Index: /issm/branches/trunk-jpl-damage/configs/config-arm-linux.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-arm-linux.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/configs/config-arm-linux.sh (revision 12258) @@ -1,12 +1,13 @@ #!/bin/sh - -pythonversion=2.7 ./configure \ --prefix=$ISSM_DIR \ - --with-python-dir=$ISSM_DIR/externalpackages/python/install\ - --with-python-version=$pythonversion \ - --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --host="arm-linux" \ + --without-modules \ + CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc \ + GCC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc \ + CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-g++ \ --with-vendor=arm-linux \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ + --without-fortran-lib Index: /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/configs/config-linux64-astrid.sh (revision 12258) @@ -15,4 +15,5 @@ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ --with-petsc-arch=$ISSM_ARCH \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ @@ -30,2 +31,3 @@ --with-numthreads=32 \ --enable-debugging + #--with-serial=no \ Index: /issm/branches/trunk-jpl-damage/configs/config-linux64-ubuntu64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-linux64-ubuntu64.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/configs/config-linux64-ubuntu64.sh (revision 12258) @@ -0,0 +1,26 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl -ldl" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-fortran-lib="-lgfortran"\ + --with-numthreads=8 \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --enable-debugging + + Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-helene.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-helene.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-helene.sh (revision 12258) @@ -0,0 +1,26 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 Index: /issm/branches/trunk-jpl-damage/configure.ac =================================================================== --- /issm/branches/trunk-jpl-damage/configure.ac (revision 12257) +++ /issm/branches/trunk-jpl-damage/configure.ac (revision 12258) @@ -10,5 +10,5 @@ AC_PROG_CPP AC_PROG_CXX([cccl cl icl g++]) -AC_PROG_F77([ifort g77 gfortran]) +#AC_PROG_F77([ifort g77 gfortran]) #Libraries and linking AC_PROG_RANLIB Index: /issm/branches/trunk-jpl-damage/cron/nightlyrun.sh =================================================================== --- /issm/branches/trunk-jpl-damage/cron/nightlyrun.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/cron/nightlyrun.sh (revision 12258) @@ -65,5 +65,4 @@ #Export ISSM_* variables{{{1 export ISSM_DIR -export ISSM_TIER export ISSM_ARCH #}}} @@ -90,5 +89,5 @@ #only update ISSM - cd $ISSM_TIER + cd $ISSM_DIR svn update @@ -109,9 +108,9 @@ #Create cluster's settings{{{1 #create simpler cluster.rc file, with only the cluster we are interested in. -cd $ISSM_TIER/test/NightlyRun/ +cd $ISSM_DIR/test/NightlyRun/ if [ "$MACHINE" = "win7" ]; then cat << END > $HOST_NAME"_settings.m" cluster.login='$USER'; -cluster.codepath='`cygpath -m $ISSM_TIER/bin`'; +cluster.codepath='`cygpath -m $ISSM_DIR/bin`'; cluster.executionpath='`cygpath -m $EXECUTION_PATH`'; END @@ -119,8 +118,8 @@ cat << END > $HOST_NAME"_settings.m" cluster.login='$USER'; -cluster.codepath='$ISSM_TIER/bin'; +cluster.codepath='$ISSM_DIR/bin'; cluster.executionpath='$EXECUTION_PATH'; END - cat << END > $ISSM_TIER/externalpackages/matlab/install.sh + cat << END > $ISSM_DIR/externalpackages/matlab/install.sh #!/bin/bash rm -rf install @@ -131,5 +130,5 @@ #}}} #Source environment variables with new matlab path {{{1 -cd $ISSM_TIER/etc +cd $ISSM_DIR/etc source environment.sh MATLAB_DIR=$MATLAB_PATH #}}} @@ -138,5 +137,5 @@ then - cd $ISSM_TIER/externalpackages + cd $ISSM_DIR/externalpackages #number of packages: numpackages=`echo $EXTERNALPACKAGES | wc -w` @@ -156,5 +155,5 @@ #erase externapackages, and link with externalpackages_dir - cd $ISSM_TIER + cd $ISSM_DIR rm -rf externalpackages cp -Rf $EXTERNALPACKAGESDIR ./ @@ -164,5 +163,5 @@ #erase externapackages, and link with externalpackages_dir - cd $ISSM_TIER + cd $ISSM_DIR rm -rf externalpackages ln -s $EXTERNALPACKAGESDIR . @@ -186,5 +185,5 @@ then - cd $ISSM_TIER + cd $ISSM_DIR make clean make distclean @@ -214,7 +213,7 @@ #Prepare run #create softlink to startup {{{1 -cd $ISSM_TIER/test/NightlyRun/ +cd $ISSM_DIR/test/NightlyRun/ rm startup.m #in case it alreade exists -cp $ISSM_TIER/startup.m . +cp $ISSM_DIR/startup.m . #}}} #Create nightlylog directory and info.log {{{1 @@ -222,7 +221,7 @@ INSTALL_TIME=$(timer) ELAPSED_INSTALL=$(timer $START_TIME) -rm -rf $ISSM_TIER/nightlylog -mkdir $ISSM_TIER/nightlylog -cat << END > $ISSM_TIER/nightlylog/info.log +rm -rf $ISSM_DIR/nightlylog +mkdir $ISSM_DIR/nightlylog +cat << END > $ISSM_DIR/nightlylog/info.log today: $(echo $TODAY) user: $(echo $USER) @@ -245,7 +244,7 @@ #on Matlab and windows machines, we'll need a windows style path: {{{ if [ "$MACHINE" = "win7" ]; then - MATLAB_TIER=`cygpath -m $ISSM_TIER` + MATLAB_TIER=`cygpath -m $ISSM_DIR` else - MATLAB_TIER=$ISSM_TIER + MATLAB_TIER=$ISSM_DIR fi #}}} @@ -254,5 +253,5 @@ do #Launch matlab and the nightly run script - cat > $ISSM_TIER/nightlylog/matlab_run$i.m << EOF + cat > $ISSM_DIR/nightlylog/matlab_run$i.m << EOF warning off %necessary to avoid a info.log of several Go for parallel runs try, @@ -263,5 +262,4 @@ echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" else - #echo "runme('id',[101 102]);" echo "runme($NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" fi @@ -271,5 +269,5 @@ message=getReport(me) directory=strsplit(pwd,'/'); - fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at'); + fid=fopen([issmdir '/nightlylog/matlaberror.log'], 'at'); fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end}); fprintf(fid,'%s',message); @@ -281,5 +279,5 @@ #Start run from nightlylog directory - cd $ISSM_TIER/nightlylog/ + cd $ISSM_DIR/nightlylog/ MATLABBIN=$MATLAB_PATH/bin/matlab @@ -298,5 +296,5 @@ #}}} #concatenate all reports {{{1 -cd $ISSM_TIER/nightlylog/ +cd $ISSM_DIR/nightlylog/ cp matlab_log1.log matlab_log.log for (( i=2;i<=$NUMCPUS_RUN;i++ )) @@ -315,5 +313,5 @@ ELAPSED_RUN=$(timer $INSTALL_TIME) ELAPSED_TOTAL=$(timer $START_TIME) -cat << END >> $ISSM_TIER/nightlylog/info.log +cat << END >> $ISSM_DIR/nightlylog/info.log elapsed_run: $(echo $ELAPSED_RUN) elapsed_total: $(echo $ELAPSED_TOTAL) @@ -324,7 +322,7 @@ #Send Report #Build html report {{{1 -cd $ISSM_TIER/nightlylog/ +cd $ISSM_DIR/nightlylog/ sh ../scripts/report.sh -echo "html report located in $ISSM_TIER/nightlylog/report.html" +echo "html report located in $ISSM_DIR/nightlylog/report.html" #}}} #send mail if requested (SKIPMAIL) {{{1 @@ -332,14 +330,14 @@ then echo "sending report..." - source $ISSM_TIER/cron/mailinglist + source $ISSM_DIR/cron/mailinglist for i in `echo $MAILINGLIST`; do if [ "$MACHINE" = "win7" ] then - email -html -s "Nightly runs on $HOST_NAME (version: $ISSM_RELEASE)" -n "ISSM Nightly run" -f echo $EMAIL_ADRESS $i < $ISSM_TIER/nightlylog/report.html + email -html -s "Nightly runs on $HOST_NAME (version: $ISSM_RELEASE)" -n "ISSM Nightly run" -f echo $EMAIL_ADRESS $i < $ISSM_DIR/nightlylog/report.html else if [ "$MACHINE" = "astrid" ] then -cat - $ISSM_TIER/nightlylog/report.html < To: $i @@ -349,5 +347,5 @@ HERE else -cat - $ISSM_TIER/nightlylog/report.html < To: $i Index: /issm/branches/trunk-jpl-damage/etc/environment.sh =================================================================== --- /issm/branches/trunk-jpl-damage/etc/environment.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/etc/environment.sh (revision 12258) @@ -215,5 +215,5 @@ #APPSCAN export PATH="$PATH:$APPSCAN_DIR/install/bin" -export PATH="$PATH:$APPSCAN_DIR/bin"] +export PATH="$PATH:$APPSCAN_DIR/bin" #CPPCHECK @@ -253,4 +253,6 @@ #GSL export PATH="$PATH:$GSL_DIR/bin" +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GSL_DIR/lib" +export LD_RUN_PATH="$LD_RUN_PATH:$GSL_DIR/lib" #GMAKE @@ -261,5 +263,9 @@ export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/src/modules/python" export LD_LIBRARY_PATH=$ISSM_DIR/src/modules/python:$LD_LIBRARY_PATH +export PYTHONSTARTUP #MODELE export PATH="$MODELE_DIR/src/exec:$PATH" + +#GIT +export PATH="$PATH:$GIT_DIR/install/bin" Index: /issm/branches/trunk-jpl-damage/etc/environment_variables.sh =================================================================== --- /issm/branches/trunk-jpl-damage/etc/environment_variables.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/etc/environment_variables.sh (revision 12258) @@ -193,5 +193,10 @@ #PYTHON PYTHON_DIR="$ISSM_DIR/externalpackages/python/install" +PYTHONSTARTUP="$ISSM_DIR/startup.py" #MODELE MODELE_DIR="$ISSM_DIR/externalpackages/modelE" + + +#GIT +GIT_DIR="$ISSM_DIR/externalpackages/git" Index: /issm/branches/trunk-jpl-damage/externalpackages/adolc/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/adolc/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/adolc/install.sh (revision 12258) @@ -5,4 +5,7 @@ #Some cleanup rm -rf install ADOL-C-2.2.0 src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' #Create install directories Index: /issm/branches/trunk-jpl-damage/externalpackages/autoconf/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/autoconf/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/autoconf/install.sh (revision 12258) @@ -4,9 +4,12 @@ rm -rf install autoconf-2.68 src +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.68.tar.gz' 'autoconf-2.68.tar.gz' + #Create install directories mkdir install #Untar -tar -zxvf autoconf-2.68.tar.gz +tar -zxvf autoconf-2.68.tar.gz #Move autoconf into src directory Index: /issm/branches/trunk-jpl-damage/externalpackages/automake/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/automake/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/automake/install.sh (revision 12258) @@ -3,4 +3,7 @@ #Some cleanup rm -rf install automake-1.11.3 src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.11.3.tar.gz' 'automake-1.11.3.tar.gz' #Create install directories Index: /issm/branches/trunk-jpl-damage/externalpackages/bbftp/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/bbftp/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/bbftp/install.sh (revision 12258) @@ -3,4 +3,7 @@ #Some cleanup rm -rf src install bbftp-client-3.2.0 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/bbftp-client-3.2.0.tar.gz' 'bbftp-client-3.2.0.tar.gz' #Create install directories Index: /issm/branches/trunk-jpl-damage/externalpackages/blas/configs/linux64/make.inc =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/blas/configs/linux64/make.inc (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/blas/configs/linux64/make.inc (revision 12258) @@ -0,0 +1,34 @@ +#################################################################### +# BLAS make include file. # +# March 2007 # +#################################################################### +# +SHELL = /bin/sh +# +# The machine (platform) identifier to append to the library names +# +PLAT = _LINUX +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O3 +DRVOPTS = $(OPTS) +NOOPT = +LOADER = gfortran +LOADOPTS = +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# The location and name of the Reference BLAS library. +# +BLASLIB = blas$(PLAT).a Index: /issm/branches/trunk-jpl-damage/externalpackages/blas/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/blas/install-linux64.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/blas/install-linux64.sh (revision 12258) @@ -0,0 +1,28 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install BLAS blas.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/blas.tgz' 'blas.tgz' + +#Untar +tar -zxvf blas.tgz + +#Move blas into install directory +mv BLAS/* src +rm -rf BLAS + +#install +cd src +cp ../configs/linux64/make.inc ./ +make + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/*.a . +ln -s blas_LINUX.a blas.a +ln -s blas_LINUX.a libblas.a Index: /issm/branches/trunk-jpl-damage/externalpackages/boost/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/boost/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/boost/install.sh (revision 12258) @@ -7,9 +7,10 @@ #to get the boost library to include python support without doing that. - - #Some cleanup rm -rf install boost_1_49_0 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/bsdtar/install-win7.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/bsdtar/install-win7.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/bsdtar/install-win7.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install src libarchive-3.0.3 mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libarchive-3.0.3.tar.gz' 'libarchive-3.0.3.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/cccl/install-win7.orig.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/cccl/install-win7.orig.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/cccl/install-win7.orig.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install cccl-0.03 mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cccl-0.03.tar.gz' 'cccl-0.03.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/cccl/issm/cccl =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/cccl/issm/cccl (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/cccl/issm/cccl (revision 12258) @@ -74,4 +74,17 @@ esac ;; + -fPIC) + #do nothing + ;; + -g) + #do nothing + ;; + -pthread) + #do nothing + ;; + -fno-omit-frame-pointer) + #do nothing + ;; + *) #do nothing @@ -83,4 +96,7 @@ shift done + +#Some default options: +opts="$opts /nologo" #echo "$prog $opts" Index: /issm/branches/trunk-jpl-damage/externalpackages/chaco/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/chaco/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/chaco/install.sh (revision 12258) @@ -6,4 +6,7 @@ rm -rf install mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz' # Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/cmake/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/cmake/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/cmake/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install cmake-2.8.5 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cmake-2.8.5.tar.gz' 'cmake-2.8.5.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/colpack/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/colpack/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/colpack/install.sh (revision 12258) @@ -3,4 +3,7 @@ #Erase install rm -rf install src ColPack + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ColPack-1.0.3.tar.gz' 'ColPack-1.0.3.tar.gz' #install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/cppcheck/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/cppcheck/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/cppcheck/install.sh (revision 12258) @@ -5,4 +5,6 @@ mkdir src +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cppcheck-1.48.tar' 'cppcheck-1.48.tar' tar -xvf cppcheck-1.48.tar Index: /issm/branches/trunk-jpl-damage/externalpackages/dace/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dace/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/dace/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install dace mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dace.zip' 'dace.zip' #uncompress Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-altix64-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-altix64-cosmos.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-altix64-cosmos.sh (revision 12258) @@ -9,4 +9,7 @@ rm -rf install mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-astrid.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-astrid.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-astrid.sh (revision 12258) @@ -9,4 +9,7 @@ rm -rf install mkdir src install + +#Download from ISSM server +$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 Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-murdo.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-linux64-murdo.sh (revision 12258) @@ -9,4 +9,7 @@ rm -rf install mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh (revision 12258) @@ -9,4 +9,7 @@ rm -rf install mkdir src install + +#Download from ISSM server +$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 Index: /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-pleiades.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/dakota/install-pleiades.sh (revision 12258) @@ -9,4 +9,7 @@ rm -rf install mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/distribute/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/distribute/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/distribute/install.sh (revision 12258) @@ -1,4 +1,5 @@ #!/bin/bash -curl -O http://python-distribute.org/distribute_setup.py +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://python-distribute.org/distribute_setup.py' 'distribute_setup.py' python distribute_setup.py Index: /issm/branches/trunk-jpl-damage/externalpackages/findbugs/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/findbugs/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/findbugs/install.sh (revision 12258) @@ -5,4 +5,6 @@ mkdir install +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/findbugs-1.3.9.tar.gz' 'findbugs-1.3.9.tar.gz' tar -zxvf findbugs-1.3.9.tar.gz Index: /issm/branches/trunk-jpl-damage/externalpackages/freetype/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/freetype/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/freetype/install.sh (revision 12258) @@ -6,4 +6,7 @@ rm -rf freetype-2.4.9 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/freetype-2.4.9.tar.gz' 'freetype-2.4.9.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/gdal/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gdal/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/gdal/install.sh (revision 12258) @@ -6,4 +6,7 @@ rm -rf gdal-1.6.0 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/gdaltokmz/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gdaltokmz/install.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/gdaltokmz/install.sh (revision 12258) @@ -0,0 +1,4 @@ +#!/bin/bash + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdaltokmz-1.0.tar.gz' 'gdaltokmz-1.0.tar.gz' Index: /issm/branches/trunk-jpl-damage/externalpackages/git/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/git/install.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/git/install.sh (revision 12258) @@ -0,0 +1,22 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install git-1.7.10.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/git-1.7.10.2.tar.gz' 'git-1.7.10.2.tar.gz' + +#Untar +tar -zxvf git-1.7.10.2.tar.gz + +#Move git into install directory +mv git-1.7.10.2/* src +rm -rf git-1.7.10.2 + +#install +cd src +./configure --prefix="$ISSM_DIR/externalpackages/git/install" + +#Compile +make install Index: /issm/branches/trunk-jpl-damage/externalpackages/gmake/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gmake/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/gmake/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install src make-3.82 mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/make-3.82.tar.gz' 'make-3.82.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/graphviz/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/graphviz/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/graphviz/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/graphviz-2.24.0.tar.gz' 'graphviz-2.24.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-android-4.0.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-android-4.0.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-android-4.0.