Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-ad.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-ad.sh (revision 11684) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-ad.sh (revision 11684) @@ -0,0 +1,44 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +./configure \ + --with-serial=no\ + --prefix=$ISSM_TIER \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/lib/libgfortran.a" \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ + --with-adolc-dir=$ISSM_TIER/externalpackages/adolc/install/ \ + --with-numthreads=8 \ + --without-thermal \ + --without-control \ + --without-hydrology \ + --without-diagnostic \ + --without-balanced \ + --without-responses \ + --without-slope \ + --without-rifts \ + --without-steadystate \ + --without-transient \ + --without-3d \ + --without-groundingline + +#--without-prognostic \ + + Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour.sh (revision 11684) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour.sh (revision 11684) @@ -0,0 +1,27 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/lib/libgfortran.a" \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-nicole.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-nicole.sh (revision 11684) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-nicole.sh (revision 11684) @@ -0,0 +1,28 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ + --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 Index: /issm/branches/trunk-jpl-damage/configure.ac =================================================================== --- /issm/branches/trunk-jpl-damage/configure.ac (revision 11683) +++ /issm/branches/trunk-jpl-damage/configure.ac (revision 11684) @@ -19,5 +19,4 @@ src/Makefile src/c/Makefile - src/ad/Makefile src/mex/Makefile src/m/Makefile @@ -50,4 +49,6 @@ src/m/utils/Ecco3/Makefile src/m/utils/Exp/Makefile + src/m/utils/Exp/manipulation/Makefile + src/m/utils/Exp/readwrite/Makefile src/m/utils/Geometry/Makefile src/m/utils/ImageProcessing/Makefile Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_daily =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_daily (revision 11684) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_daily (revision 11684) @@ -0,0 +1,100 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full paths) +ISSM_DIR="/u/astrid-r1b/cborstad/issmuci" +ISSM_TIER="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/cborstad/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="cborstad@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=8 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" + Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_nightly =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_nightly (revision 11684) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_nightly (revision 11684) @@ -0,0 +1,100 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/cborstad/issmuci" +ISSM_TIER="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/cborstad/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="cborstad@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" + Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_ucitrunk =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_ucitrunk (revision 11684) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_ucitrunk (revision 11684) @@ -0,0 +1,99 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/cborstad/issmuci" +ISSM_TIER="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/cron/trunk" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/cborstad/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="cborstad@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_validation =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_validation (revision 11684) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_borstad_validation (revision 11684) @@ -0,0 +1,99 @@ +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/cborstad/issmuci" +ISSM_TIER="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/cborstad/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco yams" + +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh install.sh" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="cborstad@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="'benchmark','all'" + Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_daily =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_daily (revision 11683) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_daily (revision 11684) @@ -19,4 +19,7 @@ #COMPILATION CONFIGURATION FILE COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" #----------------------# @@ -57,5 +60,4 @@ #Corresponding list of installation files to use EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" -EXTERNALPACKAGES_NUMCPUS=" 8 8 8 8 8 8" #---------------------# @@ -97,10 +99,2 @@ NROPTIONS="" -#------------------------# -# 7: Matlab# -#------------------------# - -#MATLAB path -MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" - -MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_nightly =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_nightly (revision 11683) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_nightly (revision 11684) @@ -19,4 +19,7 @@ #COMPILATION CONFIGURATION FILE COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" #----------------------# @@ -57,5 +60,4 @@ #Corresponding list of installation files to use EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" -EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" #---------------------# @@ -97,11 +99,2 @@ NROPTIONS="" - -#------------------------# -# 7: Matlab# -#------------------------# - -#MATLAB path -MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" - -MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_ucitrunk =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_ucitrunk (revision 11683) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_ucitrunk (revision 11684) @@ -16,4 +16,7 @@ #Machine configuration MACHINE="astrid" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-linux64-astrid.sh" #MATLAB path @@ -55,4 +58,7 @@ EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" + #---------------------# # 4: ISSM Compilation # Index: /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_validation =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_validation (revision 11683) +++ /issm/branches/trunk-jpl-damage/cron/configs/linux64_schlegel_validation (revision 11684) @@ -18,4 +18,7 @@ #COMPILATION CONFIGURATION FILE COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" #----------------------# @@ -55,6 +58,5 @@ #Corresponding list of installation files to use -EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" -EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh install.sh" #---------------------# @@ -96,10 +98,2 @@ NROPTIONS="'benchmark','all'" -#------------------------# -# 7: Matlab# -#------------------------# - -#MATLAB path -MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" - -MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" Index: /issm/branches/trunk-jpl-damage/cron/configs/macosx64_borstad =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/macosx64_borstad (revision 11684) +++ /issm/branches/trunk-jpl-damage/cron/configs/macosx64_borstad (revision 11684) @@ -0,0 +1,98 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/Users/cborstad/issmuci" +ISSM_TIER="/Users/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" + +#ISSM Architecture +ISSM_ARCH="macosx-gnu" + +#Machine configuration +MACHINE="macosx-gil" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-macosx64-chris.sh" + +#MATLAB path +MATLAB_PATH="/Applications/MATLAB_R2011b.app/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" + +#execution path used for parallel runs +EXECUTION_PATH="/Users/cborstad/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/Users/cborstad/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="cborstad@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=4 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="'exclude',[137 425:434 527]" + Index: /issm/branches/trunk-jpl-damage/cron/configs/macosx64_borstad_daily =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/macosx64_borstad_daily (revision 11684) +++ /issm/branches/trunk-jpl-damage/cron/configs/macosx64_borstad_daily (revision 11684) @@ -0,0 +1,98 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/Users/cborstad/issmuci" +ISSM_TIER="/Users/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" + +#ISSM Architecture +ISSM_ARCH="macosx-gnu" + +#Machine configuration +MACHINE="macosx-gil" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-macosx64-nicole.sh" + +#MATLAB path +MATLAB_PATH="/Applications/MATLAB_R2011b.app/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" + +#execution path used for parallel runs +EXECUTION_PATH="/Users/cborstad/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="/Users/cborstad/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="cborstad@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=4 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=4 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="'exclude',[137 425:434 527]" + Index: /issm/branches/trunk-jpl-damage/cron/configs/macosx64_larour =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/macosx64_larour (revision 11683) +++ /issm/branches/trunk-jpl-damage/cron/configs/macosx64_larour (revision 11684) @@ -48,5 +48,5 @@ # - "none" leave external packages as is # ->skip to section 4 -ISSM_EXTERNALPACKAGES="install" +ISSM_EXTERNALPACKAGES="copy" EXTERNALPACKAGESDIR="/Users/larour/issm-uci/trunk-jpl/externalpackages" @@ -73,8 +73,8 @@ #Mail delivery. If SKIPMAIL="no", the html nightly run report will be #sent to the adresses present in $ISSM_TIER/cron/mailinglist. -SKIPMAIL="no" +SKIPMAIL="yes" #Sender email address -EMAIL_ADRESS="schlegel@jpl.nasa.gov" +EMAIL_ADRESS="eric.larour@jpl.nasa.gov" #------------------------# @@ -84,8 +84,8 @@ #number of cpus used in ISSM installation and compilation (one is usually #safer as some packages are very sensitive to parallel compilation) -NUMCPUS_INSTALL=1 +NUMCPUS_INSTALL=4 #number of cpus used in the nightly runs. -NUMCPUS_RUN=7 +NUMCPUS_RUN=1 #Nightly run options. The matlab routine nightlyrun.m will be called @@ -102,5 +102,5 @@ #MATLAB path -MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" +MATLAB_PATH="/Applications/MATLAB_R2010a.app/" -MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" +MATLABBIN="/Applications/MATLAB_R2010a.app/bin/matlab" Index: /issm/branches/trunk-jpl-damage/cron/configs/macosx64_larour_validation =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/macosx64_larour_validation (revision 11684) +++ /issm/branches/trunk-jpl-damage/cron/configs/macosx64_larour_validation (revision 11684) @@ -0,0 +1,108 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/Users/larour/issm-uci" +ISSM_TIER="/Users/larour/issm-uci/trunk-jpl/cron/trunk-jpl" + +#ISSM Architecture +ISSM_ARCH="macosx-gnu" + +#Machine configuration +MACHINE="macosx-gil" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-macosx64-larour.sh" + + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" + +#execution path used for parallel runs +EXECUTION_PATH="/Users/larour/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="link" +EXTERNALPACKAGESDIR="/Users/larour/issm-uci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" +EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="yes" + +#Sender email address +EMAIL_ADRESS="eric.larour@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=8 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=1 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="'id',101:151" + +#------------------------# +# 7: Matlab# +#------------------------# + +#MATLAB path +MATLAB_PATH="/Applications/MATLAB_R2010a.app/" + +MATLABBIN="/Applications/MATLAB_R2010a.app/bin/matlab" + +#Specialty one: +export FC=gfortran Index: /issm/branches/trunk-jpl-damage/cron/configs/macosx64_schlegel =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/macosx64_schlegel (revision 11684) +++ /issm/branches/trunk-jpl-damage/cron/configs/macosx64_schlegel (revision 11684) @@ -0,0 +1,98 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/Users/schlegel/issmuci" +ISSM_TIER="/Users/schlegel/issmuci/trunk-jpl/cron/trunk-jpl" + +#ISSM Architecture +ISSM_ARCH="macosx-gnu" + +#Machine configuration +MACHINE="macosx-gil" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-macosx64-nicole.sh" + +#MATLAB path +MATLAB_PATH="/Applications/MATLAB_R2011b.app/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" + +#execution path used for parallel runs +EXECUTION_PATH="/Users/schlegel/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/Users/schlegel/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="schlegel@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=4 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="'exclude',[137 425:434 527]" + Index: /issm/branches/trunk-jpl-damage/cron/configs/macosx64_schlegel_daily =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/macosx64_schlegel_daily (revision 11684) +++ /issm/branches/trunk-jpl-damage/cron/configs/macosx64_schlegel_daily (revision 11684) @@ -0,0 +1,98 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/Users/schlegel/issmuci" +ISSM_TIER="/Users/schlegel/issmuci/trunk-jpl/cron/trunk-jpl" + +#ISSM Architecture +ISSM_ARCH="macosx-gnu" + +#Machine configuration +MACHINE="macosx-gil" + +#COMPILATION CONFIGURATION FILE +COMPILE_CONFIG_FILE="config-macosx64-nicole.sh" + +#MATLAB path +MATLAB_PATH="/Applications/MATLAB_R2011b.app/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" + +#execution path used for parallel runs +EXECUTION_PATH="/Users/schlegel/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="/Users/schlegel/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#Corresponding list of installation files to use +EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="schlegel@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=4 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=4 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="'exclude',[137 425:434 527]" + Index: /issm/branches/trunk-jpl-damage/cron/cronfiles/mac_cronfile =================================================================== --- /issm/branches/trunk-jpl-damage/cron/cronfiles/mac_cronfile (revision 11683) +++ /issm/branches/trunk-jpl-damage/cron/cronfiles/mac_cronfile (revision 11684) @@ -1,8 +1,9 @@ #use /bin/bash to run commands, overriding the default set by cron SHELL=/bin/bash +PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/bin -#mail output to Helene -MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov +#mail output to issm +MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov,Christopher.P.Borstad@jpl.nasa.gov,Nicole-Jeanne.Schlegel@jpl.nasa.gov,Feras.A.Habbal@jpl.nasa.gov #cronjob: issm 9:00pm -50 9 * * * cd /Users/seroussi/Desktop/backup/svn/issm/trunk/cron/ && ./nightlyrun.sh configs/macosx32_seroussi +30 00 * * 1 cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel Index: /issm/branches/trunk-jpl-damage/cron/nightlyrun.sh =================================================================== --- /issm/branches/trunk-jpl-damage/cron/nightlyrun.sh (revision 11683) +++ /issm/branches/trunk-jpl-damage/cron/nightlyrun.sh (revision 11684) @@ -122,4 +122,10 @@ cluster.executionpath='$EXECUTION_PATH'; END + cat << END > $ISSM_TIER/externalpackages/matlab/install.sh +#!/bin/bash +rm -rf install +ln -s $MATLAB_PATH install +END + fi #}}} @@ -153,4 +159,12 @@ rm -rf externalpackages cp -Rf $EXTERNALPACKAGESDIR ./ + +elif [ "$ISSM_EXTERNALPACKAGES" == "link" ] +then + + #erase externapackages, and link with externalpackages_dir + cd $ISSM_TIER + rm -rf externalpackages + ln -s $EXTERNALPACKAGESDIR . elif [ "$ISSM_EXTERNALPACKAGES" == "none" ] @@ -177,4 +191,14 @@ ./scripts/automakererun.sh source ./configs/$COMPILE_CONFIG_FILE + + #4: compile and install ISSM + if [ $NUMCPUS_INSTALL -gt 1 ] + then + echo "Making with " $NUMCPUS_INSTALL "cpus" + make -j $NUMCPUS_INSTALL install + else + make install + fi + make install @@ -259,4 +283,5 @@ cd $ISSM_TIER/nightlylog/ + MATLABBIN=$MATLAB_PATH/bin/matlab #Start test $MATLABBIN -nojvm -nosplash -r matlab_run$i -logfile matlab_log$i.log & @@ -312,6 +337,5 @@ if [ "$MACHINE" = "win7" ] then - echo $i - email -html -s "Nightly runs of $ISSM_RELEASE , configuration: $MACHINE, host: $HOST_NAME, user: $USER. " $i < $ISSM_TIER/nightlylog/report.html + email -html -s "Nightly runs on $HOST_NAME (version: $ISSM_RELEASE)" $i < $ISSM_TIER/nightlylog/report.html else if [ "$MACHINE" = "astrid" ] @@ -320,5 +344,5 @@ From: "ISSM Nightly run" <$EMAIL_ADRESS> To: $i -Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. +Subject: Nightly runs on $HOST_NAME (version: $ISSM_RELEASE) Mime-Version: 1.0 Content-Type: text/html @@ -328,5 +352,5 @@ From: "ISSM Nightly run" <$EMAIL_ADRESS> To: $i -Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. +Subject: Nightly runs on $HOST_NAME (version: $ISSM_RELEASE) Mime-Version: 1.0 Content-Type: text/html Index: /issm/branches/trunk-jpl-damage/etc/environment.sh =================================================================== --- /issm/branches/trunk-jpl-damage/etc/environment.sh (revision 11683) +++ /issm/branches/trunk-jpl-damage/etc/environment.sh (revision 11684) @@ -233,2 +233,14 @@ #CCCL export PATH="$PATH:$CCCL_DIR/bin" + +#PACKAGEMAKER +export PATH="$PATH:$PACKAGEMAKER_DIR" + +#ANDROID_NDK: +export PATH="$PATH:$ANDROID_NDK_DIR/" + +#ANDROID_SDK +export PATH="$PATH:$ANDROID_SDK_DIR/" + +#ANDROID_ANT +export PATH="$PATH:$ANDROID_ANT_DIR/" Index: /issm/branches/trunk-jpl-damage/etc/environment_variables.sh =================================================================== --- /issm/branches/trunk-jpl-damage/etc/environment_variables.sh (revision 11683) +++ /issm/branches/trunk-jpl-damage/etc/environment_variables.sh (revision 11684) @@ -169,2 +169,14 @@ #cccl CCCL_DIR="$ISSM_TIER/externalpackages/cccl/install" + +#packagemaker +PACKAGEMAKER_DIR="$ISSM_TIER/externalpackages/packagemaker/install" + +#android-ndk +ANDROID_NDK_DIR="$ISSM_TIER/externalpackages/android-ndk/install" + +#android-sdk +ANDROID_SDK_DIR="$ISSM_TIER/externalpackages/android-sdk/install-sdk" + +#android-ant +ANDROID_ANT_DIR="$ISSM_TIER/externalpackages/android-sdk/install-ant" Index: /issm/branches/trunk-jpl-damage/examples/Jakobshavn/Domain.exp =================================================================== --- /issm/branches/trunk-jpl-damage/examples/Jakobshavn/Domain.exp (revision 11684) +++ /issm/branches/trunk-jpl-damage/examples/Jakobshavn/Domain.exp (revision 11684) @@ -0,0 +1,34 @@ +## Name:JksOutline +## Icon:0 +# Points Count Value +28 1.000000 +# X pos Y pos +-442320.3882147236 -2277080.6549030584 +-415649.3149820761 -2315476.9356749961 +-356259.6577274340 -2351834.4758754564 +-309585.2795717255 -2384114.5349311619 +-279812.9187561168 -2353193.6362587260 +-274850.8586214480 -2287953.9379578433 +-294854.1635456266 -2263149.2609987380 +-309585.2795753506 -2232228.3623235333 +-348041.2456311518 -2191113.7607873622 +-376728.1557929466 -2197909.5626934194 +-391614.3362011510 -2203685.9943137392 +-417355.0231571503 -2206404.3150757281 +-420122.3381705935 -2211830.0535394503 +-421889.2049176788 -2218344.8015625700 +-420705.1891998384 -2226200.5387845989 +-425774.4833068820 -2230306.5097973733 +-429242.2244052034 -2235353.9400299159 +-427025.7933000360 -2240741.0910965428 +-431045.5636035603 -2255158.9014255330 +-424708.0734753361 -2261343.7626088522 +-423137.8820362946 -2268466.9593191240 +-428054.2739333302 -2272589.0010017036 +-432362.3262468725 -2272393.9161962867 +-435068.8255516959 -2273140.2906106352 +-437641.3726878429 -2272612.1952726739 +-439529.7800752302 -2272929.1351353633 +-442475.4525940326 -2275381.7044264446 +-442320.3882147236 -2277080.6549030584 + Index: /issm/branches/trunk-jpl-damage/examples/Jakobshavn/Front.exp =================================================================== --- /issm/branches/trunk-jpl-damage/examples/Jakobshavn/Front.exp (revision 11684) +++ /issm/branches/trunk-jpl-damage/examples/Jakobshavn/Front.exp (revision 11684) @@ -0,0 +1,15 @@ +## Name:Front +## Icon:0 +# Points Count Value +9 1.000000 +# X pos Y pos +-443691.7204476296 -2241744.0087129781 +-444020.9148401438 -2244124.0631026439 +-443856.3176438867 -2245205.9060070375 +-441551.9568962874 -2244773.1688452801 +-440399.7765224879 -2243474.9573600078 +-439905.9849337166 -2240662.1658085845 +-441387.3597000304 -2238065.7428380400 +-443856.3176438867 -2237633.0056762826 +-443691.7204476296 -2241744.0087129781 + Index: /issm/branches/trunk-jpl-damage/examples/Jakobshavn/Jks.par =================================================================== --- /issm/branches/trunk-jpl-damage/examples/Jakobshavn/Jks.par (revision 11684) +++ /issm/branches/trunk-jpl-damage/examples/Jakobshavn/Jks.par (revision 11684) @@ -0,0 +1,61 @@ + +%Name and hemisphere +md.mesh.hemisphere='n'; +md.miscellaneous.name='Jakobshavn'; + +%Load SeaRISE dataset +disp(' Loading SeaRISE data from NetCDF'); +ncdata = './Greenland_5km_v1.1.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +thk = ncread(ncdata,'thk')'; +topg = ncread(ncdata,'topg')'; +velx = ncread(ncdata,'surfvelx')'; +vely = ncread(ncdata,'surfvely')'; +temp = ncread(ncdata,'airtemp2m')'; +smb = ncread(ncdata,'smb')'; + +disp(' Interpolating thicknesses'); +md.geometry.thickness=InterpFromGridToMesh(x1,y1,thk,md.mesh.x,md.mesh.y,0); +pos0=find(md.geometry.thickness<=10); +md.geometry.thickness(pos0)=10; + +disp(' Interpolating bedrock topography'); +md.geometry.bed=InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); + +disp(' Constructing surface elevation'); +md.geometry.surface=md.geometry.thickness+md.geometry.bed; + +disp(' Interpolating velocities'); +md.inversion.vx_obs = InterpFromGridToMesh(x1,y1,velx,md.mesh.x,md.mesh.y,0); +md.inversion.vy_obs = InterpFromGridToMesh(x1,y1,vely,md.mesh.x,md.mesh.y,0); +md.inversion.vel_obs = sqrt(md.inversion.vx_obs.^2+md.inversion.vy_obs.^2); +md.initialization.vx = md.inversion.vx_obs; +md.initialization.vy = md.inversion.vy_obs; +md.initialization.vel= md.inversion.vel_obs; + +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; %convert to Kelvin + +disp(' Interpolating surface mass balance'); +md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; + +disp(' Construct basal friction parameters'); +md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +pos=find(md.mask.vertexonfloatingice); +md.friction.coefficient(pos)=0; %no friction applied on floating ice +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +%Reduce viscosity along the shear margins +weakb=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'WeakB.exp','node',2); +pos=find(weakb);md.materials.rheology_B(pos)=.3*md.materials.rheology_B(pos); + +disp(' Set other boundary conditions'); +md=SetMarineIceSheetBC(md,'./Front.exp'); +md.diagnostic.icefront(:,end)=1; %Apply water pressure at the ice front +md.basalforcings.melting_rate=zeros(md.mesh.numberofvertices,1); Index: /issm/branches/trunk-jpl-damage/examples/Jakobshavn/WeakB.exp =================================================================== --- /issm/branches/trunk-jpl-damage/examples/Jakobshavn/WeakB.exp (revision 11684) +++ /issm/branches/trunk-jpl-damage/examples/Jakobshavn/WeakB.exp (revision 11684) @@ -0,0 +1,60 @@ +## Name:WeakB +## Icon:0 +# Points Count Value +24 1.000000 +# X pos Y pos +-441022.7144520371 -2238435.7116546673 +-441639.8422268176 -2239053.0142011684 +-439171.3311276956 -2240699.1543251718 +-437319.9478033541 -2241727.9919026736 +-435879.9829955329 -2241933.7594181742 +-432382.9256051101 -2242756.8294801759 +-430942.9607972889 -2242962.5969956759 +-429708.7052477279 -2243991.4345731782 +-428680.1589564271 -2245020.2721506800 +-427651.6126651262 -2246049.1097281822 +-425800.2293407847 -2247077.9473056840 +-424565.9737912237 -2247695.2498521851 +-419341.0001274022 -2251604.8326466926 +-416049.6519952395 -2253868.2753171972 +-416049.6519952395 -2252222.1351931938 +-418312.4538361013 -2249341.3899761885 +-423331.7182416627 -2245843.3422126817 +-425594.5200825246 -2245226.0396661805 +-426623.0663738254 -2244402.9696041788 +-427445.9034068661 -2243991.4345731782 +-428885.8682146872 -2242756.8294801759 +-431148.6700555491 -2241522.2243871735 +-436497.1107703134 -2239670.3167476696 +-441022.7144520371 -2238435.7116546673 + +## Name:WeakB +## Icon:0 +# Points Count Value +24 1.000000 +# X pos Y pos +-442668.3885181184 -2245226.0396661805 +-440405.5866772566 -2245843.3422126817 +-438759.9126111752 -2246049.1097281822 +-437525.6570616142 -2246460.6447591828 +-435879.9829955329 -2246872.1797901839 +-434028.5996711914 -2248106.7848831862 +-431354.3793138092 -2249547.1574916886 +-430120.1237642482 -2249341.3899761885 +-429297.2867312076 -2250164.4600381902 +-427857.3219233864 -2249958.6925226897 +-426623.0663738254 -2250164.4600381902 +-424771.6830494839 -2250575.9950691909 +-423537.4274999229 -2250781.7625846914 +-422714.5904668822 -2251399.0651311926 +-415226.8149621988 -2259629.7657512082 +-419135.2908691420 -2259218.2307202076 +-422838.0575178250 -2255720.1829567007 +-424977.3923077441 -2252016.3676776937 +-426623.0663738254 -2251810.6001621932 +-428268.7404399067 -2251399.0651311926 +-429708.7052477279 -2251399.0651311926 +-431560.0885720694 -2251399.0651311926 +-443902.6440676794 -2246460.6447591828 +-442668.3885181184 -2245226.0396661805 + Index: /issm/branches/trunk-jpl-damage/examples/Jakobshavn/runme.m =================================================================== --- /issm/branches/trunk-jpl-damage/examples/Jakobshavn/runme.