Index: sm/trunk/configs/config-ios-armv7.sh =================================================================== --- /issm/trunk/configs/config-ios-armv7.sh (revision 21728) +++ (revision ) @@ -1,32 +1,0 @@ -#!/bin/sh -set -eu - -export DEVROOT=`xcode-select --print-path` -export SDKROOT="$DEVROOT/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS7.1.sdk" -export CLANG="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -export CLANGXX="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++" -export CC=$CLANG -export LD=$DEVROOT/usr/bin/ld -export CPPFLAGS="-isysroot $SDKROOT/usr/include" -export CXX=$CLANGXX -export CXXFLAGS="-O -arch armv7 -isysroot $SDKROOT -I$SDKROOT/usr/include" -export CFLAGS="-O -arch armv7 -isysroot $SDKROOT -I$SDKROOT/usr/include" -export AR=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar -export AS=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/as -export LDFLAGS="-lstdc++ -arch armv7 -isysroot $SDKROOT" -export LIBTOOL=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/libtool -export STRIP=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip -export RANLIB=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib - -./configure \ - --prefix=$ISSM_DIR \ - --build="i386-apple-darwin13.1.0" \ - --host="armv7-apple-darwin14.0.0" \ - --enable-shared \ - --with-ios=yes \ - --with-Gia=no \ - --without-fortran \ - --without-wrappers \ - --without-kriging \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: sm/trunk/configs/config-ios-armv7s.sh =================================================================== --- /issm/trunk/configs/config-ios-armv7s.sh (revision 21728) +++ (revision ) @@ -1,32 +1,0 @@ -#!/bin/sh -set -eu - -export DEVROOT=`xcode-select --print-path` -export SDKROOT="$DEVROOT/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS7.1.sdk" -export CLANG="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -export CLANGXX="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++" -export CC=$CLANG -export LD=$DEVROOT/usr/bin/ld -export CPPFLAGS="-isysroot $SDKROOT/usr/include" -export CXX=$CLANGXX -export CXXFLAGS="-O -arch armv7s -isysroot $SDKROOT -I$SDKROOT/usr/include" -export CFLAGS="-O -arch armv7s -isysroot $SDKROOT -I$SDKROOT/usr/include" -export AR=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar -export AS=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/as -export LDFLAGS="-lstdc++ -arch armv7s -isysroot $SDKROOT" -export LIBTOOL=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/libtool -export STRIP=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip -export RANLIB=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib - -./configure \ - --prefix=$ISSM_DIR \ - --build="i386-apple-darwin13.1.0" \ - --host="armv7s-apple-darwin14.0.0" \ - --enable-shared \ - --with-ios=yes \ - --with-Gia=no \ - --without-fortran \ - --without-wrappers \ - --without-kriging \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: sm/trunk/configs/config-ios-linux.sh =================================================================== --- /issm/trunk/configs/config-ios-linux.sh (revision 21728) +++ (revision ) @@ -1,28 +1,0 @@ -#!/bin/sh - -export DEVROOT="/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/" -export SDKROOT="$DEVROOT/SDKs/iPhoneOS6.0.sdk/" -export CC=$DEVROOT/usr/bin/gcc -export LD=$DEVROOT/usr/bin/ld -export CPP=$DEVROOT/usr/bin/cpp -export CXX=$DEVROOT/usr/bin/g++ -export CXXFLAGS="-O -arch armv7 -isysroot $SDKROOT" -export CFLAGS="-O -arch armv7 -isysroot $SDKROOT" -export AR=$DEVROOT/usr/bin/ar -export AS=$DEVROOT/usr/bin/as -export LDFLAGS="-lstdc++ -arch armv7 -isysroot $SDKROOT" -export LIBTOOL=$DEVROOT/usr/bin/libtool -export STRIP=$DEVROOT/usr/bin/strip -export RANLIB=$DEVROOT/usr/bin/ranlib - -./configure \ - --prefix=$ISSM_DIR \ - --build="i386-apple-darwin10.8.0" \ - --host="arm-apple-darwin10" \ - --enable-shared \ - --with-ios=yes \ - --without-fortran \ - --without-wrappers \ - --without-kriging \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: sm/trunk/configs/config-ios-simulator.sh =================================================================== --- /issm/trunk/configs/config-ios-simulator.sh (revision 21728) +++ (revision ) @@ -1,31 +1,0 @@ -#!/bin/sh -set -eu - -export DEVROOT=`xcode-select --print-path` -export SDKROOT="$DEVROOT/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator7.1.sdk" -export CLANG="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -export CLANGXX="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++" -export CC=$CLANG -export CXX=$CLANGXX -export LD=$DEVROOT/usr/bin/ld -export CPPFLAGS="-isysroot $SDKROOT/usr/include" -export CXXFLAGS="-O -arch i386 -miphoneos-version-min=7.1 -isysroot $SDKROOT -I$SDKROOT/usr/include" -export CFLAGS="-O -arch i386 -miphoneos-version-min=7.1 -isysroot $SDKROOT -I$SDKROOT/usr/include" -export AR=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar -export AS=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/as -export LDFLAGS="-lstdc++ -arch i386 -isysroot $SDKROOT" -export LIBTOOL=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/libtool -export STRIP=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip -export RANLIB=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib - -./configure \ - --prefix=$ISSM_DIR \ - --target="i386-apple-darwin13.1.0" \ - --enable-shared \ - --with-ios=yes \ - --with-Gia=no \ - --without-fortran \ - --without-wrappers \ - --without-kriging \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: sm/trunk/configs/config-pleiades-petsc3.4.sh =================================================================== --- /issm/trunk/configs/config-pleiades-petsc3.4.sh (revision 21728) +++ (revision ) @@ -1,20 +1,0 @@ -#!/bin/csh - -./configure \ - --prefix=$ISSM_DIR \ - --with-wrappers=no \ - --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ - --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-tao-dir="$ISSM_DIR/externalpackages/tao/install" \ - --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ - --with-mpi-libflags="-L/nasa/sgi/mpt/2.06rp16/ -lmpi" \ - --with-mkl-dir="/nasa/intel/Compiler/2013.1.117/composer_xe_2013.1.117/mkl/lib/intel64" \ - --with-gsl-dir="$ISSM_DIR/externalpackages/gsl/install" \ - --with-dakota-dir="$ISSM_DIR/externalpackages/dakota/install" \ - --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-hypre-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-graphics-lib="/usr/lib64/libX11.so" \ - --with-cxxoptflags="-O3" \ - --with-vendor="intel-pleiades" Index: sm/trunk/configs/config-win10.sh =================================================================== --- /issm/trunk/configs/config-win10.sh (revision 21728) +++ (revision ) @@ -1,19 +1,0 @@ -#!/bin/bash - -./configure --prefix=$ISSM_DIR \ - --with-vendor=MSVC-Win64 \ - --with-cxxoptflags='' \ - --disable-static \ - --enable-standalone-libraries \ - --with-fortran=no \ - --without-Gia \ - --without-kriging \ - --without-kml \ - --with-matlab-dir=$MATLAB_PATH \ - --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ - --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ - --with-mpi-libdir="$ISSM_DIR/externalpackages/petsc/install/lib" \ - --with-mpi-libflags="-Wl,libpetsc.lib" \ - --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include/petsc/mpiuni" Index: sm/trunk/configs/configure.sh =================================================================== --- /issm/trunk/configs/configure.sh (revision 21728) +++ (revision ) @@ -1,17 +1,0 @@ -#!/bin/sh - -#Default configuration script -#petsc 3.4 -#mpich 1.4 - -./configure \ - --prefix=$ISSM_DIR \ - --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ - --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ - --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \ - --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ - --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \ - --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \ - --with-numthreads=2 Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 21728) +++ /issm/trunk/configure.ac (revision 21729) @@ -2,5 +2,5 @@ #AUTOCONF -AC_INIT([Ice Sheet System Model (ISSM)],[4.11],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([Ice Sheet System Model (ISSM)],[4.12],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 Index: /issm/trunk/etc/environment.csh =================================================================== --- /issm/trunk/etc/environment.csh (revision 21728) +++ /issm/trunk/etc/environment.csh (revision 21729) @@ -3,12 +3,4 @@ #Load ISSM scripts setenv PATH {$PATH}:{$ISSM_DIR}/scripts - -##MATLAB -#set MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install" -#if (-e $MATLAB_DIR) then -# setenv MATLAB_DIR {$MATLAB_DIR} -# setenv PATH {$MATLAB_DIR}/bin:{$PATH} -# setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$MATLAB_DIR}/bin/glnxa64 -#endif #MPI Index: /issm/trunk/etc/environment.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 21728) +++ /issm/trunk/etc/environment.sh (revision 21729) @@ -67,14 +67,11 @@ pathappend "$ISSM_DIR/scripts" -#MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install" -#export MATLAB_DIR -#pathprepend "$MATLAB_DIR/bin" #take precedence over /usr/local/bin/matlab -#libpathappend "$MATLAB_DIR/lib" - #GMT GMT_DIR="$ISSM_DIR/externalpackages/gmt/install" -export GMT_DIR -pathprepend "$GMT_DIR/bin" -libpathappend "$GMT_DIR/lib" +if [ -d "$GMT_DIR" ]; then + export GMT_DIR + pathprepend "$GMT_DIR/bin" + libpathappend "$GMT_DIR/lib" +fi #legacy mpich2 (To be removed) @@ -89,9 +86,8 @@ if [ -d "$MPI_DIR" ]; then export MPI_DIR + export MPI_INC_DIR="$MPI_DIR/include" pathprepend "$MPI_DIR/bin" libpathappend "$MPI_DIR/lib" fi - -export MPI_INC_DIR="$MPI_DIR/include" PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" @@ -328,2 +324,8 @@ #GMT pathprepend "$ISSM_DIR/externalpackages/gmt/install/bin" + +#NEOPZ +NEOPZ_DIR="$ISSM_DIR/externalpackages/neopz/install" +if [ -d "$NEOPZ_DIR" ]; then + export REFPATTERNDIR="$NEOPZ_DIR/include/refpatterns" +fi Index: /issm/trunk/examples/Jakobshavn/runme.m =================================================================== --- /issm/trunk/examples/Jakobshavn/runme.m (revision 21728) +++ /issm/trunk/examples/Jakobshavn/runme.m (revision 21729) @@ -8,5 +8,5 @@ ncdata='../Data/Greenland_5km_dev1.2.nc'; if ~exist(ncdata,'file'), - error('File Greenland_5km_dev1.2.nc not downloaded in Data Directory. Please cd ../Data and run the download script.'); + error('File Greenland_5km_dev1.2.nc not downloaded in Data Directory'); end x1 = ncread(ncdata,'x1'); @@ -74,12 +74,11 @@ plotmodel(md,'unit#all','km','axis#all','equal',... - 'FontSize#all',12,... 'data',md.inversion.vel_obs,'title','Observed velocity',... 'data',md.results.StressbalanceSolution.Vel,'title','Modeled Velocity',... - 'colorbar#1','off','colorbar#2','on','colorbartitle#2','[m/yr]',... + 'colorbar#1','off','colorbartitle#2','(m/yr)',... 'caxis#1-2',[0,7000],... 'data',md.geometry.base,'title','Base elevation',... 'data',md.results.StressbalanceSolution.FrictionCoefficient,... 'title','Friction Coefficient',... - 'colorbar#3','on','colorbartitle#3','[m]','colorbar#4','on'); + 'colorbartitle#3','(m)'); end Index: /issm/trunk/examples/Pig/runme.m =================================================================== --- /issm/trunk/examples/Pig/runme.m (revision 21728) +++ /issm/trunk/examples/Pig/runme.m (revision 21729) @@ -12,8 +12,4 @@ % Generate an initial uniform mesh (resolution = hinit m) md=bamg(model,'domain',domain,'hmax',hinit); - - %ploting - plotmodel(md,'data','mesh') - return; % Load Velocities @@ -104,9 +100,9 @@ % Control general md.inversion.iscontrol=1; - md.inversion.maxstepss=20; + md.inversion.maxsteps=20; md.inversion.maxiter=40; md.inversion.dxmin=0.1; md.inversion.gttol=1.0e-4; - md.verbose=verbose('solution',true,'control',true); + md.verbose=verbose('control',true); % Cost functions @@ -145,15 +141,12 @@ md = loadmodel('./Models/PIG_Control_drag'); - plotmodel(md,'axis#all','equal',... - 'xlim#all',[min(md.mesh.x) max(md.mesh.x)]/10^3,... - 'ylim#all',[min(md.mesh.y) max(md.mesh.y)]/10^3,... - 'FontSize#all',12,... + plotmodel(md,... 'data',md.initialization.vel,'title','Observed velocity',... 'data',md.results.StressbalanceSolution.Vel,'title','Modeled Velocity',... 'data',md.geometry.base,'title','Bed elevation',... 'data',md.results.StressbalanceSolution.FrictionCoefficient,'title','Friction Coefficient',... - 'colorbar#all','on','colorbartitle#1-2','[m/yr]',... + 'colorbar#all','on','colorbartitle#1-2','(m/yr)',... 'caxis#1-2',([1.5,4000]),... - 'colorbartitle#3','[m]', 'log#1-2',10); + 'colorbartitle#3','(m)', 'log#1-2',10); end @@ -183,7 +176,4 @@ plotmodel(mdHO,'nlines',3,'ncols',2,'axis#all','equal',... - 'xlim#all',[min(mdHO.mesh.x) max(mdHO.mesh.x)]/10^3,... - 'ylim#all',[min(mdHO.mesh.y) max(mdHO.mesh.y)]/10^3,... - 'FontSize#all',12,... 'data',mdHO.initialization.vel,'title','Observed velocity',... 'data',(mdHO.results.StressbalanceSolution.Vel(surf)-mdHO.initialization.vel(surf)),'title','(HO-observed) velocities',... @@ -194,5 +184,5 @@ 'caxis#1',([1.5,4000]),'caxis#3',([1.5,4000]),'caxis#5',([1.5,4000]),... 'colorbar#all','on','view#all',2,... - 'colorbartitle#all','[m/yr]',... + 'colorbartitle#all','(m/yr)',... 'layer#5',1, 'log#1', 10,'log#3', 10,'log#5', 10); end Index: /issm/trunk/externalpackages/adjoinablempi/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/adjoinablempi/install-macosx64.sh (revision 21728) +++ /issm/trunk/externalpackages/adjoinablempi/install-macosx64.sh (revision 21729) @@ -5,6 +5,13 @@ rm -rf src install +# Keeping this for potential future use #Mercurial cloning: -hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src +#hg clone -r 268 http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz' + +#Untar ADOL-C +tar -zxf adjoinablempi.tar.gz export C_INCLUDE_PATH=:/usr/include/sys/:$C_INCLUDE_PATH @@ -12,6 +19,4 @@ #Configure adjoinablempi cd src -autoreconf -fi - ./configure \ --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ Index: /issm/trunk/externalpackages/adjoinablempi/install-pleaides-gcc.sh =================================================================== --- /issm/trunk/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 21728) +++ /issm/trunk/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 21729) @@ -5,11 +5,16 @@ rm -rf src install +# Keeping this for potential future use #Mercurial cloning: -hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src +#hg clone -r 268 http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz' + +#Untar ADOL-C +tar -zxf adjoinablempi.tar.gz #Configure adjoinablempi cd src -autoreconf -fi - ./configure \ --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ Index: /issm/trunk/externalpackages/adjoinablempi/install-pleaides.sh =================================================================== --- /issm/trunk/externalpackages/adjoinablempi/install-pleaides.sh (revision 21728) +++ /issm/trunk/externalpackages/adjoinablempi/install-pleaides.sh (revision 21729) @@ -5,11 +5,16 @@ rm -rf src install +# Keeping this for potential future use #Mercurial cloning: -hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src +#hg clone -r 268 http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz' + +#Untar ADOL-C +tar -zxf adjoinablempi.tar.gz #Configure adjoinablempi cd src -autoreconf -fi - ./configure \ --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ Index: /issm/trunk/externalpackages/adjoinablempi/install.sh =================================================================== --- /issm/trunk/externalpackages/adjoinablempi/install.sh (revision 21728) +++ /issm/trunk/externalpackages/adjoinablempi/install.sh (revision 21729) @@ -5,11 +5,16 @@ rm -rf src install +# Keeping this for potential future use #Mercurial cloning: -hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src +#hg clone -r 268 http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz' + +#Untar ADOL-C +tar -zxf adjoinablempi.tar.gz #Configure adjoinablempi cd src -autoreconf -fi - ./configure \ --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ Index: /issm/trunk/externalpackages/adolc/install-withampi-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi-macosx64.sh (revision 21728) +++ /issm/trunk/externalpackages/adolc/install-withampi-macosx64.sh (revision 21729) @@ -5,15 +5,18 @@ rm -rf install src -git clone https://gitlab.com/adol-c/adol-c.git src -#git clone -b ampi git://git.mcs.anl.gov/adol-c.git src -#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C' 'ADOL-C.tar.gz' + +#Untar ADOL-C +tar -zxf ADOL-C.tar.gz #Compile ADOL-C -cd src -autoreconf -f -i - export CFLAGS="-O2 -L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich" export CXXFLAGS="-O2 -L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich" +cd src ./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ @@ -21,5 +24,5 @@ --enable-ampi \ --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ - --with-soname=adolc \ + --with-soname=adolc \ --disable-tapedoc-values Index: /issm/trunk/externalpackages/adolc/install-withampi-pleiades-gcc.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 21728) +++ /issm/trunk/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 21729) @@ -5,11 +5,15 @@ rm -rf install src -git clone -b ampi git://git.mcs.anl.gov/adol-c.git src -#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C' 'ADOL-C.tar.gz' + +#Untar ADOL-C +tar -zxf ADOL-C.tar.gz #Compile ADOL-C cd src -autoreconf -f -i - ./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ @@ -17,5 +21,5 @@ --enable-ampi \ --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ - --with-soname=adolc \ + --with-soname=adolc \ --disable-tapedoc-values Index: /issm/trunk/externalpackages/adolc/install-withampi-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi-pleiades.sh (revision 21728) +++ /issm/trunk/externalpackages/adolc/install-withampi-pleiades.sh (revision 21729) @@ -5,11 +5,15 @@ rm -rf install src -git clone -b ampi git://git.mcs.anl.gov/adol-c.git src -#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C' 'ADOL-C.tar.gz' + +#Untar ADOL-C +tar -zxf ADOL-C.tar.gz #Compile ADOL-C cd src -autoreconf -f -i - ./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ @@ -17,5 +21,5 @@ --enable-ampi \ --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ - --with-soname=adolc \ + --with-soname=adolc \ --disable-tapedoc-values Index: /issm/trunk/externalpackages/adolc/install-withampi.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-withampi.sh (revision 21728) +++ /issm/trunk/externalpackages/adolc/install-withampi.sh (revision 21729) @@ -5,11 +5,15 @@ rm -rf install src -git clone https://gitlab.com/adol-c/adol-c.git src -#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C' 'ADOL-C.tar.gz' + +#Untar ADOL-C +tar -zxf ADOL-C.tar.gz #Compile ADOL-C cd src -autoreconf -f -i - ./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ Index: /issm/trunk/externalpackages/adolc/install.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install.sh (revision 21728) +++ /issm/trunk/externalpackages/adolc/install.sh (revision 21729) @@ -5,11 +5,15 @@ rm -rf install src -git clone https://gitlab.com/adol-c/adol-c.git src -#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad +# Keeping the following commented line for potential future use. +#git clone https://gitlab.com/adol-c/adol-c.git src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C' 'ADOL-C.tar.gz' + +#Untar ADOL-C +tar -zxf ADOL-C.tar.gz #Compile ADOL-C cd src - -autoreconf -f -i ./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ --libdir=$ISSM_DIR/externalpackages/adolc/install/lib Index: sm/trunk/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch =================================================================== --- /issm/trunk/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch (revision 21728) +++ (revision ) @@ -1,7 +1,0 @@ -33,34c33,35 -< || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ -< ) ---- -> ) -> // || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ -> // ) Index: /issm/trunk/externalpackages/boost/install-1.55-lonestar.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-lonestar.sh (revision 21728) +++ /issm/trunk/externalpackages/boost/install-1.55-lonestar.sh (revision 21729) @@ -22,5 +22,5 @@ rm -rf boost_1_55_0 -patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.lonestar.patch +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch #Configure and compile Index: /issm/trunk/externalpackages/boost/install-1.55-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-pleiades.sh (revision 21728) +++ /issm/trunk/externalpackages/boost/install-1.55-pleiades.sh (revision 21729) @@ -22,9 +22,5 @@ rm -rf boost_1_55_0 -#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch -#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch -#patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch -#patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch -#patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch #Configure and compile @@ -32,14 +28,9 @@ ./bootstrap.sh \ --prefix="$ISSM_DIR/externalpackages/boost/install" \ - --with-python=python2.7 \ - --with-python-root="$ISSM_DIR/externalpackages/python/install" \ - --with-toolset=intel-linux + --with-python=python3.2 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" #Compile boost -# Need gcc with iconv installed in a location that has been added to your path -./b2 toolset=intel-linux cxxflags=-static-libstdc++ linkflags=-static-libstdc++ threading=multi install -#./bjam install - -#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal +./bjam install #put bjam into install also: Index: sm/trunk/externalpackages/boost/install-1.55-pleiades_dakota6.2.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-1.55-pleiades_dakota6.2.sh (revision 21728) +++ (revision ) @@ -1,38 +1,0 @@ -#!/bin/bash -set -eu - -#Note of caution: stop after boostrap phase, and run -#bjam --debug-configuration, to figure out which paths boost is using to include -#python. make sure everyone of these paths is covered by python. If not, just make -#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY -#to get the boost library to include python support without doing that. - -#Some cleanup -rm -rf install boost_1_55_0 src -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' - -#Untar -tar -zxvf boost_1_55_0.tar.gz - -#Move boost into install directory -mv boost_1_55_0/* src -rm -rf boost_1_55_0 - -patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.lonestar.patch - -#Configure and compile -cd src -./bootstrap.sh \ - --prefix="$ISSM_DIR/externalpackages/boost/install" \ - --with-python=python3.2 \ - --with-python-root="$ISSM_DIR/externalpackages/python/install" - -#Compile boost -./bjam install - -#put bjam into install also: -mkdir ../install/bin -cp bjam ../install/bin Index: /issm/trunk/externalpackages/chaco/chaco_njs_notes.txt =================================================================== --- /issm/trunk/externalpackages/chaco/chaco_njs_notes.txt (revision 21728) +++ /issm/trunk/externalpackages/chaco/chaco_njs_notes.txt (revision 21729) @@ -2,2 +2,7 @@ sudo ln -s /usr/include/malloc/malloc.h /usr/include/malloc.h or else make sure you include the malloc directory in path + +if on sierra, you must download a version of malloc.h - +one can be found here: http://web.mit.edu/jhawk/mnt/spo/phone-project/include/malloc.h +place this file in /usr/local/include/, and run the sierra install script + Index: /issm/trunk/externalpackages/chaco/install-macosx64-sierra.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install-macosx64-sierra.sh (revision 21729) +++ /issm/trunk/externalpackages/chaco/install-macosx64-sierra.sh (revision 21729) @@ -0,0 +1,55 @@ +#!/bin/bash +set -eu + +# Some cleanup +rm -rf Chaco-2.2 +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf' + +# Untar +tar -xvzf Chaco-2.2.tar.gz + +# Move chaco to src directory +mv Chaco-2.2/* src +rm -rf Chaco-2.2 + +# Apply patches (all at once) +# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch) +patch -R -p0 < chaco.patch + +# Patch src/code/Makefile +patch ./src/code/Makefile ./patches/Makefile.macosx64-sierra.patch + + +# Build chaco +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Populate install directory +cp -p src/exec/README install +cp -p src/exec/User_Params install +cp -p src/exec/*.coords install +cp -p src/exec/*.graph install +mkdir install/include +cp -p src/code/main/defs.h install/include/defs.h +cp -p src/code/main/params.h install/include/params.h +cp -p chaco.h install/include/chaco.h +mkdir install/lib +mv src/code/chaco.a install/lib/libchaco.a +mv src/code/chacominusblas.a install/lib/libchacominusblas.a +mkdir install/exec +mv src/exec/chaco install/exec Index: /issm/trunk/externalpackages/chaco/patches/Makefile.macosx64-sierra.patch =================================================================== --- /issm/trunk/externalpackages/chaco/patches/Makefile.macosx64-sierra.patch (revision 21729) +++ /issm/trunk/externalpackages/chaco/patches/Makefile.macosx64-sierra.patch (revision 21729) @@ -0,0 +1,11 @@ +--- ./src/code/Makefile 2016-02-16 19:39:30.000000000 -0800 ++++ ./Makefile 2016-02-16 19:37:49.000000000 -0800 +@@ -6,7 +6,7 @@ + #CFLAGS = -O2 + #OFLAGS = -O2 + #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +-CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g ++CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/local/include/ + #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB + OFLAGS = -O2 + #AR = /usr/ccs/bin/ar rcv # for solaris 2 Index: /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch =================================================================== --- /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 21728) +++ /issm/trunk/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 21729) @@ -3,4 +3,4 @@ --- > # TODO: Can't this be integrated into the following logic? -> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") -> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") +> set(BLAS_LIBS "-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: sm/trunk/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh (revision 21728) +++ (revision ) @@ -1,103 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch -patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ ---prefix="$ISSM_DIR/externalpackages/dakota/install/" \ ---without-graphics \ ---with-pic \ ---disable-mpi \ ---with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ ---with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " - -#--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ -#--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" -#--with-blas="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" \ -#--with-lapack="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" - -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: sm/trunk/externalpackages/dakota/install-4.2-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-4.2-pleiades.sh (revision 21728) +++ (revision ) @@ -1,97 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' - -#Untar -tar -zxvf Dakota_4_3.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch -patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch -patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch -patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? -#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch - -#Configure dakota -cd src -./configure \ ---prefix="$ISSM_DIR/externalpackages/dakota/install/" \ ---without-graphics \ ---with-pic \ ---disable-mpi \ ---with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ ---with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" -cd .. - -#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages -#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC -#flag to the compilation. -cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/NCSUOpt/Makefile - -cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/pebbl/src/Makefile - -cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-nappspack/Makefile - -cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile - -cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile - -cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile - -cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/colin/src/Makefile - -cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/coliny/src/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile - -cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. - -#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! -cd install/lib -mv libamplsolver.a libamplsolver.a.bak -ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: sm/trunk/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh (revision 21728) +++ (revision ) @@ -1,59 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' - -#Untar -tar -zxvf Dakota_5_2.src.tar.gz - -#Move Dakota to src directory -mv Dakota/* src -rm -rf Dakota - -#Apply patches -patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch -patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch -#patch src/src/NIDRProblemDescDB.C configs/5.2/NIDRProblemDescDB.C.patch # causes segfault in 5.2 -patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch -patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch -patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? -patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch - -#Configure dakota -cd src -./configure \ ---prefix="$ISSM_DIR/externalpackages/dakota/install/" \ ---without-graphics \ ---with-pic \ ---disable-mpi \ ---with-plugin \ ---with-blas="-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ ---with-lapack="-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread" - -#--with-blas=/nasa/intel/Compiler/2012.0.032/mkl/lib/intel64/libmkl_intel_lp64.a \ -#--with-lapack=/nasa/intel/Compiler/2012.0.032/mkl/lib/intel64/libmkl_intel_lp64.a -#--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ -#--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" -#--with-blas="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" \ -#--with-lapack="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" - -cd .. - -#Compile and install dakota -cd src -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. Index: sm/trunk/externalpackages/dakota/install-5.3.1-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-5.3.1-pleiades.sh (revision 21728) +++ (revision ) @@ -1,51 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf Dakota -rm -rf src -rm -rf build -rm -rf install -mkdir src build install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' - -#Untar -tar -zxvf dakota-5.3.1-public-src.tar.gz - -#Move Dakota to src directory -mv dakota-5.3.1.src/* src -rm -rf dakota-5.3.1.src - -#Set up Dakota cmake variables and config -export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src -export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build -cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake -patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch -patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch -patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.pfe.patch - -#Apply patches -patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch -patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch -patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch -patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch -patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch - -#Configure dakota -cd $DAK_BUILD -cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC -cd .. - -#Compile and install dakota -cd $DAK_BUILD -if [ $# -eq 0 ]; -then - make - make install -else - make -j $1 - make -j $1 install -fi -cd .. Index: /issm/trunk/externalpackages/export_fig/eps2pdf.m =================================================================== --- /issm/trunk/externalpackages/export_fig/eps2pdf.m (revision 21728) +++ /issm/trunk/externalpackages/export_fig/eps2pdf.m (revision 21729) @@ -56,4 +56,5 @@ % 04/10/15: Suggest a workaround for issue #41 (missing font path; thanks Mariia Fedotenkova) % 22/02/16: Bug fix from latest release of this file (workaround for issue #41) +% 20/03/17: Added informational message in case of GS croak (issue #186) % Intialise the options string for ghostscript @@ -159,4 +160,5 @@ fprintf(2, ' or maybe the%s option(s) are not accepted by your GS version\n', gs_options); end + fprintf(2, ' or maybe you have another gs executable in your system''s path\n'); fprintf(2, 'Ghostscript options: %s\n\n', orig_options); error(message); Index: /issm/trunk/externalpackages/export_fig/export_fig.m =================================================================== --- /issm/trunk/externalpackages/export_fig/export_fig.m (revision 21728) +++ /issm/trunk/externalpackages/export_fig/export_fig.m (revision 21729) @@ -25,4 +25,5 @@ % export_fig ... -update % export_fig ... -nofontswap +% export_fig ... -linecaps % export_fig(..., handle) % @@ -43,4 +44,5 @@ % - Vector formats: pdf, eps % - Bitmap formats: png, tiff, jpg, bmp, export to workspace +% - Rounded line-caps (optional; pdf & eps only) % % This function is especially suited to exporting figures for use in @@ -153,4 +155,5 @@ % done in vector formats (only): 11 standard Matlab fonts are % replaced by the original figure fonts. This option prevents this. +% -linecaps - option to create rounded line-caps (vector formats only). % handle - The handle of the figure, axes or uipanels (can be an array of % handles, but the objects must be in the same figure) to be @@ -241,4 +244,8 @@ % 17/05/16: Fixed case of image YData containing more than 2 elements (issue #151) % 08/08/16: Enabled exporting transparency to TIF, in addition to PNG/PDF (issue #168) +% 11/12/16: Added alert in case of error creating output PDF/EPS file (issue #179) +% 13/12/16: Minor fix to the commit for issue #179 from 2 days ago +% 22/03/17: Fixed issue #187: only set manual ticks when no exponent is present +% 09/04/17: Added -linecaps option (idea by Baron Finer, issue #192) %} @@ -271,5 +278,5 @@ else % Check we have a figure - if ~isequal(get(fig, 'Type'), 'figure'); + if ~isequal(get(fig, 'Type'), 'figure') error('Handle must be that of a figure, axes or uipanel'); end @@ -583,5 +590,5 @@ if hasTransparency || hasPatches % This is *MUCH* slower, but more accurate for patches and transparent annotations (issue #39) - renderer = '-painters'; + renderer = '-painters'; %ISSM fix else renderer = '-painters'; @@ -655,5 +662,18 @@ eps2pdf(tmp_nam, pdf_nam_tmp, 1, options.append, options.colourspace==2, options.quality, options.gs_options); % Ghostscript croaks on % chars in the output PDF file, so use tempname and then rename the file - try movefile(pdf_nam_tmp, pdf_nam, 'f'); catch, end + try + % Rename the file (except if it is already the same) + % Abbie K's comment on the commit for issue #179 (#commitcomment-20173476) + if ~isequal(pdf_nam_tmp, pdf_nam) + movefile(pdf_nam_tmp, pdf_nam, 'f'); + end + catch + % Alert in case of error creating output PDF/EPS file (issue #179) + if exist(pdf_nam_tmp, 'file') + error(['Could not create ' pdf_nam ' - perhaps the folder does not exist, or you do not have write permissions']); + else + error('Could not generate the intermediary EPS file.'); + end + end catch ex % Delete the eps @@ -663,5 +683,5 @@ % Delete the eps delete(tmp_nam); - if options.eps + if options.eps || options.linecaps try % Generate an eps from the pdf @@ -669,5 +689,20 @@ eps_nam_tmp = strrep(pdf_nam_tmp,'.pdf','.eps'); pdf2eps(pdf_nam, eps_nam_tmp); - movefile(eps_nam_tmp, [options.name '.eps'], 'f'); + + % Issue #192: enable rounded line-caps + if options.linecaps + fstrm = read_write_entire_textfile(eps_nam_tmp); + fstrm = regexprep(fstrm, '[02] J', '1 J'); + read_write_entire_textfile(eps_nam_tmp, fstrm); + if options.pdf + eps2pdf(eps_nam_tmp, pdf_nam, 1, options.append, options.colourspace==2, options.quality, options.gs_options); + end + end + + if options.eps + movefile(eps_nam_tmp, [options.name '.eps'], 'f'); + else % if options.pdf + try delete(eps_nam_tmp); catch, end + end catch ex if ~options.pdf @@ -856,4 +891,5 @@ 'update', false, ... 'fontswap', true, ... + 'linecaps', false, ... 'gs_options', {{}}); end @@ -946,4 +982,6 @@ case 'nofontswap' options.fontswap = false; + case 'linecaps' + options.linecaps = true; otherwise try @@ -1161,5 +1199,5 @@ function A = rgb2grey(A) - A = cast(reshape(reshape(single(A), [], 3) * single([0.299; 0.587; 0.114]), size(A, 1), size(A, 2)), class(A)); %#ok + A = cast(reshape(reshape(single(A), [], 3) * single([0.299; 0.587; 0.114]), size(A, 1), size(A, 2)), class(A)); % #ok end @@ -1257,7 +1295,20 @@ M = {M}; end - M = cellfun(@(c) strcmp(c, 'linear'), M); - set(Hlims(M), [ax 'TickMode'], 'manual'); - %set(Hlims(M), [ax 'TickLabelMode'], 'manual'); % this hides exponent label in HG2! + %idx = cellfun(@(c) strcmp(c, 'linear'), M); + idx = find(strcmp(M,'linear')); + %set(Hlims(idx), [ax 'TickMode'], 'manual'); % issue #187 + %set(Hlims(idx), [ax 'TickLabelMode'], 'manual'); % this hides exponent label in HG2! + for idx2 = 1 : numel(idx) + try + % Fix for issue #187 - only set manual ticks when no exponent is present + hAxes = Hlims(idx(idx2)); + props = {[ax 'TickMode'],'manual', [ax 'TickLabelMode'],'manual'}; + if isempty(strtrim(hAxes.([ax 'Ruler']).SecondaryLabel.String)) + set(hAxes, props{:}); % no exponent, so update moth ticks and tick labels to manual + end + catch % probably HG1 + set(hAxes, props{:}); % revert back to old behavior + end + end end Index: /issm/trunk/externalpackages/export_fig/pdftops.m =================================================================== --- /issm/trunk/externalpackages/export_fig/pdftops.m (revision 21728) +++ /issm/trunk/externalpackages/export_fig/pdftops.m (revision 21729) @@ -33,5 +33,5 @@ % Call pdftops - [varargout{1:nargout}] = system(sprintf('"%s" %s', xpdf_path, cmd)); + [varargout{1:nargout}] = system([xpdf_command(xpdf_path()) cmd]); end @@ -138,5 +138,5 @@ function good = check_xpdf_path(path_) % Check the path is valid - [good, message] = system(sprintf('"%s" -h', path_)); %#ok + [good, message] = system([xpdf_command(path_) '-h']); %#ok % system returns good = 1 even when the command runs % Look for something distinct in the help text @@ -149,2 +149,19 @@ end end + +function cmd = xpdf_command(path_) + % Initialize any required system calls before calling ghostscript + % TODO: in Unix/Mac, find a way to determine whether to use "export" (bash) or "setenv" (csh/tcsh) + shell_cmd = ''; + if isunix + % Avoids an error on Linux with outdated MATLAB lib files + % R20XXa/bin/glnxa64/libtiff.so.X + % R20XXa/sys/os/glnxa64/libstdc++.so.X + shell_cmd = 'export LD_LIBRARY_PATH=""; '; + end + if ismac + shell_cmd = 'export DYLD_LIBRARY_PATH=""; '; + end + % Construct the command string + cmd = sprintf('%s"%s" ', shell_cmd, path_); +end Index: /issm/trunk/externalpackages/export_fig/print2array.m =================================================================== --- /issm/trunk/externalpackages/export_fig/print2array.m (revision 21728) +++ /issm/trunk/externalpackages/export_fig/print2array.m (revision 21729) @@ -50,4 +50,5 @@ % 28/05/15: Fixed issue #69: patches with LineWidth==0.75 appear wide (internal bug in Matlab's print() func) % 07/07/15: Fixed issue #83: use numeric handles in HG1 +% 11/12/16: Fixed cropping issue reported by Harry D. %} @@ -102,34 +103,41 @@ end if nargin > 2 && strcmp(renderer, '-painters') - % Print to eps file - if isTempDirOk - tmp_eps = [tempname '.eps']; - else - tmp_eps = fullfile(fpath,[fname '.eps']); - end - print2eps(tmp_eps, fig, 0, renderer, '-loose'); + % First try to print directly to tif file try - % Initialize the command to export to tiff using ghostscript - cmd_str = ['-dEPSCrop -q -dNOPAUSE -dBATCH ' res_str ' -sDEVICE=tiff24nc']; - % Set the font path - fp = font_path(); - if ~isempty(fp) - cmd_str = [cmd_str ' -sFONTPATH="' fp '"']; - end - % Add the filenames - cmd_str = [cmd_str ' -sOutputFile="' tmp_nam '" "' tmp_eps '"' gs_options]; - % Execute the ghostscript command - ghostscript(cmd_str); - catch me + % Print the file into a temporary TIF file and read it into array A + [A, err, ex] = read_tif_img(fig, res_str, renderer, tmp_nam); + if err, rethrow(ex); end + catch % error - try to print to EPS and then using Ghostscript to TIF + % Print to eps file + if isTempDirOk + tmp_eps = [tempname '.eps']; + else + tmp_eps = fullfile(fpath,[fname '.eps']); + end + print2eps(tmp_eps, fig, 0, renderer, '-loose'); + try + % Initialize the command to export to tiff using ghostscript + cmd_str = ['-dEPSCrop -q -dNOPAUSE -dBATCH ' res_str ' -sDEVICE=tiff24nc']; + % Set the font path + fp = font_path(); + if ~isempty(fp) + cmd_str = [cmd_str ' -sFONTPATH="' fp '"']; + end + % Add the filenames + cmd_str = [cmd_str ' -sOutputFile="' tmp_nam '" "' tmp_eps '"' gs_options]; + % Execute the ghostscript command + ghostscript(cmd_str); + catch me + % Delete the intermediate file + delete(tmp_eps); + rethrow(me); + end % Delete the intermediate file delete(tmp_eps); - rethrow(me); - end - % Delete the intermediate file - delete(tmp_eps); - % Read in the generated bitmap - A = imread(tmp_nam); - % Delete the temporary bitmap file - delete(tmp_nam); + % Read in the generated bitmap + A = imread(tmp_nam); + % Delete the temporary bitmap file + delete(tmp_nam); + end % Set border pixels to the correct colour if isequal(bcol, 'none') @@ -168,28 +176,6 @@ renderer = '-opengl'; end - err = false; - % Set paper size - old_pos_mode = get(fig, 'PaperPositionMode'); - old_orientation = get(fig, 'PaperOrientation'); - set(fig, 'PaperPositionMode', 'auto', 'PaperOrientation', 'portrait'); - try - % Workaround for issue #69: patches with LineWidth==0.75 appear wide (internal bug in Matlab's print() function) - fp = []; % in case we get an error below - fp = findall(fig, 'Type','patch', 'LineWidth',0.75); - set(fp, 'LineWidth',0.5); - % Fix issue #83: use numeric handles in HG1 - if ~using_hg2(fig), fig = double(fig); end - % Print to tiff file - print(fig, renderer, res_str, '-dtiff', tmp_nam); - % Read in the printed file - A = imread(tmp_nam); - % Delete the temporary file - delete(tmp_nam); - catch ex - err = true; - end - set(fp, 'LineWidth',0.75); % restore original figure appearance - % Reset paper size - set(fig, 'PaperPositionMode', old_pos_mode, 'PaperOrientation', old_orientation); + % Print the file into a temporary TIF file and read it into array A + [A, err, ex] = read_tif_img(fig, res_str, renderer, tmp_nam); % Throw any error that occurred if err @@ -220,4 +206,33 @@ end +% Function to create a TIF image of the figure and read it into an array +function [A, err, ex] = read_tif_img(fig, res_str, renderer, tmp_nam) + err = false; + ex = []; + % Temporarily set the paper size + old_pos_mode = get(fig, 'PaperPositionMode'); + old_orientation = get(fig, 'PaperOrientation'); + set(fig, 'PaperPositionMode','auto', 'PaperOrientation','portrait'); + try + % Workaround for issue #69: patches with LineWidth==0.75 appear wide (internal bug in Matlab's print() function) + fp = []; % in case we get an error below + fp = findall(fig, 'Type','patch', 'LineWidth',0.75); + set(fp, 'LineWidth',0.5); + % Fix issue #83: use numeric handles in HG1 + if ~using_hg2(fig), fig = double(fig); end + % Print to tiff file + print(fig, renderer, res_str, '-dtiff', tmp_nam); + % Read in the printed file + A = imread(tmp_nam); + % Delete the temporary file + delete(tmp_nam); + catch ex + err = true; + end + set(fp, 'LineWidth',0.75); % restore original figure appearance + % Reset the paper size + set(fig, 'PaperPositionMode',old_pos_mode, 'PaperOrientation',old_orientation); +end + % Function to return (and create, where necessary) the font path function fp = font_path() Index: /issm/trunk/externalpackages/export_fig/print2eps.m =================================================================== --- /issm/trunk/externalpackages/export_fig/print2eps.m (revision 21728) +++ /issm/trunk/externalpackages/export_fig/print2eps.m (revision 21729) @@ -27,4 +27,5 @@ % fontswap - Whether to swap non-default fonts in figure. Default: true % renderer - Renderer used to generate bounding-box. Default: 'opengl' +% (available only via the struct alternative) % crop_amounts - 4-element vector of crop amounts: [top,right,bottom,left] % (available only via the struct alternative) Index: /issm/trunk/externalpackages/git/install-macosx64-sierra.sh =================================================================== --- /issm/trunk/externalpackages/git/install-macosx64-sierra.sh (revision 21729) +++ /issm/trunk/externalpackages/git/install-macosx64-sierra.sh (revision 21729) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install git-1.7.10.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/git-1.7.10.2.tar.gz' 'git-1.7.10.2.tar.gz' + +#Untar +tar -zxvf git-1.7.10.2.tar.gz + +#Move git into install directory +mv git-1.7.10.2/* src +rm -rf git-1.7.10.2 + +#install +cd src +./configure CFLAGS="-I/usr/local/include" --prefix="$ISSM_DIR/externalpackages/git/install" +# --with-python="$ISSM_DIR/externalpackages/python/install/bin/python" #Do we really need this line? + +#Compile +make install Index: /issm/trunk/externalpackages/modules/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/modules/install-macosx64.sh (revision 21728) +++ /issm/trunk/externalpackages/modules/install-macosx64.sh (revision 21729) @@ -4,21 +4,21 @@ #Some cleanup rm -rf install -rm -rf modules-3.2.10 +rm -rf modules-3.2.9c mkdir install #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/modules-3.2.10.tar.gz' 'modules-3.2.10.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/modules-3.2.9c.tar.gz' 'modules-3.2.9c.tar.gz' #Untar -tar -zxvf modules-3.2.10.tar.gz +tar -zxvf modules-3.2.9c.tar.gz #Move modules into src directory #Configure modules -cd modules-3.2.10 -sudo ./configure \ - --prefix=/usr/local/modules \ - --with-tcl-lib=$ISSM_DIR/externalpackages/tcl/install/Library/Frameworks/Tcl.framework/Versions/8.5\ - --with-tcl-inc=$ISSM_DIR/externalpackages/tcl/install/Library/Frameworks/Tcl.framework/Versions/8.5/Headers\ +cd modules-3.2.9 +./configure \ + --prefix=$ISSM_DIR/externalpackages/modules/install\ + --with-tcl-lib=$ISSM_DIR/externalpackages/tcl/install/lib\ + --with-tcl-inc=$ISSM_DIR/externalpackages/tcl/install/include\ --with-tcl-ver=8.5 \ --with-tclx-lib=$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4\ @@ -33,7 +33,7 @@ #Compile and install modules if [ $# -eq 0 ]; then - sudo make + make else - sudo make -j $1 + make -j $1 fi sudo make install Index: /issm/trunk/externalpackages/mpich/install-3.2-linux64-static.sh =================================================================== --- /issm/trunk/externalpackages/mpich/install-3.2-linux64-static.sh (revision 21729) +++ /issm/trunk/externalpackages/mpich/install-3.2-linux64-static.sh (revision 21729) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich-3.2 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.2.tar.gz' 'mpich-3.2.tar.gz' + +#Untar +tar -zxvf mpich-3.2.tar.gz + +#Move mpich into src directory +mv mpich-3.2/* src +rm -rf mpich-3.2 + +#Configure mpich +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --disable-shared \ + +#Compile mpich (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/mpich/install-3.2-linux64.sh =================================================================== --- /issm/trunk/externalpackages/mpich/install-3.2-linux64.sh (revision 21729) +++ /issm/trunk/externalpackages/mpich/install-3.2-linux64.sh (revision 21729) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich-3.2 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.2.tar.gz' 'mpich-3.2.tar.gz' + +#Untar +tar -zxvf mpich-3.2.tar.gz + +#Move mpich into src directory +mv mpich-3.2/* src +rm -rf mpich-3.2 + +#Configure mpich +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-shared + +#Compile mpich (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/mpich/install-3.2-macosx64-static.sh =================================================================== --- /issm/trunk/externalpackages/mpich/install-3.2-macosx64-static.sh (revision 21729) +++ /issm/trunk/externalpackages/mpich/install-3.2-macosx64-static.sh (revision 21729) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich-3.2 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.2.tar.gz' 'mpich-3.2.tar.gz' + +#Untar +tar -zxvf mpich-3.2.tar.gz + +#Move mpich into src directory +mv mpich-3.2/* src +rm -rf mpich-3.2 + +#patch from http://lists.mpich.org/pipermail/discuss/2016-May/004764.html +cat src/src/include/mpiimpl.h | sed -e 's/} MPID_Request ATTRIBUTE((__aligned__(32)));/} ATTRIBUTE((__aligned__(32))) MPID_Request;/g' > TEMP +mv TEMP src/src/include/mpiimpl.h + +#Configure mpich +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" + +#Compile mpich (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/mpich/install-3.2-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/mpich/install-3.2-macosx64.sh (revision 21729) +++ /issm/trunk/externalpackages/mpich/install-3.2-macosx64.sh (revision 21729) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich-3.2 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.2.tar.gz' 'mpich-3.2.tar.gz' + +#Untar +tar -zxvf mpich-3.2.tar.gz + +#Move mpich into src directory +mv mpich-3.2/* src +rm -rf mpich-3.2 + +#patch from http://lists.mpich.org/pipermail/discuss/2016-May/004764.html +cat src/src/include/mpiimpl.h | sed -e 's/} MPID_Request ATTRIBUTE((__aligned__(32)));/} ATTRIBUTE((__aligned__(32))) MPID_Request;/g' > TEMP +mv TEMP src/src/include/mpiimpl.h + +#Configure mpich +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-shared + +#Compile mpich (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/neopz/install.sh =================================================================== --- /issm/trunk/externalpackages/neopz/install.sh (revision 21729) +++ /issm/trunk/externalpackages/neopz/install.sh (revision 21729) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install +mkdir install + +#Download from GitHub server +#GIT must be installed first. See $ISSM_DIR/externalpackages/git +git clone https://github.com/labmec/neopz.git + +#Untar and set src directory +mv neopz/ install/ + +#Set neopz CMake variables +#CMake must be installed first. See $ISSM_DIR/externalpackages/git +export PROJECT_SOURCE_DIR=$ISSM_DIR/externalpackages/neopz/install/neopz +export PROJECT_BINARY_DIR=$ISSM_DIR/externalpackages/neopz/install/ + +#Configure neopz using cmake +cd $PROJECT_SOURCE_DIR +cmake -DCMAKE_INSTALL_PREFIX:PATH=$PROJECT_BINARY_DIR + +cd $PROJECT_SOURCE_DIR +#Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi +cd $PROJECT_BINARY_DIR/pzlib +mv lib ../ +mv include ../ +cd .. +rm -rf pzlib +cd .. Index: /issm/trunk/externalpackages/pcatool/install.sh =================================================================== --- /issm/trunk/externalpackages/pcatool/install.sh (revision 21729) +++ /issm/trunk/externalpackages/pcatool/install.sh (revision 21729) @@ -0,0 +1,12 @@ +#!/bin/bash + +#Some cleanup +rm -rf install pcatool +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/pcatool.tar.gz' 'pcatool.tar.gz' + +#Untar into install +cd install +tar -zxvf ../pcatool.tar.gz Index: /issm/trunk/externalpackages/petsc/install-3.6-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-macosx64.sh (revision 21728) +++ /issm/trunk/externalpackages/petsc/install-3.6-macosx64.sh (revision 21729) @@ -13,4 +13,8 @@ mv petsc-3.6.3/* src/ rm -rf petsc-3.6.3 + +#patch +cat src/config/BuildSystem/config/packages/metis.py | sed -e "s/metis-5.1.0-p1/metis-5.1.0-p3/g" > TEMP +mv TEMP src/config/BuildSystem/config/packages/metis.py #configure Index: /issm/trunk/externalpackages/petsc/install-3.6-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.6-pleiades.sh (revision 21728) +++ /issm/trunk/externalpackages/petsc/install-3.6-pleiades.sh (revision 21729) @@ -20,7 +20,5 @@ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/" \ - --with-mpi-lib="/nasa/sgi/mpt/2.12r16/lib/libmpi.so" \ - --with-mpi-include="/nasa/sgi/mpt/2.12r16/include" \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/" \ --known-mpi-shared-libraries=1 \ --with-debugging=0 \ @@ -44,6 +42,6 @@ . /usr/share/modules/init/bash -module load comp-intel/2015.0.090 -module load mpi-sgi/mpt.2.12r16 +module load comp-intel/2016.2.181 +module load mpi-sgi/mpt export PATH="$PATH:." Index: /issm/trunk/externalpackages/petsc/install-3.7-greenplanet.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-greenplanet.sh (revision 21728) +++ /issm/trunk/externalpackages/petsc/install-3.7-greenplanet.sh (revision 21729) @@ -5,14 +5,14 @@ #Some cleanup -rm -rf install petsc-3.7.2 src +rm -rf install petsc-3.7.6 src mkdir install src #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.2.tar.gz' 'petsc-3.7.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' #Untar and move petsc to install directory -tar -zxvf petsc-3.7.2.tar.gz -mv petsc-3.7.2/* src/ -rm -rf petsc-3.7.2 +tar -zxvf petsc-3.7.6.tar.gz +mv petsc-3.7.6/* src/ +rm -rf petsc-3.7.6 #configure Index: /issm/trunk/externalpackages/petsc/install-3.7-hpc.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-hpc.sh (revision 21728) +++ /issm/trunk/externalpackages/petsc/install-3.7-hpc.sh (revision 21729) @@ -5,14 +5,14 @@ #Some cleanup -rm -rf install petsc-3.7.2 src +rm -rf install petsc-3.7.6 src mkdir install src #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.2.tar.gz' 'petsc-3.7.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' #Untar and move petsc to install directory -tar -zxvf petsc-3.7.2.tar.gz -mv petsc-3.7.2/* src/ -rm -rf petsc-3.7.2 +tar -zxvf petsc-3.7.6.tar.gz +mv petsc-3.7.6/* src/ +rm -rf petsc-3.7.6 #configure Index: /issm/trunk/externalpackages/petsc/install-3.7-linux64-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-linux64-static.sh (revision 21729) +++ /issm/trunk/externalpackages/petsc/install-3.7-linux64-static.sh (revision 21729) @@ -0,0 +1,36 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.7.6 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.7.6.tar.gz +mv petsc-3.7.6/* src/ +rm -rf petsc-3.7.6 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-shared-libraries=0 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-mumps=1 \ + --download-fblaslapack=1 \ + --download-scalapack=1 \ + --with-pic=1 + +#Compile and intall +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.7-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-linux64.sh (revision 21728) +++ /issm/trunk/externalpackages/petsc/install-3.7-linux64.sh (revision 21729) @@ -3,14 +3,14 @@ #Some cleanup -rm -rf install petsc-3.7.2 src +rm -rf install petsc-3.7.6 src mkdir install src #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.2.tar.gz' 'petsc-3.7.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' #Untar and move petsc to install directory -tar -zxvf petsc-3.7.2.tar.gz -mv petsc-3.7.2/* src/ -rm -rf petsc-3.7.2 +tar -zxvf petsc-3.7.6.tar.gz +mv petsc-3.7.6/* src/ +rm -rf petsc-3.7.6 #configure Index: /issm/trunk/externalpackages/petsc/install-3.7-macosx64-static.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-macosx64-static.sh (revision 21729) +++ /issm/trunk/externalpackages/petsc/install-3.7-macosx64-static.sh (revision 21729) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.7.6 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.7.6.tar.gz +mv petsc-3.7.6/* src/ +rm -rf petsc-3.7.6 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-shared-libraries=0 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-mumps=1 \ + --download-fblaslapack=1 \ + --download-scalapack=1 + +#Compile and intall +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.7-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-macosx64.sh (revision 21728) +++ /issm/trunk/externalpackages/petsc/install-3.7-macosx64.sh (revision 21729) @@ -3,25 +3,22 @@ #Some cleanup -rm -rf install petsc-3.7.2 src +rm -rf install petsc-3.7.6 src mkdir install src #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.2.tar.gz' 'petsc-3.7.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' #Untar and move petsc to install directory -tar -zxvf petsc-3.7.2.tar.gz -mv petsc-3.7.2/* src/ -rm -rf petsc-3.7.2 +tar -zxvf petsc-3.7.6.tar.gz +mv petsc-3.7.6/* src/ +rm -rf petsc-3.7.6 #configure cd src ./config/configure.py \ - --CXXOPTFLAGS="-g -O3" \ - --COPTFLAGS="-g -O3" \ - --FOPTFLAGS="-g -O3" \ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ + --with-debugging=1 \ --with-valgrind=0 \ --with-x=0 \ Index: /issm/trunk/externalpackages/petsc/install-3.7-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.7-pleiades.sh (revision 21728) +++ /issm/trunk/externalpackages/petsc/install-3.7-pleiades.sh (revision 21729) @@ -3,14 +3,14 @@ #Some cleanup -rm -rf install petsc-3.7.2 src +rm -rf install petsc-3.7.6 src mkdir install src #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.2.tar.gz' 'petsc-3.7.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.7.6.tar.gz' 'petsc-3.7.6.tar.gz' #Untar and move petsc to install directory -tar -zxvf petsc-3.7.2.tar.gz -mv petsc-3.7.2/* src/ -rm -rf petsc-3.7.2 +tar -zxvf petsc-3.7.6.tar.gz +mv petsc-3.7.6/* src/ +rm -rf petsc-3.7.6 #configure @@ -20,7 +20,5 @@ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort \ - --with-blas-lapack-dir="/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/" \ - --with-mpi-lib="/nasa/sgi/mpt/2.12r16/lib/libmpi.so" \ - --with-mpi-include="/nasa/sgi/mpt/2.12r16/include" \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/" \ --known-mpi-shared-libraries=1 \ --with-debugging=0 \ @@ -33,13 +31,4 @@ --download-parmetis=1 \ --download-mumps=1 \ - --download-scalapack=1 \ - --download-ml=1 \ - --download-pastix=1 \ - --download-ptscotch=1 \ - --download-hypre=1 \ - --download-euclid=1 \ - --download-spooles=1 \ - --download-spai=1 \ - --download-superlu_dist=1 \ --download-scalapack=1 @@ -53,6 +42,7 @@ . /usr/share/modules/init/bash -module load comp-intel/2015.0.090 -module load mpi-sgi/mpt.2.12r16 +module load pkgsrc +module load comp-intel/2016.2.181 +module load mpi-sgi/mpt export PATH="$PATH:." Index: /issm/trunk/externalpackages/tclx/install.sh =================================================================== --- /issm/trunk/externalpackages/tclx/install.sh (revision 21728) +++ /issm/trunk/externalpackages/tclx/install.sh (revision 21729) @@ -22,5 +22,5 @@ ./configure --prefix="$ISSM_DIR/externalpackages/tclx/install" \ --exec-prefix="$ISSM_DIR/externalpackages/tclx/install" \ - --with-tcl=$ISSM_DIR/externalpackages/tcl/install/Library/Frameworks/Tcl.framework + --with-tcl=$ISSM_DIR/externalpackages/tcl/install/lib #Compile and install tclx Index: /issm/trunk/externalpackages/valgrind/issm.supp =================================================================== --- /issm/trunk/externalpackages/valgrind/issm.supp (revision 21728) +++ /issm/trunk/externalpackages/valgrind/issm.supp (revision 21729) @@ -39,4 +39,20 @@ fun:_ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag fun:_ZNSsC1EPKcRKSaIcE +} +{ + + Memcheck:Cond + obj:/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0 + obj:/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0 + obj:/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0 + fun:call_init.part.0 + fun:call_init + fun:_dl_init + obj:/lib/x86_64-linux-gnu/ld-2.15.so + obj:* + obj:* + obj:* + obj:* + obj:* } #}}} @@ -227,3 +243,19 @@ fun:PCSetUp_LU } +{ + + Memcheck:Cond + fun:MPIC_Waitall + fun:MPIR_Alltoall_intra + fun:MPIR_Alltoall + fun:MPIR_Alltoall_impl + fun:PMPI_Alltoall + fun:PMPI_ALLTOALL + fun:dmumps_numvolsndrcv_ + fun:dmumps_simscaleabsuns_ + fun:dmumps_simscaleabs_ + fun:dmumps_fac_driver_ + fun:dmumps_ + fun:dmumps_f77_ +} #}}} Index: /issm/trunk/jenkins/linux64_caladan =================================================================== --- /issm/trunk/jenkins/linux64_caladan (revision 21728) +++ /issm/trunk/jenkins/linux64_caladan (revision 21729) @@ -13,5 +13,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -40,6 +40,6 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh - petsc install-3.6-linux64.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh triangle install-linux64.sh boost install.sh Index: /issm/trunk/jenkins/linux64_caladan_ad =================================================================== --- /issm/trunk/jenkins/linux64_caladan_ad (revision 21728) +++ /issm/trunk/jenkins/linux64_caladan_ad (revision 21729) @@ -29,6 +29,6 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh - petsc install-3.6-linux64.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh metis install-5.0.1-linux64.sh triangle install-linux64.sh Index: /issm/trunk/jenkins/linux64_caladan_ampi =================================================================== --- /issm/trunk/jenkins/linux64_caladan_ampi (revision 21728) +++ /issm/trunk/jenkins/linux64_caladan_ampi (revision 21729) @@ -19,5 +19,5 @@ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -38,6 +38,6 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh - petsc install-3.6-linux64.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh metis install-5.0.1-linux64.sh triangle install-linux64.sh Index: /issm/trunk/jenkins/linux64_ross =================================================================== --- /issm/trunk/jenkins/linux64_ross (revision 21728) +++ /issm/trunk/jenkins/linux64_ross (revision 21729) @@ -13,5 +13,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -38,5 +38,5 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh + mpich install-3.2-linux64.sh petsc install-3.7-linux64.sh triangle install-linux64.sh Index: /issm/trunk/jenkins/linux64_ross_ad =================================================================== --- /issm/trunk/jenkins/linux64_ross_ad (revision 21728) +++ /issm/trunk/jenkins/linux64_ross_ad (revision 21729) @@ -13,5 +13,5 @@ --without-kriging \ --without-kml \ - --without-Gia \ + --without-GiaIvins \ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ @@ -33,5 +33,5 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh + mpich install-3.2-linux64.sh petsc install-3.7-linux64.sh metis install-5.0.1-linux64.sh Index: /issm/trunk/jenkins/linux64_ross_ampi =================================================================== --- /issm/trunk/jenkins/linux64_ross_ampi (revision 21728) +++ /issm/trunk/jenkins/linux64_ross_ampi (revision 21729) @@ -12,5 +12,5 @@ --without-kriging \ --without-kml \ - --without-Gia \ + --without-GiaIvins \ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ @@ -21,5 +21,5 @@ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -41,5 +41,5 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh + mpich install-3.2-linux64.sh petsc install-3.7-linux64.sh metis install-5.0.1-linux64.sh Index: /issm/trunk/jenkins/linux64_ross_dakota =================================================================== --- /issm/trunk/jenkins/linux64_ross_dakota (revision 21728) +++ /issm/trunk/jenkins/linux64_ross_dakota (revision 21729) @@ -13,5 +13,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -38,5 +38,5 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh + mpich install-3.2-linux64.sh petsc install-3.7-linux64.sh triangle install-linux64.sh Index: /issm/trunk/jenkins/linux64_ross_gia =================================================================== --- /issm/trunk/jenkins/linux64_ross_gia (revision 21728) +++ /issm/trunk/jenkins/linux64_ross_gia (revision 21729) @@ -13,5 +13,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -38,6 +38,6 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh - petsc install-3.6-linux64.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh triangle install-linux64.sh math77 install.sh Index: /issm/trunk/jenkins/linux64_ross_iceocean =================================================================== --- /issm/trunk/jenkins/linux64_ross_iceocean (revision 21728) +++ /issm/trunk/jenkins/linux64_ross_iceocean (revision 21729) @@ -13,5 +13,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -34,7 +34,7 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh + mpich install-3.2-linux64.sh cmake install.sh - petsc install-3.6-linux64.sh + petsc install-3.7-linux64.sh triangle install-linux64.sh shell2junit install.sh" Index: /issm/trunk/jenkins/linux64_ross_python =================================================================== --- /issm/trunk/jenkins/linux64_ross_python (revision 21728) +++ /issm/trunk/jenkins/linux64_ross_python (revision 21729) @@ -12,5 +12,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpifort" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -36,5 +36,5 @@ #List of external pakages to be installed and their installation scripts -EXTERNALPACKAGES="mpich install-3.0-linux64.sh +EXTERNALPACKAGES="mpich install-3.2-linux64.sh petsc install-3.7-linux64.sh triangle install-linux64.sh Index: /issm/trunk/jenkins/linux64_ross_se =================================================================== --- /issm/trunk/jenkins/linux64_ross_se (revision 21728) +++ /issm/trunk/jenkins/linux64_ross_se (revision 21729) @@ -15,5 +15,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -37,7 +37,7 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh + mpich install-3.2-linux64.sh cmake install.sh - petsc install-3.6-linux64.sh + petsc install-3.7-linux64.sh triangle install-linux64.sh boost install.sh Index: /issm/trunk/jenkins/linux64_ross_static =================================================================== --- /issm/trunk/jenkins/linux64_ross_static (revision 21728) +++ /issm/trunk/jenkins/linux64_ross_static (revision 21729) @@ -16,5 +16,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ @@ -37,7 +37,7 @@ EXTERNALPACKAGES="autotools install.sh cmake install.sh - mpich install-3.0-linux64-static.sh + mpich install-3.2-linux64-static.sh m1qn3 install.sh - petsc install-3.6-linux64-static.sh + petsc install-3.7-linux64-static.sh triangle install-linux64.sh shell2junit install.sh" Index: /issm/trunk/jenkins/linux64_ross_test =================================================================== --- /issm/trunk/jenkins/linux64_ross_test (revision 21728) +++ /issm/trunk/jenkins/linux64_ross_test (revision 21729) @@ -13,5 +13,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -40,6 +40,6 @@ #List of external pakages to be installed and their installation scripts EXTERNALPACKAGES="autotools install.sh - mpich install-3.0-linux64.sh - petsc install-3.6-linux64.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh triangle install-linux64.sh boost install.sh Index: /issm/trunk/jenkins/macosx_pine-island =================================================================== --- /issm/trunk/jenkins/macosx_pine-island (revision 21728) +++ /issm/trunk/jenkins/macosx_pine-island (revision 21729) @@ -12,5 +12,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich -lmpich -lmpl" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ @@ -33,7 +33,7 @@ EXTERNALPACKAGES="autotools install.sh cmake install.sh - mpich install-3.0-macosx64.sh + mpich install-3.2-macosx64.sh m1qn3 install.sh - petsc install-3.6-macosx64.sh + petsc install-3.7-macosx64.sh triangle install-macosx64.sh shell2junit install.sh" Index: /issm/trunk/jenkins/macosx_pine-island_dakota =================================================================== --- /issm/trunk/jenkins/macosx_pine-island_dakota (revision 21728) +++ /issm/trunk/jenkins/macosx_pine-island_dakota (revision 21729) @@ -12,5 +12,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich -lmpich -lmpl" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ @@ -36,8 +36,8 @@ EXTERNALPACKAGES="autotools install.sh cmake install.sh - mpich install-3.0-macosx64.sh + mpich install-3.2-macosx64.sh chaco install-macosx64.sh m1qn3 install.sh - petsc install-3.5-macosx64.sh + petsc install-3.7-macosx64.sh triangle install-macosx64.sh boost install-1.55-macosx-el_capitan.sh Index: /issm/trunk/jenkins/macosx_pine-island_dakota_static =================================================================== --- /issm/trunk/jenkins/macosx_pine-island_dakota_static (revision 21728) +++ /issm/trunk/jenkins/macosx_pine-island_dakota_static (revision 21729) @@ -14,5 +14,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich -lmpich -lmpl" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi " \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ @@ -39,7 +39,7 @@ cmake install.sh chaco install-macosx64.sh - mpich install-3.0-macosx64-static.sh + mpich install-3.2-macosx64-static.sh m1qn3 install.sh - petsc install-3.6-macosx64-static.sh + petsc install-3.7-macosx64-static.sh triangle install-macosx64.sh boost install-1.55-macosx-el_capitan.sh Index: /issm/trunk/jenkins/macosx_pine-island_examples =================================================================== --- /issm/trunk/jenkins/macosx_pine-island_examples (revision 21728) +++ /issm/trunk/jenkins/macosx_pine-island_examples (revision 21729) @@ -12,5 +12,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich -lmpich -lmpl" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ @@ -34,7 +34,7 @@ EXTERNALPACKAGES="autotools install.sh cmake install.sh - mpich install-3.0-macosx64.sh + mpich install-3.2-macosx64.sh m1qn3 install.sh - petsc install-3.6-macosx64.sh + petsc install-3.7-macosx64.sh triangle install-macosx64.sh shell2junit install.sh" Index: /issm/trunk/jenkins/macosx_pine-island_static =================================================================== --- /issm/trunk/jenkins/macosx_pine-island_static (revision 21728) +++ /issm/trunk/jenkins/macosx_pine-island_static (revision 21729) @@ -15,5 +15,5 @@ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ - --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich -lmpich -lmpl" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ @@ -36,7 +36,7 @@ EXTERNALPACKAGES="autotools install.sh cmake install.sh - mpich install-3.0-macosx64-static.sh + mpich install-3.2-macosx64-static.sh m1qn3 install.sh - petsc install-3.6-macosx64-static.sh + petsc install-3.7-macosx64-static.sh triangle install-macosx64.sh shell2junit install.sh" Index: /issm/trunk/jenkins/windows =================================================================== --- /issm/trunk/jenkins/windows (revision 21728) +++ /issm/trunk/jenkins/windows (revision 21729) @@ -14,5 +14,5 @@ --enable-standalone-libraries \ --with-fortran=no \ - --without-Gia \ + --without-GiaIvins \ --without-kriging \ --without-kml \ @@ -60,4 +60,4 @@ #In Windows, we don't yet have MUMPS, can't do full stokes, so exclude all FS runs. Also exclude all runs with Dakota. And exclude higher order runs that have penalties. And 800+ tests because we don't want to have --with-development since we do the binaries with this version -MATLAB_NROPTIONS="'exclude',[104, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341,460]" +MATLAB_NROPTIONS="'exclude',[104, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341,460,243]" PYTHON_NROPTIONS="" Index: /issm/trunk/m4/analyses.m4 =================================================================== --- /issm/trunk/m4/analyses.m4 (revision 21728) +++ /issm/trunk/m4/analyses.m4 (revision 21729) @@ -790,28 +790,28 @@ dnl }}} -dnl with-Gia{{{ - -AC_ARG_WITH([Gia], - - AS_HELP_STRING([--with-Gia = YES], [compile with Gia capabilities (default is yes)]), - - [GIA=$withval],[GIA=yes]) - -AC_MSG_CHECKING(for Gia capability compilation) - - -HAVE_GIA=no - -if test "x$GIA" = "xyes"; then - - HAVE_GIA=yes - - AC_DEFINE([_HAVE_GIA_],[1],[with Gia capability]) - -fi - -AM_CONDITIONAL([GIA], [test x$HAVE_GIA = xyes]) - -AC_MSG_RESULT($HAVE_GIA) +dnl with-GiaIvins{{{ + +AC_ARG_WITH([GiaIvins], + + AS_HELP_STRING([--with-GiaIvins = YES], [compile with GiaIvins capabilities (default is yes)]), + + [GIAIVINS=$withval],[GIAIVINS=yes]) + +AC_MSG_CHECKING(for GiaIvins capability compilation) + + +HAVE_GIAIVINS=no + +if test "x$GIAIVINS" = "xyes"; then + + HAVE_GIAIVINS=yes + + AC_DEFINE([_HAVE_GIAIVINS_],[1],[with GiaIvins capability]) + +fi + +AM_CONDITIONAL([GIAIVINS], [test x$HAVE_GIAIVINS = xyes]) + +AC_MSG_RESULT($HAVE_GIAIVINS) dnl }}} Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 21728) +++ /issm/trunk/m4/issm_options.m4 (revision 21729) @@ -770,4 +770,5 @@ ADOLCLIB="-L$ADOLC_ROOT/lib -ladolc" AC_DEFINE([_HAVE_ADOLC_],[1],[with adolc in ISSM src]) + AC_DEFINE([_HAVE_AD_],[1],[with AD in ISSM src]) AC_SUBST([ADOLCINCL]) AC_SUBST([ADOLCLIB]) @@ -1852,4 +1853,31 @@ AM_CONDITIONAL([SNOWPACK], [test x$HAVE_SNOWPACK = xyes]) dnl }}} + dnl neopz{{{ + AC_ARG_WITH([neopz-dir], + AS_HELP_STRING([--with-neopz-dir=DIR], [neopz root directory.]), + [NEOPZ_ROOT=$withval],[NEOPZ_ROOT="no"]) + + dnl Check whether neopz is enabled + AC_MSG_CHECKING([for neopz]) + if test "x$NEOPZ_ROOT" = "xno" ; then + HAVE_NEOPZ=no + else + HAVE_NEOPZ=yes + if ! test -d "$NEOPZ_ROOT"; then + AC_MSG_ERROR([neopz directory provided ($NEOPZ_ROOT) does not exist]); + fi + fi + AC_MSG_RESULT($HAVE_NEOPZ) + + dnl neopz headers and libraries + if test "x$HAVE_NEOPZ" == "xyes"; then + NEOPZLIB="$NEOPZ_ROOT/lib/libpz.a" + NEOPZINCL=-I"$NEOPZ_ROOT/include" + AC_DEFINE([_HAVE_NEOPZ_],[1],[with NEOPZ in ISSM src]) + AC_SUBST([NEOPZINCL]) + AC_SUBST([NEOPZLIB]) + fi + AM_CONDITIONAL([NEOPZ], [test x$HAVE_NEOPZ = xyes]) + dnl }}} dnl Capabilities @@ -1867,4 +1895,18 @@ AM_CONDITIONAL([BAMG], [test x$HAVE_BAMG = xyes]) AC_MSG_RESULT($HAVE_BAMG) + dnl }}} + dnl with-ocean{{{ + AC_ARG_WITH([ocean], + AS_HELP_STRING([--with-ocean = YES],[compile with ice/ocean coupling (default is no)]), + [OCEAN=$withval],[OCEAN=no]) + AC_MSG_CHECKING(for ice/ocean capability compilation) + + HAVE_OCEAN=no + if test "x$OCEAN" = "xyes"; then + HAVE_OCEAN=yes + AC_DEFINE([_HAVE_OCEAN_],[1],[with ice/ocean coupling capability]) + fi + AM_CONDITIONAL([OCEAN], [test x$HAVE_OCEAN = xyes]) + AC_MSG_RESULT($HAVE_OCEAN) dnl }}} dnl with-kml{{{ Index: /issm/trunk/scripts/BinRead.py =================================================================== --- /issm/trunk/scripts/BinRead.py (revision 21728) +++ /issm/trunk/scripts/BinRead.py (revision 21729) @@ -129,21 +129,21 @@ """ - if strcmpi(format,'Boolean'): + if format=='Boolean': code=1 - elif strcmpi(format,'Integer'): + elif format=='Integer': code=2 - elif strcmpi(format,'Double'): + elif format=='Double': code=3 - elif strcmpi(format,'String'): + elif format=='String': code=4 - elif strcmpi(format,'BooleanMat'): + elif format=='BooleanMat': code=5 - elif strcmpi(format,'IntMat'): + elif format=='IntMat': code=6 - elif strcmpi(format,'DoubleMat'): + elif format=='DoubleMat': code=7 - elif strcmpi(format,'MatArray'): + elif format=='MatArray': code=8 - elif strcmpi(format,'StringArray'): + elif format=='StringArray': code=9 else: @@ -201,6 +201,4 @@ args = parser.parse_args() - from MatlabFuncs import * - BinRead(args.filin, args.filout,args.verbose) #}}} Index: /issm/trunk/src/c/Makefile.am =================================================================== --- /issm/trunk/src/c/Makefile.am (revision 21728) +++ /issm/trunk/src/c/Makefile.am (revision 21729) @@ -1,3 +1,3 @@ -AM_CPPFLAGS = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJ4INCL@ +AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJ4INCL@ AUTOMAKE_OPTIONS = subdir-objects @@ -20,6 +20,38 @@ #Core sources +#BAMG sources {{{ +issm_sources = +if BAMG +issm_sources += ./bamg/BamgGeom.cpp\ + ./bamg/BamgMesh.cpp\ + ./bamg/BamgOpts.cpp\ + ./bamg/CrackedEdge.cpp\ + ./bamg/Curve.cpp\ + ./bamg/Edge.cpp\ + ./bamg/GeomEdge.cpp\ + ./bamg/GeomSubDomain.cpp\ + ./bamg/GeomVertex.cpp\ + ./bamg/Geometry.cpp\ + ./bamg/ListofIntersectionTriangles.cpp\ + ./bamg/EigenMetric.cpp\ + ./bamg/Metric.cpp\ + ./bamg/BamgQuadtree.cpp\ + ./bamg/SetOfE4.cpp\ + ./bamg/SubDomain.cpp\ + ./bamg/AdjacentTriangle.cpp\ + ./bamg/Triangle.cpp\ + ./bamg/BamgVertex.cpp\ + ./bamg/VertexOnEdge.cpp\ + ./bamg/VertexOnGeom.cpp\ + ./bamg/VertexOnVertex.cpp\ + ./bamg/Mesh.cpp\ + ./shared/Bamg/BigPrimeNumber.cpp\ + ./modules/Bamgx/Bamgx.cpp\ + ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\ + ./modules/BamgTriangulatex/BamgTriangulatex.cpp +endif +#}}} #Core sources{{{ -issm_sources = ./datastructures/DataSet.cpp\ +issm_sources += ./datastructures/DataSet.cpp\ ./classes/gauss/GaussSeg.cpp\ ./classes/gauss/GaussTria.cpp\ @@ -265,4 +297,5 @@ ./modules/ModelProcessorx/CreateOutputDefinitions.cpp\ ./modules/OutputDefinitionsResponsex/OutputDefinitionsResponsex.cpp\ + ./modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp\ ./classes/Inputs/PentaInput.cpp\ ./classes/Inputs/TetraInput.cpp @@ -279,36 +312,4 @@ ./modules/ModelProcessorx/Dakota/UpdateElementsAndMaterialsDakota.cpp\ ./cores/dakota_core.cpp -endif -#}}} -#BAMG sources {{{ -if BAMG -issm_sources += ./bamg/BamgGeom.cpp\ - ./bamg/BamgMesh.cpp\ - ./bamg/BamgOpts.cpp\ - ./bamg/CrackedEdge.cpp\ - ./bamg/Curve.cpp\ - ./bamg/Direction.cpp\ - ./bamg/Edge.cpp\ - ./bamg/GeomEdge.cpp\ - ./bamg/GeomSubDomain.cpp\ - ./bamg/GeomVertex.cpp\ - ./bamg/Geometry.cpp\ - ./bamg/ListofIntersectionTriangles.cpp\ - ./bamg/EigenMetric.cpp\ - ./bamg/Metric.cpp\ - ./bamg/BamgQuadtree.cpp\ - ./bamg/SetOfE4.cpp\ - ./bamg/SubDomain.cpp\ - ./bamg/AdjacentTriangle.cpp\ - ./bamg/Triangle.cpp\ - ./bamg/BamgVertex.cpp\ - ./bamg/VertexOnEdge.cpp\ - ./bamg/VertexOnGeom.cpp\ - ./bamg/VertexOnVertex.cpp\ - ./bamg/Mesh.cpp\ - ./shared/Bamg/BigPrimeNumber.cpp\ - ./modules/Bamgx/Bamgx.cpp\ - ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\ - ./modules/BamgTriangulatex/BamgTriangulatex.cpp endif #}}} @@ -453,7 +454,7 @@ #}}} #Gia sources {{{ -if GIA +if GIAIVINS issm_sources += ./cores/gia_core.cpp\ - ./analyses/GiaAnalysis.cpp\ + ./analyses/GiaIvinsAnalysis.cpp\ ./modules/GiaDeflectionCorex/GiaDeflectionCorex.cpp\ ./modules/GiaDeflectionCorex/distme.f\ @@ -530,4 +531,7 @@ ./kml/KMLFileReadUtils.cpp #}}} +#NEOPZ sources {{{ +neopz_sources = ./classes/AdaptiveMeshRefinement.cpp +#}}} #Modules sources{{{ modules_sources= ./shared/Threads/LaunchThread.cpp\ @@ -546,5 +550,4 @@ ./modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp\ ./modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp\ - ./modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp\ ./modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp\ ./modules/InterpFromMeshToGridx/InterpFromMeshToGridx.cpp\ @@ -604,4 +607,8 @@ endif +if NEOPZ +libISSMCore_la_SOURCES += $(neopz_sources) +endif + if WRAPPERS libISSMModules_la_SOURCES = $(modules_sources) @@ -613,4 +620,5 @@ libISSMModules_la_SOURCES += $(kml_sources) endif + libISSMModules_la_CXXFLAGS = $(ALLCXXFLAGS) if !WINDOWS @@ -674,5 +682,5 @@ #External packages -LDADD += $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(PETSCLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJ4LIB) +LDADD += $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(PETSCLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJ4LIB) if FORTRAN @@ -686,4 +694,9 @@ issm_slr_CXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS) +if OCEAN +bin_PROGRAMS += issm_ocean +issm_ocean_SOURCES = main/issm_ocean.cpp +issm_ocean_CXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS) +endif if KRIGING Index: /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp (revision 21729) @@ -5,4 +5,5 @@ #include "../modules/modules.h" #include "../solutionsequences/solutionsequences.h" +#include "../cores/cores.h" /*Model processing*/ @@ -13,4 +14,5 @@ int M,N; bool spcpresent = false; + int finiteelement; IssmDouble heatcapacity; IssmDouble referencetemperature; @@ -24,4 +26,5 @@ iomodel->FindConstant(&heatcapacity,"md.materials.heatcapacity"); iomodel->FindConstant(&referencetemperature,"md.constants.referencetemperature"); + iomodel->FindConstant(&finiteelement,"md.thermal.fe"); /*return if 2d mesh*/ @@ -31,58 +34,26 @@ iomodel->FetchData(&spcvector,&M,&N,"md.thermal.spctemperature"); - //FIX ME: SHOULD USE IOMODELCREATECONSTRAINTS - /*Transient or static?:*/ - if(M==iomodel->numberofvertices){ - /*static: just create Constraints objects*/ - count=0; - - for(int i=0;inumberofvertices;i++){ - /*keep only this partition's nodes:*/ - if((iomodel->my_vertices[i])){ - - if (!xIsNan(spcvector[i])){ - - constraints->AddObject(new SpcStatic(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,0,heatcapacity*(spcvector[i]-referencetemperature),EnthalpyAnalysisEnum)); - count++; - - } - } - } - } - else if (M==(iomodel->numberofvertices+1)){ - /*transient: create transient SpcTransient objects. Same logic, except we need to retrieve - * various times and values to initialize an SpcTransient object: */ - count=0; - - /*figure out times: */ - times=xNew(N); + /*Convert spcs from temperatures to enthalpy*/ + _assert_(N>0); _assert_(M>=iomodel->numberofvertices); + for(int i=0;inumberofvertices;i++){ for(int j=0;jnumberofvertices;i++){ - - /*keep only this partition's nodes:*/ - if((iomodel->my_vertices[i])){ - - /*figure out times and values: */ - values=xNew(N); - spcpresent=false; - for(int j=0;j(values[j]))spcpresent=true; //NaN means no spc by default - } - - if(spcpresent){ - constraints->AddObject(new SpcTransient(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,0,N,times,values,EnthalpyAnalysisEnum)); - count++; - } - xDelete(values); - } - } + spcvector[i*N+j] = heatcapacity*(spcvector[i*N+j]-referencetemperature); + } + } + + /*Specific case for PDD, we want the constaints to be updated by the PDD scheme itself*/ + bool isdynamic = false; + if (iomodel->solution_enum==TransientSolutionEnum){ + int smb_model; + iomodel->FindConstant(&smb_model,"md.smb.model"); + if(smb_model==SMBpddEnum) isdynamic=true; + if(smb_model==SMBd18opddEnum) isdynamic=true; + } + + if(isdynamic){ + IoModelToDynamicConstraintsx(constraints,iomodel,spcvector,M,N,EnthalpyAnalysisEnum,finiteelement); } else{ - _error_("Size of field " << EnumToStringx(ThermalSpctemperatureEnum) << " not supported"); + IoModelToConstraintsx(constraints,iomodel,spcvector,M,N,EnthalpyAnalysisEnum,finiteelement); } @@ -98,6 +69,9 @@ void EnthalpyAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel){/*{{{*/ + int finiteelement; + iomodel->FindConstant(&finiteelement,"md.thermal.fe"); + if(iomodel->domaintype==Domain3DEnum) iomodel->FetchData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); - ::CreateNodes(nodes,iomodel,EnthalpyAnalysisEnum,P1Enum); + ::CreateNodes(nodes,iomodel,EnthalpyAnalysisEnum,finiteelement); iomodel->DeleteData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); }/*}}}*/ @@ -108,5 +82,5 @@ bool dakota_analysis,ismovingfront,isenthalpy; - int frictionlaw,basalforcing_model; + int frictionlaw,basalforcing_model,materialstype; int FrictionCoupling; @@ -120,4 +94,8 @@ /*Fetch data needed: */ iomodel->FetchData(3,"md.initialization.temperature","md.initialization.waterfraction","md.initialization.pressure"); + + /*Finite element type*/ + int finiteelement; + iomodel->FindConstant(&finiteelement,"md.thermal.fe"); /*Update elements: */ @@ -126,5 +104,5 @@ if(iomodel->my_elements[i]){ Element* element=(Element*)elements->GetObjectByOffset(counter); - element->Update(i,iomodel,analysis_counter,analysis_type,P1Enum); + element->Update(i,iomodel,analysis_counter,analysis_type,finiteelement); counter++; } @@ -134,4 +112,5 @@ iomodel->FindConstant(&ismovingfront,"md.transient.ismovingfront"); iomodel->FindConstant(&frictionlaw,"md.friction.law"); + iomodel->FindConstant(&materialstype,"md.materials.type"); iomodel->FetchDataToInput(elements,"md.geometry.thickness",ThicknessEnum); @@ -145,6 +124,4 @@ iomodel->FetchDataToInput(elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); } - iomodel->FetchDataToInput(elements,"md.materials.rheology_B",MaterialsRheologyBEnum); - iomodel->FetchDataToInput(elements,"md.materials.rheology_n",MaterialsRheologyNEnum); iomodel->FetchDataToInput(elements,"md.initialization.pressure",PressureEnum); iomodel->FetchDataToInput(elements,"md.initialization.temperature",TemperatureEnum); @@ -171,4 +148,25 @@ iomodel->FetchDataToInput(elements,"md.basalforcings.geothermalflux",BasalforcingsGeothermalfluxEnum); break; + } + + /*Rheology type*/ + iomodel->FetchDataToInput(elements,"md.materials.rheology_B",MaterialsRheologyBEnum); + switch(materialstype){ + case MatenhancediceEnum: + iomodel->FetchDataToInput(elements,"md.materials.rheology_n",MaterialsRheologyNEnum); + iomodel->FetchDataToInput(elements,"md.materials.rheology_E",MaterialsRheologyEEnum); + break; + case MatdamageiceEnum: + iomodel->FetchDataToInput(elements,"md.materials.rheology_n",MaterialsRheologyNEnum); + break; + case MatestarEnum: + iomodel->FetchDataToInput(elements,"md.materials.rheology_Ec",MaterialsRheologyEcEnum); + iomodel->FetchDataToInput(elements,"md.materials.rheology_Es",MaterialsRheologyEsEnum); + break; + case MaticeEnum: + iomodel->FetchDataToInput(elements,"md.materials.rheology_n",MaterialsRheologyNEnum); + break; + default: + _error_("not supported"); } @@ -212,4 +210,10 @@ iomodel->FetchDataToInput(elements,"md.initialization.temperature",TemperatureEnum); break; + case 9: + iomodel->FetchDataToInput(elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(elements,"md.friction.pressure_adjusted_temperature",FrictionPressureAdjustedTemperatureEnum); + InputUpdateFromConstantx(elements,1.,FrictionPEnum); + InputUpdateFromConstantx(elements,1.,FrictionQEnum); + break; default: _error_("not supported"); @@ -242,4 +246,5 @@ if(frictionlaw==4 || frictionlaw==6) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); if(frictionlaw==3) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); + if(frictionlaw==9) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); }/*}}}*/ @@ -247,7 +252,5 @@ void EnthalpyAnalysis::ApplyBasalConstraints(IssmDouble* serial_spc,Element* element){/*{{{*/ - /* Check if ice in element */ - if(!element->IsIceInElement()) return; - + /* Do not check if ice in element, this may lead to inconsistencies between cpu partitions */ /* Only update constraints at the base. */ if(!(element->IsOnBase())) return; @@ -279,10 +282,12 @@ /*apply or release spc*/ node=element->GetNode(indices[i]); + if(!node->IsActive()) continue; if(serial_spc[node->Sid()]==1.){ pressure_input->GetInputValue(&pressure, gauss); node->ApplyConstraint(0,PureIceEnthalpy(element,pressure)); } - else + else { node->DofInFSet(0); + } } @@ -312,5 +317,5 @@ const int dim=3; int i,is,state; - int vertexdown,vertexup,numvertices,numsegments; + int nodedown,nodeup,numnodes,numsegments; int enthalpy_enum; IssmDouble vec_heatflux[dim],normal_base[dim],d1enthalpy[dim],d1pressure[dim]; @@ -353,25 +358,25 @@ /******** MELTING RATES ************************************//*{{{*/ element->NormalBase(&normal_base[0],xyz_list_base); - element->VerticalSegmentIndices(&pairindices,&numsegments); + element->VerticalSegmentIndicesBase(&pairindices,&numsegments); IssmDouble* meltingrate_enthalpy = xNew(numsegments); IssmDouble* heating = xNew(numsegments); - numvertices=element->GetNumberOfVertices(); - IssmDouble* enthalpies = xNew(numvertices); - IssmDouble* pressures = xNew(numvertices); - IssmDouble* watercolumns = xNew(numvertices); - IssmDouble* basalmeltingrates = xNew(numvertices); - element->GetInputListOnVertices(enthalpies,enthalpy_enum); - element->GetInputListOnVertices(pressures,PressureEnum); - element->GetInputListOnVertices(watercolumns,WatercolumnEnum); - element->GetInputListOnVertices(basalmeltingrates,BasalforcingsGroundediceMeltingRateEnum); + numnodes=element->GetNumberOfNodes(); + IssmDouble* enthalpies = xNew(numnodes); + IssmDouble* pressures = xNew(numnodes); + IssmDouble* watercolumns = xNew(numnodes); + IssmDouble* basalmeltingrates = xNew(numnodes); + element->GetInputListOnNodes(enthalpies,enthalpy_enum); + element->GetInputListOnNodes(pressures,PressureEnum); + element->GetInputListOnNodes(watercolumns,WatercolumnEnum); + element->GetInputListOnNodes(basalmeltingrates,BasalforcingsGroundediceMeltingRateEnum); Gauss* gauss=element->NewGauss(); for(is=0;isGaussVertex(vertexdown); - - state=GetThermalBasalCondition(element, enthalpies[vertexdown], enthalpies[vertexup], pressures[vertexdown], pressures[vertexup], watercolumns[vertexdown], basalmeltingrates[vertexdown]); + nodedown = pairindices[is*2+0]; + nodeup = pairindices[is*2+1]; + gauss->GaussNode(element->GetElementType(),nodedown); + + state=GetThermalBasalCondition(element, enthalpies[nodedown], enthalpies[nodeup], pressures[nodedown], pressures[nodeup], watercolumns[nodedown], basalmeltingrates[nodedown]); switch (state) { case 0: @@ -388,5 +393,5 @@ case 4: // temperate, thick melting base: set grad H*n=0 - kappa_mix=GetWetIceConductivity(element, enthalpies[vertexdown], pressures[vertexdown]); + kappa_mix=GetWetIceConductivity(element, enthalpies[nodedown], pressures[nodedown]); pressure_input->GetInputDerivativeValue(&d1pressure[0],xyz_list,gauss); for(i=0;i<3;i++) vec_heatflux[i]=kappa_mix*beta*d1pressure[i]; @@ -414,35 +419,35 @@ /******** UPDATE MELTINGRATES AND WATERCOLUMN **************//*{{{*/ for(is=0;is=0.); _assert_(lambda<1.); - watercolumns[vertexdown]=0.; - basalmeltingrates[vertexdown]=lambda*meltingrate_enthalpy[is]; // restrict freeze on only to size of watercolumn - enthalpies[vertexdown]+=(1.-lambda)*dt/yts*meltingrate_enthalpy[is]*latentheat*rho_ice; // use rest of energy to cool down base: dE=L*m, m=(1-lambda)*meltingrate*rho_ice + if(watercolumns[nodedown]+meltingrate_enthalpy[is]*dt<0.){ // prevent too much freeze on + lambda = -watercolumns[nodedown]/(dt*meltingrate_enthalpy[is]); _assert_(lambda>=0.); _assert_(lambda<1.); + watercolumns[nodedown]=0.; + basalmeltingrates[nodedown]=lambda*meltingrate_enthalpy[is]; // restrict freeze on only to size of watercolumn + enthalpies[nodedown]+=(1.-lambda)*dt/yts*meltingrate_enthalpy[is]*latentheat*rho_ice; // use rest of energy to cool down base: dE=L*m, m=(1-lambda)*meltingrate*rho_ice } else{ - basalmeltingrates[vertexdown]=meltingrate_enthalpy[is]; - watercolumns[vertexdown]+=dt*meltingrate_enthalpy[is]; + basalmeltingrates[nodedown]=meltingrate_enthalpy[is]; + watercolumns[nodedown]+=dt*meltingrate_enthalpy[is]; } } else{ - basalmeltingrates[vertexdown]=meltingrate_enthalpy[is]; - if(watercolumns[vertexdown]+meltingrate_enthalpy[is]<0.) - watercolumns[vertexdown]=0.; + basalmeltingrates[nodedown]=meltingrate_enthalpy[is]; + if(watercolumns[nodedown]+meltingrate_enthalpy[is]<0.) + watercolumns[nodedown]=0.; else - watercolumns[vertexdown]+=meltingrate_enthalpy[is]; + watercolumns[nodedown]+=meltingrate_enthalpy[is]; } - basalmeltingrates[vertexdown]*=rho_water/rho_ice; // convert meltingrate from water to ice equivalent - _assert_(watercolumns[vertexdown]>=0.); + basalmeltingrates[nodedown]*=rho_water/rho_ice; // convert meltingrate from water to ice equivalent + _assert_(watercolumns[nodedown]>=0.); }/*}}}*/ /*feed updated variables back into model*/ if(dt!=0.){ - element->AddInput(enthalpy_enum,enthalpies,P1Enum); //TODO: distinguis for steadystate and transient run - element->AddInput(WatercolumnEnum,watercolumns,P1Enum); - } - element->AddInput(BasalforcingsGroundediceMeltingRateEnum,basalmeltingrates,P1Enum); + element->AddInput(enthalpy_enum,enthalpies,element->GetElementType()); + element->AddInput(WatercolumnEnum,watercolumns,element->GetElementType()); + } + element->AddInput(BasalforcingsGroundediceMeltingRateEnum,basalmeltingrates,element->GetElementType()); /*Clean up and return*/ @@ -589,5 +594,5 @@ } - /*Artifficial diffusivity*/ + /*Artificial diffusivity*/ if(stabilization==1){ element->ElementSizes(&hx,&hy,&hz); @@ -976,111 +981,123 @@ void EnthalpyAnalysis::DrainWaterfraction(FemModel* femmodel){/*{{{*/ /*Drain excess water fraction in ice column: */ - for(int i=0;ielements->Size();i++){ - Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); - DrainWaterfractionIcecolumn(element); - } -}/*}}}*/ -void EnthalpyAnalysis::DrainWaterfraction(Element* element, IssmDouble* pdrainrate_element){/*{{{*/ - - /* Check if ice in element */ - if(!element->IsIceInElement()) return; - - /*Intermediaries*/ - int iv,is,vertexdown,vertexup,numsegments; - IssmDouble dt, height_element; - IssmDouble rho_water, rho_ice; - int numvertices = element->GetNumberOfVertices(); - - IssmDouble* xyz_list = NULL; - IssmDouble* enthalpies = xNew(numvertices); - IssmDouble* pressures = xNew(numvertices); - IssmDouble* temperatures = xNew(numvertices); - IssmDouble* waterfractions = xNew(numvertices); - IssmDouble* deltawaterfractions = xNew(numvertices); - int *pairindices = NULL; + ComputeWaterfractionDrainage(femmodel); + DrainageUpdateWatercolumn(femmodel); + DrainageUpdateEnthalpy(femmodel); +}/*}}}*/ +void EnthalpyAnalysis::ComputeWaterfractionDrainage(FemModel* femmodel){/*{{{*/ + + int i,k,numnodes; + IssmDouble dt; + Element* element= NULL; + + femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + + for(i=0;ielements->Size();i++){ + element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + numnodes=element->GetNumberOfNodes(); + IssmDouble* waterfractions= xNew(numnodes); + IssmDouble* drainage= xNew(numnodes); + + element->GetInputListOnNodes(waterfractions,WaterfractionEnum); + for(k=0; kAddInput(WaterfractionDrainageEnum,drainage,element->GetElementType()); + + xDelete(waterfractions); + xDelete(drainage); + } +}/*}}}*/ +void EnthalpyAnalysis::DrainageUpdateWatercolumn(FemModel* femmodel){/*{{{*/ + + int i,k,numnodes, numbasalnodes; + IssmDouble dt; + int* basalnodeindices=NULL; + Element* element= NULL; - rho_ice=element->GetMaterialParameter(MaterialsRhoIceEnum); - rho_water=element->GetMaterialParameter(MaterialsRhoSeawaterEnum); - - element->GetVerticesCoordinates(&xyz_list); - element->GetInputListOnVertices(enthalpies,EnthalpyEnum); - element->GetInputListOnVertices(pressures,PressureEnum); - - element->FindParam(&dt,TimesteppingTimeStepEnum); - for(iv=0;ivEnthalpyToThermal(&temperatures[iv],&waterfractions[iv], enthalpies[iv],pressures[iv]); - deltawaterfractions[iv]=DrainageFunctionWaterfraction(waterfractions[iv], dt); - } - - /*drain waterfraction, feed updated variables back into model*/ - for(iv=0;iv(dt)) - waterfractions[iv]-=deltawaterfractions[iv]*dt; - else - waterfractions[iv]-=deltawaterfractions[iv]; - element->ThermalToEnthalpy(&enthalpies[iv], temperatures[iv], waterfractions[iv], pressures[iv]); - } - element->AddInput(EnthalpyEnum,enthalpies,P1Enum); - element->AddInput(WaterfractionEnum,waterfractions,P1Enum); - - /*return meltwater column equivalent to drained water*/ - element->VerticalSegmentIndices(&pairindices,&numsegments); - for(is=0;is=0.); - } - - /*Clean up and return*/ - xDelete(pairindices); - xDelete(xyz_list); - xDelete(enthalpies); - xDelete(pressures); - xDelete(temperatures); - xDelete(waterfractions); - xDelete(deltawaterfractions); -}/*}}}*/ -void EnthalpyAnalysis::DrainWaterfractionIcecolumn(Element* element){/*{{{*/ - - /* Check if ice in element */ - if(!element->IsIceInElement()) return; - - /* Only drain waterfraction of ice column from element at base*/ - if(!element->IsOnBase()) return; //FIXME: allow freeze on for floating elements - - /* Intermediaries*/ - int is, numvertices, numsegments; - int *pairindices = NULL; - - numvertices=element->GetNumberOfVertices(); - element->VerticalSegmentIndices(&pairindices,&numsegments); - - IssmDouble* watercolumn = xNew(numvertices); - IssmDouble* drainrate_column = xNew(numsegments); - IssmDouble* drainrate_element = xNew(numsegments); - - element->GetInputListOnVertices(watercolumn,WatercolumnEnum); - - for(is=0;isIsOnSurface()) break; - elementi=elementi->GetUpperElement(); - } - /* add drained water to water column*/ - for(is=0;isAddInput(WatercolumnEnum,watercolumn,P1Enum); - - xDelete(pairindices); - xDelete(drainrate_column); - xDelete(drainrate_element); - xDelete(watercolumn); + femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + + /*depth-integrate the drained water fraction */ + femmodel->parameters->SetParam(WaterfractionDrainageEnum,InputToDepthaverageInEnum); + femmodel->parameters->SetParam(WaterfractionDrainageIntegratedEnum,InputToDepthaverageOutEnum); + depthaverage_core(femmodel); + femmodel->parameters->SetParam(WaterfractionDrainageIntegratedEnum,InputToExtrudeEnum); + extrudefrombase_core(femmodel); + /*multiply depth-average by ice thickness*/ + for(i=0;ielements->Size();i++){ + element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + numnodes=element->GetNumberOfNodes(); + IssmDouble* drainage_int= xNew(numnodes); + IssmDouble* thicknesses= xNew(numnodes); + + element->GetInputListOnNodes(drainage_int,WaterfractionDrainageIntegratedEnum); + element->GetInputListOnNodes(thicknesses,ThicknessEnum); + for(k=0;kAddInput(WaterfractionDrainageIntegratedEnum, drainage_int, element->GetElementType()); + + xDelete(drainage_int); + xDelete(thicknesses); + } + + /*update water column*/ + for(i=0;ielements->Size();i++){ + element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + /* Check if ice in element */ + if(!element->IsIceInElement()) continue; + if(!element->IsOnBase()) continue; + + numnodes=element->GetNumberOfNodes(); + IssmDouble* watercolumn= xNew(numnodes); + IssmDouble* drainage_int= xNew(numnodes); + element->GetInputListOnNodes(watercolumn,WatercolumnEnum); + element->GetInputListOnNodes(drainage_int,WaterfractionDrainageIntegratedEnum); + + element->BasalNodeIndices(&numbasalnodes,&basalnodeindices,element->GetElementType()); + for(k=0;kAddInput(WatercolumnEnum, watercolumn, element->GetElementType()); + + xDelete(watercolumn); + xDelete(drainage_int); + } + xDelete(basalnodeindices); +}/*}}}*/ +void EnthalpyAnalysis::DrainageUpdateEnthalpy(FemModel* femmodel){/*{{{*/ + + int i,k,numnodes; + IssmDouble dt; + Element* element= NULL; + femmodel->parameters->FindParam(&dt,TimesteppingTimeStepEnum); + + for(i=0;ielements->Size();i++){ + element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + numnodes=element->GetNumberOfNodes(); + IssmDouble* enthalpies= xNew(numnodes); + IssmDouble* pressures= xNew(numnodes); + IssmDouble* temperatures= xNew(numnodes); + IssmDouble* waterfractions= xNew(numnodes); + IssmDouble* drainage= xNew(numnodes); + + element->GetInputListOnNodes(pressures,PressureEnum); + element->GetInputListOnNodes(temperatures,TemperatureEnum); + element->GetInputListOnNodes(waterfractions,WaterfractionEnum); + element->GetInputListOnNodes(drainage,WaterfractionDrainageEnum); + + for(k=0;kThermalToEnthalpy(&enthalpies[k], temperatures[k], waterfractions[k], pressures[k]); + } + element->AddInput(WaterfractionEnum,waterfractions,element->GetElementType()); + element->AddInput(EnthalpyEnum,enthalpies,element->GetElementType()); + + xDelete(enthalpies); + xDelete(pressures); + xDelete(temperatures); + xDelete(waterfractions); + xDelete(drainage); + } }/*}}}*/ IssmDouble EnthalpyAnalysis::EnthalpyDiffusionParameter(Element* element,IssmDouble enthalpy,IssmDouble pressure){/*{{{*/ @@ -1452,4 +1469,5 @@ int i,rheology_law; IssmDouble B_average,s_average,T_average=0.,P_average=0.; + IssmDouble n=3.0; int *doflist = NULL; IssmDouble *xyz_list = NULL; @@ -1477,4 +1495,5 @@ /*Get all inputs and parameters*/ + if(element->material->ObjectEnum()!=MatestarEnum) n=element->GetMaterialParameter(MaterialsRheologyNEnum); element->GetInputValue(&converged,ConvergedEnum); element->GetInputListOnNodes(&pressure[0],PressureEnum); @@ -1497,4 +1516,8 @@ /*Do nothing: B is not temperature dependent*/ break; + case BuddJackaEnum: + for(i=0;iAddInput(MaterialsRheologyBEnum,&B[0],element->GetElementType()); + break; case CuffeyEnum: for(i=0;iGetMaterialParameter(MaterialsRheologyNEnum)); + for(i=0;iAddInput(MaterialsRheologyBEnum,&B[0],element->GetElementType()); break; @@ -1511,9 +1534,9 @@ case ArrheniusEnum: element->GetVerticesCoordinates(&xyz_list); - for(i=0;iGetMaterialParameter(MaterialsRheologyNEnum)); + for(i=0;iAddInput(MaterialsRheologyBEnum,&B[0],element->GetElementType()); break; case LliboutryDuvalEnum: - for(i=0;iGetMaterialParameter(MaterialsRheologyNEnum),element->GetMaterialParameter(MaterialsBetaEnum),element->GetMaterialParameter(ConstantsReferencetemperatureEnum),element->GetMaterialParameter(MaterialsHeatcapacityEnum),element->GetMaterialParameter(MaterialsLatentheatEnum)); + for(i=0;iGetMaterialParameter(MaterialsBetaEnum),element->GetMaterialParameter(ConstantsReferencetemperatureEnum),element->GetMaterialParameter(MaterialsHeatcapacityEnum),element->GetMaterialParameter(MaterialsLatentheatEnum)); element->AddInput(MaterialsRheologyBEnum,&B[0],element->GetElementType()); break; Index: /issm/trunk/src/c/analyses/EnthalpyAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/EnthalpyAnalysis.h (revision 21728) +++ /issm/trunk/src/c/analyses/EnthalpyAnalysis.h (revision 21729) @@ -36,6 +36,7 @@ ElementVector* CreatePVectorShelf(Element* element); static void DrainWaterfraction(FemModel* femmodel); - static void DrainWaterfraction(Element* element, IssmDouble* pdrainrate_element); - static void DrainWaterfractionIcecolumn(Element* element); + static void ComputeWaterfractionDrainage(FemModel* femmodel); + static void DrainageUpdateWatercolumn(FemModel* femmodel); + static void DrainageUpdateEnthalpy(FemModel* femmodel); static IssmDouble EnthalpyDiffusionParameter(Element* element,IssmDouble enthalpy,IssmDouble pressure); static IssmDouble EnthalpyDiffusionParameterVolume(Element* element,int enthalpy_enum); Index: /issm/trunk/src/c/analyses/EnumToAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/EnumToAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/EnumToAnalysis.cpp (revision 21729) @@ -104,6 +104,6 @@ case UzawaPressureAnalysisEnum : return new UzawaPressureAnalysis(); #endif - #ifdef _HAVE_GIA_ - case GiaAnalysisEnum : return new GiaAnalysis(); + #ifdef _HAVE_GIAIVINS_ + case GiaIvinsAnalysisEnum : return new GiaIvinsAnalysis(); #endif #ifdef _HAVE_ESA_ Index: /issm/trunk/src/c/analyses/ExtrapolationAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/ExtrapolationAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/ExtrapolationAnalysis.cpp (revision 21729) @@ -84,12 +84,12 @@ /*Intermediaries */ - int dim, domaintype, extrapolationcase; - int i,row,col,stabilization; - bool extrapolatebydiffusion; - IssmDouble Jdet,D_scalar,h; - IssmDouble norm_dlsf; - IssmDouble hx,hy,hz,kappa; - IssmDouble* xyz_list = NULL; - Element* workelement=NULL; + bool extrapolatebydiffusion = true; + int dim, domaintype, extrapolationcase; + int i,row,col,stabilization; + IssmDouble Jdet,D_scalar,h; + IssmDouble norm_dlsf; + IssmDouble hx,hy,hz,kappa; + IssmDouble *xyz_list = NULL; + Element *workelement = NULL; /*Get problem case*/ @@ -102,10 +102,12 @@ case 1: case 2: case 3: workelement=element; break; } + /* get extrapolation dimension */ workelement->FindParam(&domaintype,DomainTypeEnum); switch(domaintype){ - case Domain2DverticalEnum: dim=1; break; + case Domain2DverticalEnum: dim=1; break; case Domain2DhorizontalEnum: dim=2; break; - case Domain3DEnum: dim=3; break; + case Domain3DEnum: dim=3; break; + default: _error_("not supported yet"); } @@ -117,7 +119,7 @@ IssmDouble* B = xNew(dim*numnodes); IssmDouble* Bprime = xNew(dim*numnodes); - IssmDouble* D = xNew(dim*dim); - IssmDouble* dlsf = xNew(dim); - IssmDouble* normal= xNew(dim); + IssmDouble* dlsf = xNew(dim); + IssmDouble* normal = xNew(dim); + IssmDouble* D = xNewZeroInit(dim*dim); /*Retrieve all inputs and parameters*/ @@ -126,7 +128,16 @@ workelement->GetVerticesCoordinates(&xyz_list); + /* In 3d we are going to extrude using horizontal diffusion. Since the layers are 3d, + * we change the geometry of the element to make it flat. That way, the diffusion is + * handled along the layers + */ + if(element->ObjectEnum()==PentaEnum){ + for(i=0;i<3;i++) xyz_list[3*i+2] = 0.; + for(i=3;i<6;i++) xyz_list[3*i+2] = 1.; + } + /* Start looping on the number of gaussian points: */ Gauss* gauss=workelement->NewGauss(2); - for(int ig=gauss->begin();igend();ig++){/*{{{*/ + for(int ig=gauss->begin();igend();ig++){ gauss->GaussPoint(ig); @@ -137,13 +148,8 @@ D_scalar=gauss->weight*Jdet; - extrapolatebydiffusion=true; if(extrapolatebydiffusion){ - /* diffuse values outward */ - for(row=0;rowvalues[0],1); - /* stabilization *//*{{{*/ + /* stabilization */ /* do not use streamline upwinding for extrapolation: it yields oscillating results due to diffusion along normal direction, but none across */ stabilization=1; @@ -200,7 +206,6 @@ &Ke->values[0],1); } - /*}}}*/ } - }/*}}}*/ + } /*Clean up and return*/ @@ -217,28 +222,6 @@ }/*}}}*/ ElementVector* ExtrapolationAnalysis::CreatePVector(Element* element){/*{{{*/ - - /*Intermediaries */ - Element* workelement=NULL; - - /*Get problem dimension*/ - int extrapolationcase=GetExtrapolationCase(element); - switch(extrapolationcase){ - case 0: - if(!element->IsOnBase()) return NULL; - workelement = element->SpawnBasalElement(); - break; - case 1: case 2: case 3: workelement=element; break; - } - - /*Fetch number of nodes */ - int numnodes = workelement->GetNumberOfNodes(); - - /*Initialize Element vector*/ - ElementVector* pe = workelement->NewElementVector(); - for(int i=0;ivalues[i]=0.; - - if(extrapolationcase==0){workelement->DeleteMaterials(); delete workelement;}; - return pe; + return NULL; + }/*}}}*/ void ExtrapolationAnalysis::GetB(IssmDouble* B,Element* element,IssmDouble* xyz_list,Gauss* gauss, int dim){/*{{{*/ @@ -326,12 +309,17 @@ int domaintype, extrapolationvariable; int extrapolationcase; + element->FindParam(&domaintype,DomainTypeEnum); switch(domaintype){ - case Domain2DverticalEnum: extrapolationcase=0; break; - case Domain2DhorizontalEnum: extrapolationcase=1;break; - case Domain3DEnum: + case Domain2DverticalEnum: extrapolationcase=0; break; + case Domain2DhorizontalEnum: extrapolationcase=1; break; + case Domain3DEnum: element->FindParam(&extrapolationvariable, ExtrapolationVariableEnum); - if(extrapolationvariable==ThicknessEnum) extrapolationcase=2; // scalar fields that are constant along z-axis - else extrapolationcase=3; // scalar fields that vary along z-axis + if(extrapolationvariable==ThicknessEnum){ + extrapolationcase=2; // scalar fields that are constant along z-axis + } + else{ + extrapolationcase=3; // scalar fields that vary along z-axis + } break; } Index: sm/trunk/src/c/analyses/GiaAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/GiaAnalysis.cpp (revision 21728) +++ (revision ) @@ -1,69 +1,0 @@ -#include "./GiaAnalysis.h" -#include "../toolkits/toolkits.h" -#include "../classes/classes.h" -#include "../shared/shared.h" -#include "../modules/modules.h" - -/*Model processing*/ -void GiaAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/ - /*No constraints*/ -}/*}}}*/ -void GiaAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/ - /*No loads*/ -}/*}}}*/ -void GiaAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel){/*{{{*/ - ::CreateNodes(nodes,iomodel,GiaAnalysisEnum,P1Enum); -}/*}}}*/ -int GiaAnalysis::DofsPerNode(int** doflist,int domaintype,int approximation){/*{{{*/ - return 1; -}/*}}}*/ -void GiaAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ - - /*Update elements: */ - int counter=0; - for(int i=0;inumberofelements;i++){ - if(iomodel->my_elements[i]){ - Element* element=(Element*)elements->GetObjectByOffset(counter); - element->Update(i,iomodel,analysis_counter,analysis_type,P1Enum); - counter++; - } - } - - iomodel->FetchDataToInput(elements,"md.geometry.thickness",ThicknessEnum); - iomodel->FetchDataToInput(elements,"md.gia.mantle_viscosity",GiaMantleViscosityEnum); - iomodel->FetchDataToInput(elements,"md.gia.lithosphere_thickness",GiaLithosphereThicknessEnum); - iomodel->FetchDataToInput(elements,"md.mask.ice_levelset",MaskIceLevelsetEnum); -}/*}}}*/ -void GiaAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ -}/*}}}*/ - -/*Finite Element Analysis*/ -void GiaAnalysis::Core(FemModel* femmodel){/*{{{*/ - _error_("not implemented"); -}/*}}}*/ -ElementVector* GiaAnalysis::CreateDVector(Element* element){/*{{{*/ - /*Default, return NULL*/ - return NULL; -}/*}}}*/ -ElementMatrix* GiaAnalysis::CreateJacobianMatrix(Element* element){/*{{{*/ -_error_("Not implemented"); -}/*}}}*/ -ElementMatrix* GiaAnalysis::CreateKMatrix(Element* element){/*{{{*/ - _error_("not implemented yet"); -}/*}}}*/ -ElementVector* GiaAnalysis::CreatePVector(Element* element){/*{{{*/ -_error_("not implemented yet"); -}/*}}}*/ -void GiaAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/ - _error_("not implemented yet"); -}/*}}}*/ -void GiaAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_index){/*{{{*/ - _error_("Not implemented yet"); -}/*}}}*/ -void GiaAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ - _error_("not implemented yet"); -}/*}}}*/ -void GiaAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ - /*Default, do nothing*/ - return; -}/*}}}*/ Index: sm/trunk/src/c/analyses/GiaAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/GiaAnalysis.h (revision 21728) +++ (revision ) @@ -1,33 +1,0 @@ -/*! \file GiaAnalysis.h - * \brief: header file for generic external result object - */ - -#ifndef _GiaAnalysis_ -#define _GiaAnalysis_ - -/*Headers*/ -#include "./Analysis.h" - -class GiaAnalysis: public Analysis{ - - public: - /*Model processing*/ - void CreateConstraints(Constraints* constraints,IoModel* iomodel); - void CreateLoads(Loads* loads, IoModel* iomodel); - void CreateNodes(Nodes* nodes,IoModel* iomodel); - int DofsPerNode(int** doflist,int domaintype,int approximation); - void UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type); - void UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum); - - /*Finite element Analysis*/ - void Core(FemModel* femmodel); - ElementVector* CreateDVector(Element* element); - ElementMatrix* CreateJacobianMatrix(Element* element); - ElementMatrix* CreateKMatrix(Element* element); - ElementVector* CreatePVector(Element* element); - void GetSolutionFromInputs(Vector* solution,Element* element); - void GradientJ(Vector* gradient,Element* element,int control_type,int control_index); - void InputUpdateFromSolution(IssmDouble* solution,Element* element); - void UpdateConstraints(FemModel* femmodel); -}; -#endif Index: /issm/trunk/src/c/analyses/GiaIvinsAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/GiaIvinsAnalysis.cpp (revision 21729) +++ /issm/trunk/src/c/analyses/GiaIvinsAnalysis.cpp (revision 21729) @@ -0,0 +1,69 @@ +#include "./GiaIvinsAnalysis.h" +#include "../toolkits/toolkits.h" +#include "../classes/classes.h" +#include "../shared/shared.h" +#include "../modules/modules.h" + +/*Model processing*/ +void GiaIvinsAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/ + /*No constraints*/ +}/*}}}*/ +void GiaIvinsAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/ + /*No loads*/ +}/*}}}*/ +void GiaIvinsAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel){/*{{{*/ + ::CreateNodes(nodes,iomodel,GiaIvinsAnalysisEnum,P1Enum); +}/*}}}*/ +int GiaIvinsAnalysis::DofsPerNode(int** doflist,int domaintype,int approximation){/*{{{*/ + return 1; +}/*}}}*/ +void GiaIvinsAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ + + /*Update elements: */ + int counter=0; + for(int i=0;inumberofelements;i++){ + if(iomodel->my_elements[i]){ + Element* element=(Element*)elements->GetObjectByOffset(counter); + element->Update(i,iomodel,analysis_counter,analysis_type,P1Enum); + counter++; + } + } + + iomodel->FetchDataToInput(elements,"md.geometry.thickness",ThicknessEnum); + iomodel->FetchDataToInput(elements,"md.gia.mantle_viscosity",GiaMantleViscosityEnum); + iomodel->FetchDataToInput(elements,"md.gia.lithosphere_thickness",GiaLithosphereThicknessEnum); + iomodel->FetchDataToInput(elements,"md.mask.ice_levelset",MaskIceLevelsetEnum); +}/*}}}*/ +void GiaIvinsAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ +}/*}}}*/ + +/*Finite Element Analysis*/ +void GiaIvinsAnalysis::Core(FemModel* femmodel){/*{{{*/ + _error_("not implemented"); +}/*}}}*/ +ElementVector* GiaIvinsAnalysis::CreateDVector(Element* element){/*{{{*/ + /*Default, return NULL*/ + return NULL; +}/*}}}*/ +ElementMatrix* GiaIvinsAnalysis::CreateJacobianMatrix(Element* element){/*{{{*/ +_error_("Not implemented"); +}/*}}}*/ +ElementMatrix* GiaIvinsAnalysis::CreateKMatrix(Element* element){/*{{{*/ + _error_("not implemented yet"); +}/*}}}*/ +ElementVector* GiaIvinsAnalysis::CreatePVector(Element* element){/*{{{*/ +_error_("not implemented yet"); +}/*}}}*/ +void GiaIvinsAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/ + _error_("not implemented yet"); +}/*}}}*/ +void GiaIvinsAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_index){/*{{{*/ + _error_("Not implemented yet"); +}/*}}}*/ +void GiaIvinsAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ + _error_("not implemented yet"); +}/*}}}*/ +void GiaIvinsAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ + /*Default, do nothing*/ + return; +}/*}}}*/ Index: /issm/trunk/src/c/analyses/GiaIvinsAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/GiaIvinsAnalysis.h (revision 21729) +++ /issm/trunk/src/c/analyses/GiaIvinsAnalysis.h (revision 21729) @@ -0,0 +1,33 @@ +/*! \file GiaIvinsAnalysis.h + * \brief: header file for generic external result object + */ + +#ifndef _GiaIvinsAnalysis_ +#define _GiaIvinsAnalysis_ + +/*Headers*/ +#include "./Analysis.h" + +class GiaIvinsAnalysis: public Analysis{ + + public: + /*Model processing*/ + void CreateConstraints(Constraints* constraints,IoModel* iomodel); + void CreateLoads(Loads* loads, IoModel* iomodel); + void CreateNodes(Nodes* nodes,IoModel* iomodel); + int DofsPerNode(int** doflist,int domaintype,int approximation); + void UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type); + void UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum); + + /*Finite element Analysis*/ + void Core(FemModel* femmodel); + ElementVector* CreateDVector(Element* element); + ElementMatrix* CreateJacobianMatrix(Element* element); + ElementMatrix* CreateKMatrix(Element* element); + ElementVector* CreatePVector(Element* element); + void GetSolutionFromInputs(Vector* solution,Element* element); + void GradientJ(Vector* gradient,Element* element,int control_type,int control_index); + void InputUpdateFromSolution(IssmDouble* solution,Element* element); + void UpdateConstraints(FemModel* femmodel); +}; +#endif Index: /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 21729) @@ -9,4 +9,5 @@ return 1; }/*}}}*/ + void HydrologyDCEfficientAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ @@ -33,7 +34,6 @@ iomodel->FetchData(&eplthickcomp,"md.hydrology.epl_thick_comp"); parameters->AddObject(new IntParam(HydrologydcEplThickCompEnum,eplthickcomp)); - - -}/*}}}*/ +}/*}}}*/ + void HydrologyDCEfficientAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ @@ -83,5 +83,7 @@ if(!isefficientlayer) return; - if(iomodel->domaintype!=Domain2DhorizontalEnum) iomodel->FetchData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); + if(iomodel->domaintype!=Domain2DhorizontalEnum){ + iomodel->FetchData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); + } ::CreateNodes(nodes,iomodel,HydrologyDCEfficientAnalysisEnum,P1Enum); iomodel->DeleteData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); @@ -104,14 +106,21 @@ void HydrologyDCEfficientAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/ - /*Nothing for now*/ - - /*Fetch parameters: */ + + /*Do we really want DC?*/ int hydrology_model; iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); if(hydrology_model!=HydrologydcEnum) return; - if(iomodel->domaintype==Domain3DEnum) iomodel->FetchData(1,"md.mesh.vertexonbase"); - - //create penalties for nodes: no node can have water above the max + /*Do we want an efficient layer*/ + bool isefficientlayer; + iomodel->FindConstant(&isefficientlayer,"md.hydrology.isefficientlayer"); + if(!isefficientlayer) return; + + /*Fetch parameters: */ + if(iomodel->domaintype==Domain3DEnum){ + iomodel->FetchData(1,"md.mesh.vertexonbase"); + } + + //Add moulin inputs as loads CreateSingleNodeToElementConnectivity(iomodel); for(int i=0;inumberofvertices;i++){ @@ -132,6 +141,6 @@ void HydrologyDCEfficientAnalysis::InitZigZagCounter(FemModel* femmodel){/*{{{*/ + int* eplzigzag_counter =NULL; - eplzigzag_counter=xNewZeroInit(femmodel->nodes->Size()); femmodel->parameters->AddObject(new IntVecParam(EplZigZagCounterEnum,eplzigzag_counter,femmodel->nodes->Size())); @@ -142,9 +151,6 @@ int* eplzigzag_counter=NULL; - Element* element=NULL; - femmodel->parameters->FindParam(&eplzigzag_counter,NULL,EplZigZagCounterEnum); for(int i=0;inodes->Size();i++){ - eplzigzag_counter[i]=0; } @@ -201,6 +207,7 @@ /* Intermediaries */ IssmDouble D_scalar,Jdet,dt; - IssmDouble epl_thickness; IssmDouble transfer; + IssmDouble epl_transmitivity; + IssmDouble epl_storing; IssmDouble *xyz_list = NULL; @@ -219,21 +226,18 @@ Input* epl_thick_input = basalelement->GetInput(HydrologydcEplThicknessEnum); _assert_(epl_thick_input); - Input* sed_head_input = basalelement->GetInput(SedimentHeadEnum); - Input* epl_head_input = basalelement->GetInput(EplHeadEnum); - Input* thick_input = basalelement->GetInput(ThicknessEnum); - Input* base_input = basalelement->GetInput(BaseEnum); - - IssmDouble epl_specificstoring = EplSpecificStoring(basalelement); - IssmDouble epl_conductivity = basalelement->GetMaterialParameter(HydrologydcEplConductivityEnum); + Input* epl_head_input = basalelement->GetInput(EplHeadEnum); _assert_(epl_head_input); + Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); /* Start looping on the number of gaussian points: */ - Gauss* gauss=basalelement->NewGauss(2); + Gauss* gauss = basalelement->NewGauss(2); for(int ig=gauss->begin();igend();ig++){ gauss ->GaussPoint(ig); basalelement ->JacobianDeterminant(&Jdet,xyz_list,gauss); - epl_thick_input ->GetInputValue(&epl_thickness,gauss); + + epl_transmitivity = EplTransmitivity(basalelement,gauss,epl_thick_input,epl_head_input,base_input); + epl_storing = EplStoring(basalelement,gauss,epl_thick_input,epl_head_input,base_input); /*Diffusivity*/ - D_scalar=epl_conductivity*epl_thickness*gauss->weight*Jdet; + D_scalar=epl_transmitivity*gauss->weight*Jdet; if(dt!=0.) D_scalar=D_scalar*dt; D[0][0]=D_scalar; @@ -248,5 +252,5 @@ if(dt!=0.){ basalelement->NodalFunctions(&basis[0],gauss); - D_scalar=epl_specificstoring*epl_thickness*gauss->weight*Jdet; + D_scalar=epl_storing*gauss->weight*Jdet; TripleMultiply(basis,numnodes,1,0, &D_scalar,1,1,0, @@ -256,5 +260,5 @@ /*Transfer EPL part*/ - transfer=GetHydrologyKMatrixTransfer(basalelement,gauss,sed_head_input,epl_head_input,thick_input,base_input); + transfer=GetHydrologyKMatrixTransfer(basalelement); D_scalar=dt*transfer*gauss->weight*Jdet; TripleMultiply(basis,numnodes,1,0, @@ -299,5 +303,5 @@ /*Check that all nodes are active, else return empty matrix*/ if(!active_element) { - if(domaintype!=Domain2DhorizontalEnum){ + if(domaintype!=Domain2DhorizontalEnum){ basalelement->DeleteMaterials(); delete basalelement; @@ -308,5 +312,5 @@ IssmDouble dt,scalar,water_head; IssmDouble water_load,transfer; - IssmDouble epl_thickness; + IssmDouble epl_storing; IssmDouble Jdet; IssmDouble residual,connectivity; @@ -328,38 +332,32 @@ Input* epl_thick_input = basalelement->GetInput(HydrologydcEplThicknessEnum); _assert_(epl_thick_input); - Input* sed_head_input = basalelement->GetInput(SedimentHeadEnum); - Input* epl_head_input = basalelement->GetInput(EplHeadEnum); - Input* thick_input = basalelement->GetInput(ThicknessEnum); - Input* base_input = basalelement->GetInput(BaseEnum); + Input* sed_head_input = basalelement->GetInput(SedimentHeadEnum); _assert_(sed_head_input); + Input* epl_head_input = basalelement->GetInput(EplHeadEnum); _assert_(epl_head_input); Input* water_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(water_input); - Input* residual_input = basalelement->GetInput(SedimentHeadResidualEnum); _assert_(residual_input); - if(dt!= 0.){old_wh_input = basalelement->GetInput(EplHeadOldEnum); _assert_(old_wh_input);} - - IssmDouble epl_specificstoring = EplSpecificStoring(basalelement); - + Input* residual_input = basalelement->GetInput(SedimentHeadResidualEnum); _assert_(residual_input); + Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); + + if(dt!= 0.){ + old_wh_input = basalelement->GetInput(EplHeadOldEnum); _assert_(old_wh_input); + } /* Start looping on the number of gaussian points: */ - Gauss* gauss=basalelement->NewGauss(2); + Gauss* gauss = basalelement->NewGauss(2); for(int ig=gauss->begin();igend();ig++){ gauss->GaussPoint(ig); - basalelement ->JacobianDeterminant(&Jdet,xyz_list,gauss); basalelement ->NodalFunctions(basis,gauss); - + epl_storing = EplStoring(basalelement,gauss,epl_thick_input,epl_head_input,base_input); /*Loading term*/ water_input->GetInputValue(&water_load,gauss); scalar = Jdet*gauss->weight*(water_load); if(dt!=0.) scalar = scalar*dt; - for(int i=0;ivalues[i]+=scalar*basis[i]; - } + for(int i=0;ivalues[i]+=scalar*basis[i]; /*Transient and transfer terms*/ if(dt!=0.){ - old_wh_input ->GetInputValue(&water_head,gauss); - epl_thick_input ->GetInputValue(&epl_thickness,gauss); - + old_wh_input->GetInputValue(&water_head,gauss); /*Dealing with the epl part of the transfer term*/ - transfer=GetHydrologyPVectorTransfer(basalelement,gauss,sed_head_input,epl_head_input,thick_input,base_input); - scalar = Jdet*gauss->weight*((water_head*epl_specificstoring*epl_thickness)+(dt*transfer)); + transfer=GetHydrologyPVectorTransfer(basalelement,gauss,sed_head_input); + scalar = Jdet*gauss->weight*((water_head*epl_storing)+(dt*transfer)); for(int i=0;ivalues[i]+=scalar*basis[i]; } @@ -371,11 +369,8 @@ for(int iv=0;ivGaussVertex(iv); - connectivity = IssmDouble(basalelement->VertexConnectivity(iv)); residual_input->GetInputValue(&residual,gauss); pe->values[iv]+=residual/connectivity; - - } - + } /*Clean up and return*/ xDelete(xyz_list); @@ -395,19 +390,21 @@ void HydrologyDCEfficientAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ - - bool active_element; - int domaintype,i; - Element* basalelement=NULL; - + /*Intermediaries*/ + bool active_element; + int domaintype; + Element* basalelement=NULL; + + /*Get basal element*/ element->FindParam(&domaintype,DomainTypeEnum); - - if(domaintype!=Domain2DhorizontalEnum){ - if(!element->IsOnBase()) return; - basalelement=element->SpawnBasalElement(); - } - else{ - basalelement = element; - } - + switch(domaintype){ + case Domain2DhorizontalEnum: + basalelement = element; + break; + case Domain3DEnum: + if(!element->IsOnBase()) return; + basalelement = element->SpawnBasalElement(); + break; + default: _error_("mesh "<(numnodes); IssmDouble* eplHeads = xNew(numnodes); - basalelement->GetDofList(&doflist,NoneApproximationEnum,GsetEnum); - basalelement->GetInputListOnVertices(&sedhead[0],SedimentHeadEnum); Input* active_element_input=basalelement->GetInput(HydrologydcMaskEplactiveEltEnum); _assert_(active_element_input); @@ -427,15 +421,23 @@ /*Use the dof list to index into the solution vector: */ - for(i=0;i(eplHeads[i])) _error_("NaN found in solution vector"); - if(xIsInf(eplHeads[i])) _error_("Inf found in solution vector"); + /*If the EPL is not active we revert to the bedrock elevation*/ + if(active_element){ + for(int i=0;i(eplHeads[i])) _error_("NaN found in solution vector"); + if(xIsInf(eplHeads[i])) _error_("Inf found in solution vector"); + } + } + else{ + basalelement->GetInputListOnVertices(&eplHeads[0],BaseEnum); + for(int i=0;i(eplHeads[i])) _error_("NaN found in solution vector"); + if(xIsInf(eplHeads[i])) _error_("Inf found in solution vector"); + } } /*Add input to the element: */ element->AddBasalInput(EplHeadEnum,eplHeads,P1Enum); - /*Free ressources:*/ xDelete(eplHeads); - xDelete(sedhead); xDelete(doflist); if(domaintype!=Domain2DhorizontalEnum){basalelement->DeleteMaterials(); delete basalelement;}; @@ -448,34 +450,33 @@ /*Intermediaries*/ -IssmDouble HydrologyDCEfficientAnalysis::EplSpecificStoring(Element* element){/*{{{*/ - IssmDouble rho_freshwater = element->GetMaterialParameter(MaterialsRhoFreshwaterEnum); - IssmDouble g = element->GetMaterialParameter(ConstantsGEnum); - IssmDouble epl_porosity = element->GetMaterialParameter(HydrologydcEplPorosityEnum); - IssmDouble epl_compressibility = element->GetMaterialParameter(HydrologydcEplCompressibilityEnum); - IssmDouble water_compressibility = element->GetMaterialParameter(HydrologydcWaterCompressibilityEnum); - return rho_freshwater*g*epl_porosity*(water_compressibility+(epl_compressibility/epl_porosity)); -}/*}}}*/ - -IssmDouble HydrologyDCEfficientAnalysis::SedimentStoring(Element* element){/*{{{*/ - IssmDouble rho_freshwater = element->GetMaterialParameter(MaterialsRhoFreshwaterEnum); - IssmDouble g = element->GetMaterialParameter(ConstantsGEnum); - IssmDouble sediment_porosity = element->GetMaterialParameter(HydrologydcSedimentPorosityEnum); - IssmDouble sediment_thickness = element->GetMaterialParameter(HydrologydcSedimentThicknessEnum); - IssmDouble sediment_compressibility = element->GetMaterialParameter(HydrologydcSedimentCompressibilityEnum); - IssmDouble water_compressibility = element->GetMaterialParameter(HydrologydcWaterCompressibilityEnum); - return rho_freshwater*g*sediment_porosity*sediment_thickness*(water_compressibility+(sediment_compressibility/sediment_porosity)); -}/*}}}*/ - -IssmDouble HydrologyDCEfficientAnalysis::GetHydrologyKMatrixTransfer(Element* element, Gauss* gauss, Input* sed_head_input, Input* epl_head_input, Input* thick_input, Input* base_input){/*{{{*/ +IssmDouble HydrologyDCEfficientAnalysis::GetHydrologyKMatrixTransfer(Element* element){/*{{{*/ int transfermethod; - IssmDouble hmax; - IssmDouble epl_head,sediment_head; IssmDouble leakage,transfer; - IssmDouble continuum, factor; - HydrologyDCInefficientAnalysis* inefanalysis = NULL; element->FindParam(&transfermethod,HydrologydcTransferFlagEnum); - + /*Switch between the different transfer methods cases*/ + switch(transfermethod){ + case 0: + /*Just keepping the transfer to zero*/ + transfer=0.0; + break; + case 1: + element->FindParam(&leakage,HydrologydcLeakageFactorEnum); + transfer=leakage; + break; + default: + _error_("no case higher than 1 for the Transfer method"); + } + return transfer; +}/*}}}*/ + +IssmDouble HydrologyDCEfficientAnalysis::GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* sed_head_input){/*{{{*/ + + int transfermethod; + IssmDouble sediment_head; + IssmDouble leakage,transfer; + + element->FindParam(&transfermethod,HydrologydcTransferFlagEnum); /*Switch between the different transfer methods cases*/ switch(transfermethod){ @@ -486,66 +487,7 @@ case 1: _assert_(sed_head_input); - _assert_(epl_head_input); - - inefanalysis = new HydrologyDCInefficientAnalysis(); - hmax = inefanalysis->GetHydrologyDCInefficientHmax(element,gauss,thick_input,base_input); - delete inefanalysis; - sed_head_input->GetInputValue(&sediment_head,gauss); - epl_head_input->GetInputValue(&epl_head,gauss); element->FindParam(&leakage,HydrologydcLeakageFactorEnum); - - //Computing continuum function to apply to transfer term, transfer is null only if - // epl_head>sediment_head AND sediment_head>h_max - //let's try without that for a while - /* continuum=((1.0/(1.0+exp(-20.0*(sediment_head-epl_head)))))+(1.0/(1.0+exp(-20.0*(hmax-sediment_head)))); */ - /* factor=min(continuum,1.0); */ - /* transfer=leakage*factor; */ - transfer=leakage; - break; - default: - _error_("no case higher than 1 for the Transfer method"); - } - return transfer; -}/*}}}*/ - -IssmDouble HydrologyDCEfficientAnalysis::GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* sed_head_input, Input* epl_head_input, Input* thick_input, Input* base_input){/*{{{*/ - - int transfermethod; - IssmDouble hmax; - IssmDouble epl_head,sediment_head; - IssmDouble leakage,transfer; - IssmDouble continuum, factor; - - HydrologyDCInefficientAnalysis* inefanalysis = NULL; - - element->FindParam(&transfermethod,HydrologydcTransferFlagEnum); - - /*Switch between the different transfer methods cases*/ - switch(transfermethod){ - case 0: - /*Just keepping the transfer to zero*/ - transfer=0.0; - break; - case 1: - _assert_(sed_head_input); - _assert_(epl_head_input); - - inefanalysis = new HydrologyDCInefficientAnalysis(); - hmax = inefanalysis->GetHydrologyDCInefficientHmax(element,gauss,thick_input,base_input); - delete inefanalysis; - - sed_head_input->GetInputValue(&sediment_head,gauss); - epl_head_input->GetInputValue(&epl_head,gauss); - element->FindParam(&leakage,HydrologydcLeakageFactorEnum); - - //Computing continuum function to apply to transfer term, transfer is null only if - // epl_head>sediment_head AND sediment_head>h_max - //let's try without that for a while - /* continuum=((1.0/(1.0+exp(-20.0*(sediment_head-epl_head)))))+(1.0/(1.0+exp(-20.0*(hmax-sediment_head)))); */ - /* factor=min(continuum,1.0); */ - /* transfer=sediment_head*leakage*factor; */ transfer=sediment_head*leakage; - break; default: @@ -564,13 +506,12 @@ IssmDouble EPLgrad2; IssmDouble EPL_N; - femmodel->parameters->FindParam(&domaintype,DomainTypeEnum); + femmodel->parameters->FindParam(&iseplthickcomp,HydrologydcEplThickCompEnum); + if(iseplthickcomp==0) return; for(int j=0;jelements->Size();j++){ Element* element=(Element*)femmodel->elements->GetObjectByOffset(j); - element->parameters->FindParam(&iseplthickcomp,HydrologydcEplThickCompEnum); - if(iseplthickcomp==0) return; switch(domaintype){ @@ -619,5 +560,4 @@ if(!active_element){ - /*Keeping thickness to initial value if EPL is not active*/ for(int i=0;imax_thick){ @@ -691,5 +624,4 @@ bool active_element; - int i,j; int domaintype; IssmDouble h_max; @@ -716,4 +648,5 @@ IssmDouble* eplhead =xNew(numnodes); IssmDouble* residual =xNew(numnodes); + IssmDouble* base =xNew(numnodes); IssmDouble init_thick =basalelement->GetMaterialParameter(HydrologydcEplInitialThicknessEnum); @@ -728,36 +661,45 @@ basalelement-> GetInputListOnVertices(&eplhead[0],EplHeadEnum); basalelement-> GetInputListOnVertices(&residual[0],SedimentHeadResidualEnum); + basalelement-> GetInputListOnVertices(&base[0],BaseEnum); /*Get minimum sediment head of the element*/ sedheadmin=sedhead[0]; - for(i=1;i0.){ + for(int i=1;inodes[i]); + /*If mask was already one, keep one or colapse*/ + if(old_active[i]>0.){ vec_mask->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); - if(old_active[i]==0.) recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); - } - /*If mask was already one, keep one or colapse*/ - else if(old_active[i]>0.){ - vec_mask->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); - /*If epl thickness gets under colapse thickness, close the layer*/ + /* If epl thickness gets under colapse thickness, close the layer */ if(epl_thickness[i]SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); } + /* //If epl head gets under base elevation, close the layer */ + /* else if(eplhead[i]<(base[i]-1.0e-8)){ */ + /* vec_mask->SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); */ + /* recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); */ + /* } */ + } + /*If node is now closed bring its thickness back to initial*/ + if (old_active[i]==0.){ + epl_thickness[i]=init_thick; + /*Activate if we have a residual from sediment*/ + if(residual[i]>0.){ + vec_mask->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + if(old_active[i]==0.){ + recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + } + } } /*Increase of the efficient system is needed if the epl head reach the maximum value (sediment max value for now)*/ - GetHydrologyDCInefficientHmax(&h_max,basalelement,basalelement->nodes[i]); if(eplhead[i]>=h_max && active_element){ - for(j=0;jSetValue(basalelement->nodes[j]->Sid(),1.,INS_VAL); - if(old_active[i]==0.) recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + if(old_active[j]==0.){ + recurence->SetValue(basalelement->nodes[j]->Sid(),1.,INS_VAL); + } } } @@ -772,8 +714,57 @@ xDelete(eplhead); xDelete(residual); + xDelete(base); } /*}}}*/ - -void HydrologyDCEfficientAnalysis::HydrologyEPLGetActive(Vector* active_vec, Element* element){ +IssmDouble HydrologyDCEfficientAnalysis::EplStoring(Element* element,Gauss* gauss, Input* epl_thick_input, Input* epl_head_input, Input* base_input){/*{{{*/ + IssmDouble epl_storing; + IssmDouble water_sheet,storing; + IssmDouble epl_thickness,prestep_head,base_elev; + IssmDouble rho_freshwater = element->GetMaterialParameter(MaterialsRhoFreshwaterEnum); + IssmDouble g = element->GetMaterialParameter(ConstantsGEnum); + IssmDouble epl_porosity = element->GetMaterialParameter(HydrologydcEplPorosityEnum); + IssmDouble epl_compressibility = element->GetMaterialParameter(HydrologydcEplCompressibilityEnum); + IssmDouble water_compressibility = element->GetMaterialParameter(HydrologydcWaterCompressibilityEnum); + + epl_thick_input->GetInputValue(&epl_thickness,gauss); + epl_head_input->GetInputValue(&prestep_head,gauss); + base_input->GetInputValue(&base_elev,gauss); + water_sheet=max(0.0,(prestep_head-base_elev)); + + storing=rho_freshwater*g*epl_porosity*epl_thickness*(water_compressibility+(epl_compressibility/epl_porosity)); + + /* //porosity for unconfined region */ + /* if (water_sheet<=0.9*epl_thickness){ */ + /* epl_storing=epl_porosity; */ + /* } */ + /* //continuity ramp */ + /* else if((water_sheet0.9*epl_thickness)){ */ + /* epl_storing=(epl_thickness-water_sheet)*(epl_porosity-storing)/(0.1*epl_thickness)+storing; */ + /* } */ + /* //storing coefficient for confined */ + /* else{ */ + /* epl_storing=storing; */ + /* } */ + /* return epl_storing; */ + return storing; +}/*}}}*/ + +IssmDouble HydrologyDCEfficientAnalysis::EplTransmitivity(Element* element,Gauss* gauss, Input* epl_thick_input, Input* epl_head_input, Input* base_input){/*{{{*/ + IssmDouble epl_transmitivity; + IssmDouble water_sheet; + IssmDouble epl_thickness,base_elev,prestep_head; + IssmDouble epl_conductivity = element->GetMaterialParameter(HydrologydcEplConductivityEnum); + epl_thick_input->GetInputValue(&epl_thickness,gauss); + epl_head_input->GetInputValue(&prestep_head,gauss); + base_input->GetInputValue(&base_elev,gauss); + + water_sheet=max(0.0,(prestep_head-base_elev)); + + epl_transmitivity=epl_conductivity*epl_thickness; + //epl_transmitivity=max(1.0e-6,(epl_conductivity*min(water_sheet,epl_thickness))); + return epl_transmitivity; +}/*}}}*/ + +void HydrologyDCEfficientAnalysis::HydrologyEPLGetActive(Vector* active_vec, Element* element){/*{{{*/ /*Constants*/ int domaintype; @@ -796,8 +787,8 @@ IssmDouble flag = 0.; IssmDouble* active = xNew(numnodes); + bool active_element; /*Pass the activity mask from elements to nodes*/ basalelement->GetInputListOnVertices(&active[0],HydrologydcMaskEplactiveNodeEnum); - bool active_element; Input* active_element_input=basalelement->GetInput(HydrologydcMaskEplactiveEltEnum); _assert_(active_element_input); active_element_input->GetInputValue(&active_element); @@ -823,4 +814,5 @@ xDelete(active); } +/*}}}*/ void HydrologyDCEfficientAnalysis::GetHydrologyDCInefficientHmax(IssmDouble* ph_max,Element* element, Node* innode){/*{{{*/ Index: /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.h (revision 21728) +++ /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.h (revision 21729) @@ -36,8 +36,8 @@ /*Intermediaries*/ void GetB(IssmDouble* B,Element* element,IssmDouble* xyz_list,Gauss* gauss); - IssmDouble EplSpecificStoring(Element* element); - IssmDouble SedimentStoring(Element* element); - IssmDouble GetHydrologyKMatrixTransfer(Element* element, Gauss* gauss, Input* sed_head_input, Input* epl_head_input, Input* thick_input, Input* base_input); - IssmDouble GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* sed_head_input, Input* epl_head_input, Input* thick_input, Input* base_input); + IssmDouble GetHydrologyKMatrixTransfer(Element* element); + IssmDouble GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* sed_head_input); + IssmDouble EplStoring(Element* element,Gauss* gauss, Input* epl_thick_input, Input* epl_head_input, Input* base_input); + IssmDouble EplTransmitivity(Element* element,Gauss* gauss, Input* epl_thick_input, Input* epl_head_input, Input* base_input); void HydrologyEPLGetMask(Vector* vec_mask, Vector* recurence, int* eplzigzag_counter, Element* element); void HydrologyEPLGetActive(Vector* active_vec, Element* element); Index: /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 21729) @@ -19,8 +19,8 @@ int hydro_maxiter; bool isefficientlayer; + IssmDouble penalty_factor; + IssmDouble rel_tol; + IssmDouble leakagefactor; IssmDouble sedimentlimit; - IssmDouble penalty_factor; - IssmDouble leakagefactor; - IssmDouble rel_tol; /*retrieve some parameters: */ @@ -30,30 +30,28 @@ if(hydrology_model!=HydrologydcEnum) return; - iomodel->FetchData(&isefficientlayer, "md.hydrology.isefficientlayer"); iomodel->FetchData(&sedimentlimit_flag, "md.hydrology.sedimentlimit_flag" ); iomodel->FetchData(&transfer_flag, "md.hydrology.transfer_flag" ); iomodel->FetchData(&penalty_factor, "md.hydrology.penalty_factor" ); + iomodel->FetchData(&isefficientlayer, "md.hydrology.isefficientlayer"); + iomodel->FetchData(&hydro_maxiter, "md.hydrology.max_iter" ); + iomodel->FetchData(&penalty_lock, "md.hydrology.penalty_lock" ); iomodel->FetchData(&rel_tol, "md.hydrology.rel_tol" ); - iomodel->FetchData(&penalty_lock, "md.hydrology.penalty_lock" ); - iomodel->FetchData(&hydro_maxiter, "md.hydrology.max_iter" ); - + + parameters->AddObject(new IntParam(HydrologyModelEnum,hydrology_model)); + parameters->AddObject(new IntParam(HydrologydcSedimentlimitFlagEnum,sedimentlimit_flag)); + parameters->AddObject(new IntParam(HydrologydcTransferFlagEnum,transfer_flag)); + parameters->AddObject(new IntParam(HydrologydcPenaltyLockEnum,penalty_lock)); + parameters->AddObject(new IntParam(HydrologydcMaxIterEnum,hydro_maxiter)); + parameters->AddObject(new BoolParam(HydrologydcIsefficientlayerEnum,isefficientlayer)); + parameters->AddObject(new DoubleParam(HydrologydcPenaltyFactorEnum,penalty_factor)); + parameters->AddObject(new DoubleParam(HydrologydcRelTolEnum,rel_tol)); + if(transfer_flag==1){ + iomodel->FetchData(&leakagefactor,"md.hydrology.leakage_factor"); + parameters->AddObject(new DoubleParam(HydrologydcLeakageFactorEnum,leakagefactor)); + } if(sedimentlimit_flag==1){ iomodel->FetchData(&sedimentlimit,"md.hydrology.sedimentlimit"); parameters->AddObject(new DoubleParam(HydrologydcSedimentlimitEnum,sedimentlimit)); } - - if(transfer_flag==1){ - iomodel->FetchData(&leakagefactor,"md.hydrology.leakage_factor"); - parameters->AddObject(new DoubleParam(HydrologydcLeakageFactorEnum,leakagefactor)); - } - - parameters->AddObject(new DoubleParam(HydrologydcPenaltyFactorEnum,penalty_factor)); - parameters->AddObject(new IntParam(HydrologyModelEnum,hydrology_model)); - parameters->AddObject(new BoolParam(HydrologydcIsefficientlayerEnum,isefficientlayer)); - parameters->AddObject(new IntParam(HydrologydcSedimentlimitFlagEnum,sedimentlimit_flag)); - parameters->AddObject(new IntParam(HydrologydcTransferFlagEnum,transfer_flag)); - parameters->AddObject(new DoubleParam(HydrologydcRelTolEnum,rel_tol)); - parameters->AddObject(new IntParam(HydrologydcPenaltyLockEnum,penalty_lock)); - parameters->AddObject(new IntParam(HydrologydcMaxIterEnum,hydro_maxiter)); }/*}}}*/ @@ -109,5 +107,7 @@ if(hydrology_model!=HydrologydcEnum) return; - if(iomodel->domaintype!=Domain2DhorizontalEnum) iomodel->FetchData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); + if(iomodel->domaintype!=Domain2DhorizontalEnum){ + iomodel->FetchData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); + } ::CreateNodes(nodes,iomodel,HydrologyDCInefficientAnalysisEnum,P1Enum); iomodel->DeleteData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); @@ -131,6 +131,7 @@ if(hydrology_model!=HydrologydcEnum) return; - if(iomodel->domaintype==Domain3DEnum) iomodel->FetchData(1,"md.mesh.vertexonbase"); - + if(iomodel->domaintype==Domain3DEnum){ + iomodel->FetchData(1,"md.mesh.vertexonbase"); + } //create penalties for nodes: no node can have water above the max CreateSingleNodeToElementConnectivity(iomodel); @@ -190,5 +191,5 @@ IssmDouble D_scalar,Jdet,dt; IssmDouble sediment_transmitivity; - IssmDouble transfer; + IssmDouble transfer,sediment_storing; IssmDouble *xyz_list = NULL; @@ -211,9 +212,6 @@ Input* SedTrans_input = basalelement->GetInput(HydrologydcSedimentTransmitivityEnum); _assert_(SedTrans_input); Input* sed_head_input = basalelement->GetInput(SedimentHeadEnum); - Input* epl_head_input = basalelement->GetInput(EplHeadEnum); - Input* thick_input = basalelement->GetInput(ThicknessEnum); Input* base_input = basalelement->GetInput(BaseEnum); - IssmDouble sediment_storing = SedimentStoring(basalelement); /*Transfer related Inputs*/ if(isefficientlayer){ @@ -226,5 +224,8 @@ gauss -> GaussPoint(ig); basalelement -> JacobianDeterminant(&Jdet,xyz_list,gauss); - SedTrans_input -> GetInputValue(&sediment_transmitivity,gauss); + + sediment_transmitivity = SedimentTransmitivity(basalelement,gauss,sed_head_input,base_input,SedTrans_input); + sediment_storing = SedimentStoring(basalelement,gauss,sed_head_input,base_input); + /*Diffusivity*/ D_scalar=sediment_transmitivity*gauss->weight*Jdet; @@ -251,5 +252,5 @@ active_element_input->GetInputValue(&active_element); if(active_element){ - transfer=GetHydrologyKMatrixTransfer(basalelement,gauss,sed_head_input,epl_head_input,thick_input,base_input); + transfer=GetHydrologyKMatrixTransfer(basalelement); basalelement->NodalFunctions(&basis[0],gauss); D_scalar=dt*transfer*gauss->weight*Jdet; @@ -292,5 +293,5 @@ /*Intermediaries */ bool active_element,isefficientlayer; - IssmDouble dt,scalar; + IssmDouble dt,scalar,sediment_storing; IssmDouble water_head; IssmDouble water_load,transfer; @@ -298,6 +299,6 @@ IssmDouble *xyz_list = NULL; - Input* old_wh_input = NULL; Input* active_element_input = NULL; + Input* old_wh_input = NULL; /*Fetch number of nodes and dof for this finite element*/ @@ -313,13 +314,11 @@ basalelement->FindParam(&isefficientlayer,HydrologydcIsefficientlayerEnum); - Input* sed_head_input = basalelement->GetInput(SedimentHeadEnum); - Input* epl_head_input = basalelement->GetInput(EplHeadEnum); - Input* thick_input = basalelement->GetInput(ThicknessEnum); - Input* base_input = basalelement->GetInput(BaseEnum); - Input* water_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(water_input); - if(dt!= 0.){old_wh_input = basalelement->GetInput(SedimentHeadOldEnum); _assert_(old_wh_input);} - - IssmDouble sediment_storing = SedimentStoring(basalelement); - + Input* sed_head_input = basalelement->GetInput(SedimentHeadEnum); + Input* epl_head_input = basalelement->GetInput(EplHeadEnum); + Input* base_input = basalelement->GetInput(BaseEnum); + Input* water_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(water_input); + if(dt!= 0.){ + old_wh_input = basalelement->GetInput(SedimentHeadOldEnum); _assert_(old_wh_input); + } /*Transfer related Inputs*/ if(isefficientlayer){ @@ -331,5 +330,4 @@ for(int ig=gauss->begin();igend();ig++){ gauss->GaussPoint(ig); - basalelement->JacobianDeterminant(&Jdet,xyz_list,gauss); basalelement->NodalFunctions(basis,gauss); @@ -347,5 +345,5 @@ /*if EPL is present and active input is there not here*/ active_element_input->GetInputValue(&active_element); - if(!active_element){ + if(!active_element){ water_input->GetInputValue(&water_load,gauss); scalar = Jdet*gauss->weight*(water_load); @@ -356,12 +354,14 @@ } } + /*Transient and transfer terms*/ if(dt!=0.){ - old_wh_input ->GetInputValue(&water_head,gauss); + old_wh_input->GetInputValue(&water_head,gauss); + sediment_storing = SedimentStoring(basalelement,gauss,sed_head_input,base_input); if(isefficientlayer){ /*Dealing with the sediment part of the transfer term*/ active_element_input->GetInputValue(&active_element); if(active_element){ - transfer=GetHydrologyPVectorTransfer(basalelement,gauss,sed_head_input,epl_head_input,thick_input,base_input); + transfer=GetHydrologyPVectorTransfer(basalelement,gauss,epl_head_input); } else{ @@ -423,17 +423,23 @@ void HydrologyDCInefficientAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ - int domaintype; - bool converged; - int* doflist=NULL; - Element* basalelement=NULL; - + /*Intermediaries*/ + int domaintype; + Element* basalelement=NULL; + bool converged; + int* doflist = NULL; + + /*Get basal element*/ element->FindParam(&domaintype,DomainTypeEnum); - if(domaintype!=Domain2DhorizontalEnum){ - if(!element->IsOnBase()) return; - basalelement=element->SpawnBasalElement(); - } - else{ - basalelement = element; - } + switch(domaintype){ + case Domain2DhorizontalEnum: + basalelement = element; + break; + case Domain3DEnum: + if(!element->IsOnBase()) return; + basalelement = element->SpawnBasalElement(); + break; + default: _error_("mesh "<GetNode(i)); if(values[i]>h_max) { @@ -483,5 +488,6 @@ } //adding base in min to take into account heads under bed wich don't change N - pressure[i]=(rho_ice*g*thickness[i])-(rho_freshwater*g*(max((min(h_max,values[i])-base[i]),0.0))); + //pressure[i]=(rho_ice*g*thickness[i])-(rho_freshwater*g*(max((min(h_max,values[i])-base[i]),0.0))); + pressure[i]=(rho_ice*g*thickness[i])-(rho_freshwater*g*(values[i]-base[i])); } xDelete(thickness); @@ -507,6 +513,8 @@ }/*}}}*/ -/*Intermediaries*/ -IssmDouble HydrologyDCInefficientAnalysis::SedimentStoring(Element* element){/*{{{*/ +IssmDouble HydrologyDCInefficientAnalysis::SedimentStoring(Element* element,Gauss* gauss,Input* sed_head_input, Input* base_input){/*{{{*/ + IssmDouble sediment_storing; + IssmDouble storing; + IssmDouble base_elev,prestep_head,water_sheet; IssmDouble rho_freshwater = element->GetMaterialParameter(MaterialsRhoFreshwaterEnum); IssmDouble g = element->GetMaterialParameter(ConstantsGEnum); @@ -515,52 +523,33 @@ IssmDouble sediment_compressibility = element->GetMaterialParameter(HydrologydcSedimentCompressibilityEnum); IssmDouble water_compressibility = element->GetMaterialParameter(HydrologydcWaterCompressibilityEnum); - return rho_freshwater*g*sediment_porosity*sediment_thickness*(water_compressibility+(sediment_compressibility/sediment_porosity)); -}/*}}}*/ - -IssmDouble HydrologyDCInefficientAnalysis::EplSpecificStoring(Element* element){/*{{{*/ - IssmDouble rho_freshwater = element->GetMaterialParameter(MaterialsRhoFreshwaterEnum); - IssmDouble g = element->GetMaterialParameter(ConstantsGEnum); - IssmDouble epl_porosity = element->GetMaterialParameter(HydrologydcEplPorosityEnum); - IssmDouble epl_compressibility = element->GetMaterialParameter(HydrologydcEplCompressibilityEnum); - IssmDouble water_compressibility = element->GetMaterialParameter(HydrologydcWaterCompressibilityEnum); - return rho_freshwater*g*epl_porosity*(water_compressibility+(epl_compressibility/epl_porosity)); -}/*}}}*/ - -IssmDouble HydrologyDCInefficientAnalysis::GetHydrologyDCInefficientHmax(Element* element, Gauss* gauss, Input* thick_input, Input* base_input){/*{{{*/ - int hmax_flag; - IssmDouble h_max; - IssmDouble rho_ice,rho_water; - IssmDouble thickness,bed; - /*Get the flag to the limitation method*/ - element->FindParam(&hmax_flag,HydrologydcSedimentlimitFlagEnum); + base_input->GetInputValue(&base_elev,gauss); + sed_head_input->GetInputValue(&prestep_head,gauss); + water_sheet=max(0.0,(prestep_head-(base_elev-sediment_thickness))); + + storing=rho_freshwater*g*sediment_porosity*sediment_thickness*(water_compressibility+(sediment_compressibility/sediment_porosity)); - /*Switch between the different cases*/ - switch(hmax_flag){ - case 0: - h_max=1.0e+10; - break; - case 1: - element->FindParam(&h_max,HydrologydcSedimentlimitEnum); - break; - case 2: - - rho_water = element->GetMaterialParameter(MaterialsRhoFreshwaterEnum); - rho_ice = element->GetMaterialParameter(MaterialsRhoIceEnum); - - _assert_(thick_input); - _assert_(base_input); - - /*Compute max*/ - thick_input->GetInputValue(&thickness,gauss); - base_input->GetInputValue(&bed,gauss); - h_max=((rho_ice*thickness)/rho_water)+bed; - break; - case 3: - _error_("Using normal stress not supported yet"); - break; - default: - _error_("no case higher than 3 for SedimentlimitFlag"); - } - return h_max; + //Heavyside approximation (1/(1+exp(-2kx))) with k=25 centering at thickness minus 1% + sediment_storing=(sediment_porosity*exp(-20.*(water_sheet-0.99*sediment_thickness))+storing)/(1+exp(-20.*(water_sheet-0.99*sediment_thickness))); + + return sediment_storing; +}/*}}}*/ + +IssmDouble HydrologyDCInefficientAnalysis::SedimentTransmitivity(Element* element,Gauss* gauss,Input* sed_head_input, Input* base_input,Input* SedTrans_input){/*{{{*/ + IssmDouble sediment_transmitivity; + IssmDouble FullLayer_transmitivity; + IssmDouble base_elev,prestep_head,water_sheet; + IssmDouble sediment_thickness = element->GetMaterialParameter(HydrologydcSedimentThicknessEnum); + base_input->GetInputValue(&base_elev,gauss); + sed_head_input->GetInputValue(&prestep_head,gauss); + SedTrans_input->GetInputValue(&FullLayer_transmitivity,gauss); + water_sheet=max(0.0,(prestep_head-(base_elev-sediment_thickness))); + + if (water_sheet<=sediment_thickness){ + sediment_transmitivity=FullLayer_transmitivity*water_sheet/sediment_thickness; + } + else{ + sediment_transmitivity=FullLayer_transmitivity; + } + return sediment_transmitivity; }/*}}}*/ @@ -601,12 +590,8 @@ /*}}}*/ -IssmDouble HydrologyDCInefficientAnalysis::GetHydrologyKMatrixTransfer(Element* element, Gauss* gauss, Input* sed_head_input, Input* epl_head_input, Input* thick_input, Input* base_input){/*{{{*/ +IssmDouble HydrologyDCInefficientAnalysis::GetHydrologyKMatrixTransfer(Element* element){/*{{{*/ int transfermethod; - IssmDouble hmax; - IssmDouble epl_head,sediment_head; IssmDouble leakage,transfer; - IssmDouble continuum, factor; - element->FindParam(&transfermethod,HydrologydcTransferFlagEnum); @@ -618,21 +603,6 @@ break; case 1: - _assert_(sed_head_input); - _assert_(epl_head_input); - - sed_head_input->GetInputValue(&sediment_head,gauss); - epl_head_input->GetInputValue(&epl_head,gauss); element->FindParam(&leakage,HydrologydcLeakageFactorEnum); - - hmax=GetHydrologyDCInefficientHmax(element, gauss, thick_input, base_input); - - //Computing continuum function to apply to transfer term, transfer is null only if - //epl_head>sediment_head AND sediment_head>h_max - //let's try without that for a while - /* continuum=((1.0/(1.0+exp(-20.0*(sediment_head-epl_head)))))+(1.0/(1.0+exp(-20.0*(hmax-sediment_head)))); */ - /* factor=min(continuum,1.0); */ - /* transfer=leakage*factor; */ transfer=leakage; - break; default: @@ -642,12 +612,9 @@ }/*}}}*/ -IssmDouble HydrologyDCInefficientAnalysis::GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* sed_head_input, Input* epl_head_input, Input* thick_input, Input* base_input){/*{{{*/ +IssmDouble HydrologyDCInefficientAnalysis::GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* epl_head_input){/*{{{*/ int transfermethod; - IssmDouble hmax; - IssmDouble epl_head,sediment_head; + IssmDouble epl_head; IssmDouble leakage,transfer; - IssmDouble continuum, factor; - element->FindParam(&transfermethod,HydrologydcTransferFlagEnum); @@ -659,22 +626,8 @@ break; case 1: - _assert_(sed_head_input); _assert_(epl_head_input); - - sed_head_input->GetInputValue(&sediment_head,gauss); epl_head_input->GetInputValue(&epl_head,gauss); element->FindParam(&leakage,HydrologydcLeakageFactorEnum); - - hmax=GetHydrologyDCInefficientHmax(element, gauss, thick_input, base_input); - - //Computing continuum function to apply to transfer term, transfer is null only if - //epl_head>sediment_head AND sediment_head>h_max - //let's try without that for a while - /* continuum=((1.0/(1.0+exp(-20.0*(sediment_head-epl_head)))))+(1.0/(1.0+exp(-20.0*(hmax-sediment_head)))); */ - /* factor=min(continuum,1.0); */ - /* transfer=epl_head*leakage*factor; */ - transfer=epl_head*leakage; - break; default: Index: /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.h =================================================================== --- /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.h (revision 21728) +++ /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.h (revision 21729) @@ -34,10 +34,9 @@ /*Intermediaries*/ void GetB(IssmDouble* B,Element* element,IssmDouble* xyz_list,Gauss* gauss); - IssmDouble SedimentStoring(Element* element); - IssmDouble EplSpecificStoring(Element* element); - IssmDouble GetHydrologyDCInefficientHmax(Element* element, Gauss* gauss, Input* thickness_input, Input* base_input); + IssmDouble SedimentStoring(Element* element, Gauss* gauss, Input* sed_head_input, Input* base_input); + IssmDouble SedimentTransmitivity(Element* element,Gauss* gauss,Input* sed_head_input, Input* base_input,Input* SedTrans_input); void GetHydrologyDCInefficientHmax(IssmDouble* ph_max,Element* element, Node* innode); - IssmDouble GetHydrologyKMatrixTransfer(Element* element, Gauss* gauss, Input* sed_head_input, Input* epl_head_input, Input* thick_input, Input* base_input); - IssmDouble GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* sed_head_input, Input* epl_head_input, Input* thick_input, Input* base_input); + IssmDouble GetHydrologyKMatrixTransfer(Element* element); + IssmDouble GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* epl_head_input); void ElementizeEplMask(FemModel* femmodel); }; Index: /issm/trunk/src/c/analyses/HydrologySommersAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/HydrologySommersAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/HydrologySommersAnalysis.cpp (revision 21729) @@ -120,6 +120,6 @@ iomodel->FetchDataToInput(elements,"md.initialization.vx",VxEnum); iomodel->FetchDataToInput(elements,"md.initialization.vy",VyEnum); - //iomodel->FetchDataToInput(elements,"md.hydrology.eff_pressure",EffectivePressureEnum); iomodel->FindConstant(&frictionlaw,"md.friction.law"); + /*Friction law variables*/ switch(frictionlaw){ @@ -147,4 +147,6 @@ parameters->AddObject(new IntParam(HydrologyModelEnum,hydrology_model)); parameters->AddObject(iomodel->CopyConstantObject("md.friction.law",FrictionLawEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.relaxation",HydrologyRelaxationEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.hydrology.storage",HydrologyStorageEnum)); }/*}}}*/ @@ -172,4 +174,5 @@ ElementMatrix* Ke = element->NewElementMatrix(); IssmDouble* dbasis = xNew(2*numnodes); + IssmDouble* basis = xNew(numnodes); /*Retrieve all inputs and parameters*/ @@ -178,7 +181,9 @@ /*Get conductivity from inputs*/ IssmDouble conductivity = GetConductivity(element); -//if(element->Id()==1){ -// printf("Conductivity at CreateKMatrix: %g \n",conductivity); -//} + + /*Get englacial storage coefficient*/ + IssmDouble storage,dt; + element->FindParam(&storage,HydrologyStorageEnum); + element->FindParam(&dt,TimesteppingTimeStepEnum); /* Start looping on the number of gaussian points: */ @@ -189,8 +194,10 @@ element->JacobianDeterminant(&Jdet,xyz_list,gauss); element->NodalFunctionsDerivatives(dbasis,xyz_list,gauss); + element->NodalFunctions(basis,gauss); for(int i=0;ivalues[i*numnodes+j] += conductivity*gauss->weight*Jdet*(dbasis[0*numnodes+i]*dbasis[0*numnodes+j] + dbasis[1*numnodes+i]*dbasis[1*numnodes+j]); + Ke->values[i*numnodes+j] += conductivity*gauss->weight*Jdet*(dbasis[0*numnodes+i]*dbasis[0*numnodes+j] + dbasis[1*numnodes+i]*dbasis[1*numnodes+j]) + + gauss->weight*Jdet*storage/dt*basis[i]*basis[j]; } } @@ -245,7 +252,9 @@ /*Get conductivity from inputs*/ IssmDouble conductivity = GetConductivity(element); -//if(element->Id()==1){ -// printf("Conductivity in CreatePVector: %g \n",conductivity); -//} + + /*Get englacial storage coefficient*/ + IssmDouble storage,dt; + element->FindParam(&storage,HydrologyStorageEnum); + element->FindParam(&dt,TimesteppingTimeStepEnum); /*Build friction element, needed later: */ @@ -306,11 +315,12 @@ meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1])-PMPheat); _assert_(meltrate>0.); - + for(int i=0;ivalues[i]+=Jdet*gauss->weight* ( meltrate*(1/rho_water-1/rho_ice) - +A*pow(fabs(pressure_ice - pressure_water_old),n-1)*(pressure_ice - pressure_water_old)*gap + +A*pow(fabs(pressure_ice - pressure_water),n-1)*(pressure_ice - pressure_water)*gap -beta*sqrt(vx*vx+vy*vy) +ieb + +storage*head_old/dt )*basis[i]; } @@ -354,4 +364,10 @@ element->GetInputListOnNodes(&bed[0],BaseEnum); + /*Get head from previous time-step and under-relaxation coefficient to use in under-relaxation for nonlinear convergence*/ + IssmDouble* head_old = xNew(numnodes); + element->GetInputListOnNodes(&head_old[0],HydrologyHeadEnum); + IssmDouble relaxation; + element->FindParam(&relaxation,HydrologyRelaxationEnum); + /*Use the dof list to index into the solution vector: */ for(int i=0;iAddInput(HydrologyReynoldsEnum,&reynolds,P0Enum); - /*Free ressources:*/ + /*Free resources:*/ xDelete(values); xDelete(thickness); @@ -395,4 +414,5 @@ xDelete(doflist); xDelete(eff_pressure); + xDelete(head_old); }/*}}}*/ void HydrologySommersAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ @@ -445,4 +465,5 @@ IssmDouble* xyz_list = NULL; IssmDouble dpressure_water[2],dbed[2],PMPheat; + IssmDouble q = 0.; /*Retrieve all inputs and parameters*/ @@ -468,7 +489,5 @@ /*Get conductivity from inputs*/ IssmDouble conductivity = GetConductivity(element); -//if(element->Id()==1){ -// printf("Conductivity at gap update: %g \n",conductivity); -//} + /*Build friction element, needed later: */ Friction* friction=new Friction(element,2); @@ -533,9 +552,12 @@ )); totalweights +=gauss->weight*Jdet; + + /* Compute basal water flux */ + q += gauss->weight*Jdet*(conductivity*sqrt(dh[0]*dh[0]+dh[1]*dh[1])); } /*Divide by connectivity*/ newgap = newgap/totalweights; - IssmDouble mingap = 1e-5; + IssmDouble mingap = 1e-6; if(newgapthickness) newgap = thickness; - /*Add new gap as an input*/ element->AddInput(HydrologyGapHeightEnum,&newgap,P0Enum); + + /*Divide by connectivity, add basal flux as an input*/ + q = q/totalweights; + element->AddInput(HydrologyBasalFluxEnum,&q,P0Enum); /*Clean up and return*/ Index: /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 21729) @@ -61,5 +61,4 @@ break; case CalvingDevEnum: - iomodel->FetchDataToInput(elements,"md.calving.coeff",CalvingdevCoeffEnum); iomodel->FetchDataToInput(elements,"md.calving.meltingrate",CalvingMeltingrateEnum); break; @@ -75,4 +74,5 @@ parameters->AddObject(iomodel->CopyConstantObject("md.levelset.stabilization",LevelsetStabilizationEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.levelset.reinit_frequency",LevelsetReinitFrequencyEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.levelset.calving_max",CalvingMaxEnum)); int calvinglaw; iomodel->FindConstant(&calvinglaw,"md.calving.law"); @@ -80,5 +80,8 @@ case DefaultCalvingEnum: case CalvingLevermannEnum: + break; case CalvingDevEnum: + parameters->AddObject(iomodel->CopyConstantObject("md.calving.stress_threshold_groundedice",CalvingStressThresholdGroundediceEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.calving.stress_threshold_floatingice",CalvingStressThresholdFloatingiceEnum)); break; case CalvingMinthicknessEnum: @@ -138,5 +141,6 @@ IssmDouble h,hx,hy,hz; IssmDouble vel; - IssmDouble norm_dlsf, norm_calving, calvingrate, meltingrate; + IssmDouble norm_dlsf, norm_calving, calvingrate, meltingrate, groundedice; + IssmDouble calvingmax; IssmDouble* xyz_list = NULL; @@ -152,4 +156,6 @@ } + /*Calving threshold*/ + /*Fetch number of nodes and dof for this finite element*/ int numnodes = basalelement->GetNumberOfNodes(); @@ -170,4 +176,5 @@ basalelement->GetVerticesCoordinates(&xyz_list); basalelement->FindParam(&dt,TimesteppingTimeStepEnum); + basalelement->FindParam(&calvingmax,CalvingMaxEnum); Input* vx_input = NULL; Input* vy_input = NULL; @@ -178,4 +185,5 @@ Input* calvingrate_input = NULL; Input* meltingrate_input = NULL; + Input* gr_input = NULL; /*Load velocities*/ @@ -187,8 +195,10 @@ vx_input=basalelement->GetInput(VxEnum); _assert_(vx_input); vy_input=basalelement->GetInput(VyEnum); _assert_(vy_input); + gr_input=basalelement->GetInput(MaskGroundediceLevelsetEnum); _assert_(gr_input); break; case Domain3DEnum: vx_input=basalelement->GetInput(VxAverageEnum); _assert_(vx_input); vy_input=basalelement->GetInput(VyAverageEnum); _assert_(vy_input); + gr_input=basalelement->GetInput(MaskGroundediceLevelsetEnum); _assert_(gr_input); break; default: _error_("mesh "<GetInputValue(&v[0],gauss); vy_input->GetInputValue(&v[1],gauss); + gr_input->GetInputValue(&groundedice,gauss); /*Get calving speed*/ @@ -262,4 +273,9 @@ calvingrate_input->GetInputValue(&calvingrate,gauss); meltingrate_input->GetInputValue(&meltingrate,gauss); + + /*Limit calving rate to c <= v + 3 km/yr */ + vel=sqrt(v[0]*v[0] + v[1]*v[1]); + if(calvingrate>calvingmax+vel) calvingrate = vel+calvingmax; + if(groundedice<0) meltingrate = 0.; norm_dlsf=0.; Index: /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 21729) @@ -267,20 +267,8 @@ element->FindParam(&domaintype,DomainTypeEnum); element->FindParam(&stabilization,MasstransportStabilizationEnum); - Input* vxaverage_input=NULL; + Input* vxaverage_input=element->GetInput(VxAverageEnum); _assert_(vxaverage_input); Input* vyaverage_input=NULL; - if(domaintype==Domain2DhorizontalEnum){ - vxaverage_input=element->GetInput(VxEnum); _assert_(vxaverage_input); - vyaverage_input=element->GetInput(VyEnum); _assert_(vyaverage_input); - } - else{ - if(dim==1){ - vxaverage_input=element->GetInput(VxAverageEnum); _assert_(vxaverage_input); - } - if(dim==2){ - vxaverage_input=element->GetInput(VxAverageEnum); _assert_(vxaverage_input); - vyaverage_input=element->GetInput(VyAverageEnum); _assert_(vyaverage_input); - } - - } + if(dim==2) vyaverage_input=element->GetInput(VyAverageEnum); _assert_(vyaverage_input); + h = element->CharacteristicLength(); @@ -406,14 +394,6 @@ element->FindParam(&dt,TimesteppingTimeStepEnum); element->FindParam(&domaintype,DomainTypeEnum); - Input* vxaverage_input=NULL; - Input* vyaverage_input=NULL; - if(domaintype==Domain2DhorizontalEnum){ - vxaverage_input=element->GetInput(VxEnum); _assert_(vxaverage_input); - vyaverage_input=element->GetInput(VyEnum); _assert_(vyaverage_input); - } - else{ - vxaverage_input=element->GetInput(VxAverageEnum); _assert_(vxaverage_input); - vyaverage_input=element->GetInput(VyAverageEnum); _assert_(vyaverage_input); - } + Input* vxaverage_input=element->GetInput(VxAverageEnum); _assert_(vxaverage_input); + Input* vyaverage_input=element->GetInput(VyAverageEnum); _assert_(vyaverage_input); /* Start looping on the number of gaussian points: */ Index: /issm/trunk/src/c/analyses/SealevelriseAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/SealevelriseAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/SealevelriseAnalysis.cpp (revision 21729) @@ -73,4 +73,7 @@ parameters->AddObject(iomodel->CopyConstantObject("md.slr.tide_love_h",SealevelriseTidalLoveHEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.slr.tide_love_k",SealevelriseTidalLoveKEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.slr.fluid_love",SealevelriseFluidLoveEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.slr.equatorial_moi",SealevelriseEquatorialMoiEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.slr.polar_moi",SealevelrisePolarMoiEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.slr.angular_velocity",SealevelriseAngularVelocityEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.slr.ocean_area_scaling",SealevelriseOceanAreaScalingEnum)); Index: /issm/trunk/src/c/analyses/SmbAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 21729) @@ -105,4 +105,11 @@ iomodel->FetchDataToInput(elements,"md.smb.b_neg",SmbBNegEnum); break; + case SMBgradientselaEnum: + iomodel->FetchDataToInput(elements,"md.smb.ela",SmbElaEnum); + iomodel->FetchDataToInput(elements,"md.smb.b_pos",SmbBPosEnum); + iomodel->FetchDataToInput(elements,"md.smb.b_neg",SmbBNegEnum); + iomodel->FetchDataToInput(elements,"md.smb.b_max",SmbBMaxEnum); + iomodel->FetchDataToInput(elements,"md.smb.b_min",SmbBMinEnum); + break; case SMBhenningEnum: iomodel->FetchDataToInput(elements,"md.smb.smbref",SmbSmbrefEnum,0.); @@ -212,7 +219,11 @@ parameters->AddObject(iomodel->CopyConstantObject("md.smb.dpermil",SmbDpermilEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.f",SmbFEnum)); } break; case SMBgradientsEnum: + /*Nothing to add to parameters*/ + break; + case SMBgradientselaEnum: /*Nothing to add to parameters*/ break; @@ -282,4 +293,8 @@ SmbGradientsx(femmodel); break; + case SMBgradientselaEnum: + if(VerboseSolution())_printf0_(" call smb gradients ela module\n"); + SmbGradientsElax(femmodel); + break; case SMBhenningEnum: if(VerboseSolution())_printf0_(" call smb Henning module\n"); Index: /issm/trunk/src/c/analyses/StressbalanceAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/StressbalanceAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/StressbalanceAnalysis.cpp (revision 21729) @@ -823,4 +823,11 @@ iomodel->FetchDataToInput(elements,"md.friction.q",FrictionQEnum); break; + case 9: + iomodel->FetchDataToInput(elements,"md.initialization.temperature",TemperatureEnum); + iomodel->FetchDataToInput(elements,"md.friction.coefficient",FrictionCoefficientEnum); + iomodel->FetchDataToInput(elements,"md.friction.pressure_adjusted_temperature",FrictionPressureAdjustedTemperatureEnum); + InputUpdateFromConstantx(elements,1.,FrictionPEnum); + InputUpdateFromConstantx(elements,1.,FrictionQEnum); + break; default: _error_("not supported"); @@ -888,4 +895,5 @@ if(frictionlaw==3) parameters->AddObject(iomodel->CopyConstantObject("md.friction.coupling",FrictionCouplingEnum)); if(frictionlaw==5) parameters->AddObject(iomodel->CopyConstantObject("md.friction.f",FrictionFEnum)); + if(frictionlaw==9) parameters->AddObject(iomodel->CopyConstantObject("md.friction.gamma",FrictionGammaEnum)); }/*}}}*/ @@ -1301,5 +1309,5 @@ /*build friction object, used later on: */ - Friction* friction=new Friction(element,1); + Friction* friction=new Friction(element,dim); /*Recover portion of element that is grounded*/ @@ -2330,5 +2338,5 @@ /*build friction object, used later on: */ - Friction* friction=new Friction(element,2); + Friction* friction=new Friction(element,dim==3?2:1); /*Recover portion of element that is grounded*/ @@ -3045,5 +3053,5 @@ IssmDouble rho_water = element->GetMaterialParameter(MaterialsRhoSeawaterEnum); IssmDouble gravity = element->GetMaterialParameter(ConstantsGEnum); - Input* surface_input = element->GetInput(SurfaceEnum); _assert_(surface_input); + Input* base_input = element->GetInput(BaseEnum); _assert_(base_input); /* Start looping on the number of gaussian points: */ @@ -3052,5 +3060,5 @@ gauss->GaussPoint(ig); - surface_input->GetInputDerivativeValue(&slope[0],xyz_list,gauss); + base_input->GetInputDerivativeValue(&slope[0],xyz_list,gauss); element->NodalFunctionsVelocity(vbasis,gauss); element->JacobianDeterminantBase(&Jdet,xyz_list_base,gauss); @@ -3898,6 +3906,5 @@ int i,dim; - IssmDouble Jdet,water_pressure,bed; - IssmDouble normal[3]; + IssmDouble Jdet,water_pressure,base; IssmDouble *xyz_list_base = NULL; @@ -3936,20 +3943,11 @@ element->NodalFunctionsVelocity(vbasis,gauss); - element->NormalBase(&normal[0],xyz_list_base); - _assert_(normal[dim-1]<0.); - base_input->GetInputValue(&bed, gauss); - water_pressure=gravity*rho_water*bed; + base_input->GetInputValue(&base, gauss); + water_pressure=gravity*rho_water*base; for(i=0;ivalues[i*dim+0] += water_pressure*gauss->weight*Jdet*vbasis[i]*normal[0]; - pe->values[i*dim+1] += water_pressure*gauss->weight*Jdet*vbasis[i]*normal[1]; - if(dim==3){ - pe->values[i*dim+2]+=water_pressure*gauss->weight*Jdet*vbasis[i]*normal[2]; - } - } - } - - /*Transform coordinate system*/ - element->TransformLoadVectorCoord(pe,cs_list); + pe->values[i*dim+(dim-1)]+=-water_pressure*gauss->weight*Jdet*vbasis[i]; + } + } /* shelf dampening*/ @@ -3958,5 +3956,5 @@ if(shelf_dampening) { Input* mb_input=element->GetInput(BasalforcingsFloatingiceMeltingRateEnum); _assert_(mb_input); - IssmDouble dt,mb,normal_b; + IssmDouble dt,mb; element->FindParam(&dt,TimesteppingTimeStepEnum); for(int ig=gauss->begin();igend();ig++){ @@ -3964,13 +3962,12 @@ element->JacobianDeterminantBase(&Jdet,xyz_list_base,gauss); element->NodalFunctionsVelocity(vbasis,gauss); - element->NormalBase(&normal[0],xyz_list_base); - if (dim==2) normal_b=normal[1]; - else if (dim==3) normal_b=sqrt(normal[0]*normal[0]+normal[1]*normal[1]); mb_input->GetInputValue(&mb, gauss); for(i=0;ivalues[i*dim+1] += dt*rho_water*gravity*mb*gauss->weight*Jdet*vbasis[i]*normal_b; + pe->values[i*dim+(dim-1)] += -dt*rho_water*gravity*mb*gauss->weight*Jdet*vbasis[i]; } } } + + /*DO NOT Transform Coordinate System: this stiffness matrix is already expressed in tangential coordinates*/ /*Clean up and return*/ Index: /issm/trunk/src/c/analyses/StressbalanceSIAAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/StressbalanceSIAAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/StressbalanceSIAAnalysis.cpp (revision 21729) @@ -381,4 +381,5 @@ ub=0.; vb=0.; + break; default: _error_("Not supported yet"); Index: /issm/trunk/src/c/analyses/ThermalAnalysis.cpp =================================================================== --- /issm/trunk/src/c/analyses/ThermalAnalysis.cpp (revision 21728) +++ /issm/trunk/src/c/analyses/ThermalAnalysis.cpp (revision 21729) @@ -9,5 +9,7 @@ /*Intermediary*/ - int finiteelement = P1Enum; + int finiteelement; + iomodel->FindConstant(&finiteelement,"md.thermal.fe"); + _assert_(finiteelement==P1Enum); /*Only 3d mesh supported*/ @@ -62,5 +64,7 @@ void ThermalAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel){/*{{{*/ - int finiteelement = P1Enum; + int finiteelement; + iomodel->FindConstant(&finiteelement,"md.thermal.fe"); + _assert_(finiteelement==P1Enum); if(iomodel->domaintype==Domain3DEnum) iomodel->FetchData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); @@ -73,5 +77,5 @@ void ThermalAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ - int frictionlaw,basalforcing_model; + int frictionlaw,basalforcing_model,materialstype; int FrictionCoupling; /*Now, is the model 3d? otherwise, do nothing: */ @@ -79,5 +83,7 @@ /*Update elements: */ - int finiteelement = P1Enum; + int finiteelement; + iomodel->FindConstant(&finiteelement,"md.thermal.fe"); + _assert_(finiteelement==P1Enum); int counter=0; for(int i=0;inumberofelements;i++){ @@ -93,4 +99,5 @@ iomodel->FindConstant(&ismovingfront,"md.transient.ismovingfront"); iomodel->FindConstant(&frictionlaw,"md.friction.law"); + iomodel->FindConstant(&materialstype,"md.materials.type"); iomodel->FetchDataToInput(elements,"md.geometry.thickness",ThicknessEnum); @@ -106,6 +113,4 @@ iomodel->FetchDataToInput(elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum); iomodel->FetchDataToInput(elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); - iomodel->FetchDataToInput(elements,"md.materials.rheology_B",MaterialsRheologyBEnum); - iomodel->FetchDataToInput(elements,"md.materials.rheology_n",MaterialsRheologyNEnum); iomodel->FetchDataToInput(elements,"md.initialization.pressure",PressureEnum); iomodel->FetchDataToInput(elements,"md.initialization.temperature",TemperatureEnum); @@ -116,4 +121,25 @@ InputUpdateFromConstantx(elements,0.,VyMeshEnum); InputUpdateFromConstantx(elements,0.,VzMeshEnum); + + /*Rheology type*/ + iomodel->FetchDataToInput(elements,"md.materials.rheology_B",MaterialsRheologyBEnum); + switch(materialstype){ + case MatenhancediceEnum: + iomodel->FetchDataToInput(elements,"md.materials.rheology_n",MaterialsRheologyNEnum); + iomodel->FetchDataToInput(elements,"md.materials.rheology_E",MaterialsRheologyEEnum); + break; + case MatdamageiceEnum: + iomodel->FetchDataToInput(elements,"md.materials.rheology_n",MaterialsRheologyNEnum); + break; + case MatestarEnum: + iomodel->FetchDataToInput(elements,"md.materials.rheology_Ec",MaterialsRheologyEcEnum); + iomodel->FetchDataToInput(elements,"md.materials.rheology_Es",MaterialsRheologyEsEnum); + break; + case MaticeEnum: + iomodel->FetchDataToInput(elements,"md.materials.rheology_n",MaterialsRheologyNEnum); + break; + default: + _error_("not supported"); + } if(ismovingfront){ iomodel->FetchDataToInput(elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum); // required for updating active nodes @@ -722,4 +748,5 @@ int *doflist = NULL; IssmDouble *xyz_list = NULL; + IssmDouble n=3.0; bool hack = false; @@ -756,4 +783,5 @@ /*Get all inputs and parameters*/ + if(element->material->ObjectEnum()!