionEnum (688 = log(0.001)/log(0.99): decaying time of inluence of phi[0]=0.99 to 0.001 of beta_0*/ + int nspin = 688; for(Object* &object:femmodel->elements->objects){ Element* element = xDynamicCast(object); //generate element object Index: /issm/trunk/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h =================================================================== --- /issm/trunk/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h (revision 27034) +++ /issm/trunk/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h (revision 27035) @@ -9,9 +9,10 @@ /* local prototypes: */ void GetVectorFromInputsx(Vector** pvector,FemModel* femmodel,int name,int type); -void GetVectoronBaseFromInputsx(Vector** pvector,FemModel* femmodel,int name,int type); void GetVectorFromInputsx(Vector** pvector,FemModel* femmodel,int name,int type,IssmDouble time); void GetVectorFromInputsx(IssmDouble** pvector,FemModel* femmodel,int name,int type); -void GetVectoronBaseFromInputsx(IssmDouble** pvector,FemModel* femmodel,int name,int type); void GetVectorFromInputsx(IssmDouble** pvector,int* pvector_size, FemModel* femmodel,int name); +void GetVectoronBaseFromInputsx(IssmDouble** pvector,FemModel* femmodel,int name,int type); +void GetVectoronBaseFromInputsx(Vector** pvector,FemModel* femmodel,int name,int type); + #endif /* _GETVECTORFROMINPUTSXX_H */ Index: /issm/trunk/src/c/modules/KillIcebergsx/KillIcebergsx.cpp =================================================================== --- /issm/trunk/src/c/modules/KillIcebergsx/KillIcebergsx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/KillIcebergsx/KillIcebergsx.cpp (revision 27035) @@ -9,5 +9,5 @@ #include "../InputUpdateFromVectorx/InputUpdateFromVectorx.h" -void KillIcebergsx(FemModel* femmodel){ +int KillIcebergsx(FemModel* femmodel){ /*Intermediaries*/ @@ -18,4 +18,5 @@ IssmDouble *local_mask = xNewZeroInit(nbv_local); bool *element_flag = xNewZeroInit(femmodel->elements->Size()); + IssmDouble ice; /*Step 1, go through all elements and put 1 in local_mask if the element is grounded*/ @@ -27,8 +28,18 @@ element_flag[i] = true; } - else{ - if(element->IsGrounded()){ + else { + if(element->IsAllGrounded()){ + /* only look at element with ice but not fully grounded */ int numvertices = element->GetNumberOfVertices(); - for(int v=0;vvertices[v]->Lid()] = 1.; + Gauss* gauss=element->NewGauss(); + Input* icelevel_input = element->GetInput(MaskIceLevelsetEnum); _assert_(icelevel_input); + + for(int v=0;vGaussVertex(v); + icelevel_input->GetInputValue(&ice,gauss); + /* The initial mask is very strict, we look at all grounded elements and set the mask for ice nodes only. */ + if (ice < 0) local_mask[element->vertices[v]->Lid()] = 1.; + } + delete gauss; } } @@ -48,5 +59,4 @@ /*Local iterations on partition*/ bool keepgoing = true; - int didsomething = 0; int iter = 1; while(keepgoing){ @@ -54,5 +64,4 @@ keepgoing = false; - didsomething = 0; int i=0; for(Object* & object : femmodel->elements->objects){ @@ -62,7 +71,11 @@ int numvertices = element->GetNumberOfVertices(); bool found1 = false; + IssmDouble sumlocalmask = 0.; + for(int j=0;jvertices[j]->Lid(); - if(local_mask[lid]>0.){ + /*we need to have at least a sharing edge, to extend the mask*/ + sumlocalmask += local_mask[lid]; + if(sumlocalmask > 1.5){ found1 = true; break; @@ -73,10 +86,7 @@ for(int j=0;jvertices[j]->Lid(); - if(local_mask[lid]==0.){ - local_mask[lid]=1.; - keepgoing = true; - didsomething = 1; - } + local_mask[lid]=1.; } + keepgoing = true; } } @@ -99,4 +109,5 @@ xDelete(element_flag); + int killbergReinit = 0; /*OK, now deactivate iceberg and count the number of deactivated vertices*/ for(Object* & object : femmodel->elements->objects){ @@ -120,9 +131,12 @@ element->AddInput(MaskIceLevelsetEnum,values,P1Enum); xDelete(values); + killbergReinit += 1; } } } - /*cleanup*/ xDelete(local_mask); + + /*Recompute the sign distance for the levelset function*/ + return killbergReinit; } Index: /issm/trunk/src/c/modules/KillIcebergsx/KillIcebergsx.h =================================================================== --- /issm/trunk/src/c/modules/KillIcebergsx/KillIcebergsx.h (revision 27034) +++ /issm/trunk/src/c/modules/KillIcebergsx/KillIcebergsx.h (revision 27035) @@ -6,5 +6,5 @@ /* local prototypes: */ -void KillIcebergsx(FemModel* femmodel); +int KillIcebergsx(FemModel* femmodel); #endif Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 27034) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 27035) @@ -311,27 +311,28 @@ /*cfsurfacelogvel variables: */ int num_cfsurfacelogvels; - char** cfsurfacelogvel_name = NULL; - char** cfsurfacelogvel_definitionstring = NULL; - IssmDouble** cfsurfacelogvel_vxobs = NULL; - IssmDouble** cfsurfacelogvel_vyobs = NULL; - char** cfsurfacelogvel_vxobs_string = NULL; - char** cfsurfacelogvel_vyobs_string = NULL; - int* cfsurfacelogvel_observation_M = NULL; - int* cfsurfacelogvel_observation_N = NULL; - IssmDouble** cfsurfacelogvel_weights = NULL; - int* cfsurfacelogvel_weights_M = NULL; - int* cfsurfacelogvel_weights_N = NULL; - char** cfsurfacelogvel_weightstring = NULL; - IssmDouble* cfsurfacelogvel_datatime = NULL; - - /*Fetch name, modeltring, observation, observationtring, etc ... (see src/m/classes/cfsurfacelogvel.m): */ - iomodel->FetchMultipleData(&cfsurfacelogvel_name,&num_cfsurfacelogvels, "md.cfsurfacelogvel.name"); - iomodel->FetchMultipleData(&cfsurfacelogvel_definitionstring,&num_cfsurfacelogvels, "md.cfsurfacelogvel.definitionstring"); - iomodel->FetchMultipleData(&cfsurfacelogvel_vxobs,&cfsurfacelogvel_observation_M,&cfsurfacelogvel_observation_N,&num_cfsurfacelogvels, "md.cfsurfacelogvel.vxobs"); - iomodel->FetchMultipleData(&cfsurfacelogvel_vxobs_string,&num_cfsurfacelogvels, "md.cfsurfacelogvel.vxobs_string"); - iomodel->FetchMultipleData(&cfsurfacelogvel_vyobs,&cfsurfacelogvel_observation_M,&cfsurfacelogvel_observation_N,&num_cfsurfacelogvels, "md.cfsurfacelogvel.vyobs"); - iomodel->FetchMultipleData(&cfsurfacelogvel_vyobs_string,&num_cfsurfacelogvels, "md.cfsurfacelogvel.vyobs_string"); iomodel->FetchMultipleData(&cfsurfacelogvel_weights,&cfsurfacelogvel_weights_M,&cfsurfacelogvel_weights_N,&num_cfsurfacelogvels, "md.cfsurfacelogvel.weights"); - iomodel->FetchMultipleData(&cfsurfacelogvel_weightstring,&num_cfsurfacelogvels, "md.cfsurfacelogvel.weights_string"); - iomodel->FetchMultipleData(&cfsurfacelogvel_datatime,&num_cfsurfacelogvels, "md.cfsurfacelogvel.datatime"); + char **cfsurfacelogvel_name = NULL; + char **cfsurfacelogvel_definitionstring = NULL; + IssmDouble **cfsurfacelogvel_vxobs = NULL; + IssmDouble **cfsurfacelogvel_vyobs = NULL; + char **cfsurfacelogvel_vxobs_string = NULL; + char **cfsurfacelogvel_vyobs_string = NULL; + int *cfsurfacelogvel_observation_M = NULL; + int *cfsurfacelogvel_observation_N = NULL; + IssmDouble **cfsurfacelogvel_weights = NULL; + int *cfsurfacelogvel_weights_M = NULL; + int *cfsurfacelogvel_weights_N = NULL; + char **cfsurfacelogvel_weightstring = NULL; + IssmDouble *cfsurfacelogvel_datatime = NULL; + + /*Fetch name, modeltring, observation, observationtring, etc ... (see src/m/classes/cfsurfacelogvel.m): */ + iomodel->FetchMultipleData(&cfsurfacelogvel_name,&num_cfsurfacelogvels,"md.cfsurfacelogvel.name"); + iomodel->FetchMultipleData(&cfsurfacelogvel_definitionstring,&num_cfsurfacelogvels,"md.cfsurfacelogvel.definitionstring"); + iomodel->FetchMultipleData(&cfsurfacelogvel_vxobs,&cfsurfacelogvel_observation_M,&cfsurfacelogvel_observation_N,&num_cfsurfacelogvels,"md.cfsurfacelogvel.vxobs"); + iomodel->FetchMultipleData(&cfsurfacelogvel_vxobs_string,&num_cfsurfacelogvels,"md.cfsurfacelogvel.vxobs_string"); + iomodel->FetchMultipleData(&cfsurfacelogvel_vyobs,NULL,NULL,&num_cfsurfacelogvels,"md.cfsurfacelogvel.vyobs"); + iomodel->FetchMultipleData(&cfsurfacelogvel_vyobs_string,&num_cfsurfacelogvels,"md.cfsurfacelogvel.vyobs_string"); + iomodel->FetchMultipleData(&cfsurfacelogvel_weights,&cfsurfacelogvel_weights_M,&cfsurfacelogvel_weights_N,&num_cfsurfacelogvels,"md.cfsurfacelogvel.weights"); + iomodel->FetchMultipleData(&cfsurfacelogvel_weightstring,&num_cfsurfacelogvels,"md.cfsurfacelogvel.weights_string"); + iomodel->FetchMultipleData(&cfsurfacelogvel_datatime,&num_cfsurfacelogvels,"md.cfsurfacelogvel.datatime"); for(j=0;jAddObject(iomodel->CopyConstantObject("md.basalforcings.num_basins",BasalforcingsLinearNumBasinsEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.basalforcings.ar_order",BasalforcingsAutoregressiveOrderEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.basalforcings.ar_initialtime",BasalforcingsAutoregressionInitialTimeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.basalforcings.ar_timestep",BasalforcingsAutoregressionTimestepEnum)); + iomodel->FetchData(&transparam,&M,&N,"md.basalforcings.beta0"); + parameters->AddObject(new DoubleVecParam(BasalforcingsBeta0Enum,transparam,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.basalforcings.beta1"); + parameters->AddObject(new DoubleVecParam(BasalforcingsBeta1Enum,transparam,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.basalforcings.phi"); + parameters->AddObject(new DoubleMatParam(BasalforcingsPhiEnum,transparam,M,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.basalforcings.upperwater_melting_rate"); + parameters->AddObject(new DoubleVecParam(BasalforcingsUpperwaterMeltingRateEnum,transparam,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.basalforcings.upperwater_elevation"); + parameters->AddObject(new DoubleVecParam(BasalforcingsUpperwaterElevationEnum,transparam,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.basalforcings.deepwater_elevation"); + parameters->AddObject(new DoubleVecParam(BasalforcingsDeepwaterElevationEnum,transparam,N)); + xDelete(transparam); break; default: @@ -403,4 +428,5 @@ parameters->AddObject(iomodel->CopyConstantObject("md.smb.ar_initialtime",SmbAutoregressionInitialTimeEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.smb.ar_timestep",SmbAutoregressionTimestepEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.num_bins",SmbNumElevationBinsEnum)); iomodel->FetchData(&transparam,&M,&N,"md.smb.beta0"); parameters->AddObject(new DoubleVecParam(SmbBeta0Enum,transparam,N)); @@ -412,5 +438,14 @@ parameters->AddObject(new DoubleMatParam(SmbPhiEnum,transparam,M,N)); xDelete(transparam); - break; + iomodel->FetchData(&transparam,&M,&N,"md.smb.lapserates"); + parameters->AddObject(new DoubleMatParam(SmbLapseRatesEnum,transparam,M,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.smb.elevationbins"); + parameters->AddObject(new DoubleMatParam(SmbElevationBinsEnum,transparam,M,N)); + xDelete(transparam); + iomodel->FetchData(&transparam,&M,&N,"md.smb.refelevation"); + parameters->AddObject(new DoubleVecParam(SmbRefElevationEnum,transparam,N)); + xDelete(transparam); + break; case SMBgembEnum: parameters->AddObject(iomodel->CopyConstantObject("md.smb.aIce",SmbAIceEnum)); @@ -486,4 +521,7 @@ } else if(hydrology_model==HydrologyGlaDSEnum){ + /*Nothing to add*/ + } + else if(hydrology_model==HydrologyTwsEnum){ /*Nothing to add*/ } @@ -508,4 +546,5 @@ parameters->AddObject(iomodel->CopyConstantObject("md.stochasticforcing.num_fields",StochasticForcingNumFieldsEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.stochasticforcing.defaultdimension",StochasticForcingDefaultDimensionEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.stochasticforcing.stochastictimestep",StochasticForcingTimestepEnum)); iomodel->FindConstant(&fields,&num_fields,"md.stochasticforcing.fields"); if(num_fields<1) _error_("no stochasticforcing fields found"); Index: /issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.cpp (revision 27035) @@ -81,6 +81,8 @@ UpdateElementsAndMaterialsDakota(elements,inputs,materials,iomodel); #endif - if(solution_enum==TransientSolutionEnum) UpdateElementsTransient(elements,parameters,inputs,iomodel); - + if(solution_enum==TransientSolutionEnum){ + UpdateParametersTransient(parameters,iomodel); + UpdateElementsTransient(elements,parameters,inputs,iomodel); + } /*Output definitions dataset: */ if(VerboseMProcessor()) _printf0_(" creating output definitions" << "\n"); Index: /issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.h =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.h (revision 27034) +++ /issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.h (revision 27035) @@ -24,4 +24,5 @@ void UpdateElementsAndMaterialsDakota(Elements* elements,Inputs* inputs,Materials* materials, IoModel* iomodel); void UpdateElementsTransient(Elements* elements,Parameters* parameters,Inputs* inputs,IoModel* iomodel); +void UpdateParametersTransient(Parameters* parameters,IoModel* iomodel); void CreateNodes(Nodes*nodes, IoModel* iomodel,int analysis,int finite_element,bool isamr=false,int approximation=NoneApproximationEnum,int* approximations=NULL); Index: /issm/trunk/src/c/modules/ModelProcessorx/Transient/UpdateParametersTransient.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/Transient/UpdateParametersTransient.cpp (revision 27035) +++ /issm/trunk/src/c/modules/ModelProcessorx/Transient/UpdateParametersTransient.cpp (revision 27035) @@ -0,0 +1,25 @@ +/* + * UpdateParametersTransient.cpp: + */ + +#include "../../../toolkits/toolkits.h" +#include "../../../classes/classes.h" +#include "../../../shared/shared.h" +#include "../../MeshPartitionx/MeshPartitionx.h" +#include "../ModelProcessorx.h" + +void UpdateParametersTransient(Parameters* parameters,IoModel* iomodel){/*{{{*/ + + bool isgroundingline; + int numoutputs; + char** requestedoutputs; + parameters->FindParam(&isgroundingline,TransientIsgroundinglineEnum); + if(isgroundingline){ + iomodel->FindConstant(&requestedoutputs,&numoutputs,"md.groundingline.requested_outputs"); + parameters->AddObject(new IntParam(GroundinglineNumRequestedOutputsEnum,numoutputs)); + if(numoutputs)parameters->AddObject(new StringArrayParam(GroundinglineRequestedOutputsEnum,requestedoutputs,numoutputs)); + iomodel->DeleteData(&requestedoutputs,numoutputs,"md.groundingline.requested_outputs"); + } +}/*}}}*/ + + Index: /issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp =================================================================== --- /issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 27035) @@ -40,2 +40,26 @@ xDelete(serial_vector); } +#ifdef _HAVE_AD_ +void SetControlInputsFromVectorx(FemModel* femmodel,IssmPDouble* vector){ + + /*Get total size and recast*/ + int num_controls; + int* M = NULL; + int* N = NULL; + femmodel->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); + femmodel->parameters->FindParam(&M,NULL,ControlInputSizeMEnum); + femmodel->parameters->FindParam(&N,NULL,ControlInputSizeNEnum); + + int size = 0; + for(int i=0;i(size); + for(int i=0;i(vector[i]); + + SetControlInputsFromVectorx(femmodel,serial_vector); + + xDelete(serial_vector); + xDelete(M); + xDelete(N); +} +#endif Index: /issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h =================================================================== --- /issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h (revision 27034) +++ /issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h (revision 27035) @@ -11,3 +11,7 @@ void SetControlInputsFromVectorx(FemModel* femmodel,IssmDouble* vector); +#ifdef _HAVE_AD_ +void SetControlInputsFromVectorx(FemModel* femmodel,IssmPDouble* vector); +#endif + #endif Index: /issm/trunk/src/c/modules/Solverx/Solverx.cpp =================================================================== --- /issm/trunk/src/c/modules/Solverx/Solverx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/Solverx/Solverx.cpp (revision 27035) @@ -65,5 +65,5 @@ /*Check convergence*/ if(solver_residue>solver_residue_threshold){ - _printf0_("solver residue too high!: norm(KU-F)/norm(F)=" << solver_residue << " > "< "<parameters->FindParam(&timeVV,TimeEnum); - femmodel->parameters->FindParam(&dtVV,TimesteppingTimeStepEnum); - femmodel->parameters->FindParam(&starttimeVV,TimesteppingStartTimeEnum); - IssmDouble valMean = 0; - IssmDouble valSdev = 0.5; - int seed; - //seed = reCast((timeVV-starttimeVV)/dtVV); - seed = -1; - IssmDouble rdmVV; - univariateNormal_test0(&rdmVV,valMean,valSdev,seed); - _printf_("VV rdmVV: "<parameters->FindParam(&covariance,&M,&N,StochasticForcingCovarianceEnum); _assert_(M==dimtot); _assert_(N==dimtot); + /*Check if this is a timestep for new noiseterms computation*/ + bool isstepforstoch = false; + IssmDouble time,dt,starttime,tstep_stoch; + femmodel->parameters->FindParam(&time,TimeEnum); + femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + femmodel->parameters->FindParam(&starttime,TimesteppingStartTimeEnum); + femmodel->parameters->FindParam(&tstep_stoch,StochasticForcingTimestepEnum); + + #ifndef _HAVE_AD_ + if((fmod(time,tstep_stoch)(dimtot); - my_rank=IssmComm::GetRank(); - if(my_rank==0){ - int fixedseed; - IssmDouble time,dt,starttime; - femmodel->parameters->FindParam(&time,TimeEnum); - femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); - femmodel->parameters->FindParam(&starttime,TimesteppingStartTimeEnum); - /*Determine whether random seed is fixed to time step (randomflag==false) or random seed truly random (randomflag==true)*/ - if(randomflag) fixedseed=-1; - else fixedseed = reCast((time-starttime)/dt); - /*multivariateNormal needs to be passed a NULL pointer to avoid memory leak issues*/ - IssmDouble* temparray = NULL; - multivariateNormal(&temparray,dimtot,0.0,covariance,fixedseed); - for(int i=0;i(temparray); - } - ISSM_MPI_Bcast(noiseterms,dimtot,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); - + IssmDouble* noiseterms = xNew(dimtot); + if(isstepforstoch){ + my_rank=IssmComm::GetRank(); + if(my_rank==0){ + int fixedseed; + /*Determine whether random seed is fixed to time step (randomflag==false) or random seed truly random (randomflag==true)*/ + if(randomflag) fixedseed=-1; + else fixedseed = reCast((time-starttime)/dt); + /*multivariateNormal needs to be passed a NULL pointer to avoid memory leak issues*/ + IssmDouble* temparray = NULL; + multivariateNormal(&temparray,dimtot,0.0,covariance,fixedseed); + for(int i=0;i(temparray); + } + ISSM_MPI_Bcast(noiseterms,dimtot,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + femmodel->parameters->SetParam(noiseterms,dimtot,StochasticForcingNoisetermsEnum); + } + else{ + IssmDouble* temparray = NULL; + femmodel->parameters->FindParam(&temparray,&N,StochasticForcingNoisetermsEnum); _assert_(N==dimtot); + for(int i=0;i(temparray); + } + int i=0; for(int j=0;jinputs->DeleteInput(BasalforcingsSpatialDeepwaterMeltingRateEnum); + for(Object* &object:femmodel->elements->objects){ + Element* element = xDynamicCast(object); + int numvertices = element->GetNumberOfVertices(); + IssmDouble baselinedeepwatermelt; + IssmDouble deepwatermelt_tot[numvertices]; + Input* baselinedeepwatermelt_input = NULL; + baselinedeepwatermelt_input = element->GetInput(BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum); _assert_(baselinedeepwatermelt_input); + element->GetInputValue(&dimensionid,StochasticForcingDefaultIdEnum); + Gauss* gauss = element->NewGauss(); + for(int i=0;iGaussVertex(i); + baselinedeepwatermelt_input->GetInputValue(&baselinedeepwatermelt,gauss); + deepwatermelt_tot[i] = baselinedeepwatermelt+noisefield[dimensionid]; + } + element->AddInput(BasalforcingsSpatialDeepwaterMeltingRateEnum,&deepwatermelt_tot[0],P1DGEnum); + delete gauss; + } + break; case DefaultCalvingEnum: /*Delete CalvingCalvingrateEnum at previous time step (required if it is transient)*/ @@ -136,5 +165,6 @@ gauss->GaussVertex(i); baselinefloatingicemeltrate_input->GetInputValue(&baselinefloatingicemeltrate,gauss); - floatingicemeltrate_tot[i] = max(0.0,baselinefloatingicemeltrate+noisefield[dimensionid]); + /*No check for positive melt rate because basal accretion is allowed*/ + floatingicemeltrate_tot[i] = baselinefloatingicemeltrate+noisefield[dimensionid]; } element->AddInput(BasalforcingsFloatingiceMeltingRateEnum,&floatingicemeltrate_tot[0],P1DGEnum); @@ -142,5 +172,25 @@ } break; - //VV working(29Nov2021) + case SMBforcingEnum: + /*Delete SmbMassBalanceEnum at previous time step (required if it is transient)*/ + femmodel->inputs->DeleteInput(SmbMassBalanceEnum); + for(Object* &object:femmodel->elements->objects){ + Element* element = xDynamicCast(object); + int numvertices = element->GetNumberOfVertices(); + IssmDouble baselinesmb; + IssmDouble smb_tot[numvertices]; + Input* baselinesmb_input = NULL; + baselinesmb_input = element->GetInput(BaselineSmbMassBalanceEnum); _assert_(baselinesmb_input); + element->GetInputValue(&dimensionid,StochasticForcingDefaultIdEnum); + Gauss* gauss = element->NewGauss(); + for(int i=0;iGaussVertex(i); + baselinesmb_input->GetInputValue(&baselinesmb,gauss); + smb_tot[i] = baselinesmb+noisefield[dimensionid]; + } + element->AddInput(SmbMassBalanceEnum,&smb_tot[0],P1DGEnum); + delete gauss; + } + break; case FrictionWaterPressureEnum: /*Specify that WaterPressure is stochastic*/ @@ -165,27 +215,4 @@ } break; - - /* - case FrictionEffectivePressureEnum: - femmodel->parameters->SetParam(true,StochasticForcingIsEffectivePressureEnum); - for(Object* &object:femmodel->elements->objects){ - Element* element = xDynamicCast(object); - int numvertices = element->GetNumberOfVertices(); - IssmDouble Neff[numvertices]; - element->GetInputValue(&dimensionid,StochasticForcingDefaultIdEnum); - Gauss* gauss=element->NewGauss(); - Friction* friction = new Friction(element); - for(int i=0;iGaussVertex(i); - Neff[i] = friction->EffectivePressure(gauss); - Neff[i] = Neff[i]+noisefield[dimensionid]; - } - element->AddInput(FrictionEffectivePressureEnum,Neff,P1DGEnum); - delete gauss; - delete friction; - } - break; - */ - default: _error_("Field "<GetInput(VxSurfaceEnum); _assert_(vx_input); Index: /issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp (revision 27035) @@ -74,5 +74,5 @@ Input* vyobs_input = NULL; - /*Read SurfaceEnum from 2D models:SSA, L1L2, MLHO*/ + /*Read SurfaceEnum from 2D models:SSA, L1L2, MOLHO*/ if (domaintype == Domain2DhorizontalEnum) { vx_input = topelement->GetInput(VxSurfaceEnum); _assert_(vx_input); Index: /issm/trunk/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp (revision 27035) @@ -68,5 +68,5 @@ Input* vyobs_input = NULL; - /*Read SurfaceEnum from 2D models:SSA, L1L2, MLHO*/ + /*Read SurfaceEnum from 2D models:SSA, L1L2, MOLHO*/ if (domaintype == Domain2DhorizontalEnum) { vx_input = topelement->GetInput(VxSurfaceEnum); _assert_(vx_input); Index: /issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp (revision 27035) @@ -68,5 +68,5 @@ Input* vyobs_input = NULL; - /*Read SurfaceEnum from 2D models:SSA, L1L2, MLHO*/ + /*Read SurfaceEnum from 2D models:SSA, L1L2, MOLHO*/ if (domaintype == Domain2DhorizontalEnum) { vx_input = topelement->GetInput(VxSurfaceEnum); _assert_(vx_input); Index: /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp (revision 27034) +++ /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp (revision 27035) @@ -164,6 +164,6 @@ femmodel->parameters->FindParam(&phi,&M,&Nphi,SmbPhiEnum); _assert_(M==numbasins); _assert_(Nphi==arorder); - /*AR model spin-up with 0 noise to initialize SmbValuesAutoregressionEnum*/ - int nspin{2*arorder+5}; + /*AR model spin-up with 0 noise to initialize SmbValuesAutoregressionEnum (688 = log(0.001)/log(0.99): decaying time of inluence of phi[0]=0.99 to 0.001 of beta_0*/ + int nspin = 688; for(Object* &object:femmodel->elements->objects){ Element* element = xDynamicCast(object); //generate element object @@ -198,16 +198,23 @@ bool isstochastic; bool issmbstochastic = false; - int M,N,Nphi,arorder,numbasins,my_rank; + int M,N,Nphi,arorder,numbasins,numelevbins,my_rank; femmodel->parameters->FindParam(&numbasins,SmbNumBasinsEnum); femmodel->parameters->FindParam(&arorder,SmbAutoregressiveOrderEnum); + femmodel->parameters->FindParam(&numelevbins,SmbNumElevationBinsEnum); IssmDouble tinit_ar; - IssmDouble* beta0 = NULL; - IssmDouble* beta1 = NULL; - IssmDouble* phi = NULL; + IssmDouble* beta0 = NULL; + IssmDouble* beta1 = NULL; + IssmDouble* phi = NULL; + IssmDouble* lapserates = NULL; + IssmDouble* elevbins = NULL; + IssmDouble* refelevation = NULL; femmodel->parameters->FindParam(&tinit_ar,SmbAutoregressionInitialTimeEnum); - femmodel->parameters->FindParam(&beta0,&M,SmbBeta0Enum); _assert_(M==numbasins); - femmodel->parameters->FindParam(&beta1,&M,SmbBeta1Enum); _assert_(M==numbasins); - femmodel->parameters->FindParam(&phi,&M,&Nphi,SmbPhiEnum); _assert_(M==numbasins); _assert_(Nphi==arorder); + femmodel->parameters->FindParam(&beta0,&M,SmbBeta0Enum); _assert_(M==numbasins); + femmodel->parameters->FindParam(&beta1,&M,SmbBeta1Enum); _assert_(M==numbasins); + femmodel->parameters->FindParam(&phi,&M,&Nphi,SmbPhiEnum); _assert_(M==numbasins); _assert_(Nphi==arorder); + femmodel->parameters->FindParam(&lapserates,&M,&N,SmbLapseRatesEnum); _assert_(M==numbasins); _assert_(N==numelevbins); + femmodel->parameters->FindParam(&elevbins,&M,&N,SmbElevationBinsEnum); _assert_(M==numbasins); _assert_(N==numelevbins-1); + femmodel->parameters->FindParam(&refelevation,&M,SmbRefElevationEnum); _assert_(M==numbasins); femmodel->parameters->FindParam(&isstochastic,StochasticForcingIsStochasticForcingEnum); @@ -228,6 +235,9 @@ for(Object* &object:femmodel->elements->objects){ Element* element = xDynamicCast(object); - element->Autoregression(isstepforar,arorder,telapsed_ar,beta0,beta1,phi,issmbstochastic,SMBautoregressionEnum); - } + /*Compute autoregression*/ + element->Autoregression(isstepforar,arorder,telapsed_ar,beta0,beta1,phi,issmbstochastic,SMBautoregressionEnum); + /*Compute lapse rate adjustment*/ + element->LapseRateBasinSMB(numelevbins,lapserates,elevbins,refelevation); + } /*Cleanup*/ @@ -235,4 +245,7 @@ xDelete(beta1); xDelete(phi); + xDelete(lapserates); + xDelete(elevbins); + xDelete(refelevation); }/*}}}*/ void Delta18oParameterizationx(FemModel* femmodel){/*{{{*/ Index: /issm/trunk/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp (revision 27034) +++ /issm/trunk/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp (revision 27035) @@ -68,5 +68,5 @@ Input* vyobs_input = NULL; - /*Read SurfaceEnum from 2D models:SSA, L1L2, MLHO*/ + /*Read SurfaceEnum from 2D models:SSA, L1L2, MOLHO*/ if (domaintype == Domain2DhorizontalEnum) { vx_input = topelement->GetInput(VxSurfaceEnum); _assert_(vx_input); Index: /issm/trunk/src/c/shared/Enum/Enum.vim =================================================================== --- /issm/trunk/src/c/shared/Enum/Enum.vim (revision 27034) +++ /issm/trunk/src/c/shared/Enum/Enum.vim (revision 27035) @@ -64,4 +64,9 @@ syn keyword cConstant BalancethicknessStabilizationEnum syn keyword cConstant BarystaticContributionsEnum +syn keyword cConstant BasalforcingsAutoregressionInitialTimeEnum +syn keyword cConstant BasalforcingsAutoregressionTimestepEnum +syn keyword cConstant BasalforcingsAutoregressiveOrderEnum +syn keyword cConstant BasalforcingsBeta0Enum +syn keyword cConstant BasalforcingsBeta1Enum syn keyword cConstant BasalforcingsBottomplumedepthEnum syn keyword cConstant BasalforcingsCrustthicknessEnum @@ -77,7 +82,9 @@ syn keyword cConstant BasalforcingsIsmip6NumBasinsEnum syn keyword cConstant BasalforcingsIsmip6TfDepthsEnum +syn keyword cConstant BasalforcingsLinearNumBasinsEnum syn keyword cConstant BasalforcingsLowercrustheatEnum syn keyword cConstant BasalforcingsMantleconductivityEnum syn keyword cConstant BasalforcingsNusseltEnum +syn keyword cConstant BasalforcingsPhiEnum syn keyword cConstant BasalforcingsPicoAverageOverturningEnum syn keyword cConstant BasalforcingsPicoAverageSalinityEnum @@ -105,4 +112,11 @@ syn keyword cConstant CalvingLawEnum syn keyword cConstant CalvingMinthicknessEnum +syn keyword cConstant CalvingTestSpeedfactorEnum +syn keyword cConstant CalvingTestIndependentRateEnum +syn keyword cConstant CalvingUseParamEnum +syn keyword cConstant CalvingScaleThetaEnum +syn keyword cConstant CalvingAmpAlphaEnum +syn keyword cConstant CalvingMidpointEnum +syn keyword cConstant CalvingNonlinearLawEnum syn keyword cConstant ConfigurationTypeEnum syn keyword cConstant ConstantsGEnum @@ -162,5 +176,5 @@ syn keyword cConstant FlowequationIsHOEnum syn keyword cConstant FlowequationIsL1L2Enum -syn keyword cConstant FlowequationIsMLHOEnum +syn keyword cConstant FlowequationIsMOLHOEnum syn keyword cConstant FlowequationIsSIAEnum syn keyword cConstant FlowequationIsSSAEnum @@ -189,4 +203,6 @@ syn keyword cConstant GroundinglineMeltInterpolationEnum syn keyword cConstant GroundinglineMigrationEnum +syn keyword cConstant GroundinglineNumRequestedOutputsEnum +syn keyword cConstant GroundinglineRequestedOutputsEnum syn keyword cConstant HydrologyAveragingEnum syn keyword cConstant HydrologyCavitySpacingEnum @@ -263,4 +279,5 @@ syn keyword cConstant LockFileNameEnum syn keyword cConstant LoveAllowLayerDeletionEnum +syn keyword cConstant LoveChandlerWobbleEnum syn keyword cConstant LoveCoreMantleBoundaryEnum syn keyword cConstant LoveEarthMassEnum @@ -283,4 +300,5 @@ syn keyword cConstant LoveStartingLayerEnum syn keyword cConstant LoveUnderflowTolEnum +syn keyword cConstant LovePostWidderThresholdEnum syn keyword cConstant MassFluxSegmentsEnum syn keyword cConstant MassFluxSegmentsPresentEnum @@ -352,10 +370,8 @@ syn keyword cConstant ModelnameEnum syn keyword cConstant SamplingAlphaEnum -syn keyword cConstant SamplingPhiEnum syn keyword cConstant SamplingNumRequestedOutputsEnum syn keyword cConstant SamplingRequestedOutputsEnum syn keyword cConstant SamplingRobinEnum syn keyword cConstant SamplingSeedEnum -syn keyword cConstant SamplingTauEnum syn keyword cConstant SaveResultsEnum syn keyword cConstant SolidearthPartitionIceEnum @@ -369,5 +385,4 @@ syn keyword cConstant SolidearthSettingsAbstolEnum syn keyword cConstant SolidearthSettingsCrossSectionShapeEnum -syn keyword cConstant RotationalAngularVelocityEnum syn keyword cConstant SolidearthSettingsElasticEnum syn keyword cConstant SolidearthSettingsViscousEnum @@ -376,5 +391,13 @@ syn keyword cConstant SealevelchangeViscousTimesEnum syn keyword cConstant SealevelchangeViscousIndexEnum +syn keyword cConstant SealevelchangeViscousPolarMotionEnum +syn keyword cConstant SealevelchangeRunCountEnum +syn keyword cConstant SealevelchangeTransitionsEnum +syn keyword cConstant SealevelchangeRequestedOutputsEnum +syn keyword cConstant RotationalAngularVelocityEnum syn keyword cConstant RotationalEquatorialMoiEnum +syn keyword cConstant RotationalPolarMoiEnum +syn keyword cConstant LovePolarMotionTransferFunctionColinearEnum +syn keyword cConstant LovePolarMotionTransferFunctionOrthogonalEnum syn keyword cConstant TidalLoveHEnum syn keyword cConstant TidalLoveKEnum @@ -388,9 +411,16 @@ syn keyword cConstant SealevelchangeGSelfAttractionEnum syn keyword cConstant SealevelchangeGViscoElasticEnum +syn keyword cConstant SealevelchangeUViscoElasticEnum +syn keyword cConstant SealevelchangeHViscoElasticEnum +syn keyword cConstant SealevelchangePolarMotionTransferFunctionColinearEnum +syn keyword cConstant SealevelchangePolarMotionTransferFunctionOrthogonalEnum +syn keyword cConstant SealevelchangePolarMotionTransferFunctionZEnum +syn keyword cConstant SealevelchangeTidalK2Enum +syn keyword cConstant SealevelchangeTidalH2Enum +syn keyword cConstant SealevelchangeTidalL2Enum syn keyword cConstant SolidearthSettingsSealevelLoadingEnum syn keyword cConstant SolidearthSettingsGRDEnum syn keyword cConstant SolidearthSettingsRunFrequencyEnum syn keyword cConstant SolidearthSettingsTimeAccEnum -syn keyword cConstant SealevelchangeHViscoElasticEnum syn keyword cConstant SolidearthSettingsHorizEnum syn keyword cConstant SolidearthSettingsMaxiterEnum @@ -404,15 +434,12 @@ syn keyword cConstant StochasticForcingIsStochasticForcingEnum syn keyword cConstant StochasticForcingIsWaterPressureEnum +syn keyword cConstant StochasticForcingNoisetermsEnum syn keyword cConstant StochasticForcingNumFieldsEnum syn keyword cConstant StochasticForcingRandomflagEnum -syn keyword cConstant RotationalPolarMoiEnum +syn keyword cConstant StochasticForcingTimestepEnum syn keyword cConstant SolidearthSettingsReltolEnum -syn keyword cConstant SealevelchangeRequestedOutputsEnum syn keyword cConstant SolidearthSettingsSelfAttractionEnum syn keyword cConstant SolidearthSettingsRotationEnum syn keyword cConstant SolidearthSettingsMaxSHCoeffEnum -syn keyword cConstant SealevelchangeRunCountEnum -syn keyword cConstant SealevelchangeTransitionsEnum -syn keyword cConstant SealevelchangeUViscoElasticEnum syn keyword cConstant SettingsIoGatherEnum syn keyword cConstant SettingsNumResultsOnNodesEnum @@ -439,4 +466,5 @@ syn keyword cConstant SmbDpermilEnum syn keyword cConstant SmbDsnowIdxEnum +syn keyword cConstant SmbElevationBinsEnum syn keyword cConstant SmbCldFracEnum syn keyword cConstant SmbDelta18oEnum @@ -466,9 +494,12 @@ syn keyword cConstant SmbIsturbulentfluxEnum syn keyword cConstant SmbKEnum +syn keyword cConstant SmbLapseRatesEnum syn keyword cConstant SmbNumBasinsEnum +syn keyword cConstant SmbNumElevationBinsEnum syn keyword cConstant SmbNumRequestedOutputsEnum syn keyword cConstant SmbPfacEnum syn keyword cConstant SmbPhiEnum syn keyword cConstant SmbRdlEnum +syn keyword cConstant SmbRefElevationEnum syn keyword cConstant SmbRequestedOutputsEnum syn keyword cConstant SmbRlapsEnum @@ -579,8 +610,16 @@ syn keyword cConstant BalancethicknessThickeningRateEnum syn keyword cConstant BasalCrevasseEnum +syn keyword cConstant BasalforcingsDeepwaterMeltingRateAutoregressionEnum +syn keyword cConstant BasalforcingsDeepwaterMeltingRateNoiseEnum +syn keyword cConstant BasalforcingsDeepwaterMeltingRateValuesAutoregressionEnum syn keyword cConstant BasalforcingsFloatingiceMeltingRateEnum syn keyword cConstant BasalforcingsGeothermalfluxEnum syn keyword cConstant BasalforcingsGroundediceMeltingRateEnum +syn keyword cConstant BasalforcingsLinearBasinIdEnum syn keyword cConstant BasalforcingsPerturbationMeltingRateEnum +syn keyword cConstant BasalforcingsSpatialDeepwaterElevationEnum +syn keyword cConstant BasalforcingsSpatialDeepwaterMeltingRateEnum +syn keyword cConstant BasalforcingsSpatialUpperwaterElevationEnum +syn keyword cConstant BasalforcingsSpatialUpperwaterMeltingRateEnum syn keyword cConstant BasalforcingsIsmip6BasinIdEnum syn keyword cConstant BasalforcingsIsmip6TfEnum @@ -604,6 +643,8 @@ syn keyword cConstant BaseSlopeYEnum syn keyword cConstant BaselineBasalforcingsFloatingiceMeltingRateEnum +syn keyword cConstant BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum syn keyword cConstant BaselineCalvingCalvingrateEnum syn keyword cConstant BaselineFrictionEffectivePressureEnum +syn keyword cConstant BaselineSmbMassBalanceEnum syn keyword cConstant BedEnum syn keyword cConstant BedGRDEnum @@ -618,11 +659,10 @@ syn keyword cConstant CalvingCalvingrateEnum syn keyword cConstant CalvingHabFractionEnum +syn keyword cConstant CalvingAblationrateEnum syn keyword cConstant CalvingMeltingrateEnum syn keyword cConstant CalvingStressThresholdFloatingiceEnum syn keyword cConstant CalvingStressThresholdGroundediceEnum syn keyword cConstant CalvinglevermannCoeffEnum -syn keyword cConstant CalvingratexAverageEnum syn keyword cConstant CalvingratexEnum -syn keyword cConstant CalvingrateyAverageEnum syn keyword cConstant CalvingrateyEnum syn keyword cConstant CalvingFluxLevelsetEnum @@ -803,6 +843,10 @@ syn keyword cConstant RheologyBbarAbsGradientEnum syn keyword cConstant SampleEnum +syn keyword cConstant SampleOldEnum +syn keyword cConstant SampleNoiseEnum syn keyword cConstant SamplingBetaEnum syn keyword cConstant SamplingKappaEnum +syn keyword cConstant SamplingPhiEnum +syn keyword cConstant SamplingTauEnum syn keyword cConstant SealevelEnum syn keyword cConstant SealevelGRDEnum @@ -839,16 +883,4 @@ syn keyword cConstant BslcRateEnum syn keyword cConstant GmtslcEnum -syn keyword cConstant SealevelGrotm1Enum -syn keyword cConstant SealevelGrotm2Enum -syn keyword cConstant SealevelGrotm3Enum -syn keyword cConstant SealevelGUrotm1Enum -syn keyword cConstant SealevelGUrotm2Enum -syn keyword cConstant SealevelGUrotm3Enum -syn keyword cConstant SealevelGNrotm1Enum -syn keyword cConstant SealevelGNrotm2Enum -syn keyword cConstant SealevelGNrotm3Enum -syn keyword cConstant SealevelGErotm1Enum -syn keyword cConstant SealevelGErotm2Enum -syn keyword cConstant SealevelGErotm3Enum syn keyword cConstant SealevelRSLBarystaticEnum syn keyword cConstant SealevelRSLRateEnum @@ -862,4 +894,8 @@ syn keyword cConstant SealevelchangeGEEnum syn keyword cConstant SealevelchangeGNEnum +syn keyword cConstant SealevelchangeGrotEnum +syn keyword cConstant SealevelchangeGUrotEnum +syn keyword cConstant SealevelchangeGNrotEnum +syn keyword cConstant SealevelchangeGErotEnum syn keyword cConstant SealevelchangeGsubelOceanEnum syn keyword cConstant SealevelchangeGUsubelOceanEnum @@ -1195,4 +1231,5 @@ syn keyword cConstant ArrheniusEnum syn keyword cConstant AutodiffJacobianEnum +syn keyword cConstant AutoregressionLinearFloatingMeltRateEnum syn keyword cConstant Balancethickness2AnalysisEnum syn keyword cConstant Balancethickness2SolutionEnum @@ -1218,4 +1255,6 @@ syn keyword cConstant CalvingHabEnum syn keyword cConstant CalvingLevermannEnum +syn keyword cConstant CalvingTestEnum +syn keyword cConstant CalvingParameterizationEnum syn keyword cConstant CalvingVonmisesEnum syn keyword cConstant CfdragcoeffabsgradEnum @@ -1346,5 +1385,5 @@ syn keyword cConstant JEnum syn keyword cConstant L1L2ApproximationEnum -syn keyword cConstant MLHOApproximationEnum +syn keyword cConstant MOLHOApproximationEnum syn keyword cConstant L2ProjectionBaseAnalysisEnum syn keyword cConstant L2ProjectionEPLAnalysisEnum @@ -1358,12 +1397,17 @@ syn keyword cConstant LoadsEnum syn keyword cConstant LoveAnalysisEnum -syn keyword cConstant LoveHiEnum -syn keyword cConstant LoveHrEnum +syn keyword cConstant LoveHfEnum +syn keyword cConstant LoveHtEnum syn keyword cConstant LoveKernelsImagEnum syn keyword cConstant LoveKernelsRealEnum -syn keyword cConstant LoveKiEnum -syn keyword cConstant LoveKrEnum -syn keyword cConstant LoveLiEnum -syn keyword cConstant LoveLrEnum +syn keyword cConstant LoveKfEnum +syn keyword cConstant LoveKtEnum +syn keyword cConstant LoveLfEnum +syn keyword cConstant LoveLtEnum +syn keyword cConstant LoveTidalHtEnum +syn keyword cConstant LoveTidalKtEnum +syn keyword cConstant LoveTidalLtEnum +syn keyword cConstant LovePMTF1tEnum +syn keyword cConstant LovePMTF2tEnum syn keyword cConstant LoveSolutionEnum syn keyword cConstant MINIEnum @@ -1477,7 +1521,7 @@ syn keyword cConstant SealevelAbsoluteEnum syn keyword cConstant SealevelEmotionEnum -syn keyword cConstant SealevelInertiaTensorXZEnum -syn keyword cConstant SealevelInertiaTensorYZEnum -syn keyword cConstant SealevelInertiaTensorZZEnum +syn keyword cConstant SealevelchangePolarMotionXEnum +syn keyword cConstant SealevelchangePolarMotionYEnum +syn keyword cConstant SealevelchangePolarMotionZEnum syn keyword cConstant SealevelchangePolarMotionEnum syn keyword cConstant SealevelNmotionEnum @@ -1580,5 +1624,4 @@ syn keyword cType Cfsurfacesquare syn keyword cType Channel -syn keyword cType classes syn keyword cType Constraint syn keyword cType Constraints @@ -1587,6 +1630,6 @@ syn keyword cType ControlInput syn keyword cType Covertree +syn keyword cType DataSetParam syn keyword cType DatasetInput -syn keyword cType DataSetParam syn keyword cType Definition syn keyword cType DependentObject @@ -1601,6 +1644,6 @@ syn keyword cType ElementInput syn keyword cType ElementMatrix +syn keyword cType ElementVector syn keyword cType Elements -syn keyword cType ElementVector syn keyword cType ExponentialVariogram syn keyword cType ExternalResult @@ -1609,10 +1652,9 @@ syn keyword cType Friction syn keyword cType Gauss -syn keyword cType GaussianVariogram -syn keyword cType gaussobjects syn keyword cType GaussPenta syn keyword cType GaussSeg syn keyword cType GaussTetra syn keyword cType GaussTria +syn keyword cType GaussianVariogram syn keyword cType GenericExternalResult syn keyword cType GenericOption @@ -1630,5 +1672,4 @@ syn keyword cType IssmDirectApplicInterface syn keyword cType IssmParallelDirectApplicInterface -syn keyword cType krigingobjects syn keyword cType Load syn keyword cType Loads @@ -1641,5 +1682,4 @@ syn keyword cType Matice syn keyword cType Matlitho -syn keyword cType matrixobjects syn keyword cType MatrixParam syn keyword cType Misfit @@ -1654,6 +1694,6 @@ syn keyword cType Observations syn keyword cType Option +syn keyword cType OptionUtilities syn keyword cType Options -syn keyword cType OptionUtilities syn keyword cType Param syn keyword cType Parameters @@ -1669,11 +1709,11 @@ syn keyword cType Regionaloutput syn keyword cType Results +syn keyword cType RiftStruct syn keyword cType Riftfront -syn keyword cType RiftStruct syn keyword cType SealevelGeometry syn keyword cType Seg syn keyword cType SegInput +syn keyword cType SegRef syn keyword cType Segment -syn keyword cType SegRef syn keyword cType SpcDynamic syn keyword cType SpcStatic @@ -1694,4 +1734,8 @@ syn keyword cType Vertex syn keyword cType Vertices +syn keyword cType classes +syn keyword cType gaussobjects +syn keyword cType krigingobjects +syn keyword cType matrixobjects syn keyword cType AdjointBalancethickness2Analysis syn keyword cType AdjointBalancethicknessAnalysis Index: /issm/trunk/src/c/shared/Enum/EnumDefinitions.h =================================================================== --- /issm/trunk/src/c/shared/Enum/EnumDefinitions.h (revision 27034) +++ /issm/trunk/src/c/shared/Enum/EnumDefinitions.h (revision 27035) @@ -58,4 +58,9 @@ BalancethicknessStabilizationEnum, BarystaticContributionsEnum, + BasalforcingsAutoregressionInitialTimeEnum, + BasalforcingsAutoregressionTimestepEnum, + BasalforcingsAutoregressiveOrderEnum, + BasalforcingsBeta0Enum, + BasalforcingsBeta1Enum, BasalforcingsBottomplumedepthEnum, BasalforcingsCrustthicknessEnum, @@ -71,7 +76,9 @@ BasalforcingsIsmip6NumBasinsEnum, BasalforcingsIsmip6TfDepthsEnum, + BasalforcingsLinearNumBasinsEnum, BasalforcingsLowercrustheatEnum, BasalforcingsMantleconductivityEnum, BasalforcingsNusseltEnum, + BasalforcingsPhiEnum, BasalforcingsPicoAverageOverturningEnum, BasalforcingsPicoAverageSalinityEnum, @@ -99,4 +106,11 @@ CalvingLawEnum, CalvingMinthicknessEnum, + CalvingTestSpeedfactorEnum, + CalvingTestIndependentRateEnum, + CalvingUseParamEnum, + CalvingScaleThetaEnum, + CalvingAmpAlphaEnum, + CalvingMidpointEnum, + CalvingNonlinearLawEnum, ConfigurationTypeEnum, ConstantsGEnum, @@ -156,5 +170,5 @@ FlowequationIsHOEnum, FlowequationIsL1L2Enum, - FlowequationIsMLHOEnum, + FlowequationIsMOLHOEnum, FlowequationIsSIAEnum, FlowequationIsSSAEnum, @@ -183,4 +197,6 @@ GroundinglineMeltInterpolationEnum, GroundinglineMigrationEnum, + GroundinglineNumRequestedOutputsEnum, + GroundinglineRequestedOutputsEnum, HydrologyAveragingEnum, HydrologyCavitySpacingEnum, @@ -257,4 +273,5 @@ LockFileNameEnum, LoveAllowLayerDeletionEnum, + LoveChandlerWobbleEnum, LoveCoreMantleBoundaryEnum, LoveEarthMassEnum, @@ -277,4 +294,5 @@ LoveStartingLayerEnum, LoveUnderflowTolEnum, + LovePostWidderThresholdEnum, MassFluxSegmentsEnum, MassFluxSegmentsPresentEnum, @@ -346,10 +364,8 @@ ModelnameEnum, SamplingAlphaEnum, - SamplingPhiEnum, SamplingNumRequestedOutputsEnum, SamplingRequestedOutputsEnum, SamplingRobinEnum, SamplingSeedEnum, - SamplingTauEnum, SaveResultsEnum, SolidearthPartitionIceEnum, @@ -363,5 +379,4 @@ SolidearthSettingsAbstolEnum, SolidearthSettingsCrossSectionShapeEnum, - RotationalAngularVelocityEnum, SolidearthSettingsElasticEnum, SolidearthSettingsViscousEnum, @@ -370,5 +385,13 @@ SealevelchangeViscousTimesEnum, SealevelchangeViscousIndexEnum, + SealevelchangeViscousPolarMotionEnum, + SealevelchangeRunCountEnum, + SealevelchangeTransitionsEnum, + SealevelchangeRequestedOutputsEnum, + RotationalAngularVelocityEnum, RotationalEquatorialMoiEnum, + RotationalPolarMoiEnum, + LovePolarMotionTransferFunctionColinearEnum, + LovePolarMotionTransferFunctionOrthogonalEnum, TidalLoveHEnum, TidalLoveKEnum, @@ -382,9 +405,16 @@ SealevelchangeGSelfAttractionEnum, SealevelchangeGViscoElasticEnum, + SealevelchangeUViscoElasticEnum, + SealevelchangeHViscoElasticEnum, + SealevelchangePolarMotionTransferFunctionColinearEnum, + SealevelchangePolarMotionTransferFunctionOrthogonalEnum, + SealevelchangePolarMotionTransferFunctionZEnum, + SealevelchangeTidalK2Enum, + SealevelchangeTidalH2Enum, + SealevelchangeTidalL2Enum, SolidearthSettingsSealevelLoadingEnum, SolidearthSettingsGRDEnum, SolidearthSettingsRunFrequencyEnum, SolidearthSettingsTimeAccEnum, - SealevelchangeHViscoElasticEnum, SolidearthSettingsHorizEnum, SolidearthSettingsMaxiterEnum, @@ -398,15 +428,12 @@ StochasticForcingIsStochasticForcingEnum, StochasticForcingIsWaterPressureEnum, + StochasticForcingNoisetermsEnum, StochasticForcingNumFieldsEnum, StochasticForcingRandomflagEnum, - RotationalPolarMoiEnum, + StochasticForcingTimestepEnum, SolidearthSettingsReltolEnum, - SealevelchangeRequestedOutputsEnum, SolidearthSettingsSelfAttractionEnum, SolidearthSettingsRotationEnum, SolidearthSettingsMaxSHCoeffEnum, - SealevelchangeRunCountEnum, - SealevelchangeTransitionsEnum, - SealevelchangeUViscoElasticEnum, SettingsIoGatherEnum, SettingsNumResultsOnNodesEnum, @@ -433,4 +460,5 @@ SmbDpermilEnum, SmbDsnowIdxEnum, + SmbElevationBinsEnum, SmbCldFracEnum, SmbDelta18oEnum, @@ -460,9 +488,12 @@ SmbIsturbulentfluxEnum, SmbKEnum, + SmbLapseRatesEnum, SmbNumBasinsEnum, + SmbNumElevationBinsEnum, SmbNumRequestedOutputsEnum, SmbPfacEnum, SmbPhiEnum, SmbRdlEnum, + SmbRefElevationEnum, SmbRequestedOutputsEnum, SmbRlapsEnum, @@ -534,5 +565,5 @@ TransientIsgroundinglineEnum, TransientIshydrologyEnum, - TransientIsmasstransportEnum, + TransientIsmasstransportEnum, TransientIsoceantransportEnum, TransientIsmovingfrontEnum, @@ -575,8 +606,16 @@ BalancethicknessThickeningRateEnum, BasalCrevasseEnum, + BasalforcingsDeepwaterMeltingRateAutoregressionEnum, + BasalforcingsDeepwaterMeltingRateNoiseEnum, + BasalforcingsDeepwaterMeltingRateValuesAutoregressionEnum, BasalforcingsFloatingiceMeltingRateEnum, BasalforcingsGeothermalfluxEnum, BasalforcingsGroundediceMeltingRateEnum, + BasalforcingsLinearBasinIdEnum, BasalforcingsPerturbationMeltingRateEnum, + BasalforcingsSpatialDeepwaterElevationEnum, + BasalforcingsSpatialDeepwaterMeltingRateEnum, + BasalforcingsSpatialUpperwaterElevationEnum, + BasalforcingsSpatialUpperwaterMeltingRateEnum, BasalforcingsIsmip6BasinIdEnum, BasalforcingsIsmip6TfEnum, @@ -600,6 +639,8 @@ BaseSlopeYEnum, BaselineBasalforcingsFloatingiceMeltingRateEnum, + BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum, BaselineCalvingCalvingrateEnum, BaselineFrictionEffectivePressureEnum, + BaselineSmbMassBalanceEnum, BedEnum, BedGRDEnum, @@ -614,11 +655,10 @@ CalvingCalvingrateEnum, CalvingHabFractionEnum, + CalvingAblationrateEnum, CalvingMeltingrateEnum, CalvingStressThresholdFloatingiceEnum, CalvingStressThresholdGroundediceEnum, CalvinglevermannCoeffEnum, - CalvingratexAverageEnum, CalvingratexEnum, - CalvingrateyAverageEnum, CalvingrateyEnum, CalvingFluxLevelsetEnum, @@ -799,6 +839,10 @@ RheologyBbarAbsGradientEnum, SampleEnum, + SampleOldEnum, + SampleNoiseEnum, SamplingBetaEnum, SamplingKappaEnum, + SamplingPhiEnum, + SamplingTauEnum, SealevelEnum, SealevelGRDEnum, @@ -835,16 +879,4 @@ BslcRateEnum, GmtslcEnum, - SealevelGrotm1Enum, - SealevelGrotm2Enum, - SealevelGrotm3Enum, - SealevelGUrotm1Enum, - SealevelGUrotm2Enum, - SealevelGUrotm3Enum, - SealevelGNrotm1Enum, - SealevelGNrotm2Enum, - SealevelGNrotm3Enum, - SealevelGErotm1Enum, - SealevelGErotm2Enum, - SealevelGErotm3Enum, SealevelRSLBarystaticEnum, SealevelRSLRateEnum, @@ -858,4 +890,8 @@ SealevelchangeGEEnum, SealevelchangeGNEnum, + SealevelchangeGrotEnum, + SealevelchangeGUrotEnum, + SealevelchangeGNrotEnum, + SealevelchangeGErotEnum, SealevelchangeGsubelOceanEnum, SealevelchangeGUsubelOceanEnum, @@ -1036,5 +1072,5 @@ TemperatureSEMICEnum, ThermalforcingAutoregressionNoiseEnum, - ThermalforcingValuesAutoregressionEnum, + ThermalforcingValuesAutoregressionEnum, ThermalSpctemperatureEnum, ThicknessAbsGradientEnum, @@ -1194,4 +1230,5 @@ ArrheniusEnum, AutodiffJacobianEnum, + AutoregressionLinearFloatingMeltRateEnum, Balancethickness2AnalysisEnum, Balancethickness2SolutionEnum, @@ -1217,4 +1254,6 @@ CalvingHabEnum, CalvingLevermannEnum, + CalvingTestEnum, + CalvingParameterizationEnum, CalvingVonmisesEnum, CfdragcoeffabsgradEnum, @@ -1345,5 +1384,5 @@ JEnum, L1L2ApproximationEnum, - MLHOApproximationEnum, + MOLHOApproximationEnum, L2ProjectionBaseAnalysisEnum, L2ProjectionEPLAnalysisEnum, @@ -1357,12 +1396,17 @@ LoadsEnum, LoveAnalysisEnum, - LoveHiEnum, - LoveHrEnum, + LoveHfEnum, + LoveHtEnum, LoveKernelsImagEnum, LoveKernelsRealEnum, - LoveKiEnum, - LoveKrEnum, - LoveLiEnum, - LoveLrEnum, + LoveKfEnum, + LoveKtEnum, + LoveLfEnum, + LoveLtEnum, + LoveTidalHtEnum, + LoveTidalKtEnum, + LoveTidalLtEnum, + LovePMTF1tEnum, + LovePMTF2tEnum, LoveSolutionEnum, MINIEnum, @@ -1476,7 +1520,7 @@ SealevelAbsoluteEnum, SealevelEmotionEnum, - SealevelInertiaTensorXZEnum, - SealevelInertiaTensorYZEnum, - SealevelInertiaTensorZZEnum, + SealevelchangePolarMotionXEnum, + SealevelchangePolarMotionYEnum, + SealevelchangePolarMotionZEnum, SealevelchangePolarMotionEnum, SealevelNmotionEnum, Index: /issm/trunk/src/c/shared/Enum/EnumToStringx.cpp =================================================================== --- /issm/trunk/src/c/shared/Enum/EnumToStringx.cpp (revision 27034) +++ /issm/trunk/src/c/shared/Enum/EnumToStringx.cpp (revision 27035) @@ -66,4 +66,9 @@ case BalancethicknessStabilizationEnum : return "BalancethicknessStabilization"; case BarystaticContributionsEnum : return "BarystaticContributions"; + case BasalforcingsAutoregressionInitialTimeEnum : return "BasalforcingsAutoregressionInitialTime"; + case BasalforcingsAutoregressionTimestepEnum : return "BasalforcingsAutoregressionTimestep"; + case BasalforcingsAutoregressiveOrderEnum : return "BasalforcingsAutoregressiveOrder"; + case BasalforcingsBeta0Enum : return "BasalforcingsBeta0"; + case BasalforcingsBeta1Enum : return "BasalforcingsBeta1"; case BasalforcingsBottomplumedepthEnum : return "BasalforcingsBottomplumedepth"; case BasalforcingsCrustthicknessEnum : return "BasalforcingsCrustthickness"; @@ -79,7 +84,9 @@ case BasalforcingsIsmip6NumBasinsEnum : return "BasalforcingsIsmip6NumBasins"; case BasalforcingsIsmip6TfDepthsEnum : return "BasalforcingsIsmip6TfDepths"; + case BasalforcingsLinearNumBasinsEnum : return "BasalforcingsLinearNumBasins"; case BasalforcingsLowercrustheatEnum : return "BasalforcingsLowercrustheat"; case BasalforcingsMantleconductivityEnum : return "BasalforcingsMantleconductivity"; case BasalforcingsNusseltEnum : return "BasalforcingsNusselt"; + case BasalforcingsPhiEnum : return "BasalforcingsPhi"; case BasalforcingsPicoAverageOverturningEnum : return "BasalforcingsPicoAverageOverturning"; case BasalforcingsPicoAverageSalinityEnum : return "BasalforcingsPicoAverageSalinity"; @@ -107,4 +114,11 @@ case CalvingLawEnum : return "CalvingLaw"; case CalvingMinthicknessEnum : return "CalvingMinthickness"; + case CalvingTestSpeedfactorEnum : return "CalvingTestSpeedfactor"; + case CalvingTestIndependentRateEnum : return "CalvingTestIndependentRate"; + case CalvingUseParamEnum : return "CalvingUseParam"; + case CalvingScaleThetaEnum : return "CalvingScaleTheta"; + case CalvingAmpAlphaEnum : return "CalvingAmpAlpha"; + case CalvingMidpointEnum : return "CalvingMidpoint"; + case CalvingNonlinearLawEnum : return "CalvingNonlinearLaw"; case ConfigurationTypeEnum : return "ConfigurationType"; case ConstantsGEnum : return "ConstantsG"; @@ -164,5 +178,5 @@ case FlowequationIsHOEnum : return "FlowequationIsHO"; case FlowequationIsL1L2Enum : return "FlowequationIsL1L2"; - case FlowequationIsMLHOEnum : return "FlowequationIsMLHO"; + case FlowequationIsMOLHOEnum : return "FlowequationIsMOLHO"; case FlowequationIsSIAEnum : return "FlowequationIsSIA"; case FlowequationIsSSAEnum : return "FlowequationIsSSA"; @@ -191,4 +205,6 @@ case GroundinglineMeltInterpolationEnum : return "GroundinglineMeltInterpolation"; case GroundinglineMigrationEnum : return "GroundinglineMigration"; + case GroundinglineNumRequestedOutputsEnum : return "GroundinglineNumRequestedOutputs"; + case GroundinglineRequestedOutputsEnum : return "GroundinglineRequestedOutputs"; case HydrologyAveragingEnum : return "HydrologyAveraging"; case HydrologyCavitySpacingEnum : return "HydrologyCavitySpacing"; @@ -265,4 +281,5 @@ case LockFileNameEnum : return "LockFileName"; case LoveAllowLayerDeletionEnum : return "LoveAllowLayerDeletion"; + case LoveChandlerWobbleEnum : return "LoveChandlerWobble"; case LoveCoreMantleBoundaryEnum : return "LoveCoreMantleBoundary"; case LoveEarthMassEnum : return "LoveEarthMass"; @@ -285,4 +302,5 @@ case LoveStartingLayerEnum : return "LoveStartingLayer"; case LoveUnderflowTolEnum : return "LoveUnderflowTol"; + case LovePostWidderThresholdEnum : return "LovePostWidderThreshold"; case MassFluxSegmentsEnum : return "MassFluxSegments"; case MassFluxSegmentsPresentEnum : return "MassFluxSegmentsPresent"; @@ -354,10 +372,8 @@ case ModelnameEnum : return "Modelname"; case SamplingAlphaEnum : return "SamplingAlpha"; - case SamplingPhiEnum : return "SamplingPhi"; case SamplingNumRequestedOutputsEnum : return "SamplingNumRequestedOutputs"; case SamplingRequestedOutputsEnum : return "SamplingRequestedOutputs"; case SamplingRobinEnum : return "SamplingRobin"; case SamplingSeedEnum : return "SamplingSeed"; - case SamplingTauEnum : return "SamplingTau"; case SaveResultsEnum : return "SaveResults"; case SolidearthPartitionIceEnum : return "SolidearthPartitionIce"; @@ -371,5 +387,4 @@ case SolidearthSettingsAbstolEnum : return "SolidearthSettingsAbstol"; case SolidearthSettingsCrossSectionShapeEnum : return "SolidearthSettingsCrossSectionShape"; - case RotationalAngularVelocityEnum : return "RotationalAngularVelocity"; case SolidearthSettingsElasticEnum : return "SolidearthSettingsElastic"; case SolidearthSettingsViscousEnum : return "SolidearthSettingsViscous"; @@ -378,5 +393,13 @@ case SealevelchangeViscousTimesEnum : return "SealevelchangeViscousTimes"; case SealevelchangeViscousIndexEnum : return "SealevelchangeViscousIndex"; + case SealevelchangeViscousPolarMotionEnum : return "SealevelchangeViscousPolarMotion"; + case SealevelchangeRunCountEnum : return "SealevelchangeRunCount"; + case SealevelchangeTransitionsEnum : return "SealevelchangeTransitions"; + case SealevelchangeRequestedOutputsEnum : return "SealevelchangeRequestedOutputs"; + case RotationalAngularVelocityEnum : return "RotationalAngularVelocity"; case RotationalEquatorialMoiEnum : return "RotationalEquatorialMoi"; + case RotationalPolarMoiEnum : return "RotationalPolarMoi"; + case LovePolarMotionTransferFunctionColinearEnum : return "LovePolarMotionTransferFunctionColinear"; + case LovePolarMotionTransferFunctionOrthogonalEnum : return "LovePolarMotionTransferFunctionOrthogonal"; case TidalLoveHEnum : return "TidalLoveH"; case TidalLoveKEnum : return "TidalLoveK"; @@ -390,9 +413,16 @@ case SealevelchangeGSelfAttractionEnum : return "SealevelchangeGSelfAttraction"; case SealevelchangeGViscoElasticEnum : return "SealevelchangeGViscoElastic"; + case SealevelchangeUViscoElasticEnum : return "SealevelchangeUViscoElastic"; + case SealevelchangeHViscoElasticEnum : return "SealevelchangeHViscoElastic"; + case SealevelchangePolarMotionTransferFunctionColinearEnum : return "SealevelchangePolarMotionTransferFunctionColinear"; + case SealevelchangePolarMotionTransferFunctionOrthogonalEnum : return "SealevelchangePolarMotionTransferFunctionOrthogonal"; + case SealevelchangePolarMotionTransferFunctionZEnum : return "SealevelchangePolarMotionTransferFunctionZ"; + case SealevelchangeTidalK2Enum : return "SealevelchangeTidalK2"; + case SealevelchangeTidalH2Enum : return "SealevelchangeTidalH2"; + case SealevelchangeTidalL2Enum : return "SealevelchangeTidalL2"; case SolidearthSettingsSealevelLoadingEnum : return "SolidearthSettingsSealevelLoading"; case SolidearthSettingsGRDEnum : return "SolidearthSettingsGRD"; case SolidearthSettingsRunFrequencyEnum : return "SolidearthSettingsRunFrequency"; case SolidearthSettingsTimeAccEnum : return "SolidearthSettingsTimeAcc"; - case SealevelchangeHViscoElasticEnum : return "SealevelchangeHViscoElastic"; case SolidearthSettingsHorizEnum : return "SolidearthSettingsHoriz"; case SolidearthSettingsMaxiterEnum : return "SolidearthSettingsMaxiter"; @@ -406,15 +436,12 @@ case StochasticForcingIsStochasticForcingEnum : return "StochasticForcingIsStochasticForcing"; case StochasticForcingIsWaterPressureEnum : return "StochasticForcingIsWaterPressure"; + case StochasticForcingNoisetermsEnum : return "StochasticForcingNoiseterms"; case StochasticForcingNumFieldsEnum : return "StochasticForcingNumFields"; case StochasticForcingRandomflagEnum : return "StochasticForcingRandomflag"; - case RotationalPolarMoiEnum : return "RotationalPolarMoi"; + case StochasticForcingTimestepEnum : return "StochasticForcingTimestep"; case SolidearthSettingsReltolEnum : return "SolidearthSettingsReltol"; - case SealevelchangeRequestedOutputsEnum : return "SealevelchangeRequestedOutputs"; case SolidearthSettingsSelfAttractionEnum : return "SolidearthSettingsSelfAttraction"; case SolidearthSettingsRotationEnum : return "SolidearthSettingsRotation"; case SolidearthSettingsMaxSHCoeffEnum : return "SolidearthSettingsMaxSHCoeff"; - case SealevelchangeRunCountEnum : return "SealevelchangeRunCount"; - case SealevelchangeTransitionsEnum : return "SealevelchangeTransitions"; - case SealevelchangeUViscoElasticEnum : return "SealevelchangeUViscoElastic"; case SettingsIoGatherEnum : return "SettingsIoGather"; case SettingsNumResultsOnNodesEnum : return "SettingsNumResultsOnNodes"; @@ -441,4 +468,5 @@ case SmbDpermilEnum : return "SmbDpermil"; case SmbDsnowIdxEnum : return "SmbDsnowIdx"; + case SmbElevationBinsEnum : return "SmbElevationBins"; case SmbCldFracEnum : return "SmbCldFrac"; case SmbDelta18oEnum : return "SmbDelta18o"; @@ -468,9 +496,12 @@ case SmbIsturbulentfluxEnum : return "SmbIsturbulentflux"; case SmbKEnum : return "SmbK"; + case SmbLapseRatesEnum : return "SmbLapseRates"; case SmbNumBasinsEnum : return "SmbNumBasins"; + case SmbNumElevationBinsEnum : return "SmbNumElevationBins"; case SmbNumRequestedOutputsEnum : return "SmbNumRequestedOutputs"; case SmbPfacEnum : return "SmbPfac"; case SmbPhiEnum : return "SmbPhi"; case SmbRdlEnum : return "SmbRdl"; + case SmbRefElevationEnum : return "SmbRefElevation"; case SmbRequestedOutputsEnum : return "SmbRequestedOutputs"; case SmbRlapsEnum : return "SmbRlaps"; @@ -581,8 +612,16 @@ case BalancethicknessThickeningRateEnum : return "BalancethicknessThickeningRate"; case BasalCrevasseEnum : return "BasalCrevasse"; + case BasalforcingsDeepwaterMeltingRateAutoregressionEnum : return "BasalforcingsDeepwaterMeltingRateAutoregression"; + case BasalforcingsDeepwaterMeltingRateNoiseEnum : return "BasalforcingsDeepwaterMeltingRateNoise"; + case BasalforcingsDeepwaterMeltingRateValuesAutoregressionEnum : return "BasalforcingsDeepwaterMeltingRateValuesAutoregression"; case BasalforcingsFloatingiceMeltingRateEnum : return "BasalforcingsFloatingiceMeltingRate"; case BasalforcingsGeothermalfluxEnum : return "BasalforcingsGeothermalflux"; case BasalforcingsGroundediceMeltingRateEnum : return "BasalforcingsGroundediceMeltingRate"; + case BasalforcingsLinearBasinIdEnum : return "BasalforcingsLinearBasinId"; case BasalforcingsPerturbationMeltingRateEnum : return "BasalforcingsPerturbationMeltingRate"; + case BasalforcingsSpatialDeepwaterElevationEnum : return "BasalforcingsSpatialDeepwaterElevation"; + case BasalforcingsSpatialDeepwaterMeltingRateEnum : return "BasalforcingsSpatialDeepwaterMeltingRate"; + case BasalforcingsSpatialUpperwaterElevationEnum : return "BasalforcingsSpatialUpperwaterElevation"; + case BasalforcingsSpatialUpperwaterMeltingRateEnum : return "BasalforcingsSpatialUpperwaterMeltingRate"; case BasalforcingsIsmip6BasinIdEnum : return "BasalforcingsIsmip6BasinId"; case BasalforcingsIsmip6TfEnum : return "BasalforcingsIsmip6Tf"; @@ -606,6 +645,8 @@ case BaseSlopeYEnum : return "BaseSlopeY"; case BaselineBasalforcingsFloatingiceMeltingRateEnum : return "BaselineBasalforcingsFloatingiceMeltingRate"; + case BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum : return "BaselineBasalforcingsSpatialDeepwaterMeltingRate"; case BaselineCalvingCalvingrateEnum : return "BaselineCalvingCalvingrate"; case BaselineFrictionEffectivePressureEnum : return "BaselineFrictionEffectivePressure"; + case BaselineSmbMassBalanceEnum : return "BaselineSmbMassBalance"; case BedEnum : return "Bed"; case BedGRDEnum : return "BedGRD"; @@ -620,11 +661,10 @@ case CalvingCalvingrateEnum : return "CalvingCalvingrate"; case CalvingHabFractionEnum : return "CalvingHabFraction"; + case CalvingAblationrateEnum : return "CalvingAblationrate"; case CalvingMeltingrateEnum : return "CalvingMeltingrate"; case CalvingStressThresholdFloatingiceEnum : return "CalvingStressThresholdFloatingice"; case CalvingStressThresholdGroundediceEnum : return "CalvingStressThresholdGroundedice"; case CalvinglevermannCoeffEnum : return "CalvinglevermannCoeff"; - case CalvingratexAverageEnum : return "CalvingratexAverage"; case CalvingratexEnum : return "Calvingratex"; - case CalvingrateyAverageEnum : return "CalvingrateyAverage"; case CalvingrateyEnum : return "Calvingratey"; case CalvingFluxLevelsetEnum : return "CalvingFluxLevelset"; @@ -805,6 +845,10 @@ case RheologyBbarAbsGradientEnum : return "RheologyBbarAbsGradient"; case SampleEnum : return "Sample"; + case SampleOldEnum : return "SampleOld"; + case SampleNoiseEnum : return "SampleNoise"; case SamplingBetaEnum : return "SamplingBeta"; case SamplingKappaEnum : return "SamplingKappa"; + case SamplingPhiEnum : return "SamplingPhi"; + case SamplingTauEnum : return "SamplingTau"; case SealevelEnum : return "Sealevel"; case SealevelGRDEnum : return "SealevelGRD"; @@ -841,16 +885,4 @@ case BslcRateEnum : return "BslcRate"; case GmtslcEnum : return "Gmtslc"; - case SealevelGrotm1Enum : return "SealevelGrotm1"; - case SealevelGrotm2Enum : return "SealevelGrotm2"; - case SealevelGrotm3Enum : return "SealevelGrotm3"; - case SealevelGUrotm1Enum : return "SealevelGUrotm1"; - case SealevelGUrotm2Enum : return "SealevelGUrotm2"; - case SealevelGUrotm3Enum : return "SealevelGUrotm3"; - case SealevelGNrotm1Enum : return "SealevelGNrotm1"; - case SealevelGNrotm2Enum : return "SealevelGNrotm2"; - case SealevelGNrotm3Enum : return "SealevelGNrotm3"; - case SealevelGErotm1Enum : return "SealevelGErotm1"; - case SealevelGErotm2Enum : return "SealevelGErotm2"; - case SealevelGErotm3Enum : return "SealevelGErotm3"; case SealevelRSLBarystaticEnum : return "SealevelRSLBarystatic"; case SealevelRSLRateEnum : return "SealevelRSLRate"; @@ -864,4 +896,8 @@ case SealevelchangeGEEnum : return "SealevelchangeGE"; case SealevelchangeGNEnum : return "SealevelchangeGN"; + case SealevelchangeGrotEnum : return "SealevelchangeGrot"; + case SealevelchangeGUrotEnum : return "SealevelchangeGUrot"; + case SealevelchangeGNrotEnum : return "SealevelchangeGNrot"; + case SealevelchangeGErotEnum : return "SealevelchangeGErot"; case SealevelchangeGsubelOceanEnum : return "SealevelchangeGsubelOcean"; case SealevelchangeGUsubelOceanEnum : return "SealevelchangeGUsubelOcean"; @@ -1197,4 +1233,5 @@ case ArrheniusEnum : return "Arrhenius"; case AutodiffJacobianEnum : return "AutodiffJacobian"; + case AutoregressionLinearFloatingMeltRateEnum : return "AutoregressionLinearFloatingMeltRate"; case Balancethickness2AnalysisEnum : return "Balancethickness2Analysis"; case Balancethickness2SolutionEnum : return "Balancethickness2Solution"; @@ -1220,4 +1257,6 @@ case CalvingHabEnum : return "CalvingHab"; case CalvingLevermannEnum : return "CalvingLevermann"; + case CalvingTestEnum : return "CalvingTest"; + case CalvingParameterizationEnum : return "CalvingParameterization"; case CalvingVonmisesEnum : return "CalvingVonmises"; case CfdragcoeffabsgradEnum : return "Cfdragcoeffabsgrad"; @@ -1348,5 +1387,5 @@ case JEnum : return "J"; case L1L2ApproximationEnum : return "L1L2Approximation"; - case MLHOApproximationEnum : return "MLHOApproximation"; + case MOLHOApproximationEnum : return "MOLHOApproximation"; case L2ProjectionBaseAnalysisEnum : return "L2ProjectionBaseAnalysis"; case L2ProjectionEPLAnalysisEnum : return "L2ProjectionEPLAnalysis"; @@ -1360,12 +1399,17 @@ case LoadsEnum : return "Loads"; case LoveAnalysisEnum : return "LoveAnalysis"; - case LoveHiEnum : return "LoveHi"; - case LoveHrEnum : return "LoveHr"; + case LoveHfEnum : return "LoveHf"; + case LoveHtEnum : return "LoveHt"; case LoveKernelsImagEnum : return "LoveKernelsImag"; case LoveKernelsRealEnum : return "LoveKernelsReal"; - case LoveKiEnum : return "LoveKi"; - case LoveKrEnum : return "LoveKr"; - case LoveLiEnum : return "LoveLi"; - case LoveLrEnum : return "LoveLr"; + case LoveKfEnum : return "LoveKf"; + case LoveKtEnum : return "LoveKt"; + case LoveLfEnum : return "LoveLf"; + case LoveLtEnum : return "LoveLt"; + case LoveTidalHtEnum : return "LoveTidalHt"; + case LoveTidalKtEnum : return "LoveTidalKt"; + case LoveTidalLtEnum : return "LoveTidalLt"; + case LovePMTF1tEnum : return "LovePMTF1t"; + case LovePMTF2tEnum : return "LovePMTF2t"; case LoveSolutionEnum : return "LoveSolution"; case MINIEnum : return "MINI"; @@ -1479,7 +1523,7 @@ case SealevelAbsoluteEnum : return "SealevelAbsolute"; case SealevelEmotionEnum : return "SealevelEmotion"; - case SealevelInertiaTensorXZEnum : return "SealevelInertiaTensorXZ"; - case SealevelInertiaTensorYZEnum : return "SealevelInertiaTensorYZ"; - case SealevelInertiaTensorZZEnum : return "SealevelInertiaTensorZZ"; + case SealevelchangePolarMotionXEnum : return "SealevelchangePolarMotionX"; + case SealevelchangePolarMotionYEnum : return "SealevelchangePolarMotionY"; + case SealevelchangePolarMotionZEnum : return "SealevelchangePolarMotionZ"; case SealevelchangePolarMotionEnum : return "SealevelchangePolarMotion"; case SealevelNmotionEnum : return "SealevelNmotion"; Index: /issm/trunk/src/c/shared/Enum/Enumjl.vim =================================================================== --- /issm/trunk/src/c/shared/Enum/Enumjl.vim (revision 27034) +++ /issm/trunk/src/c/shared/Enum/Enumjl.vim (revision 27035) @@ -57,4 +57,9 @@ syn keyword juliaConstC BalancethicknessStabilizationEnum syn keyword juliaConstC BarystaticContributionsEnum +syn keyword juliaConstC BasalforcingsAutoregressionInitialTimeEnum +syn keyword juliaConstC BasalforcingsAutoregressionTimestepEnum +syn keyword juliaConstC BasalforcingsAutoregressiveOrderEnum +syn keyword juliaConstC BasalforcingsBeta0Enum +syn keyword juliaConstC BasalforcingsBeta1Enum syn keyword juliaConstC BasalforcingsBottomplumedepthEnum syn keyword juliaConstC BasalforcingsCrustthicknessEnum @@ -70,7 +75,9 @@ syn keyword juliaConstC BasalforcingsIsmip6NumBasinsEnum syn keyword juliaConstC BasalforcingsIsmip6TfDepthsEnum +syn keyword juliaConstC BasalforcingsLinearNumBasinsEnum syn keyword juliaConstC BasalforcingsLowercrustheatEnum syn keyword juliaConstC BasalforcingsMantleconductivityEnum syn keyword juliaConstC BasalforcingsNusseltEnum +syn keyword juliaConstC BasalforcingsPhiEnum syn keyword juliaConstC BasalforcingsPicoAverageOverturningEnum syn keyword juliaConstC BasalforcingsPicoAverageSalinityEnum @@ -98,4 +105,11 @@ syn keyword juliaConstC CalvingLawEnum syn keyword juliaConstC CalvingMinthicknessEnum +syn keyword juliaConstC CalvingTestSpeedfactorEnum +syn keyword juliaConstC CalvingTestIndependentRateEnum +syn keyword juliaConstC CalvingUseParamEnum +syn keyword juliaConstC CalvingScaleThetaEnum +syn keyword juliaConstC CalvingAmpAlphaEnum +syn keyword juliaConstC CalvingMidpointEnum +syn keyword juliaConstC CalvingNonlinearLawEnum syn keyword juliaConstC ConfigurationTypeEnum syn keyword juliaConstC ConstantsGEnum @@ -155,5 +169,5 @@ syn keyword juliaConstC FlowequationIsHOEnum syn keyword juliaConstC FlowequationIsL1L2Enum -syn keyword juliaConstC FlowequationIsMLHOEnum +syn keyword juliaConstC FlowequationIsMOLHOEnum syn keyword juliaConstC FlowequationIsSIAEnum syn keyword juliaConstC FlowequationIsSSAEnum @@ -182,4 +196,6 @@ syn keyword juliaConstC GroundinglineMeltInterpolationEnum syn keyword juliaConstC GroundinglineMigrationEnum +syn keyword juliaConstC GroundinglineNumRequestedOutputsEnum +syn keyword juliaConstC GroundinglineRequestedOutputsEnum syn keyword juliaConstC HydrologyAveragingEnum syn keyword juliaConstC HydrologyCavitySpacingEnum @@ -256,4 +272,5 @@ syn keyword juliaConstC LockFileNameEnum syn keyword juliaConstC LoveAllowLayerDeletionEnum +syn keyword juliaConstC LoveChandlerWobbleEnum syn keyword juliaConstC LoveCoreMantleBoundaryEnum syn keyword juliaConstC LoveEarthMassEnum @@ -276,4 +293,5 @@ syn keyword juliaConstC LoveStartingLayerEnum syn keyword juliaConstC LoveUnderflowTolEnum +syn keyword juliaConstC LovePostWidderThresholdEnum syn keyword juliaConstC MassFluxSegmentsEnum syn keyword juliaConstC MassFluxSegmentsPresentEnum @@ -345,10 +363,8 @@ syn keyword juliaConstC ModelnameEnum syn keyword juliaConstC SamplingAlphaEnum -syn keyword juliaConstC SamplingPhiEnum syn keyword juliaConstC SamplingNumRequestedOutputsEnum syn keyword juliaConstC SamplingRequestedOutputsEnum syn keyword juliaConstC SamplingRobinEnum syn keyword juliaConstC SamplingSeedEnum -syn keyword juliaConstC SamplingTauEnum syn keyword juliaConstC SaveResultsEnum syn keyword juliaConstC SolidearthPartitionIceEnum @@ -362,5 +378,4 @@ syn keyword juliaConstC SolidearthSettingsAbstolEnum syn keyword juliaConstC SolidearthSettingsCrossSectionShapeEnum -syn keyword juliaConstC RotationalAngularVelocityEnum syn keyword juliaConstC SolidearthSettingsElasticEnum syn keyword juliaConstC SolidearthSettingsViscousEnum @@ -369,5 +384,13 @@ syn keyword juliaConstC SealevelchangeViscousTimesEnum syn keyword juliaConstC SealevelchangeViscousIndexEnum +syn keyword juliaConstC SealevelchangeViscousPolarMotionEnum +syn keyword juliaConstC SealevelchangeRunCountEnum +syn keyword juliaConstC SealevelchangeTransitionsEnum +syn keyword juliaConstC SealevelchangeRequestedOutputsEnum +syn keyword juliaConstC RotationalAngularVelocityEnum syn keyword juliaConstC RotationalEquatorialMoiEnum +syn keyword juliaConstC RotationalPolarMoiEnum +syn keyword juliaConstC LovePolarMotionTransferFunctionColinearEnum +syn keyword juliaConstC LovePolarMotionTransferFunctionOrthogonalEnum syn keyword juliaConstC TidalLoveHEnum syn keyword juliaConstC TidalLoveKEnum @@ -381,9 +404,16 @@ syn keyword juliaConstC SealevelchangeGSelfAttractionEnum syn keyword juliaConstC SealevelchangeGViscoElasticEnum +syn keyword juliaConstC SealevelchangeUViscoElasticEnum +syn keyword juliaConstC SealevelchangeHViscoElasticEnum +syn keyword juliaConstC SealevelchangePolarMotionTransferFunctionColinearEnum +syn keyword juliaConstC SealevelchangePolarMotionTransferFunctionOrthogonalEnum +syn keyword juliaConstC SealevelchangePolarMotionTransferFunctionZEnum +syn keyword juliaConstC SealevelchangeTidalK2Enum +syn keyword juliaConstC SealevelchangeTidalH2Enum +syn keyword juliaConstC SealevelchangeTidalL2Enum syn keyword juliaConstC SolidearthSettingsSealevelLoadingEnum syn keyword juliaConstC SolidearthSettingsGRDEnum syn keyword juliaConstC SolidearthSettingsRunFrequencyEnum syn keyword juliaConstC SolidearthSettingsTimeAccEnum -syn keyword juliaConstC SealevelchangeHViscoElasticEnum syn keyword juliaConstC SolidearthSettingsHorizEnum syn keyword juliaConstC SolidearthSettingsMaxiterEnum @@ -397,15 +427,12 @@ syn keyword juliaConstC StochasticForcingIsStochasticForcingEnum syn keyword juliaConstC StochasticForcingIsWaterPressureEnum +syn keyword juliaConstC StochasticForcingNoisetermsEnum syn keyword juliaConstC StochasticForcingNumFieldsEnum syn keyword juliaConstC StochasticForcingRandomflagEnum -syn keyword juliaConstC RotationalPolarMoiEnum +syn keyword juliaConstC StochasticForcingTimestepEnum syn keyword juliaConstC SolidearthSettingsReltolEnum -syn keyword juliaConstC SealevelchangeRequestedOutputsEnum syn keyword juliaConstC SolidearthSettingsSelfAttractionEnum syn keyword juliaConstC SolidearthSettingsRotationEnum syn keyword juliaConstC SolidearthSettingsMaxSHCoeffEnum -syn keyword juliaConstC SealevelchangeRunCountEnum -syn keyword juliaConstC SealevelchangeTransitionsEnum -syn keyword juliaConstC SealevelchangeUViscoElasticEnum syn keyword juliaConstC SettingsIoGatherEnum syn keyword juliaConstC SettingsNumResultsOnNodesEnum @@ -432,4 +459,5 @@ syn keyword juliaConstC SmbDpermilEnum syn keyword juliaConstC SmbDsnowIdxEnum +syn keyword juliaConstC SmbElevationBinsEnum syn keyword juliaConstC SmbCldFracEnum syn keyword juliaConstC SmbDelta18oEnum @@ -459,9 +487,12 @@ syn keyword juliaConstC SmbIsturbulentfluxEnum syn keyword juliaConstC SmbKEnum +syn keyword juliaConstC SmbLapseRatesEnum syn keyword juliaConstC SmbNumBasinsEnum +syn keyword juliaConstC SmbNumElevationBinsEnum syn keyword juliaConstC SmbNumRequestedOutputsEnum syn keyword juliaConstC SmbPfacEnum syn keyword juliaConstC SmbPhiEnum syn keyword juliaConstC SmbRdlEnum +syn keyword juliaConstC SmbRefElevationEnum syn keyword juliaConstC SmbRequestedOutputsEnum syn keyword juliaConstC SmbRlapsEnum @@ -572,8 +603,16 @@ syn keyword juliaConstC BalancethicknessThickeningRateEnum syn keyword juliaConstC BasalCrevasseEnum +syn keyword juliaConstC BasalforcingsDeepwaterMeltingRateAutoregressionEnum +syn keyword juliaConstC BasalforcingsDeepwaterMeltingRateNoiseEnum +syn keyword juliaConstC BasalforcingsDeepwaterMeltingRateValuesAutoregressionEnum syn keyword juliaConstC BasalforcingsFloatingiceMeltingRateEnum syn keyword juliaConstC BasalforcingsGeothermalfluxEnum syn keyword juliaConstC BasalforcingsGroundediceMeltingRateEnum +syn keyword juliaConstC BasalforcingsLinearBasinIdEnum syn keyword juliaConstC BasalforcingsPerturbationMeltingRateEnum +syn keyword juliaConstC BasalforcingsSpatialDeepwaterElevationEnum +syn keyword juliaConstC BasalforcingsSpatialDeepwaterMeltingRateEnum +syn keyword juliaConstC BasalforcingsSpatialUpperwaterElevationEnum +syn keyword juliaConstC BasalforcingsSpatialUpperwaterMeltingRateEnum syn keyword juliaConstC BasalforcingsIsmip6BasinIdEnum syn keyword juliaConstC BasalforcingsIsmip6TfEnum @@ -597,6 +636,8 @@ syn keyword juliaConstC BaseSlopeYEnum syn keyword juliaConstC BaselineBasalforcingsFloatingiceMeltingRateEnum +syn keyword juliaConstC BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum syn keyword juliaConstC BaselineCalvingCalvingrateEnum syn keyword juliaConstC BaselineFrictionEffectivePressureEnum +syn keyword juliaConstC BaselineSmbMassBalanceEnum syn keyword juliaConstC BedEnum syn keyword juliaConstC BedGRDEnum @@ -611,11 +652,10 @@ syn keyword juliaConstC CalvingCalvingrateEnum syn keyword juliaConstC CalvingHabFractionEnum +syn keyword juliaConstC CalvingAblationrateEnum syn keyword juliaConstC CalvingMeltingrateEnum syn keyword juliaConstC CalvingStressThresholdFloatingiceEnum syn keyword juliaConstC CalvingStressThresholdGroundediceEnum syn keyword juliaConstC CalvinglevermannCoeffEnum -syn keyword juliaConstC CalvingratexAverageEnum syn keyword juliaConstC CalvingratexEnum -syn keyword juliaConstC CalvingrateyAverageEnum syn keyword juliaConstC CalvingrateyEnum syn keyword juliaConstC CalvingFluxLevelsetEnum @@ -796,6 +836,10 @@ syn keyword juliaConstC RheologyBbarAbsGradientEnum syn keyword juliaConstC SampleEnum +syn keyword juliaConstC SampleOldEnum +syn keyword juliaConstC SampleNoiseEnum syn keyword juliaConstC SamplingBetaEnum syn keyword juliaConstC SamplingKappaEnum +syn keyword juliaConstC SamplingPhiEnum +syn keyword juliaConstC SamplingTauEnum syn keyword juliaConstC SealevelEnum syn keyword juliaConstC SealevelGRDEnum @@ -832,16 +876,4 @@ syn keyword juliaConstC BslcRateEnum syn keyword juliaConstC GmtslcEnum -syn keyword juliaConstC SealevelGrotm1Enum -syn keyword juliaConstC SealevelGrotm2Enum -syn keyword juliaConstC SealevelGrotm3Enum -syn keyword juliaConstC SealevelGUrotm1Enum -syn keyword juliaConstC SealevelGUrotm2Enum -syn keyword juliaConstC SealevelGUrotm3Enum -syn keyword juliaConstC SealevelGNrotm1Enum -syn keyword juliaConstC SealevelGNrotm2Enum -syn keyword juliaConstC SealevelGNrotm3Enum -syn keyword juliaConstC SealevelGErotm1Enum -syn keyword juliaConstC SealevelGErotm2Enum -syn keyword juliaConstC SealevelGErotm3Enum syn keyword juliaConstC SealevelRSLBarystaticEnum syn keyword juliaConstC SealevelRSLRateEnum @@ -855,4 +887,8 @@ syn keyword juliaConstC SealevelchangeGEEnum syn keyword juliaConstC SealevelchangeGNEnum +syn keyword juliaConstC SealevelchangeGrotEnum +syn keyword juliaConstC SealevelchangeGUrotEnum +syn keyword juliaConstC SealevelchangeGNrotEnum +syn keyword juliaConstC SealevelchangeGErotEnum syn keyword juliaConstC SealevelchangeGsubelOceanEnum syn keyword juliaConstC SealevelchangeGUsubelOceanEnum @@ -1188,4 +1224,5 @@ syn keyword juliaConstC ArrheniusEnum syn keyword juliaConstC AutodiffJacobianEnum +syn keyword juliaConstC AutoregressionLinearFloatingMeltRateEnum syn keyword juliaConstC Balancethickness2AnalysisEnum syn keyword juliaConstC Balancethickness2SolutionEnum @@ -1211,4 +1248,6 @@ syn keyword juliaConstC CalvingHabEnum syn keyword juliaConstC CalvingLevermannEnum +syn keyword juliaConstC CalvingTestEnum +syn keyword juliaConstC CalvingParameterizationEnum syn keyword juliaConstC CalvingVonmisesEnum syn keyword juliaConstC CfdragcoeffabsgradEnum @@ -1339,5 +1378,5 @@ syn keyword juliaConstC JEnum syn keyword juliaConstC L1L2ApproximationEnum -syn keyword juliaConstC MLHOApproximationEnum +syn keyword juliaConstC MOLHOApproximationEnum syn keyword juliaConstC L2ProjectionBaseAnalysisEnum syn keyword juliaConstC L2ProjectionEPLAnalysisEnum @@ -1351,12 +1390,17 @@ syn keyword juliaConstC LoadsEnum syn keyword juliaConstC LoveAnalysisEnum -syn keyword juliaConstC LoveHiEnum -syn keyword juliaConstC LoveHrEnum +syn keyword juliaConstC LoveHfEnum +syn keyword juliaConstC LoveHtEnum syn keyword juliaConstC LoveKernelsImagEnum syn keyword juliaConstC LoveKernelsRealEnum -syn keyword juliaConstC LoveKiEnum -syn keyword juliaConstC LoveKrEnum -syn keyword juliaConstC LoveLiEnum -syn keyword juliaConstC LoveLrEnum +syn keyword juliaConstC LoveKfEnum +syn keyword juliaConstC LoveKtEnum +syn keyword juliaConstC LoveLfEnum +syn keyword juliaConstC LoveLtEnum +syn keyword juliaConstC LoveTidalHtEnum +syn keyword juliaConstC LoveTidalKtEnum +syn keyword juliaConstC LoveTidalLtEnum +syn keyword juliaConstC LovePMTF1tEnum +syn keyword juliaConstC LovePMTF2tEnum syn keyword juliaConstC LoveSolutionEnum syn keyword juliaConstC MINIEnum @@ -1470,7 +1514,7 @@ syn keyword juliaConstC SealevelAbsoluteEnum syn keyword juliaConstC SealevelEmotionEnum -syn keyword juliaConstC SealevelInertiaTensorXZEnum -syn keyword juliaConstC SealevelInertiaTensorYZEnum -syn keyword juliaConstC SealevelInertiaTensorZZEnum +syn keyword juliaConstC SealevelchangePolarMotionXEnum +syn keyword juliaConstC SealevelchangePolarMotionYEnum +syn keyword juliaConstC SealevelchangePolarMotionZEnum syn keyword juliaConstC SealevelchangePolarMotionEnum syn keyword juliaConstC SealevelNmotionEnum Index: /issm/trunk/src/c/shared/Enum/StringToEnumx.cpp =================================================================== --- /issm/trunk/src/c/shared/Enum/StringToEnumx.cpp (revision 27034) +++ /issm/trunk/src/c/shared/Enum/StringToEnumx.cpp (revision 27035) @@ -66,4 +66,9 @@ else if (strcmp(name,"BalancethicknessStabilization")==0) return BalancethicknessStabilizationEnum; else if (strcmp(name,"BarystaticContributions")==0) return BarystaticContributionsEnum; + else if (strcmp(name,"BasalforcingsAutoregressionInitialTime")==0) return BasalforcingsAutoregressionInitialTimeEnum; + else if (strcmp(name,"BasalforcingsAutoregressionTimestep")==0) return BasalforcingsAutoregressionTimestepEnum; + else if (strcmp(name,"BasalforcingsAutoregressiveOrder")==0) return BasalforcingsAutoregressiveOrderEnum; + else if (strcmp(name,"BasalforcingsBeta0")==0) return BasalforcingsBeta0Enum; + else if (strcmp(name,"BasalforcingsBeta1")==0) return BasalforcingsBeta1Enum; else if (strcmp(name,"BasalforcingsBottomplumedepth")==0) return BasalforcingsBottomplumedepthEnum; else if (strcmp(name,"BasalforcingsCrustthickness")==0) return BasalforcingsCrustthicknessEnum; @@ -79,7 +84,9 @@ else if (strcmp(name,"BasalforcingsIsmip6NumBasins")==0) return BasalforcingsIsmip6NumBasinsEnum; else if (strcmp(name,"BasalforcingsIsmip6TfDepths")==0) return BasalforcingsIsmip6TfDepthsEnum; + else if (strcmp(name,"BasalforcingsLinearNumBasins")==0) return BasalforcingsLinearNumBasinsEnum; else if (strcmp(name,"BasalforcingsLowercrustheat")==0) return BasalforcingsLowercrustheatEnum; else if (strcmp(name,"BasalforcingsMantleconductivity")==0) return BasalforcingsMantleconductivityEnum; else if (strcmp(name,"BasalforcingsNusselt")==0) return BasalforcingsNusseltEnum; + else if (strcmp(name,"BasalforcingsPhi")==0) return BasalforcingsPhiEnum; else if (strcmp(name,"BasalforcingsPicoAverageOverturning")==0) return BasalforcingsPicoAverageOverturningEnum; else if (strcmp(name,"BasalforcingsPicoAverageSalinity")==0) return BasalforcingsPicoAverageSalinityEnum; @@ -107,4 +114,11 @@ else if (strcmp(name,"CalvingLaw")==0) return CalvingLawEnum; else if (strcmp(name,"CalvingMinthickness")==0) return CalvingMinthicknessEnum; + else if (strcmp(name,"CalvingTestSpeedfactor")==0) return CalvingTestSpeedfactorEnum; + else if (strcmp(name,"CalvingTestIndependentRate")==0) return CalvingTestIndependentRateEnum; + else if (strcmp(name,"CalvingUseParam")==0) return CalvingUseParamEnum; + else if (strcmp(name,"CalvingScaleTheta")==0) return CalvingScaleThetaEnum; + else if (strcmp(name,"CalvingAmpAlpha")==0) return CalvingAmpAlphaEnum; + else if (strcmp(name,"CalvingMidpoint")==0) return CalvingMidpointEnum; + else if (strcmp(name,"CalvingNonlinearLaw")==0) return CalvingNonlinearLawEnum; else if (strcmp(name,"ConfigurationType")==0) return ConfigurationTypeEnum; else if (strcmp(name,"ConstantsG")==0) return ConstantsGEnum; @@ -123,5 +137,8 @@ else if (strcmp(name,"CumBslcOceanPartition")==0) return CumBslcOceanPartitionEnum; else if (strcmp(name,"CumGmtslc")==0) return CumGmtslcEnum; - else if (strcmp(name,"CumGmslc")==0) return CumGmslcEnum; + else stage=2; + } + if(stage==2){ + if (strcmp(name,"CumGmslc")==0) return CumGmslcEnum; else if (strcmp(name,"DamageC1")==0) return DamageC1Enum; else if (strcmp(name,"DamageC2")==0) return DamageC2Enum; @@ -137,8 +154,5 @@ else if (strcmp(name,"DamageMaxDamage")==0) return DamageMaxDamageEnum; else if (strcmp(name,"DamageStabilization")==0) return DamageStabilizationEnum; - else stage=2; - } - if(stage==2){ - if (strcmp(name,"DamageStressThreshold")==0) return DamageStressThresholdEnum; + else if (strcmp(name,"DamageStressThreshold")==0) return DamageStressThresholdEnum; else if (strcmp(name,"DamageStressUBound")==0) return DamageStressUBoundEnum; else if (strcmp(name,"DebugProfiling")==0) return DebugProfilingEnum; @@ -167,5 +181,5 @@ else if (strcmp(name,"FlowequationIsHO")==0) return FlowequationIsHOEnum; else if (strcmp(name,"FlowequationIsL1L2")==0) return FlowequationIsL1L2Enum; - else if (strcmp(name,"FlowequationIsMLHO")==0) return FlowequationIsMLHOEnum; + else if (strcmp(name,"FlowequationIsMOLHO")==0) return FlowequationIsMOLHOEnum; else if (strcmp(name,"FlowequationIsSIA")==0) return FlowequationIsSIAEnum; else if (strcmp(name,"FlowequationIsSSA")==0) return FlowequationIsSSAEnum; @@ -194,4 +208,6 @@ else if (strcmp(name,"GroundinglineMeltInterpolation")==0) return GroundinglineMeltInterpolationEnum; else if (strcmp(name,"GroundinglineMigration")==0) return GroundinglineMigrationEnum; + else if (strcmp(name,"GroundinglineNumRequestedOutputs")==0) return GroundinglineNumRequestedOutputsEnum; + else if (strcmp(name,"GroundinglineRequestedOutputs")==0) return GroundinglineRequestedOutputsEnum; else if (strcmp(name,"HydrologyAveraging")==0) return HydrologyAveragingEnum; else if (strcmp(name,"HydrologyCavitySpacing")==0) return HydrologyCavitySpacingEnum; @@ -244,5 +260,8 @@ else if (strcmp(name,"InversionAlgorithm")==0) return InversionAlgorithmEnum; else if (strcmp(name,"InversionControlParameters")==0) return InversionControlParametersEnum; - else if (strcmp(name,"InversionControlScalingFactors")==0) return InversionControlScalingFactorsEnum; + else stage=3; + } + if(stage==3){ + if (strcmp(name,"InversionControlScalingFactors")==0) return InversionControlScalingFactorsEnum; else if (strcmp(name,"InversionCostFunctions")==0) return InversionCostFunctionsEnum; else if (strcmp(name,"InversionDxmin")==0) return InversionDxminEnum; @@ -260,8 +279,5 @@ else if (strcmp(name,"InversionNumCostFunctions")==0) return InversionNumCostFunctionsEnum; else if (strcmp(name,"InversionStepThreshold")==0) return InversionStepThresholdEnum; - else stage=3; - } - if(stage==3){ - if (strcmp(name,"InversionType")==0) return InversionTypeEnum; + else if (strcmp(name,"InversionType")==0) return InversionTypeEnum; else if (strcmp(name,"Ivins")==0) return IvinsEnum; else if (strcmp(name,"IsSlcCoupling")==0) return IsSlcCouplingEnum; @@ -271,4 +287,5 @@ else if (strcmp(name,"LockFileName")==0) return LockFileNameEnum; else if (strcmp(name,"LoveAllowLayerDeletion")==0) return LoveAllowLayerDeletionEnum; + else if (strcmp(name,"LoveChandlerWobble")==0) return LoveChandlerWobbleEnum; else if (strcmp(name,"LoveCoreMantleBoundary")==0) return LoveCoreMantleBoundaryEnum; else if (strcmp(name,"LoveEarthMass")==0) return LoveEarthMassEnum; @@ -291,4 +308,5 @@ else if (strcmp(name,"LoveStartingLayer")==0) return LoveStartingLayerEnum; else if (strcmp(name,"LoveUnderflowTol")==0) return LoveUnderflowTolEnum; + else if (strcmp(name,"LovePostWidderThreshold")==0) return LovePostWidderThresholdEnum; else if (strcmp(name,"MassFluxSegments")==0) return MassFluxSegmentsEnum; else if (strcmp(name,"MassFluxSegmentsPresent")==0) return MassFluxSegmentsPresentEnum; @@ -360,12 +378,13 @@ else if (strcmp(name,"Modelname")==0) return ModelnameEnum; else if (strcmp(name,"SamplingAlpha")==0) return SamplingAlphaEnum; - else if (strcmp(name,"SamplingPhi")==0) return SamplingPhiEnum; else if (strcmp(name,"SamplingNumRequestedOutputs")==0) return SamplingNumRequestedOutputsEnum; else if (strcmp(name,"SamplingRequestedOutputs")==0) return SamplingRequestedOutputsEnum; else if (strcmp(name,"SamplingRobin")==0) return SamplingRobinEnum; else if (strcmp(name,"SamplingSeed")==0) return SamplingSeedEnum; - else if (strcmp(name,"SamplingTau")==0) return SamplingTauEnum; else if (strcmp(name,"SaveResults")==0) return SaveResultsEnum; - else if (strcmp(name,"SolidearthPartitionIce")==0) return SolidearthPartitionIceEnum; + else stage=4; + } + if(stage==4){ + if (strcmp(name,"SolidearthPartitionIce")==0) return SolidearthPartitionIceEnum; else if (strcmp(name,"SolidearthPartitionHydro")==0) return SolidearthPartitionHydroEnum; else if (strcmp(name,"SolidearthPartitionOcean")==0) return SolidearthPartitionOceanEnum; @@ -377,5 +396,4 @@ else if (strcmp(name,"SolidearthSettingsAbstol")==0) return SolidearthSettingsAbstolEnum; else if (strcmp(name,"SolidearthSettingsCrossSectionShape")==0) return SolidearthSettingsCrossSectionShapeEnum; - else if (strcmp(name,"RotationalAngularVelocity")==0) return RotationalAngularVelocityEnum; else if (strcmp(name,"SolidearthSettingsElastic")==0) return SolidearthSettingsElasticEnum; else if (strcmp(name,"SolidearthSettingsViscous")==0) return SolidearthSettingsViscousEnum; @@ -383,9 +401,14 @@ else if (strcmp(name,"SealevelchangeViscousNumSteps")==0) return SealevelchangeViscousNumStepsEnum; else if (strcmp(name,"SealevelchangeViscousTimes")==0) return SealevelchangeViscousTimesEnum; - else stage=4; - } - if(stage==4){ - if (strcmp(name,"SealevelchangeViscousIndex")==0) return SealevelchangeViscousIndexEnum; + else if (strcmp(name,"SealevelchangeViscousIndex")==0) return SealevelchangeViscousIndexEnum; + else if (strcmp(name,"SealevelchangeViscousPolarMotion")==0) return SealevelchangeViscousPolarMotionEnum; + else if (strcmp(name,"SealevelchangeRunCount")==0) return SealevelchangeRunCountEnum; + else if (strcmp(name,"SealevelchangeTransitions")==0) return SealevelchangeTransitionsEnum; + else if (strcmp(name,"SealevelchangeRequestedOutputs")==0) return SealevelchangeRequestedOutputsEnum; + else if (strcmp(name,"RotationalAngularVelocity")==0) return RotationalAngularVelocityEnum; else if (strcmp(name,"RotationalEquatorialMoi")==0) return RotationalEquatorialMoiEnum; + else if (strcmp(name,"RotationalPolarMoi")==0) return RotationalPolarMoiEnum; + else if (strcmp(name,"LovePolarMotionTransferFunctionColinear")==0) return LovePolarMotionTransferFunctionColinearEnum; + else if (strcmp(name,"LovePolarMotionTransferFunctionOrthogonal")==0) return LovePolarMotionTransferFunctionOrthogonalEnum; else if (strcmp(name,"TidalLoveH")==0) return TidalLoveHEnum; else if (strcmp(name,"TidalLoveK")==0) return TidalLoveKEnum; @@ -399,9 +422,16 @@ else if (strcmp(name,"SealevelchangeGSelfAttraction")==0) return SealevelchangeGSelfAttractionEnum; else if (strcmp(name,"SealevelchangeGViscoElastic")==0) return SealevelchangeGViscoElasticEnum; + else if (strcmp(name,"SealevelchangeUViscoElastic")==0) return SealevelchangeUViscoElasticEnum; + else if (strcmp(name,"SealevelchangeHViscoElastic")==0) return SealevelchangeHViscoElasticEnum; + else if (strcmp(name,"SealevelchangePolarMotionTransferFunctionColinear")==0) return SealevelchangePolarMotionTransferFunctionColinearEnum; + else if (strcmp(name,"SealevelchangePolarMotionTransferFunctionOrthogonal")==0) return SealevelchangePolarMotionTransferFunctionOrthogonalEnum; + else if (strcmp(name,"SealevelchangePolarMotionTransferFunctionZ")==0) return SealevelchangePolarMotionTransferFunctionZEnum; + else if (strcmp(name,"SealevelchangeTidalK2")==0) return SealevelchangeTidalK2Enum; + else if (strcmp(name,"SealevelchangeTidalH2")==0) return SealevelchangeTidalH2Enum; + else if (strcmp(name,"SealevelchangeTidalL2")==0) return SealevelchangeTidalL2Enum; else if (strcmp(name,"SolidearthSettingsSealevelLoading")==0) return SolidearthSettingsSealevelLoadingEnum; else if (strcmp(name,"SolidearthSettingsGRD")==0) return SolidearthSettingsGRDEnum; else if (strcmp(name,"SolidearthSettingsRunFrequency")==0) return SolidearthSettingsRunFrequencyEnum; else if (strcmp(name,"SolidearthSettingsTimeAcc")==0) return SolidearthSettingsTimeAccEnum; - else if (strcmp(name,"SealevelchangeHViscoElastic")==0) return SealevelchangeHViscoElasticEnum; else if (strcmp(name,"SolidearthSettingsHoriz")==0) return SolidearthSettingsHorizEnum; else if (strcmp(name,"SolidearthSettingsMaxiter")==0) return SolidearthSettingsMaxiterEnum; @@ -415,15 +445,12 @@ else if (strcmp(name,"StochasticForcingIsStochasticForcing")==0) return StochasticForcingIsStochasticForcingEnum; else if (strcmp(name,"StochasticForcingIsWaterPressure")==0) return StochasticForcingIsWaterPressureEnum; + else if (strcmp(name,"StochasticForcingNoiseterms")==0) return StochasticForcingNoisetermsEnum; else if (strcmp(name,"StochasticForcingNumFields")==0) return StochasticForcingNumFieldsEnum; else if (strcmp(name,"StochasticForcingRandomflag")==0) return StochasticForcingRandomflagEnum; - else if (strcmp(name,"RotationalPolarMoi")==0) return RotationalPolarMoiEnum; + else if (strcmp(name,"StochasticForcingTimestep")==0) return StochasticForcingTimestepEnum; else if (strcmp(name,"SolidearthSettingsReltol")==0) return SolidearthSettingsReltolEnum; - else if (strcmp(name,"SealevelchangeRequestedOutputs")==0) return SealevelchangeRequestedOutputsEnum; else if (strcmp(name,"SolidearthSettingsSelfAttraction")==0) return SolidearthSettingsSelfAttractionEnum; else if (strcmp(name,"SolidearthSettingsRotation")==0) return SolidearthSettingsRotationEnum; else if (strcmp(name,"SolidearthSettingsMaxSHCoeff")==0) return SolidearthSettingsMaxSHCoeffEnum; - else if (strcmp(name,"SealevelchangeRunCount")==0) return SealevelchangeRunCountEnum; - else if (strcmp(name,"SealevelchangeTransitions")==0) return SealevelchangeTransitionsEnum; - else if (strcmp(name,"SealevelchangeUViscoElastic")==0) return SealevelchangeUViscoElasticEnum; else if (strcmp(name,"SettingsIoGather")==0) return SettingsIoGatherEnum; else if (strcmp(name,"SettingsNumResultsOnNodes")==0) return SettingsNumResultsOnNodesEnum; @@ -450,4 +477,5 @@ else if (strcmp(name,"SmbDpermil")==0) return SmbDpermilEnum; else if (strcmp(name,"SmbDsnowIdx")==0) return SmbDsnowIdxEnum; + else if (strcmp(name,"SmbElevationBins")==0) return SmbElevationBinsEnum; else if (strcmp(name,"SmbCldFrac")==0) return SmbCldFracEnum; else if (strcmp(name,"SmbDelta18o")==0) return SmbDelta18oEnum; @@ -477,9 +505,15 @@ else if (strcmp(name,"SmbIsturbulentflux")==0) return SmbIsturbulentfluxEnum; else if (strcmp(name,"SmbK")==0) return SmbKEnum; - else if (strcmp(name,"SmbNumBasins")==0) return SmbNumBasinsEnum; + else if (strcmp(name,"SmbLapseRates")==0) return SmbLapseRatesEnum; + else stage=5; + } + if(stage==5){ + if (strcmp(name,"SmbNumBasins")==0) return SmbNumBasinsEnum; + else if (strcmp(name,"SmbNumElevationBins")==0) return SmbNumElevationBinsEnum; else if (strcmp(name,"SmbNumRequestedOutputs")==0) return SmbNumRequestedOutputsEnum; else if (strcmp(name,"SmbPfac")==0) return SmbPfacEnum; else if (strcmp(name,"SmbPhi")==0) return SmbPhiEnum; else if (strcmp(name,"SmbRdl")==0) return SmbRdlEnum; + else if (strcmp(name,"SmbRefElevation")==0) return SmbRefElevationEnum; else if (strcmp(name,"SmbRequestedOutputs")==0) return SmbRequestedOutputsEnum; else if (strcmp(name,"SmbRlaps")==0) return SmbRlapsEnum; @@ -506,8 +540,5 @@ else if (strcmp(name,"Step")==0) return StepEnum; else if (strcmp(name,"Steps")==0) return StepsEnum; - else stage=5; - } - if(stage==5){ - if (strcmp(name,"StressbalanceAbstol")==0) return StressbalanceAbstolEnum; + else if (strcmp(name,"StressbalanceAbstol")==0) return StressbalanceAbstolEnum; else if (strcmp(name,"StressbalanceFSreconditioning")==0) return StressbalanceFSreconditioningEnum; else if (strcmp(name,"StressbalanceIsnewton")==0) return StressbalanceIsnewtonEnum; @@ -593,8 +624,19 @@ else if (strcmp(name,"BalancethicknessThickeningRate")==0) return BalancethicknessThickeningRateEnum; else if (strcmp(name,"BasalCrevasse")==0) return BasalCrevasseEnum; + else if (strcmp(name,"BasalforcingsDeepwaterMeltingRateAutoregression")==0) return BasalforcingsDeepwaterMeltingRateAutoregressionEnum; + else if (strcmp(name,"BasalforcingsDeepwaterMeltingRateNoise")==0) return BasalforcingsDeepwaterMeltingRateNoiseEnum; + else if (strcmp(name,"BasalforcingsDeepwaterMeltingRateValuesAutoregression")==0) return BasalforcingsDeepwaterMeltingRateValuesAutoregressionEnum; else if (strcmp(name,"BasalforcingsFloatingiceMeltingRate")==0) return BasalforcingsFloatingiceMeltingRateEnum; else if (strcmp(name,"BasalforcingsGeothermalflux")==0) return BasalforcingsGeothermalfluxEnum; - else if (strcmp(name,"BasalforcingsGroundediceMeltingRate")==0) return BasalforcingsGroundediceMeltingRateEnum; + else stage=6; + } + if(stage==6){ + if (strcmp(name,"BasalforcingsGroundediceMeltingRate")==0) return BasalforcingsGroundediceMeltingRateEnum; + else if (strcmp(name,"BasalforcingsLinearBasinId")==0) return BasalforcingsLinearBasinIdEnum; else if (strcmp(name,"BasalforcingsPerturbationMeltingRate")==0) return BasalforcingsPerturbationMeltingRateEnum; + else if (strcmp(name,"BasalforcingsSpatialDeepwaterElevation")==0) return BasalforcingsSpatialDeepwaterElevationEnum; + else if (strcmp(name,"BasalforcingsSpatialDeepwaterMeltingRate")==0) return BasalforcingsSpatialDeepwaterMeltingRateEnum; + else if (strcmp(name,"BasalforcingsSpatialUpperwaterElevation")==0) return BasalforcingsSpatialUpperwaterElevationEnum; + else if (strcmp(name,"BasalforcingsSpatialUpperwaterMeltingRate")==0) return BasalforcingsSpatialUpperwaterMeltingRateEnum; else if (strcmp(name,"BasalforcingsIsmip6BasinId")==0) return BasalforcingsIsmip6BasinIdEnum; else if (strcmp(name,"BasalforcingsIsmip6Tf")==0) return BasalforcingsIsmip6TfEnum; @@ -618,6 +660,8 @@ else if (strcmp(name,"BaseSlopeY")==0) return BaseSlopeYEnum; else if (strcmp(name,"BaselineBasalforcingsFloatingiceMeltingRate")==0) return BaselineBasalforcingsFloatingiceMeltingRateEnum; + else if (strcmp(name,"BaselineBasalforcingsSpatialDeepwaterMeltingRate")==0) return BaselineBasalforcingsSpatialDeepwaterMeltingRateEnum; else if (strcmp(name,"BaselineCalvingCalvingrate")==0) return BaselineCalvingCalvingrateEnum; else if (strcmp(name,"BaselineFrictionEffectivePressure")==0) return BaselineFrictionEffectivePressureEnum; + else if (strcmp(name,"BaselineSmbMassBalance")==0) return BaselineSmbMassBalanceEnum; else if (strcmp(name,"Bed")==0) return BedEnum; else if (strcmp(name,"BedGRD")==0) return BedGRDEnum; @@ -629,17 +673,13 @@ else if (strcmp(name,"BedSlopeY")==0) return BedSlopeYEnum; else if (strcmp(name,"BottomPressure")==0) return BottomPressureEnum; - else stage=6; - } - if(stage==6){ - if (strcmp(name,"BottomPressureOld")==0) return BottomPressureOldEnum; + else if (strcmp(name,"BottomPressureOld")==0) return BottomPressureOldEnum; else if (strcmp(name,"CalvingCalvingrate")==0) return CalvingCalvingrateEnum; else if (strcmp(name,"CalvingHabFraction")==0) return CalvingHabFractionEnum; + else if (strcmp(name,"CalvingAblationrate")==0) return CalvingAblationrateEnum; else if (strcmp(name,"CalvingMeltingrate")==0) return CalvingMeltingrateEnum; else if (strcmp(name,"CalvingStressThresholdFloatingice")==0) return CalvingStressThresholdFloatingiceEnum; else if (strcmp(name,"CalvingStressThresholdGroundedice")==0) return CalvingStressThresholdGroundediceEnum; else if (strcmp(name,"CalvinglevermannCoeff")==0) return CalvinglevermannCoeffEnum; - else if (strcmp(name,"CalvingratexAverage")==0) return CalvingratexAverageEnum; else if (strcmp(name,"Calvingratex")==0) return CalvingratexEnum; - else if (strcmp(name,"CalvingrateyAverage")==0) return CalvingrateyAverageEnum; else if (strcmp(name,"Calvingratey")==0) return CalvingrateyEnum; else if (strcmp(name,"CalvingFluxLevelset")==0) return CalvingFluxLevelsetEnum; @@ -712,5 +752,8 @@ else if (strcmp(name,"FrictionP")==0) return FrictionPEnum; else if (strcmp(name,"FrictionPressureAdjustedTemperature")==0) return FrictionPressureAdjustedTemperatureEnum; - else if (strcmp(name,"FrictionQ")==0) return FrictionQEnum; + else stage=7; + } + if(stage==7){ + if (strcmp(name,"FrictionQ")==0) return FrictionQEnum; else if (strcmp(name,"FrictionSedimentCompressibilityCoefficient")==0) return FrictionSedimentCompressibilityCoefficientEnum; else if (strcmp(name,"FrictionTillFrictionAngle")==0) return FrictionTillFrictionAngleEnum; @@ -752,8 +795,5 @@ else if (strcmp(name,"HydrologyHeadOld")==0) return HydrologyHeadOldEnum; else if (strcmp(name,"HydrologyMoulinInput")==0) return HydrologyMoulinInputEnum; - else stage=7; - } - if(stage==7){ - if (strcmp(name,"HydrologyNeumannflux")==0) return HydrologyNeumannfluxEnum; + else if (strcmp(name,"HydrologyNeumannflux")==0) return HydrologyNeumannfluxEnum; else if (strcmp(name,"HydrologyReynolds")==0) return HydrologyReynoldsEnum; else if (strcmp(name,"HydrologySheetConductivity")==0) return HydrologySheetConductivityEnum; @@ -823,6 +863,10 @@ else if (strcmp(name,"RheologyBbarAbsGradient")==0) return RheologyBbarAbsGradientEnum; else if (strcmp(name,"Sample")==0) return SampleEnum; + else if (strcmp(name,"SampleOld")==0) return SampleOldEnum; + else if (strcmp(name,"SampleNoise")==0) return SampleNoiseEnum; else if (strcmp(name,"SamplingBeta")==0) return SamplingBetaEnum; else if (strcmp(name,"SamplingKappa")==0) return SamplingKappaEnum; + else if (strcmp(name,"SamplingPhi")==0) return SamplingPhiEnum; + else if (strcmp(name,"SamplingTau")==0) return SamplingTauEnum; else if (strcmp(name,"Sealevel")==0) return SealevelEnum; else if (strcmp(name,"SealevelGRD")==0) return SealevelGRDEnum; @@ -831,5 +875,8 @@ else if (strcmp(name,"SealevelBarystaticIceWeights")==0) return SealevelBarystaticIceWeightsEnum; else if (strcmp(name,"SealevelBarystaticIceArea")==0) return SealevelBarystaticIceAreaEnum; - else if (strcmp(name,"SealevelBarystaticIceLatbar")==0) return SealevelBarystaticIceLatbarEnum; + else stage=8; + } + if(stage==8){ + if (strcmp(name,"SealevelBarystaticIceLatbar")==0) return SealevelBarystaticIceLatbarEnum; else if (strcmp(name,"SealevelBarystaticIceLongbar")==0) return SealevelBarystaticIceLongbarEnum; else if (strcmp(name,"SealevelBarystaticIceLoad")==0) return SealevelBarystaticIceLoadEnum; @@ -859,24 +906,9 @@ else if (strcmp(name,"BslcRate")==0) return BslcRateEnum; else if (strcmp(name,"Gmtslc")==0) return GmtslcEnum; - else if (strcmp(name,"SealevelGrotm1")==0) return SealevelGrotm1Enum; - else if (strcmp(name,"SealevelGrotm2")==0) return SealevelGrotm2Enum; - else if (strcmp(name,"SealevelGrotm3")==0) return SealevelGrotm3Enum; - else if (strcmp(name,"SealevelGUrotm1")==0) return SealevelGUrotm1Enum; - else if (strcmp(name,"SealevelGUrotm2")==0) return SealevelGUrotm2Enum; - else if (strcmp(name,"SealevelGUrotm3")==0) return SealevelGUrotm3Enum; - else if (strcmp(name,"SealevelGNrotm1")==0) return SealevelGNrotm1Enum; - else if (strcmp(name,"SealevelGNrotm2")==0) return SealevelGNrotm2Enum; - else if (strcmp(name,"SealevelGNrotm3")==0) return SealevelGNrotm3Enum; - else if (strcmp(name,"SealevelGErotm1")==0) return SealevelGErotm1Enum; - else if (strcmp(name,"SealevelGErotm2")==0) return SealevelGErotm2Enum; - else if (strcmp(name,"SealevelGErotm3")==0) return SealevelGErotm3Enum; else if (strcmp(name,"SealevelRSLBarystatic")==0) return SealevelRSLBarystaticEnum; else if (strcmp(name,"SealevelRSLRate")==0) return SealevelRSLRateEnum; else if (strcmp(name,"SealevelUGrd")==0) return SealevelUGrdEnum; else if (strcmp(name,"SealevelNGrd")==0) return SealevelNGrdEnum; - else stage=8; - } - if(stage==8){ - if (strcmp(name,"SealevelUEastEsa")==0) return SealevelUEastEsaEnum; + else if (strcmp(name,"SealevelUEastEsa")==0) return SealevelUEastEsaEnum; else if (strcmp(name,"SealevelUNorthEsa")==0) return SealevelUNorthEsaEnum; else if (strcmp(name,"SealevelchangeIndices")==0) return SealevelchangeIndicesEnum; @@ -885,4 +917,8 @@ else if (strcmp(name,"SealevelchangeGE")==0) return SealevelchangeGEEnum; else if (strcmp(name,"SealevelchangeGN")==0) return SealevelchangeGNEnum; + else if (strcmp(name,"SealevelchangeGrot")==0) return SealevelchangeGrotEnum; + else if (strcmp(name,"SealevelchangeGUrot")==0) return SealevelchangeGUrotEnum; + else if (strcmp(name,"SealevelchangeGNrot")==0) return SealevelchangeGNrotEnum; + else if (strcmp(name,"SealevelchangeGErot")==0) return SealevelchangeGErotEnum; else if (strcmp(name,"SealevelchangeGsubelOcean")==0) return SealevelchangeGsubelOceanEnum; else if (strcmp(name,"SealevelchangeGUsubelOcean")==0) return SealevelchangeGUsubelOceanEnum; @@ -962,5 +998,8 @@ else if (strcmp(name,"SmbGdnini")==0) return SmbGdniniEnum; else if (strcmp(name,"SmbGsp")==0) return SmbGspEnum; - else if (strcmp(name,"SmbGspini")==0) return SmbGspiniEnum; + else stage=9; + } + if(stage==9){ + if (strcmp(name,"SmbGspini")==0) return SmbGspiniEnum; else if (strcmp(name,"SmbHref")==0) return SmbHrefEnum; else if (strcmp(name,"SmbIsInitialized")==0) return SmbIsInitializedEnum; @@ -998,8 +1037,5 @@ else if (strcmp(name,"SmbSizeini")==0) return SmbSizeiniEnum; else if (strcmp(name,"SmbSmbCorr")==0) return SmbSmbCorrEnum; - else stage=9; - } - if(stage==9){ - if (strcmp(name,"SmbSmbref")==0) return SmbSmbrefEnum; + else if (strcmp(name,"SmbSmbref")==0) return SmbSmbrefEnum; else if (strcmp(name,"SmbSzaValue")==0) return SmbSzaValueEnum; else if (strcmp(name,"SmbT")==0) return SmbTEnum; @@ -1085,5 +1121,8 @@ else if (strcmp(name,"VxSurface")==0) return VxSurfaceEnum; else if (strcmp(name,"VyAverage")==0) return VyAverageEnum; - else if (strcmp(name,"VyBase")==0) return VyBaseEnum; + else stage=10; + } + if(stage==10){ + if (strcmp(name,"VyBase")==0) return VyBaseEnum; else if (strcmp(name,"Vy")==0) return VyEnum; else if (strcmp(name,"VyMesh")==0) return VyMeshEnum; @@ -1121,8 +1160,5 @@ else if (strcmp(name,"Outputdefinition19")==0) return Outputdefinition19Enum; else if (strcmp(name,"Outputdefinition20")==0) return Outputdefinition20Enum; - else stage=10; - } - if(stage==10){ - if (strcmp(name,"Outputdefinition21")==0) return Outputdefinition21Enum; + else if (strcmp(name,"Outputdefinition21")==0) return Outputdefinition21Enum; else if (strcmp(name,"Outputdefinition22")==0) return Outputdefinition22Enum; else if (strcmp(name,"Outputdefinition23")==0) return Outputdefinition23Enum; @@ -1208,5 +1244,8 @@ else if (strcmp(name,"Outputdefinition96")==0) return Outputdefinition96Enum; else if (strcmp(name,"Outputdefinition97")==0) return Outputdefinition97Enum; - else if (strcmp(name,"Outputdefinition98")==0) return Outputdefinition98Enum; + else stage=11; + } + if(stage==11){ + if (strcmp(name,"Outputdefinition98")==0) return Outputdefinition98Enum; else if (strcmp(name,"Outputdefinition99")==0) return Outputdefinition99Enum; else if (strcmp(name,"Outputdefinition9")==0) return Outputdefinition9Enum; @@ -1224,4 +1263,5 @@ else if (strcmp(name,"Arrhenius")==0) return ArrheniusEnum; else if (strcmp(name,"AutodiffJacobian")==0) return AutodiffJacobianEnum; + else if (strcmp(name,"AutoregressionLinearFloatingMeltRate")==0) return AutoregressionLinearFloatingMeltRateEnum; else if (strcmp(name,"Balancethickness2Analysis")==0) return Balancethickness2AnalysisEnum; else if (strcmp(name,"Balancethickness2Solution")==0) return Balancethickness2SolutionEnum; @@ -1244,10 +1284,9 @@ else if (strcmp(name,"Boundary")==0) return BoundaryEnum; else if (strcmp(name,"BuddJacka")==0) return BuddJackaEnum; - else stage=11; - } - if(stage==11){ - if (strcmp(name,"CalvingDev2")==0) return CalvingDev2Enum; + else if (strcmp(name,"CalvingDev2")==0) return CalvingDev2Enum; else if (strcmp(name,"CalvingHab")==0) return CalvingHabEnum; else if (strcmp(name,"CalvingLevermann")==0) return CalvingLevermannEnum; + else if (strcmp(name,"CalvingTest")==0) return CalvingTestEnum; + else if (strcmp(name,"CalvingParameterization")==0) return CalvingParameterizationEnum; else if (strcmp(name,"CalvingVonmises")==0) return CalvingVonmisesEnum; else if (strcmp(name,"Cfdragcoeffabsgrad")==0) return CfdragcoeffabsgradEnum; @@ -1328,5 +1367,8 @@ else if (strcmp(name,"GaussTetra")==0) return GaussTetraEnum; else if (strcmp(name,"GaussTria")==0) return GaussTriaEnum; - else if (strcmp(name,"GenericOption")==0) return GenericOptionEnum; + else stage=12; + } + if(stage==12){ + if (strcmp(name,"GenericOption")==0) return GenericOptionEnum; else if (strcmp(name,"GenericParam")==0) return GenericParamEnum; else if (strcmp(name,"GenericExternalResult")==0) return GenericExternalResultEnum; @@ -1367,8 +1409,5 @@ else if (strcmp(name,"Indexed")==0) return IndexedEnum; else if (strcmp(name,"IntExternalResult")==0) return IntExternalResultEnum; - else stage=12; - } - if(stage==12){ - if (strcmp(name,"ElementInput")==0) return ElementInputEnum; + else if (strcmp(name,"ElementInput")==0) return ElementInputEnum; else if (strcmp(name,"IntMatExternalResult")==0) return IntMatExternalResultEnum; else if (strcmp(name,"IntMatParam")==0) return IntMatParamEnum; @@ -1381,5 +1420,5 @@ else if (strcmp(name,"J")==0) return JEnum; else if (strcmp(name,"L1L2Approximation")==0) return L1L2ApproximationEnum; - else if (strcmp(name,"MLHOApproximation")==0) return MLHOApproximationEnum; + else if (strcmp(name,"MOLHOApproximation")==0) return MOLHOApproximationEnum; else if (strcmp(name,"L2ProjectionBaseAnalysis")==0) return L2ProjectionBaseAnalysisEnum; else if (strcmp(name,"L2ProjectionEPLAnalysis")==0) return L2ProjectionEPLAnalysisEnum; @@ -1393,12 +1432,17 @@ else if (strcmp(name,"Loads")==0) return LoadsEnum; else if (strcmp(name,"LoveAnalysis")==0) return LoveAnalysisEnum; - else if (strcmp(name,"LoveHi")==0) return LoveHiEnum; - else if (strcmp(name,"LoveHr")==0) return LoveHrEnum; + else if (strcmp(name,"LoveHf")==0) return LoveHfEnum; + else if (strcmp(name,"LoveHt")==0) return LoveHtEnum; else if (strcmp(name,"LoveKernelsImag")==0) return LoveKernelsImagEnum; else if (strcmp(name,"LoveKernelsReal")==0) return LoveKernelsRealEnum; - else if (strcmp(name,"LoveKi")==0) return LoveKiEnum; - else if (strcmp(name,"LoveKr")==0) return LoveKrEnum; - else if (strcmp(name,"LoveLi")==0) return LoveLiEnum; - else if (strcmp(name,"LoveLr")==0) return LoveLrEnum; + else if (strcmp(name,"LoveKf")==0) return LoveKfEnum; + else if (strcmp(name,"LoveKt")==0) return LoveKtEnum; + else if (strcmp(name,"LoveLf")==0) return LoveLfEnum; + else if (strcmp(name,"LoveLt")==0) return LoveLtEnum; + else if (strcmp(name,"LoveTidalHt")==0) return LoveTidalHtEnum; + else if (strcmp(name,"LoveTidalKt")==0) return LoveTidalKtEnum; + else if (strcmp(name,"LoveTidalLt")==0) return LoveTidalLtEnum; + else if (strcmp(name,"LovePMTF1t")==0) return LovePMTF1tEnum; + else if (strcmp(name,"LovePMTF2t")==0) return LovePMTF2tEnum; else if (strcmp(name,"LoveSolution")==0) return LoveSolutionEnum; else if (strcmp(name,"MINI")==0) return MINIEnum; @@ -1446,5 +1490,8 @@ else if (strcmp(name,"Nodal")==0) return NodalEnum; else if (strcmp(name,"Nodalvalue")==0) return NodalvalueEnum; - else if (strcmp(name,"NodeSId")==0) return NodeSIdEnum; + else stage=13; + } + if(stage==13){ + if (strcmp(name,"NodeSId")==0) return NodeSIdEnum; else if (strcmp(name,"NoneApproximation")==0) return NoneApproximationEnum; else if (strcmp(name,"None")==0) return NoneEnum; @@ -1490,8 +1537,5 @@ else if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; else if (strcmp(name,"SamplingAnalysis")==0) return SamplingAnalysisEnum; - else stage=13; - } - if(stage==13){ - if (strcmp(name,"SamplingSolution")==0) return SamplingSolutionEnum; + else if (strcmp(name,"SamplingSolution")==0) return SamplingSolutionEnum; else if (strcmp(name,"SIAApproximation")==0) return SIAApproximationEnum; else if (strcmp(name,"SMBautoregression")==0) return SMBautoregressionEnum; @@ -1515,7 +1559,7 @@ else if (strcmp(name,"SealevelAbsolute")==0) return SealevelAbsoluteEnum; else if (strcmp(name,"SealevelEmotion")==0) return SealevelEmotionEnum; - else if (strcmp(name,"SealevelInertiaTensorXZ")==0) return SealevelInertiaTensorXZEnum; - else if (strcmp(name,"SealevelInertiaTensorYZ")==0) return SealevelInertiaTensorYZEnum; - else if (strcmp(name,"SealevelInertiaTensorZZ")==0) return SealevelInertiaTensorZZEnum; + else if (strcmp(name,"SealevelchangePolarMotionX")==0) return SealevelchangePolarMotionXEnum; + else if (strcmp(name,"SealevelchangePolarMotionY")==0) return SealevelchangePolarMotionYEnum; + else if (strcmp(name,"SealevelchangePolarMotionZ")==0) return SealevelchangePolarMotionZEnum; else if (strcmp(name,"SealevelchangePolarMotion")==0) return SealevelchangePolarMotionEnum; else if (strcmp(name,"SealevelNmotion")==0) return SealevelNmotionEnum; @@ -1569,5 +1613,8 @@ else if (strcmp(name,"TotalSmbScaled")==0) return TotalSmbScaledEnum; else if (strcmp(name,"TransientArrayParam")==0) return TransientArrayParamEnum; - else if (strcmp(name,"TransientInput")==0) return TransientInputEnum; + else stage=14; + } + if(stage==14){ + if (strcmp(name,"TransientInput")==0) return TransientInputEnum; else if (strcmp(name,"TransientParam")==0) return TransientParamEnum; else if (strcmp(name,"TransientSolution")==0) return TransientSolutionEnum; @@ -1604,5 +1651,5 @@ else if (strcmp(name,"TriangleInterp")==0) return TriangleInterpEnum; else if (strcmp(name,"MaximumNumberOfDefinitions")==0) return MaximumNumberOfDefinitionsEnum; - else stage=14; + else stage=15; } /*If we reach this point, the string provided has not been found*/ Index: /issm/trunk/src/c/shared/Enum/Synchronize.sh =================================================================== --- /issm/trunk/src/c/shared/Enum/Synchronize.sh (revision 27034) +++ /issm/trunk/src/c/shared/Enum/Synchronize.sh (revision 27035) @@ -193,4 +193,26 @@ END #}}} +#Build issmenum.jl {{{ +#Header +cat < $ISSM_DIR/src/c/shared/Enum/issmenums.jl +# WARNING: DO NOT MODIFY THIS FILE +# this file has been automatically generated by Synchronize.sh +# Please read README for more information + +@enum IssmEnum begin +END +cat temp | awk '{print "\t" $1}' >> $ISSM_DIR/src/c/shared/Enum/issmenums.jl +#Move on to EnumToString +cat <> $ISSM_DIR/src/c/shared/Enum/issmenums.jl +end + +function EnumToString(enum::IssmEnum) +END +cat temp | awk '{print "\tif(enum==" $1 ") return \"" substr($1,1,length($1)-4) "\" end"}' >> $ISSM_DIR/src/c/shared/Enum/issmenums.jl +#Move on to StringToEnumx +cat <> $ISSM_DIR/src/c/shared/Enum/issmenums.jl +end +END +#}}} #vim file Index: /issm/trunk/src/c/shared/Exceptions/Exceptions.cpp =================================================================== --- /issm/trunk/src/c/shared/Exceptions/Exceptions.cpp (revision 27034) +++ /issm/trunk/src/c/shared/Exceptions/Exceptions.cpp (revision 27035) @@ -15,7 +15,4 @@ #include #include "./exceptions.h" -#include "../io/Print/Print.h" -#include "../io/Comm/IssmComm.h" -#include "../MemOps/MemOps.h" ErrorException::ErrorException(const string & what_arg){/*{{{*/ @@ -31,24 +28,26 @@ }/*}}}*/ -ErrorException::ErrorException(const string& what_file, const string& what_function,int what_line, const string& what_arg){/*{{{*/ +ErrorException::ErrorException(int what_rank,const string& what_file, const string& what_function,int what_line, const string& what_arg){/*{{{*/ + /*Intermediaries*/ int len; - len = strlen(what_arg.c_str())+1; - what_str = new char[len]; - memcpy(what_str,what_arg.c_str(),len); + this->rank = what_rank; + this->file_line= what_line; - len = strlen(what_file.c_str())+1; - file_name = new char[len]; - memcpy(file_name,what_file.c_str(),len); + len = strlen(what_arg.c_str())+1; + this->what_str = new char[len]; + memcpy(this->what_str,what_arg.c_str(),len); - len = strlen(what_function.c_str())+1; - function_name = new char[len]; - memcpy(function_name,what_function.c_str(),len); + len = strlen(what_file.c_str())+1; + this->file_name = new char[len]; + memcpy(this->file_name,what_file.c_str(),len); - file_line= what_line; - /*When error messages are not shown properly, uncomment the following line*/ - this->Report(); + len = strlen(what_function.c_str())+1; + this->function_name = new char[len]; + memcpy(this->function_name,what_function.c_str(),len); + /*Uncomment if messages do not print properly*/ + //this->Report(); }/*}}}*/ ErrorException::~ErrorException() throw(){/*{{{*/ @@ -58,5 +57,4 @@ }/*}}}*/ const char* ErrorException::what() const throw(){/*{{{*/ - //this->Report(); return what_str; }/*}}}*/ @@ -64,21 +62,11 @@ /*WINDOWS*/ - if(!function_name || file_line==0){ - _printf_("Error message: " << what()); + if(!this->function_name || this->file_line==0){ + cerr << "Error message: " << what() << endl; return; } - /*recover my_rank and num_procs:*/ - int my_rank = IssmComm::GetRank(); - int num_procs = IssmComm::GetSize(); - - if(num_procs==1){ - _printf_("\n??? Error in ==> " << file_name << ":" << file_line << "\n"); - _printf_(function_name << " error message: " << what() << "\n\n"); - } - else{ - _printf_("\n[" << my_rank<< "] ??? Error using ==> " << file_name << ":" << file_line << "\n"); - _printf_( "[" << my_rank << "] " << function_name << " error message: " << what() << "\n\n"); - } + cerr <<"\n[" << this->rank<< "] ??? Error using ==> " << this->file_name << ":" << this->file_line << + "\n[" << this->rank<< "] " << this->function_name << " error message: " << what() << "\n" << endl; return; @@ -91,5 +79,5 @@ /*WINDOWS*/ - if(!function_name || file_line==0){ + if(!this->function_name || this->file_line==0){ buffer << " error message: " << this->what_str; } @@ -101,5 +89,7 @@ /*Convert std::ostringstream to std::string and then create char* */ std::string buffer2 = buffer.str(); - message = xNew(strlen(buffer2.c_str())+1); sprintf(message,"%s",buffer2.c_str()); + message = new char[strlen(buffer2.c_str())+1]; + sprintf(message,"%s",buffer2.c_str()); + return message; }/*}}}*/ Index: /issm/trunk/src/c/shared/Exceptions/exceptions.h =================================================================== --- /issm/trunk/src/c/shared/Exceptions/exceptions.h (revision 27034) +++ /issm/trunk/src/c/shared/Exceptions/exceptions.h (revision 27035) @@ -28,5 +28,6 @@ #include -/*macros: */ +/*macros: (should move somewhere else)*/ +#include "../io/Comm/IssmComm.h" /* _assert_ {{{*/ /*Assertion macro: do nothing if macro _ISSM_DEBUG_ undefined*/ @@ -50,5 +51,5 @@ do{std::ostringstream aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy; \ aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy << StreamArgs << std::ends; \ - throw ErrorException(__FILE__,__func__,__LINE__,aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy.str());}while(0) + throw ErrorException(IssmComm::GetRank(),__FILE__,__func__,__LINE__,aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy.str());}while(0) #endif /*}}}*/ @@ -78,5 +79,5 @@ /*ISSM exception class: */ -class ErrorException: public exception { /*{{{*/ +class ErrorException: public exception{ /*{{{*/ char* what_str; @@ -84,8 +85,11 @@ char* file_name; int file_line; + int rank; public: - ErrorException(const string &what_arg); //for windows - ErrorException(const string &what_file,const string& what_function,int what_line,const string& what_arg);//UNIX + /*Windows*/ + ErrorException(const string &what_arg); + /*Linux/macOS*/ + ErrorException(int what_rank,const string &what_file,const string& what_function,int what_line,const string& what_arg); ~ErrorException() throw(); virtual const char *what() const throw(); Index: /issm/trunk/src/c/shared/MemOps/MemOps.h =================================================================== --- /issm/trunk/src/c/shared/MemOps/MemOps.h (revision 27034) +++ /issm/trunk/src/c/shared/MemOps/MemOps.h (revision 27035) @@ -151,5 +151,5 @@ template T* xMemCpy(T* dest, const T* src, unsigned int size) {/*{{{*/ assert(dest); assert(src); - #if defined(_HAVE_ADOLC_) + #if defined(_HAVE_ADOLC_) || defined(_HAVE_CODIPACK_) for (int i=0; idouble_count(value)); + + /*Comment out this assert, some parameters are NaN (e.g. abstol) by default*/ + //_assert_(!xIsNan(value)); + this->tape_codi->registerInput(value); #if _CODIPACK_MAJOR_==2 @@ -137,5 +140,5 @@ }/*}}}*/ void RegisterOutputFunctor::call(IssmDouble & value){/*{{{*/ - _assert_(!xIsNan(value)); + //_assert_(!xIsNan(value)); this->tape_codi->registerOutput(value); this->double_count++; Index: /issm/trunk/src/c/solutionsequences/convergence.cpp =================================================================== --- /issm/trunk/src/c/solutionsequences/convergence.cpp (revision 27034) +++ /issm/trunk/src/c/solutionsequences/convergence.cpp (revision 27035) @@ -90,6 +90,6 @@ //compute max(du) duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); - ndu=duf->Norm(NORM_TWO); nduinf=duf->Norm(NORM_INF); - if (xIsNan(ndu) || xIsNan(nu)) _error_("convergence criterion is NaN!"); + nduinf=duf->Norm(NORM_INF); + if (xIsNan(nduinf)) _error_("convergence criterion is NaN!"); //clean up Index: /issm/trunk/src/c/solutionsequences/solutionsequence_sampling.cpp =================================================================== --- /issm/trunk/src/c/solutionsequences/solutionsequence_sampling.cpp (revision 27034) +++ /issm/trunk/src/c/solutionsequences/solutionsequence_sampling.cpp (revision 27035) @@ -13,12 +13,7 @@ void GaussianVector(Vector* ppf,int seed){/*{{{*/ - - /*Intermediaries*/ - double rdnumber; - /*Define seed*/ rnd::linear_congruential_engine random_engine; - if(seed>=0) - { + if(seed>=0){ int my_rank; ISSM_MPI_Comm_rank(ISSM_MPI_COMM_WORLD,&my_rank); @@ -28,5 +23,4 @@ /* Define univariate distribution */ - rnd::normal_distribution distribution(0.0,1.0); @@ -38,9 +32,13 @@ ppf->GetLocalSize(&M); for(int i=0;iSetValue(local_indices[i],rdnumber,INS_VAL); } ppf->Assemble(); + /*Cleanup*/ + random_engine.free_resources(); + xDelete(local_indices); + xDelete(local_vector); }/*}}}*/ void solutionsequence_sampling(FemModel* femmodel){ @@ -51,6 +49,5 @@ Vector* ug = NULL; Vector* uf = NULL; - Vector* old_uf = NULL; // previous solution vector (for transient) - Vector* pf = NULL; + Vector* pf = NULL; Vector* df = NULL; Vector* ys=NULL; @@ -62,24 +59,9 @@ /*parameters:*/ - int solution_type, alpha, step, seed, nsize; - IssmDouble phi, tau; + int alpha, seed, nsize; /*Recover parameters: */ - femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); femmodel->parameters->FindParam(&seed,SamplingSeedEnum); femmodel->parameters->FindParam(&alpha,SamplingAlphaEnum); - femmodel->parameters->FindParam(&tau,SamplingTauEnum); - - /*Recover parameters for transient simulation: */ - if(solution_type==TransientSolutionEnum) - { - femmodel->parameters->FindParam(&step,StepEnum); - femmodel->parameters->FindParam(&phi,SamplingPhiEnum); - if(seed>=0) seed = seed + 13923272*step; // change default seed for transient simulations (by considering an arbitrary shif based on the step number) - - GetSolutionFromInputsx(&ug,femmodel); - Reducevectorgtofx(&uf, ug, femmodel->nodes,femmodel->parameters); - old_uf=uf->Duplicate(); - } /*CreateAnalysis*/ @@ -101,7 +83,4 @@ Reduceloadx(pf, Kfs, ys); delete Kfs; - - /*Copy old solution for transient run */ - if(solution_type==TransientSolutionEnum) uf->Copy(old_uf); /* Generate random RHS */ @@ -130,10 +109,4 @@ } - /* Divide results by tau */ - uf->Scale(1.0/tau); - - /* Update solution x_{t+1} = phi x_{t} + noise for transient */ - if(solution_type==TransientSolutionEnum) uf->AXPY(old_uf,phi); - /* Update input */ Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters); @@ -141,5 +114,5 @@ /*clean-up*/ - delete Kff; delete pf; delete df; delete uf; delete ys; delete old_uf; + delete Kff; delete pf; delete df; delete uf; delete ys; delete Ml; delete Mscale; delete analysis; Index: sm/trunk/src/m/boundaryconditions/SetMLHOBC.m =================================================================== --- /issm/trunk/src/m/boundaryconditions/SetMLHOBC.m (revision 27034) +++ (revision ) @@ -1,16 +1,0 @@ -function md=SetMLHOBC(md) -%SETMLHOBC - Create the boundary conditions for stressbalance for MLHO: VxBase, VyBase, VxShear, VyShear -% -% Usage: -% md=SetMLHOBC(md) -% - - -%node on Dirichlet -if md.flowequation.isMLHO - md.stressbalance.spcvx_base=md.stressbalance.spcvx; - md.stressbalance.spcvy_base=md.stressbalance.spcvy; - - md.stressbalance.spcvx_shear=NaN*ones(size(md.stressbalance.spcvx_base)); - md.stressbalance.spcvy_shear=NaN*ones(size(md.stressbalance.spcvy_base)); -end Index: sm/trunk/src/m/boundaryconditions/SetMLHOBC.py =================================================================== --- /issm/trunk/src/m/boundaryconditions/SetMLHOBC.py (revision 27034) +++ (revision ) @@ -1,22 +1,0 @@ -import numpy as np - - -def SetMLHOBC(md): - """ - SETMLHOBC - Create the boundary conditions for stressbalance for MLHO: VxBase, VyBase, VxShear, VyShear - - Usage: - md = SetIceShelfBC(md, varargin) - - Example: - md = SetIceShelfBC(md) - - """ - - #node on Dirichlet (boundary and ~icefront) - md.stressbalance.spcvx_base = md.stressbalance.spcvx - md.stressbalance.spcvy_base = md.stressbalance.spcvy - md.stressbalance.spcvx_shear = np.nan * md.stressbalance.spcvx - md.stressbalance.spcvy_shear = np.nan * md.stressbalance.spcvy - - return md Index: /issm/trunk/src/m/boundaryconditions/SetMOLHOBC.m =================================================================== --- /issm/trunk/src/m/boundaryconditions/SetMOLHOBC.m (revision 27035) +++ /issm/trunk/src/m/boundaryconditions/SetMOLHOBC.m (revision 27035) @@ -0,0 +1,16 @@ +function md=SetMOLHOBC(md) +%SETMOLHOBC - Create the boundary conditions for stressbalance for MOLHO: VxBase, VyBase, VxShear, VyShear +% +% Usage: +% md=SetMOLHOBC(md) +% + + +%node on Dirichlet +if md.flowequation.isMOLHO + md.stressbalance.spcvx_base=md.stressbalance.spcvx; + md.stressbalance.spcvy_base=md.stressbalance.spcvy; + + md.stressbalance.spcvx_shear=NaN*ones(size(md.stressbalance.spcvx_base)); + md.stressbalance.spcvy_shear=NaN*ones(size(md.stressbalance.spcvy_base)); +end Index: /issm/trunk/src/m/boundaryconditions/SetMOLHOBC.py =================================================================== --- /issm/trunk/src/m/boundaryconditions/SetMOLHOBC.py (revision 27035) +++ /issm/trunk/src/m/boundaryconditions/SetMOLHOBC.py (revision 27035) @@ -0,0 +1,21 @@ +import numpy as np + +def SetMOLHOBC(md): + """ + SETMOLHOBC - Create the boundary conditions for stressbalance for MOLHO: VxBase, VyBase, VxShear, VyShear + + Usage: + md = SetIceShelfBC(md, varargin) + + Example: + md = SetIceShelfBC(md) + + """ + + #node on Dirichlet (boundary and ~icefront) + md.stressbalance.spcvx_base = md.stressbalance.spcvx + md.stressbalance.spcvy_base = md.stressbalance.spcvy + md.stressbalance.spcvx_shear = np.nan * md.stressbalance.spcvx + md.stressbalance.spcvy_shear = np.nan * md.stressbalance.spcvy + + return md Index: /issm/trunk/src/m/classes/SMBautoregression.m =================================================================== --- /issm/trunk/src/m/classes/SMBautoregression.m (revision 27034) +++ /issm/trunk/src/m/classes/SMBautoregression.m (revision 27035) @@ -14,4 +14,7 @@ phi = NaN; basin_id = NaN; + lapserates = NaN; + elevationbins = NaN; + refelevation = NaN; steps_per_step = 1; averaging = 0; @@ -59,5 +62,5 @@ self.ar_order = 0.0; %autoregression model of order 0 end % }}} - function md = checkconsistency(self,md,solution,analyses) + function md = checkconsistency(self,md,solution,analyses) % {{{ if ismember('MasstransportAnalysis',analyses), @@ -70,14 +73,32 @@ md = checkfield(md,'fieldname','smb.ar_timestep','numel',1,'NaN',1,'Inf',1,'>=',md.timestepping.time_step); %autoregression time step cannot be finer than ISSM timestep md = checkfield(md,'fieldname','smb.phi','NaN',1,'Inf',1,'size',[md.smb.num_basins,md.smb.ar_order]); + + if (any(isnan(md.smb.refelevation)==0) || numel(md.smb.refelevation)>1) + md = checkfield(md,'fieldname','smb.refelevation','NaN',1,'Inf',1,'>=',0,'size',[1,md.smb.num_basins],'numel',md.smb.num_basins); + end + [nbas,nbins] = size(md.smb.lapserates); + if (any(isnan(reshape(md.smb.lapserates,[1,nbas*nbins]))==0) || numel(md.smb.lapserates)>1) + md = checkfield(md,'fieldname','smb.lapserates','NaN',1,'Inf',1,'size',[md.smb.num_basins,nbins],'numel',md.smb.num_basins*nbins); + md = checkfield(md,'fieldname','smb.elevationbins','NaN',1,'Inf',1,'size',[md.smb.num_basins,nbins-1],'numel',md.smb.num_basins*(nbins-1)); + if(issorted(md.smb.elevationbins,2)==0) + error('md.smb.elevationbins should have rows in order of increasing elevation'); + end + elseif (isnan(md.smb.elevationbins(1,1))==0 || numel(md.smb.elevationbins)>1) + %elevationbins specified but not lapserates: this will inevitably lead to inconsistencies + [nbas,nbins] = size(md.smb.elevationbins); + nbins = nbins+1; + md = checkfield(md,'fieldname','smb.lapserates','NaN',1,'Inf',1,'size',[md.smb.num_basins,nbins],'numel',md.smb.num_basins*nbins); + md = checkfield(md,'fieldname','smb.elevationbins','NaN',1,'Inf',1,'size',[md.smb.num_basins,nbins-1],'numel',md.smb.num_basins*(nbins-1)); + end end md = checkfield(md,'fieldname','smb.steps_per_step','>=',1,'numel',[1]); md = checkfield(md,'fieldname','smb.averaging','numel',[1],'values',[0 1 2]); md = checkfield(md,'fieldname','smb.requested_outputs','stringrow',1); - end + end % }}} function disp(self) % {{{ disp(sprintf(' surface forcings parameters:')); fielddisplay(self,'num_basins','number of different basins [unitless]'); fielddisplay(self,'basin_id','basin number assigned to each element [unitless]'); - fielddisplay(self,'beta0','basin-specific intercept values [m ice eq./yr]'); + fielddisplay(self,'beta0','basin-specific intercept values [m ice eq./yr] (if beta_1==0 mean=beta_0/(1-sum(phi)))'); fielddisplay(self,'beta1','basin-specific trend values [m ice eq. yr^(-2)]'); fielddisplay(self,'ar_order','order of the autoregressive model [unitless]'); @@ -85,4 +106,7 @@ fielddisplay(self,'ar_timestep','time resolution of the autoregressive model [yr]'); fielddisplay(self,'phi','basin-specific vectors of lag coefficients [unitless]'); + fielddisplay(self,'lapserates','basin-specific SMB lapse rates applied in each elevation bin, 1 row per basin, 1 column per bin [m ice eq yr^-1 m^-1] (default: no lapse rate)'); + fielddisplay(self,'elevationbins','basin-specific separations between elevation bins, 1 row per basin, 1 column per limit between bins [m] (default: no basin separation)'); + fielddisplay(self,'refelevation','basin-specific reference elevations at which SMB is calculated, and from which SMB is downscaled using lapserates (default: basin mean elevation) [m]'); fielddisplay(self, 'steps_per_step', 'number of smb steps per time step'); fielddisplay(self, 'averaging', 'averaging methods from short to long steps'); @@ -97,5 +121,31 @@ yts=md.constants.yts; - WriteData(fid,prefix,'name','md.smb.model','data',55,'format','Integer'); + templapserates = md.smb.lapserates; + tempelevationbins = md.smb.elevationbins; + temprefelevation = md.smb.refelevation; + [nbas,nbins] = size(md.smb.lapserates); + if(any(isnan(reshape(md.smb.lapserates,[1,nbas*nbins])))) + templapserates = zeros(md.smb.num_basins,2); + disp(' smb.lapserates not specified: set to 0'); + tempelevationbins = zeros(md.smb.num_basins,1); %dummy elevation bins + end + if(any(isnan(md.smb.refelevation))) + temprefelevation = zeros(1,md.smb.num_basins); + areas = GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y); + for ii=1:md.smb.num_basins + indices = find(md.smb.basin_id==ii); + elemsh = zeros(numel(indices),1); + for jj=1:numel(indices) + elemsh(jj) = mean(md.geometry.surface(md.mesh.elements(indices(jj),:))); + end + temprefelevation(ii) = sum(areas(indices).*elemsh)/sum(areas(indices)); + end + if(any(reshape(md.smb.lapserates,[1,nbas*nbins])~=0)) + disp(' smb.refelevation not specified: Reference elevations set to mean surface elevation of basins'); + end + end + [nbas,nbins] = size(templapserates); + + WriteData(fid,prefix,'name','md.smb.model','data',13,'format','Integer'); WriteData(fid,prefix,'object',self,'class','smb','fieldname','num_basins','format','Integer'); WriteData(fid,prefix,'object',self,'class','smb','fieldname','ar_order','format','Integer'); @@ -106,4 +156,8 @@ WriteData(fid,prefix,'object',self,'class','smb','fieldname','beta1','format','DoubleMat','name','md.smb.beta1','scale',1./(yts^2),'yts',yts); WriteData(fid,prefix,'object',self,'class','smb','fieldname','phi','format','DoubleMat','name','md.smb.phi','yts',yts); + WriteData(fid,prefix,'data',templapserates,'format','DoubleMat','name','md.smb.lapserates','scale',1./yts,'yts',yts); + WriteData(fid,prefix,'data',tempelevationbins,'format','DoubleMat','name','md.smb.elevationbins'); + WriteData(fid,prefix,'data',temprefelevation,'format','DoubleMat','name','md.smb.refelevation'); + WriteData(fid,prefix,'data',nbins,'format','Integer','name','md.smb.num_bins'); WriteData(fid,prefix,'object',self,'fieldname','steps_per_step','format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','averaging','format','Integer'); Index: /issm/trunk/src/m/classes/SMBautoregression.py =================================================================== --- /issm/trunk/src/m/classes/SMBautoregression.py (revision 27034) +++ /issm/trunk/src/m/classes/SMBautoregression.py (revision 27035) @@ -5,5 +5,5 @@ from project3d import * from WriteData import * - +from GetAreas import * class SMBautoregression(object): @@ -23,4 +23,7 @@ self.phi = np.nan self.basin_id = np.nan + self.lapserates = np.nan + self.elevationbins = np.nan + self.refelevation = np.nan self.steps_per_step = 1 self.averaging = 0 @@ -38,5 +41,5 @@ s += '{}\n'.format(fielddisplay(self, 'num_basins', 'number of different basins [unitless]')) s += '{}\n'.format(fielddisplay(self, 'basin_id', 'basin number assigned to each element [unitless]')) - s += '{}\n'.format(fielddisplay(self, 'beta0', 'basin-specific intercept values [m ice eq./yr]')) + s += '{}\n'.format(fielddisplay(self, 'beta0', 'basin-specific intercept values [m ice eq./yr] (if beta_1==0 mean=beta_0/(1-sum(phi)))')) s += '{}\n'.format(fielddisplay(self, 'beta1', 'basin-specific trend values [m ice eq. yr^(-2)]')) s += '{}\n'.format(fielddisplay(self, 'ar_order', 'order of the autoregressive model [unitless]')) @@ -44,6 +47,7 @@ s += '{}\n'.format(fielddisplay(self, 'ar_timestep', 'time resolution of the autoregressive model [yr]')) s += '{}\n'.format(fielddisplay(self, 'phi', 'basin-specific vectors of lag coefficients [unitless]')) - s += '{}\n'.format(fielddisplay(self, 'covmat', 'inter-basin covariance matrix for multivariate normal noise at each time step [m^2 ice eq. yr^(-2)]')) - s += '{}\n'.format(fielddisplay(self, 'randomflag', 'whether to apply real randomness (true) or pseudo-randomness with fixed seed (false)')) + s += '{}\n'.format(fielddisplay(self, 'lapserates', 'basin-specific SMB lapse rates applied in each elevation bin, 1 row per basin, 1 column per bin [m ice eq yr^-1 m^-1] (default: no lapse rate)')) + s += '{}\n'.format(fielddisplay(self, 'elevationbins', 'basin-specific SMB lapse rates applied in range of SMB<0 [m ice eq yr^-1 m^-1] (default: no lapse rate)')) + s += '{}\n'.format(fielddisplay(self, 'refelevation', 'basin-specific reference elevations at which SMB is calculated, and from which SMB is downscaled using lapserates (default: basin mean elevation) [m]')) s += '{}\n'.format(fielddisplay(self, 'steps_per_step', 'number of smb steps per time step')) s += '{}\n'.format(fielddisplay(self, 'averaging', 'averaging methods from short to long steps')) @@ -91,4 +95,7 @@ md = checkfield(md, 'fieldname', 'smb.num_basins', 'numel', 1, 'NaN', 1, 'Inf', 1, '>', 0) md = checkfield(md, 'fieldname', 'smb.basin_id', 'Inf', 1, '>=', 0, '<=', md.smb.num_basins, 'size', [md.mesh.numberofelements]) + if len(np.shape(self.beta0)) == 1: + self.beta0 = np.array([self.beta0]) + self.beta1 = np.array([self.beta1]) md = checkfield(md, 'fieldname', 'smb.beta0', 'NaN', 1, 'Inf', 1, 'size', [1, md.smb.num_basins], 'numel', md.smb.num_basins) # Scheme fails if passed as column vector md = checkfield(md, 'fieldname', 'smb.beta1', 'NaN', 1, 'Inf', 1, 'size', [1, md.smb.num_basins], 'numel', md.smb.num_basins) # Scheme fails if passed as column vector; NOTE: As opposed to MATLAB implementation, pass list @@ -97,4 +104,33 @@ md = checkfield(md, 'fieldname', 'smb.ar_timestep', 'numel', 1, 'NaN', 1, 'Inf', 1, '>=', md.timestepping.time_step) # Autoregression time step cannot be finer than ISSM timestep md = checkfield(md, 'fieldname', 'smb.phi', 'NaN', 1, 'Inf', 1, 'size', [md.smb.num_basins, md.smb.ar_order]) + + if(np.any(np.isnan(self.refelevation) is False) or np.size(self.refelevation) > 1): + if len(np.shape(self.refelevation)) == 1: + self.refelevation = np.array([self.refelevation]) + md = checkfield(md, 'fieldname', 'smb.refelevation', 'NaN', 1, 'Inf', 1, '>=', 0, 'size', [1, md.smb.num_basins], 'numel', md.smb.num_basins) + + if(np.any(np.isnan(self.lapserates) is False) or np.size(self.lapserates) > 1): + if len(np.shape(self.lapserates)) == 1: + self.lapserates = np.array([self.lapserates]) + nbins = 1 + else: + nbins = np.shape(self.lapserates)[1] + if len(np.shape(self.elevationbins)) == 1: + self.elevationbins = np.array([self.elevationbins]) + md = checkfield(md, 'fieldname', 'smb.lapserates', 'NaN', 1, 'Inf', 1, 'size', [md.smb.num_basins, nbins], 'numel', md.smb.num_basins*nbins) + md = checkfield(md, 'fieldname', 'smb.elevationbins', 'NaN', 1, 'Inf', 1, 'size', [md.smb.num_basins, nbins-1], 'numel', md.smb.num_basins*(nbins-1)) + for rr in range(md.smb.num_basins): + if(np.all(self.elevationbins[rr,0:-1]<=self.elevationbins[rr,1:])==False): + raise TypeError('md.smb.elevationbins should have rows in order of increasing elevation') + elif(np.any(np.isnan(self.elevationbins) is False) or np.size(self.elevationbins) > 1): + #elevationbins specified but not lapserates: this will inevitably lead to inconsistencies + if len(np.shape(self.elevationbins)) == 1: + self.elevationbins = np.array([self.elevationbins]) + nbins = 1 + else: + nbins = np.shape(self.elevationbins)[1]+1 + md = checkfield(md, 'fieldname', 'smb.lapserates', 'NaN', 1, 'Inf', 1, 'size', [md.smb.num_basins, nbins], 'numel', md.smb.num_basins*nbins) + md = checkfield(md, 'fieldname', 'smb.elevationbins', 'NaN', 1, 'Inf', 1, 'size', [md.smb.num_basins, nbins-1], 'numel', md.smb.num_basins*(nbins-1)) + md = checkfield(md, 'fieldname', 'smb.steps_per_step', '>=', 1, 'numel', [1]) md = checkfield(md, 'fieldname', 'smb.averaging', 'numel', [1], 'values', [0, 1, 2]) @@ -106,13 +142,37 @@ yts = md.constants.yts - WriteData(fid, prefix, 'name', 'md.smb.model', 'data', 55, 'format', 'Integer') + templapserates = np.copy(md.smb.lapserates) + tempelevationbins = np.copy(md.smb.elevationbins) + temprefelevation = np.copy(md.smb.refelevation) + if(np.any(np.isnan(md.smb.lapserates))): + templapserates = np.zeros((md.smb.num_basins,2)) + print(' smb.lapserates not specified: set to 0') + tempelevationbins = np.zeros((md.smb.num_basins,1)) #dummy elevation bins + if(np.any(np.isnan(md.smb.refelevation))): + temprefelevation = np.zeros((md.smb.num_basins)).reshape(1,md.smb.num_basins) + areas = GetAreas(md.mesh.elements, md.mesh.x, md.mesh.y) + for ii, bid in enumerate(np.unique(md.smb.basin_id)): + indices = np.where(md.smb.basin_id == bid)[0] + elemsh = np.zeros((len(indices))) + for jj in range(len(indices)): + elemsh[jj] = np.mean(md.geometry.surface[md.mesh.elements[indices[jj], :] - 1]) + temprefelevation[0, ii] = np.sum(areas[indices] * elemsh) / np.sum(areas[indices]) + if(np.any(templapserates != 0)): + print(' smb.refelevation not specified: Reference elevations set to mean surface elevation of basins') + nbins = np.shape(templapserates)[1] + + WriteData(fid, prefix, 'name', 'md.smb.model', 'data', 13, 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'num_basins', 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'ar_order', 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'ar_initialtime', 'format', 'Double', 'scale', yts) WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'ar_timestep', 'format', 'Double', 'scale', yts) - WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'basin_id', 'data', self.basin_id, 'name', 'md.smb.basin_id', 'format', 'IntMat', 'mattype', 2) # 0-indexed + WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'basin_id', 'data', self.basin_id - 1, 'name', 'md.smb.basin_id', 'format', 'IntMat', 'mattype', 2) # 0-indexed WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'beta0', 'format', 'DoubleMat', 'name', 'md.smb.beta0', 'scale', 1 / yts, 'yts', yts) WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'beta1', 'format', 'DoubleMat', 'name', 'md.smb.beta1', 'scale', 1 / (yts ** 2), 'yts', yts) WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'phi', 'format', 'DoubleMat', 'name', 'md.smb.phi', 'yts', yts) + WriteData(fid, prefix, 'data', templapserates, 'name', 'md.smb.lapserates', 'format', 'DoubleMat', 'scale', 1 / yts, 'yts', yts) + WriteData(fid, prefix, 'data', tempelevationbins, 'name', 'md.smb.elevationbins', 'format', 'DoubleMat') + WriteData(fid, prefix, 'data', temprefelevation, 'name', 'md.smb.refelevation', 'format', 'DoubleMat') + WriteData(fid, prefix, 'data', nbins, 'name', 'md.smb.num_bins', 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'fieldname', 'steps_per_step', 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'fieldname', 'averaging', 'format', 'Integer') Index: /issm/trunk/src/m/classes/SMBpddSicopolis.py =================================================================== --- /issm/trunk/src/m/classes/SMBpddSicopolis.py (revision 27034) +++ /issm/trunk/src/m/classes/SMBpddSicopolis.py (revision 27035) @@ -129,5 +129,5 @@ WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 's0t', 'format', 'DoubleMat', 'mattype', 1) WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'rlaps', 'format', 'Double') - WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'monthlytemperatures', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts) + WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'monthlytemperatures', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts) WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'precipitation', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts) WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'temperature_anomaly', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts) Index: /issm/trunk/src/m/classes/autoregressionlinearbasalforcings.m =================================================================== --- /issm/trunk/src/m/classes/autoregressionlinearbasalforcings.m (revision 27035) +++ /issm/trunk/src/m/classes/autoregressionlinearbasalforcings.m (revision 27035) @@ -0,0 +1,117 @@ +%AUTOREGRESSION LINEAR BASAL FORCINGS class definition +% +% Usage: +% autoregressionlinearbasalforcings=spatiallinearbasalforcings(); + +classdef autoregressionlinearbasalforcings + + %VV: not verified yet (27Jan2022) + + properties (SetAccess=public) + num_basins = 0; + beta0 = NaN; + beta1 = NaN; + ar_order = 0; + ar_initialtime = 0; + ar_timestep = 0; + phi = NaN; + basin_id = NaN; + groundedice_melting_rate = NaN; + deepwater_elevation = NaN; + upperwater_melting_rate = NaN; + upperwater_elevation = NaN; + geothermalflux = NaN; + end + methods + function self = autoregressionlinearbasalforcings(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + otherwise + error('constructor not supported'); + end + end % }}} + function self = extrude(self,md) % {{{ + self.groundedice_melting_rate=project3d(md,'vector',self.groundedice_melting_rate,'type','node','layer',1); + self.deepwater_elevation=project3d(md,'vector',self.deepwater_elevation,'type','node','layer',1); + self.upperwater_melting_rate=project3d(md,'vector',self.upperwater_melting_rate,'type','node','layer',1); + self.upperwater_elevation=project3d(md,'vector',self.upperwater_elevation,'type','node','layer',1); + self.geothermalflux=project3d(md,'vector',self.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux + end % }}} + function self = initialize(self,md) % {{{ + + if isnan(self.groundedice_melting_rate), + self.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + disp(' no basalforcings.groundedice_melting_rate specified: values set as zero'); + end + + end % }}} + function self = setdefaultparameters(self) % {{{ + %Nothing for now + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + + if ismember('MasstransportAnalysis',analyses) & ~(strcmp(solution,'TransientSolution') & md.transient.ismasstransport==0), + md = checkfield(md,'fieldname','basalforcings.num_basins','numel',1,'NaN',1,'Inf',1,'>',0); + md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1); + md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','NaN',1,'Inf',1,'size',[1,md.basalforcings.num_basins],'numel',md.basalforcings.num_basins); + md = checkfield(md,'fieldname','basalforcings.upperwater_melting_rate','NaN',1,'Inf',1,'>=',0,'size',[1,md.basalforcings.num_basins],'numel',md.basalforcings.num_basins); + md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','NaN',1,'Inf',1,'<=',0,'size',[1,md.basalforcings.num_basins],'numel',md.basalforcings.num_basins); + md = checkfield(md,'fieldname','basalforcings.basin_id','Inf',1,'>=',0,'<=',md.basalforcings.num_basins,'size',[md.mesh.numberofelements,1]); + md = checkfield(md,'fieldname','basalforcings.beta0','NaN',1,'Inf',1,'size',[1,md.basalforcings.num_basins],'numel',md.basalforcings.num_basins); + md = checkfield(md,'fieldname','basalforcings.beta1','NaN',1,'Inf',1,'size',[1,md.basalforcings.num_basins],'numel',md.basalforcings.num_basins); + md = checkfield(md,'fieldname','basalforcings.ar_order','numel',1,'NaN',1,'Inf',1,'>=',0); + md = checkfield(md,'fieldname','basalforcings.ar_initialtime','numel',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','basalforcings.ar_timestep','numel',1,'NaN',1,'Inf',1,'>=',md.timestepping.time_step); %autoregression time step cannot be finer than ISSM timestep + md = checkfield(md,'fieldname','basalforcings.phi','NaN',1,'Inf',1,'size',[md.basalforcings.num_basins,md.basalforcings.ar_order]); + end + if ismember('BalancethicknessAnalysis',analyses), + error('not implemented yet!'); + end + if ismember('ThermalAnalysis',analyses) & ~(strcmp(solution,'TransientSolution') & md.transient.isthermal==0), + error('not implemented yet!'); + end + if numel(md.basalforcings.geothermalflux)>1 + md = checkfield(md,'fieldname','basalforcings.geothermalflux','NaN',1,'Inf',1,'timeseries',1,'>=',0); + end + end % }}} + function disp(self) % {{{ + disp(sprintf(' autoregression linear basal forcings parameters:')); + disp(sprintf(' autoregressive model is applied for deepwater_melting_rate')); + + fielddisplay(self,'num_basins','number of different basins [unitless]'); + fielddisplay(self,'basin_id','basin number assigned to each element [unitless]'); + fielddisplay(self,'beta0','basin-specific intercept values [m/yr] (if beta_1==0 mean=beta_0/(1-sum(phi)))'); + fielddisplay(self,'beta1','basin-specific trend values [m yr^(-2)]'); + fielddisplay(self,'ar_order','order of the autoregressive model [unitless]'); + fielddisplay(self,'ar_initialtime','initial time assumed in the autoregressive model parameterization [yr]'); + fielddisplay(self,'ar_timestep','time resolution of the autoregressive model [yr]'); + fielddisplay(self,'phi','basin-specific vectors of lag coefficients [unitless]'); + fielddisplay(self,'deepwater_elevation','basin-specific elevation of ocean deepwater [m]'); + fielddisplay(self,'upperwater_melting_rate','basin-specific basal melting rate (positive if melting applied for floating ice whith base >= upperwater_elevation) [m/yr]'); + fielddisplay(self,'upperwater_elevation','basin-specific elevation of ocean upperwater [m]'); + fielddisplay(self,'groundedice_melting_rate','node-specific basal melting rate (positive if melting) [m/yr]'); + fielddisplay(self,'geothermalflux','node-specific geothermal heat flux [W/m^2]'); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ + + yts=md.constants.yts; + + WriteData(fid,prefix,'name','md.basalforcings.model','data',9,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','groundedice_melting_rate','format','DoubleMat','name','md.basalforcings.groundedice_melting_rate','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'fieldname','geothermalflux','name','md.basalforcings.geothermalflux','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'fieldname','num_basins','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','ar_order','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','ar_initialtime','format','Double','scale',yts); + WriteData(fid,prefix,'object',self,'fieldname','ar_timestep','format','Double','scale',yts); + WriteData(fid,prefix,'object',self,'fieldname','basin_id','data',self.basin_id-1,'name','md.basalforcings.basin_id','format','IntMat','mattype',2); %0-indexed + WriteData(fid,prefix,'object',self,'fieldname','beta0','format','DoubleMat','name','md.basalforcings.beta0','scale',1./yts,'yts',yts); + WriteData(fid,prefix,'object',self,'fieldname','beta1','format','DoubleMat','name','md.basalforcings.beta1','scale',1./(yts^2),'yts',yts); + WriteData(fid,prefix,'object',self,'fieldname','phi','format','DoubleMat','name','md.basalforcings.phi','yts',yts); + WriteData(fid,prefix,'object',self,'fieldname','deepwater_elevation','format','DoubleMat','name','md.basalforcings.deepwater_elevation'); + WriteData(fid,prefix,'object',self,'fieldname','upperwater_melting_rate','format','DoubleMat','name','md.basalforcings.upperwater_melting_rate','scale',1./yts); + WriteData(fid,prefix,'object',self,'fieldname','upperwater_elevation','format','DoubleMat','name','md.basalforcings.upperwater_elevation'); + end % }}} + end +end Index: /issm/trunk/src/m/classes/autoregressionlinearbasalforcings.py =================================================================== --- /issm/trunk/src/m/classes/autoregressionlinearbasalforcings.py (revision 27035) +++ /issm/trunk/src/m/classes/autoregressionlinearbasalforcings.py (revision 27035) @@ -0,0 +1,122 @@ +import numpy as np + +from checkfield import * +from fielddisplay import fielddisplay +from project3d import * +from WriteData import * + +class autoregressionlinearbasalforcings(object): + """autoregressionlinearbasalforcings class definition + + Usage: + autoregressionlinearbasalforcings = autoregressionlinearbasalforcings() + """ + + def __init__(self, *args): # {{{ + self.num_basins = 0 + self.beta0 = np.nan + self.beta1 = np.nan + self.ar_order = 0 + self.ar_initialtime = 0 + self.ar_timestep = 0 + self.phi = np.nan + self.basin_id = np.nan + self.groundedice_melting_rate = np.nan + self.deepwater_elevation = np.nan + self.upperwater_melting_rate = np.nan + self.upperwater_elevation = np.nan + self.geothermalflux = np.nan + + nargs = len(args) + if nargs == 0: + self.setdefaultparameters() + else: + raise Exception('constructor not supported') + # }}} + + def __repr__(self): # {{{ + s = ' surface forcings parameters:\n' + s += ' autoregressive model is applied for deepwater_melting_rate\n' + s += '{}\n'.format(fielddisplay(self, 'num_basins', 'number of different basins [unitless]')) + s += '{}\n'.format(fielddisplay(self, 'basin_id', 'basin number assigned to each element [unitless]')) + s += '{}\n'.format(fielddisplay(self, 'beta0', 'basin-specific intercept values [m ice eq./yr] (if beta_1==0 mean=beta_0/(1-sum(phi)))')) + s += '{}\n'.format(fielddisplay(self, 'beta1', 'basin-specific trend values [m ice eq. yr^(-2)]')) + s += '{}\n'.format(fielddisplay(self, 'ar_order', 'order of the autoregressive model [unitless]')) + s += '{}\n'.format(fielddisplay(self, 'ar_initialtime', 'initial time assumed in the autoregressive model parameterization [yr]')) + s += '{}\n'.format(fielddisplay(self, 'ar_timestep', 'time resolution of the autoregressive model [yr]')) + s += '{}\n'.format(fielddisplay(self, 'phi', 'basin-specific vectors of lag coefficients [unitless]')) + s += '{}\n'.format(fielddisplay(self, 'deepwater_elevation', 'basin-specific elevation of ocean deepwater [m]')) + s += '{}\n'.format(fielddisplay(self, 'upperwater_melting_rate', 'basin-specic basal melting rate (positive if melting applied for floating ice whith base >= upperwater_elevation) [m/yr]')) + s += '{}\n'.format(fielddisplay(self, 'upperwater_elevation', 'basin-specific elevation of ocean upperwater [m]')) + s += '{}\n'.format(fielddisplay(self, 'groundedice_melting_rate','node-specific basal melting rate (positive if melting) [m/yr]')) + s += '{}\n'.format(fielddisplay(self, 'geothermalflux','node-specific geothermal heat flux [W/m^2]')) + return s + # }}} + + def setdefaultparameters(self): #{{{ + #Nothing for now + return self + # }}} + + def extrude(self, md): # {{{ + return self # Nothing for now + # }}} + + def initialize(self, md): # {{{ + if np.all(np.isnan(self.groundedice_melting_rate)): + self.groundedice_melting_rate = np.zeros((md.mesh.numberofvertices)) + print(" no basalforcings.groundedice_melting_rate specified: values set as zero") + return self + # }}} + + def checkconsistency(self, md, solution, analyses): # {{{ + if 'MasstransportAnalysis' in analyses: + md = checkfield(md, 'fieldname', 'basalforcings.num_basins', 'numel', 1, 'NaN', 1, 'Inf', 1, '>', 0) + md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1) + + if len(np.shape(self.deepwater_elevation)) == 1: + self.deepwater_elevation = np.array([self.deepwater_elevation]) + self.upperwater_elevation = np.array([self.upperwater_elevation]) + self.upperwater_melting_rate = np.array([self.upperwater_melting_rate]) + md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', 'NaN', 1, 'Inf', 1, 'size', [1, md.basalforcings.num_basins], 'numel', md.basalforcings.num_basins) + md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', 'NaN', 1, 'Inf', 1, '<=', 0, 'size', [1, md.basalforcings.num_basins], 'numel', md.basalforcings.num_basins) + md = checkfield(md, 'fieldname', 'basalforcings.upperwater_melting_rate', 'NaN', 1, 'Inf', 1,'>=', 0, 'size', [1, md.basalforcings.num_basins], 'numel', md.basalforcings.num_basins) + md = checkfield(md, 'fieldname', 'basalforcings.basin_id', 'Inf', 1, '>=', 0, '<=', md.basalforcings.num_basins, 'size', [md.mesh.numberofelements]) + + if len(np.shape(self.beta0)) == 1: + self.beta0 = np.array([self.beta0]) + self.beta1 = np.array([self.beta1]) + + md = checkfield(md, 'fieldname', 'basalforcings.beta0', 'NaN', 1, 'Inf', 1, 'size', [1, md.basalforcings.num_basins], 'numel', md.basalforcings.num_basins) # Scheme fails if passed as column vector + md = checkfield(md, 'fieldname', 'basalforcings.beta1', 'NaN', 1, 'Inf', 1, 'size', [1, md.basalforcings.num_basins], 'numel', md.basalforcings.num_basins) # Scheme fails if passed as column vector; NOTE: As opposed to MATLAB implementation, pass list + md = checkfield(md, 'fieldname', 'basalforcings.ar_order', 'numel', 1, 'NaN', 1, 'Inf', 1, '>=', 0) + md = checkfield(md, 'fieldname', 'basalforcings.ar_initialtime', 'numel', 1, 'NaN', 1, 'Inf', 1) + md = checkfield(md, 'fieldname', 'basalforcings.ar_timestep', 'numel', 1, 'NaN', 1, 'Inf', 1, '>=', md.timestepping.time_step) # Autoregression time step cannot be finer than ISSM timestep + md = checkfield(md, 'fieldname', 'basalforcings.phi', 'NaN', 1, 'Inf', 1, 'size', [md.basalforcings.num_basins, md.basalforcings.ar_order]) + if 'BalancethicknessAnalysis' in analyses: + raise Exception('not implemented yet!') + if 'ThermalAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.isthermal: + raise Exception('not implemented yet!') + + return md + # }}} + + def marshall(self, prefix, md, fid): # {{{ + yts = md.constants.yts + + WriteData(fid, prefix, 'name', 'md.basalforcings.model', 'data', 9, 'format', 'Integer') + WriteData(fid, prefix, 'object', self, 'fieldname', 'groundedice_melting_rate', 'name', 'md.basalforcings.groundedice_melting_rate', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts) + WriteData(fid, prefix, 'object', self, 'fieldname', 'geothermalflux', 'name', 'md.basalforcings.geothermalflux', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts) + WriteData(fid, prefix, 'object', self, 'fieldname', 'num_basins', 'format', 'Integer') + WriteData(fid, prefix, 'object', self, 'fieldname', 'ar_order', 'format', 'Integer') + WriteData(fid, prefix, 'object', self, 'fieldname', 'ar_initialtime', 'format', 'Double', 'scale', yts) + WriteData(fid, prefix, 'object', self, 'fieldname', 'ar_timestep', 'format', 'Double', 'scale', yts) + WriteData(fid, prefix, 'object', self, 'fieldname', 'basin_id', 'data', self.basin_id - 1, 'name', 'md.basalforcings.basin_id', 'format', 'IntMat', 'mattype', 2) # 0-indexed + WriteData(fid, prefix, 'object', self, 'fieldname', 'beta0', 'format', 'DoubleMat', 'name', 'md.basalforcings.beta0', 'scale', 1 / yts, 'yts', yts) + WriteData(fid, prefix, 'object', self, 'fieldname', 'beta1', 'format', 'DoubleMat', 'name', 'md.basalforcings.beta1', 'scale', 1 / (yts ** 2), 'yts', yts) + WriteData(fid, prefix, 'object', self, 'fieldname', 'phi', 'format', 'DoubleMat', 'name', 'md.basalforcings.phi', 'yts', yts) + WriteData(fid, prefix, 'object', self, 'fieldname', 'deepwater_elevation', 'format', 'DoubleMat', 'name', 'md.basalforcings.deepwater_elevation') + WriteData(fid, prefix, 'object', self, 'fieldname', 'upperwater_melting_rate', 'format', 'DoubleMat', 'name', 'md.basalforcings.upperwater_melting_rate', 'scale', 1 / yts, 'yts', yts) + WriteData(fid, prefix, 'object', self, 'fieldname', 'upperwater_elevation', 'format', 'DoubleMat', 'name', 'md.basalforcings.upperwater_elevation') + + # }}} Index: /issm/trunk/src/m/classes/basalforcings.m =================================================================== --- /issm/trunk/src/m/classes/basalforcings.m (revision 27034) +++ /issm/trunk/src/m/classes/basalforcings.m (revision 27035) @@ -15,4 +15,6 @@ case 0 self=setdefaultparameters(self); + case 1 + self =structtoobj(basalforcings(),varargin{1}); otherwise error('constructor not supported'); Index: /issm/trunk/src/m/classes/calvingparameterization.m =================================================================== --- /issm/trunk/src/m/classes/calvingparameterization.m (revision 27035) +++ /issm/trunk/src/m/classes/calvingparameterization.m (revision 27035) @@ -0,0 +1,98 @@ +%CALVINGPARAMETERIZATION class definition +% For test calving laws and coefficients +% Usage: +% calvingparameterization=calvingparameterization(); + +classdef calvingparameterization + properties (SetAccess=public) + stress_threshold_groundedice = 0.; + stress_threshold_floatingice = 0.; + min_thickness = 0.; + use_param = 0; + scale_theta = 0.; + amp_alpha = 0; + midp = 0; + nonlinearlaw = 0; + end + methods + function self = calvingparameterization(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + case 1 + inputstruct=varargin{1}; + list1 = properties('calvingparameterization'); + list2 = fieldnames(inputstruct); + for i=1:length(list1) + fieldname = list1{i}; + if ismember(fieldname,list2), + self.(fieldname) = inputstruct.(fieldname); + end + end + otherwise + error('constructor not supported'); + end + end % }}} + function self = extrude(self,md) % {{{ + end % }}} + function self = setdefaultparameters(self) % {{{ + + %Default sigma max + self.stress_threshold_groundedice = 1e6; + self.stress_threshold_floatingice = 150e3; + + %For now we turn this off by setting the threshold to 0 + self.min_thickness = 0.; + + %parameters for the spatial temporal seperation + %The coefficient follows: \gamma = \frac{\theta}{2}(1-\tanh(\frac{b+p}{\alpha}))+(1-\theta) + % 0 - Use bed elevation, 1 - use heigh above floatation + self.use_param = 0; + % between 0 and 1, larger theta means more reduction for shallower ice + self.scale_theta = 0; + % alpha in the denominator + self.amp_alpha = 0; + % mid-point of this step function + self.midp = 0; + % if use a nonlinear calving law + self.nonlinearlaw = 0; + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + %Early return + if (~strcmp(solution,'TransientSolution') | md.transient.ismovingfront==0), return; end + + md = checkfield(md,'fieldname','calving.stress_threshold_groundedice','>',0,'nan',1,'Inf',1); + md = checkfield(md,'fieldname','calving.stress_threshold_floatingice','>',0,'nan',1,'Inf',1); + md = checkfield(md,'fieldname','calving.min_thickness','>=',0,'NaN',1,'Inf',1,'numel',1); + md = checkfield(md,'fieldname','calving.use_param','values',[-1, 0, 1, 2, 3, 4]); + md = checkfield(md,'fieldname','calving.scale_theta','NaN',1,'Inf',1,'numel',1); + md = checkfield(md,'fieldname','calving.amp_alpha','<>',0,'NaN',1,'Inf',1,'numel',1); + md = checkfield(md,'fieldname','calving.midp','NaN',1,'Inf',1,'numel',1); + md = checkfield(md,'fieldname','calving.nonlinearlaw','values',[0, 1]); + end % }}} + function disp(self) % {{{ + disp(sprintf(' Calving test parameters:')); + fielddisplay(self,'stress_threshold_groundedice','sigma_max applied to grounded ice only [Pa]'); + fielddisplay(self,'stress_threshold_floatingice','sigma_max applied to floating ice only [Pa]'); + fielddisplay(self,'min_thickness','minimum thickness below which no ice is allowed [m]'); + fielddisplay(self,'use_param','0 - Use bed elevation, 1 - use heigh above floatation, 2 - use ice thickness'); + fielddisplay(self,'scale_theta','larger than 0, larger theta means more reduction for shallower ice'); + fielddisplay(self,'amp_alpha','alpha'); + fielddisplay(self,'midp','mid-point'); + fielddisplay(self,'nonlinearlaw','use a nonlinear law'); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ + yts=md.constants.yts; + WriteData(fid,prefix,'name','md.calving.law','data',9,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','stress_threshold_groundedice','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','stress_threshold_floatingice','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','min_thickness','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','use_param','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','scale_theta','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','amp_alpha','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','midp','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','nonlinearlaw','format','Integer'); + end % }}} + end +end Index: /issm/trunk/src/m/classes/calvingtest.m =================================================================== --- /issm/trunk/src/m/classes/calvingtest.m (revision 27035) +++ /issm/trunk/src/m/classes/calvingtest.m (revision 27035) @@ -0,0 +1,54 @@ +%CALVINGTEST class definition +% For testing calving laws and coefficients +% Usage: +% calvingtest=calvingtest(); + +classdef calvingtest + properties (SetAccess=public) + speedfactor = 1; + independentrate = 0; + end + methods + function self = calvingtest(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + case 1 + inputstruct=varargin{1}; + list1 = properties('calvingtest'); + list2 = fieldnames(inputstruct); + for i=1:length(list1) + fieldname = list1{i}; + if ismember(fieldname,list2), + self.(fieldname) = inputstruct.(fieldname); + end + end + otherwise + error('constructor not supported'); + end + end % }}} + function self = extrude(self,md) % {{{ + end % }}} + function self = setdefaultparameters(self) % {{{ + self.speedfactor = 1; + self.independentrate = 0; + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + %Early return + if (~strcmp(solution,'TransientSolution') | md.transient.ismovingfront==0), return; end + md = checkfield(md,'fieldname','calving.speedfactor','>=',0,'NaN',1,'Inf',1, 'singletimeseries', 1); + md = checkfield(md,'fieldname','calving.independentrate','NaN',1,'Inf',1, 'singletimeseries', 1); + end % }}} + function disp(self) % {{{ + disp(sprintf(' Calving test parameters:')); + fielddisplay(self,'speedfactor','calving rate is proportional to the ice velocity (e.g. speedfactor=1 -> calving front should not move)'); + fielddisplay(self,'independentrate','calving rate is independent of the ice velocity.'); + end % }}} + function marshall(self,prefix,md,fid) % {{{ + yts=md.constants.yts; + WriteData(fid,prefix,'name','md.calving.law','data',8,'format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','speedfactor','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'fieldname','independentrate','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts,'scale',1./yts); + end % }}} + end +end Index: /issm/trunk/src/m/classes/calvingvonmises.m =================================================================== --- /issm/trunk/src/m/classes/calvingvonmises.m (revision 27034) +++ /issm/trunk/src/m/classes/calvingvonmises.m (revision 27035) @@ -44,6 +44,6 @@ if (~strcmp(solution,'TransientSolution') | md.transient.ismovingfront==0), return; end - md = checkfield(md,'fieldname','calving.stress_threshold_groundedice','>',0,'NaN',1,'Inf',1); - md = checkfield(md,'fieldname','calving.stress_threshold_floatingice','>',0,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','calving.stress_threshold_groundedice','>',0,'NaN',1,'Inf',1,'size','universal'); + md = checkfield(md,'fieldname','calving.stress_threshold_floatingice','>',0,'NaN',1,'Inf',1,'size','universal'); md = checkfield(md,'fieldname','calving.min_thickness','>=',0,'NaN',1,'Inf',1,'numel',1); end % }}} @@ -58,6 +58,6 @@ yts=md.constants.yts; WriteData(fid,prefix,'name','md.calving.law','data',2,'format','Integer'); - WriteData(fid,prefix,'object',self,'fieldname','stress_threshold_groundedice','format','DoubleMat','mattype',1); - WriteData(fid,prefix,'object',self,'fieldname','stress_threshold_floatingice','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','stress_threshold_groundedice','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'fieldname','stress_threshold_floatingice','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); WriteData(fid,prefix,'object',self,'fieldname','min_thickness','format','Double'); end % }}} Index: /issm/trunk/src/m/classes/calvingvonmises.py =================================================================== --- /issm/trunk/src/m/classes/calvingvonmises.py (revision 27034) +++ /issm/trunk/src/m/classes/calvingvonmises.py (revision 27035) @@ -48,6 +48,6 @@ return - md = checkfield(md, 'fieldname', 'calving.stress_threshold_groundedice', '>', 0, 'nan', 1, 'Inf', 1) - md = checkfield(md, 'fieldname', 'calving.stress_threshold_floatingice', '>', 0, 'nan', 1, 'Inf', 1) + md = checkfield(md, 'fieldname', 'calving.stress_threshold_groundedice', '>', 0, 'nan', 1, 'Inf', 1, 'size', 'universal') + md = checkfield(md, 'fieldname', 'calving.stress_threshold_floatingice', '>', 0, 'nan', 1, 'Inf', 1, 'size', 'universal') md = checkfield(md, 'fieldname', 'calving.min_thickness', '>=', 0, 'NaN', 1, 'Inf', 1, 'numel', [1]) @@ -56,7 +56,8 @@ def marshall(self, prefix, md, fid): # {{{ + yts = md.constants.yts WriteData(fid, prefix, 'name', 'md.calving.law', 'data', 2, 'format', 'Integer') - WriteData(fid, prefix, 'object', self, 'fieldname', 'stress_threshold_groundedice', 'format', 'DoubleMat', 'mattype', 1) - WriteData(fid, prefix, 'object', self, 'fieldname', 'stress_threshold_floatingice', 'format', 'DoubleMat', 'mattype', 1) + WriteData(fid, prefix, 'object', self, 'fieldname', 'stress_threshold_groundedice', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts ) + WriteData(fid, prefix, 'object', self, 'fieldname', 'stress_threshold_floatingice', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts) WriteData(fid, prefix, 'object', self, 'fieldname', 'min_thickness', 'format', 'Double') # }}} Index: /issm/trunk/src/m/classes/clusters/computecanada.m =================================================================== --- /issm/trunk/src/m/classes/clusters/computecanada.m (revision 27035) +++ /issm/trunk/src/m/classes/clusters/computecanada.m (revision 27035) @@ -0,0 +1,133 @@ +%COMPUTECANADA class definition +% +% Usage: +% cluster=computecanada(); +% cluster=computecanada('np',3); +% cluster=computecanada('np',3,'login','username'); + +classdef computecanada + properties (SetAccess=public) + % {{{ + name = '' + login = ''; + numtasks = 1; + cpuspertask = 8; + port = 0; + projectaccount = ''; + codepath = ''; + executionpath = ''; + time = 24*60; + memory = 2; + email = ''; + mailtype = ''; + end + %}}} + methods + function cluster=computecanada(varargin) % {{{ + + %initialize cluster using default settings if provided + if (exist('computecanada_settings')==2), computecanada_settings; end + + %use provided options to change fields + cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); + end + %}}} + function disp(cluster) % {{{ + % display the object + disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); + disp(sprintf(' name: %s',cluster.name)); + disp(sprintf(' login: %s',cluster.login)); + disp(sprintf(' port: %i',cluster.port)); + disp(sprintf(' numtasks: %i',cluster.numtasks)); + disp(sprintf(' cpuspertask: %i',cluster.cpuspertask)); + disp(sprintf(' projectaccount: %s',cluster.projectaccount)); + disp(sprintf(' codepath: %s',cluster.codepath)); + disp(sprintf(' executionpath: %s',cluster.executionpath)); + disp(sprintf(' time: %i',cluster.time)); + disp(sprintf(' memory: %i',cluster.memory)); + disp(sprintf(' email: %s', cluster.email)); + disp(sprintf(' mailtype: %s', cluster.mailtype)); + + end + %}}} + function numprocs=np(cluster) % {{{ + %compute number of processors + numprocs=cluster.numtasks*cluster.cpuspertask; + end + %}}} + function md = checkconsistency(cluster,md,solution,analyses) % {{{ + if isempty(cluster.name), md = checkmessage(md,'name empty'); end + if isempty(cluster.login), md = checkmessage(md,'login empty'); end + if ~(cluster.numtasks > 0), md = checkmessage(md,'numtasks must be > 0'); end + if ~(cluster.cpuspertask > 0), md = checkmessage(md,'cpuspertask must be > 0'); end + if ~(cluster.port >= 0), md = checkmessage(md,'port must be >= 0'); end + if isempty(cluster.projectaccount), md = checkmessage(md,'projectaccount empty'); end + if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end + if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end + if ~(cluster.time > 0), md = checkmessage(md,'time must be > 0'); end + if ~(cluster.memory > 0), md = checkmessage(md,'memory must be > 0'); end + end + %}}} + function BuildKrigingQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ + error('not implemented yet'); + end + %}}} + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ + + if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end + if(isgprof), disp('gprof not supported by cluster, ignoring...'); end + + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!