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/examples/Jakobshavn/runme.m (revision 11684) @@ -0,0 +1,92 @@ +steps=[1]; + +if any(steps==1) + disp(' Step 1: Mesh creation'); + md=triangle(model,'Domain.exp',2000); + + %Get observed velocity field on mesh nodes + ncdata='Greenland_5km_v1.1.nc'; + if ~exist(ncdata,'file'), + error('Download Greenland5km_v1.1.nc first on http://websrv.cs.umt.edu/isis/index.php/Present_Day_Greenland'); + end + x1 = ncread(ncdata,'x1'); + y1 = ncread(ncdata,'y1'); + velx = ncread(ncdata,'surfvelx'); + vely = ncread(ncdata,'surfvely'); + vx = InterpFromGridToMesh(x1,y1,velx',md.mesh.x,md.mesh.y,0); + vy = InterpFromGridToMesh(x1,y1,vely',md.mesh.x,md.mesh.y,0); + vel = sqrt(vx.^2+vy.^2); + + %refine mesh using surface velocities as metric + md=bamg(md,'hmin',1200,'hmax',15000,'field',vel,'err',5); + [md.mesh.lat,md.mesh.long] = xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + + save JksMesh.mdl md +end +if any(steps==2) + disp(' Step 2: Parameterization'); + md=loadmodel('JksMesh.mdl'); + + md=setmask(md,'',''); + md=parameterize(md,'Jks.par'); + + %zones of shear margin softening + weakb=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'WeakB.exp','node',2); + pos=find(weakb); + md.materials.rheology_B(pos)=.3*md.materials.rheology_B(pos); + + save JksPar.mdl md +end +if any(steps==3) + disp(' Step 3: Control method friction'); + md=loadmodel('JksPar.mdl'); + + md=setflowequation(md,'macayeal','all'); + + %Control general + md.inversion.iscontrol=1; + md.inversion.nsteps=20; + md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); + md.inversion.maxiter_per_step=5*ones(md.inversion.nsteps,1); + md.verbose=verbose('solution',true,'control',true); + + %Cost functions + md.inversion.cost_functions=[101*ones(md.inversion.nsteps,1) 103*ones(md.inversion.nsteps,1)]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); + md.inversion.cost_functions_coefficients(:,1)=40; + md.inversion.cost_functions_coefficients(:,2)=1; + + %Controls + md.inversion.control_parameters={'FrictionCoefficient'}; + md.inversion.gradient_scaling(1:md.inversion.nsteps)=30; + md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); + + %Additional parameters + md.diagnostic.restol=0.01; + md.diagnostic.reltol=0.1; + md.diagnostic.abstol=NaN; + + %Go solve + md.cluster=generic('name',oshostname,'np',4); + md.solver=addoptions(md.solver,NoneAnalysisEnum,asmoptions); + md.solver=addoptions(md.solver,DiagnosticVertAnalysisEnum,jacobiasmoptions); + md=solve(md,DiagnosticSolutionEnum); + + save JksControl.mdl md +end +if any(steps==4) + disp(' Plotting') + md=loadmodel('JksControl.mdl'); + + plotmodel(md,'unit#all','km','axis#all','equal',... + 'FontSize#all',12,... + 'data',md.inversion.vel_obs,'title','Observed velocity',... + 'data',md.results.DiagnosticSolution.Vel,'title','Modeled Velocity',... + 'colorbar#1','off','colorbar#2','on','colorbartitle#2','[m/yr]',... + 'caxis#1-2',[0,7000],... + 'data',md.geometry.bed,'title','Bed elevation',... + 'data',md.results.DiagnosticSolution.FrictionCoefficient,... + 'title','Friction Coefficient',... + 'colorbar#3','on','colorbartitle#3','[m]','colorbar#4','on'); +end Index: /issm/branches/trunk-jpl-damage/examples/SquareIceShelf/runme.m =================================================================== --- /issm/branches/trunk-jpl-damage/examples/SquareIceShelf/runme.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/examples/SquareIceShelf/runme.m (revision 11684) @@ -4,3 +4,4 @@ md=parameterize(md,'Square.par'); md=setflowequation(md,'macayeal','all'); +md.cluster=generic('name',oshostname,'np',2); md=solve(md,DiagnosticSolutionEnum); Index: /issm/branches/trunk-jpl-damage/externalpackages/android-ndk/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/android-ndk/install.sh (revision 11684) +++ /issm/branches/trunk-jpl-damage/externalpackages/android-ndk/install.sh (revision 11684) @@ -0,0 +1,18 @@ +#This installs the Android NDK (Native Development Kit) +#which is needed for the compilation of C/C++ code into the +#native architecture of the Android device. + +#The android-ndk-r7b-darwin-x86.tar.bz2 dummy.tar.bz2 file was downloaded +#from the android developer website: + +#Cleanup the install +rm -rf install + +# Install Android SDK and NDK. +cp android-ndk-r7b-darwin-x86.tar.bz2 dummy.tar.bz2 +bunzip2 dummy.tar.bz2 +tar -xvf dummy.tar +rm -rf dummy.tar dummy.tar.bz2 + +#Move to install +mv android-ndk-r7b install Index: /issm/branches/trunk-jpl-damage/externalpackages/android-sdk/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/android-sdk/install.sh (revision 11684) +++ /issm/branches/trunk-jpl-damage/externalpackages/android-sdk/install.sh (revision 11684) @@ -0,0 +1,60 @@ +#This installs the Android SDK (Software Development Kit) +#which is needed for the compilation of the Java project. + +step=1; + +#Different steps here. +#1: install sdk, ant and sdk tools +#2: install an emulator. +#3: test the emulator +#4: cleanup + +present_dir=`pwd`; + +if [[ $step == "1" ]]; then + + #Cleanup the install + rm -rf install-sdk install-ant + + # Install Android SDK and NDK. + unzip -o android-sdk-r16-macosx.zip + unzip -o apache-ant-1.8.2-bin.zip + + #Move to install + mv android-sdk-macosx install-sdk + mv apache-ant-1.8.2 install-ant + + #Post_install configuration: + #We need specific settings for specific platforms, for the SDK to + #function properly + + #For now, we need to install: + #android sdk platform tools + #a specific android api: API 15 + + cd install-sdk/tools/ && source ./android +fi + +if [[ $step == "2" ]]; then + + #Once this is done, we need to install an emulator. Location will default to ~/.android/avd, + #which we will move to $ISSM_TIER/externalpackages/android-emulators. + #For now, it's called: Android-4.0.3 + + cd $present_dir/install-sdk/tools + ./android avd + mv ~/.android/avd/Android-4.0.3.* $ISSM_TIER/externalpackages/android-emulators + +fi + + +if [[ $step == "3" ]]; then + + cd $present_dir/install-sdk/platform-tools + ./adb -p "$ISSM_TIER/externalpackages/android-emulators" devices + +fi + +if [[ $step == "4" ]]; then + rm -rf install-sdk install-ant +fi Index: /issm/branches/trunk-jpl-damage/externalpackages/chaco/chaco_njs_notes.txt =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/chaco/chaco_njs_notes.txt (revision 11684) +++ /issm/branches/trunk-jpl-damage/externalpackages/chaco/chaco_njs_notes.txt (revision 11684) @@ -0,0 +1,3 @@ +chaco build must be able to see malloc.h +sudo ln -s /usr/include/malloc/malloc.h /usr/include/malloc.h +or else make sure you include the malloc directory in path Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/dakota_njs_notes_macos64.txt =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/dakota_njs_notes_macos64.txt (revision 11684) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/dakota_njs_notes_macos64.txt (revision 11684) @@ -0,0 +1,5 @@ +Matlab might try to use its local /Applications/MATLAB_R2011b.app/sys/os/maci64/ fortran libraries +instead of the gfortran package libraries. Matlab library is missing some symbols, so you might +need to link to the actual gfortran library +sudo cp /Applications/MATLAB_R2011b.app/sys/os/maci64/libgfortran.3.dynlib /Applications/MATLAB_R2011b.app/sys/os/maci64/libgfortran.3.dynlib.matlab +sudo ln -s /usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.3.dylib libgfortran.3.dylib Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh (revision 11683) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh (revision 11684) @@ -28,9 +28,11 @@ #Configure dakota cd src -./configure \ - --prefix="$ISSM_TIER/externalpackages/dakota/install" \ - --without-graphics \ - --with-pic \ - --disable-mpi +./configure \ + --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas="-L$ISSM_TIER/externalpackages/petsc/install/lib -lfblas " \ + --with-lapack="-L$ISSM_TIER/externalpackages/petsc/install/lib -lflapack -lPLAPACK " cd .. @@ -44,5 +46,5 @@ mv temp ./src/methods/acro/packages/pebbl/src/Makefile -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp mv temp ./src/methods/hopspack/src-nappspack/Makefile @@ -53,5 +55,5 @@ mv temp ./src/methods/hopspack/src-shared/Makefile -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp mv temp ./src/methods/hopspack/src-shared/Makefile @@ -59,5 +61,5 @@ mv temp ./src/methods/hopspack/src-conveyor/Makefile -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp mv temp ./src/methods/hopspack/src-appspack/Makefile @@ -74,5 +76,5 @@ mv temp ./src/methods/acro/packages/tpl/3po/Makefile -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2 -D_NONSTD_SOURCE/CFLAGS = -g -O2 -fPIC/g' > temp mv temp ./src/packages/ampl/Makefile Index: /issm/branches/trunk-jpl-damage/externalpackages/matlab/install-macosx-feras.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/matlab/install-macosx-feras.sh (revision 11684) +++ /issm/branches/trunk-jpl-damage/externalpackages/matlab/install-macosx-feras.sh (revision 11684) @@ -0,0 +1,13 @@ +#!/bin/bash + +#Erase symlink +rm -rf install + +#Generic Matlab softlink for Macintosh (OSX) directory structure + +#ln -s /Applications/MATLAB_R2008a/ install +#ln -s /Applications/MATLAB_R2009a.app/ install +#ln -s /Applications/MATLAB_R2010a.app/ install +#ln -s /Applications/MATLAB_R2011b.app/ install + +ln -s /Applications/MATLAB*.app/ install Index: /issm/branches/trunk-jpl-damage/externalpackages/matlab/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/matlab/install.sh (revision 11683) +++ /issm/branches/trunk-jpl-damage/externalpackages/matlab/install.sh (revision 11684) @@ -10,6 +10,9 @@ ln -s /usr/local/matlab712/ install #ln -s /usr/local/pkgs/matlab-7.6/ install + +# Macintosh (OSX) simlink #ln -s /Applications/MATLAB_R2008a/ install #ln -s /Applications/MATLAB_R2009a.app/ install #ln -s /Applications/MATLAB_R2010a.app/ install #ln -s /Applications/MATLAB_R2011b.app/ install +#ln -s /Applications/MATLAB*.app/ install Index: /issm/branches/trunk-jpl-damage/m4/issm_options.m4 =================================================================== --- /issm/branches/trunk-jpl-damage/m4/issm_options.m4 (revision 11683) +++ /issm/branches/trunk-jpl-damage/m4/issm_options.m4 (revision 11684) @@ -250,6 +250,16 @@ HAVE_DAKOTA=yes DAKOTAINCL=-I$DAKOTA_ROOT/include - DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" - dnl DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lgslcblas -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + case "${host_os}" in + *cygwin*) + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + ;; + *linux*) + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + ;; + *darwin*) + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack" + ;; + esac AC_DEFINE([_HAVE_DAKOTA_],[1],[with Dakota in ISSM src]) AC_SUBST([DAKOTAINCL]) @@ -306,4 +316,32 @@ fi AC_MSG_RESULT($HAVE_SCOTCH) + dnl }}} + dnl adolc{{{1 + AC_ARG_WITH([adolc-dir], + AS_HELP_STRING([--with-adolc-dir = DIR], [adolc root directory.]), + [ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) + AC_MSG_CHECKING(for ADOLC) + + if test "x$ADOLC_ROOT" = "xno"; then + HAVE_ADOLC=no + else + if test -d "$ADOLC_ROOT"; then + + dnl defaults + HAVE_ADOLC=yes + ADOLCINCL="-I$ADOLC_ROOT/include/adolc -I$ADOLC_ROOT/include" + ADOLCLIB="-L$ADOLC_ROOT/lib64 -ladolc" + + AC_DEFINE([_HAVE_ADOLC_],[1],[with adolc in ISSM src]) + AC_SUBST([ADOLCINCL]) + AC_SUBST([ADOLCLIB]) + + else + echo "Specified directory does not exist!" + exit 1 + fi + fi + AM_CONDITIONAL([ADOLC], [test x$HAVE_ADOLC = xyes]) + AC_MSG_RESULT($HAVE_ADOLC) dnl }}} dnl adic2{{{1 Index: /issm/branches/trunk-jpl-damage/src/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/Makefile.am (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/Makefile.am (revision 11684) @@ -1,8 +1,2 @@ EXTRA_DIST = perl pro SUBDIRS = c mex m - -if ADIC2 -SUBDIRS += ad -endif - - Index: sm/branches/trunk-jpl-damage/src/ad/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/ad/Makefile.am (revision 11683) +++ (revision ) @@ -1,630 +1,0 @@ -INCLUDES = @DAKOTAINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ - -#This Makefile.am is for automatic differentiation of the parallel version of ISSM. -#We do not compile in serial mode -#If user requests no parallel compilation, we compile an empty ISSM. -#Compilation can still be blocked if user has not activated --with-adic compilation - -#Library declaration {{{1 - -if NOPARALLEL -lib_LIBRARIES = -else -lib_LIBRARIES = libpISSM.a libOverload.a -endif - -if ADIC2 -lib_LIBRARIES += libAD.a libpISSMRose.a -endif - -#}}} -#Overload library, to overload any non-standard symbols. {{{1 -libOverload_a_SOURCES = ./shared/String/stricmp.c -libOverload_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) -#}}} -#ISSM library {{{1 -libpISSM_a_SOURCES = ./include/macros.h\ - ./include/typedefs.h\ - ./include/types.h\ - ./include/include.h\ - ./objects/objects.h\ - ./objects/Object.h\ - ./objects/Gauss/GaussTria.h\ - ./objects/Gauss/GaussTria.cpp\ - ./objects/Update.h\ - ./objects/Element.h\ - ./objects/FemModel.h\ - ./objects/FemModel.cpp\ - ./objects/Material.h\ - ./objects/Load.h\ - ./objects/Loads/Friction.h\ - ./objects/Loads/Friction.cpp\ - ./objects/Inputs/TransientInput.h\ - ./objects/Inputs/TransientInput.cpp\ - ./objects/Constraints/SpcTransient.cpp\ - ./objects/Constraints/SpcTransient.h\ - ./objects/DofIndexing.h\ - ./objects/DofIndexing.cpp\ - ./objects/IoModel.h\ - ./objects/IoModel.cpp\ - ./objects/Node.h\ - ./objects/Node.cpp\ - ./objects/Segment.h\ - ./objects/Segment.cpp\ - ./objects/Vertex.h\ - ./objects/Vertex.cpp\ - ./objects/Hook.h\ - ./objects/Hook.cpp\ - ./objects/Patch.h\ - ./objects/Patch.cpp\ - ./objects/ElementResults/ElementResultLocal.h\ - ./objects/ElementResults/DoubleElementResult.h\ - ./objects/ElementResults/DoubleElementResult.cpp\ - ./objects/ElementResults/TriaVertexElementResult.h\ - ./objects/ElementResults/TriaVertexElementResult.cpp\ - ./objects/ElementResults/BoolElementResult.h\ - ./objects/ElementResults/BoolElementResult.cpp\ - ./objects/ExternalResults/ExternalResult.h\ - ./objects/ExternalResults/BoolExternalResult.h\ - ./objects/ExternalResults/BoolExternalResult.cpp\ - ./objects/ExternalResults/DoubleExternalResult.h\ - ./objects/ExternalResults/DoubleExternalResult.cpp\ - ./objects/ExternalResults/DoubleVecExternalResult.h\ - ./objects/ExternalResults/DoubleVecExternalResult.cpp\ - ./objects/ExternalResults/DoubleMatExternalResult.h\ - ./objects/ExternalResults/DoubleMatExternalResult.cpp\ - ./objects/ExternalResults/IntExternalResult.h\ - ./objects/ExternalResults/IntExternalResult.cpp\ - ./objects/ExternalResults/StringExternalResult.h\ - ./objects/ExternalResults/StringExternalResult.cpp\ - ./objects/ExternalResults/PetscVecExternalResult.h\ - ./objects/ExternalResults/PetscVecExternalResult.cpp\ - ./objects/Elements/Tria.h\ - ./objects/Elements/Tria.cpp\ - ./objects/Elements/TriaHook.h\ - ./objects/Elements/TriaHook.cpp\ - ./objects/Elements/TriaRef.h\ - ./objects/Elements/TriaRef.cpp\ - ./objects/Inputs/Input.h\ - ./objects/Inputs/InputLocal.h\ - ./objects/Inputs/TriaVertexInput.h\ - ./objects/Inputs/TriaVertexInput.cpp\ - ./objects/Inputs/BoolInput.h\ - ./objects/Inputs/BoolInput.cpp\ - ./objects/Inputs/IntInput.h\ - ./objects/Inputs/IntInput.cpp\ - ./objects/Inputs/DoubleInput.h\ - ./objects/Inputs/DoubleInput.cpp\ - ./objects/Inputs/DatasetInput.h\ - ./objects/Inputs/DatasetInput.cpp\ - ./objects/Materials/Matice.h\ - ./objects/Materials/Matice.cpp\ - ./objects/Materials/Matpar.h\ - ./objects/Materials/Matpar.cpp\ - ./objects/Constraints/Constraint.h\ - ./objects/Constraints/SpcStatic.cpp\ - ./objects/Constraints/SpcStatic.h\ - ./objects/Constraints/SpcDynamic.cpp\ - ./objects/Constraints/SpcDynamic.h\ - ./objects/Loads/Penpair.cpp\ - ./objects/Loads/Penpair.h\ - ./objects/Loads/Pengrid.cpp\ - ./objects/Loads/Pengrid.h\ - ./objects/Loads/Icefront.cpp\ - ./objects/Loads/Icefront.h\ - ./objects/Loads/Numericalflux.cpp\ - ./objects/Loads/Numericalflux.h\ - ./objects/Numerics/ElementMatrix.h\ - ./objects/Numerics/ElementMatrix.cpp\ - ./objects/Numerics/ElementVector.h\ - ./objects/Numerics/ElementVector.cpp\ - ./objects/Params/Param.h\ - ./objects/Params/BoolParam.cpp\ - ./objects/Params/BoolParam.h\ - ./objects/Params/IntParam.cpp\ - ./objects/Params/IntParam.h\ - ./objects/Params/IntVecParam.cpp\ - ./objects/Params/IntVecParam.h\ - ./objects/Params/IntMatParam.cpp\ - ./objects/Params/IntMatParam.h\ - ./objects/Params/DoubleParam.cpp\ - ./objects/Params/DoubleParam.h\ - ./objects/Params/FileParam.cpp\ - ./objects/Params/FileParam.h\ - ./objects/Params/PetscMatParam.cpp\ - ./objects/Params/PetscMatParam.h\ - ./objects/Params/StringArrayParam.cpp\ - ./objects/Params/StringArrayParam.h\ - ./objects/Params/DoubleMatParam.cpp\ - ./objects/Params/DoubleMatParam.h\ - ./objects/Params/DoubleMatArrayParam.cpp\ - ./objects/Params/DoubleMatArrayParam.h\ - ./objects/Params/DoubleVecParam.cpp\ - ./objects/Params/DoubleVecParam.h\ - ./objects/Params/PetscVecParam.cpp\ - ./objects/Params/PetscVecParam.h\ - ./objects/Params/StringParam.cpp\ - ./objects/Params/StringParam.h\ - ./Container/Container.h\ - ./Container/Constraints.h\ - ./Container/Constraints.cpp\ - ./Container/DataSet.h\ - ./Container/DataSet.cpp\ - ./Container/Elements.h\ - ./Container/Elements.cpp\ - ./Container/Inputs.h\ - ./Container/Inputs.cpp\ - ./Container/Loads.h\ - ./Container/Loads.cpp\ - ./Container/Materials.h\ - ./Container/Materials.cpp\ - ./Container/Nodes.h\ - ./Container/Nodes.cpp\ - ./Container/Parameters.h\ - ./Container/Parameters.cpp\ - ./Container/Results.h\ - ./Container/Results.cpp\ - ./Container/Vertices.h\ - ./Container/Vertices.cpp\ - ./shared/shared.h\ - ./shared/Alloc/alloc.h\ - ./shared/Alloc/alloc.cpp\ - ./shared/Matrix/matrix.h\ - ./shared/Matrix/MatrixUtils.cpp\ - ./shared/Dofs/dofs.h\ - ./shared/Dofs/dofsetgen.cpp\ - ./shared/Numerics/numerics.h\ - ./shared/Numerics/Verbosity.h\ - ./shared/Numerics/Verbosity.cpp\ - ./shared/Numerics/IsInputConverged.cpp\ - ./shared/Numerics/GaussPoints.h\ - ./shared/Numerics/GaussPoints.cpp\ - ./shared/Numerics/cross.cpp\ - ./shared/Numerics/extrema.cpp\ - ./shared/Numerics/UnitConversion.cpp\ - ./shared/Numerics/PetscOptionsFromAnalysis.cpp\ - ./shared/Exceptions/exceptions.h\ - ./shared/Exceptions/Exceptions.cpp\ - ./shared/Exceptions/exprintf.cpp\ - ./shared/Sorting/binary_search.cpp\ - ./shared/Sorting/sorting.h\ - ./shared/Elements/elements.h\ - ./shared/Elements/Paterson.cpp\ - ./shared/Elements/Arrhenius.cpp\ - ./shared/Elements/GetVerticesCoordinates.cpp\ - ./shared/Elements/GetLocalDofList.cpp\ - ./shared/Elements/GetGlobalDofList.cpp\ - ./shared/Elements/GetNumberOfDofs.cpp\ - ./shared/String/sharedstring.h\ - ./toolkits/petsc\ - ./toolkits/petsc/patches\ - ./toolkits/petsc/patches/SolverEnum.h\ - ./toolkits/petsc/patches/petscpatches.h\ - ./toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp\ - ./toolkits/petsc/patches/MatlabVectorToPetscVector.cpp\ - ./toolkits/petsc/patches/PetscMatrixToMatlabMatrix.cpp\ - ./toolkits/petsc/patches/PetscVectorToMatlabVector.cpp\ - ./toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp\ - ./toolkits/petsc/patches/MatlabVectorToDoubleVector.cpp\ - ./toolkits/petsc/patches/PetscDetermineLocalSize.cpp\ - ./toolkits/petsc/patches/VecTranspose.cpp\ - ./toolkits/petsc/patches/VecToMPISerial.cpp\ - ./toolkits/petsc/patches/MatToSerial.cpp\ - ./toolkits/petsc/patches/VecMerge.cpp\ - ./toolkits/petsc/patches/NewVec.cpp\ - ./toolkits/petsc/patches/PetscOptionsDetermineSolverType.cpp\ - ./toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp\ - ./toolkits/petsc/patches/NewMat.cpp\ - ./toolkits/petsc/patches/SerialToVec.cpp\ - ./toolkits/petsc/patches/VecFree.cpp\ - ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ - ./toolkits/petsc/patches/KSPFree.cpp\ - ./toolkits/petsc/patches/ISFree.cpp\ - ./toolkits/petsc/patches/MatFree.cpp\ - ./toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp\ - ./toolkits/petsc/patches/VecPartition.cpp\ - ./toolkits/petsc/patches/MatPartition.cpp\ - ./toolkits/petsc/patches/MatInvert.cpp\ - ./toolkits/petsc/patches/MatMultPatch.cpp\ - ./toolkits/petsc/petscincludes.h\ - ./toolkits/mpi/mpiincludes.h\ - ./toolkits/mpi/patches/mpipatches.h\ - ./toolkits/mpi/patches/MPI_Upperrow.cpp\ - ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ - ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp\ - ./toolkits/metis/metisincludes.h\ - ./toolkits/metis/patches/metispatches.h\ - ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp\ - ./toolkits/triangle/triangleincludes.h\ - ./toolkits.h\ - ./io/io.h\ - ./io/Disk/diskio.h\ - ./io/Disk/pfopen.cpp\ - ./io/Disk/pfclose.cpp\ - ./io/PrintfFunction.cpp\ - ./EnumDefinitions/EnumDefinitions.h\ - ./EnumDefinitions/EnumToModelField.cpp\ - ./modules/ModelProcessorx/ModelProcessorx.h\ - ./modules/ModelProcessorx/ModelProcessorx.cpp\ - ./modules/ModelProcessorx/DistributeNumDofs.cpp\ - ./modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp\ - ./modules/ModelProcessorx/NodesPartitioning.cpp\ - ./modules/ModelProcessorx/SortDataSets.cpp\ - ./modules/ModelProcessorx/UpdateCounters.cpp\ - ./modules/ModelProcessorx/CreateDataSets.cpp\ - ./modules/ModelProcessorx/CreateParameters.cpp\ - ./modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp\ - ./modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp\ - ./modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp\ - ./modules/ParsePetscOptionsx/ParsePetscOptionsx.h\ - ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\ - ./modules/NodesDofx/NodesDofx.h\ - ./modules/NodesDofx/NodesDofx.cpp\ - ./modules/VerticesDofx/VerticesDofx.h\ - ./modules/VerticesDofx/VerticesDofx.cpp\ - ./modules/OutputResultsx/OutputResultsx.h\ - ./modules/OutputResultsx/OutputResultsx.cpp\ - ./modules/InputDuplicatex/InputDuplicatex.h\ - ./modules/InputDuplicatex/InputDuplicatex.cpp\ - ./modules/InputScalex/InputScalex.h\ - ./modules/InputScalex/InputScalex.cpp\ - ./modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h\ - ./modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp\ - ./modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h\ - ./modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp\ - ./modules/IoModelToConstraintsx/IoModelToConstraintsx.h\ - ./modules/IoModelToConstraintsx/IoModelToConstraintsx.cpp\ - ./modules/InputUpdateFromConstantx/InputUpdateFromConstantx.h\ - ./modules/InputUpdateFromConstantx/InputUpdateFromConstantx.cpp\ - ./modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h\ - ./modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp\ - ./modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h\ - ./modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp\ - ./modules/GetVectorFromInputsx/GetVectorFromInputsx.h\ - ./modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp\ - ./modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h\ - ./modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp\ - ./modules/InputArtificialNoisex/InputArtificialNoisex.h\ - ./modules/InputArtificialNoisex/InputArtificialNoisex.cpp\ - ./modules/TimeAdaptx/TimeAdaptx.h\ - ./modules/TimeAdaptx/TimeAdaptx.cpp\ - ./modules/UpdateVertexPositionsx/UpdateVertexPositionsx.h\ - ./modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp\ - ./modules/ConfigureObjectsx/ConfigureObjectsx.h\ - ./modules/ConfigureObjectsx/ConfigureObjectsx.cpp\ - ./modules/ComputeBasalStressx/ComputeBasalStressx.h\ - ./modules/ComputeBasalStressx/ComputeBasalStressx.cpp\ - ./modules/ComputeStrainRatex/ComputeStrainRatex.h\ - ./modules/ComputeStrainRatex/ComputeStrainRatex.cpp\ - ./modules/SpcNodesx/SpcNodesx.h\ - ./modules/SpcNodesx/SpcNodesx.cpp\ - ./modules/UpdateConstraintsx/UpdateConstraintsx.h\ - ./modules/UpdateConstraintsx/UpdateConstraintsx.cpp\ - ./modules/MeshPartitionx/MeshPartitionx.cpp\ - ./modules/MeshPartitionx/MeshPartitionx.h\ - ./modules/Reducevectorgtofx/Reducevectorgtofx.cpp\ - ./modules/Reducevectorgtofx/Reducevectorgtofx.h\ - ./modules/Reduceloadx/Reduceloadx.h\ - ./modules/Reduceloadx/Reduceloadx.cpp\ - ./modules/EnumToStringx/EnumToStringx.cpp\ - ./modules/EnumToStringx/EnumToStringx.h\ - ./modules/StringToEnumx/StringToEnumx.cpp\ - ./modules/StringToEnumx/StringToEnumx.h\ - ./modules/SystemMatricesx/SystemMatricesx.cpp\ - ./modules/SystemMatricesx/SystemMatricesx.h\ - ./modules/ConstraintsStatex/ConstraintsStatex.cpp\ - ./modules/ConstraintsStatex/ConstraintsStatex.h\ - ./modules/ConstraintsStatex/ConstraintsStateLocal.h\ - ./modules/RequestedOutputsx/RequestedOutputsx.h\ - ./modules/RequestedOutputsx/RequestedOutputsx.cpp\ - ./modules/ResetConstraintsx/ResetConstraintsx.h\ - ./modules/ResetConstraintsx/ResetConstraintsx.cpp\ - ./modules/Solverx/Solverx.cpp\ - ./modules/Solverx/Solverx.h\ - ./modules/Solverx/DofTypesToIndexSet.cpp\ - ./modules/VecMergex/VecMergex.cpp\ - ./modules/VecMergex/VecMergex.h\ - ./modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp\ - ./modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h\ - ./modules/InputToResultx/InputToResultx.cpp\ - ./modules/InputToResultx/InputToResultx.h\ - ./modules/InputConvergencex/InputConvergencex.cpp\ - ./modules/InputConvergencex/InputConvergencex.h\ - ./solutions/convergence.cpp\ - ./solutions/WriteLockFile.cpp\ - ./solutions/ResetBoundaryConditions.cpp\ - ./solutions/AnalysisConfiguration.cpp\ - ./solutions/CorePointerFromSolutionEnum.cpp\ - ./solvers/solver_linear.cpp\ - ./solvers/solver_nonlinear.cpp - - -libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) -#}}} -#DAKOTA sources {{{1 -if DAKOTA -libpISSM_a_SOURCES += ./objects/DakotaPlugin.h\ - ./objects/DakotaPlugin.cpp\ - ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.h\ - ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.cpp\ - ./modules/DakotaResponsesx/DakotaResponsesx.h\ - ./modules/DakotaResponsesx/DakotaResponsesx.cpp\ - ./modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h\ - ./modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp\ - ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ - ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\ - ./modules/Dakotax/Dakotax.h\ - ./modules/Dakotax/Dakotax.cpp\ - ./modules/Dakotax/DakotaMPI_Bcast.cpp\ - ./modules/Dakotax/DakotaFree.cpp\ - ./modules/Dakotax/SpawnCore.cpp\ - ./modules/Dakotax/SpawnCoreParallel.cpp\ - ./modules/Dakotax/DescriptorIndex.cpp\ - ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ - ./modules/ModelProcessorx/Qmu/CreateParametersQmu.cpp\ - ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h -endif -#}}} -#Transient sources {{{1 -if TRANSIENT -libpISSM_a_SOURCES += ./solutions/transient_core.cpp\ - ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp -endif -#}}} -#Steadystate sources {{{1 -if STEADYSTATE -libpISSM_a_SOURCES += ./solutions/steadystate_core.cpp\ - ./solutions/steadystateconvergence.cpp -endif -#}}} -#Prognostic sources {{{1 -if PROGNOSTIC -libpISSM_a_SOURCES += ./solutions/prognostic_core.cpp\ - ./modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp\ - ./modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp\ - ./modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp\ - ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp - -endif -#}}} -#Thermal sources {{{1 -if THERMAL -libpISSM_a_SOURCES += ./solutions/thermal_core.cpp\ - ./solutions/thermal_core_step.cpp\ - ./solutions/enthalpy_core.cpp\ - ./solvers/solver_thermal_nonlinear.cpp\ - ./modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp\ - ./modules/ModelProcessorx/Thermal/CreateNodesThermal.cpp\ - ./modules/ModelProcessorx/Thermal/CreateConstraintsThermal.cpp\ - ./modules/ModelProcessorx/Thermal/CreateLoadsThermal.cpp\ - ./modules/ModelProcessorx/Enthalpy/UpdateElementsEnthalpy.cpp\ - ./modules/ModelProcessorx/Enthalpy/CreateNodesEnthalpy.cpp\ - ./modules/ModelProcessorx/Enthalpy/CreateConstraintsEnthalpy.cpp\ - ./modules/ModelProcessorx/Enthalpy/CreateLoadsEnthalpy.cpp\ - ./modules/ModelProcessorx/Melting/UpdateElementsMelting.cpp\ - ./modules/ModelProcessorx/Melting/CreateNodesMelting.cpp\ - ./modules/ModelProcessorx/Melting/CreateConstraintsMelting.cpp\ - ./modules/ModelProcessorx/Melting/CreateLoadsMelting.cpp\ - ./modules/ConstraintsStatex/ThermalConstraintsState.cpp\ - ./modules/ConstraintsStatex/ThermalIsPresent.cpp\ - ./modules/ResetConstraintsx/ThermalConstraintsReset.cpp -endif -#}}} -#Control sources {{{1 -if CONTROL -libpISSM_a_SOURCES += ./solutions/control_core.cpp\ - ./solutions/controltao_core.cpp\ - ./solutions/controlrestart.cpp\ - ./solutions/controlconvergence.cpp\ - ./solutions/objectivefunctionC.cpp\ - ./solutions/gradient_core.cpp\ - ./solutions/adjointdiagnostic_core.cpp\ - ./solutions/adjointbalancethickness_core.cpp\ - ./solutions/AdjointCorePointerFromSolutionEnum.cpp\ - ./solvers/solver_adjoint_linear.cpp\ - ./modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp\ - ./modules/ControlInputGetGradientx/ControlInputGetGradientx.h\ - ./modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp\ - ./modules/ControlInputSetGradientx/ControlInputSetGradientx.h\ - ./modules/ControlInputScaleGradientx/ControlInputScaleGradientx.cpp\ - ./modules/ControlInputScaleGradientx/ControlInputScaleGradientx.h\ - ./modules/ModelProcessorx/Control/CreateParametersControl.cpp\ - ./modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp\ - ./modules/InputControlUpdatex/InputControlUpdatex.h\ - ./modules/InputControlUpdatex/InputControlUpdatex.cpp\ - ./modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.h\ - ./modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp\ - ./modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.h\ - ./modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp\ - ./modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.h\ - ./modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp\ - ./modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.h\ - ./modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp\ - ./modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.h\ - ./modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp\ - ./modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.h\ - ./modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp\ - ./modules/CostFunctionx/CostFunctionx.h\ - ./modules/CostFunctionx/CostFunctionx.cpp\ - ./modules/Orthx/Orthx.h\ - ./modules/Orthx/Orthx.cpp\ - ./modules/Gradjx/Gradjx.h\ - ./modules/Gradjx/Gradjx.cpp\ - ./modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.cpp\ - ./modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.h\ - ./modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp\ - ./modules/ThicknessAbsGradientx/ThicknessAbsGradientx.h\ - ./modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp\ - ./modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.h\ - ./objects/Inputs/ControlInput.h\ - ./objects/Inputs/ControlInput.cpp\ - ./shared/Numerics/BrentSearch.cpp\ - ./shared/Numerics/OptimalSearch.cpp\ - ./shared/Numerics/OptFunc.cpp\ - ./objects/OptArgs.h\ - ./objects/OptPars.h - -endif -#}}} -#Hydrology sources {{{1 -if HYDROLOGY -libpISSM_a_SOURCES += ./modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp\ - ./modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp\ - ./modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp\ - ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp\ - ./solutions/hydrology_core.cpp\ - ./solutions/hydrology_core_step.cpp -endif -#}}} -#Diagnostic sources {{{1 -if DIAGNOSTIC -libpISSM_a_SOURCES += ./modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp\ - ./modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp \ - ./modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp \ - ./modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp\ - ./modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp\ - ./modules/ModelProcessorx/DiagnosticVert/CreateNodesDiagnosticVert.cpp \ - ./modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp \ - ./modules/ModelProcessorx/DiagnosticVert/CreateLoadsDiagnosticVert.cpp\ - ./modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp\ - ./modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp \ - ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ - ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp\ - ./solutions/diagnostic_core.cpp\ - ./solvers/solver_stokescoupling_nonlinear.cpp -endif -#}}} -#Balanced sources {{{1 -if BALANCED -libpISSM_a_SOURCES += ./modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp\ - ./modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp\ - ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\ - ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp\ - ./solutions/balancethickness_core.cpp -endif -#}}} -#Responses sources {{{1 -if RESPONSES -libpISSM_a_SOURCES += ./modules/MinVelx/MinVelx.h\ - ./modules/MinVelx/MinVelx.cpp\ - ./modules/MaxVelx/MaxVelx.h\ - ./modules/MaxVelx/MaxVelx.cpp\ - ./modules/MaxAbsVxx/MaxAbsVxx.h\ - ./modules/MaxAbsVxx/MaxAbsVxx.cpp\ - ./modules/MaxAbsVyx/MaxAbsVyx.h\ - ./modules/MaxAbsVyx/MaxAbsVyx.cpp\ - ./modules/MaxAbsVzx/MaxAbsVzx.h\ - ./modules/MaxAbsVzx/MaxAbsVzx.cpp\ - ./modules/MaxVxx/MaxVxx.h\ - ./modules/MaxVxx/MaxVxx.cpp\ - ./modules/MaxVyx/MaxVyx.h\ - ./modules/MaxVyx/MaxVyx.cpp\ - ./modules/MaxVzx/MaxVzx.h\ - ./modules/MaxVzx/MaxVzx.cpp\ - ./modules/MinVxx/MinVxx.h\ - ./modules/MinVxx/MinVxx.cpp\ - ./modules/MinVyx/MinVyx.h\ - ./modules/MinVyx/MinVyx.cpp\ - ./modules/MinVzx/MinVzx.h\ - ./modules/MinVzx/MinVzx.cpp\ - ./modules/RheologyBbarx/RheologyBbarx.cpp\ - ./modules/RheologyBbarx/RheologyBbarx.h\ - ./modules/MassFluxx/MassFluxx.cpp\ - ./modules/MassFluxx/MassFluxx.h\ - ./modules/NodalValuex/NodalValuex.h\ - ./modules/NodalValuex/NodalValuex.cpp\ - ./modules/SurfaceAreax/SurfaceAreax.h\ - ./modules/SurfaceAreax/SurfaceAreax.cpp\ - ./modules/Responsex/Responsex.h\ - ./modules/Responsex/Responsex.cpp -endif -#}}} -#Slope sources {{{1 -if SLOPE -libpISSM_a_SOURCES += ./modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp\ - ./modules/ModelProcessorx/BedSlope/CreateNodesBedSlope.cpp \ - ./modules/ModelProcessorx/BedSlope/CreateConstraintsBedSlope.cpp\ - ./modules/ModelProcessorx/BedSlope/CreateLoadsBedSlope.cpp\ - ./modules/ModelProcessorx/SurfaceSlope/UpdateElementsSurfaceSlope.cpp\ - ./modules/ModelProcessorx/SurfaceSlope/CreateNodesSurfaceSlope.cpp \ - ./modules/ModelProcessorx/SurfaceSlope/CreateConstraintsSurfaceSlope.cpp\ - ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp\ - ./solutions/surfaceslope_core.cpp\ - ./solutions/bedslope_core.cpp -endif -#}}} -#GroundingLine sources {{{1 -if GROUNDINGLINE -libpISSM_a_SOURCES += ./modules/GroundingLineMigrationx/GroundingLineMigrationx.cpp\ - ./modules/GroundingLineMigrationx/GroundingLineMigrationx.h\ - ./modules/GroundingLineMigrationx/GroundingLineMigrationxLocal.h\ - ./modules/GroundingLineMigrationx/GroundingLineMigrationxUtils.cpp\ - ./solutions/groundinglinemigration2d_core.cpp -endif -#}}} -#Rifts sources {{{1 -if RIFTS -libpISSM_a_SOURCES += ./objects/Loads/Riftfront.cpp\ - ./objects/Loads/Riftfront.h\ - ./modules/ConstraintsStatex/RiftConstraintsState.cpp -endif -#}}} -#3D sources {{{1 -if THREED -libpISSM_a_SOURCES += ./objects/Gauss/GaussPenta.h\ - ./objects/Gauss/GaussPenta.cpp\ - ./objects/ElementResults/PentaVertexElementResult.h\ - ./objects/ElementResults/PentaVertexElementResult.cpp\ - ./objects/Inputs/PentaVertexInput.h\ - ./objects/Inputs/PentaVertexInput.cpp\ - ./objects/Elements/Penta.h\ - ./objects/Elements/Penta.cpp\ - ./objects/Elements/PentaHook.h\ - ./objects/Elements/PentaHook.cpp\ - ./objects/Elements/PentaRef.h\ - ./objects/Elements/PentaRef.cpp -endif -#}}} - -#ADIC2 library, for automatic differentiation {{{1 -if ADIC2 -#libAD_a_SOURCES = ./mini1.ad.c -libAD_a_SOURCES = -libAD_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) - -#test rose preprocessing -%.r2cpp.cpp : %.cpp - testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_PARALLEL_ -D_C_ -I. -I../.. $(INCLUDES) $< - -libpISSMRose_a_SOURCES = $(libpISSM_a_SOURCES:.cpp=.r2cpp.cpp) -libpISSMRose_a_CXXFLAGS= -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) -#Automatic differentiation rules: -%.ad.c: %.c - adic2 -mforward $< --nary -endif -#}}} -#Executable {{{1 - -if NOPARALLEL -bin_PROGRAMS = -else -bin_PROGRAMS = issm.exe issmRose.exe -endif - -#Standard libraries -LDADD = ./libOverload.a -issm_exe_LDADD = ./libpISSM.a $(LDADD) -if ADIC2 -issmRose_exe_LDADD = ./libpISSMRose.a $(LDADD) -endif - -#External packages -LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(ADIC2LIB) - - -issm_exe_SOURCES = solutions/issm.cpp -issm_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) -issmRose_exe_SOURCES = solutions/issm.cpp -issmRose_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) - -#}}} Index: sm/branches/trunk-jpl-damage/src/ad/eraselinks.sh =================================================================== --- /issm/branches/trunk-jpl-damage/src/ad/eraselinks.sh (revision 11683) +++ (revision ) @@ -1,14 +1,0 @@ -#/bin/bash -#This script soflinks all files in trunk/src/c/ directory necessary for compilation -#of trunk/src/ad/ -rm include -rm objects -rm Container -rm shared -rm toolkits -rm io -rm EnumDefinitions -rm modules -rm solutions -rm solvers -rm issm.h Index: sm/branches/trunk-jpl-damage/src/ad/softlink.sh =================================================================== --- /issm/branches/trunk-jpl-damage/src/ad/softlink.sh (revision 11683) +++ (revision ) @@ -1,14 +1,0 @@ -#/bin/bash -#This script soflinks all files in trunk/src/c/ directory necessary for compilation -#of trunk/src/ad/ -ln -s ../c/include -ln -s ../c/objects -ln -s ../c/Container -ln -s ../c/shared -ln -s ../c/toolkits -ln -s ../c/io -ln -s ../c/EnumDefinitions -ln -s ../c/modules -ln -s ../c/solutions -ln -s ../c/solvers -ln -s ../c/issm.h Index: /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/EnumDefinitions.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/EnumDefinitions.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/EnumDefinitions.h (revision 11684) @@ -482,6 +482,3 @@ }; -/*Functions on enums: */ -const char *EnumToModelField(int en); - #endif Index: /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/README =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/README (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/README (revision 11684) @@ -4,5 +4,5 @@ - EnumToStringx.cpp - src/m/enum/* -all these files are automatically synchronized with EnumDefinitions.h and EnumToModelField.cpp +all these files are automatically synchronized with EnumDefinitions.h TO ADD AN ENUM: Index: /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/Synchronize.sh =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/Synchronize.sh (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/Synchronize.sh (revision 11684) @@ -13,29 +13,4 @@ NUMENUMS=$(wc -l temp | awk '{printf("%s",$1);}'); -#Take care of EnumToModelField.m first (easy) -#Build EnumToModelField.m {{{1 -cat < $ISSM_TIER/src/m/enum/EnumToModelField.m -function string=EnumToModelField(enum) -%ENUMTOMODELFIELD - output string of model field associated to enum -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% string=EnumToModelField(enum) - -switch enum, - -END - -cat EnumToModelField.cpp | grep "case" | sed -e "s/Enum :/Enum(),/g" -e "s/\"/'/g" -e "s/return /string=/g" -e "s/;/; return/g" >> $ISSM_TIER/src/m/enum/EnumToModelField.m - -cat <> $ISSM_TIER/src/m/enum/EnumToModelField.m - otherwise, error(['Enum ' num2str(enum) ' not found associated to any model field']); - -end -END -#}}} #Build EnumToStringx.cpp {{{1 #Header Index: /issm/branches/trunk-jpl-damage/src/c/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Makefile.am (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/Makefile.am (revision 11684) @@ -1,3 +1,3 @@ -INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ +INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ EXEEXT=$(ISSMEXT) @@ -120,4 +120,8 @@ ./objects/Numerics/ElementVector.h\ ./objects/Numerics/ElementVector.cpp\ + ./objects/Numerics/Matrix.h\ + ./objects/Numerics/Matrix.cpp\ + ./objects/Numerics/Vector.h\ + ./objects/Numerics/Vector.cpp\ ./objects/Params/Param.h\ ./objects/Params/BoolParam.cpp\ @@ -204,5 +208,4 @@ ./shared/Elements/GetGlobalDofList.cpp\ ./shared/Elements/GetNumberOfDofs.cpp\ - ./shared/Elements/CoordinateSystemTransform.cpp\ ./shared/String/sharedstring.h\ ./toolkits/petsc\ @@ -253,5 +256,4 @@ ./io/PrintfFunction.cpp\ ./EnumDefinitions/EnumDefinitions.h\ - ./EnumDefinitions/EnumToModelField.cpp\ ./modules/ModelProcessorx/ModelProcessorx.h\ ./modules/ModelProcessorx/ModelProcessorx.cpp\ @@ -342,4 +344,5 @@ ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.cpp\ ./modules/Solverx/Solverx.cpp\ + ./modules/Solverx/SolverxPetsc.cpp\ ./modules/Solverx/Solverx.h\ ./modules/Solverx/DofTypesToIndexSet.cpp\ @@ -503,4 +506,5 @@ ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \ + ./shared/Elements/CoordinateSystemTransform.cpp\ ./shared/Elements/TransformLoadVectorCoord.cpp \ ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ @@ -725,4 +729,6 @@ ./toolkits/matlab/matlabincludes.h\ ./toolkits/matlab/MatlabNArrayToNArray.cpp\ + ./toolkits/matlab/MatlabMatrixToMatrix.cpp\ + ./toolkits/matlab/MatlabVectorToVector.cpp\ ./io/Matlab/matlabio.h\ ./io/Matlab/WriteMatlabData.cpp\ @@ -816,5 +822,6 @@ #ISSM sources are a combination of core sources and sources related to specific capabilities (which can -#be activated by autotools conditionals {{{1 +#be activated by autotools conditionals +#{{{1 #First the core @@ -925,7 +932,40 @@ #External packages -LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(ADIC2LIB) $(OSLIBS) +LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) issm_SOURCES = solutions/issm.cpp issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) #}}} +#Automatic differentiation: append this fold to the end of the src/c/Makefile.am to get this Makefile.am {{{ +if ADIC2 +lib_LIBRARIES += libAD.a libpISSMRose.a + +#ADIC2 library, for automatic differentiation +#libAD_a_SOURCES = ./mini1.ad.c +libAD_a_SOURCES = +libAD_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) + + + +#test rose preprocessing +%.r2cpp.cpp : %.cpp + testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_PARALLEL_ -D_C_ -I. -I../.. $(INCLUDES) $< +libpISSMRose_a_SOURCES = $(libpISSM_a_SOURCES:.cpp=.r2cpp.cpp) +libpISSMRose_a_CXXFLAGS= -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) + + + +#Automatic differentiation rules: +%.ad.c: %.c + adic2 -mforward $< --nary + + + +#Executable +bin_PROGRAMS += issmRose.exe +issmRose_exe_LDADD = ./libpISSMRose.a $(LDADD) +issmRose_exe_SOURCES = solutions/issm.cpp +issmRose_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) +LDADD += $(ADIC2LIB) + +endif #}}} Index: /issm/branches/trunk-jpl-damage/src/c/io/Matlab/FetchMatlabData.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/io/Matlab/FetchMatlabData.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/io/Matlab/FetchMatlabData.cpp (revision 11684) @@ -60,6 +60,5 @@ outmatrix=NULL; } - else if (mxIsClass(dataref,"double") ){ - + else if(mxIsClass(dataref,"double") || mxIsClass(dataref,"single")){ /*Check dataref is not pointing to NaN: */ if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ @@ -69,5 +68,4 @@ } else{ - /*Convert matlab matrix to double* matrix: */ MatlabMatrixToDoubleMatrix(&outmatrix,&outmatrix_rows,&outmatrix_cols,dataref); @@ -305,4 +303,31 @@ } /*}}}*/ +/*FUNCTION FetchMatlabData(Matrix** pmatrix,const mxArray* dataref){{{1*/ +void FetchMatlabData(Matrix** pmatrix,const mxArray* dataref){ + + Matrix* outmatrix=NULL; + int dummy=0; + + if (mxIsClass(dataref,"double") ){ + + /*Check dataref is not pointing to NaN: */ + if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ + outmatrix=NULL; + } + else{ + + /*Convert matlab matrix to petsc matrix: */ + outmatrix=MatlabMatrixToMatrix(dataref); + } + } + else{ + /*This is an error: we don't have the correct input!: */ + _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); + } + + /*Assign output pointers:*/ + *pmatrix=outmatrix; +} +/*}}}*/ /*FUNCTION FetchMatlabData(double** pvector,int* pM,const mxArray* dataref){{{1*/ void FetchMatlabData(double** pvector,int* pM,const mxArray* dataref){ @@ -442,4 +467,28 @@ /*Convert matlab vector to petsc vector: */ MatlabVectorToPetscVector(&vector,&dummy,dataref); + } + else{ + /*This is an error: we don't have the correct input!: */ + _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); + } + + /*Assign output pointers:*/ + *pvector=vector; +} +/*}}}*/ +/*FUNCTION FetchMatlabData(Vector** pvector,const mxArray* dataref){{{1*/ +void FetchMatlabData(Vector** pvector,const mxArray* dataref){ + + Vector* vector=NULL; + int dummy; + + if(mxIsEmpty(dataref)){ + /*Nothing to pick up. Just initialize matrix pointer to NULL: */ + vector=NULL; + } + else if (mxIsClass(dataref,"double") ){ + + /*Convert matlab vector to petsc vector: */ + vector=MatlabVectorToVector(dataref); } else{ Index: /issm/branches/trunk-jpl-damage/src/c/io/Matlab/WriteMatlabData.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/io/Matlab/WriteMatlabData.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/io/Matlab/WriteMatlabData.cpp (revision 11684) @@ -58,4 +58,21 @@ } /*}}}*/ +/*FUNCTION WriteMatlabData(mxArray** pdataref,Matrix* matrix){{{1*/ +void WriteMatlabData(mxArray** pdataref,Matrix* matrix){ + + mxArray* dataref=NULL; + + if(matrix){ + + /*call toolkit routine: */ + dataref=matrix->ToMatlabMatrix(); + } + else{ + dataref = mxCreateDoubleMatrix(0,0,mxREAL); + } + + *pdataref=dataref; +} +/*}}}*/ /*FUNCTION WriteMatlabData(mxArray** pdataref,double* matrix, int M,int N){{{1*/ void WriteMatlabData(mxArray** pdataref,double* matrix, int M,int N){ @@ -117,4 +134,21 @@ /*call toolkit routine: */ PetscVectorToMatlabVector(&dataref,vector); + } + else{ + dataref = mxCreateDoubleMatrix(0,0,mxREAL); + } + *pdataref=dataref; + +} +/*}}}*/ +/*FUNCTION WriteMatlabData(mxArray** pdataref,Vector* vector){{{1*/ +void WriteMatlabData(mxArray** pdataref,Vector* vector){ + + mxArray* dataref=NULL; + + if(vector){ + + /*call toolkit routine: */ + dataref=vector->ToMatlabVector(); } else{ Index: /issm/branches/trunk-jpl-damage/src/c/io/Matlab/matlabio.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/io/Matlab/matlabio.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/io/Matlab/matlabio.h (revision 11684) @@ -17,7 +17,9 @@ void WriteMatlabData(mxArray** pdataref,DataSet* dataset); void WriteMatlabData(mxArray** pdataref,Mat matrix); +void WriteMatlabData(mxArray** pdataref,Matrix* matrix); void WriteMatlabData(mxArray** pdataref,double* matrix, int M,int N); void WriteMatlabData(mxArray** pdataref,int* matrix, int M,int N); void WriteMatlabData(mxArray** pdataref,Vec vector); +void WriteMatlabData(mxArray** pdataref,Vector* vector); void WriteMatlabData(mxArray** pdataref,double* vector, int M); void WriteMatlabData(mxArray** pdataref,int integer); @@ -34,4 +36,5 @@ void FetchMatlabData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); void FetchMatlabData(Mat* pmatrix,const mxArray* dataref); +void FetchMatlabData(Matrix** pmatrix,const mxArray* dataref); void FetchMatlabData(int** pvector,int* pM,const mxArray* dataref); void FetchMatlabData(float** pvector,int* pM,const mxArray* dataref); @@ -39,4 +42,5 @@ void FetchMatlabData(bool** pvector,int* pM,const mxArray* dataref); void FetchMatlabData(Vec* pvector,const mxArray* dataref); +void FetchMatlabData(Vector** pvector,const mxArray* dataref); void FetchMatlabData(char** pstring,const mxArray* dataref); void FetchMatlabData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); Index: /issm/branches/trunk-jpl-damage/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp (revision 11684) @@ -10,5 +10,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void CreateJacobianMatrixx(Mat* pJff,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,double kmax){ +void CreateJacobianMatrixx(Matrix** pJff,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,double kmax){ int i,connectivity; @@ -17,5 +17,5 @@ Element *element = NULL; Load *load = NULL; - Mat Jff = NULL; + Matrix* Jff = NULL; /*Checks*/ @@ -29,5 +29,5 @@ /*Initialize Jacobian Matrix*/ - Jff=NewMat(fsize,fsize,connectivity,numberofdofspernode); + Jff=new Matrix(fsize,fsize,connectivity,numberofdofspernode); /*Create and assemble matrix*/ @@ -41,6 +41,5 @@ if(load->InAnalysis(configuration_type)) load->PenaltyCreateJacobianMatrix(Jff,kmax); } - MatAssemblyBegin(Jff,MAT_FINAL_ASSEMBLY); - MatAssemblyEnd(Jff,MAT_FINAL_ASSEMBLY); + Jff->Assemble(); /*Assign output pointer*/ Index: /issm/branches/trunk-jpl-damage/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h (revision 11684) @@ -10,5 +10,5 @@ /* local prototypes: */ -void CreateJacobianMatrixx(Mat* pJff,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,double kmax); +void CreateJacobianMatrixx(Matrix** pJff,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,double kmax); #endif /* _CREATEJACOBIANMATRIXX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp (revision 11684) @@ -10,5 +10,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void CreateNodalConstraintsx( Vec* pys, Nodes* nodes,int configuration_type){ +void CreateNodalConstraintsx( Vector** pys, Nodes* nodes,int configuration_type){ int i; @@ -18,5 +18,5 @@ /*output: */ - Vec ys=NULL; + Vector* ys=NULL; /*figure out how many dofs we have: */ @@ -24,5 +24,5 @@ /*allocate:*/ - ys=NewVec(numberofdofs); + ys=new Vector(numberofdofs); /*go through all nodes, and for the ones corresponding to this configuration_type, fill the @@ -36,6 +36,5 @@ /*Assemble: */ - VecAssemblyBegin(ys); - VecAssemblyEnd(ys); + ys->Assemble(); /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h (revision 11684) @@ -9,5 +9,5 @@ /* local prototypes: */ -void CreateNodalConstraintsx( Vec* pys, Nodes* nodes,int configuration_type); +void CreateNodalConstraintsx( Vector** pys, Nodes* nodes,int configuration_type); #endif /* _CREATENODALCONSTRAINTSX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp (revision 11684) @@ -9,5 +9,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void GetSolutionFromInputsx( Vec* psolution, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters){ +void GetSolutionFromInputsx( Vector** psolution, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters){ /*intermediary: */ @@ -19,5 +19,5 @@ /*output: */ - Vec solution=NULL; + Vector* solution=NULL; /*retrive parameters: */ @@ -29,5 +29,5 @@ /*Initialize solution: */ - solution=NewVec(gsize); + solution=new Vector(gsize); /*Go through elements and plug solution: */ @@ -38,6 +38,5 @@ /*Assemble vector: */ - VecAssemblyBegin(solution); - VecAssemblyEnd(solution); + solution->Assemble(); /*Assign output pointers:*/ Index: /issm/branches/trunk-jpl-damage/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h (revision 11684) @@ -10,5 +10,5 @@ /* local prototypes: */ -void GetSolutionFromInputsx( Vec* psolution, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); +void GetSolutionFromInputsx( Vector** psolution, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); #endif /* _GETSOLUTIONFROMINPUTSXX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp (revision 11684) @@ -9,10 +9,10 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec solution){ +void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* solution){ double* serial_solution=NULL; /*Serialize solution, so that elements can index into it on every CPU: */ - VecToMPISerial(&serial_solution,solution); + serial_solution=solution->ToMPISerial(); /*Call overloaded form of InputUpdateFromSolutionx: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h (revision 11684) @@ -10,9 +10,9 @@ /* local prototypes: */ -void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec solution); +void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* solution); void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,double* solution); //with timestep -void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec solution,int timestep); +void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* solution,int