=MatestarEnum) n=element->GetMaterialParameter(MaterialsRheologyNEnum); element->GetInputValue(&converged,ConvergedEnum); if(converged){ @@ -767,4 +795,8 @@ case NoneEnum: /*Do nothing: B is not temperature dependent*/ + break; + case BuddJackaEnum: + for(i=0;iAddInput(MaterialsRheologyBEnum,&B[0],element->GetElementType()); break; case CuffeyEnum: @@ -778,5 +810,5 @@ case ArrheniusEnum:{ element->GetVerticesCoordinates(&xyz_list); - for(i=0;iGetMaterialParameter(MaterialsRheologyNEnum)); + for(i=0;iAddInput(MaterialsRheologyBEnum,&B[0],element->GetElementType()); break; Index: /issm/trunk/src/c/analyses/analyses.h =================================================================== --- /issm/trunk/src/c/analyses/analyses.h (revision 21728) +++ /issm/trunk/src/c/analyses/analyses.h (revision 21729) @@ -23,5 +23,5 @@ #include "./FreeSurfaceBaseAnalysis.h" #include "./FreeSurfaceTopAnalysis.h" -#include "./GiaAnalysis.h" +#include "./GiaIvinsAnalysis.h" #include "./EsaAnalysis.h" #include "./HydrologyDCEfficientAnalysis.h" Index: /issm/trunk/src/c/bamg/BamgMesh.cpp =================================================================== --- /issm/trunk/src/c/bamg/BamgMesh.cpp (revision 21728) +++ /issm/trunk/src/c/bamg/BamgMesh.cpp (revision 21729) @@ -8,5 +8,4 @@ this->EdgesSize[0]=0, this->EdgesSize[1]=0; this->Edges=NULL; this->TrianglesSize[0]=0, this->TrianglesSize[1]=0; this->Triangles=NULL; - this->QuadrilateralsSize[0]=0, this->QuadrilateralsSize[1]=0; this->Quadrilaterals=NULL; this->SubDomainsSize[0]=0, this->SubDomainsSize[1]=0; this->SubDomains=NULL; @@ -33,5 +32,4 @@ xDelete(this->Edges); xDelete(this->Triangles); - xDelete(this->Quadrilaterals); xDelete(this->SubDomains); Index: /issm/trunk/src/c/bamg/BamgMesh.h =================================================================== --- /issm/trunk/src/c/bamg/BamgMesh.h (revision 21728) +++ /issm/trunk/src/c/bamg/BamgMesh.h (revision 21729) @@ -16,6 +16,4 @@ int TrianglesSize[2]; double* Triangles; - int QuadrilateralsSize[2]; - double* Quadrilaterals; int VerticesOnGeomVertexSize[2]; Index: /issm/trunk/src/c/bamg/BamgQuadtree.cpp =================================================================== --- /issm/trunk/src/c/bamg/BamgQuadtree.cpp (revision 21728) +++ /issm/trunk/src/c/bamg/BamgQuadtree.cpp (revision 21729) @@ -8,45 +8,9 @@ namespace bamg { - /*MACROS {{{*/ - /* - * - * J j - * ^ ^ - * | | +--------+--------+ - * | | | | | - * 1X | | | 2 | 3 | - * | | | | | - * | | +--------+--------+ - * | | | | | - * 0X | | | 0 | 1 | - * | | | | | - * | | +--------+--------+ - * | +-----------------------> i - * | - * |----------------------------> I - * X0 X1 - * - * box 0 -> I=0 J=0 IJ=00 = 0 - * box 1 -> I=1 J=0 IJ=01 = 1 - * box 2 -> I=0 J=1 IJ=10 = 2 - * box 3 -> I=1 J=1 IJ=11 = 3 - */ -#define INTER_SEG(a,b,x,y) (((y) > (a)) && ((x) <(b))) #define ABS(i) ((i)<0 ?-(i) :(i)) -#define MAX1(i,j) ((i)>(j) ?(i) :(j)) -#define NORM(i1,j1,i2,j2) MAX1(ABS((i1)-(j1)),ABS((i2)-(j2))) - - //IJ(i,j,l) returns the box number of i and j with respect to l - //if !j&l and !i&l -> 0 (box zero: lower left ) - //if !j&l and i&l -> 1 (box one: lower right) - //if j&l and !i&l -> 2 (box two: upper left ) - //if j&l and i&l -> 3 (box three:upper right) -#define IJ(i,j,l) ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 )) - - //I_IJ(k,l) returns l if first bit of k is 1, else 0 -#define I_IJ(k,l) ((k&1) ? l:0) - //J_IJ(k,l) returns l if second bit of k is 1, else 0 -#define J_IJ(k,l) ((k&2) ? l:0) - /*}}}*/ +#define MAXDEPTH 30 +#define MAXISIZE 1073741824 //2^30 +#define MAXICOORD 1073741823 //2^30 - 1 = =111...111 (29 times one) + /*DOCUMENTATION What is a BamgQuadtree? {{{ * A Quadtree is a very simple way to group vertices according @@ -100,34 +64,35 @@ BamgQuadtree::BamgQuadtree(){/*{{{*/ - /*Number of boxes and vertices*/ - NbBamgQuadtreeBox=0; - NbVertices=0; + /*Initialize fields*/ + this->NbQuadtreeBox = 0; + this->NbVertices = 0; /*Create container*/ - boxcontainer=new DataSet(); + this->boxcontainer=new DataSet(); /*Create Root, pointer toward the main box*/ - root=NewBamgQuadtreeBox(); - - } - /*}}}*/ + this->root=NewBamgQuadtreeBox(); + + } /*}}}*/ BamgQuadtree::BamgQuadtree(Mesh * t,long nbv){ /*{{{*/ - /*Number of boxes and vertices*/ - NbBamgQuadtreeBox=0; - NbVertices=0; + /*Initialize fields*/ + this->NbQuadtreeBox = 0; + this->NbVertices = 0; /*Create container*/ - boxcontainer=new DataSet(); + this->boxcontainer=new DataSet(); /*Create Root, pointer toward the main box*/ - root=NewBamgQuadtreeBox(); + this->root=NewBamgQuadtreeBox(); /*Check Sizes*/ - _assert_(MaxISize>MaxICoor); + _assert_(MAXISIZE>MAXICOORD); /*Add all vertices of the mesh*/ - if (nbv==-1) nbv=t->nbv; - for (int i=0;ivertices[i]); + if(nbv==-1) nbv=t->nbv; + for(int i=0;iAdd(t->vertices[i]); + } } @@ -140,5 +105,5 @@ /*Methods*/ - void BamgQuadtree::Add(BamgVertex &w){/*{{{*/ + void BamgQuadtree::Add(BamgVertex &w){/*{{{*/ /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/Add)*/ BamgQuadtreeBox** pb=NULL; @@ -149,5 +114,5 @@ /*Initialize level*/ - long level=MaxISize; + long level=MAXISIZE; /*Get inital box (the largest)*/ @@ -164,5 +129,5 @@ //Get next subbox according to the bit value (level) - pb = &b->b[IJ(i,j,level)]; + pb = &b->box[BoxNumber(i,j,level)]; } @@ -176,5 +141,5 @@ } - /*check that l is not 0 (this should not happen as MaxDepth = 30)*/ + /*check that l is not 0 (this should not happen as MAXDEPTH = 30)*/ _assert_(level>0); @@ -195,5 +160,5 @@ /*Initialize the 4 pointers toward the 4 subboxes*/ - b->b[0]=b->b[1]=b->b[2]=b->b[3]=NULL; + b->box[0]=b->box[1]=b->box[2]=b->box[3]=NULL; /*level = 0010000 -> 0001000*/ @@ -205,8 +170,8 @@ int ij; /*bb is the new "sub"box of b where v4[k] is located*/ - BamgQuadtreeBox *bb = b->b[ij=IJ(v4[k]->i.x,v4[k]->i.y,level)]; + BamgQuadtreeBox *bb = b->box[ij=BoxNumber(v4[k]->i.x,v4[k]->i.y,level)]; // alloc the BamgQuadtreeBox - if (!bb) bb=b->b[ij]=NewBamgQuadtreeBox(); + if (!bb) bb=b->box[ij]=NewBamgQuadtreeBox(); /*Copy the current vertex*/ @@ -215,5 +180,5 @@ /*Get the subbox where w (i,j) is located*/ - pb = &b->b[IJ(i,j,level)]; + pb = &b->box[BoxNumber(i,j,level)]; } @@ -228,48 +193,79 @@ } /*}}}*/ - BamgVertex* BamgQuadtree::NearestVertex(Icoor1 i,Icoor1 j) {/*{{{*/ - /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/NearestVertex)*/ - - /*Intermediaries*/ - BamgQuadtreeBox *pb[MaxDepth]; - int pi[MaxDepth]; - Icoor1 ii[MaxDepth]; - Icoor1 jj[MaxDepth]; - int level; - long n0; - BamgQuadtreeBox *b; - long h0; - long h = MaxISize; - long hb= MaxISize; - Icoor1 i0=0,j0=0; + int BamgQuadtree::BoxNumber(int i,int j,int l){/*{{{*/ + /* + * + * J j + * ^ ^ + * | | +--------+--------+ + * | | | | | + * 1X | | | 2 | 3 | + * | | | | | + * | | +--------+--------+ + * | | | | | + * 0X | | | 0 | 1 | + * | | | | | + * | | +--------+--------+ + * | +-----------------------> i + * | + * |----------------------------> I + * X0 X1 + * + * box 0 -> I=0 J=0 BoxNumber=00 = 0 + * box 1 -> I=1 J=0 BoxNumber=01 = 1 + * box 2 -> I=0 J=1 BoxNumber=10 = 2 + * box 3 -> I=1 J=1 BoxNumber=11 = 3 + */ + //BoxNumber(i,j,l) returns the box number of i and j with respect to l + //if !j&l and !i&l -> 0 (box zero: lower left ) + //if !j&l and i&l -> 1 (box one: lower right) + //if j&l and !i&l -> 2 (box two: upper left ) + //if j&l and i&l -> 3 (box three:upper right) + return ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 )); + }/*}}}*/ + bool BamgQuadtree::Intersection(int a,int b,int x,int y){/*{{{*/ + /*is [x y] in [a b]*/ + return ((y) > (a)) && ((x) <(b)); + }/*}}}*/ + BamgVertex* BamgQuadtree::NearestVertex(int xi,int yi) {/*{{{*/ /*initial output as NULL (no vertex found)*/ BamgVertex* nearest_v=NULL; - /*Project w coordinates (i,j) onto [0,MaxISize-1] x [0,MaxISize-1] -> (iplus,jplus)*/ - Icoor1 iplus( inbitems) return nearest_v; + if(!this->root->nbitems) return nearest_v; + + /*Project coordinates (xi,yi) onto [0,MAXICOORD-1] x [0,MAXICOORD-1]*/ + int xi2 = xi; + int yi2 = yi; + if(xi<0) xi2 = 0; + if(xi>MAXISIZE) xi2 = MAXICOORD; + if(yi<0) yi2 = 0; + if(yi>MAXISIZE) yi2 = MAXICOORD; + + /*Get inital box (the largest)*/ + BamgQuadtreeBox* b = this->root; + + /*Initialize level and sizes for largest box*/ + int levelbin = (1L<nbitems)<0){ - - Icoor1 hb2 = hb >> 1; //size of the current box - int k = IJ(iplus,jplus,hb2); //box number (0,1,2 or 3) - BamgQuadtreeBox *b0 = b->b[k]; //pointer toward current box - - /* break if NULL box or empty (Keep previous box b)*/ - if (( b0 == NULL) || (b0->nbitems == 0)) break; + while(b->nbitems<0){ + + int hb2 = hb >> 1; //size of the current box + int k = BoxNumber(xi2,yi2,hb2); //box number (0,1,2 or 3) + BamgQuadtreeBox* b0 = b->box[k]; //pointer toward current box + + /* break if box is empty (Keep previous box b)*/ + if((b0==NULL) || (b0->nbitems==0)) break; /*Get next Quadtree box*/ - b=b0; - i0 += I_IJ(k,hb2); // i orign of BamgQuadtreeBox (macro) - j0 += J_IJ(k,hb2); // j orign of BamgQuadtreeBox - hb = hb2; // size of the box (in Int) + b = b0; + hb = hb2; + this->SubBoxCoords(&i0,&j0,k,hb2); } @@ -280,18 +276,18 @@ * - i0: x coordinate of the lower left corner * - j0: y coordinate of the lower left corner*/ + int n0 = b->nbitems; /* if the current subbox is holding vertices, we are almost done*/ - if (n0>0){ - //loop over the vertices of the box and find the closest vertex + if(n0>0){ + /*loop over the vertices of the box and find the closest vertex*/ for(int k=0;kv[k]->i; - - /*Compute norm with w*/ - h0=NORM(iplus,i2.x,jplus,i2.y); + int xiv = b->v[k]->i.x; + int yiv = b->v[k]->i.y; + + + int h0 = Norm(xi2,xiv,yi2,yiv); /*is it smaller than previous value*/ - if (h0v[k]; @@ -306,4 +302,8 @@ /*Initialize search variables*/ + BamgQuadtreeBox* pb[MAXDEPTH]; + int pi[MAXDEPTH]; + int ii[MAXDEPTH]; + int jj[MAXDEPTH]; pb[0]=b; //pointer toward the box b pi[0]=b->nbitems>0?(int)b->nbitems:4;//number of boxes in b @@ -315,12 +315,11 @@ /*Main loop*/ - level=0; - do { - + int level=0; + do{ /*get current box*/ - b= pb[level]; + b = pb[level]; /*Loop over the items in current box (if not empty!)*/ - while (pi[level]){ + while(pi[level]){ /*We are looping now over the items of b. k is the current index (in [0 3])*/ @@ -330,6 +329,5 @@ /*if the current subbox is holding vertices (b->nbitems<0 is subboxes)*/ if (b->nbitems>0){ - I2 i2=b->v[k]->i; - h0 = NORM(iplus,i2.x,jplus,i2.y); + int h0 = Norm(xi2,b->v[k]->i.x,yi2,b->v[k]->i.y); if (h0b[k])){ + if((b=b->box[k])){ /*Get size (hb) and coordinates of the current sub-box lowest left corner*/ hb>>=1; - Icoor1 iii = ii[level]+I_IJ(k,hb); - Icoor1 jjj = jj[level]+J_IJ(k,hb); - - /*if the current point (iplus,jplus) is in b (modulo h), this box is good: + int iii = ii[level]; + int jjj = jj[level]; + this->SubBoxCoords(&iii,&jjj,k,hb); + + /*if the current point (xi2,yi2) is in b (modulo h), this box is good: * it is holding vertices that are close to w */ - if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)){ + if(this->Intersection(iii,iii+hb,xi2-h,xi2+h) && this->Intersection(jjj,jjj+hb,yi2-h,yi2+h)){ level++; - pb[level]= b; - pi[level]= b->nbitems>0 ?(int) b->nbitems : 4 ; - ii[level]= iii; - jj[level]= jjj; + pb[level] = b; + pi[level] = b->nbitems>0 ? b->nbitems:4 ; + ii[level] = iii; + jj[level] = jjj; } - //else go backwards + /*else go backwards*/ else{ - //shifted righ by one bit: hb=001000000 -> 01000000 + /*shifted righ by one bit: hb=001000000 -> 01000000*/ b=b0; hb<<=1; @@ -379,82 +378,103 @@ * in case there is a vertex closest to w that has not yet been tested*/ hb <<= 1; - } while (level--); - - /*return nearest_v, nearest vertex*/ + }while(level--); + + /*return nearest vertex pointer*/ return nearest_v; - } /*}}}*/ - BamgQuadtree::BamgQuadtreeBox* BamgQuadtree::NewBamgQuadtreeBox(void){/*{{{*/ - - /*Output*/ - BamgQuadtreeBox* newbox=NULL; - - /*Create and initialize a new box*/ - newbox=new BamgQuadtreeBox; - newbox->nbitems=0; - newbox->b[0]=NULL; - newbox->b[1]=NULL; - newbox->b[2]=NULL; - newbox->b[3]=NULL; - - /*Add root to the container*/ - boxcontainer->AddObject(newbox); - - /*Increase counter*/ - NbBamgQuadtreeBox++; - - /*currentbox now points toward next quadtree box*/ - return newbox; + int BamgQuadtree::Norm(int xi1,int xi2,int yi1,int yi2){/*{{{*/ + + int deltax = xi2 - xi1; + int deltay = yi2 - yi1; + + if(deltax<0) deltax = -deltax; + if(deltay<0) deltay = -deltay; + + if(deltax> deltay){ + return deltax; + } + else{ + return deltay; + } }/*}}}*/ - BamgVertex* BamgQuadtree::ToClose(BamgVertex & v,double seuil,Icoor1 hx,Icoor1 hy){/*{{{*/ - /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/ToClose)*/ - - const Icoor1 i=v.i.x; - const Icoor1 j=v.i.y; - const R2 X(v.r); - const Metric Mx(v.m); - - BamgQuadtreeBox * pb[ MaxDepth ]; - int pi[ MaxDepth ]; - Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; + void BamgQuadtree::SubBoxCoords(int* pi,int*pj,int boxnumber,int length){/*{{{*/ + /* + * j (first bit) + * ^ + * | +--------+--------+ + * | | | | + * 1X | | 2 | 3 | + * | | | | + * | +--------+--------+ + * | | | | + * 0X | | 0 | 1 | + * | | | | + * | +--------+--------+ + * +-----------------------> i (second bit) + * X0 X1 + */ + + /*Add sub-box coordinate to i and j*/ + //_assert_(!(*pi & length)); + //_assert_(!(*pj & length)); + + /*length if first bit of boxnumber is 1, elengthse 0*/ + *pi += ((boxnumber & 1) ? length:0); + /*length if second bit of boxnumber is 1, elengthse 0*/ + *pj += ((boxnumber & 2) ? length:0); + + }/*}}}*/ + BamgVertex* BamgQuadtree::TooClose(BamgVertex* v,double threshold,int hx,int hy){/*{{{*/ + + const int i=v->i.x; + const int j=v->i.y; + const double Xx = v->r.x; + const double Xy = v->r.y; + Metric* Mx = new Metric(v->m); + + BamgQuadtreeBox *pb[MAXDEPTH]; + int pi[MAXDEPTH]; + int ii[MAXDEPTH], jj[MAXDEPTH]; int l=0; // level - BamgQuadtreeBox * b; - Icoor1 hb = MaxISize; - Icoor1 i0=0,j0=0; - - // BamgVertex *vn=0; - - if (!root->nbitems) - return 0; // empty tree - - // general case ----- + BamgQuadtreeBox* b; + int hb = MAXISIZE; + int i0=0,j0=0; + + // BamgVertex *vn=0; + + if(!root->nbitems) return 0; // empty tree + + // general case pb[0]=root; - pi[0]=root->nbitems>0 ?(int) root->nbitems : 4 ; + pi[0]=root->nbitems>0 ?(int)root->nbitems:4; ii[0]=i0; jj[0]=j0; - do { + do{ b= pb[l]; - while (pi[l]--){ + while(pi[l]--){ int k = pi[l]; - if (b->nbitems>0){ // BamgVertex BamgQuadtreeBox none empty - I2 i2 = b->v[k]->i; - if ( ABS(i-i2.x) v[k]->r); - if(LengthInterpole(Mx(XY), b->v[k]->m(XY)) < seuil){ + if(b->nbitems>0){ // BamgVertex BamgQuadtreeBox none empty + int i2x = b->v[k]->i.x; + int i2y = b->v[k]->i.y; + if (ABS(i-i2x)v[k]->r.x - Xx; + double XYy = b->v[k]->r.y - Xy; + if(LengthInterpole(Mx->Length(XYx,XYy),b->v[k]->m.Length(XYx,XYy)) < threshold){ + delete Mx; return b->v[k]; } - } + } } else{ // Pointer BamgQuadtreeBox BamgQuadtreeBox *b0=b; - if ((b=b->b[k])){ + if ((b=b->box[k])){ hb >>=1 ; // div by 2 - long iii = ii[l]+I_IJ(k,hb); - long jjj = jj[l]+J_IJ(k,hb); - - if (INTER_SEG(iii,iii+hb,i-hx,i+hx) && INTER_SEG(jjj,jjj+hb,j-hy,j+hy)){ + int iii = ii[l]; + int jjj = jj[l]; + this->SubBoxCoords(&iii,&jjj,k,hb); + + if(this->Intersection(iii,iii+hb,i-hx,i+hx) && this->Intersection(jjj,jjj+hb,j-hy,j+hy)){ pb[++l]= b; pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; @@ -474,8 +494,30 @@ } hb <<= 1; // mul by 2 - } while (l--); - + }while(l--); + + delete Mx; return 0; } /*}}}*/ + + BamgQuadtree::BamgQuadtreeBox* BamgQuadtree::NewBamgQuadtreeBox(void){/*{{{*/ + + /*Output*/ + BamgQuadtreeBox* newbox=NULL; + + /*Create and initialize a new box*/ + newbox=new BamgQuadtreeBox; + newbox->nbitems=0; + newbox->box[0]=NULL; + newbox->box[1]=NULL; + newbox->box[2]=NULL; + newbox->box[3]=NULL; + + /*Add root to the container*/ + boxcontainer->AddObject(newbox); + this->NbQuadtreeBox++; + + /*currentbox now points toward next quadtree box*/ + return newbox; + }/*}}}*/ } Index: /issm/trunk/src/c/bamg/BamgQuadtree.h =================================================================== --- /issm/trunk/src/c/bamg/BamgQuadtree.h (revision 21728) +++ /issm/trunk/src/c/bamg/BamgQuadtree.h (revision 21729) @@ -5,12 +5,7 @@ #include "./include.h" #include "../datastructures/datastructures.h" +class BamgVertex; namespace bamg { - - const int MaxDepth = 30; - const long MaxISize = ( 1L << MaxDepth); // = 2^30 : 010000000000..000 (bitwise operation) - - class BamgVertex; - class BamgQuadtree{ @@ -24,9 +19,7 @@ class BamgQuadtreeBox: public Object{ public: - int nbitems; // number of current vertices in the box - union{ - BamgQuadtreeBox* b[4]; - BamgVertex* v[4]; - }; + int nbitems; + BamgQuadtreeBox *box[4]; + BamgVertex *v[4]; /*Object functions*/ void Echo() {_error_("not implemented yet"); }; @@ -44,7 +37,7 @@ /*BamgQuadtree public Fields*/ - BamgQuadtreeBox* root; - long NbBamgQuadtreeBox; - long NbVertices; + BamgQuadtreeBox *root; // main box + long NbQuadtreeBox; // total number of boxes + long NbVertices; // number of points BamgQuadtree(); @@ -52,8 +45,12 @@ ~BamgQuadtree(); - BamgVertex *NearestVertex(Icoor1 i,Icoor1 j); + void Add(BamgVertex &w); + int BoxNumber(int i,int j,int l); + bool Intersection(int a,int b,int x,int y); + BamgVertex *NearestVertex(int i,int j); BamgQuadtreeBox *NewBamgQuadtreeBox(void); - BamgVertex *ToClose(BamgVertex &,double ,Icoor1,Icoor1); - void Add(BamgVertex &w); + int Norm(int xi1,int yi1,int xi2,int yi2); + void SubBoxCoords(int* pi,int*pj,int boxcoord,int length); + BamgVertex *TooClose(BamgVertex*,double,int,int); }; } Index: /issm/trunk/src/c/bamg/BamgVertex.cpp =================================================================== --- /issm/trunk/src/c/bamg/BamgVertex.cpp (revision 21728) +++ /issm/trunk/src/c/bamg/BamgVertex.cpp (revision 21729) @@ -115,5 +115,5 @@ ret = t->Optim(IndexInTriangle,koption); if(!i){ - t =0; // for no future optime + t =0; // for no future optim IndexInTriangle= 0; } @@ -196,14 +196,5 @@ BamgVertex *v0,*v1,*v2,*v3; if (tria->det<0) ok =1; - else if (tria->Quadrangle(v0,v1,v2,v3)) - { - vP = vPsave; - double qold =QuadQuality(*v0,*v1,*v2,*v3); - vP = vPnew; - double qnew =QuadQuality(*v0,*v1,*v2,*v3); - if (qnewdet < detold/2 ) ok=1; - } tria->SetUnMarkUnSwap(0); @@ -225,33 +216,3 @@ } /*}}}*/ - - /*Intermediary*/ - double QuadQuality(const BamgVertex & a,const BamgVertex &b,const BamgVertex &c,const BamgVertex &d) {/*{{{*/ - /*Original code from Frederic Hecht (BAMG v1.01, MeshQuad.cpp/QuadQuality)*/ - - // calcul de 4 angles -- - R2 A((R2)a),B((R2)b),C((R2)c),D((R2)d); - R2 AB(B-A),BC(C-B),CD(D-C),DA(A-D); - // Move(A),Line(B),Line(C),Line(D),Line(A); - const Metric & Ma = a; - const Metric & Mb = b; - const Metric & Mc = c; - const Metric & Md = d; - - double lAB=Norme2(AB); - double lBC=Norme2(BC); - double lCD=Norme2(CD); - double lDA=Norme2(DA); - AB /= lAB; BC /= lBC; CD /= lCD; DA /= lDA; - // version aniso - double cosDAB= Ma(DA,AB)/(Ma(DA)*Ma(AB)),sinDAB= Det(DA,AB); - double cosABC= Mb(AB,BC)/(Mb(AB)*Mb(BC)),sinABC= Det(AB,BC); - double cosBCD= Mc(BC,CD)/(Mc(BC)*Mc(CD)),sinBCD= Det(BC,CD); - double cosCDA= Md(CD,DA)/(Md(CD)*Md(DA)),sinCDA= Det(CD,DA); - double sinmin=Min(Min(sinDAB,sinABC),Min(sinBCD,sinCDA)); - if (sinmin<=0) return sinmin; - return 1.0-Max(Max(Abs(cosDAB),Abs(cosABC)),Max(Abs(cosBCD),Abs(cosCDA))); - } - /*}}}*/ - } Index: /issm/trunk/src/c/bamg/BamgVertex.h =================================================================== --- /issm/trunk/src/c/bamg/BamgVertex.h (revision 21728) +++ /issm/trunk/src/c/bamg/BamgVertex.h (revision 21729) @@ -4,5 +4,4 @@ #include "./include.h" #include "./Metric.h" -#include "./Direction.h" #include "./BamgOpts.h" @@ -24,5 +23,4 @@ long ReferenceNumber; long PreviousNumber; - Direction DirOfSearch; short IndexInTriangle; // the vertex number in triangle; varies between 0 and 2 in t @@ -40,5 +38,5 @@ operator const R2 & () const {return r;} // Cast operator operator Metric () const {return m;} // Cast operator - double operator()(R2 x) const { return m(x);} // Get x in the metric m + double operator()(R2 x) const { return m.Length(x.x,x.y);} // Get x in the metric m /*methods (No constructor and no destructors...)*/ @@ -54,7 +52,4 @@ inline void Set(const BamgVertex &rec,const Mesh & ,Mesh & ){*this=rec;} }; - - //Intermediary - double QuadQuality(const BamgVertex &,const BamgVertex &,const BamgVertex &,const BamgVertex &); } #endif Index: sm/trunk/src/c/bamg/Direction.cpp =================================================================== --- /issm/trunk/src/c/bamg/Direction.cpp (revision 21728) +++ (revision ) @@ -1,33 +1,0 @@ -#include -#include -#include -#include - -#include "Direction.h" - -namespace bamg { - - /*Constructors/Destructors*/ - Direction::Direction():/*{{{*/ - dir(MaxICoor){ - - }/*}}}*/ - Direction::Direction(Icoor1 i,Icoor1 j) {/*{{{*/ - Icoor2 n2 = 2*(Abs(i)+Abs(j)); - Icoor2 r = MaxICoor* (Icoor2) i; - Icoor1 r1 = (Icoor1) (2*(r/ n2)); // odd number - dir = (j>0) ? r1 : r1+1; // odd-> j>0 even-> j<0 - }/*}}}*/ - - /*Methods*/ - int Direction::direction(Icoor1 i,Icoor1 j) {/*{{{*/ - int r =1; - if (dir!= MaxICoor) { - Icoor2 x(dir/2),y1(MaxICoor/2-Abs(x)),y((dir%2)?-y1:y1); - r = (x*i + y*j) >=0; - } - return r; - } - /*}}}*/ - -} Index: sm/trunk/src/c/bamg/Direction.h =================================================================== --- /issm/trunk/src/c/bamg/Direction.h (revision 21728) +++ (revision ) @@ -1,20 +1,0 @@ -#ifndef _DIRECTION_H_ -#define _DIRECTION_H_ - -#include "./include.h" -#include "../shared/Bamg/shared.h" - -namespace bamg { - - class Direction { - private: - Icoor1 dir; - - public: - //Methods - Direction(); - Direction(Icoor1 i,Icoor1 j); - int direction(Icoor1 i,Icoor1 j); - }; -} -#endif Index: sm/trunk/src/c/bamg/DoubleAndInt.h =================================================================== --- /issm/trunk/src/c/bamg/DoubleAndInt.h (revision 21728) +++ (revision ) @@ -1,19 +1,0 @@ -#ifndef _DOUBLEANDINT_H_ -#define _DOUBLEANDINT_H_ - -#include "./include.h" - -namespace bamg { - - class DoubleAndInt { - //class used by Mesh::MakeQuadrangles - - public: - double q; - long i3j; - - //Operators - int operator<(DoubleAndInt a){return q > a.q;} - }; -} -#endif Index: /issm/trunk/src/c/bamg/EigenMetric.cpp =================================================================== --- /issm/trunk/src/c/bamg/EigenMetric.cpp (revision 21728) +++ /issm/trunk/src/c/bamg/EigenMetric.cpp (revision 21729) @@ -37,6 +37,6 @@ lambda1=0; lambda2=0; - v.x=1; - v.y=0; + vx=1; + vy=0; } /*2: delta is small -> double root*/ @@ -44,6 +44,6 @@ lambda1=-b/2; lambda2=-b/2; - v.x=1; - v.y=0; + vx=1; + vy=0; } /*3: general case -> two roots*/ @@ -76,11 +76,11 @@ if (norm2lambda1 = r1; + this->lambda2 = r2; + this->vx = vp1.x; + this->vy = vp1.y; }/*}}}*/ @@ -104,6 +107,6 @@ _printf_(" lambda1: " << lambda1 << "\n"); _printf_(" lambda2: " << lambda2 << "\n"); - _printf_(" v.x: " << v.x << "\n"); - _printf_(" v.y: " << v.y << "\n"); + _printf_(" vx: " << vx << "\n"); + _printf_(" vy: " << vy << "\n"); return; Index: /issm/trunk/src/c/bamg/Geometry.cpp =================================================================== --- /issm/trunk/src/c/bamg/Geometry.cpp (revision 21728) +++ /issm/trunk/src/c/bamg/Geometry.cpp (revision 21729) @@ -8,6 +8,4 @@ namespace bamg { - - static const Direction NoDirOfSearch=Direction(); /*Constructors/Destructors*/ @@ -80,5 +78,4 @@ vertices[i].r.y=(double)bamggeom->Vertices[i*3+1]; vertices[i].ReferenceNumber=(long)bamggeom->Vertices[i*3+2]; - vertices[i].DirOfSearch=NoDirOfSearch; vertices[i].color =0; vertices[i].type=0; @@ -106,5 +103,6 @@ * coefIcoor = (2^30 -1)/D */ - coefIcoor=(MaxICoor)/(Max(pmax.x-pmin.x,pmax.y-pmin.y)); + int MaxICoord = 1073741823; + coefIcoor=(MaxICoord)/(Max(pmax.x-pmin.x,pmax.y-pmin.y)); if(coefIcoor<=0) _error_("coefIcoor should be positive"); } @@ -772,4 +770,5 @@ /*Original code from Frederic Hecht (BAMG v1.01, MeshGeom.cpp/ProjectOnCurve)*/ /*Add a vertex on an existing geometrical edge according to the metrics of the two vertices constituting the edge*/ + /*FIXME: should go away*/ double save_s=s; @@ -807,5 +806,5 @@ //Compute metric of new vertex as a linear interpolation of the two others - V.m=Metric(1.0-s,v0,s,v1); + V.m=Metric(1.0-s,v0.m,s,v1.m); const int mxe=100; @@ -911,5 +910,5 @@ * coefIcoor = (2^30 -1)/D */ - return I2( (Icoor1) (coefIcoor*(P.x-pmin.x)) ,(Icoor1) (coefIcoor*(P.y-pmin.y)) ); + return I2( (int) (coefIcoor*(P.x-pmin.x)) ,(int) (coefIcoor*(P.y-pmin.y)) ); }/*}}}*/ void Geometry::UnMarkEdges() {/*{{{*/ Index: /issm/trunk/src/c/bamg/Geometry.h =================================================================== --- /issm/trunk/src/c/bamg/Geometry.h (revision 21728) +++ /issm/trunk/src/c/bamg/Geometry.h (revision 21729) @@ -31,5 +31,5 @@ Curve *curves; R2 pmin,pmax; // domain extrema coordinates - double coefIcoor; // coef to integer Icoor1; + double coefIcoor; // coef to integer coordinates; double MaxCornerAngle; Index: /issm/trunk/src/c/bamg/Mesh.cpp =================================================================== --- /issm/trunk/src/c/bamg/Mesh.cpp (revision 21728) +++ /issm/trunk/src/c/bamg/Mesh.cpp (revision 21729) @@ -9,6 +9,4 @@ namespace bamg { - - static const Direction NoDirOfSearch=Direction(); /*Constructors/Destructors*/ @@ -167,5 +165,4 @@ nbsubdomains = Th.nbsubdomains; nbtout = Th.nbtout; - nbq = Th.nbq ; NbVerticesOnGeomVertex = Th.NbVerticesOnGeomVertex; if(NbVerticesOnGeomVertex) @@ -269,5 +266,4 @@ vertices[i].r.y=y[i]; vertices[i].ReferenceNumber=1; - vertices[i].DirOfSearch =NoDirOfSearch; vertices[i].m=M1; vertices[i].color=0; @@ -336,5 +332,4 @@ vertices[i].r.y=bamgmesh->Vertices[i*3+1]; vertices[i].ReferenceNumber=(long)bamgmesh->Vertices[i*3+2]; - vertices[i].DirOfSearch =NoDirOfSearch; vertices[i].m=M1; vertices[i].color=0; @@ -362,26 +357,4 @@ else{ if(verbose>5) _error_("no Triangles found in the initial mesh"); - } - - //Quadrilaterals - if(bamgmesh->Quadrilaterals){ - if(verbose>5) _printf_(" processing Quadrilaterals\n"); - long i1,i2,i3,i4; - triangles =new Triangle[nbt]; - for (i=0;iQuadrilateralsSize[0];i++){ - //divide the quad into two triangles - Triangle & t1 = triangles[2*i]; - Triangle & t2 = triangles[2*i+1]; - i1=(long)bamgmesh->Quadrilaterals[i*5+0]-1; //for C indexing - i2=(long)bamgmesh->Quadrilaterals[i*5+1]-1; //for C indexing - i3=(long)bamgmesh->Quadrilaterals[i*5+2]-1; //for C indexing - i4=(long)bamgmesh->Quadrilaterals[i*5+3]-1; //for C indexing - t1=Triangle(this,i1,i2,i3); - t2=Triangle(this,i3,i4,i1); - t1.color=(long)bamgmesh->Quadrilaterals[i*5+4]; - t2.color=(long)bamgmesh->Quadrilaterals[i*5+4]; - t1.SetHidden(OppositeEdge[1]); // two times because the adj was not created - t2.SetHidden(OppositeEdge[1]); - } } @@ -698,5 +671,5 @@ /*Triangles*/ if(verbose>5) _printf_(" writing Triangles\n"); - k=nbInT-nbq*2; + k=nbInT; num=0; bamgmesh->TrianglesSize[0]=k; @@ -713,25 +686,4 @@ bamgmesh->Triangles[num*4+3]=subdomains[reft[i]].ReferenceNumber; num=num+1; - } - } - } - - /*Quadrilaterals*/ - if(verbose>5) _printf_(" writing Quadrilaterals\n"); - bamgmesh->QuadrilateralsSize[0]=nbq; - bamgmesh->QuadrilateralsSize[1]=5; - if (nbq){ - bamgmesh->Quadrilaterals=xNew(5*nbq); - for (i=0;iQuadrilaterals[i*5+0]=GetId(v0)+1; //back to M indexing - bamgmesh->Quadrilaterals[i*5+1]=GetId(v1)+1; //back to M indexing - bamgmesh->Quadrilaterals[i*5+2]=GetId(v2)+1; //back to M indexing - bamgmesh->Quadrilaterals[i*5+3]=GetId(v3)+1; //back to M indexing - bamgmesh->Quadrilaterals[i*5+4]=subdomains[reft[i]].ReferenceNumber; } } @@ -1113,5 +1065,5 @@ // s0 tt2 s1 //------------------------------- - + /*Intermediaries*/ Triangle* tt[3]; //the three triangles @@ -1230,6 +1182,6 @@ } } - } - /*}}}*/ + + }/*}}}*/ void Mesh::BoundAnisotropy(double anisomax,double hminaniso) {/*{{{*/ /*Original code from Frederic Hecht (BAMG v1.01, Metric.cpp/BoundAnisotropy)*/ @@ -1623,5 +1575,6 @@ //Build Gh.coefIcoor - Gh.coefIcoor= (MaxICoor)/(Max(Gh.pmax.x-Gh.pmin.x,Gh.pmax.y-Gh.pmin.y)); + int MaxICoord = 1073741823; //2^30 - 1 = =111...111 (29 times one) + Gh.coefIcoor= (MaxICoord)/(Max(Gh.pmax.x-Gh.pmin.x,Gh.pmax.y-Gh.pmin.y)); if (Gh.coefIcoor<=0){ delete [] colorV; @@ -1713,5 +1666,5 @@ //unset adj for (i=0;iToClose(vi,seuil,hi,hj)){ + int hi=(int) (hx*coefIcoor),hj=(int) (hy*coefIcoor); + if(!quadtree->TooClose(&vi,seuil,hi,hj)){ // a good new point BamgVertex &vj = vertices[iv]; @@ -2999,45 +2950,4 @@ } /*}}}*/ - void Mesh::MakeQuadrangles(double costheta){/*{{{*/ - /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MakeQuadrangles)*/ - - long int verbose=0; - - if (verbose>2) _printf_("MakeQuadrangles costheta = " << costheta << "\n"); - - if (costheta >1) { - if (verbose>5) _printf_(" do nothing: costheta > 1\n"); - } - - long nbqq = (nbt*3)/2; - DoubleAndInt *qq = new DoubleAndInt[nbqq]; - - long i,ij; - int j; - long k=0; - for (i=0;i=costheta) - qq[k++].i3j=i*3+j; - // sort qq - HeapSort(qq,k); - - long kk=0; - for (ij=0;ij=costheta) - triangles[i].SetHidden(j),kk++; - } - nbq = kk; - if (verbose>2){ - _printf_(" number of quadrilaterals = " << nbq << "\n"); - _printf_(" number of triangles = " << nbt-nbtout- nbq*2 << "\n"); - _printf_(" number of outside triangles = " << nbtout << "\n"); - } - delete [] qq; - } - /*}}}*/ void Mesh::MakeBamgQuadtree() { /*{{{*/ /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MakeBamgQuadtree)*/ @@ -3073,5 +2983,5 @@ lmax = Max(lmax,l); if(l> maxsubdiv2){ - R2 AC = M.Orthogonal(AB);// the ortogonal vector of AB in M + R2 AC = M.Orthogonal(AB);// the ortogonal vector of AB in M double lc = M(AC,AC); D2xD2 Rt(AB,AC);// Rt.x = AB , Rt.y = AC; @@ -3086,5 +2996,5 @@ lmax = Max(lmax,l); if(l> maxsubdiv2){ - R2 AC = M.Orthogonal(AB);// the ortogonal vector of AB in M + R2 AC = M.Orthogonal(AB);// the ortogonal vector of AB in M double lc = M(AC,AC); D2xD2 Rt(AB,AC);// Rt.x = AB , Rt.y = AC; @@ -3127,5 +3037,5 @@ } /*}}}*/ - BamgVertex* Mesh::NearestVertex(Icoor1 i,Icoor1 j) {/*{{{*/ + BamgVertex* Mesh::NearestVertex(int i,int j) {/*{{{*/ /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/NearestVertex)*/ return quadtree->NearestVertex(i,j); @@ -3786,5 +3696,6 @@ //Compute coefIcoor - coefIcoor= (MaxICoor)/(Max(pmax.x-pmin.x,pmax.y-pmin.y)); + int MaxICoord = 1073741823; //2^30 - 1 = =111...111 (29 times one) + coefIcoor= (MaxICoord)/(Max(pmax.x-pmin.x,pmax.y-pmin.y)); if (coefIcoor<=0){ _error_("coefIcoor should be positive, a problem in the geometry is likely"); @@ -3857,8 +3768,7 @@ if (tstart[i] != &vide) // not a boundary vertex delta=Max(delta,vertices[i].Smoothing(*this,BTh,tstart[i],omega)); - if (!nbq) - for ( i=0;i3) _printf_(" move max = " << pow(delta,0.5) << ", iteration = " << k << ", nb of swap = " << NbSwap << "\n"); } @@ -3914,6 +3824,6 @@ double ll = Norme2(Aij); if (0) { - double hi = ll/vi.m(Aij); - double hj = ll/vj.m(Aij); + double hi = ll/vi.m.Length(Aij.x,Aij.y); + double hj = ll/vj.m.Length(Aij.x,Aij.y); if(hi < hj) { @@ -3928,5 +3838,5 @@ else { - double li = vi.m(Aij); + double li = vi.m.Length(Aij.x,Aij.y); if( vj.m.IntersectWith(vi.m/(1 +logseuil*li)) ) if(first_np_or_next_t1[j]<0) // if the metrix change @@ -3973,5 +3883,4 @@ vertices[nbv++].m = Metric(0.5,v0.m,0.5,v1.m); vertices[nbv].ReferenceNumber=0; - vertices[nbv].DirOfSearch = NoDirOfSearch ; } NbSplitEdge++; @@ -3992,5 +3901,4 @@ // a good new point vi.ReferenceNumber=0; - vi.DirOfSearch =NoDirOfSearch; Triangle *tcvi = TriangleFindFromCoord(vi.i,det3); if (tcvi && !tcvi->link) { @@ -4019,5 +3927,5 @@ /*}}}*/ I2 Mesh::R2ToI2(const R2 & P) const {/*{{{*/ - return I2( (Icoor1) (coefIcoor*(P.x-pmin.x)),(Icoor1) (coefIcoor*(P.y-pmin.y)) ); + return I2( (int) (coefIcoor*(P.x-pmin.x)),(int) (coefIcoor*(P.y-pmin.y)) ); } /*}}}*/ @@ -4181,5 +4089,4 @@ vertices[i].r.y=y[i]; vertices[i].ReferenceNumber=1; - vertices[i].DirOfSearch =NoDirOfSearch; vertices[i].m=M1; vertices[i].color=0; @@ -4331,5 +4238,5 @@ Metric MA = background ? BTh.MetricAt(a->r) :a->m ; //Get metric associated to A Metric MB = background ? BTh.MetricAt(b->r) :b->m ; //Get metric associated to B - double ledge = (MA(AB) + MB(AB))/2; //Get edge length in metric + double ledge = (MA.Length(AB.x,AB.y) + MB.Length(AB.x,AB.y))/2; //Get edge length in metric /* We are now creating the mesh edges from the geometrical edge selected above. @@ -4367,5 +4274,5 @@ MBs= background ? BTh.MetricAt(B) : Metric(1-x,MA,x,MB); AB = A-B; - lSubEdge[kk]=(ledge+=(MAs(AB)+MBs(AB))/2); + lSubEdge[kk]=(ledge+=(MAs.Length(AB.x,AB.y)+MBs.Length(AB.x,AB.y))/2); } } @@ -4412,5 +4319,4 @@ vb->m = Metric(aa,a->m,bb,b->m); vb->ReferenceNumber = e->ReferenceNumber; - vb->DirOfSearch =NoDirOfSearch; double abcisse = k ? bb : aa; vb->r = e->F(abcisse); @@ -4735,5 +4641,4 @@ ongequi=Gh.ProjectOnCurve(eeequi,se,*A1,*GA1); A1->ReferenceNumber = eeequi.ReferenceNumber; - A1->DirOfSearch =NoDirOfSearch; e->GeomEdgeHook = ongequi; e->v[0]=A0; Index: /issm/trunk/src/c/bamg/Mesh.h =================================================================== --- /issm/trunk/src/c/bamg/Mesh.h (revision 21728) +++ /issm/trunk/src/c/bamg/Mesh.h (revision 21729) @@ -33,5 +33,5 @@ long NbRef; // counter of ref on the this class if 0 we can delete long maxnbv,maxnbt; // nombre max de sommets , de triangles - long nbv,nbt,nbe,nbq; // nb of vertices, of triangles, of edges and quadrilaterals + long nbv,nbt,nbe; // nb of vertices, of triangles and edges long nbsubdomains; long nbtout; // Nb of oudeside triangle @@ -86,9 +86,8 @@ void SmoothMetric(double raisonmax) ; void BoundAnisotropy(double anisomax,double hminaniso= 1e-100) ; - void MaxSubDivision(double maxsubdiv); Edge** MakeGeomEdgeToEdge(); long SplitInternalEdgeWithBorderVertices(); - void MakeQuadrangles(double costheta); void MakeBamgQuadtree(); + void MaxSubDivision(double maxsubdiv); void NewPoints(Mesh &,BamgOpts* bamgopts,int KeepVertices=1); long InsertNewPoints(long nbvold,long & NbTSwap,bool random); @@ -103,5 +102,5 @@ long GetId(const Edge & t) const; long GetId(const Edge * t) const; - BamgVertex* NearestVertex(Icoor1 i,Icoor1 j) ; + BamgVertex* NearestVertex(int i,int j) ; Triangle* TriangleFindFromCoord(const I2 & ,Icoor2 [3],Triangle *tstart=0) const; void ReadMesh(int* index,double* x,double* y,int nods,int nels); Index: /issm/trunk/src/c/bamg/Metric.cpp =================================================================== --- /issm/trunk/src/c/bamg/Metric.cpp (revision 21728) +++ /issm/trunk/src/c/bamg/Metric.cpp (revision 21729) @@ -13,32 +13,49 @@ /*Constructor/Destructor*/ - Metric::Metric(double a): a11(1/(a*a)),a21(0),a22(1/(a*a)){/*{{{*/ + Metric::Metric(double a){/*{{{*/ + + /*Isotropic metric for a length of a as unit*/ + this->a11 = 1./(a*a); + this->a21 = 0.; + this->a22 = 1./(a*a); }/*}}}*/ - Metric::Metric(double a,double b,double c) :a11(a),a21(b),a22(c){/*{{{*/ + Metric::Metric(double a11_in,double a21_in,double a22_in){/*{{{*/ + + this->a11 = a11_in; + this->a21 = a21_in; + this->a22 = a22_in; }/*}}}*/ - Metric::Metric(const double a[3],const Metric& m0, const Metric& m1,const Metric& m2 ){/*{{{*/ - /*Original code from Frederic Hecht (BAMG v1.01, Metric.cpp/Metric)*/ - + Metric::Metric(const double a[3],const Metric m0,const Metric m1,const Metric m2 ){/*{{{*/ + + /*Create metric using 3 inputs*/ Metric mab(a[0]*m0.a11 + a[1]*m1.a11 + a[2]*m2.a11, a[0]*m0.a21 + a[1]*m1.a21 + a[2]*m2.a21, a[0]*m0.a22 + a[1]*m1.a22 + a[2]*m2.a22); + /*Convert to eigen metric*/ EigenMetric vab(mab); - - R2 v1(vab.v.x,vab.v.y); - R2 v2(-v1.y,v1.x); - - double h1 = a[0] / m0(v1) + a[1] / m1(v1) + a[2] / m2(v1); - double h2 = a[0] / m0(v2) + a[1] / m1(v2) + a[2] / m2(v2); - - vab.lambda1 = 1 / (h1*h1); - vab.lambda2 = 1 / (h2*h2); - *this = vab; - } - /*}}}*/ - Metric::Metric(double a,const Metric& ma, double b,const Metric& mb) { /*{{{*/ - /*Original code from Frederic Hecht (BAMG v1.01, Metric.cpp/EigenMetric)*/ + double v1x = + vab.vx; + double v1y = + vab.vy; + double v2x = - vab.vy; + double v2y = + vab.vx; + + double h1=a[0] / m0.Length(v1x,v1y) + a[1] / m1.Length(v1x,v1y) + a[2] / m2.Length(v1x,v1y); + double h2=a[0] / m0.Length(v2x,v2y) + a[1] / m1.Length(v2x,v2y) + a[2] / m2.Length(v2x,v2y); + + vab.lambda1 = 1. / (h1*h1); + vab.lambda2 = 1. / (h2*h2); + + /*Build metric from vab*/ + double v00=vab.vx*vab.vx; + double v11=vab.vy*vab.vy; + double v01=vab.vx*vab.vy; + this->a11=v00*vab.lambda1+v11*vab.lambda2; + this->a21=v01*(vab.lambda1-vab.lambda2); + this->a22=v00*vab.lambda2+v11*vab.lambda1; + + } /*}}}*/ + Metric::Metric(double a,const Metric ma,double b,const Metric mb) { /*{{{*/ /*Compute metric (linear combination of ma and mb)*/ @@ -47,13 +64,22 @@ /*Get Eigen values and vectors*/ EigenMetric vab(mab); - R2 v1(vab.v.x,vab.v.y); - R2 v2(-v1.y,v1.x); + double v1x = + vab.vx; + double v1y = + vab.vy; + double v2x = - vab.vy; + double v2y = + vab.vx; /*Modify eigen values (a+b=1)*/ - double h1 = a/ma(v1) + b/mb(v1); - double h2 = a/ma(v2) + b/mb(v2); - vab.lambda1 = 1/(h1*h1); - vab.lambda2 = 1/(h2*h2); - *this=vab; + double h1 = a/ma.Length(v1x,v1y) + b/mb.Length(v1x,v1y); + double h2 = a/ma.Length(v2x,v2y) + b/mb.Length(v2x,v2y); + vab.lambda1 = 1./(h1*h1); + vab.lambda2 = 1./(h2*h2); + + /*Build metric from vab*/ + double v00=vab.vx*vab.vx; + double v11=vab.vy*vab.vy; + double v01=vab.vx*vab.vy; + this->a11=v00*vab.lambda1+v11*vab.lambda2; + this->a21=v01*(vab.lambda1-vab.lambda2); + this->a22=v00*vab.lambda2+v11*vab.lambda1; } /*}}}*/ @@ -123,7 +149,9 @@ } /*}}}*/ - R2 Metric::mul(const R2 x)const {/*{{{*/ - return R2(a11*x.x+a21*x.y,a21*x.x+a22*x.y); - }/*}}}*/ + double Metric::Length(double Ax,double Ay) const{/*{{{*/ + /*Length of A in the current metric*/ + return sqrt(Ax*Ax*a11+2*Ax*Ay*a21+Ay*Ay*a22); + } + /*}}}*/ /*Intermediary*/ @@ -140,6 +168,6 @@ Ms1[level]=Ma; Ms2[level]=Mb; - double sa = Ma(AB); - double sb = Mb(AB); + double sa = Ma.Length(AB.x,AB.y); + double sb = Mb.Length(AB.x,AB.y); lMs1[level]=sa; lMs2[level]=sb; @@ -160,5 +188,5 @@ if( s > sstop && level < 30 && i < 500-level ) { Metric Mi(0.5,M1,0.5,M2); - double si = Mi(AB); + double si = Mi.Length(AB.x,AB.y); if( Abs((s1+s2)-(si+si)) > s1*0.001) { Index: /issm/trunk/src/c/bamg/Metric.h =================================================================== --- /issm/trunk/src/c/bamg/Metric.h (revision 21728) +++ /issm/trunk/src/c/bamg/Metric.h (revision 21729) @@ -30,8 +30,7 @@ Metric(double a); Metric(double a,double b,double c); - Metric( double a,const Metric& ma, double b,const Metric& mb); - Metric(const double a[3],const Metric& m0,const Metric& m1,const Metric& m2 ); + Metric(double a,const Metric ma,double b,const Metric mb); + Metric(const double a[3],const Metric m0,const Metric m1,const Metric m2 ); void Echo(); - R2 mul(const R2 x)const; double det() const; int IntersectWith(const Metric& M2); @@ -42,4 +41,5 @@ R2 Orthogonal(const R2 x){ return R2(-(a21*x.x+a22*x.y),a11*x.x+a21*x.y); } R2 Orthogonal(const I2 x){ return R2(-(a21*x.x+a22*x.y),a11*x.x+a21*x.y); } + double Length(double Ax,double Ay) const; //operators @@ -47,5 +47,5 @@ Metric operator/(double c) const {double c2=1/(c*c);return Metric(a11*c2,a21*c2,a22*c2);} operator D2xD2(){ return D2xD2(a11,a21,a21,a22);} - double operator()(R2 x) const { return sqrt(x.x*x.x*a11+2*x.x*x.y*a21+x.y*x.y*a22);}; // length of x in metric sqrt() + //double operator()(R2 x) const { return sqrt(x.x*x.x*a11+2*x.x*x.y*a21+x.y*x.y*a22);}; // length of x in metric sqrt() FIXME: replace by Length! double operator()(R2 x,R2 y) const { return x.x*y.x*a11+(x.x*x.y+x.y*y.x)*a21+x.y*y.y*a22;}; @@ -57,5 +57,5 @@ //fields double lambda1,lambda2; - D2 v; + double vx,vy; //friends @@ -114,7 +114,7 @@ } inline Metric::Metric(const EigenMetric& M) { - double v00=M.v.x*M.v.x; - double v11=M.v.y*M.v.y; - double v01=M.v.x*M.v.y; + double v00=M.vx*M.vx; + double v11=M.vy*M.vy; + double v01=M.vx*M.vy; a11=v00*M.lambda1+v11*M.lambda2; a21=v01*(M.lambda1-M.lambda2); Index: /issm/trunk/src/c/bamg/Triangle.cpp =================================================================== --- /issm/trunk/src/c/bamg/Triangle.cpp (revision 21728) +++ /issm/trunk/src/c/bamg/Triangle.cpp (revision 21729) @@ -145,46 +145,4 @@ } /*}}}*/ - Triangle* Triangle::Quadrangle(BamgVertex * & v0,BamgVertex * & v1,BamgVertex * & v2,BamgVertex * & v3) const{/*{{{*/ - // return the other triangle of the quad if a quad or 0 if not a quat - Triangle * t =0; - if (link) { - int a=-1; - if (AdjEdgeIndex[0] & 16 ) a=0; - if (AdjEdgeIndex[1] & 16 ) a=1; - if (AdjEdgeIndex[2] & 16 ) a=2; - if (a>=0) { - t = adj[a]; - // if (t-this<0) return 0; - v2 = vertices[VerticesOfTriangularEdge[a][0]]; - v0 = vertices[VerticesOfTriangularEdge[a][1]]; - v1 = vertices[OppositeEdge[a]]; - v3 = t->vertices[OppositeEdge[AdjEdgeIndex[a]&3]]; - } - } - return t; - } - /*}}}*/ - double Triangle::QualityQuad(int a,int option) const{/*{{{*/ - double q; - if (!link || AdjEdgeIndex[a] &4) - q= -1; - else { - Triangle * t = adj[a]; - if (t-this<0) q= -1;// because we do 2 times - else if (!t->link ) q= -1; - else if (AdjEdgeIndex[0] & 16 || AdjEdgeIndex[1] & 16 || AdjEdgeIndex[2] & 16 || t->AdjEdgeIndex[0] & 16 || t->AdjEdgeIndex[1] & 16 || t->AdjEdgeIndex[2] & 16 ) - q= -1; - else if(option){ - const BamgVertex & v2 = *vertices[VerticesOfTriangularEdge[a][0]]; - const BamgVertex & v0 = *vertices[VerticesOfTriangularEdge[a][1]]; - const BamgVertex & v1 = *vertices[OppositeEdge[a]]; - const BamgVertex & v3 = * t->vertices[OppositeEdge[AdjEdgeIndex[a]&3]]; - q = QuadQuality(v0,v1,v2,v3); // do the float part - } - else q= 1; - } - return q; - } - /*}}}*/ void Triangle::Renumbering(Triangle *tb,Triangle *te, long *renu){/*{{{*/ @@ -262,4 +220,7 @@ t->AdjEdgeIndex[AdjEdgeIndex[a] & 3] &=55; // 23 + 32 AdjEdgeIndex[a] &=55 ; + }/*}}}*/ + Triangle* Triangle::TriangleAdj(int i) const {/*{{{*/ + return adj[i&3]; }/*}}}*/ int Triangle::swap(short a,int koption){/*{{{*/ @@ -305,11 +266,11 @@ // critere de Delaunay pure isotrope Icoor2 xb1 = sb->i.x - s1->i.x, - x21 = s2->i.x - s1->i.x, - yb1 = sb->i.y - s1->i.y, - y21 = s2->i.y - s1->i.y, - xba = sb->i.x - sa->i.x, - x2a = s2->i.x - sa->i.x, - yba = sb->i.y - sa->i.y, - y2a = s2->i.y - sa->i.y; + x21 = s2->i.x - s1->i.x, + yb1 = sb->i.y - s1->i.y, + y21 = s2->i.y - s1->i.y, + xba = sb->i.x - sa->i.x, + x2a = s2->i.x - sa->i.x, + yba = sb->i.y - sa->i.y, + y2a = s2->i.y - sa->i.y; double cosb12 = double(xb1*x21 + yb1*y21), @@ -342,5 +303,5 @@ if (Abs(d) > dd*1.e-3) { R2 C(MAB+ABo*((D.x*A1o.y - D.y*A1o.x)/d)); - som = M(C - S2)/M(C - S1); + som = M.Length(C.x-S2.x,C.y-S2.y) / M.Length(C.x-S1.x,C.y-S1.y); } else {kopt=1;continue;} @@ -357,5 +318,5 @@ if(Abs(d) > dd*1.e-3) { R2 C(MAB+ABo*((D.x*A1o.y - D.y*A1o.x)/d)); - som += M(C - S2)/M(C - S1); + som += M.Length(C.x-S2.x,C.y-S2.y) / M.Length(C.x-S1.x,C.y-S1.y); } else {kopt=1;continue;} @@ -376,7 +337,4 @@ } /*}}}*/ - Triangle* Triangle::TriangleAdj(int i) const {/*{{{*/ - return adj[i&3]; - }/*}}}*/ } Index: /issm/trunk/src/c/bamg/Triangle.h =================================================================== --- /issm/trunk/src/c/bamg/Triangle.h (revision 21728) +++ /issm/trunk/src/c/bamg/Triangle.h (revision 21729) @@ -46,9 +46,7 @@ int Hidden(int a)const; int GetAllflag(int a); - double QualityQuad(int a,int option=1) const; short NuEdgeTriangleAdj(int i) const; AdjacentTriangle Adj(int i) const; Triangle *TriangleAdj(int i) const; - Triangle *Quadrangle(BamgVertex *& v0,BamgVertex *& v1,BamgVertex *& v2,BamgVertex *& v3) const; void Renumbering(Triangle *tb,Triangle *te, long *renu); void Renumbering(BamgVertex *vb,BamgVertex *ve, long *renu); Index: /issm/trunk/src/c/bamg/bamgobjects.h =================================================================== --- /issm/trunk/src/c/bamg/bamgobjects.h (revision 21728) +++ /issm/trunk/src/c/bamg/bamgobjects.h (revision 21729) @@ -11,6 +11,4 @@ #include "./BamgMesh.h" #include "./Metric.h" -#include "./DoubleAndInt.h" -#include "./Direction.h" #include "./BamgVertex.h" #include "./AdjacentTriangle.h" Index: /issm/trunk/src/c/bamg/macros.h =================================================================== --- /issm/trunk/src/c/bamg/macros.h (revision 21728) +++ /issm/trunk/src/c/bamg/macros.h (revision 21729) @@ -19,5 +19,4 @@ static const short NextVertex[3] = {1,2,0}; static const short PreviousVertex[3] = {2,0,1}; - const Icoor1 MaxICoor = 1073741823; // 2^30-1 =111...111 (29 times one) } Index: /issm/trunk/src/c/classes/AdaptiveMeshRefinement.cpp =================================================================== --- /issm/trunk/src/c/classes/AdaptiveMeshRefinement.cpp (revision 21729) +++ /issm/trunk/src/c/classes/AdaptiveMeshRefinement.cpp (revision 21729) @@ -0,0 +1,683 @@ +/*!\file AdaptiveMeshrefinement.cpp + * \brief: implementation of the adaptive mesh refinement tool based on NeoPZ library: github.com/labmec/neopz + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "./AdaptiveMeshRefinement.h" + +/*Constructor, copy, clean up and destructor*/ +AdaptiveMeshRefinement::AdaptiveMeshRefinement(){/*{{{*/ + this->Initialize(); +} +/*}}}*/ +AdaptiveMeshRefinement::AdaptiveMeshRefinement(const AdaptiveMeshRefinement &cp){/*{{{*/ + this->Initialize(); + this->operator =(cp); +} +/*}}}*/ +AdaptiveMeshRefinement & AdaptiveMeshRefinement::operator =(const AdaptiveMeshRefinement &cp){/*{{{*/ + + /*Clean all attributes*/ + this->CleanUp(); + + /*Copy all data*/ + this->fathermesh = new TPZGeoMesh(*cp.fathermesh); + this->previousmesh = new TPZGeoMesh(*cp.previousmesh); + this->levelmax = cp.levelmax; + this->elementswidth = cp.elementswidth; + this->regionlevel1 = cp.regionlevel1; + this->regionlevelmax = cp.regionlevelmax; + return *this; + +} +/*}}}*/ +AdaptiveMeshRefinement::~AdaptiveMeshRefinement(){/*{{{*/ + + bool ismismip = true; + if(ismismip){//itapopo + TPZFileStream fstr; + std::stringstream ss; + + ss << this->levelmax; + std::string AMRfile = "/home/santos/Misomip2/L" + ss.str() + "_tsai/amr.txt"; + + fstr.OpenWrite(AMRfile.c_str()); + int withclassid = 1; + this->Write(fstr,withclassid); + } + this->CleanUp(); + gRefDBase.clear(); +} +/*}}}*/ +void AdaptiveMeshRefinement::CleanUp(){/*{{{*/ + + /*Verify and delete all data*/ + if(this->fathermesh) delete this->fathermesh; + if(this->previousmesh) delete this->previousmesh; + this->levelmax = -1; + this->elementswidth = -1; + this->regionlevel1 = -1; + this->regionlevelmax = -1; +} +/*}}}*/ +void AdaptiveMeshRefinement::Initialize(){/*{{{*/ + + /*Set pointers to NULL*/ + this->fathermesh = NULL; + this->previousmesh = NULL; + this->levelmax = -1; + this->elementswidth = -1; + this->regionlevel1 = -1; + this->regionlevelmax = -1; +} +/*}}}*/ +int AdaptiveMeshRefinement::ClassId() const{/*{{{*/ + return 13829430; //Antartic area with ice shelves (km^2) +} +/*}}}*/ +void AdaptiveMeshRefinement::Read(TPZStream &buf, void *context){/*{{{*/ + + try + { + /* Read the id context*/ + TPZSaveable::Read(buf,context); + + /* Read class id*/ + int classid; + buf.Read(&classid,1); + + /* Verify the class id*/ + if (classid != this->ClassId() ) + { + std::cout << "Error in restoring AdaptiveMeshRefinement!\n"; + std::cout.flush(); + DebugStop(); + } + + /* Read simple attributes */ + buf.Read(&this->levelmax,1); + buf.Read(&this->elementswidth,1); + buf.Read(&this->regionlevel1,1); + buf.Read(&this->regionlevelmax,1); + + /* Read geometric mesh*/ + TPZSaveable *sv1 = TPZSaveable::Restore(buf,0); + this->fathermesh = dynamic_cast(sv1); + + TPZSaveable *sv2 = TPZSaveable::Restore(buf,0); + this->previousmesh = dynamic_cast(sv2); + } + catch(const std::exception& e) + { + std::cout << "Exception catched! " << e.what() << std::endl; + std::cout.flush(); + DebugStop(); + } +} +/*}}}*/ +template class TPZRestoreClass;/*{{{*/ +/*}}}*/ +void AdaptiveMeshRefinement::Write(TPZStream &buf, int withclassid){/*{{{*/ + + try + { + /* Write context (this class) class ID*/ + TPZSaveable::Write(buf,withclassid); + + /* Write this class id*/ + int classid = ClassId(); + buf.Write(&classid,1); + + /* Write simple attributes */ + buf.Write(&this->levelmax,1); + buf.Write(&this->elementswidth,1); + buf.Write(&this->regionlevel1,1); + buf.Write(&this->regionlevelmax,1); + + /* Write the geometric mesh*/ + this->fathermesh->Write(buf, this->ClassId()); + this->previousmesh->Write(buf, this->ClassId()); + } + catch(const std::exception& e) + { + std::cout << "Exception catched! " << e.what() << std::endl; + std::cout.flush(); + DebugStop(); + } +} +/*}}}*/ + +/*Mesh refinement methods*/ +#include "TPZVTKGeoMesh.h" //itapopo +#include "../shared/shared.h" //itapopo +void AdaptiveMeshRefinement::ExecuteRefinement(int &type_process,double *vx, double *vy, double *masklevelset, int &nvertices, int &nelements, int &nsegments, double** px, double** py, double** pz, int** pelements, int** psegments){/*{{{*/ + + /*IMPORTANT! pelements (and psegments) are in Matlab indexing*/ + /*NEOPZ works only in C indexing*/ + + _assert_(this->fathermesh); + _assert_(this->previousmesh); + + /*Calculate the position of the grounding line using previous mesh*/ + std::vector > GLvec; + this->CalcGroundingLinePosition(masklevelset, GLvec); + + // std::ofstream file1("/home/santos/mesh0.vtk"); + // TPZVTKGeoMesh::PrintGMeshVTK(this->fathermesh,file1 ); + + /*run refinement or unrefinement process*/ + TPZGeoMesh *newmesh; + switch (type_process) { + case 0: newmesh = this->previousmesh; break; // refine previous mesh + case 1: newmesh = new TPZGeoMesh(*this->fathermesh); break; // refine mesh 0 (unrefine process) + default: DebugStop(); break;//itapopo verificar se irá usar _assert_ + } + + this->RefinementProcess(newmesh,GLvec); + + //std::ofstream file2("/home/santos/mesh1.vtk"); + //TPZVTKGeoMesh::PrintGMeshVTK(this->previousmesh,file2 ); + + /*Set new mesh pointer. Previous mesh just have uniform elements*/ + if(type_process==1){ + if(this->previousmesh) delete this->previousmesh; + this->previousmesh = newmesh; + } + + /*Refine elements to avoid hanging nodes*/ + //TPZGeoMesh *nohangingnodesmesh = new TPZGeoMesh(*newmesh);//itapopo testando, este era o original + TPZGeoMesh *nohangingnodesmesh = this->CreateRefPatternMesh(newmesh);//itapopo testando, este eh novo metodo + + //std::ofstream file3("/home/santos/mesh2.vtk"); + //TPZVTKGeoMesh::PrintGMeshVTK(this->previousmesh,file3); + + this->RefineMeshToAvoidHangingNodes(nohangingnodesmesh); + + //std::ofstream file4("/home/santos/mesh3.vtk"); + //TPZVTKGeoMesh::PrintGMeshVTK(nohangingnodesmesh,file4); + + /*Get new geometric mesh in ISSM data structure*/ + this->GetMesh(nohangingnodesmesh,nvertices,nelements,nsegments,px,py,pz,pelements,psegments); + + /*Verify the new geometry*/ + this->CheckMesh(nvertices,nelements,nsegments,this->elementswidth,px,py,pz,pelements,psegments); + + _printf_("\trefinement process done!\n\n"); + + delete nohangingnodesmesh; +} +/*}}}*/ +void AdaptiveMeshRefinement::RefinementProcess(TPZGeoMesh *gmesh,std::vector > &GLvec){/*{{{*/ + + /*Refine mesh levelmax times*/ + _printf_("\n\trefinement process (level max = " << this->levelmax << ")\n"); + _printf_("\tprogress: "); + for(int hlevel=1;hlevel<=this->levelmax;hlevel++){ + + /*Set elements to be refined using some criteria*/ + std::vector ElemVec; //elements without children + this->SetElementsToRefine(gmesh,GLvec,hlevel,ElemVec); + + /*Refine the mesh*/ + this->RefineMesh(gmesh, ElemVec); + + _printf_("* "); + } + _printf_("\n"); +} +/*}}}*/ +void AdaptiveMeshRefinement::RefineMesh(TPZGeoMesh *gmesh, std::vector &ElemVec){/*{{{*/ + + /*Refine elements in ElemVec: uniform pattern refinement*/ + for(int i = 0; i < ElemVec.size(); i++){ + + /*Get geometric element and verify if it has already been refined*/ + int index = ElemVec[i]; + TPZGeoEl * geoel = gmesh->Element(index); + if(geoel->HasSubElement()) DebugStop(); //itapopo _assert_(!geoel->HasSubElement()); + if(geoel->MaterialId() != this->GetElemMaterialID()) DebugStop(); //itapopo verificar se usará _assert_ + + /*Divide geoel*/ + TPZVec Sons; + geoel->Divide(Sons); + + /*If a 1D segment is neighbor, it must be divided too*/ + if(this->elementswidth != 3) DebugStop(); //itapopo verificar o segment para malha 3D + + std::vector sides(3); + sides[0] = 3; sides[1] = 4; sides[2] = 5; + for(int j = 0; j < sides.size(); j++ ){ + + TPZGeoElSide Neighbour = geoel->Neighbour(sides[j]); + + if( Neighbour.Element()->MaterialId() == this->GetBoundaryMaterialID() && !Neighbour.Element()->HasSubElement() ){ + TPZVec pv2; + Neighbour.Element()->Divide(pv2); + } + } + } + + gmesh->BuildConnectivity(); + +} +/*}}}*/ +void AdaptiveMeshRefinement::RefineMeshToAvoidHangingNodes(TPZGeoMesh *gmesh){/*{{{*/ + + _printf_("\trefine to avoid hanging nodes...\n"); + /*Refine elements to avoid hanging nodes: non-uniform refinement*/ + const int NElem = gmesh->NElements(); + for(int i = 0; i < NElem; i++){ + + /*Get geometric element and verify if it has already been refined. Geoel may not have been previously refined*/ + TPZGeoEl * geoel = gmesh->Element(i); + if(!geoel) continue; + if(geoel->HasSubElement()) continue; + if(geoel->MaterialId() != this->GetElemMaterialID()) continue; + + /*Get the refinement pattern for this element and refine it*/ + TPZAutoPointer refp = TPZRefPatternTools::PerfectMatchRefPattern(geoel); + if(refp){ + TPZVec Sons; + geoel->SetRefPattern(refp); + geoel->Divide(Sons); + } + + } + + gmesh->BuildConnectivity(); + +} +/*}}}*/ +void AdaptiveMeshRefinement::GetMesh(TPZGeoMesh *gmesh,int &nvertices,int &nelements,int &nsegments,double** px,double** py,double** pz, int** pelements, int** psegments){/*{{{*/ + + /*IMPORTANT! pelements (and psegments) are in Matlab indexing*/ + /*NEOPZ works only in C indexing*/ + + /* vertices */ + int ntotalvertices = gmesh->NNodes();//total + + /* mesh coords */ + double* newmeshX = xNew(ntotalvertices); + double* newmeshY = xNew(ntotalvertices); + double* newmeshZ = xNew(ntotalvertices); + + /* getting mesh coords */ + for(int i = 0; i < ntotalvertices; i++ ){ + TPZVec coords(3,0.); + gmesh->NodeVec()[i].GetCoordinates(coords); + newmeshX[i] = coords[0]; + newmeshY[i] = coords[1]; + newmeshZ[i] = coords[2]; + } + + /* elements */ + std::vector GeoVec; GeoVec.clear(); + for(int i = 0; i < gmesh->NElements(); i++){ + if( gmesh->ElementVec()[i]->HasSubElement() ) continue; + if( gmesh->ElementVec()[i]->MaterialId() != this->GetElemMaterialID() ) continue; + GeoVec.push_back( gmesh->ElementVec()[i]); + } + + int ntotalelements = (int)GeoVec.size(); + int* newelements = xNew(ntotalelements*this->elementswidth); + + if ( !(this->elementswidth == 3) && !(this->elementswidth == 4) && !(this->elementswidth == 6) ) DebugStop(); + + for(int i=0;ielementswidth;j++) newelements[i*this->elementswidth+j]=(int)GeoVec[i]->NodeIndex(j)+1;//C to Matlab indexing + } + + /* segments */ + std::vector SegVec; SegVec.clear(); + for(int i = 0; i < gmesh->NElements(); i++){ + if( gmesh->ElementVec()[i]->HasSubElement() ) continue; + if( gmesh->ElementVec()[i]->MaterialId() != this->GetBoundaryMaterialID() ) continue; + SegVec.push_back( gmesh->ElementVec()[i]); + } + + int ntotalsegments = (int)SegVec.size(); + int *newsegments=NULL; + if(ntotalsegments>0) newsegments=xNew(ntotalsegments*3); + + for(int i=0;iNodeIndex(j)+1;//C to Matlab indexing + + int neighborindex = SegVec[i]->Neighbour(2).Element()->Index(); + int neighbourid = -1; + + for(int j = 0; j < GeoVec.size(); j++){ + if( GeoVec[j]->Index() == neighborindex || GeoVec[j]->FatherIndex() == neighborindex){ + neighbourid = j; + break; + } + } + + if(neighbourid==-1) DebugStop(); //itapopo talvez passar para _assert_ + newsegments[i*3+2] = neighbourid+1;//C to Matlab indexing + } + + //setting outputs + nvertices = ntotalvertices; + nelements = ntotalelements; + nsegments = ntotalsegments; + *px = newmeshX; + *py = newmeshY; + *pz = newmeshZ; + *pelements = newelements; + *psegments = newsegments; + +} +/*}}}*/ +void AdaptiveMeshRefinement::CalcGroundingLinePosition(double *masklevelset,std::vector > &GLvec){/*{{{*/ + + /* Find grounding line using elments center point */ + GLvec.clear(); + for(int i=0;ipreviousmesh->NElements();i++){ + + if(this->previousmesh->Element(i)->MaterialId()!=this->GetElemMaterialID()) continue; + if(this->previousmesh->Element(i)->HasSubElement()) continue; + + //itapopo apenas malha 2D triangular! + int vertex0 = this->previousmesh->Element(i)->NodeIndex(0); + int vertex1 = this->previousmesh->Element(i)->NodeIndex(1); + int vertex2 = this->previousmesh->Element(i)->NodeIndex(2); + + //itapopo inserir uma verificação para não acessar fora da memória + double mls0 = masklevelset[vertex0]; + double mls1 = masklevelset[vertex1]; + double mls2 = masklevelset[vertex2]; + + if( mls0*mls1 < 0. || mls1*mls2 < 0. ){ + const int side = 6; + TPZVec qsi(2,0.); + TPZVec X(3,0.); + this->previousmesh->Element(i)->CenterPoint(side, qsi); + this->previousmesh->Element(i)->X(qsi, X); + GLvec.push_back(X); + } + } + +// itapopo apenas para debugar +// std::ofstream fileGL("/Users/santos/Desktop/gl.nb"); +// fileGL << "ListPlot[{"; +// for(int i = 0; i < GLvec.size(); i++){ +// fileGL << "{" << GLvec[i][0] << "," << GLvec[i][1] << /*"," << 0. << */"}"; +// if(i != GLvec.size()-1) fileGL << ","; +// } +// fileGL << "}]"; +// fileGL.flush(); +// fileGL.close(); + +} +/*}}}*/ +void AdaptiveMeshRefinement::SetElementsToRefine(TPZGeoMesh *gmesh,std::vector > &GLvec,int &hlevel,std::vector &ElemVec){/*{{{*/ + + if(!gmesh) DebugStop(); //itapopo verificar se usará _assert_ + + ElemVec.clear(); + + // itapopo inserir modo de encontrar criterio TESTING!!!! Come to false! + if(false) this->TagAllElements(gmesh,ElemVec); //uniform, refine all elements! + + /* Adaptive refinement. This refines some elements following some criteria*/ + this->TagElementsNearGroundingLine(gmesh, GLvec, hlevel, ElemVec); + +} +/*}}}*/ +void AdaptiveMeshRefinement::TagAllElements(TPZGeoMesh *gmesh,std::vector &ElemVec){/*{{{*/ + + /* Uniform refinement. This refines the entire mesh */ + int nelements = gmesh->NElements(); + for(int i=0;iElement(i)->MaterialId()!=this->GetElemMaterialID()) continue; + if(gmesh->Element(i)->HasSubElement()) continue; + ElemVec.push_back(i); + } +} +/*}}}*/ +void AdaptiveMeshRefinement::TagElementsNearGroundingLine(TPZGeoMesh *gmesh,std::vector > &GLvec,int &hlevel,std::vector &ElemVec){/*{{{*/ + + /* Tag elements near grounding line */ + double D1 = this->regionlevel1; + double Dhmax = this->regionlevelmax; + int hmax = this->levelmax; + double alpha = (hmax==1) ? 0. : log(D1/Dhmax)/(hmax-1.); + double Di = D1/exp(alpha*(hlevel-1)); + + for(int i=0;iNElements();i++){ + + if(gmesh->Element(i)->MaterialId()!=this->GetElemMaterialID()) continue; + if(gmesh->Element(i)->HasSubElement()) continue; + if(gmesh->Element(i)->Level()>=hlevel) continue; + + const int side2D = 6; + TPZVec qsi(2,0.); + TPZVec centerPoint(3,0.); + gmesh->Element(i)->CenterPoint(side2D, qsi); + gmesh->Element(i)->X(qsi, centerPoint); + + REAL distance = Di; + + for (int j = 0; j < GLvec.size(); j++) { + + REAL value = ( GLvec[j][0] - centerPoint[0] ) * ( GLvec[j][0] - centerPoint[0] ); // (x2-x1)^2 + value += ( GLvec[j][1] - centerPoint[1] ) * ( GLvec[j][1] - centerPoint[1] );// (y2-y1)^2 + value = std::sqrt(value); //Radius + + //finding the min distance to the grounding line + if(value < distance) distance = value; + + } + + if(distance < Di) ElemVec.push_back(i); + } + +} +/*}}}*/ +void AdaptiveMeshRefinement::CreateInitialMesh(int &nvertices,int &nelements,int &nsegments,int &width,double* x,double* y,double* z,int* elements,int* segments){/*{{{*/ + + /*IMPORTANT! elements come in Matlab indexing*/ + /*NEOPZ works only in C indexing*/ + + _assert_(nvertices>0); + _assert_(nelements>0); + this->SetElementWidth(width); + + /*Verify and creating initial mesh*/ + if(this->fathermesh) _error_("Initial mesh already exists!"); + + this->fathermesh = new TPZGeoMesh(); + this->fathermesh->NodeVec().Resize( nvertices ); + + /*Set the vertices (geometric nodes in NeoPZ context)*/ + for(int i=0;i coord(3,0.); + coord[0]= x[i]; + coord[1]= y[i]; + coord[2]= z[i]; + /*Insert in the mesh*/ + this->fathermesh->NodeVec()[i].SetCoord(coord); + this->fathermesh->NodeVec()[i].SetNodeId(i); + } + + /*Generate the elements*/ + long index; + const int mat = this->GetElemMaterialID(); + TPZManVector elem(this->elementswidth,0); + + for(int iel=0;ielelementswidth;jel++) elem[jel]=elements[iel*this->elementswidth+jel]-1;//Convert Matlab to C indexing + + /*reftype = 0: uniform, fast / reftype = 1: uniform and non-uniform (avoid hanging nodes), it is not too fast */ + const int reftype = 0; + switch(this->elementswidth){ + case 3: this->fathermesh->CreateGeoElement(ETriangle, elem, mat, index, reftype); break; + case 4: this->fathermesh->CreateGeoElement(ETetraedro, elem, mat, index, reftype); DebugStop(); break; + case 6: this->fathermesh->CreateGeoElement(EPrisma, elem, mat, index, reftype); DebugStop(); break; + default: DebugStop();//itapopo _error_("mesh not supported yet"); + } + + /*Define the element ID*/ + this->fathermesh->ElementVec()[index]->SetId(iel); + } + + /*Generate the 1D segments elements (boundary)*/ + const int matboundary = this->GetBoundaryMaterialID(); + TPZManVector boundary(2,0.); + + for(int iel=nelements;ielfathermesh->CreateGeoElement(EOned, boundary, matboundary, index, reftype);//cria elemento unidimensional + this->fathermesh->ElementVec()[index]->SetId(iel); + } + + /*Build element and node connectivities*/ + this->fathermesh->BuildConnectivity(); + + /*Create previous mesh as a copy of father mesh*/ + this->previousmesh = new TPZGeoMesh(*this->fathermesh); + +} +/*}}}*/ +#include "pzgeotriangle.h" //itapopo +#include "pzreftriangle.h" //itapopo +using namespace pzgeom; +TPZGeoMesh* AdaptiveMeshRefinement::CreateRefPatternMesh(TPZGeoMesh* gmesh){/*{{{*/ + + TPZGeoMesh *newgmesh = new TPZGeoMesh(); + newgmesh->CleanUp(); + + int nnodes = gmesh->NNodes(); + int nelem = gmesh->NElements(); + int mat = this->GetElemMaterialID();; + int reftype = 1; + long index; + + //nodes + newgmesh->NodeVec().Resize(nnodes); + for(int i=0;iNodeVec()[i] = gmesh->NodeVec()[i]; + + //elements + for(int i=0;iElement(i); + TPZManVector elem(3,0); + for(int j=0;j<3;j++) elem[j] = geoel->NodeIndex(j); + + newgmesh->CreateGeoElement(ETriangle,elem,mat,index,reftype); + newgmesh->ElementVec()[index]->SetId(geoel->Id()); + + TPZGeoElRefPattern* newgeoel = dynamic_cast*>(newgmesh->ElementVec()[index]); + + //old neighbourhood + const int nsides = TPZGeoTriangle::NSides; + TPZVec< std::vector > neighbourhood(nsides); + TPZVec NodesSequence(0); + for(int s = 0; s < nsides; s++){ + neighbourhood[s].resize(0); + TPZGeoElSide mySide(geoel,s); + TPZGeoElSide neighS = mySide.Neighbour(); + if(mySide.Dimension() == 0){ + long oldSz = NodesSequence.NElements(); + NodesSequence.resize(oldSz+1); + NodesSequence[oldSz] = geoel->NodeIndex(s); + } + while(mySide != neighS){ + neighbourhood[s].push_back(neighS); + neighS = neighS.Neighbour(); + } + } + + //inserting in new element + for(int s = 0; s < nsides; s++){ + TPZGeoEl * tempEl = newgeoel; + TPZGeoElSide tempSide(newgeoel,s); + int byside = s; + for(unsigned long n = 0; n < neighbourhood[s].size(); n++){ + TPZGeoElSide neighS = neighbourhood[s][n]; + tempEl->SetNeighbour(byside, neighS); + tempEl = neighS.Element(); + byside = neighS.Side(); + } + tempEl->SetNeighbour(byside, tempSide); + } + + long fatherindex = geoel->FatherIndex(); + if(fatherindex>-1) newgeoel->SetFather(fatherindex); + + if(!geoel->HasSubElement()) continue; + + int nsons = geoel->NSubElements(); + + TPZAutoPointer ref = gRefDBase.GetUniformRefPattern(ETriangle); + newgeoel->SetRefPattern(ref); + + for(int j=0;jSubElement(j); + if(!son){ + DebugStop(); + } + newgeoel->SetSubElement(j,son); + } + } + newgmesh->BuildConnectivity(); + + return newgmesh; +} +/*}}}*/ +void AdaptiveMeshRefinement::SetLevelMax(int &h){/*{{{*/ + this->levelmax = h; +} +/*}}}*/ +void AdaptiveMeshRefinement::SetRegions(double &D1,double Dhmax){/*{{{*/ + this->regionlevel1 = D1; + this->regionlevelmax = Dhmax; +} +/*}}}*/ +void AdaptiveMeshRefinement::SetElementWidth(int &width){/*{{{*/ + this->elementswidth = width; +} +/*}}}*/ +void AdaptiveMeshRefinement::CheckMesh(int &nvertices,int &nelements,int &nsegments,int &width,double** px,double** py,double** pz,int** pelements, int** psegments){/*{{{*/ + + /*Basic verification*/ + if( !(nvertices > 0) || !(nelements > 0) ) DebugStop(); //itapopo verificar se irá usar o _assert_ + + if ( !(width == 3) && !(width == 4) && !(width == 6) ) DebugStop(); // itapopo verifcar se irá usar o _assert_ + + if( !px || !py || !pz || !pelements ) DebugStop(); // itapopo verifcar se irá usar o _assert_ + + /*Verify if there are orphan nodes*/ + std::set elemvertices; + elemvertices.clear(); + for(int i = 0; i < nelements; i++){ + for(int j = 0; j < width; j++) { + elemvertices.insert((*pelements)[i*width+j]); + } + } + + if( elemvertices.size() != nvertices ) DebugStop();//itapopo verificar se irá usar o _assert_ + + //Verify if there are inf or NaN in coords + for(int i = 0; i < nvertices; i++) if(isnan((*px)[i]) || isinf((*px)[i])) DebugStop(); + for(int i = 0; i < nvertices; i++) if(isnan((*py)[i]) || isinf((*py)[i])) DebugStop(); + for(int i = 0; i < nvertices; i++) if(isnan((*pz)[i]) || isinf((*pz)[i])) DebugStop(); + + for(int i = 0; i < nelements; i++){ + for(int j = 0; j < width; j++){ + if( isnan((*pelements)[i*width+j]) || isinf((*pelements)[i*width+j]) ) DebugStop(); + } + } + +} +/*}}}*/ Index: /issm/trunk/src/c/classes/AdaptiveMeshRefinement.h =================================================================== --- /issm/trunk/src/c/classes/AdaptiveMeshRefinement.h (revision 21729) +++ /issm/trunk/src/c/classes/AdaptiveMeshRefinement.h (revision 21729) @@ -0,0 +1,91 @@ +#ifndef ADAPTIVEMESHREFINEMENT +#define ADAPTIVEMESHREFINEMENT + +/*Includes*/ +/*{{{*/ +/*Common includes*/ +#include +#include +#include + +/*NeoPZ includes*/ +/*REAL and STATE definitions, NeoPZ variables itapopo should be read by NeoPZ's config.h*/ +#ifndef REFPATTERNDIR + # define REFPATTERNDIR "/home/santos/trunk-jpl/externalpackages/neopz/install/include/refpatterns" +#endif + +#ifndef REALdouble + #define REALdouble +#endif + +#ifndef STATEdouble + #define STATEdouble +#endif + +#include +#include +#include +#include +#include + +#include +#include +#include + +#include +#include +#include +#include +/*}}}*/ + +class AdaptiveMeshRefinement : public TPZSaveable { + +public: + + /*Public methods*/ + /* Constructor, destructor etc*/ + AdaptiveMeshRefinement(); // Default constructor + AdaptiveMeshRefinement(const AdaptiveMeshRefinement &cp); // Copy constructor + AdaptiveMeshRefinement & operator= (const AdaptiveMeshRefinement &cp); // Operator of copy + virtual ~AdaptiveMeshRefinement(); // Destructor + + /*Savable methods*/ + virtual int ClassId() const; // ClassId to save the class + virtual void Read(TPZStream &buf, void *context); // Read this class + virtual void Write(TPZStream &buf, int withclassid); // Write this class, using ClassId to identify + + /*General methods*/ + void CleanUp(); // Clean all attributes + void Initialize(); // Initialize the attributes with NULL and values out of usually range + void SetLevelMax(int &h); // Define the max level of refinement + void SetRegions(double &D1,double Dhmax); // Define the regions which will be refined + void SetElementWidth(int &width); // Define elements width + void ExecuteRefinement(int &type_process,double *vx,double *vy,double *masklevelset,int &nvertices,int &nelements,int &nsegments,double** px,double** py,double** pz,int** pelements,int** psegments=NULL); // A new mesh will be created and refined. This returns the new mesh + void CreateInitialMesh(int &nvertices,int &nelements,int &nsegments,int &width,double* x,double* y,double* z,int* elements,int* segments=NULL); // Create a NeoPZ geometric mesh by coords and elements + TPZGeoMesh* CreateRefPatternMesh(TPZGeoMesh* gmesh); + void CheckMesh(int &nvertices,int &nelements,int &nsegments,int &width,double** px,double** py,double** pz,int** pelements,int** psegments=NULL); // Check the consistency of the mesh + +private: + + /*Private attributes*/ + int elementswidth; // Geometric nodes for element: 3 == Tria, 4 == Tetra, 6 == Penta + int levelmax; // Max level of refinement + double regionlevel1; // Region which will be refined with level 1 + double regionlevelmax; // Region which will be refined with level max + TPZGeoMesh *fathermesh; // Father Mesh is the entire mesh without refinement + TPZGeoMesh *previousmesh; // Previous mesh is a refined mesh of last step + + /*Private methods*/ + void RefinementProcess(TPZGeoMesh *gmesh,std::vector > &GLvec); // Start the refinement process + void RefineMesh(TPZGeoMesh *gmesh, std::vector &ElemVec); // Refine the elements in ElemVec + void RefineMeshToAvoidHangingNodes(TPZGeoMesh *gmesh); // Refine the elements to avoid hanging nodes + void SetElementsToRefine(TPZGeoMesh *gmesh,std::vector > &GLvec,int &hlevel, std::vector &ElemVec); //Define wich elements will be refined + void TagAllElements(TPZGeoMesh *gmesh,std::vector &ElemVec); // This tag all elements to be refined, that is, refine all elements + void TagElementsNearGroundingLine(TPZGeoMesh *gmesh,std::vector > &GLvec,int &hlevel,std::vector &ElemVec); // This tag elements near the grounding line + void CalcGroundingLinePosition(double *masklevelset,std::vector > &GLvec); // Calculate the grounding line position using previous mesh + void GetMesh(TPZGeoMesh *gmesh,int &nvertices,int &nelements,int &nsegments,double** px,double** py,double** pz,int** pelements,int** psegments=NULL); // Return coords and elements in ISSM data structure + inline int GetElemMaterialID(){return 1;} // Return element material ID + inline int GetBoundaryMaterialID(){return 2;} // Return segment (2D boundary) material ID +}; + +#endif Index: /issm/trunk/src/c/classes/DofIndexing.cpp =================================================================== --- /issm/trunk/src/c/classes/DofIndexing.cpp (revision 21728) +++ /issm/trunk/src/c/classes/DofIndexing.cpp (revision 21729) @@ -251,8 +251,10 @@ _printf_(" freeze: " << freeze << "\n"); - _printf_(" set membership: f,s sets \n"); - for(i=0;issize << "): |"); Index: /issm/trunk/src/c/classes/Elements/Element.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Element.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Elements/Element.cpp (revision 21729) @@ -48,5 +48,5 @@ IssmDouble vx,vy,vz,vmag; IssmDouble dvx[3],dvy[3],dvz[3],dvmag[3]; - IssmDouble epso,epsprime; + IssmDouble epseff,epsprime; int dim; IssmDouble *xyz_list = NULL; @@ -101,6 +101,6 @@ dvmag[2]=1./(2*sqrt(vmag))*(2*vx*dvx[2]+2*vy*dvy[2]+2*vz*dvz[2]); } - EstarStrainrateQuantities(&epso,&epsprime,vx,vy,vz,vmag,&dvx[0],&dvy[0],&dvz[0],&dvmag[0]); - lambdas[iv]=EstarLambdaS(epso,epsprime); + EstarStrainrateQuantities(&epseff,&epsprime,vx,vy,vz,vmag,&dvx[0],&dvy[0],&dvz[0],&dvmag[0]); + lambdas[iv]=EstarLambdaS(epseff,epsprime); } @@ -527,8 +527,9 @@ IssmDouble* tmp=xNew(numvertices); IssmDouble Delta18oTime; - IssmDouble dpermil; + IssmDouble dpermil,f; IssmDouble time,yts,time_yr,month; this->parameters->FindParam(&time,TimeEnum); this->parameters->FindParam(&yts,ConstantsYtsEnum); + this->parameters->FindParam(&f,SmbFEnum); time_yr=floor(time/yts)*yts; @@ -556,5 +557,5 @@ /*Compute the temperature and precipitation*/ for(int iv=0;ivGetViscosity_B(&dmudB,eps_eff); + materialstype=this->material->ObjectEnum(); + switch(materialstype){ + case MaticeEnum: + material->GetViscosity_B(&dmudB,eps_eff); + break; + case MatestarEnum: + material->ViscosityBFS(&dmudB,dim,xyz_list,gauss,vx_input,vy_input,vz_input); + break; + default: _error_("not supported"); + } /*Assign output pointer*/ @@ -679,4 +690,5 @@ /*Intermediaries*/ + int materialstype; IssmDouble dmudB; IssmDouble epsilon3d[5];/* epsilon=[exx,eyy,exy,exy,exz,eyz]; */ @@ -696,5 +708,14 @@ } /*Get viscosity*/ - material->GetViscosity_B(&dmudB,eps_eff); + materialstype=this->material->ObjectEnum(); + switch(materialstype){ + case MaticeEnum: + material->GetViscosity_B(&dmudB,eps_eff); + break; + case MatestarEnum: + material->ViscosityBHO(&dmudB,dim,xyz_list,gauss,vx_input,vy_input); + break; + default: _error_("not supported"); + } /*Assign output pointer*/ @@ -706,4 +727,5 @@ /*Intermediaries*/ + int materialstype; IssmDouble dmudB; IssmDouble epsilon2d[3];/* epsilon=[exx,eyy,exy]; */ @@ -723,5 +745,14 @@ /*Get viscosity*/ - material->GetViscosity_B(&dmudB,eps_eff); + materialstype=this->material->ObjectEnum(); + switch(materialstype){ + case MaticeEnum: + material->GetViscosity_B(&dmudB,eps_eff); + break; + case MatestarEnum: + material->ViscosityBSSA(&dmudB,dim,xyz_list,gauss,vx_input,vy_input); + break; + default: _error_("not supported"); + } /*Assign output pointer*/ @@ -1041,4 +1072,28 @@ if(!input) _error_("Input " << EnumToStringx(inputenum) << " not found in element"); input->GetInputValue(pvalue,gauss); + +}/*}}}*/ +void Element::GetInputsInterpolations(Vector* interpolations){/*{{{*/ + + int interpolation; + + /*Go through all inputs and assign interpolation in vector*/ + _assert_(this->inputs); + for(int i=0;iinputs->Size();i++){ + Input* input=xDynamicCast(this->inputs->GetObjectByOffset(i)); + switch(input->ObjectEnum()){ + case BoolInputEnum: + case DoubleInputEnum: + case IntInputEnum: + interpolations->SetValue(input->InstanceEnum(),reCast(input->ObjectEnum()),INS_VAL); + break; + case TriaInputEnum: + interpolation = input->GetResultInterpolation(); + interpolations->SetValue(input->InstanceEnum(),interpolation,INS_VAL); + break; + default: + _error_("Input "<ObjectEnum())<<" not supported yet"); + } + } }/*}}}*/ @@ -1138,43 +1193,50 @@ int numnodes = this->GetNumberOfNodes(); int* doflist = NULL; + IssmDouble value; IssmDouble* values = NULL; + Input* input = NULL; switch(type){ - case VertexPIdEnum: - doflist = xNew(numvertices); - values = xNew(numvertices); - /*Fill in values*/ - this->GetVertexPidList(doflist); - this->GetInputListOnVertices(values,input_enum); - vector->SetValues(numvertices,doflist,values,INS_VAL); - break; - case VertexSIdEnum: - doflist = xNew(numvertices); - values = xNew(numvertices); - /*Fill in values*/ - this->GetVerticesSidList(doflist); - this->GetInputListOnVertices(values,input_enum); - vector->SetValues(numvertices,doflist,values,INS_VAL); - break; - case NodesEnum: - doflist = xNew(numnodes); - values = xNew(numnodes); - /*Fill in values*/ - this->GetInputListOnNodes(values,input_enum); - this->GetDofList(&doflist,NoneApproximationEnum,GsetEnum); - vector->SetValues(numnodes,doflist,values,INS_VAL); - break; - case NodeSIdEnum: - doflist = xNew(numnodes); - values = xNew(numnodes); - /*Fill in values*/ - this->GetNodesSidList(doflist); - this->GetInputListOnNodes(values,input_enum); - vector->SetValues(numnodes,doflist,values,INS_VAL); - break; - default: - _error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet"); - } - + case ElementSIdEnum: + input=inputs->GetInput(input_enum); _assert_(input); + input->GetInputAverage(&value); + vector->SetValue(this->sid,value,INS_VAL); + break; + case VertexPIdEnum: + doflist = xNew(numvertices); + values = xNew(numvertices); + /*Fill in values*/ + this->GetVertexPidList(doflist); + this->GetInputListOnVertices(values,input_enum); + vector->SetValues(numvertices,doflist,values,INS_VAL); + break; + case VertexSIdEnum: + doflist = xNew(numvertices); + values = xNew(numvertices); + /*Fill in values*/ + this->GetVerticesSidList(doflist); + this->GetInputListOnVertices(values,input_enum); + vector->SetValues(numvertices,doflist,values,INS_VAL); + break; + case NodesEnum: + doflist = xNew(numnodes); + values = xNew(numnodes); + /*Fill in values*/ + this->GetInputListOnNodes(values,input_enum); + this->GetDofList(&doflist,NoneApproximationEnum,GsetEnum); + vector->SetValues(numnodes,doflist,values,INS_VAL); + break; + case NodeSIdEnum: + doflist = xNew(numnodes); + values = xNew(numnodes); + /*Fill in values*/ + this->GetNodesSidList(doflist); + this->GetInputListOnNodes(values,input_enum); + vector->SetValues(numnodes,doflist,values,INS_VAL); + break; + default: + _error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet"); + } + /*Clean up*/ xDelete(doflist); @@ -1511,9 +1573,9 @@ name==OldGradientEnum || name==ConvergedEnum || + name==MaterialsRheologyEEnum || + name==MaterialsRheologyEbarEnum || name==MaterialsRheologyBEnum || name==MaterialsRheologyBbarEnum || name==MaterialsRheologyNEnum || - name==MaterialsRheologyKoEnum || - name==MaterialsRheologyKobarEnum || name==MaterialsRheologyEcEnum || name==MaterialsRheologyEcbarEnum || @@ -1530,4 +1592,8 @@ name==EsaNmotionEnum || name==EsaEmotionEnum || + name==EsaStrainratexxEnum || + name==EsaStrainratexyEnum || + name==EsaStrainrateyyEnum || + name==EsaRotationrateEnum || name==EsaDeltathicknessEnum || name==GiaWEnum || @@ -1547,5 +1613,13 @@ name==HydrologyHeadOldEnum || name==StressbalanceConvergenceNumStepsEnum || - name==MeshVertexonbaseEnum + name==MeshVertexonbaseEnum || + name==FrictionPEnum || + name==FrictionQEnum || + name==FrictionCoefficientcoulombEnum || + name==LoadingforceXEnum || + name==LoadingforceYEnum || + name==VelEnum || + name==VxPicardEnum || + name==VyPicardEnum ) { @@ -1958,7 +2032,7 @@ desfac, s0t[iv], s0p[iv],rlaps,rlapslgm,TdiffTime,sealevTime, rho_water,rho_ice); - /*Get yearlytemperatures */ + /*Get yearlytemperatures */ for(int month=0;month<12;month++) { - yearlytemperatures[iv]=yearlytemperatures[iv]+(monthlytemperatures[iv*12+month]+273.15)*mavg; // Has to be in Kelvin + yearlytemperatures[iv]=yearlytemperatures[iv]+(monthlytemperatures[iv*12+month]+273.15)*mavg; // Has to be in Kelvin } } @@ -1981,6 +2055,6 @@ switch(this->ObjectEnum()){ case TriaEnum: - // this->inputs->AddInput(new TriaInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); - this->inputs->AddInput(new TriaInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); + // this->inputs->AddInput(new TriaInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); + this->inputs->AddInput(new TriaInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); this->inputs->AddInput(new TriaInput(SmbMassBalanceEnum,&agd[0],P1Enum)); this->inputs->AddInput(new TriaInput(SmbAccumulationEnum,&accu[0],P1Enum)); @@ -1988,29 +2062,44 @@ break; case PentaEnum: - if(IsOnSurface()){ - GetInputListOnVertices(&s[0],TemperatureEnum); - yearlytemperatures[0] = s[0]; - yearlytemperatures[1] = s[1]; - yearlytemperatures[2] = s[2]; - this->inputs->AddInput(new PentaInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); - } - this->inputs->AddInput(new PentaInput(SmbMassBalanceEnum,&agd[0],P1Enum)); - this->inputs->AddInput(new PentaInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); - this->InputExtrude(TemperaturePDDEnum,-1); - this->InputExtrude(SmbMassBalanceEnum,-1); - break; + if(IsOnSurface()){ + /*Here, we want to change the BC of the thermal model, keep + * the temperatures as they are for the base of the penta and + * yse yearlytemperatures for the top*/ + GetInputListOnVertices(&s[0],TemperatureEnum); + yearlytemperatures[0] = s[0]; + yearlytemperatures[1] = s[1]; + yearlytemperatures[2] = s[2]; + this->inputs->AddInput(new PentaInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); + + bool isenthalpy; + this->parameters->FindParam(&isenthalpy,ThermalIsenthalpyEnum); + if(isenthalpy){ + /*Convert that to enthalpy for the enthalpy model*/ + IssmDouble enthalpy[6]; + GetInputListOnVertices(&enthalpy[0],EnthalpyEnum); + ThermalToEnthalpy(&enthalpy[3],yearlytemperatures[3],0.,0.); + ThermalToEnthalpy(&enthalpy[4],yearlytemperatures[4],0.,0.); + ThermalToEnthalpy(&enthalpy[5],yearlytemperatures[5],0.,0.); + this->inputs->AddInput(new PentaInput(EnthalpyEnum,&enthalpy[0],P1Enum)); + } + } + this->inputs->AddInput(new PentaInput(SmbMassBalanceEnum,&agd[0],P1Enum)); + this->inputs->AddInput(new PentaInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); + this->InputExtrude(TemperaturePDDEnum,-1); + this->InputExtrude(SmbMassBalanceEnum,-1); + break; case TetraEnum: - if(IsOnSurface()){ - GetInputListOnVertices(&s[0],TemperatureEnum); - yearlytemperatures[0] = s[0]; - yearlytemperatures[1] = s[1]; - yearlytemperatures[2] = s[2]; - this->inputs->AddInput(new TetraInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); - } - this->inputs->AddInput(new TetraInput(SmbMassBalanceEnum,&agd[0],P1Enum)); - this->inputs->AddInput(new TetraInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); - this->InputExtrude(TemperaturePDDEnum,-1); - this->InputExtrude(SmbMassBalanceEnum,-1); - break; + if(IsOnSurface()){ + GetInputListOnVertices(&s[0],TemperatureEnum); + yearlytemperatures[0] = s[0]; + yearlytemperatures[1] = s[1]; + yearlytemperatures[2] = s[2]; + this->inputs->AddInput(new TetraInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); + } + this->inputs->AddInput(new TetraInput(SmbMassBalanceEnum,&agd[0],P1Enum)); + this->inputs->AddInput(new TetraInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); + this->InputExtrude(TemperaturePDDEnum,-1); + this->InputExtrude(SmbMassBalanceEnum,-1); + break; default: _error_("Not implemented yet"); } @@ -2068,4 +2157,8 @@ case DeviatoricStresszzEnum: case DeviatoricStresseffectiveEnum: this->ComputeDeviatoricStressTensor(); break; + case EsaStrainratexxEnum: + case EsaStrainratexyEnum: + case EsaStrainrateyyEnum: + case EsaRotationrateEnum: this->ComputeEsaStrainAndVorticity(); break; case SigmaNNEnum: this->ComputeSigmaNN(); break; case LambdaSEnum: this->ComputeLambdaS(); break; @@ -2620,4 +2713,24 @@ } /*}}}*/ +void Element::StrainRateESA(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ + + /*Intermediaries*/ + IssmDouble dvx[3]; + IssmDouble dvy[3]; + + /*Check that both inputs have been found*/ + if(!vx_input || !vy_input){ + _error_("Input missing. Here are the input pointers we have for vx: " << vx_input << ", vy: " << vy_input << "\n"); + } + + /*Get strain rate assuming that epsilon has been allocated*/ + vx_input->GetInputDerivativeValue(&dvx[0],xyz_list,gauss); + vy_input->GetInputDerivativeValue(&dvy[0],xyz_list,gauss); + epsilon[0] = dvx[0]; // normal strain rate x-direction + epsilon[1] = dvy[1]; // normal strain rate y-direction + epsilon[2] = 0.5*(dvx[1] + dvy[0]); // shear strain rate + epsilon[3] = 0.5*(dvx[1] - dvy[0]); // rotation rate + +}/*}}}*/ void Element::StrainRateFS(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){/*{{{*/ /*Compute the 3d Strain Rate (6 components): Index: /issm/trunk/src/c/classes/Elements/Element.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Element.h (revision 21728) +++ /issm/trunk/src/c/classes/Elements/Element.h (revision 21729) @@ -95,4 +95,5 @@ void GetInputValue(IssmDouble* pvalue,int enum_type); void GetInputValue(IssmDouble* pvalue,Gauss* gauss,int enum_type); + void GetInputsInterpolations(Vector* interps); IssmDouble GetMaterialParameter(int enum_in); void GetNodesLidList(int* lidlist); @@ -140,4 +141,5 @@ int Sid(); void SmbGemb(); + void StrainRateESA(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); void StrainRateFS(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input); void StrainRateHO(IssmDouble* epsilon,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); @@ -174,4 +176,5 @@ virtual void AddInput(int input_enum, IssmDouble* values, int interpolation_enum)=0; virtual void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part)=0; + virtual void BasalNodeIndices(int* pnumindices,int** pindices,int finiteelement){_error_("not implemented yet");}; virtual void CalvingRateDev(void){_error_("not implemented yet");}; virtual void CalvingRateLevermann(void)=0; @@ -181,4 +184,5 @@ virtual void ComputeSigmaNN(void)=0; virtual void ComputeStressTensor(void)=0; + virtual void ComputeEsaStrainAndVorticity(void)=0; virtual void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters)=0; virtual void ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index)=0; @@ -289,9 +293,10 @@ virtual int VertexConnectivity(int vertexindex)=0; virtual void VerticalSegmentIndices(int** pindices,int* pnumseg)=0; + virtual void VerticalSegmentIndicesBase(int** pindices,int* pnumseg)=0; virtual void ViscousHeating(IssmDouble* pphi,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input)=0; virtual void WriteLevelsetSegment(DataSet* segments){_error_("not implemented yet");}; virtual void ZeroLevelsetCoordinates(IssmDouble** pxyz_zero,IssmDouble* xyz_list,int levelsetenum)=0; - #ifdef _HAVE_GIA_ + #ifdef _HAVE_GIAIVINS_ virtual void GiaDeflection(Vector* wg,Vector* dwgdt,IssmDouble* x,IssmDouble* y)=0; #endif @@ -305,4 +310,5 @@ virtual IssmDouble OceanAverage(IssmDouble* Sg)=0; virtual IssmDouble OceanArea(void)=0; + virtual void SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea)=0; virtual void SealevelriseEustatic(Vector* pSgi,IssmDouble* peustatic,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble oceanarea,IssmDouble eartharea)=0; virtual void SealevelriseNonEustatic(Vector* pSgo,IssmDouble* Sg_old,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble eartharea)=0; Index: /issm/trunk/src/c/classes/Elements/ElementHook.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/ElementHook.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Elements/ElementHook.cpp (revision 21729) @@ -136,4 +136,69 @@ /*}}}*/ +void ElementHook::DeepEcho(){/*{{{*/ + + _printf_(" ElementHook DeepEcho:\n"); + _printf_(" numanalyses : "<< this->numanalyses <<"\n"); + + _printf_(" hnodes:\n"); + if(hnodes){ + for(int i=0;inumanalyses;i++) { + if(hnodes[i]) hnodes[i]->DeepEcho(); + else _printf_(" hnodes["<< i << "] = NULL\n"); + } + } + else _printf_(" hnodes = NULL\n"); + + _printf_(" hvertices:\n"); + if(hvertices) hvertices->DeepEcho(); + else _printf_(" hvertices = NULL\n"); + + _printf_(" hmaterial:\n"); + if(hmaterial) hmaterial->DeepEcho(); + else _printf_(" hmaterial = NULL\n"); + + _printf_(" hmatpar:\n"); + if(hmatpar) hmatpar->DeepEcho(); + else _printf_(" hmatpar = NULL\n"); + + _printf_(" hneighbors:\n"); + if(hneighbors) hneighbors->DeepEcho(); + else _printf_(" hneighbors = NULL\n"); + + return; +} +/*}}}*/ +void ElementHook::Echo(){/*{{{*/ + + _printf_(" ElementHook Echo:\n"); + _printf_(" numanalyses : "<< this->numanalyses <<"\n"); + + _printf_(" hnodes:\n"); + if(hnodes){ + for(int i=0;inumanalyses;i++) { + if(hnodes[i]) hnodes[i]->Echo(); + } + } + else _printf_(" hnodes = NULL\n"); + + _printf_(" hvertices:\n"); + if(hvertices) hvertices->Echo(); + else _printf_(" hvertices = NULL\n"); + + _printf_(" hmaterial:\n"); + if(hmaterial) hmaterial->Echo(); + else _printf_(" hmaterial = NULL\n"); + + _printf_(" hmatpar:\n"); + if(hmatpar) hmatpar->Echo(); + else _printf_(" hmatpar = NULL\n"); + + _printf_(" hneighbors:\n"); + if(hneighbors) hneighbors->Echo(); + else _printf_(" hneighbors = NULL\n"); + + return; +} +/*}}}*/ void ElementHook::InitHookNeighbors(int* element_ids){/*{{{*/ this->hneighbors=new Hook(element_ids,2); Index: /issm/trunk/src/c/classes/Elements/ElementHook.h =================================================================== --- /issm/trunk/src/c/classes/Elements/ElementHook.h (revision 21728) +++ /issm/trunk/src/c/classes/Elements/ElementHook.h (revision 21729) @@ -24,5 +24,7 @@ ~ElementHook(); void Marshall(char** pmarshalled_data,int* pmarshalled_data_size, int marshall_direction); - + + void DeepEcho(); + void Echo(); void InitHookNeighbors(int* element_ids); //3d only void SetHookNodes(int* node_ids,int numnodes,int analysis_counter); Index: /issm/trunk/src/c/classes/Elements/Penta.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Penta.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Elements/Penta.cpp (revision 21729) @@ -172,6 +172,94 @@ } /*}}}*/ +void Penta::BasalNodeIndices(int* pnumindices,int** pindices,int finiteelement){/*{{{*/ + + PentaRef::BasalNodeIndices(pnumindices,pindices,finiteelement); + +} +/*}}}*/ void Penta::AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part){/*{{{*/ _error_("Not supported yet!"); +} +/*}}}*/ +void Penta::CalvingRateDev(){/*{{{*/ + + if(!this->IsOnBase()) return; + + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble epsilon[3]; /* epsilon=[exx,eyy,exy];*/ + IssmDouble calvingratex[NUMVERTICES]; + IssmDouble calvingratey[NUMVERTICES]; + IssmDouble calvingrate[NUMVERTICES]; + IssmDouble lambda1,lambda2,ex,ey,vx,vy,vel; + IssmDouble sigma_vm,sigma_max,sigma_max_floating,sigma_max_grounded; + IssmDouble epse_2,groundedice; + + /* Get node coordinates and dof list: */ + ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + + /*Depth average B for stress calculation*/ + this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum); + this->InputDepthAverageAtBase(VxEnum,VxAverageEnum); + this->InputDepthAverageAtBase(VyEnum,VyAverageEnum); + + /*Retrieve all inputs and parameters we will need*/ + Input* vx_input = inputs->GetInput(VxAverageEnum); _assert_(vx_input); + Input* vy_input = inputs->GetInput(VyAverageEnum); _assert_(vy_input); + Input* gr_input = inputs->GetInput(MaskGroundediceLevelsetEnum); _assert_(gr_input); + IssmDouble B = this->GetMaterialParameter(MaterialsRheologyBbarEnum); + IssmDouble n = this->GetMaterialParameter(MaterialsRheologyNEnum); + this->parameters->FindParam(&sigma_max_floating,CalvingStressThresholdFloatingiceEnum); + this->parameters->FindParam(&sigma_max_grounded,CalvingStressThresholdGroundediceEnum); + + /* Start looping on the number of vertices: */ + GaussPenta* gauss=new GaussPenta(); + for(int iv=0;iv<3;iv++){ + gauss->GaussVertex(iv); + + /*Get velocity components and thickness*/ + vx_input->GetInputValue(&vx,gauss); + vy_input->GetInputValue(&vy,gauss); + gr_input->GetInputValue(&groundedice,gauss); + vel=sqrt(vx*vx+vy*vy)+1.e-14; + + /*Compute strain rate and viscosity: */ + this->StrainRateSSA(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input); + + /*Get Eigen values*/ + Matrix2x2Eigen(&lambda1,&lambda2,&ex,&ey,epsilon[0],epsilon[2],epsilon[1]); + _assert_(!xIsNan(lambda1)); + _assert_(!xIsNan(lambda2)); + + /*Process Eigen values (only account for extension)*/ + lambda1 = max(lambda1,0.); + lambda2 = max(lambda2,0.); + + /*Calculate sigma_vm*/ + epse_2 = 1./2. *(lambda1*lambda1 + lambda2*lambda2); + sigma_vm = sqrt(3.) * B * pow(epse_2,1./(2.*n)); + + /*Tensile stress threshold*/ + if(groundedice<0) + sigma_max = sigma_max_floating; + else + sigma_max = sigma_max_grounded; + + /*Assign values*/ + calvingratex[iv]=vx*sigma_vm/sigma_max; + calvingratey[iv]=vy*sigma_vm/sigma_max; + calvingrate[iv]=sqrt(calvingratex[iv]*calvingratex[iv] + calvingratey[iv]*calvingratey[iv]); + } + + /*Add input*/ + this->inputs->AddInput(new PentaInput(CalvingratexEnum,&calvingratex[0],P1Enum)); + this->inputs->AddInput(new PentaInput(CalvingrateyEnum,&calvingratey[0],P1Enum)); + this->inputs->AddInput(new PentaInput(CalvingCalvingrateEnum,&calvingrate[0],P1Enum)); + + this->InputExtrude(CalvingratexEnum,-1); + this->InputExtrude(CalvingrateyEnum,-1); + this->InputExtrude(CalvingCalvingrateEnum,-1); + + /*Clean up and return*/ + delete gauss; } /*}}}*/ @@ -2213,8 +2301,73 @@ } /*}}}*/ +void Penta::ResetLevelsetFromSegmentlist(IssmDouble* segments,int numsegments){/*{{{*/ + + /*Intermediaries*/ + IssmDouble d,xn,yn; + + /*Get current levelset and vertex coordinates*/ + IssmDouble ls[NUMVERTICES]; + IssmDouble xyz_list[NUMVERTICES][3]; + ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + GetInputListOnVertices(&ls[0],MaskIceLevelsetEnum); + InputDuplicate(MaskIceLevelsetEnum,PressureEnum); + + /*Get distance from list of segments and reset ls*/ + for(int j=0;j 1.0){ + // Beyond the 'w' end of the segment + d = (x-segments[4*i+2])*(x-segments[4*i+2])+(y-segments[4*i+3])*(y-segments[4*i+3]); + } + else{ + // Projection falls on the segment + xn = segments[4*i+0] + t * (segments[4*i+2] - segments[4*i+0]); + yn = segments[4*i+1] + t * (segments[4*i+3] - segments[4*i+1]); + d = (x-xn)*(x-xn)+(y-yn)*(y-yn); + } + + if(d10000) dmin=10000; + if(ls[j]>0){ + ls[j] = dmin; + } + else{ + ls[j] = - dmin; + } + } + + /*Update Levelset*/ + this->inputs->AddInput(new PentaInput(MaskIceLevelsetEnum,&ls[0],P1Enum)); +} +/*}}}*/ void Penta::SetClone(int* minranks){/*{{{*/ _error_("not implemented yet"); } + /*}}}*/ void Penta::SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index){/*{{{*/ @@ -2287,7 +2440,8 @@ this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum); if(this->material->IsDamage())this->InputDepthAverageAtBase(DamageDEnum,DamageDbarEnum); + if(this->material->IsEnhanced())this->InputDepthAverageAtBase(MaterialsRheologyEEnum,MaterialsRheologyEbarEnum); break; case MatestarEnum: - this->InputDepthAverageAtBase(MaterialsRheologyKoEnum,MaterialsRheologyKobarEnum); + this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum); this->InputDepthAverageAtBase(MaterialsRheologyEcEnum,MaterialsRheologyEcbarEnum); this->InputDepthAverageAtBase(MaterialsRheologyEsEnum,MaterialsRheologyEsbarEnum); @@ -3222,4 +3376,11 @@ } /*}}}*/ +void Penta::VerticalSegmentIndicesBase(int** pindices,int* pnumseg){/*{{{*/ + + PentaRef::VerticalSegmentIndicesBase(pindices,pnumseg,this->GetElementType()); + + return; +} +/*}}}*/ void Penta::ViscousHeating(IssmDouble* pphi,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){/*{{{*/ @@ -3394,5 +3555,5 @@ /*}}}*/ -#ifdef _HAVE_GIA_ +#ifdef _HAVE_GIAIVINS_ void Penta::GiaDeflection(Vector* wg,Vector* dwgdt,IssmDouble* x,IssmDouble* y){/*{{{*/ _error_("GIA deflection not implemented yet!"); Index: /issm/trunk/src/c/classes/Elements/Penta.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Penta.h (revision 21728) +++ /issm/trunk/src/c/classes/Elements/Penta.h (revision 21729) @@ -48,8 +48,11 @@ void AddInput(int input_enum, IssmDouble* values, int interpolation_enum); void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part); + void BasalNodeIndices(int* pnumindices,int** pindices,int finiteelement); + void CalvingRateDev(); void CalvingRateLevermann(); IssmDouble CharacteristicLength(void){_error_("not implemented yet");}; void ComputeBasalStress(Vector* sigma_b); void ComputeDeviatoricStressTensor(); + void ComputeEsaStrainAndVorticity(){_error_("not implemented yet!");}; void ComputeSigmaNN(){_error_("not implemented yet");}; void ComputeStressTensor(); @@ -146,4 +149,5 @@ void ResetFSBasalBoundaryCondition(void); void ResetHooks(); + void ResetLevelsetFromSegmentlist(IssmDouble* segments,int numsegments); void SetClone(int* minranks); void SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index); @@ -172,4 +176,5 @@ int VertexConnectivity(int vertexindex); void VerticalSegmentIndices(int** pindices,int* pnumseg); + void VerticalSegmentIndicesBase(int** pindices,int* pnumseg); void ViscousHeating(IssmDouble* pphi,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input); void ZeroLevelsetCoordinates(IssmDouble** pxyz_zero,IssmDouble* xyz_list,int levelsetenum); @@ -180,5 +185,5 @@ #endif - #ifdef _HAVE_GIA_ + #ifdef _HAVE_GIAIVINS_ void GiaDeflection(Vector* wg,Vector* dwgdt,IssmDouble* x,IssmDouble* y); #endif @@ -190,4 +195,5 @@ IssmDouble OceanArea(void){_error_("not implemented yet!");}; IssmDouble OceanAverage(IssmDouble* Sg){_error_("not implemented yet!");}; + void SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea){_error_("not implemented yet!");}; void SealevelriseEustatic(Vector* pSgi,IssmDouble* peustatic,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble oceanarea,IssmDouble eartharea){_error_("not implemented yet!");}; void SealevelriseNonEustatic(Vector* pSgo,IssmDouble* Sg_old,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble eartharea){_error_("not implemented yet!");}; Index: /issm/trunk/src/c/classes/Elements/PentaRef.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/PentaRef.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Elements/PentaRef.cpp (revision 21729) @@ -1030,4 +1030,88 @@ } /*}}}*/ +void PentaRef::VerticalSegmentIndicesBase(int** pindices,int* pnumseg,int finiteelement){/*{{{*/ + + /*Output*/ + int numseg; + int* indices = NULL; + + switch(finiteelement){ + case P1Enum: case P1DGEnum: + numseg = 3; + indices = xNew(numseg*2); + indices[0*2 + 0] = 0; indices[0*2 + 1] = 3; + indices[1*2 + 0] = 1; indices[1*2 + 1] = 4; + indices[2*2 + 0] = 2; indices[2*2 + 1] = 5; + break; + case P1bubbleEnum: case P1bubblecondensedEnum: + numseg = 3; + indices = xNew(numseg*2); + indices[0*2 + 0] = 0; indices[0*2 + 1] = 3; + indices[1*2 + 0] = 1; indices[1*2 + 1] = 4; + indices[2*2 + 0] = 2; indices[2*2 + 1] = 5; + break; + case P2xP1Enum: + numseg = 6; + indices = xNew(numseg*2); + indices[0*2 + 0] = 0; indices[0*2 + 1] = 3; + indices[1*2 + 0] = 1; indices[1*2 + 1] = 4; + indices[2*2 + 0] = 2; indices[2*2 + 1] = 5; + indices[3*2 + 0] = 6; indices[3*2 + 1] = 9; + indices[4*2 + 0] = 7; indices[4*2 + 1] = 10; + indices[5*2 + 0] = 8; indices[5*2 + 1] = 11; + break; + case P1xP2Enum: + numseg = 3; + indices = xNew(numseg*2); + indices[0*2 + 0] = 0; indices[0*2 + 1] = 6; + indices[1*2 + 0] = 1; indices[1*2 + 1] = 7; + indices[2*2 + 0] = 2; indices[2*2 + 1] = 8; + break; + case P1xP3Enum: + numseg = 3; + indices = xNew(numseg*2); + indices[0*2 + 0] = 0; indices[0*2 + 1] = 6; + indices[1*2 + 0] = 1; indices[1*2 + 1] = 7; + indices[2*2 + 0] = 2; indices[2*2 + 1] = 8; + break; + case P2Enum: + numseg = 6; + indices = xNew(numseg*2); + indices[0*2 + 0] = 0; indices[0*2 + 1] = 6; + indices[1*2 + 0] = 1; indices[1*2 + 1] = 7; + indices[2*2 + 0] = 2; indices[2*2 + 1] = 8; + indices[3*2 + 0] = 9; indices[3*2 + 1] = 15; + indices[4*2 + 0] = 10; indices[4*2 + 1] = 16; + indices[5*2 + 0] = 11; indices[5*2 + 1] = 17; + break; + case P2bubbleEnum: + numseg = 6; + indices = xNew(numseg*2); + indices[0*2 + 0] = 0; indices[0*2 + 1] = 6; + indices[1*2 + 0] = 1; indices[1*2 + 1] = 7; + indices[2*2 + 0] = 2; indices[2*2 + 1] = 8; + indices[3*2 + 0] = 9; indices[3*2 + 1] = 15; + indices[4*2 + 0] = 10; indices[4*2 + 1] = 16; + indices[5*2 + 0] = 11; indices[5*2 + 1] = 17; + break; + case P2xP4Enum: + numseg = 6; + indices = xNew(numseg*2); + indices[0*2 + 0] = 0; indices[0*2 + 1] = 6; + indices[1*2 + 0] = 1; indices[1*2 + 1] = 7; + indices[2*2 + 0] = 2; indices[2*2 + 1] = 8; + indices[3*2 + 0] = 9; indices[3*2 + 1] = 15; + indices[4*2 + 0] = 10; indices[4*2 + 1] = 16; + indices[5*2 + 0] = 11; indices[5*2 + 1] = 17; + break; + default: + _error_("Element type "<(numindices); @@ -1116,5 +1201,5 @@ indices[1] = 4; indices[2] = 5; - return; + break; case P2Enum: numindices = 6; Index: /issm/trunk/src/c/classes/Elements/PentaRef.h =================================================================== --- /issm/trunk/src/c/classes/Elements/PentaRef.h (revision 21728) +++ /issm/trunk/src/c/classes/Elements/PentaRef.h (revision 21729) @@ -28,4 +28,5 @@ void GetSegmentJacobianDeterminant(IssmDouble* Jdet, IssmDouble* xyz_list,Gauss* gauss); void GetTriaJacobianDeterminant(IssmDouble* Jdet, IssmDouble* xyz_list,Gauss* gauss); + void VerticalSegmentIndicesBase(int** pindices,int* pnumseg,int finiteelement); void Marshall(char** pmarshalled_data,int* pmarshalled_data_size, int marshall_direction){ /*do nothing */}; int NumberofNodes(int finiteelement); Index: /issm/trunk/src/c/classes/Elements/Seg.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Seg.h (revision 21728) +++ /issm/trunk/src/c/classes/Elements/Seg.h (revision 21729) @@ -48,4 +48,5 @@ void ComputeBasalStress(Vector* sigma_b){_error_("not implemented yet");}; void ComputeDeviatoricStressTensor(){_error_("not implemented yet");}; + void ComputeEsaStrainAndVorticity(){_error_("not implemented yet!");}; void ComputeSigmaNN(){_error_("not implemented yet");}; void ComputeStressTensor(){_error_("not implemented yet");}; @@ -160,4 +161,5 @@ int VertexConnectivity(int vertexindex){_error_("not implemented yet");}; void VerticalSegmentIndices(int** pindices,int* pnumseg){_error_("not implemented yet");}; + void VerticalSegmentIndicesBase(int** pindices,int* pnumseg){_error_("not implemented yet");}; void ViscousHeating(IssmDouble* pphi,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){_error_("not implemented yet");}; void ZeroLevelsetCoordinates(IssmDouble** pxyz_zero,IssmDouble* xyz_list,int levelsetenum){_error_("not implemented");}; @@ -165,5 +167,5 @@ IssmDouble GetAreaSpherical(void){_error_("not implemented yet!");}; -#ifdef _HAVE_GIA_ +#ifdef _HAVE_GIAIVINS_ void GiaDeflection(Vector* wg,Vector* dwgdt,IssmDouble* x,IssmDouble* y){_error_("not implemented yet");}; #endif @@ -173,4 +175,5 @@ #endif #ifdef _HAVE_SEALEVELRISE_ + void SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea){_error_("not implemented yet!");}; void SealevelriseEustatic(Vector* pSgi,IssmDouble* peustatic,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble oceanarea,IssmDouble eartharea){_error_("not implemented yet!");}; void SealevelriseNonEustatic(Vector* pSgo,IssmDouble* Sg_old,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble eartharea){_error_("not implemented yet!");}; Index: /issm/trunk/src/c/classes/Elements/Tetra.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Tetra.h (revision 21728) +++ /issm/trunk/src/c/classes/Elements/Tetra.h (revision 21729) @@ -50,4 +50,5 @@ void ComputeStressTensor(){_error_("not implemented yet");}; void ComputeDeviatoricStressTensor(){_error_("not implemented yet");}; + void ComputeEsaStrainAndVorticity(){_error_("not implemented yet!");}; void Configure(Elements* elements,Loads* loads,Nodes* nodesin,Vertices* verticesin,Materials* materials,Parameters* parameters); void ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index){_error_("not implemented yet");}; @@ -169,8 +170,9 @@ int VertexConnectivity(int vertexindex){_error_("not implemented yet");}; void VerticalSegmentIndices(int** pindices,int* pnumseg){_error_("not implemented yet");}; + void VerticalSegmentIndicesBase(int** pindices,int* pnumseg){_error_("not implemented yet");}; void ViscousHeating(IssmDouble* pphi,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input); void ZeroLevelsetCoordinates(IssmDouble** pxyz_zero,IssmDouble* xyz_list,int levelsetenum); -#ifdef _HAVE_GIA_ +#ifdef _HAVE_GIAIVINS_ void GiaDeflection(Vector* wg,Vector* dwgdt,IssmDouble* x,IssmDouble* y){_error_("not implemented yet");}; #endif @@ -180,4 +182,5 @@ #endif #ifdef _HAVE_SEALEVELRISE_ + void SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea){_error_("not implemented yet!");}; void SealevelriseEustatic(Vector* pSgi,IssmDouble* peustatic,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble oceanarea,IssmDouble eartharea){_error_("not implemented yet!");}; void SealevelriseNonEustatic(Vector* pSgo,IssmDouble* Sg_old,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble eartharea){_error_("not implemented yet!");}; Index: /issm/trunk/src/c/classes/Elements/Tria.cpp =================================================================== --- /issm/trunk/src/c/classes/Elements/Tria.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Elements/Tria.cpp (revision 21729) @@ -15,5 +15,5 @@ #include "../classes.h" #include "../../shared/shared.h" -#ifdef _HAVE_GIA_ +#ifdef _HAVE_GIAIVINS_ #include "../../modules/GiaDeflectionCorex/GiaDeflectionCorex.h" #endif @@ -216,5 +216,6 @@ IssmDouble calvingrate[NUMVERTICES]; IssmDouble lambda1,lambda2,ex,ey,vx,vy,vel; - IssmDouble sigma_vm,sigma_max,epse_2,groundedice; + IssmDouble sigma_vm,sigma_max,sigma_max_floating,sigma_max_grounded; + IssmDouble epse_2,groundedice; /* Get node coordinates and dof list: */ @@ -227,4 +228,6 @@ IssmDouble B = this->GetMaterialParameter(MaterialsRheologyBbarEnum); IssmDouble n = this->GetMaterialParameter(MaterialsRheologyNEnum); + this->parameters->FindParam(&sigma_max_floating,CalvingStressThresholdFloatingiceEnum); + this->parameters->FindParam(&sigma_max_grounded,CalvingStressThresholdGroundediceEnum); /* Start looping on the number of vertices: */ @@ -254,17 +257,15 @@ epse_2 = 1./2. *(lambda1*lambda1 + lambda2*lambda2); sigma_vm = sqrt(3.) * B * pow(epse_2,1./(2.*n)); - //sigma_max = 125.e+3; - sigma_max = 350.e+3; - sigma_max = 450.e+3; - sigma_max = 800.e+3; //too much - //sigma_max = 700.e+3; - //sigma_max = 670.e+3; - //sigma_max = 550.e+3; - sigma_max = 750.e+3; //too high - sigma_max = 850.e+3; //too low - sigma_max = 800.e+3; //IUGG previous test - sigma_max = 1000.e+3; //850 seems small - - if(groundedice<0) sigma_max=200.e+3; + + /*OLD (keep for a little bit)*/ + //sigma_max = 800.e+3; //IUGG previous test + //sigma_max = 1000.e+3; //GRL + //if(groundedice<0) sigma_max=150.e+3; + + /*Tensile stress threshold*/ + if(groundedice<0) + sigma_max = sigma_max_floating; + else + sigma_max = sigma_max_grounded; /*Assign values*/ @@ -294,5 +295,4 @@ IssmDouble calvingratey[NUMVERTICES]; IssmDouble calvingrate[NUMVERTICES]; - /* Get node coordinates and dof list: */ @@ -410,4 +410,46 @@ this->inputs->AddInput(new TriaInput(DeviatoricStresszzEnum,&tau_zz[0],P1Enum)); this->inputs->AddInput(new TriaInput(DeviatoricStresseffectiveEnum,&tau_e[0],P1Enum)); + + /*Clean up and return*/ + delete gauss; +} +/*}}}*/ +void Tria::ComputeEsaStrainAndVorticity(){ /*{{{*/ + + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble epsilon[4]; /* epsilon=[exx,eyy,exy+ (shear),exy- (rotation)];*/ + IssmDouble strain_xx[NUMVERTICES]; + IssmDouble strain_yy[NUMVERTICES]; + IssmDouble strain_xy[NUMVERTICES]; + IssmDouble vorticity_xy[NUMVERTICES]; + GaussTria* gauss=NULL; + + /* Get node coordinates and dof list: */ + ::GetVerticesCoordinates(&xyz_list[0][0],vertices,NUMVERTICES); + + /*Retrieve all inputs we will be needing: */ + Input* vx_input=this->GetInput(EsaEmotionEnum); _assert_(vx_input); + Input* vy_input=this->GetInput(EsaNmotionEnum); _assert_(vy_input); + + /* Start looping on the number of vertices: */ + gauss=new GaussTria(); + for (int iv=0;ivGaussVertex(iv); + + /*Compute strain rate and vorticity rate: */ + this->StrainRateESA(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input); + + /*Compute Stress*/ + strain_xx[iv]=epsilon[0]; + strain_yy[iv]=epsilon[1]; + strain_xy[iv]=epsilon[2]; + vorticity_xy[iv]=epsilon[3]; + } + + /*Add Stress tensor components into inputs*/ + this->inputs->AddInput(new TriaInput(EsaStrainratexxEnum,&strain_xx[0],P1Enum)); + this->inputs->AddInput(new TriaInput(EsaStrainrateyyEnum,&strain_yy[0],P1Enum)); + this->inputs->AddInput(new TriaInput(EsaStrainratexyEnum,&strain_xy[0],P1Enum)); + this->inputs->AddInput(new TriaInput(EsaRotationrateEnum,&vorticity_xy[0],P1Enum)); /*Clean up and return*/ @@ -3453,5 +3495,5 @@ /*}}}*/ -#ifdef _HAVE_GIA_ +#ifdef _HAVE_GIAIVINS_ void Tria::GiaDeflection(Vector* wg,Vector* dwgdt,IssmDouble* x, IssmDouble* y){/*{{{*/ @@ -3870,4 +3912,91 @@ } /*}}}*/ +void Tria::SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea){/*{{{*/ + + /*early return if we are not on an ice cap OR ocean:*/ + if(!(this->inputs->Max(MaskIceLevelsetEnum)<0) && !IsWaterInElement()) return; + + /*Compute area of element:*/ + IssmDouble area; + area=GetAreaSpherical(); + + /*Compute lat,long,radius of elemental centroid: */ + bool spherical=true; + IssmDouble llr_list[NUMVERTICES][3]; + IssmDouble late,longe,re; + /* Where is the centroid of this element?:{{{*/ + ::GetVerticesCoordinates(&llr_list[0][0],this->vertices,NUMVERTICES,spherical); + + IssmDouble minlong=400; + IssmDouble maxlong=-20; + for (int i=0;imaxlong)maxlong=llr_list[i][1]; + if(llr_list[i][1]180){ + if (llr_list[0][1]==0)llr_list[0][1]=360; + if (llr_list[1][1]==0)llr_list[1][1]=360; + if (llr_list[2][1]==0)llr_list[2][1]=360; + } + + // correction at the north pole + if(llr_list[0][0]==0)llr_list[0][1]=(llr_list[1][1]+llr_list[2][1])/2.0; + if(llr_list[1][0]==0)llr_list[1][1]=(llr_list[0][1]+llr_list[2][1])/2.0; + if(llr_list[2][0]==0)llr_list[2][1]=(llr_list[0][1]+llr_list[1][1])/2.0; + + //correction at the south pole + if(llr_list[0][0]==180)llr_list[0][1]=(llr_list[1][1]+llr_list[2][1])/2.0; + if(llr_list[1][0]==180)llr_list[1][1]=(llr_list[0][1]+llr_list[2][1])/2.0; + if(llr_list[2][0]==180)llr_list[2][1]=(llr_list[0][1]+llr_list[1][1])/2.0; + + late=(llr_list[0][0]+llr_list[1][0]+llr_list[2][0])/3.0; + longe=(llr_list[0][1]+llr_list[1][1]+llr_list[2][1])/3.0; + + late=90-late; + if(longe>180)longe=(longe-180)-180; + + late=late/180*PI; + longe=longe/180*PI; + /*}}}*/ + re=(llr_list[0][2]+llr_list[1][2]+llr_list[2][2])/3.0; + + if(IsWaterInElement()){ + IssmDouble rho_water, S; + + /*recover material parameters: */ + rho_water=matpar->GetMaterialParameter(MaterialsRhoFreshwaterEnum); + + /*From Sg_old, recover water sea level rise:*/ + S=0; for(int i=0;ivertices[i]->Sid()]/NUMVERTICES; + + /* Perturbation terms for moment of inertia (moi_list): + * computed analytically (see Wu & Peltier, eqs 10 & 32) + * also consistent with my GMD formulation! + * ALL in geographic coordinates + * */ + dI_list[0] = -4*PI*(rho_water*S*area)*pow(re,4)*(sin(late)*cos(late)*cos(longe))/eartharea; + dI_list[1] = -4*PI*(rho_water*S*area)*pow(re,4)*(sin(late)*cos(late)*sin(longe))/eartharea; + dI_list[2] = +4*PI*(rho_water*S*area)*pow(re,4)*(1-pow(sin(late),2))/eartharea; + } + else if(this->inputs->Max(MaskIceLevelsetEnum)<0){ + IssmDouble rho_ice, I; + + /*recover material parameters: */ + rho_ice=matpar->GetMaterialParameter(MaterialsRhoIceEnum); + + /*Compute ice thickness change: */ + Input* deltathickness_input=inputs->GetInput(SealevelriseDeltathicknessEnum); + if (!deltathickness_input)_error_("delta thickness input needed to compute sea level rise!"); + deltathickness_input->GetInputAverage(&I); + + dI_list[0] = -4*PI*(rho_ice*I*area)*pow(re,4)*(sin(late)*cos(late)*cos(longe))/eartharea; + dI_list[1] = -4*PI*(rho_ice*I*area)*pow(re,4)*(sin(late)*cos(late)*sin(longe))/eartharea; + dI_list[2] = +4*PI*(rho_ice*I*area)*pow(re,4)*(1-pow(sin(late),2))/eartharea; + } + + return; +}/*}}}*/ void Tria::SealevelriseEustatic(Vector* pSgi,IssmDouble* peustatic,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble oceanarea,IssmDouble eartharea){ /*{{{*/ @@ -4026,5 +4155,5 @@ IssmDouble area; IssmDouble S; //change in water water level(Farrel and Clarke, Equ. 4) - IssmDouble late,longe,re; + IssmDouble late,longe; IssmDouble lati,longi,ri; IssmDouble minlong=400; @@ -4048,5 +4177,4 @@ bool computerigid = true; bool computeelastic= true; - bool computerotation= true; /*early return if we are not on the ocean:*/ @@ -4056,13 +4184,4 @@ this->parameters->FindParam(&computerigid,SealevelriseRigidEnum); this->parameters->FindParam(&computeelastic,SealevelriseElasticEnum); - this->parameters->FindParam(&computerotation,SealevelriseRotationEnum); - - /*recover some parameters for rotational feedback: */ - IssmDouble tide_love_h, tide_love_k, omega; - if(computerotation){ - this->parameters->FindParam(&tide_love_h,SealevelriseTidalLoveHEnum); - this->parameters->FindParam(&tide_love_k,SealevelriseTidalLoveKEnum); - this->parameters->FindParam(&omega,SealevelriseAngularVelocityEnum); - } /*early return if rigid or elastic not requested:*/ @@ -4134,12 +4253,4 @@ IssmDouble delPhi,delLambda; - /* if rotation, compute m1 m2 m3 from loading function */ - IssmDouble m1, m2, m3; - if(computerotation){ - m1=0; - m2=0; - m3=0; - } - for(int i=0;i(alpha/PI*(M-1)); G_elastic[i] += G_elastic_precomputed[index]; values[i]+=3*rho_water/rho_earth*area/eartharea*S*G_elastic[i]; - } - - /*Rotational feedback: */ - if(computerotation){ - values[i]+=(1+tide_love_k-tide_love_h/9.81)*0.5*pow((omega*radius[i]),2)*(-m3*(2+m3)*(1+3*cos(2*lati)) - + 2*pow(m2,2)*(pow(cos(lati),2) + 0.5*(-1 + 3*cos(2*longi)) * pow(sin(lati),2)) - + 2*pow(m1,2)*(pow(cos(lati),2) - 0.5*(1+3*cos(2*longi)) * pow(sin(lati),2)) - - m1*(1+m3)*cos(longi)*sin(2*lati) - - 2*m1*m2*cos(longi)*pow(sin(lati),2)*sin(longi) - - m2*(1+m3)*sin(2*lati)*sin(longi)); } } Index: /issm/trunk/src/c/classes/Elements/Tria.h =================================================================== --- /issm/trunk/src/c/classes/Elements/Tria.h (revision 21728) +++ /issm/trunk/src/c/classes/Elements/Tria.h (revision 21729) @@ -57,4 +57,5 @@ void ComputeBasalStress(Vector* sigma_b); void ComputeDeviatoricStressTensor(); + void ComputeEsaStrainAndVorticity(); void ComputeSigmaNN(); void ComputeStressTensor(); @@ -138,8 +139,9 @@ int VertexConnectivity(int vertexindex); void VerticalSegmentIndices(int** pindices,int* pnumseg){_error_("not implemented yet");}; + void VerticalSegmentIndicesBase(int** pindices,int* pnumseg){_error_("not implemented yet");}; void WriteLevelsetSegment(DataSet* segments); void ZeroLevelsetCoordinates(IssmDouble** pxyz_zero,IssmDouble* xyz_list,int levelsetenum); - #ifdef _HAVE_GIA_ + #ifdef _HAVE_GIAIVINS_ void GiaDeflection(Vector* wg,Vector* dwgdt,IssmDouble* x,IssmDouble* y); #endif @@ -151,4 +153,5 @@ IssmDouble OceanArea(void); IssmDouble OceanAverage(IssmDouble* Sg); + void SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea); void SealevelriseEustatic(Vector* pSgi,IssmDouble* peustatic,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble oceanarea,IssmDouble eartharea); void SealevelriseNonEustatic(Vector* pSgo,IssmDouble* Sg_old,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble eartharea); Index: /issm/trunk/src/c/classes/ExternalResults/GenericExternalResult.h =================================================================== --- /issm/trunk/src/c/classes/ExternalResults/GenericExternalResult.h (revision 21728) +++ /issm/trunk/src/c/classes/ExternalResults/GenericExternalResult.h (revision 21729) @@ -334,4 +334,179 @@ } /*}}}*/ +/*Specific instantiations for int*: */ +template <> inline GenericExternalResult::GenericExternalResult(int in_id, int in_enum_type,int* in_values, int in_M,int in_N,int in_step,IssmDouble in_time){/*{{{*/ + + id = in_id; + M = in_M; + N = in_N; + + EnumToStringx(&this->result_name,in_enum_type); + + step = in_step; + time = in_time; + + /*Copy result in values*/ + if(M*N){ + value=xNew(M*N); + xMemCpy(value,in_values,M*N); + } + else value=NULL; +} +/*}}}*/ +template <> inline GenericExternalResult::GenericExternalResult(int in_id,const char* in_result_name,int* in_values, int in_M,int in_N,int in_step,IssmDouble in_time){/*{{{*/ + + id = in_id; + M = in_M; + N = in_N; + + /*Copy name*/ + this->result_name = xNew(strlen(in_result_name)+1); + xMemCpy(this->result_name,in_result_name,strlen(in_result_name)+1); + + step = in_step; + time = in_time; + + /*Copy result in values*/ + if(M*N){ + value=xNew(M*N); + xMemCpy(value,in_values,M*N); + } + else value=NULL; +} +/*}}}*/ +template <> inline GenericExternalResult::GenericExternalResult(int in_id, int in_enum_type,int* in_value,int in_step, IssmDouble in_time){ /*{{{*/ + _error_("you cannot initialize a GenericExternalResult without providing the dimensions of the matrix! Please use a more appropriate constructor!"); +} /*}}}*/ +template <> inline GenericExternalResult::~GenericExternalResult(){ /*{{{*/ + xDelete(result_name); + xDelete(value); +} /*}}}*/ +template <> inline void GenericExternalResult::Echo(void){ /*{{{*/ + + _printf_("GenericExternalResult:\n"); + this->GenericEcho(); + _printf_(" matrix size: " << this->M << "-" << this->N << "\n"); + +} /*}}}*/ +template <> inline void GenericExternalResult::DeepEcho(void){ /*{{{*/ + + int i,j; + + _printf_("GenericExternalResult:\n"); + this->GenericEcho(); + + _printf_(" matrix size: " << this->M << "-" << this->N << "\n"); + for (i=0;iM;i++){ + _printf_(" [ "); + for (j=0;jN;j++){ + _printf_( " " << setw(11) << this->value[i*this->N+j]); + } + _printf_(" ]\n"); + } + +} /*}}}*/ +template <> inline Object* GenericExternalResult::copy(void){ /*{{{*/ + return new GenericExternalResult(this->id,StringToEnumx(this->result_name),this->value,this->M,this->N,this->step,this->time); +} /*}}}*/ +template <> inline void GenericExternalResult::WriteData(FILE* fid,bool io_gather){ /*{{{*/ + + int my_rank; + int type; + int rows,cols; + char *name = NULL; + IssmPDouble passiveDouble; + + /*recover my_rank:*/ + my_rank=IssmComm::GetRank(); + + if(io_gather){ + /*we are gathering the data on cpu 0, don't write on other cpus: */ + if(my_rank) return; + } + + /*First write enum: */ + int length=(strlen(this->result_name)+1)*sizeof(char); + fwrite(&length,sizeof(int),1,fid); + fwrite(this->result_name,length,1,fid); + + /*Now write time and step: */ + passiveDouble=reCast(time); + fwrite(&passiveDouble,sizeof(IssmPDouble),1,fid); + fwrite(&step,sizeof(int),1,fid); + + /*writing an int array, type is 4 (see parseresultsfromdisk.m):*/ + type=4; + fwrite(&type,sizeof(int),1,fid); + rows=this->M; + fwrite(&rows,sizeof(int),1,fid); + cols=this->N; + fwrite(&cols,sizeof(int),1,fid); + fwrite(value,cols*rows*sizeof(int),1,fid); + +} +/*}}}*/ +template <> inline int GenericExternalResult::ObjectEnum(void){ /*{{{*/ + return IntMatExternalResultEnum; +} /*}}}*/ +template <> inline void GenericExternalResult::Marshall(char** pmarshalled_data,int* pmarshalled_data_size, int marshall_direction){/*{{{*/ + + MARSHALLING_ENUM(this->ObjectEnum()); + + MARSHALLING(id); + MARSHALLING(result_name); + MARSHALLING(M); + MARSHALLING(N); + MARSHALLING_DYNAMIC(value,int,M*N); + MARSHALLING(step); + MARSHALLING(time); + +} /*}}}*/ +/*Specific instantiations for int*: */ +#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. +template <> inline void GenericExternalResult::WriteData(FILE* fid,bool io_gather){ /*{{{*/ + + int i; + int my_rank; + int type; + int rows,cols; + char *name = NULL; + IssmPDouble passiveDouble; + int* passiveInts; + + /*recover my_rank:*/ + my_rank=IssmComm::GetRank(); + + if(io_gather){ + /*we are gathering the data on cpu 0, don't write on other cpus: */ + if(my_rank) return; + } + + /*First write enum: */ + int length=(strlen(this->result_name)+1)*sizeof(char); + fwrite(&length,sizeof(int),1,fid); + fwrite(this->result_name,length,1,fid); + + /*Now write time and step: */ + passiveDouble=reCast(time); + fwrite(&passiveDouble,sizeof(IssmPDouble),1,fid); + fwrite(&step,sizeof(int),1,fid); + + /*writing a int array, type is 4 (see parseresultsfromdisk.m):*/ + type=4; + fwrite(&type,sizeof(int),1,fid); + rows=this->M; + fwrite(&rows,sizeof(int),1,fid); + cols=this->N; + fwrite(&cols,sizeof(int),1,fid); + + passiveInts=xNew(this->M*this->N); + for (i=0;iM*this->N;i++)passiveInts[i]=reCast(value[i]); + fwrite(passiveInts,cols*rows*sizeof(int),1,fid); + xDelete(int); + +} +/*}}}*/ +#endif + /*Specific instantiations for IssmPDouble*: */ template <> inline GenericExternalResult::GenericExternalResult(int in_id, int in_enum_type,IssmPDouble* in_values, int in_M,int in_N,int in_step,IssmDouble in_time){/*{{{*/ Index: /issm/trunk/src/c/classes/FemModel.cpp =================================================================== --- /issm/trunk/src/c/classes/FemModel.cpp (revision 21728) +++ /issm/trunk/src/c/classes/FemModel.cpp (revision 21729) @@ -15,5 +15,4 @@ #include "./modules/modules.h" #include "../shared/Enum/Enum.h" - #include "../analyses/analyses.h" @@ -81,4 +80,8 @@ this->parameters->AddObject(new GenericParam(incomm,FemModelCommEnum)); + #ifdef _HAVE_NEOPZ_ + this->InitializeAdaptiveRefinement(); + #endif + /*Free resources */ xDelete(lockfilename); @@ -134,4 +137,8 @@ if(parameters)delete parameters; if(results)delete results; + + #ifdef _HAVE_NEOPZ_ + if(amr)delete amr; + #endif /*Now delete: */ @@ -513,5 +520,13 @@ } /*}}}*/ -void FemModel::SolutionAnalysesList(int** panalyses,int* pnumanalyses,IoModel* iomodel,int solutiontype){/*{{{*/ +int FemModel::Size(){ /*{{{*/ + int femmodel_size; + + this->Marshall(NULL,&femmodel_size,MARSHALLING_SIZE); + + return femmodel_size; +} +/*}}}*/ +void FemModel::SolutionAnalysesList(int** panalyses,int* pnumanalyses,IoModel* iomodel,int solutiontype){/*{{{*/ /*output: */ @@ -622,5 +637,5 @@ case GiaSolutionEnum: - analyses_temp[numanalyses++]=GiaAnalysisEnum; + analyses_temp[numanalyses++]=GiaIvinsAnalysisEnum; break; @@ -704,5 +719,5 @@ } if(isgia){ - analyses_temp[numanalyses++]=GiaAnalysisEnum; + analyses_temp[numanalyses++]=GiaIvinsAnalysisEnum; } @@ -1734,4 +1749,8 @@ int num_procs = IssmComm::GetSize(); + /*Get domain type (2d or 3d)*/ + int domaintype; + this->parameters->FindParam(&domaintype,DomainTypeEnum); + /*1: go throug all elements of this partition and figure out how many * segments we have (corresopnding to levelset = 0)*/ @@ -1739,5 +1758,8 @@ for(int i=0;iSize();i++){ Element* element=dynamic_cast(this->elements->GetObjectByOffset(i)); - element->WriteLevelsetSegment(segments); + if(!element->IsOnBase()) continue; + Element* basalelement = element->SpawnBasalElement(); + basalelement->WriteLevelsetSegment(segments); + if(domaintype!=Domain2DhorizontalEnum){basalelement->DeleteMaterials(); delete basalelement;}; } @@ -1771,5 +1793,20 @@ for(int i=0;iSize();i++){ Element* element=dynamic_cast(this->elements->GetObjectByOffset(i)); + if(!element->IsOnBase()) continue; element->ResetLevelsetFromSegmentlist(allsegmentlist,numseg); + } + + + /*Extrude if necessary*/ + int elementtype; + this->parameters->FindParam(&elementtype,MeshElementtypeEnum); + if(elementtype==PentaEnum){ + InputExtrudex(this,MaskIceLevelsetEnum,-1); + } + else if(elementtype==TriaEnum){ + /*no need to extrude*/ + } + else{ + _error_("not implemented yet"); } @@ -2288,5 +2325,5 @@ /*}}}*/ #endif -#ifdef _HAVE_GIA_ +#ifdef _HAVE_GIAIVINS_ void FemModel::Deflection(Vector* wg,Vector* dwgdt, IssmDouble* x, IssmDouble* y){ /*{{{*/ @@ -2459,5 +2496,5 @@ /*Go through elements, and add contribution from each element to the deflection vector wg:*/ ns = elements->Size(); - + /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ for(int i=0;iGetAreaSpherical(); } + ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); @@ -2475,16 +2513,95 @@ for(int i=0;i(elements->GetObjectByOffset(i)); - element->SealevelriseNonEustatic(pSgo, Sg_old,latitude,longitude,radius,eartharea); + element->SealevelriseNonEustatic(pSgo,Sg_old,latitude,longitude,radius,eartharea); } if(i%100==0)pSgo->Assemble(); } if(verboseconvolution)if(VerboseConvergence())_printf_("\n"); - + /*Free ressources:*/ xDelete(Sg_old); +} +/*}}}*/ +void FemModel::SealevelriseRotationalFeedback(Vector* pSgo_rot, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius){/*{{{*/ + + /*serialized vectors:*/ + IssmDouble* Sg_old=NULL; + IssmDouble eartharea=0; + IssmDouble eartharea_cpu=0; + IssmDouble tide_love_h, tide_love_k, fluid_love, moi_e, moi_p, omega, g; + IssmDouble load_love_k2 = -0.30922675; //degree 2 load Love number + IssmDouble m1, m2, m3; + IssmDouble lati, longi, radi, value; + + /*Serialize vectors from previous iteration:*/ + Sg_old=pSg_old->ToMPISerial(); + + /*First, figure out the area of the ocean, which is needed to compute the eustatic component: */ + for(int i=0;iSize();i++){ + Element* element=xDynamicCast(elements->GetObjectByOffset(i)); + eartharea_cpu += element->GetAreaSpherical(); + } + ISSM_MPI_Reduce (&eartharea_cpu,&eartharea,1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); + ISSM_MPI_Bcast(&eartharea,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + + IssmDouble moi_list[3]={0,0,0}; + IssmDouble moi_list_cpu[3]={0,0,0}; + for(int i=0;iSize();i++){ + Element* element=xDynamicCast(elements->GetObjectByOffset(i)); + element->SealevelriseMomentOfInertia(&moi_list[0],Sg_old,eartharea); + moi_list_cpu[0] += moi_list[0]; + moi_list_cpu[1] += moi_list[1]; + moi_list_cpu[2] += moi_list[2]; + } + ISSM_MPI_Reduce (&moi_list_cpu[0],&moi_list[0],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); + ISSM_MPI_Bcast(&moi_list[0],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + // + ISSM_MPI_Reduce (&moi_list_cpu[1],&moi_list[1],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); + ISSM_MPI_Bcast(&moi_list[1],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + // + ISSM_MPI_Reduce (&moi_list_cpu[2],&moi_list[2],1,ISSM_MPI_DOUBLE,ISSM_MPI_SUM,0,IssmComm::GetComm() ); + ISSM_MPI_Bcast(&moi_list[2],1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); + + /*pull out some useful parameters: */ + parameters->FindParam(&tide_love_h,SealevelriseTidalLoveHEnum); + parameters->FindParam(&tide_love_k,SealevelriseTidalLoveKEnum); + parameters->FindParam(&fluid_love,SealevelriseFluidLoveEnum); + parameters->FindParam(&moi_e,SealevelriseEquatorialMoiEnum); + parameters->FindParam(&moi_p,SealevelrisePolarMoiEnum); + parameters->FindParam(&omega,SealevelriseAngularVelocityEnum); + + /*compute perturbation terms for angular velocity vector: */ + m1 = 1/(1-tide_love_k/fluid_love) * (1+load_love_k2)/(moi_p-moi_e) * moi_list[0]; + m2 = 1/(1-tide_love_k/fluid_love) * (1+load_love_k2)/(moi_p-moi_e) * moi_list[1]; + m3 = -(1+load_love_k2)/moi_p * moi_list[2]; // term associated with fluid number (3-order-of-magnitude smaller) is negelected + + /* Green's function (1+k_2-h_2/g): checked against Glenn Milne's thesis Chapter 3 (eqs: 3.3-4, 3.10-11) + * Perturbation terms for angular velocity vector (m1, m2, m3): checked against Mitrovica (2005 Appendix) & Jensen et al (2013 Appendix A3) + * Sea level rotational feedback: checked against GMD eqs 8-9 (only first order terms, i.e., degree 2 order 0 & 1 considered) + * all DONE in Geographic coordinates: theta \in [-90,90], lambda \in [-180 180] + */ + for(int i=0;iSize();i++){ + int sid; + //Vertex* vertex=(Vertex*)vertices->GetObjectByOffset(i); + Vertex* vertex=xDynamicCast(vertices->GetObjectByOffset(i)); + sid=vertex->Sid(); + + lati=latitude[sid]/180*PI; longi=longitude[sid]/180*PI; radi=radius[sid]; + + /*only first order terms are considered now: */ + value=((1.0+tide_love_k-tide_love_h)/9.81)*pow(omega*radi,2.0)* + (-m3/6.0 + 0.5*m3*cos(2.0*lati) - 0.5*sin(2.*lati)*(m1*cos(longi)+m2*sin(longi))); + + pSgo_rot->SetValue(sid,value,INS_VAL); //INS_VAL ensures that you don't add several times + } + + /*Assemble mesh velocity*/ + pSgo_rot->Assemble(); + + /*Free ressources:*/ + xDelete(Sg_old); + } /*}}}*/ @@ -2613,6 +2730,4 @@ } } - - this->parameters->SetParam(eplzigzag_counter,this->nodes->Size(),EplZigZagCounterEnum); /*Assemble and serialize*/ @@ -2809,2 +2924,1085 @@ }/*}}}*/ #endif + +#ifdef _HAVE_NEOPZ_ +void FemModel::InitializeAdaptiveRefinement(void){/*{{{*/ + + /*Define variables*/ + int my_rank = IssmComm::GetRank(); + this->amr = NULL;//initialize amr as NULL + int numberofvertices = this->vertices->NumberOfVertices(); + int numberofelements = this->elements->NumberOfElements(); + int numberofsegments = 0; //used on matlab + IssmDouble* x = NULL; + IssmDouble* y = NULL; + IssmDouble* z = NULL; + int* elements = NULL; + int elementswidth = this->GetElementsWidth(); //just tria elements in this version. Itapopo: + int levelmax = 0; + IssmDouble regionlevel1 = 0.; + IssmDouble regionlevelmax = 0.; + + /*Get vertices coordinates of the coarse mesh (father mesh)*/ + /*elements comes in Matlab indexing*/ + this->GetMesh(this->vertices,this->elements,&x,&y,&z,&elements); + + /*Get amr parameters*/ + this->parameters->FindParam(&levelmax,AmrLevelMaxEnum); + this->parameters->FindParam(®ionlevel1,AmrRegionLevel1Enum); + this->parameters->FindParam(®ionlevelmax,AmrRegionLevelMaxEnum); + + /*Create initial mesh (coarse mesh) in neopz data structure*/ + /*Just CPU #0 should keep AMR object*/ + this->SetRefPatterns(); + if(my_rank==0){ + bool ismisomip = true; + if(ismisomip){//itapopo + TPZFileStream fstr; + std::stringstream ss; + + ss << levelmax; + std::string AMRfile = "/home/santos/Misomip2/L" + ss.str() + "_tsai/amr.txt"; + fstr.OpenRead(AMRfile.c_str()); + + TPZSaveable *sv = TPZSaveable::Restore(fstr,0); + this->amr = dynamic_cast(sv); + } + else{ + this->amr = new AdaptiveMeshRefinement(); + //this->amr->SetLevelMax(levelmax); //Set max level of refinement + //this->amr->SetRegions(regionlevel1,regionlevelmax); + this->amr->CreateInitialMesh(numberofvertices,numberofelements,numberofsegments,elementswidth,x,y,z,elements,NULL); + } + this->amr->SetLevelMax(levelmax); //Set max level of refinement + this->amr->SetRegions(regionlevel1,regionlevelmax); + } + + /*Free the vectors*/ + xDelete(x); + xDelete(y); + xDelete(z); + xDelete(elements); + +} +/*}}}*/ +void FemModel::SetRefPatterns(){/*{{{*/ + + /*Initialize the global variable of refinement patterns*/ + gRefDBase.InitializeUniformRefPattern(EOned); + gRefDBase.InitializeUniformRefPattern(ETriangle); + + //gRefDBase.InitializeRefPatterns(); + /*Insert specifics patterns to ISSM core*/ + std::string filepath = REFPATTERNDIR; + std::string filename1 = filepath + "/2D_Triang_Rib_3.rpt"; + std::string filename2 = filepath + "/2D_Triang_Rib_4.rpt"; + std::string filename3 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4.rpt"; + std::string filename4 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_4_permuted.rpt"; + std::string filename5 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5.rpt"; + std::string filename6 = filepath + "/2D_Triang_Rib_OnlyTriang_Side_3_5_permuted.rpt"; + std::string filename7 = filepath + "/2D_Triang_Rib_5.rpt"; + + TPZAutoPointer refpat1 = new TPZRefPattern(filename1); + TPZAutoPointer refpat2 = new TPZRefPattern(filename2); + TPZAutoPointer refpat3 = new TPZRefPattern(filename3); + TPZAutoPointer refpat4 = new TPZRefPattern(filename4); + TPZAutoPointer refpat5 = new TPZRefPattern(filename5); + TPZAutoPointer refpat6 = new TPZRefPattern(filename6); + TPZAutoPointer refpat7 = new TPZRefPattern(filename7); + + if(!gRefDBase.FindRefPattern(refpat1)) gRefDBase.InsertRefPattern(refpat1); + if(!gRefDBase.FindRefPattern(refpat2)) gRefDBase.InsertRefPattern(refpat2); + if(!gRefDBase.FindRefPattern(refpat3)) gRefDBase.InsertRefPattern(refpat3); + if(!gRefDBase.FindRefPattern(refpat4)) gRefDBase.InsertRefPattern(refpat4); + if(!gRefDBase.FindRefPattern(refpat5)) gRefDBase.InsertRefPattern(refpat5); + if(!gRefDBase.FindRefPattern(refpat6)) gRefDBase.InsertRefPattern(refpat6); + if(!gRefDBase.FindRefPattern(refpat7)) gRefDBase.InsertRefPattern(refpat7); +} +/*}}}*/ +void FemModel::ReMesh(void){/*{{{*/ + + /*Variables*/ + IssmDouble *newx = NULL; + IssmDouble *newy = NULL; + IssmDouble *newz = NULL; + int *newelementslist = NULL; + int newnumberofvertices = -1; + int newnumberofelements = -1; + bool* my_elements = NULL; + int* my_vertices = NULL; + int elementswidth = this->GetElementsWidth();//just tria elements in this version + + /*Execute refinement and get the new mesh*/ + /*newelementslist come in Matlab indexing*/ + this->ExecuteRefinement(newnumberofvertices,newnumberofelements,&newx,&newy,&newz,&newelementslist); + + /*Partitioning the new mesh. Maybe ElementsAndVerticesPartitioning.cpp could be modified to set this without iomodel.*/ + this->ElementsAndVerticesPartitioning(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,&my_elements,&my_vertices); + + if(this->loads->Size()!=0) _error_("not supported yet"); + + /*Create vertices*/ + Vertices* new_vertices=new Vertices(); + this->CreateVertices(newnumberofvertices,newnumberofelements,elementswidth,newelementslist,my_vertices,newx,newy,newz,new_vertices); + + /*Creating elements*/ + /*Just Tria in this version*/ + Elements* new_elements=new Elements(); + this->CreateElements(newnumberofelements,elementswidth,newelementslist,my_elements,new_elements); + + /*Creating materials*/ + Materials* new_materials=new Materials(); + this->CreateMaterials(newnumberofelements,my_elements,new_materials); + + /*Creating nodes and constraints*/ + /*Just SSA (2D) and P1 in this version*/ + Nodes* new_nodes=new Nodes(); + Constraints* new_constraints=new Constraints(); + + int nodecounter=0; + int constraintcounter=0; + for(int i=0;inummodels;i++){//create nodes for each analysis in analysis_type_list + + int analysis_enum = this->analysis_type_list[i]; + + /*As the domain is 2D, it is not necessary to create nodes for this analysis*/ + /*itapopo must verify if domain is not 3D. Only 2D in this version!*/ + if(analysis_enum==StressbalanceVerticalAnalysisEnum) continue; + + this->CreateNodes(newnumberofvertices,my_vertices,nodecounter,analysis_enum,new_nodes); + if(analysis_enum==StressbalanceAnalysisEnum) this->CreateConstraints(newnumberofvertices,newnumberofelements,nodecounter,constraintcounter,newx,newy,my_vertices,new_constraints); + this->UpdateElements(newnumberofelements,newelementslist,my_elements,nodecounter,i,new_elements); + + if(new_nodes->Size()) nodecounter=new_nodes->MaximumId(); + constraintcounter = new_constraints->NumberOfConstraints(); + /*Make sure nodecounter is at least 0 (if no node exists, maxid will be -1*/ + _assert_(nodecounter>=0); + } + + new_elements->Presort(); + new_nodes->Presort(); + new_vertices->Presort(); + this->loads->Presort(); + new_materials->Presort(); + new_constraints->Presort(); + + /*reset hooks for elements, loads and nodes: */ + new_elements->ResetHooks(); + this->loads->ResetHooks(); + new_materials->ResetHooks(); + + /*do the post-processing of the datasets to get an FemModel that can actually run analyses: */ + int analysis_type; + for(int i=0;inummodels;i++){ + analysis_type=this->analysis_type_list[i]; + //SetCurrentConfiguration(analysis_type); + + this->analysis_counter=i; + /*Now, plug analysis_counter and analysis_type inside the parameters: */ + this->parameters->SetParam(this->analysis_counter,AnalysisCounterEnum); + this->parameters->SetParam(analysis_type,AnalysisTypeEnum); + this->parameters->SetParam(analysis_type,ConfigurationTypeEnum); + + /*configure elements, loads and nodes, for this new analysis: */ + new_elements->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); + this->loads->SetCurrentConfiguration(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); + + /*take care of toolkits options, that depend on this analysis type (present only after model processor)*/ + if(this->parameters->Exist(ToolkitsOptionsStringsEnum)){ + ToolkitsOptionsFromAnalysis(this->parameters,analysis_type); + if(VerboseSolver()) _printf0_(" toolkits Options set for analysis type: " << EnumToStringx(analysis_type) << "\n"); + } + + ConfigureObjectsx(new_elements,this->loads,new_nodes,new_vertices,new_materials,this->parameters); + if(i==0){ + VerticesDofx(new_vertices,this->parameters); //only call once, we only have one set of vertices + } + SpcNodesx(new_nodes,new_constraints,this->parameters,analysis_type); + NodesDofx(new_nodes,this->parameters,analysis_type); + } + + /*Finally: interpolate all inputs and insert them into the new elements.*/ + this->InterpolateInputs(new_vertices,new_elements); + + /*Delete old structure and set new pointers*/ + delete this->vertices; this->vertices = new_vertices; + delete this->elements; this->elements = new_elements; + delete this->nodes; this->nodes = new_nodes; + delete this->constraints; this->constraints = new_constraints; + delete this->materials; this->materials = new_materials; + + GetMaskOfIceVerticesLSMx(this); + + /*Insert MISMIP+ bed topography*/ + if(true) this->BedrockFromMismipPlus(); + + /*Adjust base, thickness and mask grounded ice leve set*/ + if(true) this->AdjustBaseThicknessAndMask(); + + /*Reset current configuration: */ + analysis_type=this->analysis_type_list[this->analysis_counter]; + SetCurrentConfiguration(analysis_type); + + /*Cleanup*/ + xDelete(newx); + xDelete(newy); + xDelete(newz); + xDelete(newelementslist); + xDelete(my_vertices); + xDelete(my_elements); + + return; + +} +/*}}}*/ +void FemModel::BedrockFromMismipPlus(void){/*{{{*/ + + /*Insert bedrock from mismip+ setup*/ + /*This was used to Misomip project/simulations*/ + + IssmDouble x,y,bx,by; + int numvertices = this->GetElementsWidth(); + IssmDouble* xyz_list = NULL; + IssmDouble* r = xNew(numvertices); + + for(int el=0;elelements->Size();el++){ + Element* element=xDynamicCast(this->elements->GetObjectByOffset(el)); + + element->GetVerticesCoordinates(&xyz_list); + for(int i=0;iAddInput(BedEnum,&r[0],P1Enum); + + /*Cleanup*/ + xDelete(xyz_list); + } + + /*Delete*/ + xDelete(r); + + return; +} +/*}}}*/ +void FemModel::AdjustBaseThicknessAndMask(void){/*{{{*/ + + int numvertices = this->GetElementsWidth(); + IssmDouble rho_water,rho_ice,density,base_float; + IssmDouble* phi = xNew(numvertices); + IssmDouble* h = xNew(numvertices); + IssmDouble* s = xNew(numvertices); + IssmDouble* b = xNew(numvertices); + IssmDouble* r = xNew(numvertices); + IssmDouble* sl = xNew(numvertices); + + for(int el=0;elelements->Size();el++){ + Element* element=xDynamicCast(this->elements->GetObjectByOffset(el)); + + element->GetInputListOnVertices(&s[0],SurfaceEnum); + element->GetInputListOnVertices(&r[0],BedEnum); + element->GetInputListOnVertices(&sl[0],SealevelEnum); + rho_water = element->matpar->GetMaterialParameter(MaterialsRhoSeawaterEnum); + rho_ice = element->matpar->GetMaterialParameter(MaterialsRhoIceEnum); + density = rho_ice/rho_water; + + for(int i=0;ibase_float){ + b[i] = r[i]; + } + else { + b[i] = base_float; + } + + if(abs(sl[i])>0) _error_("Sea level value not supported!"); + /*update thickness and mask grounded ice level set*/ + h[i] = s[i]-b[i]; + phi[i] = h[i]+r[i]/density; + } + + /*Update inputs*/ + element->AddInput(MaskGroundediceLevelsetEnum,&phi[0],P1Enum); + element->AddInput(ThicknessEnum,&h[0],P1Enum); + element->AddInput(BaseEnum,&b[0],P1Enum); + + } + + /*Delete*/ + xDelete(phi); + xDelete(h); + xDelete(s); + xDelete(b); + xDelete(r); + xDelete(sl); + + return; +} +/*}}}*/ +void FemModel::WriteMeshInResults(void){/*{{{*/ + + int step = -1; + int numberofelements = -1; + int numberofvertices = -1; + IssmDouble time = -1; + IssmDouble* x = NULL; + IssmDouble* y = NULL; + IssmDouble* z = NULL; + int* elementslist = NULL; + + if(!this->elements || !this->vertices || !this->results || !this->parameters) return; + + parameters->FindParam(&step,StepEnum); + parameters->FindParam(&time,TimeEnum); + numberofelements=this->elements->NumberOfElements(); + numberofvertices=this->vertices->NumberOfVertices(); + + /*Get mesh. Elementslist comes in Matlab indexing*/ + this->GetMesh(this->vertices,this->elements,&x,&y,&z,&elementslist); + + /*Write mesh in Results*/ + this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshElementsEnum, + elementslist,numberofelements,this->GetElementsWidth(),step,time)); + + this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshXEnum, + x,numberofvertices,1,step,time)); + + this->results->AddResult(new GenericExternalResult(this->results->Size()+1,MeshYEnum, + y,numberofvertices,1,step,time)); + + /*Cleanup*/ + xDelete(x); + xDelete(y); + xDelete(z); + xDelete(elementslist); + + return; +} +/*}}}*/ +void FemModel::InterpolateInputs(Vertices* newfemmodel_vertices,Elements* newfemmodel_elements){/*{{{*/ + + int maxinputs = MaximumNumberOfDefinitionsEnum; + + /*Figure out how many inputs we have and their respective interpolation*/ + Vector* input_interpolations=new Vector(maxinputs); + if(this->elements->Size()){ + Element* element=xDynamicCast(this->elements->GetObjectByOffset(0)); + element->GetInputsInterpolations(input_interpolations); + } + input_interpolations->Assemble(); + + /*Serialize and set output*/ + IssmDouble* input_interpolations_serial = input_interpolations->ToMPISerial(); + delete input_interpolations; + + /*Count and get enums of all inputs in old mesh*/ + int numP0inputs; + int numP1inputs; + int *P0input_enums = NULL; + int *P1input_enums = NULL; + int *P0input_interp = NULL; + int *P1input_interp = NULL; + for(int step=0;step<2;step++){ + if(step){ + P0input_enums = xNew(numP0inputs); + P1input_enums = xNew(numP1inputs); + P0input_interp = xNew(numP0inputs); + P1input_interp = xNew(numP1inputs); + } + numP0inputs = 0; + numP1inputs = 0; + for(int i=0;i(input_interpolations_serial[i]); + switch(inputinterp){ + case 0: + /*Input not found, go to the next*/ + break; + case P1Enum: + if(step){ + P1input_enums[numP1inputs] = i; + P1input_interp[numP1inputs] = inputinterp; + } + numP1inputs++; + break; + case P0Enum: + case DoubleInputEnum: + case IntInputEnum: + case BoolInputEnum: + if(step){ + P0input_enums[numP0inputs] = i; + P0input_interp[numP0inputs] = inputinterp; + } + numP0inputs++; + break; + default: + _error_(EnumToStringx(inputinterp)<<" Not supported yet"); + } + } + } + + /*========== Deal with P0 inputs ==========*/ + int numelementsold = this->elements->NumberOfElements(); + int numelementsnew = newfemmodel_elements->NumberOfElements(); + int numverticesold = this->vertices->NumberOfVertices(); + int numverticesnew = newfemmodel_vertices->NumberOfVertices(); + IssmDouble* P0inputsold = xNew(numelementsold*numP0inputs); + IssmDouble* P0inputsnew = NULL; + IssmDouble* vector = NULL; + + for(int i=0;i(vector); + } + + /*========== Deal with P1 inputs ==========*/ + IssmDouble* P1inputsold = xNew(numverticesold*numP1inputs); + IssmDouble* P1inputsnew = NULL; + vector = NULL; + + for(int i=0;i(vector); + } + + /*Old mesh coordinates*/ + IssmDouble *Xold = NULL; + IssmDouble *Yold = NULL; + IssmDouble *Zold = NULL; + int *Indexold = NULL; + IssmDouble *Xnew = NULL; + IssmDouble *Ynew = NULL; + IssmDouble *Znew = NULL; + IssmDouble* XC_new = NULL; + IssmDouble* YC_new = NULL; + int *Indexnew = NULL; + + /*Get the old mesh*/ + this->GetMesh(this->vertices,this->elements,&Xold,&Yold,&Zold,&Indexold); + + /*Get the new mesh*/ + this->GetMesh(newfemmodel_vertices,newfemmodel_elements,&Xnew,&Ynew,&Znew,&Indexnew); + + /*Calculate the center points xc and xy*/ + int elementswidth = this->GetElementsWidth(); //just tria in this version + /*new mesh*/ + XC_new=xNewZeroInit(numelementsnew); + YC_new=xNewZeroInit(numelementsnew); + for(int i=0;i(numelementsnew); + for(int j=0;jSize();j++){ + Element* element=xDynamicCast(newfemmodel_elements->GetObjectByOffset(j)); + switch(P0input_interp[i]){ + case P0Enum: + case DoubleInputEnum: + element->AddInput(new DoubleInput(P0input_enums[i],vector[element->sid]));//sid because newfemmodel has just a partitioning + break; + case IntInputEnum: + element->AddInput(new IntInput(P0input_enums[i],vector[element->sid]));//sid because newfemmodel has just a partitioning + break; + case BoolInputEnum: + element->AddInput(new BoolInput(P0input_enums[i],vector[element->sid]));//sid because newfemmodel has just a partitioning + break; + default: + _error_(EnumToStringx(P0input_enums[i])<<" Not supported yet"); + } + } + + xDelete(vector); + } + + /*Insert P1 inputs into the new elements.*/ + vector=NULL; + for(int i=0;i(numverticesnew); + for(int j=0;jSize();j++){ + Element* element=xDynamicCast(newfemmodel_elements->GetObjectByOffset(j)); + element->InputUpdateFromVector(vector,P1input_enums[i],VertexSIdEnum); + } + + xDelete(vector); + } + + /*Cleanup*/ + xDelete(input_interpolations_serial); + xDelete(P0inputsold); + xDelete(P0inputsnew); + xDelete(P0input_enums); + xDelete(P0input_interp); + xDelete(P1inputsold); + xDelete(P1inputsnew); + xDelete(P1input_enums); + xDelete(P1input_interp); + xDelete(Xold); + xDelete(Yold); + xDelete(Zold); + xDelete(Indexold); + xDelete(Xnew); + xDelete(Ynew); + xDelete(Znew); + xDelete(XC_new); + xDelete(YC_new); + xDelete(Indexnew); + +} +/*}}}*/ +void FemModel::ExecuteRefinement(int &numberofvertices,int &numberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist){/*{{{*/ + + /*elements is in Matlab indexing*/ + + int my_rank = IssmComm::GetRank(); + int numberofsegments = -1; + IssmDouble* vx = NULL; //itapopo this is not being used + IssmDouble* vy = NULL; //itapopo this is not being used + IssmDouble* x = NULL; + IssmDouble* y = NULL; + IssmDouble* z = NULL; + int* elementslist = NULL; + int* segments = NULL; + IssmDouble* masklevelset = NULL; + const int elementswidth = this->GetElementsWidth();//just 2D mesh, tria elements + + /*Solutions which will be used to refine the elements*/ + this->GetGroundediceLevelSet(&masklevelset);//itapopo verificar se já existe um método igual a esse + + if(my_rank==0){ + int type_process=1; //1: it refines father mesh. See AdaptiveMeshRefinement.h (.cpp) + this->amr->ExecuteRefinement(type_process,vx,vy,masklevelset, + numberofvertices,numberofelements,numberofsegments,&x,&y,&z,&elementslist,&segments); + if(numberofvertices<=0 || numberofelements<=0 /*|| newnumberofsegments<=0*/) _error_("Error in the refinement process."); + } + else{ + x=xNew(numberofvertices); + y=xNew(numberofvertices); + z=xNew(numberofvertices); + elementslist=xNew(numberofelements*this->GetElementsWidth()); + } + + /*Send new mesh to others CPU*/ + ISSM_MPI_Bcast(&numberofvertices,1,ISSM_MPI_INT,0,IssmComm::GetComm()); + ISSM_MPI_Bcast(&numberofelements,1,ISSM_MPI_INT,0,IssmComm::GetComm()); + ISSM_MPI_Bcast(x,numberofvertices,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + ISSM_MPI_Bcast(y,numberofvertices,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + ISSM_MPI_Bcast(z,numberofvertices,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + ISSM_MPI_Bcast(elementslist,numberofelements*this->GetElementsWidth(),ISSM_MPI_INT,0,IssmComm::GetComm()); + + /*Assign the pointers*/ + (*pelementslist) = elementslist; //Matlab indexing + (*px) = x; + (*py) = y; + (*pz) = z; + + /*Cleanup*/ + if(segments) xDelete(segments); + xDelete(masklevelset); + +} +/*}}}*/ +void FemModel::GetGroundediceLevelSet(IssmDouble **pmasklevelset){/*{{{*/ + + int elementswidth = this->GetElementsWidth();//just 2D mesh, tria elements + int numberofelements = this->elements->NumberOfElements(); + int numberofvertices = this->vertices->NumberOfVertices(); + + IssmDouble* elementlevelset=xNew(elementswidth); + int* elem_vertices=xNew(elementswidth); + Vector* vmasklevelset=new Vector(numberofvertices); + + for(int i=0;ielements->Size();i++){ + Element* element=xDynamicCast(this->elements->GetObjectByOffset(i)); + element->GetInputListOnVertices(elementlevelset,MaskGroundediceLevelsetEnum); + element->GetVerticesSidList(elem_vertices); + vmasklevelset->SetValue(elem_vertices[0],elementlevelset[0],INS_VAL); + vmasklevelset->SetValue(elem_vertices[1],elementlevelset[1],INS_VAL); + vmasklevelset->SetValue(elem_vertices[2],elementlevelset[2],INS_VAL); + } + + /*Assemble*/ + vmasklevelset->Assemble(); + + /*Serialize and set output*/ + (*pmasklevelset)=vmasklevelset->ToMPISerial(); + + /*Cleanup*/ + xDelete(elementlevelset); + xDelete(elem_vertices); + delete vmasklevelset; + +} +/*}}}*/ +void FemModel::CreateVertices(int newnumberofvertices,int newnumberofelements,int elementswidth,int* newelementslist,int* my_vertices,IssmDouble* newx,IssmDouble* newy,IssmDouble* newz,Vertices* vertices){/*{{{*/ + + /*newelementslist is in Matlab indexing*/ + + /*Creating connectivity table*/ + int* connectivity=NULL; + connectivity=xNewZeroInit(newnumberofvertices); + + for (int i=0;i0 && vertexid-1id=i+1; + newvertex->sid=i; + newvertex->pid=UNDEF; + newvertex->x=newx[i]; + newvertex->y=newy[i]; + newvertex->z=newz[i]; + newvertex->domaintype=Domain2DhorizontalEnum; + newvertex->sigma=0.; + newvertex->connectivity=connectivity[i]; + newvertex->clone=false;//itapopo check this + vertices->AddObject(newvertex); + } + } + + xDelete(connectivity); +} +/*}}}*/ +void FemModel::CreateElements(int newnumberofelements,int elementswidth,int* newelementslist,bool* my_elements,Elements* elements){/*{{{*/ + + /*newlementslist is in Matlab indexing*/ + + for(int i=0;iid=i+1; + newtria->sid=i; + newtria->parameters=NULL; + newtria->inputs=new Inputs(); + newtria->nodes=NULL; + newtria->vertices=NULL; + newtria->material=NULL; + newtria->matpar=NULL; + if(this->nummodels>0){ + newtria->element_type_list=xNew(this->nummodels); + for(int j=0;jelement_type_list[j]=0; + } + else newtria->element_type_list=NULL; + + /*Element hook*/ + int matpar_id=newnumberofelements+1; //retrieve material parameter id (last pointer in femodel->materials) + int material_id=i+1; // retrieve material_id = i+1; + /*retrieve vertices ids*/ + int* vertex_ids=xNew(elementswidth); + for(int j=0;j(newelementslist[elementswidth*i+j]);//this Hook wants Matlab indexing + /*Setting the hooks*/ + newtria->numanalyses =this->nummodels; + newtria->hnodes =new Hook*[this->nummodels]; + newtria->hvertices =new Hook(&vertex_ids[0],elementswidth); + newtria->hmaterial =new Hook(&material_id,1); + newtria->hmatpar =new Hook(&matpar_id,1); + newtria->hneighbors =NULL; + /*Initialize hnodes as NULL*/ + for(int j=0;jnummodels;j++) newtria->hnodes[j]=NULL; + /*Clean up*/ + xDelete(vertex_ids); + elements->AddObject(newtria); + } + } + +} +/*}}}*/ +void FemModel::CreateMaterials(int newnumberofelements,bool* my_elements,Materials* materials){/*{{{*/ + + /*Just Matice in this version*/ + for(int i=0;iAddObject(new Matice(i+1,i,MaticeEnum)); + } + } + + /*Add new constant material property to materials, at the end: */ + Matpar *newmatpar=static_cast(this->materials->GetObjectByOffset(this->materials->Size()-1)->copy()); + newmatpar->SetMid(newnumberofelements+1); + materials->AddObject(newmatpar);//put it at the end of the materials + +} +/*}}}*/ +void FemModel::CreateNodes(int newnumberofvertices,int* my_vertices,int nodecounter,int analysis_enum,Nodes* nodes){/*{{{*/ + + int lid=0; + for(int j=0;jid=nodecounter+j+1; + newnode->sid=j; + newnode->lid=lid++; + newnode->analysis_enum=analysis_enum; + + /*Initialize coord_system: Identity matrix by default*/ + for(int k=0;k<3;k++) for(int l=0;l<3;l++) newnode->coord_system[k][l]=0.0; + for(int k=0;k<3;k++) newnode->coord_system[k][k]=1.0; + + /*indexing:*/ + newnode->indexingupdate=true; + + Analysis* analysis=EnumToAnalysis(analysis_enum); + int *doftypes=NULL; + int numdofs=analysis->DofsPerNode(&doftypes,Domain2DhorizontalEnum,SSAApproximationEnum); + newnode->indexing.Init(numdofs,doftypes); + xDelete(doftypes); + delete analysis; + if(analysis_enum==StressbalanceAnalysisEnum) + newnode->SetApproximation(SSAApproximationEnum); + else + newnode->SetApproximation(0); + + /*Stressbalance Horiz*/ + if(analysis_enum==StressbalanceAnalysisEnum){ + // itapopo this code is rarely used. + /*Coordinate system provided, convert to coord_system matrix*/ + //XZvectorsToCoordinateSystem(&this->coord_system[0][0],&iomodel->Data(StressbalanceReferentialEnum)[j*6]); + //_assert_(sqrt( coord_system[0][0]*coord_system[0][0] + coord_system[1][0]*coord_system[1][0]) >1.e-4); + + } + nodes->AddObject(newnode); + } + } + return; +} +/*}}}*/ +void FemModel::GetMesh(Vertices* femmodel_vertices, Elements* femmodel_elements,IssmDouble** px, IssmDouble** py, IssmDouble** pz, int** pelementslist){/*{{{*/ + + if(!femmodel_vertices) _error_("GetMesh: vertices are NULL."); + if(!femmodel_elements) _error_("GetMesh: elements are NULL."); + + int numberofvertices, numberofelements; + int elementswidth = this->GetElementsWidth(); // just 2D mesh in this version (just tria elements) + IssmDouble *x = NULL; + IssmDouble *y = NULL; + IssmDouble *z = NULL; + int* elementslist = NULL; + + /*Get vertices coordinates*/ + VertexCoordinatesx(&x, &y, &z, femmodel_vertices,false) ; + + numberofvertices = femmodel_vertices->NumberOfVertices(); + numberofelements = femmodel_elements->NumberOfElements(); + + /*Get element vertices*/ + int* elem_vertices=xNew(elementswidth); + Vector* vid1= new Vector(numberofelements); + Vector* vid2= new Vector(numberofelements); + Vector* vid3= new Vector(numberofelements); + + /*Go through elements, and for each element, get vertices*/ + for(int i=0;iSize();i++){ + Element* element=xDynamicCast(femmodel_elements->GetObjectByOffset(i)); + element->GetVerticesSidList(elem_vertices); + vid1->SetValue(element->sid,elem_vertices[0],INS_VAL); + vid2->SetValue(element->sid,elem_vertices[1],INS_VAL); + vid3->SetValue(element->sid,elem_vertices[2],INS_VAL); + } + + /*Assemble*/ + vid1->Assemble(); + vid2->Assemble(); + vid3->Assemble(); + + /*Serialize*/ + IssmDouble *id1 = vid1->ToMPISerial(); + IssmDouble *id2 = vid2->ToMPISerial(); + IssmDouble *id3 = vid3->ToMPISerial(); + + /*Construct elements list*/ + elementslist=xNew(numberofelements*elementswidth); + if(numberofelements*elementswidth<0) _error_("numberofelements negative."); + for(int i=0;i(elem_vertices); + xDelete(id1); + xDelete(id2); + xDelete(id3); + delete vid1; + delete vid2; + delete vid3; +} +/*}}}*/ +void FemModel::CreateConstraints(int newnumberofvertices,int newnumberofelements,int nodecounter,int constraintcounter,IssmDouble* newx,IssmDouble* newy,int* my_vertices,Constraints* constraints){/*{{{*/ + + /*itapopo ATTENTION: JUST SPCVX AND SPCVY TO TEST!!!*/ + /*OTHERS CONSTRAINTS MUST BE IMPLEMENTED!!!