/bin/bash\n'); + fprintf(fid,'#SBATCH --job-name=%s\n',modelname); + fprintf(fid,'#SBATCH --account=%s \n',cluster.projectaccount); + fprintf(fid,'#SBATCH --ntasks=%i \n',cluster.numtasks); + fprintf(fid,'#SBATCH --cpus-per-task=%i\n',cluster.cpuspertask); + fprintf(fid,'#SBATCH --time=%i\n',cluster.time); %walltime is in minutes + fprintf(fid,'#SBATCH --mem-per-cpu=%igb\n',cluster.memory); %memory in in gigabytes + fprintf(fid,'#SBATCH --mail-user=%s\n',cluster.email); %email + fprintf(fid,'#SBATCH --mail-type=%s',cluster.mailtype); + fprintf(fid,'#SBATCH --output=%s.outlog \n',modelname); + fprintf(fid,'#SBATCH --error=%s.errlog \n\n',modelname); + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME + fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname); + fprintf(fid,'srun %s/issm.exe %s %s %s\n',cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end + fclose(fid); + end %}}} + function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{ + + %compress the files into one zip. + compressstring=['tar -zcf ' dirname '.tar.gz ']; + for i=1:numel(filelist), + compressstring = [compressstring ' ' filelist{i}]; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']}); + + end %}}} + function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{ + + disp('launching solution sequence on remote cluster'); + if ~isempty(restart) + launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && hostname && sbatch ' modelname '.queue ']; + else + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... + ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && hostname && sbatch ' modelname '.queue ']; + end + issmssh(cluster.name,cluster.login,cluster.port,launchcommand); + end %}}} + function Download(cluster,dirname,filelist)% {{{ + + %copy files from cluster to current directory + directory=[cluster.executionpath '/' dirname '/']; + issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); + + end %}}} + end +end Index: /issm/trunk/src/m/classes/clusters/discovery.m =================================================================== --- /issm/trunk/src/m/classes/clusters/discovery.m (revision 27035) +++ /issm/trunk/src/m/classes/clusters/discovery.m (revision 27035) @@ -0,0 +1,170 @@ +%DISCOVERY(Dartmouth) cluster class definition +% +% Usage: +% cluster=discovery(); +% cluster=discovery('np',3); +% cluster=discovery('np',3,'login','username'); + +classdef discovery + properties (SetAccess=public) + % {{{ + name = 'discovery' + login = ''; + numnodes = 1; + cpuspernode = 16; + codepath = ''; + executionpath = ''; + interactive = 0; + time = 10; %in hours + memory = 2; %in Gb + email = 'END,FAIL'; + + end + %}}} + methods + function cluster=discovery(varargin) % {{{ + + %initialize cluster using default settings if provided + if (exist('discovery_settings')==2), discovery_settings; end + + %use provided options to change fields + cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); + end + %}}} + function disp(cluster) % {{{ + % display the object + disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); + disp(sprintf(' name: %s',cluster.name)); + disp(sprintf(' login: %s',cluster.login)); + disp(sprintf(' numnodes: %i',cluster.numnodes)); + disp(sprintf(' cpuspernode: %i',cluster.cpuspernode)); + disp(sprintf(' time: %i hours',cluster.time)); + disp(sprintf(' memory: %i Gb',cluster.memory)); + disp(sprintf(' email: %s (notifications: BEGIN,END,FAIL)',cluster.email)); + disp(sprintf(' codepath: %s',cluster.codepath)); + disp(sprintf(' executionpath: %s',cluster.executionpath)); + disp(sprintf(' interactive: %i',cluster.interactive)); + end + %}}} + function numprocs=nprocs(cluster) % {{{ + %compute number of processors + numprocs=cluster.numnodes*cluster.cpuspernode; + end + %}}} + function md = checkconsistency(cluster,md,solution,analyses) % {{{ + %Miscellaneous + if isempty(cluster.login), md = checkmessage(md,'login empty'); end + if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end + if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end + end + %}}} + function BuildKrigingQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ + + if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end + if(isgprof), disp('gprof not supported by cluster, ignoring...'); end + + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!/bin/bash\n'); + fprintf(fid,'#SBATCH --job-name=%s\n',modelname); + fprintf(fid,'#SBATCH --account=ice\n'); %Make sure we use the ICE account for this run + fprintf(fid,'#SBATCH -o %s.outlog \n',modelname); + fprintf(fid,'#SBATCH -e %s.errlog \n',modelname); + fprintf(fid,'#SBATCH --nodes=%i\n',cluster.numnodes); + fprintf(fid,'#SBATCH --ntasks-per-node=%i\n',cluster.cpuspernode); + fprintf(fid,'#SBATCH --time=%s\n',datestr(cluster.time/24,'HH:MM:SS')); %walltime is in HH:MM:SS format. cluster.time is in hour + fprintf(fid,'#SBATCH --mem=%iG\n',cluster.memory); + if ~isempty(cluster.email) + fprintf(fid,'#SBATCH --mail-type=%s\n',cluster.email); + end + fprintf(fid,'\n'); + + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); + fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); + fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname); + fprintf(fid,'srun %s/kriging.exe %s %s\n', cluster.codepath,[cluster.executionpath '/' modelname],modelname); + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end + fclose(fid); + end + %}}} + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ + + if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end + if(isgprof), disp('gprof not supported by cluster, ignoring...'); end + + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!/bin/bash\n'); + fprintf(fid,'#SBATCH --job-name=%s\n',modelname); + fprintf(fid,'#SBATCH --account=ice\n'); %Make sure we use the ICE account for this run + fprintf(fid,'#SBATCH -o %s.outlog \n',modelname); + fprintf(fid,'#SBATCH -e %s.errlog \n',modelname); + fprintf(fid,'#SBATCH --nodes=%i\n',cluster.numnodes); + fprintf(fid,'#SBATCH --ntasks-per-node=%i\n',cluster.cpuspernode); + fprintf(fid,'#SBATCH --time=%s\n',datestr(cluster.time/24,'HH:MM:SS')); %walltime is in HH:MM:SS format. cluster.time is in hour + fprintf(fid,'#SBATCH --mem=%iG\n',cluster.memory); + if ~isempty(cluster.email) + fprintf(fid,'#SBATCH --mail-type=%s\n',cluster.email); + end + fprintf(fid,'\n'); + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); + fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); + fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname); + fprintf(fid,'mpirun -n %i %s/issm.exe %s %s %s\n',cluster.nprocs(), cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end + fclose(fid); + + %in interactive mode, create a run file, and errlog and outlog file + if cluster.interactive, + fid=fopen([modelname '.run'],'w'); + fprintf(fid,'mpirun -n %i %s/issm.exe %s %s %s\n',cluster.nprocs(), cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); + if ~io_gather, %concatenate the output files: + fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); + end + fclose(fid); + fid=fopen([modelname '.errlog'],'w'); + fclose(fid); + fid=fopen([modelname '.outlog'],'w'); + fclose(fid); + end + end %}}} + function UploadQueueJob(cluster,modelname,dirname,filelist) % {{{ + + %compress the files into one zip. + compressstring=['tar -zcf ' dirname '.tar.gz ']; + for i=1:numel(filelist), + compressstring = [compressstring ' ' filelist{i}]; + end + if cluster.interactive, + compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog ']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(cluster.name,cluster.executionpath,cluster.login,0,{[dirname '.tar.gz']}); + + end %}}} + function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch) % {{{ + + disp('launching solution sequence on remote cluster'); + if ~isempty(restart) + launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && hostname && sbatch ' modelname '.queue ']; + else + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... + ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && hostname && sbatch ' modelname '.queue ']; + end + issmssh(cluster.name,cluster.login,0,launchcommand); + end %}}} + function Download(cluster,dirname,filelist) % {{{ + + %copy files from cluster to current directory + directory=[cluster.executionpath '/' dirname '/']; + issmscpin(cluster.name,cluster.login,0,directory,filelist); + + end %}}} + end +end Index: /issm/trunk/src/m/classes/clusters/generic.m =================================================================== --- /issm/trunk/src/m/classes/clusters/generic.m (revision 27034) +++ /issm/trunk/src/m/classes/clusters/generic.m (revision 27035) @@ -19,5 +19,5 @@ port = 0; interactive = 1; - codepath = [IssmConfig('ISSM_PREFIX') '/bin']; + codepath = [issmdir() '/bin']; etcpath = [issmdir() '/etc']; executionpath = [issmdir() '/execution']; Index: /issm/trunk/src/m/classes/clusters/pfe.m =================================================================== --- /issm/trunk/src/m/classes/clusters/pfe.m (revision 27034) +++ /issm/trunk/src/m/classes/clusters/pfe.m (revision 27035) @@ -11,5 +11,5 @@ name = 'pfe' login = ''; - modules = {'comp-intel/2016.2.181' 'mpt'}; + modules = {'comp-intel/2018.3.222' 'mpi-intel/2018.3.222' 'scicon/app-tools'}; numnodes = 20; cpuspernode = 8; @@ -19,4 +19,5 @@ processor = 'ivy'; srcpath = ''; + extpkgpath = ''; codepath = ''; executionpath = ''; @@ -44,6 +45,6 @@ disp(sprintf(' login: %s',cluster.login)); disp(sprintf(' modules: %s',strjoin(cluster.modules,', '))); - disp(sprintf(' numnodes: %s',cluster.numnodes)); - disp(sprintf(' cpuspernode: %s',cluster.cpuspernode)); + disp(sprintf(' numnodes: %i',cluster.numnodes)); + disp(sprintf(' cpuspernode: %i',cluster.cpuspernode)); disp(sprintf(' np: %i',cluster.nprocs())); disp(sprintf(' port: %i',cluster.port)); @@ -52,8 +53,9 @@ disp(sprintf(' processor: %i',cluster.processor)); disp(sprintf(' srcpath: %s',cluster.srcpath)); + disp(sprintf(' extpkgpath: %s',cluster.extpkgpath)); disp(sprintf(' codepath: %s',cluster.codepath)); disp(sprintf(' executionpath: %s',cluster.executionpath)); disp(sprintf(' grouplist: %s',cluster.grouplist)); - disp(sprintf(' interactive: %s',cluster.interactive)); + disp(sprintf(' interactive: %i',cluster.interactive)); disp(sprintf(' bbftp: %s',cluster.bbftp)); disp(sprintf(' numstreams: %s',cluster.numstreams)); @@ -173,9 +175,11 @@ fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); fprintf(fid,'export ISSM_DIR="%s"\n',cluster.srcpath); %FIXME + if cluster.extpkgpath + fprintf(fid,'export ISSM_EXT_PKG="%s"\n',cluster.extpkgpath); + end fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME - fprintf(fid,'export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$ISSM_DIR/externalpackages/petsc/install/lib"\n'); fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname); if ~isvalgrind, - fprintf(fid,'/u/scicon/tools/bin/toss3/several_tries mpiexec -np %i %s/%s %s %s/%s %s\n',cluster.nprocs(),cluster.codepath,executable,solution,cluster.executionpath,dirname,modelname); + fprintf(fid,'/u/scicon/tools/bin/toss3/several_tries mpiexec -np %i mbind.x -cs -n%i %s/%s %s %s/%s %s\n',cluster.nprocs(),cluster.cpuspernode,cluster.codepath,executable,solution,cluster.executionpath,dirname,modelname); else fprintf(fid,'mpiexec -np %i valgrind --leak-check=full %s/%s %s %s %s\n',cluster.nprocs(),cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); Index: /issm/trunk/src/m/classes/clusters/pfe.py =================================================================== --- /issm/trunk/src/m/classes/clusters/pfe.py (revision 27034) +++ /issm/trunk/src/m/classes/clusters/pfe.py (revision 27035) @@ -28,5 +28,5 @@ self.name = '' self.login = '' - self.modules = ['comp-intel/2016.2.181', 'mpt'] + self.modules = ['comp-intel/2018.3.222', 'mpi-intel/2018.3.222', 'scicon/app-tools'] self.numnodes = 20 self.cpuspernode = 8 @@ -36,4 +36,5 @@ self.processor = 'ivy' self.srcpath = '' + self.extpkgpath = '' self.codepath = '' self.executionpath = '' @@ -72,4 +73,5 @@ s += ' processor: {}\n'.format(self.processor) s += ' srcpath: {}\n'.format(self.srcpath) + s += ' extpkgpath: {}\n'.format(self.extpkgpath) s += ' codepath: {}\n'.format(self.codepath) s += ' executionpath: {}\n'.format(self.executionpath) @@ -177,6 +179,7 @@ fid.write('export MPI_GROUP_MAX=64\n\n') fid.write('export ISSM_DIR="{}"\n'.format(self.srcpath)) # FIXME + if self.extpkgpath: + fid.write('export ISSM_EXT_PKG="{}"\n'.format(self.extpkgpath)) fid.write('source $ISSM_DIR/etc/environment.sh\n') # FIXME - fid.write('export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$ISSM_DIR/externalpackages/petsc/install/lib"\n') fid.write('cd {}/{}/\n\n'.format(self.executionpath, dirname)) fid.write('mpiexec -np {} {}/{} {} {}/{} {}\n'.format(self.nprocs(), self.codepath, executable, solution, self.executionpath, dirname, modelname)) Index: /issm/trunk/src/m/classes/clusters/saga.py =================================================================== --- /issm/trunk/src/m/classes/clusters/saga.py (revision 27034) +++ /issm/trunk/src/m/classes/clusters/saga.py (revision 27035) @@ -119,7 +119,7 @@ fid.write('#SBATCH --nodes=%i \n' % self.numnodes) - fid.write('#SBATCH --ntasks-per-node=%i \n' % self.cpuspernode) + fid.write('#SBATCH --ntasks=%i \n' % self.cpuspernode) fid.write('#SBATCH --time={}\n'.format(timestring)) #walltime is minutes - fid.write('#SBATCH --mem-per-cpu={}MB\n'.format(int(1000 * self.mem))) # mem is in MB + fid.write('#SBATCH --mem-per-cpu={}M\n'.format(int(1000 * self.mem))) # mem is in MB fid.write('#SBATCH --account=%s\n' % self.accountname) @@ -130,6 +130,6 @@ fid.write('module purge\n') fid.write('module load CMake/3.15.3-GCCcore-8.3.0\n') - fid.write('module load PETSc/3.12.4-intel-2019b\n') - fid.write('module load ParMETIS/4.0.3-iimpi-2019b\n') + fid.write('module load PETSc/3.12.4-foss-2019b\n') + fid.write('module load ParMETIS/4.0.3-gompi-2019b\n') if isvalgrind: fid.write('module --ignore-cache load Valgrind/3.16.1-gompi-2019b \n') @@ -138,9 +138,9 @@ if isvalgrind: # profiling - #fid.write('mpirun {} --tool=callgrind {}/{} {} {}/{} {} 2>{}.errlog>{}.outlog \n'.format(self.valgrind, self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname)) + #fid.write('srun {} --tool=callgrind {}/{} {} {}/{} {} 2>{}.errlog>{}.outlog \n'.format(self.valgrind, self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname)) # leak check - fid.write('mpirun {} --leak-check=full {}/{} {} {}/{} {} 2>{}.errlog>{}.outlog '.format(self.valgrind, self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname)) + fid.write('srun {} --leak-check=full {}/{} {} {}/{} {} 2>{}.errlog>{}.outlog '.format(self.valgrind, self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname)) else: - fid.write('time mpirun {}/{} {} {}/{} {}\n'.format(self.codepath, executable, solution, self.executionpath, dirname, modelname)) + fid.write('time srun {}/{} {} {}/{} {}\n'.format(self.codepath, executable, solution, self.executionpath, dirname, modelname)) fid.close() Index: /issm/trunk/src/m/classes/flowequation.js =================================================================== --- /issm/trunk/src/m/classes/flowequation.js (revision 27034) +++ /issm/trunk/src/m/classes/flowequation.js (revision 27035) @@ -22,5 +22,5 @@ fielddisplay(this,'isSSA','is the Shelfy-Stream Approximation (SSA) used ?'); fielddisplay(this,'isL1L2','is the L1L2 approximation used ?'); - fielddisplay(this,'isMLHO','is the Mono-Layer Higher-Order approximation used?'); + fielddisplay(this,'isMOLHO','is the MOno-Layer Higher-Order (MOLHO) approximation used?'); fielddisplay(this,'isHO','is the Higher-Order (HO) approximation used ?'); fielddisplay(this,'isFS','are the Full-FS (FS) equations used ?'); @@ -41,11 +41,11 @@ }// }}} - this.extrude = function(md) {//{{{ - this.element_equation=project3d(md,'vector',this.element_equation,'type','element'); - this.vertex_equation=project3d(md,'vector',this.vertex_equation,'type','node'); - this.borderSSA=project3d(md,'vector',this.borderSSA,'type','node'); - this.borderHO=project3d(md,'vector',this.borderHO,'type','node'); - this.borderFS=project3d(md,'vector',this.borderFS,'type','node'); - return this; + this.extrude = function(md) {//{{{ + this.element_equation=project3d(md,'vector',this.element_equation,'type','element'); + this.vertex_equation=project3d(md,'vector',this.vertex_equation,'type','node'); + this.borderSSA=project3d(md,'vector',this.borderSSA,'type','node'); + this.borderHO=project3d(md,'vector',this.borderHO,'type','node'); + this.borderFS=project3d(md,'vector',this.borderFS,'type','node'); + return this; }//}}} this.checkconsistency = function(md,solution,analyses) {//{{{ @@ -59,5 +59,5 @@ checkfield(md,'fieldname','flowequation.isSSA','numel',[1],'values',[0, 1]); checkfield(md,'fieldname','flowequation.isL1L2','numel',[1],'values',[0, 1]); - checkfield(md,'fieldname','flowequation.isMLHO','numel',[1],'values',[0, 1]); + checkfield(md,'fieldname','flowequation.isMOLHO','numel',[1],'values',[0, 1]); checkfield(md,'fieldname','flowequation.isHO','numel',[1],'values',[0, 1]); checkfield(md,'fieldname','flowequation.isFS','numel',[1],'values',[0, 1]); @@ -93,5 +93,5 @@ else throw Error('Case not supported yet'); - if (!(this.isSIA | this.isSSA | this.isL1L2 | this.isMLHO | this.isHO | this.isFS)){ + if (!(this.isSIA | this.isSSA | this.isL1L2 | this.isMOLHO | this.isHO | this.isFS)){ checkmessage(md,['no element types set for this model']); } @@ -108,5 +108,5 @@ WriteData(fid,prefix,'object',this,'fieldname','isSSA','format','Boolean'); WriteData(fid,prefix,'object',this,'fieldname','isL1L2','format','Boolean'); - WriteData(fid,prefix,'object',this,'fieldname','isMLHO','format','Boolean'); + WriteData(fid,prefix,'object',this,'fieldname','isMOLHO','format','Boolean'); WriteData(fid,prefix,'object',this,'fieldname','isHO','format','Boolean'); WriteData(fid,prefix,'object',this,'fieldname','isFS','format','Boolean'); @@ -138,5 +138,5 @@ this.isSSA = 0; this.isL1L2 = 0; - this.isMLHO = 0; + this.isMOLHO = 0; this.isHO = 0; this.isFS = 0; Index: /issm/trunk/src/m/classes/flowequation.m =================================================================== --- /issm/trunk/src/m/classes/flowequation.m (revision 27034) +++ /issm/trunk/src/m/classes/flowequation.m (revision 27035) @@ -9,5 +9,5 @@ isSSA = 0; isL1L2 = 0; - isMLHO = 0; + isMOLHO = 0; isHO = 0; isFS = 0; @@ -60,10 +60,11 @@ if isfield(objstruct,'borderpattyn'), self.borderHO = objstruct.borderpattyn; end; if isfield(objstruct,'borderstokes'), self.borderFS = objstruct.borderstokes; end; - end - - %Nov 6 2021 - if any(self.vertex_equation==4) - disp(['Monolayer Higher-Order (MLHO) detected in md.flowequation, this is still under development. Please double check your settings.']); - end + + %May 31 2022 + if isfield(objstruct,'isMLHO') + self.isMOLHO = objstruct.isMLHO; + end + end + end% }}} @@ -104,5 +105,5 @@ md = checkfield(md,'fieldname','flowequation.isSSA','numel',[1],'values',[0 1]); md = checkfield(md,'fieldname','flowequation.isL1L2','numel',[1],'values',[0 1]); - md = checkfield(md,'fieldname','flowequation.isMLHO','numel',[1],'values',[0 1]); + md = checkfield(md,'fieldname','flowequation.isMOLHO','numel',[1],'values',[0 1]); md = checkfield(md,'fieldname','flowequation.isHO','numel',[1],'values',[0 1]); md = checkfield(md,'fieldname','flowequation.isFS','numel',[1],'values',[0 1]); @@ -135,5 +136,5 @@ error('Case not supported yet'); end - if ~(self.isSIA || self.isSSA || self.isL1L2 || self.isMLHO || self.isHO || self.isFS), + if ~(self.isSIA || self.isSSA || self.isL1L2 || self.isMOLHO || self.isHO || self.isFS), md = checkmessage(md,['no element types set for this model']); end @@ -153,5 +154,5 @@ fielddisplay(self,'isSSA','is the Shelfy-Stream Approximation (SSA) used?'); fielddisplay(self,'isL1L2','is the L1L2 approximation used?'); - fielddisplay(self,'isMLHO','is the Mono-Layer Higher-Order approximation used?'); + fielddisplay(self,'isMOLHO','is the MOno-Layer Higher-Order (MOLHO) approximation used?'); fielddisplay(self,'isHO','is the Higher-Order (HO) approximation used?'); fielddisplay(self,'isFS','are the Full-FS (FS) equations used?'); @@ -172,5 +173,5 @@ WriteData(fid,prefix,'object',self,'fieldname','isSSA','format','Boolean'); WriteData(fid,prefix,'object',self,'fieldname','isL1L2','format','Boolean'); - WriteData(fid,prefix,'object',self,'fieldname','isMLHO','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','isMOLHO','format','Boolean'); WriteData(fid,prefix,'object',self,'fieldname','isHO','format','Boolean'); WriteData(fid,prefix,'object',self,'fieldname','isFS','format','Boolean'); @@ -197,5 +198,5 @@ writejsdouble(fid,[modelname '.flowequation.isSSA'],self.isSSA); writejsdouble(fid,[modelname '.flowequation.isL1L2'],self.isL1L2); - writejsdouble(fid,[modelname '.flowequation.isMLHO'],self.isMLHO); + writejsdouble(fid,[modelname '.flowequation.isMOLHO'],self.isMOLHO); writejsdouble(fid,[modelname '.flowequation.isHO'],self.isHO); writejsdouble(fid,[modelname '.flowequation.isFS'],self.isFS); Index: /issm/trunk/src/m/classes/flowequation.py =================================================================== --- /issm/trunk/src/m/classes/flowequation.py (revision 27034) +++ /issm/trunk/src/m/classes/flowequation.py (revision 27035) @@ -19,5 +19,5 @@ self.isSSA = 0 self.isL1L2 = 0 - self.isMLHO = 0 + self.isMOLHO = 0 self.isHO = 0 self.isFS = 0 @@ -46,5 +46,5 @@ s += '{}\n'.format(fielddisplay(self, 'isSSA', "is the Shelfy-Stream Approximation (SSA) used?")) s += '{}\n'.format(fielddisplay(self, 'isL1L2', "are L1L2 equations used?")) - s += '{}\n'.format(fielddisplay(self, 'isMLHO', "are Mono-layer Higher-Order equations used?")) + s += '{}\n'.format(fielddisplay(self, 'isMOLHO', "are MOno-layer Higher-Order (MOLHO) equations used?")) s += '{}\n'.format(fielddisplay(self, 'isHO', "is the Higher-Order (HO) approximation used?")) s += '{}\n'.format(fielddisplay(self, 'isFS', "are the Full-FS (FS) equations used?")) @@ -90,5 +90,5 @@ md = checkfield(md, 'fieldname', 'flowequation.isSSA', 'numel', [1], 'values', [0, 1]) md = checkfield(md, 'fieldname', 'flowequation.isL1L2', 'numel', [1], 'values', [0, 1]) - md = checkfield(md, 'fieldname', 'flowequation.isMLHO', 'numel', [1], 'values', [0, 1]) + md = checkfield(md, 'fieldname', 'flowequation.isMOLHO', 'numel', [1], 'values', [0, 1]) md = checkfield(md, 'fieldname', 'flowequation.isHO', 'numel', [1], 'values', [0, 1]) md = checkfield(md, 'fieldname', 'flowequation.isFS', 'numel', [1], 'values', [0, 1]) @@ -121,5 +121,5 @@ raise RuntimeError('Case not supported yet') - if not (self.isSIA or self.isSSA or self.isL1L2 or self.isMLHO or self.isHO or self.isFS): + if not (self.isSIA or self.isSSA or self.isL1L2 or self.isMOLHO or self.isHO or self.isFS): md.checkmessage("no element types set for this model") if 'StressbalanceSIAAnalysis' in analyses: @@ -134,5 +134,5 @@ WriteData(fid, prefix, 'object', self, 'fieldname', 'isSSA', 'format', 'Boolean') WriteData(fid, prefix, 'object', self, 'fieldname', 'isL1L2', 'format', 'Boolean') - WriteData(fid, prefix, 'object', self, 'fieldname', 'isMLHO', 'format', 'Boolean') + WriteData(fid, prefix, 'object', self, 'fieldname', 'isMOLHO', 'format', 'Boolean') WriteData(fid, prefix, 'object', self, 'fieldname', 'isHO', 'format', 'Boolean') WriteData(fid, prefix, 'object', self, 'fieldname', 'isFS', 'format', 'Boolean') Index: /issm/trunk/src/m/classes/fourierlove.m =================================================================== --- /issm/trunk/src/m/classes/fourierlove.m (revision 27034) +++ /issm/trunk/src/m/classes/fourierlove.m (revision 27035) @@ -6,23 +6,25 @@ classdef fourierlove properties (SetAccess=public) - nfreq = 0; - frequencies = 0; - sh_nmax = 0; - sh_nmin = 0; - g0 = 0; - r0 = 0; - mu0 = 0; - Gravitational_Constant = 0; - allow_layer_deletion = 0; - underflow_tol = 0; - integration_steps_per_layer = 0; - istemporal = 0; - n_temporal_iterations = 0; - time = 0; - love_kernels = 0; - forcing_type = 0; - inner_core_boundary = 0; - core_mantle_boundary = 0; - complex_computation = 0; + nfreq = 0; + frequencies = 0; + sh_nmax = 0; + sh_nmin = 0; + g0 = 0; + r0 = 0; + mu0 = 0; + Gravitational_Constant = 0; + chandler_wobble = 0; + allow_layer_deletion = 0; + underflow_tol = 0; + pw_threshold = 0; + integration_steps_per_layer = 0; + istemporal = 0; + n_temporal_iterations = 0; + time = 0; + love_kernels = 0; + forcing_type = 0; + inner_core_boundary = 0; + core_mantle_boundary = 0; + complex_computation = 0; end @@ -53,6 +55,8 @@ self.mu0=1e11; % Pa self.Gravitational_Constant=6.67259e-11; % m^3 kg^-1 s^-2 + self.chandler_wobble=0; self.allow_layer_deletion=1; self.underflow_tol=1e-16; %threshold of deep to surface love number ratio to trigger the deletion of layer + self.pw_threshold=1e-3; %if relative variation across frequencies is smaller than this ratio, the post-widder transform for time-dependent love numbers is bypassed self.integration_steps_per_layer=100; self.istemporal=0; @@ -74,6 +78,8 @@ fielddisplay(self,'mu0','adimensioning constant for stress (default: 10^11) [Pa]'); fielddisplay(self,'Gravitational_Constant','Newtonian constant of gravitation (default: 6.67259e-11 [m^3 kg^-1 s^-2])'); - fielddisplay(self,'allow_layer_deletion','allow for migration of the integration boundary with increasing spherical harmonics degree (default: 1)'); + fielddisplay(self,'chandler_wobble','includes the inertial terms for the chandler wobble in the rotational feedback love numbers, only for forcing_type=11 (default: 0) (/!\ 1 is untested yet)'); + fielddisplay(self,'allow_layer_deletion','allow for migration of the integration boundary with increasing spherical harmonics degree (default: 1)'); fielddisplay(self,'underflow_tol','threshold of deep to surface love number ratio to trigger the deletion of layers (default: 1e-16)'); + fielddisplay(self,'pw_threshold','if relative variation across frequencies is smaller than this ratio, the post-widder transform for time-dependent love numbers is bypassed (default (1e-3)'); fielddisplay(self,'integration_steps_per_layer','number of radial steps to propagate the yi system from the bottom to the top of each layer (default: 100)'); fielddisplay(self,'istemporal',{'1 for time-dependent love numbers, 0 for frequency-dependent or elastic love numbers (default: 0)', 'If 1: use fourierlove function build_frequencies_from_time to meet consistency'}); @@ -98,6 +104,8 @@ md = checkfield(md,'fieldname','love.mu0','NaN',1,'Inf',1,'numel',1,'>',0); md = checkfield(md,'fieldname','love.Gravitational_Constant','NaN',1,'Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','love.chandler_wobble','values',[0 1]); md = checkfield(md,'fieldname','love.allow_layer_deletion','values',[0 1]); md = checkfield(md,'fieldname','love.underflow_tol','NaN',1,'Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','love.pw_threshold','NaN',1,'Inf',1,'numel',1,'>',0); md = checkfield(md,'fieldname','love.integration_steps_per_layer','NaN',1,'Inf',1,'numel',1,'>',0); md = checkfield(md,'fieldname','love.love_kernels','values',[0 1]); @@ -112,4 +120,8 @@ if md.love.sh_nmin<=1 & (md.love.forcing_type==1 || md.love.forcing_type==5 || md.love.forcing_type==9) error(['Degree 1 not supported for forcing type ' num2str(md.love.forcing_type) '. Use sh_min>=2 for this kind of calculation.']) + end + + if md.love.chandler_wobble==1 + disp('Warning, Chandler Wobble in Love number calculator has not been validated yet'); end @@ -137,6 +149,8 @@ WriteData(fid,prefix,'object',self,'fieldname','mu0','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','Gravitational_Constant','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','chandler_wobble','format','Boolean'); WriteData(fid,prefix,'object',self,'fieldname','allow_layer_deletion','format','Boolean'); WriteData(fid,prefix,'object',self,'fieldname','underflow_tol','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','pw_threshold','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','integration_steps_per_layer','format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','istemporal','format','Boolean'); @@ -164,5 +178,9 @@ for i=1:length(self.time) for j=1:2*self.n_temporal_iterations - self.frequencies((i-1)*2*self.n_temporal_iterations +j) = j*log(2)/self.time(i)/2/pi; + if self.time(i)==0 + self.frequencies((i-1)*2*self.n_temporal_iterations +j) =0; % convention to avoid marshalling infinite numbers + else + self.frequencies((i-1)*2*self.n_temporal_iterations +j) = j*log(2)/self.time(i)/2/pi; + end end end Index: /issm/trunk/src/m/classes/fourierlove.py =================================================================== --- /issm/trunk/src/m/classes/fourierlove.py (revision 27034) +++ /issm/trunk/src/m/classes/fourierlove.py (revision 27035) @@ -22,6 +22,8 @@ self.mu0 = 0 self.Gravitational_Constant = 0 + self.chandler_wobble = 0 self.allow_layer_deletion = 0 self.underflow_tol = 0 + self.pw_threshold = 0 self.integration_steps_per_layer = 0 self.istemporal = 0 @@ -51,6 +53,8 @@ s += '{}\n'.format(fielddisplay(self, 'allow_layer_deletion', 'allow for migration of the integration boundary with increasing spherical harmonics degree (default: 1)')) s += '{}\n'.format(fielddisplay(self, 'Gravitational_Constant', 'Newtonian constant of gravitation (default: 6.67259e-11 [m^3 kg^-1 s^-2])')) + s += '{}\n'.format(fielddisplay(self, 'chandler_wobble', 'includes the inertial terms for the chandler wobble in the rotational feedback love numbers, only for forcing_type=11 (default: 0) (/!\\ 1 has not been validated yet)')) s += '{}\n'.format(fielddisplay(self, 'allow_layer_deletion', 'allow for migration of the integration boundary with increasing spherical harmonics degree (default: 1)')) - s += '{}\n'.format(fielddisplay(self, 'underflow_tol', 'threshold of deep to surface love number ratio to trigger the deletion of layers (default: 1e-16)')) + s += '{}\n'.format(fielddisplay(self, 'pw_threshold', 'if relative variation across frequencies is smaller than this ratio, the post-widder transform for time-dependent love numbers is bypassed (default (1e-3)')) + s += '{}\n'.format(fielddisplay(self, 'chandler_wobble', 'includes the inertial terms for the chandler wobble in the rotational feedback love numbers, only for forcing_type=11 (default: 0) (/!\\ 1 is untested)')) s += '{}\n'.format(fielddisplay(self, 'integration_steps_per_layer', 'number of radial steps to propagate the yi system from the bottom to the top of each layer (default: 100)')) s += '{}\n'.format(fielddisplay(self, 'istemporal', ['1 for time-dependent love numbers, 0 for frequency-dependent or elastic love numbers (default: 0)', 'If 1: use fourierlove function build_frequencies_from_time to meet consistency'])) @@ -88,6 +92,8 @@ self.mu0 = 1e11 # Pa self.Gravitational_Constant = 6.67259e-11 # m^3 kg^-1 s^-2 + self.chandler_wobble = 0 self.allow_layer_deletion = 1 self.underflow_tol = 1e-16 # Threshold of deep to surface love number ratio to trigger the deletion of layer + self.pw_threshold = 1e-3 # If relative variation across frequencies is smaller than this ratio, the post-widder transform for time-dependent love numbers is bypassed self.integration_steps_per_layer = 100 self.istemporal = 0 @@ -113,6 +119,8 @@ md = checkfield(md, 'fieldname', 'love.mu0', 'NaN', 1, 'Inf', 1, 'numel', 1, '>', 0) md = checkfield(md, 'fieldname', 'love.Gravitational_Constant', 'NaN', 1, 'Inf', 1, 'numel', 1, '>', 0) + md = checkfield(md, 'fieldname', 'love.chandler_wobble', 'values', [0, 1]) md = checkfield(md, 'fieldname', 'love.allow_layer_deletion', 'values', [0, 1]) md = checkfield(md, 'fieldname', 'love.underflow_tol', 'NaN', 1, 'Inf', 1, 'numel', 1, '>', 0) + md = checkfield(md, 'fieldname', 'love.pw_threshold', 'NaN', 1, 'Inf', 1, 'numel', 1, '>', 0) md = checkfield(md, 'fieldname', 'love.integration_steps_per_layer', 'NaN', 1, 'Inf', 1, 'numel', 1, '>', 0) md = checkfield(md, 'fieldname', 'love.love_kernels', 'values', [0, 1]) @@ -127,9 +135,12 @@ raise RuntimeError('Degree 1 not supported for forcing type {}. Use sh_min >= 2 for this kind of calculation.'.format(md.love.forcing_type)) + if md.love.chandler_wobble == 1: + print('Warning: Chandler wobble in Love number calculator has not been validated yet') + # Need 'litho' material - if not hasattr(md.materials, 'materials') or 'litho' not in md.materials.nature: + if md.materials.__class__.__name__ != 'materials' or 'litho' not in md.materials.nature: raise RuntimeError('Need a \'litho\' material to run a Fourier Love number analysis') - mat = np.where(np.array(nature) == 'litho')[0] + mat = np.where(np.array(md.materials.nature) == 'litho')[0] if md.love.forcing_type <= 4: md = checkfield(md, 'fieldname', 'love.inner_core_boundary', 'NaN', 1, 'Inf', 1, 'numel', 1, '>', 0, '<=', md.materials[mat].numlayers) @@ -149,6 +160,8 @@ WriteData(fid, prefix, 'object', self, 'fieldname', 'mu0', 'format', 'Double') WriteData(fid, prefix, 'object', self, 'fieldname', 'Gravitational_Constant', 'format', 'Double') + WriteData(fid, prefix, 'object', self, 'fieldname', 'chandler_wobble', 'format', 'Boolean') WriteData(fid, prefix, 'object', self, 'fieldname', 'allow_layer_deletion', 'format', 'Boolean') WriteData(fid, prefix, 'object', self, 'fieldname', 'underflow_tol', 'format', 'Double') + WriteData(fid, prefix, 'object', self, 'fieldname', 'pw_threshold', 'format', 'Double') WriteData(fid, prefix, 'object', self, 'fieldname', 'integration_steps_per_layer', 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'fieldname', 'istemporal', 'format', 'Boolean') @@ -171,7 +184,11 @@ print('Temporal love numbers: Overriding md.love.nfreq and md.love.frequencies') self.nfreq = len(self.time) * 2 * self.n_temporal_iterations - self.frequencies = np.zeros((self.nfreq, 1)) + self.frequencies = np.zeros((self.nfreq,)) for i in range(len(self.time)): for j in range(2 * self.n_temporal_iterations): - self.frequencies[(i - 1) * 2 * self.n_temporal_iterations + j] = j * np.log(2) / self.time[i] / 2 / np.pi + if self.time[i] == 0: + self.frequencies[(i - 1) * 2 * self.n_temporal_iterations + j] = 0 # Convention to avoid marshalling infinite numbers + else: + self.frequencies[(i - 1) * 2 * self.n_temporal_iterations + j] = j * np.log(2) / self.time[i] / 2 / np.pi + return self #}}} Index: /issm/trunk/src/m/classes/frontalforcings.m =================================================================== --- /issm/trunk/src/m/classes/frontalforcings.m (revision 27034) +++ /issm/trunk/src/m/classes/frontalforcings.m (revision 27035) @@ -7,4 +7,5 @@ properties (SetAccess=public) meltingrate = NaN; + ablationrate = NaN; end methods @@ -29,8 +30,10 @@ function self = extrude(self,md) % {{{ self.meltingrate=project3d(md,'vector',self.meltingrate,'type','node'); + self.ablationrate=project3d(md,'vector',self.ablationrate,'type','node'); end % }}} function self = setdefaultparameters(self) % {{{ meltingrate = NaN; + ablationrate = NaN; end % }}} function md = checkconsistency(self,md,solution,analyses) % {{{ @@ -39,4 +42,7 @@ md = checkfield(md,'fieldname','frontalforcings.meltingrate','NaN',1,'Inf',1,'timeseries',1,'>=',0); + if ~isnan(md.frontalforcings.ablationrate) + md = checkfield(md,'fieldname','frontalforcings.ablationrate','Inf',1,'timeseries',1); + end end % }}} @@ -44,4 +50,5 @@ disp(sprintf(' Frontalforcings parameters:')); fielddisplay(self,'meltingrate','melting rate at given location [m/a]'); + fielddisplay(self,'ablationrate','frontal ablation rate at given location [m/a], it contains both calving and melting'); end % }}} function marshall(self,prefix,md,fid) % {{{ @@ -49,4 +56,7 @@ WriteData(fid,prefix,'name','md.frontalforcings.parameterization','data',1,'format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','meltingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts,'scale',1./yts); + if ~isnan(md.frontalforcings.ablationrate) + WriteData(fid,prefix,'object',self,'fieldname','ablationrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts,'scale',1./yts); + end end % }}} end Index: /issm/trunk/src/m/classes/frontalforcingsrignot.py =================================================================== --- /issm/trunk/src/m/classes/frontalforcingsrignot.py (revision 27034) +++ /issm/trunk/src/m/classes/frontalforcingsrignot.py (revision 27035) @@ -64,5 +64,5 @@ def marshall(self, prefix, md, fid): # {{{ WriteData(fid, prefix, 'name', 'md.frontalforcings.parameterization', 'data', 2, 'format', 'Integer') - WriteData(fid, prefix, 'object', self, 'fieldname', 'basin_id', 'data', self.basin_id, 'name', 'md.frontalforcings.basin_id', 'format', 'IntMat', 'mattype', 2) # 0-indexed + WriteData(fid, prefix, 'object', self, 'fieldname', 'basin_id', 'data', self.basin_id - 1, 'name', 'md.frontalforcings.basin_id', 'format', 'IntMat', 'mattype', 2) # 0-indexed WriteData(fid, prefix, 'object', self, 'fieldname', 'num_basins', 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'fieldname', 'subglacial_discharge', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts) Index: /issm/trunk/src/m/classes/frontalforcingsrignotautoregression.m =================================================================== --- /issm/trunk/src/m/classes/frontalforcingsrignotautoregression.m (revision 27034) +++ /issm/trunk/src/m/classes/frontalforcingsrignotautoregression.m (revision 27035) @@ -66,5 +66,5 @@ fielddisplay(self,'basin_id','basin number assigned to each element [unitless]'); fielddisplay(self,'subglacial_discharge','sum of subglacial discharge for each basin [m/d]'); - fielddisplay(self,'beta0','basin-specific intercept values [∘C]'); + fielddisplay(self,'beta0','basin-specific intercept values [∘C] (if beta_1==0 mean=beta_0/(1-sum(phi)))'); fielddisplay(self,'beta1','basin-specific trend values [∘C yr^(-1)]'); fielddisplay(self,'ar_order','order of the autoregressive model [unitless]'); @@ -75,5 +75,5 @@ function marshall(self,prefix,md,fid) % {{{ yts=md.constants.yts; - WriteData(fid,prefix,'name','md.frontalforcings.parameterization','data',55,'format','Integer'); + WriteData(fid,prefix,'name','md.frontalforcings.parameterization','data',3,'format','Integer'); WriteData(fid,prefix,'object',self,'class','frontalforcings','fieldname','num_basins','format','Integer'); WriteData(fid,prefix,'object',self,'class','frontalforcings','fieldname','subglacial_discharge','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',yts); Index: /issm/trunk/src/m/classes/frontalforcingsrignotautoregression.py =================================================================== --- /issm/trunk/src/m/classes/frontalforcingsrignotautoregression.py (revision 27034) +++ /issm/trunk/src/m/classes/frontalforcingsrignotautoregression.py (revision 27035) @@ -1,10 +1,9 @@ # -*- coding: utf-8 -*- - import numpy as np - from checkfield import checkfield from fielddisplay import fielddisplay from MatlabFuncs import * from WriteData import WriteData + class frontalforcingsrignotautoregression(object): @@ -36,5 +35,5 @@ s += '{}\n'.format(fielddisplay(self, 'basin_id', 'basin number assigned to each element [unitless]')) s += '{}\n'.format(fielddisplay(self, 'subglacial_discharge', 'sum of subglacial discharge for each basin [m/d]')) - s += '{}\n'.format(fielddisplay(self, 'beta0', 'basin-specific intercept values [°C]')) + s += '{}\n'.format(fielddisplay(self, 'beta0', 'basin-specific intercept values [°C] (if beta_1==0 mean=beta_0/(1-sum(phi)))')) s += '{}\n'.format(fielddisplay(self, 'beta1', 'basin-specific trend values [°C yr^(-1)]')) s += '{}\n'.format(fielddisplay(self, 'ar_order', 'order of the autoregressive model [unitless]')) @@ -49,5 +48,5 @@ self.num_basins = 0 self.subglacial_discharge = np.nan - self.ar_order = 0.0 # Autoregression model of order 0 + self.ar_order = 0.0 # Autoregression model of order 0 return self #}}} @@ -61,4 +60,7 @@ md = checkfield(md, 'fieldname', 'frontalforcings.basin_id', 'Inf', 1, '>=', 0, '<=', md.frontalforcings.num_basins, 'size', [md.mesh.numberofelements]) md = checkfield(md, 'fieldname', 'frontalforcings.subglacial_discharge', '>=', 0, 'NaN', 1, 'Inf', 1, 'timeseries', 1) + if len(np.shape(self.beta0)) == 1: + self.beta0 = np.array([self.beta0]) + self.beta1 = np.array([self.beta1]) md = checkfield(md, 'fieldname', 'frontalforcings.beta0', 'NaN', 1, 'Inf', 1, 'size', [1, md.frontalforcings.num_basins], 'numel', md.frontalforcings.num_basins) md = checkfield(md, 'fieldname', 'frontalforcings.beta1', 'NaN', 1, 'Inf', 1, 'size', [1, md.frontalforcings.num_basins], 'numel', md.frontalforcings.num_basins) @@ -77,5 +79,5 @@ def marshall(self, prefix, md, fid): # {{{ yts = md.constants.yts - WriteData(fid, prefix, 'name', 'md.frontalforcings.parameterization', 'data', 55, 'format', 'Integer') + WriteData(fid, prefix, 'name', 'md.frontalforcings.parameterization', 'data', 3, 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'class', 'frontalforcings', 'fieldname', 'num_basins', 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'class', 'frontalforcings', 'fieldname', 'subglacial_discharge', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts) @@ -83,5 +85,5 @@ WriteData(fid, prefix, 'object', self, 'class', 'frontalforcings', 'fieldname', 'ar_initialtime', 'format', 'Double', 'scale', yts) WriteData(fid, prefix, 'object', self, 'class', 'frontalforcings', 'fieldname', 'ar_timestep', 'format', 'Double', 'scale', yts) - WriteData(fid, prefix, 'object', self, 'class', 'frontalforcings', 'fieldname', 'basin_id', 'data', self.basin_id, 'name', 'md.frontalforcings.basin_id', 'format', 'IntMat', 'mattype', 2) # 0-indexed + WriteData(fid, prefix, 'object', self, 'class', 'frontalforcings', 'fieldname', 'basin_id', 'data', self.basin_id - 1, 'name', 'md.frontalforcings.basin_id', 'format', 'IntMat', 'mattype', 2) # 0-indexed WriteData(fid, prefix, 'object', self, 'class', 'frontalforcings', 'fieldname', 'beta0', 'format', 'DoubleMat', 'name', 'md.frontalforcings.beta0') WriteData(fid, prefix, 'object', self, 'class', 'frontalforcings', 'fieldname', 'beta1', 'format', 'DoubleMat', 'name', 'md.frontalforcings.beta1', 'scale', 1 / yts, 'yts', yts) Index: /issm/trunk/src/m/classes/geometry.py =================================================================== --- /issm/trunk/src/m/classes/geometry.py (revision 27034) +++ /issm/trunk/src/m/classes/geometry.py (revision 27035) @@ -61,5 +61,9 @@ def marshall(self, prefix, md, fid): # {{{ - length_thickness = len(self.thickness) + if isinstance(self.thickness, (list, np.ndarray)): + length_thickness = len(self.thickness) + else: + length_thickness = 1 + if (length_thickness == md.mesh.numberofvertices) or (length_thickness == md.mesh.numberofvertices + 1): WriteData(fid, prefix, 'object', self, 'fieldname', 'thickness', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts) Index: /issm/trunk/src/m/classes/groundingline.m =================================================================== --- /issm/trunk/src/m/classes/groundingline.m (revision 27034) +++ /issm/trunk/src/m/classes/groundingline.m (revision 27035) @@ -9,4 +9,5 @@ friction_interpolation = ''; melt_interpolation = ''; + requested_outputs = {}; end methods @@ -25,4 +26,6 @@ self.friction_interpolation= 'SubelementFriction1'; self.melt_interpolation = 'NoMeltOnPartiallyFloating'; + %default output + self.requested_outputs = {'default'}; end % }}} @@ -32,4 +35,5 @@ md = checkfield(md,'fieldname','groundingline.friction_interpolation','values',{'NoFrictionOnPartiallyFloating' 'SubelementFriction1' 'SubelementFriction2'}); md = checkfield(md,'fieldname','groundingline.melt_interpolation','values',{'NoMeltOnPartiallyFloating' 'SubelementMelt1' 'SubelementMelt2' 'FullMeltOnPartiallyFloating'}); + md = checkfield(md,'fieldname','groundingline.requested_outputs','stringrow',1); if ~strcmp(self.migration,'None') & strcmp(solution,'TransientSolution') & md.transient.isgroundingline==1, @@ -48,4 +52,9 @@ end % }}} + function list = defaultoutputs(self,md) % {{{ + + list = {'Surface','Base','MaskOceanLevelset'}; + + end % }}} function disp(self) % {{{ disp(sprintf(' grounding line migration parameters:')); @@ -53,4 +62,5 @@ fielddisplay(self,'friction_interpolation','type of friction interpolation for partially floating elements: ''NoFrictionOnPartiallyFloating'',''SubelementFriction1'', or ''SubelementFriction2'''); fielddisplay(self,'melt_interpolation','type of melt interpolation for partially floating elements: ''NoMeltOnPartiallyFloating'',''SubelementMelt1'',''SubelementMelt2'', or ''FullMeltOnPartiallyFloating'''); + fielddisplay(self,'requested_outputs','additional outputs requested'); end % }}} @@ -59,10 +69,20 @@ WriteData(fid,prefix,'data',self.friction_interpolation,'name','md.groundingline.friction_interpolation','format','String'); WriteData(fid,prefix,'data',self.melt_interpolation,'name','md.groundingline.melt_interpolation','format','String'); + + %process requested outputs + outputs = self.requested_outputs; + pos = find(ismember(outputs,'default')); + if ~isempty(pos), + outputs(pos) = []; %remove 'default' from outputs + outputs = [outputs defaultoutputs(self,md)]; %add defaults + end + WriteData(fid,prefix,'data',outputs,'name','md.groundingline.requested_outputs','format','StringArray') end % }}} function savemodeljs(self,fid,modelname) % {{{ writejsstring(fid,[modelname '.groundingline.migration'],self.migration); - writejsstring(fid,[modelname '.groundingline.friction_interpolation'],self.migration); - writejsstring(fid,[modelname '.groundingline.melt_interpolation'],self.migration); + writejsstring(fid,[modelname '.groundingline.friction_interpolation'],self.friction_interpolation); + writejsstring(fid,[modelname '.groundingline.melt_interpolation'],self.melt_interpolation); + writejscellstring(fid,[modelname '.groundingline.requested_outputs'],self.requested_outputs); end % }}} Index: /issm/trunk/src/m/classes/groundingline.py =================================================================== --- /issm/trunk/src/m/classes/groundingline.py (revision 27034) +++ /issm/trunk/src/m/classes/groundingline.py (revision 27035) @@ -18,4 +18,5 @@ self.friction_interpolation = '' self.melt_interpolation = '' + self.requested_outptuts = [] # Set defaults @@ -29,6 +30,12 @@ s += '{}\n'.format(fielddisplay(self, 'migration', 'type of friction interpolation on partially floating elements: ''SubelementFriction1'', ''SubelementFriction2'', ''NoFrictionOnPartiallyFloating''')) s += '{}\n'.format(fielddisplay(self, 'migration', 'type of melt interpolation on partially floating elements: \'SubelementMelt1\', \'SubelementMelt2\', \'NoMeltOnPartiallyFloating\', \'FullMeltOnPartiallyFloating\'')) + s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'additional outputs requested')) return s # }}} + + def defaultoutputs(self, md): # {{{ + return ['Surface', 'Base','MaskOceanLevelset'] + + #}}} def setdefaultparameters(self): # {{{ @@ -37,4 +44,6 @@ self.friction_interpolation = 'SubelementFriction1' self.melt_interpolation = 'NoMeltOnPartiallyFloating' + # Default output + self.requested_outputs = ['default'] return self @@ -45,4 +54,5 @@ md = checkfield(md, 'fieldname', 'groundingline.friction_interpolation', 'values', ['SubelementFriction1', 'SubelementFriction2', 'NoFrictionOnPartiallyFloating']) md = checkfield(md, 'fieldname', 'groundingline.melt_interpolation', 'values', ['SubelementMelt1', 'SubelementMelt2', 'NoMeltOnPartiallyFloating', 'FullMeltOnPartiallyFloating']) + md = checkfield(md, 'fieldname', 'groundingline.requested_outputs', 'stringrow', 1) if(not m.strcmp(self.migration, 'None') and md.transient.isgroundingline and solution == 'TransientSolution'): @@ -62,3 +72,11 @@ WriteData(fid, prefix, 'data', self.friction_interpolation, 'name', 'md.groundingline.friction_interpolation', 'format', 'String') WriteData(fid, prefix, 'data', self.melt_interpolation, 'name', 'md.groundingline.melt_interpolation', 'format', 'String') + + # Process requested outputs + outputs = self.requested_outputs + indices = [i for i, x in enumerate(outputs) if x == 'default'] + if len(indices) > 0: + outputscopy = outputs[0:max(0, indices[0] - 1)] + self.defaultoutputs(md) + outputs[indices[0] + 1:] + outputs = outputscopy + WriteData(fid, prefix, 'data', outputs, 'name', 'md.groundingline.requested_outputs', 'format', 'StringArray') # }}} Index: /issm/trunk/src/m/classes/hydrologyglads.py =================================================================== --- /issm/trunk/src/m/classes/hydrologyglads.py (revision 27034) +++ /issm/trunk/src/m/classes/hydrologyglads.py (revision 27035) @@ -58,5 +58,5 @@ def defaultoutputs(self, md): # {{{ - list = ['EffectivePressure', 'HydraulicPotential', 'HydrologySheetThickness', 'ChannelArea'] + list = ['EffectivePressure', 'HydraulicPotential', 'HydrologySheetThickness', 'ChannelArea', 'ChannelDischarge'] return list # }}} Index: /issm/trunk/src/m/classes/hydrologyshreve.m =================================================================== --- /issm/trunk/src/m/classes/hydrologyshreve.m (revision 27034) +++ /issm/trunk/src/m/classes/hydrologyshreve.m (revision 27035) @@ -35,5 +35,4 @@ end % }}} function md = checkconsistency(self,md,solution,analyses) % {{{ - %Early return if ~ismember('HydrologyShreveAnalysis',analyses) | (strcmp(solution,'TransientSolution') & md.transient.ishydrology==0), return; end Index: /issm/trunk/src/m/classes/hydrologytws.m =================================================================== --- /issm/trunk/src/m/classes/hydrologytws.m (revision 27034) +++ /issm/trunk/src/m/classes/hydrologytws.m (revision 27035) @@ -44,5 +44,5 @@ end % }}} function marshall(self,prefix,md,fid) % {{{ - WriteData(fid,prefix,'name','md.hydrology.model','data',2,'format','Integer'); + WriteData(fid,prefix,'name','md.hydrology.model','data',6,'format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','spcwatercolumn','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); outputs = self.requested_outputs; Index: /issm/trunk/src/m/classes/hydrologytws.py =================================================================== --- /issm/trunk/src/m/classes/hydrologytws.py (revision 27034) +++ /issm/trunk/src/m/classes/hydrologytws.py (revision 27035) @@ -51,9 +51,9 @@ def marshall(self, prefix, md, fid): # {{{ - WriteData(fid, prefix, 'name', 'md.hydrology.model', 'data', 2, 'format', 'Integer') + WriteData(fid, prefix, 'name', 'md.hydrology.model', 'data', 6, 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'fieldname', 'spcwatercolumn', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts) outputs = self.requested_outputs pos = find(ismember(outputs,'default')) - if not len(pos), + if not len(pos): outputs[pos] = []; # remove 'default' from outputs outputs.extend(defaultoutputs(self, md)) # add defaults Index: /issm/trunk/src/m/classes/initialization.m =================================================================== --- /issm/trunk/src/m/classes/initialization.m (revision 27034) +++ /issm/trunk/src/m/classes/initialization.m (revision 27035) @@ -39,5 +39,5 @@ function md = checkconsistency(self,md,solution,analyses) % {{{ if ismember('StressbalanceAnalysis',analyses) & ~(strcmp(solution,'TransientSolution') & md.transient.isstressbalance == 0), - if ~(isnan(md.initialization.vx) | isnan(md.initialization.vy)), + if numel(md.initialization.vx)>1 | numel(md.initialization.vy)>1 md = checkfield(md,'fieldname','initialization.vx','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1]); md = checkfield(md,'fieldname','initialization.vy','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1]); @@ -59,5 +59,5 @@ md = checkfield(md,'fieldname','initialization.vy','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1]); %Triangle with zero velocity - if any(sum(abs(md.initialization.vx(md.mesh.elements)),2)==0 & sum(abs(md.initialization.vy(md.mesh.elements)),2)==0) + if any(sum(abs(md.initialization.vx(md.mesh.elements)),2)==0 & sum(abs(md.initialization.vy(md.mesh.elements)),2)==0 & min(md.mask.ice_levelset(md.mesh.elements),[],2)<0) md = checkmessage(md,'at least one triangle has all its vertices with a zero velocity'); end Index: /issm/trunk/src/m/classes/inversion.m =================================================================== --- /issm/trunk/src/m/classes/inversion.m (revision 27034) +++ /issm/trunk/src/m/classes/inversion.m (revision 27035) @@ -104,6 +104,6 @@ %Only SSA, HO and FS are supported right now if strcmp(solution,'StressbalanceSolution') - if ~(md.flowequation.isSSA || md.flowequation.isMLHO || md.flowequation.isHO || md.flowequation.isFS || md.flowequation.isL1L2), - md = checkmessage(md,['inversion can only be performed for SSA, MLHO, HO or FS ice flow models']); + if ~(md.flowequation.isSSA || md.flowequation.isMOLHO || md.flowequation.isHO || md.flowequation.isFS || md.flowequation.isL1L2), + md = checkmessage(md,['inversion can only be performed for SSA, MOLHO, HO or FS ice flow models']); end end Index: /issm/trunk/src/m/classes/inversion.py =================================================================== --- /issm/trunk/src/m/classes/inversion.py (revision 27034) +++ /issm/trunk/src/m/classes/inversion.py (revision 27035) @@ -131,13 +131,26 @@ md = checkfield(md, 'fieldname', 'inversion.step_threshold', 'size', [md.inversion.nsteps]) md = checkfield(md, 'fieldname', 'inversion.cost_functions', 'size', [num_costfunc], 'values', supportedcostfunctions()) - md = checkfield(md, 'fieldname', 'inversion.cost_functions_coefficients', 'size', [md.mesh.numberofvertices, num_costfunc], '>=', 0) - md = checkfield(md, 'fieldname', 'inversion.gradient_scaling', 'size', [md.inversion.nsteps, num_controls]) - md = checkfield(md, 'fieldname', 'inversion.min_parameters', 'size', [md.mesh.numberofvertices, num_controls]) - md = checkfield(md, 'fieldname', 'inversion.max_parameters', 'size', [md.mesh.numberofvertices, num_controls]) + if num_costfunc == 1: + md.inversion.cost_functions_coefficients = np.squeeze(md.inversion.cost_functions_coefficients) + md = checkfield(md, 'fieldname', 'inversion.cost_functions_coefficients', 'size', [md.mesh.numberofvertices], '>=', 0) + else: + md = checkfield(md, 'fieldname', 'inversion.cost_functions_coefficients', 'size', [md.mesh.numberofvertices, num_costfunc], '>=', 0) + + if num_controls == 1: + md.inversion.gradient_scaling = np.squeeze(md.inversion.gradient_scaling) + md.inversion.min_parameters = np.squeeze(md.inversion.min_parameters) + md.inversion.max_parameters = np.squeeze(md.inversion.max_parameters) + md = checkfield(md, 'fieldname', 'inversion.gradient_scaling', 'size', [md.inversion.nsteps]) + md = checkfield(md, 'fieldname', 'inversion.min_parameters', 'size', [md.mesh.numberofvertices]) + md = checkfield(md, 'fieldname', 'inversion.max_parameters', 'size', [md.mesh.numberofvertices]) + else: + md = checkfield(md, 'fieldname', 'inversion.gradient_scaling', 'size', [md.inversion.nsteps, num_controls]) + md = checkfield(md, 'fieldname', 'inversion.min_parameters', 'size', [md.mesh.numberofvertices, num_controls]) + md = checkfield(md, 'fieldname', 'inversion.max_parameters', 'size', [md.mesh.numberofvertices, num_controls]) # Only SSA, HO and FS are supported right now if solution == 'StressbalanceSolution': - if not (md.flowequation.isSSA or md.flowequation.isMLHO or md.flowequation.isHO or md.flowequation.isFS or md.flowequation.isL1L2): - md.checkmessage("'inversion can only be performed for SSA, MLHO, HO or FS ice flow models") + if not (md.flowequation.isSSA or md.flowequation.isMOLHO or md.flowequation.isHO or md.flowequation.isFS or md.flowequation.isL1L2): + md.checkmessage("'inversion can only be performed for SSA, MOLHO, HO or FS ice flow models") if solution == 'BalancethicknessSolution': md = checkfield(md, 'fieldname', 'inversion.thickness_obs', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1) Index: /issm/trunk/src/m/classes/levelset.m =================================================================== --- /issm/trunk/src/m/classes/levelset.m (revision 27034) +++ /issm/trunk/src/m/classes/levelset.m (revision 27035) @@ -62,5 +62,5 @@ md = checkfield(md,'fieldname','levelset.spclevelset','Inf',1,'timeseries',1); - md = checkfield(md,'fieldname','levelset.stabilization','values',[0 1 2 5]); + md = checkfield(md,'fieldname','levelset.stabilization','values',[0 1 2 5 6]); md = checkfield(md,'fieldname','levelset.kill_icebergs','numel',1,'values',[0 1]); md = checkfield(md,'fieldname','levelset.migration_max','numel',1,'NaN',1,'Inf',1,'>',0); Index: /issm/trunk/src/m/classes/lovenumbers.m =================================================================== --- /issm/trunk/src/m/classes/lovenumbers.m (revision 27034) +++ /issm/trunk/src/m/classes/lovenumbers.m (revision 27035) @@ -10,14 +10,16 @@ properties (SetAccess=public) - %regular love numbers: - h = []; %provided by PREM model - k = []; %idem - l = []; %idem + %loading love numbers: + h = []; %provided by PREM model + k = []; %idem + l = []; %idem %tidal love numbers for computing rotational feedback: - th = []; - tk = []; - tl = []; - tk2secular = 0; %deg 2 secular number. + th = []; + tk = []; + tl = []; + tk2secular = 0; %deg 2 secular number. + pmtf_colinear = []; + pmtf_ortho = []; %time/frequency for visco-elastic love numbers @@ -44,4 +46,7 @@ fielddisplay(self,'tl','tidal load Love number (deg 2)'); fielddisplay(self,'tk2secular','secular fluid Love number'); + fielddisplay(self,'pmtf_colinear','Colinear component of the Polar Motion Transfer Function (e.g. x-motion due to x-component perturbation of the inertia tensor)'); + fielddisplay(self,'pmtf_ortho','Orthogonal component of the Polar Motion Transfer Function (couples x and y components, only used for Chandler Wobble)'); + fielddisplay(self,'istime','time (default: 1) or frequency love numbers (0)'); @@ -62,4 +67,10 @@ self.tk2secular=0.942; + self.pmtf_colinear=0.0; + self.pmtf_ortho=0.0; + if maxdeg>=2 + self.pmtf_colinear= (1.0+self.k(3,:))/(1.0-self.tk(3,:)/self.tk2secular); %valid only for elastic regime, not viscous. Also neglects chandler wobble + self.pmtf_ortho= 0.0; + end %time: self.istime=1; %temporal love numbers by default @@ -82,4 +93,6 @@ md = checkfield(md,'fieldname','solidearth.lovenumbers.tl','NaN',1,'Inf',1); md = checkfield(md,'fieldname','solidearth.lovenumbers.tk2secular','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','solidearth.lovenumbers.pmtf_colinear','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','solidearth.lovenumbers.pmtf_ortho','NaN',1,'Inf',1); md = checkfield(md,'fieldname','solidearth.lovenumbers.timefreq','NaN',1,'Inf',1); md = checkfield(md,'fieldname','solidearth.lovenumbers.istime','NaN',1,'Inf',1,'values',[0 1]); @@ -91,6 +104,10 @@ ntf=length(self.timefreq); - if( size(self.h,2) ~= ntf | size(self.k,2) ~= ntf | size(self.l,2) ~= ntf | size(self.th,2) ~= ntf | size(self.tk,2) ~= ntf | size(self.tl,2) ~= ntf ), + if( size(self.h,2) ~= ntf | size(self.k,2) ~= ntf | size(self.l,2) ~= ntf | size(self.th,2) ~= ntf | size(self.tk,2) ~= ntf | size(self.tl,2) ~= ntf | size(self.pmtf_colinear,2) ~= ntf | size(self.pmtf_ortho,2) ~= ntf), error('lovenumbers error message: love numbers should have as many time/frequency steps as the time/frequency vector'); + end + + if self.istime && self.timefreq(1)~=0 + error('temporal love numbers must start with elastic response, i.e timefreq(1)=0'); end @@ -108,4 +125,6 @@ WriteData(fid,prefix,'object',self,'fieldname','tk','name','md.solidearth.lovenumbers.tk','format','DoubleMat','mattype',1); WriteData(fid,prefix,'object',self,'fieldname','tl','name','md.solidearth.lovenumbers.tl','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','pmtf_colinear','name','md.solidearth.lovenumbers.pmtf_colinear','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','pmtf_ortho','name','md.solidearth.lovenumbers.pmtf_ortho','format','DoubleMat','mattype',1); WriteData(fid,prefix,'object',self,'data',self.tk2secular,'fieldname','lovenumbers.tk2secular','format','Double'); Index: /issm/trunk/src/m/classes/lovenumbers.py =================================================================== --- /issm/trunk/src/m/classes/lovenumbers.py (revision 27034) +++ /issm/trunk/src/m/classes/lovenumbers.py (revision 27035) @@ -19,8 +19,8 @@ def __init__(self, *args): #{{{ - # Regular love numbers - self.h = [] # Provided by PREM model - self.k = [] # idem - self.l = [] # idem + # Loading love numbers + self.h = [] # Provided by PREM model + self.k = [] # idem + self.l = [] # idem # Tidal love numbers for computing rotational feedback @@ -28,5 +28,9 @@ self.tk = [] self.tl = [] - self.tk2secular = 0 # deg 2 secular number + self.tk2secular = 0 # deg 2 secular number + self.pmtf_colinear = [] + self.pmtf_ortho = [] + pmtf_colinear = [] + pmtf_ortho = [] # Time/frequency for visco-elastic love numbers @@ -49,6 +53,10 @@ s += '{}\n'.format(fielddisplay(self, 'tl', 'tidal load Love number (deg 2)')) s += '{}\n'.format(fielddisplay(self, 'tk2secular', 'secular fluid Love number')) + s += '{}\n'.format(fielddisplay(self, 'pmtf_colinear', 'Colinear component of the Polar Motion Transfer Function (e.g. x-motion due to x-component perturbation of the inertia tensor)')) + s += '{}\n'.format(fielddisplay(self, 'pmtf_ortho', 'Orthogonal component of the Polar Motion Transfer Function (couples x and y components, only used for Chandler Wobble)')) s += '{}\n'.format(fielddisplay(self, 'istime', 'time (default: 1) or frequency love numbers (0)')) s += '{}\n'.format(fielddisplay(self, 'timefreq', 'time/frequency vector (yr or 1/yr)')) + s += '{}\n'.format(fielddisplay(self, 'pmtf_colinear', 'Colinear component of the Polar Motion Transfer Function (e.g. x-motion due to x-component perturbation of the inertia tensor)')) + s += '{}\n'.format(fielddisplay(self, 'pmtf_ortho', 'Orthogonal component of the Polar Motion Transfer Function (couples x and y components, only used for Chandler Wobble)')) return s #}}} @@ -65,5 +73,15 @@ # Secular fluid love number self.tk2secular = 0.942 + self.pmtf_colinear=0.0 + self.pmtf_ortho=0.0 + if maxdeg>=2: + self.pmtf_colinear= (1.0+self.k[3-1,:])/(1.0-self.tk[3-1,:]/self.tk2secular) #valid only for elastic regime, not viscous. Also neglects chandler wobble + self.pmtf_ortho= 0.0 + self.pmtf_colinear = np.array([0.0]).reshape(-1, 1) + self.pmtf_ortho = np.array([0.0]).reshape(-1, 1) + if maxdeg >= 2: + self.pmtf_colinear = ((1.0 + self.k[2, :]) / (1.0 - self.tk[2, :] / self.tk2secular)).reshape(-1, 1) # Valid only for elastic regime, not viscous. Also neglects chandler wobble. + self.pmtf_ortho = np.array([0.0]).reshape(-1, 1) # Time self.istime = 1 # Temporal love numbers by default @@ -83,4 +101,6 @@ md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.tl', 'NaN', 1, 'Inf', 1) md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.tk2secular', 'NaN', 1, 'Inf', 1) + md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.pmtf_colinear', 'NaN', 1, 'Inf', 1) + md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.pmtf_ortho', 'NaN', 1, 'Inf', 1) md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.timefreq', 'NaN', 1, 'Inf', 1) md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.istime', 'NaN', 1, 'Inf', 1, 'values', [0, 1]) @@ -91,7 +111,9 @@ ntf = len(self.timefreq) - if (np.shape(self.h)[1] != ntf or np.shape(self.k)[1] != ntf or np.shape(self.l)[1] != ntf or np.shape(self.th)[1] != ntf or np.shape(self.tk)[1] != ntf or np.shape(self.tl)[1] != ntf): + if (np.shape(self.h)[1] != ntf or np.shape(self.k)[1] != ntf or np.shape(self.l)[1] != ntf or np.shape(self.th)[1] != ntf or np.shape(self.tk)[1] != ntf or np.shape(self.tl)[1] != ntf or np.shape(self.pmtf_colinear)[1] != ntf or np.shape(self.pmtf_ortho)[1] != ntf): raise ValueError('lovenumbers error message: love numbers should have as many time/frequency steps as the time/frequency vector') + if self.istime and self.timefreq[0] != 0: + raise ValueError('temporal love numbers must start with elastic response, i.e. timefreq[0] = 0') return md #}}} @@ -109,5 +131,9 @@ WriteData(fid, prefix, 'object', self, 'fieldname', 'tk', 'name', 'md.solidearth.lovenumbers.tk', 'format', 'DoubleMat', 'mattype', 1) WriteData(fid, prefix, 'object', self, 'fieldname', 'tl', 'name', 'md.solidearth.lovenumbers.tl', 'format', 'DoubleMat', 'mattype', 1) + WriteData(fid, prefix, 'object', self, 'fieldname', 'pmtf_colinear', 'name', 'md.solidearth.lovenumbers.pmtf_colinear', 'format', 'DoubleMat', 'mattype', 1) + WriteData(fid, prefix, 'object', self, 'fieldname', 'pmtf_ortho', 'name', 'md.solidearth.lovenumbers.pmtf_ortho', 'format', 'DoubleMat', 'mattype', 1) WriteData(fid, prefix, 'object', self, 'data', self.tk2secular, 'fieldname', 'lovenumbers.tk2secular', 'format', 'Double') + WriteData(fid, prefix, 'object', self, 'fieldname', 'pmtf_colinear','name','md.solidearth.lovenumbers.pmtf_colinear','format','DoubleMat','mattype',1); + WriteData(fid, prefix, 'object', self, 'fieldname', 'pmtf_ortho','name','md.solidearth.lovenumbers.pmtf_ortho','format','DoubleMat','mattype',1); if (self.istime): @@ -118,5 +144,5 @@ WriteData(fid, prefix, 'object', self, 'fieldname', 'timefreq', 'name', 'md.solidearth.lovenumbers.timefreq', 'format', 'DoubleMat', 'mattype', 1, 'scale', scale); #}}} - + def extrude(self, md): #{{{ return Index: /issm/trunk/src/m/classes/m1qn3inversion.py =================================================================== --- /issm/trunk/src/m/classes/m1qn3inversion.py (revision 27034) +++ /issm/trunk/src/m/classes/m1qn3inversion.py (revision 27035) @@ -1,4 +1,3 @@ import numpy as np - from checkfield import checkfield from fielddisplay import fielddisplay Index: /issm/trunk/src/m/classes/massfluxatgate.py =================================================================== --- /issm/trunk/src/m/classes/massfluxatgate.py (revision 27034) +++ /issm/trunk/src/m/classes/massfluxatgate.py (revision 27035) @@ -1,2 +1,3 @@ +import numpy as np from fielddisplay import fielddisplay from pairoptions import pairoptions @@ -20,5 +21,5 @@ self.definitionstring = '' self.profilename = '' - self.segments = float('NaN') + self.segments = np.nan #set defaults Index: /issm/trunk/src/m/classes/matdamageice.py =================================================================== --- /issm/trunk/src/m/classes/matdamageice.py (revision 27034) +++ /issm/trunk/src/m/classes/matdamageice.py (revision 27035) @@ -57,5 +57,5 @@ s += '{}\n'.format(fielddisplay(self, 'rheology_law', 'law for the temperature dependance of the rheology: \'None\', \'BuddJacka\', \'Cuffey\', \'CuffeyTemperate\', \'Paterson\', \'Arrhenius\' or \'LliboutryDuval\'')) s += '{}\n'.format(fielddisplay(self, 'earth_density', 'Mantle density [kg m^-3]')) - return string + return s #}}} @@ -93,5 +93,5 @@ # Thermal exchange velocity (ice-water interface) (m/s) self.thermal_exchange_velocity = 1.00e-4 - # Rheology law: what is the temperature dependence of B with T + # Rheology law: what is the temperature dependence of B with T # available: none, paterson and arrhenius self.rheology_law = 'Paterson' Index: /issm/trunk/src/m/classes/materials.m =================================================================== --- /issm/trunk/src/m/classes/materials.m (revision 27034) +++ /issm/trunk/src/m/classes/materials.m (revision 27035) @@ -264,7 +264,7 @@ end ind=find(md.materials.issolid==0); - if sum(ismember(diff(ind),1)>=1) %if there are at least two consecutive indices that contain issolid = 0 - error(['Fluid layers detected at layers #', num2str(ind'), ', but having 2 or more adjacent fluid layers is not supported yet. Consider merging them.']) - end + %if sum(ismember(diff(ind),1)>=1) %if there are at least two consecutive indices that contain issolid = 0 + % error(['Fluid layers detected at layers #', num2str(ind'), ', but having 2 or more adjacent fluid layers is not supported yet. Consider merging them.']) + %end case 'hydro' Index: /issm/trunk/src/m/classes/materials.py =================================================================== --- /issm/trunk/src/m/classes/materials.py (revision 27034) +++ /issm/trunk/src/m/classes/materials.py (revision 27035) @@ -1,4 +1,3 @@ import numpy as np - from checkfield import checkfield from fielddisplay import fielddisplay @@ -173,9 +172,9 @@ self.rheology_n = 3 elif nat == 'litho': - # We default to a configuration that enables running GIA + # We default to a configuration that enables running GIA # solutions using giacaron and/or giaivins self.numlayers = 2 - # Center of the earth (approximation, must not be 0), then the + # Center of the earth (approximation, must not be 0), then the # lab (lithosphere/asthenosphere boundary) then the surface # (with 1d3 to avoid numerical singularities) @@ -250,6 +249,6 @@ raise RuntimeError('First layer must be solid (issolid[0] > 0 AND lame_mu[0] > 0). Add a weak inner core if necessary.') ind = np.where(md.materials.issolid == 0)[0] - if np.sum(np.in1d(np.diff(ind),1) >= 1): # If there are at least two consecutive indices that contain issolid = 0 - raise RuntimeError('Fluid layers detected at layers #' + indices + ', but having 2 or more adjacent fluid layers is not supported yet. Consider merging them.') + #if np.sum(np.in1d(np.diff(ind),1) >= 1): # If there are at least two consecutive indices that contain issolid = 0 + # raise RuntimeError('Fluid layers detected at layers #' + indices + ', but having 2 or more adjacent fluid layers is not supported yet. Consider merging them.') elif nat == 'hydro': @@ -295,5 +294,5 @@ WriteData(fid, prefix, 'object', self, 'class', 'materials', 'fieldname', 'density', 'format', 'DoubleMat', 'mattype', 3) WriteData(fid, prefix, 'object', self, 'class', 'materials', 'fieldname', 'viscosity', 'format', 'DoubleMat', 'mattype', 3) - WriteData(fid, prefix, 'object', self, 'class', 'materials', 'fieldname', 'rheologymodel', 'format', 'DoubleMat', 'mattype', 3) + WriteData(fid, prefix, 'object', self, 'class', 'materials', 'fieldname', 'rheologymodel', 'format', 'DoubleMat', 'mattype', 3) WriteData(fid, prefix, 'object', self, 'class', 'materials', 'fieldname', 'burgers_viscosity', 'format', 'DoubleMat', 'mattype', 3) WriteData(fid, prefix, 'object', self, 'class', 'materials', 'fieldname', 'burgers_mu', 'format', 'DoubleMat', 'mattype', 3) Index: /issm/trunk/src/m/classes/model.m =================================================================== --- /issm/trunk/src/m/classes/model.m (revision 27034) +++ /issm/trunk/src/m/classes/model.m (revision 27035) @@ -928,13 +928,31 @@ x_edges = 0.5*(md.mesh.x(edges(:,1)) + md.mesh.x(edges(:,2))); y_edges = 0.5*(md.mesh.y(edges(:,1)) + md.mesh.y(edges(:,2))); - md2.mesh.x = [md2.mesh.x;x_edges]; - md2.mesh.y = [md2.mesh.y;y_edges]; - md2.mesh.elements = [... + xnew = [md2.mesh.x;x_edges]; + ynew = [md2.mesh.y;y_edges]; + indexnew = [... index(:,1) nbv+edges_tria(:,3) nbv+edges_tria(:,2);... nbv+edges_tria(:,2) nbv+edges_tria(:,3) nbv+edges_tria(:,1);... nbv+edges_tria(:,2) nbv+edges_tria(:,1) index(:,3);... nbv+edges_tria(:,3) index(:,2) nbv+edges_tria(:,1)]; - md2.mesh.numberofelements = 4*nbe; - md2.mesh.numberofvertices = nbv + size(edges,1); + %md2.mesh.numberofelements = 4*nbe; + %md2.mesh.numberofvertices = nbv + size(edges,1); + + %Call Bamg to update other mesh properties + [bamgmesh_out bamggeom_out]=BamgConvertMesh(indexnew,xnew,ynew); + md2.mesh.x = bamgmesh_out.Vertices(:,1); + md2.mesh.y = bamgmesh_out.Vertices(:,2); + md2.mesh.elements = bamgmesh_out.Triangles(:,1:3); + md2.mesh.edges = bamgmesh_out.IssmEdges; + md2.mesh.segments = bamgmesh_out.IssmSegments(:,1:3); + md2.mesh.segmentmarkers = bamgmesh_out.IssmSegments(:,4); + md2.mesh.numberofelements = size(md2.mesh.elements,1); + md2.mesh.numberofvertices = length(md2.mesh.x); + md2.mesh.numberofedges = size(md2.mesh.edges,1); + md2.mesh.vertexonboundary = zeros(md2.mesh.numberofvertices,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2)) = 1; + + %Deal with boudary + md2.mesh.vertexonboundary = [md.mesh.vertexonboundary;sum(md.mesh.vertexonboundary(edges),2)==2]; + md2.mesh.elementconnectivity=bamgmesh_out.ElementConnectivity; + md2.mesh.elementconnectivity(find(isnan(md2.mesh.elementconnectivity)))=0; disp([' Old number of elements: ' num2str(nbe)]); disp([' New number of elements: ' num2str(4*nbe)]); @@ -1734,52 +1752,67 @@ end % }}} - function savemodeljs(md,modelname,websiteroot,varargin) % {{{ - - %the goal of this routine is to save the model as a javascript array that can be included in any html - %file: - - options=pairoptions(varargin{:}); - optimization=getfieldvalue(options,'optimize',0); - - - %disp: - disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']); - - %open file for writing and declare the model: - fid=fopen([websiteroot '/js/' modelname '.js'],'w'); - fprintf(fid,'var %s=new model();\n',modelname); - - %now go through all the classes and fwrite all the corresponding fields: - - fields=properties('model'); + function saveasstruct(md,filename) % {{{ + + fields=sort(properties('model')); %sort fields so that comparison of binary files is easier + disp('Converting all model fields to struct...'); + warning off MATLAB:structOnObject for i=1:length(fields), field=fields{i}; - - %Some properties do not need to be saved - if ismember(field,{'results','cluster' }), - continue; - end - - %some optimization: - if optimization==1, - %optimize for plotting only: - if ~ismember(field,{'geometry','mesh','mask'}), - continue; - end - end - - %Check that current field is an object - if ~isobject(md.(field)) - error(['field ''' char(field) ''' is not an object']); - end - - %savemodeljs for current object - %disp(['javascript saving ' field '...']); - savemodeljs(md.(field),fid,modelname); - end - - %done, close file: - fclose(fid); + md.(field) = struct(md.(field)); + end + disp('Converting model to struct...'); + md=struct(md); + warning on MATLAB:structOnObject + disp(['Saving as ' filename '...']); + save(filename,'md','-v7.3') + end % }}} +function savemodeljs(md,modelname,websiteroot,varargin) % {{{ + + %the goal of this routine is to save the model as a javascript array that can be included in any html + %file: + + options=pairoptions(varargin{:}); + optimization=getfieldvalue(options,'optimize',0); + + + %disp: + disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']); + + %open file for writing and declare the model: + fid=fopen([websiteroot '/js/' modelname '.js'],'w'); + fprintf(fid,'var %s=new model();\n',modelname); + + %now go through all the classes and fwrite all the corresponding fields: + + fields=properties('model'); + for i=1:length(fields), + field=fields{i}; + + %Some properties do not need to be saved + if ismember(field,{'results','cluster' }), + continue; end + + %some optimization: + if optimization==1, + %optimize for plotting only: + if ~ismember(field,{'geometry','mesh','mask'}), + continue; + end + end + + %Check that current field is an object + if ~isobject(md.(field)) + error(['field ''' char(field) ''' is not an object']); + end + + %savemodeljs for current object + %disp(['javascript saving ' field '...']); + savemodeljs(md.(field),fid,modelname); end - end + + %done, close file: + fclose(fid); +end + end +end Index: /issm/trunk/src/m/classes/model.py =================================================================== --- /issm/trunk/src/m/classes/model.py (revision 27034) +++ /issm/trunk/src/m/classes/model.py (revision 27035) @@ -823,7 +823,7 @@ md.inversion.max_parameters = project2d(md, md.inversion.max_parameters, md.mesh.numberoflayers) if md.smb.__class__.__name__ == 'SMBforcing' and not np.isnan(md.smb.mass_balance).all(): - md.smb.mass_balance = project2d(md, md.smb.mass_balance, md.mesh.numberoflayers) + md.smb.mass_balance = project2d(md, md.smb.mass_balance, md.mesh.numberoflayers) elif md.smb.__class__.__name__ == 'SMBhenning' and not np.isnan(md.smb.smbref).all(): - md.smb.smbref = project2d(md, md.smb.smbref, md.mesh.numberoflayers) + md.smb.smbref = project2d(md, md.smb.smbref, md.mesh.numberoflayers) # Results Index: /issm/trunk/src/m/classes/pairoptions.py =================================================================== --- /issm/trunk/src/m/classes/pairoptions.py (revision 27034) +++ /issm/trunk/src/m/classes/pairoptions.py (revision 27035) @@ -11,11 +11,16 @@ def __init__(self, *arg): # {{{ - self.functionname = '' + #self.functionname = '' self.list = OrderedDict() #get calling function name - import inspect - if len(inspect.stack()) > 1: - self.functionname = inspect.stack()[1][3] + #import inspect + #if len(inspect.stack()) > 1: + #self.functionname = inspect.stack()[1][3] + import traceback + try: + self.functionname = traceback.extract_stack(limit=2)[0][2] + except IndexError: + pass #this is probably similar to the previous if treatment (but faster) #initialize list @@ -98,6 +103,7 @@ """ - disp(['WARNING: pairoptions::displayunused is not yet implemented']) + print('WARNING: pairoptions::displayunused is not yet implemented') # }}} + def exist(self, field): # {{{ """EXIST - check if the option exists Index: /issm/trunk/src/m/classes/regionaloutput.py =================================================================== --- /issm/trunk/src/m/classes/regionaloutput.py (revision 27034) +++ /issm/trunk/src/m/classes/regionaloutput.py (revision 27035) @@ -25,7 +25,8 @@ self.name = '' + self.model= '' self.definitionstring = '' self.outputnamestring = '' - self.mask = float('NaN') + self.mask = np.nan self.maskexpstring = '' @@ -46,6 +47,6 @@ self.setmaskfromexp(modelname) - if (len(self.mask) <= 1 & np.any(np.isnan(self.mask))): - error('regionaloutput error message: ''mask'' field or ''maskexpstring'' and ''model'' fields should be defined!') + # if (len(self.mask) <= 1 & np.any(np.isnan(self.mask))): + # raise IOError('regionaloutput error message: ''mask'' field or ''maskexpstring'' and ''model'' fields should be defined!') #}}} @@ -76,4 +77,5 @@ return self # }}} + def checkconsistency(self, md, solution, analyses): # {{{ Index: /issm/trunk/src/m/classes/results.py =================================================================== --- /issm/trunk/src/m/classes/results.py (revision 27034) +++ /issm/trunk/src/m/classes/results.py (revision 27035) @@ -143,8 +143,12 @@ def __getattr__(self, key): #{{{ - if len(self.steps) == 1: - return getattr(self.steps[0], key) - else: - raise Exception('. error: Currently, can only get a field if we are not working with a transient solution.') + # NOTE: Currently only returning value from first frame of transient solution (see retrieval of md.results.TransientSolution.BedGRD in test2051.py for justification) + return getattr(self.steps[0], key) + + # Original code + # if len(self.steps) == 1: + # return getattr(self.steps[0], key) + # else: + # raise Exception('. error: Currently, can only get a field if we are not working with a transient solution.') #}}} Index: /issm/trunk/src/m/classes/rifts.py =================================================================== --- /issm/trunk/src/m/classes/rifts.py (revision 27034) +++ /issm/trunk/src/m/classes/rifts.py (revision 27035) @@ -67,29 +67,31 @@ numpairs = 0 - for rift in self.riftstruct: - numpairs += np.size(rift['penaltypairs'], axis=0) + if numrifts > 0: + for rift in self.riftstruct: + numpairs += np.size(rift['penaltypairs'], axis=0) - # Convert strings in riftstruct to hard coded numbers - FillDict = {'Air': 0, - 'Ice': 1, - 'Melange': 2, - 'Water': 3} - for rift in self.riftstruct: - if rift['fill'] in ['Air', 'Ice', 'Melange', 'Water']: - rift['fill'] = FillDict[rift['fill']] + # Convert strings in riftstruct to hard coded numbers + FillDict = {'Air': 0, + 'Ice': 1, + 'Melange': 2, + 'Water': 3} + for rift in self.riftstruct: + if rift['fill'] in ['Air', 'Ice', 'Melange', 'Water']: + rift['fill'] = FillDict[rift['fill']] - # 2 for nodes + 2 for elements + 2 for normals + 1 for length + 1 for fill + 1 for friction + 1 for fraction + 1 for fractionincrement + 1 for state. - data = np.zeros((numpairs, 12)) - count = 0 - for rift in self.riftstruct: - numpairsforthisrift = np.size(rift['penaltypairs'], 0) - data[count:count + numpairsforthisrift, 0:7] = rift['penaltypairs'] - data[count:count + numpairsforthisrift, 7] = rift['fill'] - data[count:count + numpairsforthisrift, 8] = rift['friction'] - data[count:count + numpairsforthisrift, 9] = rift['fraction'] - data[count:count + numpairsforthisrift, 10] = rift['fractionincrement'] - data[count:count + numpairsforthisrift, 11] = rift['state'].reshape(-1) - count += numpairsforthisrift - + # 2 for nodes + 2 for elements + 2 for normals + 1 for length + 1 for fill + 1 for friction + 1 for fraction + 1 for fractionincrement + 1 for state. + data = np.zeros((numpairs, 12)) + count = 0 + for rift in self.riftstruct: + numpairsforthisrift = np.size(rift['penaltypairs'], 0) + data[count:count + numpairsforthisrift, 0:7] = rift['penaltypairs'] + data[count:count + numpairsforthisrift, 7] = rift['fill'] + data[count:count + numpairsforthisrift, 8] = rift['friction'] + data[count:count + numpairsforthisrift, 9] = rift['fraction'] + data[count:count + numpairsforthisrift, 10] = rift['fractionincrement'] + data[count:count + numpairsforthisrift, 11] = rift['state'].reshape(-1) + count += numpairsforthisrift + else: + data = np.zeros((numpairs, 12)) WriteData(fid, prefix, 'data', numrifts, 'name', 'md.rifts.numrifts', 'format', 'Integer') WriteData(fid, prefix, 'data', data, 'name', 'md.rifts.riftstruct', 'format', 'DoubleMat', 'mattype', 3) Index: /issm/trunk/src/m/classes/sampling.m =================================================================== --- /issm/trunk/src/m/classes/sampling.m (revision 27034) +++ /issm/trunk/src/m/classes/sampling.m (revision 27035) @@ -9,5 +9,5 @@ tau = 0; beta = NaN; - phi = 0; + phi = NaN; alpha = 0; robin = 0; @@ -30,5 +30,5 @@ disp(sprintf('\n %s','Parameters of PDE operator (kappa^2 I-Laplacian)^(alpha/2)(tau):')); fielddisplay(self,'kappa','coefficient of the identity operator'); - fielddisplay(self,'tau','scaling coefficient of the solution (default: 1.0)'); + fielddisplay(self,'tau','scaling coefficient of the solution'); fielddisplay(self,'alpha','exponent in PDE operator, (default: 2.0, BiLaplacian covariance operator)'); @@ -47,12 +47,6 @@ function self = setdefaultparameters(self) % {{{ - %Scaling coefficient - self.tau=1; - %Apply Robin boundary conditions self.robin=0; - - %Temporal correlation factor - self.phi=0; %Exponent in fraction SPDE (default: 2, biLaplacian covariance @@ -77,10 +71,9 @@ md = checkfield(md,'fieldname','sampling.kappa','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1],'>',0); - md = checkfield(md,'fieldname','sampling.tau','NaN',1,'Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','sampling.tau','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1],'>',0); md = checkfield(md,'fieldname','sampling.robin','numel',1,'values',[0 1]); if(md.sampling.robin) md = checkfield(md,'fieldname','sampling.beta','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1],'>',0); - end - md = checkfield(md,'fieldname','sampling.phi','NaN',1,'Inf',1,'numel',1,'>=',0); + end md = checkfield(md,'fieldname','sampling.alpha','NaN',1,'Inf',1,'numel',1,'>',0); md = checkfield(md,'fieldname','sampling.seed','NaN',1,'Inf',1,'numel',1); @@ -91,7 +84,7 @@ WriteData(fid,prefix,'object',self,'fieldname','kappa','format','DoubleMat','mattype',1); - WriteData(fid,prefix,'object',self,'fieldname','tau','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','tau','format','DoubleMat','mattype',1); WriteData(fid,prefix,'object',self,'fieldname','beta','format','DoubleMat','mattype',1); - WriteData(fid,prefix,'object',self,'fieldname','phi','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','phi','format','DoubleMat','mattype',1); WriteData(fid,prefix,'object',self,'fieldname','alpha','format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','robin','format','Boolean'); @@ -110,8 +103,8 @@ nu = self.alpha-1; - KAPPA = sqrt(8*nu)/lc; - TAU = sqrt(gamma(nu)/(gamma(self.alpha)*(4*pi)*KAPPA^(2*nu)*sigma^2)); - md.sampling.kappa = KAPPA*ones(md.mesh.numberofvertices,1); - md.sampling.tau = TAU; + KAPPA = sqrt(8*nu)./lc; + TAU = sqrt(gamma(nu)./(gamma(self.alpha)*(4*pi)*KAPPA.