timestep); void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,double* solution, int timestep); Index: /issm/branches/trunk-jpl-damage/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp (revision 11684) @@ -7,8 +7,8 @@ #include "./Mergesolutionfromftogx.h" -void Mergesolutionfromftogx( Vec* pug, Vec uf, Vec ys, Nodes* nodes, Parameters* parameters, bool flag_ys0){ +void Mergesolutionfromftogx( Vector** pug, Vector* uf, Vector* ys, Nodes* nodes, Parameters* parameters, bool flag_ys0){ /*output: */ - Vec ug=NULL; + Vector* ug=NULL; /*intermediary: */ @@ -29,10 +29,10 @@ if(ssize){ if(flag_ys0){ - VecSet(ys,0.0); + ys->Set(0.0); } } /*initialize ug: */ - ug=NewVec(gsize); + ug=new Vector(gsize); /*Merge f set back into g set: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h (revision 11684) @@ -9,5 +9,5 @@ /* local prototypes: */ -void Mergesolutionfromftogx( Vec* pug, Vec uf, Vec ys, Nodes* nodes, Parameters* parameters, bool flag_ys0=false); +void Mergesolutionfromftogx( Vector** pug, Vector* uf, Vector* ys, Nodes* nodes, Parameters* parameters, bool flag_ys0=false); #endif /* _MERGESOLUTIONFROMFTOGX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ModelProcessorx/ModelProcessorx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ModelProcessorx/ModelProcessorx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ModelProcessorx/ModelProcessorx.cpp (revision 11684) @@ -64,4 +64,7 @@ if(solution_type==TransientSolutionEnum && analysis_type==DiagnosticVertAnalysisEnum && isdiagnostic==false) continue; if(solution_type==TransientSolutionEnum && analysis_type==DiagnosticHutterAnalysisEnum && isdiagnostic==false) continue; + if(solution_type==SteadystateSolutionEnum && analysis_type==ThermalAnalysisEnum && isenthalpy==true) continue; + if(solution_type==SteadystateSolutionEnum && analysis_type==MeltingAnalysisEnum && isenthalpy==true) continue; + if(solution_type==SteadystateSolutionEnum && analysis_type==EnthalpyAnalysisEnum && isenthalpy==false) continue; _printf_(VerboseMProcessor()," creating datasets for analysis %s\n",EnumToStringx(analysis_type)); Index: /issm/branches/trunk-jpl-damage/src/c/modules/Reduceloadx/Reduceloadx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11684) @@ -12,12 +12,11 @@ #include "../../io/io.h" -void Reduceloadx( Vec pf, Mat Kfs, Vec y_s,bool flag_ys0){ +void Reduceloadx( Vector* pf, Matrix* Kfs, Vector* y_s,bool flag_ys0){ /*intermediary*/ - Vec y_s0 = NULL; - Vec Kfsy_s = NULL; + Vector* y_s0 = NULL; + Vector* Kfsy_s = NULL; int Kfsm,Kfsn; int global_m,global_n; - PetscScalar a; bool fromlocalsize = true; int verbose; @@ -25,5 +24,5 @@ _printf_(VerboseModule()," Dirichlet lifting applied to load vector\n"); - MatGetSize(Kfs,&global_m,&global_n); + Kfs->GetSize(&global_m,&global_n); if(pf && global_m*global_n){ @@ -32,28 +31,26 @@ /*pf = pf - Kfs * y_s;*/ - MatGetLocalSize(Kfs,&Kfsm,&Kfsn); - Kfsy_s=NewVec(Kfsm,fromlocalsize); + Kfs->GetLocalSize(&Kfsm,&Kfsn); + Kfsy_s=new Vector(Kfsm,fromlocalsize); if (flag_ys0){ /*Create y_s0, full of 0: */ - VecDuplicate(y_s,&y_s0); - VecSet(y_s0,0.0); - VecAssemblyBegin(y_s0); - VecAssemblyEnd(y_s0); + y_s0=y_s->Duplicate(); + y_s0->Set(0.0); + y_s0->Assemble(); - MatMultPatch(Kfs,y_s0,Kfsy_s); + Kfs->MatMult(y_s0,Kfsy_s); } else{ - MatMultPatch(Kfs,y_s,Kfsy_s); + Kfs->MatMult(y_s,Kfsy_s); } - a=-1; - VecAXPY(pf,a,Kfsy_s); + pf->AXPY(Kfsy_s,-1); } /*Free ressources and return*/ - VecFree(&y_s0); - VecFree(&Kfsy_s); + delete y_s0; + delete Kfsy_s; } Index: /issm/branches/trunk-jpl-damage/src/c/modules/Reduceloadx/Reduceloadx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Reduceloadx/Reduceloadx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Reduceloadx/Reduceloadx.h (revision 11684) @@ -9,5 +9,5 @@ /* local prototypes: */ -void Reduceloadx( Vec pf, Mat Kfs, Vec ys,bool flag_ys0=false); +void Reduceloadx( Vector* pf, Matrix* Kfs, Vector* ys,bool flag_ys0=false); #endif /* _REDUCELOADX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp (revision 11684) @@ -6,8 +6,8 @@ #include "./Reducevectorgtofx.h" -void Reducevectorgtofx(Vec* puf, Vec ug, Nodes* nodes,Parameters* parameters){ +void Reducevectorgtofx(Vector** puf, Vector* ug, Nodes* nodes,Parameters* parameters){ /*output: */ - Vec uf=NULL; + Vector* uf=NULL; /*variables: */ @@ -26,10 +26,10 @@ else{ /*allocate: */ - uf=NewVec(fsize); + uf=new Vector(fsize); if(nodes->NumberOfNodes(configuration_type)){ /*serialize ug, so nodes can index into it: */ - VecToMPISerial(&ug_serial,ug); + ug_serial=ug->ToMPISerial(); /*Go through all nodes, and ask them to retrieve values from ug, and plug them into uf: */ @@ -47,6 +47,5 @@ } /*Assemble vector: */ - VecAssemblyBegin(uf); - VecAssemblyEnd(uf); + uf->Assemble(); } Index: /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.h (revision 11684) @@ -10,5 +10,5 @@ /* local prototypes: */ -void Reducevectorgtofx(Vec* puf, Vec ug, Nodes* nodes,Parameters* parameters); +void Reducevectorgtofx(Vector** puf, Vector* ug, Nodes* nodes,Parameters* parameters); #endif /* _REDUCEVECTORGTOFX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.cpp (revision 11684) @@ -6,8 +6,8 @@ #include "./Reducevectorgtosx.h" -void Reducevectorgtosx(Vec* pys, Vec yg, Nodes* nodes,Parameters* parameters){ +void Reducevectorgtosx(Vector** pys, Vector* yg, Nodes* nodes,Parameters* parameters){ /*output: */ - Vec ys=NULL; + Vector* ys=NULL; /*variables: */ @@ -26,10 +26,10 @@ else{ /*allocate: */ - ys=NewVec(ssize); + ys=new Vector(ssize); if(nodes->NumberOfNodes(configuration_type)){ /*serialize yg, so nodes can index into it: */ - VecToMPISerial(&yg_serial,yg); + yg_serial=yg->ToMPISerial(); /*Go throygh all nodes, and ask them to retrieve values from yg, and plyg them into ys: */ @@ -47,6 +47,5 @@ } /*Assemble vector: */ - VecAssemblyBegin(ys); - VecAssemblyEnd(ys); + ys->Assemble(); } Index: /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.h (revision 11684) @@ -10,5 +10,5 @@ /* local prototypes: */ -void Reducevectorgtosx(Vec* pys, Vec yg, Nodes* nodes,Parameters* parameters); +void Reducevectorgtosx(Vector** pys, Vector* yg, Nodes* nodes,Parameters* parameters); #endif /* _REDUCEVECTORGTOSX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.cpp (revision 11684) @@ -14,166 +14,20 @@ #endif -void Solverx(Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df, Parameters* parameters){ +void Solverx(Vector** puf, Matrix* Kff, Vector* pf, Vector* uf0,Vector* df, Parameters* parameters){ - /*Output: */ - Vec uf = NULL; + /*output: */ + Vector* uf=NULL; + uf=new Vector(); - /*Intermediary: */ - int local_m,local_n,global_m,global_n; - int analysis_type; + #ifdef _HAVE_PETSC_ + Vec uf0_vector=NULL; + if (uf0)uf0_vector=uf0->vector; - /*Solver */ - KSP ksp = NULL; - PC pc = NULL; - int iteration_number; - int solver_type; - bool fromlocalsize = true; - #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) - PetscTruth flag,flg; + SolverxPetsc(&uf->vector, Kff->matrix, pf->vector, uf0_vector, df->vector, parameters); + VecGetSize(uf->vector,&uf->M); #else - PetscBool flag,flg; + _error_("not supported yet!"); #endif - /*Stokes: */ - IS isv=NULL; - IS isp=NULL; - - #if _PETSC_MAJOR_ >= 3 - char ksp_type[50]; - #endif - - - /*Display message*/ - _printf_(VerboseModule()," Solving\n"); - #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) - if(VerboseSolver())PetscOptionsPrint(stdout); - #else - if(VerboseSolver())PetscOptionsView(PETSC_VIEWER_STDOUT_WORLD); - #endif - - /*First, check that f-set is not NULL, i.e. model is fully constrained: {{{*/ - _assert_(Kff); - MatGetSize(Kff,&global_m,&global_n); _assert_(global_m==global_m); - if(!global_n){ - *puf=NULL; return; - } - /*}}}*/ - /*Initial guess logic here: {{{1*/ - /*Now, check that we are not giving an initial guess to the solver, if we are running a direct solver: */ - #if _PETSC_MAJOR_ >= 3 - PetscOptionsGetString(PETSC_NULL,"-ksp_type",ksp_type,49,&flg); - if (strcmp(ksp_type,"preonly")==0)uf0=NULL; - #endif - - /*If initial guess for the solution exists, use it to create uf, otherwise, - * duplicate the right hand side so that the solution vector has the same structure*/ - if(uf0){ - VecDuplicate(uf0,&uf); VecCopy(uf0,uf); - } - else{ - MatGetLocalSize(Kff,&local_m,&local_n);uf=NewVec(local_n,fromlocalsize); - } - /*}}}*/ - /*Process petsc options to see if we are using special types of external solvers: {{{1*/ - PetscOptionsDetermineSolverType(&solver_type); - - /*In serial mode, the matrices have been loaded as MPIAIJ or AIJ matrices. - We need to convert them if we are going to run the solvers successfully: */ - #ifdef _SERIAL_ - #if _PETSC_MAJOR_ == 2 - if (solver_type==MUMPSPACKAGE_LU){ - /*Convert Kff to MATTAIJMUMPS: */ - MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==MUMPSPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_LU){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SUPERLUDISTPACKAGE){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==StokesSolverEnum){ - _error_("Petsc 2 does not support multi-physics solvers"); - } - #endif - #endif - /*}}}*/ - /*Check the solver is available: {{{1*/ - if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ - #if _PETSC_MAJOR_ >=3 - #ifndef _HAVE_MUMPS_ - _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); - #endif - - #endif - } - /*}}}*/ - /*Prepare solver:{{{1*/ - KSPCreate(MPI_COMM_WORLD,&ksp); - KSPSetOperators(ksp,Kff,Kff,DIFFERENT_NONZERO_PATTERN); - KSPSetFromOptions(ksp); - - #if defined(_SERIAL_) && _PETSC_MAJOR_==3 - /*Specific solver?: */ - KSPGetPC(ksp,&pc); - if (solver_type==MUMPSPACKAGE_LU){ - #if _PETSC_MINOR_==1 - PCFactorSetMatSolverPackage(pc,MAT_SOLVER_MUMPS); - #else - PCFactorSetMatSolverPackage(pc,MATSOLVERMUMPS); - #endif - } - #endif - - #if defined(_PARALLEL_) && _PETSC_MAJOR_==3 - /*Stokes: */ - if (solver_type==StokesSolverEnum){ - /*Make indices out of doftypes: */ - if(!df)_error_("need doftypes for Stokes solver!\n"); - DofTypesToIndexSet(&isv,&isp,df,StokesSolverEnum); - - /*Set field splits: */ - KSPGetPC(ksp,&pc); - #if _PETSC_MINOR_==1 - PCFieldSplitSetIS(pc,isv); - PCFieldSplitSetIS(pc,isp); - #else - PCFieldSplitSetIS(pc,PETSC_NULL,isv); - PCFieldSplitSetIS(pc,PETSC_NULL,isp); - #endif - - } - #endif - - /*}}}*/ - /*If there is an initial guess for the solution, use it, except if we are using the MUMPS direct solver, where any initial guess will crash Petsc: {{{1*/ - if (uf0){ - if( (solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ - KSPSetInitialGuessNonzero(ksp,PETSC_TRUE); - } - } - /*}}}*/ - - if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); - - /*Solve: */ - KSPSolve(ksp,pf,uf); - - /*Check convergence*/ - KSPGetIterationNumber(ksp,&iteration_number); - if (iteration_number<0) _error_("%s%i"," Solver diverged at iteration number: ",-iteration_number); - - /*Free resources:*/ - KSPFree(&ksp); - /*Assign output pointers:*/ *puf=uf; Index: /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.h (revision 11684) @@ -9,5 +9,6 @@ /* local prototypes: */ -void Solverx( Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df,Parameters* parameters); +void Solverx(Vector** puf, Matrix* Kff, Vector* pf, Vector* uf0,Vector* df, Parameters* parameters); +void SolverxPetsc(Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df, Parameters* parameters); void DofTypesToIndexSet(IS* pisv, IS* pisp, Vec df,int typeenum); #endif /* _SOLVERX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/SolverxPetsc.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/SolverxPetsc.cpp (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/SolverxPetsc.cpp (revision 11684) @@ -0,0 +1,180 @@ +/*!\file SolverxPetsc + * \brief Petsc implementation of solver + */ + +#include "./Solverx.h" +#include "../../shared/shared.h" +#include "../../include/include.h" +#include "../../io/io.h" + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +void SolverxPetsc(Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df, Parameters* parameters){ + + /*Output: */ + Vec uf = NULL; + + /*Intermediary: */ + int local_m,local_n,global_m,global_n; + int analysis_type; + + /*Solver */ + KSP ksp = NULL; + PC pc = NULL; + int iteration_number; + int solver_type; + bool fromlocalsize = true; + #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) + PetscTruth flag,flg; + #else + PetscBool flag,flg; + #endif + + /*Stokes: */ + IS isv=NULL; + IS isp=NULL; + + #if _PETSC_MAJOR_ >= 3 + char ksp_type[50]; + #endif + + + /*Display message*/ + _printf_(VerboseModule()," Solving\n"); + #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) + if(VerboseSolver())PetscOptionsPrint(stdout); + #else + if(VerboseSolver())PetscOptionsView(PETSC_VIEWER_STDOUT_WORLD); + #endif + + /*First, check that f-set is not NULL, i.e. model is fully constrained: {{{*/ + _assert_(Kff); + MatGetSize(Kff,&global_m,&global_n); _assert_(global_m==global_m); + if(!global_n){ + *puf=NULL; return; + } + /*}}}*/ + /*Initial guess logic here: {{{1*/ + /*Now, check that we are not giving an initial guess to the solver, if we are running a direct solver: */ + #if _PETSC_MAJOR_ >= 3 + PetscOptionsGetString(PETSC_NULL,"-ksp_type",ksp_type,49,&flg); + if (strcmp(ksp_type,"preonly")==0)uf0=NULL; + #endif + + /*If initial guess for the solution exists, use it to create uf, otherwise, + * duplicate the right hand side so that the solution vector has the same structure*/ + if(uf0){ + VecDuplicate(uf0,&uf); VecCopy(uf0,uf); + } + else{ + MatGetLocalSize(Kff,&local_m,&local_n);uf=NewVec(local_n,fromlocalsize); + } + /*}}}*/ + /*Process petsc options to see if we are using special types of external solvers: {{{1*/ + PetscOptionsDetermineSolverType(&solver_type); + + /*In serial mode, the matrices have been loaded as MPIAIJ or AIJ matrices. + We need to convert them if we are going to run the solvers successfully: */ + #ifdef _SERIAL_ + #if _PETSC_MAJOR_ == 2 + if (solver_type==MUMPSPACKAGE_LU){ + /*Convert Kff to MATTAIJMUMPS: */ + MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); + } + if (solver_type==MUMPSPACKAGE_CHOL){ + /*Convert Kff to MATTSBAIJMUMPS: */ + MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); + } + if (solver_type==SPOOLESPACKAGE_LU){ + /*Convert Kff to MATTSBAIJMUMPS: */ + MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); + } + if (solver_type==SPOOLESPACKAGE_CHOL){ + /*Convert Kff to MATTSBAIJMUMPS: */ + MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); + } + if (solver_type==SUPERLUDISTPACKAGE){ + /*Convert Kff to MATTSBAIJMUMPS: */ + MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); + } + if (solver_type==StokesSolverEnum){ + _error_("Petsc 2 does not support multi-physics solvers"); + } + #endif + #endif + /*}}}*/ + /*Check the solver is available: {{{1*/ + if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ + #if _PETSC_MAJOR_ >=3 + #ifndef _HAVE_MUMPS_ + _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); + #endif + + #endif + } + /*}}}*/ + /*Prepare solver:{{{1*/ + KSPCreate(MPI_COMM_WORLD,&ksp); + KSPSetOperators(ksp,Kff,Kff,DIFFERENT_NONZERO_PATTERN); + KSPSetFromOptions(ksp); + + #if defined(_SERIAL_) && _PETSC_MAJOR_==3 + /*Specific solver?: */ + KSPGetPC(ksp,&pc); + if (solver_type==MUMPSPACKAGE_LU){ + #if _PETSC_MINOR_==1 + PCFactorSetMatSolverPackage(pc,MAT_SOLVER_MUMPS); + #else + PCFactorSetMatSolverPackage(pc,MATSOLVERMUMPS); + #endif + } + #endif + + #if defined(_PARALLEL_) && _PETSC_MAJOR_==3 + /*Stokes: */ + if (solver_type==StokesSolverEnum){ + /*Make indices out of doftypes: */ + if(!df)_error_("need doftypes for Stokes solver!\n"); + DofTypesToIndexSet(&isv,&isp,df,StokesSolverEnum); + + /*Set field splits: */ + KSPGetPC(ksp,&pc); + #if _PETSC_MINOR_==1 + PCFieldSplitSetIS(pc,isv); + PCFieldSplitSetIS(pc,isp); + #else + PCFieldSplitSetIS(pc,PETSC_NULL,isv); + PCFieldSplitSetIS(pc,PETSC_NULL,isp); + #endif + + } + #endif + + /*}}}*/ + /*If there is an initial guess for the solution, use it, except if we are using the MUMPS direct solver, where any initial guess will crash Petsc: {{{1*/ + if (uf0){ + if( (solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ + KSPSetInitialGuessNonzero(ksp,PETSC_TRUE); + } + } + /*}}}*/ + + if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); + + /*Solve: */ + KSPSolve(ksp,pf,uf); + + /*Check convergence*/ + KSPGetIterationNumber(ksp,&iteration_number); + if (iteration_number<0) _error_("%s%i"," Solver diverged at iteration number: ",-iteration_number); + + /*Free resources:*/ + KSPFree(&ksp); + + /*Assign output pointers:*/ + *puf=uf; +} Index: /issm/branches/trunk-jpl-damage/src/c/modules/StringToEnumx/StringToEnumx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 11684) @@ -137,10 +137,10 @@ else if (strcmp(name,"PrognosticHydrostaticAdjustment")==0) return PrognosticHydrostaticAdjustmentEnum; else if (strcmp(name,"PrognosticMinThickness")==0) return PrognosticMinThicknessEnum; + else if (strcmp(name,"PrognosticPenaltyFactor")==0) return PrognosticPenaltyFactorEnum; + else if (strcmp(name,"PrognosticSpcthickness")==0) return PrognosticSpcthicknessEnum; else stage=2; } if(stage==2){ - if (strcmp(name,"PrognosticPenaltyFactor")==0) return PrognosticPenaltyFactorEnum; - else if (strcmp(name,"PrognosticSpcthickness")==0) return PrognosticSpcthicknessEnum; - else if (strcmp(name,"PrognosticStabilization")==0) return PrognosticStabilizationEnum; + if (strcmp(name,"PrognosticStabilization")==0) return PrognosticStabilizationEnum; else if (strcmp(name,"PrognosticVertexPairing")==0) return PrognosticVertexPairingEnum; else if (strcmp(name,"QmuIsdakota")==0) return QmuIsdakotaEnum; Index: /issm/branches/trunk-jpl-damage/src/c/modules/SystemMatricesx/SystemMatricesx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11684) @@ -10,5 +10,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void SystemMatricesx(Mat* pKff, Mat* pKfs, Vec* ppf, Vec* pdf, double* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,bool kflag,bool pflag,bool penalty_kflag,bool penalty_pflag){ +void SystemMatricesx(Matrix** pKff, Matrix** pKfs, Vector** ppf, Vector** pdf, double* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,bool kflag,bool pflag,bool penalty_kflag,bool penalty_pflag){ /*intermediary: */ @@ -21,8 +21,8 @@ /*output: */ - Mat Kff = NULL; - Mat Kfs = NULL; - Vec pf = NULL; - Vec df=NULL; + Matrix* Kff = NULL; + Matrix* Kfs = NULL; + Vector* pf = NULL; + Vector* df=NULL; double kmax = 0; @@ -49,7 +49,7 @@ if(kflag){ - Kff=NewMat(fsize,fsize,connectivity,numberofdofspernode); - Kfs=NewMat(fsize,ssize,connectivity,numberofdofspernode); - df=NewVec(fsize); + Kff=new Matrix(fsize,fsize,connectivity,numberofdofspernode); + Kfs=new Matrix(fsize,ssize,connectivity,numberofdofspernode); + df=new Vector(fsize); /*Fill stiffness matrix from elements: */ @@ -66,17 +66,8 @@ /*Assemble matrix and doftypes and compress matrix to save memory: */ - MatAssemblyBegin(Kff,MAT_FINAL_ASSEMBLY); - MatAssemblyEnd(Kff,MAT_FINAL_ASSEMBLY); - #if _PETSC_MAJOR_ == 2 - MatCompress(Kff); - #endif + Kff->Assemble(); + Kfs->Assemble(); + df->Assemble(); - MatAssemblyBegin(Kfs,MAT_FINAL_ASSEMBLY); - MatAssemblyEnd(Kfs,MAT_FINAL_ASSEMBLY); - #if _PETSC_MAJOR_ == 2 - MatCompress(Kfs); - #endif - VecAssemblyBegin(df); - VecAssemblyEnd(df); } @@ -84,5 +75,5 @@ if(pflag){ - pf=NewVec(fsize); + pf=new Vector(fsize); /*Fill right hand side vector, from elements: */ @@ -98,10 +89,9 @@ } - VecAssemblyBegin(pf); - VecAssemblyEnd(pf); + pf->Assemble(); } /*Now, figure out maximum value of K_gg, so that we can penalize it correctly: */ - MatNorm(Kff,NORM_INFINITY,&kmax); + kmax=Kff->Norm(NORM_INFINITY); /*Now, deal with penalties*/ @@ -115,15 +105,6 @@ /*Assemble matrix and compress matrix to save memory: */ - MatAssemblyBegin(Kff,MAT_FINAL_ASSEMBLY); - MatAssemblyEnd(Kff,MAT_FINAL_ASSEMBLY); - #if _PETSC_MAJOR_ == 2 - MatCompress(Kff); - #endif - - MatAssemblyBegin(Kfs,MAT_FINAL_ASSEMBLY); - MatAssemblyEnd(Kfs,MAT_FINAL_ASSEMBLY); - #if _PETSC_MAJOR_ == 2 - MatCompress(Kfs); - #endif + Kff->Assemble(); + Kfs->Assemble(); } @@ -137,17 +118,17 @@ } - VecAssemblyBegin(pf); - VecAssemblyEnd(pf); + pf->Assemble(); + pf->Assemble(); } /*Assign output pointers: */ if(pKff) *pKff=Kff; - else MatFree(&Kff); + else delete Kff; if(pKfs) *pKfs=Kfs; - else MatFree(&Kfs); + else delete Kfs; if(ppf) *ppf=pf; - else VecFree(&pf); + else delete pf; if(pdf) *pdf=df; - else VecFree(&df); + else delete df; if(pkmax) *pkmax=kmax; } Index: /issm/branches/trunk-jpl-damage/src/c/modules/SystemMatricesx/SystemMatricesx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SystemMatricesx/SystemMatricesx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SystemMatricesx/SystemMatricesx.h (revision 11684) @@ -10,5 +10,5 @@ /* local prototypes: */ -void SystemMatricesx(Mat* pKff, Mat* pKfs, Vec* ppf, Vec* pdf, double* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters, +void SystemMatricesx(Matrix** pKff, Matrix** pKfs, Vector** ppf, Vector** pdf, double* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters, bool kflag=true,bool pflag=true,bool penalty_kflag=true,bool penalty_pflag=true); Index: /issm/branches/trunk-jpl-damage/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp (revision 11684) @@ -10,5 +10,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vec yg){ +void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vector* yg){ int configuration_type; @@ -19,5 +19,5 @@ /*serialize yg, so nodes can index into it: */ - VecToMPISerial(&yg_serial,yg); + yg_serial=yg->ToMPISerial(); for(int i=0;iSize();i++){ Index: /issm/branches/trunk-jpl-damage/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h (revision 11684) @@ -9,5 +9,5 @@ #include "../../objects/objects.h" -void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vec yg); +void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vector* yg); #endif /* _UPDATESPCSX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/VecMergex/VecMergex.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/VecMergex/VecMergex.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/VecMergex/VecMergex.cpp (revision 11684) @@ -10,5 +10,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void VecMergex(Vec ug, Vec uf, Nodes* nodes, Parameters* parameters, int SetEnum){ +void VecMergex(Vector* ug, Vector* uf, Nodes* nodes, Parameters* parameters, int SetEnum){ /*variables: */ @@ -21,5 +21,6 @@ /*serialize uf: */ - VecToMPISerial(&uf_serial,uf); + uf_serial=uf->ToMPISerial(); + /*Do we have any nodes for this configuration? :*/ @@ -43,6 +44,4 @@ /*Assemble vector: */ - VecAssemblyBegin(ug); - VecAssemblyEnd(ug); - + ug->Assemble(); } Index: /issm/branches/trunk-jpl-damage/src/c/modules/VecMergex/VecMergex.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/VecMergex/VecMergex.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/modules/VecMergex/VecMergex.h (revision 11684) @@ -10,5 +10,5 @@ /* local prototypes: */ -void VecMergex(Vec ug, Vec uf, Nodes* nodes, Parameters* parameters, int SetEnum); +void VecMergex(Vector* ug, Vector* uf, Nodes* nodes, Parameters* parameters, int SetEnum); #endif /* _VECMERGEX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Mesh.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Mesh.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Mesh.cpp (revision 11684) @@ -1028,8 +1028,10 @@ Triangle &t=triangles[i]; if (t.det>0 && !(t.Hidden(0)||t.Hidden(1) || t.Hidden(2) )){ - index[num*3+0]=GetId(t[0])+1; //back to M indexing - index[num*3+1]=GetId(t[1])+1; //back to M indexing - index[num*3+2]=GetId(t[2])+1; //back to M indexing - num=num+1; + if(t.Anisotropy()<2 & t.Length()<1.e+5){ + index[num*3+0]=GetId(t[0])+1; //back to M indexing + index[num*3+1]=GetId(t[1])+1; //back to M indexing + index[num*3+2]=GetId(t[2])+1; //back to M indexing + num=num+1; + } } } @@ -1038,5 +1040,5 @@ /*Assign output pointers*/ *pindex=index; - *pnels=k; + *pnels=num; } /*}}}1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Triangle.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Triangle.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Triangle.cpp (revision 11684) @@ -50,4 +50,55 @@ AdjacentTriangle Triangle::Adj(int i) const { return AdjacentTriangle(adj[i],AdjEdgeIndex[i]&3); + };/*}}}*/ + /*FUNCTION Triangle::Anisotropy{{{1*/ + double Triangle::Anisotropy() const{ + + double lmin,lmax; + + /*Get three vertices A,B and C*/ + R2 A=*this->vertices[0]; + R2 B=*this->vertices[1]; + R2 C=*this->vertices[2]; + + /*Compute edges*/ + R2 e1=B-A; + R2 e2=C-A; + R2 e3=B-C; + + /*Compute edge length*/ + double l1=Norme2(e1); + double l2=Norme2(e2); + double l3=Norme2(e3); + + lmin=l1; + lmin=min(lmin,l2); + lmin=min(lmin,l3); + lmax=l1; + lmax=max(lmax,l2); + lmax=max(lmax,l3); + + return lmax/lmin; + };/*}}}*/ + /*FUNCTION Triangle::Length{{{1*/ + double Triangle::Length() const{ + + double l; + + /*Get three vertices A,B and C*/ + R2 A=*this->vertices[0]; + R2 B=*this->vertices[1]; + R2 C=*this->vertices[2]; + + /*Compute edges*/ + R2 e1=B-A; + R2 e2=C-A; + R2 e3=B-C; + + /*Compute edge length*/ + l=Norme2(e1); + l=max(l,Norme2(e2)); + l=max(l,Norme2(e3)); + + return l; };/*}}}*/ /*FUNCTION Triangle::Echo {{{1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Triangle.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Triangle.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Triangle.h (revision 11684) @@ -41,4 +41,6 @@ //Methods void Echo(); + double Anisotropy() const; + double Length() const; int swap(short a1,int=0); long Optim(short a,int =0); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Element.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Element.