Context Navigation

-              r14310
+              r15396
 ./configure \
         --prefix=$ISSM_DIR \
     --build="i386-apple-darwin10.8.0" \
     --host="arm-linux-androideabi" \
     --enable-shared \
     --with-android=jni \
         --with-android-ndk=$ISSM_DIR/externalpackages/android/android-ndk/install \
     --without-fortran \
         --without-wrappers \
         --without-kriging \
         --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \
         --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
     --disable-static
+   --prefix=$ISSM_DIR\
+   --libdir=$ISSM_DIR/src/mobile/android/ISSM_APP/libs/armeabi\
+   --build="i386-apple-darwin10.8.0"\
+   --host="arm-linux-androideabi"\
+   --enable-shared\
+   --with-android=jni\
+   --with-android-ndk=$ISSM_DIR/externalpackages/android/android-ndk/install\
+   --without-fortran\
+   --without-wrappers\
+   --without-kriging\
+   --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\
+   --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install\

issm/trunk/configs/config-discover.sh

r13975	r15396
13	13	--with-mkl-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \
14	14	--with-mpi-include="/usr/local/intel/mpi/4.0.3.008/include64/" \
15		--with-mpi-lib="-L/usr/local/intel/mpi/4.0.3.008/lib64/ -lmpi -lmpiif" \
	15	--with-mpi-libflags="-L/usr/local/intel/mpi/4.0.3.008/lib64/ -lmpi -lmpiif" \
16	16	--with-petsc-arch=$ISSM_ARCH \
17	17	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \

issm/trunk/configs/config-greenplanet.sh

r14067	r15396
12	12	--with-tao-dir=$ISSM_DIR/externalpackages/tao/install \
13	13	--with-mpi-include="/sopt/mpi/openmpi-1.5.4_psm/intel/include/" \
14		--with-mpi-lib="-L/sopt/mpi/openmpi-1.5.4_psm/intel/lib/ -lmpi -lmpi_f77" \
	14	--with-mpi-libflags="-L/sopt/mpi/openmpi-1.5.4_psm/intel/lib/ -lmpi -lmpi_f77" \
15	15	--with-petsc-arch=$ISSM_ARCH \
16	16	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \

issm/trunk/configs/config-hoffman2.sh

r14310	r15396
7	7	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
8	8	--with-mpi-include=/u/local/intel/11.1/openmpi/1.4.5/include \
9		--with-mpi-lib="-L/u/local/intel/11.1/openmpi/1.4.5/include -lmpi" \
	9	--with-mpi-libflags="-L/u/local/intel/11.1/openmpi/1.4.5/include -lmpi" \
10	10	--with-petsc-arch=$ISSM_ARCH \
11	11	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \

issm/trunk/configs/config-linux64-cloud.sh

-              r13975
+              r15396
  --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
  --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \
  --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
  --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \
+ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
+ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl " \
  --with-petsc-arch=$ISSM_ARCH \
  --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \

issm/trunk/configs/config-linux64-murdo-nopetsc.sh

-              r12332
+              r15396
 ./configure \
  --prefix=$ISSM_DIR \
  --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
  --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \
+ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
+ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \
  --with-matlab-dir=$MATLAB_DIR \
  --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \

issm/trunk/configs/config-linux64-murdo.sh

-              r13975
+              r15396
         --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
         --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
         --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
         --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \
+        --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
+        --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \
         --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
         --with-python-dir=$ISSM_DIR/externalpackages/python/install\

issm/trunk/configs/config-linux64-ubuntu64.sh

-              r12332
+              r15396
  --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-mpi-include="/usr/lib/mpich/include" \
+ --with-mpi-libflags="-L/usr/lib/mpich/lib -lmpich -lmpl -ldl" \
  --with-petsc-arch=$ISSM_ARCH \
  --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
 …
  --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
  --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\
  --with-fortran-lib="-lgfortran"\
+ --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.7/ -lgfortran"\
  --with-numthreads=8 \
  --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \

issm/trunk/configs/config-macosx64-nicole.sh

-              r13395
+              r15396
 #petsc 3.2
 #mpich 1.4
+export F77='/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran'
 ./configure \
 …
         --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 $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
+        --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
+        --with-mpi-libflags=" $ISSM_DIR/externalpackages/mpich/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpl.a " \
         --with-petsc-arch=$ISSM_ARCH \
         --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \

issm/trunk/configs/config-macosx64-ogive.sh

-              r12332
+              r15396
         --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 $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
+        --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
+        --with-mpi-libflags=" $ISSM_DIR/externalpackages/mpich/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpl.a " \
         --with-petsc-arch=$ISSM_ARCH \
         --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \

issm/trunk/configs/config-macosx64.sh

-              r14023
+              r15396
 #petsc 3.2
 #mpich 1.4
+pythonversion=2.7
+#python 2.7
 ./configure \
         --prefix=$ISSM_DIR \
         --with-matlab-dir=$MATLAB_DIR \
         --with-python-dir=$ISSM_DIR/externalpackages/python/install\
         --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\
         --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
         --with-metis-dir=$ISSM_DIR/externalpackages/metis/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 $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
         --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
+        --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \
+        --with-python-dir="$ISSM_DIR/externalpackages/python/install" \
+        --with-python-numpy-dir="$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy" \
+        --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
+        --with-metis-dir="$ISSM_DIR/externalpackages/metis/install" \
+        --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \
+        --with-mpi-libflags=" $ISSM_DIR/externalpackages/mpich/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpl.a " \
+        --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/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 \
         --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
         --with-petsc-arch=$ISSM_ARCH \
         --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
         --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
         --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
         --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
         --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install
+        --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
+        --with-petsc-arch="$ISSM_ARCH" \
+        --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
+        --with-blacs-dir="$ISSM_DIR/externalpackages/petsc/install/" \
+        --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \
+        --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \
+        --with-dakota-dir="$ISSM_DIR/externalpackages/dakota/install"

issm/trunk/configs/config-pleiades-petscdev.sh

r13975	r15396
9	9	--with-tao-dir=$ISSM_DIR/externalpackages/tao/install \
10	10	--with-mpi-include=/nasa/sgi/mpt/2.04/include \
11		--with-mpi-lib="-L/nasa/sgi/mpt/2.04/lib/ -lmpi -lpthread -lgfortran" \
	11	--with-mpi-libflags="-L/nasa/sgi/mpt/2.04/lib/ -lmpi -lpthread -lgfortran" \
12	12	--with-petsc-arch=$ISSM_ARCH \
13	13	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \

issm/trunk/configs/config-win7-32.sh

-              r12332
+              r15396
 #!/bin/sh
-#Dos style path needed for the windows sdk 7.1 cl compiler:
-ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"`
 #get configure.sh to pick up the win7 Visual Studio compiler
 ./configure --prefix=$ISSM_DIR \
+        --with-vendor=intel-win7-32  \
+        --with-matlab-dir=$MATLAB_DIR \
+        --with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \
+        --with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \
+        --with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \
+        --with-petsc-arch=$ISSM_ARCH  \
+        --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/  \
+        --with-mpi-lib="$ISSM_DIR_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \
+        --with-mpi-include="$ISSM_DIR_WIN/externalpackages/petsc/install/include/mpiuni"
+   --disable-static \
+   --with-vendor=intel-win7-32  \
+   --with-matlab-dir="$MATLAB_DIR" \
+   --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
+   --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
+   --with-metis-dir="$ISSM_DIR/externalpackages/metis/install" \
+   --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
+   --with-petsc-arch=$ISSM_ARCH  \
+   --with-mpi-libdir="$ISSM_DIR/externalpackages/petsc/install/lib" \
+   --with-mpi-libflags="-Wl,libpetsc.lib" \
+   --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include/mpiuni"

issm/trunk/configs/config-win7-64.sh

-              r12332
+              r15396
 #!/bin/sh
-#Dos style path needed for the windows sdk 7.1 cl compiler:
-ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"`
 #get configure.sh to pick up the win7 Visual Studio compiler
 ./configure --prefix=$ISSM_DIR \
+   --disable-static \
         --with-vendor=intel-win7-64  \
         --with-matlab-dir=$MATLAB_DIR \
         --with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \
         --with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \
         --with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \
+        --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-petsc-arch=$ISSM_ARCH  \
         --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/  \
+        --with-mpi-lib="$ISSM_DIR_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \
+        --with-mpi-include="$ISSM_DIR_WIN/externalpackages/petsc/install/include/mpiuni"
+        --with-mpi-libflags-dir="$ISSM_DIR/externalpackages/petsc/install/lib" \
+   --with-mpi-libflagss="-Wl,libpetsc.lib" \
+        --with-mpi-include-dir="$ISSM_DIR/externalpackages/petsc/install/include/mpiuni"

issm/trunk/configure.ac

-              r14310
+              r15396
 #AUTOCONF
 AC_INIT([ISSM],[4.2.5],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure
+AC_INIT([ISSM],[4.3],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure
 AC_CONFIG_AUX_DIR([./aux-config])         #Put config files in aux-config
 AC_CONFIG_MACRO_DIR([m4])                 #m4 macros are located in m4
 …
 #Compilers
 AC_PROG_CC([cccl cl icl gcc])
+AC_PROG_CC([icc cccl cl icl gcc])
 AC_PROG_CPP
 AC_PROG_CXX([cccl cl icl g++])
+AC_PROG_CXX([icpc cccl cl icl g++])
 AC_PROG_F77([ifort g77 gfortran])
 …
 #Initialize automake and declare foreign so that we don't need a ChangeLog, INSTALL, etc
 AM_INIT_AUTOMAKE([foreign])
 AM_CONFIG_HEADER([./config.h])   #Config file must be config.h
+AC_CONFIG_HEADERS([./config.h])   #Config file must be config.h
 AM_SILENT_RULES([yes])           #Do not show compilation command by default
 AM_PROG_CC_C_O
 …
                         src/wrappers/python/Makefile
                         src/wrappers/matlab/Makefile
                         src/android/Makefile
                         src/android/ISSM/Makefile
+                        src/mobile/Makefile
+                        src/mobile/native/Makefile
                         src/m/Makefile])

issm/trunk/etc/environment.csh

-              r13975
+              r15396
 #ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
+#ISSM_DIR should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
 #Load ISSM scripts
 …
 if (-d $PETSC_DIR) then
         setenv PETSC_DIR {$PETSC_DIR}
         setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$PETSC_DIR/lib/{$ISSM_ARCH}
+        setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$PETSC_DIR/lib
 endif
 …
 set SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
 if (-d $SLEPC_DIR) then
         setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$SLEPC_DIR/lib/{$ISSM_ARCH}
+        setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$SLEPC_DIR/lib
 endif
 …
 set TAO_DIR="$ISSM_DIR/externalpackages/tao/install"
 if (-d $TAO_DIR) then
         setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$TAO_DIR/lib/{$ISSM_ARCH}
+        setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$TAO_DIR/lib
 endif

issm/trunk/etc/environment.sh

-              r14067
+              r15396
 libpathappend "$MATLAB_DIR/lib"
+#legacy mpich2 (To be removed)
 MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install"
 if [ -d "$MPI_DIR" ]; then
 …
 fi
+MPI_DIR="$ISSM_DIR/externalpackages/mpich/install"
+if [ -d "$MPI_DIR" ]; then
+        export MPI_DIR
+        pathprepend   "$MPI_DIR/bin"
+        libpathappend "$MPI_DIR/lib"
+fi
 PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install"
 export PETSC_DIR
 …
 SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
 libpathappend "$SLEPC_DIR/lib/$ISSM_ARCH"
+libpathappend "$SLEPC_DIR/lib"
 TAO_DIR="$ISSM_DIR/externalpackages/tao/install"
 …
 DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
 pathappend "$DAKOTA_DIR/bin"
+libpathappend "$DAKOTA_DIR/lib"
 DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
 …
 pathprepend "$GDAL_DIR/bin"
 libpathappend "$GDAL_DIR/lib"
+PROJ4_DIR="$ISSM_DIR/externalpackages/proj.4/install"
+libpathappend "$PROJ4_DIR/lib"
 MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install"
 …
 CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install"
 pathappend "$CMAKE_DIR/bin"
+pathprepend "$CMAKE_DIR/bin"
 SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install"
 …
 HDF5_DIR="$ISSM_DIR/externalpackages/hdf5/install"
+dylibpathappend "$HDF5_DIR/lib"
+libpathappend "$HDF5_DIR/lib"
 if [ -d "$HDF5_DIR" ]; then
-        dylibpathappend "$HDF5_DIR/lib"
-        libpathappend "$HDF5_DIR/lib"
         export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib"
         export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include"
 fi
-#NETCDF
 NETCDF_DIR="$ISSM_DIR/externalpackages/netcdf/install"
+pathappend "$NETCDF_DIR/bin"
+dylibpathappend "$NETCDF_DIR/lib"
+libpathappend "$NETCDF_DIR/lib"
 if [ -d "$NETCDF_DIR" ]; then
-        export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$NETCDF_DIR/lib"
-        export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$NETCDF_DIR/lib"
         export LIBRARY_PATH="$LIBRARY_PATH:$NETCDF_DIR/lib"
+        dylibpathappend "$NETCDF_DIR/lib"
+        libpathappend "$NETCDF_DIR/lib"
         export C_INCLUDE_PATH="$C_INCLUDE_PATH:$NETCDF_DIR/include"
 fi
+#SVN
+NETCDF_CXX_DIR="$ISSM_DIR/externalpackages/netcdf-cxx/install"
+libpathappend "$NETCDF_CXX_DIR/lib"
 SVN_DIR="$ISSM_DIR/externalpackages/svn/install"
+if [ -d "$SVN_DIR" ]; then
+        pathprepend   "$SVN_DIR/bin"
+        libpathappend "$SVN_DIR/lib"
+fi
+pathprepend   "$SVN_DIR/bin"
+libpathappend "$SVN_DIR/lib"
 APR_DIR="$ISSM_DIR/externalpackages/apr/install"
+if [ -d "$APR_DIR" ]; then
+        pathappend    "$APR_DIR/bin"
+        libpathappend "$APR_DIR/lib"
+fi
+pathappend    "$APR_DIR/bin"
+libpathappend "$APR_DIR/lib"
 APR_UTIL_DIR="$ISSM_DIR/externalpackages/apr-util/install"
 …
 SWIG_DIR="$ISSM_DIR/externalpackages/swig/install"
 pathappend   "$SWIG_DIR"
+#AUX-CONFIG
+pathappend   "$ISSM_DIR/aux-config"

issm/trunk/externalpackages

Property svn:ignore

-              old
+              new
+archive
+MITgcm
+OpenAD
+ivins
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/adic

Property svn:ignore

-              old
+              new
+source
+build
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/adic/tests
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/adolc

Property svn:ignore

-              old
+              new
+trunk
 adolc_issm
-adolc_v220_issm
-trunk
 *.gz
+install*
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+src-*
+configure.sh
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/adolc/install-update-dev.sh

r14310	r15396
10	10
11	11	#symlink:
12		ln -s ~~/u/astrid-r1b/larour~~/issm-uci/trunk-jpl/externalpackages/adolc/adolc_issm ./adolc_issm
	12	ln -s /proj/ice/larour2/issm-uci/trunk-jpl/externalpackages/adolc/adolc_issm ./adolc_issm
13	13
14	14	#update and compile

issm/trunk/externalpackages/android

Property svn:ignore

-              old
+              new
+arm-linux*
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/android/android-emulators

Property svn:ignore

-              old
+              new
+Android-*
+android-4.1
+*.img
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/android/android-ndk

Property svn:ignore

-              old
+              new
+android-ndk-r*
+*.bz2
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/android/android-sdk

Property svn:ignore

-              old
+              new
+install-sdk*
+*.gz
 *.zip
+install-sdk
+install-ant
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/android/android-sdk/install.sh

-              r13975
+              r15396
         # Cleanup the install
         rm -rf install-sdk
+        rm -rf install
         # Download from ISSM server
 …
         # Move to install
         mv -f android-sdk-macosx install-sdk
+        mv -f android-sdk-macosx install
         # Post_install configuration:
 …
         # Note: API 16, API 15 and 14 correspond to Android 4.1, 4.0.3 and 4.0 respectively.
         cd install-sdk/tools/ && source ./android update sdk -t platform-tool,${api_levels},system-image --no-ui
+        cd install/tools/ && source ./android update sdk -t platform-tool,${api_levels},system-image --no-ui
 fi
 …
         # Here we delete the Android-4.0.3 device if it already exists.
         cd $present_dir/install-sdk/tools
+        cd $present_dir/install/tools
     if [ -e $ANDROID_DIR/android-emulators/$default_droid ]
 …
     # a terminal in our device.
         cd $present_dir/install-sdk/tools
+        cd $present_dir/install/tools
         ./emulator -avd $default_droid -sdcard $ANDROID_DIR/android-emulators/$sd_card.img &
 …
 if [[ $step == "4" || $step == "0" ]]; then
         rm -rf install-sdk
+        rm -rf install
 fi

issm/trunk/externalpackages/angel

Property svn:ignore

-              old
+              new
+angel
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/appscan

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+logs
+logs1
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/appscan/bin
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/appscan/utils
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/apr

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+*.gz
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/apr-util

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+*.gz
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/aspell

Property svn:ignore

-              old
+              new
+src
+dicts*
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
-dicts
-*.gz
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/autotools

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+*.gz
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/bbftp

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/blas

Property svn:ignore

-              old
+              new
+*.tgz
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+install
+*.tgz
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/blas/configs
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/blas/configs/linux64
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/blas/configs/macosx64
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/boost

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/bsdtar
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/canos
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/cccl

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/cccl/issm
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/cccl/issm/cccl

-              r12332
+              r15396
                 *.mex*)
                         opts="$opts -o $1"
+                        opts="$opts /OUT:$1"
                 ;;
 …
         #do nothing
         ;;
+   -I*)
+           include=`echo $1 | sed 's/-I//g'`
+           include=`cygpath -m "$include"`
+           include="/I\"$include\""
+           includeopts="$includeopts $include"
+   ;;
+        -L*)
+                library=`echo $1 | sed 's/-L//g'`
+                library=`cygpath -m $library`
+                string="/link /LIBPATH:\"$library\""
+                opts="$opts $string"
+        ;;
         *)
                 #do nothing
 …
 done
+#Some default options:
+opts="$opts /nologo"
+#echo "$prog $opts"
+exec $prog $opts
+exit 0
+#pass all our processing through the echo command, so we are sure that the string has no quirk,
+#and that once passed by exec to cl, everything works fine.
+command=`echo "$prog "$includeopts" $opts /nologo"`
+exec $command

issm/trunk/externalpackages/chaco

Property svn:ignore

-              old
+              new
 *.pdf
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
 .ignore.txt
+old
+*.tar.gz
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/chaco/mex
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/cm_and_cb_utilities
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/cmake

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/colpack

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/cppcheck

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/dace
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/dakota

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+configure.sh
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/dakota/configs
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/dakota/configs/4.2
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/dakota/configs/5.2
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/dem
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/distribute

Property svn:ignore

-              old
+              new
+*.py
 *.gz
+distribute_setup.py
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/doxygen

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/doxygen/install.sh

-              r14067
+              r15396
 #Some cleanup
 rm -rf install src
+mkdir install
 #Download latest version
 …
 #Configure doxygen
 cd install && ./configure --prefix "$ISSM_DIR/externalpackages/doxygen/install"
+cd src && ./configure --prefix "$ISSM_DIR/externalpackages/doxygen/install"
 if [ $# -eq 0 ]; then
         make

issm/trunk/externalpackages/dyson

Property svn:ignore

-              old
+              new
+jplusers.db
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/ec2ami

Property svn:ignore

-              old
+              new
 ec2-ami-tools-*
+*.gz
 *.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/ec2api

Property svn:ignore

-              old
+              new
+ec2-api-tools.zip
+ec2-api-tools-*
+ec2-api-tools*
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/esmf

Property svn:ignore

-              old
+              new
 esmf-gfortran*
 esmf
+esmf*
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/export_fig

Property svn:ignore

-              old
+              new
 .ignore
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/export_fig/license.txt

-              r11995
+              r15396
 All rights reserved.
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
 met:
     * Redistributions of source code must retain the above copyright
+    * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.
     * Redistributions in binary form must reproduce the above copyright
       notice, this list of conditions and the following disclaimer in
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
       the documentation and/or other materials provided with the distribution
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.

issm/trunk/externalpackages/export_fig/print2eps.m

-              r14310
+              r15396
 %   options - Additional parameter strings to be passed to print.
 % Copyright (C) Oliver Woodford 2008-2012
+% Copyright (C) Oliver Woodford 2008-2013
 % The idea of editing the EPS file to change line styles comes from Jiro
 …
 %           sizes we don't want, due to listeners. Thanks to Malcolm Hudson
 %           for reporting the issue.
+% 22/03/13: Extend font swapping to axes labels. Thanks to Rasmus Ischebeck
+%           for reporting the issue.
 function print2eps(name, fig, varargin)
 …
 end
 % Find all the used fonts in the figure
 font_handles = findobj(fig, '-property', 'FontName');
+font_handles = findall(fig, '-property', 'FontName');
 fonts = get(font_handles, 'FontName');
 if ~iscell(fonts)

issm/trunk/externalpackages/export_fig/user_string.m

-              r10635
+              r15396
 %   saved - Boolean indicating whether the save was succesful
 % Copyright (C) Oliver Woodford 2011
+% Copyright (C) Oliver Woodford 2011-2013
 % This method of saving paths avoids changing .m files which might be in a
 …
 % the version control system. Thank you to Jonas Dorn for suggesting this
 % approach.
+% 10/01/2013 - Access files in text, not binary mode, as latter can cause
+% errors. Thanks to Christian for pointing this out.
 function string = user_string(string_name, string)
 …
     end
     % Write the file
     fid = fopen(string_name, 'w');
+    fid = fopen(string_name, 'wt');
     if fid == -1
         string = false;
 …
     end
     try
         fwrite(fid, string, '*char');
+        fprintf(fid, '%s', string);
     catch
         fclose(fid);
 …
 else
     % Get string
     fid = fopen(string_name, 'r');
+    fid = fopen(string_name, 'rt');
     if fid == -1
         string = '';
         return
     end
     string = fread(fid, '*char')';
+    string = fgetl(fid);
     fclose(fid);
 end

issm/trunk/externalpackages/findbugs
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/flaim

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/freetype

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/gdal

Property svn:ignore

-              old
+              new
 *.gz
+install*
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/gdal/configs
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/geos5
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/gfortran
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/git

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+*.gz
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/gmake

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/gmp

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+*.bz2
+*.tar
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/googleearthtoolbox

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/graphviz

Property svn:ignore

-              old
+              new
+install*
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+configure.sh
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/gsl

Property svn:ignore

-              old
+              new
 install-macosx*
+install-*
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/gsl/install-android.sh

-              r14310
+              r15396
     cd src
+    mv ./../Makefile.am.patch ./
+    patch Makefile.am < Makefile.am.patch
+    patch Makefile.am < ./../Makefile.am.patch
     autoreconf -i
+    autoreconf -if
     ./configure \

issm/trunk/externalpackages/gslib
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/h5py

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/hdf5

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+*.gz
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/howatmask
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/ipython

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+src-*
+*.gz
+install
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/kml

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
 license.txt
+myKML.kml
+kml_shapefile.m
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/lapack

Property svn:ignore

-              old
+              new
 *.tgz
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/lapack/configs
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/lapack/configs/linux64
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/lapack/configs/macosx64
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/latex2rtf

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+cfg
+latex2rtf-2.0.0
+.ignore.txt
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/libermate

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/libpng

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+install
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/m2html

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/matlab

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/matlab/install.sh

-              r13395
+              r15396
 set -eu
+#Erase symlink
+rm -rf install
+if [ ! -h install ];
+then
+        echo "  ****************************************************************"
+        echo "  *                                                              *"
+        echo "  * you need create a symbolic link from matlab's root directory *"
+        echo "  *                                                              *"
+        echo "  * First, you need to locate matlab's root directory            *"
+        echo "  * The easiest way to find it is to launch matlab and run the   *"
+        echo "  * following command: matlabroot                                *"
+        echo "  * Then, create a symbolic link using the command 'ln -s ' the  *"
+        echo "  * target directory should be named 'install'                   *"
+        echo "  *                                                              *"
+        echo "  * Examples:                                                    *"
+        echo "  *    ln -s /usr/local/matlab712/ install                       *"
+        echo "  *    ln -s /Applications/MATLAB_R2012a.app/ install            *"
+        echo "  *                                                              *"
+        echo "  * run ./install.sh again to check that the link is correct     *"
+        echo "  *                                                              *"
+        echo "  ****************************************************************"
+else
+#Select or create a new simlink
+#ln -s /usr/local/pkgs/matlab-7.6/ install
+#ln -s /discover/vis/mathworks/matlab_r2011b/ install
+#ln -s /usr/local/matlab704/ install
+#ln -s /usr/local/matlab711/ install
+ln -s /usr/local/matlab712/ install
+# Macintosh (OSX) simlink
+#ln -s /Applications/MATLAB_R2008a/ install
+#ln -s /Applications/MATLAB_R2009a.app/ install
+#ln -s /Applications/MATLAB_R2010a.app/ install
+#ln -s /Applications/MATLAB_R2012a.app/ install
+#ln -s /Applications/MATLAB_R2011a.app/ install
+#ln -s /Applications/MATLAB*.app/ install
+        #Read link
+        DIR=$(readlink install)
+        if [ -d $DIR ]
+        then
+                echo "Symbolic link correctly set"
+        else
+                rm -rf install
+                echo "Incorrect symbolic link:"
+                echo "provided target ($DIR) does not exist or is not a directory"
+        fi
+fi

issm/trunk/externalpackages/matplotlib

Property svn:ignore

-              old
+              new
+src-*
+matplotlib
+deps*
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+install
+matplotlib
 deps
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/mercurial

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/metis

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/metis/configs
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/altix64
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/cosmos
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/discover
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/greenplanet
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/linux64
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/macosx32
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/macosx64
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/pleiades
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/win32
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/metis/configs/4.0/win7
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/mitgcm
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/modelE

Property svn:ignore

-              old
+              new
+raid1
+cmrun
+exec
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+configs
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/modules

Property svn:ignore

-              old
+              new
+modules-*
+modules*
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/ncview

Property svn:ignore

-              old
+              new
+genoverlay*
 *.gz
+udunits.tar
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+genoverlay
+README
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/netcdf

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
-install-*
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/netcdf-python

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+*.gz
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/nose

Property svn:ignore

-              old
+              new
 *.gz
+py3k
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+src-*
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/numpy

Property svn:ignore

-              old
+              new
-scipy
-scipy-*
-numpy
 numpy-*
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/octave

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/oofem
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/openanalysis

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+openanalysis
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/openssl
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/openssl/install.sh

r13807	r15396
15	15	#Configure openssl
16	16	cd src
17		./config --prefix="$ISSM_DIR/externalpackages/openssl/install"
	17	./config --prefix="$ISSM_DIR/externalpackages/openssl/install" shared
18	18	if [ $# -eq 0 ]; then
19	19	make

issm/trunk/externalpackages/packagemaker

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/pcre

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+*.gz
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/petsc

Property svn:ignore

-              old
+              new
+install-3.2
+install-dev
+*.tgz
+petscinstall-*
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
-install-3.1
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/petsc/configs
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/petsc/configs/3.1
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/petsc/configs/3.1/win7
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/petsc/install-3.1-macosx32-mathieu.sh

-              r13395
+              r15396
  --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
  --PETSC_ARCH=macosx-gnu \
  --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
+ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
  --with-debugging=0 \
  --with-shared=0 \
 …
  --download-f-blas-lapack=yes \
  --download-plapack=yes \
  --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -arch i386" \
+ --FFLAGS="-I$ISSM_DIR/externalpackages/mpich/install/include -arch i386" \
  --COPTFLAGS="-march=opteron -O2 -arch i386" \
  --FOPTFLAGS="-march=opteron -O2 -arch i386" \

issm/trunk/externalpackages/petsc/install-3.1-macosx32-ogive.sh

-              r13395
+              r15396
         --prefix="$ISSM_DIR/externalpackages/petsc/install" \
         --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
         --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
+        --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
         --PETSC_ARCH=macosx-gnu \
         --with-fc=/usr/local/bin/gfortran \
 …
         --FOPTFLAGS="-march=opteron -O2 " \
         --CXXOPTFLAGS="-march=opteron -O2 " \
         --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran "
+        --FFLAGS="-I$ISSM_DIR/externalpackages/mpich/install/include -L$ISSM_DIR/externalpackages/mpich/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran "
 #Compile petsc and install it

issm/trunk/externalpackages/petsc/install-3.1-ubuntu64.sh

-              r13395
+              r15396
 ./config/configure.py \
  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
  --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
+ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
  --PETSC_ARCH=linux-gnu\
  --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 …
  --download-f-blas-lapack=yes \
  --download-parmetis=yes \
  --FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \
+ --FFLAGS=-I$ISSM_DIR/externalpackages/mpich/install/include \
  --download-plapack=yes \
  --COPTFLAGS="-O2" \

issm/trunk/externalpackages/petsc/install-3.1-win7.sh

-              r13395
+              r15396
 # --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 # --PETSC_ARCH=macosx-gnu \
 # --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
+# --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
 # --with-debugging=0 \
 # --with-shared=0 \
 …
 # --download-f-blas-lapack=yes \
 # --download-plapack=yes \
 # --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -arch i386" \
+# --FFLAGS="-I$ISSM_DIR/externalpackages/mpich/install/include -arch i386" \
 # --COPTFLAGS="-march=opteron -O2 -arch i386" \
 # --FOPTFLAGS="-march=opteron -O2 -arch i386" \

issm/trunk/externalpackages/petsc/install-3.2-linux64.sh

r13395	r15396
18	18	./config/configure.py \
19	19	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
20		--with-mpi-dir=~~$ISSM_DIR/externalpackages/mpich2/install~~ \
	20	--with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \
21	21	--with-clanguage=C++ \
22	22	--PETSC_ARCH=linux-gnu-amd64 \

issm/trunk/externalpackages/petsc/install-3.2-macosx64.sh

r13395	r15396
20	20	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
21	21	--PETSC_ARCH="macosx-gnu" \
22		--with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \
	22	--with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \
23	23	--with-debugging=0 \
24	24	--with-shared-libraries=1 \

issm/trunk/externalpackages/petsc/install-3.3-linux64.sh

-              r13395
+              r15396
 #Some cleanup
 rm -rf install petsc-3.3-p2 src
+rm -rf install petsc-3.3-p6 src
 mkdir install src
 #Download from ISSM server
 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p2.tar.gz' 'petsc-3.3-p2.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p6.tar.gz' 'petsc-3.3-p6.tar.gz'
 #Untar and move petsc to install directory
 tar -zxvf  petsc-3.3-p2.tar.gz
 mv petsc-3.3-p2/* src/
 rm -rf petsc-3.3-p2
+tar -zxvf  petsc-3.3-p6.tar.gz
+mv petsc-3.3-p6/* src/
+rm -rf petsc-3.3-p6
 #configure
 …
 ./config/configure.py \
         --prefix="$ISSM_DIR/externalpackages/petsc/install" \
         --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
+        --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
         --PETSC_ARCH=linux-gnu-amd64 \
         --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \

issm/trunk/externalpackages/petsc/install-3.3-macosx64.sh

-              r13395
+              r15396
 #Some cleanup
 rm -rf install petsc-3.3-p2 src
+rm -rf install petsc-3.3-p6 src
 mkdir install src
 #Download from ISSM server
 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p2.tar.gz' 'petsc-3.3-p2.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p6.tar.gz' 'petsc-3.3-p6.tar.gz'
 #Untar and move petsc to install directory
 tar -zxvf  petsc-3.3-p2.tar.gz
 mv petsc-3.3-p2/* src/
 rm -rf petsc-3.3-p2
+tar -zxvf  petsc-3.3-p6.tar.gz
+mv petsc-3.3-p6/* src/
+rm -rf petsc-3.3-p6
 #configure
 …
 ./config/configure.py \
         --prefix="$ISSM_DIR/externalpackages/petsc/install" \
         --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
+        --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
         --PETSC_ARCH="macosx-gnu" \
         --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 …
         --download-plapack=yes \
         --download-parmetis=yes \
+        --download-metis=yes
+        --download-metis=yes \
+        --with-debugging=yes
 #Compile petsc and install it

issm/trunk/externalpackages/petsc/install-3.3-pleiades.sh

-              r13975
+              r15396
 #Some cleanup
 rm -rf install petsc-3.3-p2 src
+rm -rf install petsc-3.3-p6 src
 mkdir install src
 #Download from ISSM server
 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p2.tar.gz' 'petsc-3.3-p2.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p6.tar.gz' 'petsc-3.3-p6.tar.gz'
 #Untar and move petsc to install directory
 tar -zxvf  petsc-3.3-p2.tar.gz
 mv petsc-3.3-p2/* src/
 rm -rf petsc-3.3-p2
+tar -zxvf  petsc-3.3-p6.tar.gz
+mv petsc-3.3-p6/* src/
+rm -rf petsc-3.3-p6
 #configure
 …
 ./config/configure.py \
  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
- --with-batch=1  \
  --PETSC_ARCH="$ISSM_ARCH" \
  --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+ --with-batch=1  \
  --with-debugging=0 \
  --with-shared-libraries=1 \
  --known-mpi-shared-libraries=1 \
  --with-mpi=1 \
+ --with-mpi-lib=/nasa/sgi/mpt/2.06a67/lib/libmpi.so \
+ --with-mpi-include=/nasa/sgi/mpt/2.06a67/include  \
+ --download-blas=yes \
+ --download-f-blas-lapack=yes \
+ --download-mumps=yes \
+ --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
+ --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
+ --with-blas-lapack-dir="/nasa/intel/Compiler/2013.1.117/composer_xe_2013.1.117/mkl/lib/intel64" \
  --download-scalapack=yes \
  --download-blacs=yes \
  --download-plapack=no \
+ --download-mumps=yes \
  --download-metis=yes \
  --download-parmetis=yes \
 …
  --download-euclid=yes \
  --download-hypre=yes \
- --with-cxx=icc \
- --with-fc=ifort \
  --COPTFLAGS="-lmpi -O3" \
  --FOPTFLAGS="-lmpi -O3" \
 …
 . /usr/share/modules/init/bash
+module load comp-intel/2012.0.032
+module load mpi-sgi/mpt.2.06a67
+module load math/intel_mkl_64_10.0.011
+module load comp-intel/2013.1.117
+module load mpi-sgi/mpt.2.06rp16
 export PATH="$PATH:."

issm/trunk/externalpackages/petsc/install-3.3-walgreen.sh

-              r13975
+              r15396
 #!/bin/bash
 ##Some cleanup
 #rm -rf install petsc-3.3-p2 src
 #mkdir install src
+#
 ##Download from ISSM server
 #$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p2.tar.gz' 'petsc-3.3-p2.tar.gz'
+#
 ##Untar and move petsc to install directory
 #tar -zxvf  petsc-3.3-p2.tar.gz
 #mv petsc-3.3-p2/* src/
+#rm -rf petsc-3.3-p2
+#Some cleanup
+rm -rf install petsc-3.3-p6 src
+mkdir install src
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p6.tar.gz' 'petsc-3.3-p6.tar.gz'
+#Untar and move petsc to install directory
+tar -zxvf  petsc-3.3-p6.tar.gz
+mv petsc-3.3-p6/* src/
+rm -rf petsc-3.3-p6
 #configure
 …
  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
  --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
  --with-debugging=0 \
  --with-shared-libraries=1 \
  --with-blas-lapack-dir=/opt/intel/mkl/10.0.1.014/ \
- --known-mpi-shared-libraries=1 \
- --with-mpi=1 \
  --download-mumps=yes \
  --download-blacs=yes  \
  --download-blas=yes \
  --download-f-blas-lapack=yes \
+ --download-scalapack=yes \
  --download-parmetis=yes \
  --download-metis=yes \
- --download-trilinos=yes \
- --download-euclid=yes \
- --download-spai=yes \
  --download-superlu=yes \
+ --download-hypre=yes \
+ --download-prometheus=yes \
+ --with-cc=/opt/mpich/ch-p4/bin/mpicc \
+ --with-cxx=/opt/mpich/ch-p4/bin/mpicxx \
+ --with-fc=/opt/mpich/ch-p4/bin/mpif90 \
+ --COPTFLAGS="-I/opt/mpich/ch-p4/include/ -lmpich -O3" \
+ --FOPTFLAGS="-I/opt/mpich/ch-p4/include/ -lmpich -O3" \
+ --CXXOPTFLAGS="-I/opt/mpich/ch-p4/include/ -lmpich -O3"
+ #--download-hypre=yes
+#Compile petsc and install it
+make
+make install

issm/trunk/externalpackages/petsc/install-dev-linux64.sh

-              r13975
+              r15396
 if [ $STEP -eq 1 ]; then
-        # Adapted from petsc 3.2.
         # Used Mercurial to get code
         rm -rf src
 …
         ./config/configure.py \
         --prefix="$ISSM_DIR/externalpackages/petsc/install" \
         --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \
+        --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \
         --with-clanguage=C++ \
         --PETSC_ARCH=linux-gnu-amd64 \

issm/trunk/externalpackages/polygonclipper
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/pyclips

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/pysvn

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/python

Property svn:ignore

-              old
+              new
+*.txt
+install-*
+install
+install-python*
+*.tgz
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install*
 src
+*.tgz
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/python/patches
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/qhull
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/rats

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/readline

Property svn:ignore

-              old
+              new
 *.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
 src
+src-*
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/rose

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
-build
-source
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/satstress

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/scipy

Property svn:ignore

-              old
+              new
+numpy
 scipy
+scipy-*
+numpy
+numpy-*
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/scotch

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/scotch/install.sh

-              r13975
+              r15396
 tar -xvzf scotch_5.1.6.tar.gz
+# Apply patches (all at once, since many)
+# (written by diff -rc old_src new_src > scotch.patch)
+patch -p0 < scotch.patch
 # Move scotch to src directory
 mv scotch_5.1/* src
 rm -rf scotch_5.1
-# Apply patches (all at once, since many)
-# (written by diff -rc old_src new_src > scotch.patch)
-patch -p0 < scotch.patch
 # Build scotch

issm/trunk/externalpackages/scotch/mex
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/scotch/scotch.patch

-              r4705
+              r15396
 Only in new5: bin
 Only in new5: include
 Only in new5: lib
 diff -rc src/src/libscotch/arch.c new5/src/libscotch/arch.c
 *** src/src/libscotch/arch.c    2008-09-27 07:48:01.000000000 -0700
 --- new5/src/libscotch/arch.c   2010-07-21 17:13:15.583257119 -0700
+Only in src: bin
+Only in src: include
+Only in src: lib
+diff -crB scotch_5.1/src/libscotch/arch.c src/src/libscotch/arch.c
+*** scotch_5.1/src/libscotch/arch.c     2008-09-27 07:48:01.000000000 -0700
+--- src/src/libscotch/arch.c    2013-05-06 14:14:11.000000000 -0700
 ***************
 *** 173,187 ****
 …
         memset     (archptr, 0, sizeof (Arch));     /* Initialize architecture body */
         return     (1);
 diff -rc src/src/libscotch/arch_cmplt.c new5/src/libscotch/arch_cmplt.c
 *** src/src/libscotch/arch_cmplt.c      2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_cmplt.c     2010-07-21 17:13:15.585257133 -0700
+diff -crB scotch_5.1/src/libscotch/arch_cmplt.c src/src/libscotch/arch_cmplt.c
+*** scotch_5.1/src/libscotch/arch_cmplt.c       2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_cmplt.c      2013-05-06 14:14:11.000000000 -0700
 ***************
 *** 90,99 ****
 …
       return     (1);
+    }
 diff -rc src/src/libscotch/arch_cmplt.h new5/src/libscotch/arch_cmplt.h
 *** src/src/libscotch/arch_cmplt.h      2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_cmplt.h     2010-07-21 17:13:15.588257154 -0700
+diff -crB scotch_5.1/src/libscotch/arch_cmplt.h src/src/libscotch/arch_cmplt.h
+*** scotch_5.1/src/libscotch/arch_cmplt.h       2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_cmplt.h      2013-05-06 14:14:11.000000000 -0700
 ***************
 *** 87,93 ****
 …
   #define archCmpltArchFree           NULL
   ArchDomNum                  archCmpltDomNum     (const ArchCmplt * const, const ArchCmpltDom * const);
 diff -rc src/src/libscotch/arch_cmpltw.c new5/src/libscotch/arch_cmpltw.c
 *** src/src/libscotch/arch_cmpltw.c     2008-08-27 14:22:22.000000000 -0700
 --- new5/src/libscotch/arch_cmpltw.c    2010-07-21 17:13:15.590257168 -0700
+diff -crB scotch_5.1/src/libscotch/arch_cmpltw.c src/src/libscotch/arch_cmpltw.c
+*** scotch_5.1/src/libscotch/arch_cmpltw.c      2008-08-27 14:22:22.000000000 -0700
+--- src/src/libscotch/arch_cmpltw.c     2013-05-06 14:14:12.000000000 -0700
 ***************
 *** 200,211 ****
 …
         return     (1);
+      }
 diff -rc src/src/libscotch/arch_cmpltw.h new5/src/libscotch/arch_cmpltw.h
 *** src/src/libscotch/arch_cmpltw.h     2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_cmpltw.h    2010-07-21 17:13:15.592257181 -0700
+diff -crB scotch_5.1/src/libscotch/arch_cmpltw.h src/src/libscotch/arch_cmpltw.h
+*** scotch_5.1/src/libscotch/arch_cmpltw.h      2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_cmpltw.h     2013-05-06 14:14:12.000000000 -0700
 ***************
 *** 86,92 ****
 …
   int                         archCmpltwArchFree  (ArchCmpltw * restrict const);
   ArchDomNum                  archCmpltwDomNum    (const ArchCmpltw * const, const ArchCmpltwDom * const);
 diff -rc src/src/libscotch/arch_deco.c new5/src/libscotch/arch_deco.c
 *** src/src/libscotch/arch_deco.c       2008-09-28 06:35:27.000000000 -0700
 --- new5/src/libscotch/arch_deco.c      2010-07-21 17:13:15.595257202 -0700
+diff -crB scotch_5.1/src/libscotch/arch_deco.c src/src/libscotch/arch_deco.c
+*** scotch_5.1/src/libscotch/arch_deco.c        2008-09-28 06:35:27.000000000 -0700
+--- src/src/libscotch/arch_deco.c       2013-05-06 14:14:12.000000000 -0700
 ***************
 *** 211,217 ****
 …
     if ((sizeof (ArchDeco)    > sizeof (ArchDummy)) ||
         (sizeof (ArchDecoDom) > sizeof (ArchDomDummy))) {
 diff -rc src/src/libscotch/arch_deco.h new5/src/libscotch/arch_deco.h
 *** src/src/libscotch/arch_deco.h       2008-09-27 07:49:46.000000000 -0700
 --- new5/src/libscotch/arch_deco.h      2010-07-21 17:13:15.597257216 -0700
+diff -crB scotch_5.1/src/libscotch/arch_deco.h src/src/libscotch/arch_deco.h
+*** scotch_5.1/src/libscotch/arch_deco.h        2008-09-27 07:49:46.000000000 -0700
+--- src/src/libscotch/arch_deco.h       2013-05-06 14:14:13.000000000 -0700
 ***************
 *** 113,119 ****
 …
   int                         archDecoArchFree    (ArchDeco * const);
   Anum                        archDecoArchSize    (ArchDeco * const, const Anum);
 diff -rc src/src/libscotch/arch.h new5/src/libscotch/arch.h
 *** src/src/libscotch/arch.h    2009-04-28 08:11:27.000000000 -0700
 --- new5/src/libscotch/arch.h   2010-07-21 17:13:15.600257237 -0700
+diff -crB scotch_5.1/src/libscotch/arch.h src/src/libscotch/arch.h
+*** scotch_5.1/src/libscotch/arch.h     2009-04-28 08:11:27.000000000 -0700
+--- src/src/libscotch/arch.h    2013-05-06 14:14:13.000000000 -0700
 ***************
 *** 175,181 ****
 …
   char *                      archName            (const Arch * const);
   const ArchClass *           archClass           (const char * const);
 diff -rc src/src/libscotch/arch_hcub.c new5/src/libscotch/arch_hcub.c
 *** src/src/libscotch/arch_hcub.c       2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_hcub.c      2010-07-21 17:13:15.602257251 -0700
+diff -crB scotch_5.1/src/libscotch/arch_hcub.c src/src/libscotch/arch_hcub.c
+*** scotch_5.1/src/libscotch/arch_hcub.c        2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_hcub.c       2013-05-06 14:14:13.000000000 -0700
 ***************
 *** 88,95 ****
 …
   ArchHcub * restrict const   archptr,
 ! FILE * restrict const       stream)
 ! {
+  {
   #ifdef SCOTCH_DEBUG_ARCH1
     if ((sizeof (ArchHcub)    > sizeof (ArchDummy)) ||
 …
 ! #endif /* NOFILEIO */
 !                                    )
 ! {
 ! #ifdef NOFILEIO
 ! //  printf("archHcubArchLoad - napar=%d,archpar=%p\n",napar,archpar);
 ! #endif /* NOFILEIO */
+!
+  {
++ #ifdef NOFILEIO
++ //  printf("archHcubArchLoad - napar=%d,archpar=%p\n",napar,archpar);
++ #endif /* NOFILEIO */
++
   #ifdef SCOTCH_DEBUG_ARCH1
     if ((sizeof (ArchHcub)    > sizeof (ArchDummy)) ||
 …
       errorPrint ("archHcubArchLoad: bad input");
       return     (1);
 diff -rc src/src/libscotch/arch_hcub.h new5/src/libscotch/arch_hcub.h
 *** src/src/libscotch/arch_hcub.h       2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_hcub.h      2010-07-21 17:13:15.604257265 -0700
+diff -crB scotch_5.1/src/libscotch/arch_hcub.h src/src/libscotch/arch_hcub.h
+*** scotch_5.1/src/libscotch/arch_hcub.h        2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_hcub.h       2013-05-06 14:14:14.000000000 -0700
 ***************
 *** 85,91 ****
 …
   #define archHcubArchFree            NULL
   ArchDomNum                  archHcubDomNum      (const ArchHcub * const, const ArchHcubDom * const);
 diff -rc src/src/libscotch/arch_mesh.c new5/src/libscotch/arch_mesh.c
 *** src/src/libscotch/arch_mesh.c       2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_mesh.c      2010-07-21 17:13:15.607257286 -0700
+diff -crB scotch_5.1/src/libscotch/arch_mesh.c src/src/libscotch/arch_mesh.c
+*** scotch_5.1/src/libscotch/arch_mesh.c        2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_mesh.c       2013-05-06 14:14:14.000000000 -0700
 ***************
 *** 96,103 ****
 …
       return     (1);
+    }
 diff -rc src/src/libscotch/arch_mesh.h new5/src/libscotch/arch_mesh.h
 *** src/src/libscotch/arch_mesh.h       2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_mesh.h      2010-07-21 17:13:15.610257307 -0700
+diff -crB scotch_5.1/src/libscotch/arch_mesh.h src/src/libscotch/arch_mesh.h
+*** scotch_5.1/src/libscotch/arch_mesh.h        2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_mesh.h       2013-05-06 14:14:14.000000000 -0700
 ***************
 *** 96,102 ****
 …
   #define archMesh3ArchFree           NULL
   ArchDomNum                  archMesh3DomNum     (const ArchMesh3 * const, const ArchMesh3Dom * const);
 diff -rc src/src/libscotch/arch_tleaf.c new5/src/libscotch/arch_tleaf.c
 *** src/src/libscotch/arch_tleaf.c      2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_tleaf.c     2010-07-21 17:13:15.612257320 -0700
+diff -crB scotch_5.1/src/libscotch/arch_tleaf.c src/src/libscotch/arch_tleaf.c
+*** scotch_5.1/src/libscotch/arch_tleaf.c       2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_tleaf.c      2013-05-06 14:14:14.000000000 -0700
 ***************
 *** 92,99 ****
 …
   ArchTleaf * restrict const  archptr,
 ! FILE * restrict const       stream)
 ! {
+  {
   #ifdef SCOTCH_DEBUG_ARCH1
     if ((sizeof (ArchTleaf)    > sizeof (ArchDummy)) ||
 …
 ! #endif /* NOFILEIO */
 !                                    )
 ! {
 ! #ifdef NOFILEIO
 ! //  printf("archTleafArchLoad - napar=%d,archpar=%p\n",napar,archpar);
 ! #endif /* NOFILEIO */
+!
+  {
++ #ifdef NOFILEIO
++ //  printf("archTleafArchLoad - napar=%d,archpar=%p\n",napar,archpar);
++ #endif /* NOFILEIO */
++
   #ifdef SCOTCH_DEBUG_ARCH1
     if ((sizeof (ArchTleaf)    > sizeof (ArchDummy)) ||
 …
       return     (1);
+    }
 diff -rc src/src/libscotch/arch_tleaf.h new5/src/libscotch/arch_tleaf.h
 *** src/src/libscotch/arch_tleaf.h      2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_tleaf.h     2010-07-21 17:13:15.615257341 -0700
+diff -crB scotch_5.1/src/libscotch/arch_tleaf.h src/src/libscotch/arch_tleaf.h
+*** scotch_5.1/src/libscotch/arch_tleaf.h       2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_tleaf.h      2013-05-06 14:14:15.000000000 -0700
 ***************
 *** 89,95 ****
 …
   #define archTleafArchFree           NULL
   ArchDomNum                  archTleafDomNum     (const ArchTleaf * const, const ArchTleafDom * const);
 diff -rc src/src/libscotch/arch_torus.c new5/src/libscotch/arch_torus.c
 *** src/src/libscotch/arch_torus.c      2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_torus.c     2010-07-21 17:13:15.618257362 -0700
+diff -crB scotch_5.1/src/libscotch/arch_torus.c src/src/libscotch/arch_torus.c
+*** scotch_5.1/src/libscotch/arch_torus.c       2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_torus.c      2013-05-06 14:14:15.000000000 -0700
 ***************
 *** 90,97 ****
 …
       return     (1);
+    }
 diff -rc src/src/libscotch/arch_torus.h new5/src/libscotch/arch_torus.h
 *** src/src/libscotch/arch_torus.h      2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/arch_torus.h     2010-07-21 17:13:15.620257376 -0700
+diff -crB scotch_5.1/src/libscotch/arch_torus.h src/src/libscotch/arch_torus.h
+*** scotch_5.1/src/libscotch/arch_torus.h       2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/arch_torus.h      2013-05-06 14:14:15.000000000 -0700
 ***************
 *** 96,102 ****
 …
   #define archTorus3ArchFree          NULL
   ArchDomNum                  archTorus3DomNum    (const ArchTorus3 * const, const ArchTorus3Dom * const);
 diff -rc src/src/libscotch/common.c new5/src/libscotch/common.c
 *** src/src/libscotch/common.c  2008-05-22 06:44:41.000000000 -0700
 --- new5/src/libscotch/common.c 2010-07-21 17:13:15.622257390 -0700
+diff -crB scotch_5.1/src/libscotch/common.c src/src/libscotch/common.c
+*** scotch_5.1/src/libscotch/common.c   2008-05-22 06:44:41.000000000 -0700
+--- src/src/libscotch/common.c  2013-05-06 14:14:15.000000000 -0700
 ***************
 *** 100,106 ****
 …
 + #endif /* MATLAB */
+  }
 diff -rc src/src/libscotch/common.h new5/src/libscotch/common.h
 *** src/src/libscotch/common.h  2009-02-06 14:20:55.000000000 -0800
 --- new5/src/libscotch/common.h 2010-07-21 17:15:06.061025001 -0700
+diff -crB scotch_5.1/src/libscotch/common.h src/src/libscotch/common.h
+*** scotch_5.1/src/libscotch/common.h   2009-02-06 14:20:55.000000000 -0800
+--- src/src/libscotch/common.h  2013-05-09 11:49:35.317220518 -0700
 ***************
 *** 1,3 ****
 …
 --- 109,114 ----
+***************
+*** 171,179 ****
+  /** The file structure. **/
+  typedef struct File_ {
+!   char *                    name;                 /*+ File name    +*/
+    FILE *                    pntr;                 /*+ File pointer +*/
+!   char *                    mode;                 /*+ Opening mode +*/
+  } File;
+  /*
+--- 172,180 ----
+  /** The file structure. **/
+  typedef struct File_ {
+!   const char *              name;                 /*+ File name    +*/
+    FILE *                    pntr;                 /*+ File pointer +*/
+!   const char *              mode;                 /*+ Opening mode +*/
+  } File;
+  /*
 ***************
 *** 190,216 ****
 …
++
 + #endif //#ifndef _SCOTCH_COMMON_H_
 diff -rc src/src/libscotch/common_integer.c new5/src/libscotch/common_integer.c
 *** src/src/libscotch/common_integer.c  2009-01-21 01:32:32.000000000 -0800
 --- new5/src/libscotch/common_integer.c 2010-07-21 17:13:15.628257432 -0700
+diff -crB scotch_5.1/src/libscotch/common_integer.c src/src/libscotch/common_integer.c
+*** scotch_5.1/src/libscotch/common_integer.c   2009-01-21 01:32:32.000000000 -0800
+--- src/src/libscotch/common_integer.c  2013-05-06 14:14:16.000000000 -0700
 ***************
 *** 191,196 ****
 …
   /*********************/
 diff -rc src/src/libscotch/common_memory.c new5/src/libscotch/common_memory.c
 *** src/src/libscotch/common_memory.c   2009-01-03 02:16:11.000000000 -0800
 --- new5/src/libscotch/common_memory.c  2010-07-21 17:13:15.630257445 -0700
+diff -crB scotch_5.1/src/libscotch/common_memory.c src/src/libscotch/common_memory.c
+*** scotch_5.1/src/libscotch/common_memory.c    2009-01-03 02:16:11.000000000 -0800
+--- src/src/libscotch/common_memory.c   2013-05-06 14:14:16.000000000 -0700
 ***************
 *** 87,93 ****
 …
+  }
   #endif /* COMMON_MEMORY_TRACE */
 diff -rc src/src/libscotch/dummysizes.c new5/src/libscotch/dummysizes.c
 *** src/src/libscotch/dummysizes.c      2009-05-09 16:08:02.000000000 -0700
 --- new5/src/libscotch/dummysizes.c     2010-07-21 17:13:15.633257466 -0700
+diff -crB scotch_5.1/src/libscotch/dummysizes.c src/src/libscotch/dummysizes.c
+*** scotch_5.1/src/libscotch/dummysizes.c       2009-05-09 16:08:02.000000000 -0700
+--- src/src/libscotch/dummysizes.c      2013-05-06 14:14:16.000000000 -0700
 ***************
 *** 267,271 ****
 …
 + #endif /* MATLAB */
+  }
 diff -rc src/src/libscotch/graph.c new5/src/libscotch/graph.c
 *** src/src/libscotch/graph.c   2008-05-22 06:44:42.000000000 -0700
 --- new5/src/libscotch/graph.c  2010-07-21 17:13:15.635257480 -0700
+diff -crB scotch_5.1/src/libscotch/graph.c src/src/libscotch/graph.c
+*** scotch_5.1/src/libscotch/graph.c    2008-05-22 06:44:42.000000000 -0700
+--- src/src/libscotch/graph.c   2013-05-06 14:14:17.000000000 -0700
 ***************
 *** 135,141 ****
 …
       if ((grafptr->edlotax != NULL) &&
           ((grafptr->flagval & GRAPHEDGEGROUP) == 0))
 diff -rc src/src/libscotch/graph.h new5/src/libscotch/graph.h
 *** src/src/libscotch/graph.h   2008-06-01 02:49:11.000000000 -0700
 --- new5/src/libscotch/graph.h  2010-07-21 17:13:15.637257494 -0700
+diff -crB scotch_5.1/src/libscotch/graph.h src/src/libscotch/graph.h
+*** scotch_5.1/src/libscotch/graph.h    2008-06-01 02:49:11.000000000 -0700
+--- src/src/libscotch/graph.h   2013-05-06 14:14:17.000000000 -0700
 ***************
 *** 159,165 ****
 …
   int                         graphSave           (const Graph * const, FILE * const);
   Gnum                        graphBase           (Graph * const, const Gnum);
 diff -rc src/src/libscotch/graph_io.c new5/src/libscotch/graph_io.c
 *** src/src/libscotch/graph_io.c        2008-05-22 06:44:42.000000000 -0700
 --- new5/src/libscotch/graph_io.c       2010-07-21 17:13:15.639257508 -0700
+diff -crB scotch_5.1/src/libscotch/graph_io.c src/src/libscotch/graph_io.c
+*** scotch_5.1/src/libscotch/graph_io.c 2008-05-22 06:44:42.000000000 -0700
+--- src/src/libscotch/graph_io.c        2013-05-06 14:14:17.000000000 -0700
 ***************
 *** 86,92 ****
 …
+    }
 diff -rc src/src/libscotch/graph_io_scot.c new5/src/libscotch/graph_io_scot.c
 *** src/src/libscotch/graph_io_scot.c   2008-05-22 06:44:42.000000000 -0700
 --- new5/src/libscotch/graph_io_scot.c  2010-07-21 17:13:15.641257522 -0700
+diff -crB scotch_5.1/src/libscotch/graph_io_scot.c src/src/libscotch/graph_io_scot.c
+*** scotch_5.1/src/libscotch/graph_io_scot.c    2008-05-22 06:44:42.000000000 -0700
+--- src/src/libscotch/graph_io_scot.c   2013-05-06 14:14:17.000000000 -0700
 ***************
 *** 89,95 ****
 …
+    }
 diff -rc src/src/libscotch/library_arch.c new5/src/libscotch/library_arch.c
 *** src/src/libscotch/library_arch.c    2008-05-22 06:44:42.000000000 -0700
 --- new5/src/libscotch/library_arch.c   2010-07-21 17:13:15.643257536 -0700
+diff -crB scotch_5.1/src/libscotch/library_arch.c src/src/libscotch/library_arch.c
+*** scotch_5.1/src/libscotch/library_arch.c     2008-05-22 06:44:42.000000000 -0700
+--- src/src/libscotch/library_arch.c    2013-05-06 14:14:17.000000000 -0700
 ***************
 *** 120,128 ****
 …
   /*+ This routine saves the given opaque
 diff -rc src/src/libscotch/library_arch_f.c new5/src/libscotch/library_arch_f.c
 *** src/src/libscotch/library_arch_f.c  2008-05-22 06:44:42.000000000 -0700
 --- new5/src/libscotch/library_arch_f.c 2010-07-21 17:13:15.645257550 -0700
+diff -crB scotch_5.1/src/libscotch/library_arch_f.c src/src/libscotch/library_arch_f.c
+*** scotch_5.1/src/libscotch/library_arch_f.c   2008-05-22 06:44:42.000000000 -0700
+--- src/src/libscotch/library_arch_f.c  2013-05-06 14:14:18.000000000 -0700
 ***************
 *** 121,127 ****
 …
     fclose (stream);                                /* This closes filenum too */
 diff -rc src/src/libscotch/library_error_exit.c new5/src/libscotch/library_error_exit.c
 *** src/src/libscotch/library_error_exit.c      2009-01-20 00:36:33.000000000 -0800
 --- new5/src/libscotch/library_error_exit.c     2010-07-21 17:13:15.648257570 -0700
+diff -crB scotch_5.1/src/libscotch/library_error_exit.c src/src/libscotch/library_error_exit.c
+*** scotch_5.1/src/libscotch/library_error_exit.c       2009-01-20 00:36:33.000000000 -0800
+--- src/src/libscotch/library_error_exit.c      2013-05-06 14:14:18.000000000 -0700
 ***************
 *** 114,119 ****
 …
 + #endif /* MATLAB */
+  }
 diff -rc src/src/libscotch/library_graph.c new5/src/libscotch/library_graph.c
 *** src/src/libscotch/library_graph.c   2008-05-22 07:28:12.000000000 -0700
 --- new5/src/libscotch/library_graph.c  2010-07-21 17:13:15.650257584 -0700
+diff -crB scotch_5.1/src/libscotch/library_graph.c src/src/libscotch/library_graph.c
+*** scotch_5.1/src/libscotch/library_graph.c    2008-05-22 07:28:12.000000000 -0700
+--- src/src/libscotch/library_graph.c   2013-05-06 14:14:18.000000000 -0700
 ***************
 *** 137,143 ****
 …
   /*+ This routine saves the contents of the given
 diff -rc src/src/libscotch/library_graph_f.c new5/src/libscotch/library_graph_f.c
 *** src/src/libscotch/library_graph_f.c 2008-05-22 06:44:43.000000000 -0700
 --- new5/src/libscotch/library_graph_f.c        2010-07-21 17:13:15.652257598 -0700
+diff -crB scotch_5.1/src/libscotch/library_graph_f.c src/src/libscotch/library_graph_f.c
+*** scotch_5.1/src/libscotch/library_graph_f.c  2008-05-22 06:44:43.000000000 -0700
+--- src/src/libscotch/library_graph_f.c 2013-05-06 14:14:18.000000000 -0700
 ***************
 *** 136,142 ****
 …
     fclose (stream);                                /* This closes filenum too */
 diff -rc src/src/libscotch/library_graph_map.c new5/src/libscotch/library_graph_map.c
 *** src/src/libscotch/library_graph_map.c       2008-09-28 04:04:05.000000000 -0700
 --- new5/src/libscotch/library_graph_map.c      2010-07-21 17:13:15.654257612 -0700
+diff -crB scotch_5.1/src/libscotch/library_graph_map.c src/src/libscotch/library_graph_map.c
+*** scotch_5.1/src/libscotch/library_graph_map.c        2008-09-28 04:04:05.000000000 -0700
+--- src/src/libscotch/library_graph_map.c       2013-05-06 14:14:19.000000000 -0700
 ***************
 *** 182,192 ****
 …
   /*+ This routine computes a mapping
 diff -rc src/src/libscotch/library_graph_map_f.c new5/src/libscotch/library_graph_map_f.c
 *** src/src/libscotch/library_graph_map_f.c     2008-06-28 03:44:26.000000000 -0700
 --- new5/src/libscotch/library_graph_map_f.c    2010-07-21 17:13:15.656257626 -0700
+diff -crB scotch_5.1/src/libscotch/library_graph_map_f.c src/src/libscotch/library_graph_map_f.c
+*** scotch_5.1/src/libscotch/library_graph_map_f.c      2008-06-28 03:44:26.000000000 -0700
+--- src/src/libscotch/library_graph_map_f.c     2013-05-06 14:14:19.000000000 -0700
 ***************
 *** 183,189 ****
 …
     fclose (stream);                                /* This closes filenum too */
 diff -rc src/src/libscotch/library.h new5/src/libscotch/library.h
 *** src/src/libscotch/library.h 2009-05-09 16:08:03.000000000 -0700
 --- new5/src/libscotch/library.h        2010-07-21 17:13:15.660257654 -0700
+diff -crB scotch_5.1/src/libscotch/library.h src/src/libscotch/library.h
+*** scotch_5.1/src/libscotch/library.h  2009-05-09 16:08:03.000000000 -0700
+--- src/src/libscotch/library.h 2013-05-06 14:14:19.000000000 -0700
 ***************
 *** 1,3 ****
 …
++
 + #endif //#ifndef _SCOTCH_H_
 diff -rc src/src/libscotch/Makefile new5/src/libscotch/Makefile
 *** src/src/libscotch/Makefile  2009-05-09 16:08:04.000000000 -0700
 --- new5/src/libscotch/Makefile 2010-07-21 17:13:15.665257689 -0700
+diff -crB scotch_5.1/src/libscotch/Makefile src/src/libscotch/Makefile
+*** scotch_5.1/src/libscotch/Makefile   2009-05-09 16:08:04.000000000 -0700
+--- src/src/libscotch/Makefile  2013-05-06 14:14:19.000000000 -0700
 ***************
 *** 49,55 ****
 …
 +                                       $(AR) $(ARFLAGS) $(@) $(?)
 +                                       -$(RANLIB) $(@)
 diff -rc src/src/libscotch/mapping.h new5/src/libscotch/mapping.h
 *** src/src/libscotch/mapping.h 2008-10-27 08:27:47.000000000 -0700
 --- new5/src/libscotch/mapping.h        2010-07-21 17:13:15.667257702 -0700
+diff -crB scotch_5.1/src/libscotch/mapping.h src/src/libscotch/mapping.h
+*** scotch_5.1/src/libscotch/mapping.h  2008-10-27 08:27:47.000000000 -0700
+--- src/src/libscotch/mapping.h 2013-05-06 14:14:20.000000000 -0700
 ***************
 *** 106,112 ****
 …
   #undef static
 diff -rc src/src/libscotch/mapping_io.c new5/src/libscotch/mapping_io.c
 *** src/src/libscotch/mapping_io.c      2008-05-22 06:44:43.000000000 -0700
 --- new5/src/libscotch/mapping_io.c     2010-07-21 17:13:15.670257723 -0700
+diff -crB scotch_5.1/src/libscotch/mapping_io.c src/src/libscotch/mapping_io.c
+*** scotch_5.1/src/libscotch/mapping_io.c       2008-05-22 06:44:43.000000000 -0700
+--- src/src/libscotch/mapping_io.c      2013-05-06 14:14:20.000000000 -0700
 ***************
 *** 199,204 ****
 …
     return (0);
+  }
 diff -rc src/src/libscotch/mesh_io_scot.c new5/src/libscotch/mesh_io_scot.c
 *** src/src/libscotch/mesh_io_scot.c    2008-05-22 06:44:43.000000000 -0700
 --- new5/src/libscotch/mesh_io_scot.c   2010-07-21 17:13:15.672257737 -0700
+diff -crB scotch_5.1/src/libscotch/mesh_io_scot.c src/src/libscotch/mesh_io_scot.c
+*** scotch_5.1/src/libscotch/mesh_io_scot.c     2008-05-22 06:44:43.000000000 -0700
+--- src/src/libscotch/mesh_io_scot.c    2013-05-06 14:14:20.000000000 -0700
 ***************
 *** 85,91 ****
 …
+    }
 diff -rc src/src/libscotch/module.h new5/src/libscotch/module.h
 *** src/src/libscotch/module.h  2009-04-26 23:07:14.000000000 -0700
 --- new5/src/libscotch/module.h 2010-07-21 17:13:15.675257758 -0700
+diff -crB scotch_5.1/src/libscotch/module.h src/src/libscotch/module.h
+*** scotch_5.1/src/libscotch/module.h   2009-04-26 23:07:14.000000000 -0700
+--- src/src/libscotch/module.h  2013-05-06 14:14:20.000000000 -0700
 ***************
 *** 1,3 ****
 …
++
 + #endif //#ifndef _SCOTCH_MODULE_H_
 diff -rc src/src/libscotch/parser_ll.l new5/src/libscotch/parser_ll.l
 *** src/src/libscotch/parser_ll.l       2008-05-22 06:44:43.000000000 -0700
 --- new5/src/libscotch/parser_ll.l      2010-07-21 17:13:15.677257772 -0700
+diff -crB scotch_5.1/src/libscotch/parser_ll.l src/src/libscotch/parser_ll.l
+*** scotch_5.1/src/libscotch/parser_ll.l        2008-05-22 06:44:43.000000000 -0700
+--- src/src/libscotch/parser_ll.l       2013-05-06 14:14:21.000000000 -0700
 ***************
 *** 192,197 ****
 …
     yyrestart (yyin);                               /* (Re-)initialize the parser */
   #endif /* FLEX_SCANNER */
 diff -rc src/src/libscotch/parser_yy.y new5/src/libscotch/parser_yy.y
 *** src/src/libscotch/parser_yy.y       2008-10-22 15:12:48.000000000 -0700
 --- new5/src/libscotch/parser_yy.y      2010-07-21 17:13:15.679257786 -0700
+diff -crB scotch_5.1/src/libscotch/parser_yy.y src/src/libscotch/parser_yy.y
+*** scotch_5.1/src/libscotch/parser_yy.y        2008-10-22 15:12:48.000000000 -0700
+--- src/src/libscotch/parser_yy.y       2013-05-06 14:14:21.000000000 -0700
 ***************
 *** 774,779 ****
 …
     if (stratParserParse2 () != 0) {                /* Parse the strategy string */
       if (parserstratcurr != NULL)
 diff -rc src/src/libscotch/vgraph_separate_vw.c new5/src/libscotch/vgraph_separate_vw.c
 *** src/src/libscotch/vgraph_separate_vw.c      2008-05-22 06:44:43.000000000 -0700
 --- new5/src/libscotch/vgraph_separate_vw.c     2010-07-21 17:13:15.682257807 -0700
+diff -crB scotch_5.1/src/libscotch/vgraph_separate_vw.c src/src/libscotch/vgraph_separate_vw.c
+*** scotch_5.1/src/libscotch/vgraph_separate_vw.c       2008-05-22 06:44:43.000000000 -0700
+--- src/src/libscotch/vgraph_separate_vw.c      2013-05-06 14:14:21.000000000 -0700
 ***************
 *** 83,88 ****
 …
     return (0);
+  }
 diff -rc src/src/Makefile new5/src/Makefile
 *** src/src/Makefile    2008-09-15 05:50:51.000000000 -0700
 --- new5/src/Makefile   2010-07-21 17:13:15.684257821 -0700
+diff -crB scotch_5.1/src/Makefile src/src/Makefile
+*** scotch_5.1/src/Makefile     2008-09-15 05:50:51.000000000 -0700
+--- src/src/Makefile    2013-05-06 14:14:21.000000000 -0700
 ***************
 *** 97,102 ****
 …
                                         -$(CP) -f ../bin/[agm]*$(EXE) $(bindir)
                                         -$(CP) -f ../include/*scotch*.h $(includedir)
 Only in new5/src: Makefile.inc
 diff -rc src/src/scotch/gmap.h new5/src/scotch/gmap.h
 *** src/src/scotch/gmap.h       2008-06-18 11:05:17.000000000 -0700
 --- new5/src/scotch/gmap.h      2010-07-21 17:13:15.686257834 -0700
+Only in src/src: Makefile.inc
+diff -crB scotch_5.1/src/scotch/gmap.h src/src/scotch/gmap.h
+*** scotch_5.1/src/scotch/gmap.h        2008-06-18 11:05:17.000000000 -0700
+--- src/src/scotch/gmap.h       2013-05-06 14:14:22.000000000 -0700
 ***************
 *** 1,3 ****
 …
++
 + #endif //#ifndef _SCOTCH_GMAP_H_
 Only in new5/src/scotch: gmap_mex.c
 Only in new5/src/scotch: gmapx.c
 diff -rc src/src/scotch/Makefile new5/src/scotch/Makefile
 *** src/src/scotch/Makefile     2009-04-27 02:19:43.000000000 -0700
 --- new5/src/scotch/Makefile    2010-07-21 17:13:15.689257855 -0700
+Only in src/src/scotch: gmap_mex.c
+Only in src/src/scotch: gmapx.c
+diff -crB scotch_5.1/src/scotch/Makefile src/src/scotch/Makefile
+*** scotch_5.1/src/scotch/Makefile      2009-04-27 02:19:43.000000000 -0700
+--- src/src/scotch/Makefile     2013-05-06 14:14:22.000000000 -0700
 ***************
 *** 49,59 ****

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issm/trunk/externalpackages/vim/addons/vim/indent
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/vim/addons/vim/plugin
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/vim/addons/vim/plugin/file_line.vim

-              r4230
+              r15396
+" Avoid installing twice or when in unsupported Vim version.
+if exists('g:loaded_file_line') || (v:version < 700)
+        finish
+endif
+let g:loaded_file_line = 1
 function! s:gotoline()
         let file = bufname("%")
-        let names =  matchlist( file, '\(.*\):\(\d\+\)')
+        if len(names) != 0 && filereadable(names[1])
+        " :e command calls BufRead even though the file is a new one.
+        " As a workarround Jonas Pfenniger<jonas@pfenniger.name> added an
+        " AutoCmd BufRead, this will test if this file actually exists before
+        " searching for a file and line to goto.
+        if (filereadable(file))
+                return
+        endif
+        " Accept file:line:column: or file:line:column and file:line also
+        let nocol = 0
+        let names =  matchlist( file, '\(.\{-1,}\):\%(\(\d\+\)\%(:\(\d*\):\?\)\?\)\?$')
+        if empty(names)
+                "no column provided maybe?
+                let names =  matchlist( file, '\(.*\):\(\d\+\)')
+                let nocol = 1
+                if empty(names)
+                        return
+                endif
+        endif
+        let file_name =  names[1]
+        let line_num  =  names[2] == ''? '0' : names[2]
+        let  col_num  = (names[3] == '' && !nocol) ? '0' : names[3]
+        if filereadable(file_name)
                 let l:bufn = bufnr("%")
+                exec ":e " . names[1]
+                exec ":" . names[2]
+                exec ":bdelete " . l:bufn
+                if foldlevel(names[2]) > 0
+                        exec ":foldopen!"
+                exec ":bwipeout " l:bufn
+                exec "keepalt edit " . file_name
+                exec ":" . line_num
+                exec "normal! " . col_num . '|'
+                if foldlevel(line_num) > 0
+                        exec "normal! zv"
                 endif
+                exec "normal! zz"
         endif
 endfunction
 autocmd! BufNewFile *:* nested call s:gotoline()
+autocmd! BufRead *:* nested call s:gotoline()

issm/trunk/externalpackages/vim/addons/vim/syntax
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/vim/addons/vim/syntax/Synchronize.sh

-              r13395
+              r15396
 cat c.vim | sed "/ISSM's Enums begin/,/vim: ts=8/d" > temp
 echo "\"ISSM's Enums begin" >> temp
 cat ../../../../../src/c/EnumDefinitions/EnumDefinitions.h | grep -e "[0-9]Enum," -e "[a-z]Enum," -e "[A-Z]Enum," | grep -v StringToEnum | sed -e "s/,//g" | awk '{ printf "syn keyword cConstant " $1 "\n"}' >> temp
+cat ../../../../../src/c/shared/Enum/EnumDefinitions.h | grep -e "[0-9]Enum," -e "[a-z]Enum," -e "[A-Z]Enum," | grep -v StringToEnum | sed -e "s/,//g" | awk '{ printf "syn keyword cConstant " $1 "\n"}' >> temp
 echo "\"ISSM's Enums end" >> temp
 cat c.vim | sed "1,/ISSM's Enums end/d" >> temp
 mv temp c.vim
-exit 1
 #Synchronize objects
 cat c.vim | sed "/ISSM's objects begin/,/vim: ts=8/d" > temp
 echo "\"ISSM's objects begin" >> temp
 find ../../../../../src/c/classes -name "*.h" | sed -e "s/\// /g" -e "s/\.h//"| awk '{print  $(NF)}' | awk '{ printf "syn keyword cType " $1 "\n"}'>> temp
+find ../../../../../src/c/classes -name "*.cpp" | sed -e "s/\// /g" -e "s/\.cpp//"| awk '{print  $(NF)}' | awk '{ printf "syn keyword cType " $1 "\n"}'>> temp
 echo "\"ISSM's objects end" >> temp
 cat c.vim | sed "1,/ISSM's objects end/d" >> temp

issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim

-              r13975
+              r15396
 "   please try to keep the alphabetical ordering                                                                    "
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-"ISSM containers:
-syn keyword     cType           Constraints DataSet Elements Inputs Loads Materials Nodes Parameters Results Vertices Options
 "Petsc
 syn keyword     cType           Vec Mat SeqVec SeqMat
 "other ISSM's syntax
+syn keyword     cType           mxArray ErrorException QuadtreeBox IssmDouble IssmPDouble Observations
+syn keyword     cType           mxArray ErrorException QuadtreeBox
+syn keyword     cType           IssmDouble IssmPDouble
 "ISSM's objects begin
+syn keyword cType GaussPenta
+syn keyword cType gaussobjects
+syn keyword cType GaussTria
+syn keyword cType objects
+syn keyword cType Material
+syn keyword cType Matdamageice
+syn keyword cType Materials
 syn keyword cType Matice
 syn keyword cType Matpar
+syn keyword cType objects
+syn keyword cType Contour
+syn keyword cType DoubleInput
+syn keyword cType Input
+syn keyword cType DofIndexing
+syn keyword cType IntVecParam
+syn keyword cType BoolParam
+syn keyword cType IntMatParam
+syn keyword cType DoubleTransientMatParam
+syn keyword cType StringParam
+syn keyword cType DoubleVecParam
+syn keyword cType DoubleMatParam
+syn keyword cType FileParam
+syn keyword cType Parameters
+syn keyword cType DataSetParam
+syn keyword cType IntParam
+syn keyword cType VectorParam
+syn keyword cType MatrixParam
+syn keyword cType StringArrayParam
+syn keyword cType TransientParam
+syn keyword cType DoubleParam
+syn keyword cType DoubleMatArrayParam
+syn keyword cType ExponentialVariogram
+syn keyword cType PowerVariogram
+syn keyword cType Quadtree
+syn keyword cType Observations
+syn keyword cType GaussianVariogram
+syn keyword cType SphericalVariogram
+syn keyword cType Observation
+syn keyword cType RiftStruct
+syn keyword cType OptionUtilities
+syn keyword cType Options
+syn keyword cType Penpair
+syn keyword cType Loads
+syn keyword cType Icefront
+syn keyword cType Friction
+syn keyword cType Riftfront
+syn keyword cType Numericalflux
+syn keyword cType Pengrid
+syn keyword cType Contours
+syn keyword cType Vertex
+syn keyword cType ElementMatrix
+syn keyword cType ElementVector
+syn keyword cType Profiler
+syn keyword cType Results
+syn keyword cType PentaP1ElementResult
+syn keyword cType DoubleElementResult
+syn keyword cType BoolElementResult
+syn keyword cType TriaP1ElementResult
+syn keyword cType Elements
+syn keyword cType TriaHook
+syn keyword cType PentaHook
+syn keyword cType Tria
+syn keyword cType Penta
+syn keyword cType TriaRef
+syn keyword cType PentaRef
+syn keyword cType GaussTria
+syn keyword cType GaussPenta
+syn keyword cType DependentObject
+syn keyword cType Patch
+syn keyword cType Hook
 syn keyword cType ControlInput
 syn keyword cType DatasetInput
 syn keyword cType IntInput
 syn keyword cType BoolInput
 syn keyword cType TriaP1Input
+syn keyword cType Inputs
 syn keyword cType TransientInput
 syn keyword cType PentaP1Input
+syn keyword cType KML_Icon
+syn keyword cType KML_Point
+syn keyword cType KML_LinearRing
+syn keyword cType KML_Feature
+syn keyword cType KMLFileReadUtils
+syn keyword cType KML_StyleSelector
+syn keyword cType KML_LatLonBox
+syn keyword cType KML_Attribute
+syn keyword cType KML_PolyStyle
+syn keyword cType KML_Object
+syn keyword cType KML_SubStyle
+syn keyword cType KML_LineString
+syn keyword cType KML_Overlay
+syn keyword cType KML_Container
+syn keyword cType KML_Polygon
+syn keyword cType KML_Geometry
+syn keyword cType KML_ColorStyle
+syn keyword cType KML_Placemark
+syn keyword cType KML_Unknown
+syn keyword cType KML_GroundOverlay
+syn keyword cType KML_Style
+syn keyword cType KML_Comment
+syn keyword cType KML_MultiGeometry
+syn keyword cType KML_LineStyle
+syn keyword cType KML_Folder
+syn keyword cType KML_Document
+syn keyword cType KML_File
+syn keyword cType DoubleVecParam
+syn keyword cType DoubleParam
+syn keyword cType DoubleMatArrayParam
+syn keyword cType DoubleMatParam
+syn keyword cType Param
+syn keyword cType FileParam
+syn keyword cType IntVecParam
+syn keyword cType IntParam
+syn keyword cType BoolParam
+syn keyword cType IntMatParam
+syn keyword cType VectorParam
+syn keyword cType DoubleTransientMatParam
+syn keyword cType MatrixParam
+syn keyword cType StringArrayParam
+syn keyword cType StringParam
+syn keyword cType TransientParam
+syn keyword cType OptionStruct
+syn keyword cType OptionDouble
+syn keyword cType OptionLogical
+syn keyword cType OptionUtilities
+syn keyword cType OptionChar
+syn keyword cType Option
+syn keyword cType OptionCell
+syn keyword cType Segment
+syn keyword cType Icefront
+syn keyword cType Friction
+syn keyword cType Riftfront
+syn keyword cType Numericalflux
+syn keyword cType Penpair
+syn keyword cType Load
+syn keyword cType Pengrid
+syn keyword cType Object
+syn keyword cType DoubleVecExternalResult
+syn keyword cType DoubleExternalResult
+syn keyword cType IntExternalResult
+syn keyword cType BoolExternalResult
+syn keyword cType DoubleMatExternalResult
+syn keyword cType PetscVecExternalResult
+syn keyword cType ExternalResult
+syn keyword cType StringExternalResult
+syn keyword cType Vertex
+syn keyword cType DoubleInput
+syn keyword cType TriaInput
+syn keyword cType Constraints
 syn keyword cType SpcDynamic
 syn keyword cType SpcStatic
 syn keyword cType SpcTransient
+syn keyword cType Constraint
+syn keyword cType TriaP1ElementResult
+syn keyword cType PentaP1ElementResult
+syn keyword cType DoubleElementResult
+syn keyword cType ElementResultLocal
+syn keyword cType BoolElementResult
+syn keyword cType ElementResult
+syn keyword cType Nodes
+syn keyword cType IndependentObject
+syn keyword cType Vertices
 syn keyword cType Node
-syn keyword cType TriaRef
-syn keyword cType TriaHook
-syn keyword cType PentaRef
-syn keyword cType PentaHook
-syn keyword cType Tria
-syn keyword cType Element
-syn keyword cType Penta
-syn keyword cType classes
-syn keyword cType DofIndexing
-syn keyword cType Patch
-syn keyword cType Hook
-syn keyword cType Quadtree
-syn keyword cType Observation
-syn keyword cType ExponentialVariogram
-syn keyword cType GaussianVariogram
-syn keyword cType SphericalVariogram
-syn keyword cType PowerVariogram
-syn keyword cType krigingobjects
-syn keyword cType Variogram
-syn keyword cType DakotaPlugin
-syn keyword cType ElementVector
-syn keyword cType ElementMatrix
-syn keyword cType matrixobjects
-syn keyword cType Vector
-syn keyword cType Matrix
-syn keyword cType GeomSubDomain
-syn keyword cType Geometry
-syn keyword cType AdjacentTriangle
-syn keyword cType VertexOnEdge
-syn keyword cType BamgQuadtree
-syn keyword cType Edge
-syn keyword cType BamgVertex
-syn keyword cType SetOfE4
-syn keyword cType GeomEdge
-syn keyword cType Direction
-syn keyword cType VertexOnGeom
-syn keyword cType R2
-syn keyword cType Mesh
-syn keyword cType ListofIntersectionTriangles
-syn keyword cType Triangle
-syn keyword cType DoubleAndInt
-syn keyword cType VertexOnVertex
-syn keyword cType BamgOpts
-syn keyword cType BamgGeom
-syn keyword cType bamgobjects
-syn keyword cType CrackedEdge
-syn keyword cType SubDomain
-syn keyword cType BamgMesh
-syn keyword cType Metric
-syn keyword cType include
-syn keyword cType typedefs
-syn keyword cType Curve
-syn keyword cType macros
-syn keyword cType GeomVertex
-syn keyword cType OptArgs
-syn keyword cType Update
-syn keyword cType OptPars
 syn keyword cType IoModel
 syn keyword cType FemModel
 …
 syn keyword cConstant DiagnosticVertexPairingEnum
 syn keyword cConstant DiagnosticViscosityOvershootEnum
+syn keyword cConstant LoadingforceXEnum
+syn keyword cConstant LoadingforceYEnum
+syn keyword cConstant LoadingforceZEnum
 syn keyword cConstant FlowequationBordermacayealEnum
 syn keyword cConstant FlowequationBorderpattynEnum
 …
 syn keyword cConstant FrictionQEnum
 syn keyword cConstant GeometryHydrostaticRatioEnum
+syn keyword cConstant HydrologyCREnum
+syn keyword cConstant HydrologyKnEnum
+syn keyword cConstant HydrologyNEnum
+syn keyword cConstant HydrologyPEnum
+syn keyword cConstant HydrologyQEnum
+syn keyword cConstant HydrologySpcwatercolumnEnum
+syn keyword cConstant HydrologyStabilizationEnum
+syn keyword cConstant HydrologyModelEnum
+syn keyword cConstant HydrologyshreveEnum
+syn keyword cConstant HydrologyshreveCREnum
+syn keyword cConstant HydrologyshreveKnEnum
+syn keyword cConstant HydrologyshreveNEnum
+syn keyword cConstant HydrologyshrevePEnum
+syn keyword cConstant HydrologyshreveQEnum
+syn keyword cConstant HydrologyshreveSpcwatercolumnEnum
+syn keyword cConstant HydrologyshreveStabilizationEnum
+syn keyword cConstant HydrologydcEnum
+syn keyword cConstant SedimentHeadEnum
+syn keyword cConstant SedimentHeadOldEnum
+syn keyword cConstant SedimentHeadResidualEnum
+syn keyword cConstant EplHeadEnum
+syn keyword cConstant EplHeadOldEnum
+syn keyword cConstant HydrologydcRelTolEnum
+syn keyword cConstant HydrologydcSpcsedimentHeadEnum
+syn keyword cConstant HydrologydcSedimentCompressibilityEnum
+syn keyword cConstant HydrologydcSedimentPorosityEnum
+syn keyword cConstant HydrologydcSedimentThicknessEnum
+syn keyword cConstant HydrologydcSedimentTransmitivityEnum
+syn keyword cConstant HydrologydcWaterCompressibilityEnum
+syn keyword cConstant HydrologydcSpceplHeadEnum
+syn keyword cConstant HydrologydcMaskEplactiveEnum
+syn keyword cConstant HydrologydcEplCompressibilityEnum
+syn keyword cConstant HydrologydcEplPorosityEnum
+syn keyword cConstant HydrologydcEplThicknessEnum
+syn keyword cConstant HydrologydcEplTransmitivityEnum
+syn keyword cConstant HydrologydcIsefficientlayerEnum
+syn keyword cConstant HydrologydcSedimentlimitFlagEnum
+syn keyword cConstant HydrologydcSedimentlimitEnum
+syn keyword cConstant HydrologydcTransferFlagEnum
+syn keyword cConstant HydrologydcLeakageFactorEnum
+syn keyword cConstant HydrologydcPenaltyFactorEnum
+syn keyword cConstant HydrologyLayerEnum
+syn keyword cConstant HydrologySedimentEnum
+syn keyword cConstant HydrologyEfficientEnum
+syn keyword cConstant HydrologySedimentKmaxEnum
+syn keyword cConstant BasisIntegralEnum
+syn keyword cConstant WaterTransferEnum
 syn keyword cConstant IndependentObjectEnum
 syn keyword cConstant InversionControlParametersEnum
-syn keyword cConstant InversionCostFunctionEnum
 syn keyword cConstant InversionCostFunctionThresholdEnum
 syn keyword cConstant InversionCostFunctionsCoefficientsEnum
 …
 syn keyword cConstant MaterialsThermalExchangeVelocityEnum
 syn keyword cConstant MaterialsThermalconductivityEnum
+syn keyword cConstant MaterialsLithosphereShearModulusEnum
+syn keyword cConstant MaterialsLithosphereDensityEnum
+syn keyword cConstant MaterialsMantleShearModulusEnum
+syn keyword cConstant MaterialsMantleDensityEnum
 syn keyword cConstant MeshAverageVertexConnectivityEnum
 syn keyword cConstant MeshDimensionEnum
 …
 syn keyword cConstant SurfaceforcingsMassBalanceEnum
 syn keyword cConstant SurfaceforcingsIspddEnum
+syn keyword cConstant SurfaceforcingsDesfacEnum
+syn keyword cConstant SurfaceforcingsS0pEnum
 syn keyword cConstant SurfaceforcingsIssmbgradientsEnum
 syn keyword cConstant SurfaceforcingsMonthlytemperaturesEnum
-syn keyword cConstant SurfaceforcingsHcEnum
 syn keyword cConstant SurfaceforcingsHrefEnum
 syn keyword cConstant SurfaceforcingsSmbrefEnum
-syn keyword cConstant SurfaceforcingsSmbPosMaxEnum
-syn keyword cConstant SurfaceforcingsSmbPosMinEnum
-syn keyword cConstant SurfaceforcingsAPosEnum
 syn keyword cConstant SurfaceforcingsBPosEnum
-syn keyword cConstant SurfaceforcingsANegEnum
 syn keyword cConstant SurfaceforcingsBNegEnum
 syn keyword cConstant ThermalMaxiterEnum
 …
 syn keyword cConstant ThermalStabilizationEnum
 syn keyword cConstant ThermalIsenthalpyEnum
+syn keyword cConstant GiaMantleViscosityEnum
+syn keyword cConstant GiaLithosphereThicknessEnum
 syn keyword cConstant ThicknessEnum
 syn keyword cConstant TimesteppingStartTimeEnum
 …
 syn keyword cConstant TransientIsprognosticEnum
 syn keyword cConstant TransientIsthermalEnum
+syn keyword cConstant TransientIsgiaEnum
 syn keyword cConstant TransientNumRequestedOutputsEnum
 syn keyword cConstant TransientRequestedOutputsEnum
 …
 syn keyword cConstant AdjointSolutionEnum
 syn keyword cConstant AnalysisCounterEnum
+syn keyword cConstant NoneAnalysisEnum
+syn keyword cConstant DefaultAnalysisEnum
 syn keyword cConstant BalancethicknessAnalysisEnum
 syn keyword cConstant BalancethicknessSolutionEnum
+syn keyword cConstant WeakBalancethicknessAnalysisEnum
+syn keyword cConstant WeakBalancethicknessSolutionEnum
 syn keyword cConstant BedSlopeAnalysisEnum
 syn keyword cConstant BedSlopeSolutionEnum
 …
 syn keyword cConstant FlaimAnalysisEnum
 syn keyword cConstant FlaimSolutionEnum
+syn keyword cConstant HydrologyAnalysisEnum
+syn keyword cConstant HydrologyShreveAnalysisEnum
+syn keyword cConstant HydrologyDCInefficientAnalysisEnum
+syn keyword cConstant HydrologyDCEfficientAnalysisEnum
 syn keyword cConstant HydrologySolutionEnum
 syn keyword cConstant MeltingAnalysisEnum
-syn keyword cConstant NoneAnalysisEnum
 syn keyword cConstant PrognosticAnalysisEnum
 syn keyword cConstant PrognosticSolutionEnum
 …
 syn keyword cConstant ThermalSolutionEnum
 syn keyword cConstant TransientSolutionEnum
+syn keyword cConstant GiaSolutionEnum
+syn keyword cConstant GiaAnalysisEnum
 syn keyword cConstant ApproximationEnum
 syn keyword cConstant NoneApproximationEnum
 …
 syn keyword cConstant MaterialsEnum
 syn keyword cConstant NodesEnum
+syn keyword cConstant ContoursEnum
 syn keyword cConstant ParametersEnum
 syn keyword cConstant VerticesEnum
 …
 syn keyword cConstant IntVecParamEnum
 syn keyword cConstant TransientParamEnum
+syn keyword cConstant IceFrontTypeEnum
 syn keyword cConstant MacAyeal2dIceFrontEnum
 syn keyword cConstant MacAyeal3dIceFrontEnum
 …
 syn keyword cConstant NodeEnum
 syn keyword cConstant NumericalfluxEnum
+syn keyword cConstant NumericalfluxTypeEnum
 syn keyword cConstant ParamEnum
 syn keyword cConstant L1L2IceFrontEnum
 …
 syn keyword cConstant ProfilerEnum
 syn keyword cConstant MatrixParamEnum
+syn keyword cConstant NodeSIdEnum
 syn keyword cConstant VectorParamEnum
 syn keyword cConstant RiftfrontEnum
+syn keyword cConstant RiftfrontTypeEnum
 syn keyword cConstant SegmentEnum
 syn keyword cConstant SegmentRiftfrontEnum
 …
 syn keyword cConstant StringParamEnum
 syn keyword cConstant TriaEnum
 syn keyword cConstant TriaP1InputEnum
+syn keyword cConstant TriaInputEnum
 syn keyword cConstant VertexEnum
+syn keyword cConstant VertexPIdEnum
+syn keyword cConstant VertexSIdEnum
 syn keyword cConstant AirEnum
 syn keyword cConstant IceEnum
 …
 syn keyword cConstant AdjointyEnum
 syn keyword cConstant AdjointzEnum
+syn keyword cConstant BalancethicknessMisfitEnum
 syn keyword cConstant BedSlopeXEnum
 syn keyword cConstant BedSlopeYEnum
 …
 syn keyword cConstant ConstantEnum
 syn keyword cConstant ConvergedEnum
-syn keyword cConstant ExtToIuEnum
 syn keyword cConstant FillEnum
 syn keyword cConstant FractionIncrementEnum
 …
 syn keyword cConstant GroundinglineMeltingRateEnum
 syn keyword cConstant InternalEnum
-syn keyword cConstant IuToExtEnum
 syn keyword cConstant MassFluxEnum
 syn keyword cConstant MaxPenetrationEnum
 …
 syn keyword cConstant QmuSurfaceEnum
 syn keyword cConstant QmuMeltingEnum
+syn keyword cConstant AndroidFrictionCoefficientEnum
 syn keyword cConstant ResetPenaltiesEnum
 syn keyword cConstant SegmentOnIceShelfEnum
 …
 syn keyword cConstant TemperatureOldEnum
 syn keyword cConstant TemperaturePicardEnum
-syn keyword cConstant TemperatureSurfaceEnum
-syn keyword cConstant TemperatureBasalEnum
 syn keyword cConstant ThicknessAbsMisfitEnum
-syn keyword cConstant TypeEnum
 syn keyword cConstant VelEnum
 syn keyword cConstant VelocityEnum
 …
 syn keyword cConstant DragCoefficientAbsGradientEnum
 syn keyword cConstant TransientInputEnum
-syn keyword cConstant OutputfilenameEnum
 syn keyword cConstant WaterfractionEnum
 syn keyword cConstant WatercolumnEnum
 …
 syn keyword cConstant StressTensoryzEnum
 syn keyword cConstant StressTensorzzEnum
+syn keyword cConstant GiaCrossSectionShapeEnum
+syn keyword cConstant GiadWdtEnum
+syn keyword cConstant GiaWEnum
 syn keyword cConstant P0Enum
 syn keyword cConstant P1Enum
 syn keyword cConstant P1DGEnum
+syn keyword cConstant MINIEnum
+syn keyword cConstant P2Enum
 syn keyword cConstant SaveResultsEnum
 syn keyword cConstant BoolElementResultEnum
 …
 syn keyword cConstant DoubleExternalResultEnum
 syn keyword cConstant DoubleMatExternalResultEnum
-syn keyword cConstant DoubleVecExternalResultEnum
 syn keyword cConstant IntExternalResultEnum
 syn keyword cConstant JEnum
 …
 syn keyword cConstant PatchVerticesEnum
 syn keyword cConstant PentaP1ElementResultEnum
-syn keyword cConstant PetscVecExternalResultEnum
 syn keyword cConstant StringExternalResultEnum
 syn keyword cConstant StepEnum
 …
 syn keyword cConstant IceVolumeEnum
 syn keyword cConstant TotalSmbEnum
-syn keyword cConstant RelativeEnum
 syn keyword cConstant AbsoluteEnum
 syn keyword cConstant IncrementalEnum
 …
 syn keyword cConstant NoneEnum
 syn keyword cConstant SoftMigrationEnum
+syn keyword cConstant SubelementMigrationEnum
+syn keyword cConstant SubelementMigration2Enum
+syn keyword cConstant GLlevelsetEnum
 syn keyword cConstant StokesSolverEnum
 syn keyword cConstant AdjointEnum
 …
 syn keyword cConstant OutputFileNameEnum
 syn keyword cConstant LockFileNameEnum
 syn keyword cConstant PetscOptionsAnalysesEnum
 syn keyword cConstant PetscOptionsStringsEnum
+syn keyword cConstant ToolkitsOptionsAnalysesEnum
+syn keyword cConstant ToolkitsOptionsStringsEnum
 syn keyword cConstant QmuErrNameEnum
 syn keyword cConstant QmuInNameEnum
 …
 syn keyword cConstant XYEnum
 syn keyword cConstant XYZPEnum
+syn keyword cConstant DenseEnum
+syn keyword cConstant MpiDenseEnum
+syn keyword cConstant SeqEnum
+syn keyword cConstant MpiEnum
 syn keyword cConstant OptionEnum
 syn keyword cConstant GenericOptionEnum

issm/trunk/externalpackages/vim/addons/vim/xtr
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/vim/addons/vim/xtr/skeleton
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles
issm/trunk/externalpackages/vim/addons/vim/zipfiles
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/vim/addons/vimrc

-              r13975
+              r15396
 " Abbreviations {{{
 " ----------------------------------------------------------------------
 "func Eatchar(pat)
 "       let c = nr2char(getchar())
 "       return (c =~ a:pat) ? '' : c
 "endfunc
 "au BufRead,BufNewFile *.html     iabbr <silent> H1 <h1></h1><Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.html     iabbr <silent> H2 <h2></h2><Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.html     iabbr <silent> H3 <h3></h3><Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.html     iabbr <silent> CO <code></code><Left><Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.html     iabbr <silent> PP <p></p><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.m        iabbr <silent> p1  disp('');<Left><Left><Left><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.m        iab <expr> p0  "disp('-------------- file: ".expand('%')." line: ".line(".")."');"
 "au BufRead,BufNewFile *.c*       iabbr <silent> p1  printf("\n");<Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.c*,*.h   iabbr <silent> ER  _error_("");<Left><Left><Left><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.c*       ab VV VecView(ug,PETSC_VIEWER_STDOUT_WORLD);
 "au BufRead,BufNewFile *.c*       ab AS _assert_();
 "au BufRead,BufNewFile *.c*       iab <expr> p0  "printf(\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);"
 "au BufRead,BufNewFile *.c*       iab <expr> pp0 "PetscSynchronizedPrintf(MPI_COMM_WORLD,\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);\nPetscSynchronizedFlush(MPI_COMM_WORLD);"
 ""tex
 "au BufRead,BufNewFile *.tex iab EQ
 "                       \\begin{equation}
 "                       \<CR>\end{equation}<up><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.tex iab IT
 "                       \\begin{itemize}
 "                       \<CR>\item
 "                       \<CR>\end{itemize}<up><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.tex iab EN
 "                       \\begin{enumerate}
 "                       \<CR>\item
 "                       \<CR>\end{enumerate}<up><C-R>=Eatchar('\s')<CR>
 "au BufRead,BufNewFile *.tex ab (()) \left( \right)
+func Eatchar(pat)
+        let c = nr2char(getchar())
+        return (c =~ a:pat) ? '' : c
+endfunc
+au BufRead,BufNewFile *.html     iabbr <silent> H1 <h1></h1><Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.html     iabbr <silent> H2 <h2></h2><Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.html     iabbr <silent> H3 <h3></h3><Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.html     iabbr <silent> CO <code></code><Left><Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.html     iabbr <silent> PP <p></p><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.m        iabbr <silent> p1  disp('');<Left><Left><Left><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.m        iab <expr> p0  "disp('-------------- file: ".expand('%')." line: ".line(".")."');"
+au BufRead,BufNewFile *.c*       iabbr <silent> p1  printf("\n");<Left><Left><Left><Left><Left><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.c*,*.h   iabbr <silent> ER  _error_("");<Left><Left><Left><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.c*       ab VV VecView(ug,PETSC_VIEWER_STDOUT_WORLD);
+au BufRead,BufNewFile *.c*       ab AS _assert_();
+au BufRead,BufNewFile *.c*       iab <expr> p0  "printf(\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);"
+au BufRead,BufNewFile *.c*       iab <expr> pp0 "PetscSynchronizedPrintf(MPI_COMM_WORLD,\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);\nPetscSynchronizedFlush(MPI_COMM_WORLD);"
+"tex
+au BufRead,BufNewFile *.tex iab EQ
+                        \\begin{equation}
+                        \<CR>\end{equation}<up><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.tex iab IT
+                        \\begin{itemize}
+                        \<CR>\item
+                        \<CR>\end{itemize}<up><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.tex iab EN
+                        \\begin{enumerate}
+                        \<CR>\item
+                        \<CR>\end{enumerate}<up><C-R>=Eatchar('\s')<CR>
+au BufRead,BufNewFile *.tex ab (()) \left( \right)
 "}}}
 " Skeletons {{{

issm/trunk/externalpackages/vim/install.sh

-              r13395
+              r15396
 cd src/src
 ./configure \
+        --prefix "$ISSM_DIR/externalpackages/vim/install" \
+        --with-gcc "/usr/bin/gcc"
+        --prefix="$ISSM_DIR/externalpackages/vim/install" \
+        --with-gcc="/usr/bin/gcc" \
+        --with-tlib="/lib/"
 #Compile vim

issm/trunk/externalpackages/windows
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/windows/README

-              r11995
+              r15396
 We'll try the compile with the Microsoft Windows SDK 7.1: http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=8279
+MPICH2:
+to run in parallel.  First install MPICH2 from www.mpich.org/downloads. Make
+sure the install directory in C:\Program Files\MPICH2, otherwise, ISSM will
+not be able to figure out where the mpi libraries are installed on your windows platform.
+Then fire up smpd in a command line under Administrator privileges:
+smpd -install
+Then:
+mpiexe.exe -remove
+mpiexe.exe -register (type enter for username, for password, type your windows password, do not chose anything else!)
+mpiexe.exe -validate (should return SUCCESS)
+Then you are ready to run parallel.
+To do: how do we document this? Create webpage for all of this. + get a fortran compiler giong!

issm/trunk/externalpackages/windows/configs
- Property svn:ignore set to
  *.gz
  *.zip
  *.a
  *.so
  *.o
  *.la
  *.cmake
  *.cache
  *.exe
  *.in
  *.log
  *.deps
  *.metadata
  install
  src
  CMakeCache.txt
  Makefile
  CMakeFiles

issm/trunk/externalpackages/windows/windows_environment.sh

r12332	r15396
37	37	ISSM_DIR_WIN=`cygpath -m $ISSM_DIR`
38	38	export ISSM_DIR_WIN
	39
	40	#Now source for fortran environment:
	41	#source $ISSM_DIR/externalpackages/windows/fortran_environment.sh

issm/trunk/externalpackages/xaifbooster

Property svn:ignore

-              old
+              new
+xaifBooster
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
+install
+src
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/xerces

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/externalpackages/yams

Property svn:ignore

-              old
+              new
+*.gz
+*.zip
+*.a
+*.so
+*.o
+*.la
+*.cmake
+*.cache
+*.exe
+*.in
+*.log
+*.deps
+*.metadata
 install
 src
+.ignore.txt
+CMakeCache.txt
+Makefile
+CMakeFiles

issm/trunk/m4/issm_options.m4

-              r14310
+              r15396
                         export CXXFLAGS="-DWIN32 -D_INTEL_WIN_"
                 elif  test $VENDOR = intel-win7-32; then
                         export CC=cccl
+                        export CC=cl
                         export CXX=cccl
                         export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
                         export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+                        export AR=lib
+                        export AR="ar-lib lib"
+                        export OS_LDFLAG="-Wl,"
                         export RANLIB=true
                         OSLIBS="kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib"
+                        OSLIBS="-Wl,kernel32.lib -Wl,user32.lib -Wl,gdi32.lib -Wl,winspool.lib -Wl,comdlg32.lib -Wl,advapi32.lib -Wl,shell32.lib -Wl,ole32.lib -Wl,oleaut32.lib -Wl,uuid.lib -Wl,odbc32.lib -Wl,odbccp32.lib"
                 elif  test $VENDOR = intel-win7-64; then
                         export CC=cccl
+                        export CC=cl
                         export CXX=cccl
                         export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
                         export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+                        export AR=lib
+                        export AR="ar-lib lib"
+                        export OS_LDFLAG="-Wl,"
                         export RANLIB=true
                         OSLIBS="kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib"
+                        OSLIBS="-Wl,kernel32.lib -Wl,user32.lib -Wl,gdi32.lib -Wl,winspool.lib -Wl,comdlg32.lib -Wl,advapi32.lib -Wl,shell32.lib -Wl,ole32.lib -Wl,oleaut32.lib -Wl,uuid.lib -Wl,odbc32.lib -Wl,odbccp32.lib"
                 elif test $VENDOR = intel-linux; then
                         export CC=icc
 …
                         export CC=icc
                         export CXX=icpc
                         export CXXFLAGS=" -O3 -xS -D_INTEL_LINUX_ "
                         export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ "
+                        export CXXFLAGS=" -O3 -D_INTEL_LINUX_ "
+                        export CFLAGS=" -O3 -D_INTEL_LINUX_ "
         else
                 AC_MSG_ERROR([unknow compiler vendor!])
+                AC_MSG_ERROR([unknown compiler vendor!])
                 fi
         fi
 …
                 AC_MSG_CHECKING(for matlab headers and libraries in $MATLAB_ROOT)
+                MATLABINCL=-I"$MATLAB_ROOT/extern/include";
+                MATLABINCL="-I$MATLAB_ROOT/extern/include/"
                 dnl 4. get MEXLIB MEXLINK and MEXEXT (experimental)
+                MEXLINK=$(mex -v 2>&1 < /dev/null | grep LDFLAGS     | sed -e "s/         LDFLAGS            = //g")
+                MEXLIB=$( mex -v 2>&1 < /dev/null | grep CXXLIBS     | sed -e "s/         CXXLIBS            = //g")
+                MEXEXT=$( mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/         LDEXTENSION        = //g")
+      dnl OS-dependent variables and checks
+                case "${host_os}" in
+                        *cygwin*)
+                                if  test $VENDOR = intel-win7-32; then
+                                        MEXLIB="-Wl,./../../c/libISSMCore.a -Wl,libISSMApi.a -Wl,libISSMMatlab.a -Wl,./../../c/libISSMModules.a -Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib"
+               MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win32/microsoft` -no-undefined -Wl,/export:mexFunction"
+                                elif  test l-win7-64; then
+                                        MEXLIB="-Wl,./../../c/libISSMCore.a -Wl,libISSMApi.a -Wl,libISSMMatlab.a -Wl,./../../c/libISSMModules.a -Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib"
+               MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -no-undefined -Wl,/export:mexFunction"
+                                fi
+                                MEXEXT=`$MATLAB_ROOT/bin/mexext.bat`
+                                MEXEXT=".$MEXEXT"
+                        ;;
+                   *)
+                      MEXLINK=$(mex -v 2>&1 < /dev/null | grep LDFLAGS     | sed -e "s/         LDFLAGS            = //g")
+                 MEXLIB=$( mex -v 2>&1 < /dev/null | grep CXXLIBS     | sed -e "s/         CXXLIBS            = //g")
+                      MEXEXT=$( mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/         LDEXTENSION        = //g")
+                        ;;
+      esac
            AC_MSG_RESULT(done)
 …
                 MATLABWRAPPEREXT=$MEXEXT
                 AC_SUBST([MATLABWRAPPEREXT])
             AC_SUBST([MEXLIB])
+           AC_SUBST([MEXLIB])
                 AC_SUBST([MEXLINK])
         fi
 …
                 case "${host_os}" in
                                 *cygwin*)
                                 TRIANGLELIB=$TRIANGLE_ROOT/triangle.lib
+                                TRIANGLELIB="-Wl,`cygpath -m $TRIANGLE_ROOT/`triangle.lib"
                                 ;;
                                 *linux*)
 …
                 DAKOTAINCL=-I$DAKOTA_ROOT/include
                 AC_MSG_CHECKING(for dakota version)
+                DAKOTA_VERSION=`cat $DAKOTA_ROOT/include/dakota_config.h | grep "#define PACKAGE_VERSION" | sed 's/#define PACKAGE_VERSION//' | sed 's/ //g' | sed -e 's/\"//g' `
+                if test -f "$DAKOTA_ROOT/../src/src/CommandLineHandler.C"; then
+                        DAKOTA_VERSION=`cat $DAKOTA_ROOT/../src/src/CommandLineHandler.C | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
+                else if test -f "$DAKOTA_ROOT/../src/src/CommandLineHandler.cpp"; then
+                        DAKOTA_VERSION=`cat $DAKOTA_ROOT/../src/src/CommandLineHandler.cpp | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
+                else
+                        AC_MSG_ERROR([Dakota CommandLineHandler.C or CommandLineHandler.cpp file not found to determine DAKOTA_VERSION!]);
+                fi
+                fi
                 AC_MSG_RESULT($DAKOTA_VERSION)
+                AC_DEFINE_UNQUOTED([DAKOTA_VERSION],"$DAKOTA_VERSION",[Dakota version number])
+                AC_DEFINE_UNQUOTED([_DAKOTA_VERSION_],"$DAKOTA_VERSION",[Dakota version number])
+                DAKOTAFLAGS=""
                 case "${host_os}" in
                         *cygwin*)
                                 if      test x$DAKOTA_VERSION = x4.2; then
+                                if      test x$DAKOTA_VERSION = x4.2 || test x$DAKOTA_VERSION = x4.2+; then
                                         DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver"
                                 else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
 …
                         ;;
                         *linux*)
                                 if      test x$DAKOTA_VERSION = x4.2; then
+                                if      test x$DAKOTA_VERSION = x4.2 || test x$DAKOTA_VERSION = x4.2+; then
                                         DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver"
                                 else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
+                                        DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
+                                        DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system -ldl"
+                                else if test x$DAKOTA_VERSION = x5.3 || test x$DAKOTA_VERSION = x5.3.1; then
+                                        DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
+                                        DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -lmods -lmod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack_fortran -lutilib -lcolin -linterfaces -lscolib -l3po -lpebbl -ltinyxml -lconmin -ldace -lanalyzer -lrandom -lsampling -lbose -lfsudace -lhopspack -ljega -ljega_fe -lmoga -lsoga -leutils -lutilities -lncsuopt -lcport -loptpp -lpsuade -lamplsolver"
                                 else
                                         AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
                                 fi
                                 fi
+                                fi
                         ;;
                         *darwin*)
                                 if      test x$DAKOTA_VERSION = x4.2; then
+                                if      test x$DAKOTA_VERSION = x4.2 || test x$DAKOTA_VERSION = x4.2+; then
                                         DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver"
                                         dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack"
 …
                 esac
                 AC_DEFINE([_HAVE_DAKOTA_],[1],[with Dakota in ISSM src])
+                case $DAKOTA_VERSION in
+                        @<:@1-9@:>@.@<:@0-9@:>@.@<:@0-9@:>@)
+                                DAKOTA_MAJOR=`echo $DAKOTA_VERSION | sed -e 's/^\(@<:@0-9@:>@*\)\..*/\1/'`
+                                DAKOTA_MINOR=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\)\..*/\1/'`
+                                DAKOTA_BUILD=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/'`
+                        ;;
+                        @<:@1-9@:>@.@<:@0-9@:>@)
+                                DAKOTA_MAJOR=`echo $DAKOTA_VERSION | sed -e 's/^\(@<:@0-9@:>@*\)\..*/\1/'`
+                                DAKOTA_MINOR=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/'`
+                                DAKOTA_BUILD=0
+                        ;;
+                        @<:@1-9@:>@.@<:@0-9@:>@+)
+                                DAKOTA_MAJOR=`echo $DAKOTA_VERSION | sed -e 's/^\(@<:@0-9@:>@*\)\..*/\1/'`
+                                DAKOTA_MINOR=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/'`
+                                DAKOTA_BUILD=0
+                        ;;
+                        *)
+                                AC_MSG_ERROR([Dakota version ($DAKOTA_VERSION) not supported!]);
+                   ;;
+                esac
+                AC_MSG_CHECKING(for dakota major version)
+                AC_MSG_RESULT($DAKOTA_MAJOR)
+                AC_DEFINE_UNQUOTED([_DAKOTA_MAJOR_],$DAKOTA_MAJOR,[Dakota major version number])
+                AC_MSG_CHECKING(for dakota minor version)
+                AC_MSG_RESULT($DAKOTA_MINOR)
+                AC_DEFINE_UNQUOTED([_DAKOTA_MINOR_],$DAKOTA_MINOR,[Dakota minor version number])
+                AC_MSG_CHECKING(for dakota build version)
+                AC_MSG_RESULT($DAKOTA_BUILD)
+                AC_DEFINE_UNQUOTED([_DAKOTA_BUILD_],$DAKOTA_BUILD,[Dakota build version number])
                 AC_SUBST([DAKOTAINCL])
+                AC_SUBST([DAKOTAFLAGS])
                 AC_SUBST([DAKOTALIB])
 …
                 AC_MSG_RESULT($HAVE_DAKOTA)
         fi
         AM_CONDITIONAL([DAKOTA], [test x$HAVE_DAKOTA = xyes])
         dnl }}}
 …
         dnl mpi{{{
         AC_MSG_CHECKING(for mpi)
-        AC_ARG_WITH([mpi-lib],
-                AS_HELP_STRING([--with-mpi-lib = options],[mpi options, for ex: "-L$MPIROOT -lmpich]),
-                [MPILIB=$withval],[MPILIB=""])
         AC_ARG_WITH([mpi-include],
           AS_HELP_STRING([--with-mpi-include=DIR],[mpi include directory, necessary for parallel build]),
           [MPI_INCLUDE=$withval],[MPI_INCLUDE=""])
+        if test -z "$MPILIB" ; then
+        AC_ARG_WITH([mpi-libdir],
+          AS_HELP_STRING([--with-mpi-libdir=DIR],[mpi lib directory, necessary for parallel build]),
+          [MPI_LIBDIR=$withval],[MPI_LIBDIR=""])
+        AC_ARG_WITH([mpi-libflags],
+          AS_HELP_STRING([--with-mpi-libflags=LIBS],[mpi libraries to be used, necessary for parallel build]),
+          [MPI_LIBFLAGS=$withval],[MPI_LIBFLAGS=""])
+        if test -z "$MPI_INCLUDE" ; then
                 HAVE_MPI=no
         else
+                if test -z "$MPI_INCLUDE" ; then
+                        HAVE_MPI=no
+                HAVE_MPI=yes
+                dnl Processing for windows
+                if  test x$VENDOR = xintel-win7-32; then
+                        MPI_LIBDIR=`cygpath -m $MPI_LIBDIR`
+                        MPIINCL=`cygpath -m $MPI_INCLUDE`
+                elif test x$VENDOR = xintel-win7-64; then
+                        MPI_LIBDIR=`cygpath -m $MPI_LIBDIR`
+                        MPI_INCLUDE=`cygpath -m $MPI_INCLUDE`
+                fi
+                if test -z "$MPI_LIBDIR"; then
+                        MPIINCL=-I"$MPI_INCLUDE"
+                        MPILIB="$MPI_LIBFLAGS"
                 else
-                        HAVE_MPI=yes
                         MPIINCL=-I"$MPI_INCLUDE"
+                        AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src])
+                        AC_DEFINE([HAVE_MPI],[1],[Mpi Flag for Dakota (DO NOT REMOVE)])
+                        AC_SUBST([MPIINCL])
+                        AC_SUBST([MPILIB])
+                fi
+        fi
+                        MPILIB="-L$MPI_LIBDIR $MPI_LIBFLAGS"
+                fi
+                AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src])
+                AC_DEFINE([HAVE_MPI],[1],[Mpi Flag for Dakota (DO NOT REMOVE)])
+                AC_SUBST([MPIINCL])
+                AC_SUBST([MPILIB])
+        fi
         AM_CONDITIONAL([MPI], [test x$HAVE_MPI = xyes])
         AC_MSG_RESULT($HAVE_MPI)
 …
                 PETSC_VERSION_DATE_HG=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_DATE_HG" | sed 's/#define PETSC_VERSION_DATE_HG//' | sed 's/ //g' | sed -e 's/\"//g' `
+                PETSC_RELEASE=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_RELEASE" | sed 's/#define PETSC_VERSION_RELEASE//' | sed 's/ //g'`
                 AC_MSG_CHECKING(whether petsc is the development version)
+                if test x$PETSC_VERSION_DATE_HG = xunknown; then
+                        AC_DEFINE([_HAVE_PETSCDEV_],[1],[with PETSc-dev])
+                dnl if test x$PETSC_VERSION_DATE_HG = xunknown; then
+                if test "$PETSC_RELEASE" = "0"; then
+                   AC_DEFINE([_HAVE_PETSCDEV_],[1],[with PETSc-dev])
                         AC_MSG_RESULT(yes)
                 else
 …
                         *cygwin*)
                         if test $PETSC_MAJOR -lt 3 ; then
                                 PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" libpetscksp.lib libpetscdm.lib libpetscmat.lib libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib"
+                                PETSCLIB=-Wl,/LIBPATH:`cygpath -w $PETSC_ROOT/lib`  -Wl,libpetscksp.lib  -Wl,libpetscdm.lib  -Wl,libpetscmat.lib  -Wl,libpetscvec.lib  -Wl,libpetscsnes.lib  -Wl,libpetscts.lib  -Wl,libmpiuni.lib  -Wl,libpetsc.lib
                         else
                                 PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" libpetsc.lib"
                                 if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" libmetis.lib"; fi
+                                PETSCLIB="-L$PETSC_ROOT/lib  -Wl,libpetsc.lib"
+                                if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+="  -Wl,libmetis.lib"; fi
                         fi
                         ;;
                         *linux*)
                         if test $PETSC_MAJOR -lt 3 ; then
                                 PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc  -lpetscsnes -lpetscts"
+                                PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lmpiuni -lpetsc"
                         else
                                 PETSCLIB="-L$PETSC_ROOT/lib -lpetsc -ldl"
 …
                                 case "${host_os}" in
                                         *cygwin*)
                                         METISLIB="-LIBPATH:\"$METIS_ROOT\" libmetis.lib"
+                                        METISLIB="-L$METIS_ROOT -Wl,libmetis.lib"
                                         ;;
                                         *linux*)
 …
                                 case "${host_os}" in
                                         *cygwin*)
                                         METISLIB="-LIBPATH:\"$METIS_ROOT\" libmetis.lib"
+                                        METISLIB="-L$METIS_ROOT libmetis.lib"
                                         ;;
                                         *linux*)
 …
                 case "${host_os}" in
                         *cygwin*)
                         BLASLAPACKLIB="-link -LIBPATH:\"$BLASLAPACK_ROOT\" libf2cblas.lib  libf2clapack.lib"
+                        BLASLAPACKLIB="-L`cygpath -m $BLASLAPACK_ROOT` -Wl,libf2cblas.lib  -Wl,libf2clapack.lib"
                         ;;
                         *linux*)
                         BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lflapack -lfblas "
+                        BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas "
                         ;;
                         *darwin*)
                         BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lflapack -lfblas "
+                        BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas "
                         ;;
                 esac
 …
                 HAVE_MKL=yes
                 MKLINCL=""
+                MKLLIB=-L"$MKL_ROOT -lmkl -lmkl_lapack -lmkl_scalapack_ilp64   -lmkl_blacs_sgimpt_ilp64 -lguide  -lpthread"
+                if test x$VENDOR = xintel-pleiades; then
+                 MKLLIB=-L"$MKL_ROOT -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
+                else
+                 MKLLIB=-L"$MKL_ROOT -lmkl -lmkl_lapack -lmkl_scalapack_ilp64 -lmkl_blacs_sgimpt_ilp64 -lguide -lpthread"
+                fi
                 AC_DEFINE([_HAVE_MKL_],[1],[with mkl in ISSM src])
                 AC_SUBST([MKLLIB])
 …
                 HAVE_MUMPS=no
         fi
+        AM_CONDITIONAL([MUMPS], [test x$HAVE_MUMPS = xyes])
         AC_MSG_RESULT($HAVE_MUMPS)
         dnl }}}
 …
                 dnl defaults
                 HAVE_ML=yes
                 MLINCL=""
                 MLLIB=-L"$ML_ROOT/ -lml"
+                MLINCL=-I"$ML_ROOT/include"
+                MLLIB=-L"$ML_ROOT/lib -lml"
                 AC_DEFINE([_HAVE_ML_],[1],[with Blacs in ISSM src])
 …
         AC_MSG_RESULT($HAVE_ML)
         dnl }}}
+        dnl math{{{
+        dnl umfpack{{{
+                AC_ARG_WITH([umfpack-dir],
+                  AS_HELP_STRING([--with-umfpack-dir=DIR],[UMFPACK root directory]),
+                                        [UMFPACK_ROOT=$withval],[UMFPACK_ROOT=""])
+                AC_MSG_CHECKING(for UMFPACK headers and libraries in $UMFPACK_ROOT)
+                if test -d "$UMFPACK_ROOT"; then
+                        dnl defaults
+                        HAVE_UMFPACK=yes
+                        UMFPACKINCL=""
+                        UMFPACKLIB=-L"$UMFPACK_ROOT/lib -lumfpack -lumfpack.5.5.1"
+                        AC_DEFINE([_HAVE_UMFPACK_],[1],[with UMFPACK in ISSM src])
+                        AC_SUBST([UMFPACKINCL])
+                        AC_SUBST([UMFPACKLIB])
+                else
+                        HAVE_UMFPACK=no
+                fi
+                AC_MSG_RESULT($HAVE_UMFPACK)
+        dnl }}}
+dnl math{{{
         AC_MSG_CHECKING(for math library)
         AC_ARG_WITH([math-lib],
 …
                                 fi
                          fi
                                 AC_MSG_ERROR([frtran library provided ($FORTRAN_LIB$) does not exist!]);
+                                AC_MSG_ERROR([fortran library provided ($FORTRAN_LIB) does not exist!]);
                         fi
                 fi
 …
         AM_CONDITIONAL([RIFTS], [test x$HAVE_RIFTS = xyes])
         AC_MSG_RESULT($HAVE_RIFTS)
+        dnl }}}
+        dnl math77{{{
+        AC_ARG_WITH([math77-dir],
+                AS_HELP_STRING([--with-math77-dir=DIR], [math77 root directory.]),
+                [MATH77_ROOT=$withval],[MATH77_ROOT=""])
+        AC_MSG_CHECKING(for math77)
+        if test -d "$MATH77_ROOT"; then
+          HAVE_MATH77=yes
+          MATH77LIB="-L$MATH77_ROOT/ -lmath77"
+          AC_DEFINE([_HAVE_MATH77_],[1],[with math77 in ISSM src])
+          AC_SUBST([MATH77LIB])
+        else
+                HAVE_MATH77=no
+        fi
+        AC_MSG_RESULT($HAVE_MATH77)
+        dnl }}}
+        dnl with-gia{{{
+        AC_ARG_WITH([gia],
+                AS_HELP_STRING([--with-gia = YES], [compile with gia capabilities (default is yes)]),
+                [GIA=$withval],[GIA=no])
+        AC_MSG_CHECKING(for gia capability compilation)
+        if test "x$GIA" = "xyes"; then
+          if test "x$HAVE_MATH77" = "xno"; then
+                  HAVE_GIA=no
+                  AC_MSG_ERROR([gia requires compilation of math77 library! Reconfigure with --with-math77 option on]);
+          else
+                dnl defaults
+                HAVE_GIA=yes
+                AC_DEFINE([_HAVE_GIA_],[1],[with gia capability])
+          fi
+        else
+                HAVE_GIA=no
+        fi
+        AM_CONDITIONAL([GIA], [test x$HAVE_GIA = xyes])
+        AC_MSG_RESULT($HAVE_GIA)
+        dnl }}}
+        dnl with-ios{{{
+        AC_ARG_WITH([ios],
+                AS_HELP_STRING([--with-ios = YES], [compile with iOS capabilities (default is no, alternatives are yes)]),
+                [IOS=$withval],[IOS=no])
+        AC_MSG_CHECKING(for iOS compilation)
+        if test "x$IOS" = "xyes"; then
+                dnl defaults
+                HAVE_IOS=yes
+                AC_DEFINE([_HAVE_IOS_],[1],[with android capability])
+        elif test "x$IOS" = "xno"; then
+                HAVE_IOS=no
+        else
+          AC_MSG_ERROR([--with-ios should be either no or yes])
+        fi
+        AM_CONDITIONAL([IOS], [test x$HAVE_IOS != xno])
+        AC_MSG_RESULT($HAVE_IOS)
         dnl }}}
         dnl with-android{{{

