Index: /issm/trunk/Makefile.am =================================================================== --- /issm/trunk/Makefile.am (revision 13394) +++ /issm/trunk/Makefile.am (revision 13395) @@ -1,3 +1,6 @@ -EXTRA_DIST = reconf scripts test m4 examples cron etc doc packages contributors.txt -SUBDIRS = src bin +EXTRA_DIST = reconf scripts test m4 examples cron etc doc packages contributors.txt +SUBDIRS = src bin_SCRIPTS=config.h startup.m README.rtf + +ACLOCAL_AMFLAGS = -I m4 + Index: /issm/trunk/configs/config-arm-linux.sh =================================================================== --- /issm/trunk/configs/config-arm-linux.sh (revision 13394) +++ /issm/trunk/configs/config-arm-linux.sh (revision 13395) @@ -5,6 +5,8 @@ --build="i386-apple-darwin10.8.0" \ --host="arm-linux-androideabi" \ + --enable-shared \ --without-fortran \ --without-modules \ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --disable-static Index: /issm/trunk/configs/config-discover.sh =================================================================== --- /issm/trunk/configs/config-discover.sh (revision 13394) +++ /issm/trunk/configs/config-discover.sh (revision 13395) @@ -18,8 +18,7 @@ --with-scalapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ --with-blacs-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ - --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ --with-blas-lapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ --with-graphics-lib=/usr/lib64/libX11.so \ --with-cxxoptflags="-O3 -xS" \ Index: /issm/trunk/configs/config-greenplanet.sh =================================================================== --- /issm/trunk/configs/config-greenplanet.sh (revision 13394) +++ /issm/trunk/configs/config-greenplanet.sh (revision 13395) @@ -1,3 +1,3 @@ -#!/bin/csh +#!/bin/sh #PETSc 3.2 Index: /issm/trunk/configs/config-linux64-ad.sh =================================================================== --- /issm/trunk/configs/config-linux64-ad.sh (revision 13394) +++ /issm/trunk/configs/config-linux64-ad.sh (revision 13395) @@ -18,3 +18,3 @@ --without-groundingline \ --without-kriging \ - --with-adolc-dir=$ADOLC_DIR + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install Index: /issm/trunk/configs/config-linux64-astrid-ad.sh =================================================================== --- /issm/trunk/configs/config-linux64-astrid-ad.sh (revision 13394) +++ /issm/trunk/configs/config-linux64-astrid-ad.sh (revision 13395) @@ -2,35 +2,10 @@ ./configure \ - --prefix=$ISSM_DIR \ - --with-serial=no\ - --with-metis-dir=$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$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ - --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ - --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-graphics-lib=/usr/lib64/libX11.so \ - --with-cxxoptflags="-march=opteron -O2" \ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ - --with-rose-dir=$ISSM_DIR/externalpackages/rose/install/ \ - --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ - --with-numthreads=24 \ - --without-thermal \ - --without-control \ - --without-hydrology \ - --without-diagnostic \ - --without-balanced \ - --without-responses \ - --without-slope \ - --without-rifts \ - --without-steadystate \ - --without-transient \ - --without-3d \ - --without-groundingline - -#--without-prognostic \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --without-kml \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ + --with-adolc-version=3 \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: /issm/trunk/configs/config-linux64-astrid-petsc3.3.sh =================================================================== --- /issm/trunk/configs/config-linux64-astrid-petsc3.3.sh (revision 13395) +++ /issm/trunk/configs/config-linux64-astrid-petsc3.3.sh (revision 13395) @@ -0,0 +1,33 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.3 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/src/externalpackages/metis-5.0.2-p3 \ + --with-petsc-dir=$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$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2" \ + --with-numthreads=16 \ + --enable-debugging + #--with-serial=no \ Index: /issm/trunk/configs/config-linux64-astrid-petscdev.sh =================================================================== --- /issm/trunk/configs/config-linux64-astrid-petscdev.sh (revision 13394) +++ /issm/trunk/configs/config-linux64-astrid-petscdev.sh (revision 13395) @@ -1,6 +1,4 @@ #!/bin/sh -#External packages versions: -#petsc Dev: FH trying out #mpich 1.4 @@ -17,6 +15,4 @@ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ @@ -24,14 +20,10 @@ --with-spai-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-prometheus-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-superlu-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-spooles-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-pastix-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ --with-graphics-lib=/usr/lib64/libX11.so \ - --with-cxxoptflags="-march=opteron -O2" \ + --with-cxxoptflags="-march=opteron -O3" \ --with-numthreads=32 \ --enable-debugging Index: /issm/trunk/configs/config-linux64-astrid-python.sh =================================================================== --- /issm/trunk/configs/config-linux64-astrid-python.sh (revision 13394) +++ /issm/trunk/configs/config-linux64-astrid-python.sh (revision 13395) @@ -13,19 +13,10 @@ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-petsc-dir=$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$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich " \ --with-petsc-arch=$ISSM_ARCH \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ - --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ - --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ --with-graphics-lib=/usr/lib64/libX11.so \ Index: /issm/trunk/configs/config-linux64-astrid.sh =================================================================== --- /issm/trunk/configs/config-linux64-astrid.sh (revision 13394) +++ /issm/trunk/configs/config-linux64-astrid.sh (revision 13395) @@ -7,14 +7,17 @@ ./configure \ --prefix=$ISSM_DIR \ - --with-matlab-dir=$MATLAB_DIR \ + --with-matlab-dir=$ISSM_DIR/externalpackages/matlab/install \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-python-version=2.7\ --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ --with-petsc-arch=$ISSM_ARCH \ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ @@ -29,5 +32,4 @@ --with-graphics-lib=/usr/lib64/libX11.so \ --with-cxxoptflags="-march=opteron -O2" \ - --with-numthreads=32 \ + --with-numthreads=16 \ --enable-debugging - #--with-serial=no \ Index: /issm/trunk/configs/config-macosx64-chris-bothapis.sh =================================================================== --- /issm/trunk/configs/config-macosx64-chris-bothapis.sh (revision 13395) +++ /issm/trunk/configs/config-macosx64-chris-bothapis.sh (revision 13395) @@ -0,0 +1,33 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +pythonversion=2.7 + +./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy\ + --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-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 \ + --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-numthreads=8 + #--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ Index: /issm/trunk/configs/config-macosx64-chris-python.sh =================================================================== --- /issm/trunk/configs/config-macosx64-chris-python.sh (revision 13395) +++ /issm/trunk/configs/config-macosx64-chris-python.sh (revision 13395) @@ -0,0 +1,34 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +pythonversion=2.7 + +./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --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-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-numthreads=8 + #--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ Index: sm/trunk/configs/config-macosx64-helene.sh =================================================================== --- /issm/trunk/configs/config-macosx64-helene.sh (revision 13394) +++ (revision ) @@ -1,26 +1,0 @@ -#!/bin/sh - -#petsc 3.2 -#mpich 1.4 - -./configure \ - --prefix=$ISSM_DIR \ - --with-matlab-dir=$MATLAB_DIR \ - --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a" \ - --with-petsc-arch=$ISSM_ARCH \ - --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ - --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ - --with-math-lib="/usr/lib/libm.dylib" \ - --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ - --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ - --with-numthreads=8 Index: /issm/trunk/configs/config-macosx64-larour-ad.sh =================================================================== --- /issm/trunk/configs/config-macosx64-larour-ad.sh (revision 13394) +++ /issm/trunk/configs/config-macosx64-larour-ad.sh (revision 13395) @@ -3,18 +3,9 @@ ./configure \ --prefix=$ISSM_DIR \ - --without-modules\ - --without-thermal \ - --without-control \ - --without-hydrology \ - --without-diagnostic \ - --without-balanced \ - --without-responses \ - --without-slope \ - --without-rifts \ - --without-steadystate \ - --without-transient \ - --without-3d \ - --without-groundingline \ --without-kriging \ - --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install - #--with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install\ + --without-kml \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + Index: /issm/trunk/configs/config-macosx64-larour-python.sh =================================================================== --- /issm/trunk/configs/config-macosx64-larour-python.sh (revision 13394) +++ /issm/trunk/configs/config-macosx64-larour-python.sh (revision 13395) @@ -4,9 +4,12 @@ #mpich 1.4 +pythonversion=2.7 + ./configure \ --prefix=$ISSM_DIR \ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ --with-python-dir=$ISSM_DIR/externalpackages/python/install\ - --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ Index: /issm/trunk/configs/config-macosx64-larour.sh =================================================================== --- /issm/trunk/configs/config-macosx64-larour.sh (revision 13394) +++ /issm/trunk/configs/config-macosx64-larour.sh (revision 13395) @@ -24,4 +24,4 @@ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ - #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install Index: /issm/trunk/configs/config-macosx64-lion-helene.sh =================================================================== --- /issm/trunk/configs/config-macosx64-lion-helene.sh (revision 13395) +++ /issm/trunk/configs/config-macosx64-lion-helene.sh (revision 13395) @@ -0,0 +1,34 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +pythonversion=2.7 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --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-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="-L/usr/X11R6/lib -lX11" \ + --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=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-numthreads=8 + #--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + #--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ + #--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ Index: /issm/trunk/configs/config-macosx64-nicole.sh =================================================================== --- /issm/trunk/configs/config-macosx64-nicole.sh (revision 13394) +++ /issm/trunk/configs/config-macosx64-nicole.sh (revision 13395) @@ -15,10 +15,7 @@ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install -lPLAPACK" \ - --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ - --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ Index: /issm/trunk/configure.ac =================================================================== --- /issm/trunk/configure.ac (revision 13394) +++ /issm/trunk/configure.ac (revision 13395) @@ -2,8 +2,10 @@ #AUTOCONF -AC_INIT([ISSM],[4.2.1],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_INIT([ISSM],[4.2.2],[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 +m4_include([m4/issm_options.m4]) AC_CANONICAL_TARGET #Determine the system type + #Compilers AC_PROG_CC([cccl cl icl gcc]) @@ -11,6 +13,6 @@ AC_PROG_CXX([cccl cl icl g++]) AC_PROG_F77([ifort g77 gfortran]) + #Libraries and linking -AC_PROG_RANLIB AC_F77_LIBRARY_LDFLAGS AC_PATH_XTRA #figure out X library and include paths @@ -22,14 +24,11 @@ AM_SILENT_RULES([yes]) #Do not show compilation command by default AM_PROG_CC_C_O +AM_PROG_AR -##LIBTOOL? -#AC_PROG_LIBTOOL -#LT_INIT +#Libtool +LT_INIT #Run issm_options.m4 ISSM_OPTIONS - -#AM_PROG_AR must be placed after ISSM_OPTIONS -AM_PROG_AR #List all Makefiles @@ -37,11 +36,8 @@ src/Makefile src/c/Makefile - src/py/Makefile - src/py/model/Makefile src/modules/Makefile src/modules/python/Makefile src/modules/matlab/Makefile - src/m/Makefile - bin/Makefile]) + src/m/Makefile]) #End of configure.ac Index: /issm/trunk/etc/environment.csh =================================================================== --- /issm/trunk/etc/environment.csh (revision 13394) +++ /issm/trunk/etc/environment.csh (revision 13395) @@ -1,140 +1,97 @@ #ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) -source $ISSM_DIR/etc/environment_variables.csh -#Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them before exporting the variables -#to environment. - -#foreach i ($@) -#eval $i -#end - -#CRON utilities -setenv PATH {$PATH}:{$ISSM_DIR}/cron - -#SCRIPTS utilities +#Load ISSM scripts setenv PATH {$PATH}:{$ISSM_DIR}/scripts #MATLAB -setenv MATLAB_DIR {$MATLAB_DIR} -setenv PATH {$MATLAB_DIR}/bin:{$PATH} -setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$MATLAB_DIR/lib +set MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install" +if (-d MATLAB_DIR) then + setenv MATLAB_DIR {$MATLAB_DIR} + setenv PATH {$MATLAB_DIR}/bin:{$PATH} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$MATLAB_DIR}/bin/glnxa64 +endif #MPI -setenv MPI_DIR {$MPI_DIR} -setenv PATH {$MPI_DIR}/bin:{$PATH} -setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$MPI_DIR/lib -setenv MANPATH {$MANPATH}:$MPI_DIR/man -setenv MPIRUN_NPROCS 8 +set MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install" +if (-d $MPI_DIR) then + setenv MPI_DIR {$MPI_DIR} + setenv PATH {$MPI_DIR}/bin:{$PATH} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$MPI_DIR/lib + setenv MANPATH {$MANPATH}:$MPI_DIR/man +endif #PETSC -setenv PETSC_DIR {$PETSC_DIR} -setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$PETSC_DIR/lib/{$ISSM_ARCH} +set PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" +if (-d $PETSC_DIR) then + setenv PETSC_DIR {$PETSC_DIR} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$PETSC_DIR/lib/{$ISSM_ARCH} +endif #SLEPC -setenv SLEPC_DIR {$SLEPC_DIR} -setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$SLEPC_DIR/lib/{$ISSM_ARCH} +set SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install" +if (-d $SLEPC_DIR) then + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$SLEPC_DIR/lib/{$ISSM_ARCH} +endif +#PETSC +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} +endif #Dakota -setenv DAKOTA_DIR {$DAKOTA_DIR} -setenv PATH {$PATH}:{$DAKOTA_DIR}/bin -setenv MANPATH {$MANPATH}:{$MPI_DIR}/man:{$DAKOTA_DIR}/docs/man:{$DAKOTA_DIR}/docs/man-ref - -#Qhull -setenv QHULL_DIR {$QHULL_DIR} -setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$QHULL_DIR}/lib - +set DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install" +if (-d $DAKOTA_DIR) then + setenv PATH {$PATH}:{$DAKOTA_DIR}/bin + setenv MANPATH {$MANPATH}:{$MPI_DIR}/man:{$DAKOTA_DIR}/docs/man:{$DAKOTA_DIR}/docs/man-ref +endif #Doxygen -setenv DOXYGEN_DIR {$DOXYGEN_DIR} -setenv MANPATH {$MANPATH}:{$DOXYGEN_DIR}/man -setenv PATH {$PATH}:{$DOXYGEN_DIR}/bin +set DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install" +if (-d $DOXYGEN_DIR) then + setenv MANPATH {$MANPATH}:{$DOXYGEN_DIR}/man + setenv PATH {$PATH}:{$DOXYGEN_DIR}/bin +endif -#MTOC -setenv MTOC_DIR {$MTOC_DIR} -setenv PATH {$PATH}:{$MTOC_DIR} +#AUTOTOOLS +set AUTOTOOLS_DIR="$ISSM_DIR/externalpackages/autotools/install" +if (-d $AUTOTOOLS_DIR) then + setenv PATH {$AUTOTOOLS_DIR}/bin:{$PATH} +endif -#MATLAB -setenv MATLAB_DIR {$MATLAB_DIR} -setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$MATLAB_DIR}/bin/glnxa64 -setenv PATH {$PATH}:{$MATLAB_DIR}/bin +#SSH +set SSH_DIR="$ISSM_DIR/externalpackages/ssh" +if (-d $SSH_DIR) then + setenv PATH {$PATH}:{$SSH_DIR} +endif -#TRIANGLE -setenv TRIANGLE_DIR {$TRIANGLE_DIR} +#VALGRIND +set VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install/bin" +if (-d $VALGRIND_DIR) then + setenv PATH {$PATH}:{$VALGRIND_DIR} +endif -#METIS -setenv METIS_DIR {$METIS_DIR} - -#BLAS -setenv BLAS_DIR {$BLAS_DIR} +#MERCURIAL +set MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install" +if (-d $MERCURIAL_DIR) then + setenv PYTHONPATH {$MERCURIAL_DIR}/mercurial/pure/ + setenv PATH {$PATH}:{$MERCURIAL_DIR} +endif -#LAPACK -setenv LAPACK_DIR {$LAPACK_DIR} +#GSL +set GSL_DIR="$ISSM_DIR/externalpackages/gsl/install" +if (-d $GSL_DIR) then + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GSL_DIR}/lib +endif -#SCALAPACK -setenv SCALAPACK_DIR {$SCALAPACK_DIR} - -#PLAPACK -setenv PLAPACK_DIR {$PLAPACK_DIR} - -#BLACS -setenv BLACS_DIR {$BLACS_DIR} +#CMAKE +set CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install" +if (-d $CMAKE_DIR) then + setenv PATH {$PATH}:{$CMAKE_DIR}/bin +endif #YAMS -setenv YAMS_DIR {$YAMS_DIR} -setenv PATH {$PATH}:{$YAMS_DIR} - -#TEX2IM -setenv TEX2IM_DIR {$TEX2IM_DIR} -setenv PATH {$PATH}:{$TEX2IM_DIR} - -#SOWING -setenv SOWING_DIR {$SOWING_DIR} -setenv PATH {$PATH}:{$SOWING_DIR}/bin -setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$SOWING_DIR}/lib -setenv MANPATH {$MANPATH}:{$SOWING_DIR}/man - -#Chaco -setenv CHACO_DIR {$CHACO_DIR} -setenv PATH {$PATH}:{$CHACO_DIR} - -#MeshPart -setenv MESHPART_DIR {$MESHPART_DIR} -setenv PATH {$PATH}:{$MESHPART_DIR} - -#SCOTCH -setenv SCOTCH_DIR {$SCOTCH_DIR} -setenv PATH {$PATH}:{$SCOTCH_DIR} -setenv MANPATH {$MANPATH}:{$SCOTCH_DIR}/man - -#AUTOCONF -setenv AUTOCONF_DIR {$AUTOCONF_DIR} -setenv PATH {$AUTOCONF_DIR}/bin:{$PATH} - -#AUTOMAKE -setenv AUTOMAKE_DIR {$AUTOMAKE_DIR} -setenv PATH {$AUTOMAKE_DIR}/bin:{$PATH} - -#BORLAND -setenv BORLAND_DIR {$BORLAND_DIR} -setenv PATH {$PATH}:{$BORLAND_DIR}/Bin - -#SSH -setenv SSH_DIR {$SSH_DIR} -setenv PATH {$PATH}:{$SSH_DIR} - -#VALGRIND -setenv VALGRIND_DIR {$VALGRIND_DIR} -setenv PATH {$PATH}:{$VALGRIND_DIR} - -#MERCURIAL -#setenv PYTHONPATH {$PYTHONPATH}:{$MERCURIAL_DIR}/mercurial/pure/ -setenv PYTHONPATH {$MERCURIAL_DIR}/mercurial/pure/ -setenv PATH {$PATH}:{$MERCURIAL_DIR} - -#GSL -setenv GSL_DIR {$GSL_DIR} -setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GSL_DIR}/lib - -#CMAKE -setenv PATH {$PATH}:{$CMAKE_DIR}/bin +set YAMS_DIR="$ISSM_DIR/externalpackages/yams/install" +if (-d $YAMS_DIR) then + setenv PATH {$PATH}:{$YAMS_DIR}/bin +endif Index: /issm/trunk/etc/environment.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 13394) +++ /issm/trunk/etc/environment.sh (revision 13395) @@ -1,3 +1,51 @@ #ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) + +pathprepend(){ #{{{ + if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then + PATH="$1:$PATH" + fi +} #}}} +pathappend(){ #{{{ + if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then + export PATH="$PATH:$1" + fi +} #}}} +libpathprepend(){ #{{{ + if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then + export LD_LIBRARY_PATH="$1:$LD_LIBRARY_PATH" + fi + if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then + export LD_RUN_PATH="$1:$LD_RUN_PATH" + fi +} #}}} +libpathappend(){ #{{{ + if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then + export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1" + fi + if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then + export LD_RUN_PATH="$LD_RUN_PATH:$1" + fi +} #}}} +dylibpathprepend(){ #{{{ + if [ -d "$1" ] && [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then + export DYLD_LIBRARY_PATH="$1:$DYLD_LIBRARY_PATH" + fi + if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then + export LD_RUN_PATH="$1:$LD_RUN_PATH" + fi +} #}}} +dylibpathappend(){ #{{{ + if [ -d "$1" ] && [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then + export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$1" + fi + if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then + export LD_RUN_PATH="$LD_RUN_PATH:$1" + fi +} #}}} + +#FIXME: during installation packages are installed one by one but environment.sh was sourced +#before so new packages are NOT in the path. +#may resource environment.sh with: +#if [ -z $(echo "$PATH" | grep "$MATLAB_DIR") ]; then export $PATH...; fi #Windows compilers: @@ -6,290 +54,214 @@ fi -source $ISSM_DIR/etc/environment_variables.sh - -#Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them after exporting the variables -#to environment. -for i in $@ -do - eval $i -done - -#CRON utilities -PATH="$PATH:$ISSM_DIR/cron" - -#scripts -PATH="$PATH:$ISSM_DIR/scripts" - -##MATLAB +#Some basic path, in case it is not included by default +libpathappend "/usr/local/lib" + +#Load ISSM scripts +pathappend "$ISSM_DIR/scripts" + +MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install" export MATLAB_DIR -PATH="$MATLAB_DIR/bin:$PATH" #take precedence over /usr/local/bin/matlab -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MATLAB_DIR/lib" -export LD_RUN_PATH="$LD_RUN_PATH:$MATLAB_DIR/lib" -#export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MATLAB_DIR/bin/glnxa64" -#export LD_RUN_PATH="$LD_RUN_PATH:$MATLAB_DIR/bin/glnxa64" - -#MPI +pathprepend "$MATLAB_DIR/bin" #take precedence over /usr/local/bin/matlab +libpathappend "$MATLAB_DIR/lib" + +MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install" export MPI_DIR -PATH="$MPI_DIR/bin:$PATH" -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MPI_DIR/lib" -export LD_RUN_PATH="$LD_RUN_PATH:$MPI_DIR/lib" -export MANPATH="$MANPATH:$MPI_DIR/man" -export MPIRUN_NPROCS=24 - -#PETSC +pathprepend "$MPI_DIR/bin" +libpathappend "$MPI_DIR/lib" + +PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" export PETSC_DIR -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PETSC_DIR/lib/$ISSM_ARCH" -export LD_RUN_PATH="$LD_RUN_PATH:$PETSC_DIR/lib/$ISSM_ARCH" - -#SLEPC -export SLEPC_DIR -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SLEPC_DIR/lib/$ISSM_ARCH" -export LD_RUN_PATH="$LD_RUN_PATH:$SLEPC_DIR/lib/$ISSM_ARCH" - -#Dakota -export DAKOTA_DIR -PATH="$PATH:$DAKOTA_DIR/bin" -export MANPATH="$MANPATH:$MPI_DIR/man:$DAKOTA_DIR/docs/man:$DAKOTA_DIR/docs/man-ref" - -#Qhull -export QHULL_DIR -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$QHULL_DIR/lib" -export LD_RUN_PATH="$LD_RUN_PATH:$QHULL_DIR/lib" - -#Doxygen -export DOXYGEN_DIR -MANPATH="$MANPATH:$DOXYGEN_DIR/man" -PATH="$PATH:$DOXYGEN_DIR/bin" - -#MTOC -export MTOC_DIR -PATH="$PATH:$MTOC_DIR" - -#TRIANGLE -export TRIANGLE_DIR - -#METIS -export METIS_DIR - -#BLAS -export BLAS_DIR - -#LAPACK -export LAPACK_DIR - -#SCALAPACK -export SCALAPACK_DIR - -#PLAPACK -export PLAPACK_DIR - -#BLACS -export BLACS_DIR - -#YAMS -export YAMS_DIR -PATH="$PATH:$YAMS_DIR" - -#BAMG -export BAMG_DIR -PATH="$PATH:$BAMG_DIR" - -#TEX2IM -export TEX2IM_DIR -PATH="$PATH:$TEX2IM_DIR" - -#SOWING -export SOWING_DIR -PATH="$PATH:$SOWING_DIR/bin" -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SOWING_DIR/lib" -export LD_RUN_PATH="$LD_RUN_PATH:$SOWING_DIR/lib" -export MANPATH="$MANPATH:$SOWING_DIR/man" - -#Chaco -export CHACO_DIR -PATH="$PATH:$CHACO_DIR" - -#MeshPart -export MESHPART_DIR -PATH="$PATH:$MESHPART_DIR" - -#SCOTCH -export SCOTCH_DIR -PATH="$PATH:$SCOTCH_DIR" -export MANPATH="$MANPATH:$SCOTCH_DIR/man" - -#AUTOCONF -export AUTOCONF_DIR -PATH="$AUTOCONF_DIR/bin:$PATH" - -#AUTOMAKE -export AUTOMAKE_DIR -PATH="$AUTOMAKE_DIR/bin:$PATH" - -export LIBTOOL_DIR -PATH="$LIBTOOL_DIR/bin:$PATH" - -#BORLAND -export BORLAND_DIR -PATH="$PATH:$BORLAND_DIR/Bin" - -#INTEL -#export INTEL_DIR -#PATH="$PATH:$INTEL_DIR" -#source $ISSM_DIR/externalpackages/intel/intel.sh - -#SDK -export SDK_DIR -PATH="$PATH:$SDK_DIR" - -#SSH -export SSH_DIR -PATH="$PATH:$SSH_DIR" - -#VALGRIND -export VALGRIND_DIR -PATH="$PATH:$VALGRIND_DIR" - -#GRAPHVIZ -export GRAPHVIZ_DIR -PATH="$PATH:$GRAPHVIZ_DIR" - -#CPPCHECK -export CPPCHECK_DIR -PATH="$PATH:$CPPCHECK_DIR" - -#GDAL -export GDAL_DIR -PATH="$GDAL_DIR/bin:$PATH" -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GDAL_DIR/lib" - -#MERCURIAL -export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/" -export PATH="$PATH:$MERCURIAL_DIR/" - -#BOOST -export BOOSTROOT -export BOOST_DIR -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$BOOST_DIR/lib" -export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$BOOST_DIR/lib" -export PATH="$PATH:$BOOST_DIR/bin" - -#XERCES -export XERCESROOT -export XERCESCROOT - -#xaifBooster -export XAIFBOOSTERROOT -export XAIFBOOSTER_HOME -export XAIF_DIR -export PLATFORM - -#angel -export ANGELROOT - -#openanalysis -export OPENANALYSISROOT -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$OPENANALYSISROOT/lib" - -#JAVA -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$JVM_DIR" - -#BBFTP -export PATH="$PATH:$BBFTP_DIR/bin" - -#ADIC -export PATH="$PATH:$ADIC_DIR/bin" -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$ADIC_DIR/lib" -export LD_RUN_PATH="$LD_RUN_PATH:$ADIC_DIR/lib" - -#COLPACK -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$COLPACK_DIR/lib" -export LD_RUN_PATH="$LD_RUN_PATH:$COLPACK_DIR/lib" - -#ECLIPSE -export PATH="$PATH:$ECLIPSE_DIR" - -#FLAIM -export FLAIM_DIR - -#APPSCAN -export PATH="$PATH:$APPSCAN_DIR/install/bin" -export PATH="$PATH:$APPSCAN_DIR/bin" - -#CPPCHECK -export PATH="$PATH:$CPPCHECK_DIR/bin" - -#RATS -export PATH="$PATH:$RATS_DIR/bin" - -#DYSON -export PATH="$PATH:$DYSON_DIR" - -#CMAKE -export PATH="$PATH:$CMAKE_DIR/bin" - -#SHAPELIB -export PATH="$PATH:$SHAPELIB_DIR/exec" - -#CCCL -export PATH="$PATH:$CCCL_DIR/bin" - -#PACKAGEMAKER -export PATH="$PATH:$PACKAGEMAKER_DIR" - -#ANDROID_NDK: -export ANDROID_NDK_DIR -export PATH="$PATH:$ANDROID_NDK_DIR/" - -#ANDROID_DIR -export ANDROID_DIR - -#ANDROID_SDK -export PATH="$PATH:$ANDROID_SDK_DIR/" - -#ANDROID_ANT -export PATH="$PATH:$ANDROID_ANT_DIR/" - -#GSL -export PATH="$PATH:$GSL_DIR/bin" -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GSL_DIR/lib" -export LD_RUN_PATH="$LD_RUN_PATH:$GSL_DIR/lib" - -#GMAKE -export PATH="$GMAKE_DIR/bin:$PATH" - -#PYTHON -export PATH="$PYTHON_DIR/bin:$PATH" -export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/src/modules/python" -export LD_LIBRARY_PATH=$ISSM_DIR/src/modules/python:$ISSM_DIR/externalpackages/python/install/lib:$LD_LIBRARY_PATH -export PYTHONSTARTUP - -#MODELE -export PATH="$MODELE_DIR/src/exec:$PATH" - -#GIT -export PATH="$PATH:$GIT_DIR/install/bin" - -#NCVIEW -export PATH="$PATH:$NCVIEW_DIR/install" - -#TCLX -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$TCLX_DIR" -export LD_RUN_PATH="$LD_RUN_PATH:$TCLX_DIR" - - -#ASPELL -export PATH="$ASPELL_DIR/install/bin:$PATH" - - -#ESMF -export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf -export ESMF_COMPILER=gfortran -export ESMF_COMM=mpich2 - -#HDF5 -export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HDF5_DIR/lib" -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HDF5_DIR/lib" -export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib" -export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include" - +libpathappend "$PETSC_DIR/lib" + +SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install" +libpathappend "$SLEPC_DIR/lib/$ISSM_ARCH" + +TAO_DIR="$ISSM_DIR/externalpackages/tao/install" +libpathappend "$TAO_DIR/lib" + +DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install" +pathappend "$DAKOTA_DIR/bin" + +DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install" +pathappend "$DOXYGEN_DIR/bin" + +AUTOTOOLS_DIR="$ISSM_DIR/externalpackages/autotools/install" +pathprepend "$AUTOTOOLS_DIR/bin" + +SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU" +pathappend "$SDK_DIR" + +SSH_DIR="$ISSM_DIR/externalpackages/ssh" +pathappend "$SSH_DIR" + +VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install" +pathprepend "$VALGRIND_DIR/bin" + +CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install" +pathappend "$CPPCHECK_DIR/bin" + +GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install" +pathprepend "$GDAL_DIR/bin:$PATH" +libpathappend "$GDAL_DIR/lib" + +MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install" +if [ -d "$MERCURIAL_DIR" ]; then + export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/" + pathappend "$MERCURIAL_DIR" +fi + +BOOST_DIR="$ISSM_DIR/externalpackages/boost/install" +BOOSTROOT="$ISSM_DIR/externalpackages/boost/install" +if [ -d "$BOOST_DIR" ]; then + export BOOSTROOT + export BOOST_DIR + libpathappend "$BOOST_DIR/lib" + dylibpathappend "$BOOST_DIR/lib" + pathappend "$BOOST_DIR/bin" +fi + +XERCESROOT="$ISSM_DIR/externalpackages/xerces/install" +XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src" +if [ -d "$XERCESROOT" ]; then + export XERCESROOT + export XERCESCROOT +fi + +XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster" +XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/" +XAIFBOOSTER_HOME="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster" +PLATFORM="x86-Linux" +if [ -d "$XAIF_DIR" ]; then + export XAIFBOOSTERROOT + export XAIFBOOSTER_HOME + export XAIF_DIR + export PLATFORM +fi + +ANGELROOT="$ISSM_DIR/externalpackages/angel/angel" +if [ -d "$ANGELROOT" ]; then + export ANGELROOT +fi + +OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install" +if [ -d "$OPENANALYSISROOT" ]; then + export OPENANALYSISROOT + libpathappend "$OPENANALYSISROOT/lib" +fi + +JVM_DIR="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/" +libpathappend "$JVM_DIR" + +BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install" +pathappend "$BBFTP_DIR/bin" + +ADIC_DIR="$ISSM_DIR/externalpackages/adic/install" +pathappend "$ADIC_DIR/bin" +libpathappend "$ADIC_DIR/lib" + +COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install" +libpathappend "$COLPACK_DIR/lib" + +ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install" +pathappend "$ECLIPSE_DIR" + +APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan/install" +pathappend "$APPSCAN_DIR/bin" + +RATS_DIR="$ISSM_DIR/externalpackages/rats/install" +pathappend "$RATS_DIR/bin" + +DYSON_DIR="$ISSM_DIR/externalpackages/dyson/" +pathappend "$DYSON_DIR" + +CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install" +pathappend "$CMAKE_DIR/bin" + +SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install" +pathappend "$SHAPELIB_DIR/exec" + +CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install" +pathappend "$CCCL_DIR/bin" + +PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install" +pathappend "$PACKAGEMAKER_DIR" + +ANDROID_NDK_DIR="$ISSM_DIR/externalpackages/android-ndk/install" +pathappend "$ANDROID_NDK_DIR/" + +ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install-sdk" +pathappend "$ANDROID_SDK_DIR/" + +GSL_DIR="$ISSM_DIR/externalpackages/gsl/install" +libpathappend "$GSL_DIR/lib" + +GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install" +pathprepend "$GMAKE_DIR/bin" + +PYTHON_DIR="$ISSM_DIR/externalpackages/python/install" +if [ -d "$PYTHON_DIR" ]; then + export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/lib" + export PYTHONSTARTUP="$ISSM_DIR/startup.py" + pathprepend "$PYTHON_DIR/bin" + libpathprepend "$ISSM_DIR/lib" + libpathprepend "$PYTHON_DIR/lib" +fi + +MODELE_DIR="$ISSM_DIR/externalpackages/modelE/install" +pathappend "$MODELE_DIR/src/exec" + +GIT_DIR="$ISSM_DIR/externalpackages/git/install" +pathappend "$GIT_DIR/bin" + +NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview/install" +pathappend "$NCVIEW_DIR" + +TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4" +libpathappend "$TCLX_DIR" + +ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/install" +pathappend "$ASPELL_DIR/bin" + +HDF5_DIR="$ISSM_DIR/externalpackages/hdf5/install" +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" +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:$NETCDF_DIR/lib" + export C_INCLUDE_PATH="$C_INCLUDE_PATH:$NETCDF_DIR/include" +fi + +#SVN +SVN_DIR="$ISSM_DIR/externalpackages/svn/install" +if [ -d "$SVN_DIR" ]; then + pathprepend "$SVN_DIR/bin" + libpathappend "$SVN_DIR/lib" +fi + +APR_DIR="$ISSM_DIR/externalpackages/apr/install" +if [ -d "$APR_DIR" ]; then + pathappend "$APR_DIR/bin" + libpathappend "$APR_DIR/lib" +fi + +APR_UTIL_DIR="$ISSM_DIR/externalpackages/apr-util/install" +pathappend "$APR_UTIL_DIR/bin:$PATH" +libpathappend "$APR_UTIL_DIR/lib" + +SQLITE_DIR="$ISSM_DIR/externalpackages/sqlite/install" +pathappend "$SQLITE_DIR/bin" +libpathappend "$SQLITE_DIR/lib" + +YAMS_DIR="$ISSM_DIR/externalpackages/yams/install" +pathappend "$YAMS_DIR" + +SWIG_DIR="$ISSM_DIR/externalpackages/swig/install" +pathappend "$SWIG_DIR" Index: sm/trunk/etc/environment_variables.csh =================================================================== --- /issm/trunk/etc/environment_variables.csh (revision 13394) +++ (revision ) @@ -1,93 +1,0 @@ -# -# -#This routine can only be run if the ISSM_DIR variable has been correctly set! -# -# - -#MATLAB -set MATLAB_DIR={$ISSM_DIR}/externalpackages/matlab/install - -#MPI -set MPI_DIR={$ISSM_DIR}/externalpackages/mpich2/install - -#PETSC -set PETSC_DIR={$ISSM_DIR}/externalpackages/petsc/install - -#SLEPC -set SLEPC_DIR={$ISSM_DIR}/externalpackages/slepc/install - -#Dakota -set DAKOTA_DIR={$ISSM_DIR}/externalpackages/dakota/install - -#Qhull -set QHULL_DIR={$ISSM_DIR}/externalpackages/qhull/install - -#Doxygen -set DOXYGEN_DIR={$ISSM_DIR}/externalpackages/doxygen/install - -#MTOC -set MTOC_DIR={$ISSM_DIR}/externalpackages/mtoc/install - -#Triangle -set TRIANGLE_DIR={$ISSM_DIR}/externalpackages/triangle/install - -#METIS -set METIS_DIR={$ISSM_DIR}/externalpackages/metis/install - -#BLAS -set BLAS_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/fblaslapack - -#LAPACK -set LAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/fblaslapack/$ISSM_ARCH - -#SCALAPACK -set SCALAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/SCALAPACK/$ISSM_ARCH - -#PLAPACK -set PLAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/PLAPACKR32 - -#BLACS -set BLACS_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/blacs-dev/$ISSM_ARCH - -#sowing -set SOWING_DIR={$ISSM_DIR}/externalpackages/sowing/install - -#YAMS -set YAMS_DIR={$ISSM_DIR}/externalpackages/yams/install - -#TEX2IM -set TEX2IM_DIR={$ISSM_DIR}/externalpackages/tex2im/install - -#Chaco -set CHACO_DIR={$ISSM_DIR}/externalpackages/chaco/install - -#MeshPart -set MESHPART_DIR={$ISSM_DIR}/externalpackages/meshpart/install - -#SCOTCH -set SCOTCH_DIR={$ISSM_DIR}/externalpackages/scotch/install - -#Development packages -#automake -set AUTOMAKE_DIR={$ISSM_DIR}/externalpackages/automake/install - -#autoconf -set AUTOCONF_DIR={$ISSM_DIR}/externalpackages/autoconf/install - -#borland -set BORLAND_DIR=/cygdrive/c/Borland - -#ssh -set SSH_DIR={$ISSM_DIR}/externalpackages/ssh - -#mercurial -set MERCURIAL_DIR={$ISSM_DIR}/externalpackages/mercurial/install - -#valgrind -set VALGRIND_DIR={$ISSM_DIR}/externalpackages/valgrind/install/bin - -#gsl -set GSL_DIR={$ISSM_DIR}/externalpackages/gsl/install - -#cmake -set CMAKE_DIR={$ISSM_DIR}/externalpackages/cmake/install Index: sm/trunk/etc/environment_variables.sh =================================================================== --- /issm/trunk/etc/environment_variables.sh (revision 13394) +++ (revision ) @@ -1,214 +1,0 @@ -# -# -#This routine can only be run if the ISSM_DIR variable has been correctly set! -# -# - -#MATLAB -MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install" - -#MPI -MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install" - -#PETSC -PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" - -#SLEPC -SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install" - -#Dakota -DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install" - -#Qhull -QHULL_DIR="$ISSM_DIR/externalpackages/qhull/install" - -#Doxygen -DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install" - -#MTOC -MTOC_DIR="$ISSM_DIR/externalpackages/mtoc/install" - -#Triangle -TRIANGLE_DIR="$ISSM_DIR/externalpackages/triangle/install" - -#METIS -METIS_DIR="$ISSM_DIR/externalpackages/metis/install" - -#BLAS -BLAS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack" - -#LAPACK -LAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH" - -#SCALAPACK -SCALAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH" - -#PLAPACK -PLAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32" - -#BLACS -BLACS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH" - -#sowing -SOWING_DIR="$ISSM_DIR/externalpackages/sowing/install" - -#BLACS -BLACS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH" - -#YAMS -YAMS_DIR="$ISSM_DIR/externalpackages/yams/install" - -#BAMG -BAMG_DIR="$ISSM_DIR/externalpackages/bamg/install" - -#Chaco -CHACO_DIR="$ISSM_DIR/externalpackages/chaco/install" - -#MeshPart -MESHPART_DIR="$ISSM_DIR/externalpackages/meshpart/install" - -#SCOTCH -SCOTCH_DIR="$ISSM_DIR/externalpackages/scotch/install" - -#Development packages -#automake -AUTOMAKE_DIR="$ISSM_DIR/externalpackages/automake/install" - -#libtool -LIBTOOL_DIR="$ISSM_DIR/externalpackages/libtool/install" - -#autoconf -AUTOCONF_DIR="$ISSM_DIR/externalpackages/autoconf/install" - -#borland -#BORLAND_DIR="/cygdrive/c/Borland/" - -#intel -#INTEL_DIR="C:/IntelInstall/Compiler/11.1/038/bin/ia32/" - -#TEX2IM -TEX2IM_DIR="$ISSM_DIR/externalpackages/tex2im/install" - -#sdk -#SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU" - -#ssh -SSH_DIR="$ISSM_DIR/externalpackages/ssh" - -#valgrind -VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install/bin" - -#graphviz -GRAPHVIZ_DIR="$ISSM_DIR/externalpackages/graphviz/install/bin" - -#cppcheck -CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install" - -#gdal -GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install" - -#mercurial -MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install" - -#boost -BOOST_DIR="$ISSM_DIR/externalpackages/boost/install" -BOOSTROOT="$ISSM_DIR/externalpackages/boost/install" - -#OpenAnalysis -OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install" - -#xerces -XERCESROOT="$ISSM_DIR/externalpackages/xerces/install" -XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src" - -#xaifBooster -XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/" -XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster" -XAIFBOOSTER_HOME="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster" -PLATFORM=x86-Linux - -#angel -ANGELROOT="$ISSM_DIR/externalpackages/angel/angel" - -#java -JVM_DIR=/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/ - -#bbftp -BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install" - -#adic2 -ADIC_DIR="$ISSM_DIR/externalpackages/adic/install" - -#colpack -COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install" - -#eclipse -ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install" - -#flaim -FLAIM_DIR="$ISSM_DIR/externalpackages/flaim/install" - -#appscan -APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan" - -#cppcheck -CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install" - -#rats -RATS_DIR="$ISSM_DIR/externalpackages/rats/install" - -#dyson -DYSON_DIR="$ISSM_DIR/externalpackages/dyson/" - -#cmake -CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install" - -#shapelib -SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install" - -#cccl -CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install" - -#packagemaker -PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install" - -#android-dev-dir -ANDROID_DIR="$ISSM_DIR/externalpackages/android" - -#android-ndk -ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install" - -#android-sdk -ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install-sdk" - -#android-ant -ANDROID_ANT_DIR="$ANDROID_DIR/android-sdk/install-ant" - -#gsl -GSL_DIR="$ISSM_DIR/externalpackages/gsl/install" - -#gnu make -GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install" - -#PYTHON -PYTHON_DIR="$ISSM_DIR/externalpackages/python/install" -PYTHONSTARTUP="$ISSM_DIR/startup.py" - -#MODELE -MODELE_DIR="$ISSM_DIR/externalpackages/modelE" - - -#GIT -GIT_DIR="$ISSM_DIR/externalpackages/git" - -#NCVIEW -NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview" - -#TCLX -TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4" - -#ASPELL -ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/" - -#HDF5 -export HDF5_DIR=$ISSM_DIR/externalpackages/hdf5/install Index: /issm/trunk/externalpackages/adic/install.sh =================================================================== --- /issm/trunk/externalpackages/adic/install.sh (revision 13394) +++ /issm/trunk/externalpackages/adic/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Erase install @@ -26,5 +27,5 @@ --with-colpack=$ISSM_DIR/externalpackages/colpack/install\ --prefix=$ISSM_DIR/externalpackages/adic/install -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/adolc/install-dev.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-dev.sh (revision 13395) +++ /issm/trunk/externalpackages/adolc/install-dev.sh (revision 13395) @@ -0,0 +1,20 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install adolc_v220_issm + +git clone -b 2.3.x_ISSM git://gitorious.org/~utke/adol-c/adolc_v220_issm.git + +#Compile ADOL-C +cd adolc_v220_issm + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: sm/trunk/externalpackages/adolc/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install-macosx64.sh (revision 13394) +++ (revision ) @@ -1,61 +1,0 @@ -#!/bin/bash - -#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. - -#Some cleanup -rm -rf install ADOL-C-2.2.0 src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' - -#Create install directories -mkdir install src - -#Untar -tar -zxvf ADOL-C-2.2.0.tar.gz - -#Move ADOL-C into install directory -mv ADOL-C-2.2.0/* src -rm -rf ADOL-C-2.2.0 - -#Compile ADOL-C -cd src - -#export CC=gcc -#export CXX=g++ -#export CFLAGS="-arch x86_64" -#export CXXFLAGS="-arch x86_64" - -./configure \ - --prefix=$ISSM_DIR/externalpackages/adolc/install \ - --enable-sparse \ - --enable-docexa \ - --enable-addexa \ - --disable-shave - -if [ -z $1 ]; then - make -else - make -j $1 -fi -make install - - -#Ok, bug with libtool: replace all LIBTOOL= by LIBTOOL=libtool -#in all Makefiles -for i in `find ./ -name Makefile ` -do - echo $i - cat $i | sed 's/LIBTOOL =/LIBTOOL = libtool/g' > $i.bak - mv $i.bak $i -done - -#remake: -if [ -z $1 ]; then - make -else - make -j $1 -fi -make install - - Index: /issm/trunk/externalpackages/adolc/install.sh =================================================================== --- /issm/trunk/externalpackages/adolc/install.sh (revision 13394) +++ /issm/trunk/externalpackages/adolc/install.sh (revision 13395) @@ -1,14 +1,15 @@ #!/bin/bash +set -eu #some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. #Some cleanup -rm -rf install ADOL-C-2.2.0 src +rm -rf install ADOL-C-2.2.0 src trunk + +#Create install directories +mkdir install src #Download from ISSM server $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' - -#Create install directories -mkdir install src #Untar @@ -22,8 +23,8 @@ cd src -export CC=gcc -export CXX=g++ -export CFLAGS="-arch x86_64" -export CXXFLAGS="-arch x86_64" +#export CC=gcc +#export CXX=g++ +#export CFLAGS="-arch x86_64" +#export CXXFLAGS="-arch x86_64" ./configure \ @@ -34,5 +35,5 @@ --disable-shave -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else @@ -40,2 +41,20 @@ fi make install + + +#Ok, bug with libtool: replace all LIBTOOL= by LIBTOOL=libtool +#in all Makefiles +for i in `find ./ -name Makefile ` +do + echo $i + cat $i | sed 's/LIBTOOL =/LIBTOOL = libtool/g' > $i.bak + mv $i.bak $i +done + +#remake: +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/android/android-ndk/install.sh =================================================================== --- /issm/trunk/externalpackages/android/android-ndk/install.sh (revision 13394) +++ /issm/trunk/externalpackages/android/android-ndk/install.sh (revision 13395) @@ -1,27 +1,32 @@ -#This installs the Android NDK (Native Development Kit) -#which is needed for the compilation of C/C++ code into the -#native architecture of the Android device. +#!/bin/bash +set -eu -#The android-ndk-r8-darwin-x86.tar.bz2 ndk.tar.bz2 file was downloaded -#from the android developer website: -source $ANDROID_DIR/android_variables.sh +# This installs the Android NDK (Native Development Kit) +# which is needed for the compilation of C/C++ code into the +# native architecture of the Android device. -#Cleanup the install -rm -rf install -rm -rf $ANDROID_DIR/arm-linux-android-${default_droid} +# The android-ndk-r8-darwin-x86.tar.bz2 ndk.tar.bz2 file was downloaded +# from the android developer website: +source $ANDROID_DIR/android_aux.sh -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-ndk-r'${ndk_rev}'-darwin-x86.tar.bz2' 'ndk.tar.bz2' +if [[ $step == "1" || $step == "0" ]]; then + # Cleanup the install + rm -rf install + rm -rf $ANDROID_DIR/arm-linux-android-${default_droid} -# Install Android SDK and NDK. -bunzip2 ndk.tar.bz2 -tar -xvf ndk.tar -rm -rf ndk.tar ndk.tar.bz2 + # Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-ndk-r'${ndk_rev}'-darwin-x86.tar.bz2' 'ndk.tar.bz2' -#Move to install -mv android-ndk-r${ndk_rev} install + # Untar + tar -zxvf ndk.tar.bz2 + rm -rf ndk.tar ndk.tar.bz2 -#Create Standalone Development Directory -#Note: API-14 corresponds to Android 4.0 although we are -#calling our toolchain 4.1 to agree with our device. -$ANDROID_NDK_DIR/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/arm-linux-android-4.0 + # Move to install + mv android-ndk-r${ndk_rev} install +fi + +# Create Standalone Development Directory +# Note: API-14 corresponds to Android 4.0. +if [[ $step == "2" || $step == "0" ]]; then + $ANDROID_NDK_DIR/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/arm-linux-android-4.0 +fi Index: /issm/trunk/externalpackages/android/android-sdk/install.sh =================================================================== --- /issm/trunk/externalpackages/android/android-sdk/install.sh (revision 13394) +++ /issm/trunk/externalpackages/android/android-sdk/install.sh (revision 13395) @@ -1,31 +1,26 @@ -#This installs the Android SDK (Software Development Kit) -#which is needed for the compilation of the Java project. -source $ANDROID_DIR/android_variables.sh +#!/bin/bash +set -eu -step=1; +# This installs the Android SDK (Software Development Kit) +# which is needed for the compilation of the Java project. -#Different steps here. -#1: install sdk, ant and sdk tools -#2: install an emulator. -#3: test the emulator -#4: cleanup +source $ANDROID_DIR/android_aux.sh + +# Different steps here. +# 0: do all +# 1: install sdk, ant and sdk tools +# 2: install an emulator. +# 3: test the emulator +# 4: cleanup present_dir=`pwd`; sd_card="issm-sdcard" -((tmp=$1 )) +if [[ $step == "1" || $step == "0" ]]; then -if [[ $tmp -ge "1" && $tmp -le "4" ]]; then - step=$1 -else - echo "Using default step: " $step -fi - -if [[ $step == "1" ]]; then - - #Cleanup the install + # Cleanup the install rm -rf install-sdk - #Download from ISSM server + # Download from ISSM server $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-sdk_r'$sdk_rev'-macosx.zip' 'android-sdk_r'${sdk_rev}'-macosx.zip' @@ -33,15 +28,15 @@ unzip -o android-sdk_r${sdk_rev}-macosx.zip - #Move to install + # Move to install mv -f android-sdk-macosx install-sdk - #Post_install configuration: - #We need specific settings for specific platforms, for the SDK to - #function properly + # Post_install configuration: + # We need specific settings for specific platforms, for the SDK to + # function properly - #For now, we need to install: - #android sdk platform tools - #and a specific android api: API 16, API 15 and API 14 - #Note: API 16, API 15 and 14 correspond to Android 4.1, 4.0.3 and 4.0 respectively. + # For now, we need to install: + # android sdk platform tools + # and a specific android api: API 16, API 15 and API 14 + # 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 @@ -49,11 +44,11 @@ fi -if [[ $step == "2" ]]; then +if [[ $step == "2" || $step == "0" ]]; then - #Once this is done, we need to install an emulator. Location will default to ~/.android/avd, - #which we will move to $ISSM_DIR/externalpackages/android-emulators. - #For now, it's called: Android-4.0.3 + # Once this is done, we need to install an emulator. Location will default to ~/.android/avd, + # which we will move to $ISSM_DIR/externalpackages/android-emulators. + # For now, it's called: Android-4.0.3 - #Here we delete the Android-4.0.3 device if it already exists. + # Here we delete the Android-4.0.3 device if it already exists. cd $present_dir/install-sdk/tools @@ -64,6 +59,6 @@ fi - #Android will prompt the user to specify hardware emulation options. For now, default - #default settings will suffice. Press 'enter' to take default settings or enter 'no'. + # Android will prompt the user to specify hardware emulation options. For now, default + # default settings will suffice. Press 'enter' to take default settings or enter 'no'. ./android create avd -f -n $default_droid -t 1 -p $ANDROID_DIR/android-emulators/$default_droid --abi armeabi-v7a @@ -72,8 +67,8 @@ fi -if [[ $step == "3" ]]; then - #Here we will start up our default emulator to test that it is working properly. - #Once the device has booted we will use the Android Debug Bridge tool to gain - #a terminal in our device. +if [[ $step == "3" || $step == "0" ]]; then + # Here we will start up our default emulator to test that it is working properly. + # Once the device has booted we will use the Android Debug Bridge tool to gain + # a terminal in our device. cd $present_dir/install-sdk/tools @@ -82,12 +77,7 @@ cd ../platform-tools ./adb wait-for-device shell - #./adb wait-for-device shell mount -o rw,remount -t yaffs2 /dev/block/mtdblock1 /system - #./adb wait-for-device shell - #./adb push $ISSM_TIER/src/c/issm.exe /data/issm.exe - #./adb shell chmod 777 /data/issm.exe - #./adb shell /data/issm.exe fi -if [[ $step == "4" ]]; then +if [[ $step == "4" || $step == "0" ]]; then rm -rf install-sdk fi Index: /issm/trunk/externalpackages/android/android_aux.sh =================================================================== --- /issm/trunk/externalpackages/android/android_aux.sh (revision 13395) +++ /issm/trunk/externalpackages/android/android_aux.sh (revision 13395) @@ -0,0 +1,30 @@ +#!/bin/bash +# +# android_aux.sh serves as an auxiliary script for all installation +# scripts with the Android suffix. +# +# TODO: include M4 macros for generic options. +# + +sdk_rev=20 +ndk_rev=8 +api_levels="android-14,android-15,android-16" +host_triplet="arm-linux-androideabi" +default_droid="android-4.1" + +step=0; +j=1; + +echo Number of arguments is: $# +for arg in $* +do + if [[ "$arg" =~ --step=([0-9])* ]]; then + step=${BASH_REMATCH[1]}; + echo "Setting step to: " $step + elif [[ "$arg" =~ -j=([1-9]+[0-9]*) || "$arg" =~ ([1-9]+[0-9]*) ]]; then + j=${BASH_REMATCH[1]}; + echo "Number of jobs set to: " $j + else + echo "Option not recognized" + fi +done Index: sm/trunk/externalpackages/android/android_variables.sh =================================================================== --- /issm/trunk/externalpackages/android/android_variables.sh (revision 13394) +++ (revision ) @@ -1,5 +1,0 @@ -sdk_rev=20 -ndk_rev=8 -api_levels="android-14,android-15,android-16" -host_triplet="arm-linux-androideabi" -default_droid="android-4.1" Index: /issm/trunk/externalpackages/angel/install.sh =================================================================== --- /issm/trunk/externalpackages/angel/install.sh (revision 13394) +++ /issm/trunk/externalpackages/angel/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/appscan/install.sh =================================================================== --- /issm/trunk/externalpackages/appscan/install.sh (revision 13394) +++ /issm/trunk/externalpackages/appscan/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #AppScan install directory. Just symlink to your existing AppScan software Index: /issm/trunk/externalpackages/apr-util/install.sh =================================================================== --- /issm/trunk/externalpackages/apr-util/install.sh (revision 13395) +++ /issm/trunk/externalpackages/apr-util/install.sh (revision 13395) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf apr-util-1.4.1 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/apr-util-1.4.1.tar.gz' 'apr-util-1.4.1.tar.gz' + +#Untar +tar -zxvf apr-util-1.4.1.tar.gz + +#Move apr-util into src directory +mv apr-util-1.4.1/* src +rm -rf apr-util-1.4.1 + +#Configure apr-util +cd src +./configure --prefix="$ISSM_DIR/externalpackages/apr-util/install" --with-apr="$ISSM_DIR/externalpackages/apr/install" + +#Compile and install apr-util +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/apr/install.sh =================================================================== --- /issm/trunk/externalpackages/apr/install.sh (revision 13395) +++ /issm/trunk/externalpackages/apr/install.sh (revision 13395) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf apr-1.4.6 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/apr-1.4.6.tar.gz' 'apr-1.4.6.tar.gz' + +#Untar +tar -zxvf apr-1.4.6.tar.gz + +#Move apr into src directory +mv apr-1.4.6/* src +rm -rf apr-1.4.6 + +#Configure apr +cd src +./configure --prefix="$ISSM_DIR/externalpackages/apr/install" + +#Compile and install apr +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/aspell/install.sh =================================================================== --- /issm/trunk/externalpackages/aspell/install.sh (revision 13394) +++ /issm/trunk/externalpackages/aspell/install.sh (revision 13395) @@ -1,8 +1,9 @@ #!/bin/bash +set -eu #0: cleanup #1: install aspell #2: install en dictionary -step=0 +step=2 Index: /issm/trunk/externalpackages/autotools/install.sh =================================================================== --- /issm/trunk/externalpackages/autotools/install.sh (revision 13395) +++ /issm/trunk/externalpackages/autotools/install.sh (revision 13395) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + +rm -rf install +mkdir install + +export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH" + +#install autoconf +echo " === INSTALLING AUTOCONF ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.68.tar.gz' 'autoconf-2.68.tar.gz' +tar -zxvf autoconf-2.68.tar.gz +mv autoconf-2.68 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install automake +echo " === INSTALLING AUTOMAKE ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.11.3.tar.gz' 'automake-1.11.3.tar.gz' +tar -zxvf automake-1.11.3.tar.gz +mv automake-1.11.3 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install libtool +echo " === INSTALLING LIBTOOL ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool-2.4.2.tar.gz' 'libtool-2.4.2.tar.gz' +tar -zxvf libtool-2.4.2.tar.gz +rm libtool-2.4.2.tar.gz +mv libtool-2.4.2 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. Index: /issm/trunk/externalpackages/bbftp/install.sh =================================================================== --- /issm/trunk/externalpackages/bbftp/install.sh (revision 13394) +++ /issm/trunk/externalpackages/bbftp/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/blas/configs/macosx64/make.inc =================================================================== --- /issm/trunk/externalpackages/blas/configs/macosx64/make.inc (revision 13395) +++ /issm/trunk/externalpackages/blas/configs/macosx64/make.inc (revision 13395) @@ -0,0 +1,34 @@ +#################################################################### +# BLAS make include file. # +# March 2007 # +#################################################################### +# +SHELL = /bin/sh +# +# The machine (platform) identifier to append to the library names +# +PLAT = _LINUX +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O3 +DRVOPTS = $(OPTS) +NOOPT = +LOADER = gfortran +LOADOPTS = +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# The location and name of the Reference BLAS library. +# +BLASLIB = blas$(PLAT).a Index: /issm/trunk/externalpackages/blas/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/blas/install-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/blas/install-linux64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/blas/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/blas/install-macosx64.sh (revision 13395) +++ /issm/trunk/externalpackages/blas/install-macosx64.sh (revision 13395) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install BLAS blas.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/blas.tgz' 'blas.tgz' + +#Untar +tar -zxvf blas.tgz + +#Move blas into install directory +mv BLAS/* src +rm -rf BLAS + +#install +cd src +cp ../configs/macosx64/make.inc ./ +make + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/*.a . +ln -s blas_LINUX.a blas.a +ln -s blas_LINUX.a libblas.a Index: /issm/trunk/externalpackages/boost/install-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/boost/install-macosx-snowleopard.sh (revision 13395) +++ /issm/trunk/externalpackages/boost/install-macosx-snowleopard.sh (revision 13395) @@ -0,0 +1,35 @@ +#!/bin/bash + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_49_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz' + +#Untar +tar -zxvf boost_1_49_0.tar.gz + +#Move boost into install directory +mv boost_1_49_0/* src +rm -rf boost_1_49_0 +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +#./b2 address-model=32 architecture=x86 cxxflags="-arch i386" variant=release threading=multi install +./b2 toolset=darwin address-model=32 architecture=x86 variant=release threading=multi install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk/externalpackages/boost/install.sh =================================================================== --- /issm/trunk/externalpackages/boost/install.sh (revision 13394) +++ /issm/trunk/externalpackages/boost/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Note of caution: stop after boostrap phase, and run Index: /issm/trunk/externalpackages/bsdtar/install-win7.sh =================================================================== --- /issm/trunk/externalpackages/bsdtar/install-win7.sh (revision 13394) +++ /issm/trunk/externalpackages/bsdtar/install-win7.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/cccl/install-win7.orig.sh =================================================================== --- /issm/trunk/externalpackages/cccl/install-win7.orig.sh (revision 13394) +++ /issm/trunk/externalpackages/cccl/install-win7.orig.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/cccl/install-win7.sh =================================================================== --- /issm/trunk/externalpackages/cccl/install-win7.sh (revision 13394) +++ /issm/trunk/externalpackages/cccl/install-win7.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/chaco/install.sh =================================================================== --- /issm/trunk/externalpackages/chaco/install.sh (revision 13394) +++ /issm/trunk/externalpackages/chaco/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu # Some cleanup @@ -23,5 +24,5 @@ # Build chaco cd src/code -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/cmake/install.sh =================================================================== --- /issm/trunk/externalpackages/cmake/install.sh (revision 13394) +++ /issm/trunk/externalpackages/cmake/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -18,5 +19,5 @@ cd install ./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/colpack/install.sh =================================================================== --- /issm/trunk/externalpackages/colpack/install.sh (revision 13394) +++ /issm/trunk/externalpackages/colpack/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Erase install @@ -15,5 +16,5 @@ #compile cd src -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/cppcheck/install.sh =================================================================== --- /issm/trunk/externalpackages/cppcheck/install.sh (revision 13394) +++ /issm/trunk/externalpackages/cppcheck/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Erase install @@ -14,5 +15,5 @@ #compile cd src -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/dace/install.sh =================================================================== --- /issm/trunk/externalpackages/dace/install.sh (revision 13394) +++ /issm/trunk/externalpackages/dace/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/dakota/install-altix64-cosmos.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-altix64-cosmos.sh (revision 13394) +++ /issm/trunk/externalpackages/dakota/install-altix64-cosmos.sh (revision 13395) @@ -1,6 +1,4 @@ #!/bin/bash - -#Get number of cpus -NUMCPUS=$1; +set -eu #Some cleanup @@ -84,11 +82,11 @@ #Compile and install dakota cd src -if [ -z $NUMCPUS ]; +if [ $# -eq 0 ]; then make make install else - make -j $NUMCPUS - make -j $NUMCPUS install + make -j $1 + make -j $1 install fi cd .. Index: /issm/trunk/externalpackages/dakota/install-discover.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-discover.sh (revision 13394) +++ /issm/trunk/externalpackages/dakota/install-discover.sh (revision 13395) @@ -1,6 +1,4 @@ #!/bin/bash - -#Get number of cpus -NUMCPUS=$1; +set -eu #Some cleanup @@ -84,11 +82,11 @@ #Compile and install dakota cd src -if [ -z $NUMCPUS ]; +if [ $# -eq 0 ]; then make make install else - make -j $NUMCPUS - make -j $NUMCPUS install + make -j $1 + make -j $1 install fi cd .. Index: /issm/trunk/externalpackages/dakota/install-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-linux64-astrid.sh (revision 13394) +++ /issm/trunk/externalpackages/dakota/install-linux64-astrid.sh (revision 13395) @@ -1,6 +1,4 @@ #!/bin/bash - -#Get number of cpus -NUMCPUS=$1; +set -eu #Some cleanup @@ -84,11 +82,11 @@ #Compile and install dakota cd src -if [ -z $NUMCPUS ]; +if [ $# -eq 0 ]; then make make install else - make -j $NUMCPUS - make -j $NUMCPUS install + make -j $1 + make -j $1 install fi cd .. Index: /issm/trunk/externalpackages/dakota/install-linux64-murdo.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-linux64-murdo.sh (revision 13394) +++ /issm/trunk/externalpackages/dakota/install-linux64-murdo.sh (revision 13395) @@ -1,6 +1,4 @@ #!/bin/bash - -#Get number of cpus -NUMCPUS=$1; +set -eu #Some cleanup @@ -84,11 +82,11 @@ #Compile and install dakota cd src -if [ -z $NUMCPUS ]; +if [ $# -eq 0 ]; then make make install else - make -j $NUMCPUS - make -j $NUMCPUS install + make -j $1 + make -j $1 install fi cd .. Index: /issm/trunk/externalpackages/dakota/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-macosx64.sh (revision 13394) +++ /issm/trunk/externalpackages/dakota/install-macosx64.sh (revision 13395) @@ -1,6 +1,4 @@ #!/bin/bash - -#Get number of cpus -NUMCPUS=$1; +set -eu #Some cleanup @@ -37,5 +35,5 @@ --disable-mpi \ --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ - --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack -lPLAPACK " + --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " cd .. @@ -84,11 +82,11 @@ #Compile and install dakota cd src -if [ -z $NUMCPUS ]; +if [ $# -eq 0 ]; then make make install else - make -j $NUMCPUS - make -j $NUMCPUS install + make -j $1 + make -j $1 install fi cd .. Index: /issm/trunk/externalpackages/dakota/install-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/dakota/install-pleiades.sh (revision 13394) +++ /issm/trunk/externalpackages/dakota/install-pleiades.sh (revision 13395) @@ -1,12 +1,10 @@ #!/bin/bash - -#Get number of cpus -NUMCPUS=$1; +set -eu #Some cleanup rm -rf Dakota -rm -rf src -rm -rf install -mkdir src install +rm -rf src +rm -rf install +mkdir src install #Download from ISSM server @@ -31,11 +29,11 @@ #Configure dakota cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/dakota/install" \ - --without-graphics \ - --with-pic \ - --disable-mpi \ - --with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ - --with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ +--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" cd .. @@ -53,17 +51,17 @@ cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-cddlib/Makefile +mv temp ./src/methods/hopspack/src-cddlib/Makefile cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile +mv temp ./src/methods/hopspack/src-shared/Makefile cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-shared/Makefile +mv temp ./src/methods/hopspack/src-shared/Makefile cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-conveyor/Makefile +mv temp ./src/methods/hopspack/src-conveyor/Makefile cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/methods/hopspack/src-appspack/Makefile +mv temp ./src/methods/hopspack/src-appspack/Makefile cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp @@ -74,21 +72,21 @@ cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile +mv temp ./src/methods/acro/packages/tpl/3po/Makefile cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp -mv temp ./src/methods/acro/packages/tpl/3po/Makefile +mv temp ./src/methods/acro/packages/tpl/3po/Makefile cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp -mv temp ./src/packages/ampl/Makefile +mv temp ./src/packages/ampl/Makefile #Compile and install dakota -cd src -if [ -z $NUMCPUS ]; +cd src +if [ $# -eq 0 ]; then make make install else - make -j $NUMCPUS - make -j $NUMCPUS install + make -j $1 + make -j $1 install fi cd .. Index: /issm/trunk/externalpackages/distribute/install.sh =================================================================== --- /issm/trunk/externalpackages/distribute/install.sh (revision 13394) +++ /issm/trunk/externalpackages/distribute/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Download from ISSM server Index: /issm/trunk/externalpackages/doxygen/install.sh =================================================================== --- /issm/trunk/externalpackages/doxygen/install.sh (revision 13394) +++ /issm/trunk/externalpackages/doxygen/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -9,5 +10,5 @@ #Configure doxygen cd install && ./configure --prefix "$ISSM_DIR/externalpackages/doxygen/install" -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/esmf/install.sh =================================================================== --- /issm/trunk/externalpackages/esmf/install.sh (revision 13394) +++ /issm/trunk/externalpackages/esmf/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #0: cleanup @@ -32,5 +33,5 @@ #Compile and install esmf - if [ -z $1 ]; then + if [ $# -eq 0 ]; then make make install @@ -43,5 +44,5 @@ if [[ $install == "2" ]]; then cd esmf - if [ -z $1 ]; then + if [ $# -eq 0 ]; then make all_tests else Index: /issm/trunk/externalpackages/findbugs/install.sh =================================================================== --- /issm/trunk/externalpackages/findbugs/install.sh (revision 13394) +++ /issm/trunk/externalpackages/findbugs/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Erase install Index: /issm/trunk/externalpackages/flaim/install.sh =================================================================== --- /issm/trunk/externalpackages/flaim/install.sh (revision 13394) +++ /issm/trunk/externalpackages/flaim/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Erase symlink Index: /issm/trunk/externalpackages/freetype/install.sh =================================================================== --- /issm/trunk/externalpackages/freetype/install.sh (revision 13394) +++ /issm/trunk/externalpackages/freetype/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -22,5 +23,5 @@ #Compile and install freetype -if [ -z $1 ]; then +if [ $# -eq 0 ]; then sudo make else Index: /issm/trunk/externalpackages/gdal/install-murdo.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install-murdo.sh (revision 13395) +++ /issm/trunk/externalpackages/gdal/install-murdo.sh (revision 13395) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --without-png \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --with-unix-stdio-64=no + +#Patch GDALmake.opt +patch GDALmake.opt ../GDALmake.opt.patch + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/gdal/install.sh =================================================================== --- /issm/trunk/externalpackages/gdal/install.sh (revision 13394) +++ /issm/trunk/externalpackages/gdal/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -22,4 +23,5 @@ --prefix="$ISSM_DIR/externalpackages/gdal/install" \ --without-python \ + --without-png \ --with-netcdf=no \ --with-jasper=no \ @@ -32,5 +34,5 @@ #Compile and install gdal -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/gdaltokmz/install.sh =================================================================== --- /issm/trunk/externalpackages/gdaltokmz/install.sh (revision 13394) +++ /issm/trunk/externalpackages/gdaltokmz/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Download from ISSM server Index: /issm/trunk/externalpackages/geos5/install.sh =================================================================== --- /issm/trunk/externalpackages/geos5/install.sh (revision 13394) +++ /issm/trunk/externalpackages/geos5/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/git/install-nopython.sh =================================================================== --- /issm/trunk/externalpackages/git/install-nopython.sh (revision 13395) +++ /issm/trunk/externalpackages/git/install-nopython.sh (revision 13395) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install git-1.7.10.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/git-1.7.10.2.tar.gz' 'git-1.7.10.2.tar.gz' + +#Untar +tar -zxvf git-1.7.10.2.tar.gz + +#Move git into install directory +mv git-1.7.10.2/* src +rm -rf git-1.7.10.2 + +#install +cd src +./configure --prefix="$ISSM_DIR/externalpackages/git/install" + +#Compile +make install Index: /issm/trunk/externalpackages/git/install.sh =================================================================== --- /issm/trunk/externalpackages/git/install.sh (revision 13394) +++ /issm/trunk/externalpackages/git/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -17,5 +18,5 @@ #install cd src -./configure --prefix="$ISSM_DIR/externalpackages/git/install" +./configure --prefix="$ISSM_DIR/externalpackages/git/install" --with-python="$ISSM_DIR/externalpackages/python/install/bin/python" #Compile Index: /issm/trunk/externalpackages/gmake/install.sh =================================================================== --- /issm/trunk/externalpackages/gmake/install.sh (revision 13394) +++ /issm/trunk/externalpackages/gmake/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -21,5 +22,5 @@ ./configure --prefix=$ISSM_DIR/externalpackages/gmake/install -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make make install Index: /issm/trunk/externalpackages/googleearthtoolbox/install.sh =================================================================== --- /issm/trunk/externalpackages/googleearthtoolbox/install.sh (revision 13394) +++ /issm/trunk/externalpackages/googleearthtoolbox/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/graphviz/install.sh =================================================================== --- /issm/trunk/externalpackages/graphviz/install.sh (revision 13394) +++ /issm/trunk/externalpackages/graphviz/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -22,5 +23,5 @@ #Compile and install cd src -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/gsl/install-android.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-android.sh (revision 13394) +++ /issm/trunk/externalpackages/gsl/install-android.sh (revision 13395) @@ -1,33 +1,45 @@ #!/bin/bash -source $ANDROID_DIR/android_variables.sh +set -eu -#Some cleanup -rm -rf src install gsl-1.15 -mkdir src install +source $ANDROID_DIR/android_aux.sh -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' +if [[ $step == "1" || $step == "0" ]]; then -#Untar -tar -zxvf gsl-1.15.tar.gz + #Some cleanup + rm -rf src install gsl-1.15 + mkdir src install -#Move gsl into src directory -mv gsl-1.15/* src -rm -rf gsl-1.15 + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.' 'gsl-1.15.tar.gz' + + #Untar + tar -zxvf gsl-1.15.tar.gz + + #Move gsl into src directory + mv gsl-1.15/* src + rm -rf gsl-1.15 +fi #Configure gsl -cd src +if [[ $step == "2" || $step == "0" ]]; then + cd src + + autoreconf -iv --force -I $LIBTOOL_DIR/share/aclocal/ -./configure \ - --build="i386-apple-darwin10.8.0" \ - --host=$host_triplet\ - --prefix="$ISSM_DIR/externalpackages/gsl/install" + ./configure \ + --build="i386-apple-darwin10.8.0" \ + --host=$host_triplet \ + --prefix="$ISSM_DIR/externalpackages/gsl/install/" \ + --disable-static +fi #Compile gsl -if [ -z $1 ]; then - make -else - make -j $1 +if [[ $step == "3" || $step == "0" ]]; then + if [ $# -eq 0 ]; then + make $j + else + make -j $j + fi + + make install fi - -make install Index: /issm/trunk/externalpackages/gsl/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/gsl/install-linux64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -22,5 +23,5 @@ #Compile gsl -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/gsl/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-macosx64.sh (revision 13394) +++ /issm/trunk/externalpackages/gsl/install-macosx64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -24,5 +25,5 @@ #Compile gsl -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/gsl/install-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/gsl/install-pleiades.sh (revision 13394) +++ /issm/trunk/externalpackages/gsl/install-pleiades.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -22,5 +23,5 @@ #Compile gsl -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/gslib/install.sh =================================================================== --- /issm/trunk/externalpackages/gslib/install.sh (revision 13394) +++ /issm/trunk/externalpackages/gslib/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/h5py/install.sh =================================================================== --- /issm/trunk/externalpackages/h5py/install.sh (revision 13394) +++ /issm/trunk/externalpackages/h5py/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #needed further along Index: /issm/trunk/externalpackages/hdf5/install.sh =================================================================== --- /issm/trunk/externalpackages/hdf5/install.sh (revision 13394) +++ /issm/trunk/externalpackages/hdf5/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -19,5 +20,5 @@ cd src ./configure --prefix="$ISSM_DIR/externalpackages/hdf5/install" -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/ipython/install.sh =================================================================== --- /issm/trunk/externalpackages/ipython/install.sh (revision 13394) +++ /issm/trunk/externalpackages/ipython/install.sh (revision 13395) @@ -1,19 +1,19 @@ #!/bin/bash +set -eu #Some cleanup rm -rf src -rm -rf install -rm -rf ipython-0.12 -mkdir src install +rm -rf ipython-0.13 +mkdir src #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ipython-0.12.tar.gz' 'ipython-0.12.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ipython-0.13.tar.gz' 'ipython-0.13.tar.gz' #Untar -tar -zxvf ipython-0.12.tar.gz +tar -zxvf ipython-0.13.tar.gz #Move ipython into src directory -mv ipython-0.12/* src -rm -rf ipython-0.12 +mv ipython-0.13/* src +rm -rf ipython-0.13 #install ipython Index: /issm/trunk/externalpackages/kml/install.sh =================================================================== --- /issm/trunk/externalpackages/kml/install.sh (revision 13394) +++ /issm/trunk/externalpackages/kml/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Download from ISSM server Index: /issm/trunk/externalpackages/lapack/configs/linux64/make.inc =================================================================== --- /issm/trunk/externalpackages/lapack/configs/linux64/make.inc (revision 13394) +++ /issm/trunk/externalpackages/lapack/configs/linux64/make.inc (revision 13395) @@ -16,5 +16,5 @@ OPTS = -fPIC -O2 DRVOPTS = $(OPTS) -NOOPT = -O0 +NOOPT = -fPIC -O0 LOADER = gfortran LOADOPTS = Index: /issm/trunk/externalpackages/lapack/configs/macosx64/make.inc =================================================================== --- /issm/trunk/externalpackages/lapack/configs/macosx64/make.inc (revision 13395) +++ /issm/trunk/externalpackages/lapack/configs/macosx64/make.inc (revision 13395) @@ -0,0 +1,71 @@ +#################################################################### +# LAPACK make include file. # +# LAPACK, Version 3.4.0 # +# April 2012 # +#################################################################### +# +SHELL = /bin/sh +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O2 +DRVOPTS = $(OPTS) +NOOPT = -fPIC -O0 +LOADER = gfortran +LOADOPTS = +# +# Timer for the SECOND and DSECND routines +# +# Default : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME +#TIMER = EXT_ETIME +# For RS6K : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME_ +# TIMER = EXT_ETIME_ +# For gfortran compiler: SECOND and DSECND will use a call to the INTERNAL FUNCTION ETIME +TIMER = INT_ETIME +# If your Fortran compiler does not provide etime (like Nag Fortran Compiler, etc...) +# SECOND and DSECND will use a call to the INTERNAL FUNCTION CPU_TIME +# TIMER = INT_CPU_TIME +# If neither of this works...you can use the NONE value... In that case, SECOND and DSECND will always return 0 +# TIMER = NONE +# +# Configuration LAPACKE: Native C interface to LAPACK +# To generate LAPACKE library: type 'make lapackelib' +# Configuration file: turned off (default) +# Complex types: C99 (default) +# Name pattern: mixed case (default) +# (64-bit) Data model: LP64 (default) +# +# CC is the C compiler, normally invoked with options CFLAGS. +# +CC = gcc +CFLAGS = -O3 +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# Location of the extended-precision BLAS (XBLAS) Fortran library +# used for building and testing extended-precision routines. The +# relevant routines will be compiled and XBLAS will be linked only if +# USEXBLAS is defined. +# +# USEXBLAS = Yes +XBLASLIB = +# XBLASLIB = -lxblas +# +# The location of the libraries to which you will link. (The +# machine-specific, optimized BLAS library should be used whenever +# possible.) +# +BLASLIB = ../../librefblas.a +LAPACKLIB = liblapack.a +TMGLIB = libtmglib.a +LAPACKELIB = liblapacke.a Index: /issm/trunk/externalpackages/lapack/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/lapack/install-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/lapack/install-linux64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -20,5 +21,5 @@ #Compile and install lapack -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make lib else Index: /issm/trunk/externalpackages/lapack/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/lapack/install-macosx64.sh (revision 13395) +++ /issm/trunk/externalpackages/lapack/install-macosx64.sh (revision 13395) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install lapack-3.4.1 lapack-3.4.1.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/lapack-3.4.1.tgz' 'lapack-3.4.1.tgz' + +#Untar +tar -zxvf lapack-3.4.1.tgz + +#Move lapack into install directory +mv lapack-3.4.1/* src +rm -rf lapack-3.4.1 + +#install +cd src +cp ../configs/macosx64/make.inc ./ + +#Compile and install lapack +if [ $# -eq 0 ]; then + make lib +else + make -j $1 lib +fi + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/liblapack.a . Index: /issm/trunk/externalpackages/latex2rtf/install.sh =================================================================== --- /issm/trunk/externalpackages/latex2rtf/install.sh (revision 13394) +++ /issm/trunk/externalpackages/latex2rtf/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/libermate/install.sh =================================================================== --- /issm/trunk/externalpackages/libermate/install.sh (revision 13394) +++ /issm/trunk/externalpackages/libermate/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/libpng/install.sh =================================================================== --- /issm/trunk/externalpackages/libpng/install.sh (revision 13394) +++ /issm/trunk/externalpackages/libpng/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -22,5 +23,5 @@ #Compile and install libpng -if [ -z $1 ]; then +if [ $# -eq 0 ]; then sudo make else Index: /issm/trunk/externalpackages/m2html/install.sh =================================================================== --- /issm/trunk/externalpackages/m2html/install.sh (revision 13394) +++ /issm/trunk/externalpackages/m2html/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/matlab/install.sh =================================================================== --- /issm/trunk/externalpackages/matlab/install.sh (revision 13394) +++ /issm/trunk/externalpackages/matlab/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Erase symlink @@ -5,9 +6,9 @@ #Select or create a new simlink -ln -s /usr/local/pkgs/matlab-7.6/ install +#ln -s /usr/local/pkgs/matlab-7.6/ install #ln -s /discover/vis/mathworks/matlab_r2011b/ install #ln -s /usr/local/matlab704/ install #ln -s /usr/local/matlab711/ install -#ln -s /usr/local/matlab712/ install +ln -s /usr/local/matlab712/ install # Macintosh (OSX) simlink @@ -16,3 +17,4 @@ #ln -s /Applications/MATLAB_R2010a.app/ install #ln -s /Applications/MATLAB_R2012a.app/ install +#ln -s /Applications/MATLAB_R2011a.app/ install #ln -s /Applications/MATLAB*.app/ install Index: /issm/trunk/externalpackages/matplotlib/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/matplotlib/install-linux64.sh (revision 13395) +++ /issm/trunk/externalpackages/matplotlib/install-linux64.sh (revision 13395) @@ -0,0 +1,14 @@ +#/bin/bash +set -eu +export GIT_SSL_NO_VERIFY=true +export CC="gcc -fPIC " +export CXX="g++ -fPIC -L$ISSM_DIR/externalpackages/tcl/install/lib" +export F77="gfortran -fPIC" +export FC="gfortran -fPIC" +export FFLAGS=-ff2c + +git clone https://github.com/matplotlib/matplotlib +mv matplotlib src +cd src +python setup.py build +python setup.py install Index: /issm/trunk/externalpackages/matplotlib/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/matplotlib/install-macosx64.sh (revision 13395) +++ /issm/trunk/externalpackages/matplotlib/install-macosx64.sh (revision 13395) @@ -0,0 +1,27 @@ +#/bin/bash +set -eu + +export C_INCLUDE_PATH="$C_INCLUDE_PATH:/usr/include/c++/4.2.1" +export GIT_SSL_NO_VERIFY=true +export CC="gcc -fPIC -arch x86_64 -I/usr/include/c++/4.2.1" +export CXX="g++ -fPIC -arch x86_64 -I/usr/include/c++/4.2.1" +export F77="gfortran -fPIC -arch x86_64 -I/usr/include/c++/4.2.1" +export FC="gfortran -fPIC -arch x86_64 -I/usr/include/c++/4.2.1" +export FFLAGS="-ff2c -arch x86_64 -I/usr/include/c++/4.2.1" +export ARCHFLAGS="-arch x86_64 -I/usr/include/c++/4.2.1" + +git clone https://github.com/matplotlib/matplotlib +mv matplotlib src +mkdir deps +cd src + +#only try this if the classic python setup.py build approach does not work. The approach in the next 3 lines can +#trigger issues of permissions with freetype. Sometimes it is better to independently install freetype2 (from the +#issm externalpackages) as sudo (or root), so that the python script can detect its existence automatically. +#sudo make -f make.osx PREFIX=$ISSM_DIR/externalpackages/matplotlib/deps PYVERSION=$pythonversion fetch deps mpl_install_std +#sudo make -f make.osx PREFIX=$ISSM_DIR/externalpackages/matplotlib/deps PYVERSION=$pythonversion mpl_install_std +#python -c "import matplotlib; print 'Installed matplotlib', matplotlib.__version__, matplotlib.__file__" + +#to be tried: first get freetype and zlib and libpng installed in sudo mode +python setup.py build +python setup.py install Index: sm/trunk/externalpackages/matplotlib/install-osx.sh =================================================================== --- /issm/trunk/externalpackages/matplotlib/install-osx.sh (revision 13394) +++ (revision ) @@ -1,10 +1,0 @@ -#/bin/bash -pythonversion=2.7 -PYTHON=python${pythonversion} - -git clone https://github.com/matplotlib/matplotlib -mv matplotlib src -mkdir deps -cd src -make -f make.osx PREFIX=$ISSM_DIR/externalpackages/matplotlib/deps PYVERSION=$pythonversion fetch deps mpl_install_std -${PYTHON} -c "import matplotlib; print 'Installed matplotlib', matplotlib.__version__, matplotlib.__file__" Index: sm/trunk/externalpackages/matplotlib/install.sh =================================================================== --- /issm/trunk/externalpackages/matplotlib/install.sh (revision 13394) +++ (revision ) @@ -1,7 +1,0 @@ -#/bin/bash - -git clone https://github.com/matplotlib/matplotlib -mv matplotlib src -cd src -python setup.py build -python setup.py install Index: /issm/trunk/externalpackages/mercurial/install.sh =================================================================== --- /issm/trunk/externalpackages/mercurial/install.sh (revision 13394) +++ /issm/trunk/externalpackages/mercurial/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-altix64.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-altix64.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-altix64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-cosmos.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-cosmos.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-cosmos.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-discover.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-discover.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-discover.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-greenplanet.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-greenplanet.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-greenplanet.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-linux64.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-linux64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-macosx32.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-macosx32.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-macosx32.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-macosx64.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-macosx64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-pleiades.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-pleiades.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-win32.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-win32.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-win32.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-4.0-win7.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-4.0-win7.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-4.0-win7.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/metis/install-5.0.1-linux64.sh =================================================================== --- /issm/trunk/externalpackages/metis/install-5.0.1-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/metis/install-5.0.1-linux64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #metis 5.0 should be used: srand48 and drand48 are being redefined in conflict to the stdlib equivalent functions. Index: /issm/trunk/externalpackages/mitgcm/install.sh =================================================================== --- /issm/trunk/externalpackages/mitgcm/install.sh (revision 13394) +++ /issm/trunk/externalpackages/mitgcm/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Do these commands once: Index: /issm/trunk/externalpackages/modelE/install.sh =================================================================== --- /issm/trunk/externalpackages/modelE/install.sh (revision 13394) +++ /issm/trunk/externalpackages/modelE/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #modelE downloaded from the gis repository of the GISS (Goddard Institute for Space Studies) #at http://www.giss.nasa.gov/tools/modelE/ Index: /issm/trunk/externalpackages/modules/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/modules/install-macosx64.sh (revision 13395) +++ /issm/trunk/externalpackages/modules/install-macosx64.sh (revision 13395) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +rm -rf modules-3.2.9 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/modules-3.2.9.tar.gz' 'modules-3.2.9.tar.gz' + +#Untar +tar -zxvf modules-3.2.9.tar.gz + +#Move modules into src directory + +#Configure modules +cd modules-3.2.9 +./configure \ + --prefix=$ISSM_DIR/externalpackages/modules/install\ + --with-module-path=$ISSM_DIR/externalpackages/modules/install/modules/files\ + --with-version-path=$ISSM_DIR/externalpackages/modules/install/modules/versions\ + --with-tcl-lib=$ISSM_DIR/externalpackages/tcl/install/Library/Frameworks/Tcl.framework/Versions/8.5\ + --with-tcl-inc=$ISSM_DIR/externalpackages/tcl/install/Library/Frameworks/Tcl.framework/Versions/8.5/Headers\ + --with-tcl-ver=8.5\ + --with-tclx-lib=$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4\ + --with-tclx-inc=$ISSM_DIR/externalpackages/tclx/install/include\ + --with-tclx-ver=8.4\ + --with-etc-path=$ISSM_DIR/externalpackages/modules/install/modules/etc\ + --with-skel-path=$ISSM_DIR/externalpackages/modules/install/modules/etc/skel\ + --disable-dependency-tracking + +#Compile and install modules +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/modules/install.sh =================================================================== --- /issm/trunk/externalpackages/modules/install.sh (revision 13394) +++ /issm/trunk/externalpackages/modules/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/mpich2/install-1.0.2-altix64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 13394) +++ /issm/trunk/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 13395) @@ -31,5 +31,5 @@ #Compile mpich2 -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/mpich2/install-1.0.2-linux64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 13395) @@ -31,5 +31,5 @@ #Compile mpich2 -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/mpich2/install-1.0.2-macosx32.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 13394) +++ /issm/trunk/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 13395) @@ -30,5 +30,5 @@ #Compile mpich2 -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/mpich2/install-1.0.2-win32.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.0.2-win32.sh (revision 13394) +++ /issm/trunk/externalpackages/mpich2/install-1.0.2-win32.sh (revision 13395) @@ -28,5 +28,5 @@ #Compile mpich2 -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/mpich2/install-1.3.1-linux64-berg.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.3.1-linux64-berg.sh (revision 13395) +++ /issm/trunk/externalpackages/mpich2/install-1.3.1-linux64-berg.sh (revision 13395) @@ -0,0 +1,48 @@ +#!/bin/bash + +#version of mpich2 +#version=1.0.2p1 +version=1.3.1 +#version=1.4 + +#Some cleanup +rm -rf src install mpich2-$version + +#Create src and install directories +mkdir src install + +#Untar +tar -zxvf mpich2-$version.tar.gz + +#Move mpich2 into src directory +mv mpich2-$version/* src +rm -rf mpich2-$version + +#Configure mpich2 +cd src +if [[ "$version" == "1.0.2p1" ]]; +then + make distclean +fi + +source ../configure.sh + +if [[ "$version" == "1.0.2p1" ]]; +then + #Apply Patch to examples + patch ./examples/Makefile ../Examples.Makefile.patch + patch -R ./src/binding/cxx/mpicxx.h ../mpicxx.h.patch + patch -R ./src/include/mpicxx.h ../mpicxx.h.patch +fi + +#Compile mpich2 +if [ $# -eq 0 ]; +then + make +else + make -j $1 +fi +make install + +cd ../install/lib +rm -rf *.so Index: /issm/trunk/externalpackages/mpich2/install-1.4-linux64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.4-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/mpich2/install-1.4-linux64.sh (revision 13395) @@ -17,4 +17,5 @@ #Configure mpich2 cd src +export -n F90 export CFLAGS="$CFLAGS -fPIC" export FFLAGS="$FFLAGS -fPIC" @@ -26,5 +27,5 @@ #Compile mpich2 -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else @@ -32,6 +33,2 @@ fi make install - -#remove so files -cd ../install/lib -rm -rf *.so Index: /issm/trunk/externalpackages/mpich2/install-1.4-macosx32.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.4-macosx32.sh (revision 13394) +++ /issm/trunk/externalpackages/mpich2/install-1.4-macosx32.sh (revision 13395) @@ -29,5 +29,5 @@ #Compile mpich2 -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else @@ -35,6 +35,2 @@ fi make install - -#remove so files -cd ../install/lib -rm -rf *.so Index: /issm/trunk/externalpackages/mpich2/install-1.4-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/mpich2/install-1.4-macosx64.sh (revision 13394) +++ /issm/trunk/externalpackages/mpich2/install-1.4-macosx64.sh (revision 13395) @@ -29,5 +29,5 @@ #Compile mpich2 -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else @@ -35,6 +35,2 @@ fi make install - -#remove so files -cd ../install/lib -rm -rf *.so Index: /issm/trunk/externalpackages/ncview/install.sh =================================================================== --- /issm/trunk/externalpackages/ncview/install.sh (revision 13394) +++ /issm/trunk/externalpackages/ncview/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/netcdf-python/install.sh =================================================================== --- /issm/trunk/externalpackages/netcdf-python/install.sh (revision 13394) +++ /issm/trunk/externalpackages/netcdf-python/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/netcdf/install-4.0.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.0.sh (revision 13395) +++ /issm/trunk/externalpackages/netcdf/install-4.0.sh (revision 13395) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install netcdf-4.0.1 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netcdf-4.0.1.tar.gz" "netcdf-4.0.1.tar.gz" + +#Untar +tar -zxvf netcdf-4.0.1.tar.gz + +#Move netcdf to install directory +rm -rf src/* +mv netcdf-4.0.1/* src/ +rm -rf netcdf-4.0.1 + +#Configure and compile +cd src +./configure --prefix="$ISSM_DIR/externalpackages/netcdf/install" +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/netcdf/install-4.2.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install-4.2.sh (revision 13395) +++ /issm/trunk/externalpackages/netcdf/install-4.2.sh (revision 13395) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu +#you need hdf5 compiled + +#Some cleanup +rm -rf src install netcdf-4.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netcdf-4.2.tar.gz" "netcdf-4.2.tar.gz" + +#Untar +tar -zxvf netcdf-4.2.tar.gz + +#Move netcdf to install directory +rm -rf src/* +mv netcdf-4.2/* src/ +rm -rf netcdf-4.2 + +#Configure and compile +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/netcdf/install" \ + --disable-doxygen +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: sm/trunk/externalpackages/netcdf/install.sh =================================================================== --- /issm/trunk/externalpackages/netcdf/install.sh (revision 13394) +++ (revision ) @@ -1,35 +1,0 @@ -#!/bin/bash - -version=4.0.1 -#version=4.2 - -#for versions 4.2, you need hdf5 compiled, as well as doxygen for the -#documentation! - -#Some cleanup -rm -rf src install netcdf-$version -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netcdf-$version.tar.gz" "netcdf-$version.tar.gz" - -#Untar -tar -zxvf netcdf-$version.tar.gz - -#Move netcdf to install directory -rm -rf src/* -mv netcdf-$version/* src/ -rm -rf netcdf-$version - -#Configure and compile -cd src - -#version dependent: -./configure --prefix="$ISSM_DIR/externalpackages/netcdf/install" - -if [ -z $1 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk/externalpackages/nose/install-linux64-python2.sh =================================================================== --- /issm/trunk/externalpackages/nose/install-linux64-python2.sh (revision 13395) +++ /issm/trunk/externalpackages/nose/install-linux64-python2.sh (revision 13395) @@ -0,0 +1,14 @@ +#!/bin/bash +#Install Python nose module + +rm -rf src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/nose-1.1.2.tar.gz' 'nose-1.1.2.tar.gz' +tar -zxvf nose-1.1.2.tar.gz +mv nose-1.1.2 src +rm -rf nose-1.1.2 + +cd src +python ./setup.py build +python ./setup.py install Index: /issm/trunk/externalpackages/nose/install-linux64-python3.sh =================================================================== --- /issm/trunk/externalpackages/nose/install-linux64-python3.sh (revision 13395) +++ /issm/trunk/externalpackages/nose/install-linux64-python3.sh (revision 13395) @@ -0,0 +1,11 @@ +#!/bin/bash +#Install Python nose module + +rm -rf src + +svn checkout http://python-nose.googlecode.com/svn/branches/py3k +mv py3k src + +cd src +python ./setup.py build +python ./setup.py install Index: /issm/trunk/externalpackages/nose/install-macosx64-python2.sh =================================================================== --- /issm/trunk/externalpackages/nose/install-macosx64-python2.sh (revision 13395) +++ /issm/trunk/externalpackages/nose/install-macosx64-python2.sh (revision 13395) @@ -0,0 +1,14 @@ +#!/bin/bash +#Install Python nose module + +rm -rf src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/nose-1.1.2.tar.gz' 'nose-1.1.2.tar.gz' +tar -zxvf nose-1.1.2.tar.gz +mv nose-1.1.2 src +rm -rf nose-1.1.2 + +cd src +python ./setup.py build +python ./setup.py install Index: /issm/trunk/externalpackages/nose/install-macosx64-python3.sh =================================================================== --- /issm/trunk/externalpackages/nose/install-macosx64-python3.sh (revision 13395) +++ /issm/trunk/externalpackages/nose/install-macosx64-python3.sh (revision 13395) @@ -0,0 +1,11 @@ +#!/bin/bash +#Install Python nose module + +rm -rf src + +svn checkout http://python-nose.googlecode.com/svn/branches/py3k +mv py3k src + +cd src +python ./setup.py build +python ./setup.py install Index: sm/trunk/externalpackages/nose/install-macosx64sh =================================================================== --- /issm/trunk/externalpackages/nose/install-macosx64sh (revision 13394) +++ (revision ) @@ -1,29 +1,0 @@ -#!/bin/bash -#Install Python nose module - -pythonversion=2 - -rm -rf src - -if [[ $pythonversion == "3" ]];then - - svn checkout http://python-nose.googlecode.com/svn/branches/py3k - mv py3k src - - cd src - python ./setup.py build - python ./setup.py install -fi - -if [[ $pythonversion == "2" ]];then - - #Download from ISSM server - $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/nose-1.1.2.tar.gz' 'nose-1.1.2.tar.gz' - tar -zxvf nose-1.1.2.tar.gz - mv nose-1.1.2 src - rm -rf nose-1.1.2 - - cd src - python ./setup.py build - python ./setup.py install -fi Index: /issm/trunk/externalpackages/numpy/README =================================================================== --- /issm/trunk/externalpackages/numpy/README (revision 13395) +++ /issm/trunk/externalpackages/numpy/README (revision 13395) @@ -0,0 +1,9 @@ +For OSX 10.7 (Lion), the instructions here can be followed: +http://www.scipy.org/Installing_SciPy/Mac_OS_X + +For OSX 10.6 (Snow Leopard), the scipy folks recommend gcc and g++ version 4.0. +However, ISSM needs the gfortran version recommended in $ISSM_DIR/externalpackages/gfortran. +On the webpage listed above, make sure the "export CC" and "export CXX" commands point to the +binaries associated with this gfortran version (likely in /usr/local/gfortran/bin by default). +Once this gfortran is installed, the install script in this directory for Snow Leopard should +work. Index: /issm/trunk/externalpackages/numpy/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/numpy/install-linux64.sh (revision 13395) +++ /issm/trunk/externalpackages/numpy/install-linux64.sh (revision 13395) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +export CC="gcc -fPIC" +export CXX="g++ -fPIC" +export F77="gfortran -fPIC" +export FC="gfortran -fPIC" +export FFLAGS=-ff2c + +#clean up +rm -rf numpy + +#download numpy first +export GIT_SSL_NO_VERIFY=true +git clone https://github.com/numpy/numpy.git + +#install numpy +cd numpy +python setup.py build +python setup.py install +cd .. +python -c "import numpy; print 'Installed NumPy', numpy.__version__" +python -c "import numpy; numpy.test()" Index: /issm/trunk/externalpackages/numpy/install-macosx-lion.sh =================================================================== --- /issm/trunk/externalpackages/numpy/install-macosx-lion.sh (revision 13395) +++ /issm/trunk/externalpackages/numpy/install-macosx-lion.sh (revision 13395) @@ -0,0 +1,14 @@ +#!/bin/bash +set -eu + +export CC=gcc +export CXX=g++ +export FFLAGS=-ff2c + +#download numpy first +git clone https://github.com/numpy/numpy.git + +#install numpy +cd numpy +python setup.py build +python setup.py install Index: /issm/trunk/externalpackages/numpy/install-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/numpy/install-macosx-snowleopard.sh (revision 13395) +++ /issm/trunk/externalpackages/numpy/install-macosx-snowleopard.sh (revision 13395) @@ -0,0 +1,17 @@ +#!/bin/bash +set -eu + +# On OSX 10.6, gfortran gets installed in /usr/local/gfortran +export CC="/usr/local/gfortran/bin/gcc" +export CXX="/usr/local/gfortran/bin/g++" + +#download numpy first +git clone https://github.com/numpy/numpy.git + +#install numpy +cd numpy +python setup.py build +python setup.py install +cd .. +python -c "import numpy; print 'Installed NumPy', numpy.__version__" +python -c "import numpy; numpy.test()" Index: /issm/trunk/externalpackages/octave/install.sh =================================================================== --- /issm/trunk/externalpackages/octave/install.sh (revision 13394) +++ /issm/trunk/externalpackages/octave/install.sh (revision 13395) @@ -1,30 +1,31 @@ #!/bin/bash +set -eu #Some cleanup -version=3.6.1 -rm -rf src install octave-$version octave-$version.tar.gz +rm -rf src install octave-3.6.2 mkdir install src #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/octave-$version.tar.gz" "octave-$version.tar.gz" +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/octave-3.6.2.tar.gz" "octave-3.6.2.tar.gz" #Untar -tar -zxvf octave-$version.tar.gz +tar -zxvf octave-3.6.2.tar.gz #Move octave into install directory -mv octave-$version/* src -rm -rf octave-$version +mv octave-3.6.2/* src +rm -rf octave-3.6.2 #install cd src +./configure \ + --prefix=$ISSM_DIR/externalpackages/octave/install \ + --disable-readline -exit -make - -#Compile -cd ../install -mkdir lib -cd lib -cp ../../src/*.a . -ln -s octave_LINUX.a octave.a -ln -s octave_LINUX.a liboctave.a +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk/externalpackages/oofem/install.sh =================================================================== --- /issm/trunk/externalpackages/oofem/install.sh (revision 13394) +++ /issm/trunk/externalpackages/oofem/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -23,5 +24,5 @@ #Compile oofem cd targets/oofem-2.0 -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/openanalysis/install.sh =================================================================== --- /issm/trunk/externalpackages/openanalysis/install.sh (revision 13394) +++ /issm/trunk/externalpackages/openanalysis/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/packagemaker/install.sh =================================================================== --- /issm/trunk/externalpackages/packagemaker/install.sh (revision 13394) +++ /issm/trunk/externalpackages/packagemaker/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Erase symlink Index: /issm/trunk/externalpackages/pcre/install.sh =================================================================== --- /issm/trunk/externalpackages/pcre/install.sh (revision 13394) +++ /issm/trunk/externalpackages/pcre/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Cleaning Index: /issm/trunk/externalpackages/petsc/install-2.3.2-altix64-castor.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Step 1: unzip and install #Step 2: After Plapack implodes Index: /issm/trunk/externalpackages/petsc/install-2.3.2-cosmos.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-2.3.2-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-eric.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Step 1: unzip and install #Step 2: After MUMPS Crashes Index: /issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-2.3.2-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-2.3.2-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Step 1: unzip and install #Step 2: After Plapack implodes Index: /issm/trunk/externalpackages/petsc/install-2.3.2-win32-eric.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-2.3.2-win7.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-2.3.2-win7.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-2.3.2-win7.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-3.1-altix64-castor.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Step 1: unzip and install #Step 2: After Plapack implodes Index: /issm/trunk/externalpackages/petsc/install-3.1-cosmos.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.1-cosmos.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.1-cosmos.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-3.1-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-3.1-macosx32-mathieu.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-3.1-macosx32-ogive.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-3.1-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.1-pleiades.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.1-pleiades.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Step 1: unzip and install #Step 2: After Plapack implodes Index: /issm/trunk/externalpackages/petsc/install-3.1-ubuntu64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.1-ubuntu64.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.1-ubuntu64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-3.1-win7.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.1-win7.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.1-win7.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-3.2-discover.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.2-discover.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.2-discover.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -21,5 +22,5 @@ --with-batch=1 \ --with-debugging=0 \ - --with-shared-libraries=0 \ + --with-shared-libraries=1 \ --known-mpi-shared-libraries=1 \ --with-mpi-dir=/usr/local/intel/mpi/4.0.3.008/lib64/ \ @@ -32,5 +33,5 @@ --download-scalapack=no \ --download-blacs=no \ - --download-plapack=yes \ + --download-plapack=no \ --download-parmetis=yes \ --with-pic=1 Index: /issm/trunk/externalpackages/petsc/install-3.2-greenplanet.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.2-greenplanet.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.2-greenplanet.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/petsc/install-3.2-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.2-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.2-linux64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -22,5 +23,5 @@ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ - --with-shared-libraries=0 \ + --with-shared-libraries=1 \ --download-mumps=yes \ --download-scalapack=yes \ Index: /issm/trunk/externalpackages/petsc/install-3.2-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.2-macosx64.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.2-macosx64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -18,13 +19,13 @@ --prefix="$ISSM_DIR/externalpackages/petsc/install" \ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --PETSC_ARCH=macosx-gnu \ + --PETSC_ARCH="macosx-gnu" \ --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \ --with-debugging=0 \ - --with-shared-libraries=0 \ + --with-shared-libraries=1 \ --download-mumps=yes \ --download-scalapack=yes \ --download-blacs=yes \ --download-blas=yes \ - --download-plapack=yes \ + --download-plapack=no \ --download-parmetis=yes \ --download-f-blas-lapack=yes Index: /issm/trunk/externalpackages/petsc/install-3.2-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.2-pleiades.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-3.2-pleiades.sh (revision 13395) @@ -1,6 +1,7 @@ #!/bin/bash +set -eu #Step 1: unzip and install #Step 2: After Plapack implodes -STEP=1 +STEP=2 if [ $STEP -eq 1 ]; then @@ -25,5 +26,5 @@ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ - --with-shared-libraries=0 \ + --with-shared-libraries=1 \ --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ --known-mpi-shared-libraries=1 \ @@ -52,5 +53,5 @@ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ - --with-shared-libraries=0 \ + --with-shared-libraries=1 \ --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ --with-mpi-lib=/nasa/sgi/mpt/1.25/lib/libmpi.so \ Index: /issm/trunk/externalpackages/petsc/install-3.3-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.3-linux64.sh (revision 13395) +++ /issm/trunk/externalpackages/petsc/install-3.3-linux64.sh (revision 13395) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.3-p2 src +mkdir install src + +#Download from ISSM server +$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 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --download-metis=yes \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/trunk/externalpackages/petsc/install-3.3-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-3.3-macosx64.sh (revision 13395) +++ /issm/trunk/externalpackages/petsc/install-3.3-macosx64.sh (revision 13395) @@ -0,0 +1,36 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.3-p2 src +mkdir install src + +#Download from ISSM server +$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 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \ + --PETSC_ARCH="macosx-gnu" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --download-metis=yes + +#Compile petsc and install it +make +make install Index: /issm/trunk/externalpackages/petsc/install-dev-linux64.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-dev-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-dev-linux64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu STEP=2 @@ -21,6 +22,6 @@ # configure script # Note: using metis from externalpackages did not work... -# for now downloading new metis -# -then rename metis in externalpackages to metis2 +# -for now download new metis +# -rename metis in externalpackages to metis2 @@ -35,14 +36,22 @@ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ --with-debugging=0 \ - --with-shared-libraries=0 \ - --download-metis=yes \ + --with-shared-libraries=1 \ --download-mumps=yes \ + --download-plapack=yes \ --download-scalapack=yes \ - --download-blacs=yes \ + --download-blacs=yes \ --download-blas=yes \ --download-f-blas-lapack=yes \ - --download-plapack=yes \ --download-parmetis=yes \ + --download-metis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-pastix=yes \ + --download-ptscotch=yes \ + --download-spooles=yes \ --download-spai=yes \ + --download-superlu=yes \ + --download-hypre=yes \ + --download-prometheus=yes \ --with-pic=1 Index: /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh (revision 13394) +++ /issm/trunk/externalpackages/petsc/install-dev-pleiades.sh (revision 13395) @@ -1,6 +1,6 @@ #!/bin/bash +set -eu #Step 0: download -#Step 1: install before plapack crasehs -#Step 2: After Plapack implodes +#Step 1: install and write script STEP=0 @@ -19,5 +19,4 @@ # cd config/BuildSystem # hg pull -u - # configure script @@ -56,6 +55,9 @@ --download-spooles=yes \ --download-spai=yes \ - --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ + --download-superlu=yes \ + --download-hypre=yes \ + --download-prometheus=yes \ --FFLAGS=-I/usr/include \ + --with-cxx=icpc \ --with-cc=icc \ --with-fc=ifort \ @@ -64,46 +66,5 @@ --CXXOPTFLAGS=" -O3 -xS" \ --with-pic=1 - echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/documentation/faq/petsc32/) ==" - echo "== Then run STEP=2 ==" -fi -if [ $STEP -eq 2 ]; then - cd src - ./config/configure.py \ - --prefix="$ISSM_DIR/externalpackages/petsc/install" \ - --with-batch=1 \ - --PETSC_ARCH="$ISSM_ARCH" \ - --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ - --with-debugging=0 \ - --with-shared-libraries=0 \ - --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ - --with-mpi-lib=/nasa/sgi/mpt/2.04/lib/libmpi.so \ - --with-mpi-include=/nasa/sgi/mpt/2.04/include \ - --known-mpi-shared-libraries=1 \ - --download-mumps=yes \ - --download-scalapack=yes \ - --download-blacs=yes \ - --download-blas=yes \ - --with-f-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ - --download-parmetis=yes \ - --download-metis=yes \ - --with-cxx=icpc \ - --download-hypre=yes \ - --download-trilinos=yes \ - --download-prometheus=yes \ - --download-euclid=yes \ - --download-pastix=yes \ - --download-ptscotch=yes \ - --download-spooles=yes \ - --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ - --with-spai-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ - --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ - --FFLAGS=-I/usr/include \ - --with-cc=icc \ - --with-fc=ifort \ - --COPTFLAGS=" -O3 -xS" \ - --FOPTFLAGS=" -O3 -xS" \ - --CXXOPTFLAGS=" -O3 -xS" \ - --with-pic=1 - cat > script.queue << EOF + cat > script.queue << EOF #PBS -S /bin/bash #PBS -q debug Index: /issm/trunk/externalpackages/polygonclipper/install.sh =================================================================== --- /issm/trunk/externalpackages/polygonclipper/install.sh (revision 13394) +++ /issm/trunk/externalpackages/polygonclipper/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/pyclips/install.sh =================================================================== --- /issm/trunk/externalpackages/pyclips/install.sh (revision 13394) +++ /issm/trunk/externalpackages/pyclips/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/pysvn/install.sh =================================================================== --- /issm/trunk/externalpackages/pysvn/install.sh (revision 13395) +++ /issm/trunk/externalpackages/pysvn/install.sh (revision 13395) @@ -0,0 +1,26 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf pysvn-1.7.6 +mkdir src + +export CC=/usr/local/gfortran/bin/gcc +export CXX=/usr/local/gfortran/bin/g++ +export FFLAGS=-ff2c + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/pysvn-1.7.6.tar.gz' 'pysvn-1.7.6.tar.gz' + +#Untar +tar -zxvf pysvn-1.7.6.tar.gz + +#Move pysvn into src directory +mv pysvn-1.7.6/* src +rm -rf pysvn-1.7.6 + +$install +cd src +python setup.py build +python setup.py install Index: /issm/trunk/externalpackages/python/install-2.7.3-linux64.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2.7.3-linux64.sh (revision 13395) +++ /issm/trunk/externalpackages/python/install-2.7.3-linux64.sh (revision 13395) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure python +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/python/install" \ + --enable-shared + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install/include +cp python2.7/* ./ +cd ../lib +ln -s libpython2.7.so.1.0 libpython.so Index: /issm/trunk/externalpackages/python/install-2.7.3-macosx-lion.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2.7.3-macosx-lion.sh (revision 13395) +++ /issm/trunk/externalpackages/python/install-2.7.3-macosx-lion.sh (revision 13395) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure and compile +cd src +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install + +#get rid of bin, because it's just a copy of +#Library/Frameworks/Python.framework/Versions/2.7/bin, and will not reflect +#new changes being made +rm -rf bin +ln -s Library/Frameworks/Python.framework/Headers include +ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib +ln -s Library/Frameworks/Python.framework/Versions/2.7/bin bin + +#Patch pyport.h: +cd include +patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: /issm/trunk/externalpackages/python/install-2.7.3-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/python/install-2.7.3-macosx-snowleopard.sh (revision 13395) +++ /issm/trunk/externalpackages/python/install-2.7.3-macosx-snowleopard.sh (revision 13395) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#exports +export MACOSX_DEPLOYMENT_TARGET=10.6 + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure doxygen +cd src +# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory +# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include +./configure --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" + +#make +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install +ln -s Library/Frameworks/Python.framework/Headers include +ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib + +#Patch pyport.h: +cd include +patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: /issm/trunk/externalpackages/python/install-3.2.2-linux64.sh =================================================================== --- /issm/trunk/externalpackages/python/install-3.2.2-linux64.sh (revision 13395) +++ /issm/trunk/externalpackages/python/install-3.2.2-linux64.sh (revision 13395) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-3.2.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz + +#exports +export CC + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* src +rm -rf Python-3.2.2 + +#Configure python +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/python/install" \ + --enable-shared + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install/bin +ln -s python3.2 python +cd ../ +ln -s Python.framework/Versions/3.2/include/python3.2m include +ln -s Python.framework/Versions/3.2/lib/ lib Index: /issm/trunk/externalpackages/python/install-3.2.2-macosx-lion.sh =================================================================== --- /issm/trunk/externalpackages/python/install-3.2.2-macosx-lion.sh (revision 13395) +++ /issm/trunk/externalpackages/python/install-3.2.2-macosx-lion.sh (revision 13395) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-3.2.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz + +#exports +export CC + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* src +rm -rf Python-3.2.2 + +#Configure doxygen +cd src +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" + +#obsolete? +#./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" + +#make +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd install/bin +ln -s python3.2 python +cd ../ +ln -s Python.framework/Versions/3.2/include/python3.2m include +ln -s Python.framework/Versions/3.2/lib/ lib Index: /issm/trunk/externalpackages/python/install-3.2.2-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/python/install-3.2.2-macosx-snowleopard.sh (revision 13395) +++ /issm/trunk/externalpackages/python/install-3.2.2-macosx-snowleopard.sh (revision 13395) @@ -0,0 +1,41 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-3.2.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz + +#exports +export CC +export MACOSX_DEPLOYMENT_TARGET=10.6 + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* src +rm -rf Python-3.2.2 + +#Configure doxygen +cd src +# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory +# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" + +#make +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install +cd .. + +cd install/bin +ln -s python3.2 python +cd ../ +ln -s Python.framework/Versions/3.2/include/python3.2m include +ln -s Python.framework/Versions/3.2/lib/ lib Index: sm/trunk/externalpackages/python/install-linux64-astrid.sh =================================================================== --- /issm/trunk/externalpackages/python/install-linux64-astrid.sh (revision 13394) +++ (revision ) @@ -1,48 +1,0 @@ -#!/bin/bash -#wget http://python.org/ftp/python/version/Python-version.tgz - -#version=3.2.2 -version=2.7.2 - -#Some cleanup -rm -rf install src -rm -rf Python-$version -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-$version.tgz Python-$version.tgz - -#exports -export CC - -#Untar and move python into install directory -tar -zxvf Python-$version.tgz -mv Python-$version/* src -rm -rf Python-$version - -#Configure python -cd src -./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-shared - -if [ -z $1 ]; then - make -else - make -j $1 -fi -make install - -#Some modifications to be done in case version is 3.2: -if [[ $version == "3.2.2" ]]; then - cd ../install/bin - ln -s python3.2 python - cd ../ - ln -s Python.framework/Versions/3.2/include/python3.2m include - ln -s Python.framework/Versions/3.2/lib/ lib -fi -if [[ $version == "2.7.2" ]]; then - cd ../install/include - cp python2.7/* ./ - cd ../lib - ln -s libpython2.7.so.1.0 libpython.so - -fi Index: sm/trunk/externalpackages/python/install-macosx-lion.sh =================================================================== --- /issm/trunk/externalpackages/python/install-macosx-lion.sh (revision 13394) +++ (revision ) @@ -1,42 +1,0 @@ -#!/bin/bash -#wget http://python.org/ftp/python/version/Python-version.tgz - -#version=3.2.2 -version=2.7.2 - -#Some cleanup -rm -rf install src -rm -rf Python-$version -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-$version.tgz Python-$version.tgz - -#exports -export CC - -#Untar and move python into install directory -tar -zxvf Python-$version.tgz -mv Python-$version/* src -rm -rf Python-$version - -#Configure doxygen -cd src -./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" -if [ -z $1 ]; then - make -else - make -j $1 -fi -make install - -#Some modifications to be done in case version is 3.2: -if [[ $version == "3.2.2" ]]; then - cd install/bin - ln -s python3.2 python - cd ../ - ln -s Python.framework/Versions/3.2/include/python3.2m include - ln -s Python.framework/Versions/3.2/lib/ lib - - -fi Index: sm/trunk/externalpackages/python/install-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/python/install-macosx-snowleopard.sh (revision 13394) +++ (revision ) @@ -1,50 +1,0 @@ -#!/bin/bash -#wget http://python.org/ftp/python/version/Python-version.tgz - -#version=3.2.2 -version=2.7.2 - -#Some cleanup -rm -rf install src -rm -rf Python-$version -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-$version.tgz Python-$version.tgz - -#exports -export CC -export MACOSX_DEPLOYMENT_TARGET=10.6 - -#Untar and move python into install directory -tar -zxvf Python-$version.tgz -mv Python-$version/* src -rm -rf Python-$version - -#Configure doxygen -cd src -# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory -# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include -./configure --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" -if [ -z $1 ]; then - make -else - make -j $1 -fi -make install - -#Some modifications to be done in case version is 3.2: -if [[ $version == "3.2.2" ]]; then - cd install/bin - ln -s python3.2 python - cd ../ - ln -s Python.framework/Versions/3.2/include/python3.2m include - ln -s Python.framework/Versions/3.2/lib/ lib -fi - -#Some modifications to be done in case version is 2.7 -if [[ $version == "2.7.2" ]]; then - cd ../install - ln -s Library/Frameworks/Python.framework/Headers include - ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib -fi Index: /issm/trunk/externalpackages/python/patches/pyport.h.patch =================================================================== --- /issm/trunk/externalpackages/python/patches/pyport.h.patch (revision 13395) +++ /issm/trunk/externalpackages/python/patches/pyport.h.patch (revision 13395) @@ -0,0 +1,22 @@ +680a681 +> #ifdef isalnum +682a684,685 +> #endif +> #ifdef isalpha +684a688,689 +> #endif +> #ifdef islower +686a692,693 +> #endif +> #ifdef isspace +688a696,697 +> #endif +> #ifdef isupper +690a700,701 +> #endif +> #ifdef tolower +692a704,705 +> #endif +> #ifdef toupper +695a709 +> #endif Index: /issm/trunk/externalpackages/python/patches/pyport.h.patch.bugreport =================================================================== --- /issm/trunk/externalpackages/python/patches/pyport.h.patch.bugreport (revision 13395) +++ /issm/trunk/externalpackages/python/patches/pyport.h.patch.bugreport (revision 13395) @@ -0,0 +1,1 @@ +http://bugs.python.org/issue10910 Index: /issm/trunk/externalpackages/qhull/install.sh =================================================================== --- /issm/trunk/externalpackages/qhull/install.sh (revision 13394) +++ /issm/trunk/externalpackages/qhull/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/rats/install.sh =================================================================== --- /issm/trunk/externalpackages/rats/install.sh (revision 13394) +++ /issm/trunk/externalpackages/rats/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Erase install Index: /issm/trunk/externalpackages/readline/install.sh =================================================================== --- /issm/trunk/externalpackages/readline/install.sh (revision 13394) +++ /issm/trunk/externalpackages/readline/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/rose/install.sh =================================================================== --- /issm/trunk/externalpackages/rose/install.sh (revision 13394) +++ /issm/trunk/externalpackages/rose/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -22,5 +23,5 @@ --srcdir=$ISSM_DIR/externalpackages/rose/source -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/satstress/install.sh =================================================================== --- /issm/trunk/externalpackages/satstress/install.sh (revision 13394) +++ /issm/trunk/externalpackages/satstress/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/scipy/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/scipy/install-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/scipy/install-linux64.sh (revision 13395) @@ -1,9 +1,4 @@ #!/bin/bash - -#1: install numpy -#2 install scipy -#3 erase -install=2 - +set -eu export CC="gcc -fPIC" @@ -13,37 +8,21 @@ export FFLAGS=-ff2c +#clean up +rm -rf scipy -if [[ $install == "1" ]];then +#download scipy +export GIT_SSL_NO_VERIFY=true +git clone https://github.com/scipy/scipy.git - #download numpy first +#install scipy +cd scipy +export BLAS_SRC=$ISSM_DIR/externalpackages/blas/install/lib +export BLAS=$ISSM_DIR/externalpackages/blas/install/lib +export LAPACK_SRC=$ISSM_DIR/externalpackages/lapack/install/lib +export LAPACK=$ISSM_DIR/externalpackages/lapack/install/lib - export GIT_SSL_NO_VERIFY=true - git clone https://github.com/numpy/numpy.git - - #install numpy - cd numpy - python setup.py build - python setup.py install - - -elif [[ $install == "2" ]];then - - #download scipy - export GIT_SSL_NO_VERIFY=true - git clone https://github.com/scipy/scipy.git - - #install scipy - cd scipy - export BLAS_SRC=$ISSM_DIR/externalpackages/blas/install/lib - export BLAS=$ISSM_DIR/externalpackages/blas/install/lib - export LAPACK_SRC=$ISSM_DIR/externalpackages/lapack/install/lib - export LAPACK=$ISSM_DIR/externalpackages/lapack/install/lib - - python setup.py build - python setup.py install - -elif [[ $install == "3" ]];then - rm -rf numpy scipy -else - echo "Choice not covered" -fi +python setup.py build +python setup.py install +cd .. +python -c "import scipy; print 'Installed SciPy', scipy.__version__" +#python -c "import scipy; scipy.test()" Index: /issm/trunk/externalpackages/scipy/install-macosx-lion.sh =================================================================== --- /issm/trunk/externalpackages/scipy/install-macosx-lion.sh (revision 13394) +++ /issm/trunk/externalpackages/scipy/install-macosx-lion.sh (revision 13395) @@ -1,39 +1,20 @@ #!/bin/bash - -#1: install numpy -#2 install scipy -#3 erase -install=2 - +set -eu export CC=gcc export CXX=g++ export FFLAGS=-ff2c + +#download scipy +git clone https://github.com/scipy/scipy.git +#install scipy +cd scipy +export BLAS_SRC=$ISSM_DIR/externalpackages/blas/install/lib +export BLAS=$ISSM_DIR/externalpackages/blas/install/lib +export LAPACK_SRC=$ISSM_DIR/externalpackages/lapack/install/lib +export LAPACK=$ISSM_DIR/externalpackages/lapack/install/lib -if [[ $install == "1" ]];then - - #download numpy first - git clone https://github.com/numpy/numpy.git - - #install numpy - cd numpy - python setup.py build - python setup.py install - - -elif [[ $install == "2" ]];then - - #download scipy - git clone https://github.com/scipy/scipy.git - - #install scipy - cd scipy - python setup.py build - python setup.py install - -elif [[ $install == "3" ]];then - rm -rf numpy scipy -else - echo "Choice not covered" -fi +#install scipy +python setup.py build +python setup.py install Index: /issm/trunk/externalpackages/scipy/install-macosx-snowleopard.sh =================================================================== --- /issm/trunk/externalpackages/scipy/install-macosx-snowleopard.sh (revision 13394) +++ /issm/trunk/externalpackages/scipy/install-macosx-snowleopard.sh (revision 13395) @@ -1,45 +1,17 @@ #!/bin/bash -PYVERSION=2.7 -PYTHON=python${PYVERSION} +set -eu -#1: install numpy -#2 install scipy -#3 erase -install=2 +# On OSX 10.6, fgortran gets installed in /usr/local/gfortran +export CC="/usr/local/gfortran/bin/gcc" +export CXX="/usr/local/gfortran/bin/g++" -# gfortran 4.6 (see ISSM_DIR/externalpackages/gfortran) is necessary for ISSM compilation. -# On OSX 10.6, this recommended version gets installed in /usr/local/gfortran -export CC=/usr/local/gfortran/bin/gcc -export CXX=/usr/local/gfortran/bin/g++ +#download scipy +git clone https://github.com/scipy/scipy.git -if [[ $install == "1" ]];then - - #download numpy first - git clone https://github.com/numpy/numpy.git - - #install numpy - cd numpy - python setup.py build - python setup.py install - cd .. - ${PYTHON} -c "import numpy; print 'Installed NumPy', numpy.__version__" - ${PYTHON} -c "import numpy; numpy.test()" - -elif [[ $install == "2" ]];then - - #download scipy - git clone https://github.com/scipy/scipy.git - - #install scipy - cd scipy - python setup.py build - python setup.py install - cd .. - ${PYTHON} -c "import scipy; print 'Installed SciPy', scipy.__version__" - ${PYTHON} -c "import scipy; scipy.test()" - -elif [[ $install == "3" ]];then - rm -rf numpy scipy -else - echo "Choice not covered" -fi +#install scipy +cd scipy +python setup.py build +python setup.py install +cd .. +python -c "import scipy; print 'Installed SciPy', scipy.__version__" +python -c "import scipy; scipy.test()" Index: /issm/trunk/externalpackages/scotch/install.sh =================================================================== --- /issm/trunk/externalpackages/scotch/install.sh (revision 13394) +++ /issm/trunk/externalpackages/scotch/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu # Some cleanup Index: /issm/trunk/externalpackages/shapelib/install.sh =================================================================== --- /issm/trunk/externalpackages/shapelib/install.sh (revision 13394) +++ /issm/trunk/externalpackages/shapelib/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu # Some cleanup @@ -25,5 +26,5 @@ # Build shapelib and run self-tests cd src -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/slepc/install.sh =================================================================== --- /issm/trunk/externalpackages/slepc/install.sh (revision 13394) +++ /issm/trunk/externalpackages/slepc/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -18,5 +19,5 @@ cd install ./config/configure.py -if [ -z $1 ]; then +if [ $# -eq 0 ]; then make else Index: /issm/trunk/externalpackages/sqlite/install.sh =================================================================== --- /issm/trunk/externalpackages/sqlite/install.sh (revision 13395) +++ /issm/trunk/externalpackages/sqlite/install.sh (revision 13395) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf sqlite-autoconf-3071300 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/sqlite-autoconf-3071300.tar.gz' 'sqlite-autoconf-3071300.tar.gz' + +#Untar +tar -zxvf sqlite-autoconf-3071300.tar.gz + +#Move sqlite-autoconf into src directory +mv sqlite-autoconf-3071300/* src +rm -rf sqlite-autoconf-3071300 + +#Configure sqlite-autoconf +cd src +./configure --prefix="$ISSM_DIR/externalpackages/sqlite/install" + +#Compile and install sqlite-autoconf +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/svn/install.sh =================================================================== --- /issm/trunk/externalpackages/svn/install.sh (revision 13395) +++ /issm/trunk/externalpackages/svn/install.sh (revision 13395) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf subversion-1.6.18 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/subversion-1.6.18.tar.gz' 'subversion-1.6.18.tar.gz' + +#Untar +tar -zxvf subversion-1.6.18.tar.gz + +#Move subversion into src directory +mv subversion-1.6.18/* src +rm -rf subversion-1.6.18 + +#Configure subversion +cd src +./configure --prefix="$ISSM_DIR/externalpackages/svn/install" \ + --with-swig="$ISSM_DIR/externalpackages/swig/install" \ + PYTHON2="$ISSM_DIR/externalpackages/python/install/bin/python" \ + --with-sqlite="$ISSM_DIR/externalpackages/sqlite/install" + +#Compile and install subversion +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/swig/install.sh =================================================================== --- /issm/trunk/externalpackages/swig/install.sh (revision 13394) +++ /issm/trunk/externalpackages/swig/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup @@ -18,12 +19,19 @@ #cp $ISSM_DIR/externalpackages/pcre/install/pcre.h ./Source/Include/ #cp $ISSM_DIR/externalpackages/pcre/install/.libs/* ./Source/Include/ -export CFLAGS="$CFLAGS -I$ISSM_DIR/externalpackages/pcre/install" +export CFLAGS="-I$ISSM_DIR/externalpackages/pcre/install" export LDFLAGS="-L$ISSM_DIR/externalpackages/pcre/install/.libs/" export LIBS="-lpcre" -#Configure doxygen +#Configure swig ./configure \ - --prefix="$ISSM_DIR/externalpackages/python/install" \ + --prefix="$ISSM_DIR/externalpackages/swig/install" \ --with-pcre-prefix="$ISSM_DIR/externalpackages/pcre/install" \ - --with-pcre-exec-prefix="$ISSM_DIR/externalpackages/pcre/install" -make + --with-pcre-exec-prefix="$ISSM_DIR/externalpackages/pcre/install" \ + --with-python="$ISSM_DIR/externalpackages/python/install/bin/python" + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi make install Index: /issm/trunk/externalpackages/tao/install-2.0.sh =================================================================== --- /issm/trunk/externalpackages/tao/install-2.0.sh (revision 13395) +++ /issm/trunk/externalpackages/tao/install-2.0.sh (revision 13395) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu +#http://www.mcs.anl.gov/research/projects/tao/download/index.html + +#Compatible with PETSc 3.2 + +#Some cleanup +rm -rf install tao-2.0-p3 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tao-2.0-p3.tar.gz' 'tao-2.0-p3.tar.gz' + +#Untar +tar -zxvf tao-2.0-p3.tar.gz + +#move into place +mv tao-2.0-p3/* install/ +rm -rf tao-2.0-p3 +cd install +export TAO_DIR="$ISSM_DIR/externalpackages/tao/install/" + +#petsc needs to be compiled with --with-clanguage=C++ +make Index: /issm/trunk/externalpackages/tao/install-2.1.sh =================================================================== --- /issm/trunk/externalpackages/tao/install-2.1.sh (revision 13395) +++ /issm/trunk/externalpackages/tao/install-2.1.sh (revision 13395) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu +#http://www.mcs.anl.gov/research/projects/tao/download/index.html + +#compatible with PETSc 3.3 + +#Some cleanup +rm -rf install tao-2.1-p0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tao-2.1-p0.tar.gz' 'tao-2.1-p0.tar.gz' + +#Untar +tar -zxvf tao-2.1-p0.tar.gz + +#move into place +mv tao-2.1-p0/* install/ +rm -rf tao-2.1-p0 +cd install +export TAO_DIR="$ISSM_DIR/externalpackages/tao/install/" + +#petsc needs to be compiled with --with-clanguage=C++ +make Index: sm/trunk/externalpackages/tao/install.sh =================================================================== --- /issm/trunk/externalpackages/tao/install.sh (revision 13394) +++ (revision ) @@ -1,22 +1,0 @@ -#!/bin/bash -#http://www.mcs.anl.gov/research/projects/tao/download/index.html -#wget http://www.mcs.anl.gov/research/projects/tao/download/tao-2.0-p3.tar.gz - -#Some cleanup -rm -rf install tao-2.0-p3 -mkdir install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tao-2.0-p3.tar.gz' 'tao-2.0-p3.tar.gz' - -#Untar -tar -zxvf tao-2.0-p3.tar.gz - -#move into place -mv tao-2.0-p3/* install/ -rm -rf tao-2.0-p3 -cd install -export TAO_DIR="$ISSM_DIR/externalpackages/tao/install/" - -#petsc needs to be compiled with --with-clanguage=C++ -make Index: /issm/trunk/externalpackages/tcl/install.sh =================================================================== --- /issm/trunk/externalpackages/tcl/install.sh (revision 13395) +++ /issm/trunk/externalpackages/tcl/install.sh (revision 13395) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + +sudochoice=0; + +#Some cleanup +rm -rf src +rm -rf install +rm -rf tcl8.5.11 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tcl8.5.11.tar.gz' 'tcl8.5.11.tar.gz' + +#Untar +tar -zxvf tcl8.5.11.tar.gz + +#Move tcl into src directory +mv tcl8.5.11/* src +rm -rf tcl8.5.11 + +#Configure tcl +ver="8.4.12" + +cd src/unix + +#User mode: +if [[ $sudochoice == "0" ]]; +then + ./configure --prefix=$ISSM_DIR/externalpackages/tcl/install + if [ $# -eq 0 ]; then + make + else + make -j $1 + fi + make install +fi + +#sudo mode: +if [[ $sudochoice == "1" ]]; +then + sudo ./configure + if [ $# -eq 0 ]; then + sudo make + else + sudo make -j $1 + fi + sudo make install +fi Index: /issm/trunk/externalpackages/tclx/install.sh =================================================================== --- /issm/trunk/externalpackages/tclx/install.sh (revision 13395) +++ /issm/trunk/externalpackages/tclx/install.sh (revision 13395) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf tclx8.4 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tclx8.4.tar.gz' 'tclx8.4.tar.gz' + +#Untar +tar -zxvf tclx8.4.tar.gz + +#Move tclx into src directory +mv tclx8.4/* src +rm -rf tclx8.4 + +#Configure tclx +cd src +./configure --prefix="$ISSM_DIR/externalpackages/tclx/install" \ + --exec-prefix="$ISSM_DIR/externalpackages/tclx/install" \ + --with-tcl=$ISSM_DIR/externalpackages/tcl/install/Library/Frameworks/Tcl.framework + +#Compile and install tclx +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk/externalpackages/tex2im/install.sh =================================================================== --- /issm/trunk/externalpackages/tex2im/install.sh (revision 13394) +++ /issm/trunk/externalpackages/tex2im/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/tk/install.sh =================================================================== --- /issm/trunk/externalpackages/tk/install.sh (revision 13395) +++ /issm/trunk/externalpackages/tk/install.sh (revision 13395) @@ -0,0 +1,46 @@ +#!/bin/bash +set -eu + +sudochoice=0; + +#Some cleanup +rm -rf src +rm -rf install +rm -rf tk8.5.12 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tk8.5.12-src.tar.gz' 'tk8.5.12.tar.gz' + +#Untar +tar -zxvf tk8.5.12.tar.gz + +#Move tk into src directory +mv tk8.5.12/* src +rm -rf tk8.5.12 + +cd src/unix + +#User mode: +if [[ $sudochoice == "0" ]]; +then + ./configure --prefix=$ISSM_DIR/externalpackages/tk/install + if [ $# -eq 0 ]; then + make + else + make -j $1 + fi + make install +fi + +#sudo mode: +if [[ $sudochoice == "1" ]]; +then + sudo ./configure + if [ $# -eq 0 ]; then + sudo make + else + sudo make -j $1 + fi + sudo make install +fi Index: /issm/trunk/externalpackages/triangle/configs/android/configure.make =================================================================== --- /issm/trunk/externalpackages/triangle/configs/android/configure.make (revision 13394) +++ /issm/trunk/externalpackages/triangle/configs/android/configure.make (revision 13395) @@ -1,6 +1,6 @@ # This makefile configures build process to cross-compile to the android platform. -# The binary tools referenced below are specifically configuered to target armeabi-v7a. +# The binary tools referenced below are specifically configured to target armeabi-v7a. # Furthermore, the compilers (which are simply wrappers around GNU GCC) are set to -# produce binaries that are EABI complient. +# produce binaries that are EABI compliant. # # Note that the AAPCS standard defines 'EABI' as a moniker used to specify @@ -9,4 +9,7 @@ # # http://www.codesourcery.com/gnu_toolchains/arm/arm_gnu_linux_abi.pdf + +source $ANDROID_DIR/android_aux.sh + CC=${toolchain_path}-gcc AR=${toolchain_path}-ar Index: /issm/trunk/externalpackages/triangle/install-altix64.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-altix64.sh (revision 13394) +++ /issm/trunk/externalpackages/triangle/install-altix64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/triangle/install-android.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-android.sh (revision 13394) +++ /issm/trunk/externalpackages/triangle/install-android.sh (revision 13395) @@ -1,8 +1,4 @@ #!/bin/bash -source $ANDROID_DIR/android_variables.sh -export toolchain_path - -#use matlab? -matlab=0 +set -eu #Some cleanup @@ -19,13 +15,9 @@ #copy new makefile -cp ../configs//android/configure.make ./ +cp ../configs/android/configure.make ./ cp ../makefile ./ #Patch triangle.c -if [[ $matlab == "1" ]];then - patch triangle.c ../triangle.c.patch.matlab -else - patch triangle.c ../triangle.c.patch.python -fi +patch triangle.c ../triangle.c.patch #Compile triangle Index: /issm/trunk/externalpackages/triangle/install-discover.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-discover.sh (revision 13394) +++ /issm/trunk/externalpackages/triangle/install-discover.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/triangle/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/triangle/install-linux64.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/triangle/install-macosx32.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-macosx32.sh (revision 13394) +++ /issm/trunk/externalpackages/triangle/install-macosx32.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/triangle/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-macosx64.sh (revision 13394) +++ /issm/trunk/externalpackages/triangle/install-macosx64.sh (revision 13395) @@ -1,7 +1,4 @@ #!/bin/bash - -#use matlab? -matlab=0 - +set -eu #Some cleanup @@ -22,9 +19,5 @@ #Patch triangle.c -if [[ $matlab == "1" ]];then - patch triangle.c ../triangle.c.patch.matlab -else - patch triangle.c ../triangle.c.patch.python -fi +patch triangle.c ../triangle.c.patch #Compile triangle Index: /issm/trunk/externalpackages/triangle/install-pleiades.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-pleiades.sh (revision 13394) +++ /issm/trunk/externalpackages/triangle/install-pleiades.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/triangle/install-win32.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-win32.sh (revision 13394) +++ /issm/trunk/externalpackages/triangle/install-win32.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/triangle/install-win7.sh =================================================================== --- /issm/trunk/externalpackages/triangle/install-win7.sh (revision 13394) +++ /issm/trunk/externalpackages/triangle/install-win7.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/triangle/triangle.c.patch =================================================================== --- /issm/trunk/externalpackages/triangle/triangle.c.patch (revision 13394) +++ /issm/trunk/externalpackages/triangle/triangle.c.patch (revision 13395) @@ -5,6 +5,6 @@ > * double precision activation in exactinit(); The rest is not changed. > * We also created the ice_makefile to compile Triangle into a library. */ -> #include -> #include +> /* #include +> #include */ > #define ANSI_DECLARATORS > #define NO_TIMER @@ -134,11 +134,11 @@ < memptr = (VOID *) malloc((unsigned int) size); --- -> memptr = (VOID *) mxMalloc((unsigned int) size); -> //memptr = (VOID *) malloc((unsigned int) size); +> //memptr = (VOID *) mxMalloc((unsigned int) size); +> memptr = (VOID *) malloc((unsigned int) size); 1447c1543,1544 < free(memptr); --- -> //free(memptr); -> mxFree(memptr); +> free(memptr); +> //mxFree(memptr); 3665,3670c3762,3767 < void printtriangle(struct mesh *m, struct behavior *b, struct otri *t) Index: sm/trunk/externalpackages/triangle/triangle.c.patch.matlab =================================================================== --- /issm/trunk/externalpackages/triangle/triangle.c.patch.matlab (revision 13394) +++ (revision ) @@ -1,164 +1,0 @@ -0a1,10 -> /*Notes for the Ice code: -> * to be able to compile Triangle within a mex function that can run within -> * matlab, we had to change the allocation routine trimalloc, as well as the -> * double precision activation in exactinit(); The rest is not changed. -> * We also created the ice_makefile to compile Triangle into a library. */ -> #include -> #include -> #define ANSI_DECLARATORS -> #define NO_TIMER -> -347a358 -> #ifndef _WIN_ -348a360 -> #endif -641d652 -< -817a829,922 -> /*Some missing prototypes: */ -> int scale_expansion_zeroelim(int elen, REAL *e, REAL b, REAL *h); -> int fast_expansion_sum_zeroelim(int elen, REAL *e, int flen, REAL *f, REAL *h); -> void poolzero(struct memorypool *pool); -> int triunsuitable(vertex triorg, vertex tridest, vertex triapex, REAL area); -> triangle *triangletraverse(struct mesh *m); -> void pooldeinit(struct memorypool *pool); -> void printtriangle(struct mesh *m, struct behavior *b, struct otri *t); -> VOID *poolalloc(struct memorypool *pool); -> void enqueuebadtriang(struct mesh *m, struct behavior *b, -> struct badtriang *badtri); -> void triangulatepolygon(struct mesh *m, struct behavior *b, -> struct otri *firstedge, struct otri *lastedge, -> int edgecount, int doflip, int triflaws); -> void triangledealloc(struct mesh *m, triangle *dyingtriangle); -> void unflip(struct mesh *m, struct behavior *b, struct otri *flipedge); -> void vertexmedian(vertex *sortarray, int arraysize, int median, int axis); -> REAL counterclockwiseadapt(vertex pa, vertex pb, vertex pc, REAL detsum); -> REAL incircleadapt(vertex pa, vertex pb, vertex pc, vertex pd, REAL permanent); -> void enqueuebadtri(struct mesh *m, struct behavior *b, struct otri *enqtri, -> REAL minedge, vertex enqapex, vertex enqorg, vertex enqdest); -> void alternateaxes(vertex *sortarray, int arraysize, int axis); -> REAL incircleadapt(vertex pa, vertex pb, vertex pc, vertex pd, REAL permanent); -> void maketriangle(struct mesh *m, struct behavior *b, struct otri *newotri); -> REAL counterclockwise(struct mesh *m, struct behavior *b, -> vertex pa, vertex pb, vertex pc); -> vertex vertextraverse(struct mesh *m); -> void mergehulls(struct mesh *m, struct behavior *b, struct otri *farleft, -> struct otri *innerleft, struct otri *innerright, -> struct otri *farright, int axis); -> REAL incircle(struct mesh *m, struct behavior *b, -> vertex pa, vertex pb, vertex pc, vertex pd); -> void poolrestart(struct memorypool *pool); -> void trifree(VOID *memptr); -> struct splaynode *splay(struct mesh *m, struct splaynode *splaytree, -> vertex searchpoint, struct otri *searchtri); -> void eventheapdelete(struct event **heap, int heapsize, int eventnum); -> void eventheapdelete(struct event **heap, int heapsize, int eventnum); -> void flip(struct mesh *m, struct behavior *b, struct otri *flipedge); -> void check4deadevent(struct otri *checktri, struct event **freeevents, -> struct event **eventheap, int *heapsize); -> REAL orient3d(struct mesh *m, struct behavior *b, -> vertex pa, vertex pb, vertex pc, vertex pd, -> REAL aheight, REAL bheight, REAL cheight, REAL dheight); -> REAL circletop(struct mesh *m, vertex pa, vertex pb, vertex pc, REAL ccwabc); -> void poolinit(struct memorypool *pool, int bytecount, int itemcount, -> int firstitemcount, int alignment); -> void eventheapinsert(struct event **heap, int heapsize, struct event *newevent); -> int rightofhyperbola(struct mesh *m, struct otri *fronttri, vertex newsite); -> void insertsubseg(struct mesh *m, struct behavior *b, struct otri *tri, -> int subsegmark); -> int scoutsegment(struct mesh *m, struct behavior *b, struct otri *searchtri, -> vertex endpoint2, int newmark); -> vertex getvertex(struct mesh *m, struct behavior *b, int number); -> void internalerror(); -> unsigned long randomnation(unsigned int choices); -> struct splaynode *splayinsert(struct mesh *m, struct splaynode *splayroot, -> struct otri *newkey, vertex searchpoint); -> void delaunayfixup(struct mesh *m, struct behavior *b, -> struct otri *fixuptri, int leftside); -> void traversalinit(struct memorypool *pool); -> enum insertvertexresult insertvertex(struct mesh *m, struct behavior *b, -> vertex newvertex, struct otri *searchtri, -> struct osub *splitseg, -> int segmentflaws, int triflaws); -> void conformingedge(struct mesh *m, struct behavior *b, -> vertex endpoint1, vertex endpoint2, int newmark); -> enum finddirectionresult finddirection(struct mesh *m, struct behavior *b, -> struct otri *searchtri, -> vertex searchpoint); -> VOID *traverse(struct memorypool *pool); -> void deletevertex(struct mesh *m, struct behavior *b, struct otri *deltri); -> void pooldealloc(struct memorypool *pool, VOID *dyingitem); -> int checkseg4encroach(struct mesh *m, struct behavior *b, -> struct osub *testsubseg); -> void badsubsegdealloc(struct mesh *m, struct badsubseg *dyingseg); -> void vertexdealloc(struct mesh *m, vertex dyingvertex); -> void vertexsort(vertex *sortarray, int arraysize); -> void tallyencs(struct mesh *m, struct behavior *b); -> void splittriangle(struct mesh *m, struct behavior *b, -> struct badtriang *badtri); -> subseg *subsegtraverse(struct mesh *m); -> enum locateresult locate(struct mesh *m, struct behavior *b, -> vertex searchpoint, struct otri *searchtri); -> void writenodes(struct mesh *m, struct behavior *b, REAL **pointlist, -> REAL **pointattriblist, int **pointmarkerlist); -> void writevoronoi(struct mesh *m, struct behavior *b, REAL **vpointlist, -> REAL **vpointattriblist, int **vpointmarkerlist, -> int **vedgelist, int **vedgemarkerlist, REAL **vnormlist); -> void writeneighbors(struct mesh *m, struct behavior *b, int **neighborlist); -> void testtriangle(struct mesh *m, struct behavior *b, struct otri *testtri); -> void triangleinit(struct mesh *m); -> -> -1408a1514 -> void triexit(int status); -1410d1515 -< #ifdef ANSI_DECLARATORS -1412,1416d1516 -< #else /* not ANSI_DECLARATORS */ -< void triexit(status) -< int status; -< #endif /* not ANSI_DECLARATORS */ -< -1421c1521 -< #ifdef ANSI_DECLARATORS ---- -> VOID *trimalloc(int size); -1423,1427d1522 -< #else /* not ANSI_DECLARATORS */ -< VOID *trimalloc(size) -< int size; -< #endif /* not ANSI_DECLARATORS */ -< -1431c1526,1527 -< memptr = (VOID *) malloc((unsigned int) size); ---- -> memptr = (VOID *) mxMalloc((unsigned int) size); -> //memptr = (VOID *) malloc((unsigned int) size); -1447c1543,1544 -< free(memptr); ---- -> //free(memptr); -> mxFree(memptr); -3665,3670c3762,3767 -< void printtriangle(struct mesh *m, struct behavior *b, struct otri *t) -< #else /* not ANSI_DECLARATORS */ -< void printtriangle(m, b, t) -< struct mesh *m; -< struct behavior *b; -< struct otri *t; ---- -> void printtriangle(struct mesh *m, struct behavior *b, struct otri *t){ -> //#else /* not ANSI_DECLARATORS */ -> //void printtriangle(m, b, t) -> //struct mesh *m; -> //struct behavior *b; -> //struct otri *t; -3673c3770 -< { ---- -> //{ -4910c5007 -< _FPU_SETCW(cword); ---- -> //_FPU_SETCW(cword); //taken care of by Matlab Index: sm/trunk/externalpackages/triangle/triangle.c.patch.python =================================================================== --- /issm/trunk/externalpackages/triangle/triangle.c.patch.python (revision 13394) +++ (revision ) @@ -1,164 +1,0 @@ -0a1,10 -> /*Notes for the Ice code: -> * to be able to compile Triangle within a mex function that can run within -> * matlab, we had to change the allocation routine trimalloc, as well as the -> * double precision activation in exactinit(); The rest is not changed. -> * We also created the ice_makefile to compile Triangle into a library. */ -> /* #include -> #include */ -> #define ANSI_DECLARATORS -> #define NO_TIMER -> -347a358 -> #ifndef _WIN_ -348a360 -> #endif -641d652 -< -817a829,922 -> /*Some missing prototypes: */ -> int scale_expansion_zeroelim(int elen, REAL *e, REAL b, REAL *h); -> int fast_expansion_sum_zeroelim(int elen, REAL *e, int flen, REAL *f, REAL *h); -> void poolzero(struct memorypool *pool); -> int triunsuitable(vertex triorg, vertex tridest, vertex triapex, REAL area); -> triangle *triangletraverse(struct mesh *m); -> void pooldeinit(struct memorypool *pool); -> void printtriangle(struct mesh *m, struct behavior *b, struct otri *t); -> VOID *poolalloc(struct memorypool *pool); -> void enqueuebadtriang(struct mesh *m, struct behavior *b, -> struct badtriang *badtri); -> void triangulatepolygon(struct mesh *m, struct behavior *b, -> struct otri *firstedge, struct otri *lastedge, -> int edgecount, int doflip, int triflaws); -> void triangledealloc(struct mesh *m, triangle *dyingtriangle); -> void unflip(struct mesh *m, struct behavior *b, struct otri *flipedge); -> void vertexmedian(vertex *sortarray, int arraysize, int median, int axis); -> REAL counterclockwiseadapt(vertex pa, vertex pb, vertex pc, REAL detsum); -> REAL incircleadapt(vertex pa, vertex pb, vertex pc, vertex pd, REAL permanent); -> void enqueuebadtri(struct mesh *m, struct behavior *b, struct otri *enqtri, -> REAL minedge, vertex enqapex, vertex enqorg, vertex enqdest); -> void alternateaxes(vertex *sortarray, int arraysize, int axis); -> REAL incircleadapt(vertex pa, vertex pb, vertex pc, vertex pd, REAL permanent); -> void maketriangle(struct mesh *m, struct behavior *b, struct otri *newotri); -> REAL counterclockwise(struct mesh *m, struct behavior *b, -> vertex pa, vertex pb, vertex pc); -> vertex vertextraverse(struct mesh *m); -> void mergehulls(struct mesh *m, struct behavior *b, struct otri *farleft, -> struct otri *innerleft, struct otri *innerright, -> struct otri *farright, int axis); -> REAL incircle(struct mesh *m, struct behavior *b, -> vertex pa, vertex pb, vertex pc, vertex pd); -> void poolrestart(struct memorypool *pool); -> void trifree(VOID *memptr); -> struct splaynode *splay(struct mesh *m, struct splaynode *splaytree, -> vertex searchpoint, struct otri *searchtri); -> void eventheapdelete(struct event **heap, int heapsize, int eventnum); -> void eventheapdelete(struct event **heap, int heapsize, int eventnum); -> void flip(struct mesh *m, struct behavior *b, struct otri *flipedge); -> void check4deadevent(struct otri *checktri, struct event **freeevents, -> struct event **eventheap, int *heapsize); -> REAL orient3d(struct mesh *m, struct behavior *b, -> vertex pa, vertex pb, vertex pc, vertex pd, -> REAL aheight, REAL bheight, REAL cheight, REAL dheight); -> REAL circletop(struct mesh *m, vertex pa, vertex pb, vertex pc, REAL ccwabc); -> void poolinit(struct memorypool *pool, int bytecount, int itemcount, -> int firstitemcount, int alignment); -> void eventheapinsert(struct event **heap, int heapsize, struct event *newevent); -> int rightofhyperbola(struct mesh *m, struct otri *fronttri, vertex newsite); -> void insertsubseg(struct mesh *m, struct behavior *b, struct otri *tri, -> int subsegmark); -> int scoutsegment(struct mesh *m, struct behavior *b, struct otri *searchtri, -> vertex endpoint2, int newmark); -> vertex getvertex(struct mesh *m, struct behavior *b, int number); -> void internalerror(); -> unsigned long randomnation(unsigned int choices); -> struct splaynode *splayinsert(struct mesh *m, struct splaynode *splayroot, -> struct otri *newkey, vertex searchpoint); -> void delaunayfixup(struct mesh *m, struct behavior *b, -> struct otri *fixuptri, int leftside); -> void traversalinit(struct memorypool *pool); -> enum insertvertexresult insertvertex(struct mesh *m, struct behavior *b, -> vertex newvertex, struct otri *searchtri, -> struct osub *splitseg, -> int segmentflaws, int triflaws); -> void conformingedge(struct mesh *m, struct behavior *b, -> vertex endpoint1, vertex endpoint2, int newmark); -> enum finddirectionresult finddirection(struct mesh *m, struct behavior *b, -> struct otri *searchtri, -> vertex searchpoint); -> VOID *traverse(struct memorypool *pool); -> void deletevertex(struct mesh *m, struct behavior *b, struct otri *deltri); -> void pooldealloc(struct memorypool *pool, VOID *dyingitem); -> int checkseg4encroach(struct mesh *m, struct behavior *b, -> struct osub *testsubseg); -> void badsubsegdealloc(struct mesh *m, struct badsubseg *dyingseg); -> void vertexdealloc(struct mesh *m, vertex dyingvertex); -> void vertexsort(vertex *sortarray, int arraysize); -> void tallyencs(struct mesh *m, struct behavior *b); -> void splittriangle(struct mesh *m, struct behavior *b, -> struct badtriang *badtri); -> subseg *subsegtraverse(struct mesh *m); -> enum locateresult locate(struct mesh *m, struct behavior *b, -> vertex searchpoint, struct otri *searchtri); -> void writenodes(struct mesh *m, struct behavior *b, REAL **pointlist, -> REAL **pointattriblist, int **pointmarkerlist); -> void writevoronoi(struct mesh *m, struct behavior *b, REAL **vpointlist, -> REAL **vpointattriblist, int **vpointmarkerlist, -> int **vedgelist, int **vedgemarkerlist, REAL **vnormlist); -> void writeneighbors(struct mesh *m, struct behavior *b, int **neighborlist); -> void testtriangle(struct mesh *m, struct behavior *b, struct otri *testtri); -> void triangleinit(struct mesh *m); -> -> -1408a1514 -> void triexit(int status); -1410d1515 -< #ifdef ANSI_DECLARATORS -1412,1416d1516 -< #else /* not ANSI_DECLARATORS */ -< void triexit(status) -< int status; -< #endif /* not ANSI_DECLARATORS */ -< -1421c1521 -< #ifdef ANSI_DECLARATORS ---- -> VOID *trimalloc(int size); -1423,1427d1522 -< #else /* not ANSI_DECLARATORS */ -< VOID *trimalloc(size) -< int size; -< #endif /* not ANSI_DECLARATORS */ -< -1431c1526,1527 -< memptr = (VOID *) malloc((unsigned int) size); ---- -> //memptr = (VOID *) mxMalloc((unsigned int) size); -> memptr = (VOID *) malloc((unsigned int) size); -1447c1543,1544 -< free(memptr); ---- -> free(memptr); -> //mxFree(memptr); -3665,3670c3762,3767 -< void printtriangle(struct mesh *m, struct behavior *b, struct otri *t) -< #else /* not ANSI_DECLARATORS */ -< void printtriangle(m, b, t) -< struct mesh *m; -< struct behavior *b; -< struct otri *t; ---- -> void printtriangle(struct mesh *m, struct behavior *b, struct otri *t){ -> //#else /* not ANSI_DECLARATORS */ -> //void printtriangle(m, b, t) -> //struct mesh *m; -> //struct behavior *b; -> //struct otri *t; -3673c3770 -< { ---- -> //{ -4910c5007 -< _FPU_SETCW(cword); ---- -> //_FPU_SETCW(cword); //taken care of by Matlab Index: /issm/trunk/externalpackages/valgrind/install-altix64.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-altix64.sh (revision 13394) +++ /issm/trunk/externalpackages/valgrind/install-altix64.sh (revision 13395) @@ -1,17 +1,18 @@ #!/bin/bash +set -eu #Some cleanup -rm -rf install valgrind-3.7.0 +rm -rf install valgrind-3.8.0 mkdir install #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.0.tar.bz2' 'valgrind-3.8.0.tar.bz2' #Untar -tar -jxvf valgrind-3.7.0.tar.bz2 +tar -jxvf valgrind-3.8.0.tar.bz2 #Move valgrind into install directory -mv valgrind-3.7.0/* install -rm -rf valgrind-3.7.0 +mv valgrind-3.8.0/* install +rm -rf valgrind-3.8.0 #configure Index: /issm/trunk/externalpackages/valgrind/install-linux64.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-linux64.sh (revision 13394) +++ /issm/trunk/externalpackages/valgrind/install-linux64.sh (revision 13395) @@ -1,17 +1,18 @@ #!/bin/bash +set -eu #Some cleanup -rm -rf install valgrind-3.7.0 +rm -rf install valgrind-3.8.0 mkdir install #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.0.tar.bz2' 'valgrind-3.8.0.tar.bz2' #Untar -tar -jxvf valgrind-3.7.0.tar.bz2 +tar -jxvf valgrind-3.8.0.tar.bz2 #Move valgrind into install directory -mv valgrind-3.7.0/* install -rm -rf valgrind-3.7.0 +mv valgrind-3.8.0/* install +rm -rf valgrind-3.8.0 #configure @@ -25,3 +26,3 @@ #final thing: if mpi is compiled in, soft link its target to a simpler name cd lib -ln -s valgrind/libmpi* ./libmpidebug.so +ln -s valgrind/libmpiwrap-* ./libmpidebug.so Index: /issm/trunk/externalpackages/valgrind/install-macosx32.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-macosx32.sh (revision 13394) +++ /issm/trunk/externalpackages/valgrind/install-macosx32.sh (revision 13395) @@ -1,17 +1,18 @@ #!/bin/bash +set -eu #Some cleanup -rm -rf install valgrind-3.7.0 +rm -rf install valgrind-3.8.0 mkdir install #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.0.tar.bz2' 'valgrind-3.8.0.tar.bz2' #Untar -tar -jxvf valgrind-3.7.0.tar.bz2 +tar -jxvf valgrind-3.8.0.tar.bz2 #Move valgrind into install directory -mv valgrind-3.7.0/* install -rm -rf valgrind-3.7.0 +mv valgrind-3.8.0/* install +rm -rf valgrind-3.8.0 #configure Index: /issm/trunk/externalpackages/valgrind/install-macosx64.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-macosx64.sh (revision 13394) +++ /issm/trunk/externalpackages/valgrind/install-macosx64.sh (revision 13395) @@ -1,17 +1,18 @@ #!/bin/bash +set -eu #Some cleanup -rm -rf install valgrind-3.7.0 +rm -rf install valgrind-3.8.0 mkdir install #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.0.tar.bz2' 'valgrind-3.8.0.tar.bz2' #Untar -tar -jxvf valgrind-3.7.0.tar.bz2 +tar -jxvf valgrind-3.8.0.tar.bz2 #Move valgrind into install directory -mv valgrind-3.7.0/* install -rm -rf valgrind-3.7.0 +mv valgrind-3.8.0/* install +rm -rf valgrind-3.8.0 #configure Index: /issm/trunk/externalpackages/valgrind/install-win32.sh =================================================================== --- /issm/trunk/externalpackages/valgrind/install-win32.sh (revision 13394) +++ /issm/trunk/externalpackages/valgrind/install-win32.sh (revision 13395) @@ -1,17 +1,18 @@ #!/bin/bash +set -eu #Some cleanup -rm -rf install valgrind-3.7.0 +rm -rf install valgrind-3.8.0 mkdir install #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.0.tar.bz2' 'valgrind-3.8.0.tar.bz2' #Untar -tar -jxvf valgrind-3.7.0.tar.bz2 +tar -jxvf valgrind-3.8.0.tar.bz2 #Move valgrind into install directory -mv valgrind-3.7.0/* install -rm -rf valgrind-3.7.0 +mv valgrind-3.8.0/* install +rm -rf valgrind-3.8.0 #configure Index: /issm/trunk/externalpackages/vim/addons/vim/syntax/Synchronize.sh =================================================================== --- /issm/trunk/externalpackages/vim/addons/vim/syntax/Synchronize.sh (revision 13394) +++ /issm/trunk/externalpackages/vim/addons/vim/syntax/Synchronize.sh (revision 13395) @@ -6,14 +6,14 @@ 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 "[aA-zZ]Enum," | grep -v StringToEnum | sed -e "s/,//g" | awk '{ printf "syn keyword cConstant " $1 "\n"}' >> 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 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 -cat ../../../../../src/c/objects/objects.h | grep "\.h" | sed -e "s/\// /g" -e "s/\.h\"//" | awk '{print $(NF)}' | awk '{ printf "syn keyword cType " $1 "\n"}' >> 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 echo "\"ISSM's objects end" >> temp cat c.vim | sed "1,/ISSM's objects end/d" >> temp Index: /issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim =================================================================== --- /issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim (revision 13394) +++ /issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim (revision 13395) @@ -408,152 +408,164 @@ syn keyword cType Vec Mat SeqVec SeqMat "other ISSM's syntax -syn keyword cType mxArray ErrorException QuadtreeBox IssmDouble IssmPDouble +syn keyword cType mxArray ErrorException QuadtreeBox IssmDouble IssmPDouble Observations "ISSM's objects begin -syn keyword cType objects.h -syn keyword cType Object -syn keyword cType Hook -syn keyword cType DofIndexing -syn keyword cType Vertex -syn keyword cType Node -syn keyword cType Segment -syn keyword cType IoModel -syn keyword cType Patch -syn keyword cType Update -syn keyword cType Constraint -syn keyword cType SpcStatic -syn keyword cType SpcTransient -syn keyword cType SpcDynamic +syn keyword cType GaussPenta +syn keyword cType gaussobjects syn keyword cType GaussTria -syn keyword cType GaussPenta -syn keyword cType Load -syn keyword cType Friction -syn keyword cType Icefront -syn keyword cType Numericalflux -syn keyword cType Riftfront -syn keyword cType Penpair -syn keyword cType Pengrid -syn keyword cType Element -syn keyword cType Penta -syn keyword cType PentaHook -syn keyword cType PentaRef -syn keyword cType Tria -syn keyword cType TriaHook -syn keyword cType TriaRef -syn keyword cType KML_Attribute -syn keyword cType KML_Comment -syn keyword cType KML_ColorStyle -syn keyword cType KML_Container -syn keyword cType KML_Document -syn keyword cType KML_Feature -syn keyword cType KML_File -syn keyword cType KML_Folder -syn keyword cType KML_Geometry -syn keyword cType KML_GroundOverlay -syn keyword cType KML_Icon -syn keyword cType KML_LatLonBox -syn keyword cType KML_LinearRing -syn keyword cType KML_LineString -syn keyword cType KML_LineStyle -syn keyword cType KML_MultiGeometry -syn keyword cType KML_Object -syn keyword cType KML_Overlay -syn keyword cType KML_Point -syn keyword cType KML_Placemark -syn keyword cType KML_Polygon -syn keyword cType KML_PolyStyle -syn keyword cType KML_Style -syn keyword cType KML_StyleSelector -syn keyword cType KML_SubStyle -syn keyword cType KML_Unknown -syn keyword cType KMLFileReadUtils -syn keyword cType Option -syn keyword cType OptionDouble -syn keyword cType OptionLogical -syn keyword cType OptionChar -syn keyword cType OptionStruct -syn keyword cType OptionCell -syn keyword cType OptionUtilities -syn keyword cType Input -syn keyword cType BoolInput -syn keyword cType DoubleInput -syn keyword cType IntInput -syn keyword cType PentaP1Input -syn keyword cType TriaP1Input -syn keyword cType ControlInput -syn keyword cType DatasetInput -syn keyword cType TransientInput -syn keyword cType ElementResult -syn keyword cType DoubleElementResult -syn keyword cType TriaP1ElementResult -syn keyword cType PentaP1ElementResult -syn keyword cType BoolElementResult -syn keyword cType ExternalResult -syn keyword cType BoolExternalResult -syn keyword cType DoubleExternalResult -syn keyword cType DoubleVecExternalResult -syn keyword cType DoubleMatExternalResult -syn keyword cType IntExternalResult -syn keyword cType PetscVecExternalResult -syn keyword cType StringExternalResult +syn keyword cType objects syn keyword cType Material 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 ControlInput +syn keyword cType DatasetInput +syn keyword cType IntInput +syn keyword cType BoolInput +syn keyword cType TriaP1Input +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 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 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 ElementVector +syn keyword cType matrixobjects syn keyword cType Vector syn keyword cType Matrix -syn keyword cType BoolParam -syn keyword cType DoubleMatParam -syn keyword cType DoubleTransientMatParam -syn keyword cType DoubleMatArrayParam -syn keyword cType DoubleParam -syn keyword cType DoubleVecParam -syn keyword cType IntParam -syn keyword cType IntVecParam -syn keyword cType IntMatParam -syn keyword cType FileParam -syn keyword cType Param -syn keyword cType MatrixParam -syn keyword cType VectorParam -syn keyword cType StringArrayParam -syn keyword cType StringParam -syn keyword cType Contour -syn keyword cType FemModel -syn keyword cType OptArgs -syn keyword cType OptPars +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 DoubleAndInt -syn keyword cType Direction -syn keyword cType BamgVertex -syn keyword cType AdjacentTriangle -syn keyword cType Edge +syn keyword cType include +syn keyword cType typedefs +syn keyword cType Curve +syn keyword cType macros syn keyword cType GeomVertex -syn keyword cType GeomEdge -syn keyword cType Curve -syn keyword cType Triangle -syn keyword cType ListofIntersectionTriangles -syn keyword cType GeomSubDomain -syn keyword cType SubDomain -syn keyword cType VertexOnGeom -syn keyword cType VertexOnVertex -syn keyword cType VertexOnEdge -syn keyword cType CrackedEdge -syn keyword cType Mesh -syn keyword cType Geometry -syn keyword cType BamgQuadtree -syn keyword cType SetOfE4 -syn keyword cType Variogram -syn keyword cType GaussianVariogram -syn keyword cType ExponentialVariogram -syn keyword cType SphericalVariogram -syn keyword cType PowerVariogram -syn keyword cType Quadtree -syn keyword cType Observation +syn keyword cType OptArgs +syn keyword cType Update +syn keyword cType OptPars +syn keyword cType IoModel +syn keyword cType FemModel "ISSM's objects end - "ISSM's Enums begin syn keyword cConstant AutodiffForwardEnum @@ -694,8 +706,14 @@ syn keyword cConstant SettingsResultsAsPatchesEnum syn keyword cConstant SettingsWaitonlockEnum -syn keyword cConstant DebugPetscProfilingEnum -syn keyword cConstant PetscProfilingCurrentMemEnum -syn keyword cConstant PetscProfilingCurrentFlopsEnum -syn keyword cConstant PetscProfilingSolutionTimeEnum +syn keyword cConstant SurfaceforcingsDelta18oEnum +syn keyword cConstant SurfaceforcingsDelta18oSurfaceEnum +syn keyword cConstant SurfaceforcingsIsdelta18oEnum +syn keyword cConstant SurfaceforcingsPrecipitationsPresentdayEnum +syn keyword cConstant SurfaceforcingsTemperaturesPresentdayEnum +syn keyword cConstant SurfaceforcingsTemperaturesLgmEnum +syn keyword cConstant DebugProfilingEnum +syn keyword cConstant ProfilingCurrentMemEnum +syn keyword cConstant ProfilingCurrentFlopsEnum +syn keyword cConstant ProfilingSolutionTimeEnum syn keyword cConstant MaxIterationConvergenceFlagEnum syn keyword cConstant SteadystateMaxiterEnum @@ -807,4 +825,5 @@ syn keyword cConstant IntParamEnum syn keyword cConstant IntVecParamEnum +syn keyword cConstant TransientParamEnum syn keyword cConstant MacAyeal2dIceFrontEnum syn keyword cConstant MacAyeal3dIceFrontEnum @@ -926,4 +945,7 @@ syn keyword cConstant StressTensorzzEnum syn keyword cConstant IceVolumeEnum +syn keyword cConstant TotalSmbEnum +syn keyword cConstant ThicknessAlongGradientEnum +syn keyword cConstant ThicknessAcrossGradientEnum syn keyword cConstant P0Enum syn keyword cConstant P1Enum @@ -1009,22 +1031,22 @@ if !exists("c_no_ansi") || exists("c_ansi_typedefs") - syn keyword cType size_t ssize_t wchar_t ptrdiff_t sig_atomic_t fpos_t - syn keyword cType clock_t time_t va_list jmp_buf FILE DIR div_t ldiv_t - syn keyword cType mbstate_t wctrans_t wint_t wctype_t - syn keyword cType lldiv_t float_t double_t fenv_t fexcept_t + syn keyword cType size_t ssize_t wchar_t ptrdiff_t sig_atomic_t fpos_t + syn keyword cType clock_t time_t va_list jmp_buf FILE DIR div_t ldiv_t + syn keyword cType mbstate_t wctrans_t wint_t wctype_t + syn keyword cType lldiv_t float_t double_t fenv_t fexcept_t endif if !exists("c_no_c99") " ISO C99 - syn keyword cType bool complex imaginary - syn keyword cType int8_t int16_t int32_t int64_t - syn keyword cType uint8_t uint16_t uint32_t uint64_t - syn keyword cType int_least8_t int_least16_t int_least32_t int_least64_t - syn keyword cType uint_least8_t uint_least16_t uint_least32_t uint_least64_t - syn keyword cType int_fast8_t int_fast16_t int_fast32_t int_fast64_t - syn keyword cType uint_fast8_t uint_fast16_t uint_fast32_t uint_fast64_t - syn keyword cType intptr_t uintptr_t - syn keyword cType intmax_t uintmax_t + syn keyword cType bool complex imaginary + syn keyword cType int8_t int16_t int32_t int64_t + syn keyword cType uint8_t uint16_t uint32_t uint64_t + syn keyword cType int_least8_t int_least16_t int_least32_t int_least64_t + syn keyword cType uint_least8_t uint_least16_t uint_least32_t uint_least64_t + syn keyword cType int_fast8_t int_fast16_t int_fast32_t int_fast64_t + syn keyword cType uint_fast8_t uint_fast16_t uint_fast32_t uint_fast64_t + syn keyword cType intptr_t uintptr_t + syn keyword cType intmax_t uintmax_t endif if exists("c_gnu") - syn keyword cType __label__ __complex__ __volatile__ + syn keyword cType __label__ __complex__ __volatile__ endif @@ -1032,89 +1054,89 @@ syn keyword cStorageClass static register auto volatile extern const VOL if exists("c_gnu") - syn keyword cStorageClass inline __attribute__ + syn keyword cStorageClass inline __attribute__ endif if !exists("c_no_c99") - syn keyword cStorageClass inline restrict + syn keyword cStorageClass inline restrict endif if !exists("c_no_ansi") || exists("c_ansi_constants") || exists("c_gnu") - if exists("c_gnu") - syn keyword cConstant __GNUC__ __FUNCTION__ __PRETTY_FUNCTION__ - endif - syn keyword cConstant __LINE__ __FILE__ __DATE__ __TIME__ __STDC__ __func__ - syn keyword cConstant __STDC_VERSION__ - syn keyword cConstant CHAR_BIT MB_LEN_MAX MB_CUR_MAX - syn keyword cConstant UCHAR_MAX UINT_MAX ULONG_MAX USHRT_MAX - syn keyword cConstant CHAR_MIN INT_MIN LONG_MIN SHRT_MIN - syn keyword cConstant CHAR_MAX INT_MAX LONG_MAX SHRT_MAX - syn keyword cConstant SCHAR_MIN SINT_MIN SLONG_MIN SSHRT_MIN - syn keyword cConstant SCHAR_MAX SINT_MAX SLONG_MAX SSHRT_MAX - if !exists("c_no_c99") - syn keyword cConstant LLONG_MIN LLONG_MAX ULLONG_MAX - syn keyword cConstant INT8_MIN INT16_MIN INT32_MIN INT64_MIN - syn keyword cConstant INT8_MAX INT16_MAX INT32_MAX INT64_MAX - syn keyword cConstant UINT8_MAX UINT16_MAX UINT32_MAX UINT64_MAX - syn keyword cConstant INT_LEAST8_MIN INT_LEAST16_MIN INT_LEAST32_MIN INT_LEAST64_MIN - syn keyword cConstant INT_LEAST8_MAX INT_LEAST16_MAX INT_LEAST32_MAX INT_LEAST64_MAX - syn keyword cConstant UINT_LEAST8_MAX UINT_LEAST16_MAX UINT_LEAST32_MAX UINT_LEAST64_MAX - syn keyword cConstant INT_FAST8_MIN INT_FAST16_MIN INT_FAST32_MIN INT_FAST64_MIN - syn keyword cConstant INT_FAST8_MAX INT_FAST16_MAX INT_FAST32_MAX INT_FAST64_MAX - syn keyword cConstant UINT_FAST8_MAX UINT_FAST16_MAX UINT_FAST32_MAX UINT_FAST64_MAX - syn keyword cConstant INTPTR_MIN INTPTR_MAX UINTPTR_MAX - syn keyword cConstant INTMAX_MIN INTMAX_MAX UINTMAX_MAX - syn keyword cConstant PTRDIFF_MIN PTRDIFF_MAX SIG_ATOMIC_MIN SIG_ATOMIC_MAX - syn keyword cConstant SIZE_MAX WCHAR_MIN WCHAR_MAX WINT_MIN WINT_MAX - endif - syn keyword cConstant FLT_RADIX FLT_ROUNDS - syn keyword cConstant FLT_DIG FLT_MANT_DIG FLT_EPSILON - syn keyword cConstant DBL_DIG DBL_MANT_DIG DBL_EPSILON - syn keyword cConstant LDBL_DIG LDBL_MANT_DIG LDBL_EPSILON - syn keyword cConstant FLT_MIN FLT_MAX FLT_MIN_EXP FLT_MAX_EXP - syn keyword cConstant FLT_MIN_10_EXP FLT_MAX_10_EXP - syn keyword cConstant DBL_MIN DBL_MAX DBL_MIN_EXP DBL_MAX_EXP - syn keyword cConstant DBL_MIN_10_EXP DBL_MAX_10_EXP - syn keyword cConstant LDBL_MIN LDBL_MAX LDBL_MIN_EXP LDBL_MAX_EXP - syn keyword cConstant LDBL_MIN_10_EXP LDBL_MAX_10_EXP - syn keyword cConstant HUGE_VAL CLOCKS_PER_SEC NULL _NO_LEAP_SECONDS _LOCALTIME - syn keyword cConstant LC_ALL LC_COLLATE LC_CTYPE LC_MONETARY - syn keyword cConstant LC_NUMERIC LC_TIME -" syn keyword cConstant SIG_DFL SIG_ERR SIG_IGN - syn keyword cAnsiFuncPtr SIG_DFL SIG_ERR SIG_IGN - syn keyword cConstant SIGABRT SIGFPE SIGILL SIGHUP SIGINT SIGSEGV SIGTERM - syn keyword cConstant INFINITY FP_SUBNORMAL FP_ILOGB0 - syn keyword cConstant NAN FP_ZERO FP_ILOGBNAN - syn keyword cConstant FP_INFINITE FP_FAST_FMA - syn keyword cConstant HUGE_VALF FP_NAN FP_FAST_FMAF - syn keyword cConstant HUGE_VALL FP_NORMAL FP_FAST_FMAL - syn keyword cConstant FE_OVERFLOW FE_TOWARDZERO - syn keyword cConstant FE_UNDERFLOW FE_UPWARD - syn keyword cConstant FE_DIVBYZERO FE_ALL_EXCEPT FE_DFL_ENV - syn keyword cConstant FE_INEXACT FE_DOWNWARD - syn keyword cConstant FE_INVALID FE_TONEAREST - syn keyword cConstant _Complex_I _Imaginary_I - " Add POSIX signals as well... - syn keyword cConstant SIGABRT SIGALRM SIGCHLD SIGCONT SIGFPE SIGHUP - syn keyword cConstant SIGILL SIGINT SIGKILL SIGPIPE SIGQUIT SIGSEGV - syn keyword cConstant SIGSTOP SIGTERM SIGTRAP SIGTSTP SIGTTIN SIGTTOU - syn keyword cConstant SIGUSR1 SIGUSR2 - syn keyword cConstant _IOFBF _IOLBF _IONBF BUFSIZ EOF WEOF - syn keyword cConstant FOPEN_MAX FILENAME_MAX L_tmpnam - syn keyword cConstant SEEK_CUR SEEK_END SEEK_SET - syn keyword cConstant TMP_MAX stderr stdin stdout - syn keyword cConstant EXIT_FAILURE EXIT_SUCCESS RAND_MAX - " Add POSIX errors as well - syn keyword cConstant E2BIG EACCES EAGAIN EBADF EBADMSG EBUSY - syn keyword cConstant ECANCELED ECHILD EDEADLK EDOM EEXIST EFAULT - syn keyword cConstant EFBIG EILSEQ EINPROGRESS EINTR EINVAL EIO EISDIR - syn keyword cConstant EMFILE EMLINK EMSGSIZE ENAMETOOLONG ENFILE ENODEV - syn keyword cConstant ENOENT ENOEXEC ENOLCK ENOMEM ENOSPC ENOSYS - syn keyword cConstant ENOTDIR ENOTEMPTY ENOTSUP ENOTTY ENXIO EPERM - syn keyword cConstant EPIPE ERANGE EROFS ESPIPE ESRCH ETIMEDOUT EXDEV - " math.h - syn keyword cConstant M_E M_LOG2E M_LOG10E M_LN2 M_LN10 M_PI M_PI_2 M_PI_4 - syn keyword cConstant M_1_PI M_2_PI M_2_SQRTPI M_SQRT2 M_SQRT1_2 + if exists("c_gnu") + syn keyword cConstant __GNUC__ __FUNCTION__ __PRETTY_FUNCTION__ + endif + syn keyword cConstant __LINE__ __FILE__ __DATE__ __TIME__ __STDC__ __func__ + syn keyword cConstant __STDC_VERSION__ + syn keyword cConstant CHAR_BIT MB_LEN_MAX MB_CUR_MAX + syn keyword cConstant UCHAR_MAX UINT_MAX ULONG_MAX USHRT_MAX + syn keyword cConstant CHAR_MIN INT_MIN LONG_MIN SHRT_MIN + syn keyword cConstant CHAR_MAX INT_MAX LONG_MAX SHRT_MAX + syn keyword cConstant SCHAR_MIN SINT_MIN SLONG_MIN SSHRT_MIN + syn keyword cConstant SCHAR_MAX SINT_MAX SLONG_MAX SSHRT_MAX + if !exists("c_no_c99") + syn keyword cConstant LLONG_MIN LLONG_MAX ULLONG_MAX + syn keyword cConstant INT8_MIN INT16_MIN INT32_MIN INT64_MIN + syn keyword cConstant INT8_MAX INT16_MAX INT32_MAX INT64_MAX + syn keyword cConstant UINT8_MAX UINT16_MAX UINT32_MAX UINT64_MAX + syn keyword cConstant INT_LEAST8_MIN INT_LEAST16_MIN INT_LEAST32_MIN INT_LEAST64_MIN + syn keyword cConstant INT_LEAST8_MAX INT_LEAST16_MAX INT_LEAST32_MAX INT_LEAST64_MAX + syn keyword cConstant UINT_LEAST8_MAX UINT_LEAST16_MAX UINT_LEAST32_MAX UINT_LEAST64_MAX + syn keyword cConstant INT_FAST8_MIN INT_FAST16_MIN INT_FAST32_MIN INT_FAST64_MIN + syn keyword cConstant INT_FAST8_MAX INT_FAST16_MAX INT_FAST32_MAX INT_FAST64_MAX + syn keyword cConstant UINT_FAST8_MAX UINT_FAST16_MAX UINT_FAST32_MAX UINT_FAST64_MAX + syn keyword cConstant INTPTR_MIN INTPTR_MAX UINTPTR_MAX + syn keyword cConstant INTMAX_MIN INTMAX_MAX UINTMAX_MAX + syn keyword cConstant PTRDIFF_MIN PTRDIFF_MAX SIG_ATOMIC_MIN SIG_ATOMIC_MAX + syn keyword cConstant SIZE_MAX WCHAR_MIN WCHAR_MAX WINT_MIN WINT_MAX + endif + syn keyword cConstant FLT_RADIX FLT_ROUNDS + syn keyword cConstant FLT_DIG FLT_MANT_DIG FLT_EPSILON + syn keyword cConstant DBL_DIG DBL_MANT_DIG DBL_EPSILON + syn keyword cConstant LDBL_DIG LDBL_MANT_DIG LDBL_EPSILON + syn keyword cConstant FLT_MIN FLT_MAX FLT_MIN_EXP FLT_MAX_EXP + syn keyword cConstant FLT_MIN_10_EXP FLT_MAX_10_EXP + syn keyword cConstant DBL_MIN DBL_MAX DBL_MIN_EXP DBL_MAX_EXP + syn keyword cConstant DBL_MIN_10_EXP DBL_MAX_10_EXP + syn keyword cConstant LDBL_MIN LDBL_MAX LDBL_MIN_EXP LDBL_MAX_EXP + syn keyword cConstant LDBL_MIN_10_EXP LDBL_MAX_10_EXP + syn keyword cConstant HUGE_VAL CLOCKS_PER_SEC NULL _NO_LEAP_SECONDS _LOCALTIME + syn keyword cConstant LC_ALL LC_COLLATE LC_CTYPE LC_MONETARY + syn keyword cConstant LC_NUMERIC LC_TIME + " syn keyword cConstant SIG_DFL SIG_ERR SIG_IGN + syn keyword cAnsiFuncPtr SIG_DFL SIG_ERR SIG_IGN + syn keyword cConstant SIGABRT SIGFPE SIGILL SIGHUP SIGINT SIGSEGV SIGTERM + syn keyword cConstant INFINITY FP_SUBNORMAL FP_ILOGB0 + syn keyword cConstant NAN FP_ZERO FP_ILOGBNAN + syn keyword cConstant FP_INFINITE FP_FAST_FMA + syn keyword cConstant HUGE_VALF FP_NAN FP_FAST_FMAF + syn keyword cConstant HUGE_VALL FP_NORMAL FP_FAST_FMAL + syn keyword cConstant FE_OVERFLOW FE_TOWARDZERO + syn keyword cConstant FE_UNDERFLOW FE_UPWARD + syn keyword cConstant FE_DIVBYZERO FE_ALL_EXCEPT FE_DFL_ENV + syn keyword cConstant FE_INEXACT FE_DOWNWARD + syn keyword cConstant FE_INVALID FE_TONEAREST + syn keyword cConstant _Complex_I _Imaginary_I + " Add POSIX signals as well... + syn keyword cConstant SIGABRT SIGALRM SIGCHLD SIGCONT SIGFPE SIGHUP + syn keyword cConstant SIGILL SIGINT SIGKILL SIGPIPE SIGQUIT SIGSEGV + syn keyword cConstant SIGSTOP SIGTERM SIGTRAP SIGTSTP SIGTTIN SIGTTOU + syn keyword cConstant SIGUSR1 SIGUSR2 + syn keyword cConstant _IOFBF _IOLBF _IONBF BUFSIZ EOF WEOF + syn keyword cConstant FOPEN_MAX FILENAME_MAX L_tmpnam + syn keyword cConstant SEEK_CUR SEEK_END SEEK_SET + syn keyword cConstant TMP_MAX stderr stdin stdout + syn keyword cConstant EXIT_FAILURE EXIT_SUCCESS RAND_MAX + " Add POSIX errors as well + syn keyword cConstant E2BIG EACCES EAGAIN EBADF EBADMSG EBUSY + syn keyword cConstant ECANCELED ECHILD EDEADLK EDOM EEXIST EFAULT + syn keyword cConstant EFBIG EILSEQ EINPROGRESS EINTR EINVAL EIO EISDIR + syn keyword cConstant EMFILE EMLINK EMSGSIZE ENAMETOOLONG ENFILE ENODEV + syn keyword cConstant ENOENT ENOEXEC ENOLCK ENOMEM ENOSPC ENOSYS + syn keyword cConstant ENOTDIR ENOTEMPTY ENOTSUP ENOTTY ENXIO EPERM + syn keyword cConstant EPIPE ERANGE EROFS ESPIPE ESRCH ETIMEDOUT EXDEV + " math.h + syn keyword cConstant M_E M_LOG2E M_LOG10E M_LN2 M_LN10 M_PI M_PI_2 M_PI_4 + syn keyword cConstant M_1_PI M_2_PI M_2_SQRTPI M_SQRT2 M_SQRT1_2 endif if !exists("c_no_c99") " ISO C99 - syn keyword cConstant true false __bool_true_false_are_defined + syn keyword cConstant true false __bool_true_false_are_defined endif @@ -1126,163 +1148,163 @@ syn match cPreCondit display "^\s*\(%:\|#\)\s*\(else\|endif\)\>" if !exists("c_no_if0") - syn region cCppOut start="^\s*\(%:\|#\)\s*if\s\+0\+\>" end=".\@=\|$" contains=cCppOut2 - syn region cCppOut2 contained start="0" end="^\s*\(%:\|#\)\s*\(endif\>\|else\>\|elif\>\)" contains=cSpaceError,cCppSkip - syn region cCppSkip contained start="^\s*\(%:\|#\)\s*\(if\>\|ifdef\>\|ifndef\>\)" skip="\\$" end="^\s*\(%:\|#\)\s*endif\>" contains=cSpaceError,cCppSkip -endif -syn region cIncluded display contained start=+"+ skip=+\\\\\|\\"+ end=+"+ -syn match cIncluded display contained "<[^>]*>" -syn match cInclude display "^\s*\(%:\|#\)\s*include\>\s*["<]" contains=cIncluded -syn match cLineSkip "\\$" -syn cluster cPreProcGroup contains=cPreConditIf,cPreCondit,cIncluded,cInclude,cDefined,cDefine,cErrInParen,cErrInBracket,cUserLabel,cUserLabel2,cGotoLabel,cSpecial,cOctalZero,cCppOut,cCppOut2,cCppSkip,cFormat,cNumber,cFloat,cOctal,cOctalError,cNumbersCom,cString,cCommentSkip,cCommentString,cComment2String,@cCommentGroup,cCommentStartError,cParen,cBracket,cMulti -"syn region cDefine start="^\s*\(%:\|#\)\s*\(define\|undef\)\>" skip="\\$" end="$" end="//"me=s-1 contains=ALLBUT,@cPreProcGroup,@Spell -syn region cDefine start="^\s*\(%:\|#\)\s*\(define\|undef\)\>" skip="\\$" end="$" end="//"me=s-1 contains=ALLBUT,@cPreProcGroup,cName,cFunction,cAnsiFunction,@Spell -syn region cPreProc start="^\s*\(%:\|#\)\s*\(pragma\>\|line\>\|warning\>\|warn\>\|error\>\)" skip="\\$" end="$" keepend contains=ALLBUT,@cPreProcGroup,@Spell - -" Highlight User Labels -syn cluster cMultiGroup contains=cIncluded,cSpecial,cCommentSkip,cCommentString,cComment2String,@cCommentGroup,cCommentStartError,cUserCont,cUserLabel,cUserLabel2,cGotoLabel,cBitField,cOctalZero,cCppOut,cCppOut2,cCppSkip,cFormat,cNumber,cFloat,cOctal,cOctalError,cNumbersCom,cCppParen,cCppBracket,cCppString -syn region cMulti transparent start='?' skip='::' end=':' contains=ALLBUT,@cMultiGroup,@Spell -" Avoid matching foo::bar() in C++ by requiring that the next char is not ':' -syn cluster cLabelGroup contains=cUserLabel -syn match cUserCont display "^\s*\I\i*\s*:$" contains=@cLabelGroup -syn match cUserCont display ";\s*\I\i*\s*:$" contains=@cLabelGroup -syn match cUserCont display "^\s*\I\i*\s*:[^:]"me=e-1 contains=@cLabelGroup -syn match cUserCont display ";\s*\I\i*\s*:[^:]"me=e-1 contains=@cLabelGroup - -syn match cUserLabel display "\I\i*" contained -syn match cUserLabel2 display "\I\i*:;\+"me=e-2 -syn match cGotoLabel display "\>\|[-+*/%&^|<>!=]\)=" -syn match cOperator "<<\|>>\|&&\|||\|++\|--\|->" -syn match cOperator "[.!~*&%<>^|=+-]" -syn match cOperator "/[^/*=]"me=e-1 -syn match cOperator "/$" -syn match cOperator "[\\]" -syn match cOperator "&&\|||" -syn match cSpecialCharacter "[,;]" -syn match cDelimiter "[][(){}]" -syn keyword cType CHAR byte BYTE uchar ushort uint ulong -syn keyword cType WORD DWORD QWORD INT INT2 INT4 UNS UNS2 UNS4 INT8 UNS8 -syn keyword cType CFG_t cfap_t cBYTE cvoid -syn keyword cType _Bool _Complex _Imaginary __int64 -if !exists("c_no_ansi") || exists("c_ansi_typedefs") - syn keyword cMC __near __far FAR __io __direct DIR -endif - -if exists("c_minlines") - let b:c_minlines = c_minlines -else - if !exists("c_no_if0") - let b:c_minlines = 50 " #if 0 constructs can be long - else - let b:c_minlines = 15 " mostly for () constructs - endif -endif -exec "syn sync ccomment cComment minlines=" . b:c_minlines - -" Define the default highlighting. -" For version 5.7 and earlier: only when not done already -" For version 5.8 and later: only when an item doesn't have highlighting yet -if version >= 508 || !exists("did_c_syn_inits") - if version < 508 - let did_c_syn_inits = 1 - command -nargs=+ HiLink hi link - else - command -nargs=+ HiLink hi def link - endif - - HiLink cFormat cSpecial - HiLink cCppString cString - HiLink cCommentL cComment - HiLink cCommentStart cComment - HiLink cLabel Label -" HiLink cUserLabel Label - HiLink cUserLabel UserLabel2 - HiLink cUserLabel2 UserLabel2 - HiLink cGotoLabel UserLabel2 - HiLink cGoto Statement - HiLink cConditional Conditional - HiLink cRepeat Repeat - HiLink cCharacter Character - HiLink cSpecialCharacter cSpecial - HiLink cNumber Number - HiLink cOctal Number - HiLink cOctalZero PreProc " link this to Error if you want - HiLink cFloat Float - HiLink cOctalError cError - HiLink cParenError cError - HiLink cErrInParen cError - HiLink cErrInBracket cError - HiLink cCommentError cError - HiLink cCommentStartError cError - HiLink cSpaceError cError - HiLink cSpecialError cError - HiLink cOperator Operator - HiLink cOperatorBold OperatorBold - HiLink cStructure Structure - HiLink cStorageClass StorageClass - HiLink cInclude Include - HiLink cPreProc PreProc - HiLink cDefine Macro - HiLink cDefined PreCondit - HiLink cIncluded cString - HiLink cError Error - HiLink cStatement Statement - HiLink cPreCondit PreCondit - HiLink cPreConditIf PreCondit - HiLink cType Type - HiLink cConstant Constant - HiLink cCommentString cString - HiLink cComment2String cString - HiLink cCommentSkip cComment - HiLink cString String - HiLink cComment Comment - HiLink cDelimiter Delimiter - HiLink cSpecial SpecialChar - HiLink cTodo Todo - HiLink cCppSkip cCppOut - HiLink cCppOut2 cCppOut - HiLink cCppOut Comment - HiLink cMulti Operator - HiLink cMultiMG Operator - HiLink cFunction Function - HiLink cAnsiFunction StdFunction - HiLink cName Name - HiLink cBitField Name - HiLink cAnsiName StdName - "HiLink cBlock BlockBraces - HiLink cBraces BlockBraces - "HiLink cBraceError Error - HiLink cMC MicroController - HiLink cAnsiFuncPtr AnsiFuncPtr - - hi Function gui=NONE guifg=#e86f00 - "hi StdFunction gui=bold guifg=#ee0040 - hi StdFunction gui=bold guifg=#e86f00 - hi Statement gui=bold guifg=#a06129 - hi UserLabel2 gui=bold guifg=#c96129 - hi Operator gui=NONE guifg=#000000 - hi OperatorBold gui=bold guifg=#000000 - hi StdName gui=bold guifg=#5276e6 - hi Name gui=NONE guifg=#5276e6 - hi BlockBraces gui=bold guifg=#000000 - hi Special gui=NONE guifg=#a000a0 - hi Comment gui=NONE guifg=grey62 - hi MicroController gui=bold guifg=#d00000 - hi AnsiFuncPtr gui=NONE guifg=#ff0000 -" hi PreProc gui=NONE guifg=#6a5acd - hi PreCondit gui=NONE guifg=#6a5acd -" hi Macro gui=NONE guifg=#0000ff - - delcommand HiLink -endif -hi Normal gui=NONE guifg=#000000 guibg=Ivory1 - -let b:current_syntax = "c" - -" vim: ts=8 + syn region cCppOut start="^\s*\(%:\|#\)\s*if\s\+0\+\>" end=".\@=\|$" contains=cCppOut2 + syn region cCppOut2 contained start="0" end="^\s*\(%:\|#\)\s*\(endif\>\|else\>\|elif\>\)" contains=cSpaceError,cCppSkip + syn region cCppSkip contained start="^\s*\(%:\|#\)\s*\(if\>\|ifdef\>\|ifndef\>\)" skip="\\$" end="^\s*\(%:\|#\)\s*endif\>" contains=cSpaceError,cCppSkip + endif + syn region cIncluded display contained start=+"+ skip=+\\\\\|\\"+ end=+"+ + syn match cIncluded display contained "<[^>]*>" + syn match cInclude display "^\s*\(%:\|#\)\s*include\>\s*["<]" contains=cIncluded + syn match cLineSkip "\\$" + syn cluster cPreProcGroup contains=cPreConditIf,cPreCondit,cIncluded,cInclude,cDefined,cDefine,cErrInParen,cErrInBracket,cUserLabel,cUserLabel2,cGotoLabel,cSpecial,cOctalZero,cCppOut,cCppOut2,cCppSkip,cFormat,cNumber,cFloat,cOctal,cOctalError,cNumbersCom,cString,cCommentSkip,cCommentString,cComment2String,@cCommentGroup,cCommentStartError,cParen,cBracket,cMulti + "syn region cDefine start="^\s*\(%:\|#\)\s*\(define\|undef\)\>" skip="\\$" end="$" end="//"me=s-1 contains=ALLBUT,@cPreProcGroup,@Spell + syn region cDefine start="^\s*\(%:\|#\)\s*\(define\|undef\)\>" skip="\\$" end="$" end="//"me=s-1 contains=ALLBUT,@cPreProcGroup,cName,cFunction,cAnsiFunction,@Spell + syn region cPreProc start="^\s*\(%:\|#\)\s*\(pragma\>\|line\>\|warning\>\|warn\>\|error\>\)" skip="\\$" end="$" keepend contains=ALLBUT,@cPreProcGroup,@Spell + + " Highlight User Labels + syn cluster cMultiGroup contains=cIncluded,cSpecial,cCommentSkip,cCommentString,cComment2String,@cCommentGroup,cCommentStartError,cUserCont,cUserLabel,cUserLabel2,cGotoLabel,cBitField,cOctalZero,cCppOut,cCppOut2,cCppSkip,cFormat,cNumber,cFloat,cOctal,cOctalError,cNumbersCom,cCppParen,cCppBracket,cCppString + syn region cMulti transparent start='?' skip='::' end=':' contains=ALLBUT,@cMultiGroup,@Spell + " Avoid matching foo::bar() in C++ by requiring that the next char is not ':' + syn cluster cLabelGroup contains=cUserLabel + syn match cUserCont display "^\s*\I\i*\s*:$" contains=@cLabelGroup + syn match cUserCont display ";\s*\I\i*\s*:$" contains=@cLabelGroup + syn match cUserCont display "^\s*\I\i*\s*:[^:]"me=e-1 contains=@cLabelGroup + syn match cUserCont display ";\s*\I\i*\s*:[^:]"me=e-1 contains=@cLabelGroup + + syn match cUserLabel display "\I\i*" contained + syn match cUserLabel2 display "\I\i*:;\+"me=e-2 + syn match cGotoLabel display "\>\|[-+*/%&^|<>!=]\)=" + syn match cOperator "<<\|>>\|&&\|||\|++\|--\|->" + syn match cOperator "[.!~*&%<>^|=+-]" + syn match cOperator "/[^/*=]"me=e-1 + syn match cOperator "/$" + syn match cOperator "[\\]" + syn match cOperator "&&\|||" + syn match cSpecialCharacter "[,;]" + syn match cDelimiter "[][(){}]" + syn keyword cType CHAR byte BYTE uchar ushort uint ulong + syn keyword cType WORD DWORD QWORD INT INT2 INT4 UNS UNS2 UNS4 INT8 UNS8 + syn keyword cType CFG_t cfap_t cBYTE cvoid + syn keyword cType _Bool _Complex _Imaginary __int64 + if !exists("c_no_ansi") || exists("c_ansi_typedefs") + syn keyword cMC __near __far FAR __io __direct DIR + endif + + if exists("c_minlines") + let b:c_minlines = c_minlines + else + if !exists("c_no_if0") + let b:c_minlines = 50 " #if 0 constructs can be long + else + let b:c_minlines = 15 " mostly for () constructs + endif + endif + exec "syn sync ccomment cComment minlines=" . b:c_minlines + + " Define the default highlighting. + " For version 5.7 and earlier: only when not done already + " For version 5.8 and later: only when an item doesn't have highlighting yet + if version >= 508 || !exists("did_c_syn_inits") + if version < 508 + let did_c_syn_inits = 1 + command -nargs=+ HiLink hi link + else + command -nargs=+ HiLink hi def link + endif + + HiLink cFormat cSpecial + HiLink cCppString cString + HiLink cCommentL cComment + HiLink cCommentStart cComment + HiLink cLabel Label + " HiLink cUserLabel Label + HiLink cUserLabel UserLabel2 + HiLink cUserLabel2 UserLabel2 + HiLink cGotoLabel UserLabel2 + HiLink cGoto Statement + HiLink cConditional Conditional + HiLink cRepeat Repeat + HiLink cCharacter Character + HiLink cSpecialCharacter cSpecial + HiLink cNumber Number + HiLink cOctal Number + HiLink cOctalZero PreProc " link this to Error if you want + HiLink cFloat Float + HiLink cOctalError cError + HiLink cParenError cError + HiLink cErrInParen cError + HiLink cErrInBracket cError + HiLink cCommentError cError + HiLink cCommentStartError cError + HiLink cSpaceError cError + HiLink cSpecialError cError + HiLink cOperator Operator + HiLink cOperatorBold OperatorBold + HiLink cStructure Structure + HiLink cStorageClass StorageClass + HiLink cInclude Include + HiLink cPreProc PreProc + HiLink cDefine Macro + HiLink cDefined PreCondit + HiLink cIncluded cString + HiLink cError Error + HiLink cStatement Statement + HiLink cPreCondit PreCondit + HiLink cPreConditIf PreCondit + HiLink cType Type + HiLink cConstant Constant + HiLink cCommentString cString + HiLink cComment2String cString + HiLink cCommentSkip cComment + HiLink cString String + HiLink cComment Comment + HiLink cDelimiter Delimiter + HiLink cSpecial SpecialChar + HiLink cTodo Todo + HiLink cCppSkip cCppOut + HiLink cCppOut2 cCppOut + HiLink cCppOut Comment + HiLink cMulti Operator + HiLink cMultiMG Operator + HiLink cFunction Function + HiLink cAnsiFunction StdFunction + HiLink cName Name + HiLink cBitField Name + HiLink cAnsiName StdName + "HiLink cBlock BlockBraces + HiLink cBraces BlockBraces + "HiLink cBraceError Error + HiLink cMC MicroController + HiLink cAnsiFuncPtr AnsiFuncPtr + + hi Function gui=NONE guifg=#e86f00 + "hi StdFunction gui=bold guifg=#ee0040 + hi StdFunction gui=bold guifg=#e86f00 + hi Statement gui=bold guifg=#a06129 + hi UserLabel2 gui=bold guifg=#c96129 + hi Operator gui=NONE guifg=#000000 + hi OperatorBold gui=bold guifg=#000000 + hi StdName gui=bold guifg=#5276e6 + hi Name gui=NONE guifg=#5276e6 + hi BlockBraces gui=bold guifg=#000000 + hi Special gui=NONE guifg=#a000a0 + hi Comment gui=NONE guifg=grey62 + hi MicroController gui=bold guifg=#d00000 + hi AnsiFuncPtr gui=NONE guifg=#ff0000 + " hi PreProc gui=NONE guifg=#6a5acd + hi PreCondit gui=NONE guifg=#6a5acd + " hi Macro gui=NONE guifg=#0000ff + + delcommand HiLink + endif + hi Normal gui=NONE guifg=#000000 guibg=Ivory1 + + let b:current_syntax = "c" + + " vim: ts=8 Index: /issm/trunk/externalpackages/vim/addons/vimrc =================================================================== --- /issm/trunk/externalpackages/vim/addons/vimrc (revision 13394) +++ /issm/trunk/externalpackages/vim/addons/vimrc (revision 13395) @@ -99,4 +99,8 @@ map :w :make map! :w :make +" make update: nice for longer documents +map :w :make update +map! :w :make update + "use paste P: re-indent and re-format at the same time @@ -190,36 +194,40 @@ " Abbreviations {{{1 " ---------------------------------------------------------------------- -func Eatchar(pat) - let c = nr2char(getchar()) - return (c =~ a:pat) ? '' : c -endfunc -au BufRead,BufNewFile *.html iabbr H1