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Element.h (revision 11684) @@ -16,4 +16,6 @@ class Parameters; class Patch; +class Matrix; +class Vector; #include "../../toolkits/toolkits.h" @@ -28,8 +30,8 @@ virtual void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters)=0; virtual void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters)=0; - virtual void CreateKMatrix(Mat Kff, Mat Kfs,Vec df)=0; - virtual void CreatePVector(Vec pf)=0; - virtual void CreateJacobianMatrix(Mat Jff)=0; - virtual void GetSolutionFromInputs(Vec solution)=0; + virtual void CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df)=0; + virtual void CreatePVector(Vector* pf)=0; + virtual void CreateJacobianMatrix(Matrix* Jff)=0; + virtual void GetSolutionFromInputs(Vector* solution)=0; virtual int GetNodeIndex(Node* node)=0; virtual int Sid()=0; @@ -58,4 +60,5 @@ virtual void RequestedOutput(int output_enum,int step,double time)=0; + virtual int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units)=0; virtual void InputScale(int enum_type,double scale_factor)=0; virtual void GetVectorFromInputs(Vec vector, int name_enum)=0; @@ -88,5 +91,4 @@ virtual void ElementResponse(double* presponse,int response_enum,bool process_units)=0; virtual double IceVolume(void)=0; - virtual int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units)=0; #endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.cpp (revision 11684) @@ -567,5 +567,5 @@ /*}}}*/ /*FUNCTION Penta::CreateKMatrix {{{1*/ -void Penta::CreateKMatrix(Mat Kff, Mat Kfs,Vec df){ +void Penta::CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df){ /*retrieve parameters: */ @@ -671,5 +671,5 @@ /*}}}*/ /*FUNCTION Penta::CreatePVector {{{1*/ -void Penta::CreatePVector(Vec pf){ +void Penta::CreatePVector(Vector* pf){ /*retrive parameters: */ @@ -773,5 +773,5 @@ /*}}}*/ /*FUNCTION Penta::CreateJacobianMatrix{{{1*/ -void Penta::CreateJacobianMatrix(Mat Jff){ +void Penta::CreateJacobianMatrix(Matrix* Jff){ /*retrieve parameters: */ @@ -1091,5 +1091,5 @@ /*}}}*/ /*FUNCTION Penta::GetSolutionFromInputs{{{1*/ -void Penta::GetSolutionFromInputs(Vec solution){ +void Penta::GetSolutionFromInputs(Vector* solution){ int analysis_type; @@ -2331,4 +2331,35 @@ extern int my_rank; return my_rank; +} +/*}}}*/ +/*FUNCTION Penta::NodalValue {{{1*/ +int Penta::NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units){ + + int i; + int found=0; + double value; + Input* data=NULL; + GaussPenta* gauss=NULL; + + /*First, serarch the input: */ + data=inputs->GetInput(natureofdataenum); + + /*figure out if we have the vertex id: */ + found=0; + for(i=0;iGetVertexId()){ + /*Do we have natureofdataenum in our inputs? :*/ + if(data){ + /*ok, we are good. retrieve value of input at vertex :*/ + gauss=new GaussPenta(); gauss->GaussVertex(i); + data->GetInputValue(&value,gauss); + found=1; + break; + } + } + } + + if(found)*pvalue=value; + return found; } /*}}}*/ @@ -3008,35 +3039,4 @@ } /*}}}*/ -/*FUNCTION Penta::NodalValue {{{1*/ -int Penta::NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units){ - - int i; - int found=0; - double value; - Input* data=NULL; - GaussPenta* gauss=NULL; - - /*First, serarch the input: */ - data=inputs->GetInput(natureofdataenum); - - /*figure out if we have the vertex id: */ - found=0; - for(i=0;iGetVertexId()){ - /*Do we have natureofdataenum in our inputs? :*/ - if(data){ - /*ok, we are good. retrieve value of input at vertex :*/ - gauss=new GaussPenta(); gauss->GaussVertex(i); - data->GetInputValue(&value,gauss); - found=1; - break; - } - } - } - - if(found)*pvalue=value; - return found; -} -/*}}}*/ /*FUNCTION Penta::MinVel{{{1*/ void Penta::MinVel(double* pminvel, bool process_units){ @@ -4190,5 +4190,5 @@ /*}}}*/ /*FUNCTION Penta::GetSolutionFromInputsThermal{{{1*/ -void Penta::GetSolutionFromInputsThermal(Vec solution){ +void Penta::GetSolutionFromInputsThermal(Vector* solution){ const int numdof=NDOF1*NUMVERTICES; @@ -4213,5 +4213,5 @@ /*Add value to global vector*/ - VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INSERT_VALUES); /*Free ressources:*/ @@ -4221,5 +4221,5 @@ /*}}}*/ /*FUNCTION Penta::GetSolutionFromInputsEnthalpy{{{1*/ -void Penta::GetSolutionFromInputsEnthalpy(Vec solution){ +void Penta::GetSolutionFromInputsEnthalpy(Vector* solution){ const int numdof=NDOF1*NUMVERTICES; @@ -4244,5 +4244,5 @@ /*Add value to global vector*/ - VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INSERT_VALUES); /*Free ressources:*/ @@ -7862,5 +7862,5 @@ /*}}}*/ /*FUNCTION Penta::GetSolutionFromInputsDiagnosticHoriz{{{1*/ -void Penta::GetSolutionFromInputsDiagnosticHoriz(Vec solution){ +void Penta::GetSolutionFromInputsDiagnosticHoriz(Vector* solution){ const int numdof=NDOF2*NUMVERTICES; @@ -7896,5 +7896,5 @@ /*Add value to global vector*/ - VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INSERT_VALUES); /*Free ressources:*/ @@ -7904,5 +7904,5 @@ /*}}}*/ /*FUNCTION Penta::GetSolutionFromInputsDiagnosticHutter{{{1*/ -void Penta::GetSolutionFromInputsDiagnosticHutter(Vec solution){ +void Penta::GetSolutionFromInputsDiagnosticHutter(Vector* solution){ const int numdof=NDOF2*NUMVERTICES; @@ -7932,5 +7932,5 @@ /*Add value to global vector*/ - VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INSERT_VALUES); /*Free ressources:*/ @@ -7940,5 +7940,5 @@ /*}}}*/ /*FUNCTION Penta::GetSolutionFromInputsDiagnosticVert{{{1*/ -void Penta::GetSolutionFromInputsDiagnosticVert(Vec solution){ +void Penta::GetSolutionFromInputsDiagnosticVert(Vector* solution){ const int numdof=NDOF1*NUMVERTICES; @@ -7965,5 +7965,5 @@ /*Add value to global vector*/ - VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INSERT_VALUES); /*Free ressources:*/ @@ -7973,5 +7973,5 @@ /*}}}*/ /*FUNCTION Penta::GetSolutionFromInputsDiagnosticStokes{{{1*/ -void Penta::GetSolutionFromInputsDiagnosticStokes(Vec solution){ +void Penta::GetSolutionFromInputsDiagnosticStokes(Vector* solution){ const int numdof=NDOF4*NUMVERTICES; @@ -8010,5 +8010,5 @@ /*Add value to global vector*/ - VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INSERT_VALUES); /*Free ressources:*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.h (revision 11684) @@ -86,10 +86,10 @@ void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); - void CreateKMatrix(Mat Kff, Mat Kfs,Vec df); - void CreatePVector(Vec pf); - void CreateJacobianMatrix(Mat Jff); + void CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df); + void CreatePVector(Vector* pf); + void CreateJacobianMatrix(Matrix* Jff); void DeleteResults(void); int GetNodeIndex(Node* node); - void GetSolutionFromInputs(Vec solution); + void GetSolutionFromInputs(Vector* solution); double GetZcoord(GaussPenta* gauss); void GetVectorFromInputs(Vec vector,int name_enum); @@ -118,4 +118,5 @@ void Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type); int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf); + int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); double TimeAdapt(); int* GetHorizontalNeighboorSids(void); @@ -129,5 +130,4 @@ void MinVy(double* pminvy, bool process_units); void MinVz(double* pminvz, bool process_units); - int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); double MassFlux(double* segment,bool process_units); void MaxAbsVx(double* pmaxabsvx, bool process_units); @@ -183,5 +183,5 @@ void GetInputValue(double* pvalue,Node* node,int enumtype); void GetPhi(double* phi, double* epsilon, double viscosity); - void GetSolutionFromInputsEnthalpy(Vec solutiong); + void GetSolutionFromInputsEnthalpy(Vector* solutiong); double GetStabilizationParameter(double u, double v, double w, double diameter, double kappa); void GetStrainRate3dPattyn(double* epsilon,double* xyz_list, GaussPenta* gauss, Input* vx_input, Input* vy_input); @@ -250,8 +250,8 @@ void InputUpdateFromSolutionDiagnosticVert( double* solutiong); void InputUpdateFromSolutionDiagnosticStokes( double* solutiong); - void GetSolutionFromInputsDiagnosticHoriz(Vec solutiong); - void GetSolutionFromInputsDiagnosticHutter(Vec solutiong); - void GetSolutionFromInputsDiagnosticStokes(Vec solutiong); - void GetSolutionFromInputsDiagnosticVert(Vec solutiong); + void GetSolutionFromInputsDiagnosticHoriz(Vector* solutiong); + void GetSolutionFromInputsDiagnosticHutter(Vector* solutiong); + void GetSolutionFromInputsDiagnosticStokes(Vector* solutiong); + void GetSolutionFromInputsDiagnosticVert(Vector* solutiong); ElementVector* CreatePVectorCouplingMacAyealStokes(void); ElementVector* CreatePVectorCouplingMacAyealStokesViscous(void); @@ -307,5 +307,5 @@ ElementVector* CreatePVectorThermalShelf(void); ElementVector* CreatePVectorThermalSheet(void); - void GetSolutionFromInputsThermal(Vec solutiong); + void GetSolutionFromInputsThermal(Vector* solutiong); void InputUpdateFromSolutionThermal( double* solutiong); void InputUpdateFromSolutionEnthalpy( double* solutiong); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.cpp (revision 11684) @@ -319,5 +319,5 @@ /*}}}*/ /*FUNCTION Tria::CreateKMatrix {{{1*/ -void Tria::CreateKMatrix(Mat Kff, Mat Kfs,Vec df){ +void Tria::CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df){ /*retreive parameters: */ @@ -672,5 +672,5 @@ /*}}}*/ /*FUNCTION Tria::CreatePVector {{{1*/ -void Tria::CreatePVector(Vec pf){ +void Tria::CreatePVector(Vector* pf){ /*retrive parameters: */ @@ -892,5 +892,5 @@ /*}}}*/ /*FUNCTION Tria::CreateJacobianMatrix{{{1*/ -void Tria::CreateJacobianMatrix(Mat Jff){ +void Tria::CreateJacobianMatrix(Matrix* Jff){ /*retrieve parameters: */ @@ -1274,5 +1274,5 @@ /*}}}*/ /*FUNCTION Tria::GetSolutionFromInputs{{{1*/ -void Tria::GetSolutionFromInputs(Vec solution){ +void Tria::GetSolutionFromInputs(Vector* solution){ /*retrive parameters: */ @@ -2124,4 +2124,35 @@ } /*}}}*/ +/*FUNCTION Tria::NodalValue {{{1*/ +int Tria::NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units){ + + int i; + int found=0; + double value; + Input* data=NULL; + GaussTria *gauss = NULL; + + /*First, serarch the input: */ + data=inputs->GetInput(natureofdataenum); + + /*figure out if we have the vertex id: */ + found=0; + for(i=0;iGetVertexId()){ + /*Do we have natureofdataenum in our inputs? :*/ + if(data){ + /*ok, we are good. retrieve value of input at vertex :*/ + gauss=new GaussTria(); gauss->GaussVertex(i); + data->GetInputValue(&value,gauss); + found=1; + break; + } + } + } + + if(found)*pvalue=value; + return found; +} +/*}}}*/ /*FUNCTION Tria::PatchFill{{{1*/ void Tria::PatchFill(int* prow, Patch* patch){ @@ -2740,35 +2771,4 @@ } /*}}}*/ -/*FUNCTION Tria::NodalValue {{{1*/ -int Tria::NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units){ - - int i; - int found=0; - double value; - Input* data=NULL; - GaussTria *gauss = NULL; - - /*First, serarch the input: */ - data=inputs->GetInput(natureofdataenum); - - /*figure out if we have the vertex id: */ - found=0; - for(i=0;iGetVertexId()){ - /*Do we have natureofdataenum in our inputs? :*/ - if(data){ - /*ok, we are good. retrieve value of input at vertex :*/ - gauss=new GaussTria(); gauss->GaussVertex(i); - data->GetInputValue(&value,gauss); - found=1; - break; - } - } - } - - if(found)*pvalue=value; - return found; -} -/*}}}*/ /*FUNCTION Tria::ElementResponse{{{1*/ void Tria::ElementResponse(double* presponse,int response_enum,bool process_units){ @@ -3143,5 +3143,5 @@ /*}}}*/ /*FUNCTION Tria::GetSolutionFromInputsDiagnosticHoriz{{{1*/ -void Tria::GetSolutionFromInputsDiagnosticHoriz(Vec solution){ +void Tria::GetSolutionFromInputsDiagnosticHoriz(Vector* solution){ const int numdof=NDOF2*NUMVERTICES; @@ -3174,5 +3174,5 @@ } - VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INSERT_VALUES); /*Free ressources:*/ @@ -3182,5 +3182,5 @@ /*}}}*/ /*FUNCTION Tria::GetSolutionFromInputsDiagnosticHutter{{{1*/ -void Tria::GetSolutionFromInputsDiagnosticHutter(Vec solution){ +void Tria::GetSolutionFromInputsDiagnosticHutter(Vector* solution){ const int numdof=NDOF2*NUMVERTICES; @@ -3213,5 +3213,5 @@ } - VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INSERT_VALUES); /*Free ressources:*/ @@ -4985,4 +4985,5 @@ } /*}}}*/ + /*FUNCTION Tria::InputUpdateFromSolutionAdjointBalancethickness {{{1*/ void Tria::InputUpdateFromSolutionAdjointBalancethickness(double* solution){ @@ -5289,5 +5290,5 @@ /*}}}*/ /*FUNCTION Tria::GetSolutionFromInputsHydrology{{{1*/ -void Tria::GetSolutionFromInputsHydrology(Vec solution){ +void Tria::GetSolutionFromInputsHydrology(Vector* solution){ const int numdof=NDOF1*NUMVERTICES; @@ -5317,5 +5318,5 @@ } - VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INSERT_VALUES); /*Free ressources:*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.h (revision 11684) @@ -82,7 +82,7 @@ void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); - void CreateKMatrix(Mat Kff, Mat Kfs,Vec df); - void CreatePVector(Vec pf); - void CreateJacobianMatrix(Mat Jff); + void CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df); + void CreatePVector(Vector* pf); + void CreateJacobianMatrix(Matrix* Jff); int GetNodeIndex(Node* node); int Sid(); @@ -92,5 +92,5 @@ bool IsNodeOnShelfFromFlags(double* flags); bool IsOnWater(); - void GetSolutionFromInputs(Vec solution); + void GetSolutionFromInputs(Vector* solution); void GetVectorFromInputs(Vec vector, int name_enum); void GetVectorFromResults(Vec vector,int offset,int interp); @@ -106,4 +106,5 @@ void MaterialUpdateFromTemperature(void){_error_("not implemented yet");}; void MigrateGroundingLine(double* oldfloating,double* sheet_ungrounding); + int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); void PotentialSheetUngrounding(Vec potential_sheet_ungrounding); void PositiveDegreeDay(void); @@ -127,5 +128,4 @@ void MinVy(double* pminvy, bool process_units); void MinVz(double* pminvz, bool process_units); - int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); double MassFlux(double* segment,bool process_units); void MaxAbsVx(double* pmaxabsvx, bool process_units); @@ -212,6 +212,6 @@ ElementVector* CreatePVectorDiagnosticHutter(void); ElementMatrix* CreateJacobianDiagnosticMacayeal(void); - void GetSolutionFromInputsDiagnosticHoriz(Vec solution); - void GetSolutionFromInputsDiagnosticHutter(Vec solution); + void GetSolutionFromInputsDiagnosticHoriz(Vector* solution); + void GetSolutionFromInputsDiagnosticHutter(Vector* solution); void InputUpdateFromSolutionDiagnosticHoriz( double* solution); void InputUpdateFromSolutionDiagnosticHutter( double* solution); @@ -232,5 +232,5 @@ ElementVector* CreatePVectorHydrology(void); void CreateHydrologyWaterVelocityInput(void); - void GetSolutionFromInputsHydrology(Vec solution); + void GetSolutionFromInputsHydrology(Vector* solution); void InputUpdateFromSolutionHydrology(double* solution); #endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.cpp (revision 11684) @@ -316,5 +316,5 @@ /*}}}*/ /*FUNCTION Icefront::CreateKMatrix {{{1*/ -void Icefront::CreateKMatrix(Mat Kff, Mat Kfs){ +void Icefront::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ /*No stiffness loads applied, do nothing: */ @@ -324,5 +324,5 @@ /*}}}*/ /*FUNCTION Icefront::CreatePVector {{{1*/ -void Icefront::CreatePVector(Vec pf){ +void Icefront::CreatePVector(Vector* pf){ /*Checks in debugging mode*/ @@ -362,10 +362,10 @@ /*}}}*/ /*FUNCTION Icefront::CreateJacobianMatrix{{{1*/ -void Icefront::CreateJacobianMatrix(Mat Jff){ +void Icefront::CreateJacobianMatrix(Matrix* Jff){ this->CreateKMatrix(Jff,NULL); } /*}}}1*/ /*FUNCTION Icefront::PenaltyCreateKMatrix {{{1*/ -void Icefront::PenaltyCreateKMatrix(Mat Kff, Mat Kfs, double kmax){ +void Icefront::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs, double kmax){ /*do nothing: */ return; @@ -373,5 +373,5 @@ /*}}}*/ /*FUNCTION Icefront::PenaltyCreatePVector{{{1*/ -void Icefront::PenaltyCreatePVector(Vec pf,double kmax){ +void Icefront::PenaltyCreatePVector(Vector* pf,double kmax){ /*do nothing: */ return; @@ -379,5 +379,5 @@ /*}}}*/ /*FUNCTION Icefront::PenaltyCreateJacobianMatrix{{{1*/ -void Icefront::PenaltyCreateJacobianMatrix(Mat Jff,double kmax){ +void Icefront::PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){ this->PenaltyCreateKMatrix(Jff,NULL,kmax); } Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Icefront.h (revision 11684) @@ -74,10 +74,10 @@ void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); - void CreateKMatrix(Mat Kff, Mat Kfs); - void CreatePVector(Vec pf); - void CreateJacobianMatrix(Mat Jff); - void PenaltyCreateKMatrix(Mat Kff, Mat kfs, double kmax); - void PenaltyCreatePVector(Vec pf, double kmax); - void PenaltyCreateJacobianMatrix(Mat Jff,double kmax); + void CreateKMatrix(Matrix* Kff, Matrix* Kfs); + void CreatePVector(Vector* pf); + void CreateJacobianMatrix(Matrix* Jff); + void PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, double kmax); + void PenaltyCreatePVector(Vector* pf, double kmax); + void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax); bool InAnalysis(int analysis_type); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Load.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Load.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Load.h (revision 11684) @@ -12,4 +12,6 @@ /*{{{1*/ class Object; +class Matrix; +class Vector; #include "../Object.h" @@ -27,10 +29,10 @@ virtual void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters)=0; virtual void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters)=0; - virtual void CreateKMatrix(Mat Kff, Mat Kfs)=0; - virtual void CreatePVector(Vec pf)=0; - virtual void CreateJacobianMatrix(Mat Jff)=0; - virtual void PenaltyCreateJacobianMatrix(Mat Jff,double kmax)=0; - virtual void PenaltyCreateKMatrix(Mat Kff, Mat Kfs, double kmax)=0; - virtual void PenaltyCreatePVector(Vec pf, double kmax)=0; + virtual void CreateKMatrix(Matrix* Kff, Matrix* Kfs)=0; + virtual void CreatePVector(Vector* pf)=0; + virtual void CreateJacobianMatrix(Matrix* Jff)=0; + virtual void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax)=0; + virtual void PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs, double kmax)=0; + virtual void PenaltyCreatePVector(Vector* pf, double kmax)=0; virtual bool InAnalysis(int analysis_type)=0; /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.cpp (revision 11684) @@ -334,5 +334,5 @@ /*}}}*/ /*FUNCTION Numericalflux::CreateKMatrix {{{1*/ -void Numericalflux::CreateKMatrix(Mat Kff, Mat Kfs){ +void Numericalflux::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ /*recover some parameters*/ @@ -365,5 +365,5 @@ /*}}}*/ /*FUNCTION Numericalflux::CreatePVector {{{1*/ -void Numericalflux::CreatePVector(Vec pf){ +void Numericalflux::CreatePVector(Vector* pf){ /*recover some parameters*/ @@ -395,5 +395,5 @@ /*}}}*/ /*FUNCTION Numericalflux::PenaltyCreateKMatrix {{{1*/ -void Numericalflux::PenaltyCreateKMatrix(Mat Kff, Mat Kfs,double kmax){ +void Numericalflux::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,double kmax){ /*No stiffness loads applied, do nothing: */ @@ -403,5 +403,5 @@ /*}}}*/ /*FUNCTION Numericalflux::PenaltyCreatePVector{{{1*/ -void Numericalflux::PenaltyCreatePVector(Vec pf,double kmax){ +void Numericalflux::PenaltyCreatePVector(Vector* pf,double kmax){ /*No penalty loads applied, do nothing: */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Numericalflux.h (revision 11684) @@ -70,10 +70,10 @@ void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); - void CreateKMatrix(Mat Kff, Mat Kfs); - void CreatePVector(Vec pf); - void CreateJacobianMatrix(Mat Jff){_error_("Not implemented yet");}; - void PenaltyCreateJacobianMatrix(Mat Jff,double kmax){_error_("Not implemented yet");}; - void PenaltyCreateKMatrix(Mat Kff, Mat kfs, double kmax); - void PenaltyCreatePVector(Vec pf, double kmax); + void CreateKMatrix(Matrix* Kff, Matrix* Kfs); + void CreatePVector(Vector* pf); + void CreateJacobianMatrix(Matrix* Jff){_error_("Not implemented yet");}; + void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){_error_("Not implemented yet");}; + void PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, double kmax); + void PenaltyCreatePVector(Vector* pf, double kmax); bool InAnalysis(int analysis_type); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.cpp (revision 11684) @@ -295,5 +295,5 @@ /*}}}1*/ /*FUNCTION Pengrid::CreateKMatrix {{{1*/ -void Pengrid::CreateKMatrix(Mat Kff, Mat Kfs){ +void Pengrid::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ /*No loads applied, do nothing: */ @@ -303,5 +303,5 @@ /*}}}1*/ /*FUNCTION Pengrid::CreatePVector {{{1*/ -void Pengrid::CreatePVector(Vec pf){ +void Pengrid::CreatePVector(Vector* pf){ /*No loads applied, do nothing: */ @@ -311,5 +311,5 @@ /*}}}1*/ /*FUNCTION Pengrid::PenaltyCreateMatrix {{{1*/ -void Pengrid::PenaltyCreateKMatrix(Mat Kff, Mat Kfs,double kmax){ +void Pengrid::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,double kmax){ /*Retrieve parameters: */ @@ -319,7 +319,10 @@ switch(analysis_type){ + #ifdef _HAVE_DIAGNOSTIC_ case DiagnosticHorizAnalysisEnum: case AdjointHorizAnalysisEnum: Ke=PenaltyCreateKMatrixDiagnosticStokes(kmax); break; + #endif + #ifdef _HAVE_THERMAL_ case ThermalAnalysisEnum: Ke=PenaltyCreateKMatrixThermal(kmax); @@ -328,4 +331,5 @@ Ke=PenaltyCreateKMatrixMelting(kmax); break; + #endif default: _error_("analysis %i (%s) not supported yet",analysis_type,EnumToStringx(analysis_type)); @@ -340,5 +344,5 @@ /*}}}1*/ /*FUNCTION Pengrid::PenaltyCreatePVector {{{1*/ -void Pengrid::PenaltyCreatePVector(Vec pf,double kmax){ +void Pengrid::PenaltyCreatePVector(Vector* pf,double kmax){ /*Retrieve parameters: */ @@ -348,7 +352,10 @@ switch(analysis_type){ + #ifdef _HAVE_DIAGNOSTIC_ case ThermalAnalysisEnum: pe=PenaltyCreatePVectorThermal(kmax); break; + #endif + #ifdef _HAVE_THERMAL_ case MeltingAnalysisEnum: pe=PenaltyCreatePVectorMelting(kmax); @@ -356,4 +363,5 @@ case DiagnosticHorizAnalysisEnum: case AdjointHorizAnalysisEnum: break; + #endif default: _error_("analysis %i (%s) not supported yet",analysis_type,EnumToStringx(analysis_type)); @@ -539,4 +547,5 @@ } /*}}}1*/ +#ifdef _HAVE_DIAGNOSTIC_ /*FUNCTION Pengrid::PenaltyCreateKMatrixDiagnosticStokes {{{1*/ ElementMatrix* Pengrid::PenaltyCreateKMatrixDiagnosticStokes(double kmax){ @@ -571,4 +580,6 @@ } /*}}}1*/ +#endif +#ifdef _HAVE_THERMAL_ /*FUNCTION Pengrid::PenaltyCreateKMatrixMelting {{{1*/ ElementMatrix* Pengrid::PenaltyCreateKMatrixMelting(double kmax){ @@ -690,4 +701,5 @@ } /*}}}1*/ +#endif /*FUNCTION Pengrid::ResetConstraint {{{1*/ void Pengrid::ResetConstraint(void){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Pengrid.h (revision 11684) @@ -75,18 +75,22 @@ void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); - void CreateKMatrix(Mat Kff, Mat Kfs); - void CreatePVector(Vec pf); - void CreateJacobianMatrix(Mat Jff){_error_("Not implemented yet");}; - void PenaltyCreateJacobianMatrix(Mat Jff,double kmax){_error_("Not implemented yet");}; - void PenaltyCreateKMatrix(Mat Kff, Mat kfs, double kmax); - void PenaltyCreatePVector(Vec pf, double kmax); + void CreateKMatrix(Matrix* Kff, Matrix* Kfs); + void CreatePVector(Vector* pf); + void CreateJacobianMatrix(Matrix* Jff){_error_("Not implemented yet");}; + void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){_error_("Not implemented yet");}; + void PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, double kmax); + void PenaltyCreatePVector(Vector* pf, double kmax); bool InAnalysis(int analysis_type); /*}}}*/ /*Pengrid management {{{1*/ + #ifdef _HAVE_DIAGNOSTIC_ ElementMatrix* PenaltyCreateKMatrixDiagnosticStokes(double kmax); + #endif + #ifdef _HAVE_THERMAL_ ElementMatrix* PenaltyCreateKMatrixThermal(double kmax); ElementMatrix* PenaltyCreateKMatrixMelting(double kmax); ElementVector* PenaltyCreatePVectorThermal(double kmax); ElementVector* PenaltyCreatePVectorMelting(double kmax); + #endif void ConstraintActivate(int* punstable); void ConstraintActivateThermal(int* punstable); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.cpp (revision 11684) @@ -199,5 +199,5 @@ /*}}}1*/ /*FUNCTION Penpair::CreateKMatrix {{{1*/ -void Penpair::CreateKMatrix(Mat Kff, Mat Kfs){ +void Penpair::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ /*If you code this piece, don't forget that a penalty will be inactive if it is dealing with clone nodes*/ /*No loads applied, do nothing: */ @@ -207,5 +207,5 @@ /*}}}1*/ /*FUNCTION Penpair::CreatePVector {{{1*/ -void Penpair::CreatePVector(Vec pf){ +void Penpair::CreatePVector(Vector* pf){ /*No loads applied, do nothing: */ @@ -215,10 +215,10 @@ /*}}}1*/ /*FUNCTION Penpair::CreateJacobianMatrix{{{1*/ -void Penpair::CreateJacobianMatrix(Mat Jff){ +void Penpair::CreateJacobianMatrix(Matrix* Jff){ this->CreateKMatrix(Jff,NULL); } /*}}}1*/ /*FUNCTION Penpair::PenaltyCreateKMatrix {{{1*/ -void Penpair::PenaltyCreateKMatrix(Mat Kff, Mat Kfs,double kmax){ +void Penpair::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,double kmax){ /*Retrieve parameters: */ @@ -246,5 +246,5 @@ /*}}}1*/ /*FUNCTION Penpair::PenaltyCreatePVector {{{1*/ -void Penpair::PenaltyCreatePVector(Vec pf,double kmax){ +void Penpair::PenaltyCreatePVector(Vector* pf,double kmax){ /*No loads applied, do nothing: */ return; @@ -252,5 +252,5 @@ /*}}}1*/ /*FUNCTION Penpair::PenaltyCreateJacobianMatrix{{{1*/ -void Penpair::PenaltyCreateJacobianMatrix(Mat Jff,double kmax){ +void Penpair::PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){ this->PenaltyCreateKMatrix(Jff,NULL,kmax); } Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Penpair.h (revision 11684) @@ -62,10 +62,10 @@ void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); - void CreateKMatrix(Mat Kff, Mat Kfs); - void CreatePVector(Vec pf); - void CreateJacobianMatrix(Mat Jff); - void PenaltyCreateKMatrix(Mat Kff,Mat Kfs,double kmax); - void PenaltyCreatePVector(Vec pf, double kmax); - void PenaltyCreateJacobianMatrix(Mat Jff,double kmax); + void CreateKMatrix(Matrix* Kff, Matrix* Kfs); + void CreatePVector(Vector* pf); + void CreateJacobianMatrix(Matrix* Jff); + void PenaltyCreateKMatrix(Matrix* Kff,Matrix* Kfs,double kmax); + void PenaltyCreatePVector(Vector* pf, double kmax); + void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax); bool InAnalysis(int analysis_type); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.cpp (revision 11684) @@ -428,5 +428,5 @@ /*}}}*/ /*FUNCTION Riftfront::PenaltyCreateKMatrix {{{1*/ -void Riftfront::PenaltyCreateKMatrix(Mat Kff, Mat Kfs,double kmax){ +void Riftfront::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,double kmax){ /*Retrieve parameters: */ @@ -454,5 +454,5 @@ /*}}}1*/ /*FUNCTION Riftfront::PenaltyCreatePVector {{{1*/ -void Riftfront::PenaltyCreatePVector(Vec pf,double kmax){ +void Riftfront::PenaltyCreatePVector(Vector* pf,double kmax){ /*Retrieve parameters: */ @@ -480,5 +480,5 @@ /*}}}1*/ /*FUNCTION Riftfront::CreateKMatrix {{{1*/ -void Riftfront::CreateKMatrix(Mat Kff, Mat Kfs){ +void Riftfront::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ /*do nothing: */ return; @@ -486,5 +486,5 @@ /*}}}1*/ /*FUNCTION Riftfront::CreatePVector {{{1*/ -void Riftfront::CreatePVector(Vec pf){ +void Riftfront::CreatePVector(Vector* pf){ /*do nothing: */ return; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Loads/Riftfront.h (revision 11684) @@ -82,10 +82,10 @@ void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); - void CreateKMatrix(Mat Kff, Mat Kfs); - void CreatePVector(Vec pf); - void CreateJacobianMatrix(Mat Jff){_error_("Not implemented yet");}; - void PenaltyCreateJacobianMatrix(Mat Jff,double kmax){_error_("Not implemented yet");}; - void PenaltyCreateKMatrix(Mat Kff, Mat kfs, double kmax); - void PenaltyCreatePVector(Vec pf, double kmax); + void CreateKMatrix(Matrix* Kff, Matrix* Kfs); + void CreatePVector(Vector* pf); + void CreateJacobianMatrix(Matrix* Jff){_error_("Not implemented yet");}; + void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){_error_("Not implemented yet");}; + void PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, double kmax); + void PenaltyCreatePVector(Vector* pf, double kmax); bool InAnalysis(int analysis_type); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Node.