*/ + + /*Get x and y of the mesh i-1*/ + int numberofvertices = this->vertices->NumberOfVertices(); + int numberofelements = this->elements->NumberOfElements(); + IssmDouble *x = NULL; + IssmDouble *y = NULL; + IssmDouble *z = NULL; + int *elementslist = NULL; + + /*elementslist is in Matlab indexing*/ + this->GetMesh(this->vertices,this->elements,&x,&y,&z,&elementslist); + + /*Get spcvx and spcvy for mesh i-1*/ + IssmDouble *spcvx = NULL; + IssmDouble *spcvy = NULL; + IssmDouble *spcvxflag = NULL; + IssmDouble *spcvyflag = NULL; + int numberofnodes_analysistype = this->nodes->NumberOfNodes(StressbalanceAnalysisEnum); + Vector* vspcvx = new Vector(numberofnodes_analysistype); + Vector* vspcvy = new Vector(numberofnodes_analysistype); + Vector* vspcvxflag = new Vector(numberofnodes_analysistype); + Vector* vspcvyflag = new Vector(numberofnodes_analysistype); + + for(int i=0;iconstraints->Size();i++){ + SpcStatic* spc = xDynamicCast(this->constraints->GetObjectByOffset(i)); + int dof = spc->GetDof(); + int node = spc->GetNodeId(); + IssmDouble spcvalue = spc->GetValue(); + int nodeindex = node-1; + + if(dof==0) {//vx + vspcvx->SetValue(nodeindex,spcvalue,INS_VAL); + vspcvxflag->SetValue(nodeindex,1,INS_VAL); + } + if(dof==1){//vy + vspcvy->SetValue(nodeindex,spcvalue,INS_VAL); + vspcvyflag->SetValue(nodeindex,1,INS_VAL); + } + } + + /*Assemble*/ + vspcvx->Assemble(); + vspcvy->Assemble(); + vspcvxflag->Assemble(); + vspcvyflag->Assemble(); + + /*Serialize*/ + spcvx = vspcvx->ToMPISerial(); + spcvy = vspcvy->ToMPISerial(); + spcvxflag = vspcvxflag->ToMPISerial(); + spcvyflag = vspcvyflag->ToMPISerial(); + + IssmDouble *newspcvx = NULL; + IssmDouble *newspcvy = NULL; + IssmDouble *newspcvxflag = NULL; + IssmDouble *newspcvyflag = NULL; + int nods_data = numberofvertices; + int nels_data = numberofelements; + int M_data = numberofvertices; + int N_data = 1; + int N_interp = newnumberofvertices; + + /*Interpolate spcvx and spcvy in the new mesh*/ + InterpFromMeshToMesh2dx(&newspcvx,elementslist,x,y,nods_data,nels_data,spcvx,M_data,N_data,newx,newy,N_interp,NULL); + InterpFromMeshToMesh2dx(&newspcvy,elementslist,x,y,nods_data,nels_data,spcvy,M_data,N_data,newx,newy,N_interp,NULL); + InterpFromMeshToMesh2dx(&newspcvxflag,elementslist,x,y,nods_data,nels_data,spcvxflag,M_data,N_data,newx,newy,N_interp,NULL); + InterpFromMeshToMesh2dx(&newspcvyflag,elementslist,x,y,nods_data,nels_data,spcvyflag,M_data,N_data,newx,newy,N_interp,NULL); + + int count = 0; + IssmDouble eps = 1.e-8; + + /*Now, insert the interpolated constraints in the data set (constraints)*/ + for(int i=0;i(newspcvx[i]) && newspcvxflag[i]>(1-eps)){ + constraints->AddObject(new SpcStatic(constraintcounter+count+1,nodecounter+i+1,0,newspcvx[i],StressbalanceAnalysisEnum)); + //add count'th spc, on node i+1, setting dof 1 to vx. + count++; + } + } + } + count=0; + for(int i=0;i(newspcvy[i]) && newspcvyflag[i]>(1-eps) ){ + constraints->AddObject(new SpcStatic(constraintcounter+count+1,nodecounter+i+1,1,newspcvy[i],StressbalanceAnalysisEnum)); + //add count'th spc, on node i+1, setting dof 1 to vx. + count++; + } + } + } + + /*Cleanup*/ + xDelete(x); + xDelete(y); + xDelete(z); + xDelete(elementslist); + xDelete(spcvx); + xDelete(spcvy); + xDelete(spcvxflag); + xDelete(spcvyflag); + xDelete(newspcvx); + xDelete(newspcvy); + xDelete(newspcvxflag); + xDelete(newspcvyflag); + delete vspcvx; + delete vspcvy; + delete vspcvxflag; + delete vspcvyflag; + +} +/*}}}*/ +void FemModel::UpdateElements(int newnumberofelements,int* newelementslist,bool* my_elements,int nodecounter,int analysis_counter,Elements* newelements){/*{{{*/ + + /*newelementslist is in Matlab indexing*/ + + /*Update elements, set hnode. + This code is in all analysis */ + int elemcounter=0; + for(int iel=0;ielGetObjectByOffset(elemcounter); + //element update + tria->element_type_list[analysis_counter]=P1Enum; + int numnodes=3; + int* tria_node_ids=xNew(numnodes); + tria_node_ids[0]=nodecounter+newelementslist[3*iel+0]; //matlab indexing + tria_node_ids[1]=nodecounter+newelementslist[3*iel+1]; //matlab indexing + tria_node_ids[2]=nodecounter+newelementslist[3*iel+2]; //matlab indexing + tria->SetHookNodes(tria_node_ids,numnodes,analysis_counter); tria->nodes=NULL; + xDelete(tria_node_ids); + elemcounter++; + } + } + return; +} +/*}}}*/ +void FemModel::ElementsAndVerticesPartitioning(int& newnumberofvertices,int& newnumberofelements,int& elementswidth,int* newelementslist,bool** pmy_elements,int** pmy_vertices){/*{{{*/ + + /*newelementslist come in Matlab indexing*/ + + int *epart = NULL; //element partitioning. + int *npart = NULL; //node partitioning. + int *index = NULL; //elements in C indexing + int edgecut = 1; + int numflag = 0; + int etype = 1; + int my_rank = IssmComm::GetRank(); + int numprocs = IssmComm::GetSize(); + bool *my_elements = NULL; + int *my_vertices = NULL; + + _assert_(newnumberofvertices>0); + _assert_(newnumberofelements>0); + epart=xNew(newnumberofelements); + npart=xNew(newnumberofvertices); + index=xNew(elementswidth*newnumberofelements); + + for (int i=0;i1){ +#ifdef _HAVE_METIS_ + METIS_PartMeshNodalPatch(&newnumberofelements,&newnumberofvertices, index, &etype, &numflag, &numprocs, &edgecut, epart, npart); +#else + _error_("metis has not beed installed. Cannot run with more than 1 cpu"); +#endif + } + else if (numprocs==1){ + /*METIS does not know how to deal with one cpu only!*/ + for (int i=0;i(newnumberofvertices); + my_elements=xNew(newnumberofelements); + for(int i=0;i(epart); + xDelete(npart); + xDelete(index); + +} +/*}}}*/ +#endif Index: /issm/trunk/src/c/classes/FemModel.h =================================================================== --- /issm/trunk/src/c/classes/FemModel.h (revision 21728) +++ /issm/trunk/src/c/classes/FemModel.h (revision 21729) @@ -20,4 +20,7 @@ class Profiler; class Elements; +#ifdef _HAVE_NEOPZ_ +#include "./AdaptiveMeshRefinement.h" +#endif /*}}}*/ @@ -44,4 +47,8 @@ Vertices *vertices; //one set of vertices + #ifdef _HAVE_NEOPZ_ + AdaptiveMeshRefinement *amr; //adaptive mesh refinement object. It keeps coarse mesh and execute refinement process + #endif + /*constructors, destructors: */ FemModel(int argc,char** argv,ISSM_MPI_Comm comm_init,bool trace=false); @@ -60,4 +67,5 @@ void SetCurrentConfiguration(int configuration_type); void SetCurrentConfiguration(int configuration_type,int analysis_type); + int Size(void); void SolutionAnalysesList(int** panalyses,int* pnumanalyses,IoModel* iomodel,int solutiontype); void Solve(void); @@ -110,5 +118,5 @@ void ThicknessAbsGradientx( IssmDouble* pJ); void ThicknessPositivex(IssmDouble* pJ); - #ifdef _HAVE_GIA_ + #ifdef _HAVE_GIAIVINS_ void Deflection(Vector* wg,Vector* dwgdt, IssmDouble* x, IssmDouble* y); #endif @@ -120,4 +128,5 @@ void SealevelriseEustatic(Vector* pSgi, IssmDouble* peustatic, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius); void SealevelriseNonEustatic(Vector* pSgo, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius,bool verboseconvolution); + void SealevelriseRotationalFeedback(Vector* pSgo_rot, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius); void SealevelriseGeodetic(Vector* pUp, Vector* pNorth, Vector* pEast, Vector* pSg_old, IssmDouble* latitude, IssmDouble* longitude, IssmDouble* radius, IssmDouble* xx, IssmDouble* yy, IssmDouble* zz); IssmDouble SealevelriseOceanAverage(Vector* Sg); @@ -136,4 +145,26 @@ void InitFromBuffers(char* buffer, int buffersize, char* toolkits, int solution_type,bool trace,IssmPDouble* X=NULL); #endif + + #ifdef _HAVE_NEOPZ_ + /*Adaptive mesh refinement methods*/ + void InitializeAdaptiveRefinement(void); + void ReMesh(void); + void BedrockFromMismipPlus(void); + void AdjustBaseThicknessAndMask(void); + void GetMesh(Vertices* femmodel_vertices,Elements* femmodel_elements,IssmDouble** px, IssmDouble** py, IssmDouble** pz, int** pelementslist); + int GetElementsWidth(){return 3;};//just tria elements in this first version + void ExecuteRefinement(int &numberofvertices,int &numberofelements,IssmDouble** px,IssmDouble** py,IssmDouble** pz,int** pelementslist); + void GetGroundediceLevelSet(IssmDouble** pmasklevelset); + void CreateVertices(int newnumberofvertices,int newnumberofelements,int elementswidth,int* newelementslist,int* my_vertices,IssmDouble* newx,IssmDouble* newy,IssmDouble* newz,Vertices* vertices); + void CreateElements(int newnumberofelements,int elementswidth,int* newelementslist,bool* my_elements,Elements* elements); + void CreateMaterials(int newnumberofelements,bool* my_elements,Materials* materials); + void CreateNodes(int newnumberofvertices,int* my_vertices,int nodecounter,int analysis_enum,Nodes* nodes); + void CreateConstraints(int newnumberofvertices,int newnumberofelements,int nodecounter,int constraintcounter,IssmDouble* newx,IssmDouble* newy,int* my_vertices,Constraints* constraints); + void InterpolateInputs(Vertices* newfemmodel_vertices,Elements* newfemmodel_elements); + void UpdateElements(int newnumberofelements,int* newelementslist,bool* my_elements,int nodecounter,int analysis_counter,Elements* newelements); + void ElementsAndVerticesPartitioning(int& newnumberofvertices,int& newnumberofelements,int& elementswidth,int* newelementslist,bool** pmy_elements,int** pmy_vertices); + void WriteMeshInResults(void); + void SetRefPatterns(void); + #endif }; Index: /issm/trunk/src/c/classes/Inputs/BoolInput.cpp =================================================================== --- /issm/trunk/src/c/classes/Inputs/BoolInput.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Inputs/BoolInput.cpp (revision 21729) @@ -133,4 +133,8 @@ } /*}}}*/ +void BoolInput::GetInputAverage(IssmDouble* pvalue){/*{{{*/ + *pvalue=reCast(value); +} +/*}}}*/ void BoolInput::GetInputValue(bool* pvalue){/*{{{*/ *pvalue=value; Index: /issm/trunk/src/c/classes/Inputs/BoolInput.h =================================================================== --- /issm/trunk/src/c/classes/Inputs/BoolInput.h (revision 21728) +++ /issm/trunk/src/c/classes/Inputs/BoolInput.h (revision 21729) @@ -50,5 +50,5 @@ void Extrude(int start); void GetInputAllTimeAverages(IssmDouble** pvalues,IssmDouble** ptimes, int* pnumtimes){_error_("not implemented yet");}; - void GetInputAverage(IssmDouble* pvalue){_error_("not implemented yet");}; + void GetInputAverage(IssmDouble* pvalue); void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, Gauss* gauss){_error_("not implemented yet");}; void GetInputDerivativeAverageValue(IssmDouble* derivativevalues, IssmDouble* xyz_list){_error_("not implemented yet");}; Index: /issm/trunk/src/c/classes/Inputs/ControlInput.cpp =================================================================== --- /issm/trunk/src/c/classes/Inputs/ControlInput.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Inputs/ControlInput.cpp (revision 21729) @@ -81,5 +81,5 @@ _printf_("---minvalues: \n"); if (minvalues) minvalues->Echo(); _printf_("---maxvalues: \n"); if (maxvalues) maxvalues->Echo(); - _printf_("---gradient: \n"); if (gradient) gradient->Echo(); + _printf_("---gradient: \n"); if (gradient){ gradient->Echo();} else{_printf_(" Not set yet\n");} } /*}}}*/ Index: /issm/trunk/src/c/classes/Inputs/IntInput.cpp =================================================================== --- /issm/trunk/src/c/classes/Inputs/IntInput.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Inputs/IntInput.cpp (revision 21729) @@ -134,4 +134,8 @@ } /*}}}*/ +void IntInput::GetInputAverage(IssmDouble* pvalue){/*{{{*/ + *pvalue=reCast(value); +} +/*}}}*/ void IntInput::GetInputValue(bool* pvalue){_error_("not supported yet!");}/*{{{*/ /*}}}*/ Index: /issm/trunk/src/c/classes/Inputs/IntInput.h =================================================================== --- /issm/trunk/src/c/classes/Inputs/IntInput.h (revision 21728) +++ /issm/trunk/src/c/classes/Inputs/IntInput.h (revision 21729) @@ -54,5 +54,5 @@ void Extrude(int start){_error_("not supported yet");}; void GetInputAllTimeAverages(IssmDouble** pvalues,IssmDouble** ptimes, int* pnumtimes){_error_("not implemented yet");}; - void GetInputAverage(IssmDouble* pvalue){_error_("not implemented yet");}; + void GetInputAverage(IssmDouble* pvalue); void GetInputDerivativeAverageValue(IssmDouble* derivativevalues, IssmDouble* xyz_list){_error_("not implemented yet");}; void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list,Gauss* gauss){_error_("not implemented yet");}; Index: /issm/trunk/src/c/classes/Inputs/PentaInput.cpp =================================================================== --- /issm/trunk/src/c/classes/Inputs/PentaInput.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Inputs/PentaInput.cpp (revision 21729) @@ -433,4 +433,6 @@ case P1Enum: case P1bubbleEnum: + case P1xP2Enum: + case P1xP3Enum: case P2Enum: { Index: /issm/trunk/src/c/classes/IoModel.cpp =================================================================== --- /issm/trunk/src/c/classes/IoModel.cpp (revision 21728) +++ /issm/trunk/src/c/classes/IoModel.cpp (revision 21729) @@ -657,4 +657,6 @@ } else if(strcmp(record_name,"md.flowequation.fe_FS")==0){ this->AddConstant(new IoConstant(StringToEnumx(string),record_name)); + } else if(strcmp(record_name,"md.thermal.fe")==0){ + this->AddConstant(new IoConstant(StringToEnumx(string),record_name)); } else if(strcmp(record_name,"md.groundingline.migration")==0){ this->AddConstant(new IoConstant(StringToEnumx(string),record_name)); @@ -681,4 +683,5 @@ case 7: case 8: + case 10: /*We are not interested in this record, too memory intensive. Skip it: */ /*skip: */ @@ -797,4 +800,6 @@ } else if(strcmp(record_name,"md.flowequation.fe_FS")==0){ this->AddConstant(new IoConstant(StringToEnumx(string),record_name)); + } else if(strcmp(record_name,"md.thermal.fe")==0){ + this->AddConstant(new IoConstant(StringToEnumx(string),record_name)); } else if(strcmp(record_name,"md.groundingline.migration")==0){ this->AddConstant(new IoConstant(StringToEnumx(string),record_name)); @@ -821,4 +826,5 @@ case 7: break; //do nothing. not interested in this type of data, which is memory intensive. case 8: break; //do nothing. not interested in this type of data, which is memory intensive. + case 10: break; //do nothing. not interested in this type of data, which is memory intensive. case 9: ISSM_MPI_Bcast(&numstrings,1,ISSM_MPI_INT,0,IssmComm::GetComm()); @@ -1128,5 +1134,5 @@ /*Set file pointer to beginning of the data: */ fid=this->SetFilePointerToData(&code,NULL,data_name); - if(code!=5 && code!=6 && code!=7)_error_("expecting a IssmDouble, integer or boolean matrix for \""<(M*N); - - /*Read matrix on node 0, then broadcast: */ - if(my_rank==0){ - if(fread(matrix,M*N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix "); - } - ISSM_MPI_Bcast(matrix,M*N,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); - - *pmatrix=xNew(M*N); - for(int i=0;i(matrix); - } - else - *pmatrix=NULL; + if(code==10){ + /*Special case for Compressed mat*/ + IssmPDouble offset,range; + if(my_rank==0) if(fread(&offset,sizeof(IssmPDouble),1,fid)!=1) _error_("could not read offset"); + ISSM_MPI_Bcast(&offset,1,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + + if(my_rank==0) if(fread(&range,sizeof(IssmPDouble),1,fid)!=1) _error_("could not read range"); + ISSM_MPI_Bcast(&range,1,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + + *pmatrix=xNew(M*N); + + /*Read matrix*/ + uint8_t* rawmatrix=xNew((M-1)*N); + if(my_rank==0) if(fread(rawmatrix,(M-1)*N*sizeof(char),1,fid)!=1) _error_("could not read matrix "); + ISSM_MPI_Bcast(rawmatrix,(M-1)*N,ISSM_MPI_CHAR,0,IssmComm::GetComm()); + + for(int i=0;i<(M-1)*N;++i) (*pmatrix)[i]=offset+range*reCast(rawmatrix[i])/255.; + xDelete(rawmatrix); + + /*read time now*/ + IssmPDouble* timematrix=xNew(N); + if(my_rank==0) if(fread(timematrix,N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read time in compressed matrix"); + ISSM_MPI_Bcast(timematrix,N,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + + for(int i=0;i(timematrix); + + } + else{ + /*Read matrix on node 0, then broadcast: */ + matrix=xNew(M*N); + if(my_rank==0) if(fread(matrix,M*N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix "); + ISSM_MPI_Bcast(matrix,M*N,ISSM_MPI_PDOUBLE,0,IssmComm::GetComm()); + + *pmatrix=xNew(M*N); + for(int i=0;i(matrix); + } + } + else{ + *pmatrix=NULL; + } /*Assign output pointers: */ if(pM) *pM=M; @@ -1538,5 +1572,5 @@ /*Defaulting only supported for double arrays*/ - if(code!=7) _error_(vector_name<<" is not a double array"); + if(code!=7 && code!=10) _error_(vector_name<<" is not a double array"); this->FetchData(&doublearray,&M,&N,vector_name); @@ -1621,4 +1655,5 @@ break; case 7: //IssmDouble vector + case 10: this->FetchData(&doublearray,&M,&N,vector_name); if(!doublearray) _error_("\""<(M*N); +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + matrix=xNew(M*N,"t"); +#else matrix=xNew(M*N); +#endif /*Read matrix on node 0, then broadcast: */ @@ -2456,5 +2497,5 @@ /*if record_code points to a vector, get its type (nodal or elementary): */ - if(5<=record_code && record_code<=7){ + if((5<=record_code && record_code<=7) || record_code==10){ if(fread(&vector_type,sizeof(int),1,fid)!=1) _error_("Could not read vector_type"); } Index: /issm/trunk/src/c/classes/Loads/Friction.cpp =================================================================== --- /issm/trunk/src/c/classes/Loads/Friction.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Loads/Friction.cpp (revision 21729) @@ -246,4 +246,7 @@ case 8: GetAlpha2Sommers(palpha2,gauss); + break; + case 9: + GetAlpha2Josh(palpha2,gauss); break; default: @@ -463,4 +466,46 @@ *palpha2=alpha2; }/*}}}*/ +void Friction::GetAlpha2Josh(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ + /*Here, we want to parameterize the friction as a function of temperature + * + * alpha2 = alpha2_viscous * 1/f(T) + * + * where f(T) = exp((T-Tpmp)/gamma) + */ + + /*Intermediaries: */ + IssmDouble T,Tpmp,deltaT,deltaTref,pressure; + IssmDouble alpha2,time,gamma; + const IssmDouble yts = 365*24*3600.; + + /*Get viscous part*/ + this->GetAlpha2Viscous(&alpha2,gauss); + + /*Get delta Refs*/ + element->GetInputValue(&deltaTref,gauss,FrictionPressureAdjustedTemperatureEnum); + + /*Compute delta T*/ + element->GetInputValue(&T,gauss,TemperatureEnum); + element->GetInputValue(&pressure,gauss,PressureEnum); + Tpmp = element->TMeltingPoint(pressure); + deltaT = T-Tpmp; + + /*Compute gamma*/ + element->parameters->FindParam(&time,TimeEnum); + element->parameters->FindParam(&gamma,FrictionGammaEnum); + //if(time<25e3*yts){ + // gamma = 10.; + //} + //else{ + // gamma = 5.; + //} + //gamma = 5.; + + /*Compute scaling parameter*/ + alpha2 = alpha2 * exp((deltaTref - deltaT)/(2*gamma)); + + /*Assign output pointers:*/ + *palpha2=alpha2; +}/*}}}*/ void Friction::GetAlpha2Viscous(IssmDouble* palpha2, Gauss* gauss){/*{{{*/ Index: /issm/trunk/src/c/classes/Loads/Friction.h =================================================================== --- /issm/trunk/src/c/classes/Loads/Friction.h (revision 21728) +++ /issm/trunk/src/c/classes/Loads/Friction.h (revision 21729) @@ -36,4 +36,5 @@ void GetAlpha2Coulomb(IssmDouble* palpha2,Gauss* gauss); void GetAlpha2Hydro(IssmDouble* palpha2,Gauss* gauss); + void GetAlpha2Josh(IssmDouble* palpha2,Gauss* gauss); void GetAlpha2Sommers(IssmDouble* palpha2,Gauss* gauss); void GetAlpha2Temp(IssmDouble* palpha2,Gauss* gauss); Index: /issm/trunk/src/c/classes/Materials/Material.h =================================================================== --- /issm/trunk/src/c/classes/Materials/Material.h (revision 21728) +++ /issm/trunk/src/c/classes/Materials/Material.h (revision 21729) @@ -43,4 +43,5 @@ virtual void GetViscosity2dDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* pepsilon)=0; virtual bool IsDamage()=0; + virtual bool IsEnhanced()=0; virtual void ResetHooks()=0; @@ -52,4 +53,7 @@ virtual void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input)=0; virtual void ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon)=0; + virtual void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input)=0; + virtual void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input)=0; + virtual void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input)=0; }; Index: /issm/trunk/src/c/classes/Materials/Matestar.cpp =================================================================== --- /issm/trunk/src/c/classes/Materials/Matestar.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Materials/Matestar.cpp (revision 21729) @@ -134,18 +134,45 @@ /*}}}*/ IssmDouble Matestar::GetA(){/*{{{*/ - _error_("not implemented yet"); + /* + * A = 1/B^n + */ + + IssmDouble B,n; + + element->inputs->GetInputAverage(&B,MaterialsRheologyBEnum); + n=this->GetN(); + + return pow(B,-n); } /*}}}*/ IssmDouble Matestar::GetAbar(){/*{{{*/ - _error_("not implemented yet"); + /* + * A = 1/B^n + */ + + IssmDouble B,n; + + element->inputs->GetInputAverage(&B,MaterialsRheologyBbarEnum); + n=this->GetN(); + + return pow(B,-n); } /*}}}*/ IssmDouble Matestar::GetB(){/*{{{*/ - _error_("not implemented yet"); + + /*Output*/ + IssmDouble B; + + element->inputs->GetInputAverage(&B,MaterialsRheologyBEnum); + return B; } /*}}}*/ IssmDouble Matestar::GetBbar(){/*{{{*/ - _error_("not implemented yet"); + /*Output*/ + IssmDouble Bbar; + + element->inputs->GetInputAverage(&Bbar,MaterialsRheologyBbarEnum); + return Bbar; } /*}}}*/ @@ -159,80 +186,77 @@ } /*}}}*/ +IssmDouble Matestar::GetEc(){/*{{{*/ + + /*Output*/ + IssmDouble Ec; + + element->inputs->GetInputAverage(&Ec,MaterialsRheologyEcEnum); + return Ec; +} +/*}}}*/ +IssmDouble Matestar::GetEcbar(){/*{{{*/ + + /*Output*/ + IssmDouble Ecbar; + + element->inputs->GetInputAverage(&Ecbar,MaterialsRheologyEcbarEnum); + return Ecbar; +} +/*}}}*/ +IssmDouble Matestar::GetEs(){/*{{{*/ + + /*Output*/ + IssmDouble Es; + + element->inputs->GetInputAverage(&Es,MaterialsRheologyEsEnum); + return Es; +} +/*}}}*/ +IssmDouble Matestar::GetEsbar(){/*{{{*/ + + /*Output*/ + IssmDouble Esbar; + + element->inputs->GetInputAverage(&Esbar,MaterialsRheologyEsbarEnum); + return Esbar; +} +/*}}}*/ IssmDouble Matestar::GetN(){/*{{{*/ - _error_("not implemented yet"); + + /*Output*/ + IssmDouble n=3.0; + return n; } /*}}}*/ void Matestar::GetViscosity(IssmDouble* pviscosity,IssmDouble eps_eff){/*{{{*/ _error_("not implemented yet"); - /*From a string tensor and a material object, return viscosity, using Glen's flow law. - (1-D) B - viscosity= ------------------------- - 2 eps_eff ^[(n-1)/n] - - where viscosity is the viscotiy, B the flow law parameter , eps_eff is the effective strain rate - and n the flow law exponent. - - If eps_eff = 0 , it means this is the first time SystemMatrices is being run, and we - return 10^14, initial viscosity. - */ +} +/*}}}*/ +void Matestar::GetViscosityBar(IssmDouble* pviscosity,IssmDouble eps_eff){/*{{{*/ + _error_("not implemented yet"); +} +/*}}}*/ +void Matestar::GetViscosityComplement(IssmDouble* pviscosity_complement, IssmDouble* epsilon){/*{{{*/ + _error_("not implemented yet"); +} +/*}}}*/ +void Matestar::GetViscosityDComplement(IssmDouble* pviscosity_complement, IssmDouble* epsilon){/*{{{*/ + _error_("not implemented yet"); +} +/*}}}*/ +void Matestar::GetViscosityDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* epsilon){/*{{{*/ + _error_("not implemented yet"); +} +/*}}}*/ +IssmDouble Matestar::GetViscosityGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,bool isdepthaveraged){/*{{{*/ /*output: */ IssmDouble viscosity; - /*Intermediary: */ - IssmDouble B,D=0.,n; - - /*Get B and n*/ - B=GetB(); _assert_(B>0.); - n=GetN(); _assert_(n>0.); - - if (n==1.){ - /*Linear Viscous behavior (Newtonian fluid) viscosity=B/2: */ - viscosity=(1.-D)*B/2.; - } - else{ - - /*if no strain rate, return maximum viscosity*/ - if(eps_eff==0.){ - viscosity = 1.e+14/2.; - //viscosity = B; - //viscosity=2.5*pow(10.,17); - } - - else{ - viscosity=(1.-D)*B/(2.*pow(eps_eff,(n-1.)/n)); - } - } - - /*Checks in debugging mode*/ - if(viscosity<=0) _error_("Negative viscosity"); - - /*Return: */ - *pviscosity=viscosity; -} -/*}}}*/ -void Matestar::GetViscosityBar(IssmDouble* pviscosity,IssmDouble eps_eff){/*{{{*/ - _error_("not implemented yet"); -} -/*}}}*/ -void Matestar::GetViscosityComplement(IssmDouble* pviscosity_complement, IssmDouble* epsilon){/*{{{*/ - _error_("not implemented yet"); -} -/*}}}*/ -void Matestar::GetViscosityDComplement(IssmDouble* pviscosity_complement, IssmDouble* epsilon){/*{{{*/ - _error_("not implemented yet"); -} -/*}}}*/ -void Matestar::GetViscosityDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* epsilon){/*{{{*/ - _error_("not implemented yet"); -} -/*}}}*/ -IssmDouble Matestar::GetViscosityGeneral(IssmDouble ko,IssmDouble Ec, IssmDouble Es,IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz){/*{{{*/ - - /*Intermediaries*/ - IssmDouble viscosity; - IssmDouble E,lambdas; - IssmDouble epso,epsprime_norm; + /*Intermediaries*/ + IssmDouble epseff,epsprime_norm; + IssmDouble lambdas; IssmDouble vmag,dvmag[3]; + IssmDouble B,Ec,Es,E,n; /*Calculate velocity magnitude and its derivative*/ @@ -249,15 +273,33 @@ } - EstarStrainrateQuantities(&epso,&epsprime_norm,vx,vy,vz,vmag,dvx,dvy,dvz,&dvmag[0]); - lambdas=EstarLambdaS(epso,epsprime_norm); + EstarStrainrateQuantities(&epseff,&epsprime_norm,vx,vy,vz,vmag,dvx,dvy,dvz,&dvmag[0]); + lambdas=EstarLambdaS(epseff,epsprime_norm); + + /*Get B and enhancement*/ + n=GetN(); _assert_(n>0.); + if (isdepthaveraged==0.){ + B=GetB(); _assert_(B>0.); + Ec=GetEc(); _assert_(Ec>=0.); + Es=GetEs(); _assert_(Es>=0.); + } + else{ + B=GetBbar(); _assert_(B>0.); + Ec=GetEcbar(); _assert_(Ec>=0.); + Es=GetEsbar(); _assert_(Es>=0.); + } /*Get total enhancement factor E(lambdas)*/ - E = Ec + (Es-Ec)*lambdas*lambdas; + E = Ec + (Es-Ec)*lambdas*lambdas; _assert_(E>0.); /*Compute viscosity*/ - _assert_(E>0.); - _assert_(ko>0.); - _assert_(epso>0.); - viscosity = 1./(2*pow(ko*E*epso*epso,1./3.)); + /*if no strain rate, return maximum viscosity*/ + if(epseff==0.){ + viscosity = 1.e+14/2.; + //viscosity = B; + //viscosity=2.5*pow(10.,17); + } + else{ + viscosity = B/(2.*pow(E,1./n)*pow(epseff,2./n)); + } /*Assign output pointer*/ @@ -265,6 +307,53 @@ } /*}}}*/ +IssmDouble Matestar::GetViscosity_BGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,bool isdepthaveraged){/*{{{*/ + + /*Intermediaries*/ + IssmDouble dmudB; + IssmDouble epseff,epsprime_norm; + IssmDouble lambdas; + IssmDouble vmag,dvmag[3]; + IssmDouble Ec,Es,E; + + /*Calculate velocity magnitude and its derivative*/ + vmag = sqrt(vx*vx+vy*vy+vz*vz); + if(vmag<1e-12){ + dvmag[0]=0; + dvmag[1]=0; + dvmag[2]=0; + } + else{ + dvmag[0]=1./(2*sqrt(vmag))*(2*vx*dvx[0]+2*vy*dvy[0]+2*vz*dvz[0]); + dvmag[1]=1./(2*sqrt(vmag))*(2*vx*dvx[1]+2*vy*dvy[1]+2*vz*dvz[1]); + dvmag[2]=1./(2*sqrt(vmag))*(2*vx*dvx[2]+2*vy*dvy[2]+2*vz*dvz[2]); + } + + EstarStrainrateQuantities(&epseff,&epsprime_norm,vx,vy,vz,vmag,dvx,dvy,dvz,&dvmag[0]); + lambdas=EstarLambdaS(epseff,epsprime_norm); + + /*Get enhancement*/ + if (isdepthaveraged==0.){ + Ec=GetEc(); _assert_(Ec>=0.); + Es=GetEs(); _assert_(Es>=0.); + } + else{ + Ec=GetEcbar(); _assert_(Ec>=0.); + Es=GetEsbar(); _assert_(Es>=0.); + } + + /*Get total enhancement factor E(lambdas)*/ + E = Ec + (Es-Ec)*lambdas*lambdas; _assert_(E>0.); + + /*Compute dmudB*/ + if(epseff==0.) dmudB = 0.; + else dmudB = 1./(2.*pow(E,1./3.)*pow(epseff,2./3.)); + + /*Assign output*/ + return dmudB; + +} +/*}}}*/ void Matestar::GetViscosity_B(IssmDouble* pdmudB,IssmDouble eps_eff){/*{{{*/ - _error_("not implemented yet"); + _error_("not implemented yet"); } /*}}}*/ @@ -319,10 +408,10 @@ } /*}}}*/ -void Matestar::ViscosityFS(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){/*{{{*/ +void Matestar::ViscosityBFS(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){/*{{{*/ /*Intermediaries*/ IssmDouble vx,vy,vz; IssmDouble dvx[3],dvy[3],dvz[3]; - IssmDouble ko,Ec,Es; + bool isdepthaveraged=0.; /*Get velocity derivatives in all directions*/ @@ -344,25 +433,14 @@ } - /*Get enhancement factors and ko*/ - Input* ec_input = element->inputs->GetInput(MaterialsRheologyEcEnum); _assert_(ec_input); - Input* es_input = element->inputs->GetInput(MaterialsRheologyEsEnum); _assert_(es_input); - Input* ko_input = element->inputs->GetInput(MaterialsRheologyKoEnum); _assert_(ko_input); - ec_input->GetInputValue(&Ec,gauss); - es_input->GetInputValue(&Es,gauss); - ko_input->GetInputValue(&ko,gauss); - - /*Compute viscosity*/ - *pviscosity=GetViscosityGeneral(ko,Ec,Es,vx,vy,vz,&dvx[0],&dvy[0],&dvz[0]); -} -/*}}}*/ -void Matestar::ViscosityFSDerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){/*{{{*/ - this->GetViscosityDerivativeEpsSquare(pmu_prime,epsilon); -}/*}}}*/ -void Matestar::ViscosityHO(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ + /*Compute dmudB*/ + *pdmudB=GetViscosity_BGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); +} +/*}}}*/ +void Matestar::ViscosityBHO(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ /*Intermediaries*/ IssmDouble vx,vy,vz; IssmDouble dvx[3],dvy[3],dvz[3]; - IssmDouble ko,Ec,Es; + bool isdepthaveraged=0.; /*Get velocity derivatives in all directions*/ @@ -384,26 +462,12 @@ dvz[0] = 0.; dvz[1] = 0.; dvz[2] = -dvx[0]-dvy[1]; - /*Get enhancement factors and ko*/ - Input* ec_input = element->inputs->GetInput(MaterialsRheologyEcEnum); _assert_(ec_input); - Input* es_input = element->inputs->GetInput(MaterialsRheologyEsEnum); _assert_(es_input); - Input* ko_input = element->inputs->GetInput(MaterialsRheologyKoEnum); _assert_(ko_input); - ec_input->GetInputValue(&Ec,gauss); - es_input->GetInputValue(&Es,gauss); - ko_input->GetInputValue(&ko,gauss); - /*Compute viscosity*/ - *pviscosity=GetViscosityGeneral(ko,Ec,Es,vx,vy,vz,&dvx[0],&dvy[0],&dvz[0]); -}/*}}}*/ -void Matestar::ViscosityHODerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){/*{{{*/ - _error_("not implemented yet"); -}/*}}}*/ -void Matestar::ViscosityL1L2(IssmDouble* pviscosity,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* surface_input){/*{{{*/ - _error_("not implemented yet"); -}/*}}}*/ -void Matestar::ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ + *pdmudB=GetViscosity_BGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); +}/*}}}*/ +void Matestar::ViscosityBSSA(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ /*Intermediaries*/ IssmDouble vx,vy,vz; IssmDouble dvx[3],dvy[3],dvz[3]; - IssmDouble ko,Ec,Es; + bool isdepthaveraged=1.; /*Get velocity derivatives in all directions*/ @@ -428,14 +492,103 @@ dvz[0] = 0.; dvz[1] = 0.; dvz[2] = -dvx[0]-dvy[1]; - /*Get enhancement factors and ko*/ - Input* ec_input = element->inputs->GetInput(MaterialsRheologyEcbarEnum); _assert_(ec_input); - Input* es_input = element->inputs->GetInput(MaterialsRheologyEsbarEnum); _assert_(es_input); - Input* ko_input = element->inputs->GetInput(MaterialsRheologyKobarEnum); _assert_(ko_input); - ec_input->GetInputValue(&Ec,gauss); - es_input->GetInputValue(&Es,gauss); - ko_input->GetInputValue(&ko,gauss); - /*Compute viscosity*/ - *pviscosity=GetViscosityGeneral(ko,Ec,Es,vx,vy,vz,&dvx[0],&dvy[0],&dvz[0]); + *pdmudB=GetViscosity_BGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); +}/*}}}*/ +void Matestar::ViscosityFS(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){/*{{{*/ + + /*Intermediaries*/ + IssmDouble vx,vy,vz; + IssmDouble dvx[3],dvy[3],dvz[3]; + bool isdepthaveraged=0.; + + /*Get velocity derivatives in all directions*/ + _assert_(dim>1); + _assert_(vx_input); + vx_input->GetInputValue(&vx,gauss); + vx_input->GetInputDerivativeValue(&dvx[0],xyz_list,gauss); + _assert_(vy_input); + vy_input->GetInputValue(&vy,gauss); + vy_input->GetInputDerivativeValue(&dvy[0],xyz_list,gauss); + if(dim==3){ + _assert_(vz_input); + vz_input->GetInputValue(&vz,gauss); + vz_input->GetInputDerivativeValue(&dvz[0],xyz_list,gauss); + } + else{ + vz = 0.; + dvz[0] = 0.; dvz[1] = 0.; dvz[2] = 0.; + } + + /*Compute viscosity*/ + *pviscosity=GetViscosityGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); +} +/*}}}*/ +void Matestar::ViscosityFSDerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){/*{{{*/ + this->GetViscosityDerivativeEpsSquare(pmu_prime,epsilon); +}/*}}}*/ +void Matestar::ViscosityHO(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ + + /*Intermediaries*/ + IssmDouble vx,vy,vz; + IssmDouble dvx[3],dvy[3],dvz[3]; + bool isdepthaveraged=0.; + + /*Get velocity derivatives in all directions*/ + _assert_(dim==2 || dim==3); + _assert_(vx_input); + vx_input->GetInputValue(&vx,gauss); + vx_input->GetInputDerivativeValue(&dvx[0],xyz_list,gauss); + if(dim==3){ + _assert_(vy_input); + vy_input->GetInputValue(&vy,gauss); + vy_input->GetInputDerivativeValue(&dvy[0],xyz_list,gauss); + } + else{ + dvx[2] = 0.; + vy = 0.; + dvy[0] = 0.; dvy[1] = 0.; dvy[2] = 0.; + } + vz = 0.; + dvz[0] = 0.; dvz[1] = 0.; dvz[2] = -dvx[0]-dvy[1]; + + /*Compute viscosity*/ + *pviscosity=GetViscosityGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); +}/*}}}*/ +void Matestar::ViscosityHODerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){/*{{{*/ + _error_("not implemented yet"); +}/*}}}*/ +void Matestar::ViscosityL1L2(IssmDouble* pviscosity,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* surface_input){/*{{{*/ + _error_("not implemented yet"); +}/*}}}*/ +void Matestar::ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){/*{{{*/ + + /*Intermediaries*/ + IssmDouble vx,vy,vz; + IssmDouble dvx[3],dvy[3],dvz[3]; + bool isdepthaveraged=1.; + + /*Get velocity derivatives in all directions*/ + _assert_(dim==1 || dim==2); + _assert_(vx_input); + vx_input->GetInputValue(&vx,gauss); + vx_input->GetInputDerivativeValue(&dvx[0],xyz_list,gauss); + if(dim==2){ + _assert_(vy_input); + vy_input->GetInputValue(&vy,gauss); + vy_input->GetInputDerivativeValue(&dvy[0],xyz_list,gauss); + } + else{ + dvx[1] = 0.; + dvx[2] = 0.; + vy = 0.; + dvy[0] = 0.; dvy[1] = 0.; dvy[2] = 0.; + } + dvx[2] = 0.; + dvy[2] = 0.; + vz = 0.; + dvz[0] = 0.; dvz[1] = 0.; dvz[2] = -dvx[0]-dvy[1]; + + /*Compute viscosity*/ + *pviscosity=GetViscosityGeneral(vx,vy,vz,&dvx[0],&dvy[0],&dvz[0],isdepthaveraged); }/*}}}*/ void Matestar::ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){/*{{{*/ Index: /issm/trunk/src/c/classes/Materials/Matestar.h =================================================================== --- /issm/trunk/src/c/classes/Materials/Matestar.h (revision 21728) +++ /issm/trunk/src/c/classes/Materials/Matestar.h (revision 21729) @@ -69,6 +69,11 @@ IssmDouble GetD(); IssmDouble GetDbar(); + IssmDouble GetEc(); + IssmDouble GetEcbar(); + IssmDouble GetEs(); + IssmDouble GetEsbar(); IssmDouble GetN(); bool IsDamage(); + bool IsEnhanced(){_error_("not supported");}; void ResetHooks(); void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); @@ -81,6 +86,10 @@ void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); void ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon); + void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input); + void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); + void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); /*}}}*/ - IssmDouble GetViscosityGeneral(IssmDouble ko,IssmDouble Ec, IssmDouble Es,IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz); + IssmDouble GetViscosityGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,bool isdepthaveraged); + IssmDouble GetViscosity_BGeneral(IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,bool isdepthaveraged); }; Index: /issm/trunk/src/c/classes/Materials/Matice.cpp =================================================================== --- /issm/trunk/src/c/classes/Materials/Matice.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Materials/Matice.cpp (revision 21729) @@ -31,4 +31,5 @@ this->element=NULL; this->isdamaged=false; + this->isenhanced=false; return; } @@ -36,26 +37,16 @@ Matice::Matice(int matice_mid,int index, IoModel* iomodel){/*{{{*/ - /*Intermediaries:*/ - int matice_eid; - - /*Initialize id*/ - this->mid=matice_mid; - - /*Hooks: */ - matice_eid=index+1; - this->helement=new Hook(&matice_eid,1); - this->element=NULL; - - /*Other perporties*/ - int materialtype; + /*Get material type and initialize object*/ + int materialtype; iomodel->FindConstant(&materialtype,"md.materials.type"); - if(materialtype==MatdamageiceEnum) this->isdamaged = true; - else if(materialtype==MaticeEnum) this->isdamaged = false; - else _error_("Material type not recognized"); - + this->Init(matice_mid,index,materialtype); + +} +/*}}}*/ +Matice::Matice(int matice_mid,int index,int materialtype){/*{{{*/ + + this->Init(matice_mid,index,materialtype); return; - -} -/*}}}*/ +} /*}}}*/ Matice::~Matice(){/*{{{*/ delete helement; @@ -63,4 +54,34 @@ } /*}}}*/ +void Matice::Init(int matice_mid,int index,int materialtype){/*{{{*/ + + /*Initialize id*/ + this->mid=matice_mid; + + /*Hooks: */ + int matice_eid=index+1; + this->helement=new Hook(&matice_eid,1); + this->element=NULL; + + /*Material specific properties*/ + switch(materialtype){ + case MatdamageiceEnum: + this->isdamaged = true; + this->isenhanced = false; + break; + case MaticeEnum: + this->isdamaged = false; + this->isenhanced = false; + break; + case MatenhancediceEnum: + this->isdamaged = false; + this->isenhanced = true; + break; + default: + _error_("Material type not recognized"); + } + + return; +} /*}}}*/ /*Object virtual functions definitions:*/ @@ -78,4 +99,5 @@ matice->element =(Element*)this->helement->delivers(); matice->isdamaged = this->isdamaged; + matice->isenhanced = this->isenhanced; return matice; @@ -95,4 +117,5 @@ matice->element =element_in; matice->isdamaged = this->isdamaged; + matice->isenhanced = this->isenhanced; return matice; @@ -103,14 +126,38 @@ _printf_("Matice:\n"); _printf_(" mid: " << mid << "\n"); + _printf_(" isdamaged: " << isdamaged << "\n"); + _printf_(" isenhanced: " << isenhanced << "\n"); + + /*helement and element DeepEcho were commented to avoid recursion.*/ + /*Example: element->DeepEcho calls matice->DeepEcho which calls element->DeepEcho etc*/ + _printf_(" helement:\n"); + _printf_(" note: helement not printed to avoid recursion.\n"); + //if(helement) helement->DeepEcho(); + //else _printf_(" helement = NULL\n"); + _printf_(" element:\n"); - helement->Echo(); + _printf_(" note: element not printed to avoid recursion.\n"); + //if(element) element->DeepEcho(); + //else _printf_(" element = NULL\n"); } /*}}}*/ void Matice::Echo(void){/*{{{*/ - + _printf_("Matice:\n"); _printf_(" mid: " << mid << "\n"); + _printf_(" isdamaged: " << isdamaged << "\n"); + _printf_(" isenhanced: " << isenhanced << "\n"); + + /*helement and element Echo were commented to avoid recursion.*/ + /*Example: element->Echo calls matice->Echo which calls element->Echo etc*/ + _printf_(" helement:\n"); + _printf_(" note: helement not printed to avoid recursion.\n"); + //if(helement) helement->Echo(); + //else _printf_(" helement = NULL\n"); + _printf_(" element:\n"); - helement->Echo(); + _printf_(" note: element not printed to avoid recursion.\n"); + //if(element) element->Echo(); + //else _printf_(" element = NULL\n"); } /*}}}*/ @@ -124,4 +171,5 @@ MARSHALLING(mid); MARSHALLING(isdamaged); + MARSHALLING(isenhanced); this->helement->Marshall(pmarshalled_data,pmarshalled_data_size,marshall_direction); this->element=(Element*)this->helement->delivers(); @@ -207,4 +255,22 @@ } /*}}}*/ +IssmDouble Matice::GetE(){/*{{{*/ + + _assert_(this->isenhanced); + /*Output*/ + IssmDouble E; + if(this->isenhanced)element->inputs->GetInputAverage(&E,MaterialsRheologyEEnum); + return E; +} +/*}}}*/ +IssmDouble Matice::GetEbar(){/*{{{*/ + + _assert_(this->isenhanced); + /*Output*/ + IssmDouble Ebar; + if(this->isenhanced)element->inputs->GetInputAverage(&Ebar,MaterialsRheologyEbarEnum); + return Ebar; +} +/*}}}*/ IssmDouble Matice::GetN(){/*{{{*/ @@ -219,4 +285,9 @@ return this->isdamaged; +} +/*}}}*/ +bool Matice::IsEnhanced(){/*{{{*/ + + return this->isenhanced; } /*}}}*/ @@ -225,8 +296,8 @@ (1-D) B viscosity= ------------------------- - 2 eps_eff ^[(n-1)/n] - - where viscosity is the viscotiy, B the flow law parameter , eps_eff is the effective strain rate - and n the flow law exponent. + 2 E^[1/n] eps_eff ^[(n-1)/n] + + where viscosity is the viscosity, B the flow law parameter , eps_eff is the effective strain rate, + n the flow law exponent, and E is the enhancement factor. If eps_eff = 0 , it means this is the first time SystemMatrices is being run, and we @@ -238,5 +309,5 @@ /*Intermediary: */ - IssmDouble B,D=0.,n; + IssmDouble B,D=0.,E=1.,n; /*Get B and n*/ @@ -247,8 +318,12 @@ _assert_(D>=0. && D<1.); } + if(this->isenhanced){ + E=GetE(); + _assert_(E>0.); + } if (n==1.){ - /*Linear Viscous behavior (Newtonian fluid) viscosity=B/2: */ - viscosity=(1.-D)*B/2.; + /*Linear Viscous behavior (Newtonian fluid) viscosity=B/2E: */ + viscosity=(1.-D)*B/(2.*E); } else{ @@ -262,5 +337,5 @@ else{ - viscosity=(1.-D)*B/(2.*pow(eps_eff,(n-1.)/n)); + viscosity=(1.-D)*B/(2.*pow(E,1./n)*pow(eps_eff,(n-1.)/n)); } } @@ -277,7 +352,8 @@ (1-D) B viscosity= ------------------------- - 2 eps_eff ^[(n-1)/n] - - where B the flow law parameter, eps_eff is the effective strain rate and n the flow law exponent. + 2 E^[1/n] eps_eff ^[(n-1)/n] + + where B the flow law parameter, eps_eff is the effective strain rate, n the flow law exponent, + and E is the enhancement factor. If eps_eff = 0 , it means this is the first time SystemMatrices is being run, and we @@ -289,5 +365,5 @@ /*Intermediary: */ - IssmDouble B,D=0.,n; + IssmDouble B,D=0.,E=1.,n; /*Get B and n*/ @@ -298,8 +374,12 @@ _assert_(D>=0. && D<1.); } + if(this->isenhanced){ + E=GetEbar(); + _assert_(E>0.); + } if (n==1.){ - /*Linear Viscous behavior (Newtonian fluid) viscosity=B/2: */ - viscosity=(1.-D)*B/2.; + /*Linear Viscous behavior (Newtonian fluid) viscosity=B/2E: */ + viscosity=(1.-D)*B/(2.*E); } else{ @@ -312,5 +392,5 @@ else{ - viscosity=(1.-D)*B/(2.*pow(eps_eff,(n-1.)/n)); + viscosity=(1.-D)*B/(2.*pow(E,1./n)*pow(eps_eff,(n-1.)/n)); } } @@ -475,5 +555,5 @@ /*Intermediary: */ - IssmDouble D=0.,n; + IssmDouble D=0.,E=1.,n; /*Get B and n*/ @@ -483,12 +563,16 @@ _assert_(D>=0. && D<1.); } + if(this->isenhanced){ + E=GetE(); + _assert_(E>0.); + } if(n==1.){ - /*Linear Viscous behavior (Newtonian fluid) dmudB=B/2: */ - dmudB=(1.-D)/2.; + /*Linear Viscous behavior (Newtonian fluid) dmudB=B/2E: */ + dmudB=(1.-D)/(2.*E); } else{ if(eps_eff==0.) dmudB = 0.; - else dmudB = (1.-D)/(2.*pow(eps_eff,(n-1.)/n)); + else dmudB = (1.-D)/(2.*pow(E,1./n)*pow(eps_eff,(n-1.)/n)); } @@ -503,5 +587,5 @@ /*Intermediary: */ - IssmDouble n,B; + IssmDouble n,B,E=1.; /*Get B and n*/ @@ -509,12 +593,16 @@ B=GetBbar(); _assert_(this->isdamaged); + if(this->isenhanced){ + E=GetE(); + _assert_(E>0.); + } if(n==1.){ - /*Linear Viscous behavior (Newtonian fluid) dmudB=B/2: */ - dmudD=-B/2.; + /*Linear Viscous behavior (Newtonian fluid) dmudB=B/2E: */ + dmudD=-B/(2.*E); } else{ if(eps_eff==0.) dmudD = 0.; - else dmudD = -B/(2.*pow(eps_eff,(n-1.)/n)); + else dmudD = -B/(2.*pow(E,1./n)*pow(eps_eff,(n-1.)/n)); } @@ -636,5 +724,5 @@ IssmDouble epsilon3d[5];/* epsilon=[exx,eyy,exy,exz,eyz];*/ IssmDouble epsilon2d[2];/* epsilon=[exx,exy]; */ - IssmDouble eps_eff; + IssmDouble eps_eff,E=1.0; if(dim==3){ Index: /issm/trunk/src/c/classes/Materials/Matice.h =================================================================== --- /issm/trunk/src/c/classes/Materials/Matice.h (revision 21728) +++ /issm/trunk/src/c/classes/Materials/Matice.h (revision 21729) @@ -27,4 +27,5 @@ int mid; bool isdamaged; + bool isenhanced; Hook *helement; Element *element; @@ -34,5 +35,7 @@ Matice(); Matice(int mid,int i, IoModel* iomodel); + Matice(int mid,int i, int materialtype); ~Matice(); + void Init(int mid,int i, int materialtype); /*}}}*/ /*Object virtual functions definitions:{{{ */ @@ -70,6 +73,9 @@ IssmDouble GetD(); IssmDouble GetDbar(); + IssmDouble GetE(); + IssmDouble GetEbar(); IssmDouble GetN(); bool IsDamage(); + bool IsEnhanced(); void ResetHooks(); void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); @@ -82,4 +88,7 @@ void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); void ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon); + void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){_error_("not supported");}; + void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; + void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; /*}}}*/ }; Index: /issm/trunk/src/c/classes/Materials/Matpar.cpp =================================================================== --- /issm/trunk/src/c/classes/Materials/Matpar.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Materials/Matpar.cpp (revision 21729) @@ -82,4 +82,5 @@ case MaticeEnum: case MatdamageiceEnum: + case MatenhancediceEnum: case MatestarEnum: iomodel->FindConstant(&this->rho_ice,"md.materials.rho_ice"); @@ -117,5 +118,7 @@ iomodel->FindConstant(&this->dpermil,"md.smb.dpermil"); case SMBgradientsEnum: - break; + /*Nothing to add*/ + break; + case SMBgradientselaEnum: /*Nothing to add*/ break; @@ -175,4 +178,8 @@ Matpar::~Matpar(){/*{{{*/ return; +} +/*}}}*/ +void Matpar::SetMid(int matpar_mid){/*{{{*/ + this->mid=matpar_mid; } /*}}}*/ @@ -253,8 +260,35 @@ _printf_(" thermal_exchange_velocity: " << thermal_exchange_velocity << "\n"); _printf_(" g: " << g << "\n"); + _printf_(" omega: " << omega << "\n"); _printf_(" desfac: " << desfac << "\n"); _printf_(" rlaps: " << rlaps << "\n"); _printf_(" rlapslgm: " << rlapslgm << "\n"); _printf_(" dpermil: " << dpermil << "\n"); + _printf_(" albedo_ice: " << albedo_ice << "\n"); + _printf_(" albedo_snow: " << albedo_snow << "\n"); + _printf_(" sediment_compressibility: " << sediment_compressibility << "\n"); + _printf_(" sediment_porosity: " << sediment_porosity << "\n"); + _printf_(" sediment_thickness: " << sediment_thickness << "\n"); + _printf_(" water_compressibility: " << water_compressibility << "\n"); + _printf_(" epl_compressibility: " << epl_compressibility << "\n"); + _printf_(" epl_porosity: " << epl_porosity << "\n"); + _printf_(" epl_init_thickness: " << epl_init_thickness << "\n"); + _printf_(" epl_colapse_thickness: " << epl_colapse_thickness << "\n"); + _printf_(" epl_max_thickness: " << epl_max_thickness << "\n"); + _printf_(" epl_conductivity: " << epl_conductivity << "\n"); + _printf_(" lithosphere_shear_modulus: " << lithosphere_shear_modulus << "\n"); + _printf_(" lithosphere_density: " << lithosphere_density << "\n"); + _printf_(" mantle_shear_modulus: " << mantle_shear_modulus << "\n"); + _printf_(" mantle_density: " << mantle_density << "\n"); + _printf_(" earth_density: " << earth_density << "\n"); + _printf_(" poisson: " << poisson << "\n"); + _printf_(" young_modulus: " << young_modulus << "\n"); + _printf_(" ridging_exponent: " << ridging_exponent << "\n"); + _printf_(" cohesion: " << cohesion << "\n"); + _printf_(" internal_friction_coef: " << internal_friction_coef << "\n"); + _printf_(" compression_coef: " << compression_coef << "\n"); + _printf_(" traction_coef: " << traction_coef << "\n"); + _printf_(" time_relaxation_stress: " << time_relaxation_stress << "\n"); + _printf_(" time_relaxation_damage: " << time_relaxation_damage << "\n"); return; } Index: /issm/trunk/src/c/classes/Materials/Matpar.h =================================================================== --- /issm/trunk/src/c/classes/Materials/Matpar.h (revision 21728) +++ /issm/trunk/src/c/classes/Materials/Matpar.h (revision 21729) @@ -77,4 +77,5 @@ Matpar(int matpar_id, IoModel* iomodel); ~Matpar(); + void SetMid(int matpar_mid); /*Object virtual functions definitions:{{{ */ @@ -114,4 +115,5 @@ IssmDouble GetN(){_error_("not supported");}; bool IsDamage(){_error_("not supported");}; + bool IsEnhanced(){_error_("not supported");}; void ResetHooks(); @@ -123,4 +125,7 @@ void ViscositySSA(IssmDouble* pviscosity,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; void ViscositySSADerivativeEpsSquare(IssmDouble* pmu_prime,IssmDouble* epsilon){_error_("not supported");}; + void ViscosityBFS(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input){_error_("not supported");}; + void ViscosityBHO(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; + void ViscosityBSSA(IssmDouble* pmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input){_error_("not supported");}; /*}}}*/ /*Numerics: {{{*/ Index: /issm/trunk/src/c/classes/Node.cpp =================================================================== --- /issm/trunk/src/c/classes/Node.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Node.cpp (revision 21729) @@ -59,5 +59,5 @@ _assert_(sqrt( coord_system[0][0]*coord_system[0][0] + coord_system[1][0]*coord_system[1][0]) >1.e-4); - if(iomodel->domaintype!=Domain2DhorizontalEnum & iomodel->domaintype!=Domain3DsurfaceEnum){ + if(iomodel->domaintype!=Domain2DhorizontalEnum && iomodel->domaintype!=Domain3DsurfaceEnum){ /*We have a 3d mesh, we may have collapsed elements, hence dead nodes. Freeze them out: */ _assert_(iomodel->Data("md.mesh.vertexonbase")); @@ -458,6 +458,7 @@ /*Put dof for this node into the f set (ie, this dof will NOT be constrained - * to a fixed value during computations. */ + * to a fixed value during computations. Only do this for active nodes. */ _assert_(dofindexing.gsize); + _assert_(this->indexing.active); if(this->indexing.f_set[dof] == 0){ @@ -494,4 +495,9 @@ return approximation; +} +/*}}}*/ +void Node::SetApproximation(int in_approximation){/*{{{*/ + + this->approximation = in_approximation; } /*}}}*/ Index: /issm/trunk/src/c/classes/Node.h =================================================================== --- /issm/trunk/src/c/classes/Node.h (revision 21728) +++ /issm/trunk/src/c/classes/Node.h (revision 21729) @@ -85,4 +85,5 @@ void VecMerge(Vector* ug, IssmDouble* vector_serial,int setenum); void VecReduce(Vector* vector, IssmDouble* ug_serial,int setnum); + void SetApproximation(int in_approximation); }; Index: /issm/trunk/src/c/classes/Params/Param.h =================================================================== --- /issm/trunk/src/c/classes/Params/Param.h (revision 21728) +++ /issm/trunk/src/c/classes/Params/Param.h (revision 21729) @@ -25,4 +25,5 @@ /*Virtual functions:*/ + virtual void DeepEcho()=0; virtual Param* copy()=0; virtual void Echo()=0; Index: /issm/trunk/src/c/classes/Params/Parameters.cpp =================================================================== --- /issm/trunk/src/c/classes/Params/Parameters.cpp (revision 21728) +++ /issm/trunk/src/c/classes/Params/Parameters.cpp (revision 21729) @@ -91,10 +91,16 @@ } /*}}}*/ -void Parameters::DeepEcho(void){/*{{{*/ - _error_("not implemented yet"); -} -/*}}}*/ -void Parameters::Echo(void){/*{{{*/ - _error_("not implemented yet"); +void Parameters::DeepEcho(void){/*{{{*/ + for(int i=0;iparams[i]) this->params[i]->DeepEcho(); + } + return; +} +/*}}}*/ +void Parameters::Echo(void){/*{{{*/ + for(int i=0;iparams[i]) this->params[i]->Echo(); + } + return; } /*}}}*/ Index: /issm/trunk/src/c/cores/CorePointerFromSolutionEnum.cpp =================================================================== --- /issm/trunk/src/c/cores/CorePointerFromSolutionEnum.cpp (revision 21728) +++ /issm/trunk/src/c/cores/CorePointerFromSolutionEnum.cpp (revision 21729) @@ -66,5 +66,5 @@ break; case GiaSolutionEnum: - #if _HAVE_GIA_ + #if _HAVE_GIAIVINS_ solutioncore=&gia_core; #else Index: /issm/trunk/src/c/cores/controlm1qn3_core.cpp =================================================================== --- /issm/trunk/src/c/cores/controlm1qn3_core.cpp (revision 21728) +++ /issm/trunk/src/c/cores/controlm1qn3_core.cpp (revision 21729) @@ -26,4 +26,13 @@ void simul(long* indic,long* n,double* X,double* pf,double* G,long izs[1],float rzs[1],void* dzs); +/*Use struct to provide arguments*/ +typedef struct{ + FemModel * femmodel; + IssmDouble* Jlist; + int M; + int N; + int* i; +} m1qn3_struct; + void controlm1qn3_core(FemModel* femmodel){ @@ -32,5 +41,5 @@ double f,dxmin,gttol; int maxsteps,maxiter; - int intn,numberofvertices,num_controls,solution_type; + int intn,numberofvertices,num_controls,num_cost_functions,solution_type; IssmDouble *scaling_factors = NULL; IssmDouble *X = NULL; @@ -40,4 +49,5 @@ femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); femmodel->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); + femmodel->parameters->FindParam(&num_cost_functions,InversionNumCostFunctionsEnum); femmodel->parameters->FindParam(&maxsteps,InversionMaxstepsEnum); femmodel->parameters->FindParam(&maxiter,InversionMaxiterEnum); @@ -86,5 +96,5 @@ } - /*Allocate m1qn3 working arrays (see doc)*/ + /*Allocate m1qn3 working arrays (see documentation)*/ long m = 100; long ndz = 4*n+m*(2*n+1); @@ -96,7 +106,15 @@ _printf0_("____________________________________________________________________\n"); + /*Prepare structure for m1qn3*/ + m1qn3_struct mystruct; + mystruct.femmodel = femmodel; + mystruct.M = maxiter; + mystruct.N = num_cost_functions+1; + mystruct.Jlist = xNewZeroInit(mystruct.M*mystruct.N); + mystruct.i = xNewZeroInit(1); + /*Initialize Gradient and cost function of M1QN3*/ - indic = 4; //adjoint and gradient required - simul(&indic,&n,X,&f,G,izs,rzs,(void*)femmodel); + indic = 4; /*gradient required*/ + simul(&indic,&n,X,&f,G,izs,rzs,(void*)&mystruct); /*Estimation of the expected decrease in f during the first iteration*/ @@ -107,5 +125,5 @@ &n,X,&f,G,&dxmin,&df1, >tol,normtype,&impres,&io,imode,&omode,&niter,&nsim,iz,dz,&ndz, - &reverse,&indic,izs,rzs,(void*)femmodel); + &reverse,&indic,izs,rzs,(void*)&mystruct); switch(int(omode)){ @@ -137,5 +155,5 @@ ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,G); femmodel->OutputControlsx(&femmodel->results); - femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,f)); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,mystruct.Jlist,(*mystruct.i),mystruct.N,0,0)); /*Finalize*/ @@ -153,4 +171,6 @@ xDelete(XL); xDelete(scaling_factors); + xDelete(mystruct.Jlist); + xDelete(mystruct.i); } @@ -158,17 +178,22 @@ void simul(long* indic,long* n,double* X,double* pf,double* G,long izs[1],float rzs[1],void* dzs){ - /*Recover Femmodel*/ - int solution_type; - FemModel *femmodel = (FemModel*)dzs; - - /*Recover number of cost functions responses*/ - int num_responses,num_controls,numberofvertices; + /*Recover Arguments*/ + m1qn3_struct *input_struct = (m1qn3_struct*)dzs; + FemModel *femmodel = input_struct->femmodel; + IssmDouble *Jlist = input_struct->Jlist; + int JlistM = input_struct->M; + int JlistN = input_struct->N; + int *Jlisti = input_struct->i; + + /*Recover some parameters*/ + int num_responses,num_controls,numberofvertices,solution_type; IssmDouble* scaling_factors = NULL; femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); femmodel->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); + femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); numberofvertices=femmodel->vertices->NumberOfVertices(); - /*Constrain input vector*/ + /*Constrain input vector and update controls*/ IssmDouble *XL = NULL; IssmDouble *XU = NULL; @@ -183,10 +208,5 @@ } } - - /*Update control input*/ SetControlInputsFromVectorx(femmodel,X); - - /*Recover some parameters*/ - femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); /*Compute solution and adjoint*/ @@ -196,8 +216,17 @@ solutioncore(femmodel); + /*Check size of Jlist to avoid crashes*/ + _assert_((*Jlisti)CostFunctionx(pf,&Jlist,NULL); + IssmDouble* Jtemp = NULL; + femmodel->CostFunctionx(pf,&Jtemp,NULL); _printf0_("f(x) = "<(Jtemp); if(*indic==0){ @@ -206,8 +235,8 @@ /*Retrieve objective functions independently*/ _printf0_(" N/A |\n"); - for(int i=0;i(Jlist); + *Jlisti = (*Jlisti) +1; xDelete(XU); xDelete(XL); @@ -241,9 +270,9 @@ /*Print info*/ _printf0_(" "<(Jlist); + *Jlisti = (*Jlisti) +1; xDelete(XU); xDelete(XL); Index: /issm/trunk/src/c/cores/depthaverage_core.cpp =================================================================== --- /issm/trunk/src/c/cores/depthaverage_core.cpp (revision 21728) +++ /issm/trunk/src/c/cores/depthaverage_core.cpp (revision 21729) @@ -14,4 +14,5 @@ /*Intermediaries*/ int domaintype,elementtype; + int inputenum,input_average_enum; if(VerboseSolution()) _printf0_("depth averaging solution...\n"); @@ -20,13 +21,15 @@ femmodel->parameters->FindParam(&domaintype,DomainTypeEnum); femmodel->parameters->FindParam(&elementtype,MeshElementtypeEnum); + femmodel->parameters->FindParam(&inputenum,InputToDepthaverageInEnum); + femmodel->parameters->FindParam(&input_average_enum,InputToDepthaverageOutEnum); - /*If this is a 2D horizontal domain, return (no need to extrude)*/ - if(domaintype==Domain2DhorizontalEnum) return; + /*If this is a 2D horizontal domain: no need to do anything, just copy input*/ + if(domaintype==Domain2DhorizontalEnum){ + InputDuplicatex(femmodel,inputenum,input_average_enum); + return; + } /*Special method for Penta, otherwise call solution sequence*/ if(elementtype==PentaEnum){ - int inputenum,input_average_enum; - femmodel->parameters->FindParam(&inputenum,InputToDepthaverageInEnum); - femmodel->parameters->FindParam(&input_average_enum,InputToDepthaverageOutEnum); InputDepthAverageAtBasex(femmodel,inputenum,input_average_enum); } Index: /issm/trunk/src/c/cores/gia_core.cpp =================================================================== --- /issm/trunk/src/c/cores/gia_core.cpp (revision 21728) +++ /issm/trunk/src/c/cores/gia_core.cpp (revision 21729) @@ -28,5 +28,5 @@ /*Call on core computations: */ - femmodel->SetCurrentConfiguration(GiaAnalysisEnum); + femmodel->SetCurrentConfiguration(GiaIvinsAnalysisEnum); /*Figure out size of g-set deflection vector and allocate solution vector: */ Index: /issm/trunk/src/c/cores/hydrology_core.cpp =================================================================== --- /issm/trunk/src/c/cores/hydrology_core.cpp (revision 21728) +++ /issm/trunk/src/c/cores/hydrology_core.cpp (revision 21729) @@ -89,6 +89,6 @@ if(save_results){ if(VerboseSolution()) _printf0_(" saving results \n"); - int outputs[3] = {HydrologyHeadEnum,HydrologyGapHeightEnum,EffectivePressureEnum}; - femmodel->RequestedOutputsx(&femmodel->results,&outputs[0],3); + int outputs[4] = {HydrologyHeadEnum,HydrologyGapHeightEnum,EffectivePressureEnum,HydrologyBasalFluxEnum}; + femmodel->RequestedOutputsx(&femmodel->results,&outputs[0],4); /*unload results*/ Index: /issm/trunk/src/c/cores/levelsetfunctionslope_core.cpp =================================================================== --- /issm/trunk/src/c/cores/levelsetfunctionslope_core.cpp (revision 21728) +++ /issm/trunk/src/c/cores/levelsetfunctionslope_core.cpp (revision 21729) @@ -33,5 +33,5 @@ } if(domaintype==Domain2DverticalEnum){ - femmodel->parameters->SetParam(LevelsetfunctionSlopeXEnum,InputToExtrudeEnum); + femmodel->parameters->SetParam(LevelsetfunctionSlopeXEnum,InputToExtrudeEnum); extrudefrombase_core(femmodel); } Index: /issm/trunk/src/c/cores/sealevelrise_core_noneustatic.cpp =================================================================== --- /issm/trunk/src/c/cores/sealevelrise_core_noneustatic.cpp (revision 21728) +++ /issm/trunk/src/c/cores/sealevelrise_core_noneustatic.cpp (revision 21729) @@ -18,4 +18,5 @@ Vector *Sgo = NULL; //ocean convolution of the perturbation to gravity potential. + Vector *Sgo_rot= NULL; // rotational feedback IssmDouble Sgo_oceanaverage = 0; //average of Sgo over the ocean. @@ -27,4 +28,5 @@ bool spherical=true; bool converged=true; + bool rotation=true; bool verboseconvolution=true; int max_nonlinear_iterations; @@ -41,4 +43,7 @@ femmodel->parameters->FindParam(&eps_abs,SealevelriseAbstolEnum); femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); + + /*computational flag: */ + femmodel->parameters->FindParam(&rotation,SealevelriseRotationEnum); /*first, recover lat,long and radius vectors from vertices: */ @@ -75,4 +80,13 @@ Sgo->Assemble(); + if(rotation){ + /*call rotational feedback module: */ + Sgo_rot = new Vector(gsize); Sgo_rot->Assemble(); + femmodel->SealevelriseRotationalFeedback(Sgo_rot,Sg_old,latitude,longitude,radius); + Sgo_rot->Assemble(); + + Sgo->AXPY(Sgo_rot,1); + } + /*we need to average Sgo over the ocean: RHS term 5 in Eq.4 of Farrel and clarke. Only the elements can do that: */ Sgo_oceanaverage=femmodel->SealevelriseOceanAverage(Sgo); Index: /issm/trunk/src/c/cores/transient_core.cpp =================================================================== --- /issm/trunk/src/c/cores/transient_core.cpp (revision 21728) +++ /issm/trunk/src/c/cores/transient_core.cpp (revision 21729) @@ -26,5 +26,5 @@ int output_frequency; int recording_frequency; - int domaintype,groundingline_migration,smb_model; + int domaintype,groundingline_migration,smb_model,amr_frequency; int numoutputs; Analysis *analysis = NULL; @@ -60,8 +60,14 @@ femmodel->parameters->FindParam(&isdamageevolution,TransientIsdamageevolutionEnum); femmodel->parameters->FindParam(&ishydrology,TransientIshydrologyEnum); + femmodel->parameters->FindParam(&amr_frequency,TransientAmrFrequencyEnum); femmodel->parameters->FindParam(&isFS,FlowequationIsFSEnum); if(isgroundingline) femmodel->parameters->FindParam(&groundingline_migration,GroundinglineMigrationEnum); femmodel->parameters->FindParam(&numoutputs,TransientNumRequestedOutputsEnum); if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,TransientRequestedOutputsEnum); + + #ifdef _HAVE_NEOPZ_ + bool ismismip = false;//itapopo testing restart + if(ismismip) femmodel->ReMesh(); + #endif while(time < finaltime - (yts*DBL_EPSILON)){ //make sure we run up to finaltime. @@ -86,7 +92,15 @@ if(isthermal && domaintype==Domain3DEnum){ if(issmb){ + bool isenthalpy; + femmodel->parameters->FindParam(&isenthalpy,ThermalIsenthalpyEnum); femmodel->parameters->FindParam(&smb_model,SmbEnum); - if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); - if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); + if(isenthalpy){ + if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); + if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); + } + else{ + if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); + if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); + } } if(VerboseSolution()) _printf0_(" computing thermal regime\n"); @@ -132,5 +146,5 @@ if(isgia){ if(VerboseSolution()) _printf0_(" computing glacial isostatic adjustment\n"); - #ifdef _HAVE_GIA_ + #ifdef _HAVE_GIAIVINS_ gia_core(femmodel); #else @@ -140,5 +154,5 @@ /*Sea level rise: */ - if(isslr | iscoupler) sealevelrise_core(femmodel); + if(isslr || iscoupler) sealevelrise_core(femmodel); /*unload results*/ @@ -159,6 +173,15 @@ femmodel->CheckPoint(); } + + /*Adaptive mesh refinement*/ + #ifdef _HAVE_NEOPZ_ + if(amr_frequency){ + if(save_results) femmodel->WriteMeshInResults(); + if(step%amr_frequency==0 && timeReMesh();//Do not refine the last step + } + #endif + } - + femmodel->RequestedDependentsx(); Index: /issm/trunk/src/c/datastructures/DataSet.cpp =================================================================== --- /issm/trunk/src/c/datastructures/DataSet.cpp (revision 21728) +++ /issm/trunk/src/c/datastructures/DataSet.cpp (revision 21729) @@ -167,4 +167,10 @@ this->AddObject(matice); } + else if(obj_enum==MatestarEnum){ + Matestar* matestar=NULL; + matestar=new Matestar(); + matestar->Marshall(pmarshalled_data,pmarshalled_data_size,marshall_direction); + this->AddObject(matestar); + } else if(obj_enum==MatparEnum){ Matpar* matpar=NULL; Index: /issm/trunk/src/c/main/issm_ocean.cpp =================================================================== --- /issm/trunk/src/c/main/issm_ocean.cpp (revision 21729) +++ /issm/trunk/src/c/main/issm_ocean.cpp (revision 21729) @@ -0,0 +1,132 @@ +/*!\file: issm_ocean.cpp + * \brief: ISSM OCEAN main program. + */ + +#include "./issm.h" + +int main(int argc,char **argv){ + +// /*diverse:*/ +// int nummodels = 2; +// int* commsizes=xNew(nummodels); +// int* rankzeros=xNew(nummodels); +// char** modelnames=xNew(nummodels); +// char** dirnames=xNew(nummodels); +// int iceid=0; +// int oceanid=1; +// int modelid; +// int my_rank; +// int count=0; +// ISSM_MPI_Comm worldcomm; +// ISSM_MPI_Comm modelcomm; +// ISSM_MPI_Comm toonceancomm; +// ISSM_MPI_Comm fromicecomms; + + /*Initialize exception trapping: */ + ExceptionTrapBegin(); + +// /*Initialize environment (MPI, PETSC, MUMPS, etc ...)*/ +// worldcomm=EnvironmentInit(argc,argv); +// +// /*What is my rank?:*/ +// ISSM_MPI_Comm_rank(worldcomm,&my_rank); +// +// /*First model is ice, second is ocean*/ +// for(int i=0;i(strlen(argv[5+3*i])+1); +// xMemCpy(string,argv[5+3*i],strlen(argv[5+3*i])+1); +// dirnames[i]=string; +// +// string=xNew(strlen(argv[5+3*i+1])+1); +// xMemCpy(string,argv[5+3*i+1],strlen(argv[5+3*i+1])+1); +// modelnames[i]=string; +// +// commsizes[i]=(int) strtol(argv[5+3*i+2], (char **)NULL, 10); +// } +// +// /*Figure out which model each cpu will belong to: */ +// count=0; +// for(int i=0;i=count && my_rank<(count+commsizes[i])){ +// modelid=i; +// break; +// } +// count+=commsizes[i]; +// } +// /*Buil array of who is rank 0 of their own group:*/ +// count=0; +// for(int i=0;i(4); +// arguments[0]=xNew(strlen(argv[0])+1); xMemCpy(arguments[0],argv[0],strlen(argv[0])+1); //executable name +// arguments[1]=xNew(strlen(argv[1])+1); xMemCpy(arguments[1],argv[1],strlen(argv[1])+1); //solution name +// arguments[2]=xNew(strlen(argv[5+3*modelid])+1); xMemCpy(arguments[2],argv[5+3*modelid],strlen(argv[5+3*modelid])+1); //directory name +// arguments[3]=xNew(strlen(argv[5+3*modelid+1])+1); xMemCpy(arguments[3],argv[5+3*modelid+1],strlen(argv[5+3*modelid+1])+1); //model name +// /*}}}*/ +// + + //REMOVE + /*Initialize environment (MPI, PETSC, MUMPS, etc ...)*/ + ISSM_MPI_Comm comm_init=EnvironmentInit(argc,argv); + /*Initialize femmodel from arguments provided command line: */ + FemModel *femmodel = new FemModel(argc,argv,comm_init); + ///*Initialize femmodel from arguments provided command line: */ + //FemModel *femmodel = new FemModel(1,arguments,modelcomm); + +// /*Now that the models are initialized, keep communicator information in the parameters datasets of each model: */ +// femmodel->parameters->AddObject(new GenericParam(worldcomm,WorldCommEnum)); +// femmodel->parameters->AddObject(new IntParam(NumModelsEnum,nummodels)); +// femmodel->parameters->AddObject(new IntParam(ModelIdEnum,oceanid)); +// femmodel->parameters->AddObject(new IntParam(EarthIdEnum,iceid)); +// if(modelid==earthid) femmodel->parameters->AddObject(new GenericParam(fromicecomms,IcecapToEarthCommEnum)); +// else femmodel->parameters->AddObject(new GenericParam(toearthcomm,IcecapToEarthCommEnum)); + + /*Solve: */ + femmodel->Solve(); + + /*Output results: */ + OutputResultsx(femmodel); + + /*Wrap up: */ + femmodel->CleanUp(); + + /*Delete Model: */ + delete femmodel; + + /*Finalize environment:*/ + EnvironmentFinalize(); + + /*Finalize exception trapping: */ + ExceptionTrapEnd(); + +// /*Free ressources:*/ +// xDelete(commsizes); +// for(int i=0;i(string); +// string=modelnames[i]; xDelete(string); +// } +// xDelete(dirnames); +// xDelete(modelnames); + + /*Return unix success: */ + return 0; +} Index: /issm/trunk/src/c/modules/Bamgx/Bamgx.cpp =================================================================== --- /issm/trunk/src/c/modules/Bamgx/Bamgx.cpp (revision 21728) +++ /issm/trunk/src/c/modules/Bamgx/Bamgx.cpp (revision 21729) @@ -21,5 +21,4 @@ int i; int noerr=1; - double costheta=2; double hminaniso=1e-100; Mesh* Thr=NULL; @@ -168,8 +167,4 @@ if (Thr != &BTh) delete Thr; - //Make quadrangle if requested - if(costheta<=1.0) Th.MakeQuadrangles(costheta); - //if () Th.SplitElement(2); - //Split corners if requested if(bamgopts->splitcorners) Th.SplitInternalEdgeWithBorderVertices(); @@ -183,9 +178,6 @@ //display info if(verbosity>0) { - if (Th.nbt-Th.nbtout-Th.nbq*2){ - _printf_(" new number of triangles = " << (Th.nbt-Th.nbtout-Th.nbq*2) << "\n"); - } - if (Th.nbq ){ - _printf_(" new number of quads = " << Th.nbq << "\n"); + if (Th.nbt-Th.nbtout){ + _printf_(" new number of triangles = " << (Th.nbt-Th.nbtout) << "\n"); } } Index: /issm/trunk/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp =================================================================== --- /issm/trunk/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp (revision 21728) +++ /issm/trunk/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp (revision 21729) @@ -13,11 +13,14 @@ switch(type){ - case VertexPIdEnum: case VertexSIdEnum: - vector=new Vector(femmodel->vertices->NumberOfVertices()); - break; - case NodesEnum:case NodeSIdEnum: - vector=new Vector(femmodel->nodes->NumberOfNodes()); - break; - default: + case ElementSIdEnum: + vector=new Vector(femmodel->elements->NumberOfElements()); + break; + case VertexPIdEnum: case VertexSIdEnum: + vector=new Vector(femmodel->vertices->NumberOfVertices()); + break; + case NodesEnum:case NodeSIdEnum: + vector=new Vector(femmodel->nodes->NumberOfNodes()); + break; + default: _error_("vector type: " << EnumToStringx(type) << " not supported yet!"); } Index: /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp =================================================================== --- /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 21728) +++ /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 21729) @@ -37,10 +37,10 @@ /*Get default*/ - if(options->GetOption("default")){ - isdefault=true; - options->Get(&defaultvalue,"default"); - } - else{ - isdefault=false; + isdefault = false; + if(options){ + if(options->GetOption("default")){ + isdefault=true; + options->Get(&defaultvalue,"default"); + } } Index: /issm/trunk/src/c/modules/IoModelToConstraintsx/IoModelToConstraintsx.cpp =================================================================== --- /issm/trunk/src/c/modules/IoModelToConstraintsx/IoModelToConstraintsx.cpp (revision 21728) +++ /issm/trunk/src/c/modules/IoModelToConstraintsx/IoModelToConstraintsx.cpp (revision 21729) @@ -504,4 +504,54 @@ } break; + case P1xP3Enum: + for(i=0;inumberofvertices;i++){ + if((iomodel->my_vertices[i])){ + + /*figure out times and values: */ + values=xNew(N); + spcpresent=false; + for(j=0;j(values[j]))spcpresent=true; //NaN means no spc by default + } + + if(spcpresent){ + constraints->AddObject(new SpcTransient(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,dof,N,times,values,analysis_type)); + count++; + } + xDelete(values); + } + } + for(i=0;inumberofedges;i++){ + if(iomodel->edges[i*3+2]==2){ + if(my_edges[i]){ + v1 = iomodel->edges[3*i+0]-1; + v2 = iomodel->edges[3*i+1]-1; + values=xNew(N); + spcpresent=false; + for(j=0;j(values[j])) spcpresent=true; //NaN means no spc by default + } + if(spcpresent){ + constraints->AddObject(new SpcTransient(iomodel->constraintcounter+count+1,iomodel->nodecounter+iomodel->numberofvertices+2*i+1,dof, + N,times,values,analysis_type)); + count++; + } + spcpresent=false; + for(j=0;j(values[j])) spcpresent=true; //NaN means no spc by default + } + if(spcpresent){ + constraints->AddObject(new SpcTransient(iomodel->constraintcounter+count+1,iomodel->nodecounter+iomodel->numberofvertices+2*i+2,dof, + N,times,values,analysis_type)); + count++; + } + xDelete(values); + } + } + } + break; case P2xP1Enum: for(i=0;inumberofvertices;i++){ @@ -562,9 +612,63 @@ /*intermediary: */ - int i,count; + int i,j,count,elementnbv,numfacevertices; + IssmDouble value; + IssmDouble *times = NULL; + IssmDouble *values = NULL; + bool spcpresent = false; + + /*Higher-order finite elements*/ + int v1,v2; + bool *my_edges = NULL; + bool *my_faces = NULL; + bool *boundaryedge = NULL; switch(finite_element){ case P1Enum: /*Nothing else to do*/ + break; + case P1bubbleEnum: + switch(iomodel->meshelementtype){ + case TriaEnum: elementnbv = 3; break; + case TetraEnum: elementnbv = 4; break; + case PentaEnum: elementnbv = 6; break; + default: _error_("mesh type not supported yet"); + } + break; + case P1bubblecondensedEnum: + /*Nothing else to do*/ + break; + case P1xP2Enum: + EdgesPartitioning(&my_edges,iomodel); + break; + case P1xP3Enum: + EdgesPartitioning(&my_edges,iomodel); + break; + case P2xP1Enum: + EdgesPartitioning(&my_edges,iomodel); + break; + case P2Enum: + EdgesPartitioning(&my_edges,iomodel); + if(iomodel->meshelementtype==PentaEnum){ + FacesPartitioning(&my_faces,iomodel); + } + EdgeOnBoundaryFlags(&boundaryedge,iomodel); + break; + case P2bubbleEnum: + EdgesPartitioning(&my_edges,iomodel); + if(iomodel->meshelementtype==PentaEnum){ + FacesPartitioning(&my_faces,iomodel); + } + EdgeOnBoundaryFlags(&boundaryedge,iomodel); + switch(iomodel->meshelementtype){ + case TriaEnum: elementnbv = 3; break; + case TetraEnum: elementnbv = 4; break; + case PentaEnum: elementnbv = 6; break; + default: _error_("mesh type not supported yet"); + } + break; + case P2xP4Enum: + EdgesPartitioning(&my_edges,iomodel); + FacesPartitioning(&my_faces,iomodel); break; default: @@ -581,4 +685,52 @@ constraints->AddObject(new SpcDynamic(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,dof,analysis_type)); count++; + } + } + } + break; + case P1xP2Enum: + for(i=0;inumberofvertices;i++){ + if((iomodel->my_vertices[i])){ + if (!xIsNan(spcdata[i])){ + constraints->AddObject(new SpcDynamic(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,dof,analysis_type)); + count++; + } + } + } + for(i=0;inumberofedges;i++){ + if(iomodel->edges[i*3+2]==2){ + if(my_edges[i]){ + v1 = iomodel->edges[3*i+0]-1; + v2 = iomodel->edges[3*i+1]-1; + if(!xIsNan(spcdata[v1]) && !xIsNan(spcdata[v2])){ + constraints->AddObject(new SpcDynamic(iomodel->constraintcounter+count+1,iomodel->nodecounter+iomodel->numberofvertices+i+1, + dof,analysis_type)); + count++; + } + } + } + } + break; + case P1xP3Enum: + for(i=0;inumberofvertices;i++){ + if((iomodel->my_vertices[i])){ + if (!xIsNan(spcdata[i])){ + constraints->AddObject(new SpcDynamic(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,dof,analysis_type)); + count++; + } + } + } + for(i=0;inumberofedges;i++){ + if(iomodel->edges[i*3+2]==2){ + if(my_edges[i]){ + v1 = iomodel->edges[3*i+0]-1; + v2 = iomodel->edges[3*i+1]-1; + if(!xIsNan(spcdata[v1]) && !xIsNan(spcdata[v2])){ + constraints->AddObject(new SpcDynamic(iomodel->constraintcounter+count+1,iomodel->nodecounter+iomodel->numberofvertices+2*i+1, + dof,analysis_type)); + constraints->AddObject(new SpcDynamic(iomodel->constraintcounter+count+2,iomodel->nodecounter+iomodel->numberofvertices+2*i+2, + dof,analysis_type)); + count=count+2; + } } } @@ -592,3 +744,10 @@ _error_("Size of spc field not supported"); } + + /*Free ressources:*/ + xDelete(times); + xDelete(values); + xDelete(my_edges); + xDelete(my_faces); + xDelete(boundaryedge); }/*}}}*/ Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp (revision 21728) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp (revision 21729) @@ -63,4 +63,20 @@ } break; + case MatenhancediceEnum: + iomodel->FetchDataToInput(elements,"md.materials.rheology_B",MaterialsRheologyBEnum); + iomodel->FetchDataToInput(elements,"md.materials.rheology_n",MaterialsRheologyNEnum); + iomodel->FetchDataToInput(elements,"md.materials.rheology_E",MaterialsRheologyEEnum); + for (i=0;inumberofelements;i++) if(iomodel->my_elements[i]) materials->AddObject(new Matice(i+1,i,iomodel)); + switch(iomodel->domaindim){ + case 2: + elements->InputDuplicate(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum); + elements->InputDuplicate(MaterialsRheologyEEnum,MaterialsRheologyEbarEnum); + break; + case 3: + break; + default: + _error_("Mesh not supported yet"); + } + break; case MatdamageiceEnum: iomodel->FetchDataToInput(elements,"md.materials.rheology_B",MaterialsRheologyBEnum); @@ -80,5 +96,5 @@ break; case MatestarEnum: - iomodel->FetchDataToInput(elements,"md.materials.rheology_ko",MaterialsRheologyKoEnum); + iomodel->FetchDataToInput(elements,"md.materials.rheology_B",MaterialsRheologyBEnum); iomodel->FetchDataToInput(elements,"md.materials.rheology_Ec",MaterialsRheologyEcEnum); iomodel->FetchDataToInput(elements,"md.materials.rheology_Es",MaterialsRheologyEsEnum); @@ -86,5 +102,5 @@ switch(iomodel->domaindim){ case 2: - elements->InputDuplicate(MaterialsRheologyKoEnum,MaterialsRheologyKobarEnum); + elements->InputDuplicate(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum); elements->InputDuplicate(MaterialsRheologyEcEnum,MaterialsRheologyEcbarEnum); elements->InputDuplicate(MaterialsRheologyEsEnum,MaterialsRheologyEsbarEnum); Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 21728) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateOutputDefinitions.cpp (revision 21729) @@ -53,7 +53,7 @@ /*Free ressources:*/ for(j=0;j(string); - char* string2= gatedefinitionstrings[j]; xDelete(string2); - IssmDouble* gate = gatesegments[j]; xDelete(gate); + char* string = gatenames[j]; xDelete(string); + char* string2 = gatedefinitionstrings[j]; xDelete(string2); + IssmDouble* gate = gatesegments[j]; xDelete(gate); } xDelete(gatenames); @@ -142,12 +142,12 @@ int numnodalvalues; char** nodalvalue_name_s = NULL; - int* nodalvalue_definitionenums_s = NULL; - int* nodalvalue_model_enum_s = NULL; + char** nodalvalue_definitionstrings = NULL; + char** nodalvalue_modelstrings = NULL; int* nodalvalue_node_s = NULL; /*Fetch name, model_enum, etc ... (see src/m/classes/nodalvalue.m): */ iomodel->FetchMultipleData(&nodalvalue_name_s,&numnodalvalues, "md.nodalvalue.name"); - iomodel->FetchMultipleData(&nodalvalue_definitionenums_s,&numnodalvalues, "md.nodalvalue.definitionenum"); - iomodel->FetchMultipleData(&nodalvalue_model_enum_s,&numnodalvalues, "md.nodalvalue.model_enum"); + iomodel->FetchMultipleData(&nodalvalue_definitionstrings,&numnodalvalues, "md.nodalvalue.definitionenum"); + iomodel->FetchMultipleData(&nodalvalue_modelstrings,&numnodalvalues, "md.nodalvalue.model_enum"); iomodel->FetchMultipleData(&nodalvalue_node_s,&numnodalvalues, "md.nodalvalue.node"); @@ -155,5 +155,5 @@ /*First create a nodalvalue object for that specific enum (nodalvalue_model_enum_s[j]):*/ - output_definitions->AddObject(new Nodalvalue(nodalvalue_name_s[j],nodalvalue_definitionenums_s[j],nodalvalue_model_enum_s[j],nodalvalue_node_s[j]-1)); //-1 because matlab to c indexing. + output_definitions->AddObject(new Nodalvalue(nodalvalue_name_s[j],StringToEnumx(nodalvalue_definitionstrings[j]),StringToEnumx(nodalvalue_modelstrings[j]),nodalvalue_node_s[j]-1)); //-1 because matlab to c indexing. } @@ -165,6 +165,6 @@ } xDelete(nodalvalue_name_s); - xDelete(nodalvalue_model_enum_s); - xDelete(nodalvalue_definitionenums_s); + xDelete(nodalvalue_modelstrings); + xDelete(nodalvalue_definitionstrings); xDelete(nodalvalue_node_s); /*}}}*/ Index: /issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21728) +++ /issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 21729) @@ -60,4 +60,5 @@ parameters->AddObject(iomodel->CopyConstantObject("md.settings.results_on_nodes",SettingsResultsOnNodesEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.settings.io_gather",SettingsIoGatherEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.settings.solver_residue_threshold",SettingsSolverResidueThresholdEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.isautodiff",AutodiffIsautodiffEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.qmu.isdakota",QmuIsdakotaEnum)); @@ -83,6 +84,11 @@ parameters->AddObject(iomodel->CopyConstantObject("md.transient.isslr",TransientIsslrEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.transient.iscoupler",TransientIscouplerEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.transient.amr_frequency",TransientAmrFrequencyEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.materials.rheology_law",MaterialsRheologyLawEnum)); parameters->AddObject(iomodel->CopyConstantObject("md.gia.cross_section_shape",GiaCrossSectionShapeEnum)); + /*amr properties*/ + parameters->AddObject(iomodel->CopyConstantObject("md.amr.level_max",AmrLevelMaxEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.amr.region_level_1",AmrRegionLevel1Enum)); + parameters->AddObject(iomodel->CopyConstantObject("md.amr.region_level_max",AmrRegionLevelMaxEnum)); /*For stress balance only*/ Index: /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp (revision 21728) +++ /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp (revision 21729) @@ -17,4 +17,5 @@ IssmDouble rho_water; // density of fresh water IssmDouble rho_ice; // density of ice + IssmDouble yts; // conversion factor year to second /*Loop over all the elements of this partition*/ @@ -44,4 +45,7 @@ rho_water=element->matpar->GetMaterialParameter(MaterialsRhoFreshwaterEnum); + /* Get constants */ + femmodel->parameters->FindParam(&yts,ConstantsYtsEnum); + // loop over all vertices for(v=0;v(s); xDelete(smb); + } + +}/*}}}*/ +void SmbGradientsElax(FemModel* femmodel){/*{{{*/ + + // void SurfaceMassBalancex(hd,agd,ni){ + // INPUT parameters: ni: working size of arrays + // INPUT: surface elevation (m): hd(NA) + // OUTPUT: surface mass-balance (m/yr ice): agd(NA) + int v; + + /*Loop over all the elements of this partition*/ + for(int i=0;ielements->Size();i++){ + Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + + /*Allocate all arrays*/ + int numvertices = element->GetNumberOfVertices(); + IssmDouble* ela = xNew(numvertices); // Equilibrium Line Altitude (m a.s.l) to which deviations are used to calculate the SMB + IssmDouble* b_pos = xNew(numvertices); // SMB gradient above ELA (m ice eq. per m elevation change) + IssmDouble* b_neg = xNew(numvertices); // SMB gradient below ELA (m ice eq. per m elevation change) + IssmDouble* b_max = xNew(numvertices); // Upper cap on SMB rate (m/y ice eq.) + IssmDouble* b_min = xNew(numvertices); // Lower cap on SMB rate (m/y ice eq.) + IssmDouble* s = xNew(numvertices); // Surface elevation (m a.s.l.) + IssmDouble* smb = xNew(numvertices); // SMB (m/y ice eq.) + + /*Recover ELA, SMB gradients, and caps*/ + element->GetInputListOnVertices(ela,SmbElaEnum); + element->GetInputListOnVertices(b_pos,SmbBPosEnum); + element->GetInputListOnVertices(b_neg,SmbBNegEnum); + element->GetInputListOnVertices(b_max,SmbBMaxEnum); + element->GetInputListOnVertices(b_min,SmbBMinEnum); + + /*Recover surface elevation at vertices: */ + element->GetInputListOnVertices(s,SurfaceEnum); + + /*Loop over all vertices, calculate SMB*/ + for(v=0;vela[v]){ + smb[v]=b_pos[v]*(s[v]-ela[v]); + } + // if surface is below or equal to the ELA + else{ + smb[v]=b_neg[v]*(s[v]-ela[v]); + } + + // if SMB is larger than upper cap, set SMB to upper cap + if(smb[v]>b_max[v]){ + smb[v]=b_max[v]; + } + // if SMB is smaller than lower cap, set SMB to lower cap + if(smb[v]AddInput(SmbMassBalanceEnum,smb,P1Enum); + xDelete(ela); + xDelete(b_pos); + xDelete(b_neg); + xDelete(b_max); + xDelete(b_min); + xDelete(s); + xDelete(smb); + } Index: /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h =================================================================== --- /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h (revision 21728) +++ /issm/trunk/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h (revision 21729) @@ -11,4 +11,5 @@ void SurfaceMassBalancex(FemModel* femmodel); void SmbGradientsx(FemModel* femmodel); +void SmbGradientsElax(FemModel* femmodel); void Delta18oParameterizationx(FemModel* femmodel); void MungsmtpParameterizationx(FemModel* femmodel); Index: /issm/trunk/src/c/shared/Elements/BuddJacka.cpp =================================================================== --- /issm/trunk/src/c/shared/Elements/BuddJacka.cpp (revision 21728) +++ /issm/trunk/src/c/shared/Elements/BuddJacka.cpp (revision 21729) @@ -15,35 +15,40 @@ /*Switch to celsius from Kelvin: */ T=temperature-273.15; + if(T<=-40.){ B=1e8*(-0.000237326134296*pow(T+50.,3)+ 0.017054655749852*pow(T+50.,2)-0.496435984007500*(T+50.)+7.670967258739796); } - else if(-40.0.); +IssmDouble EstarLambdaS(IssmDouble epseff, IssmDouble epsprime_norm){/*{{{*/ + IssmDouble lambdas; + _assert_(epsprime_norm>=0.); - return sqrt(2*epsprime_norm*epsprime_norm/(3*epso*epso)); + if(epseff==0.){ + lambdas=0.; + } + else{ + lambdas=sqrt(epsprime_norm*epsprime_norm/(epseff*epseff)); + } + return lambdas; }/*}}}*/ Index: /issm/trunk/src/c/shared/Elements/elements.h =================================================================== --- /issm/trunk/src/c/shared/Elements/elements.h (revision 21728) +++ /issm/trunk/src/c/shared/Elements/elements.h (revision 21729) @@ -15,7 +15,7 @@ IssmDouble LliboutryDuval(IssmDouble enthalpy, IssmDouble pressure, IssmDouble n, IssmDouble betaCC, IssmDouble referencetemperature, IssmDouble heatcapacity, IssmDouble latentheat); // IssmDouble LliboutryDuval(IssmDouble temperature, IssmDouble waterfraction, IssmDouble depth,IssmDouble n); -IssmDouble EstarLambdaS(IssmDouble epso, IssmDouble epsprime_norm); +IssmDouble EstarLambdaS(IssmDouble epseff, IssmDouble epsprime_norm); void EstarOmega(IssmDouble* omega,IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble vmag,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz, IssmDouble* dvmag); -void EstarStrainrateQuantities(IssmDouble *pepso, IssmDouble *pepsprime_norm, IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble vmag,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble* dvmag); +void EstarStrainrateQuantities(IssmDouble *pepseff, IssmDouble *pepsprime_norm, IssmDouble vx,IssmDouble vy,IssmDouble vz,IssmDouble vmag,IssmDouble* dvx,IssmDouble* dvy,IssmDouble* dvz,IssmDouble* dvmag); IssmDouble PddSurfaceMassBalance(IssmDouble* monthlytemperatures, IssmDouble* monthlyprec, IssmDouble* pdds, IssmDouble* pds, IssmDouble* melt, IssmDouble* accu, IssmDouble signorm, @@ -33,5 +33,5 @@ IssmDouble* TemperaturesLgm, IssmDouble* TemperaturesPresentday, IssmDouble* monthlytemperaturesout, IssmDouble* monthlyprecout); -void ComputeD18OTemperaturePrecipitationFromPD(IssmDouble d018,IssmDouble dpermil, +void ComputeD18OTemperaturePrecipitationFromPD(IssmDouble d018,IssmDouble dpermil,IssmDouble f, IssmDouble* PrecipitationPresentday,IssmDouble* TemperaturePresentday, IssmDouble* monthlytemperaturesout, IssmDouble* monthlyprecout); Index: /issm/trunk/src/c/shared/Enum/EnumDefinitions.h =================================================================== --- /issm/trunk/src/c/shared/Enum/EnumDefinitions.h (revision 21728) +++ /issm/trunk/src/c/shared/Enum/EnumDefinitions.h (revision 21729) @@ -109,4 +109,5 @@ FrictionCoefficientEnum, FrictionCoefficientcoulombEnum, + FrictionPressureAdjustedTemperatureEnum, FrictionPEnum, FrictionQEnum, @@ -174,4 +175,7 @@ HydrologyReynoldsEnum, HydrologyNeumannfluxEnum, + HydrologyRelaxationEnum, + HydrologyBasalFluxEnum, + HydrologyStorageEnum, InversionControlParametersEnum, InversionControlScalingFactorsEnum, @@ -214,6 +218,6 @@ MaterialsRheologyLawEnum, MaterialsRheologyNEnum, - MaterialsRheologyKoEnum, - MaterialsRheologyKobarEnum, + MaterialsRheologyEEnum, + MaterialsRheologyEbarEnum, MaterialsRheologyEcEnum, MaterialsRheologyEcbarEnum, @@ -255,4 +259,7 @@ CalvingratexAverageEnum, CalvingrateyAverageEnum, + CalvingStressThresholdGroundediceEnum, + CalvingStressThresholdFloatingiceEnum, + CalvingMaxEnum, StrainRateparallelEnum, StrainRateperpendicularEnum, @@ -271,4 +278,7 @@ MaterialsEarthDensityEnum, MeshAverageVertexConnectivityEnum, + MeshXEnum, + MeshYEnum, + MeshZEnum, MeshElementsEnum, MeshNumberofelementsEnum, @@ -307,4 +317,5 @@ SettingsRecordingFrequencyEnum, SettingsWaitonlockEnum, + SettingsSolverResidueThresholdEnum, DebugProfilingEnum, ProfilingCurrentMemEnum, @@ -447,4 +458,5 @@ SMBd18opddEnum, SmbDpermilEnum, + SmbFEnum, SMBgradientsEnum, SmbMonthlytemperaturesEnum, @@ -462,4 +474,9 @@ SmbRefreezeEnum, SMBgcmEnum, + /*SMBgradientsela*/ + SMBgradientselaEnum, + SmbElaEnum, + SmbBMaxEnum, + SmbBMinEnum, /*}}}*/ /*Inputs {{{*/ @@ -522,4 +539,6 @@ TransientInputEnum, WaterfractionEnum, + WaterfractionDrainageEnum, + WaterfractionDrainageIntegratedEnum, WatercolumnEnum, ViscousHeatingEnum, @@ -565,4 +584,5 @@ DoubleMatExternalResultEnum, IntExternalResultEnum, + IntMatExternalResultEnum, JEnum, StringExternalResultEnum, @@ -775,5 +795,8 @@ SealevelriseRotationEnum, SealevelriseTidalLoveHEnum, - SealevelriseTidalLoveKEnum, + SealevelriseTidalLoveKEnum, + SealevelriseFluidLoveEnum, + SealevelriseEquatorialMoiEnum, + SealevelrisePolarMoiEnum, SealevelriseAngularVelocityEnum, SealevelriseOceanAreaScalingEnum, @@ -789,4 +812,8 @@ EsaNmotionEnum, EsaEmotionEnum, + EsaStrainratexxEnum, + EsaStrainratexyEnum, + EsaStrainrateyyEnum, + EsaRotationrateEnum, EsaDeltathicknessEnum, EsaUElasticEnum, @@ -795,4 +822,10 @@ EsaRequestedOutputsEnum, EsaNumRequestedOutputsEnum, + /*}}}*/ + /*Adaptive mesh refinement (AMR){{{*/ + AmrLevelMaxEnum, + AmrRegionLevel1Enum, + AmrRegionLevelMaxEnum, + TransientAmrFrequencyEnum, /*}}}*/ ParametersENDEnum, @@ -827,4 +860,5 @@ MaticeEnum, MatdamageiceEnum, + MatenhancediceEnum, MatestarEnum, MatparEnum, @@ -841,4 +875,5 @@ MassconaxpbyEnum, NodeSIdEnum, + ElementSIdEnum, VectorParamEnum, RiftfrontEnum, @@ -914,5 +949,5 @@ UzawaPressureAnalysisEnum, GiaSolutionEnum, - GiaAnalysisEnum, + GiaIvinsAnalysisEnum, EsaSolutionEnum, EsaAnalysisEnum, Index: /issm/trunk/src/c/shared/Enum/EnumToStringx.cpp =================================================================== --- /issm/trunk/src/c/shared/Enum/EnumToStringx.cpp (revision 21728) +++ /issm/trunk/src/c/shared/Enum/EnumToStringx.cpp (revision 21729) @@ -115,4 +115,5 @@ case FrictionCoefficientEnum : return "FrictionCoefficient"; case FrictionCoefficientcoulombEnum : return "FrictionCoefficientcoulomb"; + case FrictionPressureAdjustedTemperatureEnum : return "FrictionPressureAdjustedTemperature"; case FrictionPEnum : return "FrictionP"; case FrictionQEnum : return "FrictionQ"; @@ -180,4 +181,7 @@ case HydrologyReynoldsEnum : return "HydrologyReynolds"; case HydrologyNeumannfluxEnum : return "HydrologyNeumannflux"; + case HydrologyRelaxationEnum : return "HydrologyRelaxation"; + case HydrologyBasalFluxEnum : return "HydrologyBasalFlux"; + case HydrologyStorageEnum : return "HydrologyStorage"; case InversionControlParametersEnum : return "InversionControlParameters"; case InversionControlScalingFactorsEnum : return "InversionControlScalingFactors"; @@ -220,6 +224,6 @@ case MaterialsRheologyLawEnum : return "MaterialsRheologyLaw"; case MaterialsRheologyNEnum : return "MaterialsRheologyN"; - case MaterialsRheologyKoEnum : return "MaterialsRheologyKo"; - case MaterialsRheologyKobarEnum : return "MaterialsRheologyKobar"; + case MaterialsRheologyEEnum : return "MaterialsRheologyE"; + case MaterialsRheologyEbarEnum : return "MaterialsRheologyEbar"; case MaterialsRheologyEcEnum : return "MaterialsRheologyEc"; case MaterialsRheologyEcbarEnum : return "MaterialsRheologyEcbar"; @@ -261,4 +265,7 @@ case CalvingratexAverageEnum : return "CalvingratexAverage"; case CalvingrateyAverageEnum : return "CalvingrateyAverage"; + case CalvingStressThresholdGroundediceEnum : return "CalvingStressThresholdGroundedice"; + case CalvingStressThresholdFloatingiceEnum : return "CalvingStressThresholdFloatingice"; + case CalvingMaxEnum : return "CalvingMax"; case StrainRateparallelEnum : return "StrainRateparallel"; case StrainRateperpendicularEnum : return "StrainRateperpendicular"; @@ -277,4 +284,7 @@ case MaterialsEarthDensityEnum : return "MaterialsEarthDensity"; case MeshAverageVertexConnectivityEnum : return "MeshAverageVertexConnectivity"; + case MeshXEnum : return "MeshX"; + case MeshYEnum : return "MeshY"; + case MeshZEnum : return "MeshZ"; case MeshElementsEnum : return "MeshElements"; case MeshNumberofelementsEnum : return "MeshNumberofelements"; @@ -313,4 +323,5 @@ case SettingsRecordingFrequencyEnum : return "SettingsRecordingFrequency"; case SettingsWaitonlockEnum : return "SettingsWaitonlock"; + case SettingsSolverResidueThresholdEnum : return "SettingsSolverResidueThreshold"; case DebugProfilingEnum : return "DebugProfiling"; case ProfilingCurrentMemEnum : return "ProfilingCurrentMem"; @@ -448,4 +459,5 @@ case SMBd18opddEnum : return "SMBd18opdd"; case SmbDpermilEnum : return "SmbDpermil"; + case SmbFEnum : return "SmbF"; case SMBgradientsEnum : return "SMBgradients"; case SmbMonthlytemperaturesEnum : return "SmbMonthlytemperatures"; @@ -463,4 +475,8 @@ case SmbRefreezeEnum : return "SmbRefreeze"; case SMBgcmEnum : return "SMBgcm"; + case SMBgradientselaEnum : return "SMBgradientsela"; + case SmbElaEnum : return "SmbEla"; + case SmbBMaxEnum : return "SmbBMax"; + case SmbBMinEnum : return "SmbBMin"; case AdjointpEnum : return "Adjointp"; case AdjointxEnum : return "Adjointx"; @@ -521,4 +537,6 @@ case TransientInputEnum : return "TransientInput"; case WaterfractionEnum : return "Waterfraction"; + case WaterfractionDrainageEnum : return "WaterfractionDrainage"; + case WaterfractionDrainageIntegratedEnum : return "WaterfractionDrainageIntegrated"; case WatercolumnEnum : return "Watercolumn"; case ViscousHeatingEnum : return "ViscousHeating"; @@ -562,4 +580,5 @@ case DoubleMatExternalResultEnum : return "DoubleMatExternalResult"; case IntExternalResultEnum : return "IntExternalResult"; + case IntMatExternalResultEnum : return "IntMatExternalResult"; case JEnum : return "J"; case StringExternalResultEnum : return "StringExternalResult"; @@ -757,4 +776,7 @@ case SealevelriseTidalLoveHEnum : return "SealevelriseTidalLoveH"; case SealevelriseTidalLoveKEnum : return "SealevelriseTidalLoveK"; + case SealevelriseFluidLoveEnum : return "SealevelriseFluidLove"; + case SealevelriseEquatorialMoiEnum : return "SealevelriseEquatorialMoi"; + case SealevelrisePolarMoiEnum : return "SealevelrisePolarMoi"; case SealevelriseAngularVelocityEnum : return "SealevelriseAngularVelocity"; case SealevelriseOceanAreaScalingEnum : return "SealevelriseOceanAreaScaling"; @@ -768,4 +790,8 @@ case EsaNmotionEnum : return "EsaNmotion"; case EsaEmotionEnum : return "EsaEmotion"; + case EsaStrainratexxEnum : return "EsaStrainratexx"; + case EsaStrainratexyEnum : return "EsaStrainratexy"; + case EsaStrainrateyyEnum : return "EsaStrainrateyy"; + case EsaRotationrateEnum : return "EsaRotationrate"; case EsaDeltathicknessEnum : return "EsaDeltathickness"; case EsaUElasticEnum : return "EsaUElastic"; @@ -774,4 +800,8 @@ case EsaRequestedOutputsEnum : return "EsaRequestedOutputs"; case EsaNumRequestedOutputsEnum : return "EsaNumRequestedOutputs"; + case AmrLevelMaxEnum : return "AmrLevelMax"; + case AmrRegionLevel1Enum : return "AmrRegionLevel1"; + case AmrRegionLevelMaxEnum : return "AmrRegionLevelMax"; + case TransientAmrFrequencyEnum : return "TransientAmrFrequency"; case ParametersENDEnum : return "ParametersEND"; case XYEnum : return "XY"; @@ -802,4 +832,5 @@ case MaticeEnum : return "Matice"; case MatdamageiceEnum : return "Matdamageice"; + case MatenhancediceEnum : return "Matenhancedice"; case MatestarEnum : return "Matestar"; case MatparEnum : return "Matpar"; @@ -816,4 +847,5 @@ case MassconaxpbyEnum : return "Massconaxpby"; case NodeSIdEnum : return "NodeSId"; + case ElementSIdEnum : return "ElementSId"; case VectorParamEnum : return "VectorParam"; case RiftfrontEnum : return "Riftfront"; @@ -885,5 +917,5 @@ case UzawaPressureAnalysisEnum : return "UzawaPressureAnalysis"; case GiaSolutionEnum : return "GiaSolution"; - case GiaAnalysisEnum : return "GiaAnalysis"; + case GiaIvinsAnalysisEnum : return "GiaIvinsAnalysis"; case EsaSolutionEnum : return "EsaSolution"; case EsaAnalysisEnum : return "EsaAnalysis"; Index: /issm/trunk/src/c/shared/Enum/StringToEnumx.cpp =================================================================== --- /issm/trunk/src/c/shared/Enum/StringToEnumx.cpp (revision 21728) +++ /issm/trunk/src/c/shared/Enum/StringToEnumx.cpp (revision 21729) @@ -115,4 +115,5 @@ else if (strcmp(name,"FrictionCoefficient")==0) return FrictionCoefficientEnum; else if (strcmp(name,"FrictionCoefficientcoulomb")==0) return FrictionCoefficientcoulombEnum; + else if (strcmp(name,"FrictionPressureAdjustedTemperature")==0) return FrictionPressureAdjustedTemperatureEnum; else if (strcmp(name,"FrictionP")==0) return FrictionPEnum; else if (strcmp(name,"FrictionQ")==0) return FrictionQEnum; @@ -136,9 +137,9 @@ else if (strcmp(name,"EplHead")==0) return EplHeadEnum; else if (strcmp(name,"EplHeadOld")==0) return EplHeadOldEnum; - else if (strcmp(name,"EplHeadSlopeX")==0) return EplHeadSlopeXEnum; else stage=2; } if(stage==2){ - if (strcmp(name,"EplHeadSlopeY")==0) return EplHeadSlopeYEnum; + if (strcmp(name,"EplHeadSlopeX")==0) return EplHeadSlopeXEnum; + else if (strcmp(name,"EplHeadSlopeY")==0) return EplHeadSlopeYEnum; else if (strcmp(name,"EplZigZagCounter")==0) return EplZigZagCounterEnum; else if (strcmp(name,"HydrologydcMaxIter")==0) return HydrologydcMaxIterEnum; @@ -183,4 +184,7 @@ else if (strcmp(name,"HydrologyReynolds")==0) return HydrologyReynoldsEnum; else if (strcmp(name,"HydrologyNeumannflux")==0) return HydrologyNeumannfluxEnum; + else if (strcmp(name,"HydrologyRelaxation")==0) return HydrologyRelaxationEnum; + else if (strcmp(name,"HydrologyBasalFlux")==0) return HydrologyBasalFluxEnum; + else if (strcmp(name,"HydrologyStorage")==0) return HydrologyStorageEnum; else if (strcmp(name,"InversionControlParameters")==0) return InversionControlParametersEnum; else if (strcmp(name,"InversionControlScalingFactors")==0) return InversionControlScalingFactorsEnum; @@ -223,6 +227,6 @@ else if (strcmp(name,"MaterialsRheologyLaw")==0) return MaterialsRheologyLawEnum; else if (strcmp(name,"MaterialsRheologyN")==0) return MaterialsRheologyNEnum; - else if (strcmp(name,"MaterialsRheologyKo")==0) return MaterialsRheologyKoEnum; - else if (strcmp(name,"MaterialsRheologyKobar")==0) return MaterialsRheologyKobarEnum; + else if (strcmp(name,"MaterialsRheologyE")==0) return MaterialsRheologyEEnum; + else if (strcmp(name,"MaterialsRheologyEbar")==0) return MaterialsRheologyEbarEnum; else if (strcmp(name,"MaterialsRheologyEc")==0) return MaterialsRheologyEcEnum; else if (strcmp(name,"MaterialsRheologyEcbar")==0) return MaterialsRheologyEcbarEnum; @@ -256,15 +260,18 @@ else if (strcmp(name,"CalvingDev")==0) return CalvingDevEnum; else if (strcmp(name,"CalvingMinthickness")==0) return CalvingMinthicknessEnum; - else if (strcmp(name,"DefaultCalving")==0) return DefaultCalvingEnum; + else stage=3; + } + if(stage==3){ + if (strcmp(name,"DefaultCalving")==0) return DefaultCalvingEnum; else if (strcmp(name,"CalvinglevermannCoeff")==0) return CalvinglevermannCoeffEnum; else if (strcmp(name,"CalvinglevermannMeltingrate")==0) return CalvinglevermannMeltingrateEnum; else if (strcmp(name,"CalvingdevCoeff")==0) return CalvingdevCoeffEnum; - else stage=3; - } - if(stage==3){ - if (strcmp(name,"Calvingratex")==0) return CalvingratexEnum; + else if (strcmp(name,"Calvingratex")==0) return CalvingratexEnum; else if (strcmp(name,"Calvingratey")==0) return CalvingrateyEnum; else if (strcmp(name,"CalvingratexAverage")==0) return CalvingratexAverageEnum; else if (strcmp(name,"CalvingrateyAverage")==0) return CalvingrateyAverageEnum; + else if (strcmp(name,"CalvingStressThresholdGroundedice")==0) return CalvingStressThresholdGroundediceEnum; + else if (strcmp(name,"CalvingStressThresholdFloatingice")==0) return CalvingStressThresholdFloatingiceEnum; + else if (strcmp(name,"CalvingMax")==0) return CalvingMaxEnum; else if (strcmp(name,"StrainRateparallel")==0) return StrainRateparallelEnum; else if (strcmp(name,"StrainRateperpendicular")==0) return StrainRateperpendicularEnum; @@ -283,4 +290,7 @@ else if (strcmp(name,"MaterialsEarthDensity")==0) return MaterialsEarthDensityEnum; else if (strcmp(name,"MeshAverageVertexConnectivity")==0) return MeshAverageVertexConnectivityEnum; + else if (strcmp(name,"MeshX")==0) return MeshXEnum; + else if (strcmp(name,"MeshY")==0) return MeshYEnum; + else if (strcmp(name,"MeshZ")==0) return MeshZEnum; else if (strcmp(name,"MeshElements")==0) return MeshElementsEnum; else if (strcmp(name,"MeshNumberofelements")==0) return MeshNumberofelementsEnum; @@ -319,4 +329,5 @@ else if (strcmp(name,"SettingsRecordingFrequency")==0) return SettingsRecordingFrequencyEnum; else if (strcmp(name,"SettingsWaitonlock")==0) return SettingsWaitonlockEnum; + else if (strcmp(name,"SettingsSolverResidueThreshold")==0) return SettingsSolverResidueThresholdEnum; else if (strcmp(name,"DebugProfiling")==0) return DebugProfilingEnum; else if (strcmp(name,"ProfilingCurrentMem")==0) return ProfilingCurrentMemEnum; @@ -372,5 +383,8 @@ else if (strcmp(name,"SmbRequestedOutputs")==0) return SmbRequestedOutputsEnum; else if (strcmp(name,"SmbIsInitialized")==0) return SmbIsInitializedEnum; - else if (strcmp(name,"SmbDzini")==0) return SmbDziniEnum; + else stage=4; + } + if(stage==4){ + if (strcmp(name,"SmbDzini")==0) return SmbDziniEnum; else if (strcmp(name,"SmbDini")==0) return SmbDiniEnum; else if (strcmp(name,"SmbReini")==0) return SmbReiniEnum; @@ -383,8 +397,5 @@ else if (strcmp(name,"SmbSizeini")==0) return SmbSizeiniEnum; else if (strcmp(name,"SMBforcing")==0) return SMBforcingEnum; - else stage=4; - } - if(stage==4){ - if (strcmp(name,"SmbMassBalance")==0) return SmbMassBalanceEnum; + else if (strcmp(name,"SmbMassBalance")==0) return SmbMassBalanceEnum; else if (strcmp(name,"SMBgemb")==0) return SMBgembEnum; else if (strcmp(name,"SmbInitDensityScaling")==0) return SmbInitDensityScalingEnum; @@ -457,4 +468,5 @@ else if (strcmp(name,"SMBd18opdd")==0) return SMBd18opddEnum; else if (strcmp(name,"SmbDpermil")==0) return SmbDpermilEnum; + else if (strcmp(name,"SmbF")==0) return SmbFEnum; else if (strcmp(name,"SMBgradients")==0) return SMBgradientsEnum; else if (strcmp(name,"SmbMonthlytemperatures")==0) return SmbMonthlytemperaturesEnum; @@ -472,4 +484,8 @@ else if (strcmp(name,"SmbRefreeze")==0) return SmbRefreezeEnum; else if (strcmp(name,"SMBgcm")==0) return SMBgcmEnum; + else if (strcmp(name,"SMBgradientsela")==0) return SMBgradientselaEnum; + else if (strcmp(name,"SmbEla")==0) return SmbElaEnum; + else if (strcmp(name,"SmbBMax")==0) return SmbBMaxEnum; + else if (strcmp(name,"SmbBMin")==0) return SmbBMinEnum; else if (strcmp(name,"Adjointp")==0) return AdjointpEnum; else if (strcmp(name,"Adjointx")==0) return AdjointxEnum; @@ -490,5 +506,8 @@ else if (strcmp(name,"ResetPenalties")==0) return ResetPenaltiesEnum; else if (strcmp(name,"SurfaceAbsVelMisfit")==0) return SurfaceAbsVelMisfitEnum; - else if (strcmp(name,"SurfaceArea")==0) return SurfaceAreaEnum; + else stage=5; + } + if(stage==5){ + if (strcmp(name,"SurfaceArea")==0) return SurfaceAreaEnum; else if (strcmp(name,"SurfaceAverageVelMisfit")==0) return SurfaceAverageVelMisfitEnum; else if (strcmp(name,"SurfaceLogVelMisfit")==0) return SurfaceLogVelMisfitEnum; @@ -506,8 +525,5 @@ else if (strcmp(name,"VxAverage")==0) return VxAverageEnum; else if (strcmp(name,"Vx")==0) return VxEnum; - else stage=5; - } - if(stage==5){ - if (strcmp(name,"VxPicard")==0) return VxPicardEnum; + else if (strcmp(name,"VxPicard")==0) return VxPicardEnum; else if (strcmp(name,"VyAverage")==0) return VyAverageEnum; else if (strcmp(name,"Vy")==0) return VyEnum; @@ -533,4 +549,6 @@ else if (strcmp(name,"TransientInput")==0) return TransientInputEnum; else if (strcmp(name,"Waterfraction")==0) return WaterfractionEnum; + else if (strcmp(name,"WaterfractionDrainage")==0) return WaterfractionDrainageEnum; + else if (strcmp(name,"WaterfractionDrainageIntegrated")==0) return WaterfractionDrainageIntegratedEnum; else if (strcmp(name,"Watercolumn")==0) return WatercolumnEnum; else if (strcmp(name,"ViscousHeating")==0) return ViscousHeatingEnum; @@ -574,4 +592,5 @@ else if (strcmp(name,"DoubleMatExternalResult")==0) return DoubleMatExternalResultEnum; else if (strcmp(name,"IntExternalResult")==0) return IntExternalResultEnum; + else if (strcmp(name,"IntMatExternalResult")==0) return IntMatExternalResultEnum; else if (strcmp(name,"J")==0) return JEnum; else if (strcmp(name,"StringExternalResult")==0) return StringExternalResultEnum; @@ -610,5 +629,8 @@ else if (strcmp(name,"Outputdefinition27")==0) return Outputdefinition27Enum; else if (strcmp(name,"Outputdefinition28")==0) return Outputdefinition28Enum; - else if (strcmp(name,"Outputdefinition29")==0) return Outputdefinition29Enum; + else stage=6; + } + if(stage==6){ + if (strcmp(name,"Outputdefinition29")==0) return Outputdefinition29Enum; else if (strcmp(name,"Outputdefinition30")==0) return Outputdefinition30Enum; else if (strcmp(name,"Outputdefinition31")==0) return Outputdefinition31Enum; @@ -629,8 +651,5 @@ else if (strcmp(name,"Outputdefinition46")==0) return Outputdefinition46Enum; else if (strcmp(name,"Outputdefinition47")==0) return Outputdefinition47Enum; - else stage=6; - } - if(stage==6){ - if (strcmp(name,"Outputdefinition48")==0) return Outputdefinition48Enum; + else if (strcmp(name,"Outputdefinition48")==0) return Outputdefinition48Enum; else if (strcmp(name,"Outputdefinition49")==0) return Outputdefinition49Enum; else if (strcmp(name,"Outputdefinition50")==0) return Outputdefinition50Enum; @@ -733,5 +752,8 @@ else if (strcmp(name,"QmuErrName")==0) return QmuErrNameEnum; else if (strcmp(name,"QmuInName")==0) return QmuInNameEnum; - else if (strcmp(name,"QmuOutName")==0) return QmuOutNameEnum; + else stage=7; + } + if(stage==7){ + if (strcmp(name,"QmuOutName")==0) return QmuOutNameEnum; else if (strcmp(name,"Regular")==0) return RegularEnum; else if (strcmp(name,"Scaled")==0) return ScaledEnum; @@ -752,8 +774,5 @@ else if (strcmp(name,"LliboutryDuval")==0) return LliboutryDuvalEnum; else if (strcmp(name,"ExtrapolationVariable")==0) return ExtrapolationVariableEnum; - else stage=7; - } - if(stage==7){ - if (strcmp(name,"IceMaskNodeActivation")==0) return IceMaskNodeActivationEnum; + else if (strcmp(name,"IceMaskNodeActivation")==0) return IceMaskNodeActivationEnum; else if (strcmp(name,"LevelsetfunctionSlopeX")==0) return LevelsetfunctionSlopeXEnum; else if (strcmp(name,"LevelsetfunctionSlopeY")==0) return LevelsetfunctionSlopeYEnum; @@ -775,4 +794,7 @@ else if (strcmp(name,"SealevelriseTidalLoveH")==0) return SealevelriseTidalLoveHEnum; else if (strcmp(name,"SealevelriseTidalLoveK")==0) return SealevelriseTidalLoveKEnum; + else if (strcmp(name,"SealevelriseFluidLove")==0) return SealevelriseFluidLoveEnum; + else if (strcmp(name,"SealevelriseEquatorialMoi")==0) return SealevelriseEquatorialMoiEnum; + else if (strcmp(name,"SealevelrisePolarMoi")==0) return SealevelrisePolarMoiEnum; else if (strcmp(name,"SealevelriseAngularVelocity")==0) return SealevelriseAngularVelocityEnum; else if (strcmp(name,"SealevelriseOceanAreaScaling")==0) return SealevelriseOceanAreaScalingEnum; @@ -786,4 +808,8 @@ else if (strcmp(name,"EsaNmotion")==0) return EsaNmotionEnum; else if (strcmp(name,"EsaEmotion")==0) return EsaEmotionEnum; + else if (strcmp(name,"EsaStrainratexx")==0) return EsaStrainratexxEnum; + else if (strcmp(name,"EsaStrainratexy")==0) return EsaStrainratexyEnum; + else if (strcmp(name,"EsaStrainrateyy")==0) return EsaStrainrateyyEnum; + else if (strcmp(name,"EsaRotationrate")==0) return EsaRotationrateEnum; else if (strcmp(name,"EsaDeltathickness")==0) return EsaDeltathicknessEnum; else if (strcmp(name,"EsaUElastic")==0) return EsaUElasticEnum; @@ -792,4 +818,8 @@ else if (strcmp(name,"EsaRequestedOutputs")==0) return EsaRequestedOutputsEnum; else if (strcmp(name,"EsaNumRequestedOutputs")==0) return EsaNumRequestedOutputsEnum; + else if (strcmp(name,"AmrLevelMax")==0) return AmrLevelMaxEnum; + else if (strcmp(name,"AmrRegionLevel1")==0) return AmrRegionLevel1Enum; + else if (strcmp(name,"AmrRegionLevelMax")==0) return AmrRegionLevelMaxEnum; + else if (strcmp(name,"TransientAmrFrequency")==0) return TransientAmrFrequencyEnum; else if (strcmp(name,"ParametersEND")==0) return ParametersENDEnum; else if (strcmp(name,"XY")==0) return XYEnum; @@ -820,4 +850,5 @@ else if (strcmp(name,"Matice")==0) return MaticeEnum; else if (strcmp(name,"Matdamageice")==0) return MatdamageiceEnum; + else if (strcmp(name,"Matenhancedice")==0) return MatenhancediceEnum; else if (strcmp(name,"Matestar")==0) return MatestarEnum; else if (strcmp(name,"Matpar")==0) return MatparEnum; @@ -834,4 +865,5 @@ else if (strcmp(name,"Massconaxpby")==0) return MassconaxpbyEnum; else if (strcmp(name,"NodeSId")==0) return NodeSIdEnum; + else if (strcmp(name,"ElementSId")==0) return ElementSIdEnum; else if (strcmp(name,"VectorParam")==0) return VectorParamEnum; else if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; @@ -843,5 +875,8 @@ else if (strcmp(name,"StringArrayParam")==0) return StringArrayParamEnum; else if (strcmp(name,"StringParam")==0) return StringParamEnum; - else if (strcmp(name,"Seg")==0) return SegEnum; + else stage=8; + } + if(stage==8){ + if (strcmp(name,"Seg")==0) return SegEnum; else if (strcmp(name,"SegInput")==0) return SegInputEnum; else if (strcmp(name,"Tria")==0) return TriaEnum; @@ -875,8 +910,5 @@ else if (strcmp(name,"DamageEvolutionSolution")==0) return DamageEvolutionSolutionEnum; else if (strcmp(name,"DamageEvolutionAnalysis")==0) return DamageEvolutionAnalysisEnum; - else stage=8; - } - if(stage==8){ - if (strcmp(name,"StressbalanceAnalysis")==0) return StressbalanceAnalysisEnum; + else if (strcmp(name,"StressbalanceAnalysis")==0) return StressbalanceAnalysisEnum; else if (strcmp(name,"StressbalanceSIAAnalysis")==0) return StressbalanceSIAAnalysisEnum; else if (strcmp(name,"StressbalanceSolution")==0) return StressbalanceSolutionEnum; @@ -906,5 +938,5 @@ else if (strcmp(name,"UzawaPressureAnalysis")==0) return UzawaPressureAnalysisEnum; else if (strcmp(name,"GiaSolution")==0) return GiaSolutionEnum; - else if (strcmp(name,"GiaAnalysis")==0) return GiaAnalysisEnum; + else if (strcmp(name,"GiaIvinsAnalysis")==0) return GiaIvinsAnalysisEnum; else if (strcmp(name,"EsaSolution")==0) return EsaSolutionEnum; else if (strcmp(name,"EsaAnalysis")==0) return EsaAnalysisEnum; @@ -966,5 +998,8 @@ else if (strcmp(name,"P1P1GLS")==0) return P1P1GLSEnum; else if (strcmp(name,"MINI")==0) return MINIEnum; - else if (strcmp(name,"MINIcondensed")==0) return MINIcondensedEnum; + else stage=9; + } + if(stage==9){ + if (strcmp(name,"MINIcondensed")==0) return MINIcondensedEnum; else if (strcmp(name,"TaylorHood")==0) return TaylorHoodEnum; else if (strcmp(name,"LATaylorHood")==0) return LATaylorHoodEnum; @@ -990,5 +1025,5 @@ else if (strcmp(name,"Results")==0) return ResultsEnum; else if (strcmp(name,"MaximumNumberOfDefinitions")==0) return MaximumNumberOfDefinitionsEnum; - else stage=9; + else stage=10; } /*If we reach this point, the string provided has not been found*/ Index: /issm/trunk/src/c/shared/MemOps/MemOps.cpp =================================================================== --- /issm/trunk/src/c/shared/MemOps/MemOps.cpp (revision 21728) +++ /issm/trunk/src/c/shared/MemOps/MemOps.cpp (revision 21729) @@ -15,6 +15,8 @@ #if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) -template <> adouble* xNew(unsigned int size) { - ensureContiguousLocations(size); +template <> adouble* xNew(unsigned int size, const char* const contig) { + if (*contig == 't') + ensureContiguousLocations(size); + adouble* aT_p=new adouble[size]; assert(aT_p); Index: /issm/trunk/src/c/shared/MemOps/MemOps.h =================================================================== --- /issm/trunk/src/c/shared/MemOps/MemOps.h (revision 21728) +++ /issm/trunk/src/c/shared/MemOps/MemOps.h (revision 21729) @@ -16,5 +16,12 @@ #endif +static char const DEFCONTIG = 'f'; + +// AD (mostly ADOLC) is sensitive to calls to ensurecontiguous. These changes limit its use. +#ifdef _HAVE_AD_ +template T* xNew(unsigned int size, const char* const contig = &DEFCONTIG) { /*{{{*/ +#else template T* xNew(unsigned int size) { /*{{{*/ +#endif #ifdef USE_CXX_MEMORY_MANAGMENT_FOR_NON_POD_TYPES T* aT_p=new T[size]; @@ -49,7 +56,16 @@ #endif }/*}}}*/ +// AD (mostly ADOLC) is sensitive to calls to ensurecontiguous. These changes limit its use. +#ifdef _HAVE_AD_ +template T* xNewZeroInit(unsigned int size,const char* const contig = &DEFCONTIG) {/*{{{*/ +#else template T* xNewZeroInit(unsigned int size) {/*{{{*/ +#endif #ifdef USE_CXX_MEMORY_MANAGMENT_FOR_NON_POD_TYPES +#ifdef _HAVE_AD_ + T* aT_p=xNew(size,contig); +#else T* aT_p=xNew(size); +#endif for (unsigned int i=0; i adouble* xNew(unsigned int size); +template <> adouble* xNew(unsigned int size, const char* const contig); #endif Index: /issm/trunk/src/c/shared/io/Marshalling/IoCodeConversions.cpp =================================================================== --- /issm/trunk/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 21728) +++ /issm/trunk/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 21729) @@ -28,4 +28,34 @@ fieldname=xNew((strlen(field)+1)); xMemCpy(fieldname,field,(strlen(field)+1)); } + else if(strcmp(string_in,"SmbAccumulation")==0){ + const char* field = "md.smb.accumulation"; + param_enum = SmbAccumulationEnum; + fieldname=xNew((strlen(field)+1)); xMemCpy(fieldname,field,(strlen(field)+1)); + } + else if(strcmp(string_in,"SmbMelt")==0){ + const char* field = "md.smb.melt"; + param_enum = SmbMeltEnum; + fieldname=xNew((strlen(field)+1)); xMemCpy(fieldname,field,(strlen(field)+1)); + } + else if(strcmp(string_in,"SmbRefreeze")==0){ + const char* field = "md.smb.refreeze"; + param_enum = SmbRefreezeEnum; + fieldname=xNew((strlen(field)+1)); xMemCpy(fieldname,field,(strlen(field)+1)); + } + else if(strcmp(string_in,"SmbRunoff")==0){ + const char* field = "md.smb.runoff"; + param_enum = SmbRunoffEnum; + fieldname=xNew((strlen(field)+1)); xMemCpy(fieldname,field,(strlen(field)+1)); + } + else if(strcmp(string_in,"SmbEvaporation")==0){ + const char* field = "md.smb.evaporation"; + param_enum = SmbEvaporationEnum; + fieldname=xNew((strlen(field)+1)); xMemCpy(fieldname,field,(strlen(field)+1)); + } + else if(strcmp(string_in,"BasalforcingsFloatingiceMeltingRate")==0){ + const char* field = "md.basalforcings.floatingice_melting_rate"; + param_enum = BasalforcingsFloatingiceMeltingRateEnum; + fieldname=xNew((strlen(field)+1)); xMemCpy(fieldname,field,(strlen(field)+1)); + } else if(strcmp(string_in,"FrictionCoefficient")==0){ const char* field = "md.friction.coefficient"; @@ -52,4 +82,5 @@ case 7: return SMBhenningEnum; case 8: return SMBgembEnum; + case 9: return SMBgradientselaEnum; default: _error_("Marshalled SMB code \""<SetCurrentConfiguration(HydrologyDCEfficientAnalysisEnum); /*updating mask*/ + if(VerboseSolution()) _printf0_("==updating mask...\n"); femmodel->HydrologyEPLupdateDomainx(&ThickCount); inefanalysis->ElementizeEplMask(femmodel); @@ -170,5 +171,4 @@ /*{{{*//*Retrieve the EPL head slopes and compute EPL Thickness*/ if(VerboseSolution()) _printf0_("computing EPL Head slope...\n"); - //inefanalysis->ElementizeEplMask(femmodel); femmodel->SetCurrentConfiguration(L2ProjectionEPLAnalysisEnum); femmodel->UpdateConstraintsL2ProjectionEPLx(&L2Count); Index: /issm/trunk/src/c/solutionsequences/solutionsequence_linear.cpp =================================================================== --- /issm/trunk/src/c/solutionsequences/solutionsequence_linear.cpp (revision 21728) +++ /issm/trunk/src/c/solutionsequences/solutionsequence_linear.cpp (revision 21729) @@ -19,4 +19,5 @@ Vector* ys = NULL; int configuration_type; + IssmDouble solver_residue_threshold; /*solver convergence test: */ @@ -27,8 +28,7 @@ Vector* KUF=NULL; - - /*Recover parameters: */ femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); + femmodel->parameters->FindParam(&solver_residue_threshold,SettingsSolverResidueThresholdEnum); femmodel->UpdateConstraintsx(); SystemMatricesx(&Kff,&Kfs,&pf,&df,NULL,femmodel); @@ -47,5 +47,7 @@ nF=pf->Norm(NORM_TWO); solver_residue=nKUF/nF; - if(solver_residue>1.e-6)_error_(" solver residue too high!: norm(KU-F)/norm(F)=" << solver_residue << "\n"); + + if(!xIsNan(solver_residue_threshold) && solver_residue>solver_residue_threshold)_error_(" solver residue too high!: norm(KU-F)/norm(F)=" << solver_residue << "\n"); + //clean up Index: /issm/trunk/src/c/solutionsequences/solutionsequence_nonlinear.cpp =================================================================== --- /issm/trunk/src/c/solutionsequences/solutionsequence_nonlinear.cpp (revision 21728) +++ /issm/trunk/src/c/solutionsequences/solutionsequence_nonlinear.cpp (revision 21729) @@ -101,5 +101,5 @@ } - if(VerboseConvergence()) _printf0_("\n total number of iterations: " << count-1 << "\n"); + if(VerboseConvergence()) _printf0_("\n total number of iterations: " << count << "\n"); /*clean-up*/ Index: /issm/trunk/src/c/toolkits/gsl/DenseGslSolve.cpp =================================================================== --- /issm/trunk/src/c/toolkits/gsl/DenseGslSolve.cpp (revision 21728) +++ /issm/trunk/src/c/toolkits/gsl/DenseGslSolve.cpp (revision 21729) @@ -216,6 +216,11 @@ if(Kff_M!=Kff_N)_error_("Stiffness matrix should be square!"); - ensureContiguousLocations(Kff_N); +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + IssmDouble *x = xNew(Kff_N,"t"); +#else IssmDouble *x = xNew(Kff_N); +#endif SolverxSeq(x,Kff,pf,Kff_N,parameters); @@ -227,7 +232,12 @@ void SolverxSeq(IssmDouble *X,IssmDouble *A,IssmDouble *B,int n, Parameters* parameters){/*{{{*/ // pack inputs to conform to the EDF-prescribed interface - // ensure a contiguous block of locations: - ensureContiguousLocations(n*(n+1)); - IssmDouble* adoubleEDFin=xNew(n*(n+1)); // packed inputs, i.e. matrix and right hand side +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + IssmDouble* adoubleEDFin=xNew(n*(n+1),"t"); +#else + IssmDouble* adoubleEDFin=xNew(n*(n+1)); +#endif + // packed inputs, i.e. matrix and right hand side for(int i=0; i(size); col_indices_fromcpu[i]=xNew(size); +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + values_fromcpu[i]=xNew(size,"t"); +#else values_fromcpu[i]=xNew(size); +#endif + modes_fromcpu[i]=xNew(size); } @@ -492,5 +499,12 @@ row_indices_forcpu = xNew(total_size); col_indices_forcpu = xNew(total_size); +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + values_forcpu = xNew(total_size,"t"); +#else values_forcpu = xNew(total_size); +#endif + modes_forcpu = xNew(total_size); Index: /issm/trunk/src/c/toolkits/issm/IssmMpiVec.h =================================================================== --- /issm/trunk/src/c/toolkits/issm/IssmMpiVec.h (revision 21728) +++ /issm/trunk/src/c/toolkits/issm/IssmMpiVec.h (revision 21729) @@ -67,5 +67,12 @@ if(this->M){ +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + this->vector=xNew(this->m,"t"); +#else this->vector=xNew(this->m); +#endif + xMemCpy(this->vector,buffer,this->m); } @@ -80,5 +87,12 @@ if(this->m){ +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + this->vector=xNew(this->m,"t"); +#else this->vector=xNew(this->m); +#endif + xMemCpy(this->vector,buffer,this->m); } @@ -102,5 +116,12 @@ /*Allocate: */ +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + if (m)this->vector=xNewZeroInit(this->m,"t"); +#else if (m)this->vector=xNewZeroInit(this->m); +#endif + } /*}}}*/ @@ -196,5 +217,12 @@ if(size){ row_indices_fromcpu[i]=xNew(size); +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + values_fromcpu[i]=xNew(size,"t"); +#else values_fromcpu[i]=xNew(size); +#endif + modes_fromcpu[i]=xNew(size); } @@ -375,5 +403,12 @@ /*Allocate: */ +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + buffer=xNew(M,"t"); +#else buffer=xNew(M); +#endif + recvcounts=xNew(num_procs); displs=xNew(num_procs); @@ -527,5 +562,12 @@ /*Allocate buffers: */ row_indices_forcpu = xNew(total_size); +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + values_forcpu = xNew(total_size,"t"); +#else values_forcpu = xNew(total_size); +#endif + modes_forcpu = xNew(total_size); Index: /issm/trunk/src/c/toolkits/mumps/MumpsSolve.cpp =================================================================== --- /issm/trunk/src/c/toolkits/mumps/MumpsSolve.cpp (revision 21728) +++ /issm/trunk/src/c/toolkits/mumps/MumpsSolve.cpp (revision 21729) @@ -167,5 +167,12 @@ } /*Deal with right hand side. We need to ISSM_MPI_Gather it onto cpu 0: */ +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + rhs=xNew(pf_M,"t"); +#else rhs=xNew(pf_M); +#endif + recvcounts=xNew(num_procs); @@ -246,5 +253,12 @@ } /*Deal with right hand side. We need to ISSM_MPI_Gather it onto cpu 0: */ +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + rhs=xNew(pf_M,"t"); +#else rhs=xNew(pf_M); +#endif + recvcounts=xNew(num_procs); @@ -314,5 +328,12 @@ packedDimsSparseArr[3+local_nnz+i]=jcn_loc[i]; } +// AD performance is sensitive to calls to ensurecontiguous. +// Providing "t" will cause ensurecontiguous to be called. +#ifdef _HAVE_AD_ + IssmDouble *pack_A_rhs=xNew(local_nnz+n,"t"); +#else IssmDouble *pack_A_rhs=xNew(local_nnz+n); +#endif + for (int i=0;i(n,"t"); +#else IssmDouble *sol=xNew(n); +#endif + call_ext_fct(xDynamicCast * >(parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p, packedDimsSparseArrLength, packedDimsSparseArr, Index: /issm/trunk/src/m/Makefile.am =================================================================== --- /issm/trunk/src/m/Makefile.am (revision 21728) +++ /issm/trunk/src/m/Makefile.am (revision 21729) @@ -95,5 +95,5 @@ ${ISSM_DIR}/src/m/classes/friction.js \ ${ISSM_DIR}/src/m/classes/geometry.js \ - ${ISSM_DIR}/src/m/classes/gia.js \ + ${ISSM_DIR}/src/m/classes/giaivins.js \ ${ISSM_DIR}/src/m/classes/esa.js \ ${ISSM_DIR}/src/m/classes/groundingline.js \ Index: /issm/trunk/src/m/boundaryconditions/love_numbers.py =================================================================== --- /issm/trunk/src/m/boundaryconditions/love_numbers.py (revision 21728) +++ /issm/trunk/src/m/boundaryconditions/love_numbers.py (revision 21729) @@ -1,5 +1,5 @@ from MatlabFuncs import * from model import * -from np.import * +import numpy as np def love_numbers(value,*varargin): @@ -17,10009 +17,10009 @@ raise RuntimeError('love_numbers error message: wrong usage') - if not ( strcmpi(value,'h') | strcmpi(value,'k') | strcmpi(value,'l') | strcmpi(value,'gamma') | strcmpi(value,'lambda')): + if value not in ['h','k','l','gamma','lambda']: raise RuntimeError('value should be one of ''h'',''k'',''l'',''gamma'' and ''lambda''') - love_numbers=array([\ -[ 0 , 0 ,0 ,0 ,0 ,0 ,0 ],\ -[ -1.28740059,-1.00000000,-0.89858519,1.28740059, 0.42519882 ,0.89858519 ,0.00000000 ],\ -[ -1.00025365, -0.30922675, 0.02060926, 1.69102690, 0.46358648, 0.67016399, 0.61829668],\ -[ -1.06243501, -0.19927948, 0.06801636, 1.86315553, 0.55741597, 0.73270416, 0.56270589],\ -[ -1.06779588, -0.13649834, 0.05667027, 1.93129754, 0.63672498, 0.80683140, 0.51132745],\ -[ -1.10365923, -0.10736896, 0.04401221, 1.99629027, 0.68737906, 0.84861883, 0.48642259],\ -[ -1.16440348, -0.09295485, 0.03638747, 2.07144863, 0.72031283, 0.87065768, 0.47898268],\ -[ -1.23634156, -0.08469861, 0.03202759, 2.15164295, 0.74355796, 0.88327380, 0.47955214],\ -[ -1.31140380, -0.07921412, 0.02937593, 2.23218968, 0.76126493, 0.89140995, 0.48323250],\ -[ -1.38582399, -0.07513541, 0.02762338, 2.31068858, 0.77552290, 0.89724121, 0.48795424],\ -[ -1.45807465, -0.07187005, 0.02638627, 2.38620460, 0.78744212, 0.90174369, 0.49291061],\ -[ -1.52763314, -0.06913154, 0.02547640, 2.45850160, 0.79766475, 0.90539206, 0.49779422],\ -[ -1.59437866, -0.06676258, 0.02479080, 2.52761607, 0.80659635, 0.90844662, 0.50248477],\ -[ -1.65833071, -0.06466619, 0.02426511, 2.59366452, 0.81451271, 0.91106870, 0.50693175],\ -[ -1.71954820, -0.06277732, 0.02385464, 2.65677088, 0.82161167, 0.91336804, 0.51111243],\ -[ -1.77809640, -0.06105001, 0.02352654, 2.71704639, 0.82804049, 0.91542346, 0.51501712],\ -[ -1.83403970, -0.05945081, 0.02325609, 2.77458889, 0.83391153, 0.91729309, 0.51864363],\ -[ -1.88744242, -0.05795502, 0.02302469, 2.82948740, 0.83931209, 0.91902029, 0.52199490],\ -[ -1.93837115, -0.05654418, 0.02281843, 2.88182697, 0.84431095, 0.92063739, 0.52507761],\ -[ -1.98689666, -0.05520447, 0.02262706, 2.93169219, 0.84896295, 0.92216847, 0.52790108],\ -[ -2.03309477, -0.05392545, 0.02244322, 2.97916932, 0.85331225, 0.92363132, 0.53047654],\ -[ -2.07704643, -0.05269926, 0.02226173, 3.02434717, 0.85739480, 0.92503902, 0.53281639],\ -[ -2.11883714, -0.05151988, 0.02207909, 3.06731726, 0.86124014, 0.92640103, 0.53493369],\ -[ -2.15855611, -0.05038274, 0.02189307, 3.10817337, 0.86487276, 0.92772419, 0.53684176],\ -[ -2.19629514, -0.04928430, 0.02170238, 3.14701084, 0.86831322, 0.92901331, 0.53855386],\ -[ -2.23214747, -0.04822179, 0.02150643, 3.18392568, 0.87157886, 0.93027178, 0.54008294],\ -[ -2.26620674, -0.04719301, 0.02130509, 3.21901373, 0.87468453, 0.93150190, 0.54144148],\ -[ -2.29856595, -0.04619619, 0.02109858, 3.25236976, 0.87764301, 0.93270523, 0.54264140],\ -[ -2.32931659, -0.04522983, 0.02088735, 3.28408675, 0.88046543, 0.93388282, 0.54369397],\ -[ -2.35854794, -0.04429270, 0.02067197, 3.31425524, 0.88316156, 0.93503533, 0.54460979],\ -[ -2.38634650, -0.04338368, 0.02045310, 3.34296281, 0.88574004, 0.93616321, 0.54539877],\ -[ -2.41279547, -0.04250179, 0.02023142, 3.37029367, 0.88820859, 0.93726678, 0.54607015],\ -[ -2.43797451, -0.04164613, 0.02000761, 3.39632839, 0.89057416, 0.93834626, 0.54663248],\ -[ -2.46195951, -0.04081583, 0.01978231, 3.42114367, 0.89284301, 0.93940185, 0.54709369],\ -[ -2.48482241, -0.04001011, 0.01955614, 3.44481230, 0.89502085, 0.94043375, 0.54746112],\ -[ -2.50663126, -0.03922817, 0.01932966, 3.46740309, 0.89711291, 0.94144217, 0.54774153],\ -[ -2.52745016, -0.03846928, 0.01910337, 3.48898088, 0.89912397, 0.94242735, 0.54794114],\ -[ -2.54733938, -0.03773269, 0.01887774, 3.50960670, 0.90105847, 0.94338957, 0.54806571],\ -[ -2.56635547, -0.03701769, 0.01865317, 3.52933779, 0.90292050, 0.94432915, 0.54812051],\ -[ -2.58455138, -0.03632358, 0.01843000, 3.54822780, 0.90471386, 0.94524642, 0.54811044],\ -[ -2.60197665, -0.03564968, 0.01820854, 3.56632697, 0.90644209, 0.94614178, 0.54803997],\ -[ -2.61867756, -0.03499532, 0.01798905, 3.58368224, 0.90810850, 0.94701563, 0.54791326],\ -[ -2.63469733, -0.03435985, 0.01777176, 3.60033748, 0.90971616, 0.94786840, 0.54773413],\ -[ -2.65007629, -0.03374263, 0.01755683, 3.61633367, 0.91126798, 0.94870054, 0.54750610],\ -[ -2.66485208, -0.03314303, 0.01734443, 3.63170905, 0.91276665, 0.94951253, 0.54723245],\ -[ -2.67905981, -0.03256047, 0.01713468, 3.64649934, 0.91421471, 0.95030485, 0.54691620],\ -[ -2.69273222, -0.03199435, 0.01692767, 3.66073787, 0.91561457, 0.95107798, 0.54656015],\ -[ -2.70589990, -0.03144411, 0.01672347, 3.67445580, 0.91696845, 0.95183242, 0.54616691],\ -[ -2.71859139, -0.03090919, 0.01652215, 3.68768220, 0.91827849, 0.95256866, 0.54573889],\ -[ -2.73083334, -0.03038907, 0.01632374, 3.70044427, 0.91954667, 0.95328719, 0.54527835],\ -[ -2.74265068, -0.02988323, 0.01612826, 3.71276745, 0.92077487, 0.95398851, 0.54478739],\ -[ -2.75406669, -0.02939118, 0.01593573, 3.72467551, 0.92196486, 0.95467309, 0.54426797],\ -[ -2.76510320, -0.02891245, 0.01574615, 3.73619076, 0.92311833, 0.95534141, 0.54372191],\ -[ -2.77578063, -0.02844656, 0.01555950, 3.74733406, 0.92423685, 0.95599393, 0.54315095],\ -[ -2.78611812, -0.02799309, 0.01537578, 3.75812503, 0.92532192, 0.95663113, 0.54255669],\ -[ -2.79613364, -0.02755161, 0.01519496, 3.76858203, 0.92637496, 0.95725343, 0.54194065],\ -[ -2.80584405, -0.02712170, 0.01501701, 3.77872235, 0.92739730, 0.95786128, 0.54130424],\ -[ -2.81526521, -0.02670298, 0.01484191, 3.78856223, 0.92839022, 0.95845511, 0.54064880],\ -[ -2.82441204, -0.02629506, 0.01466961, 3.79811697, 0.92935491, 0.95903532, 0.53997561],\ -[ -2.83329857, -0.02589759, 0.01450009, 3.80740098, 0.93029251, 0.95960232, 0.53928586],\ -[ -2.84193804, -0.02551021, 0.01433329, 3.81642782, 0.93120412, 0.96015649, 0.53858067],\ -[ -2.85034293, -0.02513260, 0.01416919, 3.82521033, 0.93209074, 0.96069821, 0.53786112],\ -[ -2.85852503, -0.02476443, 0.01400773, 3.83376061, 0.93295337, 0.96122784, 0.53712821],\ -[ -2.86649548, -0.02440538, 0.01384888, 3.84209010, 0.93379291, 0.96174574, 0.53638291],\ -[ -2.87426481, -0.02405518, 0.01369258, 3.85020963, 0.93461026, 0.96225224, 0.53562612],\ -[ -2.88184299, -0.02371352, 0.01353880, 3.85812947, 0.93540625, 0.96274768, 0.53485873],\ -[ -2.88923945, -0.02338014, 0.01338749, 3.86585931, 0.93618168, 0.96323236, 0.53408154],\ -[ -2.89646316, -0.02305478, 0.01323861, 3.87340838, 0.93693730, 0.96370661, 0.53329534],\ -[ -2.90352261, -0.02273718, 0.01309211, 3.88078542, 0.93767383, 0.96417071, 0.53250089],\ -[ -2.91042585, -0.02242710, 0.01294795, 3.88799874, 0.93839197, 0.96462494, 0.53169888],\ -[ -2.91718054, -0.02212431, 0.01280609, 3.89505623, 0.93909236, 0.96506960, 0.53089002],\ -[ -2.92379397, -0.02182859, 0.01266648, 3.90196538, 0.93977564, 0.96550493, 0.53007493],\ -[ -2.93027306, -0.02153971, 0.01252908, 3.90873334, 0.94044240, 0.96593120, 0.52925424],\ -[ -2.93662439, -0.02125748, 0.01239386, 3.91536691, 0.94109322, 0.96634866, 0.52842854],\ -[ -2.94285425, -0.02098169, 0.01226077, 3.92187256, 0.94172863, 0.96675754, 0.52759839],\ -[ -2.94896860, -0.02071215, 0.01212977, 3.92825645, 0.94234915, 0.96715808, 0.52676434],\ -[ -2.95497314, -0.02044868, 0.01200082, 3.93452446, 0.94295529, 0.96755050, 0.52592690],\ -[ -2.96087331, -0.02019110, 0.01187388, 3.94068220, 0.94354752, 0.96793501, 0.52508656],\ -[ -2.96667427, -0.01993924, 0.01174893, 3.94673503, 0.94412630, 0.96831183, 0.52424380],\ -[ -2.97238097, -0.01969293, 0.01162591, 3.95268804, 0.94469206, 0.96868116, 0.52339906],\ -[ -2.97799813, -0.01945201, 0.01150481, 3.95854612, 0.94524521, 0.96904318, 0.52255277],\ -[ -2.98353025, -0.01921634, 0.01138557, 3.96431391, 0.94578617, 0.96939809, 0.52170535],\ -[ -2.98898162, -0.01898576, 0.01126817, 3.96999586, 0.94631531, 0.96974607, 0.52085719],\ -[ -2.99435636, -0.01876014, 0.01115257, 3.97559622, 0.94683300, 0.97008729, 0.52000868],\ -[ -2.99965838, -0.01853932, 0.01103875, 3.98111905, 0.94733959, 0.97042193, 0.51916016],\ -[ -3.00489143, -0.01832319, 0.01092666, 3.98656824, 0.94783543, 0.97075015, 0.51831198],\ -[ -3.01005909, -0.01811161, 0.01081628, 3.99194748, 0.94832084, 0.97107211, 0.51746448],\ -[ -3.01516479, -0.01790446, 0.01070757, 3.99726033, 0.94879613, 0.97138796, 0.51661796],\ -[ -3.02021180, -0.01770162, 0.01060052, 4.00251017, 0.94926160, 0.97169786, 0.51577273],\ -[ -3.02520323, -0.01750298, 0.01049508, 4.00770025, 0.94971755, 0.97200194, 0.51492908],\ -[ -3.03014209, -0.01730842, 0.01039123, 4.01283367, 0.95016424, 0.97230035, 0.51408727],\ -[ -3.03503122, -0.01711783, 0.01028894, 4.01791339, 0.95060195, 0.97259323, 0.51324758],\ -[ -3.03987336, -0.01693111, 0.01018819, 4.02294225, 0.95103094, 0.97288070, 0.51241024],\ -[ -3.04467112, -0.01674816, 0.01008894, 4.02792295, 0.95145145, 0.97316290, 0.51157550],\ -[ -3.04942699, -0.01656889, 0.00999117, 4.03285810, 0.95186373, 0.97343995, 0.51074358],\ -[ -3.05414335, -0.01639319, 0.00989485, 4.03775017, 0.95226799, 0.97371196, 0.50991471],\ -[ -3.05882250, -0.01622097, 0.00979997, 4.04260153, 0.95266447, 0.97397906, 0.50908908],\ -[ -3.06346660, -0.01605215, 0.00970649, 4.04741445, 0.95305338, 0.97424136, 0.50826689],\ -[ -3.06807773, -0.01588664, 0.00961439, 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0.49327197], + [ -6.27342756, -0.00030954, 0.00018961, 7.27311801, 0.99905451, 0.99950084, 0.49327183], + [ -6.27342763, -0.00030951, 0.00018959, 7.27311812, 0.99905461, 0.99950089, 0.49327208], + [ -6.27342771, -0.00030948, 0.00018957, 7.27311822, 0.99905470, 0.99950094, 0.49327205], + [ -6.27342778, -0.00030945, 0.00018956, 7.27311833, 0.99905480, 0.99950099, 0.49327194]]); + if value=='h': Index: /issm/trunk/src/m/classes/SMBd18opdd.m =================================================================== --- /issm/trunk/src/m/classes/SMBd18opdd.m (revision 21728) +++ /issm/trunk/src/m/classes/SMBd18opdd.m (revision 21729) @@ -12,4 +12,5 @@ rlapslgm = 0; dpermil = 0; + f = 0; Tdiff = NaN; sealev = NaN; @@ -63,4 +64,5 @@ self.rlapslgm = 6.5; self.dpermil = 2.4; + self.f = 0.169; end % }}} @@ -78,4 +80,5 @@ md = checkfield(md,'fieldname','smb.delta18o','NaN',1,'Inf',1,'size',[2,NaN],'singletimeseries',1); md = checkfield(md,'fieldname','smb.dpermil','>=',0,'numel',1); + md = checkfield(md,'fieldname','smb.f','>=',0,'numel',1); end end @@ -96,4 +99,5 @@ fielddisplay(self,'delta18o','delta18o [per mil], required if pdd is activated and d18opd activated'); fielddisplay(self,'dpermil','degree per mil, required if d18opd is activated'); + fielddisplay(self,'f','precip/temperature scaling factor, required if d18opd is activated'); end fielddisplay(self,'requested_outputs','additional outputs requested'); @@ -123,4 +127,5 @@ WriteData(fid,prefix,'object',self,'class','smb','fieldname','delta18o','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts); WriteData(fid,prefix,'object',self,'class','smb','fieldname','dpermil','format','Double'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','f','format','Double'); end Index: /issm/trunk/src/m/classes/SMBd18opdd.py =================================================================== --- /issm/trunk/src/m/classes/SMBd18opdd.py (revision 21728) +++ /issm/trunk/src/m/classes/SMBd18opdd.py (revision 21729) @@ -20,4 +20,5 @@ self.rlapslgm = 0. self.dpermil = 0. + self.f = 0. self.Tdiff = float('NaN') self.sealev = float('NaN') @@ -83,5 +84,5 @@ self.rlapslgm = 6.5 self.dpermil = 2.4 - + self.f = 0.169 return self #}}} @@ -100,5 +101,6 @@ md = checkfield(md,'fieldname','smb.delta18o','NaN',1,'Inf',1,'size',[2,np.nan],'singletimeseries',1) md = checkfield(md,'fieldname','smb.dpermil','>=',0,'numel',[1]) - + md = checkfield(md,'fieldname','smb.f','>=',0,'numel',[1]) + md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1) @@ -126,5 +128,5 @@ WriteData(fid,prefix,'object',self,'class','smb','fieldname','delta18o','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts) WriteData(fid,prefix,'object',self,'class','smb','fieldname','dpermil','format','Double') - + WriteData(fid,prefix,'object',self,'class','smb','fieldname','f','format','Double') #process requested outputs outputs = self.requested_outputs Index: /issm/trunk/src/m/classes/SMBforcing.m =================================================================== --- /issm/trunk/src/m/classes/SMBforcing.m (revision 21728) +++ /issm/trunk/src/m/classes/SMBforcing.m (revision 21729) @@ -69,4 +69,5 @@ WriteData(fid,prefix,'name','md.smb.model','data',1,'format','Integer'); WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + %WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','CompressedMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); %process requested outputs Index: /issm/trunk/src/m/classes/SMBforcing.py =================================================================== --- /issm/trunk/src/m/classes/SMBforcing.py (revision 21728) +++ /issm/trunk/src/m/classes/SMBforcing.py (revision 21729) @@ -56,4 +56,5 @@ WriteData(fid,prefix,'name','md.smb.model','data',1,'format','Integer'); WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + #WriteData(fid,prefix,'object',self,'class','smb','fieldname','mass_balance','format','CompressedMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); #process requested outputs Index: /issm/trunk/src/m/classes/SMBgradientsela.m =================================================================== --- /issm/trunk/src/m/classes/SMBgradientsela.m (revision 21729) +++ /issm/trunk/src/m/classes/SMBgradientsela.m (revision 21729) @@ -0,0 +1,88 @@ +%SMBgradientsela Class definition +% +% Usage: +% SMBgradientsela=SMBgradientsela(); + +classdef SMBgradientsela + properties (SetAccess=public) + ela = NaN; + b_pos = NaN; + b_neg = NaN; + b_max = NaN; + b_min = NaN; + requested_outputs = {}; + end + methods + function self = SMBgradientsela(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + otherwise + error('constructor not supported'); + end + end % }}} + function self = extrude(self,md) % {{{ + + %Nothing for now + + end % }}} + function list = defaultoutputs(self,md) % {{{ + list = {''}; + end % }}} + function self = initialize(self,md) % {{{ + + %Nothing done for now + + end % }}} + function self = setdefaultparameters(self) % {{{ + + self.b_max=9999; + self.b_min=-9999; + + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + + if ismember('MasstransportAnalysis',analyses), + md = checkfield(md,'fieldname','smb.ela','timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.b_pos','timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.b_neg','timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.b_max','timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.b_min','timeseries',1,'NaN',1,'Inf',1); + end + md = checkfield(md,'fieldname','smb.requested_outputs','stringrow',1); + end % }}} + function disp(self) % {{{ + disp(sprintf(' surface forcings parameters:')); + + disp(sprintf('\n SMB gradients ela parameters:')); + fielddisplay(self,'ela',' equilibrium line altitude from which deviation is used to calculate smb using the smb gradients ela method [m a.s.l.]'); + fielddisplay(self,'b_pos',' vertical smb gradient (dB/dz) above ela'); + fielddisplay(self,'b_neg',' vertical smb gradient (dB/dz) below ela'); + fielddisplay(self,'b_max',' upper cap on smb rate, default: 9999 (no cap) [m ice eq./yr] '); + fielddisplay(self,'b_min',' lower cap on smb rate, default: -9999 (no cap) [m ice eq./yr]'); + fielddisplay(self,'requested_outputs','additional outputs requested'); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ + + yts=md.constants.yts; + + WriteData(fid,prefix,'name','md.smb.model','data',9,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','ela','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_pos','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_neg','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_max','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_min','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + + %process requested outputs + outputs = self.requested_outputs; + pos = find(ismember(outputs,'default')); + if ~isempty(pos), + outputs(pos) = []; %remove 'default' from outputs + outputs = [outputs defaultoutputs(self,md)]; %add defaults + end + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray'); + + end % }}} + end +end Index: /issm/trunk/src/m/classes/SMBgradientsela.py =================================================================== --- /issm/trunk/src/m/classes/SMBgradientsela.py (revision 21729) +++ /issm/trunk/src/m/classes/SMBgradientsela.py (revision 21729) @@ -0,0 +1,80 @@ +from fielddisplay import fielddisplay +from checkfield import checkfield +from WriteData import WriteData +from project3d import project3d + +class SMBgradientsela(object): + """ + SMBgradientsela Class definition + + Usage: + SMBgradientsela=SMBgradientsela(); + """ + + def __init__(self): # {{{ + self.ela = float('NaN') + self.b_pos = float('NaN') + self.b_neg = float('NaN') + self.b_max = float('NaN') + self.b_min = float('NaN') + self.requested_outputs = [] + #}}} + def __repr__(self): # {{{ + string=" surface forcings parameters:" + + string="%s\n%s"%(string,fielddisplay(self,'issmbgradientsela','is smb gradients ela method activated (0 or 1, default is 0)')) + string="%s\n%s"%(string,fielddisplay(self,'ela',' equilibrium line altitude from which deviation is used to calculate smb using the smb gradients ela method [m a.s.l.]')) + string="%s\n%s"%(string,fielddisplay(self,'b_pos',' vertical smb gradient (dB/dz) above ela')) + string="%s\n%s"%(string,fielddisplay(self,'b_neg',' vertical smb gradient (dB/dz) below ela')) + string="%s\n%s"%(string,fielddisplay(self,'b_max',' upper cap on smb rate, default: 9999 (no cap) [m ice eq./yr]')) + string="%s\n%s"%(string,fielddisplay(self,'b_min',' lower cap on smb rate, default: -9999 (no cap) [m ice eq./yr]')) + string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested')) + + return string + #}}} + def extrude(self,md): # {{{ + + #Nothing for now + return self + #}}} + def defaultoutputs(self,md): # {{{ + return [] + #}}} + def initialize(self,md): # {{{ + + #Nothing for now + + return self + #}}} + def checkconsistency(self,md,solution,analyses): # {{{ + + if 'MasstransportAnalysis' in analyses: + md = checkfield(md,'fieldname','smb.ela','timeseries',1,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.b_pos','timeseries',1,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.b_neg','timeseries',1,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.b_max','timeseries',1,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.b_min','timeseries',1,'NaN',1,'Inf',1) + + md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1) + return md + # }}} + def marshall(self,prefix,md,fid): # {{{ + + yts=md.constants.yts + + WriteData(fid,prefix,'name','md.smb.model','data',9,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','ela','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_pos','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_neg','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_max','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','b_min','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) + + #process requested outputs + outputs = self.requested_outputs + indices = [i for i, x in enumerate(outputs) if x == 'default'] + if len(indices) > 0: + outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] + outputs =outputscopy + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') + + # }}} Index: /issm/trunk/src/m/classes/amr.js =================================================================== --- /issm/trunk/src/m/classes/amr.js (revision 21729) +++ /issm/trunk/src/m/classes/amr.js (revision 21729) @@ -0,0 +1,56 @@ +//AMR class definition +// +// Usage: +// amr=new amr(); + +function amr (){ + //methods + this.setdefaultparameters = function(){// {{{ + //level_max: 2 to 4 + this.level_max=2; + + //region_level_1: region around (m) the discontinuity (grounding line or ice front) where the mesh will be refined once (h=1). + this.region_level_1=20000.; + + //region_level_max: region around (m) the discontinuity (grounding line or ice front) where the mesh will be refined with max level of refinement (h=level_max). + this.region_level_max=15000.; + }// }}} + this.disp= function(){// {{{ + + console.log(sprintf(' amr parameters:')); + fielddisplay(this,'level_max','maximum refinement level (1, 2, 3 or 4)'); + fielddisplay(this,'region_level_1','region which will be refined once (level 1) [ m ]'); + fielddisplay(this,'region_level_max','region which will be refined with level_max [ m ]'); + + }// }}} + this.classname= function(){// {{{ + return "amr"; + + }// }}} + this.checkconsistency = function(md,solution,analyses) { //{{{ + + checkfield(md,'fieldname','amr.level_max','numel',[1],'>=',0,'<=',4); + checkfield(md,'fieldname','amr.region_level_1','numel',[1],'>',0,'NaN',1,'Inf',1); + checkfield(md,'fieldname','amr.region_level_max','numel',[1],'>',0,'NaN',1,'Inf',1); + if (this.region_level_1-this.region_level_max<0.2*this.region_level_1){ + md.checkmessage('region_level_max should be lower than 80% of region_level_1'); + } + } // }}} + this.marshall=function(md,prefix,fid) { //{{{ + + WriteData(fid,prefix,'object',this,'fieldname','level_max','format','Integer'); + WriteData(fid,prefix,'object',this,'fieldname','region_level_1','format','Double'); + WriteData(fid,prefix,'object',this,'fieldname','region_level_max','format','Double'); + + }//}}} + this.fix=function() { //{{{ + }//}}} + //properties + // {{{ + this.level_max = 0; + this.region_level_1 = 0.; + this.region_level_max = 0.; + + this.setdefaultparameters(); + //}}} +} Index: /issm/trunk/src/m/classes/amr.m =================================================================== --- /issm/trunk/src/m/classes/amr.m (revision 21729) +++ /issm/trunk/src/m/classes/amr.m (revision 21729) @@ -0,0 +1,65 @@ +%AMR Class definition +% +% Usage: +% amr=amr(); + +classdef amr + properties (SetAccess=public) + level_max = 0; + region_level_1 = 0; + region_level_max = 0; + end + methods + function self = amr(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + otherwise + error('constructor not supported'); + end + end % }}} + function self = setdefaultparameters(self) % {{{ + + %level_max: 2 to 4 + self.level_max=2; + + %region_level_1: region around (m) the discontinuity (grounding line or ice front) where the mesh will be refined once (h=1). + self.region_level_1=20000.; + + %region_level_max: region around (m) the discontinuity (grounding line or ice front) where the mesh will be refined with max level of refinement (h=level_max). + self.region_level_max=15000.; + + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + + md = checkfield(md,'fieldname','amr.level_max','numel',[1],'>=',0,'<=',4); + md = checkfield(md,'fieldname','amr.region_level_1','numel',[1],'>',0,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','amr.region_level_max','numel',[1],'>',0,'NaN',1,'Inf',1); + if self.region_level_1-self.region_level_max<0.2*self.region_level_1, %it was adopted 20% of the region_level_1 + md = checkmessage(md,'region_level_max should be lower than 80% of region_level_1'); + end + end % }}} + function disp(self) % {{{ + disp(sprintf(' amr parameters:')); + + fielddisplay(self,'level_max',['maximum refinement level (1, 2, 3 or 4)']); + fielddisplay(self,'region_level_1',['region which will be refined once (level 1) [ m ]']); + fielddisplay(self,'region_level_max',['region which will be refined with level_max [ m ]']); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ + + scale = md.constants.yts; + WriteData(fid,prefix,'object',self,'fieldname','level_max','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','region_level_1','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','region_level_max','format','Double'); + end % }}} + function savemodeljs(self,fid,modelname) % {{{ + + writejsdouble(fid,[modelname '.amr.level_max'],self.level_max); + writejsdouble(fid,[modelname '.amr.region_level_1'],self.region_level_1); + writejsdouble(fid,[modelname '.amr.region_level_max'],self.region_level_max); + + end % }}} + end +end Index: /issm/trunk/src/m/classes/amr.py =================================================================== --- /issm/trunk/src/m/classes/amr.py (revision 21729) +++ /issm/trunk/src/m/classes/amr.py (revision 21729) @@ -0,0 +1,55 @@ +from fielddisplay import fielddisplay +from checkfield import checkfield +from WriteData import WriteData + +class amr(object): + """ + AMR Class definition + + Usage: + amr=amr(); + """ + + def __init__(self): # {{{ + self.level_max = 0. + self.region_level_1 = 0. + self.region_level_max = 0. + + #set defaults + self.setdefaultparameters() + #}}} + def __repr__(self): # {{{ + string=" amr parameters:" + string="%s\n%s"%(string,fielddisplay(self,"level_max","maximum refinement level (1, 2, 3 or 4)")) + string="%s\n%s"%(string,fielddisplay(self,"region_level_1","region which will be refined once (level 1) [ m ]")) + string="%s\n%s"%(string,fielddisplay(self,"region_level_max","region which will be refined with level_max [ m ]")) + return string + #}}} + def setdefaultparameters(self): # {{{ + + #level_max: 2 to 4 + self.level_max=2 + + #region_level_1: region around (m) the discontinuity (grounding line or ice front) where the mesh will be refined once (h=1). + self.region_level_1=20000. + + #region_level_max: region around (m) the discontinuity (grounding line or ice front) where the mesh will be refined with max level of refinement (h=level_max). + self.region_level_max=15000. + + return self + #}}} + def checkconsistency(self,md,solution,analyses): # {{{ + md = checkfield(md,'fieldname','amr.level_max','numel',[1],'>=',0,'<=',4) + md = checkfield(md,'fieldname','amr.region_level_1','numel',[1],'>',0,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','amr.region_level_max','numel',[1],'>',0,'NaN',1,'Inf',1) + #it was adopted 20% of the region_level_1 + if self.region_level_1-self.region_level_max<0.2*self.region_level_1: + md.checkmessage("region_level_max should be lower than 80% of region_level_1") + + return md + # }}} + def marshall(self,prefix,md,fid): # {{{ + WriteData(fid,prefix,'object',self,'fieldname','level_max','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','region_level_1','format','Double') + WriteData(fid,prefix,'object',self,'fieldname','region_level_max','format','Double') + # }}} Index: /issm/trunk/src/m/classes/bamgmesh.m =================================================================== --- /issm/trunk/src/m/classes/bamgmesh.m (revision 21728) +++ /issm/trunk/src/m/classes/bamgmesh.m (revision 21729) @@ -10,5 +10,4 @@ Edges=[]; Triangles=[]; - Quadrilaterals=[]; IssmEdges=[]; IssmSegments=[]; Index: /issm/trunk/src/m/classes/bamgmesh.py =================================================================== --- /issm/trunk/src/m/classes/bamgmesh.py (revision 21728) +++ /issm/trunk/src/m/classes/bamgmesh.py (revision 21729) @@ -13,5 +13,4 @@ self.Edges=np.empty((0,3)) self.Triangles=np.empty((0,0)) - self.Quadrilaterals=np.empty((0,0)) self.IssmEdges=np.empty((0,0)) self.IssmSegments=np.empty((0,0)) @@ -45,5 +44,4 @@ s+=" Edges: %s\n" % str(self.Edges) s+=" Triangles: %s\n" % str(self.Triangles) - s+=" Quadrilaterals: %s\n" % str(self.Quadrilaterals) s+=" IssmEdges: %s\n" % str(self.IssmEdges) s+=" IssmSegments: %s\n" % str(self.IssmSegments) Index: /issm/trunk/src/m/classes/calvingdev.m =================================================================== --- /issm/trunk/src/m/classes/calvingdev.m (revision 21728) +++ /issm/trunk/src/m/classes/calvingdev.m (revision 21729) @@ -6,5 +6,6 @@ classdef calvingdev properties (SetAccess=public) - coeff = NaN; + stress_threshold_groundedice = 0.; + stress_threshold_floatingice = 0.; meltingrate = NaN; end @@ -29,11 +30,11 @@ end % }}} function self = extrude(self,md) % {{{ - self.coeff=project3d(md,'vector',self.coeff,'type','node'); self.meltingrate=project3d(md,'vector',self.meltingrate,'type','node'); end % }}} function self = setdefaultparameters(self) % {{{ - %Proportionality coefficient in Pi model - self.coeff=2e13; + %Default sigma max + self.stress_threshold_groundedice = 1e6; + self.stress_threshold_floatingice = 150e3; end % }}} function md = checkconsistency(self,md,solution,analyses) % {{{ @@ -41,10 +42,12 @@ if (~strcmp(solution,'TransientSolution') | md.transient.ismovingfront==0), return; end - md = checkfield(md,'fieldname','calving.coeff','>',0,'size',[md.mesh.numberofvertices 1]); + md = checkfield(md,'fieldname','calving.stress_threshold_groundedice','>',0,'numel',1,'nan',1,'Inf',1); + md = checkfield(md,'fieldname','calving.stress_threshold_floatingice','>',0,'numel',1,'nan',1,'Inf',1); md = checkfield(md,'fieldname','calving.meltingrate','NaN',1,'Inf',1,'timeseries',1,'>=',0); end % }}} function disp(self) % {{{ disp(sprintf(' Calving Pi parameters:')); - fielddisplay(self,'coeff','proportionality coefficient in Pi model'); + fielddisplay(self,'stress_threshold_groundedice','sigma_max applied to grounded ice only [Pa]'); + fielddisplay(self,'stress_threshold_floatingice','sigma_max applied to floating ice only [Pa]'); fielddisplay(self,'meltingrate','melting rate at given location [m/a]'); @@ -53,6 +56,7 @@ yts=md.constants.yts; WriteData(fid,prefix,'name','md.calving.law','data',2,'format','Integer'); - WriteData(fid,prefix,'object',self,'fieldname','coeff','format','DoubleMat','mattype',1); - WriteData(fid,prefix,'object',self,'fieldname','meltingrate','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1,'scale',1./yts); + WriteData(fid,prefix,'object',self,'fieldname','stress_threshold_groundedice','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','stress_threshold_floatingice','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','meltingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts,'scale',1./yts); end % }}} end Index: /issm/trunk/src/m/classes/calvinglevermann.m =================================================================== --- /issm/trunk/src/m/classes/calvinglevermann.m (revision 21728) +++ /issm/trunk/src/m/classes/calvinglevermann.m (revision 21729) @@ -42,5 +42,5 @@ md = checkfield(md,'fieldname','calving.coeff','>',0,'size',[md.mesh.numberofvertices 1]); - md = checkfield(md,'fieldname','calving.meltingrate','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1],'>=',0); + md = checkfield(md,'fieldname','calving.meltingrate','NaN',1,'Inf',1,'timeseries',1,'>=',0); end % }}} function disp(self) % {{{ @@ -54,5 +54,5 @@ WriteData(fid,prefix,'name','md.calving.law','data',3,'format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','coeff','format','DoubleMat','mattype',1); - WriteData(fid,prefix,'object',self,'fieldname','meltingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts,'scale',1./yts); + WriteData(fid,prefix,'object',self,'fieldname','meltingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'scale',1./yts); end % }}} end Index: /issm/trunk/src/m/classes/calvingminthickness.m =================================================================== --- /issm/trunk/src/m/classes/calvingminthickness.m (revision 21728) +++ /issm/trunk/src/m/classes/calvingminthickness.m (revision 21729) @@ -53,5 +53,5 @@ WriteData(fid,prefix,'name','md.calving.law','data',4,'format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','min_thickness','format','Double'); - WriteData(fid,prefix,'object',self,'fieldname','meltingrate','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1,'scale',1./yts); + WriteData(fid,prefix,'object',self,'fieldname','meltingrate','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'scale',1./yts); end % }}} end Index: /issm/trunk/src/m/classes/clusters/acenet.m =================================================================== --- /issm/trunk/src/m/classes/clusters/acenet.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/acenet.m (revision 21729) @@ -56,5 +56,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end Index: /issm/trunk/src/m/classes/clusters/camhpc.m =================================================================== --- /issm/trunk/src/m/classes/clusters/camhpc.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/camhpc.m (revision 21729) @@ -71,5 +71,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end Index: /issm/trunk/src/m/classes/clusters/castor.m =================================================================== --- /issm/trunk/src/m/classes/clusters/castor.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/castor.m (revision 21729) @@ -46,5 +46,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end Index: /issm/trunk/src/m/classes/clusters/cloud.m =================================================================== --- /issm/trunk/src/m/classes/clusters/cloud.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/cloud.m (revision 21729) @@ -48,5 +48,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ %write queuing script Index: /issm/trunk/src/m/classes/clusters/cosmos.m =================================================================== --- /issm/trunk/src/m/classes/clusters/cosmos.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/cosmos.m (revision 21729) @@ -46,5 +46,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end Index: /issm/trunk/src/m/classes/clusters/cyclone.py =================================================================== --- /issm/trunk/src/m/classes/clusters/cyclone.py (revision 21728) +++ /issm/trunk/src/m/classes/clusters/cyclone.py (revision 21729) @@ -72,5 +72,5 @@ return self # }}} - def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota): + def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling): # {{{ Index: /issm/trunk/src/m/classes/clusters/discover.m =================================================================== --- /issm/trunk/src/m/classes/clusters/discover.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/discover.m (revision 21729) @@ -90,5 +90,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,ioceancoupling) % {{{ if(isgprof), disp('gprof not supported by cluster, ignoring...'); end @@ -100,4 +100,7 @@ executable='issm_dakota.exe'; end + end + if isoceancoupling, + executable='issm_ocean.exe'; end Index: /issm/trunk/src/m/classes/clusters/gemini.m =================================================================== --- /issm/trunk/src/m/classes/clusters/gemini.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/gemini.m (revision 21729) @@ -46,5 +46,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end Index: /issm/trunk/src/m/classes/clusters/generic.js =================================================================== --- /issm/trunk/src/m/classes/clusters/generic.js (revision 21728) +++ /issm/trunk/src/m/classes/clusters/generic.js (revision 21729) @@ -43,9 +43,13 @@ fid=fopen(modelname+'.queue','w'); fprintf(fid,'#!%s\n',cluster.shell); - fprintf(fid,'mpiexec -np %i %s/%s %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,executable,solution,cluster.executionpath+'/'+dirname,modelname,modelname,modelname); + fprintf(fid,'mpiexec -np %i %s/%s %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,executable,EnumToString(solution),cluster.executionpath+'/'+dirname,modelname,modelname,modelname); fclose(fid); } //}}} this.UploadAndRun = function (md,callbackfunction,callbackerrorfunction,callbackid,fid,toolkitsstring,solutionstring,name,runtimename) { //{{{ - + if (!navigator.onLine) { //{{{ + $(callbackid).html(sprintf("%-16s", "NO CONNECTION")).prop("disabled", false); + callbackerrorfunction(); + return; + } //}}} var request = new XMLHttpRequest(); $(callbackid).html(sprintf("%-16s", "CONNECTING...")).prop("disabled", true); @@ -92,8 +96,10 @@ } var responseText = window.atob(request.responseText.slice(request.position + 10).replace(/\s/g, '')); - var buffer = str2ab(responseText); + var buffer = pako.inflate(str2ab(responseText)); var returnBuffer = new Uint8Array(buffer); var returnBuffer_size = returnBuffer.byteLength; try { + //Write result buffer to file for debugging. Filename and MIME type are optional. + //writetofile(returnBuffer, "resultBuffer", "application/octet-stream"); md.results = parseresultsfrombuffer(md,returnBuffer,returnBuffer_size); $(callbackid).html(sprintf("%-16s", "RUN")).prop("disabled", false); @@ -115,33 +121,40 @@ var npbuffer = this.str2ab(md.cluster.np.toString()); + npbuffer = pako.deflate(npbuffer); var nplength = new Uint32Array(1); nplength[0] = npbuffer.byteLength; var codeversionbuffer = this.str2ab(md.cluster.codeversion.toString()); + codeversionbuffer = pako.deflate(codeversionbuffer); var codeversionlength = new Uint32Array(1); codeversionlength[0] = codeversionbuffer.byteLength; var runtimenamebuffer = this.str2ab(runtimename); + runtimenamebuffer = pako.deflate(runtimenamebuffer); var runtimenamelength = new Uint32Array(1); runtimenamelength[0] = runtimenamebuffer.byteLength; var namebuffer = this.str2ab(name); + namebuffer = pako.deflate(namebuffer); var namelength = new Uint32Array(1); namelength[0] = namebuffer.byteLength; var toolkitsbuffer = this.str2ab(toolkitsstring); + toolkitsbuffer = pako.deflate(toolkitsbuffer); var toolkitslength = new Uint32Array(1); toolkitslength[0] = toolkitsbuffer.byteLength; var solutionbuffer = this.str2ab(solutionstring); + solutionbuffer = pako.deflate(solutionbuffer); var solutionlength = new Uint32Array(1); solutionlength[0] = solutionbuffer.byteLength; - var binbuffer = new Uint8Array(fid.rawbuffer()); //seems that 16 array bytes length could be incompatible. + var binbuffer = new Uint8Array(fid.rawbuffer()); //seems that 16 bits length could be incompatible. + binbuffer = pako.deflate(binbuffer); var binlength = new Uint32Array(1); binlength[0] = binbuffer.byteLength; var data = new Blob([nplength,npbuffer,codeversionlength,codeversionbuffer,runtimenamelength,runtimenamebuffer,namelength,namebuffer,toolkitslength,toolkitsbuffer,solutionlength,solutionbuffer,binlength,binbuffer]); - + request.open("POST", this.url, true); request.responseType = 'application/octet-stream'; Index: /issm/trunk/src/m/classes/clusters/generic.m =================================================================== --- /issm/trunk/src/m/classes/clusters/generic.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/generic.m (revision 21729) @@ -72,5 +72,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ %write queuing script @@ -82,4 +82,7 @@ executable='issm_dakota.exe'; end + end + if isoceancoupling, + executable='issm_ocean.exe'; end Index: /issm/trunk/src/m/classes/clusters/generic.py =================================================================== --- /issm/trunk/src/m/classes/clusters/generic.py (revision 21728) +++ /issm/trunk/src/m/classes/clusters/generic.py (revision 21729) @@ -17,5 +17,5 @@ Usage: cluster=generic('name','astrid','np',3); - cluster=generic('name',oshostname(),'np',3,'login','username'); + cluster=generic('name',gethostname(),'np',3,'login','username'); """ @@ -68,5 +68,5 @@ return md # }}} - def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota): # {{{ + def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling): # {{{ executable='issm.exe'; @@ -76,4 +76,6 @@ if version>=6: executable='issm_dakota.exe' + if isoceancoupling: + executable='issm_ocean.exe' #write queuing script Index: /issm/trunk/src/m/classes/clusters/generic_static.m =================================================================== --- /issm/trunk/src/m/classes/clusters/generic_static.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/generic_static.m (revision 21729) @@ -49,5 +49,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ %Check that issm.exe exists in the right path @@ -67,4 +67,7 @@ executable='issm_dakota.exe'; end + end + if isoceancoupling, + executable='issm_ocean.exe'; end Index: /issm/trunk/src/m/classes/clusters/greenplanet.m =================================================================== --- /issm/trunk/src/m/classes/clusters/greenplanet.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/greenplanet.m (revision 21729) @@ -69,5 +69,5 @@ end %}}} - function BuildKrigingQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildKrigingQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end Index: /issm/trunk/src/m/classes/clusters/hexagon.py =================================================================== --- /issm/trunk/src/m/classes/clusters/hexagon.py (revision 21728) +++ /issm/trunk/src/m/classes/clusters/hexagon.py (revision 21729) @@ -41,8 +41,8 @@ #initialize cluster using user settings if provided self=hexagon_settings(self) - self.np=self.numnodes*self.procspernodes + #OK get other fields self=options.AssignObjectFields(self) - + self.np=self.numnodes*self.procspernodes # }}} def __repr__(self): @@ -81,5 +81,5 @@ return self # }}} - def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota): + def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling): # {{{ @@ -90,4 +90,6 @@ if version>=6: executable='issm_dakota.exe' + if isoceancoupling: + executable='issm_ocean.exe' #write queuing script @@ -97,5 +99,8 @@ fid.write('#PBS -N %s \n' % shortname) fid.write('#PBS -l mppwidth=%i,mppnppn=%i\n' % (self.np,self.procspernodes)) - timestring= str(datetime.timedelta(minutes=self.time)) + timeobj=datetime.timedelta(minutes=self.time) + m,s=divmod(timeobj.total_seconds(), 60) + h,m=divmod(m, 60) + timestring="%02d:%02d:%02d" % (h, m, s) fid.write('#PBS -l walltime=%s\n' % timestring) #walltime is hh:mm:ss fid.write('#PBS -l mppmem=%imb\n' % int(self.mem/self.procspernodes)) Index: /issm/trunk/src/m/classes/clusters/hpc.m =================================================================== --- /issm/trunk/src/m/classes/clusters/hpc.