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install gsl-1.15 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' #Untar Index: sm/branches/trunk-jpl-damage/externalpackages/gsl/install-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-linux64-murdo.sh (revision 12257) +++ (revision ) @@ -1,26 +1,0 @@ -#!/bin/bash - -#Some cleanup -rm -rf src install gsl-1.15 -mkdir src install - -#Untar -tar -zxvf gsl-1.15.tar.gz - -#Move gsl into src directory -mv gsl-1.15/* src -rm -rf gsl-1.15 - -#Configure gsl -cd src - -./configure \ - --prefix="$ISSM_DIR/externalpackages/gsl/install" - -#Compile gsl -if [ -z $1 ]; then - make -else - make -j $1 -fi -make install Index: /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-linux64.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-linux64.sh (revision 12258) @@ -0,0 +1,29 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-macosx64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-macosx64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install gsl-1.15 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-pleiades.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/gsl/install-pleiades.sh (revision 12258) @@ -0,0 +1,29 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-damage/externalpackages/ipython/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/ipython/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/ipython/install.sh (revision 12258) @@ -6,4 +6,7 @@ rm -rf ipython-0.12 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ipython-0.12.tar.gz' 'ipython-0.12.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/kml/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/kml/install.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/kml/install.sh (revision 12258) @@ -0,0 +1,4 @@ +#!/bin/bash + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/kml_shapefile.zip' 'kml_shapefile.zip' Index: /issm/branches/trunk-jpl-damage/externalpackages/lapack/configs/linux64/make.inc =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/lapack/configs/linux64/make.inc (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/lapack/configs/linux64/make.inc (revision 12258) @@ -0,0 +1,71 @@ +#################################################################### +# LAPACK make include file. # +# LAPACK, Version 3.4.0 # +# April 2012 # +#################################################################### +# +SHELL = /bin/sh +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O2 +DRVOPTS = $(OPTS) +NOOPT = -O0 +LOADER = gfortran +LOADOPTS = +# +# Timer for the SECOND and DSECND routines +# +# Default : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME +#TIMER = EXT_ETIME +# For RS6K : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME_ +# TIMER = EXT_ETIME_ +# For gfortran compiler: SECOND and DSECND will use a call to the INTERNAL FUNCTION ETIME +TIMER = INT_ETIME +# If your Fortran compiler does not provide etime (like Nag Fortran Compiler, etc...) +# SECOND and DSECND will use a call to the INTERNAL FUNCTION CPU_TIME +# TIMER = INT_CPU_TIME +# If neither of this works...you can use the NONE value... In that case, SECOND and DSECND will always return 0 +# TIMER = NONE +# +# Configuration LAPACKE: Native C interface to LAPACK +# To generate LAPACKE library: type 'make lapackelib' +# Configuration file: turned off (default) +# Complex types: C99 (default) +# Name pattern: mixed case (default) +# (64-bit) Data model: LP64 (default) +# +# CC is the C compiler, normally invoked with options CFLAGS. +# +CC = gcc +CFLAGS = -O3 +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# Location of the extended-precision BLAS (XBLAS) Fortran library +# used for building and testing extended-precision routines. The +# relevant routines will be compiled and XBLAS will be linked only if +# USEXBLAS is defined. +# +# USEXBLAS = Yes +XBLASLIB = +# XBLASLIB = -lxblas +# +# The location of the libraries to which you will link. (The +# machine-specific, optimized BLAS library should be used whenever +# possible.) +# +BLASLIB = ../../librefblas.a +LAPACKLIB = liblapack.a +TMGLIB = libtmglib.a +LAPACKELIB = liblapacke.a Index: /issm/branches/trunk-jpl-damage/externalpackages/lapack/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/lapack/install-linux64.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/lapack/install-linux64.sh (revision 12258) @@ -0,0 +1,32 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install lapack-3.4.1 lapack-3.4.1.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/lapack-3.4.1.tgz' 'lapack-3.4.1.tgz' + +#Untar +tar -zxvf lapack-3.4.1.tgz + +#Move lapack into install directory +mv lapack-3.4.1/* src +rm -rf lapack-3.4.1 + +#install +cd src +cp ../configs/linux64/make.inc ./ + +#Compile and install lapack +if [ -z $1 ]; then + make lib +else + make -j $1 lib +fi + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/liblapack.a . Index: /issm/branches/trunk-jpl-damage/externalpackages/latex2rtf/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/latex2rtf/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/latex2rtf/install.sh (revision 12258) @@ -3,4 +3,7 @@ #Some cleanup rm -rf latex2rtf-2.0.0 cfg install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/latex2rtf-2.0.0.tar.gz' 'latex2rtf-2.0.0.tar.gz' #untar Index: /issm/branches/trunk-jpl-damage/externalpackages/libermate/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/libermate/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/libermate/install.sh (revision 12258) @@ -6,4 +6,7 @@ mkdir install +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libermate-0.4.tgz' 'libermate-0.4.tgz' + #Untar tar -zxvf libermate-0.4.tgz Index: /issm/branches/trunk-jpl-damage/externalpackages/libpng/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/libpng/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/libpng/install.sh (revision 12258) @@ -6,4 +6,7 @@ rm -rf libpng-1.5.10 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libpng-1.5.10.tar.gz' 'libpng-1.5.10.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/libtool/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/libtool/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/libtool/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install libtool-2.2.6b src mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool-2.2.6b.tar.gz' 'libtool-2.2.6b.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/m2html/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/m2html/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/m2html/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install m2html mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/m2html.zip' 'm2html.zip' #uncompress Index: /issm/branches/trunk-jpl-damage/externalpackages/matplotlib/install-osx.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/matplotlib/install-osx.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/matplotlib/install-osx.sh (revision 12258) @@ -0,0 +1,10 @@ +#/bin/bash +pythonversion=2.7 +PYTHON=python${pythonversion} + +git clone https://github.com/matplotlib/matplotlib +mv matplotlib src +mkdir deps +cd src +make -f make.osx PREFIX=$ISSM_DIR/externalpackages/matplotlib/deps PYVERSION=$pythonversion fetch deps mpl_install_std +${PYTHON} -c "import matplotlib; print 'Installed matplotlib', matplotlib.__version__, matplotlib.__file__" Index: /issm/branches/trunk-jpl-damage/externalpackages/mercurial/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mercurial/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/mercurial/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install mercurial-1.7.3 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mercurial-1.7.3.tar.gz' 'mercurial-1.7.3.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-altix64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-altix64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-altix64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install metis-4.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-cosmos.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-cosmos.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install metis-4.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-greenplanet.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-greenplanet.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-greenplanet.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install metis-4.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-linux64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-linux64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install metis-4.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx32.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install metis-4.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install metis-4.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-pleiades.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-pleiades.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install metis-4.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-win32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-win32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-win32.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install metis-4.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-win7.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-win7.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-4.0-win7.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install metis-4.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/metis/install-5.0.1-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/metis/install-5.0.1-linux64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/metis/install-5.0.1-linux64.sh (revision 12258) @@ -5,4 +5,7 @@ rm -rf install metis-5.0.1 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-5.0.1.tar.gz' 'metis-5.0.1.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/modelE/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/modelE/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/modelE/install.sh (revision 12258) @@ -6,4 +6,7 @@ rm -rf src install modelE_AR5_branch mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/modelE_AR5_branch.2012.03.13_10.12.21.tgz' 'modelE_AR5_branch.2012.03.13_10.12.21.tgz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-altix64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install mpich2-1.0.2p1 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.0.2p1.tar.gz' 'mpich2-1.0.2p1.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install mpich2-1.0.2p1 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.0.2p1.tar.gz' 'mpich2-1.0.2p1.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install mpich2-1.0.2p1 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.0.2p1.tar.gz' 'mpich2-1.0.2p1.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-win32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-win32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-win32.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install mpich2-1.0.2p1 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.0.2p1.tar.gz' 'mpich2-1.0.2p1.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-linux64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-linux64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install mpich2-1.4 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.tar.gz' 'mpich2-1.4.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx32.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install mpich2-1.4 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.tar.gz' 'mpich2-1.4.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install mpich2-1.4 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.tar.gz' 'mpich2-1.4.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/ncview/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/ncview/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/ncview/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ncview-1.93g.tar.gz' 'ncview-1.93g.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/netcdf/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/netcdf/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/netcdf/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install netcdf-4.0.1 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/netcdf-4.0.1.tar.gz' 'netcdf-4.0.1.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/nose/install-macosx64sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/nose/install-macosx64sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/nose/install-macosx64sh (revision 12258) @@ -1,3 +1,3 @@ -#/bin/bash +#!/bin/bash #Install Python nose module @@ -18,4 +18,6 @@ if [[ $pythonversion == "2" ]];then + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/nose-1.1.2.tar.gz' 'nose-1.1.2.tar.gz' tar -zxvf nose-1.1.2.tar.gz mv nose-1.1.2 src Index: /issm/branches/trunk-jpl-damage/externalpackages/oofem/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/oofem/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/oofem/install.sh (revision 12258) @@ -5,4 +5,7 @@ rm -rf oofem-2.0 mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/oofem-2.0.tar.gz' 'oofem-2.0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/pcre/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/pcre/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/pcre/install.sh (revision 12258) @@ -5,4 +5,7 @@ rm -rf pcre-8.21 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/pcre-8.21.tar.gz' 'pcre-8.21.tar.gz' #Untar and move python into install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-altix64-castor.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 12258) @@ -8,4 +8,7 @@ rm -rf install petsc-2.3.2-p3 src mkdir install src + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-2.3.2-p3 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-linux64-astrid.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-2.3.2-p3 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-eric.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 12258) @@ -8,4 +8,7 @@ rm -rf install petsc-2.3.2-p3 src mkdir install src + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-2.3.2-p3 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-2.3.2-p3 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 12258) @@ -8,4 +8,7 @@ rm -rf install petsc-2.3.2-p3 src mkdir install src + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win32-eric.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-2.3.2-p3 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win7.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win7.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win7.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-2.3.2-p3 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-altix64-castor.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 12258) @@ -8,4 +8,7 @@ rm -rf install petsc-3.1-p7 src mkdir install src + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-cosmos.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-cosmos.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-3.1-p7 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-linux64-astrid.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-3.1-p7 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-mathieu.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-3.1-p7 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-ogive.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-3.1-p7 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-pleiades.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-pleiades.sh (revision 12258) @@ -8,4 +8,7 @@ rm -rf install petsc-3.1-p7 src mkdir install src + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-ubuntu64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-ubuntu64.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-ubuntu64.sh (revision 12258) @@ -0,0 +1,39 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --PETSC_ARCH=linux-gnu\ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-parmetis=yes \ + --FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \ + --download-plapack=yes \ + --COPTFLAGS="-O2" \ + --FOPTFLAGS="-O2" \ + --CXXOPTFLAGS="-O2" \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-win7.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-win7.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.1-win7.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-3.1-p7 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-greenplanet.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-greenplanet.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-greenplanet.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-3.2-p3 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-linux64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-linux64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-3.2-p3 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-macosx64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-macosx64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install petsc-3.2-p3 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' #Untar and move petsc to install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-pleiades.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/petsc/install-3.2-pleiades.sh (revision 12258) @@ -2,5 +2,5 @@ #Step 1: unzip and install #Step 2: After Plapack implodes -STEP=2 +STEP=1 if [ $STEP -eq 1 ]; then @@ -8,4 +8,7 @@ rm -rf install petsc-3.2-p3 src mkdir install src + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' #Untar and move petsc to install directory @@ -38,5 +41,5 @@ --CXXOPTFLAGS=" -O3 -xS" \ --with-pic=1 - echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc31/) ==" + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/documentation/faq/petsc32/) ==" echo "== Then run STEP=2 ==" fi @@ -66,4 +69,19 @@ --CXXOPTFLAGS=" -O3 -xS" \ --with-pic=1 + cat > src/script.queue << EOF +#PBS -S /bin/bash +#PBS -q debug +#PBS -l select=1:ncpus=1:model=har +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e +. /usr/share/modules/init/bash +module load comp-intel/11.1.046 +module load mpi/mpt.1.25 +module load math/intel_mkl_64_10.0.011 +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF echo "== Follow PETSc's instructions" fi Index: /issm/branches/trunk-jpl-damage/externalpackages/polygonclipper/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/polygonclipper/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/polygonclipper/install.sh (revision 12258) @@ -3,4 +3,7 @@ #Some cleanup rm -rf install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/PolygonClipper.zip' 'PolygonClipper.zip' #install Index: /issm/branches/trunk-jpl-damage/externalpackages/pyclips/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/pyclips/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/pyclips/install.sh (revision 12258) @@ -5,4 +5,7 @@ rm -rf pyclips-1.0.7.348 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/pyclips-1.0.7.348.tar.gz' 'pyclips-1.0.7.348.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/python/install-linux64-astrid.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/python/install-linux64-astrid.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/python/install-linux64-astrid.sh (revision 12258) @@ -0,0 +1,43 @@ +#!