=Eatchar('\s') -au BufRead,BufNewFile *.html iabbr H2

=Eatchar('\s') -au BufRead,BufNewFile *.html iabbr H3

=Eatchar('\s') -au BufRead,BufNewFile *.html iabbr CO =Eatchar('\s') -au BufRead,BufNewFile *.html iabbr PP

=Eatchar('\s') -au BufRead,BufNewFile *.m iabbr p1 disp('');=Eatchar('\s') -au BufRead,BufNewFile *.m iab p0 "disp('-------------- file: ".expand('%')." line: ".line(".")."');" -au BufRead,BufNewFile *.c* iabbr p1 printf("\n");=Eatchar('\s') -au BufRead,BufNewFile *.c*,*.h iabbr ER _error_("");=Eatchar('\s') -au BufRead,BufNewFile *.c* ab VV VecView(ug,PETSC_VIEWER_STDOUT_WORLD); -au BufRead,BufNewFile *.c* ab AS _assert_(); -au BufRead,BufNewFile *.c* iab p0 "printf(\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);" -au BufRead,BufNewFile *.c* iab pp0 "PetscSynchronizedPrintf(MPI_COMM_WORLD,\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);\nPetscSynchronizedFlush(MPI_COMM_WORLD);" -"tex -au BufRead,BufNewFile *.tex iab EQ - \\begin{equation} - \\end{equation}=Eatchar('\s') -au BufRead,BufNewFile *.tex iab IT - \\begin{itemize} - \\item - \\end{itemize}=Eatchar('\s') -au BufRead,BufNewFile *.tex iab EN - \\begin{enumerate} - \\item - \\end{enumerate}=Eatchar('\s') -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 H1

=Eatchar('\s') +"au BufRead,BufNewFile *.html iabbr H2

=Eatchar('\s') +"au BufRead,BufNewFile *.html iabbr H3

=Eatchar('\s') +"au BufRead,BufNewFile *.html iabbr CO =Eatchar('\s') +"au BufRead,BufNewFile *.html iabbr PP

=Eatchar('\s') +"au BufRead,BufNewFile *.m iabbr p1 disp('');=Eatchar('\s') +"au BufRead,BufNewFile *.m iab p0 "disp('-------------- file: ".expand('%')." line: ".line(".")."');" +"au BufRead,BufNewFile *.c* iabbr p1 printf("\n");=Eatchar('\s') +"au BufRead,BufNewFile *.c*,*.h iabbr ER _error_("");=Eatchar('\s') +"au BufRead,BufNewFile *.c* ab VV VecView(ug,PETSC_VIEWER_STDOUT_WORLD); +"au BufRead,BufNewFile *.c* ab AS _assert_(); +"au BufRead,BufNewFile *.c* iab p0 "printf(\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);" +"au BufRead,BufNewFile *.c* iab pp0 "PetscSynchronizedPrintf(MPI_COMM_WORLD,\"-------------- file: ".expand('%')." line: %i\\n\",__LINE__);\nPetscSynchronizedFlush(MPI_COMM_WORLD);" +""tex +"au BufRead,BufNewFile *.tex iab EQ +" \\begin{equation} +" \\end{equation}=Eatchar('\s') +"au BufRead,BufNewFile *.tex iab IT +" \\begin{itemize} +" \\item +" \\end{itemize}=Eatchar('\s') +"au BufRead,BufNewFile *.tex iab EN +" \\begin{enumerate} +" \\item +" \\end{enumerate}=Eatchar('\s') +"au BufRead,BufNewFile *.tex ab (()) \left( \right) "}}} " Skeletons {{{1 au BufNewFile letter.tex 0r ~/.vim/xtr/skeleton/letter.tex "}}} +" Copy and Paste{{{ +"vmap y:call system("pbcopy", getreg("\"")) +"nmap :call setreg("\"",system("pbpaste"))p +"}}} Index: /issm/trunk/externalpackages/vim/install.sh =================================================================== --- /issm/trunk/externalpackages/vim/install.sh (revision 13394) +++ /issm/trunk/externalpackages/vim/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/windows/install.sh =================================================================== --- /issm/trunk/externalpackages/windows/install.sh (revision 13394) +++ /issm/trunk/externalpackages/windows/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Download from ISSM server Index: /issm/trunk/externalpackages/xaifbooster/install.sh =================================================================== --- /issm/trunk/externalpackages/xaifbooster/install.sh (revision 13394) +++ /issm/trunk/externalpackages/xaifbooster/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/externalpackages/xerces/install.sh =================================================================== --- /issm/trunk/externalpackages/xerces/install.sh (revision 13394) +++ /issm/trunk/externalpackages/xerces/install.sh (revision 13395) @@ -1,3 +1,4 @@ #!/bin/bash +set -eu #Some cleanup Index: /issm/trunk/ltmain.sh =================================================================== --- /issm/trunk/ltmain.sh (revision 13394) +++ /issm/trunk/ltmain.sh (revision 13395) @@ -1,8 +1,8 @@ -# Generated from ltmain.m4sh. - -# ltmain.sh (GNU libtool) 2.2.6b + +# libtool (GNU libtool) 2.4.2 # Written by Gordon Matzigkeit , 1996 -# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc. +# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, +# 2007, 2008, 2009, 2010, 2011 Free Software Foundation, Inc. # This is free software; see the source for copying conditions. There is NO # warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. @@ -33,27 +33,32 @@ # Provide generalized library-building support services. # -# --config show all configuration variables -# --debug enable verbose shell tracing -# -n, --dry-run display commands without modifying any files -# --features display basic configuration information and exit -# --mode=MODE use operation mode MODE -# --preserve-dup-deps don't remove duplicate dependency libraries -# --quiet, --silent don't print informational messages -# --tag=TAG use configuration variables from tag TAG -# -v, --verbose print informational messages (default) -# --version print version information -# -h, --help print short or long help message +# --config show all configuration variables +# --debug enable verbose shell tracing +# -n, --dry-run display commands without modifying any files +# --features display basic configuration information and exit +# --mode=MODE use operation mode MODE +# --preserve-dup-deps don't remove duplicate dependency libraries +# --quiet, --silent don't print informational messages +# --no-quiet, --no-silent +# print informational messages (default) +# --no-warn don't display warning messages +# --tag=TAG use configuration variables from tag TAG +# -v, --verbose print more informational messages than default +# --no-verbose don't print the extra informational messages +# --version print version information +# -h, --help, --help-all print short, long, or detailed help message # # MODE must be one of the following: # -# clean remove files from the build directory -# compile compile a source file into a libtool object -# execute automatically set library path, then run a program -# finish complete the installation of libtool libraries -# install install libraries or executables -# link create a library or an executable -# uninstall remove libraries from an installed directory +# clean remove files from the build directory +# compile compile a source file into a libtool object +# execute automatically set library path, then run a program +# finish complete the installation of libtool libraries +# install install libraries or executables +# link create a library or an executable +# uninstall remove libraries from an installed directory # -# MODE-ARGS vary depending on the MODE. +# MODE-ARGS vary depending on the MODE. When passed as first option, +# `--mode=MODE' may be abbreviated as `MODE' or a unique abbreviation of that. # Try `$progname --help --mode=MODE' for a more detailed description of MODE. # @@ -61,20 +66,22 @@ # include the following information: # -# host-triplet: $host -# shell: $SHELL -# compiler: $LTCC -# compiler flags: $LTCFLAGS -# linker: $LD (gnu? $with_gnu_ld) -# $progname: (GNU libtool) 2.2.6b -# automake: $automake_version -# autoconf: $autoconf_version +# host-triplet: $host +# shell: $SHELL +# compiler: $LTCC +# compiler flags: $LTCFLAGS +# linker: $LD (gnu? $with_gnu_ld) +# $progname: (GNU libtool) 2.4.2 +# automake: $automake_version +# autoconf: $autoconf_version # # Report bugs to . - -PROGRAM=ltmain.sh +# GNU libtool home page: . +# General help using GNU software: . + +PROGRAM=libtool PACKAGE=libtool -VERSION=2.2.6b +VERSION=2.4.2 TIMESTAMP="" -package_revision=1.3017 +package_revision=1.3337 # Be Bourne compatible @@ -92,8 +99,13 @@ DUALCASE=1; export DUALCASE # for MKS sh +# A function that is used when there is no print builtin or printf. +func_fallback_echo () +{ + eval 'cat <<_LTECHO_EOF +$1 +_LTECHO_EOF' +} + # NLS nuisances: We save the old values to restore during execute mode. -# Only set LANG and LC_ALL to C if already set. -# These must not be set unconditionally because not all systems understand -# e.g. LANG=C (notably SCO). lt_user_locale= lt_safe_locale= @@ -108,22 +120,26 @@ fi" done +LC_ALL=C +LANGUAGE=C +export LANGUAGE LC_ALL $lt_unset CDPATH +# Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh +# is ksh but when the shell is invoked as "sh" and the current value of +# the _XPG environment variable is not equal to 1 (one), the special +# positional parameter $0, within a function call, is the name of the +# function. +progpath="$0" : ${CP="cp -f"} -: ${ECHO="echo"} -: ${EGREP="/bin/grep -E"} -: ${FGREP="/bin/grep -F"} -: ${GREP="/bin/grep"} -: ${LN_S="ln -s"} +test "${ECHO+set}" = set || ECHO=${as_echo-'printf %s\n'} : ${MAKE="make"} : ${MKDIR="mkdir"} : ${MV="mv -f"} : ${RM="rm -f"} -: ${SED="/bin/sed"} : ${SHELL="${CONFIG_SHELL-/bin/sh}"} : ${Xsed="$SED -e 1s/^X//"} @@ -144,4 +160,25 @@ dirname="s,/[^/]*$,," basename="s,^.*/,," + +# func_dirname file append nondir_replacement +# Compute the dirname of FILE. If nonempty, add APPEND to the result, +# otherwise set result to NONDIR_REPLACEMENT. +func_dirname () +{ + func_dirname_result=`$ECHO "${1}" | $SED "$dirname"` + if test "X$func_dirname_result" = "X${1}"; then + func_dirname_result="${3}" + else + func_dirname_result="$func_dirname_result${2}" + fi +} # func_dirname may be replaced by extended shell implementation + + +# func_basename file +func_basename () +{ + func_basename_result=`$ECHO "${1}" | $SED "$basename"` +} # func_basename may be replaced by extended shell implementation + # func_dirname_and_basename file append nondir_replacement @@ -159,31 +196,181 @@ func_dirname_and_basename () { - # Extract subdirectory from the argument. - func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"` - if test "X$func_dirname_result" = "X${1}"; then - func_dirname_result="${3}" - else - func_dirname_result="$func_dirname_result${2}" + # Extract subdirectory from the argument. + func_dirname_result=`$ECHO "${1}" | $SED -e "$dirname"` + if test "X$func_dirname_result" = "X${1}"; then + func_dirname_result="${3}" + else + func_dirname_result="$func_dirname_result${2}" + fi + func_basename_result=`$ECHO "${1}" | $SED -e "$basename"` +} # func_dirname_and_basename may be replaced by extended shell implementation + + +# func_stripname prefix suffix name +# strip PREFIX and SUFFIX off of NAME. +# PREFIX and SUFFIX must not contain globbing or regex special +# characters, hashes, percent signs, but SUFFIX may contain a leading +# dot (in which case that matches only a dot). +# func_strip_suffix prefix name +func_stripname () +{ + case ${2} in + .*) func_stripname_result=`$ECHO "${3}" | $SED "s%^${1}%%; s%\\\\${2}\$%%"`;; + *) func_stripname_result=`$ECHO "${3}" | $SED "s%^${1}%%; s%${2}\$%%"`;; + esac +} # func_stripname may be replaced by extended shell implementation + + +# These SED scripts presuppose an absolute path with a trailing slash. +pathcar='s,^/\([^/]*\).*$,\1,' +pathcdr='s,^/[^/]*,,' +removedotparts=':dotsl + s@/\./@/@g + t dotsl + s,/\.$,/,' +collapseslashes='s@/\{1,\}@/@g' +finalslash='s,/*$,/,' + +# func_normal_abspath PATH +# Remove doubled-up and trailing slashes, "." path components, +# and cancel out any ".." path components in PATH after making +# it an absolute path. +# value returned in "$func_normal_abspath_result" +func_normal_abspath () +{ + # Start from root dir and reassemble the path. + func_normal_abspath_result= + func_normal_abspath_tpath=$1 + func_normal_abspath_altnamespace= + case $func_normal_abspath_tpath in + "") + # Empty path, that just means $cwd. + func_stripname '' '/' "`pwd`" + func_normal_abspath_result=$func_stripname_result + return + ;; + # The next three entries are used to spot a run of precisely + # two leading slashes without using negated character classes; + # we take advantage of case's first-match behaviour. + ///*) + # Unusual form of absolute path, do nothing. + ;; + //*) + # Not necessarily an ordinary path; POSIX reserves leading '//' + # and for example Cygwin uses it to access remote file shares + # over CIFS/SMB, so we conserve a leading double slash if found. + func_normal_abspath_altnamespace=/ + ;; + /*) + # Absolute path, do nothing. + ;; + *) + # Relative path, prepend $cwd. + func_normal_abspath_tpath=`pwd`/$func_normal_abspath_tpath + ;; + esac + # Cancel out all the simple stuff to save iterations. We also want + # the path to end with a slash for ease of parsing, so make sure + # there is one (and only one) here. + func_normal_abspath_tpath=`$ECHO "$func_normal_abspath_tpath" | $SED \ + -e "$removedotparts" -e "$collapseslashes" -e "$finalslash"` + while :; do + # Processed it all yet? + if test "$func_normal_abspath_tpath" = / ; then + # If we ascended to the root using ".." the result may be empty now. + if test -z "$func_normal_abspath_result" ; then + func_normal_abspath_result=/ + fi + break + fi + func_normal_abspath_tcomponent=`$ECHO "$func_normal_abspath_tpath" | $SED \ + -e "$pathcar"` + func_normal_abspath_tpath=`$ECHO "$func_normal_abspath_tpath" | $SED \ + -e "$pathcdr"` + # Figure out what to do with it + case $func_normal_abspath_tcomponent in + "") + # Trailing empty path component, ignore it. + ;; + ..) + # Parent dir; strip last assembled component from result. + func_dirname "$func_normal_abspath_result" + func_normal_abspath_result=$func_dirname_result + ;; + *) + # Actual path component, append it. + func_normal_abspath_result=$func_normal_abspath_result/$func_normal_abspath_tcomponent + ;; + esac + done + # Restore leading double-slash if one was found on entry. + func_normal_abspath_result=$func_normal_abspath_altnamespace$func_normal_abspath_result +} + +# func_relative_path SRCDIR DSTDIR +# generates a relative path from SRCDIR to DSTDIR, with a trailing +# slash if non-empty, suitable for immediately appending a filename +# without needing to append a separator. +# value returned in "$func_relative_path_result" +func_relative_path () +{ + func_relative_path_result= + func_normal_abspath "$1" + func_relative_path_tlibdir=$func_normal_abspath_result + func_normal_abspath "$2" + func_relative_path_tbindir=$func_normal_abspath_result + + # Ascend the tree starting from libdir + while :; do + # check if we have found a prefix of bindir + case $func_relative_path_tbindir in + $func_relative_path_tlibdir) + # found an exact match + func_relative_path_tcancelled= + break + ;; + $func_relative_path_tlibdir*) + # found a matching prefix + func_stripname "$func_relative_path_tlibdir" '' "$func_relative_path_tbindir" + func_relative_path_tcancelled=$func_stripname_result + if test -z "$func_relative_path_result"; then + func_relative_path_result=. + fi + break + ;; + *) + func_dirname $func_relative_path_tlibdir + func_relative_path_tlibdir=${func_dirname_result} + if test "x$func_relative_path_tlibdir" = x ; then + # Have to descend all the way to the root! + func_relative_path_result=../$func_relative_path_result + func_relative_path_tcancelled=$func_relative_path_tbindir + break + fi + func_relative_path_result=../$func_relative_path_result + ;; + esac + done + + # Now calculate path; take care to avoid doubling-up slashes. + func_stripname '' '/' "$func_relative_path_result" + func_relative_path_result=$func_stripname_result + func_stripname '/' '/' "$func_relative_path_tcancelled" + if test "x$func_stripname_result" != x ; then + func_relative_path_result=${func_relative_path_result}/${func_stripname_result} fi - func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"` -} - -# Generated shell functions inserted here. - -# Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh -# is ksh but when the shell is invoked as "sh" and the current value of -# the _XPG environment variable is not equal to 1 (one), the special -# positional parameter $0, within a function call, is the name of the -# function. -progpath="$0" + + # Normalisation. If bindir is libdir, return empty string, + # else relative path ending with a slash; either way, target + # file name can be directly appended. + if test ! -z "$func_relative_path_result"; then + func_stripname './' '' "$func_relative_path_result/" + func_relative_path_result=$func_stripname_result + fi +} # The name of this program: -# In the unlikely event $progname began with a '-', it would play havoc with -# func_echo (imagine progname=-n), so we prepend ./ in that case: func_dirname_and_basename "$progpath" progname=$func_basename_result -case $progname in - -*) progname=./$progname ;; -esac # Make sure we have an absolute path for reexecution: @@ -197,5 +384,5 @@ *) save_IFS="$IFS" - IFS=: + IFS=${PATH_SEPARATOR-:} for progdir in $PATH; do IFS="$save_IFS" @@ -215,4 +402,13 @@ # Same as above, but do not quote variable references. double_quote_subst='s/\(["`\\]\)/\\\1/g' + +# Sed substitution that turns a string into a regex matching for the +# string literally. +sed_make_literal_regex='s,[].[^$\\*\/],\\&,g' + +# Sed substitution that converts a w32 file name or path +# which contains forward slashes, into one that contains +# (escaped) backslashes. A very naive implementation. +lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' # Re-`\' parameter expansions in output of double_quote_subst that were @@ -244,5 +440,5 @@ func_echo () { - $ECHO "$progname${mode+: }$mode: $*" + $ECHO "$progname: ${opt_mode+$opt_mode: }$*" } @@ -259,9 +455,16 @@ } +# func_echo_all arg... +# Invoke $ECHO with all args, space-separated. +func_echo_all () +{ + $ECHO "$*" +} + # func_error arg... # Echo program name prefixed message to standard error. func_error () { - $ECHO "$progname${mode+: }$mode: "${1+"$@"} 1>&2 + $ECHO "$progname: ${opt_mode+$opt_mode: }"${1+"$@"} 1>&2 } @@ -270,5 +473,5 @@ func_warning () { - $opt_warning && $ECHO "$progname${mode+: }$mode: warning: "${1+"$@"} 1>&2 + $opt_warning && $ECHO "$progname: ${opt_mode+$opt_mode: }warning: "${1+"$@"} 1>&2 # bash bug again: @@ -327,7 +530,7 @@ # ...otherwise throw away the child directory and loop - my_directory_path=`$ECHO "X$my_directory_path" | $Xsed -e "$dirname"` + my_directory_path=`$ECHO "$my_directory_path" | $SED -e "$dirname"` done - my_dir_list=`$ECHO "X$my_dir_list" | $Xsed -e 's,:*$,,'` + my_dir_list=`$ECHO "$my_dir_list" | $SED 's,:*$,,'` save_mkdir_p_IFS="$IFS"; IFS=':' @@ -379,5 +582,5 @@ fi - $ECHO "X$my_tmpdir" | $Xsed + $ECHO "$my_tmpdir" } @@ -393,5 +596,5 @@ case $1 in *[\\\`\"\$]*) - func_quote_for_eval_unquoted_result=`$ECHO "X$1" | $Xsed -e "$sed_quote_subst"` ;; + func_quote_for_eval_unquoted_result=`$ECHO "$1" | $SED "$sed_quote_subst"` ;; *) func_quote_for_eval_unquoted_result="$1" ;; @@ -420,5 +623,5 @@ case $1 in *[\\\`\"]*) - my_arg=`$ECHO "X$1" | $Xsed \ + my_arg=`$ECHO "$1" | $SED \ -e "$double_quote_subst" -e "$sed_double_backslash"` ;; *) @@ -489,6 +692,20 @@ } - - +# func_tr_sh +# Turn $1 into a string suitable for a shell variable name. +# Result is stored in $func_tr_sh_result. All characters +# not in the set a-zA-Z0-9_ are replaced with '_'. Further, +# if $1 begins with a digit, a '_' is prepended as well. +func_tr_sh () +{ + case $1 in + [0-9]* | *[!a-zA-Z0-9_]*) + func_tr_sh_result=`$ECHO "$1" | $SED 's/^\([0-9]\)/_\1/; s/[^a-zA-Z0-9_]/_/g'` + ;; + * ) + func_tr_sh_result=$1 + ;; + esac +} @@ -497,5 +714,15 @@ func_version () { - $SED -n '/^# '$PROGRAM' (GNU /,/# warranty; / { + $opt_debug + + $SED -n '/(C)/!b go + :more + /\./!{ + N + s/\n# / / + b more + } + :go + /^# '$PROGRAM' (GNU /,/# warranty; / { s/^# // s/^# *$// @@ -510,5 +737,7 @@ func_usage () { - $SED -n '/^# Usage:/,/# -h/ { + $opt_debug + + $SED -n '/^# Usage:/,/^# *.*--help/ { s/^# // s/^# *$// @@ -516,14 +745,18 @@ p }' < "$progpath" - $ECHO + echo $ECHO "run \`$progname --help | more' for full usage" exit $? } -# func_help -# Echo long help message to standard output and exit. +# func_help [NOEXIT] +# Echo long help message to standard output and exit, +# unless 'noexit' is passed as argument. func_help () { + $opt_debug + $SED -n '/^# Usage:/,/# Report bugs to/ { + :print s/^# // s/^# *$// @@ -535,9 +768,16 @@ s*\$LD*'"$LD"'* s/\$with_gnu_ld/'"$with_gnu_ld"'/ - s/\$automake_version/'"`(automake --version) 2>/dev/null |$SED 1q`"'/ - s/\$autoconf_version/'"`(autoconf --version) 2>/dev/null |$SED 1q`"'/ + s/\$automake_version/'"`(${AUTOMAKE-automake} --version) 2>/dev/null |$SED 1q`"'/ + s/\$autoconf_version/'"`(${AUTOCONF-autoconf} --version) 2>/dev/null |$SED 1q`"'/ p - }' < "$progpath" - exit $? + d + } + /^# .* home page:/b print + /^# General help using/b print + ' < "$progpath" + ret=$? + if test -z "$1"; then + exit $ret + fi } @@ -547,8 +787,36 @@ func_missing_arg () { - func_error "missing argument for $1" + $opt_debug + + func_error "missing argument for $1." exit_cmd=exit } + +# func_split_short_opt shortopt +# Set func_split_short_opt_name and func_split_short_opt_arg shell +# variables after splitting SHORTOPT after the 2nd character. +func_split_short_opt () +{ + my_sed_short_opt='1s/^\(..\).*$/\1/;q' + my_sed_short_rest='1s/^..\(.*\)$/\1/;q' + + func_split_short_opt_name=`$ECHO "$1" | $SED "$my_sed_short_opt"` + func_split_short_opt_arg=`$ECHO "$1" | $SED "$my_sed_short_rest"` +} # func_split_short_opt may be replaced by extended shell implementation + + +# func_split_long_opt longopt +# Set func_split_long_opt_name and func_split_long_opt_arg shell +# variables after splitting LONGOPT at the `=' sign. +func_split_long_opt () +{ + my_sed_long_opt='1s/^\(--[^=]*\)=.*/\1/;q' + my_sed_long_arg='1s/^--[^=]*=//' + + func_split_long_opt_name=`$ECHO "$1" | $SED "$my_sed_long_opt"` + func_split_long_opt_arg=`$ECHO "$1" | $SED "$my_sed_long_arg"` +} # func_split_long_opt may be replaced by extended shell implementation + exit_cmd=: @@ -556,28 +824,4 @@ - -# Check that we have a working $ECHO. -if test "X$1" = X--no-reexec; then - # Discard the --no-reexec flag, and continue. - shift -elif test "X$1" = X--fallback-echo; then - # Avoid inline document here, it may be left over - : -elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t'; then - # Yippee, $ECHO works! - : -else - # Restart under the correct shell, and then maybe $ECHO will work. - exec $SHELL "$progpath" --no-reexec ${1+"$@"} -fi - -if test "X$1" = X--fallback-echo; then - # used as fallback echo - shift - cat </dev/null || echo $max_cmd_len` +} # func_len may be replaced by extended shell implementation + + +# func_lo2o object +func_lo2o () +{ + func_lo2o_result=`$ECHO "${1}" | $SED "$lo2o"` +} # func_lo2o may be replaced by extended shell implementation + + +# func_xform libobj-or-source +func_xform () +{ + func_xform_result=`$ECHO "${1}" | $SED 's/\.[^.]*$/.lo/'` +} # func_xform may be replaced by extended shell implementation + + # func_fatal_configuration arg... # Echo program name prefixed message to standard error, followed by @@ -637,14 +920,14 @@ func_features () { - $ECHO "host: $host" + echo "host: $host" if test "$build_libtool_libs" = yes; then - $ECHO "enable shared libraries" + echo "enable shared libraries" else - $ECHO "disable shared libraries" + echo "disable shared libraries" fi if test "$build_old_libs" = yes; then - $ECHO "enable static libraries" + echo "enable static libraries" else - $ECHO "disable static libraries" + echo "disable static libraries" fi @@ -691,131 +974,4 @@ ;; esac -} - -# Parse options once, thoroughly. This comes as soon as possible in -# the script to make things like `libtool --version' happen quickly. -{ - - # Shorthand for --mode=foo, only valid as the first argument - case $1 in - clean|clea|cle|cl) - shift; set dummy --mode clean ${1+"$@"}; shift - ;; - compile|compil|compi|comp|com|co|c) - shift; set dummy --mode compile ${1+"$@"}; shift - ;; - execute|execut|execu|exec|exe|ex|e) - shift; set dummy --mode execute ${1+"$@"}; shift - ;; - finish|finis|fini|fin|fi|f) - shift; set dummy --mode finish ${1+"$@"}; shift - ;; - install|instal|insta|inst|ins|in|i) - shift; set dummy --mode install ${1+"$@"}; shift - ;; - link|lin|li|l) - shift; set dummy --mode link ${1+"$@"}; shift - ;; - uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u) - shift; set dummy --mode uninstall ${1+"$@"}; shift - ;; - esac - - # Parse non-mode specific arguments: - while test "$#" -gt 0; do - opt="$1" - shift - - case $opt in - --config) func_config ;; - - --debug) preserve_args="$preserve_args $opt" - func_echo "enabling shell trace mode" - opt_debug='set -x' - $opt_debug - ;; - - -dlopen) test "$#" -eq 0 && func_missing_arg "$opt" && break - execute_dlfiles="$execute_dlfiles $1" - shift - ;; - - --dry-run | -n) opt_dry_run=: ;; - --features) func_features ;; - --finish) mode="finish" ;; - - --mode) test "$#" -eq 0 && func_missing_arg "$opt" && break - case $1 in - # Valid mode arguments: - clean) ;; - compile) ;; - execute) ;; - finish) ;; - install) ;; - link) ;; - relink) ;; - uninstall) ;; - - # Catch anything else as an error - *) func_error "invalid argument for $opt" - exit_cmd=exit - break - ;; - esac - - mode="$1" - shift - ;; - - --preserve-dup-deps) - opt_duplicate_deps=: ;; - - --quiet|--silent) preserve_args="$preserve_args $opt" - opt_silent=: - ;; - - --verbose| -v) preserve_args="$preserve_args $opt" - opt_silent=false - ;; - - --tag) test "$#" -eq 0 && func_missing_arg "$opt" && break - preserve_args="$preserve_args $opt $1" - func_enable_tag "$1" # tagname is set here - shift - ;; - - # Separate optargs to long options: - -dlopen=*|--mode=*|--tag=*) - func_opt_split "$opt" - set dummy "$func_opt_split_opt" "$func_opt_split_arg" ${1+"$@"} - shift - ;; - - -\?|-h) func_usage ;; - --help) opt_help=: ;; - --version) func_version ;; - - -*) func_fatal_help "unrecognized option \`$opt'" ;; - - *) nonopt="$opt" - break - ;; - esac - done - - - case $host in - *cygwin* | *mingw* | *pw32* | *cegcc*) - # don't eliminate duplications in $postdeps and $predeps - opt_duplicate_compiler_generated_deps=: - ;; - *) - opt_duplicate_compiler_generated_deps=$opt_duplicate_deps - ;; - esac - - # Having warned about all mis-specified options, bail out if - # anything was wrong. - $exit_cmd $EXIT_FAILURE } @@ -856,35 +1012,216 @@ +# Shorthand for --mode=foo, only valid as the first argument +case $1 in +clean|clea|cle|cl) + shift; set dummy --mode clean ${1+"$@"}; shift + ;; +compile|compil|compi|comp|com|co|c) + shift; set dummy --mode compile ${1+"$@"}; shift + ;; +execute|execut|execu|exec|exe|ex|e) + shift; set dummy --mode execute ${1+"$@"}; shift + ;; +finish|finis|fini|fin|fi|f) + shift; set dummy --mode finish ${1+"$@"}; shift + ;; +install|instal|insta|inst|ins|in|i) + shift; set dummy --mode install ${1+"$@"}; shift + ;; +link|lin|li|l) + shift; set dummy --mode link ${1+"$@"}; shift + ;; +uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u) + shift; set dummy --mode uninstall ${1+"$@"}; shift + ;; +esac + + + +# Option defaults: +opt_debug=: +opt_dry_run=false +opt_config=false +opt_preserve_dup_deps=false +opt_features=false +opt_finish=false +opt_help=false +opt_help_all=false +opt_silent=: +opt_warning=: +opt_verbose=: +opt_silent=false +opt_verbose=false + + +# Parse options once, thoroughly. This comes as soon as possible in the +# script to make things like `--version' happen as quickly as we can. +{ + # this just eases exit handling + while test $# -gt 0; do + opt="$1" + shift + case $opt in + --debug|-x) opt_debug='set -x' + func_echo "enabling shell trace mode" + $opt_debug + ;; + --dry-run|--dryrun|-n) + opt_dry_run=: + ;; + --config) + opt_config=: +func_config + ;; + --dlopen|-dlopen) + optarg="$1" + opt_dlopen="${opt_dlopen+$opt_dlopen +}$optarg" + shift + ;; + --preserve-dup-deps) + opt_preserve_dup_deps=: + ;; + --features) + opt_features=: +func_features + ;; + --finish) + opt_finish=: +set dummy --mode finish ${1+"$@"}; shift + ;; + --help) + opt_help=: + ;; + --help-all) + opt_help_all=: +opt_help=': help-all' + ;; + --mode) + test $# = 0 && func_missing_arg $opt && break + optarg="$1" + opt_mode="$optarg" +case $optarg in + # Valid mode arguments: + clean|compile|execute|finish|install|link|relink|uninstall) ;; + + # Catch anything else as an error + *) func_error "invalid argument for $opt" + exit_cmd=exit + break + ;; +esac + shift + ;; + --no-silent|--no-quiet) + opt_silent=false +func_append preserve_args " $opt" + ;; + --no-warning|--no-warn) + opt_warning=false +func_append preserve_args " $opt" + ;; + --no-verbose) + opt_verbose=false +func_append preserve_args " $opt" + ;; + --silent|--quiet) + opt_silent=: +func_append preserve_args " $opt" + opt_verbose=false + ;; + --verbose|-v) + opt_verbose=: +func_append preserve_args " $opt" +opt_silent=false + ;; + --tag) + test $# = 0 && func_missing_arg $opt && break + optarg="$1" + opt_tag="$optarg" +func_append preserve_args " $opt $optarg" +func_enable_tag "$optarg" + shift + ;; + + -\?|-h) func_usage ;; + --help) func_help ;; + --version) func_version ;; + + # Separate optargs to long options: + --*=*) + func_split_long_opt "$opt" + set dummy "$func_split_long_opt_name" "$func_split_long_opt_arg" ${1+"$@"} + shift + ;; + + # Separate non-argument short options: + -\?*|-h*|-n*|-v*) + func_split_short_opt "$opt" + set dummy "$func_split_short_opt_name" "-$func_split_short_opt_arg" ${1+"$@"} + shift + ;; + + --) break ;; + -*) func_fatal_help "unrecognized option \`$opt'" ;; + *) set dummy "$opt" ${1+"$@"}; shift; break ;; + esac + done + + # Validate options: + + # save first non-option argument + if test "$#" -gt 0; then + nonopt="$opt" + shift + fi + + # preserve --debug + test "$opt_debug" = : || func_append preserve_args " --debug" + + case $host in + *cygwin* | *mingw* | *pw32* | *cegcc*) + # don't eliminate duplications in $postdeps and $predeps + opt_duplicate_compiler_generated_deps=: + ;; + *) + opt_duplicate_compiler_generated_deps=$opt_preserve_dup_deps + ;; + esac + + $opt_help || { + # Sanity checks first: + func_check_version_match + + if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then + func_fatal_configuration "not configured to build any kind of library" + fi + + # Darwin sucks + eval std_shrext=\"$shrext_cmds\" + + # Only execute mode is allowed to have -dlopen flags. + if test -n "$opt_dlopen" && test "$opt_mode" != execute; then + func_error "unrecognized option \`-dlopen'" + $ECHO "$help" 1>&2 + exit $EXIT_FAILURE + fi + + # Change the help message to a mode-specific one. + generic_help="$help" + help="Try \`$progname --help --mode=$opt_mode' for more information." + } + + + # Bail if the options were screwed + $exit_cmd $EXIT_FAILURE +} + + + + ## ----------- ## ## Main. ## ## ----------- ## - -$opt_help || { - # Sanity checks first: - func_check_version_match - - if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then - func_fatal_configuration "not configured to build any kind of library" - fi - - test -z "$mode" && func_fatal_error "error: you must specify a MODE." - - - # Darwin sucks - eval std_shrext=\"$shrext_cmds\" - - - # Only execute mode is allowed to have -dlopen flags. - if test -n "$execute_dlfiles" && test "$mode" != execute; then - func_error "unrecognized option \`-dlopen'" - $ECHO "$help" 1>&2 - exit $EXIT_FAILURE - fi - - # Change the help message to a mode-specific one. - generic_help="$help" - help="Try \`$progname --help --mode=$mode' for more information." -} - # func_lalib_p file @@ -951,10 +1288,7 @@ func_ltwrapper_scriptname () { - func_ltwrapper_scriptname_result="" - if func_ltwrapper_executable_p "$1"; then - func_dirname_and_basename "$1" "" "." - func_stripname '' '.exe' "$func_basename_result" - func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper" - fi + func_dirname_and_basename "$1" "" "." + func_stripname '' '.exe' "$func_basename_result" + func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper" } @@ -1002,4 +1336,35 @@ +# func_resolve_sysroot PATH +# Replace a leading = in PATH with a sysroot. Store the result into +# func_resolve_sysroot_result +func_resolve_sysroot () +{ + func_resolve_sysroot_result=$1 + case $func_resolve_sysroot_result in + =*) + func_stripname '=' '' "$func_resolve_sysroot_result" + func_resolve_sysroot_result=$lt_sysroot$func_stripname_result + ;; + esac +} + +# func_replace_sysroot PATH +# If PATH begins with the sysroot, replace it with = and +# store the result into func_replace_sysroot_result. +func_replace_sysroot () +{ + case "$lt_sysroot:$1" in + ?*:"$lt_sysroot"*) + func_stripname "$lt_sysroot" '' "$1" + func_replace_sysroot_result="=$func_stripname_result" + ;; + *) + # Including no sysroot. + func_replace_sysroot_result=$1 + ;; + esac +} + # func_infer_tag arg # Infer tagged configuration to use if any are available and @@ -1014,11 +1379,13 @@ CC_quoted= for arg in $CC; do - func_quote_for_eval "$arg" - CC_quoted="$CC_quoted $func_quote_for_eval_result" + func_append_quoted CC_quoted "$arg" done + CC_expanded=`func_echo_all $CC` + CC_quoted_expanded=`func_echo_all $CC_quoted` case $@ in # Blanks in the command may have been stripped by the calling shell, # but not from the CC environment variable when configure was run. - " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;; + " $CC "* | "$CC "* | " $CC_expanded "* | "$CC_expanded "* | \ + " $CC_quoted"* | "$CC_quoted "* | " $CC_quoted_expanded "* | "$CC_quoted_expanded "*) ;; # Blanks at the start of $base_compile will cause this to fail # if we don't check for them as well. @@ -1031,9 +1398,11 @@ for arg in $CC; do # Double-quote args containing other shell metacharacters. - func_quote_for_eval "$arg" - CC_quoted="$CC_quoted $func_quote_for_eval_result" + func_append_quoted CC_quoted "$arg" done + CC_expanded=`func_echo_all $CC` + CC_quoted_expanded=`func_echo_all $CC_quoted` case "$@ " in - " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) + " $CC "* | "$CC "* | " $CC_expanded "* | "$CC_expanded "* | \ + " $CC_quoted"* | "$CC_quoted "* | " $CC_quoted_expanded "* | "$CC_quoted_expanded "*) # The compiler in the base compile command matches # the one in the tagged configuration. @@ -1098,4 +1467,484 @@ } + +################################################## +# FILE NAME AND PATH CONVERSION HELPER FUNCTIONS # +################################################## + +# func_convert_core_file_wine_to_w32 ARG +# Helper function used by file name conversion functions when $build is *nix, +# and $host is mingw, cygwin, or some other w32 environment. Relies on a +# correctly configured wine environment available, with the winepath program +# in $build's $PATH. +# +# ARG is the $build file name to be converted to w32 format. +# Result is available in $func_convert_core_file_wine_to_w32_result, and will +# be empty on error (or when ARG is empty) +func_convert_core_file_wine_to_w32 () +{ + $opt_debug + func_convert_core_file_wine_to_w32_result="$1" + if test -n "$1"; then + # Unfortunately, winepath does not exit with a non-zero error code, so we + # are forced to check the contents of stdout. On the other hand, if the + # command is not found, the shell will set an exit code of 127 and print + # *an error message* to stdout. So we must check for both error code of + # zero AND non-empty stdout, which explains the odd construction: + func_convert_core_file_wine_to_w32_tmp=`winepath -w "$1" 2>/dev/null` + if test "$?" -eq 0 && test -n "${func_convert_core_file_wine_to_w32_tmp}"; then + func_convert_core_file_wine_to_w32_result=`$ECHO "$func_convert_core_file_wine_to_w32_tmp" | + $SED -e "$lt_sed_naive_backslashify"` + else + func_convert_core_file_wine_to_w32_result= + fi + fi +} +# end: func_convert_core_file_wine_to_w32 + + +# func_convert_core_path_wine_to_w32 ARG +# Helper function used by path conversion functions when $build is *nix, and +# $host is mingw, cygwin, or some other w32 environment. Relies on a correctly +# configured wine environment available, with the winepath program in $build's +# $PATH. Assumes ARG has no leading or trailing path separator characters. +# +# ARG is path to be converted from $build format to win32. +# Result is available in $func_convert_core_path_wine_to_w32_result. +# Unconvertible file (directory) names in ARG are skipped; if no directory names +# are convertible, then the result may be empty. +func_convert_core_path_wine_to_w32 () +{ + $opt_debug + # unfortunately, winepath doesn't convert paths, only file names + func_convert_core_path_wine_to_w32_result="" + if test -n "$1"; then + oldIFS=$IFS + IFS=: + for func_convert_core_path_wine_to_w32_f in $1; do + IFS=$oldIFS + func_convert_core_file_wine_to_w32 "$func_convert_core_path_wine_to_w32_f" + if test -n "$func_convert_core_file_wine_to_w32_result" ; then + if test -z "$func_convert_core_path_wine_to_w32_result"; then + func_convert_core_path_wine_to_w32_result="$func_convert_core_file_wine_to_w32_result" + else + func_append func_convert_core_path_wine_to_w32_result ";$func_convert_core_file_wine_to_w32_result" + fi + fi + done + IFS=$oldIFS + fi +} +# end: func_convert_core_path_wine_to_w32 + + +# func_cygpath ARGS... +# Wrapper around calling the cygpath program via LT_CYGPATH. This is used when +# when (1) $build is *nix and Cygwin is hosted via a wine environment; or (2) +# $build is MSYS and $host is Cygwin, or (3) $build is Cygwin. In case (1) or +# (2), returns the Cygwin file name or path in func_cygpath_result (input +# file name or path is assumed to be in w32 format, as previously converted +# from $build's *nix or MSYS format). In case (3), returns the w32 file name +# or path in func_cygpath_result (input file name or path is assumed to be in +# Cygwin format). Returns an empty string on error. +# +# ARGS are passed to cygpath, with the last one being the file name or path to +# be converted. +# +# Specify the absolute *nix (or w32) name to cygpath in the LT_CYGPATH +# environment variable; do not put it in $PATH. +func_cygpath () +{ + $opt_debug + if test -n "$LT_CYGPATH" && test -f "$LT_CYGPATH"; then + func_cygpath_result=`$LT_CYGPATH "$@" 2>/dev/null` + if test "$?" -ne 0; then + # on failure, ensure result is empty + func_cygpath_result= + fi + else + func_cygpath_result= + func_error "LT_CYGPATH is empty or specifies non-existent file: \`$LT_CYGPATH'" + fi +} +#end: func_cygpath + + +# func_convert_core_msys_to_w32 ARG +# Convert file name or path ARG from MSYS format to w32 format. Return +# result in func_convert_core_msys_to_w32_result. +func_convert_core_msys_to_w32 () +{ + $opt_debug + # awkward: cmd appends spaces to result + func_convert_core_msys_to_w32_result=`( cmd //c echo "$1" ) 2>/dev/null | + $SED -e 's/[ ]*$//' -e "$lt_sed_naive_backslashify"` +} +#end: func_convert_core_msys_to_w32 + + +# func_convert_file_check ARG1 ARG2 +# Verify that ARG1 (a file name in $build format) was converted to $host +# format in ARG2. Otherwise, emit an error message, but continue (resetting +# func_to_host_file_result to ARG1). +func_convert_file_check () +{ + $opt_debug + if test -z "$2" && test -n "$1" ; then + func_error "Could not determine host file name corresponding to" + func_error " \`$1'" + func_error "Continuing, but uninstalled executables may not work." + # Fallback: + func_to_host_file_result="$1" + fi +} +# end func_convert_file_check + + +# func_convert_path_check FROM_PATHSEP TO_PATHSEP FROM_PATH TO_PATH +# Verify that FROM_PATH (a path in $build format) was converted to $host +# format in TO_PATH. Otherwise, emit an error message, but continue, resetting +# func_to_host_file_result to a simplistic fallback value (see below). +func_convert_path_check () +{ + $opt_debug + if test -z "$4" && test -n "$3"; then + func_error "Could not determine the host path corresponding to" + func_error " \`$3'" + func_error "Continuing, but uninstalled executables may not work." + # Fallback. This is a deliberately simplistic "conversion" and + # should not be "improved". See libtool.info. + if test "x$1" != "x$2"; then + lt_replace_pathsep_chars="s|$1|$2|g" + func_to_host_path_result=`echo "$3" | + $SED -e "$lt_replace_pathsep_chars"` + else + func_to_host_path_result="$3" + fi + fi +} +# end func_convert_path_check + + +# func_convert_path_front_back_pathsep FRONTPAT BACKPAT REPL ORIG +# Modifies func_to_host_path_result by prepending REPL if ORIG matches FRONTPAT +# and appending REPL if ORIG matches BACKPAT. +func_convert_path_front_back_pathsep () +{ + $opt_debug + case $4 in + $1 ) func_to_host_path_result="$3$func_to_host_path_result" + ;; + esac + case $4 in + $2 ) func_append func_to_host_path_result "$3" + ;; + esac +} +# end func_convert_path_front_back_pathsep + + +################################################## +# $build to $host FILE NAME CONVERSION FUNCTIONS # +################################################## +# invoked via `$to_host_file_cmd ARG' +# +# In each case, ARG is the path to be converted from $build to $host format. +# Result will be available in $func_to_host_file_result. + + +# func_to_host_file ARG +# Converts the file name ARG from $build format to $host format. Return result +# in func_to_host_file_result. +func_to_host_file () +{ + $opt_debug + $to_host_file_cmd "$1" +} +# end func_to_host_file + + +# func_to_tool_file ARG LAZY +# converts the file name ARG from $build format to toolchain format. Return +# result in func_to_tool_file_result. If the conversion in use is listed +# in (the comma separated) LAZY, no conversion takes place. +func_to_tool_file () +{ + $opt_debug + case ,$2, in + *,"$to_tool_file_cmd",*) + func_to_tool_file_result=$1 + ;; + *) + $to_tool_file_cmd "$1" + func_to_tool_file_result=$func_to_host_file_result + ;; + esac +} +# end func_to_tool_file + + +# func_convert_file_noop ARG +# Copy ARG to func_to_host_file_result. +func_convert_file_noop () +{ + func_to_host_file_result="$1" +} +# end func_convert_file_noop + + +# func_convert_file_msys_to_w32 ARG +# Convert file name ARG from (mingw) MSYS to (mingw) w32 format; automatic +# conversion to w32 is not available inside the cwrapper. Returns result in +# func_to_host_file_result. +func_convert_file_msys_to_w32 () +{ + $opt_debug + func_to_host_file_result="$1" + if test -n "$1"; then + func_convert_core_msys_to_w32 "$1" + func_to_host_file_result="$func_convert_core_msys_to_w32_result" + fi + func_convert_file_check "$1" "$func_to_host_file_result" +} +# end func_convert_file_msys_to_w32 + + +# func_convert_file_cygwin_to_w32 ARG +# Convert file name ARG from Cygwin to w32 format. Returns result in +# func_to_host_file_result. +func_convert_file_cygwin_to_w32 () +{ + $opt_debug + func_to_host_file_result="$1" + if test -n "$1"; then + # because $build is cygwin, we call "the" cygpath in $PATH; no need to use + # LT_CYGPATH in this case. + func_to_host_file_result=`cygpath -m "$1"` + fi + func_convert_file_check "$1" "$func_to_host_file_result" +} +# end func_convert_file_cygwin_to_w32 + + +# func_convert_file_nix_to_w32 ARG +# Convert file name ARG from *nix to w32 format. Requires a wine environment +# and a working winepath. Returns result in func_to_host_file_result. +func_convert_file_nix_to_w32 () +{ + $opt_debug + func_to_host_file_result="$1" + if test -n "$1"; then + func_convert_core_file_wine_to_w32 "$1" + func_to_host_file_result="$func_convert_core_file_wine_to_w32_result" + fi + func_convert_file_check "$1" "$func_to_host_file_result" +} +# end func_convert_file_nix_to_w32 + + +# func_convert_file_msys_to_cygwin ARG +# Convert file name ARG from MSYS to Cygwin format. Requires LT_CYGPATH set. +# Returns result in func_to_host_file_result. +func_convert_file_msys_to_cygwin () +{ + $opt_debug + func_to_host_file_result="$1" + if test -n "$1"; then + func_convert_core_msys_to_w32 "$1" + func_cygpath -u "$func_convert_core_msys_to_w32_result" + func_to_host_file_result="$func_cygpath_result" + fi + func_convert_file_check "$1" "$func_to_host_file_result" +} +# end func_convert_file_msys_to_cygwin + + +# func_convert_file_nix_to_cygwin ARG +# Convert file name ARG from *nix to Cygwin format. Requires Cygwin installed +# in a wine environment, working winepath, and LT_CYGPATH set. Returns result +# in func_to_host_file_result. +func_convert_file_nix_to_cygwin () +{ + $opt_debug + func_to_host_file_result="$1" + if test -n "$1"; then + # convert from *nix to w32, then use cygpath to convert from w32 to cygwin. + func_convert_core_file_wine_to_w32 "$1" + func_cygpath -u "$func_convert_core_file_wine_to_w32_result" + func_to_host_file_result="$func_cygpath_result" + fi + func_convert_file_check "$1" "$func_to_host_file_result" +} +# end func_convert_file_nix_to_cygwin + + +############################################# +# $build to $host PATH CONVERSION FUNCTIONS # +############################################# +# invoked via `$to_host_path_cmd ARG' +# +# In each case, ARG is the path to be converted from $build to $host format. +# The result will be available in $func_to_host_path_result. +# +# Path separators are also converted from $build format to $host format. If +# ARG begins or ends with a path separator character, it is preserved (but +# converted to $host format) on output. +# +# All path conversion functions are named using the following convention: +# file name conversion function : func_convert_file_X_to_Y () +# path conversion function : func_convert_path_X_to_Y () +# where, for any given $build/$host combination the 'X_to_Y' value is the +# same. If conversion functions are added for new $build/$host combinations, +# the two new functions must follow this pattern, or func_init_to_host_path_cmd +# will break. + + +# func_init_to_host_path_cmd +# Ensures that function "pointer" variable $to_host_path_cmd is set to the +# appropriate value, based on the value of $to_host_file_cmd. +to_host_path_cmd= +func_init_to_host_path_cmd () +{ + $opt_debug + if test -z "$to_host_path_cmd"; then + func_stripname 'func_convert_file_' '' "$to_host_file_cmd" + to_host_path_cmd="func_convert_path_${func_stripname_result}" + fi +} + + +# func_to_host_path ARG +# Converts the path ARG from $build format to $host format. Return result +# in func_to_host_path_result. +func_to_host_path () +{ + $opt_debug + func_init_to_host_path_cmd + $to_host_path_cmd "$1" +} +# end func_to_host_path + + +# func_convert_path_noop ARG +# Copy ARG to func_to_host_path_result. +func_convert_path_noop () +{ + func_to_host_path_result="$1" +} +# end func_convert_path_noop + + +# func_convert_path_msys_to_w32 ARG +# Convert path ARG from (mingw) MSYS to (mingw) w32 format; automatic +# conversion to w32 is not available inside the cwrapper. Returns result in +# func_to_host_path_result. +func_convert_path_msys_to_w32 () +{ + $opt_debug + func_to_host_path_result="$1" + if test -n "$1"; then + # Remove leading and trailing path separator characters from ARG. MSYS + # behavior is inconsistent here; cygpath turns them into '.;' and ';.'; + # and winepath ignores them completely. + func_stripname : : "$1" + func_to_host_path_tmp1=$func_stripname_result + func_convert_core_msys_to_w32 "$func_to_host_path_tmp1" + func_to_host_path_result="$func_convert_core_msys_to_w32_result" + func_convert_path_check : ";" \ + "$func_to_host_path_tmp1" "$func_to_host_path_result" + func_convert_path_front_back_pathsep ":*" "*:" ";" "$1" + fi +} +# end func_convert_path_msys_to_w32 + + +# func_convert_path_cygwin_to_w32 ARG +# Convert path ARG from Cygwin to w32 format. Returns result in +# func_to_host_file_result. +func_convert_path_cygwin_to_w32 () +{ + $opt_debug + func_to_host_path_result="$1" + if test -n "$1"; then + # See func_convert_path_msys_to_w32: + func_stripname : : "$1" + func_to_host_path_tmp1=$func_stripname_result + func_to_host_path_result=`cygpath -m -p "$func_to_host_path_tmp1"` + func_convert_path_check : ";" \ + "$func_to_host_path_tmp1" "$func_to_host_path_result" + func_convert_path_front_back_pathsep ":*" "*:" ";" "$1" + fi +} +# end func_convert_path_cygwin_to_w32 + + +# func_convert_path_nix_to_w32 ARG +# Convert path ARG from *nix to w32 format. Requires a wine environment and +# a working winepath. Returns result in func_to_host_file_result. +func_convert_path_nix_to_w32 () +{ + $opt_debug + func_to_host_path_result="$1" + if test -n "$1"; then + # See func_convert_path_msys_to_w32: + func_stripname : : "$1" + func_to_host_path_tmp1=$func_stripname_result + func_convert_core_path_wine_to_w32 "$func_to_host_path_tmp1" + func_to_host_path_result="$func_convert_core_path_wine_to_w32_result" + func_convert_path_check : ";" \ + "$func_to_host_path_tmp1" "$func_to_host_path_result" + func_convert_path_front_back_pathsep ":*" "*:" ";" "$1" + fi +} +# end func_convert_path_nix_to_w32 + + +# func_convert_path_msys_to_cygwin ARG +# Convert path ARG from MSYS to Cygwin format. Requires LT_CYGPATH set. +# Returns result in func_to_host_file_result. +func_convert_path_msys_to_cygwin () +{ + $opt_debug + func_to_host_path_result="$1" + if test -n "$1"; then + # See func_convert_path_msys_to_w32: + func_stripname : : "$1" + func_to_host_path_tmp1=$func_stripname_result + func_convert_core_msys_to_w32 "$func_to_host_path_tmp1" + func_cygpath -u -p "$func_convert_core_msys_to_w32_result" + func_to_host_path_result="$func_cygpath_result" + func_convert_path_check : : \ + "$func_to_host_path_tmp1" "$func_to_host_path_result" + func_convert_path_front_back_pathsep ":*" "*:" : "$1" + fi +} +# end func_convert_path_msys_to_cygwin + + +# func_convert_path_nix_to_cygwin ARG +# Convert path ARG from *nix to Cygwin format. Requires Cygwin installed in a +# a wine environment, working winepath, and LT_CYGPATH set. Returns result in +# func_to_host_file_result. +func_convert_path_nix_to_cygwin () +{ + $opt_debug + func_to_host_path_result="$1" + if test -n "$1"; then + # Remove leading and trailing path separator characters from + # ARG. msys behavior is inconsistent here, cygpath turns them + # into '.;' and ';.', and winepath ignores them completely. + func_stripname : : "$1" + func_to_host_path_tmp1=$func_stripname_result + func_convert_core_path_wine_to_w32 "$func_to_host_path_tmp1" + func_cygpath -u -p "$func_convert_core_path_wine_to_w32_result" + func_to_host_path_result="$func_cygpath_result" + func_convert_path_check : : \ + "$func_to_host_path_tmp1" "$func_to_host_path_result" + func_convert_path_front_back_pathsep ":*" "*:" : "$1" + fi +} +# end func_convert_path_nix_to_cygwin + + # func_mode_compile arg... func_mode_compile () @@ -1138,10 +1987,10 @@ -pie | -fpie | -fPIE) - pie_flag="$pie_flag $arg" + func_append pie_flag " $arg" continue ;; -shared | -static | -prefer-pic | -prefer-non-pic) - later="$later $arg" + func_append later " $arg" continue ;; @@ -1164,6 +2013,5 @@ for arg in $args; do IFS="$save_ifs" - func_quote_for_eval "$arg" - lastarg="$lastarg $func_quote_for_eval_result" + func_append_quoted lastarg "$arg" done IFS="$save_ifs" @@ -1172,5 +2020,5 @@ # Add the arguments to base_compile. - base_compile="$base_compile $lastarg" + func_append base_compile " $lastarg" continue ;; @@ -1188,6 +2036,5 @@ # Aesthetically quote the previous argument. - func_quote_for_eval "$lastarg" - base_compile="$base_compile $func_quote_for_eval_result" + func_append_quoted base_compile "$lastarg" done # for arg @@ -1214,5 +2061,5 @@ *.ada | *.adb | *.ads | *.asm | \ *.c++ | *.cc | *.ii | *.class | *.cpp | *.cxx | \ - *.[fF][09]? | *.for | *.java | *.obj | *.sx) + *.[fF][09]? | *.for | *.java | *.go | *.obj | *.sx | *.cu | *.cup) func_xform "$libobj" libobj=$func_xform_result @@ -1289,5 +2136,5 @@ # not support -o with -c if test "$compiler_c_o" = no; then - output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext} + output_obj=`$ECHO "$srcfile" | $SED 's%^.*/%%; s%\.[^.]*$%%'`.${objext} lockfile="$output_obj.lock" else @@ -1320,15 +2167,14 @@ exit $EXIT_FAILURE fi - removelist="$removelist $output_obj" + func_append removelist " $output_obj" $ECHO "$srcfile" > "$lockfile" fi $opt_dry_run || $RM $removelist - removelist="$removelist $lockfile" + func_append removelist " $lockfile" trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15 - if test -n "$fix_srcfile_path"; then - eval srcfile=\"$fix_srcfile_path\" - fi + func_to_tool_file "$srcfile" func_convert_file_msys_to_w32 + srcfile=$func_to_tool_file_result func_quote_for_eval "$srcfile" qsrcfile=$func_quote_for_eval_result @@ -1350,5 +2196,5 @@ if test -z "$output_obj"; then # Place PIC objects in $objdir - command="$command -o $lobj" + func_append command " -o $lobj" fi @@ -1397,9 +2243,9 @@ fi if test "$compiler_c_o" = yes; then - command="$command -o $obj" + func_append command " -o $obj" fi # Suppress compiler output if we already did a PIC compilation. - command="$command$suppress_output" + func_append command "$suppress_output" func_show_eval_locale "$command" \ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' @@ -1446,5 +2292,5 @@ $opt_help || { -test "$mode" = compile && func_mode_compile ${1+"$@"} + test "$opt_mode" = compile && func_mode_compile ${1+"$@"} } @@ -1452,5 +2298,5 @@ { # We need to display help for each of the modes. - case $mode in + case $opt_mode in "") # Generic help is extracted from the usage comments @@ -1483,8 +2329,9 @@ -o OUTPUT-FILE set the output file name to OUTPUT-FILE -no-suppress do not suppress compiler output for multiple passes - -prefer-pic try to building PIC objects only - -prefer-non-pic try to building non-PIC objects only + -prefer-pic try to build PIC objects only + -prefer-non-pic try to build non-PIC objects only -shared do not build a \`.o' file suitable for static linking -static only build a \`.o' file suitable for static linking + -Wc,FLAG pass FLAG directly to the compiler COMPILE-COMMAND is a command to be used in creating a \`standard' object file @@ -1539,5 +2386,5 @@ The following components of INSTALL-COMMAND are treated specially: - -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation + -inst-prefix-dir PREFIX-DIR Use PREFIX-DIR as a staging area for installation The rest of the components are interpreted as arguments to that command (only @@ -1559,4 +2406,6 @@ -all-static do not do any dynamic linking at all -avoid-version do not add a version suffix if possible + -bindir BINDIR specify path to binaries directory (for systems where + libraries must be found in the PATH setting at runtime) -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols @@ -1587,4 +2436,9 @@ specify library version info [each variable defaults to 0] -weak LIBNAME declare that the target provides the LIBNAME interface + -Wc,FLAG + -Xcompiler FLAG pass linker-specific FLAG directly to the compiler + -Wl,FLAG + -Xlinker FLAG pass linker-specific FLAG directly to the linker + -XCClinker FLAG pass link-specific FLAG to the compiler driver (CC) All other options (arguments beginning with \`-') are ignored. @@ -1620,16 +2474,42 @@ *) - func_fatal_help "invalid operation mode \`$mode'" + func_fatal_help "invalid operation mode \`$opt_mode'" ;; esac - $ECHO + echo $ECHO "Try \`$progname --help' for more information about other modes." - - exit $? -} - - # Now that we've collected a possible --mode arg, show help if necessary - $opt_help && func_mode_help +} + +# Now that we've collected a possible --mode arg, show help if necessary +if $opt_help; then + if test "$opt_help" = :; then + func_mode_help + else + { + func_help noexit + for opt_mode in compile link execute install finish uninstall clean; do + func_mode_help + done + } | sed -n '1p; 2,$s/^Usage:/ or: /p' + { + func_help noexit + for opt_mode in compile link execute install finish uninstall clean; do + echo + func_mode_help + done + } | + sed '1d + /^When reporting/,/^Report/{ + H + d + } + $x + /information about other modes/d + /more detailed .*MODE/d + s/^Usage:.*--mode=\([^ ]*\) .*/Description of \1 mode:/' + fi + exit $? +fi @@ -1644,5 +2524,5 @@ # Handle -dlopen flags immediately. - for file in $execute_dlfiles; do + for file in $opt_dlopen; do test -f "$file" \ || func_fatal_help "\`$file' is not a file" @@ -1651,4 +2531,7 @@ case $file in *.la) + func_resolve_sysroot "$file" + file=$func_resolve_sysroot_result + # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ @@ -1672,5 +2555,5 @@ if test -f "$dir/$objdir/$dlname"; then - dir="$dir/$objdir" + func_append dir "/$objdir" else if test ! -f "$dir/$dlname"; then @@ -1713,5 +2596,5 @@ do case $file in - -*) ;; + -* | *.la | *.lo ) ;; *) # Do a test to see if this is really a libtool program. @@ -1729,6 +2612,5 @@ esac # Quote arguments (to preserve shell metacharacters). - func_quote_for_eval "$file" - args="$args $func_quote_for_eval_result" + func_append_quoted args "$file" done @@ -1755,5 +2637,5 @@ if test -n "$shlibpath_var"; then eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\"" - $ECHO "export $shlibpath_var" + echo "export $shlibpath_var" fi $ECHO "$cmd$args" @@ -1762,5 +2644,5 @@ } -test "$mode" = execute && func_mode_execute ${1+"$@"} +test "$opt_mode" = execute && func_mode_execute ${1+"$@"} @@ -1769,13 +2651,50 @@ { $opt_debug - libdirs="$nonopt" + libs= + libdirs= admincmds= + for opt in "$nonopt" ${1+"$@"} + do + if test -d "$opt"; then + func_append libdirs " $opt" + + elif test -f "$opt"; then + if func_lalib_unsafe_p "$opt"; then + func_append libs " $opt" + else + func_warning "\`$opt' is not a valid libtool archive" + fi + + else + func_fatal_error "invalid argument \`$opt'" + fi + done + + if test -n "$libs"; then + if test -n "$lt_sysroot"; then + sysroot_regex=`$ECHO "$lt_sysroot" | $SED "$sed_make_literal_regex"` + sysroot_cmd="s/\([ ']\)$sysroot_regex/\1/g;" + else + sysroot_cmd= + fi + + # Remove sysroot references + if $opt_dry_run; then + for lib in $libs; do + echo "removing references to $lt_sysroot and \`=' prefixes from $lib" + done + else + tmpdir=`func_mktempdir` + for lib in $libs; do + sed -e "${sysroot_cmd} s/\([ ']-[LR]\)=/\1/g; s/\([ ']\)=/\1/g" $lib \ + > $tmpdir/tmp-la + mv -f $tmpdir/tmp-la $lib + done + ${RM}r "$tmpdir" + fi + fi + if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then - for dir - do - libdirs="$libdirs $dir" - done - for libdir in $libdirs; do if test -n "$finish_cmds"; then @@ -1787,5 +2706,5 @@ # Do the single finish_eval. eval cmds=\"$finish_eval\" - $opt_dry_run || eval "$cmds" || admincmds="$admincmds + $opt_dry_run || eval "$cmds" || func_append admincmds " $cmds" fi @@ -1796,51 +2715,53 @@ $opt_silent && exit $EXIT_SUCCESS - $ECHO "X----------------------------------------------------------------------" | $Xsed - $ECHO "Libraries have been installed in:" - for libdir in $libdirs; do - $ECHO " $libdir" - done - $ECHO - $ECHO "If you ever happen to want to link against installed libraries" - $ECHO "in a given directory, LIBDIR, you must either use libtool, and" - $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'" - $ECHO "flag during linking and do at least one of the following:" - if test -n "$shlibpath_var"; then - $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable" - $ECHO " during execution" + if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then + echo "----------------------------------------------------------------------" + echo "Libraries have been installed in:" + for libdir in $libdirs; do + $ECHO " $libdir" + done + echo + echo "If you ever happen to want to link against installed libraries" + echo "in a given directory, LIBDIR, you must either use libtool, and" + echo "specify the full pathname of the library, or use the \`-LLIBDIR'" + echo "flag during linking and do at least one of the following:" + if test -n "$shlibpath_var"; then + echo " - add LIBDIR to the \`$shlibpath_var' environment variable" + echo " during execution" + fi + if test -n "$runpath_var"; then + echo " - add LIBDIR to the \`$runpath_var' environment variable" + echo " during linking" + fi + if test -n "$hardcode_libdir_flag_spec"; then + libdir=LIBDIR + eval flag=\"$hardcode_libdir_flag_spec\" + + $ECHO " - use the \`$flag' linker flag" + fi + if test -n "$admincmds"; then + $ECHO " - have your system administrator run these commands:$admincmds" + fi + if test -f /etc/ld.so.conf; then + echo " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'" + fi + echo + + echo "See any operating system documentation about shared libraries for" + case $host in + solaris2.[6789]|solaris2.1[0-9]) + echo "more information, such as the ld(1), crle(1) and ld.so(8) manual" + echo "pages." + ;; + *) + echo "more information, such as the ld(1) and ld.so(8) manual pages." + ;; + esac + echo "----------------------------------------------------------------------" fi - if test -n "$runpath_var"; then - $ECHO " - add LIBDIR to the \`$runpath_var' environment variable" - $ECHO " during linking" - fi - if test -n "$hardcode_libdir_flag_spec"; then - libdir=LIBDIR - eval flag=\"$hardcode_libdir_flag_spec\" - - $ECHO " - use the \`$flag' linker flag" - fi - if test -n "$admincmds"; then - $ECHO " - have your system administrator run these commands:$admincmds" - fi - if test -f /etc/ld.so.conf; then - $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'" - fi - $ECHO - - $ECHO "See any operating system documentation about shared libraries for" - case $host in - solaris2.[6789]|solaris2.1[0-9]) - $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual" - $ECHO "pages." - ;; - *) - $ECHO "more information, such as the ld(1) and ld.so(8) manual pages." - ;; - esac - $ECHO "X----------------------------------------------------------------------" | $Xsed exit $EXIT_SUCCESS } -test "$mode" = finish && func_mode_finish ${1+"$@"} +test "$opt_mode" = finish && func_mode_finish ${1+"$@"} @@ -1853,5 +2774,5 @@ if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh || # Allow the use of GNU shtool's install command. - $ECHO "X$nonopt" | $GREP shtool >/dev/null; then + case $nonopt in *shtool*) :;; *) false;; esac; then # Aesthetically quote it. func_quote_for_eval "$nonopt" @@ -1867,5 +2788,10 @@ # Aesthetically quote it. func_quote_for_eval "$arg" - install_prog="$install_prog$func_quote_for_eval_result" + func_append install_prog "$func_quote_for_eval_result" + install_shared_prog=$install_prog + case " $install_prog " in + *[\\\ /]cp\ *) install_cp=: ;; + *) install_cp=false ;; + esac # We need to accept at least all the BSD install flags. @@ -1877,8 +2803,10 @@ isdir=no stripme= + no_mode=: for arg do + arg2= if test -n "$dest"; then - files="$files $dest" + func_append files " $dest" dest=$arg continue @@ -1888,8 +2816,7 @@ -d) isdir=yes ;; -f) - case " $install_prog " in - *[\\\ /]cp\ *) ;; - *) prev=$arg ;; - esac + if $install_cp; then :; else + prev=$arg + fi ;; -g | -m | -o) @@ -1905,4 +2832,8 @@ # If the previous option needed an argument, then skip it. if test -n "$prev"; then + if test "x$prev" = x-m && test -n "$install_override_mode"; then + arg2=$install_override_mode + no_mode=false + fi prev= else @@ -1915,5 +2846,9 @@ # Aesthetically quote the argument. func_quote_for_eval "$arg" - install_prog="$install_prog $func_quote_for_eval_result" + func_append install_prog " $func_quote_for_eval_result" + if test -n "$arg2"; then + func_quote_for_eval "$arg2" + fi + func_append install_shared_prog " $func_quote_for_eval_result" done @@ -1923,4 +2858,11 @@ test -n "$prev" && \ func_fatal_help "the \`$prev' option requires an argument" + + if test -n "$install_override_mode" && $no_mode; then + if $install_cp; then :; else + func_quote_for_eval "$install_override_mode" + func_append install_shared_prog " -m $func_quote_for_eval_result" + fi + fi if test -z "$files"; then @@ -1978,8 +2920,11 @@ *.$libext) # Do the static libraries later. - staticlibs="$staticlibs $file" + func_append staticlibs " $file" ;; *.la) + func_resolve_sysroot "$file" + file=$func_resolve_sysroot_result + # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ @@ -1995,5 +2940,5 @@ case "$current_libdirs " in *" $libdir "*) ;; - *) current_libdirs="$current_libdirs $libdir" ;; + *) func_append current_libdirs " $libdir" ;; esac else @@ -2001,5 +2946,5 @@ case "$future_libdirs " in *" $libdir "*) ;; - *) future_libdirs="$future_libdirs $libdir" ;; + *) func_append future_libdirs " $libdir" ;; esac fi @@ -2007,9 +2952,9 @@ func_dirname "$file" "/" "" dir="$func_dirname_result" - dir="$dir$objdir" + func_append dir "$objdir" if test -n "$relink_command"; then # Determine the prefix the user has applied to our future dir. - inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"` + inst_prefix_dir=`$ECHO "$destdir" | $SED -e "s%$libdir\$%%"` # Don't allow the user to place us outside of our expected @@ -2024,7 +2969,7 @@ if test -n "$inst_prefix_dir"; then # Stick the inst_prefix_dir data into the link command. - relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"` + relink_command=`$ECHO "$relink_command" | $SED "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"` else - relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"` + relink_command=`$ECHO "$relink_command" | $SED "s%@inst_prefix_dir@%%"` fi @@ -2044,5 +2989,5 @@ # Install the shared library and build the symlinks. - func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \ + func_show_eval "$install_shared_prog $dir/$srcname $destdir/$realname" \ 'exit $?' tstripme="$stripme" @@ -2084,5 +3029,5 @@ # Maybe install the static library, too. - test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library" + test -n "$old_library" && func_append staticlibs " $dir/$old_library" ;; @@ -2184,5 +3129,5 @@ func_source "$lib" fi - libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test + libfile="$libdir/"`$ECHO "$lib" | $SED 's%^.*/%%g'` ### testsuite: skip nested quoting test if test -n "$libdir" && test ! -f "$libfile"; then func_warning "\`$lib' has not been installed in \`$libdir'" @@ -2203,5 +3148,5 @@ outputname="$tmpdir/$file" # Replace the output file specification. - relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'` + relink_command=`$ECHO "$relink_command" | $SED 's%@OUTPUT@%'"$outputname"'%g'` $opt_silent || { @@ -2222,5 +3167,5 @@ else # Install the binary that we compiled earlier. - file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"` + file=`$ECHO "$file$stripped_ext" | $SED "s%\([^/]*\)$%$objdir/\1%"` fi fi @@ -2258,9 +3203,11 @@ # Set up the ranlib parameters. oldlib="$destdir/$name" + func_to_tool_file "$oldlib" func_convert_file_msys_to_w32 + tool_oldlib=$func_to_tool_file_result func_show_eval "$install_prog \$file \$oldlib" 'exit $?' if test -n "$stripme" && test -n "$old_striplib"; then - func_show_eval "$old_striplib $oldlib" 'exit $?' + func_show_eval "$old_striplib $tool_oldlib" 'exit $?' fi @@ -2281,5 +3228,5 @@ } -test "$mode" = install && func_mode_install ${1+"$@"} +test "$opt_mode" = install && func_mode_install ${1+"$@"} @@ -2324,4 +3271,20 @@ #endif +#if defined(__GNUC__) && (((__GNUC__ == 4) && (__GNUC_MINOR__ >= 4)) || (__GNUC__ > 4)) +#pragma GCC diagnostic ignored \"-Wstrict-prototypes\" +#endif + +/* Keep this code in sync between libtool.m4, ltmain, lt_system.h, and tests. */ +#if defined(_WIN32) || defined(__CYGWIN__) || defined(_WIN32_WCE) +/* DATA imports from DLLs on WIN32 con't be const, because runtime + relocations are performed -- see ld's documentation on pseudo-relocs. */ +# define LT_DLSYM_CONST +#elif defined(__osf__) +/* This system does not cope well with relocations in const data. */ +# define LT_DLSYM_CONST +#else +# define LT_DLSYM_CONST const +#endif + /* External symbol declarations for the compiler. */\ " @@ -2333,8 +3296,9 @@ # Add our own program objects to the symbol list. - progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` + progfiles=`$ECHO "$objs$old_deplibs" | $SP2NL | $SED "$lo2o" | $NL2SP` for progfile in $progfiles; do - func_verbose "extracting global C symbols from \`$progfile'" - $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'" + func_to_tool_file "$progfile" func_convert_file_msys_to_w32 + func_verbose "extracting global C symbols from \`$func_to_tool_file_result'" + $opt_dry_run || eval "$NM $func_to_tool_file_result | $global_symbol_pipe >> '$nlist'" done @@ -2372,5 +3336,5 @@ eval '$MV "$nlist"T "$nlist"' case $host in - *cygwin | *mingw* | *cegcc* ) + *cygwin* | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$nlist" >> "$output_objdir/$outputname.def"' @@ -2385,8 +3349,50 @@ func_basename "$dlprefile" name="$func_basename_result" - $opt_dry_run || { - eval '$ECHO ": $name " >> "$nlist"' - eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'" - } + case $host in + *cygwin* | *mingw* | *cegcc* ) + # if an import library, we need to obtain dlname + if func_win32_import_lib_p "$dlprefile"; then + func_tr_sh "$dlprefile" + eval "curr_lafile=\$libfile_$func_tr_sh_result" + dlprefile_dlbasename="" + if test -n "$curr_lafile" && func_lalib_p "$curr_lafile"; then + # Use subshell, to avoid clobbering current variable values + dlprefile_dlname=`source "$curr_lafile" && echo "$dlname"` + if test -n "$dlprefile_dlname" ; then + func_basename "$dlprefile_dlname" + dlprefile_dlbasename="$func_basename_result" + else + # no lafile. user explicitly requested -dlpreopen . + $sharedlib_from_linklib_cmd "$dlprefile" + dlprefile_dlbasename=$sharedlib_from_linklib_result + fi + fi + $opt_dry_run || { + if test -n "$dlprefile_dlbasename" ; then + eval '$ECHO ": $dlprefile_dlbasename" >> "$nlist"' + else + func_warning "Could not compute DLL name from $name" + eval '$ECHO ": $name " >> "$nlist"' + fi + func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32 + eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe | + $SED -e '/I __imp/d' -e 's/I __nm_/D /;s/_nm__//' >> '$nlist'" + } + else # not an import lib + $opt_dry_run || { + eval '$ECHO ": $name " >> "$nlist"' + func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32 + eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe >> '$nlist'" + } + fi + ;; + *) + $opt_dry_run || { + eval '$ECHO ": $name " >> "$nlist"' + func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32 + eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe >> '$nlist'" + } + ;; + esac done @@ -2416,8 +3422,8 @@ eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"' else - $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms" + echo '/* NONE */' >> "$output_objdir/$my_dlsyms" fi - $ECHO >> "$output_objdir/$my_dlsyms" "\ + echo >> "$output_objdir/$my_dlsyms" "\ /* The mapping between symbol names and symbols. */ @@ -2426,24 +3432,7 @@ void *address; } lt_dlsymlist; -" - case $host in - *cygwin* | *mingw* | *cegcc* ) - $ECHO >> "$output_objdir/$my_dlsyms" "\ -/* DATA imports from DLLs on WIN32 con't be const, because - runtime relocations are performed -- see ld's documentation - on pseudo-relocs. */" - lt_dlsym_const= ;; - *osf5*) - echo >> "$output_objdir/$my_dlsyms" "\ -/* This system does not cope well with relocations in const data */" - lt_dlsym_const= ;; - *) - lt_dlsym_const=const ;; - esac - - $ECHO >> "$output_objdir/$my_dlsyms" "\ -extern $lt_dlsym_const lt_dlsymlist +extern LT_DLSYM_CONST lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[]; -$lt_dlsym_const lt_dlsymlist +LT_DLSYM_CONST lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[] = {\ @@ -2458,5 +3447,5 @@ ;; esac - $ECHO >> "$output_objdir/$my_dlsyms" "\ + echo >> "$output_objdir/$my_dlsyms" "\ {0, (void *) 0} }; @@ -2485,5 +3474,5 @@ # pic_flag when linking with -static. The problem exists in # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1. - *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) + *-*-freebsd2.*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;; *-*-hpux*) @@ -2501,5 +3490,5 @@ case $arg in -pie | -fpie | -fPIE) ;; - *) symtab_cflags="$symtab_cflags $arg" ;; + *) func_append symtab_cflags " $arg" ;; esac done @@ -2516,14 +3505,14 @@ *cygwin* | *mingw* | *cegcc* ) if test -f "$output_objdir/$my_outputname.def"; then - compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` - finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` + compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` + finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` else - compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` - finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` + compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$symfileobj%"` + finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$symfileobj%"` fi ;; *) - compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` - finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` + compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$symfileobj%"` + finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$symfileobj%"` ;; esac @@ -2539,6 +3528,6 @@ # Nullify the symbol file. - compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"` - finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"` + compile_command=`$ECHO "$compile_command" | $SED "s% @SYMFILE@%%"` + finalize_command=`$ECHO "$finalize_command" | $SED "s% @SYMFILE@%%"` fi } @@ -2550,4 +3539,5 @@ # Has to be a shell function in order to 'eat' the argument # that is supplied when $file_magic_command is called. +# Despite the name, also deal with 64 bit binaries. func_win32_libid () { @@ -2560,7 +3550,9 @@ ;; *ar\ archive*) # could be an import, or static + # Keep the egrep pattern in sync with the one in _LT_CHECK_MAGIC_METHOD. if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | - $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then - win32_nmres=`eval $NM -f posix -A $1 | + $EGREP 'file format (pei*-i386(.*architecture: i386)?|pe-arm-wince|pe-x86-64)' >/dev/null; then + func_to_tool_file "$1" func_convert_file_msys_to_w32 + win32_nmres=`eval $NM -f posix -A \"$func_to_tool_file_result\" | $SED -n -e ' 1,100{ @@ -2591,4 +3583,129 @@ } +# func_cygming_dll_for_implib ARG +# +# Platform-specific function to extract the +# name of the DLL associated with the specified +# import library ARG. +# Invoked by eval'ing the libtool variable +# $sharedlib_from_linklib_cmd +# Result is available in the variable +# $sharedlib_from_linklib_result +func_cygming_dll_for_implib () +{ + $opt_debug + sharedlib_from_linklib_result=`$DLLTOOL --identify-strict --identify "$1"` +} + +# func_cygming_dll_for_implib_fallback_core SECTION_NAME LIBNAMEs +# +# The is the core of a fallback implementation of a +# platform-specific function to extract the name of the +# DLL associated with the specified import library LIBNAME. +# +# SECTION_NAME is either .idata$6 or .idata$7, depending +# on the platform and compiler that created the implib. +# +# Echos the name of the DLL associated with the +# specified import library. +func_cygming_dll_for_implib_fallback_core () +{ + $opt_debug + match_literal=`$ECHO "$1" | $SED "$sed_make_literal_regex"` + $OBJDUMP -s --section "$1" "$2" 2>/dev/null | + $SED '/^Contents of section '"$match_literal"':/{ + # Place marker at beginning of archive member dllname section + s/.*/====MARK====/ + p + d + } + # These lines can sometimes be longer than 43 characters, but + # are always uninteresting + /:[ ]*file format pe[i]\{,1\}-/d + /^In archive [^:]*:/d + # Ensure marker is printed + /^====MARK====/p + # Remove all lines with less than 43 characters + /^.\{43\}/!d + # From remaining lines, remove first 43 characters + s/^.\{43\}//' | + $SED -n ' + # Join marker and all lines until next marker into a single line + /^====MARK====/ b para + H + $ b para + b + :para + x + s/\n//g + # Remove the marker + s/^====MARK====// + # Remove trailing dots and whitespace + s/[\. \t]*$// + # Print + /./p' | + # we now have a list, one entry per line, of the stringified + # contents of the appropriate section of all members of the + # archive which possess that section. Heuristic: eliminate + # all those which have a first or second character that is + # a '.' (that is, objdump's representation of an unprintable + # character.) This should work for all archives with less than + # 0x302f exports -- but will fail for DLLs whose name actually + # begins with a literal '.' or a single character followed by + # a '.'. + # + # Of those that remain, print the first one. + $SED -e '/^\./d;/^.\./d;q' +} + +# func_cygming_gnu_implib_p ARG +# This predicate returns with zero status (TRUE) if +# ARG is a GNU/binutils-style import library. Returns +# with nonzero status (FALSE) otherwise. +func_cygming_gnu_implib_p () +{ + $opt_debug + func_to_tool_file "$1" func_convert_file_msys_to_w32 + func_cygming_gnu_implib_tmp=`$NM "$func_to_tool_file_result" | eval "$global_symbol_pipe" | $EGREP ' (_head_[A-Za-z0-9_]+_[ad]l*|[A-Za-z0-9_]+_[ad]l*_iname)$'` + test -n "$func_cygming_gnu_implib_tmp" +} + +# func_cygming_ms_implib_p ARG +# This predicate returns with zero status (TRUE) if +# ARG is an MS-style import library. Returns +# with nonzero status (FALSE) otherwise. +func_cygming_ms_implib_p () +{ + $opt_debug + func_to_tool_file "$1" func_convert_file_msys_to_w32 + func_cygming_ms_implib_tmp=`$NM "$func_to_tool_file_result" | eval "$global_symbol_pipe" | $GREP '_NULL_IMPORT_DESCRIPTOR'` + test -n "$func_cygming_ms_implib_tmp" +} + +# func_cygming_dll_for_implib_fallback ARG +# Platform-specific function to extract the +# name of the DLL associated with the specified +# import library ARG. +# +# This fallback implementation is for use when $DLLTOOL +# does not support the --identify-strict option. +# Invoked by eval'ing the libtool variable +# $sharedlib_from_linklib_cmd +# Result is available in the variable +# $sharedlib_from_linklib_result +func_cygming_dll_for_implib_fallback () +{ + $opt_debug + if func_cygming_gnu_implib_p "$1" ; then + # binutils import library + sharedlib_from_linklib_result=`func_cygming_dll_for_implib_fallback_core '.idata$7' "$1"` + elif func_cygming_ms_implib_p "$1" ; then + # ms-generated import library + sharedlib_from_linklib_result=`func_cygming_dll_for_implib_fallback_core '.idata$6' "$1"` + else + # unknown + sharedlib_from_linklib_result="" + fi +} @@ -2599,5 +3716,16 @@ f_ex_an_ar_dir="$1"; shift f_ex_an_ar_oldlib="$1" - func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?' + if test "$lock_old_archive_extraction" = yes; then + lockfile=$f_ex_an_ar_oldlib.lock + until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do + func_echo "Waiting for $lockfile to be removed" + sleep 2 + done + fi + func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" \ + 'stat=$?; rm -f "$lockfile"; exit $stat' + if test "$lock_old_archive_extraction" = yes; then + $opt_dry_run || rm -f "$lockfile" + fi if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then : @@ -2670,5 +3798,5 @@ darwin_files= for darwin_file in $darwin_filelist; do - darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP` + darwin_files=`find unfat-$$ -name $darwin_file -print | sort | $NL2SP` $LIPO -create -output "$darwin_file" $darwin_files done # $darwin_filelist @@ -2685,244 +3813,9 @@ ;; esac - my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP` + my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | sort | $NL2SP` done func_extract_archives_result="$my_oldobjs" } - - - -# func_emit_wrapper_part1 [arg=no] -# -# Emit the first part of a libtool wrapper script on stdout. -# For more information, see the description associated with -# func_emit_wrapper(), below. -func_emit_wrapper_part1 () -{ - func_emit_wrapper_part1_arg1=no - if test -n "$1" ; then - func_emit_wrapper_part1_arg1=$1 - fi - - $ECHO "\ -#! $SHELL - -# $output - temporary wrapper script for $objdir/$outputname -# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION -# -# The $output program cannot be directly executed until all the libtool -# libraries that it depends on are installed. -# -# This wrapper script should never be moved out of the build directory. -# If it is, it will not operate correctly. - -# Sed substitution that helps us do robust quoting. It backslashifies -# metacharacters that are still active within double-quoted strings. -Xsed='${SED} -e 1s/^X//' -sed_quote_subst='$sed_quote_subst' - -# Be Bourne compatible -if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then - emulate sh - NULLCMD=: - # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which - # is contrary to our usage. Disable this feature. - alias -g '\${1+\"\$@\"}'='\"\$@\"' - setopt NO_GLOB_SUBST -else - case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac -fi -BIN_SH=xpg4; export BIN_SH # for Tru64 -DUALCASE=1; export DUALCASE # for MKS sh - -# The HP-UX ksh and POSIX shell print the target directory to stdout -# if CDPATH is set. -(unset CDPATH) >/dev/null 2>&1 && unset CDPATH - -relink_command=\"$relink_command\" - -# This environment variable determines our operation mode. -if test \"\$libtool_install_magic\" = \"$magic\"; then - # install mode needs the following variables: - generated_by_libtool_version='$macro_version' - notinst_deplibs='$notinst_deplibs' -else - # When we are sourced in execute mode, \$file and \$ECHO are already set. - if test \"\$libtool_execute_magic\" != \"$magic\"; then - ECHO=\"$qecho\" - file=\"\$0\" - # Make sure echo works. - if test \"X\$1\" = X--no-reexec; then - # Discard the --no-reexec flag, and continue. - shift - elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then - # Yippee, \$ECHO works! - : - else - # Restart under the correct shell, and then maybe \$ECHO will work. - exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"} - fi - fi\ -" - $ECHO "\ - - # Find the directory that this script lives in. - thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\` - test \"x\$thisdir\" = \"x\$file\" && thisdir=. - - # Follow symbolic links until we get to the real thisdir. - file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\` - while test -n \"\$file\"; do - destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\` - - # If there was a directory component, then change thisdir. - if test \"x\$destdir\" != \"x\$file\"; then - case \"\$destdir\" in - [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;; - *) thisdir=\"\$thisdir/\$destdir\" ;; - esac - fi - - file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\` - file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\` - done -" -} -# end: func_emit_wrapper_part1 - -# func_emit_wrapper_part2 [arg=no] -# -# Emit the second part of a libtool wrapper script on stdout. -# For more information, see the description associated with -# func_emit_wrapper(), below. -func_emit_wrapper_part2 () -{ - func_emit_wrapper_part2_arg1=no - if test -n "$1" ; then - func_emit_wrapper_part2_arg1=$1 - fi - - $ECHO "\ - - # Usually 'no', except on cygwin/mingw when embedded into - # the cwrapper. - WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1 - if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then - # special case for '.' - if test \"\$thisdir\" = \".\"; then - thisdir=\`pwd\` - fi - # remove .libs from thisdir - case \"\$thisdir\" in - *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;; - $objdir ) thisdir=. ;; - esac - fi - - # Try to get the absolute directory name. - absdir=\`cd \"\$thisdir\" && pwd\` - test -n \"\$absdir\" && thisdir=\"\$absdir\" -" - - if test "$fast_install" = yes; then - $ECHO "\ - program=lt-'$outputname'$exeext - progdir=\"\$thisdir/$objdir\" - - if test ! -f \"\$progdir/\$program\" || - { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\ - test \"X\$file\" != \"X\$progdir/\$program\"; }; then - - file=\"\$\$-\$program\" - - if test ! -d \"\$progdir\"; then - $MKDIR \"\$progdir\" - else - $RM \"\$progdir/\$file\" - fi" - - $ECHO "\ - - # relink executable if necessary - if test -n \"\$relink_command\"; then - if relink_command_output=\`eval \$relink_command 2>&1\`; then : - else - $ECHO \"\$relink_command_output\" >&2 - $RM \"\$progdir/\$file\" - exit 1 - fi - fi - - $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null || - { $RM \"\$progdir/\$program\"; - $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; } - $RM \"\$progdir/\$file\" - fi" - else - $ECHO "\ - program='$outputname' - progdir=\"\$thisdir/$objdir\" -" - fi - - $ECHO "\ - - if test -f \"\$progdir/\$program\"; then" - - # Export our shlibpath_var if we have one. - if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then - $ECHO "\ - # Add our own library path to $shlibpath_var - $shlibpath_var=\"$temp_rpath\$$shlibpath_var\" - - # Some systems cannot cope with colon-terminated $shlibpath_var - # The second colon is a workaround for a bug in BeOS R4 sed - $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\` - - export $shlibpath_var -" - fi - - # fixup the dll searchpath if we need to. - if test -n "$dllsearchpath"; then - $ECHO "\ - # Add the dll search path components to the executable PATH - PATH=$dllsearchpath:\$PATH -" - fi - - $ECHO "\ - if test \"\$libtool_execute_magic\" != \"$magic\"; then - # Run the actual program with our arguments. -" - case $host in - # Backslashes separate directories on plain windows - *-*-mingw | *-*-os2* | *-cegcc*) - $ECHO "\ - exec \"\$progdir\\\\\$program\" \${1+\"\$@\"} -" - ;; - - *) - $ECHO "\ - exec \"\$progdir/\$program\" \${1+\"\$@\"} -" - ;; - esac - $ECHO "\ - \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2 - exit 1 - fi - else - # The program doesn't exist. - \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2 - \$ECHO \"This script is just a wrapper for \$program.\" 1>&2 - $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2 - exit 1 - fi -fi\ -" -} -# end: func_emit_wrapper_part2 @@ -2943,186 +3836,299 @@ func_emit_wrapper () { - func_emit_wrapper_arg1=no - if test -n "$1" ; then - func_emit_wrapper_arg1=$1 - fi - - # split this up so that func_emit_cwrapperexe_src - # can call each part independently. - func_emit_wrapper_part1 "${func_emit_wrapper_arg1}" - func_emit_wrapper_part2 "${func_emit_wrapper_arg1}" -} - - -# func_to_host_path arg + func_emit_wrapper_arg1=${1-no} + + $ECHO "\ +#! $SHELL + +# $output - temporary wrapper script for $objdir/$outputname +# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # -# Convert paths to host format when used with build tools. -# Intended for use with "native" mingw (where libtool itself -# is running under the msys shell), or in the following cross- -# build environments: -# $build $host -# mingw (msys) mingw [e.g. native] -# cygwin mingw -# *nix + wine mingw -# where wine is equipped with the `winepath' executable. -# In the native mingw case, the (msys) shell automatically -# converts paths for any non-msys applications it launches, -# but that facility isn't available from inside the cwrapper. -# Similar accommodations are necessary for $host mingw and -# $build cygwin. Calling this function does no harm for other -# $host/$build combinations not listed above. +# The $output program cannot be directly executed until all the libtool +# libraries that it depends on are installed. # -# ARG is the path (on $build) that should be converted to -# the proper representation for $host. The result is stored -# in $func_to_host_path_result. -func_to_host_path () -{ - func_to_host_path_result="$1" - if test -n "$1" ; then - case $host in - *mingw* ) - lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' - case $build in - *mingw* ) # actually, msys - # awkward: cmd appends spaces to result - lt_sed_strip_trailing_spaces="s/[ ]*\$//" - func_to_host_path_tmp1=`( cmd //c echo "$1" |\ - $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` - func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ - $SED -e "$lt_sed_naive_backslashify"` - ;; - *cygwin* ) - func_to_host_path_tmp1=`cygpath -w "$1"` - func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ - $SED -e "$lt_sed_naive_backslashify"` - ;; - * ) - # Unfortunately, winepath does not exit with a non-zero - # error code, so we are forced to check the contents of - # stdout. On the other hand, if the command is not - # found, the shell will set an exit code of 127 and print - # *an error message* to stdout. So we must check for both - # error code of zero AND non-empty stdout, which explains - # the odd construction: - func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null` - if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then - func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ - $SED -e "$lt_sed_naive_backslashify"` - else - # Allow warning below. - func_to_host_path_result="" - fi - ;; - esac - if test -z "$func_to_host_path_result" ; then - func_error "Could not determine host path corresponding to" - func_error " '$1'" - func_error "Continuing, but uninstalled executables may not work." - # Fallback: - func_to_host_path_result="$1" - fi - ;; +# This wrapper script should never be moved out of the build directory. +# If it is, it will not operate correctly. + +# Sed substitution that helps us do robust quoting. It backslashifies +# metacharacters that are still active within double-quoted strings. +sed_quote_subst='$sed_quote_subst' + +# Be Bourne compatible +if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which + # is contrary to our usage. Disable this feature. + alias -g '\${1+\"\$@\"}'='\"\$@\"' + setopt NO_GLOB_SUBST +else + case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac +fi +BIN_SH=xpg4; export BIN_SH # for Tru64 +DUALCASE=1; export DUALCASE # for MKS sh + +# The HP-UX ksh and POSIX shell print the target directory to stdout +# if CDPATH is set. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + +relink_command=\"$relink_command\" + +# This environment variable determines our operation mode. +if test \"\$libtool_install_magic\" = \"$magic\"; then + # install mode needs the following variables: + generated_by_libtool_version='$macro_version' + notinst_deplibs='$notinst_deplibs' +else + # When we are sourced in execute mode, \$file and \$ECHO are already set. + if test \"\$libtool_execute_magic\" != \"$magic\"; then + file=\"\$0\"" + + qECHO=`$ECHO "$ECHO" | $SED "$sed_quote_subst"` + $ECHO "\ + +# A function that is used when there is no print builtin or printf. +func_fallback_echo () +{ + eval 'cat <<_LTECHO_EOF +\$1 +_LTECHO_EOF' +} + ECHO=\"$qECHO\" + fi + +# Very basic option parsing. These options are (a) specific to +# the libtool wrapper, (b) are identical between the wrapper +# /script/ and the wrapper /executable/ which is used only on +# windows platforms, and (c) all begin with the string "--lt-" +# (application programs are unlikely to have options which match +# this pattern). +# +# There are only two supported options: --lt-debug and +# --lt-dump-script. There is, deliberately, no --lt-help. +# +# The first argument to this parsing function should be the +# script's $0 value, followed by "$@". +lt_option_debug= +func_parse_lt_options () +{ + lt_script_arg0=\$0 + shift + for lt_opt + do + case \"\$lt_opt\" in + --lt-debug) lt_option_debug=1 ;; + --lt-dump-script) + lt_dump_D=\`\$ECHO \"X\$lt_script_arg0\" | $SED -e 's/^X//' -e 's%/[^/]*$%%'\` + test \"X\$lt_dump_D\" = \"X\$lt_script_arg0\" && lt_dump_D=. + lt_dump_F=\`\$ECHO \"X\$lt_script_arg0\" | $SED -e 's/^X//' -e 's%^.*/%%'\` + cat \"\$lt_dump_D/\$lt_dump_F\" + exit 0 + ;; + --lt-*) + \$ECHO \"Unrecognized --lt- option: '\$lt_opt'\" 1>&2 + exit 1 + ;; + esac + done + + # Print the debug banner immediately: + if test -n \"\$lt_option_debug\"; then + echo \"${outputname}:${output}:\${LINENO}: libtool wrapper (GNU $PACKAGE$TIMESTAMP) $VERSION\" 1>&2 + fi +} + +# Used when --lt-debug. Prints its arguments to stdout +# (redirection is the responsibility of the caller) +func_lt_dump_args () +{ + lt_dump_args_N=1; + for lt_arg + do + \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[\$lt_dump_args_N]: \$lt_arg\" + lt_dump_args_N=\`expr \$lt_dump_args_N + 1\` + done +} + +# Core function for launching the target application +func_exec_program_core () +{ +" + case $host in + # Backslashes separate directories on plain windows + *-*-mingw | *-*-os2* | *-cegcc*) + $ECHO "\ + if test -n \"\$lt_option_debug\"; then + \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[0]: \$progdir\\\\\$program\" 1>&2 + func_lt_dump_args \${1+\"\$@\"} 1>&2 + fi + exec \"\$progdir\\\\\$program\" \${1+\"\$@\"} +" + ;; + + *) + $ECHO "\ + if test -n \"\$lt_option_debug\"; then + \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[0]: \$progdir/\$program\" 1>&2 + func_lt_dump_args \${1+\"\$@\"} 1>&2 + fi + exec \"\$progdir/\$program\" \${1+\"\$@\"} +" + ;; + esac + $ECHO "\ + \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2 + exit 1 +} + +# A function to encapsulate launching the target application +# Strips options in the --lt-* namespace from \$@ and +# launches target application with the remaining arguments. +func_exec_program () +{ + case \" \$* \" in + *\\ --lt-*) + for lt_wr_arg + do + case \$lt_wr_arg in + --lt-*) ;; + *) set x \"\$@\" \"\$lt_wr_arg\"; shift;; + esac + shift + done ;; + esac + func_exec_program_core \${1+\"\$@\"} +} + + # Parse options + func_parse_lt_options \"\$0\" \${1+\"\$@\"} + + # Find the directory that this script lives in. + thisdir=\`\$ECHO \"\$file\" | $SED 's%/[^/]*$%%'\` + test \"x\$thisdir\" = \"x\$file\" && thisdir=. + + # Follow symbolic links until we get to the real thisdir. + file=\`ls -ld \"\$file\" | $SED -n 's/.*-> //p'\` + while test -n \"\$file\"; do + destdir=\`\$ECHO \"\$file\" | $SED 's%/[^/]*\$%%'\` + + # If there was a directory component, then change thisdir. + if test \"x\$destdir\" != \"x\$file\"; then + case \"\$destdir\" in + [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;; + *) thisdir=\"\$thisdir/\$destdir\" ;; + esac + fi + + file=\`\$ECHO \"\$file\" | $SED 's%^.*/%%'\` + file=\`ls -ld \"\$thisdir/\$file\" | $SED -n 's/.*-> //p'\` + done + + # Usually 'no', except on cygwin/mingw when embedded into + # the cwrapper. + WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_arg1 + if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then + # special case for '.' + if test \"\$thisdir\" = \".\"; then + thisdir=\`pwd\` + fi + # remove .libs from thisdir + case \"\$thisdir\" in + *[\\\\/]$objdir ) thisdir=\`\$ECHO \"\$thisdir\" | $SED 's%[\\\\/][^\\\\/]*$%%'\` ;; + $objdir ) thisdir=. ;; esac fi -} -# end: func_to_host_path - -# func_to_host_pathlist arg -# -# Convert pathlists to host format when used with build tools. -# See func_to_host_path(), above. This function supports the -# following $build/$host combinations (but does no harm for -# combinations not listed here): -# $build $host -# mingw (msys) mingw [e.g. native] -# cygwin mingw -# *nix + wine mingw -# -# Path separators are also converted from $build format to -# $host format. If ARG begins or ends with a path separator -# character, it is preserved (but converted to $host format) -# on output. -# -# ARG is a pathlist (on $build) that should be converted to -# the proper representation on $host. The result is stored -# in $func_to_host_pathlist_result. -func_to_host_pathlist () -{ - func_to_host_pathlist_result="$1" - if test -n "$1" ; then - case $host in - *mingw* ) - lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' - # Remove leading and trailing path separator characters from - # ARG. msys behavior is inconsistent here, cygpath turns them - # into '.;' and ';.', and winepath ignores them completely. - func_to_host_pathlist_tmp2="$1" - # Once set for this call, this variable should not be - # reassigned. It is used in tha fallback case. - func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\ - $SED -e 's|^:*||' -e 's|:*$||'` - case $build in - *mingw* ) # Actually, msys. - # Awkward: cmd appends spaces to result. - lt_sed_strip_trailing_spaces="s/[ ]*\$//" - func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\ - $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` - func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ - $SED -e "$lt_sed_naive_backslashify"` - ;; - *cygwin* ) - func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"` - func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ - $SED -e "$lt_sed_naive_backslashify"` - ;; - * ) - # unfortunately, winepath doesn't convert pathlists - func_to_host_pathlist_result="" - func_to_host_pathlist_oldIFS=$IFS - IFS=: - for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do - IFS=$func_to_host_pathlist_oldIFS - if test -n "$func_to_host_pathlist_f" ; then - func_to_host_path "$func_to_host_pathlist_f" - if test -n "$func_to_host_path_result" ; then - if test -z "$func_to_host_pathlist_result" ; then - func_to_host_pathlist_result="$func_to_host_path_result" - else - func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result" - fi - fi - fi - IFS=: - done - IFS=$func_to_host_pathlist_oldIFS - ;; - esac - if test -z "$func_to_host_pathlist_result" ; then - func_error "Could not determine the host path(s) corresponding to" - func_error " '$1'" - func_error "Continuing, but uninstalled executables may not work." - # Fallback. This may break if $1 contains DOS-style drive - # specifications. The fix is not to complicate the expression - # below, but for the user to provide a working wine installation - # with winepath so that path translation in the cross-to-mingw - # case works properly. - lt_replace_pathsep_nix_to_dos="s|:|;|g" - func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\ - $SED -e "$lt_replace_pathsep_nix_to_dos"` - fi - # Now, add the leading and trailing path separators back - case "$1" in - :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result" - ;; - esac - case "$1" in - *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;" - ;; - esac - ;; - esac + + # Try to get the absolute directory name. + absdir=\`cd \"\$thisdir\" && pwd\` + test -n \"\$absdir\" && thisdir=\"\$absdir\" +" + + if test "$fast_install" = yes; then + $ECHO "\ + program=lt-'$outputname'$exeext + progdir=\"\$thisdir/$objdir\" + + if test ! -f \"\$progdir/\$program\" || + { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\ + test \"X\$file\" != \"X\$progdir/\$program\"; }; then + + file=\"\$\$-\$program\" + + if test ! -d \"\$progdir\"; then + $MKDIR \"\$progdir\" + else + $RM \"\$progdir/\$file\" + fi" + + $ECHO "\ + + # relink executable if necessary + if test -n \"\$relink_command\"; then + if relink_command_output=\`eval \$relink_command 2>&1\`; then : + else + $ECHO \"\$relink_command_output\" >&2 + $RM \"\$progdir/\$file\" + exit 1 + fi + fi + + $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null || + { $RM \"\$progdir/\$program\"; + $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; } + $RM \"\$progdir/\$file\" + fi" + else + $ECHO "\ + program='$outputname' + progdir=\"\$thisdir/$objdir\" +" + fi + + $ECHO "\ + + if test -f \"\$progdir/\$program\"; then" + + # fixup the dll searchpath if we need to. + # + # Fix the DLL searchpath if we need to. Do this before prepending + # to shlibpath, because on Windows, both are PATH and uninstalled + # libraries must come first. + if test -n "$dllsearchpath"; then + $ECHO "\ + # Add the dll search path components to the executable PATH + PATH=$dllsearchpath:\$PATH +" + fi + + # Export our shlibpath_var if we have one. + if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then + $ECHO "\ + # Add our own library path to $shlibpath_var + $shlibpath_var=\"$temp_rpath\$$shlibpath_var\" + + # Some systems cannot cope with colon-terminated $shlibpath_var + # The second colon is a workaround for a bug in BeOS R4 sed + $shlibpath_var=\`\$ECHO \"\$$shlibpath_var\" | $SED 's/::*\$//'\` + + export $shlibpath_var +" + fi + + $ECHO "\ + if test \"\$libtool_execute_magic\" != \"$magic\"; then + # Run the actual program with our arguments. + func_exec_program \${1+\"\$@\"} + fi + else + # The program doesn't exist. + \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2 + \$ECHO \"This script is just a wrapper for \$program.\" 1>&2 + \$ECHO \"See the $PACKAGE documentation for more information.\" 1>&2 + exit 1 fi -} -# end: func_to_host_pathlist +fi\ +" +} + # func_emit_cwrapperexe_src @@ -3142,11 +4148,10 @@ This wrapper executable should never be moved out of the build directory. If it is, it will not operate correctly. - - Currently, it simply execs the wrapper *script* "$SHELL $output", - but could eventually absorb all of the scripts functionality and - exec $objdir/$outputname directly. */ EOF cat <<"EOF" +#ifdef _MSC_VER +# define _CRT_SECURE_NO_DEPRECATE 1 +#endif #include #include @@ -3155,5 +4160,4 @@ # include # include -# define setmode _setmode #else # include @@ -3161,10 +4165,4 @@ # ifdef __CYGWIN__ # include -# define HAVE_SETENV -# ifdef __STRICT_ANSI__ -char *realpath (const char *, char *); -int putenv (char *); -int setenv (const char *, const char *, int); -# endif # endif #endif @@ -3178,4 +4176,42 @@ #include +/* declarations of non-ANSI functions */ +#if defined(__MINGW32__) +# ifdef __STRICT_ANSI__ +int _putenv (const char *); +# endif +#elif defined(__CYGWIN__) +# ifdef __STRICT_ANSI__ +char *realpath (const char *, char *); +int putenv (char *); +int setenv (const char *, const char *, int); +# endif +/* #elif defined (other platforms) ... */ +#endif + +/* portability defines, excluding path handling macros */ +#if defined(_MSC_VER) +# define setmode _setmode +# define stat _stat +# define chmod _chmod +# define getcwd _getcwd +# define putenv _putenv +# define S_IXUSR _S_IEXEC +# ifndef _INTPTR_T_DEFINED +# define _INTPTR_T_DEFINED +# define intptr_t int +# endif +#elif defined(__MINGW32__) +# define setmode _setmode +# define stat _stat +# define chmod _chmod +# define getcwd _getcwd +# define putenv _putenv +#elif defined(__CYGWIN__) +# define HAVE_SETENV +# define FOPEN_WB "wb" +/* #elif defined (other platforms) ... */ +#endif + #if defined(PATH_MAX) # define LT_PATHMAX PATH_MAX @@ -3193,12 +4229,5 @@ #endif -#ifdef _MSC_VER -# define S_IXUSR _S_IEXEC -# define stat _stat -# ifndef _INTPTR_T_DEFINED -# define intptr_t int -# endif -#endif - +/* path handling portability macros */ #ifndef DIR_SEPARATOR # define DIR_SEPARATOR '/' @@ -3231,8 +4260,4 @@ #endif /* PATH_SEPARATOR_2 */ -#ifdef __CYGWIN__ -# define FOPEN_WB "wb" -#endif - #ifndef FOPEN_WB # define FOPEN_WB "w" @@ -3247,20 +4272,11 @@ } while (0) -#undef LTWRAPPER_DEBUGPRINTF -#if defined DEBUGWRAPPER -# define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args -static void -ltwrapper_debugprintf (const char *fmt, ...) -{ - va_list args; - va_start (args, fmt); - (void) vfprintf (stderr, fmt, args); - va_end (args); -} +#if defined(LT_DEBUGWRAPPER) +static int lt_debug = 1; #else -# define LTWRAPPER_DEBUGPRINTF(args) +static int lt_debug = 0; #endif -const char *program_name = NULL; +const char *program_name = "libtool-wrapper"; /* in case xstrdup fails */ void *xmalloc (size_t num); @@ -3272,39 +4288,25 @@ int check_executable (const char *path); char *strendzap (char *str, const char *pat); -void lt_fatal (const char *message, ...); +void lt_debugprintf (const char *file, int line, const char *fmt, ...); +void lt_fatal (const char *file, int line, const char *message, ...); +static const char *nonnull (const char *s); +static const char *nonempty (const char *s); void lt_setenv (const char *name, const char *value); char *lt_extend_str (const char *orig_value, const char *add, int to_end); -void lt_opt_process_env_set (const char *arg); -void lt_opt_process_env_prepend (const char *arg); -void lt_opt_process_env_append (const char *arg); -int lt_split_name_value (const char *arg, char** name, char** value); void lt_update_exe_path (const char *name, const char *value); void lt_update_lib_path (const char *name, const char *value); - -static const char *script_text_part1 = +char **prepare_spawn (char **argv); +void lt_dump_script (FILE *f); EOF - func_emit_wrapper_part1 yes | - $SED -e 's/\([\\"]\)/\\\1/g' \ - -e 's/^/ "/' -e 's/$/\\n"/' - echo ";" cat <"))); + + lt_debugprintf (__FILE__, __LINE__, "(main) lt_argv_zero: %s\n", + nonnull (lt_argv_zero)); for (i = 0; i < newargc; i++) { - LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : ""))); + lt_debugprintf (__FILE__, __LINE__, "(main) newargz[%d]: %s\n", + i, nonnull (newargz[i])); } @@ -3561,9 +4524,12 @@ cat <<"EOF" /* execv doesn't actually work on mingw as expected on unix */ + newargz = prepare_spawn (newargz); rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz); if (rval == -1) { /* failed to start process */ - LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno)); + lt_debugprintf (__FILE__, __LINE__, + "(main) failed to launch target \"%s\": %s\n", + lt_argv_zero, nonnull (strerror (errno))); return 127; } @@ -3587,5 +4553,5 @@ void *p = (void *) malloc (num); if (!p) - lt_fatal ("Memory exhausted"); + lt_fatal (__FILE__, __LINE__, "memory exhausted"); return p; @@ -3621,6 +4587,6 @@ struct stat st; - LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n", - path ? (*path ? path : "EMPTY!") : "NULL!")); + lt_debugprintf (__FILE__, __LINE__, "(check_executable): %s\n", + nonempty (path)); if ((!path) || (!*path)) return 0; @@ -3639,6 +4605,6 @@ struct stat st; - LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n", - path ? (*path ? path : "EMPTY!") : "NULL!")); + lt_debugprintf (__FILE__, __LINE__, "(make_executable): %s\n", + nonempty (path)); if ((!path) || (!*path)) return 0; @@ -3666,6 +4632,6 @@ char *concat_name; - LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n", - wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!")); + lt_debugprintf (__FILE__, __LINE__, "(find_executable): %s\n", + nonempty (wrapper)); if ((wrapper == NULL) || (*wrapper == '\0')) @@ -3720,5 +4686,6 @@ /* empty path: current directory */ if (getcwd (tmp, LT_PATHMAX) == NULL) - lt_fatal ("getcwd failed"); + lt_fatal (__FILE__, __LINE__, "getcwd failed: %s", + nonnull (strerror (errno))); tmp_len = strlen (tmp); concat_name = @@ -3745,5 +4712,6 @@ /* Relative path | not found in path: prepend cwd */ if (getcwd (tmp, LT_PATHMAX) == NULL) - lt_fatal ("getcwd failed"); + lt_fatal (__FILE__, __LINE__, "getcwd failed: %s", + nonnull (strerror (errno))); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); @@ -3771,6 +4739,7 @@ while (strlen (tmp_pathspec) && !has_symlinks) { - LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n", - tmp_pathspec)); + lt_debugprintf (__FILE__, __LINE__, + "checking path component for symlinks: %s\n", + tmp_pathspec); if (lstat (tmp_pathspec, &s) == 0) { @@ -3794,6 +4763,7 @@ else { - char *errstr = strerror (errno); - lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr); + lt_fatal (__FILE__, __LINE__, + "error accessing file \"%s\": %s", + tmp_pathspec, nonnull (strerror (errno))); } } @@ -3808,5 +4778,6 @@ if (tmp_pathspec == 0) { - lt_fatal ("Could not follow symlinks for %s", pathspec); + lt_fatal (__FILE__, __LINE__, + "could not follow symlinks for %s", pathspec); } return xstrdup (tmp_pathspec); @@ -3834,9 +4805,23 @@ } +void +lt_debugprintf (const char *file, int line, const char *fmt, ...) +{ + va_list args; + if (lt_debug) + { + (void) fprintf (stderr, "%s:%s:%d: ", program_name, file, line); + va_start (args, fmt); + (void) vfprintf (stderr, fmt, args); + va_end (args); + } +} + static void -lt_error_core (int exit_status, const char *mode, +lt_error_core (int exit_status, const char *file, + int line, const char *mode, const char *message, va_list ap) { - fprintf (stderr, "%s: %s: ", program_name, mode); + fprintf (stderr, "%s:%s:%d: %s: ", program_name, file, line, mode); vfprintf (stderr, message, ap); fprintf (stderr, ".\n"); @@ -3847,10 +4832,22 @@ void -lt_fatal (const char *message, ...) +lt_fatal (const char *file, int line, const char *message, ...) { va_list ap; va_start (ap, message); - lt_error_core (EXIT_FAILURE, "FATAL", message, ap); + lt_error_core (EXIT_FAILURE, file, line, "FATAL", message, ap); va_end (ap); +} + +static const char * +nonnull (const char *s) +{ + return s ? s : "(null)"; +} + +static const char * +nonempty (const char *s) +{ + return (s && !*s) ? "(empty)" : nonnull (s); } @@ -3858,7 +4855,7 @@ lt_setenv (const char *name, const char *value) { - LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n", - (name ? name : ""), - (value ? value : ""))); + lt_debugprintf (__FILE__, __LINE__, + "(lt_setenv) setting '%s' to '%s'\n", + nonnull (name), nonnull (value)); { #ifdef HAVE_SETENV @@ -3905,93 +4902,10 @@ } -int -lt_split_name_value (const char *arg, char** name, char** value) -{ - const char *p; - int len; - if (!arg || !*arg) - return 1; - - p = strchr (arg, (int)'='); - - if (!p) - return 1; - - *value = xstrdup (++p); - - len = strlen (arg) - strlen (*value); - *name = XMALLOC (char, len); - strncpy (*name, arg, len-1); - (*name)[len - 1] = '\0'; - - return 0; -} - -void -lt_opt_process_env_set (const char *arg) -{ - char *name = NULL; - char *value = NULL; - - if (lt_split_name_value (arg, &name, &value) != 0) - { - XFREE (name); - XFREE (value); - lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg); - } - - lt_setenv (name, value); - XFREE (name); - XFREE (value); -} - -void -lt_opt_process_env_prepend (const char *arg) -{ - char *name = NULL; - char *value = NULL; - char *new_value = NULL; - - if (lt_split_name_value (arg, &name, &value) != 0) - { - XFREE (name); - XFREE (value); - lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg); - } - - new_value = lt_extend_str (getenv (name), value, 0); - lt_setenv (name, new_value); - XFREE (new_value); - XFREE (name); - XFREE (value); -} - -void -lt_opt_process_env_append (const char *arg) -{ - char *name = NULL; - char *value = NULL; - char *new_value = NULL; - - if (lt_split_name_value (arg, &name, &value) != 0) - { - XFREE (name); - XFREE (value); - lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg); - } - - new_value = lt_extend_str (getenv (name), value, 1); - lt_setenv (name, new_value); - XFREE (new_value); - XFREE (name); - XFREE (value); -} - void lt_update_exe_path (const char *name, const char *value) { - LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n", - (name ? name : ""), - (value ? value : ""))); + lt_debugprintf (__FILE__, __LINE__, + "(lt_update_exe_path) modifying '%s' by prepending '%s'\n", + nonnull (name), nonnull (value)); if (name && *name && value && *value) @@ -4012,7 +4926,7 @@ lt_update_lib_path (const char *name, const char *value) { - LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n", - (name ? name : ""), - (value ? value : ""))); + lt_debugprintf (__FILE__, __LINE__, + "(lt_update_lib_path) modifying '%s' by prepending '%s'\n", + nonnull (name), nonnull (value)); if (name && *name && value && *value) @@ -4024,8 +4938,155 @@ } - EOF + case $host_os in + mingw*) + cat <<"EOF" + +/* Prepares an argument vector before calling spawn(). + Note that spawn() does not by itself call the command interpreter + (getenv ("COMSPEC") != NULL ? getenv ("COMSPEC") : + ({ OSVERSIONINFO v; v.dwOSVersionInfoSize = sizeof(OSVERSIONINFO); + GetVersionEx(&v); + v.dwPlatformId == VER_PLATFORM_WIN32_NT; + }) ? "cmd.exe" : "command.com"). + Instead it simply concatenates the arguments, separated by ' ', and calls + CreateProcess(). We must quote the arguments since Win32 CreateProcess() + interprets characters like ' ', '\t', '\\', '"' (but not '<' and '>') in a + special way: + - Space and tab are interpreted as delimiters. They are not treated as + delimiters if they are surrounded by double quotes: "...". + - Unescaped double quotes are removed from the input. Their only effect is + that within double quotes, space and tab are treated like normal + characters. + - Backslashes not followed by double quotes are not special. + - But 2*n+1 backslashes followed by a double quote become + n backslashes followed by a double quote (n >= 0): + \" -> " + \\\" -> \" + \\\\\" -> \\" + */ +#define SHELL_SPECIAL_CHARS "\"\\ \001\002\003\004\005\006\007\010\011\012\013\014\015\016\017\020\021\022\023\024\025\026\027\030\031\032\033\034\035\036\037" +#define SHELL_SPACE_CHARS " \001\002\003\004\005\006\007\010\011\012\013\014\015\016\017\020\021\022\023\024\025\026\027\030\031\032\033\034\035\036\037" +char ** +prepare_spawn (char **argv) +{ + size_t argc; + char **new_argv; + size_t i; + + /* Count number of arguments. */ + for (argc = 0; argv[argc] != NULL; argc++) + ; + + /* Allocate new argument vector. */ + new_argv = XMALLOC (char *, argc + 1); + + /* Put quoted arguments into the new argument vector. */ + for (i = 0; i < argc; i++) + { + const char *string = argv[i]; + + if (string[0] == '\0') + new_argv[i] = xstrdup ("\"\""); + else if (strpbrk (string, SHELL_SPECIAL_CHARS) != NULL) + { + int quote_around = (strpbrk (string, SHELL_SPACE_CHARS) != NULL); + size_t length; + unsigned int backslashes; + const char *s; + char *quoted_string; + char *p; + + length = 0; + backslashes = 0; + if (quote_around) + length++; + for (s = string; *s != '\0'; s++) + { + char c = *s; + if (c == '"') + length += backslashes + 1; + length++; + if (c == '\\') + backslashes++; + else + backslashes = 0; + } + if (quote_around) + length += backslashes + 1; + + quoted_string = XMALLOC (char, length + 1); + + p = quoted_string; + backslashes = 0; + if (quote_around) + *p++ = '"'; + for (s = string; *s != '\0'; s++) + { + char c = *s; + if (c == '"') + { + unsigned int j; + for (j = backslashes + 1; j > 0; j--) + *p++ = '\\'; + } + *p++ = c; + if (c == '\\') + backslashes++; + else + backslashes = 0; + } + if (quote_around) + { + unsigned int j; + for (j = backslashes; j > 0; j--) + *p++ = '\\'; + *p++ = '"'; + } + *p = '\0'; + + new_argv[i] = quoted_string; + } + else + new_argv[i] = (char *) string; + } + new_argv[argc] = NULL; + + return new_argv; +} +EOF + ;; + esac + + cat <<"EOF" +void lt_dump_script (FILE* f) +{ +EOF + func_emit_wrapper yes | + $SED -n -e ' +s/^\(.\{79\}\)\(..*\)/\1\ +\2/ +h +s/\([\\"]\)/\\\1/g +s/$/\\n/ +s/\([^\n]*\).*/ fputs ("\1", f);/p +g +D' + cat <<"EOF" +} +EOF } # end: func_emit_cwrapperexe_src + +# func_win32_import_lib_p ARG +# True if ARG is an import lib, as indicated by $file_magic_cmd +func_win32_import_lib_p () +{ + $opt_debug + case `eval $file_magic_cmd \"\$1\" 2>/dev/null | $SED -e 10q` in + *import*) : ;; + *) false ;; + esac +} # func_mode_link arg... @@ -4073,4 +5134,5 @@ avoid_version=no + bindir= dlfiles= dlprefiles= @@ -4165,4 +5227,9 @@ case $prev in + bindir) + bindir="$arg" + prev= + continue + ;; dlfiles|dlprefiles) if test "$preload" = no; then @@ -4196,7 +5263,7 @@ *) if test "$prev" = dlfiles; then - dlfiles="$dlfiles $arg" + func_append dlfiles " $arg" else - dlprefiles="$dlprefiles $arg" + func_append dlprefiles " $arg" fi prev= @@ -4222,5 +5289,5 @@ case "$deplibs " in *" $qarg.ltframework "*) ;; - *) deplibs="$deplibs $qarg.ltframework" # this is fixed later + *) func_append deplibs " $qarg.ltframework" # this is fixed later ;; esac @@ -4241,5 +5308,5 @@ for fil in `cat "$save_arg"` do -# moreargs="$moreargs $fil" +# func_append moreargs " $fil" arg=$fil # A libtool-controlled object. @@ -4270,5 +5337,5 @@ if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then - dlfiles="$dlfiles $pic_object" + func_append dlfiles " $pic_object" prev= continue @@ -4282,5 +5349,5 @@ if test "$prev" = dlprefiles; then # Preload the old-style object. - dlprefiles="$dlprefiles $pic_object" + func_append dlprefiles " $pic_object" prev= fi @@ -4352,10 +5419,10 @@ case "$rpath " in *" $arg "*) ;; - *) rpath="$rpath $arg" ;; + *) func_append rpath " $arg" ;; esac else case "$xrpath " in *" $arg "*) ;; - *) xrpath="$xrpath $arg" ;; + *) func_append xrpath " $arg" ;; esac fi @@ -4369,11 +5436,11 @@ ;; weak) - weak_libs="$weak_libs $arg" + func_append weak_libs " $arg" prev= continue ;; xcclinker) - linker_flags="$linker_flags $qarg" - compiler_flags="$compiler_flags $qarg" + func_append linker_flags " $qarg" + func_append compiler_flags " $qarg" prev= func_append compile_command " $qarg" @@ -4382,5 +5449,5 @@ ;; xcompiler) - compiler_flags="$compiler_flags $qarg" + func_append compiler_flags " $qarg" prev= func_append compile_command " $qarg" @@ -4389,6 +5456,6 @@ ;; xlinker) - linker_flags="$linker_flags $qarg" - compiler_flags="$compiler_flags $wl$qarg" + func_append linker_flags " $qarg" + func_append compiler_flags " $wl$qarg" prev= func_append compile_command " $wl$qarg" @@ -4426,4 +5493,9 @@ ;; + -bindir) + prev=bindir + continue + ;; + -dlopen) prev=dlfiles @@ -4476,7 +5548,6 @@ -L*) - func_stripname '-L' '' "$arg" - dir=$func_stripname_result - if test -z "$dir"; then + func_stripname "-L" '' "$arg" + if test -z "$func_stripname_result"; then if test "$#" -gt 0; then func_fatal_error "require no space between \`-L' and \`$1'" @@ -4485,4 +5556,6 @@ fi fi + func_resolve_sysroot "$func_stripname_result" + dir=$func_resolve_sysroot_result # We need an absolute path. case $dir in @@ -4496,22 +5569,28 @@ esac case "$deplibs " in - *" -L$dir "*) ;; + *" -L$dir "* | *" $arg "*) + # Will only happen for absolute or sysroot arguments + ;; *) - deplibs="$deplibs -L$dir" - lib_search_path="$lib_search_path $dir" + # Preserve sysroot, but never include relative directories + case $dir in + [\\/]* | [A-Za-z]:[\\/]* | =*) func_append deplibs " $arg" ;; + *) func_append deplibs " -L$dir" ;; + esac + func_append lib_search_path " $dir" ;; esac case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) - testbindir=`$ECHO "X$dir" | $Xsed -e 's*/lib$*/bin*'` + testbindir=`$ECHO "$dir" | $SED 's*/lib$*/bin*'` case :$dllsearchpath: in *":$dir:"*) ;; ::) dllsearchpath=$dir;; - *) dllsearchpath="$dllsearchpath:$dir";; + *) func_append dllsearchpath ":$dir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; - *) dllsearchpath="$dllsearchpath:$testbindir";; + *) func_append dllsearchpath ":$testbindir";; esac ;; @@ -4523,5 +5602,5 @@ if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then case $host in - *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc*) + *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc* | *-*-haiku*) # These systems don't actually have a C or math library (as such) continue @@ -4537,5 +5616,5 @@ *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C and math libraries are in the System framework - deplibs="$deplibs System.ltframework" + func_append deplibs " System.ltframework" continue ;; @@ -4557,5 +5636,5 @@ esac fi - deplibs="$deplibs $arg" + func_append deplibs " $arg" continue ;; @@ -4569,6 +5648,6 @@ # classes, name mangling, and exception handling. # Darwin uses the -arch flag to determine output architecture. - -model|-arch|-isysroot) - compiler_flags="$compiler_flags $arg" + -model|-arch|-isysroot|--sysroot) + func_append compiler_flags " $arg" func_append compile_command " $arg" func_append finalize_command " $arg" @@ -4577,11 +5656,12 @@ ;; - -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) - compiler_flags="$compiler_flags $arg" + -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe \ + |-threads|-fopenmp|-openmp|-mp|-xopenmp|-omp|-qsmp=*) + func_append compiler_flags " $arg" func_append compile_command " $arg" func_append finalize_command " $arg" case "$new_inherited_linker_flags " in *" $arg "*) ;; - * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;; + * ) func_append new_inherited_linker_flags " $arg" ;; esac continue @@ -4650,4 +5730,8 @@ case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; + =*) + func_stripname '=' '' "$dir" + dir=$lt_sysroot$func_stripname_result + ;; *) func_fatal_error "only absolute run-paths are allowed" @@ -4656,5 +5740,5 @@ case "$xrpath " in *" $dir "*) ;; - *) xrpath="$xrpath $dir" ;; + *) func_append xrpath " $dir" ;; esac continue @@ -4709,6 +5793,6 @@ IFS="$save_ifs" func_quote_for_eval "$flag" - arg="$arg $wl$func_quote_for_eval_result" - compiler_flags="$compiler_flags $func_quote_for_eval_result" + func_append arg " $func_quote_for_eval_result" + func_append compiler_flags " $func_quote_for_eval_result" done IFS="$save_ifs" @@ -4725,7 +5809,7 @@ IFS="$save_ifs" func_quote_for_eval "$flag" - arg="$arg $wl$func_quote_for_eval_result" - compiler_flags="$compiler_flags $wl$func_quote_for_eval_result" - linker_flags="$linker_flags $func_quote_for_eval_result" + func_append arg " $wl$func_quote_for_eval_result" + func_append compiler_flags " $wl$func_quote_for_eval_result" + func_append linker_flags " $func_quote_for_eval_result" done IFS="$save_ifs" @@ -4755,21 +5839,25 @@ ;; - # -64, -mips[0-9] enable 64-bit mode on the SGI compiler - # -r[0-9][0-9]* specifies the processor on the SGI compiler - # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler - # +DA*, +DD* enable 64-bit mode on the HP compiler - # -q* pass through compiler args for the IBM compiler - # -m*, -t[45]*, -txscale* pass through architecture-specific - # compiler args for GCC - # -F/path gives path to uninstalled frameworks, gcc on darwin - # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC - # @file GCC response files + # Flags to be passed through unchanged, with rationale: + # -64, -mips[0-9] enable 64-bit mode for the SGI compiler + # -r[0-9][0-9]* specify processor for the SGI compiler + # -xarch=*, -xtarget=* enable 64-bit mode for the Sun compiler + # +DA*, +DD* enable 64-bit mode for the HP compiler + # -q* compiler args for the IBM compiler + # -m*, -t[45]*, -txscale* architecture-specific flags for GCC + # -F/path path to uninstalled frameworks, gcc on darwin + # -p, -pg, --coverage, -fprofile-* profiling flags for GCC + # @file GCC response files + # -tp=* Portland pgcc target processor selection + # --sysroot=* for sysroot support + # -O*, -flto*, -fwhopr*, -fuse-linker-plugin GCC link-time optimization -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \ - -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*) + -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*|-tp=*|--sysroot=*| \ + -O*|-flto*|-fwhopr*|-fuse-linker-plugin) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" func_append compile_command " $arg" func_append finalize_command " $arg" - compiler_flags="$compiler_flags $arg" + func_append compiler_flags " $arg" continue ;; @@ -4783,5 +5871,5 @@ *.$objext) # A standard object. - objs="$objs $arg" + func_append objs " $arg" ;; @@ -4814,5 +5902,5 @@ if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then - dlfiles="$dlfiles $pic_object" + func_append dlfiles " $pic_object" prev= continue @@ -4826,5 +5914,5 @@ if test "$prev" = dlprefiles; then # Preload the old-style object. - dlprefiles="$dlprefiles $pic_object" + func_append dlprefiles " $pic_object" prev= fi @@ -4871,6 +5959,6 @@ *.$libext) # An archive. - deplibs="$deplibs $arg" - old_deplibs="$old_deplibs $arg" + func_append deplibs " $arg" + func_append old_deplibs " $arg" continue ;; @@ -4879,14 +5967,15 @@ # A libtool-controlled library. + func_resolve_sysroot "$arg" if test "$prev" = dlfiles; then # This library was specified with -dlopen. - dlfiles="$dlfiles $arg" + func_append dlfiles " $func_resolve_sysroot_result" prev= elif test "$prev" = dlprefiles; then # The library was specified with -dlpreopen. - dlprefiles="$dlprefiles $arg" + func_append dlprefiles " $func_resolve_sysroot_result" prev= else - deplibs="$deplibs $arg" + func_append deplibs " $func_resolve_sysroot_result" fi continue @@ -4926,5 +6015,5 @@ if test -n "$shlibpath_var"; then # get the directories listed in $shlibpath_var - eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\` + eval shlib_search_path=\`\$ECHO \"\${$shlibpath_var}\" \| \$SED \'s/:/ /g\'\` else shlib_search_path= @@ -4935,4 +6024,6 @@ func_dirname "$output" "/" "" output_objdir="$func_dirname_result$objdir" + func_to_tool_file "$output_objdir/" + tool_output_objdir=$func_to_tool_file_result # Create the object directory. func_mkdir_p "$output_objdir" @@ -4955,10 +6046,10 @@ # that are linked more than once (e.g. -la -lb -la) for deplib in $deplibs; do - if $opt_duplicate_deps ; then + if $opt_preserve_dup_deps ; then case "$libs " in - *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; + *" $deplib "*) func_append specialdeplibs " $deplib" ;; esac fi - libs="$libs $deplib" + func_append libs " $deplib" done @@ -4973,7 +6064,7 @@ for pre_post_dep in $predeps $postdeps; do case "$pre_post_deps " in - *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;; + *" $pre_post_dep "*) func_append specialdeplibs " $pre_post_deps" ;; esac - pre_post_deps="$pre_post_deps $pre_post_dep" + func_append pre_post_deps " $pre_post_dep" done fi @@ -5042,6 +6133,7 @@ # Ignore non-libtool-libs dependency_libs= + func_resolve_sysroot "$lib" case $lib in - *.la) func_source "$lib" ;; + *.la) func_source "$func_resolve_sysroot_result" ;; esac @@ -5049,8 +6141,9 @@ # has declared as weak libs for deplib in $dependency_libs; do - deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"` + func_basename "$deplib" + deplib_base=$func_basename_result case " $weak_libs " in *" $deplib_base "*) ;; - *) deplibs="$deplibs $deplib" ;; + *) func_append deplibs " $deplib" ;; esac done @@ -5068,14 +6161,15 @@ found=no case $deplib in - -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) + -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe \ + |-threads|-fopenmp|-openmp|-mp|-xopenmp|-omp|-qsmp=*) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else - compiler_flags="$compiler_flags $deplib" + func_append compiler_flags " $deplib" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; - * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; + * ) func_append new_inherited_linker_flags " $deplib" ;; esac fi @@ -5162,5 +6256,5 @@ case "$new_inherited_linker_flags " in *" $deplib "*) ;; - * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; + * ) func_append new_inherited_linker_flags " $deplib" ;; esac fi @@ -5175,5 +6269,6 @@ newdependency_libs="$deplib $newdependency_libs" func_stripname '-L' '' "$deplib" - newlib_search_path="$newlib_search_path $func_stripname_result" + func_resolve_sysroot "$func_stripname_result" + func_append newlib_search_path " $func_resolve_sysroot_result" ;; prog) @@ -5189,5 +6284,6 @@ fi func_stripname '-L' '' "$deplib" - newlib_search_path="$newlib_search_path $func_stripname_result" + func_resolve_sysroot "$func_stripname_result" + func_append newlib_search_path " $func_resolve_sysroot_result" ;; *) @@ -5200,9 +6296,10 @@ if test "$pass" = link; then func_stripname '-R' '' "$deplib" - dir=$func_stripname_result + func_resolve_sysroot "$func_stripname_result" + dir=$func_resolve_sysroot_result # Make sure the xrpath contains only unique directories. case "$xrpath " in *" $dir "*) ;; - *) xrpath="$xrpath $dir" ;; + *) func_append xrpath " $dir" ;; esac fi @@ -5210,5 +6307,8 @@ continue ;; - *.la) lib="$deplib" ;; + *.la) + func_resolve_sysroot "$deplib" + lib=$func_resolve_sysroot_result + ;; *.$libext) if test "$pass" = conv; then @@ -5228,5 +6328,5 @@ set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` - if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \ + if eval "\$ECHO \"$deplib\"" 2>/dev/null | $SED 10q \ | $EGREP "$match_pattern_regex" > /dev/null; then valid_a_lib=yes @@ -5238,13 +6338,13 @@ esac if test "$valid_a_lib" != yes; then - $ECHO + echo $ECHO "*** Warning: Trying to link with static lib archive $deplib." - $ECHO "*** I have the capability to make that library automatically link in when" - $ECHO "*** you link to this library. But I can only do this if you have a" - $ECHO "*** shared version of the library, which you do not appear to have" - $ECHO "*** because the file extensions .$libext of this argument makes me believe" - $ECHO "*** that it is just a static archive that I should not use here." + echo "*** I have the capability to make that library automatically link in when" + echo "*** you link to this library. But I can only do this if you have a" + echo "*** shared version of the library, which you do not appear to have" + echo "*** because the file extensions .$libext of this argument makes me believe" + echo "*** that it is just a static archive that I should not use here." else - $ECHO + echo $ECHO "*** Warning: Linking the shared library $output against the" $ECHO "*** static library $deplib is not portable!" @@ -5273,9 +6373,9 @@ # If there is no dlopen support or we're linking statically, # we need to preload. - newdlprefiles="$newdlprefiles $deplib" + func_append newdlprefiles " $deplib" compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else - newdlfiles="$newdlfiles $deplib" + func_append newdlfiles " $deplib" fi fi @@ -5319,18 +6419,18 @@ # Convert "-framework foo" to "foo.ltframework" if test -n "$inherited_linker_flags"; then - tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'` + tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'` for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do case " $new_inherited_linker_flags " in *" $tmp_inherited_linker_flag "*) ;; - *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";; + *) func_append new_inherited_linker_flags " $tmp_inherited_linker_flag";; esac done fi - dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + dependency_libs=`$ECHO " $dependency_libs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan" || { test "$linkmode" != prog && test "$linkmode" != lib; }; then - test -n "$dlopen" && dlfiles="$dlfiles $dlopen" - test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen" + test -n "$dlopen" && func_append dlfiles " $dlopen" + test -n "$dlpreopen" && func_append dlprefiles " $dlpreopen" fi @@ -5343,6 +6443,6 @@ fi # It is a libtool convenience library, so add in its objects. - convenience="$convenience $ladir/$objdir/$old_library" - old_convenience="$old_convenience $ladir/$objdir/$old_library" + func_append convenience " $ladir/$objdir/$old_library" + func_append old_convenience " $ladir/$objdir/$old_library" elif test "$linkmode" != prog && test "$linkmode" != lib; then func_fatal_error "\`$lib' is not a convenience library" @@ -5351,10 +6451,10 @@ for deplib in $dependency_libs; do deplibs="$deplib $deplibs" - if $opt_duplicate_deps ; then + if $opt_preserve_dup_deps ; then case "$tmp_libs " in - *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; + *" $deplib "*) func_append specialdeplibs " $deplib" ;; esac fi - tmp_libs="$tmp_libs $deplib" + func_append tmp_libs " $deplib" done continue @@ -5364,7 +6464,13 @@ # Get the name of the library we link against. linklib= - for l in $old_library $library_names; do - linklib="$l" - done + if test -n "$old_library" && + { test "$prefer_static_libs" = yes || + test "$prefer_static_libs,$installed" = "built,no"; }; then + linklib=$old_library + else + for l in $old_library $library_names; do + linklib="$l" + done + fi if test -z "$linklib"; then func_fatal_error "cannot find name of link library for \`$lib'" @@ -5383,7 +6489,7 @@ # dependent libraries so libltdl's deplib preloader doesn't # bomb out in the load deplibs phase. - dlprefiles="$dlprefiles $lib $dependency_libs" + func_append dlprefiles " $lib $dependency_libs" else - newdlfiles="$newdlfiles $lib" + func_append newdlfiles " $lib" fi continue @@ -5407,5 +6513,5 @@ # Find the relevant object directory and library name. if test "X$installed" = Xyes; then - if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then + if test ! -f "$lt_sysroot$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then func_warning "library \`$lib' was moved." dir="$ladir" @@ -5413,6 +6519,6 @@ libdir="$abs_ladir" else - dir="$libdir" - absdir="$libdir" + dir="$lt_sysroot$libdir" + absdir="$lt_sysroot$libdir" fi test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes @@ -5422,10 +6528,10 @@ absdir="$abs_ladir" # Remove this search path later - notinst_path="$notinst_path $abs_ladir" + func_append notinst_path " $abs_ladir" else dir="$ladir/$objdir" absdir="$abs_ladir/$objdir" # Remove this search path later - notinst_path="$notinst_path $abs_ladir" + func_append notinst_path " $abs_ladir" fi fi # $installed = yes @@ -5438,18 +6544,44 @@ func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'" fi - # Prefer using a static library (so that no silly _DYNAMIC symbols - # are required to link). - if test -n "$old_library"; then - newdlprefiles="$newdlprefiles $dir/$old_library" - # Keep a list of preopened convenience libraries to check - # that they are being used correctly in the link pass. - test -z "$libdir" && \ - dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library" - # Otherwise, use the dlname, so that lt_dlopen finds it. - elif test -n "$dlname"; then - newdlprefiles="$newdlprefiles $dir/$dlname" - else - newdlprefiles="$newdlprefiles $dir/$linklib" - fi + case "$host" in + # special handling for platforms with PE-DLLs. + *cygwin* | *mingw* | *cegcc* ) + # Linker will automatically link against shared library if both + # static and shared are present. Therefore, ensure we extract + # symbols from the import library if a shared library is present + # (otherwise, the dlopen module name will be incorrect). We do + # this by putting the import library name into $newdlprefiles. + # We recover the dlopen module name by 'saving' the la file + # name in a special purpose variable, and (later) extracting the + # dlname from the la file. + if test -n "$dlname"; then + func_tr_sh "$dir/$linklib" + eval "libfile_$func_tr_sh_result=\$abs_ladir/\$laname" + func_append newdlprefiles " $dir/$linklib" + else + func_append newdlprefiles " $dir/$old_library" + # Keep a list of preopened convenience libraries to check + # that they are being used correctly in the link pass. + test -z "$libdir" && \ + func_append dlpreconveniencelibs " $dir/$old_library" + fi + ;; + * ) + # Prefer using a static library (so that no silly _DYNAMIC symbols + # are required to link). + if test -n "$old_library"; then + func_append newdlprefiles " $dir/$old_library" + # Keep a list of preopened convenience libraries to check + # that they are being used correctly in the link pass. + test -z "$libdir" && \ + func_append dlpreconveniencelibs " $dir/$old_library" + # Otherwise, use the dlname, so that lt_dlopen finds it. + elif test -n "$dlname"; then + func_append newdlprefiles " $dir/$dlname" + else + func_append newdlprefiles " $dir/$linklib" + fi + ;; + esac fi # $pass = dlpreopen @@ -5469,5 +6601,5 @@ if test "$linkmode" = prog && test "$pass" != link; then - newlib_search_path="$newlib_search_path $ladir" + func_append newlib_search_path " $ladir" deplibs="$lib $deplibs" @@ -5482,5 +6614,6 @@ case $deplib in -L*) func_stripname '-L' '' "$deplib" - newlib_search_path="$newlib_search_path $func_stripname_result" + func_resolve_sysroot "$func_stripname_result" + func_append newlib_search_path " $func_resolve_sysroot_result" ;; esac @@ -5493,10 +6626,10 @@ newdependency_libs="$deplib $newdependency_libs" fi - if $opt_duplicate_deps ; then + if $opt_preserve_dup_deps ; then case "$tmp_libs " in - *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; + *" $deplib "*) func_append specialdeplibs " $deplib" ;; esac fi - tmp_libs="$tmp_libs $deplib" + func_append tmp_libs " $deplib" done # for deplib continue @@ -5513,5 +6646,5 @@ case "$temp_rpath:" in *"$absdir:"*) ;; - *) temp_rpath="$temp_rpath$absdir:" ;; + *) func_append temp_rpath "$absdir:" ;; esac fi @@ -5525,5 +6658,5 @@ case "$compile_rpath " in *" $absdir "*) ;; - *) compile_rpath="$compile_rpath $absdir" + *) func_append compile_rpath " $absdir" ;; esac ;; @@ -5534,5 +6667,5 @@ case "$finalize_rpath " in *" $libdir "*) ;; - *) finalize_rpath="$finalize_rpath $libdir" + *) func_append finalize_rpath " $libdir" ;; esac ;; @@ -5559,10 +6692,10 @@ *cygwin* | *mingw* | *cegcc*) # No point in relinking DLLs because paths are not encoded - notinst_deplibs="$notinst_deplibs $lib" + func_append notinst_deplibs " $lib" need_relink=no ;; *) if test "$installed" = no; then - notinst_deplibs="$notinst_deplibs $lib" + func_append notinst_deplibs " $lib" need_relink=yes fi @@ -5581,5 +6714,5 @@ done if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then - $ECHO + echo if test "$linkmode" = prog; then $ECHO "*** Warning: Linking the executable $output against the loadable module" @@ -5599,5 +6732,5 @@ case "$compile_rpath " in *" $absdir "*) ;; - *) compile_rpath="$compile_rpath $absdir" + *) func_append compile_rpath " $absdir" ;; esac ;; @@ -5608,5 +6741,5 @@ case "$finalize_rpath " in *" $libdir "*) ;; - *) finalize_rpath="$finalize_rpath $libdir" + *) func_append finalize_rpath " $libdir" ;; esac ;; @@ -5662,5 +6795,5 @@ fi # test -n "$old_archive_from_expsyms_cmds" - if test "$linkmode" = prog || test "$mode" != relink; then + if test "$linkmode" = prog || test "$opt_mode" != relink; then add_shlibpath= add_dir= @@ -5684,7 +6817,7 @@ $ECHO "*** Warning: lib $linklib is a module, not a shared library" if test -z "$old_library" ; then - $ECHO - $ECHO "*** And there doesn't seem to be a static archive available" - $ECHO "*** The link will probably fail, sorry" + echo + echo "*** And there doesn't seem to be a static archive available" + echo "*** The link will probably fail, sorry" else add="$dir/$old_library" @@ -5713,10 +6846,10 @@ add="$dir/$linklib" elif test "$hardcode_minus_L" = yes; then - add_dir="-L$dir" + add_dir="-L$absdir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) - add_dir="$add_dir -L$inst_prefix_dir$libdir" + func_append add_dir " -L$inst_prefix_dir$libdir" ;; esac @@ -5740,5 +6873,5 @@ case :$compile_shlibpath: in *":$add_shlibpath:"*) ;; - *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;; + *) func_append compile_shlibpath "$add_shlibpath:" ;; esac fi @@ -5754,5 +6887,5 @@ case :$finalize_shlibpath: in *":$libdir:"*) ;; - *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; + *) func_append finalize_shlibpath "$libdir:" ;; esac fi @@ -5760,5 +6893,5 @@ fi - if test "$linkmode" = prog || test "$mode" = relink; then + if test "$linkmode" = prog || test "$opt_mode" = relink; then add_shlibpath= add_dir= @@ -5774,5 +6907,5 @@ case :$finalize_shlibpath: in *":$libdir:"*) ;; - *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; + *) func_append finalize_shlibpath "$libdir:" ;; esac add="-l$name" @@ -5791,5 +6924,5 @@ case $libdir in [\\/]*) - add_dir="$add_dir -L$inst_prefix_dir$libdir" + func_append add_dir " -L$inst_prefix_dir$libdir" ;; esac @@ -5826,19 +6959,19 @@ # Just print a warning and add the library to dependency_libs so # that the program can be linked against the static library. - $ECHO + echo $ECHO "*** Warning: This system can not link to static lib archive $lib." - $ECHO "*** I have the capability to make that library automatically link in when" - $ECHO "*** you link to this library. But I can only do this if you have a" - $ECHO "*** shared version of the library, which you do not appear to have." + echo "*** I have the capability to make that library automatically link in when" + echo "*** you link to this library. But I can only do this if you have a" + echo "*** shared version of the library, which you do not appear to have." if test "$module" = yes; then - $ECHO "*** But as you try to build a module library, libtool will still create " - $ECHO "*** a static module, that should work as long as the dlopening application" - $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime." + echo "*** But as you try to build a module library, libtool will still create " + echo "*** a static module, that should work as long as the dlopening application" + echo "*** is linked with the -dlopen flag to resolve symbols at runtime." if test -z "$global_symbol_pipe"; then - $ECHO - $ECHO "*** However, this would only work if libtool was able to extract symbol" - $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" - $ECHO "*** not find such a program. So, this module is probably useless." - $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." + echo + echo "*** However, this would only work if libtool was able to extract symbol" + echo "*** lists from a program, using \`nm' or equivalent, but libtool could" + echo "*** not find such a program. So, this module is probably useless." + echo "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then @@ -5868,7 +7001,7 @@ case " $xrpath " in *" $temp_xrpath "*) ;; - *) xrpath="$xrpath $temp_xrpath";; + *) func_append xrpath " $temp_xrpath";; esac;; - *) temp_deplibs="$temp_deplibs $libdir";; + *) func_append temp_deplibs " $libdir";; esac done @@ -5876,5 +7009,5 @@ fi - newlib_search_path="$newlib_search_path $absdir" + func_append newlib_search_path " $absdir" # Link against this library test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs" @@ -5883,10 +7016,16 @@ for deplib in $dependency_libs; do newdependency_libs="$deplib $newdependency_libs" - if $opt_duplicate_deps ; then + case $deplib in + -L*) func_stripname '-L' '' "$deplib" + func_resolve_sysroot "$func_stripname_result";; + *) func_resolve_sysroot "$deplib" ;; + esac + if $opt_preserve_dup_deps ; then case "$tmp_libs " in - *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; + *" $func_resolve_sysroot_result "*) + func_append specialdeplibs " $func_resolve_sysroot_result" ;; esac fi - tmp_libs="$tmp_libs $deplib" + func_append tmp_libs " $func_resolve_sysroot_result" done @@ -5894,9 +7033,12 @@ # Add the search paths of all dependency libraries for deplib in $dependency_libs; do + path= case $deplib in -L*) path="$deplib" ;; *.la) + func_resolve_sysroot "$deplib" + deplib=$func_resolve_sysroot_result func_dirname "$deplib" "" "." - dir="$func_dirname_result" + dir=$func_dirname_result # We need an absolute path. case $dir in @@ -5925,6 +7067,6 @@ darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` fi - compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}" - linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}" + func_append compiler_flags " ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}" + func_append linker_flags " -dylib_file ${darwin_install_name}:${depdepl}" path= fi @@ -5959,5 +7101,5 @@ finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs" else - compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + compiler_flags="$compiler_flags "`$ECHO " $new_inherited_linker_flags" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` fi fi @@ -5976,5 +7118,5 @@ case "$lib_search_path " in *" $dir "*) ;; - *) lib_search_path="$lib_search_path $dir" ;; + *) func_append lib_search_path " $dir" ;; esac done @@ -6034,8 +7176,8 @@ case " $tmp_libs " in *" $deplib "*) ;; - *) tmp_libs="$tmp_libs $deplib" ;; + *) func_append tmp_libs " $deplib" ;; esac ;; - *) tmp_libs="$tmp_libs $deplib" ;; + *) func_append tmp_libs " $deplib" ;; esac done @@ -6053,5 +7195,5 @@ esac if test -n "$i" ; then - tmp_libs="$tmp_libs $i" + func_append tmp_libs " $i" fi done @@ -6094,5 +7236,5 @@ build_libtool_libs=no oldlibs="$output" - objs="$objs$old_deplibs" + func_append objs "$old_deplibs" ;; @@ -6127,8 +7269,8 @@ func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs" else - $ECHO + echo $ECHO "*** Warning: Linking the shared library $output against the non-libtool" $ECHO "*** objects $objs is not portable!" - libobjs="$libobjs $objs" + func_append libobjs " $objs" fi fi @@ -6189,4 +7331,5 @@ # case $version_type in + # correct linux to gnu/linux during the next big refactor darwin|linux|osf|windows|none) func_arith $number_major + $number_minor @@ -6195,5 +7338,5 @@ revision="$number_revision" ;; - freebsd-aout|freebsd-elf|sunos) + freebsd-aout|freebsd-elf|qnx|sunos) current="$number_major" revision="$number_minor" @@ -6305,5 +7448,5 @@ ;; - linux) + linux) # correct to gnu/linux during the next big refactor func_arith $current - $age major=.$func_arith_result @@ -6328,5 +7471,5 @@ # Make executables depend on our current version. - verstring="$verstring:${current}.0" + func_append verstring ":${current}.0" ;; @@ -6396,8 +7539,8 @@ func_generate_dlsyms "$libname" "$libname" "yes" - libobjs="$libobjs $symfileobj" + func_append libobjs " $symfileobj" test "X$libobjs" = "X " && libobjs= - if test "$mode" != relink; then + if test "$opt_mode" != relink; then # Remove our outputs, but don't remove object files since they # may have been created when compiling PIC objects. @@ -6415,5 +7558,5 @@ fi fi - removelist="$removelist $p" + func_append removelist " $p" ;; *) ;; @@ -6426,15 +7569,15 @@ # Now set the variables for building old libraries. if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then - oldlibs="$oldlibs $output_objdir/$libname.$libext" + func_append oldlibs " $output_objdir/$libname.$libext" # Transform .lo files to .o files. - oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP` + oldobjs="$objs "`$ECHO "$libobjs" | $SP2NL | $SED "/\.${libext}$/d; $lo2o" | $NL2SP` fi # Eliminate all temporary directories. #for path in $notinst_path; do - # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"` - # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"` - # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"` + # lib_search_path=`$ECHO "$lib_search_path " | $SED "s% $path % %g"` + # deplibs=`$ECHO "$deplibs " | $SED "s% -L$path % %g"` + # dependency_libs=`$ECHO "$dependency_libs " | $SED "s% -L$path % %g"` #done @@ -6443,8 +7586,9 @@ temp_xrpath= for libdir in $xrpath; do - temp_xrpath="$temp_xrpath -R$libdir" + func_replace_sysroot "$libdir" + func_append temp_xrpath " -R$func_replace_sysroot_result" case "$finalize_rpath " in *" $libdir "*) ;; - *) finalize_rpath="$finalize_rpath $libdir" ;; + *) func_append finalize_rpath " $libdir" ;; esac done @@ -6460,5 +7604,5 @@ case " $dlprefiles $dlfiles " in *" $lib "*) ;; - *) dlfiles="$dlfiles $lib" ;; + *) func_append dlfiles " $lib" ;; esac done @@ -6470,5 +7614,5 @@ case "$dlprefiles " in *" $lib "*) ;; - *) dlprefiles="$dlprefiles $lib" ;; + *) func_append dlprefiles " $lib" ;; esac done @@ -6477,10 +7621,10 @@ if test -n "$rpath"; then case $host in - *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*) + *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc* | *-*-haiku*) # these systems don't actually have a c library (as such)! ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C library is in the System framework - deplibs="$deplibs System.ltframework" + func_append deplibs " System.ltframework" ;; *-*-netbsd*) @@ -6499,5 +7643,5 @@ # Add libc to deplibs on all other systems if necessary. if test "$build_libtool_need_lc" = "yes"; then - deplibs="$deplibs -lc" + func_append deplibs " -lc" fi ;; @@ -6548,5 +7692,5 @@ case " $predeps $postdeps " in *" $i "*) - newdeplibs="$newdeplibs $i" + func_append newdeplibs " $i" i="" ;; @@ -6559,19 +7703,19 @@ deplib_match=$1 if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then - newdeplibs="$newdeplibs $i" + func_append newdeplibs " $i" else droppeddeps=yes - $ECHO + echo $ECHO "*** Warning: dynamic linker does not accept needed library $i." - $ECHO "*** I have the capability to make that library automatically link in when" - $ECHO "*** you link to this library. But I can only do this if you have a" - $ECHO "*** shared version of the library, which I believe you do not have" - $ECHO "*** because a test_compile did reveal that the linker did not use it for" - $ECHO "*** its dynamic dependency list that programs get resolved with at runtime." + echo "*** I have the capability to make that library automatically link in when" + echo "*** you link to this library. But I can only do this if you have a" + echo "*** shared version of the library, which I believe you do not have" + echo "*** because a test_compile did reveal that the linker did not use it for" + echo "*** its dynamic dependency list that programs get resolved with at runtime." fi fi ;; *) - newdeplibs="$newdeplibs $i" + func_append newdeplibs " $i" ;; esac @@ -6591,5 +7735,5 @@ case " $predeps $postdeps " in *" $i "*) - newdeplibs="$newdeplibs $i" + func_append newdeplibs " $i" i="" ;; @@ -6602,27 +7746,27 @@ deplib_match=$1 if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then - newdeplibs="$newdeplibs $i" + func_append newdeplibs " $i" else droppeddeps=yes - $ECHO + echo $ECHO "*** Warning: dynamic linker does not accept needed library $i." - $ECHO "*** I have the capability to make that library automatically link in when" - $ECHO "*** you link to this library. But I can only do this if you have a" - $ECHO "*** shared version of the library, which you do not appear to have" - $ECHO "*** because a test_compile did reveal that the linker did not use this one" - $ECHO "*** as a dynamic dependency that programs can get resolved with at runtime." + echo "*** I have the capability to make that library automatically link in when" + echo "*** you link to this library. But I can only do this if you have a" + echo "*** shared version of the library, which you do not appear to have" + echo "*** because a test_compile did reveal that the linker did not use this one" + echo "*** as a dynamic dependency that programs can get resolved with at runtime." fi fi else droppeddeps=yes - $ECHO + echo $ECHO "*** Warning! Library $i is needed by this library but I was not able to" - $ECHO "*** make it link in! You will probably need to install it or some" - $ECHO "*** library that it depends on before this library will be fully" - $ECHO "*** functional. Installing it before continuing would be even better." + echo "*** make it link in! You will probably need to install it or some" + echo "*** library that it depends on before this library will be fully" + echo "*** functional. Installing it before continuing would be even better." fi ;; *) - newdeplibs="$newdeplibs $i" + func_append newdeplibs " $i" ;; esac @@ -6641,5 +7785,5 @@ case " $predeps $postdeps " in *" $a_deplib "*) - newdeplibs="$newdeplibs $a_deplib" + func_append newdeplibs " $a_deplib" a_deplib="" ;; @@ -6648,6 +7792,18 @@ if test -n "$a_deplib" ; then libname=`eval "\\$ECHO \"$libname_spec\""` + if test -n "$file_magic_glob"; then + libnameglob=`func_echo_all "$libname" | $SED -e $file_magic_glob` + else + libnameglob=$libname + fi + test "$want_nocaseglob" = yes && nocaseglob=`shopt -p nocaseglob` for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do - potential_libs=`ls $i/$libname[.-]* 2>/dev/null` + if test "$want_nocaseglob" = yes; then + shopt -s nocaseglob + potential_libs=`ls $i/$libnameglob[.-]* 2>/dev/null` + $nocaseglob + else + potential_libs=`ls $i/$libnameglob[.-]* 2>/dev/null` + fi for potent_lib in $potential_libs; do # Follow soft links. @@ -6666,5 +7822,5 @@ case $potliblink in [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";; - *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";; + *) potlib=`$ECHO "$potlib" | $SED 's,[^/]*$,,'`"$potliblink";; esac done @@ -6672,5 +7828,5 @@ $SED -e 10q | $EGREP "$file_magic_regex" > /dev/null; then - newdeplibs="$newdeplibs $a_deplib" + func_append newdeplibs " $a_deplib" a_deplib="" break 2 @@ -6681,10 +7837,10 @@ if test -n "$a_deplib" ; then droppeddeps=yes - $ECHO + echo $ECHO "*** Warning: linker path does not have real file for library $a_deplib." - $ECHO "*** I have the capability to make that library automatically link in when" - $ECHO "*** you link to this library. But I can only do this if you have a" - $ECHO "*** shared version of the library, which you do not appear to have" - $ECHO "*** because I did check the linker path looking for a file starting" + echo "*** I have the capability to make that library automatically link in when" + echo "*** you link to this library. But I can only do this if you have a" + echo "*** shared version of the library, which you do not appear to have" + echo "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for file magic test)" @@ -6697,5 +7853,5 @@ *) # Add a -L argument. - newdeplibs="$newdeplibs $a_deplib" + func_append newdeplibs " $a_deplib" ;; esac @@ -6713,5 +7869,5 @@ case " $predeps $postdeps " in *" $a_deplib "*) - newdeplibs="$newdeplibs $a_deplib" + func_append newdeplibs " $a_deplib" a_deplib="" ;; @@ -6724,7 +7880,7 @@ for potent_lib in $potential_libs; do potlib="$potent_lib" # see symlink-check above in file_magic test - if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \ + if eval "\$ECHO \"$potent_lib\"" 2>/dev/null | $SED 10q | \ $EGREP "$match_pattern_regex" > /dev/null; then - newdeplibs="$newdeplibs $a_deplib" + func_append newdeplibs " $a_deplib" a_deplib="" break 2 @@ -6735,10 +7891,10 @@ if test -n "$a_deplib" ; then droppeddeps=yes - $ECHO + echo $ECHO "*** Warning: linker path does not have real file for library $a_deplib." - $ECHO "*** I have the capability to make that library automatically link in when" - $ECHO "*** you link to this library. But I can only do this if you have a" - $ECHO "*** shared version of the library, which you do not appear to have" - $ECHO "*** because I did check the linker path looking for a file starting" + echo "*** I have the capability to make that library automatically link in when" + echo "*** you link to this library. But I can only do this if you have a" + echo "*** shared version of the library, which you do not appear to have" + echo "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)" @@ -6751,5 +7907,5 @@ *) # Add a -L argument. - newdeplibs="$newdeplibs $a_deplib" + func_append newdeplibs " $a_deplib" ;; esac @@ -6758,23 +7914,23 @@ none | unknown | *) newdeplibs="" - tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \ - -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'` + tmp_deplibs=`$ECHO " $deplibs" | $SED 's/ -lc$//; s/ -[LR][^ ]*//g'` if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then for i in $predeps $postdeps ; do # can't use Xsed below, because $i might contain '/' - tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"` + tmp_deplibs=`$ECHO " $tmp_deplibs" | $SED "s,$i,,"` done fi - if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' | - $GREP . >/dev/null; then - $ECHO + case $tmp_deplibs in + *[!\ \ ]*) + echo if test "X$deplibs_check_method" = "Xnone"; then - $ECHO "*** Warning: inter-library dependencies are not supported in this platform." + echo "*** Warning: inter-library dependencies are not supported in this platform." else - $ECHO "*** Warning: inter-library dependencies are not known to be supported." + echo "*** Warning: inter-library dependencies are not known to be supported." fi - $ECHO "*** All declared inter-library dependencies are being dropped." + echo "*** All declared inter-library dependencies are being dropped." droppeddeps=yes - fi + ;; + esac ;; esac @@ -6788,5 +7944,5 @@ *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library with the System framework - newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'` + newdeplibs=`$ECHO " $newdeplibs" | $SED 's/ -lc / System.ltframework /'` ;; esac @@ -6794,15 +7950,15 @@ if test "$droppeddeps" = yes; then if test "$module" = yes; then - $ECHO - $ECHO "*** Warning: libtool could not satisfy all declared inter-library" + echo + echo "*** Warning: libtool could not satisfy all declared inter-library" $ECHO "*** dependencies of module $libname. Therefore, libtool will create" - $ECHO "*** a static module, that should work as long as the dlopening" - $ECHO "*** application is linked with the -dlopen flag." + echo "*** a static module, that should work as long as the dlopening" + echo "*** application is linked with the -dlopen flag." if test -z "$global_symbol_pipe"; then - $ECHO - $ECHO "*** However, this would only work if libtool was able to extract symbol" - $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" - $ECHO "*** not find such a program. So, this module is probably useless." - $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." + echo + echo "*** However, this would only work if libtool was able to extract symbol" + echo "*** lists from a program, using \`nm' or equivalent, but libtool could" + echo "*** not find such a program. So, this module is probably useless." + echo "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then @@ -6814,14 +7970,14 @@ fi else - $ECHO "*** The inter-library dependencies that have been dropped here will be" - $ECHO "*** automatically added whenever a program is linked with this library" - $ECHO "*** or is declared to -dlopen it." + echo "*** The inter-library dependencies that have been dropped here will be" + echo "*** automatically added whenever a program is linked with this library" + echo "*** or is declared to -dlopen it." if test "$allow_undefined" = no; then - $ECHO - $ECHO "*** Since this library must not contain undefined symbols," - $ECHO "*** because either the platform does not support them or" - $ECHO "*** it was explicitly requested with -no-undefined," - $ECHO "*** libtool will only create a static version of it." + echo + echo "*** Since this library must not contain undefined symbols," + echo "*** because either the platform does not support them or" + echo "*** it was explicitly requested with -no-undefined," + echo "*** libtool will only create a static version of it." if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" @@ -6840,7 +7996,7 @@ case $host in *-*-darwin*) - newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` - new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` - deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + newdeplibs=`$ECHO " $newdeplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` + new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` + deplibs=`$ECHO " $deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac @@ -6855,5 +8011,5 @@ case " $deplibs " in *" -L$path/$objdir "*) - new_libs="$new_libs -L$path/$objdir" ;; + func_append new_libs " -L$path/$objdir" ;; esac ;; @@ -6865,8 +8021,8 @@ case " $new_libs " in *" $deplib "*) ;; - *) new_libs="$new_libs $deplib" ;; + *) func_append new_libs " $deplib" ;; esac ;; - *) new_libs="$new_libs $deplib" ;; + *) func_append new_libs " $deplib" ;; esac done @@ -6880,4 +8036,9 @@ # Test again, we may have decided not to build it any more if test "$build_libtool_libs" = yes; then + # Remove ${wl} instances when linking with ld. + # FIXME: should test the right _cmds variable. + case $archive_cmds in + *\$LD\ *) wl= ;; + esac if test "$hardcode_into_libs" = yes; then # Hardcode the library paths @@ -6885,8 +8046,10 @@ dep_rpath= rpath="$finalize_rpath" - test "$mode" != relink && rpath="$compile_rpath$rpath" + test "$opt_mode" != relink && rpath="$compile_rpath$rpath" for libdir in $rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then + func_replace_sysroot "$libdir" + libdir=$func_replace_sysroot_result if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" @@ -6897,5 +8060,5 @@ ;; *) - hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" + func_append hardcode_libdirs "$hardcode_libdir_separator$libdir" ;; esac @@ -6903,10 +8066,10 @@ else eval flag=\"$hardcode_libdir_flag_spec\" - dep_rpath="$dep_rpath $flag" + func_append dep_rpath " $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; - *) perm_rpath="$perm_rpath $libdir" ;; + *) func_append perm_rpath " $libdir" ;; esac fi @@ -6916,9 +8079,5 @@ test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" - if test -n "$hardcode_libdir_flag_spec_ld"; then - eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\" - else - eval dep_rpath=\"$hardcode_libdir_flag_spec\" - fi + eval "dep_rpath=\"$hardcode_libdir_flag_spec\"" fi if test -n "$runpath_var" && test -n "$perm_rpath"; then @@ -6926,5 +8085,5 @@ rpath= for dir in $perm_rpath; do - rpath="$rpath$dir:" + func_append rpath "$dir:" done eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var" @@ -6934,5 +8093,5 @@ shlibpath="$finalize_shlibpath" - test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath" + test "$opt_mode" != relink && shlibpath="$compile_shlibpath$shlibpath" if test -n "$shlibpath"; then eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var" @@ -6960,9 +8119,9 @@ for link do - linknames="$linknames $link" + func_append linknames " $link" done # Use standard objects if they are pic - test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` + test -z "$pic_flag" && libobjs=`$ECHO "$libobjs" | $SP2NL | $SED "$lo2o" | $NL2SP` test "X$libobjs" = "X " && libobjs= @@ -6971,5 +8130,5 @@ $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp" export_symbols="$output_objdir/$libname.uexp" - delfiles="$delfiles $export_symbols" + func_append delfiles " $export_symbols" fi @@ -7002,11 +8161,43 @@ cmds=$export_symbols_cmds save_ifs="$IFS"; IFS='~' - for cmd in $cmds; do + for cmd1 in $cmds; do IFS="$save_ifs" - eval cmd=\"$cmd\" - func_len " $cmd" - len=$func_len_result - if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then + # Take the normal branch if the nm_file_list_spec branch + # doesn't work or if tool conversion is not needed. + case $nm_file_list_spec~$to_tool_file_cmd in + *~func_convert_file_noop | *~func_convert_file_msys_to_w32 | ~*) + try_normal_branch=yes + eval cmd=\"$cmd1\" + func_len " $cmd" + len=$func_len_result + ;; + *) + try_normal_branch=no + ;; + esac + if test "$try_normal_branch" = yes \ + && { test "$len" -lt "$max_cmd_len" \ + || test "$max_cmd_len" -le -1; } + then func_show_eval "$cmd" 'exit $?' + skipped_export=false + elif test -n "$nm_file_list_spec"; then + func_basename "$output" + output_la=$func_basename_result + save_libobjs=$libobjs + save_output=$output + output=${output_objdir}/${output_la}.nm + func_to_tool_file "$output" + libobjs=$nm_file_list_spec$func_to_tool_file_result + func_append delfiles " $output" + func_verbose "creating $NM input file list: $output" + for obj in $save_libobjs; do + func_to_tool_file "$obj" + $ECHO "$func_to_tool_file_result" + done > "$output" + eval cmd=\"$cmd1\" + func_show_eval "$cmd" 'exit $?' + output=$save_output + libobjs=$save_libobjs skipped_export=false else @@ -7030,5 +8221,5 @@ tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" - $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' + $opt_dry_run || eval '$ECHO "$include_expsyms" | $SP2NL >> "$tmp_export_symbols"' fi @@ -7042,5 +8233,5 @@ # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter - delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" + func_append delfiles " $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols @@ -7052,5 +8243,5 @@ *" $test_deplib "*) ;; *) - tmp_deplibs="$tmp_deplibs $test_deplib" + func_append tmp_deplibs " $test_deplib" ;; esac @@ -7072,8 +8263,8 @@ else gentop="$output_objdir/${outputname}x" - generated="$generated $gentop" + func_append generated " $gentop" func_extract_archives $gentop $convenience - libobjs="$libobjs $func_extract_archives_result" + func_append libobjs " $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi @@ -7082,9 +8273,9 @@ if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then eval flag=\"$thread_safe_flag_spec\" - linker_flags="$linker_flags $flag" + func_append linker_flags " $flag" fi # Make a backup of the uninstalled library when relinking - if test "$mode" = relink; then + if test "$opt_mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $? fi @@ -7131,5 +8322,6 @@ fi save_output=$output - output_la=`$ECHO "X$output" | $Xsed -e "$basename"` + func_basename "$output" + output_la=$func_basename_result # Clear the reloadable object creation command queue and @@ -7144,11 +8336,14 @@ output=${output_objdir}/${output_la}.lnkscript func_verbose "creating GNU ld script: $output" - $ECHO 'INPUT (' > $output + echo 'INPUT (' > $output for obj in $save_libobjs do - $ECHO "$obj" >> $output + func_to_tool_file "$obj" + $ECHO "$func_to_tool_file_result" >> $output done - $ECHO ')' >> $output - delfiles="$delfiles $output" + echo ')' >> $output + func_append delfiles " $output" + func_to_tool_file "$output" + output=$func_to_tool_file_result elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then output=${output_objdir}/${output_la}.lnk @@ -7164,8 +8359,10 @@ for obj do - $ECHO "$obj" >> $output + func_to_tool_file "$obj" + $ECHO "$func_to_tool_file_result" >> $output done - delfiles="$delfiles $output" - output=$firstobj\"$file_list_spec$output\" + func_append delfiles " $output" + func_to_tool_file "$output" + output=$firstobj\"$file_list_spec$func_to_tool_file_result\" else if test -n "$save_libobjs"; then @@ -7191,9 +8388,11 @@ if test "$k" -eq 1 ; then # The first file doesn't have a previous command to add. - eval concat_cmds=\"$reload_cmds $objlist $last_robj\" + reload_objs=$objlist + eval concat_cmds=\"$reload_cmds\" else # All subsequent reloadable object files will link in # the last one created. - eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\" + reload_objs="$objlist $last_robj" + eval concat_cmds=\"\$concat_cmds~$reload_cmds~\$RM $last_robj\" fi last_robj=$output_objdir/$output_la-${k}.$objext @@ -7201,5 +8400,5 @@ k=$func_arith_result output=$output_objdir/$output_la-${k}.$objext - objlist=$obj + objlist=" $obj" func_len " $last_robj" func_arith $len0 + $func_len_result @@ -7211,9 +8410,10 @@ # files will link in the last one created. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ - eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\" + reload_objs="$objlist $last_robj" + eval concat_cmds=\"\${concat_cmds}$reload_cmds\" if test -n "$last_robj"; then eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\" fi - delfiles="$delfiles $output" + func_append delfiles " $output" else @@ -7249,5 +8449,5 @@ # Restore the uninstalled library and exit - if test "$mode" = relink; then + if test "$opt_mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ @@ -7270,5 +8470,5 @@ tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" - $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' + $opt_dry_run || eval '$ECHO "$include_expsyms" | $SP2NL >> "$tmp_export_symbols"' fi @@ -7282,5 +8482,5 @@ # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter - delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" + func_append delfiles " $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols @@ -7323,8 +8523,8 @@ if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" - generated="$generated $gentop" + func_append generated " $gentop" func_extract_archives $gentop $dlprefiles - libobjs="$libobjs $func_extract_archives_result" + func_append libobjs " $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi @@ -7342,5 +8542,5 @@ # Restore the uninstalled library and exit - if test "$mode" = relink; then + if test "$opt_mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ @@ -7354,5 +8554,5 @@ # Restore the uninstalled library and exit - if test "$mode" = relink; then + if test "$opt_mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $? @@ -7435,8 +8635,8 @@ if test -n "$whole_archive_flag_spec"; then eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\" - reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'` + reload_conv_objs=$reload_objs\ `$ECHO "$tmp_whole_archive_flags" | $SED 's|,| |g'` else gentop="$output_objdir/${obj}x" - generated="$generated $gentop" + func_append generated " $gentop" func_extract_archives $gentop $convenience @@ -7445,6 +8645,9 @@ fi + # If we're not building shared, we need to use non_pic_objs + test "$build_libtool_libs" != yes && libobjs="$non_pic_objects" + # Create the old-style object. - reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test + reload_objs="$objs$old_deplibs "`$ECHO "$libobjs" | $SP2NL | $SED "/\.${libext}$/d; /\.lib$/d; $lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test output="$obj" @@ -7506,6 +8709,6 @@ *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library is the System framework - compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` - finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` + compile_deplibs=`$ECHO " $compile_deplibs" | $SED 's/ -lc / System.ltframework /'` + finalize_deplibs=`$ECHO " $finalize_deplibs" | $SED 's/ -lc / System.ltframework /'` ;; esac @@ -7518,12 +8721,12 @@ case ${MACOSX_DEPLOYMENT_TARGET-10.0} in 10.[0123]) - compile_command="$compile_command ${wl}-bind_at_load" - finalize_command="$finalize_command ${wl}-bind_at_load" + func_append compile_command " ${wl}-bind_at_load" + func_append finalize_command " ${wl}-bind_at_load" ;; esac fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" - compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` - finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + compile_deplibs=`$ECHO " $compile_deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` + finalize_deplibs=`$ECHO " $finalize_deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac @@ -7539,5 +8742,5 @@ case " $compile_deplibs " in *" -L$path/$objdir "*) - new_libs="$new_libs -L$path/$objdir" ;; + func_append new_libs " -L$path/$objdir" ;; esac ;; @@ -7549,8 +8752,8 @@ case " $new_libs " in *" $deplib "*) ;; - *) new_libs="$new_libs $deplib" ;; + *) func_append new_libs " $deplib" ;; esac ;; - *) new_libs="$new_libs $deplib" ;; + *) func_append new_libs " $deplib" ;; esac done @@ -7558,6 +8761,6 @@ - compile_command="$compile_command $compile_deplibs" - finalize_command="$finalize_command $finalize_deplibs" + func_append compile_command " $compile_deplibs" + func_append finalize_command " $finalize_deplibs" if test -n "$rpath$xrpath"; then @@ -7567,5 +8770,5 @@ case "$finalize_rpath " in *" $libdir "*) ;; - *) finalize_rpath="$finalize_rpath $libdir" ;; + *) func_append finalize_rpath " $libdir" ;; esac done @@ -7586,5 +8789,5 @@ ;; *) - hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" + func_append hardcode_libdirs "$hardcode_libdir_separator$libdir" ;; esac @@ -7592,10 +8795,10 @@ else eval flag=\"$hardcode_libdir_flag_spec\" - rpath="$rpath $flag" + func_append rpath " $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; - *) perm_rpath="$perm_rpath $libdir" ;; + *) func_append perm_rpath " $libdir" ;; esac fi @@ -7606,10 +8809,10 @@ *":$libdir:"*) ;; ::) dllsearchpath=$libdir;; - *) dllsearchpath="$dllsearchpath:$libdir";; + *) func_append dllsearchpath ":$libdir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; - *) dllsearchpath="$dllsearchpath:$testbindir";; + *) func_append dllsearchpath ":$testbindir";; esac ;; @@ -7637,5 +8840,5 @@ ;; *) - hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" + func_append hardcode_libdirs "$hardcode_libdir_separator$libdir" ;; esac @@ -7643,10 +8846,10 @@ else eval flag=\"$hardcode_libdir_flag_spec\" - rpath="$rpath $flag" + func_append rpath " $flag" fi elif test -n "$runpath_var"; then case "$finalize_perm_rpath " in *" $libdir "*) ;; - *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;; + *) func_append finalize_perm_rpath " $libdir" ;; esac fi @@ -7662,6 +8865,6 @@ if test -n "$libobjs" && test "$build_old_libs" = yes; then # Transform all the library objects into standard objects. - compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` - finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` + compile_command=`$ECHO "$compile_command" | $SP2NL | $SED "$lo2o" | $NL2SP` + finalize_command=`$ECHO "$finalize_command" | $SP2NL | $SED "$lo2o" | $NL2SP` fi @@ -7675,12 +8878,12 @@ wrappers_required=yes case $host in + *cegcc* | *mingw32ce*) + # Disable wrappers for cegcc and mingw32ce hosts, we are cross compiling anyway. + wrappers_required=no + ;; *cygwin* | *mingw* ) if test "$build_libtool_libs" != yes; then wrappers_required=no fi - ;; - *cegcc) - # Disable wrappers for cegcc, we are cross compiling anyway. - wrappers_required=no ;; *) @@ -7692,5 +8895,5 @@ if test "$wrappers_required" = no; then # Replace the output file specification. - compile_command=`$ECHO "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` + compile_command=`$ECHO "$compile_command" | $SED 's%@OUTPUT@%'"$output"'%g'` link_command="$compile_command$compile_rpath" @@ -7698,4 +8901,10 @@ exit_status=0 func_show_eval "$link_command" 'exit_status=$?' + + if test -n "$postlink_cmds"; then + func_to_tool_file "$output" + postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'` + func_execute_cmds "$postlink_cmds" 'exit $?' + fi # Delete the generated files. @@ -7721,5 +8930,5 @@ rpath= for dir in $perm_rpath; do - rpath="$rpath$dir:" + func_append rpath "$dir:" done compile_var="$runpath_var=\"$rpath\$$runpath_var\" " @@ -7729,5 +8938,5 @@ rpath= for dir in $finalize_perm_rpath; do - rpath="$rpath$dir:" + func_append rpath "$dir:" done finalize_var="$runpath_var=\"$rpath\$$runpath_var\" " @@ -7739,9 +8948,16 @@ link_command="$compile_var$compile_command$compile_rpath" # Replace the output file specification. - link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` + link_command=`$ECHO "$link_command" | $SED 's%@OUTPUT@%'"$output"'%g'` # Delete the old output file. $opt_dry_run || $RM $output # Link the executable and exit func_show_eval "$link_command" 'exit $?' + + if test -n "$postlink_cmds"; then + func_to_tool_file "$output" + postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'` + func_execute_cmds "$postlink_cmds" 'exit $?' + fi + exit $EXIT_SUCCESS fi @@ -7758,5 +8974,5 @@ link_command="$finalize_var$compile_command$finalize_rpath" if test "$fast_install" = yes; then - relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'` + relink_command=`$ECHO "$compile_var$compile_command$compile_rpath" | $SED 's%@OUTPUT@%\$progdir/\$file%g'` else # fast_install is set to needless @@ -7770,5 +8986,5 @@ # Replace the output file specification. - link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'` + link_command=`$ECHO "$link_command" | $SED 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'` # Delete the old output files. @@ -7776,4 +8992,10 @@ func_show_eval "$link_command" 'exit $?' + + if test -n "$postlink_cmds"; then + func_to_tool_file "$output_objdir/$outputname" + postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'` + func_execute_cmds "$postlink_cmds" 'exit $?' + fi # Now create the wrapper script. @@ -7794,16 +9016,5 @@ done relink_command="(cd `pwd`; $relink_command)" - relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"` - fi - - # Quote $ECHO for shipping. - if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then - case $progpath in - [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";; - *) qecho="$SHELL `pwd`/$progpath --fallback-echo";; - esac - qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"` - else - qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"` + relink_command=`$ECHO "$relink_command" | $SED "$sed_quote_subst"` fi @@ -7885,5 +9096,5 @@ oldobjs="$old_deplibs $non_pic_objects" if test "$preload" = yes && test -f "$symfileobj"; then - oldobjs="$oldobjs $symfileobj" + func_append oldobjs " $symfileobj" fi fi @@ -7893,8 +9104,8 @@ if test -n "$addlibs"; then gentop="$output_objdir/${outputname}x" - generated="$generated $gentop" + func_append generated " $gentop" func_extract_archives $gentop $addlibs - oldobjs="$oldobjs $func_extract_archives_result" + func_append oldobjs " $func_extract_archives_result" fi @@ -7907,8 +9118,8 @@ if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" - generated="$generated $gentop" + func_append generated " $gentop" func_extract_archives $gentop $dlprefiles - oldobjs="$oldobjs $func_extract_archives_result" + func_append oldobjs " $func_extract_archives_result" fi @@ -7926,7 +9137,7 @@ : else - $ECHO "copying selected object files to avoid basename conflicts..." + echo "copying selected object files to avoid basename conflicts..." gentop="$output_objdir/${outputname}x" - generated="$generated $gentop" + func_append generated " $gentop" func_mkdir_p "$gentop" save_oldobjs=$oldobjs @@ -7952,10 +9163,12 @@ done func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj" - oldobjs="$oldobjs $gentop/$newobj" + func_append oldobjs " $gentop/$newobj" ;; - *) oldobjs="$oldobjs $obj" ;; + *) func_append oldobjs " $obj" ;; esac done fi + func_to_tool_file "$oldlib" func_convert_file_msys_to_w32 + tool_oldlib=$func_to_tool_file_result eval cmds=\"$old_archive_cmds\" @@ -7963,4 +9176,14 @@ len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then + cmds=$old_archive_cmds + elif test -n "$archiver_list_spec"; then + func_verbose "using command file archive linking..." + for obj in $oldobjs + do + func_to_tool_file "$obj" + $ECHO "$func_to_tool_file_result" + done > $output_objdir/$libname.libcmd + func_to_tool_file "$output_objdir/$libname.libcmd" + oldobjs=" $archiver_list_spec$func_to_tool_file_result" cmds=$old_archive_cmds else @@ -8037,5 +9260,5 @@ # Quote the link command for shipping. relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)" - relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"` + relink_command=`$ECHO "$relink_command" | $SED "$sed_quote_subst"` if test "$hardcode_automatic" = yes ; then relink_command= @@ -8057,10 +9280,21 @@ func_basename "$deplib" name="$func_basename_result" - eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib` + func_resolve_sysroot "$deplib" + eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $func_resolve_sysroot_result` test -z "$libdir" && \ func_fatal_error "\`$deplib' is not a valid libtool archive" - newdependency_libs="$newdependency_libs $libdir/$name" + func_append newdependency_libs " ${lt_sysroot:+=}$libdir/$name" ;; - *) newdependency_libs="$newdependency_libs $deplib" ;; + -L*) + func_stripname -L '' "$deplib" + func_replace_sysroot "$func_stripname_result" + func_append newdependency_libs " -L$func_replace_sysroot_result" + ;; + -R*) + func_stripname -R '' "$deplib" + func_replace_sysroot "$func_stripname_result" + func_append newdependency_libs " -R$func_replace_sysroot_result" + ;; + *) func_append newdependency_libs " $deplib" ;; esac done @@ -8076,7 +9310,7 @@ test -z "$libdir" && \ func_fatal_error "\`$lib' is not a valid libtool archive" - newdlfiles="$newdlfiles $libdir/$name" + func_append newdlfiles " ${lt_sysroot:+=}$libdir/$name" ;; - *) newdlfiles="$newdlfiles $lib" ;; + *) func_append newdlfiles " $lib" ;; esac done @@ -8095,5 +9329,5 @@ test -z "$libdir" && \ func_fatal_error "\`$lib' is not a valid libtool archive" - newdlprefiles="$newdlprefiles $libdir/$name" + func_append newdlprefiles " ${lt_sysroot:+=}$libdir/$name" ;; esac @@ -8107,5 +9341,5 @@ *) abs=`pwd`"/$lib" ;; esac - newdlfiles="$newdlfiles $abs" + func_append newdlfiles " $abs" done dlfiles="$newdlfiles" @@ -8116,5 +9350,5 @@ *) abs=`pwd`"/$lib" ;; esac - newdlprefiles="$newdlprefiles $abs" + func_append newdlprefiles " $abs" done dlprefiles="$newdlprefiles" @@ -8122,7 +9356,25 @@ $RM $output # place dlname in correct position for cygwin + # In fact, it would be nice if we could use this code for all target + # systems that can't hard-code library paths into their executables + # and that have no shared library path variable independent of PATH, + # but it turns out we can't easily determine that from inspecting + # libtool variables, so we have to hard-code the OSs to which it + # applies here; at the moment, that means platforms that use the PE + # object format with DLL files. See the long comment at the top of + # tests/bindir.at for full details. tdlname=$dlname case $host,$output,$installed,$module,$dlname in - *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) tdlname=../bin/$dlname ;; + *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) + # If a -bindir argument was supplied, place the dll there. + if test "x$bindir" != x ; + then + func_relative_path "$install_libdir" "$bindir" + tdlname=$func_relative_path_result$dlname + else + # Otherwise fall back on heuristic. + tdlname=../bin/$dlname + fi + ;; esac $ECHO > $output "\ @@ -8183,5 +9435,5 @@ } -{ test "$mode" = link || test "$mode" = relink; } && +{ test "$opt_mode" = link || test "$opt_mode" = relink; } && func_mode_link ${1+"$@"} @@ -8203,7 +9455,7 @@ do case $arg in - -f) RM="$RM $arg"; rmforce=yes ;; - -*) RM="$RM $arg" ;; - *) files="$files $arg" ;; + -f) func_append RM " $arg"; rmforce=yes ;; + -*) func_append RM " $arg" ;; + *) func_append files " $arg" ;; esac done @@ -8214,22 +9466,21 @@ rmdirs= - origobjdir="$objdir" for file in $files; do func_dirname "$file" "" "." dir="$func_dirname_result" if test "X$dir" = X.; then - objdir="$origobjdir" + odir="$objdir" else - objdir="$dir/$origobjdir" + odir="$dir/$objdir" fi func_basename "$file" name="$func_basename_result" - test "$mode" = uninstall && objdir="$dir" - - # Remember objdir for removal later, being careful to avoid duplicates - if test "$mode" = clean; then + test "$opt_mode" = uninstall && odir="$dir" + + # Remember odir for removal later, being careful to avoid duplicates + if test "$opt_mode" = clean; then case " $rmdirs " in - *" $objdir "*) ;; - *) rmdirs="$rmdirs $objdir" ;; + *" $odir "*) ;; + *) func_append rmdirs " $odir" ;; esac fi @@ -8257,16 +9508,15 @@ # Delete the libtool libraries and symlinks. for n in $library_names; do - rmfiles="$rmfiles $objdir/$n" + func_append rmfiles " $odir/$n" done - test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library" - - case "$mode" in + test -n "$old_library" && func_append rmfiles " $odir/$old_library" + + case "$opt_mode" in clean) - case " $library_names " in - # " " in the beginning catches empty $dlname + case " $library_names " in *" $dlname "*) ;; - *) rmfiles="$rmfiles $objdir/$dlname" ;; + *) test -n "$dlname" && func_append rmfiles " $odir/$dlname" ;; esac - test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i" + test -n "$libdir" && func_append rmfiles " $odir/$name $odir/${name}i" ;; uninstall) @@ -8296,5 +9546,5 @@ if test -n "$pic_object" && test "$pic_object" != none; then - rmfiles="$rmfiles $dir/$pic_object" + func_append rmfiles " $dir/$pic_object" fi @@ -8302,5 +9552,5 @@ if test -n "$non_pic_object" && test "$non_pic_object" != none; then - rmfiles="$rmfiles $dir/$non_pic_object" + func_append rmfiles " $dir/$non_pic_object" fi fi @@ -8308,5 +9558,5 @@ *) - if test "$mode" = clean ; then + if test "$opt_mode" = clean ; then noexename=$name case $file in @@ -8318,5 +9568,5 @@ # $file with .exe has already been added to rmfiles, # add $file without .exe - rmfiles="$rmfiles $file" + func_append rmfiles " $file" ;; esac @@ -8327,5 +9577,5 @@ relink_command= func_source $func_ltwrapper_scriptname_result - rmfiles="$rmfiles $func_ltwrapper_scriptname_result" + func_append rmfiles " $func_ltwrapper_scriptname_result" else relink_command= @@ -8335,10 +9585,10 @@ # note $name still contains .exe if it was in $file originally # as does the version of $file that was added into $rmfiles - rmfiles="$rmfiles $objdir/$name $objdir/${name}S.${objext}" + func_append rmfiles " $odir/$name $odir/${name}S.${objext}" if test "$fast_install" = yes && test -n "$relink_command"; then - rmfiles="$rmfiles $objdir/lt-$name" + func_append rmfiles " $odir/lt-$name" fi if test "X$noexename" != "X$name" ; then - rmfiles="$rmfiles $objdir/lt-${noexename}.c" + func_append rmfiles " $odir/lt-${noexename}.c" fi fi @@ -8348,5 +9598,4 @@ func_show_eval "$RM $rmfiles" 'exit_status=1' done - objdir="$origobjdir" # Try to remove the ${objdir}s in the directories where we deleted files @@ -8360,8 +9609,8 @@ } -{ test "$mode" = uninstall || test "$mode" = clean; } && +{ test "$opt_mode" = uninstall || test "$opt_mode" = clean; } && func_mode_uninstall ${1+"$@"} -test -z "$mode" && { +test -z "$opt_mode" && { help="$generic_help" func_fatal_help "you must specify a MODE" @@ -8369,5 +9618,5 @@ test -z "$exec_cmd" && \ - func_fatal_help "invalid operation mode \`$mode'" + func_fatal_help "invalid operation mode \`$opt_mode'" if test -n "$exec_cmd"; then Index: sm/trunk/m4/ar-lib.m4 =================================================================== --- /issm/trunk/m4/ar-lib.m4 (revision 13394) +++ (revision ) @@ -1,61 +1,0 @@ -## -*- Autoconf -*- -# Copyright (C) 2011 Free Software Foundation, Inc. -# -# This file is free software; the Free Software Foundation -# gives unlimited permission to copy and/or distribute it, -# with or without modifications, as long as this notice is preserved. - -# serial 1 - -# AM_PROG_AR([ACT-IF-FAIL]) -# ------------------------- -# Try to determine the archiver interface, and trigger the ar-lib wrapper -# if it is needed. If the detection of archiver interface fails, run -# ACT-IF-FAIL (default is to abort configure with a proper error message). -AC_DEFUN([AM_PROG_AR], -[AC_BEFORE([$0], [LT_INIT])dnl -AC_BEFORE([$0], [AC_PROG_LIBTOOL])dnl -AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl -AC_REQUIRE_AUX_FILE([ar-lib])dnl -AC_CHECK_TOOLS([AR], [ar lib "link -lib"], [false]) -: ${AR=ar} - -AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface], - [am_cv_ar_interface=ar - AC_COMPILE_IFELSE([AC_LANG_SOURCE([[int some_variable = 0;]])], - [am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&AS_MESSAGE_LOG_FD' - AC_TRY_EVAL([am_ar_try]) - if test "$ac_status" -eq 0; then - am_cv_ar_interface=ar - else - am_ar_try='$AR -NOLOGO -OUT:conftest.lib conftest.$ac_objext >&AS_MESSAGE_LOG_FD' - AC_TRY_EVAL([am_ar_try]) - if test "$ac_status" -eq 0; then - am_cv_ar_interface=lib - else - am_cv_ar_interface=unknown - fi - fi - rm -f conftest.lib libconftest.a - ]) - ]) - -case $am_cv_ar_interface in -ar) - ;; -lib) - # Microsoft lib, so override with the ar-lib wrapper script. - # FIXME: It is wrong to rewrite AR. - # But if we don't then we get into trouble of one sort or another. - # A longer-term fix would be to have automake use am__AR in this case, - # and then we could set am__AR="$am_aux_dir/ar-lib \$(AR)" or something - # similar. - AR="$am_aux_dir/ar-lib $AR" - ;; -unknown) - m4_default([$1], - [AC_MSG_ERROR([could not determine $AR interface])]) - ;; -esac -AC_SUBST([AR])dnl -]) Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 13394) +++ /issm/trunk/m4/issm_options.m4 (revision 13395) @@ -12,5 +12,22 @@ AC_DEFINE([_ISSM_DEBUG_],[1],[Macro to enable debugging in ISSM]) fi - dnl }}} + + dnl }}} + dnl shared build {{{ + AC_ARG_ENABLE([sharedlibs], dnl feature + AS_HELP_STRING([--enable-sharedlibs], [produce libISSM.so.0]), dnl help string + [enable_sharedlibs=$enableval], dnl action if given + [enable_sharedlibs=no]) dnl action if not given + AM_CONDITIONAL([SHAREDLIBS], [test x$enable_sharedlibs = xyes]) + dnl }}} + + dnl shared build {{{ + AC_ARG_ENABLE([version], dnl feature + AS_HELP_STRING([--enable-version], [produce libISSM.so.0]), dnl help string + [enable_version=$enableval], dnl action if given + [enable_version=no]) dnl action if not given + AM_CONDITIONAL([VERSION], [test x$enable_VERSION = xyes]) + dnl }}} + dnl Modules build {{{ AC_ARG_WITH([modules], @@ -164,42 +181,46 @@ MATLABINCL=-I"$MATLAB_ROOT/extern/include"; - dnl OS-dependent variables and checks - case "${host_os}" in - *linux*) - if test "${host_cpu}" = "x86_64"; - then - MEXLIB=-L"$MATLAB_ROOT/bin/glnxa64/ -lmex" - MEXLINK="-pthread -shared -W2,--version-script,${MATLAB_ROOT}/extern/lib/glnxa64/mexFunction.map"; - else - MEXLIB=-L"$MATLAB_ROOT/bin/glnx86/ -lmex" - MEXLINK="-pthread -shared -W2,--version-script,${MATLAB_ROOT}/extern/lib/glnx86/mexFunction.map"; - fi - MEXEXT=`$MATLAB_ROOT/bin/mexext` - MEXEXT=".$MEXEXT" - ;; - *darwin*) - dnl mex -v gives all the flags for compilation of mex files - dnl if matlab version is 7.9 or more, we must use mexmaci64 (64 bits) - MEXLINK="-O -Wl,-flat_namespace -undefined suppress -arch i386 -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci/mexFunction.map" - MEXLIB=" -L$MATLAB_ROOT/bin/maci/ -lmx -lmex -lmat -lstdc++ -largeArrayDims" - if test $MATLAB_MAJOR -ge 7; then - if test $MATLAB_MINOR -ge 9; then - MEXLINK="-O -Wl,-flat_namespace -undefined suppress -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci64/mexFunction.map" - MEXLIB=" -L$MATLAB_ROOT/bin/maci64/ -lmx -lmex -lmat -lstdc++" - fi - fi - MEXEXT=`$MATLAB_ROOT/bin/mexext` - MEXEXT=".$MEXEXT" - ;; - *cygwin*) - if test $VENDOR = intel-win7-32; then - MEXLIB="-dll -export:mexFunction -LIBPATH:\"$MATLAB_ROOT\extern\lib\win32\microsoft\" libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib -NOLOGO -INCREMENTAL:NO -manifest" - elif test $VENDOR = intel-win7-64; then - MEXLIB="-dll -export:mexFunction -LIBPATH:\"$MATLAB_ROOT\extern\lib\win64\microsoft\" libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib -NOLOGO -INCREMENTAL:NO -manifest" - fi - MEXEXT=`$MATLAB_ROOT/bin/mexext.bat` - MEXEXT=".$MEXEXT" - ;; - esac + 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=$( mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/ LDEXTENSION = //g") + dnl dnl OS-dependent variables and checks (old stuff) + dnl case "${host_os}" in + dnl *linux*) + dnl if test "${host_cpu}" = "x86_64"; + dnl then + dnl MEXLIB="-Wl,-rpath-link,$MATLAB_ROOT/bin/glnxa64 -L$MATLAB_ROOT/bin/glnxa64/ -lmx -lmex -lmat -lm" + dnl MEXLINK="-pthread -shared -W2,--version-script,${MATLAB_ROOT}/extern/lib/glnxa64/mexFunction.map"; + dnl else + dnl MEXLIB=-L"$MATLAB_ROOT/bin/glnx86/ -lmex" + dnl MEXLINK="-pthread -shared -W2,--version-script,${MATLAB_ROOT}/extern/lib/glnx86/mexFunction.map"; + dnl fi + dnl MEXEXT=`$MATLAB_ROOT/bin/mexext` + dnl MEXEXT=".$MEXEXT" + dnl ;; + dnl *darwin*) + dnl dnl mex -v gives all the flags for compilation of mex files + dnl dnl if matlab version is 7.9 or more, we must use mexmaci64 (64 bits) + dnl MEXLINK="-O -Wl,-flat_namespace -undefined suppress -arch i386 -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci/mexFunction.map" + dnl MEXLIB=" -L$MATLAB_ROOT/bin/maci/ -lmx -lmex -lmat -lstdc++ -largeArrayDims" + dnl if test $MATLAB_MAJOR -ge 7; then + dnl if test $MATLAB_MINOR -ge 9; then + dnl MEXLINK="-O -Wl,-flat_namespace -undefined suppress -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci64/mexFunction.map" + dnl MEXLIB=" -L$MATLAB_ROOT/bin/maci64/ -lmx -lmex -lmat -lstdc++" + dnl fi + dnl fi + dnl MEXEXT=`$MATLAB_ROOT/bin/mexext` + dnl MEXEXT=".$MEXEXT" + dnl ;; + dnl *cygwin*) + dnl if test $VENDOR = intel-win7-32; then + dnl MEXLIB="-dll -export:mexFunction -LIBPATH:\"$MATLAB_ROOT\extern\lib\win32\microsoft\" libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib -NOLOGO -INCREMENTAL:NO -manifest" + dnl elif test $VENDOR = intel-win7-64; then + dnl MEXLIB="-dll -export:mexFunction -LIBPATH:\"$MATLAB_ROOT\extern\lib\win64\microsoft\" libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib -NOLOGO -INCREMENTAL:NO -manifest" + dnl fi + dnl MEXEXT=`$MATLAB_ROOT/bin/mexext.bat` + dnl MEXEXT=".$MEXEXT" + dnl ;; + dnl esac AC_MSG_RESULT(done) @@ -208,5 +229,5 @@ MATLABWRAPPEREXT=$MEXEXT AC_SUBST([MATLABWRAPPEREXT]) - AC_SUBST([MEXLIB]) + AC_SUBST([MEXLIB]) AC_SUBST([MEXLINK]) fi @@ -315,5 +336,22 @@ if test -d "$PYTHON_ROOT"; then dnl defaults + HAVE_PYTHON3="no" HAVE_PYTHON=yes + + AC_ARG_WITH([python-version], + AS_HELP_STRING([--with-python-version = PYTHONVERSION],[python version.]), + [PYTHONVERSION=$withval],[PYTHONVERSION=""]) + AC_MSG_CHECKING(for python version) + + dnl recover major: + PYTHON_MAJOR=${PYTHONVERSION%.*} + + if test x$PYTHON_MAJOR = x3; then + dnl are we running python 3? + HAVE_PYTHON3="yes" + fi + AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major]) + AC_MSG_RESULT($PYTHON_MAJOR) + PYTHONINCL=-I$PYTHON_ROOT/include PYTHONLIB="-L$PYTHON_ROOT/lib -lpython$PYTHONVERSION" @@ -342,25 +380,7 @@ fi AM_CONDITIONAL([PYTHON], [test x$HAVE_PYTHON = xyes]) + AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes]) AC_MSG_RESULT($HAVE_PYTHON) - dnl python-version - HAVE_PYTHON3="no" - if test x$HAVE_PYTHON = xyes; then - AC_ARG_WITH([python-version], - AS_HELP_STRING([--with-python-version = PYTHONVERSION],[python version.]), - [PYTHONVERSION=$withval],[PYTHONVERSION=""]) - AC_MSG_CHECKING(for python version) - - dnl recover major: - PYTHON_MAJOR=${PYTHONVERSION%.*} - - if test x$PYTHON_MAJOR = x3; then - dnl are we running python 3? - HAVE_PYTHON3="yes" - fi - AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major]) - AC_MSG_RESULT($PYTHON_MAJOR) - fi - AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes]) dnl }}} dnl python-numpy{{{ @@ -373,5 +393,5 @@ dnl defaults HAVE_PYTHON_NUMPY=yes - PYTHON_NUMPYINCL=-I$PYTHON_NUMPY_ROOT + PYTHON_NUMPYINCL="-I$PYTHON_NUMPY_ROOT -I$PYTHON_NUMPY_ROOT/core/include/numpy" AC_DEFINE([_HAVE_PYTHON_NUMPY_],[1],[with Python-Numpy in ISSM src]) @@ -454,4 +474,13 @@ AC_MSG_RESULT($HAVE_ADOLC) dnl }}} + dnl adolc-version{{{ + AC_ARG_WITH([adolc-version], + AS_HELP_STRING([--with-adolc-version=number], [adolc version.]), + [ADOLC_VERSION=$withval],[ADOLC_VERSION=2]) + AC_MSG_CHECKING(for adolc-version) + + AC_DEFINE_UNQUOTED([_ADOLC_VERSION_],$ADOLC_VERSION,[ADOLC version]) + AC_MSG_RESULT($ADOLC_VERSION) + dnl }}} dnl adic2{{{ AC_ARG_WITH([adic2-dir], @@ -493,5 +522,5 @@ HAVE_GSL=yes GSLINCL="-I$GSL_ROOT/include" - GSLLIB="-L$GSL_ROOT/lib/ -lgsl -lgslcblas -lm" + GSLLIB="-dy -L$GSL_ROOT/lib -lgsl -lgslcblas -lm" AC_DEFINE([_HAVE_GSL_],[1],[with gsl in ISSM src]) @@ -533,7 +562,7 @@ [METIS_ROOT=$withval],[METIS_ROOT=""]) + AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT) + if test -d "$METIS_ROOT"; then - - AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT) dnl first figure out version of metis: does the VERSION file exist? @@ -577,5 +606,5 @@ ;; esac - + METISINCL=-I"$METIS_ROOT/include" AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number]) @@ -589,9 +618,10 @@ fi AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes]) + AC_MSG_RESULT($HAVE_METIS) dnl }}} dnl mpi{{{ AC_MSG_CHECKING(for mpi) AC_ARG_WITH([mpi-lib], - AS_HELP_STRING([--with-mpi-lib = otions],[mpi options, for ex: "-L$MPIROOT -lmpich]), + AS_HELP_STRING([--with-mpi-lib = options],[mpi options, for ex: "-L$MPIROOT -lmpich]), [MPILIB=$withval],[MPILIB=""]) @@ -607,5 +637,5 @@ else HAVE_MPI=yes - MPIINCL=-I"$MPI_INCLUDE/" + 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)]) @@ -646,4 +676,7 @@ AC_MSG_CHECKING(for petsc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH) + dnl To ge PETSc's libraries: + dnl cd externalpackages/petsc/src + dnl make getlinklibs if test -d "$PETSC_ROOT"; then @@ -653,21 +686,21 @@ *cygwin*) if test "$PETSC_MAJOR" = "2" ; then - PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/$PETSC_ARCH/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetscksp.lib libpetscdm.lib libpetscmat.lib libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib" + PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetscksp.lib libpetscdm.lib libpetscmat.lib libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib" else - PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/$PETSC_ARCH/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetsc.lib" + PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetsc.lib" fi ;; *linux*) if test "$PETSC_MAJOR" = "2" ; then - PETSCLIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -lpetscsnes -lpetscts" + PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -lpetscsnes -lpetscts" else - PETSCLIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc" + PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc -ldl" fi ;; *darwin*) if test "$PETSC_MAJOR" = "2" ; then - PETSCLIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc" + PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc" else - PETSCLIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc" + PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc" fi ;; @@ -1121,4 +1154,19 @@ dnl Capabilities + dnl with-kml{{{ + AC_ARG_WITH([kml], + AS_HELP_STRING([--with-kml = YES],[compile with kml capabilities (default is yes)]), + [KML=$withval],[KML=yes]) + AC_MSG_CHECKING(for kml capability compilation) + + if test "x$KML" = "xyes"; then + HAVE_KML=yes + AC_DEFINE([_HAVE_KML_],[1],[with kml capability]) + else + HAVE_KML=no + fi + AM_CONDITIONAL([KML], [test x$HAVE_KML = xyes]) + AC_MSG_RESULT($HAVE_KML) + dnl }}} dnl with-kriging{{{ AC_ARG_WITH([kriging], Index: sm/trunk/m4/libtool.m4 =================================================================== --- /issm/trunk/m4/libtool.m4 (revision 13394) +++ (revision ) @@ -1,7357 +1,0 @@ -# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*- -# -# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, -# 2006, 2007, 2008 Free Software Foundation, Inc. -# Written by Gordon Matzigkeit, 1996 -# -# This file is free software; 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-void nm_test_func(void); -void nm_test_func(void){} -#ifdef __cplusplus -} -#endif -int main(){nm_test_var='a';nm_test_func();return(0);} -_LT_EOF - - if AC_TRY_EVAL(ac_compile); then - # Now try to grab the symbols. - nlist=conftest.nm - if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then - # Try sorting and uniquifying the output. - if sort "$nlist" | uniq > "$nlist"T; then - mv -f "$nlist"T "$nlist" - else - rm -f "$nlist"T - fi - - # Make sure that we snagged all the symbols we need. - if $GREP ' nm_test_var$' "$nlist" >/dev/null; then - if $GREP ' nm_test_func$' "$nlist" >/dev/null; then - cat <<_LT_EOF > conftest.$ac_ext -#ifdef __cplusplus -extern "C" { -#endif - -_LT_EOF - # Now generate the symbol file. - eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' - - cat <<_LT_EOF >> conftest.$ac_ext - -/* The mapping between symbol names and symbols. */ -const struct { - const char *name; - void *address; -} -lt__PROGRAM__LTX_preloaded_symbols[[]] = -{ - { "@PROGRAM@", (void *) 0 }, -_LT_EOF - $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext - cat <<\_LT_EOF >> conftest.$ac_ext - {0, (void *) 0} -}; - -/* This works around a problem in FreeBSD linker */ -#ifdef FREEBSD_WORKAROUND -static const void *lt_preloaded_setup() { - return lt__PROGRAM__LTX_preloaded_symbols; -} -#endif - -#ifdef __cplusplus -} -#endif -_LT_EOF - # Now try linking the two files. - mv conftest.$ac_objext conftstm.$ac_objext - lt_save_LIBS="$LIBS" - lt_save_CFLAGS="$CFLAGS" - LIBS="conftstm.$ac_objext" - CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)" - if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then - pipe_works=yes - fi - LIBS="$lt_save_LIBS" - CFLAGS="$lt_save_CFLAGS" - else - echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD - fi - else - echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD - fi - else - echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD - fi - else - echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD - cat conftest.$ac_ext >&5 - fi - rm -rf conftest* conftst* - - # Do not use the global_symbol_pipe unless it works. - if test "$pipe_works" = yes; then - break - else - lt_cv_sys_global_symbol_pipe= - fi -done -]) -if test -z "$lt_cv_sys_global_symbol_pipe"; then - lt_cv_sys_global_symbol_to_cdecl= -fi -if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then - AC_MSG_RESULT(failed) -else - AC_MSG_RESULT(ok) -fi - -_LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1], - [Take the output of nm and produce a listing of raw symbols and C names]) -_LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1], - [Transform the output of nm in a proper C declaration]) -_LT_DECL([global_symbol_to_c_name_address], - [lt_cv_sys_global_symbol_to_c_name_address], [1], - [Transform the output of nm in a C name address pair]) -_LT_DECL([global_symbol_to_c_name_address_lib_prefix], - [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1], - [Transform the output of nm in a C name address pair when lib prefix is needed]) -]) # _LT_CMD_GLOBAL_SYMBOLS - - -# _LT_COMPILER_PIC([TAGNAME]) -# --------------------------- -m4_defun([_LT_COMPILER_PIC], -[m4_require([_LT_TAG_COMPILER])dnl -_LT_TAGVAR(lt_prog_compiler_wl, $1)= -_LT_TAGVAR(lt_prog_compiler_pic, $1)= -_LT_TAGVAR(lt_prog_compiler_static, $1)= - -AC_MSG_CHECKING([for $compiler option to produce PIC]) -m4_if([$1], [CXX], [ - # C++ specific cases for pic, static, wl, etc. - if test "$GXX" = yes; then - _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' - _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' - - case $host_os in - aix*) - # All AIX code is PIC. - if test "$host_cpu" = ia64; then - # AIX 5 now supports IA64 processor - _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' - fi - ;; - - amigaos*) - case $host_cpu in - powerpc) - # see comment about AmigaOS4 .so support - _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' - ;; - m68k) - # FIXME: we need at least 68020 code to build shared libraries, but - # adding the `-m68020' flag to GCC prevents building anything better, - # like `-m68040'. - _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' - ;; - esac - ;; - - beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) - # PIC is the default for these OSes. - ;; - mingw* | cygwin* | os2* | pw32* | cegcc*) - # This hack is so that the source file can tell whether it is being - # built for inclusion in a dll (and should export symbols for example). - # Although the cygwin gcc ignores -fPIC, still need this for old-style - # (--disable-auto-import) libraries - m4_if([$1], [GCJ], [], - [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) - ;; 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It appears that all Alpha - # Linux and Compaq Tru64 Unix objects are PIC. - _LT_TAGVAR(lt_prog_compiler_pic, $1)= - _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' - ;; - xlc* | xlC*) - # IBM XL 8.0 on PPC - _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' - _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' - _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' - ;; - *) - case `$CC -V 2>&1 | sed 5q` in - *Sun\ C*) - # Sun C++ 5.9 - _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' - _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' - _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' - ;; - esac - ;; - esac - ;; - lynxos*) - ;; - m88k*) - ;; - mvs*) - case $cc_basename in - cxx*) - _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall' - ;; - *) - ;; - esac - ;; - netbsd*) - ;; - *qnx* | *nto*) - # QNX uses GNU C++, but need to define -shared option too, otherwise - # it will coredump. - _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' - ;; - osf3* | osf4* | osf5*) - case $cc_basename in - KCC*) - _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' - ;; - RCC*) - # Rational C++ 2.4.1 - _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' - ;; - cxx*) - # Digital/Compaq C++ - _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' - # Make sure the PIC flag is empty. 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then - # AIX 5 now supports IA64 processor - _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' - else - _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' - fi - ;; - - mingw* | cygwin* | pw32* | os2* | cegcc*) - # This hack is so that the source file can tell whether it is being - # built for inclusion in a dll (and should export symbols for example). - m4_if([$1], [GCJ], [], - [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) - ;; - - hpux9* | hpux10* | hpux11*) - _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' - # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but - # not for PA HP-UX. - case $host_cpu in - hppa*64*|ia64*) - # +Z the default - ;; - *) - _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' - ;; - esac - # Is there a better lt_prog_compiler_static that works with the bundled CC? - _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' - ;; - - irix5* | irix6* | nonstopux*) - _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' - # PIC (with -KPIC) is the default. - _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' - ;; 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For efficiency, we do not delegate to -# those functions but instead duplicate the functionality here. -func_dirname_and_basename () -{ - case ${1} in - */*) func_dirname_result="${1%/*}${2}" ;; - * ) func_dirname_result="${3}" ;; - esac - func_basename_result="${1##*/}" -} - -# func_stripname prefix suffix name -# strip PREFIX and SUFFIX off of NAME. -# PREFIX and SUFFIX must not contain globbing or regex special -# characters, hashes, percent signs, but SUFFIX may contain a leading -# dot (in which case that matches only a dot). -func_stripname () -{ - # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are - # positional parameters, so assign one to ordinary parameter first. - func_stripname_result=${3} - func_stripname_result=${func_stripname_result#"${1}"} - func_stripname_result=${func_stripname_result%"${2}"} -} - -# func_opt_split -func_opt_split () -{ - func_opt_split_opt=${1%%=*} - func_opt_split_arg=${1#*=} -} - -# func_lo2o object -func_lo2o () -{ - case ${1} in - *.lo) func_lo2o_result=${1%.lo}.${objext} ;; - *) func_lo2o_result=${1} ;; - esac -} - -# func_xform libobj-or-source -func_xform () -{ - func_xform_result=${1%.*}.lo -} - -# func_arith arithmetic-term... -func_arith () -{ - func_arith_result=$(( $[*] )) -} - -# func_len string -# STRING may not start with a hyphen. -func_len () -{ - func_len_result=${#1} -} - -_LT_EOF - ;; - *) # Bourne compatible functions. - cat << \_LT_EOF >> "$cfgfile" - -# func_dirname file append nondir_replacement -# Compute the dirname of FILE. If nonempty, add APPEND to the result, -# otherwise set result to NONDIR_REPLACEMENT. -func_dirname () -{ - # Extract subdirectory from the argument. - func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"` - if test "X$func_dirname_result" = "X${1}"; then - func_dirname_result="${3}" - else - func_dirname_result="$func_dirname_result${2}" - fi -} - -# func_basename file -func_basename () -{ - func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"` -} - -dnl func_dirname_and_basename -dnl A portable version of this function is already defined in general.m4sh -dnl so there is no need for it here. - -# func_stripname prefix suffix name -# strip PREFIX and SUFFIX off of NAME. -# PREFIX and SUFFIX must not contain globbing or regex special -# characters, hashes, percent signs, but SUFFIX may contain a leading -# dot (in which case that matches only a dot). -# func_strip_suffix prefix name -func_stripname () -{ - case ${2} in - .*) func_stripname_result=`$ECHO "X${3}" \ - | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;; - *) func_stripname_result=`$ECHO "X${3}" \ - | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;; - esac -} - -# sed scripts: -my_sed_long_opt='1s/^\(-[[^=]]*\)=.*/\1/;q' -my_sed_long_arg='1s/^-[[^=]]*=//' - -# func_opt_split -func_opt_split () -{ - func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"` - func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"` -} - -# func_lo2o object -func_lo2o () -{ - func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"` -} - -# func_xform libobj-or-source -func_xform () -{ - func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[[^.]]*$/.lo/'` -} - -# func_arith arithmetic-term... -func_arith () -{ - func_arith_result=`expr "$[@]"` -} - -# func_len string -# STRING may not start with a hyphen. -func_len () -{ - func_len_result=`expr "$[1]" : ".*" 2>/dev/null || echo $max_cmd_len` -} - -_LT_EOF -esac - -case $lt_shell_append in - yes) - cat << \_LT_EOF >> "$cfgfile" - -# func_append var value -# Append VALUE to the end of shell variable VAR. -func_append () -{ - eval "$[1]+=\$[2]" -} -_LT_EOF - ;; - *) - cat << \_LT_EOF >> "$cfgfile" - -# func_append var value -# Append VALUE to the end of shell variable VAR. -func_append () -{ - eval "$[1]=\$$[1]\$[2]" -} - -_LT_EOF - ;; - esac -]) Index: sm/trunk/m4/ltoptions.m4 =================================================================== --- /issm/trunk/m4/ltoptions.m4 (revision 13394) +++ (revision ) @@ -1,368 +1,0 @@ -# Helper functions for option handling. -*- Autoconf -*- -# -# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc. -# Written by Gary V. Vaughan, 2004 -# -# This file is free software; the Free Software Foundation gives -# unlimited permission to copy and/or distribute it, with or without -# modifications, as long as this notice is preserved. - -# serial 6 ltoptions.m4 - -# This is to help aclocal find these macros, as it can't see m4_define. -AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])]) - - -# _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME) -# ------------------------------------------ -m4_define([_LT_MANGLE_OPTION], -[[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])]) - - -# _LT_SET_OPTION(MACRO-NAME, OPTION-NAME) -# --------------------------------------- -# Set option OPTION-NAME for macro MACRO-NAME, and if there is a -# matching handler defined, dispatch to it. Other OPTION-NAMEs are -# saved as a flag. -m4_define([_LT_SET_OPTION], -[m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl -m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]), - _LT_MANGLE_DEFUN([$1], [$2]), - [m4_warning([Unknown $1 option `$2'])])[]dnl -]) - - -# _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET]) -# ------------------------------------------------------------ -# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise. -m4_define([_LT_IF_OPTION], -[m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])]) - - -# _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET) -# ------------------------------------------------------- -# Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME -# are set. -m4_define([_LT_UNLESS_OPTIONS], -[m4_foreach([_LT_Option], m4_split(m4_normalize([$2])), - [m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option), - [m4_define([$0_found])])])[]dnl -m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3 -])[]dnl -]) - - -# _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST) -# ---------------------------------------- -# OPTION-LIST is a space-separated list of Libtool options associated -# with MACRO-NAME. If any OPTION has a matching handler declared with -# LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about -# the unknown option and exit. -m4_defun([_LT_SET_OPTIONS], -[# Set options -m4_foreach([_LT_Option], m4_split(m4_normalize([$2])), - [_LT_SET_OPTION([$1], _LT_Option)]) - -m4_if([$1],[LT_INIT],[ - dnl - dnl Simply set some default values (i.e off) if boolean options were not - dnl specified: - _LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no - ]) - _LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no - ]) - dnl - dnl If no reference was made to various pairs of opposing options, then - dnl we run the default mode handler for the pair. For example, if neither - dnl `shared' nor `disable-shared' was passed, we enable building of shared - dnl archives by default: - _LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED]) - _LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC]) - _LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC]) - _LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install], - [_LT_ENABLE_FAST_INSTALL]) - ]) -])# _LT_SET_OPTIONS - - -## --------------------------------- ## -## Macros to handle LT_INIT options. ## -## --------------------------------- ## - -# _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME) -# ----------------------------------------- -m4_define([_LT_MANGLE_DEFUN], -[[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])]) - - -# LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE) -# ----------------------------------------------- -m4_define([LT_OPTION_DEFINE], -[m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl -])# LT_OPTION_DEFINE - - -# dlopen -# ------ -LT_OPTION_DEFINE([LT_INIT], [dlopen], [enable_dlopen=yes -]) - -AU_DEFUN([AC_LIBTOOL_DLOPEN], -[_LT_SET_OPTION([LT_INIT], [dlopen]) -AC_DIAGNOSE([obsolete], -[$0: Remove this warning and the call to _LT_SET_OPTION when you -put the `dlopen' option into LT_INIT's first parameter.]) -]) - -dnl aclocal-1.4 backwards compatibility: -dnl AC_DEFUN([AC_LIBTOOL_DLOPEN], []) - - -# win32-dll -# --------- -# Declare package support for building win32 dll's. -LT_OPTION_DEFINE([LT_INIT], [win32-dll], -[enable_win32_dll=yes - -case $host in -*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-cegcc*) - AC_CHECK_TOOL(AS, as, false) - AC_CHECK_TOOL(DLLTOOL, dlltool, false) - AC_CHECK_TOOL(OBJDUMP, objdump, false) - ;; -esac - -test -z "$AS" && AS=as -_LT_DECL([], [AS], [0], [Assembler program])dnl - -test -z "$DLLTOOL" && DLLTOOL=dlltool -_LT_DECL([], [DLLTOOL], [0], [DLL creation program])dnl - -test -z "$OBJDUMP" && OBJDUMP=objdump -_LT_DECL([], [OBJDUMP], [0], [Object dumper program])dnl -])# win32-dll - -AU_DEFUN([AC_LIBTOOL_WIN32_DLL], -[AC_REQUIRE([AC_CANONICAL_HOST])dnl -_LT_SET_OPTION([LT_INIT], [win32-dll]) -AC_DIAGNOSE([obsolete], -[$0: Remove this warning and the call to _LT_SET_OPTION when you -put the `win32-dll' option into LT_INIT's first parameter.]) -]) - -dnl aclocal-1.4 backwards compatibility: -dnl AC_DEFUN([AC_LIBTOOL_WIN32_DLL], []) - - -# _LT_ENABLE_SHARED([DEFAULT]) -# ---------------------------- -# implement the --enable-shared flag, and supports the `shared' and -# `disable-shared' LT_INIT options. -# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. -m4_define([_LT_ENABLE_SHARED], -[m4_define([_LT_ENABLE_SHARED_DEFAULT], [m4_if($1, no, no, yes)])dnl -AC_ARG_ENABLE([shared], - [AS_HELP_STRING([--enable-shared@<:@=PKGS@:>@], - [build shared libraries @<:@default=]_LT_ENABLE_SHARED_DEFAULT[@:>@])], - [p=${PACKAGE-default} - case $enableval in - yes) enable_shared=yes ;; - no) enable_shared=no ;; - *) - enable_shared=no - # Look at the argument we got. We use all the common list separators. - lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," - for pkg in $enableval; do - IFS="$lt_save_ifs" - if test "X$pkg" = "X$p"; then - enable_shared=yes - fi - done - IFS="$lt_save_ifs" - ;; - esac], - [enable_shared=]_LT_ENABLE_SHARED_DEFAULT) - - _LT_DECL([build_libtool_libs], [enable_shared], [0], - [Whether or not to build shared libraries]) -])# _LT_ENABLE_SHARED - -LT_OPTION_DEFINE([LT_INIT], [shared], [_LT_ENABLE_SHARED([yes])]) -LT_OPTION_DEFINE([LT_INIT], [disable-shared], [_LT_ENABLE_SHARED([no])]) - -# Old names: -AC_DEFUN([AC_ENABLE_SHARED], -[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[shared]) -]) - -AC_DEFUN([AC_DISABLE_SHARED], -[_LT_SET_OPTION([LT_INIT], [disable-shared]) -]) - -AU_DEFUN([AM_ENABLE_SHARED], [AC_ENABLE_SHARED($@)]) -AU_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)]) - -dnl aclocal-1.4 backwards compatibility: -dnl AC_DEFUN([AM_ENABLE_SHARED], []) -dnl AC_DEFUN([AM_DISABLE_SHARED], []) - - - -# _LT_ENABLE_STATIC([DEFAULT]) -# ---------------------------- -# implement the --enable-static flag, and support the `static' and -# `disable-static' LT_INIT options. -# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. -m4_define([_LT_ENABLE_STATIC], -[m4_define([_LT_ENABLE_STATIC_DEFAULT], [m4_if($1, no, no, yes)])dnl -AC_ARG_ENABLE([static], - [AS_HELP_STRING([--enable-static@<:@=PKGS@:>@], - [build static libraries @<:@default=]_LT_ENABLE_STATIC_DEFAULT[@:>@])], - [p=${PACKAGE-default} - case $enableval in - yes) enable_static=yes ;; - no) enable_static=no ;; - *) - enable_static=no - # Look at the argument we got. We use all the common list separators. - lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," - for pkg in $enableval; do - IFS="$lt_save_ifs" - if test "X$pkg" = "X$p"; then - enable_static=yes - fi - done - IFS="$lt_save_ifs" - ;; - esac], - [enable_static=]_LT_ENABLE_STATIC_DEFAULT) - - _LT_DECL([build_old_libs], [enable_static], [0], - [Whether or not to build static libraries]) -])# _LT_ENABLE_STATIC - -LT_OPTION_DEFINE([LT_INIT], [static], [_LT_ENABLE_STATIC([yes])]) -LT_OPTION_DEFINE([LT_INIT], [disable-static], [_LT_ENABLE_STATIC([no])]) - -# Old names: -AC_DEFUN([AC_ENABLE_STATIC], -[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[static]) -]) - -AC_DEFUN([AC_DISABLE_STATIC], -[_LT_SET_OPTION([LT_INIT], [disable-static]) -]) - -AU_DEFUN([AM_ENABLE_STATIC], [AC_ENABLE_STATIC($@)]) -AU_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)]) - -dnl aclocal-1.4 backwards compatibility: -dnl AC_DEFUN([AM_ENABLE_STATIC], []) -dnl AC_DEFUN([AM_DISABLE_STATIC], []) - - - -# _LT_ENABLE_FAST_INSTALL([DEFAULT]) -# ---------------------------------- -# implement the --enable-fast-install flag, and support the `fast-install' -# and `disable-fast-install' LT_INIT options. -# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. -m4_define([_LT_ENABLE_FAST_INSTALL], -[m4_define([_LT_ENABLE_FAST_INSTALL_DEFAULT], [m4_if($1, no, no, yes)])dnl -AC_ARG_ENABLE([fast-install], - [AS_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@], - [optimize for fast installation @<:@default=]_LT_ENABLE_FAST_INSTALL_DEFAULT[@:>@])], - [p=${PACKAGE-default} - case $enableval in - yes) enable_fast_install=yes ;; - no) enable_fast_install=no ;; - *) - enable_fast_install=no - # Look at the argument we got. We use all the common list separators. - lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," - for pkg in $enableval; do - IFS="$lt_save_ifs" - if test "X$pkg" = "X$p"; then - enable_fast_install=yes - fi - done - IFS="$lt_save_ifs" - ;; - esac], - [enable_fast_install=]_LT_ENABLE_FAST_INSTALL_DEFAULT) - -_LT_DECL([fast_install], [enable_fast_install], [0], - [Whether or not to optimize for fast installation])dnl -])# _LT_ENABLE_FAST_INSTALL - -LT_OPTION_DEFINE([LT_INIT], [fast-install], [_LT_ENABLE_FAST_INSTALL([yes])]) -LT_OPTION_DEFINE([LT_INIT], [disable-fast-install], [_LT_ENABLE_FAST_INSTALL([no])]) - -# Old names: -AU_DEFUN([AC_ENABLE_FAST_INSTALL], -[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[fast-install]) -AC_DIAGNOSE([obsolete], -[$0: Remove this warning and the call to _LT_SET_OPTION when you put -the `fast-install' option into LT_INIT's first parameter.]) -]) - -AU_DEFUN([AC_DISABLE_FAST_INSTALL], -[_LT_SET_OPTION([LT_INIT], [disable-fast-install]) -AC_DIAGNOSE([obsolete], -[$0: Remove this warning and the call to _LT_SET_OPTION when you put -the `disable-fast-install' option into LT_INIT's first parameter.]) -]) - -dnl aclocal-1.4 backwards compatibility: -dnl AC_DEFUN([AC_ENABLE_FAST_INSTALL], []) -dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], []) - - -# _LT_WITH_PIC([MODE]) -# -------------------- -# implement the --with-pic flag, and support the `pic-only' and `no-pic' -# LT_INIT options. -# MODE is either `yes' or `no'. If omitted, it defaults to `both'. -m4_define([_LT_WITH_PIC], -[AC_ARG_WITH([pic], - [AS_HELP_STRING([--with-pic], - [try to use only PIC/non-PIC objects @<:@default=use both@:>@])], - [pic_mode="$withval"], - [pic_mode=default]) - -test -z "$pic_mode" && pic_mode=m4_default([$1], [default]) - -_LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl -])# _LT_WITH_PIC - -LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])]) -LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])]) - -# Old name: -AU_DEFUN([AC_LIBTOOL_PICMODE], -[_LT_SET_OPTION([LT_INIT], [pic-only]) -AC_DIAGNOSE([obsolete], -[$0: Remove this warning and the call to _LT_SET_OPTION when you -put the `pic-only' option into LT_INIT's first parameter.]) -]) - -dnl aclocal-1.4 backwards compatibility: -dnl AC_DEFUN([AC_LIBTOOL_PICMODE], []) - -## ----------------- ## -## LTDL_INIT Options ## -## ----------------- ## - -m4_define([_LTDL_MODE], []) -LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive], - [m4_define([_LTDL_MODE], [nonrecursive])]) -LT_OPTION_DEFINE([LTDL_INIT], [recursive], - [m4_define([_LTDL_MODE], [recursive])]) -LT_OPTION_DEFINE([LTDL_INIT], [subproject], - [m4_define([_LTDL_MODE], [subproject])]) - -m4_define([_LTDL_TYPE], []) -LT_OPTION_DEFINE([LTDL_INIT], [installable], - [m4_define([_LTDL_TYPE], [installable])]) -LT_OPTION_DEFINE([LTDL_INIT], [convenience], - [m4_define([_LTDL_TYPE], [convenience])]) Index: sm/trunk/m4/ltsugar.m4 =================================================================== --- /issm/trunk/m4/ltsugar.m4 (revision 13394) +++ (revision ) @@ -1,123 +1,0 @@ -# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*- -# -# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc. -# Written by Gary V. Vaughan, 2004 -# -# This file is free software; the Free Software Foundation gives -# unlimited permission to copy and/or distribute it, with or without -# modifications, as long as this notice is preserved. - -# serial 6 ltsugar.m4 - -# This is to help aclocal find these macros, as it can't see m4_define. -AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])]) - - -# lt_join(SEP, ARG1, [ARG2...]) -# ----------------------------- -# Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their -# associated separator. -# Needed until we can rely on m4_join from Autoconf 2.62, since all earlier -# versions in m4sugar had bugs. -m4_define([lt_join], -[m4_if([$#], [1], [], - [$#], [2], [[$2]], - [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])]) -m4_define([_lt_join], -[m4_if([$#$2], [2], [], - [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])]) - - -# lt_car(LIST) -# lt_cdr(LIST) -# ------------ -# Manipulate m4 lists. -# These macros are necessary as long as will still need to support -# Autoconf-2.59 which quotes differently. -m4_define([lt_car], [[$1]]) -m4_define([lt_cdr], -[m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])], - [$#], 1, [], - [m4_dquote(m4_shift($@))])]) -m4_define([lt_unquote], $1) - - -# lt_append(MACRO-NAME, STRING, [SEPARATOR]) -# ------------------------------------------ -# Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'. -# Note that neither SEPARATOR nor STRING are expanded; they are appended -# to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked). -# No SEPARATOR is output if MACRO-NAME was previously undefined (different -# than defined and empty). -# -# This macro is needed until we can rely on Autoconf 2.62, since earlier -# versions of m4sugar mistakenly expanded SEPARATOR but not STRING. -m4_define([lt_append], -[m4_define([$1], - m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])]) - - - -# lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...]) -# ---------------------------------------------------------- -# Produce a SEP delimited list of all paired combinations of elements of -# PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list -# has the form PREFIXmINFIXSUFFIXn. -# Needed until we can rely on m4_combine added in Autoconf 2.62. -m4_define([lt_combine], -[m4_if(m4_eval([$# > 3]), [1], - [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl -[[m4_foreach([_Lt_prefix], [$2], - [m4_foreach([_Lt_suffix], - ]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[, - [_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])]) - - -# lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ]) -# ----------------------------------------------------------------------- -# Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited -# by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ. -m4_define([lt_if_append_uniq], -[m4_ifdef([$1], - [m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1], - [lt_append([$1], [$2], [$3])$4], - [$5])], - [lt_append([$1], [$2], [$3])$4])]) - - -# lt_dict_add(DICT, KEY, VALUE) -# ----------------------------- -m4_define([lt_dict_add], -[m4_define([$1($2)], [$3])]) - - -# lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE) -# -------------------------------------------- -m4_define([lt_dict_add_subkey], -[m4_define([$1($2:$3)], [$4])]) - - -# lt_dict_fetch(DICT, KEY, [SUBKEY]) -# ---------------------------------- -m4_define([lt_dict_fetch], -[m4_ifval([$3], - m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]), - m4_ifdef([$1($2)], [m4_defn([$1($2)])]))]) - - -# lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE]) -# ----------------------------------------------------------------- -m4_define([lt_if_dict_fetch], -[m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4], - [$5], - [$6])]) - - -# lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...]) -# -------------------------------------------------------------- -m4_define([lt_dict_filter], -[m4_if([$5], [], [], - [lt_join(m4_quote(m4_default([$4], [[, ]])), - lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]), - [lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl -]) Index: sm/trunk/m4/ltversion.m4 =================================================================== --- /issm/trunk/m4/ltversion.m4 (revision 13394) +++ (revision ) @@ -1,23 +1,0 @@ -# ltversion.m4 -- version numbers -*- Autoconf -*- -# -# Copyright (C) 2004 Free Software Foundation, Inc. -# Written by Scott James Remnant, 2004 -# -# This file is free software; the Free Software Foundation gives -# unlimited permission to copy and/or distribute it, with or without -# modifications, as long as this notice is preserved. - -# Generated from ltversion.in. - -# serial 3017 ltversion.m4 -# This file is part of GNU Libtool - -m4_define([LT_PACKAGE_VERSION], [2.2.6b]) -m4_define([LT_PACKAGE_REVISION], [1.3017]) - -AC_DEFUN([LTVERSION_VERSION], -[macro_version='2.2.6b' -macro_revision='1.3017' -_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?]) -_LT_DECL(, macro_revision, 0) -]) Index: sm/trunk/m4/lt~obsolete.m4 =================================================================== --- /issm/trunk/m4/lt~obsolete.m4 (revision 13394) +++ (revision ) @@ -1,92 +1,0 @@ -# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*- -# -# Copyright (C) 2004, 2005, 2007 Free Software Foundation, Inc. -# Written by Scott James Remnant, 2004. -# -# This file is free software; the Free Software Foundation gives -# unlimited permission to copy and/or distribute it, with or without -# modifications, as long as this notice is preserved. - -# serial 4 lt~obsolete.m4 - -# These exist entirely to fool aclocal when bootstrapping libtool. -# -# In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN) -# which have later been changed to m4_define as they aren't part of the -# exported API, or moved to Autoconf or Automake where they belong. -# -# The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN -# in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us -# using a macro with the same name in our local m4/libtool.m4 it'll -# pull the old libtool.m4 in (it doesn't see our shiny new m4_define -# and doesn't know about Autoconf macros at all.) -# -# So we provide this file, which has a silly filename so it's always -# included after everything else. This provides aclocal with the -# AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything -# because those macros already exist, or will be overwritten later. -# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6. -# -# Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here. -# Yes, that means every name once taken will need to remain here until -# we give up compatibility with versions before 1.7, at which point -# we need to keep only those names which we still refer to. - -# This is to help aclocal find these macros, as it can't see m4_define. -AC_DEFUN([LTOBSOLETE_VERSION], [m4_if([1])]) - -m4_ifndef([AC_LIBTOOL_LINKER_OPTION], [AC_DEFUN([AC_LIBTOOL_LINKER_OPTION])]) -m4_ifndef([AC_PROG_EGREP], [AC_DEFUN([AC_PROG_EGREP])]) -m4_ifndef([_LT_AC_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH])]) -m4_ifndef([_LT_AC_SHELL_INIT], [AC_DEFUN([_LT_AC_SHELL_INIT])]) -m4_ifndef([_LT_AC_SYS_LIBPATH_AIX], [AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX])]) -m4_ifndef([_LT_PROG_LTMAIN], [AC_DEFUN([_LT_PROG_LTMAIN])]) -m4_ifndef([_LT_AC_TAGVAR], [AC_DEFUN([_LT_AC_TAGVAR])]) -m4_ifndef([AC_LTDL_ENABLE_INSTALL], [AC_DEFUN([AC_LTDL_ENABLE_INSTALL])]) -m4_ifndef([AC_LTDL_PREOPEN], [AC_DEFUN([AC_LTDL_PREOPEN])]) -m4_ifndef([_LT_AC_SYS_COMPILER], [AC_DEFUN([_LT_AC_SYS_COMPILER])]) -m4_ifndef([_LT_AC_LOCK], [AC_DEFUN([_LT_AC_LOCK])]) -m4_ifndef([AC_LIBTOOL_SYS_OLD_ARCHIVE], [AC_DEFUN([AC_LIBTOOL_SYS_OLD_ARCHIVE])]) -m4_ifndef([_LT_AC_TRY_DLOPEN_SELF], [AC_DEFUN([_LT_AC_TRY_DLOPEN_SELF])]) -m4_ifndef([AC_LIBTOOL_PROG_CC_C_O], [AC_DEFUN([AC_LIBTOOL_PROG_CC_C_O])]) -m4_ifndef([AC_LIBTOOL_SYS_HARD_LINK_LOCKS], [AC_DEFUN([AC_LIBTOOL_SYS_HARD_LINK_LOCKS])]) -m4_ifndef([AC_LIBTOOL_OBJDIR], [AC_DEFUN([AC_LIBTOOL_OBJDIR])]) -m4_ifndef([AC_LTDL_OBJDIR], [AC_DEFUN([AC_LTDL_OBJDIR])]) -m4_ifndef([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH], [AC_DEFUN([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH])]) -m4_ifndef([AC_LIBTOOL_SYS_LIB_STRIP], [AC_DEFUN([AC_LIBTOOL_SYS_LIB_STRIP])]) -m4_ifndef([AC_PATH_MAGIC], [AC_DEFUN([AC_PATH_MAGIC])]) -m4_ifndef([AC_PROG_LD_GNU], [AC_DEFUN([AC_PROG_LD_GNU])]) -m4_ifndef([AC_PROG_LD_RELOAD_FLAG], [AC_DEFUN([AC_PROG_LD_RELOAD_FLAG])]) -m4_ifndef([AC_DEPLIBS_CHECK_METHOD], [AC_DEFUN([AC_DEPLIBS_CHECK_METHOD])]) -m4_ifndef([AC_LIBTOOL_PROG_COMPILER_NO_RTTI], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI])]) -m4_ifndef([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE], [AC_DEFUN([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE])]) -m4_ifndef([AC_LIBTOOL_PROG_COMPILER_PIC], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_PIC])]) -m4_ifndef([AC_LIBTOOL_PROG_LD_SHLIBS], [AC_DEFUN([AC_LIBTOOL_PROG_LD_SHLIBS])]) -m4_ifndef([AC_LIBTOOL_POSTDEP_PREDEP], [AC_DEFUN([AC_LIBTOOL_POSTDEP_PREDEP])]) -m4_ifndef([LT_AC_PROG_EGREP], [AC_DEFUN([LT_AC_PROG_EGREP])]) -m4_ifndef([LT_AC_PROG_SED], [AC_DEFUN([LT_AC_PROG_SED])]) -m4_ifndef([_LT_CC_BASENAME], [AC_DEFUN([_LT_CC_BASENAME])]) -m4_ifndef([_LT_COMPILER_BOILERPLATE], [AC_DEFUN([_LT_COMPILER_BOILERPLATE])]) -m4_ifndef([_LT_LINKER_BOILERPLATE], [AC_DEFUN([_LT_LINKER_BOILERPLATE])]) -m4_ifndef([_AC_PROG_LIBTOOL], [AC_DEFUN([_AC_PROG_LIBTOOL])]) -m4_ifndef([AC_LIBTOOL_SETUP], [AC_DEFUN([AC_LIBTOOL_SETUP])]) -m4_ifndef([_LT_AC_CHECK_DLFCN], [AC_DEFUN([_LT_AC_CHECK_DLFCN])]) -m4_ifndef([AC_LIBTOOL_SYS_DYNAMIC_LINKER], [AC_DEFUN([AC_LIBTOOL_SYS_DYNAMIC_LINKER])]) -m4_ifndef([_LT_AC_TAGCONFIG], [AC_DEFUN([_LT_AC_TAGCONFIG])]) -m4_ifndef([AC_DISABLE_FAST_INSTALL], [AC_DEFUN([AC_DISABLE_FAST_INSTALL])]) -m4_ifndef([_LT_AC_LANG_CXX], [AC_DEFUN([_LT_AC_LANG_CXX])]) -m4_ifndef([_LT_AC_LANG_F77], [AC_DEFUN([_LT_AC_LANG_F77])]) -m4_ifndef([_LT_AC_LANG_GCJ], [AC_DEFUN([_LT_AC_LANG_GCJ])]) -m4_ifndef([AC_LIBTOOL_RC], [AC_DEFUN([AC_LIBTOOL_RC])]) -m4_ifndef([AC_LIBTOOL_LANG_C_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_C_CONFIG])]) -m4_ifndef([_LT_AC_LANG_C_CONFIG], [AC_DEFUN([_LT_AC_LANG_C_CONFIG])]) -m4_ifndef([AC_LIBTOOL_LANG_CXX_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_CXX_CONFIG])]) -m4_ifndef([_LT_AC_LANG_CXX_CONFIG], [AC_DEFUN([_LT_AC_LANG_CXX_CONFIG])]) -m4_ifndef([AC_LIBTOOL_LANG_F77_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_F77_CONFIG])]) -m4_ifndef([_LT_AC_LANG_F77_CONFIG], [AC_DEFUN([_LT_AC_LANG_F77_CONFIG])]) -m4_ifndef([AC_LIBTOOL_LANG_GCJ_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_GCJ_CONFIG])]) -m4_ifndef([_LT_AC_LANG_GCJ_CONFIG], [AC_DEFUN([_LT_AC_LANG_GCJ_CONFIG])]) -m4_ifndef([AC_LIBTOOL_LANG_RC_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_RC_CONFIG])]) -m4_ifndef([_LT_AC_LANG_RC_CONFIG], [AC_DEFUN([_LT_AC_LANG_RC_CONFIG])]) -m4_ifndef([AC_LIBTOOL_CONFIG], [AC_DEFUN([AC_LIBTOOL_CONFIG])]) -m4_ifndef([_LT_AC_FILE_LTDLL_C], [AC_DEFUN([_LT_AC_FILE_LTDLL_C])]) Index: /issm/trunk/scripts/DownloadExternalPackage.py =================================================================== --- /issm/trunk/scripts/DownloadExternalPackage.py (revision 13394) +++ /issm/trunk/scripts/DownloadExternalPackage.py (revision 13395) @@ -1,37 +1,135 @@ #!/usr/bin/env python # -*- coding: ISO-8859-1 -*- +# +# TODO: Improve upon extension recognition by checking for mismatches in found targets +# and specified local file. +# -import os,sys +import os,sys,re import urllib +from HTMLParser import HTMLParser +from urllib import FancyURLopener -#Check inputs -if(len(sys.argv)!=3): raise NameError('usage: ./DownloadExternalPackage.py URL localfile') +# Start class myHTMLParser +class MyHTMLParser(HTMLParser): -url=sys.argv[1]; -localFile=sys.argv[2] + def __init__(self, pattern): + HTMLParser.__init__(self) + self.matcher = re.compile(pattern) + self.targets = [] -#Remove file if it already exists -if os.path.exists(localFile): - print "File "+ localFile +" already exists and will not be downloaded..." - sys.exit() + def handle_starttag(self, tag, attrs): + for i in attrs: + if "href" == i[0] and str(self.matcher.match(i[1])) != "None": + self.targets.append(i[1]) +# End class myHTMLParser -#Try to download from url -httpfail=-1 -try: - print "Fetching %s" % localFile - urllib.urlretrieve(url,localFile) - httpfail=0 -except Exception, e: - httpfail=1 +# Separates the URL into a directory and the file or pattern based on the +# last appearance of '/'. +if len(sys.argv) > 1: + pivot = sys.argv[1].rfind("/") + url = (sys.argv[1])[:pivot] + pivot += 1 + find = (sys.argv[1])[pivot:] +else: + print "******************************************************************************************************************************" + print "* Invalid input! *" + print "* *" + print "* Try: 'DownloadExternalPackage.py url [localFile]' *" + print "* *" + print "* Where 'URL' is the URL with an explicit package name or the URL followed by the truncated package name. And 'localFile' is *" + print "* the file name (including extension) that you would like to save as. *" + print "* *" + print "* Examples: *" + print "* *" + print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz' *" + print "* *" + print "* This is the old style and the safest way to download a package. *" + print "* *" + print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool' 'libtool.tar.gz' *" + print "* *" + print "* This is the new style. For packages like 'Libtool', which we never expect to be using multiple versions, this will *" + print "* download the most recent version and save it as the generic 'libtool.tar.gz'. *" + print "* *" + print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.' 'gsl-1.15.tar.gz' *" + print "* *" + print "* This is the new style. This is a demonstration of how this script can be used to disambiguate a package name if there *" + print "* are more than once package matching 'gsl-'. *" + print "* *" + print "* DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool' *" + print "* *" + print "* This is the new style. This will download a package with 'libtool' as a prefix and save it as its canonical name. *" + print "* *" + print "* *" + print "******************************************************************************************************************************" -#Error message in case it failed -if (httpfail): - failureMessage = ''' -=========================================================================== -Unable to download package %s from: %s -* If URL specified manually - perhaps there is a typo? -* If your network is disconnected - please reconnect -* Alternatively, you can download the above URL manually -=========================================================================== -''' % (localFile,url) - raise RuntimeError(failureMessage) +if len(sys.argv) > 2: + localFile=sys.argv[2] + print "Downloaded file will saved as: " + localFile +else: + localFile = None + print "Downloaded file will saved with the same file name." + + +print "Looking for " + find + +# As an extra precaution, if no extension is given for a particular package +# such as '.../libtool', then ensure that files found are of appropriate +# file extensions. +# +# WARNING: The external packages directory includes executable binaries with +# '.exe' extensions. As such, '.exe' is an acceptable suffix, but this is +# inherently dangerous since this script can be used to download from any +# valid website. Furthermore, if an individual attempts a "man-in-the-middle" +# attack, then the user would be capable of downloading executables from +# an untrusted source. +pattern = find + "[\w.-]*(\.tar\.gz|tar\.gz2|tgz|zip|exe)?" +parser = MyHTMLParser(pattern) + +# Creates a 'FancyURL' which allows the script to fail gracefully by catching +# HTTP error codes 30X and several 40X(where 'X' is a natural number). +urlObject = FancyURLopener() +obj = urlObject.open(url) +parser.feed(obj.read()) + +# If a file pattern was used to describe the file that should be downloaded, +# then there is the potential for multiple file matches. Currently, the script +# will detect this ambiguity and print out all the matches, while informing +# the user that he must refine his search. +# +# TODO: Prompt the user to select from a list his/her preferred target. +if len(parser.targets) > 1: + print "Could not resolve your download due to the number of hits." + print "Refine your search." + for i in parser.targets: + print i + +elif len(parser.targets) == 1: + print "Found: " + parser.targets[0] + url += "/" + parser.targets[0] + + if localFile is None: + if os.path.exists(parser.targets[0]): + print "File " + parser.targets[0] + " already exists and will not be downloaded..." + else: + urllib.urlretrieve(url, parser.targets[0]) + print "File saved as: " + parser.targets[0] + else: + if os.path.exists(localFile): + print "File "+ localFile +" already exists and will not be downloaded..." + else: + if parser.targets[0] == localFile: + print "File found and destination match." + elif parser.matcher.match(localFile) != "None": + print "File found matches destination pattern." + else: + print "WARNING: the file found \'" + parser.targets[0] + "\' does not match \'" + localFile + "\'" + print "Ensure the downloaded version is suitable." + + urllib.urlretrieve(url, localFile) + print "File saved as: " + localFile + +else: + print "No matches found!" + +obj.close() Index: /issm/trunk/scripts/automakererun.sh =================================================================== --- /issm/trunk/scripts/automakererun.sh (revision 13394) +++ /issm/trunk/scripts/automakererun.sh (revision 13395) @@ -9,3 +9,3 @@ cd $ISSM_DIR -autoreconf -iv -I m4 +autoreconf -iv Index: /issm/trunk/scripts/historyISSM.m =================================================================== --- /issm/trunk/scripts/historyISSM.m (revision 13394) +++ /issm/trunk/scripts/historyISSM.m (revision 13395) @@ -3,9 +3,6 @@ md.mesh.numberofelements md=mesh(md,'DomainOutline.exp',5000); -md=setmask(md,'',''); md=setflowequation(md,'macayeal','all'); -md=setflowequation(md,'pattyn','all','stokes','all'); md=solve(md,TransientSolutionEnum); -md=solve(md,BalancedthicknessSolutionEnum); md=solve(md,DiagnosticSolutionEnum); md=loadresultsfromcluster(md); Index: /issm/trunk/scripts/report.sh =================================================================== --- /issm/trunk/scripts/report.sh (revision 13394) +++ /issm/trunk/scripts/report.sh (revision 13395) @@ -2,143 +2,177 @@ #generate html report from info.log output file -#----------------------------# -# Initialize local variables # -#----------------------------# +#style +#{{{ +TITLE_STYLE='width="700px" cellpadding="10"' +TITLE_FONT='style="color:#6495ed; font-family:Arial, Verdana, Tahoma; font-weight: bold; font-size:25px;" align="center"' +SECTION_STYLE='width="700px" cellpadding="5"' +SECTION_FONT='style="color:#6495ed; font-family:Arial, Verdana, Tahoma; font-size:20px; font-weight: bold;" align="left"' +TABLE_STYLE='width="680px" rules=none bgcolor="#ffffdd" border=1 bordercolor="#000000" cellpadding="3"' +TABLE_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px; font-weight: normal;" align="left"' +MATLAB_STYLE='width="700px" rules=none' +MATLAB_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:12px; font-weight: normal;" align="left"' +BODY_STYLE='width="700px"' +BODY_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px;"' +BODY_FONTC=$(echo $BODY_FONT | sed -e "s/style=\"/style=\"text-align:center; /g") +BODY_FONTL=$(echo $BODY_FONT | sed -e "s/style=\"/style=\"text-align:left; /g") +FOOTER_STYLE='width="700px" cellpadding="10"' +FOOTER_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:12px; font-weight: normal;" align="center"' +#}}} #process info.log -TODAY=` cat info.log | grep "today" | awk '{printf("%s %s",$2,$3);}'` -USER=` cat info.log | grep "user" | awk '{print $2}'` -HOST_NAME=` cat info.log | grep "host" | awk '{print $2}'` -OS=` cat info.log | grep "OS" | awk '{print $2}'` -RELEASE=` cat info.log | grep "release" | awk '{print $2}'` -EL_INSTALL=`cat info.log | grep "elapsed_install" | awk '{print $2}'` -EL_RUN=` cat info.log | grep "elapsed_run" | awk '{print $2}'` -EL_TOTAL=` cat info.log | grep "elapsed_total" | awk '{print $2}'` -CRASH=` cat info.log | grep "matlab_crash:" | awk '{print $2}'` - -#Process matlab_log.log -cat matlab_log.log | egrep 'ERROR|SUCCESS|FAILURE' | grep -v "PETSC" | sed -e "s/>/\>/g" | sed -e "s/ matlab.log -cat matlab_log.log | grep "PETSC" | sed -e "s/>/\>/g" | sed -e "s/ petscerror.log -NUM_TOT=`wc -l matlab.log | awk '{print $1}'` -NUM_ERR=`cat matlab.log | grep 'ERROR' | grep -v "PETSC" | wc -l` -NUM_SUC=`cat matlab.log | grep 'SUCCESS' | wc -l` -NUM_FAI=`cat matlab.log | grep 'FAILURE' | wc -l` - -#style -H1_STYLE='width="1000px" cellpadding="20"' -H1_FONT='style="color:#6495ed; font-family:Arial, Verdana, Tahoma; font-weight: bold; font-size:35px;" align="center"' - -H2_STYLE='width="900px" cellpadding="20"' -H2_FONT='style="color:#6495ed; font-family:Arial, Verdana, Tahoma; font-size:28px; font-weight: bold;" align="left"' - -TABLE_STYLE='width="800px" rules=none bgcolor="#ffffdd" border=1 bordercolor="#000000" cellpadding="3"' -TABLE_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px; font-weight: normal;" align="left"' - -MATLAB_STYLE='width="1000px" rules=none' -MATLAB_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:12px; font-weight: normal;" align="left"' - -BODY_STYLE='width="800px"' -BODY_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px;"' - -FOOTER_STYLE='width="800px" cellpadding="10"' -FOOTER_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:12px; font-weight: normal;" align="center"' - -#style 2 -BODY_FONTC=`echo $BODY_FONT | sed -e "s/style=\"/style=\"text-align:center; /g"` -BODY_FONTL=`echo $BODY_FONT | sed -e "s/style=\"/style=\"text-align:left; /g"` - -#create some variables -if [ $(ls -1 $ISSM_DIR/bin | wc -l) -le 20 ]; -then +#{{{ +if [ ! -f info.log ]; then + echo "File info.log not found!" >&2 # Error message to stderr. + exit 1 +fi +NRNAME=$( cat info.log | grep "name:" | awk '{$1=""}1') +TODAY=$( cat info.log | grep "today" | awk '{printf("%s %s",$2,$3);}') +USER=$( cat info.log | grep "user" | awk '{print $2}') +HOST_NAME=$( cat info.log | grep "host" | awk '{print $2}') +OS=$( cat info.log | grep "OS" | awk '{print $2}') +RELEASE=$( cat info.log | grep "release" | awk '{print $2}') +EL_INSTALL=$( cat info.log | grep "elapsed_install" | awk '{print $2}') +EL_TOTAL=$( cat info.log | grep "elapsed_total" | awk '{print $2}') +IS_MATLAB=$( cat info.log | grep "is_matlab" | awk '{print $2}') +IS_PYTHON=$( cat info.log | grep "is_python" | awk '{print $2}') +EL_MATLAB=$( cat info.log | grep "elapsed_matlab" | awk '{print $2}') +EL_PYTHON=$( cat info.log | grep "elapsed_python" | awk '{print $2}') +CRASH_MATLAB=$(cat info.log | grep "matlab_crash:" | awk '{print $2}') +CRASH_PYTHON=$(cat info.log | grep "python_crash:" | awk '{print $2}') + +#Did installation work? +if [ $(ls -1 $ISSM_DIR/bin | wc -l) -le 20 ]; then IS_INSTALL=0 else IS_INSTALL=1 fi - -#-------------------# -# build report.html # -#-------------------# - -#first: summary -cat << END > summary.html +#}}} + +#1. summary table +#{{{ +rm report.html +cat << END >> report.html
-
ISSM Nightly run report
+
$NRNAME
- + - - - - - - - - - - +
host: $HOST_NAMEhost: $HOST_NAME ($OS) date: $TODAY
OS: $OS user: $USER
status: STATUS release: $RELEASE
number of successes: $NUM_SUC/$NUM_TOT total elapsed time: $EL_TOTAL
number of errors: $NUM_ERR/$NUM_TOT - installation elapsed time: $EL_INSTALL
number of failures: $NUM_FAI/$NUM_TOT -execution elapsed time: $EL_RUN
+
+END +# }}} + +#stop if did not install +#{{{ +if [ $IS_INSTALL -eq 0 ]; then + cat << END >> report.html + + +
Status: Installation failed
+
ISSM nightly run report
+
+END +exit 0 +fi +#}}} + +#2. matlab report +if [ $IS_MATLAB -eq 1 ]; then +#Process matlab_log.log {{{ +cat matlab_log.log | egrep 'ERROR|SUCCESS|FAILURE' | grep -v "PETSC" | sed -e "s/>/\>/g" | sed -e "s/ matlab.log +cat matlab.log | grep -v "SUCCESS" > matlab_short.log +cat matlab_log.log | grep "PETSC" | sed -e "s/>/\>/g" | sed -e "s/ petscerror.log +NUM_MATLAB_TOT=$(wc -l matlab.log | awk '{print $1}') +NUM_MATLAB_ERR=$(cat matlab.log | grep 'ERROR' | grep -v "PETSC" | wc -l) +NUM_MATLAB_SUC=$(cat matlab.log | grep 'SUCCESS' | wc -l) +NUM_MATLAB_FAI=$(cat matlab.log | grep 'FAILURE' | wc -l) +#}}} +#write report {{{ +cat << END >> report.html +
Matlab tests
+ +$(if [ $CRASH_MATLAB -eq 0 ]; then +echo "" +else + echo "" +fi) + + + + +
Status: all test desks have been run
Status: Matlab crashed
Total execution time: $EL_MATLAB
Number of successes: $NUM_MATLAB_SUC/$NUM_MATLAB_TOT
Number of errors: $NUM_MATLAB_ERR/$NUM_MATLAB_TOT
Number of failures: $NUM_MATLAB_FAI/$NUM_MATLAB_TOT
+END +#}}} +fi + +#2. python report +if [ $IS_PYTHON -eq 1 ]; then +#Process python_log.log {{{ +cat python_log.log | egrep 'ERROR|SUCCESS|FAILURE' | grep -v "PETSC" | sed -e "s/>/\>/g" | sed -e "s/ python.log +cat python.log | grep -v "SUCCESS" > python_short.log +cat python_log.log | grep "PETSC" | sed -e "s/>/\>/g" | sed -e "s/ petscerror.log +NUM_PYTHON_TOT=$(wc -l python.log | awk '{print $1}') +NUM_PYTHON_ERR=$(cat python.log | grep 'ERROR' | grep -v "PETSC" | wc -l) +NUM_PYTHON_SUC=$(cat python.log | grep 'SUCCESS' | wc -l) +NUM_PYTHON_FAI=$(cat python.log | grep 'FAILURE' | wc -l) +#}}} +#write report {{{ +cat << END >> report.html +
Python tests
+ +$(if [ $CRASH_PYTHON -eq 0 ]; then + echo "" +else + echo "" +fi) + + + + +
Status: all test desks have been run
Status: Python crashed
Total execution time: $EL_PYTHON
Number of successes: $NUM_PYTHON_SUC/$NUM_PYTHON_TOT
Number of errors: $NUM_PYTHON_ERR/$NUM_PYTHON_TOT
Number of failures: $NUM_PYTHON_FAI/$NUM_PYTHON_TOT
+END +#}}} +fi + +#3. Matlab and python tables +if [ $IS_MATLAB -eq 1 ]; then +#Matlab{{{ +#display table ONLY if installation worked and there has been at leat one FAILURE or ERROR +if [ $IS_INSTALL -eq 1 ] && [ $NUM_MATLAB_TOT -gt 1 ] && [ $NUM_MATLAB_SUC -ne $NUM_MATLAB_TOT ] +then + cat << END >> report.html +
List of Matlab tests
+ + + + + + + -
ResultToleranceTest idTest nameField checked
-
-END - -#update status -if [ $IS_INSTALL -eq 1 ] -then - if [ $CRASH -eq 0 ] - then - cat summary.html | sed -e "s/STATUS/all test desks have been run<\/span>/g" > summary2.html - else - cat summary.html | sed -e "s/STATUS/installation successful but Matlab crashed<\/span>/g" > summary2.html - fi -else - cat summary.html | sed -e "s/STATUS/installation failed<\/span>/g" > summary2.html -fi -mv summary2.html summary.html - -#report table -if [ $IS_INSTALL -eq 1 ]; -then - cat << END > content.html -
List of tests
- - - - - - - - -$(cat matlab.log | while read line +$(cat matlab_short.log | while read line do echo "" - - #get status STATUS=`echo $line | awk '{print $1}'` - #FAILURE if [ "$STATUS" = "FAILURE" ] then - FONTC=$(echo "$BODY_FONTC bgcolor=#ffff00"); FONTL=$(echo "$BODY_FONTL bgcolor=#ffff00"); echo $line | awk -v FONTC="$FONTC" -v FONTL="$FONTL" ' { printf("\n\n\n\n\n\n",FONTL,$1,FONTC,$3,FONTC,$6,FONTL,$9,FONTL,$11);} - '; - - else - + '; + else #SUCCESS if [ "$STATUS" = "SUCCESS" ] @@ -146,18 +180,16 @@ FONTC=$(echo "$BODY_FONTC bgcolor=#ddffdd") FONTL=$(echo "$BODY_FONTL bgcolor=#ddffdd") + #do not write anything #ERROR else FONTC=$(echo "$BODY_FONTC bgcolor=#ffdddd id=ERROR") FONTL=$(echo "$BODY_FONTL bgcolor=#ffdddd") + echo $line | awk -v FONTC="$FONTC" -v FONTL="$FONTL" ' + { printf("\n\n\n\n\n\n",FONTL,$1,FONTL,$3,$4,$5,FONTC,$8,FONTL,$11,FONTL,$13);} + '; fi - - echo $line | awk -v FONTC="$FONTC" -v FONTL="$FONTL" ' - { printf("\n\n\n\n\n\n",FONTL,$1,FONTL,$3,$4,$5,FONTC,$8,FONTL,$11,FONTL,$13);} - '; fi - echo "" - done ) @@ -165,13 +197,70 @@
END -else - mktemp content.html -fi - -#Matlab error report -if [ -e matlaberror.log ] +fi +#}}} +fi +if [ $IS_PYTHON -eq 1 ]; then +#python{{{ +#display table ONLY if installation worked and there has been at leat one FAILURE or ERROR +if [ $IS_INSTALL -eq 1 ] && [ $NUM_PYTHON_TOT -gt 1 ] && [ $NUM_PYTHON_SUC -ne $NUM_PYTHON_TOT ] then - cat << END > matlaberror.html -
ResultToleranceTest idTest nameField checked
%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s
Matlab errors
+ cat << END >> report.html +
List of Python tests
+ + + + + + + + + $(cat matlab_short.log | while read line +do + echo "" + STATUS=`echo $line | awk '{print $1}'` + + #FAILURE + if [ "$STATUS" = "FAILURE" ] + then + + FONTC=$(echo "$BODY_FONTC bgcolor=#ffff00"); + FONTL=$(echo "$BODY_FONTL bgcolor=#ffff00"); + echo $line | awk -v FONTC="$FONTC" -v FONTL="$FONTL" ' + { printf("\n\n\n\n\n\n",FONTL,$1,FONTC,$3,FONTC,$6,FONTL,$9,FONTL,$11);} + '; + + else + + #SUCCESS + if [ "$STATUS" = "SUCCESS" ] + then + FONTC=$(echo "$BODY_FONTC bgcolor=#ddffdd") + FONTL=$(echo "$BODY_FONTL bgcolor=#ddffdd") + #do not write anything + #ERROR + else + FONTC=$(echo "$BODY_FONTC bgcolor=#ffdddd id=ERROR") + FONTL=$(echo "$BODY_FONTL bgcolor=#ffdddd") + echo $line | awk -v FONTC="$FONTC" -v FONTL="$FONTL" ' + { printf("\n\n\n\n\n\n",FONTL,$1,FONTL,$3,$4,$5,FONTC,$8,FONTL,$11,FONTL,$13);} + '; + fi + + fi + echo "" +done +) +
ResultToleranceTest idTest nameField checked
%s%s%s%s%s%s%s%s%s%s%s%s
+
+END +fi +#}}} +fi + +#4. Error report +if [ $IS_MATLAB -eq 1 ] && [ -s matlaberror.log ]; then +#Matlab {{{ +cat << END >> report.html +
Matlab errors