issm/trunk/packagers/win7
- Property svn:ignore set to
  *.msi
  *.aip
  *.aic
  *Setup*

issm/trunk/packagers/win7/ISSM.initial.aip

-              r11995
+              r15396
 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <DOCUMENT Type="Advanced Installer" CreateVersion="8.9" version="8.9" Modules="simple" RootPath="." Language="en" Id="{36DC7549-63BC-4A22-AE82-A96C27BF7B21}">
+<DOCUMENT Type="Advanced Installer" CreateVersion="8.9" version="10.1" Modules="simple" RootPath="." Language="en" Id="{36DC7549-63BC-4A22-AE82-A96C27BF7B21}">
   <COMPONENT cid="caphyon.advinst.msicomp.MsiPropsComponent">
     <ROW Property="ALLUSERS" Value="2"/>
 …
     <ROW Property="ProductLanguage" Value="1033"/>
     <ROW Property="ProductName" Value="ISSM" ValueLocId="*"/>
     <ROW Property="ProductVersion" Value="1.0"/>
+    <ROW Property="ProductVersion" Value="1.0" Type="32"/>
     <ROW Property="SecureCustomProperties" Value="OLDPRODUCTS;AI_NEWERPRODUCTFOUND"/>
     <ROW Property="UpgradeCode" Value="{F12D1A74-5079-41A3-A02A-15754B89E390}"/>
 …
     <ROW Fragment="CommonUI.aip" Path="&lt;AI_FRAGS&gt;CommonUI.aip"/>
     <ROW Fragment="FolderDlg.aip" Path="&lt;AI_THEMES&gt;classic\fragments\FolderDlg.aip"/>
+    <ROW Fragment="MaintenanceTypeDlg.aip" Path="&lt;AI_THEMES&gt;classic\fragments\MaintenanceTypeDlg.aip"/>
+    <ROW Fragment="MaintenanceWelcomeDlg.aip" Path="&lt;AI_THEMES&gt;classic\fragments\MaintenanceWelcomeDlg.aip"/>
     <ROW Fragment="SequenceDialogs.aip" Path="&lt;AI_THEMES&gt;classic\fragments\SequenceDialogs.aip"/>
     <ROW Fragment="Sequences.aip" Path="&lt;AI_FRAGS&gt;Sequences.aip"/>
 …
     <ROW Fragment="UI.aip" Path="&lt;AI_THEMES&gt;classic\fragments\UI.aip"/>
     <ROW Fragment="Validation.aip" Path="&lt;AI_FRAGS&gt;Validation.aip"/>
+    <ROW Fragment="VerifyRemoveDlg.aip" Path="&lt;AI_THEMES&gt;classic\fragments\VerifyRemoveDlg.aip"/>
+    <ROW Fragment="VerifyRepairDlg.aip" Path="&lt;AI_THEMES&gt;classic\fragments\VerifyRepairDlg.aip"/>
+    <ROW Fragment="WelcomeDlg.aip" Path="&lt;AI_THEMES&gt;classic\fragments\WelcomeDlg.aip"/>
   </COMPONENT>
   <COMPONENT cid="caphyon.advinst.msicomp.MsiBinaryComponent">
 …
     <ROW Dialog_="VerifyReadyDlg" Control_="Install" Event="EndDialog" Argument="Return" Condition="AI_PATCH" Ordering="199"/>
     <ROW Dialog_="ResumeDlg" Control_="Install" Event="EndDialog" Argument="Return" Condition="AI_RESUME" Ordering="299"/>
+    <ROW Dialog_="VerifyRemoveDlg" Control_="Remove" Event="EndDialog" Argument="Return" Condition="AI_MAINT AND InstallMode = &quot;Remove&quot;" Ordering="299"/>
+    <ROW Dialog_="VerifyRepairDlg" Control_="Repair" Event="EndDialog" Argument="Return" Condition="AI_MAINT AND InstallMode = &quot;Repair&quot;" Ordering="399"/>
+    <ROW Dialog_="VerifyRemoveDlg" Control_="Back" Event="NewDialog" Argument="MaintenanceTypeDlg" Condition="AI_MAINT AND InstallMode = &quot;Remove&quot;" Ordering="1"/>
+    <ROW Dialog_="VerifyRepairDlg" Control_="Back" Event="NewDialog" Argument="MaintenanceTypeDlg" Condition="AI_MAINT AND InstallMode = &quot;Repair&quot;" Ordering="1"/>
+    <ROW Dialog_="MaintenanceTypeDlg" Control_="RemoveButton" Event="NewDialog" Argument="VerifyRemoveDlg" Condition="AI_MAINT AND InstallMode = &quot;Remove&quot;" Ordering="601"/>
+    <ROW Dialog_="MaintenanceTypeDlg" Control_="RepairButton" Event="NewDialog" Argument="VerifyRepairDlg" Condition="AI_MAINT AND InstallMode = &quot;Repair&quot;" Ordering="601"/>
   </COMPONENT>
   <COMPONENT cid="caphyon.advinst.msicomp.MsiCreateFolderComponent">
 …
     <ROW Action="AI_RESTORE_LOCATION" Type="65" Source="aicustact.dll" Target="RestoreLocation"/>
     <ROW Action="AI_ResolveKnownFolders" Type="1" Source="aicustact.dll" Target="AI_ResolveKnownFolders"/>
+    <ROW Action="AI_ResolveLocalizedCredentials" Type="1" Source="aicustact.dll" Target="GetLocalizedCredentials"/>
     <ROW Action="AI_SHOW_LOG" Type="65" Source="aicustact.dll" Target="LaunchLogFile" WithoutSeq="true"/>
     <ROW Action="AI_STORE_LOCATION" Type="51" Source="ARPINSTALLLOCATION" Target="[APPDIR]"/>
 …
     <ROW Action="AI_STORE_LOCATION" Condition="(Not Installed) OR REINSTALL" Sequence="1501"/>
     <ROW Action="AI_PREPARE_UPGRADE" Condition="AI_UPGRADE=&quot;No&quot; AND (Not Installed)" Sequence="1399"/>
+    <ROW Action="AI_ResolveKnownFolders" Sequence="51"/>
+    <ROW Action="AI_ResolveKnownFolders" Sequence="52"/>
+    <ROW Action="AI_ResolveLocalizedCredentials" Sequence="51"/>
   </COMPONENT>
   <COMPONENT cid="caphyon.advinst.msicomp.MsiInstallUISequenceComponent">
     <ROW Action="AI_RESTORE_LOCATION" Condition="APPDIR=&quot;&quot;" Sequence="749"/>
+    <ROW Action="AI_ResolveKnownFolders" Sequence="51"/>
+    <ROW Action="AI_ResolveKnownFolders" Sequence="52"/>
+    <ROW Action="AI_ResolveLocalizedCredentials" Sequence="51"/>
   </COMPONENT>
   <COMPONENT cid="caphyon.advinst.msicomp.MsiLaunchConditionsComponent">
+    <ROW Condition="Privileged" Description="[ProductName] requires administrative privileges to install." DescriptionLocId="AI.LaunchCondition.Privileged" IsPredefined="true" Builds="DefaultBuild"/>
     <ROW Condition="VersionNT" Description="[ProductName] cannot be installed on [WindowsType9XDisplay]" DescriptionLocId="AI.LaunchCondition.No9X" IsPredefined="true" Builds="DefaultBuild"/>
   </COMPONENT>

issm/trunk/scripts/getloc.sh

r12707	r15396
1	1	#!/bin/bash
2	2	#get number of lines of code
3		cloc-1.55.pl $ISSM_DIR/src $ISSM_DIR/m4 --exclude-dir=.svn --exclude-dir=ad --exclude-~~dir=android --exclude-~~ext=exp --exclude-lang=make --out=temp
	3	cloc-1.55.pl $ISSM_DIR/src $ISSM_DIR/m4 --exclude-dir=.svn --exclude-dir=ad --exclude-ext=exp --exclude-lang=make --out=temp
4	4	cat temp
5	5	./cloc2html.py

issm/trunk/scripts/issmconfiguration.sh

-              r12332
+              r15396
         LIST=`ls`
+        if [[  $# == "0" ]]; then
+                COUNT=0;
+                for STEP in $LIST
+                do
+                        let COUNT=$COUNT+1
+                        printf '%3i: %s\n' $COUNT $STEP
+                done
+        if test -d "$JPL_SVN/usr/$USER/configs"; then
+                cd $JPL_SVN/usr/$USER/configs
+                LIST2=`ls`
+        fi
+        #print choices
+        COUNT=0;
+        printf 'ISSM wide configurations\n'
+        for STEP in $LIST
+        do
+                let COUNT=$COUNT+1
+                printf '%3i: %s\n' $COUNT $STEP
+        done
+        printf 'Personal configuration\n'
+        for STEP in $LIST2
+        do
+                let COUNT=$COUNT+1
+                printf '%3i: %s\n' $COUNT $STEP
+        done
+                echo -n "Configuration choice: "
+                read choice
+        else
+                choice=$1
+        fi
+        echo -n "Configuration choice: "
+        read choice
         #Now go backto the list and retrieve the name of the configuration file:
         COUNT=0;
         for STEP in $LIST
+        do
+                let COUNT=$COUNT+1
+                if [[ $COUNT == $choice ]]; then
+                        configurename=$STEP
+                fi
+        done
+        for STEP in $LIST2
         do
                 let COUNT=$COUNT+1
 …
         cd $ISSM_DIR
+        #at this point, was a cleanup of the archive requested?
+        if [ "$1" == "clean" ];
+        then
+                make uninstall && make distclean
+        fi
         source ./scripts/automakererun.sh
+        source configs/$configurename
+        if [ -f configs/$configurename ]; then
+                source configs/$configurename
+        else
+                source $JPL_SVN/usr/$USER/configs/$configurename
+        fi
         #we are done, go back to original directory:
 …
 fi
 #alias aut='a=`pwd` && cd $ISSM_DIR && ./scripts/automakererun.sh && ./configs/config-macosx64-larour-nopetsc.sh'

issm/trunk/scripts/vil

-              r6626
+              r15396
 #!/bin/bash
+if [ ! -z $EXECUTION_DIR ];
+then
+        EXECUTION_DIR=$ISSM_DIR/execution
+fi
 cd $EXECUTION_DIR

issm/trunk/src

Property svn:mergeinfo changed

/issm/trunk-jpl/src

merged: 14311,14313,14316-14317,14319,14323-14326,14330,14332-14333,14338-14357,14359-14365,14367-14368,14370,14372-14373,14377-14378,14380-14385,14390-14394,14397-14405,14407-14408,14411-14421,14423-14426,14429,14433-14441,14443,14446-14453,14456-14465,14467,14469,14472-14474,14476-14484,14488-14491,14493,14495-14497,14501,14503-14504,14506,14508,14512-14522,14524-14525,14527-14533,14536-14538,14540,14543-14547,14549,14551,14553,14555-14556,14558-14560,14562-14564,14566-14567,14569-14570,14572-14573,14576-14577,14579-14580,14583-14585,14587-14589,14591-14592,14594,14597-14598,14601,14603,14605-14606,14608-14613,14615,14617-14637,14639-14650,14652,14655-14656,14659-14666,14668-14675,14678-14689,14692-14696,14698-14701,14703-14720,14724,14726-14728,14731,14734-14736,14739,14741-14746,14750-14753,14755,14757,14760-14761,14763-14765,14767-14771,14773-14780,14782-14785,14787-14801,14803-14804,14807-14814,14822-14825,14827-14830,14833-14841,14844-14846,14857-14862,14864-14869,14871-14878,14881-14882,14886-14901,14903-14923,14926-14928,14931-14937,14939,14941,14948-14972,14974-14992,14994-15003,15005-15017,15020-15022,15024-15026,15028-15030,15035-15043,15048-15058,15060-15063,15065-15075,15077,15079,15082-15083,15089-15091,15093,15095-15097,15099-15101,15103-15107,15109-15112,15121,15123-15137,15139-15153,15155,15160-15161,15163-15170,15172,15174-15179,15182-15183,15186,15189-15192,15194-15199,15203-15211,15214-15220,15223-15224,15229-15230,15232,15234,15237-15238,15243,15248-15254,15257,15264-15266,15269-15270,15272-15273,15275-15278,15281-15284,15286-15288,15293,15295,15297-15302,15305-15306,15312-15317,15321-15324,15326,15329,15331,15333,15335,15339-15340,15343-15345,15351-15353,15358,15365,15370,15372-15373,15375-15387,15390

issm/trunk/src/Makefile.am

-              r13975
+              r15396
+EXTRA_DIST =  perl pro
+SUBDIRS = c m wrappers
+if ANDROID
+SUBDIRS += android
+endif
+EXTRA_DIST =  perl
+SUBDIRS = c m wrappers mobile

issm/trunk/src/c/Makefile.am

-              r14310
+              r15396
 #sources
 #Core sources{{{
 core_sources = ./issm.h\
                                         ./issm-binding.h\
                                         ./include/macros.h\
                                         ./include/typedefs.h\
                                         ./include/types.h\
                                         ./include/include.h\
+core_sources = ./main/issm.h\
+                           ./main/globals.h\
+                           ./datastructures/DataSet.h\
+                                        ./datastructures/DataSet.cpp\
+                                        ./datastructures/Object.h\
+                                        ./datastructures/datastructures.h\
                                         ./classes/classes.h\
-                                        ./classes/objects.h\
-                                        ./classes/objects/Object.h\
                                         ./classes/gauss/GaussTria.h\
                                         ./classes/gauss/GaussTria.cpp\
                                         ./classes/objects/Update.h\
                                         ./classes/objects/Element.h\
+                                        ./classes/Update.h\
+                                        ./classes/Element.h\
                                         ./classes/FemModel.h\
                                         ./classes/FemModel.cpp\
+                                        ./classes/objects/Material.h\
+                                        ./classes/objects/Load.h\
+                                        ./classes/objects/Contour.h\
+                                        ./classes/objects/OptArgs.h\
+                                        ./classes/objects/OptPars.h\
+                                        ./classes/objects/Loads/Friction.h\
+                                        ./classes/objects/Loads/Friction.cpp\
+                                        ./classes/objects/Inputs/TransientInput.h\
+                                        ./classes/objects/Inputs/TransientInput.cpp\
+                                        ./classes/objects/Constraints/SpcTransient.cpp\
+                                        ./classes/objects/Constraints/SpcTransient.h\
+                                        ./classes/objects/IndependentObject.h\
+                                        ./classes/objects/IndependentObject.cpp\
+                                        ./classes/objects/DependentObject.h\
+                                        ./classes/objects/DependentObject.cpp\
+                                        ./classes/Material.h\
+                                        ./classes/Load.h\
+                                        ./classes/Contour.h\
+                                        ./classes/Loads/Friction.h\
+                                        ./classes/Loads/Friction.cpp\
+                                        ./classes/Inputs/TransientInput.h\
+                                        ./classes/Inputs/TransientInput.cpp\
+                                        ./classes/Constraints/SpcTransient.cpp\
+                                        ./classes/Constraints/SpcTransient.h\
+                                        ./classes/IndependentObject.h\
+                                        ./classes/IndependentObject.cpp\
+                                        ./classes/DependentObject.h\
+                                        ./classes/DependentObject.cpp\
                                         ./classes/DofIndexing.h\
                                         ./classes/DofIndexing.cpp\
                                         ./classes/IoModel.h\
                                         ./classes/IoModel.cpp\
+                                        ./classes/objects/Node.h\
+                                        ./classes/objects/Node.cpp\
+                                        ./classes/objects/Segment.h\
+                                        ./classes/objects/Vertex.h\
+                                        ./classes/objects/Vertex.cpp\
+                                        ./classes/objects/AdolcEdf.h\
+                                        ./classes/IssmComm.h\
+                                        ./classes/IssmComm.cpp\
+                                        ./classes/Contours.h\
+                                        ./classes/Contours.cpp\
+                                        ./classes/Nodes.h\
+                                        ./classes/Nodes.cpp\
+                                        ./classes/Vertices.h\
+                                        ./classes/Vertices.cpp\
+                                        ./classes/Node.h\
+                                        ./classes/Node.cpp\
+                                        ./classes/Segment.h\
+                                        ./classes/Vertex.h\
+                                        ./classes/Vertex.cpp\
                                         ./classes/Hook.h\
                                         ./classes/Hook.cpp\
                                         ./classes/Patch.h\
                                         ./classes/Patch.cpp\
+                                        ./classes/objects/ElementResults/ElementResultLocal.h\
+                                        ./classes/objects/ElementResults/DoubleElementResult.h\
+                                        ./classes/objects/ElementResults/DoubleElementResult.cpp\
+                                        ./classes/objects/ElementResults/TriaP1ElementResult.h\
+                                        ./classes/objects/ElementResults/TriaP1ElementResult.cpp\
+                                        ./classes/objects/ElementResults/BoolElementResult.h\
+                                        ./classes/objects/ElementResults/BoolElementResult.cpp\
+                                        ./classes/objects/ExternalResults/ExternalResult.h\
+                                        ./classes/objects/ExternalResults/GenericExternalResult.h\
+                                        ./classes/objects/Elements/Tria.h\
+                                        ./classes/objects/Elements/Tria.cpp\
+                                        ./classes/objects/Elements/TriaHook.h\
+                                        ./classes/objects/Elements/TriaHook.cpp\
+                                        ./classes/objects/Elements/TriaRef.h\
+                                        ./classes/objects/Elements/TriaRef.cpp\
+                                        ./classes/objects/Inputs/Input.h\
+                                        ./classes/objects/Inputs/InputLocal.h\
+                                        ./classes/objects/Inputs/TriaP1Input.h\
+                                        ./classes/objects/Inputs/TriaP1Input.cpp\
+                                        ./classes/objects/Inputs/BoolInput.h\
+                                        ./classes/objects/Inputs/BoolInput.cpp\
+                                        ./classes/objects/Inputs/IntInput.h\
+                                        ./classes/objects/Inputs/IntInput.cpp\
+                                        ./classes/objects/Inputs/DoubleInput.h\
+                                        ./classes/objects/Inputs/DoubleInput.cpp\
+                                        ./classes/objects/Inputs/DatasetInput.h\
+                                        ./classes/objects/Inputs/DatasetInput.cpp\
+                                        ./classes/objects/Materials/Matice.h\
+                                        ./classes/objects/Materials/Matice.cpp\
+                                        ./classes/objects/Materials/Matdamageice.h\
+                                        ./classes/objects/Materials/Matdamageice.cpp\
+                                        ./classes/objects/Materials/Matpar.h\
+                                        ./classes/objects/Materials/Matpar.cpp\
+                                        ./classes/objects/Constraints/Constraint.h\
+                                        ./classes/objects/Constraints/SpcStatic.cpp\
+                                        ./classes/objects/Constraints/SpcStatic.h\
+                                        ./classes/objects/Constraints/SpcDynamic.cpp\
+                                        ./classes/objects/Constraints/SpcDynamic.h\
+                                        ./classes/objects/Loads/Penpair.cpp\
+                                        ./classes/objects/Loads/Penpair.h\
+                                        ./classes/objects/Loads/Pengrid.cpp\
+                                        ./classes/objects/Loads/Pengrid.h\
+                                        ./classes/objects/Loads/Icefront.cpp\
+                                        ./classes/objects/Loads/Icefront.h\
+                                        ./classes/objects/Loads/Numericalflux.cpp\
+                                        ./classes/objects/Loads/Numericalflux.h\
+                                        ./classes/ElementResults/ElementResultLocal.h\
+                                        ./classes/ElementResults/DoubleElementResult.h\
+                                        ./classes/ElementResults/DoubleElementResult.cpp\
+                                        ./classes/ElementResults/TriaP1ElementResult.h\
+                                        ./classes/ElementResults/TriaP1ElementResult.cpp\
+                                        ./classes/ElementResults/BoolElementResult.h\
+                                        ./classes/ElementResults/BoolElementResult.cpp\
+                                        ./classes/ExternalResults/Results.h\
+                                        ./classes/ExternalResults/Results.cpp\
+                                        ./classes/ExternalResults/ExternalResult.h\
+                                        ./classes/ExternalResults/GenericExternalResult.h\
+                                        ./classes/Elements/Elements.h\
+                                        ./classes/Elements/Elements.cpp\
+                                        ./classes/Elements/ElementHook.h\
+                                        ./classes/Elements/ElementHook.cpp\
+                                        ./classes/Elements/Tria.h\
+                                        ./classes/Elements/Tria.cpp\
+                                        ./classes/Elements/TriaRef.h\
+                                        ./classes/Elements/TriaRef.cpp\
+                                        ./classes/Inputs/Inputs.h\
+                                        ./classes/Inputs/Inputs.cpp\
+                                        ./classes/Inputs/Input.h\
+                                        ./classes/Inputs/InputLocal.h\
+                                        ./classes/Inputs/TriaInput.h\
+                                        ./classes/Inputs/TriaInput.cpp\
+                                        ./classes/Inputs/BoolInput.h\
+                                        ./classes/Inputs/BoolInput.cpp\
+                                        ./classes/Inputs/IntInput.h\
+                                        ./classes/Inputs/IntInput.cpp\
+                                        ./classes/Inputs/DoubleInput.h\
+                                        ./classes/Inputs/DoubleInput.cpp\
+                                        ./classes/Inputs/DatasetInput.h\
+                                        ./classes/Inputs/DatasetInput.cpp\
+                                        ./classes/Materials/Materials.h\
+                                        ./classes/Materials/Materials.cpp\
+                                        ./classes/Materials/Matice.h\
+                                        ./classes/Materials/Matice.cpp\
+                                        ./classes/Materials/Matdamageice.h\
+                                        ./classes/Materials/Matdamageice.cpp\
+                                        ./classes/Materials/Matpar.h\
+                                        ./classes/Materials/Matpar.cpp\
+                                        ./classes/Constraints/Constraints.h\
+                                        ./classes/Constraints/Constraints.cpp\
+                                        ./classes/Constraints/Constraint.h\
+                                        ./classes/Constraints/SpcStatic.cpp\
+                                        ./classes/Constraints/SpcStatic.h\
+                                        ./classes/Constraints/SpcDynamic.cpp\
+                                        ./classes/Constraints/SpcDynamic.h\
+                                        ./classes/Loads/Loads.h\
+                                        ./classes/Loads/Loads.cpp\
+                                        ./classes/Loads/Penpair.cpp\
+                                        ./classes/Loads/Penpair.h\
+                                        ./classes/Loads/Pengrid.cpp\
+                                        ./classes/Loads/Pengrid.h\
+                                        ./classes/Loads/Icefront.cpp\
+                                        ./classes/Loads/Icefront.h\
+                                        ./classes/Loads/Numericalflux.cpp\
+                                        ./classes/Loads/Numericalflux.h\
                                         ./classes/matrix/matrixobjects.h\
                                         ./classes/matrix/ElementMatrix.h\
 …
                                         ./classes/matrix/ElementVector.h\
                                         ./classes/matrix/ElementVector.cpp\
+                                        ./classes/matrix/Matrix.h\
+                                        ./classes/matrix/Vector.h\
+                                        ./classes/objects/Params/Param.h\
+                                        ./classes/objects/Params/GenericParam.h\
+                                        ./classes/objects/Params/BoolParam.cpp\
+                                        ./classes/objects/Params/BoolParam.h\
+                                        ./classes/objects/Params/IntParam.cpp\
+                                        ./classes/objects/Params/IntParam.h\
+                                        ./classes/objects/Params/IntVecParam.cpp\
+                                        ./classes/objects/Params/IntVecParam.h\
+                                        ./classes/objects/Params/IntMatParam.cpp\
+                                        ./classes/objects/Params/IntMatParam.h\
+                                        ./classes/objects/Params/DoubleParam.cpp\
+                                        ./classes/objects/Params/DoubleParam.h\
+                                        ./classes/objects/Params/FileParam.cpp\
+                                        ./classes/objects/Params/FileParam.h\
+                                        ./classes/objects/Params/StringArrayParam.cpp\
+                                        ./classes/objects/Params/StringArrayParam.h\
+                                        ./classes/objects/Params/DoubleMatParam.cpp\
+                                        ./classes/objects/Params/DoubleMatParam.h\
+                                        ./classes/objects/Params/DoubleTransientMatParam.cpp\
+                                        ./classes/objects/Params/DoubleTransientMatParam.h\
+                                        ./classes/objects/Params/DoubleMatArrayParam.cpp\
+                                        ./classes/objects/Params/DoubleMatArrayParam.h\
+                                        ./classes/objects/Params/DoubleVecParam.cpp\
+                                        ./classes/objects/Params/DoubleVecParam.h\
+                                        ./classes/objects/Params/StringParam.cpp\
+                                        ./classes/objects/Params/StringParam.h\
+                                        ./classes/objects/Params/MatrixParam.h\
+                                        ./classes/objects/Params/MatrixParam.cpp\
+                                        ./classes/objects/Params/VectorParam.h\
+                                        ./classes/objects/Params/VectorParam.cpp\
+                                        ./classes/objects/Params/TransientParam.h\
+                                        ./classes/objects/Params/TransientParam.cpp\
+                                        ./classes/objects/Params/DataSetParam.h\
+                                        ./classes/objects/Params/DataSetParam.cpp\
+                                        ./classes/objects/Profiler.h\
+                                        ./classes/objects/Profiler.cpp\
+                                        ./Container/Container.h\
+                                        ./Container/Constraints.h\
+                                        ./Container/Constraints.cpp\
+                                        ./Container/DataSet.h\
+                                        ./Container/DataSet.cpp\
+                                        ./Container/Elements.h\
+                                        ./Container/Elements.cpp\
+                                        ./Container/Inputs.h\
+                                        ./Container/Inputs.cpp\
+                                        ./Container/Loads.h\
+                                        ./Container/Loads.cpp\
+                                        ./Container/Materials.h\
+                                        ./Container/Materials.cpp\
+                                        ./Container/Nodes.h\
+                                        ./Container/Nodes.cpp\
+                                        ./Container/Options.h\
+                                        ./Container/Options.cpp\
+                                        ./Container/Parameters.h\
+                                        ./Container/Parameters.cpp\
+                                        ./Container/Results.h\
+                                        ./Container/Results.cpp\
+                                        ./Container/Vertices.h\
+                                        ./Container/Vertices.cpp\
+                                        ./classes/Params/Parameters.h\
+                                        ./classes/Params/Parameters.cpp\
+                                        ./classes/Params/Param.h\
+                                        ./classes/Params/GenericParam.h\
+                                        ./classes/Params/BoolParam.cpp\
+                                        ./classes/Params/BoolParam.h\
+                                        ./classes/Params/IntParam.cpp\
+                                        ./classes/Params/IntParam.h\
+                                        ./classes/Params/IntVecParam.cpp\
+                                        ./classes/Params/IntVecParam.h\
+                                        ./classes/Params/IntMatParam.cpp\
+                                        ./classes/Params/IntMatParam.h\
+                                        ./classes/Params/DoubleParam.cpp\
+                                        ./classes/Params/DoubleParam.h\
+                                        ./classes/Params/FileParam.cpp\
+                                        ./classes/Params/FileParam.h\
+                                        ./classes/Params/StringArrayParam.cpp\
+                                        ./classes/Params/StringArrayParam.h\
+                                        ./classes/Params/DoubleMatParam.cpp\
+                                        ./classes/Params/DoubleMatParam.h\
+                                        ./classes/Params/DoubleTransientMatParam.cpp\
+                                        ./classes/Params/DoubleTransientMatParam.h\
+                                        ./classes/Params/DoubleMatArrayParam.cpp\
+                                        ./classes/Params/DoubleMatArrayParam.h\
+                                        ./classes/Params/DoubleVecParam.cpp\
+                                        ./classes/Params/DoubleVecParam.h\
+                                        ./classes/Params/StringParam.cpp\
+                                        ./classes/Params/StringParam.h\
+                                        ./classes/Params/MatrixParam.h\
+                                        ./classes/Params/MatrixParam.cpp\
+                                        ./classes/Params/VectorParam.h\
+                                        ./classes/Params/VectorParam.cpp\
+                                        ./classes/Params/TransientParam.h\
+                                        ./classes/Params/TransientParam.cpp\
+                                        ./classes/Params/DataSetParam.h\
+                                        ./classes/Params/DataSetParam.cpp\
+                                        ./classes/Profiler.h\
+                                        ./classes/Profiler.cpp\
                                         ./shared/shared.h\
+                                        ./shared/Alloc/alloc.h\
+                                        ./shared/Alloc/alloc.cpp\
+                                        ./shared/Alloc/xNewDelete.h\
+                                        ./shared/MemOps/xMemCpy.h\
+                                        ./shared/MemOps/MemOps.h\
                                         ./shared/Matrix/matrix.h\
                                         ./shared/Matrix/MatrixUtils.cpp\
+                                        ./shared/io/io.h\
+                                        ./shared/io/Disk/diskio.h\
+                                        ./shared/io/Disk/pfopen.cpp\
+                                        ./shared/io/Disk/pfclose.cpp\
+                                        ./shared/io/Disk/WriteLockFile.cpp\
+                                        ./shared/io/Print/PrintfFunction.cpp\
+                                        ./shared/io/Print/Print.h\
+                                        ./shared/io/Comm/Comm.h\
+                                        ./shared/io/Comm/CommDef.h\
+                                        ./shared/io/Comm/IssmComm.h\
+                                        ./shared/io/Comm/IssmComm.cpp\
+                                        ./shared/LatLong/Ll2xyx.cpp\
+                                        ./shared/LatLong/Xy2llx.cpp\
+                                        ./shared/Enum/Enum.h\
+                                        ./shared/Enum/EnumDefinitions.h\
+                                        ./shared/Enum/EnumToStringx.cpp\
+                                        ./shared/Enum/StringToEnumx.cpp\
                                         ./shared/Numerics/numerics.h\
+                                        ./shared/Numerics/types.h\
+                                        ./shared/Numerics/constants.h\
                                         ./shared/Numerics/Verbosity.h\
                                         ./shared/Numerics/Verbosity.cpp\
-                                        ./shared/Numerics/IsInputConverged.cpp\
                                         ./shared/Numerics/GaussPoints.h\
                                         ./shared/Numerics/GaussPoints.cpp\
 …
                                         ./shared/Numerics/extrema.cpp\
                                         ./shared/Numerics/XZvectorsToCoordinateSystem.cpp\
                                         ./shared/Numerics/UnitConversion.cpp\
                                         ./shared/Numerics/OptionsFromAnalysis.cpp\
+                                        ./shared/Numerics/OptArgs.h\
+                                        ./shared/Numerics/OptPars.h\
                                         ./shared/Exceptions/exceptions.h\
                                         ./shared/Exceptions/Exceptions.cpp\
 …
                                         ./shared/Elements/Paterson.cpp\
                                         ./shared/Elements/Arrhenius.cpp\
-                                        ./shared/Elements/GetVerticesCoordinates.cpp\
-                                        ./shared/Elements/GetLocalDofList.cpp\
-                                        ./shared/Elements/GetGlobalDofList.cpp\
-                                        ./shared/Elements/GetNumberOfDofs.cpp\
                                         ./shared/Elements/PrintArrays.cpp\
                                         ./shared/Elements/PddSurfaceMassBalance.cpp\
 …
                                         ./toolkits/metis/metisincludes.h\
                                         ./toolkits/issm/issmtoolkit.h\
+                                        ./toolkits/issm/SeqVec.h\
+                                        ./toolkits/issm/SeqMat.h\
+                                        ./toolkits/issm/IssmToolkitUtils.h\
+                                        ./toolkits/issm/IssmToolkitUtils.cpp\
+                                        ./toolkits/issm/IssmAbsMat.h\
+                                        ./toolkits/issm/IssmAbsVec.h\
+                                        ./toolkits/issm/IssmDenseMat.h\
+                                        ./toolkits/issm/IssmMat.h\
+                                        ./toolkits/issm/IssmSeqVec.h\
+                                        ./toolkits/issm/IssmVec.h\
+                                        ./toolkits/issm/IssmSolver.h\
+                                        ./toolkits/issm/IssmSolver.cpp\
+                                        ./toolkits/issm/Bucket.h\
+                                        ./toolkits/adolc/adolcincludes.h\
+                                        ./toolkits/adolc/AdolcEdf.h\
+                                        ./toolkits/ToolkitOptions.h\
+                                        ./toolkits/ToolkitOptions.cpp\
                                         ./toolkits/triangle/triangleincludes.h\
+                                        ./toolkits/objects/toolkitobjects.h\
+                                        ./toolkits/objects/Matrix.h\
+                                        ./toolkits/objects/Vector.h\
+                                        ./toolkits/objects/Solver.h\
                                         ./toolkitsenums.h\
                                         ./toolkits.h\
-                                        ./io/io.h\
-                                        ./io/Disk/diskio.h\
-                                        ./io/Disk/pfopen.cpp\
-                                        ./io/Disk/pfclose.cpp\
-                                        ./io/Disk/WriteLockFile.cpp\
-                                        ./io/PrintfFunction.cpp\
-                                        ./EnumDefinitions/EnumDefinitions.h\
                                         ./modules/ModelProcessorx/ModelProcessorx.h\
                                         ./modules/ModelProcessorx/ModelProcessorx.cpp\
 …
                                         ./modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp\
                                         ./modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp\
                                         ./modules/ParsePetscOptionsx/ParsePetscOptionsx.h\
                                         ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\
+                                        ./modules/ParseToolkitsOptionsx/ParseToolkitsOptionsx.h\
+                                        ./modules/ParseToolkitsOptionsx/ParseToolkitsOptionsx.cpp\
                                         ./modules/NodesDofx/NodesDofx.h\
                                         ./modules/NodesDofx/NodesDofx.cpp\
 …
                                         ./modules/VerticesDofx/VerticesDofx.h\
                                         ./modules/VerticesDofx/VerticesDofx.cpp\
+                                        ./modules/VertexCoordinatesx/VertexCoordinatesx.h\
+                                        ./modules/VertexCoordinatesx/VertexCoordinatesx.cpp\
                                         ./modules/OutputResultsx/OutputResultsx.h\
                                         ./modules/OutputResultsx/OutputResultsx.cpp\
 …
                                         ./modules/Reduceloadx/Reduceloadx.h\
                                         ./modules/Reduceloadx/Reduceloadx.cpp\
-                                        ./modules/EnumToStringx/EnumToStringx.cpp\
-                                        ./modules/EnumToStringx/EnumToStringx.h\
-                                        ./modules/StringToEnumx/StringToEnumx.cpp\
-                                        ./modules/StringToEnumx/StringToEnumx.h\
                                         ./modules/ConstraintsStatex/ConstraintsStatex.cpp\
                                         ./modules/ConstraintsStatex/ConstraintsStatex.h\
 …
                                         ./modules/Solverx/Solverx.cpp\
                                         ./modules/Solverx/Solverx.h\
-                                        ./modules/Solverx/SolverxSeq.cpp\
                                         ./modules/VecMergex/VecMergex.cpp\
                                         ./modules/VecMergex/VecMergex.h\
 …
                                         ./modules/InputToResultx/InputToResultx.cpp\
                                         ./modules/InputToResultx/InputToResultx.h\
                                         ./modules/InputConvergencex/InputConvergencex.cpp\
                                         ./modules/InputConvergencex/InputConvergencex.h\
                                         ./solutions/convergence.cpp\
                                         ./solutions/ProcessArguments.cpp\
                                         ./solutions/ResetBoundaryConditions.cpp\
                                         ./solutions/AnalysisConfiguration.cpp\
                                         ./solutions/WrapperCorePointerFromSolutionEnum.cpp\
                                         ./solutions/CorePointerFromSolutionEnum.cpp\
                                         ./solutions/EnvironmentInit.cpp\
                                         ./solutions/EnvironmentFinalize.cpp\
                                         ./solutions/ad_core.cpp\
                                         ./solvers/solver_linear.cpp\
                                         ./solvers/solver_nonlinear.cpp\
                                         ./solvers/solver_newton.cpp\
                                         ./classes/objects/Options/Option.h\
                                         ./classes/objects/Options/GenericOption.h\
                                         ./classes/objects/Options/OptionUtilities.cpp\
                                         ./classes/objects/Options/OptionUtilities.h\
+                                        ./analyses/ProcessArguments.cpp\
+                                        ./analyses/ResetBoundaryConditions.cpp\
+                                        ./analyses/AnalysisConfiguration.cpp\
+                                        ./analyses/WrapperCorePointerFromSolutionEnum.cpp\
+                                        ./analyses/CorePointerFromSolutionEnum.cpp\
+                                        ./analyses/EnvironmentInit.cpp\
+                                        ./analyses/EnvironmentFinalize.cpp\
+                                        ./analyses/ad_core.cpp\
+                                        ./solutionsequences/solutionsequence_linear.cpp\
+                                        ./solutionsequences/solutionsequence_nonlinear.cpp\
+                                        ./solutionsequences/solutionsequence_newton.cpp\
+                                        ./solutionsequences/convergence.cpp\
+                                        ./classes/Options/Options.h\
+                                        ./classes/Options/Options.cpp\
+                                        ./classes/Options/Option.h\
+                                        ./classes/Options/GenericOption.h\
+                                        ./classes/Options/OptionUtilities.cpp\
+                                        ./classes/Options/OptionUtilities.h\
                                         ./classes/RiftStruct.cpp\
                                         ./classes/RiftStruct.h
 #}}}
 #DAKOTA sources  {{{
+dakota_sources = ./classes/dakota/DakotaPlugin.h\
+                                          ./classes/dakota/DakotaPlugin.cpp\
+                                          ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.h\
+dakota_sources = ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.h\
                                           ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.cpp\
                                           ./modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h\
 …
                                           ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\
                                           ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\
+                                          ./solutions/dakota_core.cpp\
+                                          ./solutions/DakotaSpawnCore.cpp
+                                          ./analyses/dakota_core.cpp\
+                                          ./analyses/DakotaSpawnCore.h\
+                                          ./analyses/DakotaSpawnCore.cpp
 #}}}
 #Transient sources  {{{
 transient_sources  = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp \
                                          ./solutions/transient_core.cpp
+                                                        ./analyses/transient_core.cpp
 #}}}
 #Steadystate sources  {{{
+steadystate_sources = ./solutions/steadystate_core.cpp\
+                                          ./solutions/steadystateconvergence.cpp
+steadystate_sources = ./analyses/steadystate_core.cpp
 #}}}
 #Prognostic sources  {{{
 …
                                               ./modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp\
                                               ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp\
                                                   ./solutions/prognostic_core.cpp
+                                                        ./analyses/prognostic_core.cpp
 #}}}
 #Thermal sources  {{{
 …
                                            ./modules/ConstraintsStatex/ThermalIsPresent.cpp\
                                            ./modules/ResetConstraintsx/ThermalConstraintsReset.cpp \
                                            ./solutions/thermal_core.cpp\
                                            ./solutions/enthalpy_core.cpp\
                                            ./solvers/solver_thermal_nonlinear.cpp
+                                           ./analyses/thermal_core.cpp\
+                                           ./analyses/enthalpy_core.cpp\
+                                           ./solutionsequences/solutionsequence_thermal_nonlinear.cpp
 #}}}
 #Control sources  {{{
 …
                                           ./modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp\
                                           ./modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.h\
                                           ./classes/objects/Inputs/ControlInput.h\
                                           ./classes/objects/Inputs/ControlInput.cpp\
+                                          ./classes/Inputs/ControlInput.h\
+                                          ./classes/Inputs/ControlInput.cpp\
                                           ./shared/Numerics/BrentSearch.cpp\
                                           ./shared/Numerics/OptimalSearch.cpp \
+                                          ./solutions/control_core.cpp\
+                                          ./solutions/controltao_core.cpp\
+                                          ./solutions/controlrestart.cpp\
+                                          ./solutions/controlconvergence.cpp\
+                                          ./solutions/objectivefunction.cpp\
+                                          ./solutions/gradient_core.cpp\
+                                          ./solutions/adjointdiagnostic_core.cpp\
+                                          ./solutions/adjointbalancethickness_core.cpp\
+                                          ./solutions/AdjointCorePointerFromSolutionEnum.cpp\
+                                          ./solvers/solver_adjoint_linear.cpp
+                                          ./analyses/control_core.cpp\
+                                          ./analyses/controltao_core.cpp\
+                                          ./analyses/objectivefunction.cpp\
+                                          ./analyses/gradient_core.cpp\
+                                          ./analyses/adjointdiagnostic_core.cpp\
+                                          ./analyses/adjointbalancethickness_core.cpp\
+                                          ./analyses/AdjointCorePointerFromSolutionEnum.cpp\
+                                          ./solutionsequences/solutionsequence_adjoint_linear.cpp
 #}}}
 #Hydrology sources  {{{
+hydrology_sources  = ./modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp\
+                                              ./modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp\
+                                              ./modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp\
+                                              ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp \
+                                                  ./solutions/hydrology_core.cpp\
+                                                  ./solutions/hydrology_core_step.cpp
+hydrology_sources  = ./modules/ModelProcessorx/HydrologyShreve/UpdateElementsHydrologyShreve.cpp\
+                                              ./modules/ModelProcessorx/HydrologyShreve/CreateNodesHydrologyShreve.cpp\
+                                              ./modules/ModelProcessorx/HydrologyShreve/CreateConstraintsHydrologyShreve.cpp\
+                                              ./modules/ModelProcessorx/HydrologyShreve/CreateLoadsHydrologyShreve.cpp \
+                                                        ./modules/ModelProcessorx/HydrologyShreve/CreateParametersHydrologyShreve.cpp \
+                                                        ./modules/ModelProcessorx/HydrologyDCInefficient/UpdateElementsHydrologyDCInefficient.cpp\
+                                                        ./modules/ModelProcessorx/HydrologyDCInefficient/CreateNodesHydrologyDCInefficient.cpp\
+                                                        ./modules/ModelProcessorx/HydrologyDCInefficient/CreateConstraintsHydrologyDCInefficient.cpp\
+                                                        ./modules/ModelProcessorx/HydrologyDCInefficient/CreateLoadsHydrologyDCInefficient.cpp \
+                                                        ./modules/ModelProcessorx/HydrologyDCInefficient/CreateParametersHydrologyDCInefficient.cpp \
+                                                        ./modules/ModelProcessorx/HydrologyDCEfficient/UpdateElementsHydrologyDCEfficient.cpp\
+                                                        ./modules/ModelProcessorx/HydrologyDCEfficient/CreateNodesHydrologyDCEfficient.cpp\
+                                                        ./modules/ModelProcessorx/HydrologyDCEfficient/CreateConstraintsHydrologyDCEfficient.cpp\
+                                                        ./modules/ModelProcessorx/HydrologyDCEfficient/CreateLoadsHydrologyDCEfficient.cpp \
+                                                        ./modules/ModelProcessorx/HydrologyDCEfficient/CreateParametersHydrologyDCEfficient.cpp \
+                                                        ./analyses/hydrology_core.cpp\
+                                                        ./solutionsequences/solutionsequence_hydro_nonlinear.cpp
 #}}}
 #Diagnostic sources  {{{
 …
                                               ./modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp \
                                               ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \
+                                              ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \
+                                                  ./shared/Elements/CoordinateSystemTransform.cpp\
+                                                  ./shared/Elements/TransformLoadVectorCoord.cpp \
+                                                  ./shared/Elements/TransformStiffnessMatrixCoord.cpp \
+                                                  ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \
+                                                  ./shared/Elements/TransformSolutionCoord.cpp\
+                                                  ./solutions/diagnostic_core.cpp\
+                                                  ./solvers/solver_stokescoupling_nonlinear.cpp
+                                                        ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \
+                                                        ./analyses/diagnostic_core.cpp\
+                                                        ./solutionsequences/solutionsequence_stokescoupling_nonlinear.cpp
 #}}}
 #Balanced sources  {{{
 …
                                             ./modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp\
                                             ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\
                                                 ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp\
                                                 ./solutions/balancethickness_core.cpp \
                                                 ./solutions/dummy_core.cpp
+                                                 ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp\
+                                                 ./analyses/balancethickness_core.cpp \
+                                                 ./analyses/dummy_core.cpp
 #}}}
 #Slope sources  {{{
 …
                                           ./modules/ModelProcessorx/SurfaceSlope/CreateConstraintsSurfaceSlope.cpp\
                                           ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp\
+                                          ./solutions/surfaceslope_core.cpp\
+                                          ./solutions/bedslope_core.cpp
+                                          ./analyses/surfaceslope_core.cpp\
+                                          ./analyses/bedslope_core.cpp
+#}}}
+#Gia sources  {{{
+gia_sources =  ./analyses/gia_core.cpp\
+                                        ./modules/ModelProcessorx/Gia/UpdateElementsGia.cpp\
+                                        ./modules/ModelProcessorx/Gia/CreateNodesGia.cpp \
+                                        ./modules/ModelProcessorx/Gia/CreateConstraintsGia.cpp\
+                                        ./modules/ModelProcessorx/Gia/CreateLoadsGia.cpp\
+                                        ./modules/GiaDeflectionCorex/GiaDeflectionCorex.cpp\
+                                        ./modules/GiaDeflectionCorex/GiaDeflectionCorex.h\
+                                        ./modules/GiaDeflectionCorex/distme.f\
+                                        ./modules/GiaDeflectionCorex/freed.f\
+                                        ./modules/GiaDeflectionCorex/ojrule.f\
+                                        ./modules/GiaDeflectionCorex/pwise.f\
+                                        ./modules/GiaDeflectionCorex/qwise.f\
+                                        ./modules/GiaDeflectionCorex/stot.f\
+                                        ./modules/GiaDeflectionCorex/what0.f\
+                                        ./classes/GiaDeflectionCoreArgs.h
 #}}}
 #Groundingline sources  {{{
 …
 #}}}
 #Rifts sources  {{{
 rifts_sources = ./classes/objects/Loads/Riftfront.cpp\
                                     ./classes/objects/Loads/Riftfront.h\
+rifts_sources = ./classes/Loads/Riftfront.cpp\
+                                    ./classes/Loads/Riftfront.h\
                                     ./modules/ConstraintsStatex/RiftConstraintsState.cpp
 #}}}
 …
 threed_sources = ./classes/gauss/GaussPenta.h\
                                      ./classes/gauss/GaussPenta.cpp\
+                                     ./classes/objects/ElementResults/PentaP1ElementResult.h\
+                                     ./classes/objects/ElementResults/PentaP1ElementResult.cpp\
+                                     ./classes/objects/Inputs/PentaP1Input.h\
+                                     ./classes/objects/Inputs/PentaP1Input.cpp\
+                                     ./classes/objects/Elements/Penta.h\
+                                     ./classes/objects/Elements/Penta.cpp\
+                                     ./classes/objects/Elements/PentaHook.h\
+                                     ./classes/objects/Elements/PentaHook.cpp\
+                                     ./classes/objects/Elements/PentaRef.h\
+                                     ./classes/objects/Elements/PentaRef.cpp
+                                     ./classes/ElementResults/PentaP1ElementResult.h\
+                                     ./classes/ElementResults/PentaP1ElementResult.cpp\
+                                     ./classes/Inputs/PentaP1Input.h\
+                                     ./classes/Inputs/PentaP1Input.cpp\
+                                     ./classes/Elements/Penta.h\
+                                     ./classes/Elements/Penta.cpp\
+                                     ./classes/Elements/PentaRef.h\
+                                     ./classes/Elements/PentaRef.cpp
 #}}}
 #Bamg sources  {{{
+bamg_sources =  ./classes/bamg/bamgobjects.h\
+                                ./classes/bamg/BamgGeom.h\
+                                ./classes/bamg/BamgGeom.cpp\
+                                ./classes/bamg/BamgMesh.h\
+                                ./classes/bamg/BamgMesh.cpp\
+                                ./classes/bamg/BamgOpts.h\
+                                ./classes/bamg/BamgOpts.cpp\
+                                ./classes/bamg/CrackedEdge.h\
+                                ./classes/bamg/CrackedEdge.cpp\
+                                ./classes/bamg/Curve.h\
+                                ./classes/bamg/Curve.cpp\
+                                ./classes/bamg/Direction.h\
+                                ./classes/bamg/Direction.cpp\
+                                ./classes/bamg/DoubleAndInt.h\
+                                ./classes/bamg/Edge.h\
+                                ./classes/bamg/Edge.cpp\
+                                ./classes/bamg/GeomEdge.h\
+                                ./classes/bamg/GeomEdge.cpp\
+                                ./classes/bamg/GeomSubDomain.h\
+                                ./classes/bamg/GeomSubDomain.cpp\
+                                ./classes/bamg/GeomVertex.h\
+                                ./classes/bamg/GeomVertex.cpp\
+                                ./classes/bamg/Geometry.cpp\
+                                ./classes/bamg/Geometry.h\
+                                ./classes/bamg/ListofIntersectionTriangles.cpp\
+                                ./classes/bamg/ListofIntersectionTriangles.h\
+                                ./classes/bamg/EigenMetric.cpp\
+                                ./classes/bamg/Metric.cpp\
+                                ./classes/bamg/Metric.h\
+                                ./classes/bamg/BamgQuadtree.cpp\
+                                ./classes/bamg/BamgQuadtree.h\
+                                ./classes/bamg/R2.h\
+                                ./classes/bamg/SetOfE4.cpp\
+                                ./classes/bamg/SetOfE4.h\
+                                ./classes/bamg/SubDomain.h\
+                                ./classes/bamg/SubDomain.cpp\
+                                ./classes/bamg/AdjacentTriangle.h\
+                                ./classes/bamg/AdjacentTriangle.cpp\
+                                ./classes/bamg/Triangle.cpp\
+                                ./classes/bamg/Triangle.h\
+                                ./classes/bamg/BamgVertex.cpp\
+                                ./classes/bamg/BamgVertex.h\
+                                ./classes/bamg/VertexOnEdge.h\
+                                ./classes/bamg/VertexOnEdge.cpp\
+                                ./classes/bamg/VertexOnGeom.h\
+                                ./classes/bamg/VertexOnGeom.cpp\
+                                ./classes/bamg/VertexOnVertex.h\
+                                ./classes/bamg/VertexOnVertex.cpp\
+                                ./classes/bamg/Mesh.cpp\
+                                ./classes/bamg/Mesh.h\
+bamg_sources =  ./bamg/bamgobjects.h\
+                                ./bamg/BamgGeom.h\
+                                ./bamg/BamgGeom.cpp\
+                                ./bamg/BamgMesh.h\
+                                ./bamg/BamgMesh.cpp\
+                                ./bamg/BamgOpts.h\
+                                ./bamg/BamgOpts.cpp\
+                                ./bamg/CrackedEdge.h\
+                                ./bamg/CrackedEdge.cpp\
+                                ./bamg/Curve.h\
+                                ./bamg/Curve.cpp\
+                                ./bamg/Direction.h\
+                                ./bamg/Direction.cpp\
+                                ./bamg/DoubleAndInt.h\
+                                ./bamg/Edge.h\
+                                ./bamg/Edge.cpp\
+                                ./bamg/GeomEdge.h\
+                                ./bamg/GeomEdge.cpp\
+                                ./bamg/GeomSubDomain.h\
+                                ./bamg/GeomSubDomain.cpp\
+                                ./bamg/GeomVertex.h\
+                                ./bamg/GeomVertex.cpp\
+                                ./bamg/Geometry.cpp\
+                                ./bamg/Geometry.h\
+                                ./bamg/ListofIntersectionTriangles.cpp\
+                                ./bamg/ListofIntersectionTriangles.h\
+                                ./bamg/EigenMetric.cpp\
+                                ./bamg/Metric.cpp\
+                                ./bamg/Metric.h\
+                                ./bamg/BamgQuadtree.cpp\
+                                ./bamg/BamgQuadtree.h\
+                                ./bamg/R2.h\
+                                ./bamg/SetOfE4.cpp\
+                                ./bamg/SetOfE4.h\
+                                ./bamg/SubDomain.h\
+                                ./bamg/SubDomain.cpp\
+                                ./bamg/AdjacentTriangle.h\
+                                ./bamg/AdjacentTriangle.cpp\
+                                ./bamg/Triangle.cpp\
+                                ./bamg/det.h \
+                                ./bamg/Triangle.h\
+                                ./bamg/BamgVertex.cpp\
+                                ./bamg/BamgVertex.h\
+                                ./bamg/VertexOnEdge.h\
+                                ./bamg/VertexOnEdge.cpp\
+                                ./bamg/VertexOnGeom.h\
+                                ./bamg/VertexOnGeom.cpp\
+                                ./bamg/VertexOnVertex.h\
+                                ./bamg/VertexOnVertex.cpp\
+                                ./bamg/Mesh.cpp\
+                                ./bamg/Mesh.h\
                                 ./shared/Bamg/Abs.h \
                                 ./shared/Bamg/BigPrimeNumber.h\
                                 ./shared/Bamg/BigPrimeNumber.cpp\
                                 ./shared/Bamg/BinaryRand.h \
-                                ./shared/Bamg/det.h \
                                 ./shared/Bamg/Exchange.h \
                                 ./shared/Bamg/extrema.h \
 …
 #}}}
 #Kriging sources  {{{
 kriging_sources = ./Container/Observations.h\
                                                 ./Container/Observations.cpp\
+kriging_sources = ./classes/kriging/Observations.h\
+                                                ./classes/kriging/Observations.cpp\
                                                 ./classes/kriging/Variogram.h \
                                                 ./classes/kriging/GaussianVariogram.h\
 …
 #For parallel kriging, only difference is ./modules/Krigingx/pKrigingx.cpp with no multithreading
 pkriging_sources = ./Container/Observations.h\
                                                 ./Container/Observations.cpp\
+pkriging_sources = ./classes/kriging/Observations.h\
+                                                ./classes/kriging/Observations.cpp\
                                                 ./classes/kriging/Variogram.h \
                                                 ./classes/kriging/GaussianVariogram.h\
 …
                              ./modules/KMLOverlayx/KMLOverlayx.h\
                              ./modules/KMLOverlayx/KMLOverlayx.cpp\
+                             ./classes/objects/KML/KML_Attribute.cpp\
+                             ./classes/objects/KML/KML_Attribute.h\
+                             ./classes/objects/KML/KML_Comment.cpp\
+                             ./classes/objects/KML/KML_Comment.h\
+                             ./classes/objects/KML/KML_ColorStyle.cpp\
+                             ./classes/objects/KML/KML_ColorStyle.h\
+                             ./classes/objects/KML/KML_Container.cpp\
+                             ./classes/objects/KML/KML_Container.h\
+                             ./classes/objects/KML/KML_Document.cpp\
+                             ./classes/objects/KML/KML_Document.h\
+                             ./classes/objects/KML/KML_Feature.cpp\
+                             ./classes/objects/KML/KML_Feature.h\
+                             ./classes/objects/KML/KML_File.cpp\
+                             ./classes/objects/KML/KML_File.h\
+                             ./classes/objects/KML/KML_Folder.cpp\
+                             ./classes/objects/KML/KML_Folder.h\
+                             ./classes/objects/KML/KML_Geometry.cpp\
+                             ./classes/objects/KML/KML_Geometry.h\
+                             ./classes/objects/KML/KML_GroundOverlay.cpp\
+                             ./classes/objects/KML/KML_GroundOverlay.h\
+                             ./classes/objects/KML/KML_Icon.cpp\
+                             ./classes/objects/KML/KML_Icon.h\
+                             ./classes/objects/KML/KML_LatLonBox.cpp\
+                             ./classes/objects/KML/KML_LatLonBox.h\
+                             ./classes/objects/KML/KML_LinearRing.cpp\
+                             ./classes/objects/KML/KML_LinearRing.h\
+                             ./classes/objects/KML/KML_LineString.cpp\
+                             ./classes/objects/KML/KML_LineString.h\
+                             ./classes/objects/KML/KML_LineStyle.cpp\
+                             ./classes/objects/KML/KML_LineStyle.h\
+                             ./classes/objects/KML/KML_MultiGeometry.cpp\
+                             ./classes/objects/KML/KML_MultiGeometry.h\
+                             ./classes/objects/KML/KML_Object.cpp\
+                             ./classes/objects/KML/KML_Object.h\
+                             ./classes/objects/KML/KML_Overlay.cpp\
+                             ./classes/objects/KML/KML_Overlay.h\
+                             ./classes/objects/KML/KML_Point.cpp\
+                             ./classes/objects/KML/KML_Point.h\
+                             ./classes/objects/KML/KML_Placemark.cpp\
+                             ./classes/objects/KML/KML_Placemark.h\
+                             ./classes/objects/KML/KML_Polygon.cpp\
+                             ./classes/objects/KML/KML_Polygon.h\
+                             ./classes/objects/KML/KML_PolyStyle.cpp\
+                             ./classes/objects/KML/KML_PolyStyle.h\
+                             ./classes/objects/KML/KML_Style.cpp\
+                             ./classes/objects/KML/KML_Style.h\
+                             ./classes/objects/KML/KML_StyleSelector.cpp\
+                             ./classes/objects/KML/KML_StyleSelector.h\
+                             ./classes/objects/KML/KML_SubStyle.cpp\
+                             ./classes/objects/KML/KML_SubStyle.h\
+                             ./classes/objects/KML/KML_Unknown.cpp\
+                             ./classes/objects/KML/KML_Unknown.h\
+                             ./classes/objects/KML/KMLFileReadUtils.cpp\
+                             ./classes/objects/KML/KMLFileReadUtils.h
+                             ./kml/kmlobjects.h\
+                             ./kml/KML_Attribute.cpp\
+                             ./kml/KML_Attribute.h\
+                             ./kml/KML_Comment.cpp\
+                             ./kml/KML_Comment.h\
+                             ./kml/KML_ColorStyle.cpp\
+                             ./kml/KML_ColorStyle.h\
+                             ./kml/KML_Container.cpp\
+                             ./kml/KML_Container.h\
+                             ./kml/KML_Document.cpp\
+                             ./kml/KML_Document.h\
+                             ./kml/KML_Feature.cpp\
+                             ./kml/KML_Feature.h\
+                             ./kml/KML_File.cpp\
+                             ./kml/KML_File.h\
+                             ./kml/KML_Folder.cpp\
+                             ./kml/KML_Folder.h\
+                             ./kml/KML_Geometry.cpp\
+                             ./kml/KML_Geometry.h\
+                             ./kml/KML_GroundOverlay.cpp\
+                             ./kml/KML_GroundOverlay.h\
+                             ./kml/KML_Icon.cpp\
+                             ./kml/KML_Icon.h\
+                             ./kml/KML_LatLonBox.cpp\
+                             ./kml/KML_LatLonBox.h\
+                             ./kml/KML_LinearRing.cpp\
+                             ./kml/KML_LinearRing.h\
+                             ./kml/KML_LineString.cpp\
+                             ./kml/KML_LineString.h\
+                             ./kml/KML_LineStyle.cpp\
+                             ./kml/KML_LineStyle.h\
+                             ./kml/KML_MultiGeometry.cpp\
+                             ./kml/KML_MultiGeometry.h\
+                             ./kml/KML_Object.cpp\
+                             ./kml/KML_Object.h\
+                             ./kml/KML_Overlay.cpp\
+                             ./kml/KML_Overlay.h\
+                             ./kml/KML_Point.cpp\
+                             ./kml/KML_Point.h\
+                             ./kml/KML_Placemark.cpp\
+                             ./kml/KML_Placemark.h\
+                             ./kml/KML_Polygon.cpp\
+                             ./kml/KML_Polygon.h\
+                             ./kml/KML_PolyStyle.cpp\
+                             ./kml/KML_PolyStyle.h\
+                             ./kml/KML_Style.cpp\
+                             ./kml/KML_Style.h\
+                             ./kml/KML_StyleSelector.cpp\
+                             ./kml/KML_StyleSelector.h\
+                             ./kml/KML_SubStyle.cpp\
+                             ./kml/KML_SubStyle.h\
+                             ./kml/KML_Unknown.cpp\
+                             ./kml/KML_Unknown.h\
+                             ./kml/KMLFileReadUtils.cpp\
+                             ./kml/KMLFileReadUtils.h
 #}}}
 #Petsc sources  {{{
 …
                                         ./toolkits/petsc/objects/PetscVec.h\
                                         ./toolkits/petsc/objects/PetscVec.cpp\
+                                        ./toolkits/petsc/petscincludes.h\
+                                        ./shared/Numerics/PetscOptionsFromAnalysis.cpp\
+                                        ./modules/Solverx/SolverxPetsc.cpp\
+                                        ./modules/Solverx/DofTypesToIndexSet.cpp
+                                        ./toolkits/petsc/objects/PetscSolver.cpp\
+                                        ./toolkits/petsc/objects/PetscSolver.h\
+                                        ./toolkits/petsc/petscincludes.h
+#}}}
+#Mumps sources  {{{
+mumps_sources=      ./toolkits/mumps\
+                                        ./toolkits/mumps/mumpsincludes.h\
+                                        ./toolkits/mumps/MpiDenseMumpsSolve.cpp
+#}}}
+#Gsl sources  {{{
+gsl_sources=      ./toolkits/gsl\
+                                        ./toolkits/gsl/gslincludes.h\
+                                        ./toolkits/gsl/DenseGslSolve.cpp
 #}}}
 #Mpi sources  {{{
 mpi_sources= ./toolkits/mpi/mpiincludes.h\
                                 ./toolkits/mpi/patches/mpipatches.h\
+                                ./toolkits/mpi/patches/DetermineLocalSize.cpp
+                                ./toolkits/mpi/patches/DetermineLocalSize.cpp\
+                                ./toolkits/mpi/patches/DetermineGlobalSize.cpp\
+                                ./toolkits/mpi/patches/DetermineRowRankFromLocalSize.cpp\
+                                ./toolkits/mpi/patches/GetOwnershipBoundariesFromRange.cpp\
+                                ./toolkits/issm/IssmMpiDenseMat.h\
+                                ./toolkits/issm/IssmMpiVec.h
 #}}}
 #Metis sources  {{{
 …
                         ./shared/Threads/PartitionRange.cpp\
                         ./shared/Exp/exp.h\
+                        ./shared/Exp/IsInPoly.cpp\
+                        ./shared/Exp/IsInPolySerial.cpp\
+                        ./shared/Exp/ExpWrite.cpp\
+                        ./shared/Exp/exp.cpp\
                         ./shared/TriMesh/trimesh.h\
                         ./shared/TriMesh/AssociateSegmentToElement.cpp\
 …
                         ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp\
                         ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp\
-                        ./modules/Xy2llx/Xy2llx.h\
-                        ./modules/Xy2llx/Xy2llx.cpp\
-                        ./modules/Ll2xyx/Ll2xyx.h\
-                        ./modules/Ll2xyx/Ll2xyx.cpp\
                         ./modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp\
                         ./modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h\
 …
                         ./modules/HoleFillerx/HoleFillerx.cpp\
                         ./modules/HoleFillerx/HoleFillerx.h\
+                        ./modules/EdgeDetectionx/EdgeDetectionx.cpp\
+                        ./modules/EdgeDetectionx/EdgeDetectionx.h\
                         ./modules/AverageFilterx/AverageFilterx.cpp\
                         ./modules/AverageFilterx/AverageFilterx.h\
 …
 endif
+if MUMPS
+issm_sources  +=  $(mumps_sources)
+endif
+if GSL
+issm_sources  +=  $(gsl_sources)
+endif
 if TRANSIENT
 issm_sources  +=  $(transient_sources)
 …
 endif
+if GIA
+issm_sources  +=  $(gia_sources)
+endif
 if CONTROL
 issm_sources  +=  $(control_sources)
 …
 libISSMCore_a_SOURCES  = $(issm_sources)
+libISSMCore_a_CXXFLAGS = $(ALLCXXFLAGS)
+libISSMCore_a_CXXFLAGS = $(ALLCXXFLAGS) $(DAKOTAFLAGS)
+libISSMCore_a_FFLAGS = $(AM_FFLAGS)
 if SHAREDLIBS
 libISSM_la_SOURCES = solutions/issm.cpp
+libISSM_la_SOURCES = main/issm.cpp
 libISSM_la_LIBADD = libISSMCore.la libISSMOverload.la
 libISSMCore_la_SOURCES  = $(issm_sources)
 libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB)
+libISSMOverload_la_SOURCES = ./shared/String/stricmp.c
+libISSMCore_la_FFLAGS = $(AM_FFLAGS)
 endif
 …
 #}}}
 #Overload library, to overload any non-standard symbols. {{{
+libISSMOverload_a_SOURCES = ./shared/String/stricmp.c
+libISSMOverload_a_SOURCES = ./shared/String/stricmp.cpp\
+                                                        ./shared/String/ApiPrintf.cpp
 libISSMOverload_a_CFLAGS  = -fPIC -D_C_ $(COPTFLAGS) $(CFLAGS)
 #}}}
 …
 endif
 issm_SOURCES = solutions/issm.cpp
+issm_SOURCES = main/issm.cpp
 issm_CXXFLAGS= -fPIC $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS)
 if KRIGING
 bin_PROGRAMS += kriging
 kriging_SOURCES = solutions/kriging.cpp
+kriging_SOURCES = main/kriging.cpp
 kriging_CXXFLAGS= -fPIC $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS)
 endif
 …
 bin_PROGRAMS +=  issmRose.exe
 issmRose_exe_LDADD = ./libISSMRose.a $(LDADD)
 issmRose_exe_SOURCES = solutions/issm.cpp
+issmRose_exe_SOURCES = main/issm.cpp
 issmRose_exe_CXXFLAGS= -fPIC $(CXXOPTFLAGS) $(COPTFLAGS)
 LDADD +=  $(ADIC2LIB)

issm/trunk/src/c/classes/DofIndexing.cpp

-              r13975
+              r15396
 #endif
-#include <stdio.h>
 #include <string.h>
+#include "./classes.h"
+#include "../EnumDefinitions/EnumDefinitions.h"
+#include "../shared/shared.h"
+#include "../Container/Container.h"
+#include "../include/include.h"
+#include "./DofIndexing.h"
+#include "../shared/Numerics/types.h"
+#include "../shared/Numerics/constants.h"
+#include "../shared/io/Print/Print.h"
+#include "../shared/Exceptions/exceptions.h"
+#include "../shared/MemOps/MemOps.h"
+#include "../shared/Enum/Enum.h"
 /*DofIndexing constructors and destructor*/
 …
         this->ssize    = UNDEF;
         this->clone    = false;
+        this->active   = true;
         this->f_set    = NULL;
         this->s_set    = NULL;
 …
 /*FUNCTION DofIndexing::DofIndexing(int gsize){{{*/
 DofIndexing::DofIndexing(int in_gsize){
         this->Init(in_gsize,NULL);
+}
 /*}}}*/
 …
 DofIndexing::DofIndexing(DofIndexing* in){ //copy constructor
+        this->gsize = in->gsize;
+        this->fsize = in->fsize;
+        this->ssize = in->ssize;
+        this->clone = in->clone;
+        this->gsize  = in->gsize;
+        this->fsize  = in->fsize;
+        this->ssize  = in->ssize;
+        this->clone  = in->clone;
+        this->active = in->active;
         if(this->gsize>0){
 …
 void DofIndexing::Init(int in_gsize,int* in_doftype){
+        this->gsize=in_gsize;
+        this->clone=false;
+        /*allocate: */
+        this->gsize = in_gsize;
+        /*At this point, assume this is not a clone (will be dealt with later)*/
+        this->clone = false;
+        /*memory allocation */
         if(this->gsize>0){
+                this->f_set=xNew<bool>(this->gsize);
+                this->s_set=xNew<bool>(this->gsize);
+                this->svalues=xNew<IssmDouble>(this->gsize);
+                if(in_doftype)this->doftype=xNew<int>(this->gsize);
+                this->gdoflist=xNew<int>(this->gsize);
+        }
+                this->f_set    = xNew<bool>(this->gsize);
+                this->s_set    = xNew<bool>(this->gsize);
+                this->svalues  = xNew<IssmDouble>(this->gsize);
+                this->gdoflist = xNew<int>(this->gsize);
+                if(in_doftype)
+                 this->doftype = xNew<int>(this->gsize);
+        }
+        /*Assign values assuming no Dirichlet at this point*/
         for(int i=0;i<this->gsize;i++){
+                /*assume dof is free, no constraints, no rigid body constraint: */
+                this->f_set[i]=true;
+                this->s_set[i]=false;
+                if(this->doftype)this->doftype[i]=in_doftype[i];
+                this->svalues[i]=0; //0 constraint is the default value
+                this->gdoflist[i]=UNDEF;
+                this->f_set[i]    = true;
+                this->s_set[i]    = false;
+                this->svalues[i]  = 0.;      //0 constraint is the default value
+                this->gdoflist[i] = UNDEF;
+                if(this->doftype)
+                 this->doftype[i]=in_doftype[i];
+        }
+}
 …
                 this->fsize=size;
                 xDelete<int>(this->fdoflist);
+                if(this->fsize)this->fdoflist=xNew<int>(size);
+                else this->fdoflist=NULL;
+                if(this->fsize)
+                 this->fdoflist=xNew<int>(size);
+                else
+                 this->fdoflist=NULL;
+        }
         else if(setenum==SsetEnum){
 …
                 this->ssize=size;
                 xDelete<int>(this->sdoflist);
+                if(this->ssize)this->sdoflist=xNew<int>(size);
+                else this->sdoflist=NULL;
+                if(this->ssize)
+                 this->sdoflist=xNew<int>(size);
+                else
+                 this->sdoflist=NULL;
+        }
         else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
 …
 void DofIndexing::Echo(void){
+        _printLine_("DofIndexing:");
+        _printLine_("   gsize: " << gsize);
+        _printLine_("   clone: " << clone);
+        _printf_("DofIndexing:\n");
+        _printf_("   gsize:  " << gsize << "\n");
+        _printf_("   clone:  " << clone << "\n");
+        _printf_("   active: " << active << "\n");
+}
 /*}}}*/
 …
         int i;
+        _printLine_("DofIndexing:");
+        _printLine_("   gsize: " << gsize);
+        _printLine_("   fsize: " << fsize);
+        _printLine_("   ssize: " << ssize);
+        _printLine_("   clone: " << clone);
+        _printLine_("   set membership: f,s sets ");
+        _printf_("DofIndexing:\n");
+        _printf_("   gsize:  " << gsize << "\n");
+        _printf_("   fsize:  " << fsize << "\n");
+        _printf_("   ssize:  " << ssize << "\n");
+        _printf_("   clone:  " << clone << "\n");
+        _printf_("   active: " << active << "\n");
+        _printf_("   set membership: f,s sets \n");
         for(i=0;i<gsize;i++){
                 _printLine_("      dof " << i << ": " <<(f_set[i]?"true":"false")<< " " <<(s_set[i]?"true":"false"));
+        }
         _printString_("   svalues (" << this->ssize << "): |");
+                _printf_("      dof " << i << ": " <<(f_set[i]?"true":"false")<< " " <<(s_set[i]?"true":"false") << "\n");
+        }
+        _printf_("   svalues (" << this->ssize << "): |");
         for(i=0;i<this->gsize;i++){
                 if(this->s_set[i])_printString_(" " << svalues[i] << " |");
+        }
         _printLine_("");
+                if(this->s_set[i])_printf_(" " << svalues[i] << " |");
+        }
+        _printf_("\n");
         if(doftype){
                 _printString_("   doftype: |");
+                _printf_("   doftype: |");
                 for(i=0;i<gsize;i++){
                         _printString_(" " << doftype[i] << " |");
+                        _printf_(" " << doftype[i] << " |");
+                }
                 _printLine_("");
+        }
         else _printLine_("   doftype: NULL");
         _printString_("   g_doflist (" << this->gsize << "): |");
+                _printf_("\n");
+        }
+        else _printf_("   doftype: NULL\n");
+        _printf_("   g_doflist (" << this->gsize << "): |");
         for(i=0;i<this->gsize;i++){
                 _printString_(" " << gdoflist[i] << " |");
+        }
         _printLine_("");
         _printString_("   f_doflist (" << this->fsize << "): |");
+                _printf_(" " << gdoflist[i] << " |");
+        }
+        _printf_("\n");
+        _printf_("   f_doflist (" << this->fsize << "): |");
         for(i=0;i<this->fsize;i++){
                 _printString_(" " << fdoflist[i] << " |");
+        }
         _printLine_("");
         _printString_("   s_doflist (" << this->ssize << "): |");
+                _printf_(" " << fdoflist[i] << " |");
+        }
+        _printf_("\n");
+        _printf_("   s_doflist (" << this->ssize << "): |");
         for(i=0;i<this->ssize;i++){
                 _printString_(" " << sdoflist[i] << " |");
+        }
         _printLine_("");
+                _printf_(" " << sdoflist[i] << " |");
+        }
+        _printf_("\n");
+}
 /*}}}*/
+/*FUNCTION DofIndexing::Deactivate{{{*/
+void DofIndexing::Deactivate(void){
+        this->active = false;
+        /*Constrain to 0. at this point*/
+        for(int i=0;i<this->gsize;i++){
+                this->f_set[i]    = false;
+                this->s_set[i]    = true;
+                this->svalues[i]  = 0.;
+        }
+        return;
+}
+/*}}}*/
+/*FUNCTION DofIndexing::Activate{{{*/
+void DofIndexing::Activate(void){
+        this->active = true;
+        /*Constrain to 0. at this point*/
+        for(int i=0;i<this->gsize;i++){
+                this->f_set[i]    = true;
+                this->s_set[i]    = false;
+                this->svalues[i]  = 0.;
+        }
+        return;
+}
+/*}}}*/

issm/trunk/src/c/classes/DofIndexing.h

-              r13975
+              r15396
 #ifndef _DOFINDEXING_H_
 #define  _DOFINDEXING_H_
+#define _DOFINDEXING_H_
 #include "../include/include.h"
+#include "../shared/Numerics/types.h"
 class DofIndexing{
 …
                 /*partitioning: */
                 bool clone;   //this node is replicated from another one
+                bool active;  //Is this node active or inactive (all dofs are constrained)
                 /*boundary conditions sets: */
 …
                 /*DofIndexing management: {{{*/
                 DofIndexing* Spawn(int* indices, int numindices);
+                void Activate(void);
+                void Deactivate(void);
                 /*}}}*/

issm/trunk/src/c/classes/FemModel.cpp

-              r14310
+              r15396
 /*!\file FemModel.c
+/*!\file FemModel.cpp
  * \brief: implementation of the FemModel object
  */
 …
 #include <stdio.h>
+#include "../Container/Container.h"
+#include "../analyses/analyses.h"
+#include "../shared/io/io.h"
+#include "./classes.h"
+#include "../shared/Enum/Enum.h"
+/*module includes: {{{*/
 #include "../modules/ModelProcessorx/ModelProcessorx.h"
+#include "../solutions/solutions.h"
+#include "../io/io.h"
+#include "./classes.h"
+#include "../include/include.h"
+#include "../EnumDefinitions/EnumDefinitions.h"
+#include "../modules/modules.h"
+#include "../modules/VerticesDofx/VerticesDofx.h"
+#include "../modules/SpcNodesx/SpcNodesx.h"
+#include "../modules/ConfigureObjectsx/ConfigureObjectsx.h"
+#include "../modules/ParseToolkitsOptionsx/ParseToolkitsOptionsx.h"
+#include "../modules/OutputResultsx/OutputResultsx.h"
+#include "../modules/GetVectorFromInputsx/GetVectorFromInputsx.h"
+#include "../modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h"
+#include "../modules/NodesDofx/NodesDofx.h"
+#include "../modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.h"
+#include "../modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.h"
+#include "../modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.h"
+#include "../modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.h"
+#include "../modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.h"
+#include "../modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.h"
+#include "../modules/ThicknessAlongGradientx/ThicknessAlongGradientx.h"
+#include "../modules/ThicknessAcrossGradientx/ThicknessAcrossGradientx.h"
+#include "../modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.h"
+#include "../modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.h"
+#include "../modules/NodalValuex/NodalValuex.h"
+#include "../modules/GetVectorFromInputsx/GetVectorFromInputsx.h"
+#include "../modules/AverageOntoPartitionx/AverageOntoPartitionx.h"
+/*}}}*/
 /*Object constructors and destructor*/
 /*FUNCTION FemModel::FemModel(int argc,char** argv){{{*/
+/*FUNCTION FemModel::FemModel(int argc,char** argv,COMM incomm){{{*/
 FemModel::FemModel(int argc,char** argv,COMM incomm){
 …
         this->comm=incomm;
         this->SetStaticComm();
         /*Now, initialize PETSC: */
         #ifdef _HAVE_PETSC_
 …
+}
 /*}}}*/
 /*FUNCTION FemModel::FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){{{*/
 FemModel::FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){
+/*FUNCTION FemModel::FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* toolkitsfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){{{*/
+FemModel::FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* toolkitsfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){
         /*Call InitFromFiles. This constructor is just a wrapper: */
         this->InitFromFiles(rootpath, inputfilename, outputfilename, petscfilename, lockfilename, in_solution_type,analyses,nummodels);
+        this->InitFromFiles(rootpath, inputfilename, outputfilename, toolkitsfilename, lockfilename, in_solution_type,analyses,nummodels);
+}
 …
         this->parameters->FindParam(&lockfilename,LockFileNameEnum);
         if (waitonlock>0){
                 _pprintLine_("write lock file:");
+                _printf0_("write lock file:\n");
                 WriteLockFile(lockfilename);
+        }
 …
         /*Before we delete the profiler, report statistics for this run: */
         profiler->Tag(Finish);  //final tagging
         _pprintLine_("");
         _pprintLine_("   "<<setw(40)<<left<<"FemModel initialization elapsed time:"<<profiler->DeltaTime(StartInit,FinishInit));
         _pprintLine_("   "<<setw(40)<<left<<"Core solution elapsed time:"<<profiler->DeltaTime(StartCore,FinishCore));
         _pprintLine_("");
         _pprintLine_("   Total elapsed time:"
+        _printf0_("\n");
+        _printf0_("   "<<setw(40)<<left<<"FemModel initialization elapsed time:"<<profiler->DeltaTime(StartInit,FinishInit) << "\n");
+        _printf0_("   "<<setw(40)<<left<<"Core solution elapsed time:"<<profiler->DeltaTime(StartCore,FinishCore) << "\n");
+        _printf0_("\n");
+        _printf0_("   Total elapsed time:"
                         <<profiler->DeltaTimeModHour(Start,Finish)<<" hrs "
                         <<profiler->DeltaTimeModMin(Start,Finish)<<" min "
                         <<profiler->DeltaTimeModSec(Start,Finish)<<" sec"
                         );
         _pprintLine_("");
+        _printf0_("\n");
         /*Now delete: */
         delete profiler;
         /*Finalize PETSC for this model: */
         #ifdef _HAVE_PETSC_
         _pprintLine_("closing Petsc");
+        _printf0_("closing Petsc\n");
         PetscFinalize();
         #endif
 …
 void FemModel::Echo(void){
         _printLine_("FemModel echo: ");
         _printLine_("   number of fem models: " << nummodels);
         _printLine_("   analysis_type_list: ");
         for(int i=0;i<nummodels;i++)_printLine_("     " << i << ": " << EnumToStringx(analysis_type_list[i]));
         _printLine_("   current analysis_type: ");
         _printLine_("     " << analysis_counter << ": " << EnumToStringx(analysis_type_list[analysis_counter]));
+}
 /*}}}*/
 /*FUNCTION FemModel::InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){{{*/
 void FemModel::InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){
+        _printf_("FemModel echo: \n");
+        _printf_("   number of fem models: " << nummodels << "\n");
+        _printf_("   analysis_type_list: \n");
+        for(int i=0;i<nummodels;i++)_printf_("     " << i << ": " << EnumToStringx(analysis_type_list[i]) << "\n");
+        _printf_("   current analysis_type: \n");
+        _printf_("     " << analysis_counter << ": " << EnumToStringx(analysis_type_list[analysis_counter]) << "\n");
+}
+/*}}}*/
+/*FUNCTION FemModel::InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* toolkitsfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){{{*/
+void FemModel::InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* toolkitsfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){
         /*intermediary*/
 …
         int         analysis_type;
         FILE       *IOMODEL = NULL;
         FILE       *petscoptionsfid = NULL;
+        FILE       *toolkitsoptionsfid = NULL;
         FILE       *output_fid = NULL;
         int         my_rank;
 …
         for(i=0;i<nummodels;i++){
                 if(VerboseMProcessor()) _pprintLine_("   Processing finite element model of analysis " << EnumToStringx(analysis_type_list[i]) << ":");
+                if(VerboseMProcessor()) _printf0_("   Processing finite element model of analysis " << EnumToStringx(analysis_type_list[i]) << ":\n");
                 analysis_type=analysis_type_list[i];
                 this->SetCurrentConfiguration(analysis_type);
                 if(i==0){
                         if(VerboseMProcessor()) _pprintLine_("      creating vertex degrees of freedom");
+                        if(VerboseMProcessor()) _printf0_("      creating vertex PIDs\n");
                         VerticesDofx(vertices,parameters); //only call once, we only have one set of vertices
+                }
                 if(VerboseMProcessor()) _pprintLine_("      resolving node constraints");
+                if(VerboseMProcessor()) _printf0_("      resolving node constraints\n");
                 SpcNodesx(nodes,constraints,parameters,analysis_type);
                 if(VerboseMProcessor()) _pprintLine_("      creating nodal degrees of freedom");
+                if(VerboseMProcessor()) _printf0_("      creating nodal degrees of freedom\n");
                 NodesDofx(nodes,parameters,analysis_type);
                 if(VerboseMProcessor()) _pprintLine_("      configuring element and loads");
+                if(VerboseMProcessor()) _printf0_("      configuring element and loads\n");
                 ConfigureObjectsx(elements, loads, nodes, vertices, materials,parameters);
+        }
 …
         this->parameters->AddObject(new StringParam(LockFileNameEnum,lockfilename));
         /*Now, deal with petsc options, which need to be put into the parameters dataset: */
         petscoptionsfid=pfopen(petscfilename,"r");
         ParsePetscOptionsx(this->parameters,petscoptionsfid);
         pfclose(petscoptionsfid,petscfilename);
+        /*Now, deal with toolkits options, which need to be put into the parameters dataset: */
+        toolkitsoptionsfid=pfopen(toolkitsfilename,"r");
+        ParseToolkitsOptionsx(this->parameters,toolkitsoptionsfid);
+        pfclose(toolkitsoptionsfid,toolkitsfilename);
+}
 /*}}}*/
 …
 void FemModel::OutputResults(void){
         _pprintLine_("write results to disk:");
+        _printf0_("write results to disk:\n");
         /*Just call the OutputResultsx module: */
 …
         this->loads->SetCurrentConfiguration(elements, loads, nodes,vertices, materials,parameters);
+        #ifdef _HAVE_PETSC_
+        /*take care of petsc options, that depend on this analysis type (present only after model processor)*/
+        if(this->parameters->Exist(PetscOptionsStringsEnum)){
+                PetscOptionsFromAnalysis(this->parameters,analysis_type);
+                if(VerboseSolver()) _pprintLine_("      petsc Options set for analysis type: " << EnumToStringx(analysis_type));
+        }
+        #endif
+        /*take care of toolkits options, that depend on this analysis type (present only after model processor)*/
+        if(this->parameters->Exist(ToolkitsOptionsStringsEnum)){
+                ToolkitsOptionsFromAnalysis(this->parameters,analysis_type);
+                if(VerboseSolver()) _printf0_("      toolkits Options set for analysis type: " << EnumToStringx(analysis_type) << "\n");
+        }
+}
 …
         void (*solutioncore)(FemModel*)=NULL; //core solution function pointer
         _pprintLine_("call computational core:");
+        _printf0_("call computational core:\n");
         /*Retrieve solution_type from parameters: */
 …
                 solution_memory=profiler->Memory(FinishCore);
                 _pprintLine_("Solution elapsed time  : " << solution_time << "  Seconds");
                 _pprintLine_("Solution elapsed flops : " << solution_flops << "  Flops");
                 _pprintLine_("Solution memory used   : " << solution_memory << "  Bytes");
+                _printf0_("Solution elapsed time    : " << solution_time   << " Seconds\n");
+                _printf0_("Solution number of flops : " << solution_flops  << " Flops\n");
+                _printf0_("Solution memory used     : " << solution_memory << " Bytes\n");
                 /*Add to results: */
                 results->AddObject(new GenericExternalResult<IssmDouble>(results->Size()+1, ProfilingSolutionTimeEnum, solution_time, 1, 0));
                 results->AddObject(new GenericExternalResult<IssmDouble>(results->Size()+1, ProfilingCurrentMemEnum, solution_memory, 1, 0));
                 results->AddObject(new GenericExternalResult<IssmDouble>(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops, 1, 0));
+        }
+                #ifdef _HAVE_ADOLC_
+                solution_time=profiler->DeltaTime(StartAdCore,FinishAdCore);
+                solution_flops=profiler->DeltaFlops(StartAdCore,FinishAdCore);
+                solution_memory=profiler->Memory(FinishAdCore);
+                _printf0_("AD Solution elapsed time    : " << solution_time   << " Seconds\n");
+                _printf0_("AD Solution number of flops : " << solution_flops  << " Flops\n");
+                _printf0_("AD Solution memory used     : " << solution_memory << " Bytes\n");
+                #endif
+                        }
+}
 /*}}}*/
 …
         /*Update element inputs*/
         InputUpdateFromVectorx(elements,nodes,vertices,loads,materials,parameters,vz,VzMeshEnum,VertexEnum);
+        InputUpdateFromVectorx(elements,nodes,vertices,loads,materials,parameters,vz,VzMeshEnum,VertexPIdEnum);
         /*Free ressources:*/
         xDelete<IssmDouble>(thickness);
         xDelete<IssmDouble>(bed);
         xdelete(&vz);
+        delete vz;
         return 1;
+}
 …
 void FemModel::UpdateConstraintsx(void){ /*{{{*/
+        Element   *element = NULL;
         IssmDouble time;
         int    analysis_type;
+        int        analysis_type;
         /*retrieve parameters: */
 …
         /*start module: */
+        if(VerboseModule()) _pprintLine_("   Updating constraints for time: " << time);
+        /*First, update dof constraints in nodes, using constraints: */
+        if(VerboseModule()) _printf0_("   Updating constraints for time: " << time << "\n");
+        /*First, Nodes might be activated/deactivated by element*/
+        for(int i=0;i<elements->Size();i++){
+                element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
+                element->UpdateConstraints();
+        }
+        /*Second, constraints might be time dependent: */
         SpcNodesx(nodes,constraints,parameters,analysis_type);
 …
+}
 /*}}}*/
 void FemModel::Responsex(IssmDouble* responses,const char* response_descriptor,bool process_units,int weight_index){/*{{{*/
+void FemModel::Responsex(IssmDouble* responses,const char* response_descriptor,int weight_index){/*{{{*/
         int response_descriptor_enum=StringToEnumx(response_descriptor);
+        this->Responsex(responses, response_descriptor_enum, process_units, weight_index);
+}
+/*}}}*/
+void FemModel::Responsex(IssmDouble* responses,int response_descriptor_enum,bool process_units,int weight_index){/*{{{*/
+        this->Responsex(responses, response_descriptor_enum,weight_index);
+}
+/*}}}*/
+void FemModel::Responsex(IssmDouble* responses,int response_descriptor_enum,int weight_index){/*{{{*/
         switch (response_descriptor_enum){
                 #ifdef _HAVE_RESPONSES_
+                case IceVolumeEnum:              this->IceVolumex(responses,process_units); break;
+                case MinVelEnum:                 this->MinVelx(responses,process_units); break;
+                case MaxVelEnum:                 this->MaxVelx(                  responses,process_units); break;
+                case MinVxEnum:                  this->MinVxx(responses,process_units); break;
+                case MaxVxEnum:                  this->MaxVxx(                   responses,process_units); break;
+                case MaxAbsVxEnum:               this->MaxAbsVxx(                responses,process_units); break;
+                case MinVyEnum:                  this->MinVyx(responses,process_units); break;
+                case MaxVyEnum:                  this->MaxVyx(                   responses,process_units); break;
+                case MaxAbsVyEnum:               this->MaxAbsVyx(                responses,process_units); break;
+                case MinVzEnum:                  this->MinVzx(responses,process_units); break;
+                case MaxVzEnum:                  this->MaxVzx(                   responses,process_units); break;
+                case MaxAbsVzEnum:               this->MaxAbsVzx(                responses,process_units); break;
+                case MassFluxEnum:               this->MassFluxx(         responses,process_units); break;
+                case SurfaceAbsVelMisfitEnum:    SurfaceAbsVelMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case SurfaceRelVelMisfitEnum:    SurfaceRelVelMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case SurfaceLogVelMisfitEnum:    SurfaceLogVelMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case SurfaceLogVxVyMisfitEnum:   SurfaceLogVxVyMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case SurfaceAverageVelMisfitEnum:SurfaceAverageVelMisfitx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case ThicknessAbsMisfitEnum:     ThicknessAbsMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case ThicknessAbsGradientEnum:   this->ThicknessAbsGradientx(responses, process_units,weight_index); break;
+                case ThicknessAlongGradientEnum: ThicknessAlongGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case ThicknessAcrossGradientEnum:ThicknessAcrossGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case BalancethicknessMisfitEnum:BalancethicknessMisfitx(responses,process_units,weight_index); break;
+                case TotalSmbEnum:                                      this->TotalSmbx(responses,process_units); break;
+                case RheologyBbarAbsGradientEnum:RheologyBbarAbsGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case DragCoefficientAbsGradientEnum:DragCoefficientAbsGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break;
+                case MaterialsRheologyBbarEnum: this->ElementResponsex(responses,MaterialsRheologyBbarEnum,process_units); break;
+                case VelEnum:                   this->ElementResponsex(responses,VelEnum,process_units); break;
+                case FrictionCoefficientEnum:NodalValuex(responses, FrictionCoefficientEnum,elements,nodes, vertices, loads, materials, parameters,process_units); break;
+                case IceVolumeEnum:              this->IceVolumex(responses); break;
+                case MinVelEnum:                 this->MinVelx(responses); break;
+                case MaxVelEnum:                 this->MaxVelx(                  responses); break;
+                case MinVxEnum:                  this->MinVxx(responses); break;
+                case MaxVxEnum:                  this->MaxVxx(                   responses); break;
+                case MaxAbsVxEnum:               this->MaxAbsVxx(                responses); break;
+                case MinVyEnum:                  this->MinVyx(responses); break;
+                case MaxVyEnum:                  this->MaxVyx(                   responses); break;
+                case MaxAbsVyEnum:               this->MaxAbsVyx(                responses); break;
+                case MinVzEnum:                  this->MinVzx(responses); break;
+                case MaxVzEnum:                  this->MaxVzx(                   responses); break;
+                case MaxAbsVzEnum:               this->MaxAbsVzx(                responses); break;
+                case MassFluxEnum:               this->MassFluxx(         responses); break;
+                #ifdef _HAVE_CONTROL_
+                case SurfaceAbsVelMisfitEnum:    SurfaceAbsVelMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case SurfaceRelVelMisfitEnum:    SurfaceRelVelMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case SurfaceLogVelMisfitEnum:    SurfaceLogVelMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case SurfaceLogVxVyMisfitEnum:   SurfaceLogVxVyMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case SurfaceAverageVelMisfitEnum:SurfaceAverageVelMisfitx( responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case ThicknessAbsMisfitEnum:     ThicknessAbsMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case ThicknessAbsGradientEnum:   this->ThicknessAbsGradientx(responses,weight_index); break;
+                case ThicknessAlongGradientEnum: ThicknessAlongGradientx(responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case ThicknessAcrossGradientEnum:ThicknessAcrossGradientx(responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case RheologyBbarAbsGradientEnum:RheologyBbarAbsGradientx(responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case DragCoefficientAbsGradientEnum:DragCoefficientAbsGradientx(responses, elements,nodes, vertices, loads, materials, parameters,weight_index); break;
+                case BalancethicknessMisfitEnum:BalancethicknessMisfitx(responses,weight_index); break;
+                #endif
+                case TotalSmbEnum:                                      this->TotalSmbx(responses); break;
+                case MaterialsRheologyBbarEnum: this->ElementResponsex(responses,MaterialsRheologyBbarEnum); break;
+                case VelEnum:                   this->ElementResponsex(responses,VelEnum); break;
+                case FrictionCoefficientEnum:NodalValuex(responses, FrictionCoefficientEnum,elements,nodes, vertices, loads, materials, parameters); break;
                 default: _error_("response descriptor \"" << EnumToStringx(response_descriptor_enum) << "\" not supported yet!"); break;
                 #else
 …
 /*}}}*/
 void FemModel::RequestedOutputsx(int* requested_outputs, int numoutputs){/*{{{*/
         int      output_enum;
 …
                                 case IceVolumeEnum:
                                         Responsex(&output_value,"IceVolume",false,0);
+                                        Responsex(&output_value,"IceVolume",0);
                                         results->AddObject(new GenericExternalResult<double>(results->Size()+1,IceVolumeEnum,reCast<IssmPDouble>(output_value),step,time));
                                         break;
                                 case TotalSmbEnum:
                                         Responsex(&output_value,"TotalSmb",false,0);
+                                        Responsex(&output_value,"TotalSmb",0);
                                         results->AddObject(new GenericExternalResult<double>(results->Size()+1,TotalSmbEnum,reCast<IssmPDouble>(output_value),step,time));
                                         break;
                                 case MaxVelEnum:
                                         Responsex(&output_value,"MaxVel",false,0);
+                                        Responsex(&output_value,"MaxVel",0);
                                         results->AddObject(new GenericExternalResult<double>(results->Size()+1,MaxVelEnum,reCast<IssmPDouble>(output_value),step,time));
                                         break;
 …
 void FemModel::RequestedDependentsx(void){/*{{{*/
         bool        isautodiff      = false;
         IssmDouble  output_value;
 …
         /*Display message*/
         if(VerboseModule()) _pprintLine_("   Generating matrices");
+        if(VerboseModule()) _printf0_("   Generating matrices\n");
         /*retrive parameters: */
 …
                 for (i=0;i<this->elements->Size();i++){
                         element=dynamic_cast<Element*>(this->elements->GetObjectByOffset(i));
+                        element->CreateKMatrix(Kff_temp,NULL,NULL);
+                }
+                        element->CreateKMatrix(Kff_temp,NULL);
+                }
                 for (i=0;i<this->loads->Size();i++){
                         load=dynamic_cast<Load*>(this->loads->GetObjectByOffset(i));
 …
         for (i=0;i<this->elements->Size();i++){
                 element=dynamic_cast<Element*>(this->elements->GetObjectByOffset(i));
+                element->CreateKMatrix(Kff,Kfs,df);
+        }
+                element->CreateKMatrix(Kff,Kfs);
+        }
         for (i=0;i<this->loads->Size();i++){
                 load=dynamic_cast<Load*>(this->loads->GetObjectByOffset(i));
 …
                         if(load->InAnalysis(configuration_type)) load->PenaltyCreatePVector(pf,kmax);
+                }
+        }
+        /*Create dof vector for stiffness matrix preconditioning*/
+        for (i=0;i<this->elements->Size();i++){
+                element=dynamic_cast<Element*>(this->elements->GetObjectByOffset(i));
+                element->CreateDVector(df);
+        }
 …
         /*Assign output pointers: */
         if(pKff) *pKff=Kff;
         else      xdelete(&Kff);
+        else      delete Kff;
         if(pKfs) *pKfs=Kfs;
         else      xdelete(&Kfs);
+        else      delete Kfs;
         if(ppf)  *ppf=pf;
         else      xdelete(&pf);
+        else      delete pf;
         if(pdf)  *pdf=df;
         else      xdelete(&df);
+        else      delete df;
         if(pkmax) *pkmax=kmax;
+}
 …
 /*}}}*/
 #ifdef _HAVE_RESPONSES_
 void FemModel::MassFluxx(IssmDouble* pmass_flux,bool process_units){/*{{{*/
+void FemModel::MassFluxx(IssmDouble* pmass_flux){/*{{{*/
         int          i,j;
 …
                         if (element->Id()==element_id){
                                 /*We found the element which owns this segment, use it to compute the mass flux: */
                                 mass_flux+=element->MassFlux(segments+5*i+0,process_units);
+                                mass_flux+=element->MassFlux(segments+5*i+0);
                                 break;
+                        }
 …
 }/*}}}*/
 void FemModel::MaxAbsVxx(IssmDouble* pmaxabsvx,bool process_units){/*{{{*/
+void FemModel::MaxAbsVxx(IssmDouble* pmaxabsvx){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MaxAbsVx(&element_maxabsvx,process_units);
+                element->MaxAbsVx(&element_maxabsvx);
                 if(element_maxabsvx>maxabsvx) maxabsvx=element_maxabsvx;
+        }
 …
 }/*}}}*/
 void FemModel::MaxAbsVyx(IssmDouble* pmaxabsvy,bool process_units){/*{{{*/
+void FemModel::MaxAbsVyx(IssmDouble* pmaxabsvy){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MaxAbsVy(&element_maxabsvy,process_units);
+                element->MaxAbsVy(&element_maxabsvy);
                 if(element_maxabsvy>maxabsvy) maxabsvy=element_maxabsvy;
+        }
 …
 }/*}}}*/
 void FemModel::MaxAbsVzx(IssmDouble* pmaxabsvz,bool process_units){/*{{{*/
+void FemModel::MaxAbsVzx(IssmDouble* pmaxabsvz){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MaxAbsVz(&element_maxabsvz,process_units);
+                element->MaxAbsVz(&element_maxabsvz);
                 if(element_maxabsvz>maxabsvz) maxabsvz=element_maxabsvz;
+        }
 …
 }/*}}}*/
 void FemModel::MaxVelx(IssmDouble* pmaxvel,bool process_units){/*{{{*/
+void FemModel::MaxVelx(IssmDouble* pmaxvel){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MaxVel(&element_maxvel,process_units);
+                element->MaxVel(&element_maxvel);
                 if(element_maxvel>maxvel) maxvel=element_maxvel;
+        }
 …
 }/*}}}*/
 void FemModel::MaxVxx(IssmDouble* pmaxvx,bool process_units){/*{{{*/
+void FemModel::MaxVxx(IssmDouble* pmaxvx){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MaxVx(&element_maxvx,process_units);
+                element->MaxVx(&element_maxvx);
                 if(element_maxvx>maxvx) maxvx=element_maxvx;
+        }
 …
 }/*}}}*/
 void FemModel::MaxVyx(IssmDouble* pmaxvy,bool process_units){/*{{{*/
+void FemModel::MaxVyx(IssmDouble* pmaxvy){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MaxVy(&element_maxvy,process_units);
+                element->MaxVy(&element_maxvy);
                 if(element_maxvy>maxvy) maxvy=element_maxvy;
+        }
 …
 }/*}}}*/
 void FemModel::MaxVzx(IssmDouble* pmaxvz,bool process_units){/*{{{*/
+void FemModel::MaxVzx(IssmDouble* pmaxvz){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MaxVz(&element_maxvz,process_units);
+                element->MaxVz(&element_maxvz);
                 if(element_maxvz>maxvz) maxvz=element_maxvz;
+        }
 …
 }/*}}}*/
 void FemModel::MinVelx(IssmDouble* pminvel,bool process_units){/*{{{*/
+void FemModel::MinVelx(IssmDouble* pminvel){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MinVel(&element_minvel,process_units);
+                element->MinVel(&element_minvel);
                 if(element_minvel<minvel) minvel=element_minvel;
+        }
 …
 }/*}}}*/
 void FemModel::MinVxx(IssmDouble* pminvx,bool process_units){/*{{{*/
+void FemModel::MinVxx(IssmDouble* pminvx){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MinVx(&element_minvx,process_units);
+                element->MinVx(&element_minvx);
                 if(element_minvx<minvx) minvx=element_minvx;
+        }
 …
 }/*}}}*/
 void FemModel::MinVyx(IssmDouble* pminvy,bool process_units){/*{{{*/
+void FemModel::MinVyx(IssmDouble* pminvy){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MinVy(&element_minvy,process_units);
+                element->MinVy(&element_minvy);
                 if(element_minvy<minvy) minvy=element_minvy;
+        }
 …
 }/*}}}*/
 void FemModel::MinVzx(IssmDouble* pminvz,bool process_units){/*{{{*/
+void FemModel::MinVzx(IssmDouble* pminvz){/*{{{*/
         int i;
 …
         for(i=0;i<this->elements->Size();i++){
                 Element* element=(Element*)this->elements->GetObjectByOffset(i);
                 element->MinVz(&element_minvz,process_units);
+                element->MinVz(&element_minvz);
                 if(element_minvz<minvz) minvz=element_minvz;
+        }
 …
 }/*}}}*/
 void FemModel::TotalSmbx(IssmDouble* pSmb,bool process_units){/*{{{*/
+void FemModel::TotalSmbx(IssmDouble* pSmb){/*{{{*/
         IssmDouble local_smb = 0;
 …
 }/*}}}*/
 void FemModel::IceVolumex(IssmDouble* pV,bool process_units){/*{{{*/
+void FemModel::IceVolumex(IssmDouble* pV){/*{{{*/
         IssmDouble local_ice_volume = 0;
 …
 }/*}}}*/
 void FemModel::ElementResponsex(IssmDouble* presponse,int response_enum,bool process_units){/*{{{*/
+void FemModel::ElementResponsex(IssmDouble* presponse,int response_enum){/*{{{*/
         int found=0;
 …
         /*Ok, we found the element, compute responseocity: */
         if(my_rank==cpu_found){
                 element->ElementResponse(&response,response_enum,IuToExtEnum);
+                element->ElementResponse(&response,response_enum);
+        }
 …
 #endif
 #ifdef _HAVE_CONTROL_
 void FemModel::BalancethicknessMisfitx(IssmDouble* presponse,bool process_units,int weight_index){/*{{{*/
+void FemModel::BalancethicknessMisfitx(IssmDouble* presponse,int weight_index){/*{{{*/
         IssmDouble J = 0;
 …
         for(int i=0;i<this->elements->Size();i++){
                 Element* element=dynamic_cast<Element*>(this->elements->GetObjectByOffset(i));
                 J+=element->BalancethicknessMisfit(process_units,weight_index);
+                J+=element->BalancethicknessMisfit(weight_index);
+        }
         #ifdef _HAVE_MPI_
 …
 }/*}}}*/
+void FemModel::ThicknessAbsGradientx( IssmDouble* pJ, bool process_units, int weight_index){/*{{{*/
+void FemModel::ThicknessAbsGradientx( IssmDouble* pJ, int weight_index){/*{{{*/
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->ThicknessAbsGradient(process_units,weight_index);
+                J+=element->ThicknessAbsGradient(weight_index);
+        }
 …
 void FemModel::CostFunctionx(IssmDouble* pJ){/*{{{*/
         /*Intermediary*/
         int      num_responses;
 …
         J=0;
         for(int i=0;i<num_responses;i++){
                 this->Responsex(&Jplus,EnumToStringx(responses[i]),false,i); //False means DO NOT process units
+                this->Responsex(&Jplus,EnumToStringx(responses[i]),i);
                 J+=Jplus;
+        }
 …
 void FemModel::DakotaResponsesx(double* d_responses,char** responses_descriptors,int numresponsedescriptors,int d_numresponses){/*{{{*/
         int        i,j;
         int        my_rank;
-        bool       process_units = true;
         /*intermediary: */
 …
                         parameters->SetParam(index,IndexEnum);
                         this->Responsex(&femmodel_response,root,process_units,0);//0 is the index for weights
+                        this->Responsex(&femmodel_response,root,0);//0 is the index for weights
                         if(my_rank==0){
 …
                         /*perfectly normal response function: */
                         this->Responsex(&femmodel_response,root,process_units,0);//0 is the weight index
+                        this->Responsex(&femmodel_response,root,0);//0 is the weight index
                         if(my_rank==0){
 …
         /*Synthesize echo: {{{*/
         if(my_rank==0){
                 _printString_("   responses: " << d_numresponses << ": ");
                 for(i=0;i<d_numresponses-1;i++)_printString_(d_responses[i] << "|");
                 _printString_(d_responses[d_numresponses-1]);
                 _printLine_("");
+                _printf_("   responses: " << d_numresponses << ": ");
+                for(i=0;i<d_numresponses-1;i++)_printf_(d_responses[i] << "|");
+                _printf_(d_responses[d_numresponses-1]);
+                _printf_("\n");
+        }
         /*}}}*/
 …
 /*}}}*/
 #endif
+#ifdef _HAVE_GIA_
+void FemModel::Deflection(Vector<IssmDouble>* wg,Vector<IssmDouble>* dwgdt, IssmDouble* x, IssmDouble* y){ /*{{{*/
+  int      i;
+        /*intermediary: */
+        Element *element     = NULL;
+        /*Go through elements, and add contribution from each element to the deflection vector wg:*/
+        for (i=0;i<elements->Size();i++){
+                element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
+                element->GiaDeflection(wg,dwgdt, x,y);
+        }
+}
+/*}}}*/
+#endif
+#ifdef _HAVE_HYDROLOGY_
+void FemModel::HydrologyEPLupdateDomainx(void){ /*{{{*/
+        Vector<IssmDouble>* mask          = NULL;
+        IssmDouble*         serial_mask   = NULL;
+        Vector<IssmDouble>* active        = NULL;
+        IssmDouble*         serial_active = NULL;
+        /*Step 1: update maks, the mask might be extended by residual and/or using downstream sediment head*/
+        mask=new Vector<IssmDouble>(nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum));
+        for (int i=0;i<elements->Size();i++){
+                Element* element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
+                element->HydrologyEPLGetMask(mask);
+        }
+        /*Assemble and serialize*/
+        mask->Assemble();
+        serial_mask=mask->ToMPISerial();
+        delete mask;
+        /*Update Mask*/
+        InputUpdateFromVectorx(elements,nodes,vertices,loads,materials,parameters,serial_mask,HydrologydcMaskEplactiveEnum,NodeSIdEnum);
+        xDelete<IssmDouble>(serial_mask);
+        /*Step 2: update node activity. If one element is connected to mask=1, all nodes are active*/
+        active=new Vector<IssmDouble>(nodes->NumberOfNodes(HydrologyDCEfficientAnalysisEnum));
+        for (int i=0;i<elements->Size();i++){
+                Element* element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
+                element->HydrologyEPLGetActive(active);
+        }
+        /*Assemble and serialize*/
+        active->Assemble();
+        serial_active=active->ToMPISerial();
+        delete active;
+        /*Update node activation accordingly*/
+        int counter =0;
+        for (int i=0;i<nodes->Size();i++){
+                Node* node=dynamic_cast<Node*>(nodes->GetObjectByOffset(i));
+                if(node->InAnalysis(HydrologyDCEfficientAnalysisEnum)){
+                        if(serial_active[node->Sid()]==1.){
+                                node->Activate();
+                                counter++;
+                        }
+                        else{
+                                node->Deactivate();
+                        }
+                }
+        }
+        xDelete<IssmDouble>(serial_active);
+        #ifdef _HAVE_MPI_
+        int sum_counter;
+        MPI_Reduce(&counter,&sum_counter,1,MPI_INT,MPI_SUM,0,IssmComm::GetComm() );
+        MPI_Bcast(&sum_counter,1,MPI_INT,0,IssmComm::GetComm());
+        counter=sum_counter;
+        #endif
+        if(VerboseSolution()) _printf0_("   Number of active nodes in EPL layer: "<< counter <<"\n");
+        /*Update dof indexings*/
+        this->UpdateConstraintsx();
+}
+/*}}}*/
+void FemModel::HydrologyTransferx(void){ /*{{{*/
+        Vector<IssmDouble>* transferg=NULL;
+        /*Vector allocation*/
+        transferg=new Vector<IssmDouble>(nodes->NumberOfNodes());
+        for (int i=0;i<elements->Size();i++){
+                Element* element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
+                element->GetHydrologyTransfer(transferg);
+        }
+        /*Assemble*/
+        transferg->Assemble();
+        /*Update Inputs*/
+        InputUpdateFromVectorx(elements,nodes,vertices,loads,materials,parameters,transferg,WaterTransferEnum,NodesEnum);
+        delete transferg;
+}
+/*}}}*/
+#endif

issm/trunk/src/c/classes/FemModel.h

-              r14310
+              r15396
 /*Headers:*/
 /*{{{*/
-#include "./objects/Object.h"
 #include "../toolkits/toolkits.h"
 class DataSet;
 …
                 /*Modules*/
                 #ifdef _HAVE_RESPONSES_
                 void MassFluxx(IssmDouble* presponse,bool process_units);
                 void MaxAbsVxx(IssmDouble* presponse,bool process_units);
                 void MaxAbsVyx(IssmDouble* presponse,bool process_units);
                 void MaxAbsVzx(IssmDouble* presponse,bool process_units);
                 void MaxVelx(IssmDouble* presponse,bool process_units);
                 void MaxVxx(IssmDouble* presponse,bool process_units);
                 void MaxVyx(IssmDouble* presponse,bool process_units);
                 void MaxVzx(IssmDouble* presponse,bool process_units);
                 void MinVelx(IssmDouble* presponse,bool process_units);
                 void MinVxx(IssmDouble* presponse,bool process_units);
                 void MinVyx(IssmDouble* presponse,bool process_units);
                 void MinVzx(IssmDouble* presponse,bool process_units);
                 void TotalSmbx(IssmDouble* pSmb,bool process_units);
                 void IceVolumex(IssmDouble* pV,bool process_units);
                 void ElementResponsex(IssmDouble* presponse,int response_enum,bool process_units);
                 void BalancethicknessMisfitx(IssmDouble* pV,bool process_units,int weight_index);
+                void MassFluxx(IssmDouble* presponse);
+                void MaxAbsVxx(IssmDouble* presponse);
+                void MaxAbsVyx(IssmDouble* presponse);
+                void MaxAbsVzx(IssmDouble* presponse);
+                void MaxVelx(IssmDouble* presponse);
+                void MaxVxx(IssmDouble* presponse);
+                void MaxVyx(IssmDouble* presponse);
+                void MaxVzx(IssmDouble* presponse);
+                void MinVelx(IssmDouble* presponse);
+                void MinVxx(IssmDouble* presponse);
+                void MinVyx(IssmDouble* presponse);
+                void MinVzx(IssmDouble* presponse);
+                void TotalSmbx(IssmDouble* pSmb);
+                void IceVolumex(IssmDouble* pV);
+                void ElementResponsex(IssmDouble* presponse,int response_enum);
+                void BalancethicknessMisfitx(IssmDouble* pV,int weight_index);
                 #endif
                 #ifdef  _HAVE_DAKOTA_
 …
                 void RequestedOutputsx(int* requested_outputs, int numoutputs);
                 void RequestedDependentsx(void);
                 void Responsex(IssmDouble* presponse,int response_descriptor_enum,bool process_units,int weight_index);
                 void Responsex(IssmDouble* presponse,const char* response_descriptor,bool process_units,int weight_index);
+                void Responsex(IssmDouble* presponse,int response_descriptor_enum,int weight_index);
+                void Responsex(IssmDouble* presponse,const char* response_descriptor,int weight_index);
                 #ifdef _HAVE_CONTROL_
                 void CostFunctionx( IssmDouble* pJ);
+                void ThicknessAbsGradientx( IssmDouble* pJ, bool process_units,int weight_index);
+                void ThicknessAbsGradientx( IssmDouble* pJ,int weight_index);
+                #endif
+                #ifdef _HAVE_GIA_
+                void Deflection(Vector<IssmDouble>* wg,Vector<IssmDouble>* dwgdt, IssmDouble* x, IssmDouble* y);
                 #endif
                 void SystemMatricesx(Matrix<IssmDouble>** pKff, Matrix<IssmDouble>** pKfs, Vector<IssmDouble>** ppf, Vector<IssmDouble>** pdf, IssmDouble* pkmax);
 …
                 void UpdateConstraintsx(void);
                 int  UpdateVertexPositionsx(void);
+                void ParEplMask(void);
+                void HydrologyTransferx(void);
+                void HydrologyEPLupdateDomainx(void);
 };

issm/trunk/src/c/classes/Hook.cpp

-              r13975
+              r15396
 #include <string.h>
 #include "./classes.h"
+#include "../Container/Container.h"
+#include "../EnumDefinitions/EnumDefinitions.h"
+#include "../shared/Enum/Enum.h"
 #include "../shared/shared.h"
-#include "../include/include.h"
 /*Constructor/Destructors*/
 …
         int i;
         if (num){
                 _printLine_("   Hook: ");
                 _printLine_("      num=" << this->num);
                 _printString_("      ids: ");
                 for (i=0;i<this->num;i++) _printString_(this->ids[i] << " ");
                 _printLine_("");
                 _printString_("      offsets: ");
                 for (i=0;i<this->num;i++) _printString_(this->offsets[i] << " ");
                 _printLine_("");
+                _printf_("   Hook: \n");
+                _printf_("      num=" << this->num << "\n");
+                _printf_("      ids: ");
+                for (i=0;i<this->num;i++) _printf_(this->ids[i] << " ");
+                _printf_("\n");
+                _printf_("      offsets: ");
+                for (i=0;i<this->num;i++) _printf_(this->offsets[i] << " ");
+                _printf_("\n");
+        }
         else{
                 _printLine_("   Hook: num=0 ");
+                _printf_("   Hook: num=0 \n");
+        }
+}
 …
         int i;
         if (num){
                 _printLine_("   Hook: ");
                 _printLine_("      num=" << this->num);
                 _printString_("      ids: ");
                 for (i=0;i<this->num;i++) _printString_(this->ids[i] << " ");
                 _printLine_("");
                 _printString_("      offsets: ");
                 for (i=0;i<this->num;i++) _printString_(this->offsets[i] << " ");
                 _printLine_("");
                 if (!objects) _printLine_("      warning: object not hooked yet");
+                _printf_("   Hook: \n");
+                _printf_("      num=" << this->num << "\n");
+                _printf_("      ids: ");
+                for (i=0;i<this->num;i++) _printf_(this->ids[i] << " ");
+                _printf_("\n");
+                _printf_("      offsets: ");
+                for (i=0;i<this->num;i++) _printf_(this->offsets[i] << " ");
+                _printf_("\n");
+                if (!objects) _printf_("      warning: object not hooked yet\n");
                 else{
                         _printString_("      objects:\n   ");
+                        _printf_("      objects:\n   ");
                         for (i=0;i<this->num;i++){
                                 _printLine_("         object " << i);
+                                _printf_("         object " << i << "\n");
                                 if(objects[i]) objects[i]->DeepEcho();
                                 else           _printLine_("            no object hooked yet (not configured)");
+                                else           _printf_("            no object hooked yet (not configured)\n");
+                        }
+                }
+        }
         else{
                 _printLine_("   Hook: num=0 ");
+                _printf_("   Hook: num=0 \n");
+        }
+}

issm/trunk/src/c/classes/Hook.h

-              r13975
+              r15396
 /*Headers:*/
 /*{{{*/
+#include "./objects/Object.h"
+class DataSet;
+#include "../datastructures/datastructures.h"
 /*}}}*/

issm/trunk/src/c/classes/IoModel.cpp

-              r13975
+              r15396
 #include "./classes.h"
+#include "../io/io.h"
+#include "../Container/Parameters.h"
+#include "../shared/io/io.h"
 #include "../shared/shared.h"
-#include "../include/include.h"
 /*FUNCTION IoModel::IoModel(){{{*/
 …
         this->data=NULL;
         this->independents=NULL;
+        this->independent_objects=NULL;
         this->constants=NULL;
 …
         this->my_nodes=NULL;
         this->my_vertices=NULL;
         this->singlenodetoelementconnectivity=NULL;
         this->numbernodetoelementconnectivity=NULL;
 …
         this->my_nodes=NULL;
         this->my_vertices=NULL;
         this->singlenodetoelementconnectivity=NULL;
         this->numbernodetoelementconnectivity=NULL;
 …
                 for(int i=0;i<MaximumNumberOfEnums;i++){
                         if(this->data[i]){
                                 _pprintLine_("Info: previous pointer of " << EnumToStringx(i) << " has not been freed (DeleteData has not been called)");
+                                _printf0_("Info: previous pointer of " << EnumToStringx(i) << " has not been freed (DeleteData has not been called)\n");
+                        }
+                }
 …
                 else{
                         if(record_enum!=MaximumNumberOfEnums){
                                 _printLine_("");
                                 _printLine_("=========================================================================");
                                 _printLine_(" Enums in marshalled file are not compatible with compiled code          ");
                                 _printLine_("                                                                         ");
                                 _printLine_("   * If you are running ISSM on a remote cluster:                        ");
                                 _printLine_("     make sure that you are using the same version of ISSM on your local ");
                                 _printLine_("     machine and remote cluster (you might need to run svn update)       ");
                                 _printLine_("   * If you are running ISSM on your local machine:                      ");
                                 _printLine_("     make sure that all the code is compiled (modules and executables)   ");
                                 _printLine_("   * If you are a developer and just added a new Enum:                   ");
                                 _printLine_("     you might need to run ./Synchronize.sh in src/c/EnumDefinitions     ");
                                 _printLine_("     and recompile                                                       ");
                                 _printLine_("=========================================================================");
                                 _printLine_("");
+                                _printf0_("\n");
+                                _printf0_("=========================================================================\n");
+                                _printf0_(" Enums in marshalled file are not compatible with compiled code          \n");
+                                _printf0_("                                                                         \n");
+                                _printf0_("   * If you are running ISSM on a remote cluster:                        \n");
+                                _printf0_("     make sure that you are using the same version of ISSM on your local \n");
+                                _printf0_("     machine and remote cluster (you might need to run svn update)       \n");
+                                _printf0_("   * If you are running ISSM on your local machine:                      \n");
+                                _printf0_("     make sure that all the code is compiled (modules and executables)   \n");
+                                _printf0_("   * If you are a developer and just added a new Enum:                   \n");
+                                _printf0_("     you might need to run ./Synchronize.sh in src/c/EnumDefinitions     \n");
+                                _printf0_("     and recompile                                                       \n");
+                                _printf0_("=========================================================================\n");
+                                _printf0_("\n");
                                 _error_("Enums not consistent (See error message above)");
+                        }
 …
 void IoModel::DeclareIndependents(void){
         int         i;
         bool        autodiff                = false;
         int         num_independent_objects;
+        int  i;
+        bool autodiff = false;
+        int  num_independent_objects;
         int *names = NULL;
         int *types = NULL;
+        int         numberofvertices;
+        int         dummy;
+        bool        keep=false;
+        int  dummy;
+        bool keep=false;
         /*Initialize array detecting whether data[i] is an independent AD mode variable: */
 …
         if(autodiff){
-                this->FetchData(&numberofvertices,MeshNumberofverticesEnum);
                 #ifdef _HAVE_ADOLC_
+                /*Start trace: {{{*/
+                /*Start trace*/
                 this->FetchData(&keep,AutodiffKeepEnum);
                 if(keep)trace_on(1,1);
                 else    trace_on(1);
+                /*}}}*/
+                /*build dataset made of independent objects: {{{*/
+                /*build dataset made of independent objects:*/
                 this->independent_objects=new DataSet();
                 this->FetchData(&num_independent_objects,AutodiffNumIndependentObjectsEnum);
 …
                                 IndependentObject* independent_object=NULL;
                                 independent_object=new IndependentObject(names[i],types[i],numberofvertices);
+                                independent_object=new IndependentObject(names[i],types[i]);
                                 /*add to independent_objects dataset:*/
 …
                         xDelete<int>(names);
                         xDelete<int>(types);
+                } /*}}}*/
+                }
                 #else
                 /*if we asked for AD computations, we have a problem!: */
 …
                                 /* Read the record length and the data type code: */
                                 fread(&record_length,sizeof(int),1,this->fid);
                                 fread(&record_code,sizeof(int),1,this->fid);
+                                if(fread(&record_length,sizeof(int),1,this->fid)!=1) _error_("Cound not read record_length");
+                                if(fread(&record_code  ,sizeof(int),1,this->fid)!=1) _error_("Cound not read record_code");
                                 #ifdef _HAVE_MPI_
 …
         int*    integer_matrix=NULL;
         int code=0;
-        int vector_type=0;
         /*recover my_rank:*/
 …
         /*Set file pointer to beginning of the data: */
         fid=this->SetFilePointerToData(&code,&vector_type,data_enum);
+        fid=this->SetFilePointerToData(&code,NULL,data_enum);
         if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(data_enum));
 …
         IssmPDouble* matrix=NULL;
         int code=0;
-        int vector_type=0;
         /*recover my_rank:*/
 …
         /*Set file pointer to beginning of the data: */
         fid=this->SetFilePointerToData(&code,&vector_type,data_enum);
+        fid=this->SetFilePointerToData(&code,NULL,data_enum);
         if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(data_enum));
 …
         int my_rank;
         int        lastindex,index;
         int        record_length;
+        int lastindex,index;
+        int record_length;
         /*recover my_rank:*/
 …
                         /*read the record length, and use it to skip this record: */
                         fread(&record_length,sizeof(int),1,fid);
+                        if(fread(&record_length,sizeof(int),1,fid)!=1) _error_("Could not read record_length");
                         fseek(fid,record_length,SEEK_CUR);
                         lastindex=index;
 …
                                 /*Ok, we have found the correct string. Pass the record length, and read data type code: */
                                 fseek(fid,sizeof(int),SEEK_CUR);
                                 fread(&record_code,sizeof(int),1,fid);
+                                if(fread(&record_code,sizeof(int),1,fid)!=1) _error_("Could not read record_code");
                                 /*if record_code points to a vector, get its type (nodal or elementary): */
+                                if(5<=record_code && record_code<=7)fread(&vector_type,sizeof(int),1,fid);
+                                if(5<=record_code && record_code<=7){
+                                        if(fread(&vector_type,sizeof(int),1,fid)!=1) _error_("Could not read vector_type");
+                                }
                                 found=1;
                                 break;
 …
                         else{
                                 /*This is not the correct string, read the record length, and use it to skip this record: */
                                 fread(&record_length,sizeof(int),1,fid);
+                                if(fread(&record_length,sizeof(int),1,fid)!=1) _error_("Could not read record_length");
                                 /*skip: */
                                 fseek(fid,record_length,SEEK_CUR);

issm/trunk/src/c/classes/IoModel.h

-              r13975
+              r15396
 #define _IOMODEL_H
+#include "../include/include.h"
+#include "../EnumDefinitions/EnumDefinitions.h"
+#include "../shared/Enum/Enum.h"
 class Parameters;
 …
                 IssmDouble **data;   //this dataset holds temporary data, memory intensive.
+                /*This data needs to stay memory resident at all time, even if it's memory intensive: */
+                FILE *fid;                               //pointer to input file
+                /*pointer to input file*/
+                FILE *fid;
+                /*Partitioning*/
                 bool *my_elements;
                 bool *my_nodes;
                 int  *my_vertices;
+                /*Connectivity tables*/
                 int  *singlenodetoelementconnectivity;
                 int  *numbernodetoelementconnectivity;
                 /*Data to synchronize through low level object drivers: */
                 int nodecounter;         //keep track of how many nodes are being created in each analysis type
                 int loadcounter;         //keep track of how many loads are being created in each analysis type
                 int constraintcounter;   //keep track of how many constraints are being created in each analysis type
+                int nodecounter;         //keep track of how many nodes are being created in each analysis
+                int loadcounter;         //keep track of how many loads are being created in each analysis
+                int constraintcounter;   //keep track of how many constraints are being created in each analysis
                 /*for AD mode: to keep track of our independent variables we fetch:*/
                 bool* independents;
                 DataSet* independent_objects;
+                bool    *independents;
+                DataSet *independent_objects;
                 /*Methods*/
 …
                 void        FetchData(Option **poption,int data_enum);
                 void        FetchData(int num,...);
                 void        FetchDataToInput(Elements* elements,int vector_enum,int default_vector_enum=NoneEnum,IssmDouble default_value=0);
+                void        FetchDataToInput(Elements* elements,int vector_enum,int default_vector_enum=NoneEnum,IssmDouble default_value=0.);
                 void        LastIndex(int *pindex);
                 FILE*       SetFilePointerToData(int* pcode,int* pvector_type, int data_enum);