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Node.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Node.cpp (revision 11684) @@ -594,5 +594,5 @@ /*}}}*/ /*FUNCTION Node::CreateNodalConstraints{{{1*/ -void Node::CreateNodalConstraints(Vec ys){ +void Node::CreateNodalConstraints(Vector* ys){ int i; @@ -613,5 +613,5 @@ /*Add values into constraint vector: */ - VecSetValues(ys,this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); + ys->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); } @@ -875,5 +875,5 @@ /*}}}*/ /*FUNCTION Node::VecMerge {{{1*/ -void Node::VecMerge(Vec ug, double* vector_serial,int setenum){ +void Node::VecMerge(Vector* ug, double* vector_serial,int setenum){ double* values=NULL; @@ -897,5 +897,5 @@ /*Add values into ug: */ - VecSetValues(ug,this->indexing.fsize,indices,(const double*)values,INSERT_VALUES); + ug->SetValues(this->indexing.fsize,indices,values,INSERT_VALUES); } } @@ -915,5 +915,5 @@ /*Add values into ug: */ - VecSetValues(ug,this->indexing.ssize,indices,(const double*)values,INSERT_VALUES); + ug->SetValues(this->indexing.ssize,indices,values,INSERT_VALUES); } } @@ -926,5 +926,5 @@ /*}}}*/ /*FUNCTION Node::VecReduce {{{1*/ -void Node::VecReduce(Vec vector, double* ug_serial,int setenum){ +void Node::VecReduce(Vector* vector, double* ug_serial,int setenum){ double* values=NULL; @@ -945,5 +945,5 @@ /*Add values into ug: */ - VecSetValues(vector,this->indexing.fsize,this->indexing.fdoflist,(const double*)values,INSERT_VALUES); + vector->SetValues(this->indexing.fsize,this->indexing.fdoflist,values,INSERT_VALUES); } } @@ -961,5 +961,5 @@ /*Add values into ug: */ - VecSetValues(vector,this->indexing.ssize,this->indexing.sdoflist,(const double*)values,INSERT_VALUES); + vector->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); } } Index: /issm/branches/trunk-jpl-damage/src/c/objects/Node.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Node.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Node.h (revision 11684) @@ -16,4 +16,6 @@ class DataSet; class Vertices; +class Vector; +class Matrix; #include "./Update.h" /*}}}*/ @@ -67,5 +69,5 @@ /*Node numerical routines {{{1*/ void Configure(DataSet* nodes,Vertices* vertices); - void CreateNodalConstraints(Vec ys); + void CreateNodalConstraints(Vector* ys); void SetCurrentConfiguration(DataSet* nodes,Vertices* vertices); int Sid(void); @@ -101,6 +103,6 @@ int IsGrounded(); void UpdateSpcs(double* ys); - void VecMerge(Vec ug, double* vector_serial,int setnum); - void VecReduce(Vec vector, double* ug_serial,int setnum); + void VecMerge(Vector* ug, double* vector_serial,int setenum); + void VecReduce(Vector* vector, double* ug_serial,int setnum); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementMatrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementMatrix.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementMatrix.cpp (revision 11684) @@ -245,6 +245,6 @@ /*ElementMatrix specific routines: */ -/*FUNCTION ElementMatrix::AddToGlobal(Mat Kff, Mat Kfs){{{1*/ -void ElementMatrix::AddToGlobal(Mat Kff, Mat Kfs){ +/*FUNCTION ElementMatrix::AddToGlobal(Matrix* Kff, Matrix* Kfs){{{1*/ +void ElementMatrix::AddToGlobal(Matrix* Kff, Matrix* Kfs){ int i,j; @@ -260,46 +260,50 @@ this->CheckConsistency(); - if(this->dofsymmetrical){ - /*only use row dofs to add values into global matrices: */ - - if(this->row_fsize){ - /*first, retrieve values that are in the f-set from the g-set values matrix: */ - localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); - for(i=0;irow_fsize;i++){ - for(j=0;jrow_fsize;j++){ - *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); + #ifdef _HAVE_PETSC_ + if(this->dofsymmetrical){ + /*only use row dofs to add values into global matrices: */ + + if(this->row_fsize){ + /*first, retrieve values that are in the f-set from the g-set values matrix: */ + localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); + for(i=0;irow_fsize;i++){ + for(j=0;jrow_fsize;j++){ + *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); + } } + /*add local values into global matrix, using the fglobaldoflist: */ + MatSetValues(Kff->matrix,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); + + /*Free ressources:*/ + xfree((void**)&localvalues); } - /*add local values into global matrix, using the fglobaldoflist: */ - MatSetValues(Kff,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); - - /*Free ressources:*/ - xfree((void**)&localvalues); - } - - - if((this->row_ssize!=0) && (this->row_fsize!=0)){ - /*first, retrieve values that are in the f and s-set from the g-set values matrix: */ - localvalues=(double*)xmalloc(this->row_fsize*this->row_ssize*sizeof(double)); - for(i=0;irow_fsize;i++){ - for(j=0;jrow_ssize;j++){ - *(localvalues+this->row_ssize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_slocaldoflist[j]); + + + if((this->row_ssize!=0) && (this->row_fsize!=0)){ + /*first, retrieve values that are in the f and s-set from the g-set values matrix: */ + localvalues=(double*)xmalloc(this->row_fsize*this->row_ssize*sizeof(double)); + for(i=0;irow_fsize;i++){ + for(j=0;jrow_ssize;j++){ + *(localvalues+this->row_ssize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_slocaldoflist[j]); + } } + /*add local values into global matrix, using the fglobaldoflist: */ + MatSetValues(Kfs->matrix,this->row_fsize,this->row_fglobaldoflist,this->row_ssize,this->row_sglobaldoflist,(const double*)localvalues,ADD_VALUES); + + /*Free ressources:*/ + xfree((void**)&localvalues); } - /*add local values into global matrix, using the fglobaldoflist: */ - MatSetValues(Kfs,this->row_fsize,this->row_fglobaldoflist,this->row_ssize,this->row_sglobaldoflist,(const double*)localvalues,ADD_VALUES); - - /*Free ressources:*/ - xfree((void**)&localvalues); - } - } - else{ - _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); - } - -} -/*}}}*/ -/*FUNCTION ElementMatrix::AddToGlobal(Mat Jff){{{1*/ -void ElementMatrix::AddToGlobal(Mat Jff){ + } + else{ + _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); + } + #else + _error_("not supported yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION ElementMatrix::AddToGlobal(Matrix* Jff){{{1*/ +void ElementMatrix::AddToGlobal(Matrix* Jff){ int i,j; @@ -312,26 +316,30 @@ this->CheckConsistency(); - if(this->dofsymmetrical){ - /*only use row dofs to add values into global matrices: */ - - if(this->row_fsize){ - /*first, retrieve values that are in the f-set from the g-set values matrix: */ - localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); - for(i=0;irow_fsize;i++){ - for(j=0;jrow_fsize;j++){ - *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); + #ifdef _HAVE_PETSC_ + if(this->dofsymmetrical){ + /*only use row dofs to add values into global matrices: */ + + if(this->row_fsize){ + /*first, retrieve values that are in the f-set from the g-set values matrix: */ + localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); + for(i=0;irow_fsize;i++){ + for(j=0;jrow_fsize;j++){ + *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); + } } + /*add local values into global matrix, using the fglobaldoflist: */ + MatSetValues(Jff->matrix,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); + + /*Free ressources:*/ + xfree((void**)&localvalues); } - /*add local values into global matrix, using the fglobaldoflist: */ - MatSetValues(Jff,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); - - /*Free ressources:*/ - xfree((void**)&localvalues); - } - - } - else{ - _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); - } + + } + else{ + _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); + } + #else + _error_("not supported yet!"); + #endif } Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementMatrix.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementMatrix.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementMatrix.h (revision 11684) @@ -58,6 +58,6 @@ /*}}}*/ /*ElementMatrix specific routines {{{1*/ - void AddToGlobal(Mat Kff, Mat Kfs); - void AddToGlobal(Mat Jff); + void AddToGlobal(Matrix* Kff, Matrix* Kfs); + void AddToGlobal(Matrix* Jff); void Echo(void); void CheckConsistency(void); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementVector.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementVector.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementVector.cpp (revision 11684) @@ -160,42 +160,52 @@ /*ElementVector specific routines: */ -/*FUNCTION ElementVector::AddToGlobal(Vec pf){{{1*/ -void ElementVector::AddToGlobal(Vec pf){ +/*FUNCTION ElementVector::AddToGlobal(Vector* pf){{{1*/ +void ElementVector::AddToGlobal(Vector* pf){ int i; double* localvalues=NULL; - if(this->fsize){ - /*first, retrieve values that are in the f-set from the g-set values vector: */ - localvalues=(double*)xmalloc(this->fsize*sizeof(double)); - for(i=0;ifsize;i++){ - localvalues[i]=this->values[this->flocaldoflist[i]]; - } - /*add local values into global vector, using the fglobaldoflist: */ - VecSetValues(pf,this->fsize,this->fglobaldoflist,(const double*)localvalues,ADD_VALUES); - - /*Free ressources:*/ - xfree((void**)&localvalues); - } -} -/*}}}*/ -/*FUNCTION ElementVector::InsertIntoGlobal(Vec pf){{{1*/ -void ElementVector::InsertIntoGlobal(Vec pf){ + #ifdef _HAVE_PETSC_ + if(this->fsize){ + /*first, retrieve values that are in the f-set from the g-set values vector: */ + localvalues=(double*)xmalloc(this->fsize*sizeof(double)); + for(i=0;ifsize;i++){ + localvalues[i]=this->values[this->flocaldoflist[i]]; + } + /*add local values into global vector, using the fglobaldoflist: */ + VecSetValues(pf->vector,this->fsize,this->fglobaldoflist,(const double*)localvalues,ADD_VALUES); + + /*Free ressources:*/ + xfree((void**)&localvalues); + } + #else + _error_("not supported yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION ElementVector::InsertIntoGlobal(Vector* pf){{{1*/ +void ElementVector::InsertIntoGlobal(Vector* pf){ int i; double* localvalues=NULL; - if(this->fsize){ - /*first, retrieve values that are in the f-set from the g-set values vector: */ - localvalues=(double*)xmalloc(this->fsize*sizeof(double)); - for(i=0;ifsize;i++){ - localvalues[i]=this->values[this->flocaldoflist[i]]; - } - /*add local values into global vector, using the fglobaldoflist: */ - VecSetValues(pf,this->fsize,this->fglobaldoflist,(const double*)localvalues,INSERT_VALUES); - - /*Free ressources:*/ - xfree((void**)&localvalues); - } + #ifdef _HAVE_PETSC_ + if(this->fsize){ + /*first, retrieve values that are in the f-set from the g-set values vector: */ + localvalues=(double*)xmalloc(this->fsize*sizeof(double)); + for(i=0;ifsize;i++){ + localvalues[i]=this->values[this->flocaldoflist[i]]; + } + /*add local values into global vector, using the fglobaldoflist: */ + VecSetValues(pf->vector,this->fsize,this->fglobaldoflist,(const double*)localvalues,INSERT_VALUES); + + /*Free ressources:*/ + xfree((void**)&localvalues); + } + #else + _error_("not supported yet!"); + #endif + } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementVector.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementVector.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/ElementVector.h (revision 11684) @@ -40,6 +40,6 @@ /*}}}*/ /*ElementVector specific routines {{{1*/ - void AddToGlobal(Vec pf); - void InsertIntoGlobal(Vec pf); + void AddToGlobal(Vector* pf); + void InsertIntoGlobal(Vector* pf); void Echo(void); void Init(ElementVector* pe); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.cpp (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.cpp (revision 11684) @@ -0,0 +1,202 @@ +/*!\file Matrix.cpp + * \brief: implementation of the Matrix object + */ + +/*Headers:*/ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../shared/shared.h" +#include "../../Container/Container.h" +#include "../../include/include.h" +#include "./Matrix.h" +/*}}}*/ + +/*Matrix constructors and destructor*/ +/*FUNCTION Matrix::Matrix(){{{1*/ +Matrix::Matrix(){ + + this->M=0; + this->N=0; + + #ifdef _HAVE_PETSC_ + this->matrix=NULL; + #else + this->matrix=NULL; + #endif + #ifdef _HAVE_ADOLC_ + this->amatrix=NULL; + #endif +} +/*}}}*/ +/*FUNCTION Matrix::Matrix(int M,int N){{{1*/ +Matrix::Matrix(int pM,int pN){ + + this->M=pM; + this->N=pN; + + #ifdef _HAVE_PETSC_ + this->matrix=NewMat(pM,pN); + #else + this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); + #endif + #ifdef _HAVE_ADOLC_ + this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); + #endif +} +/*}}}*/ +/*FUNCTION Matrix::Matrix(int M,int N,double sparsity){{{1*/ +Matrix::Matrix(int pM,int pN,double sparsity){ + + this->M=pM; + this->N=pN; + + #ifdef _HAVE_PETSC_ + this->matrix=NewMat(pM,pN,sparsity); + #else + this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); + #endif + #ifdef _HAVE_ADOLC_ + this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); + #endif +} +/*}}}*/ +/*FUNCTION Matrix::Matrix(int M,int N,int connectivity,int numberofdofspernode){{{1*/ +Matrix::Matrix(int pM,int pN,int connectivity,int numberofdofspernode){ + + this->M=pM; + this->N=pN; + + #ifdef _HAVE_PETSC_ + this->matrix=NewMat(pM,pN,connectivity,numberofdofspernode); + #else + this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); + #endif + #ifdef _HAVE_ADOLC_ + this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); + #endif +} +/*}}}*/ +/*FUNCTION Matrix::~Matrix(){{{1*/ +Matrix::~Matrix(){ + + #ifdef _HAVE_PETSC_ + MatFree(&this->matrix); + #else + xfree((void**)&this->matrix); + #endif + #ifdef _HAVE_ADOLC_ + xfree((void**)&this->amatrix); + #endif +} +/*}}}*/ + +/*Matrix specific routines: */ +/*FUNCTION Matrix::Echo{{{1*/ +void Matrix::Echo(void){ + + int i,j; + + #ifdef _HAVE_PETSC_ + MatView(this->matrix,PETSC_VIEWER_STDOUT_WORLD); + #else + printf("Matrix size: %i-%i\n",M,N); + for(i=0;i>?*/ + printf("ADOLC Matrix equivalent:" ); + for(i=0;imatrix); + #else + _error_("not implemented yet!"); + #endif + return dataref; + +} +/*}}}*/ +#endif +/*FUNCTION Matrix::Assemble{{{1*/ +void Matrix::Assemble(void){ + #ifdef _HAVE_PETSC_ + MatAssemblyBegin(this->matrix,MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(this->matrix,MAT_FINAL_ASSEMBLY); + #if _PETSC_MAJOR_ == 2 + MatCompress(this->matrix); + #endif + #else + /*do nothing:*/ + #endif + +} +/*}}}*/ +/*FUNCTION Matrix::Norm{{{1*/ +double Matrix::Norm(int norm_type){ + + double norm=0; + #ifdef _HAVE_PETSC_ + MatNorm(this->matrix,(NormType)norm_type,&norm); + #else + _error_("not implemented yet!"); + #endif + return norm; +} +/*}}}*/ +/*FUNCTION Matrix::GetSize{{{1*/ +void Matrix::GetSize(int* pM,int* pN){ + + #ifdef _HAVE_PETSC_ + MatGetSize(this->matrix,pM,pN); + #else + _error_("not implemented yet!"); + #endif +} +/*}}}*/ +/*FUNCTION Matrix::GetLocalSize{{{1*/ +void Matrix::GetLocalSize(int* pM,int* pN){ + + #ifdef _HAVE_PETSC_ + MatGetLocalSize(this->matrix,pM,pN); + #else + _error_("not implemented yet!"); + #endif +} +/*}}}*/ +/*FUNCTION Matrix::MatMult{{{1*/ +void Matrix::MatMult(Vector* X,Vector* AX){ + + #ifdef _HAVE_PETSC_ + MatMultPatch(this->matrix,X->vector,AX->vector); + #else + _error_("not implemented yet!"); + #endif +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.h (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.h (revision 11684) @@ -0,0 +1,66 @@ +/*!\file: Matrix.h + * \brief wrapper to matrix objects. The goal is to control which API (PETSC,Scalpack, Plapack?) + * implements our underlying matrix format. + */ + +#ifndef _MATRIX_H_ +#define _MATRIX_H_ + +/*Headers:*/ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif +#include "../Object.h" +#include "../../toolkits/toolkits.h" +#include "../../EnumDefinitions/EnumDefinitions.h" + +#ifdef _HAVE_ADOLC_ +#include "adolc.h" +#endif + +#ifdef _SERIAL_ +#include "mex.h" +#endif +class Vector; + +/*}}}*/ + +class Matrix{ + + public: + + int M,N; + + #ifdef _HAVE_PETSC_ + Mat matrix; + #else + double* matrix; + #endif + #ifdef _HAVE_ADOLC_ + adouble* amatrix; + #endif + + /*Matrix constructors, destructors {{{1*/ + Matrix(); + Matrix(int M,int N); + Matrix(int M,int N,double sparsity); + Matrix(int M,int N,int connectivity,int numberofdofspernode); + ~Matrix(); + /*}}}*/ + /*Matrix specific routines {{{1*/ + void Echo(void); + #ifdef _SERIAL_ + mxArray* ToMatlabMatrix(void); + #endif + void Assemble(void); + double Norm(int norm_type); + void GetSize(int* pM,int* pN); + void GetLocalSize(int* pM,int* pN); + void MatMult(Vector* X,Vector* AX); + /*}}}*/ + +}; +#endif //#ifndef _MATRIX_H_ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp (revision 11684) @@ -0,0 +1,248 @@ +/*!\file Vector.cpp + * \brief: implementation of the Vector object + */ + +/*Headers:*/ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../shared/shared.h" +#include "../../Container/Container.h" +#include "../../include/include.h" +#include "./Vector.h" +/*}}}*/ + +/*Vector constructors and destructor*/ +/*FUNCTION Vector::Vector(){{{1*/ +Vector::Vector(){ + + this->M=0; + #ifdef _HAVE_PETSC_ + this->vector=NULL; + #else + this->vector=NULL; + #endif + #ifdef _HAVE_ADOLC_ + this->avector=NULL; + #endif +} +/*}}}*/ +/*FUNCTION Vector::Vector(int M,bool fromlocalsize){{{1*/ +Vector::Vector(int pM,bool fromlocalsize){ + + #ifdef _HAVE_PETSC_ + this->vector=NewVec(pM,fromlocalsize); + #else + this->M=pM; + this->vector=(double*)xcalloc(pM,sizeof(double)); + #endif + #ifdef _HAVE_ADOLC_ + this->avector=(adouble*)xmalloc(pM*sizeof(adouble)); + #endif +} +/*}}}*/ +/*FUNCTION Vector::~Vector(){{{1*/ +Vector::~Vector(){ + + #ifdef _HAVE_PETSC_ + VecFree(&this->vector); + #else + xfree((void**)&this->vector); + #endif + #ifdef _HAVE_ADOLC_ + xfree((void**)&this->avector); + #endif +} +/*}}}*/ + +/*Vector specific routines: */ +/*FUNCTION Vector::Echo{{{1*/ +void Vector::Echo(void){ + + int i; + + #ifdef _HAVE_PETSC_ + VecView(this->vector,PETSC_VIEWER_STDOUT_WORLD); + #else + printf("Vector size: %i\n",M); + for(i=0;i>?*/ + printf("ADOLC Vector equivalent:" ); + for(i=0;ivector); + #else + _error_("not implemented yet!"); + #endif + return dataref; + +} +/*}}}*/ +#endif +/*FUNCTION Vector::Assemble{{{1*/ +void Vector::Assemble(void){ + + #ifdef _HAVE_PETSC_ + VecAssemblyBegin(this->vector); + VecAssemblyEnd(this->vector); + #else + /*do nothing*/ + #endif + +} +/*}}}*/ +/*FUNCTION Vector::SetValues{{{1*/ +void Vector::SetValues(int ssize, int* list, double* values, int mode){ + + + #ifdef _HAVE_PETSC_ + VecSetValues(this->vector,ssize,list,values,(InsertMode)mode); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION Vector::GetSize{{{1*/ +void Vector::GetSize(int* pM){ + + #ifdef _HAVE_PETSC_ + VecGetSize(this->vector,pM); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION Vector::GetLocalSize{{{1*/ +void Vector::GetLocalSize(int* pM){ + + #ifdef _HAVE_PETSC_ + VecGetLocalSize(this->vector,pM); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION Vector::Duplicate{{{1*/ +Vector* Vector::Duplicate(void){ + + Vector* output=NULL; + output=new Vector(); + #ifdef _HAVE_PETSC_ + Vec vec_output=NULL; + VecDuplicate(this->vector,&vec_output); + output->vector=vec_output; + VecGetSize(output->vector,&output->M); + #else + _error_("not implemented yet!"); + #endif + return output; + +} +/*}}}*/ +/*FUNCTION Vector::Set{{{1*/ +void Vector::Set(double value){ + + #ifdef _HAVE_PETSC_ + this->Set(value); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION Vector::AXPY{{{1*/ +void Vector::AXPY(Vector* X, double a){ + + #ifdef _HAVE_PETSC_ + VecAXPY(this->vector,a,X->vector); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION Vector::AYPX{{{1*/ +void Vector::AYPX(Vector* X, double a){ + + #ifdef _HAVE_PETSC_ + VecAYPX(this->vector,a,X->vector); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION Vector::ToMPISerial{{{1*/ +double* Vector::ToMPISerial(void){ + + double* vec_serial=NULL; + + #ifdef _HAVE_PETSC_ + VecToMPISerial(&vec_serial, this->vector); + #else + _error_("not implemented yet!"); + #endif + + return vec_serial; + +} +/*}}}*/ +/*FUNCTION Vector::Copy{{{1*/ +void Vector::Copy(Vector* to){ + + #ifdef _HAVE_PETSC_ + VecCopy(this->vector,to->vector); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION Vector::Norm{{{1*/ +double Vector::Norm(int norm_type){ + + double norm=0; + #ifdef _HAVE_PETSC_ + VecNorm(this->vector,(NormType)norm_type,&norm); + #else + _error_("not implemented yet!"); + #endif + return norm; +} +/*}}}*/ +/*FUNCTION Vector::Scale{{{1*/ +void Vector::Scale(double scale_factor){ + + #ifdef _HAVE_PETSC_ + VecScale(this->vector,scale_factor); + #else + _error_("not implemented yet!"); + #endif +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h (revision 11684) @@ -0,0 +1,70 @@ +/*!\file: Vector.h + * \brief wrapper to vector objects. The goal is to control which API (PETSC,Scalpack, Plapack?) + * implements our underlying vector format. + */ + +#ifndef _VECTOR_H_ +#define _VECTOR_H_ + +/*Headers:*/ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif +#include "../Object.h" +#include "../../toolkits/toolkits.h" +#include "../../EnumDefinitions/EnumDefinitions.h" + +#ifdef _HAVE_ADOLC_ +#include "adolc.h" +#endif + + +#ifdef _SERIAL_ +#include "mex.h" +#endif + +/*}}}*/ + +class Vector{ + + public: + + int M; + + #ifdef _HAVE_PETSC_ + Vec vector; + #else + double* vector; + #endif + #ifdef _HAVE_ADOLC_ + adouble* avector; + #endif + + /*Vector constructors, destructors {{{1*/ + Vector(); + Vector(int M,bool fromlocalsize=false); + ~Vector(); + /*}}}*/ + /*Vector specific routines {{{1*/ + void Echo(void); + #ifdef _SERIAL_ + mxArray* ToMatlabVector(void); + #endif + void Assemble(void); + void SetValues(int ssize, int* list, double* values, int mode); + void GetSize(int* pM); + void GetLocalSize(int* pM); + Vector* Duplicate(void); + void Set(double value); + void AXPY(Vector* X, double a); + void AYPX(Vector* X, double a); + double* ToMPISerial(void); + void Copy(Vector* to); + double Norm(int norm_type); + void Scale(double scale_factor); + /*}}}*/ +}; +#endif //#ifndef _VECTOR_H_ Index: /issm/branches/trunk-jpl-damage/src/c/objects/objects.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/objects.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/objects/objects.h (revision 11684) @@ -120,4 +120,6 @@ #include "./Numerics/ElementMatrix.h" #include "./Numerics/ElementVector.h" +#include "./Numerics/Vector.h" +#include "./Numerics/Matrix.h" /*Params: */ Index: /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.cpp (revision 11684) @@ -29,4 +29,5 @@ #include "../Exceptions/exceptions.h" #include "../../include/include.h" +#include "../../objects/objects.h" void* xmalloc(int size){ @@ -80,4 +81,23 @@ } +void xdelete( Matrix** pv){ + + if (pv && *pv) { + + delete *pv; + *pv=NULL; + } +} + +void xdelete( Vector** pv){ + + if (pv && *pv) { + + delete *pv; + *pv=NULL; + } +} + + void* xrealloc ( void* pv, int size){ Index: /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.h (revision 11684) @@ -5,9 +5,12 @@ #ifndef _ALLOC_H_ #define _ALLOC_H_ - +class Matrix; +class Vector; void* xmalloc(int size); void* xcalloc(int n,int size); void xfree(void** pvptr); void* xrealloc ( void* pv, int size); +void xdelete(Matrix** pvptr); +void xdelete(Vector** pvptr); #endif Index: /issm/branches/trunk-jpl-damage/src/c/shared/Elements/elements.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Elements/elements.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Elements/elements.h (revision 11684) @@ -17,6 +17,6 @@ int* GetLocalDofList( Node** nodes,int numnodes,int setenum,int approximation_enum); int* GetGlobalDofList(Node** nodes,int numnodes,int setenum,int approximation_enum); +#ifdef _HAVE_DIAGNOSTIC_ void CoordinateSystemTransform(double** ptransform,Node** nodes,int numnodes,int* cs_array); -#ifdef _HAVE_DIAGNOSTIC_ void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum); void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array); Index: /issm/branches/trunk-jpl-damage/src/c/solutions/AnalysisConfiguration.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solutions/AnalysisConfiguration.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solutions/AnalysisConfiguration.cpp (revision 11684) @@ -38,5 +38,5 @@ case SteadystateSolutionEnum: - numanalyses=7; + numanalyses=8; analyses=(int*)xmalloc(numanalyses*sizeof(int)); analyses[0]=DiagnosticHorizAnalysisEnum; @@ -45,6 +45,7 @@ analyses[3]=SurfaceSlopeAnalysisEnum; analyses[4]=BedSlopeAnalysisEnum; - analyses[5]=ThermalAnalysisEnum; - analyses[6]=MeltingAnalysisEnum; + analyses[5]=EnthalpyAnalysisEnum; + analyses[6]=ThermalAnalysisEnum; + analyses[7]=MeltingAnalysisEnum; break; Index: /issm/branches/trunk-jpl-damage/src/c/solutions/ResetBoundaryConditions.