/bin/bash +#wget http://python.org/ftp/python/version/Python-version.tgz + +#version=3.2.2 +version=2.7.2 + +#Some cleanup +rm -rf install src +rm -rf Python-$version +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-$version.tgz Python-$version.tgz + +#exports +export CC + +#Untar and move python into install directory +tar -zxvf Python-$version.tgz +mv Python-$version/* src +rm -rf Python-$version + +#Configure doxygen +cd src +./configure --prefix="$ISSM_DIR/externalpackages/python/install" + +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + +#Some modifications to be done in case version is 3.2: +if [[ $version == "3.2.2" ]]; then + cd install/bin + ln -s python3.2 python + cd ../ + ln -s Python.framework/Versions/3.2/include/python3.2m include + ln -s Python.framework/Versions/3.2/lib/ lib + + +fi Index: /issm/branches/trunk-jpl-damage/externalpackages/python/install-macosx-lion.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/python/install-macosx-lion.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/python/install-macosx-lion.sh (revision 12258) @@ -0,0 +1,42 @@ +#!/bin/bash +#wget http://python.org/ftp/python/version/Python-version.tgz + +#version=3.2.2 +version=2.7.2 + +#Some cleanup +rm -rf install src +rm -rf Python-$version +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-$version.tgz Python-$version.tgz + +#exports +export CC + +#Untar and move python into install directory +tar -zxvf Python-$version.tgz +mv Python-$version/* src +rm -rf Python-$version + +#Configure doxygen +cd src +./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + +#Some modifications to be done in case version is 3.2: +if [[ $version == "3.2.2" ]]; then + cd install/bin + ln -s python3.2 python + cd ../ + ln -s Python.framework/Versions/3.2/include/python3.2m include + ln -s Python.framework/Versions/3.2/lib/ lib + + +fi Index: /issm/branches/trunk-jpl-damage/externalpackages/python/install-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/python/install-macosx-snowleopard.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/python/install-macosx-snowleopard.sh (revision 12258) @@ -0,0 +1,41 @@ +#!/bin/bash +#wget http://python.org/ftp/python/version/Python-version.tgz + +#version=3.2.2 +version=2.7.2 + +#Some cleanup +rm -rf install src +rm -rf Python-$version +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-$version.tgz Python-$version.tgz + +#exports +export CC +export MACOSX_DEPLOYMENT_TARGET=10.6 + +#Untar and move python into install directory +tar -zxvf Python-$version.tgz +mv Python-$version/* src +rm -rf Python-$version + +#Configure doxygen +cd src +./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" --enable-universalsdk --with-universal-archs="32-bit" +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + +#Some modifications to be done in case version is 3.2: +if [[ $version == "3.2.2" ]]; then + cd install/bin + ln -s python3.2 python + cd ../ + ln -s Python.framework/Versions/3.2/include/python3.2m include + ln -s Python.framework/Versions/3.2/lib/ lib +fi Index: sm/branches/trunk-jpl-damage/externalpackages/python/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/python/install.sh (revision 12257) +++ (revision ) @@ -1,39 +1,0 @@ -#!/bin/bash -#wget http://python.org/ftp/python/version/Python-version.tgz - -version=3.2.2 -#version=2.7.2 - -#Some cleanup -rm -rf install src -rm -rf Python-$version -mkdir install src - -#exports -export CC - -#Untar and move python into install directory -tar -zxvf Python-$version.tgz -mv Python-$version/* src -rm -rf Python-$version - -#Configure doxygen -cd src -./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" -if [ -z $1 ]; then - make -else - make -j $1 -fi -make install - -#Some modifications to be done in case version is 3.2: -if [[ $version == "3.2.2" ]]; then - cd install/bin - ln -s python3.2 python - cd ../ - ln -s Python.framework/Versions/3.2/include/python3.2m include - ln -s Python.framework/Versions/3.2/lib/ lib - - -fi Index: /issm/branches/trunk-jpl-damage/externalpackages/qhull/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/qhull/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/qhull/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf src install qhull-2003.1 mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/qhull-2003.1.tar.gz' 'qhull-2003.1.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/rats/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/rats/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/rats/install.sh (revision 12258) @@ -3,4 +3,7 @@ #Erase install rm -rf install src rats-2.3 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/rats-2.3.tar.gz' 'rats-2.3.tar.gz' #install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/readline/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/readline/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/readline/install.sh (revision 12258) @@ -5,4 +5,7 @@ rm -rf readline-6.2.2 mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/readline-6.2.2.tar.gz' 'readline-6.2.2.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/rose/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/rose/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/rose/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf source build install mkdir install source build + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/rose-0.9.5a-13219.tar.gz' 'rose-0.9.5a-13219.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/satstress/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/satstress/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/satstress/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install SatStress-0.1.2 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/SatStress-0.1.2.tar.gz' 'SatStress-0.1.2.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/scipy/README =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/scipy/README (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/scipy/README (revision 12258) @@ -1,2 +1,2 @@ You will find instructions on scipy at: -http://www.scipy.org/Installing_SciPy/Mac_OS_X#head-ba1926aec910a9a1deaf9eff99e38ee23103a3b3 +http://www.scipy.org/Installing_SciPy/Mac_OS_X Index: /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-linux64.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-linux64.sh (revision 12258) @@ -0,0 +1,49 @@ +#!/bin/bash + +#1: install numpy +#2 install scipy +#3 erase +install=2 + + +export CC="gcc -fPIC" +export CXX="g++ -fPIC" +export F77="gfortran -fPIC" +export FC="gfortran -fPIC" +export FFLAGS=-ff2c + + +if [[ $install == "1" ]];then + + #download numpy first + + export GIT_SSL_NO_VERIFY=true + git clone https://github.com/numpy/numpy.git + + #install numpy + cd numpy + python setup.py build + python setup.py install + + +elif [[ $install == "2" ]];then + + #download scipy + export GIT_SSL_NO_VERIFY=true + git clone https://github.com/scipy/scipy.git + + #install scipy + cd scipy + export BLAS_SRC=$ISSM_DIR/externalpackages/blas/install/lib + export BLAS=$ISSM_DIR/externalpackages/blas/install/lib + export LAPACK_SRC=$ISSM_DIR/externalpackages/lapack/install/lib + export LAPACK=$ISSM_DIR/externalpackages/lapack/install/lib + + python setup.py build + python setup.py install + +elif [[ $install == "3" ]];then + rm -rf numpy scipy +else + echo "Choice not covered" +fi Index: /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx-lion.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx-lion.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx-lion.sh (revision 12258) @@ -0,0 +1,39 @@ +#!/bin/bash + +#1: install numpy +#2 install scipy +#3 erase +install=2 + + +export CC=gcc +export CXX=g++ +export FFLAGS=-ff2c + + +if [[ $install == "1" ]];then + + #download numpy first + git clone https://github.com/numpy/numpy.git + + #install numpy + cd numpy + python setup.py build + python setup.py install + + +elif [[ $install == "2" ]];then + + #download scipy + git clone https://github.com/scipy/scipy.git + + #install scipy + cd scipy + python setup.py build + python setup.py install + +elif [[ $install == "3" ]];then + rm -rf numpy scipy +else + echo "Choice not covered" +fi Index: /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx-snowleopard.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx-snowleopard.sh (revision 12258) @@ -0,0 +1,41 @@ +#!/bin/bash +PYVERSION=2.7 +PYTHON=python${PYVERSION} + +#1: install numpy +#2 install scipy +#3 erase +install=2 + +export CC=/usr/bin/gcc-4.0 +export CXX=/usr/bin/g++-4.0 + +if [[ $install == "1" ]];then + + #download numpy first + git clone https://github.com/numpy/numpy.git + + #install numpy + cd numpy + python setup.py build + python setup.py install + cd .. + ${PYTHON} -c "import numpy; print 'Installed NumPy', numpy.__version__" + +elif [[ $install == "2" ]];then + + #download scipy + git clone https://github.com/scipy/scipy.git + + #install scipy + cd scipy + python setup.py build + python setup.py install + cd .. + ${PYTHON} -c "import scipy; print 'Installed SciPy', scipy.__version__" + +elif [[ $install == "3" ]];then + rm -rf numpy scipy +else + echo "Choice not covered" +fi Index: sm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/scipy/install-macosx64.sh (revision 12257) +++ (revision ) @@ -1,39 +1,0 @@ -#!/bin/bash - -#1: install numpy -#2 install scipy -#3 erase -install=2 - - -export CC=gcc -export CXX=g++ -export FFLAGS=-ff2c - - -if [[ $install == "1" ]];then - - #download numpy first - git clone https://github.com/numpy/numpy.git - - #install numpy - cd numpy - python setup.py build - python setup.py install - - -elif [[ $install == "2" ]];then - - #download scipy - git clone https://github.com/scipy/scipy.git - - #install scipy - cd scipy - python setup.py build - python setup.py install - -elif [[ $install == "3" ]];then - rm -rf numpy scipy -else - echo "Choice not covered" -fi Index: /issm/branches/trunk-jpl-damage/externalpackages/scotch/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/scotch/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/scotch/install.sh (revision 12258) @@ -8,4 +8,7 @@ # Create src and install directories mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/scotch_5.1.6.tar.gz' 'scotch_5.1.6.tar.gz' # Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/shapelib/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/shapelib/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/shapelib/install.sh (revision 12258) @@ -6,4 +6,8 @@ rm -rf install mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shapelib-1.2.10.tar.gz' 'shapelib-1.2.10.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shape_eg_data.zip' 'shape_eg_data.zip' # Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/slepc/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/slepc/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/slepc/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install slepc-2.3.2 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/slepc-2.3.2.tgz' 'slepc-2.3.2.tgz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/swig/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/swig/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/swig/install.sh (revision 12258) @@ -5,4 +5,7 @@ rm -rf swig-2.0.4 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/swig-2.0.4.tar.gz' 'swig-2.0.4.tar.gz' #Untar and move python into install directory Index: /issm/branches/trunk-jpl-damage/externalpackages/tao/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/tao/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/tao/install.sh (revision 12258) @@ -6,4 +6,7 @@ rm -rf install tao-2.0-p3 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tao-2.0-p3.tar.gz' 'tao-2.0-p3.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/tex2im/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/tex2im/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/tex2im/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tex2im-1.8.tar.gz' 'tex2im-1.8.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-altix64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-altix64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-altix64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install triangle mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-android-4.0.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-android-4.0.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-android-4.0.sh (revision 12258) @@ -4,8 +4,10 @@ matlab=0 - #Some cleanup rm -rf install triangle mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-linux64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-linux64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install triangle mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-macosx32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-macosx32.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install triangle mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-macosx64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-macosx64.sh (revision 12258) @@ -8,4 +8,7 @@ rm -rf install triangle mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-pleiades.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-pleiades.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install triangle mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-win32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-win32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-win32.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install triangle mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-win7.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-win7.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/triangle/install-win7.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install triangle mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-altix64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-altix64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-altix64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install valgrind-3.7.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-linux64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-linux64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install valgrind-3.7.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx32.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install valgrind-3.7.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-macosx64.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install valgrind-3.7.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-win32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-win32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/valgrind/install-win32.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install valgrind-3.7.0 mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/vim/addons/vim/syntax/c.vim =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/vim/addons/vim/syntax/c.vim (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/vim/addons/vim/syntax/c.vim (revision 12258) @@ -547,4 +547,10 @@ syn keyword cType QuadTree syn keyword cType SetOfE4 +syn keyword cType Variogram +syn keyword cType GaussianVariogram +syn keyword cType ExponentialVariogram +syn keyword cType SphericalVariogram +syn keyword cType Quadtree +syn keyword cType Observation "ISSM's objects end @@ -688,4 +694,8 @@ syn keyword cConstant SettingsResultsAsPatchesEnum syn keyword cConstant SettingsWaitonlockEnum +syn keyword cConstant DebugPetscProfilingEnum +syn keyword cConstant PetscProfilingCurrentMemEnum +syn keyword cConstant PetscProfilingCurrentFlopsEnum +syn keyword cConstant PetscProfilingSolutionTimeEnum syn keyword cConstant SteadystateMaxiterEnum syn keyword cConstant SteadystateNumRequestedOutputsEnum @@ -703,6 +713,7 @@ syn keyword cConstant ThermalIsenthalpyEnum syn keyword cConstant ThicknessEnum +syn keyword cConstant TimesteppingStartTimeEnum +syn keyword cConstant TimesteppingFinalTimeEnum syn keyword cConstant TimesteppingCflCoefficientEnum -syn keyword cConstant TimesteppingFinalTimeEnum syn keyword cConstant TimesteppingTimeAdaptEnum syn keyword cConstant TimesteppingTimeStepEnum @@ -766,4 +777,5 @@ syn keyword cConstant BoolInputEnum syn keyword cConstant BoolParamEnum +syn keyword cConstant ContourEnum syn keyword cConstant ControlInputEnum syn keyword cConstant DatasetInputEnum @@ -906,4 +918,5 @@ syn keyword cConstant P1Enum syn keyword cConstant P1DGEnum +syn keyword cConstant SaveResultsEnum syn keyword cConstant BoolElementResultEnum syn keyword cConstant BoolExternalResultEnum @@ -920,4 +933,5 @@ syn keyword cConstant PetscVecExternalResultEnum syn keyword cConstant StringExternalResultEnum +syn keyword cConstant StepEnum syn keyword cConstant TimeEnum syn keyword cConstant TriaP1ElementResultEnum Index: /issm/branches/trunk-jpl-damage/externalpackages/vim/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/vim/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/vim/install.sh (revision 12258) @@ -5,4 +5,7 @@ rm -rf vim72 mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/vim-7.2.tar.bz2' 'vim-7.2.tar.bz2' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/windows/InstallInstructions.txt =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/windows/InstallInstructions.txt (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/windows/InstallInstructions.txt (revision 12258) @@ -42,4 +42,5 @@ python: Python language interpreter unzip +cygrunsrv @@ -144,9 +145,15 @@ How to setup a Cron job? -Download exim and cron from cygwin setup. Run exim-config (don't forget to launch your cygwin terminal as -Administrator). If asked for a daemon name, type ntsec. Also, if cron complains about sendmail, -symlink /usr/lib/sendmail to /usr/sbin/sendmail. Then link /usr/sbin/sendmail -to /usr/bin/exim. Alternatively, if you have an smtp server, you can download and configure -ssmtp. Run ssmtp-config -as Administrator and link /usr/sbin/sendmail to /usr/bin/ssmtp. After the email has been configured, -run cron-config as Administrator. +First, make sure you downloaded cygrunsrv, otherwise the cron setup will only work on a per-session +basis! Also, make sure that you have an email correctly setup. In particular, cron relies on the +/usr/sbin/sendmail script. If it does not exist, cron will not send emails. Most email management +systems will create this script, but you need to check on it. +Run cron-config and fill up the questions. For daemon name, type ntsec. +Be careful, make sure that you are running your terminal as Administrator, +otherwise your settings will be only user-based. +How to setup email? + +Preferred way is through ssmtp. Download it on cygwin, and type ssmtp-config. If the ssmtp +daemon does not create /usr/sbin/sendmail, be sure to create a symlink from the email client +to the latter file. Be careful, make sure that you are running your terminal as Administrator, +otherwise your settings will be only user-based. Index: /issm/branches/trunk-jpl-damage/externalpackages/windows/configs/sdk7.1.win7-32.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/windows/configs/sdk7.1.win7-32.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/windows/configs/sdk7.1.win7-32.sh (revision 12258) @@ -1,37 +1,37 @@ declare -x ALLUSERSPROFILE="C:\\ProgramData" -declare -x CL="/AI C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319" -declare -x COMMONPROGRAMFILES="C:\\Program Files (x86)\\Common Files" +declare -x CL="/AI C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319" +declare -x COMMONPROGRAMFILES="C:\\Program Files\\Common Files" declare -x COMSPEC="C:\\Windows\\system32\\cmd.exe" -declare -x CommandPromptType="Cross" -declare -x CommonProgramW6432="C:\\Program Files\\Common Files" +declare -x CommandPromptType="Native" declare -x Configuration="Debug" declare -x FP_NO_HOST_CHECK="NO" declare -x FrameworkVersion="v4.0.30319" declare -x HOMEDRIVE="C:" -declare -x INCLUDE="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE\\gl;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\ATLMFC\\INCLUDE;" +declare -x INCLUDE="C:\\Program Files\\Microsoft Visual Studio 10.