issm/trunk/src/c/classes/Patch.cpp

-              r13975
+              r15396
 #include <math.h>
 #include "./classes.h"
-#include "../Container/Container.h"
-#include "../io/io.h"
-#include "../EnumDefinitions/EnumDefinitions.h"
 #include "../shared/shared.h"
-#include "../include/include.h"
 /*Object constructors and destructors:*/

issm/trunk/src/c/classes/RiftStruct.cpp

-              r14310
+              r15396
 #include "./classes.h"
 #include "../EnumDefinitions/EnumDefinitions.h"
+#include "../shared/Enum/Enum.h"
 #include "../shared/shared.h"
-#include "../include/include.h"
 /*RiftStruct constructors and destructor*/

issm/trunk/src/c/classes/classes.h

-              r13975
+              r15396
  */
 #ifndef ALL_CLASSES_H_
 #define ALL_CLASSES_H_
+#ifndef _ALL_CLASSES_H_
+#define _ALL_CLASSES_H_
+/*Objects derived classes, which are used in our containers: */
+#include "./objects/objects.h"
+/*Objects: */
+#include "./Contour.h"
+#include "./Vertices.h"
+#include "./Vertex.h"
+#include "./Nodes.h"
+#include "./Contours.h"
+#include "./Node.h"
+#include "./Profiler.h"
+#include "./DependentObject.h"
+#include "./IndependentObject.h"
+#include "./Segment.h"
+/*Constraints: */
+#include "./Constraints/Constraints.h"
+#include "./Constraints/Constraint.h"
+#include "./Constraints/SpcStatic.h"
+#include "./Constraints/SpcTransient.h"
+#include "./Constraints/SpcDynamic.h"
+/*Loads: */
+#include "./Loads/Loads.h"
+#include "./Loads/Load.h"
+#include "./Loads/Friction.h"
+#include "./Loads/Icefront.h"
+#include "./Loads/Numericalflux.h"
+#include "./Loads/Riftfront.h"
+#include "./Loads/Penpair.h"
+#include "./Loads/Pengrid.h"
+/*Elements: */
+#include "./Elements/Elements.h"
+#include "./Elements/Element.h"
+#include "./Elements/Penta.h"
+#include "./Elements/PentaRef.h"
+#include "./Elements/Tria.h"
+#include "./Elements/TriaRef.h"
+#include "./Elements/ElementHook.h"
+/*Option parsing objects: */
+#include "./Options/Option.h"
+#include "./Options/Options.h"
+#include "./Options/GenericOption.h"
+#include "./Options/OptionUtilities.h"
+/*Inputs: */
+#include "./Inputs/Inputs.h"
+#include "./Inputs/Input.h"
+#include "./Inputs/BoolInput.h"
+#include "./Inputs/DoubleInput.h"
+#include "./Inputs/IntInput.h"
+#include "./Inputs/PentaP1Input.h"
+#include "./Inputs/TriaInput.h"
+#include "./Inputs/ControlInput.h"
+#include "./Inputs/DatasetInput.h"
+#include "./Inputs/TransientInput.h"
+/*ElementResults: */
+#include "./ElementResults/ElementResult.h"
+#include "./ElementResults/DoubleElementResult.h"
+#include "./ElementResults/TriaP1ElementResult.h"
+#include "./ElementResults/PentaP1ElementResult.h"
+#include "./ElementResults/BoolElementResult.h"
+/*ExternalResults: */
+#include "./ExternalResults/Results.h"
+#include "./ExternalResults/ExternalResult.h"
+#include "./ExternalResults/GenericExternalResult.h"
+/*Materials: */
+#include "./Materials/Materials.h"
+#include "./Materials/Material.h"
+#include "./Materials/Matice.h"
+#include "./Materials/Matdamageice.h"
+#include "./Materials/Matpar.h"
+/*Params: */
+#include "./Params/GenericParam.h"
+#include "./Params/BoolParam.h"
+#include "./Params/DoubleMatParam.h"
+#include "./Params/DoubleTransientMatParam.h"
+#include "./Params/DoubleMatArrayParam.h"
+#include "./Params/DoubleParam.h"
+#include "./Params/DoubleVecParam.h"
+#include "./Params/IntParam.h"
+#include "./Params/IntVecParam.h"
+#include "./Params/IntMatParam.h"
+#include "./Params/FileParam.h"
+#include "./Params/Parameters.h"
+#include "./Params/Param.h"
+#include "./Params/MatrixParam.h"
+#include "./Params/VectorParam.h"
+#include "./Params/StringArrayParam.h"
+#include "./Params/StringParam.h"
+#include "./Params/TransientParam.h"
+#include "./Params/DataSetParam.h"
 /*matrix: */
 #include "./matrix/matrixobjects.h"
-/*bamg: */
-#include "./bamg/bamgobjects.h"
 /*gauss: */
 …
 #include "./Update.h"
 #include "./FemModel.h"
+#include "./OptArgs.h"
+#include "./OptPars.h"
+#include "./AdolcEdf.h"
+#include "./IssmComm.h"
+#include "./GiaDeflectionCoreArgs.h"
 #include "./RiftStruct.h"

issm/trunk/src/c/classes/gauss/GaussPenta.cpp

-              r13395
+              r15396
  */
+#include "./gaussobjects.h"
+#include "./GaussPenta.h"
+#include "./GaussTria.h"
+#include "../../shared/io/Print/Print.h"
+#include "../../shared/Exceptions/exceptions.h"
+#include "../../shared/MemOps/MemOps.h"
+#include "../../shared/Numerics/GaussPoints.h"
+#include "../../shared/Numerics/constants.h"
 /*GaussPenta constructors and destructors:*/
 …
         int     numgauss_horiz;
         int     numgauss_vert;
         double *coords1_horiz = NULL;
         double *coords2_horiz = NULL;
         double *coords3_horiz = NULL;
         double *weights_horiz  = NULL;
+        IssmDouble *coords1_horiz = NULL;
+        IssmDouble *coords2_horiz = NULL;
+        IssmDouble *coords3_horiz = NULL;
+        IssmDouble *weights_horiz  = NULL;
         double *coords_vert = NULL;
         double *weights_vert   = NULL;
 …
         /*Allocate GaussPenta fields*/
         numgauss=numgauss_horiz*numgauss_vert;
         coords1=xNew<double>(numgauss);
         coords2=xNew<double>(numgauss);
         coords3=xNew<double>(numgauss);
         coords4=xNew<double>(numgauss);
         weights=xNew<double>(numgauss);
+        coords1=xNew<IssmDouble>(numgauss);
+        coords2=xNew<IssmDouble>(numgauss);
+        coords3=xNew<IssmDouble>(numgauss);
+        coords4=xNew<IssmDouble>(numgauss);
+        weights=xNew<IssmDouble>(numgauss);
         /*Combine Horizontal and vertical points*/
 …
         /*Clean up*/
         xDelete<double>(coords1_horiz);
         xDelete<double>(coords2_horiz);
         xDelete<double>(coords3_horiz);
+        xDelete<IssmDouble>(coords1_horiz);
+        xDelete<IssmDouble>(coords2_horiz);
+        xDelete<IssmDouble>(coords3_horiz);
         xDelete<double>(coords_vert);
         xDelete<double>(weights_horiz);
+        xDelete<IssmDouble>(weights_horiz);
         xDelete<double>(weights_vert);
+}
 …
         /*Allocate GaussPenta fields*/
         coords1=xNew<double>(numgauss);
         coords2=xNew<double>(numgauss);
         coords3=xNew<double>(numgauss);
         coords4=xNew<double>(numgauss);
         weights=xNew<double>(numgauss);
+        coords1=xNew<IssmDouble>(numgauss);
+        coords2=xNew<IssmDouble>(numgauss);
+        coords3=xNew<IssmDouble>(numgauss);
+        coords4=xNew<IssmDouble>(numgauss);
+        weights=xNew<IssmDouble>(numgauss);
         if(index1==0 && index2==3){
 …
                 /*compute z coordinate*/
                 coords4=xNew<double>(numgauss);
+                coords4=xNew<IssmDouble>(numgauss);
                 for(int i=0;i<numgauss;i++) coords4[i]=-1.0;
+        }
 …
                 /*compute z coordinate*/
                 coords4=xNew<double>(numgauss);
+                coords4=xNew<IssmDouble>(numgauss);
                 for(int i=0;i<numgauss;i++) coords4[i]=1.0;
+        }
 …
         /*Allocate GaussPenta fields*/
         numgauss=order_horiz*order_vert;
         coords1=xNew<double>(numgauss);
         coords2=xNew<double>(numgauss);
         coords3=xNew<double>(numgauss);
         coords4=xNew<double>(numgauss);
         weights=xNew<double>(numgauss);
+        coords1=xNew<IssmDouble>(numgauss);
+        coords2=xNew<IssmDouble>(numgauss);
+        coords3=xNew<IssmDouble>(numgauss);
+        coords4=xNew<IssmDouble>(numgauss);
+        weights=xNew<IssmDouble>(numgauss);
         /*Quads: get the gauss points using the product of two line rules  */
 …
 /*FUNCTION GaussPenta::~GaussPenta(){{{*/
 GaussPenta::~GaussPenta(){
         xDelete<double>(weights);
         xDelete<double>(coords1);
         xDelete<double>(coords2);
         xDelete<double>(coords3);
         xDelete<double>(coords4);
+        xDelete<IssmDouble>(weights);
+        xDelete<IssmDouble>(coords1);
+        xDelete<IssmDouble>(coords2);
+        xDelete<IssmDouble>(coords3);
+        xDelete<IssmDouble>(coords4);
+}
 /*}}}*/
 …
 void GaussPenta::Echo(void){
         _printLine_("GaussPenta:");
         _printLine_("   numgauss: " << numgauss);
+        _printf_("GaussPenta:\n");
+        _printf_("   numgauss: " << numgauss << "\n");
         if (weights){
          _printString_("   weights = [");
          for(int i=0;i<numgauss;i++) _printLine_(" " << weights[i]);
          _printLine_("]");
+        }
         else _printLine_("weights = NULL");
+         _printf_("   weights = [");
+         for(int i=0;i<numgauss;i++) _printf_(" " << weights[i] << "\n");
+         _printf_("]\n");
+        }
+        else _printf_("weights = NULL\n");
         if (coords1){
          _printString_("   coords1 = [");
          for(int i=0;i<numgauss;i++) _printLine_(" " << coords1[i]);
          _printLine_("]");
+        }
         else _printLine_("coords1 = NULL");
+         _printf_("   coords1 = [");
+         for(int i=0;i<numgauss;i++) _printf_(" " << coords1[i] << "\n");
+         _printf_("]\n");
+        }
+        else _printf_("coords1 = NULL\n");
         if (coords2){
          _printString_("   coords2 = [");
          for(int i=0;i<numgauss;i++) _printLine_(" " << coords2[i]);
          _printLine_("]");
+        }
         else _printLine_("coords2 = NULL");
+         _printf_("   coords2 = [");
+         for(int i=0;i<numgauss;i++) _printf_(" " << coords2[i] << "\n");
+         _printf_("]\n");
+        }
+        else _printf_("coords2 = NULL\n");
         if (coords3){
          _printString_("   coords3 = [");
          for(int i=0;i<numgauss;i++) _printLine_(" " << coords3[i]);
          _printLine_("]");
+        }
         else _printLine_("coords3 = NULL");
+         _printf_("   coords3 = [");
+         for(int i=0;i<numgauss;i++) _printf_(" " << coords3[i] << "\n");
+         _printf_("]\n");
+        }
+        else _printf_("coords3 = NULL\n");
         if (coords4){
                 _printString_("   coords4 = [");
                 for(int i=0;i<numgauss;i++) _printLine_(" " << coords4[i]);
                 _printLine_("]");
+        }
         else _printLine_("coords4 = NULL");
         _printLine_("   weight = " << weight);
         _printLine_("   coord1 = " << coord1);
         _printLine_("   coord2 = " << coord2);
         _printLine_("   coord3 = " << coord3);
         _printLine_("   coord4 = " << coord4);
+                _printf_("   coords4 = [");
+                for(int i=0;i<numgauss;i++) _printf_(" " << coords4[i] << "\n");
+                _printf_("]\n");
+        }
+        else _printf_("coords4 = NULL\n");
+        _printf_("   weight = " << weight << "\n");
+        _printf_("   coord1 = " << coord1 << "\n");
+        _printf_("   coord2 = " << coord2 << "\n");
+        _printf_("   coord3 = " << coord3 << "\n");
+        _printf_("   coord4 = " << coord4 << "\n");
+}
 …
         if(index1==0 && index2==1 && index3==2){
                 GaussLegendreTria(&numgauss,&coords1,&coords2,&coords3,&weights,order);
                 coords4=xNew<double>(numgauss);
+                coords4=xNew<IssmDouble>(numgauss);
                 for(int i=0;i<numgauss;i++) coords4[i]=-1.0;
+        }

issm/trunk/src/c/classes/gauss/GaussPenta.h

-              r13975
+              r15396
 /*Headers:*/
+/*{{{*/
+#include "./../../shared/shared.h"
+#include "../../shared/Numerics/types.h"
 class GaussTria;
-/*}}}*/
 class GaussPenta{
 …
         private:
                 int numgauss;
                 double* weights;
                 double* coords1;
                 double* coords2;
                 double* coords3;
                 double* coords4;
+                IssmDouble* weights;
+                IssmDouble* coords1;
+                IssmDouble* coords2;
+                IssmDouble* coords3;
+                IssmDouble* coords4;
         public:
                 double weight;
                 double coord1;
                 double coord2;
                 double coord3;
                 double coord4;
+                IssmDouble weight;
+                IssmDouble coord1;
+                IssmDouble coord2;
+                IssmDouble coord3;
+                IssmDouble coord4;
         public:

issm/trunk/src/c/classes/gauss/GaussTria.cpp

-              r13395
+              r15396
  */
+#include "./gaussobjects.h"
+#include "./GaussTria.h"
+#include "../../shared/shared.h"
 /*GaussTria constructors and destructors:*/
 …
         IssmPDouble *seg_coords  = NULL;
         IssmPDouble *seg_weights = NULL;
+        IssmDouble  a1,b1,c1,a2,b2,c2;
         int     i,index3;
 …
         /*Allocate GaussTria fields*/
+        coords1=xNew<IssmPDouble>(numgauss);
+        coords2=xNew<IssmPDouble>(numgauss);
+        coords3=xNew<IssmPDouble>(numgauss);
+        weights=xNew<IssmPDouble>(numgauss);
+        /*Reverse index1 and 2 if necessary*/
+        if (index1>index2){
+                index3=index1; index1=index2; index2=index3;
+                for(i=0;i<numgauss;i++) seg_coords[i]=-seg_coords[i];
+        coords1=xNew<IssmDouble>(numgauss);
+        coords2=xNew<IssmDouble>(numgauss);
+        coords3=xNew<IssmDouble>(numgauss);
+        weights=xNew<IssmDouble>(numgauss);
+        /*Figure out coords of index1 (a1,b1,c1) and index2 (a2,b2,c2)*/
+        if(index1==0){
+                a1=1; b1=0; c1=0;
+        }
+        else if(index1==1){
+                a1=0; b1=1; c1=0;
+        }
+        else if(index1==2){
+                a1=0; b1=0; c1=1;
+        }
+        else{
+                _error_("First indice provided is not supported yet (user provided " << index1 << ")");
+        }
+        if(index2==0){
+                a2=1; b2=0; c2=0;
+        }
+        else if(index2==1){
+                a2=0; b2=1; c2=0;
+        }
+        else if(index2==2){
+                a2=0; b2=0; c2=1;
+        }
+        else{
+         _error_("Second indice provided is not supported yet (user provided " << index2 << " )");
+        }
         /*Build Triangle Gauss point*/
+        if (index1==0 && index2==1){
+                for(i=0;i<numgauss;i++) coords1[i]=  0.5*(1-seg_coords[i]);
+                for(i=0;i<numgauss;i++) coords2[i]=1-0.5*(1.-seg_coords[i]);
+                for(i=0;i<numgauss;i++) coords3[i]=0;
+                for(i=0;i<numgauss;i++) weights[i]=seg_weights[i];
+        }
+        else if (index1==0 && index2==2){
+                for(i=0;i<numgauss;i++) coords1[i]=  0.5*(1-seg_coords[i]);
+                for(i=0;i<numgauss;i++) coords2[i]= 0 ;
+                for(i=0;i<numgauss;i++) coords3[i]=1-0.5*(1.-seg_coords[i]);
+                for(i=0;i<numgauss;i++) weights[i]=seg_weights[i];
+        }
+        else if (index1==1 && index2==2){
+                for(i=0;i<numgauss;i++) coords1[i]=0;
+                for(i=0;i<numgauss;i++) coords2[i]=  0.5*(1-seg_coords[i]);
+                for(i=0;i<numgauss;i++) coords3[i]=1-0.5*(1.-seg_coords[i]);
+                for(i=0;i<numgauss;i++) weights[i]=seg_weights[i];
+        }
+        else
+         _error_("The 2 indices provided are not supported yet (user provided " << index1 << " and " << index2 << ")");
+        for(i=0;i<numgauss;i++){
+                coords1[i]=0.5*(a1+a2) + 0.5*seg_coords[i]*(a2-a1);
+                coords2[i]=0.5*(b1+b2) + 0.5*seg_coords[i]*(b2-b1);
+                coords3[i]=0.5*(c1+c2) + 0.5*seg_coords[i]*(c2-c1);
+                weights[i]=seg_weights[i];
+        }
         /*Initialize static fields as undefined*/
 …
+}
 /*}}}*/
+/*FUNCTION GaussTria::GaussTria(int index,double r1,double r2,int order) {{{*/
+GaussTria::GaussTria(int index,IssmDouble r1,IssmDouble r2,bool mainlyfloating,int order){
+        /*
+         *  ^
+         *  |
+         * 1|\
+         *  |  \
+         *  |    \
+         *  |      \
+         *  |        \
+         *  |          \
+         *  |    +(x,y)  \
+         *  |              \
+         *  +---------------+-->
+         *  0               1
+         *
+         */
+        int         ig;
+        IssmDouble x,y;
+        IssmDouble xy_list[3][2];
+        if(mainlyfloating){
+                /*Get gauss points*/
+                GaussLegendreTria(&this->numgauss,&this->coords1,&this->coords2,&this->coords3,&this->weights,order);
+                xy_list[0][0]=0;  xy_list[0][1]=0;
+                xy_list[1][0]=r1; xy_list[1][1]=0;
+                xy_list[2][0]=0;  xy_list[2][1]=r2;
+                for(ig=0;ig<this->numgauss;ig++){
+                        x = this->coords1[ig]*xy_list[0][0] + this->coords2[ig]*xy_list[1][0] + this->coords3[ig]*xy_list[2][0];
+                        y = this->coords1[ig]*xy_list[0][1] + this->coords2[ig]*xy_list[1][1] + this->coords3[ig]*xy_list[2][1];
+                        switch(index){
+                                case 0:
+                                        this->coords1[ig] = 1.-x-y;
+                                        this->coords2[ig] = x;
+                                        this->coords3[ig] = y;
+                                        break;
+                                case 1:
+                                        this->coords1[ig] = y;
+                                        this->coords2[ig] = 1.-x-y;
+                                        this->coords3[ig] = x;
+                                        break;
+                                case 2:
+                                        this->coords1[ig] = x;
+                                        this->coords2[ig] = y;
+                                        this->coords3[ig] = 1.-x-y;
+                                        break;
+                                default:
+                                        _error_("index "<<index<<" not supported yet");
+                        }
+                        this->weights[ig] = this->weights[ig]*r1*r2;
+                }
+        }
+        else{
+                /*Double number of gauss points*/
+                GaussTria *gauss1    = NULL;
+                GaussTria *gauss2    = NULL;
+                gauss1=new GaussTria(order);
+                gauss2=new GaussTria(order);
+                xy_list[0][0]=r1; xy_list[0][1]=0;
+                xy_list[1][0]=0;  xy_list[1][1]=1.;
+                xy_list[2][0]=0;  xy_list[2][1]=r2;
+                        //gauss1->Echo();
+                for(ig=0;ig<gauss1->numgauss;ig++){
+                        x = gauss1->coords1[ig]*xy_list[0][0] + gauss1->coords2[ig]*xy_list[1][0] + gauss1->coords3[ig]*xy_list[2][0];
+                        y = gauss1->coords1[ig]*xy_list[0][1] + gauss1->coords2[ig]*xy_list[1][1] + gauss1->coords3[ig]*xy_list[2][1];
+                        switch(index){
+                                case 0:
+                                        gauss1->coords1[ig] = 1.-x-y;
+                                        gauss1->coords2[ig] = x;
+                                        gauss1->coords3[ig] = y;
+                                        break;
+                                case 1:
+                                        gauss1->coords1[ig] = y;
+                                        gauss1->coords2[ig] = 1.-x-y;
+                                        gauss1->coords3[ig] = x;
+                                        break;
+                                case 2:
+                                        gauss1->coords1[ig] = x;
+                                        gauss1->coords2[ig] = y;
+                                        gauss1->coords3[ig] = 1.-x-y;
+                                        break;
+                                default:
+                                        _error_("index "<<index<<" not supported yet");
+                        }
+                        gauss1->weights[ig] = gauss1->weights[ig]*r1*(1-r2);
+                }
+                        //gauss1->Echo();
+                xy_list[0][0]=r1; xy_list[0][1]=0;
+                xy_list[1][0]=1.; xy_list[1][1]=0;
+                xy_list[2][0]=0;  xy_list[2][1]=1.;
+                        //gauss2->Echo();
+                for(ig=0;ig<gauss2->numgauss;ig++){
+                        x = gauss2->coords1[ig]*xy_list[0][0] + gauss2->coords2[ig]*xy_list[1][0] + gauss2->coords3[ig]*xy_list[2][0];
+                        y = gauss2->coords1[ig]*xy_list[0][1] + gauss2->coords2[ig]*xy_list[1][1] + gauss2->coords3[ig]*xy_list[2][1];
+                        switch(index){
+                                case 0:
+                                        gauss2->coords1[ig] = 1.-x-y;
+                                        gauss2->coords2[ig] = x;
+                                        gauss2->coords3[ig] = y;
+                                        break;
+                                case 1:
+                                        gauss2->coords1[ig] = y;
+                                        gauss2->coords2[ig] = 1.-x-y;
+                                        gauss2->coords3[ig] = x;
+                                        break;
+                                case 2:
+                                        gauss2->coords1[ig] = x;
+                                        gauss2->coords2[ig] = y;
+                                        gauss2->coords3[ig] = 1.-x-y;
+                                        break;
+                                default:
+                                        _error_("index "<<index<<" not supported yet");
+                        }
+                        gauss2->weights[ig] = gauss2->weights[ig]*(1-r1);
+                }
+                this->numgauss = gauss1->numgauss + gauss2->numgauss;
+                this->coords1=xNew<IssmDouble>(this->numgauss);
+                this->coords2=xNew<IssmDouble>(this->numgauss);
+                this->coords3=xNew<IssmDouble>(this->numgauss);
+                this->weights=xNew<IssmDouble>(this->numgauss);
+                for(ig=0;ig<gauss1->numgauss;ig++){ // Add the first triangle gauss points
+                        this->coords1[ig]=gauss1->coords1[ig];
+                        this->coords2[ig]=gauss1->coords2[ig];
+                        this->coords3[ig]=gauss1->coords3[ig];
+                        this->weights[ig]=gauss1->weights[ig];
+                }
+                for(ig=0;ig<gauss2->numgauss;ig++){ // Add the second triangle gauss points
+                        this->coords1[gauss1->numgauss+ig]=gauss2->coords1[ig];
+                        this->coords2[gauss1->numgauss+ig]=gauss2->coords2[ig];
+                        this->coords3[gauss1->numgauss+ig]=gauss2->coords3[ig];
+                        this->weights[gauss1->numgauss+ig]=gauss2->weights[ig];
+                }
+                /*Delete gauss points*/
+                delete gauss1;
+                delete gauss2;
+        }
+        /*Initialize static fields as undefined*/
+        weight=UNDEF;
+        coord1=UNDEF;
+        coord2=UNDEF;
+        coord3=UNDEF;
+}
+/*}}}*/
 /*FUNCTION GaussTria::~GaussTria(){{{*/
 GaussTria::~GaussTria(){
         xDelete<IssmPDouble>(weights);
         xDelete<IssmPDouble>(coords1);
         xDelete<IssmPDouble>(coords2);
         xDelete<IssmPDouble>(coords3);
+        xDelete<IssmDouble>(weights);
+        xDelete<IssmDouble>(coords1);
+        xDelete<IssmDouble>(coords2);
+        xDelete<IssmDouble>(coords3);
+}
 /*}}}*/
 …
 void GaussTria::Echo(void){
         _printLine_("GaussTria:");
         _printLine_("   numgauss: " << numgauss);
+        _printf_("GaussTria:\n");
+        _printf_("   numgauss: " << numgauss << "\n");
         if (weights){
          _printString_("   weights = [");
          for(int i=0;i<numgauss;i++) _printLine_(" " << weights[i]);
          _printLine_("]");
+        }
         else _printLine_("weights = NULL");
+         _printf_("   weights = [");
+         for(int i=0;i<numgauss;i++) _printf_(" " << weights[i] << "\n");
+         _printf_("]\n");
+        }
+        else _printf_("weights = NULL\n");
         if (coords1){
          _printString_("   coords1 = [");
          for(int i=0;i<numgauss;i++) _printLine_(" " << coords1[i]);
          _printLine_("]");
+        }
         else _printLine_("coords1 = NULL");
+         _printf_("   coords1 = [");
+         for(int i=0;i<numgauss;i++) _printf_(" " << coords1[i] << "\n");
+         _printf_("]\n");
+        }
+        else _printf_("coords1 = NULL\n");
         if (coords2){
          _printString_("   coords2 = [");
          for(int i=0;i<numgauss;i++) _printLine_(" " << coords2[i]);
          _printLine_("]");
+        }
         else _printLine_("coords2 = NULL");
+         _printf_("   coords2 = [");
+         for(int i=0;i<numgauss;i++) _printf_(" " << coords2[i] << "\n");
+         _printf_("]\n");
+        }
+        else _printf_("coords2 = NULL\n");
         if (coords3){
          _printString_("   coords3 = [");
          for(int i=0;i<numgauss;i++) _printLine_(" " << coords3[i]);
          _printLine_("]");
+        }
         else _printLine_("coords3 = NULL");
         _printLine_("   weight = " << weight);
         _printLine_("   coord1 = " << coord1);
         _printLine_("   coord2 = " << coord2);
         _printLine_("   coord3 = " << coord3);
+         _printf_("   coords3 = [");
+         for(int i=0;i<numgauss;i++) _printf_(" " << coords3[i] << "\n");
+         _printf_("]\n");
+        }
+        else _printf_("coords3 = NULL\n");
+        _printf_("   weight = " << weight << "\n");
+        _printf_("   coord1 = " << coord1 << "\n");
+        _printf_("   coord2 = " << coord2 << "\n");
+        _printf_("   coord3 = " << coord3 << "\n");
+}
 …
         /*update static arrays*/
         switch(iv){
+                case 0:
+                        coord1=1; coord2=0; coord3=0;
+                case 0: coord1=1.; coord2=0.; coord3=0.; break;
+                case 1: coord1=0.; coord2=1.; coord3=0.; break;
+                case 2: coord1=0.; coord2=0.; coord3=1.; break;
+                default: _error_("vertex index should be in [0 2]");
+        }
+}
+/*}}}*/
+/*FUNCTION GaussTria::GaussNode{{{*/
+void GaussTria::GaussNode(int numnodes,int iv){
+        /*in debugging mode: check that the default constructor has been called*/
+        _assert_(numgauss==-1);
+        /*update static arrays*/
+        switch(numnodes){
+                case 3: //P1 Lagrange element
+                        switch(iv){
+                                case 0: coord1=1.; coord2=0.; coord3=0.; break;
+                                case 1: coord1=0.; coord2=1.; coord3=0.; break;
+                                case 2: coord1=0.; coord2=0.; coord3=1.; break;
+                                default: _error_("node index should be in [0 2]");
+                        }
                         break;
+                case 1:
+                        coord1=0; coord2=1; coord3=0;
+                case 6: //P2 Lagrange element
+                        switch(iv){
+                                case 0: coord1=1.; coord2=0.; coord3=0.; break;
+                                case 1: coord1=0.; coord2=1.; coord3=0.; break;
+                                case 2: coord1=0.; coord2=0.; coord3=1.; break;
+                                case 3: coord1=0.; coord2=.5; coord3=.5; break;
+                                case 4: coord1=.5; coord2=0.; coord3=.5; break;
+                                case 5: coord1=.5; coord2=.5; coord3=0.; break;
+                                default: _error_("node index should be in [0 5]");
+                        }
                         break;
+                case 2:
+                        coord1=0; coord2=0; coord3=1;
+                        break;
+                default:
+                        _error_("vertex index should be in [0 2]");
+                default: _error_("supported number of nodes are 3 and 6");
+        }

issm/trunk/src/c/classes/gauss/GaussTria.h

-              r13975
+              r15396
 /*Headers:*/
+/*{{{*/
+#include "./../../shared/shared.h"
+/*}}}*/
+#include "../../shared/Numerics/types.h"
 class GaussTria{
 …
         private:
                 int numgauss;
                 IssmPDouble* weights;
                 IssmPDouble* coords1;
                 IssmPDouble* coords2;
                 IssmPDouble* coords3;
+                IssmDouble* weights;
+                IssmDouble* coords1;
+                IssmDouble* coords2;
+                IssmDouble* coords3;
         public:
                 IssmPDouble weight;
+                IssmDouble weight;
                 IssmDouble coord1;
                 IssmDouble coord2;
 …
                 GaussTria(int order);
                 GaussTria(int index1,int index2,int order);
+                GaussTria(int index,IssmDouble r1, IssmDouble r2,bool maintlyfloating,int order);
                 ~GaussTria();
 …
                 void GaussPoint(int ig);
                 void GaussVertex(int iv);
+                void GaussNode(int numnodes,int iv);
                 void GaussCenter(void);
                 void GaussEdgeCenter(int index1,int index2);

issm/trunk/src/c/classes/kriging/ExponentialVariogram.cpp

-              r13975
+              r15396
 #endif
+#include <stdio.h>
+#include <string.h>
+#include "../objects/objects.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../classes.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 /*ExponentialVariogram constructors and destructor*/
 …
 /*FUNCTION ExponentialVariogram::Echo {{{*/
 void ExponentialVariogram::Echo(void){
         _printLine_("ExponentialVariogram");
         _printLine_("   nugget: " << this->nugget);
         _printLine_("   sill  : " << this->sill);
         _printLine_("   range : " << this->range);
+        _printf_("ExponentialVariogram\n");
+        _printf_("   nugget: " << this->nugget << "\n");
+        _printf_("   sill  : " << this->sill << "\n");
+        _printf_("   range : " << this->range << "\n");
+}
 /*}}}*/

issm/trunk/src/c/classes/kriging/GaussianVariogram.cpp

-              r13975
+              r15396
 #endif
+#include <stdio.h>
+#include <string.h>
+#include "../objects/objects.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../classes.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 /*GaussianVariogram constructors and destructor*/
 …
 /*FUNCTION GaussianVariogram::Echo {{{*/
 void GaussianVariogram::Echo(void){
         _printLine_("GaussianVariogram");
         _printLine_("   nugget: " << this->nugget);
         _printLine_("   sill  : " << this->sill);
         _printLine_("   range : " << this->range);
+        _printf_("GaussianVariogram\n");
+        _printf_("   nugget: " << this->nugget << "\n");
+        _printf_("   sill  : " << this->sill << "\n");
+        _printf_("   range : " << this->range << "\n");
+}
 /*}}}*/
 …
         gamma = (sill-nugget)*(1.-exp(-h2/(a*range*range))) + nugget;
         //if(h2>1000*1000) _printLine_("gamma = " << gamma << " h= " << sqrt(h2));
         _printLine_("h = " << sqrt(h2) << " gamma = " << gamma);
+        //if(h2>1000*1000) _printf_("gamma = " << gamma << " h= " << sqrt(h2) << "\n");
+        _printf_("h = " << sqrt(h2) << " gamma = " << gamma << "\n");
         return gamma;
+}

issm/trunk/src/c/classes/kriging/Observation.cpp

-              r13975
+              r15396
 #include <stdlib.h>
 #include "../objects/objects.h"
+#include "../classes.h"
 /*Observation constructors and destructor*/
 …
 void Observation::Echo(void){
         _printLine_("Observation");
         _printLine_("   index : " << this->index);
         _printLine_("   x     : " << this->x);
         _printLine_("   y     : " << this->y);
         _printLine_("   xi    : "); printbinary(this->xi); _printLine_("");
         _printLine_("   yi    : "); printbinary(this->yi); _printLine_("");
         _printLine_("   weight: " << this->weight);
         _printLine_("   value : " << this->value);
+        _printf_("Observation\n");
+        _printf_("   index : " << this->index << "\n");
+        _printf_("   x     : " << this->x << "\n");
+        _printf_("   y     : " << this->y << "\n");
+        _printf_("   xi    : \n"); printbinary(this->xi); _printf_("\n");
+        _printf_("   yi    : \n"); printbinary(this->yi); _printf_("\n");
+        _printf_("   weight: " << this->weight << "\n");
+        _printf_("   value : " << this->value << "\n");
+}
 /*}}}*/

issm/trunk/src/c/classes/kriging/Observation.h

r13975	r15396
6	6	#define _OBSERVATION_H_
7	7
8		#include "../~~objects/Object~~.h"
	8	#include "../../datastructures/datastructures.h"
9	9
10	10	class Observation: public Object{

issm/trunk/src/c/classes/kriging/PowerVariogram.cpp

-              r13975
+              r15396
 #endif
+#include <stdio.h>
+#include <string.h>
+#include "../objects/objects.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../classes.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 /*PowerVariogram constructors and destructor*/
 …
 /*FUNCTION PowerVariogram::Echo {{{*/
 void PowerVariogram::Echo(void){
         _printLine_("PowerVariogram");
         _printLine_("   nugget: " << this->nugget);
         _printLine_("   slope : " << this->slope);
         _printLine_("   power : " << this->power);
+        _printf_("PowerVariogram\n");
+        _printf_("   nugget: " << this->nugget << "\n");
+        _printf_("   slope : " << this->slope << "\n");
+        _printf_("   power : " << this->power << "\n");
+}
 /*}}}*/
 …
         gamma = this->nugget + this->slope*pow(h,this->power);
         //if(h>1000) _printLine_("gamma = " << gamma << " h=" << h);
+        //if(h>1000) _printf_("gamma = " << gamma << " h=" << h << "\n");
         return gamma;
+}

issm/trunk/src/c/classes/kriging/Quadtree.cpp

-              r13975
+              r15396
 #include "../objects/objects.h"
+#include "../classes.h"
 /*DOCUMENTATION What is a Quadtree? {{{
 …
 void  Quadtree::Echo(void){
         _printLine_("Quadtree:");
         _printLine_("   MaxDepth      = " << this->MaxDepth);
         _printLine_("   NbQuadtreeBox = " << this->NbQuadtreeBox);
         _printLine_("   NbObs         = " << this->NbObs);
         _printLine_("   root          = " << this->root);
+        _printf_("Quadtree:\n");
+        _printf_("   MaxDepth      = " << this->MaxDepth << "\n");
+        _printf_("   NbQuadtreeBox = " << this->NbQuadtreeBox << "\n");
+        _printf_("   NbObs         = " << this->NbObs << "\n");
+        _printf_("   root          = " << this->root << "\n");
 }/*}}}*/
 …
 void  Quadtree::DeepEcho(void){
         _printLine_("Quadtree:");
         _printLine_("   MaxDepth      = " << this->MaxDepth);
         _printLine_("   NbQuadtreeBox = " << this->NbQuadtreeBox);
         _printLine_("   NbObs         = " << this->NbObs);
         _printLine_("   root          = " << this->root);
+        _printf_("Quadtree:\n");
+        _printf_("   MaxDepth      = " << this->MaxDepth << "\n");
+        _printf_("   NbQuadtreeBox = " << this->NbQuadtreeBox << "\n");
+        _printf_("   NbObs         = " << this->NbObs << "\n");
+        _printf_("   root          = " << this->root << "\n");
         boxcontainer->Echo();
 …
 void  Quadtree::QuadtreeBox::Echo(void){
         _printLine_("QuadtreeBox:");
         _printLine_("   nbitems = " << this->nbitems);
         _printLine_("   xcenter = " << this->xcenter);
         _printLine_("   ycenter = " << this->ycenter);
         _printLine_("   length  = " << this->length);
+        _printf_("QuadtreeBox:\n");
+        _printf_("   nbitems = " << this->nbitems << "\n");
+        _printf_("   xcenter = " << this->xcenter << "\n");
+        _printf_("   ycenter = " << this->ycenter << "\n");
+        _printf_("   length  = " << this->length << "\n");
 }/*}}}*/

issm/trunk/src/c/classes/kriging/SphericalVariogram.cpp

-              r13975
+              r15396
 #endif
+#include <stdio.h>
+#include <string.h>
+#include "../objects/objects.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../classes.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 /*SphericalVariogram constructors and destructor*/
 …
 /*FUNCTION SphericalVariogram::Echo {{{*/
 void SphericalVariogram::Echo(void){
         _printLine_("SphericalVariogram");
         _printLine_("   nugget: " << this->nugget);
         _printLine_("   sill  : " << this->sill);
         _printLine_("   range : " << this->range);
+        _printf_("SphericalVariogram\n");
+        _printf_("   nugget: " << this->nugget << "\n");
+        _printf_("   sill  : " << this->sill << "\n");
+        _printf_("   range : " << this->range << "\n");
+}
 /*}}}*/

issm/trunk/src/c/classes/kriging/Variogram.h

r13395	r15396
6	6	#define _VARIOGRAM_H_
7	7
8		#include "../~~objects/Object~~.h"
	8	#include "../../datastructures/datastructures.h"
9	9
10	10	class Variogram: public Object{

issm/trunk/src/c/classes/kriging/krigingobjects.h

r13395	r15396
14	14	#include "./Quadtree.h"
15	15	#include "./Observation.h"
	16	#include "./Observations.h"
16	17
17	18	#endif

issm/trunk/src/c/classes/matrix/ElementMatrix.cpp

-              r13975
+              r15396
 #include "../classes.h"
 #include "../../shared/shared.h"
-#include "../../Container/Container.h"
-#include "../../include/include.h"
 /*}}}*/
 …
         IssmDouble* localvalues=NULL;
+        /*Check that Kff has been alocated in debugging mode*/
+        _assert_(Kff);
         /*If Kfs is not provided, call the other function*/
         if(!Kfs){
 …
         int i,j;
         _printLine_("Element Matrix echo:");
         _printLine_("   nrows: " << this->nrows);
         _printLine_("   ncols: " << this->ncols);
         _printLine_("   dofsymmetrical: " << (dofsymmetrical?"true":"false"));
         _printLine_("   values:");
+        _printf_("Element Matrix echo:\n");
+        _printf_("   nrows: " << this->nrows << "\n");
+        _printf_("   ncols: " << this->ncols << "\n");
+        _printf_("   dofsymmetrical: " << (dofsymmetrical?"true":"false") << "\n");
+        _printf_("   values:\n");
         for(i=0;i<nrows;i++){
                 _printString_(setw(4) << right << i << ": ");
                 for(j=0;j<ncols;j++) _printString_( " " << setw(11) << setprecision (5) << right << values[i*ncols+j]);
                 _printLine_("");
+        }
         _printString_("   gglobaldoflist (" << gglobaldoflist << "): ");
         if(gglobaldoflist) for(i=0;i<nrows;i++) _printString_(" " << gglobaldoflist[i]); _printLine_("");
         _printLine_("   row_fsize: " << row_fsize);
         _printString_("   row_flocaldoflist  (" << row_flocaldoflist << "): ");
         if(row_flocaldoflist) for(i=0;i<row_fsize;i++) _printString_(" " << row_flocaldoflist[i]); _printLine_(" ");
         _printString_("   row_fglobaldoflist  (" << row_fglobaldoflist << "): ");
         if(row_fglobaldoflist) for(i=0;i<row_fsize;i++) _printString_(" " << row_fglobaldoflist[i]); _printLine_(" ");
         _printLine_("   row_ssize: " << row_ssize);
         _printString_("   row_slocaldoflist  (" << row_slocaldoflist << "): ");
         if(row_slocaldoflist) for(i=0;i<row_ssize;i++) _printString_(" " << row_slocaldoflist[i]); _printLine_(" ");
         _printString_("   row_sglobaldoflist  (" << row_sglobaldoflist << "): ");
         if(row_sglobaldoflist) for(i=0;i<row_ssize;i++) _printString_(" " << row_sglobaldoflist[i]); _printLine_(" ");
+                _printf_(setw(4) << right << i << ": ");
+                for(j=0;j<ncols;j++) _printf_( " " << setw(11) << setprecision (5) << right << values[i*ncols+j]);
+                _printf_("\n");
+        }
+        _printf_("   gglobaldoflist (" << gglobaldoflist << "): ");
+        if(gglobaldoflist) for(i=0;i<nrows;i++) _printf_(" " << gglobaldoflist[i] << "\n"); _printf_("\n");
+        _printf_("   row_fsize: " << row_fsize << "\n");
+        _printf_("   row_flocaldoflist  (" << row_flocaldoflist << "): ");
+        if(row_flocaldoflist) for(i=0;i<row_fsize;i++) _printf_(" " << row_flocaldoflist[i] << "\n"); _printf_(" \n");
+        _printf_("   row_fglobaldoflist  (" << row_fglobaldoflist << "): ");
+        if(row_fglobaldoflist) for(i=0;i<row_fsize;i++) _printf_(" " << row_fglobaldoflist[i] << "\n"); _printf_(" \n");
+        _printf_("   row_ssize: " << row_ssize << "\n");
+        _printf_("   row_slocaldoflist  (" << row_slocaldoflist << "): ");
+        if(row_slocaldoflist) for(i=0;i<row_ssize;i++) _printf_(" " << row_slocaldoflist[i] << "\n"); _printf_(" \n");
+        _printf_("   row_sglobaldoflist  (" << row_sglobaldoflist << "): ");
+        if(row_sglobaldoflist) for(i=0;i<row_ssize;i++) _printf_(" " << row_sglobaldoflist[i] << "\n"); _printf_(" \n");
         if(!dofsymmetrical){
                 _printLine_("   col_fsize: " << col_fsize);
                 _printString_("   col_flocaldoflist  (" << col_flocaldoflist << "): ");
                 if(col_flocaldoflist) for(i=0;i<col_fsize;i++) _printString_(" " << col_flocaldoflist[i]); _printLine_(" ");
                 _printString_("   col_fglobaldoflist  (" << col_fglobaldoflist << "): ");
                 if(col_fglobaldoflist) for(i=0;i<col_fsize;i++) _printString_(" " << col_fglobaldoflist[i]); _printLine_(" ");
                 _printLine_("   col_ssize: " << col_ssize);
                 _printString_("   col_slocaldoflist  (" << col_slocaldoflist << "): ");
                 if(col_slocaldoflist) for(i=0;i<col_ssize;i++) _printString_(" " << col_slocaldoflist[i]); _printLine_(" ");
                 _printString_("   col_sglobaldoflist  (" << col_sglobaldoflist << "): ");
                 if(col_sglobaldoflist) for(i=0;i<col_ssize;i++) _printString_(" " << col_sglobaldoflist[i]); _printLine_(" ");
+                _printf_("   col_fsize: " << col_fsize << "\n");
+                _printf_("   col_flocaldoflist  (" << col_flocaldoflist << "): ");
+                if(col_flocaldoflist) for(i=0;i<col_fsize;i++) _printf_(" " << col_flocaldoflist[i] << "\n"); _printf_(" \n");
+                _printf_("   col_fglobaldoflist  (" << col_fglobaldoflist << "): ");
+                if(col_fglobaldoflist) for(i=0;i<col_fsize;i++) _printf_(" " << col_fglobaldoflist[i] << "\n"); _printf_(" \n");
+                _printf_("   col_ssize: " << col_ssize << "\n");
+                _printf_("   col_slocaldoflist  (" << col_slocaldoflist << "): ");
+                if(col_slocaldoflist) for(i=0;i<col_ssize;i++) _printf_(" " << col_slocaldoflist[i] << "\n"); _printf_(" \n");
+                _printf_("   col_sglobaldoflist  (" << col_sglobaldoflist << "): ");
+                if(col_sglobaldoflist) for(i=0;i<col_ssize;i++) _printf_(" " << col_sglobaldoflist[i] << "\n"); _printf_(" \n");
+        }
+}

issm/trunk/src/c/classes/matrix/ElementMatrix.h

-              r13975
+              r15396
 /*Headers:*/
 /*{{{*/
 #include "../objects/Object.h"
+#include "../../datastructures/datastructures.h"
 #include "../../toolkits/toolkits.h"
 #include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../shared/shared.h"
 class Node;
 template <class doublematrix> class Matrix;

issm/trunk/src/c/classes/matrix/ElementVector.cpp

-              r13975
+              r15396
 #include "../classes.h"
 #include "../../shared/shared.h"
-#include "../../Container/Container.h"
-#include "../../include/include.h"
 /*}}}*/
 …
         int i;
         _printLine_("Element Vector echo:");
         _printLine_("   nrows: " << nrows);
         _printLine_("   values:");
+        _printf_("Element Vector echo:\n");
+        _printf_("   nrows: " << nrows << "\n");
+        _printf_("   values:\n");
         for(i=0;i<nrows;i++){
                 _printLine_(setw(4) << right << i << ": " << setw(10) << values[i]);
+        }
         _printString_("   gglobaldoflist (" << gglobaldoflist << "): ");
         if(gglobaldoflist) for(i=0;i<nrows;i++) _printString_(" " << gglobaldoflist[i] );
         _printLine_(" ");
         _printLine_("   fsize: " << fsize);
         _printString_("   flocaldoflist  (" << flocaldoflist << "): ");
         if(flocaldoflist) for(i=0;i<fsize;i++) _printString_(" " << flocaldoflist[i] );
         _printLine_(" ");
         _printString_("   fglobaldoflist (" << fglobaldoflist << "): ");
         if(fglobaldoflist) for(i=0;i<fsize;i++) _printString_(" " << fglobaldoflist[i] );
         _printLine_(" ");
+                _printf_(setw(4) << right << i << ": " << setw(10) << values[i] << "\n");
+        }
+        _printf_("   gglobaldoflist (" << gglobaldoflist << "): ");
+        if(gglobaldoflist) for(i=0;i<nrows;i++) _printf_(" " << gglobaldoflist[i] );
+        _printf_(" \n");
+        _printf_("   fsize: " << fsize << "\n");
+        _printf_("   flocaldoflist  (" << flocaldoflist << "): ");
+        if(flocaldoflist) for(i=0;i<fsize;i++) _printf_(" " << flocaldoflist[i] );
+        _printf_(" \n");
+        _printf_("   fglobaldoflist (" << fglobaldoflist << "): ");
+        if(fglobaldoflist) for(i=0;i<fsize;i++) _printf_(" " << fglobaldoflist[i] );
+        _printf_(" \n");
+}
 /*}}}*/

issm/trunk/src/c/classes/matrix/ElementVector.h

-              r13975
+              r15396
 /*Headers:*/
 /*{{{*/
 #include "../objects/Object.h"
+#include "../../datastructures/datastructures.h"
 #include "../../toolkits/toolkits.h"
 #include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../shared/shared.h"
 class Node;
 template <class doubletype> class Vector;

issm/trunk/src/c/classes/matrix/matrixobjects.h

r13975	r15396
9	9	#include "./ElementMatrix.h"
10	10	#include "./ElementVector.h"
11		~~#include "./Vector.h"~~
12		~~#include "./Matrix.h"~~
13	11
14	12	#endif

issm/trunk/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp

-              r13975
+              r15396
 #include "./AverageOntoPartitionx.h"
-#include "../../Container/Container.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 #include "../../toolkits/toolkits.h"
-#include "../modules.h"
 void AverageOntoPartitionx(double** paverage, Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,double* vertex_response){
 …
         /*Free ressources:*/
         xDelete<double>(qmu_part);
         xdelete(&partition_contributions);
         xdelete(&partition_areas);
         xdelete(&vec_average);
+        delete partition_contributions;
+        delete partition_areas;
+        delete vec_average;
         /*Assign output pointers:*/

issm/trunk/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.h

-              r13395
+              r15396
 #define _AVERAGEONTOPARTITIONXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 void AverageOntoPartitionx(double** average, Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,double* vertex_response);

issm/trunk/src/c/modules/BamgConvertMeshx/BamgConvertMeshx.cpp

-              r13395
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
 #include "../../classes/bamg/bamgobjects.h"
+#include "../../bamg/bamgobjects.h"
 using namespace bamg;

issm/trunk/src/c/modules/BamgConvertMeshx/BamgConvertMeshx.h

-              r13395
+              r15396
 #define _BAMGCONVERTMESHX_H
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
+#include "../../bamg/bamgobjects.h"
 /* local prototypes: */

issm/trunk/src/c/modules/BamgTriangulatex/BamgTriangulatex.cpp

-              r13395
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
+#include "../../bamg/bamgobjects.h"
 using namespace bamg;

issm/trunk/src/c/modules/BamgTriangulatex/BamgTriangulatex.h

r13395	r15396
6	6	#define _BAMGTRIANGULATEX_H
7	7
8		#include "../../classes/~~objects/object~~s.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/Bamgx/Bamgx.cpp

-              r13975
+              r15396
  */
 #include "./Bamgx.h"
 #include "../../classes/bamg/bamgobjects.h"
+#include "../../bamg/bamgobjects.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
 …
                 //Step1: generate geometry Gh
                 if (verbosity>0) _printLine_("Construction of a mesh from a given geometry");
                 if (verbosity>1) _printLine_("   Processing geometry...");
+                if (verbosity>0) _printf_("Construction of a mesh from a given geometry\n");
+                if (verbosity>1) _printf_("   Processing geometry...\n");
                 Geometry Gh(bamggeom_in,bamgopts);
 …
                 //build metric using geometry
                 if (verbosity>1) _printLine_("   Generating Metric...");
+                if (verbosity>1) _printf_("   Generating Metric...\n");
                 for(i=0;i<Gh.nbv;i++){
                         Metric M=Gh[i];
 …
                 //generate mesh
                 if (verbosity>1) _printLine_("   Generating Mesh...");
+                if (verbosity>1) _printf_("   Generating Mesh...\n");
                 Mesh Th(maxnbv,Gh,bamgopts);
 …
                 //Build output
                 if (verbosity>1) _printLine_("   Write Mesh...");
+                if (verbosity>1) _printf_("   Write Mesh...\n");
                 Th.WriteMesh(bamgmesh_out,bamgopts);
                 if (verbosity>1) _printLine_("   Write Geometry...");
+                if (verbosity>1) _printf_("   Write Geometry...\n");
                 Gh.WriteGeometry(bamggeom_out,bamgopts);
 …
                 // read background mesh
                 if (verbosity>0) _printLine_("Anisotropic mesh adaptation");
                 if (verbosity>1) _printLine_("   Processing initial mesh and geometry...");
+                if (verbosity>0) _printf_("Anisotropic mesh adaptation\n");
+                if (verbosity>1) _printf_("   Processing initial mesh and geometry...\n");
                 Mesh BTh(bamggeom_in,bamgmesh_in,bamgopts);
 …
                 //Generate initial metric
                 if (bamgopts->metric){
                         if (verbosity>1) _printLine_("   Processing Metric...");
+                        if (verbosity>1) _printf_("   Processing Metric...\n");
                         BTh.ReadMetric(bamgopts);
+                }
                 else {
                         if (verbosity>1) _printLine_("   Generating initial Metric...");
+                        if (verbosity>1) _printf_("   Generating initial Metric...\n");
                         Metric Mhmax(bamgopts->hmax);
                         for (int iv=0;iv<BTh.nbv;iv++) BTh[iv].m = Mhmax;
 …
                 //use present fields to generate metric if present
                 if (bamgopts->field){
                         if (verbosity>1) _printLine_("   Merge metric with field provided...");
+                        if (verbosity>1) _printf_("   Merge metric with field provided...\n");
                         BTh.AddMetric(bamgopts);
+                }
 …
                 // change using hVertices if provided
                 if(bamgopts->hVertices && bamgopts->hVerticesSize[0]==BTh.nbv){
                         if (verbosity>1) _printLine_("   Merging Metric with hVertices...");
+                        if (verbosity>1) _printf_("   Merging Metric with hVertices...\n");
                         for (i=0;i<BTh.nbv;i++){
                                 if (!xIsNan<IssmPDouble>(bamgopts->hVertices[i])){
 …
                 // change using hminVertices if provided
                 if (bamgopts->hminVertices){
                         if (verbosity>1) _printLine_("   Merging Metric with hminVertices...");
+                        if (verbosity>1) _printf_("   Merging Metric with hminVertices...\n");
                         for (i=0;i<BTh.nbv;i++){
                                 if (!xIsNan<IssmPDouble>(bamgopts->hminVertices[i])){
 …
                 // change using hmaxVertices if provided
                 if (bamgopts->hmaxVertices){
                         if (verbosity>1) _printLine_("   Merging Metric with hmaxVertices...");
+                        if (verbosity>1) _printf_("   Merging Metric with hmaxVertices...\n");
                         for (i=0;i<BTh.nbv;i++){
                                 if (!xIsNan<IssmPDouble>(bamgopts->hmaxVertices[i])){
 …
                 //Build new mesh
                 if (verbosity>1) _printLine_("   Generating Mesh...");
+                if (verbosity>1) _printf_("   Generating Mesh...\n");
                 Thr=&BTh,Thb=0;
                 Mesh & Th( *(0 ?  new Mesh(*Thr,&Thr->Gh,Thb,maxnbv) :  new Mesh(maxnbv,BTh,bamgopts,bamgopts->KeepVertices)));
 …
                 if(verbosity>0) {
                         if (Th.nbt-Th.nbtout-Th.nbq*2){
                                 _printLine_("   new number of triangles = " << (Th.nbt-Th.nbtout-Th.nbq*2));
+                                _printf_("   new number of triangles = " << (Th.nbt-Th.nbtout-Th.nbq*2) << "\n");
+                        }
                         if (Th.nbq ){
                                 _printLine_("   new number of quads = " << Th.nbq);
+                                _printf_("   new number of quads = " << Th.nbq << "\n");
+                        }
+                }
                 //Build output
                 if (verbosity>1) _printLine_("   Write Mesh...");
+                if (verbosity>1) _printf_("   Write Mesh...\n");
                 Th.WriteMesh(bamgmesh_out,bamgopts);
                 if (verbosity>1) _printLine_("   Write Geometry...");
+                if (verbosity>1) _printf_("   Write Geometry...\n");
                 Th.Gh.WriteGeometry(bamggeom_out,bamgopts);
                 if (verbosity>1) _printLine_("   Write Metric...");
+                if (verbosity>1) _printf_("   Write Metric...\n");
                 BTh.WriteMetric(bamgopts);
 …
         /*No error return*/
         if (verbosity>1) _printLine_("   Exiting Bamg.");
+        if (verbosity>1) _printf_("   Exiting Bamg.\n");
         return noerr;

issm/trunk/src/c/modules/Bamgx/Bamgx.h

r13395	r15396
6	6	#define _BAMGX_H
7	7
8		#include "../../~~classes/~~bamg/bamgobjects.h"
	8	#include "../../bamg/bamgobjects.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/CMakeLists.txt

r14310	r15396
29	29	add_subdirectory(InputArtificialNoisex)
30	30	add_subdirectory(InputControlUpdatex)
31		~~add_subdirectory(InputConvergencex)~~
32	31	add_subdirectory(InputDuplicatex)
33	32	add_subdirectory(InputScalex)

issm/trunk/src/c/modules/Chacox/Chacox.cpp

-              r13975
+              r15396
         #ifdef _HAVE_CHACO_ //only works if Chaco library has been compiled in.
         extern int Using_Main;  /* is main routine being called? */
         extern char *PARAMS_FILENAME;   /* name of file with parameter updates */
         extern double EIGEN_TOLERANCE;  /* tolerance for eigen calculations */
         extern int OUTPUT_ASSIGN;       /* whether to write assignment to file */
         extern int DEBUG_MEMORY;        /* debug memory allocation and freeing? */
         extern int DEBUG_TRACE; /* trace main execution path */
         extern int DEBUG_PARAMS;        /* debug flag for reading parameters */
         extern long RANDOM_SEED;        /* seed for random number generators */
         extern int ECHO;                /* controls amount of output */
         extern int PROMPT;              /* prompt for input or not? */
         extern int PRINT_HEADERS;       /* print lines for output sections? */
         extern int MATCH_TYPE;      /* matching routine to call */
         extern double input_time;       /* times data file input */
         extern double start_time;       /* time partitioning starts */
         FILE     *params_file;  /* file with parameter value updates */
         int       global_method;        /* global partitioning method */
         int       local_method; /* local partitioning method */
         double    eigtol;               /* tolerance in eigenvector calculation */
         int       ndims;                /* dimension of recursive partitioning */
         int       architecture; /* 0 => hypercube, d => d-dimensional mesh */
         int       ndims_tot;    /* total number of cube dimensions to divide */
         int       mesh_dims[3]; /* dimensions of mesh of processors */
         long      seed;         /* for random graph mutations */
         int       rqi_flag;             /* use RQI/Symmlq eigensolver? */
         int       vmax;         /* if so, how many vertices to coarsen down to? */
         char      outassignname[NAME_LENGTH];   /* assignment output file name */
         char      outfilename[NAME_LENGTH];     /* name of output file */
         char     *outassignptr; /* name or null pointer for output assignment */
         char     *outfileptr;   /* name or null pointer for output file */
         int       nprocs;               /* number of processors being divided into */
         double    time;         /* timing marker */
         int       flag;         /* return code from input routines */
         double   *smalloc();    /* safe version of malloc */
         //double    seconds();  /* returns elapsed time in seconds */
         /*int       sfree(), interface(), affirm();
         void      input_queries(), smalloc_stats(), read_params(), clear_timing();*/
+        extern int     Using_Main;                   /* is main routine being called?                */
+        extern char   *PARAMS_FILENAME;              /* name of file with parameter updates          */
+        extern double  EIGEN_TOLERANCE;              /* tolerance for eigen calculations             */
+        extern int     OUTPUT_ASSIGN;                /* whether to write assignment to file          */
+        extern int     DEBUG_MEMORY;                 /* debug memory allocation and freeing?         */
+        extern int     DEBUG_TRACE;                  /* trace main execution path                    */
+        extern int     DEBUG_PARAMS;                 /* debug flag for reading parameters            */
+        extern long    RANDOM_SEED;                  /* seed for random number generators            */
+        extern int     ECHO;                         /* controls amount of output                    */
+        extern int     PROMPT;                       /* prompt for input or not?                     */
+        extern int     PRINT_HEADERS;                /* print lines for output sections?             */
+        extern int     MATCH_TYPE;                   /* matching routine to call                     */
+        extern double  input_time;                   /* times data file input                        */
+        extern double  start_time;                   /* time partitioning starts                     */
+        FILE          *params_file;                  /* file with parameter value updates            */
+        int            global_method;                /* global partitioning method                   */
+        int            local_method;                 /* local partitioning method                    */
+        double         eigtol;                       /* tolerance in eigenvector calculation         */
+        int            ndims;                        /* dimension of recursive partitioning          */
+        int            architecture;                 /* 0 => hypercube, d => d-dimensional mesh      */
+        int            ndims_tot;                    /* total number of cube dimensions to divide    */
+        int            mesh_dims[3];                 /* dimensions of mesh of processors             */
+        long           seed;                         /* for random graph mutations                   */
+        int            rqi_flag;                     /* use RQI/Symmlq eigensolver?                  */
+        int            vmax;                         /* if so, how many vertices to coarsen down to? */
+        char           outassignname[NAME_LENGTH];   /* assignment output file name                  */
+        char           outfilename[NAME_LENGTH];     /* name of output file                          */
+        char          *outassignptr;                 /* name or null pointer for output assignment   */
+        char          *outfileptr;                   /* name or null pointer for output file         */
+        int            nprocs;                       /* number of processors being divided into      */
+        double         time;                         /* timing marker                                */
+        int            flag;                         /* return code from input routines              */
+        double        *smalloc();                    /* safe version of malloc                       */
+        //double       seconds();                    /* returns elapsed time in seconds              */
+        /*int sfree(), interface(), affirm();
+        void input_queries()  , smalloc_stats(), read_params(), clear_timing();  */
         int i,tvwgt;
 …
         if (DEBUG_TRACE > 0) {
                 _printLine_("<Entering main>");
+                _printf_("<Entering main>\n");
+        }
         if (PRINT_HEADERS) {
                 _printLine_("\n                    Chaco 2.0");
                 _printLine_("          Sandia National Laboratories\n");
+                _printf_("\n                    Chaco 2.0\n");
+                _printf_("          Sandia National Laboratories\n\n");
+        }
 …
         params_file = fopen(PARAMS_FILENAME, "r");
         if (params_file == NULL && DEBUG_PARAMS > 1) {
+                printf("Parameter file `%s' not found; using default parameters.\n",
+                           PARAMS_FILENAME);
+                printf("Parameter file `%s' not found; using default parameters.\n",PARAMS_FILENAME);
+        }
 …
         if ((int)options[OPT_VWGTS] && vwgts) {
+                printf("%s -- Applying weights for %d vertices.\n",
+                           __FUNCT__,nvtxs);
+                printf("%s -- Applying weights for %d vertices.\n",__FUNCT__,nvtxs);
                 tvwgt = 0;
                 for (i=0; i<nvtxs; i++)
 …
                 tvwgt = nvtxs;
                 if      ( (int)options[OPT_VWGTS] && !vwgts)
+                        printf("%s -- Vertex weight flag=%d, but no vertex weights specified.\n",
+                                   __FUNCT__,options[OPT_VWGTS]);
+                        printf("%s -- Vertex weight flag=%d, but no vertex weights specified.\n",__FUNCT__,(int)options[OPT_VWGTS]);
                 else if (!(int)options[OPT_VWGTS] &&  vwgts)
+                        printf("%s -- Vertex weight flag=%d, so specified vertex weights ignored.\n",
+                                   __FUNCT__,options[OPT_VWGTS]);
+                        printf("%s -- Vertex weight flag=%d, so specified vertex weights ignored.\n",__FUNCT__,(int)options[OPT_VWGTS]);
+        }
 …
         else {
                 if      ( (int)options[OPT_EWGTS] && !ewgts)
+                        printf("%s -- Edge weight flag=%d, but no edge weights specified.\n",
+                                   __FUNCT__,options[OPT_EWGTS]);
+                        printf("%s -- Edge weight flag=%d, but no edge weights specified.\n",__FUNCT__,(int)options[OPT_EWGTS]);
                 else if (!(int)options[OPT_EWGTS] &&  ewgts)
+                        printf("%s -- Edge weight flag=%d, so specified edge weights ignored.\n",
+                                   __FUNCT__,options[OPT_EWGTS]);
+                        printf("%s -- Edge weight flag=%d, so specified edge weights ignored.\n",__FUNCT__,(int)options[OPT_EWGTS]);
+        }
 …
         for (i=0; i<start[nvtxs]; adjacency[i++]++);
+        printf("\n%s -- Calling Chaco interface:\n\n",
+                   __FUNCT__);
+        printf("\n%s -- Calling Chaco interface:\n\n",__FUNCT__);
         flag = interface(nvtxs, start, adjacency,
                   ((int)options[OPT_VWGTS] && vwgts ? vwgts : NULL),
 …
                   global_method, local_method, rqi_flag, vmax, ndims,
                   eigtol, seed);
+        printf("\n%s -- Chaco interface returning flag=%d.\n",
+                   __FUNCT__,flag);
+        printf("\n%s -- Chaco interface returning flag=%d.\n",__FUNCT__,flag);
 /*  Reset adjacency matrix in case calling function needs it.  */
 …
         if (DEBUG_MEMORY > 0) {
                 _printLine_("");
+                _printf_("\n");
                 smalloc_stats();
+        }
 …
         if (DEBUG_TRACE > 1) {
                 _printLine_("<Leaving main>");
+                _printf_("<Leaving main>\n");
+        }

issm/trunk/src/c/modules/Chacox/Chacox.h

-              r13975
+              r15396
 #endif
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/Chacox/input_parse.cpp

-              r13975
+              r15396
         if (DEBUG_TRACE > 0) {
                 _printLine_("<Entering input_parse>");
+                _printf_("<Entering input_parse>\n");
+        }
         if (PROMPT) {
                 _printLine_("Parallel machine architecture:");
                 _printLine_("  (0) Hypercube");
                 _printLine_("  (1) One-dimensional mesh");
                 _printLine_("  (2) Two-dimensional mesh");
                 _printLine_("  (3) Three-dimensional mesh");
+                _printf_("Parallel machine architecture:\n");
+                _printf_("  (0) Hypercube\n");
+                _printf_("  (1) One-dimensional mesh\n");
+                _printf_("  (2) Two-dimensional mesh\n");
+                _printf_("  (3) Three-dimensional mesh\n");
+        }
         *architecture = (int)options[OPT_ARCH];
         if (*architecture < 0 || *architecture > 3) {
+                printf("%s -- Architecture %d must be between 0 and 3.\n",
+                           __FUNCT__,options[OPT_ARCH]);
+                printf("%s -- Architecture %d must be between 0 and 3.\n",__FUNCT__,*architecture);
                 return(-1);
+        }
 …
         /* Name output assignment file. */
         if (PROMPT)
                 _printString_("Assignment output file: ");
+                _printf_("Assignment output file: ");
         outassignname = NULL;
         /* Name output results file. */
         if (PROMPT)
                 _printString_("File name for saving run results: ");
+                _printf_("File name for saving run results: ");
         outfilename = NULL;
 …
         else {
                 if (PROMPT) {
                         _printLine_("Global partitioning method:");
                         _printLine_("  (1) Multilevel-KL");
                         _printLine_("  (2) Spectral");
                         _printLine_("  (3) Inertial");
                         _printLine_("  (4) Linear");
                         _printLine_("  (5) Random");
                         _printLine_("  (6) Scattered");
                         _printLine_("  (7) Read-from-file");
+                        _printf_("Global partitioning method:\n");
+                        _printf_("  (1) Multilevel-KL\n");
+                        _printf_("  (2) Spectral\n");
+                        _printf_("  (3) Inertial\n");
+                        _printf_("  (4) Linear\n");
+                        _printf_("  (5) Random\n");
+                        _printf_("  (6) Scattered\n");
+                        _printf_("  (7) Read-from-file\n");
+                }
                 *global_method = (int)options[OPT_GLOBAL];
                 if (*global_method < 1 || *global_method > 7) {
+                        printf("%s -- Global method %d must be between 1 and 7.\n",
+                                   __FUNCT__,options[OPT_GLOBAL]);
+                        printf("%s -- Global method %d must be between 1 and 7.\n",__FUNCT__,*global_method);
                         return(-1);
+                }
 …
         if (*global_method == 7) {      /* Name and open input assignment file. */
                 if (PROMPT)
                         _printString_("Assignment input file: ");
+                        _printf_("Assignment input file: ");
+        }
         else if (*global_method == 3) {
                 if (PROMPT)
                         _printString_("Geometry input file name: ");
+                        _printf_("Geometry input file name: ");
+        }
         else if (*global_method == 2) {
                 if (PROMPT) {
                         _printLine_("Eigensolver:");
                         _printLine_("  (1) Multilevel RQI/Symmlq");
                         _printLine_("  (2) Lanczos");
+                        _printf_("Eigensolver:\n");
+                        _printf_("  (1) Multilevel RQI/Symmlq\n");
+                        _printf_("  (2) Lanczos\n");
+                }
                 eigensolver = (int)options[OPT_RQI];
                 if (eigensolver < 0 || eigensolver > 2) {
+                        printf("%s -- RQI/Symmlq flag %d must be between 0 and 2.\n",
+                                   __FUNCT__,options[OPT_RQI]);
+                        printf("%s -- RQI/Symmlq flag %d must be between 0 and 2.\n",__FUNCT__,eigensolver);
                         return(-1);
+                }
 …
                         if (MATCH_TYPE == 5) {  /* geometric matching */
                                 if (PROMPT)
                                         _printString_("Geometry input file name: ");
+                                        _printf_("Geometry input file name: ");
+                        }
                         *rqi_flag = 1;
                         if (PROMPT)
                                 _printString_("Number of vertices to coarsen down to: ");
+                                _printf_("Number of vertices to coarsen down to: ");
                         *vmax = (int)options[OPT_VMAX];
                         if (*vmax <= 0) {
+                                printf("%s -- Vmax %d must be greater then 0.\n",
+                                           __FUNCT__,options[OPT_VMAX]);
+                                printf("%s -- Vmax %d must be greater then 0.\n",__FUNCT__,*vmax);
                                 return(-1);
+                        }
 …
                 if (MATCH_TYPE == 5) {          /* geometric matching */
                         if (PROMPT)
                                 _printString_("Geometry input file name: ");
+                }
                 if (PROMPT)
                         _printString_("Number of vertices to coarsen down to: ");
+                                _printf_("Geometry input file name: ");
+                }
+                if (PROMPT)
+                        _printf_("Number of vertices to coarsen down to: ");
                 *vmax = (int)options[OPT_VMAX];
                 if (*vmax <= 0) {
+                        printf("%s -- Vmax %d must be greater then 0.\n",
+                                   __FUNCT__,options[OPT_VMAX]);
+                        printf("%s -- Vmax %d must be greater then 0.\n",__FUNCT__,*vmax);
                         return(-1);
+                }
 …
         else {
                 if (PROMPT) {
                         _printLine_("Local refinement method:");
                         _printLine_("  (1) Kernighan-Lin");
                         _printLine_("  (2) None");
+                        _printf_("Local refinement method:\n");
+                        _printf_("  (1) Kernighan-Lin\n");
+                        _printf_("  (2) None\n");
+                }
                 *local_method = (int)options[OPT_LOCAL];
                 if (*local_method < 1 || *local_method > 2) {
+                        printf("%s -- Local method %d must be 1 and 2.\n",
+                                   __FUNCT__,options[OPT_LOCAL]);
+                        printf("%s -- Local method %d must be 1 and 2.\n",__FUNCT__,*local_method);
                         return(-1);
+                }
 …
                 *ndims_tot = 0;
                 if (PROMPT)
                         _printString_("Total number of target hypercube dimensions: ");
+                        _printf_("Total number of target hypercube dimensions: ");
                 *ndims_tot = nparts[0];
                 if (*ndims_tot < 1) {
                         _printLine_(" Number of divisions must be at least 1");
+                        _printf_(" Number of divisions must be at least 1\n");
                         printf("%s -- Number of divisions %d must be at least 1.\n",
                                    __FUNCT__,nparts[0]);
 …
                 if (*architecture == 2) {
                         if (PROMPT)
                                 _printString_("X and Y extent of of 2-D mesh: ");
+                                _printf_("X and Y extent of of 2-D mesh: ");
                         mesh_dims[0] = nparts[0];
                         mesh_dims[1] = nparts[1];
 …
                 else if (*architecture == 3) {
                         if (PROMPT)
                                 _printString_("X, Y and Z extent of 3-D mesh: ");
+                                _printf_("X, Y and Z extent of 3-D mesh: ");
                         mesh_dims[0] = nparts[0];
                         mesh_dims[1] = nparts[1];
 …
                 else {                  /* Anything else => 1-D mesh */
                         if (PROMPT)
                                 _printString_("Size of 1-D mesh: ");
+                                _printf_("Size of 1-D mesh: ");
                         mesh_dims[0] = nparts[0];
                         *architecture = 1;
 …
         else if (*nprocs <= 7) {
                 if (PROMPT) {
                         _printLine_("Partitioning dimension: ");
                         _printLine_("  (1) Bisection");
                         _printLine_("  (2) Quadrisection");
+                        _printf_("Partitioning dimension: \n");
+                        _printf_("  (1) Bisection\n");
+                        _printf_("  (2) Quadrisection\n");
+                }
                 *ndims = (int)options[OPT_NDIMS];
                 if (*ndims < 1 || *ndims > 2) {
+                        printf("%s -- Ndims %d must be 1 or 2 for %d processors.\n",
+                                   __FUNCT__,options[OPT_NDIMS],*nprocs);
+                        printf("%s -- Ndims %d must be 1 or 2 for %d processors.\n",__FUNCT__,*ndims,*nprocs);
                         return(-1);
+                }
 …
         else {
                 if (PROMPT) {
                         _printLine_("Partitioning dimension: ");
                         _printLine_("  (1) Bisection");
                         _printLine_("  (2) Quadrisection");
                         _printLine_("  (3) Octasection");
+                        _printf_("Partitioning dimension: \n");
+                        _printf_("  (1) Bisection\n");
+                        _printf_("  (2) Quadrisection\n");
+                        _printf_("  (3) Octasection\n");
+                }
                 *ndims = (int)options[OPT_NDIMS];
                 if (*ndims < 1 || *ndims > 3) {
+                        printf("%s -- Ndims %d must be between 1 and 3 for %d processors.\n",
+                                   __FUNCT__,options[OPT_NDIMS],*nprocs);
+                        printf("%s -- Ndims %d must be between 1 and 3 for %d processors.\n",__FUNCT__,*ndims,*nprocs);
                         return(-1);
+                }

issm/trunk/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void    ComputeBasalStressx( Vector<IssmDouble>** psigma,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){

issm/trunk/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.h

-              r13975
+              r15396
 #define _COMPUTEBASALSTRESSX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void    ComputeStrainRatex( Vector<IssmDouble>** peps,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){

issm/trunk/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.h

-              r13975
+              r15396
 #define _COMPUTESTRAINRATEX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/ConfigureObjectsx/ConfigureObjectsx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
 #include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../classes/classes.h"
 int     ConfigureObjectsx( Elements* elements, Loads* loads, Nodes* nodes, Vertices* vertices, Materials* materials,Parameters* parameters){
         /*Intermediary*/
+        int i;
         int noerr=1;
-        int i;
-        Element* element=NULL;
-        Load* load=NULL;
-        Node* node=NULL;
-        Material* material=NULL;
         int configuration_type;
+        Element  *element  = NULL;
+        Load     *load     = NULL;
+        Node     *node     = NULL;
+        Material *material = NULL;
         /*Get analysis type: */
         parameters->FindParam(&configuration_type,ConfigurationTypeEnum);
         if(VerboseMProcessor()) _pprintLine_("      Configuring elements...");
+        if(VerboseMProcessor()) _printf0_("      Configuring elements...\n");
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 element->Configure(elements,loads,nodes,materials,parameters);
+                element->Configure(elements,loads,nodes,vertices,materials,parameters);
+        }
         if(VerboseMProcessor()) _pprintLine_("      Configuring loads...");
+        if(VerboseMProcessor()) _printf0_("      Configuring loads...\n");
         for (i=0;i<loads->Size();i++){
                 load=(Load*)loads->GetObjectByOffset(i);
 …
+                }
+        }
         if(VerboseMProcessor()) _pprintLine_("      Configuring nodes...");
+        if(VerboseMProcessor()) _printf0_("      Configuring nodes...\n");
         for (i=0;i<nodes->Size();i++){
                 node=(Node*)nodes->GetObjectByOffset(i);
 …
+        }
         if(VerboseMProcessor()) _pprintLine_("      Configuring materials...");
+        if(VerboseMProcessor()) _printf0_("      Configuring materials...\n");
         for (i=0;i<materials->Size();i++){
                 material=(Material*)materials->GetObjectByOffset(i);

issm/trunk/src/c/modules/ConfigureObjectsx/ConfigureObjectsx.h

r4236	r15396
6	6	#define _CONFIGUREOBJECTSX_H
7	7
8		#include "../../~~Container/Container~~.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/ConstraintsStatex/ConstraintsStateLocal.h

-              r13975
+              r15396
 #define _CONSTRAINTSSTATELOCAL_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /*melting: */

issm/trunk/src/c/modules/ConstraintsStatex/ConstraintsStatex.cpp

-              r13975
+              r15396
 #include "./ConstraintsStateLocal.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void ConstraintsStatex(int* pconverged, int* pnum_unstable_constraints, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads,Materials* materials,  Parameters* parameters){
 …
         /*Display message*/
         if(VerboseModule()) _pprintLine_("   Constraining penalties");
+        if(VerboseModule()) _printf0_("   Constraining penalties\n");
         /*recover parameters: */
 …
         /*Do we have penalties linked to rifts? In this case, run our special rifts penalty
          * management routine, otherwise, skip : */
+        /*No constraints management by default!:*/
+        num_unstable_constraints=0;
+        converged=1;
+        #ifdef _HAVE_RIFTS_
         if (RiftIsPresent(loads,analysis_type)){
                 RiftConstraintsState(&converged,&num_unstable_constraints,loads,min_mechanical_constraints,analysis_type);
+        }
+        #endif
         #ifdef _HAVE_THERMAL_
         else if(ThermalIsPresent(loads,analysis_type)){
+        if(ThermalIsPresent(loads,analysis_type)){
                 ThermalConstraintsState(loads,&converged,&num_unstable_constraints,analysis_type);
+        }
         #endif
-        else{
-                /*Do nothing, no constraints management!:*/
-                num_unstable_constraints=0;
-                converged=1;
+        }
         /*Assign output pointers: */

issm/trunk/src/c/modules/ConstraintsStatex/ConstraintsStatex.h

-              r13975
+              r15396
 #define _CONSTRAINTSSTATEX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp

-              r13975
+              r15396
 #include "./ConstraintsStateLocal.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../shared/shared.h"
 …
+        }
         else if(num_unstable_constraints<=min_mechanical_constraints){
                 if(VerboseModule()) _pprintLine_("   freezing constraints");
+                if(VerboseModule()) _printf0_("   freezing constraints\n");
                 RiftFreezeConstraints(loads,configuration_type);
+        }

issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshx.cpp

-              r13975
+              r15396
 #include "./ContourToMeshx.h"
 int ContourToMeshx(SeqVec<double>** pin_nod,SeqVec<double>** pin_elem, double* index, double* x, double* y,DataSet* contours,char* interptype,int nel,int nods, int edgevalue) {
+int ContourToMeshx(double** pin_nod,double** pin_elem, double* index, double* x, double* y,Contours* contours,char* interptype,int nel,int nods, int edgevalue) {
         /*Contour:*/
-        double*  in_nod_serial;
         double   value;
 …
         /*output: */
         SeqVec<double>* in_nod=NULL;
         SeqVec<double>* in_elem=NULL;
         in_nod  = new SeqVec<double>(nods);
         in_elem = new SeqVec<double>(nel);
+        double*  in_nod;
+        double*  in_elem;
+        in_nod   = xNewZeroInit<double>(nods);
+        in_elem  = xNewZeroInit<double>(nel);
         /*initialize thread parameters: */
 …
         LaunchThread(ContourToMeshxt,(void*)&gate,num);
-        /*Assemble in_nod: */
-        in_nod->Assemble();
-        /*Get in_nod serialised for next operation: */
-        in_nod_serial=in_nod->ToMPISerial();
         /*Take care of the case where an element interpolation has been requested: */
         if ((strcmp(interptype,"element")==0) || (strcmp(interptype,"element and node")==0)){
                 for(int n=0;n<nel;n++){
                         if ( (in_nod_serial[ (int)*(index+3*n+0) -1] == 1) && (in_nod_serial[ (int)*(index+3*n+1) -1] == 1) && (in_nod_serial[ (int)*(index+3*n+2) -1] == 1) ){
                                 value=1; in_elem->SetValue(n,value,INS_VAL);
+                        if ( (in_nod[ (int)*(index+3*n+0) -1] == 1) && (in_nod[ (int)*(index+3*n+1) -1] == 1) && (in_nod[ (int)*(index+3*n+2) -1] == 1) ){
+                                value=1; in_elem[n]=value;
+                        }
+                }
+        }
-        /*Assemble vectors: */
-        in_elem->Assemble();
         /*Assign output pointers: */
 …
         *pin_elem=in_elem;
-        /*Free ressources:*/
-        xDelete<double>(in_nod_serial);
         return 1;
+}

issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshx.h

-              r13975
+              r15396
 #include "../../shared/shared.h"
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /*threading: */
 typedef struct{
         DataSet *contours;
         int    nods;
         int    edgevalue;
         SeqVec<double> *in_nod;
         double *x;
         double *y;
+        Contours *contours;
+        int       nods;
+        int       edgevalue;
+        double   *in_nod;
+        double   *x;
+        double   *y;
 } ContourToMeshxThreadStruct;
 /* local prototypes: */
 int ContourToMeshx(SeqVec<double>** pin_nods,SeqVec<double>** pin_elem, double* index, double* x, double* y,DataSet* contours,char* interptype,int nel,int nods, int edgevalue);
+int ContourToMeshx(double** pin_nods,double** pin_elem, double* index, double* x, double* y,Contours* contours,char* interptype,int nel,int nods, int edgevalue);
 void* ContourToMeshxt(void* vContourToMeshxThreadStruct);

issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp

-              r13975
+              r15396
         /*Contour:*/
         DataSet* contours=NULL;
+        Contours* contours=NULL;
         /*parameters: */
 …
         double* x=NULL;
         double* y=NULL;
         SeqVec<double>* in_nod=NULL;
+        double* in_nod=NULL;
         /*recover handle and gate: */

issm/trunk/src/c/modules/ContourToNodesx/ContourToNodesx.cpp

-              r13975
+              r15396
 #include "./ContourToNodesx.h"
 int ContourToNodesx(SeqVec<IssmPDouble>** pflags,double* x, double* y, int nods, Contour<IssmPDouble>** contours,int numcontours,int edgevalue){
+int ContourToNodesx(IssmPDouble** pflags,double* x, double* y, int nods, Contour<IssmPDouble>** contours,int numcontours,int edgevalue){
         int i;
 …
         /*output: */
         SeqVec<IssmPDouble>* flags=NULL;
         flags=new SeqVec<IssmPDouble>(nods);
+        IssmPDouble* flags=NULL;
+        flags=xNew<IssmPDouble>(nods);
         /*Loop through all contours: */
 …
+        }
-        /*Assemble vector: */
-        flags->Assemble();
         /*Assign output pointers: */
         *pflags=flags;
 …
+}
 int ContourToNodesx(SeqVec<IssmPDouble>** pflags,double* x, double* y, int nods, DataSet* contours, int edgevalue){
+int ContourToNodesx(IssmPDouble** pflags,double* x, double* y, int nods, Contours* contours, int edgevalue){
         /*Contour:*/
 …
         /*output: */
         SeqVec<IssmPDouble>* flags=NULL;
         flags=new SeqVec<IssmPDouble>(nods);
+        IssmPDouble* flags=NULL;
+        flags=xNewZeroInit<IssmPDouble>(nods);
         /*Loop through all contours: */
 …
+        }
-        /*Assemble vector: */
-        flags->Assemble();
         /*Assign output pointers: */
         *pflags=flags;

issm/trunk/src/c/modules/ContourToNodesx/ContourToNodesx.h

-              r13395
+              r15396
 #include "../../shared/shared.h"
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 int ContourToNodesx(SeqVec<IssmPDouble>** pflags,double* x, double* y, int nods, Contour<IssmPDouble>** contours,int numcontours,int edgevalue);
 int ContourToNodesx(SeqVec<IssmPDouble>** pflags,double* x, double* y, int nods, DataSet* contours, int edgevalue);
+int ContourToNodesx(IssmPDouble** pflags,double* x, double* y, int nods, Contour<IssmPDouble>** contours,int numcontours,int edgevalue);
+int ContourToNodesx(IssmPDouble** pflags,double* x, double* y, int nods, Contours* contours, int edgevalue);
 #endif /* _CONTOURTONODESX_H */

issm/trunk/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp

-              r13395
+              r15396
 #include "./ControlInputGetGradientx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void ControlInputGetGradientx( Vector<IssmDouble>** pgradient, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){

issm/trunk/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.h

-              r13395
+              r15396
 #define _CONTROLINPUTGETGRADIENTX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 void    ControlInputGetGradientx( Vector<IssmDouble>** pgradient, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,  Parameters* parameters);

issm/trunk/src/c/modules/ControlInputScaleGradientx/ControlInputScaleGradientx.cpp

-              r13975
+              r15396
 #include "./ControlInputScaleGradientx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void ControlInputScaleGradientx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,IssmDouble* norm_list,int step){

issm/trunk/src/c/modules/ControlInputScaleGradientx/ControlInputScaleGradientx.h

-              r13395
+              r15396
 #define _CONTROLINPUTSSCALEGRADIENTX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 void    ControlInputScaleGradientx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,  Parameters* parameters,IssmDouble* norm_list,int step);

issm/trunk/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp

-              r13395
+              r15396
 #include "./ControlInputSetGradientx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,IssmDouble* gradient){

issm/trunk/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.h

-              r13395
+              r15396
 #define _CONTROLINPUTSSETGRADIENTX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 void    ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,  Parameters* parameters,double* gradient);

issm/trunk/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void CreateNodalConstraintsx( Vector<IssmDouble>** pys, Nodes* nodes,int configuration_type){
 …
         /*output: */
         Vector<IssmDouble>* ys=NULL;
+        int ssize;
+        int slocalsize;
+        if(VerboseModule()) _printf0_("   Create nodal constraints\n");
         /*figure out how many dofs we have: */
         int ssize=nodes->NumberOfDofs(configuration_type,SsetEnum);
         int slocalsize = nodes->NumberOfDofsLocal(configuration_type,SsetEnum);
+        ssize=nodes->NumberOfDofs(configuration_type,SsetEnum);
+        slocalsize = nodes->NumberOfDofsLocal(configuration_type,SsetEnum);
         /*allocate:*/

issm/trunk/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h

-              r13395
+              r15396
 #define _CREATENODALCONSTRAINTSX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/Delta18oParameterizationx/Delta18oParameterizationx.cpp

-              r13975
+              r15396
 #include "./Delta18oParameterizationx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void Delta18oParameterizationx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters){

issm/trunk/src/c/modules/Delta18oParameterizationx/Delta18oParameterizationx.h

-              r13395
+              r15396
 #define _DELTA18OPARAMETERIZATIONX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void DragCoefficientAbsGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units, int weight_index){
+void DragCoefficientAbsGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->DragCoefficientAbsGradient(process_units,weight_index);
+                J+=element->DragCoefficientAbsGradient(weight_index);
+        }

issm/trunk/src/c/modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.h

-              r13395
+              r15396
 #define _DRAGCOEFFABSGRADX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void DragCoefficientAbsGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void DragCoefficientAbsGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/ElementConnectivityx/ElementConnectivityx.cpp

-              r14067
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 int hascommondedge(int* element1,int* element2);

issm/trunk/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp

-              r13975
+              r15396
 #include "./Exp2Kmlx.h"
 #include "../../shared/shared.h"
+#include "../../include/include.h"
+#include "../../io/io.h"
+#include "../../kml/kmlobjects.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
-#include "../modules.h"
 int Exp2Kmlx(char* filexp,char* filkml,int sgn,bool holes){
 …
         clock0=clock();
         time0 =time(NULL);
         _pprintString_("\nExp2Kmlx Module -- " << ctime(&time0));
+        _printf0_("\nExp2Kmlx Module -- " << ctime(&time0));
         /*read exp file  */
         if (!DomainOutlineRead(&nprof,&pnvert,&pprofx,&pprofy,&closed,filexp))
+        if (!ExpRead(&nprof,&pnvert,&pprofx,&pprofy,&closed,filexp))
                 _error_("Error reading exp file.");
         _pprintLine_("Exp2Kmlx -- Reading " << nprof << " exp profiles from file \"" << filexp << "\".");
+        _printf0_("Exp2Kmlx -- Reading " << nprof << " exp profiles from file \"" << filexp << "\".\n");
 //      for (i=0; i<nprof; i++)
 //              _printLine_("i=" << i << "; nvert=" << pnvert[i] << ", closed=" << closed[i]);
+//              _printf_("i=" << i << "; nvert=" << pnvert[i] << ", closed=" << closed[i] << "\n");
 /*  construct kml file  */
 …
         if (holes && nprof && (pnvert[0] <= 1 || pprofx[0][pnvert[0]-1] != pprofx[0][0] || pprofy[0][pnvert[0]-1] != pprofy[0][0])) {
                 _pprintLine_("Warning -- Outer profile is not closed, so \"holes\" option will be ignored.");
+                _printf0_("Warning -- Outer profile is not closed, so \"holes\" option will be ignored.\n");
                 holes=false;
+        }
 …
                 for (i=1; i<nprof; i++) {
                         if (pnvert[i] <= 1 || pprofx[i][pnvert[i]-1] != pprofx[i][0] || pprofy[i][pnvert[i]-1] != pprofy[i][0]) {
                                 _pprintLine_("Warning -- Inner profile " << i+1 << " is not closed with \"holes\" specified, so it will be ignored.");
+                                _printf0_("Warning -- Inner profile " << i+1 << " is not closed with \"holes\" specified, so it will be ignored.\n");
                                 continue;
+                        }
 …
 /*  write kml file  */
         _pprintLine_("Exp2Kmlx -- Writing kml document to file \"" << filkml << "\".");
+        _printf0_("Exp2Kmlx -- Writing kml document to file \"" << filkml << "\".\n");
         fid=fopen(filkml,"w");
         fprintf(fid,"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
 …
         clock1=clock();
         time1 =time(NULL);
+        _printf_(true,"Exp2Kmlx Module -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0));
+        _printf_("Exp2Kmlx Module -- " <<((double)(clock1-clock0))/CLOCKS_PER_SEC << " CPU seconds; " <<difftime(time1,time0) << " elapsed seconds.\n\n\n");
         return(iret);

issm/trunk/src/c/modules/Exp2Kmlx/Exp2Kmlx.h

-              r13395
+              r15396
 #include <float.h>    /*  DBL_MAX  */
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp

-              r13975
+              r15396
 #include "./GetSolutionFromInputsx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void    GetSolutionFromInputsx( Vector<IssmDouble>** psolution, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,  Parameters* parameters){
 …
         /*output: */
         Vector<IssmDouble>* solution=NULL;
+        if(VerboseModule()) _printf0_("   Get solution from inputs\n");
         /*retrive parameters: */

issm/trunk/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h

-              r13975
+              r15396
 #define _GETSOLUTIONFROMINPUTSXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp

-              r13975
+              r15396
 #include "./GetVectorFromControlInputsx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void GetVectorFromControlInputsx(Vector<IssmDouble>** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){
 …
         /*Free ressources:*/
         xdelete(&vec_vector);
+        delete vec_vector;
         /*Assign output pointers:*/

issm/trunk/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h

-              r13975
+              r15396
 #define _GETVECTORFROMCONTROLINPUTSXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp

-              r13975
+              r15396
 #include "./GetVectorFromInputsx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void GetVectorFromInputsx( Vector<IssmDouble>** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, int name, int type){
 …
         /*Free ressources:*/
         xdelete(&vec_vector);
+        delete vec_vector;
         /*Assign output pointers:*/

issm/trunk/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h

-              r13975
+              r15396
 #define _GETVECTORFROMINPUTSXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/Gradjx/Gradjx.cpp

-              r13975
+              r15396
 #include "./Gradjx.h"
-#include "../modules.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void Gradjx(Vector<IssmDouble>** pgradient,IssmDouble** pnorm_list, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){
 …
         for(i=0;i<num_controls;i++){
                 gradient->AXPY(gradient_list[i],1.0);
                 xdelete(&gradient_list[i]);
+                delete gradient_list[i];
+        }

issm/trunk/src/c/modules/Gradjx/Gradjx.h

-              r13395
+              r15396
 #define _GRADJX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../io/io.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 #include "./GroundinglineMigrationx.h"
 void GroundinglineMigrationx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters){
         int      i, migration_style,analysis_type;
         IssmDouble*  vertices_potentially_ungrounding = NULL;
         IssmDouble*  vertices_ungrounding             = NULL;
         IssmDouble*  old_floatingice                  = NULL;
         Vector<IssmDouble>*      vec_old_floatingice              = NULL;
         Element* element                          = NULL;
+        int                 migration_style,analysis_type;
+        IssmDouble         *vertices_potentially_ungrounding = NULL;
+        IssmDouble         *vertices_ungrounding             = NULL;
+        IssmDouble         *old_floatingice                  = NULL;
+        Vector<IssmDouble> *vec_old_floatingice              = NULL;
+        Element            *element                          = NULL;
         if(VerboseModule()) _pprintLine_("   Migrating grounding line");
+        if(VerboseModule()) _printf0_("   Migrating grounding line\n");
         /*retrieve parameters: */
 …
         if(migration_style==NoneEnum) return;
+        if(migration_style!=AgressiveMigrationEnum && migration_style!=SoftMigrationEnum) _error_(EnumToStringx(migration_style) << " not supported yet!");
+        if(migration_style!=AgressiveMigrationEnum  &&
+                migration_style!=SoftMigrationEnum       &&
+                migration_style!=SubelementMigrationEnum &&
+                migration_style!=SubelementMigration2Enum)
+         _error_("Grounding line migration "<<EnumToStringx(migration_style) << " not supported yet!");
+        /*Set toolkit to default*/
+        ToolkitsOptionsFromAnalysis(parameters,NoneAnalysisEnum);
         if(migration_style==SoftMigrationEnum){
                 /*Create flag for grounded vertices above the hydrostatic equilibrium: */
                 vertices_potentially_ungrounding=PotentialSheetUngrounding(elements,vertices,parameters);
+                vertices_potentially_ungrounding=PotentialUngrounding(elements,vertices,parameters);
                 /*propagate ice shelf into connex areas of the ice sheet that potentially want to unground: */
 …
         /*Migrate grounding line : */
         for(i=0;i<elements->Size();i++){
+        for(int i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 element->MigrateGroundingLine(old_floatingice,vertices_ungrounding);
 …
         /*free ressouces: */
         xdelete(&vec_old_floatingice);
+        delete vec_old_floatingice;
         xDelete<IssmDouble>(vertices_potentially_ungrounding);
         xDelete<IssmDouble>(vertices_ungrounding);
 …
+}
 /*%}}}*/
 /*FUNCTION PotentialSheetUngrounding {{{*/
 IssmDouble*    PotentialSheetUngrounding(Elements* elements,Vertices* vertices,Parameters* parameters){
+/*FUNCTION PotentialUngrounding {{{*/
+IssmDouble*    PotentialUngrounding(Elements* elements,Vertices* vertices,Parameters* parameters){
         int      i,numberofvertices;
 …
         for(i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 element->PotentialSheetUngrounding(vec_vertices_potentially_ungrounding);
+                element->PotentialUngrounding(vec_vertices_potentially_ungrounding);
+        }
 …
         /*free ressouces and return: */
         xdelete(&vec_vertices_potentially_ungrounding);
+        delete vec_vertices_potentially_ungrounding;
         return vertices_potentially_ungrounding;
+}
 …
                         element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                         if(reCast<int,IssmDouble>(elements_neighboring_floatingce[element->Sid()])){
                                 local_nflipped+=element->UpdatePotentialSheetUngrounding(vertices_potentially_ungrounding,vec_nodes_on_floatingice,nodes_on_floatingice);
+                                local_nflipped+=element->UpdatePotentialUngrounding(vertices_potentially_ungrounding,vec_nodes_on_floatingice,nodes_on_floatingice);
+                        }
+                }
 …
                 #ifdef _HAVE_MPI_
                 MPI_Allreduce(&local_nflipped,&nflipped,1,MPI_INT,MPI_SUM,IssmComm::GetComm());
                 if(VerboseConvergence()) _pprintLine_("   Additional number of vertices allowed to unground: " << nflipped);
+                if(VerboseConvergence()) _printf0_("   Additional number of vertices allowed to unground: " << nflipped << "\n");
                 #else
                 nflipped=local_nflipped;
 …
                 /*Assemble and serialize:*/
                 xdelete(&vec_elements_neighboring_floatingice);
+                delete vec_elements_neighboring_floatingice;
                 nodes_on_floatingice=vec_nodes_on_floatingice->ToMPISerial();
+        }
         /*Free ressources:*/
         xdelete(&vec_nodes_on_floatingice);
+        delete vec_nodes_on_floatingice;
         xDelete<IssmDouble>(elements_neighboring_floatingce);

issm/trunk/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.h

-              r13395
+              r15396
 void       GroundinglineMigrationx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters);
 Vector<IssmDouble>*        CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type);
 IssmDouble*    PotentialSheetUngrounding(Elements* elements,Vertices* vertices,Parameters* parameters);
+Vector<IssmDouble>* CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type);
+IssmDouble*    PotentialUngrounding(Elements* elements,Vertices* vertices,Parameters* parameters);
 IssmDouble*    PropagateFloatingiceToGroundedNeighbors(Elements* elements,Nodes* nodes,Vertices* vertices,Parameters* parameters,IssmDouble* vertices_potentially_ungrounding);
 #endif  /* _GROUNDINGLINEMIGRATIONX_H */

issm/trunk/src/c/modules/HoleFillerx/HoleFillerx.cpp

-              r13975
+              r15396
+                        }
+                }
                 _printLine_( "" );
                 _printString_("Number of zeroes remaining: " << lines*samps-counter);
+                _printf_( ""  << "\n");
+                _printf_("Number of zeroes remaining: " << lines*samps-counter);
                 fflush( stdout );
         #endif
 …
+                }
                 //        n u m b e r   o f   z e r o e s   r e m a i n i n g :   1 2 3 4 5 6 7 8 9 10
                 _printString_( "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b" );
                 _printString_("Number of zeroes remaining: " << lines*samps-counter);
+                _printf_( "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b" );
+                _printf_("Number of zeroes remaining: " << lines*samps-counter);
                 fflush( stdout );
         #endif
 …
 /***************** FIRST RUN *********************/
 /*
 fprintf ( stdout, "First  Application:  " ); time(&t2); _printString_( ctime(&t2) );
+fprintf ( stdout, "First  Application:  " ); time(&t2); _printf_( ctime(&t2) );
 */
         for ( i = 0; i < lines; i++ ){
 …
                         #ifdef _DEBUG2_
                                 //_printLine_(temp << " " << elev << " " << range << " ");
+                                //_printf_(temp << " " << elev << " " << range << " \n");
                         #endif
 …
         #ifdef _DEBUG2_
                 _printString_( "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b" );
                 _printLine_("Number of zeroes remaining:          0\n");
+                _printf_( "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b" );
+                _printf_("Number of zeroes remaining:          0\n\n");
                 printf ( "\n");
         #endif

issm/trunk/src/c/modules/InputArtificialNoisex/InputArtificialNoisex.cpp

-              r13975
+              r15396
 #include "./InputArtificialNoisex.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void InputArtificialNoisex( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int enum_name,IssmDouble min,IssmDouble max){

issm/trunk/src/c/modules/InputArtificialNoisex/InputArtificialNoisex.h

-              r13395
+              r15396
 #define _INPUTARTIFICIALNOISEX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/InputControlUpdatex/InputControlUpdatex.cpp

-              r13975
+              r15396
 #include "./InputControlUpdatex.h"
 #include "../../shared/shared.h"
 #include "../../include/include.h"
+#include "../../classes/classes.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void InputControlUpdatex(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters,IssmDouble scalar,bool save_parameter){

issm/trunk/src/c/modules/InputControlUpdatex/InputControlUpdatex.h

r13395	r15396
6	6	#define _INPUTCONTROLUPDATEX_H
7	7
8		#include "../../~~Container/Container~~.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/InputDuplicatex/InputDuplicatex.cpp

-              r13975
+              r15396
 #include "./InputDuplicatex.h"
 #include "../../shared/shared.h"
 #include "../../include/include.h"
+#include "../../classes/classes.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void InputDuplicatex(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters,int original_enum, int new_enum){
 …
         for(i=0;i<materials->Size();i++){
                 Material* material=(Material*)materials->GetObjectByOffset(i);
                 //material->InputDuplicate(original_enum,new_enum);
+                material->InputDuplicate(original_enum,new_enum);
+        }

issm/trunk/src/c/modules/InputDuplicatex/InputDuplicatex.h

r13975	r15396
6	6	#define _INPUTDUPLICATEX_H
7	7
8		#include "../../~~Container/Container~~.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/InputScalex/InputScalex.cpp

-              r13975
+              r15396
 #include "./InputScalex.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
 #include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../classes/classes.h"
 void InputScalex(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters,int enum_type, IssmDouble scale_factor){

issm/trunk/src/c/modules/InputScalex/InputScalex.h

r13975	r15396
6	6	#define _SCALEINPUTX_H
7	7
8		#include "../../~~Container/Container~~.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/InputToResultx/InputToResultx.cpp

-              r13975
+              r15396
 #include "./InputToResultx.h"
 #include "../../shared/shared.h"
 #include "../../include/include.h"
+#include "../../classes/classes.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void InputToResultx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters,int enum_type){

issm/trunk/src/c/modules/InputToResultx/InputToResultx.h

r11995	r15396
6	6	#define _INPUTTORESULTX_H
7	7
8		#include "../../~~Container/Container~~.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/InputUpdateFromConstantx/InputUpdateFromConstantx.cpp

-              r13975
+              r15396
 #include "./InputUpdateFromConstantx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void InputUpdateFromConstantx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool   constant, int name){
         int i;
+        if(VerboseModule()) _printf0_("   Input updates from constant\n");
         /*Elements and loads drive the update: */
 …
         int i;
+        if(VerboseModule()) _printf0_("   Input updates from constant\n");
         /*Elements and loads drive the update: */
 …
         int i;
+        if(VerboseModule()) _printf0_("   Input updates from constant\n");
         /*Elements and loads drive the update: */

issm/trunk/src/c/modules/InputUpdateFromConstantx/InputUpdateFromConstantx.h

-              r13975
+              r15396
 #define _UPDATEINPUTSFROMCONSTANTXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/InputUpdateFromDakotax/InputUpdateFromDakotax.cpp

-              r13975
+              r15396
 #include "./InputUpdateFromDakotax.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../modules.h"
+#include "../InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.h"
+#include "../InputUpdateFromConstantx/InputUpdateFromConstantx.h"
+#include "../InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h"
 void  InputUpdateFromDakotax(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials*  materials,Parameters* parameters,double* variables,char* *variables_descriptors,int numvariables){

issm/trunk/src/c/modules/InputUpdateFromDakotax/InputUpdateFromDakotax.h

-              r13975
+              r15396
 #define _INPUTUPDATEFROMDAKOTAXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 void  InputUpdateFromDakotax(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials*  materials,Parameters* parameters,double* variables,char* *variables_descriptors,int numvariables);

issm/trunk/src/c/modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.cpp

-              r13975
+              r15396
 #include "./InputUpdateFromMatrixDakotax.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../modules.h"
+#include "../InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h"
 void InputUpdateFromMatrixDakotax( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,double* matrix,int nrows,int ncols, int name, int type){

issm/trunk/src/c/modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.h

-              r13975
+              r15396
 #define _UPDATEINPUTSFROMMATRIXDAKOTAXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp

-              r13975
+              r15396
 #include "./InputUpdateFromSolutionx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector<IssmDouble>* solution){

issm/trunk/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h

-              r13975
+              r15396
 #define _UPDATEINPUTSFROMSOLUTIONXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp

-              r13975
+              r15396
 #include "./InputUpdateFromVectorDakotax.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector<IssmDouble>* vector, int name, int type){

issm/trunk/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h

-              r13975
+              r15396
 #define _UPDATEINPUTSFROMVECTORDAKOTAXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp

-              r13975
+              r15396
 #include "./InputUpdateFromVectorx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector<IssmDouble>* vector, int name, int type){

issm/trunk/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h

-              r13975
+              r15396
 #define _UPDATEINPUTSFROMVECTORXX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp

-              r13975
+              r15396
 #include "./InterpFromGridToMeshx.h"
 #include "../../shared/shared.h"
+#include "../../include/include.h"
+#include "../../io/io.h"
+#include "../../shared/io/io.h"
 /*}}}*/
 /*InterpFromGridToMeshx{{{*/
 int InterpFromGridToMeshx(SeqVec<IssmPDouble>** pdata_mesh,double* x_in, int x_rows, double* y_in, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods,double default_value, int interpenum){
+int InterpFromGridToMeshx(IssmSeqVec<IssmPDouble>** pdata_mesh,double* x_in, int x_rows, double* y_in, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods,double default_value, int interpenum){
         /*output: */
         SeqVec<IssmPDouble>* data_mesh=NULL;
+        IssmSeqVec<IssmPDouble>* data_mesh=NULL;
         /*Intermediary*/
 …
         /*Allocate output vector: */
         data_mesh=new SeqVec<IssmPDouble>(nods);
+        data_mesh=new IssmSeqVec<IssmPDouble>(nods);
         /*Find out what kind of coordinates (x_in,y_in) have been given is input*/
 …
         /*launch the thread manager with InterpFromGridToMeshxt as a core: */
         LaunchThread(InterpFromGridToMeshxt,(void*)&gate,num);
         _printLine_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+        _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
         /*Assign output pointers:*/
         *pdata_mesh=data_mesh;
+        return 1;
+}
 /*}}}*/
 …
         double *y                     = gate->y;
         int     nods                  = gate->nods;
         SeqVec<IssmPDouble>*data_mesh = gate->data_mesh;
+        IssmSeqVec<IssmPDouble>*data_mesh = gate->data_mesh;
         double *data                  = gate->data;
         double  default_value         = gate->default_value;
 …
                 if(debug && my_thread==0)
                  _printString_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i-i0)/double(i1-i0)*100<<"%");
+                 _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i-i0)/double(i1-i0)*100<<"%");
                 x_grid=*(x_mesh+i);
                 y_grid=*(y_mesh+i);
 …
                                         break;
                                 default:
                                         _printLine_("Interpolation " << EnumToStringx(interpenum) << " not supported yet");
+                                        _printf_("Interpolation " << EnumToStringx(interpenum) << " not supported yet\n");
                                         return NULL; /*WARNING: no error because it would blow up the multithreading!*/
+                        }

issm/trunk/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h

-              r13395
+              r15396
 #define _INTERPFROMGRIDTOMESHX_H
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../toolkits/toolkits.h"
 #include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../shared/shared.h"
 /*threading: */
 …
         double*             x_mesh;
         double*             y_mesh;
         SeqVec<IssmPDouble>* data_mesh;
+        IssmSeqVec<IssmPDouble>* data_mesh;
 } InterpFromGridToMeshxThreadStruct;
 int    InterpFromGridToMeshx(SeqVec<IssmPDouble>** pdata_mesh,double* x, int x_rows, double* y, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods, double default_value, int interpenum=BilinearInterpEnum);
+int    InterpFromGridToMeshx(IssmSeqVec<IssmPDouble>** pdata_mesh,double* x, int x_rows, double* y, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods, double default_value, int interpenum=BilinearInterpEnum);
 void*  InterpFromGridToMeshxt(void* vInterpFromGridToMeshxThreadStruct);
 bool   findindices(int* pn,int* pm,double* x,int x_rows, double* y,int y_rows, double xgrid,double ygrid);

issm/trunk/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp

-              r13975
+              r15396
 #include "./InterpFromMesh2dx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
 #include "../../classes/objects/objects.h"
 #include "../modules.h"
+#include "../../classes/classes.h"
+#include "../ContourToNodesx/ContourToNodesx.h"
 int InterpFromMesh2dx(SeqVec<IssmPDouble>** pdata_prime,
+int InterpFromMesh2dx(IssmSeqVec<IssmPDouble>** pdata_prime,
                         double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length,
                         double* x_prime, double* y_prime, int nods_prime,
 …
         /*Output*/
         SeqVec<IssmPDouble>* data_prime=NULL;
+        IssmSeqVec<IssmPDouble>* data_prime=NULL;
         /*Intermediary*/
 …
         /*contours: */
-        SeqVec<IssmPDouble> *vec_incontour = NULL;
         double              *incontour     = NULL;
 …
         /*Initialize output*/
         data_prime=new SeqVec<IssmPDouble>(nods_prime);
+        data_prime=new IssmSeqVec<IssmPDouble>(nods_prime);
         if(num_default_values){
                 if(num_default_values==1)for (i=0;i<nods_prime;i++) data_prime->SetValue(i,default_values[0],INS_VAL);
 …
         /*Build indices of contour: */
         if(numcontours){
+                ContourToNodesx( &vec_incontour,x_prime,y_prime,nods_prime,contours,numcontours,1);
+                incontour=vec_incontour->ToMPISerial();
+                ContourToNodesx( &incontour,x_prime,y_prime,nods_prime,contours,numcontours,1);
+        }
         else{
 …
          xDelete<double>(incontour);
         *pdata_prime=data_prime;
+        return 1;
+}

issm/trunk/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.h

-              r13975
+              r15396
 #define _INTERPFROMMESH2DX_H
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../toolkits/toolkits.h"
 …
         double              ymin,ymax;
         int                 nods_prime;
         SeqVec<IssmPDouble> *data_prime;
+        IssmSeqVec<IssmPDouble> *data_prime;
         double              *x_prime;
         double              *y_prime;
 …
 } InterpFromMesh2dxThreadStruct;
 int InterpFromMesh2dx(SeqVec<IssmPDouble>** pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime,
+int InterpFromMesh2dx(IssmSeqVec<IssmPDouble>** pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime,
                 double* default_values,int num_default_values,Contour<IssmPDouble>** contours,int numcontours);

issm/trunk/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp

-              r13975
+              r15396
         double  ymax                    = gate->ymax;
         int     nods_prime              = gate->nods_prime;
         SeqVec<IssmPDouble>* data_prime = gate->data_prime;
+        IssmSeqVec<IssmPDouble>* data_prime = gate->data_prime;
         double *x_prime                 = gate->x_prime;
         double *y_prime                 = gate->y_prime;
 …
                 /*display current iteration*/
                 if (debug && my_thread==0 && fmod((double)i,(double)100)==0)
                  _printString_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i-i0)/double(i1-i0)*100<<"%");
+                 _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i-i0)/double(i1-i0)*100<<"%");
                 /*if there is no point inside the domain, go to next iteration*/
 …
+        }
         if(debug && my_thread==0)
          _printLine_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+         _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
         return NULL;
+}

issm/trunk/src/c/modules/InterpFromMeshToGridx/InterpFromMeshToGridx.cpp

-              r13975
+              r15396
 #include "./InterpFromMeshToGridx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 void InterpFromMeshToGridx(double** px_m,double** py_m,double** pgriddata,double* index_mesh, double* x_mesh, double* y_mesh, int nods,int nels, double* data_mesh, int data_length, double xmin,double ymax,double xposting,double yposting,int nlines,int ncols,double default_value) {
 …
         bool   debug;
         int    xflip,yflip;
         double area,ymin;
+        double area;
         double area_1,area_2,area_3;
         double x_tria_min,y_tria_min;
 …
         debug=(bool)((double)ncols*nlines*nels >= 5*pow(10.,10.));
+        /*Initialize coordintes and griddata*/
+        for(i=0;i<nlines;i++){
+                for(j=0;j<ncols; j++){
+                        griddata[i*ncols+j]=default_value;
+                }
+        }
         /*figure out if x or y are flipped*/
         if (xposting<0) xflip=1;
 …
         else yflip=0;
-        /*Compute coordinates lists*/
-        ymin=ymax-(nlines-1)*yposting;
-        for(i=0;i<nlines;i++)   y_grid[i]= ymin + yposting*i;
-        for(i=0;i<ncols; i++)   x_grid[i]= xmin + xposting*i;
-        /*Initialize coordintes and griddata*/
-        for(i=0;i<nlines;i++){
-                for(j=0;j<ncols; j++){
-                        griddata[i*ncols+j]=default_value;
+                }
+        }
         /*Get extreme coordinates of the grid*/
         if (xflip){
+                x_grid_min=x_grid[ncols-1]; x_grid_max=x_grid[0];
+                for(i=0;i<ncols; i++) x_grid[ncols-1-i] = xmin - xposting*i;
+                x_grid_min=x_grid[ncols-1];
+                x_grid_max=x_grid[0];
+        }
         else{
+                x_grid_min=x_grid[0]; x_grid_max=x_grid[ncols-1];
+                for(i=0;i<ncols; i++) x_grid[i]= xmin + xposting*i;
+                x_grid_min=x_grid[0];
+                x_grid_max=x_grid[ncols-1];
+        }
         if (yflip){
+                y_grid_min=y_grid[nlines-1]; y_grid_max=y_grid[0];
+                for(i=0;i<nlines;i++) y_grid[i] = ymax + yposting*i;
+                y_grid_min=y_grid[nlines-1];
+                y_grid_max=y_grid[0];
+        }
         else{
+                y_grid_min=y_grid[0]; y_grid_max=y_grid[nlines-1];
+                for(i=0;i<nlines;i++) y_grid[nlines-1-i]= ymax - yposting*i;
+                y_grid_min=y_grid[0];
+                y_grid_max=y_grid[nlines-1];
+        }
 …
                 /*display current iteration*/
                 if (debug && fmod((double)n,(double)100)==0)
                  _printString_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(n)/double(nels)*100<<"%");
+                 _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(n)/double(nels)*100<<"%");
                 /*Get extrema coordinates of current elements*/
 …
+        }
         if (debug)
          _printLine_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+         _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
         /*Assign output pointers:*/

issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
 #include "../../classes/objects/objects.h"
 #include "../modules.h"
+#include "../../classes/classes.h"
+#include "../../bamg/bamgobjects.h"
 using namespace bamg;
 …
         /*Loop over output nodes*/
         for(i=0;i<N_interp;i++){
                 //if(i%100==0) _printString_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i)/double(N_interp)*100.<<"%");
+                //if(i%100==0) _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i)/double(N_interp)*100.<<"%");
                 if(isdefault){
 …
+                }
+        }
         //if(N_interp>=100) _printLine_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+        //if(N_interp>=100) _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
         /*clean-up and return*/

issm/trunk/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp

-              r13395
+              r15396
 #include "./InterpFromMeshToMesh3dx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 int InterpFromMeshToMesh3dx( SeqVec<IssmPDouble>** pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value) {
+int InterpFromMeshToMesh3dx( IssmSeqVec<IssmPDouble>** pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value) {
         /*Output*/
         SeqVec<IssmPDouble>* data_prime=NULL;
+        IssmSeqVec<IssmPDouble>* data_prime=NULL;
         /*Intermediary*/
 …
         /*Initialize output*/
         data_prime=new SeqVec<IssmPDouble>(nods_prime);
+        data_prime=new IssmSeqVec<IssmPDouble>(nods_prime);
         for (i=0;i<nods_prime;i++) data_prime->SetValue(i,default_value,INS_VAL);
 …
                 /*display current iteration*/
                 if (debug && fmod((double)i,(double)100)==0)
                  _printString_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i)/double(nels_data)*100<<"%");
+                 _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i)/double(nels_data)*100<<"%");
                 /*Get extrema coordinates of current elements*/
 …
+        }
         if (debug)
          _printLine_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+         _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
         /*Assign output pointers:*/
         *pdata_prime=data_prime;
+        return 1;
+}

issm/trunk/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h

-              r13395
+              r15396
 #include "../../toolkits/toolkits.h"
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 int InterpFromMeshToMesh3dx(SeqVec<IssmPDouble>** pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value);
+int InterpFromMeshToMesh3dx(IssmSeqVec<IssmPDouble>** pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value);
 #endif /* _INTERPFROMMESHTOMESH3DX_H */

issm/trunk/src/c/modules/IoModelToConstraintsx/IoModelToConstraintsx.cpp

-              r13975
+              r15396
 #include "./IoModelToConstraintsx.h"
 #include "../../shared/shared.h"
-#include "../../io/io.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void IoModelToConstraintsx(Constraints* constraints,IoModel* iomodel,int vector_enum,int analysis_type){
 …
         /*intermediary: */
         int     i,j;
+        IssmDouble yts;
         bool        transient        = false;
         FILE       *fid              = NULL;
 …
         /*Fetch parameters: */
         iomodel->Constant(&numberofvertices,MeshNumberofverticesEnum);
+        iomodel->Constant(&yts,ConstantsYtsEnum);
         /*First of, find the record for the enum, and get code  of data type: */
 …
                 times=xNew<IssmDouble>(N);
                 for(j=0;j<N;j++){
                         times[j]=IssmDoublevector[(M-1)*N+j];
+                        times[j]=IssmDoublevector[(M-1)*N+j]*yts;
+                }
-                /*unit conversion: */
-                UnitConversion(times,N,ExtToIuEnum,TimeEnum);
                 /*Create constraints from x,y,z: */

issm/trunk/src/c/modules/IoModelToConstraintsx/IoModelToConstraintsx.h

-              r13395
+              r15396
 #define _IOMODEL_TO_CONSTRAINTS_H_
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/KMLFileReadx/KMLFileReadx.cpp

-              r13975
+              r15396
 #include "./KMLFileReadx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 KML_Object* KMLFileReadx(FILE* fid){
 …
         clock0=clock();
         time0 =time(NULL);
         _pprintString_("\nKMLFileReadx Module -- " << ctime(&time0));
+        _printf0_("\nKMLFileReadx Module -- " << ctime(&time0));
 /*  read kml file  */
 …
+                }
 //              _pprintLine_(kstr);
+//              _printf0_(kstr << "\n");
                 xDelete<char>(kstr);
+        }
         if (kxml) {
                 _pprintLine_("XML declaration:");
+                _printf0_("XML declaration:\n");
                 kxml->DeepEcho("  ");
                 delete kxml;
+        }
         if (kdtd) {
                 _pprintLine_("DTD declaration (not yet implemented):");
+                _printf0_("DTD declaration (not yet implemented):\n");
                 kdtd->DeepEcho("  ");
                 delete kdtd;
 …
         clock1=clock();
         time1 =time(NULL);
+        _printf_(true,"KMLFileReadx Module -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0));
+        _printf_("KMLFileReadx Module -- " <<((double)(clock1-clock0))/CLOCKS_PER_SEC << " CPU seconds; " <<difftime(time1,time0) << " elapsed seconds.\n\n\n");
         return(kfil);

issm/trunk/src/c/modules/KMLFileReadx/KMLFileReadx.h

-              r13395
+              r15396
 #include <float.h>    /*  DBL_MAX  */
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../kml/kmlobjects.h"
 /* local prototypes: */

issm/trunk/src/c/modules/KMLMeshWritex/KMLMeshWritex.cpp

-              r13395
+              r15396
 #include "./KMLMeshWritex.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void KMLMeshWritex(int* ierror,char* name,char* notes,int* elem,int melem,int nelem,int* nodecon,int mncon,int nncon,double* lat, double* lng,int* part,double* data, int mdata, int ndata,double* cmap, int mcmap, int ncmap,FILE* fid){
 …
         clock0=clock();
         time0 =time(NULL);
         _pprintString_("\nKMLMeshWritex Module -- " << ctime(&time0));
+        _printf0_("\nKMLMeshWritex Module -- " << ctime(&time0));
 /*  construct kml document  */
 …
         if (cmap) {
                 _pprintLine_("Writing " << mcmap << " Matlab colors as KML style templates.");
+                _printf0_("Writing " << mcmap << " Matlab colors as KML style templates.\n");
                 ipt=0;
                 for (i=0; i<mcmap; i++) {
 …
         if (!nodecon) {
                 _pprintLine_("Creating the node connectivity table.");
+                _printf0_("Creating the node connectivity table.\n");
                 nncon=mxepg+1;
                 nodecon=xNewZeroInit<int>(mncon*nncon);
 …
                 else if (mdata == mncon) {
                         _pprintLine_("Averaging nodal data to element data.");
+                        _printf0_("Averaging nodal data to element data.\n");
                         edata=xNewZeroInit<double>(melem*ndata);
                         edfree=true;
 …
         clock0a=clock();
         time0a =time(NULL);
+        _printf_(true,"  Constructed kml document -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock0a-clock0))/CLOCKS_PER_SEC,difftime(time0a,time0));
+        _printf_("  Constructed kml document -- " << ((double)(clock0a-clock0))/CLOCKS_PER_SEC << " CPU seconds; " << difftime(time0a,time0) << " elapsed seconds.\n\n\n");
 /*  write kml file  */
         _pprintLine_("Writing kml document to file.");
+        _printf0_("Writing kml document to file.\n");
         fprintf(fid,"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
         fprintf(fid,"<kml xmlns=\"http://www.opengis.net/kml/2.2\">\n");
 …
         clock0b=clock();
         time0b =time(NULL);
+        _printf_(true,"  Wrote kml file -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock0b-clock0a))/CLOCKS_PER_SEC,difftime(time0b,time0a));
+        _pprintLine_("Deleting kml document.");
+        _printf_("  Wrote kml file -- " << ((double)(clock0b-clock0a))/CLOCKS_PER_SEC << " CPU seconds; " << difftime(time0b,time0a) << " elapsed seconds.\n\n\n");
+        _printf0_("Deleting kml document.\n");
         delete kdoc;
         clock0c=clock();
         time0c =time(NULL);
+        _printf_(true,"  Deleted kml document -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock0c-clock0b))/CLOCKS_PER_SEC,difftime(time0c,time0b));
+        _printf_("  Deleted kml document -- " << ((double)(clock0c-clock0b))/CLOCKS_PER_SEC << " CPU seconds; " << difftime(time0c,time0b) << " elapsed seconds.\n\n\n");
         clock1=clock();
         time1 =time(NULL);
+        _printf_(true,"KMLMeshWritex Module -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0));
+        _printf_("KMLMeshWritex Module -- " << ((double)(clock1-clock0))/CLOCKS_PER_SEC << " CPU seconds; " << difftime(time1,time0) << " elapsed seconds.\n\n\n");
         return;
 …
 /*  write each element as a polygon placemark  */
         _pprintLine_("Writing " << melem << " tria elements as KML polygons.");
+        _printf0_("Writing " << melem << " tria elements as KML polygons.\n");
         for (i=0; i<melem; i++) {
 …
 //              if (!(int)fmod((double)(i+1),1000))
 //                      _pprintLine_("  " << (i+1) << " tria elements written.");
+//                      _printf0_("  " << (i+1) << " tria elements written.\n");
+        }
         _pprintLine_("  " << melem << " tria elements written.");
+        _printf0_("  " << melem << " tria elements written.\n");
         return(kfold);

issm/trunk/src/c/modules/KMLMeshWritex/KMLMeshWritex.h

-              r13395
+              r15396
 #include <float.h>    /*  DBL_MAX  */
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../kml/kmlobjects.h"
 /* local prototypes: */

issm/trunk/src/c/modules/KMLOverlayx/KMLOverlayx.cpp

-              r13975
+              r15396
 #include "./KMLOverlayx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
 #include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../kml/kmlobjects.h"
 void KMLOverlayx(int* ierror,
 …
         clock0=clock();
         time0 =time(NULL);
         _pprintString_("\nKMLOverlayx Module -- " << ctime(&time0));
+        _printf0_("\nKMLOverlayx Module -- " << ctime(&time0));
 /*  construct kml file  */
 …
 /*  write kml file  */
         _pprintLine_("Writing kml document to file.");
+        _printf0_("Writing kml document to file.\n");
         fprintf(fid,"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
         kfile->Write(fid,indent);
 …
         clock1=clock();
         time1 =time(NULL);
+        _printf_(true,"KMLOverlayx Module -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0));
+        _printf_("KMLOverlayx Module -- " << ((double)(clock1-clock0))/CLOCKS_PER_SEC << " CPU seconds; " << difftime(time1,time0) << " elapsed seconds.\n\n\n");
         return;

issm/trunk/src/c/modules/KMLOverlayx/KMLOverlayx.h

-              r13395
+              r15396
 #include <float.h>    /*  DBL_MAX  */
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/Kml2Expx/Kml2Expx.cpp