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/hpc.m (revision 21729) @@ -90,5 +90,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end Index: /issm/trunk/src/m/classes/clusters/lonestar.m =================================================================== --- /issm/trunk/src/m/classes/clusters/lonestar.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/lonestar.m (revision 21729) @@ -96,5 +96,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end @@ -107,4 +107,7 @@ executable='issm_dakota.exe'; end + end + if isoceancoupling, + executable='issm_ocean.exe'; end Index: /issm/trunk/src/m/classes/clusters/pfe.m =================================================================== --- /issm/trunk/src/m/classes/clusters/pfe.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/pfe.m (revision 21729) @@ -11,5 +11,5 @@ name = 'pfe' login = ''; - modules = {'comp-intel/2015.0.090' 'mpi-sgi/mpt.2.12r16'}; + modules = {'comp-intel/2016.2.181' 'mpi-sgi/mpt'}; numnodes = 20; cpuspernode = 8; @@ -20,5 +20,5 @@ codepath = ''; executionpath = ''; - grouplist = 's1010'; + grouplist = 's1690'; interactive = 0; bbftp = 0; @@ -136,5 +136,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isgprof), disp('gprof not supported by cluster, ignoring...'); end @@ -146,4 +146,7 @@ executable='issm_dakota.exe'; end + end + if isoceancoupling, + executable='issm_ocean.exe'; end @@ -160,6 +163,6 @@ fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]); fprintf(fid,'. /usr/share/modules/init/bash\n\n'); - fprintf(fid,'module load comp-intel/2015.0.090\n'); - fprintf(fid,'module load mpi-sgi/mpt.2.12r16\n'); + fprintf(fid,'module load comp-intel/2016.2.181\n'); + fprintf(fid,'module load mpi-sgi/mpt\n'); fprintf(fid,'export PATH="$PATH:."\n\n'); fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); @@ -223,6 +226,6 @@ fprintf(fid,'#PBS -e %s.errlog \n\n',[cluster.executionpath '/' dirname '/' modelname]); fprintf(fid,'. /usr/share/modules/init/bash\n\n'); - fprintf(fid,'module load comp-intel/2015.0.090\n'); - fprintf(fid,'module load mpi-sgi/mpt.2.12r16\n'); + fprintf(fid,'module load comp-intel/2016.2.181\n'); + fprintf(fid,'module load mpi-sgi/mpt\n'); fprintf(fid,'export PATH="$PATH:."\n\n'); fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); Index: /issm/trunk/src/m/classes/clusters/pfe.py =================================================================== --- /issm/trunk/src/m/classes/clusters/pfe.py (revision 21728) +++ /issm/trunk/src/m/classes/clusters/pfe.py (revision 21729) @@ -133,5 +133,5 @@ return self # }}} - def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota): + def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling): # {{{ @@ -142,4 +142,6 @@ if version>=6: executable='issm_dakota.exe' + if isoceancoupling: + executable='issm_ocean.exe' #write queuing script Index: /issm/trunk/src/m/classes/clusters/pollux.m =================================================================== --- /issm/trunk/src/m/classes/clusters/pollux.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/pollux.m (revision 21729) @@ -46,5 +46,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end Index: /issm/trunk/src/m/classes/clusters/raijin.m =================================================================== --- /issm/trunk/src/m/classes/clusters/raijin.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/raijin.m (revision 21729) @@ -63,5 +63,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end Index: /issm/trunk/src/m/classes/clusters/vilje.m =================================================================== --- /issm/trunk/src/m/classes/clusters/vilje.m (revision 21728) +++ /issm/trunk/src/m/classes/clusters/vilje.m (revision 21729) @@ -99,5 +99,5 @@ end %}}} - function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof) % {{{ + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end @@ -110,4 +110,7 @@ executable='issm_dakota.exe'; end + end + if isoceancoupling, + executable='issm_ocean.exe'; end Index: /issm/trunk/src/m/classes/clusters/vilje.py =================================================================== --- /issm/trunk/src/m/classes/clusters/vilje.py (revision 21728) +++ /issm/trunk/src/m/classes/clusters/vilje.py (revision 21729) @@ -41,10 +41,8 @@ #initialize cluster using user settings if provided self=vilje_settings(self) - self.np=self.numnodes*self.procspernodes #OK get other fields self=options.AssignObjectFields(self) - + self.np=self.numnodes*self.procspernodes # }}} - def __repr__(self): # {{{ @@ -57,5 +55,5 @@ s = "%s\n%s"%(s,fielddisplay(self,'procspernodes','number of mpi procs per nodes')) s = "%s\n%s"%(s,fielddisplay(self,'mem','node memory')) - s = "%s\n%s"%(s,fielddisplay(self,'queue','name of the queue')) + s = "%s\n%s"%(s,fielddisplay(self,'queue','name of the queue (test is an option, workq the default)')) s = "%s\n%s"%(s,fielddisplay(self,'time','walltime requested in minutes')) s = "%s\n%s"%(s,fielddisplay(self,'codepath','code path on the cluster')) @@ -65,9 +63,9 @@ return s # }}} - def checkconsistency(self,md,solution,analyses): # {{{ #Queue dictionarry gives queu name as key and max walltime and cpus as var - queuedict = {'workq' :[5*24*60, 30]} + queuedict = {'workq':[5*24*60, 30], + 'test':[30,4]} QueueRequirements(queuedict,self.queue,self.np,self.time) @@ -83,5 +81,5 @@ return self # }}} - def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota): + def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling): # {{{ @@ -92,4 +90,6 @@ if version>=6: executable='issm_dakota.exe' + if isoceancoupling: + executable='issm_ocean.exe' #write queuing script @@ -100,5 +100,8 @@ fid.write('#PBS -q %s \n' % self.queue) fid.write('#PBS -l select=%i:ncpus=%i:mpiprocs=%s\n' % (self.numnodes,self.cpuspernode,self.procspernodes)) - timestring= str(datetime.timedelta(minutes=self.time)) + timeobj=datetime.timedelta(minutes=self.time) + m,s=divmod(timeobj.total_seconds(), 60) + h,m=divmod(m, 60) + timestring="%02d:%02d:%02d" % (h, m, s) fid.write('#PBS -l walltime=%s\n' % timestring) #walltime is hh:mm:ss #fid.write('#PBS -l mem=%igb\n' % self.mem) @@ -116,8 +119,7 @@ fid.close() - # }}} + # }}} def UploadQueueJob(self,modelname,dirname,filelist): # {{{ - #compress the files into one zip. compressstring='tar -zcf %s.tar.gz ' % dirname Index: /issm/trunk/src/m/classes/clusters/yellowstone.m =================================================================== --- /issm/trunk/src/m/classes/clusters/yellowstone.m (revision 21729) +++ /issm/trunk/src/m/classes/clusters/yellowstone.m (revision 21729) @@ -0,0 +1,156 @@ +%YELLOWSTONE class definition +% +% Usage: +% cluster=yellowstone(); +% cluster=yellowstone('np',3); +% cluster=yellowstone('np',3,'login','username'); + +classdef yellowstone + properties (SetAccess=public) + % {{{ + name = 'yellowstone.ucar.edu' + login = ''; + modules = {'ncarenv/1.0' 'ncarbinlibs/1.1' 'perlmods/5.0' 'gmake/4.1' 'python/2.7.7' 'all-python-libs' 'git/2.3.0' 'intel/15.0.3' 'mkl/11.1.2' 'esmf' 'esmf-6.3.0rp1-defio-mpi-O' 'netcdf-mpi/4.3.3.1' 'pnetcdf/1.6.1' 'ncarcompilers/1.0' 'cmake/3.0.2' 'matlab/R2015b' 'issm'}; + numnodes = 1; + cpuspernode = 8; + port = 0; + queue = 'premium'; + time = 12*60; + processor = 'sandy'; + codepath = ''; + executionpath = ''; + grouplist = 'P93300301'; + end + %}}} + methods + function cluster=yellowstone(varargin) % {{{ + + %initialize cluster using default settings if provided + if (exist('yellowstone_settings')==2), yellowstone_settings; end + + %use provided options to change fields + cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); + end + %}}} + function disp(cluster) % {{{ + % display the object + disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); + disp(sprintf(' name: %s',cluster.name)); + disp(sprintf(' login: %s',cluster.login)); + modules=''; for i=1:length(cluster.modules), modules=[modules cluster.modules{i} ',']; end; modules=modules(1:end-1); + disp(sprintf(' modules: %s',modules)); + disp(sprintf(' port: %i',cluster.port)); + disp(sprintf(' numnodes: %i',cluster.numnodes)); + disp(sprintf(' cpuspernode: %i',cluster.cpuspernode)); + disp(sprintf(' np: %i',cluster.cpuspernode*cluster.numnodes)); + disp(sprintf(' queue: %s',cluster.queue)); + disp(sprintf(' time: %i',cluster.time)); + disp(sprintf(' processor: %s',cluster.processor)); + disp(sprintf(' codepath: %s',cluster.codepath)); + disp(sprintf(' executionpath: %s',cluster.executionpath)); + disp(sprintf(' grouplist: %s',cluster.grouplist)); + end + %}}} + function numprocs=np(cluster) % {{{ + %compute number of processors + numprocs=cluster.numnodes*cluster.cpuspernode; + end + %}}} + function md = checkconsistency(cluster,md,solution,analyses) % {{{ + + available_queues={'premium','regular'}; + queue_requirements_time=[12*60 12*650]; + queue_requirements_np=[16384 16384]; + + QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,cluster.time) + + %Miscelaneous + if isempty(cluster.login), md = checkmessage(md,'login empty'); end + if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end + if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end + if isempty(cluster.grouplist), md = checkmessage(md,'grouplist empty'); end + + end + %}}} + function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ + + executable='issm.exe'; + if isdakota, + version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3)); + if (version>=6), + executable='issm_dakota.exe'; + end + end + if isoceancoupling, + executable='issm_ocean.exe'; + end + + + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!/bin/tcsh\n'); + fprintf(fid,'#BSUB -P %s\n',cluster.grouplist); + fprintf(fid,'#BSUB -W %i:%i\n',floor(cluster.time/60),cluster.time-floor(cluster.time/60)*60); + fprintf(fid,'#BSUB -n %i\n',cluster.np); + fprintf(fid,'#BSUB -J %s\n',modelname); + fprintf(fid,'#BSUB -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'#BSUB -e %s.errlog \n',[cluster.executionpath '/' dirname '/' modelname]); + fprintf(fid,'#BSUB -q %s\n',cluster.queue); + + fprintf(fid,'module purge\n'); + for i=1:length(cluster.modules), + fprintf(fid,'module load %s\n',cluster.modules{i}); + end + + fprintf(fid,'setenv OMP_STACKSIZE 256M\n'); + fprintf(fid,'setenv MP_LABELIO yes\n'); + fprintf(fid,'setenv MP_INFOLEVEL 2\n'); + fprintf(fid,'setenv MP_SHARED_MEMORY yes\n'); + fprintf(fid,'setenv MP_EUILIB us\n'); + fprintf(fid,'setenv MP_STDOUTMODE unordered\n'); + fprintf(fid,'setenv MP_RC_USE_LMC yes\n'); + fprintf(fid,'setenv MP_MPILIB mpich2\n'); + fprintf(fid,'setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/opt/ibmhpc/pecurrent/mpich2/intel/lib64/\n'); + fprintf(fid,'setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/ncar/opt/intel/psxe-2015_update3/impi/5.0.3.048/lib64/\n'); + + fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname); + + fprintf(fid,'mpirun.lsf %s/%s %s %s %s\n',cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); + fclose(fid); + + end %}}} + function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{ + + %compress the files into one zip. + compressstring=['tar -zcf ' dirname '.tar.gz ']; + for i=1:numel(filelist), + compressstring = [compressstring ' ' filelist{i}]; + end + system(compressstring); + + disp('uploading input file and queueing script'); + directory=cluster.executionpath; + + issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']}); + + end + %}}} + function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{ + + %lauch command, to be executed via ssh + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... + ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && bsub < ' modelname '.queue ']; + + disp('launching solution sequence on remote cluster'); + issmssh(cluster.name,cluster.login,cluster.port,launchcommand); + end + %}}} + function Download(cluster,dirname,filelist)% {{{ + + %copy files from cluster to current directory + directory=[cluster.executionpath '/' dirname '/']; + issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); + + end %}}} + end +end Index: /issm/trunk/src/m/classes/esa.m =================================================================== --- /issm/trunk/src/m/classes/esa.m (revision 21728) +++ /issm/trunk/src/m/classes/esa.m (revision 21729) @@ -68,5 +68,5 @@ fielddisplay(self,'degacc','accuracy (default .01 deg) for numerical discretization of the Green''s functions'); fielddisplay(self,'transitions','indices into parts of the mesh that will be icecaps'); - fielddisplay(self,'requested_outputs','additional outputs requested (default: EsaUmotion)'); + fielddisplay(self,'requested_outputs','additional outputs requested (e.g., EsaUmotion, EsaStrainratexx, EsaRotationrate)'); end % }}} Index: /issm/trunk/src/m/classes/esa.py =================================================================== --- /issm/trunk/src/m/classes/esa.py (revision 21728) +++ /issm/trunk/src/m/classes/esa.py (revision 21729) @@ -2,5 +2,5 @@ from MatlabFuncs import * from model import * -from np.import * +import numpy as np from checkfield import checkfield from WriteData import WriteData @@ -15,5 +15,5 @@ def __init__(self): # {{{ - self.deltathickness = NaN + self.deltathickness = np.nan self.love_h = 0 #provided by PREM model() self.love_l = 0 #ideam Index: /issm/trunk/src/m/classes/frictioncoulomb.py =================================================================== --- /issm/trunk/src/m/classes/frictioncoulomb.py (revision 21728) +++ /issm/trunk/src/m/classes/frictioncoulomb.py (revision 21729) @@ -55,5 +55,5 @@ # }}} def marshall(self,prefix,md,fid): # {{{ - WriteData(fid,prefix,'name','md.friction.law','data',1,'format','Integer') + WriteData(fid,prefix,'name','md.friction.law','data',7,'format','Integer') WriteData(fid,prefix,'object',self,'fieldname','coefficient','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) WriteData(fid,prefix,'object',self,'fieldname','coefficientcoulomb','format','DoubleMat','mattype',1) Index: /issm/trunk/src/m/classes/frictionjosh.m =================================================================== --- /issm/trunk/src/m/classes/frictionjosh.m (revision 21729) +++ /issm/trunk/src/m/classes/frictionjosh.m (revision 21729) @@ -0,0 +1,59 @@ +%FRICTIONTEMP class definition +% +% Usage: +% frictionjosh=frictionjosh(); + +classdef frictionjosh + properties (SetAccess=public) + coefficient = NaN; + pressure_adjusted_temperature = NaN; + gamma = 0.; + end + methods + function self = extrude(self,md) % {{{ + self.coefficient=project3d(md,'vector',self.coefficient,'type','node','layer',1); + self.pressure_adjusted_temperature=project3d(md,'vector',self.pressure_adjusted_temperature,'type','node','layer',1); + end % }}} + function self = frictionjosh(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + case 1 + self=structtoobj(frictionjosh(),varargin{1}); + otherwise + error('constructor not supported'); + end + end % }}} + function self = setdefaultparameters(self) % {{{ + + %Default gamma: 1 + self.gamma = 1.; + + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + + %Early return + if ~ismember('StressbalanceAnalysis',analyses) & ~ismember('ThermalAnalysis',analyses), return; end + + md = checkfield(md,'fieldname','friction.coefficient','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','friction.pressure_adjusted_temperature','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','friction.gamma','numel',1,'NaN',1,'Inf',1,'>',0.); + + %Check that temperature is provided + md = checkfield(md,'fieldname','initialization.temperature','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1]); + end % }}} + function disp(self) % {{{ + disp(sprintf('Basal shear stress parameters: tau_b = coefficient^2 * Neff ^r * |u_b|^(s-1) * u_b * 1/f(T)\n(effective stress Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p)')); + fielddisplay(self,'coefficient','friction coefficient [SI]'); + fielddisplay(self,'pressure_adjusted_temperature','friction pressure_adjusted_temperature (T - Tpmp) [K]'); + fielddisplay(self,'gamma','(T - Tpmp)/gamma [K]'); + end % }}} + function marshall(self,prefix,md,fid) % {{{ + + WriteData(fid,prefix,'name','md.friction.law','data',9,'format','Integer'); + WriteData(fid,prefix,'class','friction','object',self,'fieldname','coefficient','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'class','friction','object',self,'fieldname','pressure_adjusted_temperature','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'class','friction','object',self,'fieldname','gamma','format','Double'); + end % }}} + end +end Index: sm/trunk/src/m/classes/gia.js =================================================================== --- /issm/trunk/src/m/classes/gia.js (revision 21728) +++ (revision ) @@ -1,64 +1,0 @@ -//GIA class definition -// -// Usage: -// gia=new gia(); - -function gia (){ - //methods - this.setdefaultparameters = function(){// {{{ - - this.cross_section_shape=1; //square as default (see iedge in GiaDeflectionCorex) - - }// }}} - this.disp= function(){// {{{ - - console.log(sprintf(' gia parameters:')); - - fielddisplay(this,'mantle_viscosity','mantle viscosity[Pa s]'); - fielddisplay(this,'lithosphere_thickness','lithosphere thickness (km)'); - fielddisplay(this,'cross_section_shape','1: square-edged (default). 2: elliptical. See iedge in GiaDeflectionCore'); - - }// }}} - this.classname= function(){// {{{ - return "gia"; - }// }}} - this.checkconsistency = function(md,solution,analyses) { // {{{ - - if(!ArrayAnyEqual(ArrayIsMember('GiaAnalysis',analyses),1))return; - - checkfield(md,'fieldname','gia.mantle_viscosity','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1],'>',0); - checkfield(md,'fieldname','gia.lithosphere_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1],'>',0); - checkfield(md,'fieldname','gia.cross_section_shape','numel',[1],'values',[1,2]); - - //be sure that if we are running a masstransport ice flow model coupled with gia, that thickness forcings - //are not provided into the future. - if (solution=='TransientSolution' & md.trans.ismasstransport & md.trans.isgia){ - //figure out if thickness is a transient forcing: - if (md.geometry.thickness.length == (md.mesh.numberofvertices+1)){ - //recover the furthest time "in time": - t=md.geometry.thickness[0].length; - if(md.geometry.thickness[md.geometry.thickness.length-1][t-1]!=md.timestepping.start_time){ - md.checkmessage('if ismasstransport is on, transient thickness forcing for the gia model should not be provided in the future. Synchronize your start_time to correspond to the most recent transient thickness forcing timestep'); - } - } - } - } // }}} - this.marshall=function(md,prefix,fid) { //{{{ - WriteData(fid,prefix,'object',this,'fieldname','mantle_viscosity','format','DoubleMat','mattype',1); - WriteData(fid,prefix,'object',this,'fieldname','lithosphere_thickness','format','DoubleMat','mattype',1,'scale',Math.pow(10,3)); //from km to m - WriteData(fid,prefix,'object',this,'fieldname','cross_section_shape','format','Integer'); - }//}}} - this.fix=function() { //{{{ - this.mantle_viscosity=NullFix(this.mantle_viscosity,NaN); - this.lithosphere_thickness=NullFix(this.lithosphere_thickness,NaN); - }//}}} - //properties - // {{{ - - this.mantle_viscosity = NaN; - this.lithosphere_thickness = NaN; - this.cross_section_shape = 0; - - this.setdefaultparameters(); - //}}} -} Index: sm/trunk/src/m/classes/gia.m =================================================================== --- /issm/trunk/src/m/classes/gia.m (revision 21728) +++ (revision ) @@ -1,72 +1,0 @@ -%GIA class definition -% -% Usage: -% gia=gia(); - -classdef gia - properties (SetAccess=public) - mantle_viscosity = NaN; - lithosphere_thickness = NaN; - cross_section_shape = 0; - end - methods - function self = extrude(self,md) % {{{ - self.mantle_viscosity=project3d(md,'vector',self.mantle_viscosity,'type','node'); - self.lithosphere_thickness=project3d(md,'vector',self.lithosphere_thickness,'type','node'); - end % }}} - function self = gia(varargin) % {{{ - switch nargin - case 0 - self=setdefaultparameters(self); - otherwise - error('constructor not supported'); - end - end % }}} - function self = setdefaultparameters(self) % {{{ - self.cross_section_shape=1; %square as default (see iedge in GiaDeflectionCorex) - end % }}} - function md = checkconsistency(self,md,solution,analyses) % {{{ - - if ~ismember('GiaAnalysis',analyses), return; end - md = checkfield(md,'fieldname','gia.mantle_viscosity','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1],'>',0); - md = checkfield(md,'fieldname','gia.lithosphere_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1],'>',0); - md = checkfield(md,'fieldname','gia.cross_section_shape','numel',[1],'values',[1,2]); - - %be sure that if we are running a masstransport ice flow model coupled with gia, that thickness forcings - %are not provided into the future. - if strcmp(solution,'TransientSolution') & md.transient.ismasstransport & md.transient.isgia, - %figure out if thickness is a transient forcing: - if size(md.geometry.thickness,1)==md.mesh.numberofvertices+1, - %recover the furthest time "in time": - if(thickness(end,end)~=md.timestepping.start_time), - md = checkmessage(md,['if ismasstransport is on, transient thickness forcing'... - ' for the gia model should not be provided in the future.'... - ' Synchronize your start_time to correspond to the most recent transient'... - ' thickness forcing timestep']); - end - end - end - - end % }}} - function disp(self) % {{{ - disp(sprintf(' gia parameters:')); - - fielddisplay(self,'mantle_viscosity','mantle viscosity[Pa s]'); - fielddisplay(self,'lithosphere_thickness','lithosphere thickness (km)'); - fielddisplay(self,'cross_section_shape','1: square-edged (default). 2: elliptical. See iedge in GiaDeflectionCore'); - - end % }}} - function marshall(self,prefix,md,fid) % {{{ - WriteData(fid,prefix,'object',self,'fieldname','mantle_viscosity','format','DoubleMat','mattype',1); - WriteData(fid,prefix,'object',self,'fieldname','lithosphere_thickness','format','DoubleMat','mattype',1,'scale',10^3); %from km to m - WriteData(fid,prefix,'object',self,'fieldname','cross_section_shape','format','Integer'); - end % }}} - function savemodeljs(self,fid,modelname) % {{{ - - writejsdouble(fid,[modelname '.gia.mantle_viscosity'],self.mantle_viscosity); - writejsdouble(fid,[modelname '.gia.lithosphere_thickness'],self.lithosphere_thickness); - writejsdouble(fid,[modelname '.gia.cross_section_shape'],self.cross_section_shape); - - end % }}} - end -end Index: sm/trunk/src/m/classes/gia.py =================================================================== --- /issm/trunk/src/m/classes/gia.py (revision 21728) +++ (revision ) @@ -1,63 +1,0 @@ -from fielddisplay import fielddisplay -from project3d import project3d -from checkfield import checkfield -from WriteData import WriteData - -class gia(object): - """ - GIA class definition - - Usage: - gia=gia(); - """ - - def __init__(self): # {{{ - self.mantle_viscosity = float('NaN'); - self.lithosphere_thickness = float('NaN'); - self.cross_section_shape = 0; - - #set defaults - self.setdefaultparameters() - - #}}} - def __repr__(self): # {{{ - - string=' gia solution parameters:' - - string="%s\n%s"%(string,fielddisplay(self,'mantle_viscosity','mantle viscosity constraints (NaN means no constraint) (Pa s)')) - string="%s\n%s"%(string,fielddisplay(self,'lithosphere_thickness','lithosphere thickness constraints (NaN means no constraint) (m)')) - string="%s\n%s"%(string,fielddisplay(self,'cross_section_shape',"1: square-edged, 2: elliptical-edged surface")) - return string - #}}} - def extrude(self,md): # {{{ - self.mantle_viscosity=project3d(md,'vector',self.mantle_viscosity,'type','node') - self.lithosphere_thickness=project3d(md,'vector',self.lithosphere_thickness,'type','node') - return self - #}}} - def setdefaultparameters(self): # {{{ - - self.cross_section_shape=1; - - return self - #}}} - def checkconsistency(self,md,solution,analyses): # {{{ - - # Early return - if ('GiaAnalysis' not in analyses): - return md - - md = checkfield(md,'fieldname','gia.mantle_viscosity','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices],'>',0) - md = checkfield(md,'fieldname','gia.lithosphere_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices],'>',0) - md = checkfield(md,'fieldname','gia.cross_section_shape','numel',[1],'values',[1,2]) - - #be sure that if we are running a masstransport ice flow model coupled with gia, that thickness forcings - #are not provided into the future. - - return md - # }}} - def marshall(self,prefix,md,fid): # {{{ - - WriteData(fid,prefix,'object',self,'fieldname','mantle_viscosity','format','DoubleMat','mattype',1); - WriteData(fid,prefix,'object',self,'fieldname','lithosphere_thickness','format','DoubleMat','mattype',1,'scale',10.**3.); - WriteData(fid,prefix,'object',self,'fieldname','cross_section_shape','format','Integer'); - # }}} Index: /issm/trunk/src/m/classes/giacaron.m =================================================================== --- /issm/trunk/src/m/classes/giacaron.m (revision 21729) +++ /issm/trunk/src/m/classes/giacaron.m (revision 21729) @@ -0,0 +1,300 @@ +%GIA class definition for Caron model (Caron et al, Geophysical Journal International, 2017) +% +% Usage: +% giacaron=giacaron(); +classdef giacaron + properties (SetAccess=public) + + %Physical constants + gravitational_constant= NaN; + surface_radius = NaN; + core_mantle_boudary_radius= NaN; + inner_core_boudary_radius= NaN; + stress_norm= NaN; + gravity_norm= NaN; + radius_norm= NaN; + + %Numerical parameters + allow_layer_deletion=NaN; + verbose_mode=NaN; + + %GIA problem setup + forcing_type=NaN; + isincompressible=NaN; + benchmark_mode=NaN; + calculate_sea_level=NaN; + calculate_rotational_feedback=NaN; + subtract_present_day=NaN; + ntime=NaN; + nphi=NaN; + + %Earth model + numlayers = NaN; + radius = NaN; + lame_mu = NaN; + lame_lambda = NaN; + issolid = NaN; + density = NaN; + viscosity = NaN; + isburger = NaN; + transient_viscosity = NaN; + transient_mu = NaN; + + %Ice history + ice_model_identifier=NaN; + ice_model_ntime=NaN; + nice_sheets=NaN; + + end + methods + function self = extrude(self,md) % {{{ + end % }}} + function self = giacaron(varargin) % {{{ + switch nargin + case 0 + otherwise + options=pairoptions(varargin{:}); + body=getfieldvalue(options,'body'); + if strcmpi(body,'earth'), + self.numlayers=getfieldvalue(options,'numlayers',5); + self.calculate_sea_level=true; + %[self.radius,self.lame_mu, self.lame_lambda, self.issolid, self.density, ... + %self.viscosity, self.isburger, self.transient_viscosity, self.transient_mu]=... + %modelinit(self.numlayers); + elseif strcmpi(body,'europa'), + error('giacaron constructor error message: ''europa'' body not implemented yet!'); + else + error('giacaron constructor error message: body not implemented yet!'); + end + end + end % }}} + function self = setdefaultparameters(self) % {{{ + %Physical constants + gravitational_constant= 6.67259e-11; + stress_norm= 1e12; + gravity_norm= 10; + radius_norm= 1.0; + + %Numerical parameters + allow_layer_deletion=true; + verbose_mode=false; + + %GIA problem setup + forcing_type=11; + isincompressible=false; + benchmark_mode=false; + calculate_sea_level=false; + calculate_rotational_feedback=true; + subtract_present_day=true; + + %Earth model + isburger = false(self.numlayers,1); + + %Ice history + nice_sheets=1; + + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + + if ~ismember('GiaAnalysis',analyses), return; end + % Physical constants + md = checkfield(md,'fieldname','gia.gravitational_constant','NaN',1,'Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','gia.surface_radius','NaN',1,'Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','gia.core_mantle_boundary_radius','Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','gia.inner_core_boundary_radius','Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','gia.radius_norm','NaN',1,'Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','gia.stress_norm','NaN',1,'Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','gia.gravity_norm','NaN',1,'Inf',1,'numel',1,'>',0); + + %Numerical parameters + md = checkfield(md,'fieldname','gia.allow_layer_deletion','values',[0 1]); + md = checkfield(md,'fieldname','gia.verbose_mode','values',[0 1]); + + %GIA problem setup + md = checkfield(md,'fieldname','gia.forcing_type','NaN',1,'Inf',1,'numel',1,'>',0, '<=', 12); + md = checkfield(md,'fieldname','gia.isincompressible','values',[0 1]); + md = checkfield(md,'fieldname','gia.benchmark_mode','values',[0 1]); + md = checkfield(md,'fieldname','gia.calculate_sea_level','values',[0 1]); + md = checkfield(md,'fieldname','gia.calculate_rotational_feedback','values',[0 1]); + md = checkfield(md,'fieldname','gia.subtract_present_day','values',[0 1]); + md = checkfield(md,'fieldname','gia.ntime','NaN',1,'Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','gia.ntheta','NaN',1,'Inf',1,'numel',1,'>',0); + md = checkfield(md,'fieldname','gia.nphi','numel',1,'values', self.ntheta*2); + + %Ice history + md = checkfield(md,'fieldname','gia.ice_model_identifier', 'stringrow', 1, 'size', [1 3]); + md = checkfield(md,'fieldname','gia.ice_model_ntime', 'NaN', 1, 'Inf', 1, 'numel', 1); + md = checkfield(md,'fieldname','gia.nice_sheets', 'NaN', 1, 'Inf', 1, '>', 0, 'numel', 1); + + %Earth parameters + md = checkfield(md,'fieldname','gia.numlayers','NaN',1,'Inf',1,'>',0,'numel',1); + md = checkfield(md,'fieldname','gia.radius','NaN',1,'Inf',1,'size',[md.gia.numlayers 1],'>',0); + md = checkfield(md,'fieldname','gia.lame_mu','NaN',1,'Inf',1,'size',[md.gia.numlayers 1],'>',0); + md = checkfield(md,'fieldname','gia.lame_lambda','NaN',1,'Inf',1,'size',[md.gia.numlayers 1],'>',0); + md = checkfield(md,'fieldname','gia.issolid','NaN',1,'Inf',1,'size',[md.gia.numlayers 1],'>',0,'<',2); + md = checkfield(md,'fieldname','gia.density','NaN',1,'Inf',1,'size',[md.gia.numlayers 1],'>',0); + md = checkfield(md,'fieldname','gia.viscosity','NaN',1,'Inf',1,'size',[md.gia.numlayers 1],'>',0); + md = checkfield(md,'fieldname','gia.isburger','NaN',1,'Inf',1,'size',[md.gia.numlayers 1],'>',0,'<',2); + md = checkfield(md,'fieldname','gia.transient_viscosity','NaN',1,'Inf',1,'size',[md.gia.numlayers 1],'>',0); + md = checkfield(md,'fieldname','gia.transient_mu','NaN',1,'Inf',1,'size',[md.gia.numlayers 1],'>',0); + end % }}} + function disp(self) % {{{ + disp(sprintf(' giacaron parameters:')); + + % Physical constants + fielddisplay(self,'gravitational_constant', 'Newton''s Gravitational constant, should be equal to approximately 6.67e-11 [m^3.kg^-1.s^-2]'); + fielddisplay(self,'surface_radius','NaN', 'Planet outer surface radius [m]'); + fielddisplay(self,'core_mantle_boundary_radius', 'Planet core mantle boundary radius (optional) [m]'); + fielddisplay(self,'inner_core_boundary_radius','Planet inner core boundary radius (optional) [m]'); + fielddisplay(self,'radius_norm', 'length normalization constant [m] (default 1.0)'); + fielddisplay(self,'stress_norm', 'stress normalization constant [Pa] (default 1e12)'); + fielddisplay(self,'gravity_norm', 'gravity normalization constant [m.s^-2] (default 10)'); + + %Numerical parameters + fielddisplay(self,'allow_layer_deletion', 'boolean allowing the migration of the starting integration radius while increasing the spherical harmonic degree (default true)'); + fielddisplay(self,'verbose_mode', 'boolean allowing the program to write more details on terminal (default false)') + + %GIA problem setup + fielddisplay(self,'forcing_type','integer indicating the nature and depth of the forcing for the Love number calculation: 1: ICB -- Volumic Potential, 2: ICB -- Pressure, 3: ICB -- Loading, 4: ICB -- Tangential traction, 5: CMB -- Volumic Potential, 6: CMB -- Pressure 7: CMB -- Loading, 8: CMB -- Tangential traction, 9: SURF -- Volumic Potential, 10: SURF -- Pressure, 11: SURF -- Loading, 12: SURF -- Tangential traction (default 11)'); + fielddisplay(self,'isincompressible', 'boolean approximating the mantle rheology to an incompressible body, sets Lame_lambda to 5e14 Pa (default false)'); + fielddisplay(self,'benchmark_mode', 'boolean to enter benchmark mode, writes a lot of outputs from the midst of the calculation (default false)'); + fielddisplay(self,'calculate_sea_level', 'boolean allowing the sea level equation solving (default false)'); + fielddisplay(self,'calculate_rotational_feedback', 'boolean allowing the calculation of rotational feedback (default true)'); + fielddisplay(self,'subtract_present_day', 'boolean, subtracts the present day signal so the calculation is expressed as the difference with the present-day topography, geoid and sea level (default true)'); + fielddisplay(self,'ntime', 'number of time steps') + fielddisplay(self,'ntheta', 'size of grid in latitude') + fielddisplay(self,'nphi', 'size of grid in longitude (should always be ntheta*2)'); + + %Ice history + fielddisplay(self,'ice_model_identifier', 'string identifier for the ice model (3 characters)') + fielddisplay(self,'ice_model_ntime', 'number of time steps in the original ice model, is used to interpolate the model on the desired time') + fielddisplay(self,'nice_sheets', 'number of ice regions to be scaled independently') + + %Earth parameters + fielddisplay(self,'numlayers','number of layers (default 5)'); + fielddisplay(self,'radius','array describing the radius for each interface (numlayers+1) [m]'); + fielddisplay(self,'lame_mu','array describing the shear modulus for each layers (numlayers) [Pa]'); + fielddisplay(self,'lame_lambda','array describing the lame lambda parameter (numlayers) [Pa]'); + fielddisplay(self,'issolid','array describing whether the layer is solid or liquid (default 1) (numlayers)'); + fielddisplay(self,'density','array describing each layer''s density (numlayers) [kg/m^3]'); + fielddisplay(self,'viscosity','array describing each layer''s viscosity (numlayers) [Pa.s]'); + fielddisplay(self,'isburger','array describing whether we adopt a MaxWell (0) or Burgers (1) rheology (default 0)'); + fielddisplay(self,'transient_viscosity','array describing each layer''s transient viscosity, only for Burgers rheologies (numlayers) [Pa.s]'); + fielddisplay(self,'transient_mu','array describing each layer''s transient shear modulus, only for Burgers rheologies (numlayers) [Pa]'); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ + WriteData(fid,prefix,'object',self,'fieldname','mantle_viscosity','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','lithosphere_thickness','format','DoubleMat','mattype',1,'scale',10^3); %from km to m + WriteData(fid,prefix,'object',self,'fieldname','cross_section_shape','format','Integer'); + + %Physical constants + WriteData(fid,prefix,'object',self,'fieldname','gravitational_constant','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','surface_radius ','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','core_mantle_boudary_radius','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','inner_core_boudary_radius','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','stress_norm','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','gravity_norm','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','radius_norm','format','Double'); + + %Numerical parameters + WriteData(fid,prefix,'object',self,'fieldname','allow_layer_deletion','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','verbose_mode','format','Boolean'); + + %GIA problem setup + WriteData(fid,prefix,'object',self,'fieldname','forcing_type','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','isincompressible','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','benchmark_mode','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','calculate_sea_level','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','calculate_rotational_feedback','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','subtract_present_day','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','ntime','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','ntheta','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','nphi','format','Integer'); + + %Earth model + WriteData(fid,prefix,'object',self,'fieldname','numlayers','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','radius','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','lame_mu','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','lame_lambda ','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','issolid','format','BooleanMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','density','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','viscosity','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','isburger','format','BooleanMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','transient_viscosity','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','transient_mu','format','DoubleMat','mattype',1); + + %Inversion +% dataset_type_dentifier= NaN + WriteData(fid,prefix,'object',self,'fieldname','ndata_std','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','ndata_minimum_val ','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','ndata_maximum_val ','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','ndata_total','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','n_forward_models','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','ice_coefficients_solving ','format','String'); + WriteData(fid,prefix,'object',self,'fieldname','ninverse_parameters','format','Integer'); + + %Ice history + WriteData(fid,prefix,'object',self,'fieldname','ice_model_identifier','format','String'); + WriteData(fid,prefix,'object',self,'fieldname','ice_model_ntime','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','nice_sheets','format','Integer'); + end % }}} + function savemodeljs(self,fid,modelname) % {{{ + +%Physical constants + writejsdouble(fid,[modelname '.gia.gravitational_constant'],self.gravitational_constant); + writejsdouble(fid,[modelname '.gia.surface_radius'],self.surface_radius); + writejsdouble(fid,[modelname '.gia.core_mantle_boudary_radius'],self.core_mantle_boudary_radius); + writejsdouble(fid,[modelname '.gia.inner_core_boudary_radius'],self.inner_core_boudary_radius); + writejsdouble(fid,[modelname '.gia.stress_norm'],self.stress_norm); + writejsdouble(fid,[modelname '.gia.gravity_norm'],self.gravity_norm); + writejsdouble(fid,[modelname '.gia.radius_norm'],self.radius_norm); + + %Numerical parameters + writejsdouble(fid,[modelname '.gia.allow_layer_deletion'],self.allow_layer_deletion); + writejsdouble(fid,[modelname '.gia.verbose_mode'],self.verbose_mode); + + %GIA problem setup + writejsdouble(fid,[modelname '.gia.forcing_type'],self.forcing_type); + writejsdouble(fid,[modelname '.gia.isincompressible'],self.isincompressible); + writejsdouble(fid,[modelname '.gia.benchmark_mode'],self.benchmark_mode); + writejsdouble(fid,[modelname '.gia.calculate_sea_level'],self.calculate_sea_level); + writejsdouble(fid,[modelname '.gia.calculate_rotational_feedback'],self.calculate_rotational_feedback); + writejsdouble(fid,[modelname '.gia.subtract_present_day'],self.subtract_present_day); + writejsdouble(fid,[modelname '.gia.ntime'],self.ntime); + writejsdouble(fid,[modelname '.gia.ntheta'],self.ntheta); + writejsdouble(fid,[modelname '.gia.nphi'],self.nphi); + + %Earth model + writejsdouble(fid,[modelname '.gia.numlayers'],self.numlayers); + writejsdouble(fid,[modelname '.gia.radius'],self.radius); + writejsdouble(fid,[modelname '.gia.lame_mu'],self.lame_mu); + writejsdouble(fid,[modelname '.gia.lame_lambda'],self.lame_lambda); + writejsdouble(fid,[modelname '.gia.issolid'],self.issolid); + writejsdouble(fid,[modelname '.gia.density'],self.density); + writejsdouble(fid,[modelname '.gia.viscosity'],self.viscosity); + writejsdouble(fid,[modelname '.gia.isburger'],self.isburger); + writejsdouble(fid,[modelname '.gia.transient_viscosity'],self.transient_viscosity); + writejsdouble(fid,[modelname '.gia.transient_mu'],self.transient_mu); + + %Inversion +% dataset_type_dentifier= NaN +% writejsdouble(fid,[modelname '.gia.ndata_std'],self.ndata_std); +% writejsdouble(fid,[modelname '.gia.ndata_minimum_val'],self.ndata_minimum_val); +% writejsdouble(fid,[modelname '.gia.ndata_maximum_val'],self.ndata_maximum_val); +% writejsdouble(fid,[modelname '.gia.ndata_total'],self.ndata_total); +% writejsdouble(fid,[modelname '.gia.n_forward_models'],self.n_forward_models); +% writejsdouble(fid,[modelname '.gia.ice_coefficients_solving'],self.ice_coefficients_solving); +% writejsdouble(fid,[modelname '.gia.ninverse_parameters'],self.ninverse_parameters); + + %Ice history + writejsdouble(fid,[modelname '.gia.ice_model_identifier'],self.ice_model_identifier); + writejsdouble(fid,[modelname '.gia.ice_model_ntime'],self.ice_model_ntime); + writejsdouble(fid,[modelname '.gia.nice_sheets'],self.nice_sheets); + writejsdouble(fid,[modelname '.gia.mantle_viscosity'],self.mantle_viscosity); + writejsdouble(fid,[modelname '.gia.lithosphere_thickness'],self.lithosphere_thickness); + writejsdouble(fid,[modelname '.gia.cross_section_shape'],self.cross_section_shape); + + end % }}} + end +end Index: /issm/trunk/src/m/classes/giaivins.js =================================================================== --- /issm/trunk/src/m/classes/giaivins.js (revision 21729) +++ /issm/trunk/src/m/classes/giaivins.js (revision 21729) @@ -0,0 +1,64 @@ +//GIA class definition for Ivins and James model +// +// Usage: +// giaivins=new giaivins(); + +function giaivins (){ + //methods + this.setdefaultparameters = function(){// {{{ + + this.cross_section_shape=1; //square as default (see iedge in GiaDeflectionCorex) + + }// }}} + this.disp= function(){// {{{ + + console.log(sprintf(' giaivins parameters:')); + + fielddisplay(this,'mantle_viscosity','mantle viscosity[Pa s]'); + fielddisplay(this,'lithosphere_thickness','lithosphere thickness (km)'); + fielddisplay(this,'cross_section_shape','1: square-edged (default). 2: elliptical. See iedge in GiaDeflectionCore'); + + }// }}} + this.classname= function(){// {{{ + return "giaivins"; + }// }}} + this.checkconsistency = function(md,solution,analyses) { // {{{ + + if(!ArrayAnyEqual(ArrayIsMember('GiaAnalysis',analyses),1))return; + + checkfield(md,'fieldname','gia.mantle_viscosity','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1],'>',0); + checkfield(md,'fieldname','gia.lithosphere_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1],'>',0); + checkfield(md,'fieldname','gia.cross_section_shape','numel',[1],'values',[1,2]); + + //be sure that if we are running a masstransport ice flow model coupled with giaivins, that thickness forcings + //are not provided into the future. + if (solution=='TransientSolution' & md.trans.ismasstransport & md.trans.isgia){ + //figure out if thickness is a transient forcing: + if (md.geometry.thickness.length == (md.mesh.numberofvertices+1)){ + //recover the furthest time "in time": + t=md.geometry.thickness[0].length; + if(md.geometry.thickness[md.geometry.thickness.length-1][t-1]!=md.timestepping.start_time){ + md.checkmessage('if ismasstransport is on, transient thickness forcing for the giaivins model should not be provided in the future. Synchronize your start_time to correspond to the most recent transient thickness forcing timestep'); + } + } + } + } // }}} + this.marshall=function(md,prefix,fid) { //{{{ + WriteData(fid,prefix,'object',this,'fieldname','mantle_viscosity','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',this,'fieldname','lithosphere_thickness','format','DoubleMat','mattype',1,'scale',Math.pow(10,3)); //from km to m + WriteData(fid,prefix,'object',this,'fieldname','cross_section_shape','format','Integer'); + }//}}} + this.fix=function() { //{{{ + this.mantle_viscosity=NullFix(this.mantle_viscosity,NaN); + this.lithosphere_thickness=NullFix(this.lithosphere_thickness,NaN); + }//}}} + //properties + // {{{ + + this.mantle_viscosity = NaN; + this.lithosphere_thickness = NaN; + this.cross_section_shape = 0; + + this.setdefaultparameters(); + //}}} +} Index: /issm/trunk/src/m/classes/giaivins.m =================================================================== --- /issm/trunk/src/m/classes/giaivins.m (revision 21729) +++ /issm/trunk/src/m/classes/giaivins.m (revision 21729) @@ -0,0 +1,72 @@ +%GIA class definition for Ivins and James model +% +% Usage: +% giaivins=giaivins(); + +classdef giaivins + properties (SetAccess=public) + mantle_viscosity = NaN; + lithosphere_thickness = NaN; + cross_section_shape = 0; + end + methods + function self = extrude(self,md) % {{{ + self.mantle_viscosity=project3d(md,'vector',self.mantle_viscosity,'type','node'); + self.lithosphere_thickness=project3d(md,'vector',self.lithosphere_thickness,'type','node'); + end % }}} + function self = giaivins(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + otherwise + error('constructor not supported'); + end + end % }}} + function self = setdefaultparameters(self) % {{{ + self.cross_section_shape=1; %square as default (see iedge in GiaDeflectionCorex) + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + + if ~ismember('GiaAnalysis',analyses), return; end + md = checkfield(md,'fieldname','gia.mantle_viscosity','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1],'>',0); + md = checkfield(md,'fieldname','gia.lithosphere_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1],'>',0); + md = checkfield(md,'fieldname','gia.cross_section_shape','numel',[1],'values',[1,2]); + + %be sure that if we are running a masstransport ice flow model coupled with giaivins, that thickness forcings + %are not provided into the future. + if strcmp(solution,'TransientSolution') & md.transient.ismasstransport & md.transient.isgia, + %figure out if thickness is a transient forcing: + if size(md.geometry.thickness,1)==md.mesh.numberofvertices+1, + %recover the furthest time "in time": + if(thickness(end,end)~=md.timestepping.start_time), + md = checkmessage(md,['if ismasstransport is on, transient thickness forcing'... + ' for the giaivins model should not be provided in the future.'... + ' Synchronize your start_time to correspond to the most recent transient'... + ' thickness forcing timestep']); + end + end + end + + end % }}} + function disp(self) % {{{ + disp(sprintf(' giaivins parameters:')); + + fielddisplay(self,'mantle_viscosity','mantle viscosity[Pa s]'); + fielddisplay(self,'lithosphere_thickness','lithosphere thickness (km)'); + fielddisplay(self,'cross_section_shape','1: square-edged (default). 2: elliptical. See iedge in GiaDeflectionCore'); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ + WriteData(fid,prefix,'object',self,'fieldname','mantle_viscosity','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','lithosphere_thickness','format','DoubleMat','mattype',1,'scale',10^3); %from km to m + WriteData(fid,prefix,'object',self,'fieldname','cross_section_shape','format','Integer'); + end % }}} + function savemodeljs(self,fid,modelname) % {{{ + + writejsdouble(fid,[modelname '.gia.mantle_viscosity'],self.mantle_viscosity); + writejsdouble(fid,[modelname '.gia.lithosphere_thickness'],self.lithosphere_thickness); + writejsdouble(fid,[modelname '.gia.cross_section_shape'],self.cross_section_shape); + + end % }}} + end +end Index: /issm/trunk/src/m/classes/giaivins.py =================================================================== --- /issm/trunk/src/m/classes/giaivins.py (revision 21729) +++ /issm/trunk/src/m/classes/giaivins.py (revision 21729) @@ -0,0 +1,63 @@ +from fielddisplay import fielddisplay +from project3d import project3d +from checkfield import checkfield +from WriteData import WriteData + +class giaivins(object): + """ + GIA class definition + + Usage: + giaivins=giaivins(); + """ + + def __init__(self): # {{{ + self.mantle_viscosity = float('NaN'); + self.lithosphere_thickness = float('NaN'); + self.cross_section_shape = 0; + + #set defaults + self.setdefaultparameters() + + #}}} + def __repr__(self): # {{{ + + string=' giaivins solution parameters:' + + string="%s\n%s"%(string,fielddisplay(self,'mantle_viscosity','mantle viscosity constraints (NaN means no constraint) (Pa s)')) + string="%s\n%s"%(string,fielddisplay(self,'lithosphere_thickness','lithosphere thickness constraints (NaN means no constraint) (m)')) + string="%s\n%s"%(string,fielddisplay(self,'cross_section_shape',"1: square-edged, 2: elliptical-edged surface")) + return string + #}}} + def extrude(self,md): # {{{ + self.mantle_viscosity=project3d(md,'vector',self.mantle_viscosity,'type','node') + self.lithosphere_thickness=project3d(md,'vector',self.lithosphere_thickness,'type','node') + return self + #}}} + def setdefaultparameters(self): # {{{ + + self.cross_section_shape=1; + + return self + #}}} + def checkconsistency(self,md,solution,analyses): # {{{ + + # Early return + if ('GiaAnalysis' not in analyses): + return md + + md = checkfield(md,'fieldname','gia.mantle_viscosity','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices],'>',0) + md = checkfield(md,'fieldname','gia.lithosphere_thickness','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices],'>',0) + md = checkfield(md,'fieldname','gia.cross_section_shape','numel',[1],'values',[1,2]) + + #be sure that if we are running a masstransport ice flow model coupled with giaivins, that thickness forcings + #are not provided into the future. + + return md + # }}} + def marshall(self,prefix,md,fid): # {{{ + + WriteData(fid,prefix,'object',self,'fieldname','mantle_viscosity','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'fieldname','lithosphere_thickness','format','DoubleMat','mattype',1,'scale',10.**3.); + WriteData(fid,prefix,'object',self,'fieldname','cross_section_shape','format','Integer'); + # }}} Index: /issm/trunk/src/m/classes/hydrologysommers.m =================================================================== --- /issm/trunk/src/m/classes/hydrologysommers.m (revision 21728) +++ /issm/trunk/src/m/classes/hydrologysommers.m (revision 21729) @@ -15,4 +15,6 @@ spchead = NaN; neumannflux = NaN; + relaxation = 0; + storage = 0; end methods @@ -30,4 +32,7 @@ end % }}} function self = setdefaultparameters(self) % {{{ + % Set under-relaxation parameter to be 1 (no under-relaxation of nonlinear iteration) + self.relaxation=1; + self.storage=0; end % }}} function md = checkconsistency(self,md,solution,analyses) % {{{ @@ -46,5 +51,7 @@ md = checkfield(md,'fieldname','hydrology.reynolds','>',0,'size',[md.mesh.numberofelements 1],'NaN',1,'Inf',1); md = checkfield(md,'fieldname','hydrology.neumannflux','timeseries',1,'NaN',1,'Inf',1); - md = checkfield(md,'fieldname','hydrology.spchead','size',[md.mesh.numberofvertices 1]); + md = checkfield(md,'fieldname','hydrology.spchead','size',[md.mesh.numberofvertices 1]); + md = checkfield(md,'fieldname','hydrology.relaxation','>=',0); + md = checkfield(md,'fieldname','hydrology.storage','>=',0); end % }}} function disp(self) % {{{ @@ -59,4 +66,6 @@ fielddisplay(self,'neumannflux','water flux applied along the model boundary (m^2/s)'); fielddisplay(self,'spchead','water head constraints (NaN means no constraint) (m)'); + fielddisplay(self,'relaxation','under-relaxation coefficient for nonlinear iteration'); + fielddisplay(self,'storage','englacial storage coefficient (void ratio)'); end % }}} function marshall(self,prefix,md,fid) % {{{ @@ -74,4 +83,6 @@ WriteData(fid,prefix,'object',self,'class','hydrology','fieldname','neumannflux','format','DoubleMat','mattype',2,'timeserieslength',md.mesh.numberofelements+1,'yts',md.constants.yts); WriteData(fid,prefix,'object',self,'class','hydrology','fieldname','spchead','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','hydrology','fieldname','relaxation','format','Double'); + WriteData(fid,prefix,'object',self,'class','hydrology','fieldname','storage','format','Double'); end % }}} end Index: /issm/trunk/src/m/classes/initialization.m =================================================================== --- /issm/trunk/src/m/classes/initialization.m (revision 21728) +++ /issm/trunk/src/m/classes/initialization.m (revision 21729) @@ -76,4 +76,9 @@ md = checkfield(md,'fieldname','initialization.waterfraction','>=',0,'size',[md.mesh.numberofvertices 1]); md = checkfield(md,'fieldname','initialization.watercolumn' ,'>=',0,'size',[md.mesh.numberofvertices 1]); + pos=find(md.initialization.waterfraction>0.); + if(~isempty(pos)), + md = checkfield(md,'fieldname', 'delta Tpmp', 'field',abs(md.initialization.temperature(pos)-(md.materials.meltingpoint-md.materials.beta*md.initialization.pressure(pos))),'<',1e-11,... + 'message','set temperature to pressure melting point at locations with waterfraction>0'); + end end if ismember('HydrologyShreveAnalysis',analyses), @@ -129,5 +134,5 @@ if md.thermal.isenthalpy, tpmp = md.materials.meltingpoint - md.materials.beta*md.initialization.pressure; - pos = find(md.initialization.temperature>=tpmp); + pos = find(md.initialization.waterfraction>0.); enthalpy = md.materials.heatcapacity*(md.initialization.temperature-md.constants.referencetemperature); enthalpy(pos) = md.materials.heatcapacity*(tpmp(pos) - md.constants.referencetemperature) + md.materials.latentheat*md.initialization.waterfraction(pos); Index: /issm/trunk/src/m/classes/initialization.py =================================================================== --- /issm/trunk/src/m/classes/initialization.py (revision 21728) +++ /issm/trunk/src/m/classes/initialization.py (revision 21729) @@ -100,4 +100,7 @@ md = checkfield(md,'fieldname','initialization.waterfraction','>=',0,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','initialization.watercolumn' ,'>=',0,'size',[md.mesh.numberofvertices]) + pos = np.nonzero(md.initialization.waterfraction > 0.)[0] + if(pos.size): + md = checkfield(md,'fieldname', 'delta Tpmp', 'field', np.absolute(md.initialization.temperature[pos]-(md.materials.meltingpoint-md.materials.beta*md.initialization.pressure[pos])),'<',1e-11, 'message','set temperature to pressure melting point at locations with waterfraction>0'); if 'HydrologyShreveAnalysis' in analyses: if hasattr(md.hydrology,'hydrologyshreve'): @@ -131,7 +134,7 @@ if md.thermal.isenthalpy: tpmp = md.materials.meltingpoint - md.materials.beta*md.initialization.pressure; - pos = np.nonzero(md.initialization.temperature > tpmp)[0] + pos = np.nonzero(md.initialization.waterfraction > 0.)[0] enthalpy = md.materials.heatcapacity*(md.initialization.temperature-md.constants.referencetemperature); - enthalpy[pos] = md.materials.heatcapacity*tpmp[pos].reshape(-1,) - md.constants.referencetemperature + md.materials.latentheat*md.initialization.waterfraction[pos].reshape(-1,) + enthalpy[pos] = md.materials.heatcapacity*(tpmp[pos].reshape(-1,) - md.constants.referencetemperature) + md.materials.latentheat*md.initialization.waterfraction[pos].reshape(-1,) WriteData(fid,prefix,'data',enthalpy,'format','DoubleMat','mattype',1,'name','md.initialization.enthalpy'); Index: /issm/trunk/src/m/classes/levelset.m =================================================================== --- /issm/trunk/src/m/classes/levelset.m (revision 21728) +++ /issm/trunk/src/m/classes/levelset.m (revision 21729) @@ -9,4 +9,5 @@ spclevelset = NaN; reinit_frequency = 5; + calving_max = 0.; end methods @@ -36,6 +37,7 @@ %stabilization = 2 by default - self.stabilization = 2; + self.stabilization = 2; self.reinit_frequency = 5; + self.calving_max = 3000.; end % }}} @@ -46,4 +48,5 @@ md = checkfield(md,'fieldname','levelset.spclevelset','Inf',1,'timeseries',1); md = checkfield(md,'fieldname','levelset.stabilization','values',[0 1 2]); + md = checkfield(md,'fieldname','levelset.calving_max','numel',1,'NaN',1,'Inf',1,'>',0); end % }}} function disp(self) % {{{ @@ -52,9 +55,14 @@ fielddisplay(self,'spclevelset','Levelset constraints (NaN means no constraint)'); fielddisplay(self,'reinit_frequency','Amount of time steps after which the levelset function in re-initialized'); + fielddisplay(self,'calving_max','maximum allowed calving rate (m/a)'); end % }}} function marshall(self,prefix,md,fid) % {{{ + + yts=md.constants.yts; + WriteData(fid,prefix,'object',self,'fieldname','stabilization','format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','spclevelset','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); WriteData(fid,prefix,'object',self,'fieldname','reinit_frequency','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','calving_max','format','Double','scale',1./yts); end % }}} function savemodeljs(self,fid,modelname) % {{{ @@ -63,4 +71,5 @@ writejs1Darray(fid,[modelname '.levelset.spclevelset'],self.spclevelset); writejs1Darray(fid,[modelname '.levelset.reinit_frequency'],self.reinit_frequency); + writejsdouble(fid,[modelname '.levelset.calving_max'],self.calving_max); end % }}} Index: /issm/trunk/src/m/classes/levelset.py =================================================================== --- /issm/trunk/src/m/classes/levelset.py (revision 21728) +++ /issm/trunk/src/m/classes/levelset.py (revision 21729) @@ -14,7 +14,8 @@ def __init__(self): # {{{ - self.stabilization = 0 - self.spclevelset = float('NaN') + self.stabilization = 0 + self.spclevelset = float('NaN') self.reinit_frequency = 0 + self.calving_max = 0. #set defaults @@ -27,4 +28,5 @@ string="%s\n%s"%(string,fielddisplay(self,'spclevelset','levelset constraints (NaN means no constraint)')) string="%s\n%s"%(string,fielddisplay(self,'reinit_frequency','Amount of time steps after which the levelset function in re-initialized')) + string="%s\n%s"%(string,fielddisplay(self,'calving_max','maximum allowed calving rate (m/a)')) return string @@ -39,4 +41,5 @@ self.stabilization = 2 self.reinit_frequency = 5 + self.calving_max = 3000 return self @@ -50,4 +53,5 @@ md = checkfield(md,'fieldname','levelset.spclevelset','Inf',1,'timeseries',1) md = checkfield(md,'fieldname','levelset.stabilization','values',[0,1,2]); + md = checkfield(md,'fieldname','levelset.calving_max','NaN',1,'Inf',1,'>',0); return md @@ -55,6 +59,9 @@ def marshall(self,prefix,md,fid): # {{{ + yts=md.constants.yts; + WriteData(fid,prefix,'object',self,'fieldname','stabilization','format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','spclevelset','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); WriteData(fid,prefix,'object',self,'fieldname','reinit_frequency','format','Integer'); + WriteData(fid,prefix,'object',self,'fieldname','calving_max','format','Double','scale',1./yts); # }}} Index: /issm/trunk/src/m/classes/linearbasalforcings.m =================================================================== --- /issm/trunk/src/m/classes/linearbasalforcings.m (revision 21728) +++ /issm/trunk/src/m/classes/linearbasalforcings.m (revision 21729) @@ -7,7 +7,7 @@ properties (SetAccess=public) groundedice_melting_rate = NaN; - deepwater_melting_rate = NaN; - deepwater_elevation = NaN; - upperwater_elevation = NaN; + deepwater_melting_rate = 0.; + deepwater_elevation = 0.; + upperwater_elevation = 0.; geothermalflux = NaN; end @@ -22,4 +22,8 @@ error('constructor not supported'); end + end % }}} + function self = extrude(self,md) % {{{ + self.groundedice_melting_rate=project3d(md,'vector',self.groundedice_melting_rate,'type','node','layer',1); + self.geothermalflux=project3d(md,'vector',self.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux end % }}} function self = initialize(self,md) % {{{ @@ -51,5 +55,5 @@ md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0,'numel',1); md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<','basalforcings.upperwater_elevation','numel',1); - md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<',0,'numel',1); + md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<=',0,'numel',1); end if ismember('ThermalAnalysis',analyses) & ~(strcmp(solution,'TransientSolution') & md.transient.isthermal==0), Index: /issm/trunk/src/m/classes/linearbasalforcings.py =================================================================== --- /issm/trunk/src/m/classes/linearbasalforcings.py (revision 21728) +++ /issm/trunk/src/m/classes/linearbasalforcings.py (revision 21729) @@ -83,5 +83,5 @@ md = checkfield(md,'fieldname','basalforcings.deepwater_melting_rate','>=',0); md = checkfield(md,'fieldname','basalforcings.deepwater_elevation','<',md.basalforcings.upperwater_elevation); - md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<',0); + md = checkfield(md,'fieldname','basalforcings.upperwater_elevation','<=',0); md = checkfield(md,'fieldname','basalforcings.geothermalflux','NaN',1,'Inf',1,'timeseries',1,'>=',0) Index: /issm/trunk/src/m/classes/matdamageice.m =================================================================== --- /issm/trunk/src/m/classes/matdamageice.m (revision 21728) +++ /issm/trunk/src/m/classes/matdamageice.m (revision 21729) @@ -22,5 +22,5 @@ rheology_law = ''; - %gia: + %giaivins: lithosphere_shear_modulus = 0.; lithosphere_density = 0.; @@ -114,5 +114,5 @@ md = checkfield(md,'fieldname','materials.rheology_B','>',0,'size',[md.mesh.numberofvertices 1]); md = checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements 1]); - md = checkfield(md,'fieldname','materials.rheology_law','values',{'None' 'Cuffey' 'CuffeyTemperate' 'Paterson' 'Arrhenius' 'LliboutryDuval'}); + md = checkfield(md,'fieldname','materials.rheology_law','values',{'None' 'BuddJacka' 'Cuffey' 'CuffeyTemperate' 'Paterson' 'Arrhenius' 'LliboutryDuval'}); if ismember('GiaAnalysis',analyses), @@ -145,5 +145,5 @@ fielddisplay(self,'rheology_B','flow law parameter [Pa/s^(1/n)]'); fielddisplay(self,'rheology_n','Glen''s flow law exponent'); - fielddisplay(self,'rheology_law',['law for the temperature dependance of the rheology: ''None'', ''Cuffey'', ''CuffeyTemperate'', ''Paterson'', ''Arrhenius'' or ''LliboutryDuval''']); + fielddisplay(self,'rheology_law',['law for the temperature dependance of the rheology: ''None'', ''BuddJacka'', ''Cuffey'', ''CuffeyTemperate'', ''Paterson'', ''Arrhenius'' or ''LliboutryDuval''']); fielddisplay(self,'lithosphere_shear_modulus','Lithosphere shear modulus [Pa]'); fielddisplay(self,'lithosphere_density','Lithosphere density [g/cm^-3]'); Index: /issm/trunk/src/m/classes/matdamageice.py =================================================================== --- /issm/trunk/src/m/classes/matdamageice.py (revision 21728) +++ /issm/trunk/src/m/classes/matdamageice.py (revision 21729) @@ -29,5 +29,5 @@ self.rheology_law = '' - #gia: + #giaivins: self.lithosphere_shear_modulus = 0. self.lithosphere_density = 0. @@ -58,5 +58,5 @@ string="%s\n%s"%(string,fielddisplay(self,"rheology_B","flow law parameter [Pa/s^(1/n)]")) string="%s\n%s"%(string,fielddisplay(self,"rheology_n","Glen's flow law exponent")) - string="%s\n%s"%(string,fielddisplay(self,"rheology_law","law for the temperature dependance of the rheology: 'None', 'Cuffey', 'CuffeyTemperate', 'Paterson', 'Arrhenius' or 'LliboutryDuval'")) + string="%s\n%s"%(string,fielddisplay(self,"rheology_law","law for the temperature dependance of the rheology: 'None', 'BuddJacka', 'Cuffey', 'CuffeyTemperate', 'Paterson', 'Arrhenius' or 'LliboutryDuval'")) string="%s\n%s"%(string,fielddisplay(self,"lithosphere_shear_modulus","Lithosphere shear modulus [Pa]")) string="%s\n%s"%(string,fielddisplay(self,"lithosphere_density","Lithosphere density [g/cm^-3]")) @@ -133,5 +133,5 @@ md = checkfield(md,'fieldname','materials.rheology_B','>',0,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements]) - md = checkfield(md,'fieldname','materials.rheology_law','values',['None','Cuffey', 'CuffeyTemperate', 'Paterson','Arrhenius','LliboutryDuval']) + md = checkfield(md,'fieldname','materials.rheology_law','values',['None', 'BuddJacka', 'Cuffey', 'CuffeyTemperate', 'Paterson','Arrhenius','LliboutryDuval']) md = checkfield(md,'fieldname','materials.lithosphere_shear_modulus','>',0,'numel',[1]); md = checkfield(md,'fieldname','materials.lithosphere_density','>',0,'numel',[1]); Index: /issm/trunk/src/m/classes/matenhancedice.m =================================================================== --- /issm/trunk/src/m/classes/matenhancedice.m (revision 21729) +++ /issm/trunk/src/m/classes/matenhancedice.m (revision 21729) @@ -0,0 +1,209 @@ +%MATICE class definition +% +% Usage: +% matenhancedice=matenhancedice(); + +classdef matenhancedice + properties (SetAccess=public) + rho_ice = 0.; + rho_water = 0.; + rho_freshwater = 0.; + mu_water = 0.; + heatcapacity = 0.; + latentheat = 0.; + thermalconductivity = 0.; + temperateiceconductivity = 0.; + meltingpoint = 0.; + beta = 0.; + mixed_layer_capacity = 0.; + thermal_exchange_velocity = 0.; + rheology_E = NaN; + rheology_B = NaN; + rheology_n = NaN; + rheology_law = ''; + + %giaivins: + lithosphere_shear_modulus = 0.; + lithosphere_density = 0.; + mantle_shear_modulus = 0.; + mantle_density = 0.; + + %slr + earth_density = 0; + + end + methods + function self = extrude(self,md) % {{{ + self.rheology_E=project3d(md,'vector',self.rheology_E,'type','node'); + self.rheology_B=project3d(md,'vector',self.rheology_B,'type','node'); + self.rheology_n=project3d(md,'vector',self.rheology_n,'type','element'); + end % }}} + function self = matenhancedice(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + case 1 + inputstruct=varargin{1}; + list1 = properties('matenhancedice'); + list2 = fieldnames(inputstruct); + for i=1:length(list1) + fieldname = list1{i}; + if ismember(fieldname,list2), + self.(fieldname) = inputstruct.(fieldname); + end + end + otherwise + error('constructor not supported'); + end + end % }}} + function self = setdefaultparameters(self) % {{{ + + %ice density (kg/m^3) + self.rho_ice=917.; + + %ocean water density (kg/m^3) + self.rho_water=1023.; + + %fresh water density (kg/m^3) + self.rho_freshwater=1000.; + + %water viscosity (N.s/m^2) + self.mu_water=0.001787; + + %ice heat capacity cp (J/kg/K) + self.heatcapacity=2093.; + + %ice latent heat of fusion L (J/kg) + self.latentheat=3.34*10^5; + + %ice thermal conductivity (W/m/K) + self.thermalconductivity=2.4; + + %wet ice thermal conductivity (W/m/K) + self.temperateiceconductivity=.24; + + %the melting point of ice at 1 atmosphere of pressure in K + self.meltingpoint=273.15; + + %rate of change of melting point with pressure (K/Pa) + self.beta=9.8*10^-8; + + %mixed layer (ice-water interface) heat capacity (J/kg/K) + self.mixed_layer_capacity=3974.; + + %thermal exchange velocity (ice-water interface) (m/s) + self.thermal_exchange_velocity=1.00*10^-4; + + %Rheology law: what is the temperature dependence of B with T + %available: none, paterson and arrhenius + self.rheology_law='Paterson'; + + % GIA: + self.lithosphere_shear_modulus = 6.7*10^10; % (Pa) + self.lithosphere_density = 3.32; % (g/cm^-3) + self.mantle_shear_modulus = 1.45*10^11; % (Pa) + self.mantle_density = 3.34; % (g/cm^-3) + + %SLR + self.earth_density= 5512; % average density of the Earth, (kg/m^3) + + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + md = checkfield(md,'fieldname','materials.rho_ice','>',0); + md = checkfield(md,'fieldname','materials.rho_water','>',0); + md = checkfield(md,'fieldname','materials.rho_freshwater','>',0); + md = checkfield(md,'fieldname','materials.mu_water','>',0); + md = checkfield(md,'fieldname','materials.rheology_E','>',0,'timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','materials.rheology_B','>',0,'timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements 1]); + md = checkfield(md,'fieldname','materials.rheology_law','values',{'None' 'BuddJacka' 'Cuffey' 'CuffeyTemperate' 'Paterson' 'Arrhenius' 'LliboutryDuval'}); + + if ismember('GiaAnalysis',analyses), + md = checkfield(md,'fieldname','materials.lithosphere_shear_modulus','>',0,'numel',1); + md = checkfield(md,'fieldname','materials.lithosphere_density','>',0,'numel',1); + md = checkfield(md,'fieldname','materials.mantle_shear_modulus','>',0,'numel',1); + md = checkfield(md,'fieldname','materials.mantle_density','>',0,'numel',1); + end + if ismember('SealevelriseAnalysis',analyses), + md = checkfield(md,'fieldname','materials.earth_density','>',0,'numel',1); + end + + end % }}} + function disp(self) % {{{ + disp(sprintf(' Materials:')); + + fielddisplay(self,'rho_ice','ice density [kg/m^3]'); + fielddisplay(self,'rho_water','ocean water density [kg/m^3]'); + fielddisplay(self,'rho_freshwater','fresh water density [kg/m^3]'); + fielddisplay(self,'mu_water','water viscosity [N s/m^2]'); + fielddisplay(self,'heatcapacity','heat capacity [J/kg/K]'); + fielddisplay(self,'thermalconductivity',['ice thermal conductivity [W/m/K]']); + fielddisplay(self,'temperateiceconductivity','temperate ice thermal conductivity [W/m/K]'); + fielddisplay(self,'meltingpoint','melting point of ice at 1atm in K'); + fielddisplay(self,'latentheat','latent heat of fusion [J/kg]'); + fielddisplay(self,'beta','rate of change of melting point with pressure [K/Pa]'); + fielddisplay(self,'mixed_layer_capacity','mixed layer capacity [W/kg/K]'); + fielddisplay(self,'thermal_exchange_velocity','thermal exchange velocity [m/s]'); + fielddisplay(self,'rheology_E','enhancement factor'); + fielddisplay(self,'rheology_B','flow law parameter [Pa/s^(1/n)]'); + fielddisplay(self,'rheology_n','Glen''s flow law exponent'); + fielddisplay(self,'rheology_law',['law for the temperature dependance of the rheology: ''None'', ''BuddJacka'', Cuffey'', ''CuffeyTemperate'', ''Paterson'', ''Arrhenius'' or ''LliboutryDuval''']); + fielddisplay(self,'lithosphere_shear_modulus','Lithosphere shear modulus [Pa]'); + fielddisplay(self,'lithosphere_density','Lithosphere density [g/cm^-3]'); + fielddisplay(self,'mantle_shear_modulus','Mantle shear modulus [Pa]'); + fielddisplay(self,'mantle_density','Mantle density [g/cm^-3]'); + fielddisplay(self,'earth_density','Mantle density [kg/m^-3]'); + end % }}} + function marshall(self,prefix,md,fid) % {{{ + WriteData(fid,prefix,'name','md.materials.type','data',4,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_ice','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_water','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_freshwater','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mu_water','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','heatcapacity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','latentheat','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','thermalconductivity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','temperateiceconductivity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','meltingpoint','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','beta','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mixed_layer_capacity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','thermal_exchange_velocity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_E','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_B','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_n','format','DoubleMat','mattype',2); + WriteData(fid,prefix,'data',self.rheology_law,'name','md.materials.rheology_law','format','String'); + + WriteData(fid,prefix,'object',self,'class','materials','fieldname','lithosphere_shear_modulus','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','lithosphere_density','format','Double','scale',10^3); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mantle_shear_modulus','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mantle_density','format','Double','scale',10^3); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','earth_density','format','Double'); + end % }}} + function savemodeljs(self,fid,modelname) % {{{ + + writejsdouble(fid,[modelname '.materials.rho_ice'],self.rho_ice); + writejsdouble(fid,[modelname '.materials.rho_water'],self.rho_water); + writejsdouble(fid,[modelname '.materials.rho_freshwater'],self.rho_freshwater); + writejsdouble(fid,[modelname '.materials.mu_water'],self.mu_water); + writejsdouble(fid,[modelname '.materials.heatcapacity'],self.heatcapacity); + writejsdouble(fid,[modelname '.materials.latentheat'],self.latentheat); + writejsdouble(fid,[modelname '.materials.thermalconductivity'],self.thermalconductivity); + writejsdouble(fid,[modelname '.materials.temperateiceconductivity'],self.temperateiceconductivity); + writejsdouble(fid,[modelname '.materials.meltingpoint'],self.meltingpoint); + writejsdouble(fid,[modelname '.materials.beta'],self.beta); + writejsdouble(fid,[modelname '.materials.mixed_layer_capacity'],self.mixed_layer_capacity); + writejsdouble(fid,[modelname '.materials.thermal_exchange_velocity'],self.thermal_exchange_velocity); + writejsdouble(fid,[modelname '.materials.mixed_layer_capacity'],self.mixed_layer_capacity); + writejs1Darray(fid,[modelname '.materials.rheology_E'],self.rheology_E); + writejs1Darray(fid,[modelname '.materials.rheology_B'],self.rheology_B); + writejs1Darray(fid,[modelname '.materials.rheology_n'],self.rheology_n); + writejsstring(fid,[modelname '.materials.rheology_law'],self.rheology_law); + writejsdouble(fid,[modelname '.materials.lithosphere_shear_modulus'],self.lithosphere_shear_modulus); + writejsdouble(fid,[modelname '.materials.lithosphere_density'],self.lithosphere_density); + writejsdouble(fid,[modelname '.materials.mantle_shear_modulus'],self.mantle_shear_modulus); + writejsdouble(fid,[modelname '.materials.mantle_density'],self.mantle_density); + writejsdouble(fid,[modelname '.materials.earth_density'],self.earth_density); + + end % }}} + end +end Index: /issm/trunk/src/m/classes/materials.m =================================================================== --- /issm/trunk/src/m/classes/materials.m (revision 21729) +++ /issm/trunk/src/m/classes/materials.m (revision 21729) @@ -0,0 +1,319 @@ +%MATERIALS class definition +% +% Usage: +% materials=materials(); + +classdef materials < dynamicprops + properties (SetAccess=public) + nature={}; + %all properties are dynamic. + end + methods + function self = materials(varargin) % {{{ + if nargin==0 + self.nature={'ice'}; + else + self.nature=varargin; + end + + %check this is acceptable: + for i=1:length(self.nature), + if ~(strcmpi(self.nature{i},'litho') | strcmpi(self.nature{i},'ice')), + error('materials constructor error message: nature of the material not supported yet! (''ice'' or ''litho'')'); + end + end + + %start filling in the dynamic fields: + for i=1:length(self.nature), + nat=self.nature{i}; + switch nat + case 'ice' + self.addprop('rho_ice'); + self.addprop('rho_water'); + self.addprop('rho_freshwater'); + self.addprop('mu_water'); + self.addprop('heatcapacity'); + self.addprop('latentheat'); + self.addprop('thermalconductivity'); + self.addprop('temperateiceconductivity'); + self.addprop('meltingpoint'); + self.addprop('beta'); + self.addprop('mixed_layer_capacity'); + self.addprop('thermal_exchange_velocity'); + self.addprop('rheology_B'); + self.addprop('rheology_n'); + self.addprop('rheology_law'); + case 'litho' + self.addprop('numlayers'); + self.addprop('radius'); + self.addprop('viscosity'); + self.addprop('lame_lambda'); + self.addprop('lame_mu'); + self.addprop('burgers_viscosity'); + self.addprop('burgers_mu'); + self.addprop('isburgers'); + self.addprop('density'); + self.addprop('issolid'); + otherwise + error('materials constructor error message: nature of the material not supported yet! (''ice'' or ''litho'')'); + end + end + %set default parameters: + self.setdefaultparameters(); + + end % }}} + function self = setdefaultparameters(self) % {{{ + + for i=1:length(self.nature), + nat=self.nature{i}; + switch nat + case 'ice' + %ice density (kg/m^3) + self.rho_ice=917.; + + %ocean water density (kg/m^3) + self.rho_water=1023.; + + %fresh water density (kg/m^3) + self.rho_freshwater=1000.; + + %water viscosity (N.s/m^2) + self.mu_water=0.001787; + + %ice heat capacity cp (J/kg/K) + self.heatcapacity=2093.; + + %ice latent heat of fusion L (J/kg) + self.latentheat=3.34*10^5; + + %ice thermal conductivity (W/m/K) + self.thermalconductivity=2.4; + + %wet ice thermal conductivity (W/m/K) + self.temperateiceconductivity=.24; + + %the melting point of ice at 1 atmosphere of pressure in K + self.meltingpoint=273.15; + + %rate of change of melting point with pressure (K/Pa) + self.beta=9.8*10^-8; + + %mixed layer (ice-water interface) heat capacity (J/kg/K) + self.mixed_layer_capacity=3974.; + + %thermal exchange velocity (ice-water interface) (m/s) + self.thermal_exchange_velocity=1.00*10^-4; + + %Rheology law: what is the temperature dependence of B with T + %available: none, paterson and arrhenius + self.rheology_law='Paterson'; + + case 'litho' + %we default to a configuration that enables running GIA solutions using giacaron and/or giaivins. + self.numlayers=2; + + %surface, then the lab (lithosphere/asthenosphere boundary) then the center of the earth + %(with 1d3 to avoid numerical singularities) + self.radius=[6378*1e3;6278*1e3;1e3]; + + self.viscosity=[1e40;1e21]; %lithosphere and mantle viscosity (respectively) [Pa.s] + self.lame_mu=[6.7*10^10;1.45*1e11]; % (Pa) %lithosphere and mantle shear modulus (respectively) [Pa] + self.lame_lambda=[6.7*10^10;1.45*1e11]; % (Pa) %lithosphere and mantle lamba parameter (respectively) [Pa] + self.burgers_viscosity=[NaN;NaN]; + self.burgers_mu=[NaN;NaN]; + self.isburgers=[false;false]; + self.density=[3.32*1e3;3.34*1e3]; % (Pa) %lithosphere and mantle density [kg/m^3] + self.issolid=[true;true]; % is layer solid or liquid. + + otherwise + error('materials constructor error message: nature of the material not supported yet! (''ice'' or ''litho'')'); + end + end + end % }}} + function disp(self) % {{{ + disp(sprintf(' Materials:')); + + for i=1:length(self.nature), + nat=self.nature{i}; + switch nat + case 'ice' + disp(sprintf(' \nIce:')); + fielddisplay(self,'rho_ice','ice density [kg/m^3]'); + fielddisplay(self,'rho_water','ocean water density [kg/m^3]'); + fielddisplay(self,'rho_freshwater','fresh water density [kg/m^3]'); + fielddisplay(self,'mu_water','water viscosity [N s/m^2]'); + fielddisplay(self,'heatcapacity','heat capacity [J/kg/K]'); + fielddisplay(self,'thermalconductivity',['ice thermal conductivity [W/m/K]']); + fielddisplay(self,'temperateiceconductivity','temperate ice thermal conductivity [W/m/K]'); + fielddisplay(self,'meltingpoint','melting point of ice at 1atm in K'); + fielddisplay(self,'latentheat','latent heat of fusion [J/kg]'); + fielddisplay(self,'beta','rate of change of melting point with pressure [K/Pa]'); + fielddisplay(self,'mixed_layer_capacity','mixed layer capacity [W/kg/K]'); + fielddisplay(self,'thermal_exchange_velocity','thermal exchange velocity [m/s]'); + fielddisplay(self,'rheology_B','flow law parameter [Pa/s^(1/n)]'); + fielddisplay(self,'rheology_n','Glen''s flow law exponent'); + fielddisplay(self,'rheology_law',['law for the temperature dependance of the rheology: ''None'', ''BuddJacka'', Cuffey'', ''CuffeyTemperate'', ''Paterson'', ''Arrhenius'' or ''LliboutryDuval''']); + case 'litho' + disp(sprintf(' \nLitho:')); + fielddisplay(self,'numlayers','number of layers (default 2)'); + fielddisplay(self,'radius','array describing the radius for each interface (numlayers+1) [m]'); + fielddisplay(self,'viscosity','array describing each layer''s viscosity (numlayers) [Pa.s]'); + fielddisplay(self,'lame_lambda','array describing the lame lambda parameter (numlayers) [Pa]'); + fielddisplay(self,'lame_mu','array describing the shear modulus for each layers (numlayers) [Pa]'); + fielddisplay(self,'burgers_viscosity','array describing each layer''s transient viscosity, only for Burgers rheologies (numlayers) [Pa.s]'); + fielddisplay(self,'burgers_mu','array describing each layer''s transient shear modulus, only for Burgers rheologies (numlayers) [Pa]'); + fielddisplay(self,'isburgers','array describing whether we adopt a MaxWell (0) or Burgers (1) rheology (default 0)'); + fielddisplay(self,'density','array describing each layer''s density (numlayers) [kg/m^3]'); + fielddisplay(self,'issolid','array describing whether the layer is solid or liquid (default 1) (numlayers)'); + otherwise + error('materials constructor error message: nature of the material not supported yet! (''ice'' or ''litho'')'); + end + end + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + + for i=1:length(self.nature), + nat=self.nature{i}; + switch nat + case 'ice' + md = checkfield(md,'fieldname','materials.rho_ice','>',0); + md = checkfield(md,'fieldname','materials.rho_water','>',0); + md = checkfield(md,'fieldname','materials.rho_freshwater','>',0); + md = checkfield(md,'fieldname','materials.mu_water','>',0); + md = checkfield(md,'fieldname','materials.rheology_B','>',0,'timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements 1]); + md = checkfield(md,'fieldname','materials.rheology_law','values',{'None' 'BuddJacka' 'Cuffey' 'CuffeyTemperate' 'Paterson' 'Arrhenius' 'LliboutryDuval'}); + case 'litho' + if ~ismember('LoveAnalysis',analyses), return; end + md = checkfield(md,'fieldname','materials.numlayers','NaN',1,'Inf',1,'>',0,'numel',1); + md = checkfield(md,'fieldname','materials.radius','NaN',1,'Inf',1,'size',[md.materials.numlayers+1 1],'>',0); + md = checkfield(md,'fieldname','materials.lame_mu','NaN',1,'Inf',1,'size',[md.materials.numlayers 1],'>',0); + md = checkfield(md,'fieldname','materials.lame_lambda','NaN',1,'Inf',1,'size',[md.materials.numlayers 1],'>',0); + md = checkfield(md,'fieldname','materials.issolid','NaN',1,'Inf',1,'size',[md.materials.numlayers 1],'>',0,'<',2); + md = checkfield(md,'fieldname','materials.density','NaN',1,'Inf',1,'size',[md.materials.numlayers 1],'>',0); + md = checkfield(md,'fieldname','materials.viscosity','NaN',1,'Inf',1,'size',[md.materials.numlayers 1],'>',0); + md = checkfield(md,'fieldname','materials.isburgers','NaN',1,'Inf',1,'size',[md.materials.numlayers 1],'>',0,'<',2); + md = checkfield(md,'fieldname','materials.burgers_viscosity','NaN',1,'Inf',1,'size',[md.materials.numlayers 1],'>',0); + md = checkfield(md,'fieldname','materials.burgers_mu','NaN',1,'Inf',1,'size',[md.materials.numlayers 1],'>',0); + + otherwise + error('materials constructor error message: nature of the material not supported yet! (''ice'' or ''litho'')'); + end + end + + end % }}} + function intnat = naturetointeger(strnat) % {{{ + intnat=zeros(length(strnat),1); + for i=1:length(strnat), + switch strnat{i}, + case 'damageice' + intnat(i)=1; + case 'estar' + intnat(i)=2; + case 'ice' + intnat(i)=3; + case 'enhancedice' + intnat(i)=4; + case 'litho' + intnat(i)=5; + otherwise + error('materials constructor error message: nature of the material not supported yet! (''ice'' or ''litho'')'); + end + end + end % }}} + function marshall(self,prefix,md,fid) % {{{ + + %1: MatdamageiceEnum 2: MatestarEnum 3: MaticeEnum 4: MatenhancediceEnum 5: MaterialsEnum + WriteData(fid,prefix,'name','md.materials.type','data',6,'format','Integer'); + WriteData(fid,prefix,'name','md.materials.nature','data',naturetointeger(self.nature),'format','IntMat','mattype',1); + + for i=1:length(self.nature), + nat=self.nature{i}; + switch nat + case 'ice' + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_ice','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_water','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rho_freshwater','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mu_water','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','heatcapacity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','latentheat','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','thermalconductivity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','temperateiceconductivity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','meltingpoint','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','beta','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','mixed_layer_capacity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','thermal_exchange_velocity','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_B','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_n','format','DoubleMat','mattype',2); + WriteData(fid,prefix,'data',self.rheology_law,'name','md.materials.rheology_law','format','String'); + case 'litho' + WriteData(fid,prefix,'object',self,'class','materials','fieldname','numlayers','format','Double'); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','radius','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','lame_mu','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','lame_lambda ','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','issolid','format','BooleanMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','density','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','viscosity','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','isburgers','format','BooleanMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','burgers_viscosity','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','burgers_mu','format','DoubleMat','mattype',1); + otherwise + error('materials constructor error message: nature of the material not supported yet! (''ice'' or ''litho'')'); + end + end + end % }}} + function self = extrude(self,md) % {{{ + for i=1:length(self.nature), + nat=self.nature{i}; + switch nat + case 'ice' + self.rheology_B=project3d(md,'vector',self.rheology_B,'type','node'); + self.rheology_n=project3d(md,'vector',self.rheology_n,'type','element'); + end + end + end % }}} + function savemodeljs(self,fid,modelname) % {{{ + + for i=1:length(self.nature), + nat=self.nature{i}; + switch nat + case 'ice' + writejsdouble(fid,[modelname '.materials.rho_ice'],self.rho_ice); + writejsdouble(fid,[modelname '.materials.rho_water'],self.rho_water); + writejsdouble(fid,[modelname '.materials.rho_freshwater'],self.rho_freshwater); + writejsdouble(fid,[modelname '.materials.mu_water'],self.mu_water); + writejsdouble(fid,[modelname '.materials.heatcapacity'],self.heatcapacity); + writejsdouble(fid,[modelname '.materials.latentheat'],self.latentheat); + writejsdouble(fid,[modelname '.materials.thermalconductivity'],self.thermalconductivity); + writejsdouble(fid,[modelname '.materials.temperateiceconductivity'],self.temperateiceconductivity); + writejsdouble(fid,[modelname '.materials.meltingpoint'],self.meltingpoint); + writejsdouble(fid,[modelname '.materials.beta'],self.beta); + writejsdouble(fid,[modelname '.materials.mixed_layer_capacity'],self.mixed_layer_capacity); + writejsdouble(fid,[modelname '.materials.thermal_exchange_velocity'],self.thermal_exchange_velocity); + writejsdouble(fid,[modelname '.materials.mixed_layer_capacity'],self.mixed_layer_capacity); + writejs1Darray(fid,[modelname '.materials.rheology_B'],self.rheology_B); + writejs1Darray(fid,[modelname '.materials.rheology_n'],self.rheology_n); + writejsstring(fid,[modelname '.materials.rheology_law'],self.rheology_law); + case 'litho' + writejsdouble(fid,[modelname '.materials.numlayers'],self.numlayers); + writejsdouble(fid,[modelname '.materials.radius'],self.radius); + writejsdouble(fid,[modelname '.materials.lame_mu'],self.lame_mu); + writejsdouble(fid,[modelname '.materials.lame_lambda'],self.lame_lambda); + writejsdouble(fid,[modelname '.materials.issolid'],self.issolid); + writejsdouble(fid,[modelname '.materials.density'],self.density); + writejsdouble(fid,[modelname '.materials.viscosity'],self.viscosity); + writejsdouble(fid,[modelname '.materials.isburgers'],self.isburgers); + writejsdouble(fid,[modelname '.materials.burgers_viscosity'],self.burgers_viscosity); + writejsdouble(fid,[modelname '.materials.burgers_mu'],self.burgers_mu); + otherwise + error('materials constructor error message: nature of the material not supported yet! (''ice'' or ''litho'')'); + end + end + + + + end % }}} + end +end + + Index: /issm/trunk/src/m/classes/matestar.m =================================================================== --- /issm/trunk/src/m/classes/matestar.m (revision 21728) +++ /issm/trunk/src/m/classes/matestar.m (revision 21729) @@ -18,10 +18,10 @@ mixed_layer_capacity = 0.; thermal_exchange_velocity = 0.; - rheology_ko = NaN; + rheology_B = NaN; rheology_Ec = NaN; rheology_Es = NaN; rheology_law = ''; - %gia: + %giaivins: lithosphere_shear_modulus = 0.; lithosphere_density = 0.; @@ -35,5 +35,5 @@ methods function self = extrude(self,md) % {{{ - self.rheology_ko=project3d(md,'vector',self.rheology_ko,'type','node'); + self.rheology_B=project3d(md,'vector',self.rheology_B,'type','node'); self.rheology_Ec=project3d(md,'vector',self.rheology_Ec,'type','node'); self.rheology_Es=project3d(md,'vector',self.rheology_Es,'type','node'); @@ -58,5 +58,5 @@ self.rheology_Es = ones(size(inputstruct.rheology_B)); self.rheology_Ec = ones(size(inputstruct.rheology_B)); - self.rheology_ko = inputstruct.rheology_B.^(-3)*3/2; + self.rheology_B = inputstruct.rheology_B; end otherwise @@ -121,8 +121,8 @@ md = checkfield(md,'fieldname','materials.rho_freshwater','>',0); md = checkfield(md,'fieldname','materials.mu_water','>',0); - md = checkfield(md,'fieldname','materials.rheology_ko','>',0,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','materials.rheology_B','>',0,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); md = checkfield(md,'fieldname','materials.rheology_Ec','>',0,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); md = checkfield(md,'fieldname','materials.rheology_Es','>',0,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); - md = checkfield(md,'fieldname','materials.rheology_law','values',{'None' 'Cuffey' 'CuffeyTemperate' 'Paterson' 'Arrhenius' 'LliboutryDuval'}); + md = checkfield(md,'fieldname','materials.rheology_law','values',{'None' 'BuddJacka' 'Cuffey' 'CuffeyTemperate' 'Paterson' 'Arrhenius' 'LliboutryDuval'}); if ismember('GiaAnalysis',analyses), @@ -152,8 +152,8 @@ fielddisplay(self,'mixed_layer_capacity','mixed layer capacity [W/kg/K]'); fielddisplay(self,'thermal_exchange_velocity','thermal exchange velocity [m/s]'); - fielddisplay(self,'rheology_ko','octahedral flow law parameter [s^-1 Pa^-2]'); + fielddisplay(self,'rheology_B','flow law parameter [Pa/s^(1/3)]'); fielddisplay(self,'rheology_Ec','compressive enhancement factor'); fielddisplay(self,'rheology_Es','shear enhancement factor'); - fielddisplay(self,'rheology_law',['law for the temperature dependance of the rheology: ''None'', ''Cuffey'', ''CuffeyTemperate'', ''Paterson'', ''Arrhenius'' or ''LliboutryDuval''']); + fielddisplay(self,'rheology_law',['law for the temperature dependance of the rheology: ''None'', ''BuddJacka'', ''Cuffey'', ''CuffeyTemperate'', ''Paterson'', ''Arrhenius'' or ''LliboutryDuval''']); fielddisplay(self,'lithosphere_shear_modulus','Lithosphere shear modulus [Pa]'); fielddisplay(self,'lithosphere_density','Lithosphere density [g/cm^-3]'); @@ -176,5 +176,5 @@ WriteData(fid,prefix,'object',self,'class','materials','fieldname','mixed_layer_capacity','format','Double'); WriteData(fid,prefix,'object',self,'class','materials','fieldname','thermal_exchange_velocity','format','Double'); - WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_ko','format','DoubleMat','mattype',1); + WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_B','format','DoubleMat','mattype',1); WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_Ec','format','DoubleMat','mattype',1); WriteData(fid,prefix,'object',self,'class','materials','fieldname','rheology_Es','format','DoubleMat','mattype',1); @@ -202,5 +202,5 @@ writejsdouble(fid,[modelname '.materials.thermal_exchange_velocity'],self.thermal_exchange_velocity); writejsdouble(fid,[modelname '.materials.mixed_layer_capacity'],self.mixed_layer_capacity); - writejs1Darray(fid,[modelname '.materials.rheology_ko'],self.rheology_ko); + writejs1Darray(fid,[modelname '.materials.rheology_B'],self.rheology_B); writejs1Darray(fid,[modelname '.materials.rheology_Ec'],self.rheology_Ec); writejs1Darray(fid,[modelname '.materials.rheology_Es'],self.rheology_Es); Index: /issm/trunk/src/m/classes/matice.js =================================================================== --- /issm/trunk/src/m/classes/matice.js (revision 21728) +++ /issm/trunk/src/m/classes/matice.js (revision 21729) @@ -76,5 +76,5 @@ fielddisplay(this,'rheology_B','flow law parameter [Pa/s^(1/n)]'); fielddisplay(this,'rheology_n',"Glen's flow law exponent"); - fielddisplay(this,'rheology_law',"law for the temperature dependance of the rheology: 'None', 'Cuffey', 'CuffeyTemperate', 'Paterson', 'Arrhenius' or 'LliboutryDuval'"); + fielddisplay(this,'rheology_law',"law for the temperature dependance of the rheology: 'None', 'BuddJacka', 'Cuffey', 'CuffeyTemperate', 'Paterson', 'Arrhenius' or 'LliboutryDuval'"); fielddisplay(this,'lithosphere_shear_modulus','Lithosphere shear modulus [Pa]'); fielddisplay(this,'lithosphere_density','Lithosphere density [g/cm^-3]'); @@ -99,5 +99,5 @@ checkfield(md,'fieldname','materials.rheology_B','>',0,'timeseries',1,'NaN',1,'Inf',1); checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements,1]); - checkfield(md,'fieldname','materials.rheology_law','values',['None','Cuffey','CuffeyTemperate','Paterson','Arrhenius','LliboutryDuval']); + checkfield(md,'fieldname','materials.rheology_law','values',['None','BuddJacka','Cuffey','CuffeyTemperate','Paterson','Arrhenius','LliboutryDuval']); if(ArrayAnyEqual(ArrayIsMember('GiaAnalysis',analyses),1)){ @@ -157,5 +157,5 @@ this.rheology_law = ''; - //gia: + //giaivins: this.lithosphere_shear_modulus = 0.; this.lithosphere_density = 0.; Index: /issm/trunk/src/m/classes/matice.m =================================================================== --- /issm/trunk/src/m/classes/matice.m (revision 21728) +++ /issm/trunk/src/m/classes/matice.m (revision 21729) @@ -22,5 +22,5 @@ rheology_law = ''; - %gia: + %giaivins: lithosphere_shear_modulus = 0.; lithosphere_density = 0.; @@ -114,5 +114,5 @@ md = checkfield(md,'fieldname','materials.rheology_B','>',0,'timeseries',1,'NaN',1,'Inf',1); md = checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements 1]); - md = checkfield(md,'fieldname','materials.rheology_law','values',{'None' 'Cuffey' 'CuffeyTemperate' 'Paterson' 'Arrhenius' 'LliboutryDuval'}); + md = checkfield(md,'fieldname','materials.rheology_law','values',{'None' 'BuddJacka' 'Cuffey' 'CuffeyTemperate' 'Paterson' 'Arrhenius' 'LliboutryDuval'}); if ismember('GiaAnalysis',analyses), @@ -144,5 +144,5 @@ fielddisplay(self,'rheology_B','flow law parameter [Pa/s^(1/n)]'); fielddisplay(self,'rheology_n','Glen''s flow law exponent'); - fielddisplay(self,'rheology_law',['law for the temperature dependance of the rheology: ''None'', ''Cuffey'', ''CuffeyTemperate'', ''Paterson'', ''Arrhenius'' or ''LliboutryDuval''']); + fielddisplay(self,'rheology_law',['law for the temperature dependance of the rheology: ''None'', ''BuddJacka'', Cuffey'', ''CuffeyTemperate'', ''Paterson'', ''Arrhenius'' or ''LliboutryDuval''']); fielddisplay(self,'lithosphere_shear_modulus','Lithosphere shear modulus [Pa]'); fielddisplay(self,'lithosphere_density','Lithosphere density [g/cm^-3]'); Index: /issm/trunk/src/m/classes/matice.py =================================================================== --- /issm/trunk/src/m/classes/matice.py (revision 21728) +++ /issm/trunk/src/m/classes/matice.py (revision 21729) @@ -29,5 +29,5 @@ self.rheology_law = '' - #gia: + #giaivins: self.lithosphere_shear_modulus = 0. self.lithosphere_density = 0. @@ -59,5 +59,5 @@ string="%s\n%s"%(string,fielddisplay(self,"rheology_B","flow law parameter [Pa/s^(1/n)]")) string="%s\n%s"%(string,fielddisplay(self,"rheology_n","Glen's flow law exponent")) - string="%s\n%s"%(string,fielddisplay(self,"rheology_law","law for the temperature dependance of the rheology: 'None', 'Cuffey', 'CuffeyTemperate', 'Paterson', 'Arrhenius' or 'LliboutryDuval'")) + string="%s\n%s"%(string,fielddisplay(self,"rheology_law","law for the temperature dependance of the rheology: 'None', 'BuddJacka', 'Cuffey', 'CuffeyTemperate', 'Paterson', 'Arrhenius' or 'LliboutryDuval'")) string="%s\n%s"%(string,fielddisplay(self,"lithosphere_shear_modulus","Lithosphere shear modulus [Pa]")) string="%s\n%s"%(string,fielddisplay(self,"lithosphere_density","Lithosphere density [g/cm^-3]")) @@ -134,5 +134,5 @@ md = checkfield(md,'fieldname','materials.rheology_B','>',0,'timeseries',1,'NaN',1,'Inf',1) md = checkfield(md,'fieldname','materials.rheology_n','>',0,'size',[md.mesh.numberofelements]) - md = checkfield(md,'fieldname','materials.rheology_law','values',['None','Cuffey','CuffeyTemperate','Paterson','Arrhenius','LliboutryDuval']) + md = checkfield(md,'fieldname','materials.rheology_law','values',['None','BuddJacka','Cuffey','CuffeyTemperate','Paterson','Arrhenius','LliboutryDuval']) md = checkfield(md,'fieldname','materials.lithosphere_shear_modulus','>',0,'numel',[1]); md = checkfield(md,'fieldname','materials.lithosphere_density','>',0,'numel',[1]); Index: /issm/trunk/src/m/classes/mesh2d.py =================================================================== --- /issm/trunk/src/m/classes/mesh2d.py (revision 21728) +++ /issm/trunk/src/m/classes/mesh2d.py (revision 21729) @@ -92,4 +92,5 @@ md = checkfield(md,'fieldname','mesh.numberofvertices','>',0) md = checkfield(md,'fieldname','mesh.average_vertex_connectivity','>=',9,'message',"'mesh.average_vertex_connectivity' should be at least 9 in 2d") + md = checkfield(md,'fieldname','mesh.segments','NaN',1,'Inf',1,'>',0,'size',[np.nan,3]); if solution=='ThermalSolution': md.checkmessage("thermal not supported for 2d mesh") @@ -117,3 +118,4 @@ WriteData(fid,prefix,'object',self,'class','mesh','fieldname','numberofvertices','format','Integer') WriteData(fid,prefix,'object',self,'class','mesh','fieldname','average_vertex_connectivity','format','Integer') + WriteData(fid,prefix,'object',self,'class','mesh','fieldname','segments','format','DoubleMat','mattype',3); # }}} Index: /issm/trunk/src/m/classes/mesh3dprisms.m =================================================================== --- /issm/trunk/src/m/classes/mesh3dprisms.m (revision 21728) +++ /issm/trunk/src/m/classes/mesh3dprisms.m (revision 21729) @@ -104,7 +104,18 @@ md = checkfield(md,'fieldname','mesh.vertexonbase','size',[md.mesh.numberofvertices 1],'values',[0 1]); md = checkfield(md,'fieldname','mesh.vertexonsurface','size',[md.mesh.numberofvertices 1],'values',[0 1]); + md = checkfield(md,'fieldname','mesh.average_vertex_connectivity','>=',24,'message','''mesh.average_vertex_connectivity'' should be at least 24 in 3d'); + + %Check that mesh follows the geometry md = checkfield(md,'fieldname','mesh.z','>=',md.geometry.base-10^-10,'message','''mesh.z'' lower than bedrock'); md = checkfield(md,'fieldname','mesh.z','<=',md.geometry.surface+10^-10,'message','''mesh.z'' higher than surface elevation'); - md = checkfield(md,'fieldname','mesh.average_vertex_connectivity','>=',24,'message','''mesh.average_vertex_connectivity'' should be at least 24 in 3d'); + if any(max(abs(project2d(md,md.mesh.z,1)-project2d(md,md.geometry.base,1)))>1e-10), + md = checkmessage(md,'md.mesh.z is not consistent with md.geometry.base, you changed the geometry after extrusion'); + end + if any(max(abs(project2d(md,md.mesh.z,md.mesh.numberoflayers)-project2d(md,md.geometry.surface,1)))>1e-10), + md = checkmessage(md,'md.mesh.z is not consistent with md.geometry.surface, you changed the geometry after extrusion !!'); + end + if any(max(abs(project2d(md,md.mesh.z,md.mesh.numberoflayers)-project2d(md,md.mesh.z,1) - project2d(md,md.geometry.thickness,1)))>1e-10), + md = checkmessage(md,'md.mesh.z is not consistent with md.geometry.thickness, you changed the geometry after extrusion !!'); + end end % }}} function disp(self) % {{{ Index: /issm/trunk/src/m/classes/mesh3dprisms.py =================================================================== --- /issm/trunk/src/m/classes/mesh3dprisms.py (revision 21728) +++ /issm/trunk/src/m/classes/mesh3dprisms.py (revision 21729) @@ -73,8 +73,8 @@ string="%s\n%s"%(string,fielddisplay(self,"vertexonbase","lower vertices flags list")) string="%s\n%s"%(string,fielddisplay(self,"vertexonsurface","upper vertices flags list")) - string="%s\n%s"%(string,fielddisplay(self,"uppervertex","upper vertex list (-1 for vertex on the upper surface)")) - string="%s\n%s"%(string,fielddisplay(self,"upperelements","upper element list (-1 for element on the upper layer)")) - string="%s\n%s"%(string,fielddisplay(self,"lowervertex","lower vertex list (-1 for vertex on the lower surface)")) - string="%s\n%s"%(string,fielddisplay(self,"lowerelements","lower element list (-1 for element on the lower layer)")) + string="%s\n%s"%(string,fielddisplay(self,"uppervertex","upper vertex list (NaN for vertex on the upper surface)")) + string="%s\n%s"%(string,fielddisplay(self,"upperelements","upper element list (NaN for element on the upper layer)")) + string="%s\n%s"%(string,fielddisplay(self,"lowervertex","lower vertex list (NaN for vertex on the lower surface)")) + string="%s\n%s"%(string,fielddisplay(self,"lowerelements","lower element list (NaN for element on the lower layer)")) string="%s\n%s"%(string,fielddisplay(self,"vertexonboundary","vertices on the boundary of the domain flag list")) string="%s\n%s"%(string,fielddisplay(self,"vertexconnectivity","list of vertices connected to vertex_i")) Index: /issm/trunk/src/m/classes/mesh3dsurface.py =================================================================== --- /issm/trunk/src/m/classes/mesh3dsurface.py (revision 21728) +++ /issm/trunk/src/m/classes/mesh3dsurface.py (revision 21729) @@ -1,5 +1,5 @@ from MatlabFuncs import * from model import * -from np.import * +import numpy as np from fielddisplay import fielddisplay from checkfield import checkfield @@ -12,26 +12,26 @@ # mesh3dsurface=mesh3dsurface(); def __init__(self,*args): # {{{ - self.x = NaN - self.y = NaN - self.z = NaN - self.elements = NaN + self.x = np.nan + self.y = np.nan + self.z = np.nan + self.elements = np.nan self.numberofelements = 0 self.numberofvertices = 0 self.numberofedges = 0 - self.lat = NaN - self.long = NaN - self.r = NaN + self.lat = np.nan + self.long = np.nan + self.r = np.nan - self.vertexonboundary = NaN - self.edges = NaN - self.segments = NaN - self.segmentmarkers = NaN - self.vertexconnectivity = NaN - self.elementconnectivity = NaN + self.vertexonboundary = np.nan + self.edges = np.nan + self.segments = np.nan + self.segmentmarkers = np.nan + self.vertexconnectivity = np.nan + self.elementconnectivity = np.nan self.average_vertex_connectivity = 0 - self.extractedvertices = NaN - self.extractedelements = NaN + self.extractedvertices = np.nan + self.extractedelements = np.nan if not len(args): @@ -115,7 +115,7 @@ md = checkfield(md,'fieldname','mesh.long','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) md = checkfield(md,'fieldname','mesh.r','NaN',1,'Inf',1,'size',[md.mesh.numberofvertices]) - md = checkfield(md,'fieldname','mesh.elements','NaN',1,'Inf',1,'>',0,'values',arange(1,md.mesh.numberofvertices+1)) + md = checkfield(md,'fieldname','mesh.elements','NaN',1,'Inf',1,'>',0,'values',np.arange(1,md.mesh.numberofvertices+1)) md = checkfield(md,'fieldname','mesh.elements','size',[md.mesh.numberofelements,3]) - if any(not ismember([md.mesh.numberofvertices],sort(unique(md.mesh.elements)))): + if np.any(np.logical_not(np.in1d(np.arange(1,md.mesh.numberofvertices+1),md.mesh.elements.flat))): md = checkmessage(md,'orphan nodes have been found. Check the mesh outline') @@ -139,5 +139,5 @@ WriteData(fid,prefix,'object',self,'fieldname','long','format','DoubleMat','mattype',1) WriteData(fid,prefix,'object',self,'fieldname','r','format','DoubleMat','mattype',1) - WriteData(fid,prefix,'name','md.mesh.z','data',zeros(md.mesh.numberofvertices),'format','DoubleMat','mattype',1) + WriteData(fid,prefix,'name','md.mesh.z','data',np.zeros(md.mesh.numberofvertices),'format','DoubleMat','mattype',1) WriteData(fid,prefix,'object',self,'fieldname','elements','format','DoubleMat','mattype',2) WriteData(fid,prefix,'object',self,'fieldname','numberofelements','format','Integer') Index: /issm/trunk/src/m/classes/mismipbasalforcings.py =================================================================== --- /issm/trunk/src/m/classes/mismipbasalforcings.py (revision 21728) +++ /issm/trunk/src/m/classes/mismipbasalforcings.py (revision 21729) @@ -6,5 +6,5 @@ class mismipbasalforcings(object): - """ + """ MISMIP Basal Forcings class definition @@ -13,5 +13,5 @@ """ - def __init__(self,md): # {{{ + def __init__(self): # {{{ self.groundedice_melting_rate = float('NaN') @@ -20,8 +20,4 @@ self.upperdepth_melt = float('NaN') self.geothermalflux = float('NaN') - - if np.all(np.isnan(self.groundedice_melting_rate)): - self.groundedice_melting_rate=np.zeros(md.mesh.numberofvertices) - print ' no basalforcings.groundedice_melting_rate specified: values set as zero' self.setdefaultparameters() @@ -41,4 +37,10 @@ self.geothermalflux=project3d(md,'vector',self.geothermalflux,'type','node','layer',1) #bedrock only gets geothermal flux return self + #}}} + def initialize(self,md): # {{{ + if np.all(np.isnan(self.groundedice_melting_rate)): + self.groundedice_melting_rate=np.zeros(md.mesh.numberofvertices) + print ' no basalforcings.groundedice_melting_rate specified: values set as zero' + return self #}}} def setdefaultparameters(self): # {{{ Index: /issm/trunk/src/m/classes/model.js =================================================================== --- /issm/trunk/src/m/classes/model.js (revision 21728) +++ /issm/trunk/src/m/classes/model.js (revision 21729) @@ -41,4 +41,5 @@ console.log(sprintf("//19s: //-22s -- //s","inversion" ,"[1x1 " + typeof(this.inversion) + "]","parameters for inverse methods")); console.log(sprintf("//19s: //-22s -- //s","qmu" ,"[1x1 " + typeof(this.qmu) + "]","dakota properties")); + console.log(sprintf("//19s: //-22s -- //s","amr" ,"[1x1 " + typeof(this.amr) + "]","adaptive mesh refinement properties")); console.log(sprintf("//19s: //-22s -- //s","outputdefinition","[1x1 " + typeof(this.outputdefinition) + "]","output definition")); console.log(sprintf("//19s: //-22s -- //s","results" ,"[1x1 " + typeof(this.results) + "]","model results")); @@ -78,8 +79,9 @@ this.levelset = new levelset(); this.calving = new calving(); - this.gia = new gia(); + this.gia = new giaivins(); this.autodiff = new autodiff(); this.inversion = new inversion(); this.qmu = new qmu(); + this.amr = new amr(); this.radaroverlay = new radaroverlay(); this.results = {}; @@ -472,5 +474,5 @@ md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1); - // gia + // giaivins if (!isNaN(md.gia.mantle_viscosity)) md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); @@ -612,4 +614,5 @@ this.inversion = 0; this.qmu = 0; + this.amr = 0; this.results = 0; Index: /issm/trunk/src/m/classes/model.m =================================================================== --- /issm/trunk/src/m/classes/model.m (revision 21728) +++ /issm/trunk/src/m/classes/model.m (revision 21729) @@ -40,5 +40,5 @@ levelset = 0; calving = 0; - gia = 0; + gia = 0; esa = 0; @@ -46,4 +46,5 @@ inversion = 0; qmu = 0; + amr = 0; results = 0; @@ -121,15 +122,17 @@ end %2014 November 12 - if isa(md.calving,'double'); - md.calving=calving(); - end + if isa(md.calving,'double'); md.calving=calving(); end %2016 February 3 - if isa(md.slr,'double'); - md.slr=slr(); - end + if isa(md.slr,'double'); md.slr=slr(); end %2016 October 11 - if isa(md.esa,'double'); - md.esa=esa(); - end + if isa(md.esa,'double'); md.esa=esa(); end + %2017 February 10th + if md.settings.solver_residue_threshold==0, + md.settings.solver_residue_threshold = 1e-6; + end + %2017 April 10th + if isa(md.gia,'gia'), md.gia=giaivins(); end + %2017 May 4th + if isa(md.amr,'double'); md.amr=amr(); end end% }}} @@ -223,5 +226,7 @@ if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end; if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end; - %gia + if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end; + if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end; + %giaivins if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end @@ -243,5 +248,6 @@ md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers); md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers); - if ~isnan(md.damage.spcdamage), md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end + if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end + if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers); @@ -270,8 +276,15 @@ md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1); end - if ~isnan(md.basalforcings.floatingice_melting_rate), + if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate), md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1); end md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux + + if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff), + md.calving.coeff=project2d(md,md.calving.coeff,1); + end + if isprop(md.calving,'meltingrate') & ~isnan(md.calving.meltingrate), + md.calving.meltingrate=project2d(md,md.calving.meltingrate,1); + end %update of connectivity matrix @@ -296,8 +309,4 @@ md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1); end - - %lat long - if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end - if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end %Initialize with the 2d mesh @@ -308,4 +317,7 @@ mesh.numberofelements=md.mesh.numberofelements2d; mesh.elements=md.mesh.elements2d; + if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end + if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end + mesh.epsg=md.mesh.epsg; if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end @@ -415,4 +427,6 @@ elseif fieldsize(1)==numberofelements1 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:); + elseif (fieldsize(1)==numberofelements1+1) + md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)]; end end @@ -426,4 +440,6 @@ elseif fieldsize(1)==numberofelements1 md2.(model_fields{i})=field(pos_elem,:); + elseif (fieldsize(1)==numberofelements1+1) + md2.(model_fields{i})=[field(pos_elem,:); field(end,:)]; end end @@ -1098,9 +1114,10 @@ md.levelset = levelset(); md.calving = calving(); - md.gia = gia(); + md.gia = giaivins(); md.esa = esa(); md.autodiff = autodiff(); md.inversion = inversion(); md.qmu = qmu(); + md.amr = amr(); md.radaroverlay = radaroverlay(); md.results = struct(); @@ -1268,11 +1285,12 @@ disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution')); disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution')); - disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)')); + disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)')); disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving')); - disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution')); + disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution')); disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution')); disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters')); disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods')); disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties')); + disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties')); disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition')); disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results')); Index: /issm/trunk/src/m/classes/model.py =================================================================== --- /issm/trunk/src/m/classes/model.py (revision 21728) +++ /issm/trunk/src/m/classes/model.py (revision 21729) @@ -45,9 +45,10 @@ from steadystate import steadystate from transient import transient -from gia import gia +from giaivins import giaivins from autodiff import autodiff from inversion import inversion from outputdefinition import outputdefinition from qmu import qmu +from amr import amr from results import results from radaroverlay import radaroverlay @@ -107,9 +108,10 @@ self.levelset = levelset() self.calving = calving() - self.gia = gia() + self.gia = giaivins() self.autodiff = autodiff() self.inversion = inversion() self.qmu = qmu() + self.amr = amr() self.results = results() @@ -150,8 +152,9 @@ 'levelset',\ 'calving',\ - 'gia',\ + 'gia',\ 'autodiff',\ 'inversion',\ 'qmu',\ + 'amr',\ 'outputdefinition',\ 'results',\ @@ -194,4 +197,5 @@ string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("inversion","[%s,%s]" % ("1x1",obj.inversion.__class__.__name__),"parameters for inverse methods")) string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("qmu","[%s,%s]" % ("1x1",obj.qmu.__class__.__name__),"dakota properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("amr","[%s,%s]" % ("1x1",obj.amr.__class__.__name__),"adaptive mesh refinement properties")) string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("outputdefinition","[%s,%s]" % ("1x1",obj.outputdefinition.__class__.__name__),"output definition")) string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("results","[%s,%s]" % ("1x1",obj.results.__class__.__name__),"model results")) @@ -696,5 +700,5 @@ if not np.isnan(md.initialization.epl_thickness).all(): md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1) - #gia + #giaivins if not np.isnan(md.gia.mantle_viscosity).all(): md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1) if not np.isnan(md.gia.lithosphere_thickness).all(): md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1) @@ -757,10 +761,4 @@ md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1) - #lat long - if isinstance(md.mesh.lat,np.ndarray): - if md.mesh.lat.size==md.mesh.numberofvertices: md.mesh.lat=project2d(md,md.mesh.lat,1) - if isinstance(md.mesh.long,np.ndarray): - if md.mesh.long.size==md.mesh.numberofvertices: md.mesh.long=project2d(md,md.mesh.long,1) - #Initialize with the 2d mesh mesh=mesh2d() @@ -772,4 +770,9 @@ if not np.isnan(md.mesh.vertexonboundary).all(): mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1) if not np.isnan(md.mesh.elementconnectivity).all(): mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1) + if isinstance(md.mesh.lat,np.ndarray): + if md.mesh.lat.size==md.mesh.numberofvertices: mesh.lat=project2d(md,md.mesh.lat,1) + if isinstance(md.mesh.long,np.ndarray): + if md.mesh.long.size==md.mesh.numberofvertices: mesh.long=project2d(md,md.mesh.long,1) + mesh.epsg=md.mesh.epsg md.mesh=mesh Index: /issm/trunk/src/m/classes/nodalvalue.m =================================================================== --- /issm/trunk/src/m/classes/nodalvalue.m (revision 21728) +++ /issm/trunk/src/m/classes/nodalvalue.m (revision 21729) @@ -60,8 +60,8 @@ function md = marshall(self,prefix,md,fid) % {{{ - WriteData(fid,prefix,'object',self,'fieldname','name','format','String'); - WriteData(fid,prefix,'object',self,'fieldname','definitionstring','format','String'); - WriteData(fid,prefix,'object',self,'fieldname','model_string','format','String'); - WriteData(fid,prefix,'object',self,'fieldname','node','format','Integer'); + WriteData(fid,prefix,'data',self.name,'name','md.nodalvalue.name','format','String'); + WriteData(fid,prefix,'data',self.definitionstring,'name','md.nodalvalue.definitionenum','format','String'); + WriteData(fid,prefix,'data',self.model_string,'name','md.nodalvalue.model_enum','format','String'); + WriteData(fid,prefix,'data',self.node,'name','md.nodalvalue.node','format','Integer'); end % }}} Index: /issm/trunk/src/m/classes/oldclasses/gia.m =================================================================== --- /issm/trunk/src/m/classes/oldclasses/gia.m (revision 21729) +++ /issm/trunk/src/m/classes/oldclasses/gia.m (revision 21729) @@ -0,0 +1,7 @@ +classdef gia + properties (SetAccess=public) + mantle_viscosity = NaN; + lithosphere_thickness = NaN; + cross_section_shape = 0; + end +end Index: /issm/trunk/src/m/classes/settings.js =================================================================== --- /issm/trunk/src/m/classes/settings.js (revision 21728) +++ /issm/trunk/src/m/classes/settings.js (revision 21729) @@ -27,4 +27,7 @@ //upload options: upload_port = 0; + + //throw an error if solver residue exceeds this value + self.solver_residue_threshold=1e-6; }// }}} @@ -43,4 +46,5 @@ fielddisplay(this,'upload_port','port login (default is 0)'); fielddisplay(this,'upload_filename','unique id generated when uploading the file to server'); + fielddisplay(this,'solver_residue_threshold','throw an error if solver residue exceeds this value'); @@ -58,4 +62,5 @@ checkfield(md,'fieldname','settings.recording_frequency','numel',[1],'>=',0); checkfield(md,'fieldname','settings.waitonlock','numel',[1]); + checkfield(md,'fieldname','settings.solver_residue_threshold','numel',[1],'>',0); } // }}} this.marshall=function(md,prefix,fid) { //{{{ @@ -65,4 +70,5 @@ WriteData(fid,prefix,'object',this,'fieldname','output_frequency','format','Integer'); WriteData(fid,prefix,'object',this,'fieldname','recording_frequency','format','Integer'); + WriteData(fid,prefix,'object',this,'fieldname','solver_residue_threshold','format','Double'); if (this.waitonlock>0) WriteData(fid,prefix,'name','md.settings.waitonlock','data',true,'format','Boolean'); else WriteData(fid,prefix,'name','md.settings.waitonlock','data',false,'format','Boolean'); @@ -83,4 +89,5 @@ this.upload_port = 0; this.upload_filename = ''; + this.solver_residue_threshold = 0; this.setdefaultparameters(); //}}} Index: /issm/trunk/src/m/classes/settings.m =================================================================== --- /issm/trunk/src/m/classes/settings.m (revision 21728) +++ /issm/trunk/src/m/classes/settings.m (revision 21729) @@ -17,4 +17,5 @@ upload_port = 0; upload_filename = ''; + solver_residue_threshold = 0; end methods @@ -48,5 +49,8 @@ %upload options: - upload_port = 0; + self.upload_port = 0; + + %throw an error if solver residue exceeds this value + self.solver_residue_threshold = 1e-6; end % }}} @@ -59,4 +63,5 @@ md = checkfield(md,'fieldname','settings.recording_frequency','numel',[1],'>=',0); md = checkfield(md,'fieldname','settings.waitonlock','numel',[1]); + md = checkfield(md,'fieldname','settings.solver_residue_threshold','numel',[1],'>',0); end % }}} @@ -75,4 +80,5 @@ fielddisplay(self,'upload_port','port login (default is 0)'); fielddisplay(self,'upload_filename','unique id generated when uploading the file to server'); + fielddisplay(self,'solver_residue_threshold','throw an error if solver residue exceeds this value (NaN to deactivate)'); end % }}} @@ -84,4 +90,5 @@ WriteData(fid,prefix,'object',self,'fieldname','recording_frequency','format','Integer'); WriteData(fid,prefix,'object',self,'fieldname','waitonlock','data',self.waitonlock>0,'format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','solver_residue_threshold','format','Double'); end % }}} function savemodeljs(self,fid,modelname) % {{{ @@ -98,5 +105,5 @@ writejsdouble(fid,[modelname '.settings.upload_port'],self.upload_port); writejsstring(fid,[modelname '.settings.upload_filename'],self.upload_filename); - + writejsstring(fid,[modelname '.settings.solver_residue_threshold'],self.solver_residue_threshold); end % }}} end Index: /issm/trunk/src/m/classes/settings.py =================================================================== --- /issm/trunk/src/m/classes/settings.py (revision 21728) +++ /issm/trunk/src/m/classes/settings.py (revision 21729) @@ -18,4 +18,5 @@ self.recording_frequency = 0 self.waitonlock = 0 + self.solver_residue_threshold = 0 #set defaults @@ -32,4 +33,5 @@ string="%s\n%s"%(string,fielddisplay(self,"recording_frequency","frequency at which the runs are being recorded, allowing for a restart")) string="%s\n%s"%(string,fielddisplay(self,"waitonlock","maximum number of minutes to wait for batch results, or return 0")) + string="%s\n%s"%(string,fielddisplay(self,"solver_residue_threshold","throw an error if solver residue exceeds this value (NaN to deactivate)")) return string #}}} @@ -55,4 +57,7 @@ self.waitonlock=2**31-1 + #throw an error if solver residue exceeds this value + self.solver_residue_threshold=1e-6; + return self #}}} @@ -64,4 +69,5 @@ md = checkfield(md,'fieldname','settings.recording_frequency','numel',[1],'>=',0) md = checkfield(md,'fieldname','settings.waitonlock','numel',[1]) + md = checkfield(md,'fieldname','settings.solver_residue_threshold','numel',[1],'>',0) return md @@ -73,4 +79,5 @@ WriteData(fid,prefix,'object',self,'fieldname','output_frequency','format','Integer') WriteData(fid,prefix,'object',self,'fieldname','recording_frequency','format','Integer') + WriteData(fid,prefix,'object',self,'fieldname','solver_residue_threshold','format','Double') if self.waitonlock>0: WriteData(fid,prefix,'name','md.settings.waitonlock','data',True,'format','Boolean'); Index: /issm/trunk/src/m/classes/slr.js =================================================================== --- /issm/trunk/src/m/classes/slr.js (revision 21728) +++ /issm/trunk/src/m/classes/slr.js (revision 21729) @@ -25,4 +25,11 @@ this.tide_love_k=0.3055; //degree 2 + //secular fluid love number: + this.fluid_love=0.942; + + //moment of inertia: + this.equatorial_moi=8.0077*10^37; // [kg m^2] + this.polar_moi =8.0345*10^37; // [kg m^2] + // mean rotational velocity of earth: this.angular_velocity=7.2921*10^-5; // [s^-1] @@ -50,4 +57,7 @@ md = checkfield(md,'fieldname','slr.tide_love_h','NaN',1,'Inf',1); md = checkfield(md,'fieldname','slr.tide_love_k','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','slr.fluid_love','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','slr.equatorial_moi','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','slr.polar_moi','NaN',1,'Inf',1); md = checkfield(md,'fieldname','slr.angular_velocity','NaN',1,'Inf',1); md = checkfield(md,'fieldname','slr.reltol','size',[1, 1]); @@ -83,4 +93,7 @@ fielddisplay(this,'tide_love_h','tidal love number (degree 2)'); fielddisplay(this,'tide_love_k','tidal love number (degree 2)'); + fielddisplay(this,'fluid_love','secular fluid Love number'); + fielddisplay(this,'equatorial_moi','mean equatorial moment of inertia [kg m^2]'); + fielddisplay(this,'polar_moi','polar moment of inertia [kg m^2]'); fielddisplay(this,'angular_velocity','mean rotational velocity of earth [per second]'); fielddisplay(this,'rigid','rigid earth graviational potential perturbation'); @@ -104,4 +117,7 @@ WriteData(fid,prefix,'object',this,'fieldname','tide_love_h','format','Double'); WriteData(fid,prefix,'object',this,'fieldname','tide_love_k','format','Double'); + WriteData(fid,prefix,'object',this,'fieldname','fluid_love','format','Double'); + WriteData(fid,prefix,'object',this,'fieldname','equatorial_moi','format','Double'); + WriteData(fid,prefix,'object',this,'fieldname','polar_moi','format','Double'); WriteData(fid,prefix,'object',this,'fieldname','angular_velocity','format','Double'); WriteData(fid,prefix,'object',this,'fieldname','rigid','format','Boolean'); @@ -134,4 +150,7 @@ this.tide_love_h=NullFix(this.tide_love_h,NaN); this.tide_love_k=NullFix(this.tide_love_k,NaN); + this.fluid_love=NullFix(this.fluid_love,NaN); + this.equatorial_moi=NullFix(this.equatorial_moi,NaN); + this.polar_moi=NullFix(this.polar_moi,NaN); this.angular_velocity=NullFix(this.angular_velocity,NaN); this.rigid=NullFix(this.rigid,NaN); @@ -153,4 +172,7 @@ this.tide_love_h = 0; this.tide_love_k = 0; + this.fluid_love = 0; + this.equatorial_moi = 0; + this.polar_moi = 0; this.angular_velocity = 0; this.rigid = 0; Index: /issm/trunk/src/m/classes/slr.m =================================================================== --- /issm/trunk/src/m/classes/slr.m (revision 21728) +++ /issm/trunk/src/m/classes/slr.m (revision 21729) @@ -16,4 +16,7 @@ tide_love_k = 0; %ideam tide_love_h = 0; %ideam + fluid_love = 0; + equatorial_moi = 0; + polar_moi = 0; angular_velocity = 0; rigid = 0; @@ -52,5 +55,12 @@ self.tide_love_h=0.6149; %degree 2 self.tide_love_k=0.3055; % degree 2 + + %secular fluid love number: + self.fluid_love=0.942; + %moment of inertia: + self.equatorial_moi=8.0077*10^37; % [kg m^2] + self.polar_moi =8.0345*10^37; % [kg m^2] + % mean rotational velocity of earth self.angular_velocity=7.2921*10^-5; % [s^-1] @@ -76,4 +86,7 @@ md = checkfield(md,'fieldname','slr.tide_love_h','NaN',1,'Inf',1); md = checkfield(md,'fieldname','slr.tide_love_k','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','slr.fluid_love','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','slr.equatorial_moi','NaN',1,'Inf',1); + md = checkfield(md,'fieldname','slr.polar_moi','NaN',1,'Inf',1); md = checkfield(md,'fieldname','slr.angular_velocity','NaN',1,'Inf',1); md = checkfield(md,'fieldname','slr.reltol','size',[1 1]); @@ -113,4 +126,7 @@ fielddisplay(self,'tide_love_k','tidal load Love number (deg 2)'); fielddisplay(self,'tide_love_h','tidal load Love number (deg 2)'); + fielddisplay(self,'fluid_love','secular fluid Love number'); + fielddisplay(self,'equatorial_moi','mean equatorial moment of inertia [kg m^2]'); + fielddisplay(self,'polar_moi','polar moment of inertia [kg m^2]'); fielddisplay(self,'angular_velocity','mean rotational velocity of earth [per second]'); fielddisplay(self,'rigid','rigid earth graviational potential perturbation'); @@ -125,4 +141,5 @@ function marshall(self,prefix,md,fid) % {{{ WriteData(fid,prefix,'object',self,'fieldname','deltathickness','format','DoubleMat','mattype',2); + %WriteData(fid,prefix,'object',self,'fieldname','deltathickness','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofelements+1); WriteData(fid,prefix,'object',self,'fieldname','sealevel','mattype',1,'format','DoubleMat','timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); WriteData(fid,prefix,'object',self,'fieldname','reltol','format','Double'); @@ -134,4 +151,7 @@ WriteData(fid,prefix,'object',self,'fieldname','tide_love_h','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','tide_love_k','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','fluid_love','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','equatorial_moi','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','polar_moi','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','angular_velocity','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','rigid','format','Boolean'); @@ -164,4 +184,7 @@ writejsdouble(fid,[modelname '.slr.tide_love_k'],self.tide_love_k); writejsdouble(fid,[modelname '.slr.tide_love_h'],self.tide_love_h); + writejsdouble(fid,[modelname '.slr.fluid_love'],self.fluid_love); + writejsdouble(fid,[modelname '.slr.equatorial_moi'],self.equatorial_moi); + writejsdouble(fid,[modelname '.slr.polar_moi'],self.polar_moi); writejsdouble(fid,[modelname '.slr.angular_velocity'],self.angular_velocity); writejsdouble(fid,[modelname '.slr.rigid'],self.rigid); Index: /issm/trunk/src/m/classes/slr.py =================================================================== --- /issm/trunk/src/m/classes/slr.py (revision 21728) +++ /issm/trunk/src/m/classes/slr.py (revision 21729) @@ -25,4 +25,7 @@ self.tide_love_h = 0 self.tide_love_k = 0 + self.fluid_love = 0; + self.equatorial_moi = 0; + self.polar_moi = 0; self.angular_velocity = 0; self.rigid = 0 @@ -48,4 +51,7 @@ string="%s\n%s"%(string,fielddisplay(self,'tide_love_k','tidal load Love number (degree 2)')) string="%s\n%s"%(string,fielddisplay(self,'tide_love_h','tidal load Love number (degree 2)')) + string="%s\n%s"%(string,fielddisplay(self,'fluid_love','secular fluid Love number')) + string="%s\n%s"%(string,fielddisplay(self,'equatorial_moi','mean equatorial moment of inertia [kg m^2]')) + string="%s\n%s"%(string,fielddisplay(self,'polar_moi','polar moment of inertia [kg m^2]')) string="%s\n%s"%(string,fielddisplay(self,'angular_velocity','mean rotational velocity of earth [per second]')); string="%s\n%s"%(string,fielddisplay(self,'rigid','rigid earth graviational potential perturbation')) @@ -77,4 +83,11 @@ self.tide_love_h=0.6149; #degree 2 self.tide_love_k=0.3055; #degree 2 + + #secular fluid love number: + self.fluid_love=0.942; + + #moment of inertia: + self.equatorial_moi=8.0077*10**37; # [kg m^2] + self.polar_moi =8.0345*10**37; # [kg m^2] #mean rotational velocity of earth @@ -107,4 +120,7 @@ md = checkfield(md,'fieldname','slr.tide_love_h','NaN',1,'Inf',1) md = checkfield(md,'fieldname','slr.tide_love_k','NaN',1,'Inf',1) + md = checkfield(md,'fieldname','slr.fluid_love','NaN',1,'Inf',1) + md = checkfield(md,'fieldname','slr.equatorial_moi','NaN',1,'Inf',1) + md = checkfield(md,'fieldname','slr.polar_moi','NaN',1,'Inf',1) md = checkfield(md,'fieldname','slr.angular_velocity','NaN',1,'Inf',1) md = checkfield(md,'fieldname','slr.reltol','size',[1,1]) @@ -133,4 +149,7 @@ WriteData(fid,prefix,'object',self,'fieldname','tide_love_h','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','tide_love_k','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','fluid_love','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','equatorial_moi','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','polar_moi','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','angular_velocity','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','rigid','format','Boolean') Index: /issm/trunk/src/m/classes/thermal.m =================================================================== --- /issm/trunk/src/m/classes/thermal.m (revision 21728) +++ /issm/trunk/src/m/classes/thermal.m (revision 21729) @@ -15,4 +15,5 @@ isenthalpy = 0; isdynamicbasalspc = 0; + fe = 'P1'; requested_outputs = {}; end @@ -66,4 +67,7 @@ self.isdynamicbasalspc=0; + %Linear elements by default + self.fe='P1'; + %default output self.requested_outputs={'default'}; @@ -76,4 +80,5 @@ md = checkfield(md,'fieldname','thermal.stabilization','numel',[1],'values',[0 1 2]); md = checkfield(md,'fieldname','thermal.spctemperature','Inf',1,'timeseries',1,'>=',0); + md = checkfield(md,'fieldname','thermal.fe','values',{'P1','P1xP2','P1xP3'}); if (ismember('EnthalpyAnalysis',analyses) & md.thermal.isenthalpy & dimension(md.mesh)==3), @@ -110,4 +115,5 @@ fielddisplay(self,'isenthalpy','use an enthalpy formulation to include temperate ice (default is 0)'); fielddisplay(self,'isdynamicbasalspc',['enable dynamic setting of basal forcing. required for enthalpy formulation (default is 0)']); + fielddisplay(self,'fe','Finite Element type: ''P1'' (default), ''P1xP2'''); fielddisplay(self,'requested_outputs','additional outputs requested'); @@ -122,4 +128,5 @@ WriteData(fid,prefix,'object',self,'fieldname','penalty_factor','format','Double'); WriteData(fid,prefix,'object',self,'fieldname','isenthalpy','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','fe','format','String'); WriteData(fid,prefix,'object',self,'fieldname','isdynamicbasalspc','format','Boolean'); Index: /issm/trunk/src/m/classes/thermal.py =================================================================== --- /issm/trunk/src/m/classes/thermal.py (revision 21728) +++ /issm/trunk/src/m/classes/thermal.py (revision 21729) @@ -23,4 +23,5 @@ self.isenthalpy = 0 self.isdynamicbasalspc = 0; + self.fe = 'P1'; self.requested_outputs = [] @@ -79,5 +80,8 @@ #will basal boundary conditions be set dynamically - self.isdynamicbasalspc=0; + self.isdynamicbasalspc=0 + + #Finite element interpolation + self.fe='P1' #default output @@ -124,4 +128,5 @@ WriteData(fid,prefix,'object',self,'fieldname','penalty_factor','format','Double') WriteData(fid,prefix,'object',self,'fieldname','isenthalpy','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','fe','format','String'); WriteData(fid,prefix,'object',self,'fieldname','isdynamicbasalspc','format','Boolean'); Index: /issm/trunk/src/m/classes/trans.js =================================================================== --- /issm/trunk/src/m/classes/trans.js (revision 21728) +++ /issm/trunk/src/m/classes/trans.js (revision 21729) @@ -20,4 +20,5 @@ this.isslr = 0; this.iscoupler = 0; + this.amr_frequency = 1; //default output @@ -40,4 +41,5 @@ fielddisplay(this,'isslr','indicates whether a sea-level rise model is used'); fielddisplay(this,'iscoupler','indicates whether different models are being run with need for coupling'); + fielddisplay(this,'amr_frequency','frequency at which mesh is refined in simulations with multiple time_steps'); fielddisplay(this,'requested_outputs','list of additional outputs requested'); @@ -63,4 +65,5 @@ checkfield(md,'fieldname','trans.iscoupler','numel',[1],'values',[0 ,1]); checkfield(md,'fieldname','trans.isslr','numel',[1],'values',[0 ,1]); + checkfield(md,'fieldname','trans.amr_frequency','numel',[1],'>=',0,'NaN',1,'Inf',1); checkfield(md,'fieldname','trans.requested_outputs','stringrow',1); } // }}} @@ -79,4 +82,5 @@ WriteData(fid,prefix,'object',this,'fieldname','isslr','format','Boolean'); WriteData(fid,prefix,'object',this,'fieldname','iscoupler','format','Boolean'); + WriteData(fid,prefix,'object',this,'fieldname','amr_frequency','format','Integer'); //process requested outputs @@ -111,4 +115,5 @@ this.isslr = 0; this.iscoupler = 0; + this.amr_frequency = 0; this.requested_outputs = []; Index: /issm/trunk/src/m/classes/transient.m =================================================================== --- /issm/trunk/src/m/classes/transient.m (revision 21728) +++ /issm/trunk/src/m/classes/transient.m (revision 21729) @@ -18,4 +18,6 @@ isslr = 0; iscoupler = 0; + amr_frequency = 0; + isoceancoupling = 0; requested_outputs = {}; end @@ -43,5 +45,7 @@ self.ishydrology = 0; self.isslr = 0; + self.isoceancoupling = 0; self.iscoupler = 0; + self.amr_frequency = 0; %default output @@ -62,5 +66,7 @@ self.ishydrology = 0; self.isslr = 0; + self.isoceancoupling = 0; self.iscoupler = 0; + self.amr_frequency = 1; %default output @@ -91,6 +97,11 @@ md = checkfield(md,'fieldname','transient.requested_outputs','stringrow',1); md = checkfield(md,'fieldname','transient.isslr','numel',[1],'values',[0 1]); + md = checkfield(md,'fieldname','transient.isoceancoupling','numel',[1],'values',[0 1]); md = checkfield(md,'fieldname','transient.iscoupler','numel',[1],'values',[0 1]); + md = checkfield(md,'fieldname','transient.amr_frequency','numel',[1],'>=',0,'NaN',1,'Inf',1); + if (~strcmp(solution,'TransientSolution') & md.transient.iscoupling==1), + md = checkmessage(md,['Coupling with ocean model can only be performed for transient simulations!']); + end end % }}} function disp(self) % {{{ @@ -108,5 +119,7 @@ fielddisplay(self,'ishydrology','indicates whether an hydrology model is used'); fielddisplay(self,'isslr','indicates whether a sea-level rise solution is used in the transient'); + fielddisplay(self,'isoceancoupling','indicates whether a coupling with an ocean model is used in the transient'); fielddisplay(self,'iscoupler','indicates whether different models are being run with need for coupling'); + fielddisplay(self,'amr_frequency','frequency at which mesh is refined in simulations with multiple time_steps'); fielddisplay(self,'requested_outputs','list of additional outputs requested'); @@ -124,5 +137,7 @@ WriteData(fid,prefix,'object',self,'fieldname','ismovingfront','format','Boolean'); WriteData(fid,prefix,'object',self,'fieldname','isslr','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','isoceancoupling','format','Boolean'); WriteData(fid,prefix,'object',self,'fieldname','iscoupler','format','Boolean'); + WriteData(fid,prefix,'object',self,'fieldname','amr_frequency','format','Integer'); %process requested outputs @@ -148,5 +163,7 @@ writejsdouble(fid,[modelname '.trans.ishydrology'],self.ishydrology); writejsdouble(fid,[modelname '.trans.isslr'],self.isslr); + writejsdouble(fid,[modelname '.trans.isoceancoupling'],self.isoceancoupling); writejsdouble(fid,[modelname '.trans.iscoupler'],self.iscoupler); + writejsdouble(fid,[modelname '.trans.amr_frequency'],self.amr_frequency); writejscellstring(fid,[modelname '.trans.requested_outputs'],self.requested_outputs); Index: /issm/trunk/src/m/classes/transient.py =================================================================== --- /issm/trunk/src/m/classes/transient.py (revision 21728) +++ /issm/trunk/src/m/classes/transient.py (revision 21729) @@ -23,5 +23,7 @@ self.ishydrology = False self.isslr = False + self.isoceancoupling = False self.iscoupler = False + amr_frequency = 0 self.requested_outputs = [] @@ -43,5 +45,7 @@ string="%s\n%s"%(string,fielddisplay(self,'ishydrology','indicates whether an hydrology model is used')) string="%s\n%s"%(string,fielddisplay(self,'isslr','indicates if a sea level rise solution is used in the transient')) + string="%s\n%s"%(string,fielddisplay(self,'isoceancoupling','indicates whether coupling with an ocean model is used in the transient')) string="%s\n%s"%(string,fielddisplay(self,'iscoupler','indicates whether different models are being run with need for coupling')) + string="%s\n%s"%(string,fielddisplay(self,'amr_frequency','frequency at which mesh is refined in simulations with multiple time_steps')) string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','list of additional outputs requested')) return string @@ -68,6 +72,8 @@ self.ismovingfront = False self.ishydrology = False + self.isoceancoupling = False self.isslr = False self.iscoupler = False + self.amr_frequency = 0 #default output @@ -89,5 +95,7 @@ self.ishydrology = False self.isslr = False + self.isoceancoupling = False self.iscoupler = False + self.amr_frequency = 1 #default output @@ -112,6 +120,11 @@ md = checkfield(md,'fieldname','transient.ismovingfront','numel',[1],'values',[0,1]); md = checkfield(md,'fieldname','transient.isslr','numel',[1],'values',[0,1]) + md = checkfield(md,'fieldname','transient.isoceancoupling','numel',[1],'values',[0,1]) md = checkfield(md,'fieldname','transient.iscoupler','numel',[1],'values',[0,1]) + md = checkfield(md,'fieldname','transient.amr_frequency','numel',[1],'>=',0,'NaN',1,'Inf',1) md = checkfield(md,'fieldname','transient.requested_outputs','stringrow',1) + + if (solution!='TransientSolution') and (md.transient.iscoupling): + md.checkmessage("Coupling with ocean can only be done in transient simulations!") return md @@ -129,5 +142,7 @@ WriteData(fid,prefix,'object',self,'fieldname','ismovingfront','format','Boolean') WriteData(fid,prefix,'object',self,'fieldname','isslr','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','isoceancoupling','format','Boolean') WriteData(fid,prefix,'object',self,'fieldname','iscoupler','format','Boolean') + WriteData(fid,prefix,'object',self,'fieldname','amr_frequency','format','Integer') #process requested outputs Index: /issm/trunk/src/m/consistency/checkfield.py =================================================================== --- /issm/trunk/src/m/consistency/checkfield.py (revision 21728) +++ /issm/trunk/src/m/consistency/checkfield.py (revision 21729) @@ -70,14 +70,14 @@ if np.isnan(fieldsize[0]): if not np.size(field,1)==fieldsize[1]: - md = md.checkmessage(options.getfieldvalue('message',\ - "field '%s' should have %d columns" % (fieldname,fieldsize[1]))) + md = md.checkmessage(options.getfieldvalue('message',"field '%s' should have %d columns" % (fieldname,fieldsize[1]))) elif np.isnan(fieldsize[1]): if not np.size(field,0)==fieldsize[0]: - md = md.checkmessage(options.getfieldvalue('message',\ - "field '%s' should have %d lines" % (fieldname,fieldsize[0]))) + md = md.checkmessage(options.getfieldvalue('message',"field '%s' should have %d lines" % (fieldname,fieldsize[0]))) + elif fieldsize[1]==1: + if (not np.size(field,0)==fieldsize[0]): + md = md.checkmessage(options.getfieldvalue('message',"field '%s' size should be %d x %d" % (fieldname,fieldsize[0],fieldsize[1]))) else: if (not np.size(field,0)==fieldsize[0]) or (not np.size(field,1)==fieldsize[1]): - md = md.checkmessage(options.getfieldvalue('message',\ - "field '%s' size should be %d x %d" % (fieldname,fieldsize[0],fieldsize[1]))) + md = md.checkmessage(options.getfieldvalue('message',"field '%s' size should be %d x %d" % (fieldname,fieldsize[0],fieldsize[1]))) #Check numel Index: /issm/trunk/src/m/consistency/ismodelselfconsistent.js =================================================================== --- /issm/trunk/src/m/consistency/ismodelselfconsistent.js (revision 21728) +++ /issm/trunk/src/m/consistency/ismodelselfconsistent.js (revision 21729) @@ -76,5 +76,5 @@ }else if(solutiontype ==='GiaSolution'){ - analyses=['GiaAnalysis']; + analyses=['GiaIvinsAnalysis']; }else if(solutiontype ==='TransientSolution'){ Index: /issm/trunk/src/m/consistency/ismodelselfconsistent.m =================================================================== --- /issm/trunk/src/m/consistency/ismodelselfconsistent.m (revision 21728) +++ /issm/trunk/src/m/consistency/ismodelselfconsistent.m (revision 21729) @@ -65,5 +65,5 @@ analyses={'L2ProjectionBaseAnalysis'}; elseif strcmp(solutiontype,'GiaSolution') - analyses={'GiaAnalysis'}; + analyses={'GiaIvinsAnalysis'}; elseif strcmp(solutiontype,'EsaSolution') analyses={'EsaAnalysis'}; Index: /issm/trunk/src/m/consistency/ismodelselfconsistent.py =================================================================== --- /issm/trunk/src/m/consistency/ismodelselfconsistent.py (revision 21728) +++ /issm/trunk/src/m/consistency/ismodelselfconsistent.py (revision 21729) @@ -32,5 +32,5 @@ elif solutiontype == 'GiaSolution': - analyses=['GiaAnalysis'] + analyses=['GiaIvinsAnalysis'] elif solutiontype == 'TransientSolution': Index: /issm/trunk/src/m/contrib/defleurian/netCDF/ClassTry.py =================================================================== --- /issm/trunk/src/m/contrib/defleurian/netCDF/ClassTry.py (revision 21728) +++ /issm/trunk/src/m/contrib/defleurian/netCDF/ClassTry.py (revision 21729) @@ -70,5 +70,5 @@ 'transient':'transient',\ 'calving':'calving',\ - 'gia':'gia',\ + 'giaivins':'giaivins',\ 'autodiff':'autodiff',\ 'inversion':'inversion',\ Index: /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.m =================================================================== --- /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.m (revision 21728) +++ /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.m (revision 21729) @@ -21,26 +21,27 @@ %gather geometry and timestepping as dimensions - Duration=md.timestepping.final_time-md.timestepping.start_time; - if Duration>0 && md.timestepping.time_step*md.settings.output_frequency>0, - StepNum=Duration/(md.timestepping.time_step*md.settings.output_frequency); + resfields=fieldnames(md.results); + Duration=size(eval(['md.results. ' resfields{1} ]),2); + if Duration>0, + StepNum=Duration; else StepNum=1; end + + dimlist=[40,2,md.mesh.numberofelements,md.mesh.numberofvertices,size(md.mesh.elements,2)]; %define netcdf dimensions - DimSize(1).index=netcdf.defDim(ncid,'Dimension1',md.mesh.numberofelements); - DimSize(2).index=netcdf.defDim(ncid,'Dimension2',md.mesh.numberofvertices); - DimSize(3).index=netcdf.defDim(ncid,'Dimension3',size(md.mesh.elements,2)); - DimSize(4).index=netcdf.defDim(ncid,'Dimension4',StepNum); - DimSize(5).index=netcdf.defDim(ncid,'Dimension5',40); - DimSize(6).index=netcdf.defDim(ncid,'Dimension6',2); - - for i=1:length(DimSize), - [DimSize(i).name,DimSize(i).value]=netcdf.inqDim(ncid,DimSize(i).index); - DimValue(i)=DimSize(i).value;% putting vallues in an array for - % further use - end - - %Needs a first turn arround for var def + DimSize(1).index=netcdf.defDim(ncid,'Dimension1',StepNum); + [DimSize(1).name,DimSize(1).value]=netcdf.inqDim(ncid,DimSize(1).index); + DimValue(1)=DimSize(1).value; + for i=1:5 + if sum(dimlist(i) == DimValue) == 0 + DimSize(i+1).index=netcdf.defDim(ncid,['Dimension' num2str(i+1)],dimlist(i)); + [DimSize(i+1).name,DimSize(i+1).value]=netcdf.inqDim(ncid,DimSize(i+1).index); + DimValue(i+1)=DimSize(i+1).value; + end + end + + typelist=[{'numeric'} {'logical'} {'string'} {'char'} {'cell'}]; %get all model classes and create respective groups @@ -51,50 +52,101 @@ %In each group gather the fields of the class groupfields=fields(md.(groups{i})); - %Special treatment for the results - if strcmp(groups(i),'results'), - for j=1:length(groupfields)%looping on the differents solutions - netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype','results'); - subgroupID=netcdf.defGrp(groupID,groupfields{j}); - netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',groupfields{j}); - %disp(sprintf('=====Field name in tree %s ',groupfields{j})); - if length(md.results.(groupfields{j}))>1, - %the solution have several timestep get last timesteps and output frequency - last_step = length(md.results.(groupfields{j})); - %grab first time step - subfields=fields(md.results.(groupfields{j})(1)); - for k=1:length(subfields), - if ~strcmp(subfields(k),'errlog') && ~strcmp(subfields(k),'outlog') && ~strcmp(subfields(k),'SolutionType'), - %disp(sprintf('==========SubField name in tree %s ',subfields{k})); - Var=md.results.(groupfields{j})(1).(subfields{k}); - [DimSize,DimValue]=DefCreateVar(ncid,Var,subgroupID,subfields{k},DimSize,DimValue,true,last_step,md,groupfields{j}); - end - end - elseif length(md.results.(groupfields{j}))==1, - %only one timestep - subfields=fields(md.results.(groupfields{j})); - for k=1:length(subfields), - %disp(sprintf('==========SubField name in tree %s ',subfields{k})); - if ~strcmp(subfields(k),'errlog') && ~strcmp(subfields(k),'outlog') && ~strcmp(subfields(k),'SolutionType'), - Var=md.results.(groupfields{1})(1).(subfields{k}); - [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,subfields{k},DimSize,DimValue,false); - end - end - else - print 'Result format not suported' - end - end - else - for j=1:length(groupfields), - disp(sprintf('=====Field name in tree %s ',groupfields{j})); + for j=1:length(groupfields), + Var=md.(groups{i}).(groupfields{j}); + if isa(Var,'cell') + Stdlist=false; + if length(Var) == 0 + Stdlist=true; + else + for k=1:length(typelist) + if isa(Var{1},typelist{k}) + Stdlist=true; + end + end + end + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',class(md.(groups{i}))); - Var=md.(groups{i}).(groupfields{j}); - [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,groupfields{j},DimSize,DimValue,false); - end - end - end - netcdf.close(ncid); + if(Stdlist) + disp(sprintf('=====Field name in tree %s ',groupfields{j})); + [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,groupfields{j},DimSize,DimValue); + else + listsize=length(Var); + subgroupID=netcdf.defGrp(groupID,groupfields{j}); + netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',class(Var)); + for l=1:listsize + if isprop(Var{l},'name') + lname=Var{l}.name; + elseif isprop(Var{l},'step') + lname=Var{l}.step + else + lname=[class(Var{l}) int2str(l)]; + end + listgroupID=netcdf.defGrp(subgroupID,lname); + netcdf.putAtt(listgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',class(Var{l})); + subfields=fields(Var{l}); + for m=1:length(subfields) + if ~strcmp(subfields{m},'outlog') + [DimSize,DimValue]=DefCreateVar(ncid,Var{l}.(subfields{m}),listgroupID,subfields{m},DimSize,DimValue); + end + end + end + end + elseif isa(Var,'struct') && ~strcmp(groupfields{j},'bamg') + classtype=class(md.(groups{i})); + if strcmp(classtype,'struct') + classtype=groups{i}; + end + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',classtype); + if length(Var)>1 + listsize=length(Var); + subgroupID=netcdf.defGrp(groupID,groupfields{j}); + classtype=class(Var); + if strcmp(classtype,'struct') + classtype=groups{i}; + end + netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',classtype); + for l=1:listsize + if isfield(Var(l),'step') + lname=[int2str(Var(l).step)]; + else + lname=[class(Var(l)) int2str(l)]; + end + classtype=class(Var(l)); + if strcmp(classtype,'struct') + classtype=groups{i}; + end + listgroupID=netcdf.defGrp(subgroupID,lname); + netcdf.putAtt(listgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',classtype); + subfields=fields(Var(l)); + for m=1:length(subfields) + if ~strcmp(subfields{m},'outlog') + [DimSize,DimValue]=DefCreateVar(ncid,Var(l).(subfields{m}),listgroupID,subfields{m},DimSize,DimValue); + end + end + end + else + subgroupID=netcdf.defGrp(groupID,groupfields{j}); + classtype=class(Var); + if strcmp(classtype,'struct') + classtype=groups{i}; + end + netcdf.putAtt(subgroupID,netcdf.getConstant('NC_GLOBAL'),'classtype',classtype); + subfields=fields(Var); + for m=1:length(subfields) + if ~strcmp(subfields{m},'outlog') + [DimSize,DimValue]=DefCreateVar(ncid,Var.(subfields{m}),subgroupID,subfields{m},DimSize,DimValue); + end + end + end + else + netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype',class(md.(groups{i}))); + [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,groupfields{j},DimSize,DimValue); + end + end + end + netcdf.close(ncid); end -function [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,field,DimSize,DimValue,istime,last,md,midfield) +function [DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,field,DimSize,DimValue,last,md,midfield) varclass=class(Var); varsize=size(Var); @@ -110,22 +162,13 @@ netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),field,Var); elseif isa(Var,'double'), %dealing with arrays - [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue,istime); + [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); varid = netcdf.defVar(groupID,field,'NC_DOUBLE',dims); - if istime, - VarTab=Var; - for i=2:last, - TimeVar=md.results.(midfield)(i).(field); - VarTab=[VarTab TimeVar]; - end - netcdf.putVar(groupID,varid,VarTab); - else - if length(Var)==0, - netcdf.putVar(groupID,varid,NaN); - else - netcdf.putVar(groupID,varid,Var); - end - end + if length(Var)==0, + netcdf.putVar(groupID,varid,NaN); + else + netcdf.putVar(groupID,varid,Var); + end elseif isa(Var,'cell'), - [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue,istime); + [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); %dirty hack to be able to pass strings varid = netcdf.defVar(groupID,field,'NC_CHAR',dims); @@ -134,49 +177,56 @@ else for i=1:length(Var), - startpoint=zeros(size(Var)); - startpoint(:,i)=i-1; if length(Var)>1, - endpoint=[min(length(Var{i}),40) 1]; + endpoint=[1,min(length(Var{i}),40)]; + startpoint=[1 0]; else endpoint=min(length(Var{i}),40); - end + startpoint=0; + end if length(Var{i})>40, - netcdf.putVar(groupID,varid,startpoint,endpoint,Var{i}(1:40)) + netcdf.putVar(groupID,varid,startpoint,extent,Var{i}(1:40)) disp(sprintf('some variable have been truncated')); - else + else netcdf.putVar(groupID,varid,startpoint,endpoint,Var{i}) - end - end - end + end + end + end elseif isa(Var,'struct'), %Start by getting the structure fields and size locfields=fields(Var); - [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,locfields,DimSize,DimValue,istime); + [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue); varid = netcdf.defVar(groupID,field,'NC_CHAR',dims); if length(locfields)==0, - netcdf.putVar(groupID,varid,[0,0],[11,1],'emptystruct') + netcdf.putVar(groupID,varid,[0,0],[1,11],'emptystruct') else for i=1:length(locfields), for j=1:2, if j==1, - startpoint=[0,0,i-1]; CharVar=locfields{i}; + if length(CharVar)==0 + CharVar='emptystruct'; + end + startpoint=[i-1,0,0]; else - startpoint=[0,1,i-1]; if isa(Var.(locfields{i}),'char'), CharVar=Var.(locfields{i}); else CharVar=num2str(Var.(locfields{i})); - end - end - endpoint=[min(length(CharVar),40),1,1]; + end + if length(CharVar)==0 + CharVar='emptystruct'; + end + startpoint=[i-1,1,0]; + end + + extent=[1,1,min(length(CharVar),40)]; if length(CharVar)>40, - netcdf.putVar(groupID,varid,startpoint,endpoint,CharVar(1:40)) + netcdf.putVar(groupID,varid,startpoint,extent,CharVar(1:40)) disp(sprintf('some variable have been truncated')); else - netcdf.putVar(groupID,varid,startpoint,endpoint,CharVar) - end - end - end + netcdf.putVar(groupID,varid,startpoint,extent,CharVar) + end + end + end end else @@ -186,62 +236,46 @@ end -function [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue,istime) +function [dims,DimSize,DimValue]=GetDims(ncid,Var,DimSize,DimValue) dims=[]; - %specific treatment for structures - if isa(Var,'struct') - varsize=size(field); %we pass here the fields of the current structure - MatOrVec=varsize>1; %checking if we have a matrix (1 1) or vector (1 0) - for i=1:sum(MatOrVec), %loop on the number of (non 1) dimensions - currentdim=varsize(i); - dimexist=DimValue==currentdim; - if sum(dimexist)==0, %dimension is new to us, need to create it - dimname=strcat('Dimension',int2str(length(DimValue)+1)); - dimindex=length(DimSize)+1; - DimSize(dimindex).index=netcdf.defDim(ncid,dimname,currentdim); - [DimSize(dimindex).name,DimSize(dimindex).value]=netcdf.inqDim(ncid,DimSize(dimindex).index); - dims(i)=DimSize(dimindex).index; - DimValue(dimindex)=currentdim; + if isa(Var,'cell'), + varsize=size(Var'); + elseif isa(Var,'struct') + varsize=length(fields(Var)); + else + varsize=size(Var); + end + dim=sum(varsize>1); + if dim>0 + for i=1:dim + indsize=find(varsize(i)==DimValue); + if length(indsize)>0 + dims=[dims DimSize(indsize).index]; else - dimindex=find(dimexist); - if DimSize(dimindex).value~=currentdim, - error('Indexation problem with the dimension structure') - end - end - dims(i)=DimSize(dimindex).index; - end - dims=[DimSize(6).index dims]; - else - %with a cell array need to grab the transposed size to work - if isa(Var,'cell'), - varsize=size(Var'); - else - varsize=size(Var); - end - MatOrVec=varsize>1; %checking if we have a matrix (1 1) or vector (1 0) - for i=1:sum(MatOrVec), %loop on the number of (non 1) dimensions - currentdim=varsize(i); - dimexist=DimValue==currentdim; - if sum(dimexist)==0, %dimension is new to us, need to create it - dimname=strcat('Dimension',int2str(length(DimValue)+1)); - dimindex=length(DimSize)+1; - DimSize(dimindex).index=netcdf.defDim(ncid,dimname,currentdim); - [DimSize(dimindex).name,DimSize(dimindex).value]=netcdf.inqDim(ncid,DimSize(dimindex).index); - dims(i)=DimSize(dimindex).index; - DimValue(dimindex)=currentdim; + indsize=length(DimSize)+1; + DimSize(indsize).index=netcdf.defDim(ncid,['Dimension' num2str(indsize)],varsize(i)); + [DimSize(indsize).name,DimSize(indsize).value]=netcdf.inqDim(ncid,DimSize(indsize).index); + DimValue(indsize)=DimSize(indsize).value; + dims=[dims DimSize(indsize).index]; + end + end + end + %if we have a cell variable we need to add a stringlength dimension + if isa(Var,'struct'), + if DimValue(3)~=2 + if DimValue(2)~=2 + dims=[dims DimSize(1).index]; else - dimindex=find(dimexist); - if DimSize(dimindex).value~=currentdim, - error('Indexation problem with the dimension structure') - end - end - dims(i)=DimSize(dimindex).index; - end - end - if istime, - dims=[dims DimSize(4).index];%adding the time dimension if necessary - end - %if we have a cell variable we need to add a stringlength dimension + dims=[dims DimSize(2).index]; + end + else + dims=[dims DimSize(3).index]; + end + end if isa(Var,'cell') || isa(Var,'struct'), - dims=[DimSize(5).index dims] - end + if DimValue(2)~=40 + dims=[dims DimSize(1).index]; + else + dims=[dims DimSize(2).index]; + end + end end Index: /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.py =================================================================== --- /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.py (revision 21728) +++ /issm/trunk/src/m/contrib/defleurian/netCDF/export_netCDF.py (revision 21729) @@ -1,4 +1,4 @@ from netCDF4 import Dataset, stringtochar -import numpy as np +import numpy as np import time import collections @@ -23,5 +23,5 @@ NCData.history = 'Created ' + time.ctime(time.time()) - #gather geometry and timestepping as dimensions + #define netCDF dimensions try: StepNum=np.shape(dict.values(md.results.__dict__))[1] @@ -39,9 +39,9 @@ DimDict[len(NewDim)]='DimNum'+str(dimindex) - #get all model classes and create respective groups typelist=[bool,str,unicode,int,float,complex, collections.OrderedDict, np.int64,np.ndarray,np.float64] groups=dict.keys(md.__dict__) + #get all model classes and create respective groups for group in groups: NCgroup=NCData.createGroup(str(group)) @@ -58,12 +58,10 @@ else: StdList=type(md.__dict__[group].__dict__[field][0]) in typelist - + NCgroup.__setattr__('classtype', md.__dict__[group].__class__.__name__) if StdList: #this is a standard or empty list just proceed - NCgroup.__setattr__('classtype', md.__dict__[group].__class__.__name__) Var=md.__dict__[group].__dict__[field] - DimDict=CreateVar(NCData,Var,field,NCgroup,DimDict,False) + DimDict=CreateVar(NCData,Var,field,NCgroup,DimDict) else: #this is a list of fields, specific treatment needed Listsize=len(md.__dict__[group].__dict__[field]) - NCgroup.__setattr__('classtype', md.__dict__[group].__class__.__name__) Subgroup=NCgroup.createGroup(str(field)) Subgroup.__setattr__('classtype',md.__dict__[group].__dict__[field].__class__.__name__) @@ -87,10 +85,14 @@ except AttributeError: Var=md.__dict__[group].__dict__[field].__getitem__(listindex)[subfield] - DimDict=CreateVar(NCData,Var,subfield,Listgroup,DimDict,False,md.__dict__[group],field,listindex) + DimDict=CreateVar(NCData,Var,subfield,Listgroup,DimDict,md.__dict__[group],field,listindex) + #No subgroup, we directly treat the variable - elif type(md.__dict__[group].__dict__[field]) in typelist: + elif type(md.__dict__[group].__dict__[field]) in typelist or field=='bamg': NCgroup.__setattr__('classtype', md.__dict__[group].__class__.__name__) Var=md.__dict__[group].__dict__[field] - DimDict=CreateVar(NCData,Var,field,NCgroup,DimDict,False) + DimDict=CreateVar(NCData,Var,field,NCgroup,DimDict) + elif md.__dict__[group].__dict__[field] is None: + print( 'field md.{}.{} is None'.format(group,field)) + #do nothing else: NCgroup.__setattr__('classtype', str(group)) @@ -98,8 +100,9 @@ Subgroup.__setattr__('classtype',md.__dict__[group].__class__.__name__) subfields=dict.keys(md.__dict__[group].__dict__[field].__dict__) + for subfield in subfields: if str(subfield)!='outlog': Var=md.__dict__[group].__dict__[field].__dict__[subfield] - DimDict=CreateVar(NCData,Var,subfield,Subgroup,DimDict,False) + DimDict=CreateVar(NCData,Var,subfield,Subgroup,DimDict) NCData.close() @@ -107,5 +110,5 @@ #============================================================================ #Define the variables -def CreateVar(NCData,var,field,Group,DimDict,istime,*step_args): +def CreateVar(NCData,var,field,Group,DimDict,*step_args): #grab type try: @@ -135,5 +138,5 @@ #treating list as string table elif val_type==list: - dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim,istime) + dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim) #try to get the type from the first element try: @@ -149,5 +152,5 @@ #treating bool tables as string tables elif val_type=='bool': - dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim,istime) + dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim) ncvar = Group.createVariable(str(field),str,dimensions,zlib=True) for elt in range(0,val_shape[0]): @@ -155,5 +158,5 @@ #treating dictionaries as tables of strings elif val_type==collections.OrderedDict or val_type==dict: - dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim,istime) + dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim) ncvar = Group.createVariable(str(field),str,dimensions,zlib=True) for elt in range(0,val_dim): @@ -162,30 +165,19 @@ #Now dealing with numeric variables else: - dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim,istime) + dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim) ncvar = Group.createVariable(str(field),TypeDict[val_type],dimensions,zlib=True) - if istime: - md=step_args[0] - supfield=step_args[1] - index=step_args[2] - vartab=var - timevar=md.__dict__[supfield].__getitem__(index).__dict__[field] - try: - ncvar[:,:]=timevar[:,:] - except ValueError: - ncvar[:]=timevar.T[:] - else: - try: - nan_val=np.isnan(var) - if nan_val.all(): - ncvar [:] = 'NaN' - else: - ncvar[:] = var - except TypeError: #type does not accept nan, get vallue of the variable + try: + nan_val=np.isnan(var) + if nan_val.all(): + ncvar [:] = 'NaN' + else: ncvar[:] = var + except TypeError: #type does not accept nan, get vallue of the variable + ncvar[:] = var return DimDict #============================================================================ #retriev the dimension tuple from a dictionnary -def GetDim(NCData,var,shape,DimDict,i,istime): +def GetDim(NCData,var,shape,DimDict,i): output=[] #grab dimension @@ -210,5 +202,3 @@ output=[str(DimDict[np.shape(dict.keys(var))[0]])]+[DimDict[2]] break - if istime: - output=output+['DimNum1'] return tuple(output), DimDict Index: /issm/trunk/src/m/contrib/defleurian/netCDF/read_netCDF.m =================================================================== --- /issm/trunk/src/m/contrib/defleurian/netCDF/read_netCDF.m (revision 21728) +++ /issm/trunk/src/m/contrib/defleurian/netCDF/read_netCDF.m (revision 21729) @@ -1,9 +1,9 @@ function self=read_netCDF(filename) -% Different types in the netcdf standard are: -% 2 for char -% 4 for integer -% 6 for doubles - + % Different types in the netcdf standard are: + % 2 for char + % 4 for integer + % 6 for doubles + ncid=netcdf.open(filename,'NC_NOWRITE'); groupIDs=netcdf.inqGrps(ncid);%retrieve group IDs @@ -30,5 +30,5 @@ %classtype have done is job, no need to keep it any more if ~strcmp(attname,'classtype'), - attval=netcdf.getAtt(subgroupIDs(i),netcdf.getConstant('NC_GLOBAL'),attname); + attval=netcdf.getAtt(subgroupIDs(j),netcdf.getConstant('NC_GLOBAL'),attname); if strcmp(attval,'False'), self.(groupName).(subclass).(attname)=false; @@ -37,8 +37,9 @@ else self.(groupName).(subclass).(attname)=attval; - end - end - end + end + end + end %now loop on variable in group + count=0; for k=1:length(varIDs), [varname, xtype, varDimIDs, varAtts] =netcdf.inqVar(subgroupIDs(j),varIDs(k)); @@ -48,5 +49,5 @@ [dimname, dimlen] = netcdf.inqDim(ncid,varDimIDs(l)); count(l)=[dimlen]; - end + end startpoint=zeros(size(varDimIDs)); timestep=count(end); @@ -59,33 +60,8 @@ self.(groupName).(subclass)(l).('outlog')=''; self.(groupName).(subclass)(l).('SolutionType')=subclass; - end - clear count - end - end - %toolkits too require a specific treatment - elseif strcmp(whichclass,'toolkits'), - %just one variable here - varID=netcdf.inqVarIDs(groupIDs(i)); - [varname, xtype, varDimIDs, varAtts] =netcdf.inqVar(groupIDs(i),varID); - disp(sprintf('In %s, Treating variable %s of type %i',whichclass,varname,xtype)); - [dimname,numoffields] = netcdf.inqDim(ncid,varDimIDs(end)); - self.(groupName)=eval(whichclass); - for j=1:numoffields, - varval=netcdf.getVar(groupIDs(i),varID,[0,1,j-1],[40,1,1])'; - fieldname=netcdf.getVar(groupIDs(i),varID,[0,0,j-1],[40,1,1])'; - varval=cellstr(varval); - fieldname=cellstr(fieldname); - [val, status]=str2num(varval{1}); - if strcmp(varval{1},'false') |strcmp(varval{1},'true') , - status=0; - end - if status==1, - self.