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE\\gl;" declare -x INFOPATH="/usr/local/info:/usr/share/info:/usr/info:" declare -x LANG="en_US.UTF-8" -declare -x LIB="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\ATLMFC\\LIB;" -declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib;" +declare -x LIB="C:\\Program Files\\Microsoft Visual Studio 10.0\\VC\\Lib;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;" +declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files\\Microsoft Visual Studio 10.0\\VC\\Lib;" declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:" -declare -x PATH="/usr/local/bin:/usr/bin:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2011b32/runtime/win32:/cygdrive/c/MATLAB/R2011b32/bin:/cygdrive/c/MATLAB/R2011b/runtime/win64:/cygdrive/c/MATLAB/R2011b/bin:/cygdrive/c/Program Files (x86)/Microsoft SQL Server/100/Tools/Binn:/cygdrive/c/Program Files/Microsoft SQL Server/100/Tools/Binn:/cygdrive/c/Program Files/Microsoft SQL Server/100/DTS/Binn:/cygdrive/c/Program Files/Microsoft Network Monitor 3" +declare -x PATH="/usr/local/bin:/usr/bin:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/VC/Bin:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/MATLAB/R2012a/runtime/win32:/cygdrive/c/MATLAB/R2012a/bin:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit" declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC" +declare -x PRINTER="137.78.140.129#:1" declare -x PROCESSOR_ARCHITECTURE="x86" -declare -x PROCESSOR_ARCHITEW6432="AMD64" -declare -x PROCESSOR_IDENTIFIER="Intel64 Family 6 Model 42 Stepping 7, GenuineIntel" +declare -x PROCESSOR_IDENTIFIER="x86 Family 6 Model 42 Stepping 7, GenuineIntel" declare -x PROCESSOR_LEVEL="6" declare -x PROCESSOR_REVISION="2a07" -declare -x PROGRAMFILES="C:\\Program Files (x86)" +declare -x PROGRAMFILES="C:\\Program Files" declare -x PSModulePath="C:\\Windows\\system32\\WindowsPowerShell\\v1.0\\Modules\\" declare -x PUBLIC="C:\\Users\\Public" declare -x PlatformToolset="Windows7.1SDK" declare -x ProgramData="C:\\ProgramData" -declare -x ProgramW6432="C:\\Program Files" declare -x SHELL="/bin/bash" declare -x SYSTEMDRIVE="C:" declare -x SYSTEMROOT="C:\\Windows" +declare -x TARGET_CPU="x86" declare -x TARGET_PLATFORM="WIN7" declare -x TERM="cygwin" -declare -x VS100COMNTOOLS="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\Common7\\Tools\\" +declare -x ToolsVersion="4.0" +declare -x VS100COMNTOOLS="C:\\Program Files\\Microsoft Visual Studio 10.0\\Common7\\Tools\\" declare -x WINDIR="C:\\Windows" declare -x WindowsSDKDir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\" Index: /issm/branches/trunk-jpl-damage/externalpackages/windows/configs/sdk7.1.win7-64.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/windows/configs/sdk7.1.win7-64.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/windows/configs/sdk7.1.win7-64.sh (revision 12258) @@ -13,5 +13,4 @@ declare -x LIB="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib\\X64;" declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework64\\v3.5;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;" -declare -x LOCALAPPDATA="C:\\Users\\schlegel\\AppData\\Local" declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:" declare -x PATH="/usr/local/bin:/usr/bin:/usr/include:/cygdrive/c/cygwin/usr/bin:/cygdrive/c/cygwin/usr/include:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2012a/runtime/win64:/cygdrive/c/MATLAB/R2012a/bin:/cygdrive/c/MATLAB/R2012a/extern/include:/cygdrive/c/MATLAB/R2011a/runtime/win64:/cygdrive/c/MATLAB/R2011a/bin:/cygdrive/c/MATLAB/R2011a/extern/include" @@ -41,6 +40,4 @@ declare -x TMP="/tmp" declare -x ToolsVersion="4.0" -declare -x USER="schlegel" -declare -x USERNAME="schlegel" declare -x VS100COMNTOOLS="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\Common7\\Tools\\" declare -x WINDIR="C:\\Windows" Index: /issm/branches/trunk-jpl-damage/externalpackages/windows/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/windows/install.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/externalpackages/windows/install.sh (revision 12258) @@ -0,0 +1,4 @@ +#!/bin/bash + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/win7.sdk7.1.exe' 'win7.sdk7.1.exe' Index: /issm/branches/trunk-jpl-damage/externalpackages/windows/windows_environment.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/windows/windows_environment.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/windows/windows_environment.sh (revision 12258) @@ -2,5 +2,5 @@ #Where are the configuration files for each compiler: -config_dir="$ISSM_TIER/externalpackages/windows/configs" +config_dir="$ISSM_DIR/externalpackages/windows/configs" #your choise of compiler: @@ -10,5 +10,15 @@ # 4: intel compiler on WinXP -compiler=2; +#Determine OS version using uname: +version=`uname -s | grep 64` +if [[ $version == "" ]];then + compiler=1 +else + compiler=2 +fi + +#If you want to override and use intel compilers: +#compiler=3; + #source corresponding environment variables: @@ -24,5 +34,5 @@ fi -#finally, out of ISSM_TIER, we need to create an ISSM_TIER_WIN variable for Matlab to pick up on. -ISSM_TIER_WIN=`cygpath -m $ISSM_TIER` -export ISSM_TIER_WIN +#finally, out of ISSM_DIR, we need to create an ISSM_DIR_WIN variable for Matlab to pick up on. +ISSM_DIR_WIN=`cygpath -m $ISSM_DIR` +export ISSM_DIR_WIN Index: /issm/branches/trunk-jpl-damage/externalpackages/xerces/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/xerces/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/xerces/install.sh (revision 12258) @@ -4,4 +4,7 @@ rm -rf install xerces-c-src_2_8_0 src mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/xerces-c-src_2_8_0.tar.gz' 'xerces-c-src_2_8_0.tar.gz' #Untar Index: /issm/branches/trunk-jpl-damage/externalpackages/yams/install.sh =================================================================== --- /issm/branches/trunk-jpl-damage/externalpackages/yams/install.sh (revision 12257) +++ /issm/branches/trunk-jpl-damage/externalpackages/yams/install.sh (revision 12258) @@ -4,4 +4,9 @@ rm -rf install mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/yams2-linux.gz' 'yams2-linux.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/yams2-osx.gz' 'yams2-osx.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/yams2-win.exe' 'yams2-win.exe' #loop over the binaries Index: /issm/branches/trunk-jpl-damage/m4/issm_options.m4 =================================================================== --- /issm/branches/trunk-jpl-damage/m4/issm_options.m4 (revision 12257) +++ /issm/branches/trunk-jpl-damage/m4/issm_options.m4 (revision 12258) @@ -66,8 +66,10 @@ export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ " elif test $VENDOR = arm-linux; then - export CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-cc - export CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-cc - - else + export CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc + export GCC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc + export CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-g++ + export AR=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ar + export RANLIB=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib + else AC_MSG_ERROR([unknow compiler vendor!]) fi @@ -949,11 +951,17 @@ dnl check that --with-fortran-lib may have been provided + HAVE_FORTRAN=no if test -n "$FORTRAN_LIB" ; then - HAVE_FORTRAN=yes - FORTRANLIB="$FORTRAN_LIB" - - AC_DEFINE([_HAVE_FORTRAN_],[1],[with FORTRAN in ISSM src]) - AC_SUBST([FORTRANLIB]) - fi + if test x$FORTRAN_LIB = xno; then + HAVE_FORTRAN=NO + else + HAVE_FORTRAN=yes + FORTRANLIB="$FORTRAN_LIB" + + AC_DEFINE([_HAVE_FORTRAN_],[1],[with FORTRAN in ISSM src]) + AC_SUBST([FORTRANLIB]) + fi + fi + AM_CONDITIONAL([FORTRAN], [test x$HAVE_FORTRAN = xyes]) AC_MSG_RESULT(done) dnl }}} Index: /issm/branches/trunk-jpl-damage/scripts/DownloadExternalPackage.py =================================================================== --- /issm/branches/trunk-jpl-damage/scripts/DownloadExternalPackage.py (revision 12258) +++ /issm/branches/trunk-jpl-damage/scripts/DownloadExternalPackage.py (revision 12258) @@ -0,0 +1,37 @@ +#!/usr/bin/env python +# -*- coding: ISO-8859-1 -*- + +import os,sys +import urllib + +#Check inputs +if(len(sys.argv)!=3): raise NameError('usage: ./DownloadExternalPackage.py URL localfile') + +url=sys.argv[1]; +localFile=sys.argv[2] + +#Remove file if it already exists +if os.path.exists(localFile): + print "File "+ localFile +" already exists and will not be downloaded..." + sys.exit() + +#Try to download from url +httpfail=-1 +try: + print "Fetching %s" % localFile + urllib.urlretrieve(url,localFile) + httpfail=0 +except Exception, e: + httpfail=1 + +#Error message in case it failed +if (httpfail): + failureMessage = ''' +=========================================================================== +Unable to download package %s from: %s +* If URL specified manually - perhaps there is a typo? +* If your network is disconnected - please reconnect +* Alternatively, you can download the above URL manually +=========================================================================== +''' % (localFile,url) + raise RuntimeError(failureMessage) Index: /issm/branches/trunk-jpl-damage/src/android/test102/test102.petsc =================================================================== --- /issm/branches/trunk-jpl-damage/src/android/test102/test102.petsc (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/android/test102/test102.petsc (revision 12258) @@ -0,0 +1,19 @@ +%Petsc options file: test102.petsc written from Matlab solver array + ++NoneAnalysis +-mat_type aij +-ksp_type gmres +-pc_type asm +-sub_pc_type ilu +-pc_asm_overlap 5 +-ksp_max_it 100 +-ksp_rtol 1e-15 + ++DiagnosticVertAnalysis +-mat_type aij +-ksp_type gmres +-pc_type asm +-sub_pc_type ilu +-pc_asm_overlap 5 +-ksp_max_it 100 +-ksp_rtol 1e-15 Index: /issm/branches/trunk-jpl-damage/src/android/test102/test102.sh =================================================================== --- /issm/branches/trunk-jpl-damage/src/android/test102/test102.sh (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/android/test102/test102.sh (revision 12258) @@ -0,0 +1,2 @@ +#!/bin/sh +/Users/larour/issm-uci/trunk-jpl/bin/issm.exe DiagnosticSolution /Users/larour/issm-uci/trunk-jpl/src/android/test102 test102 Index: /issm/branches/trunk-jpl-damage/src/c/Container/Observations.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Observations.cpp (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Observations.cpp (revision 12258) @@ -0,0 +1,192 @@ +/* + * \file Observations.c + * \brief: implementation of the Observations class, derived from DataSet class + */ + +/*Headers: {{{*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include + +#include "./DataSet.h" +#include "./Observations.h" +#include "../shared/shared.h" +#include "../include/include.h" +#include "../EnumDefinitions/EnumDefinitions.h" + +using namespace std; +/*}}}*/ + +/*Object constructors and destructor*/ +/*FUNCTION Observations::Observations(){{{*/ +Observations::Observations(){ + this->quadtree = NULL; + return; +} +/*}}}*/ +/*FUNCTION Observations::Observations(double* observations_list,double* x,double* y,int n,Options* options){{{*/ +Observations::Observations(double* observations_list,double* x,double* y,int n,Options* options){ + + /*Intermediaries*/ + int i,maxdepth,level,counter; + int xi,yi; + double xmin,xmax,ymin,ymax; + double offset,minlength; + Observation *observation = NULL; + + /*Get extrema*/ + xmin=x[0]; ymin=y[0]; + xmax=x[0]; ymax=y[0]; + for(i=1;iGetOption("boxlength")){ + options->Get(&minlength,"boxlength"); + if(minlength<=0)_error_("boxlength should be a positive number"); + maxdepth=int(log(max(xmax-xmin,ymax-ymin)/minlength +1)/log(2.0)); + } + else{ + maxdepth = 30; + minlength=max(xmax-xmin,ymax-ymin)/double((1L<quadtree = new Quadtree(xmin,xmax,ymin,ymax,maxdepth); + + /*Add observations one by one*/ + counter = 0; + for(i=0;iquadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); + this->quadtree->QuadtreeDepth2(&level,xi,yi); + if((int)level <= maxdepth){ + observation = new Observation(x[i],y[i],xi,yi,counter++,observations_list[i]); + this->quadtree->Add(observation); + this->AddObject(observation); + } + else{ + //We need to average with the current observations (not done yet) + } + } + printf("done\n"); +} +/*}}}*/ +/*FUNCTION Observations::~Observations(){{{*/ +Observations::~Observations(){ + delete quadtree; + return; +} +/*}}}*/ + +/*Methods*/ +/*FUNCTION Observations::ObservationList{{{*/ +void Observations::ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp,double range){ + + /*Output and Intermediaries*/ + int nobs,i,index; + double *x = NULL; + double *y = NULL; + double *obs = NULL; + Observation *observation = NULL; + int *indices = NULL; + + /*Treat range*/ + if(range==0){ + range=this->quadtree->root->length; + } + + /*Find all observations that are in range*/ + this->quadtree->RangeSearch(&indices,&nobs,x_interp,y_interp,range); + + if(nobs==0){ + /*No observation found, double range*/ + //printf("No observation found within range, doubling range\n"); + xfree((void**)&indices); + this->ObservationList(&x,&y,&obs,&nobs,x_interp,y_interp,range*2); + } + else{ + //if(nobs>1000) printf("Taking more than 1000 observations\n"); + /*Allocate vectors*/ + x = (double*)xmalloc(nobs*sizeof(double)); + y = (double*)xmalloc(nobs*sizeof(double)); + obs = (double*)xmalloc(nobs*sizeof(double)); + + /*Loop over all observations and fill in x, y and obs*/ + for (i=0;iGetObjectByOffset(indices[i]); + observation->WriteXYObs(&x[i],&y[i],&obs[i]); + } + } + + /*Assign output pointer*/ + xfree((void**)&indices); + *px=x; + *py=y; + *pobs=obs; + *pnobs=nobs; +}/*}}}*/ +/*FUNCTION Observations::QuadtreeColoring{{{*/ +void Observations::QuadtreeColoring(double* A,double *x,double *y,int n){ + + int xi,yi,level; + + for(int i=0;iquadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); + this->quadtree->QuadtreeDepth(&level,xi,yi); + A[i]=(double)level; + } + +}/*}}}*/ +/*FUNCTION Observations::Variomap{{{*/ +void Observations::Variomap(double* gamma,double *x,int n){ + + /*Output and Intermediaries*/ + int nobs,i,j,k; + double range; + Observation *observation1 = NULL; + Observation *observation2 = NULL; + int *indices = NULL; + + int *counter= (int*)xmalloc(n*sizeof(int)); + for(j=0;jSize();i++){ + observation1=(Observation*)this->GetObjectByOffset(i); + + for(j=0;j=0.); + + /*Find all observations that are in range*/ + this->quadtree->RangeSearch(&indices,&nobs,observation1->x,observation1->y,range); + + for (k=0;kGetObjectByOffset(indices[k]); + gamma[j] += 1./2.*pow(observation1->value - observation2->value,2.); + } + + counter[j] += nobs; + xfree((void**)&indices); + } + } + + /*Normalize semivariogram*/ + for(j=0;j /*forward declarations */ Index: /issm/branches/trunk-jpl-damage/src/c/Container/Vertices.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Vertices.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Vertices.h (revision 12258) @@ -32,6 +32,3 @@ }; - - #endif //ifndef _VERTICES_H_ - Index: /issm/branches/trunk-jpl-damage/src/c/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Makefile.am (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/Makefile.am (revision 12258) @@ -572,6 +572,6 @@ ./objects/Bamg/Metric.cpp\ ./objects/Bamg/Metric.h\ - ./objects/Bamg/QuadTree.cpp\ - ./objects/Bamg/QuadTree.h\ + ./objects/Bamg/BamgQuadtree.cpp\ + ./objects/Bamg/BamgQuadtree.h\ ./objects/Bamg/R2.h\ ./objects/Bamg/SetOfE4.cpp\ @@ -608,4 +608,24 @@ ./modules/BamgTriangulatex/BamgTriangulatex.cpp\ ./modules/BamgTriangulatex/BamgTriangulatex.h +#}}} +#Kriging sources {{{1 +kriging_sources = ./Container/Observations.h\ + ./Container/Observations.cpp\ + ./objects/Kriging/Variogram.h \ + ./objects/Kriging/GaussianVariogram.h\ + ./objects/Kriging/GaussianVariogram.cpp\ + ./objects/Kriging/ExponentialVariogram.h\ + ./objects/Kriging/ExponentialVariogram.cpp\ + ./objects/Kriging/SphericalVariogram.h\ + ./objects/Kriging/SphericalVariogram.cpp\ + ./objects/Kriging/PowerVariogram.h\ + ./objects/Kriging/PowerVariogram.cpp\ + ./objects/Kriging/Quadtree.h\ + ./objects/Kriging/Quadtree.cpp\ + ./objects/Kriging/Observation.h\ + ./objects/Kriging/Observation.cpp\ + ./modules/Krigingx/Krigingx.cpp\ + ./modules/Krigingx/Krigingx.h + #}}} #Kml sources {{{1 @@ -820,6 +840,4 @@ ./modules/HoleFillerx/HoleFillerx.cpp\ ./modules/HoleFillerx/HoleFillerx.h\ - ./modules/Krigingx/Krigingx.cpp\ - ./modules/Krigingx/Krigingx.h\ ./modules/AverageFilterx/AverageFilterx.cpp\ ./modules/AverageFilterx/AverageFilterx.h\ @@ -946,4 +964,5 @@ libISSMModules_a_SOURCES = $(module_sources) libISSMModules_a_SOURCES += $(bamg_sources) +libISSMModules_a_SOURCES += $(kriging_sources) libISSMModules_a_SOURCES += $(kml_sources) libISSMModules_a_CXXFLAGS = $(ALLCXXFLAGS) @@ -972,5 +991,9 @@ #External packages -LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) +LDADD += $(PETSCLIB) $(TAOLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) + +if FORTRAN +LDADD += $(FLIBS) +endif issm_SOURCES = solutions/issm.cpp Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/FetchMatlabData.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/FetchMatlabData.cpp (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/FetchMatlabData.cpp (revision 12258) @@ -404,16 +404,6 @@ else if (mxIsClass(dataref,"char") ){ - /*Check dataref is not pointing to NaN: */ - if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetNumberOfElements(dataref)==1) ){ - outmatrix_numel=0; - outmatrix_ndims=0; - outmatrix_size =NULL; - outmatrix=NULL; - } - else{ - - /*Convert matlab n-dim array to char* matrix: */ - MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref); - } + /*Convert matlab n-dim array to char* matrix: */ + MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref); } else{ Index: /issm/branches/trunk-jpl-damage/src/c/matlab/io/OptionParse.