-              r13975
+              r15396
 #include "./Kml2Expx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../modules.h"
+#include "../KMLFileReadx/KMLFileReadx.h"
 int Kml2Expx(char* filkml,char* filexp,
 …
         clock0=clock();
         time0 =time(NULL);
         _pprintString_("\nKml2Expx Module -- " << ctime(&time0));
+        _printf0_("\nKml2Expx Module -- " << ctime(&time0));
 /*  read kml file  */
 …
 /*  open exp file  */
         _pprintLine_("Writing exp profiles to file.");
+        _printf0_("Writing exp profiles to file.\n");
         fido=fopen(filexp,"w");
 …
         clock1=clock();
         time1 =time(NULL);
+        _printf_(true,"Kml2Expx Module -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0));
+        _printf_("Kml2Expx Module -- " << ((double)(clock1-clock0))/CLOCKS_PER_SEC << " CPU seconds; " << difftime(time1,time0) << " elapsed seconds.\n\n\n");
         return(iret);

issm/trunk/src/c/modules/Kml2Expx/Kml2Expx.h

-              r13395
+              r15396
 #include <float.h>    /*  DBL_MAX  */
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/Krigingx/Krigingx.cpp

-              r14310
+              r15396
 #include "./Krigingx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
+#include "../../classes/objects/objects.h"
+#include "../../Container/Observations.h"
+#include "../../classes/classes.h"
 #include "../modules.h"
 #ifdef _HAVE_GSL_
 …
                 observations->ObservationList(&x,&y,&data,&nobs);
                 _printLine_("Generation Delaunay Triangulation");
+                _printf_("Generation Delaunay Triangulation\n");
                 BamgTriangulatex(&index,&nel,x,y,nobs);
                 _printLine_("Interpolating");
+                _printf_("Interpolating\n");
                 xDelete<double>(predictions);
                 InterpFromMeshToMesh2dx(&predictions,index,x,y,nobs,nel,data,nobs,1,x_interp,y_interp,n_interp,options);
 …
                 /*launch the thread manager with Krigingxt as a core: */
                 LaunchThread(NearestNeighbort,(void*)&gate,num);
                 _printLine_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+                _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
                 xDelete<int>(gate.numdone);
+        }
 …
                 /*launch the thread manager with Krigingxt as a core: */
                 LaunchThread(idwt,(void*)&gate,num);
                 _printLine_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+                _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
                 xDelete<int>(gate.numdone);
+        }
 …
                 /*launch the thread manager with Krigingxt as a core: */
                 LaunchThread(v4t,(void*)&gate,num);
                 _printLine_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+                _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
                 xDelete<int>(gate.numdone);
+        }
 …
                 /*launch the thread manager with Krigingxt as a core: */
                 LaunchThread(Krigingxt,(void*)&gate,num);
                 _printLine_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+                _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
                 xDelete<int>(gate.numdone);
+        }
 …
                         int alldone=numdone[0];
                         for(int i=1;i<num_threads;i++) alldone+=numdone[i];
                         _printString_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(alldone)/double(n_interp)*100.<<"%");
+                        _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(alldone)/double(n_interp)*100.<<"%");
+                }
 …
                         int alldone=numdone[0];
                         for(int i=1;i<num_threads;i++) alldone+=numdone[i];
                         _printString_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(alldone)/double(n_interp)*100.<<"%");
+                        _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(alldone)/double(n_interp)*100.<<"%");
+                }
 …
                         int alldone=numdone[0];
                         for(int i=1;i<num_threads;i++) alldone+=numdone[i];
                         _printString_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(alldone)/double(n_interp)*100.<<"%");
+                        _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(alldone)/double(n_interp)*100.<<"%");
+                }
 …
                         int alldone=numdone[0];
                         for(int i=1;i<num_threads;i++) alldone+=numdone[i];
                         _printString_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(alldone)/double(n_interp)*100.<<"%");
+                        _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(alldone)/double(n_interp)*100.<<"%");
+                }

issm/trunk/src/c/modules/Krigingx/Krigingx.h

r14310	r15396
6	6	#define _KRIGINGX_H
7	7
8		#include "../../classes/~~objects/object~~s.h"
	8	#include "../../classes/classes.h"
9	9	#include "../../toolkits/toolkits.h"
10	10

issm/trunk/src/c/modules/Krigingx/pKrigingx.cpp

-              r13975
+              r15396
 #include "./Krigingx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../io/io.h"
+#include "../../classes/classes.h"
+#include "../../shared/io/io.h"
 /*FUNCTION pKrigingx{{{*/
 int pKrigingx(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){
+#ifdef _HAVE_MPI_
         int num_procs;
         int my_rank;
 …
         Observations *observations = NULL;
+        /*timing*/
+        double   start, finish;
+        double   start_core, finish_core;
+        double   start_init, finish_init;
         /*Get my_rank: */
         my_rank=IssmComm::GetRank();
 …
         /*Get some Options*/
+        MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime();
         options->Get(&radius,"searchradius",0.);
         options->Get(&mindata,"mindata",1);
 …
         /*Process observation dataset*/
+        MPI_Barrier(MPI_COMM_WORLD); start_init=MPI_Wtime();
         observations=new Observations(obs_list,obs_x,obs_y,obs_length,options);
+        MPI_Barrier(MPI_COMM_WORLD); finish_init=MPI_Wtime();
         /*Allocate output*/
 …
         options->Get(&output,"output",(char*)"prediction");
+        MPI_Barrier(MPI_COMM_WORLD); start_core=MPI_Wtime( );
         if(strcmp(output,"quadtree")==0){
                 observations->QuadtreeColoring(predictions,x_interp,y_interp,n_interp);
 …
                 /*partition loop across threads: */
                 for(int idx=my_rank;idx<n_interp;idx+=num_procs){
                         _pprintLine_("      interpolation progress: "<<setw(6)<<setprecision(2)<<double(idx)/double(n_interp)*100<<"%");
+                        _printf0_("      interpolation progress: "<<fixed<<setw(6)<<setprecision(4)<<double(idx)/double(n_interp)*100.<<"%\n");
                         observations->InterpolationKriging(&predictions[idx],&error[idx],x_interp[idx],y_interp[idx],radius,mindata,maxdata,variogram);
+                }
                 _pprintLine_("      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+                _printf0_("      interpolation progress: "<<fixed<<setw(6)<<setprecision(4)<<100.<<"%\n");
 #ifdef _HAVE_MPI_
 …
 #endif
+        }
+        else if(strcmp(output,"v4")==0){
+                /*partition loop across threads: */
+                for(int idx=my_rank;idx<n_interp;idx+=num_procs){
+                        _printf0_("      interpolation progress: "<<fixed<<setw(6)<<setprecision(4)<<double(idx)/double(n_interp)*100.<<"%\n");
+                        observations->InterpolationV4(&predictions[idx],x_interp[idx],y_interp[idx],radius,mindata,maxdata);
+                }
+                _printf0_("      interpolation progress: "<<fixed<<setw(6)<<setprecision(4)<<100.<<"%\n");
+#ifdef _HAVE_MPI_
+                double *sumpredictions =xNew<double>(n_interp);
+                MPI_Allreduce(predictions,sumpredictions,n_interp,MPI_DOUBLE,MPI_SUM,IssmComm::GetComm());
+                xDelete<double>(predictions); predictions=sumpredictions;
+#endif
+        }
         else if(strcmp(output,"nearestneighbor")==0){
                 /*partition loop across threads: */
                 for(int idx=my_rank;idx<n_interp;idx+=num_procs){
                         _pprintLine_("      interpolation progress: "<<setw(6)<<setprecision(2)<<double(idx)/double(n_interp)*100<<"%");
+                        _printf0_("      interpolation progress: "<<setw(6)<<setprecision(4)<<double(idx)/double(n_interp)*100.<<"%\n");
                         observations->InterpolationNearestNeighbor(&predictions[idx],x_interp[idx],y_interp[idx],radius);
+                }
                 _pprintLine_("      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+                _printf0_("      interpolation progress: "<<fixed<<setw(6)<<setprecision(4)<<100.<<"%\n");
 #ifdef _HAVE_MPI_
 …
                 /*partition loop across threads: */
                 for(int idx=my_rank;idx<n_interp;idx+=num_procs){
                         _pprintLine_("      interpolation progress: "<<setw(6)<<setprecision(2)<<double(idx)/double(n_interp)*100<<"%");
+                        _printf0_("      interpolation progress: "<<setw(6)<<setprecision(4)<<double(idx)/double(n_interp)*100.<<"%\n");
                         observations->InterpolationIDW(&predictions[idx],x_interp[idx],y_interp[idx],radius,mindata,maxdata,power);
+                }
                 _pprintLine_("      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+                _printf0_("      interpolation progress: "<<fixed<<setw(6)<<setprecision(4)<<100.<<"%\n");
 #ifdef _HAVE_MPI_
 …
                 _error_("output '" << output << "' not supported yet");
+        }
+        MPI_Barrier(MPI_COMM_WORLD); finish_core=MPI_Wtime( );
         /*clean-up and Assign output pointer*/
 …
         *ppredictions = predictions;
         *perror       = error;
+        MPI_Barrier(MPI_COMM_WORLD); finish=MPI_Wtime( );
+        _printf0_("\n   " << setw(34) << left << "Observation fitering elapsed time: " << finish_init-start_init << " seconds  \n\n");
+        _printf0_("   " << setw(34) << left << "Kriging prediction elapsed time: " << finish_core-start_core << " seconds  \n\n");
+        _printf0_("\n   " << "Total elapsed time " << int((finish-start)/3600) << " hrs " << int(int(finish-start)%3600/60) << " min " << int(finish-start)%60 << " sec\n\n\n");
         return 1;
+#else
+        _error_("MPI not available");
+#endif
 }/*}}}*/
 void ProcessVariogram(Variogram **pvariogram,Options* options){/*{{{*/

issm/trunk/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp

-              r13975
+              r15396
 #include "../VecMergex/VecMergex.h"
 #include "../../io/io.h"
+#include "../../shared/io/io.h"
 #include "./Mergesolutionfromftogx.h"
 …
         /*Display message*/
         if(VerboseModule()) _pprintLine_("   Merging solution vector from fset to gset");
+        if(VerboseModule()) _printf0_("   Merging solution vector from fset to gset\n");
         /*first, get gsize, fsize and ssize: */

issm/trunk/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h

r13975	r15396
6	6	#define _MERGESOLUTIONFROMFTOGX_H
7	7
8		#include "../../classes/~~objects/object~~s.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/MeshPartitionx/MeshPartitionx.h

-              r13975
+              r15396
 #define _MESHPARTITIONX_H
+#include "../../include/include.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../shared/shared.h"
 /* local prototypes: */

issm/trunk/src/c/modules/MeshProfileIntersectionx/MeshProfileIntersectionx.h

r14310	r15396
7	7
8	8	#include "../../shared/shared.h"
9		#include "../../classes/~~objects/object~~s.h"
	9	#include "../../classes/classes.h"
10	10
11	11	/* local prototypes: */

issm/trunk/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
-#include "../../../io/io.h"
-#include "../../../EnumDefinitions/EnumDefinitions.h"
 #include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
-#include "../../Solverx/Solverx.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp

-              r13975
+              r15396
-#include "../../../Container/Container.h"
-#include "../../../modules/modules.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
-#include "../../../EnumDefinitions/EnumDefinitions.h"
 #include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../ModelProcessorx.h"
+#include "../../IoModelToConstraintsx/IoModelToConstraintsx.h"
 void    CreateConstraintsBalancethickness(Constraints** pconstraints, IoModel* iomodel){

issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp

-              r13395
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../modules/modules.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/BedSlope/CreateConstraintsBedSlope.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/BedSlope/CreateLoadsBedSlope.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/BedSlope/CreateNodesBedSlope.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../modules/modules.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Control/CreateParametersControl.cpp

-              r14310
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp

-              r14310
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../modules/modules.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/CreateDataSets.cpp

-              r13975
+              r15396
 #endif
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 #include "./ModelProcessorx.h"
 …
                 #ifdef _HAVE_HYDROLOGY_
+                case HydrologyAnalysisEnum:
+                        CreateNodesHydrology(pnodes, iomodel);
+                        CreateConstraintsHydrology(pconstraints,iomodel);
+                        CreateLoadsHydrology(ploads,iomodel);
+                        UpdateElementsHydrology(elements,iomodel,analysis_counter,analysis_type);
+                case HydrologyShreveAnalysisEnum:
+                        CreateNodesHydrologyShreve(pnodes, iomodel);
+                        CreateConstraintsHydrologyShreve(pconstraints,iomodel);
+                        CreateLoadsHydrologyShreve(ploads,iomodel);
+                        UpdateElementsHydrologyShreve(elements,iomodel,analysis_counter,analysis_type);
+                        break;
+                case HydrologyDCInefficientAnalysisEnum:
+                        CreateNodesHydrologyDCInefficient(pnodes, iomodel);
+                        CreateConstraintsHydrologyDCInefficient(pconstraints,iomodel);
+                        CreateLoadsHydrologyDCInefficient(ploads,iomodel);
+                        UpdateElementsHydrologyDCInefficient(elements,iomodel,analysis_counter,analysis_type);
+                        break;
+                case HydrologyDCEfficientAnalysisEnum:
+                        CreateNodesHydrologyDCEfficient(pnodes, iomodel);
+                        CreateConstraintsHydrologyDCEfficient(pconstraints,iomodel);
+                        CreateLoadsHydrologyDCEfficient(ploads,iomodel);
+                        UpdateElementsHydrologyDCEfficient(elements,iomodel,analysis_counter,analysis_type);
                         break;
                 #endif
 …
                         CreateLoadsBalancethickness(ploads,iomodel);
                         UpdateElementsBalancethickness(elements,iomodel,analysis_counter,analysis_type);
+                        break;
+                #endif
+                #ifdef _HAVE_GIA_
+                case GiaAnalysisEnum:
+                        CreateNodesGia(pnodes, iomodel);
+                        CreateConstraintsGia(pconstraints,iomodel);
+                        CreateLoadsGia(ploads,iomodel);
+                        UpdateElementsGia(elements,iomodel,analysis_counter,analysis_type);
                         break;
                 #endif

issm/trunk/src/c/modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp

-              r13975
+              r15396
  */
-#include "../../Container/Container.h"
 #include "../../toolkits/toolkits.h"
+#include "../../io/io.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../shared/shared.h"
 #include "../MeshPartitionx/MeshPartitionx.h"
-#include "../../include/include.h"
 #include "./ModelProcessorx.h"
 …
         int numberofvertices;
         bool control_analysis;
+        bool dakota_analysis;
         /*DataSets: */
 …
         iomodel->Constant(&numberofvertices,MeshNumberofverticesEnum);
         iomodel->Constant(&control_analysis,InversionIscontrolEnum);
+        iomodel->Constant(&dakota_analysis,QmuIsdakotaEnum);
         iomodel->Constant(&materials_type,MaterialsEnum);
 …
                         iomodel->FetchData(2,MaterialsRheologyBEnum,MaterialsRheologyNEnum);
                         for (i=0;i<numberofelements;i++) if(iomodel->my_elements[i]) materials->AddObject(new Matice(i+1,i,iomodel));
+                        if(dakota_analysis){
+                                if(dim==2) materials->InputDuplicate(MaterialsRheologyBbarEnum,QmuMaterialsRheologyBEnum);
+           #ifdef _HAVE_3D_
+                                else       materials->InputDuplicate(MaterialsRheologyBEnum,QmuMaterialsRheologyBEnum);
+           #endif
+                        }
                         break;
                 case MatdamageiceEnum:

issm/trunk/src/c/modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp

-              r12706
+              r15396
 #include "../../shared/shared.h"
 #include "../../io/io.h"
 #include "../../include/include.h"
+#include "../../classes/classes.h"
+#include "../../shared/io/io.h"
 #include "./ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp

-              r13975
+              r15396
 #endif
-#include "../../Container/Container.h"
 #include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../shared/shared.h"
 #include "../MeshPartitionx/MeshPartitionx.h"
-#include "../../io/io.h"
 #include "./ModelProcessorx.h"
 …
         Parameters *parameters       = NULL;
         IssmDouble *requestedoutputs = NULL;
+        bool        isdelta18o;
+        IssmDouble  time;
+        bool        ispdd,isdelta18o;
         /*parameters for mass flux: {{{*/
         int      mass_flux_num_profiles=0;
         bool     qmu_mass_flux_present=false;
         bool     autodiff_mass_flux_present=false;
         bool     mass_flux_present=false;
         IssmDouble** array=NULL;
         int*     mdims_array=NULL;
         int*     ndims_array=NULL;
         IssmDouble*  temp_matrix=NULL;
         int      temp_m,temp_n;
         IssmDouble*  matrix=NULL;
         int      count;
+        int          mass_flux_num_profiles     = 0;
+        bool         qmu_mass_flux_present      = false;
+        bool         autodiff_mass_flux_present = false;
+        bool         mass_flux_present          = false;
+        IssmDouble **array                      = NULL;
+        int         *mdims_array                = NULL;
+        int         *ndims_array                = NULL;
+        IssmDouble  *temp_matrix                = NULL;
+        int          temp_m,temp_n;
+        IssmDouble  *matrix                     = NULL;
+        int          count;
         /*}}}*/
 …
         parameters->AddObject(iomodel->CopyConstantObject(ConstantsReferencetemperatureEnum));
         parameters->AddObject(iomodel->CopyConstantObject(BalancethicknessStabilizationEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(HydrologyStabilizationEnum));
         parameters->AddObject(iomodel->CopyConstantObject(GroundinglineMeltingRateEnum));
         parameters->AddObject(iomodel->CopyConstantObject(ThermalMaxiterEnum));
 …
         parameters->AddObject(iomodel->CopyConstantObject(MeshNumberofelementsEnum));
         parameters->AddObject(iomodel->CopyConstantObject(MeshNumberofverticesEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(MeshNumberoflayersEnum));
         parameters->AddObject(iomodel->CopyConstantObject(SettingsIoGatherEnum));
         parameters->AddObject(iomodel->CopyConstantObject(SettingsResultsAsPatchesEnum));
 …
         parameters->AddObject(iomodel->CopyConstantObject(TransientIsthermalEnum));
         parameters->AddObject(iomodel->CopyConstantObject(TransientIsgroundinglineEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(TransientIsgiaEnum));
         parameters->AddObject(iomodel->CopyConstantObject(ThermalIsenthalpyEnum));
         parameters->AddObject(iomodel->CopyConstantObject(MaterialsRheologyLawEnum));
 …
         parameters->AddObject(iomodel->CopyConstantObject(SurfaceforcingsIsdelta18oEnum));
         parameters->AddObject(iomodel->CopyConstantObject(SurfaceforcingsIssmbgradientsEnum));
+        iomodel->Constant(&isdelta18o,SurfaceforcingsIsdelta18oEnum);
+        if(isdelta18o){
+                IssmDouble *temp = NULL;
+                IssmDouble  yts;
+                int         N,M;
+                iomodel->Constant(&yts,ConstantsYtsEnum);
+                iomodel->FetchData(&temp,&N,&M,SurfaceforcingsDelta18oEnum); _assert_(N==2);
+                for(i=0;i<M;i++) temp[M+i]=yts*temp[M+i];
+                parameters->AddObject(new TransientParam(SurfaceforcingsDelta18oEnum,&temp[0],&temp[M],M));
+                iomodel->DeleteData(temp,SurfaceforcingsDelta18oEnum);
+                iomodel->FetchData(&temp,&N,&M,SurfaceforcingsDelta18oSurfaceEnum); _assert_(N==2);
+                for(i=0;i<M;i++) temp[M+i]=yts*temp[M+i];
+                parameters->AddObject(new TransientParam(SurfaceforcingsDelta18oSurfaceEnum,&temp[0],&temp[M],M));
+                iomodel->DeleteData(temp,SurfaceforcingsDelta18oSurfaceEnum);
+        parameters->AddObject(iomodel->CopyConstantObject(GiaCrossSectionShapeEnum));
+        iomodel->Constant(&ispdd,SurfaceforcingsIspddEnum);
+        if(ispdd){
+                parameters->AddObject(iomodel->CopyConstantObject(SurfaceforcingsDesfacEnum));
+                parameters->AddObject(iomodel->CopyConstantObject(SurfaceforcingsS0pEnum));
+                iomodel->Constant(&isdelta18o,SurfaceforcingsIsdelta18oEnum);
+                if(isdelta18o){
+                        IssmDouble *temp = NULL;
+                        IssmDouble  yts;
+                        int         N,M;
+                        iomodel->Constant(&yts,ConstantsYtsEnum);
+                        iomodel->FetchData(&temp,&N,&M,SurfaceforcingsDelta18oEnum); _assert_(N==2);
+                        for(i=0;i<M;i++) temp[M+i]=yts*temp[M+i];
+                        parameters->AddObject(new TransientParam(SurfaceforcingsDelta18oEnum,&temp[0],&temp[M],M));
+                        iomodel->DeleteData(temp,SurfaceforcingsDelta18oEnum);
+                        iomodel->FetchData(&temp,&N,&M,SurfaceforcingsDelta18oSurfaceEnum); _assert_(N==2);
+                        for(i=0;i<M;i++) temp[M+i]=yts*temp[M+i];
+                        parameters->AddObject(new TransientParam(SurfaceforcingsDelta18oSurfaceEnum,&temp[0],&temp[M],M));
+                        iomodel->DeleteData(temp,SurfaceforcingsDelta18oSurfaceEnum);
+                }
+        }
 …
         parameters->AddObject(new IntParam(AnalysisTypeEnum,analysis_type));
         parameters->AddObject(new IntParam(AnalysisCounterEnum,analysis_counter));
+        parameters->AddObject(new DoubleParam(TimeEnum,0.0));  //start at time 0 by default for all solutions FIXME: to be deleted
+        iomodel->Constant(&time,TimesteppingStartTimeEnum);
+        parameters->AddObject(new DoubleParam(TimeEnum,time));  //start at time 0 by default for all solutions FIXME: to be deleted
         parameters->AddObject(new IntParam(StepEnum,1));  //start at time 0 by default for all solutions FIXME: to be deleted
 …
         /*}}}*/
+        /*Solution specific parameters (FIXME: extend to other params)*/
+        #ifdef _HAVE_HYDROLOGY_
+        CreateParametersHydrologyShreve(&parameters,iomodel,solution_type,analysis_type);
+        CreateParametersHydrologyDCInefficient(&parameters,iomodel,solution_type,analysis_type);
+        CreateParametersHydrologyDCEfficient(&parameters,iomodel,solution_type,analysis_type);
+        #endif
         /*Before returning, create parameters in case we are running Qmu or control types runs: */
         #ifdef _HAVE_CONTROL_
 …
         #endif
-        /*Go through all parameters, and convert units to SI: */
-        parameters->UnitConversion(ExtToIuEnum);
         /*Assign output pointer: */
         *pparameters=parameters;

issm/trunk/src/c/modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp

-              r12706
+              r15396
 #include "../../shared/shared.h"
 #include "../../io/io.h"
 #include "../../include/include.h"
+#include "../../shared/io/io.h"
+#include "../../classes/classes.h"
 #include "./ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../io/io.h"
-#include "../../../include/include.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../ModelProcessorx.h"
 …
                 timesx[j]=spcvx[(Mx-1)*Nx+j];
+        }
-        /*unit conversion: */
-        UnitConversion(timesx,Nx,ExtToIuEnum,TimeEnum);
         /*figure out times: */
         timesy=xNew<IssmDouble>(Ny);
 …
                 timesy[j]=spcvy[(My-1)*Ny+j];
+        }
-        /*unit conversion: */
-        UnitConversion(timesy,Ny,ExtToIuEnum,TimeEnum);
         /*figure out times: */
         timesz=xNew<IssmDouble>(Nz);
 …
                 timesz[j]=spcvz[(Mz-1)*Nz+j];
+        }
-        /*unit conversion: */
-        UnitConversion(timesz,Nz,ExtToIuEnum,TimeEnum);
         /*Create spcs from x,y,z, as well as the spc values on those spcs: */

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"
 …
         /*Create Riffront loads for rifts: */
+        #ifdef _HAVE_RIFTS_
         if(numrifts){
                 iomodel->FetchData(&riftinfo,&numriftsegments,NULL,RiftsRiftstructEnum);
 …
                 xDelete<IssmDouble>(riftinfo);
+        }
+        #endif
         /*Assign output pointer: */

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"
 …
+        }
+        if(false){
+                /*Quadratic element*/
+                int numberofedges;
+                int  element1,element2;
+                bool my_edge;
+                iomodel->Constant(&numberofedges,MeshNumberofedgesEnum);
+                for (i=0;i<numberofedges;i++){
+                        /*Get left and right elements*/
+                        element1=reCast<int>(iomodel->Data(MeshEdgesEnum)[4*i+2])-1; //edges are [node1 node2 elem1 elem2]
+                        element2=reCast<int>(iomodel->Data(MeshEdgesEnum)[4*i+3])-1; //edges are [node1 node2 elem1 elem2]
+                        /*Check whether we should include this edge (element2 is -2 for boundary edges)*/
+                        my_edge = iomodel->my_elements[element1];
+                        if(!my_edge && element2>=0){
+                                my_edge = iomodel->my_elements[element2];
+                        }
+                        /*Add node on edge*/
+                        if(my_edge){
+                                nodes->AddObject(new Node(iomodel->nodecounter+numberofvertices+i+1,numberofvertices+i,numberofvertices+i+1,i,iomodel,DiagnosticHorizAnalysisEnum));
+                        }
+                }
+        }
         /*Clean fetched data: */
         iomodel->DeleteData(9,MeshVertexonbedEnum,MeshVertexonsurfaceEnum,FlowequationBordermacayealEnum,FlowequationBorderstokesEnum,

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp

-              r14310
+              r15396
 #endif
-#include "../../../Container/Container.h"
-#include "../../../modules/modules.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"
 …
         iomodel->FetchDataToInput(elements,VxEnum);
         iomodel->FetchDataToInput(elements,VyEnum);
+        iomodel->FetchDataToInput(elements,LoadingforceXEnum);
+        iomodel->FetchDataToInput(elements,LoadingforceYEnum);
         if(materials_type==MatdamageiceEnum){
                 iomodel->FetchDataToInput(elements,MaterialsRheologyZEnum);
 …
                 iomodel->FetchDataToInput(elements,BasalforcingsMeltingRateEnum);
                 iomodel->FetchDataToInput(elements,FlowequationBorderstokesEnum);
+                iomodel->FetchDataToInput(elements,LoadingforceZEnum);
+        }
 …
         elements->InputDuplicate(VxEnum,InversionVxObsEnum);
         if(dakota_analysis)elements->InputDuplicate(VxEnum,QmuVxEnum);
         #ifdef _HAVE_ANDROID_
         elements->InputDuplicate(FrictionCoefficientEnum,AndroidFrictionCoefficientEnum);

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../modules/modules.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/CreateLoadsDiagnosticVert.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/CreateNodesDiagnosticVert.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../modules/modules.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/DistributeNumDofs.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
+#include "../../include/include.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../classes/classes.h"
 void DistributeNumDofs(DofIndexing* index,int analysis_type,IssmDouble* vertices_type){
 …
                 numdofs=1;
+        }
+        else if (analysis_type==HydrologyAnalysisEnum){
+        else if (analysis_type==HydrologyDCInefficientAnalysisEnum){
+                numdofs=1;
+        }
+        else if (analysis_type==HydrologyDCEfficientAnalysisEnum){
+                numdofs=1;
+        }
+        else if (analysis_type==HydrologyShreveAnalysisEnum){
                 numdofs=1;
+        }
 …
+        }
         else if (analysis_type==PrognosticAnalysisEnum){
+                numdofs=1;
+        }
+        else if (analysis_type==GiaAnalysisEnum){
                 numdofs=1;
+        }

issm/trunk/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp

-              r13975
+              r15396
 #include <string.h>
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../shared/shared.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
-#include "../../io/io.h"
-#include "../../include/include.h"
 #include "../MeshPartitionx/MeshPartitionx.h"
 #include "../ModelProcessorx/ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Enthalpy/CreateConstraintsEnthalpy.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"
 …
                         times[j]=spcvector[(M-1)*N+j];
+                }
-                /*unit conversion: */
-                UnitConversion(times,N,ExtToIuEnum,TimeEnum);
                 /*Create constraints from x,y,z: */

issm/trunk/src/c/modules/ModelProcessorx/Enthalpy/CreateLoadsEnthalpy.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Enthalpy/CreateNodesEnthalpy.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../include/include.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"

issm/trunk/src/c/modules/ModelProcessorx/Enthalpy/UpdateElementsEnthalpy.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../modules/modules.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Melting/CreateConstraintsMelting.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Melting/CreateLoadsMelting.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Melting/CreateNodesMelting.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../include/include.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"

issm/trunk/src/c/modules/ModelProcessorx/Melting/UpdateElementsMelting.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../modules/modules.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.cpp

-              r13975
+              r15396
 #endif
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../shared/shared.h"
+#include "../../io/io.h"
+#include "../../Container/Container.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../include/include.h"
+#include "../../modules/modules.h"
+#include "./ModelProcessorx.h"
 void ModelProcessorx(Elements** pelements, Nodes** pnodes, Vertices** pvertices, Materials** pmaterials, Constraints** pconstraints, Loads** ploads, Parameters** pparameters, FILE* IOMODEL,char* rootpath,const int solution_type,const int nummodels,const int* analysis_type_list){
 …
         SetVerbosityLevel(verbose);
+        if(VerboseMProcessor()) _printf0_("   starting model processor \n");
         for(i=0;i<nummodels;i++){
                 analysis_type=analysis_type_list[i];
                 /*Hack for trasient runs (to be improved)*/
+                /*Hack for trasient runs (FIXME: to be improved)*/
                 if(solution_type==TransientSolutionEnum && analysis_type==ThermalAnalysisEnum && dim==2) continue;
                 if(solution_type==TransientSolutionEnum && analysis_type==MeltingAnalysisEnum && dim==2) continue;
 …
                 if(solution_type==SteadystateSolutionEnum && analysis_type==EnthalpyAnalysisEnum && isenthalpy==false) continue;
                 if(VerboseMProcessor()) _pprintLine_("   creating datasets for analysis " << EnumToStringx(analysis_type));
+                if(VerboseMProcessor()) _printf0_("   creating datasets for analysis " << EnumToStringx(analysis_type) << "\n");
                 CreateDataSets(&elements,&nodes,&vertices,&materials,&constraints,&loads,&parameters,iomodel,rootpath,solution_type,analysis_type,nummodels,i);
+        }
+        if(VerboseMProcessor()) _printf0_("   done with model processor \n");
         /*Free resources:*/

issm/trunk/src/c/modules/ModelProcessorx/ModelProcessorx.h

-              r13975
+              r15396
 #define RIFTINFOSIZE 12
+class DataSet;
+class IoModel;
+class Parameters;
+class DofIndexing;
+#include "../../io/io.h"
+#include "../../classes/classes.h"
 void ModelProcessorx(Elements** pelements, Nodes** pnodes, Vertices** pvertices, Materials** pmaterials, Constraints** pconstraints, Loads** ploads, Parameters** pparameters, FILE* iomodel_handle,char* rootpath,const int solution_type,const int nummodels,const int* analysis_type_listh);
 …
 void  CreateElementsVerticesAndMaterials(Elements** pelements,Vertices** pvertices,Materials** pmaterials, IoModel* iomodel,const int nummodels);
 void  CreateParameters(Parameters** pparameters,IoModel* iomodel,char* rootpath,const int solution_type,int analysis_type,int analysis_counter);
+void  CreateParametersAutodiff(Parameters** pparameters,IoModel* iomodel,int solution_type,int analysis_type);
 void  CreateParametersControl(Parameters** pparameters,IoModel* iomodel,int solution_type,int analysis_type);
 void  CreateParametersDakota(Parameters** pparameters,IoModel* iomodel,char* rootpath,int solution_type,int analysis_type);
+void  CreateParametersAutodiff(Parameters** pparameters,IoModel* iomodel,int solution_type,int analysis_type);
+void  CreateParametersHydrologyShreve(Parameters** pparameters,IoModel* iomodel,int solution_type,int analysis_type);
+void  CreateParametersHydrologyDCInefficient(Parameters** pparameters,IoModel* iomodel,int solution_type,int analysis_type);
+void  CreateParametersHydrologyDCEfficient(Parameters** pparameters,IoModel* iomodel,int solution_type,int analysis_type);
 void  UpdateElementsAndMaterialsControl(Elements* elements,Materials* materials, IoModel* iomodel);
 …
 void  CreateLoadsDiagnosticHutter(Loads** ploads, IoModel* iomodel);
 void    UpdateElementsDiagnosticHutter(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type);
+#ifdef _HAVE_GIA_
+/*gia*/
+void    CreateNodesGia(Nodes** pnodes,IoModel* iomodel);
+void    CreateConstraintsGia(Constraints** pconstraints,IoModel* iomodel);
+void    CreateLoadsGia(Loads** ploads, IoModel* iomodel);
+void    UpdateElementsGia(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type);
+#endif
 /*bed slope*/
 …
 void    UpdateElementsEnthalpy(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type);
+/*hydrology:*/
+void    CreateNodesHydrology(Nodes** pnodes,IoModel* iomodel);
+void    CreateConstraintsHydrology(Constraints** pconstraints,IoModel* iomodel);
+void  CreateLoadsHydrology(Loads** ploads, IoModel* iomodel);
+void    UpdateElementsHydrology(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type);
+/*hydrology Shreve:*/
+void    CreateNodesHydrologyShreve(Nodes** pnodes,IoModel* iomodel);
+void    CreateConstraintsHydrologyShreve(Constraints** pconstraints,IoModel* iomodel);
+void  CreateLoadsHydrologyShreve(Loads** ploads, IoModel* iomodel);
+void    UpdateElementsHydrologyShreve(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type);
+/*hydrology DC:*/
+void    CreateNodesHydrologyDCInefficient(Nodes** pnodes,IoModel* iomodel);
+void    CreateConstraintsHydrologyDCInefficient(Constraints** pconstraints,IoModel* iomodel);
+void  CreateLoadsHydrologyDCInefficient(Loads** ploads, IoModel* iomodel);
+void    UpdateElementsHydrologyDCInefficient(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type);
+void    CreateNodesHydrologyDCEfficient(Nodes** pnodes,IoModel* iomodel);
+void    CreateConstraintsHydrologyDCEfficient(Constraints** pconstraints,IoModel* iomodel);
+void  CreateLoadsHydrologyDCEfficient(Loads** ploads, IoModel* iomodel);
+void    UpdateElementsHydrologyDCEfficient(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type);
 /*melting:*/

issm/trunk/src/c/modules/ModelProcessorx/NodesPartitioning.cpp

-              r13975
+              r15396
 #include <string.h>
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../shared/shared.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
-#include "../../io/io.h"
-#include "../../include/include.h"
 #include "../MeshPartitionx/MeshPartitionx.h"
 #include "../ModelProcessorx/ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp

-              r13975
+              r15396
-#include "../../../Container/Container.h"
-#include "../../../modules/modules.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../io/io.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../ModelProcessorx.h"
+#include "../../IoModelToConstraintsx/IoModelToConstraintsx.h"
 void    CreateConstraintsPrognostic(Constraints** pconstraints, IoModel* iomodel){

issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../io/io.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp

-              r14310
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../modules/modules.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"
 …
                 elements->InputDuplicate(ThicknessEnum,QmuThicknessEnum);
                 elements->InputDuplicate(SurfaceEnum,QmuSurfaceEnum);
+                elements->InputDuplicate(BasalforcingsMeltingRateEnum,QmuMeltingEnum);
+                elements->InputDuplicate(VxEnum,QmuVxEnum);
+                elements->InputDuplicate(VyEnum,QmuVyEnum);
+        }
 …
                 iomodel->FetchDataToInput(elements,PressureEnum);
                 iomodel->FetchDataToInput(elements,TemperatureEnum);
+                iomodel->FetchDataToInput(elements,VzEnum);
+                if(dakota_analysis){
+                        elements->InputDuplicate(PressureEnum,QmuPressureEnum);
+                        elements->InputDuplicate(TemperatureEnum,QmuTemperatureEnum);
+                        elements->InputDuplicate(VzEnum,QmuVzEnum);
+                }
+        }
         if(issmbgradients){

issm/trunk/src/c/modules/ModelProcessorx/SortDataSets.cpp

-              r13975
+              r15396
 #endif
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 #include "./ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/CreateConstraintsSurfaceSlope.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/CreateNodesSurfaceSlope.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/SurfaceSlope/UpdateElementsSurfaceSlope.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../modules/modules.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"

issm/trunk/src/c/modules/ModelProcessorx/Thermal/CreateConstraintsThermal.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../modules/modules.h"
-#include "../../../io/io.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../ModelProcessorx.h"
+#include "../../IoModelToConstraintsx/IoModelToConstraintsx.h"
 void    CreateConstraintsThermal(Constraints** pconstraints, IoModel* iomodel){

issm/trunk/src/c/modules/ModelProcessorx/Thermal/CreateLoadsThermal.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"
 …
         /*Intermediary*/
+        int i;
+        int    dim;
+        int    numberofvertices;
+        Pengrid*    pengrid  = NULL;
+        int      dim;
+        int      numberofvertices;
+        Pengrid *pengrid          = NULL;
         /*Recover pointer: */
 …
         CreateSingleNodeToElementConnectivity(iomodel);
         for (i=0;i<numberofvertices;i++){
+        for(int i=0;i<numberofvertices;i++){
                 /*keep only this partition's nodes:*/

issm/trunk/src/c/modules/ModelProcessorx/Thermal/CreateNodesThermal.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../include/include.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"

issm/trunk/src/c/modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp

-              r13975
+              r15396
  */
-#include "../../../Container/Container.h"
-#include "../../../modules/modules.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"
 …
         if(dakota_analysis){
                 elements->InputDuplicate(TemperatureEnum,QmuTemperatureEnum);
+                elements->InputDuplicate(PressureEnum,QmuPressureEnum);
                 elements->InputDuplicate(BasalforcingsMeltingRateEnum,QmuMeltingEnum);
+        }
         /*Free data: */
         iomodel->DeleteData(1,MeshElementsEnum);

issm/trunk/src/c/modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp

-              r13395
+              r15396
  */
-#include "../../../Container/Container.h"
 #include "../../../toolkits/toolkits.h"
+#include "../../../io/io.h"
+#include "../../../modules/modules.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../classes/objects/objects.h"
+#include "../../../classes/classes.h"
 #include "../../../shared/shared.h"
 #include "../../MeshPartitionx/MeshPartitionx.h"
-#include "../../../include/include.h"
 #include "../ModelProcessorx.h"
 void    UpdateElementsTransient(Elements* elements, Parameters* parameters,IoModel* iomodel,int analysis_counter,int analysis_type){
+        bool        isgl;
+        int         migration_style;
+        int         i,numberofvertices;
+        IssmDouble  rho_ice,rho_water;
+        IssmDouble *phi   = NULL;
+        /*Fetch data needed*/
+        iomodel->Constant(&isgl,TransientIsgroundinglineEnum);
+        iomodel->Constant(&migration_style,GroundinglineMigrationEnum);
+        if(isgl==1 && (migration_style==SubelementMigrationEnum || migration_style==SubelementMigration2Enum)){
+                /*get parameters and constants: */
+                iomodel->Constant(&rho_ice,MaterialsRhoIceEnum);
+                iomodel->Constant(&rho_water,MaterialsRhoWaterEnum);
+                iomodel->Constant(&numberofvertices,MeshNumberofverticesEnum);
+                iomodel->FetchData(3,MeshElementsEnum,ThicknessEnum,BathymetryEnum);
+                /*Create phi vector */
+                phi=xNew<IssmDouble>(numberofvertices);
+                for (i=0;i<numberofvertices;i++){
+                        if(iomodel->my_vertices[i]){
+                                phi[i] = iomodel->Data(ThicknessEnum)[i] + rho_water/rho_ice * iomodel->Data(BathymetryEnum)[i];
+                        }
+                }
+                /*Update elements: */
+                for(i=0;i<elements->Size();i++){
+                        Element* element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
+                        element->InputCreate(phi,element->Sid(),iomodel,numberofvertices,1,1,GLlevelsetEnum,1);
+                }
+                /*Free ressources:*/
+                iomodel->DeleteData(3,MeshElementsEnum,ThicknessEnum,BathymetryEnum);
+                xDelete<IssmDouble>(phi);
+        }
+}

issm/trunk/src/c/modules/ModelProcessorx/UpdateCounters.cpp

-              r13975
+              r15396
 #endif
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 #include "./ModelProcessorx.h"

issm/trunk/src/c/modules/NodalValuex/NodalValuex.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void NodalValuex( IssmDouble* pnodalvalue, int natureofdataenum,Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units){
+void NodalValuex( IssmDouble* pnodalvalue, int natureofdataenum,Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){
         int my_rank;
 …
         for(i=0;i<elements->Size();i++){
                 Element* element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 found=element->NodalValue(&value,index,natureofdataenum,process_units);
+                found=element->NodalValue(&value,index,natureofdataenum);
                 if (found){
                         cpu_found=my_rank;

issm/trunk/src/c/modules/NodalValuex/NodalValuex.h

-              r13975
+              r15396
 #define _NODALVALUEX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void NodalValuex( IssmDouble* pnodalvalue, int natureofdataenum,Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units);
+void NodalValuex( IssmDouble* pnodalvalue, int natureofdataenum,Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters);
 #endif  /* _NODALVALUEX_H */

issm/trunk/src/c/modules/NodeConnectivityx/NodeConnectivityx.cpp

-              r14310
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void    NodeConnectivityx(int** pconnectivity,int* pwidth,int* elements, int nels, int nods){

issm/trunk/src/c/modules/NodesDofx/NodesDofx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void NodesDofx(Nodes* nodes, Parameters* parameters,int configuration_type){

issm/trunk/src/c/modules/NodesDofx/NodesDofx.h

-              r13395
+              r15396
 #define _NODESDOFX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/Orthx/Orthx.h

-              r13975
+              r15396
 #define _ORTHX_H
+#include "../../classes/objects/objects.h"
+#include "../../include/include.h"
+#include "../../classes/classes.h"
 #include "../../shared/shared.h"

issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp

-              r14310
+              r15396
 #include <stdio.h>
 #include "./OutputResultsx.h"
+#include "../../Container/Container.h"
+#include "../../io/io.h"
+#include "../../classes/objects/objects.h"
+#include "../../shared/io/io.h"
+#include "../../classes/classes.h"
 void OutputResultsx(Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Results* results){
 …
         /*We have results inside our elements, loads, etc ... Get them out of there, into the results dataset: */
-        elements->ProcessResultsUnits();
         elements->ToResults(results,parameters);
         elements->DeleteResults();

issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.h

r13975	r15396
12	12	#endif
13	13
14		#include "../../~~Container/Container~~.h"
	14	#include "../../classes/classes.h"
15	15
16	16	void OutputResultsx(Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, Results* results);

issm/trunk/src/c/modules/OutputRiftsx/OutputRiftsx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void OutputRiftsx( Vec* priftproperties, Loads* loads, int numrifts){

issm/trunk/src/c/modules/OutputRiftsx/OutputRiftsx.h

r13975	r15396
6	6	#define _OUTPUTRIFTSX_H
7	7
8		#include "../../~~Container/Container~~.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp

-              r13395
+              r15396
 #include "./PointCloudFindNeighborsx.h"
 int PointCloudFindNeighborsx(SeqVec<IssmPDouble>** pflags,double* x, double* y, int nods, double mindistance,double multithread){
+int PointCloudFindNeighborsx(IssmSeqVec<IssmPDouble>** pflags,double* x, double* y, int nods, double mindistance,double multithread){
         /*output: */
         SeqVec<IssmPDouble>* flags=NULL;
         flags=new SeqVec<IssmPDouble>(nods);
+        IssmSeqVec<IssmPDouble>* flags=NULL;
+        flags=new IssmSeqVec<IssmPDouble>(nods);
         /*threading: */

issm/trunk/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h

-              r13975
+              r15396
 #include "../../shared/shared.h"
 #include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 int PointCloudFindNeighborsx(SeqVec<IssmPDouble>** pflags,double* x, double* y, int nods, double mindistance,double multithread);
+int PointCloudFindNeighborsx(IssmSeqVec<IssmPDouble>** pflags,double* x, double* y, int nods, double mindistance,double multithread);
 /*threading: */
 …
         int nods;
         double mindistance;
         SeqVec<IssmPDouble>* flags;
+        IssmSeqVec<IssmPDouble>* flags;
 } PointCloudFindNeighborsThreadStruct;

issm/trunk/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp

-              r13975
+              r15396
         int     nods;
         double  mindistance;
         SeqVec<IssmPDouble>*     flags;
+        IssmSeqVec<IssmPDouble>*     flags;
         /*recover handle and gate: */
 …
                 /*display current iteration*/
                 if (my_thread==0 && fmod((double)i,(double)100)==0)
                  _printString_("\r      loop progress: "<<setw(6)<<setprecision(2)<<double(i-i0)/double(i1-i0)*100<<"%");
+                 _printf_("\r      loop progress: "<<setw(6)<<setprecision(2)<<double(i-i0)/double(i1-i0)*100<<"%");
                 distance=mindistance+100; //make sure initialization respects min distance criterion.
 …
+        }
         if (my_thread==0)
          _printLine_("\r      loop progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%");
+         _printf_("\r      loop progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%\n");
         /*Free ressources:*/

issm/trunk/src/c/modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp

-              r13975
+              r15396
 #include "./PositiveDegreeDayx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void PositiveDegreeDayx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters){
 …
   if (itm >= NPDMAX){
     _printLine_("increase NPDMAX in massBalance.cpp");
+    _printf_("increase NPDMAX in massBalance.cpp\n");
     exit (1);
+      }
 …
   itm = reCast<int,IssmDouble>((PDCUT+2.*siglimc)/DT + 1.5);
   if (itm >= NPDCMAX){
     _printLine_("'increase NPDCMAX in p35com'");
+    _printf_("'increase NPDCMAX in p35com'\n");
     exit (1);
+      }

issm/trunk/src/c/modules/PositiveDegreeDayx/PositiveDegreeDayx.h

-              r13395
+              r15396
 #define _POSITIVEDEGREEDAYX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.cpp

r13975	r15396
5	5
6	6	#include "../../shared/shared.h"
7		~~#include "../../include/include.h"~~
8	7	#include "../../toolkits/toolkits.h"
9	8

issm/trunk/src/c/modules/PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.h

r13975	r15396
5	5	#define _PROPAGATEFLAGSFROMCONNECTIVITYX_H
6	6
7		#include "../../~~Container/Container~~.h"
	7	#include "../../classes/classes.h"
8	8
9	9	/* local prototypes: */

issm/trunk/src/c/modules/Reduceloadx/Reduceloadx.cpp

-              r13975
+              r15396
 #include "./Reduceloadx.h"
 #include "../../io/io.h"
+#include "../../shared/io/io.h"
 void    Reduceloadx( Vector<IssmDouble>* pf, Matrix<IssmDouble>* Kfs, Vector<IssmDouble>* y_s,bool flag_ys0){
 …
         bool        oldalloc  = false;
         if(VerboseModule()) _pprintLine_("   Dirichlet lifting applied to load vector");
+        if(VerboseModule()) _printf0_("   Dirichlet lifting applied to load vector\n");
         Kfs->GetSize(&global_m,&global_n);
 …
         /*Free ressources and return*/
         xdelete(&y_s0);
         xdelete(&Kfsy_s);
+        delete y_s0;
+        delete Kfsy_s;
+}

issm/trunk/src/c/modules/Reduceloadx/Reduceloadx.h

r13395	r15396
6	6	#define _REDUCELOADX_H
7	7
8		#include "../../classes/~~objects/object~~s.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp

r13975	r15396
16	16	IssmDouble *ug_serial = NULL;
17	17	bool oldalloc = false;
	18
	19	if(VerboseModule()) _printf0_(" Reduce vector from g to f set\n");
18	20
19	21	/first figure out fsize: /

issm/trunk/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.h

r13975	r15396
7	7	#define _REDUCEVECTORGTOFX_H
8	8
9		#include "../../classes/~~objects/object~~s.h"
	9	#include "../../classes/classes.h"
10	10
11	11	/* local prototypes: */

issm/trunk/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.h

r13975	r15396
7	7	#define _REDUCEVECTORGTOSX_H
8	8
9		#include "../../classes/~~objects/object~~s.h"
	9	#include "../../classes/classes.h"
10	10
11	11	/* local prototypes: */

issm/trunk/src/c/modules/ResetConstraintsx/ResetConstraintsx.cpp

-              r13975
+              r15396
  */
+#ifdef HAVE_CONFIG_H
+        #include <config.h>
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
 #include "./ResetConstraintsx.h"
-#include "../modules.h"
 #include "../../shared/shared.h"
-#include "../../io/io.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
 #include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../ConstraintsStatex/ConstraintsStatex.h"
 void ResetConstraintsx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads,Materials* materials,  Parameters* parameters){
 …
         /*Display message*/
         if(VerboseModule()) _pprintLine_("   Resetting penalties");
+        if(VerboseModule()) _printf0_("   Resetting penalties\n");
         /*recover parameters: */
 …
         /*Do we have penalties linked to rifts? In this case, run our special rifts penalty
          * management routine, otherwise, skip : */
+        #ifdef _HAVE_RIFTS_
         if (RiftIsPresent(loads,analysis_type)){
                 _error_("rift constraints reset not supported yet!");
+        }
+        else if(ThermalIsPresent(loads,analysis_type)){
+        #endif
+        #ifdef _HAVE_THERMAL_
+        if(ThermalIsPresent(loads,analysis_type)){
                 ThermalConstraintsReset(loads,analysis_type);
+        }
         else{ /*Do nothing, no constraints management!:*/}
+        #endif
+}

issm/trunk/src/c/modules/ResetConstraintsx/ResetConstraintsx.h

-              r13975
+              r15396
 #define _RESETCONSTRAINTSX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/ResetCoordinateSystemx/ResetCoordinateSystemx.cpp

r13975	r15396
5	5	#include "./ResetCoordinateSystemx.h"
6	6	#include "../../shared/shared.h"
7		~~#include "../../include/include.h"~~
8	7	#include "../../toolkits/toolkits.h"
9	8

issm/trunk/src/c/modules/ResetCoordinateSystemx/ResetCoordinateSystemx.h

-              r13395
+              r15396
 #define _RESETCOORDINATESYSTEMX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void RheologyBbarAbsGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units, int weight_index){
+void RheologyBbarAbsGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters, int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->RheologyBbarAbsGradient(process_units,weight_index);
+                J+=element->RheologyBbarAbsGradient(weight_index);
+        }

issm/trunk/src/c/modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.h

-              r13395
+              r15396
 #define _RHEOLOGYBBARGRADIENTX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void RheologyBbarAbsGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void RheologyBbarAbsGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/Scotchx/Scotchx.h

-              r13975
+              r15396
 #include <stdio.h>
 #include <string.h>
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 #ifdef _HAVE_SCOTCH_ //only works if scotch library has been compiled in.

issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp

-              r13975
+              r15396
 #include "./SetControlInputsFromVectorx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,IssmDouble* vector){

issm/trunk/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h

-              r13395
+              r15396
 #define _SETCONTROLINPUTSXFROMVECTOR_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/Shp2Expx/Shp2Expx.cpp

-              r14283
+              r15396
 #include "./Shp2Expx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../modules.h"
+#include "../../kml/kmlobjects.h"
 int Shp2Expx(char* filshp,char* filexp){
 …
         clock0=clock();
         time0 =time(NULL);
         _pprintString_("\nShp2Expx Module -- " << ctime(&time0));
+        _printf0_("\nShp2Expx Module -- " << ctime(&time0));
 /*  note that much of the following code is taken from shpdump.c in shapelib.  */
 …
                         if (pnpart[i] > 0)
+                                _printf_(true,"Warning -- Shape %d of type \"%s\" should not have %d > 0 parts.\n",
+                                                 i,SHPTypeName( pstype[i] ),pnpart[i]);
+                                _printf_("Warning -- Shape " << i << " of type \"" << SHPTypeName( pstype[i] ) << "\" should not have " << pnpart[i] << " > 0 parts.\n\n");
                         if (pnvert[i] > 1)
+                                _printf_(true,"Warning -- Shape %d of type \"%s\" should not have %d > 1 vertices.\n",
+                                                 i,SHPTypeName( pstype[i] ),pnvert[i]);
+                                _printf_("Warning -- Shape " << i << " of type \"" << SHPTypeName( pstype[i] ) << "\" should not have " << pnvert[i] << " > 1 vertices.\n\n");
                         kpoint=new KML_Point();
 …
                                 else {
                                         if (!kpoly) {
+                                                _printf_(true,"Warning -- Shape %d of type \"%s\", part %d, expected to be outer loop (cw).\n",
+                                                                 i,SHPTypeName( pstype[i] ),j);
+                                                _printf_("Warning -- Shape " << i << " of type \"" << SHPTypeName( pstype[i] ) << "\", part " << j << ", expected to be outer loop (cw).\n\n");
                                                 continue;
+                                        }
 …
                         if (pnpart[i] > 0)
+                                _printf_(true,"Warning -- Shape %d of type \"%s\" should not have %d > 0 parts.\n",
+                                                 i,SHPTypeName( pstype[i] ),pnpart[i]);
+                                _printf_("Warning -- Shape " << i << " of type \"" << SHPTypeName( pstype[i] ) << "\" should not have " << pnpart[i] << " > 0 parts.\n\n");
 /*  create a multigeometry to hold all the points  */
 …
                 else if (pstype[i] == SHPT_MULTIPATCH) {
+                        _printf_(true,"Warning -- Shape %d of type \"%s\" will be ignored.\n",
+                                         i,SHPTypeName( pstype[i] ));
+                        _printf_("Warning -- Shape " << i << " of type \"" <<SHPTypeName( pstype[i] ) << "\" will be ignored.\n\n");
                         continue;
+                }
 …
                 else {
+                        _printf_(true,"Warning -- Shape %d of type \"%s\" will be ignored.\n",
+                                         i,SHPTypeName( pstype[i] ));
+                        _printf_("Warning -- Shape " << i << " of type \"" <<SHPTypeName( pstype[i] ) << "\" will be ignored.\n\n");
+                }
+        }
 …
 /*  open exp file  */
         _pprintLine_("Writing exp profiles to file.");
+        _printf0_("Writing exp profiles to file.\n");
         fid=fopen(filexp,"w");
 …
         clock1=clock();
         time1 =time(NULL);
+        _printf_(true,"Shp2Expx Module -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0));
+        _printf_("Shp2Expx Module -- " <<((double)(clock1-clock0))/CLOCKS_PER_SEC << " CPU seconds; " <<difftime(time1,time0)  << " elapsed seconds.\n\n\n");
         return(iret);

issm/trunk/src/c/modules/Shp2Expx/Shp2Expx.h

-              r14283
+              r15396
 #endif
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/Shp2Kmlx/Shp2Kmlx.cpp

-              r13975
+              r15396
 #include "./Shp2Kmlx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../modules.h"
+#include "../../kml/kmlobjects.h"
 int Shp2Kmlx(char* filshp,char* filkml,
 …
         clock0=clock();
         time0 =time(NULL);
         _pprintString_("\nShp2Kmlx Module -- " << ctime(&time0));
+        _printf0_("\nShp2Kmlx Module -- " << ctime(&time0));
 /*  note that much of the following code is taken from shpdump.c in shapelib.  */
 …
                         if (pnpart[i] > 0)
+                                _printf_(true,"Warning -- Shape %d of type \"%s\" should not have %d > 0 parts.\n",
+                                                 i,SHPTypeName( pstype[i] ),pnpart[i]);
+                                _printf_("Warning -- Shape "<< i << " of type \"" << SHPTypeName( pstype[i] ) << "\" should not have " << pnpart[i] << " > 0 parts.\n\n");
                         if (pnvert[i] > 1)
+                                _printf_(true,"Warning -- Shape %d of type \"%s\" should not have %d > 1 vertices.\n",
+                                                 i,SHPTypeName( pstype[i] ),pnvert[i]);
+                                _printf_("Warning -- Shape " << i << " of type \"" << SHPTypeName( pstype[i] ) << "\" should not have " << pnpart[i] << " > 1 vertices.\n\n");
                         kpoint=new KML_Point();
 …
                                 else {
                                         if (!kpoly) {
+                                                _printf_(true,"Warning -- Shape %d of type \"%s\", part %d, expected to be outer loop (cw).\n",
+                                                                 i,SHPTypeName( pstype[i] ),j);
+                                                _printf_("Warning -- Shape " << i << " of type \"" << SHPTypeName( pstype[i] ) << "\", part " << j << ", expected to be outer loop (cw).\n\n");
                                                 continue;
+                                        }
 …
                         if (pnpart[i] > 0)
+                                _printf_(true,"Warning -- Shape %d of type \"%s\" should not have %d > 0 parts.\n",
+                                                 i,SHPTypeName( pstype[i] ),pnpart[i]);
+                                _printf_("Warning -- Shape " << i << " of type \"" << SHPTypeName( pstype[i] ) << "\" should not have " << pnpart[i] << " > 0 parts.\n\n");
 /*  create a multigeometry to hold all the points  */
 …
                 else if (pstype[i] == SHPT_MULTIPATCH) {
+                        _printf_(true,"Warning -- Shape %d of type \"%s\" will be ignored.\n",
+                                         i,SHPTypeName( pstype[i] ));
+                        _printf_("Warning -- Shape " << i << " of type \"" << SHPTypeName( pstype[i] ) << "\" will be ignored.\n\n");
                         continue;
+                }
 …
                 else {
+                        _printf_(true,"Warning -- Shape %d of type \"%s\" will be ignored.\n",
+                                         i,SHPTypeName( pstype[i] ));
+                        _printf_("Warning -- Shape " << i << " of type \"" << SHPTypeName( pstype[i] ) << "\" will be ignored.\n\n");
+                }
+        }
 …
 /*  write kml file  */
         _pprintLine_("Writing kml document to file.");
+        _printf0_("Writing kml document to file.\n");
         fid=fopen(filkml,"w");
         fprintf(fid,"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
 …
         clock1=clock();
         time1 =time(NULL);
+        _printf_(true,"Shp2Kmlx Module -- %f CPU seconds; %f elapsed seconds.\n\n",
+                         ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0));
+        _printf_("Shp2Kmlx Module -- " << ((double)(clock1-clock0))/CLOCKS_PER_SEC << " CPU seconds; " << difftime(time1,time0) << " elapsed seconds.\n\n\n");
         return(iret);

issm/trunk/src/c/modules/Shp2Kmlx/Shp2Kmlx.h

-              r13395
+              r15396
 #endif
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/SmbGradientsx/SmbGradientsx.cpp

-              r13975
+              r15396
 #include "./SmbGradientsx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void SmbGradientsx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters){

issm/trunk/src/c/modules/SmbGradientsx/SmbGradientsx.h

-              r13395
+              r15396
 #define _SMBGRADIENTSX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/Solverx/CMakeLists.txt

r14310	r15396
5	5	# }}}
6	6	# CORE_SOURCES {{{
7		set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/Solverx/Solverx.cpp
8		$ENV{ISSM_DIR}/src/c/modules/Solverx/SolverxSeq.cpp PARENT_SCOPE)
	7	set(CORE_SOURCES $ENV{ISSM_DIR}/src/c/modules/Solverx/Solverx.cpp PARENT_SCOPE)
9	8	# }}}

issm/trunk/src/c/modules/Solverx/Solverx.cpp

-              r13975
+              r15396
  * \brief solver
  */
-#include "./Solverx.h"
-#include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #ifdef HAVE_CONFIG_H
 …
 #endif
+#include "./Solverx.h"
+#include "../../shared/shared.h"
 void    Solverx(Vector<IssmDouble>** puf, Matrix<IssmDouble>* Kff, Vector<IssmDouble>* pf, Vector<IssmDouble>* uf0,Vector<IssmDouble>* df, Parameters* parameters){
+        /*intermediary: */
+        Solver<IssmDouble> *solver=NULL;
         /*output: */
         Vector<IssmDouble> *uf=NULL;
+        /*In debugging mode, check that stiffness matrix and load vectors are not NULL (they can be empty)*/
+        _assert_(Kff);
+        _assert_(pf);
+        if(VerboseModule()) _printf0_("   Solving matrix system\n");
         /*Initialize vector: */
         uf=new Vector<IssmDouble>();
+        /*Initialize solver: */
+        solver=new Solver<IssmDouble>(Kff,pf,uf0,df,parameters);
+        /*According to matrix type, use specific solvers: */
+        switch(Kff->type){
+                #ifdef _HAVE_PETSC_
+                case PetscMatType:{
+                        PetscVec* uf0_vector = NULL;
+                        PetscVec* df_vector  = NULL;
+                        if(uf0) uf0_vector = uf0->pvector;
+                        if(df)  df_vector  = df->pvector;
+                        SolverxPetsc(&uf->pvector,Kff->pmatrix,pf->pvector,uf0_vector,df_vector,parameters);
+                        break;}
+                #endif
+                case SeqMatType:{
+                        SolverxSeq(&uf->svector,Kff->smatrix,pf->svector,parameters);
+                        break;}
+                default:
+                          _error_("Matrix type: " << Kff->type << " not supported yet!");
+        }
+        /*Solve:*/
+        uf=solver->Solve();
+        /*Assign output pointers:*/
+        /*clean up and assign output pointers:*/
+        delete solver;
         *puf=uf;
+}

issm/trunk/src/c/modules/Solverx/Solverx.h

-              r13975
+              r15396
 #endif
 #include "../../classes/objects/objects.h"
+#include "../../toolkits/toolkits.h"
 /* local prototypes: */
 void    Solverx(Vector<IssmDouble>** puf, Matrix<IssmDouble>* Kff, Vector<IssmDouble>* pf, Vector<IssmDouble>* uf0,Vector<IssmDouble>* df, Parameters* parameters);
-#ifdef _HAVE_PETSC_
-void    SolverxPetsc(PetscVec** puf, PetscMat* Kff, PetscVec* pf, PetscVec* uf0,PetscVec* df, Parameters* parameters);
-void    SolverxPetsc(Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df, Parameters* parameters);
-void  DofTypesToIndexSet(IS* pisv, IS* pisp, Vec df,int typeenum);
-#endif
-void SolverxSeq(SeqVec<IssmDouble>** puf,SeqMat<IssmDouble>* Kff, SeqVec<IssmDouble>* pf,Parameters* parameters);
-void SolverxSeq(IssmPDouble **pX, IssmPDouble *A, IssmPDouble *B,int n);
-void SolverxSeq(IssmPDouble *X, IssmPDouble *A, IssmPDouble *B,int n);
-#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_)
-void SolverxSeq(IssmDouble *X,IssmDouble *A,IssmDouble *B,int n, Parameters* parameters);
-// call back functions:
-ADOLC_ext_fct EDF_for_solverx;
-ADOLC_ext_fct_fos_forward EDF_fos_forward_for_solverx;
-ADOLC_ext_fct_fos_reverse EDF_fos_reverse_for_solverx;
-ADOLC_ext_fct_fov_forward EDF_fov_forward_for_solverx;
-ADOLC_ext_fct_fov_reverse EDF_fov_reverse_for_solverx;
-#endif
 #endif  /* _SOLVERX_H */

issm/trunk/src/c/modules/SpcNodesx/SpcNodesx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void SpcNodesx(Nodes* nodes,Constraints* constraints,Parameters* parameters, int analysis_type){

issm/trunk/src/c/modules/SpcNodesx/SpcNodesx.h

-              r13395
+              r15396
 #define _SPCNODESX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 #include "../../toolkits/toolkits.h"

issm/trunk/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void SurfaceAbsVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units,int weight_index){
+void SurfaceAbsVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->SurfaceAbsVelMisfit(process_units,weight_index);
+                J+=element->SurfaceAbsVelMisfit(weight_index);
+        }

issm/trunk/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.h

-              r13395
+              r15396
 #define _SURFACEABSVELMISFITX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void SurfaceAbsVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void SurfaceAbsVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/SurfaceAreax/SurfaceAreax.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 #include "../InputUpdateFromConstantx/InputUpdateFromConstantx.h"

issm/trunk/src/c/modules/SurfaceAreax/SurfaceAreax.h

-              r13975
+              r15396
 #define _SURFACEAREAX_H
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 #include "../SurfaceAreax/SurfaceAreax.h"
 void SurfaceAverageVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units,int weight_index){
+void SurfaceAverageVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->SurfaceAverageVelMisfit(process_units,weight_index);
+                J+=element->SurfaceAverageVelMisfit(weight_index);
+        }

issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.h

-              r13395
+              r15396
 #define _SURFACEAVERAGEVELMISFITX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void SurfaceAverageVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void SurfaceAverageVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void SurfaceLogVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units,int weight_index){
+void SurfaceLogVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->SurfaceLogVelMisfit(process_units,weight_index);
+                J+=element->SurfaceLogVelMisfit(weight_index);
+        }

issm/trunk/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.h

-              r13395
+              r15396
 #define _SURFACELOGVELMISFITX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void SurfaceLogVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void SurfaceLogVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void SurfaceLogVxVyMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units,int weight_index){
+void SurfaceLogVxVyMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->SurfaceLogVxVyMisfit(process_units,weight_index);
+                J+=element->SurfaceLogVxVyMisfit(weight_index);
+        }

issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.h

-              r13395
+              r15396
 #define _SURFACELOGVXVYMISFITX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void SurfaceLogVxVyMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void SurfaceLogVxVyMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void SurfaceRelVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units,int weight_index){
+void SurfaceRelVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->SurfaceRelVelMisfit(process_units,weight_index);
+                J+=element->SurfaceRelVelMisfit(weight_index);
+        }

issm/trunk/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.h

-              r13395
+              r15396
 #define _SURFACERELVELMISFITX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void SurfaceRelVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void SurfaceRelVelMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void ThicknessAbsMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units, int weight_index){
+void ThicknessAbsMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters, int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->ThicknessAbsMisfit(process_units,weight_index);
+                J+=element->ThicknessAbsMisfit(weight_index);
+        }

issm/trunk/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.h

-              r13395
+              r15396
 #define _THICKNESSABSMISFITX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void ThicknessAbsMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void ThicknessAbsMisfitx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/ThicknessAcrossGradientx/ThicknessAcrossGradientx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void ThicknessAcrossGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units, int weight_index){
+void ThicknessAcrossGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->ThicknessAcrossGradient(process_units,weight_index);
+                J+=element->ThicknessAcrossGradient(weight_index);
+        }

issm/trunk/src/c/modules/ThicknessAcrossGradientx/ThicknessAcrossGradientx.h

-              r13395
+              r15396
 #define _THICKNESSACROSSGRADIENT_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void ThicknessAcrossGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void ThicknessAcrossGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/ThicknessAlongGradientx/ThicknessAlongGradientx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void ThicknessAlongGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units, int weight_index){
+void ThicknessAlongGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,int weight_index){
         /*Intermediary*/
 …
         for (i=0;i<elements->Size();i++){
                 element=dynamic_cast<Element*>(elements->GetObjectByOffset(i));
                 J+=element->ThicknessAlongGradient(process_units,weight_index);
+                J+=element->ThicknessAlongGradient(weight_index);
+        }

issm/trunk/src/c/modules/ThicknessAlongGradientx/ThicknessAlongGradientx.h

-              r13395
+              r15396
 #define _THICKNESSALONGGRADIENT_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
 void ThicknessAlongGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units,int weight_index);
+void ThicknessAlongGradientx( IssmDouble* pJ, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int weight_index);
 #endif

issm/trunk/src/c/modules/TriMeshProcessRiftsx/TriMeshProcessRiftsx.cpp

r14310	r15396
6	6	#include "../../classes/RiftStruct.h"
7	7	#include "../../shared/shared.h"
8		~~#include "../../include/include.h"~~
9	8	#include "../../toolkits/toolkits.h"
10	9

issm/trunk/src/c/modules/TriMeshx/TriMeshx.cpp

-              r14310
+              r15396
 #include "./TriMeshx.h"
 #include "../../shared/shared.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 /*ANSI_DECLARATORS needed to call triangle library: */
 #if defined(_HAVE_TRIANGLE_)
 …
 /*}}}*/
 void TriMeshx(SeqMat<int>** pindex,SeqVec<IssmPDouble>** px,SeqVec<IssmPDouble>** py,SeqMat<int>** psegments,SeqVec<int>** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area){
+void TriMeshx(int** pindex,IssmPDouble** px,IssmPDouble** py,int** psegments,int** psegmentmarkerlist,int* pnels,int* pnods, int* pnsegs,Contours* domain,Contours* rifts,double area){
 #if !defined(_HAVE_TRIANGLE_)
 …
         /*output: */
+        int         *index             = NULL;
+        SeqMat<int> *index_matrix      = NULL;
+        double      *x                 = NULL;
+        double      *y                 = NULL;
+        int         *segments          = NULL;
+        SeqMat<int> *segments_matrix   = NULL;
+        int         *segmentmarkerlist = NULL;
+        int    *index             = NULL;
+        double *x                 = NULL;
+        double *y                 = NULL;
+        int    *segments          = NULL;
+        int    *segmentmarkerlist = NULL;
         /*intermediary: */
 …
         /*Output : */
+        index_matrix=new SeqMat<int>(index,out.numberoftriangles,3,1);
+        *pindex=index_matrix;
+        segments_matrix=new SeqMat<int>(segments,out.numberofsegments,3,1);
+        *psegments=segments_matrix;
+        *px=new SeqVec<IssmPDouble>(x,out.numberofpoints);
+        *py=new SeqVec<IssmPDouble>(y,out.numberofpoints);
+        *psegmentmarkerlist=new SeqVec<int>(segmentmarkerlist,out.numberofsegments);
+        *pindex=index;
+        *px=x;
+        *py=y;
+        *psegments=segments;
+        *psegmentmarkerlist=segmentmarkerlist;
+        *pnels=out.numberoftriangles;
+        *pnods=out.numberofpoints;
+        *pnsegs=out.numberofsegments;
 #endif
+}

issm/trunk/src/c/modules/TriMeshx/TriMeshx.h

-              r14310
+              r15396
 #include <string.h>
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */
+void TriMeshx(SeqMat<int>** pindex,SeqVec<IssmPDouble>** px,SeqVec<IssmPDouble>** py,SeqMat<int>** psegments,SeqVec<int>** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area);
+void TriMeshx(int** pindex,IssmPDouble** px,IssmPDouble** py,int** psegments,int** psegmentmarkerlist,int* pnels,int* pnods, int* pnseg,Contours* domain,Contours* rifts,double area);
 #endif  /* _TRIMESHX_H */

issm/trunk/src/c/modules/TriaSearchx/TriaSearchx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
+#include "../../classes/objects/objects.h"
+#include "../modules.h"
+#include "../../bamg/bamgobjects.h"
 using namespace bamg;

issm/trunk/src/c/modules/TriaSearchx/TriaSearchx.h

r13395	r15396
6	6	#define _TRIASEARCHX_H
7	7
8		#include "../../classes/~~objects/object~~s.h"
	8	#include "../../classes/classes.h"
9	9
10	10	/* local prototypes: */

issm/trunk/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vector<IssmDouble>* yg){

issm/trunk/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h

-              r13395
+              r15396
 #define _UPDATEDYNAMICCONSTRAINTSXX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vector<IssmDouble>* yg);

issm/trunk/src/c/modules/VecMergex/VecMergex.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void VecMergex(Vector<IssmDouble>* ug, Vector<IssmDouble>* uf, Nodes* nodes, Parameters* parameters, int SetEnum){

issm/trunk/src/c/modules/VecMergex/VecMergex.h

-              r13395
+              r15396
 #define _VECMERGEX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/VerticesDofx/VerticesDofx.cpp

-              r13975
+              r15396
 #include "../../shared/shared.h"
-#include "../../include/include.h"
 #include "../../toolkits/toolkits.h"
-#include "../../EnumDefinitions/EnumDefinitions.h"
 void VerticesDofx( Vertices* vertices, Parameters* parameters) {

issm/trunk/src/c/modules/VerticesDofx/VerticesDofx.h

-              r13975
+              r15396
 #define _VERTICESDOFX_H
+#include "../../Container/Container.h"
+#include "../../classes/objects/objects.h"
+#include "../../classes/classes.h"
 /* local prototypes: */

issm/trunk/src/c/modules/modules.h

-              r14310
+              r15396
 #include "./DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.h"
 #include "./ElementConnectivityx/ElementConnectivityx.h"
+#include "./EnumToStringx/EnumToStringx.h"
+#include "./StringToEnumx/StringToEnumx.h"
+#include "./EdgeDetectionx/EdgeDetectionx.h"
 #include "./GetSolutionFromInputsx/GetSolutionFromInputsx.h"
 #include "./GetVectorFromInputsx/GetVectorFromInputsx.h"
 #include "./GetVectorFromControlInputsx/GetVectorFromControlInputsx.h"
+#include "./GiaDeflectionCorex/GiaDeflectionCorex.h"
 #include "./SetControlInputsFromVectorx/SetControlInputsFromVectorx.h"
 #include "./Gradjx/Gradjx.h"
 …
 #include "./HoleFillerx/HoleFillerx.h"
 #include "./InputControlUpdatex/InputControlUpdatex.h"
-#include "./InputConvergencex/InputConvergencex.h"
 #include "./InputDuplicatex/InputDuplicatex.h"
 #include "./InputScalex/InputScalex.h"
 …
 #include "./KMLMeshWritex/KMLMeshWritex.h"
 #include "./KMLOverlayx/KMLOverlayx.h"
-#include "./Xy2llx/Xy2llx.h"
-#include "./Ll2xyx/Ll2xyx.h"
 #include "./Exp2Kmlx/Exp2Kmlx.h"
 #include "./Kml2Expx/Kml2Expx.h"
 …
 #include "./SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.h"
 #include "./ModelProcessorx/ModelProcessorx.h"
 #include "./ParsePetscOptionsx/ParsePetscOptionsx.h"
+#include "./ParseToolkitsOptionsx/ParseToolkitsOptionsx.h"
 #include "./NodalValuex/NodalValuex.h"
 #include "./NodeConnectivityx/NodeConnectivityx.h"
 …
 #include "./UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h"
 #include "./VerticesDofx/VerticesDofx.h"
+#include "./VertexCoordinatesx/VertexCoordinatesx.h"
 #include "./VecMergex/VecMergex.h"
 #endif

issm/trunk/src/c/shared/Bamg/BigPrimeNumber.cpp

r3913	r15396
1		#include "./BigPrimeNumber.h"
	1	#include "./Abs.h"
	2	#include "./extrema.h"
2	3
3	4	namespace bamg {

issm/trunk/src/c/shared/Bamg/BigPrimeNumber.h

-              r3913
+              r15396
 #ifndef _BIGPRIMENUMBER_H_
 #define _BIGPRIMENUMBER_H_
-#include "./Abs.h"
-#include "./extrema.h"
 namespace bamg {

issm/trunk/src/c/shared/Bamg/HeapSort.h

-              r3913
+              r15396
 /*Sort a list of size n*/
+template<class T> inline void  HeapSort(T *c,long n){
+        int l,j,r,i;
+template<class T> inline void  HeapSort(T *c,long n){ /*{{{*/
+        /*Intermediaries*/
+        int i,j,l,r;
         T   crit;
+        c--;                    //the array must starts at 1 and not 0
+        if(n<=1) return;        //return if size <=1
+        l=n/2+1;                //initialize l and r
+        /*return if size <=1*/
+        if(n<=1) return;
+        /*Initialize variables*/
+        l=n/2+1;
         r=n;
+        c--; //the array must starts at 1 and not 0
+        /*Sorting algorithm*/
         for(;;){
                 if(l<=1){
+                        crit  =c[r];
+                        c[r--]=c[1];
+                        if (r==1){c[1]=crit; return;}
+                        crit   = c[r];
+                        c[r--] = c[1];
+                        if(r==1){
+                                c[1]=crit;
+                                return;
+                        }
+                }
+                else  crit = c[--l];
+                else{
+                        crit = c[--l];
+                }
                 j=l;
                 for(;;){
                         i=j;
                         j=2*j;
                         if  (j>r) {c[i]=crit;break;}
+                        i = j;
+                        j = 2*j;
+                        if  (j>r){c[i]=crit;break;}
                         if ((j<r) && (c[j] < c[j+1])) j++;//c[j+1]> c[j] -> take j+1 instead of j (larger value)
                         if (crit < c[j]) c[i]=c[j];       //c[j]  > crit -> stock this large value in i(<j)
                         else{c[i]=crit;break;}            //c[j]  < crit -> stock crit in i (<j)
+                        if (crit < c[j]) c[i]=c[j];       //c[j]  > crit -> put this large value in i(<j)
+                        else{c[i]=crit;break;}            //c[j]  < crit -> put crit in i (<j)
+                }
+        }
+}
+/*}}}*/
 /*Sort a list of size n and returns ordering*/
+template<class T> inline void  HeapSort(int** porder,T* c,int n){
+        int  l,j,r,i;
+template<class T> inline void  HeapSort(int** porder,T* c,int n){ /*{{{*/
+        /*Intermediaries*/
+        int  i,j,l,r;
         T    crit;
         int  pos;
+        int* order = new int[n];
+        int* order = NULL;
+        /*return if size <=1*/
+        if(n<=1) return;
+        /*Initialize variables*/
+        l=n/2+1;
+        r=n;
+        c--; //the array must starts at 1 and not 0
+        order = new int[n];
         for(i=0;i<n;i++) order[i]=i+1;
+        c--;                    //the array must starts at 1 and not 0
+        order--;
+        if(n<=1) return;        //return if size <=1
+        l=n/2+1;                //initialize l and r
+        r=n;
+        /*Sorting algorithm*/
         for(;;){
                 if(l<=1){
 …
+                }
+        }
+}
+}/*}}}*/
 #endif

issm/trunk/src/c/shared/Bamg/OppositeAngle.h

-              r13395
+              r15396
 #define _OPPOSITEANGLE_H_
 #include "../../classes/bamg/include.h"
+#include "../Numerics/constants.h"
 /*Return the opposite angle modulo 2 Pi*/
 namespace bamg {
         inline float  OppositeAngle(float  a){return a<0 ? fPi+a:a-fPi;}
         inline double OppositeAngle(double a){return a<0 ?  Pi+a:a- Pi;}
+        inline float  OppositeAngle(float  a){return a<0 ? PI+a:a-PI;}
+        inline double OppositeAngle(double a){return a<0 ?  PI+a:a- PI;}
+}

issm/trunk/src/c/shared/Bamg/shared.h

r13975	r15396
9	9	#include "BigPrimeNumber.h"
10	10	#include "BinaryRand.h"
11		~~#include "det.h"~~
12	11	#include "Exchange.h"
13	12	#include "extrema.h"

issm/trunk/src/c/shared/Elements/Arrhenius.cpp

-              r12706
+              r15396
  */
-#include "./elements.h"
 #include <math.h>
+#include "../Numerics/types.h"
+#include "../Exceptions/exceptions.h"
 IssmDouble Arrhenius(IssmDouble temperature,IssmDouble depth,IssmDouble n){

issm/trunk/src/c/shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp

r13395	r15396
5	5
6	6	#include "./elements.h"
	7	#include "../Numerics/numerics.h"
7	8
8	9	void ComputeDelta18oTemperaturePrecipitation(IssmDouble Delta18oSurfacePresent, IssmDouble Delta18oSurfaceLgm, IssmDouble Delta18oSurfaceTime,

issm/trunk/src/c/shared/Elements/Paterson.cpp

r13975	r15396
7	7	#include <math.h>
8	8
9		#include "../~~../include/include~~.h"
	9	#include "../Numerics/types.h"
10	10
11	11	IssmDouble Paterson(IssmDouble temperature){

issm/trunk/src/c/shared/Elements/PddSurfaceMassBalance.cpp

-              r13975
+              r15396
 #include "./elements.h"
+IssmDouble PddSurfaceMassBlance(IssmDouble* monthlytemperatures, IssmDouble* monthlyprec, IssmDouble* pdds, IssmDouble* pds, IssmDouble signorm, IssmDouble yts, IssmDouble h, IssmDouble s, IssmDouble rho_ice, IssmDouble rho_water){
+#include "../Numerics/numerics.h"
+IssmDouble PddSurfaceMassBlance(IssmDouble* monthlytemperatures, IssmDouble* monthlyprec, IssmDouble* pdds, IssmDouble* pds, IssmDouble signorm, IssmDouble yts, IssmDouble h, IssmDouble s, IssmDouble rho_ice, IssmDouble rho_water, IssmDouble desfac, IssmDouble s0p){
   // output:
   IssmDouble B;    // surface mass balance, melt+accumulation
   int    iqj,imonth;
 …
   IssmDouble sconv; //rhow_rain/rhoi / 12 months
   IssmDouble lapser=6.5/1000., sealev=0.;    // lapse rate. degrees per meter. 7.5 lev's 99 paper, 9 Marshall 99 paper
   IssmDouble desfac = 0.5;                 // desert elevation factor
   IssmDouble s0p=0.;         // should be set to elevation from precip source
+  IssmDouble lapser=6.5, sealev=0.;    // lapse rate. degrees per meter. 7.5 lev's 99 paper, 9 Marshall 99 paper
+  // IssmDouble desfac = 0.5;                 // desert elevation factor
+  // IssmDouble s0p=0.;         // should be set to elevation from precip source
   IssmDouble s0t=0.;         // should be set to elevation from temperature source
   IssmDouble st;             // elevation between altitude of the temp record and current altitude
 …
       // gaussian=T_m, so ndd=-(Tsurf-pdd)
       if (iqj>5 &&  iqj<9){ Tsum=Tsum+tstar;}
       if (tstar >= siglim) {pdd = pdd + tstar*deltm;}
       else if (tstar> -siglim){
 …
       else{frzndd = frzndd - tstar*deltm; }
   } // end of seasonal loop
   //******************************************************************
     saccu = qm;
     prect = qmp;     // total precipitation during 1 year taking into account des. ef.

issm/trunk/src/c/shared/Elements/PrintArrays.cpp

-              r14310
+              r15396
 #include "./elements.h"
 #include "../../include/macros.h"
+#include "../io/Print/Print.h"
 using namespace std;
 void printarray(IssmPDouble* array,int lines,int cols){
         _printLine_("");
+        _printf_("\n");
         for(int i=0;i<lines;i++){
                 _printString_("   [ ");
                 for(int j=0;j<cols;j++) _printString_( " " << setw(11) << setprecision (5) << array[i*cols+j]);
                 _printLine_(" ]");
+                _printf_("   [ ");
+                for(int j=0;j<cols;j++) _printf_( " " << setw(11) << setprecision (5) << array[i*cols+j]);
+                _printf_(" ]\n");
+        }
         _printLine_("");
+        _printf_("\n");
+}
 void printsparsity(IssmPDouble* array,int lines,int cols){
         int count;
         _printLine_("");
+        _printf_("\n");
         for(int i=0;i<lines;i++){
                 _printString_("   [ ");
+                _printf_("   [ ");
                 count = 0;
                 for(int j=0;j<cols;j++){
                         if(array[i*cols+j]!=0.0){
                                 _printString_( " X"); count++;
+                                _printf_( " X"); count++;
+                        }
                         else
                          _printString_( " .");
+                         _printf_( " .");
+                }
                 _printLine_(" ] "<<i<<" => "<<count);
+                _printf_(" ] "<<i<<" => "<<count << "\n");
+        }
         _printLine_("");
+        _printf_("\n");
+}
 void printarray(int* array,int lines,int cols){
         _printLine_("");
+        _printf_("\n");
         for(int i=0;i<lines;i++){
                 _printString_("   [ ");
                 for(int j=0;j<cols;j++) _printString_( " " << setw(11) << setprecision (5) << array[i*cols+j]);
                 _printLine_(" ]");
+                _printf_("   [ ");
+                for(int j=0;j<cols;j++) _printf_( " " << setw(11) << setprecision (5) << array[i*cols+j]);
+                _printf_(" ]\n");
+        }
         _printLine_("");
+        _printf_("\n");
+}
 void printarray(bool* array,int lines,int cols){
         _printLine_("");
+        _printf_("\n");
         for(int i=0;i<lines;i++){
+                _printString_("   [ ");
+                for(int j=0;j<cols;j++) _printString_( " " << array[i*cols+j]?1:0);
+                _printLine_(" ]");
+                _printf_("   [ ");
+                for(int j=0;j<cols;j++){
+                        if(array[i*cols+j]) _printf_( " 1");
+                        else _printf_( " 0");
+                }
+                _printf_(" ]\n");
+        }
         _printLine_("");
+        _printf_("\n");
+}
 void printbinary(int n){
 …
         while (i>0) {
                 if (n&i)
                  _printString_("1");
+                 _printf_("1");
                 else
                  _printString_("0");
+                 _printf_("0");
                 i>>=1;
+        }

issm/trunk/src/c/shared/Elements/elements.h

-              r14310
+              r15396
 #define _SHARED_ELEMENTS_H_
+#include "../../classes/objects/objects.h"
+#include "../../Container/Container.h"
+class ElementMatrix;
+class ElementVector;
+#include "../Numerics/types.h"
 IssmDouble Paterson(IssmDouble temperature);
 IssmDouble Arrhenius(IssmDouble temperature,IssmDouble depth,IssmDouble n);
 IssmDouble PddSurfaceMassBlance(IssmDouble* monthlytemperatures,  IssmDouble* monthlyprec, IssmDouble* pdds, IssmDouble* pds,
+                                IssmDouble signorm, IssmDouble yts, IssmDouble h, IssmDouble s, IssmDouble rho_ice, IssmDouble rho_water);
+                                IssmDouble signorm, IssmDouble yts, IssmDouble h, IssmDouble s,
+                                IssmDouble rho_ice, IssmDouble rho_water, IssmDouble desfac, IssmDouble s0p);
 void ComputeDelta18oTemperaturePrecipitation(IssmDouble Delta18oSurfacePresent, IssmDouble Delta18oSurfaceLgm, IssmDouble Delta18oSurfaceTime,
                                      IssmDouble Delta18oPresent, IssmDouble Delta18oLgm, IssmDouble Delta18oTime,
 …
                                      IssmDouble* TemperaturesLgm, IssmDouble* TemperaturesPresentday,
                                              IssmDouble* monthlytemperaturesout, IssmDouble* monthlyprecout);
-void   GetVerticesCoordinates(IssmDouble* xyz,  Node** nodes, int numvertices);
-int    GetNumberOfDofs( Node** nodes,int numnodes,int setenum,int approximation_enum);
-int*   GetLocalDofList( Node** nodes,int numnodes,int setenum,int approximation_enum);
-int*   GetGlobalDofList(Node** nodes,int numnodes,int setenum,int approximation_enum);
-#ifdef _HAVE_DIAGNOSTIC_
-void   CoordinateSystemTransform(IssmDouble** ptransform,Node** nodes,int numnodes,int* cs_array);
-void   TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum);
-void   TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array);
-void   TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum);
-void   TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array);
-void   TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int cs_enum);
-void   TransformLoadVectorCoord(ElementVector* pe,Node** nodes,int numnodes,int* cs_array);
-void   TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int cs_enum);
-void   TransformSolutionCoord(IssmDouble* solution,Node** nodes,int numnodes,int* cs_array);
-#endif
 /*Print arrays*/

issm/trunk/src/c/shared/Exceptions/Exceptions.cpp

-              r13975
+              r15396
 #endif
+#include "../shared.h"
+#include "../../include/include.h"
+#include "./exceptions.h"
+#include "../io/Print/Print.h"
+#include "../io/Comm/Comm.h"
 ErrorException::ErrorException(const string &what_arg){/*{{{*/
 …
         if (function_name=="" || file_line==0){ //WINDOWS
                 _printString_("Error message: " << what());
+                _printf_("Error message: " << what());
+        }
         else{
                 if(num_procs==1){
                         _printLine_("\n??? Error in ==> " << file_name.c_str() << ":" << file_line);
                         _printLine_(function_name.c_str() << " error message: " << what() << "\n");
+                        _printf_("\n??? Error in ==> " << file_name.c_str() << ":" << file_line << "\n");
+                        _printf_(function_name.c_str() << " error message: " << what() << "\n\n");
+                }
                 else{
                         _printLine_("\n[" << my_rank<< "] ??? Error using ==> " << file_name.c_str() << ":" << file_line);
                         _printLine_(  "[" << my_rank << "] " << function_name.c_str() << " error message: " << what() << "\n");
+                        _printf_("\n[" << my_rank<< "] ??? Error using ==> " << file_name.c_str() << ":" << file_line << "\n");
+                        _printf_(  "[" << my_rank << "] " << function_name.c_str() << " error message: " << what() << "\n\n");
+                }
+        }

issm/trunk/src/c/shared/Exceptions/exceptions.h

-              r13975
+              r15396
  */
 #ifndef MY_EXCEPTIONS_H_
 #define MY_EXCEPTIONS_H_
+#ifndef _MY_EXCEPTIONS_H_
+#define _MY_EXCEPTIONS_H_
 #include <exception>
 #include <string>
+#include <iostream>
+#include <sstream>
+#include <iomanip>
 using namespace std;
+/*We derive our classes from the c++ exception class: */
+class ErrorException: public exception {
+#ifdef HAVE_CONFIG_H
+        #include <config.h>
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+/*macros: */
+/* _assert_ {{{*/
+/*Assertion macro: do nothing if macro _ISSM_DEBUG_ undefined*/
+#ifdef _ISSM_DEBUG_
+#define _assert_(statement)\
+  if (!(statement)) _error_("Assertion \""<<#statement<<"\" failed, please report bug to "<<PACKAGE_BUGREPORT)
+#else
+#define _assert_(ignore)\
+  ((void) 0)
+#endif
+/*}}}*/
+/* _error_ {{{*/
+/*new Error exception macro*/
+#ifdef _INTEL_WIN_
+#define _error_(StreamArgs)\
+   do{std::ostringstream aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy; \
+   aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy << StreamArgs << std::ends; \
+   throw ErrorException(aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy.str());}while(0)
+#else
+#define _error_(StreamArgs)\
+        do{std::ostringstream aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy; \
+   aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy << StreamArgs << std::ends; \
+   throw ErrorException(__FILE__,__func__,__LINE__,aLoNgAnDwEiRdLoCaLnAmeFoRtHiSmAcRoOnLy.str());}while(0)
+#endif
+/*}}}*/
+/* ExceptionTrapBegin/ExceptionTrapEnd {{{*/
+/*The following macros hide the error exception handling in a matlab module. Just put
+ * ExceptionTrapBegin(); and ExceptionTrapEnd(); at the beginning and end of a module, and c++ exceptions
+ * will be trapped. Really nifty!*/
+#define ExceptionTrapBegin(); \
+        try{
+#define ExceptionTrapEnd(); }\
+        catch(ErrorException &exception){\
+                exception.Report();\
+                return 0;\
+        }\
+        catch (exception& e) {\
+                _printf_("Standard exception: " << e.what() << "\n\n");\
+                return 0;\
+        }\
+        catch(...){\
+                _printf_("An unexpected error occurred \n\n");\
+                return 0;\
+        }
+/*}}}*/
+/*ISSM exception class: */
+class ErrorException: public exception { /*{{{*/
         string   what_str;
 …
 };
+/*}}}*/
 char* exprintf(const char* format,...);
 #endif

issm/trunk/src/c/shared/Exceptions/exprintf.cpp

-              r13975
+              r15396
 #include <stdarg.h>
 #include <stdio.h>
+#include "../Alloc/xNewDelete.h"
+#include "../Alloc/alloc.h"
+#include "../MemOps/MemOps.h"
 char* exprintf(const char* format,...){

issm/trunk/src/c/shared/Exp/exp.h

-              r14310
+              r15396
 #include <cstring>
 #include "../../classes/objects/Contour.h"
 #include "../../shared/Numerics/recast.h"
 #include "../../Container/Container.h"
+#include "../Numerics/recast.h"
+#include "../Exceptions/exceptions.h"
+#include "../MemOps/MemOps.h"
 int IsInPolySerial(double* in,double* xc,double* yc,int numvertices,double* x,double* y,int nods, int edgevalue);
 int ExpWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,char* domainname);
-int ExpWrite(DataSet* contours,char* domainname);
 int pnpoly(int npol, double *xp, double *yp, double x, double y, int edgevalue);
+/*IsInPoly {{{*/
+template <class doubletype>
+int IsInPoly(SeqVec<doubletype>* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue){
+template <class doubletype> int IsInPoly(doubletype* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue){ /*{{{*/
         int i;
 …
                 //Get current value of value[i] -> do not change it if != 0
                 in->GetValue(&value,i);
+                value=in[i];
                 if (reCast<bool,doubletype>(value)){
                         /*this vertex already is inside one of the contours, continue*/
 …
                         value=pnpoly(numvertices,xc,yc,x0,y0,edgevalue);
+                }
                 in->SetValue(i,value,INS_VAL);
+                in[i]=value;
+        }
          return 1;
 }/*}}}*/
+/*DomainOutlineRead{{{*/
+template <class doubletype>
+int DomainOutlineRead(int* pnprof,int** pprofnvertices,doubletype*** ppprofx,doubletype*** ppprofy,bool** pclosed,char* domainname){
+template <class doubletype> int ExpRead(int* pnprof,int** pprofnvertices,doubletype*** ppprofx,doubletype*** ppprofy,bool** pclosed,char* domainname){ /*{{{*/
         /*indexing: */
 …
         nprof=1;
         for(;;){
+                fscanf(fid,"%255s %255s\n",chardummy,chardummy);
+                fscanf(fid,"%255s %255s\n",chardummy,chardummy);
+                fscanf(fid,"%255s %255s %255s %255s\n",chardummy,chardummy,chardummy,chardummy);
+                fscanf(fid,"%20u %255s\n",&n,chardummy);
+                fscanf(fid,"%255s %255s %255s %255s %255s\n",chardummy,chardummy,chardummy,chardummy,chardummy);
+                for (i=0;i<n;i++) fscanf(fid,"%20lf %20lf\n",&ddummy,&ddummy);
+                //## Name:filename
+                if(fscanf(fid,"%255s %255s\n",chardummy,chardummy)!=2) _error_("Could not read " << domainname);
+                //## Icon:0
+                if(fscanf(fid,"%255s %255s\n",chardummy,chardummy)!=2) _error_("Could not read " << domainname);
+                //# Points Count Value
+                if(fscanf(fid,"%255s %255s %255s %255s\n",chardummy,chardummy,chardummy,chardummy)!=4) _error_("Could not read " << domainname);
+                if(fscanf(fid,"%20u %255s\n",&n,chardummy)!=2) _error_("Could not read number of points in "<<domainname);
+                //# X pos Y pos
+                if(fscanf(fid,"%255s %255s %255s %255s %255s\n",chardummy,chardummy,chardummy,chardummy,chardummy)!=5) _error_("Could not read " << domainname);
+                for (i=0;i<n;i++){
+                        if(fscanf(fid,"%20lf %20lf\n",&ddummy,&ddummy)!=2){
+                                _error_("Could not read coordinate of vertex "<< i <<" of "<<domainname);
+                        }
+                }
                 /*check whether we are at the end of the file, otherwise, keep reading next profile:*/
                 if (feof(fid)) break;
+                if(feof(fid)) break;
                 nprof++;
+        }
 …
                 /*Skip header: */
+                fscanf(fid,"%255s %255s\n",chardummy,chardummy);
+                fscanf(fid,"%255s %255s\n",chardummy,chardummy);
+                fscanf(fid,"%255s %255s %255s %255s\n",chardummy,chardummy,chardummy,chardummy);
+                //## Name:filename
+                if(fscanf(fid,"%255s %255s\n",chardummy,chardummy)!=2) _error_("Could not read " << domainname);
+                //## Icon:0
+                if(fscanf(fid,"%255s %255s\n",chardummy,chardummy)!=2) _error_("Could not read " << domainname);
+                //# Points Count Value
+                if(fscanf(fid,"%255s %255s %255s %255s\n",chardummy,chardummy,chardummy,chardummy)!=4) _error_("Could not read " << domainname);
                 /*Get number of profile vertices: */
                 fscanf(fid,"%20u %255s\n",&n,chardummy);
+                if(fscanf(fid,"%20u %255s\n",&n,chardummy)!=2) _error_("Could not read number of points in "<<domainname);
                 /*Skip next line: */
+                fscanf(fid,"%255s %255s %255s %255s %255s\n",chardummy,chardummy,chardummy,chardummy,chardummy);
+                //# X pos Y pos
+                if(fscanf(fid,"%255s %255s %255s %255s %255s\n",chardummy,chardummy,chardummy,chardummy,chardummy)!=5) _error_("Could not read " << domainname);
                 /*Allocate vertices: */
 …
                 /*Read vertices: */
                 for (i=0;i<n;i++){
+                        fscanf(fid,"%20lf %20lf\n",&x[i],&y[i]);
+                        if(fscanf(fid,"%20lf %20lf\n",&x[i],&y[i])!=2){
+                                _error_("Could not read coordinate of vertex "<<i<<" of "<<domainname);
+                        }
+                }
 …
         if(pclosed) *pclosed=closed;
         else         xDelete<bool>(closed);
+} /*}}}*/
+/*DataSet* DomainOutlineRead(char* domainname){{{*/
+template <class doubletype>
+DataSet* DomainOutlineRead(char* domainname){
+        return 1;
-        /*intermediary: */
-        int                  nprof;
-        int                 *profnvertices = NULL;
-        doubletype         **pprofx        = NULL;
-        doubletype         **pprofy        = NULL;
-        /*output: */
-        DataSet *domain = NULL;
-        /*If domainname is an empty string, return empty dataset*/
-        if (strcmp(domainname,"")==0){
-                nprof=0;
+        }
-        else{
-                DomainOutlineRead(&nprof,&profnvertices,&pprofx, &pprofy, NULL,domainname);
+        }
-        /*now create dataset of contours: */
-        domain=new DataSet(0);
-        for(int i=0;i<nprof;i++){
-                domain->AddObject(new Contour<doubletype>(i,profnvertices[i],pprofx[i],pprofy[i],1));
+        }
-        return domain;
 } /*}}}*/

issm/trunk/src/c/shared/Matrix/MatrixUtils.cpp

-              r13395
+              r15396
 /*Headers*/
 /*{{{*/
-#include "./matrix.h"
-#include "../Exceptions/exceptions.h"
-#include "../Alloc/alloc.h"
 #include <stdio.h>
 #include <sys/types.h>
 #include <math.h>
 #include <float.h>    /*  DBL_EPSILON  */
+#include "../../include/include.h"
+#include "../../io/io.h"
+#include "./matrix.h"
+#include "../Exceptions/exceptions.h"
+#include "../MemOps/MemOps.h"
 /*}}}*/
 …
                 pindx[ipiv]++;
+                //              _printf_(true,"pivot for i=%d: irow=%d, icol=%d, pindx[%d]=%d\n",
+                //                               i,irow,icol,ipiv,pindx[ipiv]);
+                //              _printf_("pivot for i=" << i << ": irow=" << irow << ", icol=" << icol  << ", pindx[" << ipiv << "]=" << pindx[ipiv] << "\n\n");
                 /*  switch rows to put pivot element on diagonal, noting that the
 …
                 if (irow != icol) {
+                        //                      _printf_(true,"row switch for i=%d: irow=%d, icol=%d\n",
+                        //                                       i,irow,icol);
+                        //                      _printf_("row switch for i=" << i << ": irow=" << irow << ", icol=" << icol << "\n\n");
                         ipt=irow*ndim;
 …
                         icol=pivrc2[j];
+                        //                      _printf_(true,"column switch back for j=%d: irow=%d, icol=%d\n",
+                        //                                       j,irow,icol);
+                        //                      _printf_("column switch back for j=" << j << ": irow=" << irow << ", icol=" << icol << "\n\n");
                         ipt=0;

issm/trunk/src/c/shared/Matrix/matrix.h

r12706	r15396
6	6	#define _MATRIXUTILS_H_
7	7
8		#include "../~~../include/include~~.h"
	8	#include "../Numerics/types.h"
9	9
10	10	int TripleMultiply( IssmDouble* a, int nrowa, int ncola, int itrna, IssmDouble* b, int nrowb, int ncolb, int itrnb, IssmDouble* c, int nrowc, int ncolc, int itrnc, IssmDouble* d, int iaddd);

issm/trunk/src/c/shared/Numerics/BrentSearch.cpp

-              r13975
+              r15396
 #endif
-#include "./numerics.h"
-#include "../../classes/objects/objects.h"
-#include "../../include/include.h"
-#include "../../io/io.h"
-#include "../../shared/shared.h"
 #include <float.h>
 #include <iomanip>
+#include "../Exceptions/exceptions.h"
+#include "../io/io.h"
+#include "../MemOps/MemOps.h"
+#include "./Verbosity.h"
+#include "./OptPars.h"
+#include "./OptArgs.h"
+#include "./types.h"
+#include "./isnan.h"
 void BrentSearch(IssmDouble* psearch_scalar,IssmDouble* pJ,OptPars* optpars,IssmDouble (*f)(IssmDouble,OptArgs*), OptArgs* optargs){
 …
         if (xIsNan<IssmDouble>(fxmin)) _error_("Function evaluation returned NaN");
         cout<<setprecision(5);
         if(VerboseControl()) _pprintLine_("");
         if(VerboseControl()) _pprintLine_("       Iteration         x           f(x)       Tolerance         Procedure");
         if(VerboseControl()) _pprintLine_("");
         if(VerboseControl()) _pprintLine_("           N/A    "<<setw(12)<<xmin<<"  "<<setw(12)<<fxmin<<"           N/A         boundary");
+        if(VerboseControl()) _printf0_("\n");
+        if(VerboseControl()) _printf0_("       Iteration         x           f(x)       Tolerance         Procedure\n");
+        if(VerboseControl()) _printf0_("\n");
+        if(VerboseControl()) _printf0_("           N/A    "<<setw(12)<<xmin<<"  "<<setw(12)<<fxmin<<"           N/A         boundary\n");
         fxmax = (*f)(xmax,optargs);
         if (xIsNan<IssmDouble>(fxmax)) _error_("Function evaluation returned NaN");
         if(VerboseControl()) _pprintLine_("           N/A    "<<setw(12)<<xmax<<"  "<<setw(12)<<fxmax<<"           N/A         boundary");
+        if(VerboseControl()) _printf0_("           N/A    "<<setw(12)<<xmax<<"  "<<setw(12)<<fxmax<<"           N/A         boundary\n");
         /*test if jump option activated and xmin==0*/
 …
         /*4: print result*/
         if(VerboseControl())
          _pprintLine_("         "<<setw(5)<<iter<<"    "<<setw(12)<<xbest<<"  "<<setw(12)<<fxbest<<"  "<<setw(12)<<pow(pow(xbest-xm,2),0.5)<<"         initial");
+         _printf0_("         "<<setw(5)<<iter<<"    "<<setw(12)<<xbest<<"  "<<setw(12)<<fxbest<<"  "<<setw(12)<<pow(pow(xbest-xm,2),0.5)<<"         initial\n");
         if (!xIsNan<IssmDouble>(cm_jump) && (xmin==0) && ((fxbest/fxmin)<cm_jump)){
                 if(VerboseControl()) _pprintLine_("      optimization terminated: current x satisfies criteria 'cm_jump'=" << cm_jump);
+                if(VerboseControl()) _printf0_("      optimization terminated: current x satisfies criteria 'cm_jump'=" << cm_jump << "\n");
                 loop=false;
+        }
 …
                 tol2=2.0*tol1;
                 if(VerboseControl())
                  _pprintLine_("         "<<setw(5)<<iter<<"    "<<setw(12)<<x<<"  "<<setw(12)<<fx<<"  "<<setw(12)<<pow(pow(xbest-xm,2),0.5)<<
                                          "         "<<(goldenflag?"golden":"parabolic"));
+                 _printf0_("         "<<setw(5)<<iter<<"    "<<setw(12)<<x<<"  "<<setw(12)<<fx<<"  "<<setw(12)<<pow(pow(xbest-xm,2),0.5)<<
+                                         "         "<<(goldenflag?"golden":"parabolic")<<"\n");
                 /*Stop the optimization?*/
                 if (sqrt(pow(xbest-xm,2)) < (tol2-0.5*(xmax-xmin))){
                         if(VerboseControl()) _pprintLine_("      optimization terminated: current x satisfies criteria 'tolx'=" << tolerance);
+                        if(VerboseControl()) _printf0_("      optimization terminated: current x satisfies criteria 'tolx'=" << tolerance << "\n");
                         loop=false;
+                }
                 else if (iter>=maxiter){
                         if(VerboseControl()) _pprintLine_("      exiting: Maximum number of iterations has been exceeded  ('maxiter'=" << maxiter << ")");
+                        if(VerboseControl()) _printf0_("      exiting: Maximum number of iterations has been exceeded  ('maxiter'=" << maxiter << ")\n");
                         loop=false;
+                }
                 else if (!xIsNan<IssmDouble>(cm_jump) && (xmin==0) && ((fxbest/fxmin)<cm_jump)){
                         if(VerboseControl()) _pprintLine_("      optimization terminated: current x satisfies criteria 'cm_jump'=" << cm_jump);
+                        if(VerboseControl()) _printf0_("      optimization terminated: current x satisfies criteria 'cm_jump'=" << cm_jump << "\n");
                         loop=false;
+                }

issm/trunk/src/c/shared/Numerics/CMakeLists.txt

-              r14310
+              r15396
                $ENV{ISSM_DIR}/src/c/shared/Numerics/extrema.cpp
            $ENV{ISSM_DIR}/src/c/shared/Numerics/GaussPoints.cpp
-      $ENV{ISSM_DIR}/src/c/shared/Numerics/IsInputConverged.cpp
                  $ENV{ISSM_DIR}/src/c/shared/Numerics/isnan.cpp
    $ENV{ISSM_DIR}/src/c/shared/Numerics/OptionsFromAnalysis.cpp
-        $ENV{ISSM_DIR}/src/c/shared/Numerics/UnitConversion.cpp
              $ENV{ISSM_DIR}/src/c/shared/Numerics/Verbosity.cpp
 $ENV{ISSM_DIR}/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp PARENT_SCOPE)

issm/trunk/src/c/shared/Numerics/GaussPoints.cpp

-              r13395
+              r15396
 /*  Gauss point structures and prototypes  */
-#include "../../include/include.h"
-#include "./GaussPoints.h"
-#include "../Alloc/alloc.h"
-#include "../Exceptions/exceptions.h"
 #include <math.h>
 #include <float.h>
+#include "./GaussPoints.h"
+#include "../MemOps/MemOps.h"
+#include "../Exceptions/exceptions.h"
+#include "../Numerics/constants.h"
 /*General Gauss points*/
 …
                 sizeof(wgt4 )/sizeof(IssmPDouble)};
         //      _pprintLine_("Gauss-Legendre recurrence coefficients ngaus=" << ngaus);
+        //      _printf0_("Gauss-Legendre recurrence coefficients ngaus=" << ngaus << "\n");
         *pxgaus =xNew<IssmPDouble>(ngaus);
         *pxwgt  =xNew<IssmPDouble>(ngaus);
 …
 }/*}}}*/
 /*FUNCTION GaussLegendreTria{{{*/
 void GaussLegendreTria( int* pngaus, IssmPDouble** pl1, IssmPDouble** pl2, IssmPDouble** pl3, IssmPDouble** pwgt, int iord ) {
+void GaussLegendreTria( int* pngaus, IssmDouble** pl1, IssmDouble** pl2, IssmDouble** pl3, IssmDouble** pwgt, int iord ) {
         /*Gauss quadrature points for the triangle.
 …
 .116251915907597, 0.025734050548330, 0.025734050548330};
         /*}}}*/
         /*  p=13, npoint=37  {{{*/
+        /*p=13, npoint=37  {{{*/
         static IssmPDouble wgt13[]={
 .090968907790622, 0.019537784619314, 0.019537784619314,
 …
 .014663182224828};
         /*}}}*/
         /*  p=18, npoint=70  {{{*/
+        /*p=18, npoint=70  {{{*/
         static IssmPDouble wgt18[]={
 …
                 sizeof(wgt20)/sizeof(IssmPDouble)};
         //      _pprintLine_("GaussLegendreTria: iord=" << iord);
+        //      _printf0_("GaussLegendreTria: iord=" << iord << "\n");
         /*  check to see if Gauss points need to be calculated  */
 …
                 *pngaus=np[iord-1];
                 *pl1  =xNew<IssmPDouble>(*pngaus);
                 *pl2  =xNew<IssmPDouble>(*pngaus);
                 *pl3  =xNew<IssmPDouble>(*pngaus);
                 *pwgt =xNew<IssmPDouble>(*pngaus);
+                *pl1  =xNew<IssmDouble>(*pngaus);
+                *pl2  =xNew<IssmDouble>(*pngaus);
+                *pl3  =xNew<IssmDouble>(*pngaus);
+                *pwgt =xNew<IssmDouble>(*pngaus);
                 for (i=0; i<*pngaus; i++) {
 …
                 *pngaus=nigaus*nigaus;
                 *pl1  =xNew<IssmPDouble>(*pngaus);
                 *pl2  =xNew<IssmPDouble>(*pngaus);
                 *pl3  =xNew<IssmPDouble>(*pngaus);
                 *pwgt =xNew<IssmPDouble>(*pngaus);
+                *pl1  =xNew<IssmDouble>(*pngaus);
+                *pl2  =xNew<IssmDouble>(*pngaus);
+                *pl3  =xNew<IssmDouble>(*pngaus);
+                *pwgt =xNew<IssmDouble>(*pngaus);
                 /*  get the gauss points in each direction  */
 …
+        }
         //      _pprintLine_("GaussLegendreTria - ngaus=" << *pngaus);
+        //      _printf0_("GaussLegendreTria - ngaus=" << *pngaus << "\n");
         //      for (i=0; i<*pngaus; i++)
+        //              _printf_(true,"i=%d: l1gaus=%f,l2gaus=%f,l3gaus=%f,wgt=%f\n",
+        //                               i,(*pl1 )[i],(*pl2 )[i],(*pl3 )[i],(*pwgt)[i]);
+        //              _printf0_("i=" << i << ": l1gaus=" << (*pl1 )[i] << ",l2gaus=" << (*pl2 )[i] << ",l3gaus=" << (*pl3 )[i]<< ",wgt=" << (*pwgt)[i]<< "\n\n");
         return;
 …
                 sizeof(wgt6 )/sizeof(IssmPDouble)};
         //      _pprintLine_("GaussLegendreTetra: iord=" << iord);
+        //      _printf0_("GaussLegendreTetra: iord=" << iord << "\n");
         /*  check to see if Gauss points need to be calculated  */
 …
                 sizeof(wgt5 )/sizeof(IssmPDouble)};
         //      _pprintLine_("Gauss-Lobatto recurrence coefficients ngaus=" << ngaus);
+        //      _printf0_("Gauss-Lobatto recurrence coefficients ngaus=" << ngaus << "\n");
         *pxgaus =xNew<IssmPDouble>(ngaus);
         *pxwgt  =xNew<IssmPDouble>(ngaus);

issm/trunk/src/c/shared/Numerics/GaussPoints.h

-              r12706
+              r15396
  */
 #include "../../include/types.h"
+#include "../../shared/Numerics/types.h"
 #ifndef _GAUSSPOINTS_H
 #define _GAUSSPOINTS_H
 …
 void GaussLegendreLinear(IssmPDouble** pxgaus, IssmPDouble** pxwgt, int ngaus);
 #define MAX_TRIA_SYM_ORD    20
 void GaussLegendreTria(int* pngaus, IssmPDouble** pl1, IssmPDouble** pl2, IssmPDouble** pl3, IssmPDouble** pwgt, int iord);
+void GaussLegendreTria(int* pngaus, IssmDouble** pl1, IssmDouble** pl2, IssmDouble** pl3, IssmDouble** pwgt, int iord);
 #define MAX_TETRA_SYM_ORD    6
 void GaussLegendreTetra(int* pngaus, IssmPDouble** pl1, IssmPDouble** pl2, IssmPDouble** pl3, IssmPDouble** pl4, IssmPDouble** pwgt, int iord);

issm/trunk/src/c/shared/Numerics/OptimalSearch.cpp

-              r13975
+              r15396
 #endif
-#include "./numerics.h"
-#include "../../classes/objects/objects.h"
-#include "../../io/io.h"
-#include "../../include/include.h"
-#include "../../shared/shared.h"
 #include <float.h>
+#include "../Exceptions/exceptions.h"
+#include "../io/io.h"
+#include "../MemOps/MemOps.h"
+#include "./Verbosity.h"
+#include "./OptPars.h"
+#include "./OptArgs.h"
+#include "./types.h"
+#include "./isnan.h"
 void OptimalSearch(IssmDouble* psearch_scalar,IssmDouble* pJ,OptPars* optpars,IssmDouble (*f)(IssmDouble,OptArgs*), OptArgs* optargs){
 …
         if (xIsNan<IssmDouble>(fx1)) _error_("Function evaluation returned NaN");
         cout<<setprecision(5);
         if(VerboseControl()) _pprintLine_("");
         if(VerboseControl()) _pprintLine_("       Iteration         x           f(x)       Tolerance");
         if(VerboseControl()) _pprintLine_("");
         if(VerboseControl()) _pprintLine_("           N/A    "<<setw(12)<<x1<<"  "<<setw(12)<<fx1<<"           N/A");
+        if(VerboseControl()) _printf0_("\n");
+        if(VerboseControl()) _printf0_("       Iteration         x           f(x)       Tolerance\n");
+        if(VerboseControl()) _printf0_("\n");
+        if(VerboseControl()) _printf0_("           N/A    "<<setw(12)<<x1<<"  "<<setw(12)<<fx1<<"           N/A\n");
         //update tolerances
 …
                 if (xIsNan<IssmDouble>(fx2)) _error_("Function evaluation returned NaN");
                 if(VerboseControl())
                  _pprintLine_("         "<<setw(5)<<iter<<"    "<<setw(12)<<x2<<"  "<<setw(12)<<fx2<<"  "<<(fabs(x2-x1)>fabs(fx2-fx1)?fabs(fx2-fx1):fabs(x2-x1)));
+                 _printf0_("         "<<setw(5)<<iter<<"    "<<setw(12)<<x2<<"  "<<setw(12)<<fx2<<"  "<<(fabs(x2-x1)>fabs(fx2-fx1)?fabs(fx2-fx1):fabs(x2-x1)) << "\n");
                 //Stop the optimization?
                 if ((fabs(x2-x1)+seps)<tolerance || (fabs(fx2-fx1)+seps)<tolerance){
                         if(VerboseControl()) _pprintLine_("      " << "optimization terminated: the current x satisfies the termination criteria using 'tolx' of "  << tolerance);
+                        if(VerboseControl()) _printf0_("      " << "optimization terminated: the current x satisfies the termination criteria using 'tolx' of "  << tolerance << "\n");
                         loop=false;
+                }
                 else if (iter>=maxiter){
                         if(VerboseControl()) _pprintLine_("      " << "exiting: Maximum number of iterations has been exceeded  - increase 'maxiter'");
+                        if(VerboseControl()) _printf0_("      " << "exiting: Maximum number of iterations has been exceeded  - increase 'maxiter'\n");
                         loop=false;
+                }

issm/trunk/src/c/shared/Numerics/Synchronize.sh

r13975	r15396
27	27	#endif
28	28	#include "./Verbosity.h"
29		~~#include "../../include/macros.h"~~
30	29	#include "../Exceptions/exceptions.h"
31	30	/}}}/

issm/trunk/src/c/shared/Numerics/Verbosity.cpp

r13975	r15396
16	16	#endif
17	17	#include "./Verbosity.h"
18		~~#include "../../include/macros.h"~~
19	18	#include "../Exceptions/exceptions.h"
20	19	/}}}/

issm/trunk/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp

-              r13975
+              r15396
+#include "../Alloc/alloc.h"
+#include "../../include/include.h"
+#include <math.h>
+#include "../MemOps/MemOps.h"
 #include "../Exceptions/exceptions.h"
+#include "../Numerics/types.h"
 #include "./isnan.h"
-#include <math.h>
 void XZvectorsToCoordinateSystem(IssmDouble* T,IssmDouble* xzvectors){

issm/trunk/src/c/shared/Numerics/cross.cpp

r13975	r15396
9	9	#endif
10	10
11		#include ".~~./../include/include~~.h"
	11	#include "./types.h"
12	12
13	13	void cross(IssmDouble* result,IssmDouble* vector1,IssmDouble* vector2){

issm/trunk/src/c/shared/Numerics/cubic.cpp

r13395	r15396
1	1	#include <math.h>
	2
2	3	#include "./numerics.h"
3	4

issm/trunk/src/c/shared/Numerics/extrema.cpp

-              r12706
+              r15396
 #endif
 #include "../../include/include.h"
+#include "./types.h"
 IssmDouble min(IssmDouble a,IssmDouble b){
 …
         else return b;
+}
+#ifdef _HAVE_ADOLC_
+IssmPDouble  min(IssmPDouble a,IssmPDouble b){
+        if (a<b)return a;
+        else return b;
+}
+IssmPDouble  max(IssmPDouble a,IssmPDouble b){
+        if (a>b)return a;
+        else return b;
+}
+#endif

issm/trunk/src/c/shared/Numerics/isnan.cpp

r13975	r15396
7	7	#endif
8	8
9		~~#include "../../include/include.h"~~
10	9	#include "isnan.h"
11	10

issm/trunk/src/c/shared/Numerics/isnan.h

r13975	r15396
24	24
25	25	#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_)
	26	#include "./types.h"
26	27	template <> int xIsNan<adouble> (const adouble& X);
27	28	#endif

issm/trunk/src/c/shared/Numerics/numerics.h

-              r13395
+              r15396
 #define  _NUMERICS_H_
+#ifdef HAVE_CONFIG_H
+        #include <config.h>
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
 #include "./Verbosity.h"
 #include "./GaussPoints.h"
 #include "./isnan.h"
 #include "./recast.h"
+class Input;
+class Parameters;
+struct OptArgs;
+struct OptPars;
+#include "./types.h"
+#include "./constants.h"
+#include "./OptArgs.h"
+#include "./OptPars.h"
 IssmDouble  min(IssmDouble a,IssmDouble b);
 IssmDouble  max(IssmDouble a,IssmDouble b);
+#ifdef _HAVE_ADOLC_
+IssmPDouble  min(IssmPDouble a,IssmPDouble b);
+IssmPDouble  max(IssmPDouble a,IssmPDouble b);
+#endif
 int         min(int a,int b);
 int         max(int a,int b);
 …
 void        OptimalSearch(IssmDouble *psearch_scalar,IssmDouble*pJ,OptPars*optpars,IssmDouble (*f)(IssmDouble,OptArgs*), OptArgs*optargs);
 void        cross(IssmDouble *result,IssmDouble*vector1,IssmDouble*vector2);
-void        IsInputConverged(IssmDouble *peps, Input**new_inputs,Input**old_inputs,int num_inputs,int criterion_enum);
-void        UnitConversion(IssmDouble *values, int numvalues,int direction_enum, int type_enum);
-IssmDouble  UnitConversion(IssmDouble value, int direction_enum, int type_enum);
-char       *OptionsFromAnalysis(Parameters *parameters,int analysis_type);
 void        XZvectorsToCoordinateSystem(IssmDouble *T,IssmDouble*xzvectors);
 int         cubic(IssmDouble a, IssmDouble b, IssmDouble c, IssmDouble d, double X[3], int *num);
-#ifdef _HAVE_PETSC_
-void   PetscOptionsFromAnalysis(Parameters* parameters,int analysis_type);
-#endif
 #endif //ifndef _NUMERICS_H_

issm/trunk/src/c/shared/Numerics/recast.h

-              r13975
+              r15396
 #if !defined(_HAVE_ADOLC_) || defined(_WRAPPERS_)
+template<class To, class From>
+To reCast(const From& from) {
+template<class To, class From> To reCast(const From& from) {
     return (To)from;
+}
 #else
+#include "./types.h"
+template<class To, class From>
+struct ForPartialSpecialization {
+template<class To, class From> struct ForPartialSpecialization {
     static  To reCast(const From& from ) { return (To) from;}
 };
+template<class To, class From>
+To reCast(const From& from) {
+template<class To, class From> To reCast(const From& from) {
     return ForPartialSpecialization<To,From>::reCast(from);
+}
 …
  * partial specialization
  */
+template<class To>
+struct ForPartialSpecialization<To,adouble> {
+template<class To> struct ForPartialSpecialization<To,adouble> {
     static  To reCast(const adouble& from ) { return (To) (from.getValue());}
 };

issm/trunk/src/c/shared/Sorting/binary_search.cpp

-              r13975
+              r15396
 #endif
+#include "../Exceptions/exceptions.h"
 #include <stdio.h>
 …
         int *end = NULL;
         int *mid = NULL;
+        _assert_(sorted_integers);
         // point to beginning and end of the array

issm/trunk/src/c/shared/String/DescriptorIndex.cpp

-              r13975
+              r15396
 #include <string.h>
 #include <ctype.h>
+#include "../shared.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../Enum/Enum.h"
+#include "../io/io.h"
+#include "../Exceptions/exceptions.h"
 int  DescriptorIndex(char* root, int* pindex,char* descriptor){ //We assume root has already been allocated, and we just have to copy into it.