^(2*nu).*sigma.^2)); + md.sampling.kappa = KAPPA.*ones(md.mesh.numberofvertices,1); + md.sampling.tau = TAU.*ones(md.mesh.numberofvertices,1); end % }}} @@ -121,5 +114,5 @@ writejsdouble(fid,[modelname '.sampling.tau'],self.tau); writejsdouble(fid,[modelname '.sampling.beta'],self.beta); - writejsdouble(fid,[modelname '.sampling.phi'],self.beta); + writejsdouble(fid,[modelname '.sampling.phi'],self.phi); writejsdouble(fid,[modelname '.sampling.alpha'],self.alpha); writejsdouble(fid,[modelname '.sampling.robin'],self.robin); Index: /issm/trunk/src/m/classes/solidearth.py =================================================================== --- /issm/trunk/src/m/classes/solidearth.py (revision 27034) +++ /issm/trunk/src/m/classes/solidearth.py (revision 27035) @@ -1,4 +1,3 @@ import numpy as np - from checkfield import checkfield from fielddisplay import fielddisplay @@ -6,5 +5,4 @@ from MatlabFuncs import * from planetradius import planetradius -from project3d import project3d from rotational import rotational from solidearthsettings import solidearthsettings @@ -25,14 +23,14 @@ def __init__(self, *args): # {{{ - self.settings = solidearthsettings() - self.external = None - self.lovenumbers = lovenumbers() - self.rotational = rotational() - self.planetradius = planetradius('earth') - self.requested_outputs = [] - self.transitions = [] - self.partitionice = [] - self.partitionhydro = [] - self.partitionocean = [] + self.settings = solidearthsettings() + self.external = None + self.lovenumbers = lovenumbers() + self.rotational = rotational() + self.planetradius = planetradius('earth') + self.requested_outputs = [] + self.transitions = [] + self.partitionice = [] + self.partitionhydro = [] + self.partitionocean = [] nargs = len(args) @@ -44,4 +42,5 @@ raise Exception('solidearth constructor error message: zero or one argument only!') # }}} + def __repr__(self): # {{{ s = ' solidearthinputs, forcings and settings:\n' @@ -57,8 +56,11 @@ print(self.lovenumbers) print(self.rotational) - if len(self.external): + try: print(self.external) + except TypeError: + pass return s # }}} + def setdefaultparameters(self, planet): # {{{ # Output default @@ -79,4 +81,5 @@ self.planetradius = planetradius(planet) # }}} + def checkconsistency(self, md, solution, analyses): # {{{ if ('SealevelchangeAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.isslc): @@ -94,7 +97,9 @@ return md # }}} + def defaultoutputs(self, md): # {{{ return ['Sealevel'] # }}} + def marshall(self, prefix, md, fid): # {{{ WriteData(fid, prefix, 'object', self, 'fieldname', 'planetradius', 'format', 'Double') @@ -140,4 +145,5 @@ WriteData(fid, prefix, 'data', outputs, 'name', 'md.solidearth.requested_outputs', 'format', 'StringArray') # }}} + def extrude(self, md): # {{{ return self Index: /issm/trunk/src/m/classes/solidearthsettings.py =================================================================== --- /issm/trunk/src/m/classes/solidearthsettings.py (revision 27034) +++ /issm/trunk/src/m/classes/solidearthsettings.py (revision 27035) @@ -120,13 +120,13 @@ if md.mesh.__class__.__name__ == 'mesh3dsurface': if self.grdmodel == 2: - raise RuntimeException('model requires a 2D mesh to run gia Ivins computations (change mesh from mesh3dsurface to mesh2d)') + raise Exception('model requires a 2D mesh to run gia Ivins computations (change mesh from mesh3dsurface to mesh2d)') else: if self.grdmodel == 1: - raise RuntimeException('model requires a 3D surface mesh to run GRD computations (change mesh from mesh2d to mesh3dsurface)') + raise Exception('model requires a 3D surface mesh to run GRD computations (change mesh from mesh2d to mesh3dsurface)') if self.sealevelloading and not self.grdocean: - raise RuntimeException('solidearthsettings checkconsistency error message: need grdocean on if sealevelloading flag is set') + raise Exception('solidearthsettings checkconsistency error message: need grdocean on if sealevelloading flag is set') if self.compute_bp_grd and not md.solidearth.settings.isgrd: - raise RuntimeException('solidearthsettings checkconsistency error message; if bottom pressure grd patterns are requested, solidearth settings class should have isgrd flag on') + raise Exception('solidearthsettings checkconsistency error message; if bottom pressure grd patterns are requested, solidearth settings class should have isgrd flag on') return md Index: /issm/trunk/src/m/classes/spatiallinearbasalforcings.m =================================================================== --- /issm/trunk/src/m/classes/spatiallinearbasalforcings.m (revision 27034) +++ /issm/trunk/src/m/classes/spatiallinearbasalforcings.m (revision 27035) @@ -9,5 +9,7 @@ deepwater_melting_rate = NaN; deepwater_elevation = NaN; + upperwater_melting_rate = NaN; upperwater_elevation = NaN; + perturbation_melting_rate = NaN; geothermalflux = NaN; end @@ -25,5 +27,7 @@ self.deepwater_elevation=lb.deepwater_elevation*ones(nvertices,1); self.deepwater_melting_rate=lb.deepwater_melting_rate*ones(nvertices,1); + self.upperwater_melting_rate=lb.upperwater_melting_rate*ones(nvertices,1); self.upperwater_elevation=lb.upperwater_elevation*ones(nvertices,1); + self.perturbation_melting_rate=lb.perturbation_melting_rate*ones(nvertices,1); else self=structtoobj(spatiallinearbasalforcings(),varargin{1}); @@ -37,6 +41,8 @@ self.deepwater_melting_rate=project3d(md,'vector',self.deepwater_melting_rate,'type','node','layer',1); self.deepwater_elevation=project3d(md,'vector',self.deepwater_elevation,'type','node','layer',1); + self.upperwater_melting_rate=project3d(md,'vector',self.upperwater_melting_rate,'type','node','layer',1); self.upperwater_elevation=project3d(md,'vector',self.upperwater_elevation,'type','node','layer',1); self.geothermalflux=project3d(md,'vector',self.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux + self.perturbation_melting_rate=project3d(md,'vector',self.perturbation_melting_rate,'type','node','layer',1); end % }}} function self = initialize(self,md) % {{{ @@ -58,9 +64,14 @@ function md = checkconsistency(self,md,solution,analyses) % {{{ + if numel(md.basalforcings.perturbation_melting_rate)>1 + md = checkfield(md,'fieldname','basalforcings.perturbation_melting_rate','NaN',1,'Inf',1,'timeseries',1); + end + if ismember('MasstransportAnalysis',analyses) & ~(strcmp(solution,'TransientSolution') & md.transient.ismasstransport==0), md = checkfield(md,'fieldname','basalforcings.groundedice_melting_rate','NaN',1,'Inf',1,'timeseries',1); md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','NaN',1,'Inf',1,'timeseries',1,'>=',0); md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','NaN',1,'Inf',1,'timeseries',1); - md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','NaN',1,'Inf',1,'timeseries',1,'<',0); + md = checkfield(md,'fieldname','basalforcings.upperwater_melting_rate','NaN',1,'Inf',1,'timeseries',1,'>=',0); + md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','NaN',1,'Inf',1,'timeseries',1,'<=',0); end if ismember('BalancethicknessAnalysis',analyses), @@ -69,4 +80,5 @@ md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0,'numel',1); md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<','basalforcings.upperwater_elevation','numel',1); + md = checkfield(md,'fieldname','basalforcings.upperwater_melting_rate','>=',0,'numel',1); md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<=',0,'numel',1); end @@ -76,5 +88,6 @@ md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0,'numel',1); md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<','basalforcings.upperwater_elevation','numel',1); - md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<',0,'numel',1); + md = checkfield(md,'fieldname','basalforcings.upperwater_melting_rate','>=',0,'numel',1); + md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<=',0,'numel',1); md = checkfield(md,'fieldname','basalforcings.geothermalflux','NaN',1,'Inf',1,'timeseries',1,'>=',0); end @@ -86,5 +99,7 @@ fielddisplay(self,'deepwater_melting_rate','basal melting rate (positive if melting applied for floating ice whith base < deepwater_elevation) [m/yr]'); fielddisplay(self,'deepwater_elevation','elevation of ocean deepwater [m]'); + fielddisplay(self,'upperwater_melting_rate','basal melting rate (positive if melting applied for floating ice whith base >= upperwater_elevation) [m/yr]'); fielddisplay(self,'upperwater_elevation','elevation of ocean upperwater [m]'); + fielddisplay(self,'perturbation_melting_rate','basal melting rate perturbation added to computed melting rate (positive if melting) [m/yr]'); fielddisplay(self,'geothermalflux','geothermal heat flux [W/m^2]'); @@ -94,16 +109,12 @@ yts=md.constants.yts; - floatingice_melting_rate=zeros(md.mesh.numberofvertices,1); - pos=find(md.geometry.base<=md.basalforcings.deepwater_elevation); - floatingice_melting_rate(pos)=md.basalforcings.deepwater_melting_rate(pos); - pos=find(md.geometry.base>md.basalforcings.deepwater_elevation & md.geometry.base= upperwater_elevation) [m/yr]')) s += '{}\n'.format(fielddisplay(self, 'upperwater_elevation', 'elevation of ocean upperwater [m]')) + s += '{}\n'.format(fielddisplay(self, 'perturbation_melting_rate', 'basal melting rate perturbation added to computed melting rate (positive if melting) [m/yr]')) s += '{}\n'.format(fielddisplay(self, 'geothermalflux', 'geothermal heat flux [W/m^2]')) return s @@ -55,6 +61,8 @@ self.deepwater_melting_rate = project3d(md, 'vector', self.deepwater_melting_rate, 'type', 'node', 'layer', 1) self.deepwater_elevation = project3d(md, 'vector', self.deepwater_elevation, 'type', 'node', 'layer', 1) + self.upperwater_melting_rate = project3d(md, 'vector', self.upperwater_melting_rate, 'type', 'node', 'layer', 1) self.upperwater_elevation = project3d(md, 'vector', self.upperwater_elevation, 'type', 'node', 'layer', 1) self.geothermalflux = project3d(md, 'vector', self.geothermalflux, 'type', 'node', 'layer', 1) # Bedrock only gets geothermal flux + self.perturbation_melting_rate = project3d(md, 'vector', self.upperwater_melting_rate, 'type', 'node', 'layer', 1) return self #}}} @@ -72,8 +80,11 @@ def checkconsistency(self, md, solution, analyses): #{{{ + if not np.all(np.isnan(self.perturbation_melting_rate)): + md = checkfield(md, 'fieldname', 'basalforcings.perturbation_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1) if 'MasstransportAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.ismasstransport: md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1) md = checkfield(md, 'fieldname', 'basalforcings.deepwater_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1, '>=', 0) md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', 'NaN', 1, 'Inf', 1, 'timeseries', 1) + md = checkfield(md, 'fieldname', 'basalforcings.upperwater_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1, '>=', 0) md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', 'NaN', 1, 'Inf', 1, 'timeseries', 1, '<', 0) if 'BalancethicknessAnalysis' in analyses: @@ -82,4 +93,5 @@ md = checkfield(md, 'fieldname', 'basalforcings.deepwater_melting_rate', '>=', 0, 'numel', 1) md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', '<', 'basalforcings.upperwater_elevation', 'numel', 1) + md = checkfield(md, 'fieldname', 'basalforcings.upperwater_melting_rate', '>=', 0, 'numel', 1) md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', '<=', 0, 'numel', 1) if 'ThermalAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.isthermal: @@ -89,4 +101,5 @@ md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', '<', 'basalforcings.upperwater_elevation', 'numel', 1) md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', '<', 0, 'numel', 1) + md = checkfield(md, 'fieldname', 'basalforcings.deepwater_melting_rate', '>=', 0, 'numel', 1) md = checkfield(md, 'fieldname', 'basalforcings.geothermalflux', 'NaN', 1, 'Inf', 1, 'timeseries', 1, '>=', 0) return md @@ -96,15 +109,11 @@ yts = md.constants.yts - floatingice_melting_rate = np.zeros((md.mesh.numberofvertices, )) - pos = np.where(md.geometry.base <= md.basalforcings.deepwater_elevation)[0] - floatingice_melting_rate[pos] = md.basalforcings.deepwater_melting_rate[pos] - pos = np.where(np.logical_and.reduce(md.geometry.base > md.basalforcings.deepwater_elevation, md.geometry.base < md.basalforcings.upperwater_elevation)) - floatingice_melting_rate[pos] = md.basalforcings.deepwater_melting_rate[pos] * (md.geometry.base[pos] - md.basalforcings.upperwater_elevation[pos]) / (md.basalforcings.deepwater_elevation[pos] - md.basalforcings.upperwater_elevation[pos]) WriteData(fid, prefix, 'name', 'md.basalforcings.model', 'data', 6, 'format', 'Integer') - WriteData(fid, prefix, 'data', floatingice_melting_rate, 'format', 'DoubleMat', 'name', 'md.basalforcings.floatingice_melting_rate', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts) WriteData(fid, prefix, 'object', self, 'fieldname', 'groundedice_melting_rate', 'format', 'DoubleMat', 'name', 'md.basalforcings.groundedice_melting_rate', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1,'yts', md.constants.yts) WriteData(fid, prefix,'object', self, 'fieldname', 'geothermalflux', 'name', 'md.basalforcings.geothermalflux', 'format', 'DoubleMat', 'mattype', 1,'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts) WriteData(fid, prefix, 'object', self, 'fieldname', 'deepwater_melting_rate', 'format', 'DoubleMat', 'name', 'md.basalforcings.deepwater_melting_rate', 'scale', 1. / yts, 'mattype', 1) WriteData(fid, prefix, 'object', self, 'fieldname', 'deepwater_elevation', 'format', 'DoubleMat', 'name', 'md.basalforcings.deepwater_elevation', 'mattype', 1) + WriteData(fid, prefix, 'object', self, 'fieldname', 'upperwater_melting_rate', 'format', 'DoubleMat', 'name', 'md.basalforcings.upperwater_melting_rate', 'scale', 1. / yts, 'mattype', 1) WriteData(fid, prefix, 'object', self, 'fieldname', 'upperwater_elevation', 'format', 'DoubleMat', 'name', 'md.basalforcings.upperwater_elevation', 'mattype', 1) + WriteData(fid, prefix, 'object', self, 'fieldname', 'perturbation_melting_rate', 'format', 'DoubleMat', 'name', 'md.basalforcings.perturbation_melting_rate', 'scale', 1. / yts, 'mattype', 1) #}}} Index: /issm/trunk/src/m/classes/stochasticforcing.m =================================================================== --- /issm/trunk/src/m/classes/stochasticforcing.m (revision 27034) +++ /issm/trunk/src/m/classes/stochasticforcing.m (revision 27035) @@ -11,4 +11,5 @@ default_id = NaN; covariance = NaN; + stochastictimestep = 0; randomflag = 1; end @@ -35,4 +36,7 @@ num_fields = numel(self.fields); + if(self.stochastictimestep==0) + md.stochasticforcing.stochastictimestep = md.timestepping.time_step; %by default: stochastictimestep set to ISSM time step + end %Check that covariance matrix is positive definite @@ -48,5 +52,5 @@ for field=self.fields %Checking agreement of classes - if(contains(field,'SMB')) + if(contains(field,'SMBautoregression')) mdname = structstoch.mdnames(find(strcmp(structstoch.fields,char(field)))); if~(isequal(class(md.smb),char(mdname))) @@ -54,4 +58,10 @@ end end + if(contains(field,'SMBforcing')) + mdname = structstoch.mdnames(find(strcmp(structstoch.fields,char(field)))); + if~(isequal(class(md.smb),char(mdname))) + error('md.smb does not agree with stochasticforcing field %s', char(field)); + end + end if(contains(field,'FrontalForcings')) mdname = structstoch.mdnames(find(strcmp(structstoch.fields,char(field)))); @@ -67,4 +77,16 @@ end if(contains(field,'BasalforcingsFloatingice')) + mdname = structstoch.mdnames(find(strcmp(structstoch.fields,char(field)))); + if~(isequal(class(md.basalforcings),char(mdname))) + error('md.basalforcings does not agree with stochasticforcing field %s', char(field)); + end + end + if(contains(field,'BasalforcingsSpatialDeepwaterMeltingRate')) + mdname = structstoch.mdnames(find(strcmp(structstoch.fields,char(field)))); + if~(isequal(class(md.basalforcings),char(mdname))) + error('md.basalforcings does not agree with stochasticforcing field %s', char(field)); + end + end + if(contains(field,'BasalforcingsDeepwaterMeltingRateAutoregression')) mdname = structstoch.mdnames(find(strcmp(structstoch.fields,char(field)))); if~(isequal(class(md.basalforcings),char(mdname))) @@ -85,31 +107,65 @@ end %Checking for specific dimensions - if ~(strcmp(field,'SMBautoregression') || strcmp(field,'FrontalForcingsRignotAutoregression')) + if ~(strcmp(field,'SMBautoregression') || strcmp(field,'FrontalForcingsRignotAutoregression') || strcmp(field,'BasalforcingsDeepwaterMeltingRateAutoregression')) checkdefaults = true; %field with non-specific dimensionality end end - %Retrieve sum of all the field dimensionalities - size_tot = self.defaultdimension*num_fields; - indSMBar = -1; %about to check for index of SMBautoregression - indTFar = -1; %about to check for index of FrontalForcingsRignotAutoregression + %Retrieve all the field dimensionalities + dimensions = self.defaultdimension*ones(1,num_fields); + indSMBar = -1; %about to check for index of SMBautoregression + indTFar = -1; %about to check for index of FrontalForcingsRignotAutoregression + indBDWar = -1; %about to check for index of BasalforcingsDeepwaterMeltingRateAutoregression if any(contains(self.fields,'SMBautoregression')) - size_tot = size_tot-self.defaultdimension+md.smb.num_basins; - indSMBar = find(contains(self.fields,'SMBautoregression')); %index of SMBar, now check for consistency with TFar timestep (08Nov2021) + indSMBar = find(contains(self.fields,'SMBautoregression')); %index of SMBar, now check for consistency with other ar timesteps + dimensions(indSMBar) = md.smb.num_basins; + if(md.smb.ar_timestep=',md.timestepping.time_step); md = checkfield(md,'fieldname','stochasticforcing.randomflag','numel',[1],'values',[0 1]); if(checkdefaults) %need to check the defaults @@ -121,8 +177,9 @@ disp(sprintf(' stochasticforcing parameters:')); fielddisplay(self,'isstochasticforcing','is stochasticity activated?'); - fielddisplay(self,'fields','fields with stochasticity applied, ex: {''SMBautoregression''}, or {''FrontalForcingsRignotAutoregression''}'); + fielddisplay(self,'fields','fields with stochasticity applied, ex: [{''SMBautoregression''}], or [{''SMBforcing''},{''DefaultCalving''}]'); fielddisplay(self,'defaultdimension','dimensionality of the noise terms (does not apply to fields with their specific dimension)'); fielddisplay(self,'default_id','id of each element for partitioning of the noise terms (does not apply to fields with their specific partition)'); fielddisplay(self,'covariance','covariance matrix for within- and between-fields covariance (units must be squared field units)'); + fielddisplay(self,'stochastictimestep','timestep at which new stochastic noise terms are generated (default: md.timestepping.time_step)'); fielddisplay(self,'randomflag','whether to apply real randomness (true) or pseudo-randomness with fixed seed (false)'); disp('Available fields:'); @@ -140,4 +197,9 @@ return else + + if(self.stochastictimestep==0) + disp(' stochasticforcing.stocahstictimestep not specified: set to md.timestepping.time_step'); + self.stochastictimestep = md.timestepping.time_step; %by default: stochastictimestep set to ISSM time step + end %Retrieve dimensionality of each field @@ -152,9 +214,12 @@ dimensions(ind) = md.frontalforcings.num_basins; end + if(strcmp(field,'BasalforcingsDeepwaterMeltingRateAutoregression')) + dimensions(ind) = md.basalforcings.num_basins; + end ind = ind+1; end %Scaling covariance matrix (scale column-by-column and row-by-row) - scaledfields = {'DefaultCalving','FloatingMeltRate','SMBautoregression'}; %list of fields that need scaling *1/yts + scaledfields = {'BasalforcingsDeepwaterMeltingRateAutoregression','BasalforcingsSpatialDeepwaterMeltingRate','DefaultCalving','FloatingMeltRate','SMBautoregression','SMBforcing'}; %list of fields that need scaling *1/yts tempcovariance = self.covariance; %copy of covariance to avoid writing back in member variable for i=1:num_fields @@ -173,4 +238,5 @@ self.default_id = zeros(md.mesh.numberofelements,1); end + WriteData(fid,prefix,'data',num_fields,'name','md.stochasticforcing.num_fields','format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','fields','format','StringArray'); @@ -179,4 +245,5 @@ WriteData(fid,prefix,'object',self,'fieldname','defaultdimension','format','Integer'); WriteData(fid,prefix,'data',tempcovariance,'name','md.stochasticforcing.covariance','format','DoubleMat'); + WriteData(fid,prefix,'object',self,'fieldname','stochastictimestep','format','Double','scale',yts); WriteData(fid,prefix,'object',self,'fieldname','randomflag','format','Boolean'); end @@ -195,16 +262,22 @@ % supported and corresponding md names structure.fields = {... + 'BasalforcingsDeepwaterMeltingRateAutoregression',... + 'BasalforcingsSpatialDeepwaterMeltingRate',... 'DefaultCalving',... 'FloatingMeltRate',... 'FrictionWaterPressure',... 'FrontalForcingsRignotAutoregression',... - 'SMBautoregression' + 'SMBautoregression',... + 'SMBforcing' }; structure.mdnames = {... + 'autoregressionlinearbasalforcings',... + 'spatiallinearbasalforcings',... 'calving',... 'basalforcings',... 'friction',... 'frontalforcingsrignotautoregression',... - 'SMBautoregression' + 'SMBautoregression',... + 'SMBforcing' }; end % }}} Index: /issm/trunk/src/m/classes/stochasticforcing.py =================================================================== --- /issm/trunk/src/m/classes/stochasticforcing.py (revision 27034) +++ /issm/trunk/src/m/classes/stochasticforcing.py (revision 27035) @@ -18,4 +18,5 @@ self.default_id = np.nan self.covariance = np.nan + self.stochastictimestep = 0 self.randomflag = 1 @@ -28,14 +29,18 @@ s = ' stochasticforcing parameters:\n' s += '{}\n'.format(fielddisplay(self, 'isstochasticforcing', 'is stochasticity activated?')) - s += '{}\n'.format(fielddisplay(self, 'fields', 'fields with stochasticity applied, ex: [\'SMBautoregression\'], or [\'FrontalForcingsRignotAutoregression\']')) + s += '{}\n'.format(fielddisplay(self, 'fields', 'fields with stochasticity applied, ex: [\'SMBautoregression\'], or [\'SMBforcing\',\'DefaultCalving\']')) s += '{}\n'.format(fielddisplay(self, 'defaultdimension', 'dimensionality of the noise terms (does not apply to fields with their specific dimension)')) s += '{}\n'.format(fielddisplay(self, 'default_id', 'id of each element for partitioning of the noise terms (does not apply to fields with their specific partition)')) s += '{}\n'.format(fielddisplay(self, 'covariance', 'covariance matrix for within- and between-fields covariance (units must be squared field units)')) + s += '{}\n'.format(fielddisplay(self, 'stochastictimestep', 'timestep at which new stochastic noise terms are generated (default: md.timestepping.time_step)')) s += '{}\n'.format(fielddisplay(self, 'randomflag', 'whether to apply real randomness (true) or pseudo-randomness with fixed seed (false)')) s += 'Available fields:\n' + s += ' BasalforcingsSpatialDeepwaterMeltingRate\n' s += ' DefaultCalving\n' s += ' FloatingMeltRate\n' + s += ' FrictionWaterPressure\n' + s += ' FrontalForcingsRignotAutoregression (thermal forcing)\n' s += ' SMBautoregression\n' - s += ' FrontalForcingsRignotAutoregression (thermal forcing)\n' + s += ' SMBforcing\n' return s #}}} @@ -43,7 +48,7 @@ def setdefaultparameters(self): # {{{ # Type of stabilization used - self.isstochasticforcing = 0 # stochasticforcing is turned off by default - self.fields = [] # Need to initialize to list to avoid "RuntimeError: object of type 'float' has no len()" on import of class - self.randomflag = 1 # true randomness is implemented by default + self.isstochasticforcing = 0 # stochasticforcing is turned off by default + self.fields = [] # Need to initialize to list to avoid "RuntimeError: object of type 'float' has no len()" on import of class + self.randomflag = 1 # true randomness is implemented by default return self #}}} @@ -55,4 +60,7 @@ num_fields = len(self.fields) + if(self.stochastictimestep==0): + md.stochasticforcing.stochastictimestep = md.timestepping.time_step #by default: stochastictimestep set to ISSM time step + print(' stochasticforcing.stocahstictimestep not specified: set to md.timestepping.time_step') # Check that covariance matrix is positive definite (this is done internally by linalg) @@ -63,9 +71,13 @@ # Check that all fields agree with the corresponding md class and if any field needs the default params - checkdefaults = False # Need to check defaults only if one of the fields does not have its own dimensionality + checkdefaults = False # Need to check defaults only if one of the fields does not have its own dimensionality structstoch = self.structstochforcing() for field in self.fields: # Checking agreement of classes - if 'SMB' in field: + if 'SMBautoregression' in field: + mdname = structstoch[field] + if (type(md.smb).__name__ != mdname): + raise TypeError('md.smb does not agree with stochasticforcing field {}'.format(field)) + if 'SMBforcing' in field: mdname = structstoch[field] if (type(md.smb).__name__ != mdname): @@ -83,39 +95,68 @@ if (type(md.basalforcings).__name__ != mdname): raise TypeError('md.basalforcings does not agree with stochasticforcing field {}'.format(field)) + if 'BasalforcingsSpatialDeepwaterMeltingRate' in field: + mdname = structstoch[field] + if (type(md.basalforcings).__name__ != mdname): + raise TypeError('md.basalforcings does not agree with stochasticforcing field {}'.format(field)) + if 'BasalforcingsDeepwaterMeltingRateAutoregression' in field: + mdname = structstoch[field] + if (type(md.basalforcings).__name__ != mdname): + raise TypeError('md.basalforcings does not agree with stochasticforcing field {}'.format(field)) if 'WaterPressure' in field: mdname = structstoch[field] if (type(md.friction).__name__ != mdname): raise TypeError('stochasticforcing field {} is only implemented for default friction'.format(field)) - if (md.friction.coupling!=0 and md.friction.coupling!=1 and md.friction.coupling!=2): + if md.friction.coupling not in[0, 1, 2]: raise TypeError('stochasticforcing field {} is only implemented for cases md.friction.coupling 0 or 1 or 2'.format(field)) - if (np.any(md.friction.q==0)): - raise TypeError('stochasticforcing field {} requires non-zero q exponent'.format(field)) + if (np.any(md.friction.q == 0)): + raise TypeError('stochasticforcing field {} requires non-zero q exponent'.format(field)) # Checking for specific dimensions - if not (field == 'SMBautoregression' or field == 'FrontalForcingsRignotAutoregression'): - checkdefaults = True # field with non-specific dimensionality + if field not in['SMBautoregression', 'FrontalForcingsRignotAutoregression','BasalforcingsDeepwaterMeltingRateAutoregression']: + checkdefaults = True # field with non-specific dimensionality # Retrieve sum of all the field dimensionalities - size_tot = self.defaultdimension * num_fields - indSMBar = -1 # About to check for index of SMBautoregression - indTFar = -1 # About to check for index of FrontalForcingsRignotAutoregression + dimensions = self.defaultdimension*np.ones((num_fields)) + indSMBar = -1 # About to check for index of SMBautoregression + indTFar = -1 # About to check for index of FrontalForcingsRignotAutoregression + indBDWar = -1 # About to check for index of BasalforcingsDeepwaterMeltingRateAutoregression if ('SMBautoregression' in self.fields): - size_tot = size_tot - self.defaultdimension + md.smb.num_basins - indSMBar = self.fields.index('SMBautoregression') # Index of SMBar, now check for consistency with TFar timestep (08Nov2021) + indSMBar = self.fields.index('SMBautoregression') # Index of SMBar, now check for consistency with other timesteps + dimensions[indSMBar] = md.smb.num_basins + if(md.smb.ar_timestep=', md.timestepping.time_step) md = checkfield(md, 'fieldname', 'stochasticforcing.randomflag', 'numel', [1], 'values', [0, 1]) if (checkdefaults): md = checkfield(md, 'fieldname', 'stochasticforcing.defaultdimension', 'numel', 1, 'NaN', 1, 'Inf', 1, '>', 0) - md = checkfield(md, 'fieldname', 'stochasticforcing.default_id','Inf',1,'NaN',1,'>=',0,'<=',self.defaultdimension,'size', [md.mesh.numberofelements]) + md = checkfield(md, 'fieldname', 'stochasticforcing.default_id', 'Inf', 1, 'NaN', 1, '>=', 0, '<=', self.defaultdimension, 'size', [md.mesh.numberofelements]) return md # }}} @@ -128,12 +169,15 @@ def marshall(self, prefix, md, fid): # {{{ yts = md.constants.yts - num_fields = len(self.fields) WriteData(fid, prefix, 'object', self, 'fieldname', 'isstochasticforcing', 'format', 'Boolean') if not self.isstochasticforcing: return md + else: + num_fields = len(self.fields) + if(self.stochastictimestep==0): + md.stochasticforcing.stochastictimestep = md.timestepping.time_step #by default: stochastictimestep set to ISSM time step # Retrieve dimensionality of each field - dimensions = self.defaultdimension * np.ones((num_fields,)) + dimensions = self.defaultdimension * np.ones((num_fields)) for ind, field in enumerate(self.fields): # Checking for specific dimensions @@ -142,7 +186,9 @@ if (field == 'FrontalForcingsRignotAutoregression'): dimensions[ind] = md.frontalforcings.num_basins + if (field == 'BasalforcingsDeepwaterMeltingRateAutoregression'): + dimensions[ind] = md.basalforcings.num_basins # Scaling covariance matrix (scale column-by-column and row-by-row) - scaledfields = ['DefaultCalving','FloatingMeltRate','SMBautoregression'] # list of fields that need scaling * 1/yts + scaledfields = ['BasalforcingsDeepwaterMeltingRateAutoregression','BasalforcingsSpatialDeepwaterMeltingRate','DefaultCalving', 'FloatingMeltRate', 'SMBautoregression', 'SMBforcing'] # list of fields that need scaling * 1/yts tempcovariance = np.copy(self.covariance) for i in range(num_fields): @@ -157,12 +203,13 @@ self.default_id = np.zeros(md.mesh.numberofelements) # Reshape dimensions as column array for marshalling - dimensions = dimensions.reshape(1,len(dimensions)) + dimensions = dimensions.reshape(1, len(dimensions)) WriteData(fid, prefix, 'data', num_fields, 'name', 'md.stochasticforcing.num_fields', 'format', 'Integer') WriteData(fid, prefix, 'object', self, 'fieldname', 'fields', 'format', 'StringArray') - WriteData(fid, prefix, 'data', dimensions, 'name', 'md.stochasticforcing.dimensions', 'format', 'IntMat','mattype',2) - WriteData(fid, prefix, 'object', self, 'fieldname', 'default_id', 'format', 'IntMat', 'mattype', 2) #12Nov2021 make sure this is zero-indexed! + WriteData(fid, prefix, 'data', dimensions, 'name', 'md.stochasticforcing.dimensions', 'format', 'IntMat', 'mattype', 2) + WriteData(fid, prefix, 'object', self, 'fieldname', 'default_id', 'data', self.default_id - 1, 'format', 'IntMat', 'mattype', 2) #12Nov2021 make sure this is zero-indexed! WriteData(fid, prefix, 'object', self, 'fieldname', 'defaultdimension', 'format', 'Integer') WriteData(fid, prefix, 'data', tempcovariance, 'name', 'md.stochasticforcing.covariance', 'format', 'DoubleMat') + WriteData(fid, prefix, 'object', self, 'fieldname', 'stochastictimestep', 'format', 'Double', 'scale', yts) WriteData(fid, prefix, 'object', self, 'fieldname', 'randomflag', 'format', 'Boolean') # }}} @@ -180,9 +227,12 @@ supported and corresponding md names """ - structure = {'DefaultCalving': 'calving', + structure = {'BasalforcingsDeepwaterMeltingRateAutoregression': 'autoregressionlinearbasalforcings', + 'BasalforcingsSpatialDeepwaterMeltingRate': 'spatiallinearbasalforcings', + 'DefaultCalving': 'calving', 'FloatingMeltRate': 'basalforcings', 'FrictionWaterPressure': 'friction', 'FrontalForcingsRignotAutoregression': 'frontalforcingsrignotautoregression', - 'SMBautoregression': 'SMBautoregression'} + 'SMBautoregression': 'SMBautoregression', + 'SMBforcing': 'SMBforcing'} return structure # }}} Index: /issm/trunk/src/m/classes/stressbalance.m =================================================================== --- /issm/trunk/src/m/classes/stressbalance.m (revision 27034) +++ /issm/trunk/src/m/classes/stressbalance.m (revision 27035) @@ -36,6 +36,6 @@ self.loadingforce=project3d(md,'vector',self.loadingforce,'type','node'); - % for MLHO - if md.flowequation.isMLHO + % for MOLHO + if md.flowequation.isMOLHO self.spcvx_base=project3d(md,'vector',self.spcvx_base,'type','node'); self.spcvy_base=project3d(md,'vector',self.spcvy_base,'type','node'); @@ -134,6 +134,6 @@ md = checkfield(md,'fieldname','stressbalance.FSreconditioning','>',0); end - % CHECK THIS ONLY WORKS FOR MLHO - if md.flowequation.isMLHO + % CHECK THIS ONLY WORKS FOR MOLHO + if md.flowequation.isMOLHO md = checkfield(md,'fieldname','stressbalance.spcvx_base','Inf',1,'timeseries',1); md = checkfield(md,'fieldname','stressbalance.spcvy_base','Inf',1,'timeseries',1); @@ -169,5 +169,5 @@ fielddisplay(self,'spcvz','z-axis velocity constraint (NaN means no constraint) [m/yr]'); - disp(sprintf('\n %s','MLHO boundary conditions:')); + disp(sprintf('\n %s','MOLHO boundary conditions:')); fielddisplay(self,'spcvx_base','x-axis basal velocity constraint (NaN means no constraint) [m/yr]'); fielddisplay(self,'spcvy_base','y-axis basal velocity constraint (NaN means no constraint) [m/yr]'); @@ -226,6 +226,6 @@ end WriteData(fid,prefix,'data',outputs,'name','md.stressbalance.requested_outputs','format','StringArray'); - % for MLHO - if (md.flowequation.isMLHO) + % for MOLHO + if (md.flowequation.isMOLHO) WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','spcvx_base','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); WriteData(fid,prefix,'object',self,'class','stressbalance','fieldname','spcvy_base','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); Index: /issm/trunk/src/m/classes/stressbalance.py =================================================================== --- /issm/trunk/src/m/classes/stressbalance.py (revision 27034) +++ /issm/trunk/src/m/classes/stressbalance.py (revision 27035) @@ -59,5 +59,5 @@ s += '{}\n'.format(fielddisplay(self, 'spcvz', 'z-axis velocity constraint (NaN means no constraint) [m / yr]')) s += '{}\n'.format(fielddisplay(self, 'icefront', 'segments on ice front list (last column 0: Air, 1: Water, 2: Ice')) - s += ' MLHO boundary conditions:\n' + s += ' MOLHO boundary conditions:\n' s += '{}\n'.format(fielddisplay(self, 'spcvx_base', 'x-axis basal velocity constraint (NaN means no constraint) [m / yr]')) s += '{}\n'.format(fielddisplay(self, 'spcvy_base', 'y-axis basal velocity constraint (NaN means no constraint) [m / yr]')) @@ -86,5 +86,5 @@ self.loadingforce = project3d(md, 'vector', self.loadingforce, 'type', 'node') - if md.flowequation.isMLHO: + if md.flowequation.isMOLHO: self.spcvx_base = project3d(md, 'vector', self.spcvx_base, 'type', 'node') self.spcvy_base = project3d(md, 'vector', self.spcvy_base, 'type', 'node') @@ -176,5 +176,5 @@ if np.any(np.logical_not(np.isnan(md.stressbalance.referential[pos, :]))): md.checkmessage("no referential should be specified for basal vertices of grounded ice") - if md.flowequation.isMLHO: + if md.flowequation.isMOLHO: md = checkfield(md, 'fieldname', 'stressbalance.spcvx_base', 'Inf', 1, 'timeseries', 1) md = checkfield(md, 'fieldname', 'stressbalance.spcvy_base', 'Inf', 1, 'timeseries', 1) @@ -215,6 +215,6 @@ outputs = outputscopy WriteData(fid, prefix, 'data', outputs, 'name', 'md.stressbalance.requested_outputs', 'format', 'StringArray') - # MLHO - if md.flowequation.isMLHO: + # MOLHO + if md.flowequation.isMOLHO: WriteData(fid, prefix, 'object', self, 'class', 'stressbalance', 'fieldname', 'spcvx_base', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts) WriteData(fid, prefix, 'object', self, 'class', 'stressbalance', 'fieldname', 'spcvy_base', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts) Index: /issm/trunk/src/m/classes/taoinversion.py =================================================================== --- /issm/trunk/src/m/classes/taoinversion.py (revision 27034) +++ /issm/trunk/src/m/classes/taoinversion.py (revision 27035) @@ -1,7 +1,7 @@ import numpy as np - from checkfield import checkfield from IssmConfig import IssmConfig from marshallcostfunctions import marshallcostfunctions +from fielddisplay import fielddisplay from project3d import project3d from supportedcontrols import * @@ -45,37 +45,37 @@ def __repr__(self): s = ' taoinversion parameters:\n' - s += '{}'.format(fieldstring(self, 'iscontrol', 'is inversion activated?')) - s += '{}'.format(fieldstring(self, 'mantle_viscosity', 'mantle viscosity constraints (NaN means no constraint) (Pa s)')) - s += '{}'.format(fieldstring(self, 'lithosphere_thickness', 'lithosphere thickness constraints (NaN means no constraint) (m)')) - s += '{}'.format(fieldstring(self, 'cross_section_shape', "1: square-edged, 2: elliptical - edged surface")) - s += '{}'.format(fieldstring(self, 'incomplete_adjoint', '1: linear viscosity, 0: non - linear viscosity')) - s += '{}'.format(fieldstring(self, 'control_parameters', 'ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}')) - s += '{}'.format(fieldstring(self, 'maxsteps', 'maximum number of iterations (gradient computation)')) - s += '{}'.format(fieldstring(self, 'maxiter', 'maximum number of Function evaluation (forward run)')) - s += '{}'.format(fieldstring(self, 'fatol', 'convergence criterion: f(X) - f(X * ) (X: current iteration, X * : "true" solution, f: cost function)')) - s += '{}'.format(fieldstring(self, 'frtol', 'convergence criterion: |f(X) - f(X * )| / |f(X * )|')) - s += '{}'.format(fieldstring(self, 'gatol', 'convergence criterion: ||g(X)|| (g: gradient of the cost function)')) - s += '{}'.format(fieldstring(self, 'grtol', 'convergence criterion: ||g(X)|| / |f(X)|')) - s += '{}'.format(fieldstring(self, 'gttol', 'convergence criterion: ||g(X)|| / ||g(X0)|| (g(X0): gradient at initial guess X0)')) - s += '{}'.format(fieldstring(self, 'algorithm', 'minimization algorithm: ''tao_blmvm'', ''tao_cg'', ''tao_lmvm''')) - s += '{}'.format(fieldstring(self, 'cost_functions', 'indicate the type of response for each optimization step')) - s += '{}'.format(fieldstring(self, 'cost_functions_coefficients', 'cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter')) - s += '{}'.format(fieldstring(self, 'min_parameters', 'absolute minimum acceptable value of the inversed parameter on each vertex')) - s += '{}'.format(fieldstring(self, 'max_parameters', 'absolute maximum acceptable value of the inversed parameter on each vertex')) - s += '{}'.format(fieldstring(self, 'vx_obs', 'observed velocity x component [m / yr]')) - s += '{}'.format(fieldstring(self, 'vy_obs', 'observed velocity y component [m / yr]')) - s += '{}'.format(fieldstring(self, 'vel_obs', 'observed velocity magnitude [m / yr]')) - s += '{}'.format(fieldstring(self, 'thickness_obs', 'observed thickness [m]')) - s += '{}'.format(fieldstring(self, 'surface_obs', 'observed surface elevation [m]')) - s += '{}'.format('Available cost functions:') - s += '{}'.format(' 101: SurfaceAbsVelMisfit') - s += '{}'.format(' 102: SurfaceRelVelMisfit') - s += '{}'.format(' 103: SurfaceLogVelMisfit') - s += '{}'.format(' 104: SurfaceLogVxVyMisfit') - s += '{}'.format(' 105: SurfaceAverageVelMisfit') - s += '{}'.format(' 201: ThicknessAbsMisfit') - s += '{}'.format(' 501: DragCoefficientAbsGradient') - s += '{}'.format(' 502: RheologyBbarAbsGradient') - s += '{}'.format(' 503: ThicknessAbsGradient') + s += '{}\n'.format(fielddisplay(self, 'iscontrol', 'is inversion activated?')) + # s += '{}\n'.format(fielddisplay(self, 'mantle_viscosity', 'mantle viscosity constraints (NaN means no constraint) (Pa s)')) + # s += '{}\n'.format(fielddisplay(self, 'lithosphere_thickness', 'lithosphere thickness constraints (NaN means no constraint) (m)')) + # s += '{}\n'.format(fielddisplay(self, 'cross_section_shape', "1: square-edged, 2: elliptical - edged surface")) + s += '{}\n'.format(fielddisplay(self, 'incomplete_adjoint', '1: linear viscosity, 0: non - linear viscosity')) + s += '{}\n'.format(fielddisplay(self, 'control_parameters', 'ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}')) + s += '{}\n'.format(fielddisplay(self, 'maxsteps', 'maximum number of iterations (gradient computation)')) + s += '{}\n'.format(fielddisplay(self, 'maxiter', 'maximum number of Function evaluation (forward run)')) + s += '{}\n'.format(fielddisplay(self, 'fatol', 'convergence criterion: f(X) - f(X * ) (X: current iteration, X * : "true" solution, f: cost function)')) + s += '{}\n'.format(fielddisplay(self, 'frtol', 'convergence criterion: |f(X) - f(X * )| / |f(X * )|')) + s += '{}\n'.format(fielddisplay(self, 'gatol', 'convergence criterion: ||g(X)|| (g: gradient of the cost function)')) + s += '{}\n'.format(fielddisplay(self, 'grtol', 'convergence criterion: ||g(X)|| / |f(X)|')) + s += '{}\n'.format(fielddisplay(self, 'gttol', 'convergence criterion: ||g(X)|| / ||g(X0)|| (g(X0): gradient at initial guess X0)')) + s += '{}\n'.format(fielddisplay(self, 'algorithm', 'minimization algorithm: ''tao_blmvm'', ''tao_cg'', ''tao_lmvm''')) + s += '{}\n'.format(fielddisplay(self, 'cost_functions', 'indicate the type of response for each optimization step')) + s += '{}\n'.format(fielddisplay(self, 'cost_functions_coefficients', 'cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter')) + s += '{}\n'.format(fielddisplay(self, 'min_parameters', 'absolute minimum acceptable value of the inversed parameter on each vertex')) + s += '{}\n'.format(fielddisplay(self, 'max_parameters', 'absolute maximum acceptable value of the inversed parameter on each vertex')) + s += '{}\n'.format(fielddisplay(self, 'vx_obs', 'observed velocity x component [m / yr]')) + s += '{}\n'.format(fielddisplay(self, 'vy_obs', 'observed velocity y component [m / yr]')) + s += '{}\n'.format(fielddisplay(self, 'vel_obs', 'observed velocity magnitude [m / yr]')) + s += '{}\n'.format(fielddisplay(self, 'thickness_obs', 'observed thickness [m]')) + s += '{}\n'.format(fielddisplay(self, 'surface_obs', 'observed surface elevation [m]')) + s += '{}\n'.format('Available cost functions:') + s += '{}\n'.format(' 101: SurfaceAbsVelMisfit') + s += '{}\n'.format(' 102: SurfaceRelVelMisfit') + s += '{}\n'.format(' 103: SurfaceLogVelMisfit') + s += '{}\n'.format(' 104: SurfaceLogVxVyMisfit') + s += '{}\n'.format(' 105: SurfaceAverageVelMisfit') + s += '{}\n'.format(' 201: ThicknessAbsMisfit') + s += '{}\n'.format(' 501: DragCoefficientAbsGradient') + s += '{}\n'.format(' 502: RheologyBbarAbsGradient') + s += '{}\n'.format(' 503: ThicknessAbsGradient') return s Index: /issm/trunk/src/m/consistency/checkfield.py =================================================================== --- /issm/trunk/src/m/consistency/checkfield.py (revision 27034) +++ /issm/trunk/src/m/consistency/checkfield.py (revision 27035) @@ -114,5 +114,10 @@ else: if len(np.shape(field)) < len(fieldsize): - md = md.checkmessage(options.getfieldvalue('message', "field {} has size {} but should be size {}".format(fieldname, np.shape(field), fieldsize))) + if fieldsize[-1] > 1: + md = md.checkmessage(options.getfieldvalue('message', "field {} has size {} but should be size {}".format(fieldname, np.shape(field), fieldsize))) + else: + #The last dimension is one that follows matlab 2D array regulation but usually not what we do in python, we allow the difference in shape only if the number of element is equal + if np.prod(np.shape(field)) != np.prod(fieldsize): + md = md.checkmessage(options.getfieldvalue('message', "field {} has size {} but should be size {}".format(fieldname, np.shape(field), fieldsize))) else: for i in range(np.size(fieldsize)): @@ -153,5 +158,5 @@ md = md.checkmessage(options.getfieldvalue('message', "field '{}' value should be '{}'".format(fieldname, fieldvalues[0]))) elif len(fieldvalues) == 2: - md = md.checkmessage(options.getfieldvalue('message', "field '{}' values should be '{}' '{}' or '{}'".format(fieldname, fieldvalues[0], fieldvalues[1]))) + md = md.checkmessage(options.getfieldvalue('message', "field '{}' values should be '{}' or '{}'".format(fieldname, fieldvalues[0], fieldvalues[1]))) else: md = md.checkmessage(options.getfieldvalue('message', "field '{}' should have values in {}".format(fieldname, fieldvalues))) Index: /issm/trunk/src/m/consistency/comparemodels.m =================================================================== --- /issm/trunk/src/m/consistency/comparemodels.m (revision 27034) +++ /issm/trunk/src/m/consistency/comparemodels.m (revision 27035) @@ -27,8 +27,8 @@ if any(size(field1)~=size(field2)), disp([fieldname ' do not have the same size']); - elseif isnumeric(field1), + elseif isnumeric(field1) if numel(field1)==1 & isnan(field1) & isnan(field2), %Do not do anything - elseif any(field1~=field2), + elseif any(field1(:)~=field2(:)) %Deal with NaN... pos1=find(isnan(field1)); @@ -36,5 +36,5 @@ if numel(pos1)==numel(pos2) & all(pos1==pos2), field1(pos1)=0; field2(pos2)=0; - if any(field1~=field2), + if any(field1(:)~=field2(:)) disp([fieldname ' differs']); end Index: /issm/trunk/src/m/contrib/akesson/interpMAR.m =================================================================== --- /issm/trunk/src/m/contrib/akesson/interpMAR.m (revision 27035) +++ /issm/trunk/src/m/contrib/akesson/interpMAR.m (revision 27035) @@ -0,0 +1,59 @@ +function output = interpMAR(X,Y,string,loadyear) +%%%%%% %Interpolate from MAR (Fettweis et al 2017) + +%Available outputs + % -LAT + % -LON + % -ME (Melt) + % -MSK_BAM01 (Mask Bamber et al 2001 5x5 km) + % -MSK_BAM13 (Mask Bamber et al 2013 1x1 km) + % -MSK_MAR (MAR 10x10 km Ice Mask) + % -RF (Rainfall) + % -RU (Runoff) + % -SF (Snowfall) + % -SMB (Surface Mass Balance (without corrections) + % -SMBCORR (Surface Mass Balance (with corrections) + % -SRF_BAM01 (Bamber et al 2001 5x5km Surface height) + % -SRF_BAM13 (Bamber et al 2013 1x1 km Surface height) + % -SRF_MAR (MAR 10x10 km Surface height) + % -ST (Surface temperature) + % -ST (Surface temperature (with corrections) + % -SU (Sublimation/Evaporation) + % -TIME (Time) + % -X (x) + % -Y (y) +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +if nargin==2, + string = 'SMBCORR'; + loadyear = 2014; +end + +isverbose=0; + +%Define data source +ncpath='/Users/henning/issm/trunk-jpl/projects/ModelData/MAR3/MARv3.5.2-10km-yearly-ERA-Interim-1979-2014.nc'; + +% Build grid from Bamber2001 +xdata = -800000:5000:700000; +ydata = -3400000:5000:-600000; + +%Convert to MAR projections +if isverbose, disp(' -- MAR: converting coordinates'); end +[LAT,LON] = xy2ll(double(X(:)),double(Y(:)),+1,45,70); %convert model mesh xy to Bamber's projection +[xMAR,yMAR] = ll2xy(LAT,LON,+1,39,71); %convert from lat/long Bamber's to MAR projection xy + +if isverbose, disp(' -- MAR: loading data'); end +data = double(ncread(ncpath,string)); + +%Define what year to load data for 1979-2014 +startyear=1979; +year=loadyear-startyear+1; + +%Get data from given year +data2=squeeze(data(:,:,year)); + +if isverbose, disp(' -- MAR: interpolating data to grid'); end +output = InterpFromGrid(xdata,ydata,data2',xMAR,yMAR); +output = reshape(output,size(X,1),size(X,2)); + Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/README.md =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/README.md (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/README.md (revision 27035) @@ -0,0 +1,15 @@ +# Function List + +* analyzeCalvingFront.m -- Interpolate the transient solutions to the calving front positions of the given flowlines +* averageOverTime.m -- For a given range, average transient data in time +* computeGrad.m -- Compute the gradient of a given field +* extractTransientSolutions.m -- Load a model with transient solutions, and put each of the items into individual array +* interpZeroPos.m -- Find zero positions (y=0) of the given curve defined by (X,Y) +* integrateOverDomain.m -- integrate a given variable over the whole domain, can set a mask +* integrateOverTime.m -- integrate a time series over the given time steps +* inverseHistograms.m -- Compute the inverse quantile function +* npsd.m -- Compute normalized power spectral density +* projectToFlowlines.m -- Project data from a mesh to a given flowline +* psd.m -- Compute power spectral density +* rescalegradientNan.m -- Replace Nan by 0 in the cost function, then rescale it +* wfDistance.m -- Compute Wasserstein-Fourier distance Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/analyzeCalvingFront.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/analyzeCalvingFront.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/analyzeCalvingFront.m (revision 27035) @@ -0,0 +1,62 @@ +function [flowline, icemaskFL] = analyzeCalvingFront(md, flowline, transientSolutions) +%analyzeCalvingFront - to find calving front position at the given flowline, +% if the given model contains transient solutions, then +% return a time dependent calving front with +% [Xmain, positionx, positiony, time], icemask, calving rate, +% melting rate and velocity magnitude, sigma, thickness +% Author: Cheng Gong +% Last modified: 2020-09-25 + +transient = isfield(md.results,'TransientSolution'); + +if transient + % extract data from model + icemaskFL = InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,transientSolutions.ice_levelset,flowline.x,flowline.y); + + % solve for the calving front coordinates + cf = interpZeroPos([flowline.Xmain(:), flowline.x, flowline.y], icemaskFL); + positionx = cf(:, 2); + positiony = cf(:, 3); + + % Calving rate C + cRate = InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,... + transientSolutions.calvingRate,positionx, positiony); + cRate = diag(cRate); % not very efficient, but works + + % melting rate M + mRateTemp = InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,... + transientSolutions.meltingRate,positionx, positiony); + mRate = diag(mRateTemp); % not very efficient, but works + + % velocity + vel = InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,... + transientSolutions.vel, positionx, positiony); + vel = diag(vel); + + % sigmaVM + SigmaVM = InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,... + transientSolutions.SigmaVM, positionx, positiony); + SigmaVM = diag(SigmaVM); + + % calving front + calvingFront = [cf, transientSolutions.time(:)]; + + % solutions along the flowline + SigmaVM_FL = InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,... + transientSolutions.SigmaVM,flowline.x, flowline.y); + + % Thickness along the flowlines + thickness = InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,... + transientSolutions.thickness, flowline.x, flowline.y); + + % save to flowline + flowline.calvingFront = calvingFront; + flowline.cRate = cRate; + flowline.mRate = mRate; + flowline.vel = vel; + flowline.SigmaVM = SigmaVM; + flowline.SigmaVM_FL = SigmaVM_FL; + flowline.thickness = thickness; +else + error('Calving front detectiong for the steady state is not implemented yet!') +end Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/averageOverTime.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/averageOverTime.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/averageOverTime.m (revision 27035) @@ -0,0 +1,86 @@ +function averagedData = averageOverTime(data, time, startP, endP) +%averageOverTime - compute the time averaged value of data in the range [startP, endP] +% +% data: time dependent data, +% time: has same number of columns as data, sorted in ascending order +% startP: start time point for averaging, can be at any time point, or +% even not coincide with the given points in 'time' +% endP: end time point for averaging. if this is the same as the startP, +% or not given, then the output will be the linear interpolation of the +% data at startP. +% +% if out of the given time range, use constant extrapolation, +% if within the range, do linear interpolation. +% +% Author: Cheng Gong +% Last modified: 2020-09-09 +if nargin < 4 + endP = startP; +end + +Nt = length(time); +if Nt ~= size(data,2) + error('The data and time does not match!'); +end + +if startP > endP + error('The given start point has to be smaller than the end point!'); +elseif startP == endP + % extrapolation if earlier than the first time point + if startP <= time(1) + i1 = 1; + i2 = 2; + % extrapolation if later than the last time point + elseif startP >= time(Nt) + i1 = Nt-1; + i2 = Nt; + else + pos = (time > startP); + i2 = find(pos, 1, 'first'); + i1 = i2 - 1; + end + % linear interpolation + averagedData = data(:, i1) + (data(:, i1)-data(:, i2)).*(startP-time(i1))./(time(i1)-time(i2)); +else + % find the first and last ID in the time series within the given range + pos = ((time>=startP) & (time<=endP)); + firstId = find(pos, 1, 'first'); + lastId = find(pos, 1, 'last'); + if isempty(firstId) | isempty(lastId) + averagedData = nan(size(data,1), 1); + % error('Time points out of range'); + else + % computed the integral with trapzoidal rule + integData = zeros(size(data,1), 1); + for i = firstId:lastId-1 + integData = integData + (data(:,i+1) + data(:,i)) .* (time(i+1) - time(i)).*0.5; + end + + % special treatment for the first and last time step, which are not + % complete steps. + if firstId == 1 + % extrapolation + integData = integData + data(:,1) .* (time(1)-startP); + else + % interpolation + integData = integData + 0.5.*(time(firstId)-startP)./ ... + (time(firstId)-time(firstId-1)) .* ... + ((time(firstId)-startP) .* data(:,firstId-1) + ... + (time(firstId)+startP-2*time(firstId-1)).*data(:,firstId)); + end + + if lastId == Nt + % extrapolation + integData = integData + data(:,Nt) .* (endP-time(Nt)); + else + % interpolation + integData = integData + 0.5.*(time(lastId)-endP)./ ... + (time(lastId+1)-time(lastId)) .* ... + ((time(lastId)-endP) .* data(:,lastId+1) + ... + (time(lastId)+endP-2*time(lastId+1)).*data(:,lastId)); + end + + averagedData = integData ./ (endP-startP); + end +end + Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/computeGrad.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/computeGrad.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/computeGrad.m (revision 27035) @@ -0,0 +1,45 @@ +function [gradx, grady]=computeGrad(index,x,y,field) +%COMPUTEHESSIAN - compute the gradient from a field + +%some variables +numberofnodes=length(x); +numberofelements=size(index,1); +numberoftime = size(field, 2); + +%some checks +if (length(field)~=numberofnodes) && (length(field)~=numberofelements) + error('ComputeHessian error message: the given field size not supported yet'); +end +%initialization +line=index(:); +linesize=3*numberofelements; + +%get areas and nodal functions coefficients N(x,y)=alpha x + beta y + gamma +[alpha, beta]=GetNodalFunctionsCoeff(index,x,y); +areas=GetAreas(index,x,y); + +%compute weights that hold the volume of all the element holding the node i +weights=sparse(line,ones(linesize,1),repmat(areas,3,1),numberofnodes,1); + +%compute field on nodes if on elements +if length(field)==numberofelements + field=sparse(line,ones(linesize,1),repmat(areas.*field,3,1),numberofnodes,1)./weights ; +end + +%Compute gradient for each element +if numberoftime == 1 + grad_elx=sum(field(index).*alpha,2); + grad_ely=sum(field(index).*beta,2); +else + grad_elx = zeros(numberofelements,numberoftime); + grad_ely = zeros(numberofelements,numberoftime); + for i = 1:3 + grad_elx = grad_elx + field(index(:,i), :).*alpha(:,i); + grad_ely = grad_ely + field(index(:,i), :).*beta(:,i); + end +end +%Compute gradient for each node (average of the elements around) +gradx=sparse(repmat(line,1,numberoftime),cumsum(ones(linesize,numberoftime),2),repmat(areas.*grad_elx,3,1),numberofnodes,numberoftime); +grady=sparse(repmat(line,1,numberoftime),cumsum(ones(linesize,numberoftime),2),repmat(areas.*grad_ely,3,1),numberofnodes,numberoftime); +gradx=gradx./weights; +grady=grady./weights; Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/extractTransientSolutions.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/extractTransientSolutions.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/extractTransientSolutions.m (revision 27035) @@ -0,0 +1,14 @@ +function [transientSolutions]=extractTransientSolutions(md) +%extractTransientSolutions - take the transient solutions out from model +% and put each of them into an individual array. +transientSolutions.time = cell2mat({md.results.TransientSolution(:).time}); +transientSolutions.vx = cell2mat({md.results.TransientSolution(:).Vx}); +transientSolutions.vy = cell2mat({md.results.TransientSolution(:).Vy}); +transientSolutions.vel = cell2mat({md.results.TransientSolution(:).Vel}); +transientSolutions.volume = cell2mat({md.results.TransientSolution(:).IceVolume}); +transientSolutions.thickness = cell2mat({md.results.TransientSolution(:).Thickness}); +transientSolutions.SigmaVM = cell2mat({md.results.TransientSolution(:).SigmaVM}); +transientSolutions.smb = cell2mat({md.results.TransientSolution(:).SmbMassBalance}); +transientSolutions.ice_levelset = cell2mat({md.results.TransientSolution(:).MaskIceLevelset}); +transientSolutions.calvingRate = cell2mat({md.results.TransientSolution(:).CalvingCalvingrate}); +transientSolutions.meltingRate = cell2mat({md.results.TransientSolution(:).CalvingMeltingrate}); Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/fillInNan.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/fillInNan.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/fillInNan.m (revision 27035) @@ -0,0 +1,26 @@ +function newdata = fillInNan(md, data, varargin) +%fillInNan - use the mean of surrouding data to iteratidatay fill in the Nan in data +% data should have the same size as md.mesh.x +% +% Author: Cheng Gong +% Last modified: 2021-12-08 +nanvflag = find(isnan(data)); +NNanv = length(nanvflag); + +options = pairoptions(varargin{:}); +maxiter = getfieldvalue(options,'maxiter', 10); +count = 1; + +while((NNanv>0) & (count<=maxiter)) + disp(['Iter ', num2str(count), ': found ', num2str(NNanv), ' Nan in the initial data, fill in them with the mean of their surroudings.']); + for i = 1:NNanv + [eleid, ~] = find(md.mesh.elements == nanvflag(i)); + nodeid = md.mesh.elements(eleid, :); + data(nanvflag(i)) = mean(data(nodeid(:)) , 'omitnan'); + end + nanvflag = find(isnan(data)); + NNanv = length(nanvflag); + count = count + 1; +end +newdata = data; + Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/integrateOverDomain.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/integrateOverDomain.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/integrateOverDomain.m (revision 27035) @@ -0,0 +1,32 @@ +function [intData, meanData, areas] = integrateOverDomain(md, data, masked, weights) +% integrateOverDomain - integrating data over the whole domain +% +% intData: integral of the data over each element +% meanData: intData/areas +% areas: areas of the domain +if nargin < 4 + weights = ones(size(data)); + if nargin<3 + masked = []; + end +end + +% Set the area with masked=1 to nan +data(masked) = nan; +weights(masked) =nan; + +% get the mesh +elements=md.mesh.elements; +x=md.mesh.x; +y=md.mesh.y; + +%compute areas; +eleAreas=GetAreas(elements,x,y); + +% integrate nodal data to element +eleData = 1/3*eleAreas.*(data(elements(:,1),:).*weights(elements(:,1),:) + data(elements(:,2),:).*weights(elements(:,2),:) + data(elements(:,3),:).*weights(elements(:,3),:)); +eleAreas = 1/3*eleAreas.*(weights(elements(:,1),:)+weights(elements(:,2),:)+weights(elements(:,3),:)); + +intData = sum(eleData(:),'omitnan'); +areas = sum(eleAreas(:),'omitnan'); +meanData = intData / areas; Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/integrateOverTime.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/integrateOverTime.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/integrateOverTime.m (revision 27035) @@ -0,0 +1,26 @@ +function [newData, intData] = integrateOverTime(tdata, data, time, Nintdt) +% integrateOverDomain - integrating data over the whole domain +% +% Input: +% tdata: time steps of data +% data: time series of the data +% time: time steps to be used for integration +% Nintdt: number of time steps in 'time' to be used for integration +% +% Return: +% newData: data projected on to 'time' +% intData: integrated 'newData' + +dt = abs(time(2) -time(1)); +% patch the first N time steps +intTime = [[-Nintdt:-1]*dt+time(1), time]; +% integration scheme +integ = ones(1, Nintdt) * dt; + +% interpolate data from the time scheme 'tdata' to 'time' +newData = interp1(double(tdata), double(data), intTime, 'linear', 'extrap'); + +% integrated, only works for equidistance time steps for now +intData = conv(integ, newData); +intData = intData(Nintdt:end-Nintdt); +newData = newData(Nintdt+1: end); Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/interpZeroPos.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/interpZeroPos.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/interpZeroPos.m (revision 27035) @@ -0,0 +1,52 @@ +function X0 = interpZeroPos(X, Y) +%interpZeroPos - find the x values for y=0 with line interpolation of the +% given X and Y coordinates. +% X: is a matrix of size mxn, each column represent a dimension +% Y: is a matrix of size mxk, k is the number of date sets, and each +% data set must contains positive and negative values. +% The return value: +% x0: is a matrix of size kxn, the rows correspond to each column +% of X and the columns are for each data set. +% +% The method is to find the two consective values y1 and y2 where +% Y changes the sign, and the corresponding X are x1 and x2. +% x2*y1-x1*y2 +% x0 = ------------- +% y1-y2 +% Author: Cheng Gong +% Last modified: 2020-10-20 +[m, n] = size(X); +[my, k] = size(Y); +if m~=my + error('rows of X and Y are not the same!'); +end + +% find the place where Y changes signs, or y=0 at some points +mask = (Y(1:m-1,:).*Y(2:m,:) <=0); +[row, col] = find(mask); +ind = row; + +% use only the first index from each column +if length(col)>k + disp('Multiple candidates of the y=0 values are found in one data set! Be defalut, take the first y=0 from upstream.'); + [col, ia, ~] = unique(col); + ind = row(ia); +end + +if length(col)epsilon); +Sa = S(A); + +% cummulative sum +cdf = cumtrapz(S, mu); +cdfa = cdf(A); + +% set the first value to 0 and last value to 1 +cdfa(1) = 0; +Sa(1) = 0; + +if cdfa(end) < 1 + cdfa = [cdfa(:);1]; + Sa = [Sa(:);S(end)]; +end + +[~, ind] = unique(cdfa); +% linear interpolation +q_Sinv = interp1(cdfa(ind), Sa(ind), Sinv); + +end Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/movingAverage.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/movingAverage.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/movingAverage.m (revision 27035) @@ -0,0 +1,42 @@ +function outdata = movingAverage(rawdata, varargin) +% +% rawdata is an MxN matrix, where the first M-1 rows are the raw data, the row M is the time + +options = pairoptions(varargin{:}); +timeWindow = getfieldvalue(options, 'time window', 30); % unit in days +resamp = getfieldvalue(options, 'resample', 1); % resample the data set with the size of window + +% get data info {{{ +[M, N] = size(rawdata); +if M < 2 + error('The data has to be at least two rows!'); +end +if N < 2 + error('The data has to be at least two columns!'); +end + +% sort the time +time = rawdata(M, :); +[time, tI] = sort(time); +data = rawdata(1:M-1, :); +data = data(:, tI); + +dt = time(2) - time(1); +if dt < 0 + error('The time need to be in ascending order.'); +end +windowSize = ceil(timeWindow/365/dt); +%}}} +%% filter {{{ +if resamp + ind = [1:timeWindow:N]; +else + ind = [1:N]; +end +b = (1/windowSize)*ones(1,windowSize); +a = 1; +disp(['Applying filter of width ', num2str(timeWindow)]); +smoothdata = filter(b,a,data,[],2); +time = time(ind); +outdata = [smoothdata(:,ind);time]; +%}}} Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/npsd.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/npsd.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/npsd.m (revision 27035) @@ -0,0 +1,32 @@ +function [npsdx, psdx, freq] = npsd(x) +%npsd - Normalized Power Spectral Density (using fft) +% +% x: time series +% +% psdx: Power Spectral Density(right half plane, value doubled) +% freq: frequency(non-negative half) +% +% Author: Cheng Gong +% Date: 2021-08-17 + +% length of data +Nx = length(x); +% fft +xdft = fft(x); +xdft = xdft(1:floor(Nx/2+1)); +% power specturm +psdx = (1/(2*pi*Nx)) * abs(xdft).^2; +% In order to conserve the total power, multiply all frequencies that +% occur in both sets - the positive and negative frequencies — by a factor of 2 +psdx(2:end-1) = 2*psdx(2:end-1); +freq = 0:(2*pi)/Nx:pi; +% normalize(trapzoidal rule) +intS = trapz(freq, psdx); +if intS == 0 + psdx = 1 +psdx; + intS = trapz(freq, psdx); +end +npsdx = psdx ./ intS; + + +end Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/projectToFlowlines.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/projectToFlowlines.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/projectToFlowlines.m (revision 27035) @@ -0,0 +1,16 @@ +% Function to project values on the mesh to a flowline +% +% md - ISSM model with mesh +% pValue - data on the mesh +% fx - x coordinates of the flowline +% fy - y coordinates of the flowline +% +% Author: Cheng Gong +% Last modified: 2021-01-27 + +function valueC = projectToFlowlines(md, pValue, fx, fy) + temp = InterpFromMeshToMesh2d(md.mesh.elements, md.mesh.x, md.mesh.y,... + pValue, fx, fy); + temp = diag(temp); % not very efficient, but works + valueC = temp(:)'; +end Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/psd.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/psd.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/psd.m (revision 27035) @@ -0,0 +1,24 @@ +function [psdx, freq] = psd(x) +%psd - Power Spectral Density (using fft) +% +% x: time series +% +% psdx: Power Spectral Density(right half plane, value doubled) +% freq: frequency(non-negative half) +% +% Author: Cheng Gong +% Date: 2021-08-17 + +% length of data +Nx = length(x); +% fft +xdft = fft(x); +xdft = xdft(1:floor(Nx/2+1)); +% power specturm +psdx = (1/(2*pi*Nx)) * abs(xdft).^2; +% In order to conserve the total power, multiply all frequencies that +% occur in both sets - the positive and negative frequencies — by a factor of 2 +psdx(2:end-1) = 2*psdx(2:end-1); +freq = 0:(2*pi)/Nx:pi; + +end Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/rescalegradientNan.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/rescalegradientNan.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/rescalegradientNan.m (revision 27035) @@ -0,0 +1,7 @@ +% function to replace Nan by 0 in J, then rescale with the mass matrix +% +function J = rescalegradientNan(md, unscaledJ) + +nanflag = isnan(unscaledJ); +unscaledJ(nanflag) = 0; +J = rescalegradient(md, unscaledJ); Index: /issm/trunk/src/m/contrib/chenggong/dataprocessing/wfDistance.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/dataprocessing/wfDistance.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/dataprocessing/wfDistance.m (revision 27035) @@ -0,0 +1,26 @@ +function w2 = wfDistance(x, y) +%wfDistance - compute Wasserstein-Fourier Distance, according to Cazelles, E., +% Robert, A. & Tobar, F. The Wasserstein-Fourier Distance for +% Stationary Time Series. Ieee T Signal Proces 69, 709–721 (2019). +% +% x: first time series +% y: second time series +% +% w2: Wasserstein-Fourier Distance, or W2 distance of sx and sy +% +% Author: Cheng Gong +% Date: 2021-08-18 +N = length(x); +Sinv=linspace(0,1,N); + +[csx, ~, freqx] = npsd(x); +[csy, ~, freqy] = npsd(y); + +% inverse cummulative function +[~, qx] = inverseHistograms(csx, freqx, Sinv); +[~, qy] = inverseHistograms(csy, freqy, Sinv); + +% +w2 = sqrt(trapz(Sinv ,(qx-qy).^2)); + +end Index: /issm/trunk/src/m/contrib/chenggong/expxy2shpll.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/expxy2shpll.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/expxy2shpll.m (revision 27035) @@ -0,0 +1,69 @@ +function expxy2shpll(expfilename,shpfilename,geometry) +%expxy2shpll +% Convert .exp to .shp file +% +% Usage: +% expxy2shpll('glacier.exp', 'glacier.shp') +% expxy2shpll('glacier.exp', 'glacier.shp', geometry) +% +% geometry (optional)- 'MultiPoint' : point clouds +% 'Point' : single point +% 'Line' : two points line +% 'polygon' : multiple points +% + +%check file extensions +[pathstr,name,ext] = fileparts(shpfilename); +if ~strcmp(ext,'.shp'), + error(['Shapefile ' shpfilename ' does not have an extension .shp']); +end + +[pathstr,name,ext] = fileparts(expfilename); +if ~strcmp(ext,'.exp'), + error(['Exp file ' expfilename ' does not have an extension .exp']); +end + +shp=expread(expfilename); +[lat, lon] = xy2ll(shp.x, shp.y, 1, 45, 70); +shp.x = lon; +shp.y = lat; + +%initialize number of profile +count=1; + +contours=struct([]); +for i=1:length(shp), + if nargin < 3 + + %TEMP + %if contains(shp(i).name,'_pointcloud'); + % continue; + %end + + if length(shp(i).x) == 0 + continue; + elseif contains(shp(i).name,'_pointcloud'); + geometry = 'MultiPoint'; + shp(i).name = erase(shp(i).name,'_pointcloud'); + elseif length(shp(i).x) == 1 + geometry = 'Point'; + elseif length(shp(i).x) < 3 + geometry = 'Line'; + else + if (shp(i).x(end)==shp(i).x(1) && shp(i).y(end)==shp(i).y(1)), + geometry = 'Polygon'; + else + geometry = 'Line'; + end + end + end + contours(count).Geometry=geometry; + contours(count).id=i; + contours(count).Name=shp(i).name; + contours(count).X=shp(i).x; + contours(count).Y=shp(i).y; + count = count+1; +end + +%Make sure it is one single geometry otherwise it will yell at you +shapewrite(contours,shpfilename); Index: /issm/trunk/src/m/contrib/chenggong/interpFromMEaSUREsGeotiff.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/interpFromMEaSUREsGeotiff.m (revision 27034) +++ /issm/trunk/src/m/contrib/chenggong/interpFromMEaSUREsGeotiff.m (revision 27035) @@ -1,9 +1,33 @@ -% This function calls src/m/contrib/morlighem/modeldata/interpFromGeotiff.m for multiple times to load all avaliable -% tif data in /totten_1/ModelData/Greenland/VelMEaSUREs/Jakobshavn_2008_2021/ within the given time period (in decimal years) -% For some reason, each .tif file in this folder contains two sets of data, only the first dataset is useful +function dataout = interpFromMEaSUREsGeotiff(X,Y,Tstart,Tend,varargin) +%interpFromMEaSUREsGeotiff: +% This function calls src/m/contrib/morlighem/modeldata/interpFromGeotiff.m for multiple times to load all avaliable +% tif data in /totten_1/ModelData/Greenland/VelMEaSUREs/Jakobshavn_2008_2021/ within the given time period (in decimal years) +% For some reason, each .tif file in this folder contains two sets of data, only the first dataset is useful +% +% Usage: +% dataout = interpFromMEaSUREsGeotiff(X,Y,Tstart,Tend, varargin) +% +% X, Y are the coordinates of the mesh +% Tstart and Tend decimal year of the start and end time +% +% Example: +% obsData = interpFromMEaSUREsGeotiff(md.mesh.x,md.mesh.y, tstart, tend); +% +% Options: +% - 'glacier': which glacier to look for +options = pairoptions(varargin{:}); +glacier = getfieldvalue(options,'glacier','Jakobshavn'); -function dataout = interpFromMEaSUREsGeotiff(X,Y,Tstart,Tend) - -foldername = '/totten_1/ModelData/Greenland/VelMEaSUREs/Jakobshavn_2008_2021/'; +if strcmp(glacier, 'Jakobshavn') + foldername = '/totten_1/ModelData/Greenland/VelMEaSUREs/Jakobshavn_2008_2021/'; +elseif strcmp(glacier, 'Kangerlussuaq') + foldername = '/totten_1/ModelData/Greenland/VelMEaSUREs/Kangerlussuaq_2006_2021/'; +elseif strcmp(glacier, 'Store') + foldername = '/totten_1/ModelData/Greenland/VelMEaSUREs/Store_2008_2021/'; +elseif strcmp(glacier, 'Rink') + foldername = '/totten_1/ModelData/Greenland/VelMEaSUREs/Rink_2008_2022/'; +else + error(['The velocity data for ', glacier, ' is not available, please download from NSIDC first.']); +end % get the time info from file names Index: /issm/trunk/src/m/contrib/chenggong/modeldata/interpISMIP6Temp.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/modeldata/interpISMIP6Temp.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/modeldata/interpISMIP6Temp.m (revision 27035) @@ -0,0 +1,15 @@ +function temp = interpISMIP6Temp(X, Y) +%interpISMIP6Temp - interpolate land ice basal temperature to the given mesh +% +% X and Y are the coordinates of the mesh +% +% Author: Cheng Gong +% Last modified: 2021-12-06 + +filename = '/totten_1/ModelData/Greenland/ISMIP6/GreenlandISMIP6-Morlighem-2020-10-01.nc'; + +x = ncread(filename, 'x'); +y = ncread(filename, 'y'); +tb = ncread(filename, 'tb'); + +temp = InterpFromGrid(double(x), double(y), double(tb'), X, Y); Index: /issm/trunk/src/m/contrib/chenggong/visualization/imageNonUni.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/visualization/imageNonUni.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/visualization/imageNonUni.m (revision 27035) @@ -0,0 +1,23 @@ +function imageNonUni(varargin) +%imageNonUni - draw an image with non uniform grid +% +% Author: Cheng Gong +% Last modified: 2020-08-24 +x = varargin{1}; +y = varargin{2}; +C = varargin{3}; + +nx = length(x); +ny = length(y); +[ncy, ncx] = size(C); + +if ((nx ~= ncx) || (ny~=ncy)) + error('The size of x-y coordinates do not match the data!'); +end + +X = repmat(x(:)',ny , 1); +Y = repmat(y(:), 1, nx); + + +surf(X, Y, zeros(ny,nx), C, 'EdgeColor','None'); +view(2); Index: /issm/trunk/src/m/contrib/chenggong/visualization/plotCompareTransientFlowline.m =================================================================== --- /issm/trunk/src/m/contrib/chenggong/visualization/plotCompareTransientFlowline.m (revision 27035) +++ /issm/trunk/src/m/contrib/chenggong/visualization/plotCompareTransientFlowline.m (revision 27035) @@ -0,0 +1,48 @@ +function plotCompareTransientFlowline(velList, titleList, md, flowline, TStart, TEnd, xl, yl, ca) +%plotCompareTransientFlowline - to compare the solutions along a given +% flowine for the given time periods +% +% velList: a cell of transient velocities on the model mesh +% titleList: names of the velocity data +% md: ISSM model +% flowline: a flowline data structure contains flowline.x and flowline.y. +% If possible, it should also contains flowline.Xmain, which is +% the distance along the flowline from upstream to the terminus position. +% TStart: a list of start time points +% TEnd: a list of end time points +% ca: caixs value in plot +% xl: xlim value +% yl: ylim value +% +% Author: Cheng Gong +% Date: 2021-12-06 + +N = length(velList); +vel_flowline = cell(N,1); +if ~isfield(flowline, 'Xmain') + flowline.Xmain = cumsum([0;sqrt((flowline.x(2:end)- flowline.x(1:end-1)).^2 + (flowline.y(2:end)- flowline.y(1:end-1)).^2)]')/1000; +end + +for i = 1:N + vel_flowline{i} = InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,velList{i},flowline.x,flowline.y); +end + +for p = 1:N + subplot(N,1,p) + hold on + for i = 1:length(TStart) + overlay = [vel_flowline{p}(:,i), vel_flowline{p}(:,i)]'; + imAlpha = ones(size(overlay)); + imAlpha(isnan(overlay)) = 0; + imageNonUni(flowline.Xmain, [TStart(i), TEnd(i)], overlay); + end + title(titleList{p}, 'Interpreter', 'latex'); + xlim(xl) + xlabel('x(km)') + ylabel('year') + ylim(yl); + caxis(ca) + colormap('jet') + h=colorbar; + title(h,'m/a') +end Index: /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.m =================================================================== --- /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.m (revision 27034) +++ /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.m (revision 27035) @@ -1,19 +1,20 @@ function export_netCDF(md,filename) - -%Now going on Real treatment +%verbosity of the code, 0 is no messages, 5 is chatty + verbose = 5; if exist(filename), - disp(sprintf('File %s allready exist', filename)); - prompt = 'Give a new name or "delete" to replace: '; - newname = input(prompt,'s'); - if strcmp(newname,'delete') - delete(filename) - else - disp(sprintf('New file name is %s ', newname)); - filename=newname - end - end + delete(filename) + % disp(sprintf('File %s allready exist', filename)); + % prompt = 'Give a new name or "delete" to replace: '; + % newname = input(prompt,'s'); + % if strcmp(newname,'delete') + % delete(filename) + % else + % disp(sprintf('New file name is %s ', newname)); + % filename=newname + % end + end %open file and write description mode = netcdf.getConstant('NC_NETCDF4'); - mode = bitor(mode,netcdf.getConstant('NC_NOCLOBBER'));%NOCLOBBER to avoid overwrite + mode = bitor(mode,netcdf.getConstant('NC_NOCLOBBER')); %NOCLOBBER to avoid overwrite ncid = netcdf.create(filename,mode); netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'description',['Results for run ' md.miscellaneous.name]); @@ -21,138 +22,258 @@ %gather geometry and timestepping as dimensions - resfields=fieldnames(md.results); - Duration=size(eval(['md.results. ' resfields{1} ]),2); + if isempty(fieldnames(md.results)), + %results as no field so no time is present + Duration = 0; + else + resfields = fieldnames(md.results); + Duration = size(eval(['md.results. ' resfields{1} ]),2); + end if Duration>0, - StepNum=Duration; + StepNum = Duration; else StepNum=1; - end - - dimlist=[2,md.mesh.numberofelements,md.mesh.numberofvertices,size(md.mesh.elements,2)]; - - %define netcdf dimensions - DimSize(1).index=netcdf.defDim(ncid,'Time',StepNum); + end + DimSize(1).index=netcdf.defDim(ncid,'Time',StepNum); %time is the first dimension [DimSize(1).name,DimSize(1).value]=netcdf.inqDim(ncid,DimSize(1).index); DimValue(1)=DimSize(1).value; - DimSize(2).index=netcdf.defDim(ncid,'UnLim',netcdf.getConstant('NC_UNLIMITED')); + DimSize(2).index=netcdf.defDim(ncid,'UnLim',netcdf.getConstant('NC_UNLIMITED')); % we add an unlimited dimension if needed [DimSize(2).name,DimSize(2).value]=netcdf.inqDim(ncid,DimSize(2).index); DimValue(2)=DimSize(2).value; + % adding mesh related dimensions + dimlist=[2,40,md.mesh.numberofelements,md.mesh.numberofvertices,size(md.mesh.elements,2)]; + dimnames=["DictDummy" "StringLength" "EltNum" "VertNum" "VertPerElt"]; + if verbose > 0, + disp('===Creating dimensions ==='); + end + %define netcdf dimensions for i=1:5 + % do not add the dimension if it exists already if sum(dimlist(i) == DimValue) == 0 - DimSize(i+2).index=netcdf.defDim(ncid,['Dimension' num2str(i+2)],dimlist(i)); + DimSize(i+2).index=netcdf.defDim(ncid,dimnames(i),dimlist(i)); [DimSize(i+2).name,DimSize(i+2).value]=netcdf.inqDim(ncid,DimSize(i+2).index); DimValue(i+2)=DimSize(i+2).value; end end - - typelist=[{'numeric'} {'logical'} {'string'} {'char'} {'cell'}]; - + issmclasses = fieldnames(md)'; + typelist={'half', 'single','double','int8','int16'... + ,'int32','int64','uint8','uint16','uint32'... + ,'uint64','logical','char','string'}; %all malab types that are 0D + + for cl=1:length(issmclasses), + subclasses=fieldnames(md.(issmclasses{cl}))'; + for sc=1:length(subclasses), + if sum(strcmp(class(md.(issmclasses{cl}).(subclasses{sc})), typelist)) == 0, + issmclasses = [issmclasses class(md.(issmclasses{cl}).(subclasses{sc}))]; + end + end + end %get all model classes and create respective groups groups=fieldnames(md); + if verbose > 0, + disp('===Creating and populating groups==='); + end for i=1:length(groups), - disp(sprintf('group name in tree %s ',groups{i})); + if verbose >1, + disp(sprintf('===Now treating %s===',groups{i})); + end + if strcmp(groups{i}, 'qmu'), + disp('qmu is skipped until it is more stable'); + continue + end groupID=netcdf.defGrp(ncid,groups{i}); %In each group gather the fields of the class - groupfields=fieldnames(md.(groups{i})); - for j=1:length(groupfields), - Var=md.(groups{i}).(groupfields{j}); + fields=fieldnames(md.(groups{i})); + if isempty(fields), + disp(sprintf("WARNING: md.%s as no fields, we skip it.",groups{i})) + continue + end + %looping on fields in each group + for j=1:length(fields), + Var=md.(groups{i}).(fields{j}); + %treatment for lists if isa(Var,'cell') - Stdlist=false; + Stdlist=false; %first assume it is not a standard list if length(Var) == 0 - Stdlist=true; + Stdlist=true; %It is empty and so standard (for us) else for k=1:length(typelist) if isa(Var{1},typelist{k}) - Stdlist=true; + Stdlist=true; %if the list is of a known type (to matlab) if not it is probably some exotic ISSM stuff end end end - - netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',class(md.