(groupName).(varname).(fieldname{1})=val; - else - self.(groupName).(varname).(fieldname{1})=varval{1}; - end - end - %Now for the other fields - + end + count=0; + end + end else, %define the model structure @@ -106,8 +82,8 @@ self.(groupName).(attname)=true; else - self.(groupName).(attname)=attval; - end - end - end + self.(groupName).(attname)=attval; + end + end + end %now loop on variable in group for j=1:length(varIDs), @@ -127,8 +103,8 @@ else self.(groupName).(varname)=netcdf.getVar(groupIDs(i),varIDs(j)); - end - end - end - end + end + end + end + end netcdf.close(ncid) end Index: /issm/trunk/src/m/contrib/defleurian/paraview/exportVTK.py =================================================================== --- /issm/trunk/src/m/contrib/defleurian/paraview/exportVTK.py (revision 21728) +++ /issm/trunk/src/m/contrib/defleurian/paraview/exportVTK.py (revision 21729) @@ -40,5 +40,5 @@ os.mkdir(filename) - #get the element related variables + # {{{ get the element related variables if 'z' in dict.keys(model.mesh.__dict__): points=np.column_stack((model.mesh.x,model.mesh.y,model.mesh.z)) @@ -51,6 +51,6 @@ num_of_elt=np.shape(model.mesh.elements)[0] point_per_elt=np.shape(model.mesh.elements)[1] - - #Select the type of element function of the number of nodes per elements + # }}} + # {{{ Select the type of element function of the number of nodes per elements if point_per_elt==3: celltype=5 #triangles @@ -59,6 +59,6 @@ else: error('Your Element definition is not taken into account \n') - - #this is the result structure + # }}} + # {{{ this is the result structure res_struct=model.results if (len(res_struct.__dict__)>0): @@ -75,5 +75,6 @@ else: num_of_timesteps=1 - + # }}} + # {{{ write header and mesh for step in range(0,num_of_timesteps): timestep=step @@ -107,6 +108,6 @@ fid.write('POINT_DATA %s \n' %str(num_of_points)) - - #loop over the different solution structures + # }}} + # {{{ loop over the different solution structures if 'solnames' in locals(): for sol in solnames: @@ -141,22 +142,60 @@ else: fid.write('%e\n' % fieldstruct[node]) - - #loop on arguments, if something other than result is asked, do - #it now + # }}} + # {{{ loop on arguments, if something other than result is asked, do it now for other in args: other_struct=model.__dict__[other] othernames=(dict.keys(other_struct.__dict__)) for field in othernames: - if ((np.size(other_struct.__dict__[field]))==num_of_points): - fid.write('SCALARS %s float 1 \n' % field) - fid.write('LOOKUP_TABLE default\n') - for node in range(0,num_of_points): - #paraview does not like NaN, replacing - if np.isnan(other_struct.__dict__[field][node]): - fid.write('%e\n' % -9999.9999) - #also checking for verry small value that mess up - elif (abs(other_struct.__dict__[field][node])<1.0e-20): - fid.write('%e\n' % 0.0) + if np.ndim(other_struct.__dict__[field])==1: + if np.size(other_struct.__dict__[field])==num_of_points: + fid.write('SCALARS %s float 1 \n' % field) + fid.write('LOOKUP_TABLE default\n') + for node in range(0,num_of_points): + #paraview does not like NaN, replacing + if np.isnan(other_struct.__dict__[field][node]): + fid.write('%e\n' % -9999.9999) + #also checking for verry small value that mess up + elif (abs(other_struct.__dict__[field][node])<1.0e-20): + fid.write('%e\n' % 0.0) + else: + fid.write('%e\n' % other_struct.__dict__[field][node]) + elif np.ndim(other_struct.__dict__[field])==2: + #deal with forcings + if np.shape(other_struct.__dict__[field])[0]==num_of_points+1: + current_time=res_struct.__dict__[sol].__getitem__(timestep).__dict__['time']/model.__dict__['constants'].__dict__['yts'] + times=other_struct.__dict__[field][-1,:] + if np.any(times==current_time): + time_loc=np.where(times==current_time) + current_force=other_struct.__dict__[field][:-1,time_loc] else: - fid.write('%e\n' % other_struct.__dict__[field][node]) + precede_time_loc=np.where(timescurrent_time)[0][0] + time_scaling=(current_time-times[precede_time_loc])/(times[follow_time_loc]-times[precede_time_loc]) + current_force=other_struct.__dict__[field][:-1,precede_time_loc]+(other_struct.__dict__[field][:-1,follow_time_loc]-other_struct.__dict__[field][:-1,precede_time_loc])*time_scaling + fid.write('SCALARS %s float 1 \n' % field) + fid.write('LOOKUP_TABLE default\n') + for node in range(0,num_of_points): + #paraview does not like NaN, replacing + if np.isnan(current_force[node]): + fid.write('%e\n' % -9999.9999) + #also checking for verry small value that mess up + elif (abs(current_force[node])<1.0e-20): + fid.write('%e\n' % 0.0) + else: + fid.write('%e\n' % current_force[node]) + # reloaded variable are generally of dim 2 + elif np.shape(other_struct.__dict__[field])[0]==num_of_points: + fid.write('SCALARS %s float 1 \n' % field) + fid.write('LOOKUP_TABLE default\n') + for node in range(0,num_of_points): + #paraview does not like NaN, replacing + if np.isnan(other_struct.__dict__[field][node]): + fid.write('%e\n' % -9999.9999) + #also checking for verry small value that mess up + elif (abs(other_struct.__dict__[field][node])<1.0e-20): + fid.write('%e\n' % 0.0) + else: + fid.write('%e\n' % other_struct.__dict__[field][node]) + # }}} fid.close(); Index: /issm/trunk/src/m/contrib/tsantos/AMRexportVTK.m =================================================================== --- /issm/trunk/src/m/contrib/tsantos/AMRexportVTK.m (revision 21729) +++ /issm/trunk/src/m/contrib/tsantos/AMRexportVTK.m (revision 21729) @@ -0,0 +1,193 @@ +function AMRexportVTK(filename,model,varargin) +%AMREXPORTVTK - vtk export +% +% function AMRexportVTK(filename,model) +% creates a directory with the vtk files for displays in paraview +% (only work for triangle based on their number of nodes) +% By default only the results are exported +% +% USAGE: +% AMRexportVTK(filename,model,varargin) +% +% EXAMPLE: +% AMRexportVTK('ResultSimulation1',md) + +[path,name,ext]=fileparts(filename); +separator=filesep; +mkdir(filename); + +%get the element related variables +if dimension(model.mesh)==2, + points=[model.mesh.x model.mesh.y zeros(model.mesh.numberofvertices,1)]; +else + error('Dimension not supported yet \n'); +end + +[num_of_points,dim]=size(points); +[num_of_elt]=size(model.mesh.elements,1); +[point_per_elt]=size(model.mesh.elements,2); + +%Select the type of element function of the number of nodes per elements +if point_per_elt==3; + celltype=5; %triangles +elseif point_per_elt==6; + error('Element type not supported yet \n') +else + error('Your Element definition is not taken into account \n'); +end + +%this is the result structure +res_struct=model.results; +%checking for results +if (length(fields(res_struct))>0); + %Getting all the solutions of the model + solnames=fields(res_struct); + num_of_sols=length(solnames); + num_of_timesteps=1; + %building solution structure + for i=1:num_of_sols + sol_struct{i}=res_struct.(solnames{i}); + %looking for multiple time steps + if(size(sol_struct{i},2)>num_of_timesteps); + num_of_timesteps=size(sol_struct{i},2); + outstep=model.timestepping.time_step*model.settings.output_frequency; + end + end +else + num_of_timesteps=1; +end +for step=1:num_of_timesteps; + + timestep=step; + + points=[model.results.TransientSolution(step).MeshX model.results.TransientSolution(step).MeshY zeros(size(model.results.TransientSolution(step).MeshX))]; + [num_of_points,dim]=size(points); + [num_of_elt]=size(model.results.TransientSolution(step).MeshElements,1); + + fid = fopen(strcat(path,filesep,name,filesep,'timestep.vtk',int2str(timestep),'.vtk'),'w+'); + fprintf(fid,'# vtk DataFile Version 2.0 \n'); + fprintf(fid,'Data for run %s \n',model.miscellaneous.name); + fprintf(fid,'ASCII \n'); + fprintf(fid,'DATASET UNSTRUCTURED_GRID \n'); + + fprintf(fid,'POINTS %d float\n',num_of_points); + if(dim==3); + s='%f %f %f \n'; + elseif(dim==2); + s='%f %f \n'; + end + P=[points zeros(num_of_points,3-dim)]; + fprintf(fid,s,P'); + + fprintf(fid,'CELLS %d %d\n',num_of_elt,num_of_elt*(point_per_elt+1)); + s='%d'; + for j=1:point_per_elt + s=horzcat(s,{' %d'}); + end + s=cell2mat(horzcat(s,{'\n'})); + fprintf(fid,s,[(point_per_elt)*ones(num_of_elt,1) model.results.TransientSolution(step).MeshElements-1]'); + + fprintf(fid,'CELL_TYPES %d\n',num_of_elt); + s='%d\n'; + fprintf(fid,s,celltype*ones(num_of_elt,1)); + fprintf(fid,'POINT_DATA %s \n',num2str(num_of_points)); + + %loop over the different solution structures + if (exist('num_of_sols')); + for j=1:num_of_sols + %dealing with results on different timesteps + if(size(sol_struct{j},2)>timestep); + timestep = step; + else + timestep = size(sol_struct{j},2); + end + + %getting the number of fields in the solution + fieldnames=fields(sol_struct{j}(timestep)); + num_of_fields=length(fieldnames); + + %check which field is a real result and print + for k=1:num_of_fields + if ((numel(sol_struct{j}(timestep).(fieldnames{k})))==num_of_points); + %paraview does not like NaN, replacing + nanval=find(isnan(sol_struct{j}(timestep).(fieldnames{k}))); + sol_struct{j}(timestep).(fieldnames{k})(nanval)=-9999; + %also checking for verry small value that mess up + smallval=(abs(sol_struct{j}(timestep).(fieldnames{k}))<1.0e-20); + sol_struct{j}(timestep).(fieldnames{k})(smallval)=0.0; + fprintf(fid,'SCALARS %s float 1 \n',fieldnames{k}); + fprintf(fid,'LOOKUP_TABLE default\n'); + s='%e\n'; + fprintf(fid,s,sol_struct{j}(timestep).(fieldnames{k})); + end + end + end + end + %loop on arguments, if something other than result is asked, do + %it now + for j= 1:nargin-2 + res_struct=model.(varargin{j}); + fieldnames=fields(res_struct); + num_of_fields=length(fieldnames); + for k=1:num_of_fields + if ((numel(res_struct.(fieldnames{k})))==num_of_points); + %paraview does not like NaN, replacing + nanval=find(isnan(res_struct.(fieldnames{k}))); + res_struct.(fieldnames{k})(nanval)=-9999; + %also checking for verry small value that mess up + smallval=(abs(res_struct.(fieldnames{k}))<1.0e-20); + res_struct.(fieldnames{k})(smallval)=0.0; + fprintf(fid,'SCALARS %s float 1 \n',fieldnames{k}); + fprintf(fid,'LOOKUP_TABLE default\n'); + s='%e\n'; + fprintf(fid,s,res_struct.(fieldnames{k})); + %check for forcings + elseif (size(res_struct.(fieldnames{k}),1)==num_of_points+1); + %paraview does not like NaN, replacing + nanval=find(isnan(res_struct.(fieldnames{k}))); + res_struct.(fieldnames{k})(nanval)=-9999; + %also checking for verry small value that mess up + smallval=(abs(res_struct.(fieldnames{k}))<1.0e-20); + res_struct.(fieldnames{k})(smallval)=0.0; + if (size(res_struct.(fieldnames{k}),2)==num_of_timesteps), + fprintf(fid,'SCALARS %s float 1 \n',fieldnames{k}); + fprintf(fid,'LOOKUP_TABLE default\n'); + s='%e\n'; + fprintf(fid,s,res_struct.(fieldnames{k})(1:end-1,timestep)); + else, + %forcing and results not on the same timestep,need some treatment + fprintf(fid,'SCALARS %s float 1 \n',fieldnames{k}); + fprintf(fid,'LOOKUP_TABLE default\n'); + index=1; + currenttime=((timestep-1)*outstep)+model.timestepping.start_time; + while (res_struct.(fieldnames{k})(end,index)<=currenttime); + if index==size(res_struct.(fieldnames{k}),2) + break + end + index=index+1; + end + uptime=res_struct.(fieldnames{k})(end,index); + uplim=res_struct.(fieldnames{k})(1:end-1,index); + while (res_struct.(fieldnames{k})(end,index)>=currenttime); + if index==1 + break + end + index=index-1; + end + lowtime=res_struct.(fieldnames{k})(end,index); + lowlim=res_struct.(fieldnames{k})(1:end-1,index); + if uptime==currenttime, + interp=uplim; + elseif lowtime==currenttime, + interp=lowlim; + else + interp=lowlim+(uplim-lowlim)*((currenttime-lowtime)/(uptime-lowtime)); + end + s='%e\n'; + fprintf(fid,s,interp); + end + end + end + end + fclose(fid); +end Index: /issm/trunk/src/m/contrib/tsantos/mismip/MismipGLPosition.m =================================================================== --- /issm/trunk/src/m/contrib/tsantos/mismip/MismipGLPosition.m (revision 21729) +++ /issm/trunk/src/m/contrib/tsantos/mismip/MismipGLPosition.m (revision 21729) @@ -0,0 +1,29 @@ +%GLy0 : grounding line position @ y=0km +%GLy40 : grounding line position @ y=40km + +function [GLy0 GLy40] = MismipGLPosition(xGL,yGL,t), + + GLy0 = []; + GLy40 = []; + nsteps = length(t); + + for i=1:nsteps, + + xi = xGL(i,:); + yi = yGL(i,:); + + %find GL position at y=0km + pos = find(min(yi)==yi); + GLy0(i) = max(xi(pos)); %max(xi(pos)) Helene, here + + %find GL position at y=40km + pos = find(yi<45 & yi>35); + x = yi(pos); + v = xi(pos); + xq = [38:0.1:42]; + vq = interp1(x,v,xq,'linear'); + pos = find(xq==40); + GLy40(i) = vq(pos); + end + +end Index: /issm/trunk/src/m/contrib/tsantos/mismip/generate_plot.m =================================================================== --- /issm/trunk/src/m/contrib/tsantos/mismip/generate_plot.m (revision 21729) +++ /issm/trunk/src/m/contrib/tsantos/mismip/generate_plot.m (revision 21729) @@ -0,0 +1,175 @@ +%L0 and L1 {{{ +md0 = loadmodel('./L0_viscous/Transient_Steadystate_Level_0.mat'); +md1 = loadmodel('./L1/L1_viscous/Transient_steadystate.mat'); +md_L1_R5 = loadmodel('./R5/L1_viscous/Transient_steadystate.mat'); +md_L1_R15 = loadmodel('./R15/L1_viscous/Transient_steadystate.mat'); +md_L1_R30 = loadmodel('./R30/L1_viscous/Transient_steadystate.mat'); +md_L1_R40 = loadmodel('./R40/L1_viscous/Transient_steadystate.mat'); + +[ga0 iv0 ivaf0 GLy400 ne0 t0] = ice_evolution(md0); +[gaL1 ivL1 ivafL1 GLy40L1 neL1 tL1] = ice_evolution(md1); +[ga1 iv1 ivaf1 GLy401 ne1 t1] = ice_evolution(md_L1_R5); +[ga2 iv2 ivaf2 GLy402 ne2 t2] = ice_evolution(md_L1_R15); +[ga3 iv3 ivaf3 GLy403 ne3 t3] = ice_evolution(md_L1_R30); +[ga4 iv4 ivaf4 GLy404 ne4 t4] = ice_evolution(md_L1_R40); +% }}} +%L2 {{{ +md_L2_R5 = loadmodel('./R5/L2_viscous/Transient_steadystate.mat'); +md_L2_R15 = loadmodel('./R15/L2_viscous/Transient_steadystate.mat'); +md_L2_R20 = loadmodel('./R20/L2_viscous/Transient_steadystate.mat'); +md_L2_R30 = loadmodel('./R30/L2_viscous/Transient_steadystate.mat'); + +[ga5 iv5 ivaf5 GLy405 ne5 t5] = ice_evolution(md_L2_R5); +[ga6 iv6 ivaf6 GLy406 ne6 t6] = ice_evolution(md_L2_R15); +[ga7 iv7 ivaf7 GLy407 ne7 t7] = ice_evolution(md_L2_R20); +[ga8 iv8 ivaf8 GLy408 ne8 t8] = ice_evolution(md_L2_R30); +% }}} +%L3 {{{ +md_L3_R30 = loadmodel('./L3_viscous/Transient_steadystate.mat'); +[ga9 iv9 ivaf9 GLy409 ne9 t9] = ice_evolution(md_L3_R30); +% }}} + +%L4 {{{ +md_L4_R30 = loadmodel('./L4_viscous/Transient_steadystate.mat'); +[ga10 iv10 ivaf10 GLy4010 ne10 t10] = ice_evolution(md_L4_R30); +% }}} + +% Scaling {{{ +t0=t0/1000; +tL1=tL1/1000; +t1=t1/1000; +t2=t2/1000; +t3=t3/1000; +t4=t4/1000; +t5=t5/1000; +t6=t6/1000; +t7=t7/1000; +t8=t8/1000; +t9=t9/1000; +t10=t10/1000; + +GLy400=GLy400/1000; +GLy40L1=GLy40L1/1000; +GLy401=GLy401/1000; +GLy402=GLy402/1000; +GLy403=GLy403/1000; +GLy404=GLy404/1000; +GLy405=GLy405/1000; +GLy406=GLy406/1000; +GLy407=GLy407/1000; +GLy408=GLy408/1000; +GLy409=GLy409/1000; +GLy4010=GLy4010/1000; + +ivaf0=ivaf0/10^12; +ivafL1=ivafL1/10^12; +ivaf1=ivaf1/10^12; +ivaf2=ivaf2/10^12; +ivaf3=ivaf3/10^12; +ivaf4=ivaf4/10^12; +ivaf5=ivaf5/10^12; +ivaf6=ivaf6/10^12; +ivaf7=ivaf7/10^12; +ivaf8=ivaf8/10^12; +ivaf9=ivaf9/10^12; +ivaf10=ivaf10/10^12; +% }}} + +figure(1) % {{{ +hold on +plot(t0,GLy400,'*',tL1,GLy40L1,'r+',t1,GLy401,'b',t2,GLy402,'g',t3,GLy403,'m',t4,GLy404,'r','LineWidth',1.5) +axis([0 25 365 455]) +legend('L0','L1','L1-R5','L1-R15','L1-R30','L1-R40','Location','southeast') +title('\fontsize{16} Mismip+ steady state - Rmax analysis') +ylabel('GL @ y=40km (km)') +xlabel('t (kyr)') +hold off +% }}} + +figure(2) % {{{ +hold on +plot(t0,GLy400,'*',t5,GLy405,'b',t6,GLy406,'g',t7,GLy407,'m',t8,GLy408,'r','LineWidth',1.5) +axis([0 25 365 455]) +legend('L0','L2-R5','L2-R15','L2-R20','L2-R30','Location','southeast') +title('\fontsize{16} Mismip+ steady state - Rmax analysis') +ylabel('GL @ y=40km (km)') +xlabel('t (kyr)') +hold off +% }}} + +figure(3) % {{{ +res = [2 1]; +res30 = [2 1 0.5 0.25]; +r5 = [GLy401(end) GLy405(end)]; +r15 = [GLy402(end) GLy406(end)]; +r30 = [GLy403(end) GLy408(end) GLy409(end) GLy4010(end)]; +hold on +plot(log(4),GLy400(end),'^','MarkerSize',7,'MarkerFaceColor','b','MarkerEdgeColor','k'); +plot(log(2),GLy40L1(end),'^','MarkerSize',7,'MarkerFaceColor','k','MarkerEdgeColor','k'); +plot(log(res),r5,'^','MarkerSize',7,'MarkerFaceColor','g','MarkerEdgeColor','k'); +plot(log(res),r15,'^','MarkerSize',7,'MarkerFaceColor','y','MarkerEdgeColor','k'); +plot(log(res30),r30,'^','MarkerSize',7,'MarkerFaceColor','r','MarkerEdgeColor','k'); +plot(log(res(1)),GLy404(end),'^','MarkerSize',7,'MarkerFaceColor','m','MarkerEdgeColor','k'); +plot(log(res(2)),GLy407(end),'^','MarkerSize',7,'MarkerFaceColor','c','MarkerEdgeColor','k'); +axis([log(0.2) log(5) 437 458]) +legend('L0','L1','R5','R15','R30','L1-R40','L2-R20','Location','northeast') +title('\fontsize{15} Mismip+ steady state: GLpos X Rmax') +ylabel('GL @ y=40km (km)') +xlabel('Resolution (km)') +xtickslabel = [0.25 0.5 1 2 4]; +xticks = log(xtickslabel); +ytickslabel = [440 445 450 455]; +yticks = ytickslabel; +ax = gca; +set(ax,'XTick',xticks); +set(ax,'XTickLabel',xtickslabel); +set(ax,'YTick',yticks); +set(ax,'YTickLabel',ytickslabel); +box on +%set(gca,'xscale','log') +hold off +% }}} + +figure(4) % {{{ +res = [2 1]; +res30 = [2 1 0.5 0.25]; +r5 = [ivaf1(end) ivaf5(end)]; +r15 = [ivaf2(end) ivaf6(end)]; +r30 = [ivaf3(end) ivaf8(end) ivaf9(end) ivaf10(end)]; +hold on +plot(log(4),ivaf0(end),'^','MarkerSize',7,'MarkerFaceColor','b','MarkerEdgeColor','k'); +plot(log(2),ivafL1(end),'^','MarkerSize',7,'MarkerFaceColor','k','MarkerEdgeColor','k'); +plot(log(res),r5,'^','MarkerSize',7,'MarkerFaceColor','g','MarkerEdgeColor','k'); +plot(log(res),r15,'^','MarkerSize',7,'MarkerFaceColor','y','MarkerEdgeColor','k'); +plot(log(res30),r30,'^','MarkerSize',7,'MarkerFaceColor','r','MarkerEdgeColor','k'); +plot(log(res(1)),ivaf4(end),'^','MarkerSize',7,'MarkerFaceColor','m','MarkerEdgeColor','k'); +plot(log(res(2)),ivaf7(end),'^','MarkerSize',7,'MarkerFaceColor','c','MarkerEdgeColor','k'); +axis([log(0.2) log(5) 34.3 37.2]) +legend('L0','L1','R5','R15','R30','L1-R40','L2-R20','Location','northeast') +title('\fontsize{15} Mismip+ steady state: IVAF X Rmax') +ylabel('Ice volume above floatation (1000 x km3)') +xlabel('Resolution (km)') +xtickslabel = [0.25 0.5 1 2 4]; +xticks = log(xtickslabel); +ytickslabel = [34.5 35.0 35.5 36.0 36.5 37.0]; +yticks = ytickslabel; +ax = gca; +set(ax,'XTick',xticks); +set(ax,'XTickLabel',xtickslabel); +set(ax,'YTick',yticks); +set(ax,'YTickLabel',ytickslabel); +box on +%set(gca,'xscale','log') +hold off +% }}} + +figure(5) % {{{ +hold on +plot(t0,GLy400,'*',t3,GLy403,'b',t8,GLy408,'m',t9,GLy409,'r',t10,GLy4010,'g','LineWidth',1.5) +axis([0 25 365 460]) +legend('L0','L1-R30','L2-R30','L3-R30','L4-R30','Location','southeast') +title('\fontsize{16} Mismip+ steady state - Rmax analysis') +ylabel('GL @ y=40km (km)') +xlabel('t (kyr)') +hold off +% }}} Index: /issm/trunk/src/m/contrib/tsantos/mismip/gl_position.m =================================================================== --- /issm/trunk/src/m/contrib/tsantos/mismip/gl_position.m (revision 21729) +++ /issm/trunk/src/m/contrib/tsantos/mismip/gl_position.m (revision 21729) @@ -0,0 +1,187 @@ +function [glx gly] = gl_position(md,step,level), + + %initialization of some variables + data = md.results.TransientSolution(step).MaskGroundediceLevelset; + index = md.results.TransientSolution(step).MeshElements; + x = md.results.TransientSolution(step).MeshX; + y = md.results.TransientSolution(step).MeshY; + numberofelements = size(index,1); + elementslist = 1:numberofelements; + c = []; + h = []; + + %get unique edges in mesh + %1: list of edges + edges=[index(:,[1,2]); index(:,[2,3]); index(:,[3,1])]; + %2: find unique edges + [edges,I,J]=unique(sort(edges,2),'rows'); + %3: unique edge numbers + vec=J; + %4: unique edges numbers in each triangle (2 triangles sharing the same edge will have + % the same edge number) + edges_tria=[vec(elementslist), vec(elementslist+numberofelements), vec(elementslist+2*numberofelements)]; + + %segments [nodes1 nodes2] + Seg1=index(:,[1 2]); + Seg2=index(:,[2 3]); + Seg3=index(:,[3 1]); + + %segment numbers [1;4;6;...] + Seg1_num=edges_tria(:,1); + Seg2_num=edges_tria(:,2); + Seg3_num=edges_tria(:,3); + + %value of data on each tips of the segments + Data1=data(Seg1); + Data2=data(Seg2); + Data3=data(Seg3); + + %get the ranges for each segment + Range1=sort(Data1,2); + Range2=sort(Data2,2); + Range3=sort(Data3,2); + + %find the segments that contain this value + pos1=(Range1(:,1)level); + pos2=(Range2(:,1)level); + pos3=(Range3(:,1)level); + + %get elements + poselem12=(pos1 & pos2); + poselem13=(pos1 & pos3); + poselem23=(pos2 & pos3); + poselem=find(poselem12 | poselem13 | poselem23); + numelems=length(poselem); + + %if no element has been flagged, skip to the next level + if numelems==0, + return, + end + + %go through the elements and build the coordinates for each segment (1 by element) + x1=zeros(numelems,1); + x2=zeros(numelems,1); + y1=zeros(numelems,1); + y2=zeros(numelems,1); + edge_l=zeros(numelems,2); + + for j=1:numelems, + + weight1=(level-Data1(poselem(j),1))/(Data1(poselem(j),2)-Data1(poselem(j),1)); + weight2=(level-Data2(poselem(j),1))/(Data2(poselem(j),2)-Data2(poselem(j),1)); + weight3=(level-Data3(poselem(j),1))/(Data3(poselem(j),2)-Data3(poselem(j),1)); + + if poselem12(poselem(j)); + + x1(j)=x(Seg1(poselem(j),1))+weight1*(x(Seg1(poselem(j),2))-x(Seg1(poselem(j),1))); + x2(j)=x(Seg2(poselem(j),1))+weight2*(x(Seg2(poselem(j),2))-x(Seg2(poselem(j),1))); + y1(j)=y(Seg1(poselem(j),1))+weight1*(y(Seg1(poselem(j),2))-y(Seg1(poselem(j),1))); + y2(j)=y(Seg2(poselem(j),1))+weight2*(y(Seg2(poselem(j),2))-y(Seg2(poselem(j),1))); + edge_l(j,1)=Seg1_num(poselem(j)); + edge_l(j,2)=Seg2_num(poselem(j)); + + elseif poselem13(poselem(j)), + + x1(j)=x(Seg1(poselem(j),1))+weight1*(x(Seg1(poselem(j),2))-x(Seg1(poselem(j),1))); + x2(j)=x(Seg3(poselem(j),1))+weight3*(x(Seg3(poselem(j),2))-x(Seg3(poselem(j),1))); + y1(j)=y(Seg1(poselem(j),1))+weight1*(y(Seg1(poselem(j),2))-y(Seg1(poselem(j),1))); + y2(j)=y(Seg3(poselem(j),1))+weight3*(y(Seg3(poselem(j),2))-y(Seg3(poselem(j),1))); + edge_l(j,1)=Seg1_num(poselem(j)); + edge_l(j,2)=Seg3_num(poselem(j)); + + elseif poselem23(poselem(j)), + + x1(j)=x(Seg2(poselem(j),1))+weight2*(x(Seg2(poselem(j),2))-x(Seg2(poselem(j),1))); + x2(j)=x(Seg3(poselem(j),1))+weight3*(x(Seg3(poselem(j),2))-x(Seg3(poselem(j),1))); + y1(j)=y(Seg2(poselem(j),1))+weight2*(y(Seg2(poselem(j),2))-y(Seg2(poselem(j),1))); + y2(j)=y(Seg3(poselem(j),1))+weight3*(y(Seg3(poselem(j),2))-y(Seg3(poselem(j),1))); + edge_l(j,1)=Seg2_num(poselem(j)); + edge_l(j,2)=Seg3_num(poselem(j)); + else + %it shoud not go here + end + end + + %now that we have the segments, we must try to connect them... + + %loop over the subcontours + indice=0; + while ~isempty(edge_l), + indice=indice+1; + + %take the right edge of the second segment and connect it to the next segments if any + e1=edge_l(1,1); e2=edge_l(1,2); + xc=[x1(1);x2(1)]; yc=[y1(1);y2(1)]; + + %erase the lines corresponding to this edge + edge_l(1,:)=[]; + x1(1)=[]; x2(1)=[]; + y1(1)=[]; y2(1)=[]; + + [ro1,co1]=find(edge_l==e1); + + while ~isempty(ro1) + + if co1==1, + xc=[x2(ro1);xc]; yc=[y2(ro1);yc]; + + %next edge: + e1=edge_l(ro1,2); + + else + xc=[x1(ro1);xc]; yc=[y1(ro1);yc]; + + %next edge: + e1=edge_l(ro1,1); + end + + %erase the lines of this + edge_l(ro1,:)=[]; + x1(ro1)=[]; x2(ro1)=[]; + y1(ro1)=[]; y2(ro1)=[]; + + %next connection + [ro1,co1]=find(edge_l==e1); + end + + %same thing the other way (to the right) + [ro2,co2]=find(edge_l==e2); + + while ~isempty(ro2) + + if co2==1, + xc=[xc;x2(ro2)]; yc=[yc;y2(ro2)]; + + %next edge: + e2=edge_l(ro2,2); + else + xc=[xc;x1(ro2)]; yc=[yc;y1(ro2)]; + + %next edge: + e2=edge_l(ro2,1); + end + + %erase the lines of this + edge_l(ro2,:)=[]; + x1(ro2)=[]; x2(ro2)=[]; + y1(ro2)=[]; y2(ro2)=[]; + + %next connection + [ro2,co2]=find(edge_l==e2); + end + + % Update the CS data structure as per "contours.m" + % so that clabel works + c = horzcat(c,[level, xc'; length(xc), yc']); + % y0=find(c(2,:)==0); + % y50=find(c(2,:)==50000); + % gl0(glstep)=c(1,y0); + % gl50(glstep)=c(1,y50); + glx=c(1,1:end)'; + gly=c(2,1:end)'; + pos=find(glx~=0); + glx=glx(pos); + gly=gly(pos); + +end + %min(c(1,2:end)) Index: /issm/trunk/src/m/contrib/tsantos/mismip/ice_evolution.m =================================================================== --- /issm/trunk/src/m/contrib/tsantos/mismip/ice_evolution.m (revision 21729) +++ /issm/trunk/src/m/contrib/tsantos/mismip/ice_evolution.m (revision 21729) @@ -0,0 +1,34 @@ +%ga: grounded area +%iv: ice volume +%ivaf: ice volume above floatation +%GLy40 : grounding line position @ y=40km +%nelem : number of elements + +function [ga iv ivaf GLy40 nelem t] = ice_evolution(md), + + ga = []; + iv = []; + ivaf = []; + GLy40 = []; + nelem = []; + t = []; + nsteps = length(md.results.TransientSolution); + + for i=1:nsteps, + ga(i) = md.results.TransientSolution(i).GroundedArea; + iv(i) = md.results.TransientSolution(i).IceVolume; + ivaf(i) = md.results.TransientSolution(i).IceVolumeAboveFloatation; + nelem(i) = size(md.results.TransientSolution(i).MeshElements,1); + t(i) = md.results.TransientSolution(i).time; + %find GL position at y=40km + [glx gly] = gl_position(md,i,0); + pos=find(gly<45000 & gly > 35000); + x=gly(pos); + v=glx(pos); + xq=[38000:100:42000]; + vq = interp1(x,v,xq,'linear'); + pos=find(xq==40000); + GLy40(i)=vq(pos); + end + +end Index: /issm/trunk/src/m/contrib/tsantos/mismip/writeNetCDF.m =================================================================== --- /issm/trunk/src/m/contrib/tsantos/mismip/writeNetCDF.m (revision 21729) +++ /issm/trunk/src/m/contrib/tsantos/mismip/writeNetCDF.m (revision 21729) @@ -0,0 +1,112 @@ +function writeNetCDF(md0,md,step,dt,ncfile), + + xGL={}; + yGL={}; + iceThicknessGL={}; + uBaseGL={}; + vBaseGL={}; + iceVolume=[]; + iceVAF=[]; + groundedArea=[]; + time=[]; + + %Inserting time 0. md0 must be last experiment (e.g., Ice1r for Ice1ra) + x = md0.results.TransientSolution(end).MeshX; + y = md0.results.TransientSolution(end).MeshY; + time(1) = 0; + [xgl_step ygl_step] = gl_position(md0,length(md0.results.TransientSolution),0); + xGL{1} = xgl_step; + yGL{1} = ygl_step; + iceVolume(1) = md0.results.TransientSolution(end).IceVolume; + iceVAF(1) = md0.results.TransientSolution(end).IceVolumeAboveFloatation; + groundedArea(1) = md0.results.TransientSolution(end).GroundedArea; + iceThicknessGL{1} = griddata(x,y,md0.results.TransientSolution(end).Thickness,xgl_step,ygl_step); + uBaseGL{1} = griddata(x,y,md0.results.TransientSolution(end).Vx,xgl_step,ygl_step); + vBaseGL{1} = griddata(x,y,md0.results.TransientSolution(end).Vy,xgl_step,ygl_step); + + for i=2:length(step), + x = md.results.TransientSolution(step(i)).MeshX; + y = md.results.TransientSolution(step(i)).MeshY; + time(i)=md.results.TransientSolution(step(i)).time; + [xgl_step ygl_step]=gl_position(md,step(i),0); + xGL{i}=xgl_step; + yGL{i}=ygl_step; + iceVolume(i)=md.results.TransientSolution(step(i)).IceVolume; + iceVAF(i)=md.results.TransientSolution(step(i)).IceVolumeAboveFloatation; + groundedArea(i)=md.results.TransientSolution(step(i)).GroundedArea; + iceThicknessGL{i}=griddata(x,y,md.results.TransientSolution(step(i)).Thickness,xgl_step,ygl_step); + uBaseGL{i}=griddata(x,y,md.results.TransientSolution(step(i)).Vx,xgl_step,ygl_step); + vBaseGL{i}=griddata(x,y,md.results.TransientSolution(step(i)).Vy,xgl_step,ygl_step); + end + uSurfaceGL=uBaseGL; + vSurfaceGL=vBaseGL; + uMeanGL=uBaseGL; + vMeanGL=vBaseGL; + + %Create netcdf + mode = netcdf.getConstant('NETCDF4'); + mode = bitor(mode,netcdf.getConstant('CLASSIC_MODEL')); + ncid=netcdf.create(ncfile,mode); + + %General attributes + netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author','Helene Seroussi (helene.seroussi@jpl.nasa.gov)'); + netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Model','ISSM (Ice Sheet System Model)'); + netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Notes','Experiments performed at Caltech Jet Propulsion Laboratory, Pasadena'); + netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',date()); + + %Define dimensions + gl_id = netcdf.defDim(ncid,'nPointGL',netcdf.getConstant('NC_UNLIMITED')); + ntime_id = netcdf.defDim(ncid,'nTime',length(time)); + + %Define variables + volume_var_id = netcdf.defVar(ncid,'iceVolume','NC_FLOAT',[ntime_id]); + VAF_var_id = netcdf.defVar(ncid,'iceVAF','NC_FLOAT',[ntime_id]); + grounded_var_id = netcdf.defVar(ncid,'groundedArea','NC_FLOAT',[ntime_id]); + xgl_var_id = netcdf.defVar(ncid,'xGL','NC_FLOAT',[ntime_id,gl_id]); + ygl_var_id = netcdf.defVar(ncid,'yGL','NC_FLOAT',[ntime_id,gl_id]); + thickness_var_id = netcdf.defVar(ncid,'iceThicknessGL','NC_FLOAT',[ntime_id,gl_id]); + ubase_var_id = netcdf.defVar(ncid,'uBaseGL','NC_FLOAT',[ntime_id,gl_id]); + vbase_var_id = netcdf.defVar(ncid,'vBaseGL','NC_FLOAT',[ntime_id,gl_id]); + usurface_var_id = netcdf.defVar(ncid,'uSurfaceGL','NC_FLOAT',[ntime_id,gl_id]); + vsurface_var_id = netcdf.defVar(ncid,'vSurfaceGL','NC_FLOAT',[ntime_id,gl_id]); + umean_var_id = netcdf.defVar(ncid,'uMeanGL','NC_FLOAT',[ntime_id,gl_id]); + vmean_var_id = netcdf.defVar(ncid,'vMeanGL','NC_FLOAT',[ntime_id,gl_id]); + time_var_id = netcdf.defVar(ncid,'time','NC_FLOAT',[ntime_id]); + + %Define default fill values + if(false), + netcdf.defVarFill(ncid,xgl_var_id,false,NaN); + netcdf.defVarFill(ncid,ygl_var_id,false,NaN); + netcdf.defVarFill(ncid,thickness_var_id,false,NaN); + netcdf.defVarFill(ncid,ubase_var_id,false,NaN); + netcdf.defVarFill(ncid,vbase_var_id,false,NaN); + netcdf.defVarFill(ncid,usurface_var_id,false,NaN); + netcdf.defVarFill(ncid,vsurface_var_id,false,NaN); + netcdf.defVarFill(ncid,umean_var_id,false,NaN); + netcdf.defVarFill(ncid,vmean_var_id,false,NaN); + end + + netcdf.endDef(ncid); + + %Write variables + netcdf.putVar(ncid,volume_var_id,iceVolume); + netcdf.putVar(ncid,VAF_var_id,iceVAF); + netcdf.putVar(ncid,grounded_var_id,groundedArea); + for i=1:length(time), + netcdf.putVar(ncid,xgl_var_id,[i-1,0],[1,length(xGL{i})],xGL{i}'); + netcdf.putVar(ncid,ygl_var_id,[i-1,0],[1,length(xGL{i})],yGL{i}'); + netcdf.putVar(ncid,thickness_var_id,[i-1,0],[1,length(xGL{i})],iceThicknessGL{i}'); + netcdf.putVar(ncid,ubase_var_id,[i-1,0],[1,length(xGL{i})],uBaseGL{i}'); + netcdf.putVar(ncid,vbase_var_id,[i-1,0],[1,length(xGL{i})],vBaseGL{i}'); + netcdf.putVar(ncid,usurface_var_id,[i-1,0],[1,length(xGL{i})],uSurfaceGL{i}'); + netcdf.putVar(ncid,vsurface_var_id,[i-1,0],[1,length(xGL{i})],vSurfaceGL{i}'); + netcdf.putVar(ncid,umean_var_id,[i-1,0],[1,length(xGL{i})],uMeanGL{i}'); + netcdf.putVar(ncid,vmean_var_id,[i-1,0],[1,length(xGL{i})],vMeanGL{i}'); + end + netcdf.putVar(ncid,time_var_id,time+dt); + + %Close netcdf + netcdf.close(ncid) + +end + Index: /issm/trunk/src/m/contrib/tsantos/remesh.m =================================================================== --- /issm/trunk/src/m/contrib/tsantos/remesh.m (revision 21729) +++ /issm/trunk/src/m/contrib/tsantos/remesh.m (revision 21729) @@ -0,0 +1,77 @@ +function mdOut = remesh(md,parfile) +%Set the new mesh (refined) into the model md + +NewModel = model; + +% geometry +NewModel.mesh = mesh2d(); +NewModel.mesh.x = md.results.TransientSolution(end).MeshX; +NewModel.mesh.y = md.results.TransientSolution(end).MeshY; +NewModel.mesh.elements = md.results.TransientSolution(end).MeshElements; + +% build segments. CONVEX HULL: IT JUST WORKS FOR REGULAR MESHES, WITHOUT "BAYS" +disp('Building segments: searching vertices by convex hull...'); +k = convhull(NewModel.mesh.x,NewModel.mesh.y); +nsegments = length(k)-1; +nelements = size(NewModel.mesh.elements,1); +segments = zeros(nsegments,3); +segments(:,1) = k(1:nsegments); +segments(:,2) = k(2:(nsegments+1)); +disp('Building segments: searching boundary elements...'); +for s=1:nsegments, + for e=1:nelements, + if any(NewModel.mesh.elements(e,:)==segments(s,1)) && any(NewModel.mesh.elements(e,:)==segments(s,2)) + segments(s,3)=e; + break; + end + end + + if segments(s,3)==0, + error('Element not found!'); + end +end + +NewModel.mesh.segments = segments; +%NewModel.mesh.segmentmarkers = segmentmarkers; + +% connectivity +% Fill in rest of fields: +NewModel.mesh.numberofelements = size(NewModel.mesh.elements,1); +NewModel.mesh.numberofvertices = length(NewModel.mesh.x); +NewModel.mesh.vertexonboundary = zeros(NewModel.mesh.numberofvertices,1); +NewModel.mesh.vertexonboundary(NewModel.mesh.segments(:,1:2)) = 1; + +% Now, build the connectivity tables for this mesh. +NewModel.mesh.vertexconnectivity = NodeConnectivity(NewModel.mesh.elements,NewModel.mesh.numberofvertices); +NewModel.mesh.elementconnectivity = ElementConnectivity(NewModel.mesh.elements,NewModel.mesh.vertexconnectivity); + +% Building a bed topography and others parameters +NewModel = setmask(NewModel,'',''); +NewModel = parameterize(NewModel, parfile); + +% Setting initialization +NewModel.initialization.vx = md.results.TransientSolution(end).Vx; +NewModel.initialization.vy = md.results.TransientSolution(end).Vy; +NewModel.initialization.vz = zeros(md.mesh.numberofvertices,1); +NewModel.initialization.vel = md.results.TransientSolution(end).Vel; +NewModel.initialization.pressure = md.results.TransientSolution(end).Pressure; +NewModel.geometry.surface = md.results.TransientSolution(end).Surface; +NewModel.geometry.base = md.results.TransientSolution(end).Base; +%NewModel.geometry.bed = md.geometry.bed; %use from parameterize +NewModel.geometry.thickness = md.results.TransientSolution(end).Thickness; +NewModel.mask.groundedice_levelset = md.results.TransientSolution(end).MaskGroundediceLevelset; + +%copy other data +NewModel.miscellaneous = md.miscellaneous; +NewModel.timestepping = md.timestepping; +NewModel.settings = md.settings; +NewModel.stressbalance.maxiter = md.stressbalance.maxiter; +NewModel.stressbalance.abstol = md.stressbalance.abstol; +NewModel.stressbalance.restol = md.stressbalance.restol; +NewModel.verbose = md.verbose; +NewModel.cluster = md.cluster; +NewModel.transient = md.transient; + +mdOut = NewModel; + +end Index: /issm/trunk/src/m/coordsystems/gmtmask.py =================================================================== --- /issm/trunk/src/m/coordsystems/gmtmask.py (revision 21728) +++ /issm/trunk/src/m/coordsystems/gmtmask.py (revision 21729) @@ -1,5 +1,5 @@ from MatlabFuncs import * from model import * -from np.import * +import numpy as np from os import getenv, putenv import subprocess @@ -12,5 +12,5 @@ # lenlat=len(lat) - mask=empty(lenlat) + mask=np.empty(lenlat) #are we doing a recursive call? @@ -38,5 +38,5 @@ #First, write our lat,long file for gmt: nv=lenlat - savetxt('./all_vertices.txt',transpose([long, lat, arange(1,nv+1)]),delimiter='\t',fmt='%.10f') + np.savetxt('./all_vertices.txt',np.transpose([long, lat, np.arange(1,nv+1)]),delimiter='\t',fmt='%.10f') #Avoid bypassing of the ld library path by Matlab (:() @@ -72,5 +72,5 @@ fid.close() - mask=zeros([nv,1]) + mask=np.zeros([nv,1]) mask[oce_vertices]=1 Index: /issm/trunk/src/m/dev/issmversion.m =================================================================== --- /issm/trunk/src/m/dev/issmversion.m (revision 21728) +++ /issm/trunk/src/m/dev/issmversion.m (revision 21729) @@ -17,5 +17,5 @@ disp(['Compiled on ' IssmConfig('HOST_VENDOR') ' ' IssmConfig('HOST_OS') ' ' IssmConfig('HOST_ARCH') ' by ' IssmConfig('USER_NAME')]); disp([' ']); -disp(['Copyright (c) 2009-2016 California Institute of Technology']); +disp(['Copyright (c) 2009-2017 California Institute of Technology']); disp([' ']); disp([' to get started type: issmdoc']); Index: /issm/trunk/src/m/dev/issmversion.py =================================================================== --- /issm/trunk/src/m/dev/issmversion.py (revision 21728) +++ /issm/trunk/src/m/dev/issmversion.py (revision 21729) @@ -15,5 +15,5 @@ print ' ' print 'Build date: '+IssmConfig('PACKAGE_BUILD_DATE')[0] -print 'Copyright (c) 2009-2016 California Institute of Technology' +print 'Copyright (c) 2009-2017 California Institute of Technology' print ' ' print ' to get started type: issmdoc' Index: /issm/trunk/src/m/exp/exp2shp.m =================================================================== --- /issm/trunk/src/m/exp/exp2shp.m (revision 21728) +++ /issm/trunk/src/m/exp/exp2shp.m (revision 21729) @@ -1,14 +1,25 @@ -function exp2shp(shapefilename,expfilename,geometry) +function exp2shp(expfilename,shpfilename,geometry) %SHPWRITE - write a shape file from a contour structure % % Usage: -% exp2shp(shapefilename,expfilename,geometry) +% exp2shp(expfilename,shpfilename,geometry) % % Example: -% exp2shp('domainoutline.shp','domainoutline.exp') -% exp2shp('domainoutline.shp','domainoutline.exp','Polygon') -% exp2shp('massfluxgate.shp','massfluxgate.exp','Line') +% exp2shp('domainoutline.exp','domainoutline.shp') +% exp2shp('domainoutline.exp','domainoutline.shp','Polygon') +% exp2shp('massfluxgate.exp','massfluxgate.shp','Line') % % See also SHPREAD, SHPWRITE, SHP2EXP + +%check file extensions +[pathstr,name,ext] = fileparts(shpfilename); +if ~strcmp(ext,'.shp'), + error(['Shapefile ' shpfilename ' does not have an extension .shp']); +end + +[pathstr,name,ext] = fileparts(expfilename); +if ~strcmp(ext,'.exp'), + error(['Exp file ' expfilename ' does not have an extension .exp']); +end shp=expread(expfilename); @@ -34,4 +45,3 @@ end -shapewrite(contours,shapefilename); -end +shapewrite(contours,shpfilename); Index: sm/trunk/src/m/io/download.js =================================================================== --- /issm/trunk/src/m/io/download.js (revision 21728) +++ (revision ) @@ -1,31 +1,0 @@ -function download() { - //DOWNLOAD - save model/variable data to file - // - // Usage: - // download=download('id','slr-download'); - // download=download('id','slr-download','data',md.geometry.thickness,'data',md.results.Stressbalance.Vel); - - //Convert arguments to options - var args = Array.prototype.slice.call(arguments); - var options = new pairoptions(args.slice()); - - //Recover option values: - var id = options.getfieldvalue('id',''); - - document.getElementById(id).addEventListener('click', function() { - var data = {'elements':md.mesh.elements,'x':md.mesh.x,'y':md.mesh.y,'z':md.mesh.z}; - for (var i=2; i < args.length; i+=2) { - try { - data[args[i]] = args[i+1]; - } - catch (e) { - console.log(e); - } - } - string = JSONfn.stringify(data); - - var url='data:text/json:charset=utf8,' + encodeURIComponent(string); - window.open(url, '_blank'); - window.focus(); - }); -} Index: /issm/trunk/src/m/io/loadvars.py =================================================================== --- /issm/trunk/src/m/io/loadvars.py (revision 21728) +++ /issm/trunk/src/m/io/loadvars.py (revision 21729) @@ -6,6 +6,6 @@ from re import findall from os import path +from collections import OrderedDict from whichdb import whichdb -from collections import OrderedDict from model import * @@ -98,5 +98,5 @@ listtype=curclass.groups[keylist[0]].classtype if listtype=='dict': - nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = [{} for i in range(max(1,len(curclass.groups)))] + nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = [OrderedDict() for i in range(max(1,len(curclass.groups)))] else: nvdict['md'].__dict__[classtree[mod][0]].__dict__[classtree[mod][1]] = [getattr(__import__(listtype),listtype)() for i in range(max(1,len(curclass.groups)))] @@ -179,8 +179,4 @@ else: Tree.__dict__[str(var)]=varval[:,:] - try: - print('treated {}.{} with type {}'.format(mod,var,type(Tree.__dict__[str(var)]))) - except AttributeError: - print('treated {}.{} with type {}'.format(mod,var,type(Tree[0].__dict__[str(var)]))) elif vardim==3: if type(Tree)==list: @@ -232,5 +228,5 @@ classe=str(group)+'.'+str(subgroup) class_dict[classe]=[str(getattr(NCData.groups[group].groups[subgroup],'classtype')),] - if class_dict[classe][0] not in ['dict','list']: + if class_dict[classe][0] not in ['dict','list','cell']: class_dict[classe].append(__import__(class_dict[classe][0])) class_tree[classe]=[group,subgroup] @@ -239,5 +235,5 @@ try: class_dict[classe]=[str(getattr(NCData.groups[group],'classtype')),] - if class_dict[classe][0] not in ['dict','list']: + if class_dict[classe][0] not in ['dict','list','cell']: class_dict[classe].append(__import__(class_dict[classe][0])) class_tree[classe]=[group,] Index: sm/trunk/src/m/io/saveAsFile.js =================================================================== --- /issm/trunk/src/m/io/saveAsFile.js (revision 21728) +++ (revision ) @@ -1,6 +1,0 @@ -function saveAsFile(content) { - - var url='data:text/json:charset=utf8,' + encodeURIComponent(content); - window.open(url, '_blank'); - window.focus(); -} Index: /issm/trunk/src/m/mech/drivingstress.m =================================================================== --- /issm/trunk/src/m/mech/drivingstress.m (revision 21728) +++ /issm/trunk/src/m/mech/drivingstress.m (revision 21729) @@ -14,5 +14,5 @@ thickness_bar=(md.geometry.thickness(md.mesh.elements(:,1))+md.geometry.thickness(md.mesh.elements(:,2))+md.geometry.thickness(md.mesh.elements(:,3)))/3; -px=md.materials.rho_ice*md.constants.g*thickness_bar.*sx; -py=md.materials.rho_ice*md.constants.g*thickness_bar.*sy; +px=-md.materials.rho_ice*md.constants.g*thickness_bar.*sx; +py=-md.materials.rho_ice*md.constants.g*thickness_bar.*sy; pmag=sqrt(px.^2+py.^2); Index: /issm/trunk/src/m/mesh/bamg.m =================================================================== --- /issm/trunk/src/m/mesh/bamg.m (revision 21728) +++ /issm/trunk/src/m/mesh/bamg.m (revision 21729) @@ -122,8 +122,21 @@ %Check that file exists riftfile=getfieldvalue(options,'rifts'); + [pathr,namer,extr]=fileparts(riftfile); if ~exist(riftfile,'file') error(['bamg error message: file ' riftfile ' not found ']); - end - rift=expread(riftfile); + elseif strcmp(extr,'.exp'), + rift=expread(riftfile); + elseif strcmp(extr,'.shp'), + rift=shpread(riftfile); + end + %read rift file according to its extension: + [path,name,ext]=fileparts(riftfile); + if strcmp(ext,'.exp'), + rift=expread(riftfile); + elseif strcmp(ext,'.shp'), + rift=shpread(riftfile); + else + error(['bamg error message: file ' riftfile ' format not supported (.shp or .exp)']); + end for i=1:length(rift), Index: /issm/trunk/src/m/mesh/planet/gmsh/gmshplanet.py =================================================================== --- /issm/trunk/src/m/mesh/planet/gmsh/gmshplanet.py (revision 21728) +++ /issm/trunk/src/m/mesh/planet/gmsh/gmshplanet.py (revision 21729) @@ -1,4 +1,4 @@ from MatlabFuncs import * -from model import * +import numpy as np from numpy import * from pairoptions import * @@ -95,10 +95,9 @@ fid.write('View "background mesh" [;\n') for i in range(meshini.numberofelements): - fid.write('ST(%g,%g,%g,%g,%g,%g,%g,%g,%g)[%g,%g,%g];\n',\ - meshini.x(meshini.elements(i,0)), meshini.y(meshini.elements(i,0)), meshini.z(meshini.elements(i,0)),\ - meshini.x(meshini.elements(i,1)), meshini.y(meshini.elements(i,1)), meshini.z(meshini.elements(i,1)),\ - meshini.x(meshini.elements(i,2)), meshini.y(meshini.elements(i,2)), meshini.z(meshini.elements(i,2)),\ - metric(meshini.elements(i,0)), metric(meshini.elements(i,1)), metric(meshini.elements(i,2))\ - ) + fid.write('ST(%g,%g,%g,%g,%g,%g,%g,%g,%g)[%g,%g,%g];\n', + meshini.x(meshini.elements(i,0)), meshini.y(meshini.elements(i,0)), meshini.z(meshini.elements(i,0)), + meshini.x(meshini.elements(i,1)), meshini.y(meshini.elements(i,1)), meshini.z(meshini.elements(i,1)), + meshini.x(meshini.elements(i,2)), meshini.y(meshini.elements(i,2)), meshini.z(meshini.elements(i,2)), + metric(meshini.elements(i,0)), metric(meshini.elements(i,1)), metric(meshini.elements(i,2))) fid.write('];\n') @@ -132,7 +131,7 @@ mesh.numberofvertices=int(fid.readline().strip()) - mesh.x=empty(mesh.numberofvertices) - mesh.y=empty(mesh.numberofvertices) - mesh.z=empty(mesh.numberofvertices) + mesh.x=np.empty(mesh.numberofvertices) + mesh.y=np.empty(mesh.numberofvertices) + mesh.z=np.empty(mesh.numberofvertices) for i in range(mesh.numberofvertices): A=fid.readline().split() @@ -150,5 +149,5 @@ raise RuntimeError(['Expecting $Elements (', A, ')']) mesh.numberofelements=int(fid.readline().strip()) - mesh.elements=empty([mesh.numberofelements,3]) + mesh.elements=np.zeros([mesh.numberofelements,3]) for i in range(mesh.numberofelements): A=fid.readline().split() @@ -162,7 +161,7 @@ #figure out other fields in mesh3dsurface: - mesh.r=sqrt(mesh.x**2+mesh.y**2+mesh.z**2) - mesh.lat = arcsin(mesh.z/mesh.r)/pi*180 - mesh.long = arctan2(mesh.y,mesh.x)/pi*180 + mesh.r=np.sqrt(mesh.x**2+mesh.y**2+mesh.z**2) + mesh.lat=np.arcsin(mesh.z/mesh.r)/np.pi*180 + mesh.long=np.arctan2(mesh.y,mesh.x)/np.pi*180 #erase files: Index: /issm/trunk/src/m/mesh/rifts/rifttipsonmesh.m =================================================================== --- /issm/trunk/src/m/mesh/rifts/rifttipsonmesh.m (revision 21728) +++ /issm/trunk/src/m/mesh/rifts/rifttipsonmesh.m (revision 21729) @@ -3,6 +3,13 @@ % rifts. -%read rifts from outline file -rifts=expread(riftoutline); +%read rift file according to its extension: +[path,name,ext]=fileparts(riftoutline); +if strcmp(ext,'.exp'), + rifts=expread(riftoutline); +elseif strcmp(ext,'.shp'), + rifts=shpread(riftoutline); +else + error(['bamg error message: file ' riftoutline ' format not supported (.shp or .exp)']); +end tips=[]; Index: /issm/trunk/src/m/mesh/squaremesh.py =================================================================== --- /issm/trunk/src/m/mesh/squaremesh.py (revision 21728) +++ /issm/trunk/src/m/mesh/squaremesh.py (revision 21729) @@ -49,11 +49,11 @@ segments=np.zeros((2*(nx-1)+2*(ny-1),3),int) #left edge: - segments[0:ny-1,:]=np.hstack((np.arange(2,ny+1).reshape(-1,),np.arange(1,ny).reshape(-1,),(2*np.arange(1,ny)-1).reshape(-1,))) + segments[0:ny-1,:]=np.vstack((np.arange(2,ny+1),np.arange(1,ny),(2*np.arange(1,ny)-1))).T #right edge: - segments[ny-1:2*(ny-1),:]=np.hstack((np.arange(ny*(nx-1)+1,nx*ny).reshape(-1,),np.arange(ny*(nx-1)+2,nx*ny+1).reshape(-1,),2*np.arange((ny-1)*(nx-2)+1,(nx-1)*(ny-1)+1).reshape(-1,))) + segments[ny-1:2*(ny-1),:]=np.vstack((np.arange(ny*(nx-1)+1,nx*ny),np.arange(ny*(nx-1)+2,nx*ny+1),2*np.arange((ny-1)*(nx-2)+1,(nx-1)*(ny-1)+1))).T #front edge: - segments[2*(ny-1):2*(ny-1)+(nx-1),:]=np.hstack((np.arange(2*ny,ny*nx+1,ny).reshape(-1,),np.arange(ny,ny*(nx-1)+1,ny).reshape(-1,),np.arange(2*(ny-1),2*(nx-1)*(ny-1)+1,2*(ny-1)).reshape(-1,))) + segments[2*(ny-1):2*(ny-1)+(nx-1),:]=np.vstack((np.arange(2*ny,ny*nx+1,ny),np.arange(ny,ny*(nx-1)+1,ny),np.arange(2*(ny-1),2*(nx-1)*(ny-1)+1,2*(ny-1)))).T #back edge - segments[2*(ny-1)+(nx-1):2*(nx-1)+2*(ny-1),:]=np.hstack((np.arange(1,(nx-2)*ny+2,ny).reshape(-1,),np.arange(ny+1,ny*(nx-1)+2,ny).reshape(-1,),np.arange(1,2*(nx-2)*(ny-1)+2,2*(ny-1)).reshape(-1,))) + segments[2*(ny-1)+(nx-1):2*(nx-1)+2*(ny-1),:]=np.vstack((np.arange(1,(nx-2)*ny+2,ny),np.arange(ny+1,ny*(nx-1)+2,ny),np.arange(1,2*(nx-2)*(ny-1)+2,2*(ny-1)))).T #plug coordinates and nodes Index: /issm/trunk/src/m/miscellaneous/diagnostics.m =================================================================== --- /issm/trunk/src/m/miscellaneous/diagnostics.m (revision 21729) +++ /issm/trunk/src/m/miscellaneous/diagnostics.m (revision 21729) @@ -0,0 +1,71 @@ +function diagnostics(md,varargin) +%DIAGNOSTICS - output diagnostics for use in qgis +% +% +% Usage: +% diagnostics(md,options) +% +% where options include: +% 'path': where are the diagnostics file output +% 'mesh': 0 or 1 (output mesh?, default 0) +% 'gl': 0 or 1 (output grounding line position?, default 0) +% 'vel': defaults to md.initialization.vel (can suplly another field if need be) +% Suboptions include: +% 'velposting': resolution at which the tiff file will be printed. +% 'hotspots' (0 or 1, default 0). spots where md.results.TransientSolution(i).Vel>threshold +% Suboptions include: +% 'threshold': vel value +% 'hotspotsi': index into results.TransientSolution +% +% +% +% Examples: +% diagnostics(md,'vel',md.initialization.vel,'gl',1,'hotspots',1,'hotspotsi',10,'threshold',500); + + + %process options: + options=pairoptions(varargin{:}); + path=getfieldvalue(options,'path','./'); + + %mesh: + if getfieldvalue(options,'mesh',0), + mesh2shp(md,[path '/mesh']); + end + + %grounding line : + if getfieldvalue(options,'gl',0), + contours=contourlevelzero(md,md.mask.groundedice_levelset,0); + expwrite(contours,[path '/groundingline.exp']); + exp2shp([path '/groundingline.shp'],[path '/groundingline.exp']); + end + + %velocity: + if exist(options,'vel'), + vel=getfieldvalue(options,'vel',md.initialization.vel); + xposting=getfieldvalue(options,'velposting',500); + yposting=getfieldvalue(options,'velposting',500); + + xmin=min(md.mesh.x); ymax=max(md.mesh.y); + ncols=(max(md.mesh.x)-min(md.mesh.x))/xposting+1; + nlines=(max(md.mesh.y)-min(md.mesh.y))/yposting+1; + + [xm,ym,vel]=InterpFromMeshToGrid(md.mesh.elements,md.mesh.x,md.mesh.y,vel,xmin,ymax,xposting,yposting,nlines,ncols,0); + vel=uint16(flipud(vel)); + + imwrite(vel,[path '/veltemp.tif'],'tiff'); + + string=sprintf('!gdal_translate -a_srs EPSG:3031 -a_ullr %g %g %g %g %s/veltemp.tif %s/vel.tif',... + min(md.mesh.x),max(md.mesh.y),max(md.mesh.x),min(md.mesh.y),path,path); + eval(string); + delete([path '/veltemp.tif']); + end + + %hot spots: + if getfieldvalue(options,'hotspots',0), + threshold=getfieldvalue(options,'threshold',5000); + i=getfieldvalue(options,'hotspotsi',length(md.results.TransientSolution)); + pos=find(md.results.TransientSolution(i).Vel>threshold); + contour.x=md.mesh.x(pos); contour.y=md.mesh.y(pos); contour.density=1; + expwrite(contour,[path '/hotspots.exp']); + exp2shp([path '/hotspots.shp'],[path '/hotspots.exp']); + end Index: /issm/trunk/src/m/os/sessionname.m =================================================================== --- /issm/trunk/src/m/os/sessionname.m (revision 21729) +++ /issm/trunk/src/m/os/sessionname.m (revision 21729) @@ -0,0 +1,16 @@ +function name=sessionname() +%SESSIONNAME - Get screen session name +% +% Usage: +% name=sessionname() + + + [status,styname]=system('export | grep STY'); + + sessionname=styname(17:end-2); + if isempty(sessionname), + name='none'; + return; + end + index=findstr(sessionname,'.'); + name=sessionname(index+1:end); Index: /issm/trunk/src/m/plot/applyoptions.js =================================================================== --- /issm/trunk/src/m/plot/applyoptions.js (revision 21728) +++ /issm/trunk/src/m/plot/applyoptions.js (revision 21729) @@ -1,31 +1,31 @@ -function applyoptions(md,data,datatype,options,canvas,gl,node){ //{{{ +function applyoptions(md, data, datatype, options, canvas, gl, node){ //{{{ //APPLYOPTIONS - apply colobar, text, cloud, and expdisp options to current plot // // Usage: - // applyoptions(md,data,options) + // applyoptions(md, data, options) // // See also: PLOTMODEL, PARSE_OPTIONS - //colorbar {{{ + //{{{ colorbar if (options.exist('colorbar')) { if (options.getfieldvalue('colorbar')==1) { - //Handle movie data {{{ + //{{{ Handle movie data if (datatype == 5) { data = data[0]; } //}}} - //Variable options initialization {{{ - var caxis = options.getfieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]); + //{{{ Variable options initialization + var caxis = options.getfieldvalue('caxis',[ArrayMin(data), ArrayMax(data)]); var colorbarinnerlabels = options.getfieldvalue('colorbarinnerlabels','off'); - var ccanvasid,ctitleid,clabelsid,ccanvas,ctitle,clabels,ccontext,cmap,colorbar,cwidth,cheight,cgradient,color,y,x; - //}}} - //Create colorbar labels {{{ + var ccanvasid, ctitleid, clabelsid, ccanvas, ctitle, clabels, ccontext, cmap, colorbar, cwidth, cheight, cgradient, color, y, x; + //}}} + //{{{ Create colorbar labels var labels = []; - var cdivisions = options.getfieldvalue('colorbarnticks',6); + var cdivisions = options.getfieldvalue('colorbarnticks', 6); var caxisdelta = caxis[1] - caxis[0]; - var precision = options.getfieldvalue('colorbarprecision',3); + var precision = options.getfieldvalue('colorbarprecision', 3); if (options.getfieldvalue('log','off')!='off') { for (var i=cdivisions; i >= 0; i--) { - var scale = (Math.log10(caxis[1])-Math.log10(caxis[0]))/Math.log10(options.getfieldvalue('log',10)); - labels[i] = (Math.pow(options.getfieldvalue('log',10),Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log',10))+scale*(cdivisions-i)/cdivisions)).toFixed(precision); + var scale = (Math.log10(caxis[1])-Math.log10(caxis[0]))/Math.log10(options.getfieldvalue('log', 10)); + labels[i] = (Math.pow(options.getfieldvalue('log', 10), Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log', 10))+scale*(cdivisions-i)/cdivisions)).toFixed(precision); } } else { @@ -34,33 +34,33 @@ } } //}}} - //Initialize colorbar canvas {{{ - ccanvasid = options.getfieldvalue('colorbarid',options.getfieldvalue('canvasid').replace('canvas','colorbar-canvas')); + //{{{ Initialize colorbar canvas + ccanvasid = options.getfieldvalue('colorbarid', options.getfieldvalue('canvasid').replace('canvas','colorbar-canvas')); ccanvas = $('#'+ccanvasid)[0]; - cwidth = ccanvas.width*options.getfieldvalue('colorbarwidth',1); - cheight = ccanvas.height*options.getfieldvalue('colorbarheight',1); + cwidth = ccanvas.width*options.getfieldvalue('colorbarwidth', 1); + cheight = ccanvas.height*options.getfieldvalue('colorbarheight', 1); ccontext = ccanvas.getContext('2d'); - ccontext.clearRect(0,0, cwidth, cheight); + ccontext.clearRect(0, 0, cwidth, cheight); ccontext.beginPath(); cmap = options.getfieldvalue('colormap','jet'); colorbar = colorbars[cmap]; - cgradient = ccontext.createLinearGradient(0,0,0,cheight); - //}}} - //Draw colorbar gradient {{{ + cgradient = ccontext.createLinearGradient(0, 0, 0, cheight); + //}}} + //{{{ Draw colorbar gradient for (var i=0; i < colorbar.length; i++) { color = colorbar[colorbar.length-i-1]; - color = [Math.round(color[0]*255),Math.round(color[1]*255),Math.round(color[2]*255)]; - cgradient.addColorStop(i/colorbar.length*(cdivisions/(cdivisions+1.0))+(1.0/(cdivisions+1.0)),'rgba('+color.toString()+',1.0)'); + color = [Math.round(color[0]*255), Math.round(color[1]*255), Math.round(color[2]*255)]; + cgradient.addColorStop(i/colorbar.length*(cdivisions/(cdivisions+1.0))+(1.0/(cdivisions+1.0)),'rgba('+color.toString()+', 1.0)'); } ccontext.fillStyle=cgradient; - ccontext.fillRect(0,0,cwidth,cheight); - //}}} - //Draw colorbar border {{{ + ccontext.fillRect(0, 0, cwidth, cheight); + //}}} + //{{{ Draw colorbar border ccontext.beginPath(); ccontext.lineWidth='1'; ccontext.strokeStyle=options.getfieldvalue('colorbarfontcolor','black'); - ccontext.rect(0,0,cwidth,cheight); + ccontext.rect(0, 0, cwidth, cheight); ccontext.stroke(); //}}} - //Draw colorbar labels {{{ + //{{{ Draw colorbar labels clabelsid = options.getfieldvalue('colorbarid', ccanvasid).replace('canvas','labels'); clabels = $('#'+clabelsid); @@ -80,13 +80,13 @@ clabelstring += '
  • '+labels[i]+'
    • '; ccontext.beginPath(); - ccontext.moveTo(0,y); - ccontext.lineTo(x,y); - ccontext.moveTo(cwidth-x,y); - ccontext.lineTo(cwidth,y); + ccontext.moveTo(0, y); + ccontext.lineTo(x, y); + ccontext.moveTo(cwidth-x, y); + ccontext.lineTo(cwidth, y); ccontext.stroke(); } clabels.append(clabelstring); //}}} - //Draw colorbar title {{{ + //{{{ Draw colorbar title ctitleid = options.getfieldvalue('colorbarid', ccanvasid).replace('canvas','heading'); ctitle = $('#'+ctitleid); @@ -95,6 +95,6 @@ } } //}}} - //texture canvas //{{{ - var tcontext,tcanvas,tcanvasid,tURL,tgradient; + //{{{ texture canvas + var tcontext, tcanvas, tcanvasid, tURL, tgradient; tcanvasid = 'texturecanvas'; var tcanvas = document.getElementById(tcanvasid); @@ -104,5 +104,5 @@ } tcontext = tcanvas.getContext('2d'); - tgradient = tcontext.createLinearGradient(0,0,0,256); + tgradient = tcontext.createLinearGradient(0, 0, 0, 256); var cmap = options.getfieldvalue('colormap','jet'); @@ -110,18 +110,18 @@ for (var i=0; i < colorbar.length; i++) { color = colorbar[colorbar.length-i-1]; - color = [Math.round(color[0]*255),Math.round(color[1]*255),Math.round(color[2]*255)]; - tgradient.addColorStop(i/colorbar.length,'rgba('+color.toString()+',1.0)'); + color = [Math.round(color[0]*255), Math.round(color[1]*255), Math.round(color[2]*255)]; + tgradient.addColorStop(i/colorbar.length,'rgba('+color.toString()+', 1.0)'); } tcontext.fillStyle = tgradient; - tcontext.fillRect(0,0,256,256); + tcontext.fillRect(0, 0, 256, 256); tURL = tcanvas.toDataURL(); - node.texture = initTexture(gl,tURL); + node.texture = initTexture(gl, tURL); node.textureCanvas = tcanvas; - node.caxis = options.getfieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]); + node.caxis = options.getfieldvalue('caxis',[ArrayMin(data), ArrayMax(data)]); //}}} - //expdisp contours {{{ + //{{{ expdisp contours if (options.exist('expdisp')) { - canvas.nodes.expdisp = Node(gl,options); + canvas.nodes.expdisp = Node(gl, options); var node = canvas.nodes.expdisp; @@ -131,7 +131,7 @@ var colors = []; var rgbcolor = []; - var xmin,xmax; - var ymin,ymax; - var zmin,zmax; + var xmin, xmax; + var ymin, ymax; + var zmin, zmax; var scale; @@ -139,5 +139,5 @@ var x = options.getfieldvalue('expdisp').x; var y = options.getfieldvalue('expdisp').y; - var z = Array.apply(null, Array(x.length)).map(Number.prototype.valueOf,0); + var z = Array.apply(null, Array(x.length)).map(Number.prototype.valueOf, 0); if (options.getfieldvalue('expdisp').z) { @@ -147,10 +147,10 @@ //Compute coordinates and data range: //{{{ - var modelxlim = [ArrayMin(x),ArrayMax(x)]; - var modelylim = [ArrayMin(y),ArrayMax(y)]; - var modelzlim = [ArrayMin(z),ArrayMax(z)]; - var xlim = options.getfieldvalue('xlim',modelxlim); - var ylim = options.getfieldvalue('ylim',modelylim); - var zlim = options.getfieldvalue('zlim',modelzlim); + var modelxlim = [ArrayMin(x), ArrayMax(x)]; + var modelylim = [ArrayMin(y), ArrayMax(y)]; + var modelzlim = [ArrayMin(z), ArrayMax(z)]; + var xlim = options.getfieldvalue('xlim', modelxlim); + var ylim = options.getfieldvalue('ylim', modelylim); + var zlim = options.getfieldvalue('zlim', modelzlim); xmin = xlim[0]; xmax = xlim[1]; @@ -165,5 +165,5 @@ node.shaderName = 'colored'; node.shader = gl.shaders[node.shaderName].program; - node.scale = [scale, scale, scale*options.getfieldvalue('heightscale',1)]; + node.scale = [scale, scale, scale*options.getfieldvalue('heightscale', 1)]; node.translation = [(xmin + xmax) / (-2 / scale), (ymin + ymax) / (-2 / scale), (zmin + zmax) / (-2 / scale)]; node.modelMatrix = updateModelMatrix(node); @@ -178,5 +178,5 @@ //retrieve some options - var linewidth=options.getfieldvalue('linewidth',1); + var linewidth=options.getfieldvalue('linewidth', 1); var edgecolor=options.getfieldvalue('edgecolor','black'); //RGBCOLOR? @@ -199,7 +199,7 @@ node.buffers = initBuffers(gl, node.arrays); } //}}} - //cloud of points {{{ + //{{{ cloud of points if (options.exist('cloud')) { - canvas.nodes.cloud = Node(gl,options); + canvas.nodes.cloud = Node(gl, options); var node = canvas.nodes.cloud; @@ -209,7 +209,7 @@ var colors = []; var rgbcolor = []; - var xmin,xmax; - var ymin,ymax; - var zmin,zmax; + var xmin, xmax; + var ymin, ymax; + var zmin, zmax; var scale; @@ -217,5 +217,5 @@ var x = options.getfieldvalue('cloud').x; var y = options.getfieldvalue('cloud').y; - var z = Array.apply(null, Array(x.length)).map(Number.prototype.valueOf,0); + var z = Array.apply(null, Array(x.length)).map(Number.prototype.valueOf, 0); if (options.getfieldvalue('cloud').z) { @@ -225,10 +225,10 @@ //Compute coordinates and data range: //{{{ - var modelxlim = [ArrayMin(x),ArrayMax(x)]; - var modelylim = [ArrayMin(y),ArrayMax(y)]; - var modelzlim = [ArrayMin(z),ArrayMax(z)]; - var xlim = options.getfieldvalue('xlim',modelxlim); - var ylim = options.getfieldvalue('ylim',modelylim); - var zlim = options.getfieldvalue('zlim',modelzlim); + var modelxlim = [ArrayMin(x), ArrayMax(x)]; + var modelylim = [ArrayMin(y), ArrayMax(y)]; + var modelzlim = [ArrayMin(z), ArrayMax(z)]; + var xlim = options.getfieldvalue('xlim', modelxlim); + var ylim = options.getfieldvalue('ylim', modelylim); + var zlim = options.getfieldvalue('zlim', modelzlim); xmin = xlim[0]; xmax = xlim[1]; @@ -243,5 +243,5 @@ node.shaderName = 'colored'; node.shader = gl.shaders[node.shaderName].program; - node.scale = [scale, scale, scale*options.getfieldvalue('heightscale',1)]; + node.scale = [scale, scale, scale*options.getfieldvalue('heightscale', 1)]; node.translation = [(xmin + xmax) / (-2 / scale), (ymin + ymax) / (-2 / scale), (zmin + zmax) / (-2 / scale)]; node.modelMatrix = updateModelMatrix(node); @@ -256,5 +256,5 @@ //retrieve some options - var linewidth=options.getfieldvalue('linewidth',1); + var linewidth=options.getfieldvalue('linewidth', 1); var edgecolor=options.getfieldvalue('edgecolor','black'); //RGBCOLOR? @@ -277,9 +277,8 @@ node.buffers = initBuffers(gl, node.arrays); } //}}} - - //text display //{{{ + //{{{ text display if (options.exist('textlabels')) { - var textcanvas,textcanvasid; - textcanvasid = options.getfieldvalue('textcanvasid',options.getfieldvalue('canvasid')+'-text'); + var textcanvas, textcanvasid; + textcanvasid = options.getfieldvalue('textcanvasid', options.getfieldvalue('canvasid')+'-text'); textcanvas = $('#'+textcanvasid); textcanvas.textlabels = options.getfieldvalue('textlabels',[]); @@ -287,5 +286,5 @@ //setup drawing function for text canvas draw calls textcanvas.draw = function(canvas) { - var textcontext,textlabels,textlabel,textcanvaswidth,textcanvasheight,textcoordinates; + var textcontext, textlabels, textlabel, textcanvaswidth, textcanvasheight, textcoordinates; var textposition = vec3.create(); var mvpMatrix = mat4.create(); @@ -304,5 +303,5 @@ for (text in textlabels) { textlabel = textlabels[text]; - mat4.multiply(mvpMatrix, canvas.cameraMatrix, canvas.nodes.overlay.modelMatrix); + mat4.multiply(mvpMatrix, canvas.camera.vpMatrix, canvas.nodes.overlay.modelMatrix); textposition = vec3.transformMat4(textposition, textlabel.pos, mvpMatrix); if (textposition[2] > 1) { //clip coordinates with z > 1 @@ -310,5 +309,5 @@ } textcoordinates = [(textposition[0]+1.0)/2.0*textcanvaswidth, (-textposition[1]+1.0)/2.0*textcanvasheight]; //NDC to screenspace - textcontext.font = String(options.getfieldvalue('colorbarfontsize',18))+'px "Lato",Helvetica,Arial,sans-serif'; + textcontext.font = String(options.getfieldvalue('colorbarfontsize', 18))+'px "Lato", Helvetica, Arial, sans-serif'; textcontext.fillStyle = options.getfieldvalue('colorbarfontcolor','black'); textcontext.strokeStyle = options.getfieldvalue('colorbarfontcolor','black'); @@ -321,7 +320,78 @@ canvas.textcanvas = textcanvas; } //}}} - //Atmosphere {{{ + //{{{ lat long overlay + if (options.exist('latlongoverlay')) { + var overlaycanvasid = options.getfieldvalue('latlongoverlayid', options.getfieldvalue('canvasid')+'-overlay'); + var overlaycanvas = $('#'+overlaycanvasid)[0]; + var latitudes = { + //"-90": 1, + //"-65": .999, + "-60": 0.994046875, + //"-55": 0.983187500000002, + //"-50": 0.97173550854167, + "-45": 0.955729166666666, + //"-40": 0.94218750000000218, + //"-35": 0.94218750000000218, + "-30": 0.9226562500000024, + //"-25": 0.87934895833333526, + //"-20": 0.856572916666669, + //"-15": 0.830729166666665, + //"-10": 0.803552708333336, + //"-5": 0.77395833333333541, + "0": 0.74218749999999811, + //"5": 0.70950364583333347, + //"10": 0.67479166666666823, + //"15": 0.63932291666666663, + //"20": 0.60171875, + //"25": 0.563453125, + "30": 0.523390625000001, + //"35": 0.48401875, + //"40": 0.44296875, + "45": 0.4020001, + //"50": 0.3578125, + //"55": 0.311875, + "60": 0.26953124999999978, + //"65": 0.225390625, + //"70": 0.18125, + //"75": 0.13541666666666671, + //"80": 0.08953125, + //"85": 0.046250000000000013, + //"90": 0.0, + } + var longitudes = [-150, -120, -90, -60, -30, 0, 30, 60, 90, 120, 150, 180]; + overlaycanvas.draw = function(canvas) { + var rect = overlaycanvas.getBoundingClientRect(); + overlaycanvas.width = rect.width; + overlaycanvas.height = rect.height; + var ctx = overlaycanvas.getContext('2d'); + var centerx = overlaycanvas.width / 2; + var centery = overlaycanvas.height / 2; + var radius = (overlaycanvas.height) / 2; + ctx.setLineDash([5, 10]); + for(latitude in latitudes) { + ctx.beginPath(); + ctx.arc(centerx, centery, radius * latitudes[latitude], 0, 2 * Math.PI); + ctx.stroke(); + ctx.font = String(options.getfieldvalue('colorbarfontsize', 18))+'px "Lato", Helvetica, Arial, sans-serif'; + ctx.fillStyle = options.getfieldvalue('colorbarfontcolor','black'); + ctx.strokeStyle = options.getfieldvalue('colorbarfontcolor','black'); + ctx.textAlign = 'center'; + ctx.textBaseline = 'middle'; + ctx.fillText(latitude, centerx, centery + radius * latitudes[latitude]); + ctx.strokeText(latitude, centerx, centery + radius * latitudes[latitude]); + } + ctx.setLineDash([1, 0]); + for (longitude in longitudes) { + ctx.beginPath(); + ctx.moveTo(centerx, centery); + ctx.lineTo(centerx + radius * Math.sin(longitudes[longitude] * DEG2RAD), centery + radius * Math.cos(longitudes[longitude] * DEG2RAD)); + ctx.stroke(); + } + } + canvas.overlaycanvas = overlaycanvas; + } //}}} + //{{{ additional rendering nodes if (options.exist('render')) { - var meshresults = processmesh(md,data,options); + var meshresults = processmesh(md, data, options); var x = meshresults[0]; var y = meshresults[1]; @@ -331,10 +401,10 @@ var isplanet = meshresults[5]; - var modelxlim = [ArrayMin(x),ArrayMax(x)]; - var modelylim = [ArrayMin(y),ArrayMax(y)]; - var modelzlim = [ArrayMin(z),ArrayMax(z)]; - var xlim = options.getfieldvalue('xlim',modelxlim); - var ylim = options.getfieldvalue('ylim',modelylim); - var zlim = options.getfieldvalue('zlim',modelzlim); + var modelxlim = [ArrayMin(x), ArrayMax(x)]; + var modelylim = [ArrayMin(y), ArrayMax(y)]; + var modelzlim = [ArrayMin(z), ArrayMax(z)]; + var xlim = options.getfieldvalue('xlim', modelxlim); + var ylim = options.getfieldvalue('ylim', modelylim); + var zlim = options.getfieldvalue('zlim', modelzlim); xmin = xlim[0]; xmax = xlim[1]; @@ -351,33 +421,74 @@ //atmosphere var node = Node(gl); - canvas.nodes[canvas.nodes.length] = node; node.name = "atmosphere"; node.shaderName = "SkyFromSpace"; node.shader = gl.shaders[node.shaderName]; node.drawOrder = 1; + node.cullFace = gl.FRONT; node.enableCullFace = true; - node.mesh = GL.Mesh.icosahedron({size:6371000*atmosphereScale,subdivisions:6}); - node.useIndexBuffer = false; + node.mesh = GL.Mesh.icosahedron({size: 6371000*atmosphereScale, subdivisions: 6}); node.rotation = [0, 0, 0]; node.translation = translation; node.center = [0, 0, 0]; updateModelMatrix(node); + canvas.nodes[node.name] = node; } if (options.getfieldvalue('render',[]).indexOf('space')!=-1) { //skysphere node = Node(gl); - canvas.nodes[canvas.nodes.length] = node; node.name = "skysphere"; node.shaderName = "Textured"; node.shader = gl.shaders[node.shaderName]; node.drawOrder = 2; + node.cullFace = gl.FRONT; node.enableCullFace = true; - node.mesh = GL.Mesh.sphere({size:6371000*10}); - node.texture = initTexture(gl,canvas.rootPath+'textures/TychoSkymapII_t4_2k.jpg'); - node.useIndexBuffer = false; + node.mesh = GL.Mesh.sphere({size: 6371000*20}); + node.texture = initTexture(gl, canvas.rootPath+'textures/TychoSkymapII_t4_2k.jpg'); node.rotation = [0, 0, 0]; node.translation = translation; node.center = [0, 0, 0]; updateModelMatrix(node); + canvas.nodes[node.name] = node; + } + if (canvas.clouds.enabled) { + //clouds + for (var i = 0; i < canvas.clouds.quantity; i++) { + node = Node(gl); + node.name = "clouds" + i; + node.shaderName = "Clouds"; + node.shader = gl.shaders[node.shaderName]; + node.drawOrder = 2; + node.cullFace = gl.BACK; + node.enableCullFace = true; + node.mesh = GL.Mesh.fromURL(canvas.rootPath+'obj/cloud.obj'); + node.rotation = [0, 0, 0]; + node.scale = [2500, 2500, 2500]; + node.translation = [translation[0], translation[1] - 405000, translation[2]]; + node.center = [0, 0, 0]; + node.animation = {"time": Date.now(),"target": node.translation,"current": node.translation}; + updateModelMatrix(node); + canvas.nodes[node.name] = node; + //canvas.clouds.list + } + //TODO: Steven, please add total cloud nodes, randomly spread over the mesh, giving each one a new name and adding them to the canvas.clouds.list so that we can track them later. + + } + if (options.getfieldvalue('render',[]).indexOf('latlong')!=-1) { + //latlong + node = Node(gl); + node.name = "clouds"; + node.shaderName = "Clouds"; + node.shader = gl.shaders[node.shaderName]; + node.drawOrder = 2; + node.cullFace = gl.BACK; + node.enableCullFace = true; + node.mesh = GL.Mesh.fromURL(canvas.rootPath+'obj/cloud.obj'); + node.rotation = [0, 0, 0]; + node.scale = [2500, 2500, 2500]; + node.translation = [translation[0], translation[1] - 405000, translation[2]]; + node.center = [0, 0, 0]; + node.animation = {"time": Date.now(),"target": node.translation,"current": node.translation}; + updateModelMatrix(node); + canvas.nodes[node.name] = node; } } //}}} Index: /issm/trunk/src/m/plot/applyoptions.m =================================================================== --- /issm/trunk/src/m/plot/applyoptions.m (revision 21728) +++ /issm/trunk/src/m/plot/applyoptions.m (revision 21729) @@ -348,9 +348,4 @@ hold on set(gca,'pos',Axis); -end - -%axes position -if exist(options,'axesPosition') - set(gca,'Position',getfieldvalue(options,'axesPosition')); end Index: /issm/trunk/src/m/plot/applyoptions.py =================================================================== --- /issm/trunk/src/m/plot/applyoptions.py (revision 21728) +++ /issm/trunk/src/m/plot/applyoptions.py (revision 21729) @@ -10,10 +10,9 @@ from mpl_toolkits.mplot3d import Axes3D import matplotlib as mpl - import pylab as p import matplotlib.pyplot as plt except ImportError: print "could not import pylab, matplotlib has not been installed, no plotting capabilities enabled" -def applyoptions(md,data,options,fig,ax): +def applyoptions(md,data,options,fig,axgrid,gridindex): ''' APPLYOPTIONS - apply options to current plot @@ -30,5 +29,5 @@ # get handle to current figure and axes instance #fig = p.gcf() - #ax=p.gca() + ax= axgrid[gridindex] # {{{ font @@ -234,4 +233,12 @@ cb.set_alpha(1) cb.draw_all() + if options.exist('colorbarfontsize'): + colorbarfontsize=options.getfieldvalue('colorbarfontsize') + cb.ax.tick_params(labelsize=colorbarfontsize) + # cb.set_ticks([0,-10]) + # cb.set_ticklabels([-10,0,10]) + if options.exist('colorbarticks'): + colorbarticks=options.getfieldvalue('colorbarticks') + cb.set_ticks(colorbarticks) plt.sca(ax) # return to original axes control # }}} Index: /issm/trunk/src/m/plot/googlemaps.m =================================================================== --- /issm/trunk/src/m/plot/googlemaps.m (revision 21728) +++ /issm/trunk/src/m/plot/googlemaps.m (revision 21729) @@ -133,4 +133,5 @@ %If not gdal, exit if status~=0, + disp(result); disp('googlemaps info: gdal not found or not working properly, the Google image will not be transformed'); [gX gY]=meshgrid(ulx:ulx+size(final,2)-1,uly:-1:uly-size(final,1)+1); @@ -155,4 +156,5 @@ %If previous command failed, exit if ~isempty(strfind(result,'ERROR')), + disp(result); disp(' ');disp('googlemaps info: gdal not working properly (missing proj.4 library?), Google image will not be transformed'); disp(result); Index: /issm/trunk/src/m/plot/plot_BC.m =================================================================== --- /issm/trunk/src/m/plot/plot_BC.m (revision 21728) +++ /issm/trunk/src/m/plot/plot_BC.m (revision 21729) @@ -7,4 +7,8 @@ [x y z elements is2d isplanet]=processmesh(md,[],options); +spcvx=processdata(md,md.stressbalance.spcvx,options); +spcvy=processdata(md,md.stressbalance.spcvy,options); +spcvz=processdata(md,md.stressbalance.spcvz,options); +nbv = numel(x); %plot dirichlets @@ -12,17 +16,17 @@ if strcmpi(dirichleton,'on'), h1=plot3(... - x(find(~isnan(md.stressbalance.spcvx(1:md.mesh.numberofvertices,1)))),... - y(find(~isnan(md.stressbalance.spcvx(1:md.mesh.numberofvertices,1)))),... - z(find(~isnan(md.stressbalance.spcvx(1:md.mesh.numberofvertices,1)))),... + x(find(~isnan(spcvx(1:nbv,1)))),... + y(find(~isnan(spcvx(1:nbv,1)))),... + z(find(~isnan(spcvx(1:nbv,1)))),... 'ro','MarkerSize',14,'MarkerFaceColor','r'); h2=plot3(... - x(find(~isnan(md.stressbalance.spcvy(1:md.mesh.numberofvertices,1)))),... - y(find(~isnan(md.stressbalance.spcvy(1:md.mesh.numberofvertices,1)))),... - z(find(~isnan(md.stressbalance.spcvy(1:md.mesh.numberofvertices,1)))),... + x(find(~isnan(spcvy(1:nbv,1)))),... + y(find(~isnan(spcvy(1:nbv,1)))),... + z(find(~isnan(spcvy(1:nbv,1)))),... 'bo','MarkerSize',10,'MarkerFaceColor','b'); h3=plot3(... - x(find(~isnan(md.stressbalance.spcvz(1:md.mesh.numberofvertices,1)))),... - y(find(~isnan(md.stressbalance.spcvz(1:md.mesh.numberofvertices,1)))),... - z(find(~isnan(md.stressbalance.spcvz(1:md.mesh.numberofvertices,1)))),... + x(find(~isnan(spcvz(1:nbv,1)))),... + y(find(~isnan(spcvz(1:nbv,1)))),... + z(find(~isnan(spcvz(1:nbv,1)))),... 'yo','MarkerSize',6 ,'MarkerFaceColor','y'); end Index: /issm/trunk/src/m/plot/plot_BC.py =================================================================== --- /issm/trunk/src/m/plot/plot_BC.py (revision 21728) +++ /issm/trunk/src/m/plot/plot_BC.py (revision 21729) @@ -8,6 +8,7 @@ from applyoptions import applyoptions from plot_icefront import plot_icefront +from mpl_toolkits.mplot3d import Axes3D -def plot_BC(md,options,fig,ax): +def plot_BC(md,options,fig,axgrid,gridindex): ''' PLOT_BC - plot model boundary conditions @@ -18,8 +19,15 @@ See also: PLOTMODEL ''' + x,y,z,elements,is2d,isplanet=processmesh(md,[],options) + ax=axgrid[gridindex] + fig.delaxes(axgrid.cbar_axes[gridindex]) + + if not is2d: + ax=inset_locator.inset_axes(axgrid[gridindex],width='100%',height='100%',loc=3,borderpad=0,axes_class=Axes3D) + #plot neuman plot_icefront(md,options,fig,ax) - x,y,z,elements,is2d,isplanet=processmesh(md,[],options) + XLims=[np.min(x),np.max(x)] YLims=[np.min(y),np.max(y)] @@ -36,11 +44,20 @@ y[np.where(~np.isnan(md.stressbalance.spcvz))], marker='o',c='y',s=80,label='vz Dirichlet',linewidth=0) - + try: + ax.scatter(x[np.where(~np.isnan(md.hydrology.spcepl_head))], + y[np.where(~np.isnan(md.hydrology.spcepl_head))], + marker='v',c='r',s=240,label='EPL Head',linewidth=0) + ax.scatter(x[np.where(~np.isnan(md.hydrology.spcsediment_head))], + y[np.where(~np.isnan(md.hydrology.spcsediment_head))], + marker='^',c='b',s=240,label='IDS head',linewidth=0) + except AttributeError: + print ('Not treating Hydrologydc, skipping these boundaries') ax.set_xlim(XLims) ax.set_ylim(YLims) - ax.legend() + ax.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, + ncol=3, mode="expand", borderaxespad=0.) #apply options options.addfielddefault('title','Boundary conditions') options.addfielddefault('colorbar','off') - applyoptions(md,[],options,fig,ax) + applyoptions(md,[],options,fig,axgrid,gridindex) Index: /issm/trunk/src/m/plot/plot_contour.m =================================================================== --- /issm/trunk/src/m/plot/plot_contour.m (revision 21728) +++ /issm/trunk/src/m/plot/plot_contour.m (revision 21729) @@ -14,5 +14,5 @@ %check is2d -if ~is2d, +if ~is2d & ~isplanet, error('plot_contour error message: contour not supported for 3d meshes, project on a layer'); end @@ -115,4 +115,7 @@ y1=zeros(numelems,1); y2=zeros(numelems,1); + z1=zeros(numelems,1); + z2=zeros(numelems,1); + edge_l=zeros(numelems,2); @@ -129,4 +132,6 @@ y1(j)=y(Seg1(poselem(j),1))+weight1*(y(Seg1(poselem(j),2))-y(Seg1(poselem(j),1))); y2(j)=y(Seg2(poselem(j),1))+weight2*(y(Seg2(poselem(j),2))-y(Seg2(poselem(j),1))); + z1(j)=z(Seg1(poselem(j),1))+weight1*(z(Seg1(poselem(j),2))-z(Seg1(poselem(j),1))); + z2(j)=z(Seg2(poselem(j),1))+weight2*(z(Seg2(poselem(j),2))-z(Seg2(poselem(j),1))); edge_l(j,1)=Seg1_num(poselem(j)); edge_l(j,2)=Seg2_num(poselem(j)); @@ -138,4 +143,7 @@ y1(j)=y(Seg1(poselem(j),1))+weight1*(y(Seg1(poselem(j),2))-y(Seg1(poselem(j),1))); y2(j)=y(Seg3(poselem(j),1))+weight3*(y(Seg3(poselem(j),2))-y(Seg3(poselem(j),1))); + z1(j)=z(Seg1(poselem(j),1))+weight1*(z(Seg1(poselem(j),2))-z(Seg1(poselem(j),1))); + z2(j)=z(Seg3(poselem(j),1))+weight3*(z(Seg3(poselem(j),2))-z(Seg3(poselem(j),1))); + edge_l(j,1)=Seg1_num(poselem(j)); edge_l(j,2)=Seg3_num(poselem(j)); @@ -147,4 +155,6 @@ y1(j)=y(Seg2(poselem(j),1))+weight2*(y(Seg2(poselem(j),2))-y(Seg2(poselem(j),1))); y2(j)=y(Seg3(poselem(j),1))+weight3*(y(Seg3(poselem(j),2))-y(Seg3(poselem(j),1))); + z1(j)=z(Seg2(poselem(j),1))+weight2*(z(Seg2(poselem(j),2))-z(Seg2(poselem(j),1))); + z2(j)=z(Seg3(poselem(j),1))+weight3*(z(Seg3(poselem(j),2))-z(Seg3(poselem(j),1))); edge_l(j,1)=Seg2_num(poselem(j)); edge_l(j,2)=Seg3_num(poselem(j)); @@ -161,5 +171,5 @@ %take the right edge of the second segment and connect it to the next segments if any e1=edge_l(1,1); e2=edge_l(1,2); - xc=[x1(1);x2(1)]; yc=[y1(1);y2(1)]; + xc=[x1(1);x2(1)]; yc=[y1(1);y2(1)]; zc=[z1(1);z2(1)]; %erase the lines corresponding to this edge @@ -167,4 +177,5 @@ x1(1)=[]; x2(1)=[]; y1(1)=[]; y2(1)=[]; + z1(1)=[]; z2(1)=[]; [ro1,co1]=find(edge_l==e1); @@ -173,5 +184,5 @@ if co1==1, - xc=[x2(ro1);xc]; yc=[y2(ro1);yc]; + xc=[x2(ro1);xc]; yc=[y2(ro1);yc]; zc=[z2(ro1);zc]; %next edge: @@ -179,5 +190,5 @@ else - xc=[x1(ro1);xc]; yc=[y1(ro1);yc]; + xc=[x1(ro1);xc]; yc=[y1(ro1);yc]; zc=[z1(ro1);zc]; %next edge: @@ -189,4 +200,5 @@ x1(ro1)=[]; x2(ro1)=[]; y1(ro1)=[]; y2(ro1)=[]; + z1(ro1)=[]; z2(ro1)=[]; %next connection @@ -200,10 +212,10 @@ if co2==1, - xc=[xc;x2(ro2)]; yc=[yc;y2(ro2)]; + xc=[xc;x2(ro2)]; yc=[yc;y2(ro2)]; zc=[zc;z2(ro2)]; %next edge: e2=edge_l(ro2,2); else - xc=[xc;x1(ro2)]; yc=[yc;y1(ro2)]; + xc=[xc;x1(ro2)]; yc=[yc;y1(ro2)]; zc=[zc;z1(ro2)]; %next edge: @@ -215,4 +227,5 @@ x1(ro2)=[]; x2(ro2)=[]; y1(ro2)=[]; y2(ro2)=[]; + z1(ro2)=[]; z2(ro2)=[]; %next connection @@ -221,13 +234,23 @@ %we now have one subcontour ready to be plotted - zc=level*ones(length(xc)+1,1); if getfieldvalue(options,'contouronly',0), - h=[h;patch('Xdata',[xc;NaN],'Ydata',[yc;NaN],'Zdata',zc,'Cdata',zc,'facecolor','none','edgecolor','flat','linewidth',linewidth)]; + if isplanet, + h=[h;patch('Xdata',[xc;NaN],'Ydata',[yc;NaN],'Zdata',[zc;NaN],'facecolor','none','linewidth',linewidth)]; + else + h=[h;patch('Xdata',[xc;NaN],'Ydata',[yc;NaN],'Zdata',zc,'Cdata',zc,'facecolor','none','edgecolor','flat','linewidth',linewidth)]; + end hold on else - dist = 5000; - if (max(xc)-min(xc)+max(yc)-min(yc))-3)) + + #icefront check + icefront=np.where(np.abs(np.sum(md.mask.ice_levelset[elements],1))!=3) onlyice=np.where(np.sum(md.mask.ice_levelset[elements],1)==-3) noice=np.where(np.sum(md.mask.ice_levelset[elements],1)==3) @@ -24,10 +26,9 @@ #highlight elements on neumann - colors=np.asarray([0.5 for element in elements[icefront]]) - - ax.tripcolor(x,y,elements[icefront],facecolors=colors,alpha=0.5,label='elements on ice front')#,facecolor='b' + if len(icefront[0])>0: + colors=np.asarray([0.5 for element in elements[icefront]]) + ax.tripcolor(x,y,elements[icefront],facecolors=colors,alpha=0.5,label='elements on ice front') #apply options options.addfielddefault('title','Neumann boundary conditions') options.addfielddefault('colorbar','off') - applyoptions(md,[],options,fig,ax) Index: /issm/trunk/src/m/plot/plot_manager.js =================================================================== --- /issm/trunk/src/m/plot/plot_manager.js (revision 21728) +++ /issm/trunk/src/m/plot/plot_manager.js (revision 21729) @@ -15,8 +15,7 @@ var gl = canvas.gl; //TODO: each plot_ should add their node to the canvas.node array - //figure out if this is a special plot if (typeof data === 'string'){ - + switch(data){ Index: /issm/trunk/src/m/plot/plot_manager.m =================================================================== --- /issm/trunk/src/m/plot/plot_manager.m (revision 21728) +++ /issm/trunk/src/m/plot/plot_manager.m (revision 21729) @@ -21,5 +21,5 @@ plot_boundaries(md,options,subplotwidth,i); return; - case 'BC', + case {'BC','bc'}, plot_BC(md,options,subplotwidth,i,data); return; @@ -191,6 +191,7 @@ id=getfieldvalue(options,'asymsubplot',i); subplot(nlines,ncols,id); + subplotmodel(nlines,ncols,id,options); else - subplot(nlines,ncols,i); + subplotmodel(nlines,ncols,i,options); end Index: /issm/trunk/src/m/plot/plot_manager.py =================================================================== --- /issm/trunk/src/m/plot/plot_manager.py (revision 21728) +++ /issm/trunk/src/m/plot/plot_manager.py (revision 21729) @@ -8,4 +8,6 @@ from plot_mesh import plot_mesh from plot_BC import plot_BC +from plot_elementnumbering import plot_elementnumbering +from plot_vertexnumbering import plot_vertexnumbering from processmesh import processmesh from processdata import processdata @@ -23,5 +25,5 @@ from plot_overlay import plot_overlay -def plot_manager(md,options,fig,ax): +def plot_manager(md,options,fig,axgrid,gridindex): ''' PLOT_MANAGER - distribute the plots called by plotmodel @@ -45,4 +47,5 @@ options.addfielddefault('ticklabels','on') + ax=axgrid[gridindex] # {{{ basemap plot TOFIX #if options.exist('basemap'): @@ -56,16 +59,23 @@ options.addfielddefault('ylim',[min(md.mesh.y),max(md.mesh.y)]) # }}} - # {{{ dealing with special plot (mesh for now) + # {{{ dealing with special plot if isinstance(data,(str,unicode)): if data=='mesh': - plot_mesh(md,options,fig,ax) + plot_mesh(md,options,fig,axgrid,gridindex) + #fig.delaxes(fig.axes[1]) # hack to remove colorbar after the fact return elif data=='BC': - plot_BC(md,options,fig,ax) + plot_BC(md,options,fig,axgrid,gridindex) + return + elif data=='elementnumbering': + plot_elementnumbering(md,options,fig,axgrid,gridindex) + return + elif data=='vertexnumbering': + plot_vertexnumbering(md,options,fig,axgrid,gridindex) return elif data=='none': print 'no data provided to plot (TODO: write plot_none.py)' - applyoptions(md,[],options,fig,ax) + applyoptions(md,[],options,fig,axgrid,gridindex) return else: @@ -83,7 +93,7 @@ data2,datatype=processdata(md,data,options) #plot unit - plot_unit(x,y,z,elements,data2,is2d,isplanet,datatype,options,ax) + plot_unit(x,y,z,elements,data2,is2d,isplanet,datatype,options,fig,axgrid,gridindex) #apply all options - applyoptions(md,data2,options,fig,ax) + applyoptions(md,data2,options,fig,axgrid,gridindex) #ground overlay on kml plot_unit Index: /issm/trunk/src/m/plot/plot_mesh.js =================================================================== --- /issm/trunk/src/m/plot/plot_mesh.js (revision 21728) +++ /issm/trunk/src/m/plot/plot_mesh.js (revision 21729) @@ -1,22 +1,22 @@ -function plot_mesh(md,options,canvas) { //{{{ +function plot_mesh(md, options, canvas) { //{{{ //PLOT_MESH - Function for plotting wireframe mesh. // // Usage: - // plot_mesh(md,options,canvas); + // plot_mesh(md, options, canvas); // // See also: PLOTMODEL, PLOT_MANAGER - //declare variables: {{{ + //{{{ declare variables: var vertices = []; var indices = []; var colors = []; var nanindices = {}; - var xmin,xmax; - var ymin,ymax; - var zmin,zmax; - var scale,matrixscale,vertexscale; + var xmin, xmax; + var ymin, ymax; + var zmin, zmax; + var scale, matrixscale, vertexscale; //Process data and model - var meshresults = processmesh(md,[],options); + var meshresults = processmesh(md,[], options); var x = meshresults[0]; var y = meshresults[1]; @@ -28,9 +28,9 @@ //Compue scaling through matrices for 2d meshes and vertices for 3d meshes if (!md.geometry.surface) { - md.geometry.surface=NewArrayFill(md.mesh.x.length,0); + md.geometry.surface=NewArrayFill(md.mesh.x.length, 0); } if (md.mesh.classname() == 'mesh3dsurface') { matrixscale = 1; - vertexscale = options.getfieldvalue('heightscale',1); + vertexscale = options.getfieldvalue('heightscale', 1); } else { @@ -38,5 +38,5 @@ z=md.geometry.surface; } - matrixscale = options.getfieldvalue('heightscale',1); + matrixscale = options.getfieldvalue('heightscale', 1); vertexscale = 0; } @@ -44,10 +44,10 @@ //Compute coordinates and data range: - var modelxlim = [ArrayMin(x),ArrayMax(x)]; - var modelylim = [ArrayMin(y),ArrayMax(y)]; - var modelzlim = [ArrayMin(z),ArrayMax(z)]; - var xlim = options.getfieldvalue('xlim',modelxlim); - var ylim = options.getfieldvalue('ylim',modelylim); - var zlim = options.getfieldvalue('zlim',modelzlim); + var modelxlim = [ArrayMin(x), ArrayMax(x)]; + var modelylim = [ArrayMin(y), ArrayMax(y)]; + var modelzlim = [ArrayMin(z), ArrayMax(z)]; + var xlim = options.getfieldvalue('xlim', modelxlim); + var ylim = options.getfieldvalue('ylim', modelylim); + var zlim = options.getfieldvalue('zlim', modelzlim); xmin = xlim[0]; xmax = xlim[1]; @@ -65,5 +65,5 @@ node.shaderName = "Colored"; node.shader = gl.shaders[node.shaderName]; - node.lineWidth = options.getfieldvalue('linewidth',1); + node.lineWidth = options.getfieldvalue('linewidth', 1); node.scale = [1, 1, matrixscale]; node.rotation = [-90, 0, 0]; @@ -73,6 +73,6 @@ node.drawOrder = 0; node.maskEnabled = options.getfieldvalue('innermask','off') == 'on'; - node.maskHeight = options.getfieldvalue('innermaskheight',150.0)*options.getfieldvalue('heightscale',1); - node.maskColor = options.getfieldvalue('innermaskcolor',[0.0,0.0,1.0,1.0]); + node.maskHeight = options.getfieldvalue('innermaskheight', 150.0)*options.getfieldvalue('heightscale', 1); + node.maskColor = options.getfieldvalue('innermaskcolor',[0.0, 0.0, 1.0, 1.0]); updateModelMatrix(node); @@ -80,7 +80,7 @@ var edgecolor = new RGBColor(options.getfieldvalue('edgecolor','black')); if (edgecolor.ok) edgecolor = [edgecolor.r/255.0, edgecolor.g/255.0, edgecolor.b/255.0, 1.0]; - else throw Error(sprintf("s%s%s\n","initWebGL error message: cound not find out edgecolor color for curent canvas ",canvas)); + else throw Error(sprintf("s%s%s\n","initWebGL error message: cound not find out edgecolor color for curent canvas ", canvas)); - //node plot {{{ + //{{{ node plot if (elements[0].length==6){ //prisms } @@ -136,4 +136,4 @@ } //}}} - node.mesh = GL.Mesh.load({vertices:vertices, colors:colors, triangles:indices}, null, null, gl); + node.mesh = GL.Mesh.load({vertices: vertices, colors: colors, triangles: indices}, null, null, gl); } //}}} Index: /issm/trunk/src/m/plot/plot_mesh.py =================================================================== --- /issm/trunk/src/m/plot/plot_mesh.py (revision 21728) +++ /issm/trunk/src/m/plot/plot_mesh.py (revision 21729) @@ -4,8 +4,11 @@ print "could not import pylab, matplotlib has not been installed, no plotting capabilities enabled" +import numpy as np from processmesh import processmesh from applyoptions import applyoptions - -def plot_mesh(md,options,fig,ax): +from mpl_toolkits.mplot3d.art3d import Line3DCollection +from mpl_toolkits.axes_grid1 import inset_locator +from mpl_toolkits.mplot3d import Axes3D +def plot_mesh(md,options,fig,axgrid,gridindex): ''' PLOT_MESH - plot model mesh @@ -16,15 +19,41 @@ See also: PLOTMODEL ''' + x,y,z,elements,is2d,isplanet=processmesh(md,'mesh',options) - x,y,z,elements,is2d,isplanet=processmesh(md,[],options) - + ax=axgrid[gridindex] + fig.delaxes(axgrid.cbar_axes[gridindex]) + if is2d: ax.triplot(x,y,elements) else: - print 'WARNING: only 2D mesh plot is currently implemented' - + ax=inset_locator.inset_axes(axgrid[gridindex],width='100%',height='100%',loc=3,borderpad=0,axes_class=Axes3D) + + AB=elements[:,0:2] + BC=elements[:,1:3] + CA=np.vstack((elements[:,2],elements[:,0])).T + DE=elements[:,3:5] + EF=elements[:,4:] + FD=np.vstack((elements[:,5],elements[:,3])).T + AD=np.vstack((elements[:,0],elements[:,3])).T + BE=np.vstack((elements[:,1],elements[:,4])).T + CF=np.vstack((elements[:,2],elements[:,5])).T + + tmpa=np.vstack((AB,BC,CA,DE,EF,FD,AD,BE,CF)) + #deleting segments that appear multiple times + tmpb = np.ascontiguousarray(tmpa).view(np.dtype((np.void, tmpa.dtype.itemsize * tmpa.shape[1]))) + _, idx = np.unique(tmpb, return_index=True) + triel= tmpa[idx] + + for triangle in triel: + tri=zip(x[triangle],y[triangle],z[triangle]) + pl3=Line3DCollection([tri],edgecolor='r') + ax.add_collection3d(pl3) + + ax.set_xlim([min(x),max(x)]) + ax.set_ylim([min(y),max(y)]) + ax.set_zlim([min(z),max(z)]) #apply options options.addfielddefault('title','Mesh') options.addfielddefault('colorbar','off') options.addfielddefault('ticklabels','on') - applyoptions(md,[],options,fig,ax) + applyoptions(md,[],options,fig,axgrid,gridindex) Index: /issm/trunk/src/m/plot/plot_overlay.js =================================================================== --- /issm/trunk/src/m/plot/plot_overlay.js (revision 21728) +++ /issm/trunk/src/m/plot/plot_overlay.js (revision 21729) @@ -1,22 +1,22 @@ -function plot_overlay(md,data,options,canvas){ //{{{ +function plot_overlay(md, data, options, canvas){ //{{{ //PLOT_OVERLAY - Function for plotting a georeferenced image. // // Usage: - // plot_overlay(md,data,options,canvas); + // plot_overlay(md, data, options, canvas); // // See also: PLOTMODEL, PLOT_MANAGER - //declare variables: {{{ + //{{{ declare variables: var vertices = []; var indices = []; var texcoords = []; var nanindices = {}; - var xmin,xmax; - var ymin,ymax; - var zmin,zmax; - var matrixscale,vertexscale; + var xmin, xmax; + var ymin, ymax; + var zmin, zmax; + var matrixscale, vertexscale; //Process data and model - var meshresults = processmesh(md,data,options); + var meshresults = processmesh(md, data, options); var x = meshresults[0]; var y = meshresults[1]; @@ -28,9 +28,9 @@ //Compue scaling through matrices for 2d meshes and vertices for 3d meshes if (!md.geometry.surface) { - md.geometry.surface=NewArrayFill(md.mesh.x.length,0); + md.geometry.surface=NewArrayFill(md.mesh.x.length, 0); } if (md.mesh.classname() == 'mesh3dsurface') { matrixscale = 1; - vertexscale = options.getfieldvalue('heightscale',1); + vertexscale = options.getfieldvalue('heightscale', 1); } else { @@ -38,5 +38,5 @@ z=md.geometry.surface; } - matrixscale = options.getfieldvalue('heightscale',1); + matrixscale = options.getfieldvalue('heightscale', 1); vertexscale = 0; } @@ -44,10 +44,10 @@ //Compute coordinates and data range: - var modelxlim = [ArrayMin(x),ArrayMax(x)]; - var modelylim = [ArrayMin(y),ArrayMax(y)]; - var modelzlim = [ArrayMin(z),ArrayMax(z)]; - var xlim = options.getfieldvalue('xlim',modelxlim); - var ylim = options.getfieldvalue('ylim',modelylim); - var zlim = options.getfieldvalue('zlim',modelzlim); + var modelxlim = [ArrayMin(x), ArrayMax(x)]; + var modelylim = [ArrayMin(y), ArrayMax(y)]; + var modelzlim = [ArrayMin(z), ArrayMax(z)]; + var xlim = options.getfieldvalue('xlim', modelxlim); + var ylim = options.getfieldvalue('ylim', modelylim); + var zlim = options.getfieldvalue('zlim', modelzlim); xmin = xlim[0]; xmax = xlim[1]; @@ -68,10 +68,10 @@ node.translation = [0, 0, 0]; node.center = [(xmin + xmax) / 2, (ymin + ymax) / 2, (zmin + zmax) / 2]; - node.texture = initTexture(gl,options.getfieldvalue('overlay_image')); - node.alpha = options.getfieldvalue('outeralpha',1.0); + node.texture = initTexture(gl, options.getfieldvalue('overlay_image')); + node.alpha = options.getfieldvalue('outeralpha', 1.0); node.drawOrder = 1; node.maskEnabled = options.getfieldvalue('outermask','off') == 'on'; - node.maskHeight = options.getfieldvalue('outermaskheight',150.0); - node.maskColor = options.getfieldvalue('outermaskcolor',[0.0,0.0,1.0,1.0]); + node.maskHeight = options.getfieldvalue('outermaskheight', 150.0); + node.maskColor = options.getfieldvalue('outermaskcolor',[0.0, 0.0, 1.0, 1.0]); updateModelMatrix(node); @@ -88,7 +88,7 @@ //Reclaculate bounds based on otuer radaroverlay - modelxlim = [ArrayMin(x),ArrayMax(x)]; - modelylim = [ArrayMin(y),ArrayMax(y)]; - modelzlim = [ArrayMin(z),ArrayMax(z)]; + modelxlim = [ArrayMin(x), ArrayMax(x)]; + modelylim = [ArrayMin(y), ArrayMax(y)]; + modelzlim = [ArrayMin(z), ArrayMax(z)]; xmin = xlim[0]; xmax = xlim[1]; @@ -159,4 +159,4 @@ indices[indices.length] = element[2]; } - node.mesh = GL.Mesh.load({vertices:vertices, coords:texcoords, triangles:indices}, null, null, gl); + node.mesh = GL.Mesh.load({vertices: vertices, coords: texcoords, triangles: indices}, null, null, gl); } //}}} Index: /issm/trunk/src/m/plot/plot_quiver.js =================================================================== --- /issm/trunk/src/m/plot/plot_quiver.js (revision 21728) +++ /issm/trunk/src/m/plot/plot_quiver.js (revision 21729) @@ -1,21 +1,22 @@ -function plot_quiver(md,options,canvas) { //{{{ +function plot_quiver(md, options, canvas, updateVel) { //{{{ //PLOT_QUIVER - quiver plot with colors // // Usage: - // plot_quiver(md,options,canvas) + // plot_quiver(md, options, canvas) // // See also: PLOTMODEL, PLOT_MANAGER - //declare variables: {{{ + //{{{ declare variables: var vertices = []; var indices = []; var colors = []; - var xmin,xmax; - var ymin,ymax; - var zmin,zmax; - var scale,matrixscale,vertexscale; + var xmin, xmax; + var ymin, ymax; + var zmin, zmax; + var scale, matrixscale, vertexscale; //Process data and model - var meshresults = processmesh(md,[],options); + var meshresults = processmesh(md,[], options); + var x = meshresults[0]; var y = meshresults[1]; @@ -24,15 +25,15 @@ var is2d = meshresults[4]; var isplanet = meshresults[5]; - var v = md.initialization.vel; - var vx = md.initialization.vx; - var vy = md.initialization.vy; + var v = updateVel != undefined ? updateVel.vel : md.initialization.vel; + var vx = updateVel != undefined ? updateVel.vx : md.initialization.vx; + var vy = updateVel != undefined ? updateVel.vy : md.initialization.vy; //Compue scaling through matrices for 2d meshes and vertices for 3d meshes if (!md.geometry.surface) { - md.geometry.surface=NewArrayFill(md.mesh.x.length,0); + md.geometry.surface=NewArrayFill(md.mesh.x.length, 0); } if (md.mesh.classname() == 'mesh3dsurface') { matrixscale = 1; - vertexscale = options.getfieldvalue('heightscale',1); + vertexscale = options.getfieldvalue('heightscale', 1); } else { @@ -40,5 +41,5 @@ z=md.geometry.surface; } - matrixscale = options.getfieldvalue('heightscale',1); + matrixscale = options.getfieldvalue('heightscale', 1); vertexscale = 0; } @@ -46,10 +47,10 @@ //Compute coordinates and data range: - var modelxlim = [ArrayMin(x),ArrayMax(x)]; - var modelylim = [ArrayMin(y),ArrayMax(y)]; - var modelzlim = [ArrayMin(z),ArrayMax(z)]; - var xlim = options.getfieldvalue('xlim',modelxlim); - var ylim = options.getfieldvalue('ylim',modelylim); - var zlim = options.getfieldvalue('zlim',modelzlim); + var modelxlim = [ArrayMin(x), ArrayMax(x)]; + var modelylim = [ArrayMin(y), ArrayMax(y)]; + var modelzlim = [ArrayMin(z), ArrayMax(z)]; + var xlim = options.getfieldvalue('xlim', modelxlim); + var ylim = options.getfieldvalue('ylim', modelylim); + var zlim = options.getfieldvalue('zlim', modelzlim); xmin = xlim[0]; xmax = xlim[1]; @@ -62,9 +63,9 @@ var gl = canvas.gl; var node = Node(gl); - canvas.nodes[canvas.nodes.length] = node; + canvas.nodes["velocity"] = node; node.name = "quiver"; node.shaderName = "Colored"; node.shader = gl.shaders[node.shaderName]; - node.lineWidth = options.getfieldvalue('linewidth',1); + node.lineWidth = options.getfieldvalue('linewidth', 1); node.scale = [1, 1, matrixscale]; node.rotation = [-90, 0, 0]; @@ -75,6 +76,6 @@ node.drawOrder = 0; node.maskEnabled = options.getfieldvalue('innermask','off') == 'on'; - node.maskHeight = options.getfieldvalue('innermaskheight',150.0)*options.getfieldvalue('heightscale',1); - node.maskColor = options.getfieldvalue('innermaskcolor',[0.0,0.0,1.0,1.0]); + node.maskHeight = options.getfieldvalue('innermaskheight', 150.0)*options.getfieldvalue('heightscale', 1); + node.maskColor = options.getfieldvalue('innermaskcolor',[0.0, 0.0, 1.0, 1.0]); updateModelMatrix(node); @@ -82,7 +83,7 @@ var edgecolor=new RGBColor(options.getfieldvalue('edgecolor','black')); if (edgecolor.ok) edgecolor = [edgecolor.r/255.0, edgecolor.g/255.0, edgecolor.b/255.0, 1.0]; - else throw Error(sprintf("s%s%s\n","initWebGL error message: cound not find out edgecolor color for curent canvas ",canvas)); + else throw Error(sprintf("s%s%s\n","initWebGL error message: cound not find out edgecolor color for curent canvas ", canvas)); - //node plot {{{ + //{{{ node plot if (elements[0].length==6){ //prisms } @@ -98,5 +99,5 @@ var magnitude; var color = edgecolor; - var scaling = options.getfieldvalue('scaling',1); + var scaling = options.getfieldvalue('scaling', 1); var scale; for(var i = 0; i < x.length; i++){ @@ -134,4 +135,4 @@ } //}}} - node.mesh = GL.Mesh.load({vertices:vertices, colors:colors}, null, null, gl); + node.mesh = GL.Mesh.load({vertices: vertices, colors: colors}, null, null, gl); } //}}} Index: /issm/trunk/src/m/plot/plot_unit.js =================================================================== --- /issm/trunk/src/m/plot/plot_unit.js (revision 21728) +++ /issm/trunk/src/m/plot/plot_unit.js (revision 21729) @@ -1,13 +1,13 @@ -function plot_unit(md,data,datatype,options,canvas) { //{{{ +function plot_unit(md, data, datatype, options, canvas) { //{{{ //PLOT_UNIT - unit plot, display data // // Usage: - // plot_unit(md,data,options,canvas); + // plot_unit(md, data, options, canvas); // // See also: PLOTMODEL, PLOT_MANAGER - //declare variables: {{{ + //{{{ declare variables: //Process data and model - var meshresults = processmesh(md,data,options); + var meshresults = processmesh(md, data, options); var x = meshresults[0]; var y = meshresults[1]; @@ -21,17 +21,16 @@ var indices = new Uint16Array(elements.length * 3); var nanindices = {}; - var xmin,xmax; - var ymin,ymax; - var zmin,zmax; - var datamin,datamax,datadelta; - var matrixscale,vertexscale; - + var xmin, xmax; + var ymin, ymax; + var zmin, zmax; + var datamin, datamax, datadelta; + var matrixscale, vertexscale; //Compue scaling through matrices for 2d meshes and vertices for 3d meshes if (!md.geometry.surface) { - md.geometry.surface=NewArrayFill(md.mesh.x.length,0); + md.geometry.surface=NewArrayFill(md.mesh.x.length, 0); } if (md.mesh.classname() == 'mesh3dsurface') { matrixscale = 1; - vertexscale = options.getfieldvalue('heightscale',1); + vertexscale = options.getfieldvalue('heightscale', 1); } else { @@ -39,5 +38,5 @@ z=md.geometry.surface; } - matrixscale = options.getfieldvalue('heightscale',1); + matrixscale = options.getfieldvalue('heightscale', 1); vertexscale = 0; } @@ -45,10 +44,10 @@ //Compute coordinates and data range: - var modelxlim = [ArrayMin(x),ArrayMax(x)]; - var modelylim = [ArrayMin(y),ArrayMax(y)]; - var modelzlim = [ArrayMin(z),ArrayMax(z)]; - var xlim = options.getfieldvalue('xlim',modelxlim); - var ylim = options.getfieldvalue('ylim',modelylim); - var zlim = options.getfieldvalue('zlim',modelzlim); + var modelxlim = [ArrayMin(x), ArrayMax(x)]; + var modelylim = [ArrayMin(y), ArrayMax(y)]; + var modelzlim = [ArrayMin(z), ArrayMax(z)]; + var xlim = options.getfieldvalue('xlim', modelxlim); + var ylim = options.getfieldvalue('ylim', modelylim); + var zlim = options.getfieldvalue('zlim', modelzlim); xmin = xlim[0]; xmax = xlim[1]; @@ -64,4 +63,5 @@ canvas.nodes[canvas.nodes.length] = node; canvas.unitNode = node; + canvas.unitData = data; node.name = "unit"; node.shaderName = "Textured"; @@ -71,16 +71,16 @@ node.translation = [0, 0, 0]; node.center = [(xmin + xmax) / 2, (ymin + ymax) / 2, (zmin + zmax) / 2]; - node.alpha = options.getfieldvalue('alpha',1.0); + node.alpha = options.getfieldvalue('alpha', 1.0); node.drawOrder = 1; node.maskEnabled = options.getfieldvalue('innermask','off') == 'on'; - node.maskHeight = options.getfieldvalue('innermaskheight',150.0); - node.maskColor = options.getfieldvalue('innermaskcolor',[0.0,0.0,1.0,1.0]); + node.maskHeight = options.getfieldvalue('innermaskheight', 150.0); + node.maskColor = options.getfieldvalue('innermaskcolor',[0.0, 0.0, 1.0, 1.0]); node.enabled = options.getfieldvalue('nodata','off') == 'off'; updateModelMatrix(node); switch(datatype){ - //element plot {{{ + //{{{ element plot case 1: - pos=ArrayFindNot(data,NaN); //needed for element on water + pos=ArrayFindNot(data, NaN); //needed for element on water if (elements[0].length==6){ //prisms } @@ -91,5 +91,5 @@ break; //}}} - //node plot {{{ + //{{{ node plot case 2: if (elements[0].length==6){ //prisms @@ -98,6 +98,6 @@ } else{ //triangular elements - caxis = options.getfieldvalue('caxis',[ArrayMin(data),ArrayMax(data)]); - if (options.getfieldvalue('log','off')!='off') caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log',10)),Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log',10))]; + caxis = options.getfieldvalue('caxis',[ArrayMin(data), ArrayMax(data)]); + if (options.getfieldvalue('log','off')!='off') caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log', 10)), Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log', 10))]; datamin = caxis[0]; datamax = caxis[1]; @@ -145,19 +145,19 @@ } } - node.mesh = GL.Mesh.load({vertices:vertices, coords:texcoords, triangles:indices}, null, null, gl); + node.mesh = GL.Mesh.load({vertices: vertices, coords: texcoords, triangles: indices}, null, null, gl); node.mesh.octree = new GL.Octree(node.mesh); break; //}}} - //quiver plot {{{ + //{{{ quiver plot case 3: if (is2d){ - //plot_quiver(x,y,data(:,1),data(:,2),options); + //plot_quiver(x, y, data(:, 1), data(:, 2), options); } else{ - //plot_quiver3(x,y,z,data(:,1),data(:,2),data(:,3),options); - } - break; - //}}} - //node transient plot {{{ + //plot_quiver3(x, y, z, data(:, 1), data(:, 2), data(:, 3), options); + } + break; + //}}} + //{{{ node transient plot case 5: if (elements[0].length==6){ //prisms @@ -195,6 +195,6 @@ //Prevent evaluation of datasubarray min/max if caxis exists if (options.exist('caxis')) caxis = options.getfieldvalue('caxis'); - else caxis = [ArrayMin(data[0]),ArrayMax(data[0].slice(0,-1))]; - if (options.getfieldvalue('log','off')!='off') caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log',10)),Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log',10))]; + else caxis = [ArrayMin(data[0]), ArrayMax(data[0].slice(0,-1))]; + if (options.getfieldvalue('log','off')!='off') caxis = [Math.log10(caxis[0])/Math.log10(options.getfieldvalue('log', 10)), Math.log10(caxis[1])/Math.log10(options.getfieldvalue('log', 10))]; //Prepare texcoords to hold array of data values texcoords = []; @@ -222,55 +222,59 @@ //Initialize movie loop - node.movieLoop = canvas.movieOptions.loop; - node.movieInterval = 1000 / canvas.movieOptions.fps; + node.movieLoop = canvas.animation.loop; + node.movieInterval = 1000 / canvas.animation.fps; node.movieTimestamps = timestamps; node.movieLength = timestamps.length; node.movieFrame = 0; - if (canvas.movieHandler) { clearInterval(canvas.movieHandler); } - canvas.movieHandler = setInterval(function () { - node.movieFrame = canvas.movieFrame; - if (canvas.moviePlay && canvas.movieIncrement) { - if (canvas.movieReverse) { - if (node.movieFrame == 0) { - if (node.movieLoop) { - node.movieFrame = node.movieLength - 1; - } - else { - toggleMoviePlay(canvas); - } - } - else { - node.movieFrame = node.movieFrame - 1; - } + canvas.dataMarkers.values = []; + var quiverVelFrames = {}; + for(var i=0; i < md.results.length; i++){ + quiverVelFrames[Math.floor(md.results[i].time)] = md.results[i]; + } + + if (canvas.animation.handler !== 0) { + console.log("clearing..."); + clearInterval(canvas.animation.handler) + } + //TODO: Move this into webgl.js + canvas.animation.handler = setInterval(function () { + node.movieFrame = canvas.animation.frame; + if (canvas.animation.play && canvas.animation.increment) { + if (node.movieFrame == node.movieLength - 1) { + if (node.movieLoop) { + node.movieFrame = 0; } else { - if (node.movieFrame == node.movieLength - 1) { - if (node.movieLoop) { - node.movieFrame = 0; - } - else { - toggleMoviePlay(canvas); - } - } - else { - node.movieFrame = node.movieFrame + 1; - } + toggleMoviePlay(canvas); } } - if (canvas.progressBar) { - canvas.progressBar.val(node.movieFrame); - canvas.progressBar.slider('refresh'); + else { + node.movieFrame = node.movieFrame + 1; } - if (canvas.timeLabel) { canvas.timeLabel.html(node.movieTimestamps[node.movieFrame].toFixed(0) + " " + options.getfieldvalue("movietimeunit","yr")); } - - var buffer = node.mesh.getBuffer("coords"); - buffer.data = texcoords[node.movieFrame]; - buffer.upload(canvas.gl.DYNAMIC_DRAW); - node.mesh.octree = new GL.Octree(node.mesh); - - canvas.movieFrame = node.movieFrame; - }, node.movieInterval); + if (canvas.animation.lastFrame != canvas.animation.frame) { + updateMarker(canvas, false); + } + } + + if (canvas.progressBar) { + canvas.progressBar.val(node.movieFrame); + canvas.progressBar.slider('refresh'); + } + if (canvas.timeLabel) { canvas.timeLabel.html(node.movieTimestamps[node.movieFrame].toFixed(0) + " " + options.getfieldvalue("movietimeunit","yr")); } + + var buffer = node.mesh.getBuffer("coords"); + buffer.data = texcoords[node.movieFrame]; + buffer.upload(canvas.gl.DYNAMIC_DRAW); + node.mesh.octree = new GL.Octree(node.mesh); + node.texcoords = texcoords; + if(options.getfieldvalue('quiver') == 'on'){ + plot_quiver(md, options, canvas, {vel: quiverVelFrames[node.movieFrame].Vel, vx: quiverVelFrames[node.movieFrame].Vx, vy: quiverVelFrames[node.movieFrame].Vy}); + } + canvas.animation.lastFrame = canvas.animation.frame; + canvas.animation.frame = node.movieFrame; + }, node.movieInterval); + if (canvas.progressBar) { - canvas.movieFrame = 0; + canvas.animation.frame = 0; canvas.progressBar.val(0); canvas.progressBar.attr('max', node.movieLength-1); @@ -279,10 +283,10 @@ } - node.mesh = GL.Mesh.load({vertices:vertices, coords:texcoords[0], triangles:indices}, null, null, gl); + node.mesh = GL.Mesh.load({vertices: vertices, coords: texcoords[0], triangles: indices}, null, null, gl); node.mesh.octree = new GL.Octree(node.mesh); break; //}}} default: - throw Error(sprintf("%s%i%s\n",'case ',datatype,' not supported')); + throw Error(sprintf("%s%i%s\n",'case ', datatype,' not supported')); } } //}}} Index: /issm/trunk/src/m/plot/plot_unit.py =================================================================== --- /issm/trunk/src/m/plot/plot_unit.py (revision 21728) +++ /issm/trunk/src/m/plot/plot_unit.py (revision 21729) @@ -1,13 +1,16 @@ from cmaptools import truncate_colormap from plot_quiver import plot_quiver +from scipy.interpolate import griddata +import numpy as np try: - import pylab as p import matplotlib as mpl import matplotlib.pyplot as plt - import numpy as np + from mpl_toolkits.axes_grid1 import inset_locator + from mpl_toolkits.mplot3d import Axes3D + from mpl_toolkits.mplot3d.art3d import Poly3DCollection except ImportError: print "could not import pylab, matplotlib has not been installed, no plotting capabilities enabled" -def plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options,ax): +def plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options,fig,axgrid,gridindex): """ PLOT_UNIT - unit plot, display data @@ -18,5 +21,12 @@ See also: PLOTMODEL, PLOT_MANAGER """ - + #if we are plotting 3d replace the current axis + if not is2d: + axgrid[gridindex].axis('off') + ax=inset_locator.inset_axes(axgrid[gridindex],width='100%',height='100%',loc=3,borderpad=0,axes_class=Axes3D) + ax.set_axis_bgcolor((0.7,0.7,0.7)) + else: + ax=axgrid[gridindex] + #edgecolor edgecolor=options.getfieldvalue('edgecolor','None') @@ -29,5 +39,5 @@ # {{{ define wich colormap to use try: - defaultmap=plt.cm.get_cmap('viridis') + defaultmap=plt.cm.get_cmap('viridis',colorlevels) except AttributeError: print("Viridis can't be found (probably too old Matplotlib) reverting to gnuplot colormap") @@ -42,4 +52,13 @@ options.addfield('colormap',cmap) # }}} + # {{{ if plotting only one of several layers reduce dataset, same for surface + if options.getfieldvalue('layer',0)>=1: + plotlayer=options.getfieldvalue('layer',0) + if datatype==1: + slicesize=np.shape(elements)[0] + elif datatype in [2,3]: + slicesize=len(x) + data=data[(plotlayer-1)*slicesize:plotlayer*slicesize] + # }}} # {{{ Get the colormap limits if options.exist('clim'): @@ -75,5 +94,52 @@ tri=ax.tripcolor(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha,edgecolors=edgecolor) else: - raise ValueError('plot_unit error: 3D element plot not supported yet') + + + #first deal with colormap + loccmap = plt.cm.ScalarMappable(cmap=cmap) + loccmap.set_array([min(data),max(data)]) + loccmap.set_clim(vmin=min(data),vmax=max(data)) + + #dealing with prism sides + recface=np.vstack((elements[:,0],elements[:,1],elements[:,4],elements[:,3])).T + eltind=np.arange(0,np.shape(elements)[0]) + recface=np.vstack((recface,np.vstack((elements[:,1],elements[:,2],elements[:,5],elements[:,4])).T)) + eltind=np.hstack((eltind,np.arange(0,np.shape(elements)[0]))) + recface=np.vstack((recface,np.vstack((elements[:,2],elements[:,0],elements[:,3],elements[:,5])).T)) + eltind=np.hstack((eltind,np.arange(0,np.shape(elements)[0]))) + tmp = np.ascontiguousarray(np.sort(recface)).view(np.dtype((np.void, recface.dtype.itemsize * recface.shape[1]))) + _, idx, recur = np.unique(tmp, return_index=True, return_counts=True) + recel= recface[idx[np.where(recur==1)]] + recindex=eltind[idx[np.where(recur==1)]] + for i,rectangle in enumerate(recel): + rec=zip(x[rectangle],y[rectangle],z[rectangle]) + pl3=Poly3DCollection([rec]) + color=loccmap.to_rgba(data[recindex[i]]) + pl3.set_edgecolor(color) + pl3.set_color(color) + ax.add_collection3d(pl3) + + #dealing with prism bases + triface=np.vstack((elements[:,0:3],elements[:,3:6])) + eltind=np.arange(0,np.shape(elements)[0]) + eltind=np.hstack((eltind,np.arange(0,np.shape(elements)[0]))) + tmp = np.ascontiguousarray(triface).view(np.dtype((np.void, triface.dtype.itemsize * triface.shape[1]))) + _, idx,recur = np.unique(tmp, return_index=True,return_counts=True) + #we keep only top and bottom elements + triel= triface[idx[np.where(recur==1)]] + triindex=eltind[idx[np.where(recur==1)]] + for i,triangle in enumerate(triel): + tri=zip(x[triangle],y[triangle],z[triangle]) + pl3=Poly3DCollection([tri]) + color=loccmap.to_rgba(data[triindex[i]]) + pl3.set_edgecolor(color) + pl3.set_color(color) + ax.add_collection3d(pl3) + + ax.set_xlim([min(x),max(x)]) + ax.set_ylim([min(y),max(y)]) + ax.set_zlim([min(z),max(z)]) + + #raise ValueError('plot_unit error: 3D element plot not supported yet') return # }}} @@ -81,17 +147,54 @@ elif datatype==2: if is2d: - if options.exist('mask'): + if np.ma.is_masked(data): EltMask=np.asarray([np.any(np.in1d(index,np.where(data.mask))) for index in elements]) triangles=mpl.tri.Triangulation(x,y,elements,EltMask) else: triangles=mpl.tri.Triangulation(x,y,elements) - ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha) + tri=ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha) if edgecolor != 'None': ax.triplot(x,y,elements,color=edgecolor) else: - raise ValueError('plot_unit error: 3D node plot not supported yet') - return - # }}} - # {{{ plotting quiver (TODO) + #first deal with the colormap + loccmap = plt.cm.ScalarMappable(cmap=cmap) + loccmap.set_array([min(data),max(data)]) + loccmap.set_clim(vmin=min(data),vmax=max(data)) + + #deal with prism sides + recface=np.vstack((elements[:,0],elements[:,1],elements[:,4],elements[:,3])).T + recface=np.vstack((recface,np.vstack((elements[:,1],elements[:,2],elements[:,5],elements[:,4])).T)) + recface=np.vstack((recface,np.vstack((elements[:,2],elements[:,0],elements[:,3],elements[:,5])).T)) + tmp = np.ascontiguousarray(np.sort(recface)).view(np.dtype((np.void, recface.dtype.itemsize * recface.shape[1]))) + _, idx, recur = np.unique(tmp, return_index=True, return_counts=True) + recel= recface[idx[np.where(recur==1)]] + for rectangle in recel: + rec=zip(x[rectangle],y[rectangle],z[rectangle]) + pl3=Poly3DCollection([rec]) + color=loccmap.to_rgba(np.mean(data[rectangle])) + pl3.set_edgecolor(color) + pl3.set_color(color) + ax.add_collection3d(pl3) + + #deal with prism faces + triface=np.vstack((elements[:,0:3],elements[:,3:6])) + tmp = np.ascontiguousarray(triface).view(np.dtype((np.void, triface.dtype.itemsize * triface.shape[1]))) + _, idx,recur = np.unique(tmp, return_index=True,return_counts=True) + #we keep only top and bottom elements + triel= triface[idx[np.where(recur==1)]] + for triangle in triel: + tri=zip(x[triangle],y[triangle],z[triangle]) + pl3=Poly3DCollection([tri]) + color=loccmap.to_rgba(np.mean(data[triangle])) + pl3.set_edgecolor(color) + pl3.set_color(color) + ax.add_collection3d(pl3) + + ax.set_xlim([min(x),max(x)]) + ax.set_ylim([min(y),max(y)]) + ax.set_zlim([min(z),max(z)]) + #raise ValueError('plot_unit error: 3D element plot not supported yet') + return + # }}} + # {{{ plotting quiver elif datatype==3: if is2d: @@ -103,12 +206,16 @@ # }}} # {{{ plotting P1 Patch (TODO) + elif datatype==4: print 'plot_unit message: P1 patch plot not implemented yet' return + # }}} # {{{ plotting P0 Patch (TODO) + elif datatype==5: print 'plot_unit message: P0 patch plot not implemented yet' return + # }}} else: Index: /issm/trunk/src/m/plot/plot_vertexnumbering.py =================================================================== --- /issm/trunk/src/m/plot/plot_vertexnumbering.py (revision 21729) +++ /issm/trunk/src/m/plot/plot_vertexnumbering.py (revision 21729) @@ -0,0 +1,58 @@ +try: + import pylab as p +except ImportError: + print "could not import pylab, matplotlib has not been installed, no plotting capabilities enabled" + +import numpy as np +from processmesh import processmesh +from applyoptions import applyoptions +from plot_icefront import plot_icefront + +def plot_vertexnumbering(md,options,fig,axgrid,gridindex): + ''' + PLOT_VERTEXNUMBERING - plot vertex numbering + + Usage: + plot_vertexnumbering(md,options,fig,axes); + + See also: PLOTMODEL + + ''' + #process data and model + x,y,z,elements,is2d,isplanet=processmesh(md,[],options) + + ax=axgrid[gridindex] + fig.delaxes(axgrid.cbar_axes[gridindex]) + + if is2d: + ax.triplot(x,y,elements) + else: + print 'Not Implemented Yet' + + XPad=0.1*(np.max(x)-np.min(x)) + YPad=0.1*(np.max(y)-np.min(y)) + #plot mesh + ax.triplot(x,y,elements) + ax.set_xlim((np.min(x)-XPad,np.max(x)+XPad)) + ax.set_ylim((np.min(y)-XPad,np.max(y)+XPad)) + + highlightpos=options.getfieldvalue('highlight',[]) + if highlightpos!='none': + #if just one element duplicate it to avoid coloring issues + if type(highlightpos)==int: + highlightpos=[highlightpos,highlightpos] + #convert from to matlab numbering + highlightpos=[pos-1 for pos in highlightpos] + + # and numbers + for i,Xcoord in enumerate(x): + if i in highlightpos: + props = dict(boxstyle='circle', pad=0.1,color='r') + else: + props = dict(boxstyle='circle', pad=0.1,color='w') + ax.text(x[i],y[i],str(i+1),ha='center',va='center',backgroundcolor='w',clip_on=True,bbox=props) + + #apply options + options.addfielddefault('title','Vertex numbers (matlab indexation)') + options.addfielddefault('colorbar','off') + applyoptions(md,[],options,fig,axgrid,gridindex) Index: /issm/trunk/src/m/plot/plotdoc.js =================================================================== --- /issm/trunk/src/m/plot/plotdoc.js (revision 21728) +++ /issm/trunk/src/m/plot/plotdoc.js (revision 21729) @@ -18,4 +18,5 @@ console.log(' "2d": renders orthographic camera with view set to [0, 90] (default "off", ex: "on", "off")'); console.log(' "backgroundcolor": plot background color. (default "lightcyan", ex: "green","blue")'); + console.log(' "brush": specify brush options (default {"strength":0.075,"falloff":0.5})'); console.log(' "caxis": modify colorbar range. (array of type [a, b] where b>=a)'); console.log(' "colorbar": add colorbar (default "off", ex: "on", "off")'); @@ -47,4 +48,5 @@ console.log(' "overlay": overlay a radar amplitude image behind (default "off", ex: "on", "off")'); console.log(' "overlay_image": path to overlay image (default "", ex: "./images/radar.png")'); + console.log(' "quiver": add quiver plot overlay for velocities. (default "off", ex: "on", "off")'); console.log(' "scaling": scaling factor used by quiver plots. Default is 0.4'); console.log(' "alpha": transparency coefficient 0.0 to 1.0, the lower, the more transparent. (default 1.0, ex: 0.5, 0.25)'); Index: /issm/trunk/src/m/plot/plotdoc.py =================================================================== --- /issm/trunk/src/m/plot/plotdoc.py (revision 21728) +++ /issm/trunk/src/m/plot/plotdoc.py (revision 21729) @@ -7,43 +7,42 @@ pydata={'quiver':' quiver plot give data and a vector array [Vx,Vy]', 'mesh':' draw mesh using trisurf', - 'BC':' this will draw all the boundary conditions (Dirichlet and Neumann).'} + 'BC':' this will draw all the boundary conditions (Dirichlet and Neumann).', + 'elementnumbering':' numbering of elements (matlab indices)', + '3D disclaimer':'3D is implemented with plot3d for now this is not optimal and may change to mayavi at some point. The impelementation is on the development side for now so expect some issue and question your plotting before you results.'} TODOdata={'basal_drag':' plot the basal drag on the bed (in kPa) based on the velocity in md.initialization', - 'basal_dragx or basal_dragy' :' plot a component of the basal drag on the bed (in kPa)', - 'boundaries':' this will draw all the segment boundaries to the model, including rifts.', - 'icefront':' this will show segments that are used to define the icefront of the model (Neumann boundary conditions).', - 'deviatoricstress_tensor':' plot the components of the deviatoric stress tensor (tauxx,tauyy,tauzz,tauxy,tauxz,tauyz, if computed', - 'deviatoricstress_principal':' plot the deviatoricstress tensor principal axis and principal values', - 'deviatoricstress_principalaxis1':' arrow plot the first principal axis of the deviatoricstress tensor(replace 1 by 2 or 3 if needed)', - 'driving_stress':' plot the driving stress (in kPa)', - 'elements_type':' model used for each element', - 'elementnumbering':' numbering of elements', - 'vertexnumbering':' numbering of vertices', - 'highlightelements':' to highlight elements to highlight the element list', - 'highlightvertices':' to highlight vertices (use highlight option to enter the vertex list', - 'referential':' stressbalance referential', - 'riftvel':' velocities along rifts', - 'riftrelvel':' relative velocities along rifts', - 'riftpenetration':' penetration levels for a fault', - 'riftfraction':' fill fractions for every node of the rifts', - 'rifts':' plot mesh with an offset so that rifts are visible', - 'strainrate_tensor':' plot the components of the strainrate tensor (exx,eyy,ezz,exy,exz,eyz) if computed', - 'strainrate_principal':' plot the strainrate tensor principal axis and principal values)', - 'strainrate_principalaxis1':' arrow plot the first principal axis of the strainrate tensor(replace 1 by 2 or 3 if needed)', - 'stress_tensor':' plot the components of stress tensor (sxx,syy,szz,sxy,sxz,syz) if computed', - 'stress_principal':' plot the stress tensor principal axis and principal values', - 'stress_principalaxis1':' arrow plot the first principal axis of the stress tensor(replace 1 by 2 or 3 if needed)', - 'transient_results':' this will printlay all the time steps of a transient run (use steps to specify the steps requested)', - 'transient_vel':' this will printlay the velocity for the time steps requested in ''steps'' of a transient run', - 'transient_vel':' vel can be by any field of the transient results (vx, vy, vz, vel, temperature, melting, pressure, bed, thickness, surface)', - 'transient_field':' dynamic plot of results. specify ''steps'' option, as fell as ''field'' (defaults are all steps, for ''Vel'' field)', - 'transient_movie':' this will printlay the time steps of a given field of a transient run', - 'transient_movie_field':' field to be printlayed when doing transient_movie data printlay', - 'transient_movie_output':' filename if output is desired for movie', - 'transient_movie_time':' time for each image (default 2 seconds)', - 'thermaltransient_results':' this will printlay all the time steps of a thermal transient run', - 'qmuhistnorm':' histogram normal distribution. needs option qmudata', - 'qmumean':' plot of mean distribution in sampling analysis with scaled response. needs option qmudata for descriptor', - 'qmustddev':' plot of stddev distribution in sampling analysis with scaled response. needs option qmudata for descriptor', - 'part_hist':' partitioning node and area histogram'} + 'basal_dragx or basal_dragy' :' plot a component of the basal drag on the bed (in kPa)', + 'boundaries':' this will draw all the segment boundaries to the model, including rifts.', + 'icefront':' this will show segments that are used to define the icefront of the model (Neumann boundary conditions).', + 'deviatoricstress_tensor':' plot the components of the deviatoric stress tensor (tauxx,tauyy,tauzz,tauxy,tauxz,tauyz, if computed', + 'deviatoricstress_principal':' plot the deviatoricstress tensor principal axis and principal values', + 'deviatoricstress_principalaxis1':' arrow plot the first principal axis of the deviatoricstress tensor(replace 1 by 2 or 3 if needed)', + 'driving_stress':' plot the driving stress (in kPa)', + 'elements_type':' model used for each element', + 'highlightvertices':' to highlight vertices (use highlight option to enter the vertex list', + 'referential':' stressbalance referential', + 'riftvel':' velocities along rifts', + 'riftrelvel':' relative velocities along rifts', + 'riftpenetration':' penetration levels for a fault', + 'riftfraction':' fill fractions for every node of the rifts', + 'rifts':' plot mesh with an offset so that rifts are visible', + 'strainrate_tensor':' plot the components of the strainrate tensor (exx,eyy,ezz,exy,exz,eyz) if computed', + 'strainrate_principal':' plot the strainrate tensor principal axis and principal values)', + 'strainrate_principalaxis1':' arrow plot the first principal axis of the strainrate tensor(replace 1 by 2 or 3 if needed)', + 'stress_tensor':' plot the components of stress tensor (sxx,syy,szz,sxy,sxz,syz) if computed', + 'stress_principal':' plot the stress tensor principal axis and principal values', + 'stress_principalaxis1':' arrow plot the first principal axis of the stress tensor(replace 1 by 2 or 3 if needed)', + 'transient_results':' this will printlay all the time steps of a transient run (use steps to specify the steps requested)', + 'transient_vel':' this will printlay the velocity for the time steps requested in ''steps'' of a transient run', + 'transient_vel':' vel can be by any field of the transient results (vx, vy, vz, vel, temperature, melting, pressure, bed, thickness, surface)', + 'transient_field':' dynamic plot of results. specify ''steps'' option, as fell as ''field'' (defaults are all steps, for ''Vel'' field)', + 'transient_movie':' this will printlay the time steps of a given field of a transient run', + 'transient_movie_field':' field to be printlayed when doing transient_movie data printlay', + 'transient_movie_output':' filename if output is desired for movie', + 'transient_movie_time':' time for each image (default 2 seconds)', + 'thermaltransient_results':' this will printlay all the time steps of a thermal transient run', + 'qmuhistnorm':' histogram normal distribution. needs option qmudata', + 'qmumean':' plot of mean distribution in sampling analysis with scaled response. needs option qmudata for descriptor', + 'qmustddev':' plot of stddev distribution in sampling analysis with scaled response. needs option qmudata for descriptor', + 'part_hist':' partitioning node and area histogram'} pyoptions={'axis':" show ('on') or hide ('off') axes", @@ -53,4 +52,6 @@ 'axes_pad':" spacing between axes (default is 0.25)", 'colorbartitle':" colorbar title (string)", + 'colorbarticks':" set colorbar ticks manually (list)", + 'colorbarfontsize':" specify colorbar fontsize", 'colormap':" change the default colormap ('viridis' is the default)", 'contourlevels':" N or [value1,...] add the contours of the specified values or N contours", @@ -60,4 +61,5 @@ 'fontweight':" fontweight for the title 'normal', 'bold'", 'fontcolor':" TODO", + 'highlight':" highlights certain nodes or elements when using 'vetrexnumbering' or 'elementnumbering' or 'highlightvertices ' or 'highlightelements' option", 'title':" subplot title (string)", 'xlim':" limits of X axis (all subplots) (ex: [0,500])", @@ -76,93 +78,90 @@ 'log':" cutoff value for log", 'backgroundcolor':" plot background color. RGB tuple or standard string", - 'expdisp':" path (or list of paths) to the exp file to be plotted ", - 'explinewidth':" linewidth ", - 'explinestyle':" matplotlib linestyle string ", - 'explinecolor':" matplotlib color string ", - 'expfill':" (True/False) fill a closed contour ", - 'expfillcolor':" Color for a filled contour, only used if expfill is True ", - 'expfillalpha':" alpha transparency for filled contour ", - 'overlay':" True/False. Overlay a georeferenced image (radar/visible) ", - 'overlay_image':" path to overlay image ", - 'overlayhist':" plot a histogram of overlay image, used for setting overlaylims ", - 'overlaylims':" normalized limits to clip and stretch contrast of overlay image (in [0,1], ex. [0.25,0.75]) ", - 'alpha':" set transparency of plotted data (in [0,1]) " - } + 'expdisp':" path (or list of paths) to the exp file to be plotted ", + 'explinewidth':" linewidth ", + 'explinestyle':" matplotlib linestyle string ", + 'explinecolor':" matplotlib color string ", + 'expfill':" (True/False) fill a closed contour ", + 'expfillcolor':" Color for a filled contour, only used if expfill is True ", + 'expfillalpha':" alpha transparency for filled contour ", + 'overlay':" True/False. Overlay a georeferenced image (radar/visible) ", + 'overlay_image':" path to overlay image ", + 'overlayhist':" plot a histogram of overlay image, used for setting overlaylims ", + 'overlaylims':" normalized limits to clip and stretch contrast of overlay image (in [0,1], ex. [0.25,0.75]) ", + 'alpha':" set transparency of plotted data (in [0,1]) ", + 'vertexnumbering':' numbering of vertices', + 'elementnumbering':' numbering of elements (matlab indices)', + 'highlightelements':' to highlight elements to highlight the element list', + 'layer':"number of the layer to display for 3D runs"} TODOoptions={'basin':" zoom on a given basin ('pineislandglacier','ronneiceshelf', use isbasin to identify a basin", - 'figurebackgroundcolor':" figure background color. (default is 'none',", - 'coord':" 'xy' (default) or 'latlon'", - 'colorbarpos':" [x,y,dx,dy] where x,y,dx and dy are within [0 1]", - 'colorbarcornerposition':" 'West','North',etc ...", - 'colorbartitlerotation':" -90, etc ...", - 'colorbarfontsize':" specify colorbar fontsize", - 'colorbarwidth':" multiplier (default 1) to the default width colorbar", - 'colorbarheight':" multiplier (default 1) to the default height colorbar", - 'contourticks':" 'on' or 'off' to printlay the ticks of the contours", - 'contouronly':" 'on' or 'off' to printlay the contours on a white background", - 'contourcolor':" ticks and contour color", - 'density':" density of quivers (one arrow every N nodes, N integer)", - 'inset':" add an inset (zoom) of the current figure if 1 (use 'insetx', 'insety' and 'insetpos' to determine the inset position and content)", - 'insetx':" [min(x) max(x)] where min(x) and max(x) are values determining the inset content", - 'insety':" [min(y) max(y)] where min(y) and max(y) are values determining the inset content", - 'insetpos':" [x,y,dx,dy] where x,y,dx and dy are within [0 1]", - 'highlight':" highlights certain nodes or elements when using 'nodenumbering' or 'elementnumbering' or 'highlightnodes ' or 'highlightelements' option", - 'resolution':" resolution used by section value (array of type [horizontal_resolution vertical_resolution])", - 'showsection':" show section used by 'sectionvalue' (string 'on' or a number of labels)", - 'sectionvalue':" give the value of data on a profile given by an Argus file (string 'Argusfile_name.exp',", - 'profile':" give the value of data along a vertical profile ([xlocation ylocation])", - 'smooth':" smooth element data (string 'yes' or integer)", - - 'view':" same as standard matlab option (ex: 2, 3 or [90 180]", - 'zlim':" same as standard matlab option", - 'xticklabel':" specifiy xticklabel", - 'yticklabel':" specifiy yticklabel", - 'contrast':" (default 1) coefficient to add contrast to the radar amplitude image used in overlays", - 'highres':" resolution of overlayed radar amplitude image (default is 0, high resolution is 1).", - 'alpha':" transparency coefficient (the higher, the more transparent). Default is 1.5", - 'scaling':" scaling factor used by quiver plots. Default is 0.4", - 'autoscale':" set to 'off' to have all the quivers with the same size. Default is 'on'", - 'linewidth':" line width for expprint plot (use a cell of strings if more than one)", - 'border':" size of printlay border (in pixels). active only for overlay plots", - - 'nan':" value assigned to NaNs (convenient when plotting BC)", - 'partitionedges':" 'off' by default. overlay plot of partition edges", - - 'latlon':" 'on' or {latstep lonstep [resolution [color]]} where latstep,longstep and resolution are in degrees, color is a [r g b] array", - 'latlonnumbering':" 'on' or {latgap longap colornumber latangle lonangle} where latgap and longap are pixel gaps for the numbers", - 'latlonclick':" 'on' to click on latlon ticks positions colornumber is a [r g b] array and latangle and lonangle are angles to flip the numbers", - 'northarrow':" add an arrow pointing north, 'on' for default value or [x0 y0 length [ratio width fontsize]] where (x0,y0) are the coordinates of the base, ratio=headlength/length", - 'offset':" mesh offset used by 'rifts', default is 500", - 'scaleruler':" add a scale ruler, 'on' for default value or [x0 y0 length width numberofticks] where (x0,y0) are the coordinates of the lower left corner", - 'showregion':" show domain in Antarctica on an inset, use 'insetpos' properties", - 'visible':" 'off' to make figure unvisible, default is 'on'", - 'wrapping':" repeat 'n' times the colormap ('n' must be an integer)", - 'unit':" by default, in m, otherwise, 'km' is available", - 'legend_position':" by default, 'NorthEasth'", - 'qmudata':" ", - 'figposition':" position of figure: 'fullscreen', 'halfright', 'halfleft', 'portrait', 'landscape',... (hardcoded in applyoptions.m)", - 'offsetaxispos':" offset of current axis position to get more space (ex: [-0.02 0 0.04 0])", - 'axispos':" axis position to get more space", - 'hmin':" (numeric, minimum for histogram)", - 'hmax':" (numeric, maximum for histogram)", - 'hnint':" (numeric, number of intervals for histogram)", - 'ymin1':" (numeric, minimum of histogram y-axis)", - 'ymax1':" (numeric, maximum of histogram y-axis)", - 'ymin2':" (numeric, minimum of cdf y-axis)", - 'ymax2':" (numeric, maximum of cdf y-axis)", - 'cdfplt':" (char, 'off' to turn off cdf line plots)", - 'cdfleg':" (char, 'off' to turn off cdf legends)", - 'segmentnumbering':" ('off' by default)", - 'kmlgroundoverlay':" ('off' by default)", - 'kmlfilename':" ('tempfile.kml' by default)", - 'kmlroot':" ('./' by default)", - 'kmlimagename':" ('tempimage' by default)", - 'kmlimagetype':" ('png' by default)", - 'kmlresolution':" (1 by default)", - 'kmlfolder':" ('Ground Overlay' by default)", - 'kmlfolderdescription':" ('' by default)", - 'kmlgroundoverlayname':" ('' by default)", - 'kmlgroundoverlaydescription':"N/A by default')"} - + 'figurebackgroundcolor':" figure background color. (default is 'none',", + 'coord':" 'xy' (default) or 'latlon'", + 'colorbarpos':" [x,y,dx,dy] where x,y,dx and dy are within [0 1]", + 'colorbarcornerposition':" 'West','North',etc ...", + 'colorbartitlerotation':" -90, etc ...", + 'colorbarwidth':" multiplier (default 1) to the default width colorbar", + 'colorbarheight':" multiplier (default 1) to the default height colorbar", + 'contourticks':" 'on' or 'off' to printlay the ticks of the contours", + 'contouronly':" 'on' or 'off' to printlay the contours on a white background", + 'contourcolor':" ticks and contour color", + 'density':" density of quivers (one arrow every N nodes, N integer)", + 'inset':" add an inset (zoom) of the current figure if 1 (use 'insetx', 'insety' and 'insetpos' to determine the inset position and content)", + 'insetx':" [min(x) max(x)] where min(x) and max(x) are values determining the inset content", + 'insety':" [min(y) max(y)] where min(y) and max(y) are values determining the inset content", + 'insetpos':" [x,y,dx,dy] where x,y,dx and dy are within [0 1]", + 'resolution':" resolution used by section value (array of type [horizontal_resolution vertical_resolution])", + 'showsection':" show section used by 'sectionvalue' (string 'on' or a number of labels)", + 'sectionvalue':" give the value of data on a profile given by an Argus file (string 'Argusfile_name.exp',", + 'profile':" give the value of data along a vertical profile ([xlocation ylocation])", + 'smooth':" smooth element data (string 'yes' or integer)", + 'view':" same as standard matlab option (ex: 2, 3 or [90 180]", + 'zlim':" same as standard matlab option", + 'xticklabel':" specifiy xticklabel", + 'yticklabel':" specifiy yticklabel", + 'contrast':" (default 1) coefficient to add contrast to the radar amplitude image used in overlays", + 'highres':" resolution of overlayed radar amplitude image (default is 0, high resolution is 1).", + 'alpha':" transparency coefficient (the higher, the more transparent). Default is 1.5", + 'scaling':" scaling factor used by quiver plots. Default is 0.4", + 'autoscale':" set to 'off' to have all the quivers with the same size. Default is 'on'", + 'linewidth':" line width for expprint plot (use a cell of strings if more than one)", + 'border':" size of printlay border (in pixels). active only for overlay plots", + 'nan':" value assigned to NaNs (convenient when plotting BC)", + 'partitionedges':" 'off' by default. overlay plot of partition edges", + 'latlon':" 'on' or {latstep lonstep [resolution [color]]} where latstep,longstep and resolution are in degrees, color is a [r g b] array", + 'latlonnumbering':" 'on' or {latgap longap colornumber latangle lonangle} where latgap and longap are pixel gaps for the numbers", + 'latlonclick':" 'on' to click on latlon ticks positions colornumber is a [r g b] array and latangle and lonangle are angles to flip the numbers", + 'northarrow':" add an arrow pointing north, 'on' for default value or [x0 y0 length [ratio width fontsize]] where (x0,y0) are the coordinates of the base, ratio=headlength/length", + 'offset':" mesh offset used by 'rifts', default is 500", + 'scaleruler':" add a scale ruler, 'on' for default value or [x0 y0 length width numberofticks] where (x0,y0) are the coordinates of the lower left corner", + 'showregion':" show domain in Antarctica on an inset, use 'insetpos' properties", + 'visible':" 'off' to make figure unvisible, default is 'on'", + 'wrapping':" repeat 'n' times the colormap ('n' must be an integer)", + 'unit':" by default, in m, otherwise, 'km' is available", + 'legend_position':" by default, 'NorthEasth'", + 'qmudata':" ", + 'figposition':" position of figure: 'fullscreen', 'halfright', 'halfleft', 'portrait', 'landscape',... (hardcoded in applyoptions.m)", + 'offsetaxispos':" offset of current axis position to get more space (ex: [-0.02 0 0.04 0])", + 'axispos':" axis position to get more space", + 'hmin':" (numeric, minimum for histogram)", + 'hmax':" (numeric, maximum for histogram)", + 'hnint':" (numeric, number of intervals for histogram)", + 'ymin1':" (numeric, minimum of histogram y-axis)", + 'ymax1':" (numeric, maximum of histogram y-axis)", + 'ymin2':" (numeric, minimum of cdf y-axis)", + 'ymax2':" (numeric, maximum of cdf y-axis)", + 'cdfplt':" (char, 'off' to turn off cdf line plots)", + 'cdfleg':" (char, 'off' to turn off cdf legends)", + 'segmentnumbering':" ('off' by default)", + 'kmlgroundoverlay':" ('off' by default)", + 'kmlfilename':" ('tempfile.kml' by default)", + 'kmlroot':" ('./' by default)", + 'kmlimagename':" ('tempimage' by default)", + 'kmlimagetype':" ('png' by default)", + 'kmlresolution':" (1 by default)", + 'kmlfolder':" ('Ground Overlay' by default)", + 'kmlfolderdescription':" ('' by default)", + 'kmlgroundoverlayname':" ('' by default)", + 'kmlgroundoverlaydescription':"N/A by default')"} Index: /issm/trunk/src/m/plot/plotgemb.m =================================================================== --- /issm/trunk/src/m/plot/plotgemb.m (revision 21728) +++ /issm/trunk/src/m/plot/plotgemb.m (revision 21729) @@ -20,9 +20,9 @@ deltat=results(i+1).time-time; else - deltat=time-results(i-1).time; + deltat=time-results(i-1).time; end %figure out number of levels: - dz=flipud(results(i).SmbDz(element,:)') ; + dz=results(i).SmbDz(element,:); if numlevels==-1, nlevels=length(dz); @@ -30,5 +30,5 @@ nlevels=numlevels; end - dz=dz(1:nlevels); + dz=flipud(dz(1:nlevels)') ; %retrieve values: @@ -38,8 +38,4 @@ %build vertical values: nz=length(dz); - %for j=1:nz, - % patch([time-deltat/2 ;time+deltat/2; time+deltat/2; time-deltat/2],[z0; z0; z0+dz(j); z0+dz(j)],[T(j);T(j);T(j);T(j)]); - % z0=z0+dz(j); - %end xA=(time-deltat/2)*ones(nz,1); @@ -53,4 +49,5 @@ zD=zeros(nz,1); + for j=1:nz, zA(j)=z0; @@ -59,10 +56,12 @@ zD(j)=z0+dz(j); z0=z0+dz(j); - end + end + - patch([xA,xB,xC,xD]',[zA,zB,zC,zD]',[T,T,T,T]'); + patch([xA,xB,xC,xD]',[zA,zB,zC,zD]',[T,T,T,T]','EdgeColor','none'); if i>=maxstep, break; end - end + end + Index: /issm/trunk/src/m/plot/plotmodel.py =================================================================== --- /issm/trunk/src/m/plot/plotmodel.py (revision 21728) +++ /issm/trunk/src/m/plot/plotmodel.py (revision 21729) @@ -2,4 +2,6 @@ from plotoptions import plotoptions from plotdoc import plotdoc +from plot_manager import plot_manager +from math import ceil, sqrt try: @@ -7,9 +9,7 @@ import matplotlib.pyplot as plt from mpl_toolkits.axes_grid1 import ImageGrid, AxesGrid + from mpl_toolkits.mplot3d import Axes3D except ImportError: print "could not import pylab, matplotlib has not been installed, no plotting capabilities enabled" - -from plot_manager import plot_manager -from math import ceil, sqrt def plotmodel(md,*args): @@ -17,5 +17,5 @@ ''' - #First process options + #First process options options=plotoptions(*args) @@ -36,5 +36,5 @@ nrows=np.ceil(numberofplots/subplotwidth) nr=False - + if options.list[0].exist('ncols'): ncols=options.list[0].getfieldvalue('ncols') @@ -45,9 +45,9 @@ ncols=int(ncols) nrows=int(nrows) - + #check that nrows and ncols were given at the same time! if not nr==nc: raise StandardError('error: nrows and ncols need to be specified together, or not at all') - + #Go through plots if numberofplots: @@ -58,7 +58,7 @@ if options.list[0].exist('figsize'): figsize=options.list[0].getfieldvalue('figsize') - fig=plt.figure(figurenumber,figsize=(figsize[0],figsize[1]),tight_layout=True) + fig=plt.figure(figurenumber,figsize=(figsize[0],figsize[1]))#,tight_layout=True) else: - fig=plt.figure(figurenumber,tight_layout=True) + fig=plt.figure(figurenumber)#,tight_layout=True) fig.clf() @@ -82,6 +82,6 @@ cbar_size=options.list[0].getfieldvalue('colorbarsize','5%') cbar_pad=options.list[0].getfieldvalue('colorbarpad','2.5%') # None or % - - axgrid=ImageGrid(fig, 111, + + axgrid=ImageGrid(fig,111, nrows_ncols=(nrows,ncols), ngrids=plotnum, @@ -94,6 +94,5 @@ cbar_location=cbar_location, cbar_size=cbar_size, - cbar_pad=cbar_pad - ) + cbar_pad=cbar_pad) if cbar_mode=='None': @@ -101,7 +100,6 @@ fig._axstack.remove(ax) - for i in xrange(numberofplots): - plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],fig,axgrid[i]) - + for i,ax in enumerate(axgrid.axes_all): + plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],fig,axgrid,i) fig.show() else: Index: /issm/trunk/src/m/plot/processmesh.py =================================================================== --- /issm/trunk/src/m/plot/processmesh.py (revision 21728) +++ /issm/trunk/src/m/plot/processmesh.py (revision 21729) @@ -5,11 +5,11 @@ """ PROCESSMESH - process the mesh for plotting - + Usage: - x,y,z,elements,is2d=processmech(md,data,options) - + x,y,z,elements,is2d=processmech(md,data,options) + See also: PLOTMODEL, PROCESSDATA """ - + # {{{ check mesh size parameters if md.mesh.numberofvertices==0: @@ -18,52 +18,30 @@ raise ValueError('processmesh error: the number of elements is the same as the number of nodes') # }}} - # {{{ treating non data plots mesh - if len(data)==0 or not isinstance(data,dict): - if 'latlon' not in options.getfieldvalue('coord','xy').lower(): #convert to lower case for comparison - try: - x=md.mesh.x2d - except AttributeError: - x=md.mesh.x - try: - y=md.mesh.x2d - except AttributeError: - y=md.mesh.y - else: - x=md.mesh.long - y=md.mesh.lat - try: - z=md.mesh.z - except AttributeError: - z=np.zeros_like(md.mesh.x) + # {{{ treating coordinates + + try: + z=md.mesh.z + except AttributeError: + z=np.zeros(np.shape(md.mesh.x)) + elements=md.mesh.elements-1 + + if options.getfieldvalue('layer',0)>=1: + x=md.mesh.x2d + y=md.mesh.y2d + z=np.zeros(np.shape(x)) + elements=md.mesh.elements2d-1 + elif 'latlon' in options.getfieldvalue('coord','xy'): + x=md.mesh.long + y=md.mesh.lat + else: + x=md.mesh.x + y=md.mesh.y + + #is it a 2D plot? + if md.mesh.dimension()==2 or options.getfieldvalue('layer',0)>=1: + is2d=1 + else: + is2d=0 - try: - elements2d=md.mesh.elements2d-1 - except AttributeError: - elements=md.mesh.elements-1 - - #is it a 2D plot? - if md.mesh.dimension()==2 or options.getfieldvalue('layer',0)>=1: - is2d=1 - else: - is2d=0 - - #layer projection? - if options.getfieldvalue('layer',0)>=1: - if 'latlon' in options.getfieldvalue('coord','xy').lower(): - raise ValueError('processmesh error: cannot work with 3D mesh in lat-lon coords') - #we modify the mesh temporarily to a 2D mesh from which the 3D mesh was extruded - #Basile: does not seem necessary as we already picked x as x2d - # x=x2d - # y=y2d - # z=zeros(size(x2d)) - # elements=elements2d - else: - #Process mesh for plotting - if md.mesh.dimension()==2: - is2d=1 - else: - # process polycollection here for 3D plot - is2d=0 - #units if options.exist('unit'): Index: /issm/trunk/src/m/plot/scaleruler.m =================================================================== --- /issm/trunk/src/m/plot/scaleruler.m (revision 21728) +++ /issm/trunk/src/m/plot/scaleruler.m (revision 21729) @@ -26,7 +26,10 @@ %If only one tick, just draw a rectangle if numberofticks==1, - text(x0+lengthscale/2,y0+2*widthscale,2,[num2str(lengthscale*unitscale/1000) ' km'],... + t=text(x0+lengthscale/2,y0+2*widthscale,2,[num2str(lengthscale*unitscale/1000) ' km'],... 'FontSize',fontsize,'FontWeight',fontweight,'Color',fontcolor,'HorizontalAlignment','center','VerticalAlignment','baseline'); - patch([x0 x0+lengthscale x0+lengthscale x0],[y0 y0 y0+widthscale y0+widthscale],2*ones(1,4),fontcolor,'Edgecolor',fontcolor); + if ~verLessThan('matlab', '8.3') + set(t,'Layer','front'); + end + p=patch([x0 x0+lengthscale x0+lengthscale x0],[y0 y0 y0+widthscale y0+widthscale],2*ones(1,4),fontcolor,'Edgecolor',fontcolor); else %initialize some coordinates Index: /issm/trunk/src/m/plot/slider.js =================================================================== --- /issm/trunk/src/m/plot/slider.js (revision 21728) +++ /issm/trunk/src/m/plot/slider.js (revision 21729) @@ -63,10 +63,5 @@ callback(parseFloat($(selector).val())); }); - - /* - NOTE: Slider must be "refreshed" after any JavaScript change to it, as - it is an AJAX object. - */ - $(selector).slider('refresh'); + $(selector).slider('refresh'); //Slider must be "refreshed" after any JavaScript change to it, as it is an AJAX object. } //}}} @@ -89,10 +84,5 @@ */ $(selector).appendTo(selector + '-value'); - - /* - NOTE: Slider must be "refreshed" after any JavaScript change to it, as - it is an AJAX object. - */ - $(selector).slider('refresh'); + $(selector).slider('refresh'); //Slider must be "refreshed" after any JavaScript change to it, as it is an AJAX object. } //}}} @@ -130,37 +120,21 @@ $(progressBar).attr('max', 1); $(progressBar).attr('step', 1); - $(progressBar).on('slidestop', function(event, ui){ - canvas.movieIncrement = true; - canvas.movieFrame = parseInt($(progressBar).val()); + $(progressBar).on('slidestart', function(event, ui){ + onSlideStart(canvas, progressBar); }); $(progressBar).on('change', function(event, ui){ - canvas.movieFrame = parseInt($(progressBar).val()); + onSlideChange(canvas, progressBar); }); - $(progressBar).on('slidestart', function(event, ui){ - canvas.movieIncrement = false; - canvas.movieFrame = parseInt($(progressBar).val()); + $(progressBar).on('slidestop', function(event, ui){ + onSlideStop(canvas, progressBar); }); - - /* - NOTE: Slider must be "refreshed" after any JavaScript change to it, as - it is an AJAX object. - */ - $(progressBar).slider('refresh'); - - // Attach progress bar slider to simulation. - canvas.progressBar = progressBar; + $(progressBar).slider('refresh'); //Slider must be "refreshed" after any JavaScript change to it, as it is an AJAX object. playButton.click(function(){ - canvas.moviePlay = !canvas.moviePlay; - if (canvas.moviePlay){ - playButton.find("span").removeClass("fa-play"); - playButton.find("span").addClass("fa-pause"); - } - else{ - playButton.find("span").removeClass("fa-pause"); - playButton.find("span").addClass("fa-play"); - } + toggleMoviePlay(canvas); }); + canvas.progressBar = progressBar; + canvas.playButton = playButton; canvas.timeLabel = timeText; } //}}} Index: /issm/trunk/src/m/plot/webgl.js =================================================================== --- /issm/trunk/src/m/plot/webgl.js (revision 21728) +++ /issm/trunk/src/m/plot/webgl.js (revision 21729) @@ -1,99 +1,170 @@ /*This is where we have all our webgl relevant functionality for the plotting routines: */ - //{{{ Canvas Initialization function initCanvas(options) { - //Initialize open Gl for each canvas, if needed: + //Initialize open Gl for each canvas and clear any previous animation handlers, once per plotmodel call: canvas = document.getElementById(options.getfieldvalue('canvasid')); //var canvas = document.getElementById(options.getfieldvalue('canvasid')); if (!canvas.initialized) { typedArraySliceSupport(); - canvas.gl = initWebGL(canvas,options); + if (!isEmptyOrUndefined(canvas.draw) && canvas.draw.handler !== 0) { window.cancelAnimationFrame(canvas.draw.handler); } + if (!isEmptyOrUndefined(canvas.animation) && canvas.animation.handler !== 0) { clearInterval(canvas.animation.handler); } + initWebGL(canvas, options); + initializeMarker(canvas); canvas.nodes = []; - if (canvas.drawHandler) { window.cancelAnimationFrame(canvas.drawHandler); } - draw(canvas,options); + draw(canvas); canvas.initialized = true; } return canvas; } -function initWebGL(canvas,options) { //{{{ +function initWebGL(canvas, options) { //{{{ + //Initialize canvas.gl on page load, reusing gl context on additional runs var gl; - try { - if (!canvas.gl) { - gl = GL.create({canvas:canvas}); - // Enable depth testing - gl.enable(gl.DEPTH_TEST); - // Near things obscure far things - gl.depthFunc(gl.LEQUAL); - // Enable color blending/overlay - gl.enable(gl.BLEND); - // Enable face culling - gl.enable(gl.CULL_FACE); - gl.cullFace(gl.FRONT); - // Load shaders and store them in gl object - gl.shaders = loadShaders(gl,options.getfieldvalue('rootpath','../../../js/')); - - // Add event listeners for canvas - var displayview = options.getfieldvalue('displayview','off') == 'on'; - var displayzoom = options.getfieldvalue('displayzoom','off') == 'on'; - var mc = new Hammer.Manager(canvas); - - mc.add( new Hammer.Tap({ event: 'singletap' }) ); - mc.add(new Hammer.Pan({threshold:0, pointers:0})); - mc.add(new Hammer.Pinch({threshold:0})).recognizeWith(mc.get('pan')); - mc.on('singletap', function (ev) {onTap(ev,canvas);}); - mc.on('panstart panmove', function (ev) {onPan(ev,canvas,displayview);}); - mc.on('pinchstart pinchmove', function (ev) {onPinch(ev,canvas,displayview);}); - - //canvas.addEventListener('mousemove', function (ev) {onTap(ev,canvas);}, false); - canvas.addEventListener('mousewheel', function (ev) {onZoom(ev,canvas,displayzoom)}, false); - canvas.addEventListener('DOMMouseScroll', function (ev) {onZoom(ev,canvas,displayzoom)}, false); - } - else { - gl = canvas.gl; - } - } - catch(e) { - console.log(e); - return; + if (!canvas.gl) { + gl = GL.create({canvas: canvas}); + gl.enable(gl.DEPTH_TEST); // Enable depth testing + gl.depthFunc(gl.LEQUAL); // Near things obscure far things + gl.enable(gl.BLEND); // Enable color blending/overlay + gl.enable(gl.CULL_FACE); // Enable face culling + gl.cullFace(gl.FRONT); + gl.shaders = loadShaders(gl, options.getfieldvalue('rootpath', '../../../js/')); // Load shaders and store them in gl object + gl.textures = {}; + + // Add event listeners for canvas + var displayview = options.getfieldvalue('displayview', 'off') == 'on'; + var displayzoom = options.getfieldvalue('displayzoom', 'off') == 'on'; + var mc = new Hammer.Manager(canvas); + + mc.add( new Hammer.Tap({event: 'singletap' }) ); + mc.add(new Hammer.Pan({threshold: 0, pointers: 0})); + mc.add(new Hammer.Pinch({threshold: 0})).recognizeWith(mc.get('pan')); + mc.on('singletap', function (ev) {onTap(ev, canvas);}); + mc.on('panstart panmove', function (ev) {onPan(ev, canvas, displayview);}); + mc.on('pinchstart pinchmove', function (ev) {onPinch(ev, canvas, displayview);}); + + canvas.addEventListener('mousewheel', function (ev) {onZoom(ev, canvas, displayzoom)}, false); + canvas.addEventListener('DOMMouseScroll', function (ev) {onZoom(ev, canvas, displayzoom)}, false); + } + else { + gl = canvas.gl; } // Add context state variables - //TODO:Group variables in objects for organization and naming canvas.gl = gl; - canvas.rootPath = options.getfieldvalue('rootpath','../../../js/'); - canvas.cameraPosition = vec3.create(); - canvas.cameraMatrix = mat4.create(); - canvas.controlSensitivity = options.getfieldvalue('controlsensitivity',1); - canvas.dataMarkersAllowed = options.getfieldvalue('datamarkers','off') == 'on'; - canvas.dataMarkersEnabled = true; //if data marker feature is on, user can toggle feature on and off - canvas.dataMarkerImage = options.getfieldvalue('datamarkers_image',canvas.rootPath+'textures/data_marker.svg'); - canvas.dataMarkerSize = options.getfieldvalue('datamarkerssize',[32,32]); - canvas.dataMarkerOptions = options.getfieldvalue('datamarkersoptions',{'enabled':'on','image':canvas.rootPath+'textures/data_marker.svg','size':[32,32],'format':['X: %.2e
    Y: %.2e
    Z: %.2e]
    Value: %0.1f','x','y','z','value']}); - canvas.inverseCameraMatrix = mat4.create(); - canvas.id = options.getfieldvalue('canvasid','.sim-canvas'); - canvas.movieFrame = 0; - canvas.moviePlay = true; - canvas.movieReverse = false; - canvas.movieIncrement = true; - canvas.movieOptions = options.getfieldvalue('movieoptions',{'fps':4,'loop':true}); - canvas.moviefps = options.getfieldvalue('moviefps',5); - canvas.rotation = options.getfieldvalue('view',[0,90]); //0 azimuth, 90 elevation - canvas.rotationAzimuthBounds = options.getfieldvalue('azlim',[0,360]); - canvas.rotationElevationBounds = options.getfieldvalue('ellim',[-180,180]); - canvas.translation = options.getfieldvalue('origin',[0,0,0]); - canvas.twod = options.getfieldvalue('2d','off') == 'on'; - canvas.view = options.getfieldvalue('view',[0,90]); - canvas.viewPanning = options.getfieldvalue('enablepanning','off') == 'on'; - canvas.vInverseMatrix = mat4.create(); - canvas.zoomBounds = options.getfieldvalue('zoomlim',[0.001,100.0]); - canvas.zoom = clamp(options.getfieldvalue('zoom',1.0), canvas.zoomBounds[0], canvas.zoomBounds[1]); - canvas.zoomLast = canvas.zoom; - var backgroundcolor = new RGBColor(options.getfieldvalue('backgroundcolor','lightcyan')); + canvas.textcanvas = null; + canvas.overlaycanvas = null; + canvas.unitNode = {}; + canvas.unitData = {}; + canvas.controlSensitivity = options.getfieldvalue('controlsensitivity', 1); + canvas.id = options.getfieldvalue('canvasid', '.sim-canvas'); + canvas.rootPath = options.getfieldvalue('rootpath', '../../../js/'); + canvas.selector = $('#' + canvas.id); + var backgroundcolor = new RGBColor(options.getfieldvalue('backgroundcolor', 'lightcyan')); if (backgroundcolor.ok) { canvas.backgroundcolor = [backgroundcolor.r/255.0, backgroundcolor.g/255.0, backgroundcolor.b/255.0, 1.0]; } - else { throw Error(sprintf('s%s%s\n','initWebGL error message: cound not find out background color for curent canvas ',canvas)); } - - return gl; -} //}}} -function loadShaders(gl,rootPath) { //{{{ + else { throw Error(sprintf('s%s%s\n','initWebGL error message: cound not find out background color for curent canvas ', canvas)); } + + //Property intiialization, using values from options first, then from default values. + var animation = options.getfieldvalue('movies', {}); + canvas.animation = { + frame: defaultFor(animation.frame, 0), + play: defaultFor(animation.play, true), + increment: defaultFor(animation.increment, true), + fps: defaultFor(animation.fps, 4), + loop: defaultFor(animation.loop, true), + handler: defaultFor(animation.handler, 0) + } + var brush = options.getfieldvalue('brush', {}); + canvas.brush = { + enabled: defaultFor(brush.enabled, false), + strength: defaultFor(brush.strength, 0.075), + falloff: defaultFor(brush.falloff, 0.5), + hit: defaultFor(brush.hit, {}) + }; + var camera = options.getfieldvalue('camera', {}); + canvas.camera = { + position: defaultFor(camera.position, vec3.create()), + rotation: defaultFor(camera.rotation, vec3.create()), + near: defaultFor(camera.near, 1e3), + far: defaultFor(camera.far, 1e10), + fov: defaultFor(camera.fov, 45), + vMatrix: defaultFor(camera.vMatrix, mat4.create()), + pMatrix: defaultFor(camera.pMatrix, mat4.create()), + vpMatrix: defaultFor(camera.vpMatrix, mat4.create()), + vInverseMatrix: defaultFor(camera.vInverseMatrix, mat4.create()), + pInverseMatrix: defaultFor(camera.pInverseMatrix, mat4.create()), + vpInverseMatrix: defaultFor(camera.vpInverseMatrix, mat4.create()), + ready: defaultFor(camera.ready, false) + }; + var clouds = options.getfieldvalue('clouds', {}); + canvas.clouds = { + enabled: defaultFor(clouds.enabled, false), + height: defaultFor(clouds.height, 7500), + quantity: defaultFor(clouds.quantity, 10) + }; + var dataMarkers = options.getfieldvalue('datamarkers', {}); + canvas.dataMarkers = { + enabled: defaultFor(dataMarkers.enabled, true), + values: defaultFor(dataMarkers.values, []), + image: defaultFor(dataMarkers.image, canvas.rootPath+'textures/data_marker.svg'), + size: defaultFor(dataMarkers.size, [32, 32]), + format: defaultFor(dataMarkers.format, ['X: %.2e
    Y: %.2e
    Z: %.2e