issm/trunk/src/c/shared/String/sharedstring.h

r13975	r15396
12	12	#endif
13	13
	14	void ApiPrintf(const char* string);
	15
14	16	#endif //ifndef _SHAREDSTRING_H_

issm/trunk/src/c/shared/Threads/LaunchThread.cpp

-              r14067
+              r15396
 #include "./issm_threads.h"
 #include "../Alloc/xNewDelete.h"
+#include "../MemOps/MemOps.h"
 #include "../Exceptions/exceptions.h"
-#include "../../include/include.h"
 void LaunchThread(void* function(void*), void* gate,int num_threads){

issm/trunk/src/c/shared/TriMesh/SplitMeshForRifts.cpp

-              r14310
+              r15396
  */
 #include "./trimesh.h"
+#include "../Alloc/xNewDelete.h"
+#include "../Alloc/alloc.h"
+#include "../MemOps/MemOps.h"
 int SplitMeshForRifts(int* pnel,int** pindex,int* pnods,double** px,double** py,int* pnsegs,int** psegments,int** psegmentmarkerlist){

issm/trunk/src/c/shared/TriMesh/TriMeshUtils.cpp

-              r14310
+              r15396
 #include "./trimesh.h"
 #include "../Exceptions/exceptions.h"
+#include "../Alloc/xNewDelete.h"
+#include "../Alloc/alloc.h"
+#include "../../include/include.h"
+#include "../MemOps/MemOps.h"
 #define RIFTPENALTYPAIRSWIDTH 8

issm/trunk/src/c/shared/shared.h

-              r13975
+              r15396
 #define _SHARED_H_
+#include "./Alloc/alloc.h"
+#include "./Alloc/xNewDelete.h"
+#include "./MemOps/MemOps.h"
 #include "./Bamg/shared.h"
 #include "./Elements/elements.h"
+#include "./Enum/Enum.h"
 #include "./Exceptions/exceptions.h"
+#include "./io/io.h"
 #include "./Exp/exp.h"
 #include "./Matrix/matrix.h"
-#include "./MemOps/xMemCpy.h"
 #include "./Numerics/numerics.h"
 #include "./Sorting/sorting.h"
 …
 #include "./Threads/issm_threads.h"
 #include "./TriMesh/trimesh.h"
+#include "./LatLong/latlong.h"
 #endif

issm/trunk/src/c/toolkits/issm/issmtoolkit.h

-              r13395
+              r15396
 #define _ISSM_TOOLKIT_H_
+#include "./SeqMat.h"
+#include "./SeqVec.h"
+#ifdef HAVE_CONFIG_H
+        #include <config.h>
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+#include "./IssmAbsMat.h"
+#include "./IssmAbsVec.h"
+#include "./IssmDenseMat.h"
+#include "./IssmMat.h"
+#include "./IssmSeqVec.h"
+#include "./IssmVec.h"
+#include "./IssmSolver.h"
+#ifdef _HAVE_MPI_
+#include "./IssmMpiDenseMat.h"
+#include "./IssmMpiVec.h"
+#endif
 #endif

issm/trunk/src/c/toolkits/mpi/mpiincludes.h

-              r13975
+              r15396
 #define _MPI_INCLUDES_H_
+#ifdef HAVE_CONFIG_H
+        #include <config.h>
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+#ifdef _HAVE_MPI_
 /*MPI includes: */
 #include <mpi.h>
 …
 /*Patches: */
 #include "./patches/mpipatches.h"
+#endif
 #endif

issm/trunk/src/c/toolkits/mpi/patches/DetermineLocalSize.cpp

-              r13975
+              r15396
 #include <math.h>
 #include "../../../shared/shared.h"
-#include "../../../include/types.h"
 int DetermineLocalSize(int global_size,COMM comm){
 …
         MPI_Comm_rank(comm,&my_rank);
         MPI_Comm_size(comm,&num_procs);
+        /* TODO replace the following with ->
+        local_size=global_size/num_procs; // integer division
+        if (global_size%num_procs>my_rank) local_size++; // distribute the remainder
+        return local_size;
+        <- to here  */
         /*We are  not bound by any library, just use what seems most logical*/

issm/trunk/src/c/toolkits/mpi/patches/mpipatches.h

-              r13975
+              r15396
 #define MPI_PATCHES_H_
+#include "../../../include/types.h"
+#include "../../../shared/Numerics/types.h"
+#include "../../../shared/io/Comm/Comm.h"
 int DetermineLocalSize(int global_size,COMM comm);
+int* DetermineRowRankFromLocalSize(int global_size,int localsize,COMM comm);
+void GetOwnershipBoundariesFromRange(int* plower_row,int* pupper_row,int range,COMM comm);
+int DetermineGlobalSize(int local_size,COMM comm);
 #endif

issm/trunk/src/c/toolkits/petsc/objects/PetscMat.cpp

-              r13975
+              r15396
         MatInfo info;
         MatGetInfo(this->matrix,MAT_GLOBAL_SUM,&info);
+        _pprintLine_("=========================== Stiffness matrix allocation info ===========================");
+        _pprintLine_("");
+        _pprintLine_(" nz_allocated: "<<info.nz_allocated);
+        _pprintLine_(" nz_used     : "<<info.nz_used);
+        _pprintLine_(" nz_unneeded : "<<info.nz_unneeded<<" ("<<double(info.nz_unneeded)/double(info.nz_allocated)*100.<<"%)");
+        _pprintLine_("");
+        _pprintLine_("========================================================================================");
+        _printf0_("=========================== Stiffness matrix allocation info ===========================\n");
+        _printf0_("\n");
+   _printf0_(" Block size  : "<<info.block_size << "\n");
+        _printf0_(" nz_allocated: "<<info.nz_allocated << "\n");
+        _printf0_(" nz_used     : "<<info.nz_used << "\n");
+        _printf0_(" nz_unneeded : "<<info.nz_unneeded<<" ("<<double(info.nz_unneeded)/double(info.nz_allocated)*100.<<"%)\n");
+        _printf0_("\n");
+        _printf0_("========================================================================================\n");
+}
 /*}}}*/
 …
 void PetscMat::SetValues(int m,int* idxm,int n,int* idxn,IssmDouble* values,InsMode mode){
+        MatSetValues(this->matrix,m,idxm,n,idxn,values,ISSMToPetscInsertMode(mode));
+        PetscErrorCode ierr;
+        ierr = MatSetValues(this->matrix,m,idxm,n,idxn,values,ISSMToPetscInsertMode(mode));
+        if(ierr) _error_("PETSC's MatSetValues reported an error");
+}

issm/trunk/src/c/toolkits/petsc/objects/PetscMat.h

r13975	r15396
17	17
18	18	#include "../petscincludes.h"
19		#include "../../../~~include/include~~.h"
	19	#include "../../../shared/Numerics/types.h"
20	20
21	21	/}}}/

issm/trunk/src/c/toolkits/petsc/objects/PetscVec.h

r13975	r15396
17	17
18	18	#include "../petscincludes.h"
19		~~#include "../../../include/include.h"~~
20	19
21	20	/}}}/

issm/trunk/src/c/toolkits/petsc/objects/petscobjects.h

r13395	r15396
8	8	#include "./PetscMat.h"
9	9	#include "./PetscVec.h"
	10	#include "./PetscSolver.h"
10	11
11	12	#endif

issm/trunk/src/c/toolkits/petsc/patches/ISSMToPetscMatrixType.cpp

r13975	r15396
18	18	#include "../../../shared/shared.h"
19	19
20		~~const~~ MatType ISSMToPetscMatrixType(MatrixType type){
	20	MatType ISSMToPetscMatrixType(MatrixType type){
21	21
22	22	switch(type){

issm/trunk/src/c/toolkits/petsc/patches/NewMat.cpp

-              r13975
+              r15396
 #include "../../../shared/shared.h"
-#include "../../../include/include.h"
 #include "../../mpi/patches/mpipatches.h"
 …
         #if _PETSC_MAJOR_ >= 3
         #ifdef _HAVE_PETSCDEV_
+        #if defined(_HAVE_PETSCDEV_) || _PETSC_MINOR_ >=4
         MatType type;
         #else

issm/trunk/src/c/toolkits/petsc/patches/PetscOptionsDetermineSolverType.cpp

r13975	r15396
17	17
18	18	#include "../../../shared/shared.h"
19		~~#include "../../../include/include.h"~~
20	19
21	20	void PetscOptionsDetermineSolverType(int* psolver_type){

issm/trunk/src/c/toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp

r13975	r15396
17	17
18	18	#include "../../../shared/shared.h"
19		~~#include "../../../include/include.h"~~
20	19
21	20	void PetscOptionsInsertMultipleString(char* options_string){

issm/trunk/src/c/toolkits/petsc/patches/VecMerge.cpp

r13975	r15396
17	17
18	18	#include "../../../shared/shared.h"
19		~~#include "../../../include/include.h"~~
20	19
21	20	void VecMerge(Vec A, Vec B, double* row_partition_vector,int row_partition_size){

issm/trunk/src/c/toolkits/petsc/patches/petscpatches.h

-              r13975
+              r15396
 #include "./SolverEnum.h"
 #include "../../toolkitsenums.h"
 #include "../../../include/types.h"
+#include "../../../shared/io/Comm/Comm.h"
 class Parameters;
 …
 InsertMode ISSMToPetscInsertMode(InsMode mode);
 NormType ISSMToPetscNormMode(NormMode mode);
 const MatType ISSMToPetscMatrixType(MatrixType type);
+MatType ISSMToPetscMatrixType(MatrixType type);
 void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat matrix);

issm/trunk/src/c/toolkits/plapack/patches/PlapackInvertMatrix.cpp

r13975	r15396
2	2	* \brief invert petsc matrix using Plapack
3	3	*/
4		~~#include "../../../include/include.h"~~
5	4
6	5	/* petsc: */

issm/trunk/src/c/toolkits/toolkits.h

-              r13975
+              r15396
 #endif
+#ifdef _HAVE_GSL_
+#include "./gsl/gslincludes.h"
+#endif
+#ifdef _HAVE_ADOLC_
+#include "./adolc/adolcincludes.h"
+#endif
+#ifdef _HAVE_TRIANGLE_
 #include "./triangle/triangleincludes.h"
+#endif
+#include "./objects/toolkitobjects.h"
 #include "./toolkitsenums.h"
 #include "./issm/issmtoolkit.h"
+#include "./ToolkitOptions.h"
 #endif

issm/trunk/src/c/toolkits/toolkitsenums.h

r11995	r15396
13	13
14	14	typedef enum {INS_VAL, ADD_VAL} InsMode;
15		typedef enum {NORM_INF,NORM_TWO} NormMode;
	15	typedef enum {NORM_INF,NORM_TWO,NORM_FROB} NormMode;
16	16	typedef enum {DENSE_SEQUENTIAL,SPARSE_SEQUENTIAL} MatrixType;
17	17

issm/trunk/src/dox/issm.dox

-              r14067
+              r15396
 /**
   \mainpage ISSM C/C++ Source Code Browser
 …
   These pages were automatically generated by <a href="http://www.doxygen.org/">doxygen</a>,
   from comments in the ISSM source code.
+  from the ISSM source code.
   Navigate the tabs above and browse through ISSM's
 …
   <B> Helpful Links </B>
   - Fill out an ISSM download request <a href="http://issm.jpl.nasa.gov/installation/download/">here</a>.
+  - Download ISSM <a href="http://issm.jpl.nasa.gov/download/">here</a>.
+  - ISSM Installation instructions are found <a href="http://issm.jpl.nasa.gov/installation/installation/">here</a>.
+  - ISSM Installation instructions for Linux/Mac OSX are found <a href="http://issm.jpl.nasa.gov/download/unix/">here</a>.
+  - ISSM Installation instructions for Windows are found <a href="http://issm.jpl.nasa.gov/download/windows/">here</a>.
   - For help using ISSM, see our online <a href="http://issm.jpl.nasa.gov/doc_html/usersmanual.html">User's Manual</a>.
+  - For help using ISSM, see our online <a href="http://issm.jpl.nasa.gov/documentation/">Documentation</a>.
   Other documentation is also available including simple tutorials
   and FAQ.
 …
 </th>
 <tr>
 <th  bgcolor=#FFFFFF style="text-align:left;"> C++ </th><td  bgcolor=#FFFFFF style="text-align:right;">469</td><td  bgcolor=#FFFFFF style="text-align:right;">14087</td><td  bgcolor=#FFFFFF style="text-align:right;">16669</td><td  bgcolor=#FFFFFF style="text-align:right;">56706</td><td  bgcolor=#FFFFFF style="text-align:right;">87462</td>
+<th  bgcolor=#FFFFFF style="text-align:left;"> C++ </th><td  bgcolor=#FFFFFF style="text-align:right;">469</td><td  bgcolor=#FFFFFF style="text-align:right;">14505</td><td  bgcolor=#FFFFFF style="text-align:right;">16993</td><td  bgcolor=#FFFFFF style="text-align:right;">58467</td><td  bgcolor=#FFFFFF style="text-align:right;">89965</td>
 </tr>
 <tr>
 <th  bgcolor=#C6E2FF style="text-align:left;"> MATLAB </th><td  bgcolor=#C6E2FF style="text-align:right;">945</td><td  bgcolor=#C6E2FF style="text-align:right;">6583</td><td  bgcolor=#C6E2FF style="text-align:right;">13346</td><td  bgcolor=#C6E2FF style="text-align:right;">30647</td><td  bgcolor=#C6E2FF style="text-align:right;">50576</td>
+<th  bgcolor=#C6E2FF style="text-align:left;"> MATLAB </th><td  bgcolor=#C6E2FF style="text-align:right;">959</td><td  bgcolor=#C6E2FF style="text-align:right;">6773</td><td  bgcolor=#C6E2FF style="text-align:right;">13598</td><td  bgcolor=#C6E2FF style="text-align:right;">31759</td><td  bgcolor=#C6E2FF style="text-align:right;">52130</td>
 </tr>
 <tr>
 <th  bgcolor=#FFFFFF style="text-align:left;"> C/C++  Header </th><td  bgcolor=#FFFFFF style="text-align:right;">362</td><td  bgcolor=#FFFFFF style="text-align:right;">2772</td><td  bgcolor=#FFFFFF style="text-align:right;">2894</td><td  bgcolor=#FFFFFF style="text-align:right;">11914</td><td  bgcolor=#FFFFFF style="text-align:right;">17580</td>
+<th  bgcolor=#FFFFFF style="text-align:left;"> C/C++  Header </th><td  bgcolor=#FFFFFF style="text-align:right;">365</td><td  bgcolor=#FFFFFF style="text-align:right;">2786</td><td  bgcolor=#FFFFFF style="text-align:right;">2931</td><td  bgcolor=#FFFFFF style="text-align:right;">12036</td><td  bgcolor=#FFFFFF style="text-align:right;">17753</td>
 </tr>
 <tr>
 <th  bgcolor=#C6E2FF style="text-align:left;"> Python </th><td  bgcolor=#C6E2FF style="text-align:right;">109</td><td  bgcolor=#C6E2FF style="text-align:right;">3361</td><td  bgcolor=#C6E2FF style="text-align:right;">4763</td><td  bgcolor=#C6E2FF style="text-align:right;">7050</td><td  bgcolor=#C6E2FF style="text-align:right;">15174</td>
+<th  bgcolor=#C6E2FF style="text-align:left;"> Python </th><td  bgcolor=#C6E2FF style="text-align:right;">113</td><td  bgcolor=#C6E2FF style="text-align:right;">3445</td><td  bgcolor=#C6E2FF style="text-align:right;">4852</td><td  bgcolor=#C6E2FF style="text-align:right;">7316</td><td  bgcolor=#C6E2FF style="text-align:right;">15613</td>
 </tr>
 <tr>
 <th  bgcolor=#FFFFFF style="text-align:left;"> m4 </th><td  bgcolor=#FFFFFF style="text-align:right;">1</td><td  bgcolor=#FFFFFF style="text-align:right;">187</td><td  bgcolor=#FFFFFF style="text-align:right;">5</td><td  bgcolor=#FFFFFF style="text-align:right;">1247</td><td  bgcolor=#FFFFFF style="text-align:right;">1439</td>
+<th  bgcolor=#FFFFFF style="text-align:left;"> Java </th><td  bgcolor=#FFFFFF style="text-align:right;">23</td><td  bgcolor=#FFFFFF style="text-align:right;">460</td><td  bgcolor=#FFFFFF style="text-align:right;">416</td><td  bgcolor=#FFFFFF style="text-align:right;">4061</td><td  bgcolor=#FFFFFF style="text-align:right;">4937</td>
 </tr>
 <tr>
 <th  bgcolor=#C6E2FF style="text-align:left;"> Objective  C </th><td  bgcolor=#C6E2FF style="text-align:right;">9</td><td  bgcolor=#C6E2FF style="text-align:right;">96</td><td  bgcolor=#C6E2FF style="text-align:right;">0</td><td  bgcolor=#C6E2FF style="text-align:right;">370</td><td  bgcolor=#C6E2FF style="text-align:right;">466</td>
+<th  bgcolor=#C6E2FF style="text-align:left;"> m4 </th><td  bgcolor=#C6E2FF style="text-align:right;">2</td><td  bgcolor=#C6E2FF style="text-align:right;">197</td><td  bgcolor=#C6E2FF style="text-align:right;">6</td><td  bgcolor=#C6E2FF style="text-align:right;">1401</td><td  bgcolor=#C6E2FF style="text-align:right;">1604</td>
 </tr>
 <tr>
 <th  bgcolor=#FFFFFF style="text-align:left;"> Bourne  Shell </th><td  bgcolor=#FFFFFF style="text-align:right;">5</td><td  bgcolor=#FFFFFF style="text-align:right;">57</td><td  bgcolor=#FFFFFF style="text-align:right;">79</td><td  bgcolor=#FFFFFF style="text-align:right;">256</td><td  bgcolor=#FFFFFF style="text-align:right;">392</td>
+<th  bgcolor=#FFFFFF style="text-align:left;"> XML </th><td  bgcolor=#FFFFFF style="text-align:right;">38</td><td  bgcolor=#FFFFFF style="text-align:right;">89</td><td  bgcolor=#FFFFFF style="text-align:right;">10</td><td  bgcolor=#FFFFFF style="text-align:right;">783</td><td  bgcolor=#FFFFFF style="text-align:right;">882</td>
 </tr>
 <tr>
 <th  bgcolor=#C6E2FF style="text-align:left;"> Perl </th><td  bgcolor=#C6E2FF style="text-align:right;">3</td><td  bgcolor=#C6E2FF style="text-align:right;">21</td><td  bgcolor=#C6E2FF style="text-align:right;">23</td><td  bgcolor=#C6E2FF style="text-align:right;">240</td><td  bgcolor=#C6E2FF style="text-align:right;">284</td>
+<th  bgcolor=#C6E2FF style="text-align:left;"> CMake </th><td  bgcolor=#C6E2FF style="text-align:right;">163</td><td  bgcolor=#C6E2FF style="text-align:right;">0</td><td  bgcolor=#C6E2FF style="text-align:right;">871</td><td  bgcolor=#C6E2FF style="text-align:right;">631</td><td  bgcolor=#C6E2FF style="text-align:right;">1502</td>
 </tr>
 <tr>
 <th  bgcolor=#FFFFFF style="text-align:left;"> IDL </th><td  bgcolor=#FFFFFF style="text-align:right;">1</td><td  bgcolor=#FFFFFF style="text-align:right;">18</td><td  bgcolor=#FFFFFF style="text-align:right;">4</td><td  bgcolor=#FFFFFF style="text-align:right;">124</td><td  bgcolor=#FFFFFF style="text-align:right;">146</td>
+<th  bgcolor=#FFFFFF style="text-align:left;"> Objective  C </th><td  bgcolor=#FFFFFF style="text-align:right;">9</td><td  bgcolor=#FFFFFF style="text-align:right;">96</td><td  bgcolor=#FFFFFF style="text-align:right;">0</td><td  bgcolor=#FFFFFF style="text-align:right;">370</td><td  bgcolor=#FFFFFF style="text-align:right;">466</td>
 </tr>
 <tr>
 <th  bgcolor=#C6E2FF style="text-align:left;"> C </th><td  bgcolor=#C6E2FF style="text-align:right;">1</td><td  bgcolor=#C6E2FF style="text-align:right;">2</td><td  bgcolor=#C6E2FF style="text-align:right;">3</td><td  bgcolor=#C6E2FF style="text-align:right;">6</td><td  bgcolor=#C6E2FF style="text-align:right;">11</td>
+<th  bgcolor=#C6E2FF style="text-align:left;"> Bourne  Shell </th><td  bgcolor=#C6E2FF style="text-align:right;">3</td><td  bgcolor=#C6E2FF style="text-align:right;">56</td><td  bgcolor=#C6E2FF style="text-align:right;">73</td><td  bgcolor=#C6E2FF style="text-align:right;">248</td><td  bgcolor=#C6E2FF style="text-align:right;">377</td>
 </tr>
 <tr>
+<th  bgcolor=#FFFFFF style="text-align:left;"> SUM: </th><td  bgcolor=#FFFFFF style="text-align:right;">1905</td><td  bgcolor=#FFFFFF style="text-align:right;">27184</td><td  bgcolor=#FFFFFF style="text-align:right;">37786</td><td  bgcolor=#FFFFFF style="text-align:right;">108560</td><td  bgcolor=#FFFFFF style="text-align:right;">173530</td>
+<th  bgcolor=#FFFFFF style="text-align:left;"> Perl </th><td  bgcolor=#FFFFFF style="text-align:right;">1</td><td  bgcolor=#FFFFFF style="text-align:right;">6</td><td  bgcolor=#FFFFFF style="text-align:right;">9</td><td  bgcolor=#FFFFFF style="text-align:right;">196</td><td  bgcolor=#FFFFFF style="text-align:right;">211</td>
+</tr>
+<tr>
+<th  bgcolor=#C6E2FF style="text-align:left;"> C </th><td  bgcolor=#C6E2FF style="text-align:right;">2</td><td  bgcolor=#C6E2FF style="text-align:right;">10</td><td  bgcolor=#C6E2FF style="text-align:right;">3</td><td  bgcolor=#C6E2FF style="text-align:right;">81</td><td  bgcolor=#C6E2FF style="text-align:right;">94</td>
+</tr>
+<tr>
+<th  bgcolor=#FFFFFF style="text-align:left;"> SUM: </th><td  bgcolor=#FFFFFF style="text-align:right;">2147</td><td  bgcolor=#FFFFFF style="text-align:right;">28423</td><td  bgcolor=#FFFFFF style="text-align:right;">39762</td><td  bgcolor=#FFFFFF style="text-align:right;">117349</td><td  bgcolor=#FFFFFF style="text-align:right;">185534</td>
 </tr>
 </table>
         <I> Copyright (C) 2012 </I>
+        <I> Copyright (C) 2013 </I>
   */

issm/trunk/src/m/Makefile.am

r13975	r15396
22	22	./geometry/*.m \
23	23	./interp/*.m \
24		./~~latlong~~/*.m \
	24	./coordsystems/*.m \
25	25	./mech/*.m \
26	26	./mesh/*.m \

issm/trunk/src/m/boundaryconditions/SetIceSheetBC.m

r13975	r15396
16	16	md.diagnostic.spcvz(pos)=0;
17	17	md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6);
	18	md.diagnostic.loadingforce=0*ones(md.mesh.numberofvertices,3);
18	19
19	20	%Dirichlet Values

issm/trunk/src/m/boundaryconditions/SetIceSheetBC.py

r13975	r15396
22	22	md.diagnostic.spcvz[pos]=0
23	23	md.diagnostic.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6))
	24	md.diagnostic.loadingforce=0*numpy.ones((md.mesh.numberofvertices,3))
24	25
25	26	#Dirichlet Values

issm/trunk/src/m/boundaryconditions/SetIceShelfBC.m

r13395	r15396
35	35	md.diagnostic.spcvz(pos)=0;
36	36	md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6);
	37	md.diagnostic.loadingforce=0*ones(md.mesh.numberofvertices,3);
37	38
38	39	%Dirichlet Values

issm/trunk/src/m/boundaryconditions/SetIceShelfBC.py

r14310	r15396
39	39	md.diagnostic.spcvz[pos]=0
40	40	md.diagnostic.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6))
	41	md.diagnostic.loadingforce=0*numpy.ones((md.mesh.numberofvertices,3))
41	42
42	43	#Dirichlet Values

issm/trunk/src/m/boundaryconditions/SetMarineIceSheetBC.m

r13975	r15396
42	42	md.diagnostic.spcvz(pos)=0;
43	43	md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6);
	44	md.diagnostic.loadingforce=0*ones(md.mesh.numberofvertices,3);
44	45
45	46	%Dirichlet Values

issm/trunk/src/m/boundaryconditions/SetMarineIceSheetBC.py

r14310	r15396
47	47	md.diagnostic.spcvz[pos]=0
48	48	md.diagnostic.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6))
	49	md.diagnostic.loadingforce=0*numpy.ones((md.mesh.numberofvertices,3))
49	50
50	51	#Dirichlet Values

issm/trunk/src/m/classes/autodiff.m

r14310	r15396
49	49	fielddisplay(obj,'driver','ADOLC driver (''fos_forward'' or ''fov_forward'')');
50	50	end % }}}
51		function marshall(obj,fid) % {{{
	51	function marshall(obj,md,fid) % {{{
52	52
53	53	WriteData(fid,'object',obj,'fieldname','isautodiff','format','Boolean');

issm/trunk/src/m/classes/autodiff.py

-              r13975
+              r15396
-#module imports
 import numpy
 from dependent import *
 …
         """
-        #properties
         def __init__(self,*args):    # {{{
                 self.isautodiff   = False
 …
                         raise RuntimeError("constructor not supported")
         # }}}
         def __repr__(self):    # {{{
                 s ="      automatic differentiation parameters:\n"
 …
                 return s
         # }}}
         def setdefaultparameters(self):    # {{{
                 return self
         # }}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','isautodiff','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','driver','format','String')
 …
                 return
         # }}}

issm/trunk/src/m/classes/balancethickness.m

-              r13395
+              r15396
                         if solution~=BalancethicknessSolutionEnum(), return; end
                         md = checkfield(md,'balancethickness.spcthickness','forcing',1);
+                        md = checkfield(md,'balancethickness.spcthickness');
                         md = checkfield(md,'balancethickness.thickening_rate','size',[md.mesh.numberofvertices 1],'NaN',1);
                         md = checkfield(md,'balancethickness.stabilization','size',[1 1],'values',[0 1 2 3]);
 …
                         disp(sprintf('   balance thickness solution parameters:'));
                         fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint)');
                         fielddisplay(obj,'thickening_rate','ice thickening rate used in the mass conservation (dh/dt)');
+                        fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint) [m]');
+                        fielddisplay(obj,'thickening_rate','ice thickening rate used in the mass conservation (dh/dt) [m/yr]');
                         fielddisplay(obj,'stabilization','0: None, 1: SU, 2: MacAyeal''s artificial diffusivity, 3:DG');
                 end % }}}
+                function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
+                        yts=365.0*24.0*3600.0;
                         WriteData(fid,'object',obj,'fieldname','spcthickness','format','DoubleMat','mattype',1);
                         WriteData(fid,'object',obj,'fieldname','thickening_rate','format','DoubleMat','mattype',1);
+                        WriteData(fid,'object',obj,'fieldname','thickening_rate','format','DoubleMat','mattype',1,'scale',1./yts);
                         WriteData(fid,'object',obj,'fieldname','stabilization','format','Integer');
                 end % }}}

issm/trunk/src/m/classes/balancethickness.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.spcthickness      = float('NaN')
                 self.thickening_rate   = float('NaN')
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   balance thickness solution parameters:'
                 string="%s\n%s"%(string,fielddisplay(self,'spcthickness','thickness constraints (NaN means no constraint)'))
                 string="%s\n%s"%(string,fielddisplay(self,'thickening_rate','ice thickening rate used in the mass conservation (dh/dt)'))
+                string="%s\n%s"%(string,fielddisplay(self,'spcthickness','thickness constraints (NaN means no constraint) [m]'))
+                string="%s\n%s"%(string,fielddisplay(self,'thickening_rate','ice thickening rate used in the mass conservation (dh/dt) [m/yr]'))
                 string="%s\n%s"%(string,fielddisplay(self,'stabilization',"0: None, 1: SU, 2: MacAyeal's artificial diffusivity, 3:DG"))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #Type of stabilization used
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 #Early return
 …
                         return md
                 md = checkfield(md,'balancethickness.spcthickness','forcing',1)
+                md = checkfield(md,'balancethickness.spcthickness')
                 md = checkfield(md,'balancethickness.thickening_rate','size',[md.mesh.numberofvertices],'NaN',1)
                 md = checkfield(md,'balancethickness.stabilization','size',[1],'values',[0,1,2,3])
 …
                 return md
         # }}}
+        def marshall(self,md,fid):    # {{{
+        def marshall(self,fid):    # {{{
+                yts=365.0*24.0*3600.0
                 WriteData(fid,'object',self,'fieldname','spcthickness','format','DoubleMat','mattype',1)
                 WriteData(fid,'object',self,'fieldname','thickening_rate','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','thickening_rate','format','DoubleMat','mattype',1,'scale',1./yts)
                 WriteData(fid,'object',self,'fieldname','stabilization','format','Integer')
         # }}}

issm/trunk/src/m/classes/bamggeom.py

-              r13975
+              r15396
                         raise TypeError("bamggeom constructor error message: unknown type of constructor call")
         # }}}
         def __repr__(self):    # {{{
                 s ="class '%s' object '%s' = \n" % (type(self),'self')
 …
                 return s
         # }}}

issm/trunk/src/m/classes/bamgmesh.py

-              r13975
+              r15396
                         raise TypeError("bamgmesh constructor error message: unknown type of constructor call")
         # }}}
         def __repr__(self):    # {{{
                 s ="class '%s' object '%s' = \n" % (type(self),'self')
 …
                 return s
         # }}}

issm/trunk/src/m/classes/basalforcings.m

-              r13395
+              r15396
                         disp(sprintf('   basal forcings parameters:'));
                         fielddisplay(obj,'melting_rate','basal melting rate (positive if melting)');
                         fielddisplay(obj,'melting_rate_correction','additional melting applied when the grounding line retreats');
+                        fielddisplay(obj,'melting_rate','basal melting rate (positive if melting) [m/yr]');
+                        fielddisplay(obj,'melting_rate_correction','additional melting applied to compensate for dh/dt [m/yr]');
                         fielddisplay(obj,'geothermalflux','geothermal heat flux [W/m^2]');
                 end % }}}
+                function marshall(obj,fid) % {{{
+                        WriteData(fid,'object',obj,'fieldname','melting_rate','format','DoubleMat','mattype',1);
+                        WriteData(fid,'object',obj,'fieldname','melting_rate_correction','format','DoubleMat','mattype',1);
+                        WriteData(fid,'object',obj,'fieldname','geothermalflux','format','DoubleMat','mattype',1);
+                function marshall(obj,md,fid) % {{{
+                        yts=365.0*24.0*3600.0;
+                        WriteData(fid,'object',obj,'fieldname','melting_rate','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1)
+                        WriteData(fid,'object',obj,'fieldname','melting_rate_correction','format','DoubleMat','mattype',1,'scale',1./yts);
+                        WriteData(fid,'object',obj,'fieldname','geothermalflux','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1);
                 end % }}}
         end

issm/trunk/src/m/classes/basalforcings.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 from checkfield import *
 from WriteData import *
+import numpy
 class basalforcings(object):
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.melting_rate             = float('NaN')
                 self.melting_rate_correction  = float('NaN')
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   basal forcings parameters:"
                 string="%s\n%s"%(string,fielddisplay(self,"melting_rate","basal melting rate (positive if melting)"))
                 string="%s\n%s"%(string,fielddisplay(self,"melting_rate_correction","additional melting applied when the grounding line retreats"))
+                string="%s\n%s"%(string,fielddisplay(self,"melting_rate","basal melting rate (positive if melting) [m/yr]"))
+                string="%s\n%s"%(string,fielddisplay(self,"melting_rate_correction","additional melting applied to compensate for dh/dt [m/yr]"))
                 string="%s\n%s"%(string,fielddisplay(self,"geothermalflux","geothermal heat flux [W/m^2]"))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,md,fid):    # {{{
+        def marshall(self,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','melting_rate','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','melting_rate_correction','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','geothermalflux','format','DoubleMat','mattype',1)
+                yts=365.0*24.0*3600.0
+                WriteData(fid,'object',self,'fieldname','melting_rate','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1)
+                WriteData(fid,'object',self,'fieldname','melting_rate_correction','format','DoubleMat','mattype',1,'scale',1./yts)
+                WriteData(fid,'object',self,'fieldname','geothermalflux','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1)
         # }}}

issm/trunk/src/m/classes/clusters/acenet.m

-              r13395
+              r15396
                  time=10;
                  % codepath='/usr/local/issm-r11321/bin'; % this one is for issm on acenet global
                  codepath='PATH'; % this one is for issm on my acenet directory
                  executionpath='/home/klemorza/issm/execution';
+                 codepath='/home/klemorza/issm/trunk-jpl/bin'; % this one is for issm on my acenet directory
+                 executionpath='/home/klemorza/issm/trunk-jpl/execution';
                  %}}}
          end
 …
                          fprintf(fid,'#$ -cwd\n');
           fprintf(fid,'#$ -N issm\n');
           fprintf(fid,'#$ -l h_rt=10:0:0\n');
+          fprintf(fid,'#$ -l h_rt=96:0:0\n');
           fprintf(fid,'#$ -pe ompi* %i\n',cluster.np);
           fprintf(fid,'#$ -j y\n');

issm/trunk/src/m/classes/clusters/cloud.m

-              r13975
+              r15396
                         fprintf(fid,'#!/bin/bash\n');
                         if cluster.interactive
+                                fprintf(fid,'source %s%s\n',cluster.codepath,'/../etc/environment.sh');
                                 fprintf(fid,'mpiexec -np %i -f /home/mpich2.hosts %s/issm.exe %s %s %s ',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                         else
+                                fprintf(fid,'source %s%s\n',cluster.codepath,'/../etc/environment.sh');
                                 fprintf(fid,'mpiexec -np %i -f /home/mpich2.hosts %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
                         end
 …
                                 compressstring = [compressstring ' ' filelist{i}];
                         end
-                        if cluster.interactive,
-                                compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
-                        end
                         system(compressstring);
+                        if isempty(cluster.login),
+                                error('cloud BuildQueueScript: login should be supplied!');
+                        end
                         disp('uploading input file and queueing script');
                         issmstscpout(cluster.name,cluster.executionpath,cluster.login,{[dirname '.tar.gz']});
+                        disp('launching solution sequence on remote cluster');
+                        launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+                                ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && source  ' modelname '.queue '];
+                        if cluster.interactive,
+                                disp('sending files to remote cluster. once done, please log into cluster and launch job');
+                                launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+                                        ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz '];
+                        else
+                                disp('launching solution sequence on remote cluster');
+                                launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+                                        ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && source  ' modelname '.queue '];
+                        end
                         issmstssh(cluster.name,cluster.login,launchcommand);
                 end %}}}

issm/trunk/src/m/classes/clusters/discover.m

r13975	r15396
65	65
66	66	if ( strcmpi(cluster.queue,'general') & cluster.cpuspernode*cluster.numnodes < 17)
67		md = checkmessage(md,'cpus must be great than 17 for general queue');
	67	md = checkmessage(md,'cpus must be greater than 17 for general queue');
68	68	end
69	69	%now, check cluster.cpuspernode according to processor type

issm/trunk/src/m/classes/clusters/generic.m

-              r13975
+              r15396
                                 fid=fopen([modelname '.bat'],'w');
                                 fprintf(fid,'@echo off\n');
+                                if cluster.interactive
                                         fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                                 else
                                         fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
                                                 cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
+                                if cluster.np>1,
+                                        fprintf(fid,'"C:\\Program Files\\MPICH2\\bin\\mpiexec.exe" -n %i "%s/issm.exe" %s ./ %s ',cluster.np,cluster.codepath,EnumToString(solution),modelname);
+                                else
+                                        fprintf(fid,'"%s/issm.exe" %s ./ %s ',cluster.codepath,EnumToString(solution),modelname);
                                 end
                                 fclose(fid);
 …
                 function LaunchQueueJob(cluster,modelname,dirname,filelist)% {{{
+                        %compress the files into one zip.
+                        compressstring=['tar -zcf ' dirname '.tar.gz '];
+                        for i=1:numel(filelist),
+                                compressstring = [compressstring ' ' filelist{i}];
+                        end
+                        if cluster.interactive,
+                                compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
+                        end
+                        system(compressstring);
+                        disp('uploading input file and queueing script');
+                        issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
+                        disp('launching solution sequence on remote cluster');
+                        launchcommand=['source ' cluster.etcpath '/environment.sh && cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+                                ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && source  ' modelname '.queue '];
+                        issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
+                        if ~ispc,
+                                %compress the files into one zip.
+                                compressstring=['tar -zcf ' dirname '.tar.gz '];
+                                for i=1:numel(filelist),
+                                        compressstring = [compressstring ' ' filelist{i}];
+                                end
+                                if cluster.interactive,
+                                        compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
+                                end
+                                system(compressstring);
+                                disp('uploading input file and queueing script');
+                                issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
+                                disp('launching solution sequence on remote cluster');
+                                launchcommand=['source ' cluster.etcpath '/environment.sh && cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+                                        ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && source  ' modelname '.queue '];
+                                issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
+                        else
+                                system([modelname '.bat']);
+                        end
                 end %}}}
                 function Download(cluster,dirname,filelist)% {{{

issm/trunk/src/m/classes/clusters/generic.py

-              r13395
+              r15396
                 print 'launching solution sequence on remote cluster'
                 launchcommand='cd %s && rm -rf ./%s && mkdir %s && cd %s && mv ../%s.tar.gz ./ && tar -zxf %s.tar.gz  && source  %s.queue ' % \
                         (self.executionpath,dirname,dirname,dirname,dirname,dirname,modelname)
+                launchcommand='cd %s && rm -rf ./%s && mkdir %s && cd %s && mv ../%s.tar.gz ./ && tar -zxf %s.tar.gz  && chmod 777 %s.queue && ./%s.queue' % \
+                        (self.executionpath,dirname,dirname,dirname,dirname,dirname,modelname,modelname)
                 issmssh(self.name,self.login,self.port,launchcommand)
         # }}}

issm/trunk/src/m/classes/clusters/greenplanet.m

-              r14067
+              r15396
                  executionpath='';
                  interactive=0;
+                 time=24*60;
          end
          properties (SetAccess=private)
 …
                          if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end
+                 end
+                 %}}}
+                 function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
+                         if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
+                         if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
+                         %compute number of processors
+                         cluster.np=cluster.numnodes*cluster.cpuspernode;
+                         %write queuing script
+                         fid=fopen([modelname '.queue'],'w');
+                         fprintf(fid,'#PBS -S /bin/bash\n');
+                         fprintf(fid,'#PBS -N %s\n',modelname);
+                         fprintf(fid,'#PBS -q %s \n',cluster.queue);
+                         fprintf(fid,'#PBS -l nodes=%i:ppn=%i\n',cluster.numnodes,cluster.cpuspernode);
+                         fprintf(fid,'#PBS -m bea\n');
+                         fprintf(fid,'#PBS -M mmorligh@uci.edu\n');
+                         fprintf(fid,'#PBS -o %s.outlog \n',modelname);
+                         fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
+                         %fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
+                         fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
+                         if ~io_gather, %concatenate the output files:
+                                 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+                         end
+                         fclose(fid);
                  end
                  %}}}

issm/trunk/src/m/classes/clusters/pfe.m

-              r13395
+              r15396
                  function md = checkconsistency(cluster,md,solution,analyses) % {{{
                          available_queues={'long','normal','debug'};
                          queue_requirements_time=[5*24*60 8*60 2*60];
                          queue_requirements_np=[2048 2048 150];
+                         available_queues={'long','normal','debug','devel'};
+                         queue_requirements_time=[5*24*60 8*60 2*60 2*60];
+                         queue_requirements_np=[2048 2048 150 150];
                          QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,cluster.time)
 …
                          fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
                          fprintf(fid,'. /usr/share/modules/init/bash\n\n');
                          fprintf(fid,'module load comp-intel/11.1.046\n');
                          fprintf(fid,'module load mpi/mpt.1.25\n');
+                         fprintf(fid,'module load comp-intel/2013.1.117\n');
+                         fprintf(fid,'module load mpi-sgi/mpt.2.06rp16\n');
                          fprintf(fid,'module load math/intel_mkl_64_10.0.011\n\n');
                          fprintf(fid,'export PATH="$PATH:."\n\n');
 …
                          fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds.
                          fprintf(fid,'#PBS -q %s \n',cluster.queue);
                          fprintf(fid,'#PBS -W group_list=s1010\n');
+                         fprintf(fid,'#PBS -W group_list=%s\n',cluster.grouplist);
                          fprintf(fid,'#PBS -m e\n');
                          fprintf(fid,'#PBS -o %s.outlog \n',modelname);
                          fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
                          fprintf(fid,'. /usr/share/modules/init/bash\n\n');
                          fprintf(fid,'module load comp-intel/11.1.046\n');
                          fprintf(fid,'module load mpi/mpt.1.25\n');
+                         fprintf(fid,'module load comp-intel/2013.1.117\n');
+                         fprintf(fid,'module load mpi-sgi/mpt.2.06rp16\n');
                          fprintf(fid,'module load math/intel_mkl_64_10.0.011\n\n');
                          fprintf(fid,'export PATH="$PATH:."\n');

issm/trunk/src/m/classes/constants.m

-              r12706
+              r15396
                 function md = checkconsistency(obj,md,solution,analyses) % {{{
                         md = checkfield(md,'constants.g','>',0,'size',[1 1]);
+%                       md = checkfield(md,'constants.g','>',0,'size',[1 1]);
                         md = checkfield(md,'constants.yts','>',0,'size',[1 1]);
                         md = checkfield(md,'constants.referencetemperature','size',[1 1]);
 …
                         disp(sprintf('   constants parameters:'));
                         fielddisplay(obj,'g','gravitational acceleration');
                         fielddisplay(obj,'yts','number of seconds in a year');
                         fielddisplay(obj,'referencetemperature','reference temperature used in the enthalpy model');
+                        fielddisplay(obj,'g','gravitational acceleration [m/s^2]');
+                        fielddisplay(obj,'yts','number of seconds in a year [s/yr]');
+                        fielddisplay(obj,'referencetemperature','reference temperature used in the enthalpy model [K]');
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'object',obj,'fieldname','g','format','Double');
                         WriteData(fid,'object',obj,'fieldname','yts','format','Double');

issm/trunk/src/m/classes/constants.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.g                    = 0
                 self.yts                  = 0
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   constants parameters:"
                 string="%s\n%s"%(string,fielddisplay(self,"g","gravitational acceleration"))
                 string="%s\n%s"%(string,fielddisplay(self,"yts","number of seconds in a year"))
                 string="%s\n%s"%(string,fielddisplay(self,"referencetemperature","reference temperature used in the enthalpy model"))
+                string="%s\n%s"%(string,fielddisplay(self,"g","gravitational acceleration [m/s^2]"))
+                string="%s\n%s"%(string,fielddisplay(self,"yts","number of seconds in a year [s/yr]"))
+                string="%s\n%s"%(string,fielddisplay(self,"referencetemperature","reference temperature used in the enthalpy model [K]"))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #acceleration due to gravity (m/s^2)
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','g','format','Double')
                 WriteData(fid,'object',self,'fieldname','yts','format','Double')
                 WriteData(fid,'object',self,'fieldname','referencetemperature','format','Double')
         # }}}

issm/trunk/src/m/classes/debug.m

r12706	r15396
30	30
31	31	end % }}}
32		function marshall(obj,fid) % {{{
	32	function marshall(obj,md,fid) % {{{
33	33	WriteData(fid,'object',obj,'fieldname','profiling','format','Boolean');
34	34	end % }}}

issm/trunk/src/m/classes/debug.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from WriteData import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.valgrind  = False
                 self.gprof     = False
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   debug parameters:"
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','profiling','format','Boolean')
         # }}}

issm/trunk/src/m/classes/dependent.py

-              r13975
+              r15396
                         self.segments=MeshProfileIntersection(mesh.elements,mesh.x,mesh.y,self.exp)
         # }}}
         def __repr__(self):    # {{{
                 s ="   dependent variable:\n"
 …
                 return s
         # }}}
         def setdefaultparameters(self):    # {{{
                 #do nothing
                 return self
         # }}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 if strcmpi(self.name,'MassFlux'):
 …
                 return md
         # }}}
         def typetoscalar(self):    # {{{
                 if   strcmpi(self.type,'scalar'):
 …
                 return scalar
         # }}}

issm/trunk/src/m/classes/diagnostic.m

-              r13975
+              r15396
                 rift_penalty_threshold   = 0;
                 referential              = NaN;
+                loadingforce             = NaN;
                 requested_outputs        = NaN;
         end
 …
                         md = checkfield(md,'diagnostic.reltol','size',[1 1]);
                         md = checkfield(md,'diagnostic.abstol','size',[1 1]);
                         md = checkfield(md,'diagnostic.isnewton','numel',[1],'values',[0 1]);
+                        md = checkfield(md,'diagnostic.isnewton','numel',[1],'values',[0 1 2]);
                         md = checkfield(md,'diagnostic.stokesreconditioning','size',[1 1],'NaN',1);
                         md = checkfield(md,'diagnostic.viscosity_overshoot','size',[1 1],'NaN',1);
 …
                         md = checkfield(md,'diagnostic.maxiter','size',[1 1],'>=',1);
                         md = checkfield(md,'diagnostic.referential','size',[md.mesh.numberofvertices 6]);
+                        md = checkfield(md,'diagnostic.loadingforce','size',[md.mesh.numberofvertices 3]);
                         if ~isempty(md.diagnostic.requested_outputs),
                                 md = checkfield(md,'diagnostic.requested_outputs','size',[NaN 1]);
 …
                         disp(sprintf('\n      %s','Convergence criteria:'));
                         fielddisplay(obj,'restol','mechanical equilibrium residual convergence criterion');
                         fielddisplay(obj,'reltol','velocity relative convergence criterion, NaN -> not applied');
                         fielddisplay(obj,'abstol','velocity absolute convergence criterion, NaN -> not applied');
                         fielddisplay(obj,'isnewton','Apply Newton''s method instead of a Picard fixed point method');
+                        fielddisplay(obj,'reltol','velocity relative convergence criterion, NaN: not applied');
+                        fielddisplay(obj,'abstol','velocity absolute convergence criterion, NaN: not applied');
+                        fielddisplay(obj,'isnewton','0: Picard''s fixed point, 1: Newton''s method, 2: hybrid');
                         fielddisplay(obj,'maxiter','maximum number of nonlinear iterations');
                         fielddisplay(obj,'viscosity_overshoot','over-shooting constant new=new+C*(new-old)');
                         disp(sprintf('\n      %s','boundary conditions:'));
                         fielddisplay(obj,'spcvx','x-axis velocity constraint (NaN means no constraint)');
                         fielddisplay(obj,'spcvy','y-axis velocity constraint (NaN means no constraint)');
                         fielddisplay(obj,'spcvz','z-axis velocity constraint (NaN means no constraint)');
                         fielddisplay(obj,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice)');
+                        fielddisplay(obj,'spcvx','x-axis velocity constraint (NaN means no constraint) [m/yr]');
+                        fielddisplay(obj,'spcvy','y-axis velocity constraint (NaN means no constraint) [m/yr]');
+                        fielddisplay(obj,'spcvz','z-axis velocity constraint (NaN means no constraint) [m/yr]');
+                        fielddisplay(obj,'icefront','segments on ice front list (last column 0: Air, 1: Water, 2: Ice)');
                         disp(sprintf('\n      %s','Rift options:'));
 …
                         fielddisplay(obj,'stokesreconditioning','multiplier for incompressibility equation. Only for Stokes model');
                         fielddisplay(obj,'referential','local referential');
+                        fielddisplay(obj,'loadingforce','loading force applied on each point [N/m^3]');
                         fielddisplay(obj,'requested_outputs','additional outputs requested');
                 end % }}}
                 function marshall(obj,fid) % {{{
                         WriteData(fid,'object',obj,'fieldname','spcvx','format','DoubleMat','mattype',1);
                         WriteData(fid,'object',obj,'fieldname','spcvy','format','DoubleMat','mattype',1);
                         WriteData(fid,'object',obj,'fieldname','spcvz','format','DoubleMat','mattype',1);
+                function marshall(obj,md,fid) % {{{
+                        WriteData(fid,'object',obj,'fieldname','spcvx','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1);
+                        WriteData(fid,'object',obj,'fieldname','spcvy','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1);
+                        WriteData(fid,'object',obj,'fieldname','spcvz','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1);
                         WriteData(fid,'object',obj,'fieldname','restol','format','Double');
                         WriteData(fid,'object',obj,'fieldname','reltol','format','Double');
                         WriteData(fid,'object',obj,'fieldname','abstol','format','Double');
                         WriteData(fid,'object',obj,'fieldname','isnewton','format','Boolean');
+                        WriteData(fid,'object',obj,'fieldname','isnewton','format','Integer');
                         WriteData(fid,'object',obj,'fieldname','stokesreconditioning','format','Double');
                         WriteData(fid,'object',obj,'fieldname','viscosity_overshoot','format','Double');
 …
                         WriteData(fid,'object',obj,'fieldname','rift_penalty_threshold','format','Integer');
                         WriteData(fid,'object',obj,'fieldname','referential','format','DoubleMat','mattype',1);
+                        WriteData(fid,'data',obj.loadingforce(:,1),'format','DoubleMat','mattype',1,'enum',LoadingforceXEnum);
+                        WriteData(fid,'data',obj.loadingforce(:,2),'format','DoubleMat','mattype',1,'enum',LoadingforceYEnum);
+                        WriteData(fid,'data',obj.loadingforce(:,3),'format','DoubleMat','mattype',1,'enum',LoadingforceZEnum);
                         WriteData(fid,'object',obj,'fieldname','requested_outputs','format','DoubleMat','mattype',3);

issm/trunk/src/m/classes/diagnostic.py

-              r14310
+              r15396
-#module imports
 import numpy
 import sys
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.spcvx                    = float('NaN')
                 self.spcvy                    = float('NaN')
 …
                 self.rift_penalty_threshold   = 0
                 self.referential              = float('NaN')
+                self.loadingforce             = float('NaN')
                 self.requested_outputs        = float('NaN')
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   Diagnostic solution parameters:'
                 string="%s\n%s"%(string,'      Convergence criteria:')
                 string="%s\n%s"%(string,fielddisplay(self,'restol','mechanical equilibrium residual convergence criterion'))
                 string="%s\n%s"%(string,fielddisplay(self,'reltol','velocity relative convergence criterion, NaN -> not applied'))
                 string="%s\n%s"%(string,fielddisplay(self,'abstol','velocity absolute convergence criterion, NaN -> not applied'))
                 string="%s\n%s"%(string,fielddisplay(self,'isnewton',"Apply Newton's method instead of a Picard fixed point method"))
+                string="%s\n%s"%(string,fielddisplay(self,'reltol','velocity relative convergence criterion, NaN: not applied'))
+                string="%s\n%s"%(string,fielddisplay(self,'abstol','velocity absolute convergence criterion, NaN: not applied'))
+                string="%s\n%s"%(string,fielddisplay(self,'isnewton',"0: Picard's fixed point, 1: Newton's method, 2: hybrid"))
                 string="%s\n%s"%(string,fielddisplay(self,'maxiter','maximum number of nonlinear iterations'))
                 string="%s\n%s"%(string,fielddisplay(self,'viscosity_overshoot','over-shooting constant new=new+C*(new-old)'))
                 string="%s\n%s"%(string,'\n      boundary conditions:')
+                string="%s\n%s"%(string,fielddisplay(self,'spcvx','x-axis velocity constraint (NaN means no constraint)'))
+                string="%s\n%s"%(string,fielddisplay(self,'spcvy','y-axis velocity constraint (NaN means no constraint)'))
+                string="%s\n%s"%(string,fielddisplay(self,'spcvz','z-axis velocity constraint (NaN means no constraint)'))
+                string="%s\n%s"%(string,fielddisplay(self,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice'))
+                string="%s\n%s"%(string,fielddisplay(self,'spcvx','x-axis velocity constraint (NaN means no constraint) [m/yr]'))
+                string="%s\n%s"%(string,fielddisplay(self,'spcvy','y-axis velocity constraint (NaN means no constraint) [m/yr]'))
+                string="%s\n%s"%(string,fielddisplay(self,'spcvz','z-axis velocity constraint (NaN means no constraint) [m/yr]'))
+                string="%s\n%s"%(string,fielddisplay(self,'icefront','segments on ice front list (last column 0: Air, 1: Water, 2: Ice'))
                 string="%s\n%s"%(string,'\n      Rift options:')
 …
                 string="%s\n%s"%(string,fielddisplay(self,'stokesreconditioning','multiplier for incompressibility equation. Only for Stokes model'))
                 string="%s\n%s"%(string,fielddisplay(self,'referential','local referential'))
+                string="%s\n%s"%(string,fielddisplay(self,'loadingforce','loading force applied on each point [N/m^3]'))
                 string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested'))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #maximum of non-linear iterations.
                 self.maxiter=100
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 md = checkfield(md,'diagnostic.reltol','size',[1])
                 md = checkfield(md,'diagnostic.abstol','size',[1])
                 md = checkfield(md,'diagnostic.isnewton','numel',[1],'values',[0,1])
+                md = checkfield(md,'diagnostic.isnewton','numel',[1],'values',[0,1,2])
                 md = checkfield(md,'diagnostic.stokesreconditioning','size',[1],'NaN',1)
                 md = checkfield(md,'diagnostic.viscosity_overshoot','size',[1],'NaN',1)
 …
                 md = checkfield(md,'diagnostic.maxiter','size',[1],'>=',1)
                 md = checkfield(md,'diagnostic.referential','size',[md.mesh.numberofvertices,6])
+                md = checkfield(md,'diagnostic.loadingforce','size',[md.mesh.numberofvertices,3])
                 if not md.diagnostic.requested_outputs:
                         md = checkfield(md,'diagnostic.requested_outputs','size',[float('NaN'),1])
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','spcvx','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','spcvy','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','spcvz','format','DoubleMat','mattype',1)
+        def marshall(self,md,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','spcvx','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1)
+                WriteData(fid,'object',self,'fieldname','spcvy','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1)
+                WriteData(fid,'object',self,'fieldname','spcvz','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1)
                 WriteData(fid,'object',self,'fieldname','restol','format','Double')
                 WriteData(fid,'object',self,'fieldname','reltol','format','Double')
                 WriteData(fid,'object',self,'fieldname','abstol','format','Double')
                 WriteData(fid,'object',self,'fieldname','isnewton','format','Boolean')
+                WriteData(fid,'object',self,'fieldname','isnewton','format','Integer')
                 WriteData(fid,'object',self,'fieldname','stokesreconditioning','format','Double')
                 WriteData(fid,'object',self,'fieldname','viscosity_overshoot','format','Double')
 …
                 WriteData(fid,'object',self,'fieldname','rift_penalty_threshold','format','Integer')
                 WriteData(fid,'object',self,'fieldname','referential','format','DoubleMat','mattype',1)
+                WriteData(fid,'data',self.loadingforce[:,0],'format','DoubleMat','mattype',1,'enum',LoadingforceXEnum())
+                WriteData(fid,'data',self.loadingforce[:,1],'format','DoubleMat','mattype',1,'enum',LoadingforceYEnum())
+                WriteData(fid,'data',self.loadingforce[:,2],'format','DoubleMat','mattype',1,'enum',LoadingforceZEnum())
                 WriteData(fid,'object',self,'fieldname','requested_outputs','format','DoubleMat','mattype',3)
 …
                 WriteData(fid,'data',data,'enum',DiagnosticIcefrontEnum(),'format','DoubleMat','mattype',3)
         # }}}

issm/trunk/src/m/classes/flaim.py

-              r13395
+              r15396
-#module imports
 import numpy
 from collections import OrderedDict
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.targets            = ''
                 self.tracks             = ''
 …
                 self.opt_niter          = 30000
                 #}}}
+        def __repr__(self):
+                # {{{ Displa
+        def __repr__(self): # {{{
                 string='   FLAIM - Flight Line Adaptation using Ice sheet Modeling:'
 …
                 return string
                 #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}

issm/trunk/src/m/classes/flowequation.m

r13395	r15396
73	73
74	74	end % }}}
75		function marshall(obj,fid) % {{{
	75	function marshall(obj,md,fid) % {{{
76	76	WriteData(fid,'object',obj,'fieldname','ismacayealpattyn','format','Boolean');
77	77	WriteData(fid,'object',obj,'fieldname','ishutter','format','Boolean');

issm/trunk/src/m/classes/flowequation.py

-              r14310
+              r15396
-#module imports
 import numpy
 import copy
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.ismacayealpattyn     = 0
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   flow equation parameters:'
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','ismacayealpattyn','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','ishutter','format','Boolean')
 …
                 WriteData(fid,'data',data,'enum',FlowequationElementEquationEnum(),'format','DoubleMat','mattype',2)
         # }}}

issm/trunk/src/m/classes/friction.m

r13395	r15396
37	37	fielddisplay(obj,'q','q exponent');
38	38	end % }}}
39		function marshall(obj,fid) % {{{
	39	function marshall(obj,md,fid) % {{{
40	40	WriteData(fid,'object',obj,'fieldname','coefficient','format','DoubleMat','mattype',1);
41	41	WriteData(fid,'object',obj,'fieldname','p','format','DoubleMat','mattype',2);

issm/trunk/src/m/classes/friction.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.coefficient = float('NaN')
                 self.p           = float('NaN')
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="Sigma= drag^2 * Neff ^r * u ^s, with Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p"
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','coefficient','format','DoubleMat','mattype',1)
                 WriteData(fid,'object',self,'fieldname','p','format','DoubleMat','mattype',2)
                 WriteData(fid,'object',self,'fieldname','q','format','DoubleMat','mattype',2)
         # }}}

issm/trunk/src/m/classes/geometry.m

-              r13395
+              r15396
                 function md = checkconsistency(obj,md,solution,analyses) % {{{
+                        md = checkfield(md,'geometry.surface'  ,'NaN',1,'size',[md.mesh.numberofvertices 1]);
+                        md = checkfield(md,'geometry.bed'      ,'NaN',1,'size',[md.mesh.numberofvertices 1]);
+                        md = checkfield(md,'geometry.thickness','NaN',1,'size',[md.mesh.numberofvertices 1],'>',0);
+                        if any((obj.thickness-obj.surface+obj.bed)>10^-9),
+                                md = checkmessage(md,['equality thickness=surface-bed violated']);
+                        end
+                        if solution==TransientSolutionEnum() & md.transient.isgroundingline,
+                                md = checkfield(md,'geometry.bathymetry','NaN',1,'size',[md.mesh.numberofvertices 1]);
+                        if (solution==TransientSolutionEnum() & md.transient.isgia) | (solution==GiaSolutionEnum()),
+                                md = checkfield(md,'geometry.thickness','forcing',1,'NaN',1,'>=',0);
+                        else
+                                md = checkfield(md,'geometry.surface'  ,'NaN',1,'size',[md.mesh.numberofvertices 1]);
+                                md = checkfield(md,'geometry.bed'      ,'NaN',1,'size',[md.mesh.numberofvertices 1]);
+                                md = checkfield(md,'geometry.thickness','NaN',1,'size',[md.mesh.numberofvertices 1],'>',0);
+                                if any((obj.thickness-obj.surface+obj.bed)>10^-9),
+                                        md = checkmessage(md,['equality thickness=surface-bed violated']);
+                                end
+                                if solution==TransientSolutionEnum() & md.transient.isgroundingline,
+                                        md = checkfield(md,'geometry.bathymetry','NaN',1,'size',[md.mesh.numberofvertices 1]);
+                                end
                         end
                 end % }}}
 …
                         disp(sprintf('   geometry parameters:'));
                         fielddisplay(obj,'surface','surface elevation');
                         fielddisplay(obj,'thickness','ice thickness');
                         fielddisplay(obj,'bed','bed elevation');
                         fielddisplay(obj,'bathymetry','bathymetry elevation');
+                        fielddisplay(obj,'surface','surface elevation [m]');
+                        fielddisplay(obj,'thickness','ice thickness [m]');
+                        fielddisplay(obj,'bed','bed elevation [m]');
+                        fielddisplay(obj,'bathymetry','bathymetry elevation [m]');
                         fielddisplay(obj,'hydrostatic_ratio','coefficient for ice shelves'' thickness correction: hydrostatic_ratio H_obs+ (1-hydrostatic_ratio) H_hydro');
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'data',obj.surface,'format','DoubleMat','mattype',1,'enum',SurfaceEnum());
                         WriteData(fid,'data',obj.thickness,'format','DoubleMat','mattype',1,'enum',ThicknessEnum());
+                        WriteData(fid,'data',obj.thickness,'format','DoubleMat','mattype',1,'enum',ThicknessEnum(),'forcinglength',md.mesh.numberofvertices+1);
                         WriteData(fid,'data',obj.bed,'format','DoubleMat','mattype',1,'enum',BedEnum());
                         WriteData(fid,'data',obj.bathymetry,'format','DoubleMat','mattype',1,'enum',BathymetryEnum());

issm/trunk/src/m/classes/geometry.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.surface           = float('NaN')
                 self.thickness         = float('NaN')
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   geometry parameters:"
+                string="%s\n%s"%(string,fielddisplay(self,'surface','surface elevation'))
+                string="%s\n%s"%(string,fielddisplay(self,'thickness','ice thickness'))
+                string="%s\n%s"%(string,fielddisplay(self,'bed','bed elevation'))
+                string="%s\n%s"%(string,fielddisplay(self,'bathymetry','bathymetry elevation'))
+                string="%s\n%s"%(string,fielddisplay(self,'surface','surface elevation [m]'))
+                string="%s\n%s"%(string,fielddisplay(self,'thickness','ice thickness [m]'))
+                string="%s\n%s"%(string,fielddisplay(self,'bed','bed elevation [m]'))
+                string="%s\n%s"%(string,fielddisplay(self,'bathymetry','bathymetry elevation [m]'))
                 string="%s\n%s"%(string,fielddisplay(self,'hydrostatic_ratio','coefficient for ice shelves'' thickness correction: hydrostatic_ratio H_obs+ (1-hydrostatic_ratio) H_hydro'))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 md = checkfield(md,'geometry.surface'  ,'NaN',1,'size',[md.mesh.numberofvertices])
                 md = checkfield(md,'geometry.bed'      ,'NaN',1,'size',[md.mesh.numberofvertices])
                 md = checkfield(md,'geometry.thickness','NaN',1,'size',[md.mesh.numberofvertices],'>',0)
+                md = checkfield(md,'geometry.thickness','NaN',1,'size',[md.mesh.numberofvertices],'>',0,'forcing',1)
                 if any((self.thickness-self.surface+self.bed)>10**-9):
                         md.checkmessage("equality thickness=surface-bed violated")
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'data',self.surface,'format','DoubleMat','mattype',1,'enum',SurfaceEnum())
                 WriteData(fid,'data',self.thickness,'format','DoubleMat','mattype',1,'enum',ThicknessEnum())
+                WriteData(fid,'data',self.thickness,'format','DoubleMat','mattype',1,'enum',ThicknessEnum(),'forcinglength',md.mesh.numberofvertices+1)
                 WriteData(fid,'data',self.bed,'format','DoubleMat','mattype',1,'enum',BedEnum())
                 WriteData(fid,'data',self.bathymetry,'format','DoubleMat','mattype',1,'enum',BathymetryEnum())
                 WriteData(fid,'object',self,'fieldname','hydrostatic_ratio','format','DoubleMat','mattype',1)
         # }}}

issm/trunk/src/m/classes/groundingline.m

-              r13975
+              r15396
 %CONSTANTS class definition
+%GROUNDINGLINE class definition
+%
 %   Usage:
 …
                 function md = checkconsistency(obj,md,solution,analyses) % {{{
                         md = checkfield(md,'groundingline.migration','values',{'None' 'AgressiveMigration' 'SoftMigration'});
+                        md = checkfield(md,'groundingline.migration','values',{'None' 'AgressiveMigration' 'SoftMigration' 'SubelementMigration','SubelementMigration2'});
                         if ~strcmp(obj.migration,'None'),
 …
                 end % }}}
                 function disp(obj) % {{{
+                        disp(sprintf('   balance thickness solution parameters:'));
+                        disp(sprintf('   grounding line migration parameters:'));
                         fielddisplay(obj,'migration','type of grounding line migration: ''SoftMigration'',''AgressiveMigration'' or ''None''');
                         fielddisplay(obj,'melting_rate','melting rate applied when previously grounded parts start floating');
+                        fielddisplay(obj,'melting_rate','melting rate applied when previously grounded parts start floating [m/yr]');
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'data',StringToEnum(obj.migration),'enum',GroundinglineMigrationEnum(),'format','Integer');
                         WriteData(fid,'object',obj,'fieldname','melting_rate','format','Double');

issm/trunk/src/m/classes/groundingline.py

-              r14310
+              r15396
-#module imports
 import numpy
 from fielddisplay import fielddisplay
 …
 class groundingline(object):
         """
         CONSTANTS class definition
+        GROUNDINGLINE class definition
            Usage:
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.migration=''
                 self.melting_rate=float('NaN')
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+                string='   grounding line solution parameters:'
+        def __repr__(self): # {{{
+                string='   grounding line migration parameters:'
                 string="%s\n%s"%(string,fielddisplay(self,'migration','type of grounding line migration: ''SoftMigration'',''AgressiveMigration'' or ''None'''))
                 string="%s\n%s"%(string,fielddisplay(self,'melting_rate','melting rate applied when previously grounded parts start floating'))
+                string="%s\n%s"%(string,fielddisplay(self,'melting_rate','melting rate applied when previously grounded parts start floating [m/yr]'))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #Type of migration
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 md = checkfield(md,'groundingline.migration','values',['None','AgressiveMigration','SoftMigration'])
+                md = checkfield(md,'groundingline.migration','values',['None','AgressiveMigration','SoftMigration','SubelementMigration','SubelementMigration2'])
                 if not strcmp(self.migration,'None'):
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'data',StringToEnum(self.migration)[0],'enum',GroundinglineMigrationEnum(),'format','Integer')
                 WriteData(fid,'object',self,'fieldname','melting_rate','format','Double')
         # }}}

issm/trunk/src/m/classes/independent.m

-              r13975
+              r15396
                         end
                 end % }}}
                 function scalar=typetoscalar(obj) % {{{
+                function scalartype=typetoscalar(obj) % {{{
                         if strcmpi(obj.type,'scalar'),
                                 scalar=0;
+                                scalartype=0;
                         elseif strcmpi(obj.type,'vertex'),
+                                scalar=1;
+                                scalartype=1;
+                        elseif strcmpi(obj.type,'matrix'),
+                                scalartype=1;
+                        else error([obj.type ' not supported yet!']);
                         end
                 end % }}}

issm/trunk/src/m/classes/independent.py

-              r13975
+              r15396
                 self=options.AssignObjectFields(self)
         # }}}
         def __repr__(self):    # {{{
                 s ="   independent variable:\n"
 …
                 return s
         # }}}
         def setdefaultparameters(self):    # {{{
                 #do nothing
                 return self
         # }}}
         def checkconsistency(self,md,i,solution,analyses,driver):    # {{{
                 if not numpy.isnan(self.fos_forward_index):
 …
                 return md
         # }}}
         def typetoscalar(self):    # {{{
                 if   strcmpi(self.type,'scalar'):
 …
                 return scalar
         # }}}

issm/trunk/src/m/classes/initialization.m

-              r13395
+              r15396
                 pressure      = NaN;
                 temperature   = NaN;
+                surfacetemp   = NaN;
+                basaltemp     = NaN;
+                waterfraction = NaN;
+                sediment_head = NaN;
+                epl_head      = NaN;
                 watercolumn   = NaN;
-                waterfraction = NaN;
         end
         methods
 …
                                 md = checkfield(md,'initialization.vy','NaN',1,'size',[md.mesh.numberofvertices 1]);
                         end
+                        if ismember(HydrologyAnalysisEnum(),analyses),
+                                md = checkfield(md,'initialization.watercolumn','NaN',1,'size',[md.mesh.numberofvertices 1]);
+                        end
+                        if ismember(BalancethicknessAnalysisEnum(),analyses),
+                        if ismember(BalancethicknessAnalysisEnum(),analyses) & solution==BalancethicknessSolutionEnum,
                                 md = checkfield(md,'initialization.vx','NaN',1,'size',[md.mesh.numberofvertices 1]);
                                 md = checkfield(md,'initialization.vy','NaN',1,'size',[md.mesh.numberofvertices 1]);
 …
                                 md = checkfield(md,'initialization.waterfraction','>=',0,'size',[md.mesh.numberofvertices 1]);
                         end
+                        if ismember(HydrologyShreveAnalysisEnum(),analyses),
+                                if isa(md.hydrology,'hydrologyshreve'),
+                                        md = checkfield(md,'initialization.watercolumn','NaN',1,'size',[md.mesh.numberofvertices 1]);
+                                end
+                        end
+                        if ismember(HydrologyDCInefficientAnalysisEnum(),analyses),
+                                if isa(md.hydrology,'hydrologydc'),
+                                        md = checkfield(md,'initialization.sediment_head','NaN',1,'size',[md.mesh.numberofvertices 1]);
+                                end
+                        end
+                        if ismember(HydrologyDCEfficientAnalysisEnum(),analyses),
+                                if isa(md.hydrology,'hydrologydc'),
+                                        if md.hydrology.isefficientlayer==1,
+                                                md = checkfield(md,'initialization.epl_head','NaN',1,'size',[md.mesh.numberofvertices 1]);
+                                        end
+                                end
+                        end
                 end % }}}
                 function disp(obj) % {{{
                         disp(sprintf('   initial field values:'));
+                        fielddisplay(obj,'vx','x component of velocity');
+                        fielddisplay(obj,'vy','y component of velocity');
+                        fielddisplay(obj,'vz','z component of velocity');
+                        fielddisplay(obj,'vel','velocity norm');
+                        fielddisplay(obj,'pressure','pressure field');
+                        fielddisplay(obj,'temperature','temperature in Kelvins');
+                        fielddisplay(obj,'surfacetemp','surface temperature in Kelvins');
+                        fielddisplay(obj,'basaltemp','basal temperature in Kelvins');
+                        fielddisplay(obj,'watercolumn','thickness of subglacial water');
+                        fielddisplay(obj,'vx','x component of velocity [m/yr]');
+                        fielddisplay(obj,'vy','y component of velocity [m/yr]');
+                        fielddisplay(obj,'vz','z component of velocity [m/yr]');
+                        fielddisplay(obj,'vel','velocity norm [m/yr]');
+                        fielddisplay(obj,'pressure','pressure field [Pa]');
+                        fielddisplay(obj,'temperature','temperature [K]');
                         fielddisplay(obj,'waterfraction','fraction of water in the ice');
+                        fielddisplay(obj,'sediment_head','sediment water head of subglacial system [m]');
+                        fielddisplay(obj,'epl_head','epl water head of subglacial system [m]');
+                        fielddisplay(obj,'watercolumn','thickness of subglacial water [m]');
                 end % }}}
+                function marshall(obj,fid) % {{{
+                        WriteData(fid,'data',obj.vx,'format','DoubleMat','mattype',1,'enum',VxEnum);
+                        WriteData(fid,'data',obj.vy,'format','DoubleMat','mattype',1,'enum',VyEnum);
+                        WriteData(fid,'data',obj.vz,'format','DoubleMat','mattype',1,'enum',VzEnum);
+                function marshall(obj,md,fid) % {{{
+                        yts=365.0*24.0*3600.0;
+                        WriteData(fid,'data',obj.vx,'format','DoubleMat','mattype',1,'enum',VxEnum,'scale',1./yts);
+                        WriteData(fid,'data',obj.vy,'format','DoubleMat','mattype',1,'enum',VyEnum,'scale',1./yts);
+                        WriteData(fid,'data',obj.vz,'format','DoubleMat','mattype',1,'enum',VzEnum,'scale',1./yts);
                         WriteData(fid,'data',obj.pressure,'format','DoubleMat','mattype',1,'enum',PressureEnum);
                         WriteData(fid,'data',obj.temperature,'format','DoubleMat','mattype',1,'enum',TemperatureEnum);
+                        WriteData(fid,'data',obj.waterfraction,'format','DoubleMat','mattype',1,'enum',WaterfractionEnum);
+                        WriteData(fid,'data',obj.sediment_head,'format','DoubleMat','mattype',1,'enum',SedimentHeadEnum);
+                        WriteData(fid,'data',obj.epl_head,'format','DoubleMat','mattype',1,'enum',EplHeadEnum);
                         WriteData(fid,'data',obj.watercolumn,'format','DoubleMat','mattype',1,'enum',WatercolumnEnum);
-                        WriteData(fid,'data',obj.waterfraction,'format','DoubleMat','mattype',1,'enum',WaterfractionEnum);
                 end % }}}
         end

issm/trunk/src/m/classes/initialization.py

-              r14310
+              r15396
-#module imports
 import numpy
 from fielddisplay import fielddisplay
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.vx            = float('NaN')
 …
                 self.pressure      = float('NaN')
                 self.temperature   = float('NaN')
+                self.surfacetemp   = float('NaN')
+                self.basaltemp     = float('NaN')
+                self.waterfraction = float('NaN')
                 self.watercolumn   = float('NaN')
                 self.waterfraction = float('NaN')
+                self.sediment_head  = float('NaN')
                 #set defaults
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   initial field values:'
+                string="%s\n%s"%(string,fielddisplay(self,'vx','x component of velocity'))
+                string="%s\n%s"%(string,fielddisplay(self,'vy','y component of velocity'))
+                string="%s\n%s"%(string,fielddisplay(self,'vz','z component of velocity'))
+                string="%s\n%s"%(string,fielddisplay(self,'vel','velocity norm'))
+                string="%s\n%s"%(string,fielddisplay(self,'pressure','pressure field'))
+                string="%s\n%s"%(string,fielddisplay(self,'temperature','temperature in Kelvins'))
+                string="%s\n%s"%(string,fielddisplay(self,'surfacetemp','surface temperature in Kelvins'))
+                string="%s\n%s"%(string,fielddisplay(self,'basaltemp','basal temperature in Kelvins'))
+                string="%s\n%s"%(string,fielddisplay(self,'watercolumn','thickness of subglacial water'))
+                string="%s\n%s"%(string,fielddisplay(self,'vx','x component of velocity [m/yr]'))
+                string="%s\n%s"%(string,fielddisplay(self,'vy','y component of velocity [m/yr]'))
+                string="%s\n%s"%(string,fielddisplay(self,'vz','z component of velocity [m/yr]'))
+                string="%s\n%s"%(string,fielddisplay(self,'vel','velocity norm [m/yr]'))
+                string="%s\n%s"%(string,fielddisplay(self,'pressure','pressure [Pa]'))
+                string="%s\n%s"%(string,fielddisplay(self,'temperature','temperature [K]'))
                 string="%s\n%s"%(string,fielddisplay(self,'waterfraction','fraction of water in the ice'))
+                string="%s\n%s"%(string,fielddisplay(self,'watercolumn','thickness of subglacial water [m]'))
+                string="%s\n%s"%(string,fielddisplay(self,'sediment_head','sediment water head of subglacial system [m]'))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 if DiagnosticHorizAnalysisEnum() in analyses:
 …
                         md = checkfield(md,'initialization.vx','NaN',1,'size',[md.mesh.numberofvertices])
                         md = checkfield(md,'initialization.vy','NaN',1,'size',[md.mesh.numberofvertices])
-                if HydrologyAnalysisEnum() in analyses:
-                        md = checkfield(md,'initialization.watercolumn','NaN',1,'size',[md.mesh.numberofvertices])
                 if BalancethicknessAnalysisEnum() in analyses:
                         md = checkfield(md,'initialization.vx','NaN',1,'size',[md.mesh.numberofvertices])
 …
                 if (EnthalpyAnalysisEnum() in analyses and md.thermal.isenthalpy) or solution==EnthalpySolutionEnum():
                         md = checkfield(md,'initialization.waterfraction','>=',0,'size',[md.mesh.numberofvertices])
+                if HydrologyShreveAnalysisEnum() in analyses:
+                        md = checkfield(md,'initialization.watercolumn','NaN',1,'size',[md.mesh.numberofvertices])
                 return md
         # }}}
+        def marshall(self,md,fid):    # {{{
+        def marshall(self,fid):    # {{{
+                WriteData(fid,'data',self.vx,'format','DoubleMat','mattype',1,'enum',VxEnum())
+                WriteData(fid,'data',self.vy,'format','DoubleMat','mattype',1,'enum',VyEnum())
+                WriteData(fid,'data',self.vz,'format','DoubleMat','mattype',1,'enum',VzEnum())
+                yts=365.0*24.0*3600.0
+                WriteData(fid,'data',self.vx,'format','DoubleMat','mattype',1,'enum',VxEnum(),'scale',1./yts)
+                WriteData(fid,'data',self.vy,'format','DoubleMat','mattype',1,'enum',VyEnum(),'scale',1./yts)
+                WriteData(fid,'data',self.vz,'format','DoubleMat','mattype',1,'enum',VzEnum(),'scale',1./yts)
                 WriteData(fid,'data',self.pressure,'format','DoubleMat','mattype',1,'enum',PressureEnum())
                 WriteData(fid,'data',self.temperature,'format','DoubleMat','mattype',1,'enum',TemperatureEnum())
+                WriteData(fid,'data',self.waterfraction,'format','DoubleMat','mattype',1,'enum',WaterfractionEnum())
                 WriteData(fid,'data',self.watercolumn,'format','DoubleMat','mattype',1,'enum',WatercolumnEnum())
                 WriteData(fid,'data',self.waterfraction,'format','DoubleMat','mattype',1,'enum',WaterfractionEnum())
+                WriteData(fid,'data',self.sediment_head,'format','DoubleMat','mattype',1,'enum',SedimentHeadEnum())
         # }}}

issm/trunk/src/m/classes/inversion.m

-              r14310
+              r15396
                         if solution==BalancethicknessSolutionEnum()
                                 md = checkfield(md,'inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1);
                         elseif solution==WeakBalancethicknessSolutionEnum()
+                        elseif solution==BalancethicknessSoftSolutionEnum()
                                 md = checkfield(md,'inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1);
                         else
 …
                         disp(sprintf('   inversion parameters:'));
                         fielddisplay(obj,'iscontrol','is inversion activated?');
                         fielddisplay(obj,'incomplete_adjoint','do we assume linear viscosity?');
                         fielddisplay(obj,'control_parameters','parameter where inverse control is carried out; ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}');
+                        fielddisplay(obj,'incomplete_adjoint','1: linear viscosity, 0: non-linear viscosity');
+                        fielddisplay(obj,'control_parameters','ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}');
                         fielddisplay(obj,'nsteps','number of optimization searches');
                         fielddisplay(obj,'cost_functions','indicate the type of response for each optimization step');
 …
                         fielddisplay(obj,'max_parameters','absolute maximum acceptable value of the inversed parameter on each vertex');
                         fielddisplay(obj,'gradient_only','stop control method solution at gradient');
                         fielddisplay(obj,'vx_obs','observed velocity x component [m/a]');
                         fielddisplay(obj,'vy_obs','observed velocity y component [m/a]');
                         fielddisplay(obj,'vel_obs','observed velocity magnitude [m/a]');
+                        fielddisplay(obj,'vx_obs','observed velocity x component [m/yr]');
+                        fielddisplay(obj,'vy_obs','observed velocity y component [m/yr]');
+                        fielddisplay(obj,'vel_obs','observed velocity magnitude [m/yr]');
                         fielddisplay(obj,'thickness_obs','observed thickness [m]');
                         disp('Available cost functions:');
 …
                         disp('   503: ThicknessAbsGradient');
                 end % }}}
+                function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
+                        yts=365.0*24.0*3600.0;
                         WriteData(fid,'object',obj,'fieldname','iscontrol','format','Boolean');
 …
                         WriteData(fid,'object',obj,'fieldname','step_threshold','format','DoubleMat','mattype',3);
                         WriteData(fid,'object',obj,'fieldname','gradient_only','format','Boolean');
                         WriteData(fid,'object',obj,'fieldname','vx_obs','format','DoubleMat','mattype',1);
                         WriteData(fid,'object',obj,'fieldname','vy_obs','format','DoubleMat','mattype',1);
                         WriteData(fid,'object',obj,'fieldname','vz_obs','format','DoubleMat','mattype',1);
+                        WriteData(fid,'object',obj,'fieldname','vx_obs','format','DoubleMat','mattype',1,'scale',1./yts);
+                        WriteData(fid,'object',obj,'fieldname','vy_obs','format','DoubleMat','mattype',1,'scale',1./yts);
+                        WriteData(fid,'object',obj,'fieldname','vz_obs','format','DoubleMat','mattype',1,'scale',1./yts);
                         WriteData(fid,'object',obj,'fieldname','thickness_obs','format','DoubleMat','mattype',1);

issm/trunk/src/m/classes/inversion.py

-              r14310
+              r15396
-#module imports
 import numpy
 import copy
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.iscontrol                   = 0
                 self.tao                         = 0
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   inversion parameters:'
                 string="%s\n%s"%(string,fielddisplay(self,'iscontrol','is inversion activated?'))
                 string="%s\n%s"%(string,fielddisplay(self,'incomplete_adjoint','do we assume linear viscosity?'))
                 string="%s\n%s"%(string,fielddisplay(self,'control_parameters','parameter where inverse control is carried out; ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}'))
+                string="%s\n%s"%(string,fielddisplay(self,'incomplete_adjoint','1: linear viscosity, 0: non-linear viscosity'))
+                string="%s\n%s"%(string,fielddisplay(self,'control_parameters','ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}'))
                 string="%s\n%s"%(string,fielddisplay(self,'nsteps','number of optimization searches'))
                 string="%s\n%s"%(string,fielddisplay(self,'cost_functions','indicate the type of response for each optimization step'))
 …
                 string="%s\n%s"%(string,fielddisplay(self,'max_parameters','absolute maximum acceptable value of the inversed parameter on each vertex'))
                 string="%s\n%s"%(string,fielddisplay(self,'gradient_only','stop control method solution at gradient'))
                 string="%s\n%s"%(string,fielddisplay(self,'vx_obs','observed velocity x component [m/a]'))
                 string="%s\n%s"%(string,fielddisplay(self,'vy_obs','observed velocity y component [m/a]'))
                 string="%s\n%s"%(string,fielddisplay(self,'vel_obs','observed velocity magnitude [m/a]'))
+                string="%s\n%s"%(string,fielddisplay(self,'vx_obs','observed velocity x component [m/yr]'))
+                string="%s\n%s"%(string,fielddisplay(self,'vy_obs','observed velocity y component [m/yr]'))
+                string="%s\n%s"%(string,fielddisplay(self,'vel_obs','observed velocity magnitude [m/yr]'))
                 string="%s\n%s"%(string,fielddisplay(self,'thickness_obs','observed thickness [m]'))
                 string="%s\n%s"%(string,'Available cost functions:')
 …
                 return string
                 #}}}
         def setdefaultparameters(self): # {{{
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,md,fid):    # {{{
         def marshall(self,fid):    # {{{
+                yts=365.0*24.0*3600.0
                 WriteData(fid,'object',self,'fieldname','iscontrol','format','Boolean')
 …
                 WriteData(fid,'object',self,'fieldname','step_threshold','format','DoubleMat','mattype',3)
                 WriteData(fid,'object',self,'fieldname','gradient_only','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','vx_obs','format','DoubleMat','mattype',1)
                 WriteData(fid,'object',self,'fieldname','vy_obs','format','DoubleMat','mattype',1)
                 WriteData(fid,'object',self,'fieldname','vz_obs','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','vx_obs','format','DoubleMat','mattype',1,'scale',1./yts)
+                WriteData(fid,'object',self,'fieldname','vy_obs','format','DoubleMat','mattype',1,'scale',1./yts)
+                WriteData(fid,'object',self,'fieldname','vz_obs','format','DoubleMat','mattype',1,'scale',1./yts)
                 WriteData(fid,'object',self,'fieldname','thickness_obs','format','DoubleMat','mattype',1)
 …
                 WriteData(fid,'data',num_cost_functions,'enum',InversionNumCostFunctionsEnum(),'format','Integer')
         # }}}

issm/trunk/src/m/classes/mask.m

r14314	r15396
47	47	fielddisplay(obj,'vertexonrock','vertex on rock flags list');
48	48	end % }}}
49		function marshall(obj,fid) % {{{
	49	function marshall(obj,md,fid) % {{{
50	50	WriteData(fid,'object',obj,'fieldname','elementonfloatingice','format','BooleanMat','mattype',2);
51	51	WriteData(fid,'object',obj,'fieldname','elementongroundedice','format','BooleanMat','mattype',2);

issm/trunk/src/m/classes/mask.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.elementonfloatingice = float('NaN')
                 self.elementongroundedice = float('NaN')
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   masks:"
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','elementonfloatingice','format','BooleanMat','mattype',2)
                 WriteData(fid,'object',self,'fieldname','elementongroundedice','format','BooleanMat','mattype',2)
 …
                 WriteData(fid,'object',self,'fieldname','vertexonwater','format','DoubleMat','mattype',1)
         # }}}

issm/trunk/src/m/classes/matdamageice.m

-              r13395
+              r15396
                 rheology_Z   = NaN;
                 rheology_law = '';
+                %gia:
+                lithosphere_shear_modulus  = 0.;
+                lithosphere_density        = 0.;
+                mantle_shear_modulus       = 0.;
+                mantle_density             = 0.;
         end
         methods
 …
                         %available: none, paterson and arrhenius
                         obj.rheology_law='Paterson';
+                        %GIA:
+                        obj.lithosphere_shear_modulus  = 6.7*10^10;  % (Pa)
+                        obj.lithosphere_density        = 3.32;       % (g/cm^-3)
+                        obj.mantle_shear_modulus       = 1.45*10^11; % (Pa)
+                        obj.mantle_density             = 3.34;       % (g/cm^-3)
                 end % }}}
                 function md = checkconsistency(obj,md,solution,analyses) % {{{
 …
                         md = checkfield(md,'materials.rheology_Z','>',0,'size',[md.mesh.numberofvertices 1]);
                         md = checkfield(md,'materials.rheology_law','values',{'None' 'Paterson' 'Arrhenius'});
+                        if ismember(GiaAnalysisEnum(),analyses),
+                                md = checkfield(md,'materials.lithosphere_shear_modulus','>',0,'numel',1);
+                                md = checkfield(md,'materials.lithosphere_density','>',0,'numel',1);
+                                md = checkfield(md,'materials.mantle_shear_modulus','>',0,'numel',1);
+                                md = checkfield(md,'materials.mantle_density','>',0,'numel',1);
+                        end
                 end % }}}
                 function disp(obj) % {{{
 …
                         fielddisplay(obj,'rheology_Z','rheology multiplier');
                         fielddisplay(obj,'rheology_law','law for the temperature dependance of the rheology: ''None'', ''Paterson'' or ''Arrhenius''');
+                        fielddisplay(obj,'lithosphere_shear_modulus','Lithosphere shear modulus [Pa]');
+                        fielddisplay(obj,'lithosphere_density','Lithosphere density [g/cm^-3]');
+                        fielddisplay(obj,'mantle_shear_modulus','Mantle shear modulus [Pa]');
+                        fielddisplay(obj,'mantle_density','Mantle density [g/cm^-3]');
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'enum',MaterialsEnum(),'data',MatdamageiceEnum(),'format','Integer');
                         WriteData(fid,'object',obj,'class','materials','fieldname','rho_ice','format','Double');
 …
                         WriteData(fid,'object',obj,'class','materials','fieldname','rheology_Z','format','DoubleMat','mattype',1);
                         WriteData(fid,'data',StringToEnum(obj.rheology_law),'enum',MaterialsRheologyLawEnum(),'format','Integer');
+                        WriteData(fid,'object',obj,'class','materials','fieldname','lithosphere_shear_modulus','format','Double');
+                        WriteData(fid,'object',obj,'class','materials','fieldname','lithosphere_density','format','Double','scale',10^3);
+                        WriteData(fid,'object',obj,'class','materials','fieldname','mantle_shear_modulus','format','Double');
+                        WriteData(fid,'object',obj,'class','materials','fieldname','mantle_density','format','Double','scale',10^3);
                 end % }}}
         end

issm/trunk/src/m/classes/matdamageice.py

-              r13975
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
                 self.rheology_law = ''
+                #gia:
+                self.lithosphere_shear_modulus  = 0.
+                self.lithosphere_density        = 0.
+                self.mantle_shear_modulus       = 0.
+                self.mantle_density             = 0.
                 if not len(args):
                         self.setdefaultparameters()
 …
         # }}}
+        def __repr__(self):    # {{{
+                s ='   Materials:\n'
+                s+="%s\n" % fielddisplay(self,"rho_ice","ice density [kg/m^3]")
+                s+="%s\n" % fielddisplay(self,"rho_water","ocean water density [kg/m^3]")
+                s+="%s\n" % fielddisplay(self,"rho_freshwater","fresh water density [kg/m^3]")
+                s+="%s\n" % fielddisplay(self,"mu_water","water viscosity [N s/m^2]")
+                s+="%s\n" % fielddisplay(self,"heatcapacity","heat capacity [J/kg/K]")
+                s+="%s\n" % fielddisplay(self,"thermalconductivity","ice thermal conductivity [W/m/K]")
+                s+="%s\n" % fielddisplay(self,"meltingpoint","melting point of ice at 1atm in K")
+                s+="%s\n" % fielddisplay(self,"latentheat","latent heat of fusion [J/m^3]")
+                s+="%s\n" % fielddisplay(self,"beta","rate of change of melting point with pressure [K/Pa]")
+                s+="%s\n" % fielddisplay(self,"mixed_layer_capacity","mixed layer capacity [W/kg/K]")
+                s+="%s\n" % fielddisplay(self,"thermal_exchange_velocity","thermal exchange velocity [m/s]")
+                s+="%s\n" % fielddisplay(self,"rheology_B","flow law parameter [Pa/s^(1/n)]")
+                s+="%s\n" % fielddisplay(self,"rheology_n","Glen's flow law exponent")
+                s+="%s\n" % fielddisplay(self,"rheology_Z","rheology multiplier")
+                s+="%s\n" % fielddisplay(self,"rheology_law","law for the temperature dependance of the rheology: 'None', 'Paterson' or 'Arrhenius'")
+                s+="%s\n" % fielddisplay(self,"lithosphere_shear_modulus","Lithosphere shear modulus [Pa]")
+                s+="%s\n" % fielddisplay(self,"lithosphere_density","Lithosphere density [g/cm^-3]")
+                s+="%s\n" % fielddisplay(self,"mantle_shear_modulus","Mantle shear modulus [Pa]")
+                s+="%s\n" % fielddisplay(self,"mantle_density","Mantle density [g/cm^-3]")
+                return s
+        # }}}
         def setdefaultparameters(self):    # {{{
 …
                 #available: none, paterson and arrhenius
                 self.rheology_law='Paterson'
+                # GIA:
+                self.lithosphere_shear_modulus  = 6.7*10**10;  # (Pa)
+                self.lithosphere_density        = 3.32;       # (g/cm^-3)
+                self.mantle_shear_modulus       = 1.45*10**11; # (Pa)
+                self.mantle_density             = 3.34;       # (g/cm^-3)
         # }}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 md = checkfield(md,'materials.rho_ice','>',0)
 …
                 md = checkfield(md,'materials.rheology_Z','>',0,'size',[md.mesh.numberofvertices,1])
                 md = checkfield(md,'materials.rheology_law','values',['None','Paterson','Arrhenius'])
+                md = checkfield(md,'materials.lithosphere_shear_modulus','>',0,'numel',[1]);
+                md = checkfield(md,'materials.lithosphere_density','>',0,'numel',[1]);
+                md = checkfield(md,'materials.mantle_shear_modulus','>',0,'numel',[1]);
+                md = checkfield(md,'materials.mantle_density','>',0,'numel',[1]);
                 return md
         # }}}
+        def __repr__(self):    # {{{
+                s ='   Materials:\n'
+                s+="%s\n" % fielddisplay(self,"rho_ice","ice density [kg/m^3]")
+                s+="%s\n" % fielddisplay(self,"rho_water","ocean water density [kg/m^3]")
+                s+="%s\n" % fielddisplay(self,"rho_freshwater","fresh water density [kg/m^3]")
+                s+="%s\n" % fielddisplay(self,"mu_water","water viscosity [N s/m^2]")
+                s+="%s\n" % fielddisplay(self,"heatcapacity","heat capacity [J/kg/K]")
+                s+="%s\n" % fielddisplay(self,"thermalconductivity","ice thermal conductivity [W/m/K]")
+                s+="%s\n" % fielddisplay(self,"meltingpoint","melting point of ice at 1atm in K")
+                s+="%s\n" % fielddisplay(self,"latentheat","latent heat of fusion [J/m^3]")
+                s+="%s\n" % fielddisplay(self,"beta","rate of change of melting point with pressure [K/Pa]")
+                s+="%s\n" % fielddisplay(self,"mixed_layer_capacity","mixed layer capacity [W/kg/K]")
+                s+="%s\n" % fielddisplay(self,"thermal_exchange_velocity","thermal exchange velocity [m/s]")
+                s+="%s\n" % fielddisplay(self,"rheology_B","flow law parameter [Pa/s^(1/n)]")
+                s+="%s\n" % fielddisplay(self,"rheology_n","Glen's flow law exponent")
+                s+="%s\n" % fielddisplay(self,"rheology_Z","rheology multiplier")
+                s+="%s\n" % fielddisplay(self,"rheology_law","law for the temperature dependance of the rheology: 'None', 'Paterson' or 'Arrhenius'")
+                return s
+        # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'enum',MaterialsEnum(),'data',MatdamageiceEnum(),'format','Integer')
                 WriteData(fid,'object',self,'class','materials','fieldname','rho_ice','format','Double')
 …
                 WriteData(fid,'object',self,'class','materials','fieldname','rheology_Z','format','DoubleMat','mattype',1)
                 WriteData(fid,'data',StringToEnum(self.rheology_law)[0],'enum',MaterialsRheologyLawEnum(),'format','Integer')
+                WriteData(fid,'object',self,'class','materials','fieldname','lithosphere_shear_modulus','format','Double');
+                WriteData(fid,'object',self,'class','materials','fieldname','lithosphere_density','format','Double','scale',10.**3.);
+                WriteData(fid,'object',self,'class','materials','fieldname','mantle_shear_modulus','format','Double');
+                WriteData(fid,'object',self,'class','materials','fieldname','mantle_density','format','Double','scale',10.**3.);
         # }}}

issm/trunk/src/m/classes/matice.m

-              r14310
+              r15396
                 rheology_n   = NaN;
                 rheology_law = '';
+                %gia:
+                lithosphere_shear_modulus  = 0.;
+                lithosphere_density        = 0.;
+                mantle_shear_modulus       = 0.;
+                mantle_density             = 0.;
         end
         methods
 …
                         %available: none, paterson and arrhenius
                         obj.rheology_law='Paterson';
+                        % GIA:
+                        obj.lithosphere_shear_modulus  = 6.7*10^10;  % (Pa)
+                        obj.lithosphere_density        = 3.32;       % (g/cm^-3)
+                        obj.mantle_shear_modulus       = 1.45*10^11; % (Pa)
+                        obj.mantle_density             = 3.34;       % (g/cm^-3)
                 end % }}}
                 function md = checkconsistency(obj,md,solution,analyses) % {{{
 …
                         md = checkfield(md,'materials.rheology_n','>',0,'size',[md.mesh.numberofelements 1]);
                         md = checkfield(md,'materials.rheology_law','values',{'None' 'Paterson' 'Arrhenius'});
+                        if ismember(GiaAnalysisEnum(),analyses),
+                                md = checkfield(md,'materials.lithosphere_shear_modulus','>',0,'numel',1);
+                                md = checkfield(md,'materials.lithosphere_density','>',0,'numel',1);
+                                md = checkfield(md,'materials.mantle_shear_modulus','>',0,'numel',1);
+                                md = checkfield(md,'materials.mantle_density','>',0,'numel',1);
+                        end
                 end % }}}
                 function disp(obj) % {{{
 …
                         fielddisplay(obj,'rheology_n','Glen''s flow law exponent');
                         fielddisplay(obj,'rheology_law','law for the temperature dependance of the rheology: ''None'', ''Paterson'' or ''Arrhenius''');
+                        fielddisplay(obj,'lithosphere_shear_modulus','Lithosphere shear modulus [Pa]');
+                        fielddisplay(obj,'lithosphere_density','Lithosphere density [g/cm^-3]');
+                        fielddisplay(obj,'mantle_shear_modulus','Mantle shear modulus [Pa]');
+                        fielddisplay(obj,'mantle_density','Mantle density [g/cm^-3]');
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'enum',MaterialsEnum(),'data',MaticeEnum(),'format','Integer');
                         WriteData(fid,'object',obj,'class','materials','fieldname','rho_ice','format','Double');
 …
                         WriteData(fid,'object',obj,'class','materials','fieldname','rheology_n','format','DoubleMat','mattype',2);
                         WriteData(fid,'data',StringToEnum(obj.rheology_law),'enum',MaterialsRheologyLawEnum(),'format','Integer');
+                        WriteData(fid,'object',obj,'class','materials','fieldname','lithosphere_shear_modulus','format','Double');
+                        WriteData(fid,'object',obj,'class','materials','fieldname','lithosphere_density','format','Double','scale',10^3);
+                        WriteData(fid,'object',obj,'class','materials','fieldname','mantle_shear_modulus','format','Double');
+                        WriteData(fid,'object',obj,'class','materials','fieldname','mantle_density','format','Double','scale',10^3);
                 end % }}}
         end

issm/trunk/src/m/classes/matice.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+                self.rho_ice                    = 0.
+                self.rho_water                  = 0.
+                self.rho_freshwater             = 0.
+                self.mu_water                   = 0.
+                self.heatcapacity               = 0.
+                self.latentheat                 = 0.
+                self.thermalconductivity        = 0.
+                self.meltingpoint               = 0.
+                self.beta                       = 0.
+                self.mixed_layer_capacity       = 0.
+                self.thermal_exchange_velocity  = 0.
+                self.rheology_B   = float('NaN')
+                self.rheology_n   = float('NaN')
+                self.rheology_law = ''
+        def __init__(self): # {{{
+                self.rho_ice                   = 0.
+                self.rho_water                 = 0.
+                self.rho_freshwater            = 0.
+                self.mu_water                  = 0.
+                self.heatcapacity              = 0.
+                self.latentheat                = 0.
+                self.thermalconductivity       = 0.
+                self.meltingpoint              = 0.
+                self.beta                      = 0.
+                self.mixed_layer_capacity      = 0.
+                self.thermal_exchange_velocity = 0.
+                self.rheology_B                = float('NaN')
+                self.rheology_n                = float('NaN')
+                self.rheology_law              = ''
+                #gia:
+                self.lithosphere_shear_modulus  = 0.
+                self.lithosphere_density        = 0.
+                self.mantle_shear_modulus       = 0.
+                self.mantle_density             = 0.
                 self.setdefaultparameters()
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   Materials:"
 …
                 string="%s\n%s"%(string,fielddisplay(self,"rheology_n","Glen's flow law exponent"))
                 string="%s\n%s"%(string,fielddisplay(self,"rheology_law","law for the temperature dependance of the rheology: 'None', 'Paterson' or 'Arrhenius'"))
+                string="%s\n%s"%(string,fielddisplay(self,"lithosphere_shear_modulus","Lithosphere shear modulus [Pa]"))
+                string="%s\n%s"%(string,fielddisplay(self,"lithosphere_density","Lithosphere density [g/cm^-3]"))
+                string="%s\n%s"%(string,fielddisplay(self,"mantle_shear_modulus","Mantle shear modulus [Pa]"))
+                string="%s\n%s"%(string,fielddisplay(self,"mantle_density","Mantle density [g/cm^-3]"))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #ice density (kg/m^3)
                 self.rho_ice=917.
 …
                 #available: none, paterson and arrhenius
                 self.rheology_law='Paterson'
+                # GIA:
+                self.lithosphere_shear_modulus  = 6.7*10**10  # (Pa)
+                self.lithosphere_density        = 3.32        # (g/cm^-3)
+                self.mantle_shear_modulus       = 1.45*10**11 # (Pa)
+                self.mantle_density             = 3.34        # (g/cm^-3)
                 return self
                 #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 md = checkfield(md,'materials.rho_ice','>',0)
 …
                 md = checkfield(md,'materials.rheology_n','>',0,'size',[md.mesh.numberofelements])
                 md = checkfield(md,'materials.rheology_law','values',['None','Paterson','Arrhenius'])
+                md = checkfield(md,'materials.lithosphere_shear_modulus','>',0,'numel',[1]);
+                md = checkfield(md,'materials.lithosphere_density','>',0,'numel',[1]);
+                md = checkfield(md,'materials.mantle_shear_modulus','>',0,'numel',[1]);
+                md = checkfield(md,'materials.mantle_density','>',0,'numel',[1]);
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'enum',MaterialsEnum(),'data',MaticeEnum(),'format','Integer');
                 WriteData(fid,'object',self,'class','materials','fieldname','rho_ice','format','Double')
 …
                 WriteData(fid,'object',self,'class','materials','fieldname','rheology_n','format','DoubleMat','mattype',2)
                 WriteData(fid,'data',StringToEnum(self.rheology_law)[0],'enum',MaterialsRheologyLawEnum(),'format','Integer')
+                WriteData(fid,'object',self,'class','materials','fieldname','lithosphere_shear_modulus','format','Double');
+                WriteData(fid,'object',self,'class','materials','fieldname','lithosphere_density','format','Double','scale',10.**3.);
+                WriteData(fid,'object',self,'class','materials','fieldname','mantle_shear_modulus','format','Double');
+                WriteData(fid,'object',self,'class','materials','fieldname','mantle_density','format','Double','scale',10.**3.);
         # }}}

issm/trunk/src/m/classes/mesh.m

-              r13975
+              r15396
                 extractedvertices           = NaN
                 extractedelements           = NaN
+        end
+        methods (Static)
+                function obj = loadobj(obj) % {{{
+                        % This function is directly called by matlab when a model object is
+                        % loaded. Update old properties here
+                        %2012 June 28th
+                        if numel(obj.edges)>1 & any(isnan(obj.edges(:)))
+                                disp('Update model edges from previous version');
+                                obj.edges(isnan(obj.edges))=-1;
+                        end
+                end% }}}
         end
         methods
 …
                                 fielddisplay(obj,'numberofelements2d','number of elements');
                                 fielddisplay(obj,'numberofvertices2d','number of vertices');
                                 fielddisplay(obj,'elements2d','index into (x,y,z), coordinates of the vertices');
                                 fielddisplay(obj,'x2d','vertices x coordinate');
                                 fielddisplay(obj,'y2d','vertices y coordinate');
+                                fielddisplay(obj,'elements2d','vertex indices of the mesh elements');
+                                fielddisplay(obj,'x2d','vertices x coordinate [m]');
+                                fielddisplay(obj,'y2d','vertices y coordinate [m]');
                                 disp(sprintf('\n      Elements and vertices of the extruded 3d mesh:'));
 …
                         fielddisplay(obj,'numberofelements','number of elements');
                         fielddisplay(obj,'numberofvertices','number of vertices');
                         fielddisplay(obj,'elements','index into (x,y,z), coordinates of the vertices');
                         fielddisplay(obj,'x','vertices x coordinate');
                         fielddisplay(obj,'y','vertices y coordinate');
                         fielddisplay(obj,'z','vertices z coordinate');
+                        fielddisplay(obj,'elements','vertex indices of the mesh elements');
+                        fielddisplay(obj,'x','vertices x coordinate [m]');
+                        fielddisplay(obj,'y','vertices y coordinate [m]');
+                        fielddisplay(obj,'z','vertices z coordinate [m]');
                         fielddisplay(obj,'edges','edges of the 2d mesh (vertex1 vertex2 element1 element2)');
                         fielddisplay(obj,'numberofedges','number of edges of the 2d mesh');
                         disp(sprintf('\n      Properties:'));
                         fielddisplay(obj,'dimension','mesh dimension (2d or 3d)');
+                        fielddisplay(obj,'dimension','mesh dimension');
                         fielddisplay(obj,'numberoflayers','number of extrusion layers');
                         fielddisplay(obj,'vertexonbed','lower vertices flags list');
 …
                         disp(sprintf('\n      Projection:'));
                         fielddisplay(obj,'lat','vertices latitude');
                         fielddisplay(obj,'long','vertices longitude');
+                        fielddisplay(obj,'lat','vertices latitude [degrees]');
+                        fielddisplay(obj,'long','vertices longitude [degrees]');
                         fielddisplay(obj,'hemisphere','Indicate hemisphere ''n'' or ''s'' ');
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'object',obj,'fieldname','x','format','DoubleMat','mattype',1);
                         WriteData(fid,'object',obj,'fieldname','y','format','DoubleMat','mattype',1);

issm/trunk/src/m/classes/mesh.py

-              r14310
+              r15396
-#module imports
 import numpy
 from fielddisplay import fielddisplay
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.x                           = float('NaN');
                 self.y                           = float('NaN');
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   Mesh:"
 …
                         string="%s\n%s"%(string,fielddisplay(self,"numberofelements2d","number of elements"))
                         string="%s\n%s"%(string,fielddisplay(self,"numberofvertices2d","number of vertices"))
                         string="%s\n%s"%(string,fielddisplay(self,"elements2d","index into (x,y,z), coordinates of the vertices"))
                         string="%s\n%s"%(string,fielddisplay(self,"x2d","vertices x coordinate"))
                         string="%s\n%s"%(string,fielddisplay(self,"y2d","vertices y coordinate"))
+                        string="%s\n%s"%(string,fielddisplay(self,"elements2d","vertex indices of the mesh elements"))
+                        string="%s\n%s"%(string,fielddisplay(self,"x2d","vertices x coordinate [m]"))
+                        string="%s\n%s"%(string,fielddisplay(self,"y2d","vertices y coordinate [m]"))
                         string="%s\n%s"%(string,"\n\n      Elements and vertices of the extruded 3d mesh:")
 …
                 string="%s\n%s"%(string,fielddisplay(self,"numberofelements","number of elements"))
                 string="%s\n%s"%(string,fielddisplay(self,"numberofvertices","number of vertices"))
                 string="%s\n%s"%(string,fielddisplay(self,"elements","index into (x,y,z), coordinates of the vertices"))
                 string="%s\n%s"%(string,fielddisplay(self,"x","vertices x coordinate"))
                 string="%s\n%s"%(string,fielddisplay(self,"y","vertices y coordinate"))
                 string="%s\n%s"%(string,fielddisplay(self,"z","vertices z coordinate"))
+                string="%s\n%s"%(string,fielddisplay(self,"elements","vertex indices of the mesh elements"))
+                string="%s\n%s"%(string,fielddisplay(self,"x","vertices x coordinate [m]"))
+                string="%s\n%s"%(string,fielddisplay(self,"y","vertices y coordinate [m]"))
+                string="%s\n%s"%(string,fielddisplay(self,"z","vertices z coordinate [m]"))
                 string="%s\n%s"%(string,fielddisplay(self,"edges","edges of the 2d mesh (vertex1 vertex2 element1 element2)"))
                 string="%s\n%s"%(string,fielddisplay(self,"numberofedges","number of edges of the 2d mesh"))
 …
                 string="%s%s"%(string,"\n\n      Projection:")
                 string="%s\n%s"%(string,fielddisplay(self,"lat","vertices latitude"))
                 string="%s\n%s"%(string,fielddisplay(self,"long","vertices longitude"))
+                string="%s\n%s"%(string,fielddisplay(self,"lat","vertices latitude [degrees]"))
+                string="%s\n%s"%(string,fielddisplay(self,"long","vertices longitude [degrees]"))
                 string="%s\n%s"%(string,fielddisplay(self,"hemisphere","Indicate hemisphere 'n' or 's'"))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #the connectivity is the averaged number of nodes linked to a
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','x','format','DoubleMat','mattype',1)
                 WriteData(fid,'object',self,'fieldname','y','format','DoubleMat','mattype',1)
 …
                 WriteData(fid,'object',self,'fieldname','numberofelements2d','format','Integer')
         # }}}

issm/trunk/src/m/classes/miscellaneous.m

r13395	r15396
35	35
36	36	end % }}}
37		function marshall(obj,fid) % {{{
	37	function marshall(obj,md,fid) % {{{
38	38	WriteData(fid,'object',obj,'fieldname','name','format','String');
39	39	end % }}}

issm/trunk/src/m/classes/miscellaneous.py

-              r14310
+              r15396
-#module imports
 from collections import OrderedDict
 from fielddisplay import fielddisplay
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.notes = ''
                 self.name  = ''
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   miscellaneous parameters:'
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 md = checkfield(md,'miscellaneous.name','empty',1)
                 return md
         # }}}
+        def marshall(self,fid):    #  {{{
+        def marshall(self,md,fid):    #  {{{
                 WriteData(fid,'object',self,'fieldname','name','format','String')
         # }}}

issm/trunk/src/m/classes/model/model.m

-              r14310
+              r15396
                 verbose          = 0;
                 settings         = 0;
                 solver           = 0;
+                toolkits         = 0;
                 cluster          = 0;
 …
                 steadystate      = 0;
                 transient        = 0;
+                gia              = 0;
                 autodiff         = 0;
 …
                                 end
                         end
+                        %2012 June 28th
+                        if sum(sum(isnan(md.mesh.edges)))>0
+                                disp('Update model edges from previous version');
+                                md.mesh.edges(isnan(md.mesh.edges))=-1;
+                        %2013 April 12
+                        if numel(md.diagnostic.loadingforce==1)
+                                md.diagnostic.loadingforce=0*ones(md.mesh.numberofvertices,3);
+                        end
+                        %2013 April 17
+                        if isa(md.hydrology,'hydrology'),
+                                disp('Recovering old hydrology class');
+                                md.hydrology=hydrologyshreve(md.materials);
                         end
 …
                         if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
+                        %gia
+                        if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
+                        if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
                         %bedinfo and surface info
                         md.mesh.elementonbed=ones(md.mesh.numberofelements2d,1);
 …
                         md.diagnostic.spcvz=project2d(md,md.diagnostic.spcvz,md.mesh.numberoflayers);
                         md.diagnostic.referential=project2d(md,md.diagnostic.referential,md.mesh.numberoflayers);
+                        md.diagnostic.loadingforce=project2d(md,md.diagnostic.loadingforce,md.mesh.numberoflayers);
                         md.prognostic.spcthickness=project2d(md,md.prognostic.spcthickness,md.mesh.numberoflayers);
                         md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
 …
                         md.mask.elementonwater=project2d(md,md.mask.elementonwater,1);
                         md.mask.vertexonwater=project2d(md,md.mask.vertexonwater,1);
                         md.mask.vertexonrock=project2d(md,md.mask.vertexonrock,1);
+                        %md.mask.vertexonrock=project2d(md,md.mask.vertexonrock,1);
                         %lat long
 …
                         md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
                         md.diagnostic.referential=project3d(md,'vector',md.diagnostic.referential,'type','node');
+                        md.diagnostic.loadingforce=project3d(md,'vector',md.diagnostic.loadingforce,'type','node');
                         %in 3d, pressureload: [node1 node2 node3 node4 element]
 …
                         md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
                         md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
+                        md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
+                        md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
                         md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
                         md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
 …
                         if isfield(structmd,'gridonwater'), md.mask.vertexonwater=structmd.gridonwater; end
                         if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
                         if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.solver=structmd.petscoptions; end
+                        if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
                         if isfield(structmd,'g'), md.constants.g=structmd.g; end
                         if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
 …
                                 pos=find(~isnan(structmd.spcvz)); md.diagnostic.spcvz(pos)=structmd.spcvz(pos);
                         end
+                        if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
+                                pos=find(structmd.pressureload(:,end)==120); md.diagnostic.icefront(pos,end)=0;
+                                pos=find(structmd.pressureload(:,end)==118); md.diagnostic.icefront(pos,end)=1;
+                                pos=find(structmd.pressureload(:,end)==119); md.diagnostic.icefront(pos,end)=2;
+                        if isfield(structmd,'pressureload'),
+                                if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
+                                        pos=find(structmd.pressureload(:,end)==120); md.diagnostic.icefront(pos,end)=0;
+                                        pos=find(structmd.pressureload(:,end)==118); md.diagnostic.icefront(pos,end)=1;
+                                        pos=find(structmd.pressureload(:,end)==119); md.diagnostic.icefront(pos,end)=2;
+                                end
                         end
                         if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
 …
                         end
+                        if ~isfield(structmd,'loadingforce');
+                                md.diagnostic.loadingforce=0*ones(md.mesh.numberofvertices,3);
+                        end
                 end% }}}
                 function md = setdefaultparameters(md) % {{{
 …
                         md.flowequation     = flowequation();
                         md.debug            = debug();
                         md.verbose          = verbose('solution',true,'qmu',true,'control',true);
+                        md.verbose          = verbose();
                         md.settings         = settings();
+                        md.solver           = solver();
+                        if ismumps(),
+                                md.solver           = addoptions(md.solver,DiagnosticVertAnalysisEnum(),mumpsoptions());
+                        else
+                                md.solver           = addoptions(md.solver,DiagnosticVertAnalysisEnum(),iluasmoptions());
+                        end
+                        md.toolkits         = toolkits();
                         md.cluster          = generic();
                         md.balancethickness = balancethickness();
                         md.diagnostic       = diagnostic();
                         md.hydrology        = hydrology();
+                        md.hydrology        = hydrologyshreve();
                         md.prognostic       = prognostic();
                         md.thermal          = thermal();
                         md.steadystate      = steadystate();
                         md.transient        = transient();
+                        md.gia              = gia();
                         md.autodiff         = autodiff();
                         md.flaim            = flaim();
 …
                         disp(sprintf('%19s: %-22s -- %s','verbose'         ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
                         disp(sprintf('%19s: %-22s -- %s','settings'        ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
                         disp(sprintf('%19s: %-22s -- %s','solver'          ,['[1x1 ' class(obj.solver) ']'],'PETSc options for each solution'));
+                        disp(sprintf('%19s: %-22s -- %s','toolkits'          ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
                         disp(sprintf('%19s: %-22s -- %s','cluster'         ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
                         disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
 …
                         disp(sprintf('%19s: %-22s -- %s','steadystate'     ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
                         disp(sprintf('%19s: %-22s -- %s','transient'       ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
+                        disp(sprintf('%19s: %-22s -- %s','gia'       ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
                         disp(sprintf('%19s: %-22s -- %s','autodiff'        ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
                         disp(sprintf('%19s: %-22s -- %s','flaim'           ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
 …
                 end % }}}
                 function memory(obj) % {{{
+                disp(sprintf('\nMemory imprint: '));
+                objects=fields(obj);
+                memory=0;
+                disp(sprintf('\nMemory imprint:\n'));
+                fields=properties('model');
+                mem=0;
+                for i=1:length(fields),
+                        field=obj.(fields{i});
+                        s=whos('field');
+                        mem=mem+s.bytes/1e6;
+                        disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
+                end
+                disp(sprintf('%19s--%10s','--------------','--------------'));
+                disp(sprintf('%19s: %g Mb','Total',mem));
+                end % }}}
+                function netcdf(obj,filename) % {{{
+                %NETCDF - save model as netcdf
+                %
+                %   Usage:
+                %      netcdf(md,filename)
+                %
+                %   Example:
+                %      netcdf(md,'model.nc');
+                disp('Saving model as NetCDF');
+                %1. Create NetCDF file
+                ncid=netcdf.create(filename,'CLOBBER');
+                netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
+                netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
+                netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
+                netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
+                %Preallocate variable id, needed to write variables in netcdf file
+                var_id=zeros(1000,1);%preallocate
+                for step=1:2,
+                        counter=0;
+                        [var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
+                        if step==1, netcdf.endDef(ncid); end
+                end
+                if counter>1000,
+                        warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
+                end
+                netcdf.close(ncid)
+                end % }}}
+                function xylim(obj) % {{{
+                        xlim([min(obj.mesh.x) max(obj.mesh.x)]);
+                        ylim([min(obj.mesh.y) max(obj.mesh.y)])
+                end % }}}
+                function md=upload(md) % {{{
+                %the goal of this routine is to upload the model onto a server, and to empty it.
+                %So first, save the model with a unique name and upload the file to the server:
+                random_part=fix(rand(1)*10000);
+                id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part)  '-' getenv('USER') '-' oshostname() '.upload'];
+                eval(['save ' id ' md']);
+                %Now, upload the file:
+                issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
+                %Now, empty this model of everything except settings, and record name of file we just uploaded!
+                settings_back=md.settings;
+                md=model();
+                md.settings=settings_back;
+                md.settings.upload_filename=id;
+                %get locally rid of file that was uploaded
+                eval(['delete ' id]);
+                end % }}}
+                function md=download(md) % {{{
+                for i=1:length(objects),
+                        field=objects{i};
+                        realobject=obj.(field);
+                        s=whos('realobject');
+                        memory=memory+s.bytes/1e6;
+                        disp(sprintf('%19s: %g Mb',field,s.bytes/1e6));
+                end
+                disp(sprintf('Overall: %g Mb',memory));
+                %the goal of this routine is to download the internals of the current model from a server, because
+                %this model is empty, except for the settings which tell us where to go and find this model!
+                %Download the file:
+                issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
+                name=md.settings.upload_filename;
+                %Now, load this model:
+                md=loadmodel(md.settings.upload_filename);
+                %get locally rid of file that was downloaded
+                eval(['delete ' name]);
                 end % }}}
         end

issm/trunk/src/m/classes/model/model.py

-              r14310
+              r15396
 from verbose import verbose
 from settings import settings
 from solver import solver
+from toolkits import toolkits
 from generic import generic
 from balancethickness import balancethickness
 from diagnostic import diagnostic
 from groundingline import groundingline
 from hydrology import hydrology
+from hydrologyshreve import hydrologyshreve
 from prognostic import prognostic
 from thermal import thermal
 from steadystate import steadystate
 from transient import transient
+from gia import gia
 from autodiff import autodiff
 from flaim import flaim
 …
 class model(object):
         #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self):#{{{
                 self.mesh             = mesh()
                 self.mask             = mask()
 …
                 self.debug            = debug()
                 self.verbose          = verbose('solution',True,'qmu',True,'control',True)
+                self.verbose          = verbose()
                 self.settings         = settings()
+                self.solver           = solver()
+                if ismumps():
+                        self.solver.addoptions(DiagnosticVertAnalysisEnum(),mumpsoptions())
+                else:
+                        self.solver.addoptions(DiagnosticVertAnalysisEnum(),iluasmoptions())
+                self.toolkits         = toolkits()
                 self.cluster          = generic()
 …
                 self.diagnostic       = diagnostic()
                 self.groundingline    = groundingline()
                 self.hydrology        = hydrology()
+                self.hydrology        = hydrologyshreve()
                 self.prognostic       = prognostic()
                 self.thermal          = thermal()
                 self.steadystate      = steadystate()
                 self.transient        = transient()
+                self.gia              = gia()
                 self.autodiff         = autodiff()
 …
                 self.private          = private()
                 #}}}
         def properties(self):    # {{{
                 # ordered list of properties since vars(self) is random
 …
                         'verbose',\
                         'settings',\
                         'solver',\
+                        'toolkits',\
                         'cluster',\
                         'balancethickness',\
 …
                         'steadystate',\
                         'transient',\
+                                  'gia',\
                         'autodiff',\
                         'flaim',\
 …
                         'private']
         # }}}
+        def __repr__(obj):
+                # {{{ Display
+        def __repr__(obj): #{{{
                 #print "Here %s the number: %d" % ("is", 37)
                 string="%19s: %-22s -- %s" % ("mesh","[%s,%s]" % ("1x1",obj.mesh.__class__.__name__),"mesh properties")
 …
                 string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("verbose","[%s,%s]" % ("1x1",obj.verbose.__class__.__name__),"verbosity level in solve"))
                 string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("settings","[%s,%s]" % ("1x1",obj.settings.__class__.__name__),"settings properties"))
                 string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("solver","[%s,%s]" % ("1x1",obj.solver.__class__.__name__),"PETSc options for each solution"))
+                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("toolkits","[%s,%s]" % ("1x1",obj.toolkits.__class__.__name__),"PETSc options for each solution"))
                 string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("cluster","[%s,%s]" % ("1x1",obj.cluster.__class__.__name__),"cluster parameters (number of cpus...)"))
                 string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("balancethickness","[%s,%s]" % ("1x1",obj.balancethickness.__class__.__name__),"parameters for balancethickness solution"))
 …
                 return string
         # }}}
         def checkmessage(self,string):    # {{{
                 print ("model not consistent: %s" % string)
 …
                 return self
         # }}}
         def extract(md,area):    # {{{
                 """
 …
                 return md2
         # }}}
         def extrude(md,*args):    # {{{
                 """
 …
                 md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node')
                 md.diagnostic.referential=project3d(md,'vector',md.diagnostic.referential,'type','node')
+                md.diagnostic.loadingforce=project3d(md,'vector',md.diagnostic.loadingforce,'type','node')
                 #in 3d, pressureload: [node1 node2 node3 node4 element]
 …
                 md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node')
                 md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node')
+                md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node')
+                md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node')
                 md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node')
                 md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node')
 …
                 return md
                 # }}}

issm/trunk/src/m/classes/organizer.py

-              r13975
+              r15396
                         self.trunkprefix=trunkprefix
         #}}}
         def __repr__(self):    # {{{
                 s =""
 …
                                 s+="%s\n" % "   step #%2i: '%s'",step['id'],step['string']
         #}}}
         def load(self,string):    # {{{
 …
                 return md
         #}}}
         def loadmodel(self,string):    # {{{
 …
                         raise IOerror("Could not find '%s'" % path)
         #}}}
         def perform(self,string):    # {{{
 …
                 return bool
         #}}}
         def savemodel(self,md):    # {{{
 …
                 savevars(name,'md',md)
         #}}}

issm/trunk/src/m/classes/pairoptions.m

r14310	r15396
33	33	%check length of input
34	34	if mod((nargin-1),2),
35		error('~~error: an even number of options is required~~')
	35	error('Invalid parameter/value pair arguments')
36	36	end
37	37	numoptions = (nargin-1)/2;