(groups{i}))); - if(Stdlist) - disp(sprintf('=====Field name in tree %s ',groupfields{j})); - [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,groupfields{j},DimSize,DimValue); - else - listsize=length(Var); - subgroupID=netcdf.defGrp(groupID,groupfields{j}); - netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',class(Var)); - for l=1:listsize - if isprop(Var{l},'name') - lname=Var{l}.name; - elseif isprop(Var{l},'step') - lname=Var{l}.step - else - lname=[class(Var{l}) int2str(l)]; + %print the issm class as a classtype attribute + klass = class(md.(groups{i})); + klasstring = strcat(klass, '.',klass); + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',klasstring); + if(Stdlist) % this is a standard or empty list just proceed + if verbose > 4, + disp(sprintf("=££=creating var for %s.%s with classtype : %s",groups{i}, fields{j}, klasstring)) + end + if ~isempty(Var) && isa(Var{1}, 'char'), % we have a char array, pad it to a given length + Var=char(Var)'; + end + [DimSize,DimValue,varid]=CreateVar(ncid,Var,groupID,fields{j},DimSize,DimValue); + if ~isempty(varid), + FillVar(Var,groupID,varid); + end + + else % this is a list of fields, specific treatment needed (perhaps) + if verbose > 4, + disp(sprintf("=??=we have a list of fields for %s.%s with classtype : %s",groups{i}, fields{j}, klasstring)); + end + if strcmp(groups{i}, 'outputdefinition'), + listsize=length(Var); + for k=1:listsize, + subgroupname=md.(groups{i}).(fields{j}){k}.definitionstring; + subgroupID=netcdf.defGrp(groupID,subgroupname); + klass=class(md.(groups{i}).(fields{j}){k}); + klasstring = strcat(klass, '.',klass); + netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',klasstring); + subfields=fieldnames(md.(groups{i}).(fields{j}){k}); + for l=1:length(subfields) + if verbose > 4, + disp(sprintf("=--=creating var for %s.%s[%i].%s",groups{i}, fields{j}, k, subfields{l})); + end + Var = md.(groups{i}).(fields{j}){k}.(subfields{l}); + if sum(numel(Var) == size(Var)) == 0, %this is a 2D array or more (and not a vector with dimension 2 = 1) + Var = Var'; + end + [DimSize,DimValue,varid]=CreateVar(ncid,Var,subgroupID,subfields{l},DimSize,DimValue); + if ~isempty(varid), + FillVar(Var,subgroupID,varid); + end + end end - listgroupID=netcdf.defGrp(subgroupID,lname); - netcdf.putAtt(listgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',class(Var{l})); - subfields=fieldnames(Var{l}); - for m=1:length(subfields) - if ~strcmp(subfields{m},'outlog') - [DimSize,DimValue]=DefCreateVar(ncid,Var{l}.(subfields{m}),listgroupID,subfields{m},DimSize,DimValue); - end + else + disp(sprintf("WARNING: unknown treatment for md.%s",groups{i})); + end + end + elseif sum(strcmp(class(Var), typelist))==1, %this is a standard matlab class with no subgrouping + if verbose > 4, + disp(sprintf("====creating var for %s.%s", groups{i}, fields{j})) + end + klass=class(md.(groups{i})); + klasstring = strcat(klass, '.',klass); + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',klasstring); + if sum(numel(Var) == size(Var)) == 0, %this is a 2D array or more (and not a vector with dimension 2 = 1) + Var = Var'; + end + + [DimSize,DimValue,varid]=CreateVar(ncid,Var,groupID,fields{j},DimSize,DimValue); + if ~isempty(varid), + FillVar(Var,groupID,varid); + end + + + elseif isa(Var,'struct') % structures need special treatment + if strcmp(groups{i}, 'results'), + klasstring='results.results'; + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',klasstring); + Listsize= length(md.(groups{i}).(fields{j})); + subgroupname=fields{j}; + subgroupID=netcdf.defGrp(groupID,subgroupname); + klasstring='results.solutionstep'; + netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',klasstring); + subfields=fieldnames(md.(groups{i}).(fields{j})); + if isempty(subfields), + disp(sprintf("WARNING: md.%s.%s as no subfields, we skip it.",groups{i}, fields{j})); + continue + end + for k=1:length(subfields), + if ~ismember(subfields{k}, {'errlog', 'outlog', 'SolutionType'}) + StackedVar=restable(); + for l=1:Listsize, + Var = md.(groups{i}).(fields{j})(l).(subfields{k}); + if length(Var) == 0, + %Some variables only have data on the first step + break + end + lastindex=l; + StackedVar=StackedVar.update(Var); + end + if verbose > 4, + disp(sprintf("=$$=creating var for %s.%s.%s",groups{i}, fields{j}, subfields{k})); + disp(sprintf("last index on the list is %i",lastindex)); + end + StackedVar=StackedVar.finalize(lastindex); + [DimSize,DimValue,varid]=CreateVar(ncid,StackedVar,subgroupID,subfields{k},DimSize,DimValue); + if ~isempty(varid), + FillVar(StackedVar,subgroupID,varid); + end + elseif ismember(subfields{k}, {'SolutionType'}) + %We just add solution type once as an attribute + Var = md.(groups{i}).(fields{j})(1).(subfields{k}); + [DimSize,DimValue,varid]=CreateVar(ncid,Var,subgroupID,subfields{k},DimSize,DimValue); + if ~isempty(varid), + FillVar(Var,subgroupID,varid); + end + end end - end - elseif isa(Var,'struct') && ~strcmp(groupfields{j},'bamg') - classtype=class(md.(groups{i})); - if strcmp(classtype,'struct') - classtype=groups{i}; - end - netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',classtype); - if length(Var)>1 - listsize=length(Var); - subgroupID=netcdf.defGrp(groupID,groupfields{j}); - classtype=class(Var); - if strcmp(classtype,'struct') - classtype=groups{i}; - end - netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',classtype); - for l=1:listsize - if isfield(Var(l),'step') - lname=[int2str(Var(l).step)]; - else - lname=[class(Var(l)) int2str(l)]; + elseif isempty(fieldnames(md.(groups{i}).(fields{j}))) % this is an empty struct, jus treat it as normal + klass=class(md.(groups{i})); + klasstring = strcat(klass, '.',klass); + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',klasstring); + if verbose > 4, + disp(sprintf("=[]=creating var for %s.%s",groups{i}, fields{j})); + end + + [DimSize,DimValue,varid]=CreateVar(ncid,Var,groupID,fields{j},DimSize,DimValue); + if ~isempty(varid), + FillVar(Var,groupID,varid); + end + + else + disp(sprintf("WARNING, md.%s.%s is not treated as it does not fall in one of the existing cases with class '%s'.",groups{i}, fields{j}, class(md.(groups{i}).(fields{j})))) + end + elseif sum(strcmp(class(Var), issmclasses)) == 1, % that is an issm class + if strcmp(class(Var), 'solution'), + if verbose > 4, + disp(sprintf("=$$=creating var for %s.%s",groups{i}, fields{j})) + disp("NEED treatment") + end + elseif strcmp(class(Var), 'dict'), %we have potential for a dict in py not to sure what it translates to here. + if verbose > 4, + disp(sprintf("=WW=creating var for %s.%s",groups{i}, fields{j})) + disp("NEED Treatment") + end + + else + klass=class(md.(groups{i})); + klasstring = strcat(klass, '.',klass); + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',klasstring); + subgroupID=netcdf.defGrp(groupID,fields{j}); + klass=class(md.(groups{i}).(fields{j})); + klasstring = strcat(klass, '.',klass); + netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',klasstring); + subfields=fieldnames(Var); + for k=1:length(subfields), + if sum(strcmp(subfields{k},["outlog" "errlog"])) == 0, + if verbose > 4, + disp(sprintf("+==+creating var for %s.%s.%s",groups{i}, fields{j}, subfields{k})) + end + Var=md.(groups{i}).(fields{j}).(subfields{k}); + [DimSize,DimValue,varid]=CreateVar(ncid,Var,subgroupID,subfields{k},DimSize,DimValue); + if ~isempty(varid), + FillVar(Var,subgroupID,varid); + end end - classtype=class(Var(l)); - if strcmp(classtype,'struct') - classtype=groups{i}; - end - listgroupID=netcdf.defGrp(subgroupID,lname); - netcdf.putAtt(listgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',classtype); - subfields=fieldnames(Var(l)); - for m=1:length(subfields) - if ~strcmp(subfields{m},'outlog') - [DimSize,DimValue]=DefCreateVar(ncid,Var(l).(subfields{m}),listgroupID,subfields{m},DimSize,DimValue); - end - end - end - else - subgroupID=netcdf.defGrp(groupID,groupfields{j}); - classtype=class(Var); - if strcmp(classtype,'struct') - classtype=groups{i}; - end - netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',classtype); - subfields=fieldnames(Var); - for m=1:length(subfields) - if ~strcmp(subfields{m},'outlog') - [DimSize,DimValue]=DefCreateVar(ncid,Var.(subfields{m}),subgroupID,subfields{m},DimSize,DimValue); - end - end + end + end else - netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',class(md.(groups{i}))); - [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,groupfields{j},DimSize,DimValue); - end - end - end - netcdf.close(ncid); + disp(sprintf("WARNING, md.%s.%s is not treated as it does not fall in one of the existing cases with class '%s'.",groups{i}, fields{j}, class(Var))) + end + end + end + netcdf.close(ncid); end -function [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,field,DimSize,DimValue,last,md,midfield) - varclass=class(Var); +function [DimSize,DimValue,varid]=CreateVar(ncid,Var,groupID,field,DimSize,DimValue) +% Grab dimensions varsize=size(Var); varlength=length(Var); + % treating scalar string or bool as atribute if isa(Var,'logical'), if Var, @@ -160,11 +281,85 @@ else, LogicString='False'; - end + end netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),field,LogicString); + varid=[]; + elseif isa(Var,'char'), - netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),field,Var); + if strcmp(field,'name'), % it looks like netCDF does not like attributes that are called "name" + field = 'varname'; + end + if size(Var,1) <= 1 %that is a single string or empty + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),field,Var); + varid=[]; + else % that is a character array + [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); + varid = netcdf.defVar(groupID,field,'NC_CHAR',dims); + if numel(Var)>1 + netcdf.defVarDeflate(groupID,varid,true,true,4); + end + end + elseif isa(Var,'double'), %dealing with arrays - [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); - varid = netcdf.defVar(groupID,field,'NC_DOUBLE',dims); + if all(mod(Var, 1) == 0, 'all') %those are actually integers, + [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); + varid = netcdf.defVar(groupID,field,'NC_INT64',dims); + if numel(Var)>1 + netcdf.defVarDeflate(groupID,varid,true,true,4); + end + else + [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); + varid = netcdf.defVar(groupID,field,'NC_DOUBLE',dims); + if numel(Var)>1 + netcdf.defVarDeflate(groupID,varid,true,true,4); + end + end + elseif isa(Var,'cell'), + % cells can be a range of things, what are we dealing with here + if isempty(Var), + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),field,'emptycell'); + varid=[]; + else + [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); + if isa(Var{1}, 'double'), + varid = netcdf.defVar(groupID,field,'NC_DOUBLE',dims); + if numel(Var)>1 + netcdf.defVarDeflate(groupID,varid,true,true,4); + end + else + varid = netcdf.defVar(groupID,field,'NC_CHAR',dims); + if numel(Var)>1 + netcdf.defVarDeflate(groupID,varid,true,true,4); + end + end + end + elseif isa(Var,'struct'), + if isempty(fieldnames(Var)), + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),field,'emptystruct'); + varid=[]; + else + %Start by getting the structure fields and size + [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); + varid = netcdf.defVar(groupID,field,'NC_CHAR',dims); + if numel(Var)>1 + netcdf.defVarDeflate(groupID,varid,true,true,4); + end + end + else + disp(sprintf('no support for class %s of field %s',class(Var),field)); + varid=[]; + end + return +end + + +function FillVar(Var,groupID,varid) +% Grab dimensions + varsize=size(Var); + varlength=length(Var); + % treating scalar string or bool as atribute + if isa(Var,'double'), %dealing with arrays + if all(mod(Var, 1) == 0, 'all') %those are actually integers, + Var = int64(Var); + end if length(Var)==0, netcdf.putVar(groupID,varid,NaN); @@ -172,68 +367,69 @@ netcdf.putVar(groupID,varid,Var); end - elseif isa(Var,'cell'), - [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); - %dirty hack to be able to pass strings - varid = netcdf.defVar(groupID,field,'NC_CHAR',dims); - if length(Var)==0, - netcdf.putVar(groupID,varid,0,9,'emptycell') - else - for i=1:length(Var), + elseif isa(Var,'char'), % at this point this should be a character array + netcdf.putVar(groupID,varid,Var); + elseif isa(Var,'cell'), % there can be a number of things in a cell array + for i=1:length(Var), + if isa(Var{i},'char') %for characters we limit the size to 40 for now if length(Var)>1, - endpoint=[1,min(length(Var{i}),40)]; - startpoint=[1 0]; - else - endpoint=min(length(Var{i}),40); + count=[min(length(Var{i}),40), 1]; + startpoint=[0 i-1]; + else + count=min(length(Var{i}),40); startpoint=0; end + if length(Var{i})>40, - netcdf.putVar(groupID,varid,startpoint,extent,Var{i}(1:40)) + netcdf.putVar(groupID,varid,startpoint,count,Var{i}(1:40)); disp(sprintf('some variable have been truncated')); else - netcdf.putVar(groupID,varid,startpoint,endpoint,Var{i}) - end + netcdf.putVar(groupID,varid,startpoint,count,Var{i}); + end + elseif isa(Var{i},'double') + startpoint=[i-1]; + count=[1 length(Var{i}) ndims(Var{i})]; + for j=1:ndims(Var{i}), + startpoint=[startpoint 0]; + end + netcdf.putVar(groupID,varid,startpoint,count,Var{i}); + else + disp(sprintf("WARNING: cell of class %s is not supported.",class(Var{i}))) end end elseif isa(Var,'struct'), %Start by getting the structure fields and size - locfields=fieldnames(Var); - [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); - varid = netcdf.defVar(groupID,field,'NC_CHAR',dims); - if length(locfields)==0, - netcdf.putVar(groupID,varid,[0,0],[1,11],'emptystruct') - else - for i=1:length(locfields), - for j=1:2, - if j==1, - CharVar=locfields{i}; - if length(CharVar)==0 - CharVar='emptystruct'; - end - startpoint=[i-1,0,0]; + locfields=fieldnames(Var) + for i=1:length(locfields), + for j=1:2, + if j==1, + CharVar=locfields{i}; + if length(CharVar)==0 + CharVar='emptystruct'; + end + startpoint=[i-1,0,0]; + else + if isa(Var.(locfields{i}),'char'), + CharVar=Var.(locfields{i}); else - if isa(Var.(locfields{i}),'char'), - CharVar=Var.(locfields{i}); - else - CharVar=num2str(Var.(locfields{i})); - end - if length(CharVar)==0 - CharVar='emptystruct'; - end - startpoint=[i-1,1,0]; - end - - extent=[1,1,min(length(CharVar),40)]; - if length(CharVar)>40, - netcdf.putVar(groupID,varid,startpoint,extent,CharVar(1:40)) - disp(sprintf('some variable have been truncated')); - else - netcdf.putVar(groupID,varid,startpoint,extent,CharVar) - end + CharVar=num2str(Var.(locfields{i})); + end + if length(CharVar)==0 + CharVar='emptystruct'; + end + startpoint=[i-1,1,0]; + end + + extent=[1,1,min(length(CharVar),40)]; + if length(CharVar)>40, + netcdf.putVar(groupID,varid,startpoint,extent,CharVar(1:40)); + disp(sprintf('some variable have been truncated')); + else + netcdf.putVar(groupID,varid,startpoint,extent,CharVar); end end end else - disp(sprintf('no support for class %s of field %s',varclass,field)); - end + disp(sprintf('no support for class %s',class(Var))); + end return end @@ -241,44 +437,46 @@ function [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue) dims=[]; - if isa(Var,'cell'), - varsize=size(Var'); - elseif isa(Var,'struct') + celldims=[]; + dim=ndims(Var); + if isa(Var,'struct'), varsize=length(fieldnames(Var)); else varsize=size(Var); - end - dim=sum(varsize>1); - if dim>0 - for i=1:dim - indsize=find(varsize(i)==DimValue); - if length(indsize)>0 - dims=[dims DimSize(indsize).index]; - else - indsize=length(DimSize)+1; - DimSize(indsize).index=netcdf.defDim(ncid,['Dimension' num2str(indsize)],varsize(i)); - [DimSize(indsize).name,DimSize(indsize).value]=netcdf.inqDim(ncid,DimSize(indsize).index); - DimValue(indsize)=DimSize(indsize).value; - dims=[dims DimSize(indsize).index]; - end - end - end - %if we have a cell variable we need to add a stringlength dimension + if isa(Var, 'cell') + %we add the dimension of the cells themselves, + %that will most probably fail if cells have different sizes + for i=1:dim, + newdim=size(Var{i}); + if ~ismember(newdim, celldims), + celldims=[celldims newdim]; + end + end + end + end + varsize=[varsize celldims]; + alldim=length(varsize); + if dim>0, + for i=1:alldim, + if size(Var, i)>1 || i>dim, %we skip dimensions with zero lenght but want to add dimensions from cells + indsize=find(varsize(i)==DimValue); + if length(indsize)>0 + dims=[dims DimSize(indsize).index]; + else + indsize=length(DimSize)+1; + DimSize(indsize).index=netcdf.defDim(ncid,['DimNum' num2str(indsize)],varsize(i)); + [DimSize(indsize).name,DimSize(indsize).value]=netcdf.inqDim(ncid,DimSize(indsize).index); + DimValue(indsize)=DimSize(indsize).value; + dims=[dims DimSize(indsize).index]; + end + end + end + end + if isa(Var, 'cell') && isa(Var{1}, 'char'), + %if we have an cell variable with strings we need to add a stringlength + dims=[dims DimSize(4).index]; + end + % struct also need an extra dimension 2, but only if non empty if isa(Var,'struct'), - if DimValue(3)~=2 - if DimValue(2)~=2 - dims=[dims DimSize(1).index]; - else - dims=[dims DimSize(2).index]; - end - else - dims=[dims DimSize(3).index]; - end - end - if isa(Var,'cell') || isa(Var,'struct'), - if DimValue(2)~=40 - dims=[dims DimSize(1).index]; - else - dims=[dims DimSize(2).index]; - end + dims=[dims DimSize(3).index DimSize(4).index]; end end Index: /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.py =================================================================== --- /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.py (revision 27034) +++ /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.py (revision 27035) @@ -1,4 +1,5 @@ from netCDF4 import Dataset import numpy as np +import numpy.ma as ma import time import collections @@ -13,5 +14,5 @@ def update(self, stepvar): - #if we have a scalar we just add it to the en + #if we have a scalar we just add it to the end #we save the size of the current step for further treatment if len(np.shape(stepvar)) == 0: @@ -21,39 +22,47 @@ #we save the size of the current step for further treatment else: - self.sizes.append(len(stepvar)) - for r in stepvar: - self.data.append(r) + self.sizes.append([np.shape(stepvar)]) + stackdat = np.squeeze(stepvar.flatten()) + self.data = np.hstack((self.data, stackdat)) def finalize(self, rows): #we have more scalars than steps, so we have an array if len(self.data) > rows: + datasize = np.squeeze(self.sizes) + maxsize = [] + try: + dims = np.arange(np.shape(datasize)[1]) + for dim in dims: + maxsize.append(np.nanmax(datasize[:, dim])) + except IndexError: + if datasize.ndim == 0: + maxsize.append(datasize) + else: + maxsize.append(np.nanmax(datasize[:])) + findim = np.insert(maxsize, 0, rows) #first check if all steps are the same size - SameSize = np.sum(np.asarray(self.sizes) - self.sizes[0]) == 0 + if datasize.ndim == 0: + SameSize = True + else: + SameSize = np.sum(np.abs(datasize - datasize[0])) == 0 if SameSize: #same size for all steps, just reshape - return np.reshape(self.data, newshape=(rows, int(len(self.data) / rows))) + return np.reshape(self.data, newshape=(findim)) else: #different sizes at each steps, first create a table big enough for the biggest step startpoint = 0 - datadim = len(np.shape(self.data)) - if datadim == 1: - outdat = np.nan * np.ones((rows, np.nanmax(self.sizes))) - for step in range(rows): - curlen = self.sizes[step] - outdat[step, :curlen] = self.data[startpoint: startpoint + curlen] - startpoint += curlen - elif datadim == 2: - outdat = np.nan * np.ones((rows, np.nanmax(self.sizes), np.shape(self.data)[1])) - for step in range(rows): - curlen = self.sizes[step] - outdat[step, :curlen, :] = self.data[startpoint: startpoint + curlen] - startpoint += curlen - - else: - print("ERROR, reult treatment cant cope with dimensions above 2") + outdat = np.nan * np.ones(findim) + for step in range(rows): + #slicer is the data slice in the final array + slicer = [slice(0, d) for d in datasize[step, :]] + slicer = np.insert(slicer, 0, step) + curlen = int(np.prod(datasize[step, :])) + outdat[tuple(slicer)] = np.reshape(self.data[startpoint:startpoint + curlen], newshape=(datasize[step, :])) + startpoint += curlen + #outmasked = ma.masked_array(outdat, mask=np.where(np.isnan(outdat), 1, 0)) return outdat - #as much scalars as stpes (or less) so just one value per step - else: - return np.asarray(self.data) + #as much scalars as steps (or less) so just one value per step + else: + return np.squeeze(np.asarray(self.data)) @@ -88,6 +97,6 @@ dimindex = 2 #add mesh related dimension that we know are needed - dimlist = [2, md.mesh.numberofelements, md.mesh.numberofvertices, np.shape(md.mesh.elements)[1]] - dimnames = ['DictDummy', 'EltNum', 'VertNum', 'VertPerElt'] + dimlist = [2, 40, md.mesh.numberofelements, md.mesh.numberofvertices, np.shape(md.mesh.elements)[1]] + dimnames = ['DictDummy', 'StringLength', 'EltNum', 'VertNum', 'VertPerElt'] if verbose > 0: print('===Creating dimensions ===') @@ -121,12 +130,13 @@ # looping on fields in each group for field in fields: + Var = md.__dict__[group].__dict__[field] # Special treatment for list fields - if type(md.__dict__[group].__dict__[field]) == list: + if type(Var) == list: StdList = False - if len(md.__dict__[group].__dict__[field]) == 0: + if len(Var) == 0: StdList = True #this is an empty list else: #returns False for exotic types (typicaly results) - StdList = type(md.__dict__[group].__dict__[field][0]) in typelist + StdList = type(Var[0]) in typelist klass = type(md.__dict__[group]).__module__ + '.' + type(md.__dict__[group]).__name__ NCgroup.__setattr__('classtype', klass) @@ -134,5 +144,4 @@ if verbose > 4: print("=££=creating var for {}.{} with classtype : {}".format(group, field, klass)) - Var = md.__dict__[group].__dict__[field] Var = SqueezeVar(Var) DimDict, ncvar = CreateVar(NCData, Var, field, NCgroup, DimDict) @@ -141,6 +150,6 @@ else: # this is a list of fields, specific treatment needed (usually results or outputdefinitions) if verbose > 4: - print("list of fields happens for {}.{} with classtype : {}".format(group, field, klass)) - Listsize = len(md.__dict__[group].__dict__[field]) + print("=??=we have a list of fields for {}.{} with classtype : {}".format(group, field, klass)) + Listsize = len(Var) if group == 'results': #for results we reshape the datas following time rather than subgrouping Subgroup = NCgroup.createGroup(str(field)) @@ -155,5 +164,5 @@ subfields = dict.keys(md.__dict__[group].__dict__[field].__getitem__(0)) for subfield in subfields: - if subfield not in['errlog', 'outlog']: + if subfield not in ['errlog', 'outlog']: StackedVar = ResTable() #first loop over the field (result type) to find the index of the last subfield (variable) @@ -172,5 +181,5 @@ StackedVar.update(Var) if verbose > 4: - print("=$$=creating var for {}.{}.{}".format(group, field, subfield)) + print("=@@=creating var for {}.{}.{}".format(group, field, subfield)) print("last index of the list is {}".format(lastindex)) StackedVar = SqueezeVar(StackedVar.finalize(int(lastindex))) @@ -238,5 +247,5 @@ subfields = dict.keys(md.__dict__[group].__dict__[field].__getitem__(0)) for subfield in subfields: - if subfield not in['errlog', 'outlog']: + if subfield not in ['errlog', 'outlog']: StackedVar = ResTable() for listindex in range(0, Listsize): @@ -245,9 +254,10 @@ lastindex = listindex + 1 except AttributeError: - Var = md.__dict__[group].__dict__[field].__getitem__(listindex)[subfield] + Var = md.__dict__[group].__dict__[field].__dict__[subfield] + lastindex = listindex except KeyError: #Some fields only exist for the first step lastindex = listindex - continue + break Var = SqueezeVar(Var) StackedVar.update(Var) @@ -289,5 +299,5 @@ FillVar(ncvar, Var) else: - print("WARNING, md.{}.{} is not treated as it does not fall in one of the existing cases.".format(str(group), str(field))) + print("WARNING, md.{}.{} is not treated as it does not fall in one of the existing cases.".format(group, field)) NCData.close() @@ -305,4 +315,5 @@ if val_type.startswith(' 0 + except TypeError: + #check if we are integer and under C long overflow + IsInt = np.mod(var, 1) == 0 and abs(var) < 2147483647 + if IsInt: + val_type = 'int64' + if val_shape in [(), (0,), 0] and not SupDim: + ncvar = Group.createVariable(str(field), TypeDict[val_type], zlib=True) + else: + dimensions, DimDict = GetDim(NCData, val_shape, val_type, DimDict, val_dim) + if SupDim: + dimensions = SupDim + dimensions + ncvar = Group.createVariable(str(field), TypeDict[val_type], dimensions=dimensions, zlib=True) + elif val_type in [int, 'int64']: if val_shape in [(), (0,), 0] and not SupDim: ncvar = Group.createVariable(str(field), TypeDict[val_type], zlib=True) @@ -410,5 +452,5 @@ elif val_type == 'bool': for elt in range(0, val_shape[0]): - ncvar[elt] = str(invar[elt]) + ncvar[elt] = int(invar[elt]) #str(invar[elt]) # treating dictionaries as tables of strings elif val_type in [collections.OrderedDict, dict]: Index: /issm/trunk/src/m/contrib/defleurian/netCDF/restable.m =================================================================== --- /issm/trunk/src/m/contrib/defleurian/netCDF/restable.m (revision 27035) +++ /issm/trunk/src/m/contrib/defleurian/netCDF/restable.m (revision 27035) @@ -0,0 +1,60 @@ +classdef restable + properties(SetAccess=public) + data=[]; + sizes=[]; + end + methods + function self = update(self, stepvar) + if length(stepvar) == 1 + %if we have a scalar we just add it to the end + %we save the size of the current step for further treatment + self.sizes=[self.sizes;1]; + self.data=[self.data;stepvar]; + else + % if it is an array we add the values one by one + %we save the size of the current step for further treatment + self.sizes=[self.sizes;fliplr(size(stepvar))]; + %we need to transpose to follow the indexing + flatdata=reshape(stepvar', 1, []); + self.data=[self.data,flatdata]; + end + end + function outdat = finalize(self, rows) + if length(self.data)>rows, + if size(self.sizes, 1)==1, + %just one step, data don't need treatment + outdat=self.data; + else, + %we have more scalars than steps, so we have an array + maxsize=[]; + for d=1:size(self.sizes,2) + maxsize=[maxsize,max(self.sizes(:,d))]; + end + findim=[maxsize, rows]; + %first check if all steps are the same size + SameSize = sum(self.sizes - self.sizes(1, :))==0; + if SameSize, + %same size for all steps, just reshape + outdat=reshape(self.data, findim); + else, + %different sizes at each steps, first create a table big enough for the biggest step + startpoint=1; + datadim=ndims(self.data); + outdat=nan(findim); + for r=1:rows + curlen = prod(self.sizes(r, :)); + outdat(1:self.sizes(r,1), 1:self.sizes(r,2), r) = reshape(self.data(startpoint:startpoint+ ... + curlen-1),self.sizes(r,:)); + startpoint = startpoint+curlen; + end + + end + end, + else, + %as much scalars as steps (or less) so just one value per step + outdat=self.data; + + end + end + end +end Index: /issm/trunk/src/m/contrib/larour/mdanalysis.m =================================================================== --- /issm/trunk/src/m/contrib/larour/mdanalysis.m (revision 27034) +++ /issm/trunk/src/m/contrib/larour/mdanalysis.m (revision 27035) @@ -1600,10 +1600,10 @@ if strncmpi(fieldv,'Mask',4), contourexp=[tempname '.exp']; - expcontourlevelzero(md.icecaps{i},field,0, contourexp); + isoline(md.icecaps{i},field,'output',contourexp); contourlevels=1; if diff, contourdiffexp=[tempname '.exp']; - expcontourlevelzero(md.icecaps{i},dfield,0, contourdiffexp); + isoline(md.icecaps{i},dfield,'output',contourdiffexp); end end Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpBamber2001.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpBamber2001.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpBamber2001.m (revision 27035) @@ -8,4 +8,7 @@ bamber2001bedpath ='/home/ModelData/Greenland/Bamber2001/bedrock.mat'; bamber2001thxpath ='/home/ModelData/Greenland/Bamber2001/thickness.mat'; + case {'totten'} + bamber2001bedpath ='/totten_1/ModelData/Greenland/Bamber2001/bedrock.mat'; + bamber2001thxpath ='/totten_1/ModelData/Greenland/Bamber2001/thickness.mat'; otherwise error('machine not supported yet'); Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpBamber2013.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpBamber2013.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpBamber2013.m (revision 27035) @@ -22,4 +22,6 @@ case {'ronne'} bamber2013nc='/home/ModelData/Greenland/Bamber2013/Greenland_bedrock_topography_V3.nc'; + case {'totten'} + bamber2013nc='/totten_1/ModelData/Greenland/Bamber2013/Greenland_bedrock_topography_V3.nc'; otherwise error('machine not supported yet'); Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpBedmachineAntarctica.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpBedmachineAntarctica.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpBedmachineAntarctica.m (revision 27035) @@ -28,5 +28,5 @@ if nargin<5 ncdate='2020-07-15'; %BedMachine v2 - ncdate='2021-11-16'; %BedMachine v2 + ncdate='2021-11-16'; %new end basename = 'BedMachineAntarctica'; Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpBedmachineGreenland.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpBedmachineGreenland.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpBedmachineGreenland.m (revision 27035) @@ -30,4 +30,6 @@ ncdate='2017-09-25'; %BedMachine v3 ncdate='2020-04-14'; + ncdate='2021-08-27'; + ncdate='2022-03-17'; end basename = 'BedMachineGreenland'; Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpDhdt.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpDhdt.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpDhdt.m (revision 27035) @@ -4,4 +4,6 @@ case {'ronne'} dhdtpath='/home/ModelData/Greenland/DHDT/dhdt0306.tif'; + case {'totten'} + dhdtpath='/totten_1/ModelData/Greenland/DHDT/dhdt0306.tif'; otherwise error('machine not supported yet'); Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpGimpdem.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpGimpdem.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpGimpdem.m (revision 27035) @@ -6,4 +6,6 @@ case {'ronne'} howatpath='/home/ModelData/Greenland/gimpdem/gimpdem_90m.tif'; + case {'totten'} + howatpath='/totten_1/ModelData/Greenland/gimpdem/gimpdem_90m.tif'; otherwise error('machine not supported yet'); Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpJakobsson2020.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpJakobsson2020.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpJakobsson2020.m (revision 27035) @@ -4,4 +4,6 @@ case {'ronne'} ncpath ='/home/ModelData/Greenland/IBCAO/IBCAO_v4_200m.nc'; + case {'totten'} + ncpath ='/totten_1/ModelData/Greenland/IBCAO/IBCAO_v4_200m.nc'; otherwise error('machine not supported yet'); @@ -39,5 +41,5 @@ if nargout==2, - ncpath ='/home/ModelData/Greenland/IBCAO/IBCAO_v4_200m_TID.nc'; + ncpath ='/totten_1/ModelData/Greenland/IBCAO/IBCAO_v4_200m_TID.nc'; disp(' -- Jakobsson2020: loading source'); data = double(ncread(ncpath,'z',[id1x id1y],[id2x-id1x+1 id2y-id1y+1],[1 1]))'; Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpMouginotAnt2019.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpMouginotAnt2019.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpMouginotAnt2019.m (revision 27035) @@ -5,4 +5,6 @@ case {'ronne'} nc = '/home/ModelData/Antarctica/MouginotVel/v_mix.v13Mar2019.nc'; + case {'totten'} + nc = '/totten_1/ModelData/Antarctica/MouginotVel/v_mix.v8Jul2019.nc'; otherwise error('hostname not supported yet'); Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpRACMO1km.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpRACMO1km.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpRACMO1km.m (revision 27035) @@ -4,4 +4,6 @@ case {'ronne'} rootname='/home/ModelData/Greenland/RACMO2_1km/SMB_MEAN1960-1989_150m.nc'; + case {'totten'} + rootname='/totten_1/ModelData/Greenland/RACMO2_1km/SMB_MEAN1960-1989_150m.nc'; otherwise error('machine not supported yet'); Index: /issm/trunk/src/m/contrib/morlighem/modeldata/interpRignotIceShelfMelt.m =================================================================== --- /issm/trunk/src/m/contrib/morlighem/modeldata/interpRignotIceShelfMelt.m (revision 27034) +++ /issm/trunk/src/m/contrib/morlighem/modeldata/interpRignotIceShelfMelt.m (revision 27035) @@ -4,4 +4,6 @@ case {'ronne'} rignotmelt='/home/ModelData/Antarctica/RignotMeltingrate/Ant_MeltingRate.nc'; + case {'totten'} + rignotmelt='/totten_1/ModelData/Antarctica/RignotMeltingrate/Ant_MeltingRate.nc'; case {'thwaites','murdo','astrid'} rignotmelt=['/home/seroussi/Data/Ant_MeltingRate.nc']; Index: /issm/trunk/src/m/coordsystems/ll2xy.m =================================================================== --- /issm/trunk/src/m/coordsystems/ll2xy.m (revision 27034) +++ /issm/trunk/src/m/coordsystems/ll2xy.m (revision 27035) @@ -40,4 +40,18 @@ end +%Move to CoordTransform now... +if exist('CoordTransform_matlab')==3 + disp('Calling CoordTransform instead, make sure to change your MATLAB script'); + if sgn==+1 + assert(delta==45); assert(slat ==70); + [x y]=CoordTransform(lat,lon,'EPSG:4326','EPSG:3413'); + return; + else + assert(delta==0); assert(slat ==71); + [x y]=CoordTransform(lat,lon,'EPSG:4326','EPSG:3031'); + return; + end +end + % Conversion constant from degrees to radians cde = 57.29577951; Index: /issm/trunk/src/m/coordsystems/xy2ll.m =================================================================== --- /issm/trunk/src/m/coordsystems/xy2ll.m (revision 27034) +++ /issm/trunk/src/m/coordsystems/xy2ll.m (revision 27035) @@ -34,4 +34,18 @@ help xy2ll error('bad usage'); +end + +%Move to CoordTransform now... +if exist('CoordTransform_matlab')==3 + disp('Calling CoordTransform instead, make sure to change your MATLAB script'); + if sgn==+1 + assert(delta==45); assert(slat ==70); + [lat lon]=CoordTransform(x, y,'EPSG:3413','EPSG:4326'); + return; + else + assert(delta==0); assert(slat ==71); + [lat lon]=CoordTransform(x, y,'EPSG:3031','EPSG:4326'); + return; + end end Index: /issm/trunk/src/m/dev/issmversion.m =================================================================== --- /issm/trunk/src/m/dev/issmversion.m (revision 27034) +++ /issm/trunk/src/m/dev/issmversion.m (revision 27035) @@ -17,5 +17,5 @@ disp(['Compiled on ' IssmConfig('HOST_VENDOR') ' ' IssmConfig('HOST_OS') ' ' IssmConfig('HOST_ARCH') ' by ' IssmConfig('USER_NAME')]); disp([' ']); -disp(['Copyright (c) 2009-2021 California Institute of Technology']); +disp(['Copyright (c) 2009-2022 California Institute of Technology']); disp([' ']); disp([' to get started type: issmdoc']); Index: /issm/trunk/src/m/dev/issmversion.py =================================================================== --- /issm/trunk/src/m/dev/issmversion.py (revision 27034) +++ /issm/trunk/src/m/dev/issmversion.py (revision 27035) @@ -16,5 +16,5 @@ print(' ') print(('Build date: ' + IssmConfig('PACKAGE_BUILD_DATE')[0])) -print('Copyright (c) 2009-2021 California Institute of Technology') +print('Copyright (c) 2009-2022 California Institute of Technology') print(' ') print(' to get started type: issmdoc') Index: /issm/trunk/src/m/exp/contourlevelzero.m =================================================================== --- /issm/trunk/src/m/exp/contourlevelzero.m (revision 27034) +++ /issm/trunk/src/m/exp/contourlevelzero.m (revision 27035) @@ -1,229 +1,3 @@ -function contours=contourlevelzero(md,mask,level) -%CONTOURLEVELZERO - figure out the zero level (or offset thereof, specified by the level value) -% of a vectorial mask, and vectorialize it into an exp or shp compatible -%structure. -% -% Usage: -% contours=contourlevelzero(md,mask,level) -% -% See also: PLOT_CONTOUR +function contours=contourlevelzero(md,mask,level,varargin) -%process data -if dimension(md.mesh)==3, -% error('contourlevelzero error message: routine not supported for 3d meshes, project on a layer'); - x = md.mesh.x2d; - y = md.mesh.y2d; - index=md.mesh.elements2d; -else - x=md.mesh.x; - y=md.mesh.y; - index=md.mesh.elements; -end - -if isprop(md.mesh,'z'), - z=md.mesh.z; -else - z=zeros(md.mesh.numberofvertices,1); -end - -if isempty(mask), error('mask provided is empty'); end -if dimension(md.mesh)==3, - if length(mask)~=md.mesh.numberofvertices2d, error('mask provided should be specified at the vertices of the mesh'); end -else - if length(mask)~=md.mesh.numberofvertices, error('mask provided should be specified at the vertices of the mesh'); end -end - -%initialization of some variables -numberofelements=size(index,1); -elementslist=1:numberofelements; -c=[]; -h=[]; - -%get unique edges in mesh -%1: list of edges -edges=[index(:,[1,2]); index(:,[2,3]); index(:,[3,1])]; -%2: find unique edges -[edges,I,J]=unique(sort(edges,2),'rows'); -%3: unique edge numbers -vec=J; -%4: unique edges numbers in each triangle (2 triangles sharing the same edge will have -% the same edge number) -edges_tria=[vec(elementslist), vec(elementslist+numberofelements), vec(elementslist+2*numberofelements)]; - -%segments [nodes1 nodes2] -Seg1=index(:,[1 2]); -Seg2=index(:,[2 3]); -Seg3=index(:,[3 1]); - -%segment numbers [1;4;6;...] -Seg1_num=edges_tria(:,1); -Seg2_num=edges_tria(:,2); -Seg3_num=edges_tria(:,3); - -%value of data on each tips of the segments -Data1=mask(Seg1); -Data2=mask(Seg2); -Data3=mask(Seg3); - -%get the ranges for each segment -Range1=sort(Data1,2); -Range2=sort(Data2,2); -Range3=sort(Data3,2); - -%find the segments that contain this value -pos1=(Range1(:,1)=level); -pos2=(Range2(:,1)=level); -pos3=(Range3(:,1)=level); - -%get elements -poselem12=(pos1 & pos2); -poselem13=(pos1 & pos3); -poselem23=(pos2 & pos3); -poselem=find(poselem12 | poselem13 | poselem23); -numelems=length(poselem); - -%if no element has been flagged, skip to the next level -if numelems==0, - warning('contourlevelzero warning message: no elements found with corresponding level value in mask'); - contours=struct([]); - return; -end - -%go through the elements and build the coordinates for each segment (1 by element) -x1=zeros(numelems,1); -x2=zeros(numelems,1); -y1=zeros(numelems,1); -y2=zeros(numelems,1); -z1=zeros(numelems,1); -z2=zeros(numelems,1); - -edge_l=zeros(numelems,2); - -for j=1:numelems, - - weight1=(level-Data1(poselem(j),1))/(Data1(poselem(j),2)-Data1(poselem(j),1)); - weight2=(level-Data2(poselem(j),1))/(Data2(poselem(j),2)-Data2(poselem(j),1)); - weight3=(level-Data3(poselem(j),1))/(Data3(poselem(j),2)-Data3(poselem(j),1)); - - if poselem12(poselem(j)); - - x1(j)=x(Seg1(poselem(j),1))+weight1*(x(Seg1(poselem(j),2))-x(Seg1(poselem(j),1))); - x2(j)=x(Seg2(poselem(j),1))+weight2*(x(Seg2(poselem(j),2))-x(Seg2(poselem(j),1))); - y1(j)=y(Seg1(poselem(j),1))+weight1*(y(Seg1(poselem(j),2))-y(Seg1(poselem(j),1))); - y2(j)=y(Seg2(poselem(j),1))+weight2*(y(Seg2(poselem(j),2))-y(Seg2(poselem(j),1))); - z1(j)=z(Seg1(poselem(j),1))+weight1*(z(Seg1(poselem(j),2))-z(Seg1(poselem(j),1))); - z2(j)=z(Seg2(poselem(j),1))+weight2*(z(Seg2(poselem(j),2))-z(Seg2(poselem(j),1))); - - edge_l(j,1)=Seg1_num(poselem(j)); - edge_l(j,2)=Seg2_num(poselem(j)); - - elseif poselem13(poselem(j)), - - x1(j)=x(Seg1(poselem(j),1))+weight1*(x(Seg1(poselem(j),2))-x(Seg1(poselem(j),1))); - x2(j)=x(Seg3(poselem(j),1))+weight3*(x(Seg3(poselem(j),2))-x(Seg3(poselem(j),1))); - y1(j)=y(Seg1(poselem(j),1))+weight1*(y(Seg1(poselem(j),2))-y(Seg1(poselem(j),1))); - y2(j)=y(Seg3(poselem(j),1))+weight3*(y(Seg3(poselem(j),2))-y(Seg3(poselem(j),1))); - z1(j)=z(Seg1(poselem(j),1))+weight1*(z(Seg1(poselem(j),2))-z(Seg1(poselem(j),1))); - z2(j)=z(Seg3(poselem(j),1))+weight3*(z(Seg3(poselem(j),2))-z(Seg3(poselem(j),1))); - - edge_l(j,1)=Seg1_num(poselem(j)); - edge_l(j,2)=Seg3_num(poselem(j)); - - elseif poselem23(poselem(j)), - - x1(j)=x(Seg2(poselem(j),1))+weight2*(x(Seg2(poselem(j),2))-x(Seg2(poselem(j),1))); - x2(j)=x(Seg3(poselem(j),1))+weight3*(x(Seg3(poselem(j),2))-x(Seg3(poselem(j),1))); - y1(j)=y(Seg2(poselem(j),1))+weight2*(y(Seg2(poselem(j),2))-y(Seg2(poselem(j),1))); - y2(j)=y(Seg3(poselem(j),1))+weight3*(y(Seg3(poselem(j),2))-y(Seg3(poselem(j),1))); - z1(j)=z(Seg2(poselem(j),1))+weight2*(z(Seg2(poselem(j),2))-z(Seg2(poselem(j),1))); - z2(j)=z(Seg3(poselem(j),1))+weight3*(z(Seg3(poselem(j),2))-z(Seg3(poselem(j),1))); - - edge_l(j,1)=Seg2_num(poselem(j)); - edge_l(j,2)=Seg3_num(poselem(j)); - else - %it shoud not go here - end -end - -%now that we have the segments, we must try to connect them... - -%loop over the subcontours -contours=struct([]); - -while ~isempty(edge_l), - - %take the right edge of the second segment and connect it to the next segments if any - e1=edge_l(1,1); e2=edge_l(1,2); - xc=[x1(1);x2(1)]; yc=[y1(1);y2(1)]; zc=[z1(1);z2(1)]; - - - %erase the lines corresponding to this edge - edge_l(1,:)=[]; - x1(1)=[]; x2(1)=[]; - y1(1)=[]; y2(1)=[]; - z1(1)=[]; z2(1)=[]; - - [ro1,co1]=find(edge_l==e1); - - while ~isempty(ro1) - - if co1==1, - xc=[x2(ro1);xc]; yc=[y2(ro1);yc];zc=[z2(ro1);zc]; - - %next edge: - e1=edge_l(ro1,2); - - else - xc=[x1(ro1);xc]; yc=[y1(ro1);yc];zc=[z1(ro1);zc]; - - %next edge: - e1=edge_l(ro1,1); - end - - %erase the lines of this - edge_l(ro1,:)=[]; - x1(ro1)=[]; x2(ro1)=[]; - y1(ro1)=[]; y2(ro1)=[]; - z1(ro1)=[]; z2(ro1)=[]; - - %next connection - [ro1,co1]=find(edge_l==e1); - end - - %same thing the other way (to the right) - [ro2,co2]=find(edge_l==e2); - - while ~isempty(ro2) - - if co2==1, - xc=[xc;x2(ro2)]; yc=[yc;y2(ro2)];zc=[zc;z2(ro2)]; - - %next edge: - e2=edge_l(ro2,2); - else - xc=[xc;x1(ro2)]; yc=[yc;y1(ro2)]; zc=[zc;z1(ro2)]; - - %next edge: - e2=edge_l(ro2,1); - end - - %erase the lines of this - edge_l(ro2,:)=[]; - x1(ro2)=[]; x2(ro2)=[]; - y1(ro2)=[]; y2(ro2)=[]; - z1(ro2)=[]; z2(ro2)=[]; - - %next connection - [ro2,co2]=find(edge_l==e2); - end - - %save xc,yc contour: - contours(end+1).x=xc; - contours(end).y=yc; - contours(end).z=zc; - contours(end).name=''; - contours(end).nods=length(xc); - contours(end).density=1; - contours(end).closed=0; - -end + error('this function has been renamed: A = isoline(md,mask);'); Index: /issm/trunk/src/m/exp/expcontourlevelzero.m =================================================================== --- /issm/trunk/src/m/exp/expcontourlevelzero.m (revision 27034) +++ /issm/trunk/src/m/exp/expcontourlevelzero.m (revision 27035) @@ -1,14 +1,3 @@ function expcontourlevelzero(md,mask,level,filename) -%EXPCONTOURLEVELZERO - write an Argus file from a structure recovered from running contourlevelzero -% -% Usage: -% expcontourlevelzero(md,mask,level,filename) -% -% Example: -% expcontourlevelzero(md,md.geometry.thickness,10, 'Level0.exp'); -% expcontourlevelzero(md,md.mask.ocean_levelset,0, 'Level0.exp'); -% -% See also CONTOURLEVELZERO, EXPWRITE -contours=contourlevelzero(md,mask,level); -expwrite(contours,filename); +error(['this function has been renamed: isoline(md,mask,''output'',''' filename ''');']); Index: /issm/trunk/src/m/exp/exptool.m =================================================================== --- /issm/trunk/src/m/exp/exptool.m (revision 27034) +++ /issm/trunk/src/m/exp/exptool.m (revision 27035) @@ -137,4 +137,5 @@ %plot existing profile if any hold on +disableDefaultInteractivity(gca); %disables the built-in interactions for the specified axes %Build backup structre for do and redo Index: /issm/trunk/src/m/exp/expwrite.py =================================================================== --- /issm/trunk/src/m/exp/expwrite.py (revision 27034) +++ /issm/trunk/src/m/exp/expwrite.py (revision 27035) @@ -7,5 +7,5 @@ This routine writes an Argus file from a dict containing the fields: x and y of the coordinates of the points. - The first argument is the list containing the points coordinates and the + The first argument is the list containing the points coordinates and the second one the file to be written. @@ -20,26 +20,64 @@ fid = open(filename, 'w') - for x, y in zip(contours['x'], contours['y']): - if len(x) != len(y): - raise RuntimeError('contours x and y coordinates must be of identical size') - - if 'name' in contours: - fid.write('{}{}\n'.format('# Name:', contours['name'])) + #if it is a list we need to loop on several contours + if isinstance(contours, list): + for contour in contours: + #if it is some kind of array it is a contour and we loop on indexes + if isinstance(contour['x'], (list, tuple, np.ndarray)): + writegeomlist(contour, fid, filename) + #else it is an index and we just write it down + else: + writegeom(contour, fid, filename) + #if it is a dict type it means just one contour + else: + #if it is some kind of array it is a contour and we loop on indexes + if isinstance(contours['x'], (list, tuple, np.ndarray)): + writegeomlist(contours, fid, filename) + #else it is an index and we just write it down else: - fid.write('{}{}\n'.format('# Name:', filename)) - - fid.write('{}\n'.format('## Icon:0')) - fid.write('{}\n'.format('# Points Count Value')) - if 'density' in contours: - if isinstance(contours['density'], int): - fid.write('{} {}\n'.format(np.size(x), contours['density'])) - else: - fid.write('{} {}\n'.format(np.size(x), 1.)) - else: - fid.write('{} {}\n'.format(np.size(x), 1.)) - fid.write('{}\n'.format('# X pos Y pos')) - for xi, yi in zip(x, y): - fid.write('%10.10f %10.10f\n' % (xi, yi)) - fid.write('\n') + writegeom(contours, fid, filename) fid.close() + + +def writegeomlist(contour, fid, filename): + if len(contour['x']) != len(contour['y']): + raise RuntimeError('contours x and y coordinates must be of identical size') + if 'name' in contour: + fid.write('{}{}\n'.format('## Name:', contour['name'])) + else: + fid.write('{}{}\n'.format('## Name:', filename)) + + fid.write('{}\n'.format('## Icon:0')) + fid.write('{}\n'.format('# Points Count Value')) + if 'density' in contour: + if isinstance(contour['density'], int): + fid.write('{} {}\n'.format(np.size(contour['x']), contour['density'])) + else: + fid.write('{} {}\n'.format(np.size(contour['x']), 1.)) + else: + fid.write('{} {}\n'.format(np.size(contour['x']), 1.)) + fid.write('{}\n'.format('# X pos Y pos')) + for x, y in zip(contour['x'], contour['y']): + fid.write('%10.10f %10.10f\n' % (x, y)) + fid.write('\n') + + +def writegeom(contour, fid, filename): + if 'name' in contour: + fid.write('{}{}\n'.format('## Name:', contour['name'])) + else: + fid.write('{}{}\n'.format('## Name:', filename)) + + fid.write('{}\n'.format('## Icon:0')) + fid.write('{}\n'.format('# Points Count Value')) + if 'density' in contour: + if isinstance(contour['density'], int): + fid.write('{} {}\n'.format(1, contour['density'])) + else: + fid.write('{} {}\n'.format(1, 1.)) + else: + fid.write('{} {}\n'.format(1, 1.)) + fid.write('{}\n'.format('# X pos Y pos')) + fid.write('%10.10f %10.10f\n' % (contour['x'], contour['y'])) + fid.write('\n') Index: /issm/trunk/src/m/exp/isoline.m =================================================================== --- /issm/trunk/src/m/exp/isoline.m (revision 27035) +++ /issm/trunk/src/m/exp/isoline.m (revision 27035) @@ -0,0 +1,262 @@ +function contours=isoline(md,field,varargin) +%ISOLINE - construct isovalue lines based on field provided +% +% Usage: +% contours=isoline(md,field,varargin) +% +% Supported options: +% 'value': isoline value, default is 0 +% 'output': 'struct' exp structure with individual contours (default) +% 'matrix' contours are concatenated and separated by NaNs +% 'filename.exp' saved as exp file +% +% Example: +% contours=isoline(md, md.results.TransientSolution(end).MaskOceanLevelset,'value',0); +% contours=isoline(md, md.results.TransientSolution(end).MaskOceanLevelset,'output','vector'); +% contours=isoline(md, md.results.TransientSolution(end).MaskIceLevelset,'output','Icefront.exp'); + +%Process options +options = pairoptions(varargin{:}); + +%process data +if dimension(md.mesh)==3, + % error('contourlevelzero error message: routine not supported for 3d meshes, project on a layer'); + x = md.mesh.x2d; + y = md.mesh.y2d; + index=md.mesh.elements2d; +else + x=md.mesh.x; + y=md.mesh.y; + index=md.mesh.elements; +end + +%Deal with z coordinate +if isprop(md.mesh,'z'), + z=md.mesh.z; +else + z=zeros(md.mesh.numberofvertices,1); +end + +if isempty(field), error('field provided is empty'); end +if dimension(md.mesh)==3, + if length(field)~=md.mesh.numberofvertices2d + error('field provided should be of size md.mesh.numberofvertices2d'); + end +else + if length(field)~=md.mesh.numberofvertices + error('field provided should be of size md.mesh.numberofvertices'); + end +end + +%What is the value we are trying to track +level = getfieldvalue(options,'value',0.); + +%initialization of some variables +numberofelements=size(index,1); +elementslist=1:numberofelements; +c=[]; +h=[]; + +%get unique edges in mesh +%1: list of edges +edges=[index(:,[1,2]); index(:,[2,3]); index(:,[3,1])]; +%2: find unique edges +[edges,I,J]=unique(sort(edges,2),'rows'); +%3: unique edge numbers +vec=J; +%4: unique edges numbers in each triangle (2 triangles sharing the same edge will have +% the same edge number) +edges_tria=[vec(elementslist), vec(elementslist+numberofelements), vec(elementslist+2*numberofelements)]; + +%segments [nodes1 nodes2] +Seg1=index(:,[1 2]); +Seg2=index(:,[2 3]); +Seg3=index(:,[3 1]); + +%segment numbers [1;4;6;...] +Seg1_num=edges_tria(:,1); +Seg2_num=edges_tria(:,2); +Seg3_num=edges_tria(:,3); + +%value of data on each tips of the segments +Data1=field(Seg1); +Data2=field(Seg2); +Data3=field(Seg3); + +%get the ranges for each segment +Range1=sort(Data1,2); +Range2=sort(Data2,2); +Range3=sort(Data3,2); + +%find the segments that contain this value +pos1=(Range1(:,1)=level); +pos2=(Range2(:,1)=level); +pos3=(Range3(:,1)=level); + +%get elements +poselem12=(pos1 & pos2); +poselem13=(pos1 & pos3); +poselem23=(pos2 & pos3); +poselem=find(poselem12 | poselem13 | poselem23); +numelems=length(poselem); + +%if no element has been flagged, skip to the next level +if numelems==0, + warning('isoline warning message: no elements found with corresponding value'); + contours=struct([]); + return; +end + +%go through the elements and build the coordinates for each segment (1 by element) +x1=zeros(numelems,1); +x2=zeros(numelems,1); +y1=zeros(numelems,1); +y2=zeros(numelems,1); +z1=zeros(numelems,1); +z2=zeros(numelems,1); + +edge_l=zeros(numelems,2); + +for j=1:numelems, + + weight1=(level-Data1(poselem(j),1))/(Data1(poselem(j),2)-Data1(poselem(j),1)); + weight2=(level-Data2(poselem(j),1))/(Data2(poselem(j),2)-Data2(poselem(j),1)); + weight3=(level-Data3(poselem(j),1))/(Data3(poselem(j),2)-Data3(poselem(j),1)); + + if poselem12(poselem(j)); + + x1(j)=x(Seg1(poselem(j),1))+weight1*(x(Seg1(poselem(j),2))-x(Seg1(poselem(j),1))); + x2(j)=x(Seg2(poselem(j),1))+weight2*(x(Seg2(poselem(j),2))-x(Seg2(poselem(j),1))); + y1(j)=y(Seg1(poselem(j),1))+weight1*(y(Seg1(poselem(j),2))-y(Seg1(poselem(j),1))); + y2(j)=y(Seg2(poselem(j),1))+weight2*(y(Seg2(poselem(j),2))-y(Seg2(poselem(j),1))); + z1(j)=z(Seg1(poselem(j),1))+weight1*(z(Seg1(poselem(j),2))-z(Seg1(poselem(j),1))); + z2(j)=z(Seg2(poselem(j),1))+weight2*(z(Seg2(poselem(j),2))-z(Seg2(poselem(j),1))); + + edge_l(j,1)=Seg1_num(poselem(j)); + edge_l(j,2)=Seg2_num(poselem(j)); + + elseif poselem13(poselem(j)), + + x1(j)=x(Seg1(poselem(j),1))+weight1*(x(Seg1(poselem(j),2))-x(Seg1(poselem(j),1))); + x2(j)=x(Seg3(poselem(j),1))+weight3*(x(Seg3(poselem(j),2))-x(Seg3(poselem(j),1))); + y1(j)=y(Seg1(poselem(j),1))+weight1*(y(Seg1(poselem(j),2))-y(Seg1(poselem(j),1))); + y2(j)=y(Seg3(poselem(j),1))+weight3*(y(Seg3(poselem(j),2))-y(Seg3(poselem(j),1))); + z1(j)=z(Seg1(poselem(j),1))+weight1*(z(Seg1(poselem(j),2))-z(Seg1(poselem(j),1))); + z2(j)=z(Seg3(poselem(j),1))+weight3*(z(Seg3(poselem(j),2))-z(Seg3(poselem(j),1))); + + edge_l(j,1)=Seg1_num(poselem(j)); + edge_l(j,2)=Seg3_num(poselem(j)); + + elseif poselem23(poselem(j)), + + x1(j)=x(Seg2(poselem(j),1))+weight2*(x(Seg2(poselem(j),2))-x(Seg2(poselem(j),1))); + x2(j)=x(Seg3(poselem(j),1))+weight3*(x(Seg3(poselem(j),2))-x(Seg3(poselem(j),1))); + y1(j)=y(Seg2(poselem(j),1))+weight2*(y(Seg2(poselem(j),2))-y(Seg2(poselem(j),1))); + y2(j)=y(Seg3(poselem(j),1))+weight3*(y(Seg3(poselem(j),2))-y(Seg3(poselem(j),1))); + z1(j)=z(Seg2(poselem(j),1))+weight2*(z(Seg2(poselem(j),2))-z(Seg2(poselem(j),1))); + z2(j)=z(Seg3(poselem(j),1))+weight3*(z(Seg3(poselem(j),2))-z(Seg3(poselem(j),1))); + + edge_l(j,1)=Seg2_num(poselem(j)); + edge_l(j,2)=Seg3_num(poselem(j)); + else + %it shoud not go here + end +end + +%now that we have the segments, we must try to connect them... + +%loop over the subcontours +contours=struct([]); + +while ~isempty(edge_l), + + %take the right edge of the second segment and connect it to the next segments if any + e1=edge_l(1,1); e2=edge_l(1,2); + xc=[x1(1);x2(1)]; yc=[y1(1);y2(1)]; zc=[z1(1);z2(1)]; + + + %erase the lines corresponding to this edge + edge_l(1,:)=[]; + x1(1)=[]; x2(1)=[]; + y1(1)=[]; y2(1)=[]; + z1(1)=[]; z2(1)=[]; + + [ro1,co1]=find(edge_l==e1); + + while ~isempty(ro1) + + if co1==1, + xc=[x2(ro1);xc]; yc=[y2(ro1);yc];zc=[z2(ro1);zc]; + + %next edge: + e1=edge_l(ro1,2); + + else + xc=[x1(ro1);xc]; yc=[y1(ro1);yc];zc=[z1(ro1);zc]; + + %next edge: + e1=edge_l(ro1,1); + end + + %erase the lines of this + edge_l(ro1,:)=[]; + x1(ro1)=[]; x2(ro1)=[]; + y1(ro1)=[]; y2(ro1)=[]; + z1(ro1)=[]; z2(ro1)=[]; + + %next connection + [ro1,co1]=find(edge_l==e1); + end + + %same thing the other way (to the right) + [ro2,co2]=find(edge_l==e2); + + while ~isempty(ro2) + + if co2==1, + xc=[xc;x2(ro2)]; yc=[yc;y2(ro2)];zc=[zc;z2(ro2)]; + + %next edge: + e2=edge_l(ro2,2); + else + xc=[xc;x1(ro2)]; yc=[yc;y1(ro2)]; zc=[zc;z1(ro2)]; + + %next edge: + e2=edge_l(ro2,1); + end + + %erase the lines of this + edge_l(ro2,:)=[]; + x1(ro2)=[]; x2(ro2)=[]; + y1(ro2)=[]; y2(ro2)=[]; + z1(ro2)=[]; z2(ro2)=[]; + + %next connection + [ro2,co2]=find(edge_l==e2); + end + + %save xc,yc contour: + contours(end+1).x=xc; + contours(end).y=yc; + contours(end).z=zc; + contours(end).name=''; + contours(end).nods=length(xc); + contours(end).density=1; + contours(end).closed=0; +end + +%process output +outputformat = getfieldvalue(options,'output','struct'); +if strcmp(outputformat,'matrix') + x = cell2mat(cellfun(@(x) [x;NaN],{contours(:).x},'UniformOutput',0)'); + y = cell2mat(cellfun(@(x) [x;NaN],{contours(:).y},'UniformOutput',0)'); + + contours = [x y]; +elseif strcmp(outputformat(end-3:end),'.exp') + disp(['Saving output as ' outputformat]); + expwrite(contours,outputformat); +elseif strcmp(outputformat,'struct') + %nothing to do, this is the default +else + disp('output format not supported, returning struct'); +end Index: /issm/trunk/src/m/exp/operation/exp_ginput.m =================================================================== --- /issm/trunk/src/m/exp/operation/exp_ginput.m (revision 27034) +++ /issm/trunk/src/m/exp/operation/exp_ginput.m (revision 27035) @@ -5,6 +5,5 @@ % [xi yi] = exp_ginput(numclicks,options); - -ginputtype = getfieldvalue(options,'ginputtype','default'); +%ginputtype = getfieldvalue(options,'ginputtype','default'); ginputtype = getfieldvalue(options,'ginputtype','myginput'); @@ -17,4 +16,2 @@ error('not supported yet'); end - - Index: /issm/trunk/src/m/geometry/VolumeAboveFloatation.m =================================================================== --- /issm/trunk/src/m/geometry/VolumeAboveFloatation.m (revision 27034) +++ /issm/trunk/src/m/geometry/VolumeAboveFloatation.m (revision 27035) @@ -1,7 +1,9 @@ -function V = VolumeAboveFloatation(md) +function V = VolumeAboveFloatation(md,step,flags) %VOLUMEABOVEFLOATATION - returns volume above floatation % % Usage: -% V = VolumeAboveFloatation(md) +% V = VolumeAboveFloatation(md) % uses model fiels alone +% V = VolumeAboveFloatation(md,10) % Will look at step 10 of transient solution +% V = VolumeAboveFloatation(md,10,flags) % Will look at step 10 of transient solution, only flaged elements %Special case if 3d @@ -17,4 +19,5 @@ error('not supported yet'); end + %1. get some parameters rho_ice = md.materials.rho_ice; @@ -22,7 +25,25 @@ %2. compute averages -base = mean(md.geometry.base(index),2); -surface = mean(md.geometry.surface(index),2); -bathymetry = mean(md.geometry.bed(index),2); +if nargin==1 + base = mean(md.geometry.base(index),2); + surface = mean(md.geometry.surface(index),2); + bathymetry = mean(md.geometry.bed(index),2); + ice_levelset = md.mask.ice_levelset; + ocean_levelset = md.mask.ocean_levelset; +else + if isprop(md.results.TransientSolution(step),'MaskIceLevelset') + ice_levelset = md.results.TransientSolution(step).MaskIceLevelset; + else + ice_levelset = md.mask.ice_levelset; + end + ocean_levelset = md.results.TransientSolution(step).MaskOceanLevelset; + base = mean(md.results.TransientSolution(step).Base(index),2); + surface = mean(md.results.TransientSolution(step).Surface(index),2); + if isprop(md.results.TransientSolution(step),'Bed') + bathymetry = mean(md.results.TransientSolution(step).Bed(index),2); + else + bathymetry = mean(md.geometry.bed(index),2); + end +end %3. get areas of all triangles @@ -33,6 +54,11 @@ %5. take out the ones that are outside of levelset or floating -pos = find(min(md.mask.ice_levelset(index),[],2)>0 | min(md.mask.ocean_levelset(index),[],2)<0); +pos = find(min(ice_levelset(index),[],2)>0 | min(ocean_levelset(index),[],2)<0); V(pos) = 0; + +%In case we are only looking at one portion of the domain... +if nargin==3 + V(find(~flags)) = 0; +end %sum individual contributions Index: /issm/trunk/src/m/inversions/marshallcostfunctions.py =================================================================== --- /issm/trunk/src/m/inversions/marshallcostfunctions.py (revision 27034) +++ /issm/trunk/src/m/inversions/marshallcostfunctions.py (revision 27035) @@ -14,5 +14,8 @@ 505: 'ThicknessAcrossGradient'} - data = [cfDict[cf] for cf in cost_functions] + if type(cost_functions) == int: + data = [cfDict[cost_functions]] + else: + data = [cfDict[cf] for cf in cost_functions] # #copy list first # data = copy.deepcopy(cost_functions) Index: /issm/trunk/src/m/io/loadmodel.py =================================================================== --- /issm/trunk/src/m/io/loadmodel.py (revision 27034) +++ /issm/trunk/src/m/io/loadmodel.py (revision 27035) @@ -9,5 +9,5 @@ -def loadmodel(path, onlylast=False): +def loadmodel(path, singletime=None, singleres=None): """LOADMODEL - load a model @@ -31,5 +31,5 @@ # try: #recover model on file and name it md - struc = loadvars(path, onlylast=onlylast) + struc = loadvars(path, singletime=singletime, singleres=singleres) name = [key for key in list(struc.keys())] if len(name) > 1: Index: /issm/trunk/src/m/io/loadvars.py =================================================================== --- /issm/trunk/src/m/io/loadvars.py (revision 27034) +++ /issm/trunk/src/m/io/loadvars.py (revision 27035) @@ -7,6 +7,8 @@ from re import findall, split import shelve -from netCDF4 import Dataset +from netCDF4 import Dataset, chartostring import numpy as np +import numpy.ma as ma +from importlib import import_module from model import * @@ -30,5 +32,5 @@ filename = '' nvdict = {} - debug = False #print messages if true + verbose = 0 # 0 for silent 5 for chatty if len(args) >= 1 and isinstance(args[0], str): @@ -52,9 +54,11 @@ raise TypeError("Unrecognized input arguments.") - onlylast = False + timeindex = False for key, value in kwargs.items(): - if key == 'onlylast': - onlylast = value + if key == 'singletime': + timeindex = value + if key == 'singleres': + resname = value if whichdb(filename): #We used python pickle for the save @@ -87,5 +91,5 @@ for mod in dict.keys(classtype): #==== First we create the model structure {{{ - if debug: + if verbose > 0: print(' ==== Now treating classtype {}'.format(mod)) if mod not in classtree.keys(): @@ -94,5 +98,5 @@ # this points to a subclass (results.TransientSolution for example) curclass = NCFile.groups[classtree[mod][0]].groups[classtree[mod][1]] - if debug: + if verbose > 0: print(" ==> {} is of class {}".format(mod, classtype[mod])) if classtype[mod][0] == 'results.solutionstep': #Treating results {{{ @@ -100,5 +104,6 @@ #that is the current treatment #here we have a more NC approach with time being a dimension - listtype = split(r'\.', classtype[mod][0])[0] + listtype = split(r'\.', classtype[mod][0])[1] + print(listtype) if len(NCFile.dimensions['Time']) == 1: nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = getattr(classtype[mod][1], listtype)() @@ -106,5 +111,5 @@ else: #Time dimension is in all the variables so we take that as stepnumber for the results - if onlylast: #we load only the last result to save on time and memory + if timeindex: #we load only the last result to save on time and memory nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = [getattr(classtype[mod][1], listtype)()] Tree = nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] @@ -126,10 +131,8 @@ Tree = nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] else: - if onlylast: #we load only the last result to save on time and memory + if timeindex: #we load only the last result to save on time and memory nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = [getattr(classtype[mod][1], listtype)()] Tree = nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] else: - #nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = [getattr(classtype[mod][1], listtype)() for i in range(max(1, len(NCFile.dimensions['Time'])))] - #Tree = nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]][:] setattr(nvdict['md'].__dict__[classtree[mod][0]], classtree[mod][1], getattr(classtype[mod][1], 'solution')([])) for i in range(max(1, stepnum)): @@ -137,16 +140,18 @@ Tree = nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]][:] #}}} - elif classtype[mod][0] == 'massfluxatgate': #this is for output definitions {{{ + #elif classtype[mod][0] == 'massfluxatgate.massfluxatgate': #this is for output definitions {{{ + elif mod.startswith('outputdefinition'): #this is for output definitions {{{ defname = split('Output|[0-9]+', classtree[mod][1])[1] + 's' defindex = int(findall('[0-9]+', classtree[mod][1])[0]) - nvdict['md'].__dict__[classtree[mod][0]].__dict__[defname].append(getattr(classtype[mod][1], classtype[mod][0])()) + outdeftype = split(r'\.', classtype[mod][0])[0] + nvdict['md'].__dict__[classtree[mod][0]].__dict__[defname].append(getattr(classtype[mod][1], outdeftype)()) Tree = nvdict['md'].__dict__[classtree[mod][0]].__dict__[defname][defindex - 1] #}}} else: - if debug: + if verbose > 0: print(" Using the default for md.{}.{}, is that right??".format(classtree[mod][0], classtree[mod][1])) try: modulename = split(r'\.', classtype[mod][0])[0] - if debug: + if verbose > 0: print(" trying to import {} from {}".format(classtype[mod][0], modulename)) nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = getattr(classtype[mod][1], modulename)() @@ -154,4 +159,9 @@ print("WARNING: md.{}.{} is not initialized, hopefully that was done in the main group:".format(classtree[mod][0], classtree[mod][1])) Tree = nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] + elif classtype[mod][0] == 'SMBgemb.SMBgemb': + curclass = NCFile.groups[classtree[mod][0]] + modulename = split(r'\.', classtype[mod][0])[0] + nvdict['md'].__dict__[mod] = getattr(classtype[mod][1], modulename)(nvdict['md'].__dict__['mesh'], nvdict['md'].__dict__['geometry']) + Tree = nvdict['md'].__dict__[classtree[mod][0]] else: curclass = NCFile.groups[classtree[mod][0]] @@ -159,5 +169,5 @@ nvdict['md'].__dict__[mod] = getattr(classtype[mod][1], modulename)() Tree = nvdict['md'].__dict__[classtree[mod][0]] - if debug: + if verbose > 0: print(" for {} Tree is a {} with len {}".format(mod, Tree.__class__.__name__, len(curclass.groups))) # }}} @@ -165,6 +175,9 @@ #for i in range(0, max(1, len(curclass.groups))): if len(curclass.groups) > 0: #that is presumably only for old style NC where each result step had its own group - if onlylast: - groupclass = [curclass.groups[keylist[len(curclass.groups) - 1]]] + if timeindex: + if timeindex < 0: + groupclass = [curclass.groups[keylist[len(curclass.groups) - timeindex]]] + else: + groupclass = [curclass.groups[keylist[timeindex]]] else: groupclass = [curclass.groups[key] for key in keylist] @@ -174,117 +187,147 @@ for groupindex, listclass in enumerate(groupclass): for var in listclass.variables: - if var not in ['errlog', 'outlog']: - varval = listclass.variables[str(var)] - vardim = varval.ndim - if debug: - print(" ==> treating var {} of dimension {}".format(var, vardim)) - #There is a special treatment for results to account for its specific structure - #that is the new export version where time is a named dimension - NewFormat = 'Time' in NCFile.dimensions - if type(Tree) == list: # and NewFormat: - if onlylast: - if NewFormat: - if vardim == 1: - Tree[0].__dict__[str(var)] = varval[-1].data - elif vardim == 2: - Tree[0].__dict__[str(var)] = varval[-1, :].data - elif vardim == 3: - Tree[0].__dict__[str(var)] = varval[-1, :, :].data + if not resname or var == resname: + if var not in ['errlog', 'outlog']: + varval = listclass.variables[str(var)] + vardim = varval.ndim + if verbose > 0: + print(" ==> treating var {} of dimension {}".format(var, vardim)) + #There is a special treatment for results to account for its specific structure + #that is the new export version where time is a named dimension + NewFormat = 'Time' in NCFile.dimensions + if type(Tree) == list: # and NewFormat: + if timeindex: + if NewFormat: + if vardim == 0: + try: + Tree[0].__dict__[str(var)] = varval[timeindex].data + except IndexError: + print('WARNING: No data on index {} for {} reverting to last time.'.format(timeindex, str(var))) + Tree[0].__dict__[str(var)] = varval[-1].data + elif vardim == 1: + try: + Tree[0].__dict__[str(var)] = varval[timeindex].data + except IndexError: + print('WARNING: No data on index {} for {} reverting to last time.'.format(timeindex, str(var))) + Tree[0].__dict__[str(var)] = varval[-1].data + elif vardim == 2: + Tree[0].__dict__[str(var)] = varval[timeindex, :].data + elif vardim == 3: + Tree[0].__dict__[str(var)] = varval[timeindex, :, :].data + else: + print('table dimension greater than 3 not implemented yet') + else: #old format had step sorted in difeerent group so last group is last time + Tree[0].__dict__[str(var)] = varval[:].data + else: + if NewFormat: + incomplete = 'Time' not in varval.dimensions + if incomplete: + try: + chosendim = varval.dimensions[0] + timelist = np.arange(0, len(NCFile.dimensions[chosendim])) + print('WARNING, {} is not present on every times, we chose {}({}) as the dimension to write it with'.format(var, chosendim, len(NCFile.dimensions[chosendim]))) + except IndexError: + #just one step, so no dimension, we just put it on the first solutionstep + timelist = [0] + else: + timelist = np.arange(0, len(NCFile.dimensions['Time'])) + for t in timelist: + if verbose > 5: + print("filing step {} for {}".format(t, var)) + if vardim == 0: + Tree[t].__dict__[str(var)] = varval[:].data + elif vardim == 1: + stepval = ma.masked_array(varval[t].data, mask=np.where(np.isnan(varval[t]), 1, 0)) + Tree[t].__dict__[str(var)] = ma.compressed(stepval) + elif vardim == 2: + stepval = ma.masked_array(varval[t, :].data, mask=np.where(np.isnan(varval[t, :]), 1, 0)) + Tree[t].__dict__[str(var)] = ma.compressed(stepval) + elif vardim == 3: + stepval = ma.masked_array(varval[t, :, :].data, mask=np.where(np.isnan(varval[t, :, :]), 1, 0)) + Tree[t].__dict__[str(var)] = ma.compressed(stepval).reshape((stepval.count(0)[0], stepval.count(1)[0])) + else: + print('table dimension greater than 3 not implemented yet') else: - print('table dimension greater than 3 not implemented yet') - else: #old format had step sorted in difeerent group so last group is last time - Tree[0].__dict__[str(var)] = varval[:].data + if verbose > 0: + print("filing step {} for {}".format(groupindex, var)) + Tree[groupindex].__dict__[str(var)] = varval[:].data else: - if NewFormat: - incomplete = 'Time' not in varval.dimensions and NewFormat - if incomplete: - chosendim = varval.dimensions[0] - timelist = np.arange(0, len(NCFile.dimensions[chosendim])) - print('WARNING, {} is not present on every times, we chose {}({}) as the dimension to write it with'.format(var, chosendim, len(NCFile.dimensions[chosendim]))) + if vardim == 0: #that is a scalar + if str(varval[0]) in ['', '--', 'emptycell']: #no value + Tree.__dict__[str(var)] = [] + elif varval[0] == 'True': #treatin bool + Tree.__dict__[str(var)] = True + elif varval[0] == 'False': #treatin bool + Tree.__dict__[str(var)] = False else: - timelist = np.arange(0, len(NCFile.dimensions['Time'])) - for t in timelist: - if debug: - print("filing step {} for {}".format(t, var)) - if vardim == 0: - Tree[t].__dict__[str(var)] = varval[:].data - elif vardim == 1: - Tree[t].__dict__[str(var)] = varval[t].data - elif vardim == 2: - Tree[t].__dict__[str(var)] = varval[t, :].data - elif vardim == 3: - Tree[t].__dict__[str(var)] = varval[t, :, :].data - else: - print('table dimension greater than 3 not implemented yet') + Tree.__dict__[str(var)] = varval[0].item() + + elif vardim == 1: #that is a vector + if verbose > 0: + print(" for variable {} type is {}".format(str(var), varval.dtype)) + if varval.dtype == str: + if varval.shape[0] == 1: + Tree.__dict__[str(var)] = [str(varval[0]), ] + elif 'True' in varval[:] or 'False' in varval[:]: + Tree.__dict__[str(var)] = np.asarray([V == 'True' for V in varval[:]], dtype=bool) + else: + Tree.__dict__[str(var)] = [str(vallue) for vallue in varval[:]] + elif varval.dtype == "|S1": #that is for matlab chararcter arrays + stringlist = chartostring(varval[:]) + Tree.__dict__[str(var)] = [stringlist.tolist(), ] + else: + try: + #some thing specifically require a list + mdtype = type(Tree.__dict__[str(var)]) + except KeyError: + mdtype = float + if mdtype == list: + Tree.__dict__[str(var)] = [mdval for mdval in varval[:]] + else: + Tree.__dict__[str(var)] = varval[:].data + + elif vardim == 2: + #dealling with dict + if verbose > 0: + print(" for variable {} type is {}".format(str(var), varval.dtype)) + if varval.dtype == str: #that is for dictionaries + if any(varval[:, 0] == 'toolkit'): #toolkit definition have to be first + Tree.__dict__[str(var)] = OrderedDict([('toolkit', str(varval[np.where(varval[:, 0] == 'toolkit')[0][0], 1]))]) + strings1 = [str(arg[0]) for arg in varval if arg[0] != 'toolkits'] + strings2 = [str(arg[1]) for arg in varval if arg[0] != 'toolkits'] + Tree.__dict__[str(var)].update(list(zip(strings1, strings2))) + else: + strings1 = [str(arg[0]) for arg in varval] + strings2 = [str(arg[1]) for arg in varval] + Tree.__dict__[str(var)] = OrderedDict(list(zip(strings1, strings2))) + elif varval.dtype == "|S1": #that is for matlab chararcter arrays + stringlist = chartostring(varval[:, :]) + stringlist = [string.strip() for string in stringlist] + Tree.__dict__[str(var)] = stringlist + else: + if type(Tree) == list: + t = indexlist[i] + if listtype == 'dict': + Tree[t][str(var)] = varval[:, :].data + else: + Tree[t].__dict__[str(var)] = varval[:, :].data + else: + Tree.__dict__[str(var)] = varval[:, :].data + elif vardim == 3: + Tree.__dict__[str(var)] = varval[:, :, :].data else: - if debug: - print("filing step {} for {}".format(groupindex, var)) - Tree[groupindex].__dict__[str(var)] = varval[:].data - else: - if vardim == 0: #that is a scalar - if str(varval[0]) == '': #no value - Tree.__dict__[str(var)] = [] - elif varval[0] == 'True': #treatin bool - Tree.__dict__[str(var)] = True - elif varval[0] == 'False': #treatin bool - Tree.__dict__[str(var)] = False - else: - Tree.__dict__[str(var)] = varval[0].item() - - elif vardim == 1: #that is a vector - if varval.dtype == str: - if varval.shape[0] == 1: - Tree.__dict__[str(var)] = [str(varval[0]), ] - elif 'True' in varval[:] or 'False' in varval[:]: - Tree.__dict__[str(var)] = np.asarray([V == 'True' for V in varval[:]], dtype=bool) - else: - Tree.__dict__[str(var)] = [str(vallue) for vallue in varval[:]] - else: - try: - #some thing specifically require a list - mdtype = type(Tree.__dict__[str(var)]) - except KeyError: - mdtype = float - if mdtype == list: - Tree.__dict__[str(var)] = [mdval for mdval in varval[:]] - else: - Tree.__dict__[str(var)] = varval[:].data - - elif vardim == 2: - #dealling with dict - if varval.dtype == str: #that is for dictionaries - if any(varval[:, 0] == 'toolkit'): #toolkit definition have to be first - Tree.__dict__[str(var)] = OrderedDict([('toolkit', str(varval[np.where(varval[:, 0] == 'toolkit')[0][0], 1]))]) - strings1 = [str(arg[0]) for arg in varval if arg[0] != 'toolkits'] - strings2 = [str(arg[1]) for arg in varval if arg[0] != 'toolkits'] - Tree.__dict__[str(var)].update(list(zip(strings1, strings2))) - else: - strings1 = [str(arg[0]) for arg in varval] - strings2 = [str(arg[1]) for arg in varval] - Tree.__dict__[str(var)] = OrderedDict(list(zip(strings1, strings2))) - else: - if type(Tree) == list: - t = indexlist[i] - if listtype == 'dict': - Tree[t][str(var)] = varval[:, :].data - else: - Tree[t].__dict__[str(var)] = varval[:, :].data - else: - Tree.__dict__[str(var)] = varval[:, :].data - elif vardim == 3: - Tree.__dict__[str(var)] = varval[:, :, :].data - else: - print('table dimension greater than 3 not implemented yet') + print('table dimension greater than 3 not implemented yet') # }}} #==== And with atribute {{{ for attr in listclass.ncattrs(): - if debug: + if verbose > 0: print(" ==> treating attribute {}".format(attr)) if attr != 'classtype': #classtype is for treatment, don't get it back - attribute = str(attr).swapcase() #there is a reason for swapcase, no sure what it isanymore - if attr == 'VARNAME': + if attr == 'varname': attribute = 'name' + else: + attribute = attr if type(Tree) == list: - if debug: + if verbose > 0: print(" printing with index 0") if listtype == 'dict': @@ -293,9 +336,12 @@ Tree[0].__dict__[attribute] = str(listclass.getncattr(attr)) else: - Tree.__dict__[attribute] = str(listclass.getncattr(attr)) if listclass.getncattr(attr) == 'True': Tree.__dict__[attribute] = True elif listclass.getncattr(attr) == 'False': Tree.__dict__[attribute] = False + elif listclass.getncattr(attr) == 'emptycell': + Tree.__dict__[attribute] = [] + else: + Tree.