 END
-else
-	mktemp petscerror.html
-fi
-
-#last footer
-cat << END > footer.html
+#}}}
+fi
+
+#last: footer
+#{{{
+cat << END >> report.html
 

 
ISSM nightly run report

 
 END
-
-#concatenate files
-cat summary.html content.html matlaberror.html petscerror.html footer.html > report.html
-rm  summary.html content.html footer.html matlaberror.html petscerror.html matlab.log
+#}}}
Index: /issm/trunk/src/Makefile.am
===================================================================
--- /issm/trunk/src/Makefile.am	(revision 13394)
+++ /issm/trunk/src/Makefile.am	(revision 13395)
@@ -1,2 +1,2 @@
-EXTRA_DIST =  perl  pro 
-SUBDIRS = c modules m  py
+EXTRA_DIST =  perl pro py
+SUBDIRS = c modules m
Index: /issm/trunk/src/ad/todo
===================================================================
--- /issm/trunk/src/ad/todo	(revision 13394)
+++ /issm/trunk/src/ad/todo	(revision 13395)
@@ -43,2 +43,16 @@
 
 Replace memcpy, realloc with x layers.  Replace all calls to malloc and free in the code.
+
+
+
+Questions: 
+set of active IssmDouble variables different from set of independent variables activated with <<=? 
+same thing dependent variables? 
+
+
+
+Bullet points: 
+- nightly run on with adolc compiled, running from test2000 on.  once a day.
+- run valgrind on new adolc or old adolc. send a text on how to run it. 
+- make gdb wrapper.
+- think about ModelProcessor setup. need to keep track, before we partition, on cpu 0, of the independent declarations. 
Index: /issm/trunk/src/c/Container/DataSet.cpp
===================================================================
--- /issm/trunk/src/c/Container/DataSet.cpp	(revision 13394)
+++ /issm/trunk/src/c/Container/DataSet.cpp	(revision 13395)
@@ -18,5 +18,5 @@
 
 #include "./DataSet.h"
-#include "../objects/objects.h"
+#include "../classes/objects/objects.h"
 #include "../shared/shared.h"
 #include "../io/io.h"
@@ -133,5 +133,5 @@
 	vector::iterator object;
 
-	if(this==NULL)_error2_("trying to echo a NULL dataset");
+	if(this==NULL)_error_("trying to echo a NULL dataset");
 
 	_pprintLine_("DataSet echo: " << objects.size() << " objects");
@@ -150,5 +150,5 @@
 	vector::iterator object;
 
-	if(this==NULL)_error2_("trying to echo a NULL dataset");
+	if(this==NULL)_error_("trying to echo a NULL dataset");
 
 	_pprintLine_("DataSet echo: " << objects.size() << " objects");
@@ -194,9 +194,9 @@
 
 	_assert_(this);
-	if(!sorted)_error2_("trying to binary search on a non-sorted dataset!");
+	if(!sorted)_error_("trying to binary search on a non-sorted dataset!");
 
 	/*Carry out a binary search on the sorted_ids: */
 	if(!binary_search(&id_offset,eid, sorted_ids,objects.size())){
-		_error2_("could not find object with id " << eid << " in DataSet " << EnumToStringx(enum_type));
+		_error_("could not find object with id " << eid << " in DataSet " << EnumToStringx(enum_type));
 	}
 
@@ -259,6 +259,6 @@
 	/*Only sort if we are not already sorted: */
 	if(!sorted){
-		_error2_("not implemented yet!");
-	}
-}
-/*}}}*/
+		_error_("not implemented yet!");
+	}
+}
+/*}}}*/
Index: /issm/trunk/src/c/Container/DataSet.h
===================================================================
--- /issm/trunk/src/c/Container/DataSet.h	(revision 13394)
+++ /issm/trunk/src/c/Container/DataSet.h	(revision 13395)
@@ -7,10 +7,9 @@
 
 #include 
-#include "../objects/Object.h"
+#include "../classes/objects/Object.h"
 #include "../toolkits/toolkits.h"
 #include "../EnumDefinitions/EnumDefinitions.h"
 
 /*forward declarations */
-
 class Elements;
 class Loads;
Index: /issm/trunk/src/c/Container/Elements.cpp
===================================================================
--- /issm/trunk/src/c/Container/Elements.cpp	(revision 13394)
+++ /issm/trunk/src/c/Container/Elements.cpp	(revision 13395)
@@ -166,4 +166,6 @@
 void Elements::ToResults(Results* results,Parameters* parameters){
 
+	int i;
+	
 	extern int my_rank;
 	extern int num_procs;
@@ -175,5 +177,5 @@
 	IssmDouble *resultstimes = NULL;
 	IssmDouble *vector_serial= NULL;
-	Vector*     vector       = NULL;
+	Vector*     vector       = NULL;
 	bool   io_gather;
 	bool   results_as_patches;
@@ -203,5 +205,5 @@
 		/*see what the first element of this partition has in stock (this is common to all partitions)*/
 		if(my_rank==minrank){
-			if(this->Size()==0) _error2_("Cannot write results because there is no element??");
+			if(this->Size()==0) _error_("Cannot write results because there is no element??");
 			Element* element=(Element*)this->GetObjectByOffset(0);
 			element->ListResultsInfo(&resultsenums,&resultssizes,&resultstimes,&resultssteps,&numberofresults);
@@ -232,6 +234,6 @@
 			if(resultssizes[i]==P1Enum)      vectorsize=numberofvertices;
 			else if(resultssizes[i]==P0Enum) vectorsize=numberofelements;
-			else _error2_("Unkown result size: " << EnumToStringx(resultssizes[i]));
-			vector=new Vector(vectorsize);
+			else _error_("Unkown result size: " << EnumToStringx(resultssizes[i]));
+			vector=new Vector(vectorsize);
 
 			for(int j=0;jSize();j++){
@@ -245,5 +247,12 @@
 			if(my_rank==0){
 				/*No need to add this vector for all cpus*/
-				results->AddObject(new DoubleVecExternalResult(results->Size()+1,resultsenums[i],vector_serial,vectorsize,resultssteps[i],resultstimes[i]));
+				#ifdef _HAVE_ADOLC_
+				IssmPDouble* vector_serial_passive=xNew(vectorsize);
+				for(int k=0;k(vector_serial[k]);
+				results->AddObject(new GenericExternalResult(results->Size()+1,resultsenums[i],vector_serial_passive,vectorsize,1,resultssteps[i],resultstimes[i]));
+				xDelete(vector_serial_passive);
+				#else
+				results->AddObject(new GenericExternalResult(results->Size()+1,resultsenums[i],vector_serial,vectorsize,1,resultssteps[i],resultstimes[i]));
+				#endif
 			}
 
@@ -262,7 +271,14 @@
 		/*create result object and add to results dataset:*/
 		if (patch->maxvertices && patch->maxnodes){
-			results->AddObject(new IntExternalResult(results->Size()+1,PatchVerticesEnum,patch->maxvertices,1,0));
-			results->AddObject(new IntExternalResult(results->Size()+1,PatchNodesEnum,   patch->maxnodes,1,0));
-			results->AddObject(new DoubleMatExternalResult(results->Size()+1,PatchEnum,  patch->values,patch->numrows,patch->numcols,1,0));
+			results->AddObject(new GenericExternalResult(results->Size()+1,PatchVerticesEnum,patch->maxvertices,1,0));
+			results->AddObject(new GenericExternalResult(results->Size()+1,PatchNodesEnum,   patch->maxnodes,1,0));
+			#ifdef _HAVE_ADOLC_
+			IssmPDouble* values_passive=xNew(patch->numrows*patch->numcols);
+			for(int k=0;k<(patch->numrows*patch->numcols);k++)values_passive[k]=reCast(patch->values[k]);
+			results->AddObject(new GenericExternalResult(results->Size()+1,PatchEnum,  values_passive,patch->numrows,patch->numcols,1,0));
+			xDelete(values_passive);
+			#else
+			results->AddObject(new GenericExternalResult(results->Size()+1,PatchEnum,  patch->values,patch->numrows,patch->numcols,1,0));
+			#endif
 		}
 	}
Index: /issm/trunk/src/c/Container/Inputs.cpp
===================================================================
--- /issm/trunk/src/c/Container/Inputs.cpp	(revision 13394)
+++ /issm/trunk/src/c/Container/Inputs.cpp	(revision 13395)
@@ -57,5 +57,5 @@
 		/*we could not find an input with the correct enum type. No defaults values were provided, 
 		 * error out: */
-		_error2_("could not find input with enum type " << enum_type << " (" << EnumToStringx(enum_type) << ")");
+		_error_("could not find input with enum type " << enum_type << " (" << EnumToStringx(enum_type) << ")");
 	}
 
@@ -85,5 +85,5 @@
 		/*we could not find an input with the correct enum type. No defaults values were provided, 
 		 * error out: */
-		_error2_("could not find input with enum type " << enum_type << " (" << EnumToStringx(enum_type) << ")");
+		_error_("could not find input with enum type " << enum_type << " (" << EnumToStringx(enum_type) << ")");
 	}
 
@@ -113,5 +113,5 @@
 		/*we could not find an input with the correct enum type. No defaults values were provided, 
 		 * error out: */
-		_error2_("could not find input with enum type " << enum_type << " (" << EnumToStringx(enum_type) << ")");
+		_error_("could not find input with enum type " << enum_type << " (" << EnumToStringx(enum_type) << ")");
 	}
 
@@ -141,5 +141,5 @@
 		/*we could not find an input with the correct enum type. No defaults values were provided, 
 		 * error out: */
-		_error2_("could not find input with enum type " << enum_type << " (" << EnumToStringx(enum_type) << ")");
+		_error_("could not find input with enum type " << enum_type << " (" << EnumToStringx(enum_type) << ")");
 	}
 
@@ -213,5 +213,5 @@
 
 	/*some checks: */
-	if(!constrain_input) _error2_("input " << EnumToStringx(constrain_enum) << " could not be found!");
+	if(!constrain_input) _error_("input " << EnumToStringx(constrain_enum) << " could not be found!");
 
 	/*Apply ContrainMin: */
@@ -254,5 +254,5 @@
 	}
 	else{
-		_error2_("Input " << EnumToStringx(enumtype) << " not found");
+		_error_("Input " << EnumToStringx(enumtype) << " not found");
 	}
 
@@ -275,5 +275,5 @@
 	}
 	else{
-		_error2_("Input " << EnumToStringx(enumtype) << " not found");
+		_error_("Input " << EnumToStringx(enumtype) << " not found");
 	}
 
@@ -296,5 +296,5 @@
 	}
 	else{
-		_error2_("Input " << EnumToStringx(enumtype) << " not found");
+		_error_("Input " << EnumToStringx(enumtype) << " not found");
 	}
 
@@ -317,5 +317,5 @@
 	}
 	else{
-		_error2_("Input " << EnumToStringx(enumtype) << " not found");
+		_error_("Input " << EnumToStringx(enumtype) << " not found");
 	}
 
@@ -369,5 +369,5 @@
 	/*Make a copy of the original input: */
 	original=(Input*)this->GetInput(original_enum);
-	if(!original)_error2_("could not find input with enum: " << EnumToStringx(original_enum)); 
+	if(!original)_error_("could not find input with enum: " << EnumToStringx(original_enum)); 
 	copy=(Input*)original->copy();
 
@@ -416,6 +416,6 @@
 
 	/*some checks: */
-	if(!xinput) _error2_("input " << EnumToStringx(MeshXEnum) << " could not be found!");
-	if(!yinput) _error2_("input " << EnumToStringx(MeshYEnum) << " could not be found!");
+	if(!xinput) _error_("input " << EnumToStringx(MeshXEnum) << " could not be found!");
+	if(!yinput) _error_("input " << EnumToStringx(MeshYEnum) << " could not be found!");
 
 	/*Apply AXPY: */
Index: /issm/trunk/src/c/Container/Observations.cpp
===================================================================
--- /issm/trunk/src/c/Container/Observations.cpp	(revision 13394)
+++ /issm/trunk/src/c/Container/Observations.cpp	(revision 13395)
@@ -19,4 +19,6 @@
 #include "./Observations.h"
 #include "../shared/shared.h"
+#include "../Container/Container.h"
+#include "../classes/classes.h"
 #include "../include/include.h"
 #include "../modules/modules.h"
@@ -34,13 +36,12 @@
 }
 /*}}}*/
-/*FUNCTION Observations::Observations(IssmDouble* observations_list,IssmDouble* x,IssmDouble* y,int n,Options* options){{{*/
-Observations::Observations(IssmDouble* observations_list,IssmDouble* x,IssmDouble* y,int n,Options* options){
+/*FUNCTION Observations::Observations(IssmPDouble* observations_list,IssmPDouble* x,IssmPDouble* y,int n,Options* options){{{*/
+Observations::Observations(IssmPDouble* observations_list,IssmPDouble* x,IssmPDouble* y,int n,Options* options){
 
 	/*Intermediaries*/
 	int          i,j,maxdepth,level,counter,index;
 	int          xi,yi;
-	IssmDouble       xmin,xmax,ymin,ymax;
-	IssmDouble       offset,minlength,minspacing,mintrimming,maxtrimming;
-	int         *indices     = NULL;
+	IssmPDouble  xmin,xmax,ymin,ymax;
+	IssmPDouble  offset,minlength,minspacing,mintrimming,maxtrimming;
 	Observation *observation = NULL;
 
@@ -59,15 +60,15 @@
 	options->Get(&maxtrimming,"maxtrimming",+1.e+21);
 	options->Get(&minspacing,"minspacing",0.01);
-	if(minspacing<=0) _error2_("minspacing must > 0");
+	if(minspacing<=0) _error_("minspacing must > 0");
 
 	/*Get Minimum box size*/
 	if(options->GetOption("boxlength")){
 		options->Get(&minlength,"boxlength");
-		if(minlength<=0)_error2_("boxlength should be a positive number");
-		maxdepth=int(log(max(xmax-xmin,ymax-ymin)/minlength +1)/log(2.0));
+		if(minlength<=0)_error_("boxlength should be a positive number");
+		maxdepth=reCast(log(max(xmax-xmin,ymax-ymin)/minlength +1)/log(2.0));
 	}
 	else{
 		maxdepth = 30;
-		minlength=max(xmax-xmin,ymax-ymin)/IssmDouble((1L<(tempnobs);
-		dists   = xNew(tempnobs);
+		dists   = xNew(tempnobs);
 	}
 	nobs = 0;
@@ -225,12 +226,12 @@
 		}
 	}  
-	xDelete(dists);
+	xDelete(dists);
 	xDelete(tempindices);
 
 	if(nobs){
 		/*Allocate vectors*/
-		x   = xNew(nobs);
-		y   = xNew(nobs);
-		obs = xNew(nobs);
+		x   = xNew(nobs);
+		y   = xNew(nobs);
+		obs = xNew(nobs);
 
 		/*Loop over all observations and fill in x, y and obs*/
@@ -248,12 +249,12 @@
 	*pnobs=nobs;
 }/*}}}*/
-/*FUNCTION Observations::ObservationList(IssmDouble **px,IssmDouble **py,IssmDouble **pobs,int* pnobs){{{*/
-void Observations::ObservationList(IssmDouble **px,IssmDouble **py,IssmDouble **pobs,int* pnobs){
+/*FUNCTION Observations::ObservationList(IssmPDouble **px,IssmPDouble **py,IssmPDouble **pobs,int* pnobs){{{*/
+void Observations::ObservationList(IssmPDouble **px,IssmPDouble **py,IssmPDouble **pobs,int* pnobs){
 
 	/*Output and Intermediaries*/
 	int          nobs;
-	IssmDouble      *x            = NULL;
-	IssmDouble      *y            = NULL;
-	IssmDouble      *obs          = NULL;
+	IssmPDouble *x            = NULL;
+	IssmPDouble *y            = NULL;
+	IssmPDouble *obs          = NULL;
 	Observation *observation  = NULL;
 
@@ -261,7 +262,7 @@
 
 	if(nobs){
-		x   = xNew(nobs);
-		y   = xNew(nobs);
-		obs = xNew(nobs);
+		x   = xNew(nobs);
+		y   = xNew(nobs);
+		obs = xNew(nobs);
 		for(int i=0;iSize();i++){
 			observation=(Observation*)this->GetObjectByOffset(i);
@@ -277,13 +278,13 @@
 }/*}}}*/
 /*FUNCTION Observations::InterpolationIDW{{{*/
-void Observations::InterpolationIDW(IssmDouble *pprediction,IssmDouble x_interp,IssmDouble y_interp,IssmDouble radius,int mindata,int maxdata,IssmDouble power){
+void Observations::InterpolationIDW(IssmPDouble *pprediction,IssmPDouble x_interp,IssmPDouble y_interp,IssmPDouble radius,int mindata,int maxdata,IssmPDouble power){
 
 	/*Intermediaries*/
-	int    i,n_obs;
-	IssmDouble prediction;
-	IssmDouble numerator,denominator,h,weight;
-	IssmDouble *x   = NULL;
-	IssmDouble *y   = NULL;
-	IssmDouble *obs = NULL;
+	int         i,n_obs;
+	IssmPDouble prediction;
+	IssmPDouble numerator,denominator,h,weight;
+	IssmPDouble *x   = NULL;
+	IssmPDouble *y   = NULL;
+	IssmPDouble *obs = NULL;
 
 	/*Some checks*/
@@ -321,24 +322,24 @@
 	/*clean-up*/
 	*pprediction = prediction;
-	xDelete(x);
-	xDelete(y);
-	xDelete(obs);
+	xDelete(x);
+	xDelete(y);
+	xDelete(obs);
 }/*}}}*/
 /*FUNCTION Observations::InterpolationKriging{{{*/
-void Observations::InterpolationKriging(IssmDouble *pprediction,IssmDouble *perror,IssmDouble x_interp,IssmDouble y_interp,IssmDouble radius,int mindata,int maxdata,Variogram* variogram){
+void Observations::InterpolationKriging(IssmPDouble *pprediction,IssmPDouble *perror,IssmPDouble x_interp,IssmPDouble y_interp,IssmPDouble radius,int mindata,int maxdata,Variogram* variogram){
 
 	/*Intermediaries*/
 	int           i,j,n_obs;
-	IssmDouble        prediction,error;
-	IssmDouble        numerator,denominator,ratio;
-	IssmDouble       *x            = NULL;
-	IssmDouble       *y            = NULL;
-	IssmDouble       *obs          = NULL;
-	IssmDouble       *Gamma        = NULL;
-	IssmDouble       *GinvG0       = NULL;
-	IssmDouble       *Ginv1        = NULL;
-	IssmDouble       *GinvZ        = NULL;
-	IssmDouble       *gamma0       = NULL;
-	IssmDouble       *ones         = NULL;
+	IssmPDouble   prediction,error;
+	IssmPDouble   numerator,denominator,ratio;
+	IssmPDouble  *x            = NULL;
+	IssmPDouble  *y            = NULL;
+	IssmPDouble  *obs          = NULL;
+	IssmPDouble  *Gamma        = NULL;
+	IssmPDouble  *GinvG0       = NULL;
+	IssmPDouble  *Ginv1        = NULL;
+	IssmPDouble  *GinvZ        = NULL;
+	IssmPDouble  *gamma0       = NULL;
+	IssmPDouble  *ones         = NULL;
 
 	/*Some checks*/
@@ -360,7 +361,7 @@
 
 	/*Allocate intermediary matrix and vectors*/
-	Gamma  = xNew(n_obs*n_obs);
-	gamma0 = xNew(n_obs);
-	ones   = xNew(n_obs);
+	Gamma  = xNew(n_obs*n_obs);
+	gamma0 = xNew(n_obs);
+	ones   = xNew(n_obs);
 
 	/*First: Create semivariogram matrix for observations*/
@@ -380,9 +381,9 @@
 	/*Solve the three linear systems*/
 #if _HAVE_GSL_
-	SolverxGsl(&GinvG0,Gamma,gamma0,n_obs); // Gamma^-1 gamma0
-	SolverxGsl(&Ginv1, Gamma,ones,n_obs);   // Gamma^-1 ones
-	SolverxGsl(&GinvZ, Gamma,obs,n_obs);    // Gamma^-1 Z
+	SolverxSeq(&GinvG0,Gamma,gamma0,n_obs); // Gamma^-1 gamma0
+	SolverxSeq(&Ginv1, Gamma,ones,n_obs);   // Gamma^-1 ones
+	SolverxSeq(&GinvZ, Gamma,obs,n_obs);    // Gamma^-1 Z
 #else
-	_error2_("GSL is required");
+	_error_("GSL is required");
 #endif
 
@@ -401,20 +402,20 @@
 	*pprediction = prediction;
 	*perror = error;
-	xDelete(x);
-	xDelete(y);
-	xDelete(obs);
-	xDelete(Gamma);
-	xDelete(gamma0);
-	xDelete(ones);
-	xDelete(GinvG0);
-	xDelete(Ginv1);
-	xDelete(GinvZ);
+	xDelete(x);
+	xDelete(y);
+	xDelete(obs);
+	xDelete(Gamma);
+	xDelete(gamma0);
+	xDelete(ones);
+	xDelete(GinvG0);
+	xDelete(Ginv1);
+	xDelete(GinvZ);
 
 }/*}}}*/
 /*FUNCTION Observations::InterpolationNearestNeighbor{{{*/
-void Observations::InterpolationNearestNeighbor(IssmDouble *pprediction,IssmDouble x_interp,IssmDouble y_interp,IssmDouble radius){
+void Observations::InterpolationNearestNeighbor(IssmPDouble *pprediction,IssmPDouble x_interp,IssmPDouble y_interp,IssmPDouble radius){
 
 	/*Intermediaries*/
-	IssmDouble        x,y,obs;
+	IssmPDouble x,y,obs;
 
 	/*Get clostest observation*/
@@ -425,5 +426,5 @@
 }/*}}}*/
 /*FUNCTION Observations::QuadtreeColoring{{{*/
-void Observations::QuadtreeColoring(IssmDouble* A,IssmDouble *x,IssmDouble *y,int n){
+void Observations::QuadtreeColoring(IssmPDouble* A,IssmPDouble *x,IssmPDouble *y,int n){
 
 	int xi,yi,level;
@@ -432,18 +433,18 @@
 		this->quadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]);
 		this->quadtree->QuadtreeDepth(&level,xi,yi);
-		A[i]=(IssmDouble)level;
+		A[i]=(IssmPDouble)level;
 	}
 
 }/*}}}*/
 /*FUNCTION Observations::Variomap{{{*/
-void Observations::Variomap(IssmDouble* gamma,IssmDouble *x,int n){
+void Observations::Variomap(IssmPDouble* gamma,IssmPDouble *x,int n){
 
 	/*Output and Intermediaries*/
 	int          i,j,k;
-	IssmDouble       distance;
+	IssmPDouble  distance;
 	Observation *observation1 = NULL;
 	Observation *observation2 = NULL;
 
-	IssmDouble *counter = xNew(n);
+	IssmPDouble *counter = xNew(n);
 	for(j=0;j(counter);
-}/*}}}*/
+	xDelete(counter);
+}/*}}}*/
Index: /issm/trunk/src/c/Container/Observations.h
===================================================================
--- /issm/trunk/src/c/Container/Observations.h	(revision 13394)
+++ /issm/trunk/src/c/Container/Observations.h	(revision 13395)
@@ -7,4 +7,5 @@
 
 #include "../include/include.h"
+#include "../classes/objects/Options/GenericOption.h"
 
 class Quadtree;
Index: /issm/trunk/src/c/Container/Options.cpp
===================================================================
--- /issm/trunk/src/c/Container/Options.cpp	(revision 13394)
+++ /issm/trunk/src/c/Container/Options.cpp	(revision 13395)
@@ -19,4 +19,5 @@
 #include "../io/io.h"
 #include "../include/include.h"
+#include "../classes/classes.h"
 #include "../shared/shared.h"
 #include "../EnumDefinitions/EnumDefinitions.h"
@@ -40,4 +41,6 @@
 int  Options::AddOption(Option* in_option){
 
+	char* name=NULL;
+	
 	vector::iterator object;
 	Option* option=NULL;
@@ -47,8 +50,10 @@
 
 	/*Also, check the option name*/
-	if(!in_option->name) _error2_("input option has an empty name");
-	if(strchr(in_option->name,'.')) _error2_("Option \"" << in_option->name << "\" has a protected character \".\"");
-	if(strchr(in_option->name,'[')) _error2_("Option \"" << in_option->name << "\" has a protected character \"[\"");
-	if(strchr(in_option->name,']')) _error2_("Option \"" << in_option->name << "\" has a protected character \"]\"");
+	name=in_option->Name();
+
+	if(!name) _error_("input option has an empty name");
+	if(strchr(name,'.')) _error_("Option \"" << name << "\" has a protected character \".\"");
+	if(strchr(name,'[')) _error_("Option \"" << name << "\" has a protected character \"[\"");
+	if(strchr(name,']')) _error_("Option \"" << name << "\" has a protected character \"]\"");
 
 	/*Finally, check that no option of the same name already exists in the dataset*/
@@ -56,6 +61,6 @@
 
 		option=(Option*)(*object); 
-		if (!strcmp(option->name,in_option->name)){
-			_error2_("Options \"" << in_option->name << "\" found multiple times");
+		if (!strcmp(option->Name(),name)){
+			_error_("Options \"" << name << "\" found multiple times");
 			break;
 		}
@@ -66,230 +71,4 @@
 
 	return 1;
-}
-/*}}}*/
-/*FUNCTION Options::Get(int* pvalue, char* name){{{*/
-void Options::Get(int* pvalue,const char* name){
-
-	vector::iterator object;
-	Option* option=NULL;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		option->Get(pvalue);
-	}
-	/*Else, the Option does not exist, no default provided*/
-	else{
-		_error2_("option of name \"" << name << "\" not found, and no default value has been provided");
-	}
-}
-/*}}}*/
-/*FUNCTION Options::Get(int* pvalue, char* name,int default_value){{{*/
-void Options::Get(int* pvalue,const char* name,int default_value){
-
-	vector::iterator object;
-	Option* option=NULL;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		option->Get(pvalue);
-	}
-	/*Else, the Option does not exist, a default is provided here*/
-	else{
-		*pvalue=default_value;
-	}
-}
-/*}}}*/
-/*FUNCTION Options::Get(IssmDouble* pvalue, char* name){{{*/
-void Options::Get(IssmDouble* pvalue,const char* name){
-
-	vector::iterator object;
-	Option* option=NULL;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		option->Get(pvalue);
-	}
-	/*Else, the Option does not exist, no default provided*/
-	else{
-		_error2_("option of name \"" << name << "\" not found, and no default value has been provided");
-	}
-}
-/*}}}*/
-/*FUNCTION Options::Get(IssmDouble* pvalue, char* name,IssmDouble default_value){{{*/
-void Options::Get(IssmDouble* pvalue,const char* name,IssmDouble default_value){
-
-	vector::iterator object;
-	Option* option=NULL;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		option->Get(pvalue);
-	}
-	/*Else, the Option does not exist, a default is provided here*/
-	else{
-		*pvalue=default_value;
-	}
-}
-/*}}}*/
-/*FUNCTION Options::Get(bool* pvalue, char* name){{{*/
-void Options::Get(bool* pvalue,const char* name){
-
-	vector::iterator object;
-	Option* option=NULL;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		option->Get(pvalue);
-	}
-	/*Else, the Option does not exist, no default provided*/
-	else{
-		_error2_("option of name \"" << name << "\" not found, and no default value has been provided");
-	}
-}
-/*}}}*/
-/*FUNCTION Options::Get(bool* pvalue, char* name,bool default_value){{{*/
-void Options::Get(bool* pvalue,const char* name,bool default_value){
-
-	vector::iterator object;
-	Option* option=NULL;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		option->Get(pvalue);
-	}
-	/*Else, the Option does not exist, a default is provided here*/
-	else{
-		*pvalue=default_value;
-	}
-}
-/*}}}*/
-/*FUNCTION Options::Get(char** pvalue, char* name){{{*/
-void Options::Get(char** pvalue,const char* name){
-
-	vector::iterator object;
-	Option* option=NULL;
-	char* outstring=NULL;
-	int   stringsize;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		option->Get(pvalue);
-	}
-	/*Else, the Option does not exist, no default provided*/
-	else{
-		_error2_("option of name \"" << name << "\" not found, and no default value has been provided");
-	}
-
-}
-/*}}}*/
-/*FUNCTION Options::Get(char** pvalue, char* name,char* default_value){{{*/
-void Options::Get(char** pvalue,const char* name,const char* default_value){
-
-	vector::iterator object;
-	Option* option=NULL;
-	char* outstring=NULL;
-	int   stringsize;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		option->Get(pvalue);
-	}
-	/*Else, the Option does not exist, a default is provided here*/
-	else{
-		stringsize=strlen(default_value)+1;
-		outstring=xNew(stringsize);
-		xMemCpy(outstring,default_value,stringsize);
-		*pvalue=outstring;
-	}
-
-}
-/*}}}*/
-/*FUNCTION Options::Get(char*** ppvalue,int* numel,char* name){{{*/
-void Options::Get(char*** ppvalue,int* numel,const char* name){
-
-	vector::iterator object;
-	Option* option=NULL;
-	Option* option2=NULL;
-	Options* options=NULL;
-	int   i;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		/*If the object is a Cell, copy the strings from its options dataset*/ 
-		if(option->ObjectEnum()==OptionCellEnum){
-			if (option->NumEl()) {
-				*ppvalue=xNew(option->NumEl());
-				if (numel) *numel=option->NumEl();
-				option->Get(&options);
-				for (i=0; iNumEl(); i++) {
-					option2=((Option *)options->GetObjectByOffset(i));
-					if(option2->ObjectEnum()==OptionCharEnum)
-						option2->Get(&((*ppvalue)[i]));
-					else
-						((*ppvalue)[i])=NULL;
-				}
-			}
-		}
-		/*If the object is a Char, copy the strings from its concatenation*/ 
-		else if(option->ObjectEnum()==OptionCharEnum){
-			option->Get(ppvalue,numel);
-		}
-		/*Else: not supported*/
-		else{
-			_error2_("Cannot recover field \"" << name << "\" for an option of type " << EnumToStringx(option->ObjectEnum()));
-		}
-	}
-	/*Else, the Option does not exist, no default provided*/
-	else{
-		*ppvalue=NULL;
-		if (numel) *numel=0;
-	}
-
-}
-/*}}}*/
-/*FUNCTION Options::Get(IssmDouble** pvalue,int* numel,const char* name){{{*/
-void Options::Get(IssmDouble** pvalue,int* numel,const char* name){
-
-	vector::iterator object;
-	Option* option=NULL;
-
-	/*Get option*/
-	option=GetOption(name);
-
-	/*If the pointer is not NULL, the option has been found*/
-	if(option){
-		option->Get(pvalue,numel);
-	}
-	/*Else, the Option does not exist, no default provided*/
-	else{
-		_error2_("option of name \"" << name << "\" not found, and no default value has been provided");
-	}
 }
 /*}}}*/
@@ -304,8 +83,8 @@
 
 		option=(Option*)(*object); 
-		if (!strncmp(name,option->name,strlen(option->name))){
+		if (!strncmp(name,option->Name(),strlen(option->Name()))){
 
 			/*OK, now do we have a complete name? If not, it is a cell or a structure, we need to go further*/
-			if(!strcmp(name,option->name)){
+			if(!strcmp(name,option->Name())){
 				return option;
 			}
@@ -313,16 +92,18 @@
 				/*If the object is a Cell, recursive call to its options*/ 
 				if(option->ObjectEnum()==OptionCellEnum){
-					return ((OptionCell*)option)->values->GetOption(name);
+					GenericOption* celloption=(GenericOption*)option;
+					return celloption->value->GetOption(name);
 				}
 				/*If the object is a Struct loop over its size and recursive call*/
 				else if(option->ObjectEnum()==OptionStructEnum){
-					for(int i=0;inumel;i++){
-						_assert_(((OptionStruct*)option)->values[i]);
-						return ((OptionStruct*)option)->values[i]->GetOption(name);
+					for(int i=0;iNumEl();i++){
+						GenericOption* structoption=(GenericOption*)option;
+						_assert_(structoption->value[i]);
+						return structoption->value[i]->GetOption(name);
 					}
 				}
 				/*Else: not supported*/
 				else{
-					_error2_("Cannot recover field \"" << name << "\" for an option of type " << EnumToStringx(option->ObjectEnum()));
+					_error_("Cannot recover field \"" << name << "\" for an option of type " << EnumToStringx(option->ObjectEnum()));
 				}
 			}
Index: /issm/trunk/src/c/Container/Options.h
===================================================================
--- /issm/trunk/src/c/Container/Options.h	(revision 13394)
+++ /issm/trunk/src/c/Container/Options.h	(revision 13395)
@@ -5,4 +5,6 @@
 #ifndef _CONTAINER_OPTIONS_H_
 #define _CONTAINER_OPTIONS_H_
+
+#include "../classes/objects/Options/GenericOption.h"
 
 /*forward declarations */
@@ -20,15 +22,105 @@
 		int  AddOption(Option* in_oobject);
 		Option* GetOption(const char* name);
-		void Get(IssmDouble*  pvalue,const char* name);
-		void Get(IssmDouble*  pvalue,const char* name,IssmDouble default_value);
-		void Get(int*  pvalue,const char* name);
-		void Get(int*  pvalue,const char* name,int default_value);
-		void Get(bool*    pvalue,const char* name);
-		void Get(bool*    pvalue,const char* name,bool default_value);
-		void Get(char**   pvalue,const char* name);
-		void Get(char**   pvalue,const char* name,const char* default_value);
-		void Get(char***  pvalue,int* numel,const char* name);
-		void Get(IssmDouble** pvalue,int* numel,const char* name);
+		
+		
+		template  void Get(OptionType* pvalue,const char* name){ /*{{{*/
+
+			vector::iterator object;
+			GenericOption* genericoption=NULL;
+
+			/*Get option*/
+			genericoption=(GenericOption*)GetOption(name);
+
+			/*If the pointer is not NULL, the option has been found*/
+			if(genericoption){
+				genericoption->Get(pvalue);
+			}
+			/*Else, the Option does not exist, no default provided*/
+			else{
+				_error_("option of name \"" << name << "\" not found, and no default value has been provided");
+			}
+		}
+		/*}}}*/
+		template  void Get(OptionType* pvalue,int* pnumel, const char* name){ /*{{{*/
+
+			vector::iterator object;
+			GenericOption* genericoption=NULL;
+
+			/*Get option*/
+			genericoption=(GenericOption*)GetOption(name);
+
+			/*If the pointer is not NULL, the option has been found*/
+			if(genericoption){
+				genericoption->Get(pvalue);
+				*pnumel=genericoption->NumEl();
+			}
+			/*Else, the Option does not exist, no default provided*/
+			else{
+				_error_("option of name \"" << name << "\" not found, and no default value has been provided");
+			}
+		}
+		/*}}}*/
+		template  void Get(OptionType* pvalue,const char* name,OptionType default_value){ /*{{{*/
+
+			vector::iterator object;
+			GenericOption* genericoption=NULL;
+
+			/*Get option*/
+			genericoption=(GenericOption*)GetOption(name);
+
+			/*If the pointer is not NULL, the option has been found*/
+			if(genericoption){
+				genericoption->Get(pvalue);
+			}
+			else{
+				*pvalue=default_value;
+			}
+		}
+		/*}}}*/
+		template  void Get(OptionType* pvalue,int* pnumel, const char* name,OptionType default_value){ /*{{{*/
+
+			vector::iterator object;
+			GenericOption* genericoption=NULL;
+
+			/*Get option*/
+			genericoption=(GenericOption*)GetOption(name);
+
+			/*If the pointer is not NULL, the option has been found*/
+			if(genericoption){
+				genericoption->Get(pvalue);
+				*pnumel=genericoption->NumEl();
+			}
+			else{
+				*pvalue=default_value;
+			}
+		}
+		/*}}}*/
+
 };
 
 #endif //ifndef _INPUTS_H_
+
+template <> inline void Options::Get(char** pvalue,const char* name,char* default_value){ /*{{{*/
+
+	vector::iterator object;
+	GenericOption* genericoption=NULL;
+
+	/*Get option*/
+	genericoption=(GenericOption*)GetOption(name);
+
+	/*If the pointer is not NULL, the option has been found*/
+	if(genericoption){
+		genericoption->Get(pvalue);
+	}
+	else{
+		/*Make a copy*/
+		char* outstring=NULL;
+		int   stringsize;
+
+		stringsize=strlen(default_value)+1;
+		outstring=xNew(stringsize);
+		xMemCpy(outstring,default_value,stringsize);
+		*pvalue=outstring;
+	}
+}
+/*}}}*/
Index: /issm/trunk/src/c/Container/Parameters.cpp
===================================================================
--- /issm/trunk/src/c/Container/Parameters.cpp	(revision 13394)
+++ /issm/trunk/src/c/Container/Parameters.cpp	(revision 13395)
@@ -65,5 +65,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 }
 /*}}}*/
@@ -82,5 +82,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 }
 /*}}}*/
@@ -99,5 +99,22 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
+}
+/*}}}*/
+/*FUNCTION Parameters::FindParam(IssmDouble* pscalar, int enum_type,IssmDouble time){{{*/
+void Parameters::FindParam(IssmDouble* pscalar, int enum_type,IssmDouble time){ _assert_(this);
+
+	vector::iterator object;
+	Param* param=NULL;
+
+	for ( object=objects.begin() ; object < objects.end(); object++ ){
+
+		param=(Param*)(*object);
+		if(param->InstanceEnum()==enum_type){
+			param->GetParameterValue(pscalar,time);
+			return;
+		}
+	}
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 }
 /*}}}*/
@@ -116,5 +133,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 
 }
@@ -134,5 +151,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 
 }
@@ -152,5 +169,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 
 }
@@ -170,5 +187,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 
 }
@@ -188,5 +205,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 
 }
@@ -206,5 +223,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 
 }
@@ -224,9 +241,9 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
-}
-/*}}}*/
-/*FUNCTION Parameters::FindParam(Vector** pvec,int enum_type){{{*/
-void Parameters::FindParam(Vector** pvec,int enum_type){ _assert_(this);
+	_error_("could not find parameter " << EnumToStringx(enum_type));
+}
+/*}}}*/
+/*FUNCTION Parameters::FindParam(Vector** pvec,int enum_type){{{*/
+void Parameters::FindParam(Vector** pvec,int enum_type){ _assert_(this);
 	
 	vector::iterator object;
@@ -241,10 +258,10 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
-
-}
-/*}}}*/
-/*FUNCTION Parameters::FindParam(Matrix** pmat,int enum_type){{{*/
-void Parameters::FindParam(Matrix** pmat,int enum_type){ _assert_(this);
+	_error_("could not find parameter " << EnumToStringx(enum_type));
+
+}
+/*}}}*/
+/*FUNCTION Parameters::FindParam(Matrix** pmat,int enum_type){{{*/
+void Parameters::FindParam(Matrix** pmat,int enum_type){ _assert_(this);
 	
 	vector::iterator object;
@@ -259,5 +276,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 
 }
@@ -277,5 +294,5 @@
 		}
 	}
-	_error2_("could not find parameter " << EnumToStringx(enum_type));
+	_error_("could not find parameter " << EnumToStringx(enum_type));
 }
 /*}}}*/
@@ -389,6 +406,6 @@
 }
 /*}}}*/
-/*FUNCTION Parameters::SetParam(Vector* vector,int enum_type);{{{*/
-void   Parameters::SetParam(Vector* vector,int enum_type){
+/*FUNCTION Parameters::SetParam(Vector* vector,int enum_type);{{{*/
+void   Parameters::SetParam(Vector* vector,int enum_type){
 
 	Param* param=NULL;
@@ -401,6 +418,6 @@
 }
 /*}}}*/
-/*FUNCTION Parameters::SetParam(Matrix* matrix,int enum_type);{{{*/
-void   Parameters::SetParam(Matrix* matrix,int enum_type){
+/*FUNCTION Parameters::SetParam(Matrix* matrix,int enum_type);{{{*/
+void   Parameters::SetParam(Matrix* matrix,int enum_type){
 
 	Param* param=NULL;
Index: /issm/trunk/src/c/Container/Parameters.h
===================================================================
--- /issm/trunk/src/c/Container/Parameters.h	(revision 13394)
+++ /issm/trunk/src/c/Container/Parameters.h	(revision 13395)
@@ -8,6 +8,6 @@
 
 /*forward declarations */
-class Matrix;
-class Vector;
+template  class Matrix;
+template  class Vector;
 class Materials;
 class Parameters;
@@ -23,9 +23,9 @@
 	public:
 
-		/*constructors, destructors: {{{*/
+		/*constructors, destructors*/ 
 		Parameters();
 		~Parameters();
-		/*}}}*/
-		/*numerics: {{{*/
+
+		/*numerics*/
 		bool  Exist(int enum_type);
 
@@ -33,4 +33,5 @@
 		void  FindParam(int* pinteger,int enum_type);
 		void  FindParam(IssmDouble* pscalar, int enum_type);
+		void  FindParam(IssmDouble* pscalar, int enum_type,IssmDouble time);
 		void  FindParam(char** pstring,int enum_type);
 		void  FindParam(char*** pstringarray,int* pM,int enum_type);
@@ -40,6 +41,6 @@
 		void  FindParam(IssmDouble** pIssmDoublearray,int* pM,int* pN,int enum_type);
 		void  FindParam(IssmDouble*** parray,int* pM, int** pmdims_array,int** pndims_array,int enum_type);
-		void  FindParam(Vector** pvec,int enum_type);
-		void  FindParam(Matrix** pmat,int enum_type);
+		void  FindParam(Vector** pvec,int enum_type);
+		void  FindParam(Matrix** pmat,int enum_type);
 		void  FindParam(FILE** pfid,int enum_type);
 		
@@ -53,11 +54,10 @@
 		void  SetParam(int* intarray,int M,int enum_type);
 		void  SetParam(int* intarray,int M,int N,int enum_type);
-		void  SetParam(Vector* vec,int enum_type);
-		void  SetParam(Matrix* mat,int enum_type);
+		void  SetParam(Vector* vec,int enum_type);
+		void  SetParam(Matrix* mat,int enum_type);
 		void  SetParam(FILE* fid,int enum_type);
 		void  UnitConversion(int direction_enum);
 
 		Object* FindParamObject(int enum_type);
-		/*}}}*/
 
 };
Index: /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h
===================================================================
--- /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h	(revision 13394)
+++ /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h	(revision 13395)
@@ -12,7 +12,12 @@
 enum definitions{
 	/*Model fields {{{1*/
-	AutodiffForwardEnum,
 	AutodiffIsautodiffEnum, 
-	AutodiffReverseEnum,
+	AutodiffDependentsEnum,
+	AutodiffNumDependentsEnum,
+	AutodiffIndependentsEnum,
+	AutodiffNumIndependentsEnum,
+	AutodiffJacobianEnum,
+	AutodiffXpEnum,
+	AutodiffFosForwardOutputEnum,
 	BalancethicknessSpcthicknessEnum,
 	BalancethicknessStabilizationEnum,
@@ -50,4 +55,5 @@
 	FlowequationElementEquationEnum,
 	FlowequationIshutterEnum,
+	FlowequationIsl1l2Enum,
 	FlowequationIsmacayealpattynEnum,
 	FlowequationIsstokesEnum,
@@ -101,4 +107,6 @@
 	MaterialsRheologyLawEnum,
 	MaterialsRheologyNEnum,
+	MaterialsRheologyZEnum,
+	MaterialsRheologyZbarEnum,
 	MaterialsRhoIceEnum,
 	MaterialsRhoWaterEnum,
@@ -149,4 +157,10 @@
 	SettingsResultsAsPatchesEnum,
 	SettingsWaitonlockEnum,
+	SurfaceforcingsDelta18oEnum,
+	SurfaceforcingsDelta18oSurfaceEnum,
+	SurfaceforcingsIsdelta18oEnum,
+	SurfaceforcingsPrecipitationsPresentdayEnum,
+	SurfaceforcingsTemperaturesPresentdayEnum,
+	SurfaceforcingsTemperaturesLgmEnum,
 	DebugProfilingEnum,
 	ProfilingCurrentMemEnum,
@@ -230,9 +244,10 @@
 	/*Approximations {{{1*/
 	ApproximationEnum,
+	NoneApproximationEnum,
 	HutterApproximationEnum,
 	MacAyealApproximationEnum,
 	MacAyealPattynApproximationEnum,
 	MacAyealStokesApproximationEnum,
-	NoneApproximationEnum,
+	L1L2ApproximationEnum,
 	PattynApproximationEnum,
 	PattynStokesApproximationEnum,
@@ -249,4 +264,6 @@
 	/*}}}*/
 	/*Objects {{{1*/
+	GenericParamEnum,
+	AdolcParamEnum,
 	BoolInputEnum,
 	BoolParamEnum,
@@ -270,11 +287,14 @@
 	IntParamEnum,
 	IntVecParamEnum,
+	TransientParamEnum,
 	MacAyeal2dIceFrontEnum,
 	MacAyeal3dIceFrontEnum,
 	MaticeEnum,
+	MatdamageiceEnum,
 	MatparEnum,
 	NodeEnum,
 	NumericalfluxEnum,
 	ParamEnum,
+	L1L2IceFrontEnum,
 	PattynIceFrontEnum,
 	PengridEnum,
@@ -353,4 +373,6 @@
 	TemperatureOldEnum,
 	TemperaturePicardEnum,
+	TemperatureSurfaceEnum,
+	TemperatureBasalEnum,
 	ThicknessAbsMisfitEnum,
 	TypeEnum,
@@ -374,4 +396,6 @@
 	EnthalpyPicardEnum,
 	ThicknessAbsGradientEnum,
+	ThicknessAlongGradientEnum,
+	ThicknessAcrossGradientEnum,
 	StepResponsesEnum,
 	IntMatParamEnum,
@@ -394,5 +418,4 @@
 	StressTensoryzEnum,
 	StressTensorzzEnum,
-	IceVolumeEnum,
 	/*}}}*/
 	/*Element Interpolations{{{1*/
@@ -434,4 +457,6 @@
 	MaxVzEnum,
 	MaxAbsVzEnum,
+	IceVolumeEnum,
+	TotalSmbEnum,
 	/*}}}*/
 	/*Convergence{{{1*/
@@ -487,4 +512,5 @@
 	/*Options{{{1*/
 	OptionEnum,
+	GenericOptionEnum,
 	OptionCellEnum,
 	OptionCharEnum,
Index: /issm/trunk/src/c/EnumDefinitions/Synchronize.sh
===================================================================
--- /issm/trunk/src/c/EnumDefinitions/Synchronize.sh	(revision 13394)
+++ /issm/trunk/src/c/EnumDefinitions/Synchronize.sh	(revision 13395)
@@ -98,5 +98,5 @@
 cat <> $ISSM_DIR/src/c/modules/StringToEnumx/StringToEnumx.cpp
 	/*If we reach this point, the string provided has not been found*/
-	_error2_("Enum " << name << " not found");
+	_error_("Enum " << name << " not found");
 }
 END
@@ -107,4 +107,6 @@
 #Add header to pythonenum file{{{
 cat < $ISSM_DIR/src/m/enum/EnumDefinitions.py
+from StringToEnum import StringToEnum
+
 """
 
@@ -166,5 +168,5 @@
 	"""
 
-	return StringToEnum('$NAME')
+	return StringToEnum('$NAME')[0]
 
 END
Index: /issm/trunk/src/c/Makefile.am
===================================================================
--- /issm/trunk/src/c/Makefile.am	(revision 13394)
+++ /issm/trunk/src/c/Makefile.am	(revision 13395)
@@ -1,3 +1,3 @@
-INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
+AM_CPPFLAGS = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
 
 EXEEXT=$(ISSMEXT)
@@ -5,11 +5,21 @@
 #Library declaration {{{
 lib_LIBRARIES = libISSMCore.a libISSMOverload.a
+
+if SHAREDLIBS
+lib_LTLIBRARIES = libISSMCore.la libISSMOverload.la libISSM.la
+endif
 if PYTHON
 lib_LIBRARIES += libISSMPython.a 
 endif
 if MATLAB
+if SHAREDLIBS
+lib_LTLIBRARIES += libISSMMatlab.la
+endif
 lib_LIBRARIES += libISSMMatlab.a 
 endif
 if MODULES
+if SHAREDLIBS
+lib_LTLIBRARIES += libISSMModules.la
+endif
 lib_LIBRARIES += libISSMModules.a 
 endif
@@ -24,130 +34,122 @@
 					./include/types.h\
 					./include/include.h\
-					./objects/objects.h\
-					./objects/Object.h\
-					./objects/Gauss/GaussTria.h\
-					./objects/Gauss/GaussTria.cpp\
-					./objects/Update.h\
-					./objects/Element.h\
-					./objects/FemModel.h\
-					./objects/FemModel.cpp\
-					./objects/Material.h\
-					./objects/Load.h\
-					./objects/Contour.h\
-					./objects/Contour.cpp\
-					./objects/OptArgs.h\
-					./objects/OptPars.h\
-					./objects/Loads/Friction.h\
-					./objects/Loads/Friction.cpp\
-					./objects/Inputs/TransientInput.h\
-					./objects/Inputs/TransientInput.cpp\
-					./objects/Constraints/SpcTransient.cpp\
-					./objects/Constraints/SpcTransient.h\
-					./objects/DofIndexing.h\
-					./objects/DofIndexing.cpp\
-					./objects/IoModel.h\
-					./objects/IoModel.cpp\
-					./objects/Node.h\
-					./objects/Node.cpp\
-					./objects/Segment.h\
-					./objects/Segment.cpp\
-					./objects/Vertex.h\
-					./objects/Vertex.cpp\
-					./objects/Hook.h\
-					./objects/Hook.cpp\
-					./objects/Patch.h\
-					./objects/Patch.cpp\
-					./objects/ElementResults/ElementResultLocal.h\
-					./objects/ElementResults/DoubleElementResult.h\
-					./objects/ElementResults/DoubleElementResult.cpp\
-					./objects/ElementResults/TriaP1ElementResult.h\
-					./objects/ElementResults/TriaP1ElementResult.cpp\
-					./objects/ElementResults/BoolElementResult.h\
-					./objects/ElementResults/BoolElementResult.cpp\
-					./objects/ExternalResults/ExternalResult.h\
-					./objects/ExternalResults/BoolExternalResult.h\
-					./objects/ExternalResults/BoolExternalResult.cpp\
-					./objects/ExternalResults/DoubleExternalResult.h\
-					./objects/ExternalResults/DoubleExternalResult.cpp\
-					./objects/ExternalResults/DoubleVecExternalResult.h\
-					./objects/ExternalResults/DoubleVecExternalResult.cpp\
-					./objects/ExternalResults/DoubleMatExternalResult.h\
-					./objects/ExternalResults/DoubleMatExternalResult.cpp\
-					./objects/ExternalResults/IntExternalResult.h\
-					./objects/ExternalResults/IntExternalResult.cpp\
-					./objects/ExternalResults/StringExternalResult.h\
-					./objects/ExternalResults/StringExternalResult.cpp\
-					./objects/Elements/Tria.h\
-					./objects/Elements/Tria.cpp\
-					./objects/Elements/TriaHook.h\
-					./objects/Elements/TriaHook.cpp\
-					./objects/Elements/TriaRef.h\
-					./objects/Elements/TriaRef.cpp\
-					./objects/Inputs/Input.h\
-					./objects/Inputs/InputLocal.h\
-					./objects/Inputs/TriaP1Input.h\
-					./objects/Inputs/TriaP1Input.cpp\
-					./objects/Inputs/BoolInput.h\
-					./objects/Inputs/BoolInput.cpp\
-					./objects/Inputs/IntInput.h\
-					./objects/Inputs/IntInput.cpp\
-					./objects/Inputs/DoubleInput.h\
-					./objects/Inputs/DoubleInput.cpp\
-					./objects/Inputs/DatasetInput.h\
-					./objects/Inputs/DatasetInput.cpp\
-					./objects/Materials/Matice.h\
-					./objects/Materials/Matice.cpp\
-					./objects/Materials/Matpar.h\
-					./objects/Materials/Matpar.cpp\
-					./objects/Constraints/Constraint.h\
-					./objects/Constraints/SpcStatic.cpp\
-					./objects/Constraints/SpcStatic.h\
-					./objects/Constraints/SpcDynamic.cpp\
-					./objects/Constraints/SpcDynamic.h\
-					./objects/Loads/Penpair.cpp\
-					./objects/Loads/Penpair.h\
-					./objects/Loads/Pengrid.cpp\
-					./objects/Loads/Pengrid.h\
-					./objects/Loads/Icefront.cpp\
-					./objects/Loads/Icefront.h\
-					./objects/Loads/Numericalflux.cpp\
-					./objects/Loads/Numericalflux.h\
-					./objects/Numerics/ElementMatrix.h\
-					./objects/Numerics/ElementMatrix.cpp\
-					./objects/Numerics/ElementVector.h\
-					./objects/Numerics/ElementVector.cpp\
-					./objects/Numerics/Matrix.h\
-					./objects/Numerics/Matrix.cpp\
-					./objects/Numerics/Vector.h\
-					./objects/Numerics/Vector.cpp\
-					./objects/Params/Param.h\
-					./objects/Params/BoolParam.cpp\
-					./objects/Params/BoolParam.h\
-					./objects/Params/IntParam.cpp\
-					./objects/Params/IntParam.h\
-					./objects/Params/IntVecParam.cpp\
-					./objects/Params/IntVecParam.h\
-					./objects/Params/IntMatParam.cpp\
-					./objects/Params/IntMatParam.h\
-					./objects/Params/DoubleParam.cpp\
-					./objects/Params/DoubleParam.h\
-					./objects/Params/FileParam.cpp\
-					./objects/Params/FileParam.h\
-					./objects/Params/StringArrayParam.cpp\
-					./objects/Params/StringArrayParam.h\
-					./objects/Params/DoubleMatParam.cpp\
-					./objects/Params/DoubleMatParam.h\
-					./objects/Params/DoubleTransientMatParam.cpp\
-					./objects/Params/DoubleTransientMatParam.h\
-					./objects/Params/DoubleMatArrayParam.cpp\
-					./objects/Params/DoubleMatArrayParam.h\
-					./objects/Params/DoubleVecParam.cpp\
-					./objects/Params/DoubleVecParam.h\
-					./objects/Params/StringParam.cpp\
-					./objects/Params/StringParam.h\
-					./objects/Params/MatrixParam.h\
-					./objects/Params/MatrixParam.cpp\
-					./objects/Params/VectorParam.h\
-					./objects/Params/VectorParam.cpp\
+					./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/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/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/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/matrix/matrixobjects.h\
+					./classes/matrix/ElementMatrix.h\
+					./classes/matrix/ElementMatrix.cpp\
+					./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\
 					./Container/Container.h\
 					./Container/Constraints.h\
@@ -180,4 +182,5 @@
 					./shared/Matrix/matrix.h\
 					./shared/Matrix/MatrixUtils.cpp\
+					./shared/Numerics/adolc_edf.h\
 					./shared/Numerics/numerics.h\
 					./shared/Numerics/Verbosity.h\
@@ -189,4 +192,5 @@
 					./shared/Numerics/isnan.h\
 					./shared/Numerics/isnan.cpp\
+					./shared/Numerics/cubic.cpp\
 					./shared/Numerics/extrema.cpp\
 					./shared/Numerics/XZvectorsToCoordinateSystem.cpp\
@@ -205,5 +209,7 @@
 					./shared/Elements/GetGlobalDofList.cpp\
 					./shared/Elements/GetNumberOfDofs.cpp\
+					./shared/Elements/PrintArrays.cpp\
 					./shared/Elements/PddSurfaceMassBalance.cpp\
+					./shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp\
 					./shared/String/sharedstring.h\
 					./shared/Wrapper/wrappershared.h\
@@ -216,7 +222,5 @@
 					./toolkits/issm/issmtoolkit.h\
 					./toolkits/issm/SeqVec.h\
-					./toolkits/issm/SeqVec.cpp\
 					./toolkits/issm/SeqMat.h\
-					./toolkits/issm/SeqMat.cpp\
 					./toolkits/triangle/triangleincludes.h\
 					./toolkitsenums.h\
@@ -237,4 +241,5 @@
 					./modules/ModelProcessorx/CreateDataSets.cpp\
 					./modules/ModelProcessorx/CreateParameters.cpp\
+					./modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp\
 					./modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp\
 					./modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp\
@@ -288,9 +293,10 @@
 					./modules/PositiveDegreeDayx/PositiveDegreeDayx.h\
 					./modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp\
+					./modules/Delta18oParameterizationx/Delta18oParameterizationx.h\
+					./modules/Delta18oParameterizationx/Delta18oParameterizationx.cpp\
 					./modules/SmbGradientsx/SmbGradientsx.h\
 					./modules/SmbGradientsx/SmbGradientsx.cpp\
 					./modules/UpdateConstraintsx/UpdateConstraintsx.h\
 					./modules/UpdateConstraintsx/UpdateConstraintsx.cpp\
-					./modules/MeshPartitionx/MeshPartitionx.cpp\
 					./modules/MeshPartitionx/MeshPartitionx.h\
 					./modules/Reducevectorgtofx/Reducevectorgtofx.cpp\
@@ -313,4 +319,8 @@
 					./modules/RequestedOutputsx/RequestedOutputsx.h\
 					./modules/RequestedOutputsx/RequestedOutputsx.cpp\
+					./modules/RequestedDependentsx/RequestedDependentsx.h\
+					./modules/RequestedDependentsx/RequestedDependentsx.cpp\
+					./modules/AutodiffDriversx/AutodiffDriversx.h\
+					./modules/AutodiffDriversx/AutodiffDriversx.cpp\
 					./modules/ResetConstraintsx/ResetConstraintsx.h\
 					./modules/ResetConstraintsx/ResetConstraintsx.cpp\
@@ -319,4 +329,5 @@
 					./modules/Solverx/Solverx.cpp\
 					./modules/Solverx/Solverx.h\
+					./modules/Solverx/SolverxSeq.cpp\
 					./modules/VecMergex/VecMergex.cpp\
 					./modules/VecMergex/VecMergex.h\
@@ -336,17 +347,13 @@
 					./solvers/solver_nonlinear.cpp\
 					./solvers/solver_newton.cpp\
-					./objects/Options/Option.cpp\
-					./objects/Options/Option.h\
-					./objects/Options/OptionDouble.cpp\
-					./objects/Options/OptionDouble.h\
-					./objects/Options/OptionChar.cpp\
-					./objects/Options/OptionChar.h\
-					./objects/Options/OptionUtilities.cpp\
-					./objects/Options/OptionUtilities.h
+					./classes/objects/Options/Option.h\
+					./classes/objects/Options/GenericOption.h\
+					./classes/objects/Options/OptionUtilities.cpp\
+					./classes/objects/Options/OptionUtilities.h
 
 #}}}
 #DAKOTA sources  {{{
-dakota_sources = ./objects/DakotaPlugin.h\
-					  ./objects/DakotaPlugin.cpp\
+dakota_sources = ./classes/dakota/DakotaPlugin.h\
+					  ./classes/dakota/DakotaPlugin.cpp\
 					  ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.h\
 					  ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.cpp\
@@ -365,7 +372,5 @@
 					  ./modules/Dakotax/SpawnCore.cpp\
 					  ./modules/Dakotax/DescriptorIndex.cpp\
-					  ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\
 					  ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\
-					  ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\
 					  ./modules/Dakotax/SpawnCoreParallel.cpp
 #}}}
@@ -442,8 +447,12 @@
 					  ./modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp\
 					  ./modules/ThicknessAbsGradientx/ThicknessAbsGradientx.h\
+					  ./modules/ThicknessAlongGradientx/ThicknessAlongGradientx.cpp\
+					  ./modules/ThicknessAlongGradientx/ThicknessAlongGradientx.h\
+					  ./modules/ThicknessAcrossGradientx/ThicknessAcrossGradientx.cpp\
+					  ./modules/ThicknessAcrossGradientx/ThicknessAcrossGradientx.h\
 					  ./modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp\
 					  ./modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.h\
-					  ./objects/Inputs/ControlInput.h\
-					  ./objects/Inputs/ControlInput.cpp\
+					  ./classes/objects/Inputs/ControlInput.h\
+					  ./classes/objects/Inputs/ControlInput.cpp\
 					  ./shared/Numerics/BrentSearch.cpp\
 					  ./shared/Numerics/OptimalSearch.cpp \
@@ -519,4 +528,6 @@
 					     ./modules/MinVzx/MinVzx.h\
 					     ./modules/MinVzx/MinVzx.cpp\
+					     ./modules/TotalSmbx/TotalSmbx.h\
+					     ./modules/TotalSmbx/TotalSmbx.cpp\
 					     ./modules/IceVolumex/IceVolumex.h\
 					     ./modules/IceVolumex/IceVolumex.cpp\
@@ -543,72 +554,73 @@
 #}}}
 #Rifts sources  {{{
-rifts_sources = ./objects/Loads/Riftfront.cpp\
-				    ./objects/Loads/Riftfront.h\
+rifts_sources = ./classes/objects/Loads/Riftfront.cpp\
+				    ./classes/objects/Loads/Riftfront.h\
 				    ./modules/ConstraintsStatex/RiftConstraintsState.cpp
 #}}}
 #3D sources  {{{
-threed_sources = ./objects/Gauss/GaussPenta.h\
-				     ./objects/Gauss/GaussPenta.cpp\
-				     ./objects/ElementResults/PentaP1ElementResult.h\
-				     ./objects/ElementResults/PentaP1ElementResult.cpp\
-				     ./objects/Inputs/PentaP1Input.h\
-				     ./objects/Inputs/PentaP1Input.cpp\
-				     ./objects/Elements/Penta.h\
-				     ./objects/Elements/Penta.cpp\
-				     ./objects/Elements/PentaHook.h\
-				     ./objects/Elements/PentaHook.cpp\
-				     ./objects/Elements/PentaRef.h\
-				     ./objects/Elements/PentaRef.cpp
+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
 #}}}
 #Bamg sources  {{{
-bamg_sources =  ./objects/Bamg/BamgGeom.h\
-				./objects/Bamg/BamgGeom.cpp\
-				./objects/Bamg/BamgMesh.h\
-				./objects/Bamg/BamgMesh.cpp\
-				./objects/Bamg/BamgOpts.h\
-				./objects/Bamg/BamgOpts.cpp\
-				./objects/Bamg/CrackedEdge.h\
-				./objects/Bamg/CrackedEdge.cpp\
-				./objects/Bamg/Curve.h\
-				./objects/Bamg/Curve.cpp\
-				./objects/Bamg/Direction.h\
-				./objects/Bamg/Direction.cpp\
-				./objects/Bamg/DoubleAndInt.h\
-				./objects/Bamg/Edge.h\
-				./objects/Bamg/Edge.cpp\
-				./objects/Bamg/GeomEdge.h\
-				./objects/Bamg/GeomEdge.cpp\
-				./objects/Bamg/GeomSubDomain.h\
-				./objects/Bamg/GeomSubDomain.cpp\
-				./objects/Bamg/GeomVertex.h\
-				./objects/Bamg/GeomVertex.cpp\
-				./objects/Bamg/Geometry.cpp\
-				./objects/Bamg/Geometry.h\
-				./objects/Bamg/ListofIntersectionTriangles.cpp\
-				./objects/Bamg/ListofIntersectionTriangles.h\
-				./objects/Bamg/EigenMetric.cpp\
-				./objects/Bamg/Metric.cpp\
-				./objects/Bamg/Metric.h\
-				./objects/Bamg/BamgQuadtree.cpp\
-				./objects/Bamg/BamgQuadtree.h\
-				./objects/Bamg/R2.h\
-				./objects/Bamg/SetOfE4.cpp\
-				./objects/Bamg/SetOfE4.h\
-				./objects/Bamg/SubDomain.h\
-				./objects/Bamg/SubDomain.cpp\
-				./objects/Bamg/AdjacentTriangle.h\
-				./objects/Bamg/AdjacentTriangle.cpp\
-				./objects/Bamg/Triangle.cpp\
-				./objects/Bamg/Triangle.h\
-				./objects/Bamg/BamgVertex.cpp\
-				./objects/Bamg/BamgVertex.h\
-				./objects/Bamg/VertexOnEdge.h\
-				./objects/Bamg/VertexOnEdge.cpp\
-				./objects/Bamg/VertexOnGeom.h\
-				./objects/Bamg/VertexOnGeom.cpp\
-				./objects/Bamg/VertexOnVertex.h\
-				./objects/Bamg/VertexOnVertex.cpp\
-				./objects/Bamg/Mesh.cpp\
-				./objects/Bamg/Mesh.h\
+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\
 				./shared/Bamg/Abs.h \
 				./shared/Bamg/BigPrimeNumber.h\
@@ -630,17 +642,17 @@
 kriging_sources = ./Container/Observations.h\
 						./Container/Observations.cpp\
-						./objects/Kriging/Variogram.h \
-						./objects/Kriging/GaussianVariogram.h\
-						./objects/Kriging/GaussianVariogram.cpp\
-						./objects/Kriging/ExponentialVariogram.h\
-						./objects/Kriging/ExponentialVariogram.cpp\
-						./objects/Kriging/SphericalVariogram.h\
-						./objects/Kriging/SphericalVariogram.cpp\
-						./objects/Kriging/PowerVariogram.h\
-						./objects/Kriging/PowerVariogram.cpp\
-						./objects/Kriging/Quadtree.h\
-						./objects/Kriging/Quadtree.cpp\
-						./objects/Kriging/Observation.h\
-						./objects/Kriging/Observation.cpp\
+						./classes/kriging/Variogram.h \
+						./classes/kriging/GaussianVariogram.h\
+						./classes/kriging/GaussianVariogram.cpp\
+						./classes/kriging/ExponentialVariogram.h\
+						./classes/kriging/ExponentialVariogram.cpp\
+						./classes/kriging/SphericalVariogram.h\
+						./classes/kriging/SphericalVariogram.cpp\
+						./classes/kriging/PowerVariogram.h\
+						./classes/kriging/PowerVariogram.cpp\
+						./classes/kriging/Quadtree.h\
+						./classes/kriging/Quadtree.cpp\
+						./classes/kriging/Observation.h\
+						./classes/kriging/Observation.cpp\
 						./modules/Krigingx/Krigingx.cpp\
 						./modules/Krigingx/Krigingx.h
@@ -649,17 +661,17 @@
 pkriging_sources = ./Container/Observations.h\
 						./Container/Observations.cpp\
-						./objects/Kriging/Variogram.h \
-						./objects/Kriging/GaussianVariogram.h\
-						./objects/Kriging/GaussianVariogram.cpp\
-						./objects/Kriging/ExponentialVariogram.h\
-						./objects/Kriging/ExponentialVariogram.cpp\
-						./objects/Kriging/SphericalVariogram.h\
-						./objects/Kriging/SphericalVariogram.cpp\
-						./objects/Kriging/PowerVariogram.h\
-						./objects/Kriging/PowerVariogram.cpp\
-						./objects/Kriging/Quadtree.h\
-						./objects/Kriging/Quadtree.cpp\
-						./objects/Kriging/Observation.h\
-						./objects/Kriging/Observation.cpp\
+						./classes/kriging/Variogram.h \
+						./classes/kriging/GaussianVariogram.h\
+						./classes/kriging/GaussianVariogram.cpp\
+						./classes/kriging/ExponentialVariogram.h\
+						./classes/kriging/ExponentialVariogram.cpp\
+						./classes/kriging/SphericalVariogram.h\
+						./classes/kriging/SphericalVariogram.cpp\
+						./classes/kriging/PowerVariogram.h\
+						./classes/kriging/PowerVariogram.cpp\
+						./classes/kriging/Quadtree.h\
+						./classes/kriging/Quadtree.cpp\
+						./classes/kriging/Observation.h\
+						./classes/kriging/Observation.cpp\
 						./modules/Krigingx/pKrigingx.cpp\
 						./modules/Krigingx/Krigingx.h
@@ -679,58 +691,58 @@
 			     ./modules/KMLOverlayx/KMLOverlayx.h\
 			     ./modules/KMLOverlayx/KMLOverlayx.cpp\
-			     ./objects/KML/KML_Attribute.cpp\
-			     ./objects/KML/KML_Attribute.h\
-			     ./objects/KML/KML_Comment.cpp\
-			     ./objects/KML/KML_Comment.h\
-			     ./objects/KML/KML_ColorStyle.cpp\
-			     ./objects/KML/KML_ColorStyle.h\
-			     ./objects/KML/KML_Container.cpp\
-			     ./objects/KML/KML_Container.h\
-			     ./objects/KML/KML_Document.cpp\
-			     ./objects/KML/KML_Document.h\
-			     ./objects/KML/KML_Feature.cpp\
-			     ./objects/KML/KML_Feature.h\
-			     ./objects/KML/KML_File.cpp\
-			     ./objects/KML/KML_File.h\
-			     ./objects/KML/KML_Folder.cpp\
-			     ./objects/KML/KML_Folder.h\
-			     ./objects/KML/KML_Geometry.cpp\
-			     ./objects/KML/KML_Geometry.h\
-			     ./objects/KML/KML_GroundOverlay.cpp\
-			     ./objects/KML/KML_GroundOverlay.h\
-			     ./objects/KML/KML_Icon.cpp\
-			     ./objects/KML/KML_Icon.h\
-			     ./objects/KML/KML_LatLonBox.cpp\
-		  	     ./objects/KML/KML_LatLonBox.h\
-			     ./objects/KML/KML_LinearRing.cpp\
-			     ./objects/KML/KML_LinearRing.h\
-			     ./objects/KML/KML_LineString.cpp\
-			     ./objects/KML/KML_LineString.h\
-			     ./objects/KML/KML_LineStyle.cpp\
-			     ./objects/KML/KML_LineStyle.h\
-			     ./objects/KML/KML_MultiGeometry.cpp\
-			     ./objects/KML/KML_MultiGeometry.h\
-			     ./objects/KML/KML_Object.cpp\
-			     ./objects/KML/KML_Object.h\
-			     ./objects/KML/KML_Overlay.cpp\
-			     ./objects/KML/KML_Overlay.h\
-			     ./objects/KML/KML_Point.cpp\
-			     ./objects/KML/KML_Point.h\
-			     ./objects/KML/KML_Placemark.cpp\
-			     ./objects/KML/KML_Placemark.h\
-			     ./objects/KML/KML_Polygon.cpp\
-			     ./objects/KML/KML_Polygon.h\
-			     ./objects/KML/KML_PolyStyle.cpp\
-			     ./objects/KML/KML_PolyStyle.h\
-			     ./objects/KML/KML_Style.cpp\
-			     ./objects/KML/KML_Style.h\
-			     ./objects/KML/KML_StyleSelector.cpp\
-			     ./objects/KML/KML_StyleSelector.h\
-			     ./objects/KML/KML_SubStyle.cpp\
-			     ./objects/KML/KML_SubStyle.h\
-			     ./objects/KML/KML_Unknown.cpp\
-			     ./objects/KML/KML_Unknown.h\
-			     ./objects/KML/KMLFileReadUtils.cpp\
-			     ./objects/KML/KMLFileReadUtils.h
+			     ./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
 #}}}
 #Petsc sources  {{{
@@ -763,4 +775,9 @@
 					./toolkits/petsc/patches/ISSMToPetscInsertMode.cpp\
 					./toolkits/petsc/patches/ISSMToPetscNormMode.cpp\
+					./toolkits/petsc/objects/petscobjects.h\
+					./toolkits/petsc/objects/PetscMat.h\
+					./toolkits/petsc/objects/PetscMat.cpp\
+					./toolkits/petsc/objects/PetscVec.h\
+					./toolkits/petsc/objects/PetscVec.cpp\
 					./toolkits/petsc/petscincludes.h\
 					./shared/Numerics/PetscOptionsFromAnalysis.cpp\
@@ -768,7 +785,4 @@
 					./modules/Solverx/DofTypesToIndexSet.cpp
 
-#}}}
-#Gsl sources  {{{
-gsl_sources= ./modules/Solverx/SolverxGsl.cpp
 #}}}
 #Mpi sources  {{{
@@ -810,26 +824,10 @@
 #}}}
 #Matlab and Petsc sources  {{{
-matlabpetsc_sources= ./matlab/io/MatlabMatrixToPetscMatrix.cpp\
-					 ./matlab/io/MatlabVectorToPetscVector.cpp
-	
+matlabpetsc_sources= ./matlab/io/MatlabMatrixToPetscMat.cpp\
+					 ./matlab/io/MatlabVectorToPetscVec.cpp
+
 #}}}
 #Modules sources{{{
-module_sources= ./objects/Options/Option.cpp\
-			./objects/Options/Option.h\
-			./objects/Options/OptionDouble.cpp\
-			./objects/Options/OptionDouble.h\
-			./objects/Options/OptionLogical.cpp\
-			./objects/Options/OptionLogical.h\
-			./objects/Options/OptionChar.cpp\
-			./objects/Options/OptionChar.h\
-			./objects/Options/OptionStruct.cpp\
-			./objects/Options/OptionStruct.h\
-			./objects/Options/OptionCell.cpp\
-			./objects/Options/OptionCell.h\
-			./objects/Options/OptionUtilities.cpp\
-			./objects/Options/OptionUtilities.h\
-			./shared/Alloc/alloc_module.h\
-			./shared/Alloc/alloc_module.cpp\
-			./shared/Threads/issm_threads.h\
+module_sources= ./shared/Threads/issm_threads.h\
 			./shared/Threads/LaunchThread.cpp\
 			./shared/Threads/PartitionRange.cpp\
@@ -837,5 +835,4 @@
 			./shared/Exp/IsInPoly.cpp\
 			./shared/Exp/IsInPolySerial.cpp\
-			./shared/Exp/DomainOutlineRead.cpp\
 			./shared/Exp/DomainOutlineWrite.cpp\
 			./shared/TriMesh/trimesh.h\
@@ -918,8 +915,4 @@
 endif
 
-if GSL
-issm_sources  +=  $(gsl_sources)
-endif
-
 if TRANSIENT
 issm_sources  +=  $(transient_sources)
@@ -998,10 +991,28 @@
 libISSMCore_a_CXXFLAGS = $(ALLCXXFLAGS)
 
+if SHAREDLIBS
+libISSM_la_SOURCES = solutions/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
+endif
+
 if MODULES
 libISSMModules_a_SOURCES = $(module_sources)
 libISSMModules_a_SOURCES += $(bamg_sources)
+if KRIGING
 libISSMModules_a_SOURCES += $(kriging_sources)
+endif
+if KML
 libISSMModules_a_SOURCES += $(kml_sources)
+endif
 libISSMModules_a_CXXFLAGS = $(ALLCXXFLAGS)
+libISSMModules_a_LIBADD = ./libISSMCore.a
+if SHAREDLIBS
+libISSMModules_la_SOURCES = $(libISSMModules_a_SOURCES)
+endif
 endif
 