issm/trunk/src/m/classes/pairoptions.py

-              r14310
+              r15396
         """
         def __init__(self,*arg):
+        def __init__(self,*arg): # {{{
                 self.functionname = ''
                 self.list         = OrderedDict()
 …
                         self.buildlist(*arg)
         # }}}
-        def buildlist(self,*arg):    # {{{
-                """BUILDLIST - build list of objects from input"""
-                #check length of input
-                if len(arg) % 2:
-                        raise TypeError('error: an even number of options is required')
-                numoptions = len(arg)/2
-                #go through arg and build list of objects
-                for i in xrange(numoptions):
-                        if isinstance(arg[2*i],(str,unicode)):
-                                self.list[arg[2*i]] = arg[2*i+1];
-                        else:
-                                #option is not a string, ignore it
-                                print "WARNING: option number %d is not a string and will be ignored." % (i+1)
-        # }}}
-        def addfield(self,field,value):    # {{{
-                """ADDFIELD - add a field to an options list"""
-                if isinstance(field,(str,unicode)):
-                        if field in self.list:
-                                print "WARNING: field '%s' with value=%s exists and will be overwritten with value=%s." % (field,str(self.list[field]),str(value))
-                        self.list[field] = value
-        # }}}
-        def addfielddefault(self,field,value):    # {{{
-                """ADDFIELDDEFAULT - add a field to an options list if it does not already exist"""
-                if isinstance(field,(str,unicode)):
-                        if field not in self.list:
-                                self.list[field] = value
-        # }}}
-        def AssignObjectFields(self,obj2):    # {{{
-                """ASSIGNOBJECTFIELDS - assign object fields from options"""
-                for item in self.list.iteritems():
-                        if item[0] in dir(obj2):
-                                setattr(obj2,item[0],item[1])
-                        else:
-                                print "WARNING: field '%s' is not a property of '%s'." % (item[0],type(obj2))
-                return obj2
-        # }}}
-        def changefieldvalue(self,field,newvalue):    # {{{
-                """CHANGEOPTIONVALUE - change the value of an option in an option list"""
-                self.list[field]=newvalue;
-        # }}}
-#       function obj = deleteduplicates(obj,warn) % {{{
-#       %DELETEDUPLICATES - delete duplicates in an option list
+#
-#               %track the first occurrence of each option
-#               [dummy lines]=unique(obj.list(:,1),'first');
-#               clear dummy
+#
-#               %warn user if requested
-#               if warn,
-#                       numoptions=size(obj.list,1);
-#                       for i=1:numoptions,
-#                               if ~ismember(i,lines),
-#                                       disp(['WARNING: option ' obj.list{i,1} ' appeared more than once. Only its first occurrence will be kept'])
-#                               end
-#                       end
-#               end
+#
-#               %remove duplicates from the options list
-#               obj.list=obj.list(lines,:);
-#       end % }}}
         def __repr__(self):    # {{{
                 s="   functionname: '%s'\n" % self.functionname
 …
                 return s
         # }}}
+        def buildlist(self,*arg):    # {{{
+                """BUILDLIST - build list of objects from input"""
+                #check length of input
+                if len(arg) % 2:
+                        raise TypeError('Invalid parameter/value pair arguments')
+                numoptions = len(arg)/2
+                #go through arg and build list of objects
+                for i in xrange(numoptions):
+                        if isinstance(arg[2*i],(str,unicode)):
+                                self.list[arg[2*i]] = arg[2*i+1];
+                        else:
+                                #option is not a string, ignore it
+                                print "WARNING: option number %d is not a string and will be ignored." % (i+1)
+        # }}}
+        def addfield(self,field,value):    # {{{
+                """ADDFIELD - add a field to an options list"""
+                if isinstance(field,(str,unicode)):
+                        if field in self.list:
+                                print "WARNING: field '%s' with value=%s exists and will be overwritten with value=%s." % (field,str(self.list[field]),str(value))
+                        self.list[field] = value
+        # }}}
+        def addfielddefault(self,field,value):    # {{{
+                """ADDFIELDDEFAULT - add a field to an options list if it does not already exist"""
+                if isinstance(field,(str,unicode)):
+                        if field not in self.list:
+                                self.list[field] = value
+        # }}}
+        def AssignObjectFields(self,obj2):    # {{{
+                """ASSIGNOBJECTFIELDS - assign object fields from options"""
+                for item in self.list.iteritems():
+                        if item[0] in dir(obj2):
+                                setattr(obj2,item[0],item[1])
+                        else:
+                                print "WARNING: field '%s' is not a property of '%s'." % (item[0],type(obj2))
+                return obj2
+        # }}}
+        def changefieldvalue(self,field,newvalue):    # {{{
+                """CHANGEOPTIONVALUE - change the value of an option in an option list"""
+                self.list[field]=newvalue;
+        # }}}
         def exist(self,field):    # {{{
                 """EXIST - check if the option exist"""
 …
                         return False
         # }}}
-        #def fieldoccurrences(self,field): #{{{
-        #       '''
-        #       FIELDOCCURRENCES - get number of occurrence of a field
-        #       '''
+        #
-        #       #check input
-        #       if not isinstance(field,(str,unicode)):
-        #               raise TypeError("fieldoccurrences error message: field should be a string")
-        #       #get number of occurrence
-        #       # ??
-        #       #return num
-        #       #% }}}
         def getfieldvalue(self,field,default=None):    # {{{
                 """
 …
                 return value
         # }}}
         def removefield(self,field,warn):    # {{{
                 """
 …
                                 print "removefield info: option '%s' has been removed from the list of options." % field
         # }}}
+        def marshall(self,fid,firstindex):    # {{{
+        def marshall(self,md,fid,firstindex):    # {{{
                 for i,item in enumerate(self.list.iteritems()):
 …
                                 raise TypeError("Cannot marshall option '%s': format not supported yet." % name)
         # }}}

issm/trunk/src/m/classes/planetmesh.m

-              r13975
+              r15396
 %MESH class definition
+%PLANETMESH class definition
+%
 %   Usage:
 …
                 numberofelements            = 0;
                 numberofvertices            = 0;
-                lat                         = NaN
-                long                        = NaN
                 vertexconnectivity          = NaN
 …
                         md = checkfield(md,'planetmesh.numberofelements','>',0);
                         md = checkfield(md,'planetmesh.numberofvertices','>',0);
-                        %no checks for numberofedges lat long and hemisphere
                         if (md.planetmesh.dimension==2),
                                 md = checkfield(md,'planetmesh.average_vertex_connectivity','>=',9,'message','''planetmesh.average_vertex_connectivity'' should be at least 9 in 2d');
 …
                         fielddisplay(obj,'numberofelements','number of elements');
                         fielddisplay(obj,'numberofvertices','number of vertices');
                         fielddisplay(obj,'elements','index into (x,y,z), coordinates of the vertices');
                         fielddisplay(obj,'x','vertices x coordinate');
                         fielddisplay(obj,'y','vertices y coordinate');
                         fielddisplay(obj,'z','vertices z coordinate');
                         fielddisplay(obj,'r','vertices r coordinate');
                         fielddisplay(obj,'theta','vertices theta coordinate');
                         fielddisplay(obj,'phi','vertices phi coordinate');
+                        fielddisplay(obj,'elements','vertex indices of the mesh elements');
+                        fielddisplay(obj,'x','vertices x coordinate [m]');
+                        fielddisplay(obj,'y','vertices y coordinate [m]');
+                        fielddisplay(obj,'z','vertices z coordinate [m]');
+                        fielddisplay(obj,'r','vertices r coordinate [m]');
+                        fielddisplay(obj,'theta','vertices theta coordinate [degrees]');
+                        fielddisplay(obj,'phi','vertices phi coordinate [degrees]');
                         disp(sprintf('\n      Properties:'));
 …
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'object',obj,'fieldname','x','format','DoubleMat','mattype',1);
                         WriteData(fid,'object',obj,'fieldname','y','format','DoubleMat','mattype',1);

issm/trunk/src/m/classes/plotoptions.m

-              r14310
+              r15396
                          %check length of input
                          if mod((nargin-1),2),
                                  error('buildlist error message: an even number of plotoptions is required')
+                                 error('Invalid parameter/value pair arguments')
                          end
 …
                          numoptions = (nargin-1)/2;
                          rawlist=cell(numoptions,2);
+                         counter=1;
                          for i=1:numoptions,
+                                 if ischar(varargin{2*i-1}),
+                                         rawlist{i,1}=varargin{2*i-1};
+                                         rawlist{i,2}=varargin{2*i};
+                                 optionname = varargin{2*i-1};
+                                 optionval  = varargin{2*i};
+                                 if ischar(optionname),
+                                         rawlist{counter,1}=optionname;
+                                         rawlist{counter,2}=optionval;
+                                         counter=counter+1;
                                  else
                                          %option is not a string, ignore it
                                          disp(['WARNING: option number ' num2str(i) ' is not a string, it will be ignored']);
                                          rawlist(i,:)=[];
+                                         rawlist(counter,:)=[];
                                          continue
                                  end
                          end
-                         %get figure number
-                         opt.figurenumber=getfieldvalue(rawoptions,'figure',1);
                          %get number of data to be plotted
 …
                                  opt.list{i}=deleteduplicates(opt.list{i},1);
                          end
+                         %Get figure number (should be in options for subplot 1)
+                         opt.figurenumber=getfieldvalue(opt.list{1},'figure',1);
+                         removefield(opt.list{1},'figure',0);
                  end
                  %}}}

issm/trunk/src/m/classes/plotoptions.py

-              r13975
+              r15396
         '''
         def __init__(self,*arg):
+        def __init__(self,*arg):# {{{
                 self.numberofplots = 0
                 self.figurenumber  = 1
 …
                 self.buildlist(*arg)
+                #}}}
         def __repr__(self): #{{{
                 s="\n"
 …
                 #check length of input
                 if len(arg) % 2:
                         raise TypeError('error: an even number of options is required')
+                        raise TypeError('Invalid parameter/value pair arguments')
                 #go through args and build list (like pairoptions)
 …
                 #get figure number
                 self.figurenumber=rawoptions.getfieldvalue('figure',1)
+                rawoptions.removefield('figure',0)
                 #get number of subplots

issm/trunk/src/m/classes/private.py

-              r13395
+              r15396
-#module imports
 from collections import OrderedDict
 from fielddisplay import fielddisplay
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.isconsistent = True
                 self.runtimename  = ''
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   private parameters: do not change'
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 return md
         # }}}

issm/trunk/src/m/classes/prognostic.m

-              r13975
+              r15396
                 function disp(obj) % {{{
                         disp(sprintf('   Prognostic solution parameters:'));
                         fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint)');
                         fielddisplay(obj,'min_thickness','minimum ice thickness allowed');
+                        fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint) [m]');
+                        fielddisplay(obj,'min_thickness','minimum ice thickness allowed [m]');
                         fielddisplay(obj,'hydrostatic_adjustment','adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' ');
                         fielddisplay(obj,'stabilization','0->no, 1->artificial_diffusivity, 2->streamline upwinding, 3->discontinuous Galerkin');
+                        fielddisplay(obj,'stabilization','0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin');
                         disp(sprintf('\n      %s','Penalty options:'));
 …
                 end % }}}
                 function marshall(obj,fid) % {{{
                         WriteData(fid,'object',obj,'fieldname','spcthickness','format','DoubleMat','mattype',1);
+                function marshall(obj,md,fid) % {{{
+                        WriteData(fid,'object',obj,'fieldname','spcthickness','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1);
                         WriteData(fid,'object',obj,'fieldname','min_thickness','format','Double');
                         WriteData(fid,'data',StringToEnum(obj.hydrostatic_adjustment),'format','Integer','enum',PrognosticHydrostaticAdjustmentEnum());

issm/trunk/src/m/classes/prognostic.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.spcthickness           = float('NaN')
                 self.min_thickness          = 0
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   Prognostic solution parameters:'
                 string="%s\n%s"%(string,fielddisplay(self,'spcthickness','thickness constraints (NaN means no constraint)'))
                 string="%s\n%s"%(string,fielddisplay(self,'min_thickness','minimum ice thickness allowed'))
+                string="%s\n%s"%(string,fielddisplay(self,'spcthickness','thickness constraints (NaN means no constraint) [m]'))
+                string="%s\n%s"%(string,fielddisplay(self,'min_thickness','minimum ice thickness allowed [m]'))
                 string="%s\n%s"%(string,fielddisplay(self,'hydrostatic_adjustment','adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' '))
                 string="%s\n%s"%(string,fielddisplay(self,'stabilization','0->no, 1->artificial_diffusivity, 2->streamline upwinding, 3->discontinuous Galerkin'))
+                string="%s\n%s"%(string,fielddisplay(self,'stabilization','0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin'))
                 string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested'))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #Type of stabilization to use 0:nothing 1:artificial_diffusivity 3:Discontinuous Galerkin
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','spcthickness','format','DoubleMat','mattype',1)
+        def marshall(self,md,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','spcthickness','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1)
                 WriteData(fid,'object',self,'fieldname','min_thickness','format','Double')
                 WriteData(fid,'data',StringToEnum(self.hydrostatic_adjustment)[0],'format','Integer','enum',PrognosticHydrostaticAdjustmentEnum())
 …
                 WriteData(fid,'object',self,'fieldname','requested_outputs','format','DoubleMat','mattype',3);
         # }}}

issm/trunk/src/m/classes/qmu.m

r13975	r15396
140	140
141	141	end % }}}
142		function marshall(obj,fid) % {{{
	142	function marshall(obj,md,fid) % {{{
143	143	WriteData(fid,'object',obj,'fieldname','isdakota','format','Boolean');
144	144	if ~obj.isdakota,

issm/trunk/src/m/classes/qmu.py

-              r13975
+              r15396
-#module imports
 import numpy
 from collections import OrderedDict
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.isdakota                    = 0
                 self.variables                   = OrderedDict()
 …
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
 …
                 return s
         # }}}
         def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','isdakota','format','Boolean')
                 if not self.isdakota:
 …
                 WriteData(fid,'data',flag,'enum',QmuMassFluxSegmentsPresentEnum(),'format','Boolean');
         # }}}

issm/trunk/src/m/classes/qmu/@dakota_method/dmeth_params_write.m

-              r14310
+              r15396
                 param_write(fid,sbeg,'seed','             = ','\n',dm.params);
                 param_write(fid,sbeg,'fixed_seed','','\n',dm.params);
+                if (str2num(dakotaversion())>4.2)
+                dver=textscan(dakotaversion(),'%[0123456789].%[0123456789].%[0123456789]');
+                if ((str2num(dver{1}{1})==4 && str2num(dver{2}{1})>2) || str2num(dver{1}{1})>4)
                     param_write(fid,sbeg,'rng','                ','\n',dm.params);
                 end

issm/trunk/src/m/classes/radaroverlay.m

-              r11995
+              r15396
                         fielddisplay(obj,'pwr','radar power image (matrix)');
                         fielddisplay(obj,'x','corresponding x coordinates');
                         fielddisplay(obj,'y','corresponding y coordinates');
+                        fielddisplay(obj,'x','corresponding x coordinates [m]');
+                        fielddisplay(obj,'y','corresponding y coordinates [m]');
                 end % }}}

issm/trunk/src/m/classes/radaroverlay.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.pwr = float('NaN')
                 self.x   = float('NaN')
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   radaroverlay parameters:'
                 string="%s\n%s"%(string,fielddisplay(self,'pwr','radar power image (matrix)'))
                 string="%s\n%s"%(string,fielddisplay(self,'x','corresponding x coordinates'))
                 string="%s\n%s"%(string,fielddisplay(self,'y','corresponding y coordinates'))
+                string="%s\n%s"%(string,fielddisplay(self,'x','corresponding x coordinates [m]'))
+                string="%s\n%s"%(string,fielddisplay(self,'y','corresponding y coordinates [m]'))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}

issm/trunk/src/m/classes/results.py

-              r13975
+              r15396
                 pass
         # }}}
         def __repr__(self):    # {{{
                 s ="   Model results:\n"
 …
                 return s
         # }}}
         def setdefaultparameters(self):    # {{{
                 #do nothing
                 return self
         # }}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 pass
         # }}}

issm/trunk/src/m/classes/rifts.m

r13975	r15396
54	54
55	55	end % }}}
56		function marshall(obj,fid) % {{{
	56	function marshall(obj,md,fid) % {{{
57	57
58	58	%Process rift info

issm/trunk/src/m/classes/rifts.py

-              r14310
+              r15396
-#module imports
 import numpy
 from fielddisplay import fielddisplay
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.riftstruct     = []
                 self.riftproperties = []
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   rifts parameters:'
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 if (not self.riftstruct) or numpy.any(isnans(self.riftstruct)):
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 #Process rift info
 …
                 WriteData(fid,'data',data,'enum',RiftsRiftstructEnum(),'format','DoubleMat','mattype',3)
         # }}}

issm/trunk/src/m/classes/settings.m

-              r14310
+              r15396
                 output_frequency    = 0;
                 waitonlock          = 0;
+                upload_server       = '';
+                upload_path         = '';
+                upload_login        = '';
+                upload_port         = 0;
+                upload_filename     = '';
         end
         methods
 …
                         %0 to deactivate
                         obj.waitonlock=Inf;
+                        %upload options:
+                        upload_port         = 0;
                 end % }}}
                 function md = checkconsistency(obj,md,solution,analyses) % {{{
 …
                         fielddisplay(obj,'results_as_patches','provide results as patches for each element (0 or 1)');
                         fielddisplay(obj,'output_frequency','frequency at which results are saved in all solutions with multiple time_steps');
+                        fielddisplay(obj,'waitonlock','maximum number of minutes to wait for batch results, or return 0');
+                        fielddisplay(obj,'waitonlock','maximum number of minutes to wait for batch results (NaN to deactivate)');
+                        fielddisplay(obj,'upload_server','server hostname where model should be uploaded');
+                        fielddisplay(obj,'upload_path','path on server where model should be uploaded');
+                        fielddisplay(obj,'upload_login','server login');
+                        fielddisplay(obj,'upload_port','port login (default is 0)');
+                        fielddisplay(obj,'upload_filename','unique id generated when uploading the file to server');
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'object',obj,'fieldname','io_gather','format','Boolean');
                         WriteData(fid,'object',obj,'fieldname','lowmem','format','Boolean');

issm/trunk/src/m/classes/settings.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.io_gather           = 0
                 self.lowmem              = 0
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   general settings parameters:"
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #are we short in memory ? (0 faster but requires more memory)
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 md = checkfield(md,'settings.io_gather','numel',[1],'values',[0,1])
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','io_gather','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','lowmem','format','Boolean')
 …
                         WriteData(fid,'enum',SettingsWaitonlockEnum(),'data',False,'format','Boolean');
         # }}}

issm/trunk/src/m/classes/steadystate.m

r13395	r15396
47	47
48	48	end % }}}
49		function marshall(obj,fid) % {{{
	49	function marshall(obj,md,fid) % {{{
50	50	WriteData(fid,'object',obj,'fieldname','reltol','format','Double');
51	51	WriteData(fid,'object',obj,'fieldname','maxiter','format','Integer');

issm/trunk/src/m/classes/steadystate.py

-              r13395
+              r15396
-#module imports
 import numpy
 from fielddisplay import fielddisplay
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.reltol            = 0
                 self.maxiter           = 0
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   steadystate solution parameters:'
                 string="%s\n%s"%(string,fielddisplay(self,'reltol','relative tolerance criterion'))
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #maximum of steady state iterations
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','reltol','format','Double')
                 WriteData(fid,'object',self,'fieldname','maxiter','format','Integer')
                 WriteData(fid,'object',self,'fieldname','requested_outputs','format','DoubleMat','mattype',3)
         # }}}

issm/trunk/src/m/classes/surfaceforcings.m

-              r14310
+              r15396
 classdef surfaceforcings
         properties (SetAccess=public)
                 precipitation = NaN;
                 mass_balance  = NaN;
                 ispdd = 0;
                 issmbgradients = 0;
                 isdelta18o = 0;
                 href = NaN;
                 smbref = NaN;
                 b_pos = NaN;
                 b_neg = NaN;
                 monthlytemperatures = NaN;
                 delta18o = NaN;
                 delta18o_surface = NaN;
                 temperatures_presentday = NaN;
                 temperatures_lgm = NaN;
+                precipitation             = NaN;
+                mass_balance              = NaN;
+                ispdd                     = 0;
+                issmbgradients            = 0;
+                isdelta18o                = 0;
+                href                      = NaN;
+                smbref                    = NaN;
+                b_pos                     = NaN;
+                b_neg                     = NaN;
+                monthlytemperatures       = NaN;
+                delta18o                  = NaN;
+                delta18o_surface          = NaN;
+                temperatures_presentday   = NaN;
+                temperatures_lgm          = NaN;
                 precipitations_presentday = NaN;
+                desfac                    = 0.5;
+                s0p                       = 0;
         end
         methods
 …
                   obj.issmbgradients=0;
                   obj.isdelta18o=0;
+                  obj.desfac=0.5;
+                  obj.s0p=0;
                 end % }}}
                 function md = checkconsistency(obj,md,solution,analyses) % {{{
 …
                                 md = checkfield(md,'surfaceforcings.issmbgradients','numel',[1],'values',[0 1]);
                                 if(obj.ispdd)
+                                  md = checkfield(md,'surfaceforcings.desfac','<=',1,'numel',1);
+                                  md = checkfield(md,'surfaceforcings.s0p','>=',0,'numel',1);
                                         if(obj.isdelta18o==0)
                                                 md = checkfield(md,'surfaceforcings.monthlytemperatures','forcing',1,'NaN',1);
 …
                         disp(sprintf('   surface forcings parameters:'));
+                        disp(sprintf('\n   General parameters:'));
                         fielddisplay(obj,'mass_balance','surface mass balance [m/yr ice eq]');
+                        disp(sprintf('\n   PDD and deltaO18 parameters:'));
                         fielddisplay(obj,'ispdd','is pdd activated (0 or 1, default is 0)');
                         fielddisplay(obj,'isdelta18o','is temperature and precipitation delta18o parametrisation activated (0 or 1, default is 0)');
+                        fielddisplay(obj,'monthlytemperatures','monthly surface temperatures [Kelvin], required if pdd is activated and delta18o not activated');
+                        fielddisplay(obj,'desfac','desertification elevation factor (between 0 and 1, default is 0.5) [m]');
+                        fielddisplay(obj,'s0p','should be set to elevation from precip source (between 0 and a few 1000s m, default is 0) [m]');
+                        fielddisplay(obj,'monthlytemperatures','monthly surface temperatures [K], required if pdd is activated and delta18o not activated');
                         fielddisplay(obj,'precipitation','surface precipitation [m/yr water eq]');
                         fielddisplay(obj,'temperatures_presentday','monthly present day surface temperatures [Kelvin], required if pdd is activated and delta18o activated');
                         fielddisplay(obj,'temperatures_lgm','monthly LGM surface temperatures [Kelvin], required if pdd is activated and delta18o activated');
+                        fielddisplay(obj,'temperatures_presentday','monthly present day surface temperatures [K], required if pdd is activated and delta18o activated');
+                        fielddisplay(obj,'temperatures_lgm','monthly LGM surface temperatures [K], required if pdd is activated and delta18o activated');
                         fielddisplay(obj,'precipitations_presentday','monthly surface precipitation [m/yr water eq], required if pdd is activated and delta18o activated');
                         fielddisplay(obj,'delta18o','delta18o, required if pdd is activated and delta18o activated');
                         fielddisplay(obj,'delta18o_surface','surface elevation of the delta18o site, required if pdd is activated and delta18o activated');
+                        disp(sprintf('\n   SMB gradients parameters:'));
                         fielddisplay(obj,'issmbgradients','is smb gradients method activated (0 or 1, default is 0)');
                         fielddisplay(obj,'href',' reference elevation from which deviation is used to calculate SMB adjustment in smb gradients method');
 …
                 end % }}}
+                function marshall(obj,fid) % {{{
+                        WriteData(fid,'object',obj,'fieldname','precipitation','format','DoubleMat','mattype',1);
+                        WriteData(fid,'object',obj,'fieldname','mass_balance','format','DoubleMat','mattype',1);
+                function marshall(obj,md,fid) % {{{
+                        yts=365.0*24.0*3600.0;
+                        WriteData(fid,'object',obj,'fieldname','precipitation','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1);
+                        WriteData(fid,'object',obj,'fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1);
                         WriteData(fid,'object',obj,'fieldname','ispdd','format','Boolean');
                         WriteData(fid,'object',obj,'fieldname','isdelta18o','format','Boolean');
                         if obj.ispdd,
+                                WriteData(fid,'object',obj,'fieldname','desfac','format','Double');
+                                WriteData(fid,'object',obj,'fieldname','s0p','format','Double');
                                 if obj.isdelta18o
                                         WriteData(fid,'object',obj,'fieldname','temperatures_presentday','format','DoubleMat','mattype',1);
 …
                                         WriteData(fid,'object',obj,'fieldname','delta18o','format','DoubleMat','mattype',1);
                                 else
+                                        WriteData(fid,'object',obj,'fieldname','monthlytemperatures','format','DoubleMat','mattype',1);
+                                        WriteData(fid,'object',obj,'fieldname','precipitation','format','DoubleMat','mattype',1);
+                                        WriteData(fid,'object',obj,'fieldname','monthlytemperatures','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1);
                                 end
                         end
                         WriteData(fid,'object',obj,'fieldname','issmbgradients','format','Boolean');
                         if obj.issmbgradients,
                                 WriteData(fid,'object',obj,'fieldname','href','format','DoubleMat','mattype',1);
                                 WriteData(fid,'object',obj,'fieldname','smbref','format','DoubleMat','mattype',1);
                                 WriteData(fid,'object',obj,'fieldname','b_pos','format','DoubleMat','mattype',1);
                                 WriteData(fid,'object',obj,'fieldname','b_neg','format','DoubleMat','mattype',1);
+                                WriteData(fid,'object',obj,'fieldname','href','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1);
+                                WriteData(fid,'object',obj,'fieldname','smbref','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1);
+                                WriteData(fid,'object',obj,'fieldname','b_pos','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1);
+                                WriteData(fid,'object',obj,'fieldname','b_neg','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1);
                         end

issm/trunk/src/m/classes/surfaceforcings.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+                self.precipitation = float('NaN')
+                self.mass_balance  = float('NaN')
+                self.ispdd = 0
+                self.issmbgradients = 0
+                self.isdelta18o = 0
+                self.href = float('NaN')
+                self.smbref = float('NaN')
+                self.b_pos = float('NaN')
+                self.b_neg = float('NaN')
+                self.monthlytemperatures = float('NaN')
+                self.delta18o = float('NaN')
+                self.delta18o_surface = float('NaN')
+                self.temperatures_presentday = float('NaN')
+                self.temperatures_lgm = float('NaN')
+        def __init__(self): # {{{
+                self.precipitation             = float('NaN')
+                self.mass_balance              = float('NaN')
+                self.ispdd                     = 0
+                self.issmbgradients            = 0
+                self.isdelta18o                = 0
+                self.href                      = float('NaN')
+                self.smbref                    = float('NaN')
+                self.b_pos                     = float('NaN')
+                self.b_neg                     = float('NaN')
+                self.monthlytemperatures       = float('NaN')
+                self.delta18o                  = float('NaN')
+                self.delta18o_surface          = float('NaN')
+                self.temperatures_presentday   = float('NaN')
+                self.temperatures_lgm          = float('NaN')
                 self.precipitations_presentday = float('NaN')
+                self.desfac                    = 0.
+                self.s0p                       = 0.
                 #set defaults
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   surface forcings parameters:"
 …
                 string="%s\n%s"%(string,fielddisplay(self,'mass_balance','surface mass balance [m/yr ice eq]'))
                 string="%s\n%s"%(string,fielddisplay(self,'ispdd','is pdd activated (0 or 1, default is 0)'))
+                string="%s\n%s"%(string,fielddisplay(self,'desfac','desertification elevation factor (between 0 and 1, default is 0.5) [m]'))
                 string="%s\n%s"%(string,fielddisplay(self,'isdelta18o','is temperature and precipitation delta18o parametrisation activated (0 or 1, default is 0)'))
+                string="%s\n%s"%(string,fielddisplay(self,'monthlytemperatures','monthly surface temperatures [Kelvin], required if pdd is activated and delta18o not activated'))
+                string="%s\n%s"%(string,fielddisplay(self,'s0p','should be set to elevation from precip source (between 0 and a few 1000s m, default is 0) [m]'))
+                string="%s\n%s"%(string,fielddisplay(self,'monthlytemperatures','monthly surface temperatures [K], required if pdd is activated and delta18o not activated'))
                 string="%s\n%s"%(string,fielddisplay(self,'precipitation','surface precipitation [m/yr water eq]'))
                 string="%s\n%s"%(string,fielddisplay(self,'temperatures_presentday','monthly present day surface temperatures [Kelvin], required if pdd is activated and delta18o activated'))
                 string="%s\n%s"%(string,fielddisplay(self,'temperatures_lgm','monthly LGM surface temperatures [Kelvin], required if pdd is activated and delta18o activated'))
+                string="%s\n%s"%(string,fielddisplay(self,'temperatures_presentday','monthly present day surface temperatures [K], required if pdd is activated and delta18o activated'))
+                string="%s\n%s"%(string,fielddisplay(self,'temperatures_lgm','monthly LGM surface temperatures [K], required if pdd is activated and delta18o activated'))
                 string="%s\n%s"%(string,fielddisplay(self,'precipitations_presentday','monthly surface precipitation [m/yr water eq], required if pdd is activated and delta18o activated'))
                 string="%s\n%s"%(string,fielddisplay(self,'delta18o','delta18o, required if pdd is activated and delta18o activated'))
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #pdd method not used in default mode
 …
                 self.issmbgradients=0
                 self.isdelta18o=0
+                self.desfac=0.5
+                self.s0p=0.
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                         md = checkfield(md,'surfaceforcings.issmbgradients','numel',[1],'values',[0,1])
                         if   self.ispdd:
+                                md = checkfield(md,'surfaceforcings.desfac','<=',1,'numel',[1]);
+                                md = checkfield(md,'surfaceforcings.s0p','>=',0,'numel',[1]);
                                 if not self.isdelta18o:
                                         md = checkfield(md,'surfaceforcings.monthlytemperatures','forcing',1,'NaN',1)
 …
                 return md
         # }}}
+        def marshall(self,md,fid):    # {{{
+        def marshall(self,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','precipitation','format','DoubleMat','mattype',1)
+                WriteData(fid,'object',self,'fieldname','mass_balance','format','DoubleMat','mattype',1)
+                yts=365.0*24.0*3600.0
+                WriteData(fid,'object',self,'fieldname','precipitation','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1)
+                WriteData(fid,'object',self,'fieldname','mass_balance','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1)
                 WriteData(fid,'object',self,'fieldname','ispdd','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','isdelta18o','format','Boolean')
                 if self.ispdd:
+                        WriteData(fid,'object',self,'fieldname','desfac','format','Double');
+                        WriteData(fid,'object',self,'fieldname','s0p','format','Double');
                         if self.isdelta18o:
                                 WriteData(fid,'object',self,'fieldname','temperatures_presentday','format','DoubleMat','mattype',1)
 …
                                 WriteData(fid,'object',self,'fieldname','delta18o','format','DoubleMat','mattype',1)
                         else:
+                                WriteData(fid,'object',self,'fieldname','monthlytemperatures','format','DoubleMat','mattype',1)
+                                WriteData(fid,'object',self,'fieldname','precipitation','format','DoubleMat','mattype',1)
+                                WriteData(fid,'object',self,'fieldname','monthlytemperatures','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1)
                 WriteData(fid,'object',self,'fieldname','issmbgradients','format','Boolean')
                 if self.issmbgradients:
                         WriteData(fid,'object',self,'fieldname','href','format','DoubleMat','mattype',1)
                         WriteData(fid,'object',self,'fieldname','smbref','format','DoubleMat','mattype',1)
                         WriteData(fid,'object',self,'fieldname','b_pos','format','DoubleMat','mattype',1)
                         WriteData(fid,'object',self,'fieldname','b_neg','format','DoubleMat','mattype',1)
+                        WriteData(fid,'object',self,'fieldname','href','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1)
+                        WriteData(fid,'object',self,'fieldname','smbref','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1)
+                        WriteData(fid,'object',self,'fieldname','b_pos','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1)
+                        WriteData(fid,'object',self,'fieldname','b_neg','format','DoubleMat','mattype',1,'scale',1./yts,'forcinglength',md.mesh.numberofvertices+1)
         # }}}

issm/trunk/src/m/classes/taoinversion.m

-              r14310
+              r15396
 %INVERSION class definition
+%TAOINVERSION class definition
+%
 %   Usage:
 …
                         if solution==BalancethicknessSolutionEnum()
                                 md = checkfield(md,'inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1);
                         elseif solution==WeakBalancethicknessSolutionEnum()
+                        elseif solution==BalancethicknessSoftSolutionEnum()
                                 md = checkfield(md,'inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1);
                         else
 …
                         disp(sprintf('   taoinversion parameters:'));
                         fielddisplay(obj,'iscontrol','is inversion activated?');
                         fielddisplay(obj,'incomplete_adjoint','do we assume linear viscosity?');
                         fielddisplay(obj,'control_parameters','parameter where inverse control is carried out; ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}');
+                        fielddisplay(obj,'incomplete_adjoint','1: linear viscosity, 0: non-linear viscosity');
+                        fielddisplay(obj,'control_parameters','ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}');
                         fielddisplay(obj,'nsteps','number of optimization searches');
                         fielddisplay(obj,'cost_functions','indicate the type of response for each optimization step');
 …
                         fielddisplay(obj,'min_parameters','absolute minimum acceptable value of the inversed parameter on each vertex');
                         fielddisplay(obj,'max_parameters','absolute maximum acceptable value of the inversed parameter on each vertex');
                         fielddisplay(obj,'vx_obs','observed velocity x component [m/a]');
                         fielddisplay(obj,'vy_obs','observed velocity y component [m/a]');
                         fielddisplay(obj,'vel_obs','observed velocity magnitude [m/a]');
+                        fielddisplay(obj,'vx_obs','observed velocity x component [m/yr]');
+                        fielddisplay(obj,'vy_obs','observed velocity y component [m/yr]');
+                        fielddisplay(obj,'vel_obs','observed velocity magnitude [m/yr]');
                         fielddisplay(obj,'thickness_obs','observed thickness [m]');
                         disp('Available cost functions:');
 …
                         disp('   503: ThicknessAbsGradient');
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'object',obj,'class','inversion','fieldname','iscontrol','format','Boolean');

issm/trunk/src/m/classes/thermal.m

-              r13975
+              r15396
                         disp(sprintf('   Thermal solution parameters:'));
                         fielddisplay(obj,'spctemperature','temperature constraints (NaN means no constraint)');
                         fielddisplay(obj,'stabilization','0->no, 1->artificial_diffusivity, 2->SUPG');
+                        fielddisplay(obj,'spctemperature','temperature constraints (NaN means no constraint) [K]');
+                        fielddisplay(obj,'stabilization','0: no, 1: artificial_diffusivity, 2: SUPG');
                         fielddisplay(obj,'maxiter','maximum number of non linear iterations');
                         fielddisplay(obj,'penalty_lock','stabilize unstable thermal constraints that keep zigzagging after n iteration (default is 0, no stabilization)');
 …
                 end % }}}
                 function marshall(obj,fid) % {{{
                         WriteData(fid,'object',obj,'fieldname','spctemperature','format','DoubleMat','mattype',1);
+                function marshall(obj,md,fid) % {{{
+                        WriteData(fid,'object',obj,'fieldname','spctemperature','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1);
                         WriteData(fid,'object',obj,'fieldname','penalty_threshold','format','Integer');
                         WriteData(fid,'object',obj,'fieldname','stabilization','format','Integer');

issm/trunk/src/m/classes/thermal.py

-              r14310
+              r15396
-#module imports
 import numpy
 from fielddisplay import fielddisplay
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.spctemperature    = float('NaN')
                 self.penalty_threshold = 0
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   Thermal solution parameters:'
                 string="%s\n%s"%(string,fielddisplay(self,'spctemperature','temperature constraints (NaN means no constraint)'))
                 string="%s\n%s"%(string,fielddisplay(self,'stabilization','0->no, 1->artificial_diffusivity, 2->SUPG'))
+                string="%s\n%s"%(string,fielddisplay(self,'spctemperature','temperature constraints (NaN means no constraint) [K]'))
+                string="%s\n%s"%(string,fielddisplay(self,'stabilization','0: no, 1: artificial_diffusivity, 2: SUPG'))
                 string="%s\n%s"%(string,fielddisplay(self,'maxiter','maximum number of non linear iterations'))
                 string="%s\n%s"%(string,fielddisplay(self,'penalty_lock','stabilize unstable thermal constraints that keep zigzagging after n iteration (default is 0, no stabilization)'))
 …
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #Number of unstable constraints acceptable
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','spctemperature','format','DoubleMat','mattype',1)
+        def marshall(self,md,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','spctemperature','format','DoubleMat','mattype',1,'forcinglength',md.mesh.numberofvertices+1)
                 WriteData(fid,'object',self,'fieldname','penalty_threshold','format','Integer')
                 WriteData(fid,'object',self,'fieldname','stabilization','format','Integer')
 …
                 WriteData(fid,'object',self,'fieldname','isenthalpy','format','Boolean')
         # }}}

issm/trunk/src/m/classes/timestepping.m

-              r14310
+              r15396
                         disp(sprintf('   timestepping parameters:'));
                         fielddisplay(obj,'start_time','simulation starting time [yrs]');
                         fielddisplay(obj,'final_time','final time to stop the simulation [yrs]');
                         fielddisplay(obj,'time_step','length of time steps [yrs]');
+                        fielddisplay(obj,'start_time','simulation starting time [yr]');
+                        fielddisplay(obj,'final_time','final time to stop the simulation [yr]');
+                        fielddisplay(obj,'time_step','length of time steps [yr]');
                         fielddisplay(obj,'time_adapt','use cfl condition to define time step ? (0 or 1) ');
                         fielddisplay(obj,'cfl_coefficient','coefficient applied to cfl condition');
                 end % }}}
+                function marshall(obj,fid) % {{{
+                        WriteData(fid,'object',obj,'fieldname','start_time','format','Double');
+                        WriteData(fid,'object',obj,'fieldname','final_time','format','Double');
+                        WriteData(fid,'object',obj,'fieldname','time_step','format','Double');
+                function marshall(obj,md,fid) % {{{
+                        yts=365.0*24.0*3600.0;
+                        WriteData(fid,'object',obj,'fieldname','start_time','format','Double','scale',yts);
+                        WriteData(fid,'object',obj,'fieldname','final_time','format','Double','scale',yts);
+                        WriteData(fid,'object',obj,'fieldname','time_step','format','Double','scale',yts);
                         WriteData(fid,'object',obj,'fieldname','time_adapt','format','Boolean');
                         WriteData(fid,'object',obj,'fieldname','cfl_coefficient','format','Double');

issm/trunk/src/m/classes/timestepping.py

-              r14310
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.start_time      = 0.
                 self.final_time      = 0.
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string="   timestepping parameters:"
                 string="%s\n%s"%(string,fielddisplay(self,"start_time","simulation starting time [yrs]"))
                 string="%s\n%s"%(string,fielddisplay(self,"final_time","final time to stop the simulation [yrs]"))
                 string="%s\n%s"%(string,fielddisplay(self,"time_step","length of time steps [yrs]"))
+                string="%s\n%s"%(string,fielddisplay(self,"start_time","simulation starting time [yr]"))
+                string="%s\n%s"%(string,fielddisplay(self,"final_time","final time to stop the simulation [yr]"))
+                string="%s\n%s"%(string,fielddisplay(self,"time_step","length of time steps [yr]"))
                 string="%s\n%s"%(string,fielddisplay(self,"time_adapt","use cfl condition to define time step ? (0 or 1) "))
                 string="%s\n%s"%(string,fielddisplay(self,"cfl_coefficient","coefficient applied to cfl condition"))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #time between 2 time steps
 …
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 return md
         # }}}
+        def marshall(self,md,fid):    # {{{
+        def marshall(self,fid):    # {{{
+                WriteData(fid,'object',self,'fieldname','start_time','format','Double')
+                WriteData(fid,'object',self,'fieldname','final_time','format','Double')
+                WriteData(fid,'object',self,'fieldname','time_step','format','Double')
+                yts=365.0*24.0*3600.0
+                WriteData(fid,'object',self,'fieldname','start_time','format','Double','scale',yts)
+                WriteData(fid,'object',self,'fieldname','final_time','format','Double','scale',yts)
+                WriteData(fid,'object',self,'fieldname','time_step','format','Double','scale',yts)
                 WriteData(fid,'object',self,'fieldname','time_adapt','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','cfl_coefficient','format','Double')
         # }}}

issm/trunk/src/m/classes/transient.m

-              r14067
+              r15396
                 isthermal         = 0;
                 isgroundingline   = 0;
+                isgia             = 0;
                 requested_outputs = NaN;
         end
 …
                         obj.isthermal=1;
                         obj.isgroundingline=0;
+                        obj.isgia=0;
                 end % }}}
 …
                         md = checkfield(md,'transient.isthermal','numel',[1],'values',[0 1]);
                         md = checkfield(md,'transient.isgroundingline','numel',[1],'values',[0 1]);
+                        md = checkfield(md,'transient.isgia','numel',[1],'values',[0 1]);
                         md = checkfield(md,'transient.requested_outputs','size',[NaN 1]);
 …
                         fielddisplay(obj,'isthermal','indicates if a thermal solution is used in the transient');
                         fielddisplay(obj,'isgroundingline','indicates if a groundingline migration is used in the transient');
+                        fielddisplay(obj,'isgia','indicates if a postglacial rebound model is used in the transient');
                         fielddisplay(obj,'requested_outputs','list of additional outputs requested');
                 end % }}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'object',obj,'fieldname','isprognostic','format','Boolean');
                         WriteData(fid,'object',obj,'fieldname','isdiagnostic','format','Boolean');
                         WriteData(fid,'object',obj,'fieldname','isthermal','format','Boolean');
                         WriteData(fid,'object',obj,'fieldname','isgroundingline','format','Boolean');
+                        WriteData(fid,'object',obj,'fieldname','isgia','format','Boolean');
                         WriteData(fid,'object',obj,'fieldname','requested_outputs','format','DoubleMat','mattype',3);
                 end % }}}

issm/trunk/src/m/classes/transient.py

-              r14067
+              r15396
-#module imports
 from fielddisplay import fielddisplay
 from EnumDefinitions import *
 …
         """
+        #properties
+        def __init__(self):
+                # {{{ Properties
+        def __init__(self): # {{{
                 self.isprognostic      = False
                 self.isdiagnostic      = False
                 self.isthermal         = False
                 self.isgroundingline   = False
+                self.isgia             = False
                 self.requested_outputs = float('NaN')
 …
                 #}}}
+        def __repr__(self):
+                # {{{ Display
+        def __repr__(self): # {{{
                 string='   transient solution parameters:'
                 string="%s\n%s"%(string,fielddisplay(self,'isprognostic','indicates if a prognostic solution is used in the transient'))
 …
                 string="%s\n%s"%(string,fielddisplay(self,'isthermal','indicates if a thermal solution is used in the transient'))
                 string="%s\n%s"%(string,fielddisplay(self,'isgroundingline','indicates if a groundingline migration is used in the transient'))
+                string="%s\n%s"%(string,fielddisplay(self,'isgia','indicates if a postglacial rebound is used in the transient'))
                 string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','list of additional outputs requested'))
                 return string
                 #}}}
+        def setdefaultparameters(self):
+                # {{{setdefaultparameters
+        def setdefaultparameters(self): # {{{
                 #full analysis: Diagnostic, Prognostic and Thermal but no groundingline migration for now
 …
                 self.isthermal=True
                 self.isgroundingline=False
+                self.isgia=False
                 return self
         #}}}
         def checkconsistency(self,md,solution,analyses):    # {{{
 …
                 md = checkfield(md,'transient.isthermal','numel',[1],'values',[0,1])
                 md = checkfield(md,'transient.isgroundingline','numel',[1],'values',[0,1])
+                md = checkfield(md,'transient.isgia','numel',[1],'values',[0,1])
                 md = checkfield(md,'transient.requested_outputs','size',[float('NaN')])
 …
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'object',self,'fieldname','isprognostic','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','isdiagnostic','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','isthermal','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','isgroundingline','format','Boolean')
+                WriteData(fid,'object',self,'fieldname','isgia','format','Boolean')
                 WriteData(fid,'object',self,'fieldname','requested_outputs','format','DoubleMat','mattype',3)
         # }}}

issm/trunk/src/m/classes/verbose.m

-              r13975
+              r15396
                         switch(nargin),
                                 case 0,
+                                        %Don't do anything
+                                        verbose.solution=true;
+                                        verbose.qmu=true;
+                                        verbose.control=true;
                                 case 1,
                                         binary=varargin{1};
 …
                 end
                 %}}}
                 function marshall(obj,fid) % {{{
+                function marshall(obj,md,fid) % {{{
                         WriteData(fid,'data',VerboseToBinary(obj),'enum',VerboseEnum(),'format','Integer');
                 end % }}}

issm/trunk/src/m/classes/verbose.py

-              r13975
+              r15396
                 if not len(args):
                         #Don't do anything
+                        self.solution=True;
+                        self.qmu=True;
+                        self.control=True;
                         pass
 …
                                         raise TypeError("verbose supported field values are logicals only (True or False)")
         # }}}
         def __repr__(self):    # {{{
 …
                 return s
         # }}}
         def VerboseToBinary(self):    # {{{
 …
                 return binary
         # }}}
         def BinaryToVerbose(self,binary):    # {{{
 …
                 #ENDBIN2VERB
         # }}}
         def checkconsistency(self,md,solution,analyses):    # {{{
                 return md
         # }}}
+        def marshall(self,fid):    # {{{
+        def marshall(self,md,fid):    # {{{
                 WriteData(fid,'data',self.VerboseToBinary(),'enum',VerboseEnum(),'format','Integer')
         # }}}

issm/trunk/src/m/consistency/ismodelselfconsistent.m

-              r14310
+              r15396
                 analyses=[BalancethicknessAnalysisEnum()];
         case WeakBalancethicknessSolutionEnum(),
+        case BalancethicknessSoftSolutionEnum(),
                 numanalyses=1;
                 analyses=[BalancethicknessAnalysisEnum()];
 …
                 analyses=[BedSlopeAnalysisEnum()];
+        case GiaSolutionEnum(),
+                numanalyses=1;
+                analyses=[GiaAnalysisEnum()];
         case TransientSolutionEnum(),
                 numanalyses=9;
 …
         case HydrologySolutionEnum(),
                 numanalyses=3;
                 analyses=[BedSlopeAnalysisEnum();SurfaceSlopeAnalysisEnum();HydrologyAnalysisEnum()];
+                analyses=[BedSlopeAnalysisEnum();SurfaceSlopeAnalysisEnum();HydrologyShreveAnalysisEnum();HydrologyDCInefficientAnalysisEnum();HydrologyDCEfficientAnalysisEnum()];
         otherwise

issm/trunk/src/m/consistency/ismodelselfconsistent.py

-              r13395
+              r15396
                 analyses=[BedSlopeAnalysisEnum()]
+        elif solutiontype == GiaSolutionEnum():
+                numanalyses=1
+                analyses=[GiaAnalysisEnum()]
         elif solutiontype == TransientSolutionEnum():
                 numanalyses=9
 …
         elif solutiontype == HydrologySolutionEnum():
                 numanalyses=3
                 analyses=[BedSlopeAnalysisEnum(),SurfaceSlopeAnalysisEnum(),HydrologyAnalysisEnum()]
+                analyses=[BedSlopeAnalysisEnum(),SurfaceSlopeAnalysisEnum(),HydrologyShreveAnalysisEnum(),HydrologyDCInefficientAnalysisEnum(),HydrologyDCEfficientAnalysisEnum()]
         else:

issm/trunk/src/m/contrib/gslib/pkriging.m

-              r13975
+              r15396
 options=pairoptions(varargin{:});
 cluster=getfieldvalue(options,'cluster',generic('np',10));
+cluster=getfieldvalue(options,'cluster',generic('np',1));
 options=removefield(options,'cluster',0);
 name   = ['krig' num2str(feature('GetPid'))];
 …
 %Launch job on remote cluster
 BuildKrigingQueueScript(cluster,name,'',1,0,0); %gather, valgrind, gprof
-tic
 LaunchQueueJob(cluster,name,name,{[name '.bin'] [name '.queue']});
+toc
+choice=input('Is the job successfully completed? (y/n)','s');
+%Call waitonlock
+md=model; md.cluster=cluster; md.settings.waitonlock=Inf;
+waitonlock(md)
+%Download
 Download(cluster,name,{[name '.outbin']});
 structure=parseresultsfromdisk([name '.outbin'],0);
 …
 %Process results
 B=structure.AutodiffForward;
+B=structure.(EnumToString(0));
 B=reshape(B,size(x_interp,2),size(x_interp,1))';
 E=structure.AutodiffIsautodiff;
+E=structure.(EnumToString(1));
 E=reshape(E,size(x_interp,2),size(x_interp,1))';

issm/trunk/src/m/enum/AbsoluteEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AdjointBalancethicknessAnalysisEnum.m

r8287	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AdjointEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AdjointHorizAnalysisEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AdjointSolutionEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AdjointpEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AdjointxEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AdjointyEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AdjointzEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AdolcParamEnum.m

r13395	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AgressiveMigrationEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AirEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AnalysisCounterEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AnalysisTypeEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AndroidFrictionCoefficientEnum.m

r14310	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/ApproximationEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/ArrheniusEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AutodiffDependentObjectIndicesEnum.m

r13975	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/AutodiffDependentObjectNamesEnum.m

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issm/trunk/src/m/enum/AutodiffDependentObjectTypesEnum.m

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issm/trunk/src/m/enum/AutodiffDependentObjectsEnum.m

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issm/trunk/src/m/enum/AutodiffDriverEnum.m

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issm/trunk/src/m/enum/AutodiffFosForwardIndexEnum.m

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issm/trunk/src/m/enum/AutodiffFosReverseIndexEnum.m

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issm/trunk/src/m/enum/AutodiffFovForwardIndicesEnum.m

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issm/trunk/src/m/enum/AutodiffIndependentObjectNamesEnum.m

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issm/trunk/src/m/enum/AutodiffIndependentObjectTypesEnum.m

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issm/trunk/src/m/enum/AutodiffIndependentObjectsEnum.m

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issm/trunk/src/m/enum/AutodiffIsautodiffEnum.m

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issm/trunk/src/m/enum/AutodiffJacobianEnum.m

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issm/trunk/src/m/enum/AutodiffKeepEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/AutodiffMassFluxSegmentsPresentEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/AutodiffNumDependentObjectsEnum.m

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issm/trunk/src/m/enum/AutodiffNumDependentsEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/AutodiffNumIndependentObjectsEnum.m

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issm/trunk/src/m/enum/AutodiffNumIndependentsEnum.m

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issm/trunk/src/m/enum/AutodiffXpEnum.m

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issm/trunk/src/m/enum/BalancethicknessAnalysisEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BalancethicknessMisfitEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BalancethicknessSolutionEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BalancethicknessSpcthicknessEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BalancethicknessStabilizationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BalancethicknessThickeningRateEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BasalFrictionEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BasalforcingsGeothermalfluxEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BasalforcingsMeltingRateCorrectionEnum.m

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issm/trunk/src/m/enum/BasalforcingsMeltingRateEnum.m

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issm/trunk/src/m/enum/BathymetryEnum.m

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issm/trunk/src/m/enum/BedEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BedSlopeAnalysisEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BedSlopeSolutionEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BedSlopeXAnalysisEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BedSlopeXEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BedSlopeYAnalysisEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BedSlopeYEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BilinearInterpEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BoolElementResultEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BoolExternalResultEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BoolInputEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BoolParamEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/BoundaryEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ClosedEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ColinearEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ConfigurationTypeEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ConstantEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ConstantsGEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ConstantsReferencetemperatureEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ConstantsYtsEnum.m

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issm/trunk/src/m/enum/ConstraintsEnum.m

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issm/trunk/src/m/enum/ContourEnum.m

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issm/trunk/src/m/enum/ControlInputEnum.m

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issm/trunk/src/m/enum/ControlSteadyEnum.m

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issm/trunk/src/m/enum/ConvergedEnum.m

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issm/trunk/src/m/enum/DataSetParamEnum.m

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issm/trunk/src/m/enum/DatasetInputEnum.m

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issm/trunk/src/m/enum/DebugProfilingEnum.m

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issm/trunk/src/m/enum/DependentObjectEnum.m

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issm/trunk/src/m/enum/DiagnosticAbstolEnum.m

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issm/trunk/src/m/enum/DiagnosticHorizAnalysisEnum.m

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issm/trunk/src/m/enum/DiagnosticHutterAnalysisEnum.m

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issm/trunk/src/m/enum/DiagnosticIcefrontEnum.m

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issm/trunk/src/m/enum/DiagnosticIsnewtonEnum.m

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issm/trunk/src/m/enum/DiagnosticMaxiterEnum.m

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issm/trunk/src/m/enum/DiagnosticNumRequestedOutputsEnum.m

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issm/trunk/src/m/enum/DiagnosticPenaltyFactorEnum.m

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issm/trunk/src/m/enum/DiagnosticReferentialEnum.m

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issm/trunk/src/m/enum/DiagnosticReltolEnum.m

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issm/trunk/src/m/enum/DiagnosticRequestedOutputsEnum.m

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issm/trunk/src/m/enum/DiagnosticRestolEnum.m

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issm/trunk/src/m/enum/DiagnosticRiftPenaltyLockEnum.m

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issm/trunk/src/m/enum/DiagnosticRiftPenaltyThresholdEnum.m

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issm/trunk/src/m/enum/DiagnosticShelfDampeningEnum.m

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issm/trunk/src/m/enum/DiagnosticSolutionEnum.m

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issm/trunk/src/m/enum/DiagnosticSpcvxEnum.m

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issm/trunk/src/m/enum/DiagnosticSpcvyEnum.m

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issm/trunk/src/m/enum/DiagnosticSpcvzEnum.m

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issm/trunk/src/m/enum/DiagnosticStokesreconditioningEnum.m

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issm/trunk/src/m/enum/DiagnosticVertAnalysisEnum.m

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issm/trunk/src/m/enum/DiagnosticVertexPairingEnum.m

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issm/trunk/src/m/enum/DiagnosticViscosityOvershootEnum.m

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issm/trunk/src/m/enum/DofIndexingEnum.m

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issm/trunk/src/m/enum/DoubleElementResultEnum.m

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issm/trunk/src/m/enum/DoubleExternalResultEnum.m

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issm/trunk/src/m/enum/DoubleInputEnum.m

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issm/trunk/src/m/enum/DoubleMatArrayParamEnum.m

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issm/trunk/src/m/enum/DoubleMatExternalResultEnum.m

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issm/trunk/src/m/enum/DoubleMatParamEnum.m

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issm/trunk/src/m/enum/DoubleParamEnum.m

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issm/trunk/src/m/enum/DoubleVecParamEnum.m

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issm/trunk/src/m/enum/DragCoefficientAbsGradientEnum.m

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issm/trunk/src/m/enum/ElementEnum.m

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issm/trunk/src/m/enum/ElementResultEnum.m

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issm/trunk/src/m/enum/EnthalpyAnalysisEnum.m

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issm/trunk/src/m/enum/EnthalpyEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/EnthalpyPicardEnum.m

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issm/trunk/src/m/enum/EnthalpySolutionEnum.m

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issm/trunk/src/m/enum/EnumDefinitions.py

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    WARNING: DO NOT MODIFY THIS FILE
             this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh
             Please read src/c/EnumDefinitions/README for more information
+            this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+            Please read src/c/shared/Enum/README for more information
 """
 …
         AUTODIFFISAUTODIFFENUM - Enum of AutodiffIsautodiff
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffIsautodiffEnum()
 …
         AUTODIFFNUMDEPENDENTSENUM - Enum of AutodiffNumDependents
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffNumDependentsEnum()
 …
         AUTODIFFNUMDEPENDENTOBJECTSENUM - Enum of AutodiffNumDependentObjects
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffNumDependentObjectsEnum()
 …
         AUTODIFFDEPENDENTOBJECTNAMESENUM - Enum of AutodiffDependentObjectNames
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffDependentObjectNamesEnum()
 …
         AUTODIFFDEPENDENTOBJECTTYPESENUM - Enum of AutodiffDependentObjectTypes
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffDependentObjectTypesEnum()
 …
         AUTODIFFDEPENDENTOBJECTINDICESENUM - Enum of AutodiffDependentObjectIndices
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffDependentObjectIndicesEnum()
 …
         AUTODIFFDEPENDENTOBJECTSENUM - Enum of AutodiffDependentObjects
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffDependentObjectsEnum()
 …
         AUTODIFFNUMINDEPENDENTSENUM - Enum of AutodiffNumIndependents
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffNumIndependentsEnum()
 …
         AUTODIFFNUMINDEPENDENTOBJECTSENUM - Enum of AutodiffNumIndependentObjects
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffNumIndependentObjectsEnum()
 …
         AUTODIFFINDEPENDENTOBJECTNAMESENUM - Enum of AutodiffIndependentObjectNames
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffIndependentObjectNamesEnum()
 …
         AUTODIFFINDEPENDENTOBJECTTYPESENUM - Enum of AutodiffIndependentObjectTypes
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffIndependentObjectTypesEnum()
 …
         AUTODIFFINDEPENDENTOBJECTSENUM - Enum of AutodiffIndependentObjects
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffIndependentObjectsEnum()
 …
         AUTODIFFJACOBIANENUM - Enum of AutodiffJacobian
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffJacobianEnum()
 …
         AUTODIFFXPENUM - Enum of AutodiffXp
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffXpEnum()
 …
         AUTODIFFDRIVERENUM - Enum of AutodiffDriver
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffDriverEnum()
 …
         AUTODIFFFOSFORWARDINDEXENUM - Enum of AutodiffFosForwardIndex
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffFosForwardIndexEnum()
 …
         AUTODIFFFOVFORWARDINDICESENUM - Enum of AutodiffFovForwardIndices
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffFovForwardIndicesEnum()
 …
         AUTODIFFFOSREVERSEINDEXENUM - Enum of AutodiffFosReverseIndex
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffFosReverseIndexEnum()
 …
         AUTODIFFMASSFLUXSEGMENTSPRESENTENUM - Enum of AutodiffMassFluxSegmentsPresent
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffMassFluxSegmentsPresentEnum()
 …
         AUTODIFFKEEPENUM - Enum of AutodiffKeep
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AutodiffKeepEnum()
 …
         BALANCETHICKNESSSPCTHICKNESSENUM - Enum of BalancethicknessSpcthickness
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BalancethicknessSpcthicknessEnum()
 …
         BALANCETHICKNESSSTABILIZATIONENUM - Enum of BalancethicknessStabilization
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BalancethicknessStabilizationEnum()
 …
         BALANCETHICKNESSTHICKENINGRATEENUM - Enum of BalancethicknessThickeningRate
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BalancethicknessThickeningRateEnum()
 …
         BASALFORCINGSGEOTHERMALFLUXENUM - Enum of BasalforcingsGeothermalflux
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BasalforcingsGeothermalfluxEnum()
 …
         BASALFORCINGSMELTINGRATECORRECTIONENUM - Enum of BasalforcingsMeltingRateCorrection
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BasalforcingsMeltingRateCorrectionEnum()
 …
         BASALFORCINGSMELTINGRATEENUM - Enum of BasalforcingsMeltingRate
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BasalforcingsMeltingRateEnum()
 …
         BATHYMETRYENUM - Enum of Bathymetry
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BathymetryEnum()
 …
         BEDENUM - Enum of Bed
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BedEnum()
 …
         CONSTANTSGENUM - Enum of ConstantsG
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ConstantsGEnum()
 …
         CONSTANTSREFERENCETEMPERATUREENUM - Enum of ConstantsReferencetemperature
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ConstantsReferencetemperatureEnum()
 …
         CONSTANTSYTSENUM - Enum of ConstantsYts
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ConstantsYtsEnum()
 …
         DEPENDENTOBJECTENUM - Enum of DependentObject
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DependentObjectEnum()
 …
         DIAGNOSTICABSTOLENUM - Enum of DiagnosticAbstol
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticAbstolEnum()
 …
         DIAGNOSTICICEFRONTENUM - Enum of DiagnosticIcefront
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticIcefrontEnum()
 …
         DIAGNOSTICISNEWTONENUM - Enum of DiagnosticIsnewton
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticIsnewtonEnum()
 …
         DIAGNOSTICMAXITERENUM - Enum of DiagnosticMaxiter
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticMaxiterEnum()
 …
         DIAGNOSTICNUMREQUESTEDOUTPUTSENUM - Enum of DiagnosticNumRequestedOutputs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticNumRequestedOutputsEnum()
 …
         DIAGNOSTICPENALTYFACTORENUM - Enum of DiagnosticPenaltyFactor
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticPenaltyFactorEnum()
 …
         DIAGNOSTICREFERENTIALENUM - Enum of DiagnosticReferential
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticReferentialEnum()
 …
         DIAGNOSTICRELTOLENUM - Enum of DiagnosticReltol
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticReltolEnum()
 …
         DIAGNOSTICREQUESTEDOUTPUTSENUM - Enum of DiagnosticRequestedOutputs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticRequestedOutputsEnum()
 …
         DIAGNOSTICRESTOLENUM - Enum of DiagnosticRestol
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticRestolEnum()
 …
         DIAGNOSTICRIFTPENALTYLOCKENUM - Enum of DiagnosticRiftPenaltyLock
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticRiftPenaltyLockEnum()
 …
         DIAGNOSTICRIFTPENALTYTHRESHOLDENUM - Enum of DiagnosticRiftPenaltyThreshold
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticRiftPenaltyThresholdEnum()
 …
         DIAGNOSTICSHELFDAMPENINGENUM - Enum of DiagnosticShelfDampening
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticShelfDampeningEnum()
 …
         DIAGNOSTICSPCVXENUM - Enum of DiagnosticSpcvx
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticSpcvxEnum()
 …
         DIAGNOSTICSPCVYENUM - Enum of DiagnosticSpcvy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticSpcvyEnum()
 …
         DIAGNOSTICSPCVZENUM - Enum of DiagnosticSpcvz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticSpcvzEnum()
 …
         DIAGNOSTICSTOKESRECONDITIONINGENUM - Enum of DiagnosticStokesreconditioning
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticStokesreconditioningEnum()
 …
         DIAGNOSTICVERTEXPAIRINGENUM - Enum of DiagnosticVertexPairing
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticVertexPairingEnum()
 …
         DIAGNOSTICVISCOSITYOVERSHOOTENUM - Enum of DiagnosticViscosityOvershoot
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticViscosityOvershootEnum()
 …
         return StringToEnum('DiagnosticViscosityOvershoot')[0]
+def LoadingforceXEnum():
+        """
+        LOADINGFORCEXENUM - Enum of LoadingforceX
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=LoadingforceXEnum()
+        """
+        return StringToEnum('LoadingforceX')[0]
+def LoadingforceYEnum():
+        """
+        LOADINGFORCEYENUM - Enum of LoadingforceY
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=LoadingforceYEnum()
+        """
+        return StringToEnum('LoadingforceY')[0]
+def LoadingforceZEnum():
+        """
+        LOADINGFORCEZENUM - Enum of LoadingforceZ
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=LoadingforceZEnum()
+        """
+        return StringToEnum('LoadingforceZ')[0]
 def FlowequationBordermacayealEnum():
         """
         FLOWEQUATIONBORDERMACAYEALENUM - Enum of FlowequationBordermacayeal
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlowequationBordermacayealEnum()
 …
         FLOWEQUATIONBORDERPATTYNENUM - Enum of FlowequationBorderpattyn
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlowequationBorderpattynEnum()
 …
         FLOWEQUATIONBORDERSTOKESENUM - Enum of FlowequationBorderstokes
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlowequationBorderstokesEnum()
 …
         FLOWEQUATIONELEMENTEQUATIONENUM - Enum of FlowequationElementEquation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlowequationElementEquationEnum()
 …
         FLOWEQUATIONISHUTTERENUM - Enum of FlowequationIshutter
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlowequationIshutterEnum()
 …
         FLOWEQUATIONISL1L2ENUM - Enum of FlowequationIsl1l2
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlowequationIsl1l2Enum()
 …
         FLOWEQUATIONISMACAYEALPATTYNENUM - Enum of FlowequationIsmacayealpattyn
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlowequationIsmacayealpattynEnum()
 …
         FLOWEQUATIONISSTOKESENUM - Enum of FlowequationIsstokes
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlowequationIsstokesEnum()
 …
         FLOWEQUATIONVERTEXEQUATIONENUM - Enum of FlowequationVertexEquation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlowequationVertexEquationEnum()
 …
         FRICTIONCOEFFICIENTENUM - Enum of FrictionCoefficient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FrictionCoefficientEnum()
 …
         FRICTIONPENUM - Enum of FrictionP
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FrictionPEnum()
 …
         FRICTIONQENUM - Enum of FrictionQ
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FrictionQEnum()
 …
         GEOMETRYHYDROSTATICRATIOENUM - Enum of GeometryHydrostaticRatio
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=GeometryHydrostaticRatioEnum()
 …
         return StringToEnum('GeometryHydrostaticRatio')[0]
+def HydrologyCREnum():
+        """
+        HYDROLOGYCRENUM - Enum of HydrologyCR
+           Usage:
+              macro=HydrologyCREnum()
+        """
+        return StringToEnum('HydrologyCR')[0]
+def HydrologyKnEnum():
+        """
+        HYDROLOGYKNENUM - Enum of HydrologyKn
+           Usage:
+              macro=HydrologyKnEnum()
+        """
+        return StringToEnum('HydrologyKn')[0]
+def HydrologyNEnum():
+        """
+        HYDROLOGYNENUM - Enum of HydrologyN
+           Usage:
+              macro=HydrologyNEnum()
+        """
+        return StringToEnum('HydrologyN')[0]
+def HydrologyPEnum():
+        """
+        HYDROLOGYPENUM - Enum of HydrologyP
+           Usage:
+              macro=HydrologyPEnum()
+        """
+        return StringToEnum('HydrologyP')[0]
+def HydrologyQEnum():
+        """
+        HYDROLOGYQENUM - Enum of HydrologyQ
+           Usage:
+              macro=HydrologyQEnum()
+        """
+        return StringToEnum('HydrologyQ')[0]
+def HydrologySpcwatercolumnEnum():
+        """
+        HYDROLOGYSPCWATERCOLUMNENUM - Enum of HydrologySpcwatercolumn
+           Usage:
+              macro=HydrologySpcwatercolumnEnum()
+        """
+        return StringToEnum('HydrologySpcwatercolumn')[0]
+def HydrologyStabilizationEnum():
+        """
+        HYDROLOGYSTABILIZATIONENUM - Enum of HydrologyStabilization
+           Usage:
+              macro=HydrologyStabilizationEnum()
+        """
+        return StringToEnum('HydrologyStabilization')[0]
+def HydrologyModelEnum():
+        """
+        HYDROLOGYMODELENUM - Enum of HydrologyModel
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyModelEnum()
+        """
+        return StringToEnum('HydrologyModel')[0]
+def HydrologyshreveEnum():
+        """
+        HYDROLOGYSHREVEENUM - Enum of Hydrologyshreve
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyshreveEnum()
+        """
+        return StringToEnum('Hydrologyshreve')[0]
+def HydrologyshreveCREnum():
+        """
+        HYDROLOGYSHREVECRENUM - Enum of HydrologyshreveCR
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyshreveCREnum()
+        """
+        return StringToEnum('HydrologyshreveCR')[0]
+def HydrologyshreveKnEnum():
+        """
+        HYDROLOGYSHREVEKNENUM - Enum of HydrologyshreveKn
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyshreveKnEnum()
+        """
+        return StringToEnum('HydrologyshreveKn')[0]
+def HydrologyshreveNEnum():
+        """
+        HYDROLOGYSHREVENENUM - Enum of HydrologyshreveN
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyshreveNEnum()
+        """
+        return StringToEnum('HydrologyshreveN')[0]
+def HydrologyshrevePEnum():
+        """
+        HYDROLOGYSHREVEPENUM - Enum of HydrologyshreveP
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyshrevePEnum()
+        """
+        return StringToEnum('HydrologyshreveP')[0]
+def HydrologyshreveQEnum():
+        """
+        HYDROLOGYSHREVEQENUM - Enum of HydrologyshreveQ
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyshreveQEnum()
+        """
+        return StringToEnum('HydrologyshreveQ')[0]
+def HydrologyshreveSpcwatercolumnEnum():
+        """
+        HYDROLOGYSHREVESPCWATERCOLUMNENUM - Enum of HydrologyshreveSpcwatercolumn
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyshreveSpcwatercolumnEnum()
+        """
+        return StringToEnum('HydrologyshreveSpcwatercolumn')[0]
+def HydrologyshreveStabilizationEnum():
+        """
+        HYDROLOGYSHREVESTABILIZATIONENUM - Enum of HydrologyshreveStabilization
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyshreveStabilizationEnum()
+        """
+        return StringToEnum('HydrologyshreveStabilization')[0]
+def HydrologydcEnum():
+        """
+        HYDROLOGYDCENUM - Enum of Hydrologydc
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcEnum()
+        """
+        return StringToEnum('Hydrologydc')[0]
+def SedimentHeadEnum():
+        """
+        SEDIMENTHEADENUM - Enum of SedimentHead
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=SedimentHeadEnum()
+        """
+        return StringToEnum('SedimentHead')[0]
+def SedimentHeadOldEnum():
+        """
+        SEDIMENTHEADOLDENUM - Enum of SedimentHeadOld
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=SedimentHeadOldEnum()
+        """
+        return StringToEnum('SedimentHeadOld')[0]
+def SedimentHeadResidualEnum():
+        """
+        SEDIMENTHEADRESIDUALENUM - Enum of SedimentHeadResidual
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=SedimentHeadResidualEnum()
+        """
+        return StringToEnum('SedimentHeadResidual')[0]
+def EplHeadEnum():
+        """
+        EPLHEADENUM - Enum of EplHead
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=EplHeadEnum()
+        """
+        return StringToEnum('EplHead')[0]
+def EplHeadOldEnum():
+        """
+        EPLHEADOLDENUM - Enum of EplHeadOld
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=EplHeadOldEnum()
+        """
+        return StringToEnum('EplHeadOld')[0]
+def HydrologydcRelTolEnum():
+        """
+        HYDROLOGYDCRELTOLENUM - Enum of HydrologydcRelTol
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcRelTolEnum()
+        """
+        return StringToEnum('HydrologydcRelTol')[0]
+def HydrologydcSpcsedimentHeadEnum():
+        """
+        HYDROLOGYDCSPCSEDIMENTHEADENUM - Enum of HydrologydcSpcsedimentHead
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcSpcsedimentHeadEnum()
+        """
+        return StringToEnum('HydrologydcSpcsedimentHead')[0]
+def HydrologydcSedimentCompressibilityEnum():
+        """
+        HYDROLOGYDCSEDIMENTCOMPRESSIBILITYENUM - Enum of HydrologydcSedimentCompressibility
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcSedimentCompressibilityEnum()
+        """
+        return StringToEnum('HydrologydcSedimentCompressibility')[0]
+def HydrologydcSedimentPorosityEnum():
+        """
+        HYDROLOGYDCSEDIMENTPOROSITYENUM - Enum of HydrologydcSedimentPorosity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcSedimentPorosityEnum()
+        """
+        return StringToEnum('HydrologydcSedimentPorosity')[0]
+def HydrologydcSedimentThicknessEnum():
+        """
+        HYDROLOGYDCSEDIMENTTHICKNESSENUM - Enum of HydrologydcSedimentThickness
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcSedimentThicknessEnum()
+        """
+        return StringToEnum('HydrologydcSedimentThickness')[0]
+def HydrologydcSedimentTransmitivityEnum():
+        """
+        HYDROLOGYDCSEDIMENTTRANSMITIVITYENUM - Enum of HydrologydcSedimentTransmitivity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcSedimentTransmitivityEnum()
+        """
+        return StringToEnum('HydrologydcSedimentTransmitivity')[0]
+def HydrologydcWaterCompressibilityEnum():
+        """
+        HYDROLOGYDCWATERCOMPRESSIBILITYENUM - Enum of HydrologydcWaterCompressibility
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcWaterCompressibilityEnum()
+        """
+        return StringToEnum('HydrologydcWaterCompressibility')[0]
+def HydrologydcSpceplHeadEnum():
+        """
+        HYDROLOGYDCSPCEPLHEADENUM - Enum of HydrologydcSpceplHead
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcSpceplHeadEnum()
+        """
+        return StringToEnum('HydrologydcSpceplHead')[0]
+def HydrologydcMaskEplactiveEnum():
+        """
+        HYDROLOGYDCMASKEPLACTIVEENUM - Enum of HydrologydcMaskEplactive
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcMaskEplactiveEnum()
+        """
+        return StringToEnum('HydrologydcMaskEplactive')[0]
+def HydrologydcEplCompressibilityEnum():
+        """
+        HYDROLOGYDCEPLCOMPRESSIBILITYENUM - Enum of HydrologydcEplCompressibility
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcEplCompressibilityEnum()
+        """
+        return StringToEnum('HydrologydcEplCompressibility')[0]
+def HydrologydcEplPorosityEnum():
+        """
+        HYDROLOGYDCEPLPOROSITYENUM - Enum of HydrologydcEplPorosity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcEplPorosityEnum()
+        """
+        return StringToEnum('HydrologydcEplPorosity')[0]
+def HydrologydcEplThicknessEnum():
+        """
+        HYDROLOGYDCEPLTHICKNESSENUM - Enum of HydrologydcEplThickness
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcEplThicknessEnum()
+        """
+        return StringToEnum('HydrologydcEplThickness')[0]
+def HydrologydcEplTransmitivityEnum():
+        """
+        HYDROLOGYDCEPLTRANSMITIVITYENUM - Enum of HydrologydcEplTransmitivity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcEplTransmitivityEnum()
+        """
+        return StringToEnum('HydrologydcEplTransmitivity')[0]
+def HydrologydcIsefficientlayerEnum():
+        """
+        HYDROLOGYDCISEFFICIENTLAYERENUM - Enum of HydrologydcIsefficientlayer
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcIsefficientlayerEnum()
+        """
+        return StringToEnum('HydrologydcIsefficientlayer')[0]
+def HydrologydcSedimentlimitFlagEnum():
+        """
+        HYDROLOGYDCSEDIMENTLIMITFLAGENUM - Enum of HydrologydcSedimentlimitFlag
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcSedimentlimitFlagEnum()
+        """
+        return StringToEnum('HydrologydcSedimentlimitFlag')[0]
+def HydrologydcSedimentlimitEnum():
+        """
+        HYDROLOGYDCSEDIMENTLIMITENUM - Enum of HydrologydcSedimentlimit
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcSedimentlimitEnum()
+        """
+        return StringToEnum('HydrologydcSedimentlimit')[0]
+def HydrologydcTransferFlagEnum():
+        """
+        HYDROLOGYDCTRANSFERFLAGENUM - Enum of HydrologydcTransferFlag
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcTransferFlagEnum()
+        """
+        return StringToEnum('HydrologydcTransferFlag')[0]
+def HydrologydcLeakageFactorEnum():
+        """
+        HYDROLOGYDCLEAKAGEFACTORENUM - Enum of HydrologydcLeakageFactor
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcLeakageFactorEnum()
+        """
+        return StringToEnum('HydrologydcLeakageFactor')[0]
+def HydrologydcPenaltyFactorEnum():
+        """
+        HYDROLOGYDCPENALTYFACTORENUM - Enum of HydrologydcPenaltyFactor
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologydcPenaltyFactorEnum()
+        """
+        return StringToEnum('HydrologydcPenaltyFactor')[0]
+def HydrologyLayerEnum():
+        """
+        HYDROLOGYLAYERENUM - Enum of HydrologyLayer
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyLayerEnum()
+        """
+        return StringToEnum('HydrologyLayer')[0]
+def HydrologySedimentEnum():
+        """
+        HYDROLOGYSEDIMENTENUM - Enum of HydrologySediment
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologySedimentEnum()
+        """
+        return StringToEnum('HydrologySediment')[0]
+def HydrologyEfficientEnum():
+        """
+        HYDROLOGYEFFICIENTENUM - Enum of HydrologyEfficient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyEfficientEnum()
+        """
+        return StringToEnum('HydrologyEfficient')[0]
+def HydrologySedimentKmaxEnum():
+        """
+        HYDROLOGYSEDIMENTKMAXENUM - Enum of HydrologySedimentKmax
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologySedimentKmaxEnum()
+        """
+        return StringToEnum('HydrologySedimentKmax')[0]
+def BasisIntegralEnum():
+        """
+        BASISINTEGRALENUM - Enum of BasisIntegral
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=BasisIntegralEnum()
+        """
+        return StringToEnum('BasisIntegral')[0]
+def WaterTransferEnum():
+        """
+        WATERTRANSFERENUM - Enum of WaterTransfer
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=WaterTransferEnum()
+        """
+        return StringToEnum('WaterTransfer')[0]
 def IndependentObjectEnum():
 …
         INDEPENDENTOBJECTENUM - Enum of IndependentObject
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IndependentObjectEnum()
 …
         INVERSIONCONTROLPARAMETERSENUM - Enum of InversionControlParameters
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionControlParametersEnum()
 …
         return StringToEnum('InversionControlParameters')[0]
-def InversionCostFunctionEnum():
-        """
-        INVERSIONCOSTFUNCTIONENUM - Enum of InversionCostFunction
-           Usage:
-              macro=InversionCostFunctionEnum()
-        """
-        return StringToEnum('InversionCostFunction')[0]
 def InversionCostFunctionThresholdEnum():
         """
         INVERSIONCOSTFUNCTIONTHRESHOLDENUM - Enum of InversionCostFunctionThreshold
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionCostFunctionThresholdEnum()
 …
         INVERSIONCOSTFUNCTIONSCOEFFICIENTSENUM - Enum of InversionCostFunctionsCoefficients
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionCostFunctionsCoefficientsEnum()
 …
         INVERSIONCOSTFUNCTIONSENUM - Enum of InversionCostFunctions
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionCostFunctionsEnum()
 …
         INVERSIONGRADIENTONLYENUM - Enum of InversionGradientOnly
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionGradientOnlyEnum()
 …
         INVERSIONGRADIENTSCALINGENUM - Enum of InversionGradientScaling
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionGradientScalingEnum()
 …
         INVERSIONISCONTROLENUM - Enum of InversionIscontrol
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionIscontrolEnum()
 …
         INVERSIONTAOENUM - Enum of InversionTao
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionTaoEnum()
 …
         INVERSIONINCOMPLETEADJOINTENUM - Enum of InversionIncompleteAdjoint
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionIncompleteAdjointEnum()
 …
         INVERSIONMAXPARAMETERSENUM - Enum of InversionMaxParameters
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionMaxParametersEnum()
 …
         INVERSIONMAXITERPERSTEPENUM - Enum of InversionMaxiterPerStep
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionMaxiterPerStepEnum()
 …
         INVERSIONMINPARAMETERSENUM - Enum of InversionMinParameters
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionMinParametersEnum()
 …
         INVERSIONNSTEPSENUM - Enum of InversionNsteps
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionNstepsEnum()
 …
         INVERSIONNUMCONTROLPARAMETERSENUM - Enum of InversionNumControlParameters
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionNumControlParametersEnum()
 …
         INVERSIONNUMCOSTFUNCTIONSENUM - Enum of InversionNumCostFunctions
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionNumCostFunctionsEnum()
 …
         INVERSIONSTEPTHRESHOLDENUM - Enum of InversionStepThreshold
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionStepThresholdEnum()
 …
         INVERSIONTHICKNESSOBSENUM - Enum of InversionThicknessObs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionThicknessObsEnum()
 …
         INVERSIONVELOBSENUM - Enum of InversionVelObs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionVelObsEnum()
 …
         INVERSIONVXOBSENUM - Enum of InversionVxObs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionVxObsEnum()
 …
         INVERSIONVYOBSENUM - Enum of InversionVyObs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionVyObsEnum()
 …
         INVERSIONVZOBSENUM - Enum of InversionVzObs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InversionVzObsEnum()
 …
         MASKELEMENTONFLOATINGICEENUM - Enum of MaskElementonfloatingice
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaskElementonfloatingiceEnum()
 …
         MASKELEMENTONGROUNDEDICEENUM - Enum of MaskElementongroundedice
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaskElementongroundediceEnum()
 …
         MASKELEMENTONWATERENUM - Enum of MaskElementonwater
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaskElementonwaterEnum()
 …
         MASKVERTEXONFLOATINGICEENUM - Enum of MaskVertexonfloatingice
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaskVertexonfloatingiceEnum()
 …
         MASKVERTEXONGROUNDEDICEENUM - Enum of MaskVertexongroundedice
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaskVertexongroundediceEnum()
 …
         MASKVERTEXONWATERENUM - Enum of MaskVertexonwater
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaskVertexonwaterEnum()
 …
         MATERIALSBETAENUM - Enum of MaterialsBeta
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsBetaEnum()
 …
         MATERIALSHEATCAPACITYENUM - Enum of MaterialsHeatcapacity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsHeatcapacityEnum()
 …
         MATERIALSLATENTHEATENUM - Enum of MaterialsLatentheat
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsLatentheatEnum()
 …
         MATERIALSMELTINGPOINTENUM - Enum of MaterialsMeltingpoint
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsMeltingpointEnum()
 …
         MATERIALSMIXEDLAYERCAPACITYENUM - Enum of MaterialsMixedLayerCapacity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsMixedLayerCapacityEnum()
 …
         MATERIALSRHEOLOGYBENUM - Enum of MaterialsRheologyB
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsRheologyBEnum()
 …
         MATERIALSRHEOLOGYBBARENUM - Enum of MaterialsRheologyBbar
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsRheologyBbarEnum()
 …
         MATERIALSRHEOLOGYLAWENUM - Enum of MaterialsRheologyLaw
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsRheologyLawEnum()
 …
         MATERIALSRHEOLOGYNENUM - Enum of MaterialsRheologyN
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsRheologyNEnum()
 …
         MATERIALSRHEOLOGYZENUM - Enum of MaterialsRheologyZ
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsRheologyZEnum()
 …
         MATERIALSRHEOLOGYZBARENUM - Enum of MaterialsRheologyZbar
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsRheologyZbarEnum()
 …
         MATERIALSRHOICEENUM - Enum of MaterialsRhoIce
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsRhoIceEnum()
 …
         MATERIALSRHOWATERENUM - Enum of MaterialsRhoWater
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsRhoWaterEnum()
 …
         MATERIALSRHOFRESHWATERENUM - Enum of MaterialsRhoFreshwater
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsRhoFreshwaterEnum()
 …
         MATERIALSMUWATERENUM - Enum of MaterialsMuWater
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsMuWaterEnum()
 …
         MATERIALSTHERMALEXCHANGEVELOCITYENUM - Enum of MaterialsThermalExchangeVelocity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsThermalExchangeVelocityEnum()
 …
         MATERIALSTHERMALCONDUCTIVITYENUM - Enum of MaterialsThermalconductivity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsThermalconductivityEnum()
 …
         return StringToEnum('MaterialsThermalconductivity')[0]
+def MaterialsLithosphereShearModulusEnum():
+        """
+        MATERIALSLITHOSPHERESHEARMODULUSENUM - Enum of MaterialsLithosphereShearModulus
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=MaterialsLithosphereShearModulusEnum()
+        """
+        return StringToEnum('MaterialsLithosphereShearModulus')[0]
+def MaterialsLithosphereDensityEnum():
+        """
+        MATERIALSLITHOSPHEREDENSITYENUM - Enum of MaterialsLithosphereDensity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=MaterialsLithosphereDensityEnum()
+        """
+        return StringToEnum('MaterialsLithosphereDensity')[0]
+def MaterialsMantleShearModulusEnum():
+        """
+        MATERIALSMANTLESHEARMODULUSENUM - Enum of MaterialsMantleShearModulus
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=MaterialsMantleShearModulusEnum()
+        """
+        return StringToEnum('MaterialsMantleShearModulus')[0]
+def MaterialsMantleDensityEnum():
+        """
+        MATERIALSMANTLEDENSITYENUM - Enum of MaterialsMantleDensity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=MaterialsMantleDensityEnum()
+        """
+        return StringToEnum('MaterialsMantleDensity')[0]
 def MeshAverageVertexConnectivityEnum():
         """
         MESHAVERAGEVERTEXCONNECTIVITYENUM - Enum of MeshAverageVertexConnectivity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshAverageVertexConnectivityEnum()
 …
         MESHDIMENSIONENUM - Enum of MeshDimension
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshDimensionEnum()
 …
         MESHEDGESENUM - Enum of MeshEdges
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshEdgesEnum()
 …
         MESHELEMENTCONNECTIVITYENUM - Enum of MeshElementconnectivity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshElementconnectivityEnum()
 …
         MESHELEMENTONBEDENUM - Enum of MeshElementonbed
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshElementonbedEnum()
 …
         MESHELEMENTONSURFACEENUM - Enum of MeshElementonsurface
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshElementonsurfaceEnum()
 …
         MESHELEMENTS2DENUM - Enum of MeshElements2d
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshElements2dEnum()
 …
         MESHELEMENTSENUM - Enum of MeshElements
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshElementsEnum()
 …
         MESHLOWERELEMENTSENUM - Enum of MeshLowerelements
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshLowerelementsEnum()
 …
         MESHNUMBEROFEDGESENUM - Enum of MeshNumberofedges
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshNumberofedgesEnum()
 …
         MESHNUMBEROFELEMENTS2DENUM - Enum of MeshNumberofelements2d
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshNumberofelements2dEnum()
 …
         MESHNUMBEROFELEMENTSENUM - Enum of MeshNumberofelements
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshNumberofelementsEnum()
 …
         MESHNUMBEROFLAYERSENUM - Enum of MeshNumberoflayers
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshNumberoflayersEnum()
 …
         MESHNUMBEROFVERTICES2DENUM - Enum of MeshNumberofvertices2d
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshNumberofvertices2dEnum()
 …
         MESHNUMBEROFVERTICESENUM - Enum of MeshNumberofvertices
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshNumberofverticesEnum()
 …
         MESHUPPERELEMENTSENUM - Enum of MeshUpperelements
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshUpperelementsEnum()
 …
         MESHVERTEXONBEDENUM - Enum of MeshVertexonbed
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshVertexonbedEnum()
 …
         MESHVERTEXONSURFACEENUM - Enum of MeshVertexonsurface
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshVertexonsurfaceEnum()
 …
         MESHXENUM - Enum of MeshX
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshXEnum()
 …
         MESHYENUM - Enum of MeshY
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshYEnum()
 …
         MESHZENUM - Enum of MeshZ
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeshZEnum()
 …
         MISCELLANEOUSNAMEENUM - Enum of MiscellaneousName
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MiscellaneousNameEnum()
 …
         PROGNOSTICHYDROSTATICADJUSTMENTENUM - Enum of PrognosticHydrostaticAdjustment
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticHydrostaticAdjustmentEnum()
 …
         PROGNOSTICMINTHICKNESSENUM - Enum of PrognosticMinThickness
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticMinThicknessEnum()
 …
         PROGNOSTICPENALTYFACTORENUM - Enum of PrognosticPenaltyFactor
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticPenaltyFactorEnum()
 …
         PROGNOSTICSPCTHICKNESSENUM - Enum of PrognosticSpcthickness
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticSpcthicknessEnum()
 …
         PROGNOSTICSTABILIZATIONENUM - Enum of PrognosticStabilization
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticStabilizationEnum()
 …
         PROGNOSTICVERTEXPAIRINGENUM - Enum of PrognosticVertexPairing
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticVertexPairingEnum()
 …
         PROGNOSTICNUMREQUESTEDOUTPUTSENUM - Enum of PrognosticNumRequestedOutputs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticNumRequestedOutputsEnum()
 …
         PROGNOSTICREQUESTEDOUTPUTSENUM - Enum of PrognosticRequestedOutputs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticRequestedOutputsEnum()
 …
         QMUISDAKOTAENUM - Enum of QmuIsdakota
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuIsdakotaEnum()
 …
         MASSFLUXSEGMENTSENUM - Enum of MassFluxSegments
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MassFluxSegmentsEnum()
 …
         MASSFLUXSEGMENTSPRESENTENUM - Enum of MassFluxSegmentsPresent
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MassFluxSegmentsPresentEnum()
 …
         QMUMASSFLUXSEGMENTSPRESENTENUM - Enum of QmuMassFluxSegmentsPresent
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuMassFluxSegmentsPresentEnum()
 …
         QMUNUMBEROFPARTITIONSENUM - Enum of QmuNumberofpartitions
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuNumberofpartitionsEnum()
 …
         QMUNUMBEROFRESPONSESENUM - Enum of QmuNumberofresponses
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuNumberofresponsesEnum()
 …
         QMUPARTITIONENUM - Enum of QmuPartition
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuPartitionEnum()
 …
         QMURESPONSEDESCRIPTORSENUM - Enum of QmuResponsedescriptors
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuResponsedescriptorsEnum()
 …
         QMUVARIABLEDESCRIPTORSENUM - Enum of QmuVariabledescriptors
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuVariabledescriptorsEnum()
 …
         return StringToEnum('QmuVariabledescriptors')[0]
+def QmuMaterialsRheologyBEnum():
+        """
+        QMUMATERIALSRHEOLOGYBENUM - Enum of QmuMaterialsRheologyB
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=QmuMaterialsRheologyBEnum()
+        """
+        return StringToEnum('QmuMaterialsRheologyB')[0]
 def RiftsNumriftsEnum():
         """
         RIFTSNUMRIFTSENUM - Enum of RiftsNumrifts
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=RiftsNumriftsEnum()
 …
         RIFTSRIFTSTRUCTENUM - Enum of RiftsRiftstruct
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=RiftsRiftstructEnum()
 …
         SETTINGSIOGATHERENUM - Enum of SettingsIoGather
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SettingsIoGatherEnum()
 …
         SETTINGSLOWMEMENUM - Enum of SettingsLowmem
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SettingsLowmemEnum()
 …
         SETTINGSOUTPUTFREQUENCYENUM - Enum of SettingsOutputFrequency
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SettingsOutputFrequencyEnum()
 …
         SETTINGSRESULTSASPATCHESENUM - Enum of SettingsResultsAsPatches
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SettingsResultsAsPatchesEnum()
 …
         SETTINGSWAITONLOCKENUM - Enum of SettingsWaitonlock
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SettingsWaitonlockEnum()
 …
         SURFACEFORCINGSDELTA18OENUM - Enum of SurfaceforcingsDelta18o
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsDelta18oEnum()
 …
         SURFACEFORCINGSDELTA18OSURFACEENUM - Enum of SurfaceforcingsDelta18oSurface
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsDelta18oSurfaceEnum()
 …
         SURFACEFORCINGSISDELTA18OENUM - Enum of SurfaceforcingsIsdelta18o
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsIsdelta18oEnum()
 …
         SURFACEFORCINGSPRECIPITATIONSPRESENTDAYENUM - Enum of SurfaceforcingsPrecipitationsPresentday
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsPrecipitationsPresentdayEnum()
 …
         SURFACEFORCINGSTEMPERATURESPRESENTDAYENUM - Enum of SurfaceforcingsTemperaturesPresentday
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsTemperaturesPresentdayEnum()
 …
         SURFACEFORCINGSTEMPERATURESLGMENUM - Enum of SurfaceforcingsTemperaturesLgm
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsTemperaturesLgmEnum()
 …
         DEBUGPROFILINGENUM - Enum of DebugProfiling
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DebugProfilingEnum()
 …
         PROFILINGCURRENTMEMENUM - Enum of ProfilingCurrentMem
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ProfilingCurrentMemEnum()
 …
         PROFILINGCURRENTFLOPSENUM - Enum of ProfilingCurrentFlops
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ProfilingCurrentFlopsEnum()
 …
         PROFILINGSOLUTIONTIMEENUM - Enum of ProfilingSolutionTime
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ProfilingSolutionTimeEnum()
 …
         MAXITERATIONCONVERGENCEFLAGENUM - Enum of MaxIterationConvergenceFlag
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaxIterationConvergenceFlagEnum()
 …
         STEADYSTATEMAXITERENUM - Enum of SteadystateMaxiter
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SteadystateMaxiterEnum()
 …
         STEADYSTATENUMREQUESTEDOUTPUTSENUM - Enum of SteadystateNumRequestedOutputs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SteadystateNumRequestedOutputsEnum()
 …
         STEADYSTATERELTOLENUM - Enum of SteadystateReltol
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SteadystateReltolEnum()
 …
         STEADYSTATEREQUESTEDOUTPUTSENUM - Enum of SteadystateRequestedOutputs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SteadystateRequestedOutputsEnum()
 …
         SURFACEENUM - Enum of Surface
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceEnum()
 …
         SURFACEFORCINGSPRECIPITATIONENUM - Enum of SurfaceforcingsPrecipitation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsPrecipitationEnum()
 …
         SURFACEFORCINGSMASSBALANCEENUM - Enum of SurfaceforcingsMassBalance
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsMassBalanceEnum()
 …
         SURFACEFORCINGSISPDDENUM - Enum of SurfaceforcingsIspdd
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsIspddEnum()
 …
         return StringToEnum('SurfaceforcingsIspdd')[0]
+def SurfaceforcingsDesfacEnum():
+        """
+        SURFACEFORCINGSDESFACENUM - Enum of SurfaceforcingsDesfac
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=SurfaceforcingsDesfacEnum()
+        """
+        return StringToEnum('SurfaceforcingsDesfac')[0]
+def SurfaceforcingsS0pEnum():
+        """
+        SURFACEFORCINGSS0PENUM - Enum of SurfaceforcingsS0p
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=SurfaceforcingsS0pEnum()
+        """
+        return StringToEnum('SurfaceforcingsS0p')[0]
 def SurfaceforcingsIssmbgradientsEnum():
         """
         SURFACEFORCINGSISSMBGRADIENTSENUM - Enum of SurfaceforcingsIssmbgradients
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsIssmbgradientsEnum()
 …
         SURFACEFORCINGSMONTHLYTEMPERATURESENUM - Enum of SurfaceforcingsMonthlytemperatures
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsMonthlytemperaturesEnum()
 …
         SURFACEFORCINGSHREFENUM - Enum of SurfaceforcingsHref
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsHrefEnum()
 …
         SURFACEFORCINGSSMBREFENUM - Enum of SurfaceforcingsSmbref
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsSmbrefEnum()
 …
         SURFACEFORCINGSBPOSENUM - Enum of SurfaceforcingsBPos
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsBPosEnum()
 …
         SURFACEFORCINGSBNEGENUM - Enum of SurfaceforcingsBNeg
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceforcingsBNegEnum()
 …
         THERMALMAXITERENUM - Enum of ThermalMaxiter
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThermalMaxiterEnum()
 …
         THERMALPENALTYFACTORENUM - Enum of ThermalPenaltyFactor
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThermalPenaltyFactorEnum()
 …
         THERMALPENALTYLOCKENUM - Enum of ThermalPenaltyLock
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThermalPenaltyLockEnum()
 …
         THERMALPENALTYTHRESHOLDENUM - Enum of ThermalPenaltyThreshold
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThermalPenaltyThresholdEnum()
 …
         THERMALSPCTEMPERATUREENUM - Enum of ThermalSpctemperature
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThermalSpctemperatureEnum()
 …
         THERMALSTABILIZATIONENUM - Enum of ThermalStabilization
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThermalStabilizationEnum()
 …
         THERMALISENTHALPYENUM - Enum of ThermalIsenthalpy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThermalIsenthalpyEnum()
 …
         return StringToEnum('ThermalIsenthalpy')[0]
+def GiaMantleViscosityEnum():
+        """
+        GIAMANTLEVISCOSITYENUM - Enum of GiaMantleViscosity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=GiaMantleViscosityEnum()
+        """
+        return StringToEnum('GiaMantleViscosity')[0]
+def GiaLithosphereThicknessEnum():
+        """
+        GIALITHOSPHERETHICKNESSENUM - Enum of GiaLithosphereThickness
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=GiaLithosphereThicknessEnum()
+        """
+        return StringToEnum('GiaLithosphereThickness')[0]
 def ThicknessEnum():
         """
         THICKNESSENUM - Enum of Thickness
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThicknessEnum()
 …
         TIMESTEPPINGSTARTTIMEENUM - Enum of TimesteppingStartTime
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TimesteppingStartTimeEnum()
 …
         TIMESTEPPINGFINALTIMEENUM - Enum of TimesteppingFinalTime
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TimesteppingFinalTimeEnum()
 …
         TIMESTEPPINGCFLCOEFFICIENTENUM - Enum of TimesteppingCflCoefficient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TimesteppingCflCoefficientEnum()
 …
         TIMESTEPPINGTIMEADAPTENUM - Enum of TimesteppingTimeAdapt
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TimesteppingTimeAdaptEnum()
 …
         TIMESTEPPINGTIMESTEPENUM - Enum of TimesteppingTimeStep
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TimesteppingTimeStepEnum()
 …
         TRANSIENTISDIAGNOSTICENUM - Enum of TransientIsdiagnostic
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TransientIsdiagnosticEnum()
 …
         TRANSIENTISGROUNDINGLINEENUM - Enum of TransientIsgroundingline
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TransientIsgroundinglineEnum()
 …
         TRANSIENTISPROGNOSTICENUM - Enum of TransientIsprognostic
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TransientIsprognosticEnum()
 …
         TRANSIENTISTHERMALENUM - Enum of TransientIsthermal
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TransientIsthermalEnum()
 …
         return StringToEnum('TransientIsthermal')[0]
+def TransientIsgiaEnum():
+        """
+        TRANSIENTISGIAENUM - Enum of TransientIsgia
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=TransientIsgiaEnum()
+        """
+        return StringToEnum('TransientIsgia')[0]
 def TransientNumRequestedOutputsEnum():
         """
         TRANSIENTNUMREQUESTEDOUTPUTSENUM - Enum of TransientNumRequestedOutputs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TransientNumRequestedOutputsEnum()
 …
         TRANSIENTREQUESTEDOUTPUTSENUM - Enum of TransientRequestedOutputs
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TransientRequestedOutputsEnum()
 …
         SOLUTIONTYPEENUM - Enum of SolutionType
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SolutionTypeEnum()
 …
         ANALYSISTYPEENUM - Enum of AnalysisType
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AnalysisTypeEnum()
 …
         CONFIGURATIONTYPEENUM - Enum of ConfigurationType
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ConfigurationTypeEnum()
 …
         ADJOINTBALANCETHICKNESSANALYSISENUM - Enum of AdjointBalancethicknessAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AdjointBalancethicknessAnalysisEnum()
 …
         ADJOINTHORIZANALYSISENUM - Enum of AdjointHorizAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AdjointHorizAnalysisEnum()
 …
         ADJOINTSOLUTIONENUM - Enum of AdjointSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AdjointSolutionEnum()
 …
         ANALYSISCOUNTERENUM - Enum of AnalysisCounter
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AnalysisCounterEnum()
 …
         return StringToEnum('AnalysisCounter')[0]
+def NoneAnalysisEnum():
+        """
+        NONEANALYSISENUM - Enum of NoneAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=NoneAnalysisEnum()
+        """
+        return StringToEnum('NoneAnalysis')[0]
+def DefaultAnalysisEnum():
+        """
+        DEFAULTANALYSISENUM - Enum of DefaultAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=DefaultAnalysisEnum()
+        """
+        return StringToEnum('DefaultAnalysis')[0]
 def BalancethicknessAnalysisEnum():
         """
         BALANCETHICKNESSANALYSISENUM - Enum of BalancethicknessAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BalancethicknessAnalysisEnum()
 …
         BALANCETHICKNESSSOLUTIONENUM - Enum of BalancethicknessSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BalancethicknessSolutionEnum()
 …
         return StringToEnum('BalancethicknessSolution')[0]
+def WeakBalancethicknessAnalysisEnum():
+        """
+        WEAKBALANCETHICKNESSANALYSISENUM - Enum of WeakBalancethicknessAnalysis
+           Usage:
+              macro=WeakBalancethicknessAnalysisEnum()
+        """
+        return StringToEnum('WeakBalancethicknessAnalysis')[0]
+def WeakBalancethicknessSolutionEnum():
+        """
+        WEAKBALANCETHICKNESSSOLUTIONENUM - Enum of WeakBalancethicknessSolution
+           Usage:
+              macro=WeakBalancethicknessSolutionEnum()
+        """
+        return StringToEnum('WeakBalancethicknessSolution')[0]
+def BalancethicknessSoftAnalysisEnum():
+        """
+        BALANCETHICKNESSSOFTANALYSISENUM - Enum of BalancethicknessSoftAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=BalancethicknessSoftAnalysisEnum()
+        """
+        return StringToEnum('BalancethicknessSoftAnalysis')[0]
+def BalancethicknessSoftSolutionEnum():
+        """
+        BALANCETHICKNESSSOFTSOLUTIONENUM - Enum of BalancethicknessSoftSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=BalancethicknessSoftSolutionEnum()
+        """
+        return StringToEnum('BalancethicknessSoftSolution')[0]
 def BedSlopeAnalysisEnum():
 …
         BEDSLOPEANALYSISENUM - Enum of BedSlopeAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BedSlopeAnalysisEnum()
 …
         BEDSLOPESOLUTIONENUM - Enum of BedSlopeSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BedSlopeSolutionEnum()
 …
         BEDSLOPEXANALYSISENUM - Enum of BedSlopeXAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BedSlopeXAnalysisEnum()
 …
         BEDSLOPEYANALYSISENUM - Enum of BedSlopeYAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BedSlopeYAnalysisEnum()
 …
         DIAGNOSTICHORIZANALYSISENUM - Enum of DiagnosticHorizAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticHorizAnalysisEnum()
 …
         DIAGNOSTICHUTTERANALYSISENUM - Enum of DiagnosticHutterAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticHutterAnalysisEnum()
 …
         DIAGNOSTICSOLUTIONENUM - Enum of DiagnosticSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticSolutionEnum()
 …
         DIAGNOSTICVERTANALYSISENUM - Enum of DiagnosticVertAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DiagnosticVertAnalysisEnum()
 …
         ENTHALPYANALYSISENUM - Enum of EnthalpyAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=EnthalpyAnalysisEnum()
 …
         ENTHALPYSOLUTIONENUM - Enum of EnthalpySolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=EnthalpySolutionEnum()
 …
         FLAIMANALYSISENUM - Enum of FlaimAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlaimAnalysisEnum()
 …
         FLAIMSOLUTIONENUM - Enum of FlaimSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FlaimSolutionEnum()
 …
         return StringToEnum('FlaimSolution')[0]
+def HydrologyAnalysisEnum():
+        """
+        HYDROLOGYANALYSISENUM - Enum of HydrologyAnalysis
+           Usage:
+              macro=HydrologyAnalysisEnum()
+        """
+        return StringToEnum('HydrologyAnalysis')[0]
+def HydrologyShreveAnalysisEnum():
+        """
+        HYDROLOGYSHREVEANALYSISENUM - Enum of HydrologyShreveAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyShreveAnalysisEnum()
+        """
+        return StringToEnum('HydrologyShreveAnalysis')[0]
+def HydrologyDCInefficientAnalysisEnum():
+        """
+        HYDROLOGYDCINEFFICIENTANALYSISENUM - Enum of HydrologyDCInefficientAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyDCInefficientAnalysisEnum()
+        """
+        return StringToEnum('HydrologyDCInefficientAnalysis')[0]
+def HydrologyDCEfficientAnalysisEnum():
+        """
+        HYDROLOGYDCEFFICIENTANALYSISENUM - Enum of HydrologyDCEfficientAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=HydrologyDCEfficientAnalysisEnum()
+        """
+        return StringToEnum('HydrologyDCEfficientAnalysis')[0]
 def HydrologySolutionEnum():
 …
         HYDROLOGYSOLUTIONENUM - Enum of HydrologySolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=HydrologySolutionEnum()
 …
         MELTINGANALYSISENUM - Enum of MeltingAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeltingAnalysisEnum()
 …
         return StringToEnum('MeltingAnalysis')[0]
-def NoneAnalysisEnum():
-        """
-        NONEANALYSISENUM - Enum of NoneAnalysis
-           Usage:
-              macro=NoneAnalysisEnum()
-        """
-        return StringToEnum('NoneAnalysis')[0]
 def PrognosticAnalysisEnum():
         """
         PROGNOSTICANALYSISENUM - Enum of PrognosticAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticAnalysisEnum()
 …
         PROGNOSTICSOLUTIONENUM - Enum of PrognosticSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PrognosticSolutionEnum()
 …
         STEADYSTATESOLUTIONENUM - Enum of SteadystateSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SteadystateSolutionEnum()
 …
         SURFACESLOPEANALYSISENUM - Enum of SurfaceSlopeAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceSlopeAnalysisEnum()
 …
         SURFACESLOPESOLUTIONENUM - Enum of SurfaceSlopeSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceSlopeSolutionEnum()
 …
         SURFACESLOPEXANALYSISENUM - Enum of SurfaceSlopeXAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceSlopeXAnalysisEnum()
 …
         SURFACESLOPEYANALYSISENUM - Enum of SurfaceSlopeYAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceSlopeYAnalysisEnum()
 …
         THERMALANALYSISENUM - Enum of ThermalAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThermalAnalysisEnum()
 …
         THERMALSOLUTIONENUM - Enum of ThermalSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThermalSolutionEnum()
 …
         TRANSIENTSOLUTIONENUM - Enum of TransientSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TransientSolutionEnum()
 …
         return StringToEnum('TransientSolution')[0]
+def GiaSolutionEnum():
+        """
+        GIASOLUTIONENUM - Enum of GiaSolution
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=GiaSolutionEnum()
+        """
+        return StringToEnum('GiaSolution')[0]
+def GiaAnalysisEnum():
+        """
+        GIAANALYSISENUM - Enum of GiaAnalysis
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=GiaAnalysisEnum()
+        """
+        return StringToEnum('GiaAnalysis')[0]
 def ApproximationEnum():
         """
         APPROXIMATIONENUM - Enum of Approximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ApproximationEnum()
 …
         NONEAPPROXIMATIONENUM - Enum of NoneApproximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=NoneApproximationEnum()
 …
         HUTTERAPPROXIMATIONENUM - Enum of HutterApproximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=HutterApproximationEnum()
 …
         MACAYEALAPPROXIMATIONENUM - Enum of MacAyealApproximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MacAyealApproximationEnum()
 …
         MACAYEALPATTYNAPPROXIMATIONENUM - Enum of MacAyealPattynApproximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MacAyealPattynApproximationEnum()
 …
         MACAYEALSTOKESAPPROXIMATIONENUM - Enum of MacAyealStokesApproximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MacAyealStokesApproximationEnum()
 …
         L1L2APPROXIMATIONENUM - Enum of L1L2Approximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=L1L2ApproximationEnum()
 …
         PATTYNAPPROXIMATIONENUM - Enum of PattynApproximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PattynApproximationEnum()
 …
         PATTYNSTOKESAPPROXIMATIONENUM - Enum of PattynStokesApproximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PattynStokesApproximationEnum()
 …
         STOKESAPPROXIMATIONENUM - Enum of StokesApproximation
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StokesApproximationEnum()
 …
         CONSTRAINTSENUM - Enum of Constraints
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ConstraintsEnum()
 …
         LOADSENUM - Enum of Loads
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=LoadsEnum()
 …
         MATERIALSENUM - Enum of Materials
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaterialsEnum()
 …
         NODESENUM - Enum of Nodes
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=NodesEnum()
 …
         return StringToEnum('Nodes')[0]
+def ContoursEnum():
+        """
+        CONTOURSENUM - Enum of Contours
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=ContoursEnum()
+        """
+        return StringToEnum('Contours')[0]
 def ParametersEnum():
         """
         PARAMETERSENUM - Enum of Parameters
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ParametersEnum()
 …
         VERTICESENUM - Enum of Vertices
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VerticesEnum()
 …
         RESULTSENUM - Enum of Results
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ResultsEnum()
 …
         GENERICPARAMENUM - Enum of GenericParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=GenericParamEnum()
 …
         ADOLCPARAMENUM - Enum of AdolcParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AdolcParamEnum()
 …
         BOOLINPUTENUM - Enum of BoolInput
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BoolInputEnum()
 …
         BOOLPARAMENUM - Enum of BoolParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BoolParamEnum()
 …
         CONTOURENUM - Enum of Contour
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ContourEnum()
 …
         CONTROLINPUTENUM - Enum of ControlInput
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ControlInputEnum()
 …
         DATASETINPUTENUM - Enum of DatasetInput
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DatasetInputEnum()
 …
         DOFINDEXINGENUM - Enum of DofIndexing
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DofIndexingEnum()
 …
         DOUBLEINPUTENUM - Enum of DoubleInput
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DoubleInputEnum()
 …
         DATASETPARAMENUM - Enum of DataSetParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DataSetParamEnum()
 …
         DOUBLEMATARRAYPARAMENUM - Enum of DoubleMatArrayParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DoubleMatArrayParamEnum()
 …
         DOUBLEMATPARAMENUM - Enum of DoubleMatParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DoubleMatParamEnum()
 …
         DOUBLEPARAMENUM - Enum of DoubleParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DoubleParamEnum()
 …
         DOUBLEVECPARAMENUM - Enum of DoubleVecParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DoubleVecParamEnum()
 …
         ELEMENTENUM - Enum of Element
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ElementEnum()
 …
         ELEMENTRESULTENUM - Enum of ElementResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ElementResultEnum()
 …
         EXTERNALRESULTENUM - Enum of ExternalResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ExternalResultEnum()
 …
         FILEPARAMENUM - Enum of FileParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FileParamEnum()
 …
         HOOKENUM - Enum of Hook
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=HookEnum()
 …
         ICEFRONTENUM - Enum of Icefront
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IcefrontEnum()
 …
         INPUTENUM - Enum of Input
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InputEnum()
 …
         INTINPUTENUM - Enum of IntInput
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IntInputEnum()
 …
         INTPARAMENUM - Enum of IntParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IntParamEnum()
 …
         INTVECPARAMENUM - Enum of IntVecParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IntVecParamEnum()
 …
         TRANSIENTPARAMENUM - Enum of TransientParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TransientParamEnum()
 …
         return StringToEnum('TransientParam')[0]
+def IceFrontTypeEnum():
+        """
+        ICEFRONTTYPEENUM - Enum of IceFrontType
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=IceFrontTypeEnum()
+        """
+        return StringToEnum('IceFrontType')[0]
 def MacAyeal2dIceFrontEnum():
         """
         MACAYEAL2DICEFRONTENUM - Enum of MacAyeal2dIceFront
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MacAyeal2dIceFrontEnum()
 …
         MACAYEAL3DICEFRONTENUM - Enum of MacAyeal3dIceFront
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MacAyeal3dIceFrontEnum()
 …
         MATICEENUM - Enum of Matice
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaticeEnum()
 …
         MATDAMAGEICEENUM - Enum of Matdamageice
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MatdamageiceEnum()
 …
         MATPARENUM - Enum of Matpar
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MatparEnum()
 …
         NODEENUM - Enum of Node
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=NodeEnum()
 …
         NUMERICALFLUXENUM - Enum of Numericalflux
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=NumericalfluxEnum()
 …
         return StringToEnum('Numericalflux')[0]
+def NumericalfluxTypeEnum():
+        """
+        NUMERICALFLUXTYPEENUM - Enum of NumericalfluxType
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=NumericalfluxTypeEnum()
+        """
+        return StringToEnum('NumericalfluxType')[0]
 def ParamEnum():
         """
         PARAMENUM - Enum of Param
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ParamEnum()
 …
         L1L2ICEFRONTENUM - Enum of L1L2IceFront
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=L1L2IceFrontEnum()
 …
         PATTYNICEFRONTENUM - Enum of PattynIceFront
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PattynIceFrontEnum()
 …
         PENGRIDENUM - Enum of Pengrid
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PengridEnum()
 …
         PENPAIRENUM - Enum of Penpair
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PenpairEnum()
 …
         PENTAENUM - Enum of Penta
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PentaEnum()
 …
         PENTAP1INPUTENUM - Enum of PentaP1Input
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PentaP1InputEnum()
 …
         PROFILERENUM - Enum of Profiler
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ProfilerEnum()
 …
         MATRIXPARAMENUM - Enum of MatrixParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MatrixParamEnum()
 …
         return StringToEnum('MatrixParam')[0]
+def NodeSIdEnum():
+        """
+        NODESIDENUM - Enum of NodeSId
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=NodeSIdEnum()
+        """
+        return StringToEnum('NodeSId')[0]
 def VectorParamEnum():
         """
         VECTORPARAMENUM - Enum of VectorParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VectorParamEnum()
 …
         RIFTFRONTENUM - Enum of Riftfront
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=RiftfrontEnum()
 …
         return StringToEnum('Riftfront')[0]
+def RiftfrontTypeEnum():
+        """
+        RIFTFRONTTYPEENUM - Enum of RiftfrontType
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=RiftfrontTypeEnum()
+        """
+        return StringToEnum('RiftfrontType')[0]
 def SegmentEnum():
         """
         SEGMENTENUM - Enum of Segment
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SegmentEnum()
 …
         SEGMENTRIFTFRONTENUM - Enum of SegmentRiftfront
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SegmentRiftfrontEnum()
 …
         SPCDYNAMICENUM - Enum of SpcDynamic
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SpcDynamicEnum()
 …
         SPCSTATICENUM - Enum of SpcStatic
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SpcStaticEnum()
 …
         SPCTRANSIENTENUM - Enum of SpcTransient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SpcTransientEnum()
 …
         STOKESICEFRONTENUM - Enum of StokesIceFront
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StokesIceFrontEnum()
 …
         STRINGARRAYPARAMENUM - Enum of StringArrayParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StringArrayParamEnum()
 …
         STRINGPARAMENUM - Enum of StringParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StringParamEnum()
 …
         TRIAENUM - Enum of Tria
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TriaEnum()
 …
         return StringToEnum('Tria')[0]
+def TriaP1InputEnum():
+        """
+        TRIAP1INPUTENUM - Enum of TriaP1Input
+           Usage:
+              macro=TriaP1InputEnum()
+        """
+        return StringToEnum('TriaP1Input')[0]
+def TriaInputEnum():
+        """
+        TRIAINPUTENUM - Enum of TriaInput
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=TriaInputEnum()
+        """
+        return StringToEnum('TriaInput')[0]
 def VertexEnum():
 …
         VERTEXENUM - Enum of Vertex
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VertexEnum()
 …
         return StringToEnum('Vertex')[0]
+def VertexPIdEnum():
+        """
+        VERTEXPIDENUM - Enum of VertexPId
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=VertexPIdEnum()
+        """
+        return StringToEnum('VertexPId')[0]
+def VertexSIdEnum():
+        """
+        VERTEXSIDENUM - Enum of VertexSId
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=VertexSIdEnum()
+        """
+        return StringToEnum('VertexSId')[0]
 def AirEnum():
         """
         AIRENUM - Enum of Air
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AirEnum()
 …
         ICEENUM - Enum of Ice
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IceEnum()
 …
         MELANGEENUM - Enum of Melange
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MelangeEnum()
 …
         WATERENUM - Enum of Water
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=WaterEnum()
 …
         CLOSEDENUM - Enum of Closed
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ClosedEnum()
 …
         FREEENUM - Enum of Free
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FreeEnum()
 …
         OPENENUM - Enum of Open
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OpenEnum()
 …
         ADJOINTPENUM - Enum of Adjointp
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AdjointpEnum()
 …
         ADJOINTXENUM - Enum of Adjointx
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AdjointxEnum()
 …
         ADJOINTYENUM - Enum of Adjointy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AdjointyEnum()
 …
         ADJOINTZENUM - Enum of Adjointz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AdjointzEnum()
 …
         BALANCETHICKNESSMISFITENUM - Enum of BalancethicknessMisfit
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BalancethicknessMisfitEnum()
 …
         BEDSLOPEXENUM - Enum of BedSlopeX
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BedSlopeXEnum()
 …
         BEDSLOPEYENUM - Enum of BedSlopeY
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BedSlopeYEnum()
 …
         BOUNDARYENUM - Enum of Boundary
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BoundaryEnum()
 …
         CONSTANTENUM - Enum of Constant
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ConstantEnum()
 …
         CONVERGEDENUM - Enum of Converged
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ConvergedEnum()
 …
         return StringToEnum('Converged')[0]
-def ExtToIuEnum():
-        """
-        EXTTOIUENUM - Enum of ExtToIu
-           Usage:
-              macro=ExtToIuEnum()
-        """
-        return StringToEnum('ExtToIu')[0]
 def FillEnum():
         """
         FILLENUM - Enum of Fill
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FillEnum()
 …
         FRACTIONINCREMENTENUM - Enum of FractionIncrement
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FractionIncrementEnum()
 …
         FRICTIONENUM - Enum of Friction
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FrictionEnum()
 …
         GROUNDINGLINEMELTINGRATEENUM - Enum of GroundinglineMeltingRate
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=GroundinglineMeltingRateEnum()
 …
         INTERNALENUM - Enum of Internal
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=InternalEnum()
 …
         return StringToEnum('Internal')[0]
-def IuToExtEnum():
-        """
-        IUTOEXTENUM - Enum of IuToExt
-           Usage:
-              macro=IuToExtEnum()
-        """
-        return StringToEnum('IuToExt')[0]
 def MassFluxEnum():
         """
         MASSFLUXENUM - Enum of MassFlux
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MassFluxEnum()
 …
         MAXPENETRATIONENUM - Enum of MaxPenetration
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaxPenetrationEnum()
 …
         MELTINGOFFSETENUM - Enum of MeltingOffset
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MeltingOffsetEnum()
 …
         MISFITENUM - Enum of Misfit
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MisfitEnum()
 …
         NUMBERNODETOELEMENTCONNECTIVITYENUM - Enum of NumberNodeToElementConnectivity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=NumberNodeToElementConnectivityEnum()
 …
         PRESSUREENUM - Enum of Pressure
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PressureEnum()
 …
         PRESSUREPICARDENUM - Enum of PressurePicard
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PressurePicardEnum()
 …
         QMUPRESSUREENUM - Enum of QmuPressure
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuPressureEnum()
 …
         QMUVXENUM - Enum of QmuVx
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuVxEnum()
 …
         QMUVYENUM - Enum of QmuVy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuVyEnum()
 …
         QMUVZENUM - Enum of QmuVz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuVzEnum()
 …
         QMUTHICKNESSENUM - Enum of QmuThickness
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuThicknessEnum()
 …
         QMUBEDENUM - Enum of QmuBed
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuBedEnum()
 …
         QMUSURFACEENUM - Enum of QmuSurface
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuSurfaceEnum()
 …
         QMUMELTINGENUM - Enum of QmuMelting
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuMeltingEnum()
 …
         return StringToEnum('QmuMelting')[0]
+def QmuVxMeshEnum():
+        """
+        QMUVXMESHENUM - Enum of QmuVxMesh
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=QmuVxMeshEnum()
+        """
+        return StringToEnum('QmuVxMesh')[0]
+def QmuVyMeshEnum():
+        """
+        QMUVYMESHENUM - Enum of QmuVyMesh
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=QmuVyMeshEnum()
+        """
+        return StringToEnum('QmuVyMesh')[0]
+def QmuVzMeshEnum():
+        """
+        QMUVZMESHENUM - Enum of QmuVzMesh
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=QmuVzMeshEnum()
+        """
+        return StringToEnum('QmuVzMesh')[0]
 def AndroidFrictionCoefficientEnum():
         """
         ANDROIDFRICTIONCOEFFICIENTENUM - Enum of AndroidFrictionCoefficient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AndroidFrictionCoefficientEnum()
 …
         RESETPENALTIESENUM - Enum of ResetPenalties
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ResetPenaltiesEnum()
 …
         SEGMENTONICESHELFENUM - Enum of SegmentOnIceShelf
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SegmentOnIceShelfEnum()
 …
         SURFACEABSVELMISFITENUM - Enum of SurfaceAbsVelMisfit
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceAbsVelMisfitEnum()
 …
         SURFACEAREAENUM - Enum of SurfaceArea
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceAreaEnum()
 …
         SURFACEAVERAGEVELMISFITENUM - Enum of SurfaceAverageVelMisfit
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceAverageVelMisfitEnum()
 …
         SURFACELOGVELMISFITENUM - Enum of SurfaceLogVelMisfit
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceLogVelMisfitEnum()
 …
         SURFACELOGVXVYMISFITENUM - Enum of SurfaceLogVxVyMisfit
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceLogVxVyMisfitEnum()
 …
         SURFACERELVELMISFITENUM - Enum of SurfaceRelVelMisfit
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceRelVelMisfitEnum()
 …
         SURFACESLOPEXENUM - Enum of SurfaceSlopeX
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceSlopeXEnum()
 …
         SURFACESLOPEYENUM - Enum of SurfaceSlopeY
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SurfaceSlopeYEnum()
 …
         TEMPERATUREENUM - Enum of Temperature
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TemperatureEnum()
 …
         TEMPERATUREOLDENUM - Enum of TemperatureOld
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TemperatureOldEnum()
 …
         TEMPERATUREPICARDENUM - Enum of TemperaturePicard
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TemperaturePicardEnum()
 …
         return StringToEnum('TemperaturePicard')[0]
-def TemperatureSurfaceEnum():
-        """
-        TEMPERATURESURFACEENUM - Enum of TemperatureSurface
-           Usage:
-              macro=TemperatureSurfaceEnum()
-        """
-        return StringToEnum('TemperatureSurface')[0]
-def TemperatureBasalEnum():
-        """
-        TEMPERATUREBASALENUM - Enum of TemperatureBasal
-           Usage:
-              macro=TemperatureBasalEnum()
-        """
-        return StringToEnum('TemperatureBasal')[0]
 def ThicknessAbsMisfitEnum():
         """
         THICKNESSABSMISFITENUM - Enum of ThicknessAbsMisfit
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThicknessAbsMisfitEnum()
 …
         return StringToEnum('ThicknessAbsMisfit')[0]
-def TypeEnum():
-        """
-        TYPEENUM - Enum of Type
-           Usage:
-              macro=TypeEnum()
-        """
-        return StringToEnum('Type')[0]
 def VelEnum():
         """
         VELENUM - Enum of Vel
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VelEnum()
 …
         VELOCITYENUM - Enum of Velocity
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VelocityEnum()
 …
         VXAVERAGEENUM - Enum of VxAverage
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VxAverageEnum()
 …
         VXENUM - Enum of Vx
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VxEnum()
 …
         VXPICARDENUM - Enum of VxPicard
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VxPicardEnum()
 …
         VYAVERAGEENUM - Enum of VyAverage
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VyAverageEnum()
 …
         VYENUM - Enum of Vy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VyEnum()
 …
         VYPICARDENUM - Enum of VyPicard
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VyPicardEnum()
 …
         VZENUM - Enum of Vz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VzEnum()
 …
         VZMACAYEALENUM - Enum of VzMacAyeal
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VzMacAyealEnum()
 …
         VZPATTYNENUM - Enum of VzPattyn
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VzPattynEnum()
 …
         VZPICARDENUM - Enum of VzPicard
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VzPicardEnum()
 …
         VZSTOKESENUM - Enum of VzStokes
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VzStokesEnum()
 …
         VXMESHENUM - Enum of VxMesh
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VxMeshEnum()
 …
         VYMESHENUM - Enum of VyMesh
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VyMeshEnum()
 …
         VZMESHENUM - Enum of VzMesh
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VzMeshEnum()
 …
         ENTHALPYENUM - Enum of Enthalpy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=EnthalpyEnum()
 …
         ENTHALPYPICARDENUM - Enum of EnthalpyPicard
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=EnthalpyPicardEnum()
 …
         THICKNESSABSGRADIENTENUM - Enum of ThicknessAbsGradient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThicknessAbsGradientEnum()
 …
         THICKNESSALONGGRADIENTENUM - Enum of ThicknessAlongGradient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThicknessAlongGradientEnum()
 …
         THICKNESSACROSSGRADIENTENUM - Enum of ThicknessAcrossGradient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ThicknessAcrossGradientEnum()
 …
         STEPRESPONSESENUM - Enum of StepResponses
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StepResponsesEnum()
 …
         INTMATPARAMENUM - Enum of IntMatParam
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IntMatParamEnum()
 …
         RHEOLOGYBBARABSGRADIENTENUM - Enum of RheologyBbarAbsGradient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=RheologyBbarAbsGradientEnum()
 …
         DRAGCOEFFICIENTABSGRADIENTENUM - Enum of DragCoefficientAbsGradient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DragCoefficientAbsGradientEnum()
 …
         TRANSIENTINPUTENUM - Enum of TransientInput
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TransientInputEnum()
 …
         WATERFRACTIONENUM - Enum of Waterfraction
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=WaterfractionEnum()
 …
         WATERCOLUMNENUM - Enum of Watercolumn
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=WatercolumnEnum()
 …
         BASALFRICTIONENUM - Enum of BasalFriction
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BasalFrictionEnum()
 …
         VISCOUSHEATINGENUM - Enum of ViscousHeating
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ViscousHeatingEnum()
 …
         QMUTEMPERATUREENUM - Enum of QmuTemperature
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuTemperatureEnum()
 …
         HYDROLOGYWATERVXENUM - Enum of HydrologyWaterVx
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=HydrologyWaterVxEnum()
 …
         HYDROLOGYWATERVYENUM - Enum of HydrologyWaterVy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=HydrologyWaterVyEnum()
 …
         STRESSTENSORENUM - Enum of StressTensor
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StressTensorEnum()
 …
         STRESSTENSORXXENUM - Enum of StressTensorxx
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StressTensorxxEnum()
 …
         STRESSTENSORXYENUM - Enum of StressTensorxy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StressTensorxyEnum()
 …
         STRESSTENSORXZENUM - Enum of StressTensorxz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StressTensorxzEnum()
 …
         STRESSTENSORYYENUM - Enum of StressTensoryy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StressTensoryyEnum()
 …
         STRESSTENSORYZENUM - Enum of StressTensoryz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StressTensoryzEnum()
 …
         STRESSTENSORZZENUM - Enum of StressTensorzz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StressTensorzzEnum()
 …
         return StringToEnum('StressTensorzz')[0]
+def GiaCrossSectionShapeEnum():
+        """
+        GIACROSSSECTIONSHAPEENUM - Enum of GiaCrossSectionShape
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=GiaCrossSectionShapeEnum()
+        """
+        return StringToEnum('GiaCrossSectionShape')[0]
+def GiadWdtEnum():
+        """
+        GIADWDTENUM - Enum of GiadWdt
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=GiadWdtEnum()
+        """
+        return StringToEnum('GiadWdt')[0]
+def GiaWEnum():
+        """
+        GIAWENUM - Enum of GiaW
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=GiaWEnum()
+        """
+        return StringToEnum('GiaW')[0]
 def P0Enum():
         """
         P0ENUM - Enum of P0
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=P0Enum()
 …
         P1ENUM - Enum of P1
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=P1Enum()
 …
         P1DGENUM - Enum of P1DG
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=P1DGEnum()
 …
         return StringToEnum('P1DG')[0]
+def MINIEnum():
+        """
+        MINIENUM - Enum of MINI
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=MINIEnum()
+        """
+        return StringToEnum('MINI')[0]
+def P2Enum():
+        """
+        P2ENUM - Enum of P2
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=P2Enum()
+        """
+        return StringToEnum('P2')[0]
 def SaveResultsEnum():
         """
         SAVERESULTSENUM - Enum of SaveResults
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SaveResultsEnum()
 …
         BOOLELEMENTRESULTENUM - Enum of BoolElementResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BoolElementResultEnum()
 …
         BOOLEXTERNALRESULTENUM - Enum of BoolExternalResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BoolExternalResultEnum()
 …
         DOUBLEELEMENTRESULTENUM - Enum of DoubleElementResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DoubleElementResultEnum()
 …
         DOUBLEEXTERNALRESULTENUM - Enum of DoubleExternalResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DoubleExternalResultEnum()
 …
         DOUBLEMATEXTERNALRESULTENUM - Enum of DoubleMatExternalResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=DoubleMatExternalResultEnum()
 …
         return StringToEnum('DoubleMatExternalResult')[0]
-def DoubleVecExternalResultEnum():
-        """
-        DOUBLEVECEXTERNALRESULTENUM - Enum of DoubleVecExternalResult
-           Usage:
-              macro=DoubleVecExternalResultEnum()
-        """
-        return StringToEnum('DoubleVecExternalResult')[0]
 def IntExternalResultEnum():
         """
         INTEXTERNALRESULTENUM - Enum of IntExternalResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IntExternalResultEnum()
 …
         JENUM - Enum of J
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=JEnum()
 …
         PATCHENUM - Enum of Patch
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PatchEnum()
 …
         PATCHNODESENUM - Enum of PatchNodes
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PatchNodesEnum()
 …
         PATCHVERTICESENUM - Enum of PatchVertices
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PatchVerticesEnum()
 …
         PENTAP1ELEMENTRESULTENUM - Enum of PentaP1ElementResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PentaP1ElementResultEnum()
 …
         return StringToEnum('PentaP1ElementResult')[0]
-def PetscVecExternalResultEnum():
-        """
-        PETSCVECEXTERNALRESULTENUM - Enum of PetscVecExternalResult
-           Usage:
-              macro=PetscVecExternalResultEnum()
-        """
-        return StringToEnum('PetscVecExternalResult')[0]
 def StringExternalResultEnum():
         """
         STRINGEXTERNALRESULTENUM - Enum of StringExternalResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StringExternalResultEnum()
 …
         STEPENUM - Enum of Step
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StepEnum()
 …
         TIMEENUM - Enum of Time
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TimeEnum()
 …
         TRIAP1ELEMENTRESULTENUM - Enum of TriaP1ElementResult
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TriaP1ElementResultEnum()
 …
         WATERCOLUMNOLDENUM - Enum of WaterColumnOld
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=WaterColumnOldEnum()
 …
         MINVELENUM - Enum of MinVel
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MinVelEnum()
 …
         MAXVELENUM - Enum of MaxVel
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaxVelEnum()
 …
         MINVXENUM - Enum of MinVx
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MinVxEnum()
 …
         MAXVXENUM - Enum of MaxVx
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaxVxEnum()
 …
         MAXABSVXENUM - Enum of MaxAbsVx
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaxAbsVxEnum()
 …
         MINVYENUM - Enum of MinVy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MinVyEnum()
 …
         MAXVYENUM - Enum of MaxVy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaxVyEnum()
 …
         MAXABSVYENUM - Enum of MaxAbsVy
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaxAbsVyEnum()
 …
         MINVZENUM - Enum of MinVz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MinVzEnum()
 …
         MAXVZENUM - Enum of MaxVz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaxVzEnum()
 …
         MAXABSVZENUM - Enum of MaxAbsVz
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaxAbsVzEnum()
 …
         ICEVOLUMEENUM - Enum of IceVolume
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IceVolumeEnum()
 …
         TOTALSMBENUM - Enum of TotalSmb
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TotalSmbEnum()
 …
         return StringToEnum('TotalSmb')[0]
-def RelativeEnum():
-        """
-        RELATIVEENUM - Enum of Relative
-           Usage:
-              macro=RelativeEnum()
-        """
-        return StringToEnum('Relative')[0]
 def AbsoluteEnum():
         """
         ABSOLUTEENUM - Enum of Absolute
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AbsoluteEnum()
 …
         INCREMENTALENUM - Enum of Incremental
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IncrementalEnum()
 …
         AGRESSIVEMIGRATIONENUM - Enum of AgressiveMigration
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AgressiveMigrationEnum()
 …
         NONEENUM - Enum of None
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=NoneEnum()
 …
         SOFTMIGRATIONENUM - Enum of SoftMigration
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SoftMigrationEnum()
 …
         return StringToEnum('SoftMigration')[0]
+def SubelementMigrationEnum():
+        """
+        SUBELEMENTMIGRATIONENUM - Enum of SubelementMigration
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=SubelementMigrationEnum()
+        """
+        return StringToEnum('SubelementMigration')[0]
+def SubelementMigration2Enum():
+        """
+        SUBELEMENTMIGRATION2ENUM - Enum of SubelementMigration2
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=SubelementMigration2Enum()
+        """
+        return StringToEnum('SubelementMigration2')[0]
+def GLlevelsetEnum():
+        """
+        GLLEVELSETENUM - Enum of GLlevelset
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=GLlevelsetEnum()
+        """
+        return StringToEnum('GLlevelset')[0]
 def StokesSolverEnum():
         """
         STOKESSOLVERENUM - Enum of StokesSolver
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=StokesSolverEnum()
 …
         ADJOINTENUM - Enum of Adjoint
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=AdjointEnum()
 …
         COLINEARENUM - Enum of Colinear
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ColinearEnum()
 …
         CONTROLSTEADYENUM - Enum of ControlSteady
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ControlSteadyEnum()
 …
         FSETENUM - Enum of Fset
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=FsetEnum()
 …
         GRADIENT1ENUM - Enum of Gradient1
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=Gradient1Enum()
 …
         GRADIENT2ENUM - Enum of Gradient2
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=Gradient2Enum()
 …
         GRADIENT3ENUM - Enum of Gradient3
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=Gradient3Enum()
 …
         GRADIENTENUM - Enum of Gradient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=GradientEnum()
 …
         GROUNDINGLINEMIGRATIONENUM - Enum of GroundinglineMigration
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=GroundinglineMigrationEnum()
 …
         GSETENUM - Enum of Gset
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=GsetEnum()
 …
         INDEXENUM - Enum of Index
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IndexEnum()
 …
         INDEXEDENUM - Enum of Indexed
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IndexedEnum()
 …
         INTERSECTENUM - Enum of Intersect
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=IntersectEnum()
 …
         NODALENUM - Enum of Nodal
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=NodalEnum()
 …
         OLDGRADIENTENUM - Enum of OldGradient
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OldGradientEnum()
 …
         OUTPUTFILEPOINTERENUM - Enum of OutputFilePointer
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OutputFilePointerEnum()
 …
         OUTPUTFILENAMEENUM - Enum of OutputFileName
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OutputFileNameEnum()
 …
         LOCKFILENAMEENUM - Enum of LockFileName
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=LockFileNameEnum()
 …
         return StringToEnum('LockFileName')[0]
+def PetscOptionsAnalysesEnum():
+        """
+        PETSCOPTIONSANALYSESENUM - Enum of PetscOptionsAnalyses
+           Usage:
+              macro=PetscOptionsAnalysesEnum()
+        """
+        return StringToEnum('PetscOptionsAnalyses')[0]
+def PetscOptionsStringsEnum():
+        """
+        PETSCOPTIONSSTRINGSENUM - Enum of PetscOptionsStrings
+           Usage:
+              macro=PetscOptionsStringsEnum()
+        """
+        return StringToEnum('PetscOptionsStrings')[0]
+def ToolkitsOptionsAnalysesEnum():
+        """
+        TOOLKITSOPTIONSANALYSESENUM - Enum of ToolkitsOptionsAnalyses
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=ToolkitsOptionsAnalysesEnum()
+        """
+        return StringToEnum('ToolkitsOptionsAnalyses')[0]
+def ToolkitsOptionsStringsEnum():
+        """
+        TOOLKITSOPTIONSSTRINGSENUM - Enum of ToolkitsOptionsStrings
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=ToolkitsOptionsStringsEnum()
+        """
+        return StringToEnum('ToolkitsOptionsStrings')[0]
 def QmuErrNameEnum():
 …
         QMUERRNAMEENUM - Enum of QmuErrName
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuErrNameEnum()
 …
         QMUINNAMEENUM - Enum of QmuInName
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuInNameEnum()
 …
         QMUOUTNAMEENUM - Enum of QmuOutName
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=QmuOutNameEnum()
 …
         REGULARENUM - Enum of Regular
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=RegularEnum()
 …
         SCALEDENUM - Enum of Scaled
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ScaledEnum()
 …
         SEPARATEENUM - Enum of Separate
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SeparateEnum()
 …
         SSETENUM - Enum of Sset
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=SsetEnum()
 …
         VERBOSEENUM - Enum of Verbose
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=VerboseEnum()
 …
         TRIANGLEINTERPENUM - Enum of TriangleInterp
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=TriangleInterpEnum()
 …
         BILINEARINTERPENUM - Enum of BilinearInterp
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=BilinearInterpEnum()
 …
         NEARESTINTERPENUM - Enum of NearestInterp
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=NearestInterpEnum()
 …
         XYENUM - Enum of XY
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=XYEnum()
 …
         XYZPENUM - Enum of XYZP
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=XYZPEnum()
 …
         return StringToEnum('XYZP')[0]
+def DenseEnum():
+        """
+        DENSEENUM - Enum of Dense
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=DenseEnum()
+        """
+        return StringToEnum('Dense')[0]
+def MpiDenseEnum():
+        """
+        MPIDENSEENUM - Enum of MpiDense
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=MpiDenseEnum()
+        """
+        return StringToEnum('MpiDense')[0]
+def SeqEnum():
+        """
+        SEQENUM - Enum of Seq
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=SeqEnum()
+        """
+        return StringToEnum('Seq')[0]
+def MpiEnum():
+        """
+        MPIENUM - Enum of Mpi
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
+           Usage:
+              macro=MpiEnum()
+        """
+        return StringToEnum('Mpi')[0]
 def OptionEnum():
         """
         OPTIONENUM - Enum of Option
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OptionEnum()
 …
         GENERICOPTIONENUM - Enum of GenericOption
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=GenericOptionEnum()
 …
         OPTIONCELLENUM - Enum of OptionCell
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OptionCellEnum()
 …
         OPTIONCHARENUM - Enum of OptionChar
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OptionCharEnum()
 …
         OPTIONSTRUCTENUM - Enum of OptionStruct
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OptionStructEnum()
 …
         OPTIONDOUBLEENUM - Enum of OptionDouble
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OptionDoubleEnum()
 …
         OPTIONLOGICALENUM - Enum of OptionLogical
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=OptionLogicalEnum()
 …
         PATERSONENUM - Enum of Paterson
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=PatersonEnum()
 …
         ARRHENIUSENUM - Enum of Arrhenius
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=ArrheniusEnum()
 …
         MAXIMUMNUMBEROFENUMS - Enum of MaximumNumberOfEnums
+        WARNING: DO NOT MODIFY THIS FILE
+                                this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+                                Please read src/c/shared/Enum/README for more information
            Usage:
               macro=MaximumNumberOfEnums()
         """
         return 496
+        return 560

issm/trunk/src/m/enum/ExternalResultEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FileParamEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FillEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FlaimAnalysisEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FlaimSolutionEnum.m

r8222	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FlowequationBordermacayealEnum.m

r9661	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FlowequationBorderpattynEnum.m

r9661	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FlowequationBorderstokesEnum.m

r9661	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FlowequationElementEquationEnum.m

r9661	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FlowequationIshutterEnum.m

r9661	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FlowequationIsl1l2Enum.m

r13395	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/FlowequationIsmacayealpattynEnum.m

r9661	r15396
3	3	%
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issm/trunk/src/m/enum/FlowequationIsstokesEnum.m