    Value: %0.1f', 'x', 'y', 'z', 'value']), + animated: defaultFor(dataMarkers.animated, false), + labels: defaultFor(dataMarkers.labels, []), + font: defaultFor(dataMarkers.font, ''), + marker: defaultFor(dataMarkers.marker, document.getElementById('sim-data-marker-' + canvas.id)) + }; + var draw = options.getfieldvalue('draw', {}); + canvas.draw = { + ready: defaultFor(draw.ready, false), + handler: defaultFor(draw.handler, null) + }; + var view = options.getfieldvalue('view', {}); + canvas.view = { + position: defaultFor(view.position, [0.0, 0.0, 0.0]), + rotation: defaultFor(view.rotation, [0, 90]), + zoom: defaultFor(view.zoom, 1.0), + zoomLimits: defaultFor(view.zoomLimits, [0.001, 100.0]), + lastZoom: defaultFor(view.lastZoom, 1.0), + azimuthLimits: defaultFor(view.azimuthLimits, [0, 360]), + elevationLimits: defaultFor(view.elevationLimits, [-180, 180]), + panningEnabled: defaultFor(view.panningEnabled, false), + twod: defaultFor(view.twod, false) + }; + + //Override with parameters from URL, if any + //TODO: Make permalinks more robust and less interdependent on UI + if (!canvas.usedparemters) { + function getJsonFromUrl() { + var query = location.search.substr(1); + var result = {}; + query.split('&').forEach(function(part) { + var item = part.split('='); + result[item[0]] = decodeURIComponent(item[1]); + }); + return result; + } + parameters = getJsonFromUrl(); + + if (parameters['view']) { + canvas.view = JSON.parse(parameters['view']); + } + if (parameters['initial']) { + initial = JSON.parse(parameters['initial']); + if (!initial) { + if (typeof SolveGlacier == 'function') { + SolveGlacier(); + } + if (typeof SolveSlr == 'function') { + SolveSlr(); + } + } + } + canvas.usedparemters = true; + } +} //}}} +function generatePermalink() { //{{{ + var permalink = window.location.origin + window.location.pathname + '&view=' + JSON.stringify(canvas.view) + '&initial=' + JSON.stringify(initial); + window.prompt('Share this simulation: ', permalink); +} //}}} +function loadShaders(gl, rootPath) { //{{{ var shaders = {}; shaders.Colored = new GL.Shader.fromURL(rootPath+'shaders/Colored.vsh', rootPath+'shaders/Colored.fsh', null, gl); @@ -101,44 +172,49 @@ shaders.SkyFromSpace = new GL.Shader.fromURL(rootPath+'shaders/SkyFromSpace.vert', rootPath+'shaders/SkyFromSpace.frag', null, gl); shaders.GroundFromSpace = new GL.Shader.fromURL(rootPath+'shaders/GroundFromSpace.vert', rootPath+'shaders/GroundFromSpace.frag', null, gl); + shaders.Clouds = new GL.Shader.fromURL(rootPath+'shaders/Clouds.vert', rootPath+'shaders/Clouds.frag', null, gl); return shaders; } //}}} -function initTexture(gl,imageSource) { //{{{ - return GL.Texture.fromURL(imageSource, {minFilter:gl.LINEAR_MIPMAP_LINEAR, magFilter:gl.LINEAR}, null, gl); +function initTexture(gl, imageSource) { //{{{ + //Initialize textures, or load from memory if they already exist. + if (isEmptyOrUndefined(gl.textures[imageSource])) { + gl.textures[imageSource] = GL.Texture.fromURL(imageSource, {minFilter: gl.LINEAR_MIPMAP_LINEAR, magFilter: gl.LINEAR}, null, gl); + } + return gl.textures[imageSource]; } //}}} function Node(gl) { //{{{ //Returns a Node object that contains default display states for webgl object. center represents pivot point of rotation. return { - alpha:1.0, - buffers:[], - cullFace:gl.FRONT, - disableDepthTest:false, - drawMode:gl.TRIANGLES, - drawOrder:0, - enabled:true, - enableCullFace:false, - hideOcean:false, - lineWidth:1.0, - maskEnabled:false, - maskHeight:150.0, - maskColor:vec4.fromValues(0.0, 0.0, 1.0, 1.0), - mesh:null, - name:'node', - shaderName:'Colored', - shader:gl.shaders.Colored, - texture:null, - useIndexBuffer:true, - center:vec3.create(), - scale:vec3.fromValues(1, 1, 1), - rotation:vec3.create(), - translation:vec3.create(), - modelMatrix:mat4.create(), - rotationMatrix:mat4.create(), - inverseModelMatrix:mat4.create(), - inverseRotationMatrix:mat4.create() + alpha: 1.0, + buffers: [], + cullFace: gl.BACK, + disableDepthTest: false, + drawMode: gl.TRIANGLES, + drawOrder: 0, + enabled: true, + enableCullFace: true, + hideOcean: false, + lineWidth: 1.0, + maskEnabled: false, + maskHeight: 150.0, + maskColor: vec4.fromValues(0.0, 0.0, 1.0, 1.0), + mesh: null, + name: 'node', + shaderName: 'Colored', + shader: gl.shaders.Colored, + texture: null, + useIndexBuffer: true, + center: vec3.create(), + scale: vec3.fromValues(1, 1, 1), + rotation: vec3.create(), + translation: vec3.create(), + modelMatrix: mat4.create(), + rotationMatrix: mat4.create(), + inverseModelMatrix: mat4.create(), + inverseRotationMatrix: mat4.create() }; } //}}} function debugNodes(canvasid) { //{{{ var canvasid = canvasid || '.sim-canvas'; - var nodes = $(canvasid)[0].nodes; + var nodes = document.getElementById(canvasid).nodes; console.log(canvasid, 'Nodes:'); for (var node in nodes) { @@ -151,5 +227,5 @@ var translationMatrix = mat4.create(); - mat4.translate(translationMatrix, translationMatrix, [-node.center[0],-node.center[1],-node.center[2]]); //scale/rotation centering + mat4.translate(translationMatrix, translationMatrix, vec3.negate(vec3.create(), node.center)); //scale/rotation centering mat4.multiply(modelMatrix, translationMatrix, modelMatrix); @@ -181,13 +257,24 @@ node.inverseModelMatrix = mat4.invert(mat4.create(), modelMatrix); node.rotationMatrix = rotationMatrix; - node.inverseRotationMatrix = mat4.invert(mat4.create(), rotationMatrix);; + node.inverseRotationMatrix = mat4.invert(mat4.create(), rotationMatrix); } //}}} function clamp(value, min, max) { //{{{ return Math.max(min, Math.min(value, max)); } //}}} -function recover(canvasid,name,defaultvalue) { //{{{ - var canvas = document.getElementById(canvasid); - if (canvas && canvas.hasOwnProperty(name)) { return canvas[name]; } - return defaultvalue; +function defaultFor(name, value) { //{{{ + return typeof name !== 'undefined' ? name : value; +} //}}} +function isEmptyOrUndefined(object) { //{{{ + return object === undefined || Object.getOwnPropertyNames(object).length === 0; +} //}}} +function recover(canvasid, name, value) { //{{{ + //Traverse canvas object tree for property defined by dot delimited string, returning it, or a default value if it is not found. + var object = document.getElementById(canvasid); + var properties = name.split('.'); + for (var i = 0; i < properties.length; ++i) { + object = object[properties[i]]; + if (typeof object === 'undefined') { break; } + } + return defaultFor(object, value); } //}}} function typedArraySliceSupport() { //{{{ @@ -234,19 +321,4 @@ } } //}}} -function raycast(canvas, origin, ray) { //{{{ - var mesh = canvas.unitNode.mesh; - if (!mesh || mesh.ready == false) { return; } - if (!mesh.octree) { mesh.octree = new GL.Octree(mesh); } - - var hit = mesh.octree.testRay(origin, ray, 1e3, 1e10); - - if(!hit) { return; } - - hit.modelPos = vec3.copy(vec3.create(), hit.pos); - vec3.transformMat4(hit.pos, hit.pos, canvas.unitNode.modelMatrix); - vec3.transformMat4(hit.normal, hit.normal, canvas.unitNode.modelMatrix); - - return hit; -} //}}} //}}} //{{{ Interface Functions @@ -254,126 +326,19 @@ //Sets up a marker on a canvas that will track a point on the mesh. Can be dismissed by closing the display or clicking the marker. ev.preventDefault(); - if (!(canvas.dataMarkersAllowed && canvas.dataMarkersEnabled)) { return; } - updateMarker(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY, true); -} //}}} -function updateMarker(canvas, x, y, reset, origin, far) { //{{{ - //Can be called by onTap to create/reuse a marker, or by the marker's update function. Origin and far are optional and only used by the update function for recreating the raycast. - if (!canvas.unitNode) { return; } - - var inverseMVPMatrix = mat4.invert(mat4.create(), mat4.multiply(mat4.create(), canvas.cameraMatrix, canvas.unitNode.modelMatrix)); - var origin = origin || vec3.transformMat4(vec3.create(), [(x - canvas.width / 2) / (canvas.width / 2), (canvas.height / 2 - y) / (canvas.height / 2), 0], inverseMVPMatrix); - var far = far || vec3.transformMat4(vec3.create(), [(x - canvas.width / 2) / (canvas.width / 2), (canvas.height / 2 - y) / (canvas.height / 2), 1.0], inverseMVPMatrix); - var ray = vec3.subtract(vec3.create(), far, origin); - var hit = raycast(canvas, origin, ray); - - if (hit) { - var coords = canvas.unitNode.mesh.vertexBuffers.coords.data; - var latitude = md.mesh.lat; - var longitude = md.mesh.long; - var thickness; - var velocity; - if (md.results[0]) { - thickness = md.results[canvas.movieFrame].Thickness; - velocity = md.results[canvas.movieFrame].Vel; - } - else { - thickness = md.geometry.thickness; - velocity = md.initialization.vel; - } - - var hitCoords = [coords[hit.indices[0]*2], coords[hit.indices[0]*2+1],coords[hit.indices[1]*2], coords[hit.indices[1]*2+1],coords[hit.indices[2]*2], coords[hit.indices[2]*2+1]]; - var hitLatitude = [latitude[hit.indices[0]], latitude[hit.indices[1]], latitude[hit.indices[2]]]; - var hitLongitude = [longitude[hit.indices[0]], longitude[hit.indices[1]], longitude[hit.indices[2]]]; - var hitThickness = [thickness[hit.indices[0]], thickness[hit.indices[1]], thickness[hit.indices[2]]]; - var hitVelocity = [velocity[hit.indices[0]], velocity[hit.indices[1]], velocity[hit.indices[2]]]; - var u = hitCoords[0] * hit.uvw[0] + hitCoords[2] * hit.uvw[1] + hitCoords[4] * hit.uvw[2]; - var v = hitCoords[1] * hit.uvw[0] + hitCoords[3] * hit.uvw[1] + hitCoords[5] * hit.uvw[2]; - var value = canvas.unitNode.caxis[0] * (1.0 - v) + canvas.unitNode.caxis[1] * v; - var valueLatitude = Math.abs(hitLatitude[0] * hit.uvw[0] + hitLatitude[1] * hit.uvw[1] + hitLatitude[2] * hit.uvw[2]); - var valueLongitude = Math.abs(hitLongitude[0] * hit.uvw[0] + hitLongitude[1] * hit.uvw[1] + hitLongitude[2] * hit.uvw[2]); - var valueThickness = hitThickness[0] * hit.uvw[0] + hitThickness[1] * hit.uvw[1] + hitThickness[2] * hit.uvw[2]; - var valueVelocity = hitVelocity[0] * hit.uvw[0] + hitVelocity[1] * hit.uvw[1] + hitVelocity[2] * hit.uvw[2]; - - var dataMarkerSize = canvas.dataMarkerSize; - if (!canvas.marker) { - $('#' + canvas.id).after( 'data marker'); - $('#sim-data-marker-' + canvas.id).css({ - 'position': 'absolute', - 'left': (Math.round(x) - dataMarkerSize[0] / 2) + 'px', - 'top': (Math.round(y) - dataMarkerSize[1]) + 'px', - 'width': dataMarkerSize[0] + 'px', - 'height': dataMarkerSize[1] + 'px', - 'pointer-events': 'all', - 'cursor': 'pointer', - 'display': 'none' - }); - $('#sim-data-marker-' + canvas.id).tooltipster({ - maxWidth: 320, - zIndex: 2200, - trigger: 'custom', - triggerOpen: { - mouseenter: false, - originClick: true, - touchstart: false - }, - triggerClose: { - mouseleave: false, - originClick: true, - touchleave: false - } - }); - canvas.marker = $('#sim-data-marker-' + canvas.id); - canvas.marker.on('click touch', function () { - canvas.marker.fadeOut(175); - canvas.dataMarkerDisplay.tooltipster('close'); - }); - canvas.marker.fadeIn(175); - } - - - canvas.marker.hit = hit; - canvas.marker.update = function() { - if (!canvas.unitNode) { return; } - var screenPoint = vec3.transformMat4(vec3.create(), canvas.marker.hit.pos, canvas.cameraMatrix); - var x = screenPoint[0] * (canvas.width / 2) + canvas.width / 2; - var y = -screenPoint[1] * (canvas.height / 2) + canvas.height / 2; - updateMarker(canvas, Math.round(x), Math.round(y), false, origin, far); - canvas.marker.css({ - 'left': (Math.round(x) - dataMarkerSize[0] / 2) + 'px', - 'top': (Math.round(y) - dataMarkerSize[1]) + 'px' - }); - if (canvas.dataMarkerDisplay.tooltipster('status').state != 'closed') { canvas.dataMarkerDisplay.tooltipster('reposition'); } - }; - - if (!canvas.dataMarkerDisplay) { - canvas.dataMarkerDisplay = $('#sim-data-marker-' + canvas.id); - canvas.dataMarkerDisplay.tooltipster('open'); - } - if (canvas.dataMarkerOptions) { - var format = [canvas.dataMarkerOptions.format[0]]; - for (var i = 1; i < canvas.dataMarkerOptions.format.length; i++) { - var formatString = canvas.dataMarkerOptions.format[i]; - if (formatString.toLowerCase() == 'x') { format.push(hit.modelPos[0]); } - else if (formatString.toLowerCase() == 'y') { format.push(hit.modelPos[1]); } - else if (formatString.toLowerCase() == 'z') { format.push(hit.modelPos[2]); } - else if (formatString.toLowerCase() == 'lat') { format.push(valueLatitude); } - else if (formatString.toLowerCase() == 'long') { format.push(valueLongitude); } - else if (formatString.toLowerCase() == 'thickness') { format.push(valueThickness); } - else if (formatString.toLowerCase() == 'vel') { format.push(valueVelocity); } - else if (formatString.toLowerCase() == 'value') { format.push(value); } - else {format.push(formatString); } - } - - $('#tooltip-content-data-marker-' + canvas.id).html(sprintf.apply(null, format)); - $('#tooltip-content-data-marker-' + canvas.id).css({ - 'font': canvas.dataMarkerOptions.font - }); - } - - if (reset) { modifyDataMarkersEnabled(true,canvas); } - } -} //}}} -function onPan(ev,canvas,displaylog) { //{{{ + if (!canvas.dataMarkers.enabled) { return; } + var hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY); + canvas.dataMarkers.marker.hit = hit; + canvas.brush.hit = hit; + updateMarker(canvas, true); + brushModify(canvas); +} //}}} +function onPan(ev, canvas, displaylog) { //{{{ ev.preventDefault(); + + if (canvas.dataMarkers.enabled == 'on') { + canvas.brush.hit = raycast(canvas, ev.srcEvent.layerX, ev.srcEvent.layerY); + brushModify(canvas); + } + if (ev.type == 'panstart') { canvas.lastDeltaX = 0; @@ -381,68 +346,342 @@ } if (ev.srcEvent.shiftKey || ev.pointers.length == 2) { - if (!canvas.viewPanning) return; - var deltaX = (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth / canvas.zoom * 2 * canvas.controlSensitivity * 6.371e6; - var deltaY = (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight / canvas.zoom * 2 * canvas.controlSensitivity * 6.371e6; - - if (canvas.twod) { - canvas.translation[0] += Math.cos(DEG2RAD * canvas.rotation[0]) * deltaX - Math.sin(DEG2RAD * 0) * deltaY; - canvas.translation[2] += Math.sin(DEG2RAD * canvas.rotation[0]) * deltaX + Math.cos(DEG2RAD * 0) * deltaY; + if (!canvas.view.panningEnabled) return; + var deltaX = (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth / canvas.view.zoom * 2 * canvas.controlSensitivity * 6.371e6; + var deltaY = (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight / canvas.view.zoom * 2 * canvas.controlSensitivity * 6.371e6; + + if (canvas.view.twod) { + canvas.view.position[0] += Math.cos(DEG2RAD * canvas.view.rotation[0]) * deltaX - Math.sin(DEG2RAD * 0) * deltaY; + canvas.view.position[2] += Math.sin(DEG2RAD * canvas.view.rotation[0]) * deltaX + Math.cos(DEG2RAD * 0) * deltaY; } else { - canvas.translation[0] += Math.cos(DEG2RAD * canvas.rotation[0]) * deltaX - Math.sin(DEG2RAD * canvas.rotation[0]) * deltaY; - canvas.translation[2] += Math.sin(DEG2RAD * canvas.rotation[0]) * deltaX + Math.cos(DEG2RAD * canvas.rotation[0]) * deltaY; - } - } + canvas.view.position[0] += Math.cos(DEG2RAD * canvas.view.rotation[0]) * deltaX - Math.sin(DEG2RAD * canvas.view.rotation[0]) * deltaY; + canvas.view.position[2] += Math.sin(DEG2RAD * canvas.view.rotation[0]) * deltaX + Math.cos(DEG2RAD * canvas.view.rotation[0]) * deltaY; + } + } + else { - canvas.rotation[0] += (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth * -2 * canvas.controlSensitivity * RAD2DEG; - canvas.rotation[1] += (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight * -2 * canvas.controlSensitivity * RAD2DEG; - - if (canvas.rotation[0] > 360) { canvas.rotation[0] -= 360; }; - if (canvas.rotation[0] < -360) { canvas.rotation[0] += 360; }; - if (canvas.rotation[1] > 180) { canvas.rotation[1] -= 360; }; - if (canvas.rotation[1] < -180) { canvas.rotation[1] += 360; }; - - canvas.rotation[0] = clamp(canvas.rotation[0], canvas.rotationAzimuthBounds[0], canvas.rotationAzimuthBounds[1]); - canvas.rotation[1] = clamp(canvas.rotation[1], canvas.rotationElevationBounds[0], canvas.rotationElevationBounds[1]) + canvas.view.rotation[0] += (canvas.lastDeltaX - ev.deltaX) / canvas.clientWidth * -2 * canvas.controlSensitivity * RAD2DEG; + canvas.view.rotation[1] += (canvas.lastDeltaY - ev.deltaY) / canvas.clientHeight * -2 * canvas.controlSensitivity * RAD2DEG; + + if (canvas.view.rotation[0] > 360) { canvas.view.rotation[0] -= 360; }; + if (canvas.view.rotation[0] < -360) { canvas.view.rotation[0] += 360; }; + if (canvas.view.rotation[1] > 180) { canvas.view.rotation[1] -= 360; }; + if (canvas.view.rotation[1] < -180) { canvas.view.rotation[1] += 360; }; + + canvas.view.rotation[0] = clamp(canvas.view.rotation[0], canvas.view.azimuthLimits[0], canvas.view.azimuthLimits[1]); + canvas.view.rotation[1] = clamp(canvas.view.rotation[1], canvas.view.elevationLimits[0], canvas.view.elevationLimits[1]) } canvas.lastDeltaX = ev.deltaX; canvas.lastDeltaY = ev.deltaY; - - if (displaylog) { console.log(canvas.rotation); } -} //}}} -function onPinch(ev,canvas,displaylog) { //{{{ + + repositionMarker(canvas); + + if (displaylog) { console.log(canvas.view.rotation); } +} //}}} +function onPinch(ev, canvas, displaylog) { //{{{ ev.preventDefault(); - if (ev.type == 'pinchstart') { canvas.zoomLast = canvas.zoom; } - else { modifyZoom(ev.scale * canvas.zoomLast, canvas, displaylog); } -} //}}} -function onZoom(ev,canvas,displaylog) { //{{{ + if (ev.type == 'pinchstart') { canvas.view.lastZoom = canvas.view.zoom; } + else { modifyZoom(ev.scale * canvas.view.lastZoom, canvas, displaylog); } +} //}}} +function onZoom(ev, canvas, displaylog) { //{{{ ev.preventDefault(); - var delta = clamp(ev.scale || ev.wheelDelta || -ev.detail, -1, 1) * canvas.controlSensitivity * canvas.zoom / 20; - modifyZoom(canvas.zoom + delta, canvas, displaylog); -} //}}} -function modifyZoom(value,canvas,displaylog) { //{{{ - canvas.zoom = clamp(value, canvas.zoomBounds[0], canvas.zoomBounds[1]); - if (displaylog) { console.log(canvas.zoom); } -} //}}} -function modifyDataMarkersEnabled(value,canvas) { //{{{ - canvas.dataMarkersEnabled = value; - if (!canvas.dataMarkersEnabled && canvas.marker) { - canvas.marker.fadeOut(175); - canvas.dataMarkerDisplay.tooltipster('close'); - } - else if (canvas.dataMarkersEnabled && canvas.marker) { - canvas.marker.fadeIn(175); - canvas.dataMarkerDisplay.tooltipster('open'); - } + var delta = clamp(ev.scale || ev.wheelDelta || -ev.detail, -1, 1) * canvas.controlSensitivity * canvas.view.zoom / 20; + modifyZoom(canvas.view.zoom + delta, canvas, displaylog); +} //}}} +function modifyZoom(value, canvas, displaylog) { //{{{ + canvas.view.zoom = clamp(value, canvas.view.zoomLimits[0], canvas.view.zoomLimits[1]); + repositionMarker(canvas); + if (displaylog) { console.log(canvas.view.zoom); } +} //}}} +function modifyDataMarkersEnabled(value, canvas) { //{{{ + canvas.dataMarkers.enabled = value; } //}}} function toggleMoviePlay(canvas) { //{{{ - canvas.moviePlay = !canvas.moviePlay; - if (canvas.moviePlay){ - canvas.playButton.find("span").removeClass("fa-play"); - canvas.playButton.find("span").addClass("fa-pause"); + canvas.animation.play = !canvas.animation.play; + if (canvas.animation.play){ + canvas.playButton.find('span').removeClass('fa-play'); + canvas.playButton.find('span').addClass('fa-pause'); } else{ - canvas.playButton.find("span").removeClass("fa-pause"); - canvas.playButton.find("span").addClass("fa-play"); + canvas.playButton.find('span').removeClass('fa-pause'); + canvas.playButton.find('span').addClass('fa-play'); + } +} //}}} +function onSlideStart(canvas, progressBar) { //{{{ + if (!isEmptyOrUndefined(canvas.animation)) { + canvas.animation.increment = false; + canvas.animation.frame = parseInt($(progressBar).val()); + //console.log(canvas.animation.frame); + //updateMarker(canvas, false); + } +} //}}} +function onSlideChange(canvas, progressBar) { //{{{ + if (!isEmptyOrUndefined(canvas.animation)) { + canvas.animation.frame = parseInt($(progressBar).val()); + //console.log("change"); + updateMarker(canvas, false); + } +} //}}} +function onSlideStop(canvas, progressBar) { //{{{ + if (!isEmptyOrUndefined(canvas.animation)) { + canvas.animation.increment = true; + canvas.animation.frame = parseInt($(progressBar).val()); + //console.log(canvas.animation.frame); + //updateMarker(canvas, false); + } +} //}}} +//}}} +//{{{ Interaction Functions +function raycast(canvas, x, y) { //{{{ + //Performs raycast on canvas.unitNode.mesh using x/y screen coordinates. Returns hit objects with hit position, coords, and indicies of ray-triangle intersection. + //TODO: Diagnose marker issues with orthographic views and slr-eustatic updates when switching between basins. + var inverseMVPMatrix = mat4.invert(mat4.create(), mat4.multiply(mat4.create(), canvas.camera.vpMatrix, canvas.unitNode.modelMatrix)); + var origin = vec3.transformMat4(vec3.create(), [(x - canvas.width / 2) / (canvas.width / 2), (canvas.height / 2 - y) / (canvas.height / 2), 0], inverseMVPMatrix); + var far = far || vec3.transformMat4(vec3.create(), [(x - canvas.width / 2) / (canvas.width / 2), (canvas.height / 2 - y) / (canvas.height / 2), 1.0], inverseMVPMatrix); + var ray = vec3.subtract(vec3.create(), far, origin); + + var mesh = canvas.unitNode.mesh; + if (!mesh) { return; } + if (!mesh.octree) { mesh.octree = new GL.Octree(mesh); } + + var hit = mesh.octree.testRay(origin, ray, 1e3, 1e10); + + if(!hit) { return; } + + hit.modelPos = vec3.copy(vec3.create(), hit.pos); + vec3.transformMat4(hit.pos, hit.pos, canvas.unitNode.modelMatrix); + vec3.transformMat4(hit.normal, hit.normal, canvas.unitNode.modelMatrix); + + return hit; +} //}}} +function brushModify(canvas) { //{{{ + //This function takes in the canvas and x/y coordinates, performing a raycast against the mesh, and modifies the mesh using a the canvas.brush.strength and canvas.brush.falloff properties. + //Currently the brush extends to the raycasted element and its immediate neighbors. + //TODO: Allow variable brush size/additional neighbors. Allow the function to work on multiple models (currently hardcoded to md model). + if (!canvas.unitNode || canvas.brush.enabled != 'on') { return; } + + var hit = canvas.brush.hit; + + if (hit) { + var bufferVertices = canvas.unitNode.mesh.getBuffer('vertices'); + var vertices = bufferVertices.data; + var bufferCoords = canvas.unitNode.mesh.getBuffer('coords'); + var coords = bufferCoords.data; + + //Query nearby elements and store indicies of affected vertices using pregenerated vertexconnectivity list (from NodeConnectivity) + var baseIndices = new Set(hit.indices); + var connectedIndices = new Set(hit.indices); + var connectedElement; + var indices; + var lengthIndex = md.mesh.vertexconnectivity[0].length - 1; + var length; + for (var i = 0; i < 3; i++) { + length = md.mesh.vertexconnectivity[hit.indices[i]][lengthIndex]; + for (var j = 0; j < length; j++) { + //Shift elements down by one (matlab 1-based index to 0-based index) + connectedElement = md.mesh.vertexconnectivity[hit.indices[i]][j] - 1; + indices = md.mesh.elements[connectedElement]; + connectedIndices.add(indices[0] - 1); + connectedIndices.add(indices[1] - 1); + connectedIndices.add(indices[2] - 1); + } + } + + //Apply modifications to included vertices in mesh using brush strength and falloff. + var strength; + for (var index of connectedIndices) { + if (!baseIndices.has(index)) { + strength = canvas.brush.strength * canvas.brush.falloff; + } + else { + strength = canvas.brush.strength; + } + vertices[index*3+2] += strength * 100; + md.geometry.surface[index] += strength; + md.geometry.thickness[index] += strength; + coords[index*2+1] += strength; + canvas.unitData[index] += strength; + } + + //Update mesh on GPU + bufferVertices.upload(canvas.gl.DYNAMIC_DRAW); + bufferCoords.upload(canvas.gl.DYNAMIC_DRAW); + canvas.unitNode.mesh.octree = new GL.Octree(canvas.unitNode.mesh); + + //Update clouds if rendered + //TODO: Steven, once you update the cloud generation in applyoptions.js, modify this code block to move the clouds as well. We'll want to move them individually later, but moving them all is ok for now. + for (var i = 0; i < canvas.clouds.quantity; i++) { + if (canvas.nodes['clouds' + i]) { + var v1 = vec3.fromValues(vertices[hit.indices[0] * 3], vertices[hit.indices[0] * 3 + 1], vertices[hit.indices[0] * 3 + 2]); + var v2 = vec3.fromValues(vertices[hit.indices[1] * 3], vertices[hit.indices[1] * 3 + 1], vertices[hit.indices[1] * 3 + 2]); + var v3 = vec3.fromValues(vertices[hit.indices[2] * 3], vertices[hit.indices[2] * 3 + 1], vertices[hit.indices[2] * 3 + 2]); + vec3.transformMat4(v1, v1, canvas.unitNode.modelMatrix); + vec3.transformMat4(v2, v2, canvas.unitNode.modelMatrix); + vec3.transformMat4(v3, v3, canvas.unitNode.modelMatrix); + var x = (v1[0] + v2[0] + v3[0]) / 3 + Math.floor((Math.random() * (1 + 10000 - (-10000)) + (-10000))); + var y = (v1[1] + v2[1] + v3[1]) / 3 + Math.floor((Math.random() * (1 + 10000 - (-10000)) + (-10000))); + var z = (v1[2] + v2[2] + v3[2]) / 3; + canvas.nodes['clouds' + i].translation = [x, y + canvas.clouds.height, z]; + updateModelMatrix(canvas.nodes['clouds' + i]); + } + } + } +} //}}} +function initializeMarker(canvas) { //{{{ + //Initialize data marker and tooltip display once per page load + var marker = $('#' + canvas.dataMarkers.marker.id); + var size = canvas.dataMarkers.size; + if (!marker.hasClass('tooltipstered')) { + marker.css({ + 'position': 'absolute', + 'left': -size[0] + 'px', + 'top': -size[1] + '0px', + 'width': size[0] + 'px', + 'height': size[1] + 'px', + 'pointer-events': 'all', + 'cursor': 'pointer', + 'display': 'none' + }); + marker.tooltipster({ + contentAsHTML: true, + maxWidth: 320, + maxHeight: 320, + zIndex: 1000, + trigger: 'custom', + triggerOpen: { + mouseenter: false, + originClick: true, + touchstart: false + }, + triggerClose: { + mouseleave: false, + originClick: true, + touchleave: false + }, + }); + marker.on('click touch', function () { + marker.fadeOut(175); + marker.tooltipster('close'); + }); + canvas.dataMarkers.marker.selector = marker; + } + updateMarker(canvas, true); +} //}}} +function repositionMarker(canvas) { //{{{ + //Mover marker to point to mouse position, offset in y by 1 to enable immediate clicking. + if (isEmptyOrUndefined(canvas.dataMarkers.marker.hit) || !canvas.camera.ready) { return; } + var size = canvas.dataMarkers.size; + var screenPoint = vec3.transformMat4(vec3.create(), canvas.dataMarkers.marker.hit.pos, canvas.camera.vpMatrix); + //console.log(canvas, canvas.selector, $(canvas.id) + var x = (screenPoint[0] + 1.0) * (canvas.width / 2) + canvas.selector.offset().left; + var y = (-screenPoint[1] + 1.0) * (canvas.height / 2) + canvas.selector.offset().top; + canvas.dataMarkers.marker.selector.css({ + 'left': (Math.round(x) - size[0] / 2) + 'px', + 'top': (Math.round(y) - size[1] + 1) + 'px' + }); + + if (canvas.dataMarkers.marker.selector.tooltipster('status').state != 'closed') { canvas.dataMarkers.marker.selector.tooltipster('reposition'); } +} //}}} +function updateMarker(canvas, reset) { //{{{ + //Retrieve data value fields and plots them on data marker popup if a hit has been registered. + //TODO: Automatically pick up any field of size md.mesh.numberofelements + //If no marker has been placed, no update is needed. If canvas is resimulating and unitNode has not been set yet, wait and try again. + if (isEmptyOrUndefined(canvas.dataMarkers.marker.hit)) { return; } + if (isEmptyOrUndefined(canvas.unitNode)) { setTimeout( function(){ updateMarker(canvas, reset); }, 750); return; } + + var hit = canvas.dataMarkers.marker.hit; + + var coords = canvas.unitNode.mesh.vertexBuffers.coords.data; + var latitude = md.mesh.lat; + var longitude = md.mesh.long; + var thickness; + var velocity; + if (md.results[0]) { + thickness = md.results[canvas.animation.frame].Thickness; + velocity = md.results[canvas.animation.frame].Vel; + } + else { + thickness = md.geometry.thickness; + velocity = md.initialization.vel; + } + + //Determine data values at hit position. + var hitCoords = [coords[hit.indices[0]*2], coords[hit.indices[0]*2+1], coords[hit.indices[1]*2], coords[hit.indices[1]*2+1], coords[hit.indices[2]*2], coords[hit.indices[2]*2+1]]; + var hitLatitude = [latitude[hit.indices[0]], latitude[hit.indices[1]], latitude[hit.indices[2]]]; + var hitLongitude = [longitude[hit.indices[0]], longitude[hit.indices[1]], longitude[hit.indices[2]]]; + var hitThickness = [thickness[hit.indices[0]], thickness[hit.indices[1]], thickness[hit.indices[2]]]; + var hitVelocity = [velocity[hit.indices[0]], velocity[hit.indices[1]], velocity[hit.indices[2]]]; + var u = hitCoords[0] * hit.uvw[0] + hitCoords[2] * hit.uvw[1] + hitCoords[4] * hit.uvw[2]; + var v = hitCoords[1] * hit.uvw[0] + hitCoords[3] * hit.uvw[1] + hitCoords[5] * hit.uvw[2]; + var value = canvas.unitNode.caxis[0] * (1.0 - v) + canvas.unitNode.caxis[1] * v; + var valueLatitude = Math.abs(hitLatitude[0] * hit.uvw[0] + hitLatitude[1] * hit.uvw[1] + hitLatitude[2] * hit.uvw[2]); + var valueLongitude = Math.abs(hitLongitude[0] * hit.uvw[0] + hitLongitude[1] * hit.uvw[1] + hitLongitude[2] * hit.uvw[2]); + var valueThickness = hitThickness[0] * hit.uvw[0] + hitThickness[1] * hit.uvw[1] + hitThickness[2] * hit.uvw[2]; + var valueVelocity = hitVelocity[0] * hit.uvw[0] + hitVelocity[1] * hit.uvw[1] + hitVelocity[2] * hit.uvw[2]; + + //Construct new argument array of the data display format for sprintf using first first argument as the formatSpecifier string and the rest as the additional arguments. + var format = canvas.dataMarkers.format.slice(); + for (var i = 1; i < format.length; i++) { + if (format[i].toLowerCase() == 'x') { format[i] = hit.modelPos[0]; } + else if (format[i].toLowerCase() == 'y') { format[i] = hit.modelPos[1]; } + else if (format[i].toLowerCase() == 'z') { format[i] = hit.modelPos[2]; } + else if (format[i].toLowerCase() == 'lat') { format[i] = valueLatitude; } + else if (format[i].toLowerCase() == 'long') { format[i] = valueLongitude; } + else if (format[i].toLowerCase() == 'thickness') { format[i] = valueThickness; } + else if (format[i].toLowerCase() == 'vel') { format[i] = valueVelocity; } + else if (format[i].toLowerCase() == 'value') { format[i] = value; } + } + + //Apply changes to tooltip + $('#tooltip-content-data-marker-' + canvas.id).html(sprintf.apply(null, format)); + $('#tooltip-content-data-marker-' + canvas.id).css({'font': canvas.dataMarkers.font}); + + //If animated, setup animation loop to update plot as movie plays. + if (canvas.dataMarkers.animated) { + var isEmpty = (canvas.dataMarkers.values.length == 0); + var lastUpdatedIndex = (canvas.dataMarkers.values.length-1); + var newMovieFrame = (!isEmpty && canvas.dataMarkers.values[lastUpdatedIndex][0] != canvas.animation.frame); + //If new data marker has been placed, reinitialize plot. If not, push new value into plot value array. + if (reset) { + canvas.dataMarkers.values = []; + newMovieFrame = true; + for (var currentFrame = 0; currentFrame < (canvas.unitNode.movieLength); currentFrame++) { + coords = canvas.unitNode.texcoords[currentFrame]; + var hitCoords = [coords[hit.indices[0]*2], coords[hit.indices[0]*2+1], coords[hit.indices[1]*2], coords[hit.indices[1]*2+1], coords[hit.indices[2]*2], coords[hit.indices[2]*2+1]]; + var u = hitCoords[0] * hit.uvw[0] + hitCoords[2] * hit.uvw[1] + hitCoords[4] * hit.uvw[2]; + var v = hitCoords[1] * hit.uvw[0] + hitCoords[3] * hit.uvw[1] + hitCoords[5] * hit.uvw[2]; + var value = canvas.unitNode.caxis[0] * (1.0 - v) + canvas.unitNode.caxis[1] * v; + canvas.dataMarkers.values.push([currentFrame, value]); + } + } + else { + if (isEmpty || newMovieFrame) { + canvas.dataMarkers.values.push([canvas.animation.frame, value]); + } + } + + //Replot data marker popup using update data value array. + if (isEmpty || newMovieFrame) { + var dataLabels = {'latitude': valueLatitude, 'longitude': valueLongitude, 'thickness': valueThickness, 'velocity': valueVelocity, 'value': value}; + var dataDisplay = canvas.dataMarkers.values.slice(0, canvas.animation.frame+1); + plot( + 'id', '#sim-plot', + 'type', 'bar', + 'width', 400, + 'height', 300, + 'nticks', 25, + 'xlabel', 'Time', + 'ylabel', 'Value', + 'title', 'Changes Over Time', + 'datalabels', canvas.dataMarkers.labels, + 'labelvalues', dataLabels, + 'data', dataDisplay + ); + } + } + repositionMarker(canvas); + if (reset) { + canvas.dataMarkers.marker.selector.fadeIn(175); + canvas.dataMarkers.marker.selector.tooltipster('open'); } } //}}} @@ -450,5 +689,5 @@ //{{{ Drawing Functions function updateCameraMatrix(canvas) { //{{{ - //Update view matrix and multiply with projection matrix to get the view-projection (camera) matrix. + //Update view matrix and multiply with projection matrix to get the view-projection matrix. var vMatrix = mat4.create(); var pMatrix = mat4.create(); @@ -460,13 +699,12 @@ var cameraPosition = vec3.create(); - if (canvas.twod) { mat4.ortho(pMatrix, -aspectRatio*6.371e6/canvas.zoom, aspectRatio*6.371e6/canvas.zoom, -6.371e6/canvas.zoom, 6.371e6/canvas.zoom, -1.0, 1e10); } - else { mat4.perspective(pMatrix, 45 * DEG2RAD, aspectRatio, 1e3, 1e10); } + if (canvas.view.twod) { mat4.ortho(pMatrix, -aspectRatio*6.371e6/canvas.view.zoom, aspectRatio*6.371e6/canvas.view.zoom, -6.371e6/canvas.view.zoom, 6.371e6/canvas.view.zoom, canvas.camera.near, canvas.camera.far); } + else { mat4.perspective(pMatrix, canvas.camera.fov * DEG2RAD, aspectRatio, canvas.camera.near, canvas.camera.far); } //Apply worldspace translation - mat4.translate(translateMatrix, translateMatrix, [-canvas.translation[0],-canvas.translation[1],-canvas.translation[2]]); - mat4.multiply(vMatrix, translateMatrix, vMatrix); + mat4.translate(vMatrix, translateMatrix, vec3.negate(vec3.create(), canvas.view.position)); //Calculate rotation around camera focal point about worldspace origin - if (canvas.twod) { + if (canvas.view.twod) { mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, DEG2RAD * 0, [0, 1, 0]); mat4.rotate(elevationRotationMatrix, elevationRotationMatrix, DEG2RAD * 90, [1, 0, 0]); @@ -474,26 +712,29 @@ } else { - mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, DEG2RAD * canvas.rotation[0], [0, 1, 0]); - mat4.rotate(elevationRotationMatrix, elevationRotationMatrix, DEG2RAD * canvas.rotation[1], [1, 0, 0]); + mat4.rotate(azimuthRotationMatrix, azimuthRotationMatrix, DEG2RAD * canvas.view.rotation[0], [0, 1, 0]); + mat4.rotate(elevationRotationMatrix, elevationRotationMatrix, DEG2RAD * canvas.view.rotation[1], [1, 0, 0]); mat4.multiply(rotationMatrix, elevationRotationMatrix, azimuthRotationMatrix); } - + //Apply rotation transform mat4.multiply(vMatrix, rotationMatrix, vMatrix); - - //Apply screenspace translation + + //Apply screenspace translation to emulate rotation around point mat4.identity(translateMatrix); - mat4.translate(translateMatrix, translateMatrix, [0.0, 0.0, -6.371e6/canvas.zoom]); + mat4.translate(translateMatrix, translateMatrix, [0.0, 0.0, -6.371e6/canvas.view.zoom]); mat4.multiply(vMatrix, translateMatrix, vMatrix); - //Calculate fields for lighting and raycasts - mat4.invert(canvas.vInverseMatrix, vMatrix); - //Apply projection matrix to get camera matrix - mat4.multiply(canvas.cameraMatrix, pMatrix, vMatrix); - mat4.invert(canvas.inverseCameraMatrix, canvas.cameraMatrix); - vec3.transformMat4(canvas.cameraPosition, cameraPosition, canvas.inverseCameraMatrix); + mat4.copy(canvas.camera.vMatrix, vMatrix); + mat4.multiply(canvas.camera.vpMatrix, pMatrix, vMatrix); + + //Calculate inverse view matrix fields for lighting and raycasts + mat4.invert(canvas.camera.vInverseMatrix, canvas.camera.vMatrix); + mat4.invert(canvas.camera.vpInverseMatrix, canvas.camera.vpMatrix); + + vec3.transformMat4(canvas.camera.position, cameraPosition, canvas.camera.vpInverseMatrix); + canvas.camera.ready = true; }//}}} -function drawSceneGraphNode(canvas,node) { //{{{ +function drawSceneGraphNode(canvas, node) { //{{{ if (!node.enabled) { return; } @@ -502,5 +743,12 @@ var mvpMatrix = mat4.create(); - mat4.multiply(mvpMatrix, canvas.cameraMatrix, node.modelMatrix); + mat4.multiply(mvpMatrix, canvas.camera.vpMatrix, node.modelMatrix); + + var mvMatrix = mat4.create(); + mat4.multiply(mvMatrix, canvas.camera.vMatrix, node.modelMatrix); + + var normalMatrix = mat4.create(); + mat4.invert(normalMatrix, mvMatrix); + mat4.transpose(normalMatrix, normalMatrix); if (node.texture) { node.texture.bind(0); } @@ -516,5 +764,5 @@ var lightOrigin = vec3.fromValues(0, 0, 0); var cameraPositionRelative = vec3.create(); - vec3.transformMat4(origin, origin, canvas.vInverseMatrix); + vec3.transformMat4(origin, origin, canvas.camera.vInverseMatrix); vec3.normalize(lightOrigin, lightOrigin); vec3.sub(cameraPositionRelative, origin, node.translation); @@ -548,5 +796,9 @@ node.shader.uniforms({ m4MVP: mvpMatrix, + m4Normal: normalMatrix, m4Model: node.modelMatrix, + //u_lightPosition: [-lightOrigin[0], -lightOrigin[1], -lightOrigin[2]], + u_lightPosition: [1.0, 1.0, 1.0], + u_diffuseColor: [1.0, 0.9, 0.9], u_texture: 0, u_alpha: node.alpha, @@ -584,41 +836,48 @@ gl.disable(gl.CULL_FACE); } //}}} -function draw(canvas,options) { //{{{ - if (canvas.textcanvas) { canvas.textcanvas.draw(canvas); } - +function draw(canvas) { //{{{ + //Ensure all nodes are ready to render + //TODO: Come up with better way to check if shaders are ready, or move outside of main draw function var nodes = canvas.nodes; - if (nodes.length < 1) { - canvas.drawHandler = window.requestAnimationFrame(function(time) { draw(canvas,options); }); - return; - } - for (var node in nodes) { - if ((nodes[node].texture && nodes[node].texture.ready == false) || nodes[node].shader.ready == false || nodes[node].mesh.ready == false) { - canvas.drawHandler = window.requestAnimationFrame(function(time) { draw(canvas,options); }); - return; - } - } - - var rect = canvas.getBoundingClientRect(); - canvas.width = rect.width; - canvas.height = rect.height; - - var gl = canvas.gl; - gl.makeCurrent(); //litegl function to handle switching between multiple canvases - gl.viewport(0, 0, rect.width, rect.height); - gl.clearColor(canvas.backgroundcolor[0], canvas.backgroundcolor[1], canvas.backgroundcolor[2], canvas.backgroundcolor[3]); - gl.clear(gl.COLOR_BUFFER_BIT | gl.DEPTH_BUFFER_BIT); - - updateCameraMatrix(canvas); - - if (canvas.marker) { canvas.marker.update(); } - - var drawPassNumber = 3; - for (var i = drawPassNumber - 1; i >= 0; i--) { - for (var node in nodes) { - if (nodes[node].drawOrder == i) { drawSceneGraphNode(canvas,nodes[node]); } - } - } - - canvas.drawHandler = window.requestAnimationFrame(function(time) { draw(canvas,options); }); + if (!canvas.draw.ready) { + if (nodes.length !== 0) { + canvas.draw.ready = true; + for (var node in nodes) { + if (nodes[node].shader.ready == false) { + canvas.draw.ready = false; + break; + } + } + + } + } + + //Begin rendering nodes + if (canvas.draw.ready) { + if (canvas.textcanvas) { canvas.textcanvas.draw(canvas); } + if (canvas.overlaycanvas) { canvas.overlaycanvas.draw(canvas); } + + var rect = canvas.getBoundingClientRect(); + canvas.width = rect.width; + canvas.height = rect.height; + + var gl = canvas.gl; + gl.makeCurrent(); //litegl function to handle switching between multiple canvases + gl.viewport(0, 0, canvas.width, canvas.height); + gl.clearColor(canvas.backgroundcolor[0], canvas.backgroundcolor[1], canvas.backgroundcolor[2], canvas.backgroundcolor[3]); + gl.clear(gl.COLOR_BUFFER_BIT | gl.DEPTH_BUFFER_BIT); + + updateCameraMatrix(canvas); + + var drawPassNumber = 3; + for (var i = drawPassNumber - 1; i >= 0; i--) { + for (var node in nodes) { + if (nodes[node].drawOrder == i) { drawSceneGraphNode(canvas, nodes[node]); } + } + } + } + + //Regardless of ready state, schedule next frame to check for ready state and render + canvas.draw.handler = window.requestAnimationFrame(function(time) { draw(canvas); }); } //}}} //}}} Index: /issm/trunk/src/m/qmu/dakota_out_parse.m =================================================================== --- /issm/trunk/src/m/qmu/dakota_out_parse.m (revision 21728) +++ /issm/trunk/src/m/qmu/dakota_out_parse.m (revision 21729) @@ -1,2 +1,3 @@ +function [method,dresp,scm,pcm,srcm,prcm]=dakota_out_parse(filei) % {{{ % % read a Dakota .out or .dat output file and parse it. @@ -46,980 +47,950 @@ % to foreign countries or providing access to foreign persons." % -function [method,dresp,scm,pcm,srcm,prcm]=dakota_out_parse(filei) - -if ~nargin - help dakota_out_parse - return -end - -if ~exist('filei' ,'var') || isempty(filei) - filei=input('Input file? ','s'); -end -fidi=fopen(sprintf('%s',filei),'r'); -if (fidi < 0) - error('''%s'' could not be opened.',filei); -end - -%% check the first line for the Dakota tabular output file - -method=[]; -fline=fgetl(fidi); -if ~ischar(fline) - error('File ''%s'' is empty.',filei); -end - -if strncmpi(fline,'%eval_id',8) - method='unknown'; - [dresp]=dak_tab_out(fidi,fline); - return -else - fseek(fidi,0,'bof'); -end - -%% loop through the file to find the Dakota method name - -[fline]=findline(fidi,'methodName = '); -if ~ischar(fline) - %do nothing -else - % display([' ' deblank(fline)]); + + if ~nargin + help dakota_out_parse + return + end + + if ~exist('filei' ,'var') || isempty(filei) + filei=input('Input file? ','s'); + end + fidi=fopen(sprintf('%s',filei),'r'); + if (fidi < 0) + error('''%s'' could not be opened.',filei); + end + + %% check the first line for the Dakota tabular output file + + method=[]; + fline=fgetl(fidi); + if ~ischar(fline) + error('File ''%s'' is empty.',filei); + end + + if strncmpi(fline,'%eval_id',8) + method='unknown'; + [dresp]=dak_tab_out(fidi,fline); + return + else + fseek(fidi,0,'bof'); + end + + %% loop through the file to find the Dakota method name + + [fline]=findline(fidi,'methodName = '); + if ~ischar(fline) + %do nothing + else + % display([' ' deblank(fline)]); + + [ntokens,tokens]=fltokens(fline); + method=tokens{1}{3}; + display(sprintf('Dakota methodName=''%s''.',method)); + end + + dresp=struct([]); + scm =struct([]); + pcm =struct([]); + srcm=struct([]); + prcm=struct([]); + + %% loop through the file to find the function evaluation summary + + fline=''; + [nfeval]=nfeval_read(fidi,fline); + fline=fgetl(fidi); + + %% process each results section based on content of the file + + while ischar(fline) + % ipos=ftell(fidi); + if isempty(fline) + elseif strncmp(fline,'<<<<< Function evaluation summary',33) + [nfeval]=nfeval_read(fidi,fline); + elseif strncmp(fline,'Statistics based on ',20) + [nsamp]=nsamp_read(fidi,fline); + elseif strncmp(fline,'Moments for each response function',34) + [dresp]=moments_read(fidi,dresp,fline); + elseif strncmp(fline,'Moment-based statistics for each response function',50) + [dresp]=mbstats_read(fidi,dresp,fline); + elseif strncmp(fline,'95% confidence intervals for each response function',51) + [dresp]=cis_read(fidi,dresp,fline); + elseif strncmp(fline,'Probabilities for each response function',40) || ... + strncmp(fline,'Level mappings for each response function',41) + [dresp]=cdfs_read(fidi,dresp,fline); + elseif strncmp(fline,'Probability Density Function (PDF) histograms for each response function',72) + [dresp]=pdfs_read(fidi,dresp,fline); + elseif strncmp(fline,'Simple Correlation Matrix',25) + [scm]=corrmat_read(fidi,'Simple Correlation Matrix',fline); + elseif strncmp(fline,'Partial Correlation Matrix',26) + [pcm]=corrmat_read(fidi,'Partial Correlation Matrix',fline); + elseif strncmp(fline,'Simple Rank Correlation Matrix',30) + [srcm]=corrmat_read(fidi,'Simple Rank Correlation Matrix',fline); + elseif strncmp(fline,'Partial Rank Correlation Matrix',31) + [prcm]=corrmat_read(fidi,'Partial Rank Correlation Matrix',fline); + elseif strncmp(fline,'MV Statistics for ',18) + [dresp]=mvstats_read(fidi,dresp,fline); + elseif strncmp(fline,'<<<<< Best ',11) + [dresp]=best_read(fidi,dresp,fline); + elseif strncmp(fline,'The following lists volumetric uniformity measures',50) + [dresp]=vum_read(fidi,dresp,fline); + elseif strncmp(fline,'<<<<< Iterator ',15) && ... + (length(fline) > 26) && ... + ~isempty(strfind(fline(16:end),' completed.')) + [method]=itcomp_read(fidi,fline); + elseif strncmp(fline,'-----',5) + else + display(['Unexpected line: ' deblank(fline)]); + end + fline=fgetl(fidi); + % fseek(fidi,ipos,'bof'); + end + + %% loop through the file to verify the end + + % [fline]=findline(fidi,'<<<<< Single Method Strategy completed'); + % if ~ischar(fline) + % return + % end + display('End of file successfully reached.'); + fclose(fidi); + +end % }}} +function [dresp]=dak_tab_out(fidi,fline) % {{{ +%% function to parse the dakota tabular output file + + display('Reading Dakota tabular output file.'); + + % process column headings of matrix (skipping eval_id) + + [ntokens,tokens]=fltokens(fline); + + % New file DAKOTA versions>6 + if strncmpi(fline,'%eval_id interface',18) + offset=2; + else %DAKOTA versions<6 + offset=1; + end + desc=cell (1,ntokens-offset); + data=zeros(1,ntokens-offset); + + for i=1:ntokens-offset + desc(1,i)=cellstr(tokens{1}{i+offset}); + end + display(sprintf('Number of columns (Dakota V+R)=%d.',ntokens-2)); + + % process rows of matrix + + nrow=0; + while 1 + fline=fgetl(fidi); + if ~ischar(fline) || isempty(fline) + break; + end + [ntokens,tokens]=fltokens(fline); + + % add row values to matrix (skipping eval_id) + + nrow=nrow+1; + for i=1:ntokens-offset + data(nrow,i)=tokens{1}{i+offset}; + end + end + display(sprintf('Number of rows (Dakota func evals)=%d.',nrow)); + + % calculate statistics + + % since normfit doesn't have a dim argument, and matlab isvector is true + % for a 1xn matrix, handle the case of one row explicitly + if (size(data,1) > 1) + %dmean =mean (data); + %dstddev=std (data,0); + [dmean,dstddev,dmeanci,dstddevci]=... + normfit_issm(data,0.05); + else + dmean =zeros(1,size(data,2)); + dstddev =zeros(1,size(data,2)); + dmeanci =zeros(2,size(data,2)); + dstddevci=zeros(2,size(data,2)); + for i=1:size(data,2) + [dmean(1,i),dstddev(1,i),dmeanci(:,i),dstddevci(:,i)]=... + normfit_issm(data(:,i),0.05); + end + end + + dmin =min (data,[],1); + dquart1=prctile_issm(data,25,1); + dmedian=median (data,1); + dquart3=prctile_issm(data,75,1); + dmax =max (data,[],1); + dmin95=prctile_issm(data,5,1); + dmax95=prctile_issm(data,95,1); + + % same as Dakota scm, Excel correl + dcorrel=corrcoef(data); + + % divide the data into structures for consistency + + for i=1:length(desc) + dresp(i).descriptor=char(desc(i)); + dresp(i).sample =data(:,i); + dresp(i).mean =dmean(i); + dresp(i).stddev =dstddev(i); + dresp(i).meanci =dmeanci(:,i); + dresp(i).stddevci =dstddevci(:,i); + dresp(i).min =dmin(i); + dresp(i).quart1 =dquart1(i); + dresp(i).median =dmedian(i); + dresp(i).quart3 =dquart3(i); + dresp(i).max =dmax(i); + dresp(i).dmin95 =dmin95(i); + dresp(i).dmax95 =dmax95(i); + end + + % draw box plot + + % figure + % subplot(2,1,1) + % plot_boxplot(dresp); + + % draw normal probability plot + + % subplot(2,1,2) + % plot_normplot(dresp); + +end % }}} +function [nfeval]=nfeval_read(fidi,fline) % {{{ +%% function to find and read the number of function evaluations + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'<<<<< Function evaluation summary'); + if ~ischar(fline) + nfeval = 0; + return + end + end + + [ntokens,tokens]=fltokens(fline); + nfeval=tokens{1}{5}; + display(sprintf(' Dakota function evaluations=%d.',nfeval)); + +end % }}} +function [nsamp]=nsamp_read(fidi,fline) % {{{ +%% function to find and read the number of samples + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'Statistics based on '); + if ~ischar(fline) + return + end + end + + [ntokens,tokens]=fltokens(fline); + nsamp=tokens{1}{4}; + display(sprintf(' Dakota samples=%d.',nsamp)); + +end % }}} +function [dresp]=moments_read(fidi,dresp,fline) % {{{ +%% function to find and read the moments + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'Moments for each response function'); + if ~ischar(fline) + return + end + end + + display('Reading moments for response functions:'); + + while 1 + fline=fgetl(fidi); + if isempty(fline) + break; + end + [ntokens,tokens]=fltokens(fline); + + % add new response function and moments + + dresp(end+1).descriptor=tokens{1}{ 1}; + display(sprintf(' %s',dresp(end).descriptor)); + dresp(end ).mean =tokens{1}{ 4}; + dresp(end ).stddev =tokens{1}{ 8}; + dresp(end ).coefvar =tokens{1}{13}; + end + + display(sprintf(' Number of Dakota response functions=%d.',... + length(dresp))); + +end % }}} +function [dresp]=mbstats_read(fidi,dresp,fline) % {{{ +%% function to find and read the moment-based statistics + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'Moment-based statistics for each response function'); + if ~ischar(fline) + return + end + end + + display('Reading moment-based statistics for response functions:'); + + % skip column headings of moment-based statistics + + fline=fgetl(fidi); + + while 1 + fline=fgetl(fidi); + if isempty(fline) + break; + end + [ntokens,tokens]=fltokens(fline); + + % add new response function and moment-based statistics + + dresp(end+1).descriptor=tokens{1}{ 1}; + display(sprintf(' %s',dresp(end).descriptor)); + dresp(end ).mean =tokens{1}{ 2}; + dresp(end ).stddev =tokens{1}{ 3}; + dresp(end ).skewness =tokens{1}{ 4}; + dresp(end ).kurtosis =tokens{1}{ 5}; + end + + display(sprintf(' Number of Dakota response functions=%d.',... + length(dresp))); + +end % }}} +function [dresp]=cis_read(fidi,dresp,fline) % {{{ +%% function to find and read the confidence intervals + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,... + '95% confidence intervals for each response function'); + if ~ischar(fline) + return + end + end + + display('Reading 95% confidence intervals for response functions:'); + + while 1 + fline=fgetl(fidi); + if isempty(fline) + break; + end + [ntokens,tokens]=fltokens(fline); + + % check for column headings in Dakota 5.2 + + if (ntokens == 4) + fline=fgetl(fidi); + if isempty(fline) + break; + end + [ntokens,tokens]=fltokens(fline); + end + + % find response function associated with confidence intervals + + idresp=0; + for i=1:length(dresp) + if strcmpi(tokens{1}{ 1},dresp(i).descriptor) + idresp=i; + break; + end + end + if ~idresp + idresp=length(dresp)+1; + dresp(idresp).descriptor=tokens{1}{ 1}; + display(sprintf(' %s',dresp(idresp).descriptor)); + end + + % add confidence intervals to response functions + + if (ntokens == 14) + dresp(i).meanci (1,1)=tokens{1}{ 5}; + dresp(i).meanci (2,1)=tokens{1}{ 6}; + dresp(i).stddevci(1,1)=tokens{1}{12}; + dresp(i).stddevci(2,1)=tokens{1}{13}; + else + dresp(i).meanci (1,1)=tokens{1}{ 2}; + dresp(i).meanci (2,1)=tokens{1}{ 3}; + dresp(i).stddevci(1,1)=tokens{1}{ 4}; + dresp(i).stddevci(2,1)=tokens{1}{ 5}; + end + end + + display(sprintf(' Number of Dakota response functions=%d.',... + length(dresp))); + +end % }}} +function [dresp]=cdfs_read(fidi,dresp,fline) % {{{ +%% function to find and read the cdf's + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'Probabilities for each response function'); + if ~ischar(fline) + [fline]=findline(fidi,'Level mappings for each response function'); + if ~ischar(fline) + return + end + end + end + + display('Reading CDF''s for response functions:'); + + while ischar(fline) && ~isempty(fline) + fline=fgetl(fidi); + if ~ischar(fline) + break; + end + + % process header line of cdf + + while ischar(fline) && ~isempty(fline) + [ntokens,tokens]=fltokens(fline); + + % find response function associated with cdf + + idresp=0; + for i=1:length(dresp) + if strcmpi(tokens{1}{ 6},dresp(i).descriptor) + idresp=i; + break; + end + end + if ~idresp + idresp=length(dresp)+1; + dresp(idresp).descriptor=tokens{1}{ 6}; + display(sprintf(' %s',dresp(idresp).descriptor)); + end + + % skip column headings of cdf + + fline=fgetl(fidi); + fline=fgetl(fidi); + + % read and add cdf table to response function + + fline=fgetl(fidi); + icdf=0; + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'Cumulative Distribution Function',32) + [ntokens,tokens]=fltokens(fline); + icdf=icdf+1; + dresp(idresp).cdf(icdf,1:4)=NaN; + % in later versions of Dakota, uncalculated columns are now blank + itoken=0; + for i=1:length(fline)/19 + if ~isempty(deblank(fline((i-1)*19+1:i*19))) + itoken=itoken+1; + dresp(idresp).cdf(icdf,i)=tokens{1}{itoken}; + end + end + fline=fgetl(fidi); + end + end + end + + display(sprintf(' Number of Dakota response functions=%d.',... + length(dresp))); + +end % }}} +function [dresp]=pdfs_read(fidi,dresp,fline) % {{{ +%% function to find and read the pdf's + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'Probability Density Function (PDF) histograms for each response function'); + if ~ischar(fline) + return + end + end + + display('Reading PDF''s for response functions:'); + + while ischar(fline) && ~isempty(fline) + fline=fgetl(fidi); + if ~ischar(fline) + break; + end + + % process header line of pdf + + while ischar(fline) && ~isempty(fline) + [ntokens,tokens]=fltokens(fline); + + % find response function associated with pdf + + idresp=0; + for i=1:length(dresp) + if strcmpi(tokens{1}{ 3},dresp(i).descriptor) + idresp=i; + break; + end + end + if ~idresp + idresp=length(dresp)+1; + dresp(idresp).descriptor=tokens{1}{ 3}; + display(sprintf(' %s',dresp(idresp).descriptor)); + end + + % skip column headings of pdf + + fline=fgetl(fidi); + fline=fgetl(fidi); + + % read and add pdf table to response function + + fline=fgetl(fidi); + ipdf=0; + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'PDF for', 7) + [ntokens,tokens]=fltokens(fline); + ipdf=ipdf+1; + dresp(idresp).pdf(ipdf,1:3)=NaN; + for i=1:3 + dresp(idresp).pdf(ipdf,i)=tokens{1}{i}; + end + fline=fgetl(fidi); + end + end + end + + display(sprintf(' Number of Dakota response functions=%d.',... + length(dresp))); + +end % }}} +function [cmat]=corrmat_read(fidi,cmstr,fline) % {{{ +%% function to find and read a correlation matrix + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,cmstr); + if ~ischar(fline) + cmat=struct([]); + return + end + end + + display(['Reading ''' fline '''.']); + + cmat.title=fline; + + while ~isempty(fline) + fline=fgetl(fidi); + if ~ischar(fline) + break; + end + + % process column headings of matrix + + [ntokens,tokens]=fltokens(fline); + cmat.column=cell(1,ntokens); + cmat.row =cell(1,1); + cmat.matrix=zeros(1,ntokens); + + for i=1:ntokens + cmat.column(1,i)=cellstr(tokens{1}{i}); + end + + % process rows of matrix, reading until blank line + + nrow=0; + while 1 + fline=fgetl(fidi); + if isempty(fline) + break; + end + [ntokens,tokens]=fltokens(fline); + + % add row heading to matrix + + nrow=nrow+1; + cmat.row (nrow,1)=cellstr(tokens{1}{1}); + + % add row values to matrix + + for i=2:ntokens + cmat.matrix(nrow,i-1)=tokens{1}{i}; + end + end + end + +end % }}} +function [dresp]=mvstats_read(fidi,dresp,fline) % {{{ +%% function to find and read the MV statistics + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'MV Statistics for '); + if ~ischar(fline) + return + end + end + + display('Reading MV statistics for response functions:'); + ndresp=0; + + while ischar(fline) && ~isempty(fline) && ... + strncmpi(fline,'MV Statistics for ',18) + + % add new response function and moments + + [ntokens,tokens]=fltokens(fline); + dresp(end+1).descriptor=tokens{1}{4}; + display(sprintf(' %s',dresp(end).descriptor)); + fline=fgetl(fidi); + [ntokens,tokens]=fltokens(fline); + dresp(end ).mean =tokens{1}{5}; + fline=fgetl(fidi); + [ntokens,tokens]=fltokens(fline); + dresp(end ).stddev =tokens{1}{7}; + + % read and add importance factors to response function + + idvar=0; + fline=fgetl(fidi); + if ~ischar(fline) + break; + end + + while ischar(fline) && ~isempty(fline) && ... + strncmpi(fline,' Importance Factor for variable ',33) + [ntokens,tokens]=fltokens(fline); + idvar=idvar+1; + dresp(end).var (idvar,1)=cellstr(tokens{1}{ 5}); + dresp(end).impfac(idvar,1)= tokens{1}{ 7}; + if (ntokens >= 10) + dresp(end).sens (idvar,1)= tokens{1}{10}; + else + dresp(end).sens (idvar,1)=NaN; + end + + fline=fgetl(fidi); + end + + % if importance factors missing, skip to cdf + + if ~idvar + display(' Importance Factors not available.'); + dresp(end).var ={}; + dresp(end).impfac=[]; + dresp(end).sens =[]; + while ischar(fline) && ... + ~strncmpi(fline,'Cumulative Distribution Function',32) && ... + ~strncmpi(fline,'MV Statistics for ',18) && ... + ~strncmp (fline,'-',1) + fline=fgetl(fidi); + end + end + + % process header line of cdf + + icdf=0; + + while ischar(fline) && ~isempty(fline) && ... + strncmpi(fline,'Cumulative Distribution Function',32) + [ntokens,tokens]=fltokens(fline); + + % find response function associated with cdf + + idresp=0; + for i=1:length(dresp) + if strcmpi(tokens{1}{ 6},dresp(i).descriptor) + idresp=i; + break; + end + end + if ~idresp + idresp=length(dresp)+1; + dresp(idresp).descriptor=tokens{1}{ 6}; + display(sprintf(' %s',dresp(idresp).descriptor)); + end + + % skip column headings of cdf + + fline=fgetl(fidi); + fline=fgetl(fidi); + + % read and add cdf table to response function + + fline=fgetl(fidi); + while ~isempty(fline) && ... + ~strncmpi(fline,'MV Statistics for ',18) && ... + ~strncmp (fline,'-',1) + [ntokens,tokens]=fltokens(fline); + icdf=icdf+1; + dresp(idresp).cdf(icdf,1)=tokens{1}{1}; + dresp(idresp).cdf(icdf,2)=tokens{1}{2}; + if (ntokens == 4) + dresp(idresp).cdf(icdf,3)=tokens{1}{3}; + dresp(idresp).cdf(icdf,4)=tokens{1}{4}; + else + dresp(idresp).cdf(icdf,3)=NaN; + dresp(idresp).cdf(icdf,4)=NaN; + end + fline=fgetl(fidi); + end + end + + % if cdf missing, skip to end of response function + + if ~icdf + display(' Cumulative Distribution Function not available.'); + dresp(ndresp).cdf=[]; + while ischar(fline) && ... + ~strncmpi(fline,'MV Statistics for ',18) && ... + ~strncmp (fline,'-',1) + fline=fgetl(fidi); + end + end + + end + + display(sprintf(' Number of Dakota response functions=%d.',... + length(dresp))); + +end % }}} +function [dresp]=best_read(fidi,dresp,fline) % {{{ +%% function to find and read the best evaluation + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'<<<<< Best '); + if ~ischar(fline) + return + end + end + + if isempty(dresp) + dresp(end+1).best=[]; + end + display('Reading values for best function evaluation:'); + + while ischar(fline) && ~isempty(fline) && ... + strncmpi(fline,'<<<<< Best ',11) + [ntokens,tokens]=fltokens(fline); + + % read and add best parameter(s) + + if strncmpi(cellstr(tokens{1}{3}),'parameter', 9) + display([' ' deblank(fline)]); + + fline=fgetl(fidi); + dresp.best.param =[]; + dresp.best.descriptor={}; + + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'<<<<< Best ',11) + [ntokens,tokens]=fltokens(fline); + dresp.best.param (end+1,1)= tokens{1}{1}; + dresp.best.descriptor(end+1,1)=cellstr(tokens{1}{2}); + fline=fgetl(fidi); + end + + % read and add best objective function(s) + + elseif strncmpi(cellstr(tokens{1}{3}),'objective', 9) && ... + strncmpi(cellstr(tokens{1}{4}),'function' , 8) + display([' ' deblank(fline)]); + + fline=fgetl(fidi); + dresp.best.of=[]; + + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'<<<<< Best ',11) + [ntokens,tokens]=fltokens(fline); + dresp.best.of(end+1,1)= tokens{1}{1}; + fline=fgetl(fidi); + end + + % read and add best residual norms + + elseif strncmpi(cellstr(tokens{1}{3}),'residual', 8) && ... + strncmpi(cellstr(tokens{1}{4}),'norm' , 4) + display([' ' deblank(fline)]); + dresp.best.norm = tokens{1}{ 6}; + dresp.best.hnormsq= tokens{1}{11}; + + fline=fgetl(fidi); + + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'<<<<< Best ',11) + fline=fgetl(fidi); + end + + % read and add best residual term(s) + + elseif strncmpi(cellstr(tokens{1}{3}),'residual', 8) && ... + strncmpi(cellstr(tokens{1}{4}),'term' , 4) + display([' ' deblank(fline)]); + + fline=fgetl(fidi); + dresp.best.res=[]; + + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'<<<<< Best ',11) + [ntokens,tokens]=fltokens(fline); + dresp.best.res(end+1,1)= tokens{1}{1}; + fline=fgetl(fidi); + end + + % read and add best constraint value(s) + + elseif strncmpi(cellstr(tokens{1}{3}),'constraint',10) && ... + strncmpi(cellstr(tokens{1}{4}),'value' , 5) + display([' ' deblank(fline)]); + + fline=fgetl(fidi); + dresp.best.nc=[]; + + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'<<<<< Best ',11) + [ntokens,tokens]=fltokens(fline); + dresp.best.nc(end+1,1)= tokens{1}{1}; + fline=fgetl(fidi); + end + + % read and add best data captured + + elseif strncmpi(cellstr(tokens{1}{3}),'data' , 4) && ... + strncmpi(cellstr(tokens{1}{4}),'captured', 8) + display([' ' deblank(fline)]); + dresp.best.eval= tokens{1}{8}; + + fline=fgetl(fidi); + + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'<<<<< Best ',11) + fline=fgetl(fidi); + end + + % read until next best or blank or end + + else + display([' ' deblank(fline) ' (ignored)']); + + fline=fgetl(fidi); + + while ischar(fline) && ~isempty(fline) && ... + ~strncmpi(fline,'<<<<< Best ',11) + fline=fgetl(fidi); + end + end + end + +end % }}} +function [dresp]=vum_read(fidi,dresp,fline) % {{{ +%% function to find and read the volumetric uniformity measures + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + [fline]=findline(fidi,'The following lists volumetric uniformity measures'); + if ~ischar(fline) + return + end + end + + if isempty(dresp) + dresp(end+1).vum=[]; + end + display('Reading measures for volumetric uniformity.'); + + fline=fgetl(fidi); + fline=fgetl(fidi); + + while ischar(fline) && ~isempty(fline) + [ntokens,tokens]=fltokens(fline); + switch lower(tokens{1}{1}) + case 'chi' + dresp.vum.chi=tokens{1}{4}; + case 'd' + dresp.vum.d =tokens{1}{4}; + case 'h' + dresp.vum.h =tokens{1}{4}; + case 'tau' + dresp.vum.tau=tokens{1}{4}; + end + fline=fgetl(fidi); + end + +end % }}} +function [method]=itcomp_read(fidi,fline) % {{{ +%% function to find and read the iterator completion + + if ~exist('fline','var') || isempty(fline) || ~ischar(fline) + while 1 + [fline]=findline(fidi,'<<<<< Iterator '); + if ~ischar(fline) + return + end + if (length(fline) > 26) && ... + ~isempty(strfind(fline(16:end),' completed.')) + break + end + end + end [ntokens,tokens]=fltokens(fline); method=tokens{1}{3}; - display(sprintf('Dakota methodName=''%s''.',method)); -end - -dresp=struct([]); -scm =struct([]); -pcm =struct([]); -srcm=struct([]); -prcm=struct([]); - -%% loop through the file to find the function evaluation summary - -fline=''; -[nfeval]=nfeval_read(fidi,fline); -fline=fgetl(fidi); - -%% process each results section based on content of the file - -while ischar(fline) -% ipos=ftell(fidi); - if isempty(fline) - elseif strncmp(fline,'<<<<< Function evaluation summary',33) - [nfeval]=nfeval_read(fidi,fline); - elseif strncmp(fline,'Statistics based on ',20) - [nsamp]=nsamp_read(fidi,fline); - elseif strncmp(fline,'Moments for each response function',34) - [dresp]=moments_read(fidi,dresp,fline); - elseif strncmp(fline,'Moment-based statistics for each response function',50) - [dresp]=mbstats_read(fidi,dresp,fline); - elseif strncmp(fline,'95% confidence intervals for each response function',51) - [dresp]=cis_read(fidi,dresp,fline); - elseif strncmp(fline,'Probabilities for each response function',40) || ... - strncmp(fline,'Level mappings for each response function',41) - [dresp]=cdfs_read(fidi,dresp,fline); - elseif strncmp(fline,'Probability Density Function (PDF) histograms for each response function',72) - [dresp]=pdfs_read(fidi,dresp,fline); - elseif strncmp(fline,'Simple Correlation Matrix',25) - [scm]=corrmat_read(fidi,'Simple Correlation Matrix',fline); - elseif strncmp(fline,'Partial Correlation Matrix',26) - [pcm]=corrmat_read(fidi,'Partial Correlation Matrix',fline); - elseif strncmp(fline,'Simple Rank Correlation Matrix',30) - [srcm]=corrmat_read(fidi,'Simple Rank Correlation Matrix',fline); - elseif strncmp(fline,'Partial Rank Correlation Matrix',31) - [prcm]=corrmat_read(fidi,'Partial Rank Correlation Matrix',fline); - elseif strncmp(fline,'MV Statistics for ',18) - [dresp]=mvstats_read(fidi,dresp,fline); - elseif strncmp(fline,'<<<<< Best ',11) - [dresp]=best_read(fidi,dresp,fline); - elseif strncmp(fline,'The following lists volumetric uniformity measures',50) - [dresp]=vum_read(fidi,dresp,fline); - elseif strncmp(fline,'<<<<< Iterator ',15) && ... - (length(fline) > 26) && ... - ~isempty(strfind(fline(16:end),' completed.')) - [method]=itcomp_read(fidi,fline); - elseif strncmp(fline,'-----',5) - else - display(['Unexpected line: ' deblank(fline)]); - end - fline=fgetl(fidi); -% fseek(fidi,ipos,'bof'); -end - -%% loop through the file to verify the end - -% [fline]=findline(fidi,'<<<<< Single Method Strategy completed'); -% if ~ischar(fline) -% return -% end -display('End of file successfully reached.'); -fclose(fidi); - -end - -%% function to parse the dakota tabular output file - -function [dresp]=dak_tab_out(fidi,fline) - -display('Reading Dakota tabular output file.'); - -% process column headings of matrix (skipping eval_id) - -[ntokens,tokens]=fltokens(fline); - -% New file DAKOTA versions>6 -if strncmpi(fline,'%eval_id interface',18) - offset=2; -else %DAKOTA versions<6 - offset=1; -end -desc=cell (1,ntokens-offset); -data=zeros(1,ntokens-offset); - -for i=1:ntokens-offset - desc(1,i)=cellstr(tokens{1}{i+offset}); -end -display(sprintf('Number of columns (Dakota V+R)=%d.',ntokens-2)); - -% process rows of matrix - -nrow=0; -while 1 - fline=fgetl(fidi); - if ~ischar(fline) || isempty(fline) - break; - end - [ntokens,tokens]=fltokens(fline); - -% add row values to matrix (skipping eval_id) - - nrow=nrow+1; - for i=1:ntokens-offset - data(nrow,i)=tokens{1}{i+offset}; - end -end -display(sprintf('Number of rows (Dakota func evals)=%d.',nrow)); - -% calculate statistics - -% since normfit doesn't have a dim argument, and matlab isvector is true -% for a 1xn matrix, handle the case of one row explicitly -if (size(data,1) > 1) - %dmean =mean (data); - %dstddev=std (data,0); - [dmean,dstddev,dmeanci,dstddevci]=... - normfit_issm(data,0.05); -else - dmean =zeros(1,size(data,2)); - dstddev =zeros(1,size(data,2)); - dmeanci =zeros(2,size(data,2)); - dstddevci=zeros(2,size(data,2)); - for i=1:size(data,2) - [dmean(1,i),dstddev(1,i),dmeanci(:,i),dstddevci(:,i)]=... - normfit_issm(data(:,i),0.05); - end -end - -dmin =min (data,[],1); -dquart1=prctile_issm(data,25,1); -dmedian=median (data,1); -dquart3=prctile_issm(data,75,1); -dmax =max (data,[],1); -dmin95=prctile_issm(data,5,1); -dmax95=prctile_issm(data,95,1); - -% same as Dakota scm, Excel correl -dcorrel=corrcoef(data); - -% divide the data into structures for consistency - -for i=1:length(desc) - dresp(i).descriptor=char(desc(i)); - dresp(i).sample =data(:,i); - dresp(i).mean =dmean(i); - dresp(i).stddev =dstddev(i); - dresp(i).meanci =dmeanci(:,i); - dresp(i).stddevci =dstddevci(:,i); - dresp(i).min =dmin(i); - dresp(i).quart1 =dquart1(i); - dresp(i).median =dmedian(i); - dresp(i).quart3 =dquart3(i); - dresp(i).max =dmax(i); - dresp(i).dmin95 =dmin95(i); - dresp(i).dmax95 =dmax95(i); -end - -% draw box plot - -% figure -% subplot(2,1,1) -% plot_boxplot(dresp); - -% draw normal probability plot - -% subplot(2,1,2) -% plot_normplot(dresp); - -end - -%% function to find and read the number of function evaluations - -function [nfeval]=nfeval_read(fidi,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,'<<<<< Function evaluation summary'); - if ~ischar(fline) - return - end -end - -[ntokens,tokens]=fltokens(fline); -nfeval=tokens{1}{5}; -display(sprintf(' Dakota function evaluations=%d.',nfeval)); - -end - -%% function to find and read the number of samples - -function [nsamp]=nsamp_read(fidi,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,'Statistics based on '); - if ~ischar(fline) - return - end -end - -[ntokens,tokens]=fltokens(fline); -nsamp=tokens{1}{4}; -display(sprintf(' Dakota samples=%d.',nsamp)); - -end - -%% function to find and read the moments - -function [dresp]=moments_read(fidi,dresp,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,'Moments for each response function'); - if ~ischar(fline) - return - end -end - -display('Reading moments for response functions:'); - -while 1 - fline=fgetl(fidi); - if isempty(fline) - break; - end - [ntokens,tokens]=fltokens(fline); - -% add new response function and moments - - dresp(end+1).descriptor=tokens{1}{ 1}; - display(sprintf(' %s',dresp(end).descriptor)); - dresp(end ).mean =tokens{1}{ 4}; - dresp(end ).stddev =tokens{1}{ 8}; - dresp(end ).coefvar =tokens{1}{13}; -end - -display(sprintf(' Number of Dakota response functions=%d.',... - length(dresp))); - -end - -%% function to find and read the moment-based statistics - -function [dresp]=mbstats_read(fidi,dresp,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,'Moment-based statistics for each response function'); - if ~ischar(fline) - return - end -end - -display('Reading moment-based statistics for response functions:'); - -% skip column headings of moment-based statistics - - fline=fgetl(fidi); - -while 1 - fline=fgetl(fidi); - if isempty(fline) - break; - end - [ntokens,tokens]=fltokens(fline); - -% add new response function and moment-based statistics - - dresp(end+1).descriptor=tokens{1}{ 1}; - display(sprintf(' %s',dresp(end).descriptor)); - dresp(end ).mean =tokens{1}{ 2}; - dresp(end ).stddev =tokens{1}{ 3}; - dresp(end ).skewness =tokens{1}{ 4}; - dresp(end ).kurtosis =tokens{1}{ 5}; -end - -display(sprintf(' Number of Dakota response functions=%d.',... - length(dresp))); - -end - -%% function to find and read the confidence intervals - -function [dresp]=cis_read(fidi,dresp,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,... - '95% confidence intervals for each response function'); - if ~ischar(fline) - return - end -end - -display('Reading 95% confidence intervals for response functions:'); - -while 1 - fline=fgetl(fidi); - if isempty(fline) - break; - end - [ntokens,tokens]=fltokens(fline); - -% check for column headings in Dakota 5.2 - - if (ntokens == 4) - fline=fgetl(fidi); - if isempty(fline) - break; - end - [ntokens,tokens]=fltokens(fline); - end - -% find response function associated with confidence intervals - - idresp=0; - for i=1:length(dresp) - if strcmpi(tokens{1}{ 1},dresp(i).descriptor) - idresp=i; - break; - end - end - if ~idresp - idresp=length(dresp)+1; - dresp(idresp).descriptor=tokens{1}{ 1}; - display(sprintf(' %s',dresp(idresp).descriptor)); - end - -% add confidence intervals to response functions - - if (ntokens == 14) - dresp(i).meanci (1,1)=tokens{1}{ 5}; - dresp(i).meanci (2,1)=tokens{1}{ 6}; - dresp(i).stddevci(1,1)=tokens{1}{12}; - dresp(i).stddevci(2,1)=tokens{1}{13}; - else - dresp(i).meanci (1,1)=tokens{1}{ 2}; - dresp(i).meanci (2,1)=tokens{1}{ 3}; - dresp(i).stddevci(1,1)=tokens{1}{ 4}; - dresp(i).stddevci(2,1)=tokens{1}{ 5}; - end -end - -display(sprintf(' Number of Dakota response functions=%d.',... - length(dresp))); - -end - -%% function to find and read the cdf's - -function [dresp]=cdfs_read(fidi,dresp,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,'Probabilities for each response function'); - if ~ischar(fline) - [fline]=findline(fidi,'Level mappings for each response function'); - if ~ischar(fline) - return - end - end -end - -display('Reading CDF''s for response functions:'); - -while ischar(fline) && ~isempty(fline) - fline=fgetl(fidi); - if ~ischar(fline) - break; - end - -% process header line of cdf - - while ischar(fline) && ~isempty(fline) - [ntokens,tokens]=fltokens(fline); - -% find response function associated with cdf - - idresp=0; - for i=1:length(dresp) - if strcmpi(tokens{1}{ 6},dresp(i).descriptor) - idresp=i; - break; - end - end - if ~idresp - idresp=length(dresp)+1; - dresp(idresp).descriptor=tokens{1}{ 6}; - display(sprintf(' %s',dresp(idresp).descriptor)); - end - -% skip column headings of cdf - - fline=fgetl(fidi); - fline=fgetl(fidi); - -% read and add cdf table to response function - - fline=fgetl(fidi); - icdf=0; - while ischar(fline) && ~isempty(fline) && ... - ~strncmpi(fline,'Cumulative Distribution Function',32) - [ntokens,tokens]=fltokens(fline); - icdf=icdf+1; - dresp(idresp).cdf(icdf,1:4)=NaN; -% in later versions of Dakota, uncalculated columns are now blank - itoken=0; - for i=1:length(fline)/19 - if ~isempty(deblank(fline((i-1)*19+1:i*19))) - itoken=itoken+1; - dresp(idresp).cdf(icdf,i)=tokens{1}{itoken}; - end - end - fline=fgetl(fidi); - end - end -end - -display(sprintf(' Number of Dakota response functions=%d.',... - length(dresp))); - -end - -%% function to find and read the pdf's - -function [dresp]=pdfs_read(fidi,dresp,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,'Probability Density Function (PDF) histograms for each response function'); - if ~ischar(fline) - return - end -end - -display('Reading PDF''s for response functions:'); - -while ischar(fline) && ~isempty(fline) - fline=fgetl(fidi); - if ~ischar(fline) - break; - end - -% process header line of pdf - - while ischar(fline) && ~isempty(fline) - [ntokens,tokens]=fltokens(fline); - -% find response function associated with pdf - - idresp=0; - for i=1:length(dresp) - if strcmpi(tokens{1}{ 3},dresp(i).descriptor) - idresp=i; - break; - end - end - if ~idresp - idresp=length(dresp)+1; - dresp(idresp).descriptor=tokens{1}{ 3}; - display(sprintf(' %s',dresp(idresp).descriptor)); - end - -% skip column headings of pdf - - fline=fgetl(fidi); - fline=fgetl(fidi); - -% read and add pdf table to response function - - fline=fgetl(fidi); - ipdf=0; - while ischar(fline) && ~isempty(fline) && ... - ~strncmpi(fline,'PDF for', 7) - [ntokens,tokens]=fltokens(fline); - ipdf=ipdf+1; - dresp(idresp).pdf(ipdf,1:3)=NaN; - for i=1:3 - dresp(idresp).pdf(ipdf,i)=tokens{1}{i}; - end - fline=fgetl(fidi); - end - end -end - -display(sprintf(' Number of Dakota response functions=%d.',... - length(dresp))); - -end - -%% function to find and read a correlation matrix - -function [cmat]=corrmat_read(fidi,cmstr,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,cmstr); - if ~ischar(fline) - cmat=struct([]); - return - end -end - -display(['Reading ''' fline '''.']); - -cmat.title=fline; - -while ~isempty(fline) - fline=fgetl(fidi); - if ~ischar(fline) - break; - end - -% process column headings of matrix - - [ntokens,tokens]=fltokens(fline); - cmat.column=cell(1,ntokens); - cmat.row =cell(1,1); - cmat.matrix=zeros(1,ntokens); - - for i=1:ntokens - cmat.column(1,i)=cellstr(tokens{1}{i}); - end - -% process rows of matrix, reading until blank line - - nrow=0; - while 1 - fline=fgetl(fidi); - if isempty(fline) - break; - end - [ntokens,tokens]=fltokens(fline); - -% add row heading to matrix - - nrow=nrow+1; - cmat.row (nrow,1)=cellstr(tokens{1}{1}); - -% add row values to matrix - - for i=2:ntokens - cmat.matrix(nrow,i-1)=tokens{1}{i}; - end - end -end - -end - -%% function to find and read the MV statistics - -function [dresp]=mvstats_read(fidi,dresp,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,'MV Statistics for '); - if ~ischar(fline) - return - end -end - -display('Reading MV statistics for response functions:'); -ndresp=0; - -while ischar(fline) && ~isempty(fline) && ... - strncmpi(fline,'MV Statistics for ',18) - -% add new response function and moments - - [ntokens,tokens]=fltokens(fline); - dresp(end+1).descriptor=tokens{1}{4}; - display(sprintf(' %s',dresp(end).descriptor)); - fline=fgetl(fidi); - [ntokens,tokens]=fltokens(fline); - dresp(end ).mean =tokens{1}{5}; - fline=fgetl(fidi); - [ntokens,tokens]=fltokens(fline); - dresp(end ).stddev =tokens{1}{7}; - -% read and add importance factors to response function - - idvar=0; - fline=fgetl(fidi); - if ~ischar(fline) - break; - end - - while ischar(fline) && ~isempty(fline) && ... - strncmpi(fline,' Importance Factor for variable ',33) - [ntokens,tokens]=fltokens(fline); - idvar=idvar+1; - dresp(end).var (idvar,1)=cellstr(tokens{1}{ 5}); - dresp(end).impfac(idvar,1)= tokens{1}{ 7}; - if (ntokens >= 10) - dresp(end).sens (idvar,1)= tokens{1}{10}; - else - dresp(end).sens (idvar,1)=NaN; - end - - fline=fgetl(fidi); - end - -% if importance factors missing, skip to cdf - - if ~idvar - display(' Importance Factors not available.'); - dresp(end).var ={}; - dresp(end).impfac=[]; - dresp(end).sens =[]; - while ischar(fline) && ... - ~strncmpi(fline,'Cumulative Distribution Function',32) && ... - ~strncmpi(fline,'MV Statistics for ',18) && ... - ~strncmp (fline,'-',1) - fline=fgetl(fidi); - end - end - -% process header line of cdf - - icdf=0; - - while ischar(fline) && ~isempty(fline) && ... - strncmpi(fline,'Cumulative Distribution Function',32) - [ntokens,tokens]=fltokens(fline); - -% find response function associated with cdf - - idresp=0; - for i=1:length(dresp) - if strcmpi(tokens{1}{ 6},dresp(i).descriptor) - idresp=i; - break; - end - end - if ~idresp - idresp=length(dresp)+1; - dresp(idresp).descriptor=tokens{1}{ 6}; - display(sprintf(' %s',dresp(idresp).descriptor)); - end - -% skip column headings of cdf - - fline=fgetl(fidi); - fline=fgetl(fidi); - -% read and add cdf table to response function - - fline=fgetl(fidi); - while ~isempty(fline) && ... - ~strncmpi(fline,'MV Statistics for ',18) && ... - ~strncmp (fline,'-',1) - [ntokens,tokens]=fltokens(fline); - icdf=icdf+1; - dresp(idresp).cdf(icdf,1)=tokens{1}{1}; - dresp(idresp).cdf(icdf,2)=tokens{1}{2}; - if (ntokens == 4) - dresp(idresp).cdf(icdf,3)=tokens{1}{3}; - dresp(idresp).cdf(icdf,4)=tokens{1}{4}; - else - dresp(idresp).cdf(icdf,3)=NaN; - dresp(idresp).cdf(icdf,4)=NaN; - end - fline=fgetl(fidi); - end - end - -% if cdf missing, skip to end of response function - - if ~icdf - display(' Cumulative Distribution Function not available.'); - dresp(ndresp).cdf=[]; - while ischar(fline) && ... - ~strncmpi(fline,'MV Statistics for ',18) && ... - ~strncmp (fline,'-',1) - fline=fgetl(fidi); - end - end - -end - -display(sprintf(' Number of Dakota response functions=%d.',... - length(dresp))); - -end - -%% function to find and read the best evaluation - -function [dresp]=best_read(fidi,dresp,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,'<<<<< Best '); - if ~ischar(fline) - return - end -end - -if isempty(dresp) - dresp(end+1).best=[]; -end -display('Reading values for best function evaluation:'); - -while ischar(fline) && ~isempty(fline) && ... - strncmpi(fline,'<<<<< Best ',11) - [ntokens,tokens]=fltokens(fline); - -% read and add best parameter(s) - - if strncmpi(cellstr(tokens{1}{3}),'parameter', 9) - display([' ' deblank(fline)]); - - fline=fgetl(fidi); - dresp.best.param =[]; - dresp.best.descriptor={}; - - while ischar(fline) && ~isempty(fline) && ... - ~strncmpi(fline,'<<<<< Best ',11) - [ntokens,tokens]=fltokens(fline); - dresp.best.param (end+1,1)= tokens{1}{1}; - dresp.best.descriptor(end+1,1)=cellstr(tokens{1}{2}); - fline=fgetl(fidi); - end - -% read and add best objective function(s) - - elseif strncmpi(cellstr(tokens{1}{3}),'objective', 9) && ... - strncmpi(cellstr(tokens{1}{4}),'function' , 8) - display([' ' deblank(fline)]); - - fline=fgetl(fidi); - dresp.best.of=[]; - - while ischar(fline) && ~isempty(fline) && ... - ~strncmpi(fline,'<<<<< Best ',11) - [ntokens,tokens]=fltokens(fline); - dresp.best.of(end+1,1)= tokens{1}{1}; - fline=fgetl(fidi); - end - -% read and add best residual norms - - elseif strncmpi(cellstr(tokens{1}{3}),'residual', 8) && ... - strncmpi(cellstr(tokens{1}{4}),'norm' , 4) - display([' ' deblank(fline)]); - dresp.best.norm = tokens{1}{ 6}; - dresp.best.hnormsq= tokens{1}{11}; - - fline=fgetl(fidi); - - while ischar(fline) && ~isempty(fline) && ... - ~strncmpi(fline,'<<<<< Best ',11) - fline=fgetl(fidi); - end - -% read and add best residual term(s) - - elseif strncmpi(cellstr(tokens{1}{3}),'residual', 8) && ... - strncmpi(cellstr(tokens{1}{4}),'term' , 4) - display([' ' deblank(fline)]); - - fline=fgetl(fidi); - dresp.best.res=[]; - - while ischar(fline) && ~isempty(fline) && ... - ~strncmpi(fline,'<<<<< Best ',11) - [ntokens,tokens]=fltokens(fline); - dresp.best.res(end+1,1)= tokens{1}{1}; - fline=fgetl(fidi); - end - -% read and add best constraint value(s) - - elseif strncmpi(cellstr(tokens{1}{3}),'constraint',10) && ... - strncmpi(cellstr(tokens{1}{4}),'value' , 5) - display([' ' deblank(fline)]); - - fline=fgetl(fidi); - dresp.best.nc=[]; - - while ischar(fline) && ~isempty(fline) && ... - ~strncmpi(fline,'<<<<< Best ',11) - [ntokens,tokens]=fltokens(fline); - dresp.best.nc(end+1,1)= tokens{1}{1}; - fline=fgetl(fidi); - end - -% read and add best data captured - - elseif strncmpi(cellstr(tokens{1}{3}),'data' , 4) && ... - strncmpi(cellstr(tokens{1}{4}),'captured', 8) - display([' ' deblank(fline)]); - dresp.best.eval= tokens{1}{8}; - - fline=fgetl(fidi); - - while ischar(fline) && ~isempty(fline) && ... - ~strncmpi(fline,'<<<<< Best ',11) - fline=fgetl(fidi); - end - -% read until next best or blank or end - - else - display([' ' deblank(fline) ' (ignored)']); - - fline=fgetl(fidi); - - while ischar(fline) && ~isempty(fline) && ... - ~strncmpi(fline,'<<<<< Best ',11) - fline=fgetl(fidi); - end - end -end - -end - -%% function to find and read the volumetric uniformity measures - -function [dresp]=vum_read(fidi,dresp,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - [fline]=findline(fidi,'The following lists volumetric uniformity measures'); - if ~ischar(fline) - return - end -end - -if isempty(dresp) - dresp(end+1).vum=[]; -end -display('Reading measures for volumetric uniformity.'); - -fline=fgetl(fidi); -fline=fgetl(fidi); - -while ischar(fline) && ~isempty(fline) - [ntokens,tokens]=fltokens(fline); - switch lower(tokens{1}{1}) - case 'chi' - dresp.vum.chi=tokens{1}{4}; - case 'd' - dresp.vum.d =tokens{1}{4}; - case 'h' - dresp.vum.h =tokens{1}{4}; - case 'tau' - dresp.vum.tau=tokens{1}{4}; - end - fline=fgetl(fidi); -end - -end - -%% function to find and read the iterator completion - -function [method]=itcomp_read(fidi,fline) - -if ~exist('fline','var') || isempty(fline) || ~ischar(fline) - while 1 - [fline]=findline(fidi,'<<<<< Iterator '); - if ~ischar(fline) - return - end - if (length(fline) > 26) && ... - ~isempty(strfind(fline(16:end),' completed.')) - break - end - end -end - -[ntokens,tokens]=fltokens(fline); -method=tokens{1}{3}; -display(sprintf('Dakota iterator ''%s'' completed.',method)); - -end - + display(sprintf('Dakota iterator ''%s'' completed.',method)); + +end % }}} +function [fline]=findline(fidi,string) % {{{ %% function to find a file line starting with a specified string -function [fline]=findline(fidi,string) - -ipos=ftell(fidi); - -while 1 - fline=fgetl(fidi); - if ~ischar(fline) - break; - else - if (strncmpi(fline,string,length(string))) - return; - end - end -end - -% issue warning and reset file position - -warning('findline:str_not_found',... - 'String ''%s'' not found in file.',string); -fseek(fidi,ipos,'bof'); - -end - + ipos=ftell(fidi); + + while 1 + fline=fgetl(fidi); + if ~ischar(fline) + break; + else + if (strncmpi(fline,string,length(string))) + return; + end + end + end + + % issue warning and reset file position + + warning('findline:str_not_found',... + 'String ''%s'' not found in file.',string); + fseek(fidi,ipos,'bof'); + +end % }}} +function [ntokens,tokens]=fltokens(fline) % {{{ %% function to parse a file line into tokens -function [ntokens,tokens]=fltokens(fline) - -if ~ischar(fline) - ntokens=-1; - tokens={}; - return; -end -if isempty(fline) - ntokens=0; - tokens={}; - return; -end - -strings=textscan(fline,'%s','delimiter',' :'); -%for i=1:length(strings{1}) -% display(sprintf('i=%d; strings{1}{%d}=%s',i,i,strings{1}{i})) -%end -ntokens=0; -tokens{1}{length(strings)}=''; - -for i=1:length(strings{1}) - if isempty(strings{1}{i}) - continue - end - ntokens=ntokens+1; - inum=sscanf(strings{1}{i},'%f'); - if isempty(inum) - tokens{1}{ntokens}=strings{1}{i}; -% display(sprintf('i=%d; tokens{1}{%d}=%s',... -% i,ntokens,tokens{1}{ntokens})) - else - tokens{1}{ntokens}=inum; -% display(sprintf('i=%d; tokens{1}{%d}=%f',... -% i,ntokens,tokens{1}{ntokens})) - end -end - -end + if ~ischar(fline) + ntokens=-1; + tokens={}; + return; + end + if isempty(fline) + ntokens=0; + tokens={}; + return; + end + + strings=textscan(fline,'%s','delimiter',' :'); + %for i=1:length(strings{1}) + % display(sprintf('i=%d; strings{1}{%d}=%s',i,i,strings{1}{i})) + %end + ntokens=0; + tokens{1}{length(strings)}=''; + + for i=1:length(strings{1}) + if isempty(strings{1}{i}) + continue + end + ntokens=ntokens+1; + inum=sscanf(strings{1}{i},'%f'); + if isempty(inum) + tokens{1}{ntokens}=strings{1}{i}; + % display(sprintf('i=%d; tokens{1}{%d}=%s',... + % i,ntokens,tokens{1}{ntokens})) + else + tokens{1}{ntokens}=inum; + % display(sprintf('i=%d; tokens{1}{%d}=%f',... + % i,ntokens,tokens{1}{ntokens})) + end + end + +end % }}} Index: /issm/trunk/src/m/shp/shp2exp.m =================================================================== --- /issm/trunk/src/m/shp/shp2exp.m (revision 21728) +++ /issm/trunk/src/m/shp/shp2exp.m (revision 21729) @@ -1,48 +1,58 @@ -function Shp2Exp(expfilename,shapefilename) +function shp2exp(shpfilename,expfilename) %SHP2EXP- transform shape file to Argus .exp file % % Usage: -% Shp2Exp(expfilename,shapefilename); +% shp2exp(shpfilename,expfilename); % % Example: -% Shp2Exp('Domain.exp','Domain.shp'); +% shp2exp('Domain.shp','Domain.exp'); % % See also EXPMASTER, EXPDOC - if ~exist(shapefilename,'file'), - error(['Shapefile ' shapefilename ' does not exist']); +%check file extensions +[pathstr,name,ext] = fileparts(shpfilename); +if ~strcmp(ext,'.shp'), + error(['Shapefile ' shpfilename ' does not have an extension .shp']); +end + +[pathstr,name,ext] = fileparts(expfilename); +if ~strcmp(ext,'.exp'), + error(['Exp file ' expfilename ' does not have an extension .exp']); +end + +if ~exist(shpfilename,'file'), + error(['Shapefile ' shpfilename ' does not exist']); +end +shp=shaperead(shpfilename); + +expstruct=struct([]); +for i=1:length(shp), + if strcmpi(shp(i).Geometry,'Polygon'), + x=shp(i).X; y=shp(i).Y; + ids=find(isnan(x)); + x(ids)=[]; y(ids)=[]; + expstruct(end+1).x=x; + expstruct(end).y=y; + expstruct(end).nods=length(x); + expstruct(end).density=1; + expstruct(end).closed=1; + expstruct(end).name=num2str(shp(i).id); + elseif strcmpi(shp(i).Geometry,'Point'), + x=shp(i).X; y=shp(i).Y; + expstruct(end+1).x=x; + expstruct(end).y=y; + expstruct(end).nods=length(x); + expstruct(end).density=1; + expstruct(end).closed=0; + %exp(end).name=num2str(shp(i).id); + elseif strcmpi(shp(i).Geometry,'Line'), + x=shp(i).X; y=shp(i).Y; + expstruct(end+1).x=x; + expstruct(end).y=y; + expstruct(end).nods=length(x); + expstruct(end).density=1; + expstruct(end).closed=0; end - shp=shaperead(shapefilename); +end - expstruct=struct([]); - for i=1:length(shp), - if strcmpi(shp(i).Geometry,'Polygon'), - x=shp(i).X; y=shp(i).Y; - ids=find(isnan(x)); - x(ids)=[]; y(ids)=[]; - expstruct(end+1).x=x; - expstruct(end).y=y; - expstruct(end).nods=length(x); - expstruct(end).density=1; - expstruct(end).closed=1; - expstruct(end).name=num2str(shp(i).id); - elseif strcmpi(shp(i).Geometry,'Point'), - x=shp(i).X; y=shp(i).Y; - expstruct(end+1).x=x; - expstruct(end).y=y; - expstruct(end).nods=length(x); - expstruct(end).density=1; - expstruct(end).closed=1; - %exp(end).name=num2str(shp(i).id); - elseif strcmpi(shp(i).Geometry,'Line'), - x=shp(i).X; y=shp(i).Y; - x(end)=x(1); y(end)=y(1); - expstruct(end+1).x=x; - expstruct(end).y=y; - expstruct(end).nods=length(x); - expstruct(end).density=1; - expstruct(end).closed=1; - end - end - - expwrite(expstruct,expfilename); +expwrite(expstruct,expfilename); Index: /issm/trunk/src/m/shp/shp2exp.py =================================================================== --- /issm/trunk/src/m/shp/shp2exp.py (revision 21728) +++ /issm/trunk/src/m/shp/shp2exp.py (revision 21729) @@ -26,5 +26,5 @@ shp=shapefile.Reader(shapefilename) - expdict=dict(closed=1,density=1) + expdict=dict(density=1) x=[] @@ -33,4 +33,5 @@ geom=shp.shapes()[i].shapeType if geom==5: # polygon + expdict['closed']=1 tmpx=[p[0] for p in shp.shapes()[i].points] tmpy=[q[1] for q in shp.shapes()[i].points] @@ -38,4 +39,5 @@ y.append(tmpy) elif geom==3: # line + expdict['closed']=0 tmpx=[p[0] for p in shp.shapes()[i].points] tmpy=[q[1] for q in shp.shapes()[i].points] @@ -43,4 +45,5 @@ y.append(tmpy) elif geom==1: # point + expdict['closed']=0 x.append(shp.shapes()[i].points[0][0]) y.append(shp.shapes()[i].points[0][1]) Index: /issm/trunk/src/m/solve/WriteData.m =================================================================== --- /issm/trunk/src/m/solve/WriteData.m (revision 21728) +++ /issm/trunk/src/m/solve/WriteData.m (revision 21729) @@ -167,4 +167,48 @@ if s(1)*s(2), fwrite(fid,data','double'); %get to the "c" convention, hence the transpose + end + % }}} +elseif strcmpi(format,'CompressedMat'), % {{{ + + %Get size + s=size(data); + + if (s(1)==1 & s(2)==1 & isnan(data)), + s(1)=0; s(2)=0; + end + + %first write length of record + recordlength=4+4+8+8+1*(s(1)-1)*s(2)+8*s(2)+4+4; %2 integers (32 bits) + the matrix + code + matrix type + if recordlength>2^31; error(['field ' name ' cannot be marshalled because it is larger than 2^31 bytes!']); end + fwrite(fid,recordlength,'int'); + + %write data code and matrix type: + fwrite(fid,FormatToCode(format),'int'); + fwrite(fid,mattype,'int'); + + %write matrix size + fwrite(fid,s(1),'int'); + fwrite(fid,s(2),'int'); + + if s(1)*s(2), + + %Write offset and range + A = data(1:end-1,:); + offset = min(A(:)); + range = max(A(:)) - offset; + fwrite(fid,offset,'double'); + fwrite(fid,range,'double'); + + %Convert data to uint8 and write it + A=uint8((A-offset)/range*255); + fwrite(fid,A','uint8'); %get to the "c" convention, hence the transpose + + %Write last row as double (time) + fwrite(fid,data(end,:),'double'); + else + + %Write empty offset and range + fwrite(fid,0,'double'); + fwrite(fid,0,'double'); end % }}} @@ -258,4 +302,6 @@ elseif strcmpi(format,'StringArray'), code=9; + elseif strcmpi(format,'CompressedMat'), + code=10; else error('FormatToCode error message: data type not supported yet!'); Index: /issm/trunk/src/m/solve/WriteData.py =================================================================== --- /issm/trunk/src/m/solve/WriteData.py (revision 21728) +++ /issm/trunk/src/m/solve/WriteData.py (revision 21729) @@ -213,5 +213,5 @@ #first write length of record recordlength=4+4+8*np.product(s)+4+4; #2 integers (32 bits) + the double matrix + code + matrix type - if recordlength > 2**31 : + if recordlength > 4**31 : raise ValueError('field %s cannot be marshalled because it is larger than 4^31 bytes!' % enum) @@ -234,4 +234,74 @@ for j in xrange(s[1]): fid.write(struct.pack('d',float(data[i][j]))) #get to the "c" convention, hence the transpose + # }}} + + elif m.strcmpi(format,'CompressedMat'): # {{{ + + if isinstance(data,(bool,int,long,float)): + data=np.array([data]) + elif isinstance(data,(list,tuple)): + data=np.array(data).reshape(-1,) + if np.ndim(data) == 1: + if np.size(data): + data=data.reshape(np.size(data),) + else: + data=data.reshape(0,0) + + #Get size + s=data.shape + if np.ndim(data) == 1: + n2=1 + else: + n2=s[1] + + #if matrix = NaN, then do not write anything + if np.ndim(data)==1 and np.product(s)==1 and np.all(np.isnan(data)): + s=(0,0) + n2=0 + + #first write length of record + recordlength=4+4+8+8+1*(s[0]-1)*n2+8*n2+4+4 #2 integers (32 bits) + the matrix + code + matrix type + if recordlength > 4**31 : + raise ValueError('field %s cannot be marshalled because it is larger than 4^31 bytes!' % enum) + + fid.write(struct.pack('i',recordlength)) #2 integers (32 bits) + the matrix + code + matrix type + + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',mattype)) + + #Write offset and range + A = data[0:s[0]-1] + offsetA = A.min() + rangeA = A.max() - offsetA + + if rangeA == 0: + A = A*0 + else: + A = (A-offsetA)/rangeA*255. + + #now write matrix + if np.ndim(data) == 1: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) + fid.write(struct.pack('d',float(offsetA))) + fid.write(struct.pack('d',float(rangeA))) + for i in xrange(s[0]-1): + fid.write(struct.pack('B',int(A[i]))) + + fid.write(struct.pack('d',float(data[s[0]-1]))) #get to the "c" convention, hence the transpose + + elif np.product(s) > 0: + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('d',float(offsetA))) + fid.write(struct.pack('d',float(rangeA))) + for i in xrange(s[0]-1): + for j in xrange(s[1]): + fid.write(struct.pack('B',int(A[i][j]))) #get to the "c" convention, hence the transpose + + for j in xrange(s[1]): + fid.write(struct.pack('d',float(data[s[0]-1][j]))) + # }}} @@ -337,4 +407,6 @@ elif m.strcmpi(format,'StringArray'): code=9 + elif m.strcmpi(format,'CompressedMat'): + code=10 else: raise InputError('FormatToCode error message: data type not supported yet!') Index: /issm/trunk/src/m/solve/loadresultsslm.m =================================================================== --- /issm/trunk/src/m/solve/loadresultsslm.m (revision 21729) +++ /issm/trunk/src/m/solve/loadresultsslm.m (revision 21729) @@ -0,0 +1,4 @@ +function slm=loadresultslm(slm) + + for i=1:length(slm.icecaps), slm.icecaps{i}=loadresultsfromcluster(slm.icecaps{i});end; + slm.earth=loadresultsfromcluster(slm.earth); Index: /issm/trunk/src/m/solve/parseresultsfrombuffer.js =================================================================== --- /issm/trunk/src/m/solve/parseresultsfrombuffer.js (revision 21728) +++ /issm/trunk/src/m/solve/parseresultsfrombuffer.js (revision 21729) @@ -81,4 +81,8 @@ field=fid.fread(N*M,'double'); } + else if (type==4) { + N=fid.fread(1,'int'); + field=fid.fread(N*M,'int'); + } else throw Error(sprintf("%s%i",'ReadData error message: cannot read data of type ',type)); Index: /issm/trunk/src/m/solve/parseresultsfromdisk.m =================================================================== --- /issm/trunk/src/m/solve/parseresultsfromdisk.m (revision 21728) +++ /issm/trunk/src/m/solve/parseresultsfromdisk.m (revision 21729) @@ -154,4 +154,7 @@ N=fread(fid,1,'int'); field=transpose(fread(fid,[N M],'double')); + elseif type==4, + N=fread(fid,1,'int'); + field=transpose(fread(fid,[N M],'int')); else error(['cannot read data of type ' num2str(type) ]); Index: /issm/trunk/src/m/solve/parseresultsfromdisk.py =================================================================== --- /issm/trunk/src/m/solve/parseresultsfromdisk.py (revision 21728) +++ /issm/trunk/src/m/solve/parseresultsfromdisk.py (revision 21729) @@ -162,4 +162,10 @@ for i in xrange(M): field[i,:]=struct.unpack('%dd' % N,fid.read(N*struct.calcsize('d'))) + elif type==4: + N=struct.unpack('i',fid.read(struct.calcsize('i')))[0] +# field=transpose(fread(fid,[N M],'int')); + field=np.zeros(shape=(M,N),dtype=int) + for i in xrange(M): + field[i,:]=struct.unpack('%ii' % N,fid.read(N*struct.calcsize('i'))) else: raise TypeError("cannot read data of type %d" % type) Index: /issm/trunk/src/m/solve/solve.m =================================================================== --- /issm/trunk/src/m/solve/solve.m (revision 21728) +++ /issm/trunk/src/m/solve/solve.m (revision 21729) @@ -50,4 +50,6 @@ elseif strcmpi(solutionstring,'mc') || strcmpi(solutionstring,'Balancethickness') solutionstring = 'BalancethicknessSolution'; +elseif strcmpi(solutionstring,'mcsoft') || strcmpi(solutionstring,'BalancethicknessSoft') + solutionstring = 'BalancethicknessSoftSolution'; elseif strcmpi(solutionstring,'bv') || strcmpi(solutionstring,'Balancevelocity') solutionstring = 'BalancevelocitySolution'; @@ -115,5 +117,5 @@ marshall(md); % bin file ToolkitsFile(md.toolkits,[md.miscellaneous.name '.toolkits']); % toolkits file -BuildQueueScript(cluster,md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof,md.qmu.isdakota); % queue file +BuildQueueScript(cluster,md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof,md.qmu.isdakota,md.transient.isoceancoupling); % queue file %Upload all required files Index: /issm/trunk/src/m/solve/solve.py =================================================================== --- /issm/trunk/src/m/solve/solve.py (revision 21728) +++ /issm/trunk/src/m/solve/solve.py (revision 21729) @@ -113,5 +113,5 @@ marshall(md) # bin file md.toolkits.ToolkitsFile(md.miscellaneous.name+'.toolkits') # toolkits file - cluster.BuildQueueScript(md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof,md.qmu.isdakota) # queue file + cluster.BuildQueueScript(md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof,md.qmu.isdakota,md.transient.isoceancoupling) # queue file #Stop here if batch mode Index: /issm/trunk/src/py3/shp/shp2exp.py =================================================================== --- /issm/trunk/src/py3/shp/shp2exp.py (revision 21728) +++ /issm/trunk/src/py3/shp/shp2exp.py (revision 21729) @@ -26,5 +26,5 @@ shp=shapefile.Reader(shapefilename) - expdict=dict(closed=1,density=1) + expdict=dict(density=1) x=[] @@ -33,4 +33,5 @@ geom=shp.shapes()[i].shapeType if geom==5: # polygon + expdict['closed']=1 tmpx=[p[0] for p in shp.shapes()[i].points] tmpy=[q[1] for q in shp.shapes()[i].points] @@ -38,4 +39,5 @@ y.append(tmpy) elif geom==3: # line + expdict['closed']=0 tmpx=[p[0] for p in shp.shapes()[i].points] tmpy=[q[1] for q in shp.shapes()[i].points] @@ -43,4 +45,5 @@ y.append(tmpy) elif geom==1: # point + expdict['closed']=0 x.append(shp.shapes()[i].points[0][0]) y.append(shp.shapes()[i].points[0][1]) Index: /issm/trunk/src/wrappers/matlab/Makefile.am =================================================================== --- /issm/trunk/src/wrappers/matlab/Makefile.am (revision 21728) +++ /issm/trunk/src/wrappers/matlab/Makefile.am (revision 21729) @@ -1,3 +1,3 @@ -AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ +AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ AUTOMAKE_OPTIONS = subdir-objects @@ -115,14 +115,14 @@ # Module sources and dependencies {{{ if !WINDOWS -libISSMMatlab_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(MPILIB) $(MKLLIB) $(GSLLIB) $(PROJ4LIB) $(MATHLIB) $(MEXLIB) +libISSMMatlab_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(PROJ4LIB) $(MATHLIB) $(MEXLIB) endif if STANDALONE_LIBRARIES libISSMMatlab_la_LDFLAGS = -static -deps += $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) -endif - -if !WINDOWS -libISSMApi_la_LIBADD = $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) $(MATHLIB) $(MEXLIB) +deps += $(PETSCLIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) +endif + +if !WINDOWS +libISSMApi_la_LIBADD = $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) $(MATHLIB) $(MEXLIB) endif @@ -133,110 +133,110 @@ BamgMesher_matlab_la_SOURCES = ../BamgMesher/BamgMesher.cpp BamgMesher_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -BamgMesher_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +BamgMesher_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) BamgConvertMesh_matlab_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp BamgConvertMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -BamgConvertMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +BamgConvertMesh_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) BamgTriangulate_matlab_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp BamgTriangulate_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -BamgTriangulate_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +BamgTriangulate_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) if CHACO Chaco_matlab_la_SOURCES = ../Chaco/Chaco.cpp Chaco_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -Chaco_matlab_la_LIBADD = ${deps} $(MPILIB) $(CHACOLIB) $(GSLLIB) $(PROJ4LIB) $(PETSCLIB) +Chaco_matlab_la_LIBADD = ${deps} $(MPILIB) $(CHACOLIB) $(GSLLIB) $(PROJ4LIB) $(PETSCLIB) $(NEOPZLIB) endif ContourToMesh_matlab_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp ContourToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ContourToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) +ContourToMesh_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) ExpToLevelSet_matlab_la_SOURCES = ../ExpToLevelSet/ExpToLevelSet.cpp ExpToLevelSet_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ExpToLevelSet_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) +ExpToLevelSet_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) ContourToNodes_matlab_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp ContourToNodes_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ContourToNodes_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +ContourToNodes_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) DistanceToMaskBoundary_matlab_la_SOURCES = ../DistanceToMaskBoundary/DistanceToMaskBoundary.cpp DistanceToMaskBoundary_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -DistanceToMaskBoundary_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +DistanceToMaskBoundary_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) ElementConnectivity_matlab_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp ElementConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ElementConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +ElementConnectivity_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) InterpFromGridToMesh_matlab_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp InterpFromGridToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromGridToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) +InterpFromGridToMesh_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) InterpFromMeshToMesh2d_matlab_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp InterpFromMeshToMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMeshToMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) +InterpFromMeshToMesh2d_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) InterpFromMeshToMesh3d_matlab_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp InterpFromMeshToMesh3d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMeshToMesh3d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +InterpFromMeshToMesh3d_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) InterpFromMeshToGrid_matlab_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp InterpFromMeshToGrid_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMeshToGrid_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +InterpFromMeshToGrid_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) InterpFromMesh2d_matlab_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp InterpFromMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) +InterpFromMesh2d_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) IssmConfig_matlab_la_SOURCES = ../IssmConfig/IssmConfig.cpp IssmConfig_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -IssmConfig_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) +IssmConfig_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) ExpSimplify_matlab_la_SOURCES = ../ExpSimplify/ExpSimplify.cpp ExpSimplify_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ExpSimplify_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +ExpSimplify_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) Kriging_matlab_la_SOURCES = ../Kriging/Kriging.cpp Kriging_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -Kriging_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) +Kriging_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) MeshPartition_matlab_la_SOURCES = ../MeshPartition/MeshPartition.cpp MeshPartition_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -MeshPartition_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(METISLIB) $(GSLLIB) $(PROJ4LIB) +MeshPartition_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(METISLIB) $(GSLLIB) $(PROJ4LIB) M1qn3_matlab_la_SOURCES = ../M1qn3/M1qn3.cpp M1qn3_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -M1qn3_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(METISLIB) $(M1QN3LIB) $(GSLLIB) $(PROJ4LIB) +M1qn3_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(METISLIB) $(M1QN3LIB) $(GSLLIB) $(PROJ4LIB) MeshProfileIntersection_matlab_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp MeshProfileIntersection_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -MeshProfileIntersection_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +MeshProfileIntersection_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) NodeConnectivity_matlab_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp NodeConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -NodeConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +NodeConnectivity_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) PointCloudFindNeighbors_matlab_la_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp PointCloudFindNeighbors_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -PointCloudFindNeighbors_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) +PointCloudFindNeighbors_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) PropagateFlagsFromConnectivity_matlab_la_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp PropagateFlagsFromConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -PropagateFlagsFromConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +PropagateFlagsFromConnectivity_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) Scotch_matlab_la_SOURCES = ../Scotch/Scotch.cpp Scotch_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -Scotch_matlab_la_LIBADD = ${deps} $(SCOTCHLIB) $(PETSCLIB) $(MPILIB) $(BLASLAPACKLIB) +Scotch_matlab_la_LIBADD = ${deps} $(SCOTCHLIB) $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(BLASLAPACKLIB) ShpRead_matlab_la_SOURCES = ../ShpRead/ShpRead.cpp ShpRead_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ShpRead_matlab_la_LIBADD = ${deps} $(SHAPELIBLIB) $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) +ShpRead_matlab_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) TriMesh_matlab_la_SOURCES = ../TriMesh/TriMesh.cpp TriMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -TriMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(TRIANGLELIB) $(GSLLIB) $(PROJ4LIB) +TriMesh_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(TRIANGLELIB) $(GSLLIB) $(PROJ4LIB) TriMeshProcessRifts_matlab_la_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp TriMeshProcessRifts_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -TriMeshProcessRifts_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(GSLLIB) $(PROJ4LIB) -#}}} +TriMeshProcessRifts_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +#}}} Index: /issm/trunk/src/wrappers/matlab/io/WriteMatlabData.cpp =================================================================== --- /issm/trunk/src/wrappers/matlab/io/WriteMatlabData.cpp (revision 21728) +++ /issm/trunk/src/wrappers/matlab/io/WriteMatlabData.cpp (revision 21729) @@ -192,5 +192,5 @@ int i; mxArray *dataref = NULL; - const int numfields = 17; + const int numfields = 16; const char *fnames[numfields]; mwSize ndim = 2; @@ -202,5 +202,4 @@ fnames[i++] = "Edges"; fnames[i++] = "Triangles"; - fnames[i++] = "Quadrilaterals"; fnames[i++] = "IssmEdges"; fnames[i++] = "IssmSegments"; @@ -226,5 +225,4 @@ i++; SetStructureField(dataref,"Edges", bamgmesh->EdgesSize[0],bamgmesh->EdgesSize[1], bamgmesh->Edges); i++; SetStructureField(dataref,"Triangles", bamgmesh->TrianglesSize[0],bamgmesh->TrianglesSize[1], bamgmesh->Triangles); - i++; SetStructureField(dataref,"Quadrilaterals",bamgmesh->QuadrilateralsSize[0], bamgmesh->QuadrilateralsSize[1],bamgmesh->Quadrilaterals); i++; SetStructureField(dataref,"IssmEdges", bamgmesh->IssmEdgesSize[0],bamgmesh->IssmEdgesSize[1], bamgmesh->IssmEdges); i++; SetStructureField(dataref,"IssmSegments",bamgmesh->IssmSegmentsSize[0], bamgmesh->IssmSegmentsSize[1],bamgmesh->IssmSegments); Index: /issm/trunk/src/wrappers/python/io/WritePythonData.cpp =================================================================== --- /issm/trunk/src/wrappers/python/io/WritePythonData.cpp (revision 21728) +++ /issm/trunk/src/wrappers/python/io/WritePythonData.cpp (revision 21729) @@ -151,5 +151,4 @@ PyDict_SetItemString(dict,"Edges",PyArrayFromCopiedData(bamgmesh->EdgesSize,bamgmesh->Edges)); PyDict_SetItemString(dict,"Triangles",PyArrayFromCopiedData(bamgmesh->TrianglesSize,bamgmesh->Triangles)); - PyDict_SetItemString(dict,"Quadrilaterals",PyArrayFromCopiedData(bamgmesh->QuadrilateralsSize,bamgmesh->Quadrilaterals)); PyDict_SetItemString(dict,"IssmEdges",PyArrayFromCopiedData(bamgmesh->IssmEdgesSize,bamgmesh->IssmEdges)); PyDict_SetItemString(dict,"IssmSegments",PyArrayFromCopiedData(bamgmesh->IssmSegmentsSize,bamgmesh->IssmSegments)); Index: /issm/trunk/test/Exp/Strip.exp =================================================================== --- /issm/trunk/test/Exp/Strip.exp (revision 21729) +++ /issm/trunk/test/Exp/Strip.exp (revision 21729) @@ -0,0 +1,10 @@ +## Name:domainoutline +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +0 0 +100000 0 +100000 20000 +0 20000 +0 0 Index: /issm/trunk/test/NightlyRun/IdToName.py =================================================================== --- /issm/trunk/test/NightlyRun/IdToName.py (revision 21728) +++ /issm/trunk/test/NightlyRun/IdToName.py (revision 21729) @@ -12,5 +12,5 @@ file_text = infile.readlines() - string='#Test Name:'; + string='#Test Name:' name=file_text[0] name=name[len(string)+1:-1] Index: /issm/trunk/test/NightlyRun/runme.py =================================================================== --- /issm/trunk/test/NightlyRun/runme.py (revision 21728) +++ /issm/trunk/test/NightlyRun/runme.py (revision 21729) @@ -1,9 +1,9 @@ #!/usr/bin/env python import os -import glob -import socket -import numpy -import sys -import traceback +import numpy as np +from traceback import format_exc +from sys import float_info +from glob import glob +from socket import gethostname def runme(id=None,exclude=None,benchmark='nightly',procedure='check',output='none',rank=1,numprocs=1): @@ -34,5 +34,5 @@ Usage: - runme(varargin); + runme(varargin) Examples: @@ -44,6 +44,4 @@ from parallelrange import parallelrange from IdToName import IdToName - from MatlabFuncs import strcmpi - from MatlabFuncs import ismember from arch import archread from arch import archwrite @@ -55,16 +53,16 @@ #Process options #GET benchmark {{{ - if not ismember(benchmark,['all','nightly','ismip','eismint','thermal','mesh','validation','tranforcing','adolc','slr']): - print "runme warning: benchmark '%s' not supported, defaulting to test 'nightly'." % benchmark + if not benchmark in ['all','nightly','ismip','eismint','thermal','mesh','validation','tranforcing','adolc','slr','referential']: + print("runme warning: benchmark '{}' not supported, defaulting to test 'nightly'.".format(benchmark)) benchmark='nightly' # }}} #GET procedure {{{ - if not ismember(procedure,['check','update']): - print "runme warning: procedure '%s' not supported, defaulting to test 'check'." % procedure + if not procedure in ['check','update']: + print("runme warning: procedure '{}' not supported, defaulting to test 'check'.".format(procedure)) procedure='check' # }}} #GET output {{{ - if not ismember(output,['nightly','none']): - print "runme warning: output '%s' not supported, defaulting to test 'none'." % output + if not output in ['nightly','none']: + print("runme warning: output '{}' not supported, defaulting to test 'none'.".format(output)) output='none' # }}} @@ -74,5 +72,5 @@ # }}} #GET ids {{{ - flist=glob.glob('test*.py') #File name must start with 'test' and must end by '.py' and must be different than 'test.py' + flist=glob('test*.py') #File name must start with 'test' and must end by '.py' and must be different than 'test.py' list_ids=[int(file[4:-3]) for file in flist if not file == 'test.py'] #Keep test id only (skip 'test' and '.py') #print 'list_ids =',list_ids @@ -81,5 +79,5 @@ list_ids=list_ids[i1:i2+1] #print 'list_ids after parallelrange =',list_ids - + if id: if isinstance(id,list): @@ -90,5 +88,6 @@ else: test_ids=set(list_ids) - #print 'test_ids after list =',test_ids + + #print 'test_ids after list =',test_ids # }}} #GET exclude {{{ @@ -102,23 +101,23 @@ # }}} #Process Ids according to benchmarks {{{ - if strcmpi(benchmark,'nightly'): + if benchmark=='nightly': test_ids=test_ids.intersection(set(range(1,1000))) - elif strcmpi(benchmark,'validation'): + elif benchmark=='validation': test_ids=test_ids.intersection(set(range(1001,2000))) - elif strcmpi(benchmark,'ismip'): + elif benchmark=='ismip': test_ids=test_ids.intersection(set(range(1101,1200))) - elif strcmpi(benchmark,'eismint'): + elif benchmark=='eismint': test_ids=test_ids.intersection(set(range(1201,1300))) - elif strcmpi(benchmark,'thermal'): + elif benchmark=='thermal': test_ids=test_ids.intersection(set(range(1301,1400))) - elif strcmpi(benchmark,'mesh'): + elif benchmark=='mesh': test_ids=test_ids.intersection(set(range(1401,1500))) - elif strcmpi(benchmark,'tranforcing'): + elif benchmark=='tranforcing': test_ids=test_ids.intersection(set(range(1501,1503))) - elif strcmpi(benchmark,'referential'): + elif benchmark=='referential': test_ids=test_ids.intersection(set(range(1601,1603))) - elif strcmpi(benchmark,'slr'): + elif benchmark=='slr': test_ids=test_ids.intersection(set(range(2001,2500))) - elif strcmpi(benchmark,'adolc'): + elif benchmark=='adolc': test_ids=test_ids.intersection(set(range(3001,3200))) #print 'test_ids after benchmark =',test_ids @@ -141,13 +140,13 @@ #UPDATE ARCHIVE? archive_name='Archive'+str(id) - if strcmpi(procedure,'update'): + if procedure=='update': archive_file=os.path.join('..','Archives',archive_name+'.arch') if os.path.isfile(archive_file): os.remove(archive_file) for k,fieldname in enumerate(field_names): - field=numpy.array(field_values[k],dtype=float) + field=np.array(field_values[k],dtype=float) if len(field.shape) == 1: - if numpy.size(field): - field=field.reshape(numpy.size(field),1) + if np.size(field): + field=field.reshape(np.size(field),1) else: field=field.reshape(0,0) @@ -168,11 +167,10 @@ for k,fieldname in enumerate(field_names): - try: #Get field and tolerance - field=numpy.array(field_values[k]) + field=np.array(field_values[k]) if len(field.shape) == 1: - if numpy.size(field): - field=field.reshape(numpy.size(field),1) + if np.size(field): + field=field.reshape(np.size(field),1) else: field=field.reshape(0,0) @@ -181,31 +179,28 @@ #compare to archive # Matlab uses base 1, so use base 1 in labels - archive=numpy.array(archread(archive_file,archive_name+'_field'+str(k+1))) + archive=np.array(archread(archive_file,archive_name+'_field'+str(k+1))) if archive == None: raise NameError("Field name '"+archive_name+'_field'+str(k+1)+"' does not exist in archive file.") - error_diff=numpy.amax(numpy.abs(archive-field),axis=0)/ \ - (numpy.amax(numpy.abs(archive),axis=0)+sys.float_info.epsilon) + error_diff=np.amax(np.abs(archive-field),axis=0)/(np.amax(np.abs(archive),axis=0)+float_info.epsilon) #disp test result - if (numpy.any(error_diff>tolerance) or numpy.isnan(error_diff)): - print 'ERROR difference: %-7.2g > %7.2g test id: %i test name: %s field: %s' % \ - (error_diff,tolerance,id,id_string,fieldname) + if (np.any(error_diff>tolerance) or np.isnan(error_diff)): + print('ERROR difference: {} > {} test id: {} test name: {} field: {}'.format(error_diff,tolerance,id,id_string,fieldname)) else: - print 'SUCCESS difference: %-7.2g < %7.2g test id: %i test name: %s field: %s' % \ - (error_diff,tolerance,id,id_string,fieldname) + print('SUCCESS difference: {} < {} test id: {} test name: {} field: {}'.format(error_diff,tolerance,id,id_string,fieldname)) except Exception as message: #something went wrong, print failure message: - print traceback.format_exc() + print format_exc() directory=os.getcwd().split('/') # not used? - if strcmpi(output,'nightly'): + if output=='nightly': fid=open(os.path.join(ISSM_DIR,'nightlylog','pythonerror.log'), 'a') fid.write('%s' % message) fid.write('\n------------------------------------------------------------------\n') fid.close() - print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,fieldname) + print('FAILURE difference: N/A test id: {} test name: {} field: {}'.format(id,id_string,fieldname)) else: - print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,fieldname) + print('FAILURE difference: N/A test id: {} test name: {} field: {}'.format(id,id_string,fieldname)) raise RuntimeError(message) @@ -214,14 +209,14 @@ #something went wrong, print failure message: - print traceback.format_exc() + print format_exc() directory=os.getcwd().split('/') # not used? - if strcmpi(output,'nightly'): + if output=='nightly': fid=open(os.path.join(ISSM_DIR,'nightlylog','pythonerror.log'), 'a') fid.write('%s' % message) fid.write('\n------------------------------------------------------------------\n') fid.close() - print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,'N/A') + print('FAILURE difference: N/A test id: {} test name: {} field: {}'.format(id,id_string,'N/A')) else: - print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,'N/A') + print('FAILURE difference: N/A test id: {} test name: {} field: {}'.format(id,id_string,'N/A')) raise RuntimeError(message) @@ -240,5 +235,5 @@ print "PYTHONSTARTUP error: ",e else: - print "PYTHONSTARTUP file '%s' does not exist." % PYTHONSTARTUP + print("PYTHONSTARTUP file '{}' does not exist.".format(PYTHONSTARTUP)) parser = argparse.ArgumentParser(description='RUNME - test deck for ISSM nightly runs') @@ -254,6 +249,5 @@ md = runme(args.id, args.exclude, args.benchmark, args.procedure, args.output, args.rank, args.numprocs) - from MatlabFuncs import strcmpi - if strcmpi(args.output,'nightly'): + if args.output=='nightly': print "PYTHONEXITEDCORRECTLY" Index: /issm/trunk/test/NightlyRun/test101.py =================================================================== --- /issm/trunk/test/NightlyRun/test101.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test101.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressSSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * from massfluxatgate import massfluxatgate from generic import generic @@ -14,37 +14,36 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) #outputs md.stressbalance.requested_outputs=['default','DeviatoricStressxx','DeviatoricStressyy','DeviatoricStressxy','MassFlux1','MassFlux2','MassFlux3','MassFlux4','MassFlux5','MassFlux6'] -md.outputdefinition.definitions=[ - massfluxatgate('name','MassFlux1','profilename','../Exp/MassFlux1.exp','definitionstring','Outputdefinition1'), - massfluxatgate('name','MassFlux2','profilename','../Exp/MassFlux2.exp','definitionstring','Outputdefinition2'), - massfluxatgate('name','MassFlux3','profilename','../Exp/MassFlux3.exp','definitionstring','Outputdefinition3'), - massfluxatgate('name','MassFlux4','profilename','../Exp/MassFlux4.exp','definitionstring','Outputdefinition4'), - massfluxatgate('name','MassFlux5','profilename','../Exp/MassFlux5.exp','definitionstring','Outputdefinition5'), - massfluxatgate('name','MassFlux6','profilename','../Exp/MassFlux6.exp','definitionstring','Outputdefinition6') - ] +md.outputdefinition.definitions=[massfluxatgate('name','MassFlux1','profilename','../Exp/MassFlux1.exp','definitionstring','Outputdefinition1'), + massfluxatgate('name','MassFlux2','profilename','../Exp/MassFlux2.exp','definitionstring','Outputdefinition2'), + massfluxatgate('name','MassFlux3','profilename','../Exp/MassFlux3.exp','definitionstring','Outputdefinition3'), + massfluxatgate('name','MassFlux4','profilename','../Exp/MassFlux4.exp','definitionstring','Outputdefinition4'), + massfluxatgate('name','MassFlux5','profilename','../Exp/MassFlux5.exp','definitionstring','Outputdefinition5'), + massfluxatgate('name','MassFlux6','profilename','../Exp/MassFlux6.exp','definitionstring','Outputdefinition6')] md=solve(md,'Stressbalance') #Fields and tolerances to track changes -field_names =['Vx','Vy','Vel','Pressure',\ - 'DeviatoricStressxx','DeviatoricStressyy','DeviatoricStressxy','MassFlux1','MassFlux2','MassFlux3','MassFlux4','MassFlux5','MassFlux6'] -field_tolerances=[1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,\ - 1e-13, 1e-13, 1e-13, 1e-13, 1e-13, 1e-13 ] -field_values=[\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Pressure,\ - md.results.StressbalanceSolution.DeviatoricStressxx,\ - md.results.StressbalanceSolution.DeviatoricStressyy,\ - md.results.StressbalanceSolution.DeviatoricStressxy,\ - md.results.StressbalanceSolution.MassFlux1,\ - md.results.StressbalanceSolution.MassFlux2,\ - md.results.StressbalanceSolution.MassFlux3,\ - md.results.StressbalanceSolution.MassFlux4,\ - md.results.StressbalanceSolution.MassFlux5,\ - md.results.StressbalanceSolution.MassFlux6 ] +field_names =['Vx','Vy','Vel','Pressure', + 'DeviatoricStressxx','DeviatoricStressyy','DeviatoricStressxy', + 'MassFlux1','MassFlux2','MassFlux3','MassFlux4','MassFlux5','MassFlux6'] +field_tolerances=[1e-13, 1e-13, 1e-13, 1e-13, + 1e-13, 1e-13, 1e-13, + 1e-13, 1e-13, 1e-13, + 1e-13, 1e-13, 1e-13 ] +field_values=[md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Pressure, + md.results.StressbalanceSolution.DeviatoricStressxx, + md.results.StressbalanceSolution.DeviatoricStressyy, + md.results.StressbalanceSolution.DeviatoricStressxy, + md.results.StressbalanceSolution.MassFlux1, + md.results.StressbalanceSolution.MassFlux2, + md.results.StressbalanceSolution.MassFlux3, + md.results.StressbalanceSolution.MassFlux4, + md.results.StressbalanceSolution.MassFlux5, + md.results.StressbalanceSolution.MassFlux6 ] Index: /issm/trunk/test/NightlyRun/test102.py =================================================================== --- /issm/trunk/test/NightlyRun/test102.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test102.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressSSA3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000) @@ -13,5 +14,5 @@ md.extrude(3,2.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') @@ -19,10 +20,8 @@ field_names =['Vx','Vy','Vz','Vel','Pressure'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ - md.results.StressbalanceSolution.Vz,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Pressure,\ - ] +field_values=[md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy, + md.results.StressbalanceSolution.Vz, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Pressure] Index: /issm/trunk/test/NightlyRun/test103.py =================================================================== --- /issm/trunk/test/NightlyRun/test103.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test103.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressHO from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000) @@ -13,24 +14,26 @@ md.extrude(3,2.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.stressbalance.requested_outputs=['default','StressTensorxx','StressTensoryy','StressTensorzz','StressTensorxy','StressTensorxz','StressTensoryz'] md=solve(md,'Stressbalance') #Fields and tolerances to track changes -field_names =['Vx','Vy','Vz','Vel','Pressure',\ - 'StressTensorxx','StressTensoryy','StressTensorzz','StressTensorxy','StressTensorxz','StressTensoryz'] -field_tolerances=[1e-09,1e-09,1e-09,1e-09,1e-09,\ - 1e-09,1e-09,1e-09,1e-09,1e-09,1e-08] -field_values=[\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ - md.results.StressbalanceSolution.Vz,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Pressure,\ - md.results.StressbalanceSolution.StressTensorxx,\ - md.results.StressbalanceSolution.StressTensoryy,\ - md.results.StressbalanceSolution.StressTensorzz,\ - md.results.StressbalanceSolution.StressTensorxy,\ - md.results.StressbalanceSolution.StressTensorxz,\ - md.results.StressbalanceSolution.StressTensoryz,\ - ] +field_names =['Vx','Vy','Vz', + 'Vel','Pressure', + 'StressTensorxx','StressTensoryy','StressTensorzz', + 'StressTensorxy','StressTensorxz','StressTensoryz'] +field_tolerances=[1e-09,1e-09,1e-09, + 1e-09,1e-09, + 1e-09,1e-09,1e-09, + 1e-09,1e-09,1e-08] +field_values=[md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy, + md.results.StressbalanceSolution.Vz, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Pressure, + md.results.StressbalanceSolution.StressTensorxx, + md.results.StressbalanceSolution.StressTensoryy, + md.results.StressbalanceSolution.StressTensorzz, + md.results.StressbalanceSolution.StressTensorxy, + md.results.StressbalanceSolution.StressTensorxz, + md.results.StressbalanceSolution.StressTensoryz,] Index: /issm/trunk/test/NightlyRun/test104.py =================================================================== --- /issm/trunk/test/NightlyRun/test104.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test104.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressFS from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000) @@ -13,5 +14,5 @@ md.extrude(3,2.) md=setflowequation(md,'FS','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') @@ -19,9 +20,7 @@ field_names =['Vx','Vy','Vz','Vel','Pressure'] field_tolerances=[1e-08,1e-08,1e-06,1e-08,1e-08] -field_values=[\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ - md.results.StressbalanceSolution.Vz,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Pressure,\ - ] +field_values=[md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy, + md.results.StressbalanceSolution.Vz, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Pressure] Index: /issm/trunk/test/NightlyRun/test105.py =================================================================== --- /issm/trunk/test/NightlyRun/test105.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test105.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedMasstransp2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test106.py =================================================================== --- /issm/trunk/test/NightlyRun/test106.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test106.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedMasstransp2dDG from model import * +from socket import gethostname from triangle import * from meshconvert import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000) @@ -14,5 +15,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.masstransport.stabilization=3 md.masstransport.spcthickness=md.geometry.thickness Index: /issm/trunk/test/NightlyRun/test107.py =================================================================== --- /issm/trunk/test/NightlyRun/test107.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test107.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedMasstransp3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000) @@ -13,5 +14,5 @@ md=setflowequation(md,'SSA','all') md.extrude(5,3.) -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test108.py =================================================================== --- /issm/trunk/test/NightlyRun/test108.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test108.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTherStea from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000) @@ -14,5 +15,5 @@ md=setflowequation(md,'SSA','all') md.timestepping.time_step=0 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Thermal') Index: /issm/trunk/test/NightlyRun/test109.py =================================================================== --- /issm/trunk/test/NightlyRun/test109.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test109.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTherTran from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.isstressbalance=False md.transient.ismasstransport=False @@ -24,6 +25,4 @@ field_names =['Temperature','BasalforcingsGroundediceMeltingRate'] field_tolerances=[1e-13,1e-13] -field_values=[\ - md.results.TransientSolution[0].Temperature,\ - md.results.TransientSolution[0].BasalforcingsGroundediceMeltingRate,\ - ] +field_values=[md.results.TransientSolution[0].Temperature, + md.results.TransientSolution[0].BasalforcingsGroundediceMeltingRate] Index: /issm/trunk/test/NightlyRun/test110.py =================================================================== --- /issm/trunk/test/NightlyRun/test110.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test110.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTranSSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.requested_outputs=['IceVolume'] Index: /issm/trunk/test/NightlyRun/test1101.py =================================================================== --- /issm/trunk/test/NightlyRun/test1101.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1101.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: ISMIPAHO -import numpy +import numpy as np import shutil from model import * +from socket import gethostname from squaremesh import * from setmask import * @@ -8,6 +9,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * -from PythonFuncs import * """ @@ -18,5 +17,6 @@ printingflag=False -L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +#L_list=[80000.] +L_list=[80000.] results=[] minvx=[] @@ -35,23 +35,23 @@ #Create dirichlet on the bed only - md.stressbalance.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.stressbalance.spcvx=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvy=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvz=np.nan*np.ones((md.mesh.numberofvertices)) - pos=numpy.nonzero(md.mesh.vertexonbase) + pos=np.where(md.mesh.vertexonbase) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. #Create MPCs to have periodic boundary conditions - posx=numpy.nonzero(md.mesh.x==0.)[0] - posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] + posx=np.where(md.mesh.x==0.)[0] + posx2=np.where(md.mesh.x==np.max(md.mesh.x))[0] - posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times - posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + posy=np.where(np.logical_and.reduce((md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x))))[0] #Don't take the same nodes two times + posy2=np.where(np.logical_and.reduce((md.mesh.y==np.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x))))[0] - md.stressbalance.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + md.stressbalance.vertex_pairing=np.vstack((np.vstack((posx+1,posx2+1)).T,np.vstack((posy+1,posy2+1)).T)) #Compute the stressbalance - md.cluster=generic('name',oshostname(),'np',8) + md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -61,6 +61,6 @@ vz=md.results.StressbalanceSolution.Vz results.append(md.results.StressbalanceSolution) - minvx.append(numpy.min(vx[-md.mesh.numberofvertices2d:])) - maxvx.append(numpy.max(vx[-md.mesh.numberofvertices2d:])) + minvx.append(np.min(vx[-md.mesh.numberofvertices2d:])) + maxvx.append(np.max(vx[-md.mesh.numberofvertices2d:])) #Now plot vx, vy, vz and vx on a cross section @@ -69,5 +69,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipaHOvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipaHOvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipaHOvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') # plotmodel(md,'data',vy,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') @@ -75,5 +75,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipaHOvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipaHOvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipaHOvy%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') # plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') @@ -81,5 +81,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipaHOvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipaHOvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipaHOvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') @@ -111,43 +111,25 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipaHOvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipaHOvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipaHOvxsec%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') #Now plot the min and max values of vx for each size of the square -#plot([5 10 20 40 80 160],minvx);ylim([0 18]);xlim([0 160]) +#plot([5 10 20 40 80 160],minvx)ylim([0 18])xlim([0 160]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipaHOminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipaHOminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipaHOminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') -#plot([5 10 20 40 80 160],maxvx);ylim([0 120]);xlim([0 160]) +#plot([5 10 20 40 80 160],maxvx)ylim([0 120])xlim([0 160]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipaHOmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipaHOmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipaHOmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') #Fields and tolerances to track changes -field_names =[\ - 'Vx5km','Vy5km','Vz5km',\ - 'Vx10km','Vy10km','Vz10km',\ - 'Vx20km','Vy20km','Vz20km',\ - 'Vx40km','Vy40km','Vz40km',\ - 'Vx80km','Vy80km','Vz80km',\ - 'Vx160km','Vy160km','Vz160km' -] -field_tolerances=[\ - 1e-09,1e-09,1e-09,\ - 1e-10,1e-10,1e-09,\ - 1e-09,1e-09,1e-09,\ - 1e-09,1e-08,1e-09,\ - 1e-08,1e-08,1e-08,\ - 1e-08,1e-07,1e-08,\ -] +field_names =['Vx80km','Vy80km','Vz80km'] +field_tolerances=[1e-08,1e-08,1e-08] field_values=[] for result in results: - field_values=field_values+[\ - result.Vx,\ - result.Vy,\ - result.Vz,\ - ] + field_values=field_values+[result.Vx,result.Vy,result.Vz] Index: /issm/trunk/test/NightlyRun/test1102.py =================================================================== --- /issm/trunk/test/NightlyRun/test1102.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1102.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: ISMIPAFS -import numpy +import numpy as np import shutil from model import * +from socket import gethostname from squaremesh import * from setmask import * @@ -8,6 +9,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * -from PythonFuncs import * """ @@ -18,5 +17,5 @@ printingflag=False -L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +L_list=[80000.] results=[] minvx=[] @@ -31,7 +30,7 @@ # #Find elements at the corner and extract model -# posnodes=numpy.nonzero(numpy.logical_and(numpy.logical_or(md.mesh.x==0.,md.mesh.x==numpy.max(md.mesh.x)),numpy.logical_or(md.mesh.y==0.,md.mesh.y==numpy.max(md.mesh.y)))) -# a=numpy.nonzero(ismember(md.mesh.elements,posnodes))[0] -# elements=numpy.ones((md.mesh.numberofelements),int) +# posnodes=np.nonzero(np.logical_and.reduce(np.logical_or.reduce(md.mesh.x==0.,md.mesh.x==np.max(md.mesh.x)),np.logical_or.reduce(md.mesh.y==0.,md.mesh.y==np.max(md.mesh.y)))) +# a=np.nonzero(ismember(md.mesh.elements,posnodes))[0] +# elements=np.ones((md.mesh.numberofelements),int) # elements[a]=0 # md.modelextract(elements) @@ -42,25 +41,14 @@ #Create dirichlet on the bed only - pos=numpy.nonzero(md.mesh.vertexonbase) + pos=np.nonzero(md.mesh.vertexonbase) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. md.stressbalance.spcvz[pos]=0. -# #Create MPCs to have periodic boundary conditions -# posx=numpy.nonzero(md.mesh.x==0.)[0] -# posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] -# posx=numpy.nonzero(logical_and_n(md.mesh.x==0.,md.mesh.y!=0.,md.mesh.y!=numpy.max(md.mesh.y),numpy.logical_not(md.mesh.vertexonbase)))[0] -# posx2=numpy.nonzero(logical_and_n(md.mesh.x==numpy.max(md.mesh.x),md.mesh.y!=0.,md.mesh.y!=numpy.max(md.mesh.y),numpy.logical_not(md.mesh.vertexonbase)))[0] - -# posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x),numpy.logical_not(md.mesh.vertexonbase)))[0] #Don't take the same nodes two times -# posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x),numpy.logical_not(md.mesh.vertexonbase)))[0] - -# md.stressbalance.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) - #Compute the stressbalance - md.stressbalance.abstol=float('NaN') - md.stressbalance.reltol=float('NaN') + md.stressbalance.abstol=np.nan + md.stressbalance.reltol=np.nan md.stressbalance.restol=1. - md.cluster=generic('name',oshostname(),'np',8) + md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -71,6 +59,6 @@ pressure=md.results.StressbalanceSolution.Pressure results.append(md.results.StressbalanceSolution) - minvx.append(numpy.min(vx[-md.mesh.numberofvertices2d:])) - maxvx.append(numpy.max(vx[-md.mesh.numberofvertices2d:])) + minvx.append(np.min(vx[-md.mesh.numberofvertices2d:])) + maxvx.append(np.max(vx[-md.mesh.numberofvertices2d:])) #Now plot vx, vy, vz and vx on a cross section @@ -79,5 +67,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipaFSvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipaFSvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipaFSvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') # plotmodel(md,'data',vy,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',3) @@ -85,5 +73,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipaFSvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipaFSvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipaFSvy%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') # plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',4) @@ -91,5 +79,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipaFSvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipaFSvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipaFSvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') @@ -121,38 +109,24 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipaFSvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipaFSvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipaFSvxsec.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') #Now plot the min and max values of vx for each size of the square -#plot([5 10 20 40 80 160],minvx);ylim([0 18]) +#plot([5 10 20 40 80 160],minvx)ylim([0 18]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipaFSminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipaFSminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipaFSminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') -#plot([5 10 20 40 80 160],maxvx);ylim([0 120]) +#plot([5 10 20 40 80 160],maxvx)ylim([0 120]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipaFSmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipaFSmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipaFSmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestA') #Fields and tolerances to track changes -field_names =[\ - 'Vx5km','Vy5km','Vz5km',\ - 'Vx10km','Vy10km','Vz10km',\ - 'Vx20km','Vy20km','Vz20km',\ - 'Vx40km','Vy40km','Vz40km',\ - 'Vx80km','Vy80km','Vz80km',\ - 'Vx160km','Vy160km','Vz160km' -] -field_tolerances=[\ - 1e-12,1e-12,1e-12,\ - 1e-12,1e-12,1e-12,\ - 1e-12,1e-11,1e-12,\ - 1e-12,1e-11,1e-12,\ - 1e-12,1e-11,1e-12,\ - 1e-12,1e-11,1e-12,\ -] +field_names =['Vx80km','Vy80km','Vz80km'] +field_tolerances=[1e-12,1e-11,1e-12,] field_values=[] for result in results: Index: /issm/trunk/test/NightlyRun/test1103.py =================================================================== --- /issm/trunk/test/NightlyRun/test1103.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1103.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: ISMIPBHO -import numpy +import numpy as np import shutil from model import * +from socket import gethostname from squaremesh import * from setmask import * @@ -8,6 +9,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * -from PythonFuncs import * """ @@ -18,5 +17,5 @@ printingflag=False -L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +L_list=[80000.] results=[] minvx=[] @@ -35,22 +34,22 @@ #Create dirichlet on the bed only - md.stressbalance.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - pos=numpy.nonzero(md.mesh.vertexonbase) + md.stressbalance.spcvx=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvy=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvz=np.nan*np.ones((md.mesh.numberofvertices)) + pos=np.nonzero(md.mesh.vertexonbase) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. #Create MPCs to have periodic boundary conditions - posx=numpy.nonzero(md.mesh.x==0.)[0] - posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] + posx=np.where(md.mesh.x==0.)[0] + posx2=np.where(md.mesh.x==np.max(md.mesh.x))[0] - posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times - posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + posy=np.where(np.logical_and.reduce((md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x))))[0] #Don't take the same nodes two times + posy2=np.where(np.logical_and.reduce((md.mesh.y==np.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x))))[0] - md.stressbalance.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + md.stressbalance.vertex_pairing=np.vstack((np.vstack((posx+1,posx2+1)).T,np.vstack((posy+1,posy2+1)).T)) #Compute the stressbalance - md.cluster=generic('name',oshostname(),'np',8) + md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -60,6 +59,6 @@ vz=md.results.StressbalanceSolution.Vz results.append(md.results.StressbalanceSolution) - minvx.append(numpy.min(vx[md.mesh.numberofvertices2d:])) - maxvx.append(numpy.max(vx[md.mesh.numberofvertices2d:])) + minvx.append(np.min(vx[md.mesh.numberofvertices2d:])) + maxvx.append(np.max(vx[md.mesh.numberofvertices2d:])) #Now plot vx, vy, vz and vx on a cross section @@ -68,5 +67,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipbHOvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipbHOvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipbHOvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') # plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km') @@ -74,5 +73,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipbHOvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipbHOvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipbHOvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') @@ -104,43 +103,25 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipbHOvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipbHOvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipbHOvxsec%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') #Now plot the min and max values of vx for each size of the square -#plot([5 10 20 40 80 160],minvx);ylim([0 14]);xlim([0 160]) +#plot([5 10 20 40 80 160],minvx)ylim([0 14])xlim([0 160]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipbHOminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipbHOminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipbHOminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') -#plot([5 10 20 40 80 160],maxvx);ylim([0 120]);xlim([0 160]) +#plot([5 10 20 40 80 160],maxvx)ylim([0 120])xlim([0 160]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipbHOmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipbHOmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipbHOmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestB') #Fields and tolerances to track changes -field_names =[\ - 'Vx5km','Vy5km','Vz5km',\ - 'Vx10km','Vy10km','Vz10km',\ - 'Vx20km','Vy20km','Vz20km',\ - 'Vx40km','Vy40km','Vz40km',\ - 'Vx80km','Vy80km','Vz80km',\ - 'Vx160km','Vy160km','Vz160km' -] -field_tolerances=[\ - 1e-09,1e-09,1e-09,\ - 1e-09,1e-09,1e-09,\ - 1e-09,1e-09,1e-09,\ - 1e-08,1e-08,1e-08,\ - 1e-08,1e-07,1e-07,\ - 1e-07,1e-06,1e-07,\ -] +field_names =['Vx80km','Vy80km','Vz80km'] +field_tolerances=[1e-08,1e-07,1e-07] field_values=[] for result in results: - field_values=field_values+[\ - result.Vx,\ - result.Vy,\ - result.Vz,\ - ] + field_values=field_values+[result.Vx,result.Vy,result.Vz] Index: /issm/trunk/test/NightlyRun/test1104.py =================================================================== --- /issm/trunk/test/NightlyRun/test1104.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1104.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: ISMIPBFS -import numpy +import numpy as np from model import * +from socket import gethostname from squaremesh import * from setmask import * @@ -7,6 +8,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * -from PythonFuncs import * """ @@ -15,5 +14,5 @@ """ -L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +L_list=[80000.] results=[] @@ -29,29 +28,29 @@ #Create dirichlet on the bed only - md.stressbalance.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.stressbalance.spcvx=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvy=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvz=np.nan*np.ones((md.mesh.numberofvertices)) - pos=numpy.nonzero(md.mesh.vertexonbase) + pos=np.where(md.mesh.vertexonbase) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. #Create MPCs to have periodic boundary conditions - posx=numpy.nonzero(md.mesh.x==0.)[0] - posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] + posx=np.where(md.mesh.x==0.)[0] + posx2=np.where(md.mesh.x==np.max(md.mesh.x))[0] - posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times - posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + posy=np.where(np.logical_and.reduce((md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x))))[0] #Don't take the same nodes two times + posy2=np.where(np.logical_and.reduce((md.mesh.y==np.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x))))[0] - md.stressbalance.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) - + md.stressbalance.vertex_pairing=np.vstack((np.vstack((posx+1,posx2+1)).T,np.vstack((posy+1,posy2+1)).T)) + print np.shape(md.stressbalance.vertex_pairing) #Compute the stressbalance - md.stressbalance.abstol=float('NaN') - md.cluster=generic('name',oshostname(),'np',8) + md.stressbalance.abstol=np.nan + md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') - pos=numpy.nonzero(logical_or_n(md.mesh.x==0.,md.mesh.y==0.,md.mesh.x==numpy.max(md.mesh.x),md.mesh.y==numpy.max(md.mesh.y))) + pos=np.where(np.logical_or.reduce((md.mesh.x==0.,md.mesh.y==0.,md.mesh.x==np.max(md.mesh.x),md.mesh.y==np.max(md.mesh.y)))) md.stressbalance.spcvx[pos]=md.results.StressbalanceSolution.Vx[pos] md.stressbalance.spcvy[pos]=md.results.StressbalanceSolution.Vy[pos] - md.stressbalance.vertex_pairing=numpy.empty((0,2),int) + md.stressbalance.vertex_pairing=np.empty((0,2),int) md=setflowequation(md,'FS','all') md=solve(md,'Stressbalance') @@ -66,25 +65,7 @@ #Fields and tolerances to track changes -field_names =[\ - 'Vx5km','Vy5km','Vz5km',\ - 'Vx10km','Vy10km','Vz10km',\ - 'Vx20km','Vy20km','Vz20km',\ - 'Vx40km','Vy40km','Vz40km',\ - 'Vx80km','Vy80km','Vz80km',\ - 'Vx160km','Vy160km','Vz160km' -] -field_tolerances=[\ - 1e-08,1e-08,1e-08,\ - 1e-08,1e-08,1e-08,\ - 1e-08,1e-08,1e-08,\ - 1e-08,1e-08,1e-08,\ - 1e-08,1e-07,1e-08,\ - 1e-07,1e-07,1e-07,\ -] +field_names =['Vx80km','Vy80km','Vz80km'] +field_tolerances=[1e-08,1e-07,1e-08] field_values=[] for result in results: - field_values=field_values+[\ - result.Vx,\ - result.Vy,\ - result.Vz,\ - ] + field_values=field_values+[result.Vx,result.Vy,result.Vz] Index: /issm/trunk/test/NightlyRun/test1105.py =================================================================== --- /issm/trunk/test/NightlyRun/test1105.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1105.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: ISMIPCHO -import numpy +import numpy as np import shutil from model import * +from socket import gethostname from squaremesh import * from setmask import * @@ -8,6 +9,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * -from PythonFuncs import * """ @@ -18,5 +17,5 @@ printingflag=False -L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +L_list=[80000.] results=[] minvx=[] @@ -35,18 +34,18 @@ #Create MPCs to have periodic boundary conditions - md.stressbalance.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.stressbalance.spcvx=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvy=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvz=np.nan*np.ones((md.mesh.numberofvertices)) - posx=numpy.nonzero(logical_and_n(md.mesh.x==0.,md.mesh.y!=0.,md.mesh.y!=L))[0] - posx2=numpy.nonzero(logical_and_n(md.mesh.x==L,md.mesh.y!=0.,md.mesh.y!=L))[0] + posx=np.where(np.logical_and.reduce((md.mesh.x==0.,md.mesh.y!=0.,md.mesh.y!=L)))[0] + posx2=np.where(np.logical_and.reduce((md.mesh.x==L,md.mesh.y!=0.,md.mesh.y!=L)))[0] - posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=L))[0] #Don't take the same nodes two times - posy2=numpy.nonzero(logical_and_n(md.mesh.y==L,md.mesh.x!=0.,md.mesh.x!=L))[0] + posy=np.where(np.logical_and.reduce((md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=L)))[0] #Don't take the same nodes two times + posy2=np.where(np.logical_and.reduce((md.mesh.y==L,md.mesh.x!=0.,md.mesh.x!=L)))[0] - md.stressbalance.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + md.stressbalance.vertex_pairing=np.vstack((np.vstack((posx+1,posx2+1)).T,np.vstack((posy+1,posy2+1)).T)) #Add spc on the corners - pos=numpy.nonzero(logical_and_n(numpy.logical_or(md.mesh.x==0.,md.mesh.x==L),numpy.logical_or(md.mesh.y==0.,md.mesh.y==L),md.mesh.vertexonbase)) + pos=np.where(np.logical_and.reduce((np.logical_or(md.mesh.x==0.,md.mesh.x==L),np.logical_or(md.mesh.y==0.,md.mesh.y==L),md.mesh.vertexonbase))) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. @@ -71,9 +70,9 @@ #Spc the bed at zero for vz - pos=numpy.nonzero(md.mesh.vertexonbase) + pos=np.where(md.mesh.vertexonbase) md.stressbalance.spcvz[pos]=0. #Compute the stressbalance - md.cluster=generic('name',oshostname(),'np',8) + md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -83,6 +82,6 @@ vz=md.results.StressbalanceSolution.Vz results.append(md.results.StressbalanceSolution) - minvx.append(numpy.min(vx[-md.mesh.numberofvertices2d:])) - maxvx.append(numpy.max(vx[-md.mesh.numberofvertices2d:])) + minvx.append(np.min(vx[-md.mesh.numberofvertices2d:])) + maxvx.append(np.max(vx[-md.mesh.numberofvertices2d:])) #Now plot vx, vy, vz and vx on a cross section @@ -91,5 +90,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipcHOvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipcHOvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipcHOvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') # plotmodel(md,'data',vy,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',3) @@ -97,5 +96,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipcHOvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipcHOvy' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipcHOvy%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') # plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',4) @@ -103,5 +102,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipcHOvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipcHOvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipcHOvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') @@ -133,43 +132,25 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipcHOvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipcHOvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipcHOvxsec%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') #Now plot the min and max values of vx for each size of the square -#plot([5 10 20 40 80 160],minvx);ylim([4 18]);xlim([0 160]) +#plot([5 10 20 40 80 160],minvx)ylim([4 18])xlim([0 160]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipcHOminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipcHOminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipcHOminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') -#plot([5 10 20 40 80 160],maxvx);ylim([0 200]); xlim([0 160]) +#plot([5 10 20 40 80 160],maxvx)ylim([0 200]) xlim([0 160]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipcHOmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipcHOmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipcHOmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestC') #Fields and tolerances to track changes -field_names =[\ - 'Vx5km','Vy5km','Vz5km',\ - 'Vx10km','Vy10km','Vz10km',\ - 'Vx20km','Vy20km','Vz20km',\ - 'Vx40km','Vy40km','Vz40km',\ - 'Vx80km','Vy80km','Vz80km',\ - 'Vx160km','Vy160km','Vz160km' -] -field_tolerances=[\ - 1e-08,1e-07,1e-07,\ - 1e-09,1e-07,1e-07,\ - 1e-09,1e-09,1e-07,\ - 1e-09,1e-09,1e-08,\ - 1e-09,1e-08,1e-08,\ - 1e-09,1e-08,1e-08,\ -] +field_names =['Vx80km','Vy80km','Vz80km'] +field_tolerances=[1e-09,1e-08,1e-08] field_values=[] for result in results: - field_values=field_values+[\ - result.Vx,\ - result.Vy,\ - result.Vz,\ - ] + field_values=field_values+[result.Vx,result.Vy,result.Vz] Index: /issm/trunk/test/NightlyRun/test1106.py =================================================================== --- /issm/trunk/test/NightlyRun/test1106.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1106.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: ISMIPCFS -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,6 +8,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * -from PythonFuncs import * """ @@ -15,5 +14,5 @@ """ -L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +L_list=[80000.] results=[] @@ -22,9 +21,9 @@ md=setmask(md,'','') #ice sheet test md=parameterize(md,'../Par/ISMIPC.py') - md.friction.coefficient=numpy.sqrt(md.constants.yts*(1000.+1000.*numpy.sin(md.mesh.x.reshape(-1,1)*2.*numpy.pi/L)*numpy.sin(md.mesh.y.reshape(-1,1)*2.*numpy.pi/L))) + md.friction.coefficient=np.sqrt(md.constants.yts*(1000.+1000.*np.sin(md.mesh.x*2.*np.pi/L)*np.sin(md.mesh.y*2.*np.pi/L))) md.extrude(10,1.) #Add spc on the borders - pos=numpy.nonzero(logical_or_n(md.mesh.x==0.,md.mesh.x==numpy.max(md.mesh.x),md.mesh.y==0.,md.mesh.y==numpy.max(md.mesh.y))) + pos=np.where(np.logical_or.reduce((md.mesh.x==0.,md.mesh.x==np.max(md.mesh.x),md.mesh.y==0.,md.mesh.y==np.max(md.mesh.y)))) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. @@ -51,5 +50,5 @@ #Compute the stressbalance - md.cluster=generic('name',oshostname(),'np',8) + md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -63,25 +62,7 @@ #Fields and tolerances to track changes -field_names =[\ - 'Vx5km','Vy5km','Vz5km',\ - 'Vx10km','Vy10km','Vz10km',\ - 'Vx20km','Vy20km','Vz20km',\ - 'Vx40km','Vy40km','Vz40km',\ - 'Vx80km','Vy80km','Vz80km',\ - 'Vx160km','Vy160km','Vz160km' -] -field_tolerances=[\ - 1e-12,1e-12,1e-11,\ - 1e-12,1e-12,1e-12,\ - 1e-12,1e-12,1e-12,\ - 1e-12,1e-12,1e-12,\ - 1e-12,1e-12,1e-12,\ - 1e-12,1e-11,1e-12,\ -] +field_names =['Vx80km','Vy80km','Vz80km'] +field_tolerances=[1e-12,1e-12,1e-12] field_values=[] for result in results: - field_values=field_values+[\ - result.Vx,\ - result.Vy,\ - result.Vz,\ - ] + field_values=field_values+[result.Vx,result.Vy,result.Vz] Index: /issm/trunk/test/NightlyRun/test1107.py =================================================================== --- /issm/trunk/test/NightlyRun/test1107.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1107.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: ISMIPDHO -import numpy +import numpy as np import shutil from model import * +from socket import gethostname from squaremesh import * from setmask import * @@ -8,6 +9,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * -from PythonFuncs import * """ @@ -18,5 +17,5 @@ printingflag=False -L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +L_list=[80000.] results=[] minvx=[] @@ -35,21 +34,21 @@ #We need one grd on dirichlet: the 4 corners are set to zero - md.stressbalance.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.stressbalance.spcvx=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvy=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvz=np.nan*np.ones((md.mesh.numberofvertices)) #Create MPCs to have periodic boundary conditions -# posx=find(md.mesh.x==0. & ~(md.mesh.y==0. & md.mesh.vertexonbase) & ~(md.mesh.y==L & md.mesh.vertexonbase)); - posx=numpy.nonzero(logical_and_n(md.mesh.x==0.,numpy.logical_not(numpy.logical_and(md.mesh.y==0.,md.mesh.vertexonbase)),numpy.logical_not(numpy.logical_and(md.mesh.y==L,md.mesh.vertexonbase))))[0] -# posx2=find(md.mesh.x==max(md.mesh.x) & ~(md.mesh.y==0. & md.mesh.vertexonbase) & ~(md.mesh.y==L & md.mesh.vertexonbase)); - posx2=numpy.nonzero(logical_and_n(md.mesh.x==numpy.max(md.mesh.x),numpy.logical_not(numpy.logical_and(md.mesh.y==0.,md.mesh.vertexonbase)),numpy.logical_not(numpy.logical_and(md.mesh.y==L,md.mesh.vertexonbase))))[0] +# posx=find(md.mesh.x==0. & ~(md.mesh.y==0. & md.mesh.vertexonbase) & ~(md.mesh.y==L & md.mesh.vertexonbase)) + posx=np.where(np.logical_and.reduce((md.mesh.x==0.,np.logical_not(np.logical_and(md.mesh.y==0.,md.mesh.vertexonbase)),np.logical_not(np.logical_and(md.mesh.y==L,md.mesh.vertexonbase)))))[0] +# posx2=find(md.mesh.x==max(md.mesh.x) & ~(md.mesh.y==0. & md.mesh.vertexonbase) & ~(md.mesh.y==L & md.mesh.vertexonbase)) + posx2=np.where(np.logical_and.reduce((md.mesh.x==np.max(md.mesh.x),np.logical_not(np.logical_and(md.mesh.y==0.,md.mesh.vertexonbase)),np.logical_not(np.logical_and(md.mesh.y==L,md.mesh.vertexonbase)))))[0] - posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times - posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + posy=np.where(np.logical_and.reduce((md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x))))[0] #Don't take the same nodes two times + posy2=np.where(np.logical_and.reduce((md.mesh.y==np.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x))))[0] - md.stressbalance.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + md.stressbalance.vertex_pairing=np.vstack((np.vstack((posx+1,posx2+1)).T,np.vstack((posy+1,posy2+1)).T)) #Add spc on the corners - pos=numpy.nonzero(logical_and_n(numpy.logical_or(md.mesh.x==0.,md.mesh.x==L),numpy.logical_or(md.mesh.y==0.,md.mesh.y==L),md.mesh.vertexonbase)) + pos=np.where(np.logical_and.reduce((np.logical_or(md.mesh.x==0.,md.mesh.x==L),np.logical_or(md.mesh.y==0.,md.mesh.y==L),md.mesh.vertexonbase))) md.stressbalance.spcvy[:]=0. md.stressbalance.spcvx[pos]=0. @@ -68,9 +67,9 @@ #Spc the bed at zero for vz - pos=numpy.nonzero(md.mesh.vertexonbase) + pos=np.where(md.mesh.vertexonbase) md.stressbalance.spcvz[pos]=0. #Compute the stressbalance - md.cluster=generic('name',oshostname(),'np',8) + md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -80,6 +79,6 @@ vz=md.results.StressbalanceSolution.Vz results.append(md.results.StressbalanceSolution) - minvx.append(numpy.min(vx[-md.mesh.numberofvertices2d:])) - maxvx.append(numpy.max(vx[-md.mesh.numberofvertices2d:])) + minvx.append(np.min(vx[-md.mesh.numberofvertices2d:])) + maxvx.append(np.max(vx[-md.mesh.numberofvertices2d:])) #Now plot vx, vy, vz and vx on a cross section @@ -88,5 +87,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipdHOvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipdHOvx' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipdHOvx%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') # plotmodel(md,'data',vz,'layer#all',md.mesh.numberoflayers,'xlim',[0 L/10^3],'ylim',[0 L/10^3],'unit','km','figure',3) @@ -94,5 +93,5 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipdHOvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipdHOvz' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipdHOvz%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') @@ -124,43 +123,25 @@ pass # set(gcf,'Color','w') -# printmodel(['ismipdHOvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel(['ismipdHOvxsec' num2str(L)],'png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move("ismipdHOvxsec%d.png" % L,ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') #Now plot the min and max values of vx for each size of the square -#plot([5 10 20 40 80 160],minvx);ylim([2 18]);xlim([0 160]) +#plot([5 10 20 40 80 160],minvx)ylim([2 18])xlim([0 160]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipdHOminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipdHOminvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipdHOminvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') -#plot([5 10 20 40 80 160],maxvx);ylim([0 300]);xlim([0 160]) +#plot([5 10 20 40 80 160],maxvx)ylim([0 300])xlim([0 160]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('ismipdHOmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off'); +# printmodel('ismipdHOmaxvx','png','margin','on','marginsize',25,'frame','off','resolution',1.5,'hardcopy','off') # shutil.move('ismipdHOmaxvx.png',ISSM_DIR+'/website/doc_pdf/validation/Images/ISMIP/TestD') #Fields and tolerances to track changes -field_names =[\ - 'Vx5km','Vy5km','Vz5km',\ - 'Vx10km','Vy10km','Vz10km',\ - 'Vx20km','Vy20km','Vz20km',\ - 'Vx40km','Vy40km','Vz40km',\ - 'Vx80km','Vy80km','Vz80km',\ - 'Vx160km','Vy160km','Vz160km' -] -field_tolerances=[\ - 1e-07,1e-08,1e-06,\ - 1e-08,1e-08,1e-06,\ - 1e-08,1e-08,1e-07,\ - 1e-08,1e-08,1e-07,\ - 1e-08,1e-08,1e-07,\ - 1e-07,1e-08,1e-06,\ -] +field_names =['Vx80km','Vy80km','Vz80km'] +field_tolerances=[1e-08,1e-08,1e-07] field_values=[] for result in results: - field_values=field_values+[\ - result.Vx,\ - result.Vy,\ - result.Vz,\ - ] + field_values=field_values+[result.Vx,result.Vy,result.Vz] Index: /issm/trunk/test/NightlyRun/test1108.py =================================================================== --- /issm/trunk/test/NightlyRun/test1108.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1108.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: ISMIPDFS -import numpy +import numpy as np from model import * +from socket import gethostname from bamg import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from PythonFuncs import * @@ -15,5 +16,5 @@ """ -L_list=[5000.,10000.,20000.,40000.,80000.,160000.] +L_list=[80000.] results=[] @@ -30,9 +31,9 @@ #We need one grd on dirichlet: the 4 corners are set to zero - md.stressbalance.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.stressbalance.spcvx=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvy=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvz=np.nan*np.ones((md.mesh.numberofvertices)) - pos=numpy.nonzero(logical_and_n(md.mesh.vertexonbase,numpy.logical_or(md.mesh.x==0.,md.mesh.x==numpy.max(md.mesh.x)),numpy.logical_or(md.mesh.y==0.,md.mesh.y==numpy.max(md.mesh.y)))) + pos=np.nonzero(logical_and.reduce_n(md.mesh.vertexonbase,np.logical_or.reduce(md.mesh.x==0.,md.mesh.x==np.max(md.mesh.x)),np.logical_or.reduce(md.mesh.y==0.,md.mesh.y==np.max(md.mesh.y)))) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. @@ -40,24 +41,24 @@ #Create MPCs to have periodic boundary conditions - posx=numpy.nonzero(md.mesh.x==0.)[0] - posx2=numpy.nonzero(md.mesh.x==numpy.max(md.mesh.x))[0] + posx=np.nonzero(md.mesh.x==0.)[0] + posx2=np.nonzero(md.mesh.x==np.max(md.mesh.x))[0] - posy=numpy.nonzero(logical_and_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] #Don't take the same nodes two times - posy2=numpy.nonzero(logical_and_n(md.mesh.y==numpy.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=numpy.max(md.mesh.x)))[0] + posy=np.nonzero(logical_and.reduce_n(md.mesh.y==0.,md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x)))[0] #Don't take the same nodes two times + posy2=np.nonzero(logical_and.reduce_n(md.mesh.y==np.max(md.mesh.y),md.mesh.x!=0.,md.mesh.x!=np.max(md.mesh.x)))[0] - md.stressbalance.vertex_pairing=numpy.vstack((numpy.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),numpy.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) + md.stressbalance.vertex_pairing=np.vstack((np.hstack((posx.reshape(-1,1)+1,posx2.reshape(-1,1)+1)),np.hstack((posy.reshape(-1,1)+1,posy2.reshape(-1,1)+1)))) #Compute the stressbalance - md.cluster=generic('name',oshostname(),'np',8) + md.cluster=generic('name',gethostname(),'np',8) md.verbose=verbose('convergence',True) md=solve(md,'Stressbalance') - md.stressbalance.reltol=float('NaN') - md.stressbalance.abstol=float('NaN') - md.stressbalance.vertex_pairing=numpy.empty((0,2)) + md.stressbalance.reltol=np.nan + md.stressbalance.abstol=np.nan + md.stressbalance.vertex_pairing=np.empty((0,2)) #We need one grid on dirichlet: the 4 corners are set to zero - md.stressbalance.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - md.stressbalance.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) - pos=numpy.nonzero(logical_or_n(md.mesh.y==0.,md.mesh.x==0.,md.mesh.x==numpy.max(md.mesh.x),md.mesh.y==numpy.max(md.mesh.y))) #Don't take the same nodes two times + md.stressbalance.spcvx=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvy=np.nan*np.ones((md.mesh.numberofvertices)) + md.stressbalance.spcvz=np.nan*np.ones((md.mesh.numberofvertices)) + pos=np.nonzero(logical_or.reduce_n(md.mesh.y==0.,md.mesh.x==0.,md.mesh.x==np.max(md.mesh.x),md.mesh.y==np.max(md.mesh.y))) #Don't take the same nodes two times md.stressbalance.spcvx[pos]=md.results.StressbalanceSolution.Vx[pos] md.stressbalance.spcvy[pos]=md.results.StressbalanceSolution.Vy[pos] @@ -74,20 +75,6 @@ #Fields and tolerances to track changes -field_names =[\ - 'Vx5km','Vy5km','Vz5km',\ - 'Vx10km','Vy10km','Vz10km',\ - 'Vx20km','Vy20km','Vz20km',\ - 'Vx40km','Vy40km','Vz40km',\ - 'Vx80km','Vy80km','Vz80km',\ - 'Vx160km','Vy160km','Vz160km' -] -field_tolerances=[\ - 1e-07,1e-07,1e-07,\ - 1e-08,1e-08,1e-08,\ - 1e-08,1e-07,1e-07,\ - 1e-08,1e-08,1e-08,\ - 1e-08,1e-07,1e-07,\ - 1e-07,1e-06,1e-07,\ -] +field_names =['Vx80km','Vy80km','Vz80km'] +field_tolerances=[1e-08,1e-07,1e-07] field_values=[] for result in results: Index: /issm/trunk/test/NightlyRun/test111.py =================================================================== --- /issm/trunk/test/NightlyRun/test111.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test111.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTranHO from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.requested_outputs=['IceVolume'] md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test112.py =================================================================== --- /issm/trunk/test/NightlyRun/test112.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test112.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedSurfSlop2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'SurfaceSlope') Index: /issm/trunk/test/NightlyRun/test113.py =================================================================== --- /issm/trunk/test/NightlyRun/test113.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test113.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedSurfSlope3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000) @@ -13,5 +14,5 @@ md.extrude(5,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'SurfaceSlope') Index: /issm/trunk/test/NightlyRun/test114.py =================================================================== --- /issm/trunk/test/NightlyRun/test114.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test114.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedBedSlop2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'BedSlope') Index: /issm/trunk/test/NightlyRun/test115.py =================================================================== --- /issm/trunk/test/NightlyRun/test115.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test115.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedBedSlop3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000) @@ -13,5 +14,5 @@ md.extrude(5,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'BedSlope') Index: /issm/trunk/test/NightlyRun/test116.py =================================================================== --- /issm/trunk/test/NightlyRun/test116.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test116.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfConstrainedBalThic2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000) @@ -13,8 +14,8 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') #Add boundary conditions on thickness on the border -pos=numpy.nonzero(md.mesh.vertexonboundary) +pos=np.nonzero(md.mesh.vertexonboundary) md.balancethickness.spcthickness[pos]=md.geometry.thickness[pos] md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Balancethickness') Index: /issm/trunk/test/NightlyRun/test119.py =================================================================== --- /issm/trunk/test/NightlyRun/test119.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test119.py (revision 21729) @@ -1,8 +1,9 @@ #Test Name: SquareBamgMesh -import numpy +import numpy as np import time from model import * +from socket import gethostname from bamg import * -from MatlabFuncs import * + #Simple mesh @@ -12,5 +13,5 @@ #hVertices -md=bamg(model(),'domain','../Exp/Square.exp','hmax',300000.,'hVertices',numpy.array([10000.,100000.,400000.,100000.]).reshape(-1,1),'rand',False) +md=bamg(model(),'domain','../Exp/Square.exp','hmax',300000.,'hVertices',np.array([10000.,100000.,400000.,100000.]).reshape(-1,1),'rand',False) x2=md.mesh.x y2=md.mesh.y Index: /issm/trunk/test/NightlyRun/test120.py =================================================================== --- /issm/trunk/test/NightlyRun/test120.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test120.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfConstrainedEnthalpyStea -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000) @@ -15,10 +16,10 @@ md=setflowequation(md,'SSA','all') md.timestepping.time_step=0 -md.initialization.waterfraction=numpy.zeros(md.mesh.numberofvertices) -md.initialization.watercolumn=numpy.zeros(md.mesh.numberofvertices) -md.thermal.isenthalpy = 1; -md.thermal.isdynamicbasalspc = 1; +md.initialization.waterfraction=np.zeros(md.mesh.numberofvertices) +md.initialization.watercolumn=np.zeros(md.mesh.numberofvertices) +md.thermal.isenthalpy = 1 +md.thermal.isdynamicbasalspc = 1 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Thermal') @@ -26,7 +27,5 @@ field_names =['Enthalpy','Waterfraction','Temperature'] field_tolerances=[1e-13,2e-10,1e-13] -field_values=[\ - md.results.ThermalSolution.Enthalpy,\ - md.results.ThermalSolution.Waterfraction,\ - md.results.ThermalSolution.Temperature,\ - ] +field_values=[md.results.ThermalSolution.Enthalpy, + md.results.ThermalSolution.Waterfraction, + md.results.ThermalSolution.Temperature] Index: /issm/trunk/test/NightlyRun/test1201.py =================================================================== --- /issm/trunk/test/NightlyRun/test1201.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1201.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: EISMINTMassConservation -import numpy +import numpy as np from model import * +from socket import gethostname from bamg import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -14,5 +15,4 @@ printingflag=False - results=[] @@ -24,9 +24,9 @@ md.smb.mass_balance[:]=0. md=setflowequation(md,'SSA','all') - md.cluster=generic('name',oshostname(),'np',8) + md.cluster=generic('name',gethostname(),'np',8) print " initial velocity" - md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) - md.initialization.vy=-400.*numpy.ones((md.mesh.numberofvertices,1)) + md.initialization.vx=np.zeros((md.mesh.numberofvertices)) + md.initialization.vy=-400.*np.ones((md.mesh.numberofvertices)) #Stabilization @@ -37,11 +37,11 @@ #spc thickness - pos=numpy.nonzero(md.mesh.y>199999.9)[0] - times=numpy.arange(0,501) - md.masstransport.