@@ -1014,6 +1025,14 @@
 libISSMMatlab_a_SOURCES = $(matlab_sources)
 libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS)
-endif
-
+if SHAREDLIBS
+libISSMMatlab_la_SOURCES = $(libISSMMatlab_a_SOURCES)
+endif
+endif
+
+if VERSION
+AM_LDFLAGS =
+else
+AM_LDFLAGS = -avoid-version
+endif
 #}}}
 #Overload library, to overload any non-standard symbols. {{{
Index: /issm/trunk/src/c/classes/DofIndexing.cpp
===================================================================
--- /issm/trunk/src/c/classes/DofIndexing.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/DofIndexing.cpp	(revision 13395)
@@ -0,0 +1,210 @@
+/*!\file DofIndexing.c
+ * \brief: implementation of the DofIndexing object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include "./classes.h"
+#include 
+#include "../EnumDefinitions/EnumDefinitions.h"
+#include "../shared/shared.h"
+#include "../Container/Container.h"
+#include "../include/include.h"
+
+/*DofIndexing constructors and destructor*/
+/*FUNCTION DofIndexing::DofIndexing(){{{*/
+DofIndexing::DofIndexing(){
+
+	this->gsize=UNDEF;
+	this->fsize=UNDEF;
+	this->ssize=UNDEF;
+	this->clone=0;
+	this->f_set=NULL;
+	this->s_set=NULL;
+	this->svalues=NULL;
+	this->doftype=NULL;
+	this->gdoflist=NULL;
+	this->fdoflist=NULL;
+	this->sdoflist=NULL;
+
+}
+/*}}}*/
+/*FUNCTION DofIndexing::DofIndexing(int gsize){{{*/
+DofIndexing::DofIndexing(int in_gsize){
+	this->Init(in_gsize,NULL);
+}
+/*}}}*/
+/*FUNCTION DofIndexing::DofIndexing(DofIndexing* in)  -> copy{{{*/
+DofIndexing::DofIndexing(DofIndexing* in){ //copy constructor
+
+	int i;
+	this->gsize=in->gsize;
+	this->fsize=in->fsize;
+	this->ssize=in->ssize;
+	
+	this->clone=in->clone;
+
+	if(this->gsize>0){
+		this->f_set=xNew(this->gsize);
+		this->s_set=xNew(this->gsize);
+		this->svalues=xNew(this->gsize);
+		if(in->doftype)this->doftype=xNew(this->gsize); 
+		this->gdoflist=xNew(this->gsize); 
+	}
+	else{
+		this->f_set=NULL;
+		this->s_set=NULL;
+		this->svalues=NULL;
+		this->doftype=NULL;
+		this->gdoflist=NULL;
+	}
+	if(this->fsize>0 && this->fsize!=UNDEF)this->fdoflist=xNew(this->fsize); else this->fdoflist=NULL;
+	if(this->ssize>0 && this->ssize!=UNDEF)this->sdoflist=xNew(this->ssize); else this->sdoflist=NULL;
+
+	if(this->gsize>0){
+		memcpy(this->f_set,in->f_set,this->gsize*sizeof(bool));
+		memcpy(this->s_set,in->s_set,this->gsize*sizeof(bool));
+		xMemCpy(this->svalues,in->svalues,this->gsize);
+		if(this->doftype)memcpy(this->doftype,in->doftype,this->gsize*sizeof(int));
+		memcpy(this->gdoflist,in->gdoflist,this->gsize*sizeof(int));
+	}
+	if(this->fsize>0 && this->fsize!=UNDEF)memcpy(this->fdoflist,in->fdoflist,this->fsize*sizeof(int));
+	if(this->ssize>0 && this->ssize!=UNDEF)memcpy(this->sdoflist,in->sdoflist,this->ssize*sizeof(int));
+
+}
+/*}}}*/
+/*FUNCTION DofIndexing::~DofIndexing() {{{*/
+DofIndexing::~DofIndexing(){ //destructor
+
+	xDelete(f_set); 
+	xDelete(s_set); 
+	xDelete(svalues);
+	xDelete(doftype); 
+	xDelete(gdoflist);
+	xDelete(fdoflist);
+	xDelete(sdoflist);
+
+}
+/*}}}*/
+/*FUNCTION DofIndexing::Init{{{*/
+void DofIndexing::Init(int in_gsize,int* in_doftype){
+
+	int i;
+	this->gsize=in_gsize;
+	
+	this->clone=0;
+
+	/*allocate: */
+	if(this->gsize>0){
+		this->f_set=xNew(this->gsize);
+		this->s_set=xNew(this->gsize);
+		this->svalues=xNew(this->gsize);
+		if(in_doftype)this->doftype=xNew(this->gsize);
+		this->gdoflist=xNew(this->gsize);
+	}
+
+	for (i=0;igsize;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;
+	}
+}
+/*}}}*/
+/*FUNCTION DofIndexing::InitSet{{{*/
+void DofIndexing::InitSet(int setenum){
+
+	int i;
+	int size=0;
+
+	/*go through sets, and figure out how many dofs belong to this set, except for g-set, 
+	 * which has already been initialized: */
+	if(setenum==FsetEnum){
+		size=0;
+		for(i=0;igsize;i++) if(f_set[i])size++;
+		this->fsize=size;
+		xDelete(this->fdoflist);
+		if(this->fsize)this->fdoflist=xNew(size);
+		else this->fdoflist=NULL;
+	}
+	else if(setenum==SsetEnum){
+		size=0;
+		for(i=0;igsize;i++) if(s_set[i])size++;
+		this->ssize=size;
+		xDelete(this->sdoflist);
+		if(this->ssize)this->sdoflist=xNew(size);
+		else this->sdoflist=NULL;
+	}
+	else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+}
+/*}}}*/
+
+/*Some of the Object functionality: */
+/*FUNCTION DofIndexing::Echo{{{*/
+void DofIndexing::Echo(void){
+
+	int i;
+
+	_printLine_("DofIndexing:");
+	_printLine_("   gsize: " << gsize);
+	_printLine_("   clone: " << clone);
+}
+/*}}}*/
+/*FUNCTION DofIndexing::DeepEcho{{{*/
+void DofIndexing::DeepEcho(void){
+
+	int i;
+
+	_printLine_("DofIndexing:");
+	_printLine_("   gsize: " << gsize);
+	_printLine_("   fsize: " << fsize);
+	_printLine_("   ssize: " << ssize);
+	_printLine_("   clone: " << clone);
+	
+	_printLine_("   set membership: f,s sets ");
+	for(i=0;issize << "): |");
+	for(i=0;igsize;i++){
+		if(this->s_set[i])_printString_(" " << svalues[i] << " |");
+	}
+	_printLine_("");
+
+	if(doftype){
+		_printString_("   doftype: |");
+		for(i=0;igsize << "): |");
+	for(i=0;igsize;i++){
+		_printString_(" " << gdoflist[i] << " |");
+	}
+	_printLine_("");
+
+	_printString_("   f_doflist (" << this->fsize << "): |");
+	for(i=0;ifsize;i++){
+		_printString_(" " << fdoflist[i] << " |");
+	}
+	_printLine_("");
+
+	_printString_("   s_doflist (" << this->ssize << "): |");
+	for(i=0;issize;i++){
+		_printString_(" " << sdoflist[i] << " |");
+	}
+	_printLine_("");
+}		
+/*}}}*/
+
Index: /issm/trunk/src/c/classes/DofIndexing.h
===================================================================
--- /issm/trunk/src/c/classes/DofIndexing.h	(revision 13395)
+++ /issm/trunk/src/c/classes/DofIndexing.h	(revision 13395)
@@ -0,0 +1,54 @@
+/*!\file: DofIndexing.h
+ * \brief prototype for DofIndexing.h
+ */ 
+
+#ifndef _DOFINDEXING_H_
+#define  _DOFINDEXING_H_
+
+#include "../include/include.h"
+
+class DofIndexing{
+	
+	public:
+
+		/*sizes: */
+		int gsize; //number of dofs for a node
+		int fsize; //number of dofs solver for
+		int ssize; //number of constrained dofs
+
+		/*partitioning: */
+		int     clone;   //this node is replicated from another one 
+
+		/*boundary conditions sets: */
+		bool*     f_set; //is dof on f-set (on which we solve)
+		bool*     s_set; //is dof on s-set (on which boundary conditions -dirichlet- are applied)
+		IssmDouble*   svalues; //list of constraint values. size g_size, for ease of use.
+
+		/*types of dofs: */
+		int*     doftype; //approximation type of the dofs (used only for coupling), size g_size
+		
+		/*list of degrees of freedom: */
+		int*     gdoflist; //dof list in g_set
+		int*     fdoflist; //dof list in f_set
+		int*     sdoflist; //dof list in s_set
+
+
+		/*DofIndexing constructors, destructors {{{*/
+		DofIndexing();
+		DofIndexing(int g_size);
+		void Init(int g_size,int* doftype);
+		void InitSet(int setenum);
+		DofIndexing(DofIndexing* properties);
+		~DofIndexing();
+		/*}}}*/
+		/*Object like functionality: {{{*/
+		void  Echo(void); 
+		void  DeepEcho(void); 
+		void  copy(DofIndexing* properties);
+		/*}}}*/
+		/*DofIndexing management: {{{*/
+		DofIndexing* Spawn(int* indices, int numindices);
+		/*}}}*/
+
+};
+#endif //ifndef _DOFINDEXING_H_
Index: /issm/trunk/src/c/classes/FemModel.cpp
===================================================================
--- /issm/trunk/src/c/classes/FemModel.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/FemModel.cpp	(revision 13395)
@@ -0,0 +1,159 @@
+/*!\file FemModel.c
+ * \brief: implementation of the FemModel object
+ */
+
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include "../Container/Container.h"
+#include "../modules/ModelProcessorx/ModelProcessorx.h"
+#include "../io/io.h"
+#include "./classes.h"
+#include "../include/include.h"
+#include "../EnumDefinitions/EnumDefinitions.h"
+#include "../modules/modules.h"
+
+/*Object constructors and destructor*/
+/*FUNCTION FemModel::constructor {{{*/
+FemModel::FemModel(char* rootpath, char* inputfilename, char* outputfilename, const int in_solution_type,const int* analyses,const int nummodels){
+
+	/*intermediary*/
+	int         i;
+	int         analysis_type;
+	FILE       *IOMODEL = NULL;
+	extern int  my_rank;
+
+	/*Open input file on cpu 0: */
+	if(my_rank==0) IOMODEL = pfopen(inputfilename ,"rb");
+
+	/*Initialize internal data: */
+	this->nummodels=nummodels;
+	this->solution_type=in_solution_type;
+	this->analysis_counter=nummodels-1; //point to last analysis_type carried out.
+	this->results=new Results(); //not initialized by CreateDataSets
+	
+	/*Dynamically allocate whatever is a list of length nummodels: */
+	analysis_type_list=xNew(nummodels);
+
+	/*Initialize: */
+	for(i=0;ielements,&this->nodes,&this->vertices,&this->materials,&this->constraints,&this->loads,&this->parameters,IOMODEL,rootpath,this->solution_type,nummodels,analyses);
+
+	/*do the post-processing of the datasets to get an FemModel that can actually run analyses: */
+	for(i=0;iSetCurrentConfiguration(analysis_type);
+	
+		if(i==0){
+			if(VerboseMProcessor()) _pprintLine_("      creating vertex degrees of freedom");
+			VerticesDofx(vertices,parameters); //only call once, we only have one set of vertices
+		}
+
+		if(VerboseMProcessor()) _pprintLine_("      resolving node constraints");
+		SpcNodesx(nodes,constraints,parameters,analysis_type); 
+
+		if(VerboseMProcessor()) _pprintLine_("      creating nodal degrees of freedom");
+		NodesDofx(nodes,parameters,analysis_type);
+	
+		if(VerboseMProcessor()) _pprintLine_("      configuring element and loads");
+		ConfigureObjectsx(elements, loads, nodes, vertices, materials,parameters);
+	}
+	
+	/*Close input file descriptors: */
+	if(my_rank==0) pfclose(IOMODEL,inputfilename);
+
+	/*Add output file name to parameters: */
+	this->parameters->AddObject(new StringParam(OutputfilenameEnum,outputfilename));
+
+}
+
+/*}}}*/
+/*FUNCTION FemModel::destructor {{{*/
+FemModel::~FemModel(){
+
+	/*Intermediary*/
+	int i;
+
+	/*Delete all the datasets: */
+	xDelete(analysis_type_list);
+	delete elements;
+	delete nodes;
+	delete vertices;
+	delete constraints;
+	delete loads;
+	delete materials;
+	delete parameters;
+	delete results;
+
+}
+/*}}}*/
+
+/*Object management*/
+/*FUNCTION FemModel::Echo {{{*/
+void FemModel::Echo(void){
+
+	_printLine_("FemModel echo: ");
+	_printLine_("   number of fem models: " << nummodels);
+	_printLine_("   analysis_type_list: ");
+	for(int i=0;iparameters->SetParam(analysis_counter,AnalysisCounterEnum);
+	this->parameters->SetParam(analysis_type,AnalysisTypeEnum);
+	this->parameters->SetParam(configuration_type,ConfigurationTypeEnum);
+
+	/*configure elements, loads and nodes, for this new analysis: */
+	this->elements->SetCurrentConfiguration(elements,loads, nodes,vertices, materials,parameters);
+	this->nodes->SetCurrentConfiguration(elements,loads, nodes,vertices, materials,parameters);
+	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
+
+}
+/*}}}*/
+/*FUNCTION FemModel::SetCurrentConfiguration(int configuration_type){{{*/
+void FemModel::SetCurrentConfiguration(int configuration_type){
+
+	/*overload: analysis_type = configuration_type: */
+	this->SetCurrentConfiguration(configuration_type,configuration_type);
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/FemModel.h
===================================================================
--- /issm/trunk/src/c/classes/FemModel.h	(revision 13395)
+++ /issm/trunk/src/c/classes/FemModel.h	(revision 13395)
@@ -0,0 +1,57 @@
+/*
+ * FemModel.h: 
+ */
+
+#ifndef _FEMMODEL_H_
+#define _FEMMODEL_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./objects/Object.h"
+#include "../toolkits/toolkits.h"
+class DataSet;
+class Parameters;
+class NodeSets;
+class Nodes;
+class Vertices;
+class Results;
+class Constraints;
+class Loads;
+class Materials;
+/*}}}*/
+
+
+class FemModel {
+
+	/*no private members, as we need access to these datasets quite often!:*/
+
+	public:
+
+		int                 nummodels;
+		int                 solution_type;
+		int*                analysis_type_list; //list of analyses this femmodel is going to carry out
+		int                 analysis_counter; //counter into analysis_type_list
+		
+		Elements*           elements; //elements (one set for all analyses)
+		Nodes*              nodes; //one set of nodes
+		Vertices*           vertices; //one set of vertices
+		Constraints*        constraints; //one set of constraints. each constraint knows which analysis_type it handles
+		Loads*              loads;  //one set of constraints. each constraint knows which analysis_type it handles
+		Materials*          materials;  //one set of materials, for each element
+		Parameters*         parameters; //one set of parameters, independent of the analysis_type
+		Results*            results; //results that cannot be fit into the elements (such as one time constants, arrays, strings, etc ...)
+
+		/*constructors, destructors: */
+		FemModel(char* rootpath, char* inputfilename, char* outputfilename, const int solution_type,const int* analyses,const int nummodels);
+		~FemModel();
+
+		/*Methods: */
+		void Echo();
+
+		/*Fem: */
+		void  SetCurrentConfiguration(int configuration_type);
+		void  SetCurrentConfiguration(int configuration_type,int analysis_type);
+
+};
+
+#endif
Index: /issm/trunk/src/c/classes/Hook.cpp
===================================================================
--- /issm/trunk/src/c/classes/Hook.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/Hook.cpp	(revision 13395)
@@ -0,0 +1,266 @@
+/*!\file Hook.cpp
+ * \brief: implementation of the Hook object: see Hook.h for more explanations.
+ */
+
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "./classes.h"
+#include "../Container/Container.h"
+#include "../EnumDefinitions/EnumDefinitions.h"
+#include "../shared/shared.h"
+#include "../include/include.h"
+
+
+/*Constructor/Destructors*/
+/*FUNCTION Hook::Hook(){{{*/
+Hook::Hook(){
+	this->num=0;
+	this->objects=NULL;
+	this->ids=NULL;
+	this->offsets=NULL;
+	return;
+}
+/*}}}*/
+/*FUNCTION Hook::Hook(int* ids, int num){{{*/
+Hook::Hook(int* in_ids, int in_num){
+
+	/*Intermediaries*/
+	int i;
+
+	/*Get number of objects to hook*/
+	this->num=in_num;
+
+	/*Get out if num=0*/
+	if (num==0){
+		/*Empty hook*/
+		this->ids=NULL;
+		this->objects=NULL;
+		this->offsets=NULL;
+	}
+	else{
+		/*Allocate: */
+		this->objects=xNew(this->num);
+		this->ids=xNew(this->num);
+		this->offsets=xNew(this->num);
+
+		/*Copy ids: */
+		for (i=0;inum;i++){
+			this->ids[i]=in_ids[i];
+			this->objects[i]=NULL;
+			this->offsets[i]=0;
+		}
+	}
+}
+/*}}}*/
+/*FUNCTION Hook::~Hook(){{{*/
+Hook::~Hook(){
+	/*deallocate: */
+	xDelete(this->objects);
+	xDelete(this->ids);
+	xDelete(this->offsets);
+	return;
+}
+/*}}}*/
+
+/*Some of the Object functionality: */
+/*FUNCTION Hook::Echo{{{*/
+void Hook::Echo(void){
+
+	int i;
+	if (num){
+		_printLine_("   Hook: ");
+		_printLine_("      num=" << this->num);
+		_printString_("      ids: ");
+		for (i=0;inum;i++) _printString_(this->ids[i] << " ");
+		_printLine_("");
+		_printString_("      offsets: ");
+		for (i=0;inum;i++) _printString_(this->offsets[i] << " ");
+		_printLine_("");
+	}
+	else{
+		_printLine_("   Hook: num=0 ");
+	}
+}
+/*}}}*/
+/*FUNCTION Hook::DeepEcho{{{*/
+void Hook::DeepEcho(void){
+
+	int i;
+	if (num){
+		_printLine_("   Hook: ");
+		_printLine_("      num=" << this->num);
+		_printString_("      ids: ");
+		for (i=0;inum;i++) _printString_(this->ids[i] << " ");
+		_printLine_("");
+		_printString_("      offsets: ");
+		for (i=0;inum;i++) _printString_(this->offsets[i] << " ");
+		_printLine_("");
+		if (!objects) _printLine_("      warning: object not hooked yet");
+		else{
+			_printString_("      objects:\n   ");
+			for (i=0;inum;i++){
+				_printLine_("         object " << i);
+				if(objects[i]) objects[i]->DeepEcho();
+				else           _printLine_("            no object hooked yet (not configured)");
+			}
+		}
+	}
+	else{
+		_printLine_("   Hook: num=0 ");
+	}
+}
+/*}}}*/
+/*FUNCTION Hook::copy {{{*/
+Object* Hook::copy(void){
+
+	int i;
+
+	/*output: */
+	Hook* output=NULL;
+
+	/*initalize output: */
+	output=new Hook();
+
+	/*copy in the fields: */
+	output->num=this->num;
+	if(output->num){
+		output->objects=xNew(output->num);
+		output->ids=xNew(output->num);
+		output->offsets=xNew(output->num);
+	}
+	
+	for(i=0;inum;i++){
+		output->objects[i]=this->objects[i];
+		output->offsets[i]=this->offsets[i];
+		output->ids[i]=this->ids[i];
+	}
+
+	return (Object*)output;
+}
+/*}}}*/
+
+/*Hook management: */
+/*FUNCTION Hook::configure{{{*/
+void Hook::configure(DataSet* dataset){
+
+	/*intermediary: */
+	Object* object=NULL;
+	int i;
+
+	/*Checks if debugging mode*/
+	_assert_(this->num==0 || this->ids!=NULL);
+
+	for(i=0;inum;i++){
+
+		/*is this object id -1? If so, drop this search, it was not requested: */
+		if (this->ids[i]==-1) continue;
+
+		/*Check whether existing this->objects are correct: */
+		if(this->objects[i]){
+			if(this->objects[i]->Id()==this->ids[i]) continue; //this node is good.
+			else this->objects[i]=NULL; //this node was incorrect, reset it.
+		}
+
+		/*May be the object this->offsets into this->objects are valid?: */
+		if(this->offsets[i]!=UNDEF){
+			/* Look at the this->offsets[i]'th node in the nodes dataset. If it has the correct id, 
+			 * we are good: */
+			object=(Object*)dataset->GetObjectByOffset(this->offsets[i]);
+			if (object->Id()==this->ids[i]){
+				this->objects[i]=object;
+				continue;
+			}
+			else this->offsets[i]=UNDEF; //object offset was wrong, reset it.
+		}
+
+		/*Now, for this->objects that did not get resolved, and for which we have no offset, chase them in the dataset, by id: */
+		if(this->objects[i]==NULL){
+			this->objects[i]=(Object*)dataset->GetObjectById(this->offsets+i,this->ids[i]); //remember the offset for later on.
+			/*check the id is correct!: */
+			if (this->objects[i]->Id()!=this->ids[i]) _error_("wrong id: " << this->objects[i]->Id() << " vs " << this->ids[i] << "  in resolved pointer!");
+		}
+	}
+}
+/*}}}*/
+/*FUNCTION Hook::delivers{{{*/
+Object* Hook::delivers(void){
+	
+	/*first, check that we only have one T object in our object list: */
+	if (this->num!=1) _error_("trying to delivery a single hook object when hook holds " << this->num << " objects" << "\n");
+
+	/*check NULL: */
+	if (this->objects==NULL) _error_("hook is not pointing to any object, objects pointer is NULL");
+
+	return *objects;
+}
+
+/*}}}*/
+/*FUNCTION Hook::deliverp{{{*/
+Object** Hook::deliverp(void){
+	return objects;
+}
+/*}}}*/
+/*FUNCTION Hook::Ids{{{*/
+int* Hook::Ids(void){
+	return this->ids;
+}
+/*}}}*/
+/*FUNCTION Hook::GetNum{{{*/
+int Hook::GetNum(void){
+	return this->num;
+}
+/*}}}*/
+/*FUNCTION Hook::GetObjects{{{*/
+Object** Hook::GetObjects(void){
+	return this->objects;
+}
+/*}}}*/
+/*FUNCTION Hook::GetOffsets{{{*/
+int* Hook::GetOffsets(void){
+	return this->offsets;
+}
+/*}}}*/
+/*FUNCTION Hook::Spawn{{{*/
+Hook* Hook::Spawn(int* indices, int numindices){
+
+	int i;
+
+	/*output: */
+	Hook* output=NULL;
+
+	/*allocate: */
+	output=new Hook();
+
+	/*If this Hook is empty, simply return*/
+	if(this->num==0){
+		output->num=0;
+		return output;
+	}
+
+	/*Else, check that we are requesting a half of num*/
+	if (numindices>this->num) _error_("Cannot spawn hook with " << numindices << " objects from a Hook of " << this->num << " objects");
+
+	/*go pickup the correct objects, ids and offsets :*/
+	output->num=numindices;
+	if(output->num<1) _error_("Trying to spawn an empty ElementProperties!");
+
+	output->objects=xNew(output->num);
+	output->ids=xNew(output->num);
+	output->offsets=xNew(output->num);
+
+	for(i=0;inum;i++){
+		output->objects[i]=this->objects[indices[i]];
+		output->ids[i]=this->ids[indices[i]];
+		output->offsets[i]=this->offsets[indices[i]];
+	}
+
+	return output;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/Hook.h
===================================================================
--- /issm/trunk/src/c/classes/Hook.h	(revision 13395)
+++ /issm/trunk/src/c/classes/Hook.h	(revision 13395)
@@ -0,0 +1,50 @@
+/*!\file Hook.h
+ * \brief: header file for hook object.
+ * A hook is a class  that can store the id, offset, and object corresponding to this id and offset into a dataset.
+ * For example, an element has a hook to its nodes. A node has a hook to its vertex.  The hook abstracts the need for having
+ * ids and offsets (necesarry for proper configuration of an object) in our objects. 
+ */
+
+#ifndef _HOOK_H_
+#define _HOOK_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./objects/Object.h"
+class DataSet;
+/*}}}*/
+
+class Hook{
+
+	private: 
+
+		int	   num; //number of objects being hooked onto
+		Object**	   objects; //list of object pointers. we do not allocate objects, just a list a pointers, that will get to point to the real objects from a dataset.
+		int*   ids;     //list of object ids, to go look for them in datasets.
+		int*   offsets;  //list of object offsets into datasets, to speed up lookup.
+
+	public:
+
+		/*Hook constructors, destructors: {{{*/
+		Hook();
+		Hook(int* ids, int num);
+		~Hook();
+		/*}}}*/
+		/*Object like functionality:{{{*/
+		void       Echo(void);
+		void       DeepEcho(void);
+		Object*    copy(void);
+		/*}}}*/
+		/*Hook management: {{{*/
+		Object*    delivers(void); //single object deliver
+		Object**   deliverp(void); //deliver all objects
+		void       configure(DataSet* dataset);
+		Hook*      Spawn(int* indices, int numindices);
+		Object**   GetObjects(void);
+		int*       Ids(void);
+		int*       GetOffsets(void);
+		int        GetNum(void);
+		/*}}}*/
+};
+
+#endif  /* _HOOK_H_ */
Index: /issm/trunk/src/c/classes/IoModel.cpp
===================================================================
--- /issm/trunk/src/c/classes/IoModel.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/IoModel.cpp	(revision 13395)
@@ -0,0 +1,1375 @@
+/*! \file IoModel.cpp
+ * \brief  file containing the methods that will help in processing the input data coming 
+ * into ISSM, from Matlab, or through a binary file opened for reading.
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include 
+#include 
+
+#include "./classes.h"
+#include "../io/io.h"
+#include "./Container/Parameters.h"
+#include "../shared/shared.h"
+#include "../io/io.h"
+#include "../include/include.h"
+
+/*FUNCTION IoModel::IoModel(){{{*/
+IoModel::IoModel(){
+	this->fid=NULL;
+	this->data=NULL;
+	this->independents=NULL;
+	this->constants=NULL;
+	
+	this->my_elements=NULL;
+	this->my_nodes=NULL;
+	this->my_vertices=NULL;
+	this->singlenodetoelementconnectivity=NULL;
+	this->numbernodetoelementconnectivity=NULL;
+	
+	this->nodecounter=0;
+	this->loadcounter=0;
+	this->constraintcounter=0;
+}
+/*}}}*/
+/*FUNCTION IoModel::IoModel(FILE*  iomodel_handle){{{*/
+IoModel::IoModel(FILE* iomodel_handle){
+	
+	/*First, keep track of the file handle: */
+	this->fid=iomodel_handle;
+
+	/*Check that Enums are Synchronized*/
+	this->CheckEnumSync();
+
+	/*Initialize and read constants:*/
+	this->constants=new Parameters();
+	this->FetchConstants(); /*this routine goes through the input file, and fetches bools, ints, IssmDoubles and strings only, nothing memory intensive*/
+
+	/*Initialize data: */
+	this->data=xNew(MaximumNumberOfEnums);
+	for(int i=0;idata[i]=NULL;
+
+	/*Initialize array detecting whether data[i] is an independent AD mode variable: */
+	this->independents=xNew(MaximumNumberOfEnums);
+	for(int i=0;iindependents[i]=false;
+	
+	/*Initialize permanent data: */
+	this->my_elements=NULL;
+	this->my_nodes=NULL;
+	this->my_vertices=NULL;
+	this->singlenodetoelementconnectivity=NULL;
+	this->numbernodetoelementconnectivity=NULL;
+	
+	this->nodecounter=0;
+	this->loadcounter=0;
+	this->constraintcounter=0;
+}
+/*}}}*/
+/*FUNCTION IoModel::~IoModel(){{{*/
+IoModel::~IoModel(){
+
+	if(this->constants) delete this->constants;
+
+	/*Some checks in debugging mode*/
+	#ifdef _ISSM_DEBUG_
+	if(this->data){
+		for(int i=0;idata[i]){
+				_pprintLine_("Info: previous pointer of " << EnumToStringx(i) << " has not been freed (DeleteData has not been called)");
+			}
+		}
+	}
+	#endif
+
+	xDelete(this->data);
+	xDelete(this->independents);
+	xDelete(this->my_elements);
+	xDelete(this->my_nodes);
+	xDelete(this->my_vertices);
+	xDelete(this->singlenodetoelementconnectivity);
+	xDelete(this->numbernodetoelementconnectivity);
+}
+/*}}}*/
+
+/*FUNCTION IoModel::CheckEnumSync{{{*/
+void  IoModel::CheckEnumSync(void){
+
+	extern int my_rank;
+	int record_enum = 0;
+
+	/*Check that some fields have been allocated*/
+	_assert_(this->fid || my_rank);
+
+	/*Go find in the binary file, the position of the data we want to fetch: */
+	if(my_rank==0){ //cpu 0
+
+		/*First set FILE* position to the beginning of the file: */
+		fseek(this->fid,0,SEEK_SET);
+
+		/*Get first Enum*/
+		if(fread(&record_enum,sizeof(int),1,this->fid)==0){
+			_error_("Marshalled file is empty");
+		}
+		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_("");
+				_error_("Enums not consistent (See error message above)");
+			}
+		}
+	}
+}
+/*}}}*/
+/*FUNCTION IoModel::Constant(bool* poutput,int constant_enum){{{*/
+void IoModel::Constant(bool* poutput,int constant_enum){
+
+	_assert_(constant_enum>=0);
+	_assert_(this->constants);
+
+	this->constants->FindParam(poutput,constant_enum);
+}
+/*}}}*/
+/*FUNCTION IoModel::Constant(int* poutput,int constant_enum){{{*/
+void IoModel::Constant(int* poutput,int constant_enum){
+
+	_assert_(constant_enum>=0);
+	_assert_(this->constants);
+
+	this->constants->FindParam(poutput,constant_enum);
+}
+/*}}}*/
+/*FUNCTION IoModel::Constant(IssmDouble* poutput,int constant_enum){{{*/
+void IoModel::Constant(IssmDouble* poutput,int constant_enum){
+
+	_assert_(constant_enum>=0);
+	_assert_(this->constants);
+
+	this->constants->FindParam(poutput,constant_enum);
+}
+/*}}}*/
+/*FUNCTION IoModel::Constant(char** poutput,int constant_enum){{{*/
+void IoModel::Constant(char** poutput,int constant_enum){
+
+	_assert_(constant_enum>=0);
+	_assert_(this->constants);
+
+	this->constants->FindParam(poutput,constant_enum);
+}
+/*}}}*/
+/*FUNCTION IoModel::CopyConstantObject{{{*/
+Param* IoModel::CopyConstantObject(int constant_enum){
+
+	_assert_(this->constants);
+
+	/*Find constant*/
+	Param* param=(Param*)this->constants->FindParamObject(constant_enum);
+	if(!param) _error_("Constant " << EnumToStringx(constant_enum) << " not found in iomodel");
+
+	return (Param*)param->copy();
+}
+/*}}}*/
+/*FUNCTION IoModel::Data{{{*/
+IssmDouble* IoModel::Data(int data_enum){
+
+	_assert_(data_enum=0);
+
+	return this->data[data_enum];
+}
+/*}}}*/
+/*FUNCTION IoModel::DeleteData(int num,...){{{*/
+void  IoModel::DeleteData(int num,...){
+
+	va_list ap;
+	int     dataenum;
+	int     i;
+	DoubleMatParam* parameter=NULL;
+
+	/*Go through the entire list of enums and delete the corresponding data from the iomodel-data dataset: */
+
+	va_start(ap,num);
+	for(i = 0; i independents[dataenum]) xDelete(this->data[dataenum]);
+	}
+	va_end(ap);
+} /*}}}*/
+/*FUNCTION IoModel::DeleteData(IssmDouble* {{{*/
+void  IoModel::DeleteData(IssmDouble* vector, int dataenum){
+
+	/*do not erase independent variables for the AD mode computations!: */
+	if(vector)if (!this->independents[dataenum]) xDelete(vector);
+
+} /*}}}*/
+/*FUNCTION IoModel::FetchConstants{{{*/
+void  IoModel::FetchConstants(void){
+
+	extern int my_rank;
+	extern int num_procs;
+	
+	/*record descriptions; */
+	int record_enum;
+	int record_length;
+	int record_code; //1 to 7 number
+
+	/*records: */
+	int  booleanint=0;
+	int  integer=0;
+	IssmPDouble scalar=0;
+	char* string=NULL;
+	int   string_size;
+
+	/*Check that some fields have been allocated*/
+	_assert_(this->fid || my_rank);
+	_assert_(this->constants);
+
+	/*Go find in the binary file, the position of the data we want to fetch: */
+	if(my_rank==0){ //cpu 0{{{
+	
+		/*First set FILE* position to the beginning of the file: */
+		fseek(this->fid,0,SEEK_SET);
+
+		/*Now march through file looking for the correct data identifiers (bool,int,IssmDouble or string): */
+		for(;;){
+			if(fread(&record_enum,sizeof(int),1,this->fid)==0){
+
+				/*Ok, we have reached the end of the file. break: */
+				record_code=0; //0 means bailout
+				#ifdef _HAVE_MPI_
+				MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD);  /*tell others cpus we are bailing: */
+				#endif
+				break;
+			}
+			else{
+			
+				/* 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);
+					
+				#ifdef _HAVE_MPI_
+				/*Tell other cpus what we are doing: */
+				MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD);  /*tell other cpus what we are going to do: */
+
+				/*Tell other cpus the name of the data, then branch according to the data type: */
+				MPI_Bcast(&record_enum,1,MPI_INT,0,MPI_COMM_WORLD);  
+				MPI_Bcast(&record_length,1,MPI_INT,0,MPI_COMM_WORLD);  
+				#endif
+				
+				switch(record_code){
+					case 1: 
+						/*Read the boolean and broadcast it to other cpus:*/
+						if(fread(&booleanint,sizeof(int),1,this->fid)!=1) _error_("could not read boolean ");
+						#ifdef _HAVE_MPI_
+						MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); 
+						#endif
+
+						/*create BoolParam: */
+						this->constants->AddObject(new BoolParam(record_enum,(bool)booleanint)); //cast to boolean
+
+						break;
+					case 2:
+						/*Read the integer and broadcast it to other cpus:*/
+						if(fread(&integer,sizeof(int),1,this->fid)!=1) _error_("could not read integer ");
+						#ifdef _HAVE_MPI_
+						MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); 
+						#endif
+
+						/*create IntParam: */
+						this->constants->AddObject(new IntParam(record_enum,integer));
+
+						break;
+					case 3:
+						/*Read the scalar and broadcast it to other cpus:*/
+						if(fread(&scalar,sizeof(IssmPDouble),1,this->fid)!=1) _error_("could not read scalar ");
+						#ifdef _HAVE_MPI_
+						MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); 
+						#endif
+
+						/*create DoubleParam: */
+						this->constants->AddObject(new DoubleParam(record_enum,scalar));
+
+						break;
+					case 4: 
+						/*We have to read a string from disk. First read the dimensions of the string, then the string: */
+						if(fread(&string_size,sizeof(int),1,this->fid)!=1) _error_("could not read length of string ");
+						#ifdef _HAVE_MPI_
+						MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); 
+						#endif
+
+						if(string_size){
+							string=xNew(string_size+1);
+							string[string_size]='\0';
+
+							/*Read string, then broadcast: */
+							if(fread(string,string_size*sizeof(char),1,this->fid)!=1)_error_(" could not read string ");
+							#ifdef _HAVE_MPI_
+							MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); 
+							#endif
+						}
+						else{
+							string=xNew(1);
+							string[0]='\0';
+						}
+						
+						/*Add string to parameters: */
+						this->constants->AddObject(new StringParam(record_enum,string));
+
+						/*Free string*/
+						xDelete(string);
+
+						break;
+					case 5: 
+							/*We are not interested in this record, too memory intensive. Skip it: */
+							/*skip: */
+							fseek(fid,-sizeof(int),SEEK_CUR); //backtrak 1 integer
+							fseek(fid,record_length,SEEK_CUR);
+							break;
+					case 6: 
+							/*We are not interested in this record, too memory intensive. Skip it: */
+							/*skip: */
+							fseek(fid,-sizeof(int),SEEK_CUR); //backtrak 1 integer
+							fseek(fid,record_length,SEEK_CUR);
+							break;
+					case 7: 
+							/*We are not interested in this record, too memory intensive. Skip it: */
+							/*skip: */
+							fseek(fid,-sizeof(int),SEEK_CUR); //backtrak 1 integer
+							fseek(fid,record_length,SEEK_CUR);
+							break;
+
+					case 8: 
+							/*We are not interested in this record, too memory intensive. Skip it: */
+							/*skip: */
+							fseek(fid,-sizeof(int),SEEK_CUR); //backtrak 1 integer
+							fseek(fid,record_length,SEEK_CUR);
+							break;
+
+					case 9: 
+							/*We are not interested in this record, too memory intensive. Skip it: */
+							/*skip: */
+							fseek(fid,-sizeof(int),SEEK_CUR); //backtrak 1 integer
+							fseek(fid,record_length,SEEK_CUR);
+							break;
+
+					default: 
+						_error_("unknown record type:" << record_code); 
+						break;;
+				}
+			}
+		}
+	} //}}}
+	#ifdef _HAVE_MPI_
+	else{ //cpu ~0 {{{
+		for(;;){ //wait on cpu 0
+			MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD);  /*get from cpu 0 what we are going to do: */
+			if(record_code==0){
+				break; //we are done, break from the loop
+			}
+			else{
+				MPI_Bcast(&record_enum,1,MPI_INT,0,MPI_COMM_WORLD);   //get from cpu 0 name of the data
+				MPI_Bcast(&record_length,1,MPI_INT,0,MPI_COMM_WORLD);  
+				switch(record_code){
+				case 1: 
+					/*boolean. get it from cpu 0 */
+					MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); 
+						
+					/*create BoolParam: */
+					this->constants->AddObject(new BoolParam(record_enum,(bool)booleanint)); //cast to a boolean
+					break;
+
+				case 2:
+					/*integer. get it from cpu 0 */
+					MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); 
+						
+					/*create IntParam: */
+					this->constants->AddObject(new IntParam(record_enum,integer));
+
+					break;
+				case 3:
+					/*scalar. get it from cpu 0 */
+					MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); 
+						
+					/*create DoubleParam: */
+					this->constants->AddObject(new DoubleParam(record_enum,scalar));
+
+					break;
+				case 4: 
+					MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); 
+					if(string_size){
+						string=xNew((string_size+1));
+						string[string_size]='\0';
+
+						/*Read string from cpu 0: */
+						MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); 
+					}
+					else{
+						string=xNew(1);
+						string[0]='\0';
+					}
+					/*Add string to parameters: */
+					this->constants->AddObject(new StringParam(record_enum,string));
+
+					/*Free string*/
+					xDelete(string);
+
+					break;
+				case 5: break; //do nothing. not interested in this type of data, which is memory intensive.
+				case 6: break; //do nothing. not interested in this type of data, which is memory intensive.
+				case 7: break; //do nothing. not interested in this type of data, which is memory intensive.
+				case 8: break; //do nothing. not interested in this type of data, which is memory intensive.
+				case 9: break; //do nothing. not interested in this type of data, which is memory intensive.
+
+				default: 
+					_error_("unknown record type:" << record_code); 
+					break;;
+				}
+
+
+			}
+		}
+	} //}}}
+	#endif
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(bool*     pbool,int data_enum){{{*/
+void  IoModel::FetchData(bool* pboolean,int data_enum){
+
+	extern int my_rank;
+	extern int num_procs;
+	
+
+	/*output: */
+	int   booleanint;
+	int   code;
+	
+	/*Set file pointer to beginning of the data: */
+	fid=this->SetFilePointerToData(&code,NULL,data_enum);
+
+	if(code!=1)_error_("expecting a boolean for enum " << EnumToStringx(data_enum));
+	
+	/*We have to read a boolean from disk. */
+	if(my_rank==0){  
+		if(fread(&booleanint,sizeof(int),1,fid)!=1) _error_("could not read boolean ");
+	}
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	/*cast to bool: */
+	/*Assign output pointers: */
+	*pboolean=(bool)booleanint;
+
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(int*      pinteger,int data_enum){{{*/
+void  IoModel::FetchData(int* pinteger,int data_enum){
+
+	extern int my_rank;
+	extern int num_procs;
+
+	/*output: */
+	int   integer;
+	int   code;
+	
+	/*Set file pointer to beginning of the data: */
+	fid=this->SetFilePointerToData(&code,NULL,data_enum);
+	
+	if(code!=2)_error_("expecting an integer for enum " << EnumToStringx(data_enum));
+	
+	/*We have to read a integer from disk. First read the dimensions of the integer, then the integer: */
+	if(my_rank==0){  
+		if(fread(&integer,sizeof(int),1,fid)!=1) _error_("could not read integer ");
+	}
+
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	/*Assign output pointers: */
+	*pinteger=integer;
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(IssmDouble*   pscalar,int data_enum){{{*/
+void  IoModel::FetchData(IssmDouble* pscalar,int data_enum){
+
+
+	extern int my_rank;
+	extern int num_procs;
+	
+
+	/*output: */
+	IssmPDouble   scalar;
+	int      code;
+
+	/*Set file pointer to beginning of the data: */
+	fid=this->SetFilePointerToData(&code,NULL,data_enum);
+	
+	if(code!=3)_error_("expecting a IssmDouble for enum " << EnumToStringx(data_enum));
+	
+	/*We have to read a scalar from disk. First read the dimensions of the scalar, then the scalar: */
+	if(my_rank==0){
+		if(fread(&scalar,sizeof(IssmPDouble),1,fid)!=1)_error_("could not read scalar ");
+	}
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); 
+	#endif
+
+	/*Assign output pointers: */
+	*pscalar=scalar;
+		 
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(char**    pstring,int data_enum){{{*/
+void  IoModel::FetchData(char** pstring,int data_enum){
+
+	extern int my_rank;
+	extern int num_procs;
+	
+
+	/*output: */
+	char* string=NULL;
+	int   string_size;
+	int code=0;
+
+	/*Set file pointer to beginning of the data: */
+	fid=this->SetFilePointerToData(&code,NULL,data_enum);
+	
+	if(code!=4)_error_("expecting a string for enum " << EnumToStringx(data_enum));
+	
+	/*Now fetch: */
+	
+	/*We have to read a string from disk. First read the dimensions of the string, then the string: */
+	if(my_rank==0){  
+		if(fread(&string_size,sizeof(int),1,fid)!=1) _error_("could not read length of string ");
+	}
+
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	/*Now allocate string: */
+	if(string_size){
+		string=xNew((string_size+1));
+		string[string_size]='\0';
+
+		/*Read string on node 0, then broadcast: */
+		if(my_rank==0){  
+			if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string ");
+		}
+		#ifdef _HAVE_MPI_
+		MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); 
+		#endif
+	}
+	else{
+		string=xNew(1);
+		string[0]='\0';
+	}
+
+
+	/*Assign output pointers: */
+	*pstring=string;
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(int**     pintegerematrix,int* pM,int* pN,int data_enum){{{*/
+void  IoModel::FetchData(int** pmatrix,int* pM,int* pN,int data_enum){
+
+	extern int my_rank;
+	extern int num_procs;
+	int i,j;
+
+	/*output: */
+	int M,N;
+	IssmPDouble* matrix=NULL;
+	int*    integer_matrix=NULL;
+	int code=0;
+	int vector_type=0;
+
+
+	/*Set file pointer to beginning of the data: */
+	fid=this->SetFilePointerToData(&code,&vector_type,data_enum);
+
+	if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(data_enum));
+	
+	/*Now fetch: */
+
+	/*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */
+	/*numberofelements: */
+	if(my_rank==0){  
+		if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix ");
+	}
+
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	if(my_rank==0){  
+		if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix ");
+	}
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD);
+	#endif
+
+	/*Now allocate matrix: */
+	if(M*N){
+		matrix=xNew(M*N);
+
+		/*Read matrix on node 0, then broadcast: */
+		if(my_rank==0){  
+			if(fread(matrix,M*N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix ");
+		}
+		
+		#ifdef _HAVE_MPI_
+		MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); 
+		#endif
+	}
+
+	/*Now cast to integer: */
+	if(M*N){
+		integer_matrix=xNew(M*N);
+		for (i=0;i(matrix);
+
+	/*Assign output pointers: */
+	*pmatrix=integer_matrix;
+	if (pM)*pM=M;
+	if (pN)*pN=N;
+
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(IssmDouble**  pIssmDoublematrix,int* pM,int* pN,int data_enum){{{*/
+void  IoModel::FetchData(IssmDouble** pmatrix,int* pM,int* pN,int data_enum){
+
+	extern int my_rank;
+	extern int num_procs;
+
+	/*output: */
+	int M,N;
+	IssmPDouble* matrix=NULL;
+	int code=0;
+	int vector_type=0;
+
+	/*Set file pointer to beginning of the data: */
+	fid=this->SetFilePointerToData(&code,&vector_type,data_enum);
+	if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(data_enum));
+	
+	/*Now fetch: */
+
+	/*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */
+	/*numberofelements: */
+	if(my_rank==0){  
+		if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix ");
+	}
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	if(my_rank==0){  
+		if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix ");
+	}
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	/*Now allocate matrix: */
+	if(M*N){
+		matrix=xNew(M*N);
+
+		/*Read matrix on node 0, then broadcast: */
+		if(my_rank==0){  
+			if(fread(matrix,M*N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix ");
+		}
+		#ifdef _HAVE_MPI_
+		MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); 
+		#endif
+
+		_assert_(this->independents);
+		if (this->independents[data_enum]){
+			/*this data has already been checked out! So cancel all that we've done here, and return 
+			 * the data[data_enum] directly: */
+			*pmatrix=this->data[data_enum];
+		}
+		else{
+			*pmatrix=xNew(M*N);
+			for (int i=0;i(matrix);
+	}
+	else
+	  *pmatrix=NULL;
+	/*Assign output pointers: */
+	if (pM)*pM=M;
+	if (pN)*pN=N;
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(char***   pstrings,int* pnumstrings,int data_enum){{{*/
+void  IoModel::FetchData(char*** pstrings,int* pnumstrings,int data_enum){
+
+	extern int my_rank;
+	extern int num_procs;
+	
+	int i;
+
+	/*output: */
+	int   numstrings=0;
+	char** strings=NULL;
+	
+	/*intermediary: */
+	char* string=NULL;
+	int   string_size;
+	int   code;
+	
+	/*Set file pointer to beginning of the data: */
+	fid=this->SetFilePointerToData(&code,NULL,data_enum);
+	
+	if(code!=9)_error_("expecting a string array for enum " << EnumToStringx(data_enum));
+	
+	/*We have to read a bunch of strings from disk. First read the number of strings, and allocate: */
+	if(my_rank==0){  
+		if(fread(&numstrings,sizeof(int),1,fid)!=1) _error_("could not read length of string array");
+	}
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&numstrings,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	/*Now allocate string array: */
+	if(numstrings){
+		strings=xNew(numstrings);
+		for(i=0;i((string_size+1));
+				string[string_size]='\0';
+
+				/*Read string on node 0, then broadcast: */
+				if(my_rank==0){  
+					if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string ");
+				}
+				#ifdef _HAVE_MPI_
+				MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); 
+				#endif
+			}
+			else{
+				string=xNew(1);
+				string[0]='\0';
+			}
+
+			strings[i]=string;
+		}
+	}
+
+	/*Assign output pointers: */
+	*pstrings=strings;
+	*pnumstrings=numstrings;
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(IssmDouble*** pmatrices,int** pmdims,int** pndims, int* pM,int data_enum){{{*/
+void  IoModel::FetchData(IssmDouble*** pmatrices,int** pmdims,int** pndims, int* pnumrecords,int data_enum){
+
+	int i;
+
+	extern int my_rank;
+	extern int num_procs;
+
+	/*output: */
+	IssmDouble** matrices=NULL;
+	int*     mdims=NULL;
+	int*     ndims=NULL;
+	int      numrecords=0;
+
+	/*intermediary: */
+	int     M, N;
+	IssmPDouble *matrix = NULL;
+	int     code;
+	
+	/*Set file pointer to beginning of the data: */
+	fid=this->SetFilePointerToData(&code,NULL,data_enum);
+	if(code!=8)_error_("expecting a IssmDouble mat array for enum " << EnumToStringx(data_enum));
+	
+	/*Now fetch: */
+	if(my_rank==0){  
+		if(fread(&numrecords,sizeof(int),1,fid)!=1) _error_("could not read number of records in matrix array ");
+	}
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&numrecords,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	if(numrecords){
+
+		/*Allocate matrices :*/
+		matrices=xNew(numrecords);
+		mdims=xNew(numrecords);
+		ndims=xNew(numrecords);
+
+		for(i=0;i(M*N);
+
+				/*Read matrix on node 0, then broadcast: */
+				if(my_rank==0){  
+					if(fread(matrix,M*N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix ");
+				}
+
+				#ifdef _HAVE_MPI_
+				MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); 
+				#endif
+				matrices[i]=xNew(M*N);
+				for (int j=0;j(matrix);
+			}
+			else
+			  matrices[i]=NULL;
+			/*Assign: */
+			mdims[i]=M;
+			ndims[i]=N;
+		}
+	}
+
+	/*Assign output pointers: */
+	*pmatrices=matrices;
+	*pmdims=mdims;
+	*pndims=ndims;
+	*pnumrecords=numrecords;
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(Option**  poption,int data_enum){{{*/
+void  IoModel::FetchData(Option** poption,int index){
+
+	extern int my_rank;
+	extern int num_procs;
+
+	/*output: */
+	int     code;
+	char   *name        = NULL;
+
+	/*First get option name*/
+	this->FetchData(&name,index);
+
+	/*Get option value*/
+	fid=this->SetFilePointerToData(&code,NULL,index+1);
+	switch(code){
+		case 3: {//IssmDouble
+					GenericOption* option;
+					IssmDouble value;
+					FetchData(&value,index+1);
+					option = new GenericOption();
+					option->value = value;
+					option->name  = name;
+					option->numel = 1;
+					option->ndims = 1;
+					option->size  = NULL;
+					/*Assign output pointers: */
+					*poption=option;
+					break;
+				}
+		case 4: {//char
+					GenericOption* option;
+					char* value = NULL;
+					FetchData(&value,index+1);
+					option = new GenericOption();
+					option->value = value;
+					option->name  = name;
+					option->numel = 1;
+					option->ndims = 1;
+					option->size  = NULL;
+					*poption=option;
+					break;
+				}
+		default:
+			  _error_("Option of format " << code << " not supported yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchData(int num,...){{{*/
+void  IoModel::FetchData(int num,...){
+
+	va_list ap;
+	int     dataenum;
+	IssmDouble* matrix=NULL;
+	int     M,N;
+	int     i;
+
+	/*Go through the entire list of enums and fetch the corresponding data. Add it to the iomodel->data dataset. Everything
+	 *we fetch is a IssmDouble* : */
+	
+	va_start(ap,num);
+	for(i=0; iindependents[dataenum]){
+			/*this data has already been checked out! Continue: */
+			continue;
+		}
+
+		/*Some checks in debugging mode*/
+		/*{{{*/
+		#ifdef _ISSM_DEBUG_
+		_assert_(dataenumdata[dataenum]){
+			_error_("Info: trying to fetch " << EnumToStringx(dataenum) << " but previous pointer has not been freed (DeleteData has not been called)");
+		}
+		#endif
+		/*}}}*/
+
+		/*Add to this->data: */
+		this->FetchData(&matrix,&M,&N,dataenum);
+		this->data[dataenum]=matrix;
+	}
+	va_end(ap);
+
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchDataToInput{{{*/
+void IoModel::FetchDataToInput(Elements* elements,int vector_enum,int default_vector_enum,IssmDouble default_value){
+
+	/*intermediary: */
+	int     i;
+	bool    defaulting    = false;
+	bool    transient     = false;
+
+	FILE   *fid           = NULL;
+	int     code          = 0;
+	int     vector_layout = 0;
+	int     counter;
+	int     nods;
+	int     nel;
+	int     numberofelements;
+
+
+	/*variables being fetched: */
+	bool    boolean;
+	int     integer;
+	IssmDouble  scalar;
+	char   *string        = NULL;
+	IssmDouble *IssmDoublevector  = NULL;
+	int     M,N;
+
+	/*Fetch parameters: */
+	this->constants->FindParam(&numberofelements,MeshNumberofelementsEnum);
+
+	/*First of, find the record for the enum, and get code  of data type: */
+	fid=this->SetFilePointerToData(&code, &vector_layout,vector_enum);
+
+	switch(code){
+		case 1: //boolean constant.  {{{
+			this->FetchData(&boolean,vector_enum);
+
+			/*Add boolean constant input to all elements: */
+			counter=0;
+			for (i=0;imy_elements[i]){
+					Element* element=(Element*)elements->GetObjectByOffset(counter);
+					element->InputCreate((IssmDouble)boolean,vector_enum,code);
+					counter++;
+				}
+			}
+			break; /*}}}*/
+		case 2: //integer constant.  {{{
+			this->FetchData(&integer,vector_enum);
+
+			/*Add integer constant input to all elements: */
+			counter=0;
+			for (i=0;imy_elements[i]){
+					Element* element=(Element*)elements->GetObjectByOffset(counter);
+					element->InputCreate((IssmDouble)integer,vector_enum,code);
+					counter++;
+				}
+			}
+			break; /*}}}*/
+		case 3: //IssmDouble constant.  {{{
+			this->FetchData(&scalar,vector_enum);
+
+			/*Add IssmDouble constant input to all elements: */
+			counter=0;
+			for (i=0;imy_elements[i]){
+					Element* element=(Element*)elements->GetObjectByOffset(counter);
+					element->InputCreate(scalar,vector_enum,code); 
+					counter++;
+				}
+			}
+			break; /*}}}*/
+		case 5: //boolean vector.  {{{
+
+			/*Fetch vector:*/
+			this->FetchData(&IssmDoublevector,&M,&N,vector_enum); //we still have a IssmDoublevector, because it might include times in transient mode
+			/*Check we got something, otherwise fetch default: */
+			if(IssmDoublevector){
+				defaulting=false;  //we are not defaulting, because  we do have a vector
+			}
+			else{
+				/*do we have a default enum to go fetch? */
+				if(default_vector_enum!=NoneEnum){
+					/*yes. fetch it: */
+					this->FetchData(&IssmDoublevector,&M,&N,default_vector_enum);
+					if(IssmDoublevector){
+						defaulting=false;  //we are not defaulting, because  we do have a vector
+					}
+					else{
+						/*even the default vector is non existent. we are defaulting to the default value: */
+						defaulting=true;
+					}
+				}
+				else{
+					/*we are left with the default value: */
+					defaulting=true;
+				}
+			}
+
+			/*Create inputs:*/
+			counter=0;
+			for (i=0;imy_elements[i]){
+					Element* element=(Element*)elements->GetObjectByOffset(counter);
+					if(defaulting) element->InputCreate(default_value,vector_enum,code); 
+					else           element->InputCreate(IssmDoublevector,i,this,M,N,vector_layout,vector_enum,code);//we need i to index into elements.
+					counter++;
+				}
+			}
+			break; /*}}}*/
+		case 6: //int vector{{{
+
+			/*Fetch vector:*/
+			this->FetchData(&IssmDoublevector,&M,&N,vector_enum); //we still have a IssmDoublevector, because it might include times in transient mode
+			/*Check we got something, otherwise fetch default: */
+			if(IssmDoublevector){
+				defaulting=false;  //we are not defaulting, because  we do have a vector
+			}
+			else{
+				/*do we have a default enum to go fetch? */
+				if(default_vector_enum!=NoneEnum){
+					/*yes. fetch it: */
+					this->FetchData(&IssmDoublevector,&M,&N,default_vector_enum);
+					if(IssmDoublevector){
+						defaulting=false;  //we are not defaulting, because  we do have a vector
+					}
+					else{
+						/*even the default vector is non existent. we are defaulting to the default value: */
+						defaulting=true;
+					}
+				}
+				else{
+					/*we are left with the default value: */
+					defaulting=true;
+				}
+			}
+
+			/*Create inputs:*/
+			counter=0;
+			for (i=0;imy_elements[i]){
+					Element* element=(Element*)elements->GetObjectByOffset(counter);
+					if(defaulting) element->InputCreate(default_value,vector_enum,code); 
+					else           element->InputCreate(IssmDoublevector,i,this,M,N,vector_layout,vector_enum,code);//we need i to index into elements.
+					counter++;
+				}
+			}
+			break; /*}}}*/
+		case 7: //IssmDouble vector{{{
+
+			/*Fetch vector:*/
+			this->FetchData(&IssmDoublevector,&M,&N,vector_enum);
+			/*Check we got something, otherwise fetch default: */
+			if(IssmDoublevector){
+				defaulting=false;  //we are not defaulting, because  we do have a vector
+			}
+			else{
+				/*do we have a default enum to go fetch? */
+				if(default_vector_enum!=NoneEnum){
+					/*yes. fetch it: */
+					this->FetchData(&IssmDoublevector,&M,&N,default_vector_enum);
+					if(IssmDoublevector){
+						defaulting=false;  //we are not defaulting, because  we do have a vector
+					}
+					else{
+						/*even the default vector is non existent. we are defaulting to the default value: */
+						defaulting=true;
+					}
+				}
+				else{
+					/*we are left with the default value: */
+					defaulting=true;
+				}
+			}
+
+			/*Create inputs:*/
+			counter=0;
+			for (i=0;imy_elements[i]){
+					Element* element=(Element*)elements->GetObjectByOffset(counter);
+					if(defaulting) element->InputCreate(default_value,vector_enum,code); 
+					else           element->InputCreate(IssmDoublevector,i,this,M,N,vector_layout,vector_enum,code);//we need i to index into elements.
+					counter++;
+				}
+			}
+
+			break; /*}}}*/
+		default: /*{{{*/
+			_error_("data code " << code << " not supported yet!");
+			break;
+			/*}}}*/
+	}
+	/*Free ressources. Pay attention to not freeing an AD mode independent variable though!:*/
+	if (!this->independents[vector_enum] && !this->independents[default_vector_enum]) xDelete(IssmDoublevector);
+	xDelete(string);
+}
+/*}}}*/
+/*FUNCTION IoModel::LastIndex{{{*/
+void IoModel::LastIndex(int *pindex){
+
+	extern int my_rank;
+	int        lastindex,index;
+	int        record_length;
+
+	/*Go find in the binary file, the position of the data we want to fetch: */
+	if(my_rank==0){
+
+		/*First set FILE* position to the beginning of the file: */
+		fseek(fid,0,SEEK_SET);
+
+		/*Now march through file looking for the correct data identifier: */
+		for(;;){
+			/*Read enum for this size of first string name: */
+			if(fread(&index,sizeof(int),1,fid)==0){
+				/*Ok, we have reached the end of the file. break: */
+				break;
+			}
+
+			/*read the record length, and use it to skip this record: */
+			fread(&record_length,sizeof(int),1,fid);
+			fseek(fid,record_length,SEEK_CUR);
+			lastindex=index;
+		}
+	}
+	/*Broadcast code and vector type: */
+#ifdef _HAVE_MPI_
+	MPI_Bcast(&lastindex,1,MPI_INT,0,MPI_COMM_WORLD); 
+#endif
+
+	/*Assign output pointers:*/
+	*pindex=lastindex;
+}
+/*}}}*/
+/*FUNCTION IoModel::SetFilePointerToData{{{*/
+FILE* IoModel::SetFilePointerToData(int* pcode,int* pvector_type, int data_enum){
+
+	extern int my_rank;
+	extern int num_procs;
+
+	int found=0;
+	int record_enum;
+	int record_length;
+	int record_code; //1 to 7 number
+	int vector_type; //nodal or elementary
+
+	/*Go find in the binary file, the position of the data we want to fetch: */
+	if(my_rank==0){
+
+		/*First set FILE* position to the beginning of the file: */
+		fseek(fid,0,SEEK_SET);
+
+		/*Now march through file looking for the correct data identifier: */
+		for(;;){
+			/*Read enum for this size of first string name: */
+			if(fread(&record_enum,sizeof(int),1,fid)==0){
+				/*Ok, we have reached the end of the file. break: */
+				found=0;
+				break;
+			}
+
+			/*Is this the record sought for? : */
+			if (data_enum==record_enum){
+				/*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 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);
+				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);
+				/*skip: */
+				fseek(fid,record_length,SEEK_CUR);
+			}
+		}
+	}
+#ifdef _HAVE_MPI_
+	MPI_Bcast(&found,1,MPI_INT,0,MPI_COMM_WORLD); 
+	if(!found)_error_("could not find data with name" << " " << EnumToStringx(data_enum) << " ");
+#endif
+
+	/*Broadcast code and vector type: */
+#ifdef _HAVE_MPI_
+	MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); 
+	MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); 
+	if(record_code==5) MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); 
+#endif
+
+	/*Assign output pointers:*/
+	*pcode=record_code;
+	if(pvector_type)*pvector_type=vector_type;
+
+	return fid;
+}
+/*}}}*/
+/*FUNCTION IoModel::DeclareIndependents{{{*/
+void IoModel::DeclareIndependents(void){
+
+	bool autodiff=false;
+	int  dummy;
+	int i;
+	int  num_independents;
+	int* independents=NULL;
+
+	#ifdef _HAVE_ADOLC_
+	/*recover independent enums: */
+	this->Constant(&num_independents,AutodiffNumIndependentsEnum);
+	if(num_independents){
+		this->FetchData(&independents,&dummy,&dummy,AutodiffIndependentsEnum);
+
+		/*now go fetch the independent variables for each independent enum: */
+		for(i=0;iFetchIndependent(independents[i]);
+		}
+		xDelete(independents);
+	}
+	#else
+	/*if we asked for AD computations, we have a problem!: */
+	this->Constant(&autodiff,AutodiffIsautodiffEnum);
+	if(autodiff)_error_("Cannot carry out AD mode computations without support of ADOLC compiled in!");
+	#endif
+
+}
+/*}}}*/
+/*FUNCTION IoModel::FetchIndependent{{{*/
+void IoModel::FetchIndependent(int independent_enum){
+
+	#ifdef _HAVE_ADOLC_ //cannot come here unless you are running AD mode, from DeclaredIndependents:
+	extern int my_rank;
+	extern int num_procs;
+
+	/*output: */
+	int M,N;
+	IssmPDouble* buffer=NULL; //a buffer to read the data from disk
+	IssmDouble* matrix=NULL; //our independent variable
+	int code=0;
+	int vector_type=0;
+	
+	/*Set file pointer to beginning of the data: */
+	fid=this->SetFilePointerToData(&code,&vector_type,independent_enum);
+	if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(independent_enum));
+	
+	/*Now fetch: */
+
+	/*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */
+	/*numberofelements: */
+	if(my_rank==0){  
+		if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix ");
+	}
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	if(my_rank==0){  
+		if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix ");
+	}
+	#ifdef _HAVE_MPI_
+	MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); 
+	#endif
+
+	/*Now allocate matrix: */
+	if(M*N){
+		buffer=xNew(M*N);
+		matrix=xNew(M*N);
+
+		/*Read matrix on node 0, then broadcast: */
+		if(my_rank==0){  
+			if(fread(buffer,M*N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix ");
+			
+			/*Now, before we even broadcast this to other nodes, declare the whole matrix as a independent variable!: */
+			for (int i=0;i(buffer);
+	}
+	else _error_("cannot declare the independent variable " << EnumToStringx(independent_enum) <<  "if it's empty!");
+
+	/*Ok, we are almost done. Matrix is now a independent matrix. We don't want this matrix to be fetched again in the 
+	 *future, which would effectively write over the independency in the ADOLC tape! So we are going to keep track of this 
+	 independent matrix inthe iomodel->data[independent_enum] data slot: */
+	this->data[independent_enum]=matrix;
+	this->independents[independent_enum]=true;
+ 	#endif
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/IoModel.h
===================================================================
--- /issm/trunk/src/c/classes/IoModel.h	(revision 13395)
+++ /issm/trunk/src/c/classes/IoModel.h	(revision 13395)
@@ -0,0 +1,75 @@
+/* \file IoModel.h
+ * \brief  Header file defining the IoModel structure that will help in processing the input data coming 
+ * into ISSM, from Matlab, or through a binary file opened for reading.
+ * \sa IoModel.cpp
+ */
+
+#ifndef _IOMODEL_H
+#define _IOMODEL_H
+
+#include "../include/include.h"
+#include "../EnumDefinitions/EnumDefinitions.h"
+
+class Parameters;
+class Elements;
+class Param;
+class Option;
+
+class IoModel {
+
+	private: 
+		Parameters  *constants;   //this dataset holds all IssmDouble, int, bool and char *parameters read in from the input file.*
+	
+	public:
+		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
+		bool *my_elements;
+		bool *my_nodes;
+		int  *my_vertices;
+		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
+		
+		/*for AD mode: to keep track of our independent variables we fetch:*/
+		bool* independents;
+
+		/*Methods*/
+		~IoModel();
+		IoModel();
+		IoModel(FILE* iomodel_handle);
+
+		/*Input/Output*/
+		void        CheckEnumSync(void);
+		void        Constant(bool *poutput,int constant_enum);
+		void        Constant(int *poutput,int constant_enum);
+		void        Constant(IssmDouble *poutput,int constant_enum);
+		void        Constant(char **poutput,int constant_enum);
+		Param      *CopyConstantObject(int constant_enum);
+		IssmDouble *Data(int dataenum);
+		void        DeleteData(int num,...);
+		void        DeleteData(IssmDouble* vector, int dataenum);
+		void        FetchConstants(void);
+		void        FetchData(bool* pboolean,int data_enum);
+		void        FetchData(int* pinteger,int data_enum);
+		void        FetchData(IssmDouble* pscalar,int data_enum);
+		void        FetchData(char** pstring,int data_enum);
+		void        FetchData(int** pmatrix,int* pM,int* pN,int data_enum);
+		void        FetchData(IssmDouble**  pscalarmatrix,int* pM,int* pN,int data_enum);
+		void        FetchData(char***   pstringarray,int* pnumstrings,int data_enum);
+		void        FetchData(IssmDouble*** pmatrixarray,int** pmdims,int** pndims, int* pnumrecords,int data_enum);
+		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        LastIndex(int *pindex);
+		FILE*       SetFilePointerToData(int* pcode,int* pvector_type, int data_enum);
+		void        DeclareIndependents(void);
+		void        FetchIndependent(int dependent_enum);
+};
+
+#endif  /* _IOMODEL_H */
Index: /issm/trunk/src/c/classes/OptArgs.h
===================================================================
--- /issm/trunk/src/c/classes/OptArgs.h	(revision 13395)
+++ /issm/trunk/src/c/classes/OptArgs.h	(revision 13395)
@@ -0,0 +1,13 @@
+/*!\file:  OptArgs.h
+ * \brief place holder for optimization function arguments
+ */ 
+
+#ifndef _OPTARGS_H_
+#define _OPTARGS_H_
+
+class Model;
+struct OptArgs{
+	FemModel* femmodel;
+};
+
+#endif
Index: /issm/trunk/src/c/classes/OptPars.h
===================================================================
--- /issm/trunk/src/c/classes/OptPars.h	(revision 13395)
+++ /issm/trunk/src/c/classes/OptPars.h	(revision 13395)
@@ -0,0 +1,17 @@
+/*!\file:  OptPars.h
+ * \brief place holder for optimization parameters
+ */ 
+
+#ifndef _OPTPARS_H_
+#define _OPTPARS_H_
+
+struct OptPars{
+
+	IssmDouble xmin;
+	IssmDouble xmax;
+	IssmDouble cm_jump;
+	int maxiter;
+
+};
+
+#endif
Index: /issm/trunk/src/c/classes/Patch.cpp
===================================================================
--- /issm/trunk/src/c/classes/Patch.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/Patch.cpp	(revision 13395)
@@ -0,0 +1,175 @@
+/*!\file Patch.c
+ * \brief: implementation of the Patch object
+ */
+
+/*Include files: {{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include 
+#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:*/
+/*FUNCTION Patch::Patch() default constructor {{{*/
+Patch::Patch(){
+	this->numrows=0;
+	this->numcols=0;
+	this->maxvertices=0;
+	this->maxnodes=0;
+	this->values=NULL;
+}
+/*}}}*/
+/*FUNCTION Patch::Patch(int numrows, int maxvertices, int maxnodes){{{*/
+Patch::Patch(int in_numrows, int in_maxvertices, int in_maxnodes){
+
+	int i,j;
+	this->numrows=in_numrows;
+	this->maxvertices=in_maxvertices;
+	this->maxnodes=in_maxnodes;
+    
+	this->numcols=1  //enum_type
+		+1           //step
+		+1           //time 
+		+1           //element id
+		+1           //interpolation type
+		+maxvertices //vertices
+		+maxnodes;   //nodes
+
+	//Allocate values and fill with NaN:
+	if (this->numcols*this->numrows==0){
+		this->values=NULL;
+	}
+	else{
+	        this->values=xNew(this->numcols*this->numrows);
+		for(i=0;inumrows;i++){
+			for(j=0;jnumcols;j++){
+				this->values[i*this->numcols+j]=NAN;
+			}
+		}
+	}
+
+}
+/*}}}*/
+/*FUNCTION Patch::~Patch(){{{*/
+Patch::~Patch(){
+	xDelete(values);
+}
+/*}}}*/
+
+/*Object methods*/
+/*FUNCTION Patch::fillelementinfo{{{*/
+void Patch::fillelementinfo(int count, int element_id, int* vertices_ids, int num_vertices){
+
+	int i;
+	IssmDouble* row=NULL;
+
+	/*point to the start of the row: */
+	row=this->values+count*this->numcols;
+
+	/*Let's remember what is on a row: 
+	 enum_type step time element_id interpolation vertices_ids nodal_values
+	 */
+	row[3]=element_id;
+	for(i=0;ivalues+count*this->numcols;
+
+	/*Let's remember what is on a row: 
+	 enum_type step time element_id interpolation vertices_ids nodal_values
+	 */
+	row[0]=enum_type;
+	row[1]=(IssmDouble)step;
+	row[2]=time;
+	row[4]=interpolation;
+	for(i=0;imaxvertices+i]=nodal_values[i];
+	}
+
+}
+/*}}}*/
+/*FUNCTION Patch::Gather{{{*/
+void Patch::Gather(void){
+
+	int         i;
+	int         count;
+	extern int  my_rank;
+	extern int  num_procs;
+	int         total_numrows;
+	int         node_numrows;
+	IssmDouble     *total_values  = NULL;
+	#ifdef _HAVE_MPI_
+	MPI_Status  status;
+	#endif
+
+	/*First, figure out total number of rows combining all the cpus: */
+	#ifdef _HAVE_MPI_
+	MPI_Reduce(&this->numrows,&total_numrows,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD );
+	MPI_Bcast(&total_numrows,1,MPI_INT,0,MPI_COMM_WORLD);
+	#else
+	total_numrows=this->numrows;
+	#endif
+
+	/*return if patch empty*/
+	if(total_numrows==0) return;
+
+	/*Now, allocate buffer to holds all the values, on node 0: */
+	if(my_rank==0)total_values=xNew(this->numcols*total_numrows);
+
+	/*Start by copying node 0 values onto total_values: */
+	if(my_rank==0){
+		count=0;
+		xMemCpy(total_values+count,this->values,this->numcols*this->numrows);
+		count+=this->numrows*this->numcols;
+	}
+
+	/*Now, ask other nodes to send their values: */
+	#ifdef _HAVE_MPI_
+	for (i=1;inumrows,1,MPI_INT,0,1,MPI_COMM_WORLD);   
+			if (this->numrows)MPI_Send(this->values,this->numrows*this->numcols,MPI_DOUBLE,0,1,MPI_COMM_WORLD); 
+		}
+		if (my_rank==0){
+			MPI_Recv(&node_numrows,1,MPI_INT,i,1,MPI_COMM_WORLD,&status); 
+			if (node_numrows)MPI_Recv(total_values+count,node_numrows*this->numcols,MPI_DOUBLE,i,1,MPI_COMM_WORLD,&status);
+			count+=node_numrows*this->numcols;
+		}
+	}	
+	#endif
+
+	/*Now, node 0 has total_values, of size total_numrows*this->numcols. Update the fields in the patch, to reflect this new 
+	 * reality. For other cpus, no point in keeping their data anymore: */
+	if(my_rank==0){
+		this->numrows=total_numrows;
+		xDelete(this->values);
+		this->values=total_values;
+	}
+	#ifdef _HAVE_MPI_
+	else{
+		this->numrows=0;
+		xDelete(this->values);
+	}
+	#endif
+}/*}}}*/
Index: /issm/trunk/src/c/classes/Patch.h
===================================================================
--- /issm/trunk/src/c/classes/Patch.h	(revision 13395)
+++ /issm/trunk/src/c/classes/Patch.h	(revision 13395)
@@ -0,0 +1,46 @@
+/*!\file: Patch.h
+ * \brief prototypes for Patch.h
+ */ 
+
+/*A Patch object is used to store all results held in elements, in a serial way, and to dump them to disk. 
+	
+	Each row of the Patch object is made of the following information: 
+	- the result enum_type, 
+	- the step and time, 
+	- the id of the element, 
+	- the interpolation type, 
+	- the vertices ids, 
+	- and the values at the nodes (could be different from the vertices).
+	
+	For ex: 
+	1. on a Beam element, Vx, at step 1, time .5, element id 1, interpolation type P0 (constant), vertices ids 1 and 2, one constant value 4.5
+	   VxEnum 1  .5  1 P0  1 2       4.5 NaN  NaN
+	2. on a Tria element, Vz, at step 2, time .8, element id 2, interpolation type P1 (linear), vertices ids 1 3 and 4, with values at 3 nodes 4.5, 3.2, 2.5
+	   VzEnum 2  .8  2 P1  1 3 4     4.5 3.2  2.5
+*/
+
+
+#ifndef _PATCH_H_
+#define  _PATCH_H_
+
+/*Headers:*/
+class Patch{
+
+	public:
+
+		int     numrows; //number of results held in Patch object
+		int     numcols; //number of columns
+		int     maxvertices; //maxvertices corresponds to largest amount of vertices on a given element, determined by the geometry.
+		int     maxnodes;    // maxnodes corresponds to the largest amout of nodes on a given element, determined by the interpolation type.
+		
+		IssmDouble* values;  //result values
+
+		Patch();
+		Patch(int numrows, int maxvertices, int maxnodes);
+		~Patch();
+		void fillelementinfo(int row, int element_id, int* vertices_ids, int num_vertices);
+		void fillresultinfo(int row,int enum_type,int step, IssmDouble time, int interpolation, IssmDouble* nodal_values, int num_nodes);
+		void Gather(void);
+
+};
+#endif //ifndef _PATCH_H_
Index: /issm/trunk/src/c/classes/Update.h
===================================================================
--- /issm/trunk/src/c/classes/Update.h	(revision 13395)
+++ /issm/trunk/src/c/classes/Update.h	(revision 13395)
@@ -0,0 +1,35 @@
+/*!\file: Update.h: abstract class used by some objects to update their properties
+ * \brief prototypes for Update.h
+ */ 
+
+#ifndef _UPDATE_H_
+#define  _UPDATE_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../shared/shared.h"
+/*}}}*/
+
+class Update{
+
+	public:
+
+		virtual void  InputUpdateFromVector(IssmDouble* vector, int name, int type)=0;
+		virtual void  InputUpdateFromVector(int* vector, int name, int type)=0;
+		virtual void  InputUpdateFromVector(bool* vector, int name, int type)=0; 
+		#ifdef _HAVE_DAKOTA_
+		virtual void  InputUpdateFromMatrixDakota(IssmDouble* matrix, int rows, int ncols, int name, int type)=0;
+		virtual void  InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type)=0;
+		virtual void  InputUpdateFromVectorDakota(int* vector, int name, int type)=0;
+		virtual void  InputUpdateFromVectorDakota(bool* vector, int name, int type)=0;
+		#endif
+		virtual void  InputUpdateFromConstant(IssmDouble constant, int name)=0;
+		virtual void  InputUpdateFromConstant(int constant, int name)=0;
+		virtual void  InputUpdateFromConstant(bool constant, int name)=0;
+		virtual void  InputUpdateFromSolution(IssmDouble* solution)=0;
+		virtual void  InputUpdateFromIoModel(int index, IoModel* iomodel)=0;
+
+};
+
+#endif //ifndef _UPDATE_H_
+
Index: /issm/trunk/src/c/classes/bamg/AdjacentTriangle.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/AdjacentTriangle.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/AdjacentTriangle.cpp	(revision 13395)
@@ -0,0 +1,76 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "AdjacentTriangle.h"
+#include "Mesh.h"
+
+namespace bamg {
+
+
+	/*Constructors/Destructors*/
+	//See header file
+
+	/*Methods*/
+	/*FUNCTION AdjacentTriangle::Locked {{{*/
+	int  AdjacentTriangle::Locked() const {
+		return t->AdjEdgeIndex[a] & 4;
+	}
+	/*}}}*/
+	/*FUNCTION AdjacentTriangle::MarkUnSwap {{{*/
+	int  AdjacentTriangle::MarkUnSwap() const {
+		return t->AdjEdgeIndex[a] & 8;
+	}
+	/*}}}*/
+	/*FUNCTION AdjacentTriangle::GetAllFlag_UnSwap {{{*/
+	int  AdjacentTriangle::GetAllFlag_UnSwap() const {
+		// take all flag except MarkUnSwap
+		return t->AdjEdgeIndex[a] & 1012;
+	}
+	/*}}}*/
+	/*FUNCTION AdjacentTriangle::SetLock {{{*/
+	void AdjacentTriangle::SetLock(){
+		t->SetLocked(a);
+	}
+	/*}}}*/
+	/*FUNCTION AdjacentTriangle::Adj {{{*/
+	AdjacentTriangle AdjacentTriangle::Adj() const {
+		return  t->Adj(a);
+	}
+	/*}}}*/
+	/*FUNCTION AdjacentTriangle::EdgeVertex {{{*/
+	BamgVertex* AdjacentTriangle::EdgeVertex(const int & i) const {
+		return t->vertices[VerticesOfTriangularEdge[a][i]];
+	}
+	/*}}}*/
+	/*FUNCTION AdjacentTriangle::OppositeVertex {{{*/
+	BamgVertex* AdjacentTriangle::OppositeVertex() const {
+		return t->vertices[bamg::OppositeVertex[a]]; 
+	}
+	/*}}}*/
+	/*FUNCTION AdjacentTriangle::det {{{*/
+	Icoor2 & AdjacentTriangle::det() const {
+		return t->det;
+	}
+	/*}}}*/
+	/*FUNCTION AdjacentTriangle::swap {{{*/
+	int AdjacentTriangle::swap(){
+		return  t->swap(a);
+	}
+	/*}}}*/
+	/*FUNCTION AdjacentTriangle::SetAdj2 {{{*/
+	void AdjacentTriangle::SetAdj2(const AdjacentTriangle & ta, int l  ){
+		//set Adjacent Triangle of a triangle
+		if(t) {
+			t->adj[a]=ta.t;
+			t->AdjEdgeIndex[a]=ta.a|l;
+		}
+		if(ta.t) {
+			ta.t->adj[ta.a] = t ;
+			ta.t->AdjEdgeIndex[ta.a] = a| l ;
+		}
+	}
+	/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/AdjacentTriangle.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/AdjacentTriangle.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/AdjacentTriangle.h	(revision 13395)
@@ -0,0 +1,46 @@
+#ifndef _TRIANGLEADJACENT_H_
+#define _TRIANGLEADJACENT_H_
+
+#include "./include.h"
+#include "./BamgVertex.h"
+
+namespace bamg {
+
+	//classes
+	class Triangle;
+	class Triangle;
+
+	class AdjacentTriangle {
+
+		public:
+			Triangle* t; //pointer toward the triangle
+			int  a;      //Edge number
+
+			//Constructors
+			AdjacentTriangle():a(0),t(NULL) {};
+			AdjacentTriangle(Triangle* tt,int  aa): t(tt),a(aa &3) {};
+
+			//Operators
+			operator Triangle * () const {return t;}
+			operator Triangle & () const {return *t;}
+			operator int() const {return a;}
+			AdjacentTriangle & operator++(){ a= NextEdge[a]; return *this; }
+			AdjacentTriangle operator--(){ a= PreviousEdge[a]; return *this; }
+
+			//Methods
+
+			//Methods
+			int  Locked() const;
+			int  MarkUnSwap() const;
+			int  GetAllFlag_UnSwap() const;
+			void SetLock();
+			void SetAdj2(const AdjacentTriangle &ta, int l=0);
+			int  swap();
+			AdjacentTriangle Adj() const;
+			BamgVertex* EdgeVertex(const int & i) const;
+			BamgVertex* OppositeVertex() const;
+			Icoor2& det() const;
+	};
+}
+#endif
+
Index: /issm/trunk/src/c/classes/bamg/BamgGeom.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgGeom.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgGeom.cpp	(revision 13395)
@@ -0,0 +1,34 @@
+#include 
+#include "../objects.h"
+#include "../../io/io.h"
+#include "../../shared/shared.h"
+
+/*Constructors/Destructors*/
+/*FUNCTION BamgGeom::BamgGeom(){{{*/
+BamgGeom::BamgGeom(){
+
+	this->VerticesSize[0]=0,          this->VerticesSize[1]=0;          this->Vertices=NULL;
+	this->EdgesSize[0]=0,             this->EdgesSize[1]=0;             this->Edges=NULL;
+	this->TangentAtEdgesSize[0]=0,    this->TangentAtEdgesSize[1]=0;    this->TangentAtEdges=NULL;
+	this->CornersSize[0]=0,           this->CornersSize[1]=0;           this->Corners=NULL;
+	this->RequiredVerticesSize[0]=0,  this->RequiredVerticesSize[1]=0;  this->RequiredVertices=NULL;
+	this->RequiredEdgesSize[0]=0,     this->RequiredEdgesSize[1]=0;     this->RequiredEdges=NULL;
+	this->CrackedEdgesSize[0]=0,      this->CrackedEdgesSize[1]=0;      this->CrackedEdges=NULL;
+	this->SubDomainsSize[0]=0,        this->SubDomainsSize[1]=0;        this->SubDomains=NULL;
+
+}
+/*}}}*/
+/*FUNCTION BamgGeom::~BamgGeom(){{{*/
+BamgGeom::~BamgGeom(){
+
+	xDelete(this->Vertices);
+	xDelete(this->Edges);
+	xDelete(this->TangentAtEdges);
+	xDelete(this->Corners);
+	xDelete(this->RequiredVertices);
+	xDelete(this->RequiredEdges);
+	xDelete(this->CrackedEdges);
+	xDelete(this->SubDomains);
+
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/bamg/BamgGeom.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgGeom.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgGeom.h	(revision 13395)
@@ -0,0 +1,31 @@
+/*!\file:  BamgGeom.h
+ */ 
+
+#ifndef _BAMGGEOM_H_
+#define _BAMGGEOM_H_
+
+class BamgGeom{
+
+	public:
+		int     VerticesSize[2];
+		double* Vertices;
+		int     EdgesSize[2];
+		double* Edges;
+		int     TangentAtEdgesSize[2];
+		double* TangentAtEdges;
+		int     CornersSize[2];
+		double* Corners;
+		int     RequiredVerticesSize[2];
+		double* RequiredVertices;
+		int     RequiredEdgesSize[2];
+		double* RequiredEdges;
+		int     CrackedEdgesSize[2];
+		double* CrackedEdges;
+		int     SubDomainsSize[2];
+		double* SubDomains;
+
+		BamgGeom();
+		~BamgGeom();
+};
+
+#endif
Index: /issm/trunk/src/c/classes/bamg/BamgMesh.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgMesh.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgMesh.cpp	(revision 13395)
@@ -0,0 +1,56 @@
+#include 
+#include "../objects.h"
+#include "../../io/io.h"
+#include "../../shared/shared.h"
+
+/*Constructors/Destructors*/
+/*FUNCTION BamgMesh::BamgMesh(){{{*/
+BamgMesh::BamgMesh(){
+
+	this->VerticesSize[0]=0,                  this->VerticesSize[1]=0;                 this->Vertices=NULL;
+	this->EdgesSize[0]=0,                     this->EdgesSize[1]=0;                    this->Edges=NULL;
+	this->TrianglesSize[0]=0,                 this->TrianglesSize[1]=0;                this->Triangles=NULL;
+	this->QuadrilateralsSize[0]=0,            this->QuadrilateralsSize[1]=0;           this->Quadrilaterals=NULL;
+
+	this->SubDomainsSize[0]=0,                this->SubDomainsSize[1]=0;               this->SubDomains=NULL;
+	this->SubDomainsFromGeomSize[0]=0,        this->SubDomainsFromGeomSize[1]=0;       this->SubDomainsFromGeom=NULL;
+	this->CrackedVerticesSize[0]=0,           this->CrackedVerticesSize[1]=0;          this->CrackedVertices=NULL;
+	this->CrackedEdgesSize[0]=0,              this->CrackedEdgesSize[1]=0;             this->CrackedEdges=NULL;
+
+	this->VerticesOnGeomVertexSize[0]=0,      this->VerticesOnGeomVertexSize[1]=0;     this->VerticesOnGeomVertex=NULL;
+	this->VerticesOnGeomEdgeSize[0]=0,        this->VerticesOnGeomEdgeSize[1]=0;       this->VerticesOnGeomEdge=NULL;
+	this->EdgesOnGeomEdgeSize[0]=0,           this->EdgesOnGeomEdgeSize[1]=0;          this->EdgesOnGeomEdge=NULL;
+
+	this->IssmEdgesSize[0]=0,                 this->IssmEdgesSize[1]=0;                this->IssmEdges=NULL;
+	this->IssmSegmentsSize[0]=0,              this->IssmSegmentsSize[1]=0;             this->IssmSegments=NULL;
+
+	this->ElementConnectivitySize[0]=0,       this->ElementConnectivitySize[1]=0;      this->ElementConnectivity=NULL;
+	this->NodalConnectivitySize[0]=0,         this->NodalConnectivitySize[1]=0;        this->NodalConnectivity=NULL;
+	this->NodalElementConnectivitySize[0]=0,  this->NodalElementConnectivitySize[1]=0; this->NodalElementConnectivity=NULL;
+}
+/*}}}*/
+/*FUNCTION BamgMesh::~BamgMesh(){{{*/
+BamgMesh::~BamgMesh(){
+
+	xDelete(this->Vertices);
+	xDelete(this->Edges);
+	xDelete(this->Triangles);
+	xDelete(this->Quadrilaterals);
+
+	xDelete(this->SubDomains);
+	xDelete(this->SubDomainsFromGeom);
+	xDelete(this->CrackedVertices);
+	xDelete(this->CrackedEdges);
+
+	xDelete(this->VerticesOnGeomVertex);
+	xDelete(this->VerticesOnGeomEdge);
+	xDelete(this->EdgesOnGeomEdge);
+
+	xDelete(this->IssmEdges);
+	xDelete(this->IssmSegments);
+
+	xDelete(this->ElementConnectivity);
+	xDelete(this->NodalConnectivity);
+	xDelete(this->NodalElementConnectivity);
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/bamg/BamgMesh.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgMesh.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgMesh.h	(revision 13395)
@@ -0,0 +1,52 @@
+/*!\file:  BamgMesh.h
+ */ 
+
+#ifndef _BAMGMESH_H_
+#define _BAMGMESH_H_
+
+class BamgMesh{
+
+	public:
+
+		int     VerticesSize[2];
+		double* Vertices;
+		int     EdgesSize[2];
+		double* Edges;
+		int     TrianglesSize[2];
+		double* Triangles;
+		int     QuadrilateralsSize[2];
+		double* Quadrilaterals;
+
+		int     VerticesOnGeomVertexSize[2];
+		double* VerticesOnGeomVertex;
+		int     VerticesOnGeomEdgeSize[2];
+		double* VerticesOnGeomEdge;
+		int     EdgesOnGeomEdgeSize[2];
+		double* EdgesOnGeomEdge;
+
+		int     SubDomainsSize[2];
+		double* SubDomains;
+		int     SubDomainsFromGeomSize[2];
+		double* SubDomainsFromGeom;
+		int     CrackedVerticesSize[2];
+		double* CrackedVertices;
+		int     CrackedEdgesSize[2];
+		double* CrackedEdges;
+
+		/*Output for ISSM*/
+		int     IssmEdgesSize[2];
+		double* IssmEdges;
+		int     IssmSegmentsSize[2];
+		double* IssmSegments;
+		int     ElementConnectivitySize[2];
+		double* ElementConnectivity;
+		int     NodalConnectivitySize[2];
+		double* NodalConnectivity;
+		int     NodalElementConnectivitySize[2];
+		double* NodalElementConnectivity;
+
+		BamgMesh();
+		~BamgMesh();
+};
+
+#endif
Index: /issm/trunk/src/c/classes/bamg/BamgOpts.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgOpts.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgOpts.cpp	(revision 13395)
@@ -0,0 +1,89 @@
+#include 
+#include "../../shared/shared.h"
+#include "../../include/include.h"
+#include "../objects.h"
+#include "../../io/io.h"
+
+/*Constructors/Destructors*/
+/*FUNCTION BamgOpts::BamgOpts() {{{*/
+BamgOpts::BamgOpts(){
+
+	this->anisomax=0;
+	this->cutoff=0;
+	this->coeff=0;
+	this->errg=0;
+	this->gradation=0;
+	this->Hessiantype=0;
+	this->MaxCornerAngle=0;
+	this->maxnbv=0;
+	this->maxsubdiv=0;
+	this->Metrictype=0;
+	this->nbjacobi=0;
+	this->nbsmooth=0;
+	this->omega=0;
+	this->power=0;
+	this->verbose=0;
+
+	this->Crack=0;
+	this->geometricalmetric=0;
+	this->KeepVertices=0;
+	this->splitcorners=0;
+
+	this->hmin=0;
+	this->hmax=0;
+	this->hminVertices=NULL; this->hminVerticesSize[0]=this->hminVerticesSize[1]=0;
+	this->hmaxVertices=NULL; this->hmaxVerticesSize[0]=this->hmaxVerticesSize[1]=0;
+	this->hVertices=NULL;    this->hVerticesSize[0]=this->hVerticesSize[1]=0;
+	this->metric=NULL;       this->metricSize[0]=this->metricSize[1]=0;
+	this->field=NULL;        this->fieldSize[0]=this->fieldSize[1]=0;
+	this->err=NULL;          this->errSize[0]=this->errSize[1]=0;
+
+}
+/*}}}*/
+/*FUNCTION BamgOpts::~BamgOpts() {{{*/
+BamgOpts::~BamgOpts(){
+
+	xDelete(this->hminVertices);
+	xDelete(this->hmaxVertices);
+	xDelete(this->hVertices);
+	xDelete(this->metric);
+	xDelete(this->field);
+	xDelete(this->err);
+
+}
+/*}}}*/
+
+/*Methods*/
+/*FUNCTION BamgOpts::Check{{{*/
+void BamgOpts::Check(void){
+
+	int i;
+
+	if (this->anisomax<1) _error_("'anisomax' option should be >=1");
+	if (this->coeff==0) _error_("'coeff' should be positive");
+	if (this->errg<0) _error_("'errg' option should be >0");
+	if (this->gradation<1) _error_("'gradation' option should be >=1");
+	if (this->Hessiantype!=0  && this->Hessiantype!=1) _error_("'Hessiantype' supported options are 0 and 1");
+	if (this->maxnbv<3) _error_("'maxnbv' option should be >3");
+	if (this->maxsubdiv<=1) _error_("'maxsubdiv' should be >1");
+	if (this->Metrictype!=0   && this->Metrictype!=1 && this->Metrictype!=2) _error_("'Metrictype' supported options are 0, 1 and 2");
+	if (this->nbjacobi<=0) _error_("'nbjacobi' option should be >0");
+	if (this->nbsmooth<=0) _error_("'nbsmooth' option should be >0");
+
+	if (this->Crack!=0  && this->Crack!=1) _error_("'Crack' supported options are 0 and 1");
+	if (this->KeepVertices!=0 && this->KeepVertices!=1) _error_("'KeepVertices' supported options are 0 and 1");
+	if (this->geometricalmetric!=0  && this->geometricalmetric!=1) _error_("'geometricalmetric' supported options are 0 and 1");
+
+	if (this->hmin<=0) _error_("'hmin' option should be >0");
+	if (this->hmax<=0 || this->hmaxhmin) _error_("'hmax' option should be between 0 and hmin=" << this->hmin);
+	if (this->hminVertices && this->hminVerticesSize[1]!=1) _error_("'hminVertices' should be a column");
+	if (this->hmaxVertices && this->hmaxVerticesSize[1]!=1) _error_("'hmaxVertices' should be a column");
+	if (this->hVertices && this->hVerticesSize[1]!=1) _error_("'hVertices' should be a column");
+	if (this->metric && (this->metricSize[1]!=1 && this->metricSize[1]!=3)) _error_("'metric' should have either 1 (iso) or 3 (aniso) columns.");
+	if (this->field){
+		if (this->errSize[0]!=1 || this->errSize[1]!=this->fieldSize[1]) _error_("'err' should be of size " << 1 << " x " << this->fieldSize[1]);
+		for (i=0;ifieldSize[1];i++) {if (this->err[i]<=0) _error_("'err' option should be >0");};
+	}
+
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/bamg/BamgOpts.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgOpts.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgOpts.h	(revision 13395)
@@ -0,0 +1,57 @@
+/*!\file:  BamgOpts.h
+ * \brief place holder for optimization function arguments
+ */ 
+
+#ifndef _BAMGOPTS_H_
+#define _BAMGOPTS_H_
+
+class BamgOpts{
+
+	public:
+
+		/*Parameters*/
+		double  anisomax;
+		double  cutoff;
+		double  coeff;
+		double  errg;
+		double  gradation;
+		int     Hessiantype;
+		double  MaxCornerAngle;
+		int     maxnbv;
+		double  maxsubdiv;
+		int     Metrictype;
+		int     nbjacobi;
+		int     nbsmooth;
+		double  omega;
+		double  power;
+		int     verbose;
+
+		/*Flags*/
+		int     Crack;
+		int     geometricalmetric;
+		int     KeepVertices;
+		int     splitcorners;
+
+		/*Metric related*/
+		double  hmin;
+		double  hmax;
+		int     hminVerticesSize[2];
+		double* hminVertices;
+		int     hmaxVerticesSize[2];
+		double* hmaxVertices;
+		int     hVerticesSize[2];
+		double* hVertices;
+		int     metricSize[2];
+		double* metric;
+		int     fieldSize[2];
+		double* field;
+		int     errSize[2];
+		double* err;
+
+		BamgOpts();
+		~BamgOpts();
+
+		void Check(void);
+
+};
+#endif
Index: /issm/trunk/src/c/classes/bamg/BamgQuadtree.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgQuadtree.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgQuadtree.cpp	(revision 13395)
@@ -0,0 +1,598 @@
+#include 
+#include 
+#include 
+
+#include "../objects.h"
+
+namespace bamg {
+
+	/*MACROS {{{*/
+	/* 
+	 * 
+	 *    J    j
+	 *    ^    ^
+	 *    |    | +--------+--------+
+	 *    |    | |        |        |
+	 * 1X |    | |   2    |   3    |
+	 *    |    | |        |        |
+	 *    |    | +--------+--------+
+	 *    |    | |        |        |
+	 * 0X |    | |   0    |   1    |
+	 *    |    | |        |        |
+	 *    |    | +--------+--------+
+	 *    |    +-----------------------> i
+	 *    |         
+	 *    |----------------------------> I
+	 *              X0        X1  
+	 *
+	 * box 0 -> I=0 J=0 IJ=00  = 0
+	 * box 1 -> I=1 J=0 IJ=01  = 1
+	 * box 2 -> I=0 J=1 IJ=10  = 2
+	 * box 3 -> I=1 J=1 IJ=11  = 3
+	 */
+#define INTER_SEG(a,b,x,y) (((y) > (a)) && ((x) <(b)))
+#define ABS(i) ((i)<0 ?-(i) :(i))
+#define MAX1(i,j) ((i)>(j) ?(i) :(j))
+#define NORM(i1,j1,i2,j2) MAX1(ABS((i1)-(j1)),ABS((i2)-(j2)))
+
+	//IJ(i,j,l) returns the box number of i and j with respect to l
+	//if !j&l and !i&l -> 0 (box zero: lower left )
+	//if !j&l and  i&l -> 1 (box one:  lower right)
+	//if  j&l and !i&l -> 2 (box two:  upper left )
+	//if  j&l and  i&l -> 3 (box three:upper right)
+#define IJ(i,j,l)  ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 ))
+
+	//I_IJ(k,l) returns l if first  bit of k is 1, else 0
+#define I_IJ(k,l)  ((k&1) ? l:0)
+	//J_IJ(k,l) returns l if second bit of k is 1, else 0
+#define J_IJ(k,l)  ((k&2) ? l:0)
+	/*}}}*/
+	/*DOCUMENTATION What is a BamgQuadtree? {{{
+	 * A Quadtree is a very simple way to group vertices according
+	 * to their locations. A square that holds all the points of the mesh
+	 * (or the geometry) is divided into 4 boxes. As soon as one box
+	 * hold more than 4 vertices, it is divided into 4 new boxes, etc...
+	 * There cannot be more than MAXDEEP (=30) subdivision.
+	 * This process is like a Dichotomy in dimension 2
+	 *
+	 *  + - -  -    - -    -    - - + -   - + - + - + - -     - - +
+	 *  |                           |       |   | X |             |
+	 *                                      + - + - +
+	 *  |                           |       |   |   |             |
+	 *                              + -   - + - + - +             +
+	 *  |                           |       |       |             |
+	 *                         
+	 *  |                           |       |       |             |
+	 *  + - -  -    - -    -    - - + -   - + -   - + - -     - - +
+	 *  |                           |               |             |
+	 *                         
+	 *  |                           |               |             |
+	 *                         
+	 *  |                           |               |             |
+	 *  |                           |               |             |
+	 *  + - -  -    - -    -    - - + -   -   -   - + - -     - - +
+	 *  |                           |                             |
+	 *                         
+	 *  |                           |                             |
+	 *                         
+	 *  |                           |                             |
+	 *                         
+	 *  |                           |                             |
+	 *  |                           |                             |
+	 *  |                           |                             |
+	 *  |                           |                             |
+	 *  |                           |                             |
+	 *  + - -  -    - -    -    - - + -   -   -   -   - -     - - +
+	 *
+	 * The coordinate system used in a quadtree are integers to avoid
+	 * round-off errors. The vertex in the lower left box has the coordinates
+	 * (0 0) 
+	 * The upper right vertex has the follwing coordinates:
+	 * 2^30 -1           2^30 -1        in decimal
+	 * 0 1 1 1 .... 1    0 1 1 1 .... 1 in binary
+	 *  \--   29  --/     \--   29  --/
+	 * Using binaries is therefore very easy to locate a vertex in a box:
+	 * we just need to look at the bits from the left to the right (See ::Add)
+	 }}}*/
+
+	/*Constructors/Destructors*/
+	/*FUNCTION BamgQuadtree::BamgQuadtree(){{{*/
+	BamgQuadtree::BamgQuadtree(){
+
+		/*Number of boxes and vertices*/
+		NbBamgQuadtreeBox=0;
+		NbVertices=0;
+
+		/*Create container*/
+		boxcontainer=new DataSet();
+
+		/*Create Root, pointer toward the main box*/
+		root=NewBamgQuadtreeBox();
+
+		}
+	/*}}}*/
+	/*FUNCTION BamgQuadtree::BamgQuadtree(Mesh * t,long nbv){{{*/
+	BamgQuadtree::BamgQuadtree(Mesh * t,long nbv){ 
+
+		/*Number of boxes and vertices*/
+		NbBamgQuadtreeBox=0;
+		NbVertices=0;
+
+		/*Create container*/
+		boxcontainer=new DataSet();
+
+		/*Create Root, pointer toward the main box*/
+		root=NewBamgQuadtreeBox();
+
+		/*Check Sizes*/
+		_assert_(MaxISize>MaxICoor);
+
+		/*Add all vertices of the mesh*/
+		if (nbv==-1) nbv=t->nbv;
+		for (int i=0;ivertices[i]);
+
+	}
+	/*}}}*/
+	/*FUNCTION BamgQuadtree::~BamgQuadtree(){{{*/
+	BamgQuadtree::~BamgQuadtree() {
+		delete boxcontainer;
+		root=NULL;
+	}
+	/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION BamgQuadtree::Add{{{*/
+	void  BamgQuadtree::Add(BamgVertex &w){
+		/*Original code from Frederic Hecht  (BAMG v1.01, BamgQuadtree.cpp/Add)*/
+		BamgQuadtreeBox** pb=NULL;
+		BamgQuadtreeBox*  b=NULL;
+
+		/*Get integer coodinate of current point w*/
+		register long i=w.i.x, j=w.i.y;
+
+		/*Initialize level*/
+		register long level=MaxISize;
+
+		/*Get inital box (the largest)*/
+		pb = &root;
+
+		/*Find the smallest box where w is located*/
+		while((b=*pb) && (b->nbitems<0)){ 
+
+			//shift b->nbitems by -1
+			b->nbitems--;
+
+			//shifted righ by one bit: level=00000010 -> 00000001
+			level >>= 1;
+
+			//Get next subbox according to the bit value (level)
+			pb = &b->b[IJ(i,j,level)];
+		}
+
+		/*OK, we have found b, a Subbox holding vertices (might be full)
+		  check that the vertex is not already in the box*/
+		if (b){      
+			if (b->nbitems > 3 &&  b->v[3] == &w) return;
+			if (b->nbitems > 2 &&  b->v[2] == &w) return;
+			if (b->nbitems > 1 &&  b->v[1] == &w) return;
+			if (b->nbitems > 0 &&  b->v[0] == &w) return;
+		}
+
+		/*check that l is not 0 (this should not happen as MaxDepth = 30)*/
+		_assert_(level>0);
+
+		/*Now, try to add the vertex, if the subbox is full (nbitems=4), we have to divide it
+		  in 4 new subboxes*/
+		while ((b= *pb) && (b->nbitems == 4)){ // the BamgQuadtreeBox is full
+
+			/*Copy the 4 vertices in the current BamgQuadtreebox*/
+			BamgVertex* v4[4];
+			v4[0]= b->v[0];
+			v4[1]= b->v[1];
+			v4[2]= b->v[2];
+			v4[3]= b->v[3];
+
+			/*set nbitems as negative 
+			 * (box full -> holds 4 pointers toward subboxes and not 4 vertices)*/
+			b->nbitems = -b->nbitems;
+
+			/*Initialize the 4 pointers toward the 4 subboxes*/
+			b->b[0]=b->b[1]=b->b[2]=b->b[3]=NULL;
+
+			/*level = 0010000 -> 0001000*/
+			level >>= 1;
+
+			/*Put the four vertices in the new boxes*/
+			for (int k=0;k<4;k++){
+
+				int          ij;
+				/*bb is the new "sub"box of b where v4[k] is located*/
+				BamgQuadtreeBox *bb = b->b[ij=IJ(v4[k]->i.x,v4[k]->i.y,level)];
+
+				// alloc the BamgQuadtreeBox
+				if (!bb) bb=b->b[ij]=NewBamgQuadtreeBox(); 
+
+				/*Copy the current vertex*/
+				bb->v[bb->nbitems++] = v4[k];
+			}
+
+			/*Get the subbox where w (i,j) is located*/
+			pb = &b->b[IJ(i,j,level)];
+		}
+
+		/*alloc the BamgQuadtreeBox if necessary*/
+		if (!(b=*pb)) b=*pb= NewBamgQuadtreeBox();
+
+		/*Add w*/
+		b->v[b->nbitems++]=&w;
+
+		//Increase NbVertices by one (we have one new vertex)
+		NbVertices++;
+	}
+	/*}}}*/
+	/*FUNCTION BamgQuadtree::NearestVertex{{{*/
+	BamgVertex*  BamgQuadtree::NearestVertex(Icoor1 i,Icoor1 j) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, BamgQuadtree.cpp/NearestVertex)*/
+
+		/*Intermediaries*/
+		BamgQuadtreeBox *pb[MaxDepth];
+		int          pi[MaxDepth];
+		Icoor1       ii[MaxDepth];
+		Icoor1       jj[MaxDepth];
+		int          level;
+		long         n0;
+		BamgQuadtreeBox *b;
+		long         h0;
+		long         h = MaxISize;
+		long         hb= MaxISize;
+		Icoor1       i0=0,j0=0;
+
+		/*initial output as NULL (no vertex found)*/
+		BamgVertex*  nearest_v=NULL;
+
+		/*Project w coordinates (i,j) onto [0,MaxISize-1] x [0,MaxISize-1] -> (iplus,jplus)*/
+		Icoor1 iplus( inbitems) return nearest_v; 
+
+		/*else, find the smallest non-empty BamgQuadtreeBox containing  the point (i,j)*/
+		while((n0=b->nbitems)<0){
+
+			Icoor1       hb2 = hb >> 1;             //size of the current box
+			int          k   = IJ(iplus,jplus,hb2); //box number (0,1,2 or 3)
+			BamgQuadtreeBox *b0  = b->b[k];             //pointer toward current box
+
+			/* break if NULL box or empty (Keep previous box b)*/
+			if (( b0 == NULL) || (b0->nbitems == 0)) break;
+
+			/*Get next Quadtree box*/
+			b=b0;	
+			i0 += I_IJ(k,hb2); // i orign of BamgQuadtreeBox (macro)
+			j0 += J_IJ(k,hb2); // j orign of BamgQuadtreeBox 
+			hb = hb2;          // size of the box (in Int)
+		}
+
+		/*The box b, is the smallest box containing the point (i,j) and
+		 * has the following properties:
+		 * - n0: number of items (>0 if vertices, else boxes)
+		 * - hb: box size (int)
+		 * - i0: x coordinate of the lower left corner
+		 * - j0: y coordinate of the lower left corner*/
+
+		/* if the current subbox is holding vertices, we are almost done*/
+		if (n0>0){  
+			//loop over the vertices of the box and find the closest vertex
+			for(int k=0;kv[k]->i;
+
+				/*Compute norm with w*/
+				h0=NORM(iplus,i2.x,jplus,i2.y);
+
+				/*is it smaller than previous value*/
+				if (h0v[k];
+				}
+			}
+			/*return closest vertex*/
+			return nearest_v;
+		}
+
+		/* general case: the current box is empty, we have to go backwards
+			and find the closest not-empty box and find the closest vertex*/
+
+		/*Initialize search variables*/
+		pb[0]=b;                             //pointer toward the box b
+		pi[0]=b->nbitems>0?(int)b->nbitems:4;//number of boxes in b
+		ii[0]=i0;                            //i coordinate of the box lowest left corner
+		jj[0]=j0;                            //j coordinate of the box lowest left corner
+
+		/*initialize h: smallest box size, containing a vertex close to w*/
+		h=hb;
+
+		/*Main loop*/
+		level=0;
+		do {
+
+			/*get current box*/
+			b= pb[level];
+
+			/*Loop over the items in current box (if not empty!)*/
+			while (pi[level]){
+
+				/*We are looping now over the items of b. k is the current index (in [0 3])*/
+				pi[level]--;
+				int k=pi[level];
+
+				/*if the current subbox is holding vertices (b->nbitems<0 is subboxes)*/
+				if (b->nbitems>0){
+					I2 i2=b->v[k]->i;
+					h0 = NORM(iplus,i2.x,jplus,i2.y);
+					if (h0v[k];
+					}
+				}
+				/*else: current box b is pointing toward 4 boxes
+				 * test sub-box k and go deeper into the tree if it is non empty
+				 * and contains the point w modulo a size h that is either the size of the smallest
+				 * non empty box containing w, or the closest point to w (so far) */
+				else{
+					BamgQuadtreeBox* b0=b;
+
+					/*if the next box exists:*/
+					if (b=b->b[k]){
+
+						/*Get size (hb) and coordinates of the current sub-box lowest left corner*/
+						hb>>=1;
+						Icoor1 iii = ii[level]+I_IJ(k,hb);
+						Icoor1 jjj = jj[level]+J_IJ(k,hb);
+
+						/*if the current point (iplus,jplus) is in b (modulo h), this box is good:
+						 * it is holding vertices that are close to w */
+						if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)){
+							level++;
+							pb[level]= b;
+							pi[level]= b->nbitems>0 ?(int)  b->nbitems : 4  ;
+							ii[level]= iii;
+							jj[level]= jjj;
+						}
+
+						//else go backwards
+						else{
+							//shifted righ by one bit: hb=001000000 -> 01000000
+							b=b0;
+							hb<<=1;
+						}
+					}
+					else{
+						/*Current box is NULL, go to next subbox of b (k=k-1)*/
+						b=b0;
+					}
+				}
+			}
+
+			/*We have found a vertex, now, let's try the other boxes of the previous level
+			 * in case there is a vertex closest to w that has not yet been tested*/
+			hb <<= 1;
+		} while (level--);
+
+		/*return nearest_v, nearest vertex*/
+		return nearest_v;
+
+	}
+	/*}}}*/
+	/*FUNCTION BamgQuadtree::NearestVertexWithNormal{{{*/
+	BamgVertex*  BamgQuadtree::NearestVertexWithNormal(Icoor1 i,Icoor1 j) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, BamgQuadtree.cpp/NearestVertexWithNormal)*/
+
+		BamgQuadtreeBox * pb[ MaxDepth ];
+		int  pi[ MaxDepth  ];
+		Icoor1 ii[  MaxDepth ], jj [ MaxDepth];
+		int l; // level
+		BamgQuadtreeBox * b;
+		long     h =MaxISize,h0;
+		long     hb=MaxISize;
+		Icoor1  i0=0,j0=0;
+		Icoor1  iplus( inbitems)
+		 return vn; // empty tree 
+
+		while( (n0 = b->nbitems) < 0) 
+		  {
+			// search the non empty 
+			// BamgQuadtreeBox containing  the point (i,j)
+			register Icoor1 hb2 = hb >> 1 ;
+			register  int k = IJ(iplus,jplus,hb2);// BamgQuadtreeBox number of size hb2 contening i;j
+			register BamgQuadtreeBox * b0= b->b[k];
+			if ( ( b0 == 0) || (b0->nbitems == 0) ) 
+			 break; // null box or empty   => break 	    
+			b=b0;	
+			i0 += I_IJ(k,hb2); // i orign of BamgQuadtreeBox
+			j0 += J_IJ(k,hb2); // j orign of BamgQuadtreeBox 
+			hb = hb2; 
+		  }
+
+
+		if ( n0 > 0) 
+		  {  
+			for(register int k=0;kv[k]->i;
+				//   try if is in the right direction -- 
+				h0 = NORM(iplus,i2.x,jplus,i2.y);
+				if (h0 v[k];}
+			  }
+			if (vn) return vn; 
+		  }
+		// general case -----
+		// INITIALISATION OF THE HEAP 
+		l =0; // level 
+		pb[0]= b;
+		pi[0]=b->nbitems>0 ?(int)  b->nbitems : 4  ;
+		ii[0]=i0;
+		jj[0]=j0;
+		h=hb;
+		do {   // walk on the tree  
+			b= pb[l];
+			while (pi[l]--) // loop on 4 element of the box
+			  { 	      
+				int k = pi[l];
+
+				if (b->nbitems>0) // BamgVertex BamgQuadtreeBox none empty
+				  { 
+					I2 i2 =  b->v[k]->i;
+					// if good direction when try -- 
+
+					h0 = NORM(iplus,i2.x,jplus,i2.y);
+					if (h0 v[k];
+					  }
+				  }
+				else // Pointer BamgQuadtreeBox 
+				  { 
+					register BamgQuadtreeBox *b0=b;
+					if ((b=b->b[k])) 
+					  {
+						hb >>=1 ; // div by 2
+						register Icoor1 iii = ii[l]+I_IJ(k,hb);
+						register Icoor1 jjj = jj[l]+J_IJ(k,hb);
+
+						if  (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)) 
+						  {
+							pb[++l]=  b;
+							pi[l]= b->nbitems>0 ?(int)  b->nbitems : 4  ;
+							ii[l]= iii;
+							jj[l]= jjj;
+
+						  }
+						else
+						 b=b0, hb <<=1 ;
+					  }
+					else
+					 b=b0;
+				  }
+			  }
+			hb <<= 1; // mul by 2 
+		} while (l--);
+
+		return vn;
+	}
+	/*}}}*/
+	/*FUNCTION BamgQuadtree::NewBamgQuadtreeBox {{{*/
+	BamgQuadtree::BamgQuadtreeBox* BamgQuadtree::NewBamgQuadtreeBox(void){
+
+		/*Output*/
+		BamgQuadtreeBox* newbox=NULL;
+
+		/*Create and initialize a new box*/
+		newbox=new BamgQuadtreeBox;
+		newbox->nbitems=0;
+		newbox->b[0]=NULL;
+		newbox->b[1]=NULL;
+		newbox->b[2]=NULL;
+		newbox->b[3]=NULL;
+
+		/*Add root to the container*/
+		boxcontainer->AddObject(newbox);
+
+		/*Increase counter*/
+		NbBamgQuadtreeBox++;
+
+		/*currentbox now points toward next quadtree box*/
+		return newbox;
+	}/*}}}*/
+	/*FUNCTION BamgQuadtree::ToClose {{{*/
+	BamgVertex*   BamgQuadtree::ToClose(BamgVertex & v,double seuil,Icoor1 hx,Icoor1 hy){
+		/*Original code from Frederic Hecht  (BAMG v1.01, BamgQuadtree.cpp/ToClose)*/
+
+		const Icoor1 i=v.i.x;
+		const Icoor1 j=v.i.y;
+		const R2 X(v.r);
+		const Metric  Mx(v.m);
+
+		BamgQuadtreeBox * pb[ MaxDepth ];
+		int  pi[ MaxDepth  ];
+		Icoor1 ii[  MaxDepth ], jj [ MaxDepth];
+		register int l=0; // level
+		register BamgQuadtreeBox * b;
+		Icoor1 h=MaxISize;
+		Icoor1 hb =  MaxISize;
+		Icoor1 i0=0,j0=0;
+
+		//  BamgVertex *vn=0;
+
+		if (!root->nbitems)
+		 return 0; // empty tree 
+
+		// general case -----
+		pb[0]=root;
+		pi[0]=root->nbitems>0 ?(int)  root->nbitems : 4  ;
+		ii[0]=i0;
+		jj[0]=j0;
+		h=hb;
+		do {    
+			b= pb[l];
+			while (pi[l]--){ 	      
+				register int k = pi[l];
+
+				if (b->nbitems>0){ // BamgVertex BamgQuadtreeBox none empty
+					I2 i2 =  b->v[k]->i;
+					if ( ABS(i-i2.x) v[k]->r);
+						double dd;
+						if( (dd= LengthInterpole(Mx(XY), b->v[k]->m(XY)))  < seuil ){
+							return b->v[k]; 
+						}
+					  }
+				}
+				else{ // Pointer BamgQuadtreeBox 
+					register BamgQuadtreeBox *b0=b;
+					if ((b=b->b[k])){
+						hb >>=1 ; // div by 2
+						register long iii = ii[l]+I_IJ(k,hb);
+						register long jjj = jj[l]+J_IJ(k,hb);
+
+						if  (INTER_SEG(iii,iii+hb,i-hx,i+hx) && INTER_SEG(jjj,jjj+hb,j-hy,j+hy)){
+							pb[++l]=  b;
+							pi[l]= b->nbitems>0 ?(int)  b->nbitems : 4  ;
+							ii[l]= iii;
+							jj[l]= jjj;
+
+						}
+						else{
+							b=b0;
+							hb <<=1 ;
+						}
+					}
+					else{
+						b=b0;
+					}
+				}
+			}
+			hb <<= 1; // mul by 2 
+		} while (l--);
+
+		return 0;
+	}
+	/*}}}*/
+}
Index: /issm/trunk/src/c/classes/bamg/BamgQuadtree.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgQuadtree.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgQuadtree.h	(revision 13395)
@@ -0,0 +1,62 @@
+/*Original code from Frederic Hecht  (BAMG v1.01, BamgQuadtree.h)*/
+#ifndef _BAMGQUADTREE_H
+#define _BAMGQUADTREE_H
+
+#include "./include.h"
+#include "../objects/Object.h"
+class DataSet;
+
+namespace bamg {
+
+	const int  MaxDepth = 30;
+	const long MaxISize = ( 1L << MaxDepth);  // = 2^30 : 010000000000..000 (bitwise operation)
+
+	class BamgVertex;
+
+	class BamgQuadtree{
+
+		private:
+
+			/*A quadtree box contains a maximum of 4 vertices. 4 other quadtree boxes are
+			 * created if a fifth vertex is added to the same box. A Quadtree box is therefore
+			 * composed of EITHER:
+			 * - up to 4 vertices
+			 * - 4 "sub" quadtree boxes*/
+			class BamgQuadtreeBox: public Object{ 
+				public:
+					int nbitems; // number of current vertices in the box
+					union{
+						BamgQuadtreeBox* b[4];
+						BamgVertex*  v[4];
+					};
+					/*Object functions*/
+					void    Echo()       {_error_("not implemented yet"); };
+					void    DeepEcho()   {_error_("not implemented yet"); };
+					int     Id()         {_error_("not implemented yet"); };
+					int     MyRank()     {_error_("not implemented yet"); };
+					int     ObjectEnum() {_error_("not implemented yet"); };
+					Object *copy()       {_error_("not implemented yet"); };
+			};
+
+			/*BamgQuadtree private Fields*/
+			DataSet* boxcontainer;
+
+		public:
+
+			/*BamgQuadtree public Fields*/
+			BamgQuadtreeBox* root;
+			long         NbBamgQuadtreeBox;
+			long         NbVertices;
+
+			BamgQuadtree();
+			BamgQuadtree(Mesh *t,long nbv=-1);
+			~BamgQuadtree();
+
+			BamgVertex      *NearestVertex(Icoor1 i,Icoor1 j);
+			BamgVertex      *NearestVertexWithNormal(Icoor1  i,Icoor1 j);
+			BamgQuadtreeBox *NewBamgQuadtreeBox(void);
+			BamgVertex      *ToClose(BamgVertex &,double ,Icoor1,Icoor1);
+			void             Add(BamgVertex &w);
+	};
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/BamgVertex.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgVertex.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgVertex.cpp	(revision 13395)
@@ -0,0 +1,256 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "../objects.h"
+
+namespace bamg {
+
+	/*Methods*/
+	/*FUNCTION BamgVertex::Echo {{{*/
+
+	void BamgVertex::Echo(void){
+
+		_printLine_("Vertex:");
+		_printLine_("  integer   coordinates i.x: " << i.x << ", i.y: " << i.y);
+		_printLine_("  Euclidean coordinates r.x: " << r.x << ", r.y: " << r.y);
+		_printLine_("  ReferenceNumber = " << ReferenceNumber);
+		m.Echo();
+
+		return;
+	}
+	/*}}}*/
+	/*FUNCTION BamgVertex::GetReferenceNumber{{{*/
+	int  BamgVertex::GetReferenceNumber() const { 
+		return ReferenceNumber;
+	}
+	/*}}}*/
+	/*FUNCTION BamgVertex::MetricFromHessian{{{*/
+	void BamgVertex::MetricFromHessian(const double Hxx,const double Hyx, const double Hyy,const double smin,const double smax,const double s,double err,BamgOpts* bamgopts){
+		/*Compute Metric from Hessian*/
+
+		/*get options*/
+		double power=(bamgopts->power);
+		double anisomax=(bamgopts->anisomax);
+		double CutOff=bamgopts->cutoff;
+		double hmin=(bamgopts->hmin);
+		double hmax=(bamgopts->hmax);
+		double coef=bamgopts->coeff;
+		int    Metrictype=(bamgopts->Metrictype);
+
+		/*Intermediary*/
+		double ci;
+
+		/*compute multiplicative coefficient depending on Metric Type (2/9 because it is 2d)*/
+
+		//Absolute Error
+		/*
+		 *            2         1       
+		 *Metric M = ---  ------------   Abs(Hessian)
+		 *            9   err * coeff^2  
+		 */
+		if (Metrictype==0){
+			ci= 2.0/9.0 * 1/(err*coef*coef);
+		}
+
+		//Relative Error
+		/*
+		 *            2         1            Abs(Hessian)
+		 *Metric M = ---  ------------  ----------------------
+		 *            9   err * coeff^2  max( |s| , cutoff*max(|s|) )
+		 *
+		 */
+		else if (Metrictype==1){
+			ci= 2.0/9.0 * 1/(err*coef*coef) * 1/Max( Abs(s), CutOff*(Max(Abs(smin),Abs(smax))));
+		}
+
+		//Rescaled absolute error
+		/*
+		 *            2         1            Abs(Hessian)
+		 *Metric M = ---  ------------  ---------------------- 
+		 *            9   err * coeff^2       (smax-smin)
+		 */
+		else if (Metrictype==2){
+			ci= 2.0/9.0 * 1/(err*coef*coef) * 1/(smax-smin);
+		}
+		else{
+			_error_("Metrictype " << Metrictype << " not supported yet (use 0,1 or 2(default))");
+		}
+
+		//initialize metric Miv with ci*H
+		Metric Miv(Hxx*ci,Hyx*ci,Hyy*ci);
+
+		//Get eigen values and vectors of Miv
+		EigenMetric Vp(Miv);
+
+		//move eigen valuse to their absolute values
+		Vp.Abs();
+
+		//Apply a power if requested by user
+		if(power!=1.0) Vp.pow(power);
+
+		//modify eigen values according to hmin and hmax
+		Vp.Maxh(hmax);
+		Vp.Minh(hmin);
+
+		//Bound anisotropy by 1/(anisomax)^2
+		Vp.BoundAniso2(1/(anisomax*anisomax));
+
+		//rebuild Metric from Vp
+		Metric MVp(Vp);
+
+		//Apply Metric to vertex
+		m.IntersectWith(MVp);
+
+	}
+	/*}}}*/
+	/*FUNCTION BamgVertex::Optim {{{*/
+	long BamgVertex::Optim(int i,int koption){ 
+		long ret=0;
+		if ( t && (IndexInTriangle >= 0 ) && (IndexInTriangle <3) ){
+			ret = t->Optim(IndexInTriangle,koption);
+			if(!i){
+				t =0; // for no future optime 
+				IndexInTriangle= 0;
+			}
+		}
+		return ret;
+	}
+	/*}}}*/
+	/*FUNCTION BamgVertex::Smoothing{{{*/
+	double  BamgVertex::Smoothing(Mesh &Th,const Mesh &BTh,Triangle* &tstart ,double omega){
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/Smoothing)*/
+
+		register BamgVertex* s=this;
+		BamgVertex &vP = *s,vPsave=vP;
+
+		register Triangle* tbegin= t , *tria = t , *ttc;
+
+		register int k=0,kk=0,j = EdgesVertexTriangle[IndexInTriangle][0],jc;
+		R2 P(s->r),PNew(0,0);
+		do {
+			k++; 
+
+			if (!tria->Hidden(j)){
+				BamgVertex &vQ = (*tria)[VerticesOfTriangularEdge[j][0]]; 
+
+				R2 Q = vQ,QP(P-Q);
+				double lQP = LengthInterpole(vP,vQ,QP);
+				PNew += Q+QP/Max(lQP,1e-20);
+				kk ++;
+			}
+			ttc =  tria->TriangleAdj(j);
+			jc = NextEdge[tria->NuEdgeTriangleAdj(j)];
+			tria = ttc;
+			j = NextEdge[jc];
+			if (k>=2000){
+				_error_("k>=2000 (Maximum number of iterations reached)");
+			}
+		} while ( tbegin != tria); 
+		if (kk<4) return 0;
+		PNew = PNew/(double)kk;
+		R2 Xmove((PNew-P)*omega);
+		PNew = P+Xmove;
+		double delta=Norme2_2(Xmove); 
+
+		Icoor2 deta[3];
+		I2 IBTh  = BTh.R2ToI2(PNew);
+
+		tstart=BTh.TriangleFindFromCoord(IBTh,deta,tstart);  
+
+		if (tstart->det <0){ // outside
+			double ba,bb;
+			AdjacentTriangle edge= CloseBoundaryEdge(IBTh,tstart,ba,bb) ;
+			tstart = edge;
+			vP.m= Metric(ba,*edge.EdgeVertex(0),bb,*edge.EdgeVertex(1));
+		}
+		else { // inside
+			double   aa[3];
+			double s = deta[0]+deta[1]+deta[2];
+			aa[0]=deta[0]/s;
+			aa[1]=deta[1]/s;
+			aa[2]=deta[2]/s;
+			vP.m = Metric(aa,(*tstart)[0],(*tstart)[1],(*tstart)[2]);
+		}
+
+		// recompute the det of the triangle
+		vP.r = PNew;
+
+		vP.i = Th.R2ToI2(PNew);
+
+		BamgVertex vPnew = vP;
+
+		int ok=1;
+		int loop=1;
+		k=0;
+		while (ok){
+			ok =0;
+			do {
+				k++; 
+				double detold = tria->det;
+				tria->det =  bamg::det( (*tria)[0],(*tria)[1]  ,(*tria)[2]);
+				if (loop) {
+					BamgVertex *v0,*v1,*v2,*v3;
+					if (tria->det<0) ok =1;			       
+					else if (tria->Quadrangle(v0,v1,v2,v3))
+					  {
+						vP = vPsave;
+						double qold =QuadQuality(*v0,*v1,*v2,*v3);
+						vP = vPnew;
+						double qnew =QuadQuality(*v0,*v1,*v2,*v3);
+						if (qnewdet < detold/2 ) ok=1;
+
+				}
+				tria->SetUnMarkUnSwap(0);
+				tria->SetUnMarkUnSwap(1);
+				tria->SetUnMarkUnSwap(2);
+				ttc =  tria->TriangleAdj(j);
+				jc = NextEdge[tria->NuEdgeTriangleAdj(j)];
+				tria = ttc;
+				j = NextEdge[jc];
+				if (k>=2000){
+					_error_("k>=2000");
+				}
+			}while ( tbegin != tria); 
+
+			if (ok && loop) vP=vPsave; // no move 
+			loop=0;
+		}
+		return delta;
+	}
+	/*}}}*/
+
+	/*Intermediary*/
+	/*FUNCTION QuadQuality{{{*/
+	double QuadQuality(const BamgVertex & a,const BamgVertex &b,const BamgVertex &c,const BamgVertex &d) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, MeshQuad.cpp/QuadQuality)*/
+
+		// calcul de 4 angles --
+		R2 A((R2)a),B((R2)b),C((R2)c),D((R2)d);
+		R2 AB(B-A),BC(C-B),CD(D-C),DA(A-D);
+		//  Move(A),Line(B),Line(C),Line(D),Line(A);
+		const Metric & Ma  = a;
+		const Metric & Mb  = b;
+		const Metric & Mc  = c;
+		const Metric & Md  = d;
+
+		double lAB=Norme2(AB);
+		double lBC=Norme2(BC);
+		double lCD=Norme2(CD);
+		double lDA=Norme2(DA);
+		AB /= lAB;  BC /= lBC;  CD /= lCD;  DA /= lDA;
+		// version aniso 
+		double cosDAB= Ma(DA,AB)/(Ma(DA)*Ma(AB)),sinDAB= Det(DA,AB);
+		double cosABC= Mb(AB,BC)/(Mb(AB)*Mb(BC)),sinABC= Det(AB,BC);
+		double cosBCD= Mc(BC,CD)/(Mc(BC)*Mc(CD)),sinBCD= Det(BC,CD);
+		double cosCDA= Md(CD,DA)/(Md(CD)*Md(DA)),sinCDA= Det(CD,DA);
+		double sinmin=Min(Min(sinDAB,sinABC),Min(sinBCD,sinCDA));
+		if (sinmin<=0) return sinmin;
+		return 1.0-Max(Max(Abs(cosDAB),Abs(cosABC)),Max(Abs(cosBCD),Abs(cosCDA)));
+	}
+	/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/BamgVertex.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/BamgVertex.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/BamgVertex.h	(revision 13395)
@@ -0,0 +1,58 @@
+#ifndef _BAMGVERTEX_H_
+#define _BAMGVERTEX_H_
+
+#include "./include.h"
+#include "./Metric.h"
+#include "./Direction.h"
+#include "./BamgOpts.h"
+
+namespace bamg {
+
+	//classes
+	class Triangle;
+	class Mesh;
+	class VertexOnGeom;
+	class VertexOnEdge;
+
+	class BamgVertex {
+
+		public:
+
+			/*Fields*/
+			I2        i;                 // integer coordinates
+			R2        r;                 // real coordinates
+			Metric    m;
+			long      ReferenceNumber;
+			Direction DirOfSearch;
+			short     IndexInTriangle;              // the vertex number in triangle; varies between 0 and 2 in t
+
+			union {
+				Triangle     *t;                      // one triangle which is containing the vertex
+				long          color;
+				BamgVertex   *MeshVertexHook;         // used in geometry BamgVertex to know the Mesh Vertex associated
+				VertexOnGeom *GeomEdgeHook;    // if IndexInTriangle == 8; // set with Mesh::SetVertexFieldOn()
+				BamgVertex   *BackgroundVertexHook;   // if IndexInTriangle == 16 on Background vertex Mesh::SetVertexFieldOnBTh()
+				VertexOnEdge *BackgroundEdgeHook;     // if IndexInTriangle == 32 on Background edge
+			};
+
+			/*Operators*/
+			operator I2() const {return i;}             // Cast operator
+			operator const R2 & () const {return r;}    // Cast operator
+			operator Metric () const {return m;}        // Cast operator
+			double operator()(R2 x) const { return m(x);} // Get x in the metric m
+
+			/*methods (No constructor and no destructors...)*/
+			double Smoothing(Mesh & ,const Mesh & ,Triangle  * & ,double =1);
+			void   MetricFromHessian(const double Hxx,const double Hyx, const double Hyy, const double smin,const double smax,const double s,const double err,BamgOpts* bamgopts);
+			void   Echo();
+			int    GetReferenceNumber() const;
+			long   Optim(int =1,int =0); 
+
+			//inline functions
+			inline void Set(const BamgVertex &rec,const Mesh & ,Mesh & ){*this=rec;}
+	};
+
+	//Intermediary
+	double QuadQuality(const BamgVertex &,const BamgVertex &,const BamgVertex &,const BamgVertex &);
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/CrackedEdge.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/CrackedEdge.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/CrackedEdge.cpp	(revision 13395)
@@ -0,0 +1,33 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "CrackedEdge.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+	/*FUNCTION CrackedEdge() {{{*/
+	CrackedEdge::CrackedEdge() {
+		a=NULL;
+		b=NULL;
+		E=NULL;
+		e1=NULL;
+		e2=NULL;
+		indexa[0]=-1;
+		indexa[1]=-1;
+		indexa[2]=-1;
+		indexb[0]=-1;
+		indexb[1]=-1;
+		indexb[2]=-1;
+		length=0;
+		normal.x=0;
+		normal.y=0;
+
+	}
+	/*}}}*/
+
+	/*Methods*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/CrackedEdge.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/CrackedEdge.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/CrackedEdge.h	(revision 13395)
@@ -0,0 +1,31 @@
+#ifndef _CRACKEDEDGE_H_
+#define _CRACKEDEDGE_H_
+
+#include "./typedefs.h"
+
+namespace bamg {
+
+	//classes
+	class Triangle;
+	class GeomEdge;
+	class Edge;
+
+	class CrackedEdge {
+
+		public:
+			Triangle* a;
+			Triangle* b; 
+			GeomEdge* E;
+			Edge* e1;
+			Edge* e2;
+			double length;
+			R2     normal;
+			long   indexa[3];
+			long   indexb[3];
+
+			//Constructors
+			CrackedEdge();
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/Curve.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/Curve.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Curve.cpp	(revision 13395)
@@ -0,0 +1,37 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "Curve.h"
+#include "Geometry.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+	/*FUNCTION Curve::Curve(){{{*/
+	Curve::Curve(){
+		FirstEdge=NULL;
+		LastEdge=NULL;
+		FirstVertexIndex=0;
+		LastVertexIndex=0;
+	} 
+	/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION Curve::Reverse {{{*/
+	void Curve::Reverse() {
+		/*reverse the direction of the curve */
+		Exchange(FirstEdge,LastEdge);
+		Exchange(FirstVertexIndex,LastVertexIndex);
+	}
+	/*}}}*/
+	/*FUNCTION Curve::Set {{{*/
+	void Curve::Set(const Curve & rec,const Geometry & Gh ,Geometry & GhNew){
+		*this = rec;
+		FirstEdge = GhNew.edges + Gh.GetId(FirstEdge);    
+		LastEdge = GhNew.edges + Gh.GetId(LastEdge); 
+	}
+	/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/Curve.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/Curve.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Curve.h	(revision 13395)
@@ -0,0 +1,27 @@
+#ifndef _CURVE_H_
+#define _CURVE_H_
+
+#include "../../shared/Bamg/shared.h"
+
+namespace bamg {
+
+	//classes
+	class GeomEdge;
+	class Curve;
+	class Geometry;
+
+	class Curve {
+		public:
+			GeomEdge *FirstEdge; //First edge of the curve
+			GeomEdge *LastEdge;  //Last edge of the curve
+			int FirstVertexIndex;       //Last vertex index in the last edge
+			int LastVertexIndex;        //First Vertex index in the first edge
+
+			//Methods
+			Curve();
+			void Reverse(void);
+			void Set(const Curve & rec,const Geometry & Th ,Geometry & ThNew);
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/Direction.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/Direction.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Direction.cpp	(revision 13395)
@@ -0,0 +1,36 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "Direction.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+	/*FUNCTION Direction() {{{*/
+	Direction::Direction():
+		dir(MaxICoor){
+
+	}/*}}}*/
+	/*FUNCTION Direction(Icoor1 i,Icoor1 j) {{{*/
+	Direction::Direction(Icoor1 i,Icoor1 j) {
+		Icoor2 n2 = 2*(Abs(i)+Abs(j));  
+		Icoor2 r  = MaxICoor* (Icoor2) i;
+		Icoor1 r1 = (Icoor1) (2*(r/ n2)); // odd number 
+		dir = (j>0) ? r1 : r1+1;          // odd-> j>0 even-> j<0
+	}/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION Direction::direction{{{*/
+	int Direction::direction(Icoor1 i,Icoor1 j) {
+		int r =1; 
+		if (dir!= MaxICoor) {
+			Icoor2 x(dir/2),y1(MaxICoor/2-Abs(x)),y(dir%2?-y1:y1);
+			r = (x*i + y*j) >=0;
+		}
+		return r;
+	}
+	/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/Direction.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/Direction.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Direction.h	(revision 13395)
@@ -0,0 +1,21 @@
+#ifndef _DIRECTION_H_
+#define _DIRECTION_H_
+
+#include "./include.h"
+#include "../../shared/Bamg/shared.h"
+
+namespace bamg {
+
+	class Direction {
+		private:
+			Icoor1 dir;
+
+		public:
+			//Methods
+			Direction();
+			Direction(Icoor1 i,Icoor1 j);
+			int direction(Icoor1 i,Icoor1 j);
+	};
+}
+#endif
+
Index: /issm/trunk/src/c/classes/bamg/DoubleAndInt.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/DoubleAndInt.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/DoubleAndInt.h	(revision 13395)
@@ -0,0 +1,19 @@
+#ifndef _DOUBLEANDINT_H_
+#define _DOUBLEANDINT_H_
+
+#include "./include.h"
+
+namespace bamg {
+
+	class DoubleAndInt {
+		//class used by Mesh::MakeQuadrangles
+
+		public:
+			double q;
+			long i3j;
+
+			//Operators
+			int operator<(DoubleAndInt a){return q > a.q;}
+	};
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/Edge.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/Edge.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Edge.cpp	(revision 13395)
@@ -0,0 +1,54 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "Edge.h"
+#include "Mesh.h"
+#include "Geometry.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+
+	/*Methods*/
+	/*FUNCTION Edge::Set {{{*/
+	void Edge::Set(const Mesh & Th ,long i,Mesh & ThNew){ 
+		*this = Th.edges[i];
+		v[0] = ThNew.vertices + Th.GetId(v[0]);    
+		v[1] = ThNew.vertices + Th.GetId(v[1]);
+		if (GeomEdgeHook) 
+		 GeomEdgeHook =  ThNew.Gh.edges+Th.Gh.GetId(GeomEdgeHook);
+		if (adj[0]) adj[0] =   ThNew.edges +   Th.GetId(adj[0]);
+		if (adj[1]) adj[1] =   ThNew.edges +   Th.GetId(adj[1]);
+	}
+	/*}}}*/
+	/*FUNCTION Edge::Echo {{{*/
+	void Edge::Echo(void){ 
+		_printLine_("Edge:");
+		_printLine_("   pointers towards two vertices: " << v[0] << " " << v[1]);
+		_printLine_("   ReferenceNumber = " << ReferenceNumber);
+		_printLine_("   GeomEdgeHook = " << GeomEdgeHook);
+		_printLine_("   two adjacent edges on the same curve: " << adj[0] << " " << adj[1]);
+	}
+	/*}}}*/
+	/*FUNCTION Edge::Renumbering{{{*/
+	void Edge::Renumbering(BamgVertex *vb,BamgVertex *ve, long *renu){
+
+		if (v[0] >=vb && v[0] =vb && v[1] 
+#include 
+#include 
+#include 
+
+#include "Metric.h"
+
+namespace bamg {
+
+	/*Constructor*/
+	/*FUNCTION EigenMetric::EigenMetric(const Metric M){{{*/
+	EigenMetric::EigenMetric(const Metric& M){
+		/*From a metric (a11,a21,a22), get eigen values lambda1 and lambda2 and one eigen vector v*/
+
+		/*Intermediaries*/
+		double a11=M.a11,a21=M.a21,a22=M.a22;
+		double normM;
+		double delta,b;
+
+		/*To get the eigen values, we must solve the following equation:
+		 *     | a11 - lambda    a21        |
+		 * det |                            | = 0
+		 *     | a21             a22-lambda |
+		 *
+		 * We have to solve the following polynom:
+		 *  lamda^2 + ( -a11 -a22)*lambda + (a11*a22-a21*a21) = 0*/
+
+		/*Compute polynom determinant*/
+		b=-a11-a22;
+		delta=b*b - 4*(a11*a22-a21*a21);
+
+
+		/*Compute norm of M to avoid round off errors*/
+		normM=a11*a11 + a22*a22 + a21*a21;
+
+		/*1: normM too small: eigen values = 0*/
+		if(normM<1.e-30){
+			lambda1=0;
+			lambda2=0;
+			v.x=1;
+			v.y=0;
+		}
+		/*2: delta is small -> double root*/
+		else if (delta < 1.e-5*normM){
+			lambda1=-b/2;
+			lambda2=-b/2;
+			v.x=1;
+			v.y=0;
+		}
+		/*3: general case -> two roots*/
+		else{
+			delta     = sqrt(delta);
+			lambda1   = (-b-delta)/2.0;
+			lambda2   = (-b+delta)/2.0;
+
+			/*Now, one must find the eigen vectors. For that we use the following property of the inner product
+			 *     = 
+			 * Here, M'(M-lambda*Id) is symmetrical, which gives:
+			 *    ∀(x,y)∈R²xR²  = 
+			 * And we have the following:
+			 *    if y∈Ker(M'), ∀x∈R²  =  = 0
+			 * We have shown that
+			 *    Im(M') ⊥ Ker(M')
+			 *
+			 * To find the eigen vectors of M, we only have to find two vectors
+			 * of the image of M' and take their perpendicular as long as they are
+			 * not 0.
+			 * To do that, we take the images (1,0) and (0,1):
+			 *  x1 = (a11 - lambda)      x2 = a21
+			 *  y1 = a21                 y2 = (a22-lambda)
+			 *
+			 * We take the vector that has the larger norm and take its perpendicular.*/
+
+			double norm1 = (a11-lambda1)*(a11-lambda1) + a21*a21; 
+			double norm2 = a21*a21 + (a22-lambda1)*(a22-lambda1);
+
+			if (norm2
+#include 
+#include 
+
+#include "../../include/include.h"
+#include "../../shared/Exceptions/exceptions.h"
+
+#include "GeomEdge.h"
+#include "Geometry.h"
+
+using namespace std;
+
+namespace bamg {
+
+	/*Constructor/Destructor*/
+
+	/*Methods*/
+	/*FUNCTION GeomEdge::Cracked{{{*/
+	int    GeomEdge::Cracked() const  {
+		return type &1;  
+	}/*}}}*/
+	/*FUNCTION GeomEdge::F{{{*/
+	R2 GeomEdge::F(double theta) const{
+		/*Original code from Frederic Hecht  (BAMG v1.01, MeshGeom.cpp/F)*/
+		// parametrization of the curve edge
+
+	   R2 A=v[0]->r,B=v[1]->r;
+		double ca,cb,cta,ctb;
+
+		//Check that theta is in [0 1]
+		_assert_(theta>-1e-12 && theta<1+1e-12);
+
+		if (TgA()){ 
+			if (TgB()){ //Hermite interpolation
+				cb =  theta*theta*(3-2*theta);
+				ca =  1-cb;     
+				cta = (1-theta)*(1-theta)*theta;
+				ctb = (theta-1)*theta*theta ;
+			}
+			else {
+				double t = theta;
+				cb = t*t;
+				ca = 1-cb;
+				cta= t-cb;
+				ctb=0;    
+			}
+		}
+		else{
+			if (TgB()){
+				double t = 1-theta;
+				ca = t*t;
+				cb = 1-ca;
+				ctb= -t+ca;
+				cta=0;    
+			}
+			else { // lagrange P1
+				ca =(1-theta);
+				cb = theta;
+				cta=ctb=0;
+			}
+		}
+		return A*ca + B*cb + tg[0]*cta + tg[1]*ctb;
+	  }
+	/*}}}*/
+	/*FUNCTION GeomEdge::Mark{{{*/
+	int    GeomEdge::Mark()    const  {
+		return type &16; 
+	}/*}}}*/
+	/*FUNCTION GeomEdge::R1tg{{{*/
+	double GeomEdge::R1tg(double theta,R2 & t) const{
+		/*Original code from Frederic Hecht  (BAMG v1.01, MeshGeom.cpp/R1tg)*/
+		// 1/R of radius of cuvature
+
+		R2 A=v[0]->r,B=v[1]->r;
+		double dca,dcb,dcta,dctb;
+		double ddca,ddcb,ddcta,ddctb;
+		double tt = theta*theta;
+
+		//check theta
+		_assert_(theta>=0 && theta<=1);
+
+		if (TgA()){ 
+			if (TgB()){
+				// Tangent A and B provided:
+				// interpolation d'hermite
+				dcb = 6*theta*(1-theta);
+				ddcb = 6*(1-2*theta);
+				dca = -dcb;
+				ddca = -ddcb;
+				dcta =  (3*theta - 4)*theta + 1;
+				ddcta=6*theta-4;
+				dctb = 3*tt - 2*theta;
+				ddctb = 6*theta-2;
+			}
+			else {
+				//Tangent A provided but tangent B not provided
+				// 1-t*t, t-t*t, t*t
+				double t = theta;
+				dcb = 2*t;
+				ddcb = 2;
+				dca = -dcb;
+				ddca = -2;
+				dcta = 1-dcb;
+				ddcta = -ddcb;
+				dctb=0;    
+				ddctb=0;    
+			}
+		}
+		else{
+			if (TgB()){
+				//Tangent B provided but tangent A not provided
+				double t = 1-theta;
+				dca = -2*t;
+				ddca = 2;
+				dcb = -dca;
+				ddcb = -2;
+				dctb = 1+dca;
+				ddctb= ddca;
+				dcta =0;
+				ddcta =0;
+			}
+			else {
+				//Neither thangent A nor tangent B provided
+				// lagrange P1
+				t=B-A;
+				return 0;
+			} 
+		}
+		R2 d  =  A*dca  + B*dcb  + tg[0]* dcta  + tg[1] * dctb;
+		R2 dd =  A*ddca + B*ddcb + tg[0]* ddcta + tg[1] * ddctb;
+		double d2=(d,d);
+		double sd2 = sqrt(d2);
+		t=d;
+		if(d2>1.0e-20){
+			t/=sd2;
+			return Abs(Det(d,dd))/(d2*sd2);
+		}
+		else return 0;
+	}
+	/*}}}*/
+	/*FUNCTION GeomEdge::Required{{{*/
+	int    GeomEdge::Required()       {
+		return type &64; 
+	}/*}}}*/
+	/*FUNCTION GeomEdge::Set {{{*/
+	void GeomEdge::Set(const GeomEdge & rec,const Geometry & Gh ,Geometry & GhNew){ 
+		*this = rec;
+		v[0] = GhNew.vertices + Gh.GetId(v[0]);    
+		v[1] = GhNew.vertices + Gh.GetId(v[1]); 
+		if (Adj[0]) Adj[0] =  GhNew.edges + Gh.GetId(Adj[0]);     
+		if (Adj[1]) Adj[1] =  GhNew.edges + Gh.GetId(Adj[1]);     
+	}
+	/*}}}*/
+	/*FUNCTION GeomEdge::SetCracked{{{*/
+	void   GeomEdge::SetCracked()     { 
+		type |= 1;/*=>1st digit to 1*/
+	}/*}}}*/
+	/*FUNCTION GeomEdge::SetTgA{{{*/
+	void   GeomEdge::SetTgA()         { 
+		type |=4; /*=>2d digit to 1*/
+	}/*}}}*/
+	/*FUNCTION GeomEdge::SetTgB{{{*/
+	void   GeomEdge::SetTgB()         { 
+		type |=8; /*=> 3d digit to 1*/
+	}/*}}}*/
+	/*FUNCTION GeomEdge::SetMark{{{*/
+	void   GeomEdge::SetMark()        { 
+		type |=16;/*=> 4th digiy to 1*/
+	}/*}}}*/
+	/*FUNCTION GeomEdge::SetUnMark{{{*/
+	void   GeomEdge::SetUnMark()      { 
+		type &= 1007 /* 1023-16 = 000111110111 => 4th digit to 0*/;
+	}/*}}}*/
+	/*FUNCTION GeomEdge::SetRequired{{{*/
+	void   GeomEdge::SetRequired()    { 
+		type |= 64;/*=>6th digit to 1*/ 
+	}/*}}}*/
+	  /*FUNCTION GeomEdge::Tg{{{*/
+	int    GeomEdge::Tg(int i) const  {
+		return i==0 ? TgA() : TgB();
+	}/*}}}*/
+	/*FUNCTION GeomEdge::TgA{{{*/
+	int    GeomEdge::TgA()     const  {
+		return type &4;  
+	}/*}}}*/
+	/*FUNCTION GeomEdge::TgB{{{*/
+	int    GeomEdge::TgB()     const  {
+		return type &8;  
+	}/*}}}*/
+}
Index: /issm/trunk/src/c/classes/bamg/GeomEdge.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/GeomEdge.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/GeomEdge.h	(revision 13395)
@@ -0,0 +1,47 @@
+#ifndef _GEOMETRICALEDGE_H_
+#define _GEOMETRICALEDGE_H_
+
+#include "./include.h"
+
+namespace bamg {
+
+	//classes
+	class GeomVertex;
+	class Geometry;
+
+	class GeomEdge {
+
+		public:
+			GeomVertex *v[2];
+			long               ReferenceNumber;
+			long               CurveNumber;
+			R2                 tg[2];              // the 2 tangentes (tg[0] =0 => no continuity)
+			GeomEdge   *Adj[2];
+			int                AdjVertexIndex[2]; // for a given vertex, this gives the index of the vertex in the adjacent edge (0 or 1)
+			int                type;
+
+			//Operators
+			GeomVertex       & operator[](int i){return *v[i];};
+			const GeomVertex & operator[](int i) const { return *v[i];};
+			GeomVertex       * operator()(int i){return v[i];};  
+
+			//Methods
+			R2     F(double theta) const ; // parametrization of the curve edge
+			double R1tg(double theta,R2 &t) const ; // 1/radius of curvature + tangente
+			int    Tg(int i) const;
+			int    Cracked() const;
+			int    TgA()     const;
+			int    TgB()     const;
+			int    Mark()    const;
+			int    Required();
+			void   SetCracked();
+			void   SetTgA();
+			void   SetTgB();
+			void   SetMark();
+			void   SetUnMark();
+			void   SetRequired();
+			void   Set(const GeomEdge & rec,const Geometry & Th ,Geometry & ThNew);
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/GeomSubDomain.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/GeomSubDomain.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/GeomSubDomain.cpp	(revision 13395)
@@ -0,0 +1,20 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "GeomSubDomain.h"
+#include "Geometry.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+
+	/*Methods*/
+	/*FUNCTION GeomSubDomain::Set {{{*/
+	void GeomSubDomain::Set(const GeomSubDomain & rec,const Geometry & Gh ,const Geometry & GhNew){
+		*this = rec;
+		edge = Gh.GetId(edge) + GhNew.edges;
+	}/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/GeomSubDomain.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/GeomSubDomain.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/GeomSubDomain.h	(revision 13395)
@@ -0,0 +1,23 @@
+#ifndef _GEOMETRICALSUBDOMAIN_H_
+#define _GEOMETRICALSUBDOMAIN_H_
+
+#include "./include.h"
+
+namespace bamg {
+
+	//classes
+	class GeomEdge;
+	class Geometry;
+
+	class GeomSubDomain {
+		public:
+			GeomEdge *edge;
+			int              direction;   // -1 or 1
+			long             ReferenceNumber;
+
+			//Methods
+			void Set(const GeomSubDomain &,const Geometry & ,const Geometry &);
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/GeomVertex.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/GeomVertex.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/GeomVertex.cpp	(revision 13395)
@@ -0,0 +1,38 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "GeomVertex.h"
+#include "../../include/include.h"
+#include "../../shared/Exceptions/exceptions.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+	//See header file
+
+	/*Methods*/
+	/*FUNCTION GeomVertex::Corner {{{*/
+	int  GeomVertex::Corner() const {
+		return type & 4;
+	}
+	/*}}}*/
+	/*FUNCTION GeomVertex::Required {{{*/
+	int  GeomVertex::Required()const {
+		// a corner is required
+		return type & 6;
+	}
+	/*}}}*/
+	/*FUNCTION GeomVertex::SetCorner {{{*/
+	void GeomVertex::SetCorner(){
+		type |= 4;
+	}
+	/*}}}*/
+	/*FUNCTION GeomVertex::SetRequired {{{*/
+	void GeomVertex::SetRequired(){
+		type |= 2;
+	}
+	/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/GeomVertex.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/GeomVertex.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/GeomVertex.h	(revision 13395)
@@ -0,0 +1,30 @@
+#ifndef _GEOMETRICALVERTEX_H_
+#define _GEOMETRICALVERTEX_H_
+
+#include "./include.h"
+#include "BamgVertex.h"
+
+namespace bamg {
+
+	class Geometry;
+
+	class GeomVertex : public BamgVertex { 
+
+		public:
+			friend class Geometry;
+
+			int type;
+
+			//Constructors
+			GeomVertex():type(0){};
+
+			//Methods
+			int  Corner() const;
+			int  Required()const;
+			void SetCorner();
+			void SetRequired();
+
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/Geometry.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/Geometry.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Geometry.cpp	(revision 13395)
@@ -0,0 +1,973 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "../objects.h"
+#include "../../include/include.h"
+#include "../../shared/Exceptions/exceptions.h"
+
+namespace bamg {
+
+	static const  Direction NoDirOfSearch=Direction();
+
+	/*Constructors/Destructors*/
+	/*FUNCTION Geometry::Geometry(){{{*/
+	Geometry::Geometry(){
+		Init();
+	}
+	/*}}}*/
+	/*FUNCTION Geometry::Geometry(BamgGeom* bamggeom, BamgOpts* bamgopts){{{*/
+	Geometry::Geometry(BamgGeom* bamggeom, BamgOpts* bamgopts){
+		Init();
+		ReadGeometry(bamggeom,bamgopts);
+		PostRead();
+	}
+	/*}}}*/
+	/*FUNCTION Geometry::Geometry(const Geometry & Gh) (COPY operator){{{*/
+	Geometry::Geometry(const Geometry & Gh) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, MeshGeom.cpp/Geometry)*/
+
+		long i;
+		*this = Gh;
+		NbRef =0;
+		quadtree=0;
+		vertices = nbv ? new GeomVertex[nbv] : NULL;
+		edges = nbe ? new GeomEdge[nbe]:NULL;
+		curves= nbcurves ? new Curve[nbcurves]:NULL;
+		subdomains = nbsubdomains ? new GeomSubDomain[nbsubdomains]:NULL;
+		for (i=0;i (BAMG v1.01, MeshGeom.cpp/~Geometry)*/
+		if(NbRef>0){   _printString_("Trying to delete geometry and NbRef>0, probably due to an error"); return;}
+		if(vertices)   delete [] vertices;  vertices=0;
+		if(edges)      delete [] edges;     edges=0;
+		if(quadtree)   delete    quadtree;  quadtree=0;
+		if(curves)     delete [] curves;    curves=0;nbcurves=0;
+		if(subdomains) delete [] subdomains;subdomains=0;
+		Init();
+	}
+	/*}}}*/
+
+	/*IO*/
+	/*FUNCTION Geometry::ReadGeometry{{{*/
+	void Geometry::ReadGeometry(BamgGeom* bamggeom,BamgOpts* bamgopts){
+
+		int verbose;
+		nbv=0;
+		nbe=0;
+		nbcurves=0;
+
+		double Hmin = HUGE_VAL;// the infinie value 
+		int i,j,k,n,i0,i1,i2,i3;
+
+		/*initialize some variables*/
+		verbose= bamgopts->verbose;
+		nbv    = bamggeom->VerticesSize[0];
+		nbe    = bamggeom->EdgesSize[0];
+
+		//some checks
+		if (bamggeom->Vertices==NULL) _error_("the domain provided does not contain any vertex");
+		if (bamggeom->Edges==NULL) _error_("the domain provided does not contain any edge");
+
+		//Vertices
+		if (bamggeom->Vertices){
+			if(verbose>5) _printLine_("      processing Vertices");
+			if (bamggeom->VerticesSize[1]!=3) _error_("Vertices should have 3 columns");
+			vertices = new GeomVertex[nbv];
+			for (i=0;iVertices[i*3+0];
+				vertices[i].r.y=(double)bamggeom->Vertices[i*3+1];
+				vertices[i].ReferenceNumber=(long)bamggeom->Vertices[i*3+2];
+				vertices[i].DirOfSearch=NoDirOfSearch;
+				vertices[i].color =0;
+				vertices[i].type=0;
+			}
+			/*find domain extrema (pmin,pmax) that will define the square box used for by the quadtree*/
+			pmin =  vertices[0].r;
+			pmax =  vertices[0].r;
+			for (i=0;iEdges){
+			R2      zerovector(0,0);
+			double* verticeslength=NULL;
+
+			if(verbose>5) _printLine_("      processing Edges");
+			if (bamggeom->EdgesSize[1]!=3) _error_("Edges should have 3 columns");
+			edges = new GeomEdge[nbe];
+
+			//initialize verticeslength (sum of the lengths of the edges holding vertex)
+			verticeslength = new double[nbv];
+			for(i=0;iEdges[i*3+0]-1; //-1 for C indexing
+				i2=(int)bamggeom->Edges[i*3+1]-1; //-1 for C indexing
+				edges[i].v[0]= vertices + i1;     //pointer toward vertex i1 (=&vertices[i1])
+				edges[i].v[1]= vertices + i2;     //pointer toward vertex i2
+				edges[i].ReferenceNumber=(long)bamggeom->Edges[i*3+2];
+
+				//get length of edge
+				R2     x12=vertices[i2].r-vertices[i1].r;
+				double l12=sqrt((x12,x12));
+				Hmin=Min(Hmin,l12);
+
+				//initialize other fields
+				edges[i].tg[0]=zerovector;
+				edges[i].tg[1]=zerovector;
+				edges[i].AdjVertexIndex[0] = edges[i].AdjVertexIndex[1] = -1;
+				edges[i].Adj[0] = edges[i].Adj[1] = NULL;
+				edges[i].type = 0;
+
+				//Cracked?
+				if (edges[i].ReferenceNumber!=1) edges[i].SetCracked();
+
+				//prepare metric
+				vertices[i1].color++;
+				vertices[i2].color++;
+				verticeslength[i1] += l12;
+				verticeslength[i2] += l12;
+			}
+
+			// definition the default of the given mesh size 
+			for (i=0;i 0) 
+				 vertices[i].m=Metric(verticeslength[i] /(double) vertices[i].color);
+				else 
+				 vertices[i].m=Metric(Hmin);
+			}
+			delete [] verticeslength;
+			
+		}
+		else{
+			_error_("No edges provided");
+		}
+
+		//hVertices
+		if(bamgopts->hVertices && bamgopts->hVerticesSize[0]==nbv){
+			if(verbose>5) _printLine_("      processing hVertices");
+			for (i=0;i< nbv;i++){
+				if (!xIsNan(bamgopts->hVertices[i])){
+					vertices[i].m=Metric((double)bamgopts->hVertices[i]);
+				}
+			}
+		}
+
+		//MetricVertices
+		if(bamgopts->metric && bamgopts->metric[0]==nbv){
+			if(verbose>5) _printLine_("      processing MetricVertices");
+			for (i=0;i< nbv;i++) {
+				vertices[i].m = Metric((double)bamgopts->metric[i*3+0],(double)bamgopts->metric[i*3+1],(double)bamgopts->metric[i*3+2]);
+			}
+		}
+
+		//MaxCornerAngle
+		if (bamgopts->MaxCornerAngle){
+			if(verbose>5) _printLine_("      processing MaxCornerAngle");
+			MaxCornerAngle=bamgopts->MaxCornerAngle*Pi/180;
+		}
+
+		//TangentAtEdges
+		if (bamggeom->TangentAtEdges){
+			if(verbose>5) _printString_("      processing TangentAtEdges");
+			if (bamggeom->TangentAtEdgesSize[1]!=4) _error_("TangentAtEdges should have 4 columns");
+			int n,i,j,k;
+			R2 tg;
+
+			n=bamggeom->TangentAtEdgesSize[0];
+			for (k=0;kTangentAtEdges[k*4+0]-1; //for C indexing
+				j=(int)bamggeom->TangentAtEdges[k*4+1]-1; //for C indexing
+				tg.x=bamggeom->TangentAtEdges[k*4+2];
+				tg.y=bamggeom->TangentAtEdges[k*4+3];
+				if (i<0 || i>=nbe) _error_("TangentAtEdges first index exceeds matrix dimension");
+				if (j!=0 && j!=1)  _error_("TangentAtEdges second index should be 1 or 2 only");
+				edges[i].tg[j] = tg;
+			}
+		}
+
+		//Corners
+		if(bamggeom->Corners){
+			if(verbose>5) _printString_("      processing Corners");
+			if (bamggeom->CornersSize[1]!=1) _error_("Corners should have 1 column");
+			n=bamggeom->CornersSize[0];
+			for (i=0;iCorners[i]-1; //for C indexing
+				if (j>nbv-1 || j<0) _error_("Bad corner definition: should in [0 " << nbv << "]");
+				/*Required => at the same time SetRequired and SetCorner*/
+				vertices[j].SetCorner();
+				vertices[j].SetRequired();
+			}
+		}
+
+		//RequiredVertices
+		if(bamggeom->RequiredVertices){
+			if(verbose>5) _printLine_("      processing RequiredVertices");
+			if (bamggeom->RequiredVerticesSize[1]!=1) _error_("RequiredVertices should have 1 column");
+			n=bamggeom->RequiredVerticesSize[0];
+			for (i=0;iRequiredVertices[i]-1; //for C indexing
+				if (j>nbv-1 || j<0) _error_("Bad RequiredVerticess  definition: should in [0 " << nbv << "]");
+				vertices[j].SetRequired();
+			}
+		}
+
+		//RequiredEdges
+		if(bamggeom->RequiredEdges){
+			if(verbose>5) _printLine_("      processing RequiredEdges");
+			if (bamggeom->RequiredEdgesSize[1]!=1) _error_("RequiredEdges should have 1 column");
+			n=bamggeom->RequiredEdgesSize[0];
+			for (i=0;iRequiredEdges[i]-1; //for C indexing
+				if (j>nbe-1 || j<0) _error_("Bad RequiredEdges definition: should in [0 " << nbe << "]");
+				edges[j].SetRequired();  
+			}
+		}
+
+		//SubDomain
+		if(bamggeom->SubDomains){
+			if(verbose>5) _printLine_("      processing SubDomains");
+			if (bamggeom->SubDomainsSize[1]!=4) _error_("SubDomains should have 4 columns");
+			nbsubdomains=bamggeom->SubDomainsSize[0];
+			subdomains = new GeomSubDomain[nbsubdomains];
+			for (i=0;iSubDomains[i*4+0];
+				i1=(int)bamggeom->SubDomains[i*4+1];
+				i2=(int)bamggeom->SubDomains[i*4+2];
+				i3=(int)bamggeom->SubDomains[i*4+3];
+				if (i0!=2) _error_("Bad Subdomain definition: first number should be 2 (for Edges)");
+				if (i1>nbe || i1<=0) _error_("Bad Subdomain definition: second number should in [1 " << nbe << "] (edge number)");
+				subdomains[i].edge=edges + (i1-1);
+				subdomains[i].direction = (int) i2;
+				subdomains[i].ReferenceNumber = i3;
+			}
+		}
+	}
+	/*}}}*/
+	/*FUNCTION Geometry::WriteGeometry{{{*/
+	void Geometry::WriteGeometry(BamgGeom* bamggeom, BamgOpts* bamgopts){
+
+		int verbose;
+		int nbreq=0;
+		int nbreqv=0;
+		int nbtan=0;
+		int nbcracked=0;
+		int i,count;
+
+		/*Get options*/
+		verbose=bamgopts->verbose;
+
+		/*Vertices*/
+		if(verbose>5) _printLine_("      writing Vertices");
+		bamggeom->VerticesSize[0]=nbv;
+		bamggeom->VerticesSize[1]=3;
+		if (nbv){
+			bamggeom->Vertices=xNew(3*nbv);
+			for (i=0;iVertices[i*3+0]=vertices[i].r.x;
+				bamggeom->Vertices[i*3+1]=vertices[i].r.y;
+				bamggeom->Vertices[i*3+2]=vertices[i].GetReferenceNumber();
+
+				//update counters
+				if (vertices[i].Required()) nbreqv++;
+			}
+		}
+
+		/*Edges*/
+		if(verbose>5) _printLine_("      writing Edges");
+		bamggeom->EdgesSize[0]=nbe;
+		bamggeom->EdgesSize[1]=3;
+		if (nbe){
+			bamggeom->Edges=xNew(3*nbe);
+			for (i=0;iEdges[i*3+0]=GetId(edges[i][0])+1; //back to Matlab indexing
+				bamggeom->Edges[i*3+1]=GetId(edges[i][1])+1; //back to Matlab indexing
+				bamggeom->Edges[i*3+2]=(double)edges[i].ReferenceNumber;
+
+				//update counters
+				if (edges[i].Required()) nbreq++;
+				if (edges[i].TgA() && edges[i][0].Corner()) nbtan++;
+				if (edges[i].TgB() && edges[i][1].Corner()) nbtan++;
+			}
+		}
+
+		/*RequiredEdges*/
+		if(verbose>5) _printLine_("      writing " << nbreq << " RequiredEdges");
+		bamggeom->RequiredEdgesSize[0]=nbreq;
+		bamggeom->RequiredEdgesSize[1]=1;
+		if (nbreq){
+			bamggeom->RequiredEdges=xNew(1*nbreq);
+			count=0;
+			for (i=0;iRequiredEdges[count]=i+1; //back to Matlab indexing
+					count=count+1;
+				}
+			}
+		}
+
+		//No corners
+
+		/*RequiredVertices*/
+		if(verbose>5) _printLine_("      writing " << nbreqv << " RequiredVertices");
+		bamggeom->RequiredVerticesSize[0]=nbreqv;
+		bamggeom->RequiredVerticesSize[1]=1;
+		if (nbreqv){
+			bamggeom->RequiredVertices=xNew(1*nbreqv);
+			count=0;
+			for (i=0;iRequiredVertices[count]=i+1; //back to Matlab indexing
+					count=count+1;
+				}
+			}
+		}
+
+		/*SubDomains*/
+		if(verbose>5) _printLine_("      writing SubDomains");
+		bamggeom->SubDomainsSize[0]=nbsubdomains;
+		bamggeom->SubDomainsSize[1]=4;
+		if (nbsubdomains){
+			bamggeom->SubDomains=xNew(4*nbsubdomains);
+			for (i=0;iSubDomains[4*i+0]=2;
+				bamggeom->SubDomains[4*i+1]=GetId(subdomains[i].edge)+1; //back to Matlab indexing
+				bamggeom->SubDomains[4*i+2]=subdomains[i].direction;
+				bamggeom->SubDomains[4*i+3]=subdomains[i].ReferenceNumber;
+			}
+		}
+
+		/*TangentAtEdges*/
+		if(verbose>5) _printLine_("      writing TangentAtEdges");
+		bamggeom->TangentAtEdgesSize[0]=nbtan;
+		bamggeom->TangentAtEdgesSize[1]=4;
+		if (nbtan){
+			bamggeom->TangentAtEdges=xNew(4*nbtan);
+			count=0;
+			for (i=0;iTangentAtEdges[4*i+0]=i+1; //back to Matlab indexing
+					bamggeom->TangentAtEdges[4*i+1]=1;
+					bamggeom->TangentAtEdges[4*i+2]=edges[i].tg[0].x;
+					bamggeom->TangentAtEdges[4*i+3]=edges[i].tg[0].y;
+				}
+				if (edges[i].TgB() && edges[i][1].Corner()){
+					bamggeom->TangentAtEdges[4*i+0]=i+1; //back to Matlab indexing
+					bamggeom->TangentAtEdges[4*i+1]=2;
+					bamggeom->TangentAtEdges[4*i+2]=edges[i].tg[1].x;
+					bamggeom->TangentAtEdges[4*i+3]=edges[i].tg[1].y;
+				}
+				count=count+1;
+			}
+		}
+	}
+	/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION Geometry::Echo {{{*/
+	void Geometry::Echo(void){
+
+		_printLine_("Geometry:");
+		_printLine_("   nbv  (number of vertices) : " << nbv);
+		_printLine_("   nbe  (number of edges)    : " << nbe);
+		_printLine_("   nbsubdomains: " << nbsubdomains);
+		_printLine_("   nbcurves: " << nbcurves);
+		_printLine_("   vertices: " << vertices);
+		_printLine_("   edges: " << edges);
+		_printLine_("   quadtree: " << quadtree);
+		_printLine_("   subdomains: " << subdomains);
+		_printLine_("   curves: " << curves);
+		_printLine_("   pmin (x,y): (" << pmin.x << " " << pmin.y << ")");
+		_printLine_("   pmax (x,y): (" << pmax.x << " " << pmax.y << ")");
+		_printLine_("   coefIcoor: " << coefIcoor);
+		_printLine_("   MaxCornerAngle: " << MaxCornerAngle);
+
+		return;
+	}
+	/*}}}*/
+	/*FUNCTION Geometry::Init{{{*/
+	void Geometry::Init(void){
+		/*Original code from Frederic Hecht  (BAMG v1.01, MeshGeom.cpp/EmptyGeometry)*/
+
+		NbRef=0;
+		nbv=0;
+		nbe=0;
+		quadtree=NULL;
+		curves=NULL;
+		edges=NULL;
+		vertices=NULL;
+		nbsubdomains=0;
+		nbcurves=0;
+		subdomains=NULL;
+		MaxCornerAngle = 10*Pi/180; //default is 10 degres
+	}
+	/*}}}*/
+	/*FUNCTION Geometry::MinimalHmin{{{*/
+	double Geometry::MinimalHmin() {
+		/* coeffIcoor = (2^30-1)/D
+		 * We cannot go beyond hmin = D/2^30 because of the quadtree
+		 * hmin is therefore approximately 2/coeffIcoor */
+		return 2.0/coefIcoor;
+	}/*}}}*/
+	/*FUNCTION Geometry::MaximalHmax{{{*/
+	double Geometry::MaximalHmax() {
+		return Max(pmax.x-pmin.x,pmax.y-pmin.y);
+	}/*}}}*/
+	/*FUNCTION Geometry::GetId(const GeomVertex &t){{{*/
+	long Geometry::GetId(const GeomVertex & t) const  {
+		return &t - vertices;
+	}/*}}}*/
+	/*FUNCTION Geometry::GetId(const GeomVertex * t){{{*/
+	long Geometry::GetId(const GeomVertex * t) const  {
+		return t - vertices;
+	}/*}}}*/
+	/*FUNCTION Geometry::GetId(const GeomEdge & t){{{*/
+	long Geometry::GetId(const GeomEdge & t) const  {
+		return &t - edges;
+	}/*}}}*/
+	/*FUNCTION Geometry::GetId(const GeomEdge * t){{{*/
+	long Geometry::GetId(const GeomEdge * t) const  {
+		return t - edges;
+	}/*}}}*/
+	/*FUNCTION Geometry::GetId(const Curve * c){{{*/
+	long Geometry::GetId(const Curve * c) const  {
+		return c - curves;
+	}/*}}}*/
+	/*FUNCTION Geometry::Containing{{{*/
+	GeomEdge* Geometry::Containing(const R2 P,  GeomEdge * start) const {
+		/*Original code from Frederic Hecht  (BAMG v1.01, MeshGeom.cpp/Contening)*/
+
+		GeomEdge* on =start,* pon=0;
+		// walk with the cos on geometry
+		int counter=0;
+		while(pon != on){  
+			counter++;
+			_assert_(counter<100);
+			pon = on;
+			R2 A= (*on)[0];
+			R2 B= (*on)[1];
+			R2 AB = B-A;
+			R2 AP = P-A;
+			R2 BP = P-B;
+			if ( (AB,AP) < 0) 
+			 on = on->Adj[0];
+			else if ( (AB,BP)  > 0) 
+			 on = on->Adj[1];
+			else
+			 return on;
+		}
+		return on;
+	}
+	/*}}}*/
+	/*FUNCTION Geometry::PostRead{{{*/
+	void Geometry::PostRead(){
+		/*Original code from Frederic Hecht  (BAMG v1.01, MeshGeom.cpp/AfterRead)*/
+
+		long               i,j,k;
+		int                jj;
+		long              *head_v   = new long[nbv];
+		long              *next_p   = new long[2*nbe];
+		float             *eangle   = new float[nbe];
+		double             eps      = 1e-20;
+		BamgQuadtree           quadtree; // build quadtree to find duplicates
+		BamgVertex        *v0       = vertices;
+		GeomVertex *v0g      = (GeomVertex*) (void*)v0;
+
+		k=0;
+
+		//build quadtree for this geometry
+		for (i=0;i [0 2^30-1[^2 for a quadtree of depth 30*/
+			vertices[i].i=R2ToI2(vertices[i].r); 
+
+			/*find nearest vertex already present in the quadtree (NULL if empty)*/
+			BamgVertex* v=quadtree.NearestVertex(vertices[i].i.x,vertices[i].i.y); 
+
+			/*if there is a vertex found that is to close to vertices[i] -> error*/
+			if( v && Norme1(v->r - vertices[i].r) < eps ){
+				_printLine_("reference numbers: " << v->ReferenceNumber << " " << vertices[i].ReferenceNumber);
+				_printLine_("Id: " << i+1);
+				_printLine_("Coords: ["<r.x<<" "<r.y<<"] ["<r - edges[i].v[0]->r;
+			double lv10=Norme2(v10);
+			//check that its length is not 0
+			if(lv10==0){
+				delete [] next_p;
+				delete [] head_v;
+				delete [] eangle;
+				_error_("Length of edge " << i << " is 0");
+			}
+			//compute angle in [-Pi Pi]
+			eangle[i] = atan2(v10.y,v10.x);
+			//build chains head_v and next_p
+			for (j=0;j<2;j++){
+				long v=GetId(edges[i].v[j]);
+				next_p[k]=head_v[v];
+				head_v[v]=k++; //post increment: head_v[v]=k; and then k=k+1;
+			}
+		}
+
+		//sort head_v by order of increasing edges angle
+		for (i=0;i=0){
+					ord++;
+					long  i1=n/2;       // i1 = floor (n/2)      -> Edge number
+					long  j1=n%2;       // j1 = 1 if n is odd    -> Vertex index for this edge (0 or 1)
+					long* pn=next_p+n;
+
+					//Next vertex index
+					n=*pn;                       
+
+					//compute angle between horizontal axis and v0->v1
+					float angle = j1 ? OppositeAngle(eangle[i1]):  eangle[i1]; 
+
+					//exchange if the current edge angle is smaller than the previous one
+					if (angleold > angle){
+						exch=1;
+						*pn=*po;  // next_p[n] = n + 1
+						*po=*p;   // 
+						*p=n;     // next_p[n+1] = n
+						po=pn;    // po now point toward pn (invert next and current)
+					}
+
+					//else, continue going to the next edge position
+					else{                        //  to have : po -> p -> pn
+						angleold=angle; // update maximum angle
+						po=p;           // po now point toward p  (current position)
+						p=pn;           // p  now point toward pn (next position)
+					}
+				}
+			}
+
+			// angular test on current vertex to guess whether it is a corner (ord = number of edges holding i)
+			if(ord==2) { 
+				long  n1 = head_v[i];
+				long  n2 = next_p[n1];
+				long  i1 = n1/2, i2 = n2/2; // edge number
+				long  j1 = n1%2, j2 = n2%2; // vertex in the edge 
+				float angle1=  j1 ? OppositeAngle(eangle[i1]) : eangle[i1];
+				float angle2= !j2 ? OppositeAngle(eangle[i2]) : eangle[i2];
+				float da12 = Abs(angle2-angle1);
+				if (( da12 >= MaxCornerAngle ) && (da12 <= 2*Pi -MaxCornerAngle)) {
+					vertices[i].SetCorner() ; 
+				}
+				// if the edge type/referencenumber a changing then is SetRequired();
+				if (edges[i1].type != edges[i2].type || edges[i1].Required()){
+					vertices[i].SetRequired();
+				}
+				if (edges[i1].ReferenceNumber != edges[i2].ReferenceNumber) {
+					vertices[i].SetRequired();
+				}
+			}
+			if(ord != 2) {
+				vertices[i].SetCorner();
+			}
+
+			/*close the list around the vertex to have a circular loop*/
+			long no=-1, ne = head_v[i];
+			while (ne >=0) ne = next_p[no=ne];        
+			if(no>=0) next_p[no] = head_v[i];
+		}
+
+		/*Check that the list makes sense (we have all the time the same vertex)
+		 * and build adjacent edges*/
+		k =0;
+		for (i=0;ir -edges[i].v[0]->r;// AB = vertex0 -> vertex1
+			double lAB=Norme2(AB);                       // Get length of AB
+			double ltg2[2]={0.0};                        // initialize tangent
+
+			//loop over the 2 vertices of the edge
+			for (j=0;j<2;j++) {
+				R2     tg =edges[i].tg[j];
+				double ltg=Norme2(tg);
+
+				//by default, tangent=[0 0]
+				if(ltg==0){
+					//if the current vertex of the edge is not a corner
+					if(!edges[i].v[j]->Corner()){
+						/*The tangent is set as the vector between the
+						 * previous and next vertices connected to current vertex
+						 * normed by the edge length*/
+						tg = edges[i].v[1-j]->r - edges[i].Adj[j]->v[1-edges[i].AdjVertexIndex[j]]->r;
+						ltg= Norme2(tg);
+						tg = tg *(lAB/ltg);
+						ltg= lAB;
+					}
+					//else:  a Corner no tangent => nothing to do    
+				}
+				else{
+					//tangent has already been computed
+					tg = tg*(lAB/ltg),ltg=lAB;
+				}
+
+				ltg2[j] = ltg;
+
+				if ((tg,AB)<0) tg = -tg;
+
+				edges[i].tg[j]=tg;
+			}
+			if (ltg2[0]!=0) edges[i].SetTgA();
+			if (ltg2[1]!=0) edges[i].SetTgB();
+		} 
+
+		/* generation of  all curves (from corner to corner)*/
+		/*We proceed in 2 steps: first allocate, second build*/
+		for (int step=0;step<2;step++){
+
+			//unmark all edges
+			for (i=0;iSetMark();
+								nb_marked_edges++;
+								e->CurveNumber=nbcurves;
+								GeomVertex *b=(*e)(k1);
+
+								//break if we have reached the other end of the curve
+								if (a==b || b->Required()){
+									if(curves){
+										curves[nbcurves].LastEdge=e;
+										curves[nbcurves].LastVertexIndex=k1;
+									}
+									break;
+								}
+								//else: go to next edge (adjacent)
+								else{
+									k0 = e->AdjVertexIndex[k1];//  vertex in next edge
+									e  = e->Adj[k1]; // next edge
+								}
+							}
+							nbcurves++;
+							if(level) a->SetRequired();
+						}
+					}
+				} 
+			}
+			_assert_(nb_marked_edges && nbe);
+			//allocate if first step
+			if(step==0) curves=new Curve[nbcurves];
+		} 
+
+		/*clean up*/
+		delete [] next_p;
+		delete [] head_v;
+		delete [] eangle;
+
+	}
+	/*}}}*/
+	/*FUNCTION Geometry::ProjectOnCurve {{{*/
+	GeomEdge* Geometry::ProjectOnCurve(const Edge &e,double s,BamgVertex &V,VertexOnGeom &GV) const {
+		/*Original code from Frederic Hecht  (BAMG v1.01, MeshGeom.cpp/ProjectOnCurve)*/
+		/*Add a vertex on an existing geometrical edge according to the metrics of the two vertices constituting the edge*/
+
+		double save_s=s;
+		int NbTry=0;
+
+retry:
+
+		s=save_s;
+		GeomEdge* on=e.GeomEdgeHook;
+		if (!on){
+			_error_("ProjectOnCurve error message: edge provided should be on geometry");
+		}
+		if (!e[0].GeomEdgeHook ||  !e[1].GeomEdgeHook){
+			_error_("ProjectOnCurve error message: at least one of the vertex of the edge provided is not on geometry");
+		}
+
+		//Get the two vertices of the edge
+		const BamgVertex &v0=e[0];
+		const BamgVertex &v1=e[1];
+
+		//Get position of V0, V1 and vector v0->v1
+		R2 V0=v0,V1=v1,V01=V1-V0;
+
+		//Get geometrical vertices corresponding to v0 and v1
+		VertexOnGeom  vg0=*v0.GeomEdgeHook,  vg1=*v1.GeomEdgeHook;
+
+		//build two pointers towrad current geometrical edge
+		GeomEdge *eg0=on, *eg1=on;
+
+		//Get edge direction and swap v0 and v1 if necessary
+		R2 Ag=(R2)(*on)[0],Bg=(R2)(*on)[1],AB=Bg-Ag; 
+		int OppositeSens = (V01,AB)<0;
+		int direction0=0,direction1=1;
+		if (OppositeSens) s=1-s,Exchange(vg0,vg1),Exchange(V0,V1);
+
+		//Compute metric of new vertex as a linear interpolation of the two others
+		V.m=Metric(1.0-s,v0,s,v1);
+
+		const int mxe=100;
+		GeomEdge* ge[mxe+1];
+		int     directionge[mxe+1];
+		double  lge[mxe+1];
+		int bge=mxe/2,tge=bge;
+		ge[bge] = e.GeomEdgeHook;
+		directionge[bge]=1;
+
+		while (eg0!=(GeomEdge*)vg0 && (*eg0)(direction0)!=(GeomVertex*)vg0){ 
+			if (bge<=0) {
+				if(NbTry) {
+					_printLine_("Fatal Error: on the class Mesh before call Geometry::ProjectOnCurve");
+					_printLine_("That bug might come from:");
+					_printLine_(" 1)  a mesh edge  containing more than " << mxe/2 << " geometrical edges");
+					_printLine_(" 2)  code bug : be sure that we call   Mesh::SetVertexFieldOn() before");
+					_printLine_("To solve the problem do a coarsening of the geometrical mesh or change the constant value of mxe (dangerous)");
+					_error_("see above");
+				}
+				NbTry++;
+				goto retry;
+			}
+			GeomEdge* tmpge = eg0;
+			ge[--bge] =eg0 = eg0->Adj[direction0];
+			_assert_(bge>=0 && bge<=mxe);
+			direction0 = 1-( directionge[bge] = tmpge->AdjVertexIndex[direction0]);
+		}
+		while (eg1 != (GeomEdge*) vg1  &&  (*eg1)(direction1) != (GeomVertex*) vg1) { 
+			if(tge>=mxe ) { 
+				_printLine_("WARNING: on the class Mesh before call Geometry::ProjectOnCurve is having issues (isn't it Eric?)");
+				NbTry++;
+				if (NbTry<2) goto retry;
+				_printLine_("Fatal Error: on the class Mesh before call Geometry::ProjectOnCurve");
+				_printLine_("That bug might come from:");
+				_printLine_(" 1)  a mesh edge  contening more than " << mxe/2 << " geometrical edges");
+				_printLine_(" 2)  code bug : be sure that we call   Mesh::SetVertexFieldOn() before");
+				_printLine_("To solve the problem do a coarsening of the geometrical mesh or change the constant value of mxe (dangerous)");
+				_error_("see above");
+			}
+			GeomEdge* tmpge = eg1;
+			ge[++tge] =eg1 = eg1->Adj[direction1];
+			directionge[tge]= direction1 = 1-tmpge->AdjVertexIndex[direction1];
+			_assert_(tge>=0 && tge<=mxe);
+		}
+
+
+		if ((*eg0)(direction0)==(GeomVertex*)vg0)
+		 vg0=VertexOnGeom(*(BamgVertex*) vg0,*eg0,direction0); //vg0 = absisce
+
+		if ((*eg1)(direction1)==(GeomVertex*)vg1)
+		 vg1=VertexOnGeom(*(BamgVertex*) vg1,*eg1,direction1);
+
+		double sg;
+		if (eg0 == eg1) { 
+			register double s0=vg0,s1=vg1;
+			sg =  s0*(1.0-s) +  s*s1;
+			on=eg0;
+		}
+		else {
+			R2 AA=V0,BB;
+			double s0,s1;
+			int i=bge;
+			double ll=0;
+			for(i=bge;i=0 && i<=mxe);
+				BB =  (*ge[i])[directionge[i]];
+				lge[i]=ll += Norme2(AA-BB);
+				AA=BB ;}
+				lge[tge]=ll+=Norme2(AA-V1); 
+				// search the geometrical edge
+				_assert_(s<=1.0);
+				double ls= s*ll;
+				on =0;
+				s0 = vg0;
+				s1= directionge[bge];
+				double l0=0,l1;
+				i=bge;
+				while (  (l1=lge[i]) < ls ) {
+					_assert_(i>=0 && i<=mxe);
+					i++,s0=1-(s1=directionge[i]),l0=l1;
+				}
+				on=ge[i];
+				if (i==tge) 
+				 s1=vg1;
+
+				s  =(ls-l0)/(l1-l0);
+				sg =s0*(1.0-s)+s*s1;    
+		} 
+		_assert_(on);
+		V.r= on->F(sg);
+		GV=VertexOnGeom(V,*on,sg);
+		return on;
+	}
+	/*}}}*/
+	/*FUNCTION Geometry::R2ToI2{{{*/
+	I2 Geometry::R2ToI2(const R2 & P) const {
+		/*coefIcoor is the coefficient used for integer coordinates:
+		 *                       (x-pmin.x)
+		 * Icoor x = (2^30 -1) ------------ 
+		 *                          D
+		 * where D is the longest side of the domain (direction x or y)
+		 * so that (x-pmin.x)/D is in ]0 1[
+		 *
+		 * coefIcoor = (2^30 -1)/D
+		 */
+		return  I2( (Icoor1) (coefIcoor*(P.x-pmin.x)) ,(Icoor1) (coefIcoor*(P.y-pmin.y)) );
+	}/*}}}*/
+	/*FUNCTION Geometry::UnMarkEdges{{{*/
+	void Geometry::UnMarkEdges() {
+		for (int i=0;i
+#include 
+#include 
+#include 
+
+#include "../objects.h"
+
+namespace bamg {
+
+	/*Constructors Destructors*/
+	/*FUNCTION ListofIntersectionTriangles::ListofIntersectionTriangles{{{*/
+	ListofIntersectionTriangles::ListofIntersectionTriangles(int n,int m)
+	  : MaxSize(n), Size(0), len(-1),state(-1),lIntTria(new IntersectionTriangles[n]) ,
+	  NbSeg(0), MaxNbSeg(m), lSegsI(new SegInterpolation[m]){
+	  }
+	/*}}}*/
+	/*FUNCTION ListofIntersectionTriangles::~ListofIntersectionTriangles{{{*/
+	ListofIntersectionTriangles::~ListofIntersectionTriangles(){
+		if (lIntTria) delete [] lIntTria,lIntTria=0;
+		if (lSegsI) delete [] lSegsI,lSegsI=0;
+	} 
+	/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION ListofIntersectionTriangles::Init{{{*/
+	void ListofIntersectionTriangles::Init(void){
+		state=0;
+		len=0;
+		Size=0;
+	}
+	/*}}}*/
+	/*FUNCTION ListofIntersectionTriangles::Length{{{*/
+	double  ListofIntersectionTriangles::Length(){
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/Length)*/
+
+		// computation of the length
+
+		// check Size
+		if (Size<=0){
+			_error_("Size<=0");
+		}
+
+		Metric Mx,My;
+		int ii,jj;
+		R2 x,y,xy;
+
+		SegInterpolation* SegI=lSegsI;
+		SegI=lSegsI;
+		lSegsI[NbSeg].last=Size;
+		int EndSeg=Size;
+
+		y = lIntTria[0].x;
+		double sxy, s = 0;
+		lIntTria[0].s =0;
+		SegI->lBegin=s;
+
+		for (jj=0,ii=1;iilEnd=s;
+				SegI++;
+				EndSeg=SegI->last;
+				SegI->lBegin=s;
+			}
+		}
+		len = s;
+		SegI->lEnd=s;
+
+		return s;
+	}
+	/*}}}*/
+	/*FUNCTION ListofIntersectionTriangles::NewItem(Triangle * tt,double d0,double d1,double d2) {{{*/
+	int  ListofIntersectionTriangles::NewItem(Triangle * tt,double d0,double d1,double d2) { 
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/NewItem)*/
+
+		register int n;
+		R2 x(0,0);
+		if ( d0) x =      (*tt)[0].r * d0;
+		if ( d1) x = x +  (*tt)[1].r * d1;
+		if ( d2) x = x +  (*tt)[2].r * d2;
+		// newer add same point 
+		if(!Size ||  Norme2_2(lIntTria[Size-1].x-x)) {
+			if (Size==MaxSize) ReShape();
+			lIntTria[Size].t=tt;
+			lIntTria[Size].bary[0]=d0;
+			lIntTria[Size].bary[1]=d1;
+			lIntTria[Size].bary[2]=d2;
+			lIntTria[Size].x = x;
+			Metric m0,m1,m2;
+			register BamgVertex * v;
+			if ((v=(*tt)(0))) m0    = v->m;
+			if ((v=(*tt)(1))) m1    = v->m;
+			if ((v=(*tt)(2))) m2    = v->m;
+			lIntTria[Size].m =  Metric(lIntTria[Size].bary,m0,m1,m2);
+			n=Size++;}
+		else n=Size-1;
+		return n;
+	}
+	/*}}}*/
+	/*FUNCTION ListofIntersectionTriangles::NewItem(R2 A,const Metric & mm){{{*/
+	int ListofIntersectionTriangles::NewItem(R2 A,const Metric & mm) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/NewItem)*/
+
+		register int n;
+		if(!Size ||  Norme2_2(lIntTria[Size-1].x-A)) {
+			if (Size==MaxSize) ReShape();
+			lIntTria[Size].t=0;
+			lIntTria[Size].x=A;
+			lIntTria[Size].m=mm;
+			n=Size++;
+		}
+		else  n=Size-1;
+		return  n; 
+	}
+	/*}}}*/
+	/*FUNCTION ListofIntersectionTriangles::NewPoints{{{*/
+	long ListofIntersectionTriangles::NewPoints(BamgVertex* vertices,long &nbv,long maxnbv){
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/NewPoints)*/
+
+		//If length<1.5, do nothing
+		double s=Length();
+		if (s<1.5) return 0;
+
+		const long nbvold=nbv;
+		int ii = 1 ;
+		R2 y,x;
+		Metric My,Mx ;
+		double sx =0,sy;
+		int nbi=Max(2,(int) (s+0.5));
+		double sint=s/nbi;
+		double si  =sint;
+
+		int EndSeg=Size;
+		SegInterpolation* SegI=NULL;
+		if (NbSeg) SegI=lSegsI,EndSeg=SegI->last;
+
+		for (int k=1;klast;
+				}
+			}
+
+			int ii1=ii-1;
+			x  =lIntTria[ii1].x;
+			sx =lIntTria[ii1].s;
+			Metric Mx=lIntTria[ii1].m;
+			y  =lIntTria[ii].x;
+			sy =lIntTria[ii].s;
+			Metric My=lIntTria[ii].m;
+			double lxy = sy-sx;
+			double cy = abscisseInterpole(Mx,My,y-x,(si-sx)/lxy);
+
+			R2 C;
+			double cx = 1-cy;
+			C = SegI ? SegI->F(si): x * cx + y *cy;
+			//C.Echo();
+			//x.Echo();
+			//y.Echo();
+			//_printLine_("cx = " << cx << ", cy=" << cy);
+
+			si += sint;
+			if ( nbv=MaxNbSeg) {
+			int mneo= MaxNbSeg;
+			MaxNbSeg *= 2;
+			if (verbosity>3){
+				_printLine_("   reshape lSegsI from " << mneo << " to " << MaxNbSeg);
+			}
+			_assert_(lSegsI && NbSeg3) _printLine_("   ListofIntersectionTriangles  ReShape Maxsize " << MaxSize << " -> " << MaxNbSeg);
+		MaxSize = newsize; 
+		delete [] lIntTria;// remove old
+		lIntTria = nw; // copy pointer
+	}
+	/*}}}*/
+	/*FUNCTION ListofIntersectionTriangles::SplitEdge{{{*/
+	void ListofIntersectionTriangles::SplitEdge(const Mesh & Bh, const R2 &A,const R2  &B,int nbegin) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/ListofIntersectionTriangles)*/
+
+		Triangle *tbegin, *t;
+
+		long int verbose=2;
+		Icoor2 deta[3], deti,detj;
+		double ba[3];
+		int nbt =0,ifirst=-1,ilast;
+		int i0,i1,i2;
+		int ocut,i,j,k=-1;
+		//  int OnAVertices =0;
+		Icoor2 dt[3];
+		I2 a = Bh.R2ToI2(A) ,b= Bh.R2ToI2(B);// compute  the Icoor a,b
+		I2 vi,vj;  
+		int iedge =-1;// not a edge
+
+		if(nbegin)  {// optimisation 
+			// we suppose  knowing the starting  triangle
+			t=tbegin=lIntTria[ilast=(Size-1)].t;
+			if (tbegin->det>=0) 
+			 ifirst = ilast;}  
+		else {// not optimisation 
+			Init();
+			t=tbegin = Bh.TriangleFindFromCoord(a,deta);
+			if( t->det>=0)
+			 ilast=NewItem(t,double(deta[0])/t->det,double(deta[1])/t->det,double(deta[2])/t->det);
+			else 
+			  {// find the nearest boundary edge  of the vertex A
+				// find a edge or such normal projection a the edge IJ is on the edge
+				//   <=> IJ.IA >=0 && IJ.AJ >=0
+				ilast=ifirst;
+				double ba,bb;
+				AdjacentTriangle edge=CloseBoundaryEdge(a,t,ba,bb);
+				BamgVertex & v0 = *edge.EdgeVertex(0), & v1 = *edge.EdgeVertex(1);
+				NewItem(A,Metric(ba,v0,bb,v1));
+				t=edge;
+				// test if the point b is in the same side
+				if (det(v0.i,v1.i,b)>=0) {
+					AdjacentTriangle edge=CloseBoundaryEdge(a,t,ba,bb);
+					BamgVertex & v0 = *edge.EdgeVertex(0), & v1 = *edge.EdgeVertex(1);
+					NewItem(A,Metric(ba,v0,bb,v1));
+					return;
+				}
+			  } // find the nearest boundary edge  of the vertex A
+		} // end not optimisation 
+		if (t->det<0) {  // outside departure
+			while (t->det <0) { // intersection boundary edge and a,b,
+				k=(*t)(0) ?  ((  (*t)(1) ? ( (*t)(2) ? -1 : 2) : 1  )) : 0;
+				if (k<0){
+					_error_("k<0");
+				}
+				ocut = OppositeEdge[k];
+				i=VerticesOfTriangularEdge[ocut][0];
+				j=VerticesOfTriangularEdge[ocut][1];
+				vi=(*t)[i];
+				vj=(*t)[j];
+				deti = bamg::det(a,b,vi);
+				detj = bamg::det(a,b,vj);
+				if (deti>0) // go to  i direction on gamma
+				 ocut = PreviousEdge[ocut];      
+				else if (detj<=0) // go to j direction on gamma
+				 ocut = NextEdge[ocut];         
+				AdjacentTriangle tadj =t->Adj(ocut);
+				t = tadj;
+				iedge= tadj; 
+				if (t == tbegin) { // 
+					double ba,bb;
+					long int verbose=2;
+					AdjacentTriangle edge=CloseBoundaryEdge(a,t,ba,bb);
+					BamgVertex & v0 = *edge.EdgeVertex(0), & v1 = *edge.EdgeVertex(1);
+					NewItem(A,Metric(ba,v0,bb,v1));
+					return;
+				}
+			} //  end while (t->det <0)
+			// theoriticaly we have: deti =<0 and detj>0
+
+			// computation of barycentric coor
+			// test if the point b is on size on t
+			// we revert vi,vj because vi,vj is def in Adj triangle
+			if ( det(vi,vj,b)>=0) {
+				t=tbegin;
+				double ba,bb;
+				AdjacentTriangle edge=CloseBoundaryEdge(b,t,ba,bb);
+				NewItem(B,Metric(ba,*edge.EdgeVertex(0),bb,*edge.EdgeVertex(1)));
+				return;
+			}
+			else
+			  {
+				k = OppositeVertex[iedge];
+				i=VerticesOfTriangularEdge[iedge][0];
+				j=VerticesOfTriangularEdge[iedge][1];
+				double dij = detj-deti;
+				if (i+j+k != 0 + 1 +2){
+					_error_("i+j+k != 0 + 1 +2");
+				}
+				ba[j] =  detj/dij;
+				ba[i] = -deti/dij;
+				ba[k] = 0;
+				ilast=NewItem(t,ba[0],ba[1],ba[2]); }
+		}  //  outside departure
+
+
+
+		// recherche the intersection of [a,b] with Bh Mesh.
+		// we know  a triangle ta contening the vertex a
+		// we have 2 case for intersection [a,b] with a edge [A,B] of Bh
+		// 1) the intersection point is in ]A,B[
+		// 2)                        is A or B
+		// first version --- 
+		for (;;) {
+			//    t->Draw();
+			if (iedge < 0) {
+				i0 =0;i1=1;i2=2;
+				dt[0] =bamg::det(a,b,(*t)[0]);
+				dt[1] =bamg::det(a,b,(*t)[1]);
+				dt[2] =bamg::det(a,b,(*t)[2]);}
+			else {
+				i2 = iedge;
+				i0 = NextEdge[i2];
+				i1 = NextEdge[i0]; 
+				dt[VerticesOfTriangularEdge[iedge][0]] = detj;// we revert i,j because
+				dt[VerticesOfTriangularEdge[iedge][1]] = deti;// we take the Triangle by the other side
+				dt[iedge] = det(a,b,(*t)[OppositeVertex[iedge]]);}
+
+				// so we have just to see the transition from - to + of the det0..2 on edge of t
+				// because we are going from a to b
+				if       ((dt[i=VerticesOfTriangularEdge[i0][0]] <  0) &&
+							( dt[j=VerticesOfTriangularEdge[i0][1]] > 0))
+				 ocut =i0;
+				else  if ((dt[i=VerticesOfTriangularEdge[i1][0]] <  0) &&
+							(dt[j=VerticesOfTriangularEdge[i1][1]] >  0))
+				 ocut =i1;
+				else  if ((dt[i=VerticesOfTriangularEdge[i2][0]] <  0) && 
+							(dt[j=VerticesOfTriangularEdge[i2][1]] >  0))
+				 ocut =i2;
+				else if   ((dt[i=VerticesOfTriangularEdge[i0][0]] == 0) &&
+							( dt[j=VerticesOfTriangularEdge[i0][1]] >  0))
+				 ocut =i0;
+				else  if ((dt[i=VerticesOfTriangularEdge[i1][0]] == 0) &&
+							(dt[j=VerticesOfTriangularEdge[i1][1]] >  0))
+				 ocut =i1;
+				else  if ((dt[i=VerticesOfTriangularEdge[i2][0]] == 0) && 
+							(dt[j=VerticesOfTriangularEdge[i2][1]] >  0))
+				 ocut =i2;
+				else if   ((dt[i=VerticesOfTriangularEdge[i0][0]] <  0) &&
+							( dt[j=VerticesOfTriangularEdge[i0][1]] == 0))
+				 ocut =i0;
+				else  if ((dt[i=VerticesOfTriangularEdge[i1][0]] <  0) &&
+							(dt[j=VerticesOfTriangularEdge[i1][1]] == 0))
+				 ocut =i1;
+				else  if ((dt[i=VerticesOfTriangularEdge[i2][0]] <  0) && 
+							(dt[j=VerticesOfTriangularEdge[i2][1]] == 0))
+				 ocut =i2;
+				else { //  On a edge (2 zero)
+					k =0;
+					if (dt[0]) ocut=0,k++; 
+					if (dt[1]) ocut=1,k++; 
+					if (dt[2]) ocut=2,k++;
+					if(k == 1) {
+						if (dt[ocut] >0) // triangle upper AB
+						 ocut = NextEdge[ocut];
+						i= VerticesOfTriangularEdge[ocut][0];
+						j= VerticesOfTriangularEdge[ocut][1];
+					}
+					else {
+						_error_("Bug Split Edge");
+					}
+				}
+
+				k = OppositeVertex[ocut];
+
+				Icoor2 detbij = bamg::det((*t)[i],(*t)[j],b);
+
+
+				if (detbij >= 0) { //we find the triangle contening b
+					dt[0]=bamg::det((*t)[1],(*t)[2],b);
+					dt[1]=bamg::det((*t)[2],(*t)[0],b);
+					dt[2]=bamg::det((*t)[0],(*t)[1],b);
+					double dd = t->det;
+					NewItem(t,dt[0]/dd,dt[1]/dd,dt[2]/dd);      
+					return ;}
+				else { // next triangle by  adjacent by edge ocut 
+					deti = dt[i];
+					detj = dt[j];
+					double dij = detj-deti;
+					ba[i] =  detj/dij;
+					ba[j] = -deti/dij;
+					ba[3-i-j ] = 0;
+					ilast=NewItem(t, ba[0],ba[1],ba[2]);      
+
+					AdjacentTriangle ta =t->Adj(ocut);
+					t = ta;
+					iedge= ta; 
+					if (t->det <= 0)  {
+						double ba,bb;
+						AdjacentTriangle edge=CloseBoundaryEdge(b,t,ba,bb);
+						NewItem(B,Metric(ba,*edge.EdgeVertex(0),bb,*edge.EdgeVertex(1)));
+						return;
+					}
+				}// we  go outside of omega 
+		} // for(;;)
+	}
+	/*}}}*/
+
+}
Index: /issm/trunk/src/c/classes/bamg/ListofIntersectionTriangles.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/ListofIntersectionTriangles.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/ListofIntersectionTriangles.h	(revision 13395)
@@ -0,0 +1,73 @@
+#ifndef _LISTOFINTERSECTIONTRIANGLES_H_
+#define _LISTOFINTERSECTIONTRIANGLES_H_
+
+#include "./include.h"
+
+namespace bamg {
+
+	class Triangle;
+
+	class ListofIntersectionTriangles {
+
+		class IntersectionTriangles {
+
+			public: 
+				Triangle *t;
+				double    bary[3];   // use if t != 0
+				R2        x;
+				Metric    m;
+				double    s;         // curvilinear coordinate
+				double    sp;        // length of the previous segment in m
+				double    sn;        // length of the next segment in m
+		};
+
+		class SegInterpolation {
+
+			public:
+				GeomEdge *e;
+				double           sBegin  ,sEnd; // abscisse of the seg on edge parameter
+				double           lBegin  ,lEnd; // length abscisse set in ListofIntersectionTriangles::Length
+				int              last;          // last index in ListofIntersectionTriangles for this Sub seg of edge
+
+				//Methods
+				R2 F(double s){ 
+					double c01=lEnd-lBegin, c0=(lEnd-s)/c01, c1=(s-lBegin)/c01;
+					if (lBegin>s || s>lEnd){
+						_error_("lBegin>s || s>lEnd");
+					}
+					return e->F(sBegin*c0+sEnd*c1);
+				}
+		};
+
+		public:
+
+			int                    MaxSize;
+			int                    Size;
+			double                 len;
+			int                    state;
+			IntersectionTriangles *lIntTria;
+			int                    NbSeg;
+			int                    MaxNbSeg;
+			SegInterpolation      *lSegsI;
+
+			//Constructors/Destructors
+			ListofIntersectionTriangles(int n=256,int m=16);
+			~ListofIntersectionTriangles();
+
+			//Operators
+			IntersectionTriangles & operator[](int i) {return lIntTria[i];}
+			operator int&() {return Size;}
+
+			//Methods
+			void   Init();
+			int    NewItem(Triangle *tt,double d0,double d1,double d2);
+			int    NewItem(R2 ,const Metric &);
+			void   SplitEdge(const Mesh &,const R2 &,const R2 &,int nbegin=0);
+			double Length();
+			long   NewPoints(BamgVertex *,long &nbv,long maxnbv);
+			void   NewSubSeg(GeomEdge *e,double s0,double s1);
+			void   ReShape();
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/Mesh.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/Mesh.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Mesh.cpp	(revision 13395)
@@ -0,0 +1,5856 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "../objects.h"
+
+namespace bamg {
+
+	static const  Direction NoDirOfSearch=Direction();
+
+	/*Constructors/Destructors*/
+	/*FUNCTION Mesh::Mesh(BamgGeom* bamggeom,BamgMesh* bamgmesh, BamgOpts* bamgopts){{{*/
+	Mesh::Mesh(BamgGeom* bamggeom,BamgMesh* bamgmesh, BamgOpts* bamgopts):Gh(*(new Geometry())),BTh(*this){ 
+
+		/*Initialize fields*/
+		Init(0);
+
+		/*Read Geometry if provided*/
+		if(bamggeom->Edges) {
+			Gh.ReadGeometry(bamggeom,bamgopts);
+			Gh.PostRead();
+		}
+
+		/*Read background mesh*/
+		ReadMesh(bamgmesh,bamgopts);
+
+		/*Build Geometry if not provided*/
+		if(bamggeom->Edges==NULL) {
+			/*Recreate geometry if needed*/
+			_printLine_("WARNING: mesh present but no geometry found. Reconstructing...");
+			BuildGeometryFromMesh(bamgopts);
+			Gh.PostRead();
+		}
+
+		/*Set integer coordinates*/
+		SetIntCoor();
+
+		/*Fill holes and generate mesh properties*/
+		ReconstructExistingMesh();
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::Mesh(int* index,double* x,double* y,int nods,int nels){{{*/
+	Mesh::Mesh(int* index,double* x,double* y,int nods,int nels):Gh(*(new Geometry())),BTh(*this){
+
+		Init(0);
+		ReadMesh(index,x,y,nods,nels);
+		SetIntCoor();
+		ReconstructExistingMesh();
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::Mesh(double* x,double* y,int nods){{{*/
+	Mesh::Mesh(double* x,double* y,int nods):Gh(*(new Geometry())),BTh(*this){
+		Triangulate(x,y,nods);
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::Mesh(const Mesh & Tho,const int *flag ,const int *bb){{{*/
+	Mesh::Mesh(const Mesh & Tho,const int *flag ,const int *bb,BamgOpts* bamgopts) : Gh(*(new Geometry())), BTh(*this) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/Triangles)*/
+
+		  int i,k,itadj;
+		  int kt=0;
+		  int * kk    = new int [Tho.nbv];
+		  long * reft = new long[Tho.nbt];
+		  long nbInT =    Tho.TriangleReferenceList(reft);
+		  long * refv = new long[Tho.nbv];
+
+		  for (i=0;i=0 && flag[i]) 
+			  {
+				const Triangle & t = Tho.triangles[i];
+				kt++;
+				kk[Tho.GetId(t[0])]=1;
+				kk[Tho.GetId(t[1])]=1;
+				kk[Tho.GetId(t[2])]=1;
+				itadj=Tho.GetId(t.TriangleAdj(0));
+				if (  reft[itadj] >=0 && !flag[itadj])
+				  { nbNewBedge++;
+					refv[Tho.GetId(t[VerticesOfTriangularEdge[0][0]])]=bb[i];
+					refv[Tho.GetId(t[VerticesOfTriangularEdge[0][1]])]=bb[i];
+				  }
+				itadj=Tho.GetId(t.TriangleAdj(1));
+				if (  reft[itadj] >=0 && !flag[itadj])
+				  { nbNewBedge++;
+					refv[Tho.GetId(t[VerticesOfTriangularEdge[1][0]])]=bb[i];
+					refv[Tho.GetId(t[VerticesOfTriangularEdge[1][1]])]=bb[i];}
+					itadj=Tho.GetId(t.TriangleAdj(2));
+					if (  reft[itadj] >=0 && !flag[itadj])
+					  { nbNewBedge++;
+						refv[Tho.GetId(t[VerticesOfTriangularEdge[2][0]])]=bb[i];
+						refv[Tho.GetId(t[VerticesOfTriangularEdge[2][1]])]=bb[i];}
+			  }
+		  k=0;
+		  for (i=0;i=0) kk[i]=k++;
+			}
+		  _printLine_("   number of vertices " << k << ", remove = " << Tho.nbv - k);
+		  _printLine_("   number of triangles " << kt << ", remove = " << nbInT-kt);
+		  _printLine_("   number of New boundary edge " << nbNewBedge);
+		  long imaxnbv =k;
+		  Init(imaxnbv);
+		  for (i=0;i=0) 
+			  {
+				vertices[nbv] = Tho.vertices[i];
+				if (!vertices[nbv].GetReferenceNumber())
+				 vertices[nbv].ReferenceNumber = refv[i];
+				nbv++;
+			  }
+		  if (imaxnbv != nbv){
+			  delete [] kk;
+			  delete [] refv;
+			  _error_("imaxnbv != nbv");
+		  }
+		  for (i=0;i=0 && flag[i]) 
+			  {
+				const Triangle & t = Tho.triangles[i];
+				int i0 = Tho.GetId(t[0]);
+				int i1 = Tho.GetId(t[1]);
+				int i2 = Tho.GetId(t[2]);
+				if (i0<0 || i1<0 || i2<0){
+					delete [] refv;
+					_error_("i0<0 || i1<0 || i2< 0");
+				}
+				if (i0>=Tho.nbv || i1>=Tho.nbv || i2>=Tho.nbv){
+					_error_("i0>=Tho.nbv || i1>=Tho.nbv || i2>=Tho.nbv");
+				}
+				triangles[nbt] = Triangle(this,kk[i0],kk[i1],kk[i2]);