__dict__[attribute] = str(listclass.getncattr(attr)) # }}} # }}} @@ -328,10 +374,10 @@ try: modulename = split(r'\.', class_dict[classe][0])[0] - class_dict[classe].append(__import__(modulename)) + class_dict[classe].append(import_module(modulename)) except ModuleNotFoundError: #submodule probably has a different name modulename = str(getattr(NCData.groups[group].groups[subgroup], 'classtype')) print("WARNING importing {} rather than {}".format(modulename, class_dict[classe][0])) - class_dict[classe].append(__import__(modulename)) + class_dict[classe].append(import_module(modulename)) class_tree[classe] = [group, subgroup] else: @@ -344,5 +390,5 @@ print("WARNING: module {} does not exist anymore and is skipped".format(modulename)) else: - class_dict[classe].append(__import__(modulename)) + class_dict[classe].append(import_module(modulename)) class_tree[classe] = [group, ] except AttributeError: Index: /issm/trunk/src/m/mesh/ExportGmsh.py =================================================================== --- /issm/trunk/src/m/mesh/ExportGmsh.py (revision 27035) +++ /issm/trunk/src/m/mesh/ExportGmsh.py (revision 27035) @@ -0,0 +1,51 @@ +import numpy as np +""" +EXPORTGMSH - export mesh to gmsh format + + Usage: + ExportGmsh(md,filename) +""" + + +def ExportGmsh(md, filename): + + print('writing gmsh mesh file') + with open(filename, 'w+') as GmshFile: + + #initialization + GmshFile.write('$MeshFormat \n') + GmshFile.write('2.2 0 8 \n') + GmshFile.write('$EndMeshFormat \n') + GmshFile.write('$Nodes \n') + GmshFile.write('{} \n'.format(md.mesh.numberofvertices)) + + #printing point positions + for j, eX in enumerate(md.mesh.x): + GmshFile.write('{:g} {:14.7e} {:14.7e} 0.0 \n'.format(j + 1, eX, md.mesh.y[j])) + + GmshFile.write('$EndNodes \n') + GmshFile.write('$Elements \n') + GmshFile.write('{:d} \n'.format(md.mesh.numberofelements + np.shape(md.mesh.segments)[0])) + + #printing elements caracteristics for boundaries + for ind, segment in enumerate(md.mesh.segments): + if md.mesh.x[segment[0]] == np.nanmax(md.mesh.x) and md.mesh.x[segment[1]] == np.nanmax(md.mesh.x): + bc_id = 1 + elif md.mesh.y[segment[0]] == np.nanmax(md.mesh.y) and md.mesh.y[segment[1]] == np.nanmax(md.mesh.y): + bc_id = 2 + elif md.mesh.x[segment[0]] == np.nanmin(md.mesh.x) and md.mesh.x[segment[1]] == np.nanmin(md.mesh.x): + bc_id = 3 + elif md.mesh.y[segment[0]] == np.nanmin(md.mesh.y) and md.mesh.y[segment[1]] == np.nanmin(md.mesh.y): + bc_id = 4 + else: + bc_id = 0 + + GmshFile.write('{:g} 1 2 {:g} 1 {:g} {:g} \n'.format(ind + 1, bc_id, segment[0], segment[1])) + + #and for the body + body_id = 1 + for elt, element in enumerate(md.mesh.elements): + GmshFile.write('{:g} 2 2 {:g} 3 {:g} {:g} {:g} \n'.format(elt + 1, body_id, element[0], element[1], element[2])) + GmshFile.write('$EndElements \n') + #close + GmshFile.close() Index: /issm/trunk/src/m/mesh/meshconvert.m =================================================================== --- /issm/trunk/src/m/mesh/meshconvert.m (revision 27034) +++ /issm/trunk/src/m/mesh/meshconvert.m (revision 27035) @@ -40,2 +40,4 @@ md.mesh.numberofedges = size(md.mesh.edges,1); md.mesh.vertexonboundary = zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2)) = 1; +md.mesh.elementconnectivity=md.private.bamg.mesh.ElementConnectivity; +md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0; Index: /issm/trunk/src/m/mesh/roundmesh.m =================================================================== --- /issm/trunk/src/m/mesh/roundmesh.m (revision 27034) +++ /issm/trunk/src/m/mesh/roundmesh.m (revision 27035) @@ -1,3 +1,3 @@ -function md=roundmesh(md,radius,resolution) +function md=roundmesh(md,radius,resolution,varargin) %ROUNDMESH - create an unstructured round mesh % @@ -8,7 +8,12 @@ % Usage: % md=roundmesh(md,radius,resolution) +% md=roundmesh(md,radius,resolution,'domain.exp') %First we have to create the domain outline -expname = [tempname() '.exp']; +if nargin<4 + expname = [tempname() '.exp']; +else + expname = varargin{1}; +end %Get number of points on the circle @@ -32,5 +37,7 @@ %delete domain -delete(expname); +if nargin<4 + delete(expname); +end end Index: /issm/trunk/src/m/mesh/roundmesh.py =================================================================== --- /issm/trunk/src/m/mesh/roundmesh.py (revision 27034) +++ /issm/trunk/src/m/mesh/roundmesh.py (revision 27035) @@ -26,6 +26,6 @@ y_list = roundsigfig(radius * np.sin(theta), 12) A = OrderedDict() - A['x'] = [x_list] - A['y'] = [y_list] + A['x'] = x_list + A['y'] = y_list A['density'] = 1. expwrite(A, 'RoundDomainOutline.exp') Index: /issm/trunk/src/m/miscellaneous/MatlabFuncs.py =================================================================== --- /issm/trunk/src/m/miscellaneous/MatlabFuncs.py (revision 27034) +++ /issm/trunk/src/m/miscellaneous/MatlabFuncs.py (revision 27035) @@ -2,6 +2,6 @@ functions of the same, respective name. -Where possible, users are encouraged to use native and/or the most efficient -methods in Python, but we provide these functions as a way to make translations +Where possible, users are encouraged to use native and/or the most efficient +methods in Python, but we provide these functions as a way to make translations from the MATLAB to the Python ISSM API more seamless. """ @@ -82,5 +82,5 @@ def cosdsingle(x): # {{{ - """function cosdsingle - Helper function for cosd to reduce repetition of + """function cosdsingle - Helper function for cosd to reduce repetition of logic @@ -162,5 +162,5 @@ NOTE: - Only the following functionality is currently implemented: - - C = intersect(A,B) returns the data common to both A and B, with no + - C = intersect(A,B) returns the data common to both A and B, with no repetitions. C is in sorted order. @@ -175,5 +175,5 @@ NOTE: - - Takes a type as its second argument (in contrast to the MATLAB function + - Takes a type as its second argument (in contrast to the MATLAB function that it replicates, which takes a string representing the name of a type) """ @@ -204,5 +204,4 @@ def ismember(a, s): # {{{ import numpy as np - if not isinstance(s, (tuple, list, dict, np.ndarray)): s = [s] @@ -215,10 +214,9 @@ else: if not isinstance(s, np.ndarray): - b = np.empty_like(a) + b = np.empty_like(a).flat for i, item in enumerate(a.flat): - b.flat[i] = item in s + b[i] = item in s else: b = np.in1d(a.flat, s.flat).reshape(a.shape) - return b # }}} @@ -272,6 +270,7 @@ def oshostname(): # {{{ import socket - - return socket.gethostname() + hostname = socket.gethostname() + + return hostname.lower() # }}} @@ -298,5 +297,5 @@ def sindsingle(x): # {{{ - """function sindsingle - Helper function for sind to reduce repetition of + """function sindsingle - Helper function for sind to reduce repetition of logic Index: /issm/trunk/src/m/miscellaneous/diagnostics.m =================================================================== --- /issm/trunk/src/m/miscellaneous/diagnostics.m (revision 27034) +++ /issm/trunk/src/m/miscellaneous/diagnostics.m (revision 27035) @@ -35,5 +35,5 @@ %grounding line : if getfieldvalue(options,'gl',0), - contours=contourlevelzero(md,md.mask.ocean_levelset,0); + contours=isoline(md,md.mask.ocean_levelset); expwrite(contours,[path '/groundingline.exp']); exp2shp([path '/groundingline.shp'],[path '/groundingline.exp']); Index: /issm/trunk/src/m/miscellaneous/fielddisplay.py =================================================================== --- /issm/trunk/src/m/miscellaneous/fielddisplay.py (revision 27034) +++ /issm/trunk/src/m/miscellaneous/fielddisplay.py (revision 27035) @@ -110,5 +110,5 @@ -def displayunit(offset, name, characterization, comment): #{{{ +def displayunit(offset, name, characterization, comment): #{{{ #take care of name if len(name) > 23: @@ -116,5 +116,5 @@ #take care of characterization - if m.strcmp(characterization, "''") or m.strcmp(characterization, '""') or m.strcmpi(characterization, 'nan'): + if characterization in ["''", '""', 'nan', np.nan, 'NaN', "[0x1]"]: characterization = "N/A" Index: /issm/trunk/src/m/modules/CoordTransform.m =================================================================== --- /issm/trunk/src/m/modules/CoordTransform.m (revision 27034) +++ /issm/trunk/src/m/modules/CoordTransform.m (revision 27035) @@ -4,23 +4,23 @@ % Usage: % [xout,yout] = CoordTransform(xin,yin,projin,projout) -% -% xin, yin : input coordinates -% xout, yout: output coordinates (in new projection) -% projin,projout: input/output projection string (PROJ) +% - xin, yin : input coordinates +% - xout, yout: output coordinates (in new projection) +% - projin,projout: input/output projection string (PROJ) +% +% Examples: +% [md.mesh.lat md.mesh.long] = CoordTransform(md.mesh.x, md.mesh.y, 'EPSG:3413','EPSG:4326'); +% [md.mesh.x md.mesh.y] = CoordTransform(md.mesh.lat,md.mesh.long,'EPSG:4326','EPSG:3413'); % % Example of Projections: +% lat/lon = 'EPSG:4326' or lat/lon = '+proj=longlat +datum=WGS84' +% Greenland = 'EPSG:3413' (polar stereographic 70N 45W) +% Antarctica = 'EPSG:3031' (polar stereographic 71S 0E) +% +% ll2xy previous default equivalent (uses with Hugues Ellispoid S) +% Greenland = '+proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs' +% Antarctica = '+proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs' +% Bamber Greenland = '+proj=stere +lat_0=90 +lat_ts=71 +lon_0=-39 +k=1 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' % -% lat/lon = '+init=epsg:4326' -% lat/lon = '+proj=longlat +datum=WGS84' -% -% ll2xy default equivalent (uses with Hugues Ellispoid S) -% Greenland = '+proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs' -% Antarctica = '+proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.448564109 +units=m +no_defs' -% Bamber Greenland = '+proj=stere +lat_0=90 +lat_ts=71 +lon_0=-39 +k=1 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' -% -% For latitude/longitude, x is longitude and y latitude and the angles are in -% rad -% -% This function will only work if PROJ has been installed and --with-proj-dir +% This function will only work if PROJ has been installed and --with-proj-dir % option has been set to its location in ISSM configuration Index: /issm/trunk/src/m/os/issmscpin.py =================================================================== --- /issm/trunk/src/m/os/issmscpin.py (revision 27034) +++ /issm/trunk/src/m/os/issmscpin.py (revision 27035) @@ -22,5 +22,5 @@ pass #if hostname and host are the same, do a simple copy - if hostname == host: + if strcmpi(hostname, host): #hostname == host: for package in packages: try: Index: /issm/trunk/src/m/os/issmscpout.py =================================================================== --- /issm/trunk/src/m/os/issmscpout.py (revision 27034) +++ /issm/trunk/src/m/os/issmscpout.py (revision 27035) @@ -1,4 +1,3 @@ import os -from socket import gethostname import subprocess from MatlabFuncs import * @@ -17,5 +16,5 @@ #if hostname and host are the same, do a simple copy - if host == hostname: + if strcmpi(host, hostname): #host == hostname: for package in packages: here = os.getcwd() Index: /issm/trunk/src/m/os/issmssh.py =================================================================== --- /issm/trunk/src/m/os/issmssh.py (revision 27034) +++ /issm/trunk/src/m/os/issmssh.py (revision 27035) @@ -37,5 +37,5 @@ subprocess.call('ssh -l %s -p %d localhost "%s"' % (login, port, command), shell=True) else: - subprocess.call('ssh -l %s %s "%s"' % (login, host, command), shell=True) + subprocess.call('ssh -l {} {} "{}"'.format(login, host, command), shell=True) # The following code was added to fix: Index: /issm/trunk/src/m/parameterization/killberg.m =================================================================== --- /issm/trunk/src/m/parameterization/killberg.m (revision 27034) +++ /issm/trunk/src/m/parameterization/killberg.m (revision 27035) @@ -25,9 +25,10 @@ %do not go through elements that are grounded, mark flag as 1 (done) need at least 2 vertices! %and initialize mask as 1 for all vertices of these elements -isgrounded=(sum(md.mask.ocean_levelset(md.mesh.elements)>0,2)>1); +isgrounded=(sum(md.mask.ocean_levelset(md.mesh.elements)>0,2)>2); %isgrounded = max(md.mask.ocean_levelset(md.mesh.elements),[],2)>0; pos = find(isgrounded); -element_flag(pos) = 1; +%element_flag(pos) = 1; mask(md.mesh.elements(pos,:)) = 1; +mask(md.mask.ice_levelset>=0) = 0; iter = 1; Index: /issm/trunk/src/m/parameterization/reinitializelevelset.m =================================================================== --- /issm/trunk/src/m/parameterization/reinitializelevelset.m (revision 27034) +++ /issm/trunk/src/m/parameterization/reinitializelevelset.m (revision 27035) @@ -15,5 +15,5 @@ %First: extract segments -contours=contourlevelzero(md,levelset,0); +contours=isoline(md,levelset,'value',0); %Now, make this a distance field (might not be closed) Index: /issm/trunk/src/m/parameterization/setflowequation.js =================================================================== --- /issm/trunk/src/m/parameterization/setflowequation.js (revision 27034) +++ /issm/trunk/src/m/parameterization/setflowequation.js (revision 27035) @@ -3,5 +3,5 @@ // // This routine works like plotmodel: it works with an even number of inputs -// 'SIA','SSA','L1L2','MLHO','HO','FS' and 'fill' are the possible options +// 'SIA','SSA','L1L2','MOLHO','HO','FS' and 'fill' are the possible options // that must be followed by the corresponding exp file or flags list // It can either be a domain file (argus type, .exp extension), or an array of element flags. @@ -11,5 +11,5 @@ // a string 'all' will be considered as the entire domain // You can specify the type of coupling, 'penalties' or 'tiling', to use with the input 'coupling' -// NB: L1L2 and MLHO cannot currently be coupled to any other ice flow model +// NB: L1L2 and MOLHO cannot currently be coupled to any other ice flow model // // Usage: @@ -38,5 +38,5 @@ HOflag = FlagElements(md,options.getfieldvalue('HO','')); L1L2flag = FlagElements(md,options.getfieldvalue('L1L2','')); - MLHOflag = FlagElements(md,options.getfieldvalue('MLHO','')); + MOLHOflag = FlagElements(md,options.getfieldvalue('MOLHO','')); FSflag = FlagElements(md,options.getfieldvalue('FS','')); filltype = options.getfieldvalue('fill','none'); @@ -55,9 +55,9 @@ //check that each element has at least one flag - for(var i=0;i1), +if any(SIAflag+SSAflag+HOflag+L1L2flag+MOLHOflag+FSflag>1), disp('setflowequation.m: Warning: some elements have several types, higher order type is used for them') SIAflag(find(SIAflag & SSAflag))=0; @@ -70,6 +70,6 @@ error('L1L2 cannot be coupled to any other model'); end -if any(MLHOflag) & any(SIAflag | SSAflag | HOflag | FSflag) - error('MLHO cannot be coupled to any other model'); +if any(MOLHOflag) & any(SIAflag | SSAflag | HOflag | FSflag) + error('MOLHO cannot be coupled to any other model'); end @@ -91,5 +91,5 @@ nodeonHO=zeros(md.mesh.numberofvertices,1); nodeonHO(md.mesh.elements(find(HOflag),:))=1; nodeonL1L2=zeros(md.mesh.numberofvertices,1); nodeonL1L2(md.mesh.elements(find(L1L2flag),:))=1; -nodeonMLHO=zeros(md.mesh.numberofvertices,1); nodeonMLHO(md.mesh.elements(find(MLHOflag),:))=1; +nodeonMOLHO=zeros(md.mesh.numberofvertices,1); nodeonMOLHO(md.mesh.elements(find(MOLHOflag),:))=1; nodeonFS=zeros(md.mesh.numberofvertices,1); noneflag=zeros(md.mesh.numberofelements,1); @@ -248,5 +248,5 @@ md.flowequation.element_equation(find(SSAflag))=2; md.flowequation.element_equation(find(L1L2flag))=3; -md.flowequation.element_equation(find(MLHOflag))=4; +md.flowequation.element_equation(find(MOLHOflag))=4; md.flowequation.element_equation(find(HOflag))=5; md.flowequation.element_equation(find(FSflag))=6; @@ -264,5 +264,5 @@ pos=find(nodeonSSA); md.flowequation.vertex_equation(pos)=2; pos=find(nodeonL1L2); md.flowequation.vertex_equation(pos)=3; -pos=find(nodeonMLHO); md.flowequation.vertex_equation(pos)=4; +pos=find(nodeonMOLHO); md.flowequation.vertex_equation(pos)=4; pos=find(nodeonHO); md.flowequation.vertex_equation(pos)=5; pos=find(nodeonFS); md.flowequation.vertex_equation(pos)=6; @@ -287,5 +287,5 @@ md.flowequation.isSSA = double(any(md.flowequation.element_equation == 2)); md.flowequation.isL1L2 = double(any(md.flowequation.element_equation == 3)); -md.flowequation.isMLHO = double(any(md.flowequation.element_equation == 4)); +md.flowequation.isMOLHO = double(any(md.flowequation.element_equation == 4)); md.flowequation.isHO = double(any(md.flowequation.element_equation == 5)); md.flowequation.isFS = double(any(md.flowequation.element_equation == 6)); Index: /issm/trunk/src/m/parameterization/setflowequation.py =================================================================== --- /issm/trunk/src/m/parameterization/setflowequation.py (revision 27034) +++ /issm/trunk/src/m/parameterization/setflowequation.py (revision 27035) @@ -9,5 +9,5 @@ This routine works like plotmodel: it works with an even number of inputs - 'SIA', 'SSA', 'HO', 'L1L2', 'MLHO', 'FS' and 'fill' are the possible + 'SIA', 'SSA', 'HO', 'L1L2', 'MOLHO', 'FS' and 'fill' are the possible options that must be followed by the corresponding exp file or flags list. It can either be a domain file (argus type, .exp extension), or an array of @@ -45,5 +45,5 @@ HOflag = FlagElements(md, options.getfieldvalue('HO', '')) L1L2flag = FlagElements(md, options.getfieldvalue('L1L2', '')) - MLHOflag = FlagElements(md, options.getfieldvalue('MLHO', '')) + MOLHOflag = FlagElements(md, options.getfieldvalue('MOLHO', '')) FSflag = FlagElements(md, options.getfieldvalue('FS', '')) filltype = options.getfieldvalue('fill', 'none') @@ -57,9 +57,9 @@ HOflag = ~SIAflag & ~SSAflag & ~FSflag #check that each element has at least one flag - if not any(SIAflag + SSAflag + L1L2flag + MLHOflag + HOflag + FSflag): + if not any(SIAflag + SSAflag + L1L2flag + MOLHOflag + HOflag + FSflag): raise TypeError("elements type not assigned, supported models are 'SIA', 'SSA', 'HO' and 'FS'") #check that each element has only one flag - if any(SIAflag + SSAflag + L1L2flag + MLHOflag + HOflag + FSflag > 1): + if any(SIAflag + SSAflag + L1L2flag + MOLHOflag + HOflag + FSflag > 1): print('Warning: setflowequation.py: some elements have several types, higher order type is used for them') SIAflag[np.where(np.logical_and(SIAflag, SSAflag))] = False @@ -67,9 +67,9 @@ SSAflag[np.where(np.logical_and(SSAflag, HOflag))] = False - #check that L1L2 and MLHO is not coupled to any other model for now + #check that L1L2 and MOLHO is not coupled to any other model for now if any(L1L2flag) and any(SIAflag + SSAflag + HOflag + FSflag): raise TypeError('L1L2 cannot be coupled to any other model') - if any(MLHOflag) and any(SIAflag + SSAflag + HOflag + FSflag): - raise TypeError('MLHO cannot be coupled to any other model') + if any(MOLHOflag) and any(SIAflag + SSAflag + HOflag + FSflag): + raise TypeError('MOLHO cannot be coupled to any other model') #Check that no HO or FS for 2d mesh @@ -89,6 +89,6 @@ nodeonL1L2 = np.zeros(md.mesh.numberofvertices, bool) nodeonL1L2[md.mesh.elements[np.where(L1L2flag), :] - 1] = True - nodeonMLHO = np.zeros(md.mesh.numberofvertices, bool) - nodeonMLHO[md.mesh.elements[np.where(MLHOflag), :] - 1] = True + nodeonMOLHO = np.zeros(md.mesh.numberofvertices, bool) + nodeonMOLHO[md.mesh.elements[np.where(MOLHOflag), :] - 1] = True nodeonHO = np.zeros(md.mesh.numberofvertices, bool) nodeonHO[md.mesh.elements[np.where(HOflag), :] - 1] = True @@ -241,5 +241,5 @@ md.flowequation.element_equation[np.where(SSAflag)] = 2 md.flowequation.element_equation[np.where(L1L2flag)] = 3 - md.flowequation.element_equation[np.where(MLHOflag)] = 4 + md.flowequation.element_equation[np.where(MOLHOflag)] = 4 md.flowequation.element_equation[np.where(HOflag)] = 5 md.flowequation.element_equation[np.where(FSflag)] = 6 @@ -259,5 +259,5 @@ pos = np.where(nodeonL1L2) md.flowequation.vertex_equation[pos] = 3 - pos = np.where(nodeonMLHO) + pos = np.where(nodeonMOLHO) md.flowequation.vertex_equation[pos] = 4 pos = np.where(nodeonHO) @@ -283,5 +283,5 @@ md.flowequation.isSSA = any(md.flowequation.element_equation == 2) md.flowequation.isL1L2= any(md.flowequation.element_equation == 3) - md.flowequation.isMLHO= any(md.flowequation.element_equation == 4) + md.flowequation.isMOLHO= any(md.flowequation.element_equation == 4) md.flowequation.isHO = any(md.flowequation.element_equation == 5) md.flowequation.isFS = any(md.flowequation.element_equation == 6) Index: /issm/trunk/src/m/plot/applyoptions.py =================================================================== --- /issm/trunk/src/m/plot/applyoptions.py (revision 27034) +++ /issm/trunk/src/m/plot/applyoptions.py (revision 27035) @@ -53,6 +53,6 @@ #title font titlefont = font.copy() - titlefont['size'] = titlefontsize - titlefont['weight'] = titlefontweight + titlefont['fontsize'] = titlefontsize + titlefont['fontweight'] = titlefontweight ax.set_title(title, **titlefont) # }}} Index: /issm/trunk/src/m/plot/plot_elementstype.m =================================================================== --- /issm/trunk/src/m/plot/plot_elementstype.m (revision 27034) +++ /issm/trunk/src/m/plot/plot_elementstype.m (revision 27035) @@ -37,5 +37,5 @@ end end -legend(p,'None','SIA','SSA','L1L2','MLHO','HO',... +legend(p,'None','SIA','SSA','L1L2','MOLHO','HO',... 'SSAHO','FS','SSAFS','HOFS'); Index: /issm/trunk/src/m/plot/plot_manager.m =================================================================== --- /issm/trunk/src/m/plot/plot_manager.m (revision 27034) +++ /issm/trunk/src/m/plot/plot_manager.m (revision 27035) @@ -129,9 +129,13 @@ case 'transient_results', plot_transient_results(md,options,subplotwidth,i); + return case 'transient_field', plot_transient_field(md,options,subplotwidth,i); return; otherwise, - if ismember(data,properties('model')), + if isfield(md.results,'TransientSolution') && isfield(md.results.TransientSolution,data) + plot_transient_movie(md,options,subplotwidth,i); + return + elseif ismember(data,properties('model')), data=eval(['md.' data ';']); else Index: /issm/trunk/src/m/plot/plot_transient_movie.m =================================================================== --- /issm/trunk/src/m/plot/plot_transient_movie.m (revision 27034) +++ /issm/trunk/src/m/plot/plot_transient_movie.m (revision 27035) @@ -12,4 +12,6 @@ if exist(options,'transient_movie_field'), field=getfieldvalue(options,'transient_movie_field'); + elseif ischar(getfieldvalue(options,'data')) + field=getfieldvalue(options,'data'); else disp('List of available fields:'); @@ -37,7 +39,31 @@ steps=[limit(1):limit(end)]; elseif exist(options,'transient_movie_steps'), + warning('option ''transient_movie_steps'' is now ''steps'', please update your script'); steps = getfieldvalue(options,'transient_movie_steps'); + elseif exist(options,'steps'), + steps = getfieldvalue(options,'steps'); else steps=1:length(results); + end + + %Do we have an output? + isavi = 0; + isgif = 0; + ismp4 = 0; + if exist(options,'transient_movie_output'), + filename=getfieldvalue(options,'transient_movie_output'); + [pathstr,name,ext] = fileparts(filename); + if strcmp(ext,'.gif') + isgif = 1; + elseif strcmp(ext,'.mp4') + ismp4 = 1; + elseif strcmp(ext,'.avi') + isavi = 1; + end + end + if isavi || ismp4 + vid=VideoWriter([filename(1:end-4),'.avi'],'Motion JPEG AVI'); + vid.FrameRate = 2; + open(vid); end @@ -53,4 +79,8 @@ end + + %Process mesh once for all + [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options); + %display movie nstep=1; @@ -60,14 +90,51 @@ if ~isempty(results(i).(field)), %process data - [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options); [data datatype]=processdata(md,results(i).(field),options); clf; - titlestring=[field ' at time ' num2str(results(i).time,'%7.2f') ' year']; + titlestring=[field ' (time ' num2str(results(i).time,'%7.2f') ' yr)']; plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) - apply_options_movie(md,options,titlestring); + apply_options_movie(md,data,options,titlestring); - if exist(options,'transient_movie_output'), - set(gcf,'Renderer','zbuffer','color','white'); %fixes a bug on Mac OS X (not needed in future Matlab version) + %Add grounding line + if exist(options,'groundingline') + if dimension(md.mesh)==2 + contours=isoline(md, results(i).MaskOceanLevelset,'output','matrix'); + else + ocean = project2d(md, results(i).MaskOceanLevelset, 1); + contours=isoline(md, ocean,'output','matrix'); + end + hold on + plot(contours(:,1),contours(:,2),getfieldvalue(options,'groundingline')); + end + + %Add ice front + if exist(options,'icefront') + if dimension(md.mesh)==2 + contours=isoline(md, results(i).MaskIceLevelset,'output','matrix'); + else + ice = project2d(md, results(i).MaskIceLevelset, 1); + contours=isoline(md, ice,'output','matrix'); + end + hold on + plot(contours(:,1),contours(:,2),getfieldvalue(options,'icefront')); + end + + if isgif + frame=getframe(gcf); + im = frame2im(frame); + [imind,cmap] = rgb2ind(im,256); + if i==1 + imwrite(imind, cmap, filename, 'DelayTime',getfieldvalue(options,'transient_movie_time',.5), 'LoopCount',inf) + else + imwrite(imind, cmap, filename, 'WriteMode','append'); + end + elseif isavi || ismp4 + F=getframe(gcf); + writeVideo(vid, F); + end + + if exist(options,'transient_movie_output') + %set(gcf,'Renderer','zbuffer','color','white'); %fixes a bug on Mac OS X (not needed in future Matlab version) if nstep==1, %initialize images and frame @@ -87,15 +154,26 @@ %output movie if requested. - if exist(options,'transient_movie_output'), - filename=getfieldvalue(options,'transient_movie_output'); - imwrite(images,map,filename,'DelayTime',getfieldvalue(options,'transient_movie_time',2),'LoopCount',inf) + if isavi || ismp4 + close(vid); + end + if ismp4 + filename = filename(1:end-4); + while(~exist([filename '.avi'])) + disp(['Waiting for ' filename '.avi']); + pause(1) + end + command=sprintf('ffmpeg -y -i %s.avi -c:v libx264 -crf 19 -preset slow -c:a libfaac -b:a 192k -ac 2 -vf "pad=ceil(iw/2)*2:ceil(ih/2)*2" %s.mp4',filename,filename); + system(command); + end + if isgif + imwrite(images,map,filename,'DelayTime',getfieldvalue(options,'transient_movie_time',.5),'LoopCount',inf) end end %function -function apply_options_movie(md,options,titlestring) +function apply_options_movie(md,data,options,titlestring) %apply options options=changefieldvalue(options,'title',titlestring); options=addfielddefault(options,'colorbar',1); - applyoptions(md,[],options); + applyoptions(md,data,options); end Index: /issm/trunk/src/m/plot/plot_vertexnumbering.m =================================================================== --- /issm/trunk/src/m/plot/plot_vertexnumbering.m (revision 27034) +++ /issm/trunk/src/m/plot/plot_vertexnumbering.m (revision 27035) @@ -20,6 +20,13 @@ %numbering - text(x,y,z,num2str(vertexnumbers),... - 'backgroundcolor',[0.8 0.9 0.8],'HorizontalAlignment','center','VerticalAlignment','middle'); + X = x; + Y = y; + NUM = vertexnumbers; + if exist(options,'axis') + AXIS = getfieldvalue(options,'axis'); + pos = find(X>AXIS(1) & XAXIS(3) & YAXIS(1) & XAXIS(3) & 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Index: /issm/trunk/test/MITgcm/code_4003/shelfice_step_icemass.F =================================================================== --- /issm/trunk/test/MITgcm/code_4003/shelfice_step_icemass.F (revision 27034) +++ /issm/trunk/test/MITgcm/code_4003/shelfice_step_icemass.F (revision 27035) @@ -45,8 +45,4 @@ C i,j, bi,bj :: loop indices INTEGER bi,bj,i,j -#ifdef ALLOW_CPL_ISSM - _RL issm_density - issm_density = 917. -#endif /* ALLOW_CPL_ISSM */ IF ( SHELFICEMassStepping ) THEN @@ -77,6 +73,5 @@ DO j=1-OLy,sNy+OLy-1 DO i=1-OLx+1,sNx+OLx-1 - shelficeMass(i,j,bi,bj) = - & R_shelfIce(i,j,bi,bj) * issm_density + shelficeMass(i,j,bi,bj) = -R_shelfIce(i,j,bi,bj) * rhoConst ENDDO ENDDO Index: /issm/trunk/test/MITgcm/coupling_rules.txt =================================================================== --- /issm/trunk/test/MITgcm/coupling_rules.txt (revision 27034) +++ /issm/trunk/test/MITgcm/coupling_rules.txt (revision 27035) @@ -10,8 +10,8 @@ xC Nx*Ny Real*8 10001005 yC Nx*Ny Real*8 10001006 -IceBase Nx*Ny Real*8 10001007 - (in m, 0 is sea level, negative is below sea level, 9999 is no ice, - use density 917 kg/m^3) -OceanMelt Nx*Ny Real*8 10001008 +OceanMelt Nx*Ny Real*8 10001007 + melt_mesh[i]=-melt_mesh[i]/rho_ice; //heat flux provided by ocean is in kg/m^2/s +IceBase Nx*Ny Real*8 10001008 + in m, 0 is sea level, negative is below sea level, 9999 is no ice >>>> INITIALIZATION FROM SCRATCH Index: /issm/trunk/test/MITgcm/input_4003/data.shelfice =================================================================== --- /issm/trunk/test/MITgcm/input_4003/data.shelfice (revision 27034) +++ /issm/trunk/test/MITgcm/input_4003/data.shelfice (revision 27035) @@ -17,6 +17,4 @@ #-- SHELFICEtopoFile='shelficeTopo.Lin.bin', - SHELFICEmassFile='shelficeMass.Lin.bin', - SHELFICEMassDynTendFile='shelfice_dMdt.r02.bin', -#SHELFICEwriteState = .TRUE., + SHELFICEwriteState = .TRUE., & Index: sm/trunk/test/MITgcm/input_4003/data_uncoupled =================================================================== --- /issm/trunk/test/MITgcm/input_4003/data_uncoupled (revision 27034) +++ (revision ) @@ -1,109 +1,0 @@ -# ==================== -# | Model parameters | -# ==================== -# -# Continuous equation parameters - &PARM01 - tRef = 90*-1.9, - sRef = 90*34.4, - eosType='JMD95Z', - HeatCapacity_Cp = 3974.0, - rhoConst=1030., - gravity=9.81, - viscAr=1.E-3, - viscAh= 300., - no_slip_sides=.FALSE., - no_slip_bottom=.FALSE., - diffKhT= 10., - diffKrT=5.E-5, - diffKhS= 10., - diffKrS=5.E-5, - bottomDragQuadratic=2.5E-3, - staggerTimestep = .TRUE., - tempAdvScheme=77, - saltAdvScheme=77, - vectorInvariantMomentum = .TRUE., -# momImplVertAdv=.TRUE., -#tempImplVertAdv=.TRUE., -#saltImplVertAdv=.TRUE., - implicitDiffusion = .TRUE., - implicitViscosity = .TRUE., - selectImplicitDrag = 2, - implicitFreeSurface=.TRUE., - useRealFreshWaterFlux = .TRUE., - exactConserv=.TRUE., -# start NLFS (without rstar) - nonlinFreeSurf=4, - hFacInf=0.05, - hFacSup=2.0, -# end NLFS - hFacMin=0.10, -#integr_GeoPot = 1, - ivdc_kappa = 1., - useJamartWetPoints=.TRUE., - selectBotDragQuadr=1, -#bottomVisc_pCell=.TRUE., -#- - readBinaryPrec=64, - writeBinaryPrec=64, - useSingleCpuIO=.TRUE., -#globalFiles=.TRUE., - debuglevel = 2, - plotLevel = 0, - & - -# Elliptic solver parameters - &PARM02 - cg2dMaxIters=300, - cg2dTargetResidual=1.E-11, -#printResidualFreq=100, - & - -#Time stepping parameters - &PARM03 -#nIter0=2880, -#nTimeSteps=288, -#startTime=0., -#endTime=2592000., - deltaT=300.0, - forcing_In_AB = .FALSE., - abEps=0.1, - pChkptFreq= 2592000., - chkptFreq = 2592000., - dumpFreq = 86400., - monitorFreq= 7200., - monitorSelect=1, - monitorFreq=1800., - dumpFreq = 10800., -#- for testing purpose: - nIter0=2898, - nTimeSteps=20, -#dumpFreq = 1200., - monitorFreq=1., - & - -# Gridding parameters - &PARM04 - usingCartesianGrid=.FALSE., - usingSphericalPolarGrid=.TRUE., - delR=90*10., - delX=1*.125, - delY=200*.0078125, - xgOrigin = 0., - ygOrigin = -75.5, - pCellMix_select=20, - pcellMix_delR = 10., -#interViscAr_pCell = .TRUE., -#interDiffKr_pCell = .TRUE., - pCellMix_viscAr = 90*1.E-3, - pCellMix_diffKr = 90*1.E-4, -# current default: diffKzT=5.E-5, viscAz=1.E-3, - & - -# Input datasets - &PARM05 - bathyFile='bathy_flat.bin', - hydrogThetaFile='temp_ini.bin', - hydrogSaltFile ='salt_ini.bin', -# pSurfInitFile ='etai_ini.bin' - & Index: /issm/trunk/test/MITgcm/input_4004/data =================================================================== --- /issm/trunk/test/MITgcm/input_4004/data (revision 27035) +++ /issm/trunk/test/MITgcm/input_4004/data (revision 27035) @@ -0,0 +1,100 @@ +# ==================== +# | Model parameters | +# ==================== +# +# Continuous equation parameters + &PARM01 + tRef = 90*-1.9, + sRef = 90*34.4, + eosType='JMD95Z', + HeatCapacity_Cp = 3974.0, + rhoConst=1030., + gravity=9.81, + viscAr=1.E-3, + viscAh= 300., + no_slip_sides=.FALSE., + no_slip_bottom=.FALSE., + diffKhT= 10., + diffKrT=5.E-5, + diffKhS= 10., + diffKrS=5.E-5, + bottomDragQuadratic=2.5E-3, + staggerTimestep = .TRUE., + tempAdvScheme=77, + saltAdvScheme=77, + vectorInvariantMomentum = .TRUE., +# momImplVertAdv=.TRUE., +#tempImplVertAdv=.TRUE., +#saltImplVertAdv=.TRUE., + implicitDiffusion = .TRUE., + implicitViscosity = .TRUE., + selectImplicitDrag = 2, + implicitFreeSurface=.TRUE., + useRealFreshWaterFlux = .TRUE., + exactConserv=.TRUE., +# start NLFS (without rstar) + nonlinFreeSurf=4, + hFacInf=0.05, + hFacSup=2.0, +# end NLFS + hFacMin=0.10, +#integr_GeoPot = 1, + ivdc_kappa = 1., + useJamartWetPoints=.TRUE., + selectBotDragQuadr=1, +#bottomVisc_pCell=.TRUE., +#- + readBinaryPrec=64, +#writeBinaryPrec=64, + useSingleCpuIO=.TRUE., +#globalFiles=.TRUE., + debuglevel = 5, + plotLevel = 0, + & + +# Elliptic solver parameters + &PARM02 + cg2dMaxIters=300, + cg2dTargetResidual=1.E-11, +#printResidualFreq=100, + & + +#Time stepping parameters + &PARM03 + startTime=0., + nTimeSteps=192, +#endTime=2592000., + deltaT=450.0, + forcing_In_AB = .FALSE., + abEps=0.1, + pChkptFreq= 2592000., + chkptFreq = 2592000., + dumpFreq = 450., + monitorFreq=1., + & + +# Gridding parameters + &PARM04 + usingCartesianGrid=.FALSE., + usingSphericalPolarGrid=.TRUE., + delR=90*10., + delX=3*.125, + delY=200*.0078125, + xgOrigin = 0., + ygOrigin = -75.5, + pCellMix_select=20, + pcellMix_delR = 10., +#interViscAr_pCell = .TRUE., +#interDiffKr_pCell = .TRUE., + pCellMix_viscAr = 90*1.E-3, + pCellMix_diffKr = 90*1.E-4, +# current default: diffKzT=5.E-5, viscAz=1.E-3, + & + +# Input datasets + &PARM05 + bathyFile='bathy_flat.bin', + hydrogThetaFile='temp_ini.bin', + hydrogSaltFile ='salt_ini.bin', +# pSurfInitFile ='etai_ini.bin' + & Index: /issm/trunk/test/MITgcm/input_4004/data.diagnostics =================================================================== --- /issm/trunk/test/MITgcm/input_4004/data.diagnostics (revision 27035) +++ /issm/trunk/test/MITgcm/input_4004/data.diagnostics (revision 27035) @@ -0,0 +1,69 @@ +# Diagnostic Package Choices +#----------------- +# for each output-stream: +# filename(n) : prefix of the output file name (only 8.c long) for outp.stream n +# frequency(n):< 0 : write snap-shot output every |frequency| seconds +# > 0 : write time-average output every frequency seconds +# timePhase(n) : write at time = timePhase + multiple of |frequency| +# averagingFreq(n) : frequency (in s) for periodic averaging interval +# averagingPhase(n): phase (in s) for periodic averaging interval +# repeatCycle(n) : number of averaging intervals in 1 cycle +# levels(:,n) : list of levels to write to file (Notes: declared as REAL) +# when this entry is missing, select all common levels of this list +# fields(:,n) : list of diagnostics fields (8.c) (see "available_diagnostics.log" +# file for the list of all available diag. in this particular config) +#----------------- + &DIAGNOSTICS_LIST +# diag_mnc = .FALSE., + dumpAtLast = .TRUE., + fields(1:13,1) = 'ETAN ','RSURF ','oceTAUX ','oceTAUY ', + 'oceQnet ','oceFWflx','MXLDEPTH', + 'SHIfwFlx','SHIhtFlx','SHIgammT','SHIgammS', + 'SHI_mass','SHIuStar', +# 'surForcT','surForcS','TFLUX ','SFLUX ','oceFreez', +# 'TRELAX ','SRELAX ', +# fields(1,1)='ETAN' + filename(1) = 'surfDiag', + frequency(1) = 450., +#- + fields(1:10,2) = 'UVEL ','VVEL ','WVEL ', + 'THETA ','SALT ','RHOAnoma', 'CONVADJ' + 'hFactorC','hFactorW','hFactorS', + filename(2) = 'dynDiag', + fileFlags(2) = ' h ', + frequency(2) = 450., +#- + fields(1:7,3) = 'ETAN ','RSURF ', + 'oceQnet ','oceFWflx', + 'SHIfwFlx','SHIhtFlx','SHIuStar', +# filename(3) = 'surfInst', + frequency(3) = -450., + timePhase(3) = 0., +#- + fields(1:8,4) = 'UVEL ','VVEL ','WVEL ', + 'THETA ','SALT ', + 'hFactorC','hFactorW','hFactorS', +# filename(4) = 'dynInst', + frequency(4) = -450., + timePhase(4) = 0., + & + +#-------------------- +# Parameter for Diagnostics of per level statistics: +#-------------------- +# diagSt_mnc (logical): write stat-diags to NetCDF files (default=diag_mnc) +# diagSt_regMaskFile : file containing the region-mask to read-in +# nSetRegMskFile : number of region-mask sets within the region-mask file +# set_regMask(i) : region-mask set-index that identifies the region "i" +# val_regMask(i) : region "i" identifier value in the region mask +#--for each output-stream: +# stat_fName(n) : prefix of the output file name (max 80c long) for outp.stream n +# stat_freq(n):< 0 : write snap-shot output every |stat_freq| seconds +# > 0 : write time-average output every stat_freq seconds +# stat_phase(n) : write at time = stat_phase + multiple of |stat_freq| +# stat_region(:,n) : list of "regions" (default: 1 region only=global) +# stat_fields(:,n) : list of selected diagnostics fields (8.c) in outp.stream n +# (see "available_diagnostics.log" file for the full list of diags) +#-------------------- + &DIAG_STATIS_PARMS + & Index: /issm/trunk/test/MITgcm/input_4004/data.obcs =================================================================== --- /issm/trunk/test/MITgcm/input_4004/data.obcs (revision 27035) +++ /issm/trunk/test/MITgcm/input_4004/data.obcs (revision 27035) @@ -0,0 +1,32 @@ +# Open-boundaries + &OBCS_PARM01 + OB_Jnorth=3*200, + useOBCSprescribe=.TRUE., +#OBWuFile='uVel_obc.bin', + OBNvFile='vVel_obc.bin', + OBNtFile='temp_obc.bin', + OBNsFile='salt_obc.bin', + OBCS_u1_adv_T=1, + OBCS_u1_adv_S=1, +#-- + useOBCSsponge=.TRUE., + useLinearSponge = .TRUE., +#- default is =T for these specific switches: +#OBCSsponge_VatNS=.TRUE., + OBCSsponge_UatNS=.FALSE., +#-- + OBCSprintDiags = .FALSE., + & + +# Orlanski parameters (skipped with #undef ALLOW_ORLANSKI) +#&OBCS_PARM02 +#Cmax=0.45, +#cVelTimeScale=1000., +#& + +# Sponge layer parameters + &OBCS_PARM03 + spongeThickness = 10, + Vrelaxobcsbound = 864000., + Urelaxobcsbound = 864000., + & Index: /issm/trunk/test/MITgcm/input_4004/data.pkg =================================================================== --- /issm/trunk/test/MITgcm/input_4004/data.pkg (revision 27035) +++ /issm/trunk/test/MITgcm/input_4004/data.pkg (revision 27035) @@ -0,0 +1,6 @@ +# Packages (lines beginning "#" are comments) + &PACKAGES + useOBCS=.TRUE., + useShelfIce=.TRUE., + useDiagnostics = .TRUE., + & Index: /issm/trunk/test/MITgcm/input_4004/data.shelfice =================================================================== --- /issm/trunk/test/MITgcm/input_4004/data.shelfice (revision 27035) +++ /issm/trunk/test/MITgcm/input_4004/data.shelfice (revision 27035) @@ -0,0 +1,20 @@ +# =================================== +# | Parameters for SHELFICE package | +# =================================== + &SHELFICE_PARM01 + SHELFICEconserve = .TRUE., + SHELFICEuseGammaFrict = .TRUE., + SHELFICEDragQuadratic = 0.0015, + shiCdrag = 0.0015, + SHELFICEselectDragQuadr= 2, + SHELFICEMassStepping = .TRUE., +#-- + SHELFICEremeshFrequency = 450.0, +#- need to satisfy: splitThrs > 1 + mergeThrs / Sdz +# with: Sdz = min{ delR(k+1)/delR(k) }_[k=1:Nr-1] + SHELFICEsplitThreshold = 1.12, + SHELFICEmergeThreshold = 0.10, +#-- + SHELFICEtopoFile='shelficeTopo.Lin.bin', + SHELFICEwriteState = .TRUE., + & Index: /issm/trunk/test/MITgcm/input_4004/eedata =================================================================== --- /issm/trunk/test/MITgcm/input_4004/eedata (revision 27035) +++ /issm/trunk/test/MITgcm/input_4004/eedata (revision 27035) @@ -0,0 +1,11 @@ +# Example "eedata" file +# Lines beginning "#" are comments +# nTx :: No. threads per process in X +# nTy :: No. threads per process in Y +# debugMode :: print debug msg (sequence of S/R calls) + &EEPARMS + useCoupler=.TRUE., + debugMode=.TRUE., + & +# Note: Some systems use & as the namelist terminator (as shown here). +# Other systems use a / character. Index: /issm/trunk/test/MITgcm/input_4004/eedata_uncoupled =================================================================== --- /issm/trunk/test/MITgcm/input_4004/eedata_uncoupled (revision 27035) +++ /issm/trunk/test/MITgcm/input_4004/eedata_uncoupled (revision 27035) @@ -0,0 +1,10 @@ +# Example "eedata" file +# Lines beginning "#" are comments +# nTx :: No. threads per process in X +# nTy :: No. threads per process in Y +# debugMode :: print debug msg (sequence of S/R calls) + &EEPARMS + useCoupler=.FALSE., + & +# Note: Some systems use & as the namelist terminator (as shown here). +# Other systems use a / character. Index: /issm/trunk/test/MITgcm/install.sh =================================================================== --- /issm/trunk/test/MITgcm/install.sh (revision 27034) +++ /issm/trunk/test/MITgcm/install.sh (revision 27035) @@ -7,9 +7,9 @@ ################################################################################ -# Download source -git clone --depth=1 https://github.com/MITgcm/MITgcm.git +# # Download source +# git clone --depth=1 https://github.com/MITgcm/MITgcm.git -# Move source to 'install' directory -mv MITgcm install +# # Move source to 'install' directory +# mv MITgcm install ################################################################################ @@ -18,10 +18,14 @@ # -# # Download source -# wget https://github.com/MITgcm/MITgcm/archive/refs/tags/checkpoint67x.tar.gz +# Constants +# +VER="68h" -# # Uncompress source -# tar -xvzf checkpoint67x.tar.gz +# Download source +wget https://github.com/MITgcm/MITgcm/archive/refs/tags/checkpoint${VER}.tar.gz -# # Move source to 'install' directory -# mv MITgcm-checkpoint67x install +# Uncompress source +tar -xvzf checkpoint${VER}.tar.gz + +# Move source to 'install' directory +mv MITgcm-checkpoint${VER} install Index: /issm/trunk/test/MITgcm/tools/lookat_4003.m =================================================================== --- /issm/trunk/test/MITgcm/tools/lookat_4003.m (revision 27035) +++ /issm/trunk/test/MITgcm/tools/lookat_4003.m (revision 27035) @@ -0,0 +1,124 @@ +pn='~/mitgcm/slr/components/issm/trunk-jpl/test/NightlyRun/'; +p1=[pn 'RunUncoupled/']; +p2=[pn 'run/']; + +for ts=30:34 + v1=readbin([p2 'R_shelfIce1_' myint2str(ts,10) '.data'],[3 200]); + v2=readbin([p2 'R_shelfIce2_' myint2str(ts,10) '.data'],[3 200]); + u=readbin([p2 'U.' myint2str(ts,10) '.data'],[3 200 90]); + v=readbin([p2 'V.' myint2str(ts,10) '.data'],[3 200 90]); + w=readbin([p2 'W.' myint2str(ts,10) '.data'],[3 200 90]); + clf, subplot(511), plot(v1(2,:)), title(ts) + subplot(512), plot(v2(2,:)-v1(2,:)), title('draft change') + subplot(513), mypcolor(1:200,-1:-1:-90,squeeze(u(2,:,:))'); title('U'), colorbar + subplot(514), mypcolor(1:200,-1:-1:-90,squeeze(v(2,:,:))'); title('V'), colorbar + subplot(515), mypcolor(1:200,-1:-1:-90,squeeze(w(2,:,:))'); title('W'), colorbar + pause +end + + + clf + subplot(311), mypcolor(v1), title(ts) + subplot(312), mypcolor(v2), title(ts) + subplot(313), mypcolor(v2-v1) + +for ts=1:10 + v1=readbin([p2 'SHICE_fwFlux.' myint2str(ts,10) '.data'],[3 200]); + clf + subplot(311), mypcolor(v1), title(ts), colorbar +pause +end + + + v2=readbin([p2 'SHICE_fwFlux.' myint2str(ts,10) '.data'],[3 200]); + + +clf +for ts=5, disp(ts) + T=readbin([p2 'T.' myint2str(ts,10) '.data'],[3 200 90]); + S=readbin([p2 'S.' myint2str(ts,10) '.data'],[3 200 90]); + U=readbin([p2 'U.' myint2str(ts,10) '.data'],[3 200 90]); + V=readbin([p2 'V.' myint2str(ts,10) '.data'],[3 200 90]); + W=readbin([p2 'W.' myint2str(ts,10) '.data'],[3 200 90]); + for k=1:90, disp(k) + clf + subplot(321), plot(S(2,:,k)), title('S') + subplot(322), plot(T(2,:,k)), title('T') + subplot(323), plot(U(2,:,k)), title('U') + subplot(324), plot(V(2,:,k)), title('V') + subplot(325), plot(W(2,:,k)), title('W') + pause + end +end + + +clf +for ts=1:8, disp(ts) + T=readbin([p2 'T.' myint2str(ts,10) '.data'],[3 200 90]); + S=readbin([p2 'S.' myint2str(ts,10) '.data'],[3 200 90]); + U=readbin([p2 'U.' myint2str(ts,10) '.data'],[3 200 90]); + V=readbin([p2 'V.' myint2str(ts,10) '.data'],[3 200 90]); + W=readbin([p2 'W.' myint2str(ts,10) '.data'],[3 200 90]); + clf + subplot(321), mypcolor(squeeze(S(2,:,:))'), title('S'), colorbar + subplot(322), mypcolor(squeeze(T(2,:,:))'), title('T'), colorbar + subplot(323), mypcolor(squeeze(U(2,:,:))'), title('U'), colorbar + subplot(324), mypcolor(squeeze(V(2,:,:))'), title('V'), colorbar + subplot(325), mypcolor(squeeze(W(2,:,:))'), title('W'), colorbar + pause +end + + + + + + +ts=8; +v1=readbin([p2 'R_shelfIce1_' myint2str(ts,10) '.data'],[3 200]); +v2=readbin([p2 'R_shelfIce2_' myint2str(ts,10) '.data'],[3 200]); +clf +subplot(311), mypcolor(v1); title('R_shelfIce1'), colorbar +subplot(312), mypcolor(v2); title('R_shelfIce2'), colorbar +subplot(313), mypcolor(v2-v1); title('diff'), colorbar + +figure(2) +clf +plot(1:200,v1(2,:),'o-',1:200,v2(2,:),'o-',1:200,v2(2,:)-v1(2,:),'o-') + +ts=0; +fld='R_shelfIce1_'; +v1=readbin([p2 fld myint2str(ts,10) '.data'],[3 200]); +fld='R_shelfIce2_'; +for ts=0:8:184 + v2=readbin([p2 fld myint2str(ts,10) '.data'],[3 200]); + clf + subplot(311), mypcolor(v1); title(ts-8), colorbar + subplot(312), mypcolor(v2); title(ts), colorbar + subplot(313), mypcolor(v2-v1); title('diff'), colorbar + pause + v1=v2; +end + +fld='surfDiag'; +ts=2; +v1=rdmds([p1 fld],ts); +v2=rdmds([p2 fld],ts); +clf +fld={'ETAN','RSURF','oceTAUX','oceTAUY','oceQnet','oceFWflx', ... + 'MXLDEPTH','SHIfwFlx','SHIhtFlx','SHIgammT','SHIgammS', ... + 'SHI_mass','SHIuStar'}; +for i=1:length(fld) + subplot(311), mypcolor(v1(:,:,i)); title(fld{i}), colorbar + subplot(312), mypcolor(v2(:,:,i)); title('coupled'), colorbar + subplot(313), mypcolor(v2(:,:,i)-v1(:,:,i)); title('coupled-uncoupled'), colorbar + pause +end + +fld='Eta'; +ts=1; +v1=rdmds([p1 fld],ts); +v2=rdmds([p2 fld],ts); +clf +subplot(311), mypcolor(v1); title(fld), colorbar +subplot(312), mypcolor(v2); title('coupled'), colorbar +subplot(313), mypcolor(v2-v1); title('coupled-uncoupled'), colorbar Index: /issm/trunk/test/MITgcm/tools/lookat_4004.m =================================================================== --- /issm/trunk/test/MITgcm/tools/lookat_4004.m (revision 27035) +++ /issm/trunk/test/MITgcm/tools/lookat_4004.m (revision 27035) @@ -0,0 +1,44 @@ +clear, close all +pn='~/mitgcm/slr/components/issm/trunk-jpl/test/NightlyRun/run/'; +figure(1), clf, orient tall, wysiwyg +for ts=0:4 + r1=readbin([pn 'R_shelfIce1_' myint2str(ts+1,10) '.data'],[3 200]); + r2=readbin([pn 'R_shelfIce2_' myint2str(ts,10) '.data'],[3 200]); + subplot(5,1,ts+1), mypcolor(r2-r1); colorbar +end + +for ts=1:5 + figure(ts+1), clf, orient tall, wysiwyg + e=readbin([pn 'Eta.' myint2str(ts,10) '.data'],[3 200]); + p=readbin([pn 'PHL.' myint2str(ts,10) '.data'],[3 200]); + f=readbin([pn 'SHICE_fwFlux.' myint2str(ts,10) '.data'],[3 200]); + h=readbin([pn 'SHICE_heatFlux.' myint2str(ts,10) '.data'],[3 200]); + ph=readbin([pn 'PH.' myint2str(ts,10) '.data'],[3 200 90]); + clf, subplot(511), mypcolor(e); title(['Eta @ ts=' int2str(ts)]), colorbar + subplot(512), mypcolor(p); title('PHL'), colorbar + subplot(513), mypcolor(f); title('SHICE fwFlux'), colorbar + subplot(514), mypcolor(h); title('SHICE heatFlux'), colorbar + subplot(515), mypcolor(1:200,-1:-1:-90,squeeze(ph(2,:,:))'); title('PH'), colorbar +end + +for ts=0:5 + figure(ts+7), clf, orient tall, wysiwyg + r2=readbin([pn 'R_shelfIce2_' myint2str(ts,10) '.data'],[3 200]); + if ts<5 + r1=readbin([pn 'R_shelfIce1_' myint2str(ts+1,10) '.data'],[3 200]); + end + s =readbin([pn 'S.' myint2str(ts,10) '.data'],[3 200 90]); + t =readbin([pn 'T.' myint2str(ts,10) '.data'],[3 200 90]); + u =readbin([pn 'U.' myint2str(ts,10) '.data'],[3 200 90]); + v =readbin([pn 'V.' myint2str(ts,10) '.data'],[3 200 90]); + w =readbin([pn 'W.' myint2str(ts,10) '.data'],[3 200 90]); + in=find(~s); s(in)=nan; t(in)=nan; + clf, + subplot(711), mypcolor(r2); title(['draft @ ts=' int2str(ts)]), colorbar + subplot(712), mypcolor(r2-r1); title('draft change'), colorbar + subplot(713), pcolorcen(1:200,-1:-1:-90,squeeze(s(2,:,:))'); title('S'), colorbar + subplot(714), pcolorcen(1:200,-1:-1:-90,squeeze(t(2,:,:))'); title('T'), colorbar + subplot(715), pcolorcen(1:200,-1:-1:-90,squeeze(u(2,:,:))'); title('U'), colorbar + subplot(716), pcolorcen(1:200,-1:-1:-90,squeeze(v(2,:,:))'); title('V'), colorbar + subplot(717), pcolorcen(1:200,-1:-1:-90,squeeze(w(2,:,:))'); title('W'), colorbar +end Index: /issm/trunk/test/NightlyRun/runme.m =================================================================== --- /issm/trunk/test/NightlyRun/runme.m (revision 27034) +++ /issm/trunk/test/NightlyRun/runme.m (revision 27035) @@ -2,5 +2,5 @@ %RUNME - test deck for ISSM nightly runs % -% In a test deck directory (for example, test/NightlyRun) the following +% In a test deck directory (for example, test/NightlyRun) the following % command will launch all existing tests, % @@ -29,4 +29,5 @@ % 'update': update the archive % 'valgrind': check for memory leaks (default value of md.debug.valgrind needs to be changed manually) +% 'ncExport': export netCDF file % 'stoponerror' 1 or 0 % @@ -69,5 +70,5 @@ %GET procedure {{{ procedure=getfieldvalue(options,'procedure','check'); -if ~ismember(procedure,{'check','update','valgrind'}) +if ~ismember(procedure,{'check','update','valgrind','ncExport'}) disp('runme warning: procedure not supported, defaulting to test ''check''') procedure='check'; @@ -217,4 +218,8 @@ end + %PRODUCE nc files? + elseif strcmpi(procedure,'ncExport'), + export_netCDF(md, ['test' num2str(id) 'ma.nc']) + %ELSE: CHECK TEST else, Index: /issm/trunk/test/NightlyRun/runme.py =================================================================== --- /issm/trunk/test/NightlyRun/runme.py (revision 27034) +++ /issm/trunk/test/NightlyRun/runme.py (revision 27035) @@ -10,5 +10,5 @@ from glob import glob import os -import re +from re import search, split from sys import float_info from traceback import format_exc @@ -18,5 +18,5 @@ try: from arch import archread -except: # ISSM_DIR is not on path +except: # ISSM_DIR is not on path import devpath @@ -26,4 +26,7 @@ from IdToName import IdToName from parallelrange import parallelrange +from loadmodel import loadmodel +from solve import solve +from importlib import import_module @@ -31,5 +34,5 @@ """RUNME - test deck for ISSM nightly runs - In a test deck directory (for example, test/NightlyRun) the following + In a test deck directory (for example, test/NightlyRun) the following command will launch all existing tests, @@ -41,8 +44,8 @@ Options: - -i/--id Followed by the list of ids or (parts of) test names + -i/--id Followed by the list of ids or (parts of) test names requested - -e/--exclude Ids or (parts of) test names to be excluded (same - format as id). Does nothing if 'id' is specified with + -e/--exclude Ids or (parts of) test names to be excluded (same + format as id). Does nothing if 'id' is specified with different values. -b/--benchmark 'all' : (all of the tests) @@ -60,4 +63,6 @@ -p/--procedure 'check' : run the test (default) 'update' : update the archive + 'runFromNC' : run from an existing nc file + Usage: @@ -80,8 +85,8 @@ TODO: - - At '#disp test result', make sure precision of output matches that of + - At '#disp test result', make sure precision of output matches that of MATLAB. - - Check for failures that do not raise exceptions (for example, 'Standard - exception'; see also jenkins/jenkins.sh). These should be counted as + - Check for failures that do not raise exceptions (for example, 'Standard + exception'; see also jenkins/jenkins.sh). These should be counted as failures. """ @@ -97,5 +102,5 @@ # }}} #GET procedure {{{ - if procedure not in ['check', 'update']: + if procedure not in ['check', 'update', 'runFromNC']: print(("runme warning: procedure '{}' not supported, defaulting to test 'check'.".format(procedure))) procedure = 'check' @@ -112,5 +117,5 @@ #GET ids {{{ flist = glob('test*.py') #File name must start with 'test' and must end by '.py' and must be different than 'test.py' - list_ids = [int(re.search(r'\d+',file.split('.')[0]).group()) for file in flist if not file == 'test.py'] # Keep test id only (skip 'test' and '.py') + list_ids = [int(search(r'\d+',file.split('.')[0]).group()) for file in flist if not file == 'test.py'] # Keep test id only (skip 'test' and '.py') i1, i2 = parallelrange(rank, numprocs, len(list_ids)) #Get tests for this cpu only @@ -128,4 +133,18 @@ test_ids = test_ids.difference(exclude_ids) # }}} + if procedure == 'runFromNC': + #That is a bamg test + test_ids = test_ids.difference([119, 514]) + # that is smbGEMB format is weird for the test + test_ids = test_ids.difference([243, 244, 252, 253]) + #those are amr runs where the index is missing from fieldnames + test_ids = test_ids.difference([462, 463, 464, 465]) + #test247 solves for thermal and transient which makes it complex to check + test_ids = test_ids.difference([247]) + #test 902 is running two models with different stepping + test_ids = test_ids.difference([902]) + #I have a size issue in 517 needs investigation + test_ids = test_ids.difference([517]) + #Process Ids according to benchmarks {{{ if benchmark == 'nightly': @@ -165,5 +184,9 @@ os.chdir(root) id_string = IdToName(id) - exec(compile(open('test{}.py'.format(id)).read(), 'test{}.py'.format(id), 'exec'), globals()) + print(("----------------running-----------------------")) + if procedure == 'runFromNC': + Tmod = import_module('test{}'.format(id)) + else: + exec(compile(open('test{}.py'.format(id)).read(), 'test{}.py'.format(id), 'exec'), globals()) #UPDATE ARCHIVE? @@ -185,5 +208,133 @@ archwrite(archive_file, archive_name + '_field' + str(k + 1), field) print(("File {} saved. \n".format(os.path.join('..', 'Archives', archive_name + '.arch')))) - + elif procedure == 'runFromNC': + print(("----------------loadingNC-----------------------")) + mdl = loadmodel('test{}ma.nc'.format(id)) + for key in mdl.results.__dict__.keys(): + if 'Solution' in key: + solvetype = split('Solution', key)[0] + + #we save the results, scrap them and solve. + loaded_res = mdl.results + mdl.results = [] + mdl = solve(mdl, solvetype) + + #we loop on the field_names from the nghtly test + for k, fieldname in enumerate(Tmod.field_names): + try: + #first look for indexing + if search(r'\d+$', fieldname): + index = int(search(r'\d+$', fieldname).group()) - 1 + fieldname = fieldname[:search(r'\d+$', fieldname).start()] + elif 'FirstStep' in fieldname: + index = 0 + fieldname = fieldname[:search('FirstStep', fieldname).start()] + elif 'SecondStep' in fieldname: + index = 1 + fieldname = fieldname[:search('SecondStep', fieldname).start()] + elif 'ThirdStep' in fieldname: + index = 2 + fieldname = fieldname[:search('ThirdStep', fieldname).start()] + else: + index = 0 + + #Then check if the key exists in the loaded results + try: + reskeys = mdl.results.__dict__[solvetype + 'Solution'][index].__dict__.keys() + except TypeError: + # most probably a steady state so no subscripting + reskeys = mdl.results.__dict__[solvetype + 'Solution'].__dict__.keys() + if fieldname not in reskeys: + sufixes = ["P1bubble", "P1bubbleCondensed", "LliboutryDuval", "CuffeyTemperate", "SSA", "HO", "FS", "P1xP", "P2xP", + 'MINI', 'MINIcondensed', 'TaylorHood', 'XTaylorHood', 'LATaylorHood', 'CrouzeixRaviart', 'LACrouzeixRaviart'] + namedifs = {'Misfits': 'J', + 'D': 'DamageDbar', + 'F': 'DamageF', + 'MaterialsRheologyB': 'MaterialsRheologyBbar', + 'SedimentWaterHead': 'SedimentHead', + 'EplWaterHead': 'EplHead', + 'SedimentWaterHeadSubstep': 'SedimentHeadSubstep', + 'EplWaterHeadSubstep': 'EplHeadSubstep', + 'Volume': 'IceVolume', + 'Bed': 'Base', + 'SMB': 'SmbMassBalance'} + + if fieldname in namedifs.keys(): + #Some fields are not consistent + fieldname = namedifs[fieldname] + elif any([suf in fieldname for suf in sufixes]): + #some test have loops that mess up with naming + try: + sufix = sufixes[np.squeeze(np.where([suf in fieldname for suf in sufixes]))] + except TypeError: + #probably severalmatches, we take the last one which should be the good one (Needs to be controled in the list above) + sufix = sufixes[np.squeeze(np.where([suf in fieldname for suf in sufixes]))[-1]] + fieldname = fieldname[:search(sufix, fieldname).start()] + elif fieldname.endswith("P") and index == 1: + #we are looking for P2 but 2 as been considered as an index and so shifted by -1 + fieldname = fieldname[:-1] + else: + # could be that the index selected above is part of the name + fieldname = fieldname + str(index + 1) + try: + field = mdl.results.__dict__[solvetype + 'Solution'][index].__dict__[fieldname] + loaded_field = loaded_res.__dict__[solvetype + 'Solution'][index].__dict__[fieldname] + except TypeError: + # most probably a steady state so no subscripting + try: + field = mdl.results.__dict__[solvetype + 'Solution'].__dict__[fieldname] + loaded_field = loaded_res.__dict__[solvetype + 'Solution'].__dict__[fieldname] + except KeyError: + print("WARNING: {}{} does not exist and checking will be skipped".format(fieldname, index + 1)) + continue + except KeyError: + print("WARNING: {}{} does not exist and checking will be skipped".format(fieldname, index + 1)) + continue + + ref = Tmod.field_values[k] + #Get tolerance + tolerance = Tmod.field_tolerances[k] + #compute differences for the results computed from the nc file + error_diff = np.amax(np.abs(ref - field), axis=0) / (np.amax(np.abs(ref), axis=0) + float_info.epsilon) + if not np.isscalar(error_diff): + error_diff = error_diff[0] + + #compute the differences for the results of the nc file + load_diff = np.amax(np.abs(np.squeeze(ref) - loaded_field), axis=0) / (np.amax(np.abs(np.squeeze(ref)), axis=0) + float_info.epsilon) + if not np.isscalar(load_diff): + load_diff = load_diff[0] + + #disp test result + if (np.any(error_diff > tolerance) or np.isnan(error_diff)) and (np.any(load_diff > tolerance) or np.isnan(load_diff)): + if abs(error_diff - load_diff) < tolerance: + print(('WARNING difference: {:7.2g} > {:7.2g} test id: {} field: {}{} differs from computation but equal to saved results'.format(error_diff, tolerance, id, fieldname, index + 1))) + else: + print(('ERROR difference: {:7.2g} > {:7.2g} test id: {} field: {}{} is false in both loaded and computed results'.format(error_diff, tolerance, id, fieldname, index + 1))) + errorcount += 1 + erroredtest_list.append(id) + elif (np.any(error_diff > tolerance) or np.isnan(error_diff)): + print(('ERROR difference: {:7.2g} > {:7.2g} test id: {} test name: {} field: {}{}'.format(error_diff, tolerance, id, id_string, fieldname, index + 1))) + errorcount += 1 + erroredtest_list.append(id) + elif (np.any(load_diff > tolerance) or np.isnan(load_diff)): + print(('SAVEERROR difference: {:7.2g} > {:7.2g} test id: {} test name: {} saved result : {}{}'.format(load_diff, tolerance, id, id_string, fieldname, index + 1))) + errorcount += 1 + erroredtest_list.append(id) + else: + print(('SUCCESS difference: {:7.2g} < {:7.2g} test id: {} test name: {} field: {}{}'.format(error_diff, tolerance, id, id_string, fieldname, index + 1))) + #disp only if errors for the results + + except Exception as message: + #something went wrong, print failure message: + print((format_exc())) + if output == 'nightly': + fid = open(os.path.join(ISSM_DIR, 'nightlylog', 'pythonerror.log'), 'a') + fid.write('%s' % message) + fid.write('\n------------------------------------------------------------------\n') + fid.close() + print(('FAILURE difference: N/A test id: {} test name: {} field: {}'.format(id, id_string, fieldname))) + else: + print(('FAILURE difference: N/A test id: {} test name: {} field: {}'.format(id, id_string, fieldname))) + raise RuntimeError(message) #ELSE: CHECK TEST else: Index: /issm/trunk/test/NightlyRun/test101.py =================================================================== --- /issm/trunk/test/NightlyRun/test101.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test101.py (revision 27035) @@ -2,9 +2,9 @@ from model import * from socket import gethostname -from triangle import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve from massfluxatgate import massfluxatgate from generic import generic Index: /issm/trunk/test/NightlyRun/test124.js =================================================================== --- /issm/trunk/test/NightlyRun/test124.js (revision 27034) +++ /issm/trunk/test/NightlyRun/test124.js (revision 27035) @@ -22,7 +22,7 @@ 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3']; field_tolerances=[ - 2e-09,3e-9,3e-9,3e-9,1e-13,1e-12,1e-12, - 2e-09,3e-9,3e-9,3e-9,1e-10,1e-10,1e-10, - 3e-09,3e-9,3e-9,3e-9,1e-10,1e-10,1e-10]; + 2e-09,3e-9,3e-9,3e-9,1e-13,1e-12,7e-8, + 2e-09,3e-9,3e-9,3e-9,1e-10,1e-10,2e-7, + 3e-09,3e-9,3e-9,3e-9,1e-10,1e-10,3e-7]; field_values=[ (md.results.TransientSolution[0](1).Vx), Index: /issm/trunk/test/NightlyRun/test124.m =================================================================== --- /issm/trunk/test/NightlyRun/test124.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test124.m (revision 27035) @@ -21,7 +21,7 @@ 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'}; field_tolerances={... - 2e-09,3e-9,3e-9,3e-9,1e-13,1e-12,1e-12,... - 2e-09,3e-9,3e-9,3e-9,1e-10,1e-10,1e-10,... - 3e-09,3e-9,3e-9,3e-9,1e-10,1e-10,1e-10}; + 2e-09,3e-9,3e-9,3e-9,1e-13,1e-12,7e-8,... + 2e-09,3e-9,3e-9,3e-9,1e-10,1e-10,2e-7,... + 3e-09,3e-9,3e-9,3e-9,1e-10,1e-10,3e-7}; field_values={... (md.results.TransientSolution(1).Vx),... Index: /issm/trunk/test/NightlyRun/test124.py =================================================================== --- /issm/trunk/test/NightlyRun/test124.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test124.py (revision 27035) @@ -27,7 +27,7 @@ 'Vx2', 'Vy2', 'Vel2', 'Pressure2', 'Bed2', 'Surface2', 'Thickness2', 'Vx3', 'Vy3', 'Vel3', 'Pressure3', 'Bed3', 'Surface3', 'Thickness3'] -field_tolerances = [2e-09, 3e-9, 3e-9, 3e-9, 1e-13, 1e-12, 1e-12, - 2e-09, 3e-9, 3e-9, 3e-9, 1e-10, 1e-10, 1e-10, - 3e-09, 3e-9, 3e-9, 3e-9, 1e-10, 1e-10, 1e-10] +field_tolerances = [2e-09, 3e-9, 3e-9, 3e-9, 1e-13, 1e-12, 7e-8, + 2e-09, 3e-9, 3e-9, 3e-9, 1e-10, 1e-10, 2e-7, + 3e-09, 3e-9, 3e-9, 3e-9, 1e-10, 1e-10, 3e-7] field_values = [md.results.TransientSolution[0].Vx, md.results.TransientSolution[0].Vy, Index: /issm/trunk/test/NightlyRun/test127.m =================================================================== --- /issm/trunk/test/NightlyRun/test127.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test127.m (revision 27035) @@ -1,11 +1,11 @@ -%Test Name: SquareShelfConstrainedStressMLHO2d +%Test Name: SquareShelfConstrainedStressMOLHO2d md=triangle(model(),'../Exp/Square.exp',50000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',2); %output -%FIXME compute the stress components for MLHO +%FIXME compute the stress components for MOLHO md.stressbalance.requested_outputs={'default','VxSurface','VySurface','VxShear','VyShear','VxBase','VyBase','MassFlux1','MassFlux2','MassFlux3','MassFlux4','MassFlux5','MassFlux6'}; %md.stressbalance.requested_outputs={'default','DeviatoricStressxx','DeviatoricStressyy','DeviatoricStressxy','MassFlux1','MassFlux2','MassFlux3','MassFlux4','MassFlux5','MassFlux6'}; @@ -18,5 +18,5 @@ massfluxatgate('name','MassFlux6','profilename',['../Exp/MassFlux6.exp'],'definitionstring','Outputdefinition6')... }; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Stressbalance'); Index: /issm/trunk/test/NightlyRun/test127.py =================================================================== --- /issm/trunk/test/NightlyRun/test127.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test127.py (revision 27035) @@ -1,3 +1,3 @@ -#Test Name: SquareShelfConstrainedStressMLHO2d +#Test Name: SquareShelfConstrainedStressMOLHO2d from model import * from socket import gethostname @@ -9,13 +9,13 @@ from massfluxatgate import massfluxatgate from generic import generic -from SetMLHOBC import SetMLHOBC +from SetMOLHOBC import SetMOLHOBC md = triangle(model(), '../Exp/Square.exp', 50000) md = setmask(md, 'all', '') md = parameterize(md, '../Par/SquareShelfConstrained.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 2) #outputs -#FIXME compute the stress components for MLHO +#FIXME compute the stress components for MOLHO md.stressbalance.requested_outputs = ['default', 'VxSurface', 'VySurface', 'VxShear', 'VyShear', 'VxBase', 'VyBase', 'MassFlux1', 'MassFlux2', 'MassFlux3', 'MassFlux4', 'MassFlux5', 'MassFlux6'] #md.stressbalance.requested_outputs = ['default', 'DeviatoricStressxx', 'DeviatoricStressyy', 'DeviatoricStressxy', 'MassFlux1', 'MassFlux2', 'MassFlux3', 'MassFlux4', 'MassFlux5', 'MassFlux6'] @@ -26,5 +26,5 @@ massfluxatgate('name', 'MassFlux5', 'profilename', '../Exp/MassFlux5.exp', 'definitionstring', 'Outputdefinition5'), massfluxatgate('name', 'MassFlux6', 'profilename', '../Exp/MassFlux6.exp', 'definitionstring', 'Outputdefinition6')] -md = SetMLHOBC(md) +md = SetMOLHOBC(md) md = solve(md, 'Stressbalance') Index: /issm/trunk/test/NightlyRun/test128.m =================================================================== --- /issm/trunk/test/NightlyRun/test128.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test128.m (revision 27035) @@ -1,11 +1,11 @@ -%Test Name: SquareShelfConstrainedTranMLHO2d +%Test Name: SquareShelfConstrainedTranMOLHO2d md=triangle(model(),'../Exp/Square.exp',150000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); md.transient.requested_outputs={'IceVolume','VxShear','VyShear','VxBase','VyBase','VxSurface','VySurface'}; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test128.py =================================================================== --- /issm/trunk/test/NightlyRun/test128.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test128.py (revision 27035) @@ -1,4 +1,5 @@ -#Test Name: SquareShelfConstrainedTranMLHO2d +#Test Name: SquareShelfConstrainedTranMOLHO2d from model import * +from SetMOLHOBC import SetMOLHOBC from socket import gethostname from triangle import * @@ -12,14 +13,14 @@ md = setmask(md, 'all', '') md = parameterize(md, '../Par/SquareShelfConstrained.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) md.transient.requested_outputs = ['IceVolume','VxSurface','VySurface','VxShear','VyShear','VxBase','VyBase'] -md = SetMLHOBC(md); +md = SetMOLHOBC(md) md = solve(md, 'Transient') #Fields and tolerances to track changes -field_names = ['Vx1', 'Vy1', 'Vel1', 'Pressure1', 'VxShear1', 'VyShear1', 'VxBase1', 'VyBase1', 'VxSurface1', 'VySurface1', 'Bed1', 'Surface1', 'Thickness1', 'Volume1', - 'Vx2', 'Vy2', 'Vel2', 'Pressure2', 'VxShear2', 'VyShear2', 'VxBase2', 'VyBase2', 'VxSurface2', 'VySurface2', 'Bed2', 'Surface2', 'Thickness2', 'Volume2', +field_names = ['Vx1', 'Vy1', 'Vel1', 'Pressure1', 'VxShear1', 'VyShear1', 'VxBase1', 'VyBase1', 'VxSurface1', 'VySurface1', 'Bed1', 'Surface1', 'Thickness1', 'Volume1', + 'Vx2', 'Vy2', 'Vel2', 'Pressure2', 'VxShear2', 'VyShear2', 'VxBase2', 'VyBase2', 'VxSurface2', 'VySurface2', 'Bed2', 'Surface2', 'Thickness2', 'Volume2', 'Vx3', 'Vy3', 'Vel3', 'Pressure3', 'VxShear3', 'VyShear3', 'VxBase3', 'VyBase3', 'VxSurface3', 'VySurface3', 'Bed3', 'Surface3', 'Thickness3', 'Volume3'] field_tolerances = [1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, Index: /issm/trunk/test/NightlyRun/test129.m =================================================================== --- /issm/trunk/test/NightlyRun/test129.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test129.m (revision 27035) @@ -1,7 +1,7 @@ -%Test Name: SquareShelfConstrainedRestartTranMLHO2d +%Test Name: SquareShelfConstrainedRestartTranMOLHO2d md=triangle(model(),'../Exp/Square.exp',150000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareShelfConstrained.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',1); md.transient.requested_outputs={'IceVolume','TotalSmb','VxShear','VyShear','VxBase','VyBase','VxSurface','VySurface'}; @@ -14,5 +14,5 @@ md.settings.output_frequency=2; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); md2=solve(md,'Transient','restart',1); Index: /issm/trunk/test/NightlyRun/test129.py =================================================================== --- /issm/trunk/test/NightlyRun/test129.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test129.py (revision 27035) @@ -1,5 +1,6 @@ -#Test Name: SquareShelfConstrainedRestartTranMLHO2d +#Test Name: SquareShelfConstrainedRestartTranMOLHO2d from model import * from socket import gethostname +from SetMOLHOBC import SetMOLHOBC from triangle import * from setmask import * @@ -13,5 +14,5 @@ md = setmask(md, 'all', '') md = parameterize(md, '../Par/SquareShelfConstrained.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 1) md.transient.requested_outputs = ['IceVolume', 'TotalSmb', 'VxShear','VyShear','VxBase','VyBase','VxSurface','VySurface'] @@ -23,5 +24,5 @@ md.timestepping.final_time = 19 md.settings.output_frequency = 2 -md = SetMLHOBC(md); +md = SetMOLHOBC(md) md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test134.m =================================================================== --- /issm/trunk/test/NightlyRun/test134.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test134.m (revision 27035) @@ -5,5 +5,7 @@ md = md.sampling.setparameters(md,2e5,1); md.sampling.seed = 100; +md.sampling.phi = zeros(md.mesh.numberofvertices,1); md.cluster=generic('name',oshostname(),'np',1); +md.cluster.np=1; md=solve(md,'smp'); Index: /issm/trunk/test/NightlyRun/test2002.m =================================================================== --- /issm/trunk/test/NightlyRun/test2002.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2002.m (revision 27035) @@ -3,5 +3,13 @@ %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); + +% %Generate and save mesh +% SlcMesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); +% save('../Data/SlcTestMesh.mat','SlcMesh'); +% md.mesh=SlcMesh; + +%Load precomputed mesh +load('../Data/SlcTestMesh.mat'); +md.mesh=SlcMesh; %700 km resolution mesh %Geometry for the bed, arbitrary thickness of 100: @@ -83,5 +91,5 @@ md.transient.ismasstransport=1; md.transient.isslc=1; -md.solidearth.requested_outputs={'Sealevel','Bed'}; +md.solidearth.requested_outputs={'Sealevel','Bed','SealevelBarystaticIceLoad', 'SealevelBarystaticIceArea', 'SealevelBarystaticIceWeights'}; % max number of iteration reverted back to 10 (i.e., the original default value) Index: /issm/trunk/test/NightlyRun/test2002.py =================================================================== --- /issm/trunk/test/NightlyRun/test2002.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2002.py (revision 27035) @@ -1,6 +1,6 @@ #Test Name: EarthSlc import numpy as np - -from gmshplanet import * +import pickle +#from gmshplanet import * from gmtmask import * from lovenumbers import * @@ -12,5 +12,13 @@ md = model() -md.mesh = gmshplanet('radius', 6.371012 * 1e3, 'resolution', 700.) # 700 km resolution mesh + +## Generate and save mesh (need to uncomment import of gmshplanet as well) +# md.mesh = gmshplanet('radius', 6.371012 * 1e3, 'resolution', 700.) # 700 km resolution mesh +# with open('../Data/SlcTestMesh.pkl', 'wb') as slc_test_mesh_file: +# pickle.dump(md.mesh, slc_test_mesh_file) + +# Load precomputed mesh +with open('../Data/SlcTestMesh.pkl', 'rb') as slc_test_mesh_file: + md.mesh = pickle.load(slc_test_mesh_file) # Geometry for the bed, arbitrary thickness of 100 @@ -97,5 +105,5 @@ md.transient.ismasstransport = 1 md.transient.isslc = 1 -md.solidearth.requested_outputs = ['Sealevel', 'Bed'] +md.solidearth.requested_outputs = ['Sealevel', 'Bed', 'SealevelBarystaticIceLoad', 'SealevelBarystaticIceArea', 'SealevelBarystaticIceWeights'] # Max number of iterations reverted back to 10 (i.e., the original default value) Index: /issm/trunk/test/NightlyRun/test2003.m =================================================================== --- /issm/trunk/test/NightlyRun/test2003.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2003.m (revision 27035) @@ -1,7 +1,9 @@ %Test Name: EarthSlc_rotationalFeedback + %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh %Geometry for the bed, arbitrary thickness of 1000: Index: /issm/trunk/test/NightlyRun/test2003.py =================================================================== --- /issm/trunk/test/NightlyRun/test2003.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2003.py (revision 27035) @@ -1,6 +1,6 @@ #Test Name: EarthSlc_rotationalFeedback import numpy as np +import pickle from socket import gethostname -from gmshplanet import * from gmtmask import * from lovenumbers import * @@ -12,5 +12,8 @@ md = model() -md.mesh = gmshplanet('radius', 6.371012 * 1e3, 'resolution', 700.) # 700 km resolution mesh + +# Load precomputed mesh +with open('../Data/SlcTestMesh.pkl', 'rb') as slc_test_mesh_file: + md.mesh = pickle.load(slc_test_mesh_file) # Geometry for the bed, arbitrary thickness of 100 Index: /issm/trunk/test/NightlyRun/test2004.m =================================================================== --- /issm/trunk/test/NightlyRun/test2004.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2004.m (revision 27035) @@ -362,5 +362,5 @@ if plotting, flags=ones(sl.earth.mesh.numberofelements,1); - for i=1:length(sl.eltransitions), + for i=1:length(sl.eltransitions) flags(sl.eltransitions{i})=i; end @@ -422,6 +422,6 @@ md.solidearth.settings.viscous=0; md.solidearth.requested_outputs= {'default',... - 'DeltaIceThickness','Sealevel','SealevelUGrd',... - 'SealevelchangeBarystaticMask','SealevelchangeBarystaticOceanMask'}; + 'DeltaIceThickness','Sealevel','Bed',... + 'SealevelBarystaticIceMask','SealevelBarystaticOceanMask'}; md=solve(md,'Transient'); Seustatic=md.results.TransientSolution.Sealevel; Index: /issm/trunk/test/NightlyRun/test2004.py =================================================================== --- /issm/trunk/test/NightlyRun/test2004.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2004.py (revision 27035) @@ -465,7 +465,7 @@ 'DeltaIceThickness', 'Sealevel', - 'SealevelUGrd', - 'SealevelchangeBarystaticMask', - 'SealevelchangeBarystaticOceanMask', + 'Bed', + 'SealevelBarystaticIceMask', + 'SealevelBarystaticOceanMask', ] md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test2005.m =================================================================== --- /issm/trunk/test/NightlyRun/test2005.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2005.m (revision 27035) @@ -3,5 +3,6 @@ %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh %Geometry for the bed, arbitrary thickness of 100: Index: /issm/trunk/test/NightlyRun/test2005.py =================================================================== --- /issm/trunk/test/NightlyRun/test2005.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2005.py (revision 27035) @@ -1,6 +1,5 @@ #Test Name: EarthSlc import numpy as np - -from gmshplanet import * +import pickle from gmtmask import * from lovenumbers import * @@ -14,5 +13,8 @@ # Mesh earth md = model() -md.mesh = gmshplanet('radius', 6.371012 * 1e3, 'resolution', 700.) #700 km resolution mesh + +# Load precomputed mesh +with open('../Data/SlcTestMesh.pkl', 'rb') as slc_test_mesh_file: + md.mesh = pickle.load(slc_test_mesh_file) # Geometry for the bed, arbitrary thickness of 100 Index: /issm/trunk/test/NightlyRun/test2006.m =================================================================== --- /issm/trunk/test/NightlyRun/test2006.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2006.m (revision 27035) @@ -3,5 +3,6 @@ %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh %Geometry for the bed, arbitrary thickness of 100: Index: /issm/trunk/test/NightlyRun/test2006.py =================================================================== --- /issm/trunk/test/NightlyRun/test2006.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2006.py (revision 27035) @@ -1,7 +1,7 @@ #Test Name: EarthSlc Dakota Sampling glaciers import numpy as np +import pickle from socket import gethostname from dmeth_params_set import * -from gmshplanet import * from gmtmask import * from lovenumbers import * @@ -18,5 +18,8 @@ md = model() md.cluster = generic('name', gethostname(), 'np', 5) -md.mesh = gmshplanet('radius', 6.371012 * 1e3, 'resolution', 700.) #700 km resolution mesh + +# Load precomputed mesh +with open('../Data/SlcTestMesh.pkl', 'rb') as slc_test_mesh_file: + md.mesh = pickle.load(slc_test_mesh_file) # Geometry for the bed, arbitrary thickness of 100 Index: /issm/trunk/test/NightlyRun/test2007.m =================================================================== --- /issm/trunk/test/NightlyRun/test2007.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2007.m (revision 27035) @@ -3,5 +3,6 @@ %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh %Geometry for the bed, arbitrary @@ -15,4 +16,5 @@ longe=md.mesh.long; time=0:0.5:5; +%The offline solution pattern is a degree (2,1) spherical harmonic md.solidearth.external=offlinesolidearthsolution; md.solidearth.external.displacementup=.5*sind(late).*cosd(late).*cosd(longe) .*time; Index: /issm/trunk/test/NightlyRun/test2008.m =================================================================== --- /issm/trunk/test/NightlyRun/test2008.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2008.m (revision 27035) @@ -3,5 +3,6 @@ %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh %Geometry for the bed, arbitrary thickness of 100: @@ -99,5 +100,5 @@ longe=md.mesh.long; time=0:1; -Y22=1.5*(1.+cosd(2.*late)).*cosd(2.*longe); +Y22=1.5*(1.+cosd(2.*late)).*cosd(2.*longe);%The additional solidearth signal is a degree (2,2) spherical harmonic md.solidearth.external=additionalsolidearthsolution; md.solidearth.external.displacementup=0.5*Y22 .*time; Index: /issm/trunk/test/NightlyRun/test2010.m =================================================================== --- /issm/trunk/test/NightlyRun/test2010.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2010.m (revision 27035) @@ -3,5 +3,6 @@ %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh %Geometry for the bed, arbitrary thickness of 100: @@ -98,13 +99,11 @@ eus=md.results.TransientSolution.Bslc; slc=md.results.TransientSolution.Sealevel; -moixz=md.results.TransientSolution.SealevelInertiaTensorXZ / (1/(1-tide_love_k2/tide_love_k2secular) * (1+load_love_k2)/(moi_p-moi_e) ); -moiyz=md.results.TransientSolution.SealevelInertiaTensorYZ / (1/(1-tide_love_k2/tide_love_k2secular) * (1+load_love_k2)/(moi_p-moi_e) ); -moizz=md.results.TransientSolution.SealevelInertiaTensorZZ / ( -(1+load_love_k2)/moi_p); +moixz=md.results.TransientSolution.SealevelchangePolarMotionX / (1/(1-tide_love_k2/tide_love_k2secular) * (1+load_love_k2)/(moi_p-moi_e) ); +moiyz=md.results.TransientSolution.SealevelchangePolarMotionY / (1/(1-tide_love_k2/tide_love_k2secular) * (1+load_love_k2)/(moi_p-moi_e) ); +moizz=md.results.TransientSolution.SealevelchangePolarMotionZ / ( -(1+load_love_k2)/moi_p); areaice=md.results.TransientSolution.SealevelBarystaticIceArea; +areaice(isnan(areaice))=0; loadice=md.results.TransientSolution.SealevelBarystaticIceLoad; - -% analytical moi => just checking FOR ICE only!!! {{{ -% ...have to mute ** slc induced MOI in Tria.cpp ** prior to the comparison rad_e = md.solidearth.planetradius; @@ -113,6 +112,6 @@ moi_xz = sum(-loadice.*areaice.*rad_e^2.*sin(lat).*cos(lat).*cos(lon)); moi_yz = sum(-loadice.*areaice.*rad_e^2.*sin(lat).*cos(lat).*sin(lon)); -moi_zz = sum(-loadice.*areaice.*rad_e^2.*(1.0-sin(lat).^2)); -theoretical_value_check=[moixz/moi_xz moiyz/moi_yz moizz/moi_zz] +moi_zz = sum(-loadice.*areaice.*rad_e^2.*(-1.0/3.0+sin(lat).^2)); +theoretical_value_check=[moixz/moi_xz moiyz/moi_yz moizz/moi_zz]; % should yield [1.0 1.0 1.0] % }}} Index: /issm/trunk/test/NightlyRun/test2010.py =================================================================== --- /issm/trunk/test/NightlyRun/test2010.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2010.py (revision 27035) @@ -1,6 +1,6 @@ #Test Name: MomentOfIntertia import numpy as np +import pickle from socket import gethostname -from gmshplanet import * from gmtmask import * from lovenumbers import * @@ -12,5 +12,8 @@ # Mesh earth md = model() -md.mesh = gmshplanet('radius', 6.371012 * 1e3, 'resolution', 700.) #700 km resolution mesh + +# Load precomputed mesh +with open('../Data/SlcTestMesh.pkl', 'rb') as slc_test_mesh_file: + md.mesh = pickle.load(slc_test_mesh_file) # Geometry for the bed, arbitrary thickness of 100 @@ -115,13 +118,13 @@ eus = md.results.TransientSolution.Bslc slc = md.results.TransientSolution.Sealevel -moixz = md.results.TransientSolution.SealevelInertiaTensorXZ / (1 / (1 - tide_love_k2 / tide_love_k2secular) * (1 + load_love_k2) / (moi_p - moi_e)) -moiyz = md.results.TransientSolution.SealevelInertiaTensorYZ / (1 / (1 - tide_love_k2 / tide_love_k2secular) * (1 + load_love_k2) / (moi_p - moi_e)) -moizz = md.results.TransientSolution.SealevelInertiaTensorZZ / ( -(1 + load_love_k2) / moi_p) +moixz = md.results.TransientSolution.SealevelchangePolarMotionX / (1 / (1 - tide_love_k2 / tide_love_k2secular) * (1 + load_love_k2) / (moi_p - moi_e)) +moiyz = md.results.TransientSolution.SealevelchangePolarMotionY / (1 / (1 - tide_love_k2 / tide_love_k2secular) * (1 + load_love_k2) / (moi_p - moi_e)) +moizz = md.results.TransientSolution.SealevelchangePolarMotionZ / ( -(1 + load_love_k2) / moi_p) areaice = md.results.TransientSolution.SealevelBarystaticIceArea +areaice[np.isnan(areaice)] = 0 +print(np.isnan(areaice)) +print(np.sum(areaice)) loadice = md.results.TransientSolution.SealevelBarystaticIceLoad - -# analytical moi = > just checking FOR ICE only!!! {{{ -# ...have to mute ** slc induced MOI in Tria.cpp**prior to the comparison rad_e = md.solidearth.planetradius @@ -130,8 +133,6 @@ moi_xz = sum(-loadice * areaice * pow(rad_e, 2) * np.sin(lat) * np.cos(lat) * np.cos(lon)) moi_yz = sum(-loadice * areaice * pow(rad_e, 2) * np.sin(lat) * np.cos(lat) * np.sin(lon)) -moi_zz = sum(-loadice * areaice * pow(rad_e, 2) * (1 - np.sin(lat) ** 2)) -theoretical_value_check = [moixz / moi_xz, moiyz / moi_yz, moizz / moi_zz] -print('\ntheoretical_value_check =\n') -print('\t{}\n'.format(theoretical_value_check)) +moi_zz = sum(-loadice * areaice * pow(rad_e, 2) * (-1.0 / 3.0 + np.sin(lat) ** 2)) +theoretical_value_check = [moixz / moi_xz, moiyz / moi_yz, moizz / moi_zz] # Should yield [1.0, 1.0, 1.0] # }}} Index: /issm/trunk/test/NightlyRun/test2011.m =================================================================== --- /issm/trunk/test/NightlyRun/test2011.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2011.m (revision 27035) @@ -3,5 +3,6 @@ %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh %Geometry for the bed, arbitrary thickness of 1000: @@ -111,6 +112,10 @@ bslc2=-sum(dHavg.*area)*md.materials.rho_ice/md.materials.rho_water/oceanarea; +%need to change precision before subtraction because of differences in results +%at high precision under macOS versus Linux (print values of bslc and bslc2 to %verify that the difference is negligible) +bslc_diff=single(bslc2)-single(bslc); + %Fields and tolerances to track changes field_names={'BarystaticIce','BarystaticIce2','BarystaticIceDiff'}; field_tolerances={1e-13,1e-13,1e-13}; -field_values={bslc,bslc2,bslc2-bslc}; +field_values={bslc,bslc2,bslc_diff}; Index: /issm/trunk/test/NightlyRun/test2012.m =================================================================== --- /issm/trunk/test/NightlyRun/test2012.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test2012.m (revision 27035) @@ -0,0 +1,134 @@ +%Test Name: EarthSlc Hydrology loading + +%mesh earth: +md=model; +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh + +%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; + +%solidearth loading: {{{ +md.hydrology=hydrologytws(); +md.hydrology.spcwatercolumn=[md.geometry.thickness;0]; +md.smb.mass_balance=zeros(md.mesh.numberofvertices,1); + +%antarctica +xe=md.mesh.x(md.mesh.elements)*[1;1;1]/3; +ye=md.mesh.y(md.mesh.elements)*[1;1;1]/3; +ze=md.mesh.z(md.mesh.elements)*[1;1;1]/3; +re=sqrt(xe.^2+ye.^2+ze.^2); + +late=asind(ze./re); +longe=atan2d(ye,xe); +pos=find(late < -80); +md.hydrology.spcwatercolumn(md.mesh.elements(pos,:))=md.hydrology.spcwatercolumn(md.mesh.elements(pos,:))-100; +posant=pos; + +%greenland +pos=find(late>60 & late<90 & longe>-75 & longe<-15); +md.hydrology.spcwatercolumn(md.mesh.elements(pos,:))=md.hydrology.spcwatercolumn(md.mesh.elements(pos,:))-100; +posgre=pos; + +%elastic loading from love numbers: +md.solidearth.lovenumbers=lovenumbers('maxdeg',1000); + +%}}} +%mask: {{{ +mask=gmtmask(md.mesh.lat,md.mesh.long); +oceanmask=-ones(md.mesh.numberofvertices,1); +pos=find(mask==0); oceanmask(pos)=1; + +icemask=ones(md.mesh.numberofvertices,1); +icemask(md.mesh.elements(posant))=-1; +icemask(md.mesh.elements(posgre))=-1; + +md.mask.ice_levelset=icemask; +md.mask.ocean_levelset=oceanmask; +% }}} + +%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.initialization.watercolumn=zeros(md.mesh.numberofvertices,1); + +%Materials: +md.materials=materials('hydro'); + +%Miscellaneous +md.miscellaneous.name='test2012'; + +%Solution parameters +md.cluster.np=3; +md.solidearth.settings.reltol=NaN; +md.solidearth.settings.abstol=1e-3; +md.solidearth.settings.sealevelloading=1; +md.solidearth.settings.isgrd=1; +md.solidearth.settings.ocean_area_scaling=0; +md.solidearth.settings.grdmodel=1; + +%Physics: +md.transient.issmb=0; +md.transient.isstressbalance=0; +md.transient.isthermal=0; +md.transient.ismasstransport=0; +md.transient.ishydrology=1; +md.transient.isslc=1; +md.solidearth.requested_outputs={'Sealevel','Bed'}; + +% max number of iteration reverted back to 10 (i.e., the original default value) +md.solidearth.settings.maxiter=10; + +%eustatic run: +md.solidearth.settings.selfattraction=0; +md.solidearth.settings.elastic=0; +md.solidearth.settings.rotation=0; +md.solidearth.settings.viscous=0; + +md=solve(md,'Transient'); +Seustatic=md.results.TransientSolution.Sealevel; +Beustatic=md.results.TransientSolution.Bed; + +%eustatic + selfattraction run: +md.solidearth.settings.selfattraction=1; +md.solidearth.settings.elastic=0; +md.solidearth.settings.rotation=0; +md.solidearth.settings.viscous=0; +md=solve(md,'tr'); +Sselfattraction=md.results.TransientSolution.Sealevel; +Bselfattraction=md.results.TransientSolution.Bed; + +%eustatic + selfattraction + elastic run: +md.solidearth.settings.selfattraction=1; +md.solidearth.settings.elastic=1; +md.solidearth.settings.rotation=0; +md.solidearth.settings.viscous=0; +md=solve(md,'tr'); +Selastic=md.results.TransientSolution.Sealevel; +Belastic=md.results.TransientSolution.Bed; + +%eustatic + selfattraction + elastic + rotation run: +md.solidearth.settings.selfattraction=1; +md.solidearth.settings.elastic=1; +md.solidearth.settings.rotation=1; +md.solidearth.settings.viscous=0; +md=solve(md,'tr'); +Srotation=md.results.TransientSolution.Sealevel; +Brotation=md.results.TransientSolution.Bed; + +%Fields and tolerances to track changes +field_names={'Seustatic','Sselfattraction','Selastic','Srotation','Beustatic','Bselfattraction','Belastic','Brotation'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +field_values={Seustatic,Sselfattraction,Selastic,Srotation,Beustatic,Bselfattraction,Belastic,Brotation}; Index: /issm/trunk/test/NightlyRun/test2013.m =================================================================== --- /issm/trunk/test/NightlyRun/test2013.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test2013.m (revision 27035) @@ -0,0 +1,159 @@ +%Test Name: EarthSlc_Geometry + +step=[1 2]; +if any(step==1) +%mesh earth: +md=model; +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh + +%Geometry for the bed, arbitrary thickness of 1000: +md.geometry.bed=-ones(md.mesh.numberofvertices,1); +md.geometry.base=md.geometry.bed; +md.geometry.thickness=1000*ones(md.mesh.numberofvertices,1); +md.geometry.surface=md.geometry.bed+md.geometry.thickness; + +%parameterize slc solution: +%solidearth loading: {{{ +md.masstransport.spcthickness=[md.geometry.thickness;0]; +md.smb.mass_balance=zeros(md.mesh.numberofvertices,1); + +xe=md.mesh.x(md.mesh.elements)*[1;1;1]/3; +ye=md.mesh.y(md.mesh.elements)*[1;1;1]/3; +ze=md.mesh.z(md.mesh.elements)*[1;1;1]/3; +re=sqrt(xe.^2+ye.^2+ze.^2); + +late=asind(ze./re); +longe=atan2d(ye,xe); + +%greenland +pos=find(late>60 & late<90 & longe>-75 & longe<-15); +md.masstransport.spcthickness(md.mesh.elements(:,:))= md.masstransport.spcthickness(md.mesh.elements(:,:))-1000; +posice=pos; + +%elastic loading from love numbers: +md.solidearth.lovenumbers=lovenumbers('maxdeg',100); +%}}} +%mask: {{{ +mask=gmtmask(md.mesh.lat,md.mesh.long); +icemask=ones(md.mesh.numberofvertices,1); +icemask(md.mesh.elements(posice,:))=-1; +md.mask.ice_levelset=icemask; +oceanmask=-ones(md.mesh.numberofvertices,1); +pos=find(mask==0); oceanmask(pos)=3; +md.mask.ocean_levelset=oceanmask; + +% use model representation of ocean area (not the true area) +md.solidearth.settings.ocean_area_scaling = 0; + +%materials +md.initialization.temperature=273.25*ones(md.mesh.numberofvertices,1); +md.initialization.sealevel=zeros(md.mesh.numberofvertices,1); +md.initialization.str=0; + +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); + +%Miscellaneous +md.miscellaneous.name='test2013'; + +%Solution parameters +md.solidearth.settings.reltol=NaN; +md.solidearth.settings.abstol=1e-3; +md.solidearth.settings.sealevelloading=0; +md.solidearth.settings.grdocean=0; +md.solidearth.settings.isgrd=1; +md.solidearth.settings.ocean_area_scaling=0; +md.solidearth.settings.grdmodel=1; +md.solidearth.settings.horiz=1; +md.settings.results_on_nodes = {'SealevelBarystaticIceWeights'}; +md.solidearth.requested_outputs={'SealevelBarystaticIceLoad', 'SealevelBarystaticIceWeights', 'SealevelBarystaticIceArea', 'SealevelBarystaticIceMask', 'SealevelBarystaticIceLatbar', 'SealevelBarystaticIceLongbar'}; + +%Physics: +md.transient.issmb=0; +md.transient.isstressbalance=0; +md.transient.isthermal=0; +md.transient.ismasstransport=1; +md.transient.isslc=1; + +md.timestepping.start_time=0; +md.timestepping.time_step=1; +md.timestepping.final_time=1; + +%slc: +md.solidearth.settings.selfattraction=1; +md.solidearth.settings.elastic=0; +md.solidearth.settings.rotation=0; +md.solidearth.settings.viscous=0; +md.cluster=generic('name',oshostname(),'np',3); +%md.verbose=verbose('111111111'); +md=solve(md,'Transient'); + +weights=md.results.TransientSolution.SealevelBarystaticIceWeights; +mask=md.results.TransientSolution.SealevelBarystaticIceMask; +loads=md.results.TransientSolution.SealevelBarystaticIceLoad; +areas=md.results.TransientSolution.SealevelBarystaticIceArea; +longbar=md.results.TransientSolution.SealevelBarystaticIceLongbar; +latbar=md.results.TransientSolution.SealevelBarystaticIceLatbar; + + +%Fields and tolerances to track changes +field_names ={'Mask', 'LoadAreas', 'SurfaceLoad', 'LoadWeights','LatitudeLoadBarycenter', 'LongitudeLoadBarycenter'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +field_values={mask,areas,loads,weights,latbar, longbar}; + + +end +if any(step==2) +%use this to check visually the load-related inputs + + plotmodel(md,'data',md.mask.ocean_levelset,'contourlevels', {0},'contouronly',1, 'contourcolor', 'b') + co=get(gca,'children'); + coo=struct; + for i=1:length(co) + coo(i).XData=co(i).XData; + coo(i).YData=co(i).YData; + coo(i).ZData=co(i).ZData; + end + + plotmodel(md,'data',md.mask.ice_levelset,'contourlevels', {0},'contouronly',1, 'contourcolor', 'r') + ci=get(gca,'children'); + cii=struct; + for i=1:length(ci) + cii(i).XData=ci(i).XData; + cii(i).YData=ci(i).YData; + cii(i).ZData=ci(i).ZData; + end + + close all + + subplot(2,2,1) + for i=1:md.mesh.numberofelements + patch('XData',md.mesh.x(md.mesh.elements(i,:)), 'YData',md.mesh.y(md.mesh.elements(i,:)), 'ZData',md.mesh.z(md.mesh.elements(i,:)),'facecolor', 'interp', 'facevertexcdata',weights(i,:)') + hold on + end + + for i=1:length(coo) + plot3(coo(i).XData,coo(i).YData,coo(i).ZData, 'color', [0 0 .8],'linewidth',1.5) + end + + for i=1:length(cii) + plot3(cii(i).XData,cii(i).YData,cii(i).ZData, 'color', [.7 0 .7],'linewidth',1.5) + end + + x=md.solidearth.planetradius* (cosd(latbar).*cosd(longbar)); + y=md.solidearth.planetradius* (cosd(latbar).