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issm/trunk/src/m/enum/FlowequationVertexEquationEnum.m

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issm/trunk/src/m/enum/FractionIncrementEnum.m

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issm/trunk/src/m/enum/FreeEnum.m

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issm/trunk/src/m/enum/FrictionCoefficientEnum.m

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issm/trunk/src/m/enum/FrictionEnum.m

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issm/trunk/src/m/enum/FrictionPEnum.m

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issm/trunk/src/m/enum/FrictionQEnum.m

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issm/trunk/src/m/enum/FsetEnum.m

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issm/trunk/src/m/enum/GenericOptionEnum.m

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issm/trunk/src/m/enum/GenericParamEnum.m

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issm/trunk/src/m/enum/GeometryHydrostaticRatioEnum.m

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issm/trunk/src/m/enum/Gradient1Enum.m

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issm/trunk/src/m/enum/Gradient2Enum.m

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issm/trunk/src/m/enum/Gradient3Enum.m

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issm/trunk/src/m/enum/GradientEnum.m

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issm/trunk/src/m/enum/GroundinglineMeltingRateEnum.m

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issm/trunk/src/m/enum/GroundinglineMigrationEnum.m

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issm/trunk/src/m/enum/GsetEnum.m

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issm/trunk/src/m/enum/HookEnum.m

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issm/trunk/src/m/enum/HutterApproximationEnum.m

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issm/trunk/src/m/enum/HydrologySolutionEnum.m

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issm/trunk/src/m/enum/HydrologyWaterVxEnum.m

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issm/trunk/src/m/enum/HydrologyWaterVyEnum.m

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issm/trunk/src/m/enum/IceEnum.m

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issm/trunk/src/m/enum/IceVolumeEnum.m

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issm/trunk/src/m/enum/IcefrontEnum.m

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issm/trunk/src/m/enum/IncrementalEnum.m

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issm/trunk/src/m/enum/IndependentObjectEnum.m

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issm/trunk/src/m/enum/IndexEnum.m

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issm/trunk/src/m/enum/IndexedEnum.m

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issm/trunk/src/m/enum/InputEnum.m

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issm/trunk/src/m/enum/IntExternalResultEnum.m

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issm/trunk/src/m/enum/IntInputEnum.m

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issm/trunk/src/m/enum/IntMatParamEnum.m

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issm/trunk/src/m/enum/IntParamEnum.m

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issm/trunk/src/m/enum/IntVecParamEnum.m

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issm/trunk/src/m/enum/InternalEnum.m

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issm/trunk/src/m/enum/IntersectEnum.m

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issm/trunk/src/m/enum/InversionControlParametersEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/InversionCostFunctionThresholdEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/InversionCostFunctionsCoefficientsEnum.m

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issm/trunk/src/m/enum/InversionCostFunctionsEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/InversionGradientOnlyEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/InversionGradientScalingEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/InversionIncompleteAdjointEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/InversionIscontrolEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/InversionMaxParametersEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/InversionMaxiterPerStepEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/InversionMinParametersEnum.m

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issm/trunk/src/m/enum/InversionNstepsEnum.m

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issm/trunk/src/m/enum/InversionNumControlParametersEnum.m

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issm/trunk/src/m/enum/InversionNumCostFunctionsEnum.m

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issm/trunk/src/m/enum/InversionStepThresholdEnum.m

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issm/trunk/src/m/enum/InversionTaoEnum.m

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issm/trunk/src/m/enum/InversionThicknessObsEnum.m

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issm/trunk/src/m/enum/InversionVelObsEnum.m

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issm/trunk/src/m/enum/InversionVxObsEnum.m

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issm/trunk/src/m/enum/InversionVyObsEnum.m

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issm/trunk/src/m/enum/InversionVzObsEnum.m

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issm/trunk/src/m/enum/JEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/L1L2ApproximationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/L1L2IceFrontEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/LoadsEnum.m

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issm/trunk/src/m/enum/LockFileNameEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MacAyeal2dIceFrontEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MacAyeal3dIceFrontEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MacAyealApproximationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MacAyealPattynApproximationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MacAyealStokesApproximationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaskElementonfloatingiceEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaskElementongroundediceEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaskElementonwaterEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaskVertexonfloatingiceEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaskVertexongroundediceEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaskVertexonwaterEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MassFluxEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MassFluxSegmentsEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MassFluxSegmentsPresentEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MatdamageiceEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsBetaEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsHeatcapacityEnum.m

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issm/trunk/src/m/enum/MaterialsLatentheatEnum.m

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issm/trunk/src/m/enum/MaterialsMeltingpointEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsMixedLayerCapacityEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsMuWaterEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsRheologyBEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsRheologyBbarEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsRheologyLawEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsRheologyNEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsRheologyZEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsRheologyZbarEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsRhoFreshwaterEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsRhoIceEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsRhoWaterEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsThermalExchangeVelocityEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaterialsThermalconductivityEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/MaticeEnum.m

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5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MatparEnum.m

r8222	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MatrixParamEnum.m

r11995	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaxAbsVxEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaxAbsVyEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaxAbsVzEnum.m

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	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaxIterationConvergenceFlagEnum.m

r12329	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaxPenetrationEnum.m

r8222	r15396
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	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaxVelEnum.m

r8222	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaxVxEnum.m

r8222	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaxVyEnum.m

r8222	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaxVzEnum.m

r8222	r15396
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4	4	% WARNING: DO NOT MODIFY THIS FILE
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MaximumNumberOfEnums.m

-              r14310
+              r15396
+%
 %   WARNING: DO NOT MODIFY THIS FILE
 %            this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh
 %            Please read src/c/EnumDefinitions/README for more information
+%            this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
+%            Please read src/c/shared/Enum/README for more information
+%
 %   Usage:
 %      macro=MaximumNumberOfEnums()
 macro=496;
+macro=560;

issm/trunk/src/m/enum/MelangeEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeltingAnalysisEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeltingOffsetEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshAverageVertexConnectivityEnum.m

r9705	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshDimensionEnum.m

r9719	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshEdgesEnum.m

r9733	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshElementconnectivityEnum.m

r9728	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshElementonbedEnum.m

r9729	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshElementonsurfaceEnum.m

r9729	r15396
3	3	%
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshElements2dEnum.m

r9733	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshElementsEnum.m

r9733	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshLowerelementsEnum.m

r9728	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshNumberofedgesEnum.m

r9725	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshNumberofelements2dEnum.m

r9725	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshNumberofelementsEnum.m

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	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshNumberoflayersEnum.m

r9725	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
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issm/trunk/src/m/enum/MeshNumberofvertices2dEnum.m

r9725	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshNumberofverticesEnum.m

r9725	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshUpperelementsEnum.m

r9728	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshVertexonbedEnum.m

r9729	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshVertexonsurfaceEnum.m

r9729	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshXEnum.m

r9734	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshYEnum.m

r9734	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MeshZEnum.m

r9734	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MinVelEnum.m

r8222	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MinVxEnum.m

r8222	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MinVyEnum.m

r8222	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MinVzEnum.m

r8222	r15396
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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MiscellaneousNameEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/MisfitEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/NearestInterpEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/NodalEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/NodeEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
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issm/trunk/src/m/enum/NodesEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
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issm/trunk/src/m/enum/NoneAnalysisEnum.m

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6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
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issm/trunk/src/m/enum/NoneApproximationEnum.m

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	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/NoneEnum.m

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issm/trunk/src/m/enum/NumberNodeToElementConnectivityEnum.m

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issm/trunk/src/m/enum/NumericalfluxEnum.m

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issm/trunk/src/m/enum/OldGradientEnum.m

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issm/trunk/src/m/enum/OpenEnum.m

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issm/trunk/src/m/enum/OptionCellEnum.m

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issm/trunk/src/m/enum/OptionCharEnum.m

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issm/trunk/src/m/enum/OptionDoubleEnum.m

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issm/trunk/src/m/enum/OptionEnum.m

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issm/trunk/src/m/enum/OptionLogicalEnum.m

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issm/trunk/src/m/enum/OptionStructEnum.m

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issm/trunk/src/m/enum/OutputFileNameEnum.m

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issm/trunk/src/m/enum/OutputFilePointerEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/P0Enum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/P1DGEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/P1Enum.m

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issm/trunk/src/m/enum/ParamEnum.m

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issm/trunk/src/m/enum/ParametersEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PatchEnum.m

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issm/trunk/src/m/enum/PatchNodesEnum.m

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issm/trunk/src/m/enum/PatchVerticesEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PatersonEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PattynApproximationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PattynIceFrontEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PattynStokesApproximationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PengridEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PenpairEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PentaEnum.m

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issm/trunk/src/m/enum/PentaP1ElementResultEnum.m

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issm/trunk/src/m/enum/PentaP1InputEnum.m

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issm/trunk/src/m/enum/PressureEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PressurePicardEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ProfilerEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ProfilingCurrentFlopsEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ProfilingCurrentMemEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ProfilingSolutionTimeEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticAnalysisEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticHydrostaticAdjustmentEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticMinThicknessEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticNumRequestedOutputsEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticPenaltyFactorEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticRequestedOutputsEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticSolutionEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticSpcthicknessEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticStabilizationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/PrognosticVertexPairingEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/QmuBedEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/QmuErrNameEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/QmuInNameEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/QmuIsdakotaEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/QmuMassFluxSegmentsPresentEnum.m

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issm/trunk/src/m/enum/QmuMeltingEnum.m

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issm/trunk/src/m/enum/QmuNumberofpartitionsEnum.m

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issm/trunk/src/m/enum/QmuNumberofresponsesEnum.m

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issm/trunk/src/m/enum/QmuOutNameEnum.m

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issm/trunk/src/m/enum/QmuPartitionEnum.m

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issm/trunk/src/m/enum/QmuPressureEnum.m

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issm/trunk/src/m/enum/QmuResponsedescriptorsEnum.m

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issm/trunk/src/m/enum/QmuSurfaceEnum.m

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issm/trunk/src/m/enum/QmuTemperatureEnum.m

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issm/trunk/src/m/enum/QmuThicknessEnum.m

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issm/trunk/src/m/enum/QmuVariabledescriptorsEnum.m

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issm/trunk/src/m/enum/QmuVxEnum.m

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issm/trunk/src/m/enum/QmuVyEnum.m

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issm/trunk/src/m/enum/QmuVzEnum.m

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issm/trunk/src/m/enum/RegularEnum.m

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issm/trunk/src/m/enum/ResetPenaltiesEnum.m

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issm/trunk/src/m/enum/ResultsEnum.m

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issm/trunk/src/m/enum/RheologyBbarAbsGradientEnum.m

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issm/trunk/src/m/enum/RiftfrontEnum.m

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issm/trunk/src/m/enum/RiftsNumriftsEnum.m

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issm/trunk/src/m/enum/RiftsRiftstructEnum.m

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issm/trunk/src/m/enum/SaveResultsEnum.m

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issm/trunk/src/m/enum/ScaledEnum.m

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issm/trunk/src/m/enum/SegmentEnum.m

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issm/trunk/src/m/enum/SegmentOnIceShelfEnum.m

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issm/trunk/src/m/enum/SegmentRiftfrontEnum.m

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issm/trunk/src/m/enum/SeparateEnum.m

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issm/trunk/src/m/enum/SettingsIoGatherEnum.m

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issm/trunk/src/m/enum/SettingsLowmemEnum.m

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issm/trunk/src/m/enum/SettingsOutputFrequencyEnum.m

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issm/trunk/src/m/enum/SettingsResultsAsPatchesEnum.m

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issm/trunk/src/m/enum/SettingsWaitonlockEnum.m

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issm/trunk/src/m/enum/SoftMigrationEnum.m

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issm/trunk/src/m/enum/SolutionTypeEnum.m

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issm/trunk/src/m/enum/SpcDynamicEnum.m

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issm/trunk/src/m/enum/SpcStaticEnum.m

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issm/trunk/src/m/enum/SpcTransientEnum.m

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issm/trunk/src/m/enum/SsetEnum.m

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issm/trunk/src/m/enum/SteadystateMaxiterEnum.m

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issm/trunk/src/m/enum/SteadystateNumRequestedOutputsEnum.m

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issm/trunk/src/m/enum/SteadystateReltolEnum.m

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issm/trunk/src/m/enum/SteadystateRequestedOutputsEnum.m

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issm/trunk/src/m/enum/SteadystateSolutionEnum.m

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issm/trunk/src/m/enum/StepEnum.m

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issm/trunk/src/m/enum/StepResponsesEnum.m

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issm/trunk/src/m/enum/StokesApproximationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StokesIceFrontEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StokesSolverEnum.m

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issm/trunk/src/m/enum/StressTensorEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StressTensorxxEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StressTensorxyEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StressTensorxzEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StressTensoryyEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StressTensoryzEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StressTensorzzEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StringArrayParamEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/StringExternalResultEnum.m

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issm/trunk/src/m/enum/StringParamEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceAbsVelMisfitEnum.m

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issm/trunk/src/m/enum/SurfaceAreaEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceAverageVelMisfitEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceLogVelMisfitEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceLogVxVyMisfitEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceRelVelMisfitEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceSlopeAnalysisEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceSlopeSolutionEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceSlopeXAnalysisEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceSlopeXEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceSlopeYAnalysisEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceSlopeYEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsBNegEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsBPosEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsDelta18oEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsDelta18oSurfaceEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsHrefEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsIsdelta18oEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsIspddEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsIssmbgradientsEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsMassBalanceEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsMonthlytemperaturesEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsPrecipitationEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsPrecipitationsPresentdayEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsSmbrefEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsTemperaturesLgmEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/SurfaceforcingsTemperaturesPresentdayEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TemperatureEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TemperatureOldEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TemperaturePicardEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ThermalAnalysisEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ThermalIsenthalpyEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ThermalMaxiterEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ThermalPenaltyFactorEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ThermalPenaltyLockEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ThermalPenaltyThresholdEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ThermalSolutionEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ThermalSpctemperatureEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ThermalStabilizationEnum.m

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issm/trunk/src/m/enum/ThicknessAbsGradientEnum.m

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issm/trunk/src/m/enum/ThicknessAbsMisfitEnum.m

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issm/trunk/src/m/enum/ThicknessAcrossGradientEnum.m

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issm/trunk/src/m/enum/ThicknessAlongGradientEnum.m

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issm/trunk/src/m/enum/ThicknessEnum.m

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issm/trunk/src/m/enum/TimeEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TimesteppingCflCoefficientEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TimesteppingFinalTimeEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TimesteppingStartTimeEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TimesteppingTimeAdaptEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TimesteppingTimeStepEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TotalSmbEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TransientInputEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TransientIsdiagnosticEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TransientIsgroundinglineEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TransientIsprognosticEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TransientIsthermalEnum.m

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issm/trunk/src/m/enum/TransientNumRequestedOutputsEnum.m

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issm/trunk/src/m/enum/TransientParamEnum.m

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issm/trunk/src/m/enum/TransientRequestedOutputsEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TransientSolutionEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TriaEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TriaP1ElementResultEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/TriangleInterpEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VectorParamEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VelEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VelocityEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VerboseEnum.m

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issm/trunk/src/m/enum/VertexEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VerticesEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/ViscousHeatingEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VxAverageEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VxEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VxMeshEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VxPicardEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VyAverageEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VyEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VyMeshEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VyPicardEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VzEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VzMacAyealEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VzMeshEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VzPattynEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VzPicardEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/VzStokesEnum.m

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	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/WaterColumnOldEnum.m

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	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/WaterEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/WatercolumnEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
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issm/trunk/src/m/enum/WaterfractionEnum.m

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	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/XYEnum.m

r10565	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/enum/XYZPEnum.m

r10565	r15396
3	3	%
4	4	% WARNING: DO NOT MODIFY THIS FILE
5		% this file has been automatically generated by src/c/~~EnumDefinitions~~/Synchronize.sh
6		% Please read src/c/~~EnumDefinitions~~/README for more information
	5	% this file has been automatically generated by src/c/shared/Enum/Synchronize.sh
	6	% Please read src/c/shared/Enum/README for more information
7	7	%
8	8	% Usage:

issm/trunk/src/m/exp/expcreateprofile.m

r13975	r15396
12	12
13	13	%Get root of filename
14		[path root ext ~~ver~~]=fileparts(filename);
	14	[path root ext]=fileparts(filename);
15	15
16	16	%Get profile

issm/trunk/src/m/exp/expflip.m

r13975	r15396
6	6	%
7	7
8		a=expread(domainname,1);
	8	a=expread(domainname);
9	9
10	10	for i=1:length(a),

issm/trunk/src/m/exp/exptool.m

r13975	r15396
1	1	function exptool(newfile,varargin)
2		%EXP~~MASTER~~ - allow to create, modify, add, cut, .. segments of domain outline together
	2	%EXPTOOL - allow to create, modify, add, cut, .. segments of domain outline together
3	3	%
4	4	% this routine is used to create, modify, cut,... an Argus file (.exp)

issm/trunk/src/m/exp/flowlines.m

-              r14310
+              r15396
 %check seed points
 %tria=TriaSearch(index,x,y,x0,y0);
 tria=tsearch(x,y,index,x0,y0);
+tria=TriaSearch(index,x,y,x0,y0);
+%tria=tsearch(x,y,index,x0,y0);
 pos=find(isnan(tria));
 x0(pos)=[];
 …
         %find current triangle
         queue=find(~done);
         %tria=TriaSearch(index,x,y,X(queue),Y(queue));
         tria=tsearch(x,y,index,X(queue),Y(queue));
+        tria=TriaSearch(index,x,y,X(queue),Y(queue));
+        %tria=tsearch(x,y,index,X(queue),Y(queue));
         %check that the point is actually inside a triangle of the mesh
 …
 %same process but reverse (vel=-vel) to have a vcomplete flow line
+queue=[];
 counter=1;
 X=x0; Y=y0;
 …
         %find current triangle
         queue=find(~done);
         %tria=TriaSearch(index,x,y,X(queue),Y(queue));
         tria=tsearch(x,y,index,X(queue),Y(queue));
+        tria=TriaSearch(index,x,y,X(queue),Y(queue));
+        %tria=tsearch(x,y,index,X(queue),Y(queue));
         %check that the point is actually inside a triangle of the mesh

issm/trunk/src/m/geometry/slope.m

-              r13395
+              r15396
 function [sx,sy,s]=slope(md)
+function [sx,sy,s]=slope(md,surf)
 %SLOPE - compute the surface slope
+%
 %   Usage:
 %      [sx,sy,s]=slope(md)
+%      [sx,sy,s]=slope(md,md.results.TransientSolution(1).Surface)
 %load some variables (it is much faster if the variab;es are loaded from md once for all)
 …
 end
+if nargin==1,
+        surf=md.geometry.surface;
+end
 %compute nodal functions coefficients N(x,y)=alpha x + beta y + gamma
 [alpha beta]=GetNodalFunctionsCoeff(index,x,y);
 summation=[1;1;1];
 sx=(md.geometry.surface(index).*alpha)*summation;
 sy=(md.geometry.surface(index).*beta)*summation;
+sx=(surf(index).*alpha)*summation;
+sy=(surf(index).*beta)*summation;
 s=sqrt(sx.^2+sy.^2);

issm/trunk/src/m/mesh/ProfileProjectOntoMesh.m

r13395	r15396
53	53	% (profile may start and/or end externally and/or cross holes in the model)
54	54
55		ind=find(node_in_element(:,9)>0);
	55	ind=find(node_in_element(:,end)>0);
56	56	newx=newx(ind,:);
57	57	newy=newy(ind,:);

issm/trunk/src/m/mesh/bamg.m

r13975	r15396
19	19	% to apply several fields, use one column per field
20	20	% - gradation : maximum ratio between two adjacent edges
21		% - Hessiantype : 0 -> use double P2 projection (default)
	21	% - Hessiantype : 0 -> use double L2 projection (default)
22	22	% 1 -> use Green formula
23	23	% - KeepVertices : try to keep initial vertices when adaptation is done on an existing mesh (default 1)

issm/trunk/src/m/mesh/roundmesh.m

r13975	r15396
46	46
47	47	end
48

issm/trunk/src/m/miscellaneous/normcdf_issm.m

r14310	r15396
7	7
8	8	end
9

issm/trunk/src/m/miscellaneous/normfit_issm.m

-              r14310
+              r15396
 function [muhat,sigmahat,muci,sigmaci]=normfit_issm(x,alpha)
+%  remove any NaN
+        if ~exist('alpha','var')
+                alpha=0.05;
+        end
+        x=x(~isnan(x(:)));
+        n=length(x);
+%  check for any NaN in any columns
+        if ~any(any((isnan(x))))
 %  explicitly calculate the moments
         muhat   =mean(x);
         sigmahat=std(x);
+                muhat   =mean(x);
+                sigmahat=std(x);
+        if (nargout>2)
+                if ~exist('alpha','var')
+                        alpha=0.05;
+                if (nargout>2)
+                        prob=1.-alpha/2.;
+                        if (size(x,1) == 1)
+                                % operate like matlab normfit, mean, std, etc.
+                                n=length(x);
+                        else
+                                n=size(x,1);
+                        end
+                        muci    =zeros(2,length(muhat   ));
+                        sigmaci =zeros(2,length(sigmahat));
+                        try
+                                muci(1,:)   =muhat-tinv(prob,n-1)*sigmahat/sqrt(n);
+                                muci(2,:)   =muhat+tinv(prob,n-1)*sigmahat/sqrt(n);
+                                sigmaci(1,:)=sigmahat*sqrt((n-1)/chi2inv(prob   ,n-1));
+                                sigmaci(2,:)=sigmahat*sqrt((n-1)/chi2inv(1.-prob,n-1));
+                        catch me
+                                muci(1,:)   =muhat;
+                                muci(2,:)   =muhat;
+                                sigmaci(1,:)=sigmahat;
+                                sigmaci(2,:)=sigmahat;
+                        end
                 end
-                prob=1.-alpha/2.;
+                try
+                        muci(1,1)   =muhat-tinv(prob,n-1)*sigmahat/sqrt(n);
+                        muci(2,1)   =muhat+tinv(prob,n-1)*sigmahat/sqrt(n);
+                        sigmaci(1,1)=sigmahat*sqrt((n-1)/chi2inv(prob   ,n-1));
+                        sigmaci(2,1)=sigmahat*sqrt((n-1)/chi2inv(1.-prob,n-1));
+                catch me
+                        muci(1,1)   =muhat;
+                        muci(2,1)   =muhat;
+                        sigmaci(1,1)=sigmahat;
+                        sigmaci(2,1)=sigmahat;
+        else
+%  must loop over columns, since number of elements could be different
+                muhat   =zeros(1,size(x,2));
+                sigmahat=zeros(1,size(x,2));
+                muci    =zeros(2,size(x,2));
+                sigmaci =zeros(2,size(x,2));
+%  remove any NaN and recursively call column
+                for j=1:size(x,2)
+                        [muhat(j),sigmahat(j),muci(:,j),sigmaci(:,j)]=normfit_issm(x(~isnan(x(:,j)),j),alpha);
                 end
         end
 end

issm/trunk/src/m/miscellaneous/norminv_issm.m

r14310	r15396
7	7
8	8	end
9

issm/trunk/src/m/miscellaneous/prctile_issm.m

-              r14310
+              r15396
 %  check for any NaN in any columns
                 if ~any(isnan(x))
+                if ~any(any((isnan(x))))
                         x=sort(x,1);
                         n=size(x,1);
 …
 end

issm/trunk/src/m/os/dakotaversion.m

-              r14310
+              r15396
         tline=fgets(fid);
         if ~ischar(tline), break, end
         if  strncmp(tline,'#define DAKOTA_VERSION',22),
                 DAKOTA_VERSION=strtrim(strrep(tline(24:end),'"',''));
+        if  strncmp(tline,'#define _DAKOTA_VERSION_',24),
+                DAKOTA_VERSION=strtrim(strrep(tline(26:end),'"',''));
         end
 end

issm/trunk/src/m/os/dakotaversion.py

-              r14310
+              r15396
         for tline in fid:
                 if strncmp(tline,'#define DAKOTA_VERSION',22):
                         DAKOTA_VERSION=tline[23:].replace('"','').strip()
+                if strncmp(tline,'#define _DAKOTA_VERSION_',24):
+                        DAKOTA_VERSION=tline[25:].replace('"','').strip()
                         break

issm/trunk/src/m/os/issmscpout.m

-              r13975
+              r15396
 function issmscpout(host,path,login,port,packages)
+function issmscpout(host,path,login,port,packages,varargin)
 %ISSMSCPOUT send packages to a host, using scp on unix, and pscp on windows
+%
 %   usage: issmscpout(host,path,packages)
+%   usage: issmscpout(host,path,login,port,packages)
+%
+%
 …
 %get hostname
 hostname=oshostname();
+%are we dis-allowing symbolic links?
+if nargin==6,
+        no_symlinks=1;
+else
+        no_symlinks=0;
+end
 %if hostname and host are the same, do a simple copy
 …
                 eval(['cd ' path])
                 system(['rm -rf ' packages{i} ]);
+                system(['ln -s ' here '/' packages{i} ' .']);
+                if no_symlinks,
+                        system(['cp  ' here '/' packages{i} ' .']);
+                else
+                        system(['ln -s ' here '/' packages{i} ' .']);
+                end
                 eval(['cd ' here]);
         end

issm/trunk/src/m/os/oshostname.m

r13975	r15396
7	7
8	8	if ispc(),
9		[status,hostname]=system('hostname ~~\| sed ''s/-//g''~~');
	9	[status,hostname]=system('hostname');
10	10	if status,
11	11	error('oshostname error message: could not run hostname command on windows os');

issm/trunk/src/m/parameterization/contourenvelope.m

r14310	r15396
138	138	end
139	139	segments=segments(1:count-1,:);
140

issm/trunk/src/m/plot/applyoptions.m

-              r14310
+              r15396
 filename=(getfieldvalue(options,'expdisp'));
 style=(getfieldvalue(options,'expstyle'));
+linewidth=(getfieldvalue(options,'linewidth',1));
 for i=1:length(getfieldvalue(options,'expdisp')),
         filenamei=filename{i};
         stylei=style{i};
+        expdisp(filenamei,gcf,stylei,getfieldvalue(options,'linewidth',1),getfieldvalue(options,'unit',1));
+        if length(linewidth)==1,
+                linewidthi=linewidth;
+        else
+                linewidthi=linewidth{i};
+        end
+        expdisp(filenamei,gcf,stylei,linewidthi,getfieldvalue(options,'unit',1));
 end
 …
         %box off
         if strcmpi(md.mesh.hemisphere,'n') | strcmpi(md.mesh.hemisphere,'north'),
                 A=expread([ jplsvn() '/projects/Exp/GreenlandBoxFront.exp']);
+                A=expread([ jplsvn() '/projects/ModelData/Exp/GreenlandBoxFront.exp']);
                 [A.x A.y]=ll2xy(A.x,A.y,+1,45,70);
                 A.x = A.x(1:30:end);
                 A.y = A.y(1:30:end);
         elseif strcmpi(md.mesh.hemisphere,'s') | strcmpi(md.mesh.hemisphere,'south'),
                 A=expread([ jplsvn() '/projects/Exp/Antarctica.exp']);
+                A=expread([ jplsvn() '/projects/ModelData/Exp/Antarctica.exp']);
         else
                 error('applyoptions error message: hemisphere not defined');
 …
         %get current plot position
         cplotpos=get(gca,'pos');
+        %compute inset position
+        PosInset=[cplotpos(1)+insetpos(1)*cplotpos(3),cplotpos(2)+insetpos(2)*cplotpos(4), insetpos(3)*cplotpos(3), insetpos(4)*cplotpos(4)];
+        %show pos
         X1=getfieldvalue(options,'insetx',xlim);
         Y1=getfieldvalue(options,'insety',ylim);
+        if strcmpi(getfieldvalue(options,'showinset','off'),'on')
+                line(X1([1 2 2 1 1]),Y1([1 1 2 2 1]),zeros(1,5),'Color','k','LineWidth',2);
+        end
+        %Get current figure
+        ax1=gca;
+        %plot inset
+        axes('pos',PosInset);
+        copyobj(get(ax1,'children'),gca);
+        patch('Faces',[1 2 3 4 1],'Vertices',[X1([1 2 2 1])' Y1([1 1 2 2])'],'FaceColor','None','EdgeColor','k','LineWidth',2);
+        %applay options
+        options=removefield(options,'text',0);
+        options=removefield(options,'title',0);
+        options=removefield(options,'xlabel',0);
+        options=removefield(options,'ylabel',0);
+        options=removefield(options,'inset',0);
+        options=removefield(options,'offsetaxispos',0);
+        options=removefield(options,'showregion',0);
+        options=changefieldvalue(options,'colorbar',0);
+        options=changefieldvalue(options,'latlon','off');
+        options=changefieldvalue(options,'axis','equal off');
+        options=changefieldvalue(options,'xlim',getfieldvalue(options,'insetx',xlim));
+        options=changefieldvalue(options,'ylim',getfieldvalue(options,'insety',ylim));
+        applyoptions(md,data,options);
+        %back to main gca
+        set(gcf,'CurrentAxes',maingca)
+end
+        for i=1:length(getfieldvalue(options,'insetx')),
+                if length(insetpos)==4,
+                        insetposi=insetpos;
+                else
+                        insetposi=insetpos{i};
+                end
+                PosInseti=[cplotpos(1)+insetposi(1)*cplotpos(3),cplotpos(2)+insetposi(2)*cplotpos(4), insetposi(3)*cplotpos(3), insetposi(4)*cplotpos(4)];
+                %show pos
+                if iscell(X1),
+                        X1i=X1{i};
+                else
+                        X1i=X1;
+                end
+                if iscell(Y1),
+                        Y1i=Y1{i};
+                else
+                        Y1i=Y1;
+                end
+                if strcmpi(getfieldvalue(options,'showinset','off'),'on')
+                        line(X1i([1 2 2 1 1]),Y1i([1 1 2 2 1]),zeros(1,5),'Color','k','LineWidth',2);
+                end
+                %Get current figure
+                ax1=gca;
+                %plot inset
+                axes('pos',PosInseti);
+                copyobj(get(ax1,'children'),gca);
+                patch('Faces',[1 2 3 4 1],'Vertices',[X1i([1 2 2 1])' Y1i([1 1 2 2])'],'FaceColor','None','EdgeColor','k','LineWidth',2);
+                %apply options
+                options=removefield(options,'text',0);
+                options=removefield(options,'title',0);
+                options=removefield(options,'xlabel',0);
+                options=removefield(options,'ylabel',0);
+                options=removefield(options,'inset',0);
+                options=removefield(options,'offsetaxispos',0);
+                options=removefield(options,'showregion',0);
+                options=changefieldvalue(options,'colorbar',0);
+                options=changefieldvalue(options,'latlon','off');
+                options=changefieldvalue(options,'axis','equal off');
+                options=changefieldvalue(options,'xlim',X1i);
+                options=changefieldvalue(options,'ylim',Y1i);
+                applyoptions(md,data,options);
+                %back to main gca
+                set(gcf,'CurrentAxes',maingca)
+        end
+end

issm/trunk/src/m/plot/colormaps/demmap.m

-              r14310
+              r15396
 function cmap = demmap(ncolors,minZ,maxZ);
+function cmap = demmap(ncolors,minZ,maxZ,varargin);
 %DEMMAP - concatenate sea and land color depending on zmin and zmax
+%
 %   Usage:
+%      cmap = demmap(n,zmin,zmax)
+%      cmap = demmap(n,zmin,zmax,varargin)
+%
+%   Example:
+%      cmap = demmap(50,-300,1200);
+%      cmap = demmap(50,-300,1200,'dem');
+%      cmap = demmap(50,-300,1200,'ibcao');
+%Input checks
 if nargin<3,
         help landseacolor
+        error('3 arguments necessary');
+        error('3 or 4 arguments necessary');
+elseif nargin>4,
+        help landseacolor
+        error('3 or 4 arguments necessary');
 end
+if minZ == maxZ;
+        maxZ = minZ+1;
+if nargin==4,
+        colorscheme = varargin{1};
+        if ~ischar(colorscheme), error('color scheme should be a string'); end
+else
+        colorscheme = 'dem';
 end
 …
 clim = [cmn cmx];
+cmap = [seacolor(nsea);landcolor(nland).^1.3];
+if strcmpi(colorscheme,'dem'),
+        cmap = [seacolor(nsea);landcolor(nland).^1.3];
+elseif strcmpi(colorscheme,'ibcao');
+        cmap = ibcao(nsea,nland);
+end

issm/trunk/src/m/plot/colormaps/getcolormap.m

-              r14067
+              r15396
         map = jet(256);
         map = map(128:end,:);
+elseif strcmpi(map,'damage'),
+        v=ver;
+        if any(strcmp('Image Processing Toolbox',{v.Name})),
+                map = color_scale(256,0,70,'ccw');
+                map = flipud(map);
+                map(1:2,:)=[0.7476    1.0000    1.0000; 0.7476    1.0000    1.0000];
+        else
+                error('damage colormap requires Image Processing Toolbox, please try another colormap');
+        end
 elseif strcmpi(map,'redblue'),
         map = hsv(256);
+        map = hsv(128);
         map = rgb2hsv(map);
         map(:,2)       = max(min( abs(map(:,1)-0.5)/0.5 ,1),0);
         map(1:128,1)   = 0.7;
         map(129:end,1) = 1;
+        map(1:64,1)   = 0.7;
+        map(65:end,1) = 1;
         map = hsv2rgb(map);
 elseif strcmpi(map,'Rignot'),

issm/trunk/src/m/plot/colormaps/seacolor.m

r14310	r15396
56	56	end
57	57	y = interp1(1:l,J,linspace(1,l,n),'*linear');
58

issm/trunk/src/m/plot/curvedarrow.m

-              r13975
+              r15396
         %compute some values out of (x1,y1) and (x2,y2)
         length=distance*angle;
         if exist(options,'widthratio'),
                 widthratio=getfieldvalue(options,'widthratio');
 …
                 m=-m;
         end
         if exist(options,'arrowlength'),
                 d=arrowlength;
 …
                 d=abs((distance*angle)*ratio);
         end
         %G is d distance from middle of E and F:
         G=(E+F)/2+d*m;

issm/trunk/src/m/plot/plot_gridded.m

-              r14310
+              r15396
 %shading interp;
+h=imagesc(xlim,ylim,data_grid);set(gca,'YDir','normal');
+if exist(options,'forcecolormap'),
+        image_rgb = ind2rgb(uint16((data_grid - data_min)*(length(map)/(data_max-data_min))),map);
+        h=imagesc(xlim,ylim,image_rgb);
+else
+        h=imagesc(xlim,ylim,data_grid);
+end
+axis xy
 %last step: mesh gridded?

issm/trunk/src/m/plot/plot_manager.m

-              r13975
+              r15396
 %Figure out if this is a semi-transparent plot.
+if exist(options,'googlemaps'),
+        plot_googlemaps(md,data,options,nlines,ncols,i);
+        return;
+end
+%Figure out if this is a semi-transparent plot.
 if exist(options,'gridded'),
         plot_gridded(md,data,options,nlines,ncols,i);
 …
 %standard plot:
+subplot(nlines,ncols,i);
+if exist(options,'asymsubplot')
+        id=getfieldvalue(options,'asymsubplot',i);
+        subplot(nlines,ncols,id);
+else
+        subplot(nlines,ncols,i);
+end
 %plot unit

issm/trunk/src/m/plot/plot_streamlines.m

-              r13395
+              r15396
 %initialize flowpath
 streamlines=getfieldvalue(options,'streamlines');
+edgecolor=getfieldvalue(options,'streamlines_color','y');
 if ischar(streamlines) & strcmpi(streamlines,'on');
         streamlines=60;
 …
 hold on
 for i=1:length(flowpath)
         patch('Xdata',[flowpath(i).x;NaN],'Ydata',[flowpath(i).y;NaN],'facecolor','none','edgecolor','y');
+        patch('Xdata',[flowpath(i).x;NaN],'Ydata',[flowpath(i).y;NaN],'facecolor','none','edgecolor',edgecolor);
 end

issm/trunk/src/m/plot/plot_transient_movie.m

r13975	r15396
65	65	function apply_options_movie(md,options,titlestring)
66	66	%apply options
67		options=~~addfielddefault~~(options,'title',titlestring);
	67	options=changefieldvalue(options,'title',titlestring);
68	68	options=addfielddefault(options,'colorbar',1);
69	69	applyoptions(md,[],options);

issm/trunk/src/m/plot/plotdoc.m

r13395	r15396
115	115	disp(' ''expdisp'': plot exp file on top of a data plot. provide exp file as an argument (use a cell of strings if more than one)');
116	116	disp(' ''expstyle'': marker style for expdisp plot (use a cell of strings if more than one)');
117		disp(' ''linewidth'': line width for expdisp plot');
	117	disp(' ''linewidth'': line width for expdisp plot (use a cell of strings if more than one)');
118	118	disp(' ''border'': size of display border (in pixels). active only for overlay plots');
119	119	disp(' ''text'': print string, use a cell of strings if more than one');

issm/trunk/src/m/plot/plotmodel.m

-              r14310
+              r15396
 subplotwidth=ceil(sqrt(options.numberofplots));
+%Get figure number and number of plots
+figurenumber=options.figurenumber;
+numberofplots=options.numberofplots;
 %if nlines and ncols specified, then bypass.
 if exist(options.list{1},'nlines'),
         nlines=getfieldvalue(options.list{1},'nlines');
 else
         nlines=subplotwidth;
+        nlines=ceil(numberofplots/subplotwidth);
 end
 …
         error('plotmodel error message: nlines and ncols  need to be specified together, or not at all');
 end
-%Get figure number and number of plots
-figurenumber=options.figurenumber;
-numberofplots=options.numberofplots;
 %go through subplots

issm/trunk/src/m/plot/scaleruler.m

-              r13395
+              r15396
 %get options
+structure=getfieldvalue(options,'scaleruler');
+fontsize=getfieldvalue(options,'scaleruler_fontsize',16);
+structure  = getfieldvalue(options,'scaleruler');
+fontcolor  = getfieldvalue(options,'fontcolor','k');
+fontweight = getfieldvalue(options,'fontweight','n');
+fontsize   = getfieldvalue(options,'scaleruler_fontsize',16);
 %Go through structure and fill missing arguments
 …
 end
 %retrieve north arrow parameters
 x0=structure(1);
 y0=structure(2);
 lengthscale=structure(3);
 widthscale=structure(4);
 numberofticks=structure(5);
+%retrieve scale parameters
+x0            = structure(1);
+y0            = structure(2);
+lengthscale   = structure(3);
+widthscale    = structure(4);
+numberofticks = structure(5);
+%initialize some coordinates
+unitlength=lengthscale/(numberofticks -1);
+flag=-1;
+%If only one tick, just draw a rectangle
+if numberofticks==1,
+        text(x0+lengthscale/2,y0+2*widthscale,2,[num2str(lengthscale/1000) 'km'],...
+                'FontSize',fontsize,'FontWeight',fontweight,'Color',fontcolor,'HorizontalAlignment','center','VerticalAlignment','baseline');
+        patch([x0 x0+lengthscale x0+lengthscale x0],[y0 y0 y0+widthscale y0+widthscale],2*ones(1,4),fontcolor,'Edgecolor',fontcolor);
+else
+        %initialize some coordinates
+        unitlength=lengthscale/(numberofticks -1);
+        flag=-1;
+Bd=[x0 y0];
+Bu=[x0 y0+widthscale];
+Tick=0;
+%Text
+xt=Bu(1);
+yt=Bu(2)+widthscale;
+text(xt,yt,num2str(Tick),'FontSize',fontsize,'FontWeight','n','HorizontalAlignment','left','VerticalAlignment','baseline');
+%loope over the patches
+for i=1:numberofticks-1,
+        Au=Bu;
+        Ad=Bd;
+        Bu=[Au(1)+unitlength Ad(2)+widthscale];
+        Bd=[Ad(1)+unitlength Ad(2)];
+        Tick=Tick+unitlength;
+        %pathes
+        if flag==-1
+                p=patch([Ad(1) Bd(1) Bu(1) Au(1)],[Ad(2) Bd(2) Bu(2) Au(2)],'Black','FaceAlpha',0.5);
+        else
+                p=patch([Ad(1) Bd(1) Bu(1) Au(1)],[Ad(2) Bd(2) Bu(2) Au(2)],'White','FaceAlpha',0.3);
+        end
+        %flip flag
+        flag=-flag;
+        Bd=[x0 y0];
+        Bu=[x0 y0+widthscale];
+        Tick=0;
         %Text
         xt=Bu(1);
         yt=Bu(2)+widthscale;
+        if i~=numberofticks-1,
+                text(xt,yt,num2str(round_ice(Tick/1000,3)),'FontSize',fontsize,'FontWeight','n','HorizontalAlignment','left','VerticalAlignment','baseline');
+        text(xt,yt,2,num2str(Tick),'FontSize',fontsize,'FontWeight',fontweight,'Color',fontcolor,'HorizontalAlignment','center','VerticalAlignment','baseline');
+        %loope over the patches
+        for i=1:numberofticks-1,
+                Au=Bu;
+                Ad=Bd;
+                Bu=[Au(1)+unitlength Ad(2)+widthscale];
+                Bd=[Ad(1)+unitlength Ad(2)];
+                Tick=Tick+unitlength;
+                %pathes
+                if flag==-1
+                        p=patch([Ad(1) Bd(1) Bu(1) Au(1)],[Ad(2) Bd(2) Bu(2) Au(2)],2*ones(1,4),'Black');
+                else
+                        p=patch([Ad(1) Bd(1) Bu(1) Au(1)],[Ad(2) Bd(2) Bu(2) Au(2)],2*ones(1,4),'White');
+                end
+                %flip flag
+                flag=-flag;
+                %Text
+                xt=Bu(1);
+                yt=Bu(2)+widthscale;
+                if i~=numberofticks-1,
+                        text(xt,yt,2,num2str(round_ice(Tick/1000,3)),'FontSize',fontsize,'FontWeight',fontweight,'Color',fontcolor,'HorizontalAlignment','center','VerticalAlignment','baseline');
+                end
         end
+        text(xt,yt,2,num2str(round_ice(Tick/1000,3)),'FontSize',fontsize,'FontWeight',fontweight,'Color',fontcolor,'HorizontalAlignment','center','VerticalAlignment','baseline');
+        % add leading spaces depending on length of label string
+        str=' km';
+        for i=1:numel(num2str(round_ice(Tick/1000,3))),
+                str=[' ' str];
+        end
+        text(xt,yt,2,str,'FontSize',fontsize,'FontWeight',fontweight,'Color',fontcolor,'HorizontalAlignment','left','VerticalAlignment','baseline');
 end
-text(xt,yt,[num2str(round_ice(Tick/1000,3)) ' km'],'FontSize',fontsize,'FontWeight','n','HorizontalAlignment','left','VerticalAlignment','baseline');

issm/trunk/src/m/plot/subplotmodel.m

-              r13975
+              r15396
 %Regular subplot
 if ~exist(options,'tightsubplot')
+        subplot(nlines,ncols,num);
+        return;
+        if exist(options,'asymsubplot')
+                id=getfieldvalue(options,'asymsubplot',num);
+                subplot(nlines,ncols,id);
+                return
+        else
+                subplot(nlines,ncols,num);
+                return;
+        end
 end

issm/trunk/src/m/solve/WriteData.m

-              r13975
+              r15396
 format  = getfieldvalue(options,'format');
 mattype = getfieldvalue(options,'mattype',0);    %only required for matrices
+forcinglength = getfieldvalue(options,'forcinglength',-1);
 %Process sparse matrices
 if issparse(data),
         data=full(data);
+end
+%Scale data if necesarry
+if exist(options,'scale'),
+        scale = getfieldvalue(options,'scale');
+        if size(data,1)==forcinglength,
+                data(1:end-1,:) = scale.*data(1:end-1,:);
+        else
+                data  = scale.*data;
+        end
 end

issm/trunk/src/m/solve/WriteData.py

-              r14067
+              r15396
         format  = options.getfieldvalue('format')
         mattype = options.getfieldvalue('mattype',0)    #only required for matrices
+        forcinglength = options.getfieldvalue('forcinglength',-1)
         #Process sparse matrices
 …
 #               data=full(data);
 #       end
+        #Scale data if necesarry
+        if options.exist('scale'):
+                scale = options.getfieldvalue('scale')
+                if numpy.size(data) > 1 :
+                        if numpy.size(data,0)==forcinglength:
+                                data=numpy.array(data)
+                                data[0:-1,:] = scale*data[0:-1,:]
+                        else:
+                                data  = scale*data
+                else:
+                        data  = scale*data
         #Step 1: write the enum to identify this record uniquely

issm/trunk/src/m/solve/loadresultsfromcluster.m

r13395	r15396
51	51	else
52	52	delete([md.miscellaneous.name '.bin']);
53		delete([md.miscellaneous.name '.~~petsc~~']);
	53	delete([md.miscellaneous.name '.toolkits']);
54	54	if ~ispc(),
55	55	delete([md.miscellaneous.name '.queue']);

issm/trunk/src/m/solve/loadresultsfromcluster.py

r13395	r15396
52	52	else:
53	53	os.remove(md.miscellaneous.name+'.bin')
54		os.remove(md.miscellaneous.name+'.~~petsc~~')
	54	os.remove(md.miscellaneous.name+'.toolkits')
55	55	if not ispc():
56	56	os.remove(md.miscellaneous.name+'.queue')

issm/trunk/src/m/solve/marshall.m

-              r13975
+              r15396
         %Some properties do not need to be marshalled
         if ismember(field,{'results' 'radaroverlay' 'solver' 'cluster'  'flaim' 'private'}),
+        if ismember(field,{'results' 'radaroverlay' 'toolkits' 'cluster'  'flaim' 'private'}),
                 continue;
         end
 …
         %Marshall current object
         %disp(['marshalling ' field '...']);
         marshall(md.(field),fid);
+        marshall(md.(field),md,fid);
 end

issm/trunk/src/m/solve/marshall.py

-              r13395
+              r15396
                 #Some properties do not need to be marshalled
                 if field in ['results','radaroverlay','solver','cluster','flaim','private']:
+                if field in ['results','radaroverlay','toolkits','cluster','flaim','private']:
                         continue
 …
                 #Marshall current object
                 #print "marshalling %s ..." % field
                 exec("md.%s.marshall(fid)" % field)
+                exec("md.%s.marshall(md,fid)" % field)
         #close file

issm/trunk/src/m/solve/parseresultsfromdisk.m

-              r13975
+              r15396
         %read next result
+        result=ReadData(fid);
+        try,
+                result=ReadData(fid);
+        catch me,
+                disp('WARNING: file corrupted, results partial recovery');
+                result=[];
+        end
 end
 …
         %read next result
+        result=ReadData(fid);
+        try,
+                result=ReadData(fid);
+        catch me,
+                disp('WARNING: file corrupted, results partial recovery');
+                result=[];
+        end
 end
 …
         end
+        %Process units here FIXME: this should not be done here!
+        yts=365.0*24.0*3600.0;
+        if strcmp(fieldname,'BalancethicknessThickeningRate'),
+                field = field*yts;
+        elseif strcmp(fieldname,'Time'),
+                field = field/yts;
+        elseif strcmp(fieldname,'HydrologyWaterVx'),
+                field = field*yts;
+        elseif strcmp(fieldname,'HydrologyWaterVy'),
+                field = field*yts;
+        elseif strcmp(fieldname,'Vx'),
+                field = field*yts;
+        elseif strcmp(fieldname,'Vy'),
+                field = field*yts;
+        elseif strcmp(fieldname,'Vz'),
+                field = field*yts;
+        elseif strcmp(fieldname,'Vel'),
+                field = field*yts;
+        elseif strcmp(fieldname,'BasalforcingsMeltingRate'),
+                field = field*yts;
+        elseif strcmp(fieldname,'TotalSmb'),
+                field = field/10.^12*yts; %(GigaTon/year)
+        elseif strcmp(fieldname,'SurfaceforcingsMassBalance'),
+                field = field*yts;
+        end
         result.fieldname=fieldname;
         result.time=time;
         result.step=step;
         result.field=field;
 end
 % }}}

issm/trunk/src/m/solve/parseresultsfromdisk.py

-              r14310
+              r15396
         return results
         # }}}
 def parseresultsfromdiskiosplit(filename):    # {{{
         """
 …
         return results
         # }}}
 def ReadData(fid):    # {{{
         """
 …
                         raise TypeError("cannot read data of type %d" % type)
+                #Process units here FIXME: this should not be done here!
+                yts=365.0*24.0*3600.0
+                if strcmp(fieldname,'BalancethicknessThickeningRate'):
+                        field = field*yts
+                elif strcmp(fieldname,'Time'):
+                        field = field/yts
+                elif strcmp(fieldname,'HydrologyWaterVx'):
+                        field = field*yts
+                elif strcmp(fieldname,'HydrologyWaterVy'):
+                        field = field*yts
+                elif strcmp(fieldname,'Vx'):
+                        field = field*yts
+                elif strcmp(fieldname,'Vy'):
+                        field = field*yts
+                elif strcmp(fieldname,'Vz'):
+                        field = field*yts
+                elif strcmp(fieldname,'Vel'):
+                        field = field*yts
+                elif strcmp(fieldname,'BasalforcingsMeltingRate'):
+                        field = field*yts
+                elif strcmp(fieldname,'TotalSmb'):
+                        field = field/10.**12.*yts #(GigaTon/year)
+                elif strcmp(fieldname,'SurfaceforcingsMassBalance'):
+                        field = field*yts
                 result=OrderedDict()
                 result['fieldname']=fieldname
 …
         return result
         # }}}
 def ReadDataDimensions(fid):    # {{{
         """
 …
         return result
         # }}}

issm/trunk/src/m/solve/process_solve_options.m

-              r14310
+              r15396
 if ~ismember(solution_type,[DiagnosticSolutionEnum(),PrognosticSolutionEnum(),ThermalSolutionEnum(),...
                 SteadystateSolutionEnum(),TransientSolutionEnum(),EnthalpySolutionEnum(),...
                 BalancethicknessSolutionEnum(),WeakBalancethicknessSolutionEnum(),BedSlopeSolutionEnum(),...
                 SurfaceSlopeSolutionEnum(),HydrologySolutionEnum(),FlaimSolutionEnum()]),
+                BalancethicknessSolutionEnum(),BalancethicknessSoftSolutionEnum(),BedSlopeSolutionEnum(),...
+                SurfaceSlopeSolutionEnum(),HydrologySolutionEnum(),FlaimSolutionEnum(),GiaSolutionEnum()]),
         error(['process_solve_options error message: solution_type ' EnumToString(solution_type) ' not supported yet!']);
 end

issm/trunk/src/m/solve/process_solve_options.py

-              r13395
+              r15396
         if solution_type not in (DiagnosticSolutionEnum(),PrognosticSolutionEnum(),ThermalSolutionEnum(),\
                         SteadystateSolutionEnum(),TransientSolutionEnum(),EnthalpySolutionEnum(),\
+                        BalancethicknessSolutionEnum(),BedSlopeSolutionEnum(),SurfaceSlopeSolutionEnum(),HydrologySolutionEnum(),FlaimSolutionEnum()):
+                        BalancethicknessSolutionEnum(),BedSlopeSolutionEnum(),SurfaceSlopeSolutionEnum(),\
+                        HydrologySolutionEnum(),FlaimSolutionEnum(),GiaSolutionEnum()):
                 raise ValueError("process_solve_options error message: solution_type '%s' not supported yet!" % EnumToString(solution_type)[0])
         outoptions['solution_type']=solution_type

issm/trunk/src/m/solve/solve.m

-              r13975
+              r15396
 end
-%we need to make sure we have PETSC support, otherwise, we run with only one cpu:
-if ~ispetsc(),
-        disp('PETSc support not included, running on 1 cpu only!');
-        cluster.np=1;
-end
 %Write all input files
 marshall(md);                                          % bin file
 PetscFile(md.solver,[md.miscellaneous.name '.petsc']); % petsc file
+ToolkitsFile(md.toolkits,[md.miscellaneous.name '.toolkits']); % toolkits file
 BuildQueueScript(cluster,md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof); % queue file
 …
 %Launch job
 modelname = md.miscellaneous.name;
+filelist  = {[modelname '.bin '] [modelname '.petsc '] [modelname '.queue ']};
+filelist  = {[modelname '.bin '] [modelname '.toolkits ']};
+if ispc,
+        filelist{end+1}=[modelname '.bat '];
+else
+        filelist{end+1}=[modelname '.queue '];
+end
 if md.qmu.isdakota,
         filelist{end+1} = [modelname '.qmu.in'];
 …
 %wait on lock
 if md.settings.waitonlock>0,
         %we wait for the done file
         islock=waitonlock(md);
         if islock==0, %no results to be loaded
                 disp('The results must be loaded manually with md=loadresultsfromcluster(md).');
         else          %load results
                 disp('loading results from cluster');
+if isnan(md.settings.waitonlock),
+        %load when user enters 'y'
+        disp('solution launched on remote cluster. log in to detect job completion.');
+        choice=input('Is the job successfully completed? (y/n)','s');
+        if ~strcmp(choice,'y'),
+                disp('Results not loaded... exiting');
+        else
                 md=loadresultsfromcluster(md);
         end
+elseif md.settings.waitonlock>0,
+        %we wait for the done file
+        done=waitonlock(md);
+        disp('loading results from cluster');
+        md=loadresultsfromcluster(md);
+elseif md.settings.waitonlock==0,
+         disp('Model results must be loaded manually with md=loadresultsfromcluster(md);');
 end

issm/trunk/src/m/solve/solve.py

-              r13395
+              r15396
         #Write all input files
         marshall(md)                                           # bin file
         md.solver.PetscFile(md.miscellaneous.name+'.petsc')    # petsc file
+        md.toolkits.ToolkitsFile(md.miscellaneous.name+'.toolkits')    # toolkits file
         cluster.BuildQueueScript(md.private.runtimename,md.miscellaneous.name,md.private.solution,md.settings.io_gather,md.debug.valgrind,md.debug.gprof)    # queue file
-        #we need to make sure we have PETSC support, otherwise, we run with only one cpu:
-        if not ispetsc():
-                print "PETSC support not included, running on 1 cpu only!"
-                cluster.np=1
         #Stop here if batch mode
 …
         #Launch job
         modelname = md.miscellaneous.name
         filelist  = [modelname+'.bin ',modelname+'.petsc ',modelname+'.queue ']
+        filelist  = [modelname+'.bin ',modelname+'.toolkits ',modelname+'.queue ']
         if md.qmu.isdakota:
                 filelist.append(modelname+'.qmu.in')

issm/trunk/src/m/solve/waitonlock.m

-              r13975
+              r15396
 function flag=waitonlock(md)
+function ispresent=waitonlock(md)
 %WAITONLOCK - wait for a file
+%
+%   This routine will return when a file named 'filename' is written to disk.
+%   This routine will return when a file named 'lockfilename' is written to disk.
+%   Also check for outlog file be cause it might bewritten several seconds
+%   after the lock file.
 %   If the time limit given in input is exceeded, return 0
+%
 …
 %      flag=waitonlock(md)
+%Get filename (lock file) and options
+executionpath=md.cluster.executionpath;
+cluster=md.cluster.name;
+login=md.cluster.login;
+if isprop(md.cluster,'port')
+        port=md.cluster.port;
+%Return if waitonlock < 0 (no need to wait)
+%Get lockfilename (lock file) and options
+executionpath = md.cluster.executionpath;
+timelimit     = md.settings.waitonlock;
+cluster       = md.cluster;
+lockfilename  = [executionpath '/' md.private.runtimename '/' md.miscellaneous.name '.lock'];
+logfilename   = [executionpath '/' md.private.runtimename '/' md.miscellaneous.name '.outlog'];
+%If we are using the generic cluster in interactive mode, job is already complete
+if isa(cluster,'generic') & cluster.interactive
+        %We are in interactive mode, no need to check for job completion
+        ispresent=1;
+        return;
 end
-timelimit=md.settings.waitonlock;
-filename=[executionpath '/' md.private.runtimename '/' md.miscellaneous.name '.lock'];
+%waitonlock will work if the lock is on the same machine only:
+if ~strcmpi(oshostname(),cluster),
+%initialize time and file presence test flag
+time=0; ispresent=0; time0=clock;
+disp(['waiting for ' lockfilename ' hold on... (Ctrl+C to exit)'])
+        disp('solution launched on remote cluster. log in to detect job completion.');
+        choice=input('Is the job successfully completed? (y/n)','s');
+        if ~strcmp(choice,'y'),
+                disp('Results not loaded... exiting');
+                flag=0;
+%prepare command if the job is not running on the local machine
+if ~strcmpi(oshostname(),cluster.name),
+        login = cluster.login;
+        port  = 0;
+        if isprop(cluster,'port')
+                port = cluster.port;
+        end
+        if port,
+                command = ['ssh -l ' login ' -p ' num2str(port) ' localhost "[ -f ' lockfilename ' ] && [ -f ' logfilename ' ]" 2>/dev/null'];
         else
+                flag=1;
+        end
+%job is running on the same machine
+else
+        if ismember('interactive',properties(md.cluster)) & md.cluster.interactive
+                %We are in interactive mode, no need to check for job completion
+                flag=1;
+                return;
+        end
+        %initialize time and file presence test flag
+        time=0; ispresent=0;
+        disp(['waiting for ' filename ' hold on... (Ctrl+C to exit)'])
+        %loop till file .lock exist or time is up
+        while (ispresent==0 & time<timelimit)
+                ispresent=exist(filename,'file');
+                pause(1);
+                time=time+1/60;
+        end
+        %build output
+        if (time>timelimit),
+                disp('Time limit exceeded. Increase md.settings.waitonlock');
+                disp('The results must be loaded manually with md=loadresultsfromcluster(md).');
+                error(['waitonlock error message: time limit exceeded']);
+                flag=0;
+        else
+                flag=1;
+                command = ['ssh -l ' login ' ' cluster.name ' "[ -f ' lockfilename ' ] && [ -f ' logfilename ' ]" 2>/dev/null'];
         end
 end
+%loop till file .lock exist or time is up
+while (ispresent==0 & time<timelimit)
+        if strcmpi(oshostname(),cluster.name),
+                pause(1);
+                ispresent=(exist(lockfilename,'file') & exist(logfilename,'file'));
+                time=etime(clock,time0)/60;
+        else
+                pause(10);
+                time=etime(clock,time0);
+                fprintf('\rchecking for job completion (time: %i min %i sec)      ',floor(time/60),floor(rem(time,60)));
+                time=time/60; %converts time from sec to min
+                ispresent=~system(command);
+                if ispresent, fprintf('\n'); end
+        end
+end
+%build output
+if (time>timelimit),
+        disp('Time limit exceeded. Increase md.settings.waitonlock');
+        disp('The results must be loaded manually with md=loadresultsfromcluster(md).');
+        error(['waitonlock error message: time limit exceeded']);
+end

issm/trunk/src/m/solvers/asmoptions.m

r13975	r15396
10	10
11	11	%default asm options
	12	asm.toolkit='petsc';
12	13	asm.mat_type=getfieldvalue(options,'mat_type','aij');
13	14	asm.ksp_type=getfieldvalue(options,'ksp_type','gmres');

issm/trunk/src/m/solvers/asmoptions.py

r13395	r15396
12	12	arguments=pairoptions(*args)
13	13
14		options=[['mat_type','aij'],['ksp_type','gmres'],['pc_type','asm'],['sub_pc_type','lu'],['pc_asm_overlap',3],['ksp_max_it',100],['ksp_rtol',1e-30]];
	14	options=[['toolkit','petsc'],['mat_type','aij'],['ksp_type','gmres'],['pc_type','asm'],['sub_pc_type','lu'],['pc_asm_overlap',3],['ksp_max_it',100],['ksp_rtol',1e-30]];
15	15
16	16	#now, go through our arguments, and write over default options.

issm/trunk/src/m/solvers/iluasmoptions.m

r13975	r15396
10	10
11	11	%default iluasm options
	12	iluasm.toolkit='petsc';
12	13	iluasm.mat_type=getfieldvalue(options,'mat_type','aij');
13	14	iluasm.ksp_type=getfieldvalue(options,'ksp_type','gmres');

issm/trunk/src/m/solvers/iluasmoptions.py

r13395	r15396
15	15
16	16	#default iluasm options
	17	iluasm['toolkit']='petsc'
17	18	iluasm['mat_type']=options.getfieldvalue('mat_type','aij')
18	19	iluasm['ksp_type']=options.getfieldvalue('ksp_type','gmres')

issm/trunk/src/m/solvers/jacobiasmoptions.m

r13975	r15396
10	10
11	11	%default jacobiasm options
	12	jacobiasm.toolkit='petsc';
12	13	jacobiasm.mat_type=getfieldvalue(options,'mat_type','aij');
13	14	jacobiasm.ksp_type=getfieldvalue(options,'ksp_type','gmres');

issm/trunk/src/m/solvers/jacobiasmoptions.py

r13395	r15396
12	12	arguments=pairoptions(*args)
13	13
14		options=[['mat_type','aij'],['ksp_type','gmres'],['pc_type','asm'],['sub_pc_type','jacobi'],['pc_asm_overlap',3],['ksp_max_it',100],['ksp_rtol',1e-15]];
	14	options=[['toolkit','petsc'],['mat_type','aij'],['ksp_type','gmres'],['pc_type','asm'],['sub_pc_type','jacobi'],['pc_asm_overlap',3],['ksp_max_it',100],['ksp_rtol',1e-15]];
15	15
16	16	#now, go through our arguments, and write over default options.

issm/trunk/src/m/solvers/jacobicgoptions.m

r13975	r15396
10	10
11	11	%default jacobiasm options
	12	jacobicg.toolkit='petsc';
12	13	jacobicg.mat_type=getfieldvalue(options,'mat_type','aij');
13	14	jacobicg.ksp_type=getfieldvalue(options,'ksp_type','cg');

issm/trunk/src/m/solvers/jacobicgoptions.py

r13395	r15396
12	12	arguments=pairoptions(*args)
13	13
14		options=[['mat_type','aij'],['ksp_type','cg'],['ksp_max_it',100],['ksp_rtol',1e-15]];
	14	options=[['toolkit','petsc'],['mat_type','aij'],['ksp_type','cg'],['ksp_max_it',100],['ksp_rtol',1e-15]];
15	15
16	16	#now, go through our arguments, and write over default options.

issm/trunk/src/m/solvers/matlaboptions.m

r13975	r15396
10	10
11	11	%default matlab options
	12	maltab.toolkit='petsc';
12	13	maltab.ksp_type='matlab';

issm/trunk/src/m/solvers/matlaboptions.py

r13395	r15396
12	12	arguments=pairoptions(*args)
13	13
14		options=[['ksp_type','matlab']];
	14	options=[['toolkit','petsc'],['ksp_type','matlab']];
15	15
16	16	#now, go through our arguments, and write over default options.

issm/trunk/src/m/solvers/mumpsoptions.m

-              r13395
+              r15396
 PETSC_VERSION=petscversion();
 if PETSC_VERSION==2,
+        mumps.toolkit='petsc';
         mumps.mat_type=getfieldvalue(options,'mat_type','aijmumps');
         mumps.ksp_type=getfieldvalue(options,'ksp_type','preonly');
 …
 end
 if PETSC_VERSION==3,
+        mumps.toolkit='petsc';
         mumps.mat_type=getfieldvalue(options,'mat_type','mpiaij');
         mumps.ksp_type=getfieldvalue(options,'ksp_type','preonly');

issm/trunk/src/m/solvers/mumpsoptions.py

-              r13395
+              r15396
         PETSC_VERSION=petscversion()
         if PETSC_VERSION==2:
+                mumps['toolkit']='petsc'
                 mumps['mat_type']=options.getfieldvalue('mat_type','aijmumps')
                 mumps['ksp_type']=options.getfieldvalue('ksp_type','preonly')
 …
                 mumps['pc_factor_shift_positive_definite']=options.getfieldvalue('pc_factor_shift_positive_definite','true')
         if PETSC_VERSION==3:
+                mumps['toolkit']='petsc'
                 mumps['mat_type']=options.getfieldvalue('mat_type','mpiaij')
                 mumps['ksp_type']=options.getfieldvalue('ksp_type','preonly')

issm/trunk/src/m/solvers/soroptions.m

r13975	r15396
10	10
11	11	%default sor options
	12	sor.toolkit='petsc';
12	13	sor.mat_type=getfieldvalue(options,'mat_type','aij');
13	14	sor.ksp_type=getfieldvalue(options,'ksp_type','cg');

issm/trunk/src/m/solvers/soroptions.py

r13395	r15396
12	12	arguments=pairoptions(*args)
13	13
14		options=[['mat_type','aij'],['ksp_type','cg'],['pc_type','sor'],['pc_sor_omega',1.1],['pc_sor_its',2]];
	14	options=[['toolkit','petsc'],['mat_type','aij'],['ksp_type','cg'],['pc_type','sor'],['pc_sor_omega',1.1],['pc_sor_its',2]];
15	15
16	16	#now, go through our arguments, and write over default options.

issm/trunk/src/m/solvers/stokesoptions.m

r13395	r15396
15	15	end
16	16	if PETSC_VERSION==3,
	17	stokes.toolkit='petsc';
17	18	stokes.mat_type=getfieldvalue(options,'mat_type','mpiaij');
18	19	stokes.ksp_max_it=getfieldvalue(options,'ksp_max_it',1000);

issm/trunk/src/m/solvers/stokesoptions.py

r13395	r15396
19	19	raise RuntimeError('stokesoptions error message: multi-physics options not supported in Petsc 2')
20	20	if PETSC_VERSION==3:
21		options=[['mat_type','mpiaij'],['ksp_max_it',1000],['ksp_type','gmres'],['pc_type','fieldsplit'],['pc_field_split_type','schur'],\
	21	options=[['toolkit','petsc'],['mat_type','mpiaij'],['ksp_max_it',1000],['ksp_type','gmres'],['pc_type','fieldsplit'],['pc_field_split_type','schur'],\
22	22	['fieldsplit_0_pc_type','hypre'],['fieldsplit_0_ksp_type','gmres'],['fieldsplit_0_pc_hypre_type','boomerang'],\
23	23	['fieldsplit_1_pc_type','jacobi'],['fieldsplit_1_ksp_type','preonly'],['issm_option_solver','stokes']]

issm/trunk/src/wrappers/AverageFilter/AverageFilter.cpp

-              r13236
+              r15396
 void AverageFilterUsage(void){/*{{{*/
         _printLine_("   AverageFilter usage:");
         _printLine_("   [image_out]=AverageFilter(image_in,pixels);\n");
         _printLine_("   where:");
         _printLine_("      image_in in double format");
         _printLine_("      pixels: characteristic size of smoothing");
         _printLine_("      image_out in double format");
         _printLine_("");
+        _printf_("   AverageFilter usage:\n");
+        _printf_("   [image_out]=AverageFilter(image_in,pixels)\n");
+        _printf_("   where:\n");
+        _printf_("      image_in in double format\n");
+        _printf_("      pixels: characteristic size of smoothing\n");
+        _printf_("      image_out in double format\n");
+        _printf_("\n");
 }/*}}}*/
 WRAPPER(AverageFilter){
 …
         int     smooth;
         /* output: */
-        mxArray* pfield=NULL;
         double* imageout=NULL;
         int     imageout_rows,imageout_cols;
 …
         FetchData(&imagein,&imagein_rows,&imagein_cols,IMAGEIN);
         FetchData(&smooth,SMOOTH);
         /*Run core hole filler routine: */
         AverageFilterx( &imageout,imagein,imagein_rows,imagein_cols,smooth);
 …
         WriteData(IMAGEOUT,imageout,imagein_rows,imagein_cols);
+        /*free ressources: */
+        xDelete<double>(imagein);
+        xDelete<double>(imageout);
         /*end module: */
         MODULEEND();

issm/trunk/src/wrappers/AverageFilter/AverageFilter.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/BamgConvertMesh/BamgConvertMesh.cpp

-              r13243
+              r15396
 void BamgConvertMeshUsage(void){/*{{{*/
         _pprintString_("BAMGCONVERTMESH - convert [x y index] to a bamg geom and mesh geom");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      [bamggeom bamgmesh]=BamgConvertMesh(index,x,y);");
         _pprintLine_("      index: index of the mesh");
         _pprintLine_("      x,y: coordinates of the nodes");
         _pprintLine_("");
+        _printf0_("BAMGCONVERTMESH - convert [x y index] to a bamg geom and mesh geom");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      [bamggeom bamgmesh]=BamgConvertMesh(index,x,y)\n");
+        _printf0_("      index: index of the mesh\n");
+        _printf0_("      x,y: coordinates of the nodes\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(BamgConvertMesh){
 …
         /*Clean up*/
+        xDelete<int>(index);
+        xDelete<double>(x);
+        xDelete<double>(y);
         delete bamggeom;
         delete bamgmesh;

issm/trunk/src/wrappers/BamgConvertMesh/BamgConvertMesh.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
+#include "../bindings.h"
+#include "../../c/io/io.h"
+#include "../../c/shared/io/io.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/BamgMesher/BamgMesher.cpp

-              r13287
+              r15396
 void BamgMesherUsage(void){/*{{{*/
         _pprintLine_("");
         _pprintLine_("   usage: [bamgmesh,bamggeom]=" << __FUNCT__ << "(bamgmesh,bamggeom,bamgoptions);");
         _pprintLine_("");
+        _printf0_("\n");
+        _printf0_("   usage: [bamgmesh,bamggeom]=" << __FUNCT__ << "(bamgmesh,bamggeom,bamgoptions)\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(BamgMesher){
         /*Intermediary*/
         BamgOpts *bamgopts=NULL;
         BamgMesh *bamgmesh_in=NULL;
         BamgGeom *bamggeom_in=NULL;
         BamgMesh *bamgmesh_out=NULL;
         BamgGeom *bamggeom_out=NULL;
+        BamgOpts *bamgopts     = NULL;
+        BamgMesh *bamgmesh_in  = NULL;
+        BamgGeom *bamggeom_in  = NULL;
+        BamgMesh *bamgmesh_out = NULL;
+        BamgGeom *bamggeom_out = NULL;
         /*Boot module*/

issm/trunk/src/wrappers/BamgMesher/BamgMesher.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/BamgTriangulate/BamgTriangulate.cpp

-              r13236
+              r15396
 void BamgTriangulateUsage(void){/*{{{*/
         _pprintString_("BAMGTRIANGULATE - Delaunay Triangulation of a list of points");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      index=BamgTriangulate(x,y);");
         _pprintLine_("      index: index of the triangulation");
         _pprintLine_("      x,y: coordinates of the nodes");
         _pprintLine_("");
+        _printf0_("BAMGTRIANGULATE - Delaunay Triangulation of a list of points");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      index=BamgTriangulate(x,y);\n");
+        _printf0_("      index: index of the triangulation\n");
+        _printf0_("      x,y: coordinates of the nodes\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(BamgTriangulate){
 …
         int     x_cols;
         int     y_rows,y_cols;
         int nods;
+        int     nods;
         /*Output*/
 …
         /*Input datasets: */
         if (verbose) _printLine_("Fetching inputs");
+        if (verbose) _printf_("Fetching inputs\n");
         FetchData(&x,&nods,&x_cols,XHANDLE);
         FetchData(&y,&y_rows,&y_cols,YHANDLE);
 …
         /* Run core computations: */
         if (verbose) _printLine_("Call core");
+        if (verbose) _printf_("Call core\n");
         BamgTriangulatex(&index,&nels,x,y,nods);
 …
         WriteData(INDEX,index,nels,3);
+        /*Clean up*/
+        xDelete<int>(index);
+        xDelete<double>(x);
+        xDelete<double>(y);
         /*end module: */
         MODULEEND();

issm/trunk/src/wrappers/BamgTriangulate/BamgTriangulate.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/Chaco/Chaco.cpp

-              r13250
+              r15396
 void ChacoUsage(void){/*{{{*/
         _pprintLine_("");
         _pprintLine_("Usage: [assgn] = Chaco(A,vwgts,ewgts,x,y,z,options,nparts,goal);");
         _pprintLine_("");
+        _printf0_("\n");
+        _printf0_("Usage: [assgn] = Chaco(A,vwgts,ewgts,x,y,z,options,nparts,goal);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(Chaco){
         int i;
         int nterms;
 …
         nparts=xNew<int>(1); nparts[0]=npart; //weird Chacox interface ain't it?
         FetchData(&goal,&nterms,GOAL_IN);
         /*Some debugging print: {{{*/
         #ifdef _DEBUG_
         _printLine_("nvtxs: " << nvtxs);
         _printString_("options: [");
         for(i=0;i<10;i++)_printString_(options[i] << "|");
         _printLine_("]");
         _printLine_("start: ");
         for (i=0; i<nvtxs+1;i++)_printString_(start[i] << " ");
         _printLine_("");
         _printLine_("adjacency: ");
         for (i=0; i<mxGetNzmax(A_IN);i++)_printString_("" <<adjacency[i]<< " ");i++)
         _printLine_("");
         _printLine_("nedges: " << nedges << " " << ewgts);
         if(ewgts) for (i = 0; i < nedges; i++)_printString_(ewgts[i] << " ");
         _printLine_("");
         _printLine_("vwgts:");
         for (i = 0; i < nvtxs; i++)_printString_(vwgts[i] << " ");
         _printLine_("");
         _printLine_("nparts: " << nparts[0]);
         _printLine_("goal: " << goal);
+        _printf_("nvtxs: " << nvtxs << "\n");
+        _printf_("options: [");
+        for(i=0;i<10;i++)_printf_(options[i] << "|");
+        _printf_("]\n");
+        _printf_("start: \n");
+        for (i=0; i<nvtxs+1;i++)_printf_(start[i] << " ");
+        _printf_("\n");
+        _printf_("adjacency: \n");
+        for (i=0; i<mxGetNzmax(A_IN);i++)_printf_("" <<adjacency[i]<< " ");i++)
+        _printf_("\n");
+        _printf_("nedges: " << nedges << " " << ewgts << "\n");
+        if(ewgts) for (i = 0; i < nedges; i++)_printf_(ewgts[i] << " ");
+        _printf_("\n");
+        _printf_("vwgts:\n");
+        for (i = 0; i < nvtxs; i++)_printf_(vwgts[i] << " ");
+        _printf_("\n");
+        _printf_("nparts: " << nparts[0] << "\n");
+        _printf_("goal: " << goal << "\n");
         #endif
         /*}}}*/
         /*Allocate output: */
         assignment = xNewZeroInit<short>(nvtxs);
     /*Call core: */
         Chacox(nvtxs, start, adjacency, vwgts, ewgts, x, y, z, assignment, options, nparts, goal);

issm/trunk/src/wrappers/Chaco/Chaco.h

-              r13749
+              r15396
 /*headers*/
+#include "../bindings.h" /*Should always come first to avoid python's warnings*/
 #include <stdio.h>
 #include <string.h>    /*  strcasecmp  */
 #include <time.h>      /*  clock,time,difftime  */
 #include "../../c/include/globals.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/ContourToMesh/ContourToMesh.cpp

-              r13447
+              r15396
     are inside this contour.
 */
 #include "./ContourToMesh.h"
 void ContourToMeshUsage(void){/*{{{*/
         _printLine_("CONTOURTOMESH - Flag the elements or nodes inside a contour");
         _printLine_("");
         _printLine_("      Usage: ");
         _printLine_("         [in_nod,in_elem]=ContourToMesh(index,x,y,contourname,interptype,edgevalue)\n");
         _printLine_("");
         _printLine_("         index,x,y: mesh triangulation.");
         _printLine_("         contourname: name of .exp file containing the contours.");
         _printLine_("         interptype: string definining type of interpolation ('element', or 'node').");
         _printLine_("         edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons.");
         _printLine_("         in_nod: vector of flags (0 or 1), of size nods if interptype is set to 'node' or 'element and node', ");
         _printLine_("            or of size 0 otherwise.");
         _printLine_("         in_elem: vector of flags (0 or 1), of size nel if interptype is set to 'element' or 'element and node', ");
         _printLine_("            or of size 0 otherwise.");
         _printLine_("");
         _printLine_("      Example: ");
         _printLine_("         in_nod=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','node',1)");
         _printLine_("         in_elements=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','element',0)");
         _printLine_("         [in_nodes,in_elements]=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','element and node',0)");
         _printLine_("");
+        _printf_("CONTOURTOMESH - Flag the elements or nodes inside a contour\n");
+        _printf_("\n");
+        _printf_("      Usage: \n");
+        _printf_("         [in_nod,in_elem]=ContourToMesh(index,x,y,contourname,interptype,edgevalue)\n");
+        _printf_("\n");
+        _printf_("         index,x,y: mesh triangulation.\n");
+        _printf_("         contourname: name of .exp file containing the contours.\n");
+        _printf_("         interptype: string definining type of interpolation ('element', or 'node').\n");
+        _printf_("         edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons.\n");
+        _printf_("         in_nod: vector of flags (0 or 1), of size nods if interptype is set to 'node' or 'element and node', \n");
+        _printf_("            or of size 0 otherwise.\n");
+        _printf_("         in_elem: vector of flags (0 or 1), of size nel if interptype is set to 'element' or 'element and node', \n");
+        _printf_("            or of size 0 otherwise.\n");
+        _printf_("\n");
+        _printf_("      Example: \n");
+        _printf_("         in_nod=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','node',1)\n");
+        _printf_("         in_elements=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','element',0)\n");
+        _printf_("         [in_nodes,in_elements]=ContourToMesh(md.elements,md.x,md.y,'Contour.exp','element and node',0)\n");
+        _printf_("\n");
 }/*}}}*/
 WRAPPER(ContourToMesh){
         /* required input: */
+        int      edgevalue;
+        double  *index       = NULL;
+        int      nel;
+        double  *x           = NULL;
+        int      nods;
+        double  *y           = NULL;
+        char    *interptype  = NULL;
+        DataSet *contours    = NULL;
+        int       edgevalue;
+        int       nel,nods;
+        double   *index       = NULL;
+        double   *x           = NULL;
+        double   *y           = NULL;
+        char     *interptype  = NULL;
+        Contours *contours    = NULL;
         /* output: */
         SeqVec<double> *in_nod  = NULL;
         SeqVec<double> *in_elem = NULL;
+        double *in_nod  = NULL;
+        double *in_elem = NULL;
         /*Boot module: */
 …
         /* output: */
         if (strcmp(interptype,"node")==0){
                 WriteData(PLHS0,in_nod);
+                WriteData(PLHS0,in_nod,nods);
                 WriteData(PLHS1);
+        }
         else if (strcmp(interptype,"element")==0){
                 WriteData(PLHS0,in_elem);
+                WriteData(PLHS0,in_elem,nel);
                 WriteData(PLHS1);
+        }
         else if (strcmp(interptype,"element and node")==0){
                 WriteData(PLHS0,in_nod);
                 WriteData(PLHS1,in_elem);
+                WriteData(PLHS0,in_nod,nods);
+                WriteData(PLHS1,in_elem,nel);
+        }
         else _error_("wrong interpolation type");
+        /*Clean up*/
+        xDelete<double>(index);
+        xDelete<double>(x);
+        xDelete<double>(y);
+        xDelete<char>(interptype);
+        delete contours;
+        delete in_nod;
+        delete in_elem;
         /*end module: */
         MODULEEND();

issm/trunk/src/wrappers/ContourToMesh/ContourToMesh.h

-              r13749
+              r15396
 /*Header files: */
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/toolkits/toolkits.h"
-#include "../../c/include/include.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
+#include "../bindings.h"
+#include "../../c/io/io.h"
+#include "../../c/EnumDefinitions/EnumDefinitions.h"
+#include "../../c/shared/io/io.h"
+#include "../../c/shared/Enum/Enum.h"
 #undef __FUNCT__
 …
 #endif  /* _CONTOURTOMESH_H */

issm/trunk/src/wrappers/ContourToNodes/ContourToNodes.cpp

-              r13353
+              r15396
     \brief: takes a  contour file, and figures out which nodes  (x,y list)
 */
 #include "./ContourToNodes.h"
 void ContourToNodesUsage(void){/*{{{*/
         _printLine_("   usage:");
         _printLine_("   [flags]=ContourToNodes(x,y,contourname,edgevalue);\n");
         _printLine_("   where:");
         _printLine_("      x,y: list of nodes.");
         _printLine_("      contourname: name of .exp file containing the contours, or resulting structure from call to expread.");
         _printLine_("      edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons.");
         _printLine_("      flags: vector of flags (0 or 1), of size nods.");
         _printLine_("");
+        _printf_("   usage:\n");
+        _printf_("   [flags]=ContourToNodes(x,y,contourname,edgevalue);\n");
+        _printf_("   where:\n");
+        _printf_("      x,y: list of nodes.\n");
+        _printf_("      contourname: name of .exp file containing the contours, or resulting structure from call to expread.\n");
+        _printf_("      edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons.\n");
+        _printf_("      flags: vector of flags (0 or 1), of size nods.\n");
+        _printf_("\n");
 }/*}}}*/
 WRAPPER(ContourToNodes){
         /* input: */
         int      edgevalue,nods;
         double  *x           = NULL;
         double  *y           = NULL;
         char    *contourname = NULL;
         DataSet *contours    = NULL;
+        int       edgevalue,nods;
+        double   *x           = NULL;
+        double   *y           = NULL;
+        char     *contourname = NULL;
+        Contours *contours    = NULL;
         /* output: */
         SeqVec<double> *flags = NULL;
+        double *flags = NULL;
         /*Boot module: */
 …
         /*checks on arguments on the matlab side: */
         CHECKARGUMENTS(NLHS,NRHS,&ContourToNodesUsage);
         /*Fetch inputs: */
         FetchData(&x,&nods,NULL,XHANDLE);
 …
         /* output: */
+        WriteData(FLAGS,flags);
+        WriteData(FLAGS,flags,nods);
+        /*Clean up*/
+        xDelete<double>(x);
+        xDelete<double>(y);
+        xDelete<char>(contourname);
+        delete contours;
         /*end module: */

issm/trunk/src/wrappers/ContourToNodes/ContourToNodes.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__
 …
 #endif  /* _CONTOURTONODES_H */

issm/trunk/src/wrappers/ElementConnectivity/ElementConnectivity.cpp

-              r14067
+              r15396
 void ElementConnectivityUsage(void) {/*{{{*/
         _pprintLine_("");
         _pprintLine_("   usage: elementconnectivity = " << __FUNCT__ << "(elements, nodeconnectivity);");
         _pprintLine_("");
+        _printf0_("\n");
+        _printf0_("   usage: elementconnectivity = " << __FUNCT__ << "(elements, nodeconnectivity);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(ElementConnectivity){
 …
         /*checks on arguments: */
         CHECKARGUMENTS(NLHS,NRHS,&ElementConnectivityUsage);
         /*Input datasets: */
         FetchData(&elements,&nels,NULL,ELEMENTS);
 …
         WriteData(ELEMENTCONNECTIVITY,elementconnectivity,nels,3);
+        /*Clean up*/
+        xDelete<int>(nodeconnectivity);
+        xDelete<int>(elementconnectivity);
         /*end module: */
         MODULEEND();

issm/trunk/src/wrappers/ElementConnectivity/ElementConnectivity.h

-              r13749
+              r15396
 /*Header files: */
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/toolkits/toolkits.h"
-#include "../../c/include/include.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
+#include "../bindings.h"
+#include "../../c/io/io.h"
+#include "../../c/EnumDefinitions/EnumDefinitions.h"
+#include "../../c/shared/io/io.h"
+#include "../../c/shared/Enum/Enum.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/EnumToString/EnumToString.cpp

-              r13236
+              r15396
 void EnumToStringUsage(void){/*{{{*/
         _pprintLine_("");
         _pprintLine_("   usage: " << __FUNCT__ << "string = EnumToString(enum);");
         _pprintLine_("");
+        _printf0_("\n");
+        _printf0_("   usage: " << __FUNCT__ << "string = EnumToString(enum);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(EnumToString){
 …
         WriteData(NAME,name);
+        /*Clean up*/
+        xDelete<char>(name);
         /*end module: */
         MODULEEND();

issm/trunk/src/wrappers/EnumToString/EnumToString.h

-              r13749
+              r15396
 /*Header files: */
 #include "../../c/include/globals.h"
 #include "../../c/modules/modules.h"
 #include "../../c/Container/Container.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
+#include "../../c/shared/Enum/Enum.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__
 #define __FUNCT__  "EnumToString"
 #ifdef _HAVE_MATLAB_MODULES_
 /* serial input macros: */

issm/trunk/src/wrappers/Exp2Kml/Exp2Kml.cpp

-              r13250
+              r15396
 void Exp2KmlUsage(void){/*{{{*/
         _pprintLine_("Exp2Kml - exp to kml file conversion module:");
         _pprintLine_("");
         _pprintLine_("   This module converts a file from exp to kml format.");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      [ret]=Exp2Kml(filexp,filkml,sgn,'param name',param,...);");
         _pprintLine_("");
         _pprintLine_("      filexp      file name of exp file to be read (char)");
         _pprintLine_("      filkml      file name of kml file to be written (char)");
         _pprintLine_("      sgn         sign for hemisphere (double, +1 (north) or -1 (south))");
         _pprintLine_("");
         _pprintLine_("      central_meridian     central meridian (double, optional, but must specify with sp)");
         _pprintLine_("      standard_parallel    standard parallel (double, optional, but must specify with cm)");
         _pprintLine_("      holes       flag for treatment of multiple profiles (char, optional, 'yes' for holes))");
         _pprintLine_("");
         _pprintLine_("      ret         return code (non-zero for warning)");
         _pprintLine_("");
         _pprintLine_("   Examples:");
         _pprintLine_("      [ret]=Exp2Kml('file.exp','file.kml', 1);");
         _pprintLine_("      [ret]=Exp2Kml('file.exp','file.kml', 1,'central_meridian',45,'standard_parallel',70,'holes','yes');");
         _pprintLine_("      [ret]=Exp2Kml('file.exp','file.kml',-1,'central_meridian', 0,'standard_parallel',71,'holes','yes');");
         _pprintLine_("");
+        _printf0_("Exp2Kml - exp to kml file conversion module:\n");
+        _printf0_("\n");
+        _printf0_("   This module converts a file from exp to kml format.\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      [ret]=Exp2Kml(filexp,filkml,sgn,'param name',param,...);\n");
+        _printf0_("\n");
+        _printf0_("      filexp      file name of exp file to be read (char)\n");
+        _printf0_("      filkml      file name of kml file to be written (char)\n");
+        _printf0_("      sgn         sign for hemisphere (double, +1 (north) or -1 (south))\n");
+        _printf0_("\n");
+        _printf0_("      central_meridian     central meridian (double, optional, but must specify with sp)\n");
+        _printf0_("      standard_parallel    standard parallel (double, optional, but must specify with cm)\n");
+        _printf0_("      holes       flag for treatment of multiple profiles (char, optional, 'yes' for holes))\n");
+        _printf0_("\n");
+        _printf0_("      ret         return code (non-zero for warning)\n");
+        _printf0_("\n");
+        _printf0_("   Examples:\n");
+        _printf0_("      [ret]=Exp2Kml('file.exp','file.kml', 1);\n");
+        _printf0_("      [ret]=Exp2Kml('file.exp','file.kml', 1,'central_meridian',45,'standard_parallel',70,'holes','yes');\n");
+        _printf0_("      [ret]=Exp2Kml('file.exp','file.kml',-1,'central_meridian', 0,'standard_parallel',71,'holes','yes');\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(Exp2Kml){
 …
         if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) {
                 options->Get(&cm,"central_meridian");
                 if (verbose) _printLine_("  cm=" << cm);
+                if (verbose) _printf_("  cm=" << cm << "\n");
                 options->Get(&sp,"standard_parallel");
                 if (verbose) _printLine_("  sp=" << sp);
+                if (verbose) _printf_("  sp=" << sp << "\n");
+        }

issm/trunk/src/wrappers/Exp2Kml/Exp2Kml.h

-              r14310
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/ExpSimplify/ExpSimplify.cpp

-              r14294
+              r15396
 void ExpSimplifyUsage(void){/*{{{*/
+        _pprintLine_("ExpSimplify - Simplify Exp contour");
+        _pprintLine_("");
+        _pprintLine_("   Recursive Douglas-Peucker Polygon Simplification");
+        _pprintLine_("");
+        _pprintLine_("   Usage:");
+        _pprintLine_("      ExpSimplify(expfile,tol);");
+        _pprintLine_("      - expfile: name of the exp file");
+        _pprintLine_("      - tol:  tolerance (maximal euclidean distance allowed between the new line and a vertex)");
+        _pprintLine_("");
+        _pprintLine_("   Example:");
+        _pprintLine_("      ExpSimplify('file.exp',100);");
+        _printf_("ExpSimplify - Simplify Exp contour\n");
+        _printf_("\n");
+        _printf_("   Recursive Douglas-Peucker Polygon Simplification\n");
+        _printf_("\n");
+        _printf_("   Usage:\n");
+        _printf_("      ExpSimplify(expfile,tol);\n");
+        _printf_("      - expfile: name of the exp file\n");
+        _printf_("      - tol:  tolerance (maximal euclidean distance allowed between the new line and a vertex)\n");
+        _printf_("      Additional options:\n");
+        _printf_("      - 'min': minimum number of vertices to save contours in exp file (default is 3)\n");
+        _printf_("\n");
+        _printf_("   Example:\n");
+        _printf_("      ExpSimplify('file.exp',100);\n");
+        _printf_("      ExpSimplify('file.exp',100,'remove1',false);\n");
 }/*}}}*/
 void simplify(Contour<double>* contour,bool* flags,int ind0,int ind1,double tolerance){/*{{{*/
 …
         double  distance,beta,dx,dy;
         double  maxdistance;
         int     index;
+        int     index  = -1;
         double *x      = contour->x;
         double *y      = contour->y;
 …
                 /*calculate the shortest distance of all vertices between ind0 and ind1*/
                 for(int i=ind0;i<ind1;i++){
                         distance = sqrt((x[i]-x[i+1])*(x[i]-x[i+1]) + (y[i]-y[i+1])*(y[i]-y[i+1]));
+                for(int i=ind0;i<ind1-1;i++){
+                        distance = sqrt((x[ind0]-x[i+1])*(x[ind0]-x[i+1]) + (y[ind0]-y[i+1])*(y[ind0]-y[i+1]));
                         if(i==ind0 || distance>maxdistance){
                                 maxdistance=distance;
                                 index = i;
+                                index = i + 1;
+                        }
+                }
 …
+                 *
                  * So: beta = <x-x0,xend-x0>/<xend-x0,xend-x0>  */
                 for(int i=ind0+1;i<ind1;i++){
+                for(int i=ind0+1;i<=ind1;i++){
                         beta = ((x[i]-x[ind0])*(x[ind1]-x[ind0]) + (y[i]-y[ind0])*(y[ind1]-y[ind0]))/((x[ind1]-x[ind0])*(x[ind1]-x[ind0])+(y[ind1]-y[ind0])*(y[ind1]-y[ind0]));
                         dx   = x[i]-beta*x[ind1]+(beta-1.)*x[ind0];
 …
                 /*if not, call simplifyrec for the segments between ind0 and index
                  * (index and ind1)*/
+                _assert_(index!=-1);
+                _assert_(index!=ind1);
+                _assert_(index!=ind0);
                 simplify(contour,flags,ind0 ,index,tolerance);
                 simplify(contour,flags,index,ind1, tolerance);
+        }
 }/*}}}*/
 …
         char*    expfile  = NULL;
         double   tolerance;
+        Options *options      = NULL;
+        double   minimumvertices_double;
+        int      minimumvertices;
         /*output*/
         DataSet* oldcontours = NULL;
         DataSet* newcontours = NULL;
+        Contours* oldcontours = NULL;
+        Contours* newcontours = NULL;
         /*Boot module: */
 …
         /*checks on arguments: */
+        CHECKARGUMENTS(NLHS,NRHS,&ExpSimplifyUsage);
+        /*checks on arguments on the matlab side: */
+        if (nrhs<NRHS || nlhs>NLHS){
+                ExpSimplifyUsage(); _error_("ExpSimplify usage error");
+        }
         /*Input datasets: */
         FetchData(&expfile,  EXPFILE);
         FetchData(&tolerance,TOLERANCE);
+        FetchData(&options,NRHS,nrhs,prhs);
         /*some checks*/
 …
         double distance;
+        /*Process options*/
+        options->Get(&minimumvertices_double,"min",3.);
+        if(minimumvertices_double<1.) _error_("'min' (minimum number of verties) should be a positive integer");
+        minimumvertices = int(minimumvertices_double);
         /*Read old contours and allocate new contours*/
         oldcontours=DomainOutlineRead<double>(expfile);
         newcontours=new DataSet(0);
+        oldcontours=ExpRead<double>(expfile);
+        newcontours=new Contours();
         for(int counter=0;counter<oldcontours->Size();counter++){
 …
                 x       = contour->x;
                 y       = contour->y;
                 printf("   Initial number of vertices in contour #%i: %i\n",counter+1,nods);
+                _printf_("   Initial number of vertices in contour #"<<counter+1<<": "<<nods << "\n");
                 /*Allocate flags (1=keep, 0=remove)*/
 …
                 newnods = 0;
                 for(int i=0;i<nods;i++) if(flags[i]) newnods++;
+                printf("   New     number of vertices in contour #%i: %i\n",counter+1,newnods);
+                if(newnods){
+                        newcontour       = xNew<Contour<double> >(1);
+                /*Do we save new profile?*/
+                if(newnods>=minimumvertices){
+                        _printf_("   Final   number of vertices in contour #"<<counter+1<<": "<<newnods << "\n");
+                        newcontour       = new Contour<double>();
                         newcontour->nods = newnods;
                         newcontour->x    = xNew<double>(newnods);
 …
                         newcontours->AddObject(newcontour);
+                }
+                else{
+                        _printf_("   Final   number of vertices in contour #"<<counter+1<<": "<<newnods<<" (not saved)\n");
+                }
                 /*cleanup*/
                 xDelete<bool>(flags);
+        }
+        _printf_("   Initial number of contours: "<<oldcontours->Size() << "\n");
+        _printf_("   Final   number of contours: "<<newcontours->Size() << "\n");
         /*Write data: */
 …
         /*Clean-up*/
         xDelete<char>(expfile);
+        delete options;
         /*end module: */

issm/trunk/src/wrappers/ExpSimplify/ExpSimplify.h

-              r14294
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/HoleFiller/HoleFiller.cpp

-              r13236
+              r15396
 void HoleFillerUsage(void){/*{{{*/
         _printLine_("   HoleFiller usage:");
         _printLine_("   [image_out]=HoleFiller(image_in,smooth);\n");
         _printLine_("   where:");
         _printLine_("      image_in in double format");
         _printLine_("      smooth: 1 to smooth with a box filer, 0 to leave data raw");
         _printLine_("      image_out in double format");
         _printLine_("");
+        _printf_("   HoleFiller usage:\n");
+        _printf_("   [image_out]=HoleFiller(image_in,smooth);\n");
+        _printf_("   where:\n");
+        _printf_("      image_in in double format\n");
+        _printf_("      smooth: 1 to smooth with a box filer, 0 to leave data raw\n");
+        _printf_("      image_out in double format\n");
+        _printf_("\n");
 }/*}}}*/
 WRAPPER(HoleFiller){
-        int i,j;
         /* required input: */
 …
         int     smooth;
         /* output: */
-        mxArray* pfield=NULL;
         double* imageout=NULL;
         int     imageout_rows,imageout_cols;
 …
         FetchData(&imagein,&imagein_rows,&imagein_cols,IMAGEIN);
         FetchData(&smooth_flag,SMOOTH);
         /*Get smooth flag setup: */
         if (smooth_flag==0)
 …
         WriteData(IMAGEOUT,imageout,imagein_rows,imagein_cols);
+        /*Clean up*/
+        xDelete<double>(imagein);
+        xDelete<double>(imageout);
+        xDelete<double>(imagein);
         /*end module: */
         MODULEEND();

issm/trunk/src/wrappers/HoleFiller/HoleFiller.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/InternalFront/InternalFront.cpp

-              r14310
+              r15396
 void InternalFrontUsage(void) {/*{{{*/
         _pprintLine_("");
         _pprintLine_("   usage: icefront = " << __FUNCT__ << "(md);");
         _pprintLine_("");
+        _printf0_("\n");
+        _printf0_("   usage: icefront = " << __FUNCT__ << "(md);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(InternalFront){

issm/trunk/src/wrappers/InternalFront/InternalFront.h

-              r14310
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/shared/shared.h"
+#include "../bindings.h"
+#include "../../c/io/io.h"
+#include "../../c/shared/io/io.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/InterpFromGridToMesh/InterpFromGridToMesh.cpp

-              r13923
+              r15396
  * \brief: data interpolation from a list of (x,y,values) into mesh vertices
 */
 #include "./InterpFromGridToMesh.h"
 void InterpFromGridToMeshUsage(void){/*{{{*/
         _pprintLine_("INTERPFROMGRIDTOMESH - interpolation from a grid onto a list of points");
         _pprintLine_("");
         _pprintLine_("   This function is a multi-threaded mex file that interpolates a field");
         _pprintLine_("   defined on a grid onto a list of points");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      data_mesh=InterpFromGridToMesh(x,y,data,x_mesh,y_mesh,default_value);");
         _pprintLine_("");
         _pprintLine_("      data: matrix holding the data to be interpolated onto the mesh.");
         _pprintLine_("      x,y: coordinates of matrix data. (x and y must be in increasing order)");
         _pprintLine_("      x_mesh,y_mesh: coordinates of the points onto which we interpolate.");
         _pprintLine_("      default_value: default value if no data is found (holes).");
         _pprintLine_("      data_mesh: vector of mesh interpolated data.");
         _pprintLine_("");
         _pprintLine_("   Example:");
         _pprintLine_("      load('velocities.mat');");
         _pprintLine_("      md.inversion.vx_obs=InterpFromGridToMesh(x_n,y_m,vx,md.mesh.x,md.mesh.y,0);");
         _pprintLine_("");
+        _printf0_("INTERPFROMGRIDTOMESH - interpolation from a grid onto a list of points\n");
+        _printf0_("\n");
+        _printf0_("   This function is a multi-threaded mex file that interpolates a field\n");
+        _printf0_("   defined on a grid onto a list of points\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      data_mesh=InterpFromGridToMesh(x,y,data,x_mesh,y_mesh,default_value);\n");
+        _printf0_("\n");
+        _printf0_("      data: matrix holding the data to be interpolated onto the mesh.\n");
+        _printf0_("      x,y: coordinates of matrix data. (x and y must be in increasing order)\n");
+        _printf0_("      x_mesh,y_mesh: coordinates of the points onto which we interpolate.\n");
+        _printf0_("      default_value: default value if no data is found (holes).\n");
+        _printf0_("      data_mesh: vector of mesh interpolated data.\n");
+        _printf0_("\n");
+        _printf0_("   Example:\n");
+        _printf0_("      load('velocities.mat');\n");
+        _printf0_("      md.inversion.vx_obs=InterpFromGridToMesh(x_n,y_m,vx,md.mesh.x,md.mesh.y,0);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(InterpFromGridToMesh){
 …
         /* output: */
         SeqVec<double>*  data_mesh=NULL;
+        IssmSeqVec<double>*  data_mesh=NULL;
         /*Boot module: */

issm/trunk/src/wrappers/InterpFromGridToMesh/InterpFromGridToMesh.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/InterpFromMesh2d/InterpFromMesh2d.cpp

-              r13236
+              r15396
  * \brief: data interpolation from a list of (x,y,values) into mesh vertices
 */
 #include "./InterpFromMesh2d.h"
 void InterpFromMesh2dUsage(void){/*{{{*/
         _pprintLine_("   usage:");
         _pprintLine_("         data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime);\n");
         _pprintLine_("      or data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime,default_value);\n");
         _pprintLine_("      or data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime,default_value,contourname);\n");
         _pprintLine_("   where:");
         _pprintLine_("      x,y: coordinates of the nodes where data is defined");
         _pprintLine_("      index: index of the mesh where data is defined");
         _pprintLine_("      data - vector holding the data to be interpolated onto the points.");
         _pprintLine_("      x_prime,y_prime: coordinates of the mesh vertices onto which we interpolate.");
         _pprintLine_("      default_value: a scalar or vector of size length(x_prime).");
         _pprintLine_("      contourname: linear interpolation will happen on all x_interp,y_interp inside the contour, default value will be adopted on the rest of the mesh.");
         _pprintLine_("      data_prime:  vector of prime interpolated data.");
         _pprintLine_("");
+        _printf0_("   usage:\n");
+        _printf0_("         data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime);\n");
+        _printf0_("      or data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime,default_value);\n");
+        _printf0_("      or data_prime=InterpFromMesh2d(index,x,y,data,x_prime,y_prime,default_value,contourname);\n");
+        _printf0_("   where:\n");
+        _printf0_("      x,y: coordinates of the nodes where data is defined\n");
+        _printf0_("      index: index of the mesh where data is defined\n");
+        _printf0_("      data - vector holding the data to be interpolated onto the points.\n");
+        _printf0_("      x_prime,y_prime: coordinates of the mesh vertices onto which we interpolate.\n");
+        _printf0_("      default_value: a scalar or vector of size length(x_prime).\n");
+        _printf0_("      contourname: linear interpolation will happen on all x_interp,y_interp inside the contour, default value will be adopted on the rest of the mesh.\n");
+        _printf0_("      data_prime:  vector of prime interpolated data.\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(InterpFromMesh2d){
 …
         double* x_data=NULL;
         int     x_data_rows;
         double* y_data=NULL;
         int     y_data_rows;
 …
         double* x_prime=NULL;
         double* y_prime=NULL;
         int     x_prime_rows;
         int     y_prime_rows;
         double* default_values=NULL;
 …
         /* output: */
         SeqVec<double> *data_prime = NULL;
+        IssmSeqVec<double> *data_prime = NULL;
         /*Boot module: */
 …
         if(nrhs>=8){
                 /*Call expread on filename to build a contour array in the matlab workspace: */
                 mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread");
 …
                 for(i=0;i<numcontours;i++){
                         //allocate
                         contouri=xNew<Contour<double> >(1);
+                        contouri=new Contour<double>();
                         //retrieve dimension of this contour.
                         contouri->nods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods"));
 …
                 /* Debugging of contours :{{{1*/
                 /*for(i=0;i<numcontours;i++){
                   _printLine_("\nContour echo: contour number  " << i+1 << " / " << numcontours);
+                  _printf_("\nContour echo: contour number  " << i+1 << " / " << numcontours << "\n");
                   contouri=*(contours+i);
                   _printLine_("   Number of vertices " << contouri->nods);
+                  _printf_("   Number of vertices " << contouri->nods << "\n");
                   for (j=0;j<contouri->nods;j++){
                   _printLine_("   " << *(contouri->x+j) << "f " << *(contouri->y+j) << "f");
+                  _printf_("   " << *(contouri->x+j) << "f " << *(contouri->y+j) << "f\n");
+                  }
                   }*/
 …
+        }
         /*some checks*/
         if (x_data_rows!=y_data_rows){
 …
                 _error_("vectors x_prime and y_prime should have the same length!");
+        }
         /*get number of elements and number of nodes in the data*/
         nels_data=index_data_rows;

issm/trunk/src/wrappers/InterpFromMesh2d/InterpFromMesh2d.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/InterpFromMeshToGrid/InterpFromMeshToGrid.cpp

-              r13236
+              r15396
 void InterpFromMeshToGridUsage(void){/*{{{*/
         _pprintLine_("INTERPFROMMESHTOGRID - interpolation of a data defined on a mesh onto a grid");
         _pprintLine_("");
         _pprintLine_("   This function is a multi-threaded mex file that interpolates a field");
         _pprintLine_("   defined on a triangular mesh onto a regular grid");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      [x_m,y_m,griddata]=InterpFromMeshToGrid(index,x,y,data,xmin,ymax,xposting,yposting,nlines,ncols,default_value)");
         _pprintLine_("");
         _pprintLine_("      index,x,y: delaunay triangulation defining the mesh.");
         _pprintLine_("      meshdata: vertex values of data to be interpolated.");
         _pprintLine_("      xmin,ymax,posting,nlines,ncols: parameters that define the grid");
         _pprintLine_("      default_value: value of points located out of the mesh.");
         _pprintLine_("");
+        _printf0_("INTERPFROMMESHTOGRID - interpolation of a data defined on a mesh onto a grid\n");
+        _printf0_("\n");
+        _printf0_("   This function is a multi-threaded mex file that interpolates a field\n");
+        _printf0_("   defined on a triangular mesh onto a regular grid\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      [x_m,y_m,griddata]=InterpFromMeshToGrid(index,x,y,data,xmin,ymax,xposting,yposting,nlines,ncols,default_value)\n");
+        _printf0_("\n");
+        _printf0_("      index,x,y: delaunay triangulation defining the mesh.\n");
+        _printf0_("      meshdata: vertex values of data to be interpolated.\n");
+        _printf0_("      xmin,ymax,posting,nlines,ncols: parameters that define the grid\n");
+        _printf0_("      default_value: value of points located out of the mesh.\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(InterpFromMeshToGrid){
 …
         double* x_m=NULL;
         double* y_m=NULL;
         /*Boot module: */
 …
         /*Free ressources: */
         //let matlab do this.
         /*end module: */
         MODULEEND();

issm/trunk/src/wrappers/InterpFromMeshToGrid/InterpFromMeshToGrid.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp

-              r13236
+              r15396
 void InterpFromMeshToMesh2dUsage(void){/*{{{*/
         _pprintLine_("INTERFROMMESHTOMESH2D - interpolation from a 2d triangular mesh onto a list of point");
         _pprintLine_("");
         _pprintLine_("   This function is a multi-threaded mex file that interpolates a field");
         _pprintLine_("   defined on a Delaunay triangulation onto a list of point");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("         data_interp=InterpFromMeshToMesh2d(index,x,y,data,x_interp,y_interp);");
         _pprintLine_("      or data_interp=InterpFromMeshToMesh2d(index,x,y,data,x_interp,y_interp,OPTIONS);");
         _pprintLine_("");
         _pprintLine_("      index             : index of the mesh where data is defined");
         _pprintLine_("      x,y               : coordinates of the nodes where data is defined");
         _pprintLine_("      data              : matrix holding the data to be interpolated onto the mesh. (one column per field)");
         _pprintLine_("      x_interp,y_interp : coordinates of the points onto which we interpolate.");
         _pprintLine_("      data_interp       : vector of mesh interpolated data.");
         _pprintLine_("      Available options :");
         _pprintLine_("         - 'default' : default value if point is outsite of triangulation (instead of linear interolation)");
         _pprintLine_("");
         _pprintLine_("   Example:");
         _pprintLine_("      load('temperature.mat');");
         _pprintLine_("      md.initialization.temperature=InterpFromMeshToMesh2d(index,x,y,temperature,md.mesh.x,md.mesh.y);");
         _pprintLine_("      md.initialization.temperature=InterpFromMeshToMesh2d(index,x,y,temperature,md.mesh.x,md.mesh.y,'default',253);");
         _pprintLine_("");
+        _printf0_("INTERFROMMESHTOMESH2D - interpolation from a 2d triangular mesh onto a list of point\n");
+        _printf0_("\n");
+        _printf0_("   This function is a multi-threaded mex file that interpolates a field\n");
+        _printf0_("   defined on a Delaunay triangulation onto a list of point\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("         data_interp=InterpFromMeshToMesh2d(index,x,y,data,x_interp,y_interp);\n");
+        _printf0_("      or data_interp=InterpFromMeshToMesh2d(index,x,y,data,x_interp,y_interp,OPTIONS);\n");
+        _printf0_("\n");
+        _printf0_("      index             : index of the mesh where data is defined\n");
+        _printf0_("      x,y               : coordinates of the nodes where data is defined\n");
+        _printf0_("      data              : matrix holding the data to be interpolated onto the mesh. (one column per field)\n");
+        _printf0_("      x_interp,y_interp : coordinates of the points onto which we interpolate.\n");
+        _printf0_("      data_interp       : vector of mesh interpolated data.\n");
+        _printf0_("      Available options :\n");
+        _printf0_("         - 'default' : default value if point is outsite of triangulation (instead of linear interolation)\n");
+        _printf0_("\n");
+        _printf0_("   Example:\n");
+        _printf0_("      load('temperature.mat');\n");
+        _printf0_("      md.initialization.temperature=InterpFromMeshToMesh2d(index,x,y,temperature,md.mesh.x,md.mesh.y);\n");
+        _printf0_("      md.initialization.temperature=InterpFromMeshToMesh2d(index,x,y,temperature,md.mesh.x,md.mesh.y,'default',253);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(InterpFromMeshToMesh2d){

issm/trunk/src/wrappers/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h

-              r13749
+              r15396
 /*Header files: */
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/toolkits/toolkits.h"
-#include "../../c/include/include.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
+#include "../bindings.h"
+#include "../../c/io/io.h"
+#include "../../c/EnumDefinitions/EnumDefinitions.h"
+#include "../../c/shared/io/io.h"
+#include "../../c/shared/Enum/Enum.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp