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices+1,numpy.size(times))) + pos=np.where(md.mesh.y>199999.9)[0] + times=np.arange(0,501) + md.masstransport.spcthickness=np.nan*np.ones((md.mesh.numberofvertices+1,np.size(times))) md.masstransport.spcthickness[-1,:]=times - md.masstransport.spcthickness[pos,:]=numpy.tile(500.+100.*numpy.sin(2.*numpy.pi*times/200.),(numpy.size(pos),1)) + md.masstransport.spcthickness[pos,:]=500.+100.*np.sin(2.*np.pi*times/200.) if stabilization==3: - pos=numpy.nonzero(numpy.isnan(md.masstransport.spcthickness)) + pos=np.nonzero(np.isnan(md.masstransport.spcthickness)) md.masstransport.spcthickness[pos]=500. #No NaN for DG @@ -54,8 +54,8 @@ #plot results -#[elements,x,y,z,s,h1]=SectionValues(md,results[0],'../Exp/CrossLineEISMINT.exp',100.); -#[elements,x,y,z,s,h2]=SectionValues(md,results[1],'../Exp/CrossLineEISMINT.exp',100.); -#[elements,x,y,z,s,h3]=SectionValues(md,results[2],'../Exp/CrossLineEISMINT.exp',100.); -#[elements,x,y,z,s,hth]=SectionValues(md, 500+100*sin(2*pi/200*(500-md.mesh.y/400)),'../Exp/CrossLineEISMINT.exp',100.); +#[elements,x,y,z,s,h1]=SectionValues(md,results[0],'../Exp/CrossLineEISMINT.exp',100.) +#[elements,x,y,z,s,h2]=SectionValues(md,results[1],'../Exp/CrossLineEISMINT.exp',100.) +#[elements,x,y,z,s,h3]=SectionValues(md,results[2],'../Exp/CrossLineEISMINT.exp',100.) +#[elements,x,y,z,s,hth]=SectionValues(md, 500+100*sin(2*pi/200*(500-md.mesh.y/400)),'../Exp/CrossLineEISMINT.exp',100.) #plot(s,h1,'r',s,h2,'b',s,h3,'g',s,hth,'k') #legend('Art. diff.','No Art. diff.','D.G.','Theoretical') @@ -63,16 +63,8 @@ pass # set(gcf,'Color','w') -# export_fig([issmdir() '/website/doc_pdf/validation/Images/EISMINT/IceShelf/eismintmasscthickness.pdf']); +# export_fig([issmdir() '/website/doc_pdf/validation/Images/EISMINT/IceShelf/eismintmasscthickness.pdf']) #Fields and tolerances to track changes -field_names =[ \ - 'ThicknessArtDiff','ThicknessNoArtDiff','ThicknessDG' \ -] -field_tolerances=[\ - 1e-13, 1e-13, 1e-13\ -] -field_values=[ - results[0], \ - results[1], \ - results[2], \ -] +field_names =['ThicknessArtDiff','ThicknessNoArtDiff','ThicknessDG'] +field_tolerances=[1e-13, 1e-13, 1e-13] +field_values=[results[0],results[1],results[2]] Index: /issm/trunk/test/NightlyRun/test1202.py =================================================================== --- /issm/trunk/test/NightlyRun/test1202.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1202.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: EISMINTStress1 -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -23,5 +24,5 @@ #Compute solution for SSA's model -md.cluster=generic('name',oshostname(),'np',8) +md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -35,6 +36,6 @@ pass # set(gcf,'Color','w') -# printmodel('eismintdiag1vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); -# system(['mv eismintdiag1vx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); +# printmodel('eismintdiag1vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off') +# system(['mv eismintdiag1vx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']) #plotmodel(md,'data',vy,'contourlevels',{-100,-200,-300,-400,-500,-600,-700,-800,-900,-1000},... @@ -43,12 +44,9 @@ pass # set(gcf,'Color','w') -# printmodel('eismintdiag1vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); -# system(['mv eismintdiag1vy.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); +# printmodel('eismintdiag1vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off') +# system(['mv eismintdiag1vy.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']) #Fields and tolerances to track changes field_names =['Vx','Vy'] field_tolerances=[1e-13,1e-13] -field_values=[\ - vx, \ - vy, \ - ] +field_values=[vx,vy] Index: /issm/trunk/test/NightlyRun/test1203.py =================================================================== --- /issm/trunk/test/NightlyRun/test1203.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1203.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: EISMINTStress2 -import numpy +import numpy as np import sys from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -24,9 +25,11 @@ #Impose a non zero velocity on the upper boundary condition (y=max(y)) -pos=numpy.nonzero(md.mesh.y==numpy.max(md.mesh.y)) -md.stressbalance.spcvy[pos]=400.*(((md.mesh.x[pos].reshape(-1,1)-100000.)/25000.)**2-numpy.ones((numpy.size(pos),1)))*heaviside((1.+sys.float_info.epsilon)*numpy.ones((numpy.size(pos),1))-((md.mesh.x[pos].reshape(-1,1)-100000.)/25000.)**2) +pos=np.where(md.mesh.y==np.max(md.mesh.y)) +heavyside=np.where(np.logical_and(md.mesh.y==np.max(md.mesh.y),((1.+sys.float_info.epsilon)*np.ones((np.size(md.mesh.y)))-((md.mesh.x-100000.)/25000.)**2)>0)) +md.stressbalance.spcvy[pos]=np.zeros((np.size(pos))) +md.stressbalance.spcvy[heavyside]=400.*(((md.mesh.x[heavyside]-100000.)/25000.)**2-np.ones((np.size(heavyside)))) #Compute solution for SSA's model -md.cluster=generic('name',oshostname(),'np',8) +md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -40,6 +43,6 @@ pass # set(gcf,'Color','w') -# printmodel('eismintdiag2vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); -# system(['mv eismintdiag2vx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); +# printmodel('eismintdiag2vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off') +# system(['mv eismintdiag2vx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']) #plotmodel(md,'data',vy,'contourlevels',{-100,-200,-300,-400,-500,-600,-700,-800,-900,-1000},... # 'contourcolor','k') @@ -47,12 +50,9 @@ pass # set(gcf,'Color','w') -# printmodel('eismintdiag2vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); -# system(['mv eismintdiag2vy.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); +# printmodel('eismintdiag2vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off') +# system(['mv eismintdiag2vy.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']) #Fields and tolerances to track changes field_names =['Vx','Vy'] field_tolerances=[1e-13,1e-13] -field_values=[\ - vx, \ - vy, \ - ] +field_values=[vx,vy] Index: /issm/trunk/test/NightlyRun/test1204.py =================================================================== --- /issm/trunk/test/NightlyRun/test1204.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1204.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: EISMINTTran2 -import numpy +import numpy as np import sys from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -24,9 +25,11 @@ #Impose a non zero velocity on the upper boundary condition (y=max(y)) -pos=numpy.nonzero(md.mesh.y==max(md.mesh.y)) -md.stressbalance.spcvy[pos]=400.*(((md.mesh.x[pos].reshape(-1,1)-100000.)/25000.)**2-numpy.ones((numpy.size(pos),1)))*heaviside((1.+sys.float_info.epsilon)*numpy.ones((numpy.size(pos),1))-((md.mesh.x[pos].reshape(-1,1)-100000.)/25000.)**2) +pos=np.where(md.mesh.y==np.max(md.mesh.y)) +heavyside=np.where(np.logical_and(md.mesh.y==np.max(md.mesh.y),((1.+sys.float_info.epsilon)*np.ones((np.size(md.mesh.y)))-((md.mesh.x-100000.)/25000.)**2)>0)) +md.stressbalance.spcvy[pos]=np.zeros((np.size(pos))) +md.stressbalance.spcvy[heavyside]=400.*(((md.mesh.x[heavyside]-100000.)/25000.)**2-np.ones((np.size(heavyside)))) #Compute solution for SSA's model -md.cluster=generic('name',oshostname(),'np',8) +md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -44,6 +47,6 @@ pass # set(gcf,'Color','w') -# printmodel('eisminttrans2vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); -# system(['mv eisminttrans2vx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); +# printmodel('eisminttrans2vx','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off') +# system(['mv eisminttrans2vx.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']) #plotmodel(md,'data',(md.results.TransientSolution(end).Vy)) @@ -51,6 +54,6 @@ pass # set(gcf,'Color','w') -# printmodel('eisminttrans2vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); -# system(['mv eisminttrans2vy.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); +# printmodel('eisminttrans2vy','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off') +# system(['mv eisminttrans2vy.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']) #plotmodel(md,'data',(md.results.TransientSolution(end).Thickness)) @@ -58,13 +61,11 @@ pass # set(gcf,'Color','w') -# printmodel('eisminttrans2thickness','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off'); -# system(['mv eisminttrans2thickness.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']); +# printmodel('eisminttrans2thickness','png','margin','on','marginsize',25,'frame','off','resolution',2,'hardcopy','off') +# system(['mv eisminttrans2thickness.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceShelf ']) #Fields and tolerances to track changes field_names =['Vx','Vy','Thickness'] field_tolerances=[1e-13,1e-13,1e-13] -field_values=[\ - md.results.TransientSolution[-1].Vx, \ - md.results.TransientSolution[-1].Vy, \ - md.results.TransientSolution[-1].Thickness, \ - ] +field_values=[md.results.TransientSolution[-1].Vx, + md.results.TransientSolution[-1].Vy, + md.results.TransientSolution[-1].Thickness] Index: /issm/trunk/test/NightlyRun/test1205.py =================================================================== --- /issm/trunk/test/NightlyRun/test1205.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1205.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: EISMINTRoundIceSheetStaticSIA -import numpy +import numpy as np from model import * +from socket import gethostname from roundmesh import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -28,12 +29,12 @@ vx_obs=constant/2.*md.mesh.x*(md.geometry.thickness)**-1 vy_obs=constant/2.*md.mesh.y*(md.geometry.thickness)**-1 -vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) +vel_obs=np.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) #We extrude the model to have a 3d model -md.extrude(numlayers,1.); +md.extrude(numlayers,1.) md=setflowequation(md,'SIA','all') #Spc the nodes on the bed -pos=numpy.nonzero(md.mesh.vertexonbase) +pos=np.where(md.mesh.vertexonbase) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. @@ -41,5 +42,5 @@ #Now we can solve the problem -md.cluster=generic('name',oshostname(),'np',8) +md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -47,13 +48,11 @@ vx=md.results.StressbalanceSolution.Vx vy=md.results.StressbalanceSolution.Vy -vel=numpy.zeros((md.mesh.numberofvertices2d,1)) +vel=np.zeros((md.mesh.numberofvertices2d)) for i in xrange(0,md.mesh.numberofvertices2d): node_vel=0. for j in xrange(0,md.mesh.numberoflayers-1): - node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*\ - (numpy.sqrt(vx[i+(j+1)*md.mesh.numberofvertices2d,0]**2+vy[i+(j+1)*md.mesh.numberofvertices2d,0]**2)+\ - numpy.sqrt(vx[i+j*md.mesh.numberofvertices2d,0]**2+vy[i+j*md.mesh.numberofvertices2d,0]**2)) - vel[i,0]=node_vel + node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*(np.sqrt(vx[i+(j+1)*md.mesh.numberofvertices2d,0]**2+vy[i+(j+1)*md.mesh.numberofvertices2d,0]**2)+np.sqrt(vx[i+j*md.mesh.numberofvertices2d,0]**2+vy[i+j*md.mesh.numberofvertices2d,0]**2)) + vel[i]=node_vel #Plot of the velocity from the exact and calculated solutions @@ -62,48 +61,42 @@ #subplot(2,2,1) #p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... -#vel,'FaceColor','interp','EdgeColor','none'); +#vel,'FaceColor','interp','EdgeColor','none') #title('Modelled velocity','FontSize',14,'FontWeight','bold') -#colorbar; -#caxis([0 200]); +#colorbar +#caxis([0 200]) #subplot(2,2,2) #p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... -#vel_obs,'FaceColor','interp','EdgeColor','none'); +#vel_obs,'FaceColor','interp','EdgeColor','none') #title('Analytical velocity','FontSize',14,'FontWeight','bold') -#colorbar; -#caxis([0 200]); +#colorbar +#caxis([0 200]) #subplot(2,2,3) -#hold on; -#plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); -#plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); -#title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold'); -#xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold'); -#ylabel('velocity [m/yr]','FontSize',14,'FontWeight','bold'); -#legend('calculated velocity','exact velocity'); -#axis([0 750000 0 200]); -#hold off; +#hold on +#plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.') +#plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.') +#title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold') +#xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold') +#ylabel('velocity [m/yr]','FontSize',14,'FontWeight','bold') +#legend('calculated velocity','exact velocity') +#axis([0 750000 0 200]) +#hold off #subplot(2,2,4) #p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... -#abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none'); +#abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none') #title('Relative misfit [%]','FontSize',14,'FontWeight','bold') -#colorbar; -#caxis([0 100]); +#colorbar +#caxis([0 100]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('SIAstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); -# system(['mv SIAstatic.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceSheet']); +# printmodel('SIAstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') +# system(['mv SIAstatic.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceSheet']) #Fields and tolerances to track changes -field_names =[ \ - 'Vx','Vy','Vel', \ -] -field_tolerances=[ \ - 1e-13,1e-13,1e-13, \ -] -field_values=[ \ - vx,vy,vel, \ -] +field_names =['Vx','Vy','Vel'] +field_tolerances=[1e-13,1e-13,1e-13] +field_values=[vx,vy,vel] Index: /issm/trunk/test/NightlyRun/test1206.py =================================================================== --- /issm/trunk/test/NightlyRun/test1206.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1206.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: EISMINTRoundIceSheetStaticHO -import numpy +import numpy as np from model import * +from socket import gethostname from roundmesh import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -26,7 +27,7 @@ #Calculation of the analytical 2d velocity field constant=0.3 -vx_obs=constant/2.*md.mesh.x.reshape(-1,1)*(md.geometry.thickness)**-1 -vy_obs=constant/2.*md.mesh.y.reshape(-1,1)*(md.geometry.thickness)**-1 -vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) +vx_obs=constant/2.*md.mesh.x*(md.geometry.thickness)**-1 +vy_obs=constant/2.*md.mesh.y*(md.geometry.thickness)**-1 +vel_obs=np.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) #We extrude the model to have a 3d model @@ -35,5 +36,5 @@ #Spc the nodes on the bed -pos=numpy.nonzero(md.mesh.vertexonbase) +pos=np.where(md.mesh.vertexonbase) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. @@ -41,5 +42,5 @@ #Now we can solve the problem -md.cluster=generic('name',oshostname(),'np',8) +md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -47,5 +48,5 @@ vx=md.results.StressbalanceSolution.Vx vy=md.results.StressbalanceSolution.Vy -vel=numpy.zeros((md.mesh.numberofvertices2d,1)) +vel=np.zeros((md.mesh.numberofvertices2d)) for i in xrange(0,md.mesh.numberofvertices2d): @@ -53,7 +54,7 @@ for j in xrange(0,md.mesh.numberoflayers-1): node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*\ - (numpy.sqrt(vx[i+(j+1)*md.mesh.numberofvertices2d,0]**2+vy[i+(j+1)*md.mesh.numberofvertices2d,0]**2)+\ - numpy.sqrt(vx[i+j*md.mesh.numberofvertices2d,0]**2+vy[i+j*md.mesh.numberofvertices2d,0]**2)) - vel[i,0]=node_vel + (np.sqrt(vx[i+(j+1)*md.mesh.numberofvertices2d,0]**2+vy[i+(j+1)*md.mesh.numberofvertices2d,0]**2)+\ + np.sqrt(vx[i+j*md.mesh.numberofvertices2d,0]**2+vy[i+j*md.mesh.numberofvertices2d,0]**2)) + vel[i]=node_vel #Plot of the velocity from the exact and calculated solutions @@ -61,48 +62,42 @@ #subplot(2,2,1) #p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... -#vel,'FaceColor','interp','EdgeColor','none'); +#vel,'FaceColor','interp','EdgeColor','none') #title('Modelled velocity','FontSize',14,'FontWeight','bold') -#colorbar; -#caxis([0 200]); +#colorbar +#caxis([0 200]) #subplot(2,2,2) #p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... -#vel_obs,'FaceColor','interp','EdgeColor','none'); +#vel_obs,'FaceColor','interp','EdgeColor','none') #title('Analytical velocity','FontSize',14,'FontWeight','bold') -#colorbar; -#caxis([0 200]); +#colorbar +#caxis([0 200]) #subplot(2,2,3) -#hold on; -#plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); -#plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); -#title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold'); -#xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold'); -#ylabel('velocity [m/yr]','FontSize',14,'FontWeight','bold'); -#legend('calculated velocity','exact velocity'); -#axis([0 750000 0 200]); -#hold off; +#hold on +#plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.') +#plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.') +#title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold') +#xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold') +#ylabel('velocity [m/yr]','FontSize',14,'FontWeight','bold') +#legend('calculated velocity','exact velocity') +#axis([0 750000 0 200]) +#hold off #subplot(2,2,4) #p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... -#abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none'); +#abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none') #title('Relative misfit [%]','FontSize',14,'FontWeight','bold') -#colorbar; -#caxis([0 100]); +#colorbar +#caxis([0 100]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('HOstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); -# system(['mv HOstatic.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceSheet']); +# printmodel('HOstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') +# system(['mv HOstatic.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceSheet']) #Fields and tolerances to track changes -field_names =[ \ - 'Vx','Vy','Vel', \ -] -field_tolerances=[ \ - 1e-12,1e-12,1e-12, \ -] -field_values=[ \ - vx,vy,vel, \ -] +field_names =['Vx','Vy','Vel'] +field_tolerances=[1e-12,1e-12,1e-12] +field_values=[vx,vy,vel] Index: /issm/trunk/test/NightlyRun/test1207.py =================================================================== --- /issm/trunk/test/NightlyRun/test1207.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1207.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: EISMINTRoundIceSheetStaticFS -import numpy +import numpy as np from model import * +from socket import gethostname from roundmesh import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -26,7 +27,7 @@ #Calculation of the analytical 2d velocity field constant=0.3 -vx_obs=constant/2.*md.mesh.x.reshape(-1,1)*(md.geometry.thickness)**-1 -vy_obs=constant/2.*md.mesh.y.reshape(-1,1)*(md.geometry.thickness)**-1 -vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) +vx_obs=constant/2.*md.mesh.x*(md.geometry.thickness)**-1 +vy_obs=constant/2.*md.mesh.y*(md.geometry.thickness)**-1 +vel_obs=np.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) #We extrude the model to have a 3d model @@ -35,5 +36,5 @@ #Spc the nodes on the bed -pos=numpy.nonzero(md.mesh.vertexonbase) +pos=np.where(md.mesh.vertexonbase) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. @@ -41,5 +42,5 @@ #Now we can solve the problem -md.cluster=generic('name',oshostname(),'np',8) +md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Stressbalance') @@ -47,5 +48,5 @@ vx=md.results.StressbalanceSolution.Vx vy=md.results.StressbalanceSolution.Vy -vel=numpy.zeros((md.mesh.numberofvertices2d,1)) +vel=np.zeros((md.mesh.numberofvertices2d)) for i in xrange(0,md.mesh.numberofvertices2d): @@ -53,7 +54,7 @@ for j in xrange(0,md.mesh.numberoflayers-1): node_vel=node_vel+1./(2.*(md.mesh.numberoflayers-1))*\ - (numpy.sqrt(vx[i+(j+1)*md.mesh.numberofvertices2d,0]**2+vy[i+(j+1)*md.mesh.numberofvertices2d,0]**2)+\ - numpy.sqrt(vx[i+j*md.mesh.numberofvertices2d,0]**2+vy[i+j*md.mesh.numberofvertices2d,0]**2)) - vel[i,0]=node_vel + (np.sqrt(vx[i+(j+1)*md.mesh.numberofvertices2d,0]**2+vy[i+(j+1)*md.mesh.numberofvertices2d,0]**2)+\ + np.sqrt(vx[i+j*md.mesh.numberofvertices2d,0]**2+vy[i+j*md.mesh.numberofvertices2d,0]**2)) + vel[i]=node_vel #Plot of the velocity from the exact and calculated solutions @@ -61,48 +62,42 @@ #subplot(2,2,1) #p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... -#vel,'FaceColor','interp','EdgeColor','none'); +#vel,'FaceColor','interp','EdgeColor','none') #title('Modelled velocity','FontSize',14,'FontWeight','bold') -#colorbar; -#caxis([0 200]); +#colorbar +#caxis([0 200]) #subplot(2,2,2) #p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... -#vel_obs,'FaceColor','interp','EdgeColor','none'); +#vel_obs,'FaceColor','interp','EdgeColor','none') #title('Analytical velocity','FontSize',14,'FontWeight','bold') -#colorbar; -#caxis([0 200]); +#colorbar +#caxis([0 200]) #subplot(2,2,3) -#hold on; -#plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.'); -#plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); -#title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold'); -#xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold'); -#ylabel('velocity [m/yr]','FontSize',14,'FontWeight','bold'); -#legend('calculated velocity','exact velocity'); -#axis([0 750000 0 200]); -#hold off; +#hold on +#plot(sqrt((md.mesh.x(1:md.mesh.numberofvertices2d)).^2+(md.mesh.y(1:md.mesh.numberofvertices2d)).^2),vel,'r.') +#plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.') +#title('Analytical vs calculated velocity','FontSize',14,'FontWeight','bold') +#xlabel('distance to the center of the icesheet [m]','FontSize',14,'FontWeight','bold') +#ylabel('velocity [m/yr]','FontSize',14,'FontWeight','bold') +#legend('calculated velocity','exact velocity') +#axis([0 750000 0 200]) +#hold off #subplot(2,2,4) #p=patch('Faces',md.mesh.elements2d,'Vertices',[md.mesh.x2d md.mesh.y2d],'FaceVertexCData',... -#abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none'); +#abs(vel-vel_obs)./vel_obs*100,'FaceColor','interp','EdgeColor','none') #title('Relative misfit [%]','FontSize',14,'FontWeight','bold') -#colorbar; -#caxis([0 100]); +#colorbar +#caxis([0 100]) if printingflag: pass # set(gcf,'Color','w') -# printmodel('FSstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); -# system(['mv FSstatic.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceSheet']); +# printmodel('FSstatic','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') +# system(['mv FSstatic.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT/IceSheet']) #Fields and tolerances to track changes -field_names =[ \ - 'Vx','Vy','Vel', \ -] -field_tolerances=[ \ - 1e-12,1e-12,1e-12, \ -] -field_values=[ \ - vx,vy,vel, \ -] +field_names =['Vx','Vy','Vel'] +field_tolerances=[1e-12,1e-12,1e-12] +field_values=[vx,vy,vel] Index: /issm/trunk/test/NightlyRun/test1208.py =================================================================== --- /issm/trunk/test/NightlyRun/test1208.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1208.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: EISMINTA -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -26,5 +27,5 @@ #Spc the nodes on the bed -pos=numpy.nonzero(md.mesh.vertexonbase) +pos=np.where(md.mesh.vertexonbase) md.stressbalance.spcvx[pos]=0. md.stressbalance.spcvy[pos]=0. @@ -39,5 +40,5 @@ #Now we can solve the problem -md.cluster=generic('name',oshostname(),'np',8) +md.cluster=generic('name',gethostname(),'np',8) md=solve(md,'Transient') @@ -45,14 +46,12 @@ field_names =['Vx','Vy','Vz','Vel','Pressure','Thickness','Base','Surface','Temperature','BasalforcingsGroundediceMeltingRate'] field_tolerances=[1e-08,1e-08,1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-07,1e-07] -field_values=[\ - md.results.TransientSolution[-1].Vx,\ - md.results.TransientSolution[-1].Vy,\ - md.results.TransientSolution[-1].Vz,\ - md.results.TransientSolution[-1].Vel,\ - md.results.TransientSolution[-1].Pressure,\ - md.results.TransientSolution[-1].Thickness,\ - md.results.TransientSolution[-1].Base,\ - md.results.TransientSolution[-1].Surface,\ - md.results.TransientSolution[-1].Temperature,\ - md.results.TransientSolution[-1].BasalforcingsGroundediceMeltingRate,\ - ] +field_values=[md.results.TransientSolution[-1].Vx, + md.results.TransientSolution[-1].Vy, + md.results.TransientSolution[-1].Vz, + md.results.TransientSolution[-1].Vel, + md.results.TransientSolution[-1].Pressure, + md.results.TransientSolution[-1].Thickness, + md.results.TransientSolution[-1].Base, + md.results.TransientSolution[-1].Surface, + md.results.TransientSolution[-1].Temperature, + md.results.TransientSolution[-1].BasalforcingsGroundediceMeltingRate] Index: /issm/trunk/test/NightlyRun/test121.py =================================================================== --- /issm/trunk/test/NightlyRun/test121.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test121.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedEnthalpyTran from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000) @@ -13,7 +14,7 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3); -md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.watercolumn=numpy.zeros((md.mesh.numberofvertices,1)) +md.cluster=generic('name',gethostname(),'np',3) +md.initialization.waterfraction=np.zeros((md.mesh.numberofvertices)) +md.initialization.watercolumn=np.zeros((md.mesh.numberofvertices)) md.transient.isstressbalance=False md.transient.ismasstransport=False Index: /issm/trunk/test/NightlyRun/test122.py =================================================================== --- /issm/trunk/test/NightlyRun/test122.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test122.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTransHOEnth from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000) @@ -13,10 +14,10 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.watercolumn=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.waterfraction=np.zeros((md.mesh.numberofvertices)) +md.initialization.watercolumn=np.zeros((md.mesh.numberofvertices)) md.thermal.isenthalpy=1 md.thermal.isdynamicbasalspc=1 md.thermal.stabilization=2 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test125.py =================================================================== --- /issm/trunk/test/NightlyRun/test125.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test125.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedRestartTranSSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from massfluxatgate import massfluxatgate from generic import generic @@ -15,8 +16,8 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.transient.requested_outputs=['IceVolume','TotalSmb'] -md.verbose=verbose('solution',1); +md.verbose=verbose('solution',1) md.settings.recording_frequency=5 @@ -29,5 +30,5 @@ #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','TotalSmb1','Bed1','Surface1','Thickness1','Volume1','Vx2','Vy2','Vel2','TotalSmb2','Bed2','Surface2','Thickness2','Volume2','Vx3','Vy3','Vel3','TotalSmb3','Bed3','Surface3','Thickness3','Volume3']; +field_names =['Vx1','Vy1','Vel1','TotalSmb1','Bed1','Surface1','Thickness1','Volume1','Vx2','Vy2','Vel2','TotalSmb2','Bed2','Surface2','Thickness2','Volume2','Vx3','Vy3','Vel3','TotalSmb3','Bed3','Surface3','Thickness3','Volume3'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ Index: /issm/trunk/test/NightlyRun/test126.py =================================================================== --- /issm/trunk/test/NightlyRun/test126.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test126.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedRestartTranHO3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from massfluxatgate import massfluxatgate from generic import generic @@ -14,10 +15,10 @@ md=setmask(md,'all','') md=parameterize(md,'../Par/SquareShelfConstrained.py') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.transient.requested_outputs=['IceVolume','TotalSmb'] md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.verbose=verbose('solution',1); +md.verbose=verbose('solution',1) md.settings.recording_frequency=5 @@ -30,5 +31,5 @@ #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','TotalSmb1','Bed1','Surface1','Thickness1','Volume1','Temperature1','Pressure1','Vx2','Vy2','Vel2','TotalSmb2','Bed2','Surface2','Thickness2','Volume2','Temperature2','Pressure2','Vx3','Vy3','Vel3','TotalSmb3','Bed3','Surface3','Thickness3','Volume3','Temperature3','Pressure3']; +field_names =['Vx1','Vy1','Vel1','TotalSmb1','Bed1','Surface1','Thickness1','Volume1','Temperature1','Pressure1','Vx2','Vy2','Vel2','TotalSmb2','Bed2','Surface2','Thickness2','Volume2','Temperature2','Pressure2','Vx3','Vy3','Vel3','TotalSmb3','Bed3','Surface3','Thickness3','Volume3','Temperature3','Pressure3'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ Index: /issm/trunk/test/NightlyRun/test1301.py =================================================================== --- /issm/trunk/test/NightlyRun/test1301.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1301.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: ThermalMelting -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from paterson import * from solve import * -from MatlabFuncs import * + """ @@ -27,7 +28,7 @@ #Some conditions specific to melting test -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1),int) -md.initialization.temperature=273.15*numpy.ones((md.mesh.numberofvertices,1)) -pos=numpy.nonzero(md.mesh.vertexonsurface)[0] +md.initialization.pressure=np.zeros((md.mesh.numberofvertices,1),int) +md.initialization.temperature=273.15*np.ones((md.mesh.numberofvertices)) +pos=np.nonzero(md.mesh.vertexonsurface)[0] md.thermal.spctemperature[pos]=md.initialization.temperature[pos] md.materials.rheology_B=paterson(md.initialization.temperature) @@ -39,11 +40,11 @@ #modeled results -md.cluster=generic('name',oshostname(),'np',2) +md.cluster=generic('name',gethostname(),'np',2) md=solve(md,'Thermal') #plot results comp_melting=md.results.ThermalSolution.BasalforcingsGroundediceMeltingRate -relative=numpy.abs((comp_melting-melting)/melting)*100. -relative[numpy.nonzero(comp_melting==melting)[0]]=0. +relative=np.abs((comp_melting-melting)/melting)*100. +relative[np.nonzero(comp_melting==melting)[0]]=0. #plotmodel(md,'data',comp_melting,'title','Modeled melting','data',melting,'title','Analytical melting',... # 'data',comp_melting-melting,'title','Absolute error','data',relative,'title','Relative error [%]',... @@ -52,6 +53,6 @@ pass # set(gcf,'Color','w') -# printmodel('thermalmelting','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); -# system(['mv thermalmelting.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']); +# printmodel('thermalmelting','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') +# system(['mv thermalmelting.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']) #Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test1302.py =================================================================== --- /issm/trunk/test/NightlyRun/test1302.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1302.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: ThermalAdvection -import numpy +import numpy as np import sys from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -26,11 +27,11 @@ #Thermal boundary conditions -pos1=numpy.nonzero(md.mesh.elementonbase)[0] +pos1=np.where(np.isnan(md.mesh.lowerelements))[0] md.thermal.spctemperature[md.mesh.elements[pos1,0:3]-1]=10. -pos2=numpy.nonzero(md.mesh.elementonsurface)[0] +pos2=np.where(np.isnan(md.mesh.upperelements))[0] md.thermal.spctemperature[md.mesh.elements[pos2,3:6]-1]=0. -md.initialization.vz=0.1*numpy.ones((md.mesh.numberofvertices,1)) -md.initialization.vel=numpy.sqrt( md.initialization.vx**2+ md.initialization.vy**2+ md.initialization.vz**2) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1),int) +md.initialization.vz=0.1*np.ones((md.mesh.numberofvertices)) +md.initialization.vel=np.sqrt(md.initialization.vx**2+ md.initialization.vy**2+ md.initialization.vz**2) +md.initialization.pressure=np.zeros((md.mesh.numberofvertices),int) md.thermal.stabilization=2 @@ -38,16 +39,16 @@ #d2T/dz2-w*rho_ice*c/k*dT/dz=0 T(surface)=0 T(bed)=10 => T=A exp(alpha z)+B alpha=0.1/md.constants.yts*md.materials.rho_ice*md.materials.heatcapacity/md.materials.thermalconductivity #alpha=w rho_ice c /k and w=0.1m/an -A=10./(numpy.exp(alpha*(-1000.))-1.) #A=T(bed)/(exp(alpha*bed)-1) with bed=-1000 T(bed)=10 +A=10./(np.exp(alpha*(-1000.))-1.) #A=T(bed)/(exp(alpha*bed)-1) with bed=-1000 T(bed)=10 B=-A -md.initialization.temperature=A*numpy.exp(alpha*md.mesh.z)+B +md.initialization.temperature=A*np.exp(alpha*md.mesh.z)+B #modeled results -md.cluster=generic('name',oshostname(),'np',2) +md.cluster=generic('name',gethostname(),'np',2) md=solve(md,'Thermal') #plot results comp_temp=md.results.ThermalSolution.Temperature -relative=numpy.abs((comp_temp-md.initialization.temperature)/md.initialization.temperature)*100. -relative[numpy.nonzero(comp_temp==md.initialization.temperature)[0]]=0. +relative=np.abs((comp_temp-md.initialization.temperature)/md.initialization.temperature)*100. +relative[np.nonzero(comp_temp==md.initialization.temperature)[0]]=0. #plotmodel(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,... # 'title','Analytical temperature [K]','view',3,'data',comp_temp-md.initialization.temperature,... @@ -57,6 +58,6 @@ pass # set(gcf,'Color','w') -# printmodel('thermaladvection','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); -# system(['mv thermaladvection.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT ']); +# printmodel('thermaladvection','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') +# system(['mv thermaladvection.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT ']) #Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test1303.py =================================================================== --- /issm/trunk/test/NightlyRun/test1303.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1303.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: ThermalConduction -import numpy +import numpy as np import sys from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -26,9 +27,10 @@ md=setflowequation(md,'HO','all') -pos1=numpy.nonzero(md.mesh.elementonbase)[0] + +pos1=np.where(np.isnan(md.mesh.lowerelements))[0] md.thermal.spctemperature[md.mesh.elements[pos1,0:3]-1]=10. -pos2=numpy.nonzero(md.mesh.elementonsurface)[0] +pos2=np.where(np.isnan(md.mesh.upperelements))[0] md.thermal.spctemperature[md.mesh.elements[pos2,3:6]-1]=0. -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1),int) +md.initialization.pressure=np.zeros((md.mesh.numberofvertices),int) #analytical results @@ -38,11 +40,11 @@ #modeled results -md.cluster=generic('name',oshostname(),'np',2) +md.cluster=generic('name',gethostname(),'np',2) md=solve(md,'Thermal') #plot results comp_temp=md.results.ThermalSolution.Temperature -relative=numpy.abs((comp_temp-md.initialization.temperature)/md.initialization.temperature)*100. -relative[numpy.nonzero(comp_temp==md.initialization.temperature)[0]]=0. +relative=np.abs((comp_temp-md.initialization.temperature)/md.initialization.temperature)*100. +relative[np.nonzero(comp_temp==md.initialization.temperature)[0]]=0. #plotmodel(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,... # 'title','Analytical temperature [K]','view',3,'data',comp_temp-md.initialization.temperature,... @@ -52,6 +54,6 @@ pass # set(gcf,'Color','w') -# printmodel('thermalconduction','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); -# system(['mv thermalconduction.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']); +# printmodel('thermalconduction','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') +# system(['mv thermalconduction.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']) #Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test1304.py =================================================================== --- /issm/trunk/test/NightlyRun/test1304.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1304.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: ThermalGeothermalFlux -import numpy +import numpy as np import sys from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + """ @@ -26,7 +27,7 @@ md=setflowequation(md,'HO','all') -pos2=numpy.nonzero(md.mesh.elementonsurface)[0] +pos2=np.where(np.isnan(md.mesh.upperelements))[0] md.thermal.spctemperature[md.mesh.elements[pos2,3:6]-1]=0. -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1),int) +md.initialization.pressure=np.zeros((md.mesh.numberofvertices),int) md.basalforcings.geothermalflux[:]=0.1 #100mW/m^2 @@ -37,11 +38,11 @@ #modeled results -md.cluster=generic('name',oshostname(),'np',2) +md.cluster=generic('name',gethostname(),'np',2) md=solve(md,'Thermal') #plot results comp_temp=md.results.ThermalSolution.Temperature -relative=numpy.abs((comp_temp-md.initialization.temperature)/md.initialization.temperature)*100. -relative[numpy.nonzero(comp_temp==md.initialization.temperature)[0]]=0. +relative=np.abs((comp_temp-md.initialization.temperature)/md.initialization.temperature)*100. +relative[np.where(comp_temp==md.initialization.temperature)[0]]=0. #plotmodel(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,... # 'title','Analytical temperature','view',3,'data',comp_temp-md.initialization.temperature,... @@ -51,6 +52,6 @@ pass # set(gcf,'Color','w') -# printmodel('thermalgeothermalflux','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off'); -# system(['mv thermalgeothermalflux.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']); +# printmodel('thermalgeothermalflux','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') +# system(['mv thermalgeothermalflux.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']) #Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test1501.m =================================================================== --- /issm/trunk/test/NightlyRun/test1501.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test1501.m (revision 21729) @@ -108,5 +108,5 @@ for t=starttime:endtime thickness = [thickness (md.results.TransientSolution(t).Thickness)]; - volume = [volume mean(md.results.TransientSolution(t).Thickness.value,2).*areas]; + volume = [volume mean(md.results.TransientSolution(t).Thickness(md.mesh.elements),2).*areas]; massbal = [massbal (md.results.TransientSolution(t).SmbMassBalance)]; velocity = [velocity (md.results.TransientSolution(t).Vel)]; @@ -132,5 +132,5 @@ [data datatype]=processdata(md,results(i).(field),options); - titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year']; + titlestring=[field ' at time ' num2str(results(i).time) ' year']; plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) options=changefieldvalue(options,'title',titlestring); @@ -147,5 +147,5 @@ [data datatype]=processdata(md,results(i).(field),options); - titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year']; + titlestring=[field ' at time ' num2str(results(i).time) ' year']; plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) options=changefieldvalue(options,'title',titlestring); @@ -196,5 +196,5 @@ else frame=getframe(gcf); - images(:,:,1,count) = rgb2ind(frame.cdata,map,'nodither'); + images(:,:,1,count) = rgb2ind(frame.cdata,[map; map],'nodither'); end Index: /issm/trunk/test/NightlyRun/test1501.py =================================================================== --- /issm/trunk/test/NightlyRun/test1501.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1501.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfTranSawTooth2d -import numpy +import numpy as np import sys from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + printingflag = False @@ -16,5 +17,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.isthermal=False @@ -24,5 +25,5 @@ #Solve for thinning rate -> -1 * surface mass balance -smb= 2.*numpy.ones((md.mesh.numberofvertices,1)) +smb= 2.*np.ones((md.mesh.numberofvertices)) md.smb.mass_balance= smb md.basalforcings.groundedice_melting_rate= smb @@ -37,12 +38,12 @@ smb = md.smb.mass_balance -#tooth= [ [ones(400,1)*(smb') - 10.]' [ones(400,1)*(smb')]' ]; -tooth=numpy.hstack((numpy.tile(smb-10.,(1,400)),numpy.tile(smb,(1,400)))) -#smb=[ [ones(399,1)*(smb')]' smb tooth tooth]; -smb=numpy.hstack((numpy.tile(smb,(1,399)),smb,tooth,tooth)) - -#md.smb.mass_balance= smb; -#md.smb.mass_balance(end+1,:)=[1.:2000.]; -md.smb.mass_balance=numpy.vstack((smb,numpy.arange(1,2001))) +#tooth= [ [ones(400,1)*(smb') - 10.]' [ones(400,1)*(smb')]' ] +tooth=np.hstack((np.tile(smb-10.,(1,400)),np.tile(smb,(1,400)))) +#smb=[ [ones(399,1)*(smb')]' smb tooth tooth] +smb=np.hstack((np.tile(smb,(1,399)),smb,tooth,tooth)) + +#md.smb.mass_balance= smb +#md.smb.mass_balance(end+1,:)=[1.:2000.] +md.smb.mass_balance=np.vstack((smb,np.arange(1,2001))) md=solve(md,'Transient') @@ -106,65 +107,65 @@ """ - starttime = 360; - endtime = 2000; - res = 40; - ts = [starttime:res:endtime]; - - index = md.mesh.elements; - x1=md.mesh.x(index(:,1)); x2=md.mesh.x(index(:,2)); x3=md.mesh.x(index(:,3)); - y1=md.mesh.y(index(:,1)); y2=md.mesh.y(index(:,2)); y3=md.mesh.y(index(:,3)); - areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))); - - thickness = []; - volume = []; - massbal = []; - velocity = []; + starttime = 360 + endtime = 2000 + res = 40 + ts = [starttime:res:endtime] + + index = md.mesh.elements + x1=md.mesh.x(index(:)) x2=md.mesh.x(index(:,2)) x3=md.mesh.x(index(:,3)) + y1=md.mesh.y(index(:)) y2=md.mesh.y(index(:,2)) y3=md.mesh.y(index(:,3)) + areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))) + + thickness = [] + volume = [] + massbal = [] + velocity = [] for t=starttime:endtime - thickness = [thickness (md.results.TransientSolution(t).Thickness)]; - volume = [volume mean(md.results.TransientSolution(t).Thickness.value,2).*areas]; - massbal = [massbal (md.results.TransientSolution(t).SmbMassBalance)]; - velocity = [velocity (md.results.TransientSolution(t).Vel)]; + thickness = [thickness (md.results.TransientSolution(t).Thickness)] + volume = [volume mean(md.results.TransientSolution(t).Thickness.value,2).*areas] + massbal = [massbal (md.results.TransientSolution(t).SmbMassBalance)] + velocity = [velocity (md.results.TransientSolution(t).Vel)] end figure('Position', [0 0 860 932]) - options = plotoptions('data','transient_movie','unit','km'); - options = options.list{1}; - options = checkplotoptions(md,options); + options = plotoptions('data','transient_movie','unit','km') + options = options.list{1} + options = checkplotoptions(md,options) %loop over the time steps - results=md.results.TransientSolution; - count = 1; + results=md.results.TransientSolution + count = 1 for i=ts subplot(5,9,[28:31 37:40]) set(gca,'pos',get(gca,'pos')+[-0.08 -0.08 0.07 0.08]) - field = 'Thickness'; + field = 'Thickness' %process data - [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options); - [data datatype]=processdata(md,results(i).(field),options); - - titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year']; + [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options) + [data datatype]=processdata(md,results(i).(field),options) + + titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year'] plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) - options=changefieldvalue(options,'title',titlestring); - options=addfielddefault(options,'colorbar',1); - options=changefieldvalue(options,'caxis',[0 max(max(thickness))]); - applyoptions(md,[],options); + options=changefieldvalue(options,'title',titlestring) + options=addfielddefault(options,'colorbar',1) + options=changefieldvalue(options,'caxis',[0 max(max(thickness))]) + applyoptions(md,[],options) subplot(5,9,[33:36 42:45]) set(gca,'pos',get(gca,'pos')+[-0.00 -0.08 0.07 0.08]) - field = 'Vel'; + field = 'Vel' %process data - [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options); - [data datatype]=processdata(md,results(i).(field),options); - - titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year']; + [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options) + [data datatype]=processdata(md,results(i).(field),options) + + titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year'] plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) - options=changefieldvalue(options,'title',titlestring); - options=addfielddefault(options,'colorbar',1); - options=changefieldvalue(options,'caxis',[0 max(max(velocity))]); - applyoptions(md,[],options); + options=changefieldvalue(options,'title',titlestring) + options=addfielddefault(options,'colorbar',1) + options=changefieldvalue(options,'caxis',[0 max(max(velocity))]) + applyoptions(md,[],options) subplot(5,4,1:4) @@ -173,7 +174,7 @@ plot(starttime:endtime,mean(massbal),'k','LineWidth', 4) hold on - ya = ylim; + ya = ylim plot([i i], ya, 'r', 'LineWidth',6) - ylim(ya); xlim([starttime endtime]); + ylim(ya) xlim([starttime endtime]) title('Surface Mass Balance','FontSize',14) ylabel('m/year','FontSize',14) @@ -184,7 +185,7 @@ plot(starttime:endtime,sum(volume)/1000/1000/1000,'LineWidth',4) hold on - ya = ylim; + ya = ylim plot([i i], ya, 'r', 'LineWidth',6) - ylim(ya); xlim([starttime endtime]); + ylim(ya) xlim([starttime endtime]) title('Ice Volume','FontSize',14) ylabel('km^3','FontSize',14) @@ -195,27 +196,27 @@ plot(starttime:endtime,mean(velocity)/1000, 'LineWidth', 4) hold on - ya = ylim; + ya = ylim plot([i i], ya, 'r', 'LineWidth',6) - ylim(ya); xlim([starttime endtime]); + ylim(ya) xlim([starttime endtime]) title('Mean Velocity','FontSize', 14) ylabel('km/year','FontSize', 14) xlabel('year','FontSize', 14) - set(gcf,'Renderer','zbuffer','color','white'); %fixes a bug on Mac OS X (not needed in future Matlab version) + set(gcf,'Renderer','zbuffer','color','white') %fixes a bug on Mac OS X (not needed in future Matlab version) if i==starttime, %initialize images and frame - frame=getframe(gcf); - [images,map]=rgb2ind(frame.cdata,256,'nodither'); - images(1,1,1,length(ts))=0; + frame=getframe(gcf) + [images,map]=rgb2ind(frame.cdata,256,'nodither') + images(1,1,1,length(ts))=0 else - frame=getframe(gcf); - images(:,:,1,count) = rgb2ind(frame.cdata,map,'nodither'); + frame=getframe(gcf) + images(:,:,1,count) = rgb2ind(frame.cdata,map,'nodither') end - count = count+1; + count = count+1 end - filename='transawtooth2d.gif'; + filename='transawtooth2d.gif' imwrite(images,map,filename,'DelayTime',1.0,'LoopCount',inf) """ Index: /issm/trunk/test/NightlyRun/test1502.py =================================================================== --- /issm/trunk/test/NightlyRun/test1502.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1502.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfTranSawTooth3d -import numpy +import numpy as np import sys from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + printingflag = False @@ -17,5 +18,5 @@ md=setflowequation(md,'SSA','all') md.extrude(3,1.) -md.cluster=generic('name',oshostname(),'np',2) +md.cluster=generic('name',gethostname(),'np',2) md.transient.isthermal=False @@ -25,5 +26,5 @@ #Solve for thinning rate -> -1 * surface mass balance -smb= 2.*numpy.ones((md.mesh.numberofvertices,1)) +smb= 2.*np.ones((md.mesh.numberofvertices)) md.smb.mass_balance= smb md.basalforcings.groundedice_melting_rate= smb @@ -38,12 +39,12 @@ smb = md.smb.mass_balance -#tooth= [ [ones(400,1)*(smb') - 10.]' [ones(400,1)*(smb')]' ]; -tooth=numpy.hstack((numpy.tile(smb-10.,(1,400)),numpy.tile(smb,(1,400)))) -#smb=[ [ones(399,1)*(smb')]' smb tooth tooth]; -smb=numpy.hstack((numpy.tile(smb,(1,399)),smb,tooth,tooth)) - -#md.smb.mass_balance= smb; -#md.smb.mass_balance(end+1,:)=[1.:2000.]; -md.smb.mass_balance=numpy.vstack((smb,numpy.arange(1,2001))) +#tooth= [ [ones(400,1)*(smb') - 10.]' [ones(400,1)*(smb')]' ] +tooth=np.hstack((np.tile(smb-10.,(1,400)),np.tile(smb,(1,400)))) +#smb=[ [ones(399,1)*(smb')]' smb tooth tooth] +smb=np.hstack((np.tile(smb,(1,399)),smb,tooth,tooth)) + +#md.smb.mass_balance= smb +#md.smb.mass_balance(end+1,:)=[1.:2000.] +md.smb.mass_balance=np.vstack((smb,np.arange(1,2001))) md=solve(md,'Transient') @@ -112,65 +113,65 @@ """ - starttime = 360; - endtime = 2000; - res = 40; - ts = [starttime:res:endtime]; - - index = md.mesh.elements; - x1=md.mesh.x(index(:,1)); x2=md.mesh.x(index(:,2)); x3=md.mesh.x(index(:,3)); - y1=md.mesh.y(index(:,1)); y2=md.mesh.y(index(:,2)); y3=md.mesh.y(index(:,3)); - areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))); - - thickness = []; - volume = []; - massbal = []; - velocity = []; + starttime = 360 + endtime = 2000 + res = 40 + ts = [starttime:res:endtime] + + index = md.mesh.elements + x1=md.mesh.x(index(:)) x2=md.mesh.x(index(:,2)) x3=md.mesh.x(index(:,3)) + y1=md.mesh.y(index(:)) y2=md.mesh.y(index(:,2)) y3=md.mesh.y(index(:,3)) + areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))) + + thickness = [] + volume = [] + massbal = [] + velocity = [] for t=starttime:endtime - thickness = [thickness (md.results.TransientSolution(t).Thickness)]; - volume = [volume mean(md.results.TransientSolution(t).Thickness.value,2).*areas]; - massbal = [massbal (md.results.TransientSolution(t).SmbMassBalance)]; - velocity = [velocity (md.results.TransientSolution(t).Vel)]; + thickness = [thickness (md.results.TransientSolution(t).Thickness)] + volume = [volume mean(md.results.TransientSolution(t).Thickness.value,2).*areas] + massbal = [massbal (md.results.TransientSolution(t).SmbMassBalance)] + velocity = [velocity (md.results.TransientSolution(t).Vel)] end figure('Position', [0 0 1060 1060]) - options = plotoptions('data','transient_movie','unit','km'); - options = options.list{1}; - options = checkplotoptions(md,options); + options = plotoptions('data','transient_movie','unit','km') + options = options.list{1} + options = checkplotoptions(md,options) %loop over the time steps - results=md.results.TransientSolution; - count = 1; + results=md.results.TransientSolution + count = 1 for i=ts subplot(5,9,[28:31 37:40]) set(gca,'pos',get(gca,'pos')+[-0.08 -0.08 0.07 0.08]) - field = 'Thickness'; + field = 'Thickness' %process data - [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options); - [data datatype]=processdata(md,results(i).(field),options); - - titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year']; + [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options) + [data datatype]=processdata(md,results(i).(field),options) + + titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year'] plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) - options=changefieldvalue(options,'title',titlestring); - options=addfielddefault(options,'colorbar',1); - options=changefieldvalue(options,'caxis',[0 max(max(thickness))]); - applyoptions(md,[],options); + options=changefieldvalue(options,'title',titlestring) + options=addfielddefault(options,'colorbar',1) + options=changefieldvalue(options,'caxis',[0 max(max(thickness))]) + applyoptions(md,[],options) subplot(5,9,[33:36 42:45]) set(gca,'pos',get(gca,'pos')+[-0.01 -0.08 0.07 0.08]) - field = 'Vel'; + field = 'Vel' %process data - [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options); - [data datatype]=processdata(md,results(i).(field),options); - - titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year']; + [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options) + [data datatype]=processdata(md,results(i).(field),options) + + titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year'] plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) - options=changefieldvalue(options,'title',titlestring); - options=addfielddefault(options,'colorbar',1); - options=changefieldvalue(options,'caxis',[0 max(max(velocity))]); - applyoptions(md,[],options); + options=changefieldvalue(options,'title',titlestring) + options=addfielddefault(options,'colorbar',1) + options=changefieldvalue(options,'caxis',[0 max(max(velocity))]) + applyoptions(md,[],options) subplot(5,4,1:4) @@ -179,7 +180,7 @@ plot(starttime:endtime,mean(massbal),'k','LineWidth', 4) hold on - ya = ylim; + ya = ylim plot([i i], ya, 'r', 'LineWidth',6) - ylim(ya); xlim([starttime endtime]); + ylim(ya) xlim([starttime endtime]) title('Surface Mass Balance','FontSize',14) ylabel('m/year','FontSize',14) @@ -190,7 +191,7 @@ plot(starttime:endtime,sum(volume)/1000/1000/1000,'LineWidth',4) hold on - ya = ylim; + ya = ylim plot([i i], ya, 'r', 'LineWidth',6) - ylim(ya); xlim([starttime endtime]); + ylim(ya) xlim([starttime endtime]) title('Ice Volume','FontSize',14) ylabel('km^3','FontSize',14) @@ -201,27 +202,27 @@ plot(starttime:endtime,mean(velocity)/1000, 'LineWidth', 4) hold on - ya = ylim; + ya = ylim plot([i i], ya, 'r', 'LineWidth',6) - ylim(ya); xlim([starttime endtime]); + ylim(ya) xlim([starttime endtime]) title('Mean Velocity','FontSize', 14) ylabel('km/year','FontSize', 14) xlabel('year','FontSize', 14) - set(gcf,'Renderer','zbuffer','color','white'); %fixes a bug on Mac OS X (not needed in future Matlab version) + set(gcf,'Renderer','zbuffer','color','white') %fixes a bug on Mac OS X (not needed in future Matlab version) if i==starttime, %initialize images and frame - frame=getframe(gcf); - [images,map]=rgb2ind(frame.cdata,256,'nodither'); - images(1,1,1,length(ts))=0; + frame=getframe(gcf) + [images,map]=rgb2ind(frame.cdata,256,'nodither') + images(1,1,1,length(ts))=0 else - frame=getframe(gcf); - images(:,:,1,count) = rgb2ind(frame.cdata,map,'nodither'); + frame=getframe(gcf) + images(:,:,1,count) = rgb2ind(frame.cdata,map,'nodither') end - count = count+1; + count = count+1 end - filename='transawtooth3d.gif'; + filename='transawtooth3d.gif' imwrite(images,map,filename,'DelayTime',1.0,'LoopCount',inf) """ Index: /issm/trunk/test/NightlyRun/test1601.py =================================================================== --- /issm/trunk/test/NightlyRun/test1601.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1601.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfSSA2dRotation -import numpy +import numpy as np import sys from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,43 +15,39 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.stressbalance.spcvx[numpy.nonzero(md.mesh.y>0.)]=float('NaN') +md.stressbalance.spcvx[np.where(md.mesh.y>0.)]=np.nan md.initialization.vx[:]=0. md.initialization.vy[:]=0. -md.initialization.vel=numpy.zeros_like(md.initialization.vx) +md.initialization.vel=np.zeros((md.mesh.numberofvertices)) -md.cluster=generic('name',oshostname(),'np',2) +md.cluster=generic('name',gethostname(),'np',2) md=solve(md,'Stressbalance') vel0=md.results.StressbalanceSolution.Vel - -theta=30.*numpy.pi/180. +theta=30.*np.pi/180. x=md.mesh.x y=md.mesh.y -md.mesh.x=numpy.cos(theta)*x-numpy.sin(theta)*y -md.mesh.y=numpy.sin(theta)*x+numpy.cos(theta)*y +md.mesh.x=np.cos(theta)*x-np.sin(theta)*y +md.mesh.y=np.sin(theta)*x+np.cos(theta)*y -md.stressbalance.referential[:,0:3]=numpy.tile([numpy.cos(theta),numpy.sin(theta),0],(md.mesh.numberofvertices,1)) -md.stressbalance.referential[:,3: ]=numpy.tile([0,0,1],(md.mesh.numberofvertices,1)) +rotation_array=np.array([np.cos(theta),np.sin(theta),0]) +md.stressbalance.referential[:,0:3]=(np.tile(rotation_array,(md.mesh.numberofvertices,1))) +md.stressbalance.referential[:,3: ]=np.tile([0,0,1],(md.mesh.numberofvertices,1)) md=solve(md,'Stressbalance') vel1=md.results.StressbalanceSolution.Vel - #plotmodel(md,'data',vel0,'data',vel1,'data',vel1-vel0,'title','Cartesian CS','title','Rotated CS','title','difference') -print "Error between Cartesian and rotated CS: %g" % (numpy.max(numpy.abs(vel0-vel1))/(numpy.max(numpy.abs(vel0))+sys.float_info.epsilon)) +print "Error between Cartesian and rotated CS: %g" % (np.max(np.abs(vel0-vel1))/(np.max(np.abs(vel0))+sys.float_info.epsilon)) #Now, put CS back to normal except on the side where the spc are applied -pos=numpy.nonzero(numpy.logical_or(x==0.,x==1000000.))[0] -md.stressbalance.referential[:]=float('NaN') -md.stressbalance.referential[pos,0:3]=numpy.tile([numpy.cos(theta),numpy.sin(theta),0],(len(pos),1)) -md.stressbalance.referential[pos,3: ]=numpy.tile([0,0,1],(len(pos),1)) +pos=np.where(np.logical_or(x==0.,x==1000000.))[0] +md.stressbalance.referential[:]=np.nan +md.stressbalance.referential[pos,0:3]=np.tile([np.cos(theta),np.sin(theta),0],(len(pos),1)) +md.stressbalance.referential[pos,3: ]=np.tile([0,0,1],(len(pos),1)) md=solve(md,'Stressbalance') vel2=md.results.StressbalanceSolution.Vel #plotmodel(md,'data',vel0,'data',vel2,'data',vel2-vel0,'title','Cartesian CS','title','Rotated CS','title','difference') -print "Error between Cartesian and rotated CS: %g" % (numpy.max(numpy.abs(vel0-vel2))/(numpy.max(numpy.abs(vel0))+sys.float_info.epsilon)) +print "Error between Cartesian and rotated CS: %g" % (np.max(np.abs(vel0-vel2))/(np.max(np.abs(vel0))+sys.float_info.epsilon)) #Fields and tolerances to track changes field_names =['vel1','vel2'] field_tolerances=[1e-11,1e-11] -field_values=[\ - vel1, \ - vel2, \ - ] +field_values=[vel1,vel2] Index: /issm/trunk/test/NightlyRun/test1602.py =================================================================== --- /issm/trunk/test/NightlyRun/test1602.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test1602.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfHORotation -import numpy +import numpy as np import sys from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -15,31 +16,29 @@ md.extrude(5,1.) md=setflowequation(md,'HO','all') -md.stressbalance.spcvx[numpy.nonzero(md.mesh.y>0.)]=float('NaN') +md.stressbalance.spcvx[np.nonzero(md.mesh.y>0.)]=np.nan md.initialization.vx[:]=0. md.initialization.vy[:]=0. -md.initialization.vel=numpy.zeros_like(md.initialization.vx) +md.initialization.vel=np.zeros_like(md.initialization.vx) -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') vel0=md.results.StressbalanceSolution.Vel -theta=30.*numpy.pi/180. +theta=30.*np.pi/180. x=md.mesh.x y=md.mesh.y -md.mesh.x=numpy.cos(theta)*x-numpy.sin(theta)*y -md.mesh.y=numpy.sin(theta)*x+numpy.cos(theta)*y +md.mesh.x=np.cos(theta)*x-np.sin(theta)*y +md.mesh.y=np.sin(theta)*x+np.cos(theta)*y -md.stressbalance.referential[:,0:3]=numpy.tile([numpy.cos(theta),numpy.sin(theta),0],(md.mesh.numberofvertices,1)) -md.stressbalance.referential[:,3: ]=numpy.tile([0,0,1],(md.mesh.numberofvertices,1)) +md.stressbalance.referential[:,0:3]=np.tile([np.cos(theta),np.sin(theta),0],(md.mesh.numberofvertices,1)) +md.stressbalance.referential[:,3: ]=np.tile([0,0,1],(md.mesh.numberofvertices,1)) md=solve(md,'Stressbalance') vel1=md.results.StressbalanceSolution.Vel #plotmodel(md,'data',vel0,'data',vel1,'data',vel1-vel0,'title','Cartesian CS','title','Rotated CS','title','difference','view#all',2) -print "Error between Cartesian and rotated CS: %g" % (numpy.max(numpy.abs(vel0-vel1))/(numpy.max(numpy.abs(vel0))+sys.float_info.epsilon)) +print "Error between Cartesian and rotated CS: %g" % (np.max(np.abs(vel0-vel1))/(np.max(np.abs(vel0))+sys.float_info.epsilon)) #Fields and tolerances to track changes field_names =['vel1'] field_tolerances=[1e-9] -field_values=[\ - vel1, \ - ]; +field_values=[vel1] Index: /issm/trunk/test/NightlyRun/test2001.py =================================================================== --- /issm/trunk/test/NightlyRun/test2001.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test2001.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetConstrainedGia2d -import numpy +import numpy as np import copy from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + #Define a model @@ -22,14 +23,12 @@ md.timestepping.start_time=2400000 # 2,400 kyr md.timestepping.final_time=2500000 # 2,500 kyr -md.geometry.thickness=numpy.hstack((\ - numpy.vstack((md.geometry.thickness*0.0, 0.0)),\ - numpy.vstack((md.geometry.thickness/2.0, 0.1)),\ - numpy.vstack((md.geometry.thickness, 0.2)),\ - numpy.vstack((md.geometry.thickness, 1.0)),\ - numpy.vstack((md.geometry.thickness, md.timestepping.start_time)),\ - )) +md.geometry.thickness=np.vstack((np.hstack((md.geometry.thickness*0.0, 0.0)), + np.hstack((md.geometry.thickness/2.0, 0.1)), + np.hstack((md.geometry.thickness, 0.2)), + np.hstack((md.geometry.thickness, 1.0)), + np.hstack((md.geometry.thickness, md.timestepping.start_time)))).T #Solve for GIA deflection -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Gia') @@ -37,7 +36,5 @@ field_names =['GiaW','GiadWdt'] field_tolerances=[1e-13,1e-13] -field_values =[\ - md.results.GiaSolution.GiaW,\ - md.results.GiaSolution.GiadWdt,\ - ] +field_values =[md.results.GiaSolution.GiaW, + md.results.GiaSolution.GiadWdt] Index: /issm/trunk/test/NightlyRun/test2002.m =================================================================== --- /issm/trunk/test/NightlyRun/test2002.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2002.m (revision 21729) @@ -44,4 +44,6 @@ % }}} +md.slr.ocean_area_scaling=0; + %geometry di=md.materials.rho_ice/md.materials.rho_water; Index: /issm/trunk/test/NightlyRun/test2002.py =================================================================== --- /issm/trunk/test/NightlyRun/test2002.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test2002.py (revision 21729) @@ -1,7 +1,6 @@ #Test Name: EarthSlr -from MatlabFuncs import * -from PythonFuncs import * from model import * -from numpy import * +from socket import gethostname +import numpy as np from parameterize import * from solve import * @@ -12,62 +11,62 @@ from love_numbers import * -#mesh earth: -md=model() +#mesh earth: +md=model() md.mesh=gmshplanet('radius',6.371012*10**3,'resolution',700.) #500 km resolution mesh #parameterize slr solution: -#slr loading: {{{ -md.slr.deltathickness=zeros((md.mesh.numberofelements,1)) -md.slr.sealevel=zeros((md.mesh.numberofvertices,1)) +#slr loading: +md.slr.deltathickness=np.zeros((md.mesh.numberofelements)) +md.slr.sealevel=np.zeros((md.mesh.numberofvertices)) #antarctica -late=numpy.sum(md.mesh.lat[md.mesh.elements-1],axis=1)/3 -longe=numpy.sum(md.mesh.long[md.mesh.elements-1],axis=1)/3 -pos=numpy.nonzero(late <-80) +late=np.sum(md.mesh.lat[md.mesh.elements-1],axis=1)/3 +longe=np.sum(md.mesh.long[md.mesh.elements-1],axis=1)/3 +pos=np.where(late <-80) md.slr.deltathickness[pos]=-100 #greenland -pos=numpy.nonzero(logical_and_n(late > 70,late < 80,longe>-60,longe<-30)) +pos=np.where(np.logical_and.reduce((late > 70,late < 80,longe>-60,longe<-30))) md.slr.deltathickness[pos]=-100 -#elastic loading from love numbers: +#elastic loading from love numbers: nlov=101 -md.slr.love_h = love_numbers('h')[:nlov]; -md.slr.love_k = love_numbers('k')[:nlov]; -md.slr.love_l = love_numbers('l')[:nlov]; +md.slr.love_h = love_numbers('h')[:nlov] +md.slr.love_k = love_numbers('k')[:nlov] +md.slr.love_l = love_numbers('l')[:nlov] -#}}} -#mask: {{{ -md.mask=maskpsl() # use maskpsl class (instead of mask) to store the ocean function as a ocean_levelset -mask=gmtmask(md.mesh.lat,md.mesh.long) +#mask: +md.mask=maskpsl() # use maskpsl class (instead of mask) to store the ocean function as a ocean_levelset +mask=gmtmask(md.mesh.lat,md.mesh.long) -icemask=ones((md.mesh.numberofvertices,1)) -pos=nonzero(mask==0)[0]; icemask[pos]=-1 -pos=nonzero(sum(mask[md.mesh.elements.astype(int)-1],axis=1)<3)[0] +icemask=np.ones((md.mesh.numberofvertices)) +pos=np.where(mask==0)[0] +icemask[pos]=-1 +pos=np.where(np.sum(mask[md.mesh.elements.astype(int)-1],axis=1)<3)[0] icemask[md.mesh.elements[pos,:].astype(int)-1]=-1 md.mask.ice_levelset=icemask -md.mask.ocean_levelset=zeros((md.mesh.numberofvertices,1)) -pos=numpy.nonzero(md.mask.ice_levelset==1) +md.mask.ocean_levelset=np.zeros((md.mesh.numberofvertices)) +pos=np.where(md.mask.ice_levelset==1) md.mask.ocean_levelset[pos]=1 #make sure that the ice level set is all inclusive: -md.mask.land_levelset=zeros((md.mesh.numberofvertices,1)) -md.mask.groundedice_levelset=-ones((md.mesh.numberofvertices,1)) +md.mask.land_levelset=np.zeros((md.mesh.numberofvertices)) +md.mask.groundedice_levelset=-np.ones((md.mesh.numberofvertices)) -#make sure wherever there is an ice load, that the mask is set to ice: -pos=nonzero(md.slr.deltathickness)[0]; +#make sure wherever there is an ice load, that the mask is set to ice: +pos=np.nonzero(md.slr.deltathickness)[0] icemask[md.mesh.elements[pos,:]-1]=-1 -# }}} + #geometry di=md.materials.rho_ice/md.materials.rho_water -md.geometry.thickness=ones((md.mesh.numberofvertices,1)) -md.geometry.surface=(1-di)*zeros((md.mesh.numberofvertices,1)) +md.geometry.thickness=np.ones((md.mesh.numberofvertices)) +md.geometry.surface=(1-di)*np.zeros((md.mesh.numberofvertices)) md.geometry.base=md.geometry.surface-md.geometry.thickness md.geometry.bed=md.geometry.base #materials -md.initialization.temperature=273.25*ones((md.mesh.numberofvertices,1)) +md.initialization.temperature=273.25*np.ones((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3*ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3*np.ones((md.mesh.numberofelements)) #Miscellaneous @@ -75,5 +74,5 @@ #Solution parameters -md.slr.reltol=NaN +md.slr.reltol=np.nan md.slr.abstol=1e-3 @@ -82,5 +81,5 @@ md.slr.elastic=0 md=solve(md,'Sealevelrise') -Seustatic=md.results.SealevelriseSolution.Sealevel; +Seustatic=md.results.SealevelriseSolution.Sealevel #eustatic + rigid run: @@ -88,5 +87,5 @@ md.slr.elastic=0 md=solve(md,'Sealevelrise') -Srigid=md.results.SealevelriseSolution.Sealevel; +Srigid=md.results.SealevelriseSolution.Sealevel #eustatic + rigid + elastic run: @@ -94,12 +93,12 @@ md.slr.elastic=1 md=solve(md,'Sealevelrise') -Selastic=md.results.SealevelriseSolution.Sealevel; +Selastic=md.results.SealevelriseSolution.Sealevel #eustatic + rigid + elastic + rotation run: md.slr.rigid=1 md.slr.elastic=1 -md.slr.rotation=1; -md=solve(md,'Sealevelrise'); -Srotation=md.results.SealevelriseSolution.Sealevel; +md.slr.rotation=1 +md=solve(md,'Sealevelrise') +Srotation=md.results.SealevelriseSolution.Sealevel #Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test2003.m =================================================================== --- /issm/trunk/test/NightlyRun/test2003.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2003.m (revision 21729) @@ -12,6 +12,6 @@ late=sum(md.mesh.lat(md.mesh.elements),2)/3; longe=sum(md.mesh.long(md.mesh.elements),2)/3; -pos=find(late <-80); -md.slr.deltathickness(pos)=-100; +pos=find(late <-75 & longe <0); +md.slr.deltathickness(pos)=-1; %elastic loading from love numbers: @@ -64,5 +64,7 @@ %eustatic + rigid + elastic run: -md.slr.rigid=1; md.slr.elastic=1; md.slr.rotation=0; +md.slr.rigid=1; md.slr.elastic=1; md.slr.rotation=0; +md.cluster=generic('name',oshostname(),'np',3); +%md.verbose=verbose('111111111'); md=solve(md,'Sealevelrise'); SnoRotation=md.results.SealevelriseSolution.Sealevel; @@ -70,9 +72,11 @@ %eustatic + rigid + elastic + rotation run: md.slr.rigid=1; md.slr.elastic=1; md.slr.rotation=1; +md.cluster=generic('name',oshostname(),'np',3); +%md.verbose=verbose('111111111'); md=solve(md,'Sealevelrise'); -Srotation=md.results.SealevelriseSolution.Sealevel; +SRotation=md.results.SealevelriseSolution.Sealevel; %Fields and tolerances to track changes field_names ={'noRotation','Rotation'}; field_tolerances={1e-13,1e-13}; -field_values={SnoRotation,Srotation}; +field_values={SnoRotation,SRotation}; Index: /issm/trunk/test/NightlyRun/test201.py =================================================================== --- /issm/trunk/test/NightlyRun/test201.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test201.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressSSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from ContourToMesh import * @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') @@ -19,8 +20,6 @@ field_names =['Vx','Vy','Vel','Pressure'] field_tolerances=[1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Pressure,\ - ] +field_values=[md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Pressure] Index: /issm/trunk/test/NightlyRun/test202.py =================================================================== --- /issm/trunk/test/NightlyRun/test202.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test202.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfStressSSA3d -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.extrude(3,2.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test203.py =================================================================== --- /issm/trunk/test/NightlyRun/test203.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test203.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfStressHO -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.extrude(3,2.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test204.py =================================================================== --- /issm/trunk/test/NightlyRun/test204.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test204.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfStressFS -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,9 +16,9 @@ md.extrude(3,2.) md=setflowequation(md,'FS','all') -md.cluster=generic('name',oshostname(),'np',3) -md.stressbalance.shelf_dampening=1; -md.timestepping.time_step=0; +md.cluster=generic('name',gethostname(),'np',3) +md.stressbalance.shelf_dampening=1 +md.timestepping.time_step=0 md1=solve(md,'Stressbalance') -md.stressbalance.shelf_dampening=0; +md.stressbalance.shelf_dampening=0 md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test205.py =================================================================== --- /issm/trunk/test/NightlyRun/test205.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test205.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfStressMHOPenalties -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.extrude(3,2.) md=setflowequation(md,'HO','../Exp/SquareHalfRight.exp','fill','SSA','coupling','penalties') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test2051.m =================================================================== --- /issm/trunk/test/NightlyRun/test2051.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2051.m (revision 21729) @@ -1,7 +1,7 @@ -%Test Name: GiaBenchmarksAB2dA1 +%Test Name: GiaIvinsBenchmarksAB2dA1 % Benchmark experiments (Figure A2a Ivins and James, 1999, Geophys. J. Int.) md=triangle(model(),'../Exp/RoundFrontEISMINT.exp',200000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/GiaBenchmarksAB.par'); +md=parameterize(md,'../Par/GiaIvinsBenchmarksAB.par'); %% indicate what you want to compute Index: /issm/trunk/test/NightlyRun/test2052.m =================================================================== --- /issm/trunk/test/NightlyRun/test2052.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2052.m (revision 21729) @@ -1,7 +1,7 @@ -%Test Name: GiaBenchmarksAB2dA2 +%Test Name: GiaIvinsBenchmarksAB2dA2 % Benchmark experiments (Figure A2a Ivins and James, 1999, Geophys. J. Int.) md=triangle(model(),'../Exp/RoundFrontEISMINT.exp',200000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/GiaBenchmarksAB.par'); +md=parameterize(md,'../Par/GiaIvinsBenchmarksAB.par'); %% indicate what you want to compute Index: /issm/trunk/test/NightlyRun/test2053.m =================================================================== --- /issm/trunk/test/NightlyRun/test2053.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2053.m (revision 21729) @@ -1,7 +1,7 @@ -%Test Name: GiaBenchmarksAB2dA3 +%Test Name: GiaIvinsBenchmarksAB2dA3 % Benchmark experiments (Figure A2a Ivins and James, 1999, Geophys. J. Int.) md=triangle(model(),'../Exp/RoundFrontEISMINT.exp',200000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/GiaBenchmarksAB.par'); +md=parameterize(md,'../Par/GiaIvinsBenchmarksAB.par'); %% indicate what you want to compute Index: /issm/trunk/test/NightlyRun/test206.py =================================================================== --- /issm/trunk/test/NightlyRun/test206.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test206.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfTherStea -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -16,5 +17,5 @@ md=setflowequation(md,'SSA','all') md.timestepping.time_step=0 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Thermal') @@ -24,6 +25,4 @@ field_names =['Temperature','BasalforcingsGroundediceMeltingRate'] field_tolerances=[1e-13,5e-6] -field_values=[\ - md.results.ThermalSolution.Temperature,\ - md.results.ThermalSolution.BasalforcingsGroundediceMeltingRate,\ - ] +field_values=[md.results.ThermalSolution.Temperature, + md.results.ThermalSolution.BasalforcingsGroundediceMeltingRate] Index: /issm/trunk/test/NightlyRun/test207.py =================================================================== --- /issm/trunk/test/NightlyRun/test207.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test207.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfTherTran -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.isstressbalance=False md.transient.ismasstransport=False Index: /issm/trunk/test/NightlyRun/test2071.m =================================================================== --- /issm/trunk/test/NightlyRun/test2071.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2071.m (revision 21729) @@ -1,7 +1,7 @@ -%Test Name: GiaBenchmarksAB2dC1 +%Test Name: GiaIvinsBenchmarksAB2dC1 % Benchmark experiments (Figure A2c Ivins and James, 1999, Geophys. J. Int.) md=triangle(model(),'../Exp/RoundFrontEISMINT.exp',200000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/GiaBenchmarksCD.par'); +md=parameterize(md,'../Par/GiaIvinsBenchmarksCD.par'); %% indicate what you want to compute Index: /issm/trunk/test/NightlyRun/test2072.m =================================================================== --- /issm/trunk/test/NightlyRun/test2072.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2072.m (revision 21729) @@ -1,7 +1,7 @@ -%Test Name: GiaBenchmarksAB2dC2 +%Test Name: GiaIvinsBenchmarksAB2dC2 % Benchmark experiments (Figure A2c Ivins and James, 1999, Geophys. J. Int.) md=triangle(model(),'../Exp/RoundFrontEISMINT.exp',200000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/GiaBenchmarksCD.par'); +md=parameterize(md,'../Par/GiaIvinsBenchmarksCD.par'); %% indicate what you want to compute Index: /issm/trunk/test/NightlyRun/test2073.m =================================================================== --- /issm/trunk/test/NightlyRun/test2073.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2073.m (revision 21729) @@ -1,7 +1,7 @@ -%Test Name: GiaBenchmarksAB2dC3 +%Test Name: GiaIvinsBenchmarksAB2dC3 % Benchmark experiments (Figure A2c Ivins and James, 1999, Geophys. J. Int.) md=triangle(model(),'../Exp/RoundFrontEISMINT.exp',200000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/GiaBenchmarksCD.par'); +md=parameterize(md,'../Par/GiaIvinsBenchmarksCD.par'); %% indicate what you want to compute Index: /issm/trunk/test/NightlyRun/test208.py =================================================================== --- /issm/trunk/test/NightlyRun/test208.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test208.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfTranSSA2d -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.basalforcings.floatingice_melting_rate[:]=1. md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.requested_outputs=['default','FloatingArea','GroundedArea','TotalFloatingBmb','TotalGroundedBmb'] md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test2081.m =================================================================== --- /issm/trunk/test/NightlyRun/test2081.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2081.m (revision 21729) @@ -1,7 +1,7 @@ -%Test Name: GiaBenchmarksAB2dD1 +%Test Name: GiaIvinsBenchmarksAB2dD1 % Benchmark experiments (Figure A2d Ivins and James, 1999, Geophys. J. Int.) md=triangle(model(),'../Exp/RoundFrontEISMINT.exp',200000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/GiaBenchmarksCD.par'); +md=parameterize(md,'../Par/GiaIvinsBenchmarksCD.par'); %% indicate what you want to compute Index: /issm/trunk/test/NightlyRun/test2082.m =================================================================== --- /issm/trunk/test/NightlyRun/test2082.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2082.m (revision 21729) @@ -1,7 +1,7 @@ -%Test Name: GiaBenchmarksAB2dD2 +%Test Name: GiaIvinsBenchmarksAB2dD2 % Benchmark experiments (Figure A2d Ivins and James, 1999, Geophys. J. Int.) md=triangle(model(),'../Exp/RoundFrontEISMINT.exp',200000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/GiaBenchmarksCD.par'); +md=parameterize(md,'../Par/GiaIvinsBenchmarksCD.par'); %% indicate what you want to compute Index: /issm/trunk/test/NightlyRun/test2083.m =================================================================== --- /issm/trunk/test/NightlyRun/test2083.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2083.m (revision 21729) @@ -1,7 +1,7 @@ -%Test Name: GiaBenchmarksAB2dD3 +%Test Name: GiaIvinsBenchmarksAB2dD3 % Benchmark experiments (Figure A2d Ivins and James, 1999, Geophys. J. Int.) md=triangle(model(),'../Exp/RoundFrontEISMINT.exp',200000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/GiaBenchmarksCD.par'); +md=parameterize(md,'../Par/GiaIvinsBenchmarksCD.par'); %% indicate what you want to compute Index: /issm/trunk/test/NightlyRun/test209.py =================================================================== --- /issm/trunk/test/NightlyRun/test209.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test209.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfTranSSA3d -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test210.py =================================================================== --- /issm/trunk/test/NightlyRun/test210.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test210.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfTranHO -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test211.py =================================================================== --- /issm/trunk/test/NightlyRun/test211.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test211.py (revision 21729) @@ -1,6 +1,6 @@ #Test Name: SquareShelfTranFS -from MatlabFuncs import * from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,6 +15,6 @@ md.extrude(3,1.) md=setflowequation(md,'FS','all') -md.stressbalance.reltol=NaN -md.cluster=generic('name',oshostname(),'np',3) +md.stressbalance.reltol=np.NaN +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') @@ -22,42 +22,38 @@ # Fields and tolerances to track changes -field_names=[\ - 'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsGroundediceMeltingRate1', \ - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', \ - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'] -field_tolerances=[\ - 2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,\ - 5e-06,5e-06,8e-05,5e-06,1e-07,5e-07,5e-07,5e-07,3e-06,5e-05,\ - 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vz,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].Temperature,\ - md.results.TransientSolution[0].BasalforcingsGroundediceMeltingRate,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vz,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].Temperature,\ - md.results.TransientSolution[1].BasalforcingsGroundediceMeltingRate,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vz,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].Temperature,\ - md.results.TransientSolution[2].BasalforcingsGroundediceMeltingRate,\ - ] +field_names=['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsGroundediceMeltingRate1', + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'] +field_tolerances=[2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08, + 5e-06,5e-06,8e-05,5e-06,1e-07,5e-07,5e-07,5e-07,3e-06,5e-05, + 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vz, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Temperature, + md.results.TransientSolution[0].BasalforcingsGroundediceMeltingRate, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vz, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Temperature, + md.results.TransientSolution[1].BasalforcingsGroundediceMeltingRate, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vz, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Temperature, + md.results.TransientSolution[2].BasalforcingsGroundediceMeltingRate] Index: /issm/trunk/test/NightlyRun/test2110.m =================================================================== --- /issm/trunk/test/NightlyRun/test2110.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test2110.m (revision 21729) @@ -17,6 +17,4 @@ %love numbers: nlov=10001; % horizontal displacements do not work for low degree truncation, e.g., 101 -%md.esa.love_h = love_numbers('h','CM'); md.esa.love_h(nlov+1:end)=[]; -%md.esa.love_l = love_numbers('l','CM'); md.esa.love_l(nlov+1:end)=[]; md.esa.love_h = love_numbers('h'); md.esa.love_h(nlov+1:end)=[]; md.esa.love_l = love_numbers('l'); md.esa.love_l(nlov+1:end)=[]; @@ -51,5 +49,6 @@ % solve esa -md.esa.requested_outputs = {'EsaUmotion','EsaNmotion','EsaEmotion'}; +md.esa.requested_outputs = {'EsaUmotion','EsaNmotion','EsaEmotion',... + 'EsaStrainratexx','EsaStrainratexy','EsaStrainrateyy','EsaRotationrate'}; md.cluster=generic('name',oshostname(),'np',3); md.verbose=verbose('111111111'); @@ -57,10 +56,15 @@ %Fields and tolerances to track changes -field_names ={'EsaUmotion','EsaNmotion','EsaEmotion'}; -field_tolerances={1e-13,1e-13,1e-13}; +field_names ={'EsaUmotion','EsaNmotion','EsaEmotion',... + 'EsaStrainratexx','EsaStrainratexy','EsaStrainrateyy','EsaRotationrate'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; field_values={... (md.results.EsaSolution.EsaUmotion),... (md.results.EsaSolution.EsaNmotion),... (md.results.EsaSolution.EsaEmotion),... + (md.results.EsaSolution.EsaStrainratexx),... + (md.results.EsaSolution.EsaStrainratexy),... + (md.results.EsaSolution.EsaStrainrateyy),... + (md.results.EsaSolution.EsaRotationrate),... }; Index: /issm/trunk/test/NightlyRun/test212.py =================================================================== --- /issm/trunk/test/NightlyRun/test212.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test212.py (revision 21729) @@ -1,6 +1,6 @@ #Test Name: SquareShelfCMBSSA2d -from MatlabFuncs import * from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,22 +15,21 @@ md=setflowequation(md,'SSA','all') - # control parameters md.inversion.iscontrol=1 md.inversion.control_parameters=['MaterialsRheologyBbar'] -md.inversion.min_parameters=10**6*ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=2.*10**9*ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.0e6*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=2.0e9*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[101] -md.inversion.cost_functions_coefficients=ones((md.mesh.numberofvertices,1)) -md.inversion.gradient_scaling=10**7*ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2.*ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.3*ones((md.inversion.nsteps,1)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices)) +md.inversion.gradient_scaling=1.0e7*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2.*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.3*np.ones((md.inversion.nsteps)) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') @@ -40,11 +39,9 @@ field_names =['Gradient','Misfits','MaterialsRheologyBbar','Pressure','Vel','Vx','Vy'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ -md.results.StressbalanceSolution.Gradient1,\ -md.results.StressbalanceSolution.J,\ -md.results.StressbalanceSolution.MaterialsRheologyBbar,\ -md.results.StressbalanceSolution.Pressure,\ -md.results.StressbalanceSolution.Vel,\ -md.results.StressbalanceSolution.Vx,\ -md.results.StressbalanceSolution.Vy,\ -] +field_values=[md.results.StressbalanceSolution.Gradient1, + md.results.StressbalanceSolution.J, + md.results.StressbalanceSolution.MaterialsRheologyBbar, + md.results.StressbalanceSolution.Pressure, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy] Index: /issm/trunk/test/NightlyRun/test213.py =================================================================== --- /issm/trunk/test/NightlyRun/test213.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test213.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfCMBSSA3d -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -21,17 +22,17 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['MaterialsRheologyBbar'] -md.inversion.min_parameters=10**6*ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=2.*10**9*ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=10**6*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=2.*10**9*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[101] -md.inversion.cost_functions_coefficients=ones((md.mesh.numberofvertices,1)) -md.inversion.gradient_scaling=10**7*ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2.*ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.3*ones((md.inversion.nsteps,1)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices)) +md.inversion.gradient_scaling=10**7*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2.*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.3*np.ones((md.inversion.nsteps)) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') @@ -42,11 +43,9 @@ field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] #field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.StressbalanceSolution.Gradient1,\ - md.results.StressbalanceSolution.J,\ - md.results.StressbalanceSolution.MaterialsRheologyBbar,\ - md.results.StressbalanceSolution.Pressure,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ -] +field_values=[md.results.StressbalanceSolution.Gradient1, + md.results.StressbalanceSolution.J, + md.results.StressbalanceSolution.MaterialsRheologyBbar, + md.results.StressbalanceSolution.Pressure, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy] Index: /issm/trunk/test/NightlyRun/test214.py =================================================================== --- /issm/trunk/test/NightlyRun/test214.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test214.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfCMBHO -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -21,17 +22,17 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['MaterialsRheologyBbar'] -md.inversion.min_parameters=10**6*ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=2.*10**9*ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1e6*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=2.*1e9*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[101] -md.inversion.cost_functions_coefficients=ones((md.mesh.numberofvertices,1)) -md.inversion.gradient_scaling=10**7*ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2.*ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.3*ones((md.inversion.nsteps,1)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices)) +md.inversion.gradient_scaling=1e7*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2.*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.3*np.ones((md.inversion.nsteps)) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') @@ -41,11 +42,9 @@ field_names =['Gradient','Misfits','MaterialsRheologyBbar','Pressure','Vel','Vx','Vy'] field_tolerances=[1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08] -field_values=[\ - md.results.StressbalanceSolution.Gradient1,\ - md.results.StressbalanceSolution.J,\ - md.results.StressbalanceSolution.MaterialsRheologyBbar,\ - md.results.StressbalanceSolution.Pressure,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy -] +field_values=[md.results.StressbalanceSolution.Gradient1, + md.results.StressbalanceSolution.J, + md.results.StressbalanceSolution.MaterialsRheologyBbar, + md.results.StressbalanceSolution.Pressure, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy] Index: /issm/trunk/test/NightlyRun/test215.py =================================================================== --- /issm/trunk/test/NightlyRun/test215.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test215.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfCMBFS -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -21,17 +22,17 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['MaterialsRheologyBbar'] -md.inversion.min_parameters=10**6*ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=2.*10**9*ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1e6*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=2e9*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[101] -md.inversion.cost_functions_coefficients=ones((md.mesh.numberofvertices,1)) -md.inversion.gradient_scaling=10**7*ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2.*ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.3*ones((md.inversion.nsteps,1)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices)) +md.inversion.gradient_scaling=1e7*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2.*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.3*np.ones((md.inversion.nsteps)) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') @@ -41,11 +42,9 @@ field_names =['Gradient','Misfits','MaterialsRheologyBbar','Pressure','Vel','Vx','Vy'] field_tolerances=[4.6e-08,1e-08,2e-09,1e-08,2e-09,5e-09,2e-09] -field_values=[\ - md.results.StressbalanceSolution.Gradient1,\ - md.results.StressbalanceSolution.J,\ - md.results.StressbalanceSolution.MaterialsRheologyBbar,\ - md.results.StressbalanceSolution.Pressure,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy -] +field_values=[md.results.StressbalanceSolution.Gradient1, + md.results.StressbalanceSolution.J, + md.results.StressbalanceSolution.MaterialsRheologyBbar, + md.results.StressbalanceSolution.Pressure, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy] Index: /issm/trunk/test/NightlyRun/test216.py =================================================================== --- /issm/trunk/test/NightlyRun/test216.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test216.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfStressSSA2dRift -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from meshprocessrifts import * @@ -16,5 +17,5 @@ md=parameterize(md,'../Par/SquareShelf2.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) # rift settings Index: /issm/trunk/test/NightlyRun/test217.py =================================================================== --- /issm/trunk/test/NightlyRun/test217.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test217.py (revision 21729) @@ -1,6 +1,6 @@ #Test Name: SquareShelfConstrained -from MatlabFuncs import * from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +15,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) # redo the parameter file for this special shelf. @@ -22,5 +22,5 @@ # tighten -md.stressbalance.restol=10**-4 +md.stressbalance.restol=1e-4 # needed later @@ -33,37 +33,37 @@ h=1000. -md.geometry.thickness=h*ones((md.mesh.numberofvertices,1)) +md.geometry.thickness=h*np.ones((md.mesh.numberofvertices)) md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness md.geometry.surface=md.geometry.base+md.geometry.thickness # Initial velocity and pressure -md.initialization.vx=zeros((md.mesh.numberofvertices,1)) -md.initialization.vy=zeros((md.mesh.numberofvertices,1)) -md.initialization.vz=zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=zeros((md.mesh.numberofvertices,1)) +md.initialization.vx=np.zeros((md.mesh.numberofvertices)) +md.initialization.vy=np.zeros((md.mesh.numberofvertices)) +md.initialization.vz=np.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=np.zeros((md.mesh.numberofvertices)) # Materials -md.initialization.temperature=(273.-20.)*ones((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.-20.)*np.ones((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3.*np.ones((md.mesh.numberofelements)) # Boundary conditions: -md.stressbalance.spcvx=float(nan)*ones((md.mesh.numberofvertices,1)) -md.stressbalance.spcvy=float(nan)*ones((md.mesh.numberofvertices,1)) -md.stressbalance.spcvz=float(nan)*ones((md.mesh.numberofvertices,1)) +md.stressbalance.spcvx=np.nan*np.ones((md.mesh.numberofvertices)) +md.stressbalance.spcvy=np.nan*np.ones((md.mesh.numberofvertices)) +md.stressbalance.spcvz=np.nan*np.ones((md.mesh.numberofvertices)) # constrain flanks to 0 normal velocity -pos=numpy.nonzero(numpy.logical_or(md.mesh.x==xmin,md.mesh.x==xmax)) +pos=np.where(np.logical_or(md.mesh.x==xmin,md.mesh.x==xmax)) md.stressbalance.spcvx[pos]=0 -md.stressbalance.spcvz[pos]=float(nan) +md.stressbalance.spcvz[pos]=np.nan # constrain grounding line to 0 velocity -pos=numpy.nonzero(md.mesh.y==ymin) +pos=np.where(md.mesh.y==ymin) md.stressbalance.spcvx[pos]=0 md.stressbalance.spcvy[pos]=0 # icefront -nodeonicefront=zeros(md.mesh.numberofvertices) -pos=numpy.nonzero(md.mesh.y==ymax) +nodeonicefront=np.zeros(md.mesh.numberofvertices) +pos=np.where(md.mesh.y==ymax) nodeonicefront[pos]=1 md.mask.ice_levelset=-1+nodeonicefront @@ -72,11 +72,9 @@ # create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. -# ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; -# vy_c=ey_c.*md.mesh.y*md.constants.yts; +# ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3 +# vy_c=ey_c.*md.mesh.y*md.constants.yts # Fields and tolerances to track changes field_names =['Vy'] field_tolerances=[1e-13] -field_values=[\ - md.results.StressbalanceSolution.Vy,\ - ] +field_values=[md.results.StressbalanceSolution.Vy] Index: /issm/trunk/test/NightlyRun/test219.py =================================================================== --- /issm/trunk/test/NightlyRun/test219.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test219.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfStressSSAHOTiling -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.extrude(3,2.) md=setflowequation(md,'HO','../Exp/SquareHalfRight.exp','fill','SSA') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test220.py =================================================================== --- /issm/trunk/test/NightlyRun/test220.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test220.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfStressHOFS3dTiling -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.extrude(2,1.) md=setflowequation(md,'FS','../Exp/SquareHalfRight.exp','fill','HO') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test221.py =================================================================== --- /issm/trunk/test/NightlyRun/test221.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test221.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressSSAFS3dTiling from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',120000.) @@ -13,5 +14,5 @@ md.extrude(2,1.) md=setflowequation(md,'FS','../Exp/SquareHalfRight.exp','fill','SSA') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.stressbalance.viscosity_overshoot=0 md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test222.py =================================================================== --- /issm/trunk/test/NightlyRun/test222.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test222.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressSSA2dTransientIncrHydro from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.masstransport.hydrostatic_adjustment='Incremental' md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test223.py =================================================================== --- /issm/trunk/test/NightlyRun/test223.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test223.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressSSA2dTransientIncrNonHydro from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,5 +15,5 @@ md.geometry.base=md.geometry.base+50. md.geometry.surface=md.geometry.surface+50. -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.masstransport.hydrostatic_adjustment='Incremental' md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test224.py =================================================================== --- /issm/trunk/test/NightlyRun/test224.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test224.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressHOTransientIncrHydro from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.masstransport.hydrostatic_adjustment='Incremental' md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test225.py =================================================================== --- /issm/trunk/test/NightlyRun/test225.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test225.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressHOTransientIncrNonHydro from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -15,5 +16,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.masstransport.hydrostatic_adjustment='Incremental' md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test226.py =================================================================== --- /issm/trunk/test/NightlyRun/test226.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test226.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfTranCflSSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_adapt=1. md.timestepping.final_time=15. Index: /issm/trunk/test/NightlyRun/test227.py =================================================================== --- /issm/trunk/test/NightlyRun/test227.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test227.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfTranCflHO from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_adapt=1. md.timestepping.final_time=20. Index: /issm/trunk/test/NightlyRun/test228.py =================================================================== --- /issm/trunk/test/NightlyRun/test228.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test228.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranForceNeg2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. @@ -20,8 +21,8 @@ #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*-1.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*-1.)).T -md.smb.mass_balance=numpy.vstack((smb,[1.5,3.])) +md.smb.mass_balance=np.vstack((smb,[1.5,3.])) md.transient.isthermal=False @@ -29,44 +30,42 @@ #Fields and tolerances to track changes -field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] -field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] +field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test229.py =================================================================== --- /issm/trunk/test/NightlyRun/test229.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test229.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranForcePos2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. @@ -20,8 +21,8 @@ #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*2.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*2.)).T -md.smb.mass_balance=numpy.vstack((smb,[1.5,3.])) +md.smb.mass_balance=np.vstack((smb,[1.5,3.])) md.transient.isthermal=False @@ -29,44 +30,42 @@ #Fields and tolerances to track changes -field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] -field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] +field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test230.py =================================================================== --- /issm/trunk/test/NightlyRun/test230.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test230.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranForceNeg3d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',350000.) @@ -14,5 +15,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. @@ -21,8 +22,8 @@ #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*-1.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*-1.)).T -md.smb.mass_balance=numpy.vstack((smb,[1.5,3.])) +md.smb.mass_balance=np.vstack((smb,[1.5,3.])) md.transient.isthermal=False @@ -30,48 +31,46 @@ #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassbalance4'] -field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vz,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vz,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vz,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vz,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassbalance4'] +field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vz, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vz, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vz, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vz, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test231.py =================================================================== --- /issm/trunk/test/NightlyRun/test231.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test231.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranForcePos3d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',350000.) @@ -14,5 +15,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. @@ -21,8 +22,8 @@ #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*2.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*2.)).T -md.smb.mass_balance=numpy.vstack((smb,[1.5,3.])) +md.smb.mass_balance=np.vstack((smb,[1.5,3.])) md.transient.isthermal=False @@ -30,48 +31,46 @@ #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassbalance4'] -field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vz,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vz,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vz,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vz,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassbalance4'] +field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vz, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vz, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vz, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vz, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test232.py =================================================================== --- /issm/trunk/test/NightlyRun/test232.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test232.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTherTranForcTemp -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -14,6 +15,6 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) -md.thermal.spctemperature=numpy.vstack((numpy.vstack((md.thermal.spctemperature, md.thermal.spctemperature+5., md.thermal.spctemperature+10., md.thermal.spctemperature+15.)).T, [1.5,2.5,3.5,4.])) +md.cluster=generic('name',gethostname(),'np',3) +md.thermal.spctemperature=np.vstack((np.vstack((md.thermal.spctemperature, md.thermal.spctemperature+5., md.thermal.spctemperature+10., md.thermal.spctemperature+15.)).T, [1.5,2.5,3.5,4.])) md.timestepping.time_step=1. md.timestepping.final_time=4. Index: /issm/trunk/test/NightlyRun/test233.py =================================================================== --- /issm/trunk/test/NightlyRun/test233.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test233.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranHOForcTemp -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -14,6 +15,6 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) -md.thermal.spctemperature=numpy.vstack((numpy.vstack((md.thermal.spctemperature, md.thermal.spctemperature+5.)).T, [1.,2.])) +md.cluster=generic('name',gethostname(),'np',3) +md.thermal.spctemperature=np.vstack((np.vstack((md.thermal.spctemperature, md.thermal.spctemperature+5.)).T, [1.,2.])) md.timestepping.time_step=0.5 md.timestepping.final_time=2. Index: /issm/trunk/test/NightlyRun/test236.py =================================================================== --- /issm/trunk/test/NightlyRun/test236.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test236.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranIspddIsdeltaSSA2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,5 +15,5 @@ # Use of ispdd and isdelta18o methods -md.smb = SMBpdd(); +md.smb = SMBpdd() md.smb.isdelta18o=1 md.smb.ismungsm=0 @@ -20,15 +21,15 @@ # Add temperature, precipitation and delta18o needed to measure the surface mass balance # creating delta18o -delta18o=numpy.loadtxt('../Data/delta18o.data') +delta18o=np.loadtxt('../Data/delta18o.data') md.smb.delta18o=delta18o # creating delta18oSurface -md.smb.delta18o_surface = numpy.zeros((2,numpy.size(delta18o,axis=1))) +md.smb.delta18o_surface = np.zeros((2,np.size(delta18o,axis=1))) md.smb.delta18o_surface[1,:] = delta18o[1,:] # creating Present day and lgm temperatures # Same temperature over the all region: -tmonth=numpy.ones(12)*(238.15+20.) -md.smb.temperatures_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) -md.smb.temperatures_lgm=numpy.zeros((md.mesh.numberofvertices+1,12)) +tmonth=np.ones(12)*(238.15+20.) +md.smb.temperatures_presentday=np.zeros((md.mesh.numberofvertices+1,12)) +md.smb.temperatures_lgm=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.temperatures_presentday[0:md.mesh.numberofvertices,imonth]=tmonth[imonth] @@ -39,8 +40,8 @@ # creating initialization and spc temperatures initialization and spc -md.thermal.spctemperature=numpy.mean(md.smb.temperatures_lgm[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) #-10*ones(md.mesh.numberofvertices,1) -md.thermal.spctemperature=numpy.tile(md.thermal.spctemperature,(1,md.timestepping.final_time/md.timestepping.time_step)) -itemp=numpy.arange(0,md.timestepping.final_time,md.timestepping.time_step) -md.thermal.spctemperature=numpy.vstack((md.thermal.spctemperature,itemp.reshape(1,-1))) +md.thermal.spctemperature=np.mean(md.smb.temperatures_lgm[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) #-10*ones(md.mesh.numberofvertices,1) +md.thermal.spctemperature=np.tile(md.thermal.spctemperature,(1,md.timestepping.final_time/md.timestepping.time_step)) +itemp=np.arange(0,md.timestepping.final_time,md.timestepping.time_step) +md.thermal.spctemperature=np.vstack((md.thermal.spctemperature,itemp.reshape(1,-1))) md.initialization.temperature=md.smb.temperatures_lgm[0:md.mesh.numberofvertices,0] #*ones(md.mesh.numberofvertices,1) @@ -48,6 +49,6 @@ # creating precipitation -md.smb.precipitations_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) -md.smb.precipitations_lgm=numpy.zeros((md.mesh.numberofvertices+1,12)) +md.smb.precipitations_presentday=np.zeros((md.mesh.numberofvertices+1,12)) +md.smb.precipitations_lgm=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.precipitations_presentday[0:md.mesh.numberofvertices,imonth]=-0.4*10**(-6)*md.mesh.y+0.5 @@ -57,9 +58,9 @@ # Interpolation factors -md.smb.Tdiff=0.5*numpy.ones((2,md.timestepping.final_time)) -md.smb.sealev=0.5*numpy.ones((2,md.timestepping.final_time)) +md.smb.Tdiff=0.5*np.ones((2,md.timestepping.final_time)) +md.smb.sealev=0.5*np.ones((2,md.timestepping.final_time)) # Year of each data point -md.smb.Tdiff[1,1:md.timestepping.final_time]=numpy.arange(1.,md.timestepping.final_time) -md.smb.sealev[1,1:md.timestepping.final_time]=numpy.arange(1.,md.timestepping.final_time) +md.smb.Tdiff[1,1:md.timestepping.final_time]=np.arange(1.,md.timestepping.final_time) +md.smb.sealev[1,1:md.timestepping.final_time]=np.arange(1.,md.timestepping.final_time) # time steps and resolution @@ -71,5 +72,5 @@ md.transient.requested_outputs=['default','SmbMonthlytemperatures'] md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') @@ -77,8 +78,8 @@ field_names =['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMonthlytemperatures1','SmbMassBalance1',\ 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMonthlytemperatures2','SmbMassBalance2',\ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMonthlytemperatures3','SmbMassBalance3']; + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMonthlytemperatures3','SmbMassBalance3'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13]; + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] field_values=[\ md.results.TransientSolution[0].Vx,\ Index: /issm/trunk/test/NightlyRun/test237.py =================================================================== --- /issm/trunk/test/NightlyRun/test237.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test237.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranIspddIsdeltaSSA3d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from generic import generic @@ -15,5 +16,5 @@ # Use of ispdd and isdelta18o methods -md.smb = SMBpdd(); +md.smb = SMBpdd() md.smb.isdelta18o=0 md.smb.ismungsm=1 @@ -26,7 +27,7 @@ # creating Present day and lgm temperatures # Same temperature over the all region: -tmonth=numpy.ones(12)*(238.15+20.) -md.smb.temperatures_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) -md.smb.temperatures_lgm=numpy.zeros((md.mesh.numberofvertices+1,12)) +tmonth=np.ones(12)*(238.15+20.) +md.smb.temperatures_presentday=np.zeros((md.mesh.numberofvertices+1,12)) +md.smb.temperatures_lgm=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.temperatures_presentday[0:md.mesh.numberofvertices,imonth]=tmonth[imonth] @@ -37,8 +38,8 @@ # creating initialization and spc temperatures initialization and spc -md.thermal.spctemperature=numpy.mean(md.smb.temperatures_lgm[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) #-10*ones(md.mesh.numberofvertices,1) -md.thermal.spctemperature=numpy.tile(md.thermal.spctemperature,(1,md.timestepping.final_time/md.timestepping.time_step)) -itemp=numpy.arange(0,md.timestepping.final_time,md.timestepping.time_step) -md.thermal.spctemperature=numpy.vstack((md.thermal.spctemperature,itemp.reshape(1,-1))) +md.thermal.spctemperature=np.mean(md.smb.temperatures_lgm[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) #-10*ones(md.mesh.numberofvertices,1) +md.thermal.spctemperature=np.tile(md.thermal.spctemperature,(1,md.timestepping.final_time/md.timestepping.time_step)) +itemp=np.arange(0,md.timestepping.final_time,md.timestepping.time_step) +md.thermal.spctemperature=np.vstack((md.thermal.spctemperature,itemp.reshape(1,-1))) md.initialization.temperature=md.smb.temperatures_lgm[0:md.mesh.numberofvertices,0].reshape(-1,1) #*ones(md.mesh.numberofvertices,1) @@ -46,6 +47,6 @@ # creating precipitation -md.smb.precipitations_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) -md.smb.precipitations_lgm=numpy.zeros((md.mesh.numberofvertices+1,12)) +md.smb.precipitations_presentday=np.zeros((md.mesh.numberofvertices+1,12)) +md.smb.precipitations_lgm=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.precipitations_presentday[0:md.mesh.numberofvertices,imonth]=-0.4*10**(-6)*md.mesh.y+0.5 @@ -55,7 +56,7 @@ fsize=int(md.timestepping.final_time/md.timestepping.time_step)+2 -md.smb.Pfac=numpy.zeros((2,fsize)) -md.smb.Tdiff=numpy.zeros((2,fsize)) -md.smb.sealev=numpy.zeros((2,fsize)) +md.smb.Pfac=np.zeros((2,fsize)) +md.smb.Tdiff=np.zeros((2,fsize)) +md.smb.sealev=np.zeros((2,fsize)) for iint in xrange(0,fsize): # Interpolation factors @@ -72,5 +73,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md=solve(md,'Transient') @@ -78,8 +79,8 @@ field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsGroundediceMeltingRate1','SmbMonthlytemperatures1','SmbMassBalance1',\ 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2','SmbMonthlytemperatures2','SmbMassBalance2',\ - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3','SmbMonthlytemperatures3','SmbMassBalance3']; + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3','SmbMonthlytemperatures3','SmbMassBalance3'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-8,1e-8,1e-8,1e-13,1e-8,1e-13,1e-13,\ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-8,1e-8,1e-8,7e-13,1e-7,1e-13,1e-13,\ - 1e-13,1e-13,1e-08,1e-13,1e-13,1e-8,1e-8,1e-8,7e-13,5e-7,1e-13,1e-13]; + 1e-13,1e-13,1e-08,1e-13,1e-13,1e-8,1e-8,1e-8,7e-13,5e-7,1e-13,1e-13] field_values=[\ md.results.TransientSolution[0].Vx,\ Index: /issm/trunk/test/NightlyRun/test238.py =================================================================== --- /issm/trunk/test/NightlyRun/test238.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test238.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranIspddIsdeltaO18pdSSA2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,16 +15,16 @@ # Use of ispdd and isdelta18o methods -md.smb = SMBd18opdd(); -md.smb.isd18opd=1; +md.smb = SMBd18opdd() +md.smb.isd18opd=1 # Add temperature, precipitation and delta18o needed to measure the surface mass balance # creating delta18o -delta18o=numpy.loadtxt('../Data/delta18o.data') +delta18o=np.loadtxt('../Data/delta18o.data') md.smb.delta18o=delta18o # creating Present day temperatures # Same temperature over the all region: -tmonth=numpy.ones(12)*(238.15+20.) -md.smb.temperatures_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) +tmonth=np.ones(12)*(238.15+20.) +md.smb.temperatures_presentday=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.temperatures_presentday[0:md.mesh.numberofvertices,imonth]=tmonth[imonth] @@ -32,5 +33,5 @@ # creating initialization and spc temperatures initialization and spc -md.thermal.spctemperature=numpy.mean(md.smb.temperatures_presentday[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) +md.thermal.spctemperature=np.mean(md.smb.temperatures_presentday[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) md.thermal.spctemperature=md.thermal.spctemperature-10 md.initialization.temperature=md.thermal.spctemperature @@ -38,5 +39,5 @@ # creating precipitation -md.smb.precipitations_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) +md.smb.precipitations_presentday=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.precipitations_presentday[0:md.mesh.numberofvertices,imonth]=-0.4*10**(-6)*md.mesh.y+0.5 @@ -44,12 +45,12 @@ # time steps and resolution -md.timestepping.time_step=20; -md.settings.output_frequency=1; -md.timestepping.final_time=60; +md.timestepping.time_step=20 +md.settings.output_frequency=1 +md.timestepping.final_time=60 # md.transient.requested_outputs=['default','SmbMonthlytemperatures'] md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') @@ -57,8 +58,8 @@ field_names =['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMonthlytemperatures1','SmbMassBalance1',\ 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMonthlytemperatures2','SmbMassBalance2',\ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMonthlytemperatures3','SmbMassBalance3']; + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMonthlytemperatures3','SmbMassBalance3'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13]; + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] field_values=[\ md.results.TransientSolution[0].Vx,\ Index: /issm/trunk/test/NightlyRun/test239.py =================================================================== --- /issm/trunk/test/NightlyRun/test239.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test239.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranIspddIsdeltaO18pdInterpSSA2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,16 +15,16 @@ # Use of ispdd and isdelta18o methods -md.smb = SMBd18opdd(); -md.smb.isd18opd=1; +md.smb = SMBd18opdd() +md.smb.isd18opd=1 # Add temperature, precipitation and delta18o needed to measure the surface mass balance # creating delta18o -delta18o=numpy.loadtxt('../Data/delta18o.data') +delta18o=np.loadtxt('../Data/delta18o.data') md.smb.delta18o=delta18o # creating Present day temperatures # Same temperature over the all region: -tmonth=numpy.ones(12)*(238.15+20.) -md.smb.temperatures_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) +tmonth=np.ones(12)*(238.15+20.) +md.smb.temperatures_presentday=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.temperatures_presentday[0:md.mesh.numberofvertices,imonth]=tmonth[imonth] @@ -32,5 +33,5 @@ # creating initialization and spc temperatures initialization and spc -md.thermal.spctemperature=numpy.mean(md.smb.temperatures_presentday[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) +md.thermal.spctemperature=np.mean(md.smb.temperatures_presentday[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) md.thermal.spctemperature=md.thermal.spctemperature-10 md.initialization.temperature=md.thermal.spctemperature @@ -38,5 +39,5 @@ # creating precipitation -md.smb.precipitations_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) +md.smb.precipitations_presentday=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.precipitations_presentday[0:md.mesh.numberofvertices,imonth]=-0.4*10**(-6)*md.mesh.y+0.5 @@ -44,12 +45,12 @@ # time steps and resolution -md.timestepping.time_step=0.5; -md.settings.output_frequency=1; -md.timestepping.final_time=2; +md.timestepping.time_step=0.5 +md.settings.output_frequency=1 +md.timestepping.final_time=2 # md.transient.requested_outputs=['default','SmbMonthlytemperatures'] md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') @@ -57,8 +58,8 @@ field_names =['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMonthlytemperatures1','SmbMassBalance1',\ 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMonthlytemperatures2','SmbMassBalance2',\ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMonthlytemperatures3','SmbMassBalance3']; + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMonthlytemperatures3','SmbMassBalance3'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13]; + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] field_values=[\ md.results.TransientSolution[0].Vx,\ Index: /issm/trunk/test/NightlyRun/test240.py =================================================================== --- /issm/trunk/test/NightlyRun/test240.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test240.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranIspddIsdeltaO18pdNoInterpSSA2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,16 +15,16 @@ # Use of ispdd and isdelta18o methods -md.smb = SMBd18opdd(); -md.smb.isd18opd=1; +md.smb = SMBd18opdd() +md.smb.isd18opd=1 # Add temperature, precipitation and delta18o needed to measure the surface mass balance # creating delta18o -delta18o=numpy.loadtxt('../Data/delta18o.data') +delta18o=np.loadtxt('../Data/delta18o.data') md.smb.delta18o=delta18o # creating Present day temperatures # Same temperature over the all region: -tmonth=numpy.ones(12)*(238.15+20.) -md.smb.temperatures_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) +tmonth=np.ones(12)*(238.15+20.) +md.smb.temperatures_presentday=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.temperatures_presentday[0:md.mesh.numberofvertices,imonth]=tmonth[imonth] @@ -32,5 +33,5 @@ # creating initialization and spc temperatures initialization and spc -md.thermal.spctemperature=numpy.mean(md.smb.temperatures_presentday[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) +md.thermal.spctemperature=np.mean(md.smb.temperatures_presentday[0:md.mesh.numberofvertices,:],axis=1).reshape(-1,1) md.thermal.spctemperature=md.thermal.spctemperature-10 md.initialization.temperature=md.thermal.spctemperature @@ -38,5 +39,5 @@ # creating precipitation -md.smb.precipitations_presentday=numpy.zeros((md.mesh.numberofvertices+1,12)) +md.smb.precipitations_presentday=np.zeros((md.mesh.numberofvertices+1,12)) for imonth in xrange(0,12): md.smb.precipitations_presentday[0:md.mesh.numberofvertices,imonth]=-0.4*10**(-6)*md.mesh.y+0.5 @@ -44,13 +45,13 @@ # time steps and resolution -md.timestepping.time_step=0.5; -md.settings.output_frequency=1; -md.timestepping.final_time=2; -md.timestepping.interp_forcings=0; +md.timestepping.time_step=0.5 +md.settings.output_frequency=1 +md.timestepping.final_time=2 +md.timestepping.interp_forcings=0 # md.transient.requested_outputs=['default','SmbMonthlytemperatures'] md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') @@ -58,8 +59,8 @@ field_names =['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMonthlytemperatures1','SmbMassBalance1',\ 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMonthlytemperatures2','SmbMassBalance2',\ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMonthlytemperatures3','SmbMassBalance3']; + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMonthlytemperatures3','SmbMassBalance3'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13]; + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] field_values=[\ md.results.TransientSolution[0].Vx,\ Index: /issm/trunk/test/NightlyRun/test241.py =================================================================== --- /issm/trunk/test/NightlyRun/test241.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test241.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranForceNoInterp2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. @@ -21,8 +22,8 @@ #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*-1.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*-1.)).T -md.smb.mass_balance=numpy.vstack((smb,[1.5,3.])) +md.smb.mass_balance=np.vstack((smb,[1.5,3.])) md.transient.isthermal=False @@ -30,44 +31,42 @@ #Fields and tolerances to track changes -field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] -field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] +field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test242.py =================================================================== --- /issm/trunk/test/NightlyRun/test242.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test242.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfTranForceNoInterp3d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',350000.) @@ -14,5 +15,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. @@ -22,8 +23,8 @@ #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*-1.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*-1.)).T -md.smb.mass_balance=numpy.vstack((smb,[1.5,3.])) +md.smb.mass_balance=np.vstack((smb,[1.5,3.])) md.transient.isthermal=False @@ -31,49 +32,46 @@ #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassbalance4'] -field_tolerances=[\ - 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-13,\ - 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-13,\ - 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-13,\ - 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-13] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vz,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vz,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vz,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vz,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassbalance4'] +field_tolerances=[1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-13, + 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-13, + 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-13, + 1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-13] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vz, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vz, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vz, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vz, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test260.m =================================================================== --- /issm/trunk/test/NightlyRun/test260.m (revision 21729) +++ /issm/trunk/test/NightlyRun/test260.m (revision 21729) @@ -0,0 +1,21 @@ +%Test Name: SquareShelfStressSSA2dEnhanced +md=triangle(model(),'../Exp/Square.exp',150000.); +md=setmask(md,'all',''); +md.materials=matenhancedice(); +md.materials.rheology_B=3.15e8*ones(md.mesh.numberofvertices,1); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_E=ones(md.mesh.numberofvertices,1); +md=parameterize(md,'../Par/SquareShelf.par'); +md=setflowequation(md,'SSA','all'); +md.cluster=generic('name',oshostname(),'np',3); +md=solve(md,'Stressbalance'); + +%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.StressbalanceSolution.Vx),... + (md.results.StressbalanceSolution.Vy),... + (md.results.StressbalanceSolution.Vel),... + (md.results.StressbalanceSolution.Pressure),... + }; Index: /issm/trunk/test/NightlyRun/test261.m =================================================================== --- /issm/trunk/test/NightlyRun/test261.m (revision 21729) +++ /issm/trunk/test/NightlyRun/test261.m (revision 21729) @@ -0,0 +1,28 @@ +%Test Name: SquareShelfConstrainedTranEnhanced +md=triangle(model(),'../Exp/Square.exp',180000.); +md=setmask(md,'all',''); +md=parameterize(md,'../Par/SquareShelfConstrained.par'); +md=extrude(md,3,1.); +md=setflowequation(md,'SSA','all'); +md.cluster=generic('name',oshostname(),'np',3); +md.materials=matenhancedice(); +md.materials.rheology_B=3.15e8*ones(md.mesh.numberofvertices,1); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_E=ones(md.mesh.numberofvertices,1); +md.transient.isstressbalance=1; +md.transient.ismasstransport=0; +md.transient.issmb=1; +md.transient.isthermal=1; +md.transient.isgroundingline=0; +md=solve(md,'Transient'); + +%Fields and tolerances to track changes +field_names ={'Vx','Vy','Vel','Temperature','BasalforcingsGroundediceMeltingRate'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; +field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... + (md.results.TransientSolution(1).Vel),... + (md.results.TransientSolution(1).Temperature),... + (md.results.TransientSolution(1).BasalforcingsGroundediceMeltingRate),... + }; Index: /issm/trunk/test/NightlyRun/test270.py =================================================================== --- /issm/trunk/test/NightlyRun/test270.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test270.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfStressSSA2dDamage -import numpy -from model import model +import numpy as np +from model import * +from socket import gethostname from triangle import triangle from setmask import setmask @@ -9,5 +10,5 @@ from matdamageice import matdamageice from generic import generic -from socket import gethostname as oshostname +from socket import gethostname md=triangle(model(),'../Exp/Square.exp',150000.) @@ -16,8 +17,8 @@ md=parameterize(md,'../Par/SquareShelf.py') md.damage.isdamage=1 -md.damage.D=0.5*numpy.ones(md.mesh.numberofvertices) -md.damage.spcdamage=numpy.nan*numpy.ones(md.mesh.numberofvertices) +md.damage.D=0.5*np.ones(md.mesh.numberofvertices) +md.damage.spcdamage=np.nan*np.ones(md.mesh.numberofvertices) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') @@ -25,8 +26,6 @@ field_names =['Vx','Vy','Vel','Pressure'] field_tolerances=[1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Pressure,\ - ] +field_values=[md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Pressure] Index: /issm/trunk/test/NightlyRun/test272.py =================================================================== --- /issm/trunk/test/NightlyRun/test272.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test272.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfCMDSSA2dDamage -import numpy -from model import model +import numpy as np +from model import * +from socket import gethostname from triangle import triangle from setmask import setmask @@ -7,5 +8,5 @@ from setflowequation import setflowequation from solve import solve -from socket import gethostname as oshostname +from socket import gethostname from matdamageice import matdamageice from generic import generic @@ -16,6 +17,6 @@ md=parameterize(md,'../Par/SquareShelf.py') md.damage.isdamage=1 -md.damage.D=0.5*numpy.ones(md.mesh.numberofvertices) -md.damage.spcdamage=numpy.nan*numpy.ones(md.mesh.numberofvertices) +md.damage.D=0.5*np.ones(md.mesh.numberofvertices) +md.damage.spcdamage=np.nan*np.ones(md.mesh.numberofvertices) md=setflowequation(md,'SSA','all') @@ -23,16 +24,16 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['DamageDbar'] -md.inversion.min_parameters=10**-13*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=10**-13*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[101] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.gradient_scaling=0.9*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.99*numpy.ones((md.inversion.nsteps,1)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices)) +md.inversion.gradient_scaling=0.9*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2.*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.99*np.ones((md.inversion.nsteps)) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') @@ -40,11 +41,9 @@ field_names =['Gradient','Misfits','DamageDbar','Pressure','Vel','Vx','Vy'] field_tolerances=[1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12] -field_values=[\ - md.results.StressbalanceSolution.Gradient1,\ - md.results.StressbalanceSolution.J,\ - md.results.StressbalanceSolution.DamageDbar,\ - md.results.StressbalanceSolution.Pressure,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ -] +field_values=[md.results.StressbalanceSolution.Gradient1, + md.results.StressbalanceSolution.J, + md.results.StressbalanceSolution.DamageDbar, + md.results.StressbalanceSolution.Pressure, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy] Index: /issm/trunk/test/NightlyRun/test273.py =================================================================== --- /issm/trunk/test/NightlyRun/test273.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test273.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfStressSSA2dDamageUpdate -import numpy -from model import model +import numpy as np +from model import * +from socket import gethostname from triangle import triangle from setmask import setmask @@ -9,5 +10,5 @@ from matdamageice import matdamageice from generic import generic -from socket import gethostname as oshostname +from socket import gethostname md=triangle(model(),'../Exp/Square.exp',150000.) @@ -16,8 +17,8 @@ md=parameterize(md,'../Par/SquareShelf.py') md.damage.isdamage=1 -md.damage.D=0.*numpy.ones(md.mesh.numberofvertices) -md.damage.spcdamage=numpy.nan*numpy.ones(md.mesh.numberofvertices) +md.damage.D=0.*np.ones(md.mesh.numberofvertices) +md.damage.spcdamage=np.nan*np.ones(md.mesh.numberofvertices) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.stressbalance.requested_outputs=['default','NewDamage'] @@ -30,9 +31,7 @@ field_names =['Vx','Vy','Vel','Pressure','NewDamage'] field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Pressure,\ - md.results.StressbalanceSolution.NewDamage,\ - ] +field_values=[md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Pressure, + md.results.StressbalanceSolution.NewDamage] Index: /issm/trunk/test/NightlyRun/test274.py =================================================================== --- /issm/trunk/test/NightlyRun/test274.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test274.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfStressSSA2dDamageRift -import numpy -from model import model +import numpy as np +from model import * +from socket import gethostname from triangle import triangle from setmask import setmask @@ -7,5 +8,5 @@ from setflowequation import setflowequation from solve import solve -from socket import gethostname as oshostname +from socket import gethostname from matdamageice import matdamageice from meshprocessrifts import meshprocessrifts @@ -18,9 +19,9 @@ md=parameterize(md,'../Par/SquareShelf2.py') md.damage.isdamage=1 -md.damage.D=0.5*numpy.ones(md.mesh.numberofvertices) -md.damage.spcdamage=numpy.nan*numpy.ones(md.mesh.numberofvertices) +md.damage.D=0.5*np.ones(md.mesh.numberofvertices) +md.damage.spcdamage=np.nan*np.ones(md.mesh.numberofvertices) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) print md.rifts.riftstruct[0]['fill'] md=solve(md,'Stressbalance') @@ -29,8 +30,6 @@ field_names =['Vx','Vy','Vel','Pressure'] field_tolerances=[7e-8,3e-8,3e-8,1e-11] -field_values=[\ - md.results.StressbalanceSolution.Vx,\ - md.results.StressbalanceSolution.Vy,\ - md.results.StressbalanceSolution.Vel,\ - md.results.StressbalanceSolution.Pressure,\ - ] +field_values=[md.results.StressbalanceSolution.Vx, + md.results.StressbalanceSolution.Vy, + md.results.StressbalanceSolution.Vel, + md.results.StressbalanceSolution.Pressure] Index: /issm/trunk/test/NightlyRun/test275.py =================================================================== --- /issm/trunk/test/NightlyRun/test275.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test275.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfDamageEvolutionSSA2dPralong -import numpy +import numpy as np from triangle import triangle -from model import model +from model import * +from socket import gethostname from setmask import setmask from parameterize import parameterize @@ -8,5 +9,5 @@ from setflowequation import setflowequation from generic import generic -from socket import gethostname as oshostname +from socket import gethostname from solve import solve from matdamageice import matdamageice @@ -17,6 +18,6 @@ md=parameterize(md,'../Par/SquareShelf.py') md.damage.isdamage=1 -md.damage.D=0.1*numpy.ones(md.mesh.numberofvertices) -md.damage.spcdamage=numpy.nan*numpy.ones(md.mesh.numberofvertices) +md.damage.D=0.1*np.ones(md.mesh.numberofvertices) +md.damage.spcdamage=np.nan*np.ones(md.mesh.numberofvertices) md.damage.law=1 @@ -31,11 +32,9 @@ md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'DamageEvolution') field_names=['D','F'] field_tolerances=[1.e-13,1.e-13] -field_values=[\ - md.results.DamageEvolutionSolution.DamageDbar,\ - md.results.DamageEvolutionSolution.DamageF,\ - ] +field_values=[md.results.DamageEvolutionSolution.DamageDbar, + md.results.DamageEvolutionSolution.DamageF] Index: /issm/trunk/test/NightlyRun/test280.py =================================================================== --- /issm/trunk/test/NightlyRun/test280.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test280.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressSSA2dHigherOrder from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from ContourToMesh import * @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) field_names=[] Index: /issm/trunk/test/NightlyRun/test285.py =================================================================== --- /issm/trunk/test/NightlyRun/test285.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test285.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressHOHigherOrder from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,13 +7,13 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from ContourToMesh import * -md=triangle(model(),'../Exp/Square.exp',150000.); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.py'); +md=triangle(model(),'../Exp/Square.exp',150000.) +md=setmask(md,'all','') +md=parameterize(md,'../Par/SquareShelf.py') md.extrude(3,2.) -md=setflowequation(md,'HO','all'); -md.cluster=generic('name',oshostname(),'np',3); +md=setflowequation(md,'HO','all') +md.cluster=generic('name',gethostname(),'np',3) field_names=[] Index: /issm/trunk/test/NightlyRun/test290.py =================================================================== --- /issm/trunk/test/NightlyRun/test290.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test290.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressFSP2P1 from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,18 +7,18 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from ContourToMesh import * -md=triangle(model(),'../Exp/Square.exp',150000.); -md=setmask(md,'all',''); -md=parameterize(md,'../Par/SquareShelf.py'); +md=triangle(model(),'../Exp/Square.exp',150000.) +md=setmask(md,'all','') +md=parameterize(md,'../Par/SquareShelf.py') md.extrude(3,2.) -md=setflowequation(md,'FS','all'); -md.flowequation.fe_FS='TaylorHood'; -md.cluster=generic('name',oshostname(),'np',3); -md=solve(md,'Stressbalance'); +md=setflowequation(md,'FS','all') +md.flowequation.fe_FS='TaylorHood' +md.cluster=generic('name',gethostname(),'np',3) +md=solve(md,'Stressbalance') #Fields and tolerances to track changes -field_names =['Vx', 'Vy', 'Vz', 'Vel','Pressure']; +field_names =['Vx', 'Vy', 'Vz', 'Vel','Pressure'] field_tolerances=[5e-5,5e-5,8e-5,5e-5,1e-7] field_values=[\ @@ -27,3 +28,3 @@ md.results.StressbalanceSolution.Vel,\ md.results.StressbalanceSolution.Pressure,\ - ]; + ] Index: /issm/trunk/test/NightlyRun/test291.py =================================================================== --- /issm/trunk/test/NightlyRun/test291.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test291.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfStressFSP4z from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from ContourToMesh import * @@ -15,9 +16,9 @@ md=setflowequation(md,'FS','all') md.flowequation.fe_FS='OneLayerP4z' -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md=solve(md,'Stressbalance') #Fields and tolerances to track changes -field_names =['Vx', 'Vy', 'Vz', 'Vel','Pressure']; +field_names =['Vx', 'Vy', 'Vz', 'Vel','Pressure'] field_tolerances=[5e-5,5e-5,8e-5,5e-5,1e-7] field_values=[\ @@ -27,3 +28,3 @@ md.results.StressbalanceSolution.Vel,\ md.results.StressbalanceSolution.Pressure,\ - ]; + ] Index: /issm/trunk/test/NightlyRun/test292.py =================================================================== --- /issm/trunk/test/NightlyRun/test292.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test292.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfTranSSA2dFloatingMeltParam -from MatlabFuncs import * + from model import * -from numpy import * +from socket import gethostname +import numpy as np from triangle import * from setmask import * @@ -15,5 +16,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.basalforcings=linearbasalforcings(md.basalforcings) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test3001.py =================================================================== --- /issm/trunk/test/NightlyRun/test3001.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3001.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressSSA2dAdolc from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',50000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.stressbalance.requested_outputs=['default','DeviatoricStressxx','DeviatoricStressyy','DeviatoricStressxy'] md.autodiff.isautodiff=True Index: /issm/trunk/test/NightlyRun/test3002.py =================================================================== --- /issm/trunk/test/NightlyRun/test3002.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3002.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressSSA3dAdolc from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,2.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.autodiff.isautodiff=True md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test3003.py =================================================================== --- /issm/trunk/test/NightlyRun/test3003.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3003.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressHOAdolc from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,2.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.stressbalance.requested_outputs=['default','StressTensorxx','StressTensoryy','StressTensorzz','StressTensorxy','StressTensorxz','StressTensoryz'] md.autodiff.isautodiff=True Index: /issm/trunk/test/NightlyRun/test3004.py =================================================================== --- /issm/trunk/test/NightlyRun/test3004.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3004.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressFSAdolc from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,2.) md=setflowequation(md,'FS','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.autodiff.isautodiff=True md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test3005.py =================================================================== --- /issm/trunk/test/NightlyRun/test3005.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3005.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedMasstransp2dAdolc from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.autodiff.isautodiff=True md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test3006.py =================================================================== --- /issm/trunk/test/NightlyRun/test3006.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3006.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedMasstransp2dDGAdolc from model import * +from socket import gethostname from triangle import * from meshconvert import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,5 +15,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.masstransport.stabilization=3 md.masstransport.spcthickness=md.geometry.thickness Index: /issm/trunk/test/NightlyRun/test3007.py =================================================================== --- /issm/trunk/test/NightlyRun/test3007.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3007.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedMasstransp3dAdolc from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,5 +14,5 @@ md=setflowequation(md,'SSA','all') md.extrude(5,3.) -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.autodiff.isautodiff=True md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test3008.py =================================================================== --- /issm/trunk/test/NightlyRun/test3008.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3008.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTherSteaAdolc from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -14,5 +15,5 @@ md=setflowequation(md,'SSA','all') md.timestepping.time_step=0 -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.autodiff.isautodiff=True md=solve(md,'Thermal') Index: /issm/trunk/test/NightlyRun/test3009.py =================================================================== --- /issm/trunk/test/NightlyRun/test3009.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3009.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTherTranAdolc from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.transient.isstressbalance=False md.transient.ismasstransport=False Index: /issm/trunk/test/NightlyRun/test301.py =================================================================== --- /issm/trunk/test/NightlyRun/test301.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test301.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedStressSSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareSheetConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test3010.py =================================================================== --- /issm/trunk/test/NightlyRun/test3010.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3010.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTranSSA2dAdolc from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.transient.requested_outputs=['IceVolume'] Index: /issm/trunk/test/NightlyRun/test3015.py =================================================================== --- /issm/trunk/test/NightlyRun/test3015.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3015.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfConstrainedMasstransp2dAdolcForwardDifference -import numpy +import numpy as np import copy from model import * +from socket import gethostname from triangle import * from setmask import * @@ -11,5 +12,5 @@ from SetIceShelfBC import * from solve import * -from MatlabFuncs import * + #This test runs test3005 with autodiff on, and checks that @@ -21,5 +22,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.masstransport.requested_outputs=['IceVolume'] md.verbose=verbose('autodiff',True) Index: /issm/trunk/test/NightlyRun/test3019.py =================================================================== --- /issm/trunk/test/NightlyRun/test3019.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3019.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareShelfConstrainedTherTranAdolcReverseVsForward -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -9,5 +10,5 @@ from dependent import * from solve import * -from MatlabFuncs import * + #test reverse scalar vs forward vectorial drivers in ADOLC, using the test3009 setup, equivalent to test109 setup. @@ -16,5 +17,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) #md.toolkits.DefaultAnalysis=issmgslsolver() @@ -33,5 +34,5 @@ #now run vectorial forward mode -md.autodiff.independents=[independent('name','md.geometry.thickness','type','vertex','nods',md.mesh.numberofvertices,'fov_forward_indices',numpy.arange(1,md.mesh.numberofvertices+1))] +md.autodiff.independents=[independent('name','md.geometry.thickness','type','vertex','nods',md.mesh.numberofvertices,'fov_forward_indices',np.arange(1,md.mesh.numberofvertices+1))] md.autodiff.dependents=[dependent('name','MaxVel','type','scalar')] md.autodiff.driver='fov_forward' Index: /issm/trunk/test/NightlyRun/test302.py =================================================================== --- /issm/trunk/test/NightlyRun/test302.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test302.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedStressSIA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareSheetConstrained.py') md=setflowequation(md,'SIA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test3020.py =================================================================== --- /issm/trunk/test/NightlyRun/test3020.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3020.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareShelfConstrainedTranAdolcReverseVsForward -import numpy +import numpy as np import copy from model import * +from socket import gethostname from triangle import * from setmask import * @@ -11,5 +12,5 @@ from SetIceShelfBC import * from solve import * -from MatlabFuncs import * + #This test runs test3020 with autodiff on, and checks that @@ -21,5 +22,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.transient.requested_outputs=['IceVolume','MaxVel'] md.verbose=verbose('autodiff',True) Index: /issm/trunk/test/NightlyRun/test303.py =================================================================== --- /issm/trunk/test/NightlyRun/test303.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test303.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedStressSIASSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareSheetConstrained.py') md=setflowequation(md,'SIA','../Exp/SquareHalfRight.exp','fill','SSA') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test304.py =================================================================== --- /issm/trunk/test/NightlyRun/test304.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test304.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedStressSSA3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,2.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test305.py =================================================================== --- /issm/trunk/test/NightlyRun/test305.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test305.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedStressSIA3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(5,2.) md=setflowequation(md,'SIA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test306.py =================================================================== --- /issm/trunk/test/NightlyRun/test306.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test306.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedStressSIASSA3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(4,2.) md=setflowequation(md,'SIA','../Exp/SquareHalfRight.exp','fill','SSA') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test307.py =================================================================== --- /issm/trunk/test/NightlyRun/test307.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test307.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedStressHO from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test308.py =================================================================== --- /issm/trunk/test/NightlyRun/test308.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test308.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedStressFS from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'FS','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test309.py =================================================================== --- /issm/trunk/test/NightlyRun/test309.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test309.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedMasstransp2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareSheetConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test310.py =================================================================== --- /issm/trunk/test/NightlyRun/test310.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test310.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedMasstransp2dDG from model import * +from socket import gethostname from triangle import * from meshconvert import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -16,5 +17,5 @@ md.masstransport.stabilization=3 md.masstransport.spcthickness=md.geometry.thickness -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test3101.py =================================================================== --- /issm/trunk/test/NightlyRun/test3101.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3101.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressSSA2dAdolcMumps from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',50000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.stressbalance.requested_outputs=['default','DeviatoricStressxx','DeviatoricStressyy','DeviatoricStressxy'] Index: /issm/trunk/test/NightlyRun/test3102.py =================================================================== --- /issm/trunk/test/NightlyRun/test3102.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3102.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressSSA3dAdolcMumps from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,2.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.autodiff.isautodiff=True Index: /issm/trunk/test/NightlyRun/test3103.py =================================================================== --- /issm/trunk/test/NightlyRun/test3103.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3103.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressHOAdolcMumps from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,2.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.stressbalance.requested_outputs=['default','StressTensorxx','StressTensoryy','StressTensorzz','StressTensorxy','StressTensorxz','StressTensoryz'] Index: /issm/trunk/test/NightlyRun/test3104.py =================================================================== --- /issm/trunk/test/NightlyRun/test3104.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3104.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedStressFSAdolcMumps from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,2.) md=setflowequation(md,'FS','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.autodiff.isautodiff=True Index: /issm/trunk/test/NightlyRun/test3105.py =================================================================== --- /issm/trunk/test/NightlyRun/test3105.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3105.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedMasstransp2dAdolcMumps from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.autodiff.isautodiff=True Index: /issm/trunk/test/NightlyRun/test3106.py =================================================================== --- /issm/trunk/test/NightlyRun/test3106.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3106.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedMasstransp2dDGAdolcMumps from model import * +from socket import gethostname from triangle import * from meshconvert import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,5 +15,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.masstransport.stabilization=3 md.masstransport.spcthickness=md.geometry.thickness Index: /issm/trunk/test/NightlyRun/test3107.py =================================================================== --- /issm/trunk/test/NightlyRun/test3107.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3107.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedMasstransp3dAdolcMumps from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,5 +14,5 @@ md=setflowequation(md,'SSA','all') md.extrude(5,3.) -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.autodiff.isautodiff=True Index: /issm/trunk/test/NightlyRun/test3108.py =================================================================== --- /issm/trunk/test/NightlyRun/test3108.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3108.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTherSteaAdolcMumps from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -14,5 +15,5 @@ md=setflowequation(md,'SSA','all') md.timestepping.time_step=0 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.autodiff.isautodiff=True Index: /issm/trunk/test/NightlyRun/test3109.py =================================================================== --- /issm/trunk/test/NightlyRun/test3109.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3109.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTherTranAdolcMumps from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.isstressbalance=False md.transient.ismasstransport=False Index: /issm/trunk/test/NightlyRun/test311.py =================================================================== --- /issm/trunk/test/NightlyRun/test311.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test311.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedMasstransp3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,5 +14,5 @@ md=setflowequation(md,'SSA','all') md.extrude(5,0.5) -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test3110.py =================================================================== --- /issm/trunk/test/NightlyRun/test3110.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3110.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareShelfConstrainedTranSSA2dAdolcMumps from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.requested_outputs=['IceVolume'] Index: /issm/trunk/test/NightlyRun/test3119.py =================================================================== --- /issm/trunk/test/NightlyRun/test3119.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3119.py (revision 21729) @@ -1,4 +1,5 @@ -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from dependent import * from solve import * -from MatlabFuncs import * + #test reverse scalar vs forward vectorial drivers in ADOLC, using the test3009 setup, equivalent to test109 setup. @@ -15,5 +16,5 @@ md=parameterize(md,'../Par/SquareShelfConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.autodiff.isautodiff=True Index: /issm/trunk/test/NightlyRun/test312.py =================================================================== --- /issm/trunk/test/NightlyRun/test312.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test312.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedTherStea from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -14,5 +15,5 @@ md=setflowequation(md,'SSA','all') md.timestepping.time_step=0. -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Thermal') Index: /issm/trunk/test/NightlyRun/test313.py =================================================================== --- /issm/trunk/test/NightlyRun/test313.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test313.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedTherTran from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.verbose=verbose('convergence',True,'solution',True) md.transient.isstressbalance=False Index: /issm/trunk/test/NightlyRun/test314.py =================================================================== --- /issm/trunk/test/NightlyRun/test314.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test314.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedTranSIA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareSheetConstrained.py') md=setflowequation(md,'SIA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.requested_outputs=['default','GroundedArea','FloatingArea','IceVolume'] md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test315.py =================================================================== --- /issm/trunk/test/NightlyRun/test315.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test315.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedTranSIA3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,5 +14,5 @@ md.extrude(5,1.2) md=setflowequation(md,'SIA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test316.py =================================================================== --- /issm/trunk/test/NightlyRun/test316.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test316.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedTranSSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/SquareSheetConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test317.py =================================================================== --- /issm/trunk/test/NightlyRun/test317.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test317.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedTranHO from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -14,5 +15,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.requested_outputs=['default','GroundedArea','FloatingArea','TotalFloatingBmb','TotalGroundedBmb'] md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test318.py =================================================================== --- /issm/trunk/test/NightlyRun/test318.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test318.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: SquareSheetConstrainedSteaSIA3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -13,5 +14,5 @@ md.extrude(4,1.) md=setflowequation(md,'SIA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0 md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test319.py =================================================================== --- /issm/trunk/test/NightlyRun/test319.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test319.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedCMDragSSA2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -17,17 +18,17 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['FrictionCoefficient'] -md.inversion.min_parameters=1.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=200.*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[103,501] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,2)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices,2)) md.inversion.cost_functions_coefficients[:,1]=2.*10**-7 -md.inversion.gradient_scaling=3.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2*numpy.ones(md.inversion.nsteps) -md.inversion.step_threshold=0.3*numpy.ones(md.inversion.nsteps) +md.inversion.gradient_scaling=3.*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2*np.ones(md.inversion.nsteps) +md.inversion.step_threshold=0.3*np.ones(md.inversion.nsteps) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test320.py =================================================================== --- /issm/trunk/test/NightlyRun/test320.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test320.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedCMDragSSA3d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -18,17 +19,17 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['FrictionCoefficient'] -md.inversion.min_parameters=1.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=200.*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[103,501] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,2)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices,2)) md.inversion.cost_functions_coefficients[:,1]=2.*10**-7 -md.inversion.gradient_scaling=3.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2*numpy.ones(md.inversion.nsteps) -md.inversion.step_threshold=0.3*numpy.ones(md.inversion.nsteps) +md.inversion.gradient_scaling=3.*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2*np.ones(md.inversion.nsteps) +md.inversion.step_threshold=0.3*np.ones(md.inversion.nsteps) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test321.py =================================================================== --- /issm/trunk/test/NightlyRun/test321.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test321.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedCMDragHO -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -18,17 +19,17 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['FrictionCoefficient'] -md.inversion.min_parameters=1.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=200.*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[102,501] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,2)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices,2)) md.inversion.cost_functions_coefficients[:,1]=2*10**-7 -md.inversion.gradient_scaling=3.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2*numpy.ones(md.inversion.nsteps) -md.inversion.step_threshold=0.3*numpy.ones(md.inversion.nsteps) +md.inversion.gradient_scaling=3.*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2*np.ones(md.inversion.nsteps) +md.inversion.step_threshold=0.3*np.ones(md.inversion.nsteps) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test322.py =================================================================== --- /issm/trunk/test/NightlyRun/test322.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test322.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedCMDragFS -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -18,17 +19,17 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['FrictionCoefficient'] -md.inversion.min_parameters=1.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=200.*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[104,501] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,2)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices,2)) md.inversion.cost_functions_coefficients[:,1]=2.*10**-7 -md.inversion.gradient_scaling=3.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2*numpy.ones(md.inversion.nsteps) -md.inversion.step_threshold=0.3*numpy.ones(md.inversion.nsteps) +md.inversion.gradient_scaling=3.*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2*np.ones(md.inversion.nsteps) +md.inversion.step_threshold=0.3*np.ones(md.inversion.nsteps) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test323.py =================================================================== --- /issm/trunk/test/NightlyRun/test323.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test323.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedTranCflSSA2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/SquareSheetConstrained.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_adapt=1 md.timestepping.final_time=1120. Index: /issm/trunk/test/NightlyRun/test324.py =================================================================== --- /issm/trunk/test/NightlyRun/test324.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test324.