*sind(longbar)); + z=md.solidearth.planetradius* (sind(latbar)); + ind=find(mask>0); + plot3(x(ind),y(ind),z(ind), 'kx') + axis tight; title('Load weights & barycenters');set(gca,'Fontsize', 14); + + plotmodel(md,'data', loads,'subplot',[2 2 2]);title('Average load [kg.m^-2]') + plotmodel(md,'data', mask,'subplot',[2 2 3]); title('Phi') + plotmodel(md,'data', areas,'subplot',[2 2 4]); title('Load areas [m^2]') + + +end + Index: /issm/trunk/test/NightlyRun/test2021.m =================================================================== --- /issm/trunk/test/NightlyRun/test2021.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2021.m (revision 27035) @@ -4,5 +4,6 @@ md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); %700 km resolution mesh +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh % read in love numbers. Index: /issm/trunk/test/NightlyRun/test2051.m =================================================================== --- /issm/trunk/test/NightlyRun/test2051.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2051.m (revision 27035) @@ -5,20 +5,31 @@ md=parameterize(md,'../Par/GiaIvinsBenchmarksAB.par'); +%GIA Ivins, 2 layer model. +md.solidearth.settings.grdmodel=2; +md.solidearth.settings.isgrd=1; +md.initialization.sealevel=zeros(md.mesh.numberofvertices,1); + %% indicate what you want to compute -md.gia.cross_section_shape=1; % for square-edged x-section +md.solidearth.settings.cross_section_shape=1; % for square-edged x-section +md.solidearth.settings.grdocean=0; %do not compute sea level, only deformation +md.solidearth.settings.sealevelloading=0; %do not compute sea level, only deformation % evaluation time (termed start_time) -md.timestepping.start_time=2002100; % after 2 kyr of deglaciation + +md.timestepping.time_step=2002100; % after 2 kyr of deglaciation +md.timestepping.start_time=-md.timestepping.time_step; % need one time step before t=0 to generate a thickness change at t=0 md.timestepping.final_time=2500000; % 2,500 kyr %% define loading history {{{ -md.geometry.thickness=[... +md.masstransport.spcthickness=[... [md.geometry.thickness*0.0; 0.0],... [md.geometry.thickness; 1000],... [md.geometry.thickness; 2000000],... [md.geometry.thickness*0.0; 2000100],... - [md.geometry.thickness*0.0; md.timestepping.start_time],... + [md.geometry.thickness*0.0; md.timestepping.start_time+2*md.timestepping.time_step],... ]; % }}} + +md.geometry.bed=zeros(md.mesh.numberofvertices,1); % find out elements that have zero loads throughout the loading history. @@ -26,39 +37,52 @@ md.mask.ice_levelset(pos)=1; % no ice +%Physics: +md.transient.issmb=0; +md.transient.isstressbalance=0; +md.transient.isthermal=0; +md.transient.ismasstransport=1; +md.transient.isslc=1; + md.cluster=generic('name',oshostname(),'np',3); md.verbose=verbose('1111111'); +md.solidearth.requested_outputs={'Sealevel','BedGRD'}; %% solve for GIA deflection -md=solve(md,'Gia'); +md=solve(md,'Transient'); %Test Name: GiaIvinsBenchmarksAB2dA1 -U_AB2dA1 = md.results.GiaSolution.UGia; -URate_AB2dA1 = md.results.GiaSolution.UGiaRate; +U_AB2dA1 = md.results.TransientSolution.BedGRD; +%URate_AB2dA1 = md.results.TransientSolution.UGiaRate; %Test Name: GiaIvinsBenchmarksAB2dA2 %% different evaluation time. {{{ -md.timestepping.start_time=2005100; % after 5 kyr of deglaciation -md.geometry.thickness(end,end) = md.timestepping.start_time; +md.timestepping.time_step=2005100;% after 5 kyr of deglaciation +md.timestepping.start_time=-md.timestepping.time_step; % need one time step before t=0 to generate a thickness change at t=0 +md.masstransport.spcthickness(end,end) = md.timestepping.start_time+2*md.timestepping.time_step; -md=solve(md,'Gia'); +md=solve(md,'Transient'); -U_AB2dA2 = md.results.GiaSolution.UGia; -URate_AB2dA2 = md.results.GiaSolution.UGiaRate; +U_AB2dA2 = md.results.TransientSolution.BedGRD; +%URate_AB2dA2 = md.results.TransientSolution.BedGRDRate; % }}} %Test Name: GiaIvinsBenchmarksAB2dA3 %% different evaluation time. {{{ -md.timestepping.start_time=2010100; % after 10 kyr of deglaciation -md.geometry.thickness(end,end) = md.timestepping.start_time; +md.timestepping.time_step=2010100;% after 10 kyr of deglaciation +md.timestepping.start_time=-md.timestepping.time_step; % need one time step before t=0 to generate a thickness change at t=0 +md.masstransport.spcthickness(end,end) = md.timestepping.start_time+2*md.timestepping.time_step; -md=solve(md,'Gia'); +md=solve(md,'Transient'); -U_AB2dA3 = md.results.GiaSolution.UGia; -URate_AB2dA3 = md.results.GiaSolution.UGiaRate; +U_AB2dA3 = md.results.TransientSolution.BedGRD; +%URate_AB2dA3 = md.results.TransientSolution.UGiaRate; % }}} %Fields and tolerances to track changes -field_names ={'U_AB2dA1','URate_AB2dA1','U_AB2dA2','URate_AB2dA2','U_AB2dA3','URate_AB2dA3'}; -field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; -field_values={U_AB2dA1,URate_AB2dA1,U_AB2dA2,URate_AB2dA2,U_AB2dA3,URate_AB2dA3}; +field_names ={'U_AB2dA1','U_AB2dA2','U_AB2dA3'}; +field_tolerances={1e-13,1e-13,1e-13}; +field_values={U_AB2dA1,U_AB2dA2,U_AB2dA3}; +% field_names ={'U_AB2dA1','URate_AB2dA1','U_AB2dA2','URate_AB2dA2','U_AB2dA3','URate_AB2dA3'}; +% field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; +% field_values={U_AB2dA1,URate_AB2dA1,U_AB2dA2,URate_AB2dA2,U_AB2dA3,URate_AB2dA3}; Index: /issm/trunk/test/NightlyRun/test2051.py =================================================================== --- /issm/trunk/test/NightlyRun/test2051.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2051.py (revision 27035) @@ -16,58 +16,81 @@ md = parameterize(md, '../Par/GiaIvinsBenchmarksAB.py') -# indicate what you want to compute -md.gia.cross_section_shape = 1 # for square-edged x-section +# GIA Ivins, 2 layer model +md.solidearth.settings.grdmodel = 2 +md.solidearth.settings.isgrd = 1 +md.initialization.sealevel = np.zeros((md.mesh.numberofvertices,)) -# evaluation time (termed start_time) -md.timestepping.start_time = 2002100 # after 2 kyr of deglaciation -md.timestepping.final_time = 2500000 # 2,500 kyr +# Indicate what you want to compute +md.solidearth.settings.cross_section_shape = 1 # For square-edged x-section +md.solidearth.settings.grdocean = 0 # Do not compute sea level, only deformation +md.solidearth.settings.sealevelloading = 0 # Do not compute sea level, only deformation -# define loading history -md.geometry.thickness = np.array([ +# Evaluation time (termed start_time) +md.timestepping.time_step = 2002100 # after 2 kyr of deglaciation +md.timestepping.start_time = -md.timestepping.time_step # Need one time step before t = 0 to generate a thickness change at t = 0 +md.timestepping.final_time = 2500000 # 2,500 kyr + +# Define loading history +md.masstransport.spcthickness = np.array([ np.append(md.geometry.thickness * 0.0, 0.0), np.append(md.geometry.thickness, 1000), np.append(md.geometry.thickness, 2000000), np.append(md.geometry.thickness * 0.0, 2000100), - np.append(md.geometry.thickness * 0.0, md.timestepping.start_time) + np.append(md.geometry.thickness * 0.0, md.timestepping.start_time + 2 * md.timestepping.time_step) ]).T -# find out the elements that have zero loads throughout the loading history +md.geometry.bed = np.zeros((md.mesh.numberofvertices,)) + +# Find out the elements that have zero loads throughout the loading history pos = np.where(np.abs(md.geometry.thickness[0:-2, :].sum(axis=1)) == 0)[0] -md.mask.ice_levelset[pos] = 1 # no ice +md.mask.ice_levelset[pos] = 1 # No ice + +# Physics +md.transient.issmb = 0 +md.transient.isstressbalance = 0 +md.transient.isthermal = 0 +md.transient.ismasstransport = 1 +md.transient.isslc = 1 md.cluster = generic('name', gethostname(), 'np', 3) md.verbose = verbose('1111111') +md.solidearth.requested_outputs = ['Sealevel', 'BedGRD'] -# solve for GIA deflection -md = solve(md, 'Gia') +# Solve for GIA deflection +md = solve(md, 'Transient') # Test Name: GiaIvinsBenchmarksAB2dA1 -U_AB2dA1 = md.results.GiaSolution.UGia -URate_AB2dA1 = md.results.GiaSolution.UGiaRate +U_AB2dA1 = md.results.TransientSolution.BedGRD +#URate_AB2dA1 = md.results.TransientSolution.UGiaRate # Test Name: GiaIvinsBenchmarksAB2dA2 # different evaluation time # {{{ -md.timestepping.start_time = 2005100 # after 5 kyr of deglaciation -md.geometry.thickness[-1, -1] = md.timestepping.start_time +md.timestepping.time_step = 2005100 # After 5 kyr of deglaciation +md.timestepping.start_time = -md.timestepping.time_step # Need one time step before t = 0 to generate a thickness change at t = 0 +md.masstransport.spcthickness[-1, -1] = md.timestepping.start_time + 2 * md.timestepping.time_step -md = solve(md, 'Gia') +md = solve(md, 'Transient') -U_AB2dA2 = md.results.GiaSolution.UGia -URate_AB2dA2 = md.results.GiaSolution.UGiaRate +U_AB2dA2 = md.results.TransientSolution.BedGRD +#URate_AB2dA2 = md.results.TransientSolution.BedGRDRate # }}} # Test Name: GiaIvinsBenchmarksAB2dA3 # different evaluation time # {{{ -md.timestepping.start_time = 2010100 # after 10 kyr of deglaciation -md.geometry.thickness[-1, -1] = md.timestepping.start_time +md.timestepping.time_step = 2010100 # After 10 kyr of deglaciation +md.timestepping.start_time = -md.timestepping.time_step # Need one time step before t = 0 to generate a thickness change at t = 0 +md.masstransport.spcthickness[-1, -1] = md.timestepping.start_time + 2 * md.timestepping.time_step -md = solve(md, 'Gia') +md = solve(md, 'Transient') -U_AB2dA3 = md.results.GiaSolution.UGia -URate_AB2dA3 = md.results.GiaSolution.UGiaRate +U_AB2dA3 = md.results.TransientSolution.BedGRD +#URate_AB2dA3 = md.results.TransientSolution.UGiaRate # }}} # Fields and tolerances to track changes -field_names = ['U_AB2dA1','URate_AB2dA1','U_AB2dA2','URate_AB2dA2','U_AB2dA3','URate_AB2dA3'] -field_tolerances = [1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13] -field_values = [U_AB2dA1, URate_AB2dA1, U_AB2dA2, URate_AB2dA2, U_AB2dA3, URate_AB2dA3] +field_names = ['U_AB2dA1','U_AB2dA2','U_AB2dA3'] +field_tolerances = [1e-13, 1e-13, 1e-13] +field_values = [U_AB2dA1, U_AB2dA2, U_AB2dA3] +# field_names = ['U_AB2dA1','URate_AB2dA1','U_AB2dA2','URate_AB2dA2','U_AB2dA3','URate_AB2dA3'] +# field_tolerances = [1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13] +# field_values = [U_AB2dA1, URate_AB2dA1, U_AB2dA2, URate_AB2dA2, U_AB2dA3, URate_AB2dA3] Index: /issm/trunk/test/NightlyRun/test2070.m =================================================================== --- /issm/trunk/test/NightlyRun/test2070.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test2070.m (revision 27035) @@ -0,0 +1,71 @@ +%Test Name: ElasticLoveNumbers +%Forward Love number solution for a viscoelastic earth, model M3-L70-V01 from +%Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., Martinec, Z., +%Gasperini, P., Lund, B., Wolf, D., Vermeersen, L. L. A. and King, M. A. +%(2011), A benchmark study for glacial isostatic adjustment codes. Geophysical +%Journal International, 185: 106--132. doi:10.1111/j.1365-246X.2011.04952.x + +md=model(); +md.cluster=generic('name',oshostname(),'np',2); + +md.materials=materials('litho'); +md.miscellaneous.name='test2070'; +md.groundingline.migration='None'; + +md.verbose=verbose('all'); +md.verbose=verbose('1111111111111111'); +cst=365.25*24*3600*1000; + +md.materials.numlayers=6; +md.materials.radius = [10 1222.5 3.4800e+03 5.7010e+03 5.9510e+03 6.3010e+03 6.3710e+03]'*1e3; +md.materials.density= [1.0750e4 1.0750e+04 4.9780e+03 3.8710e+03 3.4380e+03 3.0370e+03]'; +md.materials.lame_mu= [1e-5 0 2.2834e+00 1.0549e+00 7.0363e-01 5.0605e-01]'*1e11; +md.materials.viscosity=[0 0 2.0000e+00 1.0000e+00 1.0000e+00 1.0000e+25]'*1e21; +md.materials.lame_lambda=md.materials.lame_mu*0+5e17; +md.materials.issolid=[1 0 1 1 1 1]'; +md.materials.rheologymodel=zeros(md.materials.numlayers,1); +md.materials.burgers_mu=md.materials.lame_mu/3; +md.materials.burgers_viscosity=md.materials.viscosity/10; +md.materials.ebm_alpha= ones(md.materials.numlayers,1)*.9; +md.materials.ebm_delta= ones(md.materials.numlayers,1)*0.2; +md.materials.ebm_taul= ones(md.materials.numlayers,1)*54*60; %54min +md.materials.ebm_tauh= ones(md.materials.numlayers,1)*18.6*cst/1e3; %18.6yr + +md.love.allow_layer_deletion=1; +md.love.frequencies=[0]; +md.love.nfreq=length(md.love.frequencies); +md.love.sh_nmin=1; +md.love.sh_nmax=10000; +md.love.underflow_tol=1e-20; +md.love.pw_threshold=1e-3; +md.love.Gravitational_Constant=6.6732e-11; +md.love.integration_steps_per_layer=100; +md.love.allow_layer_deletion=1; +md.love.forcing_type=11; +md.love.chandler_wobble=0; +md.love.complex_computation=0; +md.love.istemporal=0; +%md.love.time=(linspace(1/12,10, 10*12))'*cst/1e3; + +md.love.love_kernels=1; + +md=solve(md,'lv'); + +h=md.results.LoveSolution.LoveHf; +l=md.results.LoveSolution.LoveLf; +k=md.results.LoveSolution.LoveKf; + +md.love.forcing_type=9; +md.love.sh_nmin=2; +md=solve(md,'lv'); + +th=md.results.LoveSolution.LoveHf; +tl=md.results.LoveSolution.LoveLf; +tk=md.results.LoveSolution.LoveKf; + +%Fields and tolerances to track changes + +field_names ={'LoveH_loading_elastic','LoveK_loading_elastic','LoveL_loading_elastic','LoveH_tidal_elastic','LoveK_tidal_elastic','LoveL_tidal_elastic'}; +field_tolerances={2.0e-8,2.0e-8,2.0e-8,2.0e-8,2.0e-8,2.0e-8}; +field_values={h,k,l,th,tk,tl}; + Index: /issm/trunk/test/NightlyRun/test2071.m =================================================================== --- /issm/trunk/test/NightlyRun/test2071.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test2071.m (revision 27035) @@ -0,0 +1,126 @@ +%Test Name: TemporalLoveNumbers +%Forward Love number solution for a viscoelastic earth, model M3-L70-V01 from +%Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., Martinec, Z., +%Gasperini, P., Lund, B., Wolf, D., Vermeersen, L. L. A. and King, M. A. +%(2011), A benchmark study for glacial isostatic adjustment codes. Geophysical +%Journal International, 185: 106--132. doi:10.1111/j.1365-246X.2011.04952.x + +md=model(); +md.cluster=generic('name',oshostname(),'np',3); + +md.materials=materials('litho'); +md.miscellaneous.name='test2071'; +md.groundingline.migration='None'; + +md.verbose=verbose('all'); +md.verbose=verbose('1111111111111111'); +yts=365.25*24*3600; + +md.materials.numlayers=6; +md.materials.radius = [10 1222.5 3.4800e+03 5.7010e+03 5.9510e+03 6.3010e+03 6.3710e+03]'*1e3; +md.materials.density= [1.0750e4 1.0750e+04 4.9780e+03 3.8710e+03 3.4380e+03 3.0370e+03]'; +md.materials.lame_mu= [1e-5 0 2.2834e+00 1.0549e+00 7.0363e-01 5.0605e-01]'*1e11; +md.materials.viscosity=[0 0 2.0000e+00 1.0000e+00 1.0000e+00 1.0000e+25]'*1e21; +md.materials.lame_lambda=md.materials.lame_mu*0+5e17; +md.materials.issolid=[1 0 1 1 1 1]'; +md.materials.rheologymodel=zeros(md.materials.numlayers,1); +md.materials.burgers_mu=md.materials.lame_mu/3; +md.materials.burgers_viscosity=md.materials.viscosity/10; +md.materials.ebm_alpha= ones(md.materials.numlayers,1)*.9; +md.materials.ebm_delta= ones(md.materials.numlayers,1)*0.2; +md.materials.ebm_taul= ones(md.materials.numlayers,1)*54*60; %54min +md.materials.ebm_tauh= ones(md.materials.numlayers,1)*18.6*yts; %18.6yr + +md.love.allow_layer_deletion=1; +md.love.frequencies=[0]; +md.love.nfreq=length(md.love.frequencies); +md.love.sh_nmin=1; +md.love.sh_nmax=1000; +md.love.underflow_tol=1e-20; +md.love.pw_threshold=1e-3; +md.love.Gravitational_Constant=6.6732e-11; +md.love.integration_steps_per_layer=100; +md.love.allow_layer_deletion=1; +md.love.forcing_type=11; +md.love.chandler_wobble=0; +md.love.complex_computation=0; + +md.love.istemporal=1; +md.love.n_temporal_iterations=8; +md.love.time=[0; (logspace(0,4.3, 99))'*yts]; +md.love=md.love.build_frequencies_from_time; +md.love.love_kernels=1; +md.solidearth.lovenumbers.tk2secular= 0.9668; +md.solidearth.rotational.equatorialmoi=8.0131e37; +md.solidearth.rotational.polarmoi=8.0394e37; +md.solidearth.rotational.angularvelocity=7.292115e-5; + +md=solve(md,'lv'); + +h=md.results.LoveSolution.LoveHt; +l=md.results.LoveSolution.LoveLt; +k=md.results.LoveSolution.LoveKt; + +%Fields and tolerances to track changes +field_names ={'LoveH_loading_temporal','LoveK_loading_temporal','LoveL_loading_temporal'}; +field_tolerances={3.0e-7,3.0e-7,8.0e-8}; +field_values={h,k,l}; + +spada=0; +if (spada) + t=md.love.time/yts; + addpath ../Data/ + load spada.mat + load spada_n1.mat; + s_weak=[9 12 15]; + + hspada(:,s_weak)=[]; + kspada(:,s_weak)=[]; + lspada(:,s_weak)=[]; + + hts=zeros(length(t),257); + lts=zeros(length(t),257); + kts=zeros(length(t),257); + + d=1; + hts(:,d+1)=hspada_n1(2); + lts(:,d+1)=lspada_n1(2); + kts(:,d+1)=-1; + for mo=1:9 + hts(:,d+1)=hts(:,d+1)-hspada_n1(3+mo)./sspada_n1(1+mo).*(1-exp(t/1e3*sspada_n1(1+mo))); + lts(:,d+1)=lts(:,d+1)-lspada_n1(3+mo)./sspada_n1(1+mo).*(1-exp(t/1e3*sspada_n1(1+mo))); + end + + for d=2:256 + hts(:,d+1)=hspada(d-1,2); + lts(:,d+1)=lspada(d-1,2); + kts(:,d+1)=kspada(d-1,2); + for mo=1:9 + hts(:,d+1)=hts(:,d+1)-hspada(d-1,3+mo)./sspada(d-1,1+mo).*(1-exp(t/1e3*sspada(d-1,1+mo))); + lts(:,d+1)=lts(:,d+1)-lspada(d-1,3+mo)./sspada(d-1,1+mo).*(1-exp(t/1e3*sspada(d-1,1+mo))); + kts(:,d+1)=kts(:,d+1)-kspada(d-1,3+mo)./sspada(d-1,1+mo).*(1-exp(t/1e3*sspada(d-1,1+mo))); + end + end +end + +return + + +h=md.results.LoveSolution.LoveHt; +l=md.results.LoveSolution.LoveLt; +k=md.results.LoveSolution.LoveKt; +ht=h'; +lt=l'; +kt=k'; +th=md.results.LoveSolution.LoveTidalHt'; +tl=md.results.LoveSolution.LoveTidalLt'; +tk=md.results.LoveSolution.LoveTidalKt'; +tht=ht*0;tht(3,:)=th(3,:); +tkt=kt*0;tkt(3,:)=tk(3,:); +tlt=lt*0;tlt(3,:)=tl(3,:); +pmtf1=md.results.LoveSolution.LovePMTF1t(:,3)'; +pmtf2=md.results.LoveSolution.LovePMTF2t(:,3)'; +time=md.love.time/yts; + +save ../Data/lnb_temporal ht kt lt tht tkt tlt pmtf1 pmtf2 time; + Index: /issm/trunk/test/NightlyRun/test2072.m =================================================================== --- /issm/trunk/test/NightlyRun/test2072.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test2072.m (revision 27035) @@ -0,0 +1,70 @@ +%Test Name: ElasticLoveNumbers_HighlyLayeredEarth +%Forward Love number solution for a viscoelastic earth, model M3-L70-V01 from +%Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., Martinec, Z., +%Gasperini, P., Lund, B., Wolf, D., Vermeersen, L. L. A. and King, M. A. +%(2011), A benchmark study for glacial isostatic adjustment codes. Geophysical +%Journal International, 185: 106--132. doi:10.1111/j.1365-246X.2011.04952.x + +md=model(); +md.cluster=generic('name',oshostname(),'np',3); + +md.materials=materials('litho'); +md.miscellaneous.name='test2072'; +md.groundingline.migration='None'; + +md.verbose=verbose('all'); +md.verbose=verbose('1111111111111111'); +cst=365.25*24*3600*1000; + + +%Model VSS96 from Vermeersen, L.L.A., Sabadini, R. & Spada, G., 1996a. Analytical visco-elastic relaxation models, Geophys. Res. Lett., 23, 697–700. +md.materials.radius=[10, 1222.5, 3480., 3600., 3630.5, 3700., 3900., 4000., 4200., 4300., 4500., 4600., 4800., 4900., 5100., 5200., 5400., 5500., 5600.5, 5650., 5701., 5736., 5771.5, 5821., 5951., 5970.5, 6016., 6061., 6150.5, 6151.5, 6251., 6371.]'*1e3; +md.materials.lame_mu=[1e-5, 0., 2.933, 2.8990002, 2.8550003, 2.7340002, 2.675, 2.559, 2.502, 2.388, 2.331, 2.215, 2.157, 2.039, 1.979, 1.8560001, 1.794, 1.73, 1.639, 1.2390001, 1.224, 1.21, 1.128, 0.97700006, 0.906, 0.79, 0.773, 0.741, 0.656, 0.665, 0.602]'*1e11; +md.materials.density=[10925., 10925., 5506.42, 5491.45, 5456.57, 5357.06, 5307.24, 5207.13, 5156.69, 5054.69, 5002.99, 4897.83, 4844.22, 4734.6, 4678.44, 4563.07, 4503.72, 4443.16, 4412.41, 3992.14, 3983.99, 3975.84, 3912.82, 3786.78, 3723.78, 3516.39, 3489.51, 3435.78, 3359.5, 3367.1, 3184.3]'; +md.materials.viscosity=[0., 0., 7.999999999999999E+21, 8.5E+21, 8.999999999999999E+21, 3.E+22, 4.E+22, 5.0000000000000004E+22, 6.E+22, 5.0000000000000004E+22, 4.5E+22, 3.E+22, 2.5000000000000002E+22, 1.7999999999999998E+22, 1.3E+22, 7.999999999999999E+21, 6.999999999999999E+21, 6.5E+21, 6.E+21, 5.5E+21, 5.E+21, 4.4999999999999995E+21, 3.9999999999999995E+21, 2.5E+21, 1.9999999999999997E+21, 1.5E+21, 9.999999999999999E+20, 6.E+20, 5.5000000000000007E+20, 2.E+20, 1.E40]'; +md.materials.lame_lambda=md.materials.lame_mu*0+5e17; +md.materials.issolid=md.materials.lame_mu>0; +md.materials.numlayers=length(md.materials.lame_mu); +md.materials.burgers_mu=md.materials.lame_mu; +md.materials.burgers_viscosity=md.materials.viscosity; +md.materials.rheologymodel=md.materials.issolid*0; +md.materials.burgers_mu=md.materials.lame_mu/3; +md.materials.burgers_viscosity=md.materials.viscosity/10; +md.materials.ebm_alpha= ones(md.materials.numlayers,1)*.9; +md.materials.ebm_delta= ones(md.materials.numlayers,1)*0.2; +md.materials.ebm_taul= ones(md.materials.numlayers,1)*54*60; %54min +md.materials.ebm_tauh= ones(md.materials.numlayers,1)*18.6*cst/1e3; %18.6yr + +md.love.allow_layer_deletion=1; +md.love.frequencies=[0]; +md.love.nfreq=length(md.love.frequencies); +md.love.sh_nmin=1; +md.love.sh_nmax=256; +md.love.underflow_tol=1e-20; +md.love.pw_threshold=1e-3; +md.love.Gravitational_Constant=6.6732e-11; +md.love.integration_steps_per_layer=100; +md.love.allow_layer_deletion=1; +md.love.forcing_type=11; +md.love.chandler_wobble=0; +md.love.complex_computation=0; +md.love.istemporal=1; +md.love.n_temporal_iterations=8; +%md.love.time=[0; (logspace(-3,6, 202))'*cst]; +md.love.time=[0; 10.^([-3.0000e+00 -2.1045e+00 -1.2090e+00 -3.1343e-01 5.8209e-01 1.4776e+00 2.3731e+00 3.2687e+00 4.1642e+00 5.0597e+00 5.9552e+00])'*cst]; +md.love=md.love.build_frequencies_from_time; + +md.love.love_kernels=1; + +md=solve(md,'lv'); + +h=md.results.LoveSolution.LoveHt; +l=md.results.LoveSolution.LoveLt; +k=md.results.LoveSolution.LoveKt; + +%Fields and tolerances to track changes + +field_names ={'LoveH_loading_elastic','LoveK_loading_elastic','LoveL_loading_elastic'}; +field_tolerances={3.0e-6,1.0e-5,5.0e-7}; +field_values={h,k,l}; + Index: /issm/trunk/test/NightlyRun/test2084.m =================================================================== --- /issm/trunk/test/NightlyRun/test2084.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2084.m (revision 27035) @@ -7,7 +7,7 @@ md=model(); -md.cluster=generic('name',oshostname(),'np',1); +md.cluster=generic('name',oshostname(),'np',8); -% set validation=1 for comparing against the Spada benchark. +% set validation=1 for comparing against the Spada benchmark. validation=0; @@ -17,4 +17,5 @@ md.verbose=verbose('all'); +md.verbose=verbose('1111111111111111'); cst=365.25*24*3600*1000; @@ -36,16 +37,23 @@ md.love.allow_layer_deletion=1; -md.love.frequencies=([0]*2*pi)'/cst; +md.love.frequencies=[0; (logspace(-6,3, 1000))'/cst]; md.love.nfreq=length(md.love.frequencies); md.love.sh_nmin=1; -md.love.sh_nmax=256; +md.love.sh_nmax=1000; md.love.underflow_tol=1e-20; +md.love.pw_threshold=1e-3; md.love.Gravitational_Constant=6.6732e-11; -md.love.integration_steps_per_layer=200; +md.love.integration_steps_per_layer=100; +md.love.allow_layer_deletion=1; +md.love.forcing_type=11; +md.love.chandler_wobble=0; +md.love.complex_computation=0; md.love.istemporal=1; md.love.n_temporal_iterations=8; -%md.love.time=(logspace(-4,5, 2))'*cst; -md.love.time=(logspace(-1,2, 50))'*cst; +%md.love.time=(logspace(-6,5, 2))'*cst; +md.love.time=[0; (logspace(-3,5, 24))'*cst]; + +%md.love.time=(linspace(1/12,10, 10*12))'*cst/1e3; md.love.love_kernels=1; if md.love.istemporal @@ -55,7 +63,7 @@ md=solve(md,'lv'); -ht2=md.results.LoveSolution.LoveHr; -lt2=md.results.LoveSolution.LoveLr; -kt2=md.results.LoveSolution.LoveKr; +ht=md.results.LoveSolution.LoveHt'; +lt=md.results.LoveSolution.LoveLt'; +kt=md.results.LoveSolution.LoveKt'; t=md.love.time/cst*1e3; @@ -69,8 +77,83 @@ field_tolerances={2.0e-8,2.0e-8,2.0e-8}; field_values={... - (md.results.LoveSolution.LoveHr(:,1)),... - (md.results.LoveSolution.LoveKr(:,1)),... - (md.results.LoveSolution.LoveLr(:,1)),... + (md.results.LoveSolution.LoveHt(:,1)),... + (md.results.LoveSolution.LoveKt(:,1)),... + (md.results.LoveSolution.LoveLt(:,1)),... }; + +return + +if false +addpath('../../../../invGIA/Spada_benchmark/') +load spada.mat +s_weak=[9 12 15]; + +hspada(:,s_weak)=[]; +kspada(:,s_weak)=[]; +lspada(:,s_weak)=[]; + +hts=zeros(length(t),md.love.sh_nmax+1); +lts=zeros(length(t),md.love.sh_nmax+1); +kts=zeros(length(t),md.love.sh_nmax+1); +for d=max(2,md.love.sh_nmin):md.love.sh_nmax +hts(:,d+1)=hspada(d-1,2); +lts(:,d+1)=lspada(d-1,2); +kts(:,d+1)=kspada(d-1,2); +for mo=1:9 +hts(:,d+1)=hts(:,d+1)-hspada(d-1,3+mo)./sspada(d-1,1+mo).*(1-exp(t/1e3*sspada(d-1,1+mo))); +lts(:,d+1)=lts(:,d+1)-lspada(d-1,3+mo)./sspada(d-1,1+mo).*(1-exp(t/1e3*sspada(d-1,1+mo))); +kts(:,d+1)=kts(:,d+1)-kspada(d-1,3+mo)./sspada(d-1,1+mo).*(1-exp(t/1e3*sspada(d-1,1+mo))); +end +end +close all + +if md.love.sh_nmin==md.love.sh_nmax +subplot(2,3,1) +plot(t/cst*1e3,ht(:,md.love.sh_nmin+1),'x-',t/cst*1e3,hts); +set(gca, 'xscale', 'log'); shading flat; +title('h') + +subplot(2,3,2) +plot(t/cst*1e3,lt(:,md.love.sh_nmin+1),'x-',t/cst*1e3,lts); +set(gca, 'xscale', 'log'); shading flat; +title('l') + +subplot(2,3,3) +plot(t/cst*1e3,kt(:,md.love.sh_nmin+1),'x-',t/cst*1e3,kts); +set(gca, 'xscale', 'log'); shading flat; +title('k') + +subplot(2,3,4) +plot(t/cst*1e3,log10(abs((ht-hts)./hts))'); +set(gca, 'xscale', 'log'); shading flat; + +subplot(2,3,5) +plot(t/cst*1e3,log10(abs((lt-lts)./lts))'); +set(gca, 'xscale', 'log'); shading flat; +title('l') + +subplot(2,3,6) +plot(t/cst*1e3,log10(abs((kt-kts)./kts))'); +set(gca, 'xscale', 'log'); shading flat; +title('k') +else + +[T,N]=meshgrid(t/cst*1e3,0:md.love.sh_nmax); +subplot(1,3,1) +pcolor(T,N,log10(abs((ht-hts)./hts))'); +set(gca, 'xscale', 'log'); shading flat;colorbar; +title('h') + +subplot(1,3,2) +pcolor(T,N,log10(abs((lt-lts)./lts))'); +set(gca, 'xscale', 'log'); shading flat;colorbar; +title('l') + +subplot(1,3,3) +pcolor(T,N,log10(abs((kt-kts)./kts))'); +set(gca, 'xscale', 'log'); shading flat;colorbar; +title('k') +end + % validate elastic loading solutions against the Spada benchmark. {{{ @@ -100,147 +183,5 @@ % end + +end % }}} - -md.love.frequencies=([1e-3 1e-2 1e-1 1 -1e-3 -1e-2 -1e-1 -1]*2*pi)'/cst; -md.love.nfreq=length(md.love.frequencies); -md.love.sh_nmax=256; -md.materials.burgers_mu=md.materials.lame_mu; -md.materials.burgers_viscosity=md.materials.viscosity; - -md=solve(md,'lv'); - -%Fields and tolerances to track changes -field_names ={field_names{:},'LoveH_loading_realpart','LoveK_loading_realpart','LoveL_loading_realpart','LoveH_loading_imagpart','LoveK_loading_imagpart','LoveL_loading_imagpart'}; -field_tolerances={field_tolerances{:},5e-7,5e-7,5e-7,5e-7,5e-7,5e-7}; -field_values={field_values{:},... - (md.results.LoveSolution.LoveHr(:,:)),... - (md.results.LoveSolution.LoveKr(:,:)),... - (md.results.LoveSolution.LoveLr(:,:)),... - (md.results.LoveSolution.LoveHi(:,:)),... - (md.results.LoveSolution.LoveKi(:,:)),... - (md.results.LoveSolution.LoveLi(:,:)),... - }; - -md.love.forcing_type=9; -md.love.sh_nmin=2; -md.love.frequencies=([0 1e-3 1e-2 1e-1 1 -1e-3 -1e-2 -1e-1 -1]*2*pi)'/cst; -md.love.nfreq=length(md.love.frequencies); -md=solve(md,'lv'); - -% validate elastic tidal solutions against the Spada benchmark. {{{ -if validation - spada_solutions = load('spada_elastic_tidal_deg_h_l_k'); - spada_d = spada_solutions(:,1); - spada_h = spada_solutions(:,2); - spada_l = spada_solutions(:,3); - spada_k = spada_solutions(:,4); - - %rename ISSM solutions. - issm_d = [2:md.love.sh_nmax]; - issm_h = md.results.LoveSolution.LoveHr(3:end,1); - issm_l = md.results.LoveSolution.LoveLr(3:end,1); - issm_k = md.results.LoveSolution.LoveKr(3:end,1); - - % relative difference for each degree, except for zero and one. - diff_h = 1 - issm_h./spada_h; - diff_l = 1 - issm_l./spada_l; - diff_k = 1 - issm_k./spada_k; - - % k seems to have larger relative difference at higher degrees, although values approach zero. - figure - plot(spada_d,issm_k./spada_k); - - figure - plot(spada_d,[diff_h diff_l diff_k]); grid on; - legend('h','l','k'); title('tidal love'); -else - % -end -% }}} - -%tidal love numbers -field_names ={field_names{:},'LoveH_tidal_elastic','LoveK_tidal_elastic','LoveL_tidal_elastic','LoveH_tidal_realpart','LoveK_tidal_realpart','LoveL_tidal_realpart','LoveH_tidal_imagpart','LoveK_tidal_imagpart','LoveL_tidal_imagpart'}; -field_tolerances={field_tolerances{:},8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6}; -field_values={field_values{:},... - (md.results.LoveSolution.LoveHr(:,1)),... - (md.results.LoveSolution.LoveKr(:,1)),... - (md.results.LoveSolution.LoveLr(:,1)),... - (md.results.LoveSolution.LoveHr(:,2:end)),... - (md.results.LoveSolution.LoveKr(:,2:end)),... - (md.results.LoveSolution.LoveLr(:,2:end)),... - (md.results.LoveSolution.LoveHi(:,2:end)),... - (md.results.LoveSolution.LoveKi(:,2:end)),... - (md.results.LoveSolution.LoveLi(:,2:end)),... - }; - -%Many layers PREM-based model -%data=load('../Data/PREM_500layers'); -%md.love.sh_nmin=1; -%md.materials.radius=data(2:end-2,1); -%md.materials.density=data(3:end-2,2); -%md.materials.lame_lambda=data(3:end-2,3); -%md.materials.lame_mu=data(3:end-2,4); -%md.materials.issolid=data(3:end-2,4)>0; -%ind=find(md.materials.issolid==0); -%md.materials.density(ind(1))=sum((md.materials.radius(ind+1).^3-md.materials.radius(ind).^3).*md.materials.density(ind))/(md.materials.radius(ind(end)+1).^3-md.materials.radius(ind(1)+1).^3); -%md.materials.lame_lambda(ind(1))=sum((md.materials.radius(ind+1).^3-md.materials.radius(ind).^3).*md.materials.lame_lambda(ind))/(md.materials.radius(ind(end)+1).^3-md.materials.radius(ind(1)+1).^3); -%md.materials.lame_mu(ind(1))=sum((md.materials.radius(ind+1).^3-md.materials.radius(ind).^3).*md.materials.lame_mu(ind))/(md.materials.radius(ind(end)+1).^3-md.materials.radius(ind(1)).^3); -%md.materials.radius(ind(2:end)+1)=[]; -%md.materials.density(ind(2:end))=[]; -%md.materials.lame_lambda(ind(2:end))=[]; -%md.materials.lame_mu(ind(2:end))=[]; -%md.materials.issolid(ind(2:end))=[]; -%md.materials.viscosity=10.^interp1([0 3479e3 3480e3 3680e3 5720e3 5800e3 6270e3 6371e3], log10([1e8 1e8 5e21 1e23 1e22 1e20 1e21 1e40]), md.materials.radius(2:end),'PCHIP'); -%md.materials.viscosity=md.materials.viscosity.*md.materials.issolid; -%md.materials.burgers_mu=md.materials.lame_mu; -%md.materials.burgers_viscosity=md.materials.viscosity; -%md.materials.rheologymodel=md.materials.issolid*0; -%md.love.forcing_type=11; -%md.materials.numlayers=length(md.materials.viscosity); -%md=solve(md,'lv'); -% -%field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; -%field_tolerances={field_tolerances{:},2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6}; -%field_values={field_values{:},... -% (md.results.LoveSolution.LoveHr(:,1)),... -% (md.results.LoveSolution.LoveKr(:,1)),... -% (md.results.LoveSolution.LoveLr(:,1)),... -% (md.results.LoveSolution.LoveHr(:,2:end)),... -% (md.results.LoveSolution.LoveKr(:,2:end)),... -% (md.results.LoveSolution.LoveLr(:,2:end)),... -% (md.results.LoveSolution.LoveHi(:,2:end)),... -% (md.results.LoveSolution.LoveKi(:,2:end)),... -% (md.results.LoveSolution.LoveLi(:,2:end)),... -% }; - -%Model VSS96 from Vermeersen, L.L.A., Sabadini, R. & Spada, G., 1996a. Analytical visco-elastic relaxation models, Geophys. Res. Lett., 23, 697–700. -md.materials.radius=[10, 1222.5, 3480., 3600., 3630.5, 3700., 3900., 4000., 4200., 4300., 4500., 4600., 4800., 4900., 5100., 5200., 5400., 5500., 5600.5, 5650., 5701., 5736., 5771.5, 5821., 5951., 5970.5, 6016., 6061., 6150.5, 6151.5, 6251., 6371.]'*1e3; -md.materials.lame_mu=[1e-5, 0., 2.933, 2.8990002, 2.8550003, 2.7340002, 2.675, 2.559, 2.502, 2.388, 2.331, 2.215, 2.157, 2.039, 1.979, 1.8560001, 1.794, 1.73, 1.639, 1.2390001, 1.224, 1.21, 1.128, 0.97700006, 0.906, 0.79, 0.773, 0.741, 0.656, 0.665, 0.602]'*1e11; -md.materials.density=[10925., 10925., 5506.42, 5491.45, 5456.57, 5357.06, 5307.24, 5207.13, 5156.69, 5054.69, 5002.99, 4897.83, 4844.22, 4734.6, 4678.44, 4563.07, 4503.72, 4443.16, 4412.41, 3992.14, 3983.99, 3975.84, 3912.82, 3786.78, 3723.78, 3516.39, 3489.51, 3435.78, 3359.5, 3367.1, 3184.3]'; -md.materials.viscosity=[0., 0., 7.999999999999999E+21, 8.5E+21, 8.999999999999999E+21, 3.E+22, 4.E+22, 5.0000000000000004E+22, 6.E+22, 5.0000000000000004E+22, 4.5E+22, 3.E+22, 2.5000000000000002E+22, 1.7999999999999998E+22, 1.3E+22, 7.999999999999999E+21, 6.999999999999999E+21, 6.5E+21, 6.E+21, 5.5E+21, 5.E+21, 4.4999999999999995E+21, 3.9999999999999995E+21, 2.5E+21, 1.9999999999999997E+21, 1.5E+21, 9.999999999999999E+20, 6.E+20, 5.5000000000000007E+20, 2.E+20, 1.E40]'; -md.materials.lame_lambda=md.materials.lame_mu*0+5e14; -md.materials.issolid=md.materials.lame_mu>0; -md.materials.numlayers=length(md.materials.lame_mu); -md.materials.burgers_mu=md.materials.lame_mu; -md.materials.burgers_viscosity=md.materials.viscosity; -md.materials.rheologymodel=md.materials.issolid*0; -md.love.forcing_type=11; -md.love.sh_nmin=1; -md.love.sh_nmax=100; -md=solve(md,'lv'); -md.love.frequencies=([0 1e-3 1e-2 1 -1e-3 -1e-2 -1]*2*pi)'/cst; -md.love.nfreq=length(md.love.frequencies); - -field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; -field_tolerances={field_tolerances{:},2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6}; -field_values={field_values{:},... - (md.results.LoveSolution.LoveHr(:,1)),... - (md.results.LoveSolution.LoveKr(:,1)),... - (md.results.LoveSolution.LoveLr(:,1)),... - (md.results.LoveSolution.LoveHr(:,2:end)),... - (md.results.LoveSolution.LoveKr(:,2:end)),... - (md.results.LoveSolution.LoveLr(:,2:end)),... - (md.results.LoveSolution.LoveHi(:,2:end)),... - (md.results.LoveSolution.LoveKi(:,2:end)),... - (md.results.LoveSolution.LoveLi(:,2:end)),... - }; Index: /issm/trunk/test/NightlyRun/test2084.py =================================================================== --- /issm/trunk/test/NightlyRun/test2084.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2084.py (revision 27035) @@ -15,7 +15,7 @@ md = model() -md.cluster = generic('name', gethostname(), 'np', 1) +md.cluster = generic('name', gethostname(), 'np', 8) -# Set validation=1 for comparing against the Spada benchark +# Set validation=1 for comparing against the Spada benchmark validation = 0 @@ -25,4 +25,5 @@ md.verbose = verbose('all') +md.verbose = verbose('1111111111111111') cst = 365.25 * 24 * 3600 * 1000 @@ -48,199 +49,46 @@ md.love.allow_layer_deletion = 1 -md.love.frequencies = (np.array([0]) * 2 * np.pi).reshape(-1, 1) / cst +md.love.frequencies = np.vstack(([0], np.logspace(-6, 3, 1000).reshape(-1, 1) / cst)) md.love.nfreq = len(md.love.frequencies) md.love.sh_nmin = 1 -md.love.sh_nmax = 256 +md.love.sh_nmax = 1000 md.love.underflow_tol = 1e-20 +md.love.pw_threshold = 1e-3 md.love.Gravitational_Constant = 6.6732e-11 -md.love.integration_steps_per_layer = 200 +md.love.integration_steps_per_layer = 100 +md.love.allow_layer_deletion = 1 +md.love.forcing_type = 11 +md.love.chandler_wobble = 0 +md.love.complex_computation = 0 md.love.istemporal = 1 md.love.n_temporal_iterations = 8 -#md.love.time = np.logspace(-4, 5, 2).reshape(-1, 1) * cst -md.love.time = np.logspace(-1, 2, 50).reshape(-1, 1) * cst +#md.love.time = np.logspace(-6, 5, 2).reshape(-1, 1) * cst +md.love.time = np.vstack(([0], np.logspace(-3, 5, 24).reshape(-1, 1) * cst)) + +#md.love.time = np.linspace(1/12, 10, 10 * 12).reshape(-1, 1) * cst / 1e3 md.love.love_kernels = 1 if md.love.istemporal: - md.love = md.love.build_frequencies_from_time + md.love = md.love.build_frequencies_from_time() md = solve(md, 'lv') -ht2 = md.results.LoveSolution.LoveHr -lt2 = md.results.LoveSolution.LoveLr -kt2 = md.results.LoveSolution.LoveKr +ht = md.results.LoveSolution.LoveHt.reshape(-1, 1) +lt = md.results.LoveSolution.LoveLt.reshape(-1, 1) +kt = md.results.LoveSolution.LoveKt.reshape(-1, 1) t = md.love.time / cst * 1e3 -#Fields and tolerances to track changes -#loading love numbers +# Fields and tolerances to track changes +# loading love numbers field_names = ['LoveH_loading_elastic', 'LoveK_loading_elastic', 'LoveL_loading_elastic'] field_tolerances = [2.0e-8, 2.0e-8, 2.0e-8] field_values = [ - np.array(md.results.LoveSolution.LoveHr)[:, 0], - np.array(md.results.LoveSolution.LoveKr)[:, 0], - np.array(md.results.LoveSolution.LoveLr)[:, 0] + np.array(md.results.LoveSolution.LoveHt)[:, 0], + np.array(md.results.LoveSolution.LoveKt)[:, 0], + np.array(md.results.LoveSolution.LoveLt)[:, 0] ] - -# Validate elastic loading solutions against the Spada benchmark {{{ # TODO: # - Implement read from file and comparison # - Implement plot -# - -#}}} - -md.love.frequencies = (np.array([1e-3, 1e-2, 1e-1, 1, -1e-3, -1e-2, -1e-1, -1]) * 2 * np.np.pi).reshape(-1, 1) / cst -md.love.nfreq = len(md.love.frequencies) -md.love.sh_nmax = 256 -md.materials.burgers_mu = md.materials.lame_mu -md.materials.burgers_viscosity = md.materials.viscosity - -md = solve(md, 'lv') - -#Fields and tolerances to track changes -field_names += ['LoveH_loading_realpart', 'LoveK_loading_realpart', 'LoveL_loading_realpart', 'LoveH_loading_imagpart', 'LoveK_loading_imagpart', 'LoveL_loading_imagpart'] -field_tolerances += [5e-7, 5e-7, 5e-7, 5e-7, 5e-7, 5e-7] -field_values += [ - np.array(md.results.LoveSolution.LoveHr), - np.array(md.results.LoveSolution.LoveKr), - np.array(md.results.LoveSolution.LoveLr), - np.array(md.results.LoveSolution.LoveHi), - np.array(md.results.LoveSolution.LoveKi), - np.array(md.results.LoveSolution.LoveLi) -] - -md.love.forcing_type = 9 -md.love.sh_nmin = 2 -md.love.frequencies = ((np.array([0, 1e-3, 1e-2, 1e-1, 1, -1e-3, -1e-2, -1e-1, -1]) * 2 * np.pi).reshape(-1, 1) / cst) -md.love.nfreq = len(md.love.frequencies) -md = solve(md, 'lv') - -# Validate elastic tidal solutions against the Spada benchmark #{{{ - -# TODO: -# - Implement read from file and comparison -# - Implement plot -# - -#}}} - -#tidal love numbers, check -field_names += ['LoveH_tidal_elastic', 'LoveK_tidal_elastic', 'LoveL_tidal_elastic', 'LoveH_tidal_realpart', 'LoveK_tidal_realpart', 'LoveL_tidal_realpart', 'LoveH_tidal_imagpart', 'LoveK_tidal_imagpart', 'LoveL_tidal_imagpart'] -field_tolerances += [8e-6, 8e-6, 8e-6, 8e-6, 8e-6, 8e-6, 8e-6, 8e-6, 8e-6] -field_values += [ - np.array(md.results.LoveSolution.LoveHr)[:, 0], - np.array(md.results.LoveSolution.LoveKr)[:, 0], - np.array(md.results.LoveSolution.LoveLr)[:, 0], - np.array(md.results.LoveSolution.LoveHr)[:, 1:], - np.array(md.results.LoveSolution.LoveKr)[:, 1:], - np.array(md.results.LoveSolution.LoveLr)[:, 1:], - np.array(md.results.LoveSolution.LoveHi)[:, 1:], - np.array(md.results.LoveSolution.LoveKi)[:, 1:], - np.array(md.results.LoveSolution.LoveLi)[:, 1:] -] - -# Many layers PREM-based model -#data = load('../Data/PREM_500layers') -#md.love.sh_nmin = 1 -#md.materials.radius = data(2:end - 2, 1) -#md.materials.density = data(3:end - 2, 2) -#md.materials.lame_lambda = data(3:end - 2, 3) -#md.materials.lame_mu = data(3:end - 2, 4) -#md.materials.issolid = data(3:end - 2, 4) > 0 -#ind = find(md.materials.issolid = 0) -#md.materials.density(ind(1))=sum((md.materials.radius(ind + 1).^3 - md.materials.radius(ind).^3). * md.materials.density(ind)) / (md.materials.radius(ind(end) + 1).^3 - md.materials.radius(ind(1) + 1).^3) -#md.materials.lame_lambda(ind(1))=sum((md.materials.radius(ind + 1).^3 - md.materials.radius(ind).^3). * md.materials.lame_lambda(ind)) / (md.materials.radius(ind(end) + 1).^3 - md.materials.radius(ind(1) + 1).^3) -#md.materials.lame_mu(ind(1))=sum((md.materials.radius(ind + 1).^3 - md.materials.radius(ind).^3). * md.materials.lame_mu(ind)) / (md.materials.radius(ind(end) + 1).^3 - md.materials.radius(ind(1)).^3) -#md.materials.radius(ind(2:end) + 1) = [] -#md.materials.density(ind(2:end)) = [] -#md.materials.lame_lambda(ind(2:end)) = [] -#md.materials.lame_mu(ind(2:end)) = [] -#md.materials.issolid(ind(2:end)) = [] -#md.materials.viscosity = 10.^interp1([0 3479e3 3480e3 3680e3 5720e3 5800e3 6270e3 6371e3], log10([1e8 1e8 5e21 1e23 1e22 1e20 1e21 1e40]), md.materials.radius(2:end), 'PCHIP') -#md.materials.viscosity = md.materials.viscosity. * md.materials.issolid -#md.materials.burgers_mu = md.materials.lame_mu -#md.materials.burgers_viscosity = md.materials.viscosity -#md.materials.rheologymodel = md.materials.issolid * 0 -#md.love.forcing_type = 11 -#md.materials.numlayers = len(md.materials.viscosity) -#md = solve(md, 'lv') -# -#field_names = [field_names, 'LoveH_loadingVSS96_elastic', 'LoveK_loadingVSS96_elastic', 'LoveL_loadingVSS96_elastic', 'LoveH_loadingVSS96_realpart', 'LoveK_loadingVSS96_realpart', 'LoveL_loadingVSS96_realpart', 'LoveH_loadingVSS96_imagpart', 'LoveK_loadingVSS96_imagpart', 'LoveL_loadingVSS96_imagpart'] -#field_tolerances = [field_tolerances, 4.3e-9, 4.3e-9, 4.3e-9, 4.3e-9, 4.3e-9, 4.3e-9, 4.3e-9, 4.3e-9, 4.3e-9] -#field_values = [field_values, -# (md.results.LoveSolution.LoveHr[:][0]), -# (md.results.LoveSolution.LoveKr[:][0]), -# (md.results.LoveSolution.LoveLr[:][0]), -# (md.results.LoveSolution.LoveHr[:][1:]), -# (md.results.LoveSolution.LoveKr[:][1:]), -# (md.results.LoveSolution.LoveLr[:][1:]), -# (md.results.LoveSolution.LoveHi[:][1:]), -# (md.results.LoveSolution.LoveKi[:][1:]), -# (md.results.LoveSolution.LoveLi[:][1:]), -# ] - -# Model VSS96 from Vermeersen, L.L.A., Sabadini, R. & Spada, G., 1996a. Analytical visco-elastic relaxation models, Geophys. Res. Lett., 23, 697-700. -md.materials.radius = np.array([10, 1222.5, 3480., 3600., 3630.5, 3700., 3900., 4000., - 4200., 4300., 4500., 4600., 4800., 4900., 5100., 5200., - 5400., 5500., 5600.5, 5650., 5701., 5736., 5771.5, - 5821., 5951., 5970.5, 6016., 6061., 6150.5, 6151.5, - 6251., 6371.]).reshape(-1, 1) * 1e3 -md.materials.lame_mu = np.array([1e-5, 0., 2.933, 2.8990002, 2.8550003, 2.7340002, 2.675, - 2.559, 2.502, 2.388, 2.331, 2.215, 2.157, 2.039, 1.979, - 1.8560001, 1.794, 1.73, 1.639, 1.2390001, 1.224, 1.21, - 1.128, 0.97700006, 0.906, 0.79, 0.773, 0.741, 0.656, 0.665, - 0.602]).reshape(-1, 1) * 1e11 -md.materials.density = np.array([10925., 10925., 5506.42, 5491.45, 5456.57, 5357.06, - 5307.24, 5207.13, 5156.69, 5054.69, 5002.99, 4897.83, - 4844.22, 4734.6, 4678.44, 4563.07, 4503.72, 4443.16, - 4412.41, 3992.14, 3983.99, 3975.84, 3912.82, 3786.78, - 3723.78, 3516.39, 3489.51, 3435.78, 3359.5, 3367.1, - 3184.3]).reshape(-1, 1) -md.materials.viscosity = np.array([0., 0., 7.999999999999999e+21, 8.5e+21, - 8.999999999999999e+21, 3.e+22, 4.e+22, - 5.0000000000000004e+22, 6.e+22, - 5.0000000000000004e+22, 4.5e+22, 3.e+22, - 2.5000000000000002e+22, 1.7999999999999998e+22, - 1.3e+22, 7.999999999999999e+21, 6.999999999999999e+21, - 6.5e+21, 6.e+21, 5.5e+21, 5.e+21, 4.4999999999999995e+21, - 3.9999999999999995e+21, 2.5e+21, - 1.9999999999999997e+21, 1.5e+21, 9.999999999999999e+20, - 6.e+20, 5.5000000000000007e+20, 2.e+20, - 1.E40]).reshape(-1, 1) -md.materials.lame_lambda = np.array(md.materials.lame_mu) * 0 + 5e14 -md.materials.issolid = np.ones(len(md.materials.lame_mu)).reshape(-1, 1) -md.materials.issolid[1] = 0 -md.materials.numlayers = len(md.materials.lame_mu) -md.materials.burgers_mu = md.materials.lame_mu -md.materials.burgers_viscosity = md.materials.viscosity -md.materials.rheologymodel = md.materials.issolid * 0 -md.love.forcing_type = 11 -md.love.sh_nmin = 1 -md.love.sh_nmax = 100 -md = solve(md, 'lv') -md.love.frequencies = (np.array([0, 1e-3, 1e-2, 1, -1e-3, -1e-2, -1]) * 2 * np.pi).reshape(-1, 1) / cst -md.love.nfreq = len(md.love.frequencies) - -field_names += [ - 'LoveH_loadingVSS96_elastic', - 'LoveK_loadingVSS96_elastic', - 'LoveL_loadingVSS96_elastic', - 'LoveH_loadingVSS96_realpart', - 'LoveK_loadingVSS96_realpart', - 'LoveL_loadingVSS96_realpart', - 'LoveH_loadingVSS96_imagpart', - 'LoveK_loadingVSS96_imagpart', - 'LoveL_loadingVSS96_imagpart' -] -field_tolerances += [2e-6, 2e-6, 2e-6, 2e-6, 2e-6, 2e-6, 2e-6, 2e-6, 2e-6] -field_values += [ - np.array(md.results.LoveSolution.LoveHr)[:, 0], - np.array(md.results.LoveSolution.LoveKr)[:, 0], - np.array(md.results.LoveSolution.LoveLr)[:, 0], - np.array(md.results.LoveSolution.LoveHr)[:, 1:], - np.array(md.results.LoveSolution.LoveKr)[:, 1:], - np.array(md.results.LoveSolution.LoveLr)[:, 1:], - np.array(md.results.LoveSolution.LoveHi)[:, 1:], - np.array(md.results.LoveSolution.LoveKi)[:, 1:], - np.array(md.results.LoveSolution.LoveLi)[:, 1:] -] +# - Implement validation of elastic loading solutions against the Spada benchmark Index: /issm/trunk/test/NightlyRun/test2085.m =================================================================== --- /issm/trunk/test/NightlyRun/test2085.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2085.m (revision 27035) @@ -8,65 +8,75 @@ % for volumetric potential - md=model(); - - md.materials=materials('litho'); - - md.materials.numlayers = 40; - md.love.forcing_type = 9; - - md.materials.density=zeros(md.materials.numlayers,1)+5511; - md.materials.lame_mu=zeros(md.materials.numlayers,1)+0.75e11; - md.materials.viscosity=zeros(md.materials.numlayers,1)+1e21; - md.materials.lame_lambda=zeros(md.materials.numlayers,1)+5e17; - md.materials.issolid=ones(md.materials.numlayers,1); - md.materials.isburgers=zeros(md.materials.numlayers,1); - md.materials.burgers_mu=md.materials.lame_mu/3; - md.materials.burgers_viscosity=md.materials.viscosity/10; - - md.materials.radius = linspace(10e3,6371e3,md.materials.numlayers+1)'; - md.love.g0 = 9.8134357285509388; % directly grabbed from fourierlovesolver for this particular case. - - md.love.allow_layer_deletion=1; - md.love.frequencies=0; - md.love.nfreq=length(md.love.frequencies); % TODO: Why are we grabbing length of a scalar here? - - md.love.sh_nmin = 2; - md.love.sh_nmax = 200; - md.love.love_kernels=1; - - md.miscellaneous.name='kernels'; - md.cluster=generic('name',oshostname(),'np',1); - md.verbose=verbose('111111101'); - - md=solve(md,'lv'); - - % save yi's for all layers except for the inner-most one, at select degrees. - degrees = [2 20 200]; % we archive solutions for degrees 2, 20, 200 - - % extract love kernels {{{ - % degree 2. - y1_tidal_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,1))); - y2_tidal_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,2))); - y3_tidal_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,3))); - y4_tidal_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,4))); - y5_tidal_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,5))); - y6_tidal_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,6))); - - % degree 20. - y1_tidal_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,1))); - y2_tidal_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,2))); - y3_tidal_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,3))); - y4_tidal_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,4))); - y5_tidal_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,5))); - y6_tidal_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,6))); - - % degree 200. - y1_tidal_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,1))); - y2_tidal_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,2))); - y3_tidal_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,3))); - y4_tidal_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,4))); - y5_tidal_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,5))); - y6_tidal_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,6))); - % }}} +md=model(); +md.groundingline.migration='None'; + +md.materials=materials('litho'); +cst=365.25*24*3600*1000; + +md.materials.numlayers = 40; +md.love.forcing_type = 9; + +md.materials.density=zeros(md.materials.numlayers,1)+5511; +md.materials.lame_mu=zeros(md.materials.numlayers,1)+0.75e11; +md.materials.lame_lambda=zeros(md.materials.numlayers,1)+5e17; +md.materials.issolid=ones(md.materials.numlayers,1); +md.materials.rheologymodel=zeros(md.materials.numlayers,1); + +%the following isn't used here but needs to have arrays of consistent size with the rest of the materials +md.materials.viscosity=zeros(md.materials.numlayers,1)+1e21; +md.materials.burgers_mu=md.materials.lame_mu/3; +md.materials.burgers_viscosity=md.materials.viscosity/10; +md.materials.ebm_alpha= ones(md.materials.numlayers,1)*0.9; +md.materials.ebm_delta= ones(md.materials.numlayers,1)*0.2; +md.materials.ebm_taul= ones(md.materials.numlayers,1)*54*60; %54min +md.materials.ebm_tauh= ones(md.materials.numlayers,1)*18.6*cst/1e3; %18.6yr + +md.materials.radius = linspace(10e3,6371e3,md.materials.numlayers+1)'; +md.love.g0 = 9.8134357285509388; % directly grabbed from fourierlovesolver for this particular case. + +md.love.allow_layer_deletion=1; +md.love.frequencies=0; +md.love.nfreq=1; +md.love.istemporal=0; + +md.love.sh_nmin = 2; +md.love.sh_nmax = 200; +md.love.love_kernels=1; + +md.miscellaneous.name='kernels'; +md.cluster=generic('name',oshostname(),'np',3); +md.verbose=verbose('111111101'); + +md=solve(md,'lv'); + +% save yi's for all layers except for the inner-most one, at select degrees. +degrees = [2 20 200]; % we archive solutions for degrees 2, 20, 200 +kernels=reshape(md.results.LoveSolution.LoveKernels, [md.love.sh_nmax+1 md.love.nfreq md.materials.numlayers+1 6]); + +% extract love kernels {{{ +% degree 2. +y1_tidal_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,1)); +y2_tidal_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,2)); +y3_tidal_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,3)); +y4_tidal_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,4)); +y5_tidal_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,5)); +y6_tidal_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,6)); + +% degree 20. +y1_tidal_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,1)); +y2_tidal_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,2)); +y3_tidal_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,3)); +y4_tidal_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,4)); +y5_tidal_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,5)); +y6_tidal_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,6)); + +% degree 200. +y1_tidal_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,1)); +y2_tidal_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,2)); +y3_tidal_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,3)); +y4_tidal_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,4)); +y5_tidal_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,5)); +y6_tidal_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,6)); +% }}} % validate tidal potential solutions against the analytic solutions. {{{ @@ -100,10 +110,11 @@ depth = (max(param.radius)-param.radius)/1000; % km. - y1 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,1))); - y2 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,2))); - y3 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,3))); - y4 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,4))); - y5 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,5))); - y6 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,6))); + kernels=reshape(md.results.LoveSolution.LoveKernels, [md.love.sh_nmax+1 md.love.nfreq md.materials.numlayers+1 6]); + y1 = squeeze(kernels(:,1,:,1)); + y2 = squeeze(kernels(:,1,:,2)); + y3 = squeeze(kernels(:,1,:,3)); + y4 = squeeze(kernels(:,1,:,4)); + y5 = squeeze(kernels(:,1,:,5)); + y6 = squeeze(kernels(:,1,:,6)); set(0,'DefaultAxesFontSize',16,'DefaultTextFontSize',15,'DefaultAxesLineWidth',1,... @@ -165,5 +176,4 @@ legend(axes6,'n=2','n=4','n=8','n=16','n=32'); %export_fig('/Users/adhikari/issm/trunk-jpl/src/m/contrib/adhikari/issm_vs_analytic_loading_homogeneous.pdf'); - else % @@ -172,33 +182,33 @@ % for surface load. - - md.love.forcing_type = 11; - md=solve(md,'lv'); - - % extract love kernels {{{ - % degree 2. - y1_loading_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,1))); - y2_loading_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,2))); - y3_loading_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,3))); - y4_loading_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,4))); - y5_loading_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,5))); - y6_loading_degree002 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(1)+1,1,2:end,6))); - - % degree 20. - y1_loading_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,1))); - y2_loading_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,2))); - y3_loading_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,3))); - y4_loading_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,4))); - y5_loading_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,5))); - y6_loading_degree020 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(2)+1,1,2:end,6))); - - % degree 200. - y1_loading_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,1))); - y2_loading_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,2))); - y3_loading_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,3))); - y4_loading_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,4))); - y5_loading_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,5))); - y6_loading_degree200 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(degrees(3)+1,1,2:end,6))); - % }}} +md.love.forcing_type = 11; +md=solve(md,'lv'); +kernels=reshape(md.results.LoveSolution.LoveKernels, [md.love.sh_nmax+1 md.love.nfreq md.materials.numlayers+1 6]); + +% extract love kernels {{{ +% degree 2. +y1_loading_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,1)); +y2_loading_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,2)); +y3_loading_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,3)); +y4_loading_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,4)); +y5_loading_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,5)); +y6_loading_degree002 = squeeze(kernels(degrees(1)+1,1,2:end,6)); + +% degree 20. +y1_loading_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,1)); +y2_loading_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,2)); +y3_loading_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,3)); +y4_loading_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,4)); +y5_loading_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,5)); +y6_loading_degree020 = squeeze(kernels(degrees(2)+1,1,2:end,6)); + +% degree 200. +y1_loading_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,1)); +y2_loading_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,2)); +y3_loading_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,3)); +y4_loading_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,4)); +y5_loading_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,5)); +y6_loading_degree200 = squeeze(kernels(degrees(3)+1,1,2:end,6)); +% }}} % validate loading solutions against the analytic solutions. {{{ @@ -225,10 +235,11 @@ depth = (max(param.radius)-param.radius)/1000; % km. - y1 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,1))); - y2 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,2))); - y3 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,3))); - y4 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,4))); - y5 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,5))); - y6 = squeeze(cell2mat(md.results.LoveSolution.LoveKernelsReal(:,1,:,6))); + kernels=reshape(md.results.LoveSolution.LoveKernels, [md.love.sh_nmax+1 md.love.nfreq md.materials.numlayers+1 6]); + y1 = squeeze(kernels(:,1,:,1)); + y2 = squeeze(kernels(:,1,:,2)); + y3 = squeeze(kernels(:,1,:,3)); + y4 = squeeze(kernels(:,1,:,4)); + y5 = squeeze(kernels(:,1,:,5)); + y6 = squeeze(kernels(:,1,:,6)); set(0,'DefaultAxesFontSize',16,'DefaultTextFontSize',15,'DefaultAxesLineWidth',1,... @@ -290,5 +301,4 @@ legend(axes6,'n=2','n=4','n=8','n=16','n=32'); %export_fig('/Users/adhikari/issm/trunk-jpl/src/m/contrib/adhikari/issm_vs_analytic_tidal_homogeneous.pdf'); - else % Index: /issm/trunk/test/NightlyRun/test2085.py =================================================================== --- /issm/trunk/test/NightlyRun/test2085.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2085.py (revision 27035) @@ -16,6 +16,8 @@ # For volumetric potential md = model() +md.groundingline.migration = 'None' md.materials = materials('litho') +cst = 365.25 * 24 * 3600 * 1000 md.materials.numlayers = 40 @@ -24,10 +26,16 @@ md.materials.density = np.zeros((md.materials.numlayers, 1)) + 5511 md.materials.lame_mu = np.zeros((md.materials.numlayers, 1)) + 0.75e11 +md.materials.lame_lambda = np.zeros((md.materials.numlayers, 1)) + 5e17 +md.materials.issolid = np.ones((md.materials.numlayers, 1)) +md.materials.rheologymodel = np.zeros((md.materials.numlayers, 1)) + +# The following isn't used here but needs to hhave arrays of consistent size with the rest of the materials md.materials.viscosity = np.zeros((md.materials.numlayers, 1)) + 1e21 -md.materials.lame_lambda = np.zeros((md.materials.numlayers, 1)) + 0.5e17 -md.materials.issolid = np.ones((md.materials.numlayers, 1)) -md.materials.isburgers = np.zeros((md.materials.numlayers, 1)) md.materials.burgers_mu = md.materials.lame_mu / 3 md.materials.burgers_viscosity = md.materials.viscosity / 10 +md.materials.ebm_alpha = np.ones((md.materials.numlayers, 1)) * 0.9 +md.materials.ebm_delta = np.ones((md.materials.numlayers, 1)) * 0.2 +md.materials.ebm_taul = np.ones((md.materials.numlayers, 1)) * 54 * 60 # 54 min +md.materials.ebm_tauh = np.ones((md.materials.numlayers, 1)) * 18.6 * cst / 1e3 # 18.6 yr md.materials.radius = np.linspace(10e3, 6371e3, md.materials.numlayers + 1).reshape(-1, 1) @@ -37,4 +45,5 @@ md.love.frequencies = 0 md.love.nfreq = 1 +md.love.istemporal = 0 md.love.sh_nmin = 2 @@ -43,5 +52,5 @@ md.miscellaneous.name = 'kernels' -md.cluster = generic('name', gethostname(), 'np', 1) +md.cluster = generic('name', gethostname(), 'np', 3) md.verbose = verbose('111111101') @@ -49,61 +58,62 @@ # Save yi's for all layers except for the inner-most one, at select degrees. -degrees = [2, 20, 200] # we archive solutions for degrees 2, 20, 200 +degrees = [1, 19, 199] # we archive solutions for degrees 2, 20, 200 +kernels = np.reshape(md.results.LoveSolution.LoveKernels, (md.love.sh_nmax + 1, md.love.nfreq, md.materials.numlayers + 1, 6), order='F') # Extract love kernels #{{{ # degree 2 -y1_tidal_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,0].squeeze() -y2_tidal_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,1].squeeze() -y3_tidal_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,2].squeeze() -y4_tidal_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,3].squeeze() -y5_tidal_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,4].squeeze() -y6_tidal_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,5].squeeze() +y1_tidal_degree002 = kernels[degrees[0]+1,0,1:,0].squeeze() +y2_tidal_degree002 = kernels[degrees[0]+1,0,1:,1].squeeze() +y3_tidal_degree002 = kernels[degrees[0]+1,0,1:,2].squeeze() +y4_tidal_degree002 = kernels[degrees[0]+1,0,1:,3].squeeze() +y5_tidal_degree002 = kernels[degrees[0]+1,0,1:,4].squeeze() +y6_tidal_degree002 = kernels[degrees[0]+1,0,1:,5].squeeze() # degree 20 -y1_tidal_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,0].squeeze() -y2_tidal_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,1].squeeze() -y3_tidal_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,2].squeeze() -y4_tidal_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,3].squeeze() -y5_tidal_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,4].squeeze() -y6_tidal_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,5].squeeze() +y1_tidal_degree020 = kernels[degrees[1]+1,0,1:,0].squeeze() +y2_tidal_degree020 = kernels[degrees[1]+1,0,1:,1].squeeze() +y3_tidal_degree020 = kernels[degrees[1]+1,0,1:,2].squeeze() +y4_tidal_degree020 = kernels[degrees[1]+1,0,1:,3].squeeze() +y5_tidal_degree020 = kernels[degrees[1]+1,0,1:,4].squeeze() +y6_tidal_degree020 = kernels[degrees[1]+1,0,1:,5].squeeze() # degree 200 -y1_tidal_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,0].squeeze() -y2_tidal_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,1].squeeze() -y3_tidal_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,2].squeeze() -y4_tidal_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,3].squeeze() -y5_tidal_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,4].squeeze() -y6_tidal_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,5].squeeze() +y1_tidal_degree200 = kernels[degrees[2]+1,0,1:,0].squeeze() +y2_tidal_degree200 = kernels[degrees[2]+1,0,1:,1].squeeze() +y3_tidal_degree200 = kernels[degrees[2]+1,0,1:,2].squeeze() +y4_tidal_degree200 = kernels[degrees[2]+1,0,1:,3].squeeze() +y5_tidal_degree200 = kernels[degrees[2]+1,0,1:,4].squeeze() +y6_tidal_degree200 = kernels[degrees[2]+1,0,1:,5].squeeze() #}}} # For surface load md.love.forcing_type = 11 - md = solve(md,'lv') +kernels = np.reshape(md.results.LoveSolution.LoveKernels, (md.love.sh_nmax + 1, md.love.nfreq, md.materials.numlayers + 1, 6), order='F') # Extract love kernels #{{{ # degree 2 -y1_loading_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,0].squeeze() -y2_loading_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,1].squeeze() -y3_loading_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,2].squeeze() -y4_loading_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,3].squeeze() -y5_loading_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,4].squeeze() -y6_loading_degree002 = md.results.LoveSolution.LoveKernelsReal[degrees[0],0,1:,5].squeeze() +y1_loading_degree002 = kernels[degrees[0]+1,0,1:,0].squeeze() +y2_loading_degree002 = kernels[degrees[0]+1,0,1:,1].squeeze() +y3_loading_degree002 = kernels[degrees[0]+1,0,1:,2].squeeze() +y4_loading_degree002 = kernels[degrees[0]+1,0,1:,3].squeeze() +y5_loading_degree002 = kernels[degrees[0]+1,0,1:,4].squeeze() +y6_loading_degree002 = kernels[degrees[0]+1,0,1:,5].squeeze() # degree 20 -y1_loading_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,0].squeeze() -y2_loading_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,1].squeeze() -y3_loading_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,2].squeeze() -y4_loading_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,3].squeeze() -y5_loading_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,4].squeeze() -y6_loading_degree020 = md.results.LoveSolution.LoveKernelsReal[degrees[1],0,1:,5].squeeze() +y1_loading_degree020 = kernels[degrees[1]+1,0,1:,0].squeeze() +y2_loading_degree020 = kernels[degrees[1]+1,0,1:,1].squeeze() +y3_loading_degree020 = kernels[degrees[1]+1,0,1:,2].squeeze() +y4_loading_degree020 = kernels[degrees[1]+1,0,1:,3].squeeze() +y5_loading_degree020 = kernels[degrees[1]+1,0,1:,4].squeeze() +y6_loading_degree020 = kernels[degrees[1]+1,0,1:,5].squeeze() # degree 200 -y1_loading_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,0].squeeze() -y2_loading_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,1].squeeze() -y3_loading_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,2].squeeze() -y4_loading_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,3].squeeze() -y5_loading_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,4].squeeze() -y6_loading_degree200 = md.results.LoveSolution.LoveKernelsReal[degrees[2],0,1:,5].squeeze() +y1_loading_degree200 = kernels[degrees[2]+1,0,1:,0].squeeze() +y2_loading_degree200 = kernels[degrees[2]+1,0,1:,1].squeeze() +y3_loading_degree200 = kernels[degrees[2]+1,0,1:,2].squeeze() +y4_loading_degree200 = kernels[degrees[2]+1,0,1:,3].squeeze() +y5_loading_degree200 = kernels[degrees[2]+1,0,1:,4].squeeze() +y6_loading_degree200 = kernels[degrees[2]+1,0,1:,5].squeeze() #}}} Index: /issm/trunk/test/NightlyRun/test2090.m =================================================================== --- /issm/trunk/test/NightlyRun/test2090.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2090.m (revision 27035) @@ -3,5 +3,6 @@ %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700.); +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh %Geometry for the bed, arbitrary thickness of 1000: @@ -37,16 +38,18 @@ %still use the lovenumbers constructor to initialize the fields: load ../Data/lnb_temporal.mat -md.solidearth.lovenumbers=lovenumbers('maxdeg',1000); -md.solidearth.lovenumbers.timefreq=[0]; +%md.solidearth.lovenumbers=lovenumbers('maxdeg',1000); +%md.solidearth.lovenumbers.timefreq=[0]; -md.solidearth.lovenumbers.h=[h1']; -md.solidearth.lovenumbers.k=[k1']; -md.solidearth.lovenumbers.l=[l1']; +md.solidearth.lovenumbers.h=[ht]; +md.solidearth.lovenumbers.k=[kt]; +md.solidearth.lovenumbers.l=[lt]; %md.solidearth.lovenumbers.h=repmat(md.solidearth.lovenumbers.h,1,100); %md.solidearth.lovenumbers.k=repmat(md.solidearth.lovenumbers.k,1,100); %md.solidearth.lovenumbers.l=repmat(md.solidearth.lovenumbers.l,1,100); -md.solidearth.lovenumbers.th=repmat(md.solidearth.lovenumbers.th,1,101); -md.solidearth.lovenumbers.tk=repmat(md.solidearth.lovenumbers.tk,1,101); -md.solidearth.lovenumbers.tl=repmat(md.solidearth.lovenumbers.tl,1,101); +md.solidearth.lovenumbers.th=tht; +md.solidearth.lovenumbers.tk=tkt; +md.solidearth.lovenumbers.tl=tlt; +md.solidearth.lovenumbers.pmtf_colinear=pmtf1; +md.solidearth.lovenumbers.pmtf_ortho=pmtf2; md.solidearth.lovenumbers.timefreq=time; @@ -92,5 +95,5 @@ %Solution parameters -md.cluster.np=3; +md.cluster.np=10; md.solidearth.settings.reltol=NaN; md.solidearth.settings.abstol=1e-3; @@ -117,5 +120,5 @@ md.solidearth.settings.elastic=1; md.solidearth.settings.viscous=1; -md.solidearth.settings.rotation=0; +md.solidearth.settings.rotation=1; md=solve(md,'tr'); Index: /issm/trunk/test/NightlyRun/test2091.m =================================================================== --- /issm/trunk/test/NightlyRun/test2091.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test2091.m (revision 27035) @@ -0,0 +1,273 @@ +%Test Name: ViscoElasticEarthSlc + +%mesh earth: +md=model;md.mesh=mesh3dsurface(); +re= md.solidearth.planetradius; +phi1=(0:10:360)/180*pi; +phi2=(0:10:360)/180*pi; + +dom=struct; +dom.x=cos(phi1')*re*pi; +dom.y=sin(phi1')*re*pi;dom.y(end)=dom.y(1); +dom.nods=length(dom.x); + +co=struct; +rad=re*pi*[linspace(1e-3,1,3)/18]; +for i=1:length(rad); +co(i).x=cos(phi2')*rad(i); +co(i).y=sin(phi2')*rad(i);co(i).y(end)=co(i).y(1); +co(i).nods=length(co(i).x);co(i).closed=1;co(i).density=1;co(i).name='Icedisklimit';co(i).Geometry='Polygon'; +co(i).BoundingBox=[min(co(i).x) min(co(i).y); max(co(i).x) max(co(i).y)]; +end + +defaultoptions={'KeepVertices',0,'MaxCornerAngle',0.0000000001,'NoBoundaryRefinement',1}; +md2d=bamg(model,'domain',dom,'subdomains',co,'hmin',100e3,'hmax',10000e3,defaultoptions{:}); + +colat=sqrt(md2d.mesh.x.^2+md2d.mesh.y.^2)/re; +lon=atan2(md2d.mesh.y,md2d.mesh.x); + +x=sin(colat).*cos(lon)*re; +y=sin(colat).*sin(lon)*re; +z=cos(colat)*re; + +md.mesh.x=x;md.mesh.y=y;md.mesh.z=z;md.mesh.lat=90-colat*180/pi;md.mesh.long=lon*180/pi; +md.mesh.r=sqrt(x.^2+y.^2+z.^2); +md.mesh.numberofelements=md2d.mesh.numberofelements;md.mesh.numberofvertices=md2d.mesh.numberofvertices; +md.mesh.elements=md2d.mesh.elements; +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +md.mesh.area=GetAreas3DTria(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.z); + + +%md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',500.); + +%Geometry for the bed, arbitrary thickness of 1000: +md.geometry.bed=-zeros(md.mesh.numberofvertices,1); +md.geometry.base=md.geometry.bed; +md.geometry.thickness=0*ones(md.mesh.numberofvertices,1); +md.geometry.surface=md.geometry.bed+md.geometry.thickness; + + +%parameterize solidearth solution: +%solidearth loading: {{{ +md.masstransport.spcthickness=[md.geometry.thickness;0]; +md.materials.rho_ice=931; + + +md.smb.mass_balance=zeros(md.mesh.numberofvertices,1); +%antarctica +xe=md.mesh.x(md.mesh.elements)*[1;1;1]/3; +ye=md.mesh.y(md.mesh.elements)*[1;1;1]/3; +ze=md.mesh.z(md.mesh.elements)*[1;1;1]/3; +re=sqrt(xe.^2+ye.^2+ze.^2); + +late=asind(ze./re); +longe=atan2d(ye,xe); +%arctic +pos=find(late>=80); +pos1=find(md.mesh.lat>=80); +md.masstransport.spcthickness(:)=0; +md.masstransport.spcthickness(pos1)=md.masstransport.spcthickness(pos1) +1500*sqrt((cosd(90-md.mesh.lat(pos1))-cosd(10))./(1-cosd(10))); +%md.masstransport.spcthickness(pos1)=md.masstransport.spcthickness(pos1) +1000; +posgre=pos; + +%visco-elastic loading from love numbers that we load ourselves. We +%still use the lovenumbers constructor to initialize the fields: +load ../Data/lnb_temporal.mat +%md.solidearth.lovenumbers=lovenumbers('maxdeg',1000); +%md.solidearth.lovenumbers.timefreq=[0]; + +maxdeg=129; +mindeg=1; + +md.solidearth.lovenumbers.h=ht; +md.solidearth.lovenumbers.h(maxdeg+1,:)=0; +%md.solidearth.lovenumbers.h(maxdeg+2,:)=0; +%md.solidearth.lovenumbers.h(maxdeg+3:end,:)=[]; +md.solidearth.lovenumbers.h(1:mindeg,:)=0; +md.solidearth.lovenumbers.k=kt; +md.solidearth.lovenumbers.k(maxdeg+1,:)=-1; +%md.solidearth.lovenumbers.k(maxdeg+2,:)=0; +%md.solidearth.lovenumbers.k(maxdeg+3:end,:)=[]; +md.solidearth.lovenumbers.k(1:mindeg,:)=-1; +md.solidearth.lovenumbers.l=lt; +md.solidearth.lovenumbers.l(maxdeg+1,:)=0; +%md.solidearth.lovenumbers.l(maxdeg+2,:)=0; +%md.solidearth.lovenumbers.l(maxdeg+3:end,:)=[]; +md.solidearth.lovenumbers.l(1:mindeg,:)=0; +%md.solidearth.lovenumbers.h=repmat(md.solidearth.lovenumbers.h,1,100); +%md.solidearth.lovenumbers.k=repmat(md.solidearth.lovenumbers.k,1,100); +%md.solidearth.lovenumbers.l=repmat(md.solidearth.lovenumbers.l,1,100); +md.solidearth.lovenumbers.th=tht(1:maxdeg+1,:); +md.solidearth.lovenumbers.tk=tkt(1:maxdeg+1,:); +md.solidearth.lovenumbers.tl=tlt(1:maxdeg+1,:); +md.solidearth.lovenumbers.pmtf_colinear=pmtf1; +md.solidearth.lovenumbers.pmtf_ortho=pmtf2; +md.solidearth.lovenumbers.timefreq=time; + +%}}} +%mask: {{{ +%mask=gmtmask(md.mesh.lat,md.mesh.long); +oceanmask=ones(md.mesh.numberofvertices,1); + +icemask=ones(md.mesh.numberofvertices,1); +icemask(pos1)=-1; + + +md.mask.ice_levelset=icemask*1e-3; +md.mask.ocean_levelset=oceanmask; +% }}} + +%time stepping: +md.timestepping.start_time=0; +md.timestepping.time_step=1000; +md.timestepping.final_time=12000; + +time1=md.timestepping.start_time:md.timestepping.time_step:md.timestepping.final_time; +md.masstransport.spcthickness=repmat(md.masstransport.spcthickness, [1 length(time1)]); +%md.masstransport.spcthickness(1:end-1,3:end)=0; +md.masstransport.spcthickness(end,:)=time1; + +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.bottompressure=zeros(md.mesh.numberofvertices,1); +md.initialization.dsl=zeros(md.mesh.numberofvertices,1); +md.initialization.str=0; + +%Materials: +md.materials=materials('hydro'); + +%Miscellaneous +md.miscellaneous.name='test2091'; + +%Solution parameters +md.cluster.np=3; +md.solidearth.settings.reltol=NaN; +md.solidearth.settings.abstol=1e-3; +md.solidearth.settings.sealevelloading=0; +md.solidearth.settings.grdocean=0; +md.solidearth.settings.isgrd=1; +md.solidearth.settings.ocean_area_scaling=0; +md.solidearth.settings.grdmodel=1; +md.solidearth.settings.timeacc=md.timestepping.time_step; +md.solidearth.settings.degacc=.01; + +%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={'SealevelGRD','BedGRD', 'BedNorthGRD', 'BedEastGRD', 'SealevelBarystaticIceLoad', 'SealevelBarystaticIceWeights', 'SealevelBarystaticIceArea', 'SealevelBarystaticIceMask', 'SealevelBarystaticIceLatbar', 'SealevelBarystaticIceLongbar'}; +md.settings.results_on_nodes = {'SealevelBarystaticIceWeights'}; + +% max number of iteration reverted back to 10 (i.e., the original default value) +md.solidearth.settings.maxiter=10; + +%eustatic + selfattraction + elastic + rotation run: +md.solidearth.settings.selfattraction=1; +md.solidearth.settings.elastic=1; +md.solidearth.settings.viscous=1; +md.solidearth.settings.rotation=0; +md.solidearth.settings.horiz=1; + +md=solve(md,'tr'); + + + +%%validation against spada curves +clear S B H E +for i=1:length(time1)-1 +S(:,i)=md.results.TransientSolution(i).SealevelGRD; +B(:,i)=md.results.TransientSolution(i).BedGRD; +H(:,i)=md.results.TransientSolution(i).BedNorthGRD; +E(:,i)=md.results.TransientSolution(i).BedEastGRD; +end + +S=cumsum(S,2); +B=cumsum(B,2); +H=cumsum(H,2); +E=cumsum(E,2); %E should theoretically be 0, in practice there is a residual due to the resolution and imperfect symmetry of the ice load. This can serve as an accuracy check of the horizontals + +%Fields and tolerances to track changes +field_names={'Sealevel','Bed', 'Horizontals'}; +field_tolerances={1e-13,1e-13,1e-13}; +field_values={S,B,H}; + +return +%Spada benchmark curves +[ali,ia,~]=unique(90-md.mesh.lat); +fid=fopen('../Data/SpadaBenchmark/T1-2/GS-disp_t0_d1_cap.dat'); + dat=textscan(fid,'%f','headerlines',16); + dat2=reshape(dat{1}, [5 180*10+2]); + ur(:,1)=dat2(2,:); + ut(:,1)=dat2(3,:); + g(:,1)=dat2(5,:); + fid=fopen('../Data/SpadaBenchmark/T1-2/GS-disp_t1_d1_cap.dat'); + dat=textscan(fid,'%f','headerlines',16); + dat2=reshape(dat{1}, [5 180*10+2]); + ur(:,end+1)=dat2(2,:); + ut(:,end+1)=dat2(3,:); + g(:,end+1)=dat2(5,:); + fid=fopen('../Data/SpadaBenchmark/T1-2/GS-disp_t2_d1_cap.dat'); + dat=textscan(fid,'%f','headerlines',16); + dat2=reshape(dat{1}, [5 180*10+2]); + ur(:,end+1)=dat2(2,:); + ut(:,end+1)=dat2(3,:); + g(:,end+1)=dat2(5,:); + fid=fopen('../Data/SpadaBenchmark/T1-2/GS-disp_t5_d1_cap.dat'); + dat=textscan(fid,'%f','headerlines',16); + dat2=reshape(dat{1}, [5 180*10+2]); + ur(:,end+1)=dat2(2,:); + ut(:,end+1)=dat2(3,:); + g(:,end+1)=dat2(5,:); + fid=fopen('../Data/SpadaBenchmark/T1-2/GS-disp_t10_d1_cap.dat'); + dat=textscan(fid,'%f','headerlines',16); + dat2=reshape(dat{1}, [5 180*10+2]); + ur(:,end+1)=dat2(2,:); + ut(:,end+1)=dat2(3,:); + g(:,end+1)=dat2(5,:); + +%correction factor for total mass in Spada vs us +fact=3.607171340900778E+018/sum(md.results.TransientSolution(1).SealevelBarystaticIceLoad.*md.results.TransientSolution(1).SealevelBarystaticIceArea); +[ali,ia,~]=unique(90-md.mesh.lat); + +clear uri; +clear uti; +clear gi; +for i=1:5 + uri(:,i)=interp1(dat2(1,1:end-1)',ur(1:end-1,i),ali); + uti(:,i)=interp1(dat2(1,1:end-1)',ut(1:end-1,i),ali); + gi(:,i)=interp1(dat2(1,1:end-1)',g(1:end-1,i),ali); +end +indB=[1 2 3 6 11];%curves at 0, 1, 2, 5 and 10kyr + + +return +subplot(2,3,1) +plot(ali,B(ia,indB)*fact,'.',ali,uri) +title('bedrock up'); + +subplot(2,3,2) +plot(ali,-H(ia,indB)*fact,'.', ali,uti) %minus sign is because unit vector e_North=-e_theta (colatitude direction) +title('bedrock horiz'); + +subplot(2,3,3) +plot(ali,(S(ia,indB))*fact,'.',ali,gi) +title('Geoid'); + +subplot(2,3,4) +plot(ali,B(ia,indB)*fact-uri) +title('Bedrock up error'); + +subplot(2,3,5) +plot(ali,-H(ia,indB)*fact-uti) +title('Bedrock horiz error'); + +subplot(2,3,6) +plot(ali,(S(ia,indB))*fact-gi) +title('Geoid error'); + + Index: /issm/trunk/test/NightlyRun/test2092.m =================================================================== --- /issm/trunk/test/NightlyRun/test2092.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test2092.m (revision 27035) @@ -0,0 +1,217 @@ +%Test Name: PolarMotion + +%mesh earth: +md=model;md.mesh=mesh3dsurface(); +re= md.solidearth.planetradius; +phi1=(0:10:360)/180*pi; +phi2=(0:10:360)/180*pi; + +dom=struct; +dom.x=cos(phi1')*re*pi; +dom.y=sin(phi1')*re*pi;dom.y(end)=dom.y(1); +dom.nods=length(dom.x); + +co=struct; +rad=re*pi*[linspace(1e-1,1,3)/18]; +for i=1:length(rad); +co(i).x=cos(phi2')*rad(i); +co(i).y=sin(phi2')*rad(i);co(i).y(end)=co(i).y(1); +co(i).nods=length(co(i).x);co(i).closed=1;co(i).density=1;co(i).name='Icedisklimit';co(i).Geometry='Polygon'; +co(i).BoundingBox=[min(co(i).x) min(co(i).y); max(co(i).x) max(co(i).y)]; +end + +defaultoptions={'KeepVertices',0,'MaxCornerAngle',0.0000000001,'NoBoundaryRefinement',1}; +md2d=bamg(model,'domain',dom,'subdomains',co,'hmin',50e3,'hmax',10000e3,defaultoptions{:}); + +colat=sqrt(md2d.mesh.x.^2+md2d.mesh.y.^2)/re; +lon=atan2(md2d.mesh.y,md2d.mesh.x); + +x=sin(colat).*cos(lon)*re; +y=sin(colat).*sin(lon)*re; +z=cos(colat)*re; + +%load +longL=75; +latL=65; + +%rotate mesh around load center +R1=[cosd(90-latL) 0 sind(90-latL) ;0 1 0; -sind(90-latL) 0 cosd(90-latL)]; +R2=[cosd(longL) -sind(longL) 0; sind(longL) cosd(longL) 0; 0 0 1]; + +for i=1:length(x); + coord= R2*R1*[x(i);y(i);z(i)]; + x(i)=coord(1); + y(i)=coord(2); + z(i)=coord(3); +end + +colat=acos(z/re); +lon=atan2(y,x); + + +md.mesh.x=x;md.mesh.y=y;md.mesh.z=z;md.mesh.lat=90-colat*180/pi;md.mesh.long=lon*180/pi; +md.mesh.r=sqrt(x.^2+y.^2+z.^2); +md.mesh.numberofelements=md2d.mesh.numberofelements;md.mesh.numberofvertices=md2d.mesh.numberofvertices; +md.mesh.elements=md2d.mesh.elements; +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +%md.mesh.area=averaging(md,GetAreas3DTria(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.z),4); +md.mesh.area=GetAreas3DTria(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.z); + +%Geometry for the bed +md.geometry.bed=-zeros(md.mesh.numberofvertices,1); +md.geometry.base=md.geometry.bed; +md.geometry.thickness=0*ones(md.mesh.numberofvertices,1); +md.geometry.surface=md.geometry.bed+md.geometry.thickness; + + +%parameterize solidearth solution: +%solidearth loading: {{{ +md.masstransport.spcthickness=[md.geometry.thickness;0]; +md.materials.rho_ice=931; + + +md.smb.mass_balance=zeros(md.mesh.numberofvertices,1); +%antarctica +xe=md.mesh.x(md.mesh.elements)*[1;1;1]/3; +ye=md.mesh.y(md.mesh.elements)*[1;1;1]/3; +ze=md.mesh.z(md.mesh.elements)*[1;1;1]/3; +re=sqrt(xe.^2+ye.^2+ze.^2); + +late=asind(ze./re); +longe=atan2d(ye,xe); + + +longi=md.mesh.long; +lati=md.mesh.lat; +delPhi=abs(lati-latL); delLambda=abs(longi-longL); if (delLambda>pi)delLambda=2*pi-delLambda; end +alpha=2.*asin(sqrt(sind(delPhi/2).^2+cosd(lati).*cosd(latL).*sind(delLambda/2).^2)); + +pos=find(alpha<=10/180*pi-0.01); + +%mass=3.607171340900778E+018; +area_element=GetAreasSphericalTria(md.mesh.elements,md.mesh.lat,md.mesh.long,md.solidearth.planetradius); + +%md.masstransport.spcthickness(md.mesh.elements(pos,:))=mass/md.materials.rho_ice/area_element(pos); +md.masstransport.spcthickness(pos,1)=1500 * sqrt( (cos(alpha(pos)) - cosd(10)) /(1-cosd(10)) ); + + +%visco-elastic loading from love numbers that we load ourselves. We +%still use the lovenumbers constructor to initialize the fields: +load ../Data/lnb_temporal.mat +%md.solidearth.lovenumbers=lovenumbers('maxdeg',1000); +%md.solidearth.lovenumbers.timefreq=[0]; + +maxdeg=3; +mindeg=2; + +md.solidearth.lovenumbers.h=ht; +md.solidearth.lovenumbers.h(maxdeg+1,:)=0; +%md.solidearth.lovenumbers.h(maxdeg+2,:)=0; +%md.solidearth.lovenumbers.h(maxdeg+3:end,:)=[]; +md.solidearth.lovenumbers.h(1:mindeg,:)=0; +md.solidearth.lovenumbers.k=kt; +md.solidearth.lovenumbers.k(maxdeg+1,:)=-1; +%md.solidearth.lovenumbers.k(maxdeg+2,:)=0; +%md.solidearth.lovenumbers.k(maxdeg+3:end,:)=[]; +md.solidearth.lovenumbers.k(1:mindeg,:)=-1; +md.solidearth.lovenumbers.l=lt; +md.solidearth.lovenumbers.l(maxdeg+1,:)=0; +%md.solidearth.lovenumbers.l(maxdeg+2,:)=0; +%md.solidearth.lovenumbers.l(maxdeg+3:end,:)=[]; +md.solidearth.lovenumbers.l(1:mindeg,:)=0; +md.solidearth.lovenumbers.th=tht(1:maxdeg+1,:); +md.solidearth.lovenumbers.tk=tkt(1:maxdeg+1,:); +md.solidearth.lovenumbers.tl=tlt(1:maxdeg+1,:); +md.solidearth.lovenumbers.pmtf_colinear=pmtf1; +md.solidearth.lovenumbers.pmtf_ortho=pmtf2; +md.solidearth.lovenumbers.timefreq=time; +md.solidearth.rotational.equatorialmoi=8.0131e37; +md.solidearth.rotational.polarmoi=8.0394e37; +md.solidearth.rotational.angularvelocity=7.292115e-5; + +%}}} +%mask: {{{ +oceanmask=ones(md.mesh.numberofvertices,1); +icemask=ones(md.mesh.numberofvertices,1); +icemask(pos)=-1; + + +md.mask.ice_levelset=icemask; +md.mask.ocean_levelset=oceanmask; +% }}} + +%time stepping: +md.timestepping.start_time=0; +md.timestepping.time_step=1000; +md.timestepping.final_time=11000; + +time1=md.timestepping.start_time:md.timestepping.time_step:md.timestepping.final_time; +md.masstransport.spcthickness=repmat(md.masstransport.spcthickness, [1 length(time1)]); +%md.masstransport.spcthickness(1:end-1,3:end)=0; +md.masstransport.spcthickness(end,:)=time1; + +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.bottompressure=zeros(md.mesh.numberofvertices,1); +md.initialization.dsl=zeros(md.mesh.numberofvertices,1); +md.initialization.str=0; + +%Materials: +md.materials=materials('hydro'); + +%Miscellaneous +md.miscellaneous.name='test2092'; + +%Solution parameters +md.cluster.np=3; +md.solidearth.settings.reltol=NaN; +md.solidearth.settings.abstol=1e-3; +md.solidearth.settings.sealevelloading=0; +md.solidearth.settings.grdocean=0; +md.solidearth.settings.isgrd=1; +md.solidearth.settings.ocean_area_scaling=0; +md.solidearth.settings.grdmodel=1; +md.solidearth.settings.timeacc=md.timestepping.time_step; +md.solidearth.settings.degacc=.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={'SealevelBarystaticIceLoad'}; + +% max number of iteration reverted back to 10 (i.e., the original default value) +md.solidearth.settings.maxiter=10; + +%eustatic + selfattraction + elastic + rotation run: +md.solidearth.settings.selfattraction=1; +md.solidearth.settings.elastic=1; +md.solidearth.settings.viscous=1; +md.solidearth.settings.rotation=1; +md.solidearth.settings.horiz=0; + +md=solve(md,'tr'); +clear m1 m2 m3 +for i=1:length(time1)-1 +m1(i)=md.results.TransientSolution(i).SealevelchangePolarMotionX; +m2(i)=md.results.TransientSolution(i).SealevelchangePolarMotionY; +m3(i)=md.results.TransientSolution(i).SealevelchangePolarMotionZ; +end + +%Fields and tolerances to track changes +field_names={'PolarmotionX','PolarmotionY', 'PolarmotionZ'}; +field_tolerances={1e-13,1e-13,1e-13}; +field_values={m1,m2,m3}; + +return +subplot(1,2,1) +plot(time1(2:end-1),m1(2:end)*180/pi *1e6/md.timestepping.time_step, time1(2:end-1),m2(2:end)*180/pi*1e6/md.timestepping.time_step); + +subplot(1,2,2) +plot(time1(1:end-1),cumsum(m1)*180/pi, time1(1:end-1),cumsum(m2)*180/pi) + Index: /issm/trunk/test/NightlyRun/test2101.m =================================================================== --- /issm/trunk/test/NightlyRun/test2101.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test2101.m (revision 27035) @@ -4,5 +4,6 @@ %mesh earth: md=model; -md.mesh=gmshplanet('radius',6.371012*10^3,'resolution',700); +load ../Data/SlcTestMesh.mat; +md.mesh=SlcMesh; %700 km resolution mesh % define load Index: /issm/trunk/test/NightlyRun/test2101.py =================================================================== --- /issm/trunk/test/NightlyRun/test2101.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test2101.py (revision 27035) @@ -1,9 +1,7 @@ #Test Name: EarthEsa #Elastostatic adjustment for an elemental ice unloading +import numpy as np +import pickle from socket import gethostname - -import numpy as np - -from gmshplanet import * from gmtmask import * from lovenumbers import * @@ -15,5 +13,8 @@ #mesh earth: md = model() -md.mesh = gmshplanet('radius', 6.371012 * 1e3, 'resolution', 700) + +# Load precomputed mesh +with open('../Data/SlcTestMesh.pkl', 'rb') as slc_test_mesh_file: + md.mesh = pickle.load(slc_test_mesh_file) #define load Index: /issm/trunk/test/NightlyRun/test233.js =================================================================== --- /issm/trunk/test/NightlyRun/test233.js (revision 27034) +++ /issm/trunk/test/NightlyRun/test233.js (revision 27035) @@ -17,5 +17,5 @@ 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3', 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','Temperature4','BasalforcingsGroundediceMeltingRate4']; -field_tolerances=[1e-09,2e-09,1e-09,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, +field_tolerances=[2e-09,2e-09,1e-09,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, 1e-09,2e-09,1e-08,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06, 1e-08,2e-09,1e-08,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06, Index: /issm/trunk/test/NightlyRun/test233.m =================================================================== --- /issm/trunk/test/NightlyRun/test233.