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/matlab/io/OptionParse.cpp (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/matlab/io/OptionParse.cpp (revision 12258) @@ -41,5 +41,5 @@ /*check and parse the name */ ological=new OptionLogical; - ological->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); + ological->name =(char*)xmalloc((strlen(name)+1)*sizeof(char)); memcpy(ological->name,name,(strlen(name)+1)*sizeof(char)); @@ -59,6 +59,6 @@ /*check and parse the name */ - ochar=new OptionChar; - ochar->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); + ochar=new OptionChar(); + ochar->name =(char*)xmalloc((strlen(name)+1)*sizeof(char)); memcpy(ochar->name,name,(strlen(name)+1)*sizeof(char)); Index: /issm/branches/trunk-jpl-damage/src/c/modules/Bamgx/Bamgx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Bamgx/Bamgx.cpp (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Bamgx/Bamgx.cpp (revision 12258) @@ -92,5 +92,5 @@ //Make Quadtree from background mesh - BTh.MakeQuadTree(); + BTh.MakeBamgQuadtree(); //Bound hmin and hmax Index: /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.cpp (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.cpp (revision 12258) @@ -8,15 +8,241 @@ #include "../../toolkits/toolkits.h" #include "../../objects/objects.h" +#include "../../Container/Observations.h" #include "../modules.h" -int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp){ +#ifdef _HAVE_GSL_ +#include +#endif + +#include "../../objects/Kriging/GaussianVariogram.h" +/*FUNCTION Krigingx{{{*/ +int Krigingx(double** ppredictions,double **perror,double* obs_x, double* obs_y, double* obs_list, int obs_length,double* x_interp,double* y_interp,int n_interp,Options* options){ /*output*/ double *predictions = NULL; + double *error = NULL; + + /*Intermediaries*/ + double range; + char *output = NULL; + Variogram *variogram = NULL; + Observations *observations = NULL; + + /*threading: */ + KrigingxThreadStruct gate; + int num=1; +#ifdef _MULTITHREADING_ + num=_NUMTHREADS_; +#endif + + /*Get Variogram from Options*/ + ProcessVariogram(&variogram,options); + options->Get(&range,"searchrange",0.); + + /*Process observation dataset*/ + observations=new Observations(obs_list,obs_x,obs_y,obs_length,options); /*Allocate output*/ - predictions=(double*)xmalloc(n_interp*sizeof(double)); + predictions =(double*)xcalloc(n_interp,sizeof(double)); + error =(double*)xcalloc(n_interp,sizeof(double)); + + /*Get output*/ + options->Get(&output,"output","prediction"); + + if(strcmp(output,"quadtree")==0){ + observations->QuadtreeColoring(predictions,x_interp,y_interp,n_interp); + } + else if(strcmp(output,"variomap")==0){ + observations->Variomap(predictions,x_interp,n_interp); + } + else if(strcmp(output,"prediction")==0){ + + /*initialize thread parameters: */ + gate.n_interp = n_interp; + gate.x_interp = x_interp; + gate.y_interp = y_interp; + gate.range = range; + gate.variogram = variogram; + gate.observations = observations; + gate.predictions = predictions; + gate.error = error; + gate.percent = (double*)xcalloc(num,sizeof(double)); + + /*launch the thread manager with Krigingxt as a core: */ + LaunchThread(Krigingxt,(void*)&gate,num); + printf("\r interpolation progress: 100.00%%\n"); + xfree((void**)&gate.percent); + } + else{ + _error_("output '%s' not supported yet",output); + } + + /*clean-up and Assign output pointer*/ + delete variogram; + delete observations; + xfree((void**)&output); + *ppredictions = predictions; + *perror = error; + return 1; +}/*}}}*/ +/*FUNCTION Krigingxt{{{*/ +void* Krigingxt(void* vpthread_handle){ + + /*gate variables :*/ + KrigingxThreadStruct *gate = NULL; + pthread_handle *handle = NULL; + int my_thread; + int num_threads; + int i0,i1; + + /*recover handle and gate: */ + handle = (pthread_handle*)vpthread_handle; + gate = (KrigingxThreadStruct*)handle->gate; + my_thread = handle->id; + num_threads = handle->num; + + /*recover parameters :*/ + int n_interp = gate->n_interp; + double *x_interp = gate->x_interp; + double *y_interp = gate->y_interp; + double range = gate->range; + Variogram *variogram = gate->variogram; + Observations *observations = gate->observations; + double *predictions = gate->predictions; + double *error = gate->error; + double *percent = gate->percent; + + /*Intermediaries*/ + int i,j,n_obs; + double numerator,denominator,ratio,localpercent; + double *x = NULL; + double *y = NULL; + double *obs = NULL; + double *Gamma = NULL; + double *GinvG0 = NULL; + double *Ginv1 = NULL; + double *GinvZ = NULL; + double *gamma0 = NULL; + double *ones = NULL; + + /*partition loop across threads: */ + PartitionRange(&i0,&i1,n_interp,num_threads,my_thread); + for(int idx=i0;idxObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx],range); + + /*Allocate intermediary matrix and vectors*/ + Gamma = (double*)xmalloc(n_obs*n_obs*sizeof(double)); + gamma0 = (double*)xmalloc(n_obs*sizeof(double)); + ones = (double*)xmalloc(n_obs*sizeof(double)); + + /*First: Create semivariogram matrix for observations*/ + for(i=0;iSemiVariogram(x[i]-x[j],y[i]-y[j]); + Gamma[j*n_obs+i] = Gamma[i*n_obs+j]; + } + } + for(i=0;iSemiVariogram(x[i]-x_interp[idx],y[i]-y_interp[idx]); + + /*Solve the three linear systems*/ + GslSolve(&GinvG0,Gamma,gamma0,n_obs); // Gamma^-1 gamma0 + GslSolve(&Ginv1, Gamma,ones,n_obs); // Gamma^-1 ones + GslSolve(&GinvZ, Gamma,obs,n_obs); // Gamma^-1 Z + + /*Prepare predictor*/ + numerator=-1.; denominator=0.; + for(i=0;iGetOption("model")){ + options->Get(&model,"model"); + if (strcmp(model,"gaussian")==0) variogram = new GaussianVariogram(options); + else if(strcmp(model,"exponential")==0) variogram = new ExponentialVariogram(options); + else if(strcmp(model,"spherical")==0) variogram = new SphericalVariogram(options); + else if(strcmp(model,"power")==0) variogram = new PowerVariogram(options); + else _error_("variogram %s not supported yet (list of supported variogram: gaussian, exponential, spherical and power)",model); + } + else variogram = new GaussianVariogram(options); /*Assign output pointer*/ - *ppredictions=predictions; -} + xfree((void**)&model); + *pvariogram = variogram; +}/*}}}*/ +void GslSolve(double** pX,double* A,double* B,int n){/*{{{*/ +#ifdef _HAVE_GSL_ + + /*GSL Matrices and vectors: */ + int s; + gsl_matrix_view a; + gsl_vector_view b; + gsl_vector *x = NULL; + gsl_permutation *p = NULL; + + /*A will be modified by LU decomposition. Use copy*/ + double* Acopy = (double*)xmalloc(n*n*sizeof(double)); + memcpy(Acopy,A,n*n*sizeof(double)); + + /*Initialize gsl matrices and vectors: */ + a = gsl_matrix_view_array (Acopy,n,n); + b = gsl_vector_view_array (B,n); + x = gsl_vector_alloc (n); + + /*Run LU and solve: */ + p = gsl_permutation_alloc (n); + gsl_linalg_LU_decomp (&a.matrix, p, &s); + gsl_linalg_LU_solve (&a.matrix, p, &b.vector, x); + + //printf ("x = \n"); + //gsl_vector_fprintf (stdout, x, "%g"); + + /*Copy result*/ + double* X = (double*)xmalloc(n*sizeof(double)); + memcpy(X,gsl_vector_ptr(x,0),n*sizeof(double)); + + /*Clean up and assign output pointer*/ + xfree((void**)&Acopy); + gsl_permutation_free(p); + gsl_vector_free(x); + *pX=X; +#else + _error_("GSL support required"); +#endif + }/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Krigingx/Krigingx.h (revision 12258) @@ -9,7 +9,24 @@ #include "../../toolkits/toolkits.h" +class Observations; +class Variogram; -int Krigingx(double** ppredictions,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp); +int Krigingx(double** ppredictions,double **perror,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options); +void ProcessVariogram(Variogram **pvariogram,Options* options); +void GslSolve(double** pX,double* A,double* B,int n); +/*threading: */ +typedef struct{ + int n_interp; + double *x_interp; + double *y_interp; + double range; + Variogram *variogram; + Observations *observations; + double *predictions; + double *error; + double *percent; +}KrigingxThreadStruct; + +void* Krigingxt(void*); #endif /* _KRIGINGX_H */ - Index: /issm/branches/trunk-jpl-damage/src/c/modules/Shp2Kmlx/Shp2Kmlx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Shp2Kmlx/Shp2Kmlx.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Shp2Kmlx/Shp2Kmlx.h (revision 12258) @@ -22,8 +22,6 @@ /* local prototypes: */ -int Shp2Kmlx(char* filshp,char* filkml, - int sgn); -int Shp2Kmlx(char* filshp,char* filkml, - int sgn,double cm,double sp); +int Shp2Kmlx(char* filshp,char* filkml, int sgn); +int Shp2Kmlx(char* filshp,char* filkml, int sgn,double cm,double sp); #endif /* _SHP2KMLX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgQuadtree.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgQuadtree.cpp (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgQuadtree.cpp (revision 12258) @@ -0,0 +1,598 @@ +#include +#include +#include + +#include "../objects.h" + +namespace bamg { + + /*MACROS {{{1*/ + /* + * + * 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) + /*}}}*/ + /*DOCUMENTATION What is a BamgQuadtree? {{{1 + * A Quadtree is a very simple way to group vertices according + * to their locations. A square that holds all the points of the mesh + * (or the geometry) is divided into 4 boxes. As soon as one box + * hold more than 4 vertices, it is divided into 4 new boxes, etc... + * There cannot be more than MAXDEEP (=30) subdivision. + * This process is like a Dichotomy in dimension 2 + * + * + - - - - - - - - + - - + - + - + - - - - + + * | | | | X | | + * + - + - + + * | | | | | | + * + - - + - + - + + + * | | | | | + * + * | | | | | + * + - - - - - - - - + - - + - - + - - - - + + * | | | | + * + * | | | | + * + * | | | | + * | | | | + * + - - - - - - - - + - - - - + - - - - + + * | | | + * + * | | | + * + * | | | + * + * | | | + * | | | + * | | | + * | | | + * | | | + * + - - - - - - - - + - - - - - - - - + + * + * The coordinate system used in a quadtree are integers to avoid + * round-off errors. The vertex in the lower left box has the coordinates + * (0 0) + * The upper right vertex has the follwing coordinates: + * 2^30 -1 2^30 -1 in decimal + * 0 1 1 1 .... 1 0 1 1 1 .... 1 in binary + * \-- 29 --/ \-- 29 --/ + * Using binaries is therefore very easy to locate a vertex in a box: + * we just need to look at the bits from the left to the right (See ::Add) + }}}1*/ + + /*Constructors/Destructors*/ + /*FUNCTION BamgQuadtree::BamgQuadtree(){{{1*/ + BamgQuadtree::BamgQuadtree(){ + + /*Number of boxes and vertices*/ + NbBamgQuadtreeBox=0; + NbVertices=0; + + /*Create container*/ + boxcontainer=new DataSet(); + + /*Create Root, pointer toward the main box*/ + root=NewBamgQuadtreeBox(); + + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::BamgQuadtree(Mesh * t,long nbv){{{1*/ + BamgQuadtree::BamgQuadtree(Mesh * t,long nbv){ + + /*Number of boxes and vertices*/ + NbBamgQuadtreeBox=0; + NbVertices=0; + + /*Create container*/ + boxcontainer=new DataSet(); + + /*Create Root, pointer toward the main box*/ + root=NewBamgQuadtreeBox(); + + /*Check Sizes*/ + _assert_(MaxISize>MaxICoor); + + /*Add all vertices of the mesh*/ + if (nbv==-1) nbv=t->nbv; + for (int i=0;ivertices[i]); + + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::~BamgQuadtree(){{{1*/ + BamgQuadtree::~BamgQuadtree() { + delete boxcontainer; + root=NULL; + } + /*}}}1*/ + + /*Methods*/ + /*FUNCTION BamgQuadtree::Add{{{1*/ + void BamgQuadtree::Add(BamgVertex &w){ + /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/Add)*/ + BamgQuadtreeBox** pb=NULL; + BamgQuadtreeBox* b=NULL; + + /*Get integer coodinate of current point w*/ + register long i=w.i.x, j=w.i.y; + + /*Initialize level*/ + register long level=MaxISize; + + /*Get inital box (the largest)*/ + pb = &root; + + /*Find the smallest box where w is located*/ + while((b=*pb) && (b->nbitems<0)){ + + //shift b->nbitems by -1 + b->nbitems--; + + //shifted righ by one bit: level=00000010 -> 00000001 + level >>= 1; + + //Get next subbox according to the bit value (level) + pb = &b->b[IJ(i,j,level)]; + } + + /*OK, we have found b, a Subbox holding vertices (might be full) + check that the vertex is not already in the box*/ + if (b){ + if (b->nbitems > 3 && b->v[3] == &w) return; + if (b->nbitems > 2 && b->v[2] == &w) return; + if (b->nbitems > 1 && b->v[1] == &w) return; + if (b->nbitems > 0 && b->v[0] == &w) return; + } + + /*check that l is not 0 (this should not happen as MaxDepth = 30)*/ + _assert_(level>0); + + /*Now, try to add the vertex, if the subbox is full (nbitems=4), we have to divide it + in 4 new subboxes*/ + while ((b= *pb) && (b->nbitems == 4)){ // the BamgQuadtreeBox is full + + /*Copy the 4 vertices in the current BamgQuadtreebox*/ + BamgVertex* v4[4]; + v4[0]= b->v[0]; + v4[1]= b->v[1]; + v4[2]= b->v[2]; + v4[3]= b->v[3]; + + /*set nbitems as negative + * (box full -> holds 4 pointers toward subboxes and not 4 vertices)*/ + b->nbitems = -b->nbitems; + + /*Initialize the 4 pointers toward the 4 subboxes*/ + b->b[0]=b->b[1]=b->b[2]=b->b[3]=NULL; + + /*level = 0010000 -> 0001000*/ + level >>= 1; + + /*Put the four vertices in the new boxes*/ + for (int k=0;k<4;k++){ + + 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)]; + + // alloc the BamgQuadtreeBox + if (!bb) bb=b->b[ij]=NewBamgQuadtreeBox(); + + /*Copy the current vertex*/ + bb->v[bb->nbitems++] = v4[k]; + } + + /*Get the subbox where w (i,j) is located*/ + pb = &b->b[IJ(i,j,level)]; + } + + /*alloc the BamgQuadtreeBox if necessary*/ + if (!(b=*pb)) b=*pb= NewBamgQuadtreeBox(); + + /*Add w*/ + b->v[b->nbitems++]=&w; + + //Increase NbVertices by one (we have one new vertex) + NbVertices++; + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::NearestVertex{{{1*/ + 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; + + /*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; + + /*else, find the smallest non-empty BamgQuadtreeBox containing the point (i,j)*/ + while((n0=b->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; + + /*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) + } + + /*The box b, is the smallest box containing the point (i,j) and + * has the following properties: + * - n0: number of items (>0 if vertices, else boxes) + * - hb: box size (int) + * - i0: x coordinate of the lower left corner + * - j0: y coordinate of the lower left corner*/ + + /* 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 + for(int k=0;kv[k]->i; + + /*Compute norm with w*/ + h0=NORM(iplus,i2.x,jplus,i2.y); + + /*is it smaller than previous value*/ + if (h0v[k]; + } + } + /*return closest vertex*/ + return nearest_v; + } + + /* general case: the current box is empty, we have to go backwards + and find the closest not-empty box and find the closest vertex*/ + + /*Initialize search variables*/ + pb[0]=b; //pointer toward the box b + pi[0]=b->nbitems>0?(int)b->nbitems:4;//number of boxes in b + ii[0]=i0; //i coordinate of the box lowest left corner + jj[0]=j0; //j coordinate of the box lowest left corner + + /*initialize h: smallest box size, containing a vertex close to w*/ + h=hb; + + /*Main loop*/ + level=0; + do { + + /*get current box*/ + b= pb[level]; + + /*Loop over the items in current box (if not empty!)*/ + while (pi[level]){ + + /*We are looping now over the items of b. k is the current index (in [0 3])*/ + pi[level]--; + int k=pi[level]; + + /*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); + if (h0v[k]; + } + } + /*else: current box b is pointing toward 4 boxes + * test sub-box k and go deeper into the tree if it is non empty + * and contains the point w modulo a size h that is either the size of the smallest + * non empty box containing w, or the closest point to w (so far) */ + else{ + BamgQuadtreeBox* b0=b; + + /*if the next box exists:*/ + if (b=b->b[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: + * 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)){ + level++; + pb[level]= b; + pi[level]= b->nbitems>0 ?(int) b->nbitems : 4 ; + ii[level]= iii; + jj[level]= jjj; + } + + //else go backwards + else{ + //shifted righ by one bit: hb=001000000 -> 01000000 + b=b0; + hb<<=1; + } + } + else{ + /*Current box is NULL, go to next subbox of b (k=k-1)*/ + b=b0; + } + } + } + + /*We have found a vertex, now, let's try the other boxes of the previous level + * in case there is a vertex closest to w that has not yet been tested*/ + hb <<= 1; + } while (level--); + + /*return nearest_v, nearest vertex*/ + return nearest_v; + + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::NearestVertexWithNormal{{{1*/ + BamgVertex* BamgQuadtree::NearestVertexWithNormal(Icoor1 i,Icoor1 j) { + /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/NearestVertexWithNormal)*/ + + BamgQuadtreeBox * pb[ MaxDepth ]; + int pi[ MaxDepth ]; + Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; + int l; // level + BamgQuadtreeBox * b; + long h =MaxISize,h0; + long hb=MaxISize; + Icoor1 i0=0,j0=0; + Icoor1 iplus( inbitems) + return vn; // empty tree + + while( (n0 = b->nbitems) < 0) + { + // search the non empty + // BamgQuadtreeBox containing the point (i,j) + register Icoor1 hb2 = hb >> 1 ; + register int k = IJ(iplus,jplus,hb2);// BamgQuadtreeBox number of size hb2 contening i;j + register BamgQuadtreeBox * b0= b->b[k]; + if ( ( b0 == 0) || (b0->nbitems == 0) ) + break; // null box or empty => break + b=b0; + i0 += I_IJ(k,hb2); // i orign of BamgQuadtreeBox + j0 += J_IJ(k,hb2); // j orign of BamgQuadtreeBox + hb = hb2; + } + + + if ( n0 > 0) + { + for(register int k=0;kv[k]->i; + // try if is in the right direction -- + h0 = NORM(iplus,i2.x,jplus,i2.y); + if (h0 v[k];} + } + if (vn) return vn; + } + // general case ----- + // INITIALISATION OF THE HEAP + l =0; // level + pb[0]= b; + pi[0]=b->nbitems>0 ?(int) b->nbitems : 4 ; + ii[0]=i0; + jj[0]=j0; + h=hb; + do { // walk on the tree + b= pb[l]; + while (pi[l]--) // loop on 4 element of the box + { + int k = pi[l]; + + if (b->nbitems>0) // BamgVertex BamgQuadtreeBox none empty + { + I2 i2 = b->v[k]->i; + // if good direction when try -- + + h0 = NORM(iplus,i2.x,jplus,i2.y); + if (h0 v[k]; + } + } + else // Pointer BamgQuadtreeBox + { + register BamgQuadtreeBox *b0=b; + if ((b=b->b[k])) + { + hb >>=1 ; // div by 2 + register Icoor1 iii = ii[l]+I_IJ(k,hb); + register Icoor1 jjj = jj[l]+J_IJ(k,hb); + + if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)) + { + pb[++l]= b; + pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; + ii[l]= iii; + jj[l]= jjj; + + } + else + b=b0, hb <<=1 ; + } + else + b=b0; + } + } + hb <<= 1; // mul by 2 + } while (l--); + + return vn; + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::NewBamgQuadtreeBox {{{1*/ + 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; + }/*}}}*/ + /*FUNCTION BamgQuadtree::ToClose {{{1*/ + 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]; + register int l=0; // level + register BamgQuadtreeBox * b; + Icoor1 h=MaxISize; + Icoor1 hb = MaxISize; + Icoor1 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 ; + ii[0]=i0; + jj[0]=j0; + h=hb; + do { + b= pb[l]; + while (pi[l]--){ + register 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); + double dd; + if( (dd= LengthInterpole(Mx(XY), b->v[k]->m(XY))) < seuil ){ + return b->v[k]; + } + } + } + else{ // Pointer BamgQuadtreeBox + register BamgQuadtreeBox *b0=b; + if ((b=b->b[k])){ + hb >>=1 ; // div by 2 + register long iii = ii[l]+I_IJ(k,hb); + register 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)){ + pb[++l]= b; + pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; + ii[l]= iii; + jj[l]= jjj; + + } + else{ + b=b0; + hb <<=1 ; + } + } + else{ + b=b0; + } + } + } + hb <<= 1; // mul by 2 + } while (l--); + + return 0; + } + /*}}}1*/ +} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgQuadtree.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgQuadtree.h (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/BamgQuadtree.h (revision 12258) @@ -0,0 +1,60 @@ +/*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.h)*/ +#ifndef _BAMGQUADTREE_H +#define _BAMGQUADTREE_H + +#include "./include.h" + +namespace bamg { + + const int MaxDepth = 30; + const long MaxISize = ( 1L << MaxDepth); // = 2^30 : 010000000000..000 (bitwise operation) + + class BamgVertex; + + class BamgQuadtree{ + + private: + + /*A quadtree box contains a maximum of 4 vertices. 4 other quadtree boxes are + * created if a fifth vertex is added to the same box. A Quadtree box is therefore + * composed of EITHER: + * - up to 4 vertices + * - 4 "sub" quadtree boxes*/ + class BamgQuadtreeBox: public Object{ + public: + int nbitems; // number of current vertices in the box + union{ + BamgQuadtreeBox* b[4]; + BamgVertex* v[4]; + }; + /*Object functions*/ + void Echo() {_error_("not implemented yet"); }; + void DeepEcho() {_error_("not implemented yet"); }; + int Id() {_error_("not implemented yet"); }; + int MyRank() {_error_("not implemented yet"); }; + int ObjectEnum() {_error_("not implemented yet"); }; + Object *copy() {_error_("not implemented yet"); }; + }; + + /*BamgQuadtree private Fields*/ + DataSet* boxcontainer; + + public: + + /*BamgQuadtree public Fields*/ + BamgQuadtreeBox* root; + long NbBamgQuadtreeBox; + long NbVertices; + + BamgQuadtree(); + BamgQuadtree(Mesh *t,long nbv=-1); + ~BamgQuadtree(); + + BamgVertex *NearestVertex(Icoor1 i,Icoor1 j); + BamgVertex *NearestVertexWithNormal(Icoor1 i,Icoor1 j); + BamgQuadtreeBox *NewBamgQuadtreeBox(void); + BamgVertex *ToClose(BamgVertex &,double ,Icoor1,Icoor1); + void Add(BamgVertex &w); + }; +} +#endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Geometry.