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solutions/ResetBoundaryConditions.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solutions/ResetBoundaryConditions.cpp (revision 11684) @@ -11,5 +11,5 @@ /*variables: */ - Vec yg = NULL; + Vector* yg = NULL; Nodes *nodes = NULL; int i; @@ -30,4 +30,4 @@ /*Free ressources:*/ - VecFree(&yg); + delete yg; } Index: /issm/branches/trunk-jpl-damage/src/c/solutions/convergence.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solutions/convergence.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solutions/convergence.cpp (revision 11684) @@ -8,5 +8,5 @@ #include "../EnumDefinitions/EnumDefinitions.h" -void convergence(bool* pconverged, Mat Kff,Vec pf,Vec uf,Vec old_uf,Parameters* parameters){ +void convergence(bool* pconverged, Matrix* Kff,Vector* pf,Vector* uf,Vector* old_uf,Parameters* parameters){ /*output*/ @@ -14,9 +14,9 @@ /*intermediary*/ - Vec KU=NULL; - Vec KUF=NULL; - Vec KUold=NULL; - Vec KUoldF=NULL; - Vec duf=NULL; + Vector* KU=NULL; + Vector* KUF=NULL; + Vector* KUold=NULL; + Vector* KUoldF=NULL; + Vector* duf=NULL; double ndu,nduinf,nu; double nKUF; @@ -48,16 +48,16 @@ //compute KUF = KU - F = K*U - F - VecDuplicate(uf,&KU); MatMultPatch(Kff,uf,KU); - VecDuplicate(KU,&KUF);VecCopy(KU,KUF); VecAYPX(KUF,-1.0,pf); + KU=uf->Duplicate(); Kff->MatMult(uf,KU); + KUF=KU->Duplicate(); KU->Copy(KUF); KUF->AYPX(pf,-1.0); //compute norm(KUF), norm(F) and residue - VecNorm(KUF,NORM_2,&nKUF); - VecNorm(pf,NORM_2,&nF); + nKUF=KUF->Norm(NORM_2); + nF=pf->Norm(NORM_2); solver_residue=nKUF/nF; _printf_(true,"\n%s%g\n"," solver residue: norm(KU-F)/norm(F)=",solver_residue); //clean up - VecFree(&KU); - VecFree(&KUF); + delete KU; + delete KUF; } @@ -65,8 +65,8 @@ //compute K[n]U[n-1]F = K[n]U[n-1] - F - VecDuplicate(uf,&KUold); MatMultPatch(Kff,old_uf,KUold); - VecDuplicate(KUold,&KUoldF);VecCopy(KUold,KUoldF); VecAYPX(KUoldF,-1.0,pf); - VecNorm(KUoldF,NORM_2,&nKUoldF); - VecNorm(pf,NORM_2,&nF); + KUold=uf->Duplicate(); Kff->MatMult(old_uf,KUold); + KUoldF=KUold->Duplicate();KUold->Copy(KUoldF); KUoldF->AYPX(pf,-1.0); + nKUoldF=KUoldF->Norm(NORM_2); + nF=pf->Norm(NORM_2); res=nKUoldF/nF; if (isnan(res)){ @@ -76,6 +76,6 @@ //clean up - VecFree(&KUold); - VecFree(&KUoldF); + delete KUold; + delete KUoldF; //print @@ -93,11 +93,11 @@ //compute norm(du)/norm(u) - VecDuplicate(old_uf,&duf);VecCopy(old_uf,duf); VecAYPX(duf,-1.0,uf); - VecNorm(duf,NORM_2,&ndu); VecNorm(old_uf,NORM_2,&nu); + duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); + ndu=duf->Norm(NORM_2); nu=old_uf->Norm(NORM_2); if (isnan(ndu) || isnan(nu)) _error_("convergence criterion is NaN!"); //clean up - VecFree(&duf); + delete duf; //print @@ -119,10 +119,10 @@ //compute max(du) - VecDuplicate(old_uf,&duf);VecCopy(old_uf,duf); VecAYPX(duf,-1.0,uf); - VecNorm(duf,NORM_2,&ndu); VecNorm(duf,NORM_INFINITY,&nduinf); + duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); + ndu=duf->Norm(NORM_2); nduinf=duf->Norm(NORM_INFINITY); if (isnan(ndu) || isnan(nu)) _error_("convergence criterion is NaN!"); //clean up - VecFree(&duf); + delete duf; //print Index: /issm/branches/trunk-jpl-damage/src/c/solutions/solutions.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solutions/solutions.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solutions/solutions.h (revision 11684) @@ -35,5 +35,5 @@ //convergence: -void convergence(bool* pconverged, Mat K_ff,Vec p_f,Vec u_f,Vec u_f_old,Parameters* parameters); +void convergence(bool* pconverged, Matrix* K_ff,Vector* p_f,Vector* u_f,Vector* u_f_old,Parameters* parameters); bool controlconvergence(double J,double tol_cm); bool steadystateconvergence(FemModel* femmodel); Index: /issm/branches/trunk-jpl-damage/src/c/solutions/steadystate_core.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solutions/steadystate_core.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solutions/steadystate_core.cpp (revision 11684) @@ -25,8 +25,8 @@ /*parameters: */ - int dim; - int solution_type; - int maxiter; - bool control_analysis; + bool control_analysis,isenthalpy; + int dim; + int solution_type; + int maxiter; int numoutputs = 0; int *requested_outputs = NULL; @@ -38,4 +38,5 @@ femmodel->parameters->FindParam(&maxiter,SteadystateMaxiterEnum); femmodel->parameters->FindParam(&numoutputs,SteadystateNumRequestedOutputsEnum); + femmodel->parameters->FindParam(&isenthalpy,ThermalIsenthalpyEnum); if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,SteadystateRequestedOutputsEnum); @@ -47,5 +48,10 @@ _printf_(VerboseSolution(),"%s%i\n"," computing temperature and velocity for step: ",step); #ifdef _HAVE_THERMAL_ - thermal_core(femmodel); + if(isenthalpy==0){ + thermal_core(femmodel); + } + else{ + enthalpy_core(femmodel); + } #else _error_("ISSM was not compiled with thermal capabilities. Exiting"); @@ -83,5 +89,7 @@ InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,PressureEnum); InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,TemperatureEnum); - InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,BasalforcingsMeltingRateEnum); + if(isenthalpy) InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,WaterfractionEnum); + if(isenthalpy) InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,EnthalpyEnum); + if(!isenthalpy) InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,BasalforcingsMeltingRateEnum); RequestedOutputsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,requested_outputs,numoutputs); } Index: /issm/branches/trunk-jpl-damage/src/c/solvers/solver_adjoint_linear.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solvers/solver_adjoint_linear.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solvers/solver_adjoint_linear.cpp (revision 11684) @@ -13,9 +13,11 @@ /*intermediary: */ - Mat Kff = NULL, Kfs = NULL; - Vec ug = NULL, uf = NULL; - Vec pf = NULL; - Vec df = NULL; - Vec ys = NULL; + Matrix* Kff = NULL; + Matrix* Kfs = NULL; + Vector* ug = NULL; + Vector* uf = NULL; + Vector* pf = NULL; + Vector* df = NULL; + Vector* ys = NULL; int configuration_type; @@ -26,8 +28,8 @@ SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf, Kfs, ys,true); MatFree(&Kfs); //true means spc = 0 - Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); MatFree(&Kff); VecFree(&pf); VecFree(&df); - Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters,true); VecFree(&uf);VecFree(&ys); //true means spc0 + Reduceloadx(pf, Kfs, ys,true); xdelete(&Kfs); //true means spc = 0 + Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); xdelete(&Kff); xdelete(&pf); xdelete(&df); + Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters,true); xdelete(&uf);xdelete(&ys); //true means spc0 InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); - VecFree(&ug); VecFree(&uf); + xdelete(&ug); xdelete(&uf); } Index: /issm/branches/trunk-jpl-damage/src/c/solvers/solver_linear.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solvers/solver_linear.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solvers/solver_linear.cpp (revision 11684) @@ -11,10 +11,11 @@ /*intermediary: */ - Mat Kff = NULL, Kfs = NULL; - Vec ug = NULL; - Vec uf = NULL; - Vec pf = NULL; - Vec df = NULL; - Vec ys = NULL; + Matrix* Kff = NULL; + Matrix* Kfs = NULL; + Vector* ug = NULL; + Vector* uf = NULL; + Vector* pf = NULL; + Vector* df = NULL; + Vector* ys = NULL; int configuration_type; @@ -25,8 +26,9 @@ SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf, Kfs, ys); MatFree(&Kfs); - Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); MatFree(&Kff); VecFree(&pf); VecFree(&df); - Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);VecFree(&uf);VecFree(&ys); + Reduceloadx(pf, Kfs, ys); xdelete(&Kfs); + Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); + xdelete(&Kff); xdelete(&pf); xdelete(&df); + Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&uf); xdelete(&ys); InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); - VecFree(&ug); VecFree(&uf); + xdelete(&ug); xdelete(&uf); } Index: /issm/branches/trunk-jpl-damage/src/c/solvers/solver_newton.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solvers/solver_newton.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solvers/solver_newton.cpp (revision 11684) @@ -18,10 +18,16 @@ int count; double kmax; - Mat Kff = NULL, Kfs = NULL, Jff = NULL; - Vec ug = NULL, old_ug = NULL; - Vec uf = NULL, old_uf = NULL, duf = NULL; - Vec pf = NULL, pJf = NULL; - Vec df = NULL; - Vec ys = NULL; + Matrix* Kff = NULL; + Matrix* Kfs = NULL; + Matrix* Jff = NULL; + Vector* ug = NULL; + Vector* old_ug = NULL; + Vector* uf = NULL; + Vector* old_uf = NULL; + Vector* duf = NULL; + Vector* pf = NULL; + Vector* pJf = NULL; + Vector* df = NULL; + Vector* ys = NULL; /*parameters:*/ @@ -47,18 +53,18 @@ for(;;){ - VecFree(&old_ug);old_ug=ug; - VecFree(&old_uf);old_uf=uf; + xdelete(&old_ug);old_ug=ug; + xdelete(&old_uf);old_uf=uf; /*Solver forward model*/ SystemMatricesx(&Kff,&Kfs,&pf,&df,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf,Kfs,ys);MatFree(&Kfs); - Solverx(&uf,Kff,pf,old_uf,df,femmodel->parameters);VecFree(&df); - Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);VecFree(&ys); - InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug);VecFree(&ug); + Reduceloadx(pf,Kfs,ys);xdelete(&Kfs); + Solverx(&uf,Kff,pf,old_uf,df,femmodel->parameters);xdelete(&df); + Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&ys); + InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug);xdelete(&ug); /*Check convergence*/ convergence(&converged,Kff,pf,uf,old_uf,femmodel->parameters); - MatFree(&Kff);VecFree(&pf); + xdelete(&Kff); xdelete(&pf); if(converged==true) break; if(count>=max_nonlinear_iterations){ @@ -70,15 +76,13 @@ SystemMatricesx(&Kff,&Kfs,&pf,NULL,&kmax,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf,Kfs,ys); MatFree(&Kfs); + Reduceloadx(pf,Kfs,ys); xdelete(&Kfs); - VecDuplicate(pf,&pJf); - MatMultPatch(Kff,uf,pJf); MatFree(&Kff); - VecScale(pJf,-1.); - VecAXPY(pJf,+1.,pf); VecFree(&pf); + pJf=pf->Duplicate(); Kff->MatMult(uf,pJf); xdelete(&Kff); + pJf->Scale(-1.0); pJf->AXPY(pf,+1.0); xdelete(&pf); CreateJacobianMatrixx(&Jff,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,kmax); - Solverx(&duf,Jff,pJf,NULL,NULL,femmodel->parameters); MatFree(&Jff);VecFree(&pJf); - VecAXPY(uf,1.,duf); VecFree(&duf); - Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);VecFree(&ys); + Solverx(&duf,Jff,pJf,NULL,NULL,femmodel->parameters); xdelete(&Jff); xdelete(&pJf); + uf->AXPY(duf, 1.0); xdelete(&duf); + Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&ys); InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug); @@ -89,7 +93,7 @@ /*clean-up*/ - VecFree(&uf); - VecFree(&ug); - VecFree(&old_ug); - VecFree(&old_uf); + xdelete(&uf); + xdelete(&ug); + xdelete(&old_ug); + xdelete(&old_uf); } Index: /issm/branches/trunk-jpl-damage/src/c/solvers/solver_nonlinear.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solvers/solver_nonlinear.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solvers/solver_nonlinear.cpp (revision 11684) @@ -14,10 +14,13 @@ /*intermediary: */ - Mat Kff = NULL, Kfs = NULL; - Vec ug = NULL, old_ug = NULL; - Vec uf = NULL, old_uf = NULL; - Vec pf = NULL; - Vec df = NULL; - Vec ys = NULL; + Matrix* Kff = NULL; + Matrix* Kfs = NULL; + Vector* ug = NULL; + Vector* old_ug = NULL; + Vector* uf = NULL; + Vector* old_uf = NULL; + Vector* pf = NULL; + Vector* df = NULL; + Vector* ys = NULL; Loads* loads=NULL; @@ -56,14 +59,14 @@ //save pointer to old velocity - VecFree(&old_ug);old_ug=ug; - VecFree(&old_uf);old_uf=uf; + xdelete(&old_ug);old_ug=ug; + xdelete(&old_uf);old_uf=uf; SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,loads,femmodel->materials,femmodel->parameters); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf, Kfs, ys); MatFree(&Kfs); + Reduceloadx(pf, Kfs, ys); xdelete(&Kfs); Solverx(&uf, Kff, pf, old_uf, df, femmodel->parameters); - Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);VecFree(&ys); + Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&ys); - convergence(&converged,Kff,pf,uf,old_uf,femmodel->parameters); MatFree(&Kff);VecFree(&pf); VecFree(&df); + convergence(&converged,Kff,pf,uf,old_uf,femmodel->parameters); xdelete(&Kff); xdelete(&pf); xdelete(&df); InputUpdateFromConstantx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,converged,ConvergedEnum); InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); @@ -96,7 +99,7 @@ /*clean-up*/ if(conserve_loads) delete loads; - VecFree(&uf); - VecFree(&ug); - VecFree(&old_ug); - VecFree(&old_uf); + xdelete(&uf); + xdelete(&ug); + xdelete(&old_ug); + xdelete(&old_uf); } Index: /issm/branches/trunk-jpl-damage/src/c/solvers/solver_stokescoupling_nonlinear.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solvers/solver_stokescoupling_nonlinear.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solvers/solver_stokescoupling_nonlinear.cpp (revision 11684) @@ -14,13 +14,18 @@ /*intermediary: */ - Mat Kff_horiz = NULL, Kfs_horiz = NULL; - Vec ug_horiz = NULL, uf_horiz = NULL, old_uf_horiz = NULL; - Vec pf_horiz = NULL; - Vec df_horiz = NULL; - Mat Kff_vert = NULL, Kfs_vert = NULL; - Vec ug_vert = NULL, uf_vert = NULL; - Vec pf_vert = NULL; - Vec df_vert = NULL; - Vec ys = NULL; + Matrix* Kff_horiz = NULL; + Matrix* Kfs_horiz = NULL; + Vector* ug_horiz = NULL; + Vector* uf_horiz = NULL; + Vector* old_uf_horiz = NULL; + Vector* pf_horiz = NULL; + Vector* df_horiz = NULL; + Matrix* Kff_vert = NULL; + Matrix* Kfs_vert = NULL; + Vector* ug_vert = NULL; + Vector* uf_vert = NULL; + Vector* pf_vert = NULL; + Vector* df_vert = NULL; + Vector* ys = NULL; bool converged; int constraints_converged; @@ -54,18 +59,18 @@ //Update once again the solution to make sure that vx and vxold are similar (for next step in transient or steadystate) InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug_horiz); - VecFree(&ug_horiz); + xdelete(&ug_horiz); //save pointer to old velocity - VecFree(&old_uf_horiz);old_uf_horiz=uf_horiz; + xdelete(&old_uf_horiz); old_uf_horiz=uf_horiz; /*solve: */ SystemMatricesx(&Kff_horiz, &Kfs_horiz, &pf_horiz, &df_horiz, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf_horiz, Kfs_horiz, ys); MatFree(&Kfs_horiz); + Reduceloadx(pf_horiz, Kfs_horiz, ys); xdelete(&Kfs_horiz); Solverx(&uf_horiz, Kff_horiz, pf_horiz, old_uf_horiz, df_horiz,femmodel->parameters); - Mergesolutionfromftogx(&ug_horiz, uf_horiz,ys,femmodel->nodes,femmodel->parameters); VecFree(&ys); + Mergesolutionfromftogx(&ug_horiz, uf_horiz,ys,femmodel->nodes,femmodel->parameters); xdelete(&ys); InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug_horiz); - convergence(&converged,Kff_horiz,pf_horiz,uf_horiz,old_uf_horiz,femmodel->parameters); MatFree(&Kff_horiz);VecFree(&pf_horiz); VecFree(&df_horiz); + convergence(&converged,Kff_horiz,pf_horiz,uf_horiz,old_uf_horiz,femmodel->parameters); xdelete(&Kff_horiz); xdelete(&pf_horiz); xdelete(&df_horiz); /*Second compute vertical velocity: */ @@ -76,9 +81,9 @@ SystemMatricesx(&Kff_vert, &Kfs_vert, &pf_vert, &df_vert,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf_vert, Kfs_vert, ys); MatFree(&Kfs_vert); - Solverx(&uf_vert, Kff_vert, pf_vert, NULL, df_vert,femmodel->parameters); MatFree(&Kff_vert); VecFree(&pf_vert); VecFree(&df_vert); - Mergesolutionfromftogx(&ug_vert, uf_vert,ys,femmodel->nodes,femmodel->parameters);VecFree(&uf_vert); VecFree(&ys); + Reduceloadx(pf_vert, Kfs_vert, ys); xdelete(&Kfs_vert); + Solverx(&uf_vert, Kff_vert, pf_vert, NULL, df_vert,femmodel->parameters); xdelete(&Kff_vert); xdelete(&pf_vert); xdelete(&df_vert); + Mergesolutionfromftogx(&ug_vert, uf_vert,ys,femmodel->nodes,femmodel->parameters);xdelete(&uf_vert); xdelete(&ys); InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug_vert); - VecFree(&ug_vert); VecFree(&uf_vert); + xdelete(&ug_vert); xdelete(&uf_vert); /*Increase count: */ @@ -92,7 +97,7 @@ /*clean-up*/ - VecFree(&old_uf_horiz); - VecFree(&uf_horiz); - VecFree(&ug_horiz); - VecFree(&ys); + xdelete(&old_uf_horiz); + xdelete(&uf_horiz); + xdelete(&ug_horiz); + xdelete(&ys); } Index: /issm/branches/trunk-jpl-damage/src/c/solvers/solver_thermal_nonlinear.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solvers/solver_thermal_nonlinear.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/solvers/solver_thermal_nonlinear.cpp (revision 11684) @@ -12,15 +12,15 @@ /*solution : */ - Vec tg=NULL; - Vec tf=NULL; - Vec tf_old=NULL; - Vec ys=NULL; + Vector* tg=NULL; + Vector* tf=NULL; + Vector* tf_old=NULL; + Vector* ys=NULL; double melting_offset; /*intermediary: */ - Mat Kff=NULL; - Mat Kfs=NULL; - Vec pf=NULL; - Vec df=NULL; + Matrix* Kff=NULL; + Matrix* Kfs=NULL; + Vector* pf=NULL; + Vector* df=NULL; bool converged; @@ -56,9 +56,9 @@ SystemMatricesx(&Kff, &Kfs, &pf,&df, &melting_offset,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); - Reduceloadx(pf, Kfs, ys); MatFree(&Kfs); VecFree(&tf); + Reduceloadx(pf, Kfs, ys); xdelete(&Kfs); xdelete(&tf); Solverx(&tf, Kff, pf,tf_old, df, femmodel->parameters); - VecFree(&tf_old); VecDuplicatePatch(&tf_old,tf); - MatFree(&Kff);VecFree(&pf);VecFree(&tg); VecFree(&df); - Mergesolutionfromftogx(&tg, tf,ys,femmodel->nodes,femmodel->parameters); VecFree(&ys); + xdelete(&tf_old); tf_old=tf->Duplicate(); + xdelete(&Kff);xdelete(&pf);xdelete(&tg); xdelete(&df); + Mergesolutionfromftogx(&tg, tf,ys,femmodel->nodes,femmodel->parameters); xdelete(&ys); InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,tg); @@ -84,7 +84,7 @@ /*Free ressources: */ - VecFree(&tg); - VecFree(&tf); - VecFree(&tf_old); - VecFree(&ys); + xdelete(&tg); + xdelete(&tf); + xdelete(&tf_old); + xdelete(&ys); } Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp (revision 11684) @@ -0,0 +1,36 @@ +/* \file MatlabMatrixToMatrix.cpp + * \brief: convert a sparse or dense matlab matrix to a matrix: + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#ifdef _SERIAL_ + +/*Matlab includes: */ +#include "mex.h" +#include "../../objects/objects.h" + +Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ + + Matrix* matrix=NULL; + + #ifdef _HAVE_PETSC_ + /*allocate matrix object: */ + matrix=new Matrix(); + + /*Call Matlab to Petsc API: */ + MatlabMatrixToPetscMatrix(&matrix->matrix,&matrix->M,&matrix->N,mxmatrix); + + #else + _error_("not supported yet!"); + #endif + + return matrix; +} +#endif Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/matlab/MatlabVectorToVector.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/matlab/MatlabVectorToVector.cpp (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/matlab/MatlabVectorToVector.cpp (revision 11684) @@ -0,0 +1,36 @@ +/* \file MatlabVectorToVector.cpp + * \brief: convert a sparse or dense matlab vector to a vector: + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#ifdef _SERIAL_ + +/*Matlab includes: */ +#include "mex.h" +#include "../../objects/objects.h" + +Vector* MatlabVectorToVector(const mxArray* mxvector){ + + Vector* vector=NULL; + + #ifdef _HAVE_PETSC_ + /*allocate vector object: */ + vector=new Vector(); + + /*Call Matlab to Petsc API: */ + MatlabVectorToPetscVector(&vector->vector,&vector->M,mxvector); + + #else + _error_("not supported yet!"); + #endif + + return vector; +} +#endif Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/matlab/matlabincludes.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/matlab/matlabincludes.h (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/matlab/matlabincludes.h (revision 11684) @@ -8,7 +8,12 @@ #ifdef _SERIAL_ #include +class Matrix; +class Vector; + int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); +Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); +Vector* MatlabVectorToVector(const mxArray* mxvector); #endif Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp (revision 11684) @@ -25,8 +25,7 @@ int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ - int rows, cols; - double* mxmatrix_ptr=NULL; - int ierr; - int i,j; + int i,j,count,rows,cols; + double *pmxdoublematrix = NULL; + float *pmxsinglematrix = NULL; /*output: */ @@ -36,8 +35,4 @@ mwIndex* ir=NULL; mwIndex* jc=NULL; - double* pr=NULL; - int count; - int nnz; - int nz; /*Ok, first check if we are dealing with a sparse or full matrix: */ @@ -45,14 +40,10 @@ /*Dealing with sparse matrix: recover size first: */ - mxmatrix_ptr=(double*)mxGetPr(mxmatrix); + pmxdoublematrix=(double*)mxGetPr(mxmatrix); rows=mxGetM(mxmatrix); cols=mxGetN(mxmatrix); - nnz=mxGetNzmax(mxmatrix); - nz=(int)((double)nnz/(double)rows); - matrix=(double*)xcalloc(rows*cols,sizeof(double)); /*Now, get ir,jc and pr: */ - pr=mxGetPr(mxmatrix); ir=mxGetIr(mxmatrix); jc=mxGetJc(mxmatrix); @@ -62,5 +53,5 @@ for(i=0;i=',1); checkfield(md,'inversion.maxiter_per_step','size',[md.inversion.nsteps 1],'>=',0); Index: /issm/branches/trunk-jpl-damage/src/m/classes/model/model.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/model/model.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/classes/model/model.m (revision 11684) @@ -158,7 +158,9 @@ if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end - if isfield(structmd,'riftproperties'), - md.rifts=rifts; + if isfield(structmd,'riftproperties'), %old implementation + md.rifts=rifts(); md.rifts.riftproperties=structmd.riftproperties; + md.rifts.riftstruct=structmd.rifts; + md.rifts.riftproperties=structmd.riftinfo; end if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end @@ -273,6 +275,7 @@ if isfield(structmd,'z'), md.mesh.z=structmd.z; end if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end - if isfield(structmd,'pressureload'), md.diagnostic.icefront=structmd.pressureload; end + if isfield(structmd,'pressureload'), md.diagnostic.icefront=structmd.pressureload; end if isfield(structmd,'diagnostic_ref'), md.diagnostic.referential=structmd.diagnostic_ref; end + %Field changes @@ -359,4 +362,5 @@ pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503; end + if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2, md.thermal.stabilization=2; Index: /issm/branches/trunk-jpl-damage/src/m/enum/EnumToModelField.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/enum/EnumToModelField.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/enum/EnumToModelField.m (revision 11684) @@ -1,28 +1,0 @@ -function string=EnumToModelField(enum) -%ENUMTOMODELFIELD - output string of model field associated to enum -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% string=EnumToModelField(enum) - -switch enum, - - case ThicknessEnum(), string='thickness'; return - case FrictionCoefficientEnum(), string='drag_coefficient'; return - case MaterialsRheologyBEnum(), string='rheology_B'; return - case MaterialsRheologyBbarEnum(), string='rheology_B'; return - case MaterialsRheologyZEnum(), string='rheology_Z'; return - case MaterialsRheologyZbarEnum(), string='rheology_Z'; return - case BalancethicknessThickeningRateEnum: string='dhdt'; return - case VxEnum(), string='vx'; return - case InversionVxObsEnum(), string='vx_obs'; return - case VyEnum(), string='vy'; return - case InversionVyObsEnum(), string='vy_obs'; return - case BasalforcingsMeltingRateEnum(), string='basal_melting_rate'; return - case SurfaceforcingsMassBalanceEnum(), string='surface_mass_balance'; return - otherwise, error(['Enum ' num2str(enum) ' not found associated to any model field']); - -end Index: /issm/branches/trunk-jpl-damage/src/m/model/EnumToModelField.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/EnumToModelField.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/m/model/EnumToModelField.m (revision 11684) @@ -0,0 +1,26 @@ +function string=EnumToModelField(enum) +%ENUMTOMODELFIELD - output string of model field associated to enum +% +% Usage: +% string=EnumToModelField(enum) + +disp('Warning: EnumToModelField is deprecated, it cannot work with new model definition. This function will be removed in the future'); + +switch enum, + + case ThicknessEnum(), string='thickness'; return + case FrictionCoefficientEnum(), string='drag_coefficient'; return + case MaterialsRheologyBEnum(), string='rheology_B'; return + case MaterialsRheologyBbarEnum(), string='rheology_B'; return + case BalancethicknessThickeningRateEnum: string='dhdt'; return + case VxEnum(), string='vx'; return + case InversionVxObsEnum(), string='vx_obs'; return + case VyEnum(), string='vy'; return + case InversionVyObsEnum(), string='vy_obs'; return + case BasalforcingsMeltingRateEnum(), string='basal_melting_rate'; return + case SurfaceforcingsAccumulationRateEnum(), string='surface_accumulation_rate'; return + case SurfaceforcingsAblationRateEnum(), string='surface_ablation_rate'; return + case SurfaceforcingsMassBalanceEnum(), string='surface_mass_balance'; return + otherwise, error(['Enum ' num2str(enum) ' not found associated to any model field']); + +end Index: /issm/branches/trunk-jpl-damage/src/m/model/SectionValues.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/SectionValues.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/model/SectionValues.m (revision 11684) @@ -82,5 +82,6 @@ %Interpolation of data on specified points - data_interp=InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,data,X,Y); + data_interp=InterpFromMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,data,X,Y); + %data_interp=InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,data,X,Y); %data_interp=griddata(md.mesh.x,md.mesh.y,data,X,Y); Index: /issm/branches/trunk-jpl-damage/src/m/model/collapse.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/collapse.