+				triangles[nbt].color = Tho.subdomains[reft[i]].ReferenceNumber; 
+				nbt++;           
+			  }
+		  if (kt!=nbt){
+			  _error_("kt!=nbt");
+		  }
+		  if (nbt==0 && nbv==0) {
+			  _error_("All triangles have been removed");
+		  }
+		  delete [] kk;
+		  delete [] reft;
+		  delete [] refv;
+		  //double cutoffradian = 10.0/180.0*Pi;
+		  BuildGeometryFromMesh(bamgopts);
+		  Gh.PostRead(); 
+		  SetIntCoor();
+		  ReconstructExistingMesh();
+
+		  if (!nbsubdomains){
+			  _error_("nbsubdomains==0");
+		  }
+		  if (!subdomains[0].head || !subdomains[0].head->link){
+			  _error_("!subdomains[0].head || !subdomains[0].head->link");
+		  }
+
+	  }
+	/*}}}*/
+	/*FUNCTION Mesh::Mesh(Mesh & Th,Geometry * pGh,Mesh * pBth,long maxnbv_in) COPY{{{*/
+	Mesh::Mesh(Mesh & Th,Geometry * pGh,Mesh * pBth,long maxnbv_in)
+	  : Gh(*(pGh?pGh:&Th.Gh)), BTh(*(pBth?pBth:this)) {
+		  /*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/Triangles)*/
+		  Gh.NbRef++;
+		  maxnbv_in = Max(maxnbv_in,Th.nbv); 
+		  long i;
+		  // do all the allocation to be sure all the pointer existe
+
+		  Init(maxnbv_in);// to make the allocation 
+		  // copy of triangles
+		  nbv = Th.nbv;
+		  nbt = Th.nbt;
+		  nbe = Th.nbe;
+		  nbsubdomains = Th.nbsubdomains;
+		  nbtout = Th.nbtout;
+		  nbq =  Th.nbq ;
+		  NbVerticesOnGeomVertex = Th.NbVerticesOnGeomVertex;
+		  if(NbVerticesOnGeomVertex)
+			VerticesOnGeomVertex = new VertexOnGeom[NbVerticesOnGeomVertex];
+		  NbVerticesOnGeomEdge = Th.NbVerticesOnGeomEdge;
+		  if (NbVerticesOnGeomEdge)
+			VerticesOnGeomEdge = new VertexOnGeom[NbVerticesOnGeomEdge] ;
+		  if (& BTh == & Th.BTh){ // same background 
+			  BTh.NbRef++;
+			  NbVertexOnBThVertex = Th.NbVertexOnBThVertex;
+			  if(NbVertexOnBThVertex)
+				VertexOnBThVertex = new VertexOnVertex[NbVertexOnBThVertex];
+			  NbVertexOnBThEdge = Th.NbVertexOnBThEdge;
+			  if(NbVertexOnBThEdge)
+				VertexOnBThEdge = new VertexOnEdge[NbVertexOnBThEdge];
+			 }
+		  else { // no add on background mesh 
+			  BTh.NbRef++;
+			  NbVertexOnBThVertex=0;
+			  VertexOnBThVertex=0;
+			  NbVertexOnBThEdge=0;
+			  VertexOnBThEdge=0;
+			 }
+
+
+		  if(nbe)
+			edges = new Edge[nbe];
+		  if(nbsubdomains)
+			subdomains = new SubDomain[nbsubdomains];
+		  pmin = Th.pmin;
+		  pmax = Th.pmax;
+		  coefIcoor = Th.coefIcoor;
+		  for(i=0;iInit(imaxnbv);
+		TriangulateFromGeom1(bamgopts,keepBackVertices);
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::Mesh(long maxnbv,Geometry & G,BamgOpts* bamgopts){{{*/
+	Mesh::Mesh(long imaxnbv,Geometry & G,BamgOpts* bamgopts):Gh(G),BTh(*this){
+		Init(imaxnbv);
+		TriangulateFromGeom0(bamgopts);
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::~Mesh(){{{*/
+	Mesh::~Mesh() {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/Triangles)*/
+
+		//if (vertices)             delete [] vertices;
+		if (edges)                delete [] edges;
+		if (triangles)            delete [] triangles;
+		if (quadtree)             delete    quadtree;
+		//if (orderedvertices)                delete [] orderedvertices;
+		if (subdomains)           delete []  subdomains;
+		if (VerticesOnGeomEdge)   delete [] VerticesOnGeomEdge;
+		if (VerticesOnGeomVertex) delete [] VerticesOnGeomVertex;
+		if (VertexOnBThVertex)    delete [] VertexOnBThVertex;
+		if (VertexOnBThEdge)      delete [] VertexOnBThEdge;
+
+		if (&Gh) {
+			if (Gh.NbRef>0) Gh.NbRef--;
+			else if (Gh.NbRef==0) delete &Gh;
+		}
+		if (&BTh && (&BTh != this)) {
+			if (BTh.NbRef>0) BTh.NbRef--;
+			else if (BTh.NbRef==0) delete &BTh;
+		}
+		Init(0); // set all to zero 
+	}
+	/*}}}*/
+
+	/*IO*/
+	/*FUNCTION Mesh::ReadMesh(int* index,double* x,double* y,int nods,int nels){{{*/
+	void Mesh::ReadMesh(int* index,double* x,double* y,int nods,int nels){
+
+		double Hmin = HUGE_VAL;// the infinie value 
+		long i1,i2,i3;
+		long i,j;
+		Metric M1(1);
+		int verbose=0;
+		bool* nodeflags=NULL;
+
+		nbv=nods;
+		maxnbv=nbv;
+		nbt=nels;
+
+		//Vertices
+		if (verbose) _printLine_("Reading vertices (" << nbv << ")");
+		vertices=xNew(nbv);
+		orderedvertices=xNew(nbv);
+		for (i=0;i(nbv);
+		for(i=0;i(nodeflags);
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::ReadMesh(BamgMesh* bamgmesh, BamgOpts* bamgopts){{{*/
+	void Mesh::ReadMesh(BamgMesh* bamgmesh, BamgOpts* bamgopts){
+
+		int    verbose;
+		double Hmin = HUGE_VAL;    // the infinie value
+		long   i1,i2,i3;
+		long   i,j;
+		Metric M1(1);
+
+		verbose=bamgopts->verbose;
+
+		nbv=bamgmesh->VerticesSize[0];
+		maxnbv=nbv;
+		nbt=bamgmesh->TrianglesSize[0];
+
+		//Vertices
+		if(bamgmesh->Vertices){
+			if(verbose>5) _printLine_("      processing Vertices");
+
+			vertices=xNew(nbv);
+			orderedvertices=xNew(nbv);
+
+			for (i=0;iVertices[i*3+0];
+				vertices[i].r.y=bamgmesh->Vertices[i*3+1];
+				vertices[i].ReferenceNumber=(long)bamgmesh->Vertices[i*3+2];
+				vertices[i].DirOfSearch =NoDirOfSearch;
+				vertices[i].m=M1;
+				vertices[i].color=0;
+			}
+			maxnbt=2*maxnbv-2; // for filling The Holes and quadrilaterals 
+		}
+		else{
+			if(verbose>5) _error_("no Vertices found in the initial mesh");
+		}
+
+		//Triangles
+		if(bamgmesh->Triangles){
+			if(verbose>5) _printLine_("      processing Triangles");
+			triangles =new Triangle[maxnbt]; //we cannot allocate only nbt triangles since 
+			//other triangles will be added for each edge
+			for (i=0;iTriangles[i*4+0]-1; //for C indexing
+				i2=(long)bamgmesh->Triangles[i*4+1]-1; //for C indexing
+				i3=(long)bamgmesh->Triangles[i*4+2]-1; //for C indexing
+				t=Triangle(this,i1,i2,i3);
+				t.color=(long)bamgmesh->Triangles[i*4+3];
+			}
+		}
+		else{
+			if(verbose>5) _error_("no Triangles found in the initial mesh");
+		}
+
+		//Quadrilaterals
+		if(bamgmesh->Quadrilaterals){
+			if(verbose>5) _printLine_("      processing Quadrilaterals");
+			long i1,i2,i3,i4,iref;
+			triangles =new Triangle[nbt];
+			for (i=0;iQuadrilateralsSize[0];i++){
+				//divide the quad into two triangles
+				Triangle & t1 = triangles[2*i];
+				Triangle & t2 = triangles[2*i+1];
+				i1=(long)bamgmesh->Quadrilaterals[i*5+0]-1; //for C indexing
+				i2=(long)bamgmesh->Quadrilaterals[i*5+1]-1; //for C indexing
+				i3=(long)bamgmesh->Quadrilaterals[i*5+2]-1; //for C indexing
+				i4=(long)bamgmesh->Quadrilaterals[i*5+3]-1; //for C indexing
+				t1=Triangle(this,i1,i2,i3);
+				t2=Triangle(this,i3,i4,i1);
+				t1.color=(long)bamgmesh->Quadrilaterals[i*5+4];
+				t2.color=(long)bamgmesh->Quadrilaterals[i*5+4];
+				t1.SetHidden(OppositeEdge[1]); // two times  because the adj was not created 
+				t2.SetHidden(OppositeEdge[1]); 
+			}
+		}
+
+		//VerticesOnGeomEdge
+		if(bamgmesh->VerticesOnGeomEdge){
+			if(verbose>5) _printLine_("      processing VerticesOnGeomEdge");
+			NbVerticesOnGeomEdge=bamgmesh->VerticesOnGeomEdgeSize[0];
+			VerticesOnGeomEdge= new  VertexOnGeom[NbVerticesOnGeomEdge] ;
+			for (i=0;iVerticesOnGeomEdge[i*3+0]-1; //for C indexing
+				i2=(long)  bamgmesh->VerticesOnGeomEdge[i*3+1]-1; //for C indexing
+				s =(double)bamgmesh->VerticesOnGeomEdge[i*3+2];
+				VerticesOnGeomEdge[i]=VertexOnGeom(vertices[i1],Gh.edges[i2],s);
+			}
+		}
+
+		//VerticesOnGeomVertex
+		if(bamgmesh->VerticesOnGeomVertexSize[0]){
+			if(verbose>5) _printLine_("      processing VerticesOnGeomVertex");
+			NbVerticesOnGeomVertex=bamgmesh->VerticesOnGeomVertexSize[0];
+			VerticesOnGeomVertex  = new  VertexOnGeom[NbVerticesOnGeomVertex] ;
+			for (i=0;iVerticesOnGeomVertex[i*2+0]-1; //for C indexing
+				i2=(long)bamgmesh->VerticesOnGeomVertex[i*2+1]-1; //for C indexing
+				VerticesOnGeomVertex[i]=VertexOnGeom(vertices[i1],Gh.vertices[i2]);
+			}
+		}
+
+		//Edges
+		if (bamgmesh->Edges){
+			int i1,i2;
+			double* len=NULL;
+
+			if(verbose>5) _printLine_("      processing Edges");
+			nbe=bamgmesh->EdgesSize[0];
+			edges= new Edge[nbe];
+			//initialize length of each edge (used to provided metric)
+			len= new double[nbv];
+			for(i=0;iEdges[i*3+0]-1; //-1 for C indexing
+				i2=(int)bamgmesh->Edges[i*3+1]-1; //-1 for C indexing
+				edges[i].ReferenceNumber=(long)bamgmesh->Edges[i*3+2];
+				edges[i].v[0]= vertices +i1;
+				edges[i].v[1]= vertices +i2;
+				edges[i].adj[0]=NULL;
+				edges[i].adj[1]=NULL;
+				R2 x12=vertices[i2].r-vertices[i1].r;
+				double l12=sqrt((x12,x12));
+
+				//prepare metric
+				vertices[i1].color++;
+				vertices[i2].color++;
+				len[i1]+=l12;
+				len[i2]+=l12;
+				Hmin = Min(Hmin,l12);
+			}
+
+			// definition  the default of the given mesh size 
+			for (i=0;i0) 
+				 vertices[i].m=Metric(len[i]/(double)vertices[i].color);
+				else 
+				 vertices[i].m=Metric(Hmin);
+			}
+			delete [] len;
+
+			// construction of edges[].adj 
+			for (i=0;icolor,j0;
+					if(i0==-1){
+						v->color=i*2+j;
+					}
+					else if (i0>=0) {// i and i0 edge are adjacent by the vertex v
+						j0 = i0%2;
+						i0 = i0/2;
+						_assert_(v==edges[i0 ].v[j0]);
+						edges[i ].adj[j ] =edges +i0;
+						edges[i0].adj[j0] =edges +i ;
+						v->color = -3;
+					}
+				}
+			}
+		}
+
+		//EdgeOnGeomEdge
+		if(bamgmesh->EdgesOnGeomEdge){
+			if(verbose>5) _printLine_("      processing EdgesOnGeomEdge");
+			int i1,i2,i,j;
+			i2=bamgmesh->EdgesOnGeomEdgeSize[0];
+			for (i1=0;i1EdgesOnGeomEdge[i1*2+0]-1; //C indexing
+				j=(int)bamgmesh->EdgesOnGeomEdge[i1*2+1]-1; //C indexing
+				//Check value
+				if(!(i>=0 && j>=0 && iSubDomains){
+			long i3,head,direction;
+			if(verbose>5) _printLine_("      processing SubDomains");
+			nbsubdomains=bamgmesh->SubDomainsSize[0];
+			subdomains = new SubDomain [ nbsubdomains ];
+			for (i=0;iSubDomains[i*3+0];
+				head=(int)bamgmesh->SubDomains[i*3+1]-1;//C indexing
+				direction=(int)bamgmesh->SubDomains[i*3+2];
+				if (i3!=23) _error_("Bad Subdomain definition: first number should be 3");
+				if (head<0 || head>=nbt) _error_("Bad Subdomain definition: head should in [1 " << nbt << "] (triangle number)");
+				subdomains[i].head = triangles+head;
+			}
+		}
+
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::WriteMesh {{{*/
+	void Mesh::WriteMesh(BamgMesh* bamgmesh,BamgOpts* bamgopts){
+
+		/*Intermediary*/
+		int i,j,k,num,i1,i2;
+		long n;
+		int* head_1=NULL;
+		int* next_1=NULL;
+		int* connectivitysize_1=NULL;
+		int  connectivitymax_1=0;
+
+		/*Get options*/
+		int verbose=bamgopts->verbose;
+
+		/*Build reft that holds the number the subdomain number of each triangle, and the real numbering of the elements*/
+		long* reft = new long[nbt];
+		long* numt = new long[nbt];
+		long nbInT = TriangleReferenceList(reft);
+		TriangleIntNumbering(numt);
+
+		/*Chaining algorithm used to generate connectivity tables and other outputs*/
+
+		//Memory Allocation
+		head_1=xNew(nbv);
+		next_1=xNew(3*nbt);
+		connectivitysize_1=xNew(nbv);
+
+		//Initialization
+		for (i=0;i=0){
+				for (j=0;j<3;j++){
+					int v=GetId(triangles[i][j]); //jth vertex of the ith triangle
+					if (k>3*nbt-1 || k<0) _error_("k = " << k << ", nbt = " << nbt);
+					next_1[k]=head_1[v];
+					if (v>nbv-1 || v<0)   _error_("v = " << v << ", nbv = " << nbv);
+					head_1[v]=k++;
+					connectivitysize_1[v]+=1;
+				}
+			}
+		}
+		//Get maximum connectivity
+		connectivitymax_1=0;
+		for (i=0;iconnectivitymax_1) connectivitymax_1=connectivitysize_1[i];
+		}
+
+		/*OK, now build outputs*/
+
+		/*Vertices*/
+		if(verbose>5) _printLine_("      writing Vertices");
+		bamgmesh->VerticesSize[0]=nbv;
+		bamgmesh->VerticesSize[1]=3;
+		if (nbv){
+			bamgmesh->Vertices=xNew(3*nbv);
+			for (i=0;iVertices[i*3+0]=vertices[i].r.x;
+				bamgmesh->Vertices[i*3+1]=vertices[i].r.y;
+				bamgmesh->Vertices[i*3+2]=vertices[i].GetReferenceNumber();
+			}
+		}
+
+		/*Edges*/
+		if(verbose>5) _printLine_("      writing Edges");
+		bamgmesh->EdgesSize[0]=nbe;
+		bamgmesh->EdgesSize[1]=3;
+		int NumIssmSegments=0;
+		if (nbe){
+			bamgmesh->Edges=xNew(3*nbe);
+			for (i=0;iEdges[i*3+0]=GetId(edges[i][0])+1; //back to M indexing
+				bamgmesh->Edges[i*3+1]=GetId(edges[i][1])+1; //back to M indexing
+				bamgmesh->Edges[i*3+2]=edges[i].ReferenceNumber;
+				if(edges[i].GeomEdgeHook){
+					NumIssmSegments++;
+				}
+			}
+		}
+
+		/*Element edges*/
+		if(verbose>5) _printLine_("      writing element edges");
+		SetOfEdges4* edge4=new SetOfEdges4(nbt*3,nbv);
+		double* elemedge=NULL;
+		elemedge=xNew(3*nbt);
+		for (i=0;i<3*nbt;i++) elemedge[i]=-2.;//will become -1
+		k=0;
+		for (i=0;i=0){
+				for  (j=0;j<3;j++) {
+					i1=GetId(triangles[i][VerticesOfTriangularEdge[j][0]]);
+					i2=GetId(triangles[i][VerticesOfTriangularEdge[j][1]]);
+					n =edge4->SortAndFind(i1,i2);
+					if (n==-1){
+						//first time
+						n=edge4->SortAndAdd(i1,i2);
+						elemedge[n*2+0]=double(k);
+					}
+					else{
+						//second time
+						elemedge[n*2+1]=double(k);
+					}
+				}
+				k++;
+			}
+		}
+		bamgmesh->IssmEdgesSize[0]=edge4->nb();
+		bamgmesh->IssmEdgesSize[1]=4;
+		bamgmesh->IssmEdges=xNew(4*edge4->nb());
+		for (i=0;inb();i++){
+			/*Invert first two vertices if necessary*/
+			bool found=false;
+			for (j=0;j<3;j++){
+				if (triangles[(int)elemedge[2*i+0]](j)==vertices+edge4->i(i)){
+					if (triangles[(int)elemedge[2*i+0]]((j+1)%3)==vertices+edge4->j(i)){
+						//trigonometric direction
+						bamgmesh->IssmEdges[i*4+0]=edge4->i(i)+1;// back to M indexing
+						bamgmesh->IssmEdges[i*4+1]=edge4->j(i)+1;// back to M indexing
+					}
+					else{
+						bamgmesh->IssmEdges[i*4+0]=edge4->j(i)+1;// back to M indexing
+						bamgmesh->IssmEdges[i*4+1]=edge4->i(i)+1;// back to M indexing
+					}
+					found=true;
+					break;
+				}
+			}
+			_assert_(found);
+			bamgmesh->IssmEdges[i*4+2]=elemedge[2*i+0]+1; // back to M indexing
+			bamgmesh->IssmEdges[i*4+3]=elemedge[2*i+1]+1; // back to M indexing
+		}
+		//clean up
+		delete edge4;
+		xDelete(elemedge);
+
+		/*IssmSegments*/
+		if(verbose>5) _printLine_("      writing IssmSegments");
+		bamgmesh->IssmSegmentsSize[0]=NumIssmSegments;
+		bamgmesh->IssmSegmentsSize[1]=4;
+		bamgmesh->IssmSegments=xNew(4*NumIssmSegments);
+		num=0;
+		for (i=0;iIssmSegments[num*4+0]=GetId(edges[i][0])+1; //back to M indexing
+								bamgmesh->IssmSegments[num*4+1]=GetId(edges[i][1])+1; //back to M indexing
+								bamgmesh->IssmSegments[num*4+2]=(int)j/3+1;            //back to M indexing
+								bamgmesh->IssmSegments[num*4+3]=edges[i].ReferenceNumber;
+								num+=1;
+								stop=true;
+								break;
+							}
+							if (GetId(triangles[(int)j/3][(int)((k+2)%3)])==i2){
+								bamgmesh->IssmSegments[num*4+0]=GetId(edges[i][1])+1; //back to M indexing
+								bamgmesh->IssmSegments[num*4+1]=GetId(edges[i][0])+1; //back to M indexing
+								bamgmesh->IssmSegments[num*4+2]=(int)j/3+1;            //back to M indexing
+								bamgmesh->IssmSegments[num*4+3]=edges[i].ReferenceNumber;
+								num+=1;
+								stop=true;
+								break;
+							}
+						}
+					}
+					if(stop) break;
+				}
+				if (!stop){
+					_error_("Element holding segment [" << i1+1 << " " << i2+1 << "] not found...");
+				}
+			}
+		}
+
+		/*Triangles*/
+		if(verbose>5) _printLine_("      writing Triangles");
+		k=nbInT-nbq*2;
+		num=0;
+		bamgmesh->TrianglesSize[0]=k;
+		bamgmesh->TrianglesSize[1]=4;
+		if (k){
+			bamgmesh->Triangles=xNew(4*k);
+			for (i=0;i=0 && !( t.Hidden(0) || t.Hidden(1) || t.Hidden(2) )){
+					bamgmesh->Triangles[num*4+0]=GetId(t[0])+1; //back to M indexing
+					bamgmesh->Triangles[num*4+1]=GetId(t[1])+1; //back to M indexing
+					bamgmesh->Triangles[num*4+2]=GetId(t[2])+1; //back to M indexing
+					bamgmesh->Triangles[num*4+3]=subdomains[reft[i]].ReferenceNumber;
+					num=num+1;
+				}
+			}
+		}
+
+		/*Quadrilaterals*/
+		if(verbose>5) _printLine_("      writing Quadrilaterals");
+		bamgmesh->QuadrilateralsSize[0]=nbq;
+		bamgmesh->QuadrilateralsSize[1]=5;
+		if (nbq){
+			bamgmesh->Quadrilaterals=xNew(5*nbq);
+			for (i=0;iQuadrilaterals[i*5+0]=GetId(v0)+1; //back to M indexing
+					bamgmesh->Quadrilaterals[i*5+1]=GetId(v1)+1; //back to M indexing
+					bamgmesh->Quadrilaterals[i*5+2]=GetId(v2)+1; //back to M indexing
+					bamgmesh->Quadrilaterals[i*5+3]=GetId(v3)+1; //back to M indexing
+					bamgmesh->Quadrilaterals[i*5+4]=subdomains[reft[i]].ReferenceNumber;
+				}
+			}
+		}
+
+		/*SubDomains*/
+		if(verbose>5) _printLine_("      writing SubDomains");
+		bamgmesh->SubDomainsSize[0]=nbsubdomains;
+		bamgmesh->SubDomainsSize[1]=4;
+		if (nbsubdomains){
+			bamgmesh->SubDomains=xNew(4*nbsubdomains);
+			for (i=0;iSubDomains[i*4+0]=3;
+				bamgmesh->SubDomains[i*4+1]=reft[GetId(subdomains[i].head)];
+				bamgmesh->SubDomains[i*4+2]=1;
+				bamgmesh->SubDomains[i*4+3]=subdomains[i].ReferenceNumber;
+			}
+		}
+
+		/*SubDomainsFromGeom*/
+		if(verbose>5) _printLine_("      writing SubDomainsFromGeom");
+		bamgmesh->SubDomainsFromGeomSize[0]=Gh.nbsubdomains;
+		bamgmesh->SubDomainsFromGeomSize[1]=4;
+		if (Gh.nbsubdomains){
+			bamgmesh->SubDomainsFromGeom=xNew(4*Gh.nbsubdomains);
+			for (i=0;iSubDomainsFromGeom[i*4+0]=2;
+				bamgmesh->SubDomainsFromGeom[i*4+1]=GetId(subdomains[i].edge)+1; //back to Matlab indexing
+				bamgmesh->SubDomainsFromGeom[i*4+2]=subdomains[i].direction;
+				bamgmesh->SubDomainsFromGeom[i*4+3]=Gh.subdomains[i].ReferenceNumber;
+			}
+		}
+
+		/*VerticesOnGeomVertex*/
+		if(verbose>5) _printLine_("      writing VerticesOnGeomVertex");
+		bamgmesh->VerticesOnGeomVertexSize[0]=NbVerticesOnGeomVertex;
+		bamgmesh->VerticesOnGeomVertexSize[1]=2;
+		if (NbVerticesOnGeomVertex){
+			bamgmesh->VerticesOnGeomVertex=xNew(2*NbVerticesOnGeomVertex);
+			for (i=0;iVerticesOnGeomVertex[i*2+0]=GetId((BamgVertex*)v)+1; //back to Matlab indexing
+				bamgmesh->VerticesOnGeomVertex[i*2+1]=Gh.GetId((GeomVertex*)v)+1; //back to Matlab indexing
+			}
+		}
+
+		/*VertexOnGeomEdge*/
+		if(verbose>5) _printLine_("      writing VerticesOnGeomEdge");
+		bamgmesh->VerticesOnGeomEdgeSize[0]=NbVerticesOnGeomEdge;
+		bamgmesh->VerticesOnGeomEdgeSize[1]=3;
+		if (NbVerticesOnGeomEdge){
+			bamgmesh->VerticesOnGeomEdge=xNew(3*NbVerticesOnGeomEdge);
+			for (i=0;iVerticesOnGeomEdge[i*3+0]=GetId((BamgVertex*)v)+1; //back to Matlab indexing
+				bamgmesh->VerticesOnGeomEdge[i*3+1]=Gh.GetId((const GeomEdge*)v)+1; //back to Matlab indexing
+				bamgmesh->VerticesOnGeomEdge[i*3+2]=(double)v; //absisce
+			}
+		}
+
+		/*EdgesOnGeomEdge*/
+		if(verbose>5) _printLine_("      writing EdgesOnGeomEdge");
+		k=0;
+		for (i=0;iEdgesOnGeomEdgeSize[0]=k;
+		bamgmesh->EdgesOnGeomEdgeSize[1]=2;
+		if (k){
+			bamgmesh->EdgesOnGeomEdge=xNew(2*(int)k);
+			int count=0;
+			for (i=0;iEdgesOnGeomEdge[count*2+0]=(double)i+1; //back to Matlab indexing
+					bamgmesh->EdgesOnGeomEdge[count*2+1]=(double)Gh.GetId(edges[i].GeomEdgeHook)+1; //back to Matlab indexing
+					count=count+1;
+				}
+			}
+		}
+
+		/*Element Connectivity*/
+		if(verbose>5) _printLine_("      writing Element connectivity");
+		bamgmesh->ElementConnectivitySize[0]=nbt-nbtout;
+		bamgmesh->ElementConnectivitySize[1]=3;
+		bamgmesh->ElementConnectivity=xNew(3*(nbt-nbtout));
+		for (i=0;i<3*(nbt-nbtout);i++) bamgmesh->ElementConnectivity[i]=NAN;
+		num=0;
+		for (i=0;i=0){
+				for (j=0;j<3;j++){
+					k=GetId(triangles[i].TriangleAdj(j));
+					if (reft[k]>=0){
+						_assert_(3*num+j<3*(nbt-nbtout));
+						bamgmesh->ElementConnectivity[3*num+j]=k+1; // back to Matlab indexing
+					}
+				}
+				num+=1;
+			}
+		}
+
+		/*ElementNodal Connectivity*/
+		if(verbose>5) _printLine_("      writing Nodal element connectivity");
+		bamgmesh->NodalElementConnectivitySize[0]=nbv;
+		bamgmesh->NodalElementConnectivitySize[1]=connectivitymax_1;
+		bamgmesh->NodalElementConnectivity=xNew(connectivitymax_1*nbv);
+		for (i=0;iNodalElementConnectivity[i]=NAN;
+		for (i=0;iNodalElementConnectivity[connectivitymax_1*i+k]=floor((double)j/3)+1;
+				k++;
+			}
+		}
+
+		/*Nodal Connectivity*/
+		if(verbose>5) _printLine_("      writing Nodal connectivity");
+		//chaining algorithm (again...)
+		int* head_2=NULL;
+		int* next_2=NULL;
+		int* connectivitysize_2=NULL;
+		int  connectivitymax_2=0;
+		i1=bamgmesh->IssmEdgesSize[0];
+		i2=bamgmesh->IssmEdgesSize[1];
+		head_2=xNew(nbv);
+		next_2=xNew(2*i1);
+		connectivitysize_2=xNew(nbv);
+		//Initialization
+		for (i=0;iIssmEdges[i*i2+j]-1; //back to C indexing
+				if (k>2*i1-1 || k<0) _error_("Index exceed matrix dimensions (k=" << k << " not in [0 " << 2*i1-1 << "]");
+				next_2[k]=head_2[v];
+				if (v>nbv-1 || v<0)   _error_("Index exceed matrix dimensions (v=" << v << " not in [0 " << nbv-1 << "])");
+				head_2[v]=k++;
+				connectivitysize_2[v]+=1;
+			}
+		}
+		//Get maximum connectivity
+		for (i=0;iconnectivitymax_2) connectivitymax_2=connectivitysize_2[i];
+		}
+		//Build output
+		bamgmesh->NodalConnectivitySize[0]=nbv;
+		bamgmesh->NodalConnectivitySize[1]=connectivitymax_2;
+		bamgmesh->NodalConnectivity=xNew(connectivitymax_2*nbv);
+		for (i=0;iNodalConnectivity[i]=NAN;
+		for (i=0;iIssmEdges[int(j/2)*i2+0];
+				if (i+1==num){ //carefull, ElementEdge is in M indexing
+					//i is the first vertex of the edge, it is therefore connected to the second vertex
+					bamgmesh->NodalConnectivity[connectivitymax_2*i+k]=bamgmesh->IssmEdges[int(j/2)*i2+1];
+				}
+				else{
+					bamgmesh->NodalConnectivity[connectivitymax_2*i+k]=num;
+				}
+				k++;
+			}
+		}
+
+		/*Cracked vertices*/
+		if(verbose>5) _printLine_("      writing Cracked vertices");
+		bamgmesh->CrackedVerticesSize[0]=NbCrackedVertices;
+		bamgmesh->CrackedVerticesSize[1]=2;
+		if (NbCrackedVertices){
+			bamgmesh->CrackedVertices=xNew(2*NbCrackedVertices);
+			for (i=0;iCrackedVertices[i*2+0]=CrackedVertices[i*2+0]+1; //M indexing
+				bamgmesh->CrackedVertices[i*2+1]=CrackedVertices[i*2+1]+1; //M indexing
+			}
+		}
+
+		/*Cracked vertices*/
+		if(verbose>5) _printLine_("      writing Cracked vertices");
+		bamgmesh->CrackedEdgesSize[0]=NbCrackedEdges;
+		bamgmesh->CrackedEdgesSize[1]=4;
+		if (NbCrackedEdges){
+			bamgmesh->CrackedEdges=xNew(2*NbCrackedEdges);
+			for (i=0;iCrackedEdges[i*2+0]=0;//CrackedEdges[i]->+1; //M indexing
+				bamgmesh->CrackedEdges[i*2+1]=0;//CrackedEdges[i]-]->+1; //M indexing
+			}
+		}
+
+		//clean up
+		xDelete(connectivitysize_1);
+		xDelete(head_1);
+		xDelete(next_1);
+		xDelete(connectivitysize_2);
+		xDelete(head_2);
+		xDelete(next_2);
+		delete [] reft;
+		delete [] numt;
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::ReadMetric{{{*/
+	void Mesh::ReadMetric(const BamgOpts* bamgopts) {
+
+		/*Intermediary*/
+		int  i,j;
+
+		if(bamgopts->verbose>3) _printLine_("      processing metric");
+		double hmin = Max(bamgopts->hmin,MinimalHmin());
+		double hmax = Min(bamgopts->hmax,MaximalHmax());
+		double coef = bamgopts->coeff;
+
+		//for now we only use j==3
+		j=3;
+
+		for (i=0;imetric[i];
+				vertices[i].m=Metric(Max(hmin,Min(hmax, h*coef)));
+			}
+			else if (j==3){
+				//do not erase metric computed by hVertices
+				if (vertices[i].m.a11==1 && vertices[i].m.a21==0 && vertices[i].m.a22==1){
+					double a,b,c;	     
+					a=bamgopts->metric[i*3+0];
+					b=bamgopts->metric[i*3+1];
+					c=bamgopts->metric[i*3+2];
+					Metric M(a,b,c);
+					EigenMetric Vp(M/coef);
+
+					Vp.Maxh(hmax);
+					Vp.Minh(hmin);
+					vertices[i].m = Vp;
+				}
+			}
+		}
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::WriteMetric{{{*/
+	void Mesh::WriteMetric(BamgOpts* bamgopts) {
+		int i;
+		xDelete(bamgopts->metric);
+		bamgopts->metric=xNew(3*nbv);
+		for (i=0;imetric[i*3+0]=vertices[i].m.a11;
+			bamgopts->metric[i*3+1]=vertices[i].m.a21;
+			bamgopts->metric[i*3+2]=vertices[i].m.a22;
+		}
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::WriteIndex{{{*/
+	void Mesh::WriteIndex(int** pindex,int* pnels){
+
+		/*Intermediary*/
+		int i,k,num;
+		int verbose=0;
+
+		/*output*/
+		int* index=NULL;
+
+		/*Get number of triangles*/
+		k=0;
+		for (i=0;i0) k++;
+		}
+
+		if (k){
+			index=xNew(3*k);
+			num=0;
+			for (i=0;i0 && !(t.Hidden(0)||t.Hidden(1) || t.Hidden(2) )){
+					//if(t.Anisotropy()<2 & t.Length()<1.e+5){
+						index[num*3+0]=GetId(t[0])+1; //back to M indexing
+						index[num*3+1]=GetId(t[1])+1; //back to M indexing
+						index[num*3+2]=GetId(t[2])+1; //back to M indexing
+						num=num+1;
+					//}
+				}
+			}
+		}
+
+		/*Assign output pointers*/
+		*pindex=index;
+		*pnels=num;
+	}
+	/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION Mesh::AddGeometryMetric{{{*/
+	void Mesh::AddGeometryMetric(BamgOpts* bamgopts){
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/IntersectGeomMetric)*/
+
+		/*Get options*/
+		int    verbose=bamgopts->verbose;
+		double anisomax =bamgopts->anisomax;
+		double errg     =bamgopts->errg;
+
+		double ss[2]={0.00001,0.99999};
+		double errC = 2*sqrt(2*errg);
+		double hmax = Gh.MaximalHmax();
+		double hmin = Gh.MinimalHmin();
+
+		//check that hmax is positive
+		if (hmax<=0){
+			_error_("hmax<=0");
+		}
+
+		//errC cannot be higher than 1
+		if (errC>1) errC=1;
+
+		//Set all vertices to "on"
+		SetVertexFieldOn();
+
+		//loop over all the vertices on edges
+		for (int  i=0;iR1tg(s,tg);
+				double  ht=hmax;
+				// err relative to the length of the edge
+				if (R1>1.0e-20) {  
+					ht = Min(Max(errC/R1,hmin),hmax);
+				}
+				double hn=Min(hmax,ht*anisomax);
+
+				if (ht<=0 || hn<=0){
+					_error_("ht<=0 || hn<=0");
+				}
+				EigenMetric Vp(1/(ht*ht),1/(hn*hn),tg);
+				Metric MVp(Vp);
+				edges[i][j].m.IntersectWith(MVp);
+			}
+		}
+		// the problem is for the vertex on vertex 
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::AddMetric{{{*/
+	void Mesh::AddMetric(BamgOpts* bamgopts){
+		//  Hessiantype = 0 =>  H is computed using double P2 projection
+		//  Hessiantype = 1 =>  H is computed with green formula
+
+		/*Options*/
+		int Hessiantype=bamgopts->Hessiantype;
+
+		if (Hessiantype==0){
+			BuildMetric0(bamgopts);
+		}
+		else if (Hessiantype==1){
+			BuildMetric1(bamgopts);
+		}
+		else{
+			_error_("Hessiantype " << Hessiantype << " not supported yet (1->use Green formula, 0-> double P2 projection)");
+		}
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::AddVertex{{{*/
+	void Mesh::AddVertex( BamgVertex &s,Triangle* t, Icoor2* det3) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/Add)*/
+		// -------------------------------
+		//             s2
+		//                               !
+		//             /|\               !
+		//            / | \              !
+		//           /  |  \             !
+		//    tt1   /   |   \ tt0        !
+		//         /    |s   \           !
+		//        /     .     \          !
+		//       /  .      `   \         !
+		//      / .           ` \        !
+		//      ----------------         !
+		//   s0       tt2       s1
+		//-------------------------------
+
+		/*Intermediaries*/
+		Triangle* tt[3];       //the three triangles
+		Icoor2 det3local[3];   //three determinants (integer)
+		int nbzerodet =0;      //number of zeros in det3
+		int izerodet=-1;       //egde containing the vertex s
+		int iedge; 
+
+		/*three vertices of t*/
+		BamgVertex &s0=(*t)[0];
+		BamgVertex &s1=(*t)[1];
+		BamgVertex &s2=(*t)[2];
+
+		//determinant of t
+		Icoor2 detOld=t->det;
+
+		/* infvertexindex = index of the infinite vertex (NULL)
+			if no infinite vertex (NULL) infvertexindex=-1
+			else if v_i is infinite, infvertexindex=i*/
+		int infvertexindex = &s0 ?  ((  &s1 ? ( &s2  ? -1 : 2) : 1  )) : 0;
+
+		//some checks
+		if (( infvertexindex <0 ) && (detOld <0) ||  ( infvertexindex >=0  ) && (detOld >0) ){
+			_error_("inconsistent configuration (Contact ISSM developers)");
+		}
+
+		// if det3 does not exist, build it 
+		if (!det3){ 
+			//allocate
+			det3 = det3local;
+			//if no infinite vertex
+			if (infvertexindex<0 ) {
+				det3[0]=bamg::det(s ,s1,s2);
+				det3[1]=bamg::det(s0,s ,s2);
+				det3[2]=bamg::det(s0,s1,s );}
+			else { 
+				// one of &s1  &s2  &s0 is NULL
+				det3[0]= &s0 ? -1 : bamg::det(s ,s1,s2) ;
+				det3[1]= &s1 ? -1 : bamg::det(s0,s ,s2) ;
+				det3[2]= &s2 ? -1 : bamg::det(s0,s1,s ) ;
+			}
+		}
+
+		if (!det3[0]) izerodet=0,nbzerodet++;
+		if (!det3[1]) izerodet=1,nbzerodet++;
+		if (!det3[2]) izerodet=2,nbzerodet++;
+
+		//if nbzerodet>0, point s is on an egde or on a vertex 
+		if  (nbzerodet>0){ 
+			/*s is on an edge*/
+			if (nbzerodet==1) {
+				iedge = OppositeEdge[izerodet];
+				AdjacentTriangle ta = t->Adj(iedge);
+
+				/*if the point is one the boundary 
+				  add the point in outside part */
+				if (t->det>=0){ // inside triangle
+					if (((Triangle*)ta)->det<0 ) {
+						// add in outside triangle 
+						AddVertex(s,( Triangle *)ta);
+						return;
+					}
+				}
+			}
+			else{
+				_error_("Cannot add a vertex more than once. Check duplicates");
+			}
+		}
+
+		// remove de MarkUnSwap edge
+		t->SetUnMarkUnSwap(0);
+		t->SetUnMarkUnSwap(1);
+		t->SetUnMarkUnSwap(2);
+
+		tt[0]= t;
+		tt[1]= &triangles[nbt++];
+		tt[2]= &triangles[nbt++];
+
+		if (nbt>maxnbt) _error_("Not enough triangles");
+
+		*tt[1]=*tt[2]=*t;
+		tt[0]->link=tt[1];
+		tt[1]->link=tt[2]; 
+
+		(*tt[0])(OppositeVertex[0])=&s;
+		(*tt[1])(OppositeVertex[1])=&s;
+		(*tt[2])(OppositeVertex[2])=&s;
+
+		tt[0]->det=det3[0];
+		tt[1]->det=det3[1];
+		tt[2]->det=det3[2];         
+
+		//  update adj des triangles externe 
+		tt[0]->SetAdjAdj(0);
+		tt[1]->SetAdjAdj(1);
+		tt[2]->SetAdjAdj(2);
+		//  update des adj des 3 triangle interne
+		const int i0 = 0;
+		const int i1= NextEdge[i0];
+		const int i2 = PreviousEdge[i0];
+
+		tt[i0]->SetAdj2(i2,tt[i2],i0);
+		tt[i1]->SetAdj2(i0,tt[i0],i1);
+		tt[i2]->SetAdj2(i1,tt[i1],i2);
+
+		tt[0]->SetSingleVertexToTriangleConnectivity();
+		tt[1]->SetSingleVertexToTriangleConnectivity();
+		tt[2]->SetSingleVertexToTriangleConnectivity();
+
+
+		// swap if the point s is on a edge
+		if(izerodet>=0) {
+			int rswap=tt[izerodet]->swap(iedge);
+
+			if (!rswap) {
+				_error_("swap the point s is on a edge");
+			}
+		}
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::BoundAnisotropy{{{*/
+	void  Mesh::BoundAnisotropy(double anisomax,double hminaniso) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/BoundAnisotropy)*/
+
+		long int verbose=0;
+		double lminaniso = 1/ (Max(hminaniso*hminaniso,1e-100));
+
+		//display info
+		if (verbose > 1)  _printLine_("   BoundAnisotropy by " << anisomax);
+
+		double h1=1.e30,h2=1e-30;
+		double coef = 1./(anisomax*anisomax);
+		double hn1=1.e30,hn2=1e-30,rnx =1.e-30,rx=0;  
+
+		//loop over all vertices
+		for (int i=0;i2){
+				h1 =Min(h1,Vp.lmin());
+				h2 =Max(h2,Vp.lmax());
+				hn1=Min(hn1,Vp.lmin());
+				hn2=Max(hn2,Vp.lmax());
+				rx =Max(rx,Vp.Aniso2());
+				rnx= Max(rnx,Vp.Aniso2());
+			}
+		}
+
+		//display info
+		if (verbose>2){
+			_printLine_("      input:  Hmin = " << pow(h2,-0.5)  << ", Hmax = " << pow(h1,-0.5) << ", factor of anisotropy max  = " << pow(rx,0.5));
+			_printLine_("      output: Hmin = " << pow(hn2,-0.5) << ", Hmax = " << pow(hn1,-0.5)<< ", factor of anisotropy max  = " < (BAMG v1.01, MeshGeom.cpp/ConsGeometry)*/
+
+		/*Reconstruct Geometry from Mesh*/
+
+		/*Intermediary*/
+		int i,j,k,kk,it,jt;
+		int    verbose=0;
+		double cutoffradian=10*Pi/180;
+
+		/*Recover options*/
+		if (bamgopts){
+			verbose=bamgopts->verbose;
+			cutoffradian=bamgopts->MaxCornerAngle*Pi/180;
+		}
+
+		//display info
+		if (verbose>1) _printLine_("   construction of the geometry from the 2d mesh");
+
+		//check that the mesh is not empty
+		if (nbt<=0 || nbv <=0 ) {
+			_error_("nbt or nbv is negative (Mesh empty?)");
+		}
+
+		//Gh is the geometry of the mesh (this), initialize MaxCornerAngle
+		if (cutoffradian>=0) Gh.MaxCornerAngle = cutoffradian;
+
+		/*Construction of the edges*/
+
+		//initialize st and edge4
+		SetOfEdges4* edge4= new SetOfEdges4(nbt*3,nbv);
+		long*        st   = new long[nbt*3];
+
+		//initialize st as -1 (chaining algorithm)
+		for (i=0;iSortAndAdd(GetId(edges[i][0]),GetId(edges[i][1]));
+		}
+		//check that there is no double edge
+		if (nbe !=  edge4->nb()){ 
+			delete [] st;
+			_error_("Some Double edge in the mesh, the number is " << nbe << ", nbe4=" << edge4->nb()); 
+		}
+		//keep nbe in nbeold
+		long nbeold = nbe;
+
+		//Go through the triangles and ass the edges in edge4 if they are not there yet
+		for (i=0;iSortAndAdd(GetId(triangles[i][VerticesOfTriangularEdge[j][0]]), GetId(triangles[i][VerticesOfTriangularEdge[j][1]]));
+				long invisible = triangles[i].Hidden(j);
+
+				//if st[k] has not been changed yet, add 3*i+j (= vertex position in the index)
+				if(st[k]==-1) st[k]=3*i+j;
+
+				//else st[k]>=0 -> the edge already exist, check
+				else if(st[k]>=0) {
+					//check that it is not an edge on boundary (should not already exist)
+					if (triangles[i].TriangleAdj(j) || triangles[st[k]/3].TriangleAdj((int) (st[k]%3))){
+						_error_("problem in Geometry reconstruction: an edge on boundary is duplicated (double element?)");
+					}
+					//OK, the element is not on boundary, is belongs to 2 triangles -> build Adjacent triangles list
+					triangles[i].SetAdj2(j,triangles + st[k] / 3,(int) (st[k]%3));
+					if (invisible)  triangles[i].SetHidden(j);
+					// if k < nbe mark the edge as on Boundary (Locked)
+					if (knb(); // the total number of edges 
+		delete edge4; edge4=NULL;
+
+		//display info
+		if(verbose>5) {
+			_printLine_("         info on Mesh:");
+			_printLine_("            - number of vertices    = " << nbv); 
+			_printLine_("            - number of triangles   = " << nbt); 
+			_printLine_("            - number of given edges = " << nbe); 
+			_printLine_("            - number of all edges   = " << nbedges); 
+			_printLine_("            - Euler number 1 - nb of holes = " << nbt-nbedges+nbv); 
+		}
+
+		// check consistency of edge[].adj and geometrical required  vertices
+		k=0; kk=0;
+		for (i=0;i=0) 
+			 kk++;
+		}
+
+		/*Constructions of edges*/
+
+		k += kk;
+		kk=0;
+		if (k) {
+			nbe = k;
+			Edge* edgessave=edges;
+			edges = new Edge[nbe];
+			k =0;
+
+			//display info
+			if(verbose>4) _printLine_("   Construction of the edges " << nbe);
+
+			for (i=0;i=0){
+					it = st[i]/3;
+					j  = (int) (st[i]%3);
+					add=k++;
+				}
+				if (add>=0 && add < nbe){
+					edges[add].v[0] = &triangles[it][VerticesOfTriangularEdge[j][0]];
+					edges[add].v[1] = &triangles[it][VerticesOfTriangularEdge[j][1]];
+					edges[add].GeomEdgeHook=NULL; 
+					//if already existed
+					if (iGetReferenceNumber(),edges[add].v[1]->GetReferenceNumber());
+				  }
+			}
+
+			//check that we have been through all edges
+			if (k!=nbe){
+				_error_("problem in edge construction process: k!=nbe (should not happen)");
+			}
+			//delete edgessave
+			if (edgessave) delete [] edgessave;
+		}
+
+		/*Color the vertices*/
+
+		//initialize color of all vertices as 0
+		for (i=0;icolor++;
+		}
+
+		//change the color: if a vertex belongs to 2 edges -1, else -2
+		for (i=0;icolor;
+				long j0;
+
+				//if color<0 (first time), no adjacent edge
+				if(i0<0) edges[i].adj[j]=NULL;
+
+				//if color=-1 (corner),change the vertex color as 2*i+j (position of the vertex in edges)
+				if(i0==-1) v->color=i*2+j;
+
+				//if color>=0 (i and i0 edge are adjacent by the vertex v)
+				else if (i0>=0) {
+					//get position of v in edges back
+					j0 =  i0%2; //column in edges
+					i0 =  i0/2; //line in edges
+
+					//check that we have the correct vertex
+					if (v!=edges[i0 ].v[j0]){
+						_error_("v!=edges[i0 ].v[j0]: this should not happen as the vertex belongs to this edge");
+					}
+
+					//Add adjacence
+					edges[i ].adj[j ]=edges +i0;
+					edges[i0].adj[j0]=edges +i ;
+
+					//change color to -3
+					v->color = -3;
+				}
+			}
+		}
+
+		/*Reconstruct subdomains info*/
+
+		//check that nbsubdomains is empty
+		if (nbsubdomains){
+			_error_("nbsubdomains should be 0");
+		}
+		nbsubdomains=0;
+
+		//color the subdomains
+		long* colorT= new long[nbt];
+		Triangle *tt,*t;
+
+		//initialize the color of each triangle as -1
+		for (it=0;it0){
+					if( (j=st[level]++)<3 ){ 
+						t = &triangles[st[level-1]];
+						tt=t->TriangleAdj((int)j);
+
+						//color the adjacent triangle
+						if ( ! t->Locked(j) && tt && (colorT[jt = GetId(tt)] == -1) && ( tt->color==kolor)) {
+							colorT[jt]=nbsubdomains;
+							st[++level]=jt;
+							st[++level]=0;
+							k++;
+						}
+					}
+					else level-=2;
+				}
+				nbsubdomains++;
+			}
+		}
+		if (verbose> 3) _printLine_("      The Number of sub domain = " << nbsubdomains); 
+
+		//build subdomains
+		long isd;
+		subdomains = new SubDomain[nbsubdomains];
+
+		//initialize subdomains[isd].head as 0
+		for (isd=0;isdcolor != triangles[it].color) && !subdomains[isd=colorT[it]].head){
+					subdomains[isd].head = triangles+it;
+					subdomains[isd].ReferenceNumber =  triangles[it].color;
+					subdomains[isd].direction = j; // hack
+					subdomains[isd].edge = 0;
+					k++;
+				}
+			}
+		}
+		//check that we have been through all subdomains
+		if (k!= nbsubdomains){
+			delete [] colorT;
+			_error_("k!= nbsubdomains");
+		}
+		//delete colorT and st
+		delete [] colorT;
+		delete [] st;
+
+		/*Reconstruct Geometry Gh*/
+
+		//build colorV -1 for all vertex and 0 for the vertices belonging to edges
+		long* colorV = new long[nbv];
+		for (i=0;i3) _printLine_("   number of vertices = " << Gh.nbv << "\n   number of edges = " << Gh.nbe);
+		NbVerticesOnGeomVertex = Gh.nbv;
+		VerticesOnGeomVertex = new VertexOnGeom[NbVerticesOnGeomVertex];
+		NbVerticesOnGeomEdge =0;
+		VerticesOnGeomEdge =0;
+
+		//Build VertexOnGeom
+		for (i=0;i=0){
+				BamgVertex & v = Gh.vertices[j];
+				v = vertices[i];
+				v.color =0;
+				VerticesOnGeomVertex[j] = VertexOnGeom(vertices[i], Gh.vertices[j]);
+			}
+		}
+
+		//Buid pmin and pmax of Gh (extrema coordinates)
+		Gh.pmin =  Gh.vertices[0].r;
+		Gh.pmax =  Gh.vertices[0].r;
+		// recherche des extrema des vertices pmin,pmax
+		for (i=0;iSetRequired();
+				Gh.edges[i].v[1]->SetRequired();
+				Gh.edges[i].SetRequired();
+			}
+
+			R2 x12 = Gh.vertices[j0].r-Gh.vertices[j1].r;
+			double l12=Norme2(x12);        
+			hmin = Min(hmin,l12);
+
+			Gh.vertices[j1].color++;
+			Gh.vertices[j0].color++;
+
+			len[j0]+= l12;
+			len[j1] += l12;
+			hmin = Min(hmin,l12);
+			Gh.edges[i].ReferenceNumber  = edges[i].ReferenceNumber;
+
+			k = edge4->SortAndAdd(i0,i1);
+			if (k != i){
+				delete [] len;
+				delete [] colorV;
+				_error_("problem in Edge4 construction: k != i");
+			}
+		}
+
+		//Build metric for all vertices of Gh
+		for (i=0;i 0) 
+		  Gh.vertices[i].m=  Metric(len[i] /(double) Gh.vertices[i].color);
+		 else 
+		  Gh.vertices[i].m=  Metric(hmin);
+		}
+		//delete len
+		delete [] len;
+
+		//Build Gh.subdomains
+		for (i=0;iSortAndFind(i0,i1);
+			if(k>=0){
+				subdomains[i].direction = (vertices + i0 == edges[k].v[0]) ? 1 : -1;
+				subdomains[i].edge = edges+k;
+				Gh.subdomains[i].edge = Gh.edges + k;
+				Gh.subdomains[i].direction  =  subdomains[i].direction;
+				Gh.subdomains[i].ReferenceNumber =  subdomains[i].ReferenceNumber;
+			}
+			else
+			 _error_("%i should be >=0");
+		  }
+
+		delete edge4;
+		delete [] colorV;
+
+		//unset adj
+		for (i=0;iverbose;
+
+		/*Get and process fields*/
+		s=bamgopts->field;
+		nbsol=bamgopts->fieldSize[1];
+
+		/*Check size*/
+		if (bamgopts->fieldSize[0] != nbv) _error_("'field' should have " << nbv << " rows");
+
+		//initialization of some variables
+		double* ss=(double*)s;
+		double  sA,sB,sC;
+		double*  detT = new double[nbt];
+		double*  sumareas = new double[nbv];
+		double*  alpha= new double[nbt*3];
+		double*  beta = new double[nbt*3];
+		double*  dx_elem    = new double[nbt];
+		double*  dy_elem    = new double[nbt];
+		double*  dx_vertex  = new double[nbv];
+		double*  dy_vertex  = new double[nbv];
+		double*  dxdx_elem  = new double[nbt];
+		double*  dxdy_elem  = new double[nbt];
+		double*  dydy_elem  = new double[nbt];
+		double*  dxdx_vertex= new double[nbv];
+		double*  dxdy_vertex= new double[nbv];
+		double*  dydy_vertex= new double[nbv];
+
+		//display infos
+		if(verbose>1) {
+			_printLine_("   Construction of Metric: number of field: " << nbsol << " (nbt=" << nbt << ", nbv=" << nbv << ")");
+		}
+
+		//first, build the chains that will be used for the Hessian computation, as weel as the area of each element
+		int* head_s=NULL;
+		head_s=xNew(nbv);
+		int* next_p=NULL;
+		next_p=xNew(3*nbt);
+		int  p=0;
+		//initialization
+		for(i=0;i2) _printLine_("      Solution " << nusol << ", Min = " << smin << ", Max = " << smax << ", Delta = " << sdelta);
+
+			//skip constant field
+			if (sdelta < 1.0e-10*Max(absmax,1e-20)){
+				_printLine_("      Solution " << nusol << " is constant, skipping...");
+				continue;
+			}
+
+			//initialize the hessian and gradient matrices
+			for ( iv=0,k=0; iverr[nusol],bamgopts);
+			}
+
+		}//for all solutions
+
+		//clean up
+		xDelete(head_s);
+		xDelete(next_p);
+		delete [] detT;
+		delete [] alpha;
+		delete [] beta;
+		delete [] sumareas;
+		delete [] dx_elem;
+		delete [] dy_elem;
+		delete [] dx_vertex;
+		delete [] dy_vertex;
+		delete [] dxdx_elem;
+		delete [] dxdy_elem;
+		delete [] dydy_elem;
+		delete [] dxdx_vertex;
+		delete [] dxdy_vertex;
+		delete [] dydy_vertex;
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::BuildMetric1 (Green formula){{{*/
+	void Mesh::BuildMetric1(BamgOpts* bamgopts){
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/IntersectConsMetric)*/
+
+		/*Options*/
+		double* s=NULL;
+		long nbsol;
+		int NbJacobi;
+		int verbose;
+
+		/*Recover options*/
+		verbose=bamgopts->verbose;
+		NbJacobi=bamgopts->nbjacobi;
+
+		/*Get and process fields*/
+		s=bamgopts->field;
+		nbsol=bamgopts->fieldSize[1];
+
+		/*Check size*/
+		if (bamgopts->fieldSize[0] != nbv) _error_("'field' should have " << nbv << " rows");
+
+		//initialization of some variables
+		long    i,k,iA,iB,iC,iv;
+		R2      O(0,0);
+		double* ss=(double*)s;
+		double  sA,sB,sC;
+		double*  detT = new double[nbt];
+		double*  Mmass= new double[nbv];
+		double*  Mmassxx= new double[nbv];
+		double*  dxdx= new double[nbv];
+		double*  dxdy= new double[nbv];
+		double*  dydy= new double[nbv];
+		double*  workT= new double[nbt];
+		double*  workV= new double[nbv];
+		int*    OnBoundary = new int[nbv];
+
+		//display infos
+		if(verbose>1) {
+			_printLine_("   Construction of Metric: number of field: " << nbsol << " (nbt=" << nbt << ", nbv=" << nbv << ")");
+		}
+
+		//initialize Mmass, OnBoundary and Massxx by zero
+		for (iv=0;ivlink){
+						//mark the two vertices of the edge as OnBoundary
+						OnBoundary[GetId(t[VerticesOfTriangularEdge[j][0]])]=1;
+						OnBoundary[GetId(t[VerticesOfTriangularEdge[j][1]])]=1;
+						nbb++;
+					}
+				}
+
+				//number of vertices on boundary for current triangle t
+				workT[i] = nbb;
+
+				//Build Mmass Mmass[i] = Mmass[i] + Area/3
+				Mmass[iA] += dett;
+				Mmass[iB] += dett;
+				Mmass[iC] += dett;
+
+				//Build Massxx = Mmass
+				Mmassxx[iA] += dett;
+				Mmassxx[iB] += dett;
+				Mmassxx[iC] += dett;
+			}
+
+			//else: the triangle is a boundary triangle -> workT=-1
+			else workT[i]=-1;
+		}
+
+		//for all Solution  
+		for (int nusol=0;nusol2) _printLine_("      Solution " << nusol << ", Min = " << smin << ", Max = " << smax << ", Delta = " << sdelta << ", number of fields = " << nbsol);
+
+			//skip constant field
+			if (sdelta < 1.0e-10*Max(absmax,1e-20) ){
+				if (verbose>2) _printLine_("      Solution " << nusol << " is constant, skipping...");
+				continue;
+			}
+
+			//pointer toward ss that is also a pointer toward s (solutions)
+			double* sf=ss; 
+
+				//initialize the hessian matrix
+				for ( iv=0,k=0; iv normal = 0
+						if ( !tBC || !tBC->link ) nBC=O;
+						if ( !tCA || !tCA->link ) nCA=O;
+						if ( !tAB || !tAB->link ) nAB=O;
+
+						// remark we forgot a 1/2 because
+						//       int_{edge} w_i = 1/2 if i is in edge 
+						//                         0  if not
+						// if we don't take the  boundary 
+						dxdx[iA] += ( nCA.x + nAB.x ) *Grads.x;
+						dxdx[iB] += ( nAB.x + nBC.x ) *Grads.x;
+						dxdx[iC] += ( nBC.x + nCA.x ) *Grads.x;
+
+						//warning optimization (1) the division by 2 is done on the metric construction
+						dxdy[iA] += (( nCA.y + nAB.y ) *Grads.x + ( nCA.x + nAB.x ) *Grads.y) ;
+						dxdy[iB] += (( nAB.y + nBC.y ) *Grads.x + ( nAB.x + nBC.x ) *Grads.y) ;
+						dxdy[iC] += (( nBC.y + nCA.y ) *Grads.x + ( nBC.x + nCA.x ) *Grads.y) ; 
+
+						dydy[iA] += ( nCA.y + nAB.y ) *Grads.y;
+						dydy[iB] += ( nAB.y + nBC.y ) *Grads.y;
+						dydy[iC] += ( nBC.y + nCA.y ) *Grads.y;
+
+					} // for real all triangles 
+				}
+
+				long kk=0;
+				for ( iv=0,k=0 ; iv0){
+						dxdx[iv] /= 2*Mmassxx[iv];
+						// warning optimization (1) on term dxdy[iv]*ci/2 
+						dxdy[iv] /= 4*Mmassxx[iv];
+						dydy[iv] /= 2*Mmassxx[iv];
+						// Compute the matrix with abs(eigen value)
+						Metric M(dxdx[iv], dxdy[iv], dydy[iv]);
+						EigenMetric Vp(M);
+						Vp.Abs();
+						M = Vp;
+						dxdx[iv] = M.a11;
+						dxdy[iv] = M.a21;
+						dydy[iv] = M.a22;
+					}
+					else kk++;
+				}
+
+				// correction of second derivative
+				// by a laplacien
+				double* d2[3] = {dxdx, dxdy, dydy};
+				double* dd;
+				for (int xy = 0;xy<3;xy++) {
+					dd = d2[xy];
+					// do leat 2 iteration for boundary problem
+					for (int ijacobi=0;ijacobi0)+(Mmassxx[iB]>0)+(Mmassxx[iC]>0)),1.);
+							 workT[i] = (dd[iA]+dd[iB]+dd[iC])/cc;
+						 }
+						for (iv=0;iverr[nusol],bamgopts);
+				}
+
+		}// end for all solution 
+
+		delete [] detT;
+		delete [] Mmass;
+		delete [] dxdx;
+		delete [] dxdy;
+		delete [] dydy;
+		delete []  workT;
+		delete [] workV;
+		delete [] Mmassxx;
+		delete []  OnBoundary;
+
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::CrackMesh{{{*/
+	void Mesh::CrackMesh(BamgOpts* bamgopts) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/CrackMesh)*/
+
+		/*Intermediary*/
+		int i,j,k,num,count;
+		int i1,i2;
+		int j1,j2;
+
+		/*Options*/
+		int verbose=bamgopts->verbose;
+
+		//  computed the number of cracked edge
+		for (k=i=0;iCracked()) k++;
+		}
+
+		//Return if no edge is cracked
+		if(k==0) return;
+		if (verbose>4) _printLine_("      number of Cracked Edges = " << k);
+
+		//Initialize Cracked edge
+		NbCrackedEdges=k;
+		CrackedEdges=new CrackedEdge[k];
+
+		//Compute number of Cracked Vertices
+		k=0;
+		NbCrackedVertices=0;
+
+		int* splitvertex=new int[nbv];
+		for (i=0;iCracked()){
+
+				//Fill edges fields of CrackedEdges
+				CrackedEdges[k  ].E =edges[i].GeomEdgeHook;
+				CrackedEdges[k++].e1=&edges[i];
+
+				//Get number of the two vertices on the edge
+				i1=GetId(edges[i][0]);
+				i2=GetId(edges[i][1]);
+				_assert_(i1>=0 && i1=0 && i24) _printLine_("      number of Cracked Vertices = " << NbCrackedVertices);
+		if (NbCrackedVertices){
+			CrackedVertices=xNew(2*NbCrackedVertices);
+			num=0;
+			for (i=0;i to renumber
+							CrackedEdges[i].b=ta.t;
+							CrackedEdges[i].length=Norme2((*ta.t)[j1].r-(*ta.t)[j2].r);
+							CrackedEdges[i].normal=Orthogonal((*ta.t)[j1].r-(*ta.t)[j2].r);
+						}
+						Edgeflags[i]++;
+						break;
+					}
+				}
+				//_printLine_(element_renu[GetId(ta.t)] << " -> " << GetId((*ta.t)[0])+1 << " " << GetId((*ta.t)[1])+1 << " " << GetId((*ta.t)[2])+1 << ", edge [" << i1 << "->" << j1 << " " << i2 << "->" << j2 << "]");
+				ta = Next(ta).Adj(); 
+				if (count++>50) _error_("Maximum number of iteration exceeded");
+			}while ((tbegin != ta)); 
+		}
+
+		//Check EdgeFlag
+		for(i=0;i (BAMG v1.01, Mesh2.cpp/ForceBoundary)*/
+
+			long int verbose=2;
+			int k=0;
+			int nbfe=0,nbswp=0,Nbswap=0;
+
+			//display
+			if (verbose > 2) _printLine_("   ForceBoundary  nb of edge: " << nbe);
+
+			//check that there is no triangle with 0 determinant
+			for (int t = 0; t < nbt; t++){
+				if (!triangles[t].det) k++;
+			}
+			if (k!=0) {
+				_error_("there is " << k << " triangles of mes = 0");
+			}
+
+			//Force Edges
+			AdjacentTriangle ta(0,0);
+			for (int i = 0; i < nbe; i++){
+
+				//Force edge i
+				nbswp =  ForceEdge(edges[i][0],edges[i][1],ta);
+				if (nbswp<0) k++;
+				else Nbswap += nbswp;
+
+				if (nbswp) nbfe++;
+				if ( nbswp < 0 && k < 5){
+					_error_("Missing Edge " << i << ", v0=" << GetId(edges[i][0]) << ",v1=" << GetId(edges[i][1]));
+				}
+			}
+
+			if (k!=0) {
+				_error_("There are " << k << " lost edges, the boundary might be crossing");
+			}
+			for (int j=0;j 3) _printLine_("      number of inforced edge = " << nbfe << ", number of swap= " << Nbswap); 
+		}
+	/*}}}*/
+	/*FUNCTION Mesh::FindSubDomain{{{*/
+	void Mesh::FindSubDomain(int OutSide) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/FindSubDomain)*/
+
+		long int verbose=0;
+
+		if (verbose >2){
+			if (OutSide) _printLine_("   Find all external sub-domain"); 
+			else _printLine_("   Find all internal sub-domain");
+		  }
+		short * HeapArete = new short[nbt];
+		Triangle  **  HeapTriangle = new Triangle*  [nbt];
+		Triangle *t,*t1;
+		long k,it;
+
+		for (int itt=0;ittlink = t ; // sd forme d'un triangle cicular link
+
+				HeapTriangle[i] =t ; 
+				HeapArete[i] = 3;
+
+				while (i >= 0) // boucle sur la pile
+				  { while ( HeapArete[i]--) // boucle sur les 3 aretes 
+					  { 
+						int na =  HeapArete[i];
+						Triangle * tc =  HeapTriangle[i]; // triangle courant
+						if( ! tc->Locked(na)) // arete non frontiere
+						  {
+							Triangle * ta = tc->TriangleAdj(na) ; // næ triangle adjacent
+							if (ta->link == 0 ) // non deja chainer => on enpile
+							  { 
+								i++;
+								ta->link = t->link ;  // on chaine les triangles
+								t->link = ta ;  // d'un meme sous domaine          
+								HeapArete[i] = 3; // pour les 3 triangles adjacents
+								HeapTriangle[i] = ta;
+							  }}
+					  } // deplie fin de boucle sur les 3 adjacences
+					i--;
+				  }          
+			}      
+		}
+
+		// supression de tous les sous domaine infini <=>  contient le sommet NULL
+		it =0;
+		nbtout = 0;
+		while (itlink;
+						t1->link=0;
+					}
+				  }
+			  }   
+			it++;} // end while (itlink;
+						mark[it]=k;
+						subdomains[k].head = t1;
+						do {
+							mark[GetId(t)]=k;
+							t=t->link;
+						} while (t!=t1);
+						mark[it]=k++;}
+						//    else if(mark[it] == -2 ) triangles[it].Draw(999);
+						it++;} // end white (it=0 && subdomains[kl].ReferenceNumber <0 && kr >=0 && subdomains[kr].ReferenceNumber>=0)
+										nbk--,subdomains[kr].ReferenceNumber=subdomains[kl].ReferenceNumber-1;
+									  if (kr >=0 && subdomains[kr].ReferenceNumber <0 && kl >=0 && subdomains[kl].ReferenceNumber>=0)
+										nbk--,subdomains[kl].ReferenceNumber=subdomains[kr].ReferenceNumber-1;
+									  if(kr<0 && kl >=0 && subdomains[kl].ReferenceNumber>=0)
+										nbk--,subdomains[kl].ReferenceNumber=-1;
+									  if(kl<0 && kr >=0 && subdomains[kr].ReferenceNumber>=0)
+										nbk--,subdomains[kr].ReferenceNumber=-1;
+								  }
+								 }
+							long  j=0;
+							for ( i=0;ilink;
+									 t1->link=0;
+								 }//while (t)
+								}
+							if(verbose>4) _printLine_("      Number of removes subdomains (OutSideMesh) = " << nbsubdomains-j);
+							nbsubdomains=j;
+						  }
+
+						delete []  mark; 
+
+			  }
+			else
+			  { // find the head for all sub domaine
+				if (Gh.nbsubdomains != nbsubdomains && subdomains)
+				 delete [] subdomains, subdomains=0;
+				if (! subdomains  ) 
+				 subdomains = new SubDomain[ Gh.nbsubdomains];
+				nbsubdomains =Gh.nbsubdomains;
+				long err=0;
+				CreateSingleVertexToTriangleConnectivity();
+				long * mark = new long[nbt];
+				Edge **GeomEdgetoEdge = MakeGeomEdgeToEdge();
+
+				for (it=0;itt;
+					int direction = Gh.subdomains[i].direction;
+					// test if ge and e is in the same direction 
+					if (((eg[0].r-eg[1].r),(e[0].r-e[1].r))<0) direction = -direction ;
+					subdomains[i].direction = direction;
+					subdomains[i].edge = &e;
+					_assert_(t && direction);
+
+					AdjacentTriangle  ta(t,EdgesVertexTriangle[v0->IndexInTriangle][0]);// previous edges
+
+					while (1) {
+						_assert_(v0==ta.EdgeVertex(1));
+						if (ta.EdgeVertex(0) == v1) { // ok we find the edge
+							if (direction>0)  
+							 subdomains[i].head=t=Adj(ta);
+							else 
+							 subdomains[i].head=t=ta;
+							if(t= triangles+nbt || t->det < 0 || t->link == 0) {
+								_error_("bad definition of SubSomain " << i);
+							}
+							long it = GetId(t);
+							if (mark[it] >=0) {
+								break;
+							}
+							if(i != inew) 
+							 Exchange(subdomains[i],subdomains[inew]);
+							inew++;
+							Triangle *tt=t;
+							long kkk=0;
+							do 
+							  {
+								kkk++;
+								if (mark[GetId(tt)]>=0){
+									_error_("mark[GetId(tt)]>=0");
+								}
+								mark[GetId(tt)]=i;
+								tt=tt->link;
+							  } while (tt!=t);
+							break;
+						}
+						ta = Previous(Adj(ta));         
+						if(t == (Triangle *) ta) {
+							_error_("bad definition of SubSomain " << i);
+						}
+					}
+				}
+
+				if (inew < nbsubdomains) {
+					if (verbose>5) _printLine_("WARNING: " << nbsubdomains-inew << " SubDomains are being removed");
+					nbsubdomains=inew;}
+
+
+					for (it=0;it (BAMG v1.01, Mesh2.cpp/PreInit)*/
+
+		/* initialize random seed: */
+		srand(19999999);
+
+		/*Initialize fields*/
+		NbRef=0;
+		quadtree=NULL;
+		nbv=0;
+		nbt=0;
+		nbe=0;
+		edges=NULL;
+		nbq=0;
+		nbsubdomains=0;
+		subdomains=NULL;
+		maxnbv=maxnbv_in;
+		maxnbt=2 *maxnbv_in-2;
+		NbVertexOnBThVertex=0;
+		VertexOnBThVertex=NULL;
+		NbVertexOnBThEdge=0;
+		VertexOnBThEdge=NULL;
+		NbCrackedVertices=0;
+		CrackedVertices =NULL;
+		NbCrackedEdges =0;
+		CrackedEdges =NULL;
+		NbVerticesOnGeomVertex=0;
+		VerticesOnGeomVertex=NULL;
+		NbVerticesOnGeomEdge=0;
+		VerticesOnGeomEdge=NULL;
+
+		/*Allocate if maxnbv_in>0*/
+		if (maxnbv_in) {
+			vertices=new BamgVertex[maxnbv];
+			_assert_(vertices);
+			orderedvertices=new (BamgVertex* [maxnbv]);
+			_assert_(orderedvertices);
+			triangles=new Triangle[maxnbt];
+			_assert_(triangles);
+		}
+		else {
+			vertices=NULL;
+			orderedvertices=NULL;
+			triangles=NULL;
+			maxnbt=0;
+		} 
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::Insert{{{*/
+	void Mesh::Insert() {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/Insert)*/
+
+		/*Insert points in the existing Geometry*/
+
+		//Intermediary
+		int i;
+
+		/*Get options*/
+		long int verbose=2;
+
+		//Display info
+		if (verbose>2) _printLine_("   Insert initial " << nbv << " vertices");
+
+		//Compute integer coordinates for the existing vertices
+		SetIntCoor();
+
+		/*Now we want to build a list (orderedvertices) of the vertices in a random
+		 * order. To do so, we use the following method:
+		 *
+		 * From an initial k0 in [0 nbv[ random (vertex number)
+		 * the next k (vertex number) is computed using a big
+		 * prime number (PN>>nbv) following:
+		 *
+		 * k_{i+1} = k_i + PN  [nbv]
+		 *
+		 * let's show that:
+		 *
+		 *   for all j in [0 nbv[, ∃! i in [0 nbv[ such that k_i=j
+		 *
+		 * Let's assume that there are 2 distinct j1 and j2 such that
+		 * k_j1 = k_j2
+		 *
+		 * This means that
+		 *  
+		 *  k0+j1*PN = k0+j2*PN [nbv]
+		 *  (j1-j2)*PN =0       [nbv]
+		 * since PN is a prime number larger than nbv, and nbv!=1
+		 *  j1-j2=0             [nbv]
+		 * BUT
+		 *  j1 and j2 are in [0 nbv[ which is impossible.
+		 *
+		 *  We hence have built a random list of nbv elements of
+		 *  [0 nbv[ all distincts*/
+
+		//Get Prime number
+		const long PrimeNumber= BigPrimeNumber(nbv);
+		int   k0=rand()%nbv; 
+
+		//Build orderedvertices
+		for (i=0; ii,orderedvertices[1]->i,orderedvertices[i]->i)==0;){
+			//if i is higher than nbv, it means that all the determinants are 0,
+			//all vertices are aligned!
+			if  (++i>=nbv) _error_("all the vertices are aligned");
+		}
+		// exchange i et 2 in "orderedvertices" so that
+		// the first 3 vertices are not aligned (real triangle)
+		Exchange(orderedvertices[2], orderedvertices[i]);
+
+		/*Take the first edge formed by the first two vertices and build
+		 * the initial simple mesh from this edge and 2 boundary triangles*/
+
+		BamgVertex *v0=orderedvertices[0], *v1=orderedvertices[1];
+
+		nbt = 2;
+		triangles[0](0) = NULL;//infinite vertex
+		triangles[0](1) = v0;
+		triangles[0](2) = v1;
+		triangles[1](0) = NULL;//infinite vertex
+		triangles[1](2) = v0;
+		triangles[1](1) = v1;
+
+		//Build adjacence
+		const int e0 = OppositeEdge[0];
+		const int e1 = NextEdge[e0];
+		const int e2 = PreviousEdge[e0];
+		triangles[0].SetAdj2(e0, &triangles[1] ,e0);
+		triangles[0].SetAdj2(e1, &triangles[1] ,e2);
+		triangles[0].SetAdj2(e2, &triangles[1] ,e1);
+
+		triangles[0].det = -1;  //boundary triangle: det = -1
+		triangles[1].det = -1;  //boundary triangle: det = -1
+
+		triangles[0].SetSingleVertexToTriangleConnectivity();
+		triangles[1].SetSingleVertexToTriangleConnectivity();
+
+		triangles[0].link=&triangles[1];
+		triangles[1].link=&triangles[0];
+
+		//build quadtree
+		if (!quadtree)  quadtree = new BamgQuadtree(this,0);
+		quadtree->Add(*v0);
+		quadtree->Add(*v1);
+
+		/*Now, add the vertices One by One*/
+		long NbSwap=0;
+		if (verbose>3) _printLine_("   Begining of insertion process...");
+
+		for (int icount=2; icounti,det3); //(newvertex->i = integer coordinates)
+
+			//Add newvertex to the quadtree
+			quadtree->Add(*newvertex); 
+
+			//Add newvertex to the existing mesh
+			AddVertex(*newvertex,tcvi,det3);
+
+			//Make the mesh Delaunay around newvertex by swaping the edges
+			NbSwap += newvertex->Optim(1,0);
+		}
+
+		//Display info
+		if (verbose>3) {
+			_printLine_("      NbSwap of insertion: " << NbSwap);
+			_printLine_("      NbSwap/nbv:          " << NbSwap/nbv);
+		}
+
+#ifdef NBLOOPOPTIM
+
+		k0 = rand()%nbv ; 
+		for (int is4=0; is4Optim(0,0);
+			if (verbose>3) {
+				_printLine_("      Optim Loop: " << Nbloop);
+				_printLine_("      NbSwap/nbv:          " << NbSwap/nbv);
+			}
+			if(!NbSwap) break;
+		}
+		CreateSingleVertexToTriangleConnectivity(); 
+		// because we break the TriangleContainingTheVertex
+#endif
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::InsertNewPoints{{{*/
+	long Mesh::InsertNewPoints(long nbvold,long & NbTSwap) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/InsertNewPoints)*/
+
+		long int verbose=0;
+		double seuil= 1.414/2 ;// for two close point 
+		long i;
+		long NbSwap=0;
+		Icoor2 det3[3];
+
+		//number of new points
+		const long nbvnew=nbv-nbvold;
+
+		//display info if required
+		if (verbose>5) _printLine_("      Try to Insert " << nbvnew << " new points");
+
+		//return if no new points
+		if (!nbvnew) return 0; 
+
+		/*construction of a random order*/
+		const long PrimeNumber= BigPrimeNumber(nbv)  ;
+		//remainder of the division of rand() by nbvnew
+		long k3 = rand()%nbvnew;
+		//loop over the new points
+		for (int is3=0; is3ReferenceNumber=i;
+		}
+
+		// for all the new point
+		long iv=nbvold;
+		for (i=nbvold;iToClose(vi,seuil,hi,hj)){
+				// a good new point 
+				BamgVertex &vj = vertices[iv];
+				long  j=vj.ReferenceNumber; 
+				if (&vj!=orderedvertices[j]){
+					_error_("&vj!= orderedvertices[j]");
+				}
+				if(i!=j){ 
+					Exchange(vi,vj);
+					Exchange(orderedvertices[j],orderedvertices[i]);
+				}
+				vj.ReferenceNumber=0; 
+				Triangle *tcvj=TriangleFindFromCoord(vj.i,det3);
+				if (tcvj && !tcvj->link){
+					tcvj->Echo();
+					_error_("problem inserting point in InsertNewPoints (tcvj=" << tcvj << " and tcvj->link=" << tcvj->link << ")");
+				}
+				quadtree->Add(vj);
+				AddVertex(vj,tcvj,det3);
+				NbSwap += vj.Optim(1);          
+				iv++;
+			}
+		} 
+		if (verbose>3) {
+			_printLine_("         number of new points: " << iv);
+			_printLine_("         number of to close (?) points: " << nbv-iv);
+			_printLine_("         number of swap after: " << NbSwap);
+		}
+		nbv = iv;
+
+		for (i=nbvold;i3) _printLine_("   NbSwap=" << NbSwap);
+
+		NbTSwap +=  NbSwap ;
+		return nbv-nbvold;
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::isCracked{{{*/
+	int Mesh::isCracked() const {
+		return NbCrackedVertices != 0;
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::MakeGeomEdgeToEdge{{{*/
+	Edge** Mesh::MakeGeomEdgeToEdge() {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/MakeGeomEdgeToEdge)*/
+
+		if (!Gh.nbe){
+			_error_("!Gh.nbe");
+		}
+		Edge **e= new (Edge* [Gh.nbe]);
+
+		long i;
+		for ( i=0;iGeomEdgeHook; 
+			e[Gh.GetId(GeomEdgeHook)] = ei;    
+		  }
+		for ( i=0;iGeomEdgeHook;
+			 int j= ii;
+			 while (!(*GeomEdgeHook)[j].Required()) { 
+				 Adj(GeomEdgeHook,j); // next geom edge
+				 j=1-j;
+				 if (e[Gh.GetId(GeomEdgeHook)])  break; // optimisation
+				 e[Gh.GetId(GeomEdgeHook)] = ei; 
+			 }
+		 }
+
+		int kk=0;
+		for ( i=0;i (BAMG v1.01, Mesh2.cpp/MakeQuadrangles)*/
+
+		long int verbose=0;
+
+		if (verbose>2) _printLine_("MakeQuadrangles costheta = " << costheta);
+
+		if (costheta >1) {
+			if (verbose>5) _printLine_("   do nothing: costheta > 1");
+		}
+
+
+			long nbqq = (nbt*3)/2;
+			DoubleAndInt *qq = new DoubleAndInt[nbqq];
+
+			long i,ij;
+			int j;
+			long k=0;
+			for (i=0;i=costheta)
+				qq[k++].i3j=i*3+j;
+			//  sort  qq
+			HeapSort(qq,k);
+
+			long kk=0;
+			for (ij=0;ij=costheta) 
+				 triangles[i].SetHidden(j),kk++;
+			  }
+			nbq = kk;
+			if (verbose>2){
+				_printLine_("   number of quadrilaterals    = " << nbq);
+				_printLine_("   number of triangles         = " << nbt-nbtout- nbq*2);
+				_printLine_("   number of outside triangles = " << nbtout);
+			}
+			delete [] qq;
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::MakeBamgQuadtree{{{*/
+	void Mesh::MakeBamgQuadtree() {  
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/MakeBamgQuadtree)*/
+
+		long int verbose=0;
+		if (  !quadtree )  quadtree = new BamgQuadtree(this);
+
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::MaxinalHmax{{{*/
+	double Mesh::MaximalHmax() {
+		return Max(pmax.x-pmin.x,pmax.y-pmin.y);
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::MaxSubDivision{{{*/
+	void  Mesh::MaxSubDivision(double maxsubdiv) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/MaxSubDivision)*/
+
+		long int verbose=0;
+
+		const  double maxsubdiv2 = maxsubdiv*maxsubdiv;
+		if(verbose>1) _printLine_("   Limit the subdivision of a edges in the new mesh by " << maxsubdiv);
+		// for all the edges 
+		// if the len of the edge is to long 
+		long it,nbchange=0;    
+		double lmax=0;
+		for (it=0;it maxsubdiv2){
+					  R2 AC = M.Orthogonal(AB);// the ortogonal vector of AB in M
+						double lc = M(AC,AC);
+						D2xD2 Rt(AB,AC);// Rt.x = AB , Rt.y = AC;
+						D2xD2 Rt1(Rt.inv());
+						D2xD2 D(maxsubdiv2,0,0,lc);
+						D2xD2 MM = Rt1*D*Rt1.t();
+						v0.m =  M = Metric(MM.x.x,MM.y.x,MM.y.y);
+						nbchange++;
+					}
+					M = v1;
+					l = M(AB,AB);
+					lmax = Max(lmax,l);
+					if(l> maxsubdiv2){
+					  R2 AC = M.Orthogonal(AB);// the ortogonal vector of AB in M
+						double lc = M(AC,AC);
+						D2xD2 Rt(AB,AC);// Rt.x = AB , Rt.y = AC;
+						D2xD2 Rt1(Rt.inv());
+						D2xD2 D(maxsubdiv2,0,0,lc);
+						D2xD2  MM = Rt1*D*Rt1.t();
+						v1.m =  M = Metric(MM.x.x,MM.y.x,MM.y.y);
+						nbchange++;
+					}
+				}
+			}
+		}
+		if(verbose>3){
+			_printLine_("      number of metric changes = " << nbchange << ", maximum number of subdivision of a edges before change = " << pow(lmax,0.5));
+		}
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::MetricAt{{{*/
+	Metric Mesh::MetricAt(const R2 & A) const { 
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/MetricAt)*/
+
+		I2 a = R2ToI2(A);
+		Icoor2 deta[3];
+		Triangle * t =TriangleFindFromCoord(a,deta);
+		if (t->det <0) { // outside
+			double ba,bb;
+			AdjacentTriangle edge= CloseBoundaryEdge(a,t,ba,bb) ;
+			return Metric(ba,*edge.EdgeVertex(0),bb,*edge.EdgeVertex(1));}
+		else { // inside
+			double   aa[3];
+			double s = deta[0]+deta[1]+deta[2];
+			aa[0]=deta[0]/s;
+			aa[1]=deta[1]/s;
+			aa[2]=deta[2]/s;
+			return Metric(aa,(*t)[0],(*t)[1],(*t)[2]);
+		}
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::MininalHmin{{{*/
+	double Mesh::MinimalHmin() {
+		return 2.0/coefIcoor;
+	}
+	/*}}}*/
+/*FUNCTION Mesh::NearestVertex{{{*/
+BamgVertex* Mesh::NearestVertex(Icoor1 i,Icoor1 j) {
+	/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/NearestVertex)*/
+	return  quadtree->NearestVertex(i,j); 
+} 
+/*}}}*/
+	/*FUNCTION Mesh::NewPoints{{{*/
+	void  Mesh::NewPoints(Mesh & Bh,BamgOpts* bamgopts,int KeepVertices){
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/NewPoints)*/
+
+		int i,j,k;
+		long NbTSwap=0;
+		long nbtold=nbt;
+		long nbvold=nbv;
+		long Headt=0;
+		long next_t;
+		long* first_np_or_next_t=new long[maxnbt];
+		Triangle* t=NULL;
+
+		/*Recover options*/
+		int verbose=bamgopts->verbose;
+
+		/*First, insert old points if requested*/
+		if (KeepVertices && (&Bh != this) && (nbv+Bh.nbv< maxnbv)){
+			if (verbose>5) _printLine_("         Inserting initial mesh points");
+			for (i=0;i5) _printLine_("         Big loop");
+		do {
+			/*Update variables*/
+			iter++;
+			nbtold=nbt;
+			nbvold=nbv;
+
+			/*We test all triangles*/
+			i=Headt;
+			next_t=-first_np_or_next_t[i];
+			for(t=&triangles[i];i=nbt ){
+					_error_("Index problem in NewPoints (i=" << i << " not in [0 " << nbt-1 << "])");
+				}
+				//change first_np_or_next_t[i]
+				first_np_or_next_t[i] = iter; 
+
+				//Loop over the edges of t
+				for(j=0;j<3;j++){
+					AdjacentTriangle tj(t,j);
+					BamgVertex &vA = *tj.EdgeVertex(0);
+					BamgVertex &vB = *tj.EdgeVertex(1);
+
+					//if t is a boundary triangle, or tj locked, continue
+					if (!t->link)     continue;
+					if (t->det <0)    continue;
+					if (t->Locked(j)) continue;
+
+					AdjacentTriangle tadjj = t->Adj(j);	  
+					Triangle* ta=tadjj;
+
+					//if the adjacent triangle is a boundary triangle, continur
+					if (ta->det<0) continue;	  
+
+					R2 A=vA;
+					R2 B=vB;
+					k=GetId(ta);
+
+					//if this edge has already been done, go to next edge of triangle
+					if(first_np_or_next_t[k]==iter) continue;
+
+					lIntTria.SplitEdge(Bh,A,B);
+					lIntTria.NewPoints(vertices,nbv,maxnbv);
+				  } // end loop for each edge 
+			  }// for triangle   
+
+			if (!InsertNewPoints(nbvold,NbTSwap)) break;
+			for (i=nbtold;it, EdgesVertexTriangle[s->IndexInTriangle][1]);
+				Triangle*        tbegin= (Triangle*) ta;
+				long kt;
+				do { 
+					kt = GetId((Triangle*) ta);
+					if (first_np_or_next_t[kt]>0){
+						first_np_or_next_t[kt]=-Headt;
+						Headt=kt;
+					}
+					if (ta.EdgeVertex(0)!=s){
+						_error_("ta.EdgeVertex(0)!=s");
+					}
+					ta = Next(Adj(ta));
+				} while ( (tbegin != (Triangle*) ta)); 
+			}
+
+		} while (nbv!=nbvold);
+
+		delete []  first_np_or_next_t;
+
+		long NbSwapf =0,NbSwp;
+
+		NbSwp = NbSwapf;
+		for (i=0;i (BAMG v1.01, MeshQuad.cpp/ProjectOnCurve)*/
+
+		void *pA=0,*pB=0;
+		double tA=0,tB=0;
+		R2 A=vA,B=vB;
+		BamgVertex * pvA=&vA, * pvB=&vB;
+		if (vA.IndexInTriangle == IsVertexOnVertex){
+			pA=vA.BackgroundVertexHook;
+		}
+		else if (vA.IndexInTriangle == IsVertexOnEdge){
+			pA=vA.BackgroundEdgeHook->be;
+			tA=vA.BackgroundEdgeHook->abcisse;
+		}
+		else {
+			_error_("ProjectOnCurve On BamgVertex " << BTh.GetId(vA) << " forget call to SetVertexFieldOnBTh");
+		} 
+
+		if (vB.IndexInTriangle == IsVertexOnVertex){
+			pB=vB.BackgroundVertexHook;
+		}
+		else if(vB.IndexInTriangle == IsVertexOnEdge){
+			pB=vB.BackgroundEdgeHook->be;
+			tB=vB.BackgroundEdgeHook->abcisse;
+		}
+		else {
+			_error_("ProjectOnCurve On BamgVertex " << BTh.GetId(vB) << " forget call to SetVertexFieldOnBTh");
+		} 
+		Edge * e = &BhAB;
+		if (!pA || !pB || !e){
+			_error_("!pA || !pB || !e");
+		}
+		// be carefull the back ground edge e is on same geom edge 
+		// of the initiale edge def by the 2 vertex A B;
+		//check Is a background Mesh;   
+		if (e=BTh.edges+BTh.nbe){
+			_error_("e=BTh.edges+BTh.nbe");
+		}
+		// walk on BTh edge 
+		//not finish ProjectOnCurve with BackGround Mesh);
+		// 1 first find a back ground edge contening the vertex A
+		// 2 walk n back gound boundary to find the final vertex B
+
+		if( vA.IndexInTriangle == IsVertexOnEdge) 
+		  { // find the start edge 
+			e = vA.BackgroundEdgeHook->be;	 
+
+		  } 
+		else if (vB.IndexInTriangle == IsVertexOnEdge) 
+		  {
+			theta = 1-theta;
+			Exchange(tA,tB);
+			Exchange(pA,pB);
+			Exchange(pvA,pvB);
+			Exchange(A,B);
+			e =  vB.BackgroundEdgeHook->be;
+
+		  } 
+		else{ // do the search by walking 
+			_error_("case not supported yet");
+		  }
+
+		// find the direction of walking with direction of edge and pA,PB;
+		R2 AB=B-A;
+
+		double cosE01AB = (( (R2) (*e)[1] - (R2) (*e)[0] ) , AB);
+		int kkk=0;
+		int direction = (cosE01AB>0) ? 1 : 0;
+
+		//   double l=0; // length of the edge AB
+		double abscisse = -1;
+
+		for (int step=0;step<2;step++){
+			// 2 times algo:
+			//    1 for computing the length l
+			//    2 for find the vertex 
+			int  iii;
+			BamgVertex  *v0=pvA,*v1; 
+			Edge *neee,*eee;
+			double lg =0; // length of the curve 
+			double te0;
+			// we suppose take the curve's abcisse 
+			for ( eee=e,iii=direction,te0=tA;
+						eee && ((( void*) eee) != pB) && (( void*) (v1=&((*eee)[iii]))) != pB ;
+						neee = eee->adj[iii],iii = 1-neee->Intersection(*eee),eee = neee,v0=v1,te0=1-iii ) { 
+
+				kkk=kkk+1;
+				_assert_(kkk<100);
+				_assert_(eee);
+				double lg0 = lg;
+				double dp = LengthInterpole(v0->m,v1->m,(R2) *v1 - (R2) *v0);
+				lg += dp;
+				if (step && abscisse <= lg) { // ok we find the geom edge 
+					double sss  =   (abscisse-lg0)/dp;
+					double thetab = te0*(1-sss)+ sss*iii;
+					_assert_(thetab>=0 && thetab<=1);
+					BR = VertexOnEdge(&R,eee,thetab);
+					return  Gh.ProjectOnCurve(*eee,thetab,R,GR);
+				  }
+			  }
+			// we find the end 
+			if (v1 != pvB){
+				if (( void*) v1 == pB)
+				 tB = iii;
+
+				double lg0 = lg;
+				_assert_(eee);
+				v1 = pvB;
+				double dp = LengthInterpole(v0->m,v1->m,(R2) *v1 - (R2) *v0);
+				lg += dp;	
+				abscisse = lg*theta;
+				if (abscisse <= lg && abscisse >= lg0 ) // small optimisation we know the lenght because end
+				  { // ok we find the geom edge 
+					double sss  =   (abscisse-lg0)/dp;
+					double thetab = te0*(1-sss)+ sss*tB;
+					_assert_(thetab>=0 && thetab<=1);
+					BR = VertexOnEdge(&R,eee,thetab);
+					return  Gh.ProjectOnCurve(*eee,thetab,R,GR);
+				  }
+			  }
+			abscisse = lg*theta;
+
+		  }
+		_error_("Big bug...");
+		return 0; // just for the compiler 
+	}                  
+	/*}}}*/
+/*FUNCTION Mesh::ReconstructExistingMesh{{{*/
+void Mesh::ReconstructExistingMesh(){
+	/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/FillHoleInMesh)*/
+
+	/*This routine reconstruct an existing mesh to make it CONVEX:
+	 * -all the holes are filled
+	 * -concave boundaries are filled
+	 * A convex mesh is required for a lot of operations. This is why every mesh
+	 * goes through this process.
+	 * This routine also generates mesh properties such as adjencies,...
+	 */
+
+	/*Intermediary*/
+	int verbose=0;
+
+	// generation of the integer coordinate
+
+	// find extrema coordinates of vertices pmin,pmax
+	long i;
+	if(verbose>2) _printLine_("      Reconstruct mesh of " << nbv << " vertices"); 
+
+	//initialize orderedvertices
+	_assert_(orderedvertices);
+	for (i=0;iSortAndAdd(GetId(edges[i][0]),GetId(edges[i][1])));
+	}
+	if (kk != nbe){ 
+		_error_("There are " << kk-nbe << " double edges in the mesh");
+	}
+
+	//Add edges of all triangles in existing mesh
+	long* st = new long[nbt*3];
+	for (i=0;iSortAndAdd(GetId(triangles[i][VerticesOfTriangularEdge[j][0]]),GetId(triangles[i][VerticesOfTriangularEdge[j][1]]));
+
+			long invisible=triangles[i].Hidden(j);
+
+			//If the edge has not been added to st, add it
+			if(st[k]==-1) st[k]=3*i+j;
+
+			//If the edge already exists, add adjacency
+			else if(st[k]>=0) {
+				_assert_(!triangles[i].TriangleAdj(j));
+				_assert_(!triangles[st[k]/3].TriangleAdj((int) (st[k]%3)));
+
+				triangles[i].SetAdj2(j,triangles+st[k]/3,(int)(st[k]%3));
+				if (invisible) triangles[i].SetHidden(j);
+				if (k5) {
+		_printLine_("         info of Mesh:");
+		_printLine_("            - number of vertices    = " << nbv << " "); 
+		_printLine_("            - number of triangles   = " << nbt << " "); 
+		_printLine_("            - number of given edges = " << nbe << " "); 
+		_printLine_("            - number of all edges   = " << edge4->nb()); 
+		_printLine_("            - Euler number 1 - nb of holes = " << nbt-edge4->nb()+nbv); 
+	}
+
+	//check the consistency of edge[].adj and the geometrical required vertex
+	long k=0;
+	for (i=0;inb();i++){
+		if (st[i]>=0){ // edge alone 
+			if (ii(i);
+				orderedvertices[i0] = vertices+i0;
+				long i1=edge4->j(i);
+				orderedvertices[i1] = vertices+i1;
+			}
+			else {
+				k=k+1;
+				if (k<10) {
+					//print only 10 edges
+					_printLine_("Lost boundary edges " << i << " : " << edge4->i(i) << " " << edge4->j(i));
+				}
+				else if (k==10){
+					_printLine_("Other lost boundary edges not shown...");
+				}
+			}
+		}
+	}
+	if(k) {
+		_error_(k << " boundary edges (from the geometry) are not defined as mesh edges");
+	}
+
+	/* mesh generation with boundary points*/
+	long nbvb=0;
+	for (i=0;ii,orderedvertices[1]->i,orderedvertices[i]->i)==0;) 
+	 if  (++i>=nbvb) {
+		 _error_("ReconstructExistingMesh: All the vertices are aligned");
+	 }
+	//Move this vertex (i) to the 2d position in orderedvertices
+	Exchange(orderedvertices[2], orderedvertices[i]);
+
+	/*Reconstruct mesh beginning with 2 triangles*/
+	BamgVertex *  v0=orderedvertices[0], *v1=orderedvertices[1];
+
+	triangles[0](0) = NULL; // Infinite vertex
+	triangles[0](1) = v0;
+	triangles[0](2) = v1;
+
+	triangles[1](0) = NULL;// Infinite vertex
+	triangles[1](2) = v0;
+	triangles[1](1) = v1;
+	const int e0 = OppositeEdge[0];
+	const int e1 = NextEdge[e0];
+	const int e2 = PreviousEdge[e0];
+	triangles[0].SetAdj2(e0, &triangles[1] ,e0);
+	triangles[0].SetAdj2(e1, &triangles[1] ,e2);
+	triangles[0].SetAdj2(e2, &triangles[1] ,e1);
+
+	triangles[0].det = -1;  // boundary triangles
+	triangles[1].det = -1;  // boundary triangles
+
+	triangles[0].SetSingleVertexToTriangleConnectivity();
+	triangles[1].SetSingleVertexToTriangleConnectivity();
+
+	triangles[0].link=&triangles[1];
+	triangles[1].link=&triangles[0];
+
+	if (!quadtree) delete quadtree; //ReInitialise;
+	quadtree = new BamgQuadtree(this,0);
+	quadtree->Add(*v0);
+	quadtree->Add(*v1);
+
+	// vertices are added one by one
+	long NbSwap=0;
+	for (int icount=2; icounti,det3);
+		quadtree->Add(*vi); 
+		AddVertex(*vi,tcvi,det3);
+		NbSwap += vi->Optim(1,1);
+	}
+
+	//enforce the boundary 
+	AdjacentTriangle ta(0,0);
+	long nbloss = 0,knbe=0;
+	for ( i = 0; i < nbe; i++){
+		if (st[i] >=0){ //edge alone => on border
+			BamgVertex &a=edges[i][0], &b=edges[i][1];
+			if (a.t && b.t){
+				knbe++;
+				if (ForceEdge(a,b,ta)<0) nbloss++;
+			}
+		}
+	}
+	if(nbloss) {
+		_error_("we lost " << nbloss << " existing edges other " << knbe);
+	}
+
+	FindSubDomain(1);
+	// remove all the hole 
+	// remove all the good sub domain
+	long krm =0;
+	for (i=0;iSortAndAdd(v0?GetId(v0):nbv,v1? GetId(v1):nbv);
+
+					_assert_(st[k]>=0);
+					tta.SetAdj2(ja,savetriangles + st[k] / 3,(int) (st[k]%3));
+					ta.SetLock();
+					st[k]=-2-st[k]; 
+				}
+			}
+		}
+	}
+	long NbTfillHoll =0;
+	for (i=0;i=0) {
+			savetriangles[savenbt]=triangles[i];
+			savetriangles[savenbt].link=0;
+			savenbt++;
+		}
+	}
+	// gestion of the adj
+	k =0;
+	Triangle * tmax = triangles + nbt;
+	for (i=0;i= triangles && ta < tmax){
+				ta= savetriangles + ta->color;
+				ti.SetAdj2(j,ta,aa);
+				if(lck) ti.SetLocked(j);
+			}
+		}
+	}
+
+	// restore triangles;
+	nbt=savenbt;
+	maxnbt=savemaxnbt;
+	delete [] triangles;
+	delete [] subdomains;
+	triangles = savetriangles;
+	subdomains = savesubdomains;
+	if (k) {
+		_error_("number of triangles edges alone = " << k);
+	}
+	FindSubDomain();
+
+	delete edge4;
+	delete [] st;
+	for (i=0;iAdd(vertices[i]);
+
+	SetVertexFieldOn();
+
+	/*Check requirements consistency*/
+	for (i=0;iIsRequiredVertex()){
+						_printLine_("ReconstructExistingMesh error message: problem with the edge number " << i+1 << ": [" << GetId(edges[i][0])+1 << " " << GetId(edges[i][1])+1 << "]");
+						_printLine_("This edge is on geometrical edge number " << Gh.GetId(edges[i].GeomEdgeHook)+1);
+						if (edges[i][j].GeomEdgeHook->OnGeomVertex())
+						 _printLine_("the vertex number " << GetId(edges[i][j])+1 << " of this edge is a geometric BamgVertex number " << Gh.GetId(edges[i][j].GeomEdgeHook->gv)+1);
+						else if (edges[i][j].GeomEdgeHook->OnGeomEdge())
+						 _printLine_("the vertex number " << GetId(edges[i][j])+1 << " of this edge is a geometric Edge number " << Gh.GetId(edges[i][j].GeomEdgeHook->ge)+1);
+						else
+						 _printLine_("Its pointer is " << edges[i][j].GeomEdgeHook);
+
+						_printLine_("This edge is on geometry and has no adjacent edge (open curve) and one of the tip is not required");
+						_error_("See above (might be cryptic...)");
+					}
+				}
+			}
+		}
+	}
+}
+/*}}}*/
+	/*FUNCTION Mesh::TrianglesRenumberBySubDomain{{{*/
+	void Mesh::TrianglesRenumberBySubDomain(bool justcompress){
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/ReNumberingTheTriangleBySubDomain)*/
+
+		long int verbose=0;
+		long *renu= new long[nbt];
+		register Triangle *t0,*t,*te=triangles+nbt;
+		register long k=0,it,i,j;
+
+		for ( it=0;it= nbt ){
+					_error_("kt<0 || kt >= nbt");
+				}
+				if (renu[kt]!=-1){
+					_error_("renu[kt]!=-1");
+				}
+				renu[kt]=k++;
+			}
+			while (t0 != (t=t->link));
+		  }
+		// take is same numbering if possible    
+		if(justcompress)
+		 for ( k=0,it=0;it=0 ) 
+			renu[it]=k++;
+
+		// put the outside triangles at the end
+		for ( it=0;it= 0) // a new sub cycle
+			{ 
+			 i=it;
+			 Triangle ti=triangles[i],tj;
+			 while ( (j=renu[i]) >= 0) 
+				{ // i is old, and j is new 
+				 renu[i] = -1; // mark 
+				 tj = triangles[j]; // save new
+				 triangles[j]= ti; // new <- old
+				 i=j;     // next 
+				 ti = tj;
+				}  
+			}
+		delete [] renu;
+
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::VerticesRenumber{{{*/
+	void Mesh::VerticesRenumber(long * renu) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/ReNumberingVertex)*/
+
+		// warning be carfull because pointer
+		// from on mesh to over mesh 
+		//  --  so do ReNumbering at the beginning
+		BamgVertex * ve = vertices+nbv;
+		long it,ie,i;
+
+		_printLine_("renumbering triangles");
+		for ( it=0;it=vertices && v < ve)
+			 VerticesOnGeomVertex[i].meshvertex=vertices+renu[GetId(v)];
+		  }
+
+		_printLine_("renumbering vertices on edge");
+		for (i=0;i< NbVerticesOnGeomEdge;i++)
+		  {
+			BamgVertex *v =VerticesOnGeomEdge[i].meshvertex;
+			if (v>=vertices && v < ve)
+			 VerticesOnGeomEdge[i].meshvertex=vertices+renu[GetId(v)];
+		  }
+
+		_printLine_("renumbering vertices on Bth vertex");
+		for (i=0;i< NbVertexOnBThVertex;i++)
+		  {
+			BamgVertex *v=VertexOnBThVertex[i].v;
+			if (v>=vertices && v < ve)
+			 VertexOnBThVertex[i].v=vertices+renu[GetId(v)];
+		  }
+
+		for (i=0;i< NbVertexOnBThEdge;i++)
+		  {
+			BamgVertex *v=VertexOnBThEdge[i].v;
+			if (v>=vertices && v < ve)
+			 VertexOnBThEdge[i].v=vertices+renu[GetId(v)];
+		  }
+
+		// move the Vertices without a copy of the array 
+		// be carefull not trivial code 
+		long j;
+		for ( it=0;it= 0) // a new sub cycle
+			{ 
+			 i=it;
+			 BamgVertex ti=vertices[i],tj;
+			 while ( (j=renu[i]) >= 0){
+				 // i is old, and j is new 
+				 renu[i] = -1-renu[i]; // mark 
+				 tj = vertices[j];     // save new
+				 vertices[j]= ti;      // new <- old
+				 i=j;     // next 
+				 ti = tj;
+				}  
+			}
+		if (quadtree){
+			delete quadtree;
+			quadtree = new BamgQuadtree(this);
+		}
+
+		for ( it=0;it (BAMG v1.01, Mesh2.cpp/SetIntCoor)*/
+
+	/*Set integer coordinate for existing vertices*/
+
+	//Get extrema coordinates of the existing vertices
+	pmin =  vertices[0].r;
+	pmax =  vertices[0].r;
+	long i;
+	for (i=0;i*/
+
+	const  double  sqrt32=sqrt(3.)*0.5; 
+	const double  aireKh=sqrt32*0.5;
+	D2  Beq(1,0),Heq(0.5,sqrt32);
+	D2xD2 Br(D2xD2(Beq,Heq).t());
+	D2xD2 B1r(Br.inv());
+	double gammamn=1e100,hmin=1e100;
+	double gammamx=0,hmax=0;
+	double beta=1e100;
+	double beta0=0;
+	double  alpha2=0;
+	double area=0,Marea=0;
+	// double cf= double(coefIcoor);
+	// double cf2= 6.*cf*cf;
+	int nt=0;
+	for (int it=0;it (BAMG v1.01, Mesh2.cpp/SmoothingVertex)*/
+
+	long int verbose=0;
+	//  if quatree exist remove it end reconstruct
+	if (quadtree) delete quadtree;
+	quadtree=0;
+	CreateSingleVertexToTriangleConnectivity();
+	Triangle vide; // a triangle to mark the boundary vertex
+	Triangle   ** tstart= new Triangle* [nbv];
+	long i,j,k;
+	//   attention si Background == Triangle alors on ne peut pas utiliser la rechech rapide 
+	if ( this == & BTh)
+	 for ( i=0;i2) _printLine_("   SmoothingVertex: nb Iteration = " << nbiter << ", Omega=" << omega);
+	for (k=0;k3) _printLine_("      move max = " << pow(delta,0.5) << ", iteration = " << k << ", nb of swap = " << NbSwap);
+	  }
+
+	delete [] tstart;
+	if (quadtree) quadtree= new BamgQuadtree(this);
+}
+/*}}}*/
+/*FUNCTION Mesh::SmoothMetric{{{*/
+void Mesh::SmoothMetric(double raisonmax) { 
+	/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/SmoothMetric)*/
+
+	long int verbose=0;
+
+	if(raisonmax<1.1) return;
+	if(verbose > 1) _printLine_("   Mesh::SmoothMetric raisonmax = " << raisonmax);
+	CreateSingleVertexToTriangleConnectivity();
+	long i,j,kch,kk,ip;
+	long *first_np_or_next_t0 = new long[nbv];
+	long *first_np_or_next_t1 = new long[nbv];
+	long Head0 =0,Head1=-1;
+	double logseuil= log(raisonmax);
+
+	for(i=0;i=0&& kk++<100) {
+		kch=0;
+		for (i=Head0;i>=0;i=first_np_or_next_t0[ip=i],first_np_or_next_t0[ip]=-1) {
+			//  pour tous les triangles autour du sommet s
+			register Triangle* t= vertices[i].t;
+			if (!t){
+				_error_("!t");
+			}
+			BamgVertex & vi = vertices[i];
+			AdjacentTriangle ta(t,EdgesVertexTriangle[vertices[i].IndexInTriangle][0]);
+			BamgVertex *pvj0 = ta.EdgeVertex(0);
+			while (1) {
+				ta=Previous(Adj(ta));
+				if (vertices+i != ta.EdgeVertex(1)){
+					_error_("vertices+i != ta.EdgeVertex(1)");
+				}
+				BamgVertex & vj = *(ta.EdgeVertex(0));
+				if ( &vj ) {
+					j= &vj-vertices;
+					if (j<0 || j >= nbv){
+						_error_("j<0 || j >= nbv");
+					}
+					R2 Aij = (R2) vj - (R2) vi;
+					double ll =  Norme2(Aij);
+					if (0) {  
+						double hi = ll/vi.m(Aij);
+						double hj = ll/vj.m(Aij);
+						if(hi < hj)
+						  {
+							double dh=(hj-hi)/ll;
+							if (dh>logseuil) {
+								vj.m.IntersectWith(vi.m/(1 +logseuil*ll/hi));
+								if(first_np_or_next_t1[j]<0)
+								 kch++,first_np_or_next_t1[j]=Head1,Head1=j;
+							}
+						  }
+					} 
+					else
+					  {
+						double li = vi.m(Aij);
+						if( vj.m.IntersectWith(vi.m/(1 +logseuil*li)) )
+						 if(first_np_or_next_t1[j]<0) // if the metrix change 
+						  kch++,first_np_or_next_t1[j]=Head1,Head1=j;
+					  }
+				}
+				if  ( &vj ==  pvj0 ) break;
+			}
+		}
+		Head0 = Head1;
+		Head1 = -1;
+		Exchange(first_np_or_next_t0,first_np_or_next_t1);
+	}
+	if(verbose>2) _printLine_("      number of iterations = " << kch); 
+	delete [] first_np_or_next_t0;
+	delete [] first_np_or_next_t1;
+}
+/*}}}*/
+	/*FUNCTION Mesh::SplitElement{{{*/
+	int  Mesh::SplitElement(int choice){
+		/*Original code from Frederic Hecht  (BAMG v1.01, MeshQuad.cpp/SplitElement)*/
+
+		long int verbose=0;
+
+		Direction NoDirOfSearch;
+		const  int withBackground = &BTh != this && &BTh;
+
+		TrianglesRenumberBySubDomain();
+		//int nswap =0;
+		const long nfortria( choice ? 4 : 6);
+		if(withBackground) 
+		  {
+			BTh.SetVertexFieldOn();
+			SetVertexFieldOnBTh();
+		  }
+		else
+		 BTh.SetVertexFieldOn();
+
+		long newnbt=0,newnbv=0;
+		long * kedge = 0;
+		long newnbq=nbq;
+		long * ksplit= 0, * ksplitarray=0;
+		long kkk=0;
+		int ret =0;
+		if (maxnbvSortAndAdd(GetId(edges[i][0]),GetId(edges[i][1])));
+			if (ong) // a geometrical edges 
+			  { 
+				if (withBackground){
+					// walk on back ground mesh 
+					//  newVertexOnBThEdge[ibe++] = VertexOnEdge(vertices[k],bedge,absicsseonBedge); 
+					// a faire -- difficile 
+					// the first PB is to now a background edge between the 2 vertices
+					if (!edgesGtoB){
+						_error_("!edgesGtoB");
+					}
+					ong= ProjectOnCurve(*edgesGtoB[Gh.GetId(edges[i].GeomEdgeHook)],
+								edges[i][0],edges[i][1],0.5,vertices[k],
+								newVertexOnBThEdge[kvb],
+								newVerticesOnGeomEdge[kvg++]);
+					vertices[k].ReferenceNumber= edges[i].ReferenceNumber;
+					vertices[k].DirOfSearch =   NoDirOfSearch;        
+					;
+					// get the Info on background mesh 
+					double s =        newVertexOnBThEdge[kvb];
+					BamgVertex &  bv0  = newVertexOnBThEdge[kvb][0];
+					BamgVertex &  bv1  = newVertexOnBThEdge[kvb][1];
+					// compute the metrix of the new points 
+					vertices[k].m =  Metric(1-s,bv0,s,bv1); 
+					kvb++;
+				  }
+				else 
+				  {
+					ong=Gh.ProjectOnCurve(edges[i],
+								0.5,vertices[k],newVerticesOnGeomEdge[kvg++]);
+					// vertices[k].i = R2ToI2( vertices[k].r);
+					vertices[k].ReferenceNumber = edges[i].ReferenceNumber;
+					vertices[k].DirOfSearch = NoDirOfSearch;
+					vertices[k].m =  Metric(0.5,edges[i][0],0.5,edges[i][1]);	      
+				  }  
+			  }
+			else // straigth line edge ---
+			  { 
+				vertices[k].r = ((R2) edges[i][0] + (R2)  edges[i][1] )*0.5;
+				vertices[k].m =  Metric(0.5,edges[i][0],0.5,edges[i][1]);
+				vertices[k].GeomEdgeHook = 0;
+			  }
+			//vertices[k].i = R2ToI2( vertices[k].r);
+			R2 AB =  vertices[k].r;
+			R2 AA = (A+AB)*0.5;
+			R2 BB = (AB+B)*0.5;
+			vertices[k].ReferenceNumber = edges[i].ReferenceNumber;
+			vertices[k].DirOfSearch = NoDirOfSearch;
+
+			newedges[ie].GeomEdgeHook = Gh.Containing(AA,ong);
+			newedges[ie++].v[1]=vertices+k;
+
+			newedges[ie]=edges[i];
+			newedges[ie].adj[0]=newedges + ie -1;
+			newedges[ie].adj[1]=newedges+(edges[i].adj[1]-edges) ;
+			newedges[ie].GeomEdgeHook =  Gh.Containing(BB,ong);
+			newedges[ie++].v[0]=vertices+k;
+			k++;
+		  }
+		if (edgesGtoB) delete [] edgesGtoB;
+		edgesGtoB=0;
+
+		newnbv=k;
+		newNbVerticesOnGeomEdge=kvg;
+		if (newnbv> maxnbv) goto Error;// bug 
+
+		nbv = k;
+
+
+		kedge = new long[3*nbt+1];
+		ksplitarray = new long[nbt+1];
+		ksplit = ksplitarray +1; // because ksplit[-1] == ksplitarray[0]
+
+		for (i=0;i<3*nbt;i++)
+		 kedge[i]=-1;
+
+		//  
+
+		for (i=0;i= lastT)
+				 t.SetAdj2(j,0,0);// unset adj
+				const BamgVertex & v0 = t[VerticesOfTriangularEdge[j][0]];
+				const BamgVertex & v1 = t[VerticesOfTriangularEdge[j][1]];
+				long  ke =edge4->SortAndFind(GetId(v0),GetId(v1));
+				if (ke>0) 
+				  {
+					long ii = GetId(tt);
+					int  jj = ta;
+					long ks = ke + nbvold;
+					kedge[3*i+j] = ks;
+					if (ii=0){
+						// warning PB roundoff error 
+						if (t.link && ( (aa=Area2( A.r    , t[1].r , t[2].r )) < 0.0 
+										||   (bb=Area2( t[0].r , A.r    , t[2].r )) < 0.0  
+										||   (cc=Area2( t[0].r , t[1].r , A.r    )) < 0.0)){
+							_printLine_(ke + nbvold << " not in triangle " << i << " In= " << !!t.link << " " << aa << " " << bb << " " << cc << " " << dd);
+							_error_("Number of triangles with P2 interpolation Problem");
+						}
+					}
+					else {
+						if (tt.link && ( (aa=Area2( A.r     , tt[1].r , tt[2].r )) < 0 
+										||   (bb=Area2( tt[0].r , A.r     , tt[2].r )) < 0 
+										||   (cc=Area2( tt[0].r , tt[1].r , A.r     )) < 0)){
+							_printLine_(ke + nbvold << " not in triangle " << ii << " In= " << !!tt.link << " " << aa << " " << bb << " " << cc << " " << dd);
+							_error_("Number of triangles with P2 interpolation Problem");
+						}
+					} 
+				  }
+			  }
+		}
+
+		for (i=0;iSortAndFind(GetId(v0),GetId(v1));
+					if (ke<0) // new 
+					  {
+						if (&tt) // internal triangles all the boundary 
+						  { // new internal edges 
+							long ii = GetId(tt);
+							int  jj = ta;
+
+							kedge[3*i+j]=k;// save the vertex number 
+							kedge[3*ii+jj]=k;
+							if (k=0
+						kedge[3*i+j]=nbvold+ke;
+						kkk[nbsplitedge++]=j;// previously splited
+					  }
+				  }
+				else 
+				 kkk[nbsplitedge++]=j;// previously splited
+
+			  } 
+			if (nbinvisible>=2){
+				_error_("nbinvisible>=2");
+			}
+			switch (nbsplitedge) {
+				case 0: ksplit[i]=10; newnbt++; break;   // nosplit
+				case 1: ksplit[i]=20+kkk[0];newnbt += 2; break; // split in 2 
+				case 2: ksplit[i]=30+3-kkk[0]-kkk[1];newnbt += 3; break; // split in 3 
+				case 3:
+						  if (nbinvisible) ksplit[i]=40+invisibleedge,newnbt += 4;
+						  else   ksplit[i]=10*nfortria,newnbt+=nfortria;
+						  break;
+			} 
+			if (ksplit[i]<40){
+				_error_("ksplit[i]<40");
+			}
+		  }
+		//  now do the element split
+		newnbq = 4*nbq;
+		nbv = k;
+		kkk = nbt;
+		ksplit[-1] = nbt;
+		// look on  old true  triangles 
+
+		for (i=0;i=7 || kk<=0){
+				_error_("kk>=7 || kk<=0");
+			}
+
+			// def the numbering   k (edge) i vertex 
+			int k0 = ke;
+			int k1 = NextEdge[k0];
+			int k2 = PreviousEdge[k0];
+			int i0 = OppositeVertex[k0];
+			int i1 = OppositeVertex[k1];
+			int i2 = OppositeVertex[k2];
+
+			Triangle &t0=triangles[i];
+			BamgVertex * v0=t0(i0);           
+			BamgVertex * v1=t0(i1);           
+			BamgVertex * v2=t0(i2);
+
+			if (nbmkadj>=10){
+				_error_("nbmkadj>=10");
+			}
+			// --------------------------
+			AdjacentTriangle ta0(t0.Adj(i0)),ta1(t0.Adj(i1)),ta2(t0.Adj(i2));
+			// save the flag Hidden
+			int hid[]={t0.Hidden(0),t0.Hidden(1),t0.Hidden(2)};
+			// un set all adj -- save Hidden flag --
+			t0.SetAdj2(0,0,hid[0]);
+			t0.SetAdj2(1,0,hid[1]);
+			t0.SetAdj2(2,0,hid[2]);
+			// --  remake 
+			switch  (kk) {
+				case 1: break;// nothing 
+				case 2: // 
+						  {
+							Triangle &t1=triangles[kkk++];
+							t1=t0;
+							if (kedge[3*i+i0]<0){
+								_error_("kedge[3*i+i0]<0");
+							}
+							BamgVertex * v3 = vertices + kedge[3*i+k0];
+
+							t0(i2) = v3;
+							t1(i1) = v3;
+							t0.SetAllFlag(k2,0);
+							t1.SetAllFlag(k1,0);
+						  } 
+						break; 
+				case 3: //
+						  {
+							Triangle &t1=triangles[kkk++];
+							Triangle &t2=triangles[kkk++];
+							t2=t1=t0;
+							if (kedge[3*i+k1]<0){
+								_error_("kedge[3*i+k1]<0");
+							}
+							if (kedge[3*i+k2]<0){
+								_error_("kedge[3*i+k2]<0");
+							}
+
+							BamgVertex * v01 = vertices + kedge[3*i+k2];
+							BamgVertex * v02 = vertices + kedge[3*i+k1]; 
+							t0(i1) = v01; 
+							t0(i2) = v02; 
+							t1(i2) = v02;
+							t1(i0) = v01; 
+							t2(i0) = v02; 
+							t0.SetAllFlag(k0,0);
+							t1.SetAllFlag(k1,0);
+							t1.SetAllFlag(k0,0);
+							t2.SetAllFlag(k2,0);
+						  } 
+						break;
+				case 4: // 
+				case 6: // split in 4 
+						  {
+							Triangle &t1=triangles[kkk++];
+							Triangle &t2=triangles[kkk++];
+							Triangle &t3=triangles[kkk++];
+							t3=t2=t1=t0;
+							if (kedge[3*i+k0] <0 || kedge[3*i+k1]<0 || kedge[3*i+k2]<0){
+								_error_("kedge[3*i+k0] <0 || kedge[3*i+k1]<0 || kedge[3*i+k2]<0");
+							}
+							BamgVertex * v12 = vertices + kedge[3*i+k0];
+							BamgVertex * v02 = vertices + kedge[3*i+k1]; 
+							BamgVertex * v01 = vertices + kedge[3*i+k2];
+							t0(i1) = v01;
+							t0(i2) = v02;
+							t0.SetAllFlag(k0,hid[k0]);
+
+							t1(i0) = v01;
+							t1(i2) = v12;
+							t0.SetAllFlag(k1,hid[k1]);
+
+							t2(i0) = v02;
+							t2(i1) = v12;
+							t2.SetAllFlag(k2,hid[k2]);
+
+							t3(i0) = v12;
+							t3(i1) = v02;
+							t3(i2) = v01;
+
+							t3.SetAllFlag(0,hid[0]);	   
+							t3.SetAllFlag(1,hid[1]);	   
+							t3.SetAllFlag(2,hid[2]);
+
+							if ( kk == 6)
+							  {
+
+								Triangle &t4=triangles[kkk++];
+								Triangle &t5=triangles[kkk++];
+
+								t4 = t3;
+								t5 = t3;
+
+								t0.SetHidden(k0);
+								t1.SetHidden(k1);
+								t2.SetHidden(k2);
+								t3.SetHidden(0);
+								t4.SetHidden(1);
+								t5.SetHidden(2);
+
+								if (nbv < maxnbv ) 
+								  {
+									vertices[nbv].r = ((R2) *v01 + (R2) *v12  + (R2) *v02 ) / 3.0;
+									vertices[nbv].ReferenceNumber =0;
+									vertices[nbv].DirOfSearch =NoDirOfSearch;
+									//vertices[nbv].i = R2ToI2(vertices[nbv].r);
+									double a3[]={1./3.,1./3.,1./3.};
+									vertices[nbv].m = Metric(a3,v0->m,v1->m,v2->m);
+									BamgVertex * vc =  vertices +nbv++;
+									t3(i0) = vc;
+									t4(i1) = vc;
+									t5(i2) = vc;
+
+								  }
+								else
+								 goto Error; 
+							  }
+
+						  } 
+						break;         
+			}
+
+			// save all the new triangles
+			mkadj[nbmkadj++]=i;
+			long jj;
+			if (t0.link) 
+			 for (jj=nbt;jj13){// 13 = 6 + 4 +
+				_error_("nbmkadj>13");
+			}
+
+			if (kk==6)  newnbq+=3;
+			for (jj=ksplit[i-1];jj= maxnbt) goto Error; // bug 
+		if (nbv>= maxnbv) goto Error; // bug 
+		// generation of the new triangles 
+
+		SetIntCoor("In SplitElement"); 
+
+		CreateSingleVertexToTriangleConnectivity();
+		if(withBackground)
+		 BTh.CreateSingleVertexToTriangleConnectivity();
+
+		delete [] edges;
+		edges = newedges;
+		nbe = newnbe;
+		nbq = newnbq;
+
+		for (i=0;i2){
+			_printLine_("   number of quadrilaterals    = " << nbq);
+			_printLine_("   number of triangles         = " << nbt-nbtout- nbq*2);
+			_printLine_("   number of outside triangles = " << nbtout);
+		}
+
+		return 0; //ok
+
+Error:
+		nbv = nbvold;
+		nbt = nbtold;
+		nbtout = nbtoutold;
+		// cleaning memory ---
+		delete [] newedges;
+		if (ksplitarray) delete [] ksplitarray;
+		if (kedge) delete [] kedge;
+		if (newVerticesOnGeomEdge) delete [] newVerticesOnGeomEdge;
+		if (edge4) delete edge4;
+		if(newVertexOnBThEdge) delete []  newVertexOnBThEdge;
+
+		return ret; // ok 
+	}
+	/*}}}*/
+/*FUNCTION Mesh::SplitInternalEdgeWithBorderVertices{{{*/
+long  Mesh::SplitInternalEdgeWithBorderVertices(){
+	/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/SplitInternalEdgeWithBorderVertices)*/
+
+	long NbSplitEdge=0;
+	SetVertexFieldOn();  
+	long it;
+	long nbvold=nbv;
+	long int verbose=2;
+	for (it=0;itlink) {
+				_printLine_("problem inserting point in SplitInternalEdgeWithBorderVertices (tcvj && !tcvj->link)");
+			}
+
+			quadtree->Add(vi);
+			if (!tcvi || tcvi->det<0){// internal
+				_error_("!tcvi || tcvi->det < 0");
+			}
+			AddVertex(vi,tcvi,det3);
+			NbSwap += vi.Optim(1);          
+			iv++;
+		}
+		if (verbose>3) {
+			_printLine_("   number of points: " << iv);
+			_printLine_("   number of swap to  split internal edges with border vertices: " << NbSwap);
+			nbv = iv;
+		}
+	}
+	if (NbSplitEdge>nbv-nbvold) _printLine_("WARNING: not enough vertices  to split all internal edges, we lost " << NbSplitEdge - ( nbv-nbvold) << " edges...");
+	if (verbose>2) _printLine_("SplitInternalEdgeWithBorderVertices: Number of splited edge " << NbSplitEdge);
+
+	return  NbSplitEdge;
+}
+/*}}}*/
+/*FUNCTION Mesh::ToI2{{{*/
+I2 Mesh::R2ToI2(const R2 & P) const {
+	return  I2( (Icoor1) (coefIcoor*(P.x-pmin.x)),(Icoor1) (coefIcoor*(P.y-pmin.y)) );
+}
+/*}}}*/
+/*FUNCTION Mesh::ToR2{{{*/
+R2 Mesh::I2ToR2(const I2 & P) const {
+	return  R2( (double) P.x/coefIcoor+pmin.x, (double) P.y/coefIcoor+pmin.y);
+}
+/*}}}*/
+/*FUNCTION Mesh::TriangleFindFromCoord{{{*/
+Triangle * Mesh::TriangleFindFromCoord(const I2 & B,Icoor2 det3[3], Triangle *tstart) const {
+	/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/FindTriangleContening)*/
+
+	Triangle * t=0;	
+	int j,jp,jn,jj;
+	int counter;
+
+	/*Get starting triangle. Take tsart if provided*/
+	if (tstart) t=tstart;
+
+	/*Else find the closest Triangle using the quadtree*/
+	else {
+
+		/*Check that the quadtree does exist*/
+		if (!quadtree) _error_("no starting triangle provided and no quadtree available");
+
+		/*Call NearestVertex*/
+		BamgVertex *a = quadtree->NearestVertex(B.x,B.y) ;
+
+		/*Check output (Vertex a)*/
+		if (!a)    _error_("problem while trying to find nearest vertex from a given point. No output found");
+		if (!a->t) _error_("no triangle is associated to vertex number " << GetId(a)+1 << " (orphan?)");
+		_assert_(a>=vertices && at;
+		_assert_(t>=triangles && tdet < 0){ 
+
+		/*Get a real vertex from this triangle (k0)*/
+		int k0=(*t)(0)?(((*t)(1)?((*t)(2)?-1:2):1)):0;
+		_assert_(k0>=0);// k0 the NULL vertex
+		int k1=NextVertex[k0],k2=PreviousVertex[k0];
+		det3[k0]=det(B,(*t)[k1],(*t)[k2]);
+		det3[k1]=det3[k2]=-1;     
+		if (det3[k0] > 0) // outside B 
+		 return t; 
+		t = t->TriangleAdj(OppositeEdge[k0]);
+		counter++;
+		_assert_(counter<2);
+	}
+
+	jj=0;
+	detop = det(*(*t)(VerticesOfTriangularEdge[jj][0]),*(*t)(VerticesOfTriangularEdge[jj][1]),B);
+
+	while(t->det>0) { 
+
+		/*Increase counter*/
+		if (++counter>=10000) _error_("Maximum number of iteration reached (threshold = " << counter << ").");
+
+		j= OppositeVertex[jj];
+		det3[j] = detop;  //det(*b,*s1,*s2);
+		jn = NextVertex[j];
+		jp = PreviousVertex[j];
+		det3[jp]= det(*(*t)(j),*(*t)(jn),B);
+		det3[jn] = t->det-det3[j] -det3[jp];
+
+		// count the number k of  det3 <0
+		int k=0,ii[3];
+		if (det3[0] < 0 ) ii[k++]=0; 
+		if (det3[1] < 0 ) ii[k++]=1;
+		if (det3[2] < 0 ) ii[k++]=2;
+		// 0 => ok
+		// 1 => go in way 1
+		// 2 => two way go in way 1 or 2 randomly
+
+		if (k==0) break;
+		if (k==2 && BinaryRand()) Exchange(ii[0],ii[1]);
+		_assert_(k<3);
+		AdjacentTriangle t1 = t->Adj(jj=ii[0]);
+		if ((t1.det() < 0 ) && (k == 2))
+		 t1 = t->Adj(jj=ii[1]);
+		t=t1;
+		j=t1;// for optimisation we now the -det[OppositeVertex[j]];
+		detop = -det3[OppositeVertex[jj]];
+		jj = j;
+	}
+
+	if (t->det<0) // outside triangle 
+	 det3[0]=det3[1]=det3[2]=-1,det3[OppositeVertex[jj]]=detop;
+	return t;
+}
+/*}}}*/
+/*FUNCTION Mesh::TriangleIntNumbering{{{*/
+void Mesh::TriangleIntNumbering(long* renumbering){
+
+	long num=0;
+	for (int i=0;i0) renumbering[i]=num++;
+		else renumbering[i]=-1;
+	}
+	return;   
+}
+/*}}}*/
+/*FUNCTION Mesh::TriangleReferenceList{{{*/
+long  Mesh::TriangleReferenceList(long* reft) const {
+	/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/ConsRefTriangle)*/
+
+	long int verbose=0;
+	register Triangle *t0,*t;
+	register long k=0, num;   
+
+	//initialize all triangles as -1 (outside)
+	for (int it=0;it=0 && numlink));
+		//stop when all triangles of subdomains have been tagged
+
+	}
+	return k;   
+}
+/*}}}*/
+/*FUNCTION Mesh::Triangulate{{{*/
+void Mesh::Triangulate(double* x,double* y,int nods){
+
+	int verbose=0;
+	int i;
+	Metric M1(1);
+
+	/*Initialize mesh*/
+	Init(nods);//this resets nbv to 0
+	nbv=nods;
+
+	//Vertices
+	if(verbose) _printLine_("Reading vertices (" << nbv << ")");
+	for (i=0;i (BAMG v1.01, Mesh2.cpp/GeomToTriangles0)*/
+		/*Generate mesh from geometry*/
+
+		/*Intermediaries*/
+		int                i,j,k;
+		int                nbcurves    = 0;
+		int                NbNewPoints,NbEdgeCurve;
+		double             lcurve,lstep,s;
+		const int          MaxSubEdge  = 10;
+
+		R2          AB;
+		GeomVertex *a, *b;
+		BamgVertex *va,*vb;
+		GeomEdge   *e;
+
+		// add a ref to GH to make sure that it is not destroyed by mistake
+		Gh.NbRef++;
+
+		/*Get options*/
+		int verbose=bamgopts->verbose;
+
+		//build background mesh flag (1 if background, else 0)
+		bool background=(&BTh != this);
+
+		/*Build VerticesOnGeomVertex*/
+
+		//Compute the number of geometrical vertices that we are going to use to mesh
+		for (i=0;i= maxnbv) _error_("too many vertices on geometry: " << NbVerticesOnGeomVertex << " >= " << maxnbv);
+		_assert_(nbv==0);
+		//Build VerticesOnGeomVertex
+		for (i=0;ibeginning of a new curve)*/
+					if (!ei.Mark() && ei[j].Required()){ 
+
+						long  nbvend=0;
+						Edge* PreviousNewEdge=NULL;
+						lstep = -1;
+
+						/*If Edge is required (do that only once for the 2 vertices)*/
+						if(ei.Required()){
+							if (j==0){
+								//do not create internal points if required (take it as is)
+								if(step==0) nbe++;
+								else{ 
+									e=&ei;
+									a=ei(0);
+									b=ei(1);
+
+									//check that edges has been allocated
+									_assert_(edges);
+									edges[nbe].v[0]=a->MeshVertexHook;
+									edges[nbe].v[1]=b->MeshVertexHook;;
+									edges[nbe].ReferenceNumber = e->ReferenceNumber;
+									edges[nbe].GeomEdgeHook = e;
+									edges[nbe].adj[0] = 0;
+									edges[nbe].adj[1] = 0;
+									nbe++;
+								}
+							}
+						}
+
+						/*If Edge is not required: we are on a curve*/
+						else {
+							for (int kstep=0;kstep<=step;kstep++){
+								//kstep=0, compute number of edges (discretize curve)
+								//kstep=1  create the points and edge
+								PreviousNewEdge=0;
+								NbNewPoints=0;
+								NbEdgeCurve=0;
+								if (nbvend>=maxnbv) _error_("maximum number of vertices too low! Check the domain outline or increase maxnbv");
+								lcurve =0;
+								s = lstep; //-1 initially, then length of each sub edge
+
+								/*reminder: i = edge number, j=[0;1] vertex index in edge*/
+								k=j;            // k = vertex index in edge (0 or 1)
+								e=&ei;          // e = reference of current edge
+								a=ei(k);        // a = pointer toward the kth vertex of the current edge
+								va = a->MeshVertexHook; // va = pointer toward mesh vertex associated
+								e->SetMark();   // Mark edge
+
+								/*Loop until we reach the end of the curve*/
+								for(;;){ 
+									k = 1-k;            // other vertx index of the curve
+									b = (*e)(k);        // b = pointer toward the other vertex of the current edge
+									AB= b->r - a->r;   // AB = vector of the current edge
+									Metric MA = background ? BTh.MetricAt(a->r) :a->m ;  //Get metric associated to A
+									Metric MB = background ? BTh.MetricAt(b->r) :b->m ;  //Get metric associated to B
+									double ledge = (MA(AB) + MB(AB))/2;                  //Get edge length in metric
+
+									/* We are now creating the mesh edges from the geometrical edge selected above.
+									 * The edge will be divided according to the metric previously computed and cannot
+									 * be divided more than 10 times (MaxSubEdge). */
+
+									//By default, there is only one subedge that is the geometrical edge itself
+									int NbSubEdge = 1;
+
+									//initialize lSubEdge, holding the length of each subedge (cannot be higher than 10)
+									double lSubEdge[MaxSubEdge];
+
+									//Build Subedges according to the edge length
+									if (ledge < 1.5){
+										//if ledge < 1.5 (between one and 2), take the edge as is
+										lSubEdge[0] = ledge;
+									}
+									//else, divide the edge
+									else {
+										//compute number of subedges (division of the edge), Maximum is 10
+										NbSubEdge = Min( MaxSubEdge, (int) (ledge +0.5));
+										/*Now, we are going to divide the edge according to the metric.
+										 * Get segment by sement along the edge.
+										 * Build lSubEdge, which holds the distance between the first vertex
+										 * of the edge and the next point on the edge according to the 
+										 * discretization (each SubEdge is AB)*/
+										R2 A,B;
+										A=a->r;
+										Metric MAs=MA,MBs;
+										ledge=0; 
+										double x =0, xstep= 1./NbSubEdge;
+										for (int kk=0; kk < NbSubEdge; kk++,A=B,MAs=MBs ) {
+											x += xstep;
+											B =  e->F(k ? x : 1-x);
+											MBs= background ? BTh.MetricAt(B) : Metric(1-x,MA,x,MB);
+											AB = A-B;
+											lSubEdge[kk]=(ledge+=(MAs(AB)+MBs(AB))/2);
+										}
+									}
+
+									double lcurveb = lcurve+ledge;
+
+									/*Now, create corresponding points*/
+									while(s>=lcurve && s<=lcurveb && nbv1){
+											if (ss < (llk=lSubEdge[kkk=(kk0+kk1)/2]))
+											 kk1=kkk,ll1=llk;
+											else
+											 kk0=kkk,ll0=llk;
+										}
+										_assert_(kk1!=kk0);
+
+										/*Curvilinear coordinate in [0 1] of ss in current edge*/
+										// WARNING: This is what we would do
+										// ssa = (ss-ll0)/(ll1-ll0);
+										// aa = (kk0+ssa)/NbSubEdge
+										// This is what Bamg does:
+										double sbb = (ss-ll0)/(ll1-ll0);
+										/*Curvilinear coordinate in [0 1] of ss in current curve*/
+										double bb = (kk1+sbb)/NbSubEdge;
+										double aa = 1-bb;
+
+										// new vertex on edge
+										vb = &vertices[nbv++];
+										vb->m = Metric(aa,a->m,bb,b->m);
+										vb->ReferenceNumber = e->ReferenceNumber;
+										vb->DirOfSearch =NoDirOfSearch;
+										double abcisse = k ? bb : aa;
+										vb->r =  e->F(abcisse);
+										VerticesOnGeomEdge[NbVerticesOnGeomEdge++]= VertexOnGeom(*vb,*e,abcisse);        
+
+										// to take into account the direction of the edge
+										s += lstep;
+										edges[nbe].v[0]=va;
+										edges[nbe].v[1]=vb;
+										edges[nbe].ReferenceNumber =e->ReferenceNumber;
+										edges[nbe].GeomEdgeHook = e;
+										edges[nbe].adj[0] = PreviousNewEdge;
+										if(PreviousNewEdge) PreviousNewEdge->adj[1]=&edges[nbe];
+										PreviousNewEdge=edges+nbe;
+										nbe++;
+										va = vb;
+									}
+									
+									/*We just added one edge to the curve: Go to the next one*/
+									lcurve = lcurveb;
+									e->SetMark();
+									a=b;
+
+									/*If b is required, we are on a new curve->break*/
+									if (b->Required()) break;
+									int kprev=k;
+									k = e->AdjVertexIndex[kprev];// next vertices
+									e = e->Adj[kprev];
+									_assert_(e);
+								}// for(;;)
+								vb = b->MeshVertexHook;
+
+								/*Number of edges in the last disretized curve*/
+								NbEdgeCurve = Max((long) (lcurve +0.5), (long) 1);
+								/*Number of internal vertices in the last disretized curve*/
+								NbNewPoints = NbEdgeCurve-1;
+								if(!kstep){
+									NbVerticesOnGeomEdge0 += NbNewPoints;
+									nbcurves++;
+								}
+								nbvend=nbv+NbNewPoints; 
+								lstep = lcurve / NbEdgeCurve; //approximately one
+							}// end of curve --
+							if (edges) { // last edges of the curves 
+								edges[nbe].v[0]=va;
+								edges[nbe].v[1]=vb;
+								edges[nbe].ReferenceNumber = e->ReferenceNumber;
+								edges[nbe].GeomEdgeHook = e;
+								edges[nbe].adj[0] = PreviousNewEdge;
+								edges[nbe].adj[1] = 0;
+								if(PreviousNewEdge) PreviousNewEdge->adj[1] = & edges[nbe];
+								nbe++;
+							}
+							else nbe += NbEdgeCurve;
+						} // end on  curve ---
+					}
+				}
+			} // for (i=0;i4) _printLine_("      -- current number of vertices = " << nbv);
+		if (verbose>3) _printLine_("      Creating initial Constrained Delaunay Triangulation...");
+		if (verbose>3) _printLine_("         Inserting boundary points");
+		Insert();
+
+		//Force the boundary
+		if (verbose>3) _printLine_("         Forcing boundaries");
+		ForceBoundary();
+
+		//Extract SubDomains
+		if (verbose>3) _printLine_("         Extracting subdomains");
+		FindSubDomain();
+
+		if (verbose>3) _printLine_("      Inserting internal points");
+		NewPoints(*this,bamgopts,0) ;
+		if (verbose>4) _printLine_("      -- current number of vertices = " << nbv);
+	}
+	/*}}}*/
+	/*FUNCTION Mesh::TriangulateFromGeom1{{{*/
+	void Mesh::TriangulateFromGeom1(BamgOpts* bamgopts,int KeepVertices){ 
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/GeomToTriangles1)*/
+
+		/*Get options*/
+		int verbose=bamgopts->verbose;
+
+		Gh.NbRef++;// add a ref to Gh
+
+		/************************************************************************* 
+		 * method in 2 steps
+		 * 1 - compute the number of new edges to allocate
+		 * 2 - construct the edges
+		 * remark:
+		 * in this part we suppose to have a background mesh with the same geometry 
+		 * 
+		 * To construct the discretization of the new mesh we have to 
+		 * rediscretize the boundary of background Mesh 
+		 * because we have only the pointeur from the background mesh to the geometry.
+		 * We need the abcisse of the background mesh vertices on geometry
+		 * so a vertex is 
+		 * 0 on GeomVertex ;
+		 * 1 on GeomEdge + abcisse
+		 * 2 internal 
+		 *************************************************************************/
+
+		//Check that background mesh and current mesh do have the same geometry
+		_assert_(&BTh.Gh==&Gh);
+		BTh.NbRef++; // add a ref to BackGround Mesh
+
+		//Initialize new mesh
+		BTh.SetVertexFieldOn();
+		int* bcurve = new int[Gh.nbcurves]; // 
+
+		/* There are 2 ways to make the loop 
+		* 1) on the geometry 
+		* 2) on the background mesh
+		*  if you do the loop on geometry, we don't have the pointeur on background,
+		*  and if you do the loop in background we have the pointeur on geometry
+		* so do the walk on  background */
+
+		NbVerticesOnGeomVertex=0;
+		NbVerticesOnGeomEdge=0;
+
+		/*STEP 1 copy of Required vertices*/
+
+		int i; 
+		for (i=0;i= maxnbv){
+			_error_("too many vertices on geometry: " << NbVerticesOnGeomVertex << " >= " << maxnbv);
+		}
+
+		VerticesOnGeomVertex = new VertexOnGeom[  NbVerticesOnGeomVertex];
+		VertexOnBThVertex    = new VertexOnVertex[NbVerticesOnGeomVertex];
+
+		//At this point there is NO vertex but vertices should have been allocated by Init
+		_assert_(vertices);
+		for (i=0;i Th
+				VerticesOnGeomVertex[nbv]= VertexOnGeom(vertices[nbv],Gh[i]);
+				nbv++;
+			}
+			else Gh[i].MeshVertexHook=0;
+		} 
+		for (i=0;iMeshVertexHook); // use of Geom -> Th
+				VertexOnBThVertex[NbVertexOnBThVertex++]=VertexOnVertex(gv->MeshVertexHook,bv);
+				gv->MeshVertexHook->m = bv->m; // for taking the metric of the background mesh
+			}
+		}
+		_assert_(NbVertexOnBThVertex==NbVerticesOnGeomVertex); /*This might be due to MaxCornerAngle too small*/
+
+		/*STEP 2: reseed boundary edges*/
+
+		//  find the begining of the curve in BTh
+		Gh.UnMarkEdges();	
+		int bfind=0;
+		for (int i=0;iIsRequiredVertex()){ 
+
+					/*Get curve number*/
+					int nc=ei.GeomEdgeHook->CurveNumber;
+					
+					//_printLine_("Dealing with curve number " << nc);
+					//_printLine_("edge on geometry is same as GhCurve? " << (ei.GeomEdgeHook==Gh.curves[nc].FirstEdge || ei.GeomEdgeHook==Gh.curves[nc].LastEdge)?"yes":"no");
+					//if(ei.GeomEdgeHook==Gh.curves[nc].FirstEdge || ei.GeomEdgeHook==Gh.curves[nc].LastEdge){
+					//	_printLine_("Do we have the right extremity? curve first vertex -> " << ((GeomVertex *)*ei[je].GeomEdgeHook==&(*Gh.curves[nc].FirstEdge)[Gh.curves[nc].FirstVertexIndex])?"yes":"no");
+					//	_printLine_("Do we have the right extremity? curve last  vertex -> " << ((GeomVertex *)*ei[je].GeomEdgeHook==&(*Gh.curves[nc].LastEdge)[Gh.curves[nc].LastVertexIndex])?"yes":"no");
+					//}
+					//BUG FIX from original bamg
+					/*Check that we are on the same edge and right vertex (0 or 1) */
+					if(ei.GeomEdgeHook==Gh.curves[nc].FirstEdge  && (GeomVertex *)*ei[je].GeomEdgeHook==&(*Gh.curves[nc].FirstEdge)[Gh.curves[nc].FirstVertexIndex]){
+						bcurve[nc]=iedge*2+je;
+						bfind++;	
+					}
+					else if ((ei.GeomEdgeHook==Gh.curves[nc].LastEdge  && (GeomVertex *)*ei[je].GeomEdgeHook==&(*Gh.curves[nc].LastEdge)[Gh.curves[nc].LastVertexIndex]) && bcurve[nc]==-1){
+						bcurve[nc]=iedge*2+je;
+						bfind++;	
+					}
+				}
+			}
+		} 
+		if (bfind!=Gh.nbcurves){
+			delete [] bcurve;
+			_error_("problem generating number of curves (" << Gh.nbcurves << " found in the geometry but " << bfind << " curve found in the mesh)");
+		}
+
+		// method in 2 + 1 step 
+		//  0.0) compute the length and the number of vertex to do allocation
+		//  1.0) recompute the length
+		//  1.1) compute the  vertex 
+
+		long nbex=0,NbVerticesOnGeomEdgex=0;
+		for (int step=0; step <2;step++){
+
+			long NbOfNewPoints=0;
+			long NbOfNewEdge=0;
+			long iedge;
+			Gh.UnMarkEdges();	
+			double L=0;
+
+			/*Go through all geometrical curve*/
+			for (int icurve=0;icurveGeomEdgeHook;
+
+					double sNew=Lstep;// abscisse of the new points (phase==1) 
+					L=0;// length of the curve
+					long i=0;// index of new points on the curve
+					register GeomVertex * GA0 = *(*peequi)[k0equi].GeomEdgeHook;
+					BamgVertex *A0;
+					A0 = GA0->MeshVertexHook;  // the vertex in new mesh
+					BamgVertex *A1;
+					VertexOnGeom *GA1;
+					Edge* PreviousNewEdge = 0;
+
+					// New Curve phase 
+					_assert_(A0-vertices>=0 && A0-verticesRequired()){
+						GeomVertex *GA1 = *(*peequi)[1-k0equi].GeomEdgeHook;
+						A1 = GA1->MeshVertexHook;  //
+					}       
+					else {
+						for(;;){
+							Edge &ee=*pe; 
+							Edge &eeequi=*peequi; 
+							k1 = 1-k0; // next vertex of the edge 
+							k1equi= 1 - k0equi;
+							_assert_(pe && ee.GeomEdgeHook);
+							ee.GeomEdgeHook->SetMark();
+							BamgVertex & v0=ee[0], & v1=ee[1];
+							R2 AB=(R2)v1-(R2)v0;
+							double L0=L,LAB;
+							LAB=LengthInterpole(v0.m,v1.m,AB);
+							L+= LAB;
+
+							if (phase){
+								// computation of the new points for the given curve
+								while ((i!=NbCreatePointOnCurve) && sNew<=L) { 
+
+									//some checks
+									_assert_(sNew>=L0);
+									_assert_(LAB);
+									_assert_(vertices && nbv=1.000000001){
+										_error_("Problem creating point on a boundary: se=" << se << " should be in [0 1]");
+									}
+									se = abscisseInterpole(v0.m,v1.m,AB,se,1);
+									if (se<0 || se>1){
+										_error_("Problem creating point on a boundary: se=" << se << " should be in [0 1]");
+									}
+									se = k1         ? se : 1. - se;
+									se = k1==k1equi ? se : 1. - se;
+									VertexOnBThEdge[NbVerticesOnGeomEdge++] = VertexOnEdge(A1,&eeequi,se); // save 
+									ongequi=Gh.ProjectOnCurve(eeequi,se,*A1,*GA1); 
+									A1->ReferenceNumber = eeequi.ReferenceNumber;
+									A1->DirOfSearch =NoDirOfSearch;
+									e->GeomEdgeHook = ongequi;
+									e->v[0]=A0;
+									e->v[1]=A1;
+									e->ReferenceNumber = eeequi.ReferenceNumber;
+									e->adj[0]=PreviousNewEdge;
+
+									if (PreviousNewEdge) PreviousNewEdge->adj[1]=e;
+									PreviousNewEdge=e;
+									A0=A1;
+									sNew += Lstep;
+									if (++i== NbCreatePointOnCurve) break;
+								}
+							}
+
+							//some checks
+							_assert_(ee.GeomEdgeHook->CurveNumber==ei.GeomEdgeHook->CurveNumber);
+							if (ee[k1].GeomEdgeHook->IsRequiredVertex()) {
+								_assert_(eeequi[k1equi].GeomEdgeHook->IsRequiredVertex());
+								register GeomVertex * GA1 = *eeequi[k1equi].GeomEdgeHook;
+								A1=GA1->MeshVertexHook;// the vertex in new mesh
+								_assert_(A1-vertices>=0 && A1-vertices= " << maxnbv);
+				}
+				edges = new Edge[NbOfNewEdge];
+				nbex = NbOfNewEdge;
+				if(NbOfNewPoints) {
+					VerticesOnGeomEdge    = new VertexOnGeom[NbOfNewPoints];
+					NbVertexOnBThEdge     = NbOfNewPoints;
+					VertexOnBThEdge       = new  VertexOnEdge[NbOfNewPoints];
+					NbVerticesOnGeomEdgex = NbOfNewPoints;
+				}
+				NbOfNewPoints =0;
+				NbOfNewEdge = 0;
+			}
+		}
+		_assert_(nbe!=0);
+		delete [] bcurve;
+
+		//Insert points inside existing triangles
+		if (verbose>4) _printLine_("      -- current number of vertices = " << nbv);
+		if (verbose>3) _printLine_("      Creating initial Constrained Delaunay Triangulation...");
+		if (verbose>3) _printLine_("         Inserting boundary points");
+		Insert();
+
+		//Force the boundary
+		if (verbose>3) _printLine_("         Forcing boundaries");
+		ForceBoundary();
+
+		//Extract SubDomains
+		if (verbose>3) _printLine_("         Extracting subdomains");
+		FindSubDomain();
+
+		if (verbose>3) _printLine_("      Inserting internal points");
+		NewPoints(BTh,bamgopts,KeepVertices) ;
+		if (verbose>4) _printLine_("      -- current number of vertices = " << nbv);
+	}
+	/*}}}*/
+
+	/*Intermediary*/
+	/*FUNCTION CloseBoundaryEdge{{{*/
+	AdjacentTriangle CloseBoundaryEdge(I2 A,Triangle *t, double &a,double &b) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/CloseBoundaryEdge)*/
+
+		int k=(*t)(0) ?  ((  (*t)(1) ? ( (*t)(2) ? -1 : 2) : 1  )) : 0;
+		int dir=0;
+		if (k<0){
+			_error_("k<0");
+		}
+		int kkk=0;  
+		Icoor2 IJ_IA,IJ_AJ;
+		AdjacentTriangle edge(t,OppositeEdge[k]);          
+		for (;;edge = dir >0 ? Next(Adj(Next(edge))) : Previous(Adj(Previous(edge)))) {  
+			kkk++;
+			if (kkk>=1000){
+				_error_("kkk>=1000");
+			}
+			BamgVertex  &vI =  *edge.EdgeVertex(0);
+			BamgVertex  &vJ =  *edge.EdgeVertex(1);
+			I2 I=vI, J=vJ, IJ= J-I;
+			IJ_IA = (IJ ,(A-I));
+			if (IJ_IA<0) {
+				if (dir>0) {a=1;b=0;return edge;}// change of signe => I
+				else {dir=-1;
+					continue;}};// go in direction i 
+					IJ_AJ = (IJ ,(J-A));
+					if (IJ_AJ<0) {
+						if(dir<0)  {a=0;b=1;return edge;}            
+						else {dir = 1;
+							continue;}}// go in direction j
+							double IJ2 = IJ_IA + IJ_AJ;
+							if (IJ2==0){
+								_error_("IJ2==0");
+							}
+							a= IJ_AJ/IJ2;
+							b= IJ_IA/IJ2;
+							return edge;
+		  } 
+	}
+	/*}}}*/
+/*FUNCTION ForceEdge{{{*/
+int ForceEdge(BamgVertex &a, BamgVertex & b,AdjacentTriangle & taret)  { 
+	/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/ForceEdge)*/
+
+	int NbSwap =0;
+	if (!a.t || !b.t){ // the 2 vertex is in a mesh
+		_error_("!a.t || !b.t");
+	}
+	int k=0;
+	taret=AdjacentTriangle(0,0); // erreur 
+
+	AdjacentTriangle tta(a.t,EdgesVertexTriangle[a.IndexInTriangle][0]);
+	BamgVertex   *v1, *v2 = tta.EdgeVertex(0),*vbegin =v2;
+	// we turn around a in the  direct direction  
+
+	Icoor2 det2 = v2 ? det(*v2,a,b): -1 , det1;
+	if(v2) // normal case 
+	 det2 = det(*v2,a,b);
+	else { // no chance infini vertex try the next
+		tta= Previous(Adj(tta));
+		v2 = tta.EdgeVertex(0);
+		vbegin =v2;
+		if (!v2){
+			_error_("!v2");
+		}
+		det2 = det(*v2,a,b);
+	}
+
+	while (v2 != &b) {
+		AdjacentTriangle tc = Previous(Adj(tta));    
+		v1 = v2; 
+		v2 = tc.EdgeVertex(0);
+		det1 = det2;
+		det2 =  v2 ? det(*v2,a,b): det2; 
+
+		if((det1 < 0) && (det2 >0)) { 
+			// try to force the edge 
+			BamgVertex * va = &a, *vb = &b;
+			tc = Previous(tc);
+			if (!v1 || !v2){
+				_error_("!v1 || !v2");
+			}
+			Icoor2 detss = 0,l=0,ks;
+			while ((ks=SwapForForcingEdge(  va,  vb, tc, detss, det1,det2,NbSwap)))
+			 if(l++ > 10000000) {
+				 _error_("Loop in forcing Egde, nb de swap=" << NbSwap << ", nb of try swap (" << l << ") too big");
+			 }
+			BamgVertex *aa = tc.EdgeVertex(0), *bb = tc.EdgeVertex(1);
+			if (( aa == &a ) && (bb == &b) ||  (bb ==  &a ) && (aa == &b)) {
+				tc.SetLock();
+				a.Optim(1,0);
+				b.Optim(1,0);
+				taret = tc;
+				return NbSwap;
+			}
+			else 
+			  {
+				taret = tc;
+				return -2; // error  boundary is crossing
+			  }
+		}
+		tta = tc;
+		k++;
+		if (k>=2000){
+			_error_("k>=2000");
+		}
+		if ( vbegin == v2 ) return -1;// error 
+	}
+
+	tta.SetLock();
+	taret=tta;
+	a.Optim(1,0);
+	b.Optim(1,0);
+	return NbSwap; 
+}
+/*}}}*/
+/*FUNCTION swap{{{*/
+void  swap(Triangle *t1,short a1, Triangle *t2,short a2, BamgVertex *s1,BamgVertex *s2,Icoor2 det1,Icoor2 det2){ 
+	/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/swap)*/
+	// --------------------------------------------------------------
+	// short a2=aa[a];// les 2 numero de l arete dans les 2 triangles
+	//                               
+	//               sb                     sb    
+	//             / | \                   /   \                      !
+	//         as1/  |  \                 /a2   \                     !
+	//           /   |   \               /    t2 \                    !
+	//       s1 /t1  | t2 \s2  -->   s1 /___as2___\s2                 !
+	//          \  a1|a2  /             \   as1   /  
+	//           \   |   /               \ t1    /   
+	//            \  |  / as2             \   a1/    
+	//             \ | /                   \   /     
+	//              sa                       sa   
+	//  -------------------------------------------------------------
+	int as1 = NextEdge[a1];
+	int as2 = NextEdge[a2];
+	int ap1 = PreviousEdge[a1];
+	int ap2 = PreviousEdge[a2];
+	(*t1)(VerticesOfTriangularEdge[a1][1]) = s2 ; // avant sb
+	(*t2)(VerticesOfTriangularEdge[a2][1]) = s1  ; // avant sa
+	// mise a jour des 2 adjacences externes 
+	AdjacentTriangle taas1 = t1->Adj(as1),
+						  taas2 = t2->Adj(as2),
+						  tas1(t1,as1), tas2(t2,as2),
+						  ta1(t1,a1),ta2(t2,a2);
+	// externe haut gauche
+	taas1.SetAdj2(ta2, taas1.GetAllFlag_UnSwap());
+	// externe bas droite
+	taas2.SetAdj2(ta1, taas2.GetAllFlag_UnSwap());
+	// remove the Mark  UnMarkSwap 
+	t1->SetUnMarkUnSwap(ap1);
+	t2->SetUnMarkUnSwap(ap2);
+	// interne 
+	tas1.SetAdj2(tas2);
+
+	t1->det = det1;
+	t2->det = det2;
+
+	t1->SetSingleVertexToTriangleConnectivity();
+	t2->SetSingleVertexToTriangleConnectivity();
+} // end swap 
+/*}}}*/
+	/*FUNCTION SwapForForcingEdge{{{*/
+	int SwapForForcingEdge(BamgVertex   *  & pva ,BamgVertex  * &   pvb ,AdjacentTriangle & tt1,Icoor2 & dets1, Icoor2 & detsa,Icoor2 & detsb, int & NbSwap) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/SwapForForcingEdge)*/
+		// l'arete ta coupe l'arete pva pvb
+		// de cas apres le swap sa coupe toujours
+		// on cherche l'arete suivante 
+		// on suppose que detsa >0 et detsb <0
+		// attention la routine echange pva et pvb 
+
+		if(tt1.Locked()) return 0; // frontiere croise 
+
+		AdjacentTriangle tt2 = Adj(tt1);
+		Triangle *t1=tt1,*t2=tt2;// les 2 triangles adjacent
+		short a1=tt1,a2=tt2;// les 2 numero de l arete dans les 2 triangles
+		if ( a1<0 || a1>=3 ){
+			_error_("a1<0 || a1>=3");
+		}
+
+		BamgVertex & sa= (* t1)[VerticesOfTriangularEdge[a1][0]];
+		BamgVertex & s1= (*t1)[OppositeVertex[a1]];
+		BamgVertex & s2= (*t2)[OppositeVertex[a2]];
+
+
+		Icoor2 dets2 = det(*pva,*pvb,s2);
+		Icoor2 det1=t1->det , det2=t2->det ;
+		Icoor2 detT = det1+det2;
+		if ((det1<=0 ) || (det2<=0)){
+			_error_("(det1<=0 ) || (det2<=0)");
+		}
+		if ( (detsa>=0) || (detsb<=0) ){ // [a,b] cut infinite line va,bb
+			_error_("(detsa>=0) || (detsb<=0)");
+		}
+		Icoor2 ndet1 = bamg::det(s1,sa,s2);
+		Icoor2 ndet2 = detT - ndet1;
+
+		int ToSwap =0; //pas de swap
+		if ((ndet1 >0) && (ndet2 >0)) 
+		  { // on peut swaper  
+			if ((dets1 <=0 && dets2 <=0) || (dets2 >=0 && detsb >=0))
+			 ToSwap =1; 
+			else // swap alleatoire 
+			 if (BinaryRand()) 
+			  ToSwap =2; 
+		  }
+		if (ToSwap) NbSwap++,
+		 bamg::swap(t1,a1,t2,a2,&s1,&s2,ndet1,ndet2);
+
+		int ret=1;
+
+		if (dets2 < 0) {// haut
+			dets1 = ToSwap ? dets1 : detsa ;
+			detsa = dets2; 
+			tt1 =  Previous(tt2) ;}
+		else if (dets2 > 0){// bas 
+			dets1 = ToSwap ? dets1 : detsb ;
+			detsb = dets2;
+			//xxxx tt1 = ToSwap ? tt1 : Next(tt2);
+			if(!ToSwap) tt1 =  Next(tt2);
+		}
+		else { // changement de direction 
+			ret = -1;
+			Exchange(pva,pvb);
+			Exchange(detsa,detsb);
+			Exchange(dets1,dets2);
+			Exchange(tt1,tt2);
+			dets1=-dets1;
+			dets2=-dets2;
+			detsa=-detsa;
+			detsb=-detsb;
+
+			if (ToSwap) 
+			 if (dets2 < 0) {// haut
+				 dets1 = (ToSwap ? dets1 : detsa) ;
+				 detsa = dets2; 
+				 tt1 =  Previous(tt2) ;}
+			 else if (dets2 > 0){// bas 
+				 dets1 = (ToSwap ? dets1 : detsb) ;
+				 detsb =  dets2;
+				 if(!ToSwap) tt1 =  Next(tt2);
+			 }
+			 else {// on a fin ???
+				 tt1 = Next(tt2);
+				 ret =0;}
+
+		}
+		return ret;
+	}
+	/*}}}*/
+
+}
Index: /issm/trunk/src/c/classes/bamg/Mesh.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/Mesh.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Mesh.h	(revision 13395)
@@ -0,0 +1,193 @@
+#ifndef _MESH_H_
+#define _MESH_H_
+
+#include "./include.h"
+#include "./BamgOpts.h"
+#include "./BamgMesh.h"
+#include "./BamgGeom.h"
+#include "./Triangle.h"
+#include "./VertexOnGeom.h"
+#include "./VertexOnVertex.h"
+#include "./VertexOnEdge.h"
+#include "./ListofIntersectionTriangles.h"
+
+namespace bamg {
+
+	//classes
+	class Geometry;
+	class CrackedEdge;
+	class BamgQuadtree;
+	class SubDomain;
+
+	class Mesh {
+
+		public:
+
+			Geometry                    & Gh;                    // Geometry
+			Mesh                        & BTh;                   // Background Mesh Bth== *this =>no background
+			BamgVertex                   *vertices;
+			Triangle                     *triangles;
+			Edge                         *edges;
+			BamgQuadtree                 *quadtree;
+			BamgVertex                  **orderedvertices;
+			SubDomain                    *subdomains;
+			long                          NbRef;                 // counter of ref on the this class if 0 we can delete
+			long                          maxnbv,maxnbt;         // nombre max de sommets , de triangles
+			long                          nbv,nbt,nbe,nbq;       // nb of vertices, of triangles, of edges and quadrilaterals
+			long                          nbsubdomains;
+			long                          nbtout;                // Nb of oudeside triangle
+
+			R2                            pmin,pmax;             // extrema
+			double                        coefIcoor;             // coef to integer Icoor1;
+			ListofIntersectionTriangles   lIntTria;
+
+			long                          NbVerticesOnGeomVertex;
+			VertexOnGeom                 *VerticesOnGeomVertex;
+			long                          NbVerticesOnGeomEdge;
+			VertexOnGeom                 *VerticesOnGeomEdge;
+			long                          NbVertexOnBThVertex;
+			VertexOnVertex               *VertexOnBThVertex;
+			long                          NbVertexOnBThEdge;
+			VertexOnEdge                 *VertexOnBThEdge;
+			long                          NbCrackedVertices;
+			long                         *CrackedVertices;
+			long                          NbCrackedEdges;
+			CrackedEdge                  *CrackedEdges;
+
+			//Constructors/Destructors
+			Mesh(BamgGeom* bamggeom,BamgMesh* bamgmesh,BamgOpts* bamgopts);
+			Mesh(int* index,double* x,double* y,int nods,int nels);/*MeshConvert*/
+			Mesh(double* x,double* y,int nods); /*BamgTriangulate*/
+			Mesh(Mesh &,Geometry * pGh=0,Mesh* pBTh=0,long maxnbv_in=0 ); //copy operator
+			Mesh(const Mesh &,const int *flag,const int *bb,BamgOpts* bamgopts); // truncature
+			Mesh(long maxnbv,Mesh & BT,BamgOpts* bamgopts,int keepBackVertices=1);
+			Mesh(long maxnbv,Geometry & G,BamgOpts* bamgopts);
+			~Mesh(); 
+
+			//Operators
+			const BamgVertex &operator[](long i) const { return vertices[i];  };
+			BamgVertex       &operator[](long i) { return vertices[i];        };
+			const Triangle   &operator()(long i) const { return triangles[i]; };
+			Triangle         &operator()(long  i) { return triangles[i];             };
+
+			//Methods
+			void SetIntCoor(const char * from =0);
+			double MinimalHmin();
+			double MaximalHmax();
+			I2 R2ToI2(const R2 & P) const;
+			R2 I2ToR2(const I2 & P) const;
+			void AddVertex(BamgVertex & s,Triangle * t,Icoor2 *  =0) ;
+			void Insert();
+			void Echo(void);
+			void ForceBoundary();
+			void FindSubDomain(int OutSide=0);
+			long TriangleReferenceList(long*) const;
+			void TriangleIntNumbering(long* renumbering);
+			void ShowHistogram() const;
+			void CrackMesh(BamgOpts* bamgopts);
+			void ShowRegulaty() const;
+			void SmoothMetric(double raisonmax) ;
+			void BoundAnisotropy(double anisomax,double hminaniso= 1e-100) ;
+			void MaxSubDivision(double maxsubdiv);
+			Edge** MakeGeomEdgeToEdge();
+			long SplitInternalEdgeWithBorderVertices();
+			void MakeQuadrangles(double costheta);
+			int  SplitElement(int choice);
+			void MakeBamgQuadtree();
+			void NewPoints(Mesh &,BamgOpts* bamgopts,int KeepVertices=1);
+			long InsertNewPoints(long nbvold,long & NbTSwap) ; 
+			void TrianglesRenumberBySubDomain(bool justcompress=false);
+			void VerticesRenumber(long * renu);
+			void SmoothingVertex(int =3,double=0.3);
+			Metric MetricAt (const R2 &) const;
+			GeomEdge* ProjectOnCurve( Edge & AB, BamgVertex &  A, BamgVertex & B,double theta, BamgVertex & R,VertexOnEdge & BR,VertexOnGeom & GR);
+			long GetId(const Triangle & t) const;
+			long GetId(const Triangle * t) const;
+			long GetId(const BamgVertex & t) const;
+			long GetId(const BamgVertex * t) const;
+			long GetId(const Edge & t) const;
+			long GetId(const Edge * t) const;
+			BamgVertex* NearestVertex(Icoor1 i,Icoor1 j) ;
+			Triangle* TriangleFindFromCoord(const I2 & ,Icoor2 [3],Triangle *tstart=0) const;
+			void ReadMesh(int* index,double* x,double* y,int nods,int nels);
+			void ReadMesh(BamgMesh* bamgmesh, BamgOpts* bamgopts);
+			void WriteMesh(BamgMesh* bamgmesh,BamgOpts* bamgopts);
+			void ReadMetric(const BamgOpts* bamgopts);
+			void WriteMetric(BamgOpts* bamgopts);
+			void WriteIndex(int** pindex,int* pnels);
+			void AddMetric(BamgOpts* bamgopts);
+			void BuildMetric0(BamgOpts* bamgopts);
+			void BuildMetric1(BamgOpts* bamgopts);
+			void AddGeometryMetric(BamgOpts* bamgopts);
+			int  isCracked() const;
+			void BuildGeometryFromMesh(BamgOpts* bamgopts=NULL);
+			void ReconstructExistingMesh();
+
+			//Inline methods
+			inline  void CreateSingleVertexToTriangleConnectivity(){
+				for (int i=0;iAdjVertexIndex[i];on=on->Adj[j];
+	}
+	inline double qualite(const BamgVertex &va,const BamgVertex &vb,const BamgVertex &vc){
+		double ret; 
+		I2 ia=va,ib=vb,ic=vc;
+		I2 ab=ib-ia,bc=ic-ib,ac=ic-ia;
+		Icoor2 deta=Det(ab,ac);
+		if (deta <=0) ret = -1;
+		else {
+			double a = sqrt((double) (ac,ac)),
+					 b = sqrt((double) (bc,bc)),
+					 c = sqrt((double) (ab,ab)),
+					 p = a+b+c;
+			double h= Max(Max(a,b),c),ro=deta/p;
+			ret = ro/h;
+		}
+		return ret;
+	}
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/Metric.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/Metric.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Metric.cpp	(revision 13395)
@@ -0,0 +1,353 @@
+#include 
+#include 
+#include 
+
+#include "Metric.h"
+#include "../../include/include.h"
+#include "../../shared/Exceptions/exceptions.h"
+
+using namespace std;
+
+namespace bamg {
+
+	SaveMetricInterpole  LastMetricInterpole;
+
+	/*Constructor/Destructor*/
+	/*FUNCTION Metric::Metric(double a){{{*/
+	Metric::Metric(double a): a11(1/(a*a)),a21(0),a22(1/(a*a)){
+	
+	}/*}}}*/
+	/*FUNCTION Metric::Metric(double a,double b,double c){{{*/
+	Metric::Metric(double a,double b,double c) :a11(a),a21(b),a22(c){
+	
+	}/*}}}*/
+	/*FUNCTION Metric::Metric(const double  a[3],const  Metric& m0, const  Metric& m1,const  Metric&  m2 ){{{*/ 
+	Metric::Metric(const double  a[3],const  Metric& m0, const  Metric& m1,const  Metric& m2 ){
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/Metric)*/
+
+		Metric mab(a[0]*m0.a11 + a[1]*m1.a11 + a[2]*m2.a11,
+					a[0]*m0.a21 + a[1]*m1.a21 + a[2]*m2.a21,
+					a[0]*m0.a22 + a[1]*m1.a22 + a[2]*m2.a22);
+
+		EigenMetric vab(mab);
+
+		R2 v1(vab.v.x,vab.v.y);
+		R2 v2(-v1.y,v1.x);
+
+		double h1 = a[0] / m0(v1) + a[1] / m1(v1) + a[2] / m2(v1);
+		double h2 = a[0] / m0(v2) + a[1] / m1(v2) + a[2] / m2(v2);
+
+		vab.lambda1 =  1 / (h1*h1);
+		vab.lambda2 =  1 / (h2*h2);
+		*this = vab;
+	}
+	/*}}}*/
+	/*FUNCTION Metric::Metric(double  a,const  Metric& ma, double  b,const  Metric& mb){{{*/
+	Metric::Metric(double  a,const  Metric& ma, double  b,const  Metric& mb) { 
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/EigenMetric)*/
+
+		/*Compute metric (linear combination of ma and mb)*/
+		Metric mab(a*ma.a11+b*mb.a11,a*ma.a21+b*mb.a21,a*ma.a22+b*mb.a22);
+
+		/*Get Eigen values and vectors*/
+		EigenMetric vab(mab);
+		R2 v1(vab.v.x,vab.v.y);
+		R2 v2(-v1.y,v1.x);
+
+		/*Modify eigen values (a+b=1)*/
+		double h1 = a/ma(v1) + b/mb(v1);
+		double h2 = a/ma(v2) + b/mb(v2);
+		vab.lambda1 =  1/(h1*h1);
+		vab.lambda2 =  1/(h2*h2);
+		*this=vab;
+	}
+	/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION Metric::det{{{*/
+	double Metric::det() const {
+		return a11*a22-a21*a21;
+	}  /*}}}*/
+	/*FUNCTION Metric::Echo {{{*/
+	void Metric::Echo(void){
+
+		_printLine_("Metric:");
+		_printLine_("   [a11 a21 a22]: [" << a11 << " " << a21 << " " << a22 << "]");
+
+		return;
+	}
+	/*}}}*/
+	/*FUNCTION Metric::IntersectWith{{{*/
+	int Metric::IntersectWith(const Metric& M2) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/IntersectWith)*/
+
+		/*Get a new metric from an existing metric (M1=this)
+		 * and a new metric given in input M2 using a 
+		 * Simultaneous Matrix Reduction:
+		 * If M1 and M2 are 2 metrics, we must build N=M1^-1 M2 (Alauzet2003 p16) 
+		 * the eigen vectors of N form a matrix P
+		 * The new metric M = M1 inter M2 is then given by:
+		 *
+		 *      -T [ max(lambda1, mu1)          0         ]  -1				 
+		 * M = P   [                                      ] P		 
+		 *         [        0            max(lambda2, mu2)] 
+		 *
+		 * where lambdai and mui can be computed using Rayleigh formula: 
+		 *    lambdai = vi' M1 vi
+		 * with vi eigen vectors of N (columns of P)
+		 */
+
+		int         change=0;
+		Metric &M1=*this;
+		D2xD2       P;
+
+		//Get P, eigen vectors of N=inv(M1) M2
+		SimultaneousMatrixReduction(*this,M2,P);
+
+		//extract the eigen vectors of P (columns)
+		R2 v1(P.x.x,P.y.x);
+		R2 v2(P.x.y,P.y.y);
+
+		//compute lambdai mui
+		double lambda1=M1(v1,v1);
+		double lambda2=M1(v2,v2);
+		double mu1=M2(v1,v1);
+		double mu2=M2(v2,v2);
+
+		//check where any change needs to be done on M1
+		if ( lambda1 < mu1 )  change=1,lambda1=mu1;
+		if ( lambda2 < mu2 )  change=1,lambda2=mu2; 
+
+		//update M1 if necessary
+		if (change) {
+			D2xD2 invP(P.inv());
+			D2xD2 D(lambda1,0,0,lambda2); 
+			D2xD2 M(invP.t()*D*invP);
+			a11=M.x.x;
+			a21=0.5*(M.x.y+M.y.x);
+			a22=M.y.y;
+		}
+		return change;
+	}
+	/*}}}*/
+	/*FUNCTION Metric::mul{{{*/
+	R2     Metric::mul(const R2 x)const {
+		return R2(a11*x.x+a21*x.y,a21*x.x+a22*x.y);
+	}/*}}}*/
+
+	/*Intermediary*/
+	/*FUNCTION LengthInterpole{{{*/
+	double LengthInterpole(const Metric& Ma,const  Metric& Mb, R2 AB) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/LengthInterpole)*/
+
+		double k=1./2.;
+		int level=0;
+		static int kkk=0;
+		static  Metric Ms1[32],Ms2[32];
+		static double lMs1[32],lMs2[32];
+		static double K[32];
+		double l=0,sss=0;
+		Ms1[level]=Ma;
+		Ms2[level]=Mb;
+		double sa =  Ma(AB);
+		double sb =  Mb(AB);
+		lMs1[level]=sa;
+		lMs2[level]=sb;
+		K[level]=k;
+		level++;
+		int i=0;
+		double * L= LastMetricInterpole.L, *S = LastMetricInterpole.S;
+		double  sstop = 0.1; // Max(0.6,(sa+sb)/5000);
+		while (level) {
+			level--;
+			Metric M1=Ms1[level];
+			Metric M2=Ms2[level];
+			k=K[level];
+			double s1=  lMs1[level];
+			double s2=  lMs2[level];
+
+			double s= (s1+s2)*k;
+			if( s > sstop   && level < 30 && i < 500-level ) {
+				Metric Mi(0.5,M1,0.5,M2);
+				double si = Mi(AB);
+				if( Abs((s1+s2)-(si+si)) > s1*0.001) 
+				  {
+					k=k/2;
+					// we begin by the end to walk in the correct direction from a to b
+					// due to the stack 
+					Ms1[level]=Mi;
+					Ms2[level]=M2;
+					lMs1[level]=si;
+					lMs2[level]=s2;
+					K[level]=k;
+					level++;
+					Ms1[level]=M1;
+					Ms2[level]=Mi;
+					lMs1[level]=s1;
+					lMs2[level]=si;
+					K[level]=k;
+					level++;
+				  }
+				else
+				 L[i]= l += s,S[i]=sss+=k,i++;
+			}
+			else 
+			 L[i]= l += s,S[i]=sss+=k,i++;
+		}
+		// warning for optimisation S is in [0:0.5] not in [0:1]
+		if (i>=512){
+			_error_("i>=512");
+		}
+		LastMetricInterpole.lab=l;
+		LastMetricInterpole.opt=i;
+		if (i>200 && kkk++<10) _printLine_("WARNING: LengthInterpole: ( i=" << i << " l=" << l << " sss=" << sss << " ) " << sstop); 
+		return l;
+	}
+	/*}}}*/
+	/*FUNCTION SimultaneousMatrixReduction{{{*/
+	void SimultaneousMatrixReduction( Metric M1,  Metric M2, D2xD2 &V) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/ReductionSimultanee)*/
+
+		/*In this routine we must return a matrix V that is composed of the 
+		 * eigen vectors of N=inv(M1) M2.
+		 * Instead of looking at N directly, we are going to use the fact that
+		 * M1 and M2 are symmetrical, positive definite. 
+		 * The eigen values of N are given by solving
+		 *    inv(M1) M2 V = lambda V
+		 * which is equivalent to
+		 *    M2 V = lambda M1 V
+		 * and we will hence solve
+		 *    (M2 - lambda M1) V = 0
+		 */
+
+		//M1 and M2 components
+		double a11=M1.a11,a21=M1.a21,a22=M1.a22;
+		double b11=M2.a11,b21=M2.a21,b22=M2.a22;
+
+		/*To get the eigen values, we solve the following problem:
+		 *    det(M2-lambda M1) = 0
+		 *    (b11 - lambda a11)(b22-lambda a22) - (b21-lambda a21)^2
+		 * and we have the following trinome:
+		 *    a lambda^2 + b lambda + c =0
+		 * with:
+		 *    a = a11 a22 - a21 a21 (=det(M1))
+		 *    b = -a11 b22 -b11 a22 + 2 b21 a21
+		 *    c = b11 b22 - b21 b21 (=det(M2))
+		 *    */
+		const double a= a11*a22  - a21*a21;
+		const double b=-a11*b22 - b11*a22+2*b21*a21;
+		const double c=-b21*b21 + b11*b22;
+		const double bb=b*b,ac=a*c;
+		const double delta= bb-4*ac;
+
+		// first, case of a double root if:
+		//  - all the terms are very small (a??)
+		//  - or : delta is very small
+		if ( (bb + Abs(ac) < 1.0e-34 ) ||  (delta < 1.0e-6*bb) ){
+			//all vectors are eigen vectors -> choose 1,0 and 0,1
+			V= D2xD2(1,0,0,1);
+		}
+
+		//general case: two distinct roots: lambda1 and lambda2
+		else {
+
+			/*Compute eigen values*/
+			const double delta2 = sqrt(delta);
+			double lambda[2];
+			lambda[0]= (-b - delta2)/(2*a);
+			lambda[1]= (-b + delta2)/(2*a);
+
+			/*compute eigen vectors*/
+			double vp[2][2];
+			double v0,v1,v2;
+			double s0,s1;
+
+			for(int i=0;i<2;i++){
+				/*Now, one must find the eigen vectors. For that we use the 
+				 * following property of the inner product
+				 *    (Ax,b) = transp(b) Ax = transp(x) transp(A) b
+				 *           = (transp(A) b ,x)
+				 * Here we are dealing with A= M2 - lambda M1 which is symmetrical:
+				 *    for all (x,y) in R2 
+				 *       ((M2 - lambda M1)x,y)=((M2 - lambda M1)y,x)
+				 * If y is in Ker(M2 - lambda M1):
+				 *    for all x in R2
+				 *       ((M2 - lambda M1)y,x)=0
+				 * This shows that:
+				 *    Ker(M2 - lambda M1) is orthogonal to Im(M2 - lambda M1)
+				 * To find the eigen vectors, we only have to find two vectors
+				 * of the image and take their perpendicular as long as they are
+				 * not 0.
+				 * To do that, we take (1,0) and (0,1) and take the larger norm*/
+
+				//compute V = M2 - lambdai M1
+				v0 = b11 - lambda[i]*a11;
+				v1 = b21 - lambda[i]*a21;
+				v2 = b22 - lambda[i]*a22;
+
+				// compute s1=norm(V(1,0)) and s0=norm(V(0,1))
+				s0 = v0*v0 + v1*v1;
+				s1 = v1*v1 + v2*v2;
+
+				//compute vp1 = (vp1x,vp1y)
+				if(s1 < s0){
+					s0=sqrt(s0);
+					vp[0][i]=   v1/s0;
+					vp[1][i]= - v0/s0;
+				}
+				else{
+					s1=sqrt(s1);
+					vp[0][i]=   v2/s1;
+					vp[1][i]= - v1/s1;
+				}
+			}
+
+			//compute V from vp
+			V=D2xD2(vp[0][0],vp[0][1],vp[1][0],vp[1][1]);
+		}
+	}
+	/*}}}*/
+	/*FUNCTION abscisseInterpole{{{*/
+	double abscisseInterpole(const Metric& Ma,const  Metric& Mb, R2 AB,double s,int optim) { 
+		/*Original code from Frederic Hecht  (BAMG v1.01, Metric.cpp/abscisseInterpole)*/
+
+		if(!optim)  LengthInterpole(Ma,Mb,AB);
+		double l  = s* LastMetricInterpole.lab,r;
+		int j=LastMetricInterpole.opt-1;
+
+		double * L= LastMetricInterpole.L, *S = LastMetricInterpole.S;
+		// warning for optimisation S is the abcisse in [0:0.5]
+		// and L is le lenght 
+		if(l<=L[0]){
+			r=2*S[0]*l/L[0];
+		}
+		else if (l>=L[j]){
+			r=1;
+		}
+		else{
+			int i=0;
+			while (j-i>1){
+				int k;
+				k= (i+j)/2;
+				if(l<=L[k]){
+					j=k;// l<=L[j] 
+				}
+				else{
+					i=k; //  L[i]1 || r<0){
+			_error_("r>1 || r<0");
+		}
+		return r ;
+	}
+	/*}}}*/
+
+}
Index: /issm/trunk/src/c/classes/bamg/Metric.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/Metric.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Metric.h	(revision 13395)
@@ -0,0 +1,138 @@
+#ifndef _METRIC_H
+#define _METRIC_H
+
+#include "./include.h"
+#include "../../shared/Bamg/shared.h"
+#include "R2.h"
+#include 
+
+namespace bamg {
+
+	typedef P2    D2;
+	typedef P2xP2 D2xD2;
+
+	class Metric;
+	class EigenMetric;
+
+	class Metric{
+
+		public:
+
+			//fields
+			double a11,a21,a22;
+
+			//friends
+			friend class EigenMetric;
+
+			//functions
+			Metric():a11(0),a21(0),a22(0){};
+			Metric(const EigenMetric&);
+			Metric(double a);
+			Metric(double a,double b,double c);
+			Metric( double  a,const  Metric& ma, double  b,const  Metric& mb);
+			Metric(const double  a[3],const  Metric& m0,const  Metric& m1,const  Metric& m2 );
+			void        Echo();
+			R2          mul(const R2 x)const;
+			double      det() const;
+			int         IntersectWith(const  Metric& M2);
+			inline void Box(double &hx,double &hy) const;
+
+			/*The following functions must remain the the header file because it is called before Metric
+			 * is compiled by other classes*/
+			R2 Orthogonal(const R2 x){ return R2(-(a21*x.x+a22*x.y),a11*x.x+a21*x.y); }
+			R2 Orthogonal(const I2 x){ return R2(-(a21*x.x+a22*x.y),a11*x.x+a21*x.y); }
+
+			//operators
+			Metric operator*(double c) const {double c2=c*c;return  Metric(a11*c2,a21*c2,a22*c2);} 
+			Metric operator/(double c) const {double c2=1/(c*c);return  Metric(a11*c2,a21*c2,a22*c2);} 
+			operator D2xD2(){ return D2xD2(a11,a21,a21,a22);}
+			double  operator()(R2 x) const { return sqrt(x.x*x.x*a11+2*x.x*x.y*a21+x.y*x.y*a22);};        // length of x in metric sqrt()
+			double  operator()(R2 x,R2 y) const { return x.x*y.x*a11+(x.x*x.y+x.y*y.x)*a21+x.y*y.y*a22;};
+
+	};
+
+	class EigenMetric{
+		public:
+
+			//fields
+			double lambda1,lambda2;
+			D2     v;
+
+			//friends
+			friend  class Metric;
+
+			//functions
+			EigenMetric(const Metric& );
+			EigenMetric(double r1,double r2,const D2& vp1);
+			void   Echo();
+			void   Abs();
+			void   pow(double  p);
+			void   Min(double  a);
+			void   Max(double  a);
+			void   Minh(double h);
+			void   Maxh(double h);
+			void   Isotrope();
+			double hmin()   const;
+			double hmax()   const;
+			double lmax()   const;
+			double lmin()   const;
+			double Aniso2() const;
+			double Aniso()  const;
+			void   BoundAniso(const  double c);
+			inline void BoundAniso2(const double coef);
+
+			//operators
+			void operator *=(double coef){ lambda1*=coef;lambda2*=coef;}
+	};
+
+	class SaveMetricInterpole {
+		friend double LengthInterpole(const Metric& Ma,const  Metric& Mb, R2 AB);
+		friend double abscisseInterpole(const Metric& Ma ,const  Metric& Mb, R2 ,double s,int optim);
+		public:
+		int opt;
+		double lab;
+		double L[1024],S[1024];
+	};
+
+	extern SaveMetricInterpole  LastMetricInterpole; // for optimization 
+	//Functions
+	void  SimultaneousMatrixReduction( Metric M1,  Metric M2,D2xD2 &V);
+	double LengthInterpole(const Metric& Ma,const  Metric& Mb, R2 AB);
+	double abscisseInterpole(const Metric& Ma,const  Metric& Mb, R2 AB,double s,int optim=0);
+
+	//inlines
+	inline void  EigenMetric::BoundAniso2(const double coef){
+		if (coef<=1.00000000001){
+			if (lambda1 < lambda2)
+			 lambda1 = bamg::Max(lambda1,lambda2*coef);
+			else
+			 lambda2 = bamg::Max(lambda2,lambda1*coef);
+		}
+		else{  //TO BE CHECKED
+			if (lambda1 > lambda2)
+			 lambda1 = bamg::Min(lambda1,lambda2*coef);
+			else
+			 lambda2 = bamg::Min(lambda2,lambda1*coef);
+		}
+	}
+	inline Metric::Metric(const EigenMetric& M) {
+		double v00=M.v.x*M.v.x;
+		double v11=M.v.y*M.v.y;
+		double v01=M.v.x*M.v.y;
+		a11=v00*M.lambda1+v11*M.lambda2;
+		a21=v01*(M.lambda1-M.lambda2);
+		a22=v00*M.lambda2+v11*M.lambda1;
+	}
+	inline   void  Metric::Box(double &hx,double &hy) const {
+		double d=  a11*a22-a21*a21;
+		hx = sqrt(a22/d);
+		hy = sqrt(a11/d);
+	}
+	inline double LengthInterpole(double la,double lb) {
+		return ( Abs(la - lb) < 1.0e-6*Max3(la,lb,1.0e-20) ) ?  (la+lb)/2  : la*lb*log(la/lb)/(la-lb);
+	}
+	inline double abscisseInterpole(double la,double lb,double lab,double s){
+		return ( Abs(la - lb) <1.0e-6*Max3(la,lb,1.0e-20))  ? s : (exp(s*lab*(la-lb)/(la*lb))-1)*lb/(la-lb);
+	}
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/R2.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/R2.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/R2.h	(revision 13395)
@@ -0,0 +1,105 @@
+/*Original code from Frederic Hecht  (BAMG v1.01, R2.h)*/
+#ifndef _R2_H
+#define _R2_H
+
+#include 
+
+namespace bamg {
+
+	template  class P2{
+
+		  public:  
+
+			  //fields
+			  R x,y;
+
+			  //functions
+			  P2 () :x(0),y(0) {};
+			  P2 (R a,R b)  :x(a),y(b)  {}
+			  P2 (P2 A,P2 B) : x(B.x-A.x),y(B.y-A.y) {}
+			  void Echo(){
+				  printf("Member of P2:\n");
+				  printf("   x: %g or %i\n",x,x);
+				  printf("   y: %g or %i\n",y,y);
+			  }
+			  //operators
+			  RR       operator,(const P2 & cc) const {return  (RR) x* (RR) cc.x+(RR) y* (RR) cc.y;} //scalar product
+			  P2 operator+(const P2 & cc) const {return P2(x+cc.x,y+cc.y);}
+			  P2 operator-(const P2 & cc) const {return P2(x-cc.x,y-cc.y);}
+			  P2 operator-()  const{return P2(-x,-y);}
+			  P2 operator*(R  cc) const {return P2(x*cc,y*cc);}
+			  P2 operator/(R  cc) const {return P2(x/cc,y/cc);}
+			  P2 operator+=(const  P2 & cc) {x += cc.x;y += cc.y;return *this;}
+			  P2 operator/=(const  R r) {x /= r;y /= r;return *this;}
+			  P2 operator*=(const  R r) {x *= r;y *= r;return *this;}
+			  P2 operator-=(const  P2 & cc) {x -= cc.x;y -= cc.y;return *this;}
+
+	  };
+
+	template  class P2xP2{
+
+		  private:
+
+			  friend P2 operator*(P2 c,P2xP2 cc){
+				  return P2(c.x*cc.x.x + c.y*cc.y.x, c.x*cc.x.y + c.y*cc.y.y);
+			  } 
+		  public:
+
+			  //fields
+			  P2 x,y; 
+
+			  //functions
+			  P2xP2 (): x(),y()  {}
+			  P2xP2 (P2 a,P2 b): x(a),y(b) {}
+			  P2xP2 (P2 a,P2 b,P2 c ): x(b-a),y(c-a) {}
+			  P2xP2 (R xx,R xy,R yx,R yy) :x(xx,xy),y(yx,yy) {}
+			  void Echo(){
+				  printf("Member of P2xP2:\n");
+				  printf("   x.x: %g   x.y: %g\n",x.x,x.y);
+				  printf("   y.x: %g   y.x: %g\n",y.x,y.y);
+			  }
+			  RR          det() const {return (RR) x.x* (RR) y.y - (RR) x.y * (RR) y.x;}
+			  P2xP2 inv()  const{
+				  RR d = (*this).det(); 
+				  return P2xP2((R)( y.y /d) ,(R)(-x.y/d),(R)( -y.x/d) ,(R)( x.x/d) );
+			  };
+			  P2xP2 t()  {return P2xP2(x.x,y.x,x.y,y.y);} //transposer 
+			  P2    tx() {return P2(x.x,y.x);} 
+			  P2    ty() {return P2(x.y,y.y);} 
+			  //Operators
+			  P2     operator*(const P2& c) const {return P2(x.x*c.x + x.y*c.y, y.x*c.x + y.y*c.y);}
+			  P2xP2  operator*(P2xP2 c) const{
+				  return  P2xP2(x.x*c.x.x + x.y*c.y.x,
+							  x.x*c.x.y + x.y*c.y.y,
+							  y.x*c.x.x + y.y*c.y.x,
+							  y.x*c.x.y + y.y*c.y.y);
+			  }
+	  };  
+
+	//inline functions
+	template    
+	  inline RR Det(const P2 x,const P2 y) {
+		  return (RR) x.x * (RR) y.y - (RR) x.y * (RR) y.x ;
+	  } 
+	template    
+	  inline RR Area2 (const P2 a,const P2 b,const P2 c) {
+		  return Det(b-a,c-a) ;
+	  }
+	template    
+	  inline R Norme1 (const P2 x) {
+		  return (Abs(x.x)+Abs(x.y)) ;
+	  } 
+	template    
+	  inline RR Norme2_2 (const P2 x) {
+		  return (RR)x.x*(RR)x.x + (RR)x.y*(RR)x.y ;
+	  } 
+	template    
+	  inline RR Norme2 (const P2 x) {
+		  return sqrt((RR)x.x*(RR)x.x + (RR)x.y*(RR)x.y) ;
+	  } 
+	template    
+	  inline P2 Orthogonal (const P2 x) {
+		  return  P2(-x.y,x.x);
+	  } 
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/SetOfE4.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/SetOfE4.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/SetOfE4.cpp	(revision 13395)
@@ -0,0 +1,120 @@
+#include "../objects.h"
+
+using namespace std;
+namespace bamg {
+
+	/*Constructor*/
+	/*FUNCTION  SetOfEdges4::SetOfEdges4(long mmx,long nnx){{{*/
+	SetOfEdges4::SetOfEdges4(long mmx,long nnx){
+		/*Original code from Frederic Hecht  (BAMG v1.01, SetOfEdges4.cpp/SetOfEdges4)*/
+
+		/*Intermediary*/
+		int i;
+
+		//initialize fields
+		nx   =nnx;   //number of vertices
+		nbax =mmx;   // 3 * number of triangles
+		NbOfEdges=0;
+		head = new long [nx];
+		Edges= new IntEdge[nbax];
+
+		//initialize head (-1 everywhere)
+		i=nx;
+		while(i--) head[i]=-1;
+	}
+	/*}}}*/
+
+	/*Methods*/ 
+	/*FUNCTION  SetOfEdges4::add{{{*/
+	long SetOfEdges4::add(long ii,long jj) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, SetOfEdges4.cpp/add)*/
+
+		/*Intermediary*/
+		int h,n;
+
+		//get n from h (usually h=ii)
+		_assert_(head);
+		n=head[h=Abs(ii)%nx];
+
+		//go through the existing edges that holds h (=ii) and check that 
+		//the edge ii jj is not already in Edge
+		while (n >= 0){
+
+			//if the edge ii jj is already in Edges, return n
+			if (ii == Edges[n].i && jj == Edges[n].j) return n;
+
+			//else go to next edge that holds ii
+			else n = Edges[n].next;
+		}
+
+		//check that nbax <=NbOfEdges
+		if (nbax <=NbOfEdges ) {
+			_error_("SetOfEdges4::add overflow: NbOfEdges=" << NbOfEdges << " > nbax=" << nbax);
+		}
+
+		//update chain
+		Edges[NbOfEdges].i=ii;
+		Edges[NbOfEdges].j=jj;
+		Edges[NbOfEdges].next= head[h];
+		head[h] = NbOfEdges;
+		return NbOfEdges ++;
+	}
+	/*}}}*/
+	/*FUNCTION  SetOfEdges4::find {{{*/
+	long SetOfEdges4::find(long ii,long jj) { 
+		/*Original code from Frederic Hecht  (BAMG v1.01, SetOfEdges4.cpp/find)*/
+
+		/*Intermediary*/
+		int n;
+
+		//check that head is not empty
+		_assert_(head);
+
+		//get n from h (usually h=ii)
+		n=head[Abs(ii)%nx];
+
+		//go through the existing edges that holds h (=ii) and return position in Edge
+		while (n >= 0){
+
+			//if the edge ii jj is already in Edges, return n
+			if (ii == Edges[n].i && jj == Edges[n].j) return n;
+
+			//else go to next edge that holds ii
+			else n = Edges[n].next;
+		}
+
+		//if we reach this point, the edge does not exist return -1
+		return -1;
+	}
+	/*}}}*/
+	/*FUNCTION  SetOfEdges4::i{{{*/
+	long SetOfEdges4::i(long k){
+		return Edges[k].i;
+	}
+	/*}}}*/
+	/*FUNCTION  SetOfEdges4::j{{{*/
+	long SetOfEdges4::j(long k){
+		return Edges[k].j;
+	}
+	/*}}}*/
+	/*FUNCTION  SetOfEdges4::nb{{{*/
+	long SetOfEdges4::nb(){
+		return NbOfEdges;
+	}
+	/*}}}*/
+	/*FUNCTION  SetOfEdges4::newarete{{{*/
+	long SetOfEdges4::newarete(long k){
+		return NbOfEdges == k+1;
+	}
+	/*}}}*/
+	/*FUNCTION  SetOfEdges4::SortAndAdd{{{*/
+	long SetOfEdges4::SortAndAdd (long ii,long jj) {
+		return ii <=jj ? add (ii,jj)  : add (jj,ii) ;
+	}
+	/*}}}*/
+	/*FUNCTION  SetOfEdges4::SortAndFind{{{*/
+	long SetOfEdges4::SortAndFind (long ii,long jj) {
+		return ii <=jj ? find (ii,jj)  : find (jj,ii) ;
+	}
+	/*}}}*/
+}
Index: /issm/trunk/src/c/classes/bamg/SetOfE4.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/SetOfE4.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/SetOfE4.h	(revision 13395)
@@ -0,0 +1,42 @@
+#ifndef _SetOfEdge4_h
+#define _SetOfEdge4_h
+
+namespace bamg {
+
+	class SetOfEdges4;
+
+	class IntEdge{
+		friend class SetOfEdges4;
+		public:
+		long i,j;
+		long next; 
+	};
+
+	class SetOfEdges4 {
+
+		private:
+			long nx,nbax,NbOfEdges;
+			long* head; 
+			IntEdge* Edges;
+
+		public:
+
+			// Constructors
+			SetOfEdges4(long ,long);// nb Edges mx , nb de sommet 
+			~SetOfEdges4() {delete [] head; delete [] Edges;}
+
+			//operators
+			IntEdge & operator[](long k){return  Edges[k];}
+
+			//Methods
+			long add (long ii,long jj);
+			long SortAndAdd (long ii,long jj);
+			long nb();
+			long find (long ii,long jj);
+			long SortAndFind (long ii,long jj);
+			long i(long k);
+			long j(long k);
+			long newarete(long k);
+	};
+}
+#endif 
Index: /issm/trunk/src/c/classes/bamg/SubDomain.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/SubDomain.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/SubDomain.cpp	(revision 13395)
@@ -0,0 +1,28 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "SubDomain.h"
+#include "Mesh.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+
+	/*Methods*/
+	/*FUNCTION SubDomain::Set {{{*/
+	void SubDomain::Set(const Mesh & Th ,long i,Mesh & ThNew){
+		*this = Th.subdomains[i];
+		if ( head-Th.triangles<0 || head-Th.triangles>=Th.nbt){
+			_error_("head-Th.triangles<0 || head-Th.triangles>=Th.nbt");
+		}
+		head = ThNew.triangles + Th.GetId(head) ; 
+		if (edge-Th.edges<0 || edge-Th.edges>=Th.nbe);{
+			_error_("edge-Th.edges<0 || edge-Th.edges>=Th.nbe");
+		}
+		edge = ThNew.edges+ Th.GetId(edge);
+	}
+	/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/SubDomain.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/SubDomain.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/SubDomain.h	(revision 13395)
@@ -0,0 +1,27 @@
+#ifndef _SUBDOMAIN_H_
+#define _SUBDOMAIN_H_
+
+#include "./include.h"
+#include "./Edge.h"
+
+namespace bamg {
+
+	//classes
+	class Triangle;
+	class Mesh;
+
+	class SubDomain {
+
+		public:
+
+			Triangle *head;
+			long      ReferenceNumber;
+			int       direction;   // -1 or 1
+			Edge     *edge;        // to geometrical
+
+			//Methods
+			void Set(const Mesh &,long,Mesh &);
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/Triangle.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/Triangle.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Triangle.cpp	(revision 13395)
@@ -0,0 +1,491 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "../objects.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+	/*FUNCTION Triangle(){{{*/
+	Triangle::Triangle(void){
+
+	}
+	/*}}}*/
+	/*FUNCTION Triangle(Mesh *Th,long i,long j,long k) {{{*/
+	Triangle::Triangle(Mesh *Th,long i,long j,long k) {
+		BamgVertex *v=Th->vertices;
+		long nbv = Th->nbv;
+		if (i<0 || j<0 || k<0){
+			_error_("i<0 || j<0 || k<0");
+		}
+		if (i>=nbv || j>=nbv || k>=nbv){
+			_error_("i>=nbv || j>=nbv || k>=nbv");
+		}
+		vertices[0]=v+i;
+		vertices[1]=v+j;
+		vertices[2]=v+k;
+		adj[0]=adj[1]=adj[2]=0;
+		AdjEdgeIndex[0]=AdjEdgeIndex[1]=AdjEdgeIndex[2]=0;
+		det=0;
+	}
+	/*}}}*/
+	/*FUNCTION Triangle(BamgVertex *v0,BamgVertex *v1,BamgVertex *v2) {{{*/
+	Triangle::Triangle(BamgVertex *v0,BamgVertex *v1,BamgVertex *v2){
+		vertices[0]=v0;
+		vertices[1]=v1;
+		vertices[2]=v2;
+		adj[0]=adj[1]=adj[2]=0;
+		AdjEdgeIndex[0]=AdjEdgeIndex[1]=AdjEdgeIndex[2]=0;
+		if (v0) det=0;
+		else {
+			det=-1;
+			link=NULL;};  
+	}
+	/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION Triangle::Adj{{{*/
+	AdjacentTriangle Triangle::Adj(int i)  const {
+		return AdjacentTriangle(adj[i],AdjEdgeIndex[i]&3);
+	};/*}}}*/
+	/*FUNCTION Triangle::Anisotropy{{{*/
+	double Triangle::Anisotropy() const{
+
+		double lmin,lmax;
+
+		/*Get three vertices A,B and C*/
+		R2 A=*this->vertices[0];
+		R2 B=*this->vertices[1];
+		R2 C=*this->vertices[2];
+
+		/*Compute edges*/
+		R2 e1=B-A;
+		R2 e2=C-A;
+		R2 e3=B-C;
+
+		/*Compute edge length*/
+		double l1=Norme2(e1);
+		double l2=Norme2(e2);
+		double l3=Norme2(e3);
+
+		lmin=l1;
+		lmin=min(lmin,l2);
+		lmin=min(lmin,l3);
+		lmax=l1;
+		lmax=max(lmax,l2);
+		lmax=max(lmax,l3);
+
+		return lmax/lmin;
+	};/*}}}*/
+	/*FUNCTION Triangle::Length{{{*/
+	double Triangle::Length() const{
+
+		double l;
+
+		/*Get three vertices A,B and C*/
+		R2 A=*this->vertices[0];
+		R2 B=*this->vertices[1];
+		R2 C=*this->vertices[2];
+
+		/*Compute edges*/
+		R2 e1=B-A;
+		R2 e2=C-A;
+		R2 e3=B-C;
+
+		/*Compute edge length*/
+		l=Norme2(e1);
+		l=max(l,Norme2(e2));
+		l=max(l,Norme2(e3));
+
+		return l;
+	};/*}}}*/
+	/*FUNCTION Triangle::Echo {{{*/
+	void Triangle::Echo(void){
+
+		int i;
+
+		_printLine_("Triangle:");
+		_printLine_("   vertices pointer towards three vertices");
+		_printLine_("      vertices[0] vertices[1] vertices[2] = " << vertices[0] << " " << vertices[1] << " " << vertices[2]);
+		_printLine_("   adj pointer towards three adjacent triangles");
+		_printLine_("      adj[0] adj[1] adj[2] = " << adj[0] << " " << adj[1] << " " << adj[2]);
+		_printLine_("   det (integer triangle determinant) = " << det);
+		if (link){
+			_printLine_("   link (pointer toward duplicate triangle)= " << link);
+		}
+		else{
+			_printLine_("   color = " << color);
+		}
+
+		_printLine_("\nThree vertices:");
+		for(i=0;i<3;i++){
+			if (vertices[i]){
+				vertices[i]->Echo();
+			}
+			else{
+				_printLine_("   vertex " << i+1 << " does not exist");
+			}
+		}
+
+		return;
+	}
+	/*}}}*/
+	/*FUNCTION Triangle::FindBoundaryEdge{{{*/
+	AdjacentTriangle Triangle::FindBoundaryEdge(int i) const{
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/FindBoundaryEdge)*/
+
+		/*Intermediary*/
+		Triangle* ttc=NULL;
+		int k,j,jc;
+
+		// call current triangle t
+		Triangle* t = (Triangle*)this;
+
+		//is the current triangle inside or outside?
+		int outside=!link  ;
+
+		// EdgesVertexTriangle[3][2] = {{1,2},{2,0},{0,1}};
+		// initialize j as the first vertex of the ith edge
+		j=EdgesVertexTriangle[i][0];
+
+		//Loop over the adjacent triangle of t
+		k=0;
+		do{
+			//keep track of outside
+			int outsidep = outside;
+			//increment k
+			k++;
+			//Get ttc, adjacent triangle of t with respect to vertex j
+			ttc =  t->adj[j];
+			//is the current triangle inside or outside?
+			outside = !ttc->link;
+			//if both previous triangle are outside, return
+			if (outside+outsidep == 1) return AdjacentTriangle(t,j);
+
+			//update t and j
+			t = ttc;
+			//NextEdge[3] = {1,2,0};
+			jc = NextEdge[t->AdjEdgeIndex[j]&3];
+			j = NextEdge[jc];
+
+			//check number of iterations
+			if (k>=2000){
+				_error_("too many iteration in Triangle::FindBoundaryEdge (k>=2000)");
+			}
+		} while (this!= t);
+		//not found, return empty triangle
+		return AdjacentTriangle(NULL,0);
+	}
+	/*}}}*/
+	/*FUNCTION Triangle::GetAllflag{{{*/
+	int    Triangle::GetAllflag(int a){
+		return AdjEdgeIndex[a] & 1020;
+	}/*}}}*/
+	/*FUNCTION Triangle::Hidden{{{*/
+	int    Triangle::Hidden(int a)const {
+		return AdjEdgeIndex[a]&16;
+	} /*}}}*/
+	/*FUNCTION Triangle::Locked{{{*/
+	int    Triangle::Locked(int a)const {
+		return AdjEdgeIndex[a]&4;
+	} /*}}}*/
+	/*FUNCTION Triangle::NuEdgeTriangleAdj{{{*/
+	short  Triangle::NuEdgeTriangleAdj(int i) const {
+		/*Number of the  adjacent edge in adj tria (make sure it is between 0 and 2*/
+		return AdjEdgeIndex[i&3]&3;
+	}/*}}}*/
+	/*FUNCTION Triangle::Optim{{{*/
+	long  Triangle::Optim(short i,int koption) {
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/Optim)*/
+
+		// turn around (positive direction)
+		Triangle *t=this;
+		long NbSwap =0;
+		int  k = 0;
+		int  j = OppositeEdge[i];
+		int  jp= PreviousEdge[j];
+
+		// initialize tp, jp the previous triangle & edge
+		Triangle *tp=adj[jp];
+		jp = AdjEdgeIndex[jp]&3;
+		do {
+			while (t->swap(j,koption)){
+				if (k>=20000) _error_("k>=20000");
+				NbSwap++;
+				k++;
+				t=  tp->adj[jp];      // set unchange t qnd j for previous triangles
+				j=  NextEdge[tp->AdjEdgeIndex[jp]&3];
+			}
+			// end on this  Triangle 
+			tp = t;
+			jp = NextEdge[j];
+
+			t=  tp->adj[jp];      // set unchange t qnd j for previous triangles
+			j=  NextEdge[tp->AdjEdgeIndex[jp]&3];
+
+		} while( t != this);
+		return NbSwap;
+	}
+	/*}}}*/
+	/*FUNCTION Triangle::Quadrangle {{{*/
+	Triangle* Triangle::Quadrangle(BamgVertex * & v0,BamgVertex * & v1,BamgVertex * & v2,BamgVertex * & v3) const{
+		// return the other triangle of the quad if a quad or 0 if not a quat
+		Triangle * t =0;
+		if (link) {
+			int a=-1;
+			if (AdjEdgeIndex[0] & 16 ) a=0;
+			if (AdjEdgeIndex[1] & 16 ) a=1;
+			if (AdjEdgeIndex[2] & 16 ) a=2;
+			if (a>=0) {
+				t = adj[a];
+				//  if (t-this<0) return 0;
+				v2 = vertices[VerticesOfTriangularEdge[a][0]];
+				v0 = vertices[VerticesOfTriangularEdge[a][1]];
+				v1 = vertices[OppositeEdge[a]];
+				v3 = t->vertices[OppositeEdge[AdjEdgeIndex[a]&3]];
+			}
+		}
+		return t;
+	}
+	/*}}}*/
+	/*FUNCTION Triangle::QualityQuad {{{*/
+	double   Triangle::QualityQuad(int a,int option) const{
+		double q;
+		if (!link || AdjEdgeIndex[a] &4)
+		 q=  -1;
+		else {
+			Triangle * t = adj[a];
+			if (t-this<0) q=  -1;// because we do 2 times 
+			else if (!t->link ) q=  -1;
+			else if (AdjEdgeIndex[0] & 16 || AdjEdgeIndex[1] & 16  || AdjEdgeIndex[2] & 16 || t->AdjEdgeIndex[0] & 16 || t->AdjEdgeIndex[1] & 16 || t->AdjEdgeIndex[2] & 16 )
+			 q= -1;
+			else if(option){ 
+				const BamgVertex & v2 = *vertices[VerticesOfTriangularEdge[a][0]];
+				const BamgVertex & v0 = *vertices[VerticesOfTriangularEdge[a][1]];
+				const BamgVertex & v1 = *vertices[OppositeEdge[a]];
+				const BamgVertex & v3 = * t->vertices[OppositeEdge[AdjEdgeIndex[a]&3]];
+				q =  QuadQuality(v0,v1,v2,v3); // do the float part
+			}
+			else q= 1;
+		}
+		return  q;
+	}
+	/*}}}*/
+	/*FUNCTION Triangle::Renumbering(Triangle *tb,Triangle *te, long *renu){{{*/
+	void  Triangle::Renumbering(Triangle *tb,Triangle *te, long *renu){
+
+		if (link  >=tb && link  =tb && adj[0] =tb && adj[1] =tb && adj[2] =vb && vertices[0] =vb && vertices[1] =vb && vertices[2] = Th.triangles && link  < Th.triangles + Th.nbt)
+		 link = ThNew.triangles + Th.GetId(link);
+	}
+	/*}}}*/
+	/*FUNCTION Triangle::SetAdjAdj{{{*/
+	void Triangle::SetAdjAdj(short a){
+		// Copy all the mark 
+		a &= 3;
+		register Triangle *tt=adj[a];
+		AdjEdgeIndex [a] &= 55; // remove MarkUnSwap
+		register short aatt = AdjEdgeIndex[a] & 3;
+		if(tt){ 
+			tt->adj[aatt]=this;
+			tt->AdjEdgeIndex[aatt]=a + (AdjEdgeIndex[a] & 60 ) ;
+		}
+	}/*}}}*/
+	/*FUNCTION Triangle::SetAdj2{{{*/
+	void Triangle::SetAdj2(short a,Triangle *t,short aat){
+		/*For current triangle:
+		 * - a is the index of the edge were the adjency is set (in [0 2])
+		 * - t is the adjacent triangle
+		 * - aat is the index of the same edge in the adjacent triangle*/
+		adj[a]=t;
+		AdjEdgeIndex[a]=aat;
+		if(t){ //if t!=NULL add adjacent triangle to t (this)
+			t->adj[aat]=this;
+			t->AdjEdgeIndex[aat]=a;
+		}
+	}/*}}}*/
+	/*FUNCTION Triangle::SetAllFlag{{{*/
+	void   Triangle::SetAllFlag(int a,int f){
+		AdjEdgeIndex[a] = (AdjEdgeIndex[a] &3) + (1020 & f);
+	}/*}}}*/
+	/*FUNCTION Triangle::SetDet{{{*/
+	void Triangle::SetDet() {
+		if(vertices[0] && vertices[1] && vertices[2])    det = bamg::det(*vertices[0],*vertices[1],*vertices[2]);
+		else det = -1; 
+	}/*}}}*/
+	/*FUNCTION Triangle::SetHidden{{{*/
+	void Triangle::SetHidden(int a){
+		//Get Adjacent Triangle number a
+		register Triangle* t = adj[a];
+		//if it exist
+		//C|=D -> C=(C|D) bitwise inclusive OR
+		if(t) t->AdjEdgeIndex[AdjEdgeIndex[a] & 3] |=16;
+		AdjEdgeIndex[a] |= 16;
+	}/*}}}*/
+	/*FUNCTION Triangle::SetLocked{{{*/
+	void Triangle::SetLocked(int a){
+		//mark the edge as on Boundary
+		register Triangle * t = adj[a];
+		t->AdjEdgeIndex[AdjEdgeIndex[a] & 3] |=4;
+		AdjEdgeIndex[a] |= 4;
+	}/*}}}*/
+	/*FUNCTION Triangle::SetMarkUnSwap{{{*/
+	void Triangle::SetMarkUnSwap(int a){
+		register Triangle * t = adj[a];
+		t->AdjEdgeIndex[AdjEdgeIndex[a] & 3] |=8;
+		AdjEdgeIndex[a] |=8 ;
+	}/*}}}*/
+	/*FUNCTION Triangle::SetSingleVertexToTriangleConnectivity{{{*/
+	void Triangle::SetSingleVertexToTriangleConnectivity() { 
+		if (vertices[0]) (vertices[0]->t=this,vertices[0]->IndexInTriangle=0);
+		if (vertices[1]) (vertices[1]->t=this,vertices[1]->IndexInTriangle=1);
+		if (vertices[2]) (vertices[2]->t=this,vertices[2]->IndexInTriangle=2);
+	}/*}}}*/
+	/*FUNCTION Triangle::SetUnMarkUnSwap{{{*/
+	void Triangle::SetUnMarkUnSwap(int a){ 
+		register Triangle * t = adj[a];
+		t->AdjEdgeIndex[AdjEdgeIndex[a] & 3] &=55; // 23 + 32 
+		AdjEdgeIndex[a] &=55 ;
+	}/*}}}*/
+	/*FUNCTION Triangle::swap{{{*/
+	int Triangle::swap(short a,int koption){
+		/*Original code from Frederic Hecht  (BAMG v1.01, Mesh2.cpp/swap)*/
+
+		if(a/4 !=0) return 0;// arete lock or MarkUnSwap
+
+		register Triangle *t1=this,*t2=adj[a];// les 2 triangles adjacent
+		register short a1=a,a2=AdjEdgeIndex[a];// les 2 numero de l arete dans les 2 triangles
+		if(a2/4 !=0) return 0; // arete lock or MarkUnSwap
+
+		register BamgVertex  *sa=t1->vertices[VerticesOfTriangularEdge[a1][0]];
+		register BamgVertex  *sb=t1->vertices[VerticesOfTriangularEdge[a1][1]];
+		register BamgVertex  *s1=t1->vertices[OppositeVertex[a1]];
+		register BamgVertex  *s2=t2->vertices[OppositeVertex[a2]];
+
+		Icoor2 det1=t1->det , det2=t2->det ;
+		Icoor2 detT = det1+det2;
+		Icoor2 detA = Abs(det1) + Abs(det2);
+		Icoor2 detMin = Min(det1,det2);
+
+		int OnSwap = 0;       
+		// si 2 triangle infini (bord) => detT = -2;
+		if (sa == 0) {// les deux triangles sont frontieres
+			det2=bamg::det(s2->i,sb->i,s1->i);
+			OnSwap = det2 >0;}
+		else if (sb == 0) { // les deux triangles sont frontieres
+			det1=bamg::det(s1->i,sa->i,s2->i);
+			OnSwap = det1 >0;}
+		else if(( s1 != 0) && (s2 != 0) ) {
+			det1 = bamg::det(s1->i,sa->i,s2->i);
+			det2 = detT - det1;
+			OnSwap = (Abs(det1) + Abs(det2)) < detA;
+
+			Icoor2 detMinNew=Min(det1,det2);
+			//     if (detMin<0 && (Abs(det1) + Abs(det2) == detA)) OnSwap=BinaryRand();// just for test   
+			if (! OnSwap &&(detMinNew>0)) {
+				OnSwap = detMin ==0;
+				if (! OnSwap) {
+					int  kopt = koption;
+					while (1)
+					 if(kopt) {
+						 // critere de Delaunay pure isotrope
+						 register Icoor2 xb1 = sb->i.x - s1->i.x,
+									 x21 = s2->i.x - s1->i.x,
+									 yb1 = sb->i.y - s1->i.y,
+									 y21 = s2->i.y - s1->i.y,
+									 xba = sb->i.x - sa->i.x, 
+									 x2a = s2->i.x - sa->i.x,
+									 yba = sb->i.y - sa->i.y,
+									 y2a = s2->i.y - sa->i.y;
+						 register double
+							cosb12 =  double(xb1*x21 + yb1*y21),
+									 cosba2 =  double(xba*x2a + yba*y2a) ,
+									 sinb12 = double(det2),
+									 sinba2 = double(t2->det);
+
+
+						 // angle b12 > angle ba2 => cotg(angle b12) < cotg(angle ba2)
+						 OnSwap =  ((double) cosb12 * (double)  sinba2) <  ((double) cosba2 * (double) sinb12);
+						 break;
+					 }
+					 else {	
+						 // critere de Delaunay anisotrope 
+						 double som;
+						 I2 AB=(I2) *sb - (I2) *sa;
+						 I2 MAB2=((I2) *sb + (I2) *sa);
+						 R2 MAB(MAB2.x*0.5,MAB2.y*0.5);
+						 I2 A1=(I2) *s1 - (I2) *sa;
+						 I2 D = (I2) * s1 - (I2) * sb ;
+						 R2 S2(s2->i.x,s2->i.y);
+						 R2 S1(s1->i.x,s1->i.y);
+							{
+							 Metric M=s1->m;
+							 R2 ABo = M.Orthogonal(AB);
+							 R2 A1o = M.Orthogonal(A1);
+							 // (A+B)+ x ABo = (S1+B)/2+ y A1 
+							 // ABo x - A1o y =  (S1+B)/2-(A+B)/2 = (S1-B)/2 = D/2
+							 double dd = Abs(ABo.x*A1o.y)+Abs(ABo.y*A1o.x);
+							 double d = (ABo.x*A1o.y - ABo.y*A1o.x)*2; // because D/2
+							 if (Abs(d) > dd*1.e-3) {
+								 R2 C(MAB+ABo*((D.x*A1o.y - D.y*A1o.x)/d));
+								 som  = M(C - S2)/M(C - S1);
+							 } else 
+								{kopt=1;continue;}
+
+							}
+							{
+							 Metric M=s2->m;
+							 R2 ABo = M.Orthogonal(AB);
+							 R2 A1o = M.Orthogonal(A1);
+							 // (A+B)+ x ABo = (S1+B)/2+ y A1 
+							 // ABo x - A1o y =  (S1+B)/2-(A+B)/2 = (S1-B)/2 = D/2 
+							 double dd = Abs(ABo.x*A1o.y)+Abs(ABo.y*A1o.x);
+							 double d = (ABo.x*A1o.y - ABo.y*A1o.x)*2; // because D/2
+							 if(Abs(d) > dd*1.e-3) {
+								 R2 C(MAB+ABo*((D.x*A1o.y - D.y*A1o.x)/d));
+								 som  += M(C - S2)/M(C -  S1);
+							 } else 
+								{kopt=1;continue;}
+							}
+						 OnSwap = som < 2;
+						 break;
+					 }
+
+				} // OnSwap 
+			} // (! OnSwap &&(det1 > 0) && (det2 > 0) )
+		}
+		if( OnSwap ) 
+		 bamg::swap(t1,a1,t2,a2,s1,s2,det1,det2);
+		else {
+			t1->SetMarkUnSwap(a1);     
+		}
+		return OnSwap;
+	}
+	/*}}}*/
+	/*FUNCTION Triangle::TriangleAdj{{{*/
+	Triangle* Triangle::TriangleAdj(int i) const {
+		return adj[i&3];
+	}/*}}}*/
+
+}
Index: /issm/trunk/src/c/classes/bamg/Triangle.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/Triangle.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/Triangle.h	(revision 13395)
@@ -0,0 +1,76 @@
+#ifndef _TRIANGLE_H_
+#define _TRIANGLE_H_
+
+#include "./include.h"
+#include "AdjacentTriangle.h"
+
+namespace bamg {
+
+	//classes
+	class Mesh;
+	class BamgVertex;
+	class Triangle;
+
+	class Triangle {
+
+		friend class AdjacentTriangle;
+
+		private:
+			BamgVertex *vertices[3];        // 3 vertices if t is triangle, t[i] allowed by access function, (*t)[i] if pointer
+			Triangle   *adj[3];             // 3 pointers toward the adjacent triangles
+			short       AdjEdgeIndex[3];   // edge id in the adjacent triangles. The edge number 1 is the edge number AdjEdgeIndex[1] in the Adjacent triangle 1
+
+		public: 
+			Icoor2 det; //Integer determinant (twice its area)
+			union { 
+				Triangle *link;
+				long      color;
+			};
+
+			//Constructors/Destructors
+			Triangle();
+			Triangle(Mesh *Th,long i,long j,long k);
+			Triangle(BamgVertex *v0,BamgVertex *v1,BamgVertex *v2);
+
+			//Operators
+			const BamgVertex & operator[](int i) const {return *vertices[i];};
+			BamgVertex & operator[](int i)  {return *vertices[i];};
+			const BamgVertex * operator()(int i) const {return vertices[i];};
+			BamgVertex * & operator()(int i)  {return vertices[i];};
+
+			//Methods
+			void              Echo();
+			double            Anisotropy() const;
+			double            Length() const;
+			int               swap(short a1,int=0);
+			long              Optim(short a,int =0);
+			int               Locked(int a)const;
+			int               Hidden(int a)const;
+			int               GetAllflag(int a);
+			void              SetAllFlag(int a,int f);
+			double            QualityQuad(int a,int option=1) const;
+			short             NuEdgeTriangleAdj(int i) const;
+			AdjacentTriangle  FindBoundaryEdge(int  i) const;
+			AdjacentTriangle  Adj(int i) const;
+			Triangle         *TriangleAdj(int i) const;
+			Triangle         *Quadrangle(BamgVertex  *& v0,BamgVertex *& v1,BamgVertex *& v2,BamgVertex *& v3) const;
+			void              Renumbering(Triangle   *tb,Triangle *te, long *renu);
+			void              Renumbering(BamgVertex *vb,BamgVertex *ve, long *renu);
+			void              SetAdjAdj(short a);
+			void              SetAdj2(short a,Triangle *t,short aat);
+			void              SetSingleVertexToTriangleConnectivity();
+			void              SetHidden(int a);
+			void              SetLocked(int a);
+			void              SetMarkUnSwap(int a);
+			void              SetUnMarkUnSwap(int a);
+			void              SetDet();
+
+			//Inline methods
+			double qualite() ;
+			void  Set(const Triangle &,const Mesh &,Mesh &);
+			int   In(BamgVertex *v) const { return vertices[0]==v || vertices[1]==v || vertices[2]==v ;}
+
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/VertexOnEdge.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/VertexOnEdge.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/VertexOnEdge.cpp	(revision 13395)
@@ -0,0 +1,25 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "VertexOnEdge.h"
+#include "Mesh.h"
+
+namespace bamg {
+
+	/*Methods*/
+	/*FUNCTION VertexOnEdge::Set {{{*/
+	void VertexOnEdge::Set(const Mesh & Th ,long i,Mesh & ThNew){
+		*this = Th.VertexOnBThEdge[i];  
+		v = ThNew.vertices + Th.GetId(v);
+	}
+	/*}}}*/
+	/*FUNCTION VertexOnEdge::SetOnBTh{{{*/
+	void VertexOnEdge::SetOnBTh(){
+		v->BackgroundEdgeHook=this;
+		v->IndexInTriangle=IsVertexOnEdge;  
+	}
+	/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/VertexOnEdge.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/VertexOnEdge.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/VertexOnEdge.h	(revision 13395)
@@ -0,0 +1,36 @@
+#ifndef _VERTEXONEDGE_H_
+#define _VERTEXONEDGE_H_
+
+#include "./include.h"
+#include "./Edge.h"
+
+namespace bamg {
+
+	//classes
+	class Mesh;
+	class BamgVertex;
+
+	class VertexOnEdge {
+
+		public:
+			BamgVertex* v;
+			Edge*   be;
+			double abcisse;
+
+			//Constructors
+			VertexOnEdge(BamgVertex * w, Edge *bw,double s) :v(w),be(bw),abcisse(s) {};
+			VertexOnEdge(){};
+
+			//Operators
+			operator double () const { return abcisse;}
+			operator BamgVertex* () const { return v;}  
+			operator Edge* () const { return be;}  
+			BamgVertex & operator[](int i) const { return (*be)[i];}
+
+			//Methods
+			void SetOnBTh();
+			void Set(const Mesh &,long,Mesh &);  
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/VertexOnGeom.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/VertexOnGeom.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/VertexOnGeom.cpp	(revision 13395)
@@ -0,0 +1,70 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "VertexOnGeom.h"
+#include "Mesh.h"
+#include "Geometry.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+	/*FUNCTION VertexOnGeom::VertexOnGeom(){{{*/
+	VertexOnGeom::VertexOnGeom(){
+		meshvertex=NULL;
+		curvilincoord=0;
+		gv=0;
+	} 
+	/*}}}*/
+	/*FUNCTION VertexOnGeom::VertexOnGeom(BamgVertex & m,GeomVertex &g){{{*/
+	VertexOnGeom::VertexOnGeom(BamgVertex & m,GeomVertex &g){
+		meshvertex=&m;
+		curvilincoord=-1;
+		gv=&g;
+	}
+	/*}}}*/
+	/*FUNCTION VertexOnGeom::VertexOnGeom(BamgVertex & m,GeomEdge &g,double s){{{*/
+	VertexOnGeom::VertexOnGeom(BamgVertex & m,GeomEdge &g,double s){
+		meshvertex=&m;
+		curvilincoord=s;
+		ge=&g;
+	}
+	/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION VertexOnGeom::Set {{{*/
+	void VertexOnGeom::Set(const VertexOnGeom & rec,const Mesh & Th ,Mesh & ThNew){
+		*this = rec;  
+		meshvertex = ThNew.vertices + Th.GetId(meshvertex);
+		if (gv)
+		 if (curvilincoord < 0 )
+		  gv = ThNew.Gh.vertices + Th.Gh.GetId(gv);
+		 else
+		  ge = ThNew.Gh.edges + Th.Gh.GetId(ge);
+
+	}
+	/*}}}*/
+	/*FUNCTION VertexOnGeom::OnGeomVertex{{{*/