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Geometry.cpp (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Geometry.cpp (revision 12258) @@ -505,5 +505,5 @@ float *eangle = new float[nbe]; double eps = 1e-20; - QuadTree quadtree; // build quadtree to find duplicates + BamgQuadtree quadtree; // build quadtree to find duplicates BamgVertex *v0 = vertices; GeomVertex *v0g = (GeomVertex*) (void*)v0; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Geometry.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Geometry.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Geometry.h (revision 12258) @@ -12,5 +12,5 @@ class Triangle; - class QuadTree; + class BamgQuadtree; class GeomSubDomain; class Edge; @@ -20,17 +20,17 @@ public: - long NbRef; // counter of ref on the this class if 0 we can delete - long nbv; // number of vertices - long nbe; // number of edges - long nbsubdomains; - long nbcurves; + long NbRef; // counter of ref on the this class if 0 we can delete + long nbv; // number of vertices + long nbe; // number of edges + long nbsubdomains; + long nbcurves; GeomVertex *vertices; GeomEdge *edges; - QuadTree *quadtree; + BamgQuadtree *quadtree; GeomSubDomain *subdomains; - Curve *curves; - R2 pmin,pmax; // domain extrema coordinates - double coefIcoor; // coef to integer Icoor1; - double MaxCornerAngle; + Curve *curves; + R2 pmin,pmax; // domain extrema coordinates + double coefIcoor; // coef to integer Icoor1; + double MaxCornerAngle; //Constructor/Destructors @@ -44,5 +44,5 @@ GeomVertex &operator[](long i) { return vertices[i]; }; const GeomEdge &operator()(long i) const { return edges[i]; }; - GeomEdge &operator()(long i) { return edges[i]; }; + GeomEdge &operator()(long i) { return edges[i]; }; //Methods Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Mesh.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Mesh.cpp (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Mesh.cpp (revision 12258) @@ -2885,5 +2885,5 @@ //build quadtree - if (!quadtree) quadtree = new QuadTree(this,0); + if (!quadtree) quadtree = new BamgQuadtree(this,0); quadtree->Add(*v0); quadtree->Add(*v1); @@ -3107,10 +3107,10 @@ } /*}}}1*/ - /*FUNCTION Mesh::MakeQuadTree{{{1*/ - void Mesh::MakeQuadTree() { - /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MakeQuadTree)*/ + /*FUNCTION Mesh::MakeBamgQuadtree{{{1*/ + void Mesh::MakeBamgQuadtree() { + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MakeBamgQuadtree)*/ long int verbose=0; - if ( !quadtree ) quadtree = new QuadTree(this); + if ( !quadtree ) quadtree = new BamgQuadtree(this); } @@ -3622,5 +3622,5 @@ if (!quadtree) delete quadtree; //ReInitialise; - quadtree = new QuadTree(this,0); + quadtree = new BamgQuadtree(this,0); quadtree->Add(*v0); quadtree->Add(*v1); @@ -3900,5 +3900,5 @@ if (quadtree){ delete quadtree; - quadtree = new QuadTree(this); + quadtree = new BamgQuadtree(this); } @@ -4116,5 +4116,5 @@ delete [] tstart; - if (quadtree) quadtree= new QuadTree(this); + if (quadtree) quadtree= new BamgQuadtree(this); } /*}}}1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Mesh.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Mesh.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/Mesh.h (revision 12258) @@ -17,5 +17,5 @@ class Geometry; class CrackedEdge; - class QuadTree; + class BamgQuadtree; class SubDomain; @@ -29,5 +29,5 @@ Triangle *triangles; Edge *edges; - QuadTree *quadtree; + BamgQuadtree *quadtree; BamgVertex **orderedvertices; SubDomain *subdomains; @@ -94,5 +94,5 @@ void MakeQuadrangles(double costheta); int SplitElement(int choice); - void MakeQuadTree(); + void MakeBamgQuadtree(); void NewPoints(Mesh &,BamgOpts* bamgopts,int KeepVertices=1); long InsertNewPoints(long nbvold,long & NbTSwap) ; Index: sm/branches/trunk-jpl-damage/src/c/objects/Bamg/QuadTree.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/QuadTree.cpp (revision 12257) +++ (revision ) @@ -1,598 +1,0 @@ -#include -#include -#include - -#include "../objects.h" - -namespace bamg { - - /*MACROS {{{1*/ - /* - * - * 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) - /*}}}*/ - /*DOCUMENTATION What is a QuadTree? {{{1 - * A Quadtree is a very simple way to group vertices according - * to their locations. A square that holds all the points of the mesh - * (or the geometry) is divided into 4 boxes. As soon as one box - * hold more than 4 vertices, it is divided into 4 new boxes, etc... - * There cannot be more than MAXDEEP (=30) subdivision. - * This process is like a Dichotomy in dimension 2 - * - * + - - - - - - - - + - - + - + - + - - - - + - * | | | | X | | - * + - + - + - * | | | | | | - * + - - + - + - + + - * | | | | | - * - * | | | | | - * + - - - - - - - - + - - + - - + - - - - + - * | | | | - * - * | | | | - * - * | | | | - * | | | | - * + - - - - - - - - + - - - - + - - - - + - * | | | - * - * | | | - * - * | | | - * - * | | | - * | | | - * | | | - * | | | - * | | | - * + - - - - - - - - + - - - - - - - - + - * - * The coordinate system used in a quadtree are integers to avoid - * round-off errors. The vertex in the lower left box has the coordinates - * (0 0) - * The upper right vertex has the follwing coordinates: - * 2^30 -1 2^30 -1 in decimal - * 0 1 1 1 .... 1 0 1 1 1 .... 1 in binary - * \-- 29 --/ \-- 29 --/ - * Using binaries is therefore very easy to locate a vertex in a box: - * we just need to look at the bits from the left to the right (See ::Add) - }}}1*/ - - /*Constructors/Destructors*/ - /*FUNCTION QuadTree::QuadTree(){{{1*/ - QuadTree::QuadTree(){ - - /*Number of boxes and vertices*/ - NbQuadTreeBox=0; - NbVertices=0; - - /*Create container*/ - boxcontainer=new DataSet(); - - /*Create Root, pointer toward the main box*/ - root=NewQuadTreeBox(); - - } - /*}}}1*/ - /*FUNCTION QuadTree::QuadTree(Mesh * t,long nbv){{{1*/ - QuadTree::QuadTree(Mesh * t,long nbv){ - - /*Number of boxes and vertices*/ - NbQuadTreeBox=0; - NbVertices=0; - - /*Create container*/ - boxcontainer=new DataSet(); - - /*Create Root, pointer toward the main box*/ - root=NewQuadTreeBox(); - - /*Check Sizes*/ - _assert_(MaxISize>MaxICoor); - - /*Add all vertices of the mesh*/ - if (nbv==-1) nbv=t->nbv; - for (int i=0;ivertices[i]); - - } - /*}}}1*/ - /*FUNCTION QuadTree::~QuadTree(){{{1*/ - QuadTree::~QuadTree() { - delete boxcontainer; - root=NULL; - } - /*}}}1*/ - - /*Methods*/ - /*FUNCTION QuadTree::Add{{{1*/ - void QuadTree::Add(BamgVertex &w){ - /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/Add)*/ - QuadTreeBox** pb=NULL; - QuadTreeBox* b=NULL; - - /*Get integer coodinate of current point w*/ - register long i=w.i.x, j=w.i.y; - - /*Initialize level*/ - register long level=MaxISize; - - /*Get inital box (the largest)*/ - pb = &root; - - /*Find the smallest box where w is located*/ - while((b=*pb) && (b->nbitems<0)){ - - //shift b->nbitems by -1 - b->nbitems--; - - //shifted righ by one bit: level=00000010 -> 00000001 - level >>= 1; - - //Get next subbox according to the bit value (level) - pb = &b->b[IJ(i,j,level)]; - } - - /*OK, we have found b, a Subbox holding vertices (might be full) - check that the vertex is not already in the box*/ - if (b){ - if (b->nbitems > 3 && b->v[3] == &w) return; - if (b->nbitems > 2 && b->v[2] == &w) return; - if (b->nbitems > 1 && b->v[1] == &w) return; - if (b->nbitems > 0 && b->v[0] == &w) return; - } - - /*check that l is not 0 (this should not happen as MaxDeep = 30)*/ - _assert_(level>0); - - /*Now, try to add the vertex, if the subbox is full (nbitems=4), we have to divide it - in 4 new subboxes*/ - while ((b= *pb) && (b->nbitems == 4)){ // the QuadTreeBox is full - - /*Copy the 4 vertices in the current QuadTreebox*/ - BamgVertex* v4[4]; - v4[0]= b->v[0]; - v4[1]= b->v[1]; - v4[2]= b->v[2]; - v4[3]= b->v[3]; - - /*set nbitems as negative - * (box full -> holds 4 pointers toward subboxes and not 4 vertices)*/ - b->nbitems = -b->nbitems; - - /*Initialize the 4 pointers toward the 4 subboxes*/ - b->b[0]=b->b[1]=b->b[2]=b->b[3]=NULL; - - /*level = 0010000 -> 0001000*/ - level >>= 1; - - /*Put the four vertices in the new boxes*/ - for (int k=0;k<4;k++){ - - int ij; - /*bb is the new "sub"box of b where v4[k] is located*/ - QuadTreeBox *bb = b->b[ij=IJ(v4[k]->i.x,v4[k]->i.y,level)]; - - // alloc the QuadTreeBox - if (!bb) bb=b->b[ij]=NewQuadTreeBox(); - - /*Copy the current vertex*/ - bb->v[bb->nbitems++] = v4[k]; - } - - /*Get the subbox where w (i,j) is located*/ - pb = &b->b[IJ(i,j,level)]; - } - - /*alloc the QuadTreeBox if necessary*/ - if (!(b=*pb)) b=*pb= NewQuadTreeBox(); - - /*Add w*/ - b->v[b->nbitems++]=&w; - - //Increase NbVertices by one (we have one new vertex) - NbVertices++; - } - /*}}}1*/ - /*FUNCTION QuadTree::NearestVertex{{{1*/ - BamgVertex* QuadTree::NearestVertex(Icoor1 i,Icoor1 j) { - /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/NearestVertex)*/ - - /*Intermediaries*/ - QuadTreeBox *pb[MaxDeep]; - int pi[MaxDeep]; - Icoor1 ii[MaxDeep]; - Icoor1 jj[MaxDeep]; - int level; - long n0; - QuadTreeBox *b; - long h0; - long h = MaxISize; - long hb= MaxISize; - Icoor1 i0=0,j0=0; - - /*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; - - /*else, find the smallest non-empty QuadTreeBox containing the point (i,j)*/ - while((n0=b->nbitems)<0){ - - Icoor1 hb2 = hb >> 1; //size of the current box - int k = IJ(iplus,jplus,hb2); //box number (0,1,2 or 3) - QuadTreeBox *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; - - /*Get next Quadtree box*/ - b=b0; - i0 += I_IJ(k,hb2); // i orign of QuadTreeBox (macro) - j0 += J_IJ(k,hb2); // j orign of QuadTreeBox - hb = hb2; // size of the box (in Int) - } - - /*The box b, is the smallest box containing the point (i,j) and - * has the following properties: - * - n0: number of items (>0 if vertices, else boxes) - * - hb: box size (int) - * - i0: x coordinate of the lower left corner - * - j0: y coordinate of the lower left corner*/ - - /* 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 - for(int k=0;kv[k]->i; - - /*Compute norm with w*/ - h0=NORM(iplus,i2.x,jplus,i2.y); - - /*is it smaller than previous value*/ - if (h0v[k]; - } - } - /*return closest vertex*/ - return nearest_v; - } - - /* general case: the current box is empty, we have to go backwards - and find the closest not-empty box and find the closest vertex*/ - - /*Initialize search variables*/ - pb[0]=b; //pointer toward the box b - pi[0]=b->nbitems>0?(int)b->nbitems:4;//number of boxes in b - ii[0]=i0; //i coordinate of the box lowest left corner - jj[0]=j0; //j coordinate of the box lowest left corner - - /*initialize h: smallest box size, containing a vertex close to w*/ - h=hb; - - /*Main loop*/ - level=0; - do { - - /*get current box*/ - b= pb[level]; - - /*Loop over the items in current box (if not empty!)*/ - while (pi[level]){ - - /*We are looping now over the items of b. k is the current index (in [0 3])*/ - pi[level]--; - int k=pi[level]; - - /*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); - if (h0v[k]; - } - } - /*else: current box b is pointing toward 4 boxes - * test sub-box k and go deeper into the tree if it is non empty - * and contains the point w modulo a size h that is either the size of the smallest - * non empty box containing w, or the closest point to w (so far) */ - else{ - QuadTreeBox* b0=b; - - /*if the next box exists:*/ - if (b=b->b[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: - * 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)){ - level++; - pb[level]= b; - pi[level]= b->nbitems>0 ?(int) b->nbitems : 4 ; - ii[level]= iii; - jj[level]= jjj; - } - - //else go backwards - else{ - //shifted righ by one bit: hb=001000000 -> 01000000 - b=b0; - hb<<=1; - } - } - else{ - /*Current box is NULL, go to next subbox of b (k=k-1)*/ - b=b0; - } - } - } - - /*We have found a vertex, now, let's try the other boxes of the previous level - * in case there is a vertex closest to w that has not yet been tested*/ - hb <<= 1; - } while (level--); - - /*return nearest_v, nearest vertex*/ - return nearest_v; - - } - /*}}}1*/ - /*FUNCTION QuadTree::NearestVertexWithNormal{{{1*/ - BamgVertex* QuadTree::NearestVertexWithNormal(Icoor1 i,Icoor1 j) { - /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/NearestVertexWithNormal)*/ - - QuadTreeBox * pb[ MaxDeep ]; - int pi[ MaxDeep ]; - Icoor1 ii[ MaxDeep ], jj [ MaxDeep]; - int l; // level - QuadTreeBox * b; - long h =MaxISize,h0; - long hb=MaxISize; - Icoor1 i0=0,j0=0; - Icoor1 iplus( inbitems) - return vn; // empty tree - - while( (n0 = b->nbitems) < 0) - { - // search the non empty - // QuadTreeBox containing the point (i,j) - register Icoor1 hb2 = hb >> 1 ; - register int k = IJ(iplus,jplus,hb2);// QuadTreeBox number of size hb2 contening i;j - register QuadTreeBox * b0= b->b[k]; - if ( ( b0 == 0) || (b0->nbitems == 0) ) - break; // null box or empty => break - b=b0; - i0 += I_IJ(k,hb2); // i orign of QuadTreeBox - j0 += J_IJ(k,hb2); // j orign of QuadTreeBox - hb = hb2; - } - - - if ( n0 > 0) - { - for(register int k=0;kv[k]->i; - // try if is in the right direction -- - h0 = NORM(iplus,i2.x,jplus,i2.y); - if (h0 v[k];} - } - if (vn) return vn; - } - // general case ----- - // INITIALISATION OF THE HEAP - l =0; // level - pb[0]= b; - pi[0]=b->nbitems>0 ?(int) b->nbitems : 4 ; - ii[0]=i0; - jj[0]=j0; - h=hb; - do { // walk on the tree - b= pb[l]; - while (pi[l]--) // loop on 4 element of the box - { - int k = pi[l]; - - if (b->nbitems>0) // BamgVertex QuadTreeBox none empty - { - I2 i2 = b->v[k]->i; - // if good direction when try -- - - h0 = NORM(iplus,i2.x,jplus,i2.y); - if (h0 v[k]; - } - } - else // Pointer QuadTreeBox - { - register QuadTreeBox *b0=b; - if ((b=b->b[k])) - { - hb >>=1 ; // div by 2 - register Icoor1 iii = ii[l]+I_IJ(k,hb); - register Icoor1 jjj = jj[l]+J_IJ(k,hb); - - if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)) - { - pb[++l]= b; - pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; - ii[l]= iii; - jj[l]= jjj; - - } - else - b=b0, hb <<=1 ; - } - else - b=b0; - } - } - hb <<= 1; // mul by 2 - } while (l--); - - return vn; - } - /*}}}1*/ - /*FUNCTION QuadTree::NewQuadTreeBox {{{1*/ - QuadTree::QuadTreeBox* QuadTree::NewQuadTreeBox(void){ - - /*Output*/ - QuadTreeBox* newbox=NULL; - - /*Create and initialize a new box*/ - newbox=new QuadTreeBox; - 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*/ - NbQuadTreeBox++; - - /*currentbox now points toward next quadtree box*/ - return newbox; - }/*}}}*/ - /*FUNCTION QuadTree::ToClose {{{1*/ - BamgVertex* QuadTree::ToClose(BamgVertex & v,double seuil,Icoor1 hx,Icoor1 hy){ - /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/ToClose)*/ - - const Icoor1 i=v.i.x; - const Icoor1 j=v.i.y; - const R2 X(v.r); - const Metric Mx(v.m); - - QuadTreeBox * pb[ MaxDeep ]; - int pi[ MaxDeep ]; - Icoor1 ii[ MaxDeep ], jj [ MaxDeep]; - register int l=0; // level - register QuadTreeBox * b; - Icoor1 h=MaxISize; - Icoor1 hb = MaxISize; - Icoor1 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 ; - ii[0]=i0; - jj[0]=j0; - h=hb; - do { - b= pb[l]; - while (pi[l]--){ - register int k = pi[l]; - - if (b->nbitems>0){ // BamgVertex QuadTreeBox none empty - I2 i2 = b->v[k]->i; - if ( ABS(i-i2.x) v[k]->r); - double dd; - if( (dd= LengthInterpole(Mx(XY), b->v[k]->m(XY))) < seuil ){ - return b->v[k]; - } - } - } - else{ // Pointer QuadTreeBox - register QuadTreeBox *b0=b; - if ((b=b->b[k])){ - hb >>=1 ; // div by 2 - register long iii = ii[l]+I_IJ(k,hb); - register 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)){ - pb[++l]= b; - pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; - ii[l]= iii; - jj[l]= jjj; - - } - else{ - b=b0; - hb <<=1 ; - } - } - else{ - b=b0; - } - } - } - hb <<= 1; // mul by 2 - } while (l--); - - return 0; - } - /*}}}1*/ -} Index: sm/branches/trunk-jpl-damage/src/c/objects/Bamg/QuadTree.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Bamg/QuadTree.h (revision 12257) +++ (revision ) @@ -1,61 +1,0 @@ -/*Original code from Frederic Hecht (BAMG v1.01, QuadTree.h)*/ -#ifndef _QUADTREE_H -#define _QUADTREE_H - -#include "./include.h" - -namespace bamg { - - const int MaxDeep = 30; - const long MaxISize = ( 1L << MaxDeep); // = 2^30 : 010000000000..000 (bitwise operation) - - class BamgVertex; - - class QuadTree{ - - private: - - /*A quadtree box contains a maximum of 4 vertices. 4 other quadtree boxes are - * created if a fifth vertex is added to the same box. A Quadtree box is therefore - * composed of EITHER: - * - up to 4 vertices - * - 4 "sub" quadtree boxes*/ - class QuadTreeBox: public Object{ - public: - int nbitems; // number of current vertices in the box - union{ - QuadTreeBox* b[4]; - BamgVertex* v[4]; - }; - /*Object functions*/ - void Echo(){_error_("not implemented yet");}; - void DeepEcho(){_error_("not implemented yet");}; - int Id(){_error_("not implemented yet");}; - int MyRank(){_error_("not implemented yet");}; - int ObjectEnum(){_error_("not implemented yet");}; - Object* copy(){_error_("not implemented yet");}; - }; - - /*QuadTree private Fields*/ - DataSet* boxcontainer; - - public: - - /*QuadTree public Fields*/ - QuadTreeBox* root; - long NbQuadTreeBox; - long NbVertices; - - QuadTree(); - QuadTree(Mesh *t,long nbv=-1); - ~QuadTree(); - - BamgVertex* NearestVertex(Icoor1 i,Icoor1 j); - BamgVertex* NearestVertexWithNormal(Icoor1 i,Icoor1 j); - QuadTreeBox* NewQuadTreeBox(void); - BamgVertex* ToClose(BamgVertex & ,double ,Icoor1,Icoor1); - void Add( BamgVertex & w); - - }; -} -#endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/Constraint.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/Constraint.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Constraints/Constraint.h (revision 12258) @@ -11,8 +11,6 @@ /*Headers:*/ /*{{{1*/ +class Nodes; #include "../Object.h" - -class Nodes; - #include "../../toolkits/toolkits.h" /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/ExponentialVariogram.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/ExponentialVariogram.cpp (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/ExponentialVariogram.cpp (revision 12258) @@ -0,0 +1,74 @@ +/*!\file ExponentialVariogram.c + * \brief: implementation of the ExponentialVariogram object + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../include/include.h" + +/*ExponentialVariogram constructors and destructor*/ +/*FUNCTION ExponentialVariogram::ExponentialVariogram(){{{1*/ +ExponentialVariogram::ExponentialVariogram(){ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + return; +} +/*}}}*/ +/*FUNCTION ExponentialVariogram::ExponentialVariogram(Options* options){{{1*/ +ExponentialVariogram::ExponentialVariogram(Options* options){ + + /*Defaults*/ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + + /*Overwrite from options*/ + if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); + if(options->GetOption("sill")) options->Get(&this->sill,"sill"); + if(options->GetOption("range")) options->Get(&this->range,"range"); + + /*Checks*/ + if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)"); +} +/*}}}*/ +/*FUNCTION ExponentialVariogram::~ExponentialVariogram(){{{1*/ +ExponentialVariogram::~ExponentialVariogram(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION ExponentialVariogram::Echo {{{1*/ +void ExponentialVariogram::Echo(void){ + printf("ExponentialVariogram\n"); + printf(" nugget: %g\n",this->nugget); + printf(" sill : %g\n",this->sill); + printf(" range : %g\n",this->range); +} +/*}}}*/ + +/*Variogram function*/ +/*FUNCTION ExponentialVariogram::SemiVariogram{{{1*/ +double ExponentialVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ + double h,a,gamma; + + /*Calculate length*/ + h=sqrt(pow(deltax,2.)+pow(deltay,2.)); + + /*return semi-variogram*/ + a = 1./3.; + gamma = (sill-nugget)*(1-exp(-h/(a*range))) + nugget; + return gamma; +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/ExponentialVariogram.