-              r13236
+              r15396
  * \brief: data interpolation from a list of (x,y,values) into mesh vertices
 */
 #include "./InterpFromMeshToMesh3d.h"
 void InterpFromMeshToMesh3dUsage(void){/*{{{*/
         _pprintLine_("INTERPFROMMESHTOMESH3D - interpolation from a 3d hexahedron mesh onto a list of point");
         _pprintLine_("");
         _pprintLine_("   This function is a multi-threaded mex file that interpolates a field");
         _pprintLine_("   defined on a triangular mesh onto a list of point");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      data_prime=InterpFromMeshToMesh3d(index,x,y,z,data,x_prime,y_prime,z_prime,default_value);");
         _pprintLine_("");
         _pprintLine_("      index: index of the mesh where data is defined");
         _pprintLine_("      x,y,z: coordinates of the nodes where data is defined");
         _pprintLine_("      data: matrix holding the data to be interpolated onto the mesh.");
         _pprintLine_("      x_prime,y_prime,z_prime: coordinates of the points onto which we interpolate.");
         _pprintLine_("      default_value: default value if no data is found (holes).");
         _pprintLine_("      data_prime: vector of mesh interpolated data.");
         _pprintLine_("");
         _pprintLine_("   Example:");
         _pprintLine_("      load('temperature.mat');");
         _pprintLine_("      md.initialization.temperature=InterpFromMeshToMesh3d(index,x,y,z,temperature,md.mesh.x,md.mesh.y,md.mesh.z,253);");
         _pprintLine_("");
+        _printf0_("INTERPFROMMESHTOMESH3D - interpolation from a 3d hexahedron mesh onto a list of point\n");
+        _printf0_("\n");
+        _printf0_("   This function is a multi-threaded mex file that interpolates a field\n");
+        _printf0_("   defined on a triangular mesh onto a list of point\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      data_prime=InterpFromMeshToMesh3d(index,x,y,z,data,x_prime,y_prime,z_prime,default_value);\n");
+        _printf0_("\n");
+        _printf0_("      index: index of the mesh where data is defined\n");
+        _printf0_("      x,y,z: coordinates of the nodes where data is defined\n");
+        _printf0_("      data: matrix holding the data to be interpolated onto the mesh.\n");
+        _printf0_("      x_prime,y_prime,z_prime: coordinates of the points onto which we interpolate.\n");
+        _printf0_("      default_value: default value if no data is found (holes).\n");
+        _printf0_("      data_prime: vector of mesh interpolated data.\n");
+        _printf0_("\n");
+        _printf0_("   Example:\n");
+        _printf0_("      load('temperature.mat');\n");
+        _printf0_("      md.initialization.temperature=InterpFromMeshToMesh3d(index,x,y,z,temperature,md.mesh.x,md.mesh.y,md.mesh.z,253);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(InterpFromMeshToMesh3d){
 …
         double* y_prime=NULL;
         double* z_prime=NULL;
         int     x_prime_rows;
         int     y_prime_rows;
 …
         /* output: */
         SeqVec<double>*  data_prime=NULL;
+        IssmSeqVec<double>*  data_prime=NULL;
         /*Boot module: */

issm/trunk/src/wrappers/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/KMLFileRead/KMLFileRead.cpp

-              r13250
+              r15396
 void KMLFileReadUsage(void){/*{{{*/
         _pprintLine_("KMLFileRead - KML file reader module:");
         _pprintLine_("");
         _pprintLine_("   This module reads a KML file.");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      [ierror]=KMLFileRead(kmlfile,'param name',param,...);");
         _pprintLine_("");
         _pprintLine_("      kmlfile      file name of kml file to be read (char)");
         _pprintLine_("");
         _pprintLine_("      echo         echo command (char, optional, 'off'/'on')");
         _pprintLine_("      deepecho     deep echo command (char, optional, 'off'/'on')");
         _pprintLine_("      write        write command (char, optional, 'off'/'stdout'/kmlfile)");
         _pprintLine_("");
         _pprintLine_("      ierror       return code (non-zero for error)");
         _pprintLine_("");
         _pprintLine_("   Examples:");
         _pprintLine_("      [ierror]=KMLFileRead('file.kml','deepecho','on');");
         _pprintLine_("      [ierror]=KMLFileRead('filin.kml','echo','on','write','filout.kml');");
         _pprintLine_("");
+        _printf0_("KMLFileRead - KML file reader module:\n");
+        _printf0_("\n");
+        _printf0_("   This module reads a KML file.\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      [ierror]=KMLFileRead(kmlfile,'param name',param,...);\n");
+        _printf0_("\n");
+        _printf0_("      kmlfile      file name of kml file to be read (char)\n");
+        _printf0_("\n");
+        _printf0_("      echo         echo command (char, optional, 'off'/'on')\n");
+        _printf0_("      deepecho     deep echo command (char, optional, 'off'/'on')\n");
+        _printf0_("      write        write command (char, optional, 'off'/'stdout'/kmlfile)\n");
+        _printf0_("\n");
+        _printf0_("      ierror       return code (non-zero for error)\n");
+        _printf0_("\n");
+        _printf0_("   Examples:\n");
+        _printf0_("      [ierror]=KMLFileRead('file.kml','deepecho','on');\n");
+        _printf0_("      [ierror]=KMLFileRead('filin.kml','echo','on','write','filout.kml');\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(KMLFileRead){
 …
         if (!strlen(filnam)) strcpy(filnam,"stdout");
         if (verbose) _printLine_("Opening file \"" << filnam << "\".");
+        if (verbose) _printf_("Opening file \"" << filnam << "\".\n");
         fidi=fopen(filnam,"r");
         /* Run core computations: */
         if (verbose) _printLine_("Calling core:");
+        if (verbose) _printf_("Calling core:\n");
         kobj=KMLFileReadx(fidi);
         if (verbose) _printLine_("Closing file \"" << filnam << "\".");
+        if (verbose) _printf_("Closing file \"" << filnam << "\".\n");
         fclose(fidi);
 …
+                        }
                         else {
                                 if (verbose) _printLine_("Opening file \"" << write << "\".");
+                                if (verbose) _printf_("Opening file \"" << write << "\".\n");
                                 fido=fopen(write,"w");
                                 kobj->Write(fido,"");
                                 if (verbose) _printLine_("Closing file \"" << write << "\".");
+                                if (verbose) _printf_("Closing file \"" << write << "\".\n");
                                 ierror=fclose(fido);
+                        }

issm/trunk/src/wrappers/KMLFileRead/KMLFileRead.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/KMLMeshWrite/KMLMeshWrite.cpp

-              r13250
+              r15396
 void KMLMeshWriteUsage(void){/*{{{*/
         _pprintLine_("KMLMeshWrite - KML mesh writer module:");
         _pprintLine_("");
         _pprintLine_("   This module writes the mesh of a model as KML polygons into the specified KML file.");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      ierror=KMLMeshWrite(name,notes,elem,nodecon,lat,long,part,data,cmap,kmlfile);");
         _pprintLine_("");
         _pprintLine_("      name       model name (string, may be empty)");
         _pprintLine_("      notes      model notes (string or cell array of strings, may be empty)");
         _pprintLine_("      elem       elements (double array)");
         _pprintLine_("      nodecon    nodal connectivity array (double array, may be empty)");
         _pprintLine_("      lat        nodal latititudes (double vector)");
         _pprintLine_("      long       nodal longitudes (double vector)");
         _pprintLine_("      part       nodal partitions (double vector, may be empty)");
         _pprintLine_("      data       nodal or element data (double vector, may be empty)");
         _pprintLine_("      cmap       color map (double nx3 array, may be empty)");
         _pprintLine_("      kmlfile    KML file name (string)");
         _pprintLine_("");
         _pprintLine_("      ierror     error flag (double, non-zero for error)");
         _pprintLine_("");
         _pprintLine_("   Example:");
         _pprintLine_("      KMLMeshWrite(md.name,md.notes,md.elements,md.nodeconnectivity,md.lat,md.long,md.part,md.fm_criterion,options.cmap,filekml);");
         _pprintLine_("");
+        _printf0_("KMLMeshWrite - KML mesh writer module:\n");
+        _printf0_("\n");
+        _printf0_("   This module writes the mesh of a model as KML polygons into the specified KML file.\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      ierror=KMLMeshWrite(name,notes,elem,nodecon,lat,long,part,data,cmap,kmlfile);\n");
+        _printf0_("\n");
+        _printf0_("      name       model name (string, may be empty)\n");
+        _printf0_("      notes      model notes (string or cell array of strings, may be empty)\n");
+        _printf0_("      elem       elements (double array)\n");
+        _printf0_("      nodecon    nodal connectivity array (double array, may be empty)\n");
+        _printf0_("      lat        nodal latititudes (double vector)\n");
+        _printf0_("      long       nodal longitudes (double vector)\n");
+        _printf0_("      part       nodal partitions (double vector, may be empty)\n");
+        _printf0_("      data       nodal or element data (double vector, may be empty)\n");
+        _printf0_("      cmap       color map (double nx3 array, may be empty)\n");
+        _printf0_("      kmlfile    KML file name (string)\n");
+        _printf0_("\n");
+        _printf0_("      ierror     error flag (double, non-zero for error)\n");
+        _printf0_("\n");
+        _printf0_("   Example:\n");
+        _printf0_("      KMLMeshWrite(md.name,md.notes,md.elements,md.nodeconnectivity,md.lat,md.long,md.part,md.fm_criterion,options.cmap,filekml);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(KMLMeshWrite){

issm/trunk/src/wrappers/KMLMeshWrite/KMLMeshWrite.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/KMLOverlay/KMLOverlay.cpp

-              r13250
+              r15396
 void KMLOverlayUsage(void){/*{{{*/
         _pprintLine_("KMLOverlay - KML file overlay module:");
         _pprintLine_("");
         _pprintLine_("   This module reads a list of image files and writes a KML or KMZ overlay file.");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      ierror=KMLOverlay(kmlfile,'param name',param,...);");
         _pprintLine_("");
         _pprintLine_("      kmlfile     KML or KMZ file name (string)");
         _pprintLine_("");
         _pprintLine_("      lataxis     latitude axis (double vector [south north], required)");
         _pprintLine_("      longaxis    longitude axis (double vector [west east], required)");
         _pprintLine_("      images      relative or http image file names (string or array of strings or cell array of strings, required)");
         _pprintLine_("      zip         flag to zip the doc.kml and image files into kmzfile (double, non-zero for kmz)");
         _pprintLine_("");
         _pprintLine_("      ierror     error flag (double, non-zero for error)");
         _pprintLine_("");
         _pprintLine_("   Example:");
         _pprintLine_("      KMLOverlay(kmlfile,'lataxis',[south north],'longaxis',[west east],'images',{'file1.png','http://issm/file2.png'},'zip',1);");
         _pprintLine_("");
+        _printf0_("KMLOverlay - KML file overlay module:\n");
+        _printf0_("\n");
+        _printf0_("   This module reads a list of image files and writes a KML or KMZ overlay file.\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      ierror=KMLOverlay(kmlfile,'param name',param,...);\n");
+        _printf0_("\n");
+        _printf0_("      kmlfile     KML or KMZ file name (string)\n");
+        _printf0_("\n");
+        _printf0_("      lataxis     latitude axis (double vector [south north], required)\n");
+        _printf0_("      longaxis    longitude axis (double vector [west east], required)\n");
+        _printf0_("      images      relative or http image file names (string or array of strings or cell array of strings, required)\n");
+        _printf0_("      zip         flag to zip the doc.kml and image files into kmzfile (double, non-zero for kmz)\n");
+        _printf0_("\n");
+        _printf0_("      ierror     error flag (double, non-zero for error)\n");
+        _printf0_("\n");
+        _printf0_("   Example:\n");
+        _printf0_("      KMLOverlay(kmlfile,'lataxis',[south north],'longaxis',[west east],'images',{'file1.png','http://issm/file2.png'},'zip',1);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(KMLOverlay){
 …
         options->Get(&lataxis ,&nlat ,(char*)"lataxis");
         if (verbose && lataxis) for (i=0; i<nlat; i++) _printLine_("  lataxis [" << i << "]=" << lataxis[i]);
+        if (verbose && lataxis) for (i=0; i<nlat; i++) _printf_("  lataxis [" << i << "]=" << lataxis[i] << "\n");
         options->Get(&longaxis,&nlong,(char*)"longaxis");
         if (verbose && longaxis) for (i=0; i<nlong; i++) _printLine_("  longaxis[" << i << "]=" << longaxis[i]);
+        if (verbose && longaxis) for (i=0; i<nlong; i++) _printf_("  longaxis[" << i << "]=" << longaxis[i] << "\n");
         options->Get(&pimages,&nimages,(char*)"images");
         if (verbose && pimages) for (i=0; i<nimages; i++) _printLine_("  pimages[" << i << "]=\"" << pimages[i] << "\"");
+        if (verbose && pimages) for (i=0; i<nimages; i++) _printf_("  pimages[" << i << "]=\"" << pimages[i] << "\"\n");
         options->Get(&dzip,(char*)"zip",0.);
         if (verbose) _printLine_("  dzip=" << dzip);
+        if (verbose) _printf_("  dzip=" << dzip << "\n");
         /*some checks*/
 …
         if(!strlen(filkml)) strcpy(filkml,"stdout");
         if(verbose) _printLine_("Opening kml overlay file \"" << filkml << "\".");
+        if(verbose) _printf_("Opening kml overlay file \"" << filkml << "\".\n");
         fid=fopen(filkml,"w");
         /* Run core computations: */
         if (verbose) _printLine_("Calling core:");
+        if (verbose) _printf_("Calling core:\n");
         KMLOverlayx(&ierror,lataxis,longaxis,nimages,pimages,fid);
         if (verbose) _printLine_("Closing file \"" << filkml << "\".");
+        if (verbose) _printf_("Closing file \"" << filkml << "\".\n");
         fclose(fid);
 …
                                 strcat(czip,pimages[i]);
+                        }
                 if (verbose) _printLine_("Zipping file \"" << filkmz << "\".");
                 if (verbose) _printLine_(czip);
+                if (verbose) _printf_("Zipping file \"" << filkmz << "\".\n");
+                if (verbose) _printf_(czip << "\n");
                 if (mexEvalString(czip)) _error_("Error zipping file \"" << filkmz << "\".");

issm/trunk/src/wrappers/KMLOverlay/KMLOverlay.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/Kml2Exp/Kml2Exp.cpp

-              r13250
+              r15396
 void Kml2ExpUsage(void){/*{{{*/
         _pprintLine_("Kml2Exp - kml to exp file conversion module:");
         _pprintLine_("");
         _pprintLine_("   This module converts a file from kml to exp format.");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      [ret]=Kml2Exp(filexp,filkml,sgn,'param name',param,...);");
         _pprintLine_("");
         _pprintLine_("      filkml      file name of kml file to be read (char)");
         _pprintLine_("      filexp      file name of exp file to be written (char)");
         _pprintLine_("      sgn         sign for hemisphere (double, +1 (north) or -1 (south))");
         _pprintLine_("");
         _pprintLine_("      central_meridian     central meridian (double, optional, but must specify with sp)");
         _pprintLine_("      standard_parallel    standard parallel (double, optional, but must specify with cm)");
         _pprintLine_("");
         _pprintLine_("      ret         return code (non-zero for warning)");
         _pprintLine_("");
         _pprintLine_("   Examples:");
         _pprintLine_("      [ret]=Kml2Exp('file.kml','file.exp', 1);");
         _pprintLine_("      [ret]=Kml2Exp('file.kml','file.exp', 1,'central_meridian',45,'standard_parallel',70);");
         _pprintLine_("      [ret]=Kml2Exp('file.kml','file.exp',-1,'central_meridian', 0,'standard_parallel',71);");
         _pprintLine_("");
+        _printf0_("Kml2Exp - kml to exp file conversion module:\n");
+        _printf0_("\n");
+        _printf0_("   This module converts a file from kml to exp format.\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      [ret]=Kml2Exp(filexp,filkml,sgn,'param name',param,...);\n");
+        _printf0_("\n");
+        _printf0_("      filkml      file name of kml file to be read (char)\n");
+        _printf0_("      filexp      file name of exp file to be written (char)\n");
+        _printf0_("      sgn         sign for hemisphere (double, +1 (north) or -1 (south))\n");
+        _printf0_("\n");
+        _printf0_("      central_meridian     central meridian (double, optional, but must specify with sp)\n");
+        _printf0_("      standard_parallel    standard parallel (double, optional, but must specify with cm)\n");
+        _printf0_("\n");
+        _printf0_("      ret         return code (non-zero for warning)\n");
+        _printf0_("\n");
+        _printf0_("   Examples:\n");
+        _printf0_("      [ret]=Kml2Exp('file.kml','file.exp', 1);\n");
+        _printf0_("      [ret]=Kml2Exp('file.kml','file.exp', 1,'central_meridian',45,'standard_parallel',70);\n");
+        _printf0_("      [ret]=Kml2Exp('file.kml','file.exp',-1,'central_meridian', 0,'standard_parallel',71);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(Kml2Exp){
 …
         if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) {
                 options->Get(&cm,"central_meridian");
                 if (verbose) _printLine_("  cm=" << cm);
+                if (verbose) _printf_("  cm=" << cm << "\n");
                 options->Get(&sp,"standard_parallel");
                 if (verbose) _printLine_("  sp=" << sp);
+                if (verbose) _printf_("  sp=" << sp << "\n");
+        }

issm/trunk/src/wrappers/Kml2Exp/Kml2Exp.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/Kriging/Kriging.cpp

-              r14067
+              r15396
         num=_NUMTHREADS_;
 #endif
         _pprintLine_("");
         _pprintLine_("   usage: predictions=" << __FUNCT__ << "(x,y,observations,x_interp,y_interp,'options');");
         _pprintLine_("   available options:");
         _pprintLine_("      -'model': Available variogram models 'gaussian' (default),'spherical','power','exponential'");
         _pprintLine_("         -'nugget': nugget effect (default 0.2)");
         _pprintLine_("         -'range':  for gaussian, spherical and exponential models (default sqrt(3))");
         _pprintLine_("         -'sill':   for gaussian, spherical and exponential models (default 1)");
         _pprintLine_("         -'slope':  for power model (default 1)");
         _pprintLine_("         -'power':  for power model (default 1)");
         _pprintLine_("      -'searchradius': search radius for each prediction (default is observations span)");
         _pprintLine_("      -'boxlength':    minimum length of quadtree boxes (useful to decrease the number of observations)");
         _pprintLine_("      -'maxdata':      minimum number of observations for a prediction (default is 50)");
         _pprintLine_("      -'mindata':      maximum number of observations for a prediction (default is 1)");
         _pprintLine_("      -'maxtrimming':  maximum trimming value (default is -1.e+21)");
         _pprintLine_("      -'mintrimming':  minimum trimming value (default is +1.e+21)");
         _pprintLine_("      -'minspacing':   minimum distance between observation (default is 0.01)");
         _pprintLine_("      -'numthreads':   number of threads, default is "<<num);
         _pprintLine_("");
+        _printf0_("\n");
+        _printf0_("   usage: predictions=" << __FUNCT__ << "(x,y,observations,x_interp,y_interp,'options');\n");
+        _printf0_("   available options:\n");
+        _printf0_("      -'model': Available variogram models 'gaussian' (default),'spherical','power','exponential'\n");
+        _printf0_("         -'nugget': nugget effect (default 0.2)\n");
+        _printf0_("         -'range':  for gaussian, spherical and exponential models (default sqrt(3))\n");
+        _printf0_("         -'sill':   for gaussian, spherical and exponential models (default 1)\n");
+        _printf0_("         -'slope':  for power model (default 1)\n");
+        _printf0_("         -'power':  for power model (default 1)\n");
+        _printf0_("      -'searchradius': search radius for each prediction (default is observations span)\n");
+        _printf0_("      -'boxlength':    minimum length of quadtree boxes (useful to decrease the number of observations)\n");
+        _printf0_("      -'maxdata':      minimum number of observations for a prediction (default is 50)\n");
+        _printf0_("      -'mindata':      maximum number of observations for a prediction (default is 1)\n");
+        _printf0_("      -'maxtrimming':  maximum trimming value (default is -1.e+21)\n");
+        _printf0_("      -'mintrimming':  minimum trimming value (default is +1.e+21)\n");
+        _printf0_("      -'minspacing':   minimum distance between observation (default is 0.01)\n");
+        _printf0_("      -'numthreads':   number of threads, default is "<<num << "\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(Kriging){

issm/trunk/src/wrappers/Kriging/Kriging.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/Ll2xy/Ll2xy.cpp

-              r13236
+              r15396
 void Ll2xyUsage(void){/*{{{*/
         _pprintLine_("Ll2xy - lat/long to x/y coordinate transformation module:");
         _pprintLine_("");
         _pprintLine_("   This module transforms lat/long to x/y coordinates.");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      [x,y]=Ll2xy(lat,lon,sgn,'param name',param,...);");
         _pprintLine_("");
         _pprintLine_("      lat         latitude coordinates (double vector)");
         _pprintLine_("      lon         longitude coordinates (double vector)");
         _pprintLine_("      sgn         sign for hemisphere (double, +1 (north) or -1 (south))");
         _pprintLine_("");
         _pprintLine_("      central_meridian     central meridian (double, optional, but must specify with sp)");
         _pprintLine_("      standard_parallel    standard parallel (double, optional, but must specify with cm)");
         _pprintLine_("");
         _pprintLine_("      x           x coordinates (double vector)");
         _pprintLine_("      y           y coordinates (double vector)");
         _pprintLine_("");
         _pprintLine_("   Examples:");
         _pprintLine_("      [x,y]=Ll2xy(lat,lon, 1);");
         _pprintLine_("      [x,y]=Ll2xy(lat,lon, 1,'central_meridian',45,'standard_parallel',70);");
         _pprintLine_("      [x,y]=Ll2xy(lat,lon,-1,'central_meridian', 0,'standard_parallel',71);");
         _pprintLine_("");
+        _printf0_("Ll2xy - lat/long to x/y coordinate transformation module:\n");
+        _printf0_("\n");
+        _printf0_("   This module transforms lat/long to x/y coordinates.\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      [x,y]=Ll2xy(lat,lon,sgn,'param name',param,...);\n");
+        _printf0_("\n");
+        _printf0_("      lat         latitude coordinates (double vector)\n");
+        _printf0_("      lon         longitude coordinates (double vector)\n");
+        _printf0_("      sgn         sign for hemisphere (double, +1 (north) or -1 (south))\n");
+        _printf0_("\n");
+        _printf0_("      central_meridian     central meridian (double, optional, but must specify with sp)\n");
+        _printf0_("      standard_parallel    standard parallel (double, optional, but must specify with cm)\n");
+        _printf0_("\n");
+        _printf0_("      x           x coordinates (double vector)\n");
+        _printf0_("      y           y coordinates (double vector)\n");
+        _printf0_("\n");
+        _printf0_("   Examples:\n");
+        _printf0_("      [x,y]=Ll2xy(lat,lon, 1);\n");
+        _printf0_("      [x,y]=Ll2xy(lat,lon, 1,'central_meridian',45,'standard_parallel',70);\n");
+        _printf0_("      [x,y]=Ll2xy(lat,lon,-1,'central_meridian', 0,'standard_parallel',71);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(Ll2xy){
 …
         if(options->GetOption("central_meridian") || options->GetOption("standard_parallel")){
                 options->Get(&cm,"central_meridian");
                 if (verbose) _printLine_("  cm=" << cm);
+                if (verbose) _printf_("  cm=" << cm << "\n");
                 options->Get(&sp,"standard_parallel");
                 if (verbose) _printLine_("  sp=" << sp);
+                if (verbose) _printf_("  sp=" << sp << "\n");
+        }
         /*some checks*/
         if (verbose) _printLine_("Checking inputs:");
+        if (verbose) _printf_("Checking inputs:\n");
         if (nlat != nlon){_error_("Must have same number of lat[" << nlat << "] and lon[" << nlon << "] coordinates.");}
         else                ncoord=nlat;

issm/trunk/src/wrappers/Ll2xy/Ll2xy.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/MeshPartition/MeshPartition.cpp

-              r13236
+              r15396
  * \brief: partition mesh according to number of areas, using Metis library.
 */
 #include "./MeshPartition.h"
 void MeshPartitionUsage(void){/*{{{*/
         _printLine_("   usage:");
         _printString_("   [element_partitioning,node_partitioning]=MeshPartition(md.mesh,numpartitions)");
         _printLine_("   where:");
         _printLine_("      element_partitioning is a vector of partitioning area numbers, for every element.");
         _printLine_("      node_partitioning is a vector of partitioning area numbers, for every node.");
         _printLine_("");
+        _printf_("   usage:\n");
+        _printf_("   [element_partitioning,node_partitioning]=MeshPartition(md.mesh,numpartitions)");
+        _printf_("   where:\n");
+        _printf_("      element_partitioning is a vector of partitioning area numbers, for every element.\n");
+        _printf_("      node_partitioning is a vector of partitioning area numbers, for every node.\n");
+        _printf_("\n");
 }/*}}}*/
 WRAPPER(MeshPartition){
 …
                 element_partitioning[i]=(double)int_element_partitioning[i]+1; //Metis indexing from 0, matlab from 1.
+        }
         node_partitioning=xNew<double>(numberofvertices);
         for (i=0;i<numberofvertices;i++){
 …
         WriteData(ELEMENTPARTITIONING,element_partitioning,numberofelements);
         WriteData(NODEPARTITIONING,node_partitioning,numberofvertices);
         /*Free ressources:*/
         //don't! let matlab do it.

issm/trunk/src/wrappers/MeshPartition/MeshPartition.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__
 …
 #define NRHS  2
 #endif  /* _MESHPARTITION_H */

issm/trunk/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.cpp

-              r14310
+              r15396
                 mesh.
 */
 #include "./MeshProfileIntersection.h"
 void MeshProfileIntersectionUsage(void){/*{{{*/
         _printLine_("   usage:");
         _printLine_("   [segments]=MeshProfileIntersection(index,x,y,filename);");
         _printLine_("   where:");
         _printLine_("   input:");
         _printLine_("        index,x,y is a triangulation");
         _printLine_("        filename: name of Argus style .exp file containing the segments (can be groups of disconnected segments)");
         _printLine_("   output:");
         _printLine_("        segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremities for a segment ");
         _printLine_("        belonging to the elemnt_id element. there are as many lines in segments as there are segments intersecting the ");
         _printLine_("        mesh.");
+        _printf_("   usage:\n");
+        _printf_("   [segments]=MeshProfileIntersection(index,x,y,filename);\n");
+        _printf_("   where:\n");
+        _printf_("   input:\n");
+        _printf_("        index,x,y is a triangulation\n");
+        _printf_("        filename: name of Argus style .exp file containing the segments (can be groups of disconnected segments)\n");
+        _printf_("   output:\n");
+        _printf_("        segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremities for a segment \n");
+        _printf_("        belonging to the elemnt_id element. there are as many lines in segments as there are segments intersecting the \n");
+        _printf_("        mesh.\n");
 }/*}}}*/
 WRAPPER(MeshProfileIntersection){
 …
         /* required input: */
         //mesh
         double* double_index=NULL;
         int*    index=NULL;
+        double *double_index = NULL;
+        int    *index        = NULL;
         int     nel;
         double* x=NULL;
         double* y=NULL;
+        double *x            = NULL;
+        double *y            = NULL;
         int     nods;
         int     dummy;
         //contours
         DataSet          *domain      = NULL;
+        Contours         *domain      = NULL;
         Contour<double> **contours=NULL;
         int               numcontours;
 …
         //contours
         FetchData(&domain,FILENAME);
         // MeshProfileIntersectionx should be modified to take DataSet directly (and perhaps SeqMat and SeqVec).
+        // MeshProfileIntersectionx should be modified to take DataSet directly (and perhaps IssmDenseMat and IssmSeqVec).
         numcontours=domain->Size();
         contours=xNew<Contour<double>*>(numcontours);

issm/trunk/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__
 …
 #endif  /* _MESHPROFILEINTERSECTION_H */

issm/trunk/src/wrappers/NodeConnectivity/NodeConnectivity.cpp

-              r14067
+              r15396
 void NodeConnectivityUsage(void){/*{{{*/
         _pprintLine_("");
         _pprintLine_("   usage: connectivity = " << __FUNCT__ << "(elements, numnodes);");
         _pprintLine_("");
+        _printf0_("\n");
+        _printf0_("   usage: connectivity = " << __FUNCT__ << "(elements, numnodes);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(NodeConnectivity){
 …
         /*checks on arguments: */
         CHECKARGUMENTS(NLHS,NRHS,&NodeConnectivityUsage);
         /*Input datasets: */
         FetchData(&elements,&nels,NULL,ELEMENTS);

issm/trunk/src/wrappers/NodeConnectivity/NodeConnectivity.h

-              r13749
+              r15396
 /*Header files: */
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/toolkits/toolkits.h"
-#include "../../c/include/include.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
+#include "../bindings.h"
+#include "../../c/io/io.h"
+#include "../../c/EnumDefinitions/EnumDefinitions.h"
+#include "../../c/shared/io/io.h"
+#include "../../c/shared/Enum/Enum.h"
 #ifdef _HAVE_MATLAB_MODULES_

issm/trunk/src/wrappers/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp

-              r13236
+              r15396
     \brief: flag points that are too near one another, within an array of point coordinates
 */
 #include "./PointCloudFindNeighbors.h"
 void PointCloudFindNeighborsUsage(void){/*{{{*/
         _printLine_("   usage:");
         _printLine_("   [flags]=PointCloudFindNeighbors(x,y,mindistance,multithread);\n");
         _printLine_("   where:");
         _printLine_("      x,y: list of points.");
         _printLine_("      mindistance: minimum distance that should exist between points in the cloud.");
         _printLine_("      multithread: run multithreaded or not. with multithreads, flags can get 1 and 2 values in duplicates.");
         _printLine_("      flags: array of flags (flag==1 means point is within mindistance of another point)");
         _printLine_("");
+        _printf_("   usage:\n");
+        _printf_("   [flags]=PointCloudFindNeighbors(x,y,mindistance,multithread);\n");
+        _printf_("   where:\n");
+        _printf_("      x,y: list of points.\n");
+        _printf_("      mindistance: minimum distance that should exist between points in the cloud.\n");
+        _printf_("      multithread: run multithreaded or not. with multithreads, flags can get 1 and 2 values in duplicates.\n");
+        _printf_("      flags: array of flags (flag==1 means point is within mindistance of another point)\n");
+        _printf_("\n");
 }/*}}}*/
 WRAPPER(PointCloudFindNeighbors){
 …
         /* output: */
         SeqVec<double> *flags = NULL;
+        IssmSeqVec<double> *flags = NULL;
         /*Boot module: */

issm/trunk/src/wrappers/PointCloudFindNeighbors/PointCloudFindNeighbors.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp

-              r13250
+              r15396
 void PropagateFlagsFromConnectivityUsage(void) {/*{{{*/
         _printLine_("");
         _printLine_("   usage: [pool] = " << __FUNCT__ << "(connectivity,pool,index,flags);");;
         _printLine_("");
+        _printf_("\n");
+        _printf_("   usage: [pool] = " << __FUNCT__ << "(connectivity,pool,index,flags);\n");;
+        _printf_("\n");
 }/*}}}*/
 WRAPPER(PropagateFlagsFromConnectivity){
 …
         int     index;
         int     dummy;
         /*Boot module: */
         MODULEBOOT();
 …
         /*checks on arguments on the matlab side: */
         CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&PropagateFlagsFromConnectivityUsage);
         /*Input datasets: */
         FetchData(&connectivity,&nel,&dummy,CONNECTIVITY);

issm/trunk/src/wrappers/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/Scotch/Scotch.cpp

r13236	r15396
35	35
36	36	/* Check for proper number of arguments */
37
	37
38	38	if (nrhs == 0 && nlhs == 0) {
39	39	GmapUsage();

issm/trunk/src/wrappers/Scotch/Scotch.h

-              r13749
+              r15396
 #define _SCOTCH_H
+#include "../bindings.h" /*Should always come first to avoid python's warnings*/
 #include <stdio.h>
 #include <string.h>    /*  strcasecmp  */
 #include <time.h>      /*  clock,time,difftime  */
 #include "../../c/include/globals.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
+#include "../bindings.h"
 #undef __FUNCT__
 #define __FUNCT__  "Scotch"

issm/trunk/src/wrappers/Shp2Exp/Shp2Exp.cpp

-              r14283
+              r15396
 void Shp2ExpUsage(void){/*{{{*/
         _pprintLine_("Shp2Exp - shp to exp file conversion module:");
         _pprintLine_("");
         _pprintLine_("   This module converts a file from shp to exp format.");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      [ret]=Shp2Exp(filshp,filexp,sgn,'param name',param,...);");
         _pprintLine_("");
         _pprintLine_("      filshp      file name of shp file to be read (char, extension optional)");
         _pprintLine_("      filexp      file name of exp file to be written (char)");
         _pprintLine_("");
         _pprintLine_("      ret         return code (non-zero for warning)");
         _pprintLine_("");
         _pprintLine_("   Examples:");
         _pprintLine_("      [ret]=Shp2Exp('file.shp','file.exp');");
         _pprintLine_("");
+        _printf0_("Shp2Exp - shp to exp file conversion module:\n");
+        _printf0_("\n");
+        _printf0_("   This module converts a file from shp to exp format.\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      [ret]=Shp2Exp(filshp,filexp,sgn,'param name',param,...);\n");
+        _printf0_("\n");
+        _printf0_("      filshp      file name of shp file to be read (char, extension optional)\n");
+        _printf0_("      filexp      file name of exp file to be written (char)\n");
+        _printf0_("\n");
+        _printf0_("      ret         return code (non-zero for warning)\n");
+        _printf0_("\n");
+        _printf0_("   Examples:\n");
+        _printf0_("      [ret]=Shp2Exp('file.shp','file.exp');\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(Shp2Exp){

issm/trunk/src/wrappers/Shp2Exp/Shp2Exp.h

-              r14283
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__
 …
 #endif

issm/trunk/src/wrappers/Shp2Kml/Shp2Kml.cpp

-              r13250
+              r15396
 void Shp2KmlUsage(void){/*{{{*/
         _pprintLine_("Shp2Kml - shp to kml file conversion module:");
         _pprintLine_("");
         _pprintLine_("   This module converts a file from shp to kml format.");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      [ret]=Shp2Kml(filshp,filkml,sgn,'param name',param,...);");
         _pprintLine_("");
         _pprintLine_("      filshp      file name of shp file to be read (char, extension optional)");
         _pprintLine_("      filkml      file name of kml file to be written (char)");
         _pprintLine_("      sgn         sign for hemisphere (double, +1 (north); -1 (south); or 0 (no translation))");
         _pprintLine_("");
         _pprintLine_("      central_meridian     central meridian (double, optional, but must specify with sp)");
         _pprintLine_("      standard_parallel    standard parallel (double, optional, but must specify with cm)");
         _pprintLine_("");
         _pprintLine_("      ret         return code (non-zero for warning)");
         _pprintLine_("");
         _pprintLine_("   Examples:");
         _pprintLine_("      [ret]=Shp2Kml('file.shp','file.kml', 0);");
         _pprintLine_("      [ret]=Shp2Kml('file.shp','file.kml', 1,'central_meridian',45,'standard_parallel',70);");
         _pprintLine_("      [ret]=Shp2Kml('file.shp','file.kml',-1,'central_meridian', 0,'standard_parallel',71);");
         _pprintLine_("");
+        _printf0_("Shp2Kml - shp to kml file conversion module:\n");
+        _printf0_("\n");
+        _printf0_("   This module converts a file from shp to kml format.\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      [ret]=Shp2Kml(filshp,filkml,sgn,'param name',param,...);\n");
+        _printf0_("\n");
+        _printf0_("      filshp      file name of shp file to be read (char, extension optional)\n");
+        _printf0_("      filkml      file name of kml file to be written (char)\n");
+        _printf0_("      sgn         sign for hemisphere (double, +1 (north) -1 (south) or 0 (no translation))\n");
+        _printf0_("\n");
+        _printf0_("      central_meridian     central meridian (double, optional, but must specify with sp)\n");
+        _printf0_("      standard_parallel    standard parallel (double, optional, but must specify with cm)\n");
+        _printf0_("\n");
+        _printf0_("      ret         return code (non-zero for warning)\n");
+        _printf0_("\n");
+        _printf0_("   Examples:\n");
+        _printf0_("      [ret]=Shp2Kml('file.shp','file.kml', 0);\n");
+        _printf0_("      [ret]=Shp2Kml('file.shp','file.kml', 1,'central_meridian',45,'standard_parallel',70);\n");
+        _printf0_("      [ret]=Shp2Kml('file.shp','file.kml',-1,'central_meridian', 0,'standard_parallel',71);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(Shp2Kml){
 …
         if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) {
                 options->Get(&cm,"central_meridian");
                 if (verbose) _printLine_("  cm=" << cm);
+                if (verbose) _printf_("  cm=" << cm << "\n");
                 options->Get(&sp,"standard_parallel");
                 if (verbose) _printLine_("  sp=" << sp);
+                if (verbose) _printf_("  sp=" << sp << "\n");
+        }

issm/trunk/src/wrappers/Shp2Kml/Shp2Kml.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__
 …
 #endif

issm/trunk/src/wrappers/StringToEnum/StringToEnum.cpp

-              r13236
+              r15396
 void StringToEnumUsage(void){/*{{{*/
         _pprintLine_("");
         _pprintLine_("   usage: " << __FUNCT__ << "enum = StringToEnum(string);");
         _pprintLine_("");
+        _printf0_("\n");
+        _printf0_("   usage: " << __FUNCT__ << "enum = StringToEnum(string);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(StringToEnum){

issm/trunk/src/wrappers/StringToEnum/StringToEnum.h

-              r13749
+              r15396
 /*Header files: */
 #include "../../c/include/globals.h"
 #include "../../c/modules/modules.h"
 #include "../../c/Container/Container.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
+#include "../../c/shared/Enum/Enum.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__
 #define __FUNCT__  "StringToEnum"
 #ifdef _HAVE_MATLAB_MODULES_
 /* serial input macros: */

issm/trunk/src/wrappers/TriMesh/TriMesh.cpp

-              r14310
+              r15396
 void TriMeshUsage(void){/*{{{*/
         _printLine_("");
         _printLine_("   usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,rifts,area) ");
         _printLine_("      where: index,x,y defines a triangulation, segments is an array made ");
         _printLine_("      of exterior segments to the mesh domain outline, segmentmarkers is an array flagging each segment, ");
         _printLine_("      outlinefilename an Argus domain outline file, ");
         _printLine_("      area is the maximum area desired for any element of the resulting mesh, ");
         _printLine_("");
+        _printf_("\n");
+        _printf_("   usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,rifts,area) \n");
+        _printf_("      where: index,x,y defines a triangulation, segments is an array made \n");
+        _printf_("      of exterior segments to the mesh domain outline, segmentmarkers is an array flagging each segment, \n");
+        _printf_("      outlinefilename an Argus domain outline file, \n");
+        _printf_("      area is the maximum area desired for any element of the resulting mesh, \n");
+        _printf_("\n");
 }/*}}}*/
 WRAPPER(TriMesh){
         /*intermediary: */
         double  area;
         DataSet *domain = NULL;
         DataSet *rifts  = NULL;
+        double    area;
+        Contours *domain = NULL;
+        Contours *rifts  = NULL;
         /* output: */
+        SeqMat<int>    *index             = NULL;
+        SeqVec<double> *x                 = NULL;
+        SeqVec<double> *y                 = NULL;
+        SeqMat<int>    *segments          = NULL;
+        SeqVec<int>    *segmentmarkerlist = NULL;
+        int    *index             = NULL;
+        double *x                 = NULL;
+        double *y                 = NULL;
+        int    *segments          = NULL;
+        int    *segmentmarkerlist = NULL;
+        int     nels,nods,nsegs;
         /*Boot module: */
 …
         /*checks on arguments: */
         CHECKARGUMENTS(NLHS,NRHS,&TriMeshUsage);
         /*Fetch data needed for meshing: */
         FetchData(&domain,DOMAINOUTLINE);
 …
         /*call x core: */
         TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,domain,rifts,area);
+        TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,&nels,&nods,&nsegs,domain,rifts,area);
         /*write outputs: */
         WriteData(INDEX,index);
         WriteData(X,x);
         WriteData(Y,y);
         WriteData(SEGMENTS,segments);
         WriteData(SEGMENTMARKERLIST,segmentmarkerlist);
+        WriteData(INDEX,index,nels,3);
+        WriteData(X,x,nods);
+        WriteData(Y,y,nods);
+        WriteData(SEGMENTS,segments,nsegs,3);
+        WriteData(SEGMENTMARKERLIST,segmentmarkerlist,nsegs);
         /*free ressources: */
         delete domain;
         delete rifts;
         delete index;
         delete x;
         delete y;
         delete segments;
         delete segmentmarkerlist;
+        xDelete<int>(index);
+        xDelete<double>(x);
+        xDelete<double>(y);
+        xDelete<int>(segments);
+        xDelete<int>(segmentmarkerlist);
         /*end module: */

issm/trunk/src/wrappers/TriMesh/TriMesh.h

-              r13749
+              r15396
 /*Header files: */
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/toolkits/toolkits.h"
-#include "../../c/include/include.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
+#include "../bindings.h"
+#include "../../c/io/io.h"
+#include "../../c/EnumDefinitions/EnumDefinitions.h"
+#include "../../c/shared/io/io.h"
+#include "../../c/shared/Enum/Enum.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/TriMeshProcessRifts/TriMeshProcessRifts.cpp

-              r14310
+              r15396
 void TriMeshProcessRiftsUsage(void){/*{{{*/
         _printLine_("");
         _printLine_("   usage: [index2,x2,y2,segments2,segmentmarkers2,rifts2]=TriMeshProcessrifts(index1,x1,y1,segments1,segmentmarkers1) ");
         _printLine_("      where: (index1,x1,y1,segments1,segmentmarkers1) is an initial triangulation.");
         _printLine_("      index2,x2,y2,segments2,segmentmarkers2,rifts2 is the resulting triangulation where rifts have been processed.");
+        _printf_("\n");
+        _printf_("   usage: [index2,x2,y2,segments2,segmentmarkers2,rifts2]=TriMeshProcessrifts(index1,x1,y1,segments1,segmentmarkers1) \n");
+        _printf_("      where: (index1,x1,y1,segments1,segmentmarkers1) is an initial triangulation.\n");
+        _printf_("      index2,x2,y2,segments2,segmentmarkers2,rifts2 is the resulting triangulation where rifts have been processed.\n");
 }/*}}}*/
 WRAPPER(TriMeshProcessRifts){

issm/trunk/src/wrappers/TriMeshProcessRifts/TriMeshProcessRifts.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/TriaSearch/TriaSearch.cpp

-              r13236
+              r15396
 void TriaSearchUsage(void){/*{{{*/
         _pprintLine_("TriaSearch- find triangle holding a point (x0,y0) in a mesh");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("         tria=TriaSearch(index,x,y,x0,y0);");
         _pprintLine_("      index,x,y: mesh triangulatrion");
         _pprintLine_("      x0,y0: coordinates of the point for which we are trying to find a triangle");
         _pprintLine_("      x0,y0 can be an array of points");
         _pprintLine_("");
+        _printf0_("TriaSearch- find triangle holding a point (x0,y0) in a mesh\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("         tria=TriaSearch(index,x,y,x0,y0);\n");
+        _printf0_("      index,x,y: mesh triangulatrion\n");
+        _printf0_("      x0,y0: coordinates of the point for which we are trying to find a triangle\n");
+        _printf0_("      x0,y0 can be an array of points\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(TriaSearch){

issm/trunk/src/wrappers/TriaSearch/TriaSearch.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/Xy2ll/Xy2ll.cpp

-              r13236
+              r15396
 void Xy2llUsage(void){/*{{{*/
         _pprintLine_("Xy2ll - x/y to lat/long coordinate transformation module:");
         _pprintLine_("");
         _pprintLine_("   This module transforms x/y to lat/long coordinates.");
         _pprintLine_("");
         _pprintLine_("   Usage:");
         _pprintLine_("      [lat,lon]=Xy2ll(x,y,sgn,'param name',param,...);");
         _pprintLine_("");
         _pprintLine_("      x           x coordinates (double vector)");
         _pprintLine_("      y           y coordinates (double vector)");
         _pprintLine_("      sgn         sign for hemisphere (double, +1 (north) or -1 (south))");
         _pprintLine_("");
         _pprintLine_("      central_meridian     central meridian (double, optional, but must specify with sp)");
         _pprintLine_("      standard_parallel    standard parallel (double, optional, but must specify with cm)");
         _pprintLine_("");
         _pprintLine_("      lat         latitude coordinates (double vector)");
         _pprintLine_("      lon         longitude coordinates (double vector)");
         _pprintLine_("");
         _pprintLine_("   Examples:");
         _pprintLine_("      [lat,lon]=Xy2ll(x,y, 1);");
         _pprintLine_("      [lat,lon]=Xy2ll(x,y, 1,'central_meridian',45,'standard_parallel',70);");
         _pprintLine_("      [lat,lon]=Xy2ll(x,y,-1,'central_meridian', 0,'standard_parallel',71);");
         _pprintLine_("");
+        _printf0_("Xy2ll - x/y to lat/long coordinate transformation module:\n");
+        _printf0_("\n");
+        _printf0_("   This module transforms x/y to lat/long coordinates.\n");
+        _printf0_("\n");
+        _printf0_("   Usage:\n");
+        _printf0_("      [lat,lon]=Xy2ll(x,y,sgn,'param name',param,...);\n");
+        _printf0_("\n");
+        _printf0_("      x           x coordinates (double vector)\n");
+        _printf0_("      y           y coordinates (double vector)\n");
+        _printf0_("      sgn         sign for hemisphere (double, +1 (north) or -1 (south))\n");
+        _printf0_("\n");
+        _printf0_("      central_meridian     central meridian (double, optional, but must specify with sp)\n");
+        _printf0_("      standard_parallel    standard parallel (double, optional, but must specify with cm)\n");
+        _printf0_("\n");
+        _printf0_("      lat         latitude coordinates (double vector)\n");
+        _printf0_("      lon         longitude coordinates (double vector)\n");
+        _printf0_("\n");
+        _printf0_("   Examples:\n");
+        _printf0_("      [lat,lon]=Xy2ll(x,y, 1);\n");
+        _printf0_("      [lat,lon]=Xy2ll(x,y, 1,'central_meridian',45,'standard_parallel',70);\n");
+        _printf0_("      [lat,lon]=Xy2ll(x,y,-1,'central_meridian', 0,'standard_parallel',71);\n");
+        _printf0_("\n");
 }/*}}}*/
 WRAPPER(Xy2ll){
 …
         if (options->GetOption("central_meridian") || options->GetOption("standard_parallel")) {
                 options->Get(&cm,"central_meridian");
                 if (verbose) _printLine_("  cm=" << cm);
+                if (verbose) _printf_("  cm=" << cm << "\n");
                 options->Get(&sp,"standard_parallel");
                 if (verbose) _printLine_("  sp=" << sp);
+                if (verbose) _printf_("  sp=" << sp << "\n");
+        }
 …
         /* Run core computations: */
         if (verbose) _printLine_("Calling core:");
+        if (verbose) _printf_("Calling core:\n");
         if (options->GetOption("central_meridian") && options->GetOption("standard_parallel"))
                 iret=Xy2llx(lat,lon,x,y,ncoord,sgn,cm,sp);

issm/trunk/src/wrappers/Xy2ll/Xy2ll.h

-              r13749
+              r15396
 #endif
+#include "../../c/include/globals.h"
+#include "../bindings.h"
+#include "../../c/main/globals.h"
 #include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
-#include "../bindings.h"
 #undef __FUNCT__

issm/trunk/src/wrappers/bindings.h

-              r13749
+              r15396
 #endif
+#ifdef  _HAVE_PYTHON_MODULES_
+#include "./python/include/pythonincludes.h"
+#include "./python/include/wrapper_macros.h"
+#include "./python/io/pythonio.h"
+#endif
 #ifdef  _HAVE_MATLAB_MODULES_
 #include "./matlab/include/matlabincludes.h"
 …
 #endif
-#ifdef  _HAVE_PYTHON_MODULES_
-#include "./python/include/pythonincludes.h"
-#include "./python/include/wrapper_macros.h"
-#include "./python/io/pythonio.h"
 #endif
-#endif

issm/trunk/src/wrappers/matlab/Makefile.am

-              r14310
+              r15396
                                 ./io/MatlabVectorToDoubleVector.cpp\
                                 ./io/MatlabMatrixToDoubleMatrix.cpp\
+                                ./io/MatlabMatrixToSeqMat.cpp\
+                                ./io/MatlabVectorToSeqVec.cpp
+                                ./io/MatlabMatrixToIssmMat.cpp\
+                                ./io/MatlabVectorToIssmVec.cpp
 if PETSC
 …
 if SHAREDLIBS
 libISSMMatlab_la_SOURCES = $(io_sources)
+endif
+#}}}
+#api io{{{
+lib_LIBRARIES += libISSMApi.a
+if SHAREDLIBS
+lib_LTLIBRARIES += libISSMApi.la
+else
+lib_LTLIBRARIES +=
+endif
+api_sources= ./io/ApiPrintf.cpp
+libISSMApi_a_SOURCES = $(api_sources)
+libISSMApi_a_CXXFLAGS= $(ALLCXXFLAGS)
+if SHAREDLIBS
+libISSMApi_la_SOURCES = $(api_sources)
 endif
 #}}}
 …
                                                  ContourToMesh.la\
                                                  ContourToNodes.la\
+                                                 EdgeDetection.la\
                                                  ElementConnectivity.la\
                                                  EnumToString.la\
 …
 endif
 #}}}
+#Flags and libraries {{{
+#if SHAREDLIBS
+#deps = ../../c/libISSMCore.la ../../c/libISSMModules.la
+#else
+#deps = ../../c/libISSMCore.a ../../c/libISSMModules.a
+#endif
+#deps +=  $(MATHLIB) ${MEXLIB}
+deps =  $(MATHLIB) ${MEXLIB}
+# Dependencies {{{
+deps =  $(MATHLIB)
 #Triangle library
 …
 AM_LDFLAGS += -avoid-version
 endif
-if SHAREDLIBS
-deps += ./libISSMMatlab.la
-else
-deps += ./libISSMMatlab.a
-AM_LDFLAGS += --no-warnings
-endif
 AM_CXXFLAGS +=  -D_HAVE_MATLAB_MODULES_  -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread
 if SHAREDLIBS
 deps +=
 else
 deps += ../../c/libISSMModules.a ../../c/libISSMCore.a
+deps += ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la ./libISSMMatlab.a
+else
+deps += ./libISSMMatlab.a ../../c/libISSMModules.a ../../c/libISSMCore.a ./libISSMApi.a
 if ADOLC
 deps += $(ADOLCLIB)
 endif
 endif
+#MEXLIB needs to be the last (undefined references on larsen)
+deps += ${MEXLIB}
 #Optimization flags:
 AM_CXXFLAGS += $(CXXOPTFLAGS)
 #}}}
+#Bin sources {{{
+# Module sources and dependencies {{{
+libISSMMatlab_la_LIBADD = $(MPILIB) $(PETSCLIB) $(GSLLIB) $(MATHLIB) $(MEXLIB) ./../../c/libISSMCore.la
+libISSMMatlab_la_LDFLAGS = -module
+libISSMApi_la_LIBADD = $(MPILIB) $(PETSCLIB) $(GSLLIB) $(MATHLIB) $(MEXLIB)
+libISSMApi_la_LDFLAGS = -module
 AverageFilter_la_SOURCES = ../AverageFilter/AverageFilter.cpp\
                                                                         ../AverageFilter/AverageFilter.h
 AverageFilter_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+AverageFilter_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 BamgMesher_la_SOURCES = ../BamgMesher/BamgMesher.cpp\
                                                                 ../BamgMesher/BamgMesher.h
 BamgMesher_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+BamgMesher_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 BamgConvertMesh_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp\
                                                                           ../BamgConvertMesh/BamgConvertMesh.h
 BamgConvertMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+BamgConvertMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 BamgTriangulate_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp\
                                                                           ../BamgTriangulate/BamgTriangulate.h
 BamgTriangulate_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+BamgTriangulate_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 Chaco_la_SOURCES = ../Chaco/Chaco.cpp\
                                                  ../Chaco/Chaco.h
 Chaco_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(CHACOLIB)
+Chaco_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(CHACOLIB) $(GSLLIB)
 ContourToMesh_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp\
                                                                         ../ContourToMesh/ContourToMesh.h
 ContourToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+ContourToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB)
 ContourToNodes_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp\
                                                                          ../ContourToNodes/ContourToNodes.h
 ContourToNodes_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+ContourToNodes_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 ElementConnectivity_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\
                                                                                         ../ElementConnectivity/ElementConnectivity.h
 ElementConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+ElementConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 EnumToString_la_SOURCES = ../EnumToString/EnumToString.cpp\
                                                                   ../EnumToString/EnumToString.h
 EnumToString_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+EnumToString_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 StringToEnum_la_SOURCES = ../StringToEnum/StringToEnum.cpp\
                                                                   ../StringToEnum/StringToEnum.h
 StringToEnum_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+StringToEnum_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 HoleFiller_la_SOURCES = ../HoleFiller/HoleFiller.cpp\
                                                                 ../HoleFiller/HoleFiller.h
 HoleFiller_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+HoleFiller_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)  $(GSLLIB)
 InternalFront_la_SOURCES = ../InternalFront/InternalFront.cpp\
                                                                         ../InternalFront/InternalFront.h
 InternalFront_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+InternalFront_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 InterpFromGridToMesh_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp\
                                                                                          ../InterpFromGridToMesh/InterpFromGridToMesh.h
 InterpFromGridToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+InterpFromGridToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB)
 InterpFromMeshToMesh2d_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\
                                                                                                 ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h
 InterpFromMeshToMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+InterpFromMeshToMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB)
 InterpFromMeshToMesh3d_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp\
                                                                                                 ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h
 InterpFromMeshToMesh3d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+InterpFromMeshToMesh3d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 InterpFromMeshToGrid_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp\
                                                                                          ../InterpFromMeshToGrid/InterpFromMeshToGrid.h
 InterpFromMeshToGrid_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+InterpFromMeshToGrid_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 InterpFromMesh2d_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp\
                                                                                 ../InterpFromMesh2d/InterpFromMesh2d.h
 InterpFromMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+InterpFromMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB)
 KMLFileRead_la_SOURCES = ../KMLFileRead/KMLFileRead.cpp\
                                                                  ../KMLFileRead/KMLFileRead.h
 KMLFileRead_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+KMLFileRead_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 KMLMeshWrite_la_SOURCES = ../KMLMeshWrite/KMLMeshWrite.cpp\
                                                                   ../KMLMeshWrite/KMLMeshWrite.h
 KMLMeshWrite_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+KMLMeshWrite_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 KMLOverlay_la_SOURCES = ../KMLOverlay/KMLOverlay.cpp\
                                                                 ../KMLOverlay/KMLOverlay.h
 KMLOverlay_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+KMLOverlay_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 Xy2ll_la_SOURCES = ../Xy2ll/Xy2ll.cpp\
                                                  ../Xy2ll/Xy2ll.h
 Xy2ll_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+Xy2ll_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 Ll2xy_la_SOURCES = ../Ll2xy/Ll2xy.cpp\
                                                  ../Ll2xy/Ll2xy.h
+Ll2xy_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+Ll2xy_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
+EdgeDetection_la_SOURCES = ../EdgeDetection/EdgeDetection.cpp\
+                                                        ../EdgeDetection/EdgeDetection.h
+EdgeDetection_la_LIBADD= ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 ExpSimplify_la_SOURCES = ../ExpSimplify/ExpSimplify.cpp\
                                                         ../ExpSimplify/ExpSimplify.h
 ExpSimplify_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+ExpSimplify_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 Exp2Kml_la_SOURCES = ../Exp2Kml/Exp2Kml.cpp\
                                                         ../Exp2Kml/Exp2Kml.h
 Exp2Kml_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+Exp2Kml_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 Kml2Exp_la_SOURCES = ../Kml2Exp/Kml2Exp.cpp\
                                                         ../Kml2Exp/Kml2Exp.h
 Kml2Exp_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+Kml2Exp_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 Kriging_la_SOURCES = ../Kriging/Kriging.cpp\
                                                         ../Kriging/Kriging.h
 Kriging_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(MULTITHREADINGLIB)
+Kriging_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(MULTITHREADINGLIB) $(GSLLIB)
 MeshPartition_la_SOURCES = ../MeshPartition/MeshPartition.cpp\
                                                                         ../MeshPartition/MeshPartition.h
 MeshPartition_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(METISLIB)
+MeshPartition_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(METISLIB) $(GSLLIB)
 MeshProfileIntersection_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\
                                                                                                  ../MeshProfileIntersection/MeshProfileIntersection.h
 MeshProfileIntersection_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+MeshProfileIntersection_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 NodeConnectivity_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\
                                                                                 ../NodeConnectivity/NodeConnectivity.h
 NodeConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+NodeConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 PointCloudFindNeighbors_la_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\
                                                                                                  ../PointCloudFindNeighbors/PointCloudFindNeighbors.h
 PointCloudFindNeighbors_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+PointCloudFindNeighbors_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB)
 PropagateFlagsFromConnectivity_la_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\
                                                                                                                   ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h
 PropagateFlagsFromConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+PropagateFlagsFromConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 Scotch_la_SOURCES = ../Scotch/Scotch.cpp\
                                                   ../Scotch/Scotch.h
 Scotch_la_LIBADD = ${deps} $(SCOTCHLIB) $(MPILIB)
+Scotch_la_LIBADD = ${deps} $(SCOTCHLIB) $(MPILIB) $(BLASLAPACKLIB)
 Shp2Exp_la_SOURCES = ../Shp2Exp/Shp2Exp.cpp\
                                                         ../Shp2Exp/Shp2Exp.h
 Shp2Exp_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB)
+Shp2Exp_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB) $(GSLLIB)
 Shp2Kml_la_SOURCES = ../Shp2Kml/Shp2Kml.cpp\
                                                         ../Shp2Kml/Shp2Kml.h
 Shp2Kml_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB)
+Shp2Kml_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB) $(GSLLIB)
 TriaSearch_la_SOURCES = ../TriaSearch/TriaSearch.cpp\
                                                                 ../TriaSearch/TriaSearch.h
 TriaSearch_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+TriaSearch_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 TriMesh_la_SOURCES = ../TriMesh/TriMesh.cpp\
                                                         ../TriMesh/TriMesh.h
 TriMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB)
+TriMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB) $(GSLLIB)
 TriMeshProcessRifts_la_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\
                                                                                         ../TriMeshProcessRifts/TriMeshProcessRifts.h
 TriMeshProcessRifts_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 #}}}
+TriMeshProcessRifts_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
+#}}}

issm/trunk/src/wrappers/matlab/io/CheckNumMatlabArguments.cpp

r13749	r15396
4	4
5	5	#include "./matlabio.h"
6		~~#include "../../c/shared/Exceptions/exceptions.h"~~
7	6
8	7	int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* THISFUNCTION, void (*function)( void )){

issm/trunk/src/wrappers/matlab/io/FetchMatlabData.cpp

-              r14067
+              r15396
 #include "./matlabio.h"
-#include "../../c/shared/shared.h"
 /*Primitive data types*/
 …
                 else{
                         if(!mxIsClass(dataref,"double") && !mxIsClass(dataref,"single")){
                                 _printLine_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'");
+                                _printf_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'\n");
+                        }
                         /*Convert matlab matrix to double* matrix: */
 …
                 else{
                         if(!mxIsClass(dataref,"double") && !mxIsClass(dataref,"single")){
                                 _printLine_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'");
+                                _printf_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'\n");
+                        }
                         /*Convert matlab n-dim array to double* matrix: */
 …
                 else{
                         if(!mxIsClass(dataref,"double") && !mxIsClass(dataref,"single")){
                                 _printLine_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'");
+                                _printf_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'\n");
+                        }
                         /*Convert matlab matrix to double* matrix: */
 …
+}
 /*}}}*/
 /*FUNCTION FetchData(DataSet** pcontours,const mxArray* dataref){{{*/
 void FetchData(DataSet** pcontours,const mxArray* dataref){
         int              numcontours,index,test1,test2;
+/*FUNCTION FetchData(Contours** pcontours,const mxArray* dataref){{{*/
+void FetchData(Contours** pcontours,const mxArray* dataref){
+        int             numcontours,index,test1,test2;
         char            *contourname = NULL;
         DataSet         *contours    = NULL;
+        Contours        *contours    = NULL;
         Contour<double> *contouri    = NULL;
         if (mxIsClass(dataref,"char")){
                 FetchData(&contourname,dataref);
                 contours=DomainOutlineRead<double>(contourname);
+                contours=ExpRead<double>(contourname);
+        }
         else if(mxIsClass(dataref,"struct")){
                 contours=new DataSet(0);
+                contours=new Contours();
                 numcontours=mxGetNumberOfElements(dataref);
                 for(int i=0;i<numcontours;i++){
                         contouri=xNew<Contour<double> >(1);
+                        contouri=new Contour<double>();
                         index = mxGetFieldNumber(dataref,"nods");

issm/trunk/src/wrappers/matlab/io/MatlabMatrixToDoubleMatrix.cpp

r13749	r15396
11	11	/Matlab includes: /
12	12	#include "./matlabio.h"
13		~~#include "../../c/shared/shared.h"~~
14	13
15	14	int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){

issm/trunk/src/wrappers/matlab/io/MatlabMatrixToMatrix.cpp

-              r13749
+              r15396
 #endif
-#include <stdio.h>
-#include <string.h>
 #include "./matlabio.h"
-#include "../../c/shared/shared.h"
-#include "../../c/toolkits/toolkits.h"
 Matrix<double>* MatlabMatrixToMatrix(const mxArray* mxmatrix){
 …
         matrix->pmatrix=MatlabMatrixToPetscMat(mxmatrix);
         #else
         matrix->smatrix=MatlabMatrixToSeqMat(mxmatrix);
+        matrix->imatrix=MatlabMatrixToIssmMat(mxmatrix);
         #endif

issm/trunk/src/wrappers/matlab/io/MatlabNArrayToNArray.cpp

r13749	r15396
10	10
11	11	#include "./matlabio.h"
12		~~#include "../../c/shared/shared.h"~~
13		~~#include "../../c/include/include.h"~~
14	12
15	13	/FUNCTION MatlabNArrayToNArray(double* pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{*/

issm/trunk/src/wrappers/matlab/io/MatlabVectorToDoubleVector.cpp

-              r13749
+              r15396
 #endif
-#include <string.h>
 /*Matlab includes: */
 #include "./matlabio.h"
-#include "../../c/shared/shared.h"
 int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){

issm/trunk/src/wrappers/matlab/io/MatlabVectorToPetscVec.cpp

-              r13749
+              r15396
 #endif
-/*Petsc includes: */
-#include <petscmat.h>
-#include <petscvec.h>
-#include <petscksp.h>
 /*Matlab includes: */
 #include "./matlabio.h"
-#include "../../c/shared/shared.h"
 PetscVec* MatlabVectorToPetscVec(const mxArray* mxvector){

issm/trunk/src/wrappers/matlab/io/MatlabVectorToVector.cpp

-              r13749
+              r15396
 #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
 #endif
-#include <stdio.h>
-#include <string.h>
 #include "./matlabio.h"
-#include "../../c/shared/shared.h"
-#include "../../c/toolkits/toolkits.h"
 Vector<double>* MatlabVectorToVector(const mxArray* mxvector){
 …
         vector->pvector=MatlabVectorToPetscVec(mxvector);
         #else
         vector->svector=MatlabVectorToSeqVec(mxvector);
+        vector->ivector=MatlabVectorToIssmVec(mxvector);
         #endif

issm/trunk/src/wrappers/matlab/io/OptionParse.cpp

-              r13749
+              r15396
 #include <cstring>
 #include "./matlabio.h"
-#include "../../c/shared/shared.h"
-#include "../../c/io/io.h"
 GenericOption<double>* OptionDoubleParse( char* name, const mxArray* prhs[]){ /*{{{*/
 …
          option=(Option*)OptionCellParse(name,prhs);
         else {
                 _pprintLine_("  Converting value of option \"" << name << "\" from unrecognized class \"" << mxGetClassName(prhs[0]) << "\" to class \"" << "struct" << "\".");
+                _printf0_("  Converting value of option \"" << name << "\" from unrecognized class \"" << mxGetClassName(prhs[0]) << "\" to class \"" << "struct" << "\".\n");
                 if (!mexCallMATLAB(1,lhs,1,(mxArray**)prhs,"struct")) {
                         option=(Option*)OptionStructParse(name,(const mxArray**)lhs);

issm/trunk/src/wrappers/matlab/io/WriteMatlabData.cpp

-              r14310
+              r15396
 #include "./matlabio.h"
 #include "../../c/shared/shared.h"
+#include "./../../../c/datastructures/datastructures.h"
 /*Primitive data types*/
 …
                 vector_matlab=(double*)mxMalloc(M*sizeof(double));
                 for(int i=0;i<M;i++) vector_matlab[i]=vector[i];
+                dataref = mxCreateDoubleMatrix(0,0,mxREAL);
+                mxSetM(dataref,(mwSize)M);
+                mxSetN(dataref,(mwSize)1);
+                mxSetPr(dataref,vector_matlab);
+        }
+        else{
+                dataref = mxCreateDoubleMatrix(0,0,mxREAL);
+        }
+        *pdataref=dataref;
+}
+/*}}}*/
+/*FUNCTION WriteData(mxArray** pdataref,int* vector, int M){{{*/
+void WriteData(mxArray** pdataref,int* vector, int M){
+        mxArray* dataref       = NULL;
+        double*  vector_matlab = NULL;
+        if(vector){
+                /*create the matlab vector with Matlab's memory manager */
+                vector_matlab=(double*)mxMalloc(M*sizeof(double));
+                for(int i=0;i<M;i++) vector_matlab[i]=double(vector[i]);
                 dataref = mxCreateDoubleMatrix(0,0,mxREAL);
                 mxSetM(dataref,(mwSize)M);
 …
+}
 /*}}}*/
 /*FUNCTION WriteData(mxArray** pdataref,SeqMat<double>* matrix){{{*/
 void WriteData(mxArray** pdataref,SeqMat<double>* matrix){
+/*FUNCTION WriteData(mxArray** pdataref,IssmDenseMat<double>* matrix){{{*/
+void WriteData(mxArray** pdataref,IssmDenseMat<double>* matrix){
         int      i,j;
 …
+}
 /*}}}*/
 /*FUNCTION WriteData(mxArray** pdataref,SeqVec<double>* vector){{{*/
 void WriteData(mxArray** pdataref,SeqVec<double>* vector){
+/*FUNCTION WriteData(mxArray** pdataref,IssmSeqVec<double>* vector){{{*/
+void WriteData(mxArray** pdataref,IssmSeqVec<double>* vector){
         mxArray* dataref=NULL;
 …
         /*Clean-up and return*/
         xDelete<double>(vector_ptr);
-        *pdataref=dataref;
+}
-/*}}}*/
-/*FUNCTION WriteData(mxArray** pdataref,SeqMat<int>* matrix){{{*/
-void WriteData(mxArray** pdataref,SeqMat<int>* matrix){
-        int      i,j;
-        int      rows,cols;
-        mxArray *dataref     = NULL;
-        int     *matrix_ptr  = NULL;
-        double  *tmatrix_ptr = NULL;
-        if(matrix){
-                matrix_ptr=matrix->ToSerial();
-                matrix->GetSize(&rows,&cols);
-                /*Now transpose the matrix and allocate with Matlab's memory manager: */
-                tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double));
-                for(i=0;i<rows;i++){
-                        for(j=0;j<cols;j++){
-                                tmatrix_ptr[j*rows+i]=(double)matrix_ptr[i*cols+j];
+                        }
+                }
-                /*create matlab matrix: */
-                dataref=mxCreateDoubleMatrix(0,0,mxREAL);
-                mxSetM(dataref,rows);
-                mxSetN(dataref,cols);
-                mxSetPr(dataref,tmatrix_ptr);
-                /*Free ressources:*/
-                xDelete<int>(matrix_ptr);
+        }
-        else{
-                dataref = mxCreateDoubleMatrix(0,0,mxREAL);
+        }
-        *pdataref=dataref;
+}
-/*}}}*/
-/*FUNCTION WriteData(mxArray** pdataref,SeqVec<int>* vector){{{*/
-void WriteData(mxArray** pdataref,SeqVec<int>* vector){
-        mxArray* dataref=NULL;
-        int*     vector_ptr=NULL;
-        double*  vector_matlab=NULL;
-        int      rows;
-        if(vector){
-                /*call toolkit routine: */
-                vector_ptr=vector->ToMPISerial();
-                vector->GetSize(&rows);
-                /*now create the matlab vector with Matlab's memory manager */
-                vector_matlab=(double*)mxMalloc(rows*sizeof(double));
-                for(int i=0;i<rows;i++) vector_matlab[i]=(double)vector_ptr[i];
-                dataref = mxCreateDoubleMatrix(0,0,mxREAL);
-                mxSetM(dataref,rows);
-                mxSetN(dataref,1);
-                mxSetPr(dataref,vector_matlab);
+        }
-        else{
-                dataref = mxCreateDoubleMatrix(0,0,mxREAL);
+        }
-        /*Clean-up and return*/
-        xDelete<int>(vector_ptr);
         *pdataref=dataref;
+}
 …
+}
 /*}}}*/
+/*FUNCTION WriteData(mxArray** pdataref,Contours* contours){{{*/
+void WriteData(mxArray** pdataref,Contours* contours){
+        /*Intermediary*/
+        int         i;
+        mxArray    *dataref           = NULL;
+        const int   numfields         = 6;
+        const char *fnames[numfields];
+        mwSize      ndim              = 2;
+        mwSize      dimensions[2]     = {1,1};
+        char        id[100];
+        /*Initialize field names*/
+        i=0;
+        fnames[i++] = "name";
+        fnames[i++] = "nods";
+        fnames[i++] = "density";
+        fnames[i++] = "x";
+        fnames[i++] = "y";
+        fnames[i++] = "closed";
+        _assert_(i==numfields);
+        /*Initialize matlab structure of dimension numrifts*/
+        dimensions[0]=contours->Size();
+        dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames);
+        /*set each matlab each field*/
+        for(int i=0;i<contours->Size();i++){
+                Contour<IssmPDouble>* contour=(Contour<IssmPDouble>*)contours->GetObjectByOffset(i);
+                /*create a name for this contour from the contour id and set it: */
+                sprintf(id,"%i",contour->id);
+                SetStructureFieldi(dataref,i,"name",id);
+                /*number of nods: */
+                SetStructureFieldi(dataref,i,"nods"         ,contour->nods);
+                /*density: */
+                SetStructureFieldi(dataref,i,"density"            ,1);
+                /*x and y: */
+                SetStructureFieldi(dataref,i,"x"             ,contour->nods, 1,contour->x);
+                SetStructureFieldi(dataref,i,"y"             ,contour->nods, 1,contour->y);
+                /*closed: */
+                SetStructureFieldi(dataref,i,"closed"         ,(int)contour->closed);
+        }
+        /*Assign output*/
+        *pdataref=dataref;
+}
+/*}}}*/
 /*Toolkit*/
 /*FUNCTION SetStructureField{{{*/
+/*FUNCTION SetStructureField(mxArray* dataref,const char* fieldname,int M,int N,double* fieldpointer){{{*/
 void SetStructureField(mxArray* dataref,const char* fieldname,int M,int N,double* fieldpointer){
 …
         /*Assign to structure*/
         mxSetField(dataref,0,fieldname,field);
+}
+/*}}}*/
+/*FUNCTION SetStructureFieldi(mxArray* dataref,const char* fieldname,char* string) {{{*/
+void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,char* string){
+        mxArray* field = NULL;
+        /*Convert field*/
+        WriteData(&field,string);
+        /*Assign to structure*/
+        mxSetField(dataref,i,fieldname,field);
+}
 /*}}}*/

issm/trunk/src/wrappers/matlab/io/matlabio.h

-              r14310
+              r15396
 #include "../include/matlabincludes.h"
+#include "../../c/classes/classes.h"
+#include "../../c/Container/Container.h"
+#include "../../c/include/include.h"
+#include "../../../c/bamg/bamgobjects.h"
+#include "../../../c/classes/classes.h"
+#include "../../../c/toolkits/toolkits.h"
+#include "../../../c/shared/shared.h"
+void WriteData(mxArray** pdataref,SeqMat<int>* matrix);
+void WriteData(mxArray** pdataref,SeqMat<double>* matrix);
+void WriteData(mxArray** pdataref,IssmDenseMat<double>* matrix);
 void WriteData(mxArray** pdataref,double* matrix, int M,int N);
 void WriteData(mxArray** pdataref,int*    matrix, int M,int N);
+void WriteData(mxArray** pdataref,SeqVec<int>* vector);
+void WriteData(mxArray** pdataref,SeqVec<double>* vector);
+void WriteData(mxArray** pdataref,IssmSeqVec<double>* vector);
 void WriteData(mxArray** pdataref,double* vector, int M);
+void WriteData(mxArray** pdataref,int* vector, int M);
 void WriteData(mxArray** pdataref,int integer);
 void WriteData(mxArray** pdataref,bool boolean);
 …
 void WriteData(mxArray** pdataref,BamgMesh* bamgmesh);
 void WriteData(mxArray** pdataref,RiftStruct* riftstruct);
+void WriteData(mxArray** pdataref,Contours* contours);
 void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref);
 …
 void FetchData(BamgOpts** bamgopts,const mxArray* dataref);
 void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref);
 void FetchData(DataSet** pcontours,const mxArray* dataref);
+void FetchData(Contours** pcontours,const mxArray* dataref);
 Option* OptionParse(char* name, const mxArray* prhs[]);
 …
 void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int field);
 void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,double field);
+void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,char* string);
 int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* THISFUNCTION, void (*function)( void ));
 …
 int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix);
 /*Matlab to SeqMat routines: */
 SeqMat<double>* MatlabMatrixToSeqMat(const mxArray* dataref);
 SeqVec<double>* MatlabVectorToSeqVec(const mxArray* dataref);
+/*Matlab to IssmDenseMat routines: */
+IssmMat<double>* MatlabMatrixToIssmMat(const mxArray* dataref);
+IssmVec<double>* MatlabVectorToIssmVec(const mxArray* dataref);
 /*Matlab to Petsc routines: */
 …
 #endif
+/*Print*/
+void ApiPrintf(const char* string);
 #endif  /* _IO_H_ */

issm/trunk/src/wrappers/python/Makefile.am

-              r13923
+              r15396
 lib_LTLIBRARIES = libISSMPython.la
 else
         lib_LTLIBRARIES =
+lib_LTLIBRARIES =
 endif
 …
 if SHAREDLIBS
 libISSMPython_la_SOURCES = $(io_sources)
+endif
+#}}}
+#api io{{{
+lib_LIBRARIES += libISSMApi.a
+if SHAREDLIBS
+lib_LTLIBRARIES += libISSMApi.la
+else
+lib_LTLIBRARIES +=
+endif
+api_sources= ./io/ApiPrintf.cpp
+libISSMApi_a_SOURCES = $(api_sources)
+libISSMApi_a_CXXFLAGS= $(ALLCXXFLAGS)
+if SHAREDLIBS
+libISSMApi_la_SOURCES = $(api_sources)
 endif
 #}}}
 …
 endif
+if SHAREDLIBS
+deps += ./libISSMApi.la
+else
+deps += ./libISSMApi.a
+endif
 endif
 …
 BamgConvertMesh_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp\
                                                                           ../BamgConvertMesh/BamgConvertMesh.h
 BamgConvertMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+BamgConvertMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 BamgMesher_la_SOURCES = ../BamgMesher/BamgMesher.cpp\
                                                                 ../BamgMesher/BamgMesher.h
 BamgMesher_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+BamgMesher_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 ContourToMesh_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp\
                                                                          ../ContourToMesh/ContourToMesh.h
 ContourToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+ContourToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 ContourToNodes_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp\
                                                                          ../ContourToNodes/ContourToNodes.h
 ContourToNodes_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+ContourToNodes_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 ElementConnectivity_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\
                                                                                         ../ElementConnectivity/ElementConnectivity.h
 ElementConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+ElementConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 EnumToString_la_SOURCES = ../EnumToString/EnumToString.cpp\
                                                                   ../EnumToString/EnumToString.h
 EnumToString_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+EnumToString_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 InterpFromMeshToMesh2d_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\
                                                                                                 ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h
 InterpFromMeshToMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+InterpFromMeshToMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB)
 InterpFromGridToMesh_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp\
                                                                                                 ../InterpFromGridToMesh/InterpFromGridToMesh.h
 InterpFromGridToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+InterpFromGridToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB)
 MeshProfileIntersection_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\
                                                                                 ../MeshProfileIntersection/MeshProfileIntersection.h
 MeshProfileIntersection_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+MeshProfileIntersection_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 NodeConnectivity_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\
                                                                                 ../NodeConnectivity/NodeConnectivity.h
 NodeConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+NodeConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 StringToEnum_la_SOURCES = ../StringToEnum/StringToEnum.cpp\
                                                                   ../StringToEnum/StringToEnum.h
 StringToEnum_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+StringToEnum_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 TriMesh_la_SOURCES = ../TriMesh/TriMesh.cpp\
                                                         ../TriMesh/TriMesh.h
 TriMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB)
+TriMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB) $(GSLLIB)
 TriMeshProcessRifts_la_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\
                                                                                         ../TriMeshProcessRifts/TriMeshProcessRifts.h
 TriMeshProcessRifts_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
+TriMeshProcessRifts_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB)
 #}}}

issm/trunk/src/wrappers/python/io/CheckNumPythonArguments.cpp

r13749	r15396
8	8	#include "./pythonio.h"
9	9	#include "../../c/shared/Exceptions/exceptions.h"
10		~~#include "../../c/include/include.h"~~
11	10
12	11	int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )){

issm/trunk/src/wrappers/python/io/FetchPythonData.cpp

-              r14310
+              r15396
 #include "./pythonio.h"
-#include "../../c/include/include.h"
 #include "../../c/shared/shared.h"
 …
         bool* bmatrix=NULL;
         int i;
+        PyObject* py_matrix2=NULL;
         if     (PyArray_Check((PyArrayObject*)py_matrix)) {
 …
                 if (M && N) {
+                        if (!PyArray_ISCONTIGUOUS((PyArrayObject*)py_matrix)) {
+                                py_matrix2=PyArray_ContiguousFromAny(py_matrix,NPY_DOUBLE,ndim,ndim);
+                                py_matrix=py_matrix2;
+                        }
                         if      (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_DOUBLE) {
                                 /*retrieve internal value: */
 …
                                 /*copy matrix: */
                                 matrix=xNew<double>(M*N);
+                                memcpy(matrix,dmatrix,(M*N)*sizeof(double));
+                        }
+                        else if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_INT64) {
+//                              if (PyArray_ISCONTIGUOUS((PyArrayObject*)py_matrix)) {
+                                        memcpy(matrix,dmatrix,(M*N)*sizeof(double));
+//                              }
+//                              else {
+//                                      int j,k,ipt=0;
+//                                      int mstride,nstride;
+//                                      mstride=(int)PyArray_STRIDE((PyArrayObject*)py_matrix,0)/PyArray_ITEMSIZE((PyArrayObject*)py_matrix);
+//                                      if (ndim > 1)
+//                                              nstride=(int)PyArray_STRIDE((PyArrayObject*)py_matrix,1)/PyArray_ITEMSIZE((PyArrayObject*)py_matrix);
+//                                      else
+//                                              nstride=1;
+//                                      for (i=0; i<M; i++) {
+//                                              k=i*mstride;
+//                                              for (j=0; j<N; j++) {
+//                                                      matrix[ipt++]=dmatrix[k];
+//                                                      k+=nstride;
+//                                              }
+//                                      }
+//                              }
+                        }
+                        else if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_LONG) {
                                 /*retrieve internal value: */
                                 lmatrix=(long*)PyArray_DATA((PyArrayObject*)py_matrix);
 …
                         else
                                 _error_("unrecognized double pyarray type in input!");
+                        if (py_matrix2)
+                                delete(py_matrix2);
+                }
                 else
 …
         bool* bmatrix=NULL;
         int i;
+        PyObject* py_matrix2=NULL;
         if     (PyArray_Check((PyArrayObject*)py_matrix)) {
 …
                 if (M && N) {
+                        if (!PyArray_ISCONTIGUOUS((PyArrayObject*)py_matrix)) {
+                                py_matrix2=PyArray_ContiguousFromAny(py_matrix,NPY_LONG,ndim,ndim);
+                                py_matrix=py_matrix2;
+                        }
                         if      (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_DOUBLE) {
                                 /*retrieve internal value: */
 …
+                        }
                         else if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_INT64) {
+                        else if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_LONG) {
                                 /*retrieve internal value: */
                                 lmatrix=(long*)PyArray_DATA((PyArrayObject*)py_matrix);
 …
                         else
                                 _error_("unrecognized int pyarray type in input!");
+                        if (py_matrix2)
+                                delete(py_matrix2);
+                }
                 else
 …
         long* lmatrix=NULL;
         int i;
+        PyObject* py_matrix2=NULL;
         if     (PyArray_Check((PyArrayObject*)py_matrix)) {
 …
                 if (M && N) {
+                        if (!PyArray_ISCONTIGUOUS((PyArrayObject*)py_matrix)) {
+                                py_matrix2=PyArray_ContiguousFromAny(py_matrix,NPY_BOOL,ndim,ndim);
+                                py_matrix=py_matrix2;
+                        }
                         if      (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_DOUBLE) {
                                 /*retrieve internal value: */
 …
+                        }
                         else if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_INT64) {
+                        else if (PyArray_TYPE((PyArrayObject*)py_matrix) == NPY_LONG) {
                                 /*retrieve internal value: */
                                 lmatrix=(long*)PyArray_DATA((PyArrayObject*)py_matrix);
 …
                         else
                                 _error_("unrecognized bool pyarray type in input!");
+                        if (py_matrix2)
+                                delete(py_matrix2);
+                }
                 else
 …
         bool* bvector=NULL;
         int i;
+        PyObject* py_vector2=NULL;
         if     (PyArray_Check((PyArrayObject*)py_vector)) {
 …
                 if (M) {
+                        if (!PyArray_ISCONTIGUOUS((PyArrayObject*)py_vector)) {
+                                py_vector2=PyArray_ContiguousFromAny(py_vector,NPY_DOUBLE,ndim,ndim);
+                                py_vector=py_vector2;
+                        }
                         if      (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_DOUBLE) {
                                 /*retrieve internal value: */
 …
+                        }
                         else if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_INT64) {
+                        else if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_LONG) {
                                 /*retrieve internal value: */
                                 lvector=(long*)PyArray_DATA((PyArrayObject*)py_vector);
 …
                         else
                                 _error_("unrecognized double pyarray type in input!");
+                        if (py_vector2)
+                                delete(py_vector2);
+                }
                 else
 …
         double* dvector=NULL;
         int i;
+        PyObject* py_vector2=NULL;
         if     (PyArray_Check((PyArrayObject*)py_vector)) {
 …
                 if (M) {
+                        if (!PyArray_ISCONTIGUOUS((PyArrayObject*)py_vector)) {
+                                py_vector2=PyArray_ContiguousFromAny(py_vector,NPY_LONG,ndim,ndim);
+                                py_vector=py_vector2;
+                        }
                         if      (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_DOUBLE) {
                                 /*retrieve internal value: */
 …
+                        }
                         else if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_INT64) {
+                        else if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_LONG) {
                                 /*retrieve internal value: */
                                 lvector=(long*)PyArray_DATA((PyArrayObject*)py_vector);
 …
                         else
                          _error_("unrecognized int pyarray type in input!");
+                        if (py_vector2)
+                                delete(py_vector2);
+                }
                 else
 …
         long* lvector=NULL;
         int i;
+        PyObject* py_vector2=NULL;
         if     (PyArray_Check((PyArrayObject*)py_vector)) {
 …
                 if (M) {
+                        if (!PyArray_ISCONTIGUOUS((PyArrayObject*)py_vector)) {
+                                py_vector2=PyArray_ContiguousFromAny(py_vector,NPY_BOOL,ndim,ndim);
+                                py_vector=py_vector2;
+                        }
                         if      (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_DOUBLE) {
                                 /*retrieve internal value: */
 …
+                        }
                         else if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_INT64) {
+                        else if (PyArray_TYPE((PyArrayObject*)py_vector) == NPY_LONG) {
                                 /*retrieve internal value: */
                                 lvector=(long*)PyArray_DATA((PyArrayObject*)py_vector);
 …
                         else
                                 _error_("unrecognized bool pyarray type in input!");
+                        if (py_vector2)
+                                delete(py_vector2);
+                }
                 else
 …
                 if(i+1 == nrhs) _error_("Argument " << i+2 << " must exist and be value of option \"" << name << "\".");
                 _pprintLine_("FetchData for Options not implemented yet, ignoring option \"" << name << "\"!");
+                _printf0_("FetchData for Options not implemented yet, ignoring option \"" << name << "\"!\n");
 //              option=(Option*)OptionParse(name,&PyTuple_GetItem(py_tuple,(Py_ssize_t)(i+1)));
 …
+}
 /*}}}*/
 /*FUNCTION FetchData(DataSet** pcontours,PyObject* py_list){{{*/
 void FetchData(DataSet** pcontours,PyObject* py_list){
+/*FUNCTION FetchData(Contours** pcontours,PyObject* py_list){{{*/
+void FetchData(Contours** pcontours,PyObject* py_list){
         int              numcontours,test1,test2;
         char            *contourname = NULL;
         DataSet         *contours    = NULL;
+        Contours         *contours    = NULL;
         Contour<double> *contouri    = NULL;
         PyObject        *py_dicti    = NULL;
 …
         if (PyString_Check(py_list)){
                 FetchData(&contourname,py_list);
                 contours=DomainOutlineRead<double>(contourname);
+                contours=ExpRead<double>(contourname);
+        }
         else if(PyList_Check(py_list)){
                 contours=new DataSet(0);
+                contours=new Contours();
                 numcontours=(int)PyList_Size(py_list);
                 for(int i=0;i<numcontours;i++){
                         contouri=xNew<Contour<double> >(1);
+                        contouri=new Contour<double>();
                         py_dicti=PyList_GetItem(py_list,(Py_ssize_t)i);

issm/trunk/src/wrappers/python/io/WritePythonData.cpp

-              r14310
+              r15396
 #include "./pythonio.h"
-#include "../../c/include/include.h"
-#include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
 #include "../../c/EnumDefinitions/EnumDefinitions.h"
+#include "../../c/shared/Enum/Enum.h"
 /*Primitive data types*/
 …
         PyTuple_SetItem(tuple, index, array);
+}/*}}}*/
+/*FUNCTION WriteData(PyObject* py_tuple,int index, double* vector, int M){{{*/
+void WriteData(PyObject* py_tuple, int index, double* vector, int M){
+        double   *buffer = NULL;
+        npy_intp  dim   = 10;
+        PyObject *array = NULL;
+        /*Copy vector*/
+        buffer=xNew<double>(M);
+        for(int i=0;i<M;i++)buffer[i]=vector[i];
+        dim=(npy_intp)M;
+        array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer);
+        PyTuple_SetItem(py_tuple, index, array);
+}/*}}}*/
+/*FUNCTION WriteData(PyObject* py_tuple,int index, int* vector, int M){{{*/
+void WriteData(PyObject* py_tuple, int index, int* vector, int M){
+        long* lvector=NULL;
+        npy_intp dim=10;
+        PyObject* array=NULL;
+        /*transform into long matrix: */
+        lvector=xNew<long>(M);
+        for(int i=0;i<M;i++)lvector[i]=(long)vector[i];
+        dim=(npy_intp)M;
+        array=PyArray_SimpleNewFromData(1,&dim,NPY_INT64,lvector);
+        PyTuple_SetItem(py_tuple, index, array);
 }/*}}}*/
 /*FUNCTION WriteData(PyObject* py_tuple,int index){{{*/
 …
+}
 /*}}}*/
 /*FUNCTION WriteData(PyObject* py_tuple,int index,SeqMat<double>* matrix){{{*/
 void WriteData(PyObject* py_tuple,int index,SeqMat<double>* matrix){
+/*FUNCTION WriteData(PyObject* py_tuple,int index,IssmDenseMat<double>* matrix){{{*/
+void WriteData(PyObject* py_tuple,int index,IssmDenseMat<double>* matrix){
         int M,N;
 …
 }/*}}}*/
 /*FUNCTION WriteData(PyObject* py_tuple,int index,SeqVec<double>* vector){{{*/
 void WriteData(PyObject* py_tuple,int index,SeqVec<double>* vector){
+/*FUNCTION WriteData(PyObject* py_tuple,int index,IssmSeqVec<double>* vector){{{*/
+void WriteData(PyObject* py_tuple,int index,IssmSeqVec<double>* vector){
         int M;
 …
         dim=(npy_intp)M;
         array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer);
-        PyTuple_SetItem(py_tuple, index, array);
+}
-/*}}}*/
-/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqMat<int>* matrix){{{*/
-void WriteData(PyObject* py_tuple,int index,SeqMat<int>* matrix){
-        int M,N;
-        int* ibuffer=NULL;
-        npy_intp dims[2]={0,0};
-        PyObject* array=NULL;
-        matrix->GetSize(&M,&N);
-        ibuffer=matrix->ToSerial();
-        /*convert to long*/
-        long* lbuffer=xNew<long>(M*N);
-        for(int i=0;i<M*N;i++) lbuffer[i]=(long)ibuffer[i];
-        xDelete<int>(ibuffer);
-        dims[0]=(npy_intp)M;
-        dims[1]=(npy_intp)N;
-        array=PyArray_SimpleNewFromData(2,dims,NPY_INT64,lbuffer);
-        PyTuple_SetItem(py_tuple, index, array);
-}/*}}}*/
-/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqVec<int>* vector){{{*/
-void WriteData(PyObject* py_tuple,int index,SeqVec<int>* vector){
-        int M;
-        int* ibuffer=NULL;
-        npy_intp dim=10;
-        PyObject* array=NULL;
-        vector->GetSize(&M);
-        ibuffer=vector->ToMPISerial();
-        /*convert to long*/
-        long* lbuffer=xNew<long>(M);
-        for(int i=0;i<M;i++) lbuffer[i]=(long)ibuffer[i];
-        xDelete<int>(ibuffer);
-        dim=(npy_intp)M;
-        array=PyArray_SimpleNewFromData(1,&dim,NPY_INT64,lbuffer);
-        PyTuple_SetItem(py_tuple, index, array);
+}
-/*}}}*/
-/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqMat<bool>* matrix){{{*/
-void WriteData(PyObject* py_tuple,int index,SeqMat<bool>* matrix){
-        int M,N;
-        bool* buffer=NULL;
-        npy_intp dims[2]={0,0};
-        PyObject* array=NULL;
-        matrix->GetSize(&M,&N);
-        buffer=matrix->ToSerial();
-        dims[0]=(npy_intp)M;
-        dims[1]=(npy_intp)N;
-        array=PyArray_SimpleNewFromData(2,dims,NPY_BOOL,buffer);
-        PyTuple_SetItem(py_tuple, index, array);
-}/*}}}*/
-/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqVec<bool>* vector){{{*/
-void WriteData(PyObject* py_tuple,int index,SeqVec<bool>* vector){
-        int M;
-        bool* buffer=NULL;
-        npy_intp dim=10;
-        PyObject* array=NULL;
-        vector->GetSize(&M);
-        buffer=vector->ToMPISerial();
-        dim=(npy_intp)M;
-        array=PyArray_SimpleNewFromData(1,&dim,NPY_BOOL,buffer);
         PyTuple_SetItem(py_tuple, index, array);

issm/trunk/src/wrappers/python/io/pythonio.h

-              r14310
+              r15396
 #include "../include/pythonincludes.h"
+#include "../../c/bamg/bamgobjects.h"
 #include "../../c/classes/classes.h"
+#include "../../c/Container/Container.h"
+#include "../../c/include/include.h"
+#include "../../c/shared/shared.h"
 void WriteData(PyObject* py_tuple,int index, double* matrix, int M,int N);
 …
 void WriteData(PyObject* py_tuple,int index, bool* matrix, int M,int N);
 void WriteData(PyObject* py_tuple,int index, int integer);
+void WriteData(PyObject* py_tuple,int index, double* vector, int M);
+void WriteData(PyObject* py_tuple,int index, int* vector, int M);
 void WriteData(PyObject* py_tuple,int index, char* string);
 void WriteData(PyObject* py_tuple,int index);
+void WriteData(PyObject* py_tuple,int index, SeqMat<double>* matrix);
+void WriteData(PyObject* py_tuple,int index, SeqVec<double>* vector);
+void WriteData(PyObject* py_tuple,int index, SeqMat<int>* matrix);
+void WriteData(PyObject* py_tuple,int index, SeqVec<int>* vector);
+void WriteData(PyObject* py_tuple,int index, SeqMat<bool>* matrix);
+void WriteData(PyObject* py_tuple,int index, SeqVec<bool>* vector);
+void WriteData(PyObject* py_tuple,int index, IssmDenseMat<double>* matrix);
+void WriteData(PyObject* py_tuple,int index, IssmSeqVec<double>* vector);
 void WriteData(PyObject* py_tuple,int index, BamgGeom* bamggeom);
 void WriteData(PyObject* py_tuple,int index, BamgMesh* bamgmesh);
 …
 void FetchData(BamgOpts** bamgopts,PyObject* py_dict);
 void FetchData(Options** poptions,int istart, int nrhs,PyObject* py_tuple);
 void FetchData(DataSet** pcontours,PyObject* py_list);
+void FetchData(Contours** pcontours,PyObject* py_list);
 int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void ));
 …
 PyObject* PyArrayFromCopiedData(int dimi,int dimj,bool* data);
+/*Print*/
+void ApiPrintf(const char* string);
 #endif  /* _IO_H_ */

issm/trunk/test

Property svn:mergeinfo changed

/issm/trunk-jpl/test

merged: 14311,14318,14371,14407,14430-14432,14505,14534-14535,14537-14539,14541-14542,14548,14550,14552,14554,14557,14565,14568,14586,14588-14590,14593,14595-14596,14599-14600,14604,14614,14650,14653,14658,14667,14676-14677,14702,14721,14724-14725,14727,14729-14730,14732-14734,14740,14746-14749,14756,14759,14762,14766,14772,14781,14803,14805,14815-14816,14818-14821,14826,14831-14832,14842-14843,14847-14856,14879,14902,14924-14925,14940,14942-14948,14973,15018-15019,15027,15059,15076,15078,15080,15084,15092,15138,15154,15156-15157,15162,15184,15187-15188,15191,15227,15233,15236,15242,15285,15311,15332,15359-15364

issm/trunk/test/NightlyRun

Property svn:ignore

old	new
	1	*.toolkits
1	2	__pycache__
2	3	*.tar.gz

issm/trunk/test/NightlyRun/IdToName.m

-              r13395
+              r15396
         case 328, name='SquareSheetConstrainedSmbGradients2d';
         case 329, name='SquareSheetConstrainedSmbGradients3d';
+        case 331, name='SquareSheetConstrainedHydrologyShreve';
+        case 332, name='SquareSheetConstrainedHydrologyDC';
+        case 333, name='SquareSheetHydrologyDCTwoLayers';
         case 401, name='SquareSheetShelfDiagM2d';
         case 402, name='SquareSheetShelfDiagM3d';
 …
         case 431, name='SquareSheetShelfSteaEnthalpyM3d';
         case 432, name='SquareSheetShelfSteaEnthalpyP3d';
+        case 433, name='RoundSheetShelfGLMigrationM3d';
         case 501, name='PigDiagM2d';
         case 502, name='PigDiagP3d';
 …
         case 1601, name='SquareShelfM2dRotation';
         case 1602, name='SquareSheetShelfP3dRotation';
+        case 2001, name='SquareSheetConstrainedGia2d';
+        case 2051, name='GiaBenchmarksAB2dA1';
+        case 2052, name='GiaBenchmarksAB2dA2';
+        case 2053, name='GiaBenchmarksAB2dA3';
+        case 2061, name='GiaBenchmarksAB2dB1';
+        case 2062, name='GiaBenchmarksAB2dB2';
+        case 2063, name='GiaBenchmarksAB2dB3';
+        case 2071, name='GiaBenchmarksAB2dC1';
+        case 2072, name='GiaBenchmarksAB2dC2';
+        case 2073, name='GiaBenchmarksAB2dC3';
+        case 2081, name='GiaBenchmarksAB2dD1';
+        case 2082, name='GiaBenchmarksAB2dD2';
+        case 2083, name='GiaBenchmarksAB2dD3';
         case 3001, name='SquareShelfConstrainedDiagM2dAdolc';
         case 3002, name='SquareShelfConstrainedDiagM3dAdolc';
 …
         case 3009, name='SquareShelfConstrainedTherTranAdolc';
         case 3010, name='SquareShelfConstrainedTranM2dAdolc';
+        case 3015, name='SquareShelfConstrainedProg2dAdolcForwardDifference';
+        case 3019, name='SquareShelfConstrainedTherTranAdolcReverseVsForward';
         otherwise, name='N/A';

issm/trunk/test/NightlyRun/IdToName.py

-              r13395
+              r15396
 : 'SquareSheetConstrainedSmbGradients2d',
 : 'SquareSheetConstrainedSmbGradients3d',
+: 'SquareSheetConstrainedHydrology',
+: 'SquareSheetConstrainedTranCflM3d',
 : 'SquareSheetShelfDiagM2d',
 : 'SquareSheetShelfDiagM3d',
 …
 : 'SquareSheetShelfGroundingLine3dSoft',
 : 'SquareSheetShelfDiagM2dNewton',
 : 'SquareSheetShelfDiagP3dNewton',
+: 'SquareSheetShelfDiagP3dNewton',
 : 'SquareSheetShelfDiagS3dNewton',
 : 'SquareSheetShelfSteaEnthalpyM3d',
 : 'SquareSheetShelfSteaEnthalpyP3d',
+: 'RoundSheetShelfGLMigrationM3d',
 : 'PigDiagM2d',
 : 'PigDiagP3d',
 …
 : 'SquareShelfM2dRotation',
 : 'SquareSheetShelfP3dRotation',
+: 'SquareSheetConstrainedGia2d',
 : 'SquareShelfConstrainedDiagM2dAdolc',
 : 'SquareShelfConstrainedDiagM3dAdolc',
 …
 : 'SquareShelfConstrainedTherTranAdolc',
 : 'SquareShelfConstrainedTranM2dAdolc',
+: 'SquareShelfConstrainedProg2dAdolcForwardDifference',
+: 'SquareShelfConstrainedTherTranAdolcReverseVsForward',
+        }

issm/trunk/test/NightlyRun/Makefile

r13395	r15396
1	1	clean:
2		rm -rf .tar.gz .bin .errlog .outlog .outbin .petsc .queue .run valgrind.log* .bat .lock qmu*
	2	rm -rf .tar.gz .bin .errlog .outlog .outbin .petsc .queue .toolkits .run valgrind.log .bat .lock qmu*

issm/trunk/test/NightlyRun/android.m

r14310	r15396
1		md=triangle(model(),'../Exp/Square.exp',100000.);
	1	md=triangle(model(),'../Exp/Square.exp',40000.);
2	2	md=setmask(md,'all','');
3	3	md=parameterize(md,'../Par/SquareShelfConstrained.par');

issm/trunk/test/NightlyRun/runme.m

-              r14310
+              r15396
 %      'id'            followed by the list of ids requested
 %      'exclude'       ids to be excluded from the test
+%      'benchmark'     'nightly' (nightly run/ daily run)
+%      'benchmark'     'all' (all of them)
+%                      'nightly' (nightly run/ daily run)
 %                      'ismip'  : validation of ismip-hom tests
 %                      'eismint': validation of eismint tests
 …
 %                      'mesh'   : validation of mesh tests
 %                      'adolc'   : validation of adolc tests
+%                      'gia'   : validation of gia tests
 %                      ...
 %      'procedure'     'check' : run the test (default)
 %                      'update': update the archive
-%                      'model' : prepare the model but no test is run
+%
 %   Usage:
 %      md=runme(varargin);
+%      runme(varargin);
+%
 %   Examples:
 %      runme;
 %      runme('exclude',101);
 %      md=runme('id',102,'procedure','model');
+%      runme('id',102,'procedure','update');
 %Get ISSM_DIR variable
 …
 %GET benchmark {{{
 benchmark=getfieldvalue(options,'benchmark','nightly');
 if ~ismember(benchmark,{'all','nightly','ismip','eismint','thermal','mesh','validation','tranforcing','adolc'})
+if ~ismember(benchmark,{'all','nightly','ismip','eismint','thermal','mesh','validation','tranforcing','adolc','gia'})
         disp('runme warning: benchmark not supported, defaulting to test ''nightly''')
         benchmark='nightly';
 …
 elseif strcmpi(benchmark,'referential'),
         test_ids=intersect(test_ids,[1601:1602]);
+elseif strcmpi(benchmark,'gia'),
+        test_ids=intersect(test_ids,[2001:2100]);
 elseif strcmpi(benchmark,'adolc'),
         test_ids=intersect(test_ids,[3001:3020]);
 …
         end
 end
-%output md if requested
-if nargout==1
-        varargout{1}=md;
-end

issm/trunk/test/NightlyRun/runme.py

-              r14067
+              r15396
                'id'            followed by the list of ids requested
                'exclude'       ids to be excluded from the test
+               'benchmark'     'nightly' (nightly run/ daily run)
+               'benchmark'     'all' (all of the tests)
+                                   'nightly' (nightly run/ daily run)
                                'ismip'  : validation of ismip-hom tests
                                'eismint': validation of eismint tests
                                'thermal': validation of thermal tests
                                'mesh'   : validation of mesh tests
+                                                   'adolc'   : validation of adolc tests
+                           'gia'   : validation of gia tests
                                ...
                'procedure'     'check' : run the test (default)
 …
             Usage:
                md=runme(varargin);
+               runme(varargin);
             Examples:
                runme()
                runme(exclude=101)
                md=runme(id=102,procedure='update')
+               runme(id=102,procedure='update')
         """
 …
         #Process options
         #GET benchmark {{{
         if not ismember(benchmark,['all','nightly','ismip','eismint','thermal','mesh','validation','tranforcing','adolc']):
+        if not ismember(benchmark,['all','nightly','ismip','eismint','thermal','mesh','validation','tranforcing','adolc','gia']):
                 print "runme warning: benchmark '%s' not supported, defaulting to test 'nightly'." % benchmark
                 benchmark='nightly'
 …
         elif strcmpi(benchmark,'referential'):
                 test_ids=test_ids.intersection(set(range(1601,1603)))
+        elif strcmpi(benchmark,'gia'):
+                test_ids=test_ids.intersection(set(range(2001,2100)))
         elif strcmpi(benchmark,'adolc'):
                 test_ids=test_ids.intersection(set(range(3001,3020)))
 …
                                                 else:
                                                         field=field.reshape(0,0)
+                                        elif len(field.shape) == 0:
+                                                field=field.reshape(1,1)
                                         # Matlab uses base 1, so use base 1 in labels
                                         f.createDimension(archive_name+'_field'+str(k+1)+'_1',numpy.size(field,0))
 …
                                 raise RuntimeError(me)
-#       #output md if requested
-#       if nargout==1
-#               varargout{1}=md;
-#       end
         return

issm/trunk/test/NightlyRun/test111.m

-              r13975
+              r15396
 field_tolerances={...
 e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-13,...
 e-09,1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,2e-11,...
 e-09,1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-11};
+e-09,1e-08,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,2e-11,...
+e-09,1e-08,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-11};
 field_values={...
         (md.results.TransientSolution(1).Vx),...

issm/trunk/test/NightlyRun/test111.py

-              r13975
+              r15396
 field_tolerances=[\
 e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-13,\
 e-09,1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,2e-11,\
 e-09,1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-11]
+e-09,1e-08,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,2e-11,\
+e-09,1e-08,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-11]
 field_values=[\
         md.results.TransientSolution[0].Vx,\

issm/trunk/test/NightlyRun/test1110.m

r14310	r15396
54	54	md.prognostic.stabilization=1;
55	55	md.diagnostic.maxiter=1;
56
	56
57	57	%Compute the diagnostic
58	58	md.cluster=generic('name',oshostname(),'np',8);

issm/trunk/test/NightlyRun/test119.m

r13975	r15396
18	18	%Fields and tolerances to track changes
19	19	field_names ={'x1','y1','x2','y2','nbelements','elapsed time'};
20		field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,0.7};
	20	field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,0.8};
21	21	field_values={...
22	22	x1, y1,...

issm/trunk/test/NightlyRun/test119.py

r13975	r15396
23	23	#Fields and tolerances to track changes
24	24	field_names =['x1','y1','x2','y2','nbelements','elapsed time']
25		field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,0.7]
	25	field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,0.8]
26	26	field_values=[\
27	27	x1, y1,\

issm/trunk/test/NightlyRun/test234.m

-              r14310
+              r15396
 md.qmu.method=dakota_method('nond_samp');
 md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),'seed',1234,'samples',20,'sample_type','lhs');
+if (str2num(dakotaversion())>4.2)
+dver=textscan(dakotaversion(),'%[0123456789].%[0123456789].%[0123456789]')
+if ((str2num(dver{1}{1})==4 && str2num(dver{2}{1})>2) || str2num(dver{1}{1})>4)
         md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),'rng','rnum2')
 end
 …
 md.qmu.params.evaluation_concurrency=1;
 md.qmu.params.interval_type='forward';
+md.qmu.params.tabular_graphics_data=true;
 md.qmu.isdakota=1;

issm/trunk/test/NightlyRun/test3001.m

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.par');
 md=setflowequation(md,'macayeal','all');
+md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
+md.toolkits.DefaultAnalysis=issmsolver();
 md.diagnostic.requested_outputs=StressTensorEnum();
 md.autodiff.isautodiff=true;
+md.toolkits.DefaultAnalysis=issmsolver();
 md.verbose=verbose('autodiff',true);
 md=solve(md,DiagnosticSolutionEnum());

issm/trunk/test/NightlyRun/test3001.py

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.py')
 md=setflowequation(md,'macayeal','all')
 md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
 md.diagnostic.requested_outputs=StressTensorEnum()
+md.toolkits.DefaultAnalysis=issmsolver()
 md.autodiff.isautodiff=True
 md=solve(md,DiagnosticSolutionEnum())

issm/trunk/test/NightlyRun/test3002.m

-              r13975
+              r15396
 md=extrude(md,3,2.);
 md=setflowequation(md,'macayeal','all');
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.autodiff.isautodiff=true;
+md.toolkits.DefaultAnalysis=issmsolver();
 md.verbose=verbose('autodiff',true);
 md=solve(md,DiagnosticSolutionEnum());

issm/trunk/test/NightlyRun/test3002.py

-              r13975
+              r15396
 md.extrude(3,2.)
 md=setflowequation(md,'macayeal','all')
 md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
 md.autodiff.isautodiff=True
+md.toolkits.DefaultAnalysis=issmsolver()
 md=solve(md,DiagnosticSolutionEnum())

issm/trunk/test/NightlyRun/test3003.m

-              r13975
+              r15396
 md=extrude(md,3,2.);
 md=setflowequation(md,'pattyn','all');
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.diagnostic.requested_outputs=StressTensorEnum();
 md.autodiff.isautodiff=true;
+md.toolkits.DefaultAnalysis=issmsolver();
 md.verbose=verbose('autodiff',true);
 md=solve(md,DiagnosticSolutionEnum());

issm/trunk/test/NightlyRun/test3003.py

-              r13975
+              r15396
 md.extrude(3,2.)
 md=setflowequation(md,'pattyn','all')
 md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
 md.diagnostic.requested_outputs=StressTensorEnum()
+md.toolkits.DefaultAnalysis=issmsolver()
 md.autodiff.isautodiff=True
 md=solve(md,DiagnosticSolutionEnum())

issm/trunk/test/NightlyRun/test3004.m

-              r13975
+              r15396
 md=extrude(md,3,2.);
 md=setflowequation(md,'stokes','all');
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.autodiff.isautodiff=true;
+md.toolkits.DefaultAnalysis=issmsolver();
 md.verbose=verbose('autodiff',true);
 md=solve(md,DiagnosticSolutionEnum());

issm/trunk/test/NightlyRun/test3004.py

-              r13975
+              r15396
 md.extrude(3,2.)
 md=setflowequation(md,'stokes','all')
+md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
+md.toolkits.DefaultAnalysis=issmsolver()
 md.autodiff.isautodiff=True
 md=solve(md,DiagnosticSolutionEnum())

issm/trunk/test/NightlyRun/test3005.m

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.par');
 md=setflowequation(md,'macayeal','all');
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.autodiff.isautodiff=true;
+md.toolkits.DefaultAnalysis=issmsolver();
 md.verbose=verbose('autodiff',true);
 md=solve(md,PrognosticSolutionEnum());

issm/trunk/test/NightlyRun/test3005.py

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.py')
 md=setflowequation(md,'macayeal','all')
+md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
+md.toolkits.DefaultAnalysis=issmsolver()
 md.autodiff.isautodiff=True
 md=solve(md,PrognosticSolutionEnum())

issm/trunk/test/NightlyRun/test3006.m

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.par');
 md=setflowequation(md,'macayeal','all');
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.prognostic.stabilization=3;
 md.prognostic.spcthickness=md.geometry.thickness;
 md.autodiff.isautodiff=true;
+md.toolkits.DefaultAnalysis=issmsolver();
 md.verbose=verbose('autodiff',true);
 md=solve(md,PrognosticSolutionEnum());

issm/trunk/test/NightlyRun/test3006.py

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.py')
 md=setflowequation(md,'macayeal','all')
 md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
 md.prognostic.stabilization=3
 md.prognostic.spcthickness=md.geometry.thickness
+md.toolkits.DefaultAnalysis=issmsolver()
 md.autodiff.isautodiff=True
 md=solve(md,PrognosticSolutionEnum())

issm/trunk/test/NightlyRun/test3007.m

-              r13975
+              r15396
 md=setflowequation(md,'macayeal','all');
 md=extrude(md,5,3.);
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.autodiff.isautodiff=true;
 md.verbose=verbose('autodiff',true);
+md.toolkits.DefaultAnalysis=issmsolver();
 md=solve(md,PrognosticSolutionEnum());

issm/trunk/test/NightlyRun/test3007.py

-              r13975
+              r15396
 md=setflowequation(md,'macayeal','all')
 md.extrude(5,3.)
+md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
+md.toolkits.DefaultAnalysis=issmsolver()
 md.autodiff.isautodiff=True
 md=solve(md,PrognosticSolutionEnum())

issm/trunk/test/NightlyRun/test3008.m

-              r13975
+              r15396
 md=setflowequation(md,'macayeal','all');
 md.timestepping.time_step=0;
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.autodiff.isautodiff=true;
 md.verbose=verbose('autodiff',true);
+md.toolkits.DefaultAnalysis=issmsolver();
 md=solve(md,ThermalSolutionEnum());

issm/trunk/test/NightlyRun/test3008.py

-              r13975
+              r15396
 md=setflowequation(md,'macayeal','all')
 md.timestepping.time_step=0
+md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
+md.toolkits.DefaultAnalysis=issmsolver()
 md.autodiff.isautodiff=True
 md=solve(md,ThermalSolutionEnum())

issm/trunk/test/NightlyRun/test3009.m

-              r13975
+              r15396
 md=extrude(md,3,1.);
 md=setflowequation(md,'macayeal','all');
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.transient.isdiagnostic=0;
 md.transient.isprognostic=0;
 …
 md.autodiff.isautodiff=true;
 md.verbose=verbose('autodiff',true);
+md.toolkits.DefaultAnalysis=issmsolver();
 md=solve(md,TransientSolutionEnum());

issm/trunk/test/NightlyRun/test3009.py

-              r14067
+              r15396
 md.extrude(3,1.)
 md=setflowequation(md,'macayeal','all')
 md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
 md.transient.isdiagnostic=False
 md.transient.isprognostic=False
 md.transient.isthermal=True
 md.transient.isgroundingline=False
+md.toolkits.DefaultAnalysis=issmsolver()
 md.autodiff.isautodiff=True
 md=solve(md,TransientSolutionEnum())

issm/trunk/test/NightlyRun/test3010.m

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.par');
 md=setflowequation(md,'macayeal','all');
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.transient.requested_outputs=IceVolumeEnum();
 md.autodiff.isautodiff=true;
 md.verbose=verbose('autodiff',true);
+md.toolkits.DefaultAnalysis=issmsolver();
 md=solve(md,TransientSolutionEnum());

issm/trunk/test/NightlyRun/test3010.py

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.py')
 md=setflowequation(md,'macayeal','all')
+md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
+md.toolkits.DefaultAnalysis=issmsolver()
 md.transient.requested_outputs=IceVolumeEnum()

issm/trunk/test/NightlyRun/test3015.m

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.par');
 md=setflowequation(md,'macayeal','all');
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.prognostic.requested_outputs=IceVolumeEnum();
 md.verbose=verbose('autodiff',true);
+md.toolkits.DefaultAnalysis=issmsolver();
 %setup autodiff parameters

issm/trunk/test/NightlyRun/test3019.m

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.par');
 md=setflowequation(md,'macayeal','all');
+md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
+md.toolkits.DefaultAnalysis=issmsolver();
 md.autodiff.isautodiff=true;
 …
 %Fields and tolerances to track changes
 field_names     ={'Jac Forward','Jac Reverse','Jac Forward - Reverse'};
 field_tolerances={1e-13,1e-13,1e-13};
+field_tolerances={1e-8,1e-8,1e-6};
 field_values={jac_forward,jac_reverse,jac_forward-jac_reverse};

issm/trunk/test/NightlyRun/test3020.m

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.par');
 md=setflowequation(md,'macayeal','all');
 md.cluster=generic('name',oshostname(),'np',3);
+md.cluster=generic('name',oshostname(),'np',1);
 md.transient.requested_outputs=[IceVolumeEnum();MaxVelEnum()];
 md.verbose=verbose('autodiff',true);
+md.diagnostic.restol=0.000001;
+md.diagnostic.restol=1e-4;
+md.toolkits.DefaultAnalysis=issmsolver();
 %setup autodiff parameters
 …
 %Fields and tolerances to track changes
 field_names     ={'dV/dh-dV/dh0','dMaxV/dh-dMaxV/dh0'};
 field_tolerances={1e-13,1e-13};
+field_tolerances={1e-8,1e-7};
 field_values={dVdh_ad-dVdh_an,dMaxVdh_an-dMaxVdh_ad};

issm/trunk/test/NightlyRun/test3020.py

-              r13975
+              r15396
 md=parameterize(md,'../Par/SquareShelfConstrained.py')
 md=setflowequation(md,'macayeal','all')
 md.cluster=generic('name',oshostname(),'np',3)
+md.cluster=generic('name',oshostname(),'np',1)
 md.transient.requested_outputs=[IceVolumeEnum(),MaxVelEnum()]
 md.verbose=verbose('autodiff',True)
 md.diagnostic.restol=0.000001
+md.toolkits.DefaultAnalysis=issmsolver()
 #setup autodiff parameters

issm/trunk/test/NightlyRun/test317.m

-              r13975
+              r15396
         'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2',...
         'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
 field_tolerances={1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
 e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
 e-09,5e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10};
+field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
+e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
+e-09,5e-10,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10};
 field_values={...
         (md.results.TransientSolution(1).Vx),...

issm/trunk/test/NightlyRun/test317.py

-              r13975
+              r15396
         'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2',\
         'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3']
 field_tolerances=[1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\
 e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\
 e-09,5e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10]
+field_tolerances=[1e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\
+e-09,1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,\
+e-09,5e-10,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10]
 field_values=[\
         md.results.TransientSolution[0].Vx,\

issm/trunk/test/NightlyRun/test405.m

r13975	r15396
9	9	%Fields and tolerances to track changes
10	10	field_names ={'Vx','Vy','Vz','Vel','Pressure'};
11		field_tolerances={~~1e-05,1e-05,1e-05,1~~e-05,1e-05};
	11	field_tolerances={5e-05,5e-05,5e-05,5e-05,1e-05};
12	12	field_values={...
13	13	(md.results.DiagnosticSolution.Vx),...

issm/trunk/test/NightlyRun/test405.py

r13975	r15396
19	19	#Fields and tolerances to track changes
20	20	field_names =['Vx','Vy','Vz','Vel','Pressure']
21		field_tolerances=[~~1e-05,1e-05,1e-05,1~~e-05,1e-05]
	21	field_tolerances=[5e-05,5e-05,5e-05,5e-05,1e-05]
22	22	field_values=[\
23	23	md.results.DiagnosticSolution.Vx,\

issm/trunk/test/NightlyRun/test415.m

r13975	r15396
24	24	%Fields and tolerances to track changes
25	25	field_names ={'Gradient','Misfits','FrictionCoefficient','Pressure','Vel','Vx','Vy','Vz','Temperature','BasalforcingsMeltingRate'};
26		field_tolerances={1e-10,1e-9,1e-10,1e-13,1e-~~10,1e-09,1e-10~~,1e-8,1e-09,1e-6};
	26	field_tolerances={1e-10,1e-9,1e-10,1e-13,1e-09,1e-09,1e-09,1e-8,1e-09,1e-6};
27	27	field_values={...
28	28	(md.results.SteadystateSolution.Gradient1),...

issm/trunk/test/NightlyRun/test415.py

r13975	r15396
36	36	#Fields and tolerances to track changes
37	37	field_names =['Gradient','Misfits','FrictionCoefficient','Pressure','Vel','Vx','Vy','Vz','Temperature','BasalforcingsMeltingRate']
38		field_tolerances=[1e-10,1e-9,1e-10,1e-13,1e-~~10,1e-09,1e-10~~,1e-8,1e-09,1e-6]
	38	field_tolerances=[1e-10,1e-9,1e-10,1e-13,1e-09,1e-09,1e-09,1e-8,1e-09,1e-6]
39	39	field_values=[\
40	40	md.results.SteadystateSolution.Gradient1,\

issm/trunk/test/NightlyRun/test423.m

-              r13975
+              r15396
 md.transient.isthermal=0;
 md.transient.isprognostic=0;
 md.transient.isdiagnostic=0;
+md.transient.isdiagnostic=1;
 md.transient.isgroundingline=1;
 …
 md=solve(md,TransientSolutionEnum());
 element_on_iceshelf_agressive=(md.results.TransientSolution.MaskElementonfloatingice);
+vel_agressive=(md.results.TransientSolution.Vel);
 md.groundingline.migration='SoftMigration';
 md=solve(md,TransientSolutionEnum());
 element_on_iceshelf_soft=(md.results.TransientSolution.MaskElementonfloatingice);
+vel_soft=(md.results.TransientSolution.Vel);
+md.groundingline.migration='SubelementMigration';
+md=solve(md,TransientSolutionEnum());
+element_on_iceshelf_subelement=(md.results.TransientSolution.GLlevelset);
+vel_subelement=(md.results.TransientSolution.Vel);
+md.groundingline.migration='SubelementMigration2';
+md=solve(md,TransientSolutionEnum());
+element_on_iceshelf_subelement2=(md.results.TransientSolution.GLlevelset);
+vel_subelement2=(md.results.TransientSolution.Vel);
 %Fields and tolerances to track changes
 field_names     ={'ElementOnIceShelfAgressive','ElementOnIceShelfSoft'};
 field_tolerances={1e-13,1e-13};
 field_values={element_on_iceshelf_agressive,element_on_iceshelf_soft};
+field_names     ={'ElementOnIceShelfAgressive','VelAgressive','ElementOnIceShelfSoft','VelSoft','ElementOnIceShelfSubelement','VelSubelement','ElementOnIceShelfSubelement2','VelSubelement2'};
+field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
+field_values={element_on_iceshelf_agressive,vel_agressive,element_on_iceshelf_soft,vel_soft,element_on_iceshelf_subelement,vel_subelement,element_on_iceshelf_subelement2,vel_subelement2};

issm/trunk/test/NightlyRun/test423.py

-              r14067
+              r15396
 md.transient.isthermal=False
 md.transient.isprognostic=False
 md.transient.isdiagnostic=False
+md.transient.isdiagnostic=True
 md.transient.isgroundingline=True
 …
 md=solve(md,TransientSolutionEnum())
 element_on_iceshelf_agressive=md.results.TransientSolution[0].MaskElementonfloatingice
+vel_agressive=md.results.TransientSolution[0].Vel
 md.groundingline.migration='SoftMigration'
 md=solve(md,TransientSolutionEnum())
 element_on_iceshelf_soft=md.results.TransientSolution[0].MaskElementonfloatingice
+vel_soft=md.results.TransientSolution[0].Vel
+md.groundingline.migration='SubelementMigration'
+md=solve(md,TransientSolutionEnum())
+element_on_iceshelf_subelement=md.results.TransientSolution[0].GLlevelset
+vel_subelement=md.results.TransientSolution[0].Vel
+md.groundingline.migration='SubelementMigration2'
+md=solve(md,TransientSolutionEnum())
+element_on_iceshelf_subelement2=md.results.TransientSolution[0].GLlevelset
+vel_subelement2=md.results.TransientSolution[0].Vel
 #Fields and tolerances to track changes
 field_names     =['ElementOnIceShelfAgressive','ElementOnIceShelfSoft']
 field_tolerances=[1e-13,1e-13]
 field_values=[element_on_iceshelf_agressive,element_on_iceshelf_soft]
+field_names     =['ElementOnIceShelfAgressive','VelAgressive','ElementOnIceShelfSoft','VelSoft','ElementOnIceShelfSubelement','VelSubelement','ElementOnIceShelfSubelement2','VelSubelement2']
+field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13]
+field_values=[element_on_iceshelf_agressive,vel_agressive,element_on_iceshelf_soft,vel_soft,element_on_iceshelf_subelement,vel_subelement,element_on_iceshelf_subelement2,vel_subelement2]

issm/trunk/test/Par/ISMIPF.par

r14310	r15396
45	45	md.thermal.stabilization=1;
46	46	md.thermal.penalty_threshold=10^5;
	47	md.transient.isthermal=0;

issm/trunk/test/Par/ISMIPF.py

r14310	r15396
48	48	md.thermal.stabilization=1
49	49	md.thermal.penalty_threshold=10**5
	50	md.transient.isthermal=0

issm/trunk/test/Par/RoundSheetShelf.par

r13975	r15396
107	107	md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices,1);
108	108	md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6);
	109	md.diagnostic.loadingforce=0*ones(md.mesh.numberofvertices,3);
109	110	md.thermal.spctemperature=737.*ones(md.mesh.numberofvertices,1);
110	111

issm/trunk/test/Par/RoundSheetShelf.py

r13975	r15396
116	116	md.prognostic.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1))
117	117	md.diagnostic.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6))
	118	md.diagnostic.loadingforce=0*numpy.ones((md.mesh.numberofvertices,3))
118	119	md.thermal.spctemperature=737.*numpy.ones((md.mesh.numberofvertices,1))
119	120

issm/trunk/test/Par/SquareSheetConstrained.par

-              r13975
+              r15396
 md.timestepping.final_time=3.;
+%GIA:
+md.gia.lithosphere_thickness=100.*ones(md.mesh.numberofvertices,1); % in km
+md.gia.mantle_viscosity=1.0*10^21*ones(md.mesh.numberofvertices,1); % in Pa.s
+md.materials.lithosphere_shear_modulus=6.7*10^10;                   % in Pa
+md.materials.lithosphere_density=3.32;                              % in g/cm^-3
+md.materials.mantle_shear_modulus=1.45*10^11;                       % in Pa
+md.materials.mantle_density=3.34;                                   % in g/cm^-3
 %Boundary conditions:
 md=SetIceSheetBC(md);

issm/trunk/test/Par/SquareSheetConstrained.py

-              r14310
+              r15396
 md.timestepping.final_time=3.
+#GIA:
+md.gia.lithosphere_thickness=100.*numpy.ones((md.mesh.numberofvertices,1)); # in km
+md.gia.mantle_viscosity=1.*10**21*numpy.ones((md.mesh.numberofvertices,1)); # in Pa.s
+md.materials.lithosphere_shear_modulus=6.7*10**10;                          # in Pa
+md.materials.lithosphere_density=3.32;                                      # in g/cm^-3
+md.materials.mantle_shear_modulus=1.45*10**11;                              # in Pa
+md.materials.mantle_density=3.34;                                           # in g/cm^-3
 #Boundary conditions:
 md=SetIceSheetBC(md)

issm/trunk/test/Par/SquareShelf.py

-              r14310
+              r15396
 vx=iVelF.variables['vx'][:]
 vy=iVelF.variables['vy'][:]
+index=iVelF.variables['index'][:].astype(float)
+index=reshape(index.T,(len(index),3),order='F')
+index=iVelF.variables['index'][:].astype(int)
 #dbg - begin

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