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/model/collapse.m (revision 11684) @@ -93,4 +93,5 @@ md.geometry.bed=project2d(md,md.geometry.bed,1); md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); +md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); md.mask.elementonfloatingice=project2d(md,md.mask.elementonfloatingice,1); md.mask.vertexonfloatingice=project2d(md,md.mask.vertexonfloatingice,1); @@ -111,4 +112,6 @@ md.mesh.lowervertex=NaN; md.mesh.uppervertex=NaN; +md.mesh.lowerelements=NaN; +md.mesh.upperelements=NaN; %Remove old mesh Index: /issm/branches/trunk-jpl-damage/src/m/model/mesh/bamg.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/mesh/bamg.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/model/mesh/bamg.m (revision 11684) @@ -4,43 +4,43 @@ % Available options (for more details see ISSM website http://issm.jpl.nasa.gov/): % -% - domain: followed by an ARGUS file that prescribes the domain outline -% - hmin : minimum edge length (default is 10^-100) -% - hmax : maximum esge length (default is 10^100) -% - hVertices : imposed edge length for each vertex (geometry or mesh) -% - hminVertices: minimum edge length for each vertex (mesh) -% - hmaxVertices: maximum edge length for each vertex (mesh) -% -% - anisomax : maximum ration between the smallest and largest edges (default is 10^30) -% - coeff : coefficient applied to the metric (2-> twice as many elements, default is 1) -% - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied -% - err : error used to generate the metric from a field -% - errg : geometrical error (default is 0.1) -% - field : field of the model that will be used to compute the metric -% to apply several fields, use one column per field -% - gradation : maximum ration between two adjacent edges -% - Hessiantype : 0 -> use double P2 projection (default) -% 1 -> use Green formula -% - KeepVertices: try to keep initial vertices when adaptation is done on an existing mesh (default 1) -% - MaxCornerAngle: maximal angle of corners in degree (default is 10) -% - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) -% - maxsubdiv : maximum subdivision of exisiting elements (default is 10) -% - metric : matrix (numberofnodes x 3) used as a metric -% - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) -% 2 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) -% 3 -> rescaled absolute error c/(err coeff^2) * Abs(H)/(smax-smin) -% - nbjacoby : correction used by Hessiantype=1 (default is 1) -% - nbsmooth : number of metric smoothing procedure (default is 3) -% - omega : relaxation parameter of the smoothing procedure (default is 1.8) -% - power : power applied to the metric (default is 1) -% - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) -% - geometricalmetric : Take the geometry into account to generate the metric (default is 0) -% - verbose : level of verbosity (default is 1) -% -% - rifts : followed by an ARGUS file that prescribes the rifts -% - toltip: tolerance to move tip on an existing point of the domain outline -% - tracks: followed by an ARGUS file that prescribes the tracks that the mesh will stick to -% - RequiredVertices: mesh vertices that are required. [x,y,ref]; ref is optional -% - tol: if the distance between 2 points of the domain outline is less than tol, they -% will be merged +% - domain : followed by an ARGUS file that prescribes the domain outline +% - hmin : minimum edge length (default is 10^-100) +% - hmax : maximum edge length (default is 10^100) +% - hVertices : imposed edge length for each vertex (geometry or mesh) +% - hminVertices : minimum edge length for each vertex (mesh) +% - hmaxVertices : maximum edge length for each vertex (mesh) +% +% - anisomax : maximum ratio between the smallest and largest edges (default is 10^30) +% - coeff : coefficient applied to the metric (2-> twice as many elements, default is 1) +% - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied +% - err : error used to generate the metric from a field +% - errg : geometric error (default is 0.1) +% - field : field of the model that will be used to compute the metric +% to apply several fields, use one column per field +% - gradation : maximum ratio between two adjacent edges +% - Hessiantype : 0 -> use double P2 projection (default) +% 1 -> use Green formula +% - KeepVertices : try to keep initial vertices when adaptation is done on an existing mesh (default 1) +% - MaxCornerAngle : maximum angle of corners in degree (default is 10) +% - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) +% - maxsubdiv : maximum subdivision of exisiting elements (default is 10) +% - metric : matrix (numberofnodes x 3) used as a metric +% - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) +% 2 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) +% 3 -> rescaled absolute error c/(err coeff^2) * Abs(H)/(smax-smin) +% - nbjacoby : correction used by Hessiantype=1 (default is 1) +% - nbsmooth : number of metric smoothing procedure (default is 3) +% - omega : relaxation parameter of the smoothing procedure (default is 1.8) +% - power : power applied to the metric (default is 1) +% - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) +% - geometricalmetric : take the geometry into account to generate the metric (default is 0) +% - verbose : level of verbosity (default is 1) +% +% - rifts : followed by an ARGUS file that prescribes the rifts +% - toltip : tolerance to move tip on an existing point of the domain outline +% - tracks : followed by an ARGUS file that prescribes the tracks that the mesh will stick to +% - RequiredVertices : mesh vertices that are required. [x,y,ref]; ref is optional +% - tol : if the distance between 2 points of the domain outline is less than tol, they +% will be merged % % Examples: Index: /issm/branches/trunk-jpl-damage/src/m/qmu/dakota_in_data.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/qmu/dakota_in_data.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/qmu/dakota_in_data.m (revision 11684) @@ -80,6 +80,6 @@ if strcmpi(params.analysis_driver,'matlab') && ... isempty(params.analysis_components) - [pathstr,name,ext,versn] = fileparts(filei); - params.analysis_components=fullfile(pathstr,[name '.m' versn]); + [pathstr,name,ext] = fileparts(filei); + params.analysis_components=fullfile(pathstr,[name '.m']); end Index: /issm/branches/trunk-jpl-damage/src/m/qmu/dakota_in_write.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/qmu/dakota_in_write.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/qmu/dakota_in_write.m (revision 11684) @@ -63,10 +63,10 @@ filei=input('Dakota input file to write? ','s'); end -[pathstr,name,ext,versn] = fileparts(filei); +[pathstr,name,ext] = fileparts(filei); if isempty(ext) % fileparts only considers '.in' to be the extension, not '.qmu.in' ext='.qmu.in'; end -filei2=fullfile(pathstr,[name ext versn]); +filei2=fullfile(pathstr,[name ext]); display(sprintf('Opening Dakota input file ''%s''.',filei2)); @@ -234,9 +234,9 @@ param_write(fidi,'\t ','evaluation_static_scheduling','','\n',params); if ~isempty(params.analysis_components) - [pathstr,name,ext,versn] = fileparts(params.analysis_components); + [pathstr,name,ext] = fileparts(params.analysis_components); if isempty(ext) ext='.m'; end - params.analysis_components=fullfile(pathstr,[name ext versn]); + params.analysis_components=fullfile(pathstr,[name ext]); param_write(fidi,'\t ','analysis_components',' = ''','''\n',params); end Index: /issm/branches/trunk-jpl-damage/src/m/solutions/AnalysisConfiguration.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/solutions/AnalysisConfiguration.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/solutions/AnalysisConfiguration.m (revision 11684) @@ -14,6 +14,6 @@ case SteadystateSolutionEnum, - numanalyses=7; - analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum;ThermalAnalysisEnum;MeltingAnalysisEnum]; + numanalyses=8; + analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum;EnthalpyAnalysisEnum;ThermalAnalysisEnum;MeltingAnalysisEnum]; case ThermalSolutionEnum, Index: /issm/branches/trunk-jpl-damage/src/m/solutions/steadystate_core.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/solutions/steadystate_core.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/solutions/steadystate_core.m (revision 11684) @@ -10,4 +10,5 @@ control_analysis=femmodel.parameters.InversionIscontrol; solution_type=femmodel.parameters.SolutionType; + isenthalpy=femmodel.parameters.ThermalIsenthalpy; %Initialize counter @@ -17,5 +18,9 @@ issmprintf(VerboseSolution,'\n%s%i\n',' computing velocities and temperatures for step: ',step); - femmodel=thermal_core(femmodel); + if (isenthalpy==0), + femmodel=thermal_core(femmodel); + else + femmodel=enthalpy_core(femmodel); + end issmprintf(VerboseSolution,'\n%s',[' computing new velocity']); @@ -46,6 +51,10 @@ femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,PressureEnum); femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,TemperatureEnum); - femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,BasalforcingsMeltingRateEnum); - end + if (isenthalpy), + femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,EnthalpyEnum); + femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,WaterfractionEnum); + else + femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,BasalforcingsMeltingRateEnum); + end end %end of function Index: /issm/branches/trunk-jpl-damage/src/m/utils/Analysis/setcluster.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Analysis/setcluster.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/m/utils/Analysis/setcluster.m (revision 11684) @@ -5,3 +5,4 @@ % md=setcluster(md,cluster); +disp('Warning: setcluster is deprecated, use md.cluster=cluster instead'); md.cluster=cluster; Index: /issm/branches/trunk-jpl-damage/src/m/utils/Exp/manipulation/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Exp/manipulation/Makefile.am (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/m/utils/Exp/manipulation/Makefile.am (revision 11684) @@ -0,0 +1,1 @@ +bin_SCRIPTS=*.m Index: /issm/branches/trunk-jpl-damage/src/m/utils/Exp/readwrite/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/Exp/readwrite/Makefile.am (revision 11684) +++ /issm/branches/trunk-jpl-damage/src/m/utils/Exp/readwrite/Makefile.am (revision 11684) @@ -0,0 +1,1 @@ +bin_SCRIPTS=*.m Index: /issm/branches/trunk-jpl-damage/src/mex/CreateJacobianMatrix/CreateJacobianMatrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/CreateJacobianMatrix/CreateJacobianMatrix.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/CreateJacobianMatrix/CreateJacobianMatrix.cpp (revision 11684) @@ -17,5 +17,5 @@ /* output datasets: */ - Mat Jff = NULL; + Matrix* Jff = NULL; /*Boot module: */ @@ -53,5 +53,5 @@ delete materials; delete parameters; - MatFree(&Jff); + delete Jff; /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp (revision 11684) @@ -12,5 +12,5 @@ /* output datasets: */ - Vec ys=NULL; + Vector* ys=NULL; /*Boot module: */ @@ -32,5 +32,5 @@ /*Free ressources: */ delete nodes; - VecFree(&ys); + delete ys; /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/GetSolutionFromInputs/GetSolutionFromInputs.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/GetSolutionFromInputs/GetSolutionFromInputs.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/GetSolutionFromInputs/GetSolutionFromInputs.cpp (revision 11684) @@ -14,5 +14,5 @@ Materials* materials=NULL; Parameters* parameters=NULL; - Vec ug=NULL; + Vector* ug=NULL; /* output datasets: elements and loads*/ Index: /issm/branches/trunk-jpl-damage/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp (revision 11684) @@ -14,5 +14,5 @@ Materials* materials=NULL; Parameters* parameters=NULL; - Vec solution=NULL; + Vector* solution=NULL; /*Boot module: */ @@ -50,5 +50,5 @@ delete materials; delete parameters; - VecFree(&solution); + delete solution; /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp (revision 11684) @@ -9,11 +9,11 @@ /*input datasets: */ bool flag_ys0; - Vec uf = NULL; - Vec ys = NULL; + Vector* uf = NULL; + Vector* ys = NULL; Nodes* nodes = NULL; Parameters* parameters = NULL; /* output datasets: */ - Vec ug=NULL; + Vector* ug=NULL; /*Boot module: */ @@ -45,7 +45,7 @@ /*Free ressources: */ - VecFree(&uf); - VecFree(&ug); - VecFree(&ys); + delete uf; + delete ug; + delete ys; delete nodes; delete parameters; Index: /issm/branches/trunk-jpl-damage/src/mex/Reduceload/Reduceload.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Reduceload/Reduceload.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/Reduceload/Reduceload.cpp (revision 11684) @@ -8,7 +8,7 @@ /*input datasets: */ - Vec pf = NULL; - Mat Kfs = NULL; - Vec ys = NULL; + Vector* pf = NULL; + Matrix* Kfs = NULL; + Vector* ys = NULL; bool flag_ys0=false; @@ -40,7 +40,7 @@ /*Free ressources: */ - VecFree(&pf); - MatFree(&Kfs); - VecFree(&ys); + delete pf; + delete Kfs; + delete ys; MODULEEND(); Index: /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtof/Reducevectorgtof.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11684) @@ -8,10 +8,10 @@ /*input datasets: */ - Vec ug=NULL; + Vector* ug=NULL; Nodes* nodes=NULL; Parameters* parameters=NULL; /* output datasets: */ - Vec uf=NULL; + Vector* uf=NULL; /*Boot module: */ @@ -35,6 +35,6 @@ delete nodes; delete parameters; - VecFree(&ug); - VecFree(&uf); + delete ug; + delete uf; /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtos/Reducevectorgtos.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtos/Reducevectorgtos.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtos/Reducevectorgtos.cpp (revision 11684) @@ -8,10 +8,10 @@ /*input datasets: */ - Vec yg=NULL; + Vector* yg=NULL; Nodes* nodes=NULL; Parameters* parameters=NULL; /* output datasets: */ - Vec ys=NULL; + Vector* ys=NULL; /*Boot module: */ @@ -35,6 +35,6 @@ delete nodes; delete parameters; - VecFree(&yg); - VecFree(&ys); + delete yg; + delete ys; /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/Solver/Solver.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Solver/Solver.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/Solver/Solver.cpp (revision 11684) @@ -8,9 +8,9 @@ /*input datasets: */ - Mat Kff = NULL; - Vec pf = NULL; - Vec uf0 = NULL; - Vec uf = NULL; - Vec df = NULL; + Matrix* Kff = NULL; + Vector* pf = NULL; + Vector* uf0 = NULL; + Vector* uf = NULL; + Vector* df = NULL; Parameters *parameters = NULL; int analysis_type; @@ -66,9 +66,9 @@ /*Free ressources: */ - MatFree(&Kff); - VecFree(&pf); - VecFree(&uf0); - VecFree(&uf); - VecFree(&df); + delete Kff; + delete pf; + delete uf0; + delete uf; + delete df; delete parameters; Index: /issm/branches/trunk-jpl-damage/src/mex/SystemMatrices/SystemMatrices.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/SystemMatrices/SystemMatrices.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/SystemMatrices/SystemMatrices.cpp (revision 11684) @@ -17,8 +17,8 @@ /* output datasets: */ - Mat Kff = NULL; - Mat Kfs = NULL; - Vec pf = NULL; - Vec df = NULL; + Matrix* Kff = NULL; + Matrix* Kfs = NULL; + Vector* pf = NULL; + Vector* df = NULL; double kmax; @@ -72,8 +72,8 @@ delete materials; delete parameters; - MatFree(&Kff); - MatFree(&Kfs); - VecFree(&pf); - VecFree(&df); + delete Kff; + delete Kfs; + delete pf; + delete df; /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp (revision 11683) +++ /issm/branches/trunk-jpl-damage/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp (revision 11684) @@ -11,5 +11,5 @@ Nodes *nodes = NULL; Parameters *parameters = NULL; - Vec yg = NULL; + Vector* yg = NULL; /*Boot module: */ @@ -32,5 +32,5 @@ /*Free ressources: */ - VecFree(&yg); + delete yg; delete constraints; delete nodes; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/IdToName.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/IdToName.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/IdToName.m (revision 11684) @@ -224,4 +224,14 @@ case 453, name='SquareSheetShelfGroundingLine3dSoftSerial'; case 454, name='SquareSheetShelfGroundingLine3dSoftParallel'; + case 455, name='SquareSheetShelfDiagM2dNewtonSerial'; + case 456, name='SquareSheetShelfDiagM2dNewtonParallel'; + case 457, name='SquareSheetShelfDiagP3dNewtonSerial'; + case 458, name='SquareSheetShelfDiagP3dNewtonParallel'; + case 459, name='SquareSheetShelfDiagS3dNewtonSerial'; + case 460, name='SquareSheetShelfDiagS3dNewtonParallel'; + case 461, name='SquareSheetShelfSteaEnthalpyM3dSerial'; + case 462, name='SquareSheetShelfSteaEnthalpyM3dParallel'; + case 463, name='SquareSheetShelfSteaEnthalpyP3dSerial'; + case 464, name='SquareSheetShelfSteaEnthalpyP3dParallel'; case 501, name='PigDiagM2dSerial'; case 502, name='PigDiagM2dParallel'; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/runme.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/runme.m (revision 11683) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/runme.m (revision 11684) @@ -180,4 +180,5 @@ disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,fieldname)); else + disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,fieldname)); rethrow(me2); end @@ -204,4 +205,5 @@ disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,'N/A')); else + disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,'N/A')); rethrow(me); end Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test455.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test455.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test455.m (revision 11684) @@ -0,0 +1,18 @@ +md=triangle(model,'../Exp/Square.exp',150000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=setflowequation(md,'macayeal','all'); +md.diagnostic.isnewton=1; +md.diagnostic.restol=0.0001; +md.cluster=none; +md=solve(md,DiagnosticSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vel','Pressure'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13}; +field_values={... + (md.results.DiagnosticSolution.Vx),... + (md.results.DiagnosticSolution.Vy),... + (md.results.DiagnosticSolution.Vel),... + (md.results.DiagnosticSolution.Pressure),... + }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test456.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test456.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test456.m (revision 11684) @@ -0,0 +1,18 @@ +md=triangle(model,'../Exp/Square.exp',150000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=setflowequation(md,'macayeal','all'); +md.diagnostic.isnewton=1; +md.diagnostic.restol=0.0001; +md.cluster=generic('name',oshostname(),'np',3); +md=solve(md,DiagnosticSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vel','Pressure'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13}; +field_values={... + (md.results.DiagnosticSolution.Vx),... + (md.results.DiagnosticSolution.Vy),... + (md.results.DiagnosticSolution.Vel),... + (md.results.DiagnosticSolution.Pressure),... + }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test457.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test457.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test457.m (revision 11684) @@ -0,0 +1,20 @@ +md=triangle(model,'../Exp/Square.exp',180000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=extrude(md,5,1); +md=setflowequation(md,'pattyn','all'); +md.diagnostic.isnewton=1; +md.diagnostic.restol=0.0001; +md.cluster=none; +md=solve(md,DiagnosticSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +field_values={... + (md.results.DiagnosticSolution.Vx),... + (md.results.DiagnosticSolution.Vy),... + (md.results.DiagnosticSolution.Vz),... + (md.results.DiagnosticSolution.Vel),... + (md.results.DiagnosticSolution.Pressure),... + }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test458.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test458.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test458.m (revision 11684) @@ -0,0 +1,20 @@ +md=triangle(model,'../Exp/Square.exp',180000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=extrude(md,5,1); +md=setflowequation(md,'pattyn','all'); +md.diagnostic.isnewton=1; +md.diagnostic.restol=0.0001; +md.cluster=generic('name',oshostname(),'np',3); +md=solve(md,DiagnosticSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; +field_values={... + (md.results.DiagnosticSolution.Vx),... + (md.results.DiagnosticSolution.Vy),... + (md.results.DiagnosticSolution.Vz),... + (md.results.DiagnosticSolution.Vel),... + (md.results.DiagnosticSolution.Pressure),... + }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test459.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test459.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test459.m (revision 11684) @@ -0,0 +1,19 @@ +md=triangle(model,'../Exp/Square.exp',180000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=extrude(md,3,1); +md=setflowequation(md,'stokes','all'); +md.diagnostic.isnewton=1; +md.diagnostic.restol=0.0001; +md=solve(md,DiagnosticSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +field_values={... + (md.results.DiagnosticSolution.Vx),... + (md.results.DiagnosticSolution.Vy),... + (md.results.DiagnosticSolution.Vz),... + (md.results.DiagnosticSolution.Vel),... + (md.results.DiagnosticSolution.Pressure),... + }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test460.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test460.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test460.m (revision 11684) @@ -0,0 +1,20 @@ +md=triangle(model,'../Exp/Square.exp',180000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=extrude(md,3,1); +md=setflowequation(md,'stokes','all'); +md.diagnostic.isnewton=1; +md.diagnostic.restol=0.0001; +md.cluster=generic('name',oshostname(),'np',3); +md=solve(md,DiagnosticSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +field_tolerances={1e-07,1e-07,1e-06,1e-07,1e-07}; +field_values={... + (md.results.DiagnosticSolution.Vx),... + (md.results.DiagnosticSolution.Vy),... + (md.results.DiagnosticSolution.Vz),... + (md.results.DiagnosticSolution.Vel),... + (md.results.DiagnosticSolution.Pressure),... + }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test461.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test461.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test461.m (revision 11684) @@ -0,0 +1,24 @@ +md=triangle(model,'../Exp/Square.exp',150000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=extrude(md,3,2); +md=setflowequation(md,'macayeal','all'); +md.cluster=none; +md.timestepping.time_step=0; +md.thermal.isenthalpy=1; +md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +md=solve(md,SteadystateSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; +field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; +field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... + (md.results.SteadystateSolution.Vz),... + (md.results.SteadystateSolution.Vel),... + (md.results.SteadystateSolution.Pressure),... + (md.results.SteadystateSolution.Temperature),... + (md.results.SteadystateSolution.Waterfraction),... + (md.results.SteadystateSolution.Enthalpy),... + }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test462.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test462.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test462.m (revision 11684) @@ -0,0 +1,24 @@ +md=triangle(model,'../Exp/Square.exp',150000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=extrude(md,3,2); +md=setflowequation(md,'macayeal','all'); +md.cluster=generic('name',oshostname(),'np',3); +md.timestepping.time_step=0; +md.thermal.isenthalpy=1; +md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +md=solve(md,SteadystateSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; +field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; +field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... + (md.results.SteadystateSolution.Vz),... + (md.results.SteadystateSolution.Vel),... + (md.results.SteadystateSolution.Pressure),... + (md.results.SteadystateSolution.Temperature),... + (md.results.SteadystateSolution.Waterfraction),... + (md.results.SteadystateSolution.Enthalpy),... + }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test463.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test463.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test463.m (revision 11684) @@ -0,0 +1,24 @@ +md=triangle(model,'../Exp/Square.exp',150000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=extrude(md,3,2); +md=setflowequation(md,'pattyn','all'); +md.cluster=none; +md.timestepping.time_step=0; +md.thermal.isenthalpy=1; +md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +md=solve(md,SteadystateSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; +field_tolerances={1e-09,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; +field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... + (md.results.SteadystateSolution.Vz),... + (md.results.SteadystateSolution.Vel),... + (md.results.SteadystateSolution.Pressure),... + (md.results.SteadystateSolution.Temperature),... + (md.results.SteadystateSolution.Waterfraction),... + (md.results.SteadystateSolution.Enthalpy),... + }; Index: /issm/branches/trunk-jpl-damage/test/NightlyRun/test464.m =================================================================== --- /issm/branches/trunk-jpl-damage/test/NightlyRun/test464.m (revision 11684) +++ /issm/branches/trunk-jpl-damage/test/NightlyRun/test464.m (revision 11684) @@ -0,0 +1,24 @@ +md=triangle(model,'../Exp/Square.exp',150000); +md=setmask(md,'../Exp/SquareShelf.exp',''); +md=parameterize(md,'../Par/SquareSheetShelf.par'); +md=extrude(md,3,2); +md=setflowequation(md,'pattyn','all'); +md.cluster=generic('name',oshostname(),'np',3); +md.timestepping.time_step=0; +md.thermal.isenthalpy=1; +md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +md=solve(md,SteadystateSolutionEnum); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; +field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-13,1e-10,1e-10,1e-10}; +field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... + (md.results.SteadystateSolution.Vz),... + (md.results.SteadystateSolution.Vel),... + (md.results.SteadystateSolution.Pressure),... + (md.results.SteadystateSolution.Temperature),... + (md.results.SteadystateSolution.Waterfraction),... + (md.results.SteadystateSolution.Enthalpy),... + };