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/ExponentialVariogram.h (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/ExponentialVariogram.h (revision 12258) @@ -0,0 +1,34 @@ +/*! \file ExponentialVariogram.h + * \brief: header file for triavertexinput object + */ + +#ifndef _EXPONENTIALVARIOGRAM_H_ +#define _EXPONENTIALVARIOGRAM_H_ + +/*Headers:*/ +#include "./Variogram.h" + +class ExponentialVariogram: public Variogram{ + + public: + double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin + double sill; //Limit of the variogram tending to infinity lag distances + double range; //The distance in which the difference of the variogram from the sill becomes negligible + + /*ExponentialVariogram constructors, destructors*/ + ExponentialVariogram(); + ExponentialVariogram(Options* options); + ~ExponentialVariogram(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); +}; +#endif /* _EXPONENTIALVARIOGRAM_H */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/GaussianVariogram.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12258) @@ -0,0 +1,74 @@ +/*!\file GaussianVariogram.c + * \brief: implementation of the GaussianVariogram object + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../include/include.h" + +/*GaussianVariogram constructors and destructor*/ +/*FUNCTION GaussianVariogram::GaussianVariogram(){{{1*/ +GaussianVariogram::GaussianVariogram(){ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + return; +} +/*}}}*/ +/*FUNCTION GaussianVariogram::GaussianVariogram(Options* options){{{1*/ +GaussianVariogram::GaussianVariogram(Options* options){ + + /*Defaults*/ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + + /*Overwrite from options*/ + if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); + if(options->GetOption("sill")) options->Get(&this->sill,"sill"); + if(options->GetOption("range")) options->Get(&this->range,"range"); + + /*Checks*/ + if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)"); +} +/*}}}*/ +/*FUNCTION GaussianVariogram::~GaussianVariogram(){{{1*/ +GaussianVariogram::~GaussianVariogram(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION GaussianVariogram::Echo {{{1*/ +void GaussianVariogram::Echo(void){ + printf("GaussianVariogram\n"); + printf(" nugget: %g\n",this->nugget); + printf(" sill : %g\n",this->sill); + printf(" range : %g\n",this->range); +} +/*}}}*/ + +/*Variogram function*/ +/*FUNCTION GaussianVariogram::SemiVariogram{{{1*/ +double GaussianVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ + double h2,a,gamma; + + /*Calculate length square*/ + h2=pow(deltax,2.)+pow(deltay,2.); + + /*return semi-variogram*/ + a = 1./3.; + gamma = (sill-nugget)*(1-exp(-h2/(a*pow(range,2.)))) + nugget; + return gamma; +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/GaussianVariogram.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/GaussianVariogram.h (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/GaussianVariogram.h (revision 12258) @@ -0,0 +1,34 @@ +/*! \file GaussianVariogram.h + * \brief: header file for triavertexinput object + */ + +#ifndef _GAUSSIANVARIOGRAM_H_ +#define _GAUSSIANVARIOGRAM_H_ + +/*Headers:*/ +#include "./Variogram.h" + +class GaussianVariogram: public Variogram{ + + public: + double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin + double sill; //Limit of the variogram tending to infinity lag distances + double range; //The distance in which the difference of the variogram from the sill becomes negligible + + /*GaussianVariogram constructors, destructors*/ + GaussianVariogram(); + GaussianVariogram(Options* options); + ~GaussianVariogram(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); +}; +#endif /* _GAUSSIANVARIOGRAM_H */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Observation.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Observation.cpp (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Observation.cpp (revision 12258) @@ -0,0 +1,55 @@ +/*!\file Observation.c + * \brief: implementation of the Observation object + */ + +#include +#include "../objects.h" + +/*Observation constructors and destructor*/ +/*FUNCTION Observation::Observation(){{{1*/ +Observation::Observation(){ + return; +} +/*}}}*/ +/*FUNCTION Observation::Observation(double x,double y,int xi,int yi,int index,double value){{{1*/ +Observation::Observation(double x_in,double y_in,int xi_in,int yi_in,int index_in,double value_in){ + + this->x = x_in; + this->y = y_in; + this->xi = xi_in; + this->yi = yi_in; + this->index = index_in; + this->value = value_in; + +} +/*}}}*/ +/*FUNCTION Observation::~Observation(){{{1*/ +Observation::~Observation(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION Observation::Echo {{{1*/ +void Observation::Echo(void){ + + int bit; + + printf("Observation\n"); + printf(" index : %i\n",this->index); + printf(" x : %g\n",this->x); + printf(" y : %g\n",this->y); + printf(" xi : "); printbinary(this->xi); printf("\n"); + printf(" yi : "); printbinary(this->yi); printf("\n"); + printf(" value : %g\n",this->value); +} +/*}}}*/ + +/*Observations functions*/ +/*FUNCTION Observation::WriteXYObs(double* px,double* py,double* pobs){{{1*/ +void Observation::WriteXYObs(double* px,double* py,double* pobs){ + *px = this->x; + *py = this->y; + *pobs = this->value; +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Observation.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Observation.h (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Observation.h (revision 12258) @@ -0,0 +1,34 @@ +/*! \file Observation.h + * \brief: header file for Observation object + */ + +#ifndef _OBSERVATION_H_ +#define _OBSERVATION_H_ + +#include "../Object.h" + +class Observation: public Object{ + + public: + double x,y; + int xi,yi; + int index; + double value; + + /*Observation constructors, destructors*/ + Observation(); + Observation(double x_in,double y_in,int xi_in,int yi_in,int index_in,double value_in); + ~Observation(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho() {_error_("Not implemented yet"); }; + int Id() {_error_("Not implemented yet"); }; + int MyRank() {_error_("Not implemented yet"); }; + int ObjectEnum(){_error_("Not implemented yet"); }; + Object *copy() {_error_("Not implemented yet"); }; + + /*Management*/ + void WriteXYObs(double* px,double* py,double* pobs); +}; +#endif /* _OBSERVATION_*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/PowerVariogram.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/PowerVariogram.cpp (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/PowerVariogram.cpp (revision 12258) @@ -0,0 +1,75 @@ +/*!\file PowerVariogram.c + * \brief: implementation of the PowerVariogram object + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../include/include.h" + +/*PowerVariogram constructors and destructor*/ +/*FUNCTION PowerVariogram::PowerVariogram(){{{1*/ +PowerVariogram::PowerVariogram(){ + this->nugget = 0.2; + this->slope = 1.; + this->power = 1.; + return; +} +/*}}}*/ +/*FUNCTION PowerVariogram::PowerVariogram(Options* options){{{1*/ +PowerVariogram::PowerVariogram(Options* options){ + + /*Defaults*/ + this->nugget = 0.2; + this->slope = 1.; + this->power = 1.; + + /*Overwrite from options*/ + if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); + if(options->GetOption("slope")) options->Get(&this->slope,"slope"); + if(options->GetOption("power")) options->Get(&this->power,"power"); + + /*Checks*/ + if(power<=0 || power>=2) _error_("power must be betwwen 0 and 2 (0 < power < 2)"); + if(slope<=0) _error_("slope must be positive"); +} +/*}}}*/ +/*FUNCTION PowerVariogram::~PowerVariogram(){{{1*/ +PowerVariogram::~PowerVariogram(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION PowerVariogram::Echo {{{1*/ +void PowerVariogram::Echo(void){ + printf("PowerVariogram\n"); + printf(" nugget: %g\n",this->nugget); + printf(" slope : %g\n",this->slope); + printf(" power : %g\n",this->power); +} +/*}}}*/ + +/*Variogram function*/ +/*FUNCTION PowerVariogram::SemiVariogram{{{1*/ +double PowerVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ + double h,gamma; + + /*Calculate length square*/ + h=sqrt(pow(deltax,2.)+pow(deltay,2.)); + + /*return semi-variogram*/ + gamma = this->nugget + this->slope*pow(h,this->power); + + return gamma; +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/PowerVariogram.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/PowerVariogram.h (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/PowerVariogram.h (revision 12258) @@ -0,0 +1,34 @@ +/*! \file PowerVariogram.h + * \brief: header file for triavertexinput object + */ + +#ifndef _POWERVARIOGRAM_H_ +#define _POWERVARIOGRAM_H_ + +/*Headers:*/ +#include "./Variogram.h" + +class PowerVariogram: public Variogram{ + + public: + double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin + double slope; + double power; + + /*PowerVariogram constructors, destructors*/ + PowerVariogram(); + PowerVariogram(Options* options); + ~PowerVariogram(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); +}; +#endif /* _POWERVARIOGRAM_H */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Quadtree.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Quadtree.cpp (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Quadtree.cpp (revision 12258) @@ -0,0 +1,511 @@ +#include "../objects.h" +/*DOCUMENTATION What is a Quadtree? {{{1 + * A Quadtree is a very simple way to group vertices according + * to their locations. A square that holds all the points of the mesh + * (or the geometry) is divided into 4 boxes. As soon as one box + * hold more than 4 vertices, it is divided into 4 new boxes, etc... + * There cannot be more than MAXDEEP (=30) subdivision. + * This process is like a Dichotomy in dimension 2 + * + * + - - - - - - - - + - - + - + - + - - - - + + * | | | | X | | + * + - + - + + * | | | | | | + * + - - + - + - + + + * | | | | | + * + * | | | | | + * + - - - - - - - - + - - + - - + - - - - + + * | | | | + * + * | | | | + * + * | | | | + * | | | | + * + - - - - - - - - + - - - - + - - - - + + * | | | + * + * | | | + * + * | | | + * + * | | | + * | | | + * | | | + * | | | + * | | | + * + - - - - - - - - + - - - - - - - - + + * + * The coordinate system used in a quadtree are integers to avoid + * round-off errors. The vertex in the lower left box has the coordinates + * (0 0) + * The upper right vertex has the follwing coordinates: + * 2^30 -1 2^30 -1 in decimal + * 0 1 1 1 .... 1 0 1 1 1 .... 1 in binary + * \-- 29 --/ \-- 29 --/ + * Using binaries is therefore very easy to locate a vertex in a box: + * we just need to look at the bits from the left to the right (See ::Add) + }}}1*/ +/*MACROS {{{1*/ +/* + * + * 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 + */ +//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 )) +/*}}}*/ + + /*Constructors/Destructors*/ +/*FUNCTION Quadtree::Quadtree(){{{1*/ +Quadtree::Quadtree(){ + _error_("Constructor not supported"); + +} +/*}}}1*/ +/*FUNCTION Quadtree::Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth){{{1*/ +Quadtree::Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth){ + + /*Intermediaries*/ + double length; + + /*Initialize fields*/ + this->MaxDepth=maxdepth; + this->NbQuadtreeBox=0; + this->NbObs=0; + + /*Create container*/ + this->boxcontainer=new DataSet(); + + /*Create Root, pointer toward the main box*/ + length=max(xmax-xmin,ymax-ymin); + this->root=NewQuadtreeBox(xmin+length/2,ymin+length/2,length); +} +/*}}}1*/ + /*FUNCTION Quadtree::~Quadtree(){{{1*/ + Quadtree::~Quadtree(){ + + delete boxcontainer; + root=NULL; + + } + /*}}}1*/ + + /*Methods*/ +/*FUNCTION Quadtree::Add{{{1*/ +void Quadtree::Add(Observation* observation){ + + /*Intermediaries*/ + int xi,yi,ij,level,levelbin; + QuadtreeBox **pbox = NULL; // pointer toward current box b + QuadtreeBox **pmaster = NULL; // pointer toward master of b + QuadtreeBox *box = NULL; // current box b + QuadtreeBox *slave = NULL; // suslaveox of b (if necessary) + Observation *obs[4]; + + /*Get integer coodinates*/ + xi = observation->xi; + yi = observation->yi; + + /*Initialize levels*/ + level = 0; + levelbin = (1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pmaster = &root; + pbox = &root; + + /*Find the smallest box where the observation is located*/ + while((box=*pbox) && (box->nbitems<0)){ + + /*Go down one level (levelbin = 00100 -> 00010)*/ + levelbin>>=1; level+=1; _assert_(levelMaxDepth); + + /*Get next box according to the bit value (levelbin)*/ + pmaster = pbox; + pbox = &box->box[IJ(xi,yi,levelbin)]; + } + _assert_(levelbin>0); + + /*Now, try to add the vertex, if the box is full (nbitems=4), we have to divide it in 4 new boxes*/ + while((box=*pbox) && (box->nbitems==4)){ + + /*Copy the 4 observation in the current Quadtreebox*/ + obs[0] = box->obs[0]; + obs[1] = box->obs[1]; + obs[2] = box->obs[2]; + obs[3] = box->obs[3]; + + /*set nbitems as -1 (now holding boxes instead of observations)*/ + box->nbitems = -1; + box->box[0] = NULL; + box->box[1] = NULL; + box->box[2] = NULL; + box->box[3] = NULL; + + /*Go down one level (levelbin = 00010 -> 00001)*/ + levelbin>>=1; level+=1; _assert_(levelMaxDepth); + + /*Put the four observations in the new boxes*/ + for (int k=0;k<4;k++){ + + /*Get box for observation number k*/ + ij = IJ(obs[k]->xi,obs[k]->yi,levelbin); + slave = box->box[ij]; + if(!slave){ + box->box[ij] = NewQuadtreeBox(box,ij); + slave = box->box[ij]; + } + slave->obs[slave->nbitems++] = obs[k]; + } + + /*Get the suslaveox where the current observation is located*/ + ij = IJ(xi,yi,levelbin); + pmaster = pbox; + pbox = &box->box[ij]; + } + + /*alloc the QuadtreeBox if necessary and add current observation*/ + box = *pbox; + if(!box){ + ij = IJ(xi,yi,levelbin); + box = *pbox = NewQuadtreeBox(*pmaster,ij); + } + box->obs[box->nbitems++]=observation; + NbObs++; + +}/*}}}*/ +/*FUNCTION Quadtree::Echo{{{1*/ +void Quadtree::Echo(void){ + + printf("Quadtree:\n"); + printf(" MaxDepth = %i\n",this->MaxDepth); + printf(" NbQuadtreeBox = %i\n",this->NbQuadtreeBox); + printf(" NbObs = %i\n",this->NbObs); + printf(" root = %p\n",this->root); + +}/*}}}*/ +/*FUNCTION Quadtree::DeepEcho{{{1*/ +void Quadtree::DeepEcho(void){ + + printf("Quadtree:\n"); + printf(" MaxDepth = %i\n",this->MaxDepth); + printf(" NbQuadtreeBox = %i\n",this->NbQuadtreeBox); + printf(" NbObs = %i\n",this->NbObs); + printf(" root = %p\n",this->root); + boxcontainer->Echo(); + +}/*}}}*/ +/*FUNCTION Quadtree::IntergerCoordinates{{{1*/ +void Quadtree::IntergerCoordinates(int *xi,int *yi,double x,double y){ + + /*Intermediaries*/ + double coefficient; + double xmin,ymin; + + /*Checks in debugging mode*/ + _assert_(xi && yi); + _assert_(this->root); + + /*coeffIcoor is the coefficient used for integer coordinates: + * (x-xmin) + * xi = (2^30 -1) --------- + * length + * coefficient = (2^30 -1)/length + */ + coefficient = double((1L<MaxDepth)-1)/(this->root->length); + xmin = this->root->xcenter - this->root->length/2; + ymin = this->root->ycenter - this->root->length/2; + + *xi=int(coefficient*(x - xmin)); + *yi=int(coefficient*(y - ymin)); +}/*}}}*/ +/*FUNCTION Quadtree::NewQuadtreeBox(double xcenter,double ycenter,double length){{{1*/ +Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(double xcenter,double ycenter,double length){ + + /*Output*/ + QuadtreeBox* newbox=NULL; + + /*Create and initialize a new box*/ + newbox=new QuadtreeBox(); + newbox->nbitems=0; + newbox->xcenter=xcenter; + newbox->ycenter=ycenter; + newbox->length=length; + newbox->box[0]=NULL; + newbox->box[1]=NULL; + newbox->box[2]=NULL; + newbox->box[3]=NULL; + + /*Add to container*/ + this->boxcontainer->AddObject(newbox); + NbQuadtreeBox++; + + /*currentbox now points toward next quadtree box*/ + return newbox; +}/*}}}*/ +/*FUNCTION Quadtree::NewQuadtreeBox(QuadtreeBox* master,int index) {{{1*/ +Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(QuadtreeBox* master,int index){ + + /*Output*/ + QuadtreeBox* newbox=NULL; + + /*Checks in debugging mode*/ + _assert_(master); + + /*Create and initialize a new box*/ + newbox=new QuadtreeBox(); + newbox->nbitems=0; + newbox->box[0]=NULL; + newbox->box[1]=NULL; + newbox->box[2]=NULL; + newbox->box[3]=NULL; + switch(index){ + case 0: + newbox->xcenter=master->xcenter - master->length/4; + newbox->ycenter=master->ycenter - master->length/4; + break; + case 1: + newbox->xcenter=master->xcenter + master->length/4; + newbox->ycenter=master->ycenter - master->length/4; + break; + case 2: + newbox->xcenter=master->xcenter - master->length/4; + newbox->ycenter=master->ycenter + master->length/4; + break; + case 3: + newbox->xcenter=master->xcenter + master->length/4; + newbox->ycenter=master->ycenter + master->length/4; + break; + default: + _error_("Case %i not supported",index); + } + newbox->length=master->length/2; + + /*Add to container*/ + this->boxcontainer->AddObject(newbox); + NbQuadtreeBox++; + + /*currentbox now points toward next quadtree box*/ + return newbox; +}/*}}}*/ +/*FUNCTION Quadtree::QuadtreeDepth{{{1*/ +void Quadtree::QuadtreeDepth(int* A,int xi,int yi){ + + QuadtreeBox **pbox = NULL; + QuadtreeBox *box = NULL; + int level,levelbin; + + /*Initialize levels*/ + level = 0; + levelbin = (1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pbox=&root; + + /*Find the smallest box where this point is located*/ + while((box=*pbox) && (box->nbitems<0)){ + + levelbin>>=1; level+=1; _assert_(levelMaxDepth); + + pbox = &box->box[IJ(xi,yi,levelbin)]; + } + if(box && box->nbitems>0){ + /*This box is not empty, add one level*/ + level+=1; + } + + *A=level; +}/*}}}*/ +/*FUNCTION Quadtree::QuadtreeDepth2{{{1*/ +void Quadtree::QuadtreeDepth2(int* A,int xi,int yi){ + + QuadtreeBox **pbox = NULL; + QuadtreeBox *box = NULL; + int level,levelbin; + + /*Initialize levels*/ + level = 0; + levelbin = (1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pbox=&root; + + /*Find the smallest box where this point is located*/ + while((box=*pbox) && (box->nbitems<0)){ + + levelbin>>=1; level+=1; + + pbox = &box->box[IJ(xi,yi,levelbin)]; + } + if(box && box->nbitems>0){ + /*This box is not empty, add one level*/ + level+=1; + } + + /*If we were to add the vertex, get level*/ + if(box && box->nbitems==4){ + int ij; + bool flag=true; + while(flag){ + + levelbin>>=1; level+=1; + if(level>this->MaxDepth){ + level+=1; + break; + } + + /*loop over the four observations*/ + ij=IJ(box->obs[0]->xi,box->obs[0]->yi,levelbin); + for (int k=1;k<4;k++){ + if(IJ(box->obs[k]->xi,box->obs[k]->yi,levelbin) != ij){ + flag = false; + } + } + if(IJ(xi,yi,levelbin)!