+	int VertexOnGeom::OnGeomVertex()const{
+		return this? curvilincoord <0 :0;
+	}
+	/*}}}*/
+	/*FUNCTION VertexOnGeom::OnGeomEdge{{{*/
+	int VertexOnGeom::OnGeomEdge() const{
+		return this? curvilincoord >=0 :0;
+	}
+	/*}}}*/
+	/*FUNCTION VertexOnGeom::IsRequiredVertex{{{*/
+	int VertexOnGeom::IsRequiredVertex() {
+		return this? ((curvilincoord<0 ? (gv?gv->Required():0):0 )) : 0;
+	}
+	/*}}}*/
+	/*FUNCTION VertexOnGeom::SetOn{{{*/
+	void VertexOnGeom::SetOn(){
+		meshvertex->GeomEdgeHook=this;
+		meshvertex->IndexInTriangle=IsVertexOnGeom;
+	}
+	/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/VertexOnGeom.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/VertexOnGeom.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/VertexOnGeom.h	(revision 13395)
@@ -0,0 +1,46 @@
+#ifndef _VERTEXONGEOM_H_
+#define _VERTEXONGEOM_H_
+
+#include "./include.h"
+#include "./GeomVertex.h"
+
+namespace bamg {
+
+	//classes
+	class Mesh;
+	class BamgVertex;
+	class GeomEdge;
+
+	class VertexOnGeom{
+
+		public:
+
+			BamgVertex* meshvertex;
+			double curvilincoord;  
+			union{ 
+				GeomVertex* gv; // if curvilincoord <0; 
+				GeomEdge*   ge; // if curvilincoord in [0..1]
+			};
+
+			//Constructors/Destructors
+			VertexOnGeom();
+			VertexOnGeom(BamgVertex & m,GeomVertex &g);
+			VertexOnGeom(BamgVertex & m,GeomEdge &g,double s);
+
+			//Operators
+			operator BamgVertex*() const  {return meshvertex;}
+			operator GeomVertex * () const  {return gv;}
+			operator GeomEdge * () const  {return ge;}
+			operator const double & () const {return curvilincoord;}
+
+			//Methods
+			int  OnGeomVertex()const;
+			int  OnGeomEdge() const;
+			int  IsRequiredVertex();
+			void SetOn();
+
+			//Inline methods
+			void Set(const VertexOnGeom&,const Mesh &,Mesh &);  
+	};
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/VertexOnVertex.cpp
===================================================================
--- /issm/trunk/src/c/classes/bamg/VertexOnVertex.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/VertexOnVertex.cpp	(revision 13395)
@@ -0,0 +1,34 @@
+#include 
+#include 
+#include 
+#include 
+
+#include "VertexOnVertex.h"
+#include "Mesh.h"
+
+namespace bamg {
+
+	/*Constructors/Destructors*/
+	/*FUNCTION VertexOnVertex::VertexOnVertex(){{{*/
+	VertexOnVertex::VertexOnVertex() {
+		v=NULL;
+		bv=NULL;
+	};/*}}}*/
+	/*FUNCTION VertexOnVertex::VertexOnVertex(BamgVertex * w,BamgVertex *bw){{{*/
+	VertexOnVertex::VertexOnVertex(BamgVertex * w,BamgVertex *bw) :v(w),bv(bw){
+	
+	}/*}}}*/
+
+	/*Methods*/
+	/*FUNCTION VertexOnVertex::Set{{{*/
+	void VertexOnVertex::Set(const Mesh &Th ,long i,Mesh &ThNew) { 
+		*this = Th.VertexOnBThVertex[i];  
+		v     = ThNew.vertices + Th.GetId(v);
+	}
+	/*}}}*/
+	/*FUNCTION VertexOnVertex::SetOnBTh{{{*/
+	void VertexOnVertex::SetOnBTh(){
+		v->BackgroundVertexHook=bv;v->IndexInTriangle=IsVertexOnVertex;
+	}/*}}}*/
+
+} 
Index: /issm/trunk/src/c/classes/bamg/VertexOnVertex.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/VertexOnVertex.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/VertexOnVertex.h	(revision 13395)
@@ -0,0 +1,28 @@
+#ifndef _VERTEXONVERTEX_H_
+#define _VERTEXONVERTEX_H_
+
+#include "./include.h"
+#include "./BamgVertex.h"
+
+namespace bamg {
+
+	//classes
+	class Mesh;
+
+	class VertexOnVertex {
+
+		public:
+			BamgVertex* v;
+			BamgVertex* bv;
+
+			//Constructors
+			VertexOnVertex();
+			VertexOnVertex(BamgVertex * w,BamgVertex *bw);
+
+			//Methods
+			void SetOnBTh();
+			void Set(const Mesh &,long,Mesh &);
+	};
+
+}
+#endif
Index: /issm/trunk/src/c/classes/bamg/bamgobjects.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/bamgobjects.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/bamgobjects.h	(revision 13395)
@@ -0,0 +1,34 @@
+/* \file bamgobjects.h
+ * \brief: prototype header for all bamg related objects.
+ */
+
+#ifndef BAMG_OBJECTS_H_
+#define BAMG_OBJECTS_H_
+
+/*Bamg: */
+#include "./BamgOpts.h"
+#include "./BamgGeom.h"
+#include "./BamgMesh.h"
+#include "./Metric.h"
+#include "./DoubleAndInt.h"
+#include "./Direction.h"
+#include "./BamgVertex.h"
+#include "./AdjacentTriangle.h"
+#include "./Edge.h"
+#include "./GeomVertex.h"
+#include "./GeomEdge.h"
+#include "./Curve.h"
+#include "./Triangle.h"
+#include "./ListofIntersectionTriangles.h"
+#include "./GeomSubDomain.h"
+#include "./SubDomain.h"
+#include "./VertexOnGeom.h"
+#include "./VertexOnVertex.h"
+#include "./VertexOnEdge.h"
+#include "./CrackedEdge.h"
+#include "./Mesh.h"
+#include "./Geometry.h"
+#include "./BamgQuadtree.h"
+#include "./SetOfE4.h"
+
+#endif
Index: /issm/trunk/src/c/classes/bamg/include.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/include.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/include.h	(revision 13395)
@@ -0,0 +1,12 @@
+/*!\file: include.h
+ * \brief prototypes for include.h
+ */ 
+
+#ifndef _INCLUDE2_H_
+#define  _INCLUDE2_H_
+
+#include "../../include/macros.h"
+#include "./macros.h"
+#include "./typedefs.h"
+
+#endif //ifndef _INCLUDE2_H_
Index: /issm/trunk/src/c/classes/bamg/macros.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/macros.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/macros.h	(revision 13395)
@@ -0,0 +1,24 @@
+#ifndef _BAMGMACROS_H
+#define _BAMGMACROS_H
+
+#include "./typedefs.h"
+
+namespace bamg {
+
+	const double Pi =3.141592653589793238462643383279502884197169399375105820974944592308;
+	const float  fPi=3.141592653589793238462643383279502884197169399375105820974944592308;
+	const  int   IsVertexOnGeom = 8;
+	const  int   IsVertexOnVertex = 16;
+	const  int   IsVertexOnEdge = 32;
+	static const short VerticesOfTriangularEdge[3][2] = {{1,2},{2,0},{0,1}};
+	static const short EdgesVertexTriangle[3][2] = {{1,2},{2,0},{0,1}};
+	static const short OppositeVertex[3] = {0,1,2};
+	static const short OppositeEdge[3] =  {0,1,2};
+	static const short NextEdge[3] = {1,2,0};
+	static const short PreviousEdge[3] = {2,0,1};
+	static const short NextVertex[3] = {1,2,0};
+	static const short PreviousVertex[3] = {2,0,1};
+	const  Icoor1 MaxICoor   = 1073741823; // 2^30-1 =111...111 (29 times one)
+}
+
+#endif
Index: /issm/trunk/src/c/classes/bamg/typedefs.h
===================================================================
--- /issm/trunk/src/c/classes/bamg/typedefs.h	(revision 13395)
+++ /issm/trunk/src/c/classes/bamg/typedefs.h	(revision 13395)
@@ -0,0 +1,17 @@
+#ifndef _BAMGTYPEDEFS_H
+#define _BAMGTYPEDEFS_H
+
+#include "./R2.h"
+
+namespace bamg {
+
+	/*Integer coordinates types*/
+	typedef int  Icoor1; 
+	typedef long Icoor2;
+
+	/*I2 and R2*/
+	typedef P2  I2;
+	typedef P2  R2;
+}
+
+#endif
Index: /issm/trunk/src/c/classes/classes.h
===================================================================
--- /issm/trunk/src/c/classes/classes.h	(revision 13395)
+++ /issm/trunk/src/c/classes/classes.h	(revision 13395)
@@ -0,0 +1,33 @@
+/* \file classes.h
+ * \brief: prototype header for all classes used in ISSM.
+ */
+
+#ifndef ALL_CLASSES_H_
+#define ALL_CLASSES_H_
+
+/*Objects derived classes, which are used in our containers: */
+#include "./objects/objects.h"
+
+/*matrix: */
+#include "./matrix/matrixobjects.h"
+
+/*bamg: */
+#include "./bamg/bamgobjects.h"
+
+/*gauss: */
+#include "./gauss/gaussobjects.h"
+
+/*kriging: */
+#include "./kriging/krigingobjects.h"
+
+/*diverse: */
+#include "./Hook.h"
+#include "./DofIndexing.h"
+#include "./IoModel.h"
+#include "./Patch.h"
+#include "./Update.h"
+#include "./FemModel.h"
+#include "./OptArgs.h"
+#include "./OptPars.h"
+
+#endif
Index: /issm/trunk/src/c/classes/dakota/DakotaPlugin.cpp
===================================================================
--- /issm/trunk/src/c/classes/dakota/DakotaPlugin.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/dakota/DakotaPlugin.cpp	(revision 13395)
@@ -0,0 +1,118 @@
+/*!\file:  DakotaPlugin.cpp (see DakotaPlugin.h for explanations)
+ * \brief  header file for derived DirectApplicInterface class. 
+ * \sa SpwanCore.cpp and \sa qmu.cpp
+ *
+ * This class needs to be understood simultaneously with qmu.cpp and SpwanCore.cpp. 
+ * This call is derived from the Dakota DirectApplicInterface class. This is the 
+ * only way to plug ISSM's own routines into the Dakota engine. The derived class 
+ * has one function called derived_map_ac, which is called by Dakota to drive the 
+ * entire snesitivity analysis. 
+ *
+ * We use this routine (which gets variables, variable_descriptors from the Dakota 
+ * engine, and requests responses from the ISSM solution sequences), to call our 
+ * own solutoin cores. This routines calls the SpawnCore routine, which will drive 
+ * the entire computations. 
+ */ 
+
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+/*Standard ISSM includes: */
+#include "../../shared/shared.h"
+#include "../../include/include.h"
+#include "../classes.h"
+#include "../../modules/Dakotax/Dakotax.h"
+
+/*Standard includes: */
+#include 
+
+#ifdef _HAVE_DAKOTA_ //only works if dakota library has been compiled in.
+
+//Dakota headers
+#include "DakotaResponse.H"
+#include "ParamResponsePair.H"
+#include "DakotaPlugin.h"
+#include "system_defs.h"
+#include "ProblemDescDB.H"
+#include "ParallelLibrary.H"
+
+namespace SIM {
+
+//constructor
+DakotaPlugin::DakotaPlugin(const Dakota::ProblemDescDB& problem_db,void* in_femmodel):Dakota::DirectApplicInterface(problem_db){
+
+
+	femmodel=in_femmodel;
+	counter=0;
+}
+
+//destructor
+DakotaPlugin::~DakotaPlugin(){ /* Virtual destructor handles referenceCount at Interface level. */ }
+
+int DakotaPlugin::derived_map_ac(const Dakota::String& driver) {
+
+	int i;
+	IssmDouble* variables=NULL;
+	char** variable_descriptors=NULL;
+	char*  variable_descriptor=NULL;
+	IssmDouble* responses=NULL;
+
+	/*increae counter: */
+	counter++;
+
+	/*Before launching analysis, we need to transfer the dakota inputs into Issm 
+	 *readable variables: */
+
+	/*First, the variables: */
+	variables=xNew(numACV);
+	for(i=0;i(numACV);
+	for(i=0;i(strlen(label.c_str())+1);
+		memcpy(variable_descriptor,label.c_str(),(strlen(label.c_str())+1)*sizeof(char));
+
+		
+		variable_descriptors[i]=variable_descriptor;
+	}
+
+	/*Initialize responses: */
+	responses=xNewZeroInit(numFns);
+
+	/*run core solution: */
+	SpawnCore(responses,numFns, variables,variable_descriptors,numACV,femmodel,counter);
+
+	/*populate responses: */
+	for(i=0;i(variables);
+	for(i=0;i(variable_descriptor);
+	}
+	xDelete(variable_descriptors);
+	xDelete(responses);
+
+	return 0;
+}
+  
+
+int DakotaPlugin::GetCounter(){
+	return counter;
+}
+
+} // namespace SIM
+
+
+#endif //only works if dakota library has been compiled in.
Index: /issm/trunk/src/c/classes/dakota/DakotaPlugin.h
===================================================================
--- /issm/trunk/src/c/classes/dakota/DakotaPlugin.h	(revision 13395)
+++ /issm/trunk/src/c/classes/dakota/DakotaPlugin.h	(revision 13395)
@@ -0,0 +1,52 @@
+/*!\file:  DakotaPlugin.h:
+ */ 
+
+#ifndef _DAKOTAPLUGIN_H
+#define _DAKOTAPLUGIN_H
+
+
+#ifdef _HAVE_DAKOTA_ //only works if dakota library has been compiled in.
+
+/*Headers:*/
+/*{{{*/
+#include "DirectApplicInterface.H"
+#include "../../toolkits/toolkits.h"
+#include "../../classes/classes.h"
+/*}}}*/
+
+namespace SIM {
+
+class DakotaPlugin: public Dakota::DirectApplicInterface
+{
+public:
+
+	DakotaPlugin(const Dakota::ProblemDescDB& problem_db,void* model);
+	~DakotaPlugin();
+
+	/*these fields are used by core solutions: */
+	void* femmodel;
+
+	int counter;
+
+protected:
+
+  // execute the input filter portion of a direct evaluation invocation
+  //int derived_map_if(const Dakota::String& if_name);
+  /// execute an analysis code portion of a direct evaluation invocation
+  int derived_map_ac(const Dakota::String& ac_name);
+  // execute the output filter portion of a direct evaluation invocation
+  //int derived_map_of(const Dakota::String& of_name);
+
+  /*add for issm: */
+  int GetCounter();
+
+private:
+
+};
+
+} // namespace SIM
+
+#endif //only works if dakota library has been compiled in.
+
+
+#endif
Index: /issm/trunk/src/c/classes/gauss/GaussPenta.cpp
===================================================================
--- /issm/trunk/src/c/classes/gauss/GaussPenta.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/gauss/GaussPenta.cpp	(revision 13395)
@@ -0,0 +1,404 @@
+/*!\file GaussPenta.c
+ * \brief: implementation of the GaussPenta object
+ */
+
+#include "./gaussobjects.h"
+
+/*GaussPenta constructors and destructors:*/
+/*FUNCTION GaussPenta::GaussPenta() {{{*/
+GaussPenta::GaussPenta(){
+
+	numgauss=-1;
+
+	weights=NULL;
+	coords1=NULL;
+	coords2=NULL;
+	coords3=NULL;
+	coords4=NULL;
+
+	weight=UNDEF;
+	coord1=UNDEF;
+	coord2=UNDEF;
+	coord3=UNDEF;
+	coord4=UNDEF;
+}
+/*}}}*/
+/*FUNCTION GaussPenta::GaussPenta(int order_horiz,int order_vert) {{{*/
+GaussPenta::GaussPenta(int order_horiz,int order_vert){
+
+	/*Intermediaries*/
+	int     ighoriz,igvert;
+	int     numgauss_horiz;
+	int     numgauss_vert;
+	double *coords1_horiz = NULL;
+	double *coords2_horiz = NULL;
+	double *coords3_horiz = NULL;
+	double *weights_horiz  = NULL;
+	double *coords_vert = NULL;
+	double *weights_vert   = NULL;
+
+	/*Get gauss points*/
+	GaussLegendreTria(&numgauss_horiz,&coords1_horiz,&coords2_horiz,&coords3_horiz,&weights_horiz,order_horiz);
+	GaussLegendreLinear(&coords_vert,&weights_vert,order_vert);
+	numgauss_vert=order_vert;
+
+	/*Allocate GaussPenta fields*/
+	numgauss=numgauss_horiz*numgauss_vert;
+	coords1=xNew(numgauss);
+	coords2=xNew(numgauss);
+	coords3=xNew(numgauss);
+	coords4=xNew(numgauss);
+	weights=xNew(numgauss);
+
+	/*Combine Horizontal and vertical points*/
+	for (ighoriz=0; ighoriz(coords1_horiz);
+	xDelete(coords2_horiz);
+	xDelete(coords3_horiz);
+	xDelete(coords_vert);
+	xDelete(weights_horiz);
+	xDelete(weights_vert);
+}
+/*}}}*/
+/*FUNCTION GaussPenta::GaussPenta(int index1, int index2, int order){{{*/
+GaussPenta::GaussPenta(int index1, int index2,int order){
+
+	/*Intermediaties*/
+	double *seg_coords  = NULL;
+	double *seg_weights = NULL;
+	int     i;
+
+	/*Get Segment gauss points*/
+	numgauss=order;
+	GaussLegendreLinear(&seg_coords,&seg_weights,numgauss);
+
+	/*Allocate GaussPenta fields*/
+	coords1=xNew(numgauss);
+	coords2=xNew(numgauss);
+	coords3=xNew(numgauss);
+	coords4=xNew(numgauss);
+	weights=xNew(numgauss);
+
+	if(index1==0 && index2==3){
+		for(i=0;i(seg_coords);
+	xDelete(seg_weights);
+
+}
+/*}}}*/
+/*FUNCTION GaussPenta::GaussPenta(int index1, int index2, int index3, int order){{{*/
+GaussPenta::GaussPenta(int index1, int index2, int index3, int order){
+
+	/*Basal Tria*/
+	if(index1==0 && index2==1 && index3==2){
+
+		/*Get GaussTria*/
+		GaussLegendreTria(&numgauss,&coords1,&coords2,&coords3,&weights,order);
+
+		/*compute z coordinate*/
+		coords4=xNew(numgauss);
+		for(int i=0;i(numgauss);
+		for(int i=0;i(numgauss);
+	coords2=xNew(numgauss);
+	coords3=xNew(numgauss);
+	coords4=xNew(numgauss);
+	weights=xNew(numgauss);
+
+	/*Quads: get the gauss points using the product of two line rules  */
+	if(index1==0 && index2==1 && index3==4 && index4==3){
+		for(i=0;i(seg_horiz_coords);
+	xDelete(seg_horiz_weights);
+	xDelete(seg_vert_coords);
+	xDelete(seg_vert_weights);
+}
+/*}}}*/
+/*FUNCTION GaussPenta::~GaussPenta(){{{*/
+GaussPenta::~GaussPenta(){
+	xDelete(weights);
+	xDelete(coords1);
+	xDelete(coords2);
+	xDelete(coords3);
+	xDelete(coords4);
+}
+/*}}}*/
+
+/*Methods*/
+/*FUNCTION GaussPenta::Echo{{{*/
+void GaussPenta::Echo(void){
+
+	_printLine_("GaussPenta:");
+	_printLine_("   numgauss: " << numgauss);
+
+	if (weights){
+	 _printString_("   weights = ["); 
+	 for(int i=0;i(numgauss);
+		for(int i=0;i0);
+	_assert_(weights);
+	_assert_(coords1);
+	_assert_(coords2);
+	_assert_(coords3);
+	_assert_(coords4);
+
+	/*return first gauss index*/
+	return 0;
+}
+/*}}}*/
+/*FUNCTION GaussPenta::end{{{*/
+int GaussPenta::end(void){
+
+	/*Check that this has been initialized*/
+	_assert_(numgauss>0);
+	_assert_(weights);
+	_assert_(coords1);
+	_assert_(coords2);
+	_assert_(coords3);
+	_assert_(coords4);
+
+	/*return last gauss index +1*/
+	return numgauss;
+}
+/*}}}*/
+/*FUNCTION GaussPenta::SynchronizeGaussTria{{{*/
+void GaussPenta::SynchronizeGaussTria(GaussTria* gauss_tria){
+
+	gauss_tria->coord1=this->coord1;
+	gauss_tria->coord2=this->coord2;
+	gauss_tria->coord3=this->coord3;
+	gauss_tria->weight=UNDEF;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/gauss/GaussPenta.h
===================================================================
--- /issm/trunk/src/c/classes/gauss/GaussPenta.h	(revision 13395)
+++ /issm/trunk/src/c/classes/gauss/GaussPenta.h	(revision 13395)
@@ -0,0 +1,51 @@
+/*!\file GaussPenta.h
+ * \brief: header file for node object
+ */
+
+#ifndef _GAUSSPENTA_H_
+#define _GAUSSPENTA_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./../../shared/shared.h"
+class GaussTria;
+/*}}}*/
+
+class GaussPenta{
+
+	private:
+		int numgauss;
+		double* weights;
+		double* coords1;
+		double* coords2;
+		double* coords3;
+		double* coords4;
+
+	public:
+		double weight;
+		double coord1;
+		double coord2;
+		double coord3;
+		double coord4;
+		
+	public:
+
+		/*GaussPenta constructors, destructors*/
+		GaussPenta();
+		GaussPenta(int order_horiz,int order_vert);
+		GaussPenta(int index1, int index2,int order);
+		GaussPenta(int index1, int index2, int index3, int order);
+		GaussPenta(int index1, int index2, int index3, int index4,int order_horiz,int order_vert);
+		~GaussPenta();
+
+		/*Methods*/
+		int  begin(void);
+		int  end(void);
+		void Echo(void);
+		void GaussPoint(int ig);
+		void GaussVertex(int iv);
+		void GaussFaceTria(int index1, int index2, int index3, int order);
+		void GaussCenter(void);
+		void SynchronizeGaussTria(GaussTria* gauss_tria);
+};
+#endif
Index: /issm/trunk/src/c/classes/gauss/GaussTria.cpp
===================================================================
--- /issm/trunk/src/c/classes/gauss/GaussTria.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/gauss/GaussTria.cpp	(revision 13395)
@@ -0,0 +1,276 @@
+/*!\file GaussTria.c
+ * \brief: implementation of the GaussTria object
+ */
+
+#include "./gaussobjects.h"
+
+/*GaussTria constructors and destructors:*/
+/*FUNCTION GaussTria::GaussTria() {{{*/
+GaussTria::GaussTria(){
+
+	numgauss=-1;
+
+	weights=NULL;
+	coords1=NULL;
+	coords2=NULL;
+	coords3=NULL;
+
+	weight=UNDEF;
+	coord1=UNDEF;
+	coord2=UNDEF;
+	coord3=UNDEF;
+}
+/*}}}*/
+/*FUNCTION GaussTria::GaussTria(int order) {{{*/
+GaussTria::GaussTria(int order){
+
+	/*Get gauss points*/
+	GaussLegendreTria(&numgauss,&coords1,&coords2,&coords3,&weights,order);
+
+	/*Initialize static fields as undefinite*/
+	weight=UNDEF;
+	coord1=UNDEF;
+	coord2=UNDEF;
+	coord3=UNDEF;
+
+}
+/*}}}*/
+/*FUNCTION GaussTria::GaussTria(int index1,int index2,int order) {{{*/
+GaussTria::GaussTria(int index1,int index2,int order){
+
+	/*Intermediaties*/
+	IssmPDouble *seg_coords  = NULL;
+	IssmPDouble *seg_weights = NULL;
+	int     i,index3;
+
+	/*Get Segment gauss points*/
+	numgauss=order;
+	GaussLegendreLinear(&seg_coords,&seg_weights,numgauss);
+
+	/*Allocate GaussTria fields*/
+	coords1=xNew(numgauss);
+	coords2=xNew(numgauss);
+	coords3=xNew(numgauss);
+	weights=xNew(numgauss);
+
+	/*Reverse index1 and 2 if necessary*/
+	if (index1>index2){
+		index3=index1; index1=index2; index2=index3;
+		for(i=0;i(seg_coords);
+	xDelete(seg_weights);
+}
+/*}}}*/
+/*FUNCTION GaussTria::~GaussTria(){{{*/
+GaussTria::~GaussTria(){
+	xDelete(weights);
+	xDelete(coords1);
+	xDelete(coords2);
+	xDelete(coords3);
+}
+/*}}}*/
+
+/*Methods*/
+/*FUNCTION GaussTria::Echo{{{*/
+void GaussTria::Echo(void){
+
+	_printLine_("GaussTria:");
+	_printLine_("   numgauss: " << numgauss);
+
+	if (weights){
+	 _printString_("   weights = ["); 
+	 for(int i=0;i=0 && ig< numgauss);
+
+	 /*update static arrays*/
+	 weight=weights[ig];
+	 coord1=coords1[ig];
+	 coord2=coords2[ig];
+	 coord3=coords3[ig];
+
+}
+/*}}}*/
+/*FUNCTION GaussTria::GaussFromCoords{{{*/
+void GaussTria::GaussFromCoords(IssmDouble x,IssmDouble y,IssmDouble* xyz_list){
+
+	/*Intermediaries*/
+	IssmDouble    area = 0;
+	IssmDouble    x1,y1,x2,y2,x3,y3;
+
+	/*in debugging mode: check that the default constructor has been called*/
+	_assert_(numgauss==-1);
+
+	x1=*(xyz_list+3*0+0); y1=*(xyz_list+3*0+1);
+	x2=*(xyz_list+3*1+0); y2=*(xyz_list+3*1+1);
+	x3=*(xyz_list+3*2+0); y3=*(xyz_list+3*2+1);
+
+	area=(x2*y3 - y2*x3 + x1*y2 - y1*x2 + x3*y1 - y3*x1)/2;
+
+	/*Get first area coordinate = det(x-x3  x2-x3 ; y-y3   y2-y3)/area*/
+	coord1=((x-x3)*(y2-y3)-(x2-x3)*(y-y3))/area;
+
+	/*Get second area coordinate = det(x1-x3  x-x3 ; y1-y3   y-y3)/area*/
+	coord2=((x1-x3)*(y-y3)-(x-x3)*(y1-y3))/area;
+
+	/*Get third  area coordinate 1-area1-area2: */
+	coord3=1-coord1-coord2;
+
+}
+/*}}}*/
+/*FUNCTION GaussTria::GaussVertex{{{*/
+void GaussTria::GaussVertex(int iv){
+
+	/*in debugging mode: check that the default constructor has been called*/
+	_assert_(numgauss==-1);
+
+	/*update static arrays*/
+	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_("vertex index should be in [0 2]");
+
+	}
+
+}
+/*}}}*/
+/*FUNCTION GaussTria::begin{{{*/
+int GaussTria::begin(void){
+
+	/*Check that this has been initialized*/
+	_assert_(numgauss>0);
+	_assert_(weights);
+	_assert_(coords1);
+	_assert_(coords2);
+	_assert_(coords3);
+
+	/*return first gauss index*/
+	return 0;
+}
+/*}}}*/
+/*FUNCTION GaussTria::end{{{*/
+int GaussTria::end(void){
+
+	/*Check that this has been initialized*/
+	_assert_(numgauss>0);
+	_assert_(weights);
+	_assert_(coords1);
+	_assert_(coords2);
+	_assert_(coords3);
+
+	/*return last gauss index +1*/
+	return numgauss;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/gauss/GaussTria.h
===================================================================
--- /issm/trunk/src/c/classes/gauss/GaussTria.h	(revision 13395)
+++ /issm/trunk/src/c/classes/gauss/GaussTria.h	(revision 13395)
@@ -0,0 +1,46 @@
+/*!\file GaussTria.h
+ * \brief: header file for node object
+ */
+
+#ifndef _GAUSSTRIA_H_
+#define _GAUSSTRIA_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./../../shared/shared.h"
+/*}}}*/
+
+class GaussTria{
+
+	private:
+		int numgauss;
+		IssmPDouble* weights;
+		IssmPDouble* coords1;
+		IssmPDouble* coords2;
+		IssmPDouble* coords3;
+
+	public:
+		IssmPDouble weight;
+		IssmDouble coord1;
+		IssmDouble coord2;
+		IssmDouble coord3;
+		
+	public:
+
+		/*GaussTria constructors, destructors*/
+		GaussTria();
+		GaussTria(int order);
+		GaussTria(int index1,int index2,int order);
+		~GaussTria();
+
+		/*Methods*/
+		int  begin(void);
+		int  end(void);
+		void Echo(void);
+		void GaussFromCoords(IssmDouble x1,IssmDouble y1,IssmDouble* xyz_list);
+		void GaussPoint(int ig);
+		void GaussVertex(int iv);
+		void GaussCenter(void);
+		void GaussEdgeCenter(int index1,int index2);
+};
+#endif  /* _GAUSSTRIA_H_ */
Index: /issm/trunk/src/c/classes/gauss/gaussobjects.h
===================================================================
--- /issm/trunk/src/c/classes/gauss/gaussobjects.h	(revision 13395)
+++ /issm/trunk/src/c/classes/gauss/gaussobjects.h	(revision 13395)
@@ -0,0 +1,11 @@
+/* \file gaussobjects.h
+ * \brief: prototype header for all gauss related objects
+ */
+
+#ifndef ALL_GAUSS_OBJECTS_H_
+#define ALL_GAUSS_OBJECTS_H_
+
+#include "./GaussTria.h"
+#include "./GaussPenta.h"
+
+#endif
Index: /issm/trunk/src/c/classes/kriging/ExponentialVariogram.cpp
===================================================================
--- /issm/trunk/src/c/classes/kriging/ExponentialVariogram.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/ExponentialVariogram.cpp	(revision 13395)
@@ -0,0 +1,95 @@
+/*!\file ExponentialVariogram.c
+ * \brief: implementation of the ExponentialVariogram object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../shared/shared.h"
+#include "../../include/include.h"
+
+/*ExponentialVariogram constructors and destructor*/
+/*FUNCTION ExponentialVariogram::ExponentialVariogram(){{{*/
+ExponentialVariogram::ExponentialVariogram(){
+	this->nugget = 0.2;
+	this->sill   = 1;
+	this->range  = SQRT3;
+	return;
+}
+/*}}}*/
+/*FUNCTION ExponentialVariogram::ExponentialVariogram(Options* options){{{*/
+ExponentialVariogram::ExponentialVariogram(Options* options){
+
+	/*Defaults*/
+	this->nugget = 0.2;
+	this->sill   = 1;
+	this->range  = SQRT3;
+
+	/*Overwrite from options*/
+	if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget");
+	if(options->GetOption("sill"))   options->Get(&this->sill,"sill");
+	if(options->GetOption("range"))  options->Get(&this->range,"range");
+
+	/*Checks*/
+	if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)");
+}
+/*}}}*/
+/*FUNCTION ExponentialVariogram::~ExponentialVariogram(){{{*/
+ExponentialVariogram::~ExponentialVariogram(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION ExponentialVariogram::Echo {{{*/
+void ExponentialVariogram::Echo(void){
+	_printLine_("ExponentialVariogram");
+	_printLine_("   nugget: " << this->nugget);
+	_printLine_("   sill  : " << this->sill);
+	_printLine_("   range : " << this->range);
+}
+/*}}}*/
+
+/*Variogram function*/
+/*FUNCTION ExponentialVariogram::Covariance{{{*/
+double ExponentialVariogram::Covariance(double deltax,double deltay){
+	/*The covariance can be deduced from the variogram from the following
+	 * relationship:
+	 *    2 gamma = C(x,x) + C(y,y) -2 C(x,y)
+	 * so
+	 *    C(h) = sill - gamma                                            */
+	double h,a,cova;
+
+	/*Calculate length*/
+	h=sqrt(pow(deltax,2.)+pow(deltay,2.));
+
+	/*If h is too small, return sill*/
+	if(h<0.0000001) return sill;
+
+	/*compute covariance*/
+	a     = 1./3.;
+	cova = (sill-nugget)*exp(-h/(a*range));
+	return cova;
+}
+/*}}}*/
+/*FUNCTION ExponentialVariogram::SemiVariogram{{{*/
+double ExponentialVariogram::SemiVariogram(double deltax,double deltay){
+	/*http://en.wikipedia.org/wiki/Variogram*/
+	double h,a,gamma;
+
+	/*Calculate length*/
+	h=sqrt(pow(deltax,2.)+pow(deltay,2.));
+
+	/*return semi-variogram*/
+	a     = 1./3.;
+	gamma = (sill-nugget)*(1-exp(-h/(a*range))) + nugget;
+	return gamma;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/kriging/ExponentialVariogram.h
===================================================================
--- /issm/trunk/src/c/classes/kriging/ExponentialVariogram.h	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/ExponentialVariogram.h	(revision 13395)
@@ -0,0 +1,35 @@
+/*! \file ExponentialVariogram.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+#ifndef _EXPONENTIALVARIOGRAM_H_
+#define _EXPONENTIALVARIOGRAM_H_
+
+/*Headers:*/
+#include "./Variogram.h"
+
+class ExponentialVariogram: public Variogram{
+
+	public:
+		double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin
+		double sill;   //Limit of the variogram tending to infinity lag distances
+		double range;  //The distance in which the difference of the variogram from the sill becomes negligible
+
+		/*ExponentialVariogram constructors, destructors*/
+		ExponentialVariogram();
+		ExponentialVariogram(Options* options);
+		~ExponentialVariogram();
+
+		/*Object virtual functions definitions*/
+		void  Echo();
+		void  DeepEcho(){_error_("Not implemented yet");};
+		int   Id(){_error_("Not implemented yet");}; 
+		int   MyRank(){_error_("Not implemented yet");};
+		int   ObjectEnum(){_error_("Not implemented yet");};
+		Object* copy(){_error_("Not implemented yet");};
+
+		/*Variogram functions*/
+		double SemiVariogram(double deltax,double deltay);
+		double Covariance(double deltax,double deltay);
+};
+#endif  /* _EXPONENTIALVARIOGRAM_H */
Index: /issm/trunk/src/c/classes/kriging/GaussianVariogram.cpp
===================================================================
--- /issm/trunk/src/c/classes/kriging/GaussianVariogram.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/GaussianVariogram.cpp	(revision 13395)
@@ -0,0 +1,99 @@
+/*!\file GaussianVariogram.c
+ * \brief: implementation of the GaussianVariogram object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../shared/shared.h"
+#include "../../include/include.h"
+
+/*GaussianVariogram constructors and destructor*/
+/*FUNCTION GaussianVariogram::GaussianVariogram(){{{*/
+GaussianVariogram::GaussianVariogram(){
+	this->nugget = 0.2;
+	this->sill   = 1;
+	this->range  = SQRT3;
+	return;
+}
+/*}}}*/
+/*FUNCTION GaussianVariogram::GaussianVariogram(Options* options){{{*/
+GaussianVariogram::GaussianVariogram(Options* options){
+
+	/*Defaults*/
+	this->nugget = 0.2;
+	this->sill   = 1;
+	this->range  = SQRT3;
+
+	/*Overwrite from options*/
+	if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget");
+	if(options->GetOption("sill"))   options->Get(&this->sill,"sill");
+	if(options->GetOption("range"))  options->Get(&this->range,"range");
+
+	/*Checks*/
+	if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)");
+}
+/*}}}*/
+/*FUNCTION GaussianVariogram::~GaussianVariogram(){{{*/
+GaussianVariogram::~GaussianVariogram(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION GaussianVariogram::Echo {{{*/
+void GaussianVariogram::Echo(void){
+	_printLine_("GaussianVariogram");
+	_printLine_("   nugget: " << this->nugget);
+	_printLine_("   sill  : " << this->sill);
+	_printLine_("   range : " << this->range);
+}
+/*}}}*/
+
+/*Variogram function*/
+/*FUNCTION GaussianVariogram::Covariance{{{*/
+double GaussianVariogram::Covariance(double deltax,double deltay){
+	/*The covariance can be deduced from the variogram from the following
+	 * relationship:
+	 *    2 gamma = C(x,x) + C(y,y) -2 C(x,y)
+	 * so
+	 *    C(h) = sill - gamma                                            */
+	double h2,a,cova;
+
+	/*Calculate length square*/
+	h2=pow(deltax,2.)+pow(deltay,2.);
+
+	/*If h is too small, return sill*/
+	if(h2<0.0000001) return sill;
+
+	/*compute covariance*/
+	a     = 1./3.;
+	cova = (sill-nugget)*exp(-h2/(a*range*range));
+
+	return cova;
+}
+/*}}}*/
+/*FUNCTION GaussianVariogram::SemiVariogram{{{*/
+double GaussianVariogram::SemiVariogram(double deltax,double deltay){
+	/*http://en.wikipedia.org/wiki/Variogram*/
+	double h2,a,gamma;
+
+	/*Calculate length square*/
+	h2=pow(deltax,2.)+pow(deltay,2.);
+
+	/*return semi-variogram*/
+	a     = 1./3.;
+	gamma = (sill-nugget)*(1.-exp(-h2/(a*range*range))) + nugget;
+
+	//if(h2>1000*1000) _printLine_("gamma = " << gamma << " h= " << sqrt(h2));
+	_printLine_("h = " << sqrt(h2) << " gamma = " << gamma);
+	return gamma;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/kriging/GaussianVariogram.h
===================================================================
--- /issm/trunk/src/c/classes/kriging/GaussianVariogram.h	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/GaussianVariogram.h	(revision 13395)
@@ -0,0 +1,36 @@
+/*! \file GaussianVariogram.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+#ifndef _GAUSSIANVARIOGRAM_H_
+#define _GAUSSIANVARIOGRAM_H_
+
+/*Headers:*/
+#include "./Variogram.h"
+class Options;
+
+class GaussianVariogram: public Variogram{
+
+	public:
+		double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin
+		double sill;   //Limit of the variogram tending to infinity lag distances
+		double range;  //The distance in which the difference of the variogram from the sill becomes negligible
+
+		/*GaussianVariogram constructors, destructors*/
+		GaussianVariogram();
+		GaussianVariogram(Options* options);
+		~GaussianVariogram();
+
+		/*Object virtual functions definitions*/
+		void  Echo();
+		void  DeepEcho(){_error_("Not implemented yet");};
+		int   Id(){_error_("Not implemented yet");}; 
+		int   MyRank(){_error_("Not implemented yet");};
+		int   ObjectEnum(){_error_("Not implemented yet");};
+		Object* copy(){_error_("Not implemented yet");};
+
+		/*Variogram functions*/
+		double SemiVariogram(double deltax,double deltay);
+		double Covariance(double deltax,double deltay);
+};
+#endif  /* _GAUSSIANVARIOGRAM_H */
Index: /issm/trunk/src/c/classes/kriging/Observation.cpp
===================================================================
--- /issm/trunk/src/c/classes/kriging/Observation.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/Observation.cpp	(revision 13395)
@@ -0,0 +1,57 @@
+/*!\file Observation.c
+ * \brief: implementation of the Observation object
+ */
+
+#include 
+#include "../objects.h"
+
+/*Observation constructors and destructor*/
+/*FUNCTION Observation::Observation(){{{*/
+Observation::Observation(){
+	return;
+}
+/*}}}*/
+/*FUNCTION Observation::Observation(double x,double y,int xi,int yi,int index,double value){{{*/
+Observation::Observation(double x_in,double y_in,int xi_in,int yi_in,int index_in,double value_in){
+
+	this->x      = x_in;
+	this->y      = y_in;
+	this->xi     = xi_in;
+	this->yi     = yi_in;
+	this->index  = index_in;
+	this->value  = value_in;
+	this->weight = 1.;
+
+}
+/*}}}*/
+/*FUNCTION Observation::~Observation(){{{*/
+Observation::~Observation(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION Observation::Echo {{{*/
+void Observation::Echo(void){
+
+	int  bit;
+
+	_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);
+}
+/*}}}*/
+
+/*Observations functions*/
+/*FUNCTION Observation::WriteXYObs(double* px,double* py,double* pobs){{{*/
+void Observation::WriteXYObs(double* px,double* py,double* pobs){
+	*px   = this->x;
+	*py   = this->y;
+	*pobs = this->value;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/kriging/Observation.h
===================================================================
--- /issm/trunk/src/c/classes/kriging/Observation.h	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/Observation.h	(revision 13395)
@@ -0,0 +1,35 @@
+/*! \file Observation.h 
+ *  \brief: header file for Observation object
+ */
+
+#ifndef _OBSERVATION_H_
+#define _OBSERVATION_H_
+
+#include "../objects/Object.h"
+
+class Observation: public Object{
+
+	public:
+		double x,y;
+		int    xi,yi;
+		int    index;
+		double weight;
+		double value;
+
+		/*Observation constructors, destructors*/
+		Observation();
+		Observation(double x_in,double y_in,int xi_in,int yi_in,int index_in,double value_in);
+		~Observation();
+
+		/*Object virtual functions definitions*/
+		void    Echo();
+		void    DeepEcho()  {_error_("Not implemented yet"); };
+		int     Id()        {_error_("Not implemented yet"); };
+		int     MyRank()    {_error_("Not implemented yet"); };
+		int     ObjectEnum(){_error_("Not implemented yet"); };
+		Object *copy()      {_error_("Not implemented yet"); };
+
+		/*Management*/
+		void WriteXYObs(double* px,double* py,double* pobs);
+};
+#endif  /* _OBSERVATION_*/
Index: /issm/trunk/src/c/classes/kriging/PowerVariogram.cpp
===================================================================
--- /issm/trunk/src/c/classes/kriging/PowerVariogram.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/PowerVariogram.cpp	(revision 13395)
@@ -0,0 +1,94 @@
+/*!\file PowerVariogram.c
+ * \brief: implementation of the PowerVariogram object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../shared/shared.h"
+#include "../../include/include.h"
+
+/*PowerVariogram constructors and destructor*/
+/*FUNCTION PowerVariogram::PowerVariogram(){{{*/
+PowerVariogram::PowerVariogram(){
+	this->nugget = 0.2;
+	this->slope  = 1.;
+	this->power  = 1.;
+	return;
+}
+/*}}}*/
+/*FUNCTION PowerVariogram::PowerVariogram(Options* options){{{*/
+PowerVariogram::PowerVariogram(Options* options){
+
+	/*Defaults*/
+	this->nugget = 0.2;
+	this->slope  = 1.;
+	this->power  = 1.;
+
+	/*Overwrite from options*/
+	if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget");
+	if(options->GetOption("slope"))  options->Get(&this->slope,"slope");
+	if(options->GetOption("power"))  options->Get(&this->power,"power");
+
+	/*Checks*/
+	if(power<=0 || power>=2) _error_("power must be betwwen 0 and 2 (0 < power < 2)");
+	if(slope<=0) _error_("slope must be positive");
+}
+/*}}}*/
+/*FUNCTION PowerVariogram::~PowerVariogram(){{{*/
+PowerVariogram::~PowerVariogram(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION PowerVariogram::Echo {{{*/
+void PowerVariogram::Echo(void){
+	_printLine_("PowerVariogram");
+	_printLine_("   nugget: " << this->nugget);
+	_printLine_("   slope : " << this->slope);
+	_printLine_("   power : " << this->power);
+}
+/*}}}*/
+
+/*Variogram function*/
+/*FUNCTION PowerVariogram::Covariance{{{*/
+double PowerVariogram::Covariance(double deltax,double deltay){
+	/*The covariance can be deduced from the variogram from the following
+	 * relationship:
+	 *    2 gamma = C(x,x) + C(y,y) -2 C(x,y)
+	 * so
+	 *    C(h) = sill - gamma                                            */
+	double h,cova;
+
+	/*Calculate length square*/
+	h=sqrt(pow(deltax,2.)+pow(deltay,2.));
+
+	/*return covariance*/
+	cova = 9999. - this->slope*pow(h,this->power);
+
+	return cova;
+}
+/*}}}*/
+/*FUNCTION PowerVariogram::SemiVariogram{{{*/
+double PowerVariogram::SemiVariogram(double deltax,double deltay){
+	/*http://en.wikipedia.org/wiki/Variogram*/
+	double h,gamma;
+
+	/*Calculate length square*/
+	h=sqrt(pow(deltax,2.)+pow(deltay,2.));
+
+	/*return semi-variogram*/
+	gamma = this->nugget + this->slope*pow(h,this->power);
+
+	//if(h>1000) _printLine_("gamma = " << gamma << " h=" << h);
+	return gamma;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/kriging/PowerVariogram.h
===================================================================
--- /issm/trunk/src/c/classes/kriging/PowerVariogram.h	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/PowerVariogram.h	(revision 13395)
@@ -0,0 +1,35 @@
+/*! \file PowerVariogram.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+#ifndef _POWERVARIOGRAM_H_
+#define _POWERVARIOGRAM_H_
+
+/*Headers:*/
+#include "./Variogram.h"
+
+class PowerVariogram: public Variogram{
+
+	public:
+		double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin
+		double slope;  
+		double power; 
+
+		/*PowerVariogram constructors, destructors*/
+		PowerVariogram();
+		PowerVariogram(Options* options);
+		~PowerVariogram();
+
+		/*Object virtual functions definitions*/
+		void  Echo();
+		void  DeepEcho(){_error_("Not implemented yet");};
+		int   Id(){_error_("Not implemented yet");}; 
+		int   MyRank(){_error_("Not implemented yet");};
+		int   ObjectEnum(){_error_("Not implemented yet");};
+		Object* copy(){_error_("Not implemented yet");};
+
+		/*Variogram functions*/
+		double SemiVariogram(double deltax,double deltay);
+		double Covariance(double deltax,double deltay);
+};
+#endif  /* _POWERVARIOGRAM_H */
Index: /issm/trunk/src/c/classes/kriging/Quadtree.cpp
===================================================================
--- /issm/trunk/src/c/classes/kriging/Quadtree.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/Quadtree.cpp	(revision 13395)
@@ -0,0 +1,607 @@
+#include "../objects.h"
+
+/*DOCUMENTATION What is a Quadtree? {{{
+ * A Quadtree is a very simple way to group vertices according
+ * to their locations. A square that holds all the points of the mesh
+ * (or the geometry) is divided into 4 boxes. As soon as one box
+ * hold more than 4 vertices, it is divided into 4 new boxes, etc...
+ * There cannot be more than MAXDEEP (=30) subdivision.
+ * This process is like a Dichotomy in dimension 2
+ *
+ *  + - -  -    - -    -    - - + -   - + - + - + - -     - - +
+ *  |                           |       |   | X |             |
+ *                                      + - + - +
+ *  |                           |       |   |   |             |
+ *                              + -   - + - + - +             +
+ *  |                           |       |       |             |
+ *                         
+ *  |                           |       |       |             |
+ *  + - -  -    - -    -    - - + -   - + -   - + - -     - - +
+ *  |                           |               |             |
+ *                         
+ *  |                           |               |             |
+ *                         
+ *  |                           |               |             |
+ *  |                           |               |             |
+ *  + - -  -    - -    -    - - + -   -   -   - + - -     - - +
+ *  |                           |                             |
+ *                         
+ *  |                           |                             |
+ *                         
+ *  |                           |                             |
+ *                         
+ *  |                           |                             |
+ *  |                           |                             |
+ *  |                           |                             |
+ *  |                           |                             |
+ *  |                           |                             |
+ *  + - -  -    - -    -    - - + -   -   -   -   - -     - - +
+ *
+ * The coordinate system used in a quadtree are integers to avoid
+ * round-off errors. The vertex in the lower left box has the coordinates
+ * (0 0) 
+ * The upper right vertex has the follwing coordinates:
+ * 2^30 -1           2^30 -1        in decimal
+ * 0 1 1 1 .... 1    0 1 1 1 .... 1 in binary
+ *  \--   29  --/     \--   29  --/
+ * Using binaries is therefore very easy to locate a vertex in a box:
+ * we just need to look at the bits from the left to the right (See ::Add)
+ }}}*/
+/*MACROS {{{*/
+/* 
+ * 
+ *    J    j
+ *    ^    ^
+ *    |    | +--------+--------+
+ *    |    | |        |        |
+ * 1X |    | |   2    |   3    |
+ *    |    | |        |        |
+ *    |    | +--------+--------+
+ *    |    | |        |        |
+ * 0X |    | |   0    |   1    |
+ *    |    | |        |        |
+ *    |    | +--------+--------+
+ *    |    +-----------------------> i
+ *    |         
+ *    |----------------------------> I
+ *              X0        X1  
+ *
+ * box 0 -> I=0 J=0 IJ=00  = 0
+ * box 1 -> I=1 J=0 IJ=01  = 1
+ * box 2 -> I=0 J=1 IJ=10  = 2
+ * box 3 -> I=1 J=1 IJ=11  = 3
+ */
+//IJ(i,j,l) returns the box number of i and j with respect to l
+//if !j&l and !i&l -> 0 (box zero: lower left )
+//if !j&l and  i&l -> 1 (box one:  lower right)
+//if  j&l and !i&l -> 2 (box two:  upper left )
+//if  j&l and  i&l -> 3 (box three:upper right)
+#define IJ(i,j,l)  ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 ))
+/*}}}*/
+
+	/*Constructors/Destructors*/
+/*FUNCTION Quadtree::Quadtree(){{{*/
+Quadtree::Quadtree(){
+	_error_("Constructor not supported");
+
+}
+/*}}}*/
+/*FUNCTION Quadtree::Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth){{{*/
+Quadtree::Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth){
+
+	/*Intermediaries*/
+	double length;
+
+	/*Initialize fields*/
+	this->MaxDepth=maxdepth;
+	this->NbQuadtreeBox=0;
+	this->NbObs=0;
+
+	/*Create container*/
+	this->boxcontainer=new DataSet();
+
+	/*Create Root, pointer toward the main box*/
+	length=max(xmax-xmin,ymax-ymin);
+	this->root=NewQuadtreeBox(xmin+length/2,ymin+length/2,length);
+}
+/*}}}*/
+	/*FUNCTION Quadtree::~Quadtree(){{{*/
+	Quadtree::~Quadtree(){
+
+		delete boxcontainer;
+		root=NULL;
+
+	}
+	/*}}}*/
+
+	/*Methods*/
+/*FUNCTION Quadtree::Add{{{*/
+void  Quadtree::Add(Observation* observation){
+
+	/*Intermediaries*/
+	int          xi,yi,ij,level,levelbin;
+	QuadtreeBox **pbox    = NULL; // pointer toward current box b
+	QuadtreeBox **pmaster = NULL; // pointer toward master of b
+	QuadtreeBox  *box     = NULL; // current box b
+	QuadtreeBox  *slave   = NULL; // suslaveox of b (if necessary)
+	Observation  *obs[4];
+
+	/*Get integer coodinates*/
+	xi = observation->xi;
+	yi = observation->yi;
+
+	/*Initialize levels*/
+	level    = 0;
+	levelbin = (1L<MaxDepth);// = 2^30
+
+	/*Get inital box (the largest)*/
+	pmaster = &root;
+	pbox    = &root;
+
+	/*Find the smallest box where the observation is located*/
+	while((box=*pbox) && (box->nbitems<0)){ 
+
+		/*Go down one level (levelbin = 00100 -> 00010)*/
+		levelbin>>=1; level+=1; _assert_(levelMaxDepth);
+
+		/*Get next box according to the bit value (levelbin)*/
+		pmaster = pbox;
+		pbox    = &box->box[IJ(xi,yi,levelbin)];
+	}
+	_assert_(levelbin>0);
+
+	/*Now, try to add the vertex, if the box is full (nbitems=4), we have to divide it in 4 new boxes*/
+	while((box=*pbox) && (box->nbitems==4)){
+
+		/*Copy the 4 observation in the current Quadtreebox*/
+		obs[0] = box->obs[0];
+		obs[1] = box->obs[1];
+		obs[2] = box->obs[2];
+		obs[3] = box->obs[3];
+
+		/*set nbitems as -1 (now holding boxes instead of observations)*/
+		box->nbitems = -1;
+		box->box[0]  = NULL;
+		box->box[1]  = NULL;
+		box->box[2]  = NULL;
+		box->box[3]  = NULL;
+
+		/*Go down one level (levelbin = 00010 -> 00001)*/
+		levelbin>>=1; level+=1; _assert_(levelMaxDepth);
+
+		/*Put the four observations in the new boxes*/
+		for (int k=0;k<4;k++){
+
+			/*Get box for observation number k*/
+			ij    = IJ(obs[k]->xi,obs[k]->yi,levelbin);
+			slave = box->box[ij];
+			if(!slave){
+				box->box[ij] = NewQuadtreeBox(box,ij);
+				slave        = box->box[ij];
+			}
+			slave->obs[slave->nbitems++] = obs[k];
+		}
+
+		/*Get the suslaveox where the current observation is located*/
+		ij      = IJ(xi,yi,levelbin);
+		pmaster = pbox;
+		pbox    = &box->box[ij];
+	}
+
+	/*alloc the QuadtreeBox if necessary and add current observation*/
+	box = *pbox;
+	if(!box){
+		ij  = IJ(xi,yi,levelbin);
+		box = *pbox = NewQuadtreeBox(*pmaster,ij);
+	}
+	box->obs[box->nbitems++]=observation;
+	NbObs++;
+
+}/*}}}*/
+/*FUNCTION Quadtree::AddAndAverage{{{*/
+void Quadtree::AddAndAverage(double x,double y,double value){
+
+	QuadtreeBox **pbox = NULL;
+	QuadtreeBox  *box  = NULL;
+	int           xi,yi;
+	int           level,levelbin;
+	int           index;
+	double        length,length2;
+
+	/*Get integer coodinates*/
+	this->IntergerCoordinates(&xi,&yi,x,y);
+
+	/*Initialize levels*/
+	level    = 0;
+	levelbin = (1L<MaxDepth);// = 2^30
+
+	/*Get inital box (the largest)*/
+	pbox=&root;
+
+	/*Find the smallest box where this point is located*/
+	while((box=*pbox) && (box->nbitems<0)){ 
+
+		levelbin>>=1; level+=1; 
+
+		pbox = &box->box[IJ(xi,yi,levelbin)];
+	}
+
+	/*Add obervation in this box (should be full)*/
+	if(box && box->nbitems==4){
+		index  = 0;
+		length = pow(box->obs[0]->x - x,2.) + pow(box->obs[0]->y - y,2.);
+		for(int i=1;i<4;i++){
+			length2 = pow(box->obs[i]->x - x,2.) + pow(box->obs[i]->y - y,2.);
+			if(length2obs[index]->x = (box->obs[index]->weight*box->obs[index]->x + x)/(box->obs[index]->weight+1);
+		box->obs[index]->y = (box->obs[index]->weight*box->obs[index]->y + y)/(box->obs[index]->weight+1);
+		box->obs[index]->xi= int((box->obs[index]->weight*double(box->obs[index]->xi) + double(xi))/(box->obs[index]->weight+1));
+		box->obs[index]->yi= int((box->obs[index]->weight*double(box->obs[index]->yi) + double(yi))/(box->obs[index]->weight+1));
+		box->obs[index]->value   = (box->obs[index]->weight*box->obs[index]->value + value)/(box->obs[index]->weight+1);
+		box->obs[index]->weight += 1;
+	}
+	else{
+		_error_("Box is not full");
+	}
+}/*}}}*/
+/*FUNCTION Quadtree::ClosestObs{{{*/
+void Quadtree::ClosestObs(int *pindex,double x,double y){
+
+	QuadtreeBox **pbox = NULL;
+	QuadtreeBox  *box  = NULL;
+	int           xi,yi;
+	int           level,levelbin;
+	int           index = -1;
+	double        length,length2;
+
+	/*Get integer coodinates*/
+	this->IntergerCoordinates(&xi,&yi,x,y);
+
+	/*Initialize levels*/
+	level    = 0;
+	levelbin = (1L<MaxDepth);// = 2^30
+
+	/*Get inital box (the largest)*/
+	pbox=&root;
+
+	/*Find the smallest box where this point is located*/
+	while((box=*pbox) && (box->nbitems<0)){ 
+
+		levelbin>>=1; level+=1; 
+
+		pbox = &box->box[IJ(xi,yi,levelbin)];
+	}
+
+	/*Add obervation in this box (should be full)*/
+	if(box && box->nbitems>0){
+		index  = box->obs[0]->index;
+		length = pow(box->obs[0]->x - x,2.) + pow(box->obs[0]->y - y,2.);
+		for(int i=1;inbitems;i++){
+			length2 = pow(box->obs[i]->x - x,2.) + pow(box->obs[i]->y - y,2.);
+			if(length2obs[i]->index;
+				length = length2;
+			}
+		}
+	}
+
+	*pindex=index;
+}/*}}}*/
+/*FUNCTION Quadtree::Echo{{{*/
+void  Quadtree::Echo(void){
+
+	_printLine_("Quadtree:");
+	_printLine_("   MaxDepth      = " << this->MaxDepth);
+	_printLine_("   NbQuadtreeBox = " << this->NbQuadtreeBox);
+	_printLine_("   NbObs         = " << this->NbObs);
+	_printLine_("   root          = " << this->root);
+
+}/*}}}*/
+/*FUNCTION Quadtree::DeepEcho{{{*/
+void  Quadtree::DeepEcho(void){
+
+	_printLine_("Quadtree:");
+	_printLine_("   MaxDepth      = " << this->MaxDepth);
+	_printLine_("   NbQuadtreeBox = " << this->NbQuadtreeBox);
+	_printLine_("   NbObs         = " << this->NbObs);
+	_printLine_("   root          = " << this->root);
+	boxcontainer->Echo();
+
+}/*}}}*/
+/*FUNCTION Quadtree::IntergerCoordinates{{{*/
+void  Quadtree::IntergerCoordinates(int *xi,int *yi,double x,double y){
+
+	/*Intermediaries*/
+	double coefficient;
+	double xmin,ymin;
+
+	/*Checks in debugging mode*/
+	_assert_(xi && yi);
+	_assert_(this->root);
+
+	/*coeffIcoor is the coefficient used for integer coordinates:
+	 *                (x-xmin)
+	 * xi = (2^30 -1) --------- 
+	 *                 length
+	 * coefficient = (2^30 -1)/length
+	 */
+	coefficient = double((1L<MaxDepth)-1)/(this->root->length);
+	xmin        = this->root->xcenter - this->root->length/2;
+	ymin        = this->root->ycenter - this->root->length/2;
+
+	*xi=int(coefficient*(x - xmin));
+	*yi=int(coefficient*(y - ymin));
+}/*}}}*/
+/*FUNCTION Quadtree::NewQuadtreeBox(double xcenter,double ycenter,double length){{{*/
+Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(double xcenter,double ycenter,double length){
+
+	/*Output*/
+	QuadtreeBox* newbox=NULL;
+
+	/*Create and initialize a new box*/
+	newbox=new QuadtreeBox();
+	newbox->nbitems=0;
+	newbox->xcenter=xcenter;
+	newbox->ycenter=ycenter;
+	newbox->length=length;
+	newbox->box[0]=NULL;
+	newbox->box[1]=NULL;
+	newbox->box[2]=NULL;
+	newbox->box[3]=NULL;
+
+	/*Add to container*/
+	this->boxcontainer->AddObject(newbox);
+	NbQuadtreeBox++;
+
+	/*currentbox now points toward next quadtree box*/
+	return newbox;
+}/*}}}*/
+/*FUNCTION Quadtree::NewQuadtreeBox(QuadtreeBox* master,int index) {{{*/
+Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(QuadtreeBox* master,int index){
+
+	/*Output*/
+	QuadtreeBox* newbox=NULL;
+
+	/*Checks in debugging mode*/
+	_assert_(master);
+
+	/*Create and initialize a new box*/
+	newbox=new QuadtreeBox();
+	newbox->nbitems=0;
+	newbox->box[0]=NULL;
+	newbox->box[1]=NULL;
+	newbox->box[2]=NULL;
+	newbox->box[3]=NULL;
+	switch(index){
+		case 0:
+			newbox->xcenter=master->xcenter - master->length/4;
+			newbox->ycenter=master->ycenter - master->length/4;
+			break;
+		case 1:
+			newbox->xcenter=master->xcenter + master->length/4;
+			newbox->ycenter=master->ycenter - master->length/4;
+			break;
+		case 2:
+			newbox->xcenter=master->xcenter - master->length/4;
+			newbox->ycenter=master->ycenter + master->length/4;
+			break;
+		case 3:
+			newbox->xcenter=master->xcenter + master->length/4;
+			newbox->ycenter=master->ycenter + master->length/4;
+			break;
+		default:
+			_error_("Case " << index << " not supported");
+	}
+	newbox->length=master->length/2;
+
+	/*Add to container*/
+	this->boxcontainer->AddObject(newbox);
+	NbQuadtreeBox++;
+
+	/*currentbox now points toward next quadtree box*/
+	return newbox;
+}/*}}}*/
+/*FUNCTION Quadtree::QuadtreeDepth{{{*/
+void Quadtree::QuadtreeDepth(int* A,int xi,int yi){
+
+	QuadtreeBox **pbox = NULL;
+	QuadtreeBox  *box  = NULL;
+	int           level,levelbin;
+
+	/*Initialize levels*/
+	level    = 0;
+	levelbin = (1L<MaxDepth);// = 2^30
+
+	/*Get inital box (the largest)*/
+	pbox=&root;
+
+	/*Find the smallest box where this point is located*/
+	while((box=*pbox) && (box->nbitems<0)){ 
+
+		levelbin>>=1; level+=1; _assert_(levelMaxDepth);
+
+		pbox = &box->box[IJ(xi,yi,levelbin)];
+	}
+	if(box && box->nbitems>0){
+		/*This box is not empty, add one level*/
+		level+=1;
+	}
+
+	*A=level;
+}/*}}}*/
+/*FUNCTION Quadtree::QuadtreeDepth2{{{*/
+void Quadtree::QuadtreeDepth2(int* A,int xi,int yi){
+
+	QuadtreeBox **pbox = NULL;
+	QuadtreeBox  *box  = NULL;
+	int           level,levelbin;
+
+	/*Initialize levels*/
+	level    = 0;
+	levelbin = (1L<MaxDepth);// = 2^30
+
+	/*Get inital box (the largest)*/
+	pbox=&root;
+
+	/*Find the smallest box where this point is located*/
+	while((box=*pbox) && (box->nbitems<0)){ 
+
+		levelbin>>=1; level+=1; 
+
+		pbox = &box->box[IJ(xi,yi,levelbin)];
+	}
+	if(box && box->nbitems>0){
+		/*This box is not empty, add one level*/
+		level+=1;
+	}
+
+	/*If we were to add the vertex, get level*/
+	if(box && box->nbitems==4){
+		int ij;
+		bool flag=true;
+		while(flag){
+
+			levelbin>>=1; level+=1;
+			if(level>this->MaxDepth){
+				level+=1;
+				break;
+			}
+
+			/*loop over the four observations*/
+			ij=IJ(box->obs[0]->xi,box->obs[0]->yi,levelbin);
+			for (int k=1;k<4;k++){
+				if(IJ(box->obs[k]->xi,box->obs[k]->yi,levelbin) != ij){
+					flag = false;
+				}
+			}
+			if(IJ(xi,yi,levelbin)!=ij){
+				flag = false;
+			}
+		}
+	}
+
+	*A=level;
+}/*}}}*/
+/*FUNCTION Quadtree::RangeSearch{{{*/
+void Quadtree::RangeSearch(int **pindices,int *pnobs,double x,double y,double range){
+
+	/*Intermediaries*/
+	int  nobs;
+	int *indices = NULL;
+
+	/*Allocate indices (maximum by default*/
+	if(this->NbObs) indices = xNew(this->NbObs);
+	nobs = 0;
+
+	if(this->root) this->root->RangeSearch(indices,&nobs,x,y,range);
+
+	/*Clean-up and return*/
+	*pnobs=nobs;
+	*pindices=indices;
+
+}/*}}}*/
+
+/*QuadtreeBox methos*/
+/*FUNCTION QuadtreeBox::Echo{{{*/
+void  Quadtree::QuadtreeBox::Echo(void){
+
+	_printLine_("QuadtreeBox:");
+	_printLine_("   nbitems = " << this->nbitems);
+	_printLine_("   xcenter = " << this->xcenter);
+	_printLine_("   ycenter = " << this->ycenter);
+	_printLine_("   length  = " << this->length);
+
+}/*}}}*/
+/*FUNCTION QuadtreeBox::IsWithinRange{{{*/
+int Quadtree::QuadtreeBox::IsWithinRange(double x,double y,double range){
+
+	/*Return 0 if the 2 boxes do not overlap*/
+	if(this->xcenter+this->length/2 < x-range) return 0;
+	if(this->xcenter-this->length/2 > x+range) return 0;
+	if(this->ycenter+this->length/2 < y-range) return 0;
+	if(this->ycenter-this->length/2 > y+range) return 0;
+
+	/*Return 2 if the this box is included in the range*/
+	if(this->xcenter+this->length/2 <= x+range &&
+		this->ycenter+this->length/2 <= y+range &&
+		this->xcenter-this->length/2 >= x-range &&
+		this->ycenter-this->length/2 >= y-range) return 2;
+
+	/*This is a simple overlap*/
+	return 1;
+
+}/*}}}*/
+/*FUNCTION QuadtreeBox::RangeSearch{{{*/
+void Quadtree::QuadtreeBox::RangeSearch(int* indices,int *pnobs,double x,double y,double range){
+
+	/*Intermediaries*/
+	int i,nobs;
+
+	/*Recover current number of observations*/
+	nobs = *pnobs;
+
+	switch(this->IsWithinRange(x,y,range)){
+		case 0:
+			/*If this box is not within range, return*/
+			break;
+		case 2:
+			/*This box is included in range*/
+			this->WriteObservations(indices,&nobs);
+			break;
+		case 1:
+			/*This box is partly included*/
+			if(this->nbitems>0){
+				/*If this box has only observations, add indices that are within range*/
+				for(i=0;inbitems;i++){
+					if(fabs(this->obs[i]->x-x) <= range && fabs(this->obs[i]->y-y) <= range){
+						indices[nobs++]=this->obs[i]->index;
+					}
+				}
+			}
+			else{
+				/*This box points toward boxes*/
+				if(this->box[0]) this->box[0]->RangeSearch(indices,&nobs,x,y,range);
+				if(this->box[1]) this->box[1]->RangeSearch(indices,&nobs,x,y,range);
+				if(this->box[2]) this->box[2]->RangeSearch(indices,&nobs,x,y,range);
+				if(this->box[3]) this->box[3]->RangeSearch(indices,&nobs,x,y,range);
+			}
+			break;
+		default:
+			_error_("Case " << this->IsWithinRange(x,y,range) << " not supported");
+	}
+
+	/*Assign output pointers: */
+	*pnobs=nobs;
+}/*}}}*/
+/*FUNCTION QuadtreeBox::WriteObservations{{{*/
+void Quadtree::QuadtreeBox::WriteObservations(int* indices,int *pnobs){
+
+	/*Intermediaries*/
+	int i,nobs;
+
+	/*Recover current number of observations*/
+	nobs = *pnobs;
+
+	if(this->nbitems>0){
+		/*If this box has only observations, add all indices*/
+		for(i=0;inbitems;i++){
+			indices[nobs++]=this->obs[i]->index;
+		}
+	}
+	else{
+		/*This box points toward boxes, */
+		if(this->box[0]) this->box[0]->WriteObservations(indices,&nobs);
+		if(this->box[1]) this->box[1]->WriteObservations(indices,&nobs);
+		if(this->box[2]) this->box[2]->WriteObservations(indices,&nobs);
+		if(this->box[3]) this->box[3]->WriteObservations(indices,&nobs);
+	}
+
+	/*Assign output pointers: */
+	*pnobs=nobs;
+}/*}}}*/
Index: /issm/trunk/src/c/classes/kriging/Quadtree.h
===================================================================
--- /issm/trunk/src/c/classes/kriging/Quadtree.h	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/Quadtree.h	(revision 13395)
@@ -0,0 +1,66 @@
+
+#ifndef _QUADTREE_H
+#define _QUADTREE_H
+
+class Observation;
+
+class Quadtree{
+
+	private:
+		/* A quadtree box contains up to 4 points (locations). 4 new quadtree boxes are
+		 * created if a fifth point is added to the same box. A Quadtree box is therefore
+		 * composed of EITHER:
+		 * - up to 4 vertices
+		 * - 4 "sub" quadtree boxes*/
+
+		class QuadtreeBox: public Object{ 
+			public:
+				int    nbitems; // number of current vertices in the box
+				double xcenter; // x position of the center (double)
+				double ycenter; // x position of the center (double)
+				double length;  // width of the box
+				union{
+					QuadtreeBox *box[4];
+					Observation *obs[4];
+				};
+
+				/*Object functions (Needed because the Quadtree uses a Container*/
+				void    Echo();
+				void    DeepEcho()  {_error_("not implemented yet"); };
+				int     Id()        {_error_("not implemented yet"); };
+				int     MyRank()    {_error_("not implemented yet"); };
+				int     ObjectEnum(){_error_("not implemented yet"); };
+				Object *copy()      {_error_("not implemented yet"); };
+
+				/*Methods*/
+				int          IsWithinRange(double  x,double y,double range);
+				void         RangeSearch(int *indices,int *pnobs,double x,double y,double range);
+				void         WriteObservations(int *indices,int *pnobs);
+
+		};
+
+		/*Quadtree private Fields*/
+		DataSet* boxcontainer;
+
+	public:
+		int          MaxDepth;          // maximum number of subdivision
+		QuadtreeBox *root;              // main box
+		int          NbQuadtreeBox;     // total number of boxes
+		int          NbObs;             // number of points
+
+		Quadtree();
+		Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth_in);
+		~Quadtree();
+		void         Add(Observation *observation);
+		void         AddAndAverage(double x,double y,double value);
+		void         ClosestObs(int *pindex,double x,double y);
+		void         DeepEcho(void);
+		void         Echo(void);
+		void         IntergerCoordinates(int *xi,int *yi,double x,double y);
+		QuadtreeBox *NewQuadtreeBox(double xcenter,double ycenter,double length);
+		QuadtreeBox *NewQuadtreeBox(QuadtreeBox* master,int index);
+		void         QuadtreeDepth(int *A,int xi,int yi);
+		void         QuadtreeDepth2(int *A,int xi,int yi);
+		void         RangeSearch(int **pindices,int *pnobs,double x,double y,double range);
+};
+#endif //_QUADTREE_H
Index: /issm/trunk/src/c/classes/kriging/SphericalVariogram.cpp
===================================================================
--- /issm/trunk/src/c/classes/kriging/SphericalVariogram.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/SphericalVariogram.cpp	(revision 13395)
@@ -0,0 +1,98 @@
+/*!\file SphericalVariogram.c
+ * \brief: implementation of the SphericalVariogram object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../shared/shared.h"
+#include "../../include/include.h"
+
+/*SphericalVariogram constructors and destructor*/
+/*FUNCTION SphericalVariogram::SphericalVariogram(){{{*/
+SphericalVariogram::SphericalVariogram(){
+	this->nugget = 0.2;
+	this->sill   = 1;
+	this->range  = SQRT3;
+	return;
+}
+/*}}}*/
+/*FUNCTION SphericalVariogram::SphericalVariogram(Options* options){{{*/
+SphericalVariogram::SphericalVariogram(Options* options){
+
+	/*Defaults*/
+	this->nugget = 0.2;
+	this->sill   = 1;
+	this->range  = SQRT3;
+
+	/*Overwrite from options*/
+	if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget");
+	if(options->GetOption("sill"))   options->Get(&this->sill,"sill");
+	if(options->GetOption("range"))  options->Get(&this->range,"range");
+
+	/*Checks*/
+	if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)");
+}
+/*}}}*/
+/*FUNCTION SphericalVariogram::~SphericalVariogram(){{{*/
+SphericalVariogram::~SphericalVariogram(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION SphericalVariogram::Echo {{{*/
+void SphericalVariogram::Echo(void){
+	_printLine_("SphericalVariogram");
+	_printLine_("   nugget: " << this->nugget);
+	_printLine_("   sill  : " << this->sill);
+	_printLine_("   range : " << this->range);
+}
+/*}}}*/
+
+/*Variogram function*/
+/*FUNCTION SphericalVariogram::Covariance{{{*/
+double SphericalVariogram::Covariance(double deltax,double deltay){
+	/*The covariance can be deduced from the variogram from the following
+	 * relationship:
+	 *    2 gamma = C(x,x) + C(y,y) -2 C(x,y)
+	 * so
+	 *    C(h) = sill - gamma                                            */
+	double h,cova;
+
+	/*Calculate length square*/
+	h=sqrt(pow(deltax,2.)+pow(deltay,2.));
+
+	/*return covariance*/
+	if(h<=range)
+	 cova = (sill-nugget)*(1 - (3*h)/(2*range) + pow(h,3.)/(2*pow(range,3.)) );
+	else
+	 cova = 0.;
+
+	return cova;
+}
+/*}}}*/
+/*FUNCTION SphericalVariogram::SemiVariogram{{{*/
+double SphericalVariogram::SemiVariogram(double deltax,double deltay){
+	/*http://en.wikipedia.org/wiki/Variogram*/
+	double h,gamma;
+
+	/*Calculate length square*/
+	h=sqrt(pow(deltax,2.)+pow(deltay,2.));
+
+	/*return semi-variogram*/
+	if(h<=range)
+	 gamma = (sill-nugget)*( (3*h)/(2*range) - pow(h,3.)/(2*pow(range,3.)) ) + nugget;
+	else
+	 gamma = sill;
+
+	return gamma;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/kriging/SphericalVariogram.h
===================================================================
--- /issm/trunk/src/c/classes/kriging/SphericalVariogram.h	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/SphericalVariogram.h	(revision 13395)
@@ -0,0 +1,35 @@
+/*! \file SphericalVariogram.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+#ifndef _SPHERICALVARIOGRAM_H_
+#define _SPHERICALVARIOGRAM_H_
+
+/*Headers:*/
+#include "./Variogram.h"
+
+class SphericalVariogram: public Variogram{
+
+	public:
+		double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin
+		double sill;   //Limit of the variogram tending to infinity lag distances
+		double range;  //The distance in which the difference of the variogram from the sill becomes negligible
+
+		/*SphericalVariogram constructors, destructors*/
+		SphericalVariogram();
+		SphericalVariogram(Options* options);
+		~SphericalVariogram();
+
+		/*Object virtual functions definitions*/
+		void  Echo();
+		void  DeepEcho(){_error_("Not implemented yet");};
+		int   Id(){_error_("Not implemented yet");}; 
+		int   MyRank(){_error_("Not implemented yet");};
+		int   ObjectEnum(){_error_("Not implemented yet");};
+		Object* copy(){_error_("Not implemented yet");};
+
+		/*Variogram functions*/
+		double SemiVariogram(double deltax,double deltay);
+		double Covariance(double deltax,double deltay);
+};
+#endif  /* _SPHERICALVARIOGRAM_H */
Index: /issm/trunk/src/c/classes/kriging/Variogram.h
===================================================================
--- /issm/trunk/src/c/classes/kriging/Variogram.h	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/Variogram.h	(revision 13395)
@@ -0,0 +1,18 @@
+/*!\file:  Variogram.h
+ * \brief abstract class for Variogram object
+ */ 
+
+#ifndef _VARIOGRAM_H_
+#define _VARIOGRAM_H_
+
+#include "../objects/Object.h"
+
+class Variogram: public Object{
+
+	public: 
+		virtual ~Variogram(){};
+		virtual double SemiVariogram(double deltax,double deltay)=0;
+		virtual double Covariance(double deltax,double deltay)=0;
+
+};
+#endif
Index: /issm/trunk/src/c/classes/kriging/krigingobjects.h
===================================================================
--- /issm/trunk/src/c/classes/kriging/krigingobjects.h	(revision 13395)
+++ /issm/trunk/src/c/classes/kriging/krigingobjects.h	(revision 13395)
@@ -0,0 +1,17 @@
+/* \file krigingobjects.h
+ * \brief: prototype header for all kriging objects.
+ */
+
+#ifndef KRIGING_OBJECTS_H_
+#define KRIGING_OBJECTS_H_
+
+/*Kriging*/
+#include "./Variogram.h"
+#include "./GaussianVariogram.h"
+#include "./ExponentialVariogram.h"
+#include "./SphericalVariogram.h"
+#include "./PowerVariogram.h"
+#include "./Quadtree.h"
+#include "./Observation.h"
+
+#endif
Index: /issm/trunk/src/c/classes/matrix/ElementMatrix.cpp
===================================================================
--- /issm/trunk/src/c/classes/matrix/ElementMatrix.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/matrix/ElementMatrix.cpp	(revision 13395)
@@ -0,0 +1,496 @@
+/*!\file ElementMatrix.cpp
+ * \brief: implementation of the ElementMatrix object, used to plug values from element into global stiffness matrix
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../classes.h"
+#include "../../shared/shared.h"
+#include "../../Container/Container.h"
+#include "../../include/include.h"
+/*}}}*/
+
+/*ElementMatrix constructors and destructor*/
+/*FUNCTION ElementMatrix::ElementMatrix(){{{*/
+ElementMatrix::ElementMatrix(){
+
+	this->nrows=0;
+	this->ncols=0;
+	this->values=NULL;
+	this->dofsymmetrical=false;
+
+	this->row_fsize=0;
+	this->row_flocaldoflist=NULL;
+	this->row_fglobaldoflist=NULL;
+	this->row_ssize=0;
+	this->row_slocaldoflist=NULL;
+	this->row_sglobaldoflist=NULL;
+
+	this->col_fsize=0;
+	this->col_flocaldoflist=NULL;
+	this->col_fglobaldoflist=NULL;
+	this->col_ssize=0;
+	this->col_slocaldoflist=NULL;
+	this->col_sglobaldoflist=NULL;
+
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::ElementMatrix(ElementMatrix* Ke){{{*/
+ElementMatrix::ElementMatrix(ElementMatrix* Ke){
+
+	if(!Ke) _error_("Input Element Matrix is a NULL pointer");
+	this->Init(Ke);
+	return;
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::ElementMatrix(ElementMatrix* Ke1, ElementMatrix* Ke2){{{*/
+ElementMatrix::ElementMatrix(ElementMatrix* Ke1, ElementMatrix* Ke2){
+
+	/*intermediaries*/
+	int i,j,counter;
+	int gsize,fsize,ssize;
+	int* P=NULL;
+	bool found;
+
+	/*If one of the two matrix is NULL, we copy the other one*/
+	if(!Ke1 && !Ke2){
+		_error_("Two input element matrices are NULL");
+	}
+	else if(!Ke1){
+		this->Init(Ke2);
+		return;
+	}
+	else if(!Ke2){
+		this->Init(Ke1);
+		return;
+	}
+
+	/*General Case: Ke1 and Ke2 are not empty*/
+	if(!Ke1->dofsymmetrical || !Ke2->dofsymmetrical) _error_("merging 2 non dofsymmetrical matrices not implemented yet");
+
+	/*Initialize itransformation matrix Ke[P[i]] = Ke2[i]*/
+	P=xNew(Ke2->nrows);
+
+	/*1: Get the new numbering of Ke2 and get size of the new matrix*/
+	gsize=Ke1->nrows;
+	for(i=0;inrows;i++){
+		found=false;
+		for(j=0;jnrows;j++){
+			if(Ke2->gglobaldoflist[i]==Ke1->gglobaldoflist[j]){
+				found=true; P[i]=j; break;
+			}
+		}
+		if(!found){
+			P[i]=gsize; gsize++;
+		}
+	}
+
+	/*2: Initialize static fields*/
+	this->nrows=gsize;
+	this->ncols=gsize;
+	this->dofsymmetrical=true;
+
+	/*Gset and values*/
+	this->gglobaldoflist=xNew(this->nrows);
+	this->values=xNewZeroInit(this->nrows*this->ncols);
+	for(i=0;inrows;i++){
+		for(j=0;jncols;j++){
+			this->values[i*this->ncols+j] += Ke1->values[i*Ke1->ncols+j];
+		}
+		this->gglobaldoflist[i]=Ke1->gglobaldoflist[i];
+	}
+	for(i=0;inrows;i++){
+		for(j=0;jncols;j++){
+			this->values[P[i]*this->ncols+P[j]] += Ke2->values[i*Ke2->ncols+j];
+		}
+		this->gglobaldoflist[P[i]]=Ke2->gglobaldoflist[i];
+	}
+
+	/*Fset*/
+	fsize=Ke1->row_fsize;
+	for(i=0;irow_fsize;i++){
+		if(P[Ke2->row_flocaldoflist[i]] >= Ke1->nrows) fsize++;
+	}
+	this->row_fsize=fsize;
+	if(fsize){
+		this->row_flocaldoflist =xNew(fsize);
+		this->row_fglobaldoflist=xNew(fsize);
+		for(i=0;irow_fsize;i++){
+			this->row_flocaldoflist[i] =Ke1->row_flocaldoflist[i];
+			this->row_fglobaldoflist[i]=Ke1->row_fglobaldoflist[i];
+		}
+		counter=Ke1->row_fsize;
+		for(i=0;irow_fsize;i++){
+			if(P[Ke2->row_flocaldoflist[i]] >= Ke1->nrows){
+				this->row_flocaldoflist[counter] =P[Ke2->row_flocaldoflist[i]];
+				this->row_fglobaldoflist[counter]=Ke2->row_fglobaldoflist[i];
+				counter++;
+			}
+		}
+	}
+	else{
+		this->row_flocaldoflist=NULL;
+		this->row_fglobaldoflist=NULL;
+	}
+
+	/*Sset*/
+	ssize=Ke1->row_ssize;
+	for(i=0;irow_ssize;i++){
+		if(P[Ke2->row_slocaldoflist[i]] >= Ke1->nrows) ssize++;
+	}
+	this->row_ssize=ssize;
+	if(ssize){
+		this->row_slocaldoflist =xNew(ssize);
+		this->row_sglobaldoflist=xNew(ssize);
+		for(i=0;irow_ssize;i++){
+			this->row_slocaldoflist[i] =Ke1->row_slocaldoflist[i];
+			this->row_sglobaldoflist[i]=Ke1->row_sglobaldoflist[i];
+		}
+		counter=Ke1->row_ssize;
+		for(i=0;irow_ssize;i++){
+			if(P[Ke2->row_slocaldoflist[i]] >= Ke1->nrows){
+				this->row_slocaldoflist[counter] =P[Ke2->row_slocaldoflist[i]];
+				this->row_sglobaldoflist[counter]=Ke2->row_sglobaldoflist[i];
+				counter++;
+			}
+		}
+	}
+	else{
+		this->row_slocaldoflist=NULL;
+		this->row_sglobaldoflist=NULL;
+	}
+
+	/*don't do cols, we can pick them up from the rows: */
+	this->col_fsize=0;
+	this->col_flocaldoflist=NULL;
+	this->col_fglobaldoflist=NULL;
+	this->col_ssize=0;
+	this->col_slocaldoflist=NULL;
+	this->col_sglobaldoflist=NULL;
+
+	/*clean-up*/
+	xDelete(P);
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::ElementMatrix(ElementMatrix* Ke1, ElementMatrix* Ke2,ElementMatrix* Ke3){{{*/
+ElementMatrix::ElementMatrix(ElementMatrix* Ke1, ElementMatrix* Ke2,ElementMatrix* Ke3){
+
+	/*Concatenate all matrices*/
+	ElementMatrix* Ke12 =new ElementMatrix(Ke1,Ke2);
+	ElementMatrix* Ke123=new ElementMatrix(Ke12,Ke3);
+
+	/*Initialize current object with this matrix*/
+	this->Init(Ke123);
+
+	/*clean-up*/
+	delete Ke12;
+	delete Ke123;
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::ElementMatrix(Node** nodes,int numnodes,Parameters* parameters,int approximation){{{*/
+ElementMatrix::ElementMatrix(Node** nodes,int numnodes,Parameters* parameters,int approximation){
+
+	/*get Matrix size and properties*/
+	this->dofsymmetrical=true;
+	this->nrows=GetNumberOfDofs(nodes,numnodes,GsetEnum,approximation);
+	this->ncols=this->nrows;
+
+	/*fill values with 0: */
+	this->values=xNewZeroInit(this->nrows*this->ncols);
+
+	/*g list*/
+	this->gglobaldoflist=GetGlobalDofList(nodes,numnodes,GsetEnum,approximation);
+
+	/*get dof lists for f and s set: */
+	this->row_fsize=GetNumberOfDofs(nodes,numnodes,FsetEnum,approximation);
+	this->row_flocaldoflist =GetLocalDofList( nodes,numnodes,FsetEnum,approximation);
+	this->row_fglobaldoflist=GetGlobalDofList(nodes,numnodes,FsetEnum,approximation);
+	this->row_ssize=GetNumberOfDofs(nodes,numnodes,SsetEnum,approximation);
+	this->row_slocaldoflist =GetLocalDofList( nodes,numnodes,SsetEnum,approximation);
+	this->row_sglobaldoflist=GetGlobalDofList(nodes,numnodes,SsetEnum,approximation);
+
+	/*Because this matrix is "dofsymmetrical" don't do cols, we can pick them up from the rows: */
+	this->col_fsize=0;
+	this->col_flocaldoflist=NULL;
+	this->col_fglobaldoflist=NULL;
+	this->col_ssize=0;
+	this->col_slocaldoflist=NULL;
+	this->col_sglobaldoflist=NULL;
+
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::~ElementMatrix(){{{*/
+ElementMatrix::~ElementMatrix(){
+	
+	xDelete(this->values);
+	xDelete(this->gglobaldoflist);
+	xDelete(this->row_flocaldoflist);
+	xDelete(this->row_fglobaldoflist);
+	xDelete(this->row_slocaldoflist);
+	xDelete(this->row_sglobaldoflist);
+	xDelete(this->col_flocaldoflist);
+	xDelete(this->col_fglobaldoflist);
+	xDelete(this->col_slocaldoflist);
+	xDelete(this->col_sglobaldoflist);
+}
+/*}}}*/
+
+/*ElementMatrix specific routines: */
+/*FUNCTION ElementMatrix::AddToGlobal(Matrix* Kff, Matrix* Kfs){{{*/
+void ElementMatrix::AddToGlobal(Matrix* Kff, Matrix* Kfs){
+
+	int i,j;
+	IssmDouble* localvalues=NULL;
+
+	/*If Kfs is not provided, call the other function*/
+	if(!Kfs){
+		this->AddToGlobal(Kff);
+		return;
+	}
+
+	/*In debugging mode, check consistency (no NaN, and values not too big)*/
+	this->CheckConsistency();
+
+	if(this->dofsymmetrical){
+		/*only use row dofs to add values into global matrices: */
+
+		if(this->row_fsize){
+			/*first, retrieve values that are in the f-set from the g-set values matrix: */
+			localvalues=xNew(this->row_fsize*this->row_fsize);
+			for(i=0;irow_fsize;i++){
+				for(j=0;jrow_fsize;j++){
+					*(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]);
+				}
+			}
+			/*add local values into global  matrix, using the fglobaldoflist: */
+			Kff->SetValues(this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,localvalues,ADD_VAL);
+
+			/*Free ressources:*/
+			xDelete(localvalues);
+		}
+
+
+		if((this->row_ssize!=0) && (this->row_fsize!=0)){
+			/*first, retrieve values that are in the f and s-set from the g-set values matrix: */
+			localvalues=xNew(this->row_fsize*this->row_ssize);
+			for(i=0;irow_fsize;i++){
+				for(j=0;jrow_ssize;j++){
+					*(localvalues+this->row_ssize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_slocaldoflist[j]);
+				}
+			}
+			/*add local values into global  matrix, using the fglobaldoflist: */
+			Kfs->SetValues(this->row_fsize,this->row_fglobaldoflist,this->row_ssize,this->row_sglobaldoflist,localvalues,ADD_VAL);
+
+			/*Free ressources:*/
+			xDelete(localvalues);
+		}
+	}
+	else{
+		_error_("non dofsymmetrical matrix AddToGlobal routine not support yet!");
+	}
+
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::AddToGlobal(Matrix* Jff){{{*/
+void ElementMatrix::AddToGlobal(Matrix* Jff){
+
+	int i,j;
+	IssmDouble* localvalues=NULL;
+
+	/*Check that Jff is not NULL*/
+	_assert_(Jff); 
+
+	/*In debugging mode, check consistency (no NaN, and values not too big)*/
+	this->CheckConsistency();
+
+	if(this->dofsymmetrical){
+		/*only use row dofs to add values into global matrices: */
+
+		if(this->row_fsize){
+			/*first, retrieve values that are in the f-set from the g-set values matrix: */
+			localvalues=xNew(this->row_fsize*this->row_fsize);
+			for(i=0;irow_fsize;i++){
+				for(j=0;jrow_fsize;j++){
+					*(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]);
+				}
+			}
+			/*add local values into global  matrix, using the fglobaldoflist: */
+			Jff->SetValues(this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,localvalues,ADD_VAL);
+
+			/*Free ressources:*/
+			xDelete(localvalues);
+		}
+
+	}
+	else{
+		_error_("non dofsymmetrical matrix AddToGlobal routine not support yet!");
+	}
+
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::CheckConsistency{{{*/
+void ElementMatrix::CheckConsistency(void){
+	/*Check element matrix values, only in debugging mode*/
+	#ifdef _ISSM_DEBUG_ 
+	for (int i=0;inrows;i++){
+		for(int j=0;jncols;j++){
+			if (xIsNan(this->values[i*this->ncols+j])) _error_("NaN found in Element Matrix");
+			if (fabs(this->values[i*this->ncols+j])>1.e+50) _error_("Element Matrix values exceeds 1.e+50");
+		}
+	}
+	#endif
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::Transpose{{{*/
+void ElementMatrix::Transpose(void){
+
+	/*Intermediaries*/
+	ElementMatrix* Ke_copy=new ElementMatrix(this);
+
+	/*Update sizes*/
+	this->nrows=Ke_copy->ncols;
+	this->ncols=Ke_copy->nrows;
+
+	/*Transpose values*/
+	for (int i=0;inrows;i++) for(int j=0;jncols;j++) this->values[i*this->ncols+j]=Ke_copy->values[j*Ke_copy->ncols+i];
+
+	/*Transpose indices*/
+	if(!dofsymmetrical){
+		_error_("not supported yet");
+	}
+
+	/*Clean up and return*/
+	delete Ke_copy;
+	return;
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::Echo{{{*/
+void ElementMatrix::Echo(void){
+
+	int i,j;
+	_printLine_("Element Matrix echo:");
+	_printLine_("   nrows: " << this->nrows);
+	_printLine_("   ncols: " << this->ncols);
+	_printLine_("   dofsymmetrical: " << (dofsymmetrical?"true":"false"));
+
+	_printLine_("   values:");
+	for(i=0;inrows =Ke->nrows;
+	this->ncols =Ke->ncols;
+	this->dofsymmetrical=Ke->dofsymmetrical;
+
+	this->values=xNew(this->nrows*this->ncols);
+	xMemCpy(this->values,Ke->values,this->nrows*this->ncols);
+
+	this->gglobaldoflist=xNew(this->nrows);
+	xMemCpy(this->gglobaldoflist,Ke->gglobaldoflist,this->nrows);
+
+	this->row_fsize=Ke->row_fsize;
+	if(this->row_fsize){
+		this->row_flocaldoflist=xNew(this->row_fsize);
+		xMemCpy(this->row_flocaldoflist,Ke->row_flocaldoflist,this->row_fsize);
+		this->row_fglobaldoflist=xNew(this->row_fsize);
+		xMemCpy(this->row_fglobaldoflist,Ke->row_fglobaldoflist,this->row_fsize);
+	}
+	else{
+		this->row_flocaldoflist=NULL;
+		this->row_fglobaldoflist=NULL;
+	}
+
+	this->row_ssize=Ke->row_ssize;
+	if(this->row_ssize){
+		this->row_slocaldoflist=xNew(this->row_ssize);
+		xMemCpy(this->row_slocaldoflist,Ke->row_slocaldoflist,this->row_ssize);
+		this->row_sglobaldoflist=xNew(this->row_ssize);
+		xMemCpy(this->row_sglobaldoflist,Ke->row_sglobaldoflist,this->row_ssize);
+	}
+	else{
+		this->row_slocaldoflist=NULL;
+		this->row_sglobaldoflist=NULL;
+	}
+
+	this->col_fsize=Ke->col_fsize;
+	if(this->col_fsize){
+		this->col_flocaldoflist=xNew(this->col_fsize);
+		xMemCpy(this->col_flocaldoflist,Ke->col_flocaldoflist,this->col_fsize);
+		this->col_fglobaldoflist=xNew(this->col_fsize);
+		xMemCpy(this->col_fglobaldoflist,Ke->col_fglobaldoflist,this->col_fsize);
+	}
+	else{
+		this->col_flocaldoflist=NULL;
+		this->col_fglobaldoflist=NULL;
+	}
+
+	this->col_ssize=Ke->col_ssize;
+	if(this->col_ssize){
+		this->col_slocaldoflist=xNew(this->col_ssize);
+		xMemCpy(this->col_slocaldoflist,Ke->col_slocaldoflist,this->col_ssize);
+		this->col_sglobaldoflist=xNew(this->col_ssize);
+		xMemCpy(this->col_sglobaldoflist,Ke->col_sglobaldoflist,this->col_ssize);
+	}
+	else{
+		this->col_slocaldoflist=NULL;
+		this->col_sglobaldoflist=NULL;
+	}
+}
+/*}}}*/
+/*FUNCTION ElementMatrix::SetDiag{{{*/
+void ElementMatrix::SetDiag(IssmDouble scalar){
+
+	int i;
+
+	if(this->nrows!=this->ncols)_error_("need square matrix in input!");
+
+	for(i=0;inrows;i++){
+		this->values[this->ncols*i+i]=scalar;
+	}
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/matrix/ElementMatrix.h
===================================================================
--- /issm/trunk/src/c/classes/matrix/ElementMatrix.h	(revision 13395)
+++ /issm/trunk/src/c/classes/matrix/ElementMatrix.h	(revision 13395)
@@ -0,0 +1,71 @@
+/*!\file:  ElementMatrix.h
+ * \brief container for information needed to plug element matrix generated by elements 
+ * into the Kff and Kfs global matrices. 
+ * This object will hold the element matrix on the g-set, the local as well as global 
+ * dof lists in the f and s sets.
+ */ 
+
+#ifndef _ELEMENT_MATRIX_H_
+#define _ELEMENT_MATRIX_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../objects/Object.h"
+#include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+class Node;
+template  class Matrix;
+class Parameters;
+/*}}}*/
+
+class ElementMatrix{
+
+	public:
+	
+		int      nrows;
+		int      ncols;
+		bool     dofsymmetrical;
+		IssmDouble*  values;
+
+		//gset
+		int*     gglobaldoflist;
+
+		/*row wise: */
+		//fset
+		int      row_fsize;
+		int*     row_flocaldoflist;
+		int*     row_fglobaldoflist;
+		//sset
+		int      row_ssize;
+		int*     row_slocaldoflist;
+		int*     row_sglobaldoflist;
+
+		/*column wise: */
+		//fset
+		int      col_fsize;
+		int*     col_flocaldoflist;
+		int*     col_fglobaldoflist;
+		//sset
+		int      col_ssize;
+		int*     col_slocaldoflist;
+		int*     col_sglobaldoflist;
+
+		/*ElementMatrix constructors, destructors {{{*/
+		ElementMatrix();
+		ElementMatrix(ElementMatrix* Ke);
+		ElementMatrix(ElementMatrix* Ke1,ElementMatrix* Ke2);
+		ElementMatrix(ElementMatrix* Ke1,ElementMatrix* Ke2,ElementMatrix* Ke3);
+		ElementMatrix(Node** nodes,int numnodes,Parameters* parameters,int approximation=NoneApproximationEnum);
+		~ElementMatrix();
+		/*}}}*/
+		/*ElementMatrix specific routines {{{*/
+		void AddToGlobal(Matrix* Kff, Matrix* Kfs);
+		void AddToGlobal(Matrix* Jff);
+		void Echo(void);
+		void CheckConsistency(void);
+		void Transpose(void);
+		void Init(ElementMatrix* Ke);
+		void SetDiag(IssmDouble scalar);
+		/*}}}*/
+};
+#endif //#ifndef _ELEMENT_MATRIX_H_
Index: /issm/trunk/src/c/classes/matrix/ElementVector.cpp
===================================================================
--- /issm/trunk/src/c/classes/matrix/ElementVector.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/matrix/ElementVector.cpp	(revision 13395)
@@ -0,0 +1,276 @@
+/*!\file ElementVector.cpp
+ * \brief: implementation of the ElementVector object, used to plug values from element into global load
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../classes.h"
+#include "../../shared/shared.h"
+#include "../../Container/Container.h"
+#include "../../include/include.h"
+/*}}}*/
+
+/*ElementVector constructors and destructor*/
+/*FUNCTION ElementVector::ElementVector(){{{*/
+ElementVector::ElementVector(){
+
+	this->nrows=0;
+	this->values=NULL;
+	this->fsize=0;
+	this->flocaldoflist=NULL;
+	this->fglobaldoflist=NULL;
+
+}
+/*}}}*/
+/*FUNCTION ElementVector::ElementVector(ElementVector* pe1, ElementVector* pe2){{{*/
+ElementVector::ElementVector(ElementVector* pe1, ElementVector* pe2){
+
+	/*intermediaries*/
+	int i,j,counter;
+	int gsize,fsize,ssize;
+	int* P=NULL;
+	bool found;
+
+	/*If one of the two matrix is NULL, we copy the other one*/
+	if(!pe1 && !pe2){
+		_error_("Two input element matrices are NULL");
+	}
+	else if(!pe1){
+		this->Init(pe2);
+		return;
+	}
+	else if(!pe2){
+		this->Init(pe1);
+		return;
+	}
+
+	/*Initialize itransformation matrix pe[P[i]] = pe2[i]*/
+	P=xNew(pe2->nrows);
+
+	/*1: Get the new numbering of pe2 and get size of the new matrix*/
+	gsize=pe1->nrows;
+	for(i=0;inrows;i++){
+		found=false;
+		for(j=0;jnrows;j++){
+			if(pe2->gglobaldoflist[i]==pe1->gglobaldoflist[j]){
+				found=true; P[i]=j; break;
+			}
+		}
+		if(!found){
+			P[i]=gsize; gsize++;
+		}
+	}
+
+	/*2: Initialize static fields*/
+	this->nrows=gsize;
+
+	/*Gset and values*/
+	this->gglobaldoflist=xNew(this->nrows);
+	this->values=xNewZeroInit(this->nrows);
+	for(i=0;inrows;i++){
+		this->values[i] += pe1->values[i];
+		this->gglobaldoflist[i]=pe1->gglobaldoflist[i];
+	}
+	for(i=0;inrows;i++){
+		this->values[P[i]] += pe2->values[i];
+		this->gglobaldoflist[P[i]]=pe2->gglobaldoflist[i];
+	}
+
+	/*Fset*/
+	fsize=pe1->fsize;
+	for(i=0;ifsize;i++){
+		if(P[pe2->flocaldoflist[i]] >= pe1->nrows) fsize++;
+	}
+	this->fsize=fsize;
+	if(fsize){
+		this->flocaldoflist =xNew(fsize);
+		this->fglobaldoflist=xNew(fsize);
+		for(i=0;ifsize;i++){
+			this->flocaldoflist[i] =pe1->flocaldoflist[i];
+			this->fglobaldoflist[i]=pe1->fglobaldoflist[i];
+		}
+		counter=pe1->fsize;
+		for(i=0;ifsize;i++){
+			if(P[pe2->flocaldoflist[i]] >= pe1->nrows){
+				this->flocaldoflist[counter] =P[pe2->flocaldoflist[i]];
+				this->fglobaldoflist[counter]=pe2->fglobaldoflist[i];
+				counter++;
+			}
+		}
+	}
+	else{
+		this->flocaldoflist=NULL;
+		this->fglobaldoflist=NULL;
+	}
+
+	/*clean-up*/
+	xDelete(P);
+}
+/*}}}*/
+/*FUNCTION ElementVector::ElementVector(ElementVector* pe1, ElementVector* pe2,ElementVector* pe3){{{*/
+ElementVector::ElementVector(ElementVector* pe1, ElementVector* pe2,ElementVector* pe3){
+
+	/*Concatenate all matrices*/
+	ElementVector* pe12 =new ElementVector(pe1,pe2);
+	ElementVector* pe123=new ElementVector(pe12,pe3);
+
+	/*Initialize current object with this matrix*/
+	this->Init(pe123);
+
+	/*clean-up*/
+	delete pe12;
+	delete pe123;
+}
+/*}}}*/
+/*FUNCTION ElementVector::ElementVector(Node** nodes,int numnodes,Parameters* parameters,int approximation){{{*/
+ElementVector::ElementVector(Node** nodes,int numnodes,Parameters* parameters,int approximation){
+
+	/*get Vector size and properties*/
+	this->nrows=GetNumberOfDofs(nodes,numnodes,GsetEnum,approximation);
+
+	/*fill values with 0: */
+	this->values=xNewZeroInit(this->nrows);
+	
+	/*g list*/
+	this->gglobaldoflist=GetGlobalDofList(nodes,numnodes,GsetEnum,approximation);
+
+	/*Get fsize*/
+	this->fsize=GetNumberOfDofs(nodes,numnodes,FsetEnum,approximation);
+	this->flocaldoflist =GetLocalDofList( nodes,numnodes,FsetEnum,approximation);
+	this->fglobaldoflist=GetGlobalDofList(nodes,numnodes,FsetEnum,approximation);
+}
+/*}}}*/
+/*FUNCTION ElementVector::~ElementVector(){{{*/
+ElementVector::~ElementVector(){
+	
+	xDelete(this->values);
+	xDelete(this->gglobaldoflist);
+	xDelete(this->flocaldoflist);
+	xDelete(this->fglobaldoflist);
+}
+/*}}}*/
+
+/*ElementVector specific routines: */
+/*FUNCTION ElementVector::AddToGlobal(Vector* pf){{{*/
+void ElementVector::AddToGlobal(Vector* pf){
+
+	int i;
+	IssmDouble* localvalues=NULL;
+
+	/*In debugging mode, check consistency (no NaN, and values not too big)*/
+	this->CheckConsistency();
+
+	if(this->fsize){
+		/*first, retrieve values that are in the f-set from the g-set values vector: */
+		localvalues=xNew(this->fsize);
+		for(i=0;ifsize;i++){
+			localvalues[i]=this->values[this->flocaldoflist[i]];
+		}
+		/*add local values into global  vector, using the fglobaldoflist: */
+		pf->SetValues(this->fsize,this->fglobaldoflist,localvalues,ADD_VAL);
+
+		/*Free ressources:*/
+		xDelete(localvalues);
+	}
+	
+}
+/*}}}*/
+/*FUNCTION ElementVector::InsertIntoGlobal(Vector* pf){{{*/
+void ElementVector::InsertIntoGlobal(Vector* pf){
+
+	int i;
+	IssmDouble* localvalues=NULL;
+
+	if(this->fsize){
+		/*first, retrieve values that are in the f-set from the g-set values vector: */
+		localvalues=xNew(this->fsize);
+		for(i=0;ifsize;i++){
+			localvalues[i]=this->values[this->flocaldoflist[i]];
+		}
+		/*add local values into global  vector, using the fglobaldoflist: */
+		pf->SetValues(this->fsize,this->fglobaldoflist,localvalues,INS_VAL);
+
+		/*Free ressources:*/
+		xDelete(localvalues);
+	}
+
+}
+/*}}}*/
+/*FUNCTION ElementVector::CheckConsistency{{{*/
+void ElementVector::CheckConsistency(void){
+	/*Check element matrix values, only in debugging mode*/
+#ifdef _ISSM_DEBUG_ 
+	for (int i=0;inrows;i++){
+		if (xIsNan(this->values[i])) _error_("NaN found in Element Vector");
+		if (fabs( this->values[i])>1.e+50) _error_("Element Vector values exceeds 1.e+50");
+	}
+#endif
+}
+/*}}}*/
+/*FUNCTION ElementVector::Echo{{{*/
+void ElementVector::Echo(void){
+
+	int i,j;
+	_printLine_("Element Vector echo:");
+	_printLine_("   nrows: " << nrows);
+	_printLine_("   values:");
+	for(i=0;inrows =pe->nrows;
+
+	this->values=xNew(this->nrows);
+	xMemCpy(this->values,pe->values,this->nrows);
+
+	this->gglobaldoflist=xNew(this->nrows);
+	xMemCpy(this->gglobaldoflist,pe->gglobaldoflist,this->nrows);
+
+	this->fsize=pe->fsize;
+	if(this->fsize){
+		this->flocaldoflist=xNew(this->fsize);
+		xMemCpy(this->flocaldoflist,pe->flocaldoflist,this->fsize);
+		this->fglobaldoflist=xNew(this->fsize);
+		xMemCpy(this->fglobaldoflist,pe->fglobaldoflist,this->fsize);
+	}
+	else{
+		this->flocaldoflist=NULL;
+		this->fglobaldoflist=NULL;
+	}
+}
+/*}}}*/
+/*FUNCTION ElementVector::SetValue{{{*/
+void ElementVector::SetValue(IssmDouble scalar){
+
+	int i;
+
+	for(i=0;inrows;i++)this->values[i]=scalar;
+
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/matrix/ElementVector.h
===================================================================
--- /issm/trunk/src/c/classes/matrix/ElementVector.h	(revision 13395)
+++ /issm/trunk/src/c/classes/matrix/ElementVector.h	(revision 13395)
@@ -0,0 +1,53 @@
+/*!\file:  ElementVector.h
+ * \brief container for information needed to plug element vector generated by elements 
+ * into the pf global load vector. 
+ * This object will hold the element vector on the g-set, the local as well as global 
+ * dof lists in the f set
+ */ 
+
+#ifndef _ELEMENT_VECTOR_H_
+#define _ELEMENT_VECTOR_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../objects/Object.h"
+#include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+class Node;
+template  class Vector;
+class Parameters;
+/*}}}*/
+
+class ElementVector{
+
+	public:
+	
+		int      nrows;
+		IssmDouble*  values;
+		
+		//gset
+		int*     gglobaldoflist;
+
+		//fset
+		int      fsize;
+		int*     flocaldoflist;
+		int*     fglobaldoflist;
+		
+		/*ElementVector constructors, destructors {{{*/
+		ElementVector();
+		ElementVector(ElementVector* pe1,ElementVector* pe2);
+		ElementVector(ElementVector* pe1,ElementVector* pe2,ElementVector* pe3);
+		ElementVector(Node** nodes,int numnodes,Parameters* parameters,int approximation=NoneApproximationEnum);
+		~ElementVector();
+		/*}}}*/
+		/*ElementVector specific routines {{{*/
+		void AddToGlobal(Vector* pf);
+		void InsertIntoGlobal(Vector* pf);
+		void Echo(void);
+		void CheckConsistency(void);
+		void Init(ElementVector* pe);
+		void SetValue(IssmDouble scalar);
+		/*}}}*/
+};
+#endif //#ifndef _ELEMENT_VECTOR_H_
+
Index: /issm/trunk/src/c/classes/matrix/Matrix.h
===================================================================
--- /issm/trunk/src/c/classes/matrix/Matrix.h	(revision 13395)
+++ /issm/trunk/src/c/classes/matrix/Matrix.h	(revision 13395)
@@ -0,0 +1,345 @@
+/*!\file:  Matrix.h
+ * \brief wrapper to matrix objects. The goal is to control which API (PETSc,Scalpack, Plapack?) 
+ * implements our underlying matrix format.
+ */ 
+
+#ifndef _MATRIX_H_
+#define _MATRIX_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+#include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+/*}}}*/
+
+enum matrixtype { PetscMatType, SeqMatType };
+
+template  class Vector;
+
+template  
+class Matrix{
+
+	public:
+
+		#ifdef _HAVE_PETSC_
+		PetscMat *pmatrix;
+		#endif
+		SeqMat   *smatrix;
+		int       type;
+
+		/*Matrix constructors, destructors*/
+		/*FUNCTION Matrix(){{{*/
+		Matrix(){
+
+			#ifdef _HAVE_PETSC_
+			pmatrix=NULL;
+			#endif
+			smatrix=NULL;
+
+			type=PetscMatType; //default
+			#ifndef _HAVE_PETSC_
+			type=SeqMatType;
+			#endif
+
+		}
+		/*}}}*/
+		/*FUNCTION Matrix(int M,int N,int in_type){{{*/
+		#ifdef _HAVE_PETSC_
+		Matrix(int M,int N,int in_type=PetscMatType){
+		#else
+		Matrix(int M,int N,int in_type=SeqMatType){
+		#endif
+
+			#ifdef _HAVE_PETSC_
+			pmatrix=NULL;
+			#endif
+			smatrix=NULL;
+			type=in_type;
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix=new PetscMat(M,N);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix=new SeqMat(M,N);
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION Matrix(int M,int N,IssmDouble sparsity,int in_type){{{*/
+		#ifdef _HAVE_PETSC_
+		Matrix(int M,int N,double sparsity,int in_type=PetscMatType){
+		#else
+		Matrix(int M,int N,double sparsity,int in_type=SeqMatType){
+		#endif
+
+			#ifdef _HAVE_PETSC_
+			pmatrix=NULL;
+			#endif
+
+			smatrix=NULL;
+			type=in_type;
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix=new PetscMat(M,N,sparsity);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix=new SeqMat(M,N,sparsity);
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+		}
+		/*}}}*/
+		/*FUNCTION Matrix(IssmDouble* serial_mat, int M,int N,IssmDouble sparsity,int in_type){{{*/
+		#ifdef _HAVE_PETSC_
+		Matrix(IssmPDouble* serial_mat,int M,int N,IssmPDouble sparsity,int in_type=PetscMatType){
+		#else
+		Matrix(IssmPDouble* serial_mat,int M,int N,IssmPDouble sparsity,int in_type=SeqMatType){
+		#endif
+
+			#ifdef _HAVE_PETSC_
+			pmatrix=NULL;
+			#endif
+			smatrix=NULL;
+			type=in_type;
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix=new PetscMat(serial_mat,M,N,sparsity);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix=new SeqMat(serial_mat,M,N,sparsity);
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION Matrix(int M,int N,int connectivity,int numberofdofspernode,int in_type){{{*/
+		#ifdef _HAVE_PETSC_
+		Matrix(int M,int N,int connectivity,int numberofdofspernode,int in_type=PetscMatType){
+		#else
+		Matrix(int M,int N,int connectivity,int numberofdofspernode,int in_type=SeqMatType){
+		#endif
+
+			#ifdef _HAVE_PETSC_
+			pmatrix=NULL;
+			#endif
+			smatrix=NULL;
+			type=in_type;
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix=new PetscMat(M,N,connectivity,numberofdofspernode);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix=new SeqMat(M,N,connectivity,numberofdofspernode);
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION ~Matrix(){{{*/
+		~Matrix(){
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				delete this->pmatrix;
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqMatType){
+				delete this->smatrix;
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+
+		/*Matrix specific routines:*/
+		/*FUNCTION Echo{{{*/
+		void Echo(void){
+			_assert_(this);
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix->Echo();
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix->Echo();
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION Assemble{{{*/
+		void Assemble(void){
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix->Assemble();
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix->Assemble();
+			}
+			else{
+				_error_("Matrix type: " << type << " not supported yet!");
+			}
+		}
+		/*}}}*/
+		/*FUNCTION Norm{{{*/
+		IssmDouble Norm(NormMode norm_type){
+
+			IssmDouble norm=0;
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				norm=this->pmatrix->Norm(norm_type);
+				#endif
+			}
+			else if(type==SeqMatType){
+				norm=this->smatrix->Norm(norm_type);
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+			return norm;
+		}
+		/*}}}*/
+		/*FUNCTION GetSize{{{*/
+		void GetSize(int* pM,int* pN){
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix->GetSize(pM,pN);
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix->GetSize(pM,pN);
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION GetLocalSize{{{*/
+		void GetLocalSize(int* pM,int* pN){
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix->GetLocalSize(pM,pN);
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix->GetLocalSize(pM,pN);
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION MatMult{{{*/
+		void MatMult(Vector* X,Vector* AX){
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix->MatMult(X->pvector,AX->pvector);
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix->MatMult(X->svector,AX->svector);
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION Duplicate{{{*/
+		Matrix* Duplicate(void){
+
+			Matrix* output=NULL;
+
+			output=new Matrix();
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				output->pmatrix=this->pmatrix->Duplicate();
+				#endif
+			}
+			else if(type==SeqMatType){
+				output->smatrix=this->smatrix->Duplicate();
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+			return output;
+		}
+		/*}}}*/
+		/*FUNCTION ToSerial{{{*/
+		doubletype* ToSerial(void){
+
+			doubletype* output=NULL;
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				output=this->pmatrix->ToSerial();
+				#endif
+			}
+			else if(type==SeqMatType){
+				output=this->smatrix->ToSerial();
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+
+
+			return output;
+		}
+		/*}}}*/
+		/*FUNCTION SetValues{{{*/
+		void SetValues(int m,int* idxm,int n,int* idxn,IssmDouble* values,InsMode mode){
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix->SetValues(m,idxm,n,idxn,values,mode);
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix->SetValues(m,idxm,n,idxn,values,mode);
+			}
+			else _error_("Matrix type: " << type << " not supported yet!");
+		}
+		/*}}}*/
+		/*FUNCTION Convert{{{*/
+		void Convert(MatrixType newtype){
+
+			if(type==PetscMatType){
+				#ifdef _HAVE_PETSC_
+				this->pmatrix->Convert(newtype);
+				#endif
+			}
+			else if(type==SeqMatType){
+				this->smatrix->Convert(newtype);
+			}
+			else{
+				_error_("Matrix type: " << type << " not supported yet!");
+			}
+
+		}
+		/*}}}*/
+};
+
+#endif //#ifndef _MATRIX_H_
Index: /issm/trunk/src/c/classes/matrix/Vector.h
===================================================================
--- /issm/trunk/src/c/classes/matrix/Vector.h	(revision 13395)
+++ /issm/trunk/src/c/classes/matrix/Vector.h	(revision 13395)
@@ -0,0 +1,469 @@
+/*!\file:  Vector.h
+ * \brief wrapper to vector objects. The goal is to control which API (PETSc,Scalpack, Plapack?) 
+ * implements our underlying vector format.
+ */ 
+
+#ifndef _VECTOR_H_
+#define _VECTOR_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+#include "../../toolkits/toolkits.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+
+/*}}}*/
+
+enum vectortype { PetscVecType, SeqVecType };
+
+template  
+class Vector{
+
+	public:
+
+		int  type;
+		#ifdef _HAVE_PETSC_
+		PetscVec* pvector;
+		#endif
+		SeqVec* svector; 
+
+		/*Vector constructors, destructors */
+		/*FUNCTION Vector(){{{*/
+		Vector(){
+
+			#ifdef _HAVE_PETSC_
+			this->pvector=NULL;
+			#endif
+			this->svector=NULL;
+
+			type=PetscVecType; //default
+			#ifndef _HAVE_PETSC_
+			type=SeqVecType;
+			#endif
+
+		}
+		/*}}}*/
+		/*FUNCTION Vector(int M,bool fromlocalsize,int in_type){{{*/
+		#ifdef _HAVE_PETSC_
+		Vector(int M,bool fromlocalsize=false,int in_type=PetscVecType){
+		#else
+		Vector(int M,bool fromlocalsize=false,int in_type=SeqVecType){
+		#endif
+
+			#ifdef _HAVE_PETSC_
+			pvector=NULL;
+			#endif
+			svector=NULL;
+			type=in_type;
+
+
+			if(type==PetscVecType){
+			#ifdef _HAVE_PETSC_
+				this->pvector=new PetscVec(M,fromlocalsize);
+			 #else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+			 #endif
+			}
+			else if(type==SeqVecType){
+				this->svector=new SeqVec(M,fromlocalsize);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION Vector(doubletype* serial_vec,int M,int in_type){{{*/
+		#ifdef _HAVE_PETSC_
+		Vector(doubletype* serial_vec,int M,int in_type=PetscVecType){
+		#else
+		Vector(doubletype* serial_vec,int M,int in_type=SeqVecType){
+			//} for vim
+		#endif
+
+			#ifdef _HAVE_PETSC_
+			pvector=NULL;
+			#endif
+
+			svector=NULL;
+			type=in_type;
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector=new PetscVec(serial_vec,M);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector=new SeqVec(serial_vec,M);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION ~Vector(){{{*/
+		~Vector(){
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				delete this->pvector;
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				delete this->svector;
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+		}
+		/*}}}*/
+		#ifdef _HAVE_PETSC_
+		/*FUNCTION Vector(Vec petsc_vector){{{*/
+		Vector(Vec petsc_vector){
+
+			this->type=PetscVecType;
+			this->svector=NULL;
+			this->pvector=new PetscVec(petsc_vector);
+
+		}
+		/*}}}*/
+		#endif
+
+		/*Vector specific routines*/
+		/*FUNCTION Echo{{{*/
+		void Echo(void){
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->Echo();
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->Echo();
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION Assemble{{{*/
+		void Assemble(void){
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->Assemble();
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->Assemble();
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION SetValues{{{*/
+		void SetValues(int ssize, int* list, doubletype* values, InsMode mode){
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->SetValues(ssize,list,values,mode);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->SetValues(ssize,list,values,mode);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+
+
+		}
+		/*}}}*/
+		/*FUNCTION SetValue{{{*/
+		void SetValue(int dof, doubletype value, InsMode mode){
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->SetValue(dof,value,mode);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->SetValue(dof,value,mode);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION GetValue{{{*/
+		void GetValue(doubletype* pvalue,int dof){
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->GetValue(pvalue,dof);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->GetValue(pvalue,dof);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION GetSize{{{*/
+		void GetSize(int* pM){
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->GetSize(pM);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->GetSize(pM);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION IsEmpty{{{*/
+		bool IsEmpty(void){
+
+			int M;
+
+			this->GetSize(&M);
+
+			if(M==0) 
+				return true;
+			else
+				return false;
+		}
+		/*}}}*/
+		/*FUNCTION GetLocalSize{{{*/
+		void GetLocalSize(int* pM){
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->GetLocalSize(pM);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->GetLocalSize(pM);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION Duplicate{{{*/
+		Vector* Duplicate(void){
+
+			Vector* output=NULL;
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				output=new Vector();
+				output->pvector=this->pvector->Duplicate();
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				output=new Vector();
+				output->svector=this->svector->Duplicate();
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+			return output;
+
+		}
+		/*}}}*/
+		/*FUNCTION Set{{{*/
+		void Set(doubletype value){
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->Set(value);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->Set(value);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION AXPY{{{*/
+		void AXPY(Vector* X, doubletype a){
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->AXPY(X->pvector,a);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->AXPY(X->svector,a);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION AYPX{{{*/
+		void AYPX(Vector* X, doubletype a){
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->AYPX(X->pvector,a);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->AYPX(X->svector,a);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+
+		}
+		/*}}}*/
+		/*FUNCTION ToMPISerial{{{*/
+		doubletype* ToMPISerial(void){
+
+			doubletype* vec_serial=NULL;
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				vec_serial=this->pvector->ToMPISerial();
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				vec_serial=this->svector->ToMPISerial();
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+			return vec_serial;
+
+		}
+		/*}}}*/
+		/*FUNCTION Copy{{{*/
+		void Copy(Vector* to){
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->Copy(to->pvector);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->Copy(to->svector);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+
+		}
+		/*}}}*/
+		/*FUNCTION Norm{{{*/
+		doubletype Norm(NormMode norm_type){
+
+			doubletype norm=0;
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				norm=this->pvector->Norm(norm_type);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				norm=this->svector->Norm(norm_type);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+			return norm;
+		}
+		/*}}}*/
+		/*FUNCTION Scale{{{*/
+		void Scale(doubletype scale_factor){
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->Scale(scale_factor);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->Scale(scale_factor);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+		/*FUNCTION Dot{{{*/
+		doubletype Dot(Vector* vector){
+
+			doubletype dot;
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				dot=this->pvector->Dot(vector->pvector);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				dot=this->svector->Dot(vector->svector);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+			return dot;
+		}
+		/*}}}*/
+		/*FUNCTION PointwiseDivide{{{*/
+		void PointwiseDivide(Vector* x,Vector* y){
+
+
+			if(type==PetscVecType){
+				#ifdef _HAVE_PETSC_
+				this->pvector->PointwiseDivide(x->pvector,y->pvector);
+				#else
+				_error_("Petsc matrix format not usable, as Petsc has not been compiled!");
+				#endif
+			}
+			else if(type==SeqVecType){
+				this->svector->PointwiseDivide(x->svector,y->svector);
+			}
+			else _error_("Vector type: " << type << " not supported yet!");
+
+		}
+		/*}}}*/
+};
+#endif //#ifndef _VECTOR_H_
Index: /issm/trunk/src/c/classes/matrix/matrixobjects.h
===================================================================
--- /issm/trunk/src/c/classes/matrix/matrixobjects.h	(revision 13395)
+++ /issm/trunk/src/c/classes/matrix/matrixobjects.h	(revision 13395)
@@ -0,0 +1,16 @@
+/* \file matrixobjects.h
+ * \brief: prototype header for all matrix objects.
+ */
+
+#ifndef ALL_MATRIX_OBJECTS_H_
+#define ALL_MATRIX_OBJECTS_H_
+
+
+/*Numerics:*/
+#include "./ElementMatrix.h"
+#include "./ElementVector.h"
+#include "./Vector.h"
+#include "./Matrix.h"
+
+
+#endif
Index: /issm/trunk/src/c/classes/objects.h
===================================================================
--- /issm/trunk/src/c/classes/objects.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects.h	(revision 13395)
@@ -0,0 +1,68 @@
+/* \file objects.h
+ * \brief: prototype header for all objects.
+ */
+
+#ifndef ALL_OBJECTS_H_
+#define ALL_OBJECTS_H_
+
+/*Abstract classes: */
+#include "./objects/objects.h"
+
+/*Objects: */
+#include "./Hook.h"
+#include "./DofIndexing.h"
+#include "./IoModel.h"
+#include "./Patch.h"
+#include "./Update.h"
+
+/*Gauss*/
+#include "./gauss/GaussTria.h"
+#include "./gauss/GaussPenta.h"
+
+/*Numerics:*/
+#include "./matrix/ElementMatrix.h"
+#include "./matrix/ElementVector.h"
+#include "./matrix/Vector.h"
+#include "./matrix/Matrix.h"
+
+/*C objects: */
+#include "./FemModel.h"
+#include "./OptArgs.h"
+#include "./OptPars.h"
+
+/*Bamg: */
+#include "./bamg/BamgOpts.h"
+#include "./bamg/BamgGeom.h"
+#include "./bamg/BamgMesh.h"
+#include "./bamg/Metric.h"
+#include "./bamg/DoubleAndInt.h"
+#include "./bamg/Direction.h"
+#include "./bamg/BamgVertex.h"
+#include "./bamg/AdjacentTriangle.h"
+#include "./bamg/Edge.h"
+#include "./bamg/GeomVertex.h"
+#include "./bamg/GeomEdge.h"
+#include "./bamg/Curve.h"
+#include "./bamg/Triangle.h"
+#include "./bamg/ListofIntersectionTriangles.h"
+#include "./bamg/GeomSubDomain.h"
+#include "./bamg/SubDomain.h"
+#include "./bamg/VertexOnGeom.h"
+#include "./bamg/VertexOnVertex.h"
+#include "./bamg/VertexOnEdge.h"
+#include "./bamg/CrackedEdge.h"
+#include "./bamg/Mesh.h"
+#include "./bamg/Geometry.h"
+#include "./bamg/BamgQuadtree.h"
+#include "./bamg/SetOfE4.h"
+
+/*Kriging*/
+#include "./kriging/Variogram.h"
+#include "./kriging/GaussianVariogram.h"
+#include "./kriging/ExponentialVariogram.h"
+#include "./kriging/SphericalVariogram.h"
+#include "./kriging/PowerVariogram.h"
+#include "./kriging/Quadtree.h"
+#include "./kriging/Observation.h"
+
+#endif
Index: /issm/trunk/src/c/classes/objects/Constraints/Constraint.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Constraints/Constraint.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Constraints/Constraint.h	(revision 13395)
@@ -0,0 +1,28 @@
+/*!\file:  Constraint.h
+ * \brief abstract class for Constraint object
+ * This class is a place holder for constraints
+ * It is derived from Object, so DataSets can contain them.
+ */ 
+
+
+#ifndef _CONSTRAINT_H_
+#define _CONSTRAINT_H_
+
+/*Headers:*/
+/*{{{*/
+class Nodes;
+#include "../Object.h"
+#include "../../../toolkits/toolkits.h"
+/*}}}*/
+
+class Constraint: public Object{
+
+	public: 
+		
+		virtual      ~Constraint(){};
+		virtual void ConstrainNode(Nodes* nodes,Parameters* parameters)=0;
+		virtual bool InAnalysis(int analysis_type)=0;
+
+
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/Constraints/SpcDynamic.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Constraints/SpcDynamic.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Constraints/SpcDynamic.cpp	(revision 13395)
@@ -0,0 +1,141 @@
+/*!\file SpcDynamic.c
+ * \brief: implementation of the SpcDynamic object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../Container/Container.h"
+#include "../objects.h"
+
+/*SpcDynamic constructors and destructor*/
+/*FUNCTION SpcDynamic::SpcDynamic(){{{*/
+SpcDynamic::SpcDynamic(){
+	return;
+}
+/*}}}*/
+/*FUNCTION SpcDynamic::SpcDynamic(int spc_sid,int spc_nodeid,...){{{*/
+SpcDynamic::SpcDynamic(int spc_sid,int spc_nodeid, int spc_dof,int spc_analysis_type){
+
+	sid=spc_sid;
+	nodeid=spc_nodeid;
+	dof=spc_dof;
+	value=0;
+	analysis_type=spc_analysis_type;
+	isset=false;
+
+	return;
+}
+/*}}}*/
+/*FUNCTION SpcDynamic::~SpcDynamic{{{*/
+SpcDynamic::~SpcDynamic(){
+	return;
+}
+/*}}}*/
+		
+/*Object virtual functions definitions:*/
+/*FUNCTION SpcDynamic::Echo {{{*/
+void SpcDynamic::Echo(void){
+
+	_printLine_("SpcDynamic:");
+	_printLine_("   sid: " << sid);
+	_printLine_("   nodeid: " << nodeid);
+	_printLine_("   dof: " << dof);
+	_printLine_("   value: " << value);
+	_printLine_("   isset: " <<(isset?"true":"false"));
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	return;
+}
+/*}}}*/
+/*FUNCTION SpcDynamic::DeepEcho {{{*/
+void SpcDynamic::DeepEcho(void){
+
+	this->Echo();
+	return;
+}		
+/*}}}*/
+/*FUNCTION SpcDynamic::Id {{{*/
+int    SpcDynamic::Id(void){ return sid; }
+/*}}}*/
+/*FUNCTION SpcDynamic::MyRank {{{*/
+int    SpcDynamic::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION SpcDynamic::ObjectEnum{{{*/
+int SpcDynamic::ObjectEnum(void){
+
+	return SpcDynamicEnum;
+
+}
+/*}}}*/
+/*FUNCTION SpcDynamic::copy {{{*/
+Object* SpcDynamic::copy() {
+	return new SpcDynamic(*this); 
+}
+/*}}}*/
+
+/*Constraint virtual functions definitions: */
+/*FUNCTION SpcDynamic::InAnalysis{{{*/
+bool SpcDynamic::InAnalysis(int in_analysis_type){
+	if (in_analysis_type==this->analysis_type) return true;
+	else return false;
+}
+/*}}}*/
+/*FUNCTION SpcDynamic::ConstrainNode{{{*/
+void SpcDynamic::ConstrainNode(Nodes* nodes,Parameters* parameters){
+
+	Node* node=NULL;
+
+	/*Chase through nodes and find the node to which this SpcDynamic applys: */
+	node=(Node*)nodes->GetObjectById(NULL,nodeid);
+
+	/*Apply constraint: */
+	if(node){ //in case the spc is dealing with a node on another cpu
+
+		/*We should first check that the value has been set... (test306)*/
+		node->ApplyConstraint(dof,value);
+	}
+}
+/*}}}*/
+
+/*SpcDynamic functions*/
+/*FUNCTION SpcDynamic::GetDof {{{*/
+int SpcDynamic::GetDof(){
+	return dof;
+}
+/*}}}*/
+/*FUNCTION SpcDynamic::GetNodeId {{{*/
+int   SpcDynamic::GetNodeId(){
+	
+	return nodeid;
+}
+/*}}}*/
+/*FUNCTION SpcDynamic::GetValue {{{*/
+IssmDouble SpcDynamic::GetValue(){
+	_assert_(this->isset);
+	_assert_(!xIsNan(value));
+	return value;
+}
+/*}}}*/
+/*FUNCTION SpcDynamic::SetDynamicConstraint {{{*/
+void SpcDynamic::SetDynamicConstraint(Nodes* nodes,IssmDouble* yg_serial){
+
+	int pos;
+
+	Node* node=(Node*)nodes->GetObjectById(NULL,nodeid);
+	pos=node->GetDof(dof-1,GsetEnum);
+
+	this->value=yg_serial[pos];
+	this->isset=true;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Constraints/SpcDynamic.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Constraints/SpcDynamic.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Constraints/SpcDynamic.h	(revision 13395)
@@ -0,0 +1,52 @@
+/*!\file SpcDynamic.h
+ * \brief: header file for spc object
+ */
+
+#ifndef _SPCDynamic_H_
+#define _SPCDynamic_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Object.h"
+class DataSet;
+/*}}}*/
+
+class SpcDynamic: public Constraint{
+
+	private: 
+		int	sid; /*! id, to track it*/
+		int	nodeid; /*!node id*/
+		int dof; /*!component*/
+		IssmDouble value; /*value*/
+		bool isset;
+		int analysis_type;
+
+	public:
+
+		/*SpcDynamic constructors, destructors:{{{*/
+		SpcDynamic();
+		SpcDynamic(int sid,int nodeid, int dof,int analysis_type);
+		~SpcDynamic();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Constraint virtual functions definitions: {{{*/
+		void   ConstrainNode(Nodes* nodes,Parameters* parameters);
+		bool   InAnalysis(int analysis_type);
+		/*}}}*/
+		/*SpcDynamic management:{{{ */
+		int    GetNodeId();
+		int    GetDof();
+		IssmDouble GetValue();
+		void   SetDynamicConstraint(Nodes* nodes,IssmDouble *yg_serial);
+		/*}}}*/
+
+};
+
+#endif  /* _SPCStatic_H_*/
Index: /issm/trunk/src/c/classes/objects/Constraints/SpcStatic.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Constraints/SpcStatic.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Constraints/SpcStatic.cpp	(revision 13395)
@@ -0,0 +1,129 @@
+/*!\file SpcStatic.c
+ * \brief: implementation of the SpcStatic object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../Container/Container.h"
+#include "../objects.h"
+
+/*SpcStatic constructors and destructor*/
+/*FUNCTION SpcStatic::SpcStatic(){{{*/
+SpcStatic::SpcStatic(){
+	return;
+}
+/*}}}*/
+/*FUNCTION SpcStatic::SpcStatic(int spc_sid,int spc_nodeid,...){{{*/
+SpcStatic::SpcStatic(int spc_sid,int spc_nodeid, int spc_dof,IssmDouble spc_value,int spc_analysis_type){
+
+	sid=spc_sid;
+	nodeid=spc_nodeid;
+	dof=spc_dof;
+	value=spc_value;
+	analysis_type=spc_analysis_type;
+
+	return;
+}
+/*}}}*/
+/*FUNCTION SpcStatic::~SpcStatic{{{*/
+SpcStatic::~SpcStatic(){
+	return;
+}
+/*}}}*/
+		
+/*Object virtual functions definitions:*/
+/*FUNCTION SpcStatic::Echo {{{*/
+void SpcStatic::Echo(void){
+
+	_printLine_("SpcStatic:");
+	_printLine_("   sid: " << sid);
+	_printLine_("   nodeid: " << nodeid);
+	_printLine_("   dof: " << dof);
+	_printLine_("   value: " << value);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	return;
+}
+/*}}}*/
+/*FUNCTION SpcStatic::DeepEcho {{{*/
+void SpcStatic::DeepEcho(void){
+
+	_printLine_("SpcStatic:");
+	_printLine_("   sid: " << sid);
+	_printLine_("   nodeid: " << nodeid);
+	_printLine_("   dof: " << dof);
+	_printLine_("   value: " << value);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	return;
+}		
+/*}}}*/
+/*FUNCTION SpcStatic::Id {{{*/
+int    SpcStatic::Id(void){ return sid; }
+/*}}}*/
+/*FUNCTION SpcStatic::MyRank {{{*/
+int    SpcStatic::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION SpcStatic::ObjectEnum{{{*/
+int SpcStatic::ObjectEnum(void){
+
+	return SpcStaticEnum;
+
+}
+/*}}}*/
+/*FUNCTION SpcStatic::copy {{{*/
+Object* SpcStatic::copy() {
+	return new SpcStatic(*this); 
+}
+/*}}}*/
+
+/*Constraint virtual functions definitions: */
+/*FUNCTION SpcStatic::InAnalysis{{{*/
+bool SpcStatic::InAnalysis(int in_analysis_type){
+	if (in_analysis_type==this->analysis_type) return true;
+	else return false;
+}
+/*}}}*/
+/*FUNCTION SpcStatic::ConstrainNode{{{*/
+void SpcStatic::ConstrainNode(Nodes* nodes,Parameters* parameters){
+
+	Node* node=NULL;
+
+	/*Chase through nodes and find the node to which this SpcStatic applys: */
+	node=(Node*)nodes->GetObjectById(NULL,nodeid);
+
+	/*Apply constraint: */
+	if(node){ //in case the spc is dealing with a node on another cpu
+		node->ApplyConstraint(dof,value);
+	}
+}
+/*}}}*/
+
+/*SpcStatic functions*/
+/*FUNCTION SpcStatic::GetDof {{{*/
+int SpcStatic::GetDof(){
+	return dof;
+}
+/*}}}*/
+/*FUNCTION SpcStatic::GetNodeId {{{*/
+int   SpcStatic::GetNodeId(){
+	
+	return nodeid;
+}
+/*}}}*/
+/*FUNCTION SpcStatic::GetValue {{{*/
+IssmDouble SpcStatic::GetValue(){
+	_assert_(!xIsNan(value));
+	return value;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Constraints/SpcStatic.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Constraints/SpcStatic.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Constraints/SpcStatic.h	(revision 13395)
@@ -0,0 +1,50 @@
+/*!\file SpcStatic.h
+ * \brief: header file for spc object
+ */
+
+#ifndef _SPCStatic_H_
+#define _SPCStatic_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Object.h"
+class DataSet;
+/*}}}*/
+
+class SpcStatic: public Constraint{
+
+	private: 
+		int	sid; /*! id, to track it*/
+		int	nodeid; /*!node id*/
+		int dof; /*!component*/
+		IssmDouble value; /*value*/
+		int analysis_type;
+
+	public:
+
+		/*SpcStatic constructors, destructors:{{{*/
+		SpcStatic();
+		SpcStatic(int sid,int nodeid, int dof,IssmDouble value,int analysis_type);
+		~SpcStatic();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Constraint virtual functions definitions: {{{*/
+		void   ConstrainNode(Nodes* nodes,Parameters* parameters);
+		bool   InAnalysis(int analysis_type);
+		/*}}}*/
+		/*SpcStatic management:{{{ */
+		int    GetNodeId();
+		int    GetDof();
+		IssmDouble GetValue();
+		/*}}}*/
+
+};
+
+#endif  /* _SPCStatic_H_*/
Index: /issm/trunk/src/c/classes/objects/Constraints/SpcTransient.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Constraints/SpcTransient.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Constraints/SpcTransient.cpp	(revision 13395)
@@ -0,0 +1,176 @@
+/*!\file SpcTransient.c
+ * \brief: implementation of the SpcTransient object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../Container/Container.h"
+#include "../objects.h"
+
+/*SpcTransient constructors and destructor*/
+/*FUNCTION SpcTransient::SpcTransient(){{{*/
+SpcTransient::SpcTransient(){
+	sid=-1;
+	nodeid=-1;
+	dof=-1;
+	values=NULL;
+	times=NULL;
+	nsteps=-1;
+	analysis_type=-1;
+	return;
+}
+/*}}}*/
+/*FUNCTION SpcTransient::SpcTransient(int spc_sid,int spc_nodeid,...){{{*/
+SpcTransient::SpcTransient(int spc_sid,int spc_nodeid, int spc_dof,int spc_nsteps, IssmDouble* spc_times, IssmDouble* spc_values,int spc_analysis_type){
+
+	sid=spc_sid;
+	nodeid=spc_nodeid;
+	dof=spc_dof;
+	nsteps=spc_nsteps;
+	if(spc_nsteps){
+		values=xNew(spc_nsteps);
+		times=xNew(spc_nsteps);
+		xMemCpy(values,spc_values,nsteps);
+		xMemCpy(times,spc_times,nsteps);
+	}
+	analysis_type=spc_analysis_type;
+	return;
+}
+/*}}}*/
+/*FUNCTION SpcTransient::~SpcTransient{{{*/
+SpcTransient::~SpcTransient(){
+	xDelete(times);
+	xDelete(values);
+	return;
+}
+/*}}}*/
+		
+/*Object virtual functions definitions:*/
+/*FUNCTION SpcTransient::Echo {{{*/
+void SpcTransient::Echo(void){
+
+	int i;
+	_printLine_("SpcTransient:");
+	_printLine_("   sid: " << sid);
+	_printLine_("   nodeid: " << nodeid);
+	_printLine_("   dof: " << dof);
+	_printLine_("   nsteps: " << nsteps);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	_printLine_("   steps|times|values");
+	for(i=0;iEcho();
+}		
+/*}}}*/
+/*FUNCTION SpcTransient::Id {{{*/
+int    SpcTransient::Id(void){ return sid; }
+/*}}}*/
+/*FUNCTION SpcTransient::MyRank {{{*/
+int    SpcTransient::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION SpcTransient::ObjectEnum{{{*/
+int SpcTransient::ObjectEnum(void){
+
+	return SpcTransientEnum;
+
+}
+/*}}}*/
+/*FUNCTION SpcTransient::copy {{{*/
+Object* SpcTransient::copy() {
+	return new SpcTransient(sid,nodeid,dof,nsteps,times,values,analysis_type);
+}
+/*}}}*/
+
+/*Constraint virtual functions definitions:*/
+/*FUNCTION SpcTransient::InAnalysis{{{*/
+bool SpcTransient::InAnalysis(int in_analysis_type){
+	
+	if (in_analysis_type==this->analysis_type) return true;
+	else return false;
+}
+/*}}}*/
+/*FUNCTION SpcTransient::ConstrainNode{{{*/
+void SpcTransient::ConstrainNode(Nodes* nodes,Parameters* parameters){
+
+	Node* node=NULL;
+	IssmDouble time=0;
+	int    i;
+	IssmDouble alpha=-1;
+	IssmDouble value;
+	bool   found=false;
+
+	/*Chase through nodes and find the node to which this SpcTransient applys: */
+	node=(Node*)nodes->GetObjectById(NULL,nodeid);
+	
+	if(node){ //in case the spc is dealing with a node on another cpu
+
+		/*Retrieve time in parameters: */
+		parameters->FindParam(&time,TimeEnum);
+
+		/*Now, go fetch value for this time: */
+		if (time<=times[0]){
+			value=values[0];
+			found=true;
+		}
+		else if (time>=times[nsteps-1]){
+			value=values[nsteps-1];
+			found=true;
+		}
+		else{
+			for(i=0;i(value)){
+			node->RelaxConstraint(dof);
+		}
+		else node->ApplyConstraint(dof,value);
+	}
+}
+/*}}}*/
+
+/*SpcTransient functions*/
+/*FUNCTION SpcTransient::GetDof {{{*/
+int SpcTransient::GetDof(){
+	return dof;
+}
+/*}}}*/
+/*FUNCTION SpcTransient::GetNodeId {{{*/
+int   SpcTransient::GetNodeId(){
+	
+	return nodeid;
+}
+/*}}}*/
+/*FUNCTION SpcTransient::GetValue {{{*/
+IssmDouble SpcTransient::GetValue(){
+	return values[0];
+}
+/*}}}*/
+
Index: /issm/trunk/src/c/classes/objects/Constraints/SpcTransient.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Constraints/SpcTransient.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Constraints/SpcTransient.h	(revision 13395)
@@ -0,0 +1,52 @@
+/*!\file SpcTransient.h
+ * \brief: header file for spc object
+ */
+
+#ifndef _SPCTRANSIENT_H_
+#define _SPCTRANSIENT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Object.h"
+class DataSet;
+/*}}}*/
+
+class SpcTransient: public Constraint{
+
+	private: 
+		int	sid; /*! id, to track it*/
+		int	nodeid; /*!node id*/
+		int dof; /*!component*/
+		IssmDouble* values; /*different values in time*/
+		IssmDouble* times; /*different time steps*/
+		int nsteps; /*number of time steps*/
+		int analysis_type;
+
+	public:
+
+		/*SpcTransient constructors, destructors:{{{*/
+		SpcTransient();
+		SpcTransient(int sid,int nodeid, int dof,int nsteps, IssmDouble* times, IssmDouble* values,int analysis_type);
+		~SpcTransient();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Constraint virtual functions definitions: {{{*/
+		void   ConstrainNode(Nodes* nodes,Parameters* parameters);
+		bool   InAnalysis(int analysis_type);
+		/*}}}*/
+		/*SpcTransient management:{{{ */
+		int    GetNodeId();
+		int    GetDof();
+		IssmDouble GetValue();
+		/*}}}*/
+
+};
+
+#endif  /* _SPCTRANSIENT_H_ */
Index: /issm/trunk/src/c/classes/objects/Contour.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Contour.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Contour.h	(revision 13395)
@@ -0,0 +1,112 @@
+/*!\file Contour.h
+ * \brief: header file for Contour object
+ */
+
+#ifndef _CONTOUR_H_
+#define _CONTOUR_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../include/include.h"
+#include "../../shared/Exceptions/exceptions.h"
+#include "../../shared/Alloc/xNewDelete.h"
+#include "../../shared/MemOps/xMemCpy.h"
+#include "../../io/io.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "./Object.h"
+/*}}}*/
+
+template 
+class Contour: public Object{
+
+	public: 
+
+		int     id;
+		int	  nods;  //number of vertices in the contour
+		doubletype* x;
+		doubletype* y;
+		bool    closed; //is this contour closed?
+
+		/*Contour constructors, destructors :*/
+		/*FUNCTION Contour() default constructor {{{*/
+		Contour(){
+			this->id=0;
+			this->nods=0;
+			this->x=NULL;
+			this->y=NULL;
+			this->closed=false;
+		}
+		/*}}}*/
+		/*FUNCTION Contour(int pid, int nods, doubletype* x, doubletype* y,bool closed) {{{*/
+		Contour(int pid,int pnods, doubletype* px, doubletype* py,bool pclosed){
+
+			this->id=pid;
+			this->nods=pnods;
+			this->closed=pclosed;
+			if(nods){
+				this->x=xNew(nods);
+				xMemCpy(this->x,px,nods);
+				this->y=xNew(nods);
+				xMemCpy(this->y,py,nods);
+			}
+		}
+		/*}}}*/
+		/*FUNCTION Contour() default constructor {{{*/
+		~Contour(){
+			xDelete(this->x);
+			xDelete(this->y);
+		}
+		/*}}}*/
+
+
+		/*Object virtual function resolutoin: */
+		/*FUNCTION Echo(){{{*/
+		void Echo(void){
+
+			int i;
+
+			_printLine_("Contour: " << id);
+			_printLine_("   nods: " << nods);
+			_printLine_("   closed: " << (closed?"true":"false"));
+			if(nods){
+				_printLine_("   x,y:");
+				for(i=0;iEcho();
+		}
+		/*}}}*/
+		/*FUNCTION Id(){{{*/
+		int Id(void){
+			return id;
+		}
+		/*}}}*/
+		/*FUNCTION MyRank{{{*/
+		int    MyRank(void){ 
+			extern int my_rank;
+
+			return my_rank; 
+		}
+		/*}}}*/
+		/*FUNCTION ObjectEnum{{{*/
+		int ObjectEnum(void){
+
+			return ContourEnum;
+
+		}
+		/*}}}*/
+		/*FUNCTION copy {{{*/
+		Object* copy() {
+
+			return new Contour(*this); 
+
+		}
+		/*}}}*/
+};
+
+#endif  /* _CONTOUR_H_ */
Index: /issm/trunk/src/c/classes/objects/ElementResults/BoolElementResult.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/BoolElementResult.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/BoolElementResult.cpp	(revision 13395)
@@ -0,0 +1,136 @@
+/*!\file BoolElementResult.c
+ * \brief: implementation of the BoolElementResult object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "./ElementResultLocal.h"
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*BoolElementResult constructors and destructor*/
+/*FUNCTION BoolElementResult::BoolElementResult(){{{*/
+BoolElementResult::BoolElementResult(){
+	return;
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::BoolElementResult(int in_enum_type,IssmDouble in_value,int in_step, IssmDouble in_time){{{*/
+BoolElementResult::BoolElementResult(int in_enum_type,bool in_value,int in_step, IssmDouble in_time){
+
+	enum_type=in_enum_type;
+	value=in_value;
+	step=in_step;
+	time=in_time;
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::~BoolElementResult(){{{*/
+BoolElementResult::~BoolElementResult(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION BoolElementResult::Echo {{{*/
+void BoolElementResult::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::DeepEcho{{{*/
+void BoolElementResult::DeepEcho(void){
+
+	_printLine_("BoolElementResult:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: "<<(this->value?"true":"false"));
+	_printLine_("   step: " << this->step);
+	_printLine_("   time: " << this->time);
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::Id{{{*/
+int    BoolElementResult::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION BoolElementResult::MyRank{{{*/
+int    BoolElementResult::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::ObjectEnum{{{*/
+int BoolElementResult::ObjectEnum(void){
+
+	return BoolElementResultEnum;
+
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::copy{{{*/
+Object* BoolElementResult::copy() {
+
+	return new BoolElementResult(this->enum_type,this->value,this->step,this->time);
+
+}
+/*}}}*/
+
+/*ElementResult management*/
+/*FUNCTION BoolElementResult::InstanceEnum{{{*/
+int BoolElementResult::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::SpawnTriaElementResult{{{*/
+ElementResult* BoolElementResult::SpawnTriaElementResult(int* indices){
+
+	/*output*/
+	BoolElementResult* outresult=new BoolElementResult();
+
+	/*copy fields: */
+	outresult->enum_type=this->enum_type;
+	outresult->value=this->value;
+	outresult->time=this->time;
+	outresult->step=this->step;
+
+	/*Assign output*/
+	return outresult;
+
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::ProcessUnits{{{*/
+void BoolElementResult::ProcessUnits(Parameters* parameters){
+// no op
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::NumberOfNodalValues{{{*/
+int BoolElementResult::NumberOfNodalValues(void){
+	return 1;
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::PatchFill{{{*/
+void BoolElementResult::PatchFill(int row, Patch* patch){
+	
+	 /*Here, we fill the result information into the patch object. First, let's remember what is in a row 
+	  * of the patch object: enum_type step time element_id interpolation vertices_ids nodal_values
+	  * Here, we will supply the enum_type, step, time, interpolation and nodal_values: */
+	IssmDouble IssmDoublevalue=this->value?1:0;
+	patch->fillresultinfo(row,this->enum_type,this->step,this->time,P0Enum,&IssmDoublevalue,1);
+
+}
+/*}}}*/
+/*FUNCTION BoolElementResult::GetVectorFromResults{{{*/
+void BoolElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){
+
+	_error_("cannot return vector on vertices");
+} /*}}}*/
+/*FUNCTION BoolElementResult::GetElementVectorFromResults{{{*/
+void BoolElementResult::GetElementVectorFromResults(Vector* vector,int dof){
+
+	vector->SetValue(dof,value,INS_VAL);
+} /*}}}*/
Index: /issm/trunk/src/c/classes/objects/ElementResults/BoolElementResult.h
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/BoolElementResult.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/BoolElementResult.h	(revision 13395)
@@ -0,0 +1,54 @@
+/*! \file BoolElementResult.h 
+ *  \brief: header file for bool result object
+ *  A boll result object is just derived from a BoolInput object, with additional time and step information.
+ */
+
+
+#ifndef _BOOLELEMENTRESULT_H_
+#define _BOOLELEMENTRESULT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Inputs/Input.h"
+#include "../../../include/include.h"
+class Parameters;
+/*}}}*/
+
+class BoolElementResult: public ElementResult{
+
+	private: 
+		int    enum_type;
+		bool   value;
+		int    step;
+		IssmDouble time;
+
+	public:
+
+		/*BoolElementResult constructors, destructors: {{{*/
+		BoolElementResult();
+		BoolElementResult(int enum_type,bool value,int step,IssmDouble time);
+		~BoolElementResult();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*ElementResult virtual functions definitions: {{{*/
+		ElementResult* SpawnTriaElementResult(int* indices);
+		IssmDouble  GetTime(void){return time;};
+		int     GetStep(void){return step;};
+		void    ProcessUnits(Parameters* parameters);
+		int     NumberOfNodalValues(void);
+		void    PatchFill(int row, Patch* patch);
+		/*}}}*/
+		/*BoolElementResult management: {{{*/
+		int   InstanceEnum();
+		void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs);
+		void GetElementVectorFromResults(Vector* vector,int dof);
+		/*}}}*/
+};
+#endif  /* _BOOLELEMENTRESULT_H */
Index: /issm/trunk/src/c/classes/objects/ElementResults/DoubleElementResult.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/DoubleElementResult.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/DoubleElementResult.cpp	(revision 13395)
@@ -0,0 +1,137 @@
+/*!\file DoubleElementResult.c
+ * \brief: implementation of the DoubleElementResult object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "./ElementResultLocal.h"
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*DoubleElementResult constructors and destructor*/
+/*FUNCTION DoubleElementResult::DoubleElementResult(){{{*/
+DoubleElementResult::DoubleElementResult(){
+	return;
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::DoubleElementResult(int in_enum_type,IssmDouble in_value,int in_step, IssmDouble in_time){{{*/
+DoubleElementResult::DoubleElementResult(int in_enum_type,IssmDouble in_value,int in_step, IssmDouble in_time){
+
+	enum_type=in_enum_type;
+	value=in_value;
+	step=in_step;
+	time=in_time;
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::~DoubleElementResult(){{{*/
+DoubleElementResult::~DoubleElementResult(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION DoubleElementResult::Echo {{{*/
+void DoubleElementResult::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::DeepEcho{{{*/
+void DoubleElementResult::DeepEcho(void){
+
+	_printLine_("DoubleElementResult:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: " << this->value);
+	_printLine_("   step: " << this->step);
+	_printLine_("   time: " << this->time);
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::Id{{{*/
+int    DoubleElementResult::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION DoubleElementResult::MyRank{{{*/
+int    DoubleElementResult::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::ObjectEnum{{{*/
+int DoubleElementResult::ObjectEnum(void){
+
+	return DoubleElementResultEnum;
+
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::copy{{{*/
+Object* DoubleElementResult::copy() {
+
+	return new DoubleElementResult(this->enum_type,this->value,this->step,this->time);
+
+}
+/*}}}*/
+
+/*ElementResult management*/
+/*FUNCTION DoubleElementResult::InstanceEnum{{{*/
+int DoubleElementResult::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::SpawnTriaElementResult{{{*/
+ElementResult* DoubleElementResult::SpawnTriaElementResult(int* indices){
+
+	/*output*/
+	DoubleElementResult* outresult=new DoubleElementResult();
+
+	/*copy fields: */
+	outresult->enum_type=this->enum_type;
+	outresult->value=this->value;
+	outresult->time=this->time;
+	outresult->step=this->step;
+
+	/*Assign output*/
+	return outresult;
+
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::ProcessUnits{{{*/
+void DoubleElementResult::ProcessUnits(Parameters* parameters){
+	
+	this->value=UnitConversion(this->value,IuToExtEnum,this->enum_type);
+
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::NumberOfNodalValues{{{*/
+int DoubleElementResult::NumberOfNodalValues(void){
+	return 1;
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::PatchFill{{{*/
+void DoubleElementResult::PatchFill(int row, Patch* patch){
+	
+	 /*Here, we fill the result information into the patch object. First, let's remember what is in a row 
+	  * of the patch object: enum_type step time element_id interpolation vertices_ids nodal_values
+	  * Here, we will supply the enum_type, step, time, interpolation and nodal_values: */
+	patch->fillresultinfo(row,this->enum_type,this->step,this->time,P0Enum,&this->value,1);
+
+}
+/*}}}*/
+/*FUNCTION DoubleElementResult::GetVectorFromResults{{{1*/
+void DoubleElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){
+
+	_error_("cannot return vector on vertices");
+} /*}}}*/
+/*FUNCTION DoubleElementResult::GetElementVectorFromResults{{{1*/
+void DoubleElementResult::GetElementVectorFromResults(Vector* vector,int dof){
+
+	vector->SetValue(dof,value,INS_VAL);
+} /*}}}*/
Index: /issm/trunk/src/c/classes/objects/ElementResults/DoubleElementResult.h
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/DoubleElementResult.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/DoubleElementResult.h	(revision 13395)
@@ -0,0 +1,54 @@
+/*! \file DoubleElementResult.h 
+ *  \brief: header file for IssmDouble result object
+ *  A IssmDouble result object is just derived from a DoubleInput object, with additional time and step information.
+ */
+
+
+#ifndef _DOUBLEELEMENTRESULT_H_
+#define _DOUBLEELEMENTRESULT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Inputs/Input.h"
+#include "../../../include/include.h"
+class Parameters;
+/*}}}*/
+
+class DoubleElementResult: public ElementResult{
+
+	private: 
+		int    enum_type;
+		IssmDouble value;
+		int    step;
+		IssmDouble time;
+
+	public:
+
+		/*DoubleElementResult constructors, destructors: {{{*/
+		DoubleElementResult();
+		DoubleElementResult(int enum_type,IssmDouble value,int step,IssmDouble time);
+		~DoubleElementResult();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*ElementResult virtual functions definitions: {{{*/
+		ElementResult* SpawnTriaElementResult(int* indices);
+		IssmDouble  GetTime(void){return time;};
+		int     GetStep(void){return step;};
+		void    ProcessUnits(Parameters* parameters);
+		int     NumberOfNodalValues(void);
+		void    PatchFill(int row, Patch* patch);
+		/*}}}*/
+		/*DoubleElementResult management: {{{*/
+		int   InstanceEnum();
+		void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs);
+		void GetElementVectorFromResults(Vector* vector,int dof);
+		/*}}}*/
+};
+#endif  /* _DOUBLEELEMENTRESULT_H */
Index: /issm/trunk/src/c/classes/objects/ElementResults/ElementResult.h
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/ElementResult.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/ElementResult.h	(revision 13395)
@@ -0,0 +1,32 @@
+/*!\file:  ElementResult.h
+ * \brief abstract class for ElementResult object
+ */ 
+
+
+#ifndef _ELEMENTRESULT_H_
+#define _ELEMENTRESULT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Object.h"
+/*}}}*/
+
+class ElementResult:public Object{
+
+	public: 
+		
+		virtual        ~ElementResult(){};
+		
+		virtual         ElementResult* SpawnTriaElementResult(int* indices)=0;
+		virtual IssmDouble  GetTime(void)=0;
+		virtual int     GetStep(void)=0;
+		virtual void    ProcessUnits(Parameters* parameters)=0;
+		virtual int     NumberOfNodalValues(void)=0;
+		virtual void    PatchFill(int row, Patch* patch)=0;
+		virtual int     InstanceEnum()=0;
+		virtual void    GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdof)=0;
+		virtual void    GetElementVectorFromResults(Vector* vector,int dof)=0;
+
+};
+
+#endif
Index: /issm/trunk/src/c/classes/objects/ElementResults/ElementResultLocal.h
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/ElementResultLocal.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/ElementResultLocal.h	(revision 13395)
@@ -0,0 +1,11 @@
+/*!\file: ElementResultLocal.h
+ * \brief prototypes for ElementResultLocal.h
+ */ 
+
+#ifndef _ELEMENTRESULTLOCAL_H_
+#define  _ELEMENTRESULTLOCAL_H_
+
+class Parameters;
+
+#endif //ifndef _ELEMENTRESULTLOCAL_H_
+
Index: /issm/trunk/src/c/classes/objects/ElementResults/PentaP1ElementResult.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/PentaP1ElementResult.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/PentaP1ElementResult.cpp	(revision 13395)
@@ -0,0 +1,153 @@
+/*!\file PentaP1ElementResult.c
+ * \brief: implementation of the PentaP1ElementResult object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "./ElementResultLocal.h"
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*PentaP1ElementResult constructors and destructor*/
+/*FUNCTION PentaP1ElementResult::PentaP1ElementResult(){{{*/
+PentaP1ElementResult::PentaP1ElementResult(){
+	return;
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::PentaP1ElementResult(int in_enum_type,IssmDouble* in_values,int in_step, IssmDouble in_time){{{*/
+PentaP1ElementResult::PentaP1ElementResult(int in_enum_type,IssmDouble* in_values,int in_step, IssmDouble in_time){
+
+	int i;
+
+	enum_type=in_enum_type;
+	for(i=0;i<6;i++)values[i]=in_values[i];
+	step=in_step;
+	time=in_time;
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::~PentaP1ElementResult(){{{*/
+PentaP1ElementResult::~PentaP1ElementResult(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION PentaP1ElementResult::Echo {{{*/
+void PentaP1ElementResult::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::DeepEcho{{{*/
+void PentaP1ElementResult::DeepEcho(void){
+
+	_printLine_("PentaP1ElementResult:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   values: [" << this->values[0] << " " << this->values[1] << " " << this->values[2] << " " << this->values[3] << " " << this->values[4] << " " << this->values[5] << "]");
+	_printLine_("   step: " << this->step);
+	_printLine_("   time: " << this->time);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::Id{{{*/
+int    PentaP1ElementResult::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::MyRank{{{*/
+int    PentaP1ElementResult::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::ObjectEnum{{{*/
+int PentaP1ElementResult::ObjectEnum(void){
+
+	return PentaP1ElementResultEnum;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::copy{{{*/
+Object* PentaP1ElementResult::copy() {
+	
+	return new PentaP1ElementResult(this->enum_type,this->values,this->step,this->time);
+
+}
+/*}}}*/
+
+/*ElementResult management*/
+/*FUNCTION PentaP1ElementResult::InstanceEnum{{{*/
+int PentaP1ElementResult::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::SpawnTriaElementResult{{{*/
+ElementResult* PentaP1ElementResult::SpawnTriaElementResult(int* indices){
+
+	/*output*/
+	TriaP1ElementResult* outresult=NULL;
+	IssmDouble newvalues[3];
+
+	/*Loop over the new indices*/
+	for(int i=0;i<3;i++){
+
+		/*Check index value*/
+		_assert_(indices[i]>=0 && indices[i]<6);
+
+		/*Assign value to new result*/
+		newvalues[i]=this->values[indices[i]];
+	}
+
+	/*Create new Tria result*/
+	outresult=new TriaP1ElementResult(this->enum_type,&newvalues[0],this->step,this->time);
+
+	/*Assign output*/
+	return outresult;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::ProcessUnits{{{*/
+void PentaP1ElementResult::ProcessUnits(Parameters* parameters){
+	
+	UnitConversion(this->values,6,IuToExtEnum,this->enum_type);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::NumberOfNodalValues{{{*/
+int PentaP1ElementResult::NumberOfNodalValues(void){
+	return 6;
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::PatchFill{{{*/
+void PentaP1ElementResult::PatchFill(int row, Patch* patch){
+	
+	 /*Here, we fill the result information into the patch object. First, let's remember what is in a row 
+	  * of the patch object: enum_type step time element_id interpolation vertices_ids nodal_values
+	  * Here, we will supply the enum_type, step, time, interpolation and nodal_values: */
+	patch->fillresultinfo(row,this->enum_type,this->step,this->time,P1Enum,this->values,6);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1ElementResult::GetVectorFromResults{{{*/
+void PentaP1ElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){
+
+	IssmDouble data[6];
+
+	if(numdofs!=6)_error_("Result " << EnumToStringx(this->enum_type) << " is a PentaP1ElementResult and cannot write vector of " << numdofs << " dofs");
+	for(int i=0;i<6;i++) data[i]=this->values[i]/(IssmDouble)connectivitylist[i];
+	vector->SetValues(numdofs,doflist,&data[0],ADD_VAL);
+
+} /*}}}*/
+/*FUNCTION PentaP1ElementResult::GetElementVectorFromResults{{{*/
+void PentaP1ElementResult::GetElementVectorFromResults(Vector* vector,int dof){
+
+	_error_("Result " << EnumToStringx(enum_type) << " is a PentaP1ElementResult and should not write vector of size numberofelemenrs");
+} /*}}}*/
Index: /issm/trunk/src/c/classes/objects/ElementResults/PentaP1ElementResult.h
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/PentaP1ElementResult.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/PentaP1ElementResult.h	(revision 13395)
@@ -0,0 +1,54 @@
+/*! \file PentaP1ElementResult.h 
+ *  \brief: header file for PentaP1ElementResult object
+ *  this object is just a PentaP1Input with additional time and step info.
+ */
+
+
+#ifndef _PENTAP1ELEMENTRESULT_H_
+#define _PENTAP1ELEMENTRESULT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Inputs/Input.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+class PentaP1ElementResult: public ElementResult{
+
+	private: 
+		int    enum_type;
+		IssmDouble values[6];
+		int    step;
+		IssmDouble time;
+
+	public:
+
+		/*PentaP1ElementResult constructors, destructors: {{{*/
+		PentaP1ElementResult();
+		PentaP1ElementResult(int enum_type,IssmDouble* values,int step, IssmDouble time);
+		~PentaP1ElementResult();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*ElementResult virtual functions definitions: {{{*/
+		ElementResult* SpawnTriaElementResult(int* indices);
+		IssmDouble  GetTime(void){return time;};
+		int     GetStep(void){return step;};
+		void    ProcessUnits(Parameters* parameters);
+		int     NumberOfNodalValues(void);
+		void    PatchFill(int row, Patch* patch);
+		/*}}}*/
+		/*PentaP1ElementResult management: {{{*/
+		int   InstanceEnum();
+		void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs);
+		void GetElementVectorFromResults(Vector* vector,int dof);
+		/*}}}*/
+
+};
+#endif  /* _PENTAP1ELEMENTRESULT_H */
Index: /issm/trunk/src/c/classes/objects/ElementResults/TriaP1ElementResult.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/TriaP1ElementResult.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/TriaP1ElementResult.cpp	(revision 13395)
@@ -0,0 +1,140 @@
+/*!\file TriaP1ElementResult.c
+ * \brief: implementation of the TriaP1ElementResult object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "./ElementResultLocal.h"
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*TriaP1ElementResult constructors and destructor*/
+/*FUNCTION TriaP1ElementResult::TriaP1ElementResult(){{{*/
+TriaP1ElementResult::TriaP1ElementResult(){
+	return;
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::TriaP1ElementResult(int in_enum_type,IssmDouble* in_values,int in_step, IssmDouble in_time){{{*/
+TriaP1ElementResult::TriaP1ElementResult(int in_enum_type,IssmDouble* in_values,int in_step, IssmDouble in_time){
+
+	enum_type=in_enum_type;
+	values[0]=in_values[0];
+	values[1]=in_values[1];
+	values[2]=in_values[2];
+	step=in_step;
+	time=in_time;
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::~TriaP1ElementResult(){{{*/
+TriaP1ElementResult::~TriaP1ElementResult(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION TriaP1ElementResult::Echo {{{*/
+void TriaP1ElementResult::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::DeepEcho{{{*/
+void TriaP1ElementResult::DeepEcho(void){
+		
+	_printLine_("TriaP1ElementResult:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   values: [" << this->values[0] << " " << this->values[1] << " " << this->values[2] << "]");
+	_printLine_("   step: " << this->step);
+	_printLine_("   time: " << this->time);
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::Id{{{*/
+int    TriaP1ElementResult::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::MyRank{{{*/
+int    TriaP1ElementResult::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::ObjectEnum{{{*/
+int TriaP1ElementResult::ObjectEnum(void){
+
+	return TriaP1ElementResultEnum;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::copy{{{*/
+Object* TriaP1ElementResult::copy() {
+	
+	return new TriaP1ElementResult(this->enum_type,this->values,this->step,this->time);
+
+}
+/*}}}*/
+
+/*ElementResult management*/
+/*FUNCTION TriaP1ElementResult::InstanceEnum{{{*/
+int TriaP1ElementResult::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::SpawnTriaElementResult{{{*/
+ElementResult* TriaP1ElementResult::SpawnTriaElementResult(int* indices){
+
+	/*output*/
+	TriaP1ElementResult* outresult=NULL;
+
+	/*Create new Tria result (copy of current result)*/
+	outresult=new TriaP1ElementResult(this->enum_type,&this->values[0],this->step,this->time);
+
+	/*Assign output*/
+	return outresult;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::ProcessUnits{{{*/
+void TriaP1ElementResult::ProcessUnits(Parameters* parameters){
+	
+	UnitConversion(this->values,3,IuToExtEnum,this->enum_type);
+
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::NumberOfNodalValues{{{*/
+int TriaP1ElementResult::NumberOfNodalValues(void){
+	return 3;
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::PatchFill{{{*/
+void TriaP1ElementResult::PatchFill(int row, Patch* patch){
+	
+	 /*Here, we fill the result information into the patch object. First, let's remember what is in a row 
+	  * of the patch object: enum_type step time element_id interpolation vertices_ids nodal_values
+	  * Here, we will supply the enum_type, step, time, interpolation and nodal_values: */
+	patch->fillresultinfo(row,this->enum_type,this->step,this->time,P1Enum,this->values,3);
+
+}
+/*}}}*/
+/*FUNCTION TriaP1ElementResult::GetVectorFromResults{{{*/
+void TriaP1ElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){
+
+	IssmDouble data[3];
+
+	if(numdofs!=3)_error_("Result " << EnumToStringx(this->enum_type) << " is a TriaP1ElementResult and cannot write vector of " << numdofs << " dofs");
+	for(int i=0;i<3;i++) data[i]=this->values[i]/(IssmDouble)connectivitylist[i];
+	vector->SetValues(numdofs,doflist,&data[0],ADD_VAL);
+
+} /*}}}*/
+/*FUNCTION TriaP1ElementResult::GetElementVectorFromResults{{{*/
+void TriaP1ElementResult::GetElementVectorFromResults(Vector* vector,int dof){
+	_error_("Result " << EnumToStringx(enum_type) << " is a TriaP1ElementResult and should not write vector of size numberofelemenrs");
+} /*}}}*/
Index: /issm/trunk/src/c/classes/objects/ElementResults/TriaP1ElementResult.h
===================================================================
--- /issm/trunk/src/c/classes/objects/ElementResults/TriaP1ElementResult.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ElementResults/TriaP1ElementResult.h	(revision 13395)
@@ -0,0 +1,53 @@
+/*! \file TriaP1ElementResult.h 
+ *  \brief: header file for TriaP1ElementResult object
+ */
+
+
+#ifndef _TRIAP1ELEMENTRESULT_H_
+#define _TRIAP1ELEMENTRESULT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Inputs/Input.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+class TriaP1ElementResult: public ElementResult{
+
+	private: 
+		int    enum_type;
+		IssmDouble values[3];
+		int    step;
+		IssmDouble time;
+
+	public:
+
+		/*TriaP1ElementResult constructors, destructors: {{{*/
+		TriaP1ElementResult();
+		TriaP1ElementResult(int enum_type,IssmDouble* values,int step,IssmDouble time);
+		~TriaP1ElementResult();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*ElementResult virtual functions definitions: {{{*/
+		ElementResult* SpawnTriaElementResult(int* indices);
+		IssmDouble  GetTime(void){return time;};
+		int     GetStep(void){return step;};
+		void    ProcessUnits(Parameters* parameters);
+		int     NumberOfNodalValues(void);
+		void    PatchFill(int row, Patch* patch);
+		/*}}}*/
+		/*TriaP1ElementResult management: {{{*/
+		int   InstanceEnum();
+		void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs);
+		void GetElementVectorFromResults(Vector* vector,int dof);
+		/*}}}*/
+
+};
+#endif  /* _TRIAP1ELEMENTRESULT_H */
Index: /issm/trunk/src/c/classes/objects/Elements/Element.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/Element.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/Element.h	(revision 13395)
@@ -0,0 +1,119 @@
+/*!\file:  Element.h
+ * \brief abstract class for Element object
+ * This class is a place holder for the Tria and the Penta elements. 
+ * It is derived from Element, so DataSets can contain them.
+ */ 
+
+
+#ifndef _ELEMENT_H_
+#define _ELEMENT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Object.h"
+
+class DataSet;
+class Parameters;
+class Patch;
+template  class Matrix;
+template  class Vector;
+
+#include "../../../toolkits/toolkits.h"
+/*}}}*/
+
+class Element: public Object,public Update{
+
+	public: 
+		
+		virtual        ~Element(){};
+	
+		virtual void   Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters)=0;
+		virtual void   SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters)=0;
+		virtual void   CreateKMatrix(Matrix* Kff, Matrix*  Kfs,Vector* df)=0;
+		virtual void   CreatePVector(Vector* pf)=0;
+		virtual void   CreateJacobianMatrix(Matrix* Jff)=0;
+		virtual void   GetSolutionFromInputs(Vector* solution)=0;
+		virtual int    GetNodeIndex(Node* node)=0;
+		virtual int    Sid()=0;
+		virtual bool   IsFloating()=0; 
+		virtual bool   IsNodeOnShelf()=0; 
+		virtual bool   IsNodeOnShelfFromFlags(IssmDouble* flags)=0; 
+		virtual bool   IsOnBed()=0;
+		virtual void   GetInputListOnVertices(IssmDouble* pvalue,int enumtype)=0;
+		virtual void   GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue)=0;
+		virtual void   GetInputValue(IssmDouble* pvalue,Node* node,int enumtype)=0;
+		
+		virtual IssmDouble SurfaceArea(void)=0;
+		virtual void   InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum)=0;
+		virtual void   ComputeBasalStress(Vector* sigma_b)=0;
+		virtual void   ComputeStrainRate(Vector* eps)=0;
+		virtual void   PatchSize(int* pnumrows, int* pnumvertices,int* pnumnodes)=0;
+		virtual void   PatchFill(int* pcount, Patch* patch)=0;
+		virtual void   ListResultsInfo(int** results_enums,int** results_size,IssmDouble** results_times,int** results_steps,int* num_results)=0;
+		virtual void   DeleteResults(void)=0;
+		virtual void   Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type)=0;
+		virtual void   InputToResult(int enum_type,int step,IssmDouble time)=0;
+		virtual void   InputDuplicate(int original_enum,int new_enum)=0;
+		virtual void   InputCreate(IssmDouble scalar,int name,int code)=0;
+		virtual void   InputCreate(IssmDouble* vector, int index,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code)=0;
+		virtual void   ProcessResultsUnits(void)=0;
+		virtual void   RequestedOutput(int output_enum,int step,IssmDouble time)=0;
+		
+		virtual int    NodalValue(IssmDouble* pvalue, int index, int natureofdataenum,bool process_units)=0;
+		virtual void   InputScale(int enum_type,IssmDouble scale_factor)=0;
+		virtual void   GetVectorFromInputs(Vector* vector, int name_enum)=0;
+		virtual void   GetVectorFromResults(Vector* vector,int id,int enum_in,int interp)=0;
+		virtual void   InputArtificialNoise(int enum_type,IssmDouble min,IssmDouble max)=0;
+		virtual bool   InputConvergence(IssmDouble* eps, int* enums,int num_enums,int* criterionenums,IssmDouble* criterionvalues,int num_criterionenums)=0;
+		virtual void   AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part)=0;
+		virtual int*   GetHorizontalNeighboorSids(void)=0;
+		virtual IssmDouble TimeAdapt()=0;
+		virtual void   MigrateGroundingLine(IssmDouble* old_floating_ice,IssmDouble* sheet_ungrounding)=0;
+		virtual void   PotentialSheetUngrounding(Vector* potential_sheet_ungrounding)=0;
+		virtual void   PositiveDegreeDay(IssmDouble* pdds,IssmDouble* pds,IssmDouble signorm)=0;
+		virtual void   Delta18oParameterization(void)=0;
+		virtual void   SmbGradients()=0;
+		virtual int    UpdatePotentialSheetUngrounding(IssmDouble* potential_sheet_ungrounding,Vector* vec_nodes_on_iceshelf,IssmDouble* nodes_on_iceshelf)=0;
+		virtual void   ResetCoordinateSystem()=0;
+		virtual void   SmearFunction(Vector* smearedvector,IssmDouble (*WeightFunction)(IssmDouble distance,IssmDouble radius),IssmDouble radius)=0;
+
+		#ifdef _HAVE_RESPONSES_
+		virtual void   MinVel(IssmDouble* pminvel, bool process_units)=0;
+		virtual void   MaxVel(IssmDouble* pmaxvel, bool process_units)=0;
+		virtual void   MinVx(IssmDouble* pminvx, bool process_units)=0;
+		virtual void   MaxVx(IssmDouble* pmaxvx, bool process_units)=0;
+		virtual void   MaxAbsVx(IssmDouble* pmaxabsvx, bool process_units)=0;
+		virtual void   MinVy(IssmDouble* pminvy, bool process_units)=0;
+		virtual void   MaxVy(IssmDouble* pmaxvy, bool process_units)=0;
+		virtual void   MaxAbsVy(IssmDouble* pmaxabsvy, bool process_units)=0;
+		virtual void   MinVz(IssmDouble* pminvz, bool process_units)=0;
+		virtual void   MaxVz(IssmDouble* pmaxvz, bool process_units)=0;
+		virtual void   MaxAbsVz(IssmDouble* pmaxabsvz, bool process_units)=0;
+		virtual IssmDouble MassFlux(IssmDouble* segment,bool process_units)=0;
+		virtual void   ElementResponse(IssmDouble* presponse,int response_enum,bool process_units)=0;
+		virtual IssmDouble IceVolume(void)=0;
+		virtual IssmDouble TotalSmb(void)=0;
+		#endif
+
+		#ifdef _HAVE_CONTROL_
+		virtual void   Gradj(Vector* gradient,int control_type,int control_index)=0;
+		virtual IssmDouble ThicknessAbsMisfit(bool process_units  ,int weight_index)=0;
+		virtual IssmDouble SurfaceAbsVelMisfit(bool process_units ,int weight_index)=0;
+		virtual IssmDouble SurfaceRelVelMisfit(bool process_units ,int weight_index)=0;
+		virtual IssmDouble SurfaceLogVelMisfit(bool process_units ,int weight_index)=0;
+		virtual IssmDouble SurfaceLogVxVyMisfit(bool process_units,int weight_index)=0;
+		virtual IssmDouble SurfaceAverageVelMisfit(bool process_units,int weight_index)=0;
+		virtual IssmDouble ThicknessAbsGradient(bool process_units,int weight_index)=0;
+		virtual IssmDouble ThicknessAlongGradient(bool process_units,int weight_index)=0;
+		virtual IssmDouble ThicknessAcrossGradient(bool process_units,int weight_index)=0;
+		virtual IssmDouble RheologyBbarAbsGradient(bool process_units,int weight_index)=0;
+		virtual IssmDouble DragCoefficientAbsGradient(bool process_units,int weight_index)=0;
+		virtual void   ControlInputGetGradient(Vector* gradient,int enum_type,int control_index)=0;
+		virtual void   ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index)=0;
+		virtual void   ControlInputScaleGradient(int enum_type, IssmDouble scale)=0;
+		virtual void   GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data)=0;
+		virtual void   SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index)=0;
+		virtual void   InputControlUpdate(IssmDouble scalar,bool save_parameter)=0;
+		#endif
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/Elements/Penta.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/Penta.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/Penta.cpp	(revision 13395)
@@ -0,0 +1,9135 @@
+/*!\file Penta.cpp
+ * \brief: implementation of the Penta object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../shared/shared.h"
+#include "../../../include/include.h"
+#include "../../../Container/Container.h"
+/*}}}*/
+
+/*Element macros*/
+#define NUMVERTICES   6
+#define NUMVERTICES2D 3
+
+/*Constructors/destructor/copy*/
+/*FUNCTION Penta::Penta(){{{*/
+Penta::Penta(){
+
+	int i;
+
+	this->nodes=NULL;
+	this->material=NULL;
+	this->matpar=NULL;
+	this->verticalneighbors=NULL;
+	this->inputs=NULL;
+	this->parameters=NULL;
+	this->results=NULL;
+	for(i=0;i<3;i++)this->horizontalneighborsids[i]=UNDEF;
+}
+/*}}}*/
+/*FUNCTION Penta::~Penta(){{{*/
+Penta::~Penta(){
+	delete inputs;
+	delete results;
+	this->parameters=NULL;
+}
+/*}}}*/
+/*FUNCTION Penta::Penta(int id, int index, IoModel* iomodel,int nummodels) {{{*/
+Penta::Penta(int penta_id, int penta_sid, int index, IoModel* iomodel,int nummodels)
+	:PentaRef(nummodels)
+	,PentaHook(nummodels,index+1,iomodel) //index+1: material id, iomodel->numberofelements+1: matpar id
+                                                                      { //i is the element index
+
+	int i;
+	int penta_elements_ids[2];
+
+	/*Checks in debugging mode*/
+	/*{{{*/
+	_assert_(iomodel->Data(MeshUpperelementsEnum));
+	_assert_(iomodel->Data(MeshLowerelementsEnum));
+	/*}}}*/
+
+	/*id: */
+	this->id=penta_id;
+	this->sid=penta_sid;
+
+	/*Build neighbors list*/
+	if (xIsNan(iomodel->Data(MeshUpperelementsEnum)[index])) penta_elements_ids[1]=this->id; //upper penta is the same penta
+	else                                    penta_elements_ids[1]=reCast((iomodel->Data(MeshUpperelementsEnum)[index]));
+	if (xIsNan(iomodel->Data(MeshLowerelementsEnum)[index])) penta_elements_ids[0]=this->id; //lower penta is the same penta
+	else                                    penta_elements_ids[0]=reCast((iomodel->Data(MeshLowerelementsEnum)[index]));
+	this->InitHookNeighbors(penta_elements_ids);
+
+	/*Build horizontalneighborsids list: */
+	_assert_(iomodel->Data(MeshElementconnectivityEnum));
+	for(i=0;i<3;i++) this->horizontalneighborsids[i]=reCast(iomodel->Data(MeshElementconnectivityEnum)[3*index+i])-1;
+
+	//this->parameters: we still can't point to it, it may not even exist. Configure will handle this.
+	this->parameters=NULL;
+
+	/*intialize inputs and results: */
+	this->inputs=new Inputs();
+	this->results=new Results();
+	
+	/*initialize pointers:*/
+	this->nodes=NULL;
+	this->material=NULL;
+	this->matpar=NULL;
+	this->verticalneighbors=NULL;
+}
+/*}}}*/
+/*FUNCTION Penta::copy {{{*/
+Object* Penta::copy() {
+
+	int i;
+
+	Penta* penta=NULL;
+
+	penta=new Penta();
+
+	//deal with PentaRef mother class
+	penta->element_type_list=xNew(this->numanalyses);
+	for(i=0;inumanalyses;i++) penta->element_type_list[i]=this->element_type_list[i];
+
+	//deal with PentaHook mother class
+	penta->numanalyses=this->numanalyses;
+	penta->hnodes=new Hook*[penta->numanalyses];
+	for(i=0;inumanalyses;i++)penta->hnodes[i]=(Hook*)this->hnodes[i]->copy();
+	penta->hmaterial=(Hook*)this->hmaterial->copy();
+	penta->hmatpar=(Hook*)this->hmatpar->copy();
+	penta->hneighbors=(Hook*)this->hneighbors->copy();
+
+	/*deal with Penta  copy fields: */
+	penta->id=this->id;
+	penta->sid=this->sid;
+	if(this->inputs){
+		penta->inputs=(Inputs*)this->inputs->Copy();
+	}
+	else{
+		penta->inputs=new Inputs();
+	}
+	if(this->results){
+		penta->results=(Results*)this->results->Copy();
+	}
+	else{
+		penta->results=new Results();
+	}
+	/*point parameters: */
+	penta->parameters=this->parameters;
+
+	/*recover objects: */
+	penta->nodes=xNew(6); //we cannot rely on an analysis_counter to tell us which analysis_type we are running, so we just copy the nodes.
+	for(i=0;i<6;i++)penta->nodes[i]=this->nodes[i];
+	penta->material=(Material*)penta->hmaterial->delivers();
+	penta->matpar=(Matpar*)penta->hmatpar->delivers();
+	penta->verticalneighbors=(Penta**)penta->hneighbors->deliverp();
+
+	/*neighbors: */
+	for(i=0;i<3;i++)penta->horizontalneighborsids[i]=this->horizontalneighborsids[i];
+
+	return penta;
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION Penta::AverageOntoPartition {{{*/
+void  Penta::AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part){
+	_error_("Not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Penta::BedNormal {{{*/
+void Penta::BedNormal(IssmDouble* bed_normal, IssmDouble xyz_list[3][3]){
+
+	int i;
+	IssmDouble v13[3],v23[3];
+	IssmDouble normal[3];
+	IssmDouble normal_norm;
+
+	for (i=0;i<3;i++){
+		v13[i]=xyz_list[0][i]-xyz_list[2][i];
+		v23[i]=xyz_list[1][i]-xyz_list[2][i];
+	}
+
+	normal[0]=v13[1]*v23[2]-v13[2]*v23[1];
+	normal[1]=v13[2]*v23[0]-v13[0]*v23[2];
+	normal[2]=v13[0]*v23[1]-v13[1]*v23[0];
+	normal_norm=sqrt( pow(normal[0],2)+pow(normal[1],2)+pow(normal[2],2) );
+
+	/*Bed normal is opposite to surface normal*/
+	*(bed_normal)=-normal[0]/normal_norm;
+	*(bed_normal+1)=-normal[1]/normal_norm;
+	*(bed_normal+2)=-normal[2]/normal_norm;
+}
+/*}}}*/
+/*FUNCTION Penta::BasalFrictionCreateInput {{{*/
+void Penta::BasalFrictionCreateInput(void){
+
+	/*Constants*/
+	const int  numdof=NUMVERTICES*NDOF1;
+
+	/*Intermediaries */
+	int    count,ig;
+	IssmDouble basalfriction[NUMVERTICES]={0,0,0,0,0,0};
+	IssmDouble alpha2,vx,vy;
+	Friction*  friction=NULL;
+	GaussPenta* gauss=NULL;
+
+
+	/* Basal friction can only be found at the base of an ice sheet: */
+	if (!IsOnBed() || IsFloating()){
+		//empty friction: 
+		this->inputs->AddInput(new PentaP1Input(BasalFrictionEnum,&basalfriction[0]));
+		return;
+	}
+
+	/*Retrieve all inputs and parameters*/
+	Input* vx_input=inputs->GetInput(VxEnum);                         _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                         _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);                         _assert_(vz_input);
+
+
+	/*Build friction element, needed later: */
+	friction=new Friction("3d",inputs,matpar,DiagnosticHorizAnalysisEnum);
+
+	/* Start looping on the number of gauss 2d (nodes on the bedrock) */
+	gauss=new GaussPenta(0,1,2,2);
+	count=0;
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		friction->GetAlpha2(&alpha2,gauss,VxEnum,VyEnum,VzEnum);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		basalfriction[count]=alpha2*(pow(vx,2.0)+pow(vy,2.0));
+		count++;
+	}
+	
+	/*Create PentaVertex input, which will hold the basal friction:*/
+	this->inputs->AddInput(new PentaP1Input(BasalFrictionEnum,&basalfriction[0]));
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+}
+/*}}}*/
+/*FUNCTION Penta::ComputeBasalStress {{{*/
+void  Penta::ComputeBasalStress(Vector* sigma_b){
+
+	int         i,j,ig;
+	int         dofv[3]={0,1,2};
+	int         dofp[1]={3};
+	int         analysis_type,approximation;
+	int         doflist[NUMVERTICES];
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      xyz_list_tria[3][3];
+	IssmDouble      rho_ice,gravity,stokesreconditioning;
+	IssmDouble      pressure,viscosity,bed,Jdet2d;
+	IssmDouble      bed_normal[3];
+	IssmDouble      basalforce[3];
+	IssmDouble      epsilon[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble      devstresstensor[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble      stresstensor[6]={0.0};
+	IssmDouble      sigma_xx,sigma_yy,sigma_zz;
+	IssmDouble      sigma_xy,sigma_xz,sigma_yz;
+	IssmDouble      surface=0,value=0;
+	GaussPenta* gauss;
+
+	/*retrive parameters: */
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*Check analysis_types*/
+	if (analysis_type!=DiagnosticHorizAnalysisEnum) _error_("Not supported yet!");
+	if (approximation!=StokesApproximationEnum) _error_("Not supported yet!");
+
+	/*retrieve some parameters: */
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	
+	if(!IsOnBed()){
+		//put zero
+		sigma_b->SetValue(id-1,0.0,INS_VAL);
+		return;
+	}
+
+	/*recovre material parameters: */
+	rho_ice=matpar->GetRhoIce();
+	gravity=matpar->GetG();
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;i<3;i++) for(j=0;j<3;j++) xyz_list_tria[i][j]=xyz_list[i][j];
+
+	/*Retrieve all inputs we will be needing: */
+	Input* pressure_input=inputs->GetInput(PressureEnum); _assert_(pressure_input);
+	Input* vx_input=inputs->GetInput(VxEnum);             _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);             _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);             _assert_(vz_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(0,1,2,2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/*Compute strain rate viscosity and pressure: */
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+		pressure_input->GetInputValue(&pressure,gauss);
+
+		/*Compute Stress*/
+		sigma_xx=2*viscosity*epsilon[0]-pressure*stokesreconditioning; // sigma = nu eps - pressure
+		sigma_yy=2*viscosity*epsilon[1]-pressure*stokesreconditioning;
+		sigma_zz=2*viscosity*epsilon[2]-pressure*stokesreconditioning;
+		sigma_xy=2*viscosity*epsilon[3];
+		sigma_xz=2*viscosity*epsilon[4];
+		sigma_yz=2*viscosity*epsilon[5];
+
+		/*Get normal vector to the bed */
+		BedNormal(&bed_normal[0],xyz_list_tria);
+
+		/*basalforce*/
+		basalforce[0] += sigma_xx*bed_normal[0] + sigma_xy*bed_normal[1] + sigma_xz*bed_normal[2];
+		basalforce[1] += sigma_xy*bed_normal[0] + sigma_yy*bed_normal[1] + sigma_yz*bed_normal[2];
+		basalforce[2] += sigma_xz*bed_normal[0] + sigma_yz*bed_normal[1] + sigma_zz*bed_normal[2];
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0],gauss);
+		value+=sigma_zz*Jdet2d*gauss->weight;
+		surface+=Jdet2d*gauss->weight;
+	}
+	value=value/surface;
+
+	/*Add value to output*/
+	sigma_b->SetValue(id-1,value,INS_VAL);
+}
+/*}}}*/
+/*FUNCTION Penta::ComputeStrainRate {{{*/
+void  Penta::ComputeStrainRate(Vector* eps){
+
+	_error_("Not implemented yet");
+
+}
+/*}}}*/
+/*FUNCTION Penta::ComputeStressTensor {{{*/
+void  Penta::ComputeStressTensor(){
+
+	int         iv;
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      pressure,viscosity;
+	IssmDouble      epsilon[6]; /* epsilon=[exx,eyy,exy];*/
+	IssmDouble      sigma_xx[NUMVERTICES];
+	IssmDouble		sigma_yy[NUMVERTICES];
+	IssmDouble		sigma_zz[NUMVERTICES];
+	IssmDouble      sigma_xy[NUMVERTICES];
+	IssmDouble		sigma_xz[NUMVERTICES];
+	IssmDouble		sigma_yz[NUMVERTICES];
+	GaussPenta* gauss=NULL;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Retrieve all inputs we will be needing: */
+	Input* pressure_input=inputs->GetInput(PressureEnum); _assert_(pressure_input);
+	Input* vx_input=inputs->GetInput(VxEnum);             _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);             _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);             _assert_(vz_input);
+
+	/* Start looping on the number of vertices: */
+	gauss=new GaussPenta();
+	for (int iv=0;ivGaussVertex(iv);
+
+		/*Compute strain rate viscosity and pressure: */
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3d(&viscosity,&epsilon[0]);
+		pressure_input->GetInputValue(&pressure,gauss);
+
+		/*Compute Stress*/
+		sigma_xx[iv]=2*viscosity*epsilon[0]-pressure; // sigma = nu eps - pressure
+		sigma_yy[iv]=2*viscosity*epsilon[1]-pressure;
+		sigma_zz[iv]=2*viscosity*epsilon[2]-pressure;
+		sigma_xy[iv]=2*viscosity*epsilon[3];
+		sigma_xz[iv]=2*viscosity*epsilon[4];
+		sigma_yz[iv]=2*viscosity*epsilon[5];
+	}
+	
+	/*Add Stress tensor components into inputs*/
+	this->inputs->AddInput(new PentaP1Input(StressTensorxxEnum,&sigma_xx[0]));
+	this->inputs->AddInput(new PentaP1Input(StressTensorxyEnum,&sigma_xy[0]));
+	this->inputs->AddInput(new PentaP1Input(StressTensorxzEnum,&sigma_xz[0]));
+	this->inputs->AddInput(new PentaP1Input(StressTensoryyEnum,&sigma_yy[0]));
+	this->inputs->AddInput(new PentaP1Input(StressTensoryzEnum,&sigma_yz[0]));
+	this->inputs->AddInput(new PentaP1Input(StressTensorzzEnum,&sigma_zz[0]));
+
+	/*Clean up and return*/
+	delete gauss;
+}
+/*}}}*/
+		/*FUNCTION Penta::Configure {{{*/
+void  Penta::Configure(Elements* elementsin, Loads* loadsin, DataSet* nodesin, Materials* materialsin, Parameters* parametersin){
+
+	int analysis_counter;
+	
+	/*go into parameters and get the analysis_counter: */
+	parametersin->FindParam(&analysis_counter,AnalysisCounterEnum);
+
+	/*Get Element type*/
+	this->element_type=this->element_type_list[analysis_counter];
+
+	/*Take care of hooking up all objects for this element, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and offsets hidden in hooks: */
+	if (this->hnodes[analysis_counter]) this->hnodes[analysis_counter]->configure(nodesin);
+	this->hmaterial->configure(materialsin);
+	this->hmatpar->configure(materialsin);
+	this->hneighbors->configure(elementsin);
+
+	/*Now, go pick up the objects inside the hooks: */
+	if (this->hnodes[analysis_counter]) this->nodes=(Node**)this->hnodes[analysis_counter]->deliverp();
+	else this->nodes=NULL;
+	this->material=(Material*)this->hmaterial->delivers();
+	this->matpar=(Matpar*)this->hmatpar->delivers();
+	this->verticalneighbors=(Penta**)this->hneighbors->deliverp();
+
+	/*point parameters to real dataset: */
+	this->parameters=parametersin;
+
+	/*get inputs configured too: */
+	this->inputs->Configure(parameters);
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrix {{{*/
+void  Penta::CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df){
+
+	/*retrieve parameters: */
+	ElementMatrix* Ke=NULL;
+	ElementVector* De=NULL;
+	int analysis_type;
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Checks in debugging {{{*/
+	_assert_(this->nodes && this->material && this->matpar && this->verticalneighbors && this->parameters && this->inputs);
+	/*}}}*/
+	
+	/*Skip if water element*/
+	if(IsOnWater()) return;
+
+	/*Just branch to the correct element stiffness matrix generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+		#ifdef _HAVE_DIAGNOSTIC_
+		case DiagnosticHorizAnalysisEnum:
+			Ke=CreateKMatrixDiagnosticHoriz(); De=CreateDVectorDiagnosticHoriz();
+			break;
+		case AdjointHorizAnalysisEnum:
+			Ke=CreateKMatrixAdjointHoriz();
+			break;
+		case DiagnosticHutterAnalysisEnum:
+			Ke=CreateKMatrixDiagnosticHutter();
+			break;
+		case DiagnosticVertAnalysisEnum:
+			Ke=CreateKMatrixDiagnosticVert();
+			break;
+		#endif
+		case BedSlopeXAnalysisEnum: case SurfaceSlopeXAnalysisEnum: case BedSlopeYAnalysisEnum: case SurfaceSlopeYAnalysisEnum:
+			Ke=CreateBasalMassMatrix();
+			break;
+		case PrognosticAnalysisEnum:
+			Ke=CreateKMatrixPrognostic();
+			break;
+		#ifdef _HAVE_BALANCED_
+		case BalancethicknessAnalysisEnum:
+			Ke=CreateKMatrixBalancethickness();
+			break;
+		#endif
+		#ifdef _HAVE_THERMAL_
+		case ThermalAnalysisEnum:
+			Ke=CreateKMatrixThermal();
+			break;
+		case EnthalpyAnalysisEnum:
+			Ke=CreateKMatrixEnthalpy();
+			break;
+		case MeltingAnalysisEnum:
+			Ke=CreateKMatrixMelting();
+			break;
+		#endif
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global matrix*/
+	if(Ke){
+		Ke->AddToGlobal(Kff,Kfs);
+		delete Ke;
+	}
+	/*Add to global Vector*/
+	if(De){
+		De->InsertIntoGlobal(df);
+		delete De;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixPrognostic {{{*/
+ElementMatrix* Penta::CreateKMatrixPrognostic(void){
+
+	if (!IsOnBed()) return NULL;
+
+	/*Depth Averaging Vx and Vy*/
+	this->InputDepthAverageAtBase(VxEnum,VxAverageEnum);
+	this->InputDepthAverageAtBase(VyEnum,VyAverageEnum);
+
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementMatrix* Ke=tria->CreateKMatrixPrognostic();
+	delete tria->material; delete tria;
+
+	/*Delete Vx and Vy averaged*/
+	this->inputs->DeleteInput(VxAverageEnum);
+	this->inputs->DeleteInput(VyAverageEnum);
+
+	/*clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateBasalMassMatrix{{{*/
+ElementMatrix* Penta::CreateBasalMassMatrix(void){
+
+	if (!IsOnBed()) return NULL;
+
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementMatrix* Ke=tria->CreateMassMatrix();
+	delete tria->material; delete tria;
+
+	/*clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVector {{{*/
+void  Penta::CreatePVector(Vector* pf){
+
+	/*retrive parameters: */
+	ElementVector* pe=NULL;
+	int analysis_type;
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*if debugging mode, check that all pointers exist {{{*/
+	_assert_(this->nodes && this->material && this->matpar && this->verticalneighbors && this->parameters && this->inputs);
+	/*}}}*/
+
+	/*Skip if water element*/
+	if(IsOnWater()) return;
+
+	/*Just branch to the correct element stiffness matrix generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+		#ifdef _HAVE_DIAGNOSTIC_
+		case DiagnosticHorizAnalysisEnum:
+			pe=CreatePVectorDiagnosticHoriz();
+			break;
+		case DiagnosticHutterAnalysisEnum:
+			pe=CreatePVectorDiagnosticHutter();
+			break;
+		case DiagnosticVertAnalysisEnum:
+			pe=CreatePVectorDiagnosticVert();
+			break;
+		#endif
+	 	#ifdef _HAVE_CONTROL_
+		case AdjointHorizAnalysisEnum:
+			pe=CreatePVectorAdjointHoriz();
+			break;
+		#endif
+		#ifdef _HAVE_THERMAL_
+		case ThermalAnalysisEnum:
+			pe=CreatePVectorThermal();
+			break;
+		case EnthalpyAnalysisEnum:
+			pe=CreatePVectorEnthalpy();
+			break;
+		case MeltingAnalysisEnum:
+			pe=CreatePVectorMelting();
+			break;
+		#endif
+		case BedSlopeXAnalysisEnum: case SurfaceSlopeXAnalysisEnum: case BedSlopeYAnalysisEnum: case SurfaceSlopeYAnalysisEnum:
+			pe=CreatePVectorSlope();
+			break;
+		case PrognosticAnalysisEnum:
+			pe=CreatePVectorPrognostic();