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test233.m (revision 27035) @@ -16,5 +16,5 @@ 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3', ... 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','Temperature4','BasalforcingsGroundediceMeltingRate4'}; -field_tolerances={1e-09,2e-09,1e-09,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ... +field_tolerances={2e-09,2e-09,1e-09,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ... 1e-09,2e-09,1e-08,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06, ... 1e-08,2e-09,1e-08,2e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06, ... Index: /issm/trunk/test/NightlyRun/test233.py =================================================================== --- /issm/trunk/test/NightlyRun/test233.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test233.py (revision 27035) @@ -26,5 +26,5 @@ 'Vx3', 'Vy3', 'Vz3', 'Vel3', 'Pressure3', 'Bed3', 'Surface3', 'Thickness3', 'Temperature3', 'BasalforcingsGroundediceMeltingRate3', 'Vx4', 'Vy4', 'Vz4', 'Vel4', 'Pressure4', 'Bed4', 'Surface4', 'Thickness4', 'Temperature4', 'BasalforcingsGroundediceMeltingRate4'] -field_tolerances = [1e-09, 2e-09, 1e-09, 2e-09, 1e-09, 1e-09, 1e-09, 1e-09, 1e-09, 1e-09, +field_tolerances = [2e-09, 2e-09, 1e-09, 2e-09, 1e-09, 1e-09, 1e-09, 1e-09, 1e-09, 1e-09, 1e-09, 2e-09, 1e-08, 2e-09, 1e-09, 1e-09, 1e-09, 1e-09, 1e-09, 1e-06, 1e-08, 2e-09, 1e-08, 2e-09, 1e-09, 1e-09, 1e-09, 1e-09, 1e-09, 1e-06, Index: /issm/trunk/test/NightlyRun/test247.py =================================================================== --- /issm/trunk/test/NightlyRun/test247.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test247.py (revision 27035) @@ -1,3 +1,3 @@ -#Test Name: SquareShelfTranIspddIsdeltaO18pdNoInterpSSA2d +#Test Name: SquareShelfTranIspddIsdeltaO18pdNoInterpSSA2d import numpy as np from model import * @@ -57,10 +57,10 @@ tim1 = np.linspace(1,12,12)/12 -md.smb.temperatures_reconstructed[md.mesh.numberofvertices,0:12] = tim1 +md.smb.temperatures_reconstructed[md.mesh.numberofvertices,0:12] = tim1 md.smb.temperatures_reconstructed[md.mesh.numberofvertices,12:24] = tim1+3 md.smb.temperatures_reconstructed[md.mesh.numberofvertices,24:36] = tim1+5 md.smb.precipitations_reconstructed[md.mesh.numberofvertices,0:12] = tim1 -md.smb.precipitations_reconstructed[md.mesh.numberofvertices,12:24] = tim1+3 +md.smb.precipitations_reconstructed[md.mesh.numberofvertices,12:24] = tim1+3 md.smb.precipitations_reconstructed[md.mesh.numberofvertices,24:36] = tim1+5 @@ -68,5 +68,5 @@ # spc md.thermal.spctemperature=np.mean(md.smb.temperatures_presentday[0:md.mesh.numberofvertices,0:12],axis=1)-10. -md.initialization.temperature=md.thermal.spctemperature +md.initialization.temperature=md.thermal.spctemperature md.smb.s0p = np.maximum(md.geometry.surface.reshape(-1, 1),np.zeros((md.mesh.numberofvertices,1))) @@ -89,5 +89,5 @@ md.thermal.isdrainicecolumn = 0 -md=solve(md,'thermal') +md = solve(md, 'thermal') md.initialization.temperature = md.results.ThermalSolution.Temperature @@ -121,54 +121,54 @@ #Fields and tolerances to track changes -field_names = ['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','Enthalpy1','SmbMassBalance1', - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','Enthalpy2','SmbMassBalance2', - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','Enthalpy3','SmbMassBalance3', - 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','Temperature4','Enthalpy4','SmbMassBalance4'] -field_tolerances=[1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-13, - 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-13, - 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-13, - 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-13] +field_names = ['Vx1', 'Vy1', 'Vz1', 'Vel1', 'Pressure1', 'Bed1', 'Surface1', 'Thickness1', 'Temperature1', 'Enthalpy1', 'SmbMassBalance1', + 'Vx2', 'Vy2', 'Vz2', 'Vel2', 'Pressure2', 'Bed2', 'Surface2', 'Thickness2', 'Temperature2', 'Enthalpy2', 'SmbMassBalance2', + 'Vx3', 'Vy3', 'Vz3', 'Vel3', 'Pressure3', 'Bed3', 'Surface3', 'Thickness3', 'Temperature3', 'Enthalpy3', 'SmbMassBalance3', + 'Vx4', 'Vy4', 'Vz4', 'Vel4', 'Pressure4', 'Bed4', 'Surface4', 'Thickness4', 'Temperature4', 'Enthalpy4', 'SmbMassBalance4'] +field_tolerances=[1e-09, 1e-09, 1e-09, 1e-09, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-13, + 1e-09, 1e-09, 1e-09, 1e-09, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-13, + 1e-09, 1e-09, 1e-09, 1e-09, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-13, + 1e-09, 1e-09, 1e-09, 1e-09, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-13] field_values = [md.results.TransientSolution[0].Vx, - md.results.TransientSolution[0].Vy, - md.results.TransientSolution[0].Vz, - md.results.TransientSolution[0].Vel, - md.results.TransientSolution[0].Pressure, - md.results.TransientSolution[0].Base, - md.results.TransientSolution[0].Surface, - md.results.TransientSolution[0].Thickness, - md.results.TransientSolution[0].Temperature, - md.results.TransientSolution[0].Enthalpy, - md.results.TransientSolution[0].SmbMassBalance, - md.results.TransientSolution[1].Vx, - md.results.TransientSolution[1].Vy, - md.results.TransientSolution[1].Vz, - md.results.TransientSolution[1].Vel, - md.results.TransientSolution[1].Pressure, - md.results.TransientSolution[1].Base, - md.results.TransientSolution[1].Surface, - md.results.TransientSolution[1].Thickness, - md.results.TransientSolution[1].Temperature, - md.results.TransientSolution[1].Enthalpy, - md.results.TransientSolution[1].SmbMassBalance, - md.results.TransientSolution[2].Vx, - md.results.TransientSolution[2].Vy, - md.results.TransientSolution[2].Vz, - md.results.TransientSolution[2].Vel, - md.results.TransientSolution[2].Pressure, - md.results.TransientSolution[2].Base, - md.results.TransientSolution[2].Surface, - md.results.TransientSolution[2].Thickness, - md.results.TransientSolution[2].Temperature, - md.results.TransientSolution[2].Enthalpy, - md.results.TransientSolution[2].SmbMassBalance, - md.results.TransientSolution[3].Vx, - md.results.TransientSolution[3].Vy, - md.results.TransientSolution[3].Vz, - md.results.TransientSolution[3].Vel, - md.results.TransientSolution[3].Pressure, - md.results.TransientSolution[3].Base, - md.results.TransientSolution[3].Surface, - md.results.TransientSolution[3].Thickness, - md.results.TransientSolution[3].Temperature, - md.results.TransientSolution[3].Enthalpy, - md.results.TransientSolution[3].SmbMassBalance] + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vz, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Temperature, + md.results.TransientSolution[0].Enthalpy, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vz, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Temperature, + md.results.TransientSolution[1].Enthalpy, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vz, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Temperature, + md.results.TransientSolution[2].Enthalpy, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vz, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].Temperature, + md.results.TransientSolution[3].Enthalpy, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test248.m =================================================================== --- /issm/trunk/test/NightlyRun/test248.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test248.m (revision 27035) @@ -1,10 +1,10 @@ -%Test Name: SquareShelfStressMLHO2d +%Test Name: SquareShelfStressMOLHO2d md=triangle(model(),'../Exp/Square.exp',150000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); md.stressbalance.requested_outputs={'default','VxSurface','VySurface','VxShear','VyShear','VxBase','VyBase'}; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Stressbalance'); Index: /issm/trunk/test/NightlyRun/test248.py =================================================================== --- /issm/trunk/test/NightlyRun/test248.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test248.py (revision 27035) @@ -1,20 +1,19 @@ -#Test Name: SquareShelfStressMLHO2d +#Test Name: SquareShelfStressMOLHO2d from model import * from socket import gethostname -from triangle import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * - -from ContourToMesh import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve +from SetMOLHOBC import SetMOLHOBC md = triangle(model(), '../Exp/Square.exp', 150000) md = setmask(md, 'all', '') md = parameterize(md, '../Par/SquareShelf.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) md.stressbalance.requested_outputs = ['default', 'VxSurface', 'VySurface', 'VxShear', 'VyShear', 'VxBase', 'VyBase'] -md = SetMLHOBC(md); +md = SetMOLHOBC(md) md = solve(md, 'Stressbalance') @@ -27,7 +26,7 @@ md.results.StressbalanceSolution.Pressure, md.results.StressbalanceSolution.VxSurface, - md.results.StressbalanceSolution.VySurface, + md.results.StressbalanceSolution.VySurface, md.results.StressbalanceSolution.VxShear, - md.results.StressbalanceSolution.VyShear, + md.results.StressbalanceSolution.VyShear, md.results.StressbalanceSolution.VxBase, md.results.StressbalanceSolution.VyBase] Index: /issm/trunk/test/NightlyRun/test249.m =================================================================== --- /issm/trunk/test/NightlyRun/test249.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test249.m (revision 27035) @@ -1,11 +1,11 @@ -%Test Name: SquareShelfTranMLHO2d +%Test Name: SquareShelfTranMOLHO2d md=triangle(model(),'../Exp/Square.exp',150000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); md.transient.requested_outputs={'default','FloatingArea','GroundedArea','TotalGroundedBmb','TotalFloatingBmb'}; md.basalforcings.floatingice_melting_rate(:)=1; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test249.py =================================================================== --- /issm/trunk/test/NightlyRun/test249.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test249.py (revision 27035) @@ -1,12 +1,13 @@ -#Test Name: SquareShelfTranMLHO2d +#Test Name: SquareShelfTranMOLHO2d from model import * from socket import gethostname -from triangle import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve from generic import generic +from SetMOLHOBC import SetMOLHOBC md = triangle(model(), '../Exp/Square.exp', 150000) @@ -14,8 +15,8 @@ md = parameterize(md, '../Par/SquareShelf.py') md.basalforcings.floatingice_melting_rate[:] = 1. -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) md.transient.requested_outputs = ['default', 'FloatingArea', 'GroundedArea', 'TotalFloatingBmb', 'TotalGroundedBmb'] -md = SetMLHOBC(md); +md = SetMOLHOBC(md) md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test252.py =================================================================== --- /issm/trunk/test/NightlyRun/test252.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test252.py (revision 27035) @@ -72,8 +72,8 @@ nlayers = md.results.TransientSolution[0].SmbT.shape[1] for i in range(1, len(md.results.TransientSolution)): - nlayers=np.minimum(md.results.TransientSolution[i].SmbT.shape[1], nlayers) + nlayers = np.minimum(md.results.TransientSolution[i].SmbT.shape[1], nlayers) #Fields and tolerances to track changes -field_names = ['Layers','SmbDz1', 'SmbT1', 'SmbD1', 'SmbRe1', 'SmbGdn1', 'SmbGsp1', 'SmbA1', 'SmbEC1', 'SmbMassBalance1', 'SmbMAdd1', 'SmbDzAdd1', 'SmbFAC1', +field_names = ['Layers', 'SmbDz1', 'SmbT1', 'SmbD1', 'SmbRe1', 'SmbGdn1', 'SmbGsp1', 'SmbA1', 'SmbEC1', 'SmbMassBalance1', 'SmbMAdd1', 'SmbDzAdd1', 'SmbFAC1', 'SmbDz2', 'SmbT2', 'SmbD2', 'SmbRe2', 'SmbGdn2', 'SmbGsp2', 'SmbA2', 'SmbEC2', 'SmbMassBalance2', 'SmbMAdd2', 'SmbDzAdd2', 'SmbFAC2', 'SmbDz3', 'SmbT3', 'SmbD3', 'SmbRe3', 'SmbGdn3', 'SmbGsp3', 'SmbA3', 'SmbEC3', 'SmbMassBalance3', 'SmbMAdd3', 'SmbDzAdd3', 'SmbFAC3', Index: /issm/trunk/test/NightlyRun/test254.m =================================================================== --- /issm/trunk/test/NightlyRun/test254.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test254.m (revision 27035) @@ -1,7 +1,7 @@ -%Test Name: SquareShelfConstrainedMLHO +%Test Name: SquareShelfConstrainedMOLHO md=triangle(model(),'../Exp/Square.exp',150000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); @@ -58,5 +58,5 @@ md.stressbalance.requested_outputs={'default','VySurface','VyShear','VyBase'}; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Stressbalance'); Index: /issm/trunk/test/NightlyRun/test254.py =================================================================== --- /issm/trunk/test/NightlyRun/test254.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test254.py (revision 27035) @@ -1,3 +1,3 @@ -#Test Name: SquareShelfConstrainedMLHO +#Test Name: SquareShelfConstrainedMOLHO from model import * from socket import gethostname @@ -9,5 +9,5 @@ from paterson import paterson from solve import solve -from SetMLHOBC import SetMLHOBC +from SetMOLHOBC import SetMOLHOBC from generic import generic @@ -15,5 +15,5 @@ md = setmask(md, 'all', '') md = parameterize(md, '../Par/SquareShelf.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) @@ -71,5 +71,5 @@ md.stressbalance.requested_outputs = ['default', 'VySurface', 'VyShear', 'VyBase'] -md = SetMLHOBC(md) +md = SetMOLHOBC(md) md = solve(md, 'Stressbalance') Index: /issm/trunk/test/NightlyRun/test255.m =================================================================== --- /issm/trunk/test/NightlyRun/test255.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test255.m (revision 27035) @@ -1,10 +1,10 @@ -%Test Name: SquareShelfStressMLHO2dTransientIncrHydro +%Test Name: SquareShelfStressMOLHO2dTransientIncrHydro md=triangle(model(),'../Exp/Square.exp',150000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); md.masstransport.hydrostatic_adjustment='Incremental'; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test255.py =================================================================== --- /issm/trunk/test/NightlyRun/test255.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test255.py (revision 27035) @@ -1,3 +1,3 @@ -#Test Name: SquareShelfStressMLHO2dTransientIncrHydro +#Test Name: SquareShelfStressMOLHO2dTransientIncrHydro from model import * from socket import gethostname @@ -7,13 +7,13 @@ from setflowequation import setflowequation from solve import solve -from SetMLHOBC import SetMLHOBC +from SetMOLHOBC import SetMOLHOBC md = triangle(model(), '../Exp/Square.exp', 150000.) md = setmask(md, 'all', '') md = parameterize(md, '../Par/SquareShelf.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) md.masstransport.hydrostatic_adjustment = 'Incremental' -md = SetMLHOBC(md) +md = SetMOLHOBC(md) md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test256.m =================================================================== --- /issm/trunk/test/NightlyRun/test256.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test256.m (revision 27035) @@ -1,11 +1,11 @@ -%Test Name: SquareShelfStressMLHO2dTransientIncrNonHydro +%Test Name: SquareShelfStressMOLHO2dTransientIncrNonHydro md=triangle(model(),'../Exp/Square.exp',150000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.geometry.base=md.geometry.base+50.; md.geometry.surface=md.geometry.surface+50.; md.cluster=generic('name',oshostname(),'np',1); md.masstransport.hydrostatic_adjustment='Incremental'; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test256.py =================================================================== --- /issm/trunk/test/NightlyRun/test256.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test256.py (revision 27035) @@ -1,10 +1,11 @@ -#Test Name: SquareShelfStressMLHO2dTransientIncrNonHydro +#Test Name: SquareShelfStressMOLHO2dTransientIncrNonHydro from model import * from socket import gethostname -from triangle import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve +from SetMOLHOBC import SetMOLHOBC @@ -12,10 +13,10 @@ md = setmask(md, 'all', '') md = parameterize(md, '../Par/SquareShelf.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.geometry.base = md.geometry.base + 50. md.geometry.surface = md.geometry.surface + 50. md.cluster = generic('name', gethostname(), 'np', 1) md.masstransport.hydrostatic_adjustment = 'Incremental' -md = SetMLHOBC(md); +md = SetMOLHOBC(md) md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test257.m =================================================================== --- /issm/trunk/test/NightlyRun/test257.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test257.m (revision 27035) @@ -45,4 +45,6 @@ md.smb.ar_timestep = 2.0; %timestep of the autoregressive model [yr] md.smb.phi = [[0.2,0.1,0.05,0.01];[0.4,0.2,-0.2,0.1];[0.4,-0.4,0.1,-0.1]]; +md.smb.lapserates = [0.01,0.0;0.01,-0.01;0.0,-0.01]; +md.smb.elevationbins = [100;150;100]; %Stochastic forcing @@ -51,4 +53,5 @@ md.stochasticforcing.covariance = [[0.15 0.08 -0.02];[0.08 0.12 -0.05];[-0.02 -0.05 0.1]]; %global covariance among- and between-fields md.stochasticforcing.randomflag = 0; %fixed random seeds +md.stochasticforcing.stochastictimestep = 1.0; md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test257.py =================================================================== --- /issm/trunk/test/NightlyRun/test257.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test257.py (revision 27035) @@ -43,5 +43,5 @@ md.smb = SMBautoregression() md.smb.num_basins = 3 # number of basins -md.smb.basin_id = idbasin - 1 # prescribe basin ID number to elements; # NOTE: offset because of 1-based vertex indexing +md.smb.basin_id = idbasin # prescribe basin ID number to elements; md.smb.beta0 = np.array([[0.5, 1.2, 1.5]]) # intercept values of SMB in basins [m ice eq./yr] md.smb.beta1 = np.array([[0.0, 0.01, -0.01]]) # trend values of SMB in basins [m ice eq./yr^2] @@ -50,4 +50,6 @@ md.smb.ar_timestep = 2.0 #timestep of the autoregressive model [yr] md.smb.phi = np.array([[0.2, 0.1, 0.05, 0.01], [0.4, 0.2, -0.2, 0.1], [0.4, -0.4, 0.1, -0.1]]) +md.smb.lapserates = np.array([[0.01,0.0],[0.01,-0.01],[0.0,-0.01]]) +md.smb.elevationbins = np.array([100,150,100]).reshape(md.smb.num_basins,1) # Stochastic forcing @@ -56,5 +58,5 @@ md.stochasticforcing.covariance = np.array([[0.15, 0.08, -0.02], [0.08, 0.12, -0.05], [-0.02, -0.05, 0.1]]) # global covariance among- and between-fields md.stochasticforcing.randomflag = 0 # fixed random seeds - +md.stochasticforcing.stochastictimestep = 1.0 md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test317.py =================================================================== --- /issm/trunk/test/NightlyRun/test317.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test317.py (revision 27035) @@ -20,5 +20,5 @@ #Fields and tolerances to track changes -field_names = ['Vx1', 'Vy1', 'Vz1', 'Vel1', 'Pressure1', 'Bed1', 'Surface1', 'Thickness1', 'Temperature1', 'BasalforcingsGroundediceMeltingRate1', 'GroundedArea1', 'FloatingArea1', 'TotalFloatingBmb1', 'TotalGroundedBmb1' +field_names = ['Vx1', 'Vy1', 'Vz1', 'Vel1', 'Pressure1', 'Bed1', 'Surface1', 'Thickness1', 'Temperature1', 'BasalforcingsGroundediceMeltingRate1', 'GroundedArea1', 'FloatingArea1', 'TotalFloatingBmb1', 'TotalGroundedBmb1', 'Vx2', 'Vy2', 'Vz2', 'Vel2', 'Pressure2', 'Bed2', 'Surface2', 'Thickness2', 'Temperature2', 'BasalforcingsGroundediceMeltingRate2', 'GroundedArea2', 'FloatingArea2', 'TotalFloatingBmb2', 'TotalGroundedBmb2', 'Vx3', 'Vy3', 'Vz3', 'Vel3', 'Pressure3', 'Bed3', 'Surface3', 'Thickness3', 'Temperature3', 'BasalforcingsGroundediceMeltingRate3', 'GroundedArea3', 'FloatingArea3', 'TotalFloatingBmb2', 'TotalGroundedBmb2'] Index: /issm/trunk/test/NightlyRun/test3204.m =================================================================== --- /issm/trunk/test/NightlyRun/test3204.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test3204.m (revision 27035) @@ -0,0 +1,112 @@ +%Test Name: SquareShelfTransientCalibrationNBEcodipackCheckpoint + +%Same as test3201 but with checkpointing 1 + +%Generate observations +md = model; +md = triangle(model(),'../Exp/Square.exp',100000.); +md = setmask(md,'all',''); +md = parameterize(md,'../Par/SquareShelf.par'); +md = setflowequation(md,'SSA','all'); +md.cluster = generic('np',2); + +%Create real time series for B +md.timestepping.interp_forcing = 0; +md.timestepping.final_time = 2*md.timestepping.time_step; +md.materials.rheology_B = 1.8e8*ones(md.mesh.numberofelements,2); +md.materials.rheology_B(find(mean(md.mesh.x(md.mesh.elements),2)0))=0; + draft=draft.*pos; + draft=draft(1:Nx,1:Ny)+draft(2:end,1:Ny)+draft(1:Nx,2:end)+draft(2:end,2:end); + pos=pos(1:Nx,1:Ny)+pos(2:end,1:Ny)+pos(1:Nx,2:end)+pos(2:end,2:end); + draft(find(pos))=draft(find(pos))./pos(find(pos)); namF='run/shelficeTopo.Lin.bin'; fid=fopen(namF,'w','b'); fwrite(fid,draft,prec);fclose(fid); - var=([1:Ny]-2)/(jEnd-2); - dMdt_fy=zeros(Nx,Ny); - for i=1:Nx - dMdt_fy(i,:)=-cos(pi*var); - dMdt_fy(i,1)=0; dMdt_fy(i,j2:Ny)=0; - end - %- rate of change due to ice-stream dynamics - rateDyn=rho_water*0.1/3600; sfx='r02'; - dMdt=rateDyn*dMdt_fy; - namF=sprintf('%s.%s.%s','run/shelfice_dMdt',sfx,'bin'); - fid=fopen(namF,'w','b'); fwrite(fid,dMdt,prec);fclose(fid); - - T_sfc = -1.9; - T_bot = 2; del_T = (T_bot - T_sfc)/(59*delZ); tref=zeros(1,Nz); @@ -440,6 +420,4 @@ fid=fopen(namF,'w','b'); fwrite(fid,tref,prec);fclose(fid); - S_sfc = 34.2; - S_bot = 34.7; del_S = (S_bot - S_sfc)/(59*delZ); sref=zeros(1,Nz); @@ -472,9 +450,4 @@ namF='run/salt_ini.bin'; fid=fopen(namF,'w','b'); fwrite(fid,var,prec);fclose(fid); - - rhoAvr=rho_water-1.345; - mIce=-rhoAvr*draft; - namF='run/shelficeMass.Lin.bin'; - fid=fopen(namF,'w','b'); fwrite(fid,mIce,prec);fclose(fid); % }}} % }}} Index: /issm/trunk/test/NightlyRun/test4004.m =================================================================== --- /issm/trunk/test/NightlyRun/test4004.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test4004.m (revision 27035) @@ -0,0 +1,427 @@ +%Test Name: IceOceanCoupling Dan Goldberg'd setup +%ISSM/MITgcm coupled set-up +% +%Script control parameters +steps=1:10; + +%To download and recompile MITgcm from scratch: +!rm -rf ${ISSM_DIR}/test/MITgcm/install +!rm -rf ${ISSM_DIR}/test/MITgcm/build/* +!rm -rf Models + +%Organizer +!mkdir Models +org=organizer('repository','Models','prefix','IceOcean.','steps',steps); + +presentdirectory=pwd; + +% {{{ Parameters: +if perform(org,'Parameters'), + Nx=3; % number of longitude cells + Ny=200; % number of latitude cells + Nz=90; % number of MITgcm vertical cells + nPx=1; % number of MITgcm processes to use in x direction + nPy=8; % number of MITgcm processes to use in y direction + xgOrigin=0; % origin of longitude + ygOrigin=-75.5; % origin of latitude + dLong=.125; % longitude grid spacing + dLat=dLong/16; % latitude grid spacing + delZ=10; % thickness of vertical levels (m) + gravity= 9.81; % gravity (m^2/s) + rho_ice=917; + rho_water=1030; + di=rho_ice/rho_water; + prec = 'real*8'; % precision of MITgcm input binary files + + % bathymetry and ice sheet geometry + H = -900; % water depth in the ice shelf cavity + Hmin = -600; % deepest point of cavern + Hmax = -300; % shallowest point of cavern + jEnd = Ny*3/4; % where ice-shelf ends + j2 = jEnd+1; + + % initial ocean conditions + T_sfc = -2; + T_bot = -1.9; + S_sfc = 34.2; + S_bot = 34.3; + + savedata(org, Nx, Ny, nPx, nPy, Nz, dLong, dLat, delZ, xgOrigin, ygOrigin, ... + rho_ice, rho_water, di, H, Hmin, Hmax, jEnd, j2, gravity, prec, ... + T_sfc,T_bot,S_sfc,S_bot); +end +% }}} +% {{{ Bathymetry: +if perform(org,'Bathymetry'), + + loaddata(org,'Parameters'); + + %create lat,lon + latg = ygOrigin+[0:Ny-1]*dLat; + latc = latg+dLat/2; + long = xgOrigin+[0:Nx-1]*dLong; + lonc = long+dLong/2; + [lat lon]=meshgrid(latc,lonc); + zC=-delZ*([1:Nz]-0.5); + zF=-delZ*[0:Nz]; + + %create bathymetry: + bathymetry = ones(Nx,Ny)*H; + bathymetry(:,end) = 0; + + %save bathymetry file for MITgcm + savedata(org,lat,lon,bathymetry); + +end +% }}} +% {{{ IceSheetGeometry: +if perform(org,'IceSheetGeometry'), + + loaddata(org,'Parameters'); + loaddata(org,'Bathymetry'); + latmin=min(lat(:)); + latmax=max(lat(:)); + + dHdy = (Hmax-Hmin)/dLat/(jEnd-2); %Slope of ice shelf + draft=bathymetry; + for i=1:Nx + draft(i,:)=Hmin+dHdy*[-1:Ny-2]*dLat; + end + draft(:,j2:Ny)=0; + + ice_mask=ones(Nx,Ny); + ice_mask(:,j2:Ny)=0; + iceshelf_mask=ice_mask; + thickness=abs(draft)/di; + + savedata(org,ice_mask,iceshelf_mask,draft,thickness); + + close all, figure(2), clf + subplot(411), pcolorcen(bathymetry); colorbar, title('bathymetry') + subplot(412), pcolorcen(ice_mask); colorbar, title('ice and iceshelf mask') + subplot(413), pcolorcen(draft); colorbar, title('draft') + subplot(414), pcolorcen(thickness); colorbar, title('thickness') + +end +% }}} + +%Configure MITgcm +% {{{ GetMITgcm: +if perform(org,'GetMITgcm'), + system([pwd '/../MITgcm/get_mitgcm.sh']); +end +% }}} +% {{{ BuildMITgcm: +if perform(org,'BuildMITgcm'), + system(['../MITgcm/build_4003.sh generic ' pwd '/../MITgcm']); +end +% }}} +addpath(recursivepath([pwd '/../MITgcm'])); +% {{{ RunUncoupledMITgcm: +if perform(org,'RunUncoupledMITgcm'), + + loaddata(org,'Parameters'); + loaddata(org,'Bathymetry'); + loaddata(org,'IceSheetGeometry'); + + % rename previous run directory and create new one + if exist ('run.old') + !\rm -rf run.old + end + if exist ('run') + !\mv run run.old + end + !\mkdir run + !\cp ../MITgcm/build/mitgcmuv run + !\cp ../MITgcm/input_4004/* run + !\cp ../MITgcm/input_4004/eedata_uncoupled run/eedata + + % {{{ Construct MITgcm binary input files + namF='run/bathy_flat.bin'; + fid=fopen(namF,'w','b'); fwrite(fid,bathymetry,prec);fclose(fid); + + namF='run/shelficeTopo.Lin.bin'; + fid=fopen(namF,'w','b'); fwrite(fid,draft,prec);fclose(fid); + + del_T = (T_bot - T_sfc)/(59*delZ); + tref=zeros(1,Nz); + for k = 1:Nz; + tref(k) = T_sfc + del_T*((k-20)*delZ); + tref(k)= max(T_sfc,min(tref(k),T_bot)); + end + namF='run/temp_obc.bin'; + tref=[tref; tref; tref]; + fid=fopen(namF,'w','b'); fwrite(fid,tref,prec);fclose(fid); + + del_S = (S_bot - S_sfc)/(59*delZ); + sref=zeros(1,Nz); + for k = 1:Nz; + sref(k) = S_sfc + del_S*((k-20)*delZ); + sref(k)= max(S_sfc,min(sref(k),S_bot)); + end + namF='run/salt_obc.bin'; + sref=[sref; sref; sref]; + fid=fopen(namF,'w','b'); fwrite(fid,sref,prec);fclose(fid); + + zax=[1:Nz]; + v1=2.5e-2; + var=1+Nz-2*zax; var=var/(Nz-1); + vobc=v1*var; + namF='run/vVel_obc.bin'; + vobc=[vobc; vobc; vobc]; + fid=fopen(namF,'w','b'); fwrite(fid,vobc,prec);fclose(fid); + + var=zeros(Nx,Ny,Nz); + for i=1:Nx, for j=1:Ny + var(i,j,:)=tref(1,:); + end, end + namF='run/temp_ini.bin'; + fid=fopen(namF,'w','b'); fwrite(fid,var,prec);fclose(fid); + + for i=1:Nx, for j=1:Ny + var(i,j,:)=sref(1,:); + end, end + namF='run/salt_ini.bin'; + fid=fopen(namF,'w','b'); fwrite(fid,var,prec);fclose(fid); + % }}} + + cd run + eval(['!mpirun -np ' int2str(nPx*nPy) ' ./mitgcmuv']); + cd .. +end +% }}} + +%Configure ISSM +% {{{ CreateMesh: +if perform(org,'CreateMesh'), + + loaddata(org,'Parameters'); + + %create model: + md=model(); + + %Grab lat,long from MITgcm: + long=readbin('run/XC.data',[Nx Ny]); + lat=readbin('run/YC.data',[Nx Ny]); + + %project lat,long: + [x,y]=ll2xy(lat(:),long(:),-1); + index=[]; + % C D + % A B + for j=1:(Ny-1), + for i=1:(Nx-1), + A=(j-1)*(Nx)+i; + B=(j-1)*(Nx)+i+1; + C=j*(Nx)+i; + D=j*(Nx)+i+1; + index(end+1,:)=[A B C]; + index(end+1,:)=[C B D]; + end + end + + %fill mesh and model: + md=meshconvert(md,index,x,y); + md.mesh.lat=lat(:); + md.mesh.long=long(:); + + savemodel(org,md); + +end +% }}} +% {{{ MeshGeometry: +if perform(org,'MeshGeometry'), + + loaddata(org,'Parameters'); + loaddata(org,'CreateMesh'); + loaddata(org,'Bathymetry'); + loaddata(org,'IceSheetGeometry'); + + %start filling some of the fields + md.geometry.bed=bathymetry(:); + md.geometry.thickness=thickness(:); + md.geometry.base=-917/1028*md.geometry.thickness; + md.geometry.surface=md.geometry.base+md.geometry.thickness; + + %nothing passes icefront: + pos=find((~ice_mask(:) & ice_mask(:)~=0) | thickness(:)==0); + md.geometry.thickness(pos)=1; + md.geometry.surface(pos)=(1-di)*md.geometry.thickness(pos); + md.geometry.base(pos)=-di*md.geometry.thickness(pos); + + %level sets: + md.mask.ice_levelset=iceshelf_mask(:); + pos=find(md.mask.ice_levelset==1); md.mask.ice_levelset(pos)=-1; + pos=find(md.mask.ice_levelset==0); md.mask.ice_levelset(pos)=1; + md.mask.ocean_levelset=-ones(md.mesh.numberofvertices,1); + + savemodel(org,md); + +end +% }}} +% {{{ ParameterizeIce: +if perform(org,'ParameterizeIce'), + + loaddata(org,'MeshGeometry'); + + %miscellaneous + md.miscellaneous.name='test4004'; + + %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); + + %friction: + md.friction.coefficient=0*ones(md.mesh.numberofvertices,1); + pos=find(md.mask.ocean_levelset>0); + md.friction.coefficient(pos)=5; + md.friction.p=ones(md.mesh.numberofelements,1); + md.friction.q=ones(md.mesh.numberofelements,1); + + %temperatures and surface mass balance: + md.initialization.temperature=(273.15-22)*ones(md.mesh.numberofvertices,1); + md.initialization.pressure=md.materials.rho_ice*md.constants.g*(md.geometry.surface-md.geometry.base); + md.smb.mass_balance = 0*ones(md.mesh.numberofvertices,1); + + %Flow law + md.materials.rheology_B=paterson(md.initialization.temperature); + md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); + md.damage.D=zeros(md.mesh.numberofvertices,1); + md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1); + + %the spcs going + 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); + md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6); + md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3); + md.masstransport.spcthickness=NaN*ones(md.mesh.numberofvertices,1); + + %get some flux at the ice divide: + pos=find(md.mesh.lat==min(md.mesh.lat)); + md.masstransport.spcthickness(pos)=md.geometry.thickness(pos); + md.stressbalance.spcvy(pos)=800; + md.stressbalance.spcvx(pos)=0; + + %deal with boundaries, excluding icefront: + pos=find(md.mesh.long==min(md.mesh.long) | md.mesh.long==max(md.mesh.long)); + md.stressbalance.spcvx(pos)=0; + + point1=find(md.mesh.y==min(md.mesh.y)); point2=find(md.mesh.x==max(md.mesh.x)); + costheta=(md.mesh.x(point2)-md.mesh.x(point1))/sqrt((md.mesh.x(point2)-md.mesh.x(point1)).^2+(md.mesh.y(point2)-md.mesh.y(point1)).^2); + sintheta=(md.mesh.y(point2)-md.mesh.y(point1))/sqrt((md.mesh.x(point2)-md.mesh.x(point1)).^2+(md.mesh.y(point2)-md.mesh.y(point1)).^2); + md.stressbalance.referential(:,1:3)=repmat([costheta,sintheta,0],md.mesh.numberofvertices,1); + md.stressbalance.referential(:,4:6)=repmat([-sintheta,costheta,0],md.mesh.numberofvertices,1); + + 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.basalforcings.geothermalflux=.064*ones(md.mesh.numberofvertices,1); + + %flow equations: + md=setflowequation(md,'SSA','all'); + + savemodel(org,md); +end +% }}} + +%Run MITgcm/ISSM +% {{{ RunCoupledMITgcmISSM: +if perform(org,'RunCoupledMITgcmISSM'), + + loaddata(org,'Parameters'); + loaddata(org,'Bathymetry'); + loaddata(org,'IceSheetGeometry'); + loaddata(org,'ParameterizeIce'); + + % {{{ prepare ISSM + md.transient.isoceancoupling=1; + md.transient.isgroundingline=0; + md.transient.isthermal=0; + md.groundingline.migration='SubelementMigration'; + md.groundingline.melt_interpolation='NoMeltOnPartiallyFloating'; + md.groundingline.friction_interpolation='SubelementFriction2'; + md.masstransport.stabilization=1; + md.timestepping.coupling_time=1/24/365/100; % 1/100 hour in decimal years + md.timestepping.time_step=1/24/365/100; % 1/100 hour in decimal years + md.timestepping.final_time=23/24/365; % hour 23 in decimal years + md.cluster=generic('name',oshostname(),'np',2); + md.cluster.npocean=nPx*nPy; + md.cluster.np=2; + md.cluster.executionpath=[pwd '/run']; + md.transient.requested_outputs={'default','MaskOceanLevelset'}; + md.masstransport.requested_outputs={'default','BasalforcingsFloatingiceMeltingRate'}; + % }}} + % {{{ prepare MITgcm + % rename previous run directory and create new one + if exist ('run.old') + !\rm -rf run.old + end + if exist ('run') + !\mv run run.old + end + !\mkdir run + !\cp ../MITgcm/build/mitgcmuv run + !\cp ../MITgcm/input_4004/* run + + % {{{ Construct MITgcm binary input files + namF='run/bathy_flat.bin'; + fid=fopen(namF,'w','b'); fwrite(fid,bathymetry,prec);fclose(fid); + + namF='run/shelficeTopo.Lin.bin'; + fid=fopen(namF,'w','b'); fwrite(fid,draft,prec);fclose(fid); + + del_T = (T_bot - T_sfc)/(59*delZ); + tref=zeros(1,Nz); + for k = 1:Nz; + tref(k) = T_sfc + del_T*((k-20)*delZ); + tref(k)= max(T_sfc,min(tref(k),T_bot)); + end + namF='run/temp_obc.bin'; + tref=[tref; tref; tref]; + fid=fopen(namF,'w','b'); fwrite(fid,tref,prec);fclose(fid); + + del_S = (S_bot - S_sfc)/(59*delZ); + sref=zeros(1,Nz); + for k = 1:Nz; + sref(k) = S_sfc + del_S*((k-20)*delZ); + sref(k)= max(S_sfc,min(sref(k),S_bot)); + end + namF='run/salt_obc.bin'; + sref=[sref; sref; sref]; + fid=fopen(namF,'w','b'); fwrite(fid,sref,prec);fclose(fid); + + zax=[1:Nz]; + v1=2.5e-2; + var=1+Nz-2*zax; var=var/(Nz-1); + vobc=v1*var; + namF='run/vVel_obc.bin'; + vobc=[vobc; vobc; vobc]; + fid=fopen(namF,'w','b'); fwrite(fid,vobc,prec);fclose(fid); + + var=zeros(Nx,Ny,Nz); + for i=1:Nx, for j=1:Ny + var(i,j,:)=tref(1,:); + end, end + namF='run/temp_ini.bin'; + fid=fopen(namF,'w','b'); fwrite(fid,var,prec);fclose(fid); + + for i=1:Nx, for j=1:Ny + var(i,j,:)=sref(1,:); + end, end + namF='run/salt_ini.bin'; + fid=fopen(namF,'w','b'); fwrite(fid,var,prec);fclose(fid); + % }}} + % }}} + + md=solveiceocean(md,'Transient','runtimename',false); + + savemodel(org,md); + + plotmodel(md,'data',md.results.TransientSolution(end).Vel,'data',md.results.TransientSolution(end).Thickness) + +%eval(['!mpiexec -np ' int2str(md.cluster.np) ' ' md.cluster.codepath '/issm_ocean.exe TransientSolution ' pwd ' ' md.miscellaneous.name ' ']); +%eval(['!mpiexec -np ' int2str(md.cluster.np) ' ' md.cluster.codepath '/issm_ocean.exe TransientSolution ' pwd ' ' md.miscellaneous.name ' : -np ' int2str(nPx*nPy) ' ./mitgcmuv']); +end +% }}} Index: /issm/trunk/test/NightlyRun/test427.py =================================================================== --- /issm/trunk/test/NightlyRun/test427.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test427.py (revision 27035) @@ -2,9 +2,9 @@ from model import * from socket import gethostname - -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve md = triangle(model(), '../Exp/Square.exp', 150000.) Index: /issm/trunk/test/NightlyRun/test436.py =================================================================== --- /issm/trunk/test/NightlyRun/test436.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test436.py (revision 27035) @@ -3,9 +3,9 @@ from model import * from socket import gethostname -from triangle import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve md = triangle(model(), '../Exp/Square.exp', 150000.) @@ -26,5 +26,5 @@ for i in ['LliboutryDuval', 'CuffeyTemperate']: print(' ') - print(' == == == Testing rheology law: ' + i + ' = ') + print(' ====== Testing rheology law: ' + i + ' = ') md.materials.rheology_law = i Index: /issm/trunk/test/NightlyRun/test443.py =================================================================== --- /issm/trunk/test/NightlyRun/test443.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test443.py (revision 27035) @@ -3,10 +3,9 @@ from model import * from socket import gethostname - -from triangle import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve from frictioncoulomb import frictioncoulomb from ContourToMesh import ContourToMesh Index: /issm/trunk/test/NightlyRun/test446.m =================================================================== --- /issm/trunk/test/NightlyRun/test446.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test446.m (revision 27035) @@ -1,10 +1,10 @@ -%Test Name: SquareSheetShelfStressMLHO2d +%Test Name: SquareSheetShelfStressMOLHO2d md=triangle(model(),'../Exp/Square.exp',150000.); md=setmask(md,'../Exp/SquareShelf.exp',''); md=parameterize(md,'../Par/SquareSheetShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); md.stressbalance.requested_outputs={'default','VxSurface','VySurface','VxShear','VyShear','VxBase','VyBase'}; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Stressbalance'); Index: /issm/trunk/test/NightlyRun/test446.py =================================================================== --- /issm/trunk/test/NightlyRun/test446.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test446.py (revision 27035) @@ -1,19 +1,19 @@ -#Test Name: SquareSheetShelfStressMLHO2d +#Test Name: SquareSheetShelfStressMOLHO2d from model import * from socket import gethostname - -from triangle import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve +from SetMOLHOBC import SetMOLHOBC md = triangle(model(), '../Exp/Square.exp', 150000.) md = setmask(md, '../Exp/SquareShelf.exp', '') md = parameterize(md, '../Par/SquareSheetShelf.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) md.stressbalance.requested_outputs = ['default', 'VxSurface', 'VySurface', 'VxShear', 'VyShear', 'VxBase', 'VyBase'] -md = SetMLHOBC(md); +md = SetMOLHOBC(md); md = solve(md, 'Stressbalance') Index: /issm/trunk/test/NightlyRun/test447.m =================================================================== --- /issm/trunk/test/NightlyRun/test447.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test447.m (revision 27035) @@ -1,3 +1,3 @@ -%Test Name: SquareSheetShelfTranMLHO2d +%Test Name: SquareSheetShelfTranMOLHO2d md=triangle(model(),'../Exp/Square.exp',150000.); md=setmask(md,'../Exp/SquareShelf.exp',''); @@ -13,8 +13,8 @@ md.transient.isthermal=0; md.transient.isgroundingline=1; -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); md.transient.requested_outputs={'default','GroundedArea','FloatingArea','TotalFloatingBmb','TotalGroundedBmb','TotalSmb'}; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test447.py =================================================================== --- /issm/trunk/test/NightlyRun/test447.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test447.py (revision 27035) @@ -1,3 +1,3 @@ -#Test Name: SquareSheetShelfTranMLHO2d +#Test Name: SquareSheetShelfTranMOLHO2d import numpy as np from model import * @@ -8,5 +8,5 @@ from setflowequation import setflowequation from solve import solve -from SetMLHOBC import SetMLHOBC +from SetMOLHOBC import SetMOLHOBC from frictioncoulomb import frictioncoulomb from generic import generic @@ -25,8 +25,8 @@ md.transient.isthermal = False md.transient.isgroundingline = True -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) md.transient.requested_outputs = ['default', 'GroundedArea', 'FloatingArea', 'TotalFloatingBmb', 'TotalGroundedBmb', 'TotalSmb'] -md = SetMLHOBC(md) +md = SetMOLHOBC(md) md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test448.m =================================================================== --- /issm/trunk/test/NightlyRun/test448.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test448.m (revision 27035) @@ -1,3 +1,3 @@ -%Test Name: RoundSheetShelfGLMigrationMLHO2d +%Test Name: RoundSheetShelfGLMigrationMOLHO2d radius=1.e6; shelfextent=2.e5; @@ -16,5 +16,5 @@ md=setmask(md,flags,''); md=parameterize(md,'../Par/RoundSheetShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); @@ -25,5 +25,5 @@ md.transient.isgroundingline=1; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); %test different grounding line dynamics. md.groundingline.migration='AggressiveMigration'; Index: /issm/trunk/test/NightlyRun/test448.py =================================================================== --- /issm/trunk/test/NightlyRun/test448.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test448.py (revision 27035) @@ -1,11 +1,12 @@ -#Test Name: RoundSheetShelfGLMigrationMLHO2d +#Test Name: RoundSheetShelfGLMigrationMOLHO2d import numpy as np from model import * from socket import gethostname -from roundmesh import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from roundmesh import roundmesh +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve +from SetMOLHOBC import SetMOLHOBC @@ -27,5 +28,5 @@ md = setmask(md, flags, '') md = parameterize(md, '../Par/RoundSheetShelf.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) @@ -38,5 +39,5 @@ #test different grounding line dynamics. md.groundingline.migration = 'AggressiveMigration' -md = SetMLHOBC(md); +md = SetMOLHOBC(md) md = solve(md, 'Transient') element_on_iceshelf_agressive = md.results.TransientSolution[0].MaskOceanLevelset Index: /issm/trunk/test/NightlyRun/test449.m =================================================================== --- /issm/trunk/test/NightlyRun/test449.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test449.m (revision 27035) @@ -1,3 +1,3 @@ -%Test Name: MISMIP3DMLHO +%Test Name: MISMIP3DMOLHO md=triangle(model(),'../Exp/Square.exp',100000.); md=setmask(md,'../Exp/SquareShelf.exp',''); @@ -12,5 +12,5 @@ md.geometry.base(pos)=md.geometry.bed(pos); md.geometry.surface=md.geometry.base+md.geometry.thickness; -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); %Boundary conditions: @@ -45,5 +45,5 @@ md.cluster=generic('name',oshostname(),'np',3); -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test449.py =================================================================== --- /issm/trunk/test/NightlyRun/test449.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test449.py (revision 27035) @@ -1,3 +1,3 @@ -#Test Name: MISMIP3DMLHO +#Test Name: MISMIP3DMOLHO import numpy as np from model import * @@ -8,5 +8,5 @@ from setflowequation import setflowequation from solve import solve -from SetMLHOBC import SetMLHOBC +from SetMOLHOBC import SetMOLHOBC from generic import generic @@ -24,5 +24,5 @@ md.geometry.base[pos] = md.geometry.bed[pos] md.geometry.surface = md.geometry.base + md.geometry.thickness -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') #Boundary conditions: @@ -59,5 +59,5 @@ md.cluster = generic('name', gethostname(), 'np', 3) -md = SetMLHOBC(md) +md = SetMOLHOBC(md) md = solve(md, 'Transient') #print md.results.TransientSolution[0].BasalforcingsFloatingiceMeltingRate Index: /issm/trunk/test/NightlyRun/test518.m =================================================================== --- /issm/trunk/test/NightlyRun/test518.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test518.m (revision 27035) @@ -1,10 +1,10 @@ -%Test Name: PigStressMLHO2d +%Test Name: PigStressMOLHO2d md=triangle(model(),'../Exp/Pig.exp',20000.); md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); md=parameterize(md,'../Par/Pig.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); md.stressbalance.requested_outputs={'default','VxSurface','VySurface','VxShear','VyShear','VxBase','VyBase'}; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Stressbalance'); Index: /issm/trunk/test/NightlyRun/test518.py =================================================================== --- /issm/trunk/test/NightlyRun/test518.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test518.py (revision 27035) @@ -1,10 +1,12 @@ -#Test Name: PigStressMLHO2d + +#Test Name: PigStressMOLHO2d from model import * from socket import gethostname -from triangle import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve +from SetMOLHOBC import SetMOLHOBC @@ -12,8 +14,8 @@ md = setmask(md, '../Exp/PigShelves.exp', '../Exp/PigIslands.exp') md = parameterize(md, '../Par/Pig.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) md.stressbalance.requested_outputs = ['default', 'VxSurface', 'VySurface', 'VxShear', 'VyShear', 'VxBase', 'VyBase'] -md = SetMLHOBC(md); +md = SetMOLHOBC(md) md = solve(md, 'Stressbalance') Index: /issm/trunk/test/NightlyRun/test519.m =================================================================== --- /issm/trunk/test/NightlyRun/test519.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test519.m (revision 27035) @@ -1,7 +1,7 @@ -%Test Name: PigTranMLHO2d +%Test Name: PigTranMOLHO2d md=triangle(model(),'../Exp/Pig.exp',20000.); md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); md=parameterize(md,'../Par/Pig.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); md.geometry.bed=md.geometry.base; @@ -9,5 +9,5 @@ md.mesh.scale_factor=0.9*ones(md.mesh.numberofvertices,1); md.transient.requested_outputs={'default','IceVolume','IceVolumeScaled','GroundedArea','GroundedAreaScaled','FloatingArea','FloatingAreaScaled','TotalSmb','TotalSmbScaled','TotalFloatingBmb','TotalFloatingBmbScaled'}; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test519.py =================================================================== --- /issm/trunk/test/NightlyRun/test519.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test519.py (revision 27035) @@ -1,3 +1,3 @@ -#Test Name: PigTranMLHO2d +#Test Name: PigTranMOLHO2d import numpy as np from model import * @@ -8,5 +8,5 @@ from setflowequation import setflowequation from solve import solve -from SetMLHOBC import SetMLHOBC +from SetMOLHOBC import SetMOLHOBC from generic import generic @@ -14,9 +14,9 @@ md = setmask(md, '../Exp/PigShelves.exp', '../Exp/PigIslands.exp') md = parameterize(md, '../Par/Pig.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.mesh.scale_factor = 0.9 * np.ones((md.mesh.numberofvertices)) md.transient.requested_outputs = ['default', 'IceVolume', 'IceVolumeScaled', 'GroundedArea', 'GroundedAreaScaled', 'FloatingArea', 'FloatingAreaScaled', 'TotalSmb', 'TotalSmbScaled', 'TotalFloatingBmb', 'TotalFloatingBmbScaled'] md.cluster = generic('name', gethostname(), 'np', 3) -md = SetMLHOBC(md) +md = SetMOLHOBC(md) md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test541.m =================================================================== --- /issm/trunk/test/NightlyRun/test541.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test541.m (revision 27035) @@ -35,6 +35,6 @@ field_tolerances={... 1e-11,2e-11,2e-11,1e-12,2e-11,6e-12,9e-12,1e-12,... - 1e-11,2e-11,2e-11,1e-12,2e-11,... - 2e-11,1e-11,1e-11,9e-12,2e-11,2e-11,2e-11,1e-11,... + 1e-11,2e-11,2e-11,2e-9,2e-11,... + 2e-11,1e-11,1e-11,9e-12,2e-11,3e-11,2e-11,1e-11,... 1e-11,2e-11,2e-11,8e-08,2e-11,... 2e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-9,... Index: /issm/trunk/test/NightlyRun/test541.py =================================================================== --- /issm/trunk/test/NightlyRun/test541.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test541.py (revision 27035) @@ -42,6 +42,6 @@ 'IceVolume10', 'IceVolumeAboveFloatation10', 'TotalSmb10', 'TotalGroundedBmb10', 'TotalFloatingBmb10'] field_tolerances = [1e-11, 2e-11, 2e-11, 1e-12, 2e-11, 6e-12, 9e-12, 1e-12, - 1e-11, 2e-11, 2e-11, 1e-12, 2e-11, - 2e-11, 1e-11, 1e-11, 9e-12, 2e-11, 2e-11, 2e-11, 1e-11, + 1e-11, 2e-11, 2e-11, 2e-9, 2e-11, + 2e-11, 1e-11, 1e-11, 9e-12, 2e-11, 3e-11, 2e-11, 1e-11, 1e-11, 2e-11, 2e-11, 8e-08, 2e-11, 2e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-9, Index: /issm/trunk/test/NightlyRun/test542.py =================================================================== --- /issm/trunk/test/NightlyRun/test542.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test542.py (revision 27035) @@ -1,14 +1,13 @@ #Test Name: PigTranFrontalforcingsrignot import numpy as np - -from calvingvonmises import * -from frontalforcingsrignot import * +from calvingvonmises import calvingvonmises +from frontalforcingsrignot import frontalforcingsrignot from socket import gethostname from model import * -from parameterize import * -from setflowequation import * -from setmask import * -from solve import * -from triangle import * +from parameterize import parameterize +from setflowequation import setflowequation +from setmask import setmask +from solve import solve +from triangle import triangle @@ -35,10 +34,10 @@ md.frontalforcings = frontalforcingsrignot() md.frontalforcings.num_basins = 2 -md.frontalforcings.basin_id = idbasin - 1 # NOTE: offset because of 1-based vertex indexing +md.frontalforcings.basin_id = idbasin md.frontalforcings.subglacial_discharge = 0.1 * np.ones((md.mesh.numberofvertices,)) md.frontalforcings.thermalforcing = 0.5 * np.ones((md.mesh.numberofvertices,)) for elem in range(md.mesh.numberofelements): if idbasin[elem] == 2: - md.frontalforcings.thermalforcing[md.mesh.elements[elem, 0:3] - 1] = 1.5 # NOTE: offset because of 1-based vertex indexing + md.frontalforcings.thermalforcing[md.mesh.elements[elem, 0:3] - 1] = 1.5 #NOTE: offset because of 1-based vertex indexing md.transient.ismovingfront = 1 @@ -51,14 +50,11 @@ # Fields and tolerances to track changes -field_names = [ - 'Vx1', 'Vy1', 'Vel1', 'Pressure1', 'Bed1', 'Surface1', 'Thickness1', 'MaskIceLevelset1', 'CalvingMetlingRate1', - 'Vx2', 'Vy2', 'Vel2', 'Pressure2', 'Bed2', 'Surface2', 'Thickness2', 'MaskIceLevelset2', 'CalvingMetlingRate2', - 'Vx10', 'Vy10', 'Vel10', 'Pressure10', 'Bed10', 'Surface10', 'Thickness10', 'MaskIceLevelset10', 'CalvingMetlingRate10' -] +field_names = ['Vx1', 'Vy1', 'Vel1', 'Pressure1', 'Bed1', 'Surface1', 'Thickness1', 'MaskIceLevelset1', 'CalvingMetlingRate1', + 'Vx2', 'Vy2', 'Vel2', 'Pressure2', 'Bed2', 'Surface2', 'Thickness2', 'MaskIceLevelset2', 'CalvingMetlingRate2', + 'Vx10', 'Vy10', 'Vel10', 'Pressure10', 'Bed10', 'Surface10', 'Thickness10', 'MaskIceLevelset10', 'CalvingMetlingRate10'] field_tolerances = [ 1e-11, 2e-11, 2e-11, 1e-12, 2e-11, 6e-12, 9e-12, 1e-12, 1e-9, 2e-11, 1e-11, 1e-11, 9e-12, 2e-1, 2e-11, 2e-11, 1e-11, 1e-9, - 2e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-9, 1e-9 -] + 2e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-10, 1e-9, 1e-9] field_values = [ md.results.TransientSolution[0].Vx, Index: /issm/trunk/test/NightlyRun/test543.py =================================================================== --- /issm/trunk/test/NightlyRun/test543.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test543.py (revision 27035) @@ -1,13 +1,12 @@ #Test Name: PigTranStochasticforcing import numpy as np - -from frontalforcingsrignotautoregression import * +from frontalforcingsrignotautoregression import frontalforcingsrignotautoregression from socket import gethostname from model import * -from parameterize import * -from setflowequation import * -from setmask import * -from solve import * -from triangle import * +from parameterize import parameterize +from setflowequation import setflowequation +from setmask import setmask +from solve import solve +from triangle import triangle @@ -41,11 +40,11 @@ idb_df[ii] = 2 #Dimensionalities -nb_tf = 2 -nb_clv = 2 +nb_tf = 2 +nb_clv = 2 nb_flmlt = 2 # Calving parameters md.mask.ice_levelset = 1e4 * (md.mask.ice_levelset + 0.5) -md.calving.calvingrate = 0.3*np.ones((md.mesh.numberofvertices,)) +md.calving.calvingrate = 0.3 * np.ones((md.mesh.numberofvertices,)) md.levelset.spclevelset = np.full((md.mesh.numberofvertices,), np.nan) md.levelset.migration_max = 10.0 @@ -53,5 +52,5 @@ md.frontalforcings = frontalforcingsrignotautoregression() md.frontalforcings.num_basins = nb_tf -md.frontalforcings.basin_id = idb_tf - 1 # NOTE: offset because of 1-based vertex indexing +md.frontalforcings.basin_id = idb_tf md.frontalforcings.subglacial_discharge = 0.1 * np.ones((md.mesh.numberofvertices,)) md.frontalforcings.beta0 = np.array([[0.05, 0.01]]) # intercept values of TF in basins [C] @@ -62,11 +61,11 @@ md.frontalforcings.phi = np.array([[0.1, -0.1, 0.01, -0.01], [0.2, -0.2, 0.1, 0.0]]) # autoregressive parameters #Floating Ice Melt parameters -md.basalforcings.floatingice_melting_rate = 0.1*np.ones((md.mesh.numberofvertices,)) +md.basalforcings.floatingice_melting_rate = 0.1 * np.ones((md.mesh.numberofvertices,)) #Covariance matrix -covtf = 1e-4*np.identity(nb_tf) -covclv = 1e-1*np.identity(nb_clv) -covclv[0,0] = 1/10*covclv[0,0] -covflmlt = 0.05*np.identity(nb_flmlt) +covtf = 1e-4 * np.identity(nb_tf) +covclv = 1e-1 * np.identity(nb_clv) +covclv[0, 0] = 1 / 10 * covclv[0, 0] +covflmlt = 0.05 * np.identity(nb_flmlt) #covglob = np.zeros([6,6]) #covglob[0:2,0:2] = covtf @@ -75,5 +74,10 @@ #Hard-coding covariance matrix because python is complaining -covglob = np.array([[1e-4,0.,0.,0.,0.,0.],[0.,1e-4,0.,0.,0.,0.],[0.,0.,1e-2,0.,0.,0.],[0.,0.,0.,1e-1,0.,0.],[0.,0.,0.,0.,0.05,0.],[0.,0.,0.,0.,0.,0.05]]) +covglob = np.array([[1e-4, 0., 0., 0., 0., 0.], + [0., 1e-4, 0., 0., 0., 0.], + [0., 0., 1e-2, 0., 0., 0.], + [0., 0., 0., 1e-1, 0., 0.], + [0., 0., 0., 0., 0.05, 0.], + [0., 0., 0., 0., 0., 0.05]]) #testchol = np.linalg.cholesky(covglob) #print(testchol) @@ -81,14 +85,14 @@ # Stochastic forcing md.stochasticforcing.isstochasticforcing = 1 -md.stochasticforcing.fields = ['FrontalForcingsRignotAutoregression','DefaultCalving','FloatingMeltRate'] +md.stochasticforcing.fields = ['FrontalForcingsRignotAutoregression', 'DefaultCalving', 'FloatingMeltRate'] md.stochasticforcing.defaultdimension = 2 -md.stochasticforcing.default_id = idb_df-1 #NOTE: offset because of 1-based vertex indexing -md.stochasticforcing.covariance = covglob # global covariance among- and between-fields -md.stochasticforcing.randomflag = 0 # determines true/false randomness +md.stochasticforcing.default_id = idb_df +md.stochasticforcing.covariance = covglob # global covariance among- and between-fields +md.stochasticforcing.randomflag = 0 # determines true/false randomness -md.transient.ismovingfront = 1 +md.transient.ismovingfront = 1 md.transient.isgroundingline = 1 -md.transient.requested_outputs = ['default', 'CalvingCalvingrate','CalvingMeltingrate','BasalforcingsFloatingiceMeltingRate'] +md.transient.requested_outputs = ['default', 'CalvingCalvingrate', 'CalvingMeltingrate', 'BasalforcingsFloatingiceMeltingRate'] md.cluster = generic('name', gethostname(), 'np', 2) md = solve(md, 'Transient') @@ -96,14 +100,12 @@ # Fields and tolerances to track changes field_names = [ - 'Vx1' ,'Vy1' ,'Vel1' ,'Thickness1' ,'MaskIceLevelset1' ,'CalvingCalvingrate1' ,'CalvingMeltingrate1' ,'BasalforcingsFloatingiceMeltingRate1', - 'Vx2' ,'Vy2' ,'Vel2' ,'Thickness2' ,'MaskIceLevelset2' ,'CalvingCalvingrate1' ,'CalvingMeltingrate2' ,'BasalforcingsFloatingiceMeltingRate2', - 'Vx10','Vy10','Vel10','Thickness10','MaskIceLevelset10','CalvingCalvingrate10','CalvingMeltingrate10','BasalforcingsFloatingiceMeltingRate10' -] + 'Vx1', 'Vy1', 'Vel1', 'Thickness1', 'MaskIceLevelset1', 'CalvingCalvingrate1', 'CalvingMeltingrate1', 'BasalforcingsFloatingiceMeltingRate1', + 'Vx2', 'Vy2', 'Vel2', 'Thickness2', 'MaskIceLevelset2', 'CalvingCalvingrate1', 'CalvingMeltingrate2', 'BasalforcingsFloatingiceMeltingRate2', + 'Vx10', 'Vy10', 'Vel10', 'Thickness10', 'MaskIceLevelset10', 'CalvingCalvingrate10', 'CalvingMeltingrate10', 'BasalforcingsFloatingiceMeltingRate10'] field_tolerances = [ - 1e-11,2e-11,2e-11,1e-11,1e-9,1e-10,1e-10,1e-10, - 2e-11,1e-11,1e-11,9e-11,2e-9,1e-10,1e-10,1e-10, - 2e-10,1e-10,1e-10,1e-10,5e-9,1e-10,1e-10,1e-10 -] + 1e-11, 2e-11, 2e-11, 1e-11, 1e-9, 1e-10, 1e-10, 1e-10, + 2e-11, 1e-11, 1e-11, 9e-11, 2e-9, 1e-10, 1e-10, 1e-10, + 2e-10, 1e-10, 1e-10, 1e-10, 5e-9, 1e-10, 1e-10, 1e-10] field_values = [ md.results.TransientSolution[0].Vx, @@ -130,4 +132,3 @@ md.results.TransientSolution[9].CalvingCalvingrate, md.results.TransientSolution[9].CalvingMeltingrate, - md.results.TransientSolution[9].BasalforcingsFloatingiceMeltingRate -] + md.results.TransientSolution[9].BasalforcingsFloatingiceMeltingRate] Index: /issm/trunk/test/NightlyRun/test544.m =================================================================== --- /issm/trunk/test/NightlyRun/test544.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test544.m (revision 27035) @@ -0,0 +1,117 @@ +%Test Name: PigTranAutoregressionAndStochasticforcings +md=triangle(model(),'../Exp/Pig.exp',8000.); +md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); +md=parameterize(md,'../Par/Pig.par'); +md=setflowequation(md,'SSA','all'); +md.timestepping.start_time = 0; +md.timestepping.time_step = 1; +md.timestepping.final_time = 10; + +%Basin separation +idb = zeros(md.mesh.numberofelements,1); +iid1 = find(md.mesh.x>=-1.6e6); +for ii=1:md.mesh.numberofelements + for vertex=1:3 + if any(iid1==md.mesh.elements(ii,vertex)) %one vertex in basin 1 + idb(ii) = 1; + end + end + if idb(ii)==0 %no vertex was found in basin 1 + idb(ii) = 2; + end +end +nb_bas = 2; + +%SMB +md.smb = SMBautoregression(); +md.smb.num_basins = nb_bas; %number of basins +md.smb.basin_id = idb; %prescribe basin ID number to elements +md.smb.beta0 = [0.5,1.2]; %intercept values of SMB in basins [m ice eq./yr] +md.smb.beta1 = [0.0,0.01]; %trend values of SMB in basins [m ice eq./yr^2] +md.smb.ar_initialtime = md.timestepping.start_time; +md.smb.ar_order = 4; +md.smb.ar_timestep = 2.0; %timestep of the autoregressive model [yr] +md.smb.phi = [[0.2,0.1,0.05,0.01];[0.4,0.2,-0.2,0.1]]; + +%Calving +md.mask.ice_levelset = 1e4*(md.mask.ice_levelset + 0.5); +md.calving.calvingrate = 0.1*ones(md.mesh.numberofvertices,1); +md.levelset.spclevelset = NaN(md.mesh.numberofvertices,1); +md.levelset.migration_max = 10.0; +md.frontalforcings.meltingrate = zeros(md.mesh.numberofvertices,1); + +% Basal forcing implementation +md.basalforcings = autoregressionlinearbasalforcings(); +md.basalforcings.num_basins = nb_bas; %number of basins +md.basalforcings.basin_id = idb; %prescribe basin ID number to elements +md.basalforcings.beta0 = [1.0,2.50]; %intercept values of DeepwaterMelt in basins [m/yr] +md.basalforcings.beta1 = [0.2,0.01]; %trend values of DeepwaterMelt in basins [m/yr^2] +md.basalforcings.ar_initialtime = md.timestepping.start_time; +md.basalforcings.ar_order = 1; +md.basalforcings.ar_timestep = 1.0; %timestep of the autoregressive model [yr] +md.basalforcings.phi = [0.0;0.1]; +md.basalforcings.deepwater_elevation = [-1000,-1520]; +md.basalforcings.upperwater_elevation = [0,-50]; +md.basalforcings.upperwater_melting_rate = [0.0,0.0]; +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); + +% Covariance matrix +covsmb = 3*eye(nb_bas); +covclv = 1e-1*eye(nb_bas); +covclv(1,1) = 1/10*covclv(1,1); +covdwm = 400*eye(nb_bas); +covglob = blkdiag(covsmb,covclv,covdwm); + +% Stochastic forcing +md.stochasticforcing.isstochasticforcing = 1; +md.stochasticforcing.fields = [{'SMBautoregression'},{'DefaultCalving'},{'BasalforcingsDeepwaterMeltingRateAutoregression'}]; +md.stochasticforcing.defaultdimension = 2; +md.stochasticforcing.default_id = idb; +md.stochasticforcing.covariance = covglob; %global covariance among- and between-fields +md.stochasticforcing.randomflag = 0; %determines true/false randomness + +md.transient.ismovingfront = 1; +md.transient.requested_outputs = {'default','SmbMassBalance','BasalforcingsFloatingiceMeltingRate','BasalforcingsSpatialDeepwaterMeltingRate'}; +md.transient.isstressbalance = 1; +md.transient.ismasstransport = 1; +md.transient.issmb = 1; +md.transient.isthermal = 0; +md.transient.isgroundingline = 1; + +md.cluster=generic('name',oshostname(),'np',2); +md=solve(md,'Transient'); + +%Fields and tolerances to track changes +field_names ={... + 'Vx1' ,'Vy1' ,'Vel1' ,'Thickness1', 'SmbMassBalance1', 'BasalforcingsFloatingiceMeltingRate1', 'BasalforcingsSpatialDeepwaterMeltingRate1',... + 'Vx2' ,'Vy2' ,'Vel2' ,'Thickness2', 'SmbMassBalance2' ,'BasalforcingsFloatingiceMeltingRate2', 'BasalforcingsSpatialDeepwaterMeltingRate2',... + 'Vx3' ,'Vy3' ,'Vel3' ,'Thickness3', 'SmbMassBalance3' ,'BasalforcingsFloatingiceMeltingRate3', 'BasalforcingsSpatialDeepwaterMeltingRate3',... + }; +field_tolerances={... + 1e-11,1e-11,2e-11,1e-11,1e-10,1e-9,1e-10,... + 1e-11,1e-11,2e-11,9e-11,1e-10,1e-9,1e-10,... + 2e-10,2e-10,2e-10,1e-10,1e-10,1e-9,1e-10,... + }; +field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... + (md.results.TransientSolution(1).Vel),... + (md.results.TransientSolution(1).Thickness),... + (md.results.TransientSolution(1).SmbMassBalance),... + (md.results.TransientSolution(1).BasalforcingsFloatingiceMeltingRate),... + (md.results.TransientSolution(1).BasalforcingsSpatialDeepwaterMeltingRate),... + (md.results.TransientSolution(5).Vx),... + (md.results.TransientSolution(5).Vy),... + (md.results.TransientSolution(5).Vel),... + (md.results.TransientSolution(5).Thickness),... + (md.results.TransientSolution(5).SmbMassBalance),... + (md.results.TransientSolution(5).BasalforcingsFloatingiceMeltingRate),... + (md.results.TransientSolution(5).BasalforcingsSpatialDeepwaterMeltingRate),... + (md.results.TransientSolution(10).Vx),... + (md.results.TransientSolution(10).Vy),... + (md.results.TransientSolution(10).Vel),... + (md.results.TransientSolution(10).Thickness),... + (md.results.TransientSolution(10).SmbMassBalance),... + (md.results.TransientSolution(10).BasalforcingsFloatingiceMeltingRate),... + (md.results.TransientSolution(10).BasalforcingsSpatialDeepwaterMeltingRate),... + }; Index: /issm/trunk/test/NightlyRun/test544.py =================================================================== --- /issm/trunk/test/NightlyRun/test544.py (revision 27035) +++ /issm/trunk/test/NightlyRun/test544.py (revision 27035) @@ -0,0 +1,126 @@ +#Test Name: PigTranAutoregressionAndStochasticforcings +import numpy as np +from autoregressionlinearbasalforcings import autoregressionlinearbasalforcings +from SMBautoregression import SMBautoregression +from stochasticforcing import stochasticforcing +from socket import gethostname +from model import * +from parameterize import parameterize +from setflowequation import setflowequation +from setmask import setmask +from solve import solve +from triangle import triangle + + +md = triangle(model(), '../Exp/Pig.exp', 8000) +md = setmask(md, '../Exp/PigShelves.exp', '../Exp/PigIslands.exp') +md = parameterize(md, '../Par/Pig.py') +md = setflowequation(md, 'SSA', 'all') +md.timestepping.start_time = 0 +md.timestepping.time_step = 1 +md.timestepping.final_time = 10 + +# Basin separation +idb = np.zeros((md.mesh.numberofelements,)) +iid1 = np.where(md.mesh.x >= -1.6e6)[0] +for ii in range(md.mesh.numberofelements): + for vertex in range(3): + if md.mesh.elements[ii][vertex] - 1 in iid1: # one vertex in basin 1; NOTE: offset because of 1-based vertex indexing + idb[ii] = 1 + if idb[ii] == 0: # no vertex was found in basin 1 + for vertex in range(3): + idb[ii] = 2 +nb_bas = 2 + +#SMB +md.smb = SMBautoregression() +md.smb.num_basins = nb_bas # number of basins +md.smb.basin_id = idb # prescribe basin ID number to elements; +md.smb.beta0 = np.array([[0.5, 1.2]]) # intercept values of SMB in basins [m ice eq./yr] +md.smb.beta1 = np.array([[0.0, 0.01]]) # trend values of SMB in basins [m ice eq./yr^2] +md.smb.ar_initialtime = md.timestepping.start_time +md.smb.ar_order = 4 +md.smb.ar_timestep = 2.0 #timestep of the autoregressive model [yr] +md.smb.phi = np.array([[0.2, 0.1, 0.05, 0.01], [0.4, 0.2, -0.2, 0.1]]) + +#Calving +md.mask.ice_levelset = 1e4*(md.mask.ice_levelset + 0.5) +md.calving.calvingrate = 0.1*np.ones((md.mesh.numberofvertices,)) +md.levelset.spclevelset = np.full((md.mesh.numberofvertices,), np.nan) +md.levelset.migration_max = 10.0 +md.frontalforcings.meltingrate = np.zeros((md.mesh.numberofvertices,)) + +#Basal forcing implementation +md.basalforcings = autoregressionlinearbasalforcings() +md.basalforcings.num_basins = nb_bas +md.basalforcings.basin_id = idb +md.basalforcings.beta0 = np.array([[1.0, 2.50]]) # intercept values of DeepwaterMelt in basins [m/yr] +md.basalforcings.beta1 = np.array([[0.2, 0.01]]) # trend values of DeepwaterMelt in basins [m/yr^2] +md.basalforcings.ar_initialtime = md.timestepping.start_time # initial time in the AR model parameterization [yr] +md.basalforcings.ar_order = 1 +md.basalforcings.ar_timestep = 1.0 # timestep of the autoregressive model [yr] +md.basalforcings.phi = np.array([[0.0], [0.1]]) # autoregressive parameters +md.basalforcings.deepwater_elevation = np.array([[-1000, -1520]]) +md.basalforcings.upperwater_elevation = np.array([[0, -50]]) +md.basalforcings.upperwater_melting_rate = np.array([[0,0]]) +md.basalforcings.groundedice_melting_rate = np.zeros((md.mesh.numberofvertices,)) + +#Covariance matrix (hard-coding) +covglob = np.array([[3.0, 0., 0., 0., 0., 0.], + [0., 3.0, 0., 0., 0., 0.], + [0., 0., 0.01, 0., 0., 0.], + [0., 0., 0., 0.1, 0., 0.], + [0., 0., 0., 0., 400, 0.], + [0., 0., 0., 0., 0., 400]]) + +#Stochastic forcing +md.stochasticforcing.isstochasticforcing = 1 +md.stochasticforcing.fields = ['SMBautoregression', 'DefaultCalving', 'BasalforcingsDeepwaterMeltingRateAutoregression'] +md.stochasticforcing.defaultdimension = 2 +md.stochasticforcing.default_id = idb +md.stochasticforcing.covariance = covglob # global covariance among- and between-fields +md.stochasticforcing.randomflag = 0 # determines true/false randomness + +md.transient.ismovingfront = 1 +md.transient.requested_outputs = ['default', 'SmbMassBalance', 'BasalforcingsFloatingiceMeltingRate', 'BasalforcingsSpatialDeepwaterMeltingRate'] +md.transient.isstressbalance = 1 +md.transient.ismasstransport = 1 +md.transient.issmb = 1 +md.transient.isthermal = 0 +md.transient.isgroundingline = 1 + +md.cluster = generic('name', gethostname(), 'np', 2) +md = solve(md, 'Transient') + +# Fields and tolerances to track changes +field_names = [ + 'Vx1', 'Vy1', 'Vel1', 'Thickness1', 'SmbMassBalance1', 'BasalforcingsFloatingiceMeltingRate1', 'BasalforcingsSpatialDeepwaterMeltingRate1', + 'Vx5', 'Vy5', 'Vel5', 'Thickness5', 'SmbMassBalance5', 'BasalforcingsFloatingiceMeltingRate5', 'BasalforcingsSpatialDeepwaterMeltingRate5', + 'Vx10', 'Vy10', 'Vel10', 'Thickness10', 'SmbMassBalance10', 'BasalforcingsFloatingiceMeltingRate10', 'BasalforcingsSpatialDeepwaterMeltingRate10'] + +field_tolerances = [ + 1e-11, 1e-11, 2e-11, 1e-11, 1e10, 1e-9, 1e-10, + 1e-11, 1e-11, 2e-11, 9e-11, 1e10, 1e-9, 1e-10, + 2e-10, 2e-10, 2e-10, 1e-10, 1e10, 1e-9, 1e-10] +field_values = [ + md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[0].BasalforcingsFloatingiceMeltingRate, + md.results.TransientSolution[0].BasalforcingsSpatialDeepwaterMeltingRate, + md.results.TransientSolution[4].Vx, + md.results.TransientSolution[4].Vy, + md.results.TransientSolution[4].Vel, + md.results.TransientSolution[4].Thickness, + md.results.TransientSolution[4].SmbMassBalance, + md.results.TransientSolution[4].BasalforcingsFloatingiceMeltingRate, + md.results.TransientSolution[4].BasalforcingsSpatialDeepwaterMeltingRate, + md.results.TransientSolution[9].Vx, + md.results.TransientSolution[9].Vy, + md.results.TransientSolution[9].Vel, + md.results.TransientSolution[9].Thickness, + md.results.TransientSolution[9].SmbMassBalance, + md.results.TransientSolution[9].BasalforcingsFloatingiceMeltingRate, + md.results.TransientSolution[9].BasalforcingsSpatialDeepwaterMeltingRate] Index: /issm/trunk/test/NightlyRun/test612.py =================================================================== --- /issm/trunk/test/NightlyRun/test612.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test612.py (revision 27035) @@ -2,5 +2,6 @@ import numpy as np from model import * -from setmask import * +from setmask import setmask +from setflowequation import setflowequation from triangle import triangle from parameterize import parameterize Index: /issm/trunk/test/NightlyRun/test621.py =================================================================== --- /issm/trunk/test/NightlyRun/test621.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test621.py (revision 27035) @@ -12,17 +12,17 @@ md = triangle(model(), '../Exp/79North.exp', 6000) -md = setmask(md, '../Exp/79NorthShelf.exp','') +md = setmask(md, '../Exp/79NorthShelf.exp', '') md = parameterize(md, '../Par/79North.py') md = setflowequation(md, 'SSA', 'all') #Default friction -md.friction = friction() -md.friction.coefficient = 30*np.ones(md.mesh.numberofvertices) -md.friction.p = 1*np.ones((md.mesh.numberofelements)) -md.friction.q = 1*np.ones((md.mesh.numberofelements)) +md.friction = friction() +md.friction.coefficient = 30 * np.ones(md.mesh.numberofvertices) +md.friction.p = np.ones((md.mesh.numberofelements)) +md.friction.q = np.ones((md.mesh.numberofelements)) # Basin separation default -idb_df = np.zeros((md.mesh.numberofelements,)) -iid1 = np.where(md.mesh.y<=-1.08e6)[0] +idb_df = np.zeros((md.mesh.numberofelements)) +iid1 = np.where(md.mesh.y <= -1.08e6)[0] for ii in range(md.mesh.numberofelements): for vertex in range(3): @@ -33,59 +33,49 @@ idb_df[ii] = 2 #Covariance matrix -covPw = np.array([[0.75e10,0.0],[0.0,0.5e10]]) +covPw = np.array([[0.75e10, 0.0], [0.0, 0.5e10]]) # Stochastic forcing md.stochasticforcing.isstochasticforcing = 1 -md.stochasticforcing.fields = ['FrictionWaterPressure'] -md.stochasticforcing.defaultdimension = 2 -md.stochasticforcing.default_id = idb_df-1 #NOTE: offset because of 1-based vertex indexing -md.stochasticforcing.covariance = covPw # global covariance -md.stochasticforcing.randomflag = 0 # determines true/false randomness +md.stochasticforcing.fields = ['FrictionWaterPressure'] +md.stochasticforcing.defaultdimension = 2 +md.stochasticforcing.default_id = idb_df +md.stochasticforcing.covariance = covPw # global covariance +md.stochasticforcing.randomflag = 0 # determines true/false randomness -md.transient.issmb = 0; -md.transient.ismasstransport = 1; -md.transient.isstressbalance = 1; -md.transient.isthermal = 0; -md.transient.isgroundingline = 0; +md.transient.issmb = 0 +md.transient.ismasstransport = 1 +md.transient.isstressbalance = 1 +md.transient.isthermal = 0 +md.transient.isgroundingline = 0 md.transient.requested_outputs = ['default', 'FrictionWaterPressure'] md.timestepping.start_time = 0 -md.timestepping.time_step = 1 +md.timestepping.time_step = 1 md.timestepping.final_time = 5 -md.cluster = generic('name',gethostname(),'np',3) +md.cluster = generic('name', gethostname(), 'np', 3) md = solve(md, 'Transient') # Fields and tolerances to track changes -field_names = [ - 'Vx1','Vy1','Vel1','Thickness1','FrictionWaterPressure1', - 'Vx2','Vy2','Vel2','Thickness2','FrictionWaterPressure2', - 'Vx10','Vy10','Vel10','Thickness10','FrictionWaterPressure10' - ] +field_names = ['Vx1', 'Vy1', 'Vel1', 'Thickness1', 'FrictionWaterPressure1', + 'Vx2', 'Vy2', 'Vel2', 'Thickness2', 'FrictionWaterPressure2', + 'Vx10', 'Vy10', 'Vel10', 'Thickness10', 'FrictionWaterPressure10'] -field_tolerances = [ - 2e-10,2e-10,2e-10,2e-10,2e-10, - 4e-10,4e-10,4e-10,4e-10,4e-10, - 8e-10,8e-10,8e-10,8e-10,8e-10 - ] +field_tolerances = [2e-10, 2e-10, 2e-10, 2e-10, 2e-10, + 4e-10, 4e-10, 4e-10, 4e-10, 4e-10, + 8e-10, 8e-10, 8e-10, 8e-10, 8e-10] -field_values = [ - md.results.TransientSolution[0].Vx, - md.results.TransientSolution[0].Vy, - md.results.TransientSolution[0].Vel, - md.results.TransientSolution[0].Thickness, - md.results.TransientSolution[0].FrictionWaterPressure, - md.results.TransientSolution[1].Vx, - md.results.TransientSolution[1].Vy, - md.results.TransientSolution[1].Vel, - md.results.TransientSolution[1].Thickness, - md.results.TransientSolution[1].FrictionWaterPressure, - md.results.TransientSolution[4].Vx, - md.results.TransientSolution[4].Vy, - md.results.TransientSolution[4].Vel, - md.results.TransientSolution[4].Thickness, - md.results.TransientSolution[4].FrictionWaterPressure - ] - - - - +field_values = [md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].FrictionWaterPressure, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].FrictionWaterPressure, + md.results.TransientSolution[4].Vx, + md.results.TransientSolution[4].Vy, + md.results.TransientSolution[4].Vel, + md.results.TransientSolution[4].Thickness, + md.results.TransientSolution[4].FrictionWaterPressure] Index: /issm/trunk/test/NightlyRun/test701.py =================================================================== --- /issm/trunk/test/NightlyRun/test701.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test701.py (revision 27035) @@ -66,5 +66,5 @@ md.flowequation.fe_FS = i md = solve(md, 'Stressbalance') - field_names = field_names + [['Vx' + i], ['Vy' + i], ['Vel' + i], ['Pressure' + i]] + field_names = field_names + ['Vx' + i, 'Vy' + i, 'Vel' + i, 'Pressure' + i] field_tolerances = field_tolerances + [9e-5, 9e-5, 9e-5, 1e-10] field_values = field_values + [md.results.StressbalanceSolution.Vx, Index: /issm/trunk/test/NightlyRun/test810.m =================================================================== --- /issm/trunk/test/NightlyRun/test810.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test810.m (revision 27035) @@ -1,7 +1,7 @@ -%Test Name: ValleyGlacierLevelsetMLHO2d +%Test Name: ValleyGlacierLevelsetMOLHO2d md=triangle(model(),'../Exp/Square.exp',50000); md=setmask(md,'',''); md=parameterize(md,'../Par/ValleyGlacierShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.levelset.stabilization=2; md.cluster=generic('name',oshostname(),'np',3); @@ -15,5 +15,5 @@ md.transient.isgroundingline=1; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test810.py =================================================================== --- /issm/trunk/test/NightlyRun/test810.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test810.py (revision 27035) @@ -1,10 +1,11 @@ -#Test Name: ValleyGlacierLevelsetMLHO2d +#Test Name: ValleyGlacierLevelsetMOLHO2d from model import * from socket import gethostname -from triangle import * -from setmask import * -from parameterize import * -from setflowequation import * -from solve import * +from triangle import triangle +from setmask import setmask +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve +from SetMOLHOBC import SetMOLHOBC md = triangle(model(), '../Exp/Square.exp', 50000) @@ -12,5 +13,5 @@ md = parameterize(md, '../Par/ValleyGlacierShelf.py') md.levelset.stabilization = 2 -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) @@ -22,5 +23,5 @@ md.transient.isthermal = False md.transient.isgroundingline = True -md = SetMLHOBC(md); +md = SetMOLHOBC(md) md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test811.m =================================================================== --- /issm/trunk/test/NightlyRun/test811.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test811.m (revision 27035) @@ -1,7 +1,7 @@ -%Test Name: ValleyGlacierLevelsetCalvingMLHO2d +%Test Name: ValleyGlacierLevelsetCalvingMOLHO2d md=triangle(model(),'../Exp/Square.exp',50000); md=setmask(md,'',''); md=parameterize(md,'../Par/ValleyGlacierShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); @@ -18,5 +18,5 @@ md.levelset.migration_max = 1e10; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test811.py =================================================================== --- /issm/trunk/test/NightlyRun/test811.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test811.py (revision 27035) @@ -1,3 +1,3 @@ -#Test Name: ValleyGlacierLevelsetCalvingMLHO2d +#Test Name: ValleyGlacierLevelsetCalvingMOLHO2d import numpy as np from model import * @@ -8,5 +8,5 @@ from setflowequation import setflowequation from solve import solve -from SetMLHOBC import SetMLHOBC +from SetMOLHOBC import SetMOLHOBC from generic import generic @@ -14,5 +14,5 @@ md = setmask(md, '', '') md = parameterize(md, '../Par/ValleyGlacierShelf.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) @@ -29,5 +29,5 @@ md.levelset.migration_max = 1e10 -md = SetMLHOBC(md) +md = SetMOLHOBC(md) md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test812.m =================================================================== --- /issm/trunk/test/NightlyRun/test812.m (revision 27034) +++ /issm/trunk/test/NightlyRun/test812.m (revision 27035) @@ -1,7 +1,7 @@ -%Test Name: SquareShelfLevelsetCalvingMLHO2dLevermann +%Test Name: SquareShelfLevelsetCalvingMOLHO2dLevermann md=triangle(model(),'../Exp/Square.exp',50000.); md=setmask(md,'all',''); md=parameterize(md,'../Par/SquareShelf.par'); -md=setflowequation(md,'MLHO','all'); +md=setflowequation(md,'MOLHO','all'); md.cluster=generic('name',oshostname(),'np',3); @@ -35,5 +35,5 @@ md.transient.requested_outputs={'default','StrainRateparallel','StrainRateperpendicular','Calvingratex','Calvingratey','CalvingCalvingrate'}; -md=SetMLHOBC(md); +md=SetMOLHOBC(md); md=solve(md,'Transient'); Index: /issm/trunk/test/NightlyRun/test812.py =================================================================== --- /issm/trunk/test/NightlyRun/test812.py (revision 27034) +++ /issm/trunk/test/NightlyRun/test812.py (revision 27035) @@ -1,3 +1,3 @@ -#Test Name: SquareShelfLevelsetCalvingMLHO2dLevermann +#Test Name: SquareShelfLevelsetCalvingMOLHO2dLevermann import numpy as np from socket import gethostname @@ -8,10 +8,10 @@ from solve import solve from triangle import triangle -from SetMLHOBC import SetMLHOBC +from SetMOLHOBC import SetMOLHOBC md = triangle(model(), '../Exp/Square.exp', 50000.) md = setmask(md, 'all', '') md = parameterize(md, '../Par/SquareShelf.py') -md = setflowequation(md, 'MLHO', 'all') +md = setflowequation(md, 'MOLHO', 'all') md.cluster = generic('name', gethostname(), 'np', 3) @@ -45,5 +45,5 @@ md.transient.requested_outputs = ['default', 'StrainRateparallel', 'StrainRateperpendicular', 'Calvingratex', 'Calvingratey', 'CalvingCalvingrate'] -md = SetMLHOBC(md); +md = SetMOLHOBC(md); md = solve(md, 'Transient') Index: /issm/trunk/test/NightlyRun/test813.m =================================================================== --- /issm/trunk/test/NightlyRun/test813.m (revision 27035) +++ /issm/trunk/test/NightlyRun/test813.m (revision 27035) @@ -0,0 +1,59 @@ +%Test Name: SquareShelfLevelsetKillberg +md=triangle(model(),'../Exp/Square.exp',50000.); +md=setmask(md,'all',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=setflowequation(md,'SSA','all'); +md.cluster=generic('name',oshostname(),'np',3); + +x = md.mesh.x; +xmin = min(x); +xmax = max(x); +Lx = (xmax-xmin); +alpha = 2./3.; +md.mask.ice_levelset = ((x - alpha*Lx)>0) - ((x - alpha*Lx)<0); + +% a very special border case that fails the previous version of killberg 20220427 +icebergid = 59; +ids = [141,144,139, 58, 263]; +md.mask.ice_levelset(ids) = 1; +md.mask.ocean_levelset = -md.mask.ice_levelset; +md.mask.ocean_levelset(142) = 1; +md.mask.ocean_levelset(141) = 1; +md.mask.ocean_levelset(143) = 1; +md.mask.ocean_levelset(144) = 1; +md.mask.ocean_levelset(139) = 1; +md.mask.ice_levelset(icebergid) = -1; + +md.levelset.kill_icebergs=1; + +md.timestepping.time_step=10; +md.timestepping.final_time=30; + +%Transient +md.transient.isstressbalance=0; +md.transient.ismasstransport=1; +md.transient.issmb=1; +md.transient.isthermal=0; +md.transient.isgroundingline=0; +md.transient.ismovingfront=1; + +md.calving.calvingrate=zeros(md.mesh.numberofvertices,1); +md.frontalforcings.meltingrate=10000*ones(md.mesh.numberofvertices,1); +md.levelset.spclevelset=md.mask.ice_levelset; + +md=solve(md,'Transient'); + +%Fields and tolerances to track changes +field_names ={'MaskIceLevelsetwithIceberg','MaskIceLevelset1',... + 'MaskIceLevelset2',... + 'MaskIceLevelset3'}; +field_tolerances={1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,... + 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,5e-11,... + 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,5e-11}; +field_values={... + md.mask.ice_levelset,... + md.results.TransientSolution(1).MaskIceLevelset,... + md.results.TransientSolution(2).MaskIceLevelset,... + md.results.TransientSolution(3).MaskIceLevelset,... + }; + Index: /issm/trunk/test/Par/GiaIvinsBenchmarksAB.par =================================================================== --- /issm/trunk/test/Par/GiaIvinsBenchmarksAB.par (revision 27034) +++ /issm/trunk/test/Par/GiaIvinsBenchmarksAB.par (revision 27035) @@ -14,15 +14,16 @@ md.geometry.surface=md.geometry.thickness+md.geometry.base; + +%GIA parameters specific to Experiments A and B + +md.materials=materials('litho','ice'); +md.materials.numlayers=2; +md.materials.radius = [10 6271e3 6371e3]; %100km litosphere, the rest is mantle material +md.materials.density= [3.38e3 3.36e3]; +md.materials.lame_mu= [1.45e11 6.7e10]; +md.materials.viscosity=[1e21 1e40]; + %Ice density used for benchmarking, not 917 kg/m^3 md.materials.rho_ice=1000; %kg m^3 - -%GIA parameters specific to Experiments A and B -md.gia=giaivins(); -md.gia.mantle_viscosity=10^21*ones(md.mesh.numberofvertices,1); %in Pa.s -md.gia.lithosphere_thickness=100*ones(md.mesh.numberofvertices,1); %in km -md.materials.lithosphere_shear_modulus=6.7*10^10; %in Pa -md.materials.lithosphere_density=3.36; %in g/cm^3 -md.materials.mantle_shear_modulus=1.45*10^11; %in Pa -md.materials.mantle_density=3.38; %in g/cm^3 Index: /issm/trunk/test/Par/GiaIvinsBenchmarksAB.py =================================================================== --- /issm/trunk/test/Par/GiaIvinsBenchmarksAB.py (revision 27034) +++ /issm/trunk/test/Par/GiaIvinsBenchmarksAB.py (revision 27035) @@ -6,9 +6,9 @@ from arch import * -from giaivins import giaivins from InterpFromMeshToMesh2d import * +from materials import * from paterson import * +from SetIceSheetBC import * from verbose import * -from SetIceSheetBC import * @@ -28,17 +28,15 @@ md.geometry.surface = md.geometry.thickness + md.geometry.base.reshape(-1, 1) #would otherwise create a 91x91 matrix -#Ice density used for benchmarking, not 917 kg/m^3 -md.materials.rho_ice = 1000 #kg/m^3 +# GIA parameters specific to Experiments A and B +md.materials = materials('litho', 'ice') +md.materials.radius = [10, 6271e3, 6371e3] # 100km lithosphere, the rest is mantle material +md.materials.density = [3.38e3, 3.36e3] +md.materials.lame_u = [1.45e11, 6.7e10] +md.materials.viscosity = [1e21, 1e40] -#GIA parameters specific to Experiments A and B -md.gia=giaivins(); -md.gia.mantle_viscosity = 1e21 * np.ones((md.mesh.numberofvertices, 1)) #in Pa.s -md.gia.lithosphere_thickness = 100 * np.ones((md.mesh.numberofvertices, 1)) #in km -md.materials.lithosphere_shear_modulus = 6.7 * 1e10 #in Pa -md.materials.lithosphere_density = 3.36 #in g/cm^3 -md.materials.mantle_shear_modulus = 1.45 * 1e11 #in Pa -md.materials.mantle_density = 3.38 #in g/cm^3 +# Ice density used for benchmarking, not 917 kg/m^3 +md.materials.rho_ice = 1000 # kg/m^3 -#Initial velocity +# Initial velocity x = archread('../Data/SquareSheetConstrained.arch', 'x') y = archread('../Data/SquareSheetConstrained.arch', 'y') @@ -57,10 +55,10 @@ md.initialization.pressure = np.zeros((md.mesh.numberofvertices, 1)) -#Materials +# Materials md.initialization.temperature = (273. - 20.) * np.ones((md.mesh.numberofvertices, 1)) md.materials.rheology_B = paterson(md.initialization.temperature) md.materials.rheology_n = 3. * np.ones((md.mesh.numberofelements, 1)) -#Friction +# Friction md.friction.coefficient = 20. * np.ones((md.mesh.numberofvertices, 1)) md.friction.coefficient[np.where(md.mask.ocean_levelset < 0.)] = 0. @@ -68,5 +66,5 @@ md.friction.q = np.ones((md.mesh.numberofelements, 1)) -#Numerical parameters +# Numerical parameters md.groundingline.migration = 'None' md.masstransport.stabilization = 1 @@ -81,8 +79,8 @@ md.timestepping.final_time = 3. -#Boundary conditions: +# Boundary conditions: md = SetIceSheetBC(md) -#Change name so that no test have the same name +# Change name so that no test have the same name if len(inspect.stack()) > 2: md.miscellaneous.name = os.path.basename(inspect.stack()[2][1]).split('.')[0]