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedTranCflSIA3d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,5 +15,5 @@ md.extrude(5,1.2) md=setflowequation(md,'SIA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_adapt=1 md.timestepping.final_time=16000. Index: /issm/trunk/test/NightlyRun/test325.py =================================================================== --- /issm/trunk/test/NightlyRun/test325.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test325.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedEnthalpyStea -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -15,10 +16,10 @@ md=setflowequation(md,'SSA','all') md.timestepping.time_step=0. -md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.watercolumn=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.waterfraction=np.zeros((md.mesh.numberofvertices)) +md.initialization.watercolumn=np.zeros((md.mesh.numberofvertices)) md.thermal.isenthalpy = 1 md.thermal.isdynamicbasalspc = 1 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Thermal') Index: /issm/trunk/test/NightlyRun/test326.py =================================================================== --- /issm/trunk/test/NightlyRun/test326.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test326.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedEnthalpyTran -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',180000.) @@ -14,7 +15,7 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) -md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.watercolumn=numpy.zeros((md.mesh.numberofvertices,1)) +md.cluster=generic('name',gethostname(),'np',3) +md.initialization.waterfraction=np.zeros((md.mesh.numberofvertices)) +md.initialization.watercolumn=np.zeros((md.mesh.numberofvertices)) md.transient.isstressbalance=False md.transient.ismasstransport=False Index: /issm/trunk/test/NightlyRun/test327.py =================================================================== --- /issm/trunk/test/NightlyRun/test327.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test327.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedTransHOEnth -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',200000.) @@ -14,9 +15,9 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) -md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.watercolumn=numpy.zeros((md.mesh.numberofvertices,1)) +md.cluster=generic('name',gethostname(),'np',3) +md.initialization.waterfraction=np.zeros((md.mesh.numberofvertices)) +md.initialization.watercolumn=np.zeros((md.mesh.numberofvertices)) md.initialization.temperature[:]=272. -md.thermal.spctemperature[numpy.nonzero(md.mesh.vertexonsurface)[0]]=272. +md.thermal.spctemperature[np.nonzero(md.mesh.vertexonsurface)[0]]=272. md.thermal.isenthalpy=1 md.thermal.isdynamicbasalspc=1 Index: /issm/trunk/test/NightlyRun/test328.py =================================================================== --- /issm/trunk/test/NightlyRun/test328.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test328.py (revision 21729) @@ -1,6 +1,6 @@ #Test Name: SquareSheetConstrainedSmbGradients2d -import numpy import copy from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +8,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,40 +13,52 @@ md=parameterize(md,'../Par/SquareSheetConstrained.py') md=setflowequation(md,'SSA','all') -md.smb = SMBgradients(); +md.smb = SMBgradients() md.smb.b_pos=-100. + 0.00005*md.mesh.x - 0.0001*md.mesh.y md.smb.b_neg=250. + 0.000051*md.mesh.x - 0.00011*md.mesh.y md.transient.requested_outputs=['default','TotalSmb'] -md.smb.href=copy.deepcopy(md.geometry.surface).reshape(-1) -md.smb.smbref= 1000. - 0.001*md.mesh.x - 0.005*md.mesh.y; -md.cluster=generic('name',oshostname(),'np',3) +md.smb.href=copy.deepcopy(md.geometry.surface) +md.smb.smbref= 1000. - 0.001*md.mesh.x - 0.005*md.mesh.y +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','Bed1','Surface1','Thickness1','SMB1','TotalSmb1','Vx2','Vy2','Vel2','Bed2','Surface2','Thickness2','SMB2','TotalSmb2','Vx3','Vy3','Vel3','Bed3','Surface3','Thickness3','SMB3','TotalSmb3'] -field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[0].TotalSmb,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].TotalSmb,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[2].TotalSmb,\ - ] +field_names =['Vx1','Vy1','Vel1', + 'Bed1','Surface1','Thickness1', + 'SMB1','TotalSmb1', + 'Vx2','Vy2','Vel2','Bed2', + 'Surface2','Thickness2', + 'SMB2','TotalSmb2','Vx3','Vy3', + 'Vel3','Bed3','Surface3', + 'Thickness3','SMB3','TotalSmb3'] +field_tolerances=[1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[0].TotalSmb, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].TotalSmb, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[2].TotalSmb] Index: /issm/trunk/test/NightlyRun/test329.py =================================================================== --- /issm/trunk/test/NightlyRun/test329.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test329.py (revision 21729) @@ -1,6 +1,6 @@ #Test Name: SquareSheetConstrainedSmbGradients3d -import numpy import copy from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +8,4 @@ from setflowequation import * from solve import * -from MatlabFuncs import * md=triangle(model(),'../Exp/Square.exp',150000.) @@ -15,48 +14,60 @@ md.extrude(3,1) md=setflowequation(md,'HO','all') -md.smb = SMBgradients(); +md.smb = SMBgradients() md.smb.b_pos=-100. + 0.00005*md.mesh.x - 0.0001*md.mesh.y md.smb.b_neg=250. + 0.000051*md.mesh.x - 0.00011*md.mesh.y -md.smb.href=copy.deepcopy(md.geometry.surface).reshape(-1) -md.smb.smbref= 1000. - 0.001*md.mesh.x - 0.005*md.mesh.y; +md.smb.href=copy.deepcopy(md.geometry.surface) +md.smb.smbref= 1000. - 0.001*md.mesh.x - 0.005*md.mesh.y md.transient.requested_outputs=['default','TotalSmb'] -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vz1','Vel1','Bed1','Surface1','Thickness1','Temperature1','SMB1','TotalSmb1','Vx2','Vy2','Vz2','Vel2','Bed2','Surface2','Thickness2','Temperature2','SMB2','TotalSmb2','Vx3','Vy3','Vz3','Vel3','Bed3','Surface3','Thickness3','Temperature3','SMB3','TotalSmb3'] -field_tolerances=[1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vz,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].Temperature,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[0].TotalSmb,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vz,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].Temperature,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[1].TotalSmb,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vz,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].Temperature,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[2].TotalSmb,\ - ] +field_names =['Vx1','Vy1','Vz1','Vel1', + 'Bed1','Surface1','Thickness1', + 'Temperature1','SMB1','TotalSmb1', + 'Vx2','Vy2','Vz2','Vel2', + 'Bed2','Surface2','Thickness2', + 'Temperature2','SMB2','TotalSmb2', + 'Vx3','Vy3','Vz3','Vel3', + 'Bed3','Surface3','Thickness3', + 'Temperature3','SMB3','TotalSmb3'] +field_tolerances=[1e-09,1e-09,1e-09,1e-09, + 1e-10,1e-10,1e-10, + 1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-09, + 1e-10,1e-10,1e-10, + 1e-10,1e-10,1e-10, + 1e-09,5e-09,1e-09,1e-09, + 1e-10,1e-10,1e-10, + 1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vz, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Temperature, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[0].TotalSmb, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vz, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Temperature, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[1].TotalSmb, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vz, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Temperature, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[2].TotalSmb] Index: /issm/trunk/test/NightlyRun/test330.m =================================================================== --- /issm/trunk/test/NightlyRun/test330.m (revision 21729) +++ /issm/trunk/test/NightlyRun/test330.m (revision 21729) @@ -0,0 +1,46 @@ +%Test Name:UnConfinedHydroDC +md=triangle(model(),'../Exp/Strip.exp',10000.); +md=setmask(md,'',''); +%reduced slab (20m long) +md.mesh.x=md.mesh.x/5.0e3; +md.mesh.y=md.mesh.y/5.0e3; +md=parameterize(md,'../Par/IceCube.par'); +md.transient=deactivateall(md.transient); +md.transient.ishydrology=1; +md=setflowequation(md,'SSA','all'); +md.cluster=generic('name',oshostname(),'np',1); +md.hydrology=(hydrologydc); +md.hydrology=initialize(md.hydrology,md); + +%Hydro Model Parameters +md.hydrology.isefficientlayer=0; +md.hydrology.sedimentlimit_flag=0; +md.hydrology.rel_tol=1.0e-6; +md.hydrology.penalty_lock=0; +md.hydrology.max_iter=200; +md.hydrology.transfer_flag=0; +md.hydrology.sediment_porosity=0.1; +%Sediment +md.hydrology.sediment_thickness=10.0; +md.hydrology.sediment_transmitivity=(1.0e-3*md.hydrology.sediment_thickness)*ones(md.mesh.numberofvertices,1); +%init +md.initialization.sediment_head=-5.0*ones(md.mesh.numberofvertices,1); +%BC +md.hydrology.spcsediment_head=NaN*ones(md.mesh.numberofvertices,1); +pos=find(md.mesh.x==0); +md.hydrology.spcsediment_head(pos)=0.5; + +md.timestepping.time_step=5/md.constants.yts; %5s steppin +md.settings.output_frequency=2; +md.timestepping.final_time=300/md.constants.yts; %500s run + +md=solve(md,'Transient'); + +%fields to track, results can also be found in +%Wang 2009 Fig 6b (jouranl of Hydrology) +field_names={'SedimentWaterHead1',... + 'SedimentWaterHead2'}; +field_tolerances={1e-13,... + 1e-13}; +field_values={md.results.TransientSolution(11).SedimentHead,... + md.results.TransientSolution(31).SedimentHead}; Index: /issm/trunk/test/NightlyRun/test330.py =================================================================== --- /issm/trunk/test/NightlyRun/test330.py (revision 21729) +++ /issm/trunk/test/NightlyRun/test330.py (revision 21729) @@ -0,0 +1,57 @@ +#Test Name:UnConfinedHydroDC +import numpy as np +import inspect +from model import * +from setmask import * +from triangle import triangle +from transient import transient +from parameterize import parameterize +from setflowequation import setflowequation +from solve import solve +from socket import gethostname +from generic import generic + +md=triangle(model(),'../Exp/Strip.exp',10000.) +md=setmask(md,'','') +#reduced slab (20m long) +md.mesh.x=md.mesh.x/5.0e3 +md.mesh.y=md.mesh.y/5.0e3 +md=parameterize(md,'../Par/IceCube.py') +md.transient=transient.setallnullparameters(md.transient) +md.transient.ishydrology=True +md=setflowequation(md,'SSA','all') +md.cluster=generic('name',gethostname(),'np',1) +md.hydrology=hydrologydc() +md.hydrology=md.hydrology.initialize(md) + +#Hydro Model Parameters +md.hydrology.isefficientlayer=0 +md.hydrology.sedimentlimit_flag=0 +md.hydrology.rel_tol=1.0e-6 +md.hydrology.penalty_lock=0 +md.hydrology.max_iter=200 +md.hydrology.transfer_flag=0 +md.hydrology.sediment_porosity=0.1 +#Sediment +md.hydrology.sediment_thickness=10.0 +md.hydrology.sediment_transmitivity=(1.0e-3*md.hydrology.sediment_thickness)*np.ones((md.mesh.numberofvertices)) +#init +md.initialization.sediment_head=-5.0*np.ones((md.mesh.numberofvertices)) +#BC +md.hydrology.spcsediment_head=np.nan*np.ones((md.mesh.numberofvertices)) +md.hydrology.spcsediment_head[np.where(md.mesh.x==0)]=0.5 + +md.timestepping.time_step=5/md.constants.yts #5s steppin +md.settings.output_frequency=2 +md.timestepping.final_time=300/md.constants.yts #500s run + +md=solve(md,'Transient') + +#fields to track, results can also be found in +#Wang 2009 Fig 6b (jouranl of Hydrology) +field_names=['SedimentWaterHead1', + 'SedimentWaterHead2'] +field_tolerances=[1e-13, + 1e-13] +field_values=[md.results.TransientSolution[10].SedimentHead, + md.results.TransientSolution[30].SedimentHead] Index: /issm/trunk/test/NightlyRun/test3300.py =================================================================== --- /issm/trunk/test/NightlyRun/test3300.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test3300.py (revision 21729) @@ -1,4 +1,5 @@ import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from generic import generic @@ -18,5 +19,5 @@ md.transient.issmb=True md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.hydrology=hydrologydc() md.hydrology=md.hydrology.initialize(md) @@ -26,13 +27,13 @@ md.hydrology.sedimentlimit=400.0 md.hydrology.sediment_thickness=20.0 -md.initialization.sediment_head=np.zeros((md.mesh.numberofvertices,1)) -md.hydrology.spcsediment_head=float('NaN')*np.ones((md.mesh.numberofvertices,1)) -md.basalforcings.groundedice_melting_rate = 2.0*np.ones((md.mesh.numberofvertices,1)) -md.hydrology.sediment_transmitivity=1.5e-4*np.ones((md.mesh.numberofvertices,1)) +md.initialization.sediment_head=np.zeros((md.mesh.numberofvertices)) +md.hydrology.spcsediment_head=np.nan*np.ones((md.mesh.numberofvertices)) +md.basalforcings.groundedice_melting_rate = 2.0*np.ones((md.mesh.numberofvertices)) +md.hydrology.sediment_transmitivity=1.5e-4*np.ones((md.mesh.numberofvertices)) -md.initialization.epl_head=np.zeros((md.mesh.numberofvertices,1)) -md.initialization.epl_thickness=np.ones((md.mesh.numberofvertices,1)) -md.hydrology.spcepl_head=float('NaN')*np.ones((md.mesh.numberofvertices,1)) -md.hydrology.mask_eplactive_node=np.zeros((md.mesh.numberofvertices,1)) +md.initialization.epl_head=np.zeros((md.mesh.numberofvertices)) +md.initialization.epl_thickness=np.ones((md.mesh.numberofvertices)) +md.hydrology.spcepl_head=np.nan*np.ones((md.mesh.numberofvertices)) +md.hydrology.mask_eplactive_node=np.zeros((md.mesh.numberofvertices)) md.hydrology.epl_conductivity=1.5e-2 @@ -61,6 +62,6 @@ totvol=np.zeros(4001) time=np.arange(0.002,8.001,0.002) -store=md.constants.g*md.hydrology.sediment_porosity*md.materials.rho_freshwater*((md.hydrology.sediment_compressibility/md.hydrology.sediment_porosity)+md.hydrology.water_compressibility); -sedstore=20.0*store; +store=md.constants.g*md.hydrology.sediment_porosity*md.materials.rho_freshwater*((md.hydrology.sediment_compressibility/md.hydrology.sediment_porosity)+md.hydrology.water_compressibility) +sedstore=20.0*store for i in range(0,4000): sedvol[i]=np.mean(md.results.TransientSolution[i].SedimentHead)*sedstore Index: /issm/trunk/test/NightlyRun/test332.m =================================================================== --- /issm/trunk/test/NightlyRun/test332.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test332.m (revision 21729) @@ -2,5 +2,5 @@ md=triangle(model(),'../Exp/Square.exp',100000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); +md=parameterize(md,'../Par/IceCube.par'); md.transient=deactivateall(md.transient); md.transient.ishydrology=1; Index: /issm/trunk/test/NightlyRun/test332.py =================================================================== --- /issm/trunk/test/NightlyRun/test332.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test332.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedHydrologyDC -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from generic import generic @@ -14,5 +15,5 @@ md=triangle(model(),'../Exp/Square.exp',100000.) md=setmask(md,'','') -md=parameterize(md,'../Par/SquareSheetConstrained.py') +md=parameterize(md,'../Par/IceCube.py') md.transient=transient.setallnullparameters(md.transient) @@ -20,5 +21,5 @@ md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.hydrology=hydrologydc() md.hydrology=md.hydrology.initialize(md) @@ -27,11 +28,11 @@ md.hydrology.sedimentlimit_flag=1 md.hydrology.sedimentlimit=8000.0 -md.initialization.sediment_head=numpy.zeros((md.mesh.numberofvertices,1)) -md.hydrology.spcsediment_head=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) -pos=numpy.nonzero(md.mesh.y==0.)[0] +md.initialization.sediment_head=np.zeros((md.mesh.numberofvertices)) +md.hydrology.spcsediment_head=np.nan*np.ones((md.mesh.numberofvertices)) +pos=np.nonzero(md.mesh.y==0.)[0] md.hydrology.spcsediment_head[pos]=0.0 -md.basalforcings.groundedice_melting_rate = 2.0*numpy.ones((md.mesh.numberofvertices,1)) -md.basalforcings.floatingice_melting_rate = 0.0*numpy.ones((md.mesh.numberofvertices,1)) -md.hydrology.sediment_transmitivity= 3.0*numpy.ones((md.mesh.numberofvertices,1)) +md.basalforcings.groundedice_melting_rate = 2.0*np.ones((md.mesh.numberofvertices)) +md.basalforcings.floatingice_melting_rate = 0.0*np.ones((md.mesh.numberofvertices)) +md.hydrology.sediment_transmitivity= 3.0*np.ones((md.mesh.numberofvertices)) md.timestepping.time_step=0 md.timestepping.final_time=1.0 @@ -41,5 +42,5 @@ #you can also compare with an analitic solution, but it is exact #only if no limits are applied -#analitic=(md.mesh.y.^2-2*md.mesh.y*1.0e6)*(-2.0/(2*md.constants.yts*md.hydrology.sediment_transmitivity)) +#analitic=(md.mesh.y**2-2*md.mesh.y*1.0e6)*(-2.0/(2*md.constants.yts*md.hydrology.sediment_transmitivity)) field_names =['SedimentWaterHead','SedimentHeadResidual'] field_tolerances=[1e-13, 3e-10] Index: /issm/trunk/test/NightlyRun/test333.m =================================================================== --- /issm/trunk/test/NightlyRun/test333.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test333.m (revision 21729) @@ -2,5 +2,5 @@ md=triangle(model(),'../Exp/Square.exp',100000.); md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.par'); +md=parameterize(md,'../Par/IceCube.par'); md.transient=deactivateall(md.transient); md.transient.ishydrology=1; Index: /issm/trunk/test/NightlyRun/test333.py =================================================================== --- /issm/trunk/test/NightlyRun/test333.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test333.py (revision 21729) @@ -2,4 +2,5 @@ import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,16 +9,15 @@ from setflowequation import * from solve import * -from MatlabFuncs import * - from generic import generic md=triangle(model(),'../Exp/Square.exp',100000.) md=setmask(md,'','') -md=parameterize(md,'../Par/SquareSheetConstrained.py') +md=parameterize(md,'../Par/IceCube.py') + md.transient=transient.setallnullparameters(md.transient) md.transient.ishydrology=True md.transient.issmb=True md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.hydrology=hydrologydc() md.hydrology=md.hydrology.initialize(md) @@ -26,15 +26,15 @@ md.hydrology.sedimentlimit_flag=1 md.hydrology.sedimentlimit=800.0 -md.initialization.sediment_head=np.zeros((md.mesh.numberofvertices,1)) -md.hydrology.spcsediment_head=float('NaN')*np.ones((md.mesh.numberofvertices,1)) +md.initialization.sediment_head=np.zeros((md.mesh.numberofvertices)) +md.hydrology.spcsediment_head=np.nan*np.ones((md.mesh.numberofvertices)) -md.basalforcings.groundedice_melting_rate = 2.0*np.ones((md.mesh.numberofvertices,1)) -md.basalforcings.floatingice_melting_rate = 0.0*np.ones((md.mesh.numberofvertices,1)) -md.hydrology.sediment_transmitivity= 3.0*np.ones((md.mesh.numberofvertices,1)) +md.basalforcings.groundedice_melting_rate = 2.0*np.ones((md.mesh.numberofvertices)) +md.basalforcings.floatingice_melting_rate = 0.0*np.ones((md.mesh.numberofvertices)) +md.hydrology.sediment_transmitivity= 3.0*np.ones((md.mesh.numberofvertices)) -md.initialization.epl_head=np.zeros((md.mesh.numberofvertices,1)) -md.initialization.epl_thickness=np.ones((md.mesh.numberofvertices,1)) -md.hydrology.spcepl_head=float('NaN')*np.ones((md.mesh.numberofvertices,1)) -md.hydrology.mask_eplactive_node=np.zeros((md.mesh.numberofvertices,1)) +md.initialization.epl_head=np.zeros((md.mesh.numberofvertices)) +md.initialization.epl_thickness=np.ones((md.mesh.numberofvertices)) +md.hydrology.spcepl_head=np.nan*np.ones((md.mesh.numberofvertices)) +md.hydrology.mask_eplactive_node=np.zeros((md.mesh.numberofvertices)) md.hydrology.epl_conductivity=30 md.hydrology.epl_initial_thickness=1 @@ -47,12 +47,12 @@ md=solve(md,'Transient') -sedvol=np.zeros(10) -eplvol=np.zeros(10) -time=np.arange(0.2,2.1,0.2) -store=md.constants.g*md.hydrology.sediment_porosity*md.materials.rho_freshwater*((md.hydrology.sediment_compressibility/md.hydrology.sediment_porosity)+md.hydrology.water_compressibility); -sedstore=20.0*store; -for i in range(0,10): - sedvol[i]=np.mean(md.results.TransientSolution[i].SedimentHead)*sedstore - eplvol[i]=np.mean(md.results.TransientSolution[i].EplHead)*store*np.mean(md.results.TransientSolution[i].HydrologydcEplThickness) +# sedvol=np.zeros(10) +# eplvol=np.zeros(10) +# time=np.arange(0.2,2.1,0.2) +# store=md.constants.g*md.hydrology.sediment_porosity*md.materials.rho_freshwater*((md.hydrology.sediment_compressibility/md.hydrology.sediment_porosity)+md.hydrology.water_compressibility) +# sedstore=20.0*store +# for i in range(0,10): +# sedvol[i]=np.mean(md.results.TransientSolution[i].SedimentHead)*sedstore +# eplvol[i]=np.mean(md.results.TransientSolution[i].EplHead)*store*np.mean(md.results.TransientSolution[i].HydrologydcEplThickness) field_names=['SedimentWaterHead1','EplWaterHead1','SedimentHeadResidual1', Index: /issm/trunk/test/NightlyRun/test334.m =================================================================== --- /issm/trunk/test/NightlyRun/test334.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test334.m (revision 21729) @@ -4,5 +4,5 @@ md.transient=deactivateall(md.transient); md.transient.ishydrology=1; -md=parameterize(md,'../Par/SquareSheetConstrained.par'); +md=parameterize(md,'../Par/IceCube.par'); md=setflowequation(md,'SSA','all'); md.cluster=generic('name',oshostname(),'np',1); Index: /issm/trunk/test/NightlyRun/test334.py =================================================================== --- /issm/trunk/test/NightlyRun/test334.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test334.py (revision 21729) @@ -2,4 +2,5 @@ import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from generic import generic @@ -14,9 +15,9 @@ md=triangle(model(),'../Exp/Square.exp',100000.) md=setmask(md,'','') -md=parameterize(md,'../Par/SquareSheetConstrained.py') +md=parameterize(md,'../Par/IceCube.py') md.transient=transient.setallnullparameters(md.transient) md.transient.ishydrology=True md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.hydrology=hydrologydc() md.hydrology=md.hydrology.initialize(md) @@ -25,11 +26,11 @@ md.hydrology.sedimentlimit_flag=1 md.hydrology.sedimentlimit=8000.0 -md.initialization.sediment_head=np.zeros((md.mesh.numberofvertices,1)) -md.hydrology.spcsediment_head=float('NaN')*np.ones((md.mesh.numberofvertices,1)) +md.initialization.sediment_head=np.zeros((md.mesh.numberofvertices)) +md.hydrology.spcsediment_head=np.nan*np.ones((md.mesh.numberofvertices)) md.hydrology.spcsediment_head[np.where(md.mesh.y==0)]=0.0 -md.basalforcings.groundedice_melting_rate = 2.0*np.ones((md.mesh.numberofvertices,1)) -md.basalforcings.floatingice_melting_rate = 0.0*np.ones((md.mesh.numberofvertices,1)) -md.hydrology.sediment_transmitivity= 3.0*np.ones((md.mesh.numberofvertices,1)) +md.basalforcings.groundedice_melting_rate = 2.0*np.ones((md.mesh.numberofvertices)) +md.basalforcings.floatingice_melting_rate = 0.0*np.ones((md.mesh.numberofvertices)) +md.hydrology.sediment_transmitivity= 3.0*np.ones((md.mesh.numberofvertices)) md.timestepping.time_step=0 Index: /issm/trunk/test/NightlyRun/test335.m =================================================================== --- /issm/trunk/test/NightlyRun/test335.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test335.m (revision 21729) @@ -5,5 +5,5 @@ md.transient.ishydrology=1; md.transient.issmb=1; -md=parameterize(md,'../Par/SquareSheetConstrained.par'); +md=parameterize(md,'../Par/IceCube.par'); md=setflowequation(md,'SSA','all'); md.cluster=generic('name',oshostname(),'np',1); Index: /issm/trunk/test/NightlyRun/test335.py =================================================================== --- /issm/trunk/test/NightlyRun/test335.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test335.py (revision 21729) @@ -2,4 +2,5 @@ import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -8,5 +9,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + from generic import generic @@ -14,10 +15,10 @@ md=triangle(model(),'../Exp/Square.exp',100000.) md=setmask(md,'','') -md=parameterize(md,'../Par/SquareSheetConstrained.py') +md=parameterize(md,'../Par/IceCube.py') md.transient=transient.setallnullparameters(md.transient) md.transient.ishydrology=True md.transient.issmb=True md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md.hydrology=hydrologydc() md.hydrology=md.hydrology.initialize(md) @@ -26,14 +27,14 @@ md.hydrology.sedimentlimit_flag=1 md.hydrology.sedimentlimit=800.0 -md.initialization.sediment_head=np.zeros((md.mesh.numberofvertices,1)) -md.hydrology.spcsediment_head=float('NaN')*np.ones((md.mesh.numberofvertices,1)) -md.basalforcings.groundedice_melting_rate = 2.0*np.ones((md.mesh.numberofvertices,1)) -md.basalforcings.floatingice_melting_rate = np.zeros((md.mesh.numberofvertices,1)) -md.hydrology.sediment_transmitivity=3*np.ones((md.mesh.numberofvertices,1)) +md.initialization.sediment_head=np.zeros((md.mesh.numberofvertices)) +md.hydrology.spcsediment_head=np.nan*np.ones((md.mesh.numberofvertices)) +md.basalforcings.groundedice_melting_rate = 2.0*np.ones((md.mesh.numberofvertices)) +md.basalforcings.floatingice_melting_rate = np.zeros((md.mesh.numberofvertices)) +md.hydrology.sediment_transmitivity=3*np.ones((md.mesh.numberofvertices)) -md.initialization.epl_head=np.zeros((md.mesh.numberofvertices,1)) -md.initialization.epl_thickness=np.ones((md.mesh.numberofvertices,1)) -md.hydrology.spcepl_head=float('NaN')*np.ones((md.mesh.numberofvertices,1)) -md.hydrology.mask_eplactive_node=np.zeros((md.mesh.numberofvertices,1)) +md.initialization.epl_head=np.zeros((md.mesh.numberofvertices)) +md.initialization.epl_thickness=np.ones((md.mesh.numberofvertices)) +md.hydrology.spcepl_head=np.nan*np.ones((md.mesh.numberofvertices)) +md.hydrology.mask_eplactive_node=np.zeros((md.mesh.numberofvertices)) md.hydrology.epl_conductivity=30 md.hydrology.epl_initial_thickness=1 Index: /issm/trunk/test/NightlyRun/test336.py =================================================================== --- /issm/trunk/test/NightlyRun/test336.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test336.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedSmbComponents2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. @@ -20,11 +21,11 @@ #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*-1.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*-1.)).T -md.smb=SMBcomponents(); -md.smb.accumulation=numpy.vstack((smb*2, [1.5,3.])); -md.smb.runoff=numpy.vstack((smb/2, [1.5,3.])); -md.smb.evaporation=numpy.vstack((smb/2, [1.5,3.])); +md.smb=SMBcomponents() +md.smb.accumulation=np.vstack((smb*2, [1.5,3.])) +md.smb.runoff=np.vstack((smb/2, [1.5,3.])) +md.smb.evaporation=np.vstack((smb/2, [1.5,3.])) md.transient.isthermal=False @@ -32,44 +33,42 @@ #Fields and tolerances to track changes -field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] -field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] +field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test337.py =================================================================== --- /issm/trunk/test/NightlyRun/test337.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test337.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedSmbComponents3d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,5 +15,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. @@ -21,11 +22,11 @@ #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*-1.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*-1.)).T -md.smb=SMBcomponents(); -md.smb.accumulation=numpy.vstack((smb*2, [1.5,3.])); -md.smb.runoff=numpy.vstack((smb/2, [1.5,3.])); -md.smb.evaporation=numpy.vstack((smb/2, [1.5,3.])); +md.smb=SMBcomponents() +md.smb.accumulation=np.vstack((smb*2, [1.5,3.])) +md.smb.runoff=np.vstack((smb/2, [1.5,3.])) +md.smb.evaporation=np.vstack((smb/2, [1.5,3.])) md.transient.isthermal=False @@ -33,45 +34,42 @@ #Fields and tolerances to track changes -field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] -field_tolerances=[\ - 5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] +field_tolerances=[5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10, + 5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10, + 5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10, + 5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test338.py =================================================================== --- /issm/trunk/test/NightlyRun/test338.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test338.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedSmbMeltComponents2d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -13,19 +14,19 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. md.settings.output_frequency=1 -md.timestepping.final_time=4. +md.timestepping.final_time=400. #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*-1.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*-1.)).T -md.smb=SMBmeltcomponents(); -md.smb.accumulation=numpy.vstack((smb, [1.5,3.])); -md.smb.evaporation=numpy.vstack((smb/2, [1.5,3.])); -md.smb.melt=numpy.vstack((smb/2, [1.5,3.])); -md.smb.refreeze=numpy.vstack((smb, [1.5,3.])); +md.smb=SMBmeltcomponents() +md.smb.accumulation=np.vstack((smb, [1.5,3.])) +md.smb.evaporation=np.vstack((smb/2, [1.5,3.])) +md.smb.melt=np.vstack((smb/2, [1.5,3.])) +md.smb.refreeze=np.vstack((smb, [1.5,3.])) md.transient.isthermal=False @@ -33,44 +34,42 @@ #Fields and tolerances to track changes -field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] -field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] +field_tolerances=[1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test339.py =================================================================== --- /issm/trunk/test/NightlyRun/test339.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test339.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedSmbMeltComponents3d -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',150000.) @@ -14,5 +15,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=1. @@ -21,12 +22,12 @@ #Set up transient -smb=numpy.ones((md.mesh.numberofvertices,1))*3.6 -smb=numpy.hstack((smb,smb*-1.)) +smb=np.ones((md.mesh.numberofvertices))*3.6 +smb=np.vstack((smb,smb*-1.)).T -md.smb=SMBmeltcomponents(); -md.smb.accumulation=numpy.vstack((smb, [1.5,3.])); -md.smb.evaporation=numpy.vstack((smb/2, [1.5,3.])); -md.smb.melt=numpy.vstack((smb/2, [1.5,3.])); -md.smb.refreeze=numpy.vstack((smb, [1.5,3.])); +md.smb=SMBmeltcomponents() +md.smb.accumulation=np.vstack((smb, [1.5,3.])) +md.smb.evaporation=np.vstack((smb/2, [1.5,3.])) +md.smb.melt=np.vstack((smb/2, [1.5,3.])) +md.smb.refreeze=np.vstack((smb, [1.5,3.])) md.transient.isthermal=False @@ -34,45 +35,42 @@ #Fields and tolerances to track changes -field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', \ - 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', \ - 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', \ - 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] -field_tolerances=[\ - 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ - 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].SmbMassBalance,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].SmbMassBalance,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].SmbMassBalance,\ - md.results.TransientSolution[3].Vx,\ - md.results.TransientSolution[3].Vy,\ - md.results.TransientSolution[3].Vel,\ - md.results.TransientSolution[3].Pressure,\ - md.results.TransientSolution[3].Base,\ - md.results.TransientSolution[3].Surface,\ - md.results.TransientSolution[3].Thickness,\ - md.results.TransientSolution[3].SmbMassBalance,\ - ] +field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SmbMassBalance1', + 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SmbMassBalance2', + 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SmbMassBalance3', + 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SmbMassBalance4'] +field_tolerances=[1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10, + 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].SmbMassBalance, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].SmbMassBalance, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].SmbMassBalance, + md.results.TransientSolution[3].Vx, + md.results.TransientSolution[3].Vy, + md.results.TransientSolution[3].Vel, + md.results.TransientSolution[3].Pressure, + md.results.TransientSolution[3].Base, + md.results.TransientSolution[3].Surface, + md.results.TransientSolution[3].Thickness, + md.results.TransientSolution[3].SmbMassBalance] Index: /issm/trunk/test/NightlyRun/test341.py =================================================================== --- /issm/trunk/test/NightlyRun/test341.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test341.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: SquareSheetConstrainedCMm1qn3DragHO -import numpy +import numpy as np from model import * +from socket import gethostname from m1qn3inversion import * from triangle import * @@ -8,28 +9,28 @@ from setflowequation import * from solve import * -from MatlabFuncs import * -md=triangle(model(),'../Exp/Square.exp',200000.); -md=setmask(md,'',''); -md=parameterize(md,'../Par/SquareSheetConstrained.py'); + +md=triangle(model(),'../Exp/Square.exp',200000.) +md=setmask(md,'','') +md=parameterize(md,'../Par/SquareSheetConstrained.py') md.extrude(3,1.) -md=setflowequation(md,'HO','all'); +md=setflowequation(md,'HO','all') #control parameters -md.inversion=m1qn3inversion(md.inversion); -md.inversion.iscontrol=1; +md.inversion=m1qn3inversion(md.inversion) +md.inversion.iscontrol=1 md.inversion.control_parameters=['FrictionCoefficient'] -md.inversion.min_parameters=1.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=200.*np.ones((md.mesh.numberofvertices)) md.inversion.maxsteps=2 md.inversion.maxiter=6 md.inversion.cost_functions=[102,501] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,2)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices,2)) md.inversion.cost_functions_coefficients[:,1]=2.*10**-7 -md.inversion.vx_obs=md.initialization.vx; -md.inversion.vy_obs=md.initialization.vy; +md.inversion.vx_obs=md.initialization.vx +md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3); -md=solve(md,'Stressbalance'); +md.cluster=generic('name',gethostname(),'np',3) +md=solve(md,'Stressbalance') #Fields and tolerances to track changes Index: /issm/trunk/test/NightlyRun/test343.m =================================================================== --- /issm/trunk/test/NightlyRun/test343.m (revision 21729) +++ /issm/trunk/test/NightlyRun/test343.m (revision 21729) @@ -0,0 +1,50 @@ +%Test Name: SquareSheetConstrainedSmbGradientsEla2d +md=triangle(model(),'../Exp/Square.exp',150000.); +md=setmask(md,'',''); +md=parameterize(md,'../Par/SquareSheetConstrained.par'); +md=setflowequation(md,'SSA','all'); +md.smb = SMBgradientsela(); +md.smb.ela=1500.*ones(md.mesh.numberofvertices+1,1); +md.smb.b_pos=0.002.*ones(md.mesh.numberofvertices+1,1); +md.smb.b_neg=0.005.*ones(md.mesh.numberofvertices+1,1); +md.smb.b_max=4.*(md.materials.rho_freshwater/md.materials.rho_ice).*ones(md.mesh.numberofvertices+1,1); +md.smb.b_min=-4.*(md.materials.rho_freshwater/md.materials.rho_ice).*ones(md.mesh.numberofvertices+1,1); + +%Change geometry +md.geometry.thickness=md.geometry.surface*30; +md.geometry.surface=md.geometry.base+md.geometry.thickness; + +%Transient options +md.transient.requested_outputs={'default','TotalSmb'}; +md.cluster=generic('name',oshostname(),'np',3); +md=solve(md,'Transient'); + +%Fields and tolerances to track changes +field_names ={'Vx1','Vy1','Vel1','Bed1','Surface1','Thickness1','SMB1','TotalSmb1','Vx2','Vy2','Vel2','Bed2','Surface2','Thickness2','SMB2','TotalSmb2','Vx3','Vy3','Vel3','Bed3','Surface3','Thickness3','SMB3','TotalSmb3'}; +field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1.5e-13,1e-13}; +field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... + (md.results.TransientSolution(1).Vel),... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... + (md.results.TransientSolution(1).Thickness),... + (md.results.TransientSolution(1).SmbMassBalance),... + (md.results.TransientSolution(1).TotalSmb),... + (md.results.TransientSolution(2).Vx),... + (md.results.TransientSolution(2).Vy),... + (md.results.TransientSolution(2).Vel),... + (md.results.TransientSolution(2).Base),... + (md.results.TransientSolution(2).Surface),... + (md.results.TransientSolution(2).Thickness),... + (md.results.TransientSolution(2).TotalSmb),... + (md.results.TransientSolution(2).SmbMassBalance),... + (md.results.TransientSolution(3).Vx),... + (md.results.TransientSolution(3).Vy),... + (md.results.TransientSolution(3).Vel),... + (md.results.TransientSolution(3).Base),... + (md.results.TransientSolution(3).Surface),... + (md.results.TransientSolution(3).Thickness),... + (md.results.TransientSolution(3).SmbMassBalance),... + (md.results.TransientSolution(3).TotalSmb),... + }; Index: /issm/trunk/test/NightlyRun/test344.m =================================================================== --- /issm/trunk/test/NightlyRun/test344.m (revision 21729) +++ /issm/trunk/test/NightlyRun/test344.m (revision 21729) @@ -0,0 +1,61 @@ +%Test Name: SquareSheetConstrainedSmbGradientsEla3d +md=triangle(model(),'../Exp/Square.exp',150000.); +md=setmask(md,'',''); +md=parameterize(md,'../Par/SquareSheetConstrained.par'); + +%Change geometry +md.geometry.thickness=md.geometry.surface*30; +md.geometry.surface=md.geometry.base+md.geometry.thickness; + +md=extrude(md,3,1.); +md=setflowequation(md,'HO','all'); +md.smb = SMBgradientsela(); +md.smb.ela=1500.*ones(md.mesh.numberofvertices+1,1); +md.smb.b_pos=0.002.*ones(md.mesh.numberofvertices+1,1); +md.smb.b_neg=0.005.*ones(md.mesh.numberofvertices+1,1); +md.smb.b_max=4.*(md.materials.rho_freshwater/md.materials.rho_ice).*ones(md.mesh.numberofvertices+1,1); +md.smb.b_min=-4.*(md.materials.rho_freshwater/md.materials.rho_ice).*ones(md.mesh.numberofvertices+1,1); + + +%Transient options +md.transient.requested_outputs={'default','TotalSmb'}; +md.cluster=generic('name',oshostname(),'np',3); +md=solve(md,'Transient'); + +%Fields and tolerances to track changes +field_names ={'Vx1','Vy1','Vz1','Vel1','Bed1','Surface1','Thickness1','Temperature1','SMB1','TotalSmb1','Vx2','Vy2','Vz2','Vel2','Bed2','Surface2','Thickness2','Temperature2','SMB2','TotalSmb2','Vx3','Vy3','Vz3','Vel3','Bed3','Surface3','Thickness3','Temperature3','SMB3','TotalSmb3'}; +field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... + 1e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,... + 1e-09,5e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10}; +field_values={... + (md.results.TransientSolution(1).Vx),... + (md.results.TransientSolution(1).Vy),... + (md.results.TransientSolution(1).Vz),... + (md.results.TransientSolution(1).Vel),... + (md.results.TransientSolution(1).Base),... + (md.results.TransientSolution(1).Surface),... + (md.results.TransientSolution(1).Thickness),... + (md.results.TransientSolution(1).Temperature),... + (md.results.TransientSolution(1).SmbMassBalance),... + (md.results.TransientSolution(1).TotalSmb),... + (md.results.TransientSolution(2).Vx),... + (md.results.TransientSolution(2).Vy),... + (md.results.TransientSolution(2).Vz),... + (md.results.TransientSolution(2).Vel),... + (md.results.TransientSolution(2).Base),... + (md.results.TransientSolution(2).Surface),... + (md.results.TransientSolution(2).Thickness),... + (md.results.TransientSolution(2).Temperature),... + (md.results.TransientSolution(2).SmbMassBalance),... + (md.results.TransientSolution(2).TotalSmb),... + (md.results.TransientSolution(3).Vx),... + (md.results.TransientSolution(3).Vy),... + (md.results.TransientSolution(3).Vz),... + (md.results.TransientSolution(3).Vel),... + (md.results.TransientSolution(3).Base),... + (md.results.TransientSolution(3).Surface),... + (md.results.TransientSolution(3).Thickness),... + (md.results.TransientSolution(3).Temperature),... + (md.results.TransientSolution(3).SmbMassBalance),... + (md.results.TransientSolution(3).TotalSmb),... + }; Index: /issm/trunk/test/NightlyRun/test401.py =================================================================== --- /issm/trunk/test/NightlyRun/test401.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test401.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressSSA2d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/SquareSheetShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test402.py =================================================================== --- /issm/trunk/test/NightlyRun/test402.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test402.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressSSA3d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(4,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test403.py =================================================================== --- /issm/trunk/test/NightlyRun/test403.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test403.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressHO -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(5,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test404.py =================================================================== --- /issm/trunk/test/NightlyRun/test404.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test404.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressFS -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(3,1.) md=setflowequation(md,'FS','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test405.py =================================================================== --- /issm/trunk/test/NightlyRun/test405.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test405.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressMHOPenalties -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(5,1.) md=setflowequation(md,'SSA','../Exp/SquareHalfRight.exp','fill','HO','coupling','penalties') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test406.py =================================================================== --- /issm/trunk/test/NightlyRun/test406.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test406.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfTherStea -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(4,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0. md=solve(md,'Thermal') Index: /issm/trunk/test/NightlyRun/test407.py =================================================================== --- /issm/trunk/test/NightlyRun/test407.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test407.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfTherTran -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(4,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.isstressbalance=False md.transient.ismasstransport=False Index: /issm/trunk/test/NightlyRun/test408.m =================================================================== --- /issm/trunk/test/NightlyRun/test408.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test408.m (revision 21729) @@ -3,6 +3,15 @@ md=setmask(md,'../Exp/SquareShelf.exp',''); md=parameterize(md,'../Par/SquareSheetShelf.par'); +md.geometry.bed=md.geometry.base; +pos=find(md.mask.groundedice_levelset<0); +md.geometry.bed(pos)=md.geometry.base(pos)-10; +md.friction=frictioncoulomb(); +md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); +md.friction.coefficientcoulomb=0.02*ones(md.mesh.numberofvertices,1); md=extrude(md,3,1); md.transient.isthermal=0; +md.transient.isgroundingline=1; md=setflowequation(md,'SSA','all'); md.cluster=generic('name',oshostname(),'np',3); Index: /issm/trunk/test/NightlyRun/test408.py =================================================================== --- /issm/trunk/test/NightlyRun/test408.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test408.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfTranSSA3d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -8,12 +9,22 @@ from setflowequation import * from solve import * +from frictioncoulomb import frictioncoulomb md=triangle(model(),'../Exp/Square.exp',150000.) md=setmask(md,'../Exp/SquareShelf.exp','') md=parameterize(md,'../Par/SquareSheetShelf.py') +md.geometry.bed=copy.deepcopy(md.geometry.base) +pos=np.nonzero(md.mask.groundedice_levelset<0.) +md.geometry.bed[pos]=md.geometry.bed[pos]-10 +md.friction=frictioncoulomb() +md.friction.coefficient=20*np.ones(md.mesh.numberofvertices) +md.friction.p=1*np.ones(md.mesh.numberofelements) +md.friction.q=1*np.ones(md.mesh.numberofelements) +md.friction.coefficientcoulomb=0.02*np.ones(md.mesh.numberofvertices) +md.transient.isthermal=False +md.transient.isgroundingline=True md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.transient.isthermal=False -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.requested_outputs=['default','GroundedArea','FloatingArea','TotalFloatingBmb','TotalGroundedBmb','TotalSmb'] md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test409.py =================================================================== --- /issm/trunk/test/NightlyRun/test409.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test409.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfTranMHOPenalties -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,6 +15,6 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','../Exp/SquareHalfRight.exp','fill','HO','coupling','penalties') -md.cluster=generic('name',oshostname(),'np',3) -md.transient.requested_outputs=['default','GroundedArea']; +md.cluster=generic('name',gethostname(),'np',3) +md.transient.requested_outputs=['default','GroundedArea'] md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test410.py =================================================================== --- /issm/trunk/test/NightlyRun/test410.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test410.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfSteaSSA3d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(3,2.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0 md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test411.py =================================================================== --- /issm/trunk/test/NightlyRun/test411.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test411.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfSteaHO -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(3,2.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0. md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test415.py =================================================================== --- /issm/trunk/test/NightlyRun/test415.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test415.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfCMDragSteaSSA3d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -18,18 +19,18 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['FrictionCoefficient'] -md.inversion.min_parameters=1.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=200.*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[103,501] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,2)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices,2)) md.inversion.cost_functions_coefficients[:,1]=2.*10**-7 -md.inversion.gradient_scaling=3.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2*numpy.ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.3*numpy.ones((md.inversion.nsteps,1)) +md.inversion.gradient_scaling=3.*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.3*np.ones((md.inversion.nsteps)) md.timestepping.time_step=0. md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test416.py =================================================================== --- /issm/trunk/test/NightlyRun/test416.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test416.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfCMDragSteaHO -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -18,18 +19,18 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['FrictionCoefficient'] -md.inversion.min_parameters=1.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=200.*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[102,501] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,2)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices,2)) md.inversion.cost_functions_coefficients[:,1]=2.*10**-7 -md.inversion.gradient_scaling=3.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2*numpy.ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.3*numpy.ones((md.inversion.nsteps,1)) +md.inversion.gradient_scaling=3.*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.3*np.ones((md.inversion.nsteps)) md.timestepping.time_step=0. md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test419.py =================================================================== --- /issm/trunk/test/NightlyRun/test419.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test419.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressSSAHOTiling -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(5,1.) md=setflowequation(md,'SSA','../Exp/SquareHalfRight.exp','fill','HO') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test421.py =================================================================== --- /issm/trunk/test/NightlyRun/test421.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test421.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressHOFS3dTiling -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(5,1.) md=setflowequation(md,'FS','../Exp/SquareHalfRight.exp','fill','HO') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test422.py =================================================================== --- /issm/trunk/test/NightlyRun/test422.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test422.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressSSAFS3dTiling -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(5,1.) md=setflowequation(md,'FS','../Exp/SquareHalfRight.exp','fill','SSA') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.stressbalance.reltol=0.4 md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test423.py =================================================================== --- /issm/trunk/test/NightlyRun/test423.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test423.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: RoundSheetShelfGLMigrationSSA2d -import numpy +import numpy as np from model import * +from socket import gethostname from roundmesh import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + radius=1.e6 @@ -14,18 +15,18 @@ md=roundmesh(model(),radius,50000.) #fix center node to 0,0 -rad=numpy.sqrt(md.mesh.x**2+md.mesh.y**2) -pos=numpy.argmin(rad) +rad=np.sqrt(md.mesh.x**2+md.mesh.y**2) +pos=np.argmin(rad) md.mesh.x[pos]=0. md.mesh.y[pos]=0. #the closest node to the center is changed to be exactly at the center -xelem=numpy.mean(md.mesh.x[md.mesh.elements.astype(int)-1],axis=1) -yelem=numpy.mean(md.mesh.y[md.mesh.elements.astype(int)-1],axis=1) -rad=numpy.sqrt(xelem**2+yelem**2) -flags=numpy.zeros(md.mesh.numberofelements) -pos=numpy.nonzero(rad>=(radius-shelfextent)) +xelem=np.mean(md.mesh.x[md.mesh.elements.astype(int)-1],axis=1) +yelem=np.mean(md.mesh.y[md.mesh.elements.astype(int)-1],axis=1) +rad=np.sqrt(xelem**2+yelem**2) +flags=np.zeros(md.mesh.numberofelements) +pos=np.nonzero(rad>=(radius-shelfextent)) flags[pos]=1 md=setmask(md,flags,'') md=parameterize(md,'../Par/RoundSheetShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.isthermal=False Index: /issm/trunk/test/NightlyRun/test424.py =================================================================== --- /issm/trunk/test/NightlyRun/test424.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test424.py (revision 21729) @@ -1,6 +1,5 @@ #Test Name: SquareSheetShelfGroundingLine2dAggressive -import numpy from model import * -from MatlabFuncs import * +from socket import gethostname from triangle import * from setmask import * @@ -15,6 +14,6 @@ md.initialization.vx[:]=0. md.initialization.vy[:]=0. -md.geometry.base=-700.-abs(md.mesh.y.reshape(-1,1)-500000.)/1000. -md.geometry.bed =-700.-abs(md.mesh.y.reshape(-1,1)-500000.)/1000. +md.geometry.base=-700.-abs(md.mesh.y-500000.)/1000. +md.geometry.bed =-700.-abs(md.mesh.y-500000.)/1000. md.geometry.thickness[:]=1000. md.geometry.surface=md.geometry.base+md.geometry.thickness @@ -25,32 +24,30 @@ md.transient.requested_outputs=['IceVolume','IceVolumeAboveFloatation'] -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') #Fields and tolerances to track changes -field_names =['Bed1','Surface1','Thickness1','Floatingice1','IceVolume1','IceVolumeAboveFloatation1',\ - 'Bed2','Surface2','Thickness2','Floatingice2','IceVolume2','IceVolumeAboveFloatation2',\ - 'Bed3','Surface3','Thickness3','Floatingice3','IceVolume3','IceVolumeAboveFloatation3'] -field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].MaskGroundediceLevelset,\ - md.results.TransientSolution[0].IceVolume,\ - md.results.TransientSolution[0].IceVolumeAboveFloatation,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].MaskGroundediceLevelset,\ - md.results.TransientSolution[1].IceVolume,\ - md.results.TransientSolution[1].IceVolumeAboveFloatation,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].MaskGroundediceLevelset,\ - md.results.TransientSolution[2].IceVolume,\ - md.results.TransientSolution[2].IceVolumeAboveFloatation,\ - ] +field_names =['Bed1','Surface1','Thickness1','Floatingice1','IceVolume1','IceVolumeAboveFloatation1', + 'Bed2','Surface2','Thickness2','Floatingice2','IceVolume2','IceVolumeAboveFloatation2', + 'Bed3','Surface3','Thickness3','Floatingice3','IceVolume3','IceVolumeAboveFloatation3'] +field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] +field_values=[md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].MaskGroundediceLevelset, + md.results.TransientSolution[0].IceVolume, + md.results.TransientSolution[0].IceVolumeAboveFloatation, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].MaskGroundediceLevelset, + md.results.TransientSolution[1].IceVolume, + md.results.TransientSolution[1].IceVolumeAboveFloatation, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].MaskGroundediceLevelset, + md.results.TransientSolution[2].IceVolume, + md.results.TransientSolution[2].IceVolumeAboveFloatation] Index: /issm/trunk/test/NightlyRun/test425.py =================================================================== --- /issm/trunk/test/NightlyRun/test425.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test425.py (revision 21729) @@ -1,6 +1,5 @@ #Test Name: SquareSheetShelfGroundingLine2dSoft -import numpy from model import * -from MatlabFuncs import * +from socket import gethostname from triangle import * from setmask import * @@ -15,6 +14,6 @@ md.initialization.vx[:]=0. md.initialization.vy[:]=0. -md.geometry.base=-700.-abs(md.mesh.y.reshape(-1,1)-500000.)/1000. -md.geometry.bed =-700.-abs(md.mesh.y.reshape(-1,1)-500000.)/1000. +md.geometry.base=-700.-abs(md.mesh.y-500000.)/1000. +md.geometry.bed =-700.-abs(md.mesh.y-500000.)/1000. md.geometry.thickness[:]=1300. md.geometry.surface=md.geometry.base+md.geometry.thickness @@ -24,26 +23,24 @@ md.groundingline.migration='SoftMigration' -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') #Fields and tolerances to track changes -field_names =['Bed1','Surface1','Thickness1','Floatingice1',\ - 'Bed2','Surface2','Thickness2','Floatingice2',\ - 'Bed3','Surface3','Thickness3','Floatingice3'] -field_tolerances=[1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13,\ - 1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].MaskGroundediceLevelset,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].MaskGroundediceLevelset,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].MaskGroundediceLevelset,\ - ] +field_names =['Bed1','Surface1','Thickness1','Floatingice1', + 'Bed2','Surface2','Thickness2','Floatingice2', + 'Bed3','Surface3','Thickness3','Floatingice3'] +field_tolerances=[1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13, + 1e-13,1e-13,1e-13,1e-13] +field_values=[md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].MaskGroundediceLevelset, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].MaskGroundediceLevelset, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].MaskGroundediceLevelset] Index: /issm/trunk/test/NightlyRun/test426.py =================================================================== --- /issm/trunk/test/NightlyRun/test426.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test426.py (revision 21729) @@ -1,6 +1,5 @@ #Test Name: SquareSheetShelfGroundingLine3dAggressive -import numpy from model import * -from MatlabFuncs import * +from socket import gethostname from triangle import * from setmask import * @@ -14,46 +13,44 @@ md.initialization.vx[:]=0. md.initialization.vy[:]=0. -md.geometry.base=-700.-abs(md.mesh.y.reshape(-1,1)-500000.)/1000. -md.geometry.bed =-700.-abs(md.mesh.y.reshape(-1,1)-500000.)/1000. +md.geometry.base=-700.-abs(md.mesh.y-500000.)/1000. +md.geometry.bed =-700.-abs(md.mesh.y-500000.)/1000. md.geometry.thickness[:]=1000. md.geometry.surface=md.geometry.base+md.geometry.thickness md.smb.mass_balance[:]=100. -md.extrude(3,1.); -md=setflowequation(md,'SSA','all'); +md.extrude(3,1.) +md=setflowequation(md,'SSA','all') md.transient.isstressbalance=False md.transient.isgroundingline=True md.groundingline.migration='AggressiveMigration' md.transient.requested_outputs=['IceVolume','IceVolumeAboveFloatation'] -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') #Fields and tolerances to track changes -field_names =['Bed1','Surface1','Thickness1','Floatingice1','IceVolume1','IceVolumeAboveFloatation1',\ - 'Bed2','Surface2','Thickness2','Floatingice2','IceVolume2','IceVolumeAboveFloatation2',\ - 'Bed3','Surface3','Thickness3','Floatingice3','IceVolume3','IceVolumeAboveFloatation3',] +field_names =['Bed1','Surface1','Thickness1','Floatingice1','IceVolume1','IceVolumeAboveFloatation1', + 'Bed2','Surface2','Thickness2','Floatingice2','IceVolume2','IceVolumeAboveFloatation2', + 'Bed3','Surface3','Thickness3','Floatingice3','IceVolume3','IceVolumeAboveFloatation3',] -field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-11,1e-10,1e-11,3e-11,2e-12,5e-12,\ - 1e-10,1e-10,1e-10,5e-11,2e-12,5e-12] +field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-11,1e-10,1e-11,3e-11,2e-12,5e-12, + 1e-10,1e-10,1e-10,5e-11,2e-12,5e-12] -field_values=[\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].MaskGroundediceLevelset,\ - md.results.TransientSolution[0].IceVolume,\ - md.results.TransientSolution[0].IceVolumeAboveFloatation,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].MaskGroundediceLevelset,\ - md.results.TransientSolution[1].IceVolume,\ - md.results.TransientSolution[1].IceVolumeAboveFloatation,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].MaskGroundediceLevelset,\ - md.results.TransientSolution[2].IceVolume,\ - md.results.TransientSolution[2].IceVolumeAboveFloatation,\ - ] +field_values=[md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].MaskGroundediceLevelset, + md.results.TransientSolution[0].IceVolume, + md.results.TransientSolution[0].IceVolumeAboveFloatation, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].MaskGroundediceLevelset, + md.results.TransientSolution[1].IceVolume, + md.results.TransientSolution[1].IceVolumeAboveFloatation, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].MaskGroundediceLevelset, + md.results.TransientSolution[2].IceVolume, + md.results.TransientSolution[2].IceVolumeAboveFloatation] Index: /issm/trunk/test/NightlyRun/test427.py =================================================================== --- /issm/trunk/test/NightlyRun/test427.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test427.py (revision 21729) @@ -1,7 +1,6 @@ #Test Name: SquareSheetShelfGroundingLine3dSoft -import numpy from model import * -from MatlabFuncs import * -from triangle import * +from socket import gethostname + from setmask import * from parameterize import * @@ -14,6 +13,6 @@ md.initialization.vx[:]=0. md.initialization.vy[:]=0. -md.geometry.base=-700.-abs(md.mesh.y.reshape(-1,1)-500000.)/1000. -md.geometry.bed =-700.-abs(md.mesh.y.reshape(-1,1)-500000.)/1000. +md.geometry.base=-700.-abs(md.mesh.y-500000.)/1000. +md.geometry.bed =-700.-abs(md.mesh.y-500000.)/1000. md.geometry.thickness[:]=1300 md.geometry.surface=md.geometry.base+md.geometry.thickness @@ -25,26 +24,24 @@ md.transient.isgroundingline=True md.groundingline.migration='SoftMigration' -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') #Fields and tolerances to track changes -field_names =['Bed1','Surface1','Thickness1','Floatingice1',\ - 'Bed2','Surface2','Thickness2','Floatingice2',\ - 'Bed3','Surface3','Thickness3','Floatingice3'] -field_tolerances=[1e-13,1e-13,1e-13,1e-13,\ - 5e-12,3e-12,7e-12,2e-11,\ - 1e-10,5e-11,1e-10,7e-10] -field_values=[\ - md.results.TransientSolution[0].Base,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].MaskGroundediceLevelset,\ - md.results.TransientSolution[1].Base,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].MaskGroundediceLevelset,\ - md.results.TransientSolution[2].Base,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].MaskGroundediceLevelset,\ - ] +field_names =['Bed1','Surface1','Thickness1','Floatingice1', + 'Bed2','Surface2','Thickness2','Floatingice2', + 'Bed3','Surface3','Thickness3','Floatingice3'] +field_tolerances=[1e-13,1e-13,1e-13,1e-13, + 5e-12,3e-12,7e-12,2e-11, + 1e-10,5e-11,1e-10,7e-10] +field_values=[md.results.TransientSolution[0].Base, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].MaskGroundediceLevelset, + md.results.TransientSolution[1].Base, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].MaskGroundediceLevelset, + md.results.TransientSolution[2].Base, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].MaskGroundediceLevelset] Index: /issm/trunk/test/NightlyRun/test428.py =================================================================== --- /issm/trunk/test/NightlyRun/test428.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test428.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressSSA2dNewton -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -15,5 +16,5 @@ md.stressbalance.isnewton=1 md.stressbalance.restol=0.0001 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test429.py =================================================================== --- /issm/trunk/test/NightlyRun/test429.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test429.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressHONewton -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -16,5 +17,5 @@ md.stressbalance.isnewton=1 md.stressbalance.restol=0.0001 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test431.py =================================================================== --- /issm/trunk/test/NightlyRun/test431.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test431.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfSteaEnthalpySSA3d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,10 +15,10 @@ md.extrude(3,2.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0. md.thermal.isenthalpy=1 md.thermal.isdynamicbasalspc=1 -md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.watercolumn=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.waterfraction=np.zeros((md.mesh.numberofvertices)) +md.initialization.watercolumn=np.zeros((md.mesh.numberofvertices)) md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test432.py =================================================================== --- /issm/trunk/test/NightlyRun/test432.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test432.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfSteaEnthalpyHO -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,9 +15,9 @@ md.extrude(3,2.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0. md.thermal.isenthalpy=1 -md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.watercolumn=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.waterfraction=np.zeros((md.mesh.numberofvertices)) +md.initialization.watercolumn=np.zeros((md.mesh.numberofvertices)) md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test433.py =================================================================== --- /issm/trunk/test/NightlyRun/test433.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test433.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: RoundSheetShelfGLMigrationSSA3d -import numpy +import numpy as np from model import * +from socket import gethostname from roundmesh import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + radius=1.e6 @@ -14,13 +15,13 @@ md=roundmesh(model(),radius,50000.) #fix center node to 0,0 -rad=numpy.sqrt(md.mesh.x**2+md.mesh.y**2) -pos=numpy.argmin(rad) +rad=np.sqrt(md.mesh.x**2+md.mesh.y**2) +pos=np.argmin(rad) md.mesh.x[pos]=0. md.mesh.y[pos]=0. #the closest node to the center is changed to be exactly at the center -xelem=numpy.mean(md.mesh.x[md.mesh.elements.astype(int)-1],axis=1) -yelem=numpy.mean(md.mesh.y[md.mesh.elements.astype(int)-1],axis=1) -rad=numpy.sqrt(xelem**2+yelem**2) -flags=numpy.zeros(md.mesh.numberofelements) -pos=numpy.nonzero(rad>=(radius-shelfextent)) +xelem=np.mean(md.mesh.x[md.mesh.elements.astype(int)-1],axis=1) +yelem=np.mean(md.mesh.y[md.mesh.elements.astype(int)-1],axis=1) +rad=np.sqrt(xelem**2+yelem**2) +flags=np.zeros(md.mesh.numberofelements) +pos=np.nonzero(rad>=(radius-shelfextent)) flags[pos]=1 md=setmask(md,flags,'') @@ -28,5 +29,5 @@ md=setflowequation(md,'SSA','all') md.extrude(3,1.) -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.isthermal=False Index: /issm/trunk/test/NightlyRun/test434.py =================================================================== --- /issm/trunk/test/NightlyRun/test434.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test434.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfL1L2 -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(4,1.) md=setflowequation(md,'L1L2','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test450.py =================================================================== --- /issm/trunk/test/NightlyRun/test450.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test450.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressSSAHigherOrder -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/SquareSheetShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) field_names=[] Index: /issm/trunk/test/NightlyRun/test455.py =================================================================== --- /issm/trunk/test/NightlyRun/test455.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test455.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: SquareSheetShelfStressHOHigherOrder -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(5,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) field_names=[] Index: /issm/trunk/test/NightlyRun/test460.m =================================================================== --- /issm/trunk/test/NightlyRun/test460.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test460.m (revision 21729) @@ -5,5 +5,5 @@ md=extrude(md,3,1.); md.materials = matestar(md.materials); -md.materials.rheology_ko = (3.15e8)^(-3)*ones(md.mesh.numberofvertices,1); +md.materials.rheology_B = 3.15e8*ones(md.mesh.numberofvertices,1); md.materials.rheology_Ec=ones(md.mesh.numberofvertices,1); md.materials.rheology_Es=3*ones(md.mesh.numberofvertices,1); Index: /issm/trunk/test/NightlyRun/test461.m =================================================================== --- /issm/trunk/test/NightlyRun/test461.m (revision 21729) +++ /issm/trunk/test/NightlyRun/test461.m (revision 21729) @@ -0,0 +1,43 @@ +%Test Name: SquareSheetShelfThermalFSEstar +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.materials = matestar(md.materials); +md.materials.rheology_B = 3.15e8*ones(md.mesh.numberofvertices,1); +md.materials.rheology_Ec=ones(md.mesh.numberofvertices,1); +md.materials.rheology_Es=3*ones(md.mesh.numberofvertices,1); + +md=setflowequation(md,'FS','all'); +md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); +md.initialization.watercolumn=zeros(md.mesh.numberofvertices,1); +md.transient.isstressbalance=0; +md.transient.ismasstransport=0; +md.transient.issmb=1; +md.transient.isthermal=1; +md.transient.isgroundingline=0; +md.thermal.isenthalpy=1; +md.thermal.isdynamicbasalspc=1; +md.cluster=generic('name',oshostname(),'np',3); +md=solve(md,'Transient'); + +%Fields and tolerances to track changes +field_names ={... + 'Enthalpy1','Waterfraction1','Temperature1',... + 'Enthalpy2','Waterfraction2','Temperature2',... + 'Enthalpy3','Waterfraction3','Temperature3'}; +field_tolerances={... + 1e-12,1e-11,1e-12,... + 1e-12,1e-10,1e-12,... + 1e-12,1e-9,1e-12}; +field_values={... + (md.results.TransientSolution(1).Enthalpy),... + (md.results.TransientSolution(1).Waterfraction),... + (md.results.TransientSolution(1).Temperature),... + (md.results.TransientSolution(2).Enthalpy),... + (md.results.TransientSolution(2).Waterfraction),... + (md.results.TransientSolution(2).Temperature),... + (md.results.TransientSolution(3).Enthalpy),... + (md.results.TransientSolution(3).Waterfraction),... + (md.results.TransientSolution(3).Temperature),... + }; Index: /issm/trunk/test/NightlyRun/test501.py =================================================================== --- /issm/trunk/test/NightlyRun/test501.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test501.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigStressSSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',20000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/Pig.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test502.py =================================================================== --- /issm/trunk/test/NightlyRun/test502.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test502.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigStressHO from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',20000.) @@ -13,5 +14,5 @@ md.extrude(3,0.9) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test503.py =================================================================== --- /issm/trunk/test/NightlyRun/test503.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test503.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigStressFS from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',20000.) @@ -13,5 +14,5 @@ md.extrude(3,0.9) md=setflowequation(md,'FS','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test504.py =================================================================== --- /issm/trunk/test/NightlyRun/test504.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test504.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigTranSSA2d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',20000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/Pig.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test505.py =================================================================== --- /issm/trunk/test/NightlyRun/test505.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test505.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigTranSSA3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',30000.) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test506.py =================================================================== --- /issm/trunk/test/NightlyRun/test506.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test506.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigTranHO from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',30000.) @@ -13,5 +14,5 @@ md.extrude(2,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test507.py =================================================================== --- /issm/trunk/test/NightlyRun/test507.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test507.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigTranFS from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',30000.) @@ -13,5 +14,5 @@ md.extrude(2,1.) md=setflowequation(md,'FS','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Transient') Index: /issm/trunk/test/NightlyRun/test508.py =================================================================== --- /issm/trunk/test/NightlyRun/test508.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test508.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigSteaSSA3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',35000.) @@ -13,5 +14,5 @@ md.extrude(3,1.1) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0. md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test509.py =================================================================== --- /issm/trunk/test/NightlyRun/test509.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test509.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigSteaHO from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',30000.) @@ -13,5 +14,5 @@ md.extrude(3,1.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0. md.thermal.penalty_threshold=7 Index: /issm/trunk/test/NightlyRun/test510.py =================================================================== --- /issm/trunk/test/NightlyRun/test510.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test510.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigSteaFS from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',20000.) @@ -13,5 +14,5 @@ md.extrude(2,1.) md=setflowequation(md,'FS','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0. md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test511.py =================================================================== --- /issm/trunk/test/NightlyRun/test511.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test511.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: PigCMBFS -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',11000.) @@ -23,16 +24,16 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['MaterialsRheologyBbar'] -md.inversion.min_parameters=10.**6*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=2.*10**9*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=10.**6*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=2.*10**9*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[101] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.gradient_scaling=10.**8*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.99*numpy.ones((md.inversion.nsteps,1)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices)) +md.inversion.gradient_scaling=10.**8*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2.*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.99*np.ones((md.inversion.nsteps)) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',1) +md.cluster=generic('name',gethostname(),'np',1) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test512.py =================================================================== --- /issm/trunk/test/NightlyRun/test512.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test512.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: PigCMDragHO -import numpy +import numpy as np from model import * +from socket import gethostname from triangle import * from setmask import * @@ -7,5 +8,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',20000.) @@ -18,17 +19,17 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['FrictionCoefficient'] -md.inversion.min_parameters=1.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=200.*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[103,501] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,2)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices,2)) md.inversion.cost_functions_coefficients[:,1]=2.*10**-7 -md.inversion.gradient_scaling=3.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=2.99*numpy.ones((md.inversion.nsteps,1)) +md.inversion.gradient_scaling=3.*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2.*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=2.99*np.ones((md.inversion.nsteps)) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Stressbalance') Index: /issm/trunk/test/NightlyRun/test513.py =================================================================== --- /issm/trunk/test/NightlyRun/test513.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test513.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigCMDragSteaSSA3d from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',30000.) @@ -17,13 +18,13 @@ md.inversion.iscontrol=1 md.inversion.control_parameters=['FrictionCoefficient'] -md.inversion.min_parameters=1.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=1.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=200.*np.ones((md.mesh.numberofvertices)) md.inversion.nsteps=2 md.inversion.cost_functions=[103,501] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,2)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices,2)) md.inversion.cost_functions_coefficients[:,1]=2.*10**-7 -md.inversion.gradient_scaling=3.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=2.*numpy.ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.99*numpy.ones((md.inversion.nsteps,1)) +md.inversion.gradient_scaling=3.*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=2.*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.99*np.ones((md.inversion.nsteps)) md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy @@ -31,5 +32,5 @@ md.thermal.penalty_lock=5 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Steadystate') Index: /issm/trunk/test/NightlyRun/test514.py =================================================================== --- /issm/trunk/test/NightlyRun/test514.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test514.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: PigBamgMesh -import numpy +import numpy as np import copy from model import * +from socket import gethostname from bamg import * from setmask import * @@ -8,8 +9,8 @@ from ComputeHessian import * from ComputeMetric import * -from MatlabFuncs import * + #Simple mesh 1 -hVertices=10000.*numpy.ones((27,1)) +hVertices=10000.*np.ones((27)) hVertices[0:5]=1000. md=bamg(model(),'domain','../Exp/Pig.exp','hmax',20000.,'hVertices',hVertices,'gradation',3.,'geometricalmetric',1) @@ -38,6 +39,6 @@ #refine existing mesh 3 -hVertices=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) -hVertices[numpy.nonzero(md.mesh.vertexonboundary)]=500. +hVertices=np.nan*np.ones((md.mesh.numberofvertices)) +hVertices[np.nonzero(md.mesh.vertexonboundary)]=500. md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'anisomax',1.,'hVertices',hVertices) x5=md2.mesh.x @@ -45,10 +46,10 @@ #refine existing mesh 4 -md2=bamg(copy.deepcopy(md),'field',md.inversion.vy_obs,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',0,'err',numpy.array([[1.]])) +md2=bamg(copy.deepcopy(md),'field',md.inversion.vy_obs,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',0,'err',np.array([[1.]])) x6=md2.mesh.x y6=md2.mesh.y #refine existing mesh 5 -md2=bamg(copy.deepcopy(md),'field',numpy.hstack((md.inversion.vy_obs,md.geometry.thickness)),'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',1,'err',numpy.array([[10.,100.]])) +md2=bamg(copy.deepcopy(md),'field',np.hstack((md.inversion.vy_obs,md.geometry.thickness)),'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',1,'err',np.array([[10.,100.]])) x7=md2.mesh.x y7=md2.mesh.y @@ -57,11 +58,3 @@ field_names =['x1','y1','x2','y2','x3','y3','x4','y4','x5','y5','x6','y6','x7','y7'] field_tolerances = [2e-10,7e-10,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ - x1, y1,\ - y2, y2,\ - y3, y3,\ - y4, y4,\ - y5, y5,\ - y6, y6,\ - y7, y7,\ - ] +field_values=[x1, y1, y2, y2, y3, y3, y4, y4, y5, y5, y6, y6, y7, y7] Index: /issm/trunk/test/NightlyRun/test515.py =================================================================== --- /issm/trunk/test/NightlyRun/test515.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test515.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigTherTranSUPG from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',30000.) @@ -14,5 +15,5 @@ md=setflowequation(md,'HO','all') md.thermal.stabilization=2 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.transient.isstressbalance=False md.transient.ismasstransport=False Index: /issm/trunk/test/NightlyRun/test516.py =================================================================== --- /issm/trunk/test/NightlyRun/test516.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test516.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: PigTherSteaSUPG -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -15,5 +16,5 @@ md=setflowequation(md,'HO','all') md.thermal.stabilization=2 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md.timestepping.time_step=0 md.thermal.penalty_threshold=40 Index: /issm/trunk/test/NightlyRun/test530.py =================================================================== --- /issm/trunk/test/NightlyRun/test530.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test530.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigBalVel1 from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',20000.) @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/Pig.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Balancevelocity') Index: /issm/trunk/test/NightlyRun/test531.py =================================================================== --- /issm/trunk/test/NightlyRun/test531.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test531.py (revision 21729) @@ -1,4 +1,5 @@ #Test Name: PigBalVel2 from model import * +from socket import gethostname from triangle import * from setmask import * @@ -6,5 +7,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Pig.exp',20000.) @@ -14,5 +15,5 @@ md.initialization.vy[:]=0. md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Balancevelocity') Index: /issm/trunk/test/NightlyRun/test601.py =================================================================== --- /issm/trunk/test/NightlyRun/test601.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test601.py (revision 21729) @@ -1,5 +1,6 @@ #Test Name: 79NorthMasstransp2d from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -12,5 +13,5 @@ md=parameterize(md,'../Par/79North.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test602.py =================================================================== --- /issm/trunk/test/NightlyRun/test602.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test602.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: 79NorthMasstransp2dDG -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from meshconvert import * @@ -17,5 +18,5 @@ md.masstransport.stabilization=3 md.masstransport.spcthickness=md.geometry.thickness -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test603.py =================================================================== --- /issm/trunk/test/NightlyRun/test603.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test603.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: 79NorthMasstransp3d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(6,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Masstransport') Index: /issm/trunk/test/NightlyRun/test604.py =================================================================== --- /issm/trunk/test/NightlyRun/test604.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test604.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: 79NorthSurfSlop2d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/79North.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'SurfaceSlope') Index: /issm/trunk/test/NightlyRun/test605.py =================================================================== --- /issm/trunk/test/NightlyRun/test605.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test605.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: 79NorthSurfSlop3d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(5,1.5) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'SurfaceSlope') Index: /issm/trunk/test/NightlyRun/test606.py =================================================================== --- /issm/trunk/test/NightlyRun/test606.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test606.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: 79NorthBedSlop2d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/79North.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'BedSlope') Index: /issm/trunk/test/NightlyRun/test607.py =================================================================== --- /issm/trunk/test/NightlyRun/test607.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test607.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: 79NorthBedSlop3d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -14,5 +15,5 @@ md.extrude(2,1.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'BedSlope') Index: /issm/trunk/test/NightlyRun/test608.py =================================================================== --- /issm/trunk/test/NightlyRun/test608.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test608.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: 79NorthBalThic2d -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -13,5 +14,5 @@ md=parameterize(md,'../Par/79North.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Balancethickness') Index: /issm/trunk/test/NightlyRun/test611.py =================================================================== --- /issm/trunk/test/NightlyRun/test611.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test611.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: 79NorthCMBalThic2dCG -import numpy +import numpy as np from model import * -from MatlabFuncs import * +from socket import gethostname + from triangle import * from setmask import * @@ -20,13 +21,13 @@ md.inversion.control_parameters=['BalancethicknessThickeningRate'] md.inversion.thickness_obs=md.geometry.thickness -md.inversion.min_parameters=-50.*numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.max_parameters=50.*numpy.ones((md.mesh.numberofvertices,1)) +md.inversion.min_parameters=-50.*np.ones((md.mesh.numberofvertices)) +md.inversion.max_parameters=50.*np.ones((md.mesh.numberofvertices)) md.inversion.cost_functions=[201] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.gradient_scaling=10./md.constants.yts*numpy.ones((md.inversion.nsteps,1)) -md.inversion.maxiter_per_step=4*numpy.ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.99*numpy.ones((md.inversion.nsteps,1)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices)) +md.inversion.gradient_scaling=10./md.constants.yts*np.ones((md.inversion.nsteps)) +md.inversion.maxiter_per_step=4*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.99*np.ones((md.inversion.nsteps)) -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Balancethickness') Index: /issm/trunk/test/NightlyRun/test613.py =================================================================== --- /issm/trunk/test/NightlyRun/test613.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test613.py (revision 21729) @@ -1,6 +1,7 @@ #Test Name: 79NorthCMBalThicVxVy -import numpy +import numpy as np import copy from model import * +from socket import gethostname from triangle import * from meshconvert import * @@ -9,5 +10,5 @@ from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/79North.exp',10000.) @@ -19,5 +20,5 @@ #Ice sheet only md=md.extract(md.mask.groundedice_levelset>0.) -pos=numpy.nonzero(md.mesh.vertexonboundary) +pos=np.nonzero(md.mesh.vertexonboundary) md.balancethickness.spcthickness[pos]=md.geometry.thickness[pos] @@ -28,14 +29,14 @@ md.inversion.control_parameters=['Vx','Vy'] md.balancethickness.stabilization=1 -md.inversion.gradient_scaling=numpy.hstack((10./md.constants.yts*numpy.ones((md.inversion.nsteps,1)),10./md.constants.yts*numpy.ones((md.inversion.nsteps,1)))) -md.inversion.min_parameters=numpy.hstack((-2000.*numpy.ones((md.mesh.numberofvertices,1)),-2000.*numpy.ones((md.mesh.numberofvertices,1)))) -md.inversion.max_parameters=numpy.hstack((+2000.*numpy.ones((md.mesh.numberofvertices,1)),+2000.*numpy.ones((md.mesh.numberofvertices,1)))) +md.inversion.gradient_scaling=np.vstack((10./md.constants.yts*np.ones((md.inversion.nsteps)),10./md.constants.yts*np.ones((md.inversion.nsteps)))).T +md.inversion.min_parameters=np.vstack((-2000.*np.ones((md.mesh.numberofvertices)),-2000.*np.ones((md.mesh.numberofvertices)))).T +md.inversion.max_parameters=np.vstack((+2000.*np.ones((md.mesh.numberofvertices)),+2000.*np.ones((md.mesh.numberofvertices)))).T md.inversion.cost_functions=[201] -md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,1)) -md.inversion.maxiter_per_step=4*numpy.ones((md.inversion.nsteps,1)) -md.inversion.step_threshold=0.99*numpy.ones((md.inversion.nsteps,1)) +md.inversion.cost_functions_coefficients=np.ones((md.mesh.numberofvertices)) +md.inversion.maxiter_per_step=4*np.ones((md.inversion.nsteps)) +md.inversion.step_threshold=0.99*np.ones((md.inversion.nsteps)) md.verbose.control=1 -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) md=solve(md,'Balancethickness') @@ -43,10 +44,8 @@ field_names =['Gradient1','Gradient2','Misfits','Vx','Vy','Thickness'] field_tolerances=[1e-12,1e-12,1e-12,1e-12,1e-12,1e-12] -field_values=[\ - md.results.BalancethicknessSolution.Gradient1,\ - md.results.BalancethicknessSolution.Gradient2,\ - md.results.BalancethicknessSolution.J,\ - md.results.BalancethicknessSolution.Vx,\ - md.results.BalancethicknessSolution.Vy,\ - md.results.BalancethicknessSolution.Thickness,\ -] +field_values=[md.results.BalancethicknessSolution.Gradient1, + md.results.BalancethicknessSolution.Gradient2, + md.results.BalancethicknessSolution.J, + md.results.BalancethicknessSolution.Vx, + md.results.BalancethicknessSolution.Vy, + md.results.BalancethicknessSolution.Thickness] Index: /issm/trunk/test/NightlyRun/test701.m =================================================================== --- /issm/trunk/test/NightlyRun/test701.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test701.m (revision 21729) @@ -52,5 +52,5 @@ field_values={}; %md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.y); -for i={'MINI','MINIcondensed','TaylorHood','XTaylorHood','LATaylorHood','CrouzeixRaviart','LACrouzeixRaviart'} +for i={'MINI','MINIcondensed','TaylorHood','LATaylorHood','CrouzeixRaviart','LACrouzeixRaviart'} disp(' '); disp(['====== Testing ' i{1} ' Full-Stokes Finite element =====']); Index: /issm/trunk/test/NightlyRun/test702.m =================================================================== --- /issm/trunk/test/NightlyRun/test702.m (revision 21728) +++ /issm/trunk/test/NightlyRun/test702.m (revision 21729) @@ -50,5 +50,5 @@ field_tolerances={}; field_values={}; -for i={'MINI','MINIcondensed','TaylorHood','XTaylorHood','LATaylorHood','CrouzeixRaviart'} +for i={'MINI','MINIcondensed','TaylorHood','XTaylorHood','LATaylorHood'} disp(' '); disp(['====== Testing ' i{1} ' Full-Stokes Finite element =====']); Index: /issm/trunk/test/NightlyRun/test801.py =================================================================== --- /issm/trunk/test/NightlyRun/test801.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test801.py (revision 21729) @@ -1,11 +1,11 @@ #Test Name: ValleyGlacierLevelsetSSA2d from model import * +from socket import gethostname from triangle import * -from squaremesh import * from setmask import * from parameterize import * from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',50000) @@ -13,5 +13,5 @@ md=parameterize(md,'../Par/ValleyGlacierShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) #Transient @@ -27,31 +27,29 @@ #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1',\ - 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2',\ - 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3'] -field_tolerances=[1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,\ - 1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,\ - 1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].MaskIceLevelset,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].MaskIceLevelset,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].MaskIceLevelset,\ - ] +field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1', + 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2', + 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3'] +field_tolerances=[1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12, + 1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12, + 1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].MaskIceLevelset, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].MaskIceLevelset, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].MaskIceLevelset] Index: /issm/trunk/test/NightlyRun/test802.py =================================================================== --- /issm/trunk/test/NightlyRun/test802.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test802.py (revision 21729) @@ -1,11 +1,11 @@ #Test Name: ValleyGlacierLevelsetThermalSSA3d from model import * +from socket import gethostname from triangle import * -from squaremesh import * from setmask import * from parameterize import * from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',50000) @@ -14,8 +14,8 @@ md.extrude(3,2.) md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) #Thermal model -pos_surf=numpy.nonzero(md.mesh.vertexonsurface)[0] +pos_surf=np.nonzero(md.mesh.vertexonsurface)[0] md.thermal.spctemperature[pos_surf]=md.initialization.temperature[pos_surf] @@ -32,34 +32,32 @@ #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1','Temperature1',\ - 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2','Temperature2',\ - 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3','Temperature3'] -field_tolerances=[1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,\ - 1e-9,1e-9,1e-10,1e-10,1e-10,1e-10,1e-10,1e-9,\ - 1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].MaskIceLevelset,\ - md.results.TransientSolution[0].Temperature,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].MaskIceLevelset,\ - md.results.TransientSolution[1].Temperature,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].MaskIceLevelset,\ - md.results.TransientSolution[2].Temperature,\ - ] +field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1','Temperature1', + 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2','Temperature2', + 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3','Temperature3'] +field_tolerances=[1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12, + 1e-9,1e-9,1e-10,1e-10,1e-10,1e-10,1e-10,1e-9, + 1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].MaskIceLevelset, + md.results.TransientSolution[0].Temperature, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].MaskIceLevelset, + md.results.TransientSolution[1].Temperature, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].MaskIceLevelset, + md.results.TransientSolution[2].Temperature] Index: /issm/trunk/test/NightlyRun/test803.py =================================================================== --- /issm/trunk/test/NightlyRun/test803.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test803.py (revision 21729) @@ -1,11 +1,11 @@ #Test Name: ValleyGlacierLevelsetEnthalpyHO3d from model import * +from socket import gethostname from triangle import * -from squaremesh import * from setmask import * from parameterize import * from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',50000) @@ -14,8 +14,8 @@ md.extrude(3,2.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) #Thermal model -pos_surf=numpy.nonzero(md.mesh.vertexonsurface)[0] +pos_surf=np.where(md.mesh.vertexonsurface)[0] md.thermal.spctemperature[pos_surf]=md.initialization.temperature[pos_surf] md.thermal.isenthalpy=True @@ -34,37 +34,35 @@ #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1','Enthalpy1','Watercolumn1',\ - 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2','Enthalpy2','Watercolumn2',\ - 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3','Enthalpy3','Watercolumn3'] -field_tolerances=[1e-10,1e-10,1e-10,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 1e-9,1e-9,1e-10,1e-10,1e-10,1e-10,1e-10,1e-9,1e-10,\ - 1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].MaskIceLevelset,\ - md.results.TransientSolution[0].Enthalpy,\ - md.results.TransientSolution[0].Watercolumn,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].MaskIceLevelset,\ - md.results.TransientSolution[1].Enthalpy,\ - md.results.TransientSolution[1].Watercolumn,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].MaskIceLevelset,\ - md.results.TransientSolution[2].Enthalpy,\ - md.results.TransientSolution[2].Watercolumn,\ - ] +field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1','Enthalpy1','Watercolumn1', + 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2','Enthalpy2','Watercolumn2', + 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3','Enthalpy3','Watercolumn3'] +field_tolerances=[1e-10,1e-10,1e-10,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 1e-9,1e-9,1e-10,1e-10,1e-10,1e-10,1e-10,1e-9,1e-10, + 1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].MaskIceLevelset, + md.results.TransientSolution[0].Enthalpy, + md.results.TransientSolution[0].Watercolumn, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].MaskIceLevelset, + md.results.TransientSolution[1].Enthalpy, + md.results.TransientSolution[1].Watercolumn, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].MaskIceLevelset, + md.results.TransientSolution[2].Enthalpy, + md.results.TransientSolution[2].Watercolumn] Index: /issm/trunk/test/NightlyRun/test804.py =================================================================== --- /issm/trunk/test/NightlyRun/test804.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test804.py (revision 21729) @@ -1,11 +1,11 @@ #Test Name: ValleyGlacierLevelsetCalvingSIA2d from model import * +from socket import gethostname from triangle import * -from squaremesh import * from setmask import * from parameterize import * from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',50000) @@ -13,5 +13,5 @@ md=parameterize(md,'../Par/ValleyGlacierShelf.py') md=setflowequation(md,'SIA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) #Transient @@ -22,40 +22,37 @@ md.transient.isgroundingline=True md.transient.isgia=False -md.transient.ismovingfront=True; +md.transient.ismovingfront=True -md.calving.calvingrate=1000.*numpy.ones((md.mesh.numberofvertices,1)) -md.calving.meltingrate=numpy.zeros((md.mesh.numberofvertices,1)) +md.calving.calvingrate=1000.*np.ones((md.mesh.numberofvertices)) +md.calving.meltingrate=np.zeros((md.mesh.numberofvertices)) md=solve(md,'Transient') #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1',\ - 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2',\ - 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3'] -field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ - 2e-13,2e-13,2e-13,1e-13,1e-13,1e-13,1e-13,\ - 2e-13,2e-13,2e-13,1e-13,1e-13,1e-13,1e-13] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].MaskIceLevelset,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].MaskIceLevelset,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].MaskIceLevelset,\ - - ] +field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1', + 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2', + 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3'] +field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13, + 2e-13,2e-13,2e-13,1e-13,1e-13,1e-13,1e-13, + 2e-13,2e-13,2e-13,1e-13,1e-13,1e-13,1e-13] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].MaskIceLevelset, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].MaskIceLevelset, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].MaskIceLevelset] Index: /issm/trunk/test/NightlyRun/test805.py =================================================================== --- /issm/trunk/test/NightlyRun/test805.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test805.py (revision 21729) @@ -1,11 +1,11 @@ #Test Name: ValleyGlacierLevelsetEnthCalvingHO3d from model import * +from socket import gethostname from triangle import * -from squaremesh import * from setmask import * from parameterize import * from setflowequation import * from solve import * -from MatlabFuncs import * + md=triangle(model(),'../Exp/Square.exp',50000) @@ -14,8 +14,8 @@ md.extrude(3,2.) md=setflowequation(md,'HO','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) #Thermal model -pos_surf=numpy.nonzero(md.mesh.vertexonsurface)[0] +pos_surf=np.nonzero(md.mesh.vertexonsurface)[0] md.thermal.spctemperature[pos_surf]=md.initialization.temperature[pos_surf] md.thermal.isenthalpy=True @@ -29,45 +29,43 @@ md.transient.isgroundingline=True md.transient.isgia=False -md.transient.ismovingfront=True; +md.transient.ismovingfront=True -md.calving.calvingrate=1000.*numpy.ones((md.mesh.numberofvertices,1)) -md.calving.meltingrate=numpy.zeros((md.mesh.numberofvertices,1)) +md.calving.calvingrate=1000.*np.ones((md.mesh.numberofvertices)) +md.calving.meltingrate=np.zeros((md.mesh.numberofvertices)) md=solve(md,'Transient') #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1','Enthalpy1','Watercolumn1',\ - 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2','Enthalpy2','Watercolumn2',\ - 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3','Enthalpy3','Watercolumn3'] -field_tolerances=[1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,\ - 1e-9,1e-9,1e-10,1e-10,1e-10,1e-10,1e-10,1e-9,1e-10,\ - 1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].MaskIceLevelset,\ - md.results.TransientSolution[0].Enthalpy,\ - md.results.TransientSolution[0].Watercolumn,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].MaskIceLevelset,\ - md.results.TransientSolution[1].Enthalpy,\ - md.results.TransientSolution[1].Watercolumn,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].MaskIceLevelset,\ - md.results.TransientSolution[2].Enthalpy,\ - md.results.TransientSolution[2].Watercolumn,\ - ] +field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1','Enthalpy1','Watercolumn1', + 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2','Enthalpy2','Watercolumn2', + 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3','Enthalpy3','Watercolumn3'] +field_tolerances=[1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11, + 1e-9,1e-9,1e-10,1e-10,1e-10,1e-10,1e-10,1e-9,1e-10, + 1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].MaskIceLevelset, + md.results.TransientSolution[0].Enthalpy, + md.results.TransientSolution[0].Watercolumn, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].MaskIceLevelset, + md.results.TransientSolution[1].Enthalpy, + md.results.TransientSolution[1].Watercolumn, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].MaskIceLevelset, + md.results.TransientSolution[2].Enthalpy, + md.results.TransientSolution[2].Watercolumn] Index: /issm/trunk/test/NightlyRun/test806.py =================================================================== --- /issm/trunk/test/NightlyRun/test806.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test806.py (revision 21729) @@ -1,12 +1,12 @@ #Test Name: SquareShelfLevelsetCalvingSSA2dLevermann from model import * +from socket import gethostname from triangle import * -from squaremesh import * from setmask import * from parameterize import * from setflowequation import * from solve import * -from MatlabFuncs import * -import numpy + +import numpy as np md=triangle(model(),'../Exp/Square.exp',50000.) @@ -14,5 +14,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) x = md.mesh.x @@ -21,5 +21,5 @@ Lx = (xmax-xmin) alpha = 2./3. -md.mask.ice_levelset = numpy.float_((x - alpha*Lx)>0) - numpy.float_((x - alpha*Lx)<0) +md.mask.ice_levelset = np.float_((x - alpha*Lx)>0) - np.float_((x - alpha*Lx)<0) md.timestepping.time_step=10 @@ -33,10 +33,10 @@ md.transient.isgroundingline=False md.transient.isgia=False -md.transient.ismovingfront=True; +md.transient.ismovingfront=True md.calving=calvinglevermann() -md.calving.coeff=4.89e13*numpy.ones((md.mesh.numberofvertices,1)) -md.calving.meltingrate=numpy.zeros((md.mesh.numberofvertices,1)) -md.levelset.spclevelset=numpy.float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.calving.coeff=4.89e13*np.ones((md.mesh.numberofvertices)) +md.calving.meltingrate=np.zeros((md.mesh.numberofvertices)) +md.levelset.spclevelset=np.nan*np.ones((md.mesh.numberofvertices)) md.transient.requested_outputs=['default','StrainRateparallel','StrainRateperpendicular','Calvingratex','Calvingratey','CalvingCalvingrate'] @@ -45,41 +45,38 @@ #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1','StrainRateparallel1','StrainRateperpendicular1','CalvingCalvingrate1',\ - 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2','StrainRateparallel2','StrainRateperpendicular2','CalvingCalvingrate2',\ - 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3','StrainRateparallel3','StrainRateperpendicular3','CalvingCalvingrate3'] -field_tolerances=[1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,\ - 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,\ - 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,1e-11,5e-11,5e-11,1e-11] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].MaskIceLevelset,\ - md.results.TransientSolution[0].StrainRateparallel,\ - md.results.TransientSolution[0].StrainRateperpendicular,\ - md.results.TransientSolution[0].CalvingCalvingrate,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].MaskIceLevelset,\ - md.results.TransientSolution[1].StrainRateparallel,\ - md.results.TransientSolution[1].StrainRateperpendicular,\ - md.results.TransientSolution[1].CalvingCalvingrate,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].MaskIceLevelset,\ - md.results.TransientSolution[2].StrainRateparallel,\ - md.results.TransientSolution[2].StrainRateperpendicular,\ - md.results.TransientSolution[2].CalvingCalvingrate,\ - - ] +field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1','StrainRateparallel1','StrainRateperpendicular1','CalvingCalvingrate1', + 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2','StrainRateparallel2','StrainRateperpendicular2','CalvingCalvingrate2', + 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3','StrainRateparallel3','StrainRateperpendicular3','CalvingCalvingrate3'] +field_tolerances=[1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11, + 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11, + 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,1e-11,5e-11,5e-11,1e-11] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].MaskIceLevelset, + md.results.TransientSolution[0].StrainRateparallel, + md.results.TransientSolution[0].StrainRateperpendicular, + md.results.TransientSolution[0].CalvingCalvingrate, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].MaskIceLevelset, + md.results.TransientSolution[1].StrainRateparallel, + md.results.TransientSolution[1].StrainRateperpendicular, + md.results.TransientSolution[1].CalvingCalvingrate, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].MaskIceLevelset, + md.results.TransientSolution[2].StrainRateparallel, + md.results.TransientSolution[2].StrainRateperpendicular, + md.results.TransientSolution[2].CalvingCalvingrate] Index: /issm/trunk/test/NightlyRun/test807.py =================================================================== --- /issm/trunk/test/NightlyRun/test807.py (revision 21728) +++ /issm/trunk/test/NightlyRun/test807.py (revision 21729) @@ -1,12 +1,12 @@ #Test Name: SquareShelfLevelsetMeltingSSA2d from model import * +from socket import gethostname from triangle import * -from squaremesh import * from setmask import * from parameterize import * from setflowequation import * from solve import * -from MatlabFuncs import * -import numpy + +import numpy as np md=triangle(model(),'../Exp/Square.exp',50000.) @@ -14,5 +14,5 @@ md=parameterize(md,'../Par/SquareShelf.py') md=setflowequation(md,'SSA','all') -md.cluster=generic('name',oshostname(),'np',3) +md.cluster=generic('name',gethostname(),'np',3) x = md.mesh.x @@ -21,5 +21,5 @@ Lx = (xmax-xmin) alpha = 2./3. -md.mask.ice_levelset = numpy.float_((x - alpha*Lx)>0) - numpy.float_((x - alpha*Lx)<0) +md.mask.ice_levelset = np.float_((x - alpha*Lx)>0) - np.float_((x - alpha*Lx)<0) md.timestepping.time_step=10 @@ -33,41 +33,38 @@ md.transient.isgroundingline=False md.transient.isgia=False -md.transient.ismovingfront=True; +md.transient.ismovingfront=True -md.calving.calvingrate=numpy.zeros((md.mesh.numberofvertices,1)) -md.calving.meltingrate=10000*numpy.ones((md.mesh.numberofvertices,1)) -md.levelset.spclevelset=numpy.float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.calving.calvingrate=np.zeros((md.mesh.numberofvertices)) +md.calving.meltingrate=10000*np.ones((md.mesh.numberofvertices)) +md.levelset.spclevelset=np.nan*np.ones((md.mesh.numberofvertices)) md=solve(md,'Transient') #Fields and tolerances to track changes -field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1',\ - 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2',\ - 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3'] -field_tolerances=[1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,\ - 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,5e-11,\ - 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,5e-11] -field_values=[\ - md.results.TransientSolution[0].Vx,\ - md.results.TransientSolution[0].Vy,\ - md.results.TransientSolution[0].Vel,\ - md.results.TransientSolution[0].Pressure,\ - md.results.TransientSolution[0].Thickness,\ - md.results.TransientSolution[0].Surface,\ - md.results.TransientSolution[0].MaskIceLevelset,\ - md.results.TransientSolution[1].Vx,\ - md.results.TransientSolution[1].Vy,\ - md.results.TransientSolution[1].Vel,\ - md.results.TransientSolution[1].Pressure,\ - md.results.TransientSolution[1].Thickness,\ - md.results.TransientSolution[1].Surface,\ - md.results.TransientSolution[1].MaskIceLevelset,\ - md.results.TransientSolution[2].Vx,\ - md.results.TransientSolution[2].Vy,\ - md.results.TransientSolution[2].Vel,\ - md.results.TransientSolution[2].Pressure,\ - md.results.TransientSolution[2].Thickness,\ - md.results.TransientSolution[2].Surface,\ - md.results.TransientSolution[2].MaskIceLevelset,\ - - ] +field_names =['Vx1','Vy1','Vel1','Pressure1','Thickness1','Surface1','MaskIceLevelset1', + 'Vx2','Vy2','Vel2','Pressure2','Thickness2','Surface2','MaskIceLevelset2', + 'Vx3','Vy3','Vel3','Pressure3','Thickness3','Surface3','MaskIceLevelset3'] +field_tolerances=[1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11, + 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,5e-11, + 2e-11,2e-11,2e-11,1e-11,1e-11,1e-11,5e-11] +field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vel, + md.results.TransientSolution[0].Pressure, + md.results.TransientSolution[0].Thickness, + md.results.TransientSolution[0].Surface, + md.results.TransientSolution[0].MaskIceLevelset, + md.results.TransientSolution[1].Vx, + md.results.TransientSolution[1].Vy, + md.results.TransientSolution[1].Vel, + md.results.TransientSolution[1].Pressure, + md.results.TransientSolution[1].Thickness, + md.results.TransientSolution[1].Surface, + md.results.TransientSolution[1].MaskIceLevelset, + md.results.TransientSolution[2].Vx, + md.results.TransientSolution[2].Vy, + md.results.TransientSolution[2].Vel, + md.results.TransientSolution[2].Pressure, + md.results.TransientSolution[2].Thickness, + md.results.TransientSolution[2].Surface, + md.results.TransientSolution[2].MaskIceLevelset] Index: /issm/trunk/test/Par/79North.py =================================================================== --- /issm/trunk/test/Par/79North.py (revision 21728) +++ /issm/trunk/test/Par/79North.py (revision 21729) @@ -26,20 +26,20 @@ #Materials -md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) md.initialization.temperature=md.initialization.temperature #Friction -md.friction.coefficient=50.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=50.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) #Ice shelf melting and surface mass balance -md.basalforcings.floatingice_melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) +md.basalforcings.floatingice_melting_rate=numpy.zeros((md.mesh.numberofvertices)) md.basalforcings.floatingice_melting_rate[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.basalforcings.groundedice_melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) -md.smb.mass_balance=15*numpy.ones((md.mesh.numberofvertices,1)) +md.basalforcings.groundedice_melting_rate=numpy.zeros((md.mesh.numberofvertices)) +md.smb.mass_balance=15*numpy.ones((md.mesh.numberofvertices)) #Numerical parameters Index: sm/trunk/test/Par/GiaBenchmarksAB.par =================================================================== --- /issm/trunk/test/Par/GiaBenchmarksAB.par (revision 21728) +++ (revision ) @@ -1,77 +1,0 @@ -%Geometry specific to Experiments A and B -rad=600000; -nv=md.mesh.numberofvertices; -for i=1:nv, - dist=sqrt(md.mesh.x(i).^2+md.mesh.y(i)^2); - if (dist <= rad) - md.geometry.thickness(i)=2000.0; - else - md.geometry.thickness(i)=1.0; % non-zero thickness - end -end -md.geometry.thickness=md.geometry.thickness'; -md.geometry.base=zeros(md.mesh.numberofvertices,1); -md.geometry.surface=md.geometry.thickness+md.geometry.base; - -%Ice density used for benchmarking, not 917 kg/m^3 -md.materials.rho_ice=1000; %kg m^3 - -%GIA parameters specific to Experiments A and B -md.gia.mantle_viscosity=10^21*ones(md.mesh.numberofvertices,1); %in Pa.s -md.gia.lithosphere_thickness=100*ones(md.mesh.numberofvertices,1); %in km -md.materials.lithosphere_shear_modulus=6.7*10^10; %in Pa -md.materials.lithosphere_density=3.36; %in g/cm^3 -md.materials.mantle_shear_modulus=1.45*10^11; %in Pa -md.materials.mantle_density=3.38; %in g/cm^3 - - -%Initial velocity -x = archread('../Data/SquareSheetConstrained.arch','x'); -y = archread('../Data/SquareSheetConstrained.arch','y'); -vx = archread('../Data/SquareSheetConstrained.arch','vx'); -vy = archread('../Data/SquareSheetConstrained.arch','vy'); -index = archread('../Data/SquareSheetConstrained.arch','index'); - -x = x{1}; -y = y{1}; -vx = vx{1}; -vy = vy{1}; -index = index{1}; - -md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); -md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); -clear vx vy x y index; -md.initialization.vz=zeros(md.mesh.numberofvertices,1); -md.initialization.pressure=zeros(md.mesh.numberofvertices,1); - -%Materials -md.initialization.temperature=(273.-20.)*ones(md.mesh.numberofvertices,1); -md.materials.rheology_B=paterson(md.initialization.temperature); -md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); - -%Friction -md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; -md.friction.p=ones(md.mesh.numberofelements,1); -md.friction.q=ones(md.mesh.numberofelements,1); - -%Numerical parameters -md.stressbalance.viscosity_overshoot=0.0; -md.masstransport.stabilization=1.; -md.thermal.stabilization=1.; -md.verbose=verbose(0); -md.settings.waitonlock=30; -md.stressbalance.restol=0.05; -md.steadystate.reltol=0.05; -md.stressbalance.reltol=0.05; -md.stressbalance.abstol=NaN; -md.timestepping.time_step=1.; -md.timestepping.final_time=3.; - -%Boundary conditions: -md=SetIceSheetBC(md); - -%Change name so that no test have the same name -A=dbstack; -if (length(A)>2), md.miscellaneous.name=A(3).file(1:end-2); end - Index: sm/trunk/test/Par/GiaBenchmarksCD.par =================================================================== --- /issm/trunk/test/Par/GiaBenchmarksCD.par (revision 21728) +++ (revision ) @@ -1,76 +1,0 @@ -%Geometry specific to Experiments C and D -rad=800000; -nv=md.mesh.numberofvertices; -for i=1:nv, - dist=sqrt(md.mesh.x(i).^2+md.mesh.y(i)^2); - if (dist <= rad) - md.geometry.thickness(i)=3000.0; - else - md.geometry.thickness(i)=1.0; % non-zero thickness - end -end -md.geometry.thickness=md.geometry.thickness'; -md.geometry.base=zeros(md.mesh.numberofvertices,1); -md.geometry.surface=md.geometry.thickness+md.geometry.base; - -%Ice density used for benchmarking, not 917 kg/m^3 -md.materials.rho_ice=1000; %kg m^3 - -%GIA parameters specific to Experiments A and B -md.gia.mantle_viscosity=10^21*ones(md.mesh.numberofvertices,1); %in Pa.s -md.gia.lithosphere_thickness=100*ones(md.mesh.numberofvertices,1); %in km -md.materials.lithosphere_shear_modulus=6.7*10^10; %in Pa -md.materials.lithosphere_density=3.32; %in g/cm^3 -md.materials.mantle_shear_modulus=1.45*10^11; %in Pa -md.materials.mantle_density=3.34; %in g/cm^3 - -%Initial velocity -x = archread('../Data/SquareSheetConstrained.arch','x'); -y = archread('../Data/SquareSheetConstrained.arch','y'); -vx = archread('../Data/SquareSheetConstrained.arch','vx'); -vy = archread('../Data/SquareSheetConstrained.arch','vy'); -index = archread('../Data/SquareSheetConstrained.arch','index'); - -x = x{1}; -y = y{1}; -vx = vx{1}; -vy = vy{1}; -index = index{1}; - -md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); -md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); -clear vx vy x y index; -md.initialization.vz=zeros(md.mesh.numberofvertices,1); -md.initialization.pressure=zeros(md.mesh.numberofvertices,1); - -%Materials -md.initialization.temperature=(273.-20.)*ones(md.mesh.numberofvertices,1); -md.materials.rheology_B=paterson(md.initialization.temperature); -md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); - -%Friction -md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); -md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; -md.friction.p=ones(md.mesh.numberofelements,1); -md.friction.q=ones(md.mesh.numberofelements,1); - -%Numerical parameters -md.stressbalance.viscosity_overshoot=0.0; -md.masstransport.stabilization=1.; -md.thermal.stabilization=1.; -md.verbose=verbose(0); -md.settings.waitonlock=30; -md.stressbalance.restol=0.05; -md.steadystate.reltol=0.05; -md.stressbalance.reltol=0.05; -md.stressbalance.abstol=NaN; -md.timestepping.time_step=1.; -md.timestepping.final_time=3.; - -%Boundary conditions: -md=SetIceSheetBC(md); - -%Change name so that no test have the same name -A=dbstack; -if (length(A)>2), md.miscellaneous.name=A(3).file(1:end-2); end - Index: /issm/trunk/test/Par/GiaIvinsBenchmarksAB.par =================================================================== --- /issm/trunk/test/Par/GiaIvinsBenchmarksAB.par (revision 21729) +++ /issm/trunk/test/Par/GiaIvinsBenchmarksAB.par (revision 21729) @@ -0,0 +1,77 @@ +%Geometry specific to Experiments A and B +rad=600000; +nv=md.mesh.numberofvertices; +for i=1:nv, + dist=sqrt(md.mesh.x(i).^2+md.mesh.y(i)^2); + if (dist <= rad) + md.geometry.thickness(i)=2000.0; + else + md.geometry.thickness(i)=1.0; % non-zero thickness + end +end +md.geometry.thickness=md.geometry.thickness'; +md.geometry.base=zeros(md.mesh.numberofvertices,1); +md.geometry.surface=md.geometry.thickness+md.geometry.base; + +%Ice density used for benchmarking, not 917 kg/m^3 +md.materials.rho_ice=1000; %kg m^3 + +%GIA parameters specific to Experiments A and B +md.gia.mantle_viscosity=10^21*ones(md.mesh.numberofvertices,1); %in Pa.s +md.gia.lithosphere_thickness=100*ones(md.mesh.numberofvertices,1); %in km +md.materials.lithosphere_shear_modulus=6.7*10^10; %in Pa +md.materials.lithosphere_density=3.36; %in g/cm^3 +md.materials.mantle_shear_modulus=1.45*10^11; %in Pa +md.materials.mantle_density=3.38; %in g/cm^3 + + +%Initial velocity +x = archread('../Data/SquareSheetConstrained.arch','x'); +y = archread('../Data/SquareSheetConstrained.arch','y'); +vx = archread('../Data/SquareSheetConstrained.arch','vx'); +vy = archread('../Data/SquareSheetConstrained.arch','vy'); +index = archread('../Data/SquareSheetConstrained.arch','index'); + +x = x{1}; +y = y{1}; +vx = vx{1}; +vy = vy{1}; +index = index{1}; + +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); +clear vx vy x y index; +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); + +%Materials +md.initialization.temperature=(273.-20.)*ones(md.mesh.numberofvertices,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); + +%Friction +md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +%Numerical parameters +md.stressbalance.viscosity_overshoot=0.0; +md.masstransport.stabilization=1.; +md.thermal.stabilization=1.; +md.verbose=verbose(0); +md.settings.waitonlock=30; +md.stressbalance.restol=0.05; +md.steadystate.reltol=0.05; +md.stressbalance.reltol=0.05; +md.stressbalance.abstol=NaN; +md.timestepping.time_step=1.; +md.timestepping.final_time=3.; + +%Boundary conditions: +md=SetIceSheetBC(md); + +%Change name so that no test have the same name +A=dbstack; +if (length(A)>2), md.miscellaneous.name=A(3).file(1:end-2); end + Index: /issm/trunk/test/Par/GiaIvinsBenchmarksCD.par =================================================================== --- /issm/trunk/test/Par/GiaIvinsBenchmarksCD.par (revision 21729) +++ /issm/trunk/test/Par/GiaIvinsBenchmarksCD.par (revision 21729) @@ -0,0 +1,76 @@ +%Geometry specific to Experiments C and D +rad=800000; +nv=md.mesh.numberofvertices; +for i=1:nv, + dist=sqrt(md.mesh.x(i).^2+md.mesh.y(i)^2); + if (dist <= rad) + md.geometry.thickness(i)=3000.0; + else + md.geometry.thickness(i)=1.0; % non-zero thickness + end +end +md.geometry.thickness=md.geometry.thickness'; +md.geometry.base=zeros(md.mesh.numberofvertices,1); +md.geometry.surface=md.geometry.thickness+md.geometry.base; + +%Ice density used for benchmarking, not 917 kg/m^3 +md.materials.rho_ice=1000; %kg m^3 + +%GIA parameters specific to Experiments A and B +md.gia.mantle_viscosity=10^21*ones(md.mesh.numberofvertices,1); %in Pa.s +md.gia.lithosphere_thickness=100*ones(md.mesh.numberofvertices,1); %in km +md.materials.lithosphere_shear_modulus=6.7*10^10; %in Pa +md.materials.lithosphere_density=3.32; %in g/cm^3 +md.materials.mantle_shear_modulus=1.45*10^11; %in Pa +md.materials.mantle_density=3.34; %in g/cm^3 + +%Initial velocity +x = archread('../Data/SquareSheetConstrained.arch','x'); +y = archread('../Data/SquareSheetConstrained.arch','y'); +vx = archread('../Data/SquareSheetConstrained.arch','vx'); +vy = archread('../Data/SquareSheetConstrained.arch','vy'); +index = archread('../Data/SquareSheetConstrained.arch','index'); + +x = x{1}; +y = y{1}; +vx = vx{1}; +vy = vy{1}; +index = index{1}; + +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); +clear vx vy x y index; +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); + +%Materials +md.initialization.temperature=(273.-20.)*ones(md.mesh.numberofvertices,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); + +%Friction +md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +%Numerical parameters +md.stressbalance.viscosity_overshoot=0.0; +md.masstransport.stabilization=1.; +md.thermal.stabilization=1.; +md.verbose=verbose(0); +md.settings.waitonlock=30; +md.stressbalance.restol=0.05; +md.steadystate.reltol=0.05; +md.stressbalance.reltol=0.05; +md.stressbalance.abstol=NaN; +md.timestepping.time_step=1.; +md.timestepping.final_time=3.; + +%Boundary conditions: +md=SetIceSheetBC(md); + +%Change name so that no test have the same name +A=dbstack; +if (length(A)>2), md.miscellaneous.name=A(3).file(1:end-2); end + Index: /issm/trunk/test/Par/ISMIPA.py =================================================================== --- /issm/trunk/test/Par/ISMIPA.py (revision 21728) +++ /issm/trunk/test/Par/ISMIPA.py (revision 21729) @@ -5,17 +5,17 @@ print " creating thickness" -md.geometry.surface=-md.mesh.x.reshape(-1,1)*numpy.tan(0.5*numpy.pi/180.) -md.geometry.base=md.geometry.surface-1000.+500.*numpy.sin(md.mesh.x.reshape(-1,1)*2.*numpy.pi/numpy.max(md.mesh.x))*numpy.sin(md.mesh.y.reshape(-1,1)*2.*numpy.pi/numpy.max(md.mesh.x)) +md.geometry.surface=-md.mesh.x*numpy.tan(0.5*numpy.pi/180.) +md.geometry.base=md.geometry.surface-1000.+500.*numpy.sin(md.mesh.x*2.*numpy.pi/numpy.max(md.mesh.x))*numpy.sin(md.mesh.y*2.*numpy.pi/numpy.max(md.mesh.x)) md.geometry.thickness=md.geometry.surface-md.geometry.base print " creating drag" -md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) print " creating flow law parameter" -md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices,1)) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) print " boundary conditions for stressbalance model" Index: /issm/trunk/test/Par/ISMIPB.py =================================================================== --- /issm/trunk/test/Par/ISMIPB.py (revision 21728) +++ /issm/trunk/test/Par/ISMIPB.py (revision 21729) @@ -5,17 +5,17 @@ print " creating thickness" -md.geometry.surface=-md.mesh.x.reshape(-1,1)*numpy.tan(0.5*numpy.pi/180.) -md.geometry.base=md.geometry.surface-1000.+500.*numpy.sin(md.mesh.x.reshape(-1,1)*2.*numpy.pi/numpy.max(md.mesh.x)) +md.geometry.surface=-md.mesh.x*numpy.tan(0.5*numpy.pi/180.) +md.geometry.base=md.geometry.surface-1000.+500.*numpy.sin(md.mesh.x*2.*numpy.pi/numpy.max(md.mesh.x)) md.geometry.thickness=md.geometry.surface-md.geometry.base print " creating drag" -md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) print " creating flow law parameter" -md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices,1)) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) print " boundary conditions for stressbalance model" Index: /issm/trunk/test/Par/ISMIPC.py =================================================================== --- /issm/trunk/test/Par/ISMIPC.py (revision 21728) +++ /issm/trunk/test/Par/ISMIPC.py (revision 21729) @@ -5,5 +5,5 @@ print " creating thickness" -md.geometry.surface=2000.-md.mesh.x.reshape(-1,1)*numpy.tan(0.1*numpy.pi/180.) #to have z>0 +md.geometry.surface=2000.-md.mesh.x*numpy.tan(0.1*numpy.pi/180.) #to have z>0 md.geometry.base=md.geometry.surface-1000. md.geometry.thickness=md.geometry.surface-md.geometry.base @@ -11,12 +11,12 @@ print " creating drag" #md.friction.coefficient=sqrt(md.constants.yts.*(1000.+1000.*sin(md.mesh.x*2.*pi/max(md.mesh.x/2.)).*sin(md.mesh.y*2.*pi/max(md.mesh.x/2.)))./(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.base))); -md.friction.coefficient=numpy.sqrt(md.constants.yts*(1000.+1000.*numpy.sin(md.mesh.x.reshape(-1,1)*2.*numpy.pi/numpy.max(md.mesh.x))*numpy.sin(md.mesh.y.reshape(-1,1)*2.*numpy.pi/numpy.max(md.mesh.x)))) +md.friction.coefficient=numpy.sqrt(md.constants.yts*(1000.+1000.*numpy.sin(md.mesh.x*2.*numpy.pi/numpy.max(md.mesh.x))*numpy.sin(md.mesh.y*2.*numpy.pi/numpy.max(md.mesh.x)))) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.zeros((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.zeros((md.mesh.numberofelements)) print " creating flow law parameter" -md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices,1)) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) print " boundary conditions for stressbalance model:" Index: /issm/trunk/test/Par/ISMIPD.py =================================================================== --- /issm/trunk/test/Par/ISMIPD.py (revision 21728) +++ /issm/trunk/test/Par/ISMIPD.py (revision 21729) @@ -5,17 +5,17 @@ print " creating thickness" -md.geometry.surface=2000.-md.mesh.x.reshape(-1,1)*numpy.tan(0.1*numpy.pi/180.) #to have z>0 +md.geometry.surface=2000.-md.mesh.x*numpy.tan(0.1*numpy.pi/180.) #to have z>0 md.geometry.base=md.geometry.surface-1000. md.geometry.thickness=md.geometry.surface-md.geometry.base print " creating drag" -md.friction.coefficient=numpy.sqrt(md.constants.yts*(1000.+1000.*numpy.sin(md.mesh.x.reshape(-1,1)*2.*numpy.pi/numpy.max(md.mesh.x)))) +md.friction.coefficient=numpy.sqrt(md.constants.yts*(1000.+1000.*numpy.sin(md.mesh.x*2.*numpy.pi/numpy.max(md.mesh.x)))) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.zeros((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.zeros((md.mesh.numberofelements)) print " creating flow law parameter" -md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices,1)) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) print " boundary conditions for stressbalance model:" Index: /issm/trunk/test/Par/ISMIPE.py =================================================================== --- /issm/trunk/test/Par/ISMIPE.py (revision 21728) +++ /issm/trunk/test/Par/ISMIPE.py (revision 21729) @@ -7,6 +7,6 @@ print " creating thickness" data = numpy.array(archread('../Data/ISMIPE.arch','data')); -md.geometry.surface=numpy.zeros((md.mesh.numberofvertices,1)) -md.geometry.base=numpy.zeros((md.mesh.numberofvertices,1)) +md.geometry.surface=numpy.zeros((md.mesh.numberofvertices)) +md.geometry.base=numpy.zeros((md.mesh.numberofvertices)) for i in xrange(0,md.mesh.numberofvertices): y=md.mesh.y[i] @@ -21,11 +21,11 @@ print " creating drag" -md.friction.coefficient=numpy.zeros((md.mesh.numberofvertices,1)) -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.coefficient=numpy.zeros((md.mesh.numberofvertices)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) print " creating flow law parameter" -md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices,1)) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_B=6.8067*10**7*numpy.ones((md.mesh.numberofvertices)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) print " boundary conditions for stressbalance model:" Index: /issm/trunk/test/Par/ISMIPF.py =================================================================== --- /issm/trunk/test/Par/ISMIPF.py (revision 21728) +++ /issm/trunk/test/Par/ISMIPF.py (revision 21729) @@ -6,17 +6,17 @@ print " creating thickness" -md.geometry.surface=-md.mesh.x.reshape(-1,1)*numpy.tan(3.*numpy.pi/180.) +md.geometry.surface=-md.mesh.x*numpy.tan(3.*numpy.pi/180.) #md.geometry.base=md.geometry.surface-1000. -md.geometry.base=md.geometry.surface-1000.+100.*numpy.exp(-((md.mesh.x.reshape(-1,1)-numpy.max(md.mesh.x)/2.)**2+(md.mesh.y.reshape(-1,1)-numpy.max(md.mesh.y)/2.)**2)/(10000.**2)) +md.geometry.base=md.geometry.surface-1000.+100.*numpy.exp(-((md.mesh.x-numpy.max(md.mesh.x)/2.)**2+(md.mesh.y-numpy.max(md.mesh.y)/2.)**2)/(10000.**2)) md.geometry.thickness=md.geometry.surface-md.geometry.base print " creating drag" -md.friction.coefficient=numpy.sqrt(md.constants.yts/(2.140373*10**-7*1000.))*numpy.ones((md.mesh.numberofvertices,1)) -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.zeros((md.mesh.numberofelements,1)) +md.friction.coefficient=numpy.sqrt(md.constants.yts/(2.140373*10**-7*1000.))*numpy.ones((md.mesh.numberofvertices)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.zeros((md.mesh.numberofelements)) print " creating flow law parameter" -md.materials.rheology_B=1.4734*10**14*numpy.ones((md.mesh.numberofvertices,1)) -md.materials.rheology_n=1.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_B=1.4734*10**14*numpy.ones((md.mesh.numberofvertices)) +md.materials.rheology_n=1.*numpy.ones((md.mesh.numberofelements)) md.materials.rheology_law='None' @@ -24,18 +24,18 @@ #Create node on boundary first (because we cannot use mesh) md=SetIceSheetBC(md) -md.stressbalance.spcvx=100.*numpy.ones((md.mesh.numberofvertices,1)) -md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vel=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.temperature=255.*numpy.ones((md.mesh.numberofvertices,1)) +md.stressbalance.spcvx=100.*numpy.ones((md.mesh.numberofvertices)) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vel=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.temperature=255.*numpy.ones((md.mesh.numberofvertices)) pos=numpy.nonzero(numpy.logical_or(numpy.logical_or(md.mesh.x==numpy.min(md.mesh.x),md.mesh.x==numpy.max(md.mesh.x)),numpy.logical_or(md.mesh.y==numpy.min(md.mesh.y),md.mesh.y==numpy.max(md.mesh.y)))) -md.balancethickness.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.balancethickness.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices)) md.balancethickness.spcthickness[pos]=md.geometry.thickness[pos] -md.masstransport.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.masstransport.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices)) md.masstransport.spcthickness[pos]=md.geometry.thickness[pos] -md.thermal.spctemperature=255.*numpy.ones((md.mesh.numberofvertices,1)) -md.basalforcings.geothermalflux=0.4*numpy.ones((md.mesh.numberofvertices,1)) +md.thermal.spctemperature=255.*numpy.ones((md.mesh.numberofvertices)) +md.basalforcings.geothermalflux=0.4*numpy.ones((md.mesh.numberofvertices)) #Parallel options Index: /issm/trunk/test/Par/IceCube.par =================================================================== --- /issm/trunk/test/Par/IceCube.par (revision 21729) +++ /issm/trunk/test/Par/IceCube.par (revision 21729) @@ -0,0 +1,46 @@ +%Start defining model parameters here + +%Geometry +md.geometry.thickness=1000.0*ones(md.mesh.numberofvertices,1); +md.geometry.base=zeros(md.mesh.numberofvertices,1); +md.geometry.surface=md.geometry.base+md.geometry.thickness; + +md.initialization.vx=zeros(md.mesh.numberofvertices,1); +md.initialization.vy=zeros(md.mesh.numberofvertices,1); +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); + +%Materials +md.initialization.temperature=(273.-20.)*ones(md.mesh.numberofvertices,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); + +%Calving +md.calving.calvingrate=zeros(md.mesh.numberofvertices,1); +md.levelset.spclevelset=NaN(md.mesh.numberofvertices,1); + +%Friction +md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +%Numerical parameters +md.stressbalance.viscosity_overshoot=0.0; +md.masstransport.stabilization=1.; +md.thermal.stabilization=1.; +md.verbose=verbose(0); +md.settings.waitonlock=30; +md.stressbalance.restol=0.05; +md.steadystate.reltol=0.05; +md.stressbalance.reltol=0.05; +md.stressbalance.abstol=NaN; +md.timestepping.time_step=1.; +md.timestepping.final_time=3.; + +%Boundary conditions: +md=SetIceSheetBC(md); + +%Change name so that no test have the same name +A=dbstack; +if (length(A)>2), md.miscellaneous.name=A(3).file(1:end-2); end Index: /issm/trunk/test/Par/IceCube.py =================================================================== --- /issm/trunk/test/Par/IceCube.py (revision 21729) +++ /issm/trunk/test/Par/IceCube.py (revision 21729) @@ -0,0 +1,55 @@ +import os.path +import numpy as np +import inspect +from verbose import verbose +from InterpFromMeshToMesh2d import InterpFromMeshToMesh2d +from paterson import paterson +from SetIceSheetBC import SetIceSheetBC +from arch import * + +#Start defining model parameters here + +#Geometry +md.geometry.thickness=1000.0*np.ones((md.mesh.numberofvertices)) +md.geometry.base=np.zeros((md.mesh.numberofvertices)) +md.geometry.surface=md.geometry.base+md.geometry.thickness + +md.initialization.vx=np.zeros((md.mesh.numberofvertices)) +md.initialization.vy=np.zeros((md.mesh.numberofvertices)) +md.initialization.vz=np.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=np.zeros((md.mesh.numberofvertices)) + +#Materials +md.initialization.temperature=(273.-20.)*np.ones((md.mesh.numberofvertices)) +md.materials.rheology_B=paterson(md.initialization.temperature) +md.materials.rheology_n=3.*np.ones((md.mesh.numberofelements)) + +#Calving +md.calving.calvingrate=np.zeros((md.mesh.numberofvertices)) +md.levelset.spclevelset=np.nan*np.ones((md.mesh.numberofvertices)) + +#Friction +md.friction.coefficient=20.*np.ones((md.mesh.numberofvertices)) +md.friction.coefficient[np.where(md.mask.groundedice_levelset<0.)[0]]=0. +md.friction.p=np.ones((md.mesh.numberofelements)) +md.friction.q=np.ones((md.mesh.numberofelements)) + +#Numerical parameters +md.stressbalance.viscosity_overshoot=0.0 +md.masstransport.stabilization=1. +md.thermal.stabilization=1. +md.verbose=verbose(0) +md.settings.waitonlock=30 +md.stressbalance.restol=0.05 +md.steadystate.reltol=0.05 +md.stressbalance.reltol=0.05 +md.stressbalance.abstol=float('NaN') +md.timestepping.time_step=1. +md.timestepping.final_time=3. + +#Boundary conditions: +md=SetIceSheetBC(md) + +#Change name so that no test have the same name +if len(inspect.stack()) > 2: + md.miscellaneous.name = os.path.basename(inspect.stack()[2][1]).split('.')[0] Index: /issm/trunk/test/Par/Pig.py =================================================================== --- /issm/trunk/test/Par/Pig.py (revision 21728) +++ /issm/trunk/test/Par/Pig.py (revision 21729) @@ -26,18 +26,18 @@ md.initialization.vx=md.inversion.vx_obs md.initialization.vy=md.inversion.vy_obs -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) #Materials -md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) md.initialization.temperature=md.initialization.temperature #Friction -md.friction.coefficient=50.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=50.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) #Numerical parameters Index: /issm/trunk/test/Par/RoundSheetEISMINT.py =================================================================== --- /issm/trunk/test/Par/RoundSheetEISMINT.py (revision 21728) +++ /issm/trunk/test/Par/RoundSheetEISMINT.py (revision 21729) @@ -4,23 +4,23 @@ #Ok, start defining model parameters here print " creating thickness" -md.geometry.thickness=10.*numpy.ones((md.mesh.numberofvertices,1)) -md.geometry.base=numpy.zeros((md.mesh.numberofvertices,1)) +md.geometry.thickness=10.*numpy.ones((md.mesh.numberofvertices)) +md.geometry.base=numpy.zeros((md.mesh.numberofvertices)) md.geometry.surface=md.geometry.base+md.geometry.thickness print " creating drag" -md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices,1)) -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) print " creating temperatures" tmin=238.15 #K st=1.67*10**-2/1000. #k/m -radius=numpy.sqrt((md.mesh.x)**2+(md.mesh.y)**2).reshape(-1,1) +radius=numpy.sqrt((md.mesh.x)**2+(md.mesh.y)**2) md.initialization.temperature=tmin+st*radius -md.basalforcings.geothermalflux=4.2*10**-2*numpy.ones((md.mesh.numberofvertices,1)) +md.basalforcings.geothermalflux=4.2*10**-2*numpy.ones((md.mesh.numberofvertices)) print " creating flow law parameter" -md.materials.rheology_B=6.81*10**7*numpy.ones((md.mesh.numberofvertices,1)) #to have the same B as the analytical solution -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_B=6.81*10**7*numpy.ones((md.mesh.numberofvertices)) #to have the same B as the analytical solution +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) print " creating surface mass balance" @@ -32,11 +32,11 @@ print " creating velocities" constant=0.3 -md.inversion.vx_obs=constant/2.*md.mesh.x.reshape(-1,1)*(md.geometry.thickness)**-1 -md.inversion.vy_obs=constant/2.*md.mesh.y.reshape(-1,1)*(md.geometry.thickness)**-1 +md.inversion.vx_obs=constant/2.*md.mesh.x*(md.geometry.thickness)**-1 +md.inversion.vy_obs=constant/2.*md.mesh.y*(md.geometry.thickness)**-1 md.inversion.vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) -md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) #Deal with boundary conditions: Index: /issm/trunk/test/Par/RoundSheetShelf.py =================================================================== --- /issm/trunk/test/Par/RoundSheetShelf.py (revision 21728) +++ /issm/trunk/test/Par/RoundSheetShelf.py (revision 21729) @@ -14,5 +14,5 @@ hmin=300. hmax=1000. -radius=numpy.sqrt(md.mesh.x.reshape(-1,1)*md.mesh.x.reshape(-1,1)+md.mesh.y.reshape(-1,1)*md.mesh.y.reshape(-1,1)) +radius=numpy.sqrt(md.mesh.x*md.mesh.x+md.mesh.y*md.mesh.y.reshape(-1)) ymin=numpy.min(radius) ymax=numpy.max(radius) @@ -58,26 +58,26 @@ #Initial velocity -md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) #Materials -md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) #Surface mass balance and basal melting -md.smb.mass_balance=-10.*numpy.ones((md.mesh.numberofvertices,1)) -md.basalforcings.groundedice_melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) +md.smb.mass_balance=-10.*numpy.ones((md.mesh.numberofvertices)) +md.basalforcings.groundedice_melting_rate=numpy.zeros((md.mesh.numberofvertices)) pos=numpy.nonzero(md.mask.groundedice_levelset>0.)[0] md.basalforcings.groundedice_melting_rate[pos]=10. -md.basalforcings.floatingice_melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) -md.basalforcings.geothermalflux=numpy.ones((md.mesh.numberofvertices,1)) +md.basalforcings.floatingice_melting_rate=numpy.zeros((md.mesh.numberofvertices)) +md.basalforcings.geothermalflux=numpy.ones((md.mesh.numberofvertices)) #Friction radius=1.e6 shelfextent=2.e5 -md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices)) xelem=numpy.mean(md.mesh.x[md.mesh.elements.astype(int)-1],axis=1) yelem=numpy.mean(md.mesh.y[md.mesh.elements.astype(int)-1],axis=1) @@ -86,6 +86,6 @@ pos=numpy.nonzero(rad>=(radius-shelfextent)) md.friction.coefficient[md.mesh.elements[pos,:]-1]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) #Numerical parameters @@ -109,7 +109,7 @@ #Deal with boundary conditions: -md.stressbalance.spcvx=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) -md.stressbalance.spcvy=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) -md.stressbalance.spcvz=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) +md.stressbalance.spcvx=float('nan')*numpy.ones((md.mesh.numberofvertices)) +md.stressbalance.spcvy=float('nan')*numpy.ones((md.mesh.numberofvertices)) +md.stressbalance.spcvz=float('nan')*numpy.ones((md.mesh.numberofvertices)) pos=numpy.nonzero(numpy.logical_and(md.mesh.x==0,md.mesh.y==0)) @@ -119,9 +119,9 @@ pos=numpy.nonzero(md.mesh.vertexonboundary) md.mask.ice_levelset[pos]=0 -md.balancethickness.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) -md.masstransport.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) +md.balancethickness.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices)) +md.masstransport.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices)) md.stressbalance.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6)) md.stressbalance.loadingforce=0*numpy.ones((md.mesh.numberofvertices,3)) -md.thermal.spctemperature=737.*numpy.ones((md.mesh.numberofvertices,1)) +md.thermal.spctemperature=737.*numpy.ones((md.mesh.numberofvertices)) #Change name so that no test have the same name Index: /issm/trunk/test/Par/RoundSheetStaticEISMINT.py =================================================================== --- /issm/trunk/test/Par/RoundSheetStaticEISMINT.py (revision 21728) +++ /issm/trunk/test/Par/RoundSheetStaticEISMINT.py (revision 21729) @@ -5,16 +5,16 @@ hmin=0.01 hmax=2756.7 -radius=numpy.sqrt((md.mesh.x)**2+(md.mesh.y)**2).reshape(-1,1) +radius=numpy.sqrt((md.mesh.x)**2+(md.mesh.y)**2) radiusmax=numpy.max(radius) radius[numpy.nonzero(radius>(1.-10**-9)*radiusmax)]=radiusmax #eliminate roundoff issues in next statement -md.geometry.thickness=hmin*numpy.ones((numpy.size(md.mesh.x),1))+hmax*(4.*((1./2.)**(4./3.)*numpy.ones((numpy.size(md.mesh.x),1))-((radius)/(2.*radiusmax))**(4./3.)))**(3./8.) +md.geometry.thickness=hmin*numpy.ones((numpy.size(md.mesh.x)))+hmax*(4.*((1./2.)**(4./3.)*numpy.ones((numpy.size(md.mesh.x)))-((radius)/(2.*radiusmax))**(4./3.)))**(3./8.) md.geometry.base=0.*md.geometry.thickness md.geometry.surface=md.geometry.base+md.geometry.thickness print " creating drag" -md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) print " creating temperatures" @@ -22,9 +22,9 @@ st=1.67*10**-2/1000. #k/m md.initialization.temperature=tmin+st*radius -md.basalforcings.geothermalflux=4.2*10**-2*numpy.ones((md.mesh.numberofvertices,1)) +md.basalforcings.geothermalflux=4.2*10**-2*numpy.ones((md.mesh.numberofvertices)) print " creating flow law parameter" -md.materials.rheology_B=6.81*10**7*numpy.ones((md.mesh.numberofvertices,1)) #to have the same B as the analytical solution -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_B=6.81*10**7*numpy.ones((md.mesh.numberofvertices)) #to have the same B as the analytical solution +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) print " creating surface mass balance" @@ -36,11 +36,11 @@ print " creating velocities" constant=0.3 -md.inversion.vx_obs=constant/2.*md.mesh.x.reshape(-1,1)*(md.geometry.thickness)**-1 -md.inversion.vy_obs=constant/2.*md.mesh.y.reshape(-1,1)*(md.geometry.thickness)**-1 +md.inversion.vx_obs=constant/2.*md.mesh.x*(md.geometry.thickness)**-1 +md.inversion.vy_obs=constant/2.*md.mesh.y*(md.geometry.thickness)**-1 md.inversion.vel_obs=numpy.sqrt((md.inversion.vx_obs)**2+(md.inversion.vy_obs)**2) -md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) #Deal with boundary conditions: Index: /issm/trunk/test/Par/SquareEISMINT.py =================================================================== --- /issm/trunk/test/Par/SquareEISMINT.py (revision 21728) +++ /issm/trunk/test/Par/SquareEISMINT.py (revision 21729) @@ -7,30 +7,30 @@ ymin=numpy.min(md.mesh.y) ymax=numpy.max(md.mesh.y) -md.geometry.thickness=500.*numpy.ones((md.mesh.numberofvertices,1)) +md.geometry.thickness=500.*numpy.ones((md.mesh.numberofvertices)) md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness md.geometry.surface=md.geometry.base+md.geometry.thickness print " creating drag" -md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) print " creating initial values" -md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) -md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vel=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices)) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vel=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) print " creating flow law parameter" -md.materials.rheology_B=1.7687*10**8*numpy.ones((md.mesh.numberofvertices,1)) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_B=1.7687*10**8*numpy.ones((md.mesh.numberofvertices)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) print " creating surface mass balance" -md.smb.mass_balance=0.2*numpy.ones((md.mesh.numberofvertices,1)) #0m/a -md.basalforcings.floatingice_melting_rate=0.*numpy.ones((md.mesh.numberofvertices,1)) #0m/a -md.basalforcings.groundedice_melting_rate=0.*numpy.ones((md.mesh.numberofvertices,1)) #0m/a +md.smb.mass_balance=0.2*numpy.ones((md.mesh.numberofvertices)) #0m/a +md.basalforcings.floatingice_melting_rate=0.*numpy.ones((md.mesh.numberofvertices)) #0m/a +md.basalforcings.groundedice_melting_rate=0.*numpy.ones((md.mesh.numberofvertices)) #0m/a print " boundary conditions" @@ -39,7 +39,7 @@ #Evolution of the ice shelf pos=numpy.nonzero(md.mesh.y==200000.) #nodes on the upper boundary condition -md.balancethickness.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.balancethickness.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices)) md.balancethickness.spcthickness[pos]=500. -md.masstransport.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.masstransport.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices)) md.masstransport.spcthickness[pos]=500. md.masstransport.stabilization=0 #Better result with no artificial diffusivity Index: /issm/trunk/test/Par/SquareSheetConstrained.py =================================================================== --- /issm/trunk/test/Par/SquareSheetConstrained.py (revision 21728) +++ /issm/trunk/test/Par/SquareSheetConstrained.py (revision 21729) @@ -1,4 +1,4 @@ import os.path -import numpy +import numpy as np import inspect from verbose import verbose @@ -13,38 +13,38 @@ hmin=300. hmax=1000. -ymin=numpy.min(md.mesh.y) -ymax=numpy.max(md.mesh.y) -xmin=min(md.mesh.x) -xmax=max(md.mesh.x) -md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y.reshape(-1,1)-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x.reshape(-1,1)-xmin)/(xmax-xmin) +ymin=np.min(md.mesh.y) +ymax=np.max(md.mesh.y) +xmin=np.min(md.mesh.x) +xmax=np.max(md.mesh.x) +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x-xmin)/(xmax-xmin) md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness+20. md.geometry.surface=md.geometry.base+md.geometry.thickness #Initial velocity -x = numpy.array(archread('../Data/SquareSheetConstrained.arch','x')) -y = numpy.array(archread('../Data/SquareSheetConstrained.arch','y')) -vx = numpy.array(archread('../Data/SquareSheetConstrained.arch','vx')); -vy = numpy.array(archread('../Data/SquareSheetConstrained.arch','vy')); +x = np.array(archread('../Data/SquareSheetConstrained.arch','x')) +y = np.array(archread('../Data/SquareSheetConstrained.arch','y')) +vx = np.array(archread('../Data/SquareSheetConstrained.arch','vx')); +vy = np.array(archread('../Data/SquareSheetConstrained.arch','vy')); index = archread('../Data/SquareSheetConstrained.arch','index').astype(int); -[md.initialization.vx]=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y) -[md.initialization.vy]=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y)[0] +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y)[0] +md.initialization.vz=np.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=np.zeros((md.mesh.numberofvertices)) #Materials -md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.-20.)*np.ones((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3.*np.ones((md.mesh.numberofelements)) #Calving -md.calving.calvingrate=0.*numpy.ones((md.mesh.numberofvertices,1)) -md.levelset.spclevelset=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.calving.calvingrate=np.zeros((md.mesh.numberofvertices)) +md.levelset.spclevelset=np.nan*np.ones((md.mesh.numberofvertices)) #Friction -md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices,1)) -md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.coefficient=20.*np.ones((md.mesh.numberofvertices)) +md.friction.coefficient[np.where(md.mask.groundedice_levelset<0.)[0]]=0. +md.friction.p=np.ones((md.mesh.numberofelements)) +md.friction.q=np.ones((md.mesh.numberofelements)) #Numerical parameters @@ -57,11 +57,11 @@ md.steadystate.reltol=0.05 md.stressbalance.reltol=0.05 -md.stressbalance.abstol=float('NaN') +md.stressbalance.abstol=np.nan md.timestepping.time_step=1. md.timestepping.final_time=3. #GIA: -md.gia.lithosphere_thickness=100.*numpy.ones((md.mesh.numberofvertices,1)); # in km -md.gia.mantle_viscosity=1.*10**21*numpy.ones((md.mesh.numberofvertices,1)); # in Pa.s +md.gia.lithosphere_thickness=100.*np.ones((md.mesh.numberofvertices)); # in km +md.gia.mantle_viscosity=1.*10**21*np.ones((md.mesh.numberofvertices)); # in Pa.s md.materials.lithosphere_shear_modulus=6.7*10**10; # in Pa md.materials.lithosphere_density=3.32; # in g/cm^-3 Index: /issm/trunk/test/Par/SquareSheetShelf.py =================================================================== --- /issm/trunk/test/Par/SquareSheetShelf.py (revision 21728) +++ /issm/trunk/test/Par/SquareSheetShelf.py (revision 21729) @@ -17,5 +17,5 @@ xmin=min(md.mesh.x) xmax=max(md.mesh.x) -md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y.reshape(-1,1)-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x.reshape(-1,1)-xmin)/(xmax-xmin) +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x-xmin)/(xmax-xmin) md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness bed_sheet=-md.materials.rho_ice/md.materials.rho_water*(hmax+(hmin-hmax)*(ymax/2-ymin)/(ymax-ymin)) @@ -33,22 +33,22 @@ [md.initialization.vx] = InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y) [md.initialization.vy] = InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) #Materials -md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) #Accumulation and melting -md.smb.mass_balance=10.*numpy.ones((md.mesh.numberofvertices,1)) -md.basalforcings.groundedice_melting_rate=5.*numpy.ones((md.mesh.numberofvertices,1)) -md.basalforcings.floatingice_melting_rate=5.*numpy.ones((md.mesh.numberofvertices,1)) +md.smb.mass_balance=10.*numpy.ones((md.mesh.numberofvertices)) +md.basalforcings.groundedice_melting_rate=5.*numpy.ones((md.mesh.numberofvertices)) +md.basalforcings.floatingice_melting_rate=5.*numpy.ones((md.mesh.numberofvertices)) #Friction -md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) #Numerical parameters Index: /issm/trunk/test/Par/SquareShelf.py =================================================================== --- /issm/trunk/test/Par/SquareShelf.py (revision 21728) +++ /issm/trunk/test/Par/SquareShelf.py (revision 21729) @@ -16,5 +16,5 @@ xmin=min(md.mesh.x) xmax=max(md.mesh.x) -md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y.reshape(-1,1)-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x.reshape(-1,1)-xmin)/(xmax-xmin) +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x-xmin)/(xmax-xmin) md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness md.geometry.surface=md.geometry.base+md.geometry.thickness @@ -35,6 +35,6 @@ [md.initialization.vx]=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y) [md.initialization.vy]=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) #dbg - begin @@ -51,13 +51,13 @@ #Materials -md.initialization.temperature = (273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.temperature = (273.-20.)*numpy.ones((md.mesh.numberofvertices)) md.materials.rheology_B = paterson(md.initialization.temperature) -md.materials.rheology_n = 3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n = 3.*numpy.ones((md.mesh.numberofelements)) #Friction -md.friction.coefficient = 20.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient = 20.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p = numpy.ones((md.mesh.numberofelements,1)) -md.friction.q = numpy.ones((md.mesh.numberofelements,1)) +md.friction.p = numpy.ones((md.mesh.numberofelements)) +md.friction.q = numpy.ones((md.mesh.numberofelements)) #Numerical parameters Index: /issm/trunk/test/Par/SquareShelf2.py =================================================================== --- /issm/trunk/test/Par/SquareShelf2.py (revision 21728) +++ /issm/trunk/test/Par/SquareShelf2.py (revision 21729) @@ -16,5 +16,5 @@ xmin=min(md.mesh.x) xmax=max(md.mesh.x) -md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y.reshape(-1,1)-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x.reshape(-1,1)-xmin)/(xmax-xmin) +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x-xmin)/(xmax-xmin) md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness md.geometry.surface=md.geometry.base+md.geometry.thickness @@ -34,6 +34,6 @@ [md.initialization.vx]=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y) [md.initialization.vy]=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) #dbg - begin @@ -50,13 +50,13 @@ #Materials -md.initialization.temperature = (273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.temperature = (273.-20.)*numpy.ones((md.mesh.numberofvertices)) md.materials.rheology_B = paterson(md.initialization.temperature) -md.materials.rheology_n = 3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n = 3.*numpy.ones((md.mesh.numberofelements)) #Friction -md.friction.coefficient = 20.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient = 20.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p = numpy.ones((md.mesh.numberofelements,1)) -md.friction.q = numpy.ones((md.mesh.numberofelements,1)) +md.friction.p = numpy.ones((md.mesh.numberofelements)) +md.friction.q = numpy.ones((md.mesh.numberofelements)) #Numerical parameters Index: /issm/trunk/test/Par/SquareShelfConstrained.py =================================================================== --- /issm/trunk/test/Par/SquareShelfConstrained.py (revision 21728) +++ /issm/trunk/test/Par/SquareShelfConstrained.py (revision 21729) @@ -1,5 +1,5 @@ import os.path from arch import * -import numpy +import numpy as np import inspect from verbose import verbose @@ -12,9 +12,9 @@ hmin=300. hmax=1000. -ymin=numpy.min(md.mesh.y) -ymax=numpy.max(md.mesh.y) +ymin=np.min(md.mesh.y) +ymax=np.max(md.mesh.y) xmin=min(md.mesh.x) xmax=max(md.mesh.x) -md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y.reshape(-1,1)-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x.reshape(-1,1)-xmin)/(xmax-xmin) +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x-xmin)/(xmax-xmin) md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness md.geometry.surface=md.geometry.base+md.geometry.thickness @@ -22,32 +22,32 @@ #Initial velocity -#x = numpy.reshape(numpy.array(archread('../Data/SquareShelfConstrained.arch','x')),(-1)) -#y = numpy.reshape(numpy.array(archread('../Data/SquareShelfConstrained.arch','y')),(-1)) -x = numpy.array(archread('../Data/SquareShelfConstrained.arch','x')) -y = numpy.array(archread('../Data/SquareShelfConstrained.arch','y')) -vx = numpy.array(archread('../Data/SquareShelfConstrained.arch','vx')) -vy = numpy.array(archread('../Data/SquareShelfConstrained.arch','vy')) -index = numpy.array(archread('../Data/SquareShelfConstrained.arch','index').astype(int)) +#x = np.reshape(np.array(archread('../Data/SquareShelfConstrained.arch','x')),(-1)) +#y = np.reshape(np.array(archread('../Data/SquareShelfConstrained.arch','y')),(-1)) +x = np.array(archread('../Data/SquareShelfConstrained.arch','x')) +y = np.array(archread('../Data/SquareShelfConstrained.arch','y')) +vx = np.array(archread('../Data/SquareShelfConstrained.arch','vx')) +vy = np.array(archread('../Data/SquareShelfConstrained.arch','vy')) +index = np.array(archread('../Data/SquareShelfConstrained.arch','index').astype(int)) [md.initialization.vx]=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y) [md.initialization.vy]=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vz=np.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=np.zeros((md.mesh.numberofvertices)) #Materials -md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.-20.)*np.ones((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3.*np.ones((md.mesh.numberofelements)) #Surface mass balance and basal melting -md.smb.mass_balance=10.*numpy.ones((md.mesh.numberofvertices,1)) -md.basalforcings.groundedice_melting_rate=5.*numpy.ones((md.mesh.numberofvertices,1)) -md.basalforcings.floatingice_melting_rate=5.*numpy.ones((md.mesh.numberofvertices,1)) +md.smb.mass_balance=10.*np.ones((md.mesh.numberofvertices)) +md.basalforcings.groundedice_melting_rate=5.*np.ones((md.mesh.numberofvertices)) +md.basalforcings.floatingice_melting_rate=5.*np.ones((md.mesh.numberofvertices)) #Friction -md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices,1)) -md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.coefficient=20.*np.ones((md.mesh.numberofvertices)) +md.friction.coefficient[np.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. +md.friction.p=np.ones((md.mesh.numberofelements)) +md.friction.q=np.ones((md.mesh.numberofelements)) #Numerical parameters Index: /issm/trunk/test/Par/SquareThermal.py =================================================================== --- /issm/trunk/test/Par/SquareThermal.py (revision 21728) +++ /issm/trunk/test/Par/SquareThermal.py (revision 21729) @@ -9,29 +9,29 @@ print " creating thickness" h=1000. -md.geometry.thickness=h*numpy.ones((md.mesh.numberofvertices,1)) -md.geometry.base=-1000.*numpy.ones((md.mesh.numberofvertices,1)) +md.geometry.thickness=h*numpy.ones((md.mesh.numberofvertices)) +md.geometry.base=-1000.*numpy.ones((md.mesh.numberofvertices)) md.geometry.surface=md.geometry.base+md.geometry.thickness; print " creating velocities" -md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) print " creating drag" -md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=200.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) print " creating temperatures" -md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices)) print " creating flow law parameter" md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) print " creating surface mass balance" -md.smb.mass_balance=numpy.ones((md.mesh.numberofvertices,1))/md.constants.yts #1m/a -md.basalforcings.melting_rate=0.*numpy.ones((md.mesh.numberofvertices,1))/md.constants.yts #1m/a +md.smb.mass_balance=numpy.ones((md.mesh.numberofvertices))/md.constants.yts #1m/a +md.basalforcings.melting_rate=0.*numpy.ones((md.mesh.numberofvertices))/md.constants.yts #1m/a #Deal with boundary conditions: @@ -41,5 +41,5 @@ print " boundary conditions for thermal model" -md.thermal.spctemperature[:]=md.initialization.temperature -md.basalforcings.geothermalflux=numpy.zeros((md.mesh.numberofvertices,1)) +md.thermal.spctemperature=md.initialization.temperature +md.basalforcings.geothermalflux=numpy.zeros((md.mesh.numberofvertices)) md.basalforcings.geothermalflux[numpy.nonzero(md.mask.groundedice_levelset>0.)[0]]=1.*10**-3 #1 mW/m^2 Index: /issm/trunk/test/Par/ValleyGlacierShelf.py =================================================================== --- /issm/trunk/test/Par/ValleyGlacierShelf.py (revision 21728) +++ /issm/trunk/test/Par/ValleyGlacierShelf.py (revision 21729) @@ -10,6 +10,6 @@ #Start defining model parameters here -x=md.mesh.x.reshape(-1,1) -y=md.mesh.y.reshape(-1,1) +x=md.mesh.x +y=md.mesh.y xmin, xmax = min(x), max(x) ymin, ymax = min(y), max(y) @@ -33,22 +33,22 @@ #Mask md.mask.ice_levelset=x - alpha*Lx -md.mask.groundedice_levelset= numpy.ones((md.mesh.numberofvertices,1)) +md.mask.groundedice_levelset= numpy.ones((md.mesh.numberofvertices)) #Initial velocity -md.initialization.vx=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vy=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.vx=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vy=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) #Materials -md.initialization.temperature=(273.15-5.)*numpy.ones((md.mesh.numberofvertices,1)) -md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) -md.initialization.watercolumn=numpy.zeros((md.mesh.numberofvertices,1)) +md.initialization.temperature=(273.15-5.)*numpy.ones((md.mesh.numberofvertices)) +md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.watercolumn=numpy.zeros((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements,1)) +md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) #Thermal md.thermal.isenthalpy=False -md.thermal.spctemperature=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) +md.thermal.spctemperature=float('nan')*numpy.ones((md.mesh.numberofvertices)) #Groundingline @@ -56,13 +56,13 @@ #Surface mass balance and basal melting -md.smb.mass_balance=0.3*numpy.ones((md.mesh.numberofvertices,1)) +md.smb.mass_balance=0.3*numpy.ones((md.mesh.numberofvertices)) md.basalforcings.groundedice_melting_rate=md.smb.mass_balance md.basalforcings.floatingice_melting_rate=md.smb.mass_balance #Friction -md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices,1)) +md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices)) md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements,1)) -md.friction.q=numpy.ones((md.mesh.numberofelements,1)) +md.friction.p=numpy.ones((md.mesh.numberofelements)) +md.friction.q=numpy.ones((md.mesh.numberofelements)) #Transient @@ -82,7 +82,7 @@ #Masstransport -md.calving.calvingrate=0.*numpy.ones((md.mesh.numberofvertices,1)) -md.calving.meltingrate=0.*numpy.ones((md.mesh.numberofvertices,1)) -md.levelset.spclevelset=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +md.calving.calvingrate=0.*numpy.ones((md.mesh.numberofvertices)) +md.calving.meltingrate=0.*numpy.ones((md.mesh.numberofvertices)) +md.levelset.spclevelset=float('NaN')*numpy.ones((md.mesh.numberofvertices)) md.masstransport.stabilization=1.