=ij){ + flag = false; + } + } + } + + *A=level; +}/*}}}*/ +/*FUNCTION Quadtree::RangeSearch{{{1*/ +void Quadtree::RangeSearch(int **pindices,int *pnobs,double x,double y,double range){ + + /*Intermediaries*/ + int nobs; + int *indices = NULL; + + /*Allocate indices (maximum by default*/ + indices = (int*)xmalloc(this->NbObs*sizeof(int)); + nobs = 0; + + this->root->RangeSearch(indices,&nobs,x,y,range); + + /*Clean-up and return*/ + *pnobs=nobs; + *pindices=indices; + +}/*}}}*/ + +/*QuadtreeBox methos*/ +/*FUNCTION QuadtreeBox::Echo{{{1*/ +void Quadtree::QuadtreeBox::Echo(void){ + + printf("QuadtreeBox:\n"); + printf(" nbitems = %i\n",this->nbitems); + printf(" xcenter = %g\n",this->xcenter); + printf(" ycenter = %g\n",this->ycenter); + printf(" length = %g\n",this->length); + +}/*}}}*/ +/*FUNCTION QuadtreeBox::IsWithinRange{{{1*/ +int Quadtree::QuadtreeBox::IsWithinRange(double x,double y,double range){ + + /*Return 0 if the 2 boxes do not overlap*/ + if(this->xcenter+this->length/2 < x-range) return 0; + if(this->xcenter-this->length/2 > x+range) return 0; + if(this->ycenter+this->length/2 < y-range) return 0; + if(this->ycenter-this->length/2 > y+range) return 0; + + /*Return 2 if the this box is included in the range*/ + if(this->xcenter+this->length/2 <= x+range && + this->ycenter+this->length/2 <= y+range && + this->xcenter-this->length/2 >= x-range && + this->ycenter-this->length/2 >= y-range) return 2; + + /*This is a simple overlap*/ + return 1; + +}/*}}}*/ +/*FUNCTION QuadtreeBox::RangeSearch{{{1*/ +void Quadtree::QuadtreeBox::RangeSearch(int* indices,int *pnobs,double x,double y,double range){ + + /*Intermediaries*/ + int i,nobs; + + /*Recover current number of observations*/ + nobs = *pnobs; + + switch(this->IsWithinRange(x,y,range)){ + case 0: + /*If this box is not within range, return*/ + break; + case 2: + /*This box is included in range*/ + this->WriteObservations(indices,&nobs); + break; + case 1: + /*This box is partly included*/ + if(this->nbitems>0){ + /*If this box has only observations, add indices that are within range*/ + for(i=0;inbitems;i++){ + if(fabs(this->obs[i]->x-x) <= range && fabs(this->obs[i]->y-y) <= range){ + indices[nobs++]=this->obs[i]->index; + } + } + } + else{ + /*This box points toward boxes*/ + if(this->box[0]) this->box[0]->RangeSearch(indices,&nobs,x,y,range); + if(this->box[1]) this->box[1]->RangeSearch(indices,&nobs,x,y,range); + if(this->box[2]) this->box[2]->RangeSearch(indices,&nobs,x,y,range); + if(this->box[3]) this->box[3]->RangeSearch(indices,&nobs,x,y,range); + } + break; + default: + _error_("Case %i not supported",this->IsWithinRange(x,y,range)); + } + + /*Assign output pointers: */ + *pnobs=nobs; +}/*}}}*/ +/*FUNCTION QuadtreeBox::WriteObservations{{{1*/ +void Quadtree::QuadtreeBox::WriteObservations(int* indices,int *pnobs){ + + /*Intermediaries*/ + int i,nobs; + + /*Recover current number of observations*/ + nobs = *pnobs; + + if(this->nbitems>0){ + /*If this box has only observations, add all indices*/ + for(i=0;inbitems;i++){ + indices[nobs++]=this->obs[i]->index; + } + } + else{ + /*This box points toward boxes, */ + if(this->box[0]) this->box[0]->WriteObservations(indices,&nobs); + if(this->box[1]) this->box[1]->WriteObservations(indices,&nobs); + if(this->box[2]) this->box[2]->WriteObservations(indices,&nobs); + if(this->box[3]) this->box[3]->WriteObservations(indices,&nobs); + } + + /*Assign output pointers: */ + *pnobs=nobs; +}/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Quadtree.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Quadtree.h (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Quadtree.h (revision 12258) @@ -0,0 +1,64 @@ + +#ifndef _QUADTREE_H +#define _QUADTREE_H + +class Observation; + +class Quadtree{ + + private: + /* A quadtree box contains up to 4 points (locations). 4 new quadtree boxes are + * created if a fifth point is added to the same box. A Quadtree box is therefore + * composed of EITHER: + * - up to 4 vertices + * - 4 "sub" quadtree boxes*/ + + class QuadtreeBox: public Object{ + public: + int nbitems; // number of current vertices in the box + double xcenter; // x position of the center (double) + double ycenter; // x position of the center (double) + double length; // width of the box + union{ + QuadtreeBox *box[4]; + Observation *obs[4]; + }; + + /*Object functions (Needed because the Quadtree uses a Container*/ + void Echo(); + void DeepEcho() {_error_("not implemented yet"); }; + int Id() {_error_("not implemented yet"); }; + int MyRank() {_error_("not implemented yet"); }; + int ObjectEnum(){_error_("not implemented yet"); }; + Object *copy() {_error_("not implemented yet"); }; + + /*Methods*/ + int IsWithinRange(double x,double y,double range); + void RangeSearch(int* indices,int *pnobs,double x,double y,double range); + void WriteObservations(int* indices,int *pnobs); + + }; + + /*Quadtree private Fields*/ + DataSet* boxcontainer; + + public: + int MaxDepth; // maximum number of subdivision + QuadtreeBox *root; // main box + long NbQuadtreeBox; // total number of boxes + long NbObs; // number of points + + Quadtree(); + Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth_in); + ~Quadtree(); + void Add(Observation *observation); + void DeepEcho(void); + void Echo(void); + void IntergerCoordinates(int *xi,int *yi,double x,double y); + QuadtreeBox *NewQuadtreeBox(double xcenter,double ycenter,double length); + QuadtreeBox *NewQuadtreeBox(QuadtreeBox* master,int index); + void QuadtreeDepth(int *A,int xi,int yi); + void QuadtreeDepth2(int *A,int xi,int yi); + void RangeSearch(int **pindices,int *pnobs,double x,double y,double range); +}; +#endif //_QUADTREE_H Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/SphericalVariogram.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/SphericalVariogram.cpp (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/SphericalVariogram.cpp (revision 12258) @@ -0,0 +1,77 @@ +/*!\file SphericalVariogram.c + * \brief: implementation of the SphericalVariogram object + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../include/include.h" + +/*SphericalVariogram constructors and destructor*/ +/*FUNCTION SphericalVariogram::SphericalVariogram(){{{1*/ +SphericalVariogram::SphericalVariogram(){ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + return; +} +/*}}}*/ +/*FUNCTION SphericalVariogram::SphericalVariogram(Options* options){{{1*/ +SphericalVariogram::SphericalVariogram(Options* options){ + + /*Defaults*/ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + + /*Overwrite from options*/ + if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); + if(options->GetOption("sill")) options->Get(&this->sill,"sill"); + if(options->GetOption("range")) options->Get(&this->range,"range"); + + /*Checks*/ + if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)"); +} +/*}}}*/ +/*FUNCTION SphericalVariogram::~SphericalVariogram(){{{1*/ +SphericalVariogram::~SphericalVariogram(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION SphericalVariogram::Echo {{{1*/ +void SphericalVariogram::Echo(void){ + printf("SphericalVariogram\n"); + printf(" nugget: %g\n",this->nugget); + printf(" sill : %g\n",this->sill); + printf(" range : %g\n",this->range); +} +/*}}}*/ + +/*Variogram function*/ +/*FUNCTION SphericalVariogram::SemiVariogram{{{1*/ +double SphericalVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ + double h,gamma; + + /*Calculate length square*/ + h=sqrt(pow(deltax,2.)+pow(deltay,2.)); + + /*return semi-variogram*/ + if(h<=range) + gamma = (sill-nugget)*( (3*h)/(2*range) - pow(h,3.)/(2*pow(range,3.)) ) + nugget; + else + gamma = sill; + + return gamma; +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/SphericalVariogram.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/SphericalVariogram.h (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/SphericalVariogram.h (revision 12258) @@ -0,0 +1,34 @@ +/*! \file SphericalVariogram.h + * \brief: header file for triavertexinput object + */ + +#ifndef _SPHERICALVARIOGRAM_H_ +#define _SPHERICALVARIOGRAM_H_ + +/*Headers:*/ +#include "./Variogram.h" + +class SphericalVariogram: public Variogram{ + + public: + double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin + double sill; //Limit of the variogram tending to infinity lag distances + double range; //The distance in which the difference of the variogram from the sill becomes negligible + + /*SphericalVariogram constructors, destructors*/ + SphericalVariogram(); + SphericalVariogram(Options* options); + ~SphericalVariogram(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); +}; +#endif /* _SPHERICALVARIOGRAM_H */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Variogram.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Variogram.h (revision 12258) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Kriging/Variogram.h (revision 12258) @@ -0,0 +1,17 @@ +/*!\file: Variogram.h + * \brief abstract class for Variogram object + */ + +#ifndef _VARIOGRAM_H_ +#define _VARIOGRAM_H_ + +#include "../Object.h" + +class Variogram: public Object{ + + public: + virtual ~Variogram(){}; + virtual double SemiVariogram(double deltax,double deltay)=0; + +}; +#endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp (revision 12258) @@ -85,5 +85,5 @@ /*}}}*/ #endif -#ifdef _HAVE_GSL_ +#if defined(_HAVE_GSL_) && !defined(_HAVE_PETSC_) /*FUNCTION Vector::Vector(SeqVec* seq_vec){{{1*/ Vector::Vector(SeqVec* seq_vec){ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h (revision 12258) @@ -43,5 +43,5 @@ Vector(Vec petsc_vec); #endif - #ifdef _HAVE_GSL_ + #if defined(_HAVE_GSL_) && !defined(_HAVE_PETSC_) Vector(SeqVec* seq_vec); #endif Index: /issm/branches/trunk-jpl-damage/src/c/objects/objects.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/objects.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/objects/objects.h (revision 12258) @@ -170,6 +170,15 @@ #include "./Bamg/Mesh.h" #include "./Bamg/Geometry.h" -#include "./Bamg/QuadTree.h" +#include "./Bamg/BamgQuadtree.h" #include "./Bamg/SetOfE4.h" +/*Kriging*/ +#include "./Kriging/Variogram.h" +#include "./Kriging/GaussianVariogram.h" +#include "./Kriging/ExponentialVariogram.h" +#include "./Kriging/SphericalVariogram.h" +#include "./Kriging/PowerVariogram.h" +#include "./Kriging/Quadtree.h" +#include "./Kriging/Observation.h" + #endif Index: /issm/branches/trunk-jpl-damage/src/c/shared/Elements/elements.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Elements/elements.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Elements/elements.h (revision 12258) @@ -47,4 +47,15 @@ printf("\n"); } +inline void printbinary(int n) { + unsigned int i=1L<<(sizeof(n)*8-1); + + while (i>0) { + if (n&i) + printf("1"); + else + printf("0"); + i>>=1; + } +} #endif //ifndef _SHARED_ELEMENTS_H_ Index: /issm/branches/trunk-jpl-damage/src/m/model/collapse.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/collapse.m (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/m/model/collapse.m (revision 12258) @@ -102,6 +102,6 @@ %lat long -if numel(md.mesh.lat)>1, md.mesh.lat=project2d(md,md.mesh.lat,1); end -if numel(md.mesh.long)>1, md.mesh.long=project2d(md,md.mesh.long,1); end +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 Index: /issm/branches/trunk-jpl-damage/src/m/model/partition/AreaAverageOntoPartition.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/model/partition/AreaAverageOntoPartition.m (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/m/model/partition/AreaAverageOntoPartition.m (revision 12258) @@ -29,5 +29,5 @@ %finally, project vector: vector=project2d(md3d,vector,layer); - md.qmu.partition=project2d(md3d,md3d.part,layer); + md.qmu.partition=project2d(md3d,md3d.qmu.partition,layer); end Index: /issm/branches/trunk-jpl-damage/src/m/utils/BC/SetIceShelfBC.py =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/utils/BC/SetIceShelfBC.py (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/m/utils/BC/SetIceShelfBC.py (revision 12258) @@ -1,3 +1,4 @@ -def SetIceShelfBC(md,icefrontfile='') +from numpy import * +def SetIceShelfBC(md,icefrontfile=''): #SETICESHELFBC - Create the boundary conditions for diagnostic and thermal models for a Ice Shelf with Ice Front # @@ -22,40 +23,41 @@ print 'SetIceShelfBC error message: ice front file '+icefrontfile+ ' not found' return [] - nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2); - nodeonicefront=double(md.mesh.vertexonboundary & nodeinsideicefront); + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2) + nodeonicefront=double(md.mesh.vertexonboundary.astype(bool) and nodeinsideicefront.astype(bool)) - pos=find(md.mesh.vertexonboundary & ~nodeonicefront); - md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); - md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); - md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); - md.diagnostic.spcvx(pos)=0; - md.diagnostic.spcvy(pos)=0; - md.diagnostic.spcvz(pos)=0; - md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6); + pos=argwhere(logical_and(md.mesh.vertexonboundary.astype(bool),~nodeonicefront.astype(bool))) + md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices); + md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices); + md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices); + md.diagnostic.spcvx[pos]=0; + md.diagnostic.spcvy[pos]=0; + md.diagnostic.spcvz[pos]=0; + md.diagnostic.referential=float('NaN')*ones((md.mesh.numberofvertices,6),float); #Dirichlet Values - if (length(md.inversion.vx_obs)==md.mesh.numberofvertices & length(md.inversion.vy_obs)==md.mesh.numberofvertices) - disp(' boundary conditions for diagnostic model: spc set as observed velocities'); - md.diagnostic.spcvx(pos)=md.inversion.vx_obs(pos); - md.diagnostic.spcvy(pos)=md.inversion.vy_obs(pos); - else - disp(' boundary conditions for diagnostic model: spc set as zero'); - end + if ~isnan(md.inversion.vx_obs) and ~isnan(md.inversion.vy_obs): + if (len(md.inversion.vx_obs)==md.mesh.numberofvertices) and (len(md.inversion.vy_obs)==md.mesh.numberofvertices): + print ' boundary conditions for diagnostic model: spc set as observed velocities' + md.diagnostic.spcvx[pos]=md.inversion.vx_obs[pos] + md.diagnostic.spcvy[pos]=md.inversion.vy_obs[pos] + else: + print ' boundary conditions for diagnostic model: spc set as zero' #segment on Ice Front #segment on Neumann (Ice Front) - pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); - if (md.mesh.dimension==2) - pressureload=md.mesh.segments(pos,:); - elseif md.mesh.dimension==3 - pressureload_layer1=[md.mesh.segments(pos,1:2) md.mesh.segments(pos,2)+md.mesh.numberofvertices2d md.mesh.segments(pos,1)+md.mesh.numberofvertices2d md.mesh.segments(pos,3)]; + segs1=md.mesh.segments[:,0].astype(int)-1 + segs2=md.mesh.segments[:,1].astype(int)-1 + + pos=argwhere(logical_and(nodeonicefront[segs1].astype(bool),nodeonicefront[segs2].astype(bool))) + if (md.mesh.dimension==2): + pressureload=md.mesh.segments[pos,:]; + elif md.mesh.dimension==3: + pressureload_layer=[md.mesh.segments[pos,0:2],md.mesh.segments[pos,1]+md.mesh.numberofvertices2d,md.mesh.segments[pos,0]+md.mesh.numberofvertices2d, md.mesh.segments[pos,2]]; pressureload=[]; - for i=1:md.mesh.numberoflayers-1, - pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.mesh.numberofvertices2d pressureload_layer1(:,5)+(i-1)*md.mesh.numberofelements2d ]; - end - end + for i in range(1,md.mesh.numberoflayers-1): + pressureload=[pressureload ,pressureload_layer1[:,1:4]+(i-1)*md.mesh.numberofvertices2d, pressureload_layer1[:,5]+(i-1)*md.mesh.numberofelements2d ]; #Add water or air enum depending on the element - pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))]; + pressureload=[pressureload, 1*md.mask.elementonfloatingice(pressureload[:,end])]; #plug onto model @@ -63,31 +65,27 @@ #Create zeros basalforcings and surfaceforcings - if isnan(md.surfaceforcings.precipitation), - md.surfaceforcings.precipitation=zeros(md.mesh.numberofvertices,1); - disp(' no surfaceforcings.precipitation specified: values set as zero'); - end - if isnan(md.surfaceforcings.mass_balance), - md.surfaceforcings.mass_balance=zeros(md.mesh.numberofvertices,1); - disp(' no surfaceforcings.mass_balance specified: values set as zero'); - end - if isnan(md.basalforcings.melting_rate), - md.basalforcings.melting_rate=zeros(md.mesh.numberofvertices,1); - disp(' no basalforcings.melting_rate specified: values set as zero'); - end - if isnan(md.balancethickness.thickening_rate), - md.balancethickness.thickening_rate=zeros(md.mesh.numberofvertices,1); - disp(' no balancethickness.thickening_rate specified: values set as zero'); - end + if isnan(md.surfaceforcings.precipitation): + md.surfaceforcings.precipitation=zeros(md.mesh.numberofvertices); + print ' no surfaceforcings.precipitation specified: values set as zero' + if isnan(md.surfaceforcings.mass_balance): + md.surfaceforcings.mass_balance=zeros(md.mesh.numberofvertices); + print ' no surfaceforcings.mass_balance specified: values set as zero' + if isnan(md.basalforcings.melting_rate): + md.basalforcings.melting_rate=zeros(md.mesh.numberofvertices) + print ' no basalforcings.melting_rate specified: values set as zero' + if isnan(md.balancethickness.thickening_rate): + md.balancethickness.thickening_rate=zeros(md.mesh.numberofvertices); + print ' no balancethickness.thickening_rate specified: values set as zero' - md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices,1); - md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices,1); + md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices); + md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices); - if (length(md.initialization.temperature)==md.mesh.numberofvertices), - md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1); - pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); #impose observed temperature on surface - if (length(md.basalforcings.geothermalflux)~=md.mesh.numberofvertices), - md.basalforcings.geothermalflux=zeros(md.mesh.numberofvertices,1); - end - else - disp(' no thermal boundary conditions created: no observed temperature found'); - end + if (len(md.initialization.temperature)==md.mesh.numberofvertices): + md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices); + pos=argwhere(md.mesh.vertexonsurface); md.thermal.spctemperature[pos]=md.initialization.temperature[pos]; #impose observed temperature on surface + if (len(md.basalforcings.geothermalflux) !=md.mesh.numberofvertices): + md.basalforcings.geothermalflux=zeros(md.mesh.numberofvertices); + else: + print ' no thermal boundary conditions created: no observed temperature found' + + return md Index: /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.cpp (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.cpp (revision 12258) @@ -7,11 +7,13 @@ /*Outputs*/ - double *x = NULL; - double *y = NULL; - double *observations = NULL; - double *x_interp = NULL; - double *y_interp = NULL; - double *predictions = NULL; - int n_interp,n,n_obs; + double *x = NULL; + double *y = NULL; + double *observations = NULL; + double *x_interp = NULL; + double *y_interp = NULL; + double *predictions = NULL; + double *error = NULL; + Options *options = NULL; + int N_interp,M_interp,M,N,n_obs; /*Boot module: */ @@ -19,18 +21,22 @@ /*checks on arguments on the matlab side: */ - CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&KrigingUsage); + if (nrhsNLHS){ + KrigingUsage(); _error_("Kriging usage error"); + } /*Fetch inputs: */ FetchData(&x,&n_obs,X); - FetchData(&y,&n,Y); if(n_obs!=n) _error_("x and y should have the same size"); - FetchData(&observations,&n,OBSERVATIONS); if(n_obs!=n) _error_("x and observations should have the same size"); - FetchData(&x_interp,&n_interp,XINTERP); - FetchData(&y_interp,&n,YINTERP); if(n_interp!=n) _error_("x_interp and y_interp should have the same size"); + FetchData(&y,&N,Y); if(n_obs!=N) _error_("x and y should have the same size"); + FetchData(&observations,&N,OBSERVATIONS); if(n_obs!=N) _error_("x and observations should have the same size"); + FetchData(&x_interp,&M_interp,&N_interp,XINTERP); + FetchData(&y_interp,&M,&N,YINTERP); if(N!=N_interp || M!=M_interp) _error_("x_interp and y_interp should have the same size"); + FetchData(&options,NRHS,nrhs,prhs); /*Call x layer*/ - Krigingx(&predictions,x,y,observations,n_obs,x_interp,y_interp,n_interp); + Krigingx(&predictions,&error,x,y,observations,n_obs,x_interp,y_interp,M_interp*N_interp,options); /*Generate output Matlab Structures*/ - WriteData(PREDICTIONS,predictions,n_interp); + if(nlhs>=1) WriteData(PREDICTIONS,predictions,M_interp,N_interp); + if(nlhs==2) WriteData(ERROR,error,M_interp,N_interp); /*Free ressources: */ @@ -41,4 +47,5 @@ xfree((void**)&y_interp); xfree((void**)&predictions); + xfree((void**)&error); /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.h (revision 12257) +++ /issm/branches/trunk-jpl-damage/src/modules/Kriging/Kriging.h (revision 12258) @@ -26,8 +26,9 @@ /* serial output macros: */ #define PREDICTIONS (mxArray**)&plhs[0] +#define ERROR (mxArray**)&plhs[1] /* serial arg counts: */ #undef NLHS -#define NLHS 1 +#define NLHS 2 #undef NRHS #define NRHS 5