+			break;
+		#ifdef _HAVE_BALANCED_
+		case BalancethicknessAnalysisEnum:
+			pe=CreatePVectorBalancethickness();
+			break;
+		#endif
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global Vector*/
+	if(pe){
+		pe->AddToGlobal(pf);
+		delete pe;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorPrognostic {{{*/
+ElementVector* Penta::CreatePVectorPrognostic(void){
+
+	if (!IsOnBed()) return NULL;
+
+	/*Depth Averaging Vx and Vy*/
+	this->InputDepthAverageAtBase(VxEnum,VxAverageEnum);
+	this->InputDepthAverageAtBase(VyEnum,VyAverageEnum);
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementVector* pe=tria->CreatePVectorPrognostic();
+	delete tria->material; delete tria;
+
+	/*Delete Vx and Vy averaged*/
+	this->inputs->DeleteInput(VxAverageEnum);
+	this->inputs->DeleteInput(VyAverageEnum);
+
+	/*Clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorSlope {{{*/
+ElementVector* Penta::CreatePVectorSlope(void){
+
+	if (!IsOnBed()) return NULL;
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementVector* pe=tria->CreatePVectorSlope();
+	delete tria->material; delete tria;
+
+	/*clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateJacobianMatrix{{{*/
+void  Penta::CreateJacobianMatrix(Matrix* Jff){
+
+	/*retrieve parameters: */
+	ElementMatrix* Ke=NULL;
+	int analysis_type;
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Checks in debugging {{{*/
+	_assert_(this->nodes && this->material && this->matpar && this->verticalneighbors && this->parameters && this->inputs);
+	/*}}}*/
+
+	/*Skip if water element*/
+	if(IsOnWater()) return;
+
+	/*Just branch to the correct element stiffness matrix generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+#ifdef _HAVE_DIAGNOSTIC_
+		case DiagnosticHorizAnalysisEnum:
+			Ke=CreateJacobianDiagnosticHoriz();
+			break;
+#endif
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global matrix*/
+	if(Ke){
+		Ke->AddToGlobal(Jff);
+		delete Ke;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::DeepEcho{{{*/
+void Penta::DeepEcho(void){
+
+	int i;
+	
+	_printLine_("Penta:");
+	_printLine_("   id: " << id);
+	nodes[0]->DeepEcho();
+	nodes[1]->DeepEcho();
+	nodes[2]->DeepEcho();
+	nodes[3]->DeepEcho();
+	nodes[4]->DeepEcho();
+	nodes[5]->DeepEcho();
+	material->DeepEcho();
+	matpar->DeepEcho();
+	_printLine_("   neighbor ids: " << verticalneighbors[0]->Id() << "-" << verticalneighbors[1]->Id());
+	_printLine_("   parameters");
+	parameters->DeepEcho();
+	_printLine_("   inputs");
+	inputs->DeepEcho();
+	_printLine_("   results");
+	results->DeepEcho();
+	_printLine_("neighboor sids: ");
+	_printLine_(" " << horizontalneighborsids[0] << " " << horizontalneighborsids[1] << " " << horizontalneighborsids[2]);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION Penta::DeleteResults {{{*/
+void  Penta::DeleteResults(void){
+
+	/*Delete and reinitialize results*/
+	delete this->results;
+	this->results=new Results();
+
+}
+/*}}}*/
+/*FUNCTION Penta::Delta18oParameterization{{{*/
+void  Penta::Delta18oParameterization(void){
+        /*Are we on the base? If not, return*/
+        if(!IsOnBed()) return;
+
+	int        i;
+	IssmDouble monthlytemperatures[NUMVERTICES][12],monthlyprec[NUMVERTICES][12];
+	IssmDouble TemperaturesPresentday[NUMVERTICES][12],TemperaturesLgm[NUMVERTICES][12];
+	IssmDouble PrecipitationsPresentday[NUMVERTICES][12];
+	IssmDouble tmp[NUMVERTICES];
+	IssmDouble Delta18oPresent,Delta18oLgm,Delta18oTime;
+	IssmDouble Delta18oSurfacePresent,Delta18oSurfaceLgm,Delta18oSurfaceTime;
+	IssmDouble time,yts,finaltime;
+	this->parameters->FindParam(&time,TimeEnum);
+	this->parameters->FindParam(&yts,ConstantsYtsEnum);
+	this->parameters->FindParam(&finaltime,TimesteppingFinalTimeEnum);
+
+	/*Recover present day temperature and precipitation*/
+	Input*     input=inputs->GetInput(SurfaceforcingsTemperaturesPresentdayEnum);    _assert_(input);
+	Input*     input2=inputs->GetInput(SurfaceforcingsTemperaturesLgmEnum);          _assert_(input2);
+	Input*     input3=inputs->GetInput(SurfaceforcingsPrecipitationsPresentdayEnum); _assert_(input3);
+	GaussPenta* gauss=new GaussPenta();
+	for(int month=0;month<12;month++) {
+		for(int iv=0;ivGaussVertex(iv);
+			input->GetInputValue(&TemperaturesPresentday[iv][month],gauss,month/12.*yts);
+			input2->GetInputValue(&TemperaturesLgm[iv][month],gauss,month/12.*yts);
+			input3->GetInputValue(&PrecipitationsPresentday[iv][month],gauss,month/12.*yts);
+			PrecipitationsPresentday[iv][month]=PrecipitationsPresentday[iv][month]/yts; // converion in m/sec
+		}
+	}
+
+	/*Recover delta18o and Delta18oSurface at present day, lgm and at time t*/
+	this->parameters->FindParam(&Delta18oPresent,SurfaceforcingsDelta18oEnum,finaltime);
+	this->parameters->FindParam(&Delta18oLgm,SurfaceforcingsDelta18oEnum,finaltime-(21000*yts));
+	this->parameters->FindParam(&Delta18oTime,SurfaceforcingsDelta18oEnum,time);
+	this->parameters->FindParam(&Delta18oSurfacePresent,SurfaceforcingsDelta18oSurfaceEnum,finaltime);
+	this->parameters->FindParam(&Delta18oSurfaceLgm,SurfaceforcingsDelta18oSurfaceEnum,finaltime-(21000*yts));
+	this->parameters->FindParam(&Delta18oSurfaceTime,SurfaceforcingsDelta18oSurfaceEnum,time);
+
+	/*Compute the temperature and precipitation*/
+	for(int iv=0;ivAddTimeInput(newmonthinput1,time+imonth/12.*yts);
+
+		for(i=0;iAddTimeInput(newmonthinput2,time+imonth/12.*yts);
+	}
+
+	this->inputs->AddInput(NewTemperatureInput);
+	this->inputs->AddInput(NewPrecipitationInput);
+
+	this->InputExtrude(SurfaceforcingsMonthlytemperaturesEnum,ElementEnum);
+	this->InputExtrude(SurfaceforcingsPrecipitationEnum,ElementEnum);
+
+	/*clean-up*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Penta::Echo{{{*/
+
+void Penta::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION Penta::ObjectEnum{{{*/
+int Penta::ObjectEnum(void){
+
+	return PentaEnum;
+
+}
+/*}}}*/
+/*FUNCTION Penta::GetBasalElement{{{*/
+Penta* Penta::GetBasalElement(void){
+
+	/*Output*/
+	Penta* penta=NULL;
+
+	/*Go through all elements till the bed is reached*/
+	penta=this;
+	for(;;){
+		/*Stop if we have reached the surface, else, take lower penta*/
+		if (penta->IsOnBed()) break;
+
+		/* get lower Penta*/
+		penta=penta->GetLowerElement();
+		_assert_(penta->Id()!=this->id);
+	}
+
+	/*return output*/
+	return penta;
+}
+/*}}}*/
+/*FUNCTION Penta::GetDofList {{{*/
+void  Penta::GetDofList(int** pdoflist,int approximation_enum,int setenum){
+
+	int  i,j,count=0;
+	int  numberofdofs=0;
+	int* doflist=NULL;
+
+	/*First, figure out size of doflist: */
+	for(i=0;i<6;i++) numberofdofs+=nodes[i]->GetNumberOfDofs(approximation_enum,setenum);
+
+	/*Allocate: */
+	doflist=xNew(numberofdofs);
+
+	/*Populate: */
+	count=0;
+	for(i=0;i<6;i++){
+		nodes[i]->GetDofList(doflist+count,approximation_enum,setenum);
+		count+=nodes[i]->GetNumberOfDofs(approximation_enum,setenum);
+	}
+
+	/*Assign output pointers:*/
+	*pdoflist=doflist;
+}
+/*}}}*/
+/*FUNCTION Penta::GetDofList1 {{{*/
+void  Penta::GetDofList1(int* doflist){
+
+	int i;
+	for(i=0;i<6;i++) doflist[i]=nodes[i]->GetDofList1();
+
+}
+/*}}}*/
+/*FUNCTION Penta::GetConnectivityList {{{*/
+void  Penta::GetConnectivityList(int* connectivity){
+	for(int i=0;iGetConnectivity();
+}
+/*}}}*/
+/*FUNCTION Penta::GetElementType {{{*/
+int Penta::GetElementType(){
+
+	/*return PentaRef field*/
+	return this->element_type;
+}
+/*}}}*/
+/*FUNCTION Penta::GetElementSizes{{{*/
+void Penta::GetElementSizes(IssmDouble* hx,IssmDouble* hy,IssmDouble* hz){
+
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble xmin,ymin,zmin;
+	IssmDouble xmax,ymax,zmax;
+
+	/*Get xyz list: */
+	GetVerticesCoordinates(&xyz_list[0][0],nodes,NUMVERTICES);
+	xmin=xyz_list[0][0]; xmax=xyz_list[0][0];
+	ymin=xyz_list[0][1]; ymax=xyz_list[0][1];
+	zmin=xyz_list[0][2]; zmax=xyz_list[0][2];
+
+	for(int i=1;ixmax) xmax=xyz_list[i][0];
+		if(xyz_list[i][1]ymax) ymax=xyz_list[i][1];
+		if(xyz_list[i][2]zmax) zmax=xyz_list[i][2];
+	}
+
+	*hx=xmax-xmin;
+	*hy=ymax-ymin;
+	*hz=zmax-zmin;
+}
+/*}}}*/
+/*FUNCTION Penta::GetHorizontalNeighboorSids {{{*/
+int* Penta::GetHorizontalNeighboorSids(){
+
+	/*return PentaRef field*/
+	return &this->horizontalneighborsids[0];
+
+}
+/*}}}*/
+/*FUNCTION Penta::GetLowerElement{{{*/
+Penta* Penta::GetLowerElement(void){
+
+	Penta* upper_penta=NULL;
+
+	upper_penta=(Penta*)verticalneighbors[0]; //first one (0) under, second one (1) above
+
+	return upper_penta;
+}
+/*}}}*/
+/*FUNCTION Penta::GetNodeIndex {{{*/
+int Penta::GetNodeIndex(Node* node){
+
+	_assert_(nodes);
+	for(int i=0;iGetInput(enumtype);
+	if (!input) _error_("Input " << EnumToStringx(enumtype) << " not found in element");
+
+	/*Checks in debugging mode*/
+	_assert_(pvalue);
+
+	/* Start looping on the number of vertices: */
+	gauss=new GaussPenta();
+	for (int iv=0;ivGaussVertex(iv);
+		input->GetInputValue(&pvalue[iv],gauss);
+	}
+
+	/*clean-up*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Penta::GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue) {{{*/
+void Penta::GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue){
+
+	/*Intermediaries*/
+	IssmDouble     value[NUMVERTICES];
+	GaussPenta *gauss              = NULL;
+
+	/*Recover input*/
+	Input* input=inputs->GetInput(enumtype);
+
+	/*Checks in debugging mode*/
+	_assert_(pvalue);
+
+	/* Start looping on the number of vertices: */
+	if (input){
+		gauss=new GaussPenta();
+		for (int iv=0;ivGaussVertex(iv);
+			input->GetInputValue(&pvalue[iv],gauss);
+		}
+	}
+	else{
+		for (int iv=0;ivGetInput(enumtype);
+	if(!input) _error_("No input of type " << EnumToStringx(enumtype) << " found in tria");
+
+	GaussPenta* gauss=new GaussPenta();
+	gauss->GaussVertex(this->GetNodeIndex(node));
+
+	input->GetInputValue(pvalue,gauss);
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Penta::GetPhi {{{*/
+void Penta::GetPhi(IssmDouble* phi, IssmDouble*  epsilon, IssmDouble viscosity){
+	/*Compute deformational heating from epsilon and viscosity */
+
+	IssmDouble epsilon_matrix[3][3];
+	IssmDouble epsilon_eff;
+	IssmDouble epsilon_sqr[3][3];
+
+	/* Build epsilon matrix */
+	epsilon_matrix[0][0]=*(epsilon+0);
+	epsilon_matrix[1][0]=*(epsilon+3);
+	epsilon_matrix[2][0]=*(epsilon+4);
+	epsilon_matrix[0][1]=*(epsilon+3);
+	epsilon_matrix[1][1]=*(epsilon+1);
+	epsilon_matrix[2][1]=*(epsilon+5);
+	epsilon_matrix[0][2]=*(epsilon+4);
+	epsilon_matrix[1][2]=*(epsilon+5);
+	epsilon_matrix[2][2]=*(epsilon+2);
+
+	/* Effective value of epsilon_matrix */
+	epsilon_sqr[0][0]=pow(epsilon_matrix[0][0],2);
+	epsilon_sqr[1][0]=pow(epsilon_matrix[1][0],2);
+	epsilon_sqr[2][0]=pow(epsilon_matrix[2][0],2);
+	epsilon_sqr[0][1]=pow(epsilon_matrix[0][1],2);
+	epsilon_sqr[1][1]=pow(epsilon_matrix[1][1],2);
+	epsilon_sqr[2][1]=pow(epsilon_matrix[2][1],2);
+	epsilon_sqr[0][2]=pow(epsilon_matrix[0][2],2);
+	epsilon_sqr[1][2]=pow(epsilon_matrix[1][2],2);
+	epsilon_sqr[2][2]=pow(epsilon_matrix[2][2],2);
+	epsilon_eff=1/pow(2,0.5)*pow((epsilon_sqr[0][0]+epsilon_sqr[0][1]+ epsilon_sqr[0][2]+ epsilon_sqr[1][0]+ epsilon_sqr[1][1]+ epsilon_sqr[1][2]+ epsilon_sqr[2][0]+ epsilon_sqr[2][1]+ epsilon_sqr[2][2]),0.5);
+
+	/*Phi = Tr(sigma * eps) 
+	 *    = Tr(sigma'* eps)
+	 *    = 2 * eps_eff * sigma'_eff
+	 *    = 4 * mu * eps_eff ^2*/
+	*phi=4*pow(epsilon_eff,2.0)*viscosity;
+}
+/*}}}*/
+/*FUNCTION Penta::GetSidList{{{*/
+void  Penta::GetSidList(int* sidlist){
+
+	int i;
+	for(i=0;iGetSidList();
+
+}
+/*}}}*/
+/*FUNCTION Penta::GetSolutionFromInputs{{{*/
+void  Penta::GetSolutionFromInputs(Vector* solution){
+
+	int analysis_type;
+
+	/*retrive parameters: */
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Just branch to the correct InputUpdateFromSolution generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+	#ifdef _HAVE_DIAGNOSTIC_
+	case DiagnosticHorizAnalysisEnum:
+		int approximation;
+		inputs->GetInputValue(&approximation,ApproximationEnum);
+		if(approximation==StokesApproximationEnum || approximation==NoneApproximationEnum){
+			GetSolutionFromInputsDiagnosticStokes(solution);
+		}
+		else if (approximation==MacAyealApproximationEnum || approximation==PattynApproximationEnum || approximation==HutterApproximationEnum){
+			GetSolutionFromInputsDiagnosticHoriz(solution);
+		}
+		else if (approximation==MacAyealPattynApproximationEnum || approximation==PattynStokesApproximationEnum || approximation==MacAyealStokesApproximationEnum){
+			return; //the elements around will create the solution
+		}
+		break;
+	case DiagnosticHutterAnalysisEnum:
+		GetSolutionFromInputsDiagnosticHutter(solution);
+		break;
+	case DiagnosticVertAnalysisEnum:
+		GetSolutionFromInputsDiagnosticVert(solution);
+		break;
+	#endif
+	#ifdef _HAVE_THERMAL_
+	case ThermalAnalysisEnum:
+		GetSolutionFromInputsThermal(solution);
+		break;
+	case EnthalpyAnalysisEnum:
+		GetSolutionFromInputsEnthalpy(solution);
+		break;
+	#endif
+	default:
+		_error_("analysis: " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::GetStabilizationParameter {{{*/
+IssmDouble Penta::GetStabilizationParameter(IssmDouble u, IssmDouble v, IssmDouble w, IssmDouble diameter, IssmDouble kappa){
+	/*Compute stabilization parameter*/
+	/*kappa=thermalconductivity/(rho_ice*hearcapacity) for thermal model*/
+	/*kappa=enthalpydiffusionparameter for enthalpy model*/
+
+	IssmDouble normu;
+	IssmDouble tau_parameter;
+
+	normu=pow(pow(u,2)+pow(v,2)+pow(w,2),0.5);
+	if(normu*diameter/(3*2*kappa)<1){ 
+		tau_parameter=pow(diameter,2)/(3*2*2*kappa);
+	}
+	else tau_parameter=diameter/(2*normu);
+
+	return tau_parameter;
+}
+/*}}}*/
+/*FUNCTION Penta::GetStrainRate3dPattyn{{{*/
+void Penta::GetStrainRate3dPattyn(IssmDouble* epsilon,IssmDouble* xyz_list, GaussPenta* gauss, Input* vx_input, Input* vy_input){
+	/*Compute the 3d Blatter/PattynStrain Rate (5 components):
+	 *
+	 * epsilon=[exx eyy exy exz eyz]
+	 *
+	 * with exz=1/2 du/dz
+	 *      eyz=1/2 dv/dz
+	 *
+	 * the contribution of vz is neglected
+	 */
+
+	int i;
+	IssmDouble epsilonvx[5];
+	IssmDouble epsilonvy[5];
+
+	/*Check that both inputs have been found*/
+	if (!vx_input || !vy_input){
+		_error_("Input missing. Here are the input pointers we have for vx: " << vx_input << ", vy: " << vy_input << "\n");
+	}
+
+	/*Get strain rate assuming that epsilon has been allocated*/
+	vx_input->GetVxStrainRate3dPattyn(epsilonvx,xyz_list,gauss);
+	vy_input->GetVyStrainRate3dPattyn(epsilonvy,xyz_list,gauss);
+
+	/*Sum all contributions*/
+	for(i=0;i<5;i++) epsilon[i]=epsilonvx[i]+epsilonvy[i];
+}
+/*}}}*/
+/*FUNCTION Penta::GetStrainRate3d{{{*/
+void Penta::GetStrainRate3d(IssmDouble* epsilon,IssmDouble* xyz_list, GaussPenta* gauss, Input* vx_input, Input* vy_input, Input* vz_input){
+	/*Compute the 3d Strain Rate (6 components):
+	 *
+	 * epsilon=[exx eyy ezz exy exz eyz]
+	 */
+
+	int i;
+	IssmDouble epsilonvx[6];
+	IssmDouble epsilonvy[6];
+	IssmDouble epsilonvz[6];
+
+	/*Check that both inputs have been found*/
+	if (!vx_input || !vy_input || !vz_input){
+		_error_("Input missing. Here are the input pointers we have for vx: " << vx_input << ", vy: " << vy_input << ", vz: " << vz_input << "\n");
+	}
+
+	/*Get strain rate assuming that epsilon has been allocated*/
+	vx_input->GetVxStrainRate3d(epsilonvx,xyz_list,gauss);
+	vy_input->GetVyStrainRate3d(epsilonvy,xyz_list,gauss);
+	vz_input->GetVzStrainRate3d(epsilonvz,xyz_list,gauss);
+
+	/*Sum all contributions*/
+	for(i=0;i<6;i++) epsilon[i]=epsilonvx[i]+epsilonvy[i]+epsilonvz[i];
+}
+/*}}}*/
+/*FUNCTION Penta::GetUpperElement{{{*/
+Penta* Penta::GetUpperElement(void){
+
+	Penta* upper_penta=NULL;
+
+	upper_penta=(Penta*)verticalneighbors[1]; //first one under, second one above
+
+	return upper_penta;
+}
+/*}}}*/
+/*FUNCTION Penta::GetVectorFromInputs{{{*/
+void  Penta::GetVectorFromInputs(Vector* vector,int input_enum){
+
+	int doflist1[NUMVERTICES];
+
+	/*Get out if this is not an element input*/
+	if (!IsInput(input_enum)) return;
+
+	/*Prepare index list*/
+	this->GetDofList1(&doflist1[0]);
+
+	/*Get input (either in element or material)*/
+	Input* input=inputs->GetInput(input_enum);
+	if(!input) _error_("Input " << EnumToStringx(input_enum) << " not found in element");
+
+	/*We found the enum.  Use its values to fill into the vector, using the vertices ids: */
+	input->GetVectorFromInputs(vector,&doflist1[0]);
+}
+/*}}}*/
+/*FUNCTION Penta::GetVectorFromResults{{{*/
+void  Penta::GetVectorFromResults(Vector* vector,int offset,int enum_in,int interp){
+
+	/*Get result*/
+	ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(offset);
+	if(elementresult->InstanceEnum()!=enum_in){
+		_error_("Results of offset "<InstanceEnum())<<" when "<GetSidList(&doflist1[0]);
+		this->GetConnectivityList(&connectivity[0]);
+		elementresult->GetVectorFromResults(vector,&doflist1[0],&connectivity[0],NUMVERTICES);
+	}
+	else if(interp==P0Enum){
+		elementresult->GetElementVectorFromResults(vector,sid);
+	}
+	else{
+		_printLine_("Interpolation " << EnumToStringx(interp) << " not supported");
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::GetZcoord {{{*/
+IssmDouble Penta::GetZcoord(GaussPenta* gauss){
+
+	int    i;
+	IssmDouble z;
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble z_list[NUMVERTICES];
+
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iinputs->GetInput(enum_type);
+	if(!input)_error_("could not find old input with enum: " << EnumToStringx(enum_type));
+
+	/*ArtificialNoise: */
+	input->ArtificialNoise(min,max);
+}
+/*}}}*/
+/*FUNCTION Penta::InputConvergence{{{*/
+bool Penta::InputConvergence(IssmDouble* eps, int* enums,int num_enums,int* criterionenums,IssmDouble* criterionvalues,int num_criterionenums){
+
+	int i;
+	bool    converged=true;
+	Input** new_inputs=NULL;
+	Input** old_inputs=NULL;
+
+	new_inputs=xNew(num_enums/2); //half the enums are for the new inputs
+	old_inputs=xNew(num_enums/2); //half the enums are for the old inputs
+
+	for(i=0;iinputs->GetInput(enums[2*i+0]);
+		old_inputs[i]=(Input*)this->inputs->GetInput(enums[2*i+1]);
+		if(!new_inputs[i])_error_("could not find input with enum " << EnumToStringx(enums[2*i+0]));
+		if(!old_inputs[i])_error_("could not find input with enum " << EnumToStringx(enums[2*i+0]));
+	}
+
+	/*ok, we've got the inputs (new and old), now loop throught the number of criterions and fill the eps array:*/
+	for(i=0;icriterionvalues[i]) converged=false; 
+	}
+
+	/*clean up*/
+	xDelete(new_inputs);
+	xDelete(old_inputs);
+
+	/*Return output*/
+	return converged;
+}
+/*}}}*/
+/*FUNCTION Penta::InputCreate(IssmDouble scalar,int enum,int code);{{{*/
+void Penta::InputCreate(IssmDouble scalar,int name,int code){
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+	
+	if ((code==5) || (code==1)){ //boolean
+		this->inputs->AddInput(new BoolInput(name,reCast(scalar)));
+	}
+	else if ((code==6) || (code==2)){ //integer
+		this->inputs->AddInput(new IntInput(name,reCast(scalar)));
+	}
+	else if ((code==7) || (code==3)){ //IssmDouble
+		this->inputs->AddInput(new DoubleInput(name,scalar));
+	}
+	else _error_("could not recognize nature of vector from code " << code);
+
+}
+/*}}}*/
+/*FUNCTION Penta::InputCreate(IssmDouble* vector,int index,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code){{{*/
+void Penta::InputCreate(IssmDouble* vector, int index,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code){//index into elements
+
+	/*Intermediaries*/
+	int    i,j,t;
+	int    penta_vertex_ids[6];
+	int    row;
+	IssmDouble nodeinputs[6];
+	IssmDouble time;
+	TransientInput* transientinput=NULL;
+
+	int    numberofvertices;
+	int    numberofelements;
+	IssmDouble yts;
+
+	/*Fetch parameters: */
+	iomodel->Constant(&numberofvertices,MeshNumberofverticesEnum);
+	iomodel->Constant(&numberofelements,MeshNumberofelementsEnum);
+	iomodel->Constant(&yts,ConstantsYtsEnum);
+
+	/*Branch on type of vector: nodal or elementary: */
+	if(vector_type==1){ //nodal vector
+
+		/*Recover vertices ids needed to initialize inputs*/
+		for(i=0;i<6;i++){ 
+			_assert_(iomodel->Data(MeshElementsEnum));
+			penta_vertex_ids[i]=reCast(iomodel->Data(MeshElementsEnum)[6*index+i]); //ids for vertices are in the elements array from Matlab
+		}
+
+		/*Are we in transient or static? */
+		if(M==numberofvertices){
+
+			/*create input values: */
+			for(i=0;i<6;i++)nodeinputs[i]=(IssmDouble)vector[penta_vertex_ids[i]-1];
+
+			/*process units: */
+			UnitConversion(&nodeinputs[0], 6 ,ExtToIuEnum, vector_enum);
+
+			/*create static input: */
+			this->inputs->AddInput(new PentaP1Input(vector_enum,nodeinputs));
+		}
+		else if(M==numberofvertices+1){
+			/*create transient input: */
+			for(t=0;tAddTimeInput(new PentaP1Input(vector_enum,nodeinputs),time);
+			}
+			this->inputs->AddInput(transientinput);
+		}
+		else _error_("nodal vector is either numberofnodes (" << numberofvertices << "), or numberofnodes+1 long. Field provided is " << M << " long. Enum " << EnumToStringx(vector_enum));
+	}
+	else if(vector_type==2){ //element vector
+		/*Are we in transient or static? */
+		if(M==numberofelements){
+
+			/*static mode: create an input out of the element value: */
+
+			if (code==5){ //boolean
+				this->inputs->AddInput(new BoolInput(vector_enum,reCast(vector[index])));
+			}
+			else if (code==6){ //integer
+				this->inputs->AddInput(new IntInput(vector_enum,reCast(vector[index])));
+			}
+			else if (code==7){ //IssmDouble
+				this->inputs->AddInput(new DoubleInput(vector_enum,vector[index]));
+			}
+			else _error_("could not recognize nature of vector from code " << code);
+		}
+		else {
+			_error_("transient elementary inputs not supported yet!");
+		}
+	}
+	else{
+		_error_("Cannot add input for vector type " << vector_type << " (not supported)");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Penta::InputDepthAverageAtBase{{{*/
+void  Penta::InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum){
+
+	int  step,i;
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	IssmDouble  Helem_list[NUMVERTICES];
+	IssmDouble  zeros_list[NUMVERTICES]={0.0};
+	Penta* penta=NULL;
+	Input* original_input=NULL;
+	Input* element_integrated_input=NULL;
+	Input* total_integrated_input=NULL;
+	Input* element_thickness_input=NULL;
+	Input* total_thickness_input=NULL;
+	Input* depth_averaged_input=NULL;
+
+	/*recover parameters: */
+
+	/*Are we on the base? If not, return*/
+	if(!IsOnBed()) return;
+
+	/*OK, we are on bed. Initialize global inputs as 0*/
+	total_thickness_input =new PentaP1Input(ThicknessEnum,zeros_list);
+
+	/*Now follow all the upper element from the base to the surface to integrate the input*/
+	penta=this;
+	step =0;
+	for(;;){
+
+		/*Step1: Get original input (to be depth avegaged): */
+		if (object_enum==MeshElementsEnum)
+		 original_input=(Input*)penta->inputs->GetInput(enum_type);
+		else if (object_enum==MaterialsEnum)
+		 original_input=(Input*)penta->material->inputs->GetInput(enum_type);
+		else
+		 _error_("object " << EnumToStringx(object_enum) << " not supported yet");
+		if(!original_input) _error_("could not find input with enum " << EnumToStringx(enum_type));
+
+		/*If first time, initialize total_integrated_input*/
+		if (step==0){
+			if (original_input->ObjectEnum()==PentaP1InputEnum)
+			 total_integrated_input=new PentaP1Input(average_enum_type,zeros_list);
+			else if (original_input->ObjectEnum()==ControlInputEnum)
+			 total_integrated_input=new PentaP1Input(average_enum_type,zeros_list);
+			else if (original_input->ObjectEnum()==DoubleInputEnum)
+			 total_integrated_input=new DoubleInput(average_enum_type,0.0);
+			else
+			 _error_("object " << EnumToStringx(original_input->ObjectEnum()) << " not supported yet");
+		}
+
+		/*Step2: Create element thickness input*/
+		GetVerticesCoordinates(&xyz_list[0][0],penta->nodes,NUMVERTICES);
+		for(i=0;i<3;i++){
+			Helem_list[i]=xyz_list[i+3][2]-xyz_list[i][2];
+			Helem_list[i+3]=Helem_list[i];
+		}
+		element_thickness_input=new PentaP1Input(ThicknessEnum,Helem_list);
+
+		/*Step3: Vertically integrate A COPY of the original*/
+		element_integrated_input=(Input*)original_input->copy();
+		element_integrated_input->VerticallyIntegrate(element_thickness_input);
+
+		/*Add contributions to global inputs*/
+		total_integrated_input->AXPY(element_integrated_input,1.0);
+		total_thickness_input ->AXPY(element_thickness_input,1.0);
+
+		/*Clean up*/
+		delete element_thickness_input;
+		delete element_integrated_input;
+
+		/*Stop if we have reached the surface, else, take upper penta*/
+		if (penta->IsOnSurface()) break;
+
+		/* get upper Penta*/
+		penta=penta->GetUpperElement();
+		_assert_(penta->Id()!=this->id);
+
+		/*increase couter*/
+		step++;
+	}
+
+	/*OK, now we only need to divide the depth integrated input by the total thickness!*/
+	depth_averaged_input=total_integrated_input->PointwiseDivide(total_thickness_input);
+	depth_averaged_input->ChangeEnum(average_enum_type);
+
+	/*Clean up*/
+	delete total_thickness_input;
+	delete total_integrated_input;
+
+	/*Finally, add to inputs*/
+	if (object_enum==MeshElementsEnum)
+	 this->inputs->AddInput((Input*)depth_averaged_input);
+	else if (object_enum==MaterialsEnum)
+	 this->material->inputs->AddInput((Input*)depth_averaged_input);
+	else
+	 _error_("object " << EnumToStringx(object_enum) << " not supported yet");
+}
+/*}}}*/
+/*FUNCTION Penta::InputDuplicate{{{*/
+void  Penta::InputDuplicate(int original_enum,int new_enum){
+
+	/*Call inputs method*/
+	if (IsInput(original_enum)) inputs->DuplicateInput(original_enum,new_enum);
+
+}
+/*}}}*/
+/*FUNCTION Penta::InputExtrude {{{*/
+void  Penta::InputExtrude(int enum_type,int object_type){
+
+	int     i,num_inputs;
+	Penta  *penta       = NULL;
+	Input  *copy        = NULL;
+	Input **base_inputs = NULL;
+
+	/*Are we on the base, not on the surface?:*/
+	if(!IsOnBed()) return;
+
+	/*Step1: Get and Extrude original input: */
+	if (object_type==ElementEnum){
+		num_inputs=1;
+		base_inputs=xNew(num_inputs);
+		base_inputs[0]=(Input*)this->inputs->GetInput(enum_type);
+	}
+	else if (object_type==MaterialsEnum){
+		num_inputs=1;
+		base_inputs=xNew(num_inputs);
+		base_inputs[0]=(Input*)material->inputs->GetInput(enum_type);
+	}
+	else if (object_type==NodeEnum){
+		num_inputs=3; //only the three upper nodes
+		base_inputs=xNew(num_inputs);
+		for(i=0;inodes[i]->inputs->GetInput(enum_type);
+		}
+	}
+	else{
+		_error_("object of type " << EnumToStringx(object_type) << " not supported yet");
+	}
+	for(i=0;iExtrude();
+	}
+
+	/*Stop if there is only one layer of element*/
+	if (this->IsOnSurface()) return;
+
+	/*Step 2: this input has been extruded for this element, now follow the upper element*/
+	penta=this;
+	for(;;){
+		/* get upper Penta*/
+		penta=penta->GetUpperElement();
+		_assert_(penta->Id()!=this->id);
+
+		/*Add input of the basal element to penta->inputs*/
+		for(i=0;icopy();
+			if (object_type==ElementEnum){
+				penta->inputs->AddInput((Input*)copy);
+			}
+			else if(object_type==MaterialsEnum){
+				penta->material->inputs->AddInput((Input*)copy);
+			}
+			else if(object_type==NodeEnum){
+				penta->nodes[i+3]->inputs->AddInput((Input*)copy); //change only the three upper nodes
+			}
+			else{
+				_error_("object of type " << EnumToStringx(object_type) << " not supported yet");
+			}
+		}
+
+		/*Stop if we have reached the surface*/
+		if (penta->IsOnSurface()) break;
+	}
+
+	/*clean-up and return*/
+	xDelete(base_inputs);
+}
+/*}}}*/
+/*FUNCTION Penta::InputScale{{{*/
+void  Penta::InputScale(int enum_type,IssmDouble scale_factor){
+
+	Input* input=NULL;
+
+	/*Make a copy of the original input: */
+	input=(Input*)this->inputs->GetInput(enum_type);
+	if(!input)_error_("could not find old input with enum: " << EnumToStringx(enum_type));
+
+	/*Scale: */
+	input->Scale(scale_factor);
+}
+/*}}}*/
+/*FUNCTION Penta::InputToResult{{{*/
+void  Penta::InputToResult(int enum_type,int step,IssmDouble time){
+
+	int    i;
+	bool   found = false;
+	Input *input = NULL;
+
+	/*Go through all the input objects, and find the one corresponding to enum_type, if it exists: */
+	if (enum_type==MaterialsRheologyBbarEnum) input=this->material->inputs->GetInput(MaterialsRheologyBEnum);
+	else if (enum_type==MaterialsRheologyZbarEnum) input=this->material->inputs->GetInput(MaterialsRheologyZEnum);
+	else input=this->inputs->GetInput(enum_type);
+	//if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found in penta->inputs"); why error out? if the requested input does not exist, we should still 
+	//try and output whatever we can instead of just failing.
+	if(!input)return;
+
+	/*If we don't find it, no big deal, just don't do the transfer. Otherwise, build a new Result 
+	 * object out of the input, with the additional step and time information: */
+	this->results->AddObject((Object*)input->SpawnResult(step,time));
+	#ifdef _HAVE_CONTROL_
+	if(input->ObjectEnum()==ControlInputEnum){
+		if(((ControlInput*)input)->gradient!=NULL) this->results->AddObject((Object*)((ControlInput*)input)->SpawnGradient(step,time));
+	}
+	#endif
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromConstant(bool value, int name);{{{*/
+void  Penta::InputUpdateFromConstant(bool constant, int name){
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	/*update input*/
+	this->inputs->AddInput(new BoolInput(name,constant));
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromConstant(IssmDouble value, int name);{{{*/
+void  Penta::InputUpdateFromConstant(IssmDouble constant, int name){
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	/*update input*/
+	this->inputs->AddInput(new DoubleInput(name,constant));
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromConstant(int value, int name);{{{*/
+void  Penta::InputUpdateFromConstant(int constant, int name){
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	/*update input*/
+	this->inputs->AddInput(new IntInput(name,constant));
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromIoModel {{{*/
+void Penta::InputUpdateFromIoModel(int index,IoModel* iomodel){ 
+
+	/*Intermediaries*/
+	IssmInt i,j;
+	int     penta_vertex_ids[6];
+	IssmDouble  nodeinputs[6];
+	IssmDouble  cmmininputs[6];
+	IssmDouble  cmmaxinputs[6];
+
+	IssmDouble  yts;
+	bool    control_analysis;
+	int     num_control_type;
+	int     num_cm_responses;
+
+	/*Fetch parameters: */
+	iomodel->Constant(&yts,ConstantsYtsEnum);
+	iomodel->Constant(&control_analysis,InversionIscontrolEnum);
+	if(control_analysis) iomodel->Constant(&num_control_type,InversionNumControlParametersEnum);
+	if(control_analysis) iomodel->Constant(&num_cm_responses,InversionNumCostFunctionsEnum);
+
+	/*Checks if debuging*/
+	/*{{{*/
+	_assert_(iomodel->Data(MeshElementsEnum));
+	/*}}}*/
+
+	/*Recover vertices ids needed to initialize inputs*/
+	for(i=0;i<6;i++){ 
+		penta_vertex_ids[i]=reCast(iomodel->Data(MeshElementsEnum)[6*index+i]); //ids for vertices are in the elements array from Matlab
+	}
+
+	/*Control Inputs*/
+	#ifdef _HAVE_CONTROL_
+	if (control_analysis && iomodel->Data(InversionControlParametersEnum)){
+		for(i=0;i(iomodel->Data(InversionControlParametersEnum)[i])){
+				case BalancethicknessThickeningRateEnum:
+					if (iomodel->Data(BalancethicknessThickeningRateEnum)){
+						for(j=0;j<6;j++)nodeinputs[j]=iomodel->Data(BalancethicknessThickeningRateEnum)[penta_vertex_ids[j]-1]/yts;
+						for(j=0;j<6;j++)cmmininputs[j]=iomodel->Data(InversionMinParametersEnum)[(penta_vertex_ids[j]-1)*num_control_type+i]/yts;
+						for(j=0;j<6;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(penta_vertex_ids[j]-1)*num_control_type+i]/yts;
+						this->inputs->AddInput(new ControlInput(BalancethicknessThickeningRateEnum,PentaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+					}
+					break;
+				case VxEnum:
+					if (iomodel->Data(VxEnum)){
+						for(j=0;j<6;j++)nodeinputs[j]=iomodel->Data(VxEnum)[penta_vertex_ids[j]-1]/yts;
+						for(j=0;j<6;j++)cmmininputs[j]=iomodel->Data(InversionMinParametersEnum)[(penta_vertex_ids[j]-1)*num_control_type+i]/yts;
+						for(j=0;j<6;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(penta_vertex_ids[j]-1)*num_control_type+i]/yts;
+						this->inputs->AddInput(new ControlInput(VxEnum,PentaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+					}
+					break;
+				case VyEnum:
+					if (iomodel->Data(VyEnum)){
+						for(j=0;j<6;j++)nodeinputs[j]=iomodel->Data(VyEnum)[penta_vertex_ids[j]-1]/yts;
+						for(j=0;j<6;j++)cmmininputs[j]=iomodel->Data(InversionMinParametersEnum)[(penta_vertex_ids[j]-1)*num_control_type+i]/yts;
+						for(j=0;j<6;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(penta_vertex_ids[j]-1)*num_control_type+i]/yts;
+						this->inputs->AddInput(new ControlInput(VyEnum,PentaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+					}
+					break;
+				case FrictionCoefficientEnum:
+					if (iomodel->Data(FrictionCoefficientEnum)){
+						for(j=0;j<6;j++)nodeinputs[j]=iomodel->Data(FrictionCoefficientEnum)[penta_vertex_ids[j]-1];
+						for(j=0;j<6;j++)cmmininputs[j]=iomodel->Data(InversionMinParametersEnum)[(penta_vertex_ids[j]-1)*num_control_type+i];
+						for(j=0;j<6;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(penta_vertex_ids[j]-1)*num_control_type+i];
+						this->inputs->AddInput(new ControlInput(FrictionCoefficientEnum,PentaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+					}
+					break;
+				case MaterialsRheologyBbarEnum:
+				case MaterialsRheologyZbarEnum:
+					/*Material will take care of it*/ break;
+				default:
+					_error_("Control " << EnumToStringx(reCast(iomodel->Data(InversionControlParametersEnum)[i])) << " not implemented yet");
+			}
+		}
+	}
+	#endif
+
+	//Need to know the type of approximation for this element
+	if(iomodel->Data(FlowequationElementEquationEnum)){
+		if (iomodel->Data(FlowequationElementEquationEnum)[index]==MacAyealApproximationEnum){
+			this->inputs->AddInput(new IntInput(ApproximationEnum,MacAyealApproximationEnum));
+		}
+		else if (iomodel->Data(FlowequationElementEquationEnum)[index]==PattynApproximationEnum){
+			this->inputs->AddInput(new IntInput(ApproximationEnum,PattynApproximationEnum));
+		}
+		else if (iomodel->Data(FlowequationElementEquationEnum)[index]==MacAyealPattynApproximationEnum){
+			this->inputs->AddInput(new IntInput(ApproximationEnum,MacAyealPattynApproximationEnum));
+		}
+		else if (iomodel->Data(FlowequationElementEquationEnum)[index]==HutterApproximationEnum){
+			this->inputs->AddInput(new IntInput(ApproximationEnum,HutterApproximationEnum));
+		}
+		else if (iomodel->Data(FlowequationElementEquationEnum)[index]==L1L2ApproximationEnum){
+			this->inputs->AddInput(new IntInput(ApproximationEnum,L1L2ApproximationEnum));
+		}
+		else if (iomodel->Data(FlowequationElementEquationEnum)[index]==StokesApproximationEnum){
+			this->inputs->AddInput(new IntInput(ApproximationEnum,StokesApproximationEnum));
+		}
+		else if (iomodel->Data(FlowequationElementEquationEnum)[index]==MacAyealStokesApproximationEnum){
+			this->inputs->AddInput(new IntInput(ApproximationEnum,MacAyealStokesApproximationEnum));
+		}
+		else if (iomodel->Data(FlowequationElementEquationEnum)[index]==PattynStokesApproximationEnum){
+			this->inputs->AddInput(new IntInput(ApproximationEnum,PattynStokesApproximationEnum));
+		}
+		else if (iomodel->Data(FlowequationElementEquationEnum)[index]==NoneApproximationEnum){
+			this->inputs->AddInput(new IntInput(ApproximationEnum,NoneApproximationEnum));
+		}
+		else{
+			_error_("Approximation type " << EnumToStringx(reCast(iomodel->Data(FlowequationElementEquationEnum)[index])) << " not supported yet");
+		}
+	}
+
+	/*DatasetInputs*/
+	if (control_analysis && iomodel->Data(InversionCostFunctionsCoefficientsEnum)) {
+
+		/*Create inputs and add to DataSetInput*/
+		DatasetInput* datasetinput=new DatasetInput(InversionCostFunctionsCoefficientsEnum);
+		for(i=0;iData(InversionCostFunctionsCoefficientsEnum)[(penta_vertex_ids[j]-1)*num_cm_responses+i];
+			datasetinput->inputs->AddObject(new PentaP1Input(InversionCostFunctionsCoefficientsEnum,nodeinputs));
+		}
+
+		/*Add datasetinput to element inputs*/
+		this->inputs->AddInput(datasetinput);
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolution {{{*/
+void  Penta::InputUpdateFromSolution(IssmDouble* solution){
+
+	int analysis_type;
+
+	/*retreive parameters: */
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Just branch to the correct InputUpdateFromSolution generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+	#ifdef _HAVE_DIAGNOSTIC_
+	case DiagnosticHorizAnalysisEnum:
+		InputUpdateFromSolutionDiagnosticHoriz( solution);
+		break;
+	case DiagnosticHutterAnalysisEnum:
+		InputUpdateFromSolutionDiagnosticHutter( solution);
+		break;
+	case DiagnosticVertAnalysisEnum:
+		InputUpdateFromSolutionDiagnosticVert( solution);
+		break;
+	#endif
+	#ifdef _HAVE_CONTROL_
+	case AdjointHorizAnalysisEnum:
+		int approximation;
+		inputs->GetInputValue(&approximation,ApproximationEnum);
+		if(approximation==StokesApproximationEnum || approximation==NoneApproximationEnum){
+			InputUpdateFromSolutionAdjointStokes( solution);
+		}
+		else{
+			InputUpdateFromSolutionAdjointHoriz( solution);
+		}
+		break;
+	#endif
+	#ifdef _HAVE_THERMAL_
+	case ThermalAnalysisEnum:
+		InputUpdateFromSolutionThermal( solution);
+		break;
+	case EnthalpyAnalysisEnum:
+		InputUpdateFromSolutionEnthalpy( solution);
+		break;
+	case MeltingAnalysisEnum:
+		InputUpdateFromSolutionOneDof(solution,BasalforcingsMeltingRateEnum);
+		break;
+	#endif
+	case BedSlopeXAnalysisEnum:
+		InputUpdateFromSolutionOneDofCollapsed(solution,BedSlopeXEnum);
+		break;
+	case BedSlopeYAnalysisEnum:
+		InputUpdateFromSolutionOneDofCollapsed(solution,BedSlopeYEnum);
+		break;
+	case SurfaceSlopeXAnalysisEnum:
+		InputUpdateFromSolutionOneDofCollapsed(solution,SurfaceSlopeXEnum);
+		break;
+	case SurfaceSlopeYAnalysisEnum:
+		InputUpdateFromSolutionOneDofCollapsed(solution,SurfaceSlopeYEnum);
+		break;
+	case PrognosticAnalysisEnum:
+		InputUpdateFromSolutionPrognostic(solution);
+		break;
+	#ifdef _HAVE_BALANCED_
+	case BalancethicknessAnalysisEnum:
+		InputUpdateFromSolutionOneDofCollapsed(solution,ThicknessEnum);
+		break;
+	#endif
+	default: 
+		_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionPrognostic{{{*/
+void  Penta::InputUpdateFromSolutionPrognostic(IssmDouble* solution){
+
+	const int  numdof   = NDOF1*NUMVERTICES;
+	const int  numdof2d = NDOF1*NUMVERTICES2D;
+
+	int    i,hydroadjustment;
+	int*   doflist = NULL;
+	IssmDouble rho_ice,rho_water,minthickness;
+	IssmDouble newthickness[numdof];
+	IssmDouble newbed[numdof];
+	IssmDouble newsurface[numdof];
+	IssmDouble oldbed[NUMVERTICES];
+	IssmDouble oldsurface[NUMVERTICES];
+	IssmDouble oldthickness[NUMVERTICES];
+	Penta  *penta   = NULL;
+
+	/*If not on bed, return*/
+	if (!IsOnBed()) return;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector and extrude it */
+	this->parameters->FindParam(&minthickness,PrognosticMinThicknessEnum);
+	for(i=0;i(newthickness[i])) _error_("NaN found in solution vector");
+		/*Constrain thickness to be at least 1m*/
+		if(newthickness[i]parameters->FindParam(&hydroadjustment,PrognosticHydrostaticAdjustmentEnum);
+
+	/*recover material parameters: */
+	rho_ice=matpar->GetRhoIce();
+	rho_water=matpar->GetRhoWater();
+
+	for(i=0;inodes[i]->IsGrounded()){
+			newsurface[i]=oldbed[i]+newthickness[i]; //surface = oldbed + newthickness
+			newbed[i]=oldbed[i];               //same bed: do nothing
+		}
+		else{ //so it is an ice shelf
+			if(hydroadjustment==AbsoluteEnum){
+				newsurface[i]=newthickness[i]*(1-rho_ice/rho_water);
+				newbed[i]=newthickness[i]*(-rho_ice/rho_water);
+			}
+			else if(hydroadjustment==IncrementalEnum){
+				newsurface[i]=oldsurface[i]+(1.0-rho_ice/rho_water)*(newthickness[i]-oldthickness[i]); //surface = oldsurface + (1-di) * dH 
+				newbed[i]=oldbed[i]-rho_ice/rho_water*(newthickness[i]-oldthickness[i]); //bed = oldbed + di * dH
+			}
+			else _error_("Hydrostatic adjustment " << hydroadjustment << " (" << EnumToStringx(hydroadjustment) << ") not supported yet");
+		}
+	}
+
+	/*Start looping over all elements above current element and update all inputs*/
+	penta=this;
+	for(;;){
+		/*Add input to the element: */
+		penta->inputs->AddInput(new PentaP1Input(ThicknessEnum,newthickness));
+		penta->inputs->AddInput(new PentaP1Input(SurfaceEnum,newsurface));
+		penta->inputs->AddInput(new PentaP1Input(BedEnum,newbed));
+
+		/*Stop if we have reached the surface*/
+		if (penta->IsOnSurface()) break;
+
+		/* get upper Penta*/
+		penta=penta->GetUpperElement(); _assert_(penta->Id()!=this->id);
+	}
+	
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionOneDof{{{*/
+void  Penta::InputUpdateFromSolutionOneDof(IssmDouble* solution,int enum_type){
+
+	const int numdof = NDOF1*NUMVERTICES;
+
+	IssmDouble values[numdof];
+	int*   doflist=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(int i=0;i(values[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Add input to the element: */
+	this->inputs->AddInput(new PentaP1Input(enum_type,values));
+	
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionOneDofCollpased{{{*/
+void  Penta::InputUpdateFromSolutionOneDofCollapsed(IssmDouble* solution,int enum_type){
+
+	const int  numdof   = NDOF1*NUMVERTICES;
+	const int  numdof2d = NDOF1*NUMVERTICES2D;
+
+	IssmDouble  values[numdof];
+	int*    doflist = NULL;
+	Penta  *penta   = NULL;
+
+	/*If not on bed, return*/
+	if (!IsOnBed()) return;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector and extrude it */
+	for(int i=0;i(values[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Start looping over all elements above current element and update all inputs*/
+	penta=this;
+	for(;;){
+		/*Add input to the element: */
+		penta->inputs->AddInput(new PentaP1Input(enum_type,values));
+
+		/*Stop if we have reached the surface*/
+		if (penta->IsOnSurface()) break;
+
+		/* get upper Penta*/
+		penta=penta->GetUpperElement(); _assert_(penta->Id()!=this->id);
+	}
+	
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromVector(IssmDouble* vector, int name, int type);{{{*/
+void  Penta::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	/*Penta update B in InputUpdateFromSolutionThermal, so don't look for B update here.*/
+
+	switch(type){
+
+		case VertexEnum:
+			{
+
+				/*New PentaVertexInpu*/
+				IssmDouble values[6];
+
+				/*Get values on the 6 vertices*/
+				for (int i=0;i<6;i++){
+					values[i]=vector[this->nodes[i]->GetVertexDof()];
+				}
+
+				/*update input*/
+				if (name==MaterialsRheologyZEnum || name==MaterialsRheologyZbarEnum){
+					material->inputs->AddInput(new PentaP1Input(name,values));
+				}
+				else{
+					this->inputs->AddInput(new PentaP1Input(name,values));
+				}
+				return;
+				break;
+			}
+
+		default:
+
+			_error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromVector(int* vector, int name, int type);{{{*/
+void  Penta::InputUpdateFromVector(int* vector, int name, int type){
+	_error_("not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromVector(bool* vector, int name, int type);{{{*/
+void  Penta::InputUpdateFromVector(bool* vector, int name, int type){
+	_error_("not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Penta::IsOnBed{{{*/
+bool Penta::IsOnBed(void){
+
+	bool onbed;
+	inputs->GetInputValue(&onbed,MeshElementonbedEnum);
+	return onbed;
+}
+/*}}}*/
+/*FUNCTION Penta::IsInput{{{*/
+bool Penta::IsInput(int name){
+	if (
+				name==ThicknessEnum ||
+				name==SurfaceEnum ||
+				name==BedEnum ||
+				name==SurfaceSlopeXEnum ||
+				name==SurfaceSlopeYEnum ||
+				name==SurfaceforcingsMassBalanceEnum ||
+				name==BasalforcingsMeltingRateEnum ||
+				name==BasalforcingsGeothermalfluxEnum ||
+				name==SurfaceAreaEnum||
+				name==PressureEnum ||
+				name==VxEnum ||
+				name==VyEnum ||
+				name==VzEnum ||
+				name==VxMeshEnum ||
+				name==VyMeshEnum ||
+				name==VzMeshEnum ||
+				name==InversionVxObsEnum ||
+				name==InversionVyObsEnum ||
+				name==InversionVzObsEnum ||
+				name==TemperatureEnum ||
+				name==EnthalpyEnum ||
+				name==EnthalpyPicardEnum ||
+				name==WaterfractionEnum||
+				name==FrictionCoefficientEnum ||
+				name==GradientEnum ||
+				name==OldGradientEnum  ||
+				name==ConvergedEnum || 
+				name==QmuVxEnum ||
+				name==QmuVyEnum ||
+				name==QmuVzEnum ||
+				name==QmuPressureEnum ||
+				name==QmuBedEnum ||
+				name==QmuThicknessEnum ||
+				name==QmuSurfaceEnum ||
+				name==QmuTemperatureEnum ||
+				name==QmuMeltingEnum
+				) {
+		return true;
+	}
+	else return false;
+}
+/*}}}*/
+/*FUNCTION Penta::IsFloating{{{*/
+bool   Penta::IsFloating(){
+
+	bool onshelf;
+	inputs->GetInputValue(&onshelf,MaskElementonfloatingiceEnum);
+	return onshelf;
+}
+/*}}}*/
+/*FUNCTION Penta::IsNodeOnShelf {{{*/
+bool   Penta::IsNodeOnShelf(){
+
+	int  i;
+	bool shelf=false;
+
+	for(i=0;i<6;i++){
+		if (nodes[i]->IsFloating()){
+			shelf=true;
+			break;
+		}
+	}
+	return shelf;
+}
+/*}}}*/
+/*FUNCTION Penta::IsNodeOnShelfFromFlags {{{*/
+bool   Penta::IsNodeOnShelfFromFlags(IssmDouble* flags){
+
+	int  i;
+	bool shelf=false;
+
+	for(i=0;i(flags[nodes[i]->Sid()])){
+			shelf=true;
+			break;
+		}
+	}
+	return shelf;
+}
+/*}}}*/
+/*FUNCTION Penta::IsOnSurface{{{*/
+bool Penta::IsOnSurface(void){
+
+	bool onsurface;
+	inputs->GetInputValue(&onsurface,MeshElementonsurfaceEnum);
+	return onsurface;
+}
+/*}}}*/
+/*FUNCTION Penta::IsOnWater {{{*/
+bool   Penta::IsOnWater(){
+
+	bool onwater;
+	inputs->GetInputValue(&onwater,MaskElementonwaterEnum);
+	return onwater;
+}
+/*}}}*/
+/*FUNCTION Penta::ListResultsInfo{{{*/
+void Penta::ListResultsInfo(int** in_resultsenums,int** in_resultssizes,IssmDouble** in_resultstimes,int** in_resultssteps,int* in_num_results){
+
+	/*Intermediaries*/
+	int     i;
+	int     numberofresults = 0;
+	int     *resultsenums   = NULL;
+	int     *resultssizes   = NULL;
+	IssmDouble  *resultstimes   = NULL;
+	int     *resultssteps   = NULL;
+
+	/*Checks*/
+	_assert_(in_num_results);
+
+	/*Count number of results*/
+	for(i=0;iresults->Size();i++){
+		ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+		numberofresults++;
+	}
+
+	if(numberofresults){
+
+		/*Allocate output*/
+		resultsenums=xNew(numberofresults);
+		resultssizes=xNew(numberofresults);
+		resultstimes=xNew(numberofresults);
+		resultssteps=xNew(numberofresults);
+
+		/*populate enums*/
+		for(i=0;iresults->Size();i++){
+			ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+			resultsenums[i]=elementresult->InstanceEnum();
+			resultstimes[i]=elementresult->GetTime();
+			resultssteps[i]=elementresult->GetStep();
+			if(elementresult->ObjectEnum()==PentaP1ElementResultEnum){
+				resultssizes[i]=P1Enum;
+			}
+			else{
+				resultssizes[i]=P0Enum;
+			}
+		}
+	}
+
+	/*Assign output pointers:*/
+	*in_num_results=numberofresults;
+	*in_resultsenums=resultsenums;
+	*in_resultssizes=resultssizes;
+	*in_resultstimes=resultstimes;
+	*in_resultssteps=resultssteps;
+
+}/*}}}*/
+/*FUNCTION Penta::MigrateGroundingLine{{{*/
+void  Penta::MigrateGroundingLine(IssmDouble* old_floating_ice,IssmDouble* sheet_ungrounding){
+
+	int     i,migration_style,unground;
+	bool    elementonshelf = false;
+	IssmDouble  bed_hydro,yts,gl_melting_rate;
+	IssmDouble  rho_water,rho_ice,density;
+	IssmDouble  melting[NUMVERTICES];
+	IssmDouble  h[NUMVERTICES],s[NUMVERTICES],b[NUMVERTICES],ba[NUMVERTICES];
+
+	if(!IsOnBed()) return;
+
+	/*Recover info at the vertices: */
+	parameters->FindParam(&migration_style,GroundinglineMigrationEnum);
+	parameters->FindParam(&yts,ConstantsYtsEnum);
+	GetInputListOnVertices(&h[0],ThicknessEnum);
+	GetInputListOnVertices(&s[0],SurfaceEnum);
+	GetInputListOnVertices(&b[0],BedEnum);
+	GetInputListOnVertices(&ba[0],BathymetryEnum);
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	density=rho_ice/rho_water;
+	
+	/*go through vertices, and update inputs, considering them to be PentaVertex type: */
+	for(i=0;i(old_floating_ice[nodes[i]->Sid()])){
+			if(b[i]<=ba[i]){ 
+				b[i]=ba[i];
+				s[i]=b[i]+h[i];
+				nodes[i]->inputs->AddInput(new BoolInput(MaskVertexonfloatingiceEnum,false));
+				nodes[i]->inputs->AddInput(new BoolInput(MaskVertexongroundediceEnum,true));
+			}
+		}
+		/*Ice sheet: if hydrostatic bed above bathymetry, ice sheet starts to unground, elso do nothing */
+		/*Change only if AgressiveMigration or if the ice sheet is in contact with the ocean*/
+		else{
+			bed_hydro=-density*h[i];
+			if (bed_hydro>ba[i]){
+				/*Unground only if the element is connected to the ice shelf*/
+				if(migration_style==AgressiveMigrationEnum){
+					s[i]=(1-density)*h[i];
+					b[i]=-density*h[i];
+					nodes[i]->inputs->AddInput(new BoolInput(MaskVertexonfloatingiceEnum,true));
+					nodes[i]->inputs->AddInput(new BoolInput(MaskVertexongroundediceEnum,false));
+				}
+				else if(migration_style==SoftMigrationEnum && reCast(sheet_ungrounding[nodes[i]->Sid()])){
+					s[i]=(1-density)*h[i];
+					b[i]=-density*h[i];
+					nodes[i]->inputs->AddInput(new BoolInput(MaskVertexonfloatingiceEnum,true));
+					nodes[i]->inputs->AddInput(new BoolInput(MaskVertexongroundediceEnum,false));
+				}
+			}
+		}
+	}
+
+	/*If at least one vertex is now floating, the element is now floating*/
+	for(i=0;iIsFloating()){
+			elementonshelf=true;
+			break;
+		}
+	}
+	
+   /*Add basal melting rate if element just ungrounded*/
+	if(!this->IsFloating() && elementonshelf==true){
+		for(i=0;iinputs->AddInput(new PentaP1Input(BasalforcingsMeltingRateEnum,&melting[0]));
+	} 
+
+	/*Update inputs*/
+	this->inputs->AddInput(new PentaP1Input(SurfaceEnum,&s[0]));
+	this->inputs->AddInput(new PentaP1Input(BedEnum,&b[0]));
+   this->inputs->AddInput(new BoolInput(MaskElementonfloatingiceEnum,elementonshelf));
+
+	/*Extrude inputs*/
+	this->InputExtrude(SurfaceEnum,ElementEnum);
+	this->InputExtrude(BedEnum,ElementEnum);
+	this->InputExtrude(MaskElementonfloatingiceEnum,ElementEnum);
+	this->InputExtrude(MaskVertexonfloatingiceEnum,NodeEnum);
+	this->InputExtrude(MaskVertexongroundediceEnum,NodeEnum);
+}
+/*}}}*/
+/*FUNCTION Penta::MinEdgeLength{{{*/
+IssmDouble Penta::MinEdgeLength(IssmDouble xyz_list[6][3]){
+	/*Return the minimum lenght of the nine egdes of the penta*/
+
+	int    i,node0,node1;
+	int    edges[9][2]={{0,1},{0,2},{1,2},{3,4},{3,5},{4,5},{0,3},{1,4},{2,5}}; //list of the nine edges
+	IssmDouble length;
+	IssmDouble minlength=-1;
+
+	for(i=0;i<9;i++){
+		/*Find the two nodes for this edge*/
+		node0=edges[i][0];
+		node1=edges[i][1];
+
+		/*Compute the length of this edge and compare it to the minimal length*/
+		length=pow(pow(xyz_list[node0][0]-xyz_list[node1][0],2.0)+pow(xyz_list[node0][1]-xyz_list[node1][1],2.0)+pow(xyz_list[node0][2]-xyz_list[node1][2],2.0),0.5);
+		if(lengthGetInput(natureofdataenum); 
+
+	/*figure out if we have the vertex id: */
+	found=0;
+	for(i=0;iGetVertexId()){
+			/*Do we have natureofdataenum in our inputs? :*/
+			if(data){
+				/*ok, we are good. retrieve value of input at vertex :*/
+				gauss=new GaussPenta(); gauss->GaussVertex(i);
+				data->GetInputValue(&value,gauss);
+				found=1;
+				break;
+			}
+		}
+	}
+
+	delete gauss;
+	if(found)*pvalue=value;
+	return found;
+}
+/*}}}*/
+/*FUNCTION Penta::PatchFill{{{*/
+void  Penta::PatchFill(int* pcount, Patch* patch){
+
+	int i,count;
+	int vertices_ids[6];
+
+	/*recover pointer: */
+	count=*pcount;
+		
+	/*will be needed later: */
+	for(i=0;i<6;i++) vertices_ids[i]=nodes[i]->GetVertexId(); //vertices id start at column 3 of the patch.
+
+	for(i=0;iresults->Size();i++){
+		ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+
+		/*For this result,fill the information in the Patch object (element id + vertices ids), and then hand 
+		 *it to the result object, to fill the rest: */
+		patch->fillelementinfo(count,this->sid+1,vertices_ids,6);
+		elementresult->PatchFill(count,patch);
+
+		/*increment counter: */
+		count++;
+	}
+
+	/*Assign output pointers:*/
+	*pcount=count;
+}/*}}}*/
+/*FUNCTION Penta::PatchSize{{{*/
+void  Penta::PatchSize(int* pnumrows, int* pnumvertices,int* pnumnodes){
+
+	int     i;
+	int     numrows       = 0;
+	int     numnodes      = 0;
+	int     temp_numnodes = 0;
+
+	/*Go through all the results objects, and update the counters: */
+	for (i=0;iresults->Size();i++){
+		ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+		/*first, we have one more result: */
+		numrows++;
+		/*now, how many vertices and how many nodal values for this result? :*/
+		temp_numnodes=elementresult->NumberOfNodalValues(); //ask result object.
+		if(temp_numnodes>numnodes)numnodes=temp_numnodes;
+	}
+
+	/*Assign output pointers:*/
+	*pnumrows=numrows;
+	*pnumvertices=NUMVERTICES;
+	*pnumnodes=numnodes;
+}
+/*}}}*/
+/*FUNCTION Penta::PositiveDegreeDay{{{*/
+void  Penta::PositiveDegreeDay(IssmDouble* pdds,IssmDouble* pds,IssmDouble signorm){
+
+   IssmDouble agd[NUMVERTICES];             // surface mass balance
+   IssmDouble monthlytemperatures[NUMVERTICES][12],monthlyprec[NUMVERTICES][12];
+   IssmDouble h[NUMVERTICES],s[NUMVERTICES]; // ,b
+   IssmDouble rho_water,rho_ice;
+
+   /*Recover monthly temperatures and precipitation*/
+   Input*     input=inputs->GetInput(SurfaceforcingsMonthlytemperaturesEnum); _assert_(input);
+   Input*     input2=inputs->GetInput(SurfaceforcingsPrecipitationEnum); _assert_(input2);
+   GaussPenta* gauss=new GaussPenta();
+   IssmDouble time,yts;
+   this->parameters->FindParam(&time,TimeEnum);
+   this->parameters->FindParam(&yts,ConstantsYtsEnum);
+   for(int month=0;month<12;month++) {
+     for(int iv=0;ivGaussVertex(iv);
+       input->GetInputValue(&monthlytemperatures[iv][month],gauss,time+month/12.*yts);
+       monthlytemperatures[iv][month]=monthlytemperatures[iv][month]-273.15; // conversion from Kelvin to celcius
+       input2->GetInputValue(&monthlyprec[iv][month],gauss,time+month/12.*yts);
+       monthlyprec[iv][month]=monthlyprec[iv][month]*yts; // convertion to m/yr
+     }
+   } 
+
+  /*Recover info at the vertices: */
+  GetInputListOnVertices(&h[0],ThicknessEnum);
+  GetInputListOnVertices(&s[0],SurfaceEnum);
+
+  /*Get material parameters :*/
+  rho_ice=matpar->GetRhoIce();
+  rho_water=matpar->GetRhoFreshwater();
+
+   /*measure the surface mass balance*/
+   for (int iv = 0; iv < NUMVERTICES; iv++){
+     agd[iv]=PddSurfaceMassBlance(&monthlytemperatures[iv][0], &monthlyprec[iv][0], pdds, pds, signorm, yts, h[iv], s[iv], rho_ice, rho_water);
+   }
+
+   /*Update inputs*/    
+   this->inputs->AddInput(new PentaP1Input(SurfaceforcingsMassBalanceEnum,&agd[0]));
+   //this->inputs->AddInput(new PentaVertexInput(ThermalSpcTemperatureEnum,&Tsurf[0]));
+   this->InputExtrude(SurfaceforcingsMassBalanceEnum,ElementEnum);
+
+	/*clean-up*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Penta::PotentialSheetUngrounding{{{*/
+void  Penta::PotentialSheetUngrounding(Vector* potential_sheet_ungrounding){
+
+	int     i;
+	IssmDouble  h[NUMVERTICES],ba[NUMVERTICES];
+	IssmDouble  bed_hydro;
+	IssmDouble  rho_water,rho_ice,density;
+	bool    elementonshelf = false;
+
+	/*material parameters: */
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	density=rho_ice/rho_water;
+	GetInputListOnVertices(&h[0],ThicknessEnum);
+	GetInputListOnVertices(&ba[0],BathymetryEnum);
+
+	/*go through vertices, and figure out which ones are on the ice sheet, and want to unground: */
+	for(i=0;iIsFloating()){
+			bed_hydro=-density*h[i];
+			if (bed_hydro>ba[i]){
+				/*Vertex that could potentially unground, flag it*/
+				potential_sheet_ungrounding->SetValue(nodes[i]->Sid(),1,INS_VAL);
+			}
+		}
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::ProcessResultsUnits{{{*/
+void  Penta::ProcessResultsUnits(void){
+
+	int i;
+
+	for(i=0;iresults->Size();i++){
+		ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+		elementresult->ProcessUnits(this->parameters);
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::ReduceMatrixStokes {{{*/
+void Penta::ReduceMatrixStokes(IssmDouble* Ke_reduced, IssmDouble* Ke_temp){
+
+	int    i,j;
+	IssmDouble Kii[24][24];
+	IssmDouble Kib[24][3];
+	IssmDouble Kbb[3][3];
+	IssmDouble Kbi[3][24];
+	IssmDouble Kbbinv[3][3];
+	IssmDouble Kright[24][24];
+
+	/*Create the four matrices used for reduction */
+	for(i=0;i<24;i++){
+		for(j=0;j<24;j++){
+			Kii[i][j]=*(Ke_temp+27*i+j);
+		}
+		for(j=0;j<3;j++){
+			Kib[i][j]=*(Ke_temp+27*i+j+24);
+		}
+	}
+	for(i=0;i<3;i++){
+		for(j=0;j<24;j++){
+			Kbi[i][j]=*(Ke_temp+27*(i+24)+j);
+		}
+		for(j=0;j<3;j++){
+			Kbb[i][j]=*(Ke_temp+27*(i+24)+j+24);
+		}
+	}
+
+	/*Inverse the matrix corresponding to bubble part Kbb */
+	Matrix3x3Invert(&Kbbinv[0][0], &Kbb[0][0]);
+
+	/*Multiply matrices to create the reduce matrix Ke_reduced */
+	TripleMultiply(&Kib[0][0],24,3,0,
+				&Kbbinv[0][0],3,3,0,
+				&Kbi[0][0],3,24,0,
+				&Kright[0][0],0);
+
+	/*Affect value to the reduced matrix */
+	for(i=0;i<24;i++) for(j=0;j<24;j++) *(Ke_reduced+24*i+j)=Kii[i][j]-Kright[i][j];
+}
+/*}}}*/
+/*FUNCTION Penta::ReduceVectorStokes {{{*/
+void Penta::ReduceVectorStokes(IssmDouble* Pe_reduced, IssmDouble* Ke_temp, IssmDouble* Pe_temp){
+
+	int    i,j;
+	IssmDouble Pi[24];
+	IssmDouble Pb[3];
+	IssmDouble Kbb[3][3];
+	IssmDouble Kib[24][3];
+	IssmDouble Kbbinv[3][3];
+	IssmDouble Pright[24];
+
+	/*Create the four matrices used for reduction */
+	for(i=0;i<24;i++) Pi[i]=*(Pe_temp+i);
+	for(i=0;i<3;i++) Pb[i]=*(Pe_temp+i+24);
+	for(j=0;j<3;j++){
+		for(i=0;i<24;i++){
+			Kib[i][j]=*(Ke_temp+3*i+j);
+		}
+		for(i=0;i<3;i++){
+			Kbb[i][j]=*(Ke_temp+3*(i+24)+j);
+		}
+	}
+
+	/*Inverse the matrix corresponding to bubble part Kbb */
+	Matrix3x3Invert(&Kbbinv[0][0], &Kbb[0][0]);
+
+	/*Multiply matrices to create the reduce matrix Ke_reduced */
+	TripleMultiply(&Kib[0][0],24,3,0,
+				&Kbbinv[0][0],3,3,0,
+				&Pb[0],3,1,0,&Pright[0],0);
+
+	/*Affect value to the reduced matrix */
+	for(i=0;i<24;i++) *(Pe_reduced+i)=Pi[i]-Pright[i];
+}
+/*}}}*/
+/*FUNCTION Penta::RequestedOutput{{{*/
+void Penta::RequestedOutput(int output_enum,int step,IssmDouble time){
+			
+	if(IsInput(output_enum)){
+		/*just transfer this input to results, and we are done: */
+		InputToResult(output_enum,step,time);
+	}
+	else{
+		/*this input does not exist, compute it, and then transfer to results: */
+		switch(output_enum){
+			case BasalFrictionEnum:
+
+				/*create input: */
+				BasalFrictionCreateInput();
+
+				/*transfer to results :*/
+				InputToResult(output_enum,step,time);
+
+				/*erase input: */
+				inputs->DeleteInput(output_enum);
+				break;
+			case ViscousHeatingEnum:
+
+				/*create input: */
+				ViscousHeatingCreateInput();
+
+				/*transfer to results :*/
+				InputToResult(output_enum,step,time);
+
+				/*erase input: */
+				inputs->DeleteInput(output_enum);
+				break;
+
+			case StressTensorEnum: 
+				this->ComputeStressTensor();
+				InputToResult(StressTensorxxEnum,step,time);
+				InputToResult(StressTensorxyEnum,step,time);
+				InputToResult(StressTensorxzEnum,step,time);
+				InputToResult(StressTensoryyEnum,step,time);
+				InputToResult(StressTensoryzEnum,step,time);
+				InputToResult(StressTensorzzEnum,step,time);
+				break;
+
+			default:
+				/*do nothing, no need to derail the computation because one of the outputs requested cannot be found: */
+				break;
+		}
+	}
+
+}
+/*}}}*/
+/*FUNCTION Penta::ResetCoordinateSystem{{{*/
+void  Penta::ResetCoordinateSystem(void){
+
+	int    approximation;
+	IssmDouble slopex[NUMVERTICES];
+	IssmDouble slopey[NUMVERTICES];
+	IssmDouble xz_plane[6];
+
+	/*For Stokes only: we want the CS to be tangential to the bedrock*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(IsFloating() || !IsOnBed() || (approximation!=StokesApproximationEnum && approximation!=MacAyealStokesApproximationEnum &&  approximation!=PattynStokesApproximationEnum)) return;
+
+	/*Get slope on each node*/
+	GetInputListOnVertices(&slopex[0],BedSlopeXEnum);
+	GetInputListOnVertices(&slopey[0],BedSlopeYEnum);
+
+	/*Loop over basal nodes (first 3) and update their CS*/
+	for(int i=0;inodes[i]->coord_system[0][0],&xz_plane[0]);
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::SetClone {{{*/
+void  Penta::SetClone(int* minranks){
+
+	_error_("not implemented yet");
+}
+/*}}}*/
+/*FUNCTION Penta::SetCurrentConfiguration {{{*/
+void  Penta::SetCurrentConfiguration(Elements* elementsin, Loads* loadsin, DataSet* nodesin, Materials* materialsin, Parameters* parametersin){
+
+	int analysis_counter;
+
+	/*go into parameters and get the analysis_counter: */
+	parametersin->FindParam(&analysis_counter,AnalysisCounterEnum);
+
+	/*Get Element type*/
+	this->element_type=this->element_type_list[analysis_counter];
+
+	/*Pick up nodes */
+	if (this->hnodes[analysis_counter]) this->nodes=(Node**)this->hnodes[analysis_counter]->deliverp();
+	else this->nodes=NULL;
+}
+/*}}}*/
+/*FUNCTION Penta::SpawnTria {{{*/
+Tria*  Penta::SpawnTria(int g0, int g1, int g2){
+
+	int   i,analysis_counter;
+	int   indices[3];
+	int   zero=0;
+	Tria*       tria            = NULL;
+	Inputs*     tria_inputs     = NULL;
+	Results*    tria_results    = NULL;
+	Parameters* tria_parameters = NULL;
+
+	/*go into parameters and get the analysis_counter: */
+	this->parameters->FindParam(&analysis_counter,AnalysisCounterEnum);
+
+	indices[0]=g0;
+	indices[1]=g1;
+	indices[2]=g2;
+
+	tria_parameters=this->parameters;
+	tria_inputs=(Inputs*)this->inputs->SpawnTriaInputs(indices);
+	tria_results=(Results*)this->results->SpawnTriaResults(indices);
+
+	tria=new Tria();
+	tria->id=this->id;
+	tria->inputs=tria_inputs;
+	tria->results=tria_results;
+	tria->parameters=tria_parameters;
+	tria->element_type=P1Enum; //Only P1 CG for now (TO BE CHANGED)
+	this->SpawnTriaHook(dynamic_cast(tria),&indices[0]);
+
+	/*Spawn material*/
+	tria->material=NULL;
+	tria->material=(Material*)this->material->copy();
+	delete tria->material->inputs;
+	tria->material->inputs=(Inputs*)this->material->inputs->SpawnTriaInputs(indices);
+
+	/*recover nodes, material and matpar: */
+	tria->nodes=(Node**)tria->hnodes[analysis_counter]->deliverp();
+	tria->matpar=(Matpar*)tria->hmatpar->delivers();
+
+	return tria;
+}
+/*}}}*/
+/*FUNCTION Penta::SmbGradients{{{*/
+void Penta::SmbGradients(void){
+
+	int i;
+
+	// input
+   IssmDouble h[NUMVERTICES];					// ice thickness (m)		
+	IssmDouble s[NUMVERTICES];					// surface elevation (m)
+	IssmDouble a_pos[NUMVERTICES];				// Hs-SMB relation parameter 
+	IssmDouble b_pos[NUMVERTICES];				// Hs-SMB relation parameter
+	IssmDouble a_neg[NUMVERTICES];				// Hs-SMB relation parameter
+	IssmDouble b_neg[NUMVERTICES];				// Hs-SMB relation paremeter
+	IssmDouble Hc[NUMVERTICES];					// elevation of transition between accumulation regime and ablation regime
+	IssmDouble smb_pos_max[NUMVERTICES];		// maximum SMB value in the accumulation regime
+	IssmDouble smb_pos_min[NUMVERTICES];		// minimum SMB value in the accumulation regime
+   IssmDouble rho_water;                   // density of fresh water
+	IssmDouble rho_ice;                     // density of ice
+
+	// output
+	IssmDouble smb[NUMVERTICES];					// surface mass balance (m/yr ice)
+
+	/*Recover SmbGradients*/
+	GetInputListOnVertices(&Hc[0],SurfaceforcingsHcEnum);
+	GetInputListOnVertices(&smb_pos_max[0],SurfaceforcingsSmbPosMaxEnum);
+	GetInputListOnVertices(&smb_pos_min[0],SurfaceforcingsSmbPosMinEnum);
+	GetInputListOnVertices(&a_pos[0],SurfaceforcingsAPosEnum);
+	GetInputListOnVertices(&b_pos[0],SurfaceforcingsBPosEnum);
+	GetInputListOnVertices(&a_neg[0],SurfaceforcingsANegEnum);
+	GetInputListOnVertices(&b_neg[0],SurfaceforcingsBNegEnum);
+	
+   /*Recover surface elevatio at vertices: */
+	GetInputListOnVertices(&h[0],ThicknessEnum);
+	GetInputListOnVertices(&s[0],SurfaceEnum);
+
+   /*Get material parameters :*/
+   rho_ice=matpar->GetRhoIce();
+   rho_water=matpar->GetRhoFreshwater();
+			
+   // loop over all vertices
+   for(i=0;iHc[i]){
+	    smb[i]=a_pos[i]+b_pos[i]*s[i];
+		 if(smb[i]>smb_pos_max[i]){smb[i]=smb_pos_max[i];}
+		 if(smb[i]inputs->AddInput(new PentaP1Input(SurfaceforcingsMassBalanceEnum,&smb[0]));
+}
+/*}}}*/
+/*FUNCTION Penta::SurfaceArea {{{*/
+IssmDouble Penta::SurfaceArea(void){
+
+	int    approximation;
+	IssmDouble S;
+	Tria*  tria=NULL;
+
+	/*retrieve inputs :*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/*Bail out if this element if:
+	 * -> Non MacAyeal not on the surface
+	 * -> MacAyeal (2d model) and not on bed) */
+	if ((approximation!=MacAyealApproximationEnum && !IsOnSurface()) || (approximation==MacAyealApproximationEnum && !IsOnBed())){
+		return 0;
+	}
+	else if (approximation==MacAyealApproximationEnum){
+
+		/*This element should be collapsed into a tria element at its base. Create this tria element, 
+		 * and compute SurfaceArea*/
+		tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria (lower face).
+		S=tria->SurfaceArea();
+		delete tria->material; delete tria;
+		return S;
+	}
+	else{
+
+		tria=(Tria*)SpawnTria(3,4,5); //nodes 3, 4 and 5 make the new tria (upper face).
+		S=tria->SurfaceArea();
+		delete tria->material; delete tria;
+		return S;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::SurfaceNormal {{{*/
+void Penta::SurfaceNormal(IssmDouble* surface_normal, IssmDouble xyz_list[3][3]){
+
+	int    i;
+	IssmDouble v13[3],v23[3];
+	IssmDouble normal[3];
+	IssmDouble normal_norm;
+
+	for (i=0;i<3;i++){
+		v13[i]=xyz_list[0][i]-xyz_list[2][i];
+		v23[i]=xyz_list[1][i]-xyz_list[2][i];
+	}
+
+	normal[0]=v13[1]*v23[2]-v13[2]*v23[1];
+	normal[1]=v13[2]*v23[0]-v13[0]*v23[2];
+	normal[2]=v13[0]*v23[1]-v13[1]*v23[0];
+
+	normal_norm=sqrt( pow(normal[0],2)+pow(normal[1],2)+pow(normal[2],2) );
+
+	*(surface_normal)=normal[0]/normal_norm;
+	*(surface_normal+1)=normal[1]/normal_norm;
+	*(surface_normal+2)=normal[2]/normal_norm;
+}
+/*}}}*/
+/*FUNCTION Penta::TimeAdapt{{{*/
+IssmDouble  Penta::TimeAdapt(void){
+
+	int    i;
+	IssmDouble C,dx,dy,dz,dt;
+	IssmDouble maxabsvx,maxabsvy,maxabsvz;
+	IssmDouble maxx,minx,maxy,miny,maxz,minz;
+	IssmDouble xyz_list[NUMVERTICES][3];
+
+	/*get CFL coefficient:*/
+	this->parameters->FindParam(&C,TimesteppingCflCoefficientEnum);
+
+	/*Get for Vx and Vy, the max of abs value: */
+	this->MaxAbsVx(&maxabsvx,false);
+	this->MaxAbsVy(&maxabsvy,false);
+	this->MaxAbsVz(&maxabsvz,false);
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], this->nodes, NUMVERTICES);
+
+	minx=xyz_list[0][0];
+	maxx=xyz_list[0][0];
+	miny=xyz_list[0][1];
+	maxy=xyz_list[0][1];
+	minz=xyz_list[0][2];
+	maxz=xyz_list[0][2];
+	
+	for(i=1;imaxx)maxx=xyz_list[i][0];
+		if (xyz_list[i][1]maxy)maxy=xyz_list[i][1];
+		if (xyz_list[i][2]maxz)maxz=xyz_list[i][2];
+	}
+	dx=maxx-minx;
+	dy=maxy-miny;
+	dz=maxz-minz;
+
+	/*CFL criterion: */
+	dt=C/(maxabsvy/dx+maxabsvy/dy+maxabsvz/dz);
+
+	return dt;
+}/*}}}*/
+/*FUNCTION Penta::Update(int index,IoModel* iomodel,int analysis_counter,int analysis_type) {{{*/
+void Penta::Update(int index,IoModel* iomodel,int analysis_counter,int analysis_type){ 
+
+	/*Intermediaries*/
+	IssmInt    i,j;
+	int        penta_type;
+	int        penta_node_ids[6];
+	int        penta_vertex_ids[6];
+	IssmDouble nodeinputs[6];
+	IssmDouble yts;
+	int        stabilization;
+	bool       dakota_analysis;
+	bool       isstokes;
+	IssmDouble beta,heatcapacity,referencetemperature,meltingpoint,latentheat;
+
+	/*Fetch parameters: */
+	iomodel->Constant(&yts,ConstantsYtsEnum);
+	iomodel->Constant(&stabilization,PrognosticStabilizationEnum);
+	iomodel->Constant(&dakota_analysis,QmuIsdakotaEnum);
+	iomodel->Constant(&isstokes,FlowequationIsstokesEnum);
+	iomodel->Constant(&beta,MaterialsBetaEnum);
+	iomodel->Constant(&heatcapacity,MaterialsHeatcapacityEnum);
+	iomodel->Constant(&referencetemperature,ConstantsReferencetemperatureEnum);
+	iomodel->Constant(&meltingpoint,MaterialsMeltingpointEnum);
+	iomodel->Constant(&latentheat,MaterialsLatentheatEnum);
+
+	/*Checks if debuging*/
+	/*{{{*/
+	_assert_(iomodel->Data(MeshElementsEnum));
+	/*}}}*/
+
+	/*Recover element type*/
+	if ((analysis_type==PrognosticAnalysisEnum || analysis_type==BalancethicknessAnalysisEnum) && stabilization==3){
+		/*P1 Discontinuous Galerkin*/
+		penta_type=P1DGEnum;
+	}
+	else{
+		/*P1 Continuous Galerkin*/
+		penta_type=P1Enum;
+	}
+	this->SetElementType(penta_type,analysis_counter);
+
+	/*Recover vertices ids needed to initialize inputs*/
+	for(i=0;i<6;i++) penta_vertex_ids[i]=reCast(iomodel->Data(MeshElementsEnum)[6*index+i]); //ids for vertices are in the elements array from Matlab
+
+	/*Recover nodes ids needed to initialize the node hook.*/
+	for(i=0;i<6;i++){ 
+		//go recover node ids, needed to initialize the node hook.
+		//WARNING: We assume P1 elements here!!!!!
+		penta_node_ids[i]=iomodel->nodecounter+reCast(iomodel->Data(MeshElementsEnum)[6*index+i]); //ids for vertices are in the elements array from Matlab
+	}
+
+	/*hooks: */
+	this->SetHookNodes(penta_node_ids,analysis_counter); this->nodes=NULL; //set hook to nodes, for this analysis type
+
+	/*Fill with IoModel*/
+	this->InputUpdateFromIoModel(index,iomodel);
+
+	/*Defaults if not provided in iomodel*/
+	switch(analysis_type){
+
+		case DiagnosticHorizAnalysisEnum:
+
+			/*default vx,vy and vz: either observation or 0 */
+			if(!iomodel->Data(VxEnum)){
+				for(i=0;i<6;i++)nodeinputs[i]=0;
+				this->inputs->AddInput(new PentaP1Input(VxEnum,nodeinputs));
+				if(dakota_analysis) this->inputs->AddInput(new PentaP1Input(QmuVxEnum,nodeinputs));
+			}
+			if(!iomodel->Data(VyEnum)){
+				for(i=0;i<6;i++)nodeinputs[i]=0;
+				this->inputs->AddInput(new PentaP1Input(VyEnum,nodeinputs));
+				if(dakota_analysis) this->inputs->AddInput(new PentaP1Input(QmuVyEnum,nodeinputs));
+			}
+			if(!iomodel->Data(VzEnum)){
+				for(i=0;i<6;i++)nodeinputs[i]=0;
+				this->inputs->AddInput(new PentaP1Input(VzEnum,nodeinputs));
+				if(dakota_analysis) this->inputs->AddInput(new PentaP1Input(QmuVzEnum,nodeinputs));
+			}
+			if(!iomodel->Data(PressureEnum)){
+				for(i=0;i<6;i++)nodeinputs[i]=0;
+				if(dakota_analysis){
+					this->inputs->AddInput(new PentaP1Input(PressureEnum,nodeinputs));
+					this->inputs->AddInput(new PentaP1Input(QmuPressureEnum,nodeinputs));
+				}
+				if(isstokes){
+					this->inputs->AddInput(new PentaP1Input(PressureEnum,nodeinputs));
+					this->inputs->AddInput(new PentaP1Input(PressurePicardEnum,nodeinputs));
+				}
+			}
+			if(*(iomodel->Data(FlowequationElementEquationEnum)+index)==PattynStokesApproximationEnum){
+				/*Create VzPattyn and VzStokes Enums*/
+				if(iomodel->Data(VzEnum) && iomodel->Data(FlowequationBorderstokesEnum)){
+					for(i=0;i<6;i++) nodeinputs[i]=iomodel->Data(VzEnum)[penta_vertex_ids[i]-1]/yts*iomodel->Data(FlowequationBorderstokesEnum)[penta_vertex_ids[i]-1];
+					this->inputs->AddInput(new PentaP1Input(VzStokesEnum,nodeinputs));
+					for(i=0;i<6;i++) nodeinputs[i]=iomodel->Data(VzEnum)[penta_vertex_ids[i]-1]/yts*(1-iomodel->Data(FlowequationBorderstokesEnum)[penta_vertex_ids[i]-1]);
+					this->inputs->AddInput(new PentaP1Input(VzPattynEnum,nodeinputs));
+				}
+				else{
+					for(i=0;i<6;i++)nodeinputs[i]=0;
+					this->inputs->AddInput(new PentaP1Input(VzStokesEnum,nodeinputs));
+					this->inputs->AddInput(new PentaP1Input(VzPattynEnum,nodeinputs));
+				}
+			}
+			if(*(iomodel->Data(FlowequationElementEquationEnum)+index)==MacAyealStokesApproximationEnum){
+				/*Create VzMacAyeal and VzStokes Enums*/
+				if(iomodel->Data(VzEnum) && iomodel->Data(FlowequationBorderstokesEnum)){
+					for(i=0;i<6;i++) nodeinputs[i]=iomodel->Data(VzEnum)[penta_vertex_ids[i]-1]/yts*iomodel->Data(FlowequationBorderstokesEnum)[penta_vertex_ids[i]-1];
+					this->inputs->AddInput(new PentaP1Input(VzStokesEnum,nodeinputs));
+					for(i=0;i<6;i++) nodeinputs[i]=iomodel->Data(VzEnum)[penta_vertex_ids[i]-1]/yts*(1-iomodel->Data(FlowequationBorderstokesEnum)[penta_vertex_ids[i]-1]);
+					this->inputs->AddInput(new PentaP1Input(VzMacAyealEnum,nodeinputs));
+				}
+				else{
+					for(i=0;i<6;i++)nodeinputs[i]=0;
+					this->inputs->AddInput(new PentaP1Input(VzStokesEnum,nodeinputs));
+					this->inputs->AddInput(new PentaP1Input(VzMacAyealEnum,nodeinputs));
+				}
+			}
+			break;
+
+		case ThermalAnalysisEnum:
+			/*Initialize mesh velocity*/
+			for(i=0;i<6;i++)nodeinputs[i]=0;
+			this->inputs->AddInput(new PentaP1Input(VxMeshEnum,nodeinputs));
+			this->inputs->AddInput(new PentaP1Input(VyMeshEnum,nodeinputs));
+			this->inputs->AddInput(new PentaP1Input(VzMeshEnum,nodeinputs));
+			break;
+
+		case EnthalpyAnalysisEnum:
+			/*Initialize mesh velocity*/
+			for(i=0;i<6;i++)nodeinputs[i]=0;
+			this->inputs->AddInput(new PentaP1Input(VxMeshEnum,nodeinputs));
+			this->inputs->AddInput(new PentaP1Input(VyMeshEnum,nodeinputs));
+			this->inputs->AddInput(new PentaP1Input(VzMeshEnum,nodeinputs));
+			if (iomodel->Data(TemperatureEnum) && iomodel->Data(WaterfractionEnum) && iomodel->Data(PressureEnum)) {
+				for(i=0;i<6;i++){
+					if(iomodel->Data(TemperatureEnum)[penta_vertex_ids[i]-1] < meltingpoint-beta*iomodel->Data(PressureEnum)[penta_vertex_ids[i]-1]){
+						nodeinputs[i]=heatcapacity*(iomodel->Data(TemperatureEnum)[penta_vertex_ids[i]-1]-referencetemperature);
+					}
+					else nodeinputs[i]=heatcapacity*
+					 (meltingpoint-beta*iomodel->Data(PressureEnum)[penta_vertex_ids[i]-1]-referencetemperature)
+						+latentheat*iomodel->Data(WaterfractionEnum)[penta_vertex_ids[i]-1];
+				}
+				this->inputs->AddInput(new PentaP1Input(EnthalpyEnum,nodeinputs));
+			}
+			else _error_("temperature and waterfraction required for the enthalpy solution");
+			break;
+
+		default:
+			/*No update for other solution types*/
+			break;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::UpdatePotentialSheetUngrounding{{{*/
+int Penta::UpdatePotentialSheetUngrounding(IssmDouble* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,IssmDouble* nodes_on_iceshelf){
+
+	int i;
+	int nflipped=0;
+
+	/*Go through nodes, and whoever is on the potential_sheet_ungrounding, ends up in nodes_on_iceshelf: */
+	for(i=0;i(vertices_potentially_ungrounding[nodes[i]->Sid()])){
+			vec_nodes_on_iceshelf->SetValue(nodes[i]->Sid(),1,INS_VAL);
+		
+			/*If node was not on ice shelf, we flipped*/
+			if(nodes_on_iceshelf[nodes[i]->Sid()]==0){
+				nflipped++;
+			}
+		}
+	}
+	return nflipped;
+}
+/*}}}*/
+/*FUNCTION Penta::ViscousHeatingCreateInput {{{*/
+void Penta::ViscousHeatingCreateInput(void){
+
+	/*Constants*/
+	const int  numdof=NUMVERTICES*NDOF1;
+
+	/*Intermediaries*/
+	int    iv;
+	IssmDouble phi;
+	IssmDouble viscosity;
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble epsilon[6];
+	IssmDouble     viscousheating[NUMVERTICES]={0,0,0,0,0,0};
+	IssmDouble     thickness;
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum); _assert_(vz_input);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+
+	/*loop over vertices: */
+	gauss=new GaussPenta();
+	for (int iv=0;ivGaussVertex(iv);
+		
+		thickness_input->GetInputValue(&thickness,gauss);
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+		GetPhi(&phi, &epsilon[0], viscosity);
+		
+
+		viscousheating[iv]=phi*thickness;
+	}
+
+	/*Create PentaVertex input, which will hold the basal friction:*/
+	this->inputs->AddInput(new PentaP1Input(ViscousHeatingEnum,&viscousheating[0]));
+
+	/*Clean up and return*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Penta::SmearFunction {{{*/
+void  Penta::SmearFunction(Vector* smearedvector,IssmDouble (*WeightFunction)(IssmDouble distance,IssmDouble radius),IssmDouble radius){
+	_error_("not implemented yet");
+}
+/*}}}*/
+
+#ifdef _HAVE_RESPONSES_
+/*FUNCTION Penta::IceVolume {{{*/
+IssmDouble Penta::IceVolume(void){
+
+	/*The volume of a troncated prism is base * 1/3 sum(length of edges)*/
+	IssmDouble base,height;
+	IssmDouble xyz_list[NUMVERTICES][3];
+
+	if(IsOnWater())return 0;
+
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*First calculate the area of the base (cross section triangle)
+	 * http://en.wikipedia.org/wiki/Pentangle
+	 * base = 1/2 abs((xA-xC)(yB-yA)-(xA-xB)(yC-yA))*/
+	base = 1./2.*fabs((xyz_list[0][0]-xyz_list[2][0])*(xyz_list[1][1]-xyz_list[0][1]) - (xyz_list[0][0]-xyz_list[1][0])*(xyz_list[2][1]-xyz_list[0][1]));
+
+	/*Now get the average height*/
+	height = 1./3.*((xyz_list[3][2]-xyz_list[0][2])+(xyz_list[4][2]-xyz_list[1][2])+(xyz_list[5][2]-xyz_list[2][2]));
+
+	/*Return: */
+	return base*height;
+}
+/*}}}*/
+/*FUNCTION Penta::MinVel{{{*/
+void  Penta::MinVel(IssmDouble* pminvel, bool process_units){
+
+	/*Get minimum:*/
+	IssmDouble minvel=this->inputs->Min(VelEnum);
+
+	/*process units if requested: */
+	if(process_units) minvel=UnitConversion(minvel,IuToExtEnum,VelEnum);
+
+	/*Assign output pointers:*/
+	*pminvel=minvel;
+}
+/*}}}*/
+/*FUNCTION Penta::MinVx{{{*/
+void  Penta::MinVx(IssmDouble* pminvx, bool process_units){
+
+	/*Get minimum:*/
+	IssmDouble minvx=this->inputs->Min(VxEnum);
+
+	/*process units if requested: */
+	if(process_units) minvx=UnitConversion(minvx,IuToExtEnum,VxEnum);
+
+	/*Assign output pointers:*/
+	*pminvx=minvx;
+}
+/*}}}*/
+/*FUNCTION Penta::MinVy{{{*/
+void  Penta::MinVy(IssmDouble* pminvy, bool process_units){
+
+	/*Get minimum:*/
+	IssmDouble minvy=this->inputs->Min(VyEnum);
+
+	/*process units if requested: */
+	if(process_units) minvy=UnitConversion(minvy,IuToExtEnum,VyEnum);
+
+	/*Assign output pointers:*/
+	*pminvy=minvy;
+}
+/*}}}*/
+/*FUNCTION Penta::MinVz{{{*/
+void  Penta::MinVz(IssmDouble* pminvz, bool process_units){
+
+	/*Get minimum:*/
+	IssmDouble minvz=this->inputs->Min(VzEnum);
+
+	/*process units if requested: */
+	if(process_units) minvz=UnitConversion(minvz,IuToExtEnum,VzEnum);
+
+	/*Assign output pointers:*/
+	*pminvz=minvz;
+}
+/*}}}*/
+/*FUNCTION Penta::MassFlux {{{*/
+IssmDouble Penta::MassFlux( IssmDouble* segment,bool process_units){
+
+	IssmDouble mass_flux=0;
+
+	if(!IsOnBed()) return mass_flux;
+
+	/*Depth Averaging Vx and Vy*/
+	this->InputDepthAverageAtBase(VxEnum,VxAverageEnum);
+	this->InputDepthAverageAtBase(VyEnum,VyAverageEnum);
+
+	/*Spawn Tria element from the base of the Penta: */
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	mass_flux=tria->MassFlux(segment,process_units);
+	delete tria->material; delete tria;
+
+	/*Delete Vx and Vy averaged*/
+	this->inputs->DeleteInput(VxAverageEnum);
+	this->inputs->DeleteInput(VyAverageEnum);
+
+	/*clean up and return*/
+	return mass_flux;
+}
+/*}}}*/
+/*FUNCTION Penta::MaxAbsVx{{{*/
+void  Penta::MaxAbsVx(IssmDouble* pmaxabsvx, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxabsvx=this->inputs->MaxAbs(VxEnum);
+
+	/*process units if requested: */
+	if(process_units) maxabsvx=UnitConversion(maxabsvx,IuToExtEnum,VxEnum);
+
+	/*Assign output pointers:*/
+	*pmaxabsvx=maxabsvx;
+}
+/*}}}*/
+/*FUNCTION Penta::MaxAbsVy{{{*/
+void  Penta::MaxAbsVy(IssmDouble* pmaxabsvy, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxabsvy=this->inputs->MaxAbs(VyEnum);
+
+	/*process units if requested: */
+	if(process_units) maxabsvy=UnitConversion(maxabsvy,IuToExtEnum,VyEnum);
+
+	/*Assign output pointers:*/
+	*pmaxabsvy=maxabsvy;
+}
+/*}}}*/
+/*FUNCTION Penta::MaxAbsVz{{{*/
+void  Penta::MaxAbsVz(IssmDouble* pmaxabsvz, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxabsvz=this->inputs->MaxAbs(VzEnum);
+
+	/*process units if requested: */
+	if(process_units) maxabsvz=UnitConversion(maxabsvz,IuToExtEnum,VyEnum);
+
+	/*Assign output pointers:*/
+	*pmaxabsvz=maxabsvz;
+}
+/*}}}*/
+/*FUNCTION Penta::MaxVel{{{*/
+void  Penta::MaxVel(IssmDouble* pmaxvel, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxvel=this->inputs->Max(VelEnum);
+
+	/*process units if requested: */
+	if(process_units) maxvel=UnitConversion(maxvel,IuToExtEnum,VelEnum);
+
+	/*Assign output pointers:*/
+	*pmaxvel=maxvel;
+
+}
+/*}}}*/
+/*FUNCTION Penta::MaxVx{{{*/
+void  Penta::MaxVx(IssmDouble* pmaxvx, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxvx=this->inputs->Max(VxEnum);
+
+	/*process units if requested: */
+	if(process_units) maxvx=UnitConversion(maxvx,IuToExtEnum,VxEnum);
+
+	/*Assign output pointers:*/
+	*pmaxvx=maxvx;
+}
+/*}}}*/
+/*FUNCTION Penta::MaxVy{{{*/
+void  Penta::MaxVy(IssmDouble* pmaxvy, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxvy=this->inputs->Max(VyEnum);
+
+	/*process units if requested: */
+	if(process_units) maxvy=UnitConversion(maxvy,IuToExtEnum,VyEnum);
+
+	/*Assign output pointers:*/
+	*pmaxvy=maxvy;
+}
+/*}}}*/
+/*FUNCTION Penta::MaxVz{{{*/
+void  Penta::MaxVz(IssmDouble* pmaxvz, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxvz=this->inputs->Max(VzEnum);
+
+	/*process units if requested: */
+	if(process_units) maxvz=UnitConversion(maxvz,IuToExtEnum,VzEnum);
+
+	/*Assign output pointers:*/
+	*pmaxvz=maxvz;
+}
+/*}}}*/
+/*FUNCTION Penta::ElementResponse{{{*/
+void Penta::ElementResponse(IssmDouble* presponse,int response_enum,bool process_units){
+
+	switch(response_enum){
+		case MaterialsRheologyBbarEnum:
+			*presponse=this->material->GetBbar();
+			break;
+		case MaterialsRheologyZbarEnum:
+			*presponse=this->material->GetZbar();
+			break;
+		case VelEnum:
+			{
+
+				/*Get input:*/
+				IssmDouble vel;
+				Input* vel_input;
+
+				vel_input=this->inputs->GetInput(VelEnum); _assert_(vel_input);
+				vel_input->GetInputAverage(&vel);
+
+				/*process units if requested: */
+				if(process_units) vel=UnitConversion(vel,IuToExtEnum,VelEnum);
+
+				/*Assign output pointers:*/
+				*presponse=vel;
+			}
+			break;
+		default:  
+			_error_("Response type " << EnumToStringx(response_enum) << " not supported yet!");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Penta::TotalSmb {{{*/
+IssmDouble Penta::TotalSmb(void){
+
+	/*The smb[Gt yr-1] of one element is area[m2] * smb [ m ice yr^-1] * rho_ice [kg m-3] / 1e+10^12 */
+	IssmDouble base,smb,rho_ice;
+	IssmDouble Total_Smb=0;
+	IssmDouble xyz_list[NUMVERTICES][3];
+
+	/*Get material parameters :*/
+	rho_ice=matpar->GetRhoIce();
+
+	if(IsOnWater() || !IsOnSurface()) return 0.;
+	
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*First calculate the area of the base (cross section triangle)
+	 * http://en.wikipedia.org/wiki/Triangle
+	 * base = 1/2 abs((xA-xC)(yB-yA)-(xA-xB)(yC-yA))*/
+	base = 1./2. * fabs((xyz_list[0][0]-xyz_list[2][0])*(xyz_list[1][1]-xyz_list[0][1]) - (xyz_list[0][0]-xyz_list[1][0])*(xyz_list[2][1]-xyz_list[0][1]));
+
+	/*Now get the average SMB over the element*/
+	Input* smb_input = inputs->GetInput(SurfaceforcingsMassBalanceEnum); _assert_(smb_input);
+	smb_input->GetInputAverage(&smb);
+	Total_Smb=rho_ice*base*smb;// smb on element in kg s-1
+	
+	/*Process units: */
+	Total_Smb=UnitConversion(Total_Smb,IuToExtEnum,TotalSmbEnum);// smb on element in GigaTon yr-1
+	
+	/*Return: */
+	return Total_Smb;
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_THERMAL_
+/*FUNCTION Penta::CreateKMatrixEnthalpy {{{*/
+ElementMatrix* Penta::CreateKMatrixEnthalpy(void){
+	
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixEnthalpyVolume();
+	ElementMatrix* Ke2=CreateKMatrixEnthalpyShelf();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+	
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixEnthalpyVolume {{{*/
+ElementMatrix* Penta::CreateKMatrixEnthalpyVolume(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        stabilization;
+	int        i,j,ig,found=0;
+	IssmDouble     Jdet,u,v,w,um,vm,wm;
+	IssmDouble     h,hx,hy,hz,vx,vy,vz,vel;
+	IssmDouble     gravity,rho_ice,rho_water;
+	IssmDouble     epsvel=2.220446049250313e-16;
+	IssmDouble     heatcapacity,thermalconductivity,dt;
+	IssmDouble     pressure,enthalpy;
+	IssmDouble     latentheat,kappa;
+	IssmDouble     tau_parameter,diameter;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     B_conduct[3][numdof];
+	IssmDouble     B_advec[3][numdof];
+	IssmDouble     Bprime_advec[3][numdof];
+	IssmDouble     L[numdof];
+	IssmDouble     dbasis[3][6];
+	IssmDouble     D_scalar_conduct,D_scalar_advec;
+	IssmDouble     D_scalar_trans,D_scalar_stab;
+	IssmDouble     D[3][3];
+	IssmDouble     K[3][3]={0.0};
+	Tria*      tria=NULL;
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	gravity=matpar->GetG();
+	heatcapacity=matpar->GetHeatCapacity();
+	latentheat=matpar->GetLatentHeat();
+	thermalconductivity=matpar->GetThermalConductivity();
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	this->parameters->FindParam(&stabilization,ThermalStabilizationEnum);
+	Input* pressure_input=inputs->GetInput(PressureEnum);      _assert_(pressure_input);
+	Input* enthalpy_input=inputs->GetInput(EnthalpyPicardEnum);_assert_(enthalpy_input); //for this iteration of the step
+	Input* vx_input=inputs->GetInput(VxEnum);                  _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                  _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);                  _assert_(vz_input);
+	Input* vxm_input=inputs->GetInput(VxMeshEnum);             _assert_(vxm_input);
+	Input* vym_input=inputs->GetInput(VyMeshEnum);             _assert_(vym_input);
+	Input* vzm_input=inputs->GetInput(VzMeshEnum);             _assert_(vzm_input);
+	if (stabilization==2) diameter=MinEdgeLength(xyz_list);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(2,2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Conduction: */  
+		/*Need to change that depending on enthalpy value -> cold or temperate ice: */  
+		GetBConduct(&B_conduct[0][0],&xyz_list[0][0],gauss); 
+
+		enthalpy_input->GetInputValue(&enthalpy, gauss);
+		pressure_input->GetInputValue(&pressure, gauss);
+		kappa=matpar->GetEnthalpyDiffusionParameter(enthalpy,pressure);
+		D_scalar_conduct=gauss->weight*Jdet*kappa;
+		if(reCast(dt)) D_scalar_conduct=D_scalar_conduct*dt;
+
+		D[0][0]=D_scalar_conduct; D[0][1]=0; D[0][2]=0;
+		D[1][0]=0; D[1][1]=D_scalar_conduct; D[1][2]=0;
+		D[2][0]=0; D[2][1]=0; D[2][2]=D_scalar_conduct;
+
+		TripleMultiply(&B_conduct[0][0],3,numdof,1,
+					&D[0][0],3,3,0,
+					&B_conduct[0][0],3,numdof,0,
+					&Ke->values[0],1);
+
+		/*Advection: */
+		GetBAdvec(&B_advec[0][0],&xyz_list[0][0],gauss); 
+		GetBprimeAdvec(&Bprime_advec[0][0],&xyz_list[0][0],gauss); 
+
+		vx_input->GetInputValue(&u, gauss); vxm_input->GetInputValue(&um,gauss); vx=u-um; 
+		vy_input->GetInputValue(&v, gauss); vym_input->GetInputValue(&vm,gauss); vy=v-vm; 
+		vz_input->GetInputValue(&w, gauss); vzm_input->GetInputValue(&wm,gauss); vz=w-wm;
+
+		D_scalar_advec=gauss->weight*Jdet;
+		if(reCast(dt)) D_scalar_advec=D_scalar_advec*dt;
+
+		D[0][0]=D_scalar_advec*vx;D[0][1]=0;                D[0][2]=0;
+		D[1][0]=0;                D[1][1]=D_scalar_advec*vy;D[1][2]=0;
+		D[2][0]=0;                D[2][1]=0;                D[2][2]=D_scalar_advec*vz;
+
+		TripleMultiply(&B_advec[0][0],3,numdof,1,
+					&D[0][0],3,3,0,
+					&Bprime_advec[0][0],3,numdof,0,
+					&Ke->values[0],1);
+
+		/*Transient: */
+		if(reCast(dt)){
+			GetNodalFunctionsP1(&L[0], gauss);
+			D_scalar_trans=gauss->weight*Jdet;
+			D_scalar_trans=D_scalar_trans;
+
+			TripleMultiply(&L[0],numdof,1,0,
+						&D_scalar_trans,1,1,0,
+						&L[0],1,numdof,0,
+						&Ke->values[0],1);
+		}
+
+		/*Artifficial diffusivity*/
+		if(stabilization==1){
+			/*Build K: */
+			GetElementSizes(&hx,&hy,&hz);
+			vel=sqrt(pow(vx,2.)+pow(vy,2.)+pow(vz,2.))+1.e-14;
+			h=sqrt( pow(hx*vx/vel,2.) + pow(hy*vy/vel,2.) + pow(hz*vz/vel,2.));
+			K[0][0]=h/(2*vel)*vx*vx;  K[0][1]=h/(2*vel)*vx*vy; K[0][2]=h/(2*vel)*vx*vz;
+			K[1][0]=h/(2*vel)*vy*vx;  K[1][1]=h/(2*vel)*vy*vy; K[1][2]=h/(2*vel)*vy*vz;
+			K[2][0]=h/(2*vel)*vz*vx;  K[2][1]=h/(2*vel)*vz*vy; K[2][2]=h/(2*vel)*vz*vz;
+			D_scalar_stab=gauss->weight*Jdet;
+			if(reCast(dt)) D_scalar_stab=D_scalar_stab*dt;
+			for(i=0;i<3;i++) for(j=0;j<3;j++) K[i][j] = D_scalar_stab*K[i][j];
+
+			GetBprimeAdvec(&Bprime_advec[0][0],&xyz_list[0][0],gauss); 
+
+			TripleMultiply(&Bprime_advec[0][0],3,numdof,1,
+						&K[0][0],3,3,0,
+						&Bprime_advec[0][0],3,numdof,0,
+						&Ke->values[0],1);
+		}
+		else if(stabilization==2){
+			GetNodalFunctionsP1Derivatives(&dbasis[0][0],&xyz_list[0][0], gauss);
+			tau_parameter=GetStabilizationParameter(u-um,v-vm,w-wm,diameter,kappa);
+
+			for(i=0;ivalues[i*numdof+j]+=tau_parameter*D_scalar_advec*
+					  ((u-um)*dbasis[0][i]+(v-vm)*dbasis[1][i]+(w-wm)*dbasis[2][i])*((u-um)*dbasis[0][j]+(v-vm)*dbasis[1][j]+(w-wm)*dbasis[2][j]);
+				}
+			}
+			if(reCast(dt)){
+				for(i=0;ivalues[i*numdof+j]+=tau_parameter*D_scalar_trans*L[j]*((u-um)*dbasis[0][i]+(v-vm)*dbasis[1][i]+(w-wm)*dbasis[2][i]);
+					}
+				}
+			}
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixEnthalpyShelf {{{*/
+ElementMatrix* Penta::CreateKMatrixEnthalpyShelf(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int       i,j,ig;
+	IssmDouble    mixed_layer_capacity,thermal_exchange_velocity;
+	IssmDouble    rho_ice,rho_water,heatcapacity;
+	IssmDouble    Jdet2d,dt;
+	IssmDouble    xyz_list[NUMVERTICES][3];
+	IssmDouble	 xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble    basis[NUMVERTICES];
+	IssmDouble    D_scalar;
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element matrix and return if necessary*/
+	if (!IsOnBed() || !IsFloating()) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	mixed_layer_capacity=matpar->GetMixedLayerCapacity();
+	thermal_exchange_velocity=matpar->GetThermalExchangeVelocity();
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	heatcapacity=matpar->GetHeatCapacity();
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;ibegin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+		
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0], gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+				
+		D_scalar=gauss->weight*Jdet2d*rho_water*mixed_layer_capacity*thermal_exchange_velocity/(rho_ice*heatcapacity);
+		if(reCast(dt)) D_scalar=dt*D_scalar;
+
+		TripleMultiply(&basis[0],numdof,1,0,
+					&D_scalar,1,1,0,
+					&basis[0],1,numdof,0,
+					&Ke->values[0],1);
+	}
+	
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixMelting {{{*/
+ElementMatrix* Penta::CreateKMatrixMelting(void){
+
+	if (!IsOnBed()) return NULL;
+
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementMatrix* Ke=tria->CreateKMatrixMelting();
+
+	delete tria->material; delete tria;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixThermal {{{*/
+ElementMatrix* Penta::CreateKMatrixThermal(void){
+	
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixThermalVolume();
+	ElementMatrix* Ke2=CreateKMatrixThermalShelf();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+	
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixThermalVolume {{{*/
+ElementMatrix* Penta::CreateKMatrixThermalVolume(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        stabilization;
+	int        i,j,ig,found=0;
+	IssmDouble     Jdet,u,v,w,um,vm,wm,vel;
+	IssmDouble     h,hx,hy,hz,vx,vy,vz;
+	IssmDouble     gravity,rho_ice,rho_water,kappa;
+	IssmDouble     heatcapacity,thermalconductivity,dt;
+	IssmDouble     tau_parameter,diameter;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     B_conduct[3][numdof];
+	IssmDouble     B_advec[3][numdof];
+	IssmDouble     Bprime_advec[3][numdof];
+	IssmDouble     L[numdof];
+	IssmDouble     dbasis[3][6];
+	IssmDouble     D_scalar_conduct,D_scalar_advec;
+	IssmDouble     D_scalar_trans,D_scalar_stab;
+	IssmDouble     D[3][3];
+	IssmDouble     K[3][3]={0.0};
+	Tria*      tria=NULL;
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	gravity=matpar->GetG();
+	heatcapacity=matpar->GetHeatCapacity();
+	thermalconductivity=matpar->GetThermalConductivity();
+	kappa=thermalconductivity/(rho_ice*heatcapacity);
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	this->parameters->FindParam(&stabilization,ThermalStabilizationEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);      _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);      _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);      _assert_(vz_input);
+	Input* vxm_input=inputs->GetInput(VxMeshEnum); _assert_(vxm_input);
+	Input* vym_input=inputs->GetInput(VyMeshEnum); _assert_(vym_input);
+	Input* vzm_input=inputs->GetInput(VzMeshEnum); _assert_(vzm_input);
+	if (stabilization==2) diameter=MinEdgeLength(xyz_list);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(2,2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Conduction: */
+
+		GetBConduct(&B_conduct[0][0],&xyz_list[0][0],gauss); 
+
+		D_scalar_conduct=gauss->weight*Jdet*kappa;
+		if(reCast(dt)) D_scalar_conduct=D_scalar_conduct*dt;
+
+		D[0][0]=D_scalar_conduct; D[0][1]=0; D[0][2]=0;
+		D[1][0]=0; D[1][1]=D_scalar_conduct; D[1][2]=0;
+		D[2][0]=0; D[2][1]=0; D[2][2]=D_scalar_conduct;
+
+		TripleMultiply(&B_conduct[0][0],3,numdof,1,
+					&D[0][0],3,3,0,
+					&B_conduct[0][0],3,numdof,0,
+					&Ke->values[0],1);
+
+		/*Advection: */
+
+		GetBAdvec(&B_advec[0][0],&xyz_list[0][0],gauss); 
+		GetBprimeAdvec(&Bprime_advec[0][0],&xyz_list[0][0],gauss); 
+
+		vx_input->GetInputValue(&u, gauss); vxm_input->GetInputValue(&um,gauss); vx=u-um;
+		vy_input->GetInputValue(&v, gauss); vym_input->GetInputValue(&vm,gauss); vy=v-vm;
+		vz_input->GetInputValue(&w, gauss); vzm_input->GetInputValue(&wm,gauss); vz=w-wm;
+
+		D_scalar_advec=gauss->weight*Jdet;
+		if(reCast(dt)) D_scalar_advec=D_scalar_advec*dt;
+
+		D[0][0]=D_scalar_advec*vx;    D[0][1]=0;                    D[0][2]=0;
+		D[1][0]=0;                    D[1][1]=D_scalar_advec*vy;    D[1][2]=0;
+		D[2][0]=0;                    D[2][1]=0;                    D[2][2]=D_scalar_advec*vz;
+
+		TripleMultiply(&B_advec[0][0],3,numdof,1,
+					&D[0][0],3,3,0,
+					&Bprime_advec[0][0],3,numdof,0,
+					&Ke->values[0],1);
+
+		/*Transient: */
+		if(reCast(dt)){
+			GetNodalFunctionsP1(&L[0], gauss);
+			D_scalar_trans=gauss->weight*Jdet;
+			D_scalar_trans=D_scalar_trans;
+
+			TripleMultiply(&L[0],numdof,1,0,
+						&D_scalar_trans,1,1,0,
+						&L[0],1,numdof,0,
+						&Ke->values[0],1);
+		}
+
+		/*Artifficial diffusivity*/
+		if(stabilization==1){
+			/*Build K: */
+			GetElementSizes(&hx,&hy,&hz);
+			vel=sqrt(pow(vx,2.)+pow(vy,2.)+pow(vz,2.))+1.e-14;
+			h=sqrt( pow(hx*vx/vel,2.) + pow(hy*vy/vel,2.) + pow(hz*vz/vel,2.));
+
+			K[0][0]=h/(2*vel)*fabs(vx*vx);  K[0][1]=h/(2*vel)*fabs(vx*vy); K[0][2]=h/(2*vel)*fabs(vx*vz);
+			K[1][0]=h/(2*vel)*fabs(vy*vx);  K[1][1]=h/(2*vel)*fabs(vy*vy); K[1][2]=h/(2*vel)*fabs(vy*vz);
+			K[2][0]=h/(2*vel)*fabs(vz*vx);  K[2][1]=h/(2*vel)*fabs(vz*vy); K[2][2]=h/(2*vel)*fabs(vz*vz);
+
+			D_scalar_stab=gauss->weight*Jdet;
+			if(reCast(dt)) D_scalar_stab=D_scalar_stab*dt;
+			for(i=0;i<3;i++) for(j=0;j<3;j++) K[i][j] = D_scalar_stab*K[i][j];
+
+			GetBprimeAdvec(&Bprime_advec[0][0],&xyz_list[0][0],gauss); 
+
+			TripleMultiply(&Bprime_advec[0][0],3,numdof,1,
+						&K[0][0],3,3,0,
+						&Bprime_advec[0][0],3,numdof,0,
+						&Ke->values[0],1);
+		}
+		else if(stabilization==2){
+			GetNodalFunctionsP1Derivatives(&dbasis[0][0],&xyz_list[0][0], gauss);
+			tau_parameter=GetStabilizationParameter(u-um,v-vm,w-wm,diameter,kappa);
+
+			for(i=0;ivalues[i*numdof+j]+=tau_parameter*D_scalar_advec*
+					  ((u-um)*dbasis[0][i]+(v-vm)*dbasis[1][i]+(w-wm)*dbasis[2][i])*((u-um)*dbasis[0][j]+(v-vm)*dbasis[1][j]+(w-wm)*dbasis[2][j]);
+				}
+			}
+			if(reCast(dt)){
+				for(i=0;ivalues[i*numdof+j]+=tau_parameter*D_scalar_trans*L[j]*((u-um)*dbasis[0][i]+(v-vm)*dbasis[1][i]+(w-wm)*dbasis[2][i]);
+					}
+				}
+			}
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixThermalShelf {{{*/
+ElementMatrix* Penta::CreateKMatrixThermalShelf(void){
+
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int       i,j,ig;
+	IssmDouble    mixed_layer_capacity,thermal_exchange_velocity;
+	IssmDouble    rho_ice,rho_water,heatcapacity;
+	IssmDouble    Jdet2d,dt;
+	IssmDouble    xyz_list[NUMVERTICES][3];
+	IssmDouble	 xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble    basis[NUMVERTICES];
+	IssmDouble    D_scalar;
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element matrix and return if necessary*/
+	if (!IsOnBed() || !IsFloating()) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	mixed_layer_capacity=matpar->GetMixedLayerCapacity();
+	thermal_exchange_velocity=matpar->GetThermalExchangeVelocity();
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	heatcapacity=matpar->GetHeatCapacity();
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;ibegin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+		
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0], gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+				
+		D_scalar=gauss->weight*Jdet2d*rho_water*mixed_layer_capacity*thermal_exchange_velocity/(heatcapacity*rho_ice);
+		if(reCast(dt)) D_scalar=dt*D_scalar;
+
+		TripleMultiply(&basis[0],numdof,1,0,
+					&D_scalar,1,1,0,
+					&basis[0],1,numdof,0,
+					&Ke->values[0],1);
+	}
+	
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorEnthalpy {{{*/
+ElementVector* Penta::CreatePVectorEnthalpy(void){
+
+	/*compute all load vectors for this element*/
+	ElementVector* pe1=CreatePVectorEnthalpyVolume();
+	ElementVector* pe2=CreatePVectorEnthalpySheet();
+	ElementVector* pe3=CreatePVectorEnthalpyShelf();
+	ElementVector* pe =new ElementVector(pe1,pe2,pe3);
+
+	/*clean-up and return*/
+	delete pe1;
+	delete pe2;
+	delete pe3;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorEnthalpyVolume {{{*/
+ElementVector* Penta::CreatePVectorEnthalpyVolume(void){
+
+	/*Constants*/
+	const int  numdof=NUMVERTICES*NDOF1;
+
+	/*Intermediaries*/
+	int    i,j,ig,found=0;
+	int    friction_type,stabilization;
+	IssmDouble Jdet,phi,dt;
+	IssmDouble rho_ice,heatcapacity;
+	IssmDouble thermalconductivity,kappa;
+	IssmDouble viscosity,pressure;
+	IssmDouble enthalpy,enthalpypicard;
+	IssmDouble tau_parameter,diameter;
+	IssmDouble u,v,w;
+	IssmDouble scalar_def,scalar_transient;
+	IssmDouble temperature_list[NUMVERTICES];
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble L[numdof];
+	IssmDouble dbasis[3][6];
+	IssmDouble epsilon[6];
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	rho_ice=matpar->GetRhoIce();
+	heatcapacity=matpar->GetHeatCapacity();
+	thermalconductivity=matpar->GetThermalConductivity();
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	this->parameters->FindParam(&stabilization,ThermalStabilizationEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);                                  _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                                  _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);                                  _assert_(vz_input);
+	Input* pressure_input=inputs->GetInput(PressureEnum);                      _assert_(pressure_input);
+	Input* enthalpy_input=NULL; 
+	Input* enthalpypicard_input=NULL; 
+	if(reCast(dt)){
+		enthalpy_input=inputs->GetInput(EnthalpyEnum); _assert_(enthalpy_input);
+	}
+	if (stabilization==2){
+		diameter=MinEdgeLength(xyz_list);
+		enthalpypicard_input=inputs->GetInput(EnthalpyPicardEnum); _assert_(enthalpypicard_input);
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(2,3);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1(&L[0], gauss);
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+		GetPhi(&phi, &epsilon[0], viscosity);
+
+		scalar_def=phi/rho_ice*Jdet*gauss->weight;
+		if(reCast(dt)) scalar_def=scalar_def*dt;
+
+		for(i=0;ivalues[i]+=scalar_def*L[i];
+
+		/* Build transient now */
+		if(reCast(dt)){
+			enthalpy_input->GetInputValue(&enthalpy, gauss);
+			scalar_transient=enthalpy*Jdet*gauss->weight;
+			for(i=0;ivalues[i]+=scalar_transient*L[i];
+		}
+
+		if(stabilization==2){
+			GetNodalFunctionsP1Derivatives(&dbasis[0][0],&xyz_list[0][0], gauss);
+
+			vx_input->GetInputValue(&u, gauss);
+			vy_input->GetInputValue(&v, gauss);
+			vz_input->GetInputValue(&w, gauss);
+			pressure_input->GetInputValue(&pressure, gauss);
+			enthalpypicard_input->GetInputValue(&enthalpypicard, gauss);
+			kappa=matpar->GetEnthalpyDiffusionParameter(enthalpy,pressure);
+			tau_parameter=GetStabilizationParameter(u,v,w,diameter,kappa);
+
+			for(i=0;ivalues[i]+=tau_parameter*scalar_def*(u*dbasis[0][i]+v*dbasis[1][i]+w*dbasis[2][i]);
+			if(reCast(dt)){
+				for(i=0;ivalues[i]+=tau_parameter*scalar_transient*(u*dbasis[0][i]+v*dbasis[1][i]+w*dbasis[2][i]);
+			}
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorEnthalpyShelf {{{*/
+ElementVector* Penta::CreatePVectorEnthalpyShelf(void){
+
+	/*Constants*/
+	const int  numdof=NUMVERTICES*NDOF1;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     Jdet2d;
+	IssmDouble     heatcapacity,h_pmp;
+	IssmDouble     mixed_layer_capacity,thermal_exchange_velocity;
+	IssmDouble     rho_ice,rho_water,pressure,dt,scalar_ocean;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble     basis[NUMVERTICES];
+	GaussPenta* gauss=NULL;
+
+	/* Ice/ocean heat exchange flux on ice shelf base */
+	if (!IsOnBed() || !IsFloating()) return NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iGetMixedLayerCapacity();
+	thermal_exchange_velocity=matpar->GetThermalExchangeVelocity();
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	heatcapacity=matpar->GetHeatCapacity();
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	Input* pressure_input=inputs->GetInput(PressureEnum); _assert_(pressure_input);
+
+	/* Start looping on the number of gauss 2d (nodes on the bedrock) */
+	gauss=new GaussPenta(0,1,2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0], gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+
+		pressure_input->GetInputValue(&pressure,gauss);
+		h_pmp=matpar->PureIceEnthalpy(pressure);
+
+		scalar_ocean=gauss->weight*Jdet2d*rho_water*mixed_layer_capacity*thermal_exchange_velocity*(h_pmp)/(rho_ice*heatcapacity);
+		if(reCast(dt)) scalar_ocean=dt*scalar_ocean;
+
+		for(i=0;ivalues[i]+=scalar_ocean*basis[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorEnthalpySheet {{{*/
+ElementVector* Penta::CreatePVectorEnthalpySheet(void){
+
+	/*Constants*/
+	const int  numdof=NUMVERTICES*NDOF1;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	int        analysis_type;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     xyz_list_tria[NUMVERTICES2D][3]={0.0};
+	IssmDouble     Jdet2d,dt;
+	IssmDouble     rho_ice,heatcapacity,geothermalflux_value;
+	IssmDouble     basalfriction,alpha2,vx,vy;
+	IssmDouble     scalar,enthalpy,enthalpyup;
+	IssmDouble     pressure,pressureup;
+	IssmDouble     basis[NUMVERTICES];
+	Friction*  friction=NULL;
+	GaussPenta* gauss=NULL;
+	GaussPenta* gaussup=NULL;
+
+	/* Geothermal flux on ice sheet base and basal friction */
+	if (!IsOnBed() || IsFloating()) return NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iFindParam(&analysis_type,AnalysisTypeEnum);
+	rho_ice=matpar->GetRhoIce();
+	heatcapacity=matpar->GetHeatCapacity();
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);                         _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                         _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);                         _assert_(vz_input);
+	Input* enthalpy_input=inputs->GetInput(EnthalpyEnum);             _assert_(enthalpy_input);
+	Input* pressure_input=inputs->GetInput(PressureEnum);             _assert_(pressure_input);
+	Input* geothermalflux_input=inputs->GetInput(BasalforcingsGeothermalfluxEnum); _assert_(geothermalflux_input);
+
+	/*Build frictoin element, needed later: */
+	friction=new Friction("3d",inputs,matpar,analysis_type);
+
+	/* Start looping on the number of gauss 2d (nodes on the bedrock) */
+	gauss=new GaussPenta(0,1,2,2);
+	gaussup=new GaussPenta(3,4,5,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+		gaussup->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0], gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+
+		enthalpy_input->GetInputValue(&enthalpy,gauss);
+		pressure_input->GetInputValue(&pressure,gauss);
+//		if(enthalpy>matpar->PureIceEnthalpy(pressure)){
+//			enthalpy_input->GetInputValue(&enthalpyup,gaussup);
+//			pressure_input->GetInputValue(&pressureup,gaussup);
+//			if(enthalpyup>matpar->PureIceEnthalpy(pressureup)){
+//				//do nothing, don't add heatflux
+//			}
+//			else{
+//				//need to change spcenthalpy according to Aschwanden 
+//				//NEED TO UPDATE
+//			}
+//		}
+//		else{
+			geothermalflux_input->GetInputValue(&geothermalflux_value,gauss);
+			friction->GetAlpha2(&alpha2,gauss,VxEnum,VyEnum,VzEnum);
+			vx_input->GetInputValue(&vx,gauss);
+			vy_input->GetInputValue(&vy,gauss);
+			basalfriction=alpha2*(pow(vx,2.0)+pow(vy,2.0));
+
+			scalar=gauss->weight*Jdet2d*(basalfriction+geothermalflux_value)/(rho_ice);
+			if(reCast(dt)) scalar=dt*scalar;
+
+			for(i=0;ivalues[i]+=scalar*basis[i];
+//		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	delete gaussup;
+	delete friction;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorMelting {{{*/
+ElementVector* Penta::CreatePVectorMelting(void){
+	return NULL;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorThermal {{{*/
+ElementVector* Penta::CreatePVectorThermal(void){
+
+	/*compute all load vectors for this element*/
+	ElementVector* pe1=CreatePVectorThermalVolume();
+	ElementVector* pe2=CreatePVectorThermalSheet();
+	ElementVector* pe3=CreatePVectorThermalShelf();
+	ElementVector* pe =new ElementVector(pe1,pe2,pe3);
+
+	/*clean-up and return*/
+	delete pe1;
+	delete pe2;
+	delete pe3;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorThermalVolume {{{*/
+ElementVector* Penta::CreatePVectorThermalVolume(void){
+
+	/*Constants*/
+	const int  numdof=NUMVERTICES*NDOF1;
+
+	/*Intermediaries*/
+	int    i,j,ig,found=0;
+	int    friction_type,stabilization;
+	IssmDouble Jdet,phi,dt;
+	IssmDouble rho_ice,heatcapacity;
+	IssmDouble thermalconductivity,kappa;
+	IssmDouble viscosity,temperature;
+	IssmDouble tau_parameter,diameter;
+	IssmDouble u,v,w;
+	IssmDouble scalar_def,scalar_transient;
+	IssmDouble temperature_list[NUMVERTICES];
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble L[numdof];
+	IssmDouble dbasis[3][6];
+	IssmDouble epsilon[6];
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	rho_ice=matpar->GetRhoIce();
+	heatcapacity=matpar->GetHeatCapacity();
+	thermalconductivity=matpar->GetThermalConductivity();
+	kappa=thermalconductivity/(rho_ice*heatcapacity);
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	this->parameters->FindParam(&stabilization,ThermalStabilizationEnum);
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum); _assert_(vz_input);
+	Input* temperature_input=NULL;
+	if (reCast(dt)) temperature_input=inputs->GetInput(TemperatureEnum); _assert_(inputs);
+	if (stabilization==2) diameter=MinEdgeLength(xyz_list);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(2,3);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1(&L[0], gauss);
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+		GetPhi(&phi, &epsilon[0], viscosity);
+
+		scalar_def=phi/(rho_ice*heatcapacity)*Jdet*gauss->weight;
+		if(reCast(dt)) scalar_def=scalar_def*dt;
+
+		for(i=0;ivalues[i]+=scalar_def*L[i];
+
+		/* Build transient now */
+		if(reCast(dt)){
+			temperature_input->GetInputValue(&temperature, gauss);
+			scalar_transient=temperature*Jdet*gauss->weight;
+			for(i=0;ivalues[i]+=scalar_transient*L[i];
+		}
+
+		if(stabilization==2){
+			GetNodalFunctionsP1Derivatives(&dbasis[0][0],&xyz_list[0][0], gauss);
+
+			vx_input->GetInputValue(&u, gauss);
+			vy_input->GetInputValue(&v, gauss);
+			vz_input->GetInputValue(&w, gauss);
+
+			tau_parameter=GetStabilizationParameter(u,v,w,diameter,kappa);
+
+			for(i=0;ivalues[i]+=tau_parameter*scalar_def*(u*dbasis[0][i]+v*dbasis[1][i]+w*dbasis[2][i]);
+			if(reCast(dt)){
+				for(i=0;ivalues[i]+=tau_parameter*scalar_transient*(u*dbasis[0][i]+v*dbasis[1][i]+w*dbasis[2][i]);
+			}
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorThermalShelf {{{*/
+ElementVector* Penta::CreatePVectorThermalShelf(void){
+
+	/*Constants*/
+	const int  numdof=NUMVERTICES*NDOF1;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     Jdet2d;
+	IssmDouble     mixed_layer_capacity,thermal_exchange_velocity;
+	IssmDouble     rho_ice,rho_water,pressure,dt,scalar_ocean;
+	IssmDouble     heatcapacity,t_pmp;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble     basis[NUMVERTICES];
+	GaussPenta* gauss=NULL;
+
+	/* Ice/ocean heat exchange flux on ice shelf base */
+	if (!IsOnBed() || !IsFloating()) return NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iGetMixedLayerCapacity();
+	thermal_exchange_velocity=matpar->GetThermalExchangeVelocity();
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	heatcapacity=matpar->GetHeatCapacity();
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	Input* pressure_input=inputs->GetInput(PressureEnum); _assert_(pressure_input);
+
+	/* Start looping on the number of gauss 2d (nodes on the bedrock) */
+	gauss=new GaussPenta(0,1,2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0], gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+
+		pressure_input->GetInputValue(&pressure,gauss);
+		t_pmp=matpar->TMeltingPoint(pressure);
+
+		scalar_ocean=gauss->weight*Jdet2d*rho_water*mixed_layer_capacity*thermal_exchange_velocity*(t_pmp)/(heatcapacity*rho_ice);
+		if(reCast(dt)) scalar_ocean=dt*scalar_ocean;
+
+		for(i=0;ivalues[i]+=scalar_ocean*basis[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorThermalSheet {{{*/
+ElementVector* Penta::CreatePVectorThermalSheet(void){
+
+	/*Constants*/
+	const int  numdof=NUMVERTICES*NDOF1;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	int        analysis_type;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     xyz_list_tria[NUMVERTICES2D][3]={0.0};
+	IssmDouble     Jdet2d,dt;
+	IssmDouble     rho_ice,heatcapacity,geothermalflux_value;
+	IssmDouble     basalfriction,alpha2,vx,vy;
+	IssmDouble     basis[NUMVERTICES];
+	IssmDouble     scalar;
+	Friction*  friction=NULL;
+	GaussPenta* gauss=NULL;
+
+	/* Geothermal flux on ice sheet base and basal friction */
+	if (!IsOnBed() || IsFloating()) return NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iFindParam(&analysis_type,AnalysisTypeEnum);
+	rho_ice=matpar->GetRhoIce();
+	heatcapacity=matpar->GetHeatCapacity();
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);                         _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                         _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);                         _assert_(vz_input);
+	Input* geothermalflux_input=inputs->GetInput(BasalforcingsGeothermalfluxEnum); _assert_(geothermalflux_input);
+
+	/*Build frictoin element, needed later: */
+	friction=new Friction("3d",inputs,matpar,analysis_type);
+
+	/* Start looping on the number of gauss 2d (nodes on the bedrock) */
+	gauss=new GaussPenta(0,1,2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0], gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+
+			geothermalflux_input->GetInputValue(&geothermalflux_value,gauss);
+			friction->GetAlpha2(&alpha2,gauss,VxEnum,VyEnum,VzEnum);
+			vx_input->GetInputValue(&vx,gauss);
+			vy_input->GetInputValue(&vy,gauss);
+			basalfriction=alpha2*(pow(vx,2.0)+pow(vy,2.0));
+
+			scalar=gauss->weight*Jdet2d*(basalfriction+geothermalflux_value)/(heatcapacity*rho_ice);
+			if(reCast(dt)) scalar=dt*scalar;
+
+			for(i=0;ivalues[i]+=scalar*basis[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::GetSolutionFromInputsThermal{{{*/
+void  Penta::GetSolutionFromInputsThermal(Vector* solution){
+
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	int         i;
+	int        *doflist = NULL;
+	IssmDouble  values[numdof];
+	IssmDouble  temp;
+	GaussPenta *gauss = NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+	Input* t_input=inputs->GetInput(TemperatureEnum); _assert_(t_input);
+
+	gauss=new GaussPenta();
+	for(i=0;iGaussVertex(i);
+		t_input->GetInputValue(&temp,gauss);
+		values[i]=temp;
+	}
+
+	/*Add value to global vector*/
+	solution->SetValues(numdof,doflist,values,INS_VAL);
+
+	/*Free ressources:*/
+	delete gauss;
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::GetSolutionFromInputsEnthalpy{{{*/
+void  Penta::GetSolutionFromInputsEnthalpy(Vector* solution){
+
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	int          i;
+	int*         doflist=NULL;
+	IssmDouble       values[numdof];
+	IssmDouble       enthalpy;
+	GaussPenta   *gauss=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+	Input* h_input=inputs->GetInput(EnthalpyEnum); _assert_(h_input);
+
+	gauss=new GaussPenta();
+	for(i=0;iGaussVertex(i);
+		h_input->GetInputValue(&enthalpy,gauss);
+		values[i]=enthalpy;
+	}
+
+	/*Add value to global vector*/
+	solution->SetValues(numdof,doflist,values,INS_VAL);
+
+	/*Free ressources:*/
+	delete gauss;
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionThermal {{{*/
+void  Penta::InputUpdateFromSolutionThermal(IssmDouble* solution){
+
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	bool   converged;
+	int    i,rheology_law;
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble values[numdof];
+	IssmDouble B[numdof];
+	IssmDouble B_average,s_average;
+	int*   doflist=NULL;
+	//IssmDouble pressure[numdof];
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;imatpar->TMeltingPoint(pressure[i])) values[i]=matpar->TMeltingPoint(pressure[i]);
+		//if(values[i]TMeltingPoint(pressure[i])-50) values[i]=matpar->TMeltingPoint(pressure[i])-50;
+
+		/*Check solution*/
+		if(xIsNan(values[i])) _error_("NaN found in solution vector");
+		//if(values[i]<0)      _printLine_("temperature < 0°K found in solution vector");
+		//if(values[i]>275)    _printLine_("temperature > 275°K found in solution vector (Paterson's rheology associated is negative)");
+	}
+
+	/*Get all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* surface_input=inputs->GetInput(SurfaceEnum); _assert_(surface_input);
+
+	this->inputs->GetInputValue(&converged,ConvergedEnum);
+	if(converged){
+		this->inputs->AddInput(new PentaP1Input(TemperatureEnum,values));
+
+		/*Update Rheology only if converged (we must make sure that the temperature is below melting point
+		 * otherwise the rheology could be negative*/
+		this->parameters->FindParam(&rheology_law,MaterialsRheologyLawEnum);
+		switch(rheology_law){
+			case NoneEnum:
+				/*Do nothing: B is not temperature dependent*/
+				break;
+			case PatersonEnum:
+				B_average=Paterson((values[0]+values[1]+values[2]+values[3]+values[4]+values[5])/6.0);
+				for(i=0;imaterial->inputs->AddInput(new PentaP1Input(MaterialsRheologyBEnum,B));
+				break;
+			case ArrheniusEnum:
+				surface_input->GetInputAverage(&s_average);
+				B_average=Arrhenius((values[0]+values[1]+values[2]+values[3]+values[4]+values[5])/6.0,
+							s_average-((xyz_list[0][2]+xyz_list[1][2]+xyz_list[2][2]+xyz_list[3][2]+xyz_list[4][2]+xyz_list[5][2])/6.0),
+							material->GetN());
+				for(i=0;imaterial->inputs->AddInput(new PentaP1Input(MaterialsRheologyBEnum,B));
+				break;
+			default:
+				_error_("Rheology law " << EnumToStringx(rheology_law) << " not supported yet");
+
+		}
+	}
+	else{
+		this->inputs->AddInput(new PentaP1Input(TemperaturePicardEnum,values));
+	}
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionEnthalpy {{{*/
+void  Penta::InputUpdateFromSolutionEnthalpy(IssmDouble* solution){
+
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	bool   converged=false;
+	int    i,rheology_law;
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble values[numdof];
+	IssmDouble pressure[NUMVERTICES];
+	IssmDouble temperatures[numdof];
+	IssmDouble waterfraction[numdof];
+	IssmDouble B[numdof];
+	IssmDouble B_average,s_average;
+	int*   doflist=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(values[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Get all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	GetInputListOnVertices(&pressure[0],PressureEnum);
+	Input* surface_input=inputs->GetInput(SurfaceEnum); _assert_(surface_input);
+	
+	this->inputs->GetInputValue(&converged,ConvergedEnum);
+	if(converged){
+		/*Convert enthalpy into temperature and water fraction*/
+		for(i=0;iEnthalpyToThermal(&temperatures[i],&waterfraction[i],values[i],pressure[i]);
+			if(waterfraction[i]<0) _error_("Negative water fraction found in solution vector");
+			//if(waterfraction[i]>1) _error_("Water fraction >1 found in solution vector");
+		}
+			
+		this->inputs->AddInput(new PentaP1Input(EnthalpyEnum,values));
+		this->inputs->AddInput(new PentaP1Input(WaterfractionEnum,waterfraction));
+		this->inputs->AddInput(new PentaP1Input(TemperatureEnum,temperatures));
+
+		/*Update Rheology only if converged (we must make sure that the temperature is below melting point
+		 * otherwise the rheology could be negative*/
+		this->parameters->FindParam(&rheology_law,MaterialsRheologyLawEnum);
+		switch(rheology_law){
+			case NoneEnum:
+				/*Do nothing: B is not temperature dependent*/
+				break;
+			case PatersonEnum:
+				B_average=Paterson((temperatures[0]+temperatures[1]+temperatures[2]+temperatures[3]+temperatures[4]+temperatures[5])/6.0);
+				for(i=0;imaterial->inputs->AddInput(new PentaP1Input(MaterialsRheologyBEnum,B));
+				break;
+			case ArrheniusEnum:
+				surface_input->GetInputAverage(&s_average);
+				B_average=Arrhenius((temperatures[0]+temperatures[1]+temperatures[2]+temperatures[3]+temperatures[4]+temperatures[5])/6.0,
+							s_average-((xyz_list[0][2]+xyz_list[1][2]+xyz_list[2][2]+xyz_list[3][2]+xyz_list[4][2]+xyz_list[5][2])/6.0),
+							material->GetN());
+				for(i=0;imaterial->inputs->AddInput(new PentaP1Input(MaterialsRheologyBEnum,B));
+				break;
+			default:
+				_error_("Rheology law " << EnumToStringx(rheology_law) << " not supported yet");
+
+		}
+	}
+	else{
+		this->inputs->AddInput(new PentaP1Input(EnthalpyPicardEnum,values));
+	}
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_CONTROL_
+/*FUNCTION Penta::ControlInputGetGradient{{{*/
+void Penta::ControlInputGetGradient(Vector* gradient,int enum_type,int control_index){
+
+	int doflist1[NUMVERTICES];
+	Input* input=NULL;
+
+	if(enum_type==MaterialsRheologyBbarEnum){
+		if(!IsOnBed()) return;
+		input=(Input*)material->inputs->GetInput(MaterialsRheologyBEnum);
+	}
+	else if(enum_type==MaterialsRheologyZbarEnum){
+		if(!IsOnBed()) return;
+		input=(Input*)material->inputs->GetInput(MaterialsRheologyZEnum);
+	}
+		
+	else{
+		input=inputs->GetInput(enum_type);
+	}
+	if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found");
+	if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
+
+	GradientIndexing(&doflist1[0],control_index);
+	((ControlInput*)input)->GetGradient(gradient,&doflist1[0]);
+
+}/*}}}*/
+/*FUNCTION Penta::ControlInputScaleGradient{{{*/
+void Penta::ControlInputScaleGradient(int enum_type,IssmDouble scale){
+
+	Input* input=NULL;
+
+	if(enum_type==MaterialsRheologyBbarEnum){
+		input=(Input*)material->inputs->GetInput(MaterialsRheologyBEnum);
+	}
+	else if(enum_type==MaterialsRheologyZbarEnum){
+		input=(Input*)material->inputs->GetInput(MaterialsRheologyZEnum);
+	}
+	else{
+		input=inputs->GetInput(enum_type);
+	}
+	if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found");
+	if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
+
+	((ControlInput*)input)->ScaleGradient(scale);
+}/*}}}*/
+/*FUNCTION Penta::ControlInputSetGradient{{{*/
+void Penta::ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index){
+
+	int    doflist1[NUMVERTICES];
+	IssmDouble grad_list[NUMVERTICES];
+	Input* grad_input=NULL;
+	Input* input=NULL;
+
+	if(enum_type==MaterialsRheologyBbarEnum){
+		input=(Input*)material->inputs->GetInput(MaterialsRheologyBEnum);
+	}
+	else if(enum_type==MaterialsRheologyZbarEnum){
+		input=(Input*)material->inputs->GetInput(MaterialsRheologyZEnum);
+	}
+	else{
+		input=inputs->GetInput(enum_type);
+	}
+	if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found");
+	if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
+
+	GradientIndexing(&doflist1[0],control_index);
+	for(int i=0;iSetGradient(grad_input);
+
+}/*}}}*/
+/*FUNCTION Penta::CreateKMatrixAdjointHoriz{{{*/
+ElementMatrix* Penta::CreateKMatrixAdjointHoriz(void){
+
+	int approximation;
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	switch(approximation){
+		case MacAyealApproximationEnum:
+			return CreateKMatrixAdjointMacAyeal2d();
+		case PattynApproximationEnum:
+			return CreateKMatrixAdjointPattyn();
+		case StokesApproximationEnum:
+			return CreateKMatrixAdjointStokes();
+		case NoneApproximationEnum:
+			return NULL;
+		default:
+			_error_("Approximation " << EnumToStringx(approximation) << " not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixAdjointMacAyeal2d{{{*/
+ElementMatrix* Penta::CreateKMatrixAdjointMacAyeal2d(void){
+
+	/*Figure out if this penta is collapsed. If so, then bailout, except if it is at the 
+	  bedrock, in which case we spawn a tria element using the 3 first nodes, and use it to build 
+	  the stiffness matrix. */
+	if (!IsOnBed()) return NULL;
+
+	/*Depth average some fields*/
+	switch(this->material->ObjectEnum()){
+		case MaticeEnum:
+			this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum,MaterialsEnum);
+			break;
+		case MatdamageiceEnum:
+			this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum,MaterialsEnum);
+			this->InputDepthAverageAtBase(MaterialsRheologyZEnum,MaterialsRheologyZbarEnum,MaterialsEnum);
+			break;
+		default:
+			_error_("material "<material->ObjectEnum())<<" not supported");
+	}
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementMatrix* Ke=tria->CreateKMatrixAdjointMacAyeal();
+	delete tria->material; delete tria;
+
+	/*Delete averaged fields*/
+	this->material->inputs->DeleteInput(MaterialsRheologyBbarEnum);
+	this->material->inputs->DeleteInput(MaterialsRheologyZbarEnum);
+
+	/*clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixAdjointPattyn{{{*/
+ElementMatrix* Penta::CreateKMatrixAdjointPattyn(void){
+
+	/*Constants*/
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	bool       incomplete_adjoint;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     Jdet;
+	IssmDouble     eps1dotdphii,eps1dotdphij;
+	IssmDouble     eps2dotdphii,eps2dotdphij;
+	IssmDouble     mu_prime;
+	IssmDouble     epsilon[5]; /* epsilon=[exx,eyy,exy,exz,eyz];*/
+	IssmDouble     eps1[3],eps2[3];
+	IssmDouble     phi[NUMVERTICES];
+	IssmDouble     dphi[3][NUMVERTICES];
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Jacobian with regular Pattyn (first part of the Gateau derivative)*/
+	parameters->FindParam(&incomplete_adjoint,InversionIncompleteAdjointEnum);
+	ElementMatrix* Ke=CreateKMatrixDiagnosticPattyn();
+	if(incomplete_adjoint) return Ke;
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1Derivatives(&dphi[0][0],&xyz_list[0][0],gauss);
+
+		this->GetStrainRate3dPattyn(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		material->GetViscosityDerivativeEpsSquare(&mu_prime,&epsilon[0]);
+		eps1[0]=2*epsilon[0]+epsilon[1];   eps2[0]=epsilon[2];
+		eps1[1]=epsilon[2];                eps2[1]=epsilon[0]+2*epsilon[1];
+		eps1[2]=epsilon[3];                eps2[2]=epsilon[4];
+
+		for(i=0;i<6;i++){
+			for(j=0;j<6;j++){
+				eps1dotdphii=eps1[0]*dphi[0][i]+eps1[1]*dphi[1][i]+eps1[2]*dphi[2][i];
+				eps1dotdphij=eps1[0]*dphi[0][j]+eps1[1]*dphi[1][j]+eps1[2]*dphi[2][j];
+				eps2dotdphii=eps2[0]*dphi[0][i]+eps2[1]*dphi[1][i]+eps2[2]*dphi[2][i];
+				eps2dotdphij=eps2[0]*dphi[0][j]+eps2[1]*dphi[1][j]+eps2[2]*dphi[2][j];
+
+				Ke->values[12*(2*i+0)+2*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps1dotdphii;
+				Ke->values[12*(2*i+0)+2*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps1dotdphii;
+				Ke->values[12*(2*i+1)+2*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps2dotdphii;
+				Ke->values[12*(2*i+1)+2*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps2dotdphii;
+			}
+		}
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixAdjointStokes{{{*/
+ElementMatrix* Penta::CreateKMatrixAdjointStokes(void){
+
+	/*Constants*/
+	const int    numdof=NDOF4*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	bool       incomplete_adjoint;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     Jdet;
+	IssmDouble     eps1dotdphii,eps1dotdphij;
+	IssmDouble     eps2dotdphii,eps2dotdphij;
+	IssmDouble     eps3dotdphii,eps3dotdphij;
+	IssmDouble     mu_prime;
+	IssmDouble     epsilon[5]; /* epsilon=[exx,eyy,exy,exz,eyz];*/
+	IssmDouble     eps1[3],eps2[3],eps3[3];
+	IssmDouble     phi[NUMVERTICES];
+	IssmDouble     dphi[3][NUMVERTICES];
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Jacobian with regular Stokes (first part of the Gateau derivative)*/
+	parameters->FindParam(&incomplete_adjoint,InversionIncompleteAdjointEnum);
+	ElementMatrix* Ke=CreateKMatrixDiagnosticStokes();
+	if(incomplete_adjoint) return Ke;
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);       _assert_(vz_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1Derivatives(&dphi[0][0],&xyz_list[0][0],gauss);
+
+		this->GetStrainRate3dPattyn(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		material->GetViscosityDerivativeEpsSquare(&mu_prime,&epsilon[0]);
+		eps1[0]=epsilon[0];   eps2[0]=epsilon[2];   eps3[0]=epsilon[3];
+		eps1[1]=epsilon[2];   eps2[1]=epsilon[1];   eps3[1]=epsilon[4];
+		eps1[2]=epsilon[3];   eps2[2]=epsilon[4];   eps3[2]= -epsilon[0] -epsilon[1];
+
+		for(i=0;i<6;i++){
+			for(j=0;j<6;j++){
+				eps1dotdphii=eps1[0]*dphi[0][i]+eps1[1]*dphi[1][i]+eps1[2]*dphi[2][i];
+				eps1dotdphij=eps1[0]*dphi[0][j]+eps1[1]*dphi[1][j]+eps1[2]*dphi[2][j];
+				eps2dotdphii=eps2[0]*dphi[0][i]+eps2[1]*dphi[1][i]+eps2[2]*dphi[2][i];
+				eps2dotdphij=eps2[0]*dphi[0][j]+eps2[1]*dphi[1][j]+eps2[2]*dphi[2][j];
+				eps3dotdphii=eps3[0]*dphi[0][i]+eps3[1]*dphi[1][i]+eps3[2]*dphi[2][i];
+				eps3dotdphij=eps3[0]*dphi[0][j]+eps3[1]*dphi[1][j]+eps3[2]*dphi[2][j];
+
+				Ke->values[numdof*(4*i+0)+4*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps1dotdphii;
+				Ke->values[numdof*(4*i+0)+4*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps1dotdphii;
+				Ke->values[numdof*(4*i+0)+4*j+2]+=gauss->weight*Jdet*2*mu_prime*eps3dotdphij*eps1dotdphii;
+
+				Ke->values[numdof*(4*i+1)+4*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps2dotdphii;
+				Ke->values[numdof*(4*i+1)+4*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps2dotdphii;
+				Ke->values[numdof*(4*i+1)+4*j+2]+=gauss->weight*Jdet*2*mu_prime*eps3dotdphij*eps2dotdphii;
+
+				Ke->values[numdof*(4*i+2)+4*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps3dotdphii;
+				Ke->values[numdof*(4*i+2)+4*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps3dotdphii;
+				Ke->values[numdof*(4*i+2)+4*j+2]+=gauss->weight*Jdet*2*mu_prime*eps3dotdphij*eps3dotdphii;
+			}
+		}
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorAdjointHoriz{{{*/
+ElementVector* Penta::CreatePVectorAdjointHoriz(void){
+
+	int approximation;
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	switch(approximation){
+		case MacAyealApproximationEnum:
+			return CreatePVectorAdjointMacAyeal();
+		case PattynApproximationEnum:
+			return CreatePVectorAdjointPattyn();
+		case NoneApproximationEnum:
+			return NULL;
+		case StokesApproximationEnum:
+			return CreatePVectorAdjointStokes();
+		default:
+			_error_("Approximation " << EnumToStringx(approximation) << " not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorAdjointMacAyeal{{{*/
+ElementVector* Penta::CreatePVectorAdjointMacAyeal(){
+
+	if (!IsOnBed()) return NULL;
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementVector* pe=tria->CreatePVectorAdjointHoriz();
+	delete tria->material; delete tria;
+
+	/*clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorAdjointPattyn{{{*/
+ElementVector* Penta::CreatePVectorAdjointPattyn(void){
+
+	if (!IsOnSurface()) return NULL;
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(3,4,5); //nodes 3, 4 and 5 make the new tria (upper face).
+	ElementVector* pe=tria->CreatePVectorAdjointHoriz();
+	delete tria->material; delete tria;
+
+	/*clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorAdjointStokes{{{*/
+ElementVector* Penta::CreatePVectorAdjointStokes(void){
+
+	if (!IsOnSurface()) return NULL;
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(3,4,5); //nodes 3, 4 and 5 make the new tria (upper face).
+	ElementVector* pe=tria->CreatePVectorAdjointStokes();
+	delete tria->material; delete tria;
+
+	/*clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::GradientIndexing{{{*/
+void Penta::GradientIndexing(int* indexing,int control_index){
+
+	/*Get some parameters*/
+	int num_controls;
+	parameters->FindParam(&num_controls,InversionNumControlParametersEnum);
+
+	/*get gradient indices*/
+	for(int i=0;inodes[i]->GetVertexDof() + control_index;
+	}
+
+}
+/*}}}*/
+/*FUNCTION Penta::Gradj {{{*/
+void  Penta::Gradj(Vector* gradient,int control_type,int control_index){
+	/*dJ/dalpha = ∂L/∂alpha = ∂J/∂alpha + ∂/∂alpha(KU-F)*/
+
+	int              i,approximation;
+	Tria*            tria=NULL;
+
+	/*If on water, skip grad (=0): */
+	if(IsOnWater())return;
+
+	/*First deal with ∂/∂alpha(KU-F)*/
+	switch(control_type){
+
+		case FrictionCoefficientEnum:
+			inputs->GetInputValue(&approximation,ApproximationEnum);
+			switch(approximation){
+				case MacAyealApproximationEnum:
+					GradjDragMacAyeal(gradient,control_index);
+					break;
+				case PattynApproximationEnum:
+					GradjDragPattyn(gradient,control_index);
+					break;
+				case StokesApproximationEnum:
+					GradjDragStokes(gradient,control_index);
+					break;
+				case NoneApproximationEnum:
+					/*Gradient is 0*/
+					break;
+				default:
+					_error_("approximation " << EnumToStringx(approximation) << " not supported yet");
+			}
+			break;
+
+		case MaterialsRheologyBbarEnum:
+			inputs->GetInputValue(&approximation,ApproximationEnum);
+			switch(approximation){
+				case MacAyealApproximationEnum:
+					GradjBbarMacAyeal(gradient,control_index);
+					break;
+				case PattynApproximationEnum:
+					GradjBbarPattyn(gradient,control_index);
+					break;
+				case StokesApproximationEnum:
+					GradjBbarStokes(gradient,control_index);
+					break;
+				case NoneApproximationEnum:
+					/*Gradient is 0*/
+					break;
+				default:
+					_error_("approximation " << EnumToStringx(approximation) << " not supported yet");
+			}
+			break;
+
+		default:
+			_error_("control type " << EnumToStringx(control_type) << " not supported yet: ");
+	}
+
+	/*Now deal with ∂J/∂alpha*/
+	int        *responses = NULL;
+	int         num_responses,resp;
+	this->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum);
+	this->parameters->FindParam(&responses,NULL,NULL,StepResponsesEnum);
+
+	for(resp=0;respGradjDragGradient(gradient,resp,control_index);
+			delete tria->material; delete tria;
+			break;
+		case RheologyBbarAbsGradientEnum:
+			if (!IsOnBed()) return;
+			tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+			tria->GradjBGradient(gradient,resp,control_index);
+			delete tria->material; delete tria;
+			break;
+		default:
+			_error_("response " << EnumToStringx(responses[resp]) << " not supported yet");
+	}
+	xDelete(responses);
+}
+/*}}}*/
+/*FUNCTION Penta::GradjDragMacAyeal {{{*/
+void  Penta::GradjDragMacAyeal(Vector* gradient,int control_index){
+
+	/*Gradient is 0 if on shelf or not on bed*/
+	if(IsFloating() || !IsOnBed()) return;
+
+	/*Spawn tria*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	tria->GradjDragMacAyeal(gradient,control_index);
+	delete tria->material; delete tria;
+
+} /*}}}*/
+/*FUNCTION Penta::GradjDragPattyn {{{*/
+void  Penta::GradjDragPattyn(Vector* gradient,int control_index){
+
+	int        i,j,ig;
+	int        analysis_type;
+	int        doflist1[NUMVERTICES];
+	IssmDouble     vx,vy,lambda,mu,alpha_complement,Jdet;
+	IssmDouble     bed,thickness,Neff,drag;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     xyz_list_tria[NUMVERTICES2D][3]={0.0};
+	IssmDouble     dk[NDOF3]; 
+	IssmDouble     grade_g[NUMVERTICES]={0.0};
+	IssmDouble     grade_g_gaussian[NUMVERTICES];
+	IssmDouble     basis[6];
+	Friction*  friction=NULL;
+	GaussPenta  *gauss=NULL;
+
+	/*Gradient is 0 if on shelf or not on bed*/
+	if(IsFloating() || !IsOnBed()) return;
+
+	/*Retrieve all inputs and parameters*/
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+	GradientIndexing(&doflist1[0],control_index);
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iGetInput(AdjointxEnum);               _assert_(adjointx_input);
+	Input* adjointy_input=inputs->GetInput(AdjointyEnum);               _assert_(adjointy_input);
+	Input* vx_input=inputs->GetInput(VxEnum);                           _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                           _assert_(vy_input);
+	Input* dragcoefficient_input=inputs->GetInput(FrictionCoefficientEnum); _assert_(dragcoefficient_input);
+
+	/*Build frictoin element, needed later: */
+	friction=new Friction("2d",inputs,matpar,analysis_type);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(0,1,2,4);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet, &xyz_list_tria[0][0],gauss);
+		GetNodalFunctionsP1(basis, gauss);
+
+		/*Build alpha_complement_list: */
+		friction->GetAlphaComplement(&alpha_complement, gauss,VxEnum,VyEnum,VzEnum);
+
+		dragcoefficient_input->GetInputValue(&drag, gauss);
+		adjointx_input->GetInputValue(&lambda, gauss);
+		adjointy_input->GetInputValue(&mu, gauss);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		dragcoefficient_input->GetInputDerivativeValue(&dk[0],&xyz_list[0][0],gauss);
+
+		/*Build gradje_g_gaussian vector (actually -dJ/ddrag): */
+		for (i=0;iweight*basis[i]; /*basis are 0 for the 3 upper nodes*/
+		}
+
+		/*Add gradje_g_gaussian vector to gradje_g: */
+		for(i=0;i(grade_g[i]));
+			grade_g[i]+=grade_g_gaussian[i];
+		}
+	}
+	gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+}
+/*}}}*/
+/*FUNCTION Penta::GradjDragStokes {{{*/
+void  Penta::GradjDragStokes(Vector* gradient,int control_index){
+
+	int        i,j,ig;
+	int        analysis_type;
+	int        doflist1[NUMVERTICES];
+	IssmDouble     bed,thickness,Neff;
+	IssmDouble     lambda,mu,xi,Jdet,vx,vy,vz;
+	IssmDouble     alpha_complement,drag;
+	IssmDouble     surface_normal[3],bed_normal[3];
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     xyz_list_tria[NUMVERTICES2D][3]={0.0};
+	IssmDouble     dk[NDOF3]; 
+	IssmDouble     basis[6];
+	IssmDouble     grade_g[NUMVERTICES]={0.0};
+	IssmDouble     grade_g_gaussian[NUMVERTICES];
+	Friction*  friction=NULL;
+	GaussPenta* gauss=NULL;
+
+	/*Gradient is 0 if on shelf or not on bed*/
+	if(IsFloating() || !IsOnBed()) return;
+
+	/*Retrieve all inputs and parameters*/
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iGetInput(FrictionCoefficientEnum); _assert_(drag_input);
+	Input* vx_input      =inputs->GetInput(VxEnum);                  _assert_(vx_input);
+	Input* vy_input      =inputs->GetInput(VyEnum);                  _assert_(vy_input);
+	Input* vz_input      =inputs->GetInput(VzEnum);                  _assert_(vz_input);
+	Input* adjointx_input=inputs->GetInput(AdjointxEnum);            _assert_(adjointx_input);
+	Input* adjointy_input=inputs->GetInput(AdjointyEnum);            _assert_(adjointy_input);
+	Input* adjointz_input=inputs->GetInput(AdjointzEnum);            _assert_(adjointz_input);
+
+	/*Build frictoin element, needed later: */
+	friction=new Friction("3d",inputs,matpar,analysis_type);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(0,1,2,4);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/*Recover alpha_complement and drag: */
+		friction->GetAlphaComplement(&alpha_complement, gauss,VxEnum,VyEnum,VzEnum);
+		drag_input->GetInputValue(&drag,gauss);
+
+		/*recover lambda mu and xi: */
+		adjointx_input->GetInputValue(&lambda,gauss);
+		adjointy_input->GetInputValue(&mu    ,gauss);
+		adjointz_input->GetInputValue(&xi    ,gauss);
+
+		/*recover vx vy and vz: */
+		vx_input->GetInputValue(&vx, gauss);
+		vy_input->GetInputValue(&vy, gauss);
+		vz_input->GetInputValue(&vz, gauss);
+
+		/*Get normal vector to the bed */
+		SurfaceNormal(&surface_normal[0],xyz_list_tria);
+
+		bed_normal[0]=-surface_normal[0]; //Function is for upper surface, so the normal to the bed is the opposite of the result
+		bed_normal[1]=-surface_normal[1];
+		bed_normal[2]=-surface_normal[2];
+
+		/* Get Jacobian determinant: */
+		GetTriaJacobianDeterminant(&Jdet,&xyz_list_tria[0][0],gauss);
+		GetNodalFunctionsP1(basis, gauss);
+
+		/*Get k derivative: dk/dx */
+		drag_input->GetInputDerivativeValue(&dk[0],&xyz_list[0][0],gauss);
+
+		/*Build gradje_g_gaussian vector (actually -dJ/ddrag): */
+		for (i=0;iweight*basis[i]; 
+		}
+
+		/*Add gradje_g_gaussian vector to gradje_g: */
+		for( i=0; iSetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+
+	delete friction;
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Penta::GradjBbarMacAyeal {{{*/
+void  Penta::GradjBbarMacAyeal(Vector* gradient,int control_index){
+
+	/*This element should be collapsed into a tria element at its base*/
+	if (!IsOnBed()) return; 
+
+	/*Depth Average B*/
+	this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum,MaterialsEnum);
+
+	/*Collapse element to the base*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria (lower face).
+	tria->GradjBMacAyeal(gradient,control_index);
+	delete tria->material; delete tria;
+
+	/*delete Average B*/
+	this->material->inputs->DeleteInput(MaterialsRheologyBbarEnum);
+
+} /*}}}*/
+/*FUNCTION Penta::GradjBbarPattyn {{{*/
+void  Penta::GradjBbarPattyn(Vector* gradient,int control_index){
+
+	/*Gradient is computed on bed only (Bbar)*/
+	if (!IsOnBed()) return;
+
+	/*Depth Average B*/
+	this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum,MaterialsEnum);
+
+	/*Collapse element to the base*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2);
+	tria->GradjBMacAyeal(gradient,control_index);    //We use MacAyeal as an estimate for now
+	delete tria->material; delete tria;
+
+	/*delete Average B*/
+	this->material->inputs->DeleteInput(MaterialsRheologyBbarEnum);
+} /*}}}*/
+/*FUNCTION Penta::GradjBbarStokes {{{*/
+void  Penta::GradjBbarStokes(Vector* gradient,int control_index){
+
+	/*Gradient is computed on bed only (Bbar)*/
+	if (!IsOnBed()) return;
+
+	/*Depth Average B*/
+	this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum,MaterialsEnum);
+
+	/*Collapse element to the base*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2);
+	tria->GradjBMacAyeal(gradient,control_index);    //We use MacAyeal as an estimate for now
+	delete tria->material; delete tria;
+
+	/*delete Average B*/
+	this->material->inputs->DeleteInput(MaterialsRheologyBbarEnum);
+} /*}}}*/
+/*FUNCTION Penta::InputControlUpdate{{{*/
+void  Penta::InputControlUpdate(IssmDouble scalar,bool save_parameter){
+
+	/*Intermediary*/
+	int    num_controls;
+	int*   control_type=NULL;
+	Input* input=NULL;
+
+	/*retrieve some parameters: */
+	this->parameters->FindParam(&num_controls,InversionNumControlParametersEnum);
+	this->parameters->FindParam(&control_type,NULL,InversionControlParametersEnum);
+
+	for(int i=0;iinputs->GetInput(MaterialsRheologyBEnum); _assert_(input);
+		}
+		else if(control_type[i]==MaterialsRheologyZbarEnum){
+			if (!IsOnBed()) goto cleanup_and_return;
+			input=(Input*)material->inputs->GetInput(MaterialsRheologyZEnum); _assert_(input);
+		}
+		else{
+			input=(Input*)this->inputs->GetInput(control_type[i]); _assert_(input);
+		}
+
+		if (input->ObjectEnum()!=ControlInputEnum) _error_("input " << EnumToStringx(control_type[i]) << " is not a ControlInput");
+
+		((ControlInput*)input)->UpdateValue(scalar);
+		((ControlInput*)input)->Constrain();
+		if (save_parameter) ((ControlInput*)input)->SaveValue();
+
+		if(control_type[i]==MaterialsRheologyBbarEnum){
+			this->InputExtrude(MaterialsRheologyBEnum,MaterialsEnum);
+		}
+		else if(control_type[i]==MaterialsRheologyZbarEnum){
+			this->InputExtrude(MaterialsRheologyZEnum,MaterialsEnum);
+		}
+	}
+
+	/*Clean up and return*/
+cleanup_and_return:
+	xDelete(control_type);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionAdjointStokes {{{*/
+void  Penta::InputUpdateFromSolutionAdjointStokes(IssmDouble* solution){
+
+	const int    numdof=NDOF4*NUMVERTICES;
+
+	int    i;
+	IssmDouble values[numdof];
+	IssmDouble lambdax[NUMVERTICES];
+	IssmDouble lambday[NUMVERTICES];
+	IssmDouble lambdaz[NUMVERTICES];
+	IssmDouble lambdap[NUMVERTICES];
+	int*   doflist=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(lambdax[i])) _error_("NaN found in solution vector");
+		if(xIsNan(lambday[i])) _error_("NaN found in solution vector");
+		if(xIsNan(lambdaz[i])) _error_("NaN found in solution vector");
+		if(xIsNan(lambdap[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new PentaP1Input(AdjointxEnum,lambdax));
+	this->inputs->AddInput(new PentaP1Input(AdjointyEnum,lambday));
+	this->inputs->AddInput(new PentaP1Input(AdjointzEnum,lambdaz));
+	this->inputs->AddInput(new PentaP1Input(AdjointpEnum,lambdap));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionAdjointHoriz {{{*/
+void  Penta::InputUpdateFromSolutionAdjointHoriz(IssmDouble* solution){
+
+	const int numdof=NDOF2*NUMVERTICES;
+
+	int    i;
+	IssmDouble values[numdof];
+	IssmDouble lambdax[NUMVERTICES];
+	IssmDouble lambday[NUMVERTICES];
+	int*   doflist=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(lambdax[i]))       _error_("NaN found in solution vector");
+		if(xIsNan(lambday[i]))       _error_("NaN found in solution vector");
+	}
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new PentaP1Input(AdjointxEnum,lambdax));
+	this->inputs->AddInput(new PentaP1Input(AdjointyEnum,lambday));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::SurfaceAverageVelMisfit {{{*/
+IssmDouble Penta::SurfaceAverageVelMisfit(bool process_units,int weight_index){
+
+	int    approximation;
+	IssmDouble J;
+	Tria*  tria=NULL;
+
+	/*retrieve inputs :*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/*Bail out if this element if:
+	 * -> Non MacAyeal and not on the surface
+	 * -> MacAyeal (2d model) and not on bed) */
+	if ((approximation!=MacAyealApproximationEnum && !IsOnSurface()) || (approximation==MacAyealApproximationEnum && !IsOnBed())){
+		return 0;
+	}
+	else if (approximation==MacAyealApproximationEnum){
+
+		/*This element should be collapsed into a tria element at its base. Create this tria element, 
+		 * and compute SurfaceAverageVelMisfit*/
+		tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria (lower face).
+		J=tria->SurfaceAverageVelMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+	else{
+
+		tria=(Tria*)SpawnTria(3,4,5); //nodes 3, 4 and 5 make the new tria (upper face).
+		J=tria->SurfaceAverageVelMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::SurfaceAbsVelMisfit {{{*/
+IssmDouble Penta::SurfaceAbsVelMisfit(bool process_units,int weight_index){
+
+	int    approximation;
+	IssmDouble J;
+	Tria*  tria=NULL;
+
+	/*retrieve inputs :*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/*Bail out if this element if:
+	 * -> Non MacAyeal and not on the surface
+	 * -> MacAyeal (2d model) and not on bed) */
+	if ((approximation!=MacAyealApproximationEnum && !IsOnSurface()) || (approximation==MacAyealApproximationEnum && !IsOnBed())){
+		return 0;
+	}
+	else if (approximation==MacAyealApproximationEnum){
+
+		/*This element should be collapsed into a tria element at its base. Create this tria element, 
+		 * and compute SurfaceAbsVelMisfit*/
+		tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria (lower face).
+		J=tria->SurfaceAbsVelMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+	else{
+
+		tria=(Tria*)SpawnTria(3,4,5); //nodes 3, 4 and 5 make the new tria (upper face).
+		J=tria->SurfaceAbsVelMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::SurfaceLogVelMisfit {{{*/
+IssmDouble Penta::SurfaceLogVelMisfit(bool process_units,int weight_index){
+
+	int    approximation;
+	IssmDouble J;
+	Tria*  tria=NULL;
+
+	/*retrieve inputs :*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/*Bail out if this element if:
+	 * -> Non MacAyeal and not on the surface
+	 * -> MacAyeal (2d model) and not on bed) */
+	if ((approximation!=MacAyealApproximationEnum && !IsOnSurface()) || (approximation==MacAyealApproximationEnum && !IsOnBed())){
+		return 0;
+	}
+	else if (approximation==MacAyealApproximationEnum){
+
+		/*This element should be collapsed into a tria element at its base. Create this tria element, 
+		 * and compute SurfaceLogVelMisfit*/
+		tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria (lower face).
+		J=tria->SurfaceLogVelMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+	else{
+
+		tria=(Tria*)SpawnTria(3,4,5); //nodes 3, 4 and 5 make the new tria (upper face).
+		J=tria->SurfaceLogVelMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::SurfaceLogVxVyMisfit {{{*/
+IssmDouble Penta::SurfaceLogVxVyMisfit(bool process_units,int weight_index){
+
+	IssmDouble J;
+	Tria* tria=NULL;
+
+	/*inputs: */
+	int  approximation;
+
+	/*retrieve inputs :*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/*Bail out if this element if:
+	 * -> Non MacAyeal and not on the surface
+	 * -> MacAyeal (2d model) and not on bed) */
+	if ((approximation!=MacAyealApproximationEnum && !IsOnSurface()) || (approximation==MacAyealApproximationEnum && !IsOnBed())){
+		return 0;
+	}
+	else if (approximation==MacAyealApproximationEnum){
+
+		/*This element should be collapsed into a tria element at its base. Create this tria element, 
+		 * and compute SurfaceLogVxVyMisfit*/
+		tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria (lower face).
+		J=tria->SurfaceLogVxVyMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+	else{
+
+		tria=(Tria*)SpawnTria(3,4,5); //nodes 3, 4 and 5 make the new tria (upper face).
+		J=tria->SurfaceLogVxVyMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::SurfaceRelVelMisfit {{{*/
+IssmDouble Penta::SurfaceRelVelMisfit(bool process_units,int weight_index){
+
+	int    approximation;
+	IssmDouble J;
+	Tria*  tria=NULL;
+
+	/*retrieve inputs :*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/*Bail out if this element if:
+	 * -> Non MacAyeal and not on the surface
+	 * -> MacAyeal (2d model) and not on bed) */
+	if ((approximation!=MacAyealApproximationEnum && !IsOnSurface()) || (approximation==MacAyealApproximationEnum && !IsOnBed())){
+		return 0;
+	}
+	else if (approximation==MacAyealApproximationEnum){
+
+		/*This element should be collapsed into a tria element at its base. Create this tria element, 
+		 * and compute SurfaceRelVelMisfit*/
+		tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria (lower face).
+		J=tria->SurfaceRelVelMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+	else{
+
+		tria=(Tria*)SpawnTria(3,4,5); //nodes 3, 4 and 5 make the new tria (upper face).
+		J=tria->SurfaceRelVelMisfit(process_units,weight_index);
+		delete tria->material; delete tria;
+		return J;
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::ThicknessAbsGradient{{{*/
+IssmDouble Penta::ThicknessAbsGradient(bool process_units,int weight_index){
+
+	_error_("Not implemented yet");
+}
+/*}}}*/
+/*FUNCTION Penta::ThicknessAbsMisfit {{{*/
+IssmDouble Penta::ThicknessAbsMisfit(bool process_units,int weight_index){
+
+	int    approximation;
+	IssmDouble J;
+	Tria*  tria=NULL;
+
+	/*retrieve inputs :*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+	_error_("Not implemented yet");
+
+	tria=(Tria*)SpawnTria(0,1,2);
+	J=tria->ThicknessAbsMisfit(process_units,weight_index);
+	delete tria->material; delete tria;
+	return J;
+}
+/*}}}*/
+/*FUNCTION Penta::DragCoefficientAbsGradient{{{*/
+IssmDouble Penta::DragCoefficientAbsGradient(bool process_units,int weight_index){
+
+	IssmDouble J;
+	Tria*  tria=NULL;
+
+	/*If on water, on shelf or not on bed, skip: */
+	if(IsOnWater()|| IsFloating() || !IsOnBed()) return 0;
+
+	tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria
+	J=tria->DragCoefficientAbsGradient(process_units,weight_index);
+	delete tria->material; delete tria;
+	return J;
+}
+/*}}}*/
+/*FUNCTION Penta::RheologyBbarAbsGradient{{{*/
+IssmDouble Penta::RheologyBbarAbsGradient(bool process_units,int weight_index){
+
+	IssmDouble J;
+	Tria*  tria=NULL;
+
+	/*If on water, on shelf or not on bed, skip: */
+	if(IsOnWater() || !IsOnBed()) return 0;
+
+	tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria
+	J=tria->RheologyBbarAbsGradient(process_units,weight_index);
+	delete tria->material; delete tria;
+	return J;
+}
+/*}}}*/
+/*FUNCTION Penta::GetVectorFromControlInputs{{{*/
+void  Penta::GetVectorFromControlInputs(Vector* vector,int control_enum,int control_index,const char* data){
+
+	int doflist1[NUMVERTICES];
+
+	/*Get out if this is not an element input*/
+	if(!IsInput(control_enum)) return;
+
+	/*Prepare index list*/
+	GradientIndexing(&doflist1[0],control_index);
+
+	/*Get input (either in element or material)*/
+	Input* input=inputs->GetInput(control_enum);
+	if(!input) _error_("Input " << EnumToStringx(control_enum) << " not found in element");
+
+	/*Check that it is a ControlInput*/
+	if (input->ObjectEnum()!=ControlInputEnum){
+		_error_("input " << EnumToStringx(control_enum) << " is not a ControlInput");
+	}
+
+	((ControlInput*)input)->GetVectorFromInputs(vector,&doflist1[0],data);
+}
+/*}}}*/
+/*FUNCTION Penta::SetControlInputsFromVector{{{*/
+void  Penta::SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index){
+
+	IssmDouble  values[NUMVERTICES];
+	int     doflist1[NUMVERTICES];
+	Input  *input     = NULL;
+	Input  *new_input = NULL;
+
+	/*Get out if this is not an element input*/
+	if(!IsInput(control_enum)) return;
+
+	/*Prepare index list*/
+	GradientIndexing(&doflist1[0],control_index);
+
+	/*Get values on vertices*/
+	for (int i=0;iinputs->GetInput(control_enum); _assert_(input);
+	}
+	else{
+		input=(Input*)this->inputs->GetInput(control_enum);   _assert_(input);
+	}
+
+	if (input->ObjectEnum()!=ControlInputEnum){
+		_error_("input " << EnumToStringx(control_enum) << " is not a ControlInput");
+	}
+
+	((ControlInput*)input)->SetInput(new_input);
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_DAKOTA_
+/*FUNCTION Penta::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type);{{{*/
+void  Penta::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){
+	
+	int i,j;
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	switch(type){
+
+		case VertexEnum:
+
+			/*New PentaP1Input*/
+			IssmDouble values[6];
+
+			/*Get values on the 6 vertices*/
+			for (i=0;i<6;i++){
+				values[i]=vector[this->nodes[i]->GetSidList()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!)
+			}
+
+			/*Branch on the specified type of update: */
+			switch(name){
+				case ThicknessEnum:
+					/*Update thickness + surface: assume bed is constant. On ice shelves, takes hydrostatic equilibrium {{{*/
+					IssmDouble  thickness[6];
+					IssmDouble  thickness_init[6];
+					IssmDouble  hydrostatic_ratio[6];
+					IssmDouble  surface[6];
+					IssmDouble  bed[6];
+					
+					/*retrieve inputs: */
+					GetInputListOnVertices(&thickness_init[0],ThicknessEnum);
+					GetInputListOnVertices(&hydrostatic_ratio[0],GeometryHydrostaticRatioEnum);
+					GetInputListOnVertices(&bed[0],BedEnum);
+					GetInputListOnVertices(&surface[0],SurfaceEnum);
+
+					/*build new thickness: */
+//					for(j=0;j<6;j++)thickness[j]=values[j];
+
+					/*build new bed and surface: */
+					if (this->IsFloating()){
+						/*hydrostatic equilibrium: */
+						IssmDouble rho_ice,rho_water,di;
+						rho_ice=this->matpar->GetRhoIce();
+						rho_water=this->matpar->GetRhoWater();
+
+						di=rho_ice/rho_water;
+
+						/*build new thickness: */
+						for (j=0; j<6; j++) {
+						/*  for observed/interpolated/hydrostatic thickness, remove scaling from any hydrostatic thickness  */
+							if     (hydrostatic_ratio[j] >= 0.)
+								thickness[j]=values[j]-(values[j]/thickness_init[j]-1.)*hydrostatic_ratio[j]*surface[j]/(1.-di);
+						/*  for minimum thickness, don't scale  */
+							else
+								thickness[j]=thickness_init[j];
+
+						/*  check the computed thickness and update bed  */
+							if (thickness[j] < 0.)
+								thickness[j]=1./(1.-di);
+							bed[j]=surface[j]-thickness[j];
+						}
+
+//						for(j=0;j<6;j++){
+//							surface[j]=(1-di)*thickness[j];
+//							bed[j]=-di*thickness[j];
+//						}
+					}
+					else{
+						/*build new thickness: */
+						for (j=0; j<6; j++) {
+						/*  for observed thickness, use scaled value  */
+							if(hydrostatic_ratio[j] >= 0.)
+								thickness[j]=values[j];
+						/*  for minimum thickness, don't scale  */
+							else
+								thickness[j]=thickness_init[j];
+						}
+
+						/*update bed on grounded ice: */
+//						for(j=0;j<6;j++)surface[j]=bed[j]+thickness[j];
+						for(j=0;j<6;j++)bed[j]=surface[j]-thickness[j];
+					}
+
+					/*Add new inputs: */
+					this->inputs->AddInput(new PentaP1Input(ThicknessEnum,thickness));
+					this->inputs->AddInput(new PentaP1Input(BedEnum,bed));
+					this->inputs->AddInput(new PentaP1Input(SurfaceEnum,surface));
+
+					/*}}}*/
+					break;
+				default:
+					this->inputs->AddInput(new PentaP1Input(name,values));
+			}
+			break;
+
+		default:
+			_error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromVectorDakota(int* vector, int name, int type);{{{*/
+void  Penta::InputUpdateFromVectorDakota(int* vector, int name, int type){
+	_error_("not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromVectorDakota(bool* vector, int name, int type);{{{*/
+void  Penta::InputUpdateFromVectorDakota(bool* vector, int name, int type){
+	_error_("not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type);{{{*/
+void  Penta::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type){
+	
+	int i,j,t;
+	TransientInput* transientinput=NULL;
+	IssmDouble values[6];
+	IssmDouble time;
+	int row;
+	IssmDouble yts;
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	switch(type){
+
+		case VertexEnum:
+			
+			/*Create transient input: */
+						
+			parameters->FindParam(&yts,ConstantsYtsEnum);
+
+			for(t=0;tnodes[i]->GetSidList();
+					values[i]=(IssmDouble)matrix[ncols*row+t];
+				}
+
+				/*time? :*/
+				time=(IssmDouble)matrix[(nrows-1)*ncols+t]*yts;
+
+				if(t==0) transientinput=new TransientInput(name);
+				transientinput->AddTimeInput(new PentaP1Input(name,values),time);
+				transientinput->Configure(parameters);
+			}
+			this->inputs->AddInput(transientinput);
+			break;
+
+		default:
+			_error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_DIAGNOSTIC_
+/*FUNCTION Penta::CreateDVectorDiagnosticHoriz {{{*/
+ElementVector* Penta::CreateDVectorDiagnosticHoriz(void){
+
+	int approximation;
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	switch(approximation){
+		case StokesApproximationEnum:
+			return CreateDVectorDiagnosticStokes();
+		default:
+			return NULL; //no need for doftypes outside of stokes approximation
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::CreateDVectorDiagnosticStokes{{{*/
+ElementVector* Penta::CreateDVectorDiagnosticStokes(void){
+
+	/*output: */
+	ElementVector* De=NULL;
+	/*intermediary: */
+	int approximation;
+	int i;
+
+	/*Initialize Element vector and return if necessary*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(approximation!=StokesApproximationEnum) return NULL;
+
+	De=new ElementVector(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	for (i=0;ivalues[i*4+0]=VelocityEnum;
+		De->values[i*4+1]=VelocityEnum;
+		De->values[i*4+2]=VelocityEnum;
+		De->values[i*4+3]=PressureEnum;
+	}
+
+	return De;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixCouplingMacAyealPattyn{{{*/
+ElementMatrix* Penta::CreateKMatrixCouplingMacAyealPattyn(void){
+	
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixCouplingMacAyealPattynViscous();
+	ElementMatrix* Ke2=CreateKMatrixCouplingMacAyealPattynFriction();
+	ElementMatrix* Ke=new ElementMatrix(Ke1,Ke2);
+	
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixCouplingMacAyealPattynViscous{{{*/
+ElementMatrix* Penta::CreateKMatrixCouplingMacAyealPattynViscous(void){
+
+	/*Constants*/
+	const int numnodes    = 2 *NUMVERTICES;
+	const int numdofm     = NDOF2 *NUMVERTICES2D;
+	const int numdofp     = NDOF2 *NUMVERTICES;
+	const int numdoftotal = 2 *NDOF2*NUMVERTICES;
+
+	/*Intermediaries */
+	int         i,j,ig;
+	IssmDouble      Jdet;
+	IssmDouble      viscosity,oldviscosity,newviscosity,viscosity_overshoot; //viscosity
+	IssmDouble      epsilon[5],oldepsilon[5]; /* epsilon=[exx,eyy,exy,exz,eyz];*/
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      B[3][numdofp];
+	IssmDouble      Bprime[3][numdofm];
+	IssmDouble      D[3][3]={0.0};            // material matrix, simple scalar matrix.
+	IssmDouble      D_scalar;
+	IssmDouble      Ke_gg[numdofp][numdofm]={0.0}; //local element stiffness matrix 
+	IssmDouble      Ke_gg_gaussian[numdofp][numdofm]; //stiffness matrix evaluated at the gaussian point.
+	GaussPenta *gauss=NULL;
+	GaussTria  *gauss_tria=NULL;
+	Node       *node_list[numnodes];
+	int         cs_list[numnodes];
+
+	/*Find penta on bed as pattyn must be coupled to the dofs on the bed: */
+	Penta* pentabase=GetBasalElement();
+	Tria*  tria=pentabase->SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+
+	/*Prepare node list*/
+	for(i=0;inodes[i];
+		node_list[i+1*NUMVERTICES] = this->nodes[i];
+		cs_list[i+0*NUMVERTICES] = XYEnum;
+		cs_list[i+1*NUMVERTICES] = XYEnum;
+	}
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke1=new ElementMatrix(pentabase->nodes,NUMVERTICES,this->parameters,MacAyealApproximationEnum);
+	ElementMatrix* Ke2=new ElementMatrix(this->nodes     ,NUMVERTICES,this->parameters,PattynApproximationEnum);
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+	delete Ke1; delete Ke2;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&viscosity_overshoot,DiagnosticViscosityOvershootEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+	Input* vxold_input=inputs->GetInput(VxPicardEnum); _assert_(vxold_input);
+	Input* vyold_input=inputs->GetInput(VyPicardEnum); _assert_(vyold_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	gauss_tria=new GaussTria();
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+		gauss->SynchronizeGaussTria(gauss_tria);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetBMacAyealPattyn(&B[0][0], &xyz_list[0][0], gauss);
+		tria->GetBprimeMacAyeal(&Bprime[0][0], &xyz_list[0][0], gauss_tria);
+
+		this->GetStrainRate3dPattyn(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		this->GetStrainRate3dPattyn(&oldepsilon[0],&xyz_list[0][0],gauss,vxold_input,vyold_input);
+		material->GetViscosity3d(&viscosity, &epsilon[0]);
+		material->GetViscosity3d(&oldviscosity, &oldepsilon[0]);
+
+		newviscosity=viscosity+viscosity_overshoot*(viscosity-oldviscosity);
+		D_scalar=2*newviscosity*gauss->weight*Jdet;
+		for (i=0;i<3;i++) D[i][i]=D_scalar;
+
+		TripleMultiply( &B[0][0],3,numdofp,1,
+					&D[0][0],3,3,0,
+					&Bprime[0][0],3,numdofm,0,
+					&Ke_gg_gaussian[0][0],0);
+
+		for( i=0; ivalues[(i+2*numdofm)*numdoftotal+j]+=Ke_gg[i][j];
+	for(i=0;ivalues[i*numdoftotal+(j+2*numdofm)]+=Ke_gg[j][i];
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,node_list,numnodes,cs_list);
+
+	/*Clean-up and return*/
+	delete tria->material; delete tria;
+	delete gauss;
+	delete gauss_tria;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixCouplingMacAyealPattynFriction{{{*/
+ElementMatrix* Penta::CreateKMatrixCouplingMacAyealPattynFriction(void){
+
+	/*Constants*/
+	const int numnodes    = 2 *NUMVERTICES;
+	const int numdof      = NDOF2 *NUMVERTICES;
+	const int numdoftotal = NDOF4 *NUMVERTICES;
+	
+	/*Intermediaries */
+	int       i,j,ig,analysis_type;
+	IssmDouble    Jdet2d,slope_magnitude,alpha2;
+	IssmDouble    xyz_list[NUMVERTICES][3];
+	IssmDouble    xyz_list_tria[NUMVERTICES2D][3]={0.0};
+	IssmDouble    slope[3]={0.0,0.0,0.0};
+	IssmDouble    MAXSLOPE=.06; // 6 %
+	IssmDouble    MOUNTAINKEXPONENT=10;
+	IssmDouble    L[2][numdof];
+	IssmDouble    DL[2][2]                  ={{ 0,0 },{0,0}}; //for basal drag
+	IssmDouble    DL_scalar;
+	IssmDouble    Ke_gg[numdof][numdof]     ={0.0};
+	IssmDouble    Ke_gg_gaussian[numdof][numdof]; //stiffness matrix contribution from drag
+	Friction  *friction = NULL;
+	GaussPenta *gauss=NULL;
+	Node       *node_list[numnodes];
+	int         cs_list[numnodes];
+
+	/*Initialize Element matrix and return if necessary*/
+	if(IsFloating() || !IsOnBed()) return NULL;
+	ElementMatrix* Ke1=new ElementMatrix(nodes,NUMVERTICES,this->parameters,MacAyealApproximationEnum);
+	ElementMatrix* Ke2=new ElementMatrix(nodes,NUMVERTICES,this->parameters,PattynApproximationEnum);
+	ElementMatrix* Ke=new ElementMatrix(Ke1,Ke2);
+	delete Ke1; delete Ke2;
+
+	/*Prepare node list*/
+	for(i=0;inodes[i];
+		node_list[i+1*NUMVERTICES] = this->nodes[i];
+		cs_list[i+0*NUMVERTICES] = XYEnum;
+		cs_list[i+1*NUMVERTICES] = XYEnum;
+	}
+
+	/*retrieve inputs :*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iFindParam(&analysis_type,AnalysisTypeEnum);
+	Input* surface_input=inputs->GetInput(SurfaceEnum); _assert_(surface_input);
+	Input* vx_input=inputs->GetInput(VxEnum);           _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);           _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);           _assert_(vz_input);
+
+	/*build friction object, used later on: */
+	friction=new Friction("2d",inputs,matpar,analysis_type);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(0,1,2,2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/*Friction: */
+		friction->GetAlpha2(&alpha2, gauss,VxEnum,VyEnum,VzEnum);
+
+		// If we have a slope > 6% for this element,  it means  we are on a mountain. In this particular case, 
+		//velocity should be = 0. To achieve this result, we set alpha2_list to a very high value: */
+		surface_input->GetInputDerivativeValue(&slope[0],&xyz_list[0][0],gauss);
+		slope_magnitude=sqrt(pow(slope[0],2)+pow(slope[1],2));
+
+		if (slope_magnitude>MAXSLOPE){
+			alpha2=pow((IssmDouble)10,MOUNTAINKEXPONENT);
+		}
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0],gauss);
+		GetL(&L[0][0], gauss,NDOF2);
+
+		DL_scalar=alpha2*gauss->weight*Jdet2d;
+		for (i=0;i<2;i++) DL[i][i]=DL_scalar; 
+		
+		/*  Do the triple producte tL*D*L: */
+		TripleMultiply( &L[0][0],2,numdof,1,
+					&DL[0][0],2,2,0,
+					&L[0][0],2,numdof,0,
+					&Ke_gg_gaussian[0][0],0);
+
+		for(i=0;ivalues[i*numdoftotal+(numdof+j)]+=Ke_gg[i][j];
+	for(i=0;ivalues[(i+numdof)*numdoftotal+j]+=Ke_gg[i][j];
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,node_list,numnodes,cs_list);
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixCouplingMacAyealStokes{{{*/
+ElementMatrix* Penta::CreateKMatrixCouplingMacAyealStokes(void){
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixCouplingMacAyealStokesViscous();
+	ElementMatrix* Ke2=CreateKMatrixCouplingMacAyealStokesFriction();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixCouplingMacAyealStokesViscous{{{*/
+ElementMatrix* Penta::CreateKMatrixCouplingMacAyealStokesViscous(void){
+
+	/*Constants*/
+	const int numnodes    = 2 *NUMVERTICES;
+	const int numdofm     = NDOF2 *NUMVERTICES2D;
+	const int numdofs     = NDOF4 *NUMVERTICES;
+	const int numdoftotal = 2 *numdofm+numdofs;
+
+	/*Intermediaries */
+	int         i,j,ig;
+	IssmDouble      Jdet;
+	IssmDouble      viscosity,stokesreconditioning; //viscosity
+	IssmDouble      epsilon[6]; /* epsilon=[exx,eyy,exy,exz,eyz];*/
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      B[4][numdofs+3];
+	IssmDouble      Bprime[4][numdofm];
+	IssmDouble      B2[3][numdofm];
+	IssmDouble      Bprime2[3][numdofs+3];
+	IssmDouble      D[4][4]={0.0};            // material matrix, simple scalar matrix.
+	IssmDouble      D2[3][3]={0.0};            // material matrix, simple scalar matrix.
+	IssmDouble      D_scalar;
+	IssmDouble      Ke_gg[numdofs][numdofm]={0.0}; //local element stiffness matrix 
+	IssmDouble      Ke_gg2[numdofm][numdofs]={0.0}; //local element stiffness matrix 
+	IssmDouble      Ke_gg_gaussian[numdofs+3][numdofm]; //stiffness matrix evaluated at the gaussian point.
+	IssmDouble      Ke_gg_gaussian2[numdofm][numdofs+3]; //stiffness matrix evaluated at the gaussian point.
+	GaussPenta *gauss=NULL;
+	GaussTria  *gauss_tria=NULL;
+	Node       *node_list[numnodes];
+	int         cs_list[numnodes];
+
+	/*Find penta on bed as stokes must be coupled to the dofs on the bed: */
+	Penta* pentabase=GetBasalElement();
+	Tria* tria=pentabase->SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+
+	/*Prepare node list*/
+	for(i=0;inodes[i];
+		node_list[i+1*NUMVERTICES] = this->nodes[i];
+		cs_list[i+0*NUMVERTICES] = XYEnum;
+		cs_list[i+1*NUMVERTICES] = XYZPEnum;
+	}
+
+	/*Initialize Element matrix and return if necessary*/
+	ElementMatrix* Ke1=new ElementMatrix(pentabase->nodes,NUMVERTICES,this->parameters,MacAyealApproximationEnum);
+	ElementMatrix* Ke2=new ElementMatrix(this->nodes     ,NUMVERTICES,this->parameters,StokesApproximationEnum);
+	ElementMatrix* Ke=new ElementMatrix(Ke1,Ke2);
+	delete Ke1; delete Ke2;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);       _assert_(vz_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	gauss_tria=new GaussTria();
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+		gauss->SynchronizeGaussTria(gauss_tria);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetBMacAyealStokes(&B[0][0], &xyz_list[0][0], gauss);
+		tria->GetBprimeMacAyealStokes(&Bprime[0][0], &xyz_list[0][0], gauss_tria);
+		tria->GetBMacAyealStokes(&B2[0][0], &xyz_list[0][0], gauss_tria);
+		GetBprimeMacAyealStokes(&Bprime2[0][0], &xyz_list[0][0], gauss);
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity, &epsilon[0]);
+
+		D_scalar=2*viscosity*gauss->weight*Jdet;
+		for (i=0;i<3;i++) D[i][i]=D_scalar;
+		D[3][3]=-gauss->weight*Jdet*stokesreconditioning;
+		for (i=0;i<3;i++) D2[i][i]=D_scalar;
+
+		TripleMultiply( &B[0][0],4,numdofs+3,1,
+					&D[0][0],4,4,0,
+					&Bprime[0][0],4,numdofm,0,
+					&Ke_gg_gaussian[0][0],0);
+
+		TripleMultiply( &B2[0][0],3,numdofm,1,
+					&D2[0][0],3,3,0,
+					&Bprime2[0][0],3,numdofs+3,0,
+					&Ke_gg_gaussian2[0][0],0);
+
+		for( i=0; ivalues[(i+2*numdofm)*numdoftotal+j]+=Ke_gg[i][j];
+	for(i=0;ivalues[i*numdoftotal+(j+2*numdofm)]+=Ke_gg2[i][j];
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,node_list,numnodes,cs_list);
+
+	/*Clean-up and return*/
+	delete tria->material; delete tria;
+	delete gauss;
+	delete gauss_tria;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixCouplingMacAyealStokesFriction {{{*/
+ElementMatrix* Penta::CreateKMatrixCouplingMacAyealStokesFriction(void){
+
+	/*Constants*/
+	const int numnodes  = 2 *NUMVERTICES;
+	const int numdof    = NUMVERTICES *NDOF4;
+	const int numdofm   = NUMVERTICES *NDOF2;
+	const int numdof2d  = NUMVERTICES2D *NDOF4;
+	const int numdof2dm = NUMVERTICES2D *NDOF2;
+	const int numdoftot = numdof+numdofm;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	int        analysis_type,approximation;
+	IssmDouble     stokesreconditioning;
+	IssmDouble     viscosity,alpha2_gauss,Jdet2d;
+	IssmDouble	  bed_normal[3];
+	IssmDouble     epsilon[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble	  xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble     LMacAyealStokes[8][numdof2dm];
+	IssmDouble     LprimeMacAyealStokes[8][numdof2d];
+	IssmDouble     DLMacAyealStokes[8][8]={0.0};
+	IssmDouble     LStokesMacAyeal[4][numdof2d];
+	IssmDouble     LprimeStokesMacAyeal[4][numdof2dm];
+	IssmDouble     DLStokesMacAyeal[4][4]={0.0};
+	IssmDouble     Ke_drag_gaussian[numdof2dm][numdof2d];
+	IssmDouble     Ke_drag_gaussian2[numdof2d][numdof2dm];
+	Friction*  friction=NULL;
+	GaussPenta *gauss=NULL;
+	Node       *node_list[numnodes];
+	int         cs_list[numnodes];
+
+	/*If on water or not Stokes, skip stiffness: */
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(IsFloating() || !IsOnBed()) return NULL;
+	ElementMatrix* Ke1=new ElementMatrix(this->nodes,NUMVERTICES,this->parameters,MacAyealApproximationEnum);
+	ElementMatrix* Ke2=new ElementMatrix(this->nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+	ElementMatrix* Ke=new ElementMatrix(Ke1,Ke2);
+	delete Ke1; delete Ke2;
+
+	/*Prepare node list*/
+	for(i=0;inodes[i];
+		node_list[i+1*NUMVERTICES] = this->nodes[i];
+		cs_list[i+0*NUMVERTICES] = XYEnum;
+		cs_list[i+1*NUMVERTICES] = XYZPEnum;
+	}
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+	parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum); _assert_(vz_input);
+	for(i=0;ibegin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0],gauss);
+		GetLMacAyealStokes(&LMacAyealStokes[0][0], gauss);
+		GetLprimeMacAyealStokes(&LprimeMacAyealStokes[0][0], &xyz_list[0][0], gauss);
+		GetLStokesMacAyeal(&LStokesMacAyeal[0][0], gauss);
+		GetLprimeStokesMacAyeal(&LprimeStokesMacAyeal[0][0], &xyz_list[0][0], gauss);
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+
+		BedNormal(&bed_normal[0],xyz_list_tria);
+		friction->GetAlpha2(&alpha2_gauss, gauss,VxEnum,VyEnum,VzEnum);
+
+		DLMacAyealStokes[0][0]=alpha2_gauss*gauss->weight*Jdet2d;
+		DLMacAyealStokes[1][1]=alpha2_gauss*gauss->weight*Jdet2d;
+		DLMacAyealStokes[2][2]=-alpha2_gauss*gauss->weight*Jdet2d*bed_normal[0]*bed_normal[2];
+		DLMacAyealStokes[3][3]=-alpha2_gauss*gauss->weight*Jdet2d*bed_normal[1]*bed_normal[2];
+		DLMacAyealStokes[4][4]=-2*viscosity*gauss->weight*Jdet2d*bed_normal[0];
+		DLMacAyealStokes[5][5]=-2*viscosity*gauss->weight*Jdet2d*bed_normal[1];
+		DLMacAyealStokes[6][6]=stokesreconditioning*gauss->weight*Jdet2d*bed_normal[0];
+		DLMacAyealStokes[7][7]=stokesreconditioning*gauss->weight*Jdet2d*bed_normal[1];
+
+		DLStokesMacAyeal[0][0]=alpha2_gauss*gauss->weight*Jdet2d;
+		DLStokesMacAyeal[1][1]=alpha2_gauss*gauss->weight*Jdet2d;
+		DLStokesMacAyeal[2][2]=-alpha2_gauss*gauss->weight*Jdet2d*bed_normal[0]*bed_normal[2];
+		DLStokesMacAyeal[3][3]=-alpha2_gauss*gauss->weight*Jdet2d*bed_normal[1]*bed_normal[2];
+		
+		TripleMultiply( &LMacAyealStokes[0][0],8,numdof2dm,1,
+					&DLMacAyealStokes[0][0],8,8,0,
+					&LprimeMacAyealStokes[0][0],8,numdof2d,0,
+					&Ke_drag_gaussian[0][0],0);
+
+		TripleMultiply( &LStokesMacAyeal[0][0],4,numdof2d,1,
+					&DLStokesMacAyeal[0][0],4,4,0,
+					&LprimeStokesMacAyeal[0][0],4,numdof2dm,0,
+					&Ke_drag_gaussian2[0][0],0);
+
+		for(i=0;ivalues[i*numdoftot+j+numdofm]+=Ke_drag_gaussian[i][j];
+		for(i=0;ivalues[(i+numdofm)*numdoftot+j]+=Ke_drag_gaussian2[i][j];
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,node_list,numnodes,cs_list);
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixCouplingPattynStokes{{{*/
+ElementMatrix* Penta::CreateKMatrixCouplingPattynStokes(void){
+
+	/*Constants*/
+	const int numnodes  = 2 *NUMVERTICES;
+	const int numdofp     = NDOF2 *NUMVERTICES;
+	const int numdofs     = NDOF4 *NUMVERTICES;
+	const int numdoftotal = (NDOF2+NDOF4) *NUMVERTICES;
+
+	/*Intermediaries*/
+	Node     *node_list[numnodes];
+	int       cs_list[numnodes];
+	int       i,j;
+
+	/*Prepare node list*/
+	for(i=0;inodes[i];
+		node_list[i+1*NUMVERTICES] = this->nodes[i];
+		cs_list[i+0*NUMVERTICES] = XYEnum;
+		cs_list[i+1*NUMVERTICES] = XYZPEnum;
+	}
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=new ElementMatrix(this->nodes,NUMVERTICES,this->parameters,PattynApproximationEnum);
+	ElementMatrix* Ke2=new ElementMatrix(this->nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+	ElementMatrix* Ke=new ElementMatrix(Ke1,Ke2);
+	delete Ke1;
+	delete Ke2;
+	Ke1=CreateKMatrixDiagnosticPattyn(); TransformInvStiffnessMatrixCoord(Ke1,this->nodes,NUMVERTICES,XYEnum);
+	Ke2=CreateKMatrixDiagnosticStokes(); TransformInvStiffnessMatrixCoord(Ke2,this->nodes,NUMVERTICES,XYZPEnum);
+
+	for(i=0;ivalues[(i+numdofp)*numdoftotal+NDOF2*j+0]+=Ke2->values[i*numdofs+NDOF4*j+0];
+		Ke->values[(i+numdofp)*numdoftotal+NDOF2*j+1]+=Ke2->values[i*numdofs+NDOF4*j+1];
+	}
+	for(i=0;ivalues[i*numdoftotal+numdofp+NDOF4*j+0]+=Ke1->values[i*numdofp+NDOF2*j+0];
+		Ke->values[i*numdoftotal+numdofp+NDOF4*j+1]+=Ke1->values[i*numdofp+NDOF2*j+1];
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,node_list,numnodes,cs_list);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticHoriz {{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticHoriz(void){
+
+	int approximation;
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	switch(approximation){
+		case MacAyealApproximationEnum:
+			return CreateKMatrixDiagnosticMacAyeal2d();
+		case L1L2ApproximationEnum:
+			return CreateKMatrixDiagnosticL1L2();
+		case PattynApproximationEnum:
+			return CreateKMatrixDiagnosticPattyn();
+		case StokesApproximationEnum:
+			return CreateKMatrixDiagnosticStokes();
+		case HutterApproximationEnum:
+			return NULL;
+		case NoneApproximationEnum:
+			return NULL;
+		case MacAyealPattynApproximationEnum:
+			return CreateKMatrixDiagnosticMacAyealPattyn();
+		case MacAyealStokesApproximationEnum:
+			return CreateKMatrixDiagnosticMacAyealStokes();
+		case PattynStokesApproximationEnum:
+			return CreateKMatrixDiagnosticPattynStokes();
+		default:
+			_error_("Approximation " << EnumToStringx(approximation) << " not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticHutter{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticHutter(void){
+
+	/*Constants*/
+	const int numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries*/
+	int         connectivity[2];
+	int         i,i0,i1,j0,j1;
+	IssmDouble  one0,one1;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Spawn 3 beam elements: */
+	for(i=0;i<3;i++){
+		/*2 dofs of first node*/
+		i0=2*i;
+		i1=2*i+1;
+		/*2 dofs of second node*/
+		j0=2*(i+3);
+		j1=2*(i+3)+1;
+
+		/*Find connectivity for the two nodes*/
+		connectivity[0]=nodes[i]->GetConnectivity();
+		connectivity[1]=nodes[i+3]->GetConnectivity();
+		one0=1/(IssmDouble)connectivity[0];
+		one1=1/(IssmDouble)connectivity[1];
+
+		/*Create matrix for these two nodes*/
+		if (IsOnBed() && IsOnSurface()){
+			Ke->values[i0*numdof+i0]=one0;
+			Ke->values[i1*numdof+i1]=one0;
+			Ke->values[j0*numdof+i0]=-one1;
+			Ke->values[j0*numdof+j0]=one1;
+			Ke->values[j1*numdof+i1]=-one1;
+			Ke->values[j1*numdof+j1]=one1;
+		}
+		else if (IsOnBed()){
+			Ke->values[i0*numdof+i0]=one0;
+			Ke->values[i1*numdof+i1]=one0;
+			Ke->values[j0*numdof+i0]=-2*one1;
+			Ke->values[j0*numdof+j0]=2*one1;
+			Ke->values[j1*numdof+i1]=-2*one1;
+			Ke->values[j1*numdof+j1]=2*one1;
+		}
+		else if (IsOnSurface()){
+			Ke->values[j0*numdof+i0]=-one1;
+			Ke->values[j0*numdof+j0]=one1;
+			Ke->values[j1*numdof+i1]=-one1;
+			Ke->values[j1*numdof+j1]=one1;
+		}
+		else{ //node is on two horizontal layers and beams include the values only once, so the have to use half of the connectivity
+			Ke->values[j0*numdof+i0]=-2*one1;
+			Ke->values[j0*numdof+j0]=2*one1;
+			Ke->values[j1*numdof+i1]=-2*one1;
+			Ke->values[j1*numdof+j1]=2*one1;
+		}
+	}
+
+	/*Clean up and return*/
+	return Ke;
+}/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticMacAyeal2d{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticMacAyeal2d(void){
+
+	/*Figure out if this penta is collapsed. If so, then bailout, except if it is at the 
+	  bedrock, in which case we spawn a tria element using the 3 first nodes, and use it to build 
+	  the stiffness matrix. */
+	if (!IsOnBed()) return NULL;
+
+	/*Depth average some fields*/
+	switch(this->material->ObjectEnum()){
+		case MaticeEnum:
+			this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum,MaterialsEnum);
+			break;
+		case MatdamageiceEnum:
+			this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum,MaterialsEnum);
+			this->InputDepthAverageAtBase(MaterialsRheologyZEnum,MaterialsRheologyZbarEnum,MaterialsEnum);
+			break;
+		default:
+			_error_("material "<material->ObjectEnum())<<" not supported");
+	}
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementMatrix* Ke=tria->CreateKMatrixDiagnosticMacAyeal();
+	delete tria->material; delete tria;
+
+	/*Delete averaged fields*/
+	this->material->inputs->DeleteInput(MaterialsRheologyBbarEnum);
+	this->material->inputs->DeleteInput(MaterialsRheologyZbarEnum);
+
+	/*clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticMacAyeal3d{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticMacAyeal3d(void){
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixDiagnosticMacAyeal3dViscous();
+	ElementMatrix* Ke2=CreateKMatrixDiagnosticMacAyeal3dFriction();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticMacAyeal3dViscous{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticMacAyeal3dViscous(void){
+
+	/*Constants*/
+	const int    numdof2d=2*NUMVERTICES2D;
+
+	/*Intermediaries */
+	int         i,j,ig,approximation;
+	IssmDouble  Jdet;
+	IssmDouble  viscosity , oldviscosity, newviscosity, viscosity_overshoot;
+	IssmDouble  epsilon[5],oldepsilon[5];       /* epsilon=[exx,eyy,exy,exz,eyz];*/
+	IssmDouble  epsilons[6];                    //6 for stokes
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	IssmDouble  B[3][numdof2d];
+	IssmDouble  Bprime[3][numdof2d];
+	IssmDouble  D[3][3]= {0.0};                 // material matrix, simple scalar matrix.
+	IssmDouble  D_scalar;
+	IssmDouble  Ke_gg_gaussian[numdof2d][numdof2d];
+	Tria       *tria       = NULL;
+	Penta      *pentabase  = NULL;
+	GaussPenta *gauss      = NULL;
+	GaussTria  *gauss_tria = NULL;
+
+	/*Find penta on bed as this is a macayeal elements: */
+	pentabase=GetBasalElement();
+	tria=pentabase->SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(tria->nodes,NUMVERTICES2D,this->parameters,MacAyealApproximationEnum);
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes,NUMVERTICES);
+	this->parameters->FindParam(&viscosity_overshoot,DiagnosticViscosityOvershootEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+	Input* vxold_input=inputs->GetInput(VxPicardEnum); _assert_(vxold_input);
+	Input* vyold_input=inputs->GetInput(VyPicardEnum); _assert_(vyold_input);
+	Input* vz_input=inputs->GetInput(VzEnum);       _assert_(vz_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	gauss_tria=new GaussTria();
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+		gauss->SynchronizeGaussTria(gauss_tria);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		tria->GetBMacAyeal(&B[0][0], &xyz_list[0][0], gauss_tria);
+		tria->GetBprimeMacAyeal(&Bprime[0][0], &xyz_list[0][0], gauss_tria);
+
+		if(approximation==MacAyealPattynApproximationEnum){
+			this->GetStrainRate3dPattyn(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+			this->GetStrainRate3dPattyn(&oldepsilon[0],&xyz_list[0][0],gauss,vxold_input,vyold_input);
+			material->GetViscosity3d(&viscosity, &epsilon[0]);
+			material->GetViscosity3d(&oldviscosity, &oldepsilon[0]);
+
+			newviscosity=viscosity+viscosity_overshoot*(viscosity-oldviscosity);
+		}
+		else if (approximation==MacAyealStokesApproximationEnum){
+			this->GetStrainRate3d(&epsilons[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+			material->GetViscosity3dStokes(&newviscosity,&epsilons[0]);
+		}
+		else _error_("approximation " << approximation << " (" << EnumToStringx(approximation) << ") not supported yet");
+
+		D_scalar=2*newviscosity*gauss->weight*Jdet;
+		for (i=0;i<3;i++) D[i][i]=D_scalar;
+
+		TripleMultiply( &B[0][0],3,numdof2d,1,
+					&D[0][0],3,3,0,
+					&Bprime[0][0],3,numdof2d,0,
+					&Ke_gg_gaussian[0][0],0);
+
+		for(i=0;ivalues[i*numdof2d+j]+=Ke_gg_gaussian[i][j];
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,tria->nodes,NUMVERTICES2D,XYEnum);
+
+	/*Clean up and return*/
+	delete tria->material;
+	delete tria;
+	delete gauss_tria;
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticMacAyeal3dFriction{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticMacAyeal3dFriction(void){
+
+	/*Initialize Element matrix and return if necessary*/
+	if(IsFloating() || !IsOnBed()) return NULL;
+
+	/*Build a tria element using the 3 nodes of the base of the penta. Then use 
+	 * the tria functionality to build a friction stiffness matrix on these 3
+	 * nodes: */
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementMatrix* Ke=tria->CreateKMatrixDiagnosticMacAyealFriction();
+	delete tria->material; delete tria;
+
+	/*clean-up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticMacAyealPattyn{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticMacAyealPattyn(void){
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixDiagnosticMacAyeal3d();
+	ElementMatrix* Ke2=CreateKMatrixDiagnosticPattyn();
+	ElementMatrix* Ke3=CreateKMatrixCouplingMacAyealPattyn();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2,Ke3);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	delete Ke3;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticMacAyealStokes{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticMacAyealStokes(void){
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixDiagnosticMacAyeal3d();
+	ElementMatrix* Ke2=CreateKMatrixDiagnosticStokes();
+	ElementMatrix* Ke3=CreateKMatrixCouplingMacAyealStokes();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2,Ke3);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	delete Ke3;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticL1L2{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticL1L2(void){
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixDiagnosticL1L2Viscous();
+	ElementMatrix* Ke2=CreateKMatrixDiagnosticL1L2Friction();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticL1L2Viscous{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticL1L2Viscous(void){
+
+	/*Constants*/
+	const int    numdof2d=2*NUMVERTICES2D;
+
+	/*Intermediaries */
+	int         i,j;
+	IssmDouble  Jdet,viscosity;
+	IssmDouble  epsilon[5];       /* epsilon=[exx,eyy,exy,exz,eyz];*/
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	IssmDouble  B[3][numdof2d];
+	IssmDouble  Bprime[3][numdof2d];
+	IssmDouble  Ke_gg_gaussian[numdof2d][numdof2d];
+	IssmDouble  D[3][3]= {0.0};                 // material matrix, simple scalar matrix.
+	Tria       *tria       = NULL;
+	Penta      *pentabase  = NULL;
+	GaussPenta *gauss      = NULL;
+	GaussTria  *gauss_tria = NULL;
+
+	/*Find penta on bed as this is a macayeal elements: */
+	pentabase=GetBasalElement();
+	tria=pentabase->SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(tria->nodes,NUMVERTICES2D,this->parameters,L1L2ApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes,NUMVERTICES);
+	Input* vx_input=inputs->GetInput(VxEnum);        _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);        _assert_(vy_input);
+	Input* surf_input=inputs->GetInput(SurfaceEnum); _assert_(surf_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	gauss_tria=new GaussTria();
+	for(int ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+		gauss->SynchronizeGaussTria(gauss_tria);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		tria->GetBMacAyeal(&B[0][0], &xyz_list[0][0], gauss_tria);
+		tria->GetBprimeMacAyeal(&Bprime[0][0], &xyz_list[0][0], gauss_tria);
+
+		/*Get viscosity for L1L2 model*/
+		GetL1L2Viscosity(&viscosity,&xyz_list[0][0],gauss,vx_input,vy_input,surf_input);
+
+		for(i=0;i<3;i++) D[i][i]=2*viscosity*gauss->weight*Jdet;
+
+		TripleMultiply( &B[0][0],3,numdof2d,1,
+					&D[0][0],3,3,0,
+					&Bprime[0][0],3,numdof2d,0,
+					&Ke_gg_gaussian[0][0],0);
+		for(i=0;ivalues[i*numdof2d+j]+=Ke_gg_gaussian[i][j];
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,tria->nodes,NUMVERTICES2D,XYEnum);
+
+	/*Clean up and return*/
+	delete tria->material;
+	delete tria;
+	delete gauss_tria;
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticL1L2Friction{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticL1L2Friction(void){
+
+	/*Initialize Element matrix and return if necessary*/
+	if(IsFloating() || !IsOnBed()) return NULL;
+
+	/*Build a tria element using the 3 nodes of the base of the penta. Then use 
+	 * the tria functionality to build a friction stiffness matrix on these 3
+	 * nodes: */
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementMatrix* Ke=tria->CreateKMatrixDiagnosticMacAyealFriction();
+	delete tria->material; delete tria;
+
+	/*clean-up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticPattyn{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticPattyn(void){
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixDiagnosticPattynViscous();
+	ElementMatrix* Ke2=CreateKMatrixDiagnosticPattynFriction();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticPattynViscous{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticPattynViscous(void){
+
+	/*Constants*/
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	int        approximation;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     Jdet;
+	IssmDouble     viscosity,oldviscosity,newviscosity,viscosity_overshoot; //viscosity
+	IssmDouble     epsilon[5],oldepsilon[5]; /* epsilon=[exx,eyy,exy,exz,eyz];*/
+	IssmDouble     D_scalar;
+	IssmDouble     D[5][5]={0.0};            // material matrix, simple scalar matrix.
+	IssmDouble     B[5][numdof];
+	IssmDouble     Bprime[5][numdof];
+	Tria*      tria=NULL;
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,PattynApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&viscosity_overshoot,DiagnosticViscosityOvershootEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+	Input* vxold_input=inputs->GetInput(VxPicardEnum); _assert_(vxold_input);
+	Input* vyold_input=inputs->GetInput(VyPicardEnum); _assert_(vyold_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetBPattyn(&B[0][0], &xyz_list[0][0], gauss);
+		GetBprimePattyn(&Bprime[0][0], &xyz_list[0][0], gauss);
+
+		this->GetStrainRate3dPattyn(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		this->GetStrainRate3dPattyn(&oldepsilon[0],&xyz_list[0][0],gauss,vxold_input,vyold_input);
+		material->GetViscosity3d(&viscosity, &epsilon[0]);
+		material->GetViscosity3d(&oldviscosity, &oldepsilon[0]);
+		newviscosity=viscosity+viscosity_overshoot*(viscosity-oldviscosity);
+
+		D_scalar=2*newviscosity*gauss->weight*Jdet;
+		for (i=0;i<5;i++) D[i][i]=D_scalar;
+
+		TripleMultiply( &B[0][0],5,numdof,1,
+					&D[0][0],5,5,0,
+					&Bprime[0][0],5,numdof,0,
+					&Ke->values[0],1);
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticPattynFriction{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticPattynFriction(void){
+
+	/*Constants*/
+	const int numdof   = NDOF2*NUMVERTICES;
+	
+	/*Intermediaries */
+	int       i,j,ig;
+	int       analysis_type;
+	IssmDouble    xyz_list[NUMVERTICES][3];
+	IssmDouble    xyz_list_tria[NUMVERTICES2D][3]={0.0};
+	IssmDouble    slope_magnitude,alpha2,Jdet;
+	IssmDouble    slope[3]={0.0,0.0,0.0};
+	IssmDouble    MAXSLOPE=.06; // 6 %
+	IssmDouble    MOUNTAINKEXPONENT=10;
+	IssmDouble    L[2][numdof];
+	IssmDouble    DL[2][2]={{ 0,0 },{0,0}}; //for basal drag
+	IssmDouble    DL_scalar;
+	Friction  *friction = NULL;
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element matrix and return if necessary*/
+	if(IsFloating() || !IsOnBed()) return NULL;
+
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,PattynApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iFindParam(&analysis_type,AnalysisTypeEnum);
+	Input* surface_input=inputs->GetInput(SurfaceEnum); _assert_(surface_input);
+	Input* vx_input=inputs->GetInput(VxEnum);           _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);           _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);           _assert_(vz_input);
+
+	/*build friction object, used later on: */
+	friction=new Friction("2d",inputs,matpar,analysis_type);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(0,1,2,2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet, &xyz_list_tria[0][0],gauss);
+		GetL(&L[0][0], gauss,NDOF2);
+
+		surface_input->GetInputDerivativeValue(&slope[0],&xyz_list[0][0],gauss);
+		friction->GetAlpha2(&alpha2, gauss,VxEnum,VyEnum,VzEnum); 
+		slope_magnitude=sqrt(pow(slope[0],2)+pow(slope[1],2));
+
+		// If we have a slope > 6% for this element,  it means  we are on a mountain. In this particular case, 
+		//velocity should be = 0. To achieve this result, we set alpha2_list to a very high value: */
+		if (slope_magnitude>MAXSLOPE){
+			alpha2=pow((IssmDouble)10,MOUNTAINKEXPONENT);
+		}
+		
+		DL_scalar=alpha2*gauss->weight*Jdet;
+		for (i=0;i<2;i++) DL[i][i]=DL_scalar;
+		
+		TripleMultiply( &L[0][0],2,numdof,1,
+					&DL[0][0],2,2,0,
+					&L[0][0],2,numdof,0,
+					&Ke->values[0],1);
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticPattynStokes{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticPattynStokes(void){
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixDiagnosticPattyn();
+	ElementMatrix* Ke2=CreateKMatrixDiagnosticStokes();
+	ElementMatrix* Ke3=CreateKMatrixCouplingPattynStokes();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2,Ke3);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	delete Ke3;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticStokes{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticStokes(void){
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixDiagnosticStokesViscous();
+	ElementMatrix* Ke2=CreateKMatrixDiagnosticStokesFriction();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticStokesViscous {{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticStokesViscous(void){
+
+	/*Intermediaries */
+	int        i,j,ig,approximation;
+	IssmDouble     Jdet,viscosity,stokesreconditioning;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     epsilon[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble     B[8][27];
+	IssmDouble     B_prime[8][27];
+	IssmDouble     D_scalar;
+	IssmDouble     D[8][8]={0.0};
+	IssmDouble     Ke_temp[27][27]={0.0}; //for the six nodes and the bubble 
+	GaussPenta *gauss=NULL;
+
+	/*If on water or not Stokes, skip stiffness: */
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(approximation!=StokesApproximationEnum && approximation!=MacAyealStokesApproximationEnum && approximation!=PattynStokesApproximationEnum) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum); _assert_(vz_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetBStokes(&B[0][0],&xyz_list[0][0],gauss); 
+		GetBprimeStokes(&B_prime[0][0],&xyz_list[0][0],gauss); 
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+
+		D_scalar=gauss->weight*Jdet;
+		for (i=0;i<6;i++) D[i][i]=D_scalar*2*viscosity;
+		for (i=6;i<8;i++) D[i][i]=-D_scalar*stokesreconditioning;
+
+		TripleMultiply( &B[0][0],8,27,1,
+					&D[0][0],8,8,0,
+					&B_prime[0][0],8,27,0,
+					&Ke_temp[0][0],1);
+	}
+
+	/*Condensation*/
+	ReduceMatrixStokes(Ke->values, &Ke_temp[0][0]);
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticStokesFriction{{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticStokesFriction(void){
+
+	/*Constants*/
+	const int numdof=NUMVERTICES*NDOF4;
+	const int numdof2d=NUMVERTICES2D*NDOF4;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	int        analysis_type,approximation;
+	IssmDouble     alpha2,Jdet2d;
+	IssmDouble     stokesreconditioning,viscosity;
+	IssmDouble     epsilon[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble	  xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble     LStokes[2][numdof2d];
+	IssmDouble     DLStokes[2][2]={0.0};
+	IssmDouble     Ke_drag_gaussian[numdof2d][numdof2d];
+	Friction*  friction=NULL;
+	GaussPenta *gauss=NULL;
+
+	/*If on water or not Stokes, skip stiffness: */
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(IsFloating() || !IsOnBed() || (approximation!=StokesApproximationEnum && approximation!=MacAyealStokesApproximationEnum &&  approximation!=PattynStokesApproximationEnum)) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+	parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum); _assert_(vz_input);
+	for(i=0;ibegin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0],gauss);
+		GetLStokes(&LStokes[0][0], gauss);
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+
+		friction->GetAlpha2(&alpha2, gauss,VxEnum,VyEnum,VzEnum);
+
+		DLStokes[0][0] = +alpha2*gauss->weight*Jdet2d; //taub_x = -alpha2 vx
+		DLStokes[1][1] = +alpha2*gauss->weight*Jdet2d; //taub_y = -alpha2 vy
+
+		TripleMultiply( &LStokes[0][0],2,numdof2d,1,
+					&DLStokes[0][0],2,2,0,
+					&LStokes[0][0],2,numdof2d,0,
+					&Ke_drag_gaussian[0][0],0);
+
+		for(i=0;ivalues[i*numdof+j]+=Ke_drag_gaussian[i][j];
+	}
+
+	/*DO NOT Transform Coordinate System: this stiffness matrix is already expressed in tangential coordinates*/
+	//TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYZPEnum);
+	
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticVert {{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticVert(void){
+	
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixDiagnosticVertVolume();
+	ElementMatrix* Ke2=CreateKMatrixDiagnosticVertSurface();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticVertVolume {{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticVertVolume(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int         i,j,ig;
+	IssmDouble      Jdet;
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      B[NDOF1][NUMVERTICES];
+	IssmDouble      Bprime[NDOF1][NUMVERTICES];
+	IssmDouble      DL_scalar;
+	GaussPenta  *gauss=NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(2,2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetBVert(&B[0][0], &xyz_list[0][0], gauss);
+		GetBprimeVert(&Bprime[0][0], &xyz_list[0][0], gauss);
+
+		DL_scalar=gauss->weight*Jdet;
+
+		TripleMultiply( &B[0][0],1,NUMVERTICES,1,
+					&DL_scalar,1,1,0,
+					&Bprime[0][0],1,NUMVERTICES,0,
+					&Ke->values[0],1);
+	} 
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateKMatrixDiagnosticVertSurface {{{*/
+ElementMatrix* Penta::CreateKMatrixDiagnosticVertSurface(void){
+
+	if (!IsOnSurface()) return NULL;
+
+	/*Constants*/
+	const int numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int       i,j,ig;
+	IssmDouble    xyz_list[NUMVERTICES][3];
+	IssmDouble    xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble    surface_normal[3];
+	IssmDouble    Jdet2d,DL_scalar;
+	IssmDouble    basis[NUMVERTICES];
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;ibegin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0],gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+
+		DL_scalar= - gauss->weight*Jdet2d*surface_normal[2]; 
+
+		TripleMultiply( basis,1,numdof,1,
+					&DL_scalar,1,1,0,
+					basis,1,numdof,0,
+					&Ke->values[0],1);
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorCouplingMacAyealStokes {{{*/
+ElementVector* Penta::CreatePVectorCouplingMacAyealStokes(void){
+
+	/*compute all load vectors for this element*/
+	ElementVector* pe1=CreatePVectorCouplingMacAyealStokesViscous();
+	ElementVector* pe2=CreatePVectorCouplingMacAyealStokesFriction();
+	ElementVector* pe =new ElementVector(pe1,pe2);
+
+	/*clean-up and return*/
+	delete pe1;
+	delete pe2;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorCouplingMacAyealStokesViscous {{{*/
+ElementVector* Penta::CreatePVectorCouplingMacAyealStokesViscous(void){
+
+	/*Constants*/
+	const int   numdof=NUMVERTICES*NDOF4;
+
+	/*Intermediaries */
+	int         i,j,ig;
+	int         approximation;
+	IssmDouble      viscosity,Jdet;
+	IssmDouble      stokesreconditioning;
+	IssmDouble      epsilon[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble      dw[3];
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      basis[6]; //for the six nodes of the penta
+	IssmDouble      dbasis[3][6]; //for the six nodes of the penta
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element vector and return if necessary*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(approximation!=MacAyealStokesApproximationEnum) return NULL;
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);               _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);               _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);               _assert_(vz_input);
+	Input* vzmacayeal_input=inputs->GetInput(VzMacAyealEnum);   _assert_(vzmacayeal_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+		GetNodalFunctionsP1Derivatives(&dbasis[0][0],&xyz_list[0][0], gauss);
+
+		vzmacayeal_input->GetInputDerivativeValue(&dw[0],&xyz_list[0][0],gauss);
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+
+		for(i=0;ivalues[i*NDOF4+0]+=-Jdet*gauss->weight*viscosity*dw[0]*dbasis[2][i];
+			pe->values[i*NDOF4+1]+=-Jdet*gauss->weight*viscosity*dw[1]*dbasis[2][i];
+			pe->values[i*NDOF4+2]+=-Jdet*gauss->weight*viscosity*(dw[0]*dbasis[0][i]+dw[1]*dbasis[1][i]+2*dw[2]*dbasis[2][i]);
+			pe->values[i*NDOF4+3]+=Jdet*gauss->weight*stokesreconditioning*dw[2]*basis[i];
+		}
+	}
+
+	/*Transform coordinate system*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorCouplingMacAyealStokesFriction{{{*/
+ElementVector* Penta::CreatePVectorCouplingMacAyealStokesFriction(void){
+
+	/*Constants*/
+	const int numdof=NUMVERTICES*NDOF4;
+
+	/*Intermediaries*/
+	int         i,j,ig;
+	int         approximation,analysis_type;
+	IssmDouble      Jdet,Jdet2d;
+	IssmDouble      stokesreconditioning;
+	IssmDouble	   bed_normal[3];
+	IssmDouble      epsilon[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble      viscosity, w, alpha2_gauss;
+	IssmDouble      dw[3];
+	IssmDouble	   xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      basis[6]; //for the six nodes of the penta
+	Tria*       tria=NULL;
+	Friction*   friction=NULL;
+	GaussPenta  *gauss=NULL;
+
+	/*Initialize Element vector and return if necessary*/
+	if(!IsOnBed() || IsFloating()) return NULL;
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(approximation!=MacAyealStokesApproximationEnum) return NULL;
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);               _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);               _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);               _assert_(vz_input);
+	Input* vzmacayeal_input=inputs->GetInput(VzMacAyealEnum);   _assert_(vzmacayeal_input);
+
+	for(i=0;ibegin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0], gauss);
+		GetNodalFunctionsP1(basis, gauss);
+
+		vzmacayeal_input->GetInputValue(&w, gauss);
+		vzmacayeal_input->GetInputDerivativeValue(&dw[0],&xyz_list[0][0],gauss);
+
+		BedNormal(&bed_normal[0],xyz_list_tria);
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+		friction->GetAlpha2(&alpha2_gauss, gauss,VxEnum,VyEnum,VzEnum);
+
+		for(i=0;ivalues[i*NDOF4+0]+=Jdet2d*gauss->weight*(alpha2_gauss*w*bed_normal[0]*bed_normal[2]+2*viscosity*dw[2]*bed_normal[0])*basis[i];
+			pe->values[i*NDOF4+1]+=Jdet2d*gauss->weight*(alpha2_gauss*w*bed_normal[1]*bed_normal[2]+2*viscosity*dw[2]*bed_normal[1])*basis[i];
+			pe->values[i*NDOF4+2]+=Jdet2d*gauss->weight*2*viscosity*(dw[0]*bed_normal[0]+dw[1]*bed_normal[1]+dw[2]*bed_normal[2])*basis[i];
+		}
+	}
+
+	/*Transform coordinate system*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorCouplingPattynStokes {{{*/
+ElementVector* Penta::CreatePVectorCouplingPattynStokes(void){
+
+	/*compute all load vectors for this element*/
+	ElementVector* pe1=CreatePVectorCouplingPattynStokesViscous();
+	ElementVector* pe2=CreatePVectorCouplingPattynStokesFriction();
+	ElementVector* pe =new ElementVector(pe1,pe2);
+
+	/*clean-up and return*/
+	delete pe1;
+	delete pe2;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorCouplingPattynStokesViscous {{{*/
+ElementVector* Penta::CreatePVectorCouplingPattynStokesViscous(void){
+
+	/*Constants*/
+	const int   numdof=NUMVERTICES*NDOF4;
+
+	/*Intermediaries */
+	int         i,j,ig;
+	int         approximation;
+	IssmDouble      viscosity,Jdet;
+	IssmDouble      stokesreconditioning;
+	IssmDouble      epsilon[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble      dw[3];
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      basis[6]; //for the six nodes of the penta
+	IssmDouble      dbasis[3][6]; //for the six nodes of the penta
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element vector and return if necessary*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(approximation!=PattynStokesApproximationEnum) return NULL;
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);               _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);               _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);               _assert_(vz_input);
+	Input* vzpattyn_input=inputs->GetInput(VzPattynEnum);   _assert_(vzpattyn_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+		GetNodalFunctionsP1Derivatives(&dbasis[0][0],&xyz_list[0][0], gauss);
+
+		vzpattyn_input->GetInputDerivativeValue(&dw[0],&xyz_list[0][0],gauss);
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+
+		for(i=0;ivalues[i*NDOF4+0]+=-Jdet*gauss->weight*viscosity*dw[0]*dbasis[2][i];
+			pe->values[i*NDOF4+1]+=-Jdet*gauss->weight*viscosity*dw[1]*dbasis[2][i];
+			pe->values[i*NDOF4+2]+=-Jdet*gauss->weight*viscosity*(dw[0]*dbasis[0][i]+dw[1]*dbasis[1][i]+2*dw[2]*dbasis[2][i]);
+			pe->values[i*NDOF4+3]+=Jdet*gauss->weight*stokesreconditioning*dw[2]*basis[i];
+		}
+	}
+
+	/*Transform coordinate system*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorCouplingPattynStokesFriction{{{*/
+ElementVector* Penta::CreatePVectorCouplingPattynStokesFriction(void){
+
+	/*Constants*/
+	const int numdof=NUMVERTICES*NDOF4;
+
+	/*Intermediaries*/
+	int         i,j,ig;
+	int         approximation,analysis_type;
+	IssmDouble      Jdet,Jdet2d;
+	IssmDouble      stokesreconditioning;
+	IssmDouble	   bed_normal[3];
+	IssmDouble      epsilon[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble      viscosity, w, alpha2_gauss;
+	IssmDouble      dw[3];
+	IssmDouble	   xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      basis[6]; //for the six nodes of the penta
+	Tria*       tria=NULL;
+	Friction*   friction=NULL;
+	GaussPenta  *gauss=NULL;
+
+	/*Initialize Element vector and return if necessary*/
+	if(!IsOnBed() || IsFloating()) return NULL;
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(approximation!=PattynStokesApproximationEnum) return NULL;
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);               _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);               _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);               _assert_(vz_input);
+	Input* vzpattyn_input=inputs->GetInput(VzPattynEnum);   _assert_(vzpattyn_input);
+
+	for(i=0;ibegin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0], gauss);
+		GetNodalFunctionsP1(basis, gauss);
+
+		vzpattyn_input->GetInputValue(&w, gauss);
+		vzpattyn_input->GetInputDerivativeValue(&dw[0],&xyz_list[0][0],gauss);
+
+		BedNormal(&bed_normal[0],xyz_list_tria);
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+		friction->GetAlpha2(&alpha2_gauss, gauss,VxEnum,VyEnum,VzEnum);
+
+		for(i=0;ivalues[i*NDOF4+0]+=Jdet2d*gauss->weight*(alpha2_gauss*w*bed_normal[0]*bed_normal[2]+2*viscosity*dw[2]*bed_normal[0])*basis[i];
+			pe->values[i*NDOF4+1]+=Jdet2d*gauss->weight*(alpha2_gauss*w*bed_normal[1]*bed_normal[2]+2*viscosity*dw[2]*bed_normal[1])*basis[i];
+			pe->values[i*NDOF4+2]+=Jdet2d*gauss->weight*2*viscosity*(dw[0]*bed_normal[0]+dw[1]*bed_normal[1]+dw[2]*bed_normal[2])*basis[i];
+		}
+	}
+
+	/*Transform coordinate system*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticHoriz{{{*/
+ElementVector* Penta::CreatePVectorDiagnosticHoriz(void){
+
+	int approximation;
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	switch(approximation){
+		case MacAyealApproximationEnum:
+			return CreatePVectorDiagnosticMacAyeal();
+		case PattynApproximationEnum:
+			return CreatePVectorDiagnosticPattyn();
+		case L1L2ApproximationEnum:
+			return CreatePVectorDiagnosticL1L2();
+		case HutterApproximationEnum:
+			return NULL;
+		case NoneApproximationEnum:
+			return NULL;
+		case StokesApproximationEnum:
+			return CreatePVectorDiagnosticStokes();
+		case MacAyealPattynApproximationEnum:
+			return CreatePVectorDiagnosticMacAyealPattyn();
+		case MacAyealStokesApproximationEnum:
+			return CreatePVectorDiagnosticMacAyealStokes();
+		case PattynStokesApproximationEnum:
+			return CreatePVectorDiagnosticPattynStokes();
+		default:
+			_error_("Approximation " << EnumToStringx(approximation) << " not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticMacAyealPattyn{{{*/
+ElementVector* Penta::CreatePVectorDiagnosticMacAyealPattyn(void){
+
+	/*compute all load vectors for this element*/
+	ElementVector* pe1=CreatePVectorDiagnosticMacAyeal();
+	ElementVector* pe2=CreatePVectorDiagnosticPattyn();
+	ElementVector* pe =new ElementVector(pe1,pe2);
+
+	/*clean-up and return*/
+	delete pe1;
+	delete pe2;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticMacAyealStokes{{{*/
+ElementVector* Penta::CreatePVectorDiagnosticMacAyealStokes(void){
+
+	/*compute all load vectors for this element*/
+	ElementVector* pe1=CreatePVectorDiagnosticMacAyeal();
+	ElementVector* pe2=CreatePVectorDiagnosticStokes();
+	ElementVector* pe3=CreatePVectorCouplingMacAyealStokes();
+	ElementVector* pe =new ElementVector(pe1,pe2,pe3);
+
+	/*clean-up and return*/
+	delete pe1;
+	delete pe2;
+	delete pe3;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticPattynStokes{{{*/
+ElementVector* Penta::CreatePVectorDiagnosticPattynStokes(void){
+
+	/*compute all load vectors for this element*/
+	ElementVector* pe1=CreatePVectorDiagnosticPattyn();
+	ElementVector* pe2=CreatePVectorDiagnosticStokes();
+	ElementVector* pe3=CreatePVectorCouplingPattynStokes();
+	ElementVector* pe =new ElementVector(pe1,pe2,pe3);
+
+	/*clean-up and return*/
+	delete pe1;
+	delete pe2;
+	delete pe3;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticHutter{{{*/
+ElementVector* Penta::CreatePVectorDiagnosticHutter(void){
+
+	/*Constants*/
+	const int numdofs=NDOF2*NUMVERTICES;
+
+	/*Intermediaries*/
+	int          i,j,k,ig;
+	int          node0,node1;
+	int          connectivity[2];
+	IssmDouble       Jdet;
+	IssmDouble       xyz_list[NUMVERTICES][3];
+	IssmDouble       xyz_list_segment[2][3];
+	IssmDouble       z_list[NUMVERTICES];
+	IssmDouble       z_segment[2],slope[2];
+	IssmDouble       slope2,constant_part;
+	IssmDouble       rho_ice,gravity,n,B;
+	IssmDouble       ub,vb,z_g,surface,thickness;
+	GaussPenta*  gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	rho_ice=matpar->GetRhoIce();
+	gravity=matpar->GetG();
+	n=material->GetN();
+	B=material->GetB();
+	Input* thickness_input=inputs->GetInput(ThicknessEnum);  _assert_(thickness_input);
+	Input* surface_input=inputs->GetInput(SurfaceEnum);      _assert_(surface_input);
+	Input* slopex_input=inputs->GetInput(SurfaceSlopeXEnum); _assert_(slopex_input);
+	Input* slopey_input=inputs->GetInput(SurfaceSlopeYEnum); _assert_(slopey_input);
+	for(i=0;iGetConnectivity();
+		connectivity[1]=nodes[node1]->GetConnectivity();
+
+		/*Loop on the Gauss points: */
+		gauss=new GaussPenta(node0,node1,3);
+		for(ig=gauss->begin();igend();ig++){
+			gauss->GaussPoint(ig);
+
+			slopex_input->GetInputValue(&slope[0],gauss);
+			slopey_input->GetInputValue(&slope[1],gauss);
+			surface_input->GetInputValue(&surface,gauss);
+			thickness_input->GetInputValue(&thickness,gauss);
+
+			slope2=pow(slope[0],2)+pow(slope[1],2);
+			constant_part=-2*pow(rho_ice*gravity,n)*pow(slope2,((n-1)/2));
+
+			PentaRef::GetInputValue(&z_g,&z_list[0],gauss);
+			GetSegmentJacobianDeterminant(&Jdet,&xyz_list_segment[0][0],gauss);
+
+			if (IsOnSurface()){
+				for(j=0;jvalues[2*node1+j]+=constant_part*pow((surface-z_g)/B,n)*slope[j]*Jdet*gauss->weight/(IssmDouble)connectivity[1];
+			}
+			else{//connectivity is too large, should take only half on it
+				for(j=0;jvalues[2*node1+j]+=constant_part*pow((surface-z_g)/B,n)*slope[j]*Jdet*gauss->weight*2/(IssmDouble)connectivity[1];
+			}
+		}
+		delete gauss;
+
+		//Deal with lower surface
+		if (IsOnBed()){
+			constant_part=-1.58*pow((IssmDouble)10.0,-(IssmDouble)10.0)*rho_ice*gravity*thickness;
+			ub=constant_part*slope[0];
+			vb=constant_part*slope[1];
+
+			pe->values[2*node0]+=ub/(IssmDouble)connectivity[0];
+			pe->values[2*node0+1]+=vb/(IssmDouble)connectivity[0];
+		}
+	}
+
+	/*Clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticMacAyeal{{{*/
+ElementVector* Penta::CreatePVectorDiagnosticMacAyeal(void){
+
+	if (!IsOnBed()) return NULL;
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementVector* pe=tria->CreatePVectorDiagnosticMacAyeal();
+	delete tria->material; delete tria;
+
+	/*Clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticL1L2{{{*/
+ElementVector* Penta::CreatePVectorDiagnosticL1L2(void){
+
+	if (!IsOnBed()) return NULL;
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementVector* pe=tria->CreatePVectorDiagnosticMacAyeal();
+	delete tria->material; delete tria;
+
+	/*Clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticPattyn{{{*/
+ElementVector* Penta::CreatePVectorDiagnosticPattyn(void){
+
+	/*Constants*/
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries*/
+	int         i,j,ig;
+	IssmDouble      Jdet;
+	IssmDouble      slope[3]; //do not put 2! this goes into GetInputDerivativeValue, which addresses slope[3] also!
+	IssmDouble      driving_stress_baseline,thickness;
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      basis[6];
+	GaussPenta  *gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,PattynApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+	Input* surface_input=inputs->GetInput(SurfaceEnum);     _assert_(surface_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(2,3);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1(basis, gauss);
+
+		thickness_input->GetInputValue(&thickness, gauss);
+		surface_input->GetInputDerivativeValue(&slope[0],&xyz_list[0][0],gauss);
+
+		driving_stress_baseline=matpar->GetRhoIce()*matpar->GetG();
+
+		for(i=0;ivalues[i*NDOF2+j]+= -driving_stress_baseline*slope[j]*Jdet*gauss->weight*basis[i];
+	}
+
+	/*Transform coordinate system*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticStokes {{{*/
+ElementVector* Penta::CreatePVectorDiagnosticStokes(void){
+
+	/*compute all load vectors for this element*/
+	ElementVector* pe1=CreatePVectorDiagnosticStokesViscous();
+	ElementVector* pe2=CreatePVectorDiagnosticStokesShelf();
+	ElementVector* pe =new ElementVector(pe1,pe2);
+
+	/*clean-up and return*/
+	delete pe1;
+	delete pe2;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticStokesViscous {{{*/
+ElementVector* Penta::CreatePVectorDiagnosticStokesViscous(void){
+
+	/*Constants*/
+	const int numdofbubble=NDOF4*NUMVERTICES+NDOF3*1;
+
+	/*Intermediaries*/
+	int        i,j,ig;
+	int        approximation;
+	IssmDouble     Jdet,viscosity;
+	IssmDouble     gravity,rho_ice,stokesreconditioning;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     epsilon[6]; /* epsilon=[exx,eyy,ezz,exy,exz,eyz];*/
+	IssmDouble     l1l7[7]; //for the six nodes and the bubble 
+	IssmDouble     B[8][numdofbubble];
+	IssmDouble     B_prime[8][numdofbubble];
+	IssmDouble     B_prime_bubble[8][3];
+	IssmDouble     D[8][8]={0.0};
+	IssmDouble     D_scalar;
+	IssmDouble     Pe_gaussian[numdofbubble]={0.0}; //for the six nodes and the bubble 
+	IssmDouble     Ke_temp[numdofbubble][3]={0.0}; //for the six nodes and the bubble 
+	IssmDouble     Ke_gaussian[numdofbubble][3];
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element vector and return if necessary*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(approximation!=StokesApproximationEnum && approximation!=MacAyealStokesApproximationEnum && approximation!=PattynStokesApproximationEnum) return NULL;
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	rho_ice=matpar->GetRhoIce();
+	gravity=matpar->GetG();
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* vx_input=inputs->GetInput(VxEnum);   _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);   _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);   _assert_(vz_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetBStokes(&B[0][0],&xyz_list[0][0],gauss); 
+		GetBprimeStokes(&B_prime[0][0],&xyz_list[0][0], gauss); 
+		GetNodalFunctionsMINI(&l1l7[0], gauss);
+
+		this->GetStrainRate3d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input,vz_input);
+		material->GetViscosity3dStokes(&viscosity,&epsilon[0]);
+
+		for(i=0;iweight*l1l7[i];
+		}
+
+		/*Get bubble part of Bprime */
+		for(i=0;i<8;i++) for(j=0;j<3;j++) B_prime_bubble[i][j]=B_prime[i][j+24];
+
+		D_scalar=gauss->weight*Jdet;
+		for (i=0;i<6;i++) D[i][i]=D_scalar*2*viscosity;
+		for (i=6;i<8;i++) D[i][i]=-D_scalar*stokesreconditioning;
+
+		TripleMultiply(&B[0][0],8,numdofbubble,1,
+					&D[0][0],8,8,0,
+					&B_prime_bubble[0][0],8,3,0,
+					&Ke_temp[0][0],1);
+	}
+
+	/*Condensation*/
+	ReduceVectorStokes(pe->values, &Ke_temp[0][0], &Pe_gaussian[0]);
+
+	/*Transform coordinate system*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticStokesShelf{{{*/
+ElementVector* Penta::CreatePVectorDiagnosticStokesShelf(void){
+
+	/*Intermediaries*/
+	int         i,j,ig;
+	int         approximation,shelf_dampening;
+	IssmDouble      gravity,rho_water,bed,water_pressure;
+	IssmDouble      damper,normal_vel,vx,vy,vz,dt;
+	IssmDouble		xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble		bed_normal[3];
+	IssmDouble      dz[3];
+	IssmDouble      basis[6]; //for the six nodes of the penta
+	IssmDouble      Jdet2d;
+	GaussPenta  *gauss=NULL;
+
+	/*Initialize Element vector and return if necessary*/
+	if(!IsOnBed() || !IsFloating()) return NULL;
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	this->parameters->FindParam(&shelf_dampening,DiagnosticShelfDampeningEnum);
+	if(approximation!=StokesApproximationEnum && approximation!=MacAyealStokesApproximationEnum && approximation!=PattynStokesApproximationEnum) return NULL;
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	rho_water=matpar->GetRhoWater();
+	gravity=matpar->GetG();
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* bed_input=inputs->GetInput(BedEnum); _assert_(bed_input);
+	Input* vx_input=inputs->GetInput(VxEnum);   _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);   _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);   _assert_(vz_input);
+
+	for(i=0;ibegin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0], gauss);
+		GetNodalFunctionsP1(basis, gauss);
+
+		BedNormal(&bed_normal[0],xyz_list_tria);
+		bed_input->GetInputValue(&bed, gauss);
+		if(shelf_dampening){ //add dampening to avoid too high vertical velocities when not in hydrostatic equilibrium
+			bed_input->GetInputDerivativeValue(&dz[0],&xyz_list[0][0],gauss);
+			vx_input->GetInputValue(&vx, gauss);
+			vy_input->GetInputValue(&vy, gauss);
+			vz_input->GetInputValue(&vz, gauss);
+			dt=0;
+			normal_vel=bed_normal[0]*vx+bed_normal[1]*vy+bed_normal[2]*vz;
+			damper=gravity*rho_water*pow(1+pow(dz[0],2)+pow(dz[1],2),0.5)*normal_vel*dt;
+		}
+		else damper=0;
+		water_pressure=gravity*rho_water*bed;
+
+		for(i=0;ivalues[i*NDOF4+j]+=(water_pressure+damper)*gauss->weight*Jdet2d*basis[i]*bed_normal[j];
+	}
+
+	/*Transform coordinate system*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticVert {{{*/
+ElementVector* Penta::CreatePVectorDiagnosticVert(void){
+
+	/*compute all load vectors for this element*/
+	ElementVector* pe1=CreatePVectorDiagnosticVertVolume();
+	ElementVector* pe2=CreatePVectorDiagnosticVertBase();
+	ElementVector* pe =new ElementVector(pe1,pe2);
+
+	/*clean-up and return*/
+	delete pe1;
+	delete pe2;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticVertVolume {{{*/
+ElementVector* Penta::CreatePVectorDiagnosticVertVolume(void){
+
+	/*Constants*/
+	const int  numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries*/
+	int        i,ig;
+	int        approximation;
+	IssmDouble     Jdet;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     dudx,dvdy,dwdz;
+	IssmDouble     du[3],dv[3],dw[3];
+	IssmDouble     basis[6];
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+	Input* vzstokes_input=NULL;
+	if(approximation==PattynStokesApproximationEnum || approximation==MacAyealStokesApproximationEnum){
+		vzstokes_input=inputs->GetInput(VzStokesEnum); _assert_(vzstokes_input);
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(2,2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1(basis, gauss);
+
+		vx_input->GetInputDerivativeValue(&du[0],&xyz_list[0][0],gauss);
+		vy_input->GetInputDerivativeValue(&dv[0],&xyz_list[0][0],gauss);
+		if(approximation==PattynStokesApproximationEnum || approximation==MacAyealStokesApproximationEnum){
+			vzstokes_input->GetInputDerivativeValue(&dw[0],&xyz_list[0][0],gauss);
+			dwdz=dw[2];
+		}
+		else dwdz=0;
+		dudx=du[0];
+		dvdy=dv[1];
+
+		for (i=0;ivalues[i] += (dudx+dvdy+dwdz)*Jdet*gauss->weight*basis[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorDiagnosticVertBase {{{*/
+ElementVector* Penta::CreatePVectorDiagnosticVertBase(void){
+
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	int        approximation;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     xyz_list_tria[NUMVERTICES2D][3];
+	IssmDouble     Jdet2d;
+	IssmDouble     vx,vy,vz,dbdx,dbdy,basalmeltingvalue;
+	IssmDouble     slope[3];
+	IssmDouble     basis[NUMVERTICES];
+	GaussPenta* gauss=NULL;
+
+	if (!IsOnBed()) return NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	for(i=0;iGetInputValue(&approximation,ApproximationEnum);
+	Input* bed_input=inputs->GetInput(BedEnum);                                _assert_(bed_input);
+	Input* basal_melting_input=inputs->GetInput(BasalforcingsMeltingRateEnum); _assert_(basal_melting_input);
+	Input* vx_input=inputs->GetInput(VxEnum);                                  _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                                  _assert_(vy_input);
+	Input* vzstokes_input=NULL;
+	if(approximation==PattynStokesApproximationEnum || approximation==MacAyealStokesApproximationEnum){
+		vzstokes_input=inputs->GetInput(VzStokesEnum);       _assert_(vzstokes_input);
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(0,1,2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		basal_melting_input->GetInputValue(&basalmeltingvalue, gauss);
+		bed_input->GetInputDerivativeValue(&slope[0],&xyz_list[0][0],gauss);
+		vx_input->GetInputValue(&vx, gauss);
+		vy_input->GetInputValue(&vy, gauss);
+		if(approximation==PattynStokesApproximationEnum || approximation==MacAyealStokesApproximationEnum){
+			vzstokes_input->GetInputValue(&vz, gauss);
+		}
+		else vz=0;
+
+		dbdx=slope[0];
+		dbdy=slope[1];
+
+		GetTriaJacobianDeterminant(&Jdet2d, &xyz_list_tria[0][0],gauss);
+		GetNodalFunctionsP1(&basis[0], gauss);
+
+		for(i=0;ivalues[i]+=-Jdet2d*gauss->weight*(vx*dbdx+vy*dbdy-vz-basalmeltingvalue)*basis[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateJacobianDiagnosticHoriz{{{*/
+ElementMatrix* Penta::CreateJacobianDiagnosticHoriz(void){
+
+	int approximation;
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	switch(approximation){
+		case MacAyealApproximationEnum:
+			return CreateJacobianDiagnosticMacayeal2d();
+		case PattynApproximationEnum:
+			return CreateJacobianDiagnosticPattyn();
+		case StokesApproximationEnum:
+			return CreateJacobianDiagnosticStokes();
+		case NoneApproximationEnum:
+			return NULL;
+		default:
+			_error_("Approximation " << EnumToStringx(approximation) << " not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::CreateJacobianDiagnosticMacayeal2d{{{*/
+ElementMatrix* Penta::CreateJacobianDiagnosticMacayeal2d(void){
+
+	/*Figure out if this penta is collapsed. If so, then bailout, except if it is at the 
+	  bedrock, in which case we spawn a tria element using the 3 first nodes, and use it to build 
+	  the stiffness matrix. */
+	if (!IsOnBed()) return NULL;
+
+	/*Depth average some fields*/
+	switch(this->material->ObjectEnum()){
+		case MaticeEnum:
+			this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum,MaterialsEnum);
+			break;
+		case MatdamageiceEnum:
+			this->InputDepthAverageAtBase(MaterialsRheologyBEnum,MaterialsRheologyBbarEnum,MaterialsEnum);
+			this->InputDepthAverageAtBase(MaterialsRheologyZEnum,MaterialsRheologyZbarEnum,MaterialsEnum);
+			break;
+		default:
+			_error_("material "<material->ObjectEnum())<<" not supported");
+	}
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementMatrix* Ke=tria->CreateJacobianDiagnosticMacayeal();
+	delete tria->material; delete tria;
+
+	/*Delete averaged inputs*/
+	this->material->inputs->DeleteInput(MaterialsRheologyBbarEnum);
+	this->material->inputs->DeleteInput(MaterialsRheologyZbarEnum);
+
+	/*clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateJacobianDiagnosticPattyn{{{*/
+ElementMatrix* Penta::CreateJacobianDiagnosticPattyn(void){
+
+	/*Constants*/
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     Jdet;
+	IssmDouble     eps1dotdphii,eps1dotdphij;
+	IssmDouble     eps2dotdphii,eps2dotdphij;
+	IssmDouble     mu_prime;
+	IssmDouble     epsilon[5]; /* epsilon=[exx,eyy,exy,exz,eyz];*/
+	IssmDouble     eps1[3],eps2[3];
+	IssmDouble     phi[NUMVERTICES];
+	IssmDouble     dphi[3][NUMVERTICES];
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Jacobian with regular Pattyn (first part of the Gateau derivative)*/
+	ElementMatrix* Ke=CreateKMatrixDiagnosticPattyn();
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1Derivatives(&dphi[0][0],&xyz_list[0][0],gauss);
+
+		this->GetStrainRate3dPattyn(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		material->GetViscosityDerivativeEpsSquare(&mu_prime,&epsilon[0]);
+		eps1[0]=2*epsilon[0]+epsilon[1];   eps2[0]=epsilon[2];
+		eps1[1]=epsilon[2];                eps2[1]=epsilon[0]+2*epsilon[1];
+		eps1[2]=epsilon[3];                eps2[2]=epsilon[4];
+
+		for(i=0;i<6;i++){
+			for(j=0;j<6;j++){
+				eps1dotdphii=eps1[0]*dphi[0][i]+eps1[1]*dphi[1][i]+eps1[2]*dphi[2][i];
+				eps1dotdphij=eps1[0]*dphi[0][j]+eps1[1]*dphi[1][j]+eps1[2]*dphi[2][j];
+				eps2dotdphii=eps2[0]*dphi[0][i]+eps2[1]*dphi[1][i]+eps2[2]*dphi[2][i];
+				eps2dotdphij=eps2[0]*dphi[0][j]+eps2[1]*dphi[1][j]+eps2[2]*dphi[2][j];
+
+				Ke->values[12*(2*i+0)+2*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps1dotdphii;
+				Ke->values[12*(2*i+0)+2*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps1dotdphii;
+				Ke->values[12*(2*i+1)+2*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps2dotdphii;
+				Ke->values[12*(2*i+1)+2*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps2dotdphii;
+			}
+		}
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreateJacobianDiagnosticStokes{{{*/
+ElementMatrix* Penta::CreateJacobianDiagnosticStokes(void){
+
+	/*Constants*/
+	const int    numdof=NDOF4*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     Jdet;
+	IssmDouble     eps1dotdphii,eps1dotdphij;
+	IssmDouble     eps2dotdphii,eps2dotdphij;
+	IssmDouble     eps3dotdphii,eps3dotdphij;
+	IssmDouble     mu_prime;
+	IssmDouble     epsilon[5]; /* epsilon=[exx,eyy,exy,exz,eyz];*/
+	IssmDouble     eps1[3],eps2[3],eps3[3];
+	IssmDouble     phi[NUMVERTICES];
+	IssmDouble     dphi[3][NUMVERTICES];
+	GaussPenta *gauss=NULL;
+
+	/*Initialize Jacobian with regular Stokes (first part of the Gateau derivative)*/
+	ElementMatrix* Ke=CreateKMatrixDiagnosticStokes();
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);       _assert_(vz_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussPenta(5,5);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsP1Derivatives(&dphi[0][0],&xyz_list[0][0],gauss);
+
+		this->GetStrainRate3dPattyn(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		material->GetViscosityDerivativeEpsSquare(&mu_prime,&epsilon[0]);
+		eps1[0]=epsilon[0];   eps2[0]=epsilon[2];   eps3[0]=epsilon[3];
+		eps1[1]=epsilon[2];   eps2[1]=epsilon[1];   eps3[1]=epsilon[4];
+		eps1[2]=epsilon[3];   eps2[2]=epsilon[4];   eps3[2]= -epsilon[0] -epsilon[1];
+
+		for(i=0;i<6;i++){
+			for(j=0;j<6;j++){
+				eps1dotdphii=eps1[0]*dphi[0][i]+eps1[1]*dphi[1][i]+eps1[2]*dphi[2][i];
+				eps1dotdphij=eps1[0]*dphi[0][j]+eps1[1]*dphi[1][j]+eps1[2]*dphi[2][j];
+				eps2dotdphii=eps2[0]*dphi[0][i]+eps2[1]*dphi[1][i]+eps2[2]*dphi[2][i];
+				eps2dotdphij=eps2[0]*dphi[0][j]+eps2[1]*dphi[1][j]+eps2[2]*dphi[2][j];
+				eps3dotdphii=eps3[0]*dphi[0][i]+eps3[1]*dphi[1][i]+eps3[2]*dphi[2][i];
+				eps3dotdphij=eps3[0]*dphi[0][j]+eps3[1]*dphi[1][j]+eps3[2]*dphi[2][j];
+
+				Ke->values[numdof*(4*i+0)+4*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps1dotdphii;
+				Ke->values[numdof*(4*i+0)+4*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps1dotdphii;
+				Ke->values[numdof*(4*i+0)+4*j+2]+=gauss->weight*Jdet*2*mu_prime*eps3dotdphij*eps1dotdphii;
+
+				Ke->values[numdof*(4*i+1)+4*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps2dotdphii;
+				Ke->values[numdof*(4*i+1)+4*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps2dotdphii;
+				Ke->values[numdof*(4*i+1)+4*j+2]+=gauss->weight*Jdet*2*mu_prime*eps3dotdphij*eps2dotdphii;
+
+				Ke->values[numdof*(4*i+2)+4*j+0]+=gauss->weight*Jdet*2*mu_prime*eps1dotdphij*eps3dotdphii;
+				Ke->values[numdof*(4*i+2)+4*j+1]+=gauss->weight*Jdet*2*mu_prime*eps2dotdphij*eps3dotdphii;
+				Ke->values[numdof*(4*i+2)+4*j+2]+=gauss->weight*Jdet*2*mu_prime*eps3dotdphij*eps3dotdphii;
+			}
+		}
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::GetSolutionFromInputsDiagnosticHoriz{{{*/
+void  Penta::GetSolutionFromInputsDiagnosticHoriz(Vector* solution){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int         i;
+	int         approximation;
+	int        *doflist        = NULL;
+	IssmDouble  vx,vy;
+	IssmDouble  values[numdof];
+	GaussPenta *gauss;
+
+	/*Get approximation enum and dof list: */
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+
+	/*If the element is a coupling, do nothing: every node is also on an other elements 
+	 * (as coupling is between MacAyeal and Pattyn) so the other element will take care of it*/
+	GetDofList(&doflist,approximation,GsetEnum);
+
+	/*Ok, we have vx and vy in values, fill in vx and vy arrays: */
+	/*P1 element only for now*/
+	gauss=new GaussPenta();
+	for(i=0;iGaussVertex(i);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		values[i*NDOF2+0]=vx;
+		values[i*NDOF2+1]=vy;
+	}
+
+	/*Add value to global vector*/
+	solution->SetValues(numdof,doflist,values,INS_VAL);
+
+	/*Free ressources:*/
+	delete gauss;
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::GetSolutionFromInputsDiagnosticHutter{{{*/
+void  Penta::GetSolutionFromInputsDiagnosticHutter(Vector* solution){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int          i;
+	int*         doflist=NULL;
+	IssmDouble       vx,vy;
+	IssmDouble       values[numdof];
+	GaussPenta*  gauss=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+
+	/*Ok, we have vx and vy in values, fill in vx and vy arrays: */
+	/*P1 element only for now*/
+	gauss=new GaussPenta();
+	for(i=0;iGaussVertex(i);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		values[i*NDOF2+0]=vx;
+		values[i*NDOF2+1]=vy;
+	}
+
+	/*Add value to global vector*/
+	solution->SetValues(numdof,doflist,values,INS_VAL);
+
+	/*Free ressources:*/
+	delete gauss;
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::GetSolutionFromInputsDiagnosticVert{{{*/
+void  Penta::GetSolutionFromInputsDiagnosticVert(Vector* solution){
+
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	int          i;
+	int*         doflist=NULL;
+	IssmDouble       vz;
+	IssmDouble       values[numdof];
+	GaussPenta*  gauss=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+	Input* vz_input=inputs->GetInput(VzEnum); _assert_(vz_input);
+
+	/*Ok, we have vx and vy in values, fill in vx and vy arrays: */
+	/*P1 element only for now*/
+	gauss=new GaussPenta();
+	for(i=0;iGaussVertex(i);
+		vz_input->GetInputValue(&vz,gauss);
+		values[i]=vz;
+	}
+
+	/*Add value to global vector*/
+	solution->SetValues(numdof,doflist,values,INS_VAL);
+
+	/*Free ressources:*/
+	delete gauss;
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::GetSolutionFromInputsDiagnosticStokes{{{*/
+void  Penta::GetSolutionFromInputsDiagnosticStokes(Vector* solution){
+
+	const int    numdof=NDOF4*NUMVERTICES;
+
+	int          i;
+	int*         doflist=NULL;
+	IssmDouble       vx,vy,vz,p;
+	IssmDouble       stokesreconditioning;
+	IssmDouble       values[numdof];
+	GaussPenta   *gauss;
+
+	/*Get dof list: */
+	GetDofList(&doflist,StokesApproximationEnum,GsetEnum);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);       _assert_(vz_input);
+	Input* p_input =inputs->GetInput(PressureEnum); _assert_(p_input);
+
+	/*Recondition pressure: */
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+
+	/*Ok, we have vx vy vz and P in values, fill in vx vy vz P arrays: */
+	/*P1 element only for now*/
+	gauss=new GaussPenta();
+	for(i=0;iGaussVertex(i);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vz_input->GetInputValue(&vz,gauss);
+		p_input ->GetInputValue(&p ,gauss);
+		values[i*NDOF4+0]=vx;
+		values[i*NDOF4+1]=vy;
+		values[i*NDOF4+2]=vz;
+		values[i*NDOF4+3]=p/stokesreconditioning;
+	}
+
+	/*Add value to global vector*/
+	solution->SetValues(numdof,doflist,values,INS_VAL);
+
+	/*Free ressources:*/
+	delete gauss;
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::GetL1L2Viscosity{{{*/
+void Penta::GetL1L2Viscosity(IssmDouble* pviscosity,IssmDouble* xyz_list, GaussPenta* gauss, Input* vx_input, Input* vy_input,Input* surface_input){
+	/*Compute the L1L2 viscosity
+	 *
+	 *      1
+	 * mu = - A^-1 (sigma'_e)^(1-n)
+	 *      2
+	 *
+	 * sigma'_e^2 = |sigma'_//|^2 + |sigma'_perp|^2 (see Perego 2012 eq. 17,18)
+	 *
+	 * L1L2 assumptions:
+	 *
+	 * (1) |eps_b|_// = A (|sigma'_//|^2 + |sigma'_perp|^2)^((n-1)/2) |sigma'_//|
+	 * (2) |sigma'_perp|^2 = |rho g (s-z) grad(s)|^2
+	 *
+	 * Assuming that n = 3, we have a polynom of degree 3 to solve (the only unkown is X=|sigma'_//|)
+	 *
+	 * A X^3 + A |rho g (s-z) grad(s)|^2 X - |eps_b|_// = 0     */
+
+	int        i;
+	IssmDouble z,s,viscosity,p,q,delta;
+	IssmDouble tau_perp,tau_par,eps_b,A;
+	IssmDouble epsilonvx[5]; /*exx eyy exy exz eyz*/
+	IssmDouble epsilonvy[5]; /*exx eyy exy exz eyz*/
+	IssmDouble epsilon[5];   /*exx eyy exy exz eyz*/
+	IssmDouble z_list[NUMVERTICES];
+	IssmDouble slope[3];
+
+	/*Check that both inputs have been found*/
+	if (!vx_input || !vy_input || !surface_input) _error_("Input missing");
+
+	/*Get tau_perp*/
+	for(i=0;iGetInputValue(&s,gauss);
+	surface_input->GetInputDerivativeValue(&slope[0],xyz_list,gauss);
+	PentaRef::GetInputValue(&z,&z_list[0],gauss);
+	tau_perp = matpar->GetRhoIce() * matpar->GetG() * fabs(s-z)*sqrt(slope[0]*slope[0]+slope[1]*slope[1]);
+
+	/* Get eps_b*/
+	vx_input->GetVxStrainRate3dPattyn(epsilonvx,xyz_list,gauss);
+	vy_input->GetVyStrainRate3dPattyn(epsilonvy,xyz_list,gauss);
+	for(i=0;i<5;i++) epsilon[i]=epsilonvx[i]+epsilonvy[i];
+	eps_b = sqrt(epsilon[0]*epsilon[0] + epsilon[1]*epsilon[1] + epsilon[0]*epsilon[1] + epsilon[2]*epsilon[2]);
+	if(eps_b==0.){
+		*pviscosity = 2.5e+17;
+		return;
+	}
+
+	/*Get A*/
+	_assert_(material->GetN()==3.0);
+	A=material->GetA();
+
+	/*Solve for tau_perp (http://fr.wikipedia.org/wiki/Méthode_de_Cardan)*/
+	p     = tau_perp *tau_perp;
+	q     = - eps_b/A;
+	delta = q *q + p*p*p*4./27.;
+	_assert_(delta>0);
+	tau_par = pow(0.5*(-q+sqrt(delta)),1./3.) - pow(0.5*(q+sqrt(delta)),1./3.);
+
+	/*Viscosity*/
+	viscosity = 1./(2.*A*(tau_par*tau_par + tau_perp*tau_perp));
+	_assert_(!isnan(viscosity));
+	_assert_(viscosity > 0.);
+
+	/*Assign output pointer*/
+	*pviscosity = viscosity;
+	return; 
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticHoriz {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticHoriz(IssmDouble* solution){
+
+	int  approximation;
+
+	/*Recover inputs*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	/*MacAyeal, everything is done by the element on bed*/
+	if (approximation==MacAyealApproximationEnum){
+		if (!IsOnBed()){
+			/*Do nothing. Element on bed will take care of it*/
+			return;
+		}
+		else{
+			InputUpdateFromSolutionDiagnosticMacAyeal(solution);
+			return;
+		}
+	}
+	if (approximation==L1L2ApproximationEnum){
+		if (!IsOnBed()) return;
+		InputUpdateFromSolutionDiagnosticL1L2(solution);
+		return;
+	}
+	else if (approximation==PattynApproximationEnum){
+		InputUpdateFromSolutionDiagnosticPattyn(solution);
+	}
+	else if (approximation==PattynStokesApproximationEnum){
+		InputUpdateFromSolutionDiagnosticPattynStokes(solution);
+	}
+	else if (approximation==MacAyealStokesApproximationEnum){
+		InputUpdateFromSolutionDiagnosticMacAyealStokes(solution);
+	}
+	else if (approximation==StokesApproximationEnum || approximation==NoneApproximationEnum){
+		InputUpdateFromSolutionDiagnosticStokes(solution);
+	}
+	else if (approximation==MacAyealPattynApproximationEnum){
+		InputUpdateFromSolutionDiagnosticMacAyealPattyn(solution);
+	}
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticMacAyeal {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticMacAyeal(IssmDouble* solution){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int     i;
+	IssmDouble  rho_ice,g;
+	IssmDouble  values[numdof];
+	IssmDouble  vx[NUMVERTICES];
+	IssmDouble  vy[NUMVERTICES];
+	IssmDouble  vz[NUMVERTICES];
+	IssmDouble  vel[NUMVERTICES];
+	IssmDouble  pressure[NUMVERTICES];
+	IssmDouble  surface[NUMVERTICES];
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	int    *doflist = NULL;
+	Penta  *penta   = NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,MacAyealApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(vx[i])) _error_("NaN found in solution vector");
+		if(xIsNan(vy[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Get parameters fro pressure computation*/
+	rho_ice=matpar->GetRhoIce();
+	g=matpar->GetG();
+
+	/*Start looping over all elements above current element and update all inputs*/
+	penta=this;
+	for(;;){
+
+		/*Get node data: */
+		GetVerticesCoordinates(&xyz_list[0][0],penta->nodes,NUMVERTICES);
+
+		/*Now Compute vel*/
+		GetInputListOnVertices(&vz[0],VzEnum,0.0); //default is 0
+		for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+		penta->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+		penta->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+		/*Add vx and vy as inputs to the tria element: */
+		penta->inputs->AddInput(new PentaP1Input(VxEnum,vx));
+		penta->inputs->AddInput(new PentaP1Input(VyEnum,vy));
+		penta->inputs->AddInput(new PentaP1Input(VelEnum,vel));
+		penta->inputs->AddInput(new PentaP1Input(PressureEnum,pressure));
+
+		/*Stop if we have reached the surface*/
+		if (penta->IsOnSurface()) break;
+
+		/* get upper Penta*/
+		penta=penta->GetUpperElement(); _assert_(penta->Id()!=this->id);
+	}
+	
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticMacAyealPattyn {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticMacAyealPattyn(IssmDouble* solution){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+	const int    numdof2d=NDOF2*NUMVERTICES2D;
+
+	int     i;
+	IssmDouble  rho_ice,g;
+	IssmDouble  macayeal_values[numdof];
+	IssmDouble  pattyn_values[numdof];
+	IssmDouble  vx[NUMVERTICES];
+	IssmDouble  vy[NUMVERTICES];
+	IssmDouble  vz[NUMVERTICES];
+	IssmDouble  vel[NUMVERTICES];
+	IssmDouble  pressure[NUMVERTICES];
+	IssmDouble  surface[NUMVERTICES];
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	int*    doflistp = NULL;
+	int*    doflistm = NULL;
+	Penta   *penta   = NULL;
+
+	/*OK, we have to add results of this element for pattyn 
+	 * and results from the penta at base for macayeal. Now recover results*/
+	penta=GetBasalElement();
+
+	/*Get dof listof this element (pattyn dofs) and of the penta at base (macayeal dofs): */
+	GetDofList(&doflistp,PattynApproximationEnum,GsetEnum);
+	penta->GetDofList(&doflistm,MacAyealApproximationEnum,GsetEnum);
+
+	/*Get node data: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;inodes,NUMVERTICES,XYEnum);
+	TransformSolutionCoord(&pattyn_values[0],   this->nodes,NUMVERTICES,XYEnum);
+
+	/*Ok, we have vx and vy in values, fill in vx and vy arrays: */
+	for(i=0;i(vx[i])) _error_("NaN found in solution vector");
+		if(xIsNan(vy[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Now Compute vel*/
+	GetInputListOnVertices(&vz[0],VzEnum,0.0); //default is 0
+	for(i=0;iGetRhoIce();
+	g=matpar->GetG();
+	GetInputListOnVertices(&surface[0],SurfaceEnum);
+	for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+	this->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+	this->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new PentaP1Input(VxEnum,vx));
+	this->inputs->AddInput(new PentaP1Input(VyEnum,vy));
+	this->inputs->AddInput(new PentaP1Input(VelEnum,vel));
+	this->inputs->AddInput(new PentaP1Input(PressureEnum,pressure));
+
+	/*Free ressources:*/
+	xDelete(doflistp);
+	xDelete(doflistm);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticMacAyealStokes {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticMacAyealStokes(IssmDouble* solution){
+
+	const int    numdofm=NDOF2*NUMVERTICES;
+	const int    numdofs=NDOF4*NUMVERTICES;
+	const int    numdof2d=NDOF2*NUMVERTICES2D;
+
+	int     i;
+	IssmDouble  stokesreconditioning;
+	IssmDouble  macayeal_values[numdofm];
+	IssmDouble  stokes_values[numdofs];
+	IssmDouble  vx[NUMVERTICES];
+	IssmDouble  vy[NUMVERTICES];
+	IssmDouble  vz[NUMVERTICES];
+	IssmDouble  vzmacayeal[NUMVERTICES];
+	IssmDouble  vzstokes[NUMVERTICES];
+	IssmDouble  vel[NUMVERTICES];
+	IssmDouble  pressure[NUMVERTICES];
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	int*    doflistm        = NULL;
+	int*    doflists        = NULL;
+	Penta   *penta          = NULL;
+
+	/*OK, we have to add results of this element for macayeal 
+	 * and results from the penta at base for macayeal. Now recover results*/
+	penta=GetBasalElement();
+
+	/*Get dof listof this element (macayeal dofs) and of the penta at base (macayeal dofs): */
+	penta->GetDofList(&doflistm,MacAyealApproximationEnum,GsetEnum);
+	GetDofList(&doflists,StokesApproximationEnum,GsetEnum);
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+
+	/*Get node data: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;inodes,NUMVERTICES,XYEnum);
+	TransformSolutionCoord(&stokes_values[0],this->nodes,NUMVERTICES,XYZPEnum);
+
+	/*Ok, we have vx and vy in values, fill in vx and vy arrays: */
+	for(i=0;i(vx[i]))       _error_("NaN found in solution vector");
+		if(xIsNan(vy[i]))       _error_("NaN found in solution vector");
+		if(xIsNan(vzstokes[i])) _error_("NaN found in solution vector");
+		if(xIsNan(pressure[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Get Vz*/
+	Input* vzmacayeal_input=inputs->GetInput(VzMacAyealEnum);
+	if (vzmacayeal_input){
+		if (vzmacayeal_input->ObjectEnum()!=PentaP1InputEnum){
+			_error_("Cannot compute Vel as VzMacAyeal is of type " << EnumToStringx(vzmacayeal_input->ObjectEnum()));
+		}
+		GetInputListOnVertices(&vzmacayeal[0],VzMacAyealEnum);
+	}
+	else{
+		_error_("Cannot update solution as VzMacAyeal is not present");
+	}
+
+	/*Now Compute vel*/
+	for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+	this->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+	this->inputs->ChangeEnum(VzEnum,VzPicardEnum);
+	this->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new PentaP1Input(VxEnum,vx));
+	this->inputs->AddInput(new PentaP1Input(VyEnum,vy));
+	this->inputs->AddInput(new PentaP1Input(VzEnum,vz));
+	this->inputs->AddInput(new PentaP1Input(VzStokesEnum,vzstokes));
+	this->inputs->AddInput(new PentaP1Input(VelEnum,vel));
+	this->inputs->AddInput(new PentaP1Input(PressureEnum,pressure));
+
+	/*Free ressources:*/
+	xDelete(doflistm);
+	xDelete(doflists);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticL1L2 {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticL1L2(IssmDouble* solution){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int     i;
+	IssmDouble  rho_ice,g;
+	IssmDouble  values[numdof];
+	IssmDouble  vx[NUMVERTICES];
+	IssmDouble  vy[NUMVERTICES];
+	IssmDouble  vz[NUMVERTICES];
+	IssmDouble  vel[NUMVERTICES];
+	IssmDouble  pressure[NUMVERTICES];
+	IssmDouble  surface[NUMVERTICES];
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	int    *doflist = NULL;
+	Penta  *penta   = NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,L1L2ApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(vx[i])) _error_("NaN found in solution vector");
+		if(xIsNan(vy[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Get parameters fro pressure computation*/
+	rho_ice=matpar->GetRhoIce();
+	g=matpar->GetG();
+
+	/*Start looping over all elements above current element and update all inputs*/
+	penta=this;
+	for(;;){
+
+		/*Get node data: */
+		GetVerticesCoordinates(&xyz_list[0][0],penta->nodes,NUMVERTICES);
+
+		/*Now Compute vel*/
+		GetInputListOnVertices(&vz[0],VzEnum,0.0); //default is 0
+		for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+		penta->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+		penta->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+		/*Add vx and vy as inputs to the tria element: */
+		penta->inputs->AddInput(new PentaP1Input(VxEnum,vx));
+		penta->inputs->AddInput(new PentaP1Input(VyEnum,vy));
+		penta->inputs->AddInput(new PentaP1Input(VelEnum,vel));
+		penta->inputs->AddInput(new PentaP1Input(PressureEnum,pressure));
+
+		/*Stop if we have reached the surface*/
+		if (penta->IsOnSurface()) break;
+
+		/* get upper Penta*/
+		penta=penta->GetUpperElement(); _assert_(penta->Id()!=this->id);
+	}
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticPattyn {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticPattyn(IssmDouble* solution){
+	
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int    i;
+	IssmDouble rho_ice,g;
+	IssmDouble values[numdof];
+	IssmDouble vx[NUMVERTICES];
+	IssmDouble vy[NUMVERTICES];
+	IssmDouble vz[NUMVERTICES];
+	IssmDouble vel[NUMVERTICES];
+	IssmDouble pressure[NUMVERTICES];
+	IssmDouble surface[NUMVERTICES];
+	IssmDouble xyz_list[NUMVERTICES][3];
+	int*   doflist = NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,PattynApproximationEnum,GsetEnum);
+
+	/*Get node data: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(vx[i])) _error_("NaN found in solution vector");
+		if(xIsNan(vy[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Get Vz*/
+	Input* vz_input=inputs->GetInput(VzEnum);
+	if (vz_input){
+		GetInputListOnVertices(&vz[0],VzEnum);
+	}
+	else{
+		for(i=0;iGetRhoIce();
+	g=matpar->GetG();
+	GetInputListOnVertices(&surface[0],SurfaceEnum);
+	for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+	this->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+	this->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new PentaP1Input(VxEnum,vx));
+	this->inputs->AddInput(new PentaP1Input(VyEnum,vy));
+	this->inputs->AddInput(new PentaP1Input(VelEnum,vel));
+	this->inputs->AddInput(new PentaP1Input(PressureEnum,pressure));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticPattynStokes {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticPattynStokes(IssmDouble* solution){
+
+	const int    numdofp=NDOF2*NUMVERTICES;
+	const int    numdofs=NDOF4*NUMVERTICES;
+
+	int    i;
+	IssmDouble pattyn_values[numdofp];
+	IssmDouble stokes_values[numdofs];
+	IssmDouble vx[NUMVERTICES];
+	IssmDouble vy[NUMVERTICES];
+	IssmDouble vz[NUMVERTICES];
+	IssmDouble vzpattyn[NUMVERTICES];
+	IssmDouble vzstokes[NUMVERTICES];
+	IssmDouble vel[NUMVERTICES];
+	IssmDouble pressure[NUMVERTICES];
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble stokesreconditioning;
+	int*   doflistp      = NULL;
+	int*   doflists      = NULL;
+	Penta  *penta        = NULL;
+
+	/*OK, we have to add results of this element for pattyn 
+	 * and results from the penta at base for macayeal. Now recover results*/
+	penta=GetBasalElement();
+
+	/*Get dof listof this element (pattyn dofs) and of the penta at base (macayeal dofs): */
+	GetDofList(&doflistp,PattynApproximationEnum,GsetEnum);
+	GetDofList(&doflists,StokesApproximationEnum,GsetEnum);
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+
+	/*Get node data: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;inodes,NUMVERTICES,XYEnum);
+	TransformSolutionCoord(&stokes_values[0],this->nodes,NUMVERTICES,XYZPEnum);
+
+	/*Ok, we have vx and vy in values, fill in vx and vy arrays: */
+	for(i=0;i(vx[i]))       _error_("NaN found in solution vector");
+		if(xIsNan(vy[i]))       _error_("NaN found in solution vector");
+		if(xIsNan(vzstokes[i])) _error_("NaN found in solution vector");
+		if(xIsNan(pressure[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Get Vz*/
+	Input* vzpattyn_input=inputs->GetInput(VzPattynEnum);
+	if (vzpattyn_input){
+		if (vzpattyn_input->ObjectEnum()!=PentaP1InputEnum){
+			_error_("Cannot compute Vel as VzPattyn is of type " << EnumToStringx(vzpattyn_input->ObjectEnum()));
+		}
+		GetInputListOnVertices(&vzpattyn[0],VzPattynEnum);
+	}
+	else{
+		_error_("Cannot update solution as VzPattyn is not present");
+	}
+
+	/*Now Compute vel*/
+	for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+	this->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+	this->inputs->ChangeEnum(VzEnum,VzPicardEnum);
+	this->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new PentaP1Input(VxEnum,vx));
+	this->inputs->AddInput(new PentaP1Input(VyEnum,vy));
+	this->inputs->AddInput(new PentaP1Input(VzEnum,vz));
+	this->inputs->AddInput(new PentaP1Input(VzStokesEnum,vzstokes));
+	this->inputs->AddInput(new PentaP1Input(VelEnum,vel));
+	this->inputs->AddInput(new PentaP1Input(PressureEnum,pressure));
+
+	/*Free ressources:*/
+	xDelete(doflistp);
+	xDelete(doflists);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticHutter {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticHutter(IssmDouble* solution){
+	
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int     i;
+	IssmDouble  rho_ice,g;
+	IssmDouble  values[numdof];
+	IssmDouble  vx[NUMVERTICES];
+	IssmDouble  vy[NUMVERTICES];
+	IssmDouble  vz[NUMVERTICES];
+	IssmDouble  vel[NUMVERTICES];
+	IssmDouble  pressure[NUMVERTICES];
+	IssmDouble  surface[NUMVERTICES];
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	int*    doflist = NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Get node data: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(vx[i])) _error_("NaN found in solution vector");
+		if(xIsNan(vy[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Now Compute vel*/
+	GetInputListOnVertices(&vz[0],VzEnum,0.0); //default is 0
+	for(i=0;iGetRhoIce();
+	g=matpar->GetG();
+	GetInputListOnVertices(&surface[0],SurfaceEnum);
+	for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+	this->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+	this->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new PentaP1Input(VxEnum,vx));
+	this->inputs->AddInput(new PentaP1Input(VyEnum,vy));
+	this->inputs->AddInput(new PentaP1Input(VelEnum,vel));
+	this->inputs->AddInput(new PentaP1Input(PressureEnum,pressure));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticVert {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticVert(IssmDouble* solution){
+
+	const int numdof=NDOF1*NUMVERTICES;
+	
+	int      i;
+	int      approximation;
+	IssmDouble   rho_ice,g;
+	IssmDouble   values[numdof];
+	IssmDouble   vx[NUMVERTICES];
+	IssmDouble   vy[NUMVERTICES];
+	IssmDouble   vz[NUMVERTICES];
+	IssmDouble   vzmacayeal[NUMVERTICES];
+	IssmDouble   vzpattyn[NUMVERTICES];
+	IssmDouble   vzstokes[NUMVERTICES];
+	IssmDouble   vel[NUMVERTICES];
+	IssmDouble   pressure[NUMVERTICES];
+	IssmDouble   surface[NUMVERTICES];
+	IssmDouble   xyz_list[NUMVERTICES][3];
+	int*     doflist      = NULL;
+
+
+	/*Get the approximation and do nothing if the element in Stokes or None*/
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(approximation==StokesApproximationEnum || approximation==NoneApproximationEnum){
+		return;
+	}
+
+	/*Get dof list and vertices coordinates: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Use the dof list to index into the solution vector vz: */
+	for(i=0;i(vz[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Get Vx and Vy*/
+	GetInputListOnVertices(&vx[0],VxEnum,0.0); //default is 0
+	GetInputListOnVertices(&vy[0],VyEnum,0.0); //default is 0
+
+	/*Do some modifications if we actually have a PattynStokes or MacAyealStokes element*/
+	if(approximation==PattynStokesApproximationEnum){
+		Input* vzstokes_input=inputs->GetInput(VzStokesEnum);
+		if (vzstokes_input){
+			if (vzstokes_input->ObjectEnum()!=PentaP1InputEnum) _error_("Cannot compute Vel as VzStokes is of type " << EnumToStringx(vzstokes_input->ObjectEnum()));
+			GetInputListOnVertices(&vzstokes[0],VzStokesEnum);
+		}
+		else _error_("Cannot compute Vz as VzStokes in not present in PattynStokes element");
+		for(i=0;iGetInput(VzStokesEnum);
+		if (vzstokes_input){
+			if (vzstokes_input->ObjectEnum()!=PentaP1InputEnum) _error_("Cannot compute Vel as VzStokes is of type " << EnumToStringx(vzstokes_input->ObjectEnum()));
+			GetInputListOnVertices(&vzstokes[0],VzStokesEnum);
+		}
+		else _error_("Cannot compute Vz as VzStokes in not present in MacAyealStokes element");
+		for(i=0;iGetRhoIce();
+		g=matpar->GetG();
+		GetInputListOnVertices(&surface[0],SurfaceEnum);
+		for(i=0;iinputs->ChangeEnum(VzEnum,VzPicardEnum);
+
+	if(approximation!=PattynStokesApproximationEnum && approximation!=MacAyealStokesApproximationEnum){
+		this->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+		this->inputs->AddInput(new PentaP1Input(PressureEnum,pressure));
+	}
+	else if(approximation==PattynStokesApproximationEnum){
+		this->inputs->AddInput(new PentaP1Input(VzPattynEnum,vzpattyn));
+	}
+	else if(approximation==MacAyealStokesApproximationEnum){
+		this->inputs->AddInput(new PentaP1Input(VzMacAyealEnum,vzmacayeal));
+	}
+	this->inputs->AddInput(new PentaP1Input(VzEnum,vz));
+	this->inputs->AddInput(new PentaP1Input(VelEnum,vel));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Penta::InputUpdateFromSolutionDiagnosticStokes {{{*/
+void  Penta::InputUpdateFromSolutionDiagnosticStokes(IssmDouble* solution){
+	
+	const int numdof=NDOF4*NUMVERTICES;
+
+	int     i;
+	IssmDouble  values[numdof];
+	IssmDouble  vx[NUMVERTICES];
+	IssmDouble  vy[NUMVERTICES];
+	IssmDouble  vz[NUMVERTICES];
+	IssmDouble  vel[NUMVERTICES];
+	IssmDouble  pressure[NUMVERTICES];
+	IssmDouble  stokesreconditioning;
+	int*    doflist=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,StokesApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(vx[i]))       _error_("NaN found in solution vector");
+		if(xIsNan(vy[i]))       _error_("NaN found in solution vector");
+		if(xIsNan(vz[i]))       _error_("NaN found in solution vector");
+		if(xIsNan(pressure[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Recondition pressure and compute vel: */
+	this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
+	for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+	this->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+	this->inputs->ChangeEnum(VzEnum,VzPicardEnum);
+	this->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new PentaP1Input(VxEnum,vx));
+	this->inputs->AddInput(new PentaP1Input(VyEnum,vy));
+	this->inputs->AddInput(new PentaP1Input(VzEnum,vz));
+	this->inputs->AddInput(new PentaP1Input(VelEnum,vel));
+	this->inputs->AddInput(new PentaP1Input(PressureEnum,pressure));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_BALANCED_
+/*FUNCTION Penta::CreateKMatrixBalancethickness {{{*/
+ElementMatrix* Penta::CreateKMatrixBalancethickness(void){
+
+	/*Figure out if this penta is collapsed. If so, then bailout, except if it is at the 
+	  bedrock, in which case we spawn a tria element using the 3 first nodes, and use it to build 
+	  the stiffness matrix. */
+	if (!IsOnBed()) return NULL;
+
+	/*Depth Averaging Vx and Vy*/
+	this->InputDepthAverageAtBase(VxEnum,VxAverageEnum);
+	this->InputDepthAverageAtBase(VyEnum,VyAverageEnum);
+
+	/*Spawn Tria element from the base of the Penta: */
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementMatrix* Ke=tria->CreateKMatrixBalancethickness();
+	delete tria->material; delete tria;
+
+	/*Delete Vx and Vy averaged*/
+	this->inputs->DeleteInput(VxAverageEnum);
+	this->inputs->DeleteInput(VyAverageEnum);
+
+	/*clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penta::CreatePVectorBalancethickness {{{*/
+ElementVector* Penta::CreatePVectorBalancethickness(void){
+
+	if (!IsOnBed()) return NULL;
+
+	/*Depth Averaging Vx and Vy*/
+	this->InputDepthAverageAtBase(VxEnum,VxAverageEnum);
+	this->InputDepthAverageAtBase(VyEnum,VyAverageEnum);
+
+	/*Call Tria function*/
+	Tria* tria=(Tria*)SpawnTria(0,1,2); //nodes 0, 1 and 2 make the new tria.
+	ElementVector* pe=tria->CreatePVectorBalancethickness();
+	delete tria->material; delete tria;
+
+	/*Delete Vx and Vy averaged*/
+	this->inputs->DeleteInput(VxAverageEnum);
+	this->inputs->DeleteInput(VyAverageEnum);
+
+	/*Clean up and return*/
+	return pe;
+}
+/*}}}*/
+#endif
+
Index: /issm/trunk/src/c/classes/objects/Elements/Penta.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/Penta.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/Penta.h	(revision 13395)
@@ -0,0 +1,325 @@
+/*! \file Penta.h 
+ *  \brief: header file for penta object
+ */
+
+#ifndef _PENTA_H_
+#define _PENTA_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Element.h"
+#include "./PentaHook.h"
+#include "./PentaRef.h"
+class  Object;
+class Parameters;
+class Inputs;
+class IoModel;
+class Node;
+class Material;
+class Matpar;
+class Tria;
+class ElementMatrix;
+class ElementVector;
+
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+/*}}}*/
+
+class Penta: public Element,public PentaHook,public PentaRef{
+
+	public:
+
+		int          id;
+		int          sid;
+
+		Node       **nodes;        // 6 nodes
+		Material    *material;       // 1 material ice
+		Matpar      *matpar;       // 1 material parameter
+		Penta      **verticalneighbors;   // 2 neighbors: first one under, second one above
+		int          horizontalneighborsids[3];
+
+		Parameters  *parameters;   //pointer to solution parameters
+		Inputs      *inputs;
+		Results      *results;
+
+		/*Penta constructors and destructor: {{{*/
+		Penta();
+		Penta(int penta_id,int penta_sid,int i, IoModel* iomodel,int nummodels);
+		~Penta();
+		/*}}}*/
+		/*Object virtual functions definitions: {{{*/
+		Object*   copy();
+		void	  DeepEcho();
+		void	  Echo();
+		int		  ObjectEnum();
+		int		  Id(); 
+		int		  MyRank();
+		/*}}}*/
+		/*Update virtual functions definitions: {{{*/
+		void  InputUpdateFromConstant(bool constant, int name);
+		void  InputUpdateFromConstant(IssmDouble constant, int name);
+		void  InputUpdateFromConstant(int constant, int name);
+		void  InputUpdateFromSolution(IssmDouble* solutiong);
+		void  InputUpdateFromVector(bool* vector, int name, int type);
+		void  InputUpdateFromVector(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVector(int* vector, int name, int type);
+		#ifdef _HAVE_DAKOTA_
+		void  InputUpdateFromVectorDakota(bool* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(int* vector, int name, int type);
+		void  InputUpdateFromMatrixDakota(IssmDouble* matrix, int nows, int ncols, int name, int type);
+		#endif
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel);
+		/*}}}*/
+		/*Element virtual functions definitions: {{{*/
+		void   AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part);
+		void   BasalFrictionCreateInput(void);
+		void   ComputeBasalStress(Vector* sigma_b);
+		void   ComputeStrainRate(Vector* eps);
+		void   ComputeStressTensor();
+		void   Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters);
+		void   SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters);
+		void   CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df);
+		void   CreatePVector(Vector* pf);
+		void   CreateJacobianMatrix(Matrix* Jff);
+		void   Delta18oParameterization(void);
+		void   DeleteResults(void);
+		int    GetNodeIndex(Node* node);
+		void   GetSolutionFromInputs(Vector* solution);
+		IssmDouble GetZcoord(GaussPenta* gauss);
+		void   GetVectorFromInputs(Vector* vector,int name_enum);
+		void   GetVectorFromResults(Vector* vector,int offset,int name_enum,int interp);
+		
+		int    Sid();
+		void   InputArtificialNoise(int enum_type,IssmDouble min, IssmDouble max);
+		bool   InputConvergence(IssmDouble* eps, int* enums,int num_enums,int* criterionenums,IssmDouble* criterionvalues,int num_criterionenums);
+		void   InputCreate(IssmDouble scalar,int name,int code);
+		void   InputCreate(IssmDouble* vector, int index,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code);
+		void   InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum=MeshElementsEnum);
+		void   InputDuplicate(int original_enum,int new_enum);
+		void   InputScale(int enum_type,IssmDouble scale_factor);
+		
+		void   InputToResult(int enum_type,int step,IssmDouble time);
+		void   MigrateGroundingLine(IssmDouble* old_floating_ice,IssmDouble* sheet_ungrounding);
+		void   PotentialSheetUngrounding(Vector* potential_sheet_ungrounding);
+		void   RequestedOutput(int output_enum,int step,IssmDouble time);
+		void   ListResultsInfo(int** results_enums,int** results_size,IssmDouble** results_times,int** results_steps,int* num_results);
+		void   PatchFill(int* pcount, Patch* patch);
+		void   PatchSize(int* pnumrows, int* pnumvertices,int* pnumnodes);
+		void   PositiveDegreeDay(IssmDouble* pdds,IssmDouble* pds,IssmDouble signorm);
+		void   ProcessResultsUnits(void);
+		void   ResetCoordinateSystem(void);
+		void   SmbGradients();
+		IssmDouble SurfaceArea(void);
+		void   Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type);
+		int    UpdatePotentialSheetUngrounding(IssmDouble* potential_sheet_ungrounding,Vector* vec_nodes_on_iceshelf,IssmDouble* nodes_on_iceshelf);
+		int    NodalValue(IssmDouble* pvalue, int index, int natureofdataenum,bool process_units);
+		IssmDouble TimeAdapt();
+		int*   GetHorizontalNeighboorSids(void);
+		void   ViscousHeatingCreateInput(void);
+		void   SmearFunction(Vector* smearedvector,IssmDouble (*WeightFunction)(IssmDouble distance,IssmDouble radius),IssmDouble radius);
+
+		 #ifdef _HAVE_RESPONSES_
+		IssmDouble IceVolume(void);
+		IssmDouble TotalSmb(void);
+		void   MinVel(IssmDouble* pminvel, bool process_units);
+		void   MinVx(IssmDouble* pminvx, bool process_units);
+		void   MinVy(IssmDouble* pminvy, bool process_units);
+		void   MinVz(IssmDouble* pminvz, bool process_units);
+		IssmDouble MassFlux(IssmDouble* segment,bool process_units);
+		void   MaxAbsVx(IssmDouble* pmaxabsvx, bool process_units);
+		void   MaxAbsVy(IssmDouble* pmaxabsvy, bool process_units);
+		void   MaxAbsVz(IssmDouble* pmaxabsvz, bool process_units);
+		void   MaxVel(IssmDouble* pmaxvel, bool process_units);
+		void   ElementResponse(IssmDouble* presponse,int response_enum,bool process_units);
+		void   MaxVx(IssmDouble* pmaxvx, bool process_units);
+		void   MaxVy(IssmDouble* pmaxvy, bool process_units);
+		void   MaxVz(IssmDouble* pmaxvz, bool process_units);
+		#endif
+
+		#ifdef _HAVE_CONTROL_
+		IssmDouble DragCoefficientAbsGradient(bool process_units,int weight_index);
+		void   GradientIndexing(int* indexing,int control_index);
+		void   Gradj(Vector* gradient,int control_type,int control_index);
+		void   GradjDragMacAyeal(Vector* gradient,int control_index);
+		void   GradjDragPattyn(Vector* gradient,int control_index);
+		void   GradjDragStokes(Vector* gradient,int control_index);
+		void   GradjBbarMacAyeal(Vector* gradient,int control_index);
+		void   GradjBbarPattyn(Vector* gradient,int control_index);
+		void   GradjBbarStokes(Vector* gradient,int control_index);
+		void   GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data);
+		void   SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index);
+		void   ControlInputGetGradient(Vector* gradient,int enum_type,int control_index);
+		void   ControlInputScaleGradient(int enum_type,IssmDouble scale);
+		void   ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index);
+		IssmDouble RheologyBbarAbsGradient(bool process_units,int weight_index);
+		IssmDouble ThicknessAbsMisfit(     bool process_units,int weight_index);
+		IssmDouble SurfaceAbsVelMisfit(    bool process_units,int weight_index);
+		IssmDouble SurfaceRelVelMisfit(    bool process_units,int weight_index);
+		IssmDouble SurfaceLogVelMisfit(    bool process_units,int weight_index);
+		IssmDouble SurfaceLogVxVyMisfit(   bool process_units,int weight_index);
+		IssmDouble SurfaceAverageVelMisfit(bool process_units,int weight_index);
+		IssmDouble ThicknessAbsGradient(bool process_units,int weight_index);
+		IssmDouble ThicknessAlongGradient( bool process_units,int weight_index){_error_("not supported");};
+		IssmDouble ThicknessAcrossGradient(bool process_units,int weight_index){_error_("not supported");};
+		void   InputControlUpdate(IssmDouble scalar,bool save_parameter);
+		#endif
+		/*}}}*/
+		/*Penta specific routines:{{{*/
+		void	  BedNormal(IssmDouble* bed_normal, IssmDouble xyz_list[3][3]);
+		ElementMatrix* CreateBasalMassMatrix(void);
+		ElementMatrix* CreateKMatrixPrognostic(void);
+		ElementVector* CreatePVectorPrognostic(void);
+		ElementVector* CreatePVectorSlope(void);
+		void	  GetDofList(int** pdoflist,int approximation_enum,int setenum);
+		void	  GetDofList1(int* doflist);
+		void    GetSidList(int* sidlist);
+		void    GetConnectivityList(int* connectivity);
+		int     GetElementType(void);
+		void    GetElementSizes(IssmDouble* hx,IssmDouble* hy,IssmDouble* hz);
+		void    GetInputListOnVertices(IssmDouble* pvalue,int enumtype);
+		void    GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue);
+		void    GetInputValue(IssmDouble* pvalue,Node* node,int enumtype);
+		void	  GetPhi(IssmDouble* phi, IssmDouble*  epsilon, IssmDouble viscosity);
+		void	  GetSolutionFromInputsEnthalpy(Vector* solutiong);
+		IssmDouble  GetStabilizationParameter(IssmDouble u, IssmDouble v, IssmDouble w, IssmDouble diameter, IssmDouble kappa);
+		void    GetStrainRate3dPattyn(IssmDouble* epsilon,IssmDouble* xyz_list, GaussPenta* gauss, Input* vx_input, Input* vy_input);
+		void    GetStrainRate3d(IssmDouble* epsilon,IssmDouble* xyz_list, GaussPenta* gauss, Input* vx_input, Input* vy_input, Input* vz_input);
+		Penta*  GetUpperElement(void);
+		Penta*  GetLowerElement(void);
+		Penta*  GetBasalElement(void);
+		void	  InputExtrude(int enum_type,int object_type);
+		void    InputUpdateFromSolutionPrognostic(IssmDouble* solutiong);
+		void    InputUpdateFromSolutionOneDof(IssmDouble* solutiong,int enum_type);
+		void    InputUpdateFromSolutionOneDofCollapsed(IssmDouble* solutiong,int enum_type);
+		bool	  IsInput(int name);
+		bool	  IsOnSurface(void);
+		bool	  IsOnBed(void);
+		bool    IsFloating(void); 
+		bool    IsNodeOnShelf(); 
+		bool    IsNodeOnShelfFromFlags(IssmDouble* flags);
+		bool    IsOnWater(void); 
+		IssmDouble  MinEdgeLength(IssmDouble xyz_list[6][3]);
+		void	  ReduceMatrixStokes(IssmDouble* Ke_reduced, IssmDouble* Ke_temp);
+		void	  ReduceVectorStokes(IssmDouble* Pe_reduced, IssmDouble* Ke_temp, IssmDouble* Pe_temp);
+		void	  SetClone(int* minranks);
+		Tria*	  SpawnTria(int g0, int g1, int g2);
+		void	  SurfaceNormal(IssmDouble* surface_normal, IssmDouble xyz_list[3][3]);
+
+		#ifdef _HAVE_DIAGNOSTIC_
+		ElementMatrix* CreateKMatrixCouplingMacAyealPattyn(void);
+		ElementMatrix* CreateKMatrixCouplingMacAyealPattynViscous(void);
+		ElementMatrix* CreateKMatrixCouplingMacAyealPattynFriction(void);
+		ElementMatrix* CreateKMatrixCouplingMacAyealStokes(void);
+		ElementMatrix* CreateKMatrixCouplingMacAyealStokesViscous(void);
+		ElementMatrix* CreateKMatrixCouplingMacAyealStokesFriction(void);
+		ElementMatrix* CreateKMatrixCouplingPattynStokes(void);
+		ElementMatrix* CreateKMatrixDiagnosticHoriz(void);
+		ElementMatrix* CreateKMatrixAdjointHoriz(void);
+		ElementVector* CreateDVectorDiagnosticHoriz(void);
+		ElementVector* CreateDVectorDiagnosticStokes(void);
+		ElementMatrix* CreateKMatrixDiagnosticHutter(void);
+		ElementMatrix* CreateKMatrixDiagnosticMacAyeal2d(void);
+		ElementMatrix* CreateKMatrixDiagnosticMacAyeal3d(void);
+		ElementMatrix* CreateKMatrixDiagnosticMacAyeal3dViscous(void);
+		ElementMatrix* CreateKMatrixDiagnosticMacAyeal3dFriction(void);
+		ElementMatrix* CreateKMatrixDiagnosticMacAyealPattyn(void);
+		ElementMatrix* CreateKMatrixDiagnosticMacAyealStokes(void);
+		ElementMatrix* CreateKMatrixDiagnosticL1L2(void);
+		ElementMatrix* CreateKMatrixDiagnosticL1L2Viscous(void);
+		ElementMatrix* CreateKMatrixDiagnosticL1L2Friction(void);
+		ElementMatrix* CreateKMatrixDiagnosticPattyn(void);
+		ElementMatrix* CreateKMatrixDiagnosticPattynViscous(void);
+		ElementMatrix* CreateKMatrixDiagnosticPattynFriction(void);
+		ElementMatrix* CreateKMatrixDiagnosticPattynStokes(void);
+		ElementMatrix* CreateKMatrixDiagnosticStokes(void);
+		ElementMatrix* CreateKMatrixDiagnosticStokesViscous(void);
+		ElementMatrix* CreateKMatrixDiagnosticStokesFriction(void);
+		ElementMatrix* CreateKMatrixDiagnosticVert(void);
+		ElementMatrix* CreateKMatrixDiagnosticVertVolume(void);
+		ElementMatrix* CreateKMatrixDiagnosticVertSurface(void);
+		ElementMatrix* CreateJacobianDiagnosticHoriz(void);
+		ElementMatrix* CreateJacobianDiagnosticMacayeal2d(void);
+		ElementMatrix* CreateJacobianDiagnosticPattyn(void);
+		ElementMatrix* CreateJacobianDiagnosticStokes(void);
+		void           InputUpdateFromSolutionDiagnosticHoriz( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionDiagnosticMacAyeal( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionDiagnosticMacAyealPattyn( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionDiagnosticMacAyealStokes( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionDiagnosticL1L2( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionDiagnosticPattyn( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionDiagnosticPattynStokes( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionDiagnosticHutter( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionDiagnosticVert( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionDiagnosticStokes( IssmDouble* solutiong);
+		void	         GetSolutionFromInputsDiagnosticHoriz(Vector* solutiong);
+		void	         GetSolutionFromInputsDiagnosticHutter(Vector* solutiong);
+		void	         GetSolutionFromInputsDiagnosticStokes(Vector* solutiong);
+		void	         GetSolutionFromInputsDiagnosticVert(Vector* solutiong);
+		ElementVector* CreatePVectorCouplingMacAyealStokes(void);
+		ElementVector* CreatePVectorCouplingMacAyealStokesViscous(void);
+		ElementVector* CreatePVectorCouplingMacAyealStokesFriction(void);
+		ElementVector* CreatePVectorCouplingPattynStokes(void);
+		ElementVector* CreatePVectorCouplingPattynStokesViscous(void);
+		ElementVector* CreatePVectorCouplingPattynStokesFriction(void);
+		ElementVector* CreatePVectorDiagnosticHoriz(void);
+		ElementVector* CreatePVectorDiagnosticHutter(void);
+		ElementVector* CreatePVectorDiagnosticMacAyeal(void);
+		ElementVector* CreatePVectorDiagnosticMacAyealPattyn(void);
+		ElementVector* CreatePVectorDiagnosticMacAyealStokes(void);
+		ElementVector* CreatePVectorDiagnosticL1L2(void);
+		ElementVector* CreatePVectorDiagnosticPattyn(void);
+		ElementVector* CreatePVectorDiagnosticPattynStokes(void);
+		ElementVector* CreatePVectorDiagnosticStokes(void);
+		ElementVector* CreatePVectorDiagnosticStokesViscous(void);
+		ElementVector* CreatePVectorDiagnosticStokesShelf(void);
+		ElementVector* CreatePVectorDiagnosticVert(void);
+		ElementVector* CreatePVectorDiagnosticVertVolume(void);
+		ElementVector* CreatePVectorDiagnosticVertBase(void);
+		void GetL1L2Viscosity(IssmDouble*, IssmDouble*, GaussPenta*, Input*, Input*, Input*);
+		#endif
+
+		#ifdef _HAVE_CONTROL_
+		ElementVector* CreatePVectorAdjointHoriz(void);
+		ElementMatrix* CreateKMatrixAdjointMacAyeal2d(void);
+		ElementMatrix* CreateKMatrixAdjointPattyn(void);
+		ElementMatrix* CreateKMatrixAdjointStokes(void);
+		ElementVector* CreatePVectorAdjointMacAyeal(void);
+		ElementVector* CreatePVectorAdjointPattyn(void);
+		ElementVector* CreatePVectorAdjointStokes(void);
+		void    InputUpdateFromSolutionAdjointHoriz( IssmDouble* solutiong);
+		void    InputUpdateFromSolutionAdjointStokes( IssmDouble* solutiong);
+		#endif
+
+		#ifdef _HAVE_HYDROLOGY_
+		void    CreateHydrologyWaterVelocityInput(void);
+		#endif
+		#ifdef _HAVE_THERMAL_
+		ElementMatrix* CreateKMatrixEnthalpy(void);
+		ElementMatrix* CreateKMatrixEnthalpyVolume(void);
+		ElementMatrix* CreateKMatrixEnthalpyShelf(void);
+		ElementMatrix* CreateKMatrixThermal(void);
+		ElementMatrix* CreateKMatrixMelting(void);
+		ElementMatrix* CreateKMatrixThermalVolume(void);
+		ElementMatrix* CreateKMatrixThermalShelf(void);
+		ElementVector* CreatePVectorEnthalpy(void);
+		ElementVector* CreatePVectorEnthalpyVolume(void);
+		ElementVector* CreatePVectorEnthalpyShelf(void);
+		ElementVector* CreatePVectorEnthalpySheet(void);
+		ElementVector* CreatePVectorMelting(void);
+		ElementVector* CreatePVectorThermal(void);
+		ElementVector* CreatePVectorThermalVolume(void);
+		ElementVector* CreatePVectorThermalShelf(void);
+		ElementVector* CreatePVectorThermalSheet(void);
+		void	       GetSolutionFromInputsThermal(Vector* solutiong);
+		void           InputUpdateFromSolutionThermal( IssmDouble* solutiong);
+		void           InputUpdateFromSolutionEnthalpy( IssmDouble* solutiong);
+		#endif
+		#ifdef _HAVE_BALANCED_
+		ElementMatrix* CreateKMatrixBalancethickness(void);
+		ElementVector* CreatePVectorBalancethickness(void);
+		#endif
+		/*}}}*/
+};
+#endif  /* _PENTA_H */
Index: /issm/trunk/src/c/classes/objects/Elements/PentaHook.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/PentaHook.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/PentaHook.cpp	(revision 13395)
@@ -0,0 +1,104 @@
+/*!\file PentaHook.c
+ * \brief: implementation of the PentaHook object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Object constructors and destructor*/
+/*FUNCTION PentaHook::PentaHook(){{{*/
+PentaHook::PentaHook(){
+	numanalyses=UNDEF;
+	this->hnodes=NULL;
+	this->hmaterial=NULL;
+	this->hmatpar=NULL;
+	this->hneighbors=NULL;
+}
+/*}}}*/
+/*FUNCTION PentaHook::~PentaHook(){{{*/
+PentaHook::~PentaHook(){
+
+	int i;
+
+	for(i=0;inumanalyses;i++){
+		if (this->hnodes[i]) delete this->hnodes[i];
+	}
+	delete [] this->hnodes;
+	delete hmaterial;
+	delete hmatpar;
+	delete hneighbors;
+}
+/*}}}*/
+/*FUNCTION PentaHook::PentaHook(int in_numanalyses,int material_id, int matpar_id){{{*/
+PentaHook::PentaHook(int in_numanalyses,int material_id, IoModel* iomodel){
+
+	/*intermediary: */
+	int matpar_id;
+	
+	/*retrieve parameters: */
+	iomodel->Constant(&matpar_id,MeshNumberofelementsEnum); matpar_id++;
+
+	this->numanalyses=in_numanalyses;
+	this->hnodes=new Hook*[in_numanalyses];
+	this->hmaterial=new Hook(&material_id,1);
+	this->hmatpar=new Hook(&matpar_id,1);
+	this->hneighbors=NULL; 
+
+	//Initialize hnodes as NULL
+	for(int i=0;inumanalyses;i++){
+		this->hnodes[i]=NULL;
+	}
+
+}
+/*}}}*/
+
+/*FUNCTION PentaHook::SetHookNodes{{{*/
+void PentaHook::SetHookNodes(int* node_ids,int analysis_counter){
+	this->hnodes[analysis_counter]= new Hook(node_ids,6);
+
+}
+/*}}}*/
+/*FUNCTION PentaHook::InitHookNeighbors{{{*/
+void PentaHook::InitHookNeighbors(int* element_ids){
+	this->hneighbors=new Hook(element_ids,2);
+
+}
+/*}}}*/
+/*FUNCTION PentaHook::SpawnTriaHook{{{*/
+void PentaHook::SpawnTriaHook(TriaHook* triahook,int* indices){
+
+	int i;
+	int zero=0;
+
+	triahook->numanalyses=this->numanalyses;
+	triahook->hnodes=new Hook*[this->numanalyses];
+
+	for(i=0;inumanalyses;i++){
+		/*Do not do anything if Hook is empty*/
+		if (!this->hnodes[i] || this->hnodes[i]->GetNum()==0){
+			triahook->hnodes[i]=NULL;
+		}
+		else{
+			/*Else, spawn Hook*/
+			triahook->hnodes[i]=this->hnodes[i]->Spawn(indices,3);
+		}
+	}
+	// do not spawn hmaterial. material will be taken care of by Penta
+	triahook->hmaterial=NULL;
+	triahook->hmatpar=(Hook*)this->hmatpar->copy();
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Elements/PentaHook.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/PentaHook.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/PentaHook.h	(revision 13395)
@@ -0,0 +1,33 @@
+/*!\file: PentaHook.h
+ * \brief prototypes for PentaHook.h
+ */ 
+
+#ifndef _PENTAHOOK_H_
+#define  _PENTAHOOK_H_
+
+class Hook;
+class TriaHook;
+class IoModel;
+
+class PentaHook{
+
+	public: 
+		int   numanalyses; //number of analysis types
+		Hook** hnodes; // 6 nodes for each analysis type
+		Hook*  hmaterial; // 1 ice material
+		Hook*  hmatpar; // 1 material parameter
+		Hook*  hneighbors; // 2 elements, first down, second up
+
+		/*FUNCTION constructors, destructors {{{*/
+		PentaHook();
+		PentaHook(int in_numanalyses,int material_id, IoModel* iomodel);
+		~PentaHook();
+		void SetHookNodes(int* node_ids,int analysis_counter);
+		void SpawnTriaHook(TriaHook* triahook,int* indices);
+		void InitHookNeighbors(int* element_ids);
+		/*}}}*/
+};
+
+
+#endif //ifndef _PENTAHOOK_H_
+
Index: /issm/trunk/src/c/classes/objects/Elements/PentaRef.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/PentaRef.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/PentaRef.cpp	(revision 13395)
@@ -0,0 +1,1267 @@
+/*!\file PentaRef.c
+ * \brief: implementation of the PentaRef object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Element macros*/
+#define NUMNODESP1    6
+#define NUMNODESP1_2d 3
+#define NUMNODESMINI  7
+
+/*Object constructors and destructor*/
+/*FUNCTION PentaRef::PentaRef(){{{*/
+PentaRef::PentaRef(){
+	this->element_type_list=NULL;
+}
+/*}}}*/
+/*FUNCTION PentaRef::PentaRef(int* types,int nummodels){{{*/
+PentaRef::PentaRef(const int nummodels){
+
+	/*Only allocate pointer*/
+	element_type_list=xNew(nummodels);
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::~PentaRef(){{{*/
+PentaRef::~PentaRef(){
+	xDelete(element_type_list);
+}
+/*}}}*/
+
+/*Management*/
+/*FUNCTION PentaRef::SetElementType{{{*/
+void PentaRef::SetElementType(int type,int type_counter){
+
+	_assert_(type==P1Enum || type==P1DGEnum);
+
+	/*initialize element type*/
+	this->element_type_list[type_counter]=type;
+}
+/*}}}*/
+
+/*Reference Element numerics*/
+/*FUNCTION PentaRef::GetBMacAyealPattyn {{{*/
+void PentaRef::GetBMacAyealPattyn(IssmDouble* B, IssmDouble* xyz_list, GaussPenta* gauss){
+	/*Compute B  matrix. B=[B1 B2 B3 B4 B5 B6] where Bi is of size 5*NDOF2. 
+	 * For node i, Bi can be expressed in the actual coordinate system
+	 * by: 
+	 *       Bi=[ dh/dx          0      ]
+	 *          [   0           dh/dy   ]
+	 *          [ 1/2*dh/dy  1/2*dh/dx  ]
+	 * where h is the interpolation function for node i.
+	 *
+	 * We assume B has been allocated already, of size: 5x(NDOF2*NUMNODESP1)
+	 */
+
+	IssmDouble dbasis[3][NUMNODESP1];
+
+	/*Get dbasis in actual coordinate system: */
+	GetNodalFunctionsP1Derivatives(&dbasis[0][0],xyz_list, gauss);
+
+	/*Build B: */
+	for (int i=0;icoord1*(1-gauss->coord4)/2.0;
+	l1l2l3[1]=gauss->coord2*(1-gauss->coord4)/2.0;
+	l1l2l3[2]=gauss->coord3*(1-gauss->coord4)/2.0;
+
+	/*Build LStokes: */
+	for (int i=0;i<3;i++){
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+0)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+1)=0.;
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+2)=0.;
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+3)=0.;
+
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+0)=0.;
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+1)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+2)=0.;
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+3)=0.;
+	}
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetLprimeStokes {{{*/
+void PentaRef::GetLprimeStokes(IssmDouble* LprimeStokes, IssmDouble* xyz_list, GaussPenta* gauss){
+
+	/*
+	 * Compute Lprime  matrix. Lprime=[Lp1 Lp2 Lp3] where Lpi is square and of size numdof. 
+	 * For node i, Lpi can be expressed in the actual coordinate system
+	 * by: 
+	 *       Lpi=[ h    0    0   0]1
+	 *		       [ 0    h    0   0]2
+	 *		       [ h    0    0   0]3
+	 *		       [ 0    h    0   0]4
+	 *		       [ 0    0    h   0]5
+	 *		       [ 0    0    h   0]6
+	 *		       [ 0    0  dh/dz 0]7
+	 *		       [ 0    0  dh/dz 0]8
+	 *		       [ 0    0  dh/dz 0]9
+	 *		       [dh/dz 0  dh/dx 0]0
+	 *		       [ 0 dh/dz dh/dy 0]1
+	 *           [ 0    0    0   h]2
+	 *           [ 0    0    0   h]3
+	 *           [ 0    0    0   h]4
+	 *
+	 *       Li=[ h    0    0   0]1
+	 *	 	      [ 0    h    0   0]2
+	 *		      [ 0    0    h   0]3
+	 *		      [ 0    0    h   0]4
+	 *	 	      [ h    0    0   0]5
+	 *	 	      [ 0    h    0   0]6
+	 *	 	      [ h    0    0   0]7
+	 *	 	      [ 0    h    0   0]8
+	 *		      [ 0    0    h   0]9
+	 *		      [ 0    0    h   0]0
+	 *		      [ 0    0    h   0]1
+	 *	 	      [ h    0    0   0]2
+	 *	 	      [ 0    h    0   0]3
+	 *		      [ 0    0    h   0]4
+	 * where h is the interpolation function for node i.
+	 */
+	int i;
+	int num_dof=4;
+
+	IssmDouble l1l2l3[NUMNODESP1_2d];
+	IssmDouble dh1dh6[3][NUMNODESP1];
+
+	/*Get l1l2l3 in actual coordinate system: */
+	l1l2l3[0]=gauss->coord1*(1-gauss->coord4)/2.0;
+	l1l2l3[1]=gauss->coord2*(1-gauss->coord4)/2.0;
+	l1l2l3[2]=gauss->coord3*(1-gauss->coord4)/2.0;
+
+	GetNodalFunctionsP1Derivatives(&dh1dh6[0][0],xyz_list,gauss);
+
+	/*Build LprimeStokes: */
+	for (i=0;i<3;i++){
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i)=l1l2l3[i]; //LprimeStokes[0][NDOF2*i]=dh1dh3[0][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+1)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+1)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*4+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*4+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*4+num_dof*i+2)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*4+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*5+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*5+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*5+num_dof*i+2)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*5+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*6+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*6+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*6+num_dof*i+2)=dh1dh6[2][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*6+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*7+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*7+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*7+num_dof*i+2)=dh1dh6[2][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*7+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*8+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*8+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*8+num_dof*i+2)=dh1dh6[2][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*8+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*9+num_dof*i)=dh1dh6[2][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*9+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*9+num_dof*i+2)=dh1dh6[0][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*9+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*10+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*10+num_dof*i+1)=dh1dh6[2][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*10+num_dof*i+2)=dh1dh6[1][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*10+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*11+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*11+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*11+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*11+num_dof*i+3)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*12+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*12+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*12+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*12+num_dof*i+3)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*13+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*13+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*13+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*13+num_dof*i+3)=l1l2l3[i];
+	}
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetLMacAyealStokes {{{*/
+void PentaRef::GetLMacAyealStokes(IssmDouble* LStokes, GaussPenta* gauss){
+	/*
+	 * Compute L  matrix. L=[L1 L2 L3] where Li is square and of size numdof. 
+	 * For node i, Li can be expressed in the actual coordinate system
+	 * by: 
+	 *       Li=[ h    0 ]
+	 *	 	      [ 0    h ]
+	 *	 	      [ h    0 ]
+	 *	 	      [ 0    h ]
+	 *	 	      [ h    0 ]
+	 *	 	      [ 0    h ]
+	 *	 	      [ h    0 ]
+	 *	 	      [ 0    h ]
+	 * where h is the interpolation function for node i.
+	 */
+
+	int i;
+	int num_dof=2;
+
+	IssmDouble l1l2l3[NUMNODESP1_2d];
+
+
+	/*Get l1l2l3 in actual coordinate system: */
+	l1l2l3[0]=gauss->coord1*(1-gauss->coord4)/2.0;
+	l1l2l3[1]=gauss->coord2*(1-gauss->coord4)/2.0;
+	l1l2l3[2]=gauss->coord3*(1-gauss->coord4)/2.0;
+
+	/*Build LStokes: */
+	for (i=0;i<3;i++){
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i)=l1l2l3[i]; //LStokes[0][NDOF2*i]=dh1dh3[0][i];
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+1)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+1)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*2+num_dof*i)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+1)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*3+num_dof*i)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+1)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*4+num_dof*i)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*4+num_dof*i+1)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*5+num_dof*i)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*5+num_dof*i+1)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*6+num_dof*i)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*6+num_dof*i+1)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*7+num_dof*i)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*7+num_dof*i+1)=l1l2l3[i];
+
+	}
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetLprimeMacAyealStokes {{{*/
+void PentaRef::GetLprimeMacAyealStokes(IssmDouble* LprimeStokes, IssmDouble* xyz_list, GaussPenta* gauss){
+
+	/*
+	 * Compute Lprime  matrix. Lprime=[Lp1 Lp2 Lp3] where Lpi is square and of size numdof. 
+	 * For node i, Lpi can be expressed in the actual coordinate system
+	 * by: 
+	 *       Lpi=[ h    0    0   0]
+	 *		       [ 0    h    0   0]
+	 *		       [ 0    0    h   0]
+	 *		       [ 0    0    h   0]
+	 *		       [ 0    0  dh/dz 0]
+	 *		       [ 0    0  dh/dz 0]
+	 *           [ 0    0    0   h]
+	 *           [ 0    0    0   h]
+	 * where h is the interpolation function for node i.
+	 */
+	int i;
+	int num_dof=4;
+
+	IssmDouble l1l2l3[NUMNODESP1_2d];
+	IssmDouble dh1dh6[3][NUMNODESP1];
+
+	/*Get l1l2l3 in actual coordinate system: */
+	l1l2l3[0]=gauss->coord1*(1-gauss->coord4)/2.0;
+	l1l2l3[1]=gauss->coord2*(1-gauss->coord4)/2.0;
+	l1l2l3[2]=gauss->coord3*(1-gauss->coord4)/2.0;
+
+	GetNodalFunctionsP1Derivatives(&dh1dh6[0][0],xyz_list,gauss);
+
+	/*Build LprimeStokes: */
+	for (i=0;i<3;i++){
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i)=l1l2l3[i]; //LprimeStokes[0][NDOF2*i]=dh1dh3[0][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+1)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+2)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+2)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*4+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*4+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*4+num_dof*i+2)=dh1dh6[2][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*4+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*5+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*5+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*5+num_dof*i+2)=dh1dh6[2][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*5+num_dof*i+3)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*6+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*6+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*6+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*6+num_dof*i+3)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*7+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*7+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*7+num_dof*i+2)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*7+num_dof*i+3)=l1l2l3[i];
+	}
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetLStokesMacAyeal {{{*/
+void PentaRef::GetLStokesMacAyeal(IssmDouble* LStokes, GaussPenta* gauss){
+	/*
+	 * Compute L  matrix. L=[L1 L2 L3] where Li is square and of size numdof. 
+	 * For node i, Li can be expressed in the actual coordinate system
+	 * by: 
+	 *       Li=[ h    0    0   0]
+	 *	 	      [ 0    h    0   0]
+	 *		      [ 0    0    h   0]
+	 *		      [ 0    0    h   0]
+	 * where h is the interpolation function for node i.
+	 */
+
+	int i;
+	int num_dof=4;
+
+	IssmDouble l1l2l3[NUMNODESP1_2d];
+
+
+	/*Get l1l2l3 in actual coordinate system: */
+	l1l2l3[0]=gauss->coord1*(1-gauss->coord4)/2.0;
+	l1l2l3[1]=gauss->coord2*(1-gauss->coord4)/2.0;
+	l1l2l3[2]=gauss->coord3*(1-gauss->coord4)/2.0;
+
+	/*Build LStokes: */
+	for (i=0;i<3;i++){
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i)=l1l2l3[i]; //LStokes[0][NDOF2*i]=dh1dh3[0][i];
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+1)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+2)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+3)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+1)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+2)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+3)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*2+num_dof*i)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+1)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+2)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+3)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*3+num_dof*i)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+1)=0;
+		*(LStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+2)=l1l2l3[i];
+		*(LStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+3)=0;
+
+	}
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetLprimeStokesMacAyeal {{{*/
+void PentaRef::GetLprimeStokesMacAyeal(IssmDouble* LprimeStokes, IssmDouble* xyz_list, GaussPenta* gauss){
+
+	/*
+	 * Compute Lprime  matrix. Lprime=[Lp1 Lp2 Lp3] where Lpi is square and of size numdof. 
+	 * For node i, Lpi can be expressed in the actual coordinate system
+	 * by: 
+	 *       Lpi=[ h    0 ]
+	 *		       [ 0    h ]
+	 *		       [ h    0 ]
+	 *		       [ 0    h ]
+	 * where h is the interpolation function for node i.
+	 */
+	int i;
+	int num_dof=2;
+
+	IssmDouble l1l2l3[NUMNODESP1_2d];
+	IssmDouble dh1dh6[3][NUMNODESP1];
+
+	/*Get l1l2l3 in actual coordinate system: */
+	l1l2l3[0]=gauss->coord1*(1-gauss->coord4)/2.0;
+	l1l2l3[1]=gauss->coord2*(1-gauss->coord4)/2.0;
+	l1l2l3[2]=gauss->coord3*(1-gauss->coord4)/2.0;
+
+	GetNodalFunctionsP1Derivatives(&dh1dh6[0][0],xyz_list,gauss);
+
+	/*Build LprimeStokes: */
+	for (i=0;i<3;i++){
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i)=l1l2l3[i]; //LprimeStokes[0][NDOF2*i]=dh1dh3[0][i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*0+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*1+num_dof*i+1)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i)=l1l2l3[i];
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*2+num_dof*i+1)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i)=0;
+		*(LprimeStokes+num_dof*NUMNODESP1_2d*3+num_dof*i+1)=l1l2l3[i];
+	}
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetJacobian {{{*/
+void PentaRef::GetJacobian(IssmDouble* J, IssmDouble* xyz_list,GaussPenta* gauss){
+
+	int i,j;
+
+	/*The Jacobian is constant over the element, discard the gaussian points. 
+	 * J is assumed to have been allocated of size NDOF2xNDOF2.*/
+
+	IssmDouble A1,A2,A3; //area coordinates
+	IssmDouble xi,eta,zi; //parametric coordinates
+
+	IssmDouble x1,x2,x3,x4,x5,x6;
+	IssmDouble y1,y2,y3,y4,y5,y6;
+	IssmDouble z1,z2,z3,z4,z5,z6;
+
+	/*Figure out xi,eta and zi (parametric coordinates), for this gaussian point: */
+	A1=gauss->coord1;
+	A2=gauss->coord2;
+	A3=gauss->coord3;
+
+	xi=A2-A1;
+	eta=SQRT3*A3;
+	zi=gauss->coord4;
+
+	x1=*(xyz_list+3*0+0);
+	x2=*(xyz_list+3*1+0);
+	x3=*(xyz_list+3*2+0);
+	x4=*(xyz_list+3*3+0);
+	x5=*(xyz_list+3*4+0);
+	x6=*(xyz_list+3*5+0);
+
+	y1=*(xyz_list+3*0+1);
+	y2=*(xyz_list+3*1+1);
+	y3=*(xyz_list+3*2+1);
+	y4=*(xyz_list+3*3+1);
+	y5=*(xyz_list+3*4+1);
+	y6=*(xyz_list+3*5+1);
+
+	z1=*(xyz_list+3*0+2);
+	z2=*(xyz_list+3*1+2);
+	z3=*(xyz_list+3*2+2);
+	z4=*(xyz_list+3*3+2);
+	z5=*(xyz_list+3*4+2);
+	z6=*(xyz_list+3*5+2);
+
+	*(J+NDOF3*0+0)=0.25*(x1-x2-x4+x5)*zi+0.25*(-x1+x2-x4+x5);
+	*(J+NDOF3*1+0)=SQRT3/12.0*(x1+x2-2*x3-x4-x5+2*x6)*zi+SQRT3/12.0*(-x1-x2+2*x3-x4-x5+2*x6);
+	*(J+NDOF3*2+0)=SQRT3/12.0*(x1+x2-2*x3-x4-x5+2*x6)*eta+1/4*(x1-x2-x4+x5)*xi +0.25*(-x1+x5-x2+x4);
+
+	*(J+NDOF3*0+1)=0.25*(y1-y2-y4+y5)*zi+0.25*(-y1+y2-y4+y5);
+	*(J+NDOF3*1+1)=SQRT3/12.0*(y1+y2-2*y3-y4-y5+2*y6)*zi+SQRT3/12.0*(-y1-y2+2*y3-y4-y5+2*y6);
+	*(J+NDOF3*2+1)=SQRT3/12.0*(y1+y2-2*y3-y4-y5+2*y6)*eta+0.25*(y1-y2-y4+y5)*xi+0.25*(y4-y1+y5-y2);
+
+	*(J+NDOF3*0+2)=0.25*(z1-z2-z4+z5)*zi+0.25*(-z1+z2-z4+z5);
+	*(J+NDOF3*1+2)=SQRT3/12.0*(z1+z2-2*z3-z4-z5+2*z6)*zi+SQRT3/12.0*(-z1-z2+2*z3-z4-z5+2*z6);
+	*(J+NDOF3*2+2)=SQRT3/12.0*(z1+z2-2*z3-z4-z5+2*z6)*eta+0.25*(z1-z2-z4+z5)*xi+0.25*(-z1+z5-z2+z4);
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetJacobianDeterminant {{{*/
+void PentaRef::GetJacobianDeterminant(IssmDouble*  Jdet, IssmDouble* xyz_list,GaussPenta* gauss){
+	/*On a penta, Jacobian varies according to coordinates. We need to get the Jacobian, and take 
+	 * the determinant of it: */
+	IssmDouble J[3][3];
+
+	/*Get Jacobian*/
+	GetJacobian(&J[0][0],xyz_list,gauss);
+
+	/*Get Determinant*/
+	Matrix3x3Determinant(Jdet,&J[0][0]);
+	if(*Jdet<0) _error_("negative jacobian determinant!");
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetTriaJacobianDeterminant{{{*/
+void PentaRef::GetTriaJacobianDeterminant(IssmDouble*  Jdet, IssmDouble* xyz_list,GaussPenta* gauss){
+	/*The Jacobian determinant is constant over the element, discard the gaussian points. 
+	 * J is assumed to have been allocated of size NDOF2xNDOF2.*/
+
+	IssmDouble x1,x2,x3,y1,y2,y3,z1,z2,z3;
+
+	x1=*(xyz_list+3*0+0);
+	y1=*(xyz_list+3*0+1);
+	z1=*(xyz_list+3*0+2);
+	x2=*(xyz_list+3*1+0);
+	y2=*(xyz_list+3*1+1);
+	z2=*(xyz_list+3*1+2);
+	x3=*(xyz_list+3*2+0);
+	y3=*(xyz_list+3*2+1);
+	z3=*(xyz_list+3*2+2);
+
+	/*Jdet = norm( AB ^ AC ) / (2 * area of the reference triangle), with areaRef=sqrt(3) */
+	*Jdet=SQRT3/6.0*pow(pow(((y2-y1)*(z3-z1)-(z2-z1)*(y3-y1)),2.0)+pow(((z2-z1)*(x3-x1)-(x2-x1)*(z3-z1)),2.0)+pow(((x2-x1)*(y3-y1)-(y2-y1)*(x3-x1)),2.0),0.5);
+	if(*Jdet<0) _error_("negative jacobian determinant!");
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetSegmentJacobianDeterminant{{{*/
+void PentaRef::GetSegmentJacobianDeterminant(IssmDouble*  Jdet, IssmDouble* xyz_list,GaussPenta* gauss){
+	/*The Jacobian determinant is constant over the element, discard the gaussian points. 
+	 * J is assumed to have been allocated of size NDOF2xNDOF2.*/
+
+	IssmDouble x1,x2,y1,y2,z1,z2;
+
+	x1=*(xyz_list+3*0+0);
+	y1=*(xyz_list+3*0+1);
+	z1=*(xyz_list+3*0+2);
+	x2=*(xyz_list+3*1+0);
+	y2=*(xyz_list+3*1+1);
+	z2=*(xyz_list+3*1+2);
+
+	*Jdet=1.0/2.0*sqrt(pow(x2-x1,2.) + pow(y2-y1,2.) + pow(z2-z1,2.));
+	if(*Jdet<0) _error_("negative jacobian determinant!");
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetJacobianInvert {{{*/
+void PentaRef::GetJacobianInvert(IssmDouble* Jinv, IssmDouble* xyz_list,GaussPenta* gauss){
+
+	/*Jacobian*/
+	IssmDouble J[3][3];
+
+	/*Call Jacobian routine to get the jacobian:*/
+	GetJacobian(&J[0][0], xyz_list, gauss);
+
+	/*Invert Jacobian matrix: */
+	Matrix3x3Invert(Jinv,&J[0][0]);
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetNodalFunctionsMINI{{{*/
+void PentaRef::GetNodalFunctionsMINI(IssmDouble* l1l7, GaussPenta* gauss){
+	/*This routine returns the values of the nodal functions  at the gaussian point.*/
+
+	l1l7[0]=gauss->coord1*(1.0-gauss->coord4)/2.0;
+	l1l7[1]=gauss->coord2*(1.0-gauss->coord4)/2.0;
+	l1l7[2]=gauss->coord3*(1.0-gauss->coord4)/2.0;
+	l1l7[3]=gauss->coord1*(1.0+gauss->coord4)/2.0;
+	l1l7[4]=gauss->coord2*(1.0+gauss->coord4)/2.0;
+	l1l7[5]=gauss->coord3*(1.0+gauss->coord4)/2.0;
+	l1l7[6]=27*gauss->coord1*gauss->coord2*gauss->coord3*(1.0+gauss->coord4)*(1.0-gauss->coord4);
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetNodalFunctionsMINIDerivatives{{{*/
+void PentaRef::GetNodalFunctionsMINIDerivatives(IssmDouble* dh1dh7,IssmDouble* xyz_list, GaussPenta* gauss){
+
+	/*This routine returns the values of the nodal functions derivatives  (with respect to the 
+	 * actual coordinate system): */
+
+	int       i;
+	IssmDouble    dh1dh7_ref[3][NUMNODESMINI];
+	IssmDouble    Jinv[3][3];
+
+	/*Get derivative values with respect to parametric coordinate system: */
+	GetNodalFunctionsMINIDerivativesReference(&dh1dh7_ref[0][0], gauss); 
+
+	/*Get Jacobian invert: */
+	GetJacobianInvert(&Jinv[0][0], xyz_list, gauss);
+
+	/*Build dh1dh6: 
+	 *
+	 * [dhi/dx]= Jinv'*[dhi/dr]
+	 * [dhi/dy]        [dhi/ds]
+	 * [dhi/dz]        [dhi/dzeta]
+	 */
+
+	for (i=0;icoord2-gauss->coord1;
+	IssmDouble s=-3.0/SQRT3*(gauss->coord1+gauss->coord2-2.0/3.0);
+	IssmDouble zeta=gauss->coord4;
+
+	/*First nodal function: */
+	*(dl1dl7+NUMNODESMINI*0+0)=-0.5*(1.0-zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*1+0)=-SQRT3/6.0*(1.0-zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*2+0)=-0.5*(-0.5*r-SQRT3/6.0*s+ONETHIRD);
+
+	/*Second nodal function: */
+	*(dl1dl7+NUMNODESMINI*0+1)=0.5*(1.0-zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*1+1)=-SQRT3/6.0*(1.0-zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*2+1)=-0.5*(0.5*r-SQRT3/6.0*s+ONETHIRD);
+
+	/*Third nodal function: */
+	*(dl1dl7+NUMNODESMINI*0+2)=0;
+	*(dl1dl7+NUMNODESMINI*1+2)=SQRT3/3.0*(1.0-zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*2+2)=-0.5*(SQRT3/3.0*s+ONETHIRD);
+
+	/*Fourth nodal function: */
+	*(dl1dl7+NUMNODESMINI*0+3)=-0.5*(1.0+zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*1+3)=-SQRT3/6.0*(1.0+zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*2+3)=0.5*(-0.5*r-SQRT3/6.0*s+ONETHIRD);
+
+	/*Fith nodal function: */
+	*(dl1dl7+NUMNODESMINI*0+4)=0.5*(1.0+zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*1+4)=-SQRT3/6.0*(1.0+zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*2+4)=0.5*(0.5*r-SQRT3/6.0*s+ONETHIRD);
+
+	/*Sixth nodal function: */
+	*(dl1dl7+NUMNODESMINI*0+5)=0;
+	*(dl1dl7+NUMNODESMINI*1+5)=SQRT3/3.0*(1.0+zeta)/2.0;
+	*(dl1dl7+NUMNODESMINI*2+5)=0.5*(SQRT3/3.0*s+ONETHIRD);
+
+	/*Seventh nodal function: */
+	*(dl1dl7+NUMNODESMINI*0+6)=9.0/2.0*r*(1.0+zeta)*(zeta-1.0)*(SQRT3*s+1.0);
+	*(dl1dl7+NUMNODESMINI*1+6)=9.0/4.0*(1+zeta)*(1-zeta)*(SQRT3*pow(s,2.0)-2.0*s-SQRT3*pow(r,2.0));
+	*(dl1dl7+NUMNODESMINI*2+6)=27*gauss->coord1*gauss->coord2*gauss->coord3*(-2.0*zeta);
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetNodalFunctionsP1 {{{*/
+void PentaRef::GetNodalFunctionsP1(IssmDouble* l1l6, GaussPenta* gauss){
+	/*This routine returns the values of the nodal functions  at the gaussian point.*/
+
+	l1l6[0]=gauss->coord1*(1-gauss->coord4)/2.0;
+	l1l6[1]=gauss->coord2*(1-gauss->coord4)/2.0;
+	l1l6[2]=gauss->coord3*(1-gauss->coord4)/2.0;
+	l1l6[3]=gauss->coord1*(1+gauss->coord4)/2.0;
+	l1l6[4]=gauss->coord2*(1+gauss->coord4)/2.0;
+	l1l6[5]=gauss->coord3*(1+gauss->coord4)/2.0;
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetNodalFunctionsP1Derivatives {{{*/
+void PentaRef::GetNodalFunctionsP1Derivatives(IssmDouble* dh1dh6,IssmDouble* xyz_list, GaussPenta* gauss){
+
+	/*This routine returns the values of the nodal functions derivatives  (with respect to the 
+	 * actual coordinate system): */
+	IssmDouble    dh1dh6_ref[NDOF3][NUMNODESP1];
+	IssmDouble    Jinv[NDOF3][NDOF3];
+
+	/*Get derivative values with respect to parametric coordinate system: */
+	GetNodalFunctionsP1DerivativesReference(&dh1dh6_ref[0][0], gauss); 
+
+	/*Get Jacobian invert: */
+	GetJacobianInvert(&Jinv[0][0], xyz_list, gauss);
+
+	/*Build dh1dh3: 
+	 *
+	 * [dhi/dx]= Jinv*[dhi/dr]
+	 * [dhi/dy]       [dhi/ds]
+	 * [dhi/dz]       [dhi/dn]
+	 */
+
+	for (int i=0;icoord1; _assert_(A1>=0 && A1<=1);//first area coordinate value. In term of xi and eta: A1=(1-xi)/2-eta/(2*SQRT3);
+	A2=gauss->coord2; _assert_(A2>=0 && A2<=1);//second area coordinate value In term of xi and eta: A2=(1+xi)/2-eta/(2*SQRT3);
+	A3=gauss->coord3; _assert_(A3>=0 && A3<=1);//third area coordinate value  In term of xi and eta: A3=y/SQRT3;
+	z =gauss->coord4; _assert_(z>=-1 &&  z<=1);//fourth vertical coordinate value. Corresponding nodal function: (1-z)/2 and (1+z)/2
+
+	/*First nodal function derivatives. The corresponding nodal function is N=A1*(1-z)/2. Its derivatives follow*/
+	*(dl1dl6+NUMNODESP1*0+0)=-0.5*(1.0-z)/2.0;
+	*(dl1dl6+NUMNODESP1*1+0)=-0.5/SQRT3*(1.0-z)/2.0;
+	*(dl1dl6+NUMNODESP1*2+0)=-0.5*A1;
+
+	/*Second nodal function: The corresponding nodal function is N=A2*(1-z)/2. Its derivatives follow*/
+	*(dl1dl6+NUMNODESP1*0+1)=0.5*(1.0-z)/2.0;
+	*(dl1dl6+NUMNODESP1*1+1)=-0.5/SQRT3*(1.0-z)/2.0;
+	*(dl1dl6+NUMNODESP1*2+1)=-0.5*A2;
+
+	/*Third nodal function: The corresponding nodal function is N=A3*(1-z)/2. Its derivatives follow*/
+	*(dl1dl6+NUMNODESP1*0+2)=0.0;
+	*(dl1dl6+NUMNODESP1*1+2)=1.0/SQRT3*(1.0-z)/2.0;
+	*(dl1dl6+NUMNODESP1*2+2)=-0.5*A3;
+
+	/*Fourth nodal function: The corresponding nodal function is N=A1*(1+z)/2. Its derivatives follow*/
+	*(dl1dl6+NUMNODESP1*0+3)=-0.5*(1.0+z)/2.0;
+	*(dl1dl6+NUMNODESP1*1+3)=-0.5/SQRT3*(1.0+z)/2.0;
+	*(dl1dl6+NUMNODESP1*2+3)=0.5*A1;
+
+	/*Fifth nodal function: The corresponding nodal function is N=A2*(1+z)/2. Its derivatives follow*/
+	*(dl1dl6+NUMNODESP1*0+4)=0.5*(1.0+z)/2.0;
+	*(dl1dl6+NUMNODESP1*1+4)=-0.5/SQRT3*(1.0+z)/2.0;
+	*(dl1dl6+NUMNODESP1*2+4)=0.5*A2;
+
+	/*Sixth nodal function: The corresponding nodal function is N=A3*(1+z)/2. Its derivatives follow*/
+	*(dl1dl6+NUMNODESP1*0+5)=0.0;
+	*(dl1dl6+NUMNODESP1*1+5)=1.0/SQRT3*(1.0+z)/2.0;
+	*(dl1dl6+NUMNODESP1*2+5)=0.5*A3;
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetQuadNodalFunctions {{{*/
+void PentaRef::GetQuadNodalFunctions(IssmDouble* l1l4,GaussPenta* gauss,int index1,int index2,int index3,int index4){
+	/*This routine returns the values of the nodal functions  at the gaussian point.*/
+
+	IssmDouble BasisFunctions[6];
+
+	GetNodalFunctionsP1(&BasisFunctions[0],gauss);
+
+	_assert_(index1>=0 && index1<6);
+	_assert_(index2>=0 && index2<6);
+	_assert_(index3>=0 && index3<6);
+	_assert_(index4>=0 && index4<6);
+
+	l1l4[0]=BasisFunctions[index1];
+	l1l4[1]=BasisFunctions[index2];
+	l1l4[2]=BasisFunctions[index3];
+	l1l4[3]=BasisFunctions[index4];
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetQuadJacobianDeterminant{{{*/
+void PentaRef::GetQuadJacobianDeterminant(IssmDouble* Jdet,IssmDouble xyz_list[4][3],GaussPenta* gauss){
+	/*This routine returns the values of the nodal functions  at the gaussian point.*/
+
+	IssmDouble x1,x2,x3,x4,y1,y2,y3,y4,z1,z2,z3,z4;
+
+	x1=xyz_list[0][0];
+	y1=xyz_list[0][1];
+	z1=xyz_list[0][2];
+	x2=xyz_list[1][0];
+	y2=xyz_list[1][1];
+	z2=xyz_list[1][2];
+	x3=xyz_list[2][0];
+	y3=xyz_list[2][1];
+	z3=xyz_list[2][2];
+	x4=xyz_list[3][0];
+	y4=xyz_list[3][1];
+	z4=xyz_list[3][2];
+
+	/*Jdet = (Area of the trapezoid)/(Area trapezoid ref) with AreaRef = 4*/
+	/*Area of a trabezoid = altitude * (base1 + base2)/2 */
+	*Jdet= pow(pow(x2-x1,2.) + pow(y2-y1,2.),0.5) * (z4-z1 + z3-z2)/8;
+	if(*Jdet<0) _error_("negative jacobian determinant!");
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetInputValue{{{*/
+void PentaRef::GetInputValue(IssmDouble* pvalue,IssmDouble* plist,GaussPenta* gauss){
+	/*P1 interpolation on Gauss point*/
+
+	/*intermediary*/
+	IssmDouble l1l6[6];
+
+	/*nodal functions: */
+	GetNodalFunctionsP1(&l1l6[0],gauss);
+
+	/*Assign output pointers:*/
+	*pvalue=l1l6[0]*plist[0]+l1l6[1]*plist[1]+l1l6[2]*plist[2]+l1l6[3]*plist[3]+l1l6[4]*plist[4]+l1l6[5]*plist[5];
+
+}
+/*}}}*/
+/*FUNCTION PentaRef::GetInputDerivativeValue{{{*/
+void PentaRef::GetInputDerivativeValue(IssmDouble* p, IssmDouble* plist,IssmDouble* xyz_list, GaussPenta* gauss){
+	/*From node values of parameter p (p_list[0], p_list[1], p_list[2], p_list[3], p_list[4] and p_list[4]), return parameter derivative value at gaussian point specified by gauss_coord:
+	 *   dp/dx=p_list[0]*dh1/dx+p_list[1]*dh2/dx+p_list[2]*dh3/dx+p_list[3]*dh4/dx+p_list[4]*dh5/dx+p_list[5]*dh6/dx;
+	 *   dp/dy=p_list[0]*dh1/dy+p_list[1]*dh2/dy+p_list[2]*dh3/dy+p_list[3]*dh4/dy+p_list[4]*dh5/dy+p_list[5]*dh6/dy;
+	 *   dp/dz=p_list[0]*dh1/dz+p_list[1]*dh2/dz+p_list[2]*dh3/dz+p_list[3]*dh4/dz+p_list[4]*dh5/dz+p_list[5]*dh6/dz;
+	 *
+	 *   p is a vector of size 3x1 already allocated.
+	 */
+	IssmDouble dh1dh6[3][NUMNODESP1];
+
+	/*Get nodal funnctions derivatives in actual coordinate system: */
+	GetNodalFunctionsP1Derivatives(&dh1dh6[0][0],xyz_list, gauss);
+
+	/*Assign output*/
+	p[0]=plist[0]*dh1dh6[0][0]+plist[1]*dh1dh6[0][1]+plist[2]*dh1dh6[0][2]+plist[3]*dh1dh6[0][3]+plist[4]*dh1dh6[0][4]+plist[5]*dh1dh6[0][5];
+	p[1]=plist[0]*dh1dh6[1][0]+plist[1]*dh1dh6[1][1]+plist[2]*dh1dh6[1][2]+plist[3]*dh1dh6[1][3]+plist[4]*dh1dh6[1][4]+plist[5]*dh1dh6[1][5];
+	p[2]=plist[0]*dh1dh6[2][0]+plist[1]*dh1dh6[2][1]+plist[2]*dh1dh6[2][2]+plist[3]*dh1dh6[2][3]+plist[4]*dh1dh6[2][4]+plist[5]*dh1dh6[2][5];
+
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Elements/PentaRef.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/PentaRef.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/PentaRef.h	(revision 13395)
@@ -0,0 +1,63 @@
+/*!\file:  PentaRef.h
+ * \brief abstract class for handling Penta oriented routines, like nodal functions, 
+ * strain rate generation, etc ...
+ */ 
+
+
+#ifndef _PENTAREF_H_
+#define _PENTAREF_H_
+
+class PentaRef{
+	
+
+	public: 
+		int* element_type_list; //P1CG, P1DG, MINI, P2...
+		int  element_type;
+		
+		PentaRef();
+		PentaRef(const int nummodels);
+		~PentaRef();
+
+		/*Management*/
+		void SetElementType(int type,int type_counter);
+
+		/*Numerics*/
+		void GetNodalFunctionsP1(IssmDouble* l1l6, GaussPenta* gauss);
+		void GetNodalFunctionsMINI(IssmDouble* l1l7, GaussPenta* gauss);
+		void GetNodalFunctionsP1Derivatives(IssmDouble* dh1dh6,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetNodalFunctionsMINIDerivatives(IssmDouble* dh1dh7,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetNodalFunctionsP1DerivativesReference(IssmDouble* dl1dl6,GaussPenta* gauss);
+		void GetNodalFunctionsMINIDerivativesReference(IssmDouble* dl1dl7,GaussPenta* gauss);
+		void GetQuadNodalFunctions(IssmDouble* l1l4,GaussPenta* gauss,int index1,int index2,int index3,int index4);
+		void GetQuadJacobianDeterminant(IssmDouble*  Jdet, IssmDouble xyz_list[4][3],GaussPenta* gauss);
+		void GetJacobian(IssmDouble* J, IssmDouble* xyz_list,GaussPenta* gauss);
+		void GetJacobianDeterminant(IssmDouble*  Jdet, IssmDouble* xyz_list,GaussPenta* gauss);
+		void GetTriaJacobianDeterminant(IssmDouble*  Jdet, IssmDouble* xyz_list,GaussPenta* gauss);
+		void GetSegmentJacobianDeterminant(IssmDouble*  Jdet, IssmDouble* xyz_list,GaussPenta* gauss);
+		void GetJacobianInvert(IssmDouble*  Jinv, IssmDouble* xyz_list,GaussPenta* gauss);
+		void GetBMacAyealPattyn(IssmDouble* B, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBMacAyealStokes(IssmDouble* B, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBPattyn(IssmDouble* B, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBStokes(IssmDouble* B, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBprimeMacAyealStokes(IssmDouble* Bprime, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBprimePattyn(IssmDouble* B, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBprimeStokes(IssmDouble* B_prime, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBprimeVert(IssmDouble* B, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBAdvec(IssmDouble* B_advec, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBConduct(IssmDouble* B_conduct, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBVert(IssmDouble* B, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetBprimeAdvec(IssmDouble* Bprime_advec, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetL(IssmDouble* L, GaussPenta* gauss,int numdof);
+		void GetLStokes(IssmDouble* LStokes, GaussPenta* gauss);
+		void GetLprimeStokes(IssmDouble* LprimeStokes, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetLMacAyealStokes(IssmDouble* LMacAyealStokes, GaussPenta* gauss);
+		void GetLprimeMacAyealStokes(IssmDouble* LprimeMacAyealStokes, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetLStokesMacAyeal(IssmDouble* LStokesMacAyeal, GaussPenta* gauss);
+		void GetLprimeStokesMacAyeal(IssmDouble* LprimeStokesMacAyeal, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetInputValue(IssmDouble* pvalue,IssmDouble* plist, GaussPenta* gauss);
+		void GetInputValue(IssmDouble* pvalue,IssmDouble* plist,GaussTria* gauss){_error_("only PentaGauss are supported");};
+		void GetInputDerivativeValue(IssmDouble* pvalues, IssmDouble* plist,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetInputDerivativeValue(IssmDouble* pvalues, IssmDouble* plist,IssmDouble* xyz_list, GaussTria* gauss){_error_("only PentaGauss are supported");};
+
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/Elements/Tria.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/Tria.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/Tria.cpp	(revision 13395)
@@ -0,0 +1,5965 @@
+/*!\file Tria.cpp
+ * \brief: implementation of the Tria object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Element macros*/
+#define NUMVERTICES 3
+
+/*Constructors/destructor/copy*/
+/*FUNCTION Tria::Tria(){{{*/
+Tria::Tria(){
+
+	int i;
+
+	this->nodes=NULL;
+	this->material=NULL;
+	this->matpar=NULL;
+	for(i=0;i<3;i++)this->horizontalneighborsids[i]=UNDEF;
+	this->inputs=NULL;
+	this->parameters=NULL;
+	this->results=NULL;
+
+}
+/*}}}*/
+/*FUNCTION Tria::Tria(int id, int sid,int index, IoModel* iomodel,int nummodels){{{*/
+Tria::Tria(int tria_id, int tria_sid, int index, IoModel* iomodel,int nummodels)
+	:TriaRef(nummodels)
+	,TriaHook(nummodels,index+1,iomodel){
+		
+		int i;
+		/*id: */
+		this->id=tria_id;
+		this->sid=tria_sid;
+
+		//this->parameters: we still can't point to it, it may not even exist. Configure will handle this.
+		this->parameters=NULL;
+
+		/*Build horizontalneighborsids list: */
+		_assert_(iomodel->Data(MeshElementconnectivityEnum));
+		//for (i=0;i<3;i++) this->horizontalneighborsids[i]=(int)iomodel->elementconnectivity[3*index+i]-1;
+
+		/*intialize inputs and results: */
+		this->inputs=new Inputs();
+		this->results=new Results();
+
+		/*initialize pointers:*/
+		this->nodes=NULL;
+		this->material=NULL;
+		this->matpar=NULL;
+
+}
+/*}}}*/
+/*FUNCTION Tria::~Tria(){{{*/
+Tria::~Tria(){
+	delete inputs;
+	delete results;
+	this->parameters=NULL;
+}
+/*}}}*/
+/*FUNCTION Tria::copy {{{*/
+Object* Tria::copy() {
+
+	int i;
+	Tria* tria=NULL;
+
+	tria=new Tria();
+
+	//deal with TriaRef mother class
+	tria->element_type_list=xNew(this->numanalyses);
+	for(i=0;inumanalyses;i++) tria->element_type_list[i]=this->element_type_list[i];
+
+	//deal with TriaHook mother class
+	tria->numanalyses=this->numanalyses;
+	tria->hnodes=new Hook*[tria->numanalyses];
+	for(i=0;inumanalyses;i++)tria->hnodes[i]=(Hook*)this->hnodes[i]->copy();
+	tria->hmaterial=(Hook*)this->hmaterial->copy();
+	tria->hmatpar=(Hook*)this->hmatpar->copy();
+
+	/*deal with Tria fields: */
+	tria->id=this->id;
+	tria->sid=this->sid;
+	if(this->inputs){
+		tria->inputs=(Inputs*)this->inputs->Copy();
+	}
+	else{
+		tria->inputs=new Inputs();
+	}
+	if(this->results){
+		tria->results=(Results*)this->results->Copy();
+	}
+	else{
+		tria->results=new Results();
+	}
+	/*point parameters: */
+	tria->parameters=this->parameters;
+
+	/*recover objects: */
+	tria->nodes=xNew(3); //we cannot rely on an analysis_counter to tell us which analysis_type we are running, so we just copy the nodes.
+	for(i=0;i<3;i++)tria->nodes[i]=this->nodes[i];
+	tria->material=(Material*)tria->hmaterial->delivers();
+	tria->matpar=(Matpar*)tria->hmatpar->delivers();
+
+	/*neighbors: */
+	for(i=0;i<3;i++)tria->horizontalneighborsids[i]=this->horizontalneighborsids[i];
+
+	return tria;
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION Tria::AverageOntoPartition {{{*/
+void  Tria::AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part){
+
+	bool      already=false;
+	int       i,j;
+	int       partition[NUMVERTICES];
+	int       offsetsid[NUMVERTICES];
+	int       offsetdof[NUMVERTICES];
+	IssmDouble    area;
+	IssmDouble    mean;
+	IssmDouble    values[3];
+
+	/*First, get the area: */
+	area=this->GetArea();
+
+	/*Figure out the average for this element: */
+	this->GetSidList(&offsetsid[0]);
+	this->GetDofList1(&offsetdof[0]);
+	mean=0;
+	for(i=0;i(qmu_part[offsetsid[i]]);
+		mean=mean+1.0/NUMVERTICES*vertex_response[offsetdof[i]];
+	}
+
+	/*Add contribution: */
+	for(i=0;iSetValue(partition[i],mean*area,ADD_VAL);
+			partition_areas->SetValue(partition[i],area,ADD_VAL);
+		};
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrix {{{*/
+void  Tria::CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df){
+
+	/*retreive parameters: */
+	ElementMatrix* Ke=NULL;
+	int analysis_type;
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Checks in debugging mode{{{*/
+	_assert_(this->nodes && this->material && this->matpar && this->parameters && this->inputs);
+	/*}}}*/
+	
+	/*Skip if water element*/
+	if(IsOnWater()) return;
+
+	/*Just branch to the correct element stiffness matrix generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+		#ifdef _HAVE_DIAGNOSTIC_
+		case DiagnosticHorizAnalysisEnum:
+			Ke=CreateKMatrixDiagnosticMacAyeal();
+			break;
+		case AdjointHorizAnalysisEnum:
+			Ke=CreateKMatrixAdjointMacAyeal();
+			break;
+		case DiagnosticHutterAnalysisEnum:
+			Ke=CreateKMatrixDiagnosticHutter();
+			break;
+		 #endif
+		case BedSlopeXAnalysisEnum: case SurfaceSlopeXAnalysisEnum: case BedSlopeYAnalysisEnum: case SurfaceSlopeYAnalysisEnum:
+			Ke=CreateMassMatrix();
+			break;
+		case PrognosticAnalysisEnum:
+			Ke=CreateKMatrixPrognostic();
+			break;
+		#ifdef _HAVE_HYDROLOGY_
+		case HydrologyAnalysisEnum:
+			Ke=CreateKMatrixHydrology();
+			break;
+		#endif
+		#ifdef _HAVE_BALANCED_
+		case BalancethicknessAnalysisEnum:
+			Ke=CreateKMatrixBalancethickness();
+			break;
+		#endif
+		#ifdef _HAVE_CONTROL_
+		case AdjointBalancethicknessAnalysisEnum:
+			Ke=CreateKMatrixAdjointBalancethickness();
+			break;
+		#endif
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global matrix*/
+	if(Ke){
+		Ke->AddToGlobal(Kff,Kfs);
+		delete Ke;
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixMelting {{{*/
+ElementMatrix* Tria::CreateKMatrixMelting(void){
+
+	/*Constants*/
+	const int  numdof=NUMVERTICES*NDOF1;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble heatcapacity,latentheat;
+	IssmDouble Jdet,D_scalar;
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble L[3];
+	GaussTria *gauss=NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	latentheat=matpar->GetLatentHeat();
+	heatcapacity=matpar->GetHeatCapacity();
+
+	/* Start looping on the number of gauss  (nodes on the bedrock) */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetL(&L[0], &xyz_list[0][0], gauss,NDOF1);
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0], gauss);
+
+		D_scalar=latentheat/heatcapacity*gauss->weight*Jdet;
+
+		TripleMultiply(&L[0],numdof,1,0,
+					&D_scalar,1,1,0,
+					&L[0],1,numdof,0,
+					&Ke->values[0],1);
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixPrognostic {{{*/
+ElementMatrix* Tria::CreateKMatrixPrognostic(void){
+
+	switch(GetElementType()){
+		case P1Enum:
+			return CreateKMatrixPrognostic_CG();
+		case P1DGEnum:
+			return CreateKMatrixPrognostic_DG();
+		default:
+			_error_("Element type " << EnumToStringx(GetElementType()) << " not supported yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixPrognostic_CG {{{*/
+ElementMatrix* Tria::CreateKMatrixPrognostic_CG(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        stabilization;
+	int        i,j,ig,dim;
+	IssmDouble     Jdettria,DL_scalar,dt,h;
+	IssmDouble     vel,vx,vy,dvxdx,dvydy;
+	IssmDouble     dvx[2],dvy[2];
+	IssmDouble     v_gauss[2]={0.0};
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     L[NUMVERTICES];
+	IssmDouble     B[2][NUMVERTICES];
+	IssmDouble     Bprime[2][NUMVERTICES];
+	IssmDouble     K[2][2]                        ={0.0};
+	IssmDouble     KDL[2][2]                      ={0.0};
+	IssmDouble     DL[2][2]                        ={0.0};
+	IssmDouble     DLprime[2][2]                   ={0.0};
+	GaussTria *gauss=NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	this->parameters->FindParam(&dim,MeshDimensionEnum);
+	this->parameters->FindParam(&stabilization,PrognosticStabilizationEnum);
+	Input* vxaverage_input=NULL;
+	Input* vyaverage_input=NULL;
+	if(dim==2){
+		vxaverage_input=inputs->GetInput(VxEnum); _assert_(vxaverage_input);
+		vyaverage_input=inputs->GetInput(VyEnum); _assert_(vyaverage_input);
+	}
+	else{
+		vxaverage_input=inputs->GetInput(VxAverageEnum); _assert_(vxaverage_input);
+		vyaverage_input=inputs->GetInput(VyAverageEnum); _assert_(vyaverage_input);
+	}
+	h=sqrt(2*this->GetArea());
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		GetL(&L[0], &xyz_list[0][0], gauss,NDOF1);
+
+		vxaverage_input->GetInputValue(&vx,gauss);
+		vyaverage_input->GetInputValue(&vy,gauss);
+		vxaverage_input->GetInputDerivativeValue(&dvx[0],&xyz_list[0][0],gauss);
+		vyaverage_input->GetInputDerivativeValue(&dvy[0],&xyz_list[0][0],gauss);
+
+		DL_scalar=gauss->weight*Jdettria;
+
+		TripleMultiply( &L[0],1,numdof,1,
+					&DL_scalar,1,1,0,
+					&L[0],1,numdof,0,
+					&Ke->values[0],1);
+
+		GetBPrognostic(&B[0][0], &xyz_list[0][0], gauss);
+		GetBprimePrognostic(&Bprime[0][0], &xyz_list[0][0], gauss);
+
+		dvxdx=dvx[0];
+		dvydy=dvy[1];
+		DL_scalar=dt*gauss->weight*Jdettria;
+
+		DL[0][0]=DL_scalar*dvxdx;
+		DL[1][1]=DL_scalar*dvydy;
+		DLprime[0][0]=DL_scalar*vx;
+		DLprime[1][1]=DL_scalar*vy;
+
+		TripleMultiply( &B[0][0],2,numdof,1,
+					&DL[0][0],2,2,0,
+					&B[0][0],2,numdof,0,
+					&Ke->values[0],1);
+
+		TripleMultiply( &B[0][0],2,numdof,1,
+					&DLprime[0][0],2,2,0,
+					&Bprime[0][0],2,numdof,0,
+					&Ke->values[0],1);
+
+		if(stabilization==2){
+			/*Streamline upwinding*/
+			vel=sqrt(vx*vx+vy*vy)+1.e-8;
+			K[0][0]=h/(2*vel)*vx*vx;
+			K[1][0]=h/(2*vel)*vy*vx;
+			K[0][1]=h/(2*vel)*vx*vy;
+			K[1][1]=h/(2*vel)*vy*vy;
+		}
+		else if(stabilization==1){
+			/*MacAyeal*/
+			vxaverage_input->GetInputAverage(&vx);
+			vyaverage_input->GetInputAverage(&vy);
+			K[0][0]=h/2.0*fabs(vx);
+			K[0][1]=0.;
+			K[1][0]=0.;
+			K[1][1]=h/2.0*fabs(vy);
+		}
+		if(stabilization==1 || stabilization==2){
+			KDL[0][0]=DL_scalar*K[0][0];
+			KDL[1][0]=DL_scalar*K[1][0];
+			KDL[0][1]=DL_scalar*K[0][1];
+			KDL[1][1]=DL_scalar*K[1][1];
+			TripleMultiply( &Bprime[0][0],2,numdof,1,
+						&KDL[0][0],2,2,0,
+						&Bprime[0][0],2,numdof,0,
+						&Ke->values[0],1);
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixPrognostic_DG {{{*/
+ElementMatrix* Tria::CreateKMatrixPrognostic_DG(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig,dim;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     Jdettria,dt,vx,vy;
+	IssmDouble     L[NUMVERTICES];
+	IssmDouble     B[2][NUMVERTICES];
+	IssmDouble     Bprime[2][NUMVERTICES];
+	IssmDouble     DL[2][2]={0.0};
+	IssmDouble     DLprime[2][2]={0.0};
+	IssmDouble     DL_scalar;
+	GaussTria  *gauss=NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	this->parameters->FindParam(&dim,MeshDimensionEnum);
+	Input* vxaverage_input=NULL;
+	Input* vyaverage_input=NULL;
+	if(dim==2){
+		vxaverage_input=inputs->GetInput(VxEnum); _assert_(vxaverage_input);
+		vyaverage_input=inputs->GetInput(VyEnum); _assert_(vyaverage_input);
+	}
+	else{
+		vxaverage_input=inputs->GetInput(VxAverageEnum); _assert_(vxaverage_input);
+		vyaverage_input=inputs->GetInput(VyAverageEnum); _assert_(vyaverage_input);
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		vxaverage_input->GetInputValue(&vx,gauss);
+		vyaverage_input->GetInputValue(&vy,gauss);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		GetL(&L[0], &xyz_list[0][0], gauss,NDOF1);
+
+		DL_scalar=gauss->weight*Jdettria;
+
+		TripleMultiply( &L[0],1,numdof,1,
+					&DL_scalar,1,1,0,
+					&L[0],1,numdof,0,
+					&Ke->values[0],1);
+
+		/*WARNING: B and Bprime are inverted compared to usual prognostic!!!!*/
+		GetBPrognostic(&Bprime[0][0], &xyz_list[0][0], gauss);
+		GetBprimePrognostic(&B[0][0], &xyz_list[0][0], gauss);
+
+		DL_scalar=-dt*gauss->weight*Jdettria;
+
+		DLprime[0][0]=DL_scalar*vx;
+		DLprime[1][1]=DL_scalar*vy;
+
+		TripleMultiply( &B[0][0],2,numdof,1,
+					&DLprime[0][0],2,2,0,
+					&Bprime[0][0],2,numdof,0,
+					&Ke->values[0],1);
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateMassMatrix {{{*/
+ElementMatrix* Tria::CreateMassMatrix(void){
+
+	/*constants: */
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/* Intermediaries */
+	IssmDouble  D,Jdet;
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	IssmDouble  L[1][3];
+	GaussTria  *gauss = NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	GetVerticesCoordinates(&xyz_list[0][0],nodes,NUMVERTICES);
+
+	/* Start looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for(int ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+		
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		D=gauss->weight*Jdet;
+
+		GetL(&L[0][0], &xyz_list[0][0], gauss,NDOF1);
+
+		TripleMultiply(&L[0][0],1,3,1,
+					&D,1,1,0,
+					&L[0][0],1,3,0,
+					&Ke->values[0],1);
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVector {{{*/
+void  Tria::CreatePVector(Vector* pf){
+
+	/*retrive parameters: */
+	ElementVector* pe=NULL;
+	int analysis_type;
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*asserts: {{{*/
+	/*if debugging mode, check that all pointers exist*/
+	_assert_(this->nodes && this->material && this->matpar && this->parameters && this->inputs);
+	/*}}}*/
+	
+	/*Skip if water element*/
+	if(IsOnWater()) return;
+
+	/*Just branch to the correct load generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+		#ifdef _HAVE_DIAGNOSTIC_
+		case DiagnosticHorizAnalysisEnum:
+			pe=CreatePVectorDiagnosticMacAyeal();
+			break;
+		case DiagnosticHutterAnalysisEnum:
+			pe=CreatePVectorDiagnosticHutter();
+			break;
+		#endif
+		case BedSlopeXAnalysisEnum: case SurfaceSlopeXAnalysisEnum: case BedSlopeYAnalysisEnum: case SurfaceSlopeYAnalysisEnum:
+			pe=CreatePVectorSlope();
+			break;
+		case PrognosticAnalysisEnum:
+			pe=CreatePVectorPrognostic();
+			break;
+		#ifdef _HAVE_HYDROLOGY_
+		case HydrologyAnalysisEnum:
+			pe=CreatePVectorHydrology();
+			break;
+		#endif
+		#ifdef _HAVE_BALANCED_
+		case BalancethicknessAnalysisEnum:
+			pe=CreatePVectorBalancethickness();
+			break;
+		#endif
+		#ifdef _HAVE_CONTROL_
+		case AdjointBalancethicknessAnalysisEnum:
+			pe=CreatePVectorAdjointBalancethickness();
+			break;
+		case AdjointHorizAnalysisEnum:
+			pe=CreatePVectorAdjointHoriz();
+			break;
+		#endif
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global Vector*/
+	if(pe){
+		pe->AddToGlobal(pf);
+		delete pe;
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorPrognostic{{{*/
+ElementVector* Tria::CreatePVectorPrognostic(void){
+
+	switch(GetElementType()){
+		case P1Enum:
+			return CreatePVectorPrognostic_CG();
+		case P1DGEnum:
+			return CreatePVectorPrognostic_DG();
+		default:
+			_error_("Element type " << EnumToStringx(GetElementType()) << " not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorPrognostic_CG {{{*/
+ElementVector* Tria::CreatePVectorPrognostic_CG(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     Jdettria,dt;
+	IssmDouble     surface_mass_balance_g,basal_melting_g,basal_melting_correction_g,thickness_g;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     L[NUMVERTICES];
+	GaussTria* gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	Input* surface_mass_balance_input=inputs->GetInput(SurfaceforcingsMassBalanceEnum); _assert_(surface_mass_balance_input);
+	Input* basal_melting_input=inputs->GetInput(BasalforcingsMeltingRateEnum);          _assert_(basal_melting_input);
+	Input* basal_melting_correction_input=inputs->GetInput(BasalforcingsMeltingRateCorrectionEnum);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum);                             _assert_(thickness_input);
+
+	/*Initialize basal_melting_correction_g to 0, do not forget!:*/
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		GetL(&L[0], &xyz_list[0][0], gauss,NDOF1);
+
+		surface_mass_balance_input->GetInputValue(&surface_mass_balance_g,gauss);
+		basal_melting_input->GetInputValue(&basal_melting_g,gauss);
+		thickness_input->GetInputValue(&thickness_g,gauss);
+		if(basal_melting_correction_input)
+		 basal_melting_correction_input->GetInputValue(&basal_melting_correction_g,gauss);
+		else
+		 basal_melting_correction_g=0.;
+
+		for(i=0;ivalues[i]+=Jdettria*gauss->weight*(thickness_g+dt*(surface_mass_balance_g-basal_melting_g-basal_melting_correction_g))*L[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorPrognostic_DG {{{*/
+ElementVector* Tria::CreatePVectorPrognostic_DG(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     Jdettria,dt;
+	IssmDouble     surface_mass_balance_g,basal_melting_g,thickness_g;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     L[NUMVERTICES];
+	GaussTria* gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* surface_mass_balance_input=inputs->GetInput(SurfaceforcingsMassBalanceEnum); _assert_(surface_mass_balance_input);
+	Input* basal_melting_input=inputs->GetInput(BasalforcingsMeltingRateEnum);          _assert_(basal_melting_input);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum);                             _assert_(thickness_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		GetL(&L[0], &xyz_list[0][0], gauss,NDOF1);
+
+		surface_mass_balance_input->GetInputValue(&surface_mass_balance_g,gauss);
+		basal_melting_input->GetInputValue(&basal_melting_g,gauss);
+		thickness_input->GetInputValue(&thickness_g,gauss);
+
+		for(i=0;ivalues[i]+=Jdettria*gauss->weight*(thickness_g+dt*(surface_mass_balance_g-basal_melting_g))*L[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorSlope {{{*/
+ElementVector* Tria::CreatePVectorSlope(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+	
+	/*Intermediaries */
+	int        i,j,ig;
+	int        analysis_type;
+	IssmDouble     Jdet;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     slope[2];
+	IssmDouble     basis[3];
+	GaussTria* gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* slope_input=NULL;
+	if ( (analysis_type==SurfaceSlopeXAnalysisEnum) || (analysis_type==SurfaceSlopeYAnalysisEnum)){
+		slope_input=inputs->GetInput(SurfaceEnum); _assert_(slope_input);
+	}
+	if ( (analysis_type==BedSlopeXAnalysisEnum) || (analysis_type==BedSlopeYAnalysisEnum)){
+		slope_input=inputs->GetInput(BedEnum);     _assert_(slope_input);
+	}
+		
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctions(basis, gauss);
+
+		slope_input->GetInputDerivativeValue(&slope[0],&xyz_list[0][0],gauss);
+
+		if ( (analysis_type==SurfaceSlopeXAnalysisEnum) || (analysis_type==BedSlopeXAnalysisEnum)){
+			for(i=0;ivalues[i]+=Jdet*gauss->weight*slope[0]*basis[i];
+		}
+		if ( (analysis_type==SurfaceSlopeYAnalysisEnum) || (analysis_type==BedSlopeYAnalysisEnum)){
+			for(i=0;ivalues[i]+=Jdet*gauss->weight*slope[1]*basis[i];
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateJacobianMatrix{{{*/
+void  Tria::CreateJacobianMatrix(Matrix* Jff){
+
+	/*retrieve parameters: */
+	ElementMatrix* Ke=NULL;
+	int analysis_type;
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Checks in debugging {{{*/
+	_assert_(this->nodes && this->material && this->matpar && this->parameters && this->inputs);
+	/*}}}*/
+
+	/*Skip if water element*/
+	if(IsOnWater()) return;
+
+	/*Just branch to the correct element stiffness matrix generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+#ifdef _HAVE_DIAGNOSTIC_
+		case DiagnosticHorizAnalysisEnum:
+			Ke=CreateJacobianDiagnosticMacayeal();
+			break;
+#endif
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global matrix*/
+	if(Ke){
+		Ke->AddToGlobal(Jff);
+		delete Ke;
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::ComputeBasalStress {{{*/
+void  Tria::ComputeBasalStress(Vector* eps){
+	_error_("Not Implemented yet");
+}
+/*}}}*/
+/*FUNCTION Tria::ComputeStrainRate {{{*/
+void  Tria::ComputeStrainRate(Vector* eps){
+	_error_("Not Implemented yet");
+}
+/*}}}*/
+/*FUNCTION Tria::ComputeStressTensor {{{*/
+void  Tria::ComputeStressTensor(){
+
+	int         iv;
+	IssmDouble      xyz_list[NUMVERTICES][3];
+	IssmDouble      pressure,viscosity;
+	IssmDouble      epsilon[3]; /* epsilon=[exx,eyy,exy];*/
+	IssmDouble      sigma_xx[NUMVERTICES];
+	IssmDouble		sigma_yy[NUMVERTICES];
+	IssmDouble		sigma_zz[NUMVERTICES]={0,0,0};
+	IssmDouble      sigma_xy[NUMVERTICES];
+	IssmDouble		sigma_xz[NUMVERTICES]={0,0,0};
+	IssmDouble		sigma_yz[NUMVERTICES]={0,0,0};
+	GaussTria* gauss=NULL;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Retrieve all inputs we will be needing: */
+	Input* pressure_input=inputs->GetInput(PressureEnum); _assert_(pressure_input);
+	Input* vx_input=inputs->GetInput(VxEnum);             _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);             _assert_(vy_input);
+
+	/* Start looping on the number of vertices: */
+	gauss=new GaussTria();
+	for (int iv=0;ivGaussVertex(iv);
+
+		/*Compute strain rate viscosity and pressure: */
+		this->GetStrainRate2d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		material->GetViscosity2d(&viscosity,&epsilon[0]);
+		pressure_input->GetInputValue(&pressure,gauss);
+
+		/*Compute Stress*/
+		sigma_xx[iv]=2*viscosity*epsilon[0]-pressure; // sigma = nu eps - pressure
+		sigma_yy[iv]=2*viscosity*epsilon[1]-pressure;
+		sigma_xy[iv]=2*viscosity*epsilon[2];
+	}
+	
+	/*Add Stress tensor components into inputs*/
+	this->inputs->AddInput(new TriaP1Input(StressTensorxxEnum,&sigma_xx[0]));
+	this->inputs->AddInput(new TriaP1Input(StressTensorxyEnum,&sigma_xy[0]));
+	this->inputs->AddInput(new TriaP1Input(StressTensorxzEnum,&sigma_xz[0]));
+	this->inputs->AddInput(new TriaP1Input(StressTensoryyEnum,&sigma_yy[0]));
+	this->inputs->AddInput(new TriaP1Input(StressTensoryzEnum,&sigma_yz[0]));
+	this->inputs->AddInput(new TriaP1Input(StressTensorzzEnum,&sigma_zz[0]));
+
+	/*Clean up and return*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::Configure {{{*/
+void  Tria::Configure(Elements* elementsin, Loads* loadsin, DataSet* nodesin, Materials* materialsin, Parameters* parametersin){
+	
+	/*go into parameters and get the analysis_counter: */
+	int analysis_counter;
+	parametersin->FindParam(&analysis_counter,AnalysisCounterEnum);
+
+	/*Get Element type*/
+	this->element_type=this->element_type_list[analysis_counter];
+
+	/*Take care of hooking up all objects for this element, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and offsets hidden in hooks: */
+	if(this->hnodes[analysis_counter]) this->hnodes[analysis_counter]->configure(nodesin);
+	this->hmaterial->configure(materialsin);
+	this->hmatpar->configure(materialsin);
+
+	/*Now, go pick up the objects inside the hooks: */
+	if(this->hnodes[analysis_counter]) this->nodes=(Node**)this->hnodes[analysis_counter]->deliverp();
+	else this->nodes=NULL;
+	this->material=(Material*)this->hmaterial->delivers();
+	this->matpar=(Matpar*)this->hmatpar->delivers();
+
+	/*point parameters to real dataset: */
+	this->parameters=parametersin;
+
+	/*get inputs configured too: */
+	this->inputs->Configure(parameters);
+
+}
+/*}}}*/
+/*FUNCTION Tria::DeepEcho{{{*/
+void Tria::DeepEcho(void){
+
+	_printLine_("Tria:");
+	_printLine_("   id: " << id);
+	if(nodes){
+		nodes[0]->DeepEcho();
+		nodes[1]->DeepEcho();
+		nodes[2]->DeepEcho();
+	}
+	else _printLine_("nodes = NULL");
+
+	if (material) material->DeepEcho();
+	else _printLine_("material = NULL");
+
+	if (matpar) matpar->DeepEcho();
+	else _printLine_("matpar = NULL");
+
+	_printLine_("   parameters");
+	if (parameters) parameters->DeepEcho();
+	else _printLine_("parameters = NULL");
+
+	_printLine_("   inputs");
+	if (inputs) inputs->DeepEcho();
+	else _printLine_("inputs=NULL");
+
+	if (results) results->DeepEcho();
+	else _printLine_("results=NULL");
+
+	_printLine_("neighboor sids: ");
+	_printLine_(" " << horizontalneighborsids[0] << " " << horizontalneighborsids[1] << " " << horizontalneighborsids[2]);
+	
+	return;
+}
+/*}}}*/
+/*FUNCTION Tria::DeleteResults {{{*/
+void  Tria::DeleteResults(void){
+
+	/*Delete and reinitialize results*/
+	delete this->results;
+	this->results=new Results();
+
+}
+/*}}}*/
+/*FUNCTION Tria::Delta18oParameterization{{{*/
+void  Tria::Delta18oParameterization(void){
+
+	int        i;
+	IssmDouble monthlytemperatures[NUMVERTICES][12],monthlyprec[NUMVERTICES][12];
+	IssmDouble TemperaturesPresentday[NUMVERTICES][12],TemperaturesLgm[NUMVERTICES][12];
+	IssmDouble PrecipitationsPresentday[NUMVERTICES][12];
+	IssmDouble tmp[NUMVERTICES];
+	IssmDouble Delta18oPresent,Delta18oLgm,Delta18oTime;
+	IssmDouble Delta18oSurfacePresent,Delta18oSurfaceLgm,Delta18oSurfaceTime;
+	IssmDouble time,yts,finaltime;
+
+	/*Recover parameters*/
+	this->parameters->FindParam(&time,TimeEnum);
+	this->parameters->FindParam(&yts,ConstantsYtsEnum);
+	this->parameters->FindParam(&finaltime,TimesteppingFinalTimeEnum);
+
+	/*Recover present day temperature and precipitation*/
+	Input* input=inputs->GetInput(SurfaceforcingsTemperaturesPresentdayEnum);    _assert_(input);
+	Input* input2=inputs->GetInput(SurfaceforcingsTemperaturesLgmEnum);          _assert_(input2);
+	Input* input3=inputs->GetInput(SurfaceforcingsPrecipitationsPresentdayEnum); _assert_(input3);
+	GaussTria* gauss=new GaussTria();
+	for(int month=0;month<12;month++){
+		for(int iv=0;ivGaussVertex(iv);
+			input->GetInputValue(&TemperaturesPresentday[iv][month],gauss,month/12.*yts);
+			input2->GetInputValue(&TemperaturesLgm[iv][month],gauss,month/12.*yts);
+			input3->GetInputValue(&PrecipitationsPresentday[iv][month],gauss,month/12.*yts);
+			PrecipitationsPresentday[iv][month]=PrecipitationsPresentday[iv][month]/yts; // converion in m/sec
+		}
+	}
+
+	/*Recover delta18o and Delta18oSurface at present day, lgm and at time t*/
+	this->parameters->FindParam(&Delta18oPresent,SurfaceforcingsDelta18oEnum,finaltime);
+	this->parameters->FindParam(&Delta18oLgm,SurfaceforcingsDelta18oEnum,(finaltime-(21000*yts)));
+	this->parameters->FindParam(&Delta18oTime,SurfaceforcingsDelta18oEnum,time);
+	this->parameters->FindParam(&Delta18oSurfacePresent,SurfaceforcingsDelta18oSurfaceEnum,finaltime);
+	this->parameters->FindParam(&Delta18oSurfaceLgm,SurfaceforcingsDelta18oSurfaceEnum,(finaltime-(21000*yts)));
+	this->parameters->FindParam(&Delta18oSurfaceTime,SurfaceforcingsDelta18oSurfaceEnum,time);
+	
+	/*Compute the temperature and precipitation*/
+	for(int iv=0;ivAddTimeInput(newmonthinput1,time+imonth/12.*yts);
+
+		for(i=0;iAddTimeInput(newmonthinput2,time+imonth/12.*yts);
+	}
+
+	this->inputs->AddInput(NewTemperatureInput);
+	this->inputs->AddInput(NewPrecipitationInput);
+
+	/*clean-up*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::Echo{{{*/
+void Tria::Echo(void){
+	_printLine_("Tria:");
+	_printLine_("   id: " << id);
+	if(nodes){
+		nodes[0]->Echo();
+		nodes[1]->Echo();
+		nodes[2]->Echo();
+	}
+	else _printLine_("nodes = NULL");
+
+	if (material) material->Echo();
+	else _printLine_("material = NULL");
+
+	if (matpar) matpar->Echo();
+	else _printLine_("matpar = NULL");
+
+	_printLine_("   parameters");
+	if (parameters) parameters->Echo();
+	else _printLine_("parameters = NULL");
+
+	_printLine_("   inputs");
+	if (inputs) inputs->Echo();
+	else _printLine_("inputs=NULL");
+
+	if (results) results->Echo();
+	else _printLine_("results=NULL");
+
+	_printLine_("neighboor sids: ");
+	_printLine_(" " << horizontalneighborsids[0] << " " << horizontalneighborsids[1] << " " << horizontalneighborsids[2]);
+}
+/*}}}*/
+/*FUNCTION Tria::ObjectEnum{{{*/
+int Tria::ObjectEnum(void){
+
+	return TriaEnum;
+
+}
+/*}}}*/
+/*FUNCTION Tria::GetArea {{{*/
+IssmDouble Tria::GetArea(void){
+
+	IssmDouble area=0;
+	IssmDouble xyz_list[NUMVERTICES][3];
+	IssmDouble x1,y1,x2,y2,x3,y3;
+
+	/*Get xyz list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	x1=xyz_list[0][0]; y1=xyz_list[0][1];
+	x2=xyz_list[1][0]; y2=xyz_list[1][1];
+	x3=xyz_list[2][0]; y3=xyz_list[2][1];
+ 
+	_assert_(x2*y3 - y2*x3 + x1*y2 - y1*x2 + x3*y1 - y3*x1>0);
+	return (x2*y3 - y2*x3 + x1*y2 - y1*x2 + x3*y1 - y3*x1)/2;
+}
+/*}}}*/
+/*FUNCTION Tria::GetDofList {{{*/
+void  Tria::GetDofList(int** pdoflist, int approximation_enum,int setenum){
+
+	int i,j;
+	int count=0;
+	int numberofdofs=0;
+	int* doflist=NULL;
+
+	/*First, figure out size of doflist and create it: */
+	for(i=0;i<3;i++) numberofdofs+=nodes[i]->GetNumberOfDofs(approximation_enum,setenum);
+	doflist=xNew(numberofdofs);
+
+	/*Populate: */
+	count=0;
+	for(i=0;i<3;i++){
+		nodes[i]->GetDofList(doflist+count,approximation_enum,setenum);
+		count+=nodes[i]->GetNumberOfDofs(approximation_enum,setenum);
+	}
+
+	/*Assign output pointers:*/
+	*pdoflist=doflist;
+}
+/*}}}*/
+/*FUNCTION Tria::GetDofList1 {{{*/
+void  Tria::GetDofList1(int* doflist){
+
+	int i;
+	for(i=0;i<3;i++) doflist[i]=nodes[i]->GetDofList1();
+
+}
+/*}}}*/
+/*FUNCTION Tria::GetElementType {{{*/
+int Tria::GetElementType(){
+
+	/*return TriaRef field*/
+	return this->element_type;
+
+}
+/*}}}*/
+/*FUNCTION Tria::GetHorizontalNeighboorSids {{{*/
+int* Tria::GetHorizontalNeighboorSids(){
+
+	/*return TriaRef field*/
+	return &this->horizontalneighborsids[0];
+
+}
+/*}}}*/
+/*FUNCTION Tria::GetNodeIndex {{{*/
+int Tria::GetNodeIndex(Node* node){
+
+	_assert_(nodes);
+	for(int i=0;iGetInput(enumtype);
+	if (!input) _error_("Input " << EnumToStringx(enumtype) << " not found in element");
+
+	/*Checks in debugging mode*/
+	_assert_(pvalue);
+
+	/* Start looping on the number of vertices: */
+	gauss=new GaussTria();
+	for (int iv=0;ivGaussVertex(iv);
+		input->GetInputValue(&pvalue[iv],gauss);
+	}
+
+	/*clean-up*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue) {{{*/
+void Tria::GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue){
+
+	IssmDouble     value[NUMVERTICES];
+	GaussTria *gauss = NULL;
+	Input     *input = inputs->GetInput(enumtype);
+
+	/*Checks in debugging mode*/
+	_assert_(pvalue);
+
+	/* Start looping on the number of vertices: */
+	if (input){
+		gauss=new GaussTria();
+		for (int iv=0;ivGaussVertex(iv);
+			input->GetInputValue(&pvalue[iv],gauss);
+		}
+	}
+	else{
+		for (int iv=0;ivGetInput(enumtype);
+
+	/*Checks in debugging mode*/
+	_assert_(pvalue);
+
+	/* Start looping on the number of vertices: */
+	if (input){
+		gauss=new GaussTria();
+		for (int iv=0;ivGaussVertex(iv);
+			input->GetInputValue(&pvalue[iv],gauss,index);
+		}
+	}
+	else{
+		for (int iv=0;ivGetInput(enumtype);
+	if(!input) _error_("No input of type " << EnumToStringx(enumtype) << " found in tria");
+
+	GaussTria* gauss=new GaussTria();
+	gauss->GaussVertex(this->GetNodeIndex(node));
+
+	input->GetInputValue(pvalue,gauss);
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::GetSidList {{{*/
+void  Tria::GetSidList(int* sidlist){
+	for(int i=0;iGetSidList();
+}
+/*}}}*/
+/*FUNCTION Tria::GetConnectivityList {{{*/
+void  Tria::GetConnectivityList(int* connectivity){
+	for(int i=0;iGetConnectivity();
+}
+/*}}}*/
+/*FUNCTION Tria::GetSolutionFromInputs{{{*/
+void  Tria::GetSolutionFromInputs(Vector* solution){
+
+	/*retrive parameters: */
+	int analysis_type;
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Just branch to the correct InputUpdateFromSolution generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+	#ifdef _HAVE_DIAGNOSTIC_
+	case DiagnosticHorizAnalysisEnum:
+		GetSolutionFromInputsDiagnosticHoriz(solution);
+		break;
+	case DiagnosticHutterAnalysisEnum:
+		GetSolutionFromInputsDiagnosticHutter(solution);
+		break;
+	#endif
+	#ifdef _HAVE_HYDROLOGY_
+	case HydrologyAnalysisEnum:
+		GetSolutionFromInputsHydrology(solution);
+		break;
+	#endif
+	default:
+		_error_("analysis: " << EnumToStringx(analysis_type) << " not supported yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Tria::GetStrainRate2d(IssmDouble* epsilon,IssmDouble* xyz_list, GaussTria* gauss, Input* vx_input, Input* vy_input){{{*/
+void Tria::GetStrainRate2d(IssmDouble* epsilon,IssmDouble* xyz_list, GaussTria* gauss, Input* vx_input, Input* vy_input){
+	/*Compute the 2d Strain Rate (3 components):
+	 * epsilon=[exx eyy exy] */
+
+	int i;
+	IssmDouble epsilonvx[3];
+	IssmDouble epsilonvy[3];
+
+	/*Check that both inputs have been found*/
+	if (!vx_input || !vy_input){
+		_error_("Input missing. Here are the input pointers we have for vx: " << vx_input << ", vy: " << vy_input << "\n");
+	}
+
+	/*Get strain rate assuming that epsilon has been allocated*/
+	vx_input->GetVxStrainRate2d(epsilonvx,xyz_list,gauss);
+	vy_input->GetVyStrainRate2d(epsilonvy,xyz_list,gauss);
+
+	/*Sum all contributions*/
+	for(i=0;i<3;i++) epsilon[i]=epsilonvx[i]+epsilonvy[i];
+}
+/*}}}*/
+/*FUNCTION Tria::GetVectorFromInputs{{{*/
+void  Tria::GetVectorFromInputs(Vector* vector,int input_enum){
+
+	int doflist1[NUMVERTICES];
+
+	/*Get out if this is not an element input*/
+	if(!IsInput(input_enum)) return;
+
+	/*Prepare index list*/
+	this->GetDofList1(&doflist1[0]);
+
+	/*Get input (either in element or material)*/
+	Input* input=inputs->GetInput(input_enum);
+	if(!input) _error_("Input " << EnumToStringx(input_enum) << " not found in element");
+
+	/*We found the enum.  Use its values to fill into the vector, using the vertices ids: */
+	input->GetVectorFromInputs(vector,&doflist1[0]);
+}
+/*}}}*/
+/*FUNCTION Tria::GetVectorFromResults{{{*/
+void  Tria::GetVectorFromResults(Vector* vector,int offset,int enum_in,int interp){
+
+	/*Get result*/
+	ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(offset);
+	if(elementresult->InstanceEnum()!=enum_in){
+		_error_("Results of offset "<InstanceEnum())<<" when "<GetSidList(&doflist1[0]);
+		this->GetConnectivityList(&connectivity[0]);
+		elementresult->GetVectorFromResults(vector,&doflist1[0],&connectivity[0],NUMVERTICES);
+	}
+	else if(interp==P0Enum){
+		elementresult->GetElementVectorFromResults(vector,sid);
+	}
+	else{
+		_printLine_("Interpolation " << EnumToStringx(interp) << " not supported");
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::Id {{{*/
+int    Tria::Id(){
+	
+	return id;
+
+}
+/*}}}*/
+/*FUNCTION Tria::Sid {{{*/
+int    Tria::Sid(){
+	
+	return sid;
+
+}
+/*}}}*/
+/*FUNCTION Tria::InputArtificialNoise{{{*/
+void  Tria::InputArtificialNoise(int enum_type,IssmDouble min,IssmDouble max){
+
+	Input* input=NULL;
+
+	/*Make a copy of the original input: */
+	input=(Input*)this->inputs->GetInput(enum_type);
+	if(!input)_error_("could not find old input with enum: " << EnumToStringx(enum_type));
+
+	/*ArtificialNoise: */
+	input->ArtificialNoise(min,max);
+}
+/*}}}*/
+/*FUNCTION Tria::InputConvergence{{{*/
+bool Tria::InputConvergence(IssmDouble* eps, int* enums,int num_enums,int* criterionenums,IssmDouble* criterionvalues,int num_criterionenums){
+
+	bool    converged=true;
+	int     i;
+	Input** new_inputs=NULL;
+	Input** old_inputs=NULL;
+
+	new_inputs=xNew(num_enums/2); //half the enums are for the new inputs
+	old_inputs=xNew(num_enums/2); //half the enums are for the old inputs
+
+	for(i=0;iinputs->GetInput(enums[2*i+0]);
+		old_inputs[i]=(Input*)this->inputs->GetInput(enums[2*i+1]);
+		if(!new_inputs[i])_error_("could not find input with enum " << EnumToStringx(enums[2*i+0]));
+		if(!old_inputs[i])_error_("could not find input with enum " << EnumToStringx(enums[2*i+0]));
+	}
+
+	/*ok, we've got the inputs (new and old), now loop throught the number of criterions and fill the eps array:*/
+	for(i=0;icriterionvalues[i]) converged=false; 
+	}
+
+	/*clean up and return*/
+	xDelete(new_inputs);
+	xDelete(old_inputs);
+	return converged;
+}
+/*}}}*/
+/*FUNCTION Tria::InputDepthAverageAtBase {{{*/
+void  Tria::InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum){
+
+	/*New input*/
+	Input* oldinput=NULL;
+	Input* newinput=NULL;
+
+	/*copy input of enum_type*/
+	if (object_enum==MeshElementsEnum)
+	 oldinput=(Input*)this->inputs->GetInput(enum_type);
+	else if (object_enum==MaterialsEnum)
+	 oldinput=(Input*)this->material->inputs->GetInput(enum_type);
+	else
+	 _error_("object " << EnumToStringx(object_enum) << " not supported yet");
+	if(!oldinput)_error_("could not find old input with enum: " << EnumToStringx(enum_type));
+	newinput=(Input*)oldinput->copy();
+
+	/*Assign new name (average)*/
+	newinput->ChangeEnum(average_enum_type);
+
+	/*Add new input to current element*/
+	if (object_enum==MeshElementsEnum)
+	 this->inputs->AddInput((Input*)newinput);
+	else if (object_enum==MaterialsEnum)
+	 this->material->inputs->AddInput((Input*)newinput);
+	else
+	 _error_("object " << EnumToStringx(object_enum) << " not supported yet");
+}
+/*}}}*/
+/*FUNCTION Tria::InputDuplicate{{{*/
+void  Tria::InputDuplicate(int original_enum,int new_enum){
+
+	/*Call inputs method*/
+	if (IsInput(original_enum)) inputs->DuplicateInput(original_enum,new_enum);
+
+}
+/*}}}*/
+/*FUNCTION Tria::InputScale{{{*/
+void  Tria::InputScale(int enum_type,IssmDouble scale_factor){
+
+	Input* input=NULL;
+
+	/*Make a copy of the original input: */
+	input=(Input*)this->inputs->GetInput(enum_type);
+	if(!input)_error_("could not find old input with enum: " << EnumToStringx(enum_type));
+
+	/*Scale: */
+	input->Scale(scale_factor);
+}
+/*}}}*/
+/*FUNCTION Tria::InputToResult{{{*/
+void  Tria::InputToResult(int enum_type,int step,IssmDouble time){
+
+	int    i;
+	Input *input = NULL;	
+
+	/*Go through all the input objects, and find the one corresponding to enum_type, if it exists: */
+	if (enum_type==MaterialsRheologyBbarEnum || enum_type==MaterialsRheologyZbarEnum) input=this->material->inputs->GetInput(enum_type);
+	else input=this->inputs->GetInput(enum_type);
+	//if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found in tria->inputs");
+	if(!input)return;
+
+	/*If we don't find it, no big deal, just don't do the transfer. Otherwise, build a new Result 
+	 * object out of the input, with the additional step and time information: */
+	this->results->AddObject((Object*)input->SpawnResult(step,time));
+	
+	#ifdef _HAVE_CONTROL_
+	if(input->ObjectEnum()==ControlInputEnum){
+		if(((ControlInput*)input)->gradient!=NULL) this->results->AddObject((Object*)((ControlInput*)input)->SpawnGradient(step,time));
+	}
+	#endif
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromConstant(int value, int name);{{{*/
+void  Tria::InputUpdateFromConstant(int constant, int name){
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	/*update input*/
+	this->inputs->AddInput(new IntInput(name,constant));
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromConstant(IssmDouble value, int name);{{{*/
+void  Tria::InputUpdateFromConstant(IssmDouble constant, int name){
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	/*update input*/
+	this->inputs->AddInput(new DoubleInput(name,constant));
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromConstant(bool value, int name);{{{*/
+void  Tria::InputUpdateFromConstant(bool constant, int name){
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	/*update input*/
+	this->inputs->AddInput(new BoolInput(name,constant));
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromIoModel{{{*/
+void Tria::InputUpdateFromIoModel(int index, IoModel* iomodel){ //i is the element index
+
+	/*Intermediaries*/
+	int        i,j;
+	int        tria_vertex_ids[3];
+	IssmDouble nodeinputs[3];
+	IssmDouble cmmininputs[3];
+	IssmDouble cmmaxinputs[3];
+	bool       control_analysis   = false;
+	int        num_control_type;
+	IssmDouble yts;
+	int        num_cm_responses;
+   
+	/*Get parameters: */
+	iomodel->Constant(&yts,ConstantsYtsEnum); 
+	iomodel->Constant(&control_analysis,InversionIscontrolEnum);
+	if(control_analysis) iomodel->Constant(&num_control_type,InversionNumControlParametersEnum);
+	if(control_analysis) iomodel->Constant(&num_cm_responses,InversionNumCostFunctionsEnum);
+
+	/*Recover vertices ids needed to initialize inputs*/
+	for(i=0;i<3;i++){ 
+		tria_vertex_ids[i]=reCast(iomodel->Data(MeshElementsEnum)[3*index+i]); //ids for vertices are in the elements array from Matlab
+	}
+
+	/*Control Inputs*/
+	#ifdef _HAVE_CONTROL_
+	if (control_analysis && iomodel->Data(InversionControlParametersEnum)){
+		for(i=0;i(iomodel->Data(InversionControlParametersEnum)[i])){
+				case BalancethicknessThickeningRateEnum:
+					if (iomodel->Data(BalancethicknessThickeningRateEnum)){
+						for(j=0;j<3;j++)nodeinputs[j]=iomodel->Data(BalancethicknessThickeningRateEnum)[tria_vertex_ids[j]-1]/yts;
+						for(j=0;j<3;j++)cmmininputs[j]=iomodel->Data(InversionMinParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i]/yts;
+						for(j=0;j<3;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i]/yts;
+						this->inputs->AddInput(new ControlInput(BalancethicknessThickeningRateEnum,TriaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+					}
+					break;
+				case VxEnum:
+					if (iomodel->Data(VxEnum)){
+						for(j=0;j<3;j++)nodeinputs[j]=iomodel->Data(VxEnum)[tria_vertex_ids[j]-1]/yts;
+						for(j=0;j<3;j++)cmmininputs[j]=iomodel->Data(InversionMinParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i]/yts;
+						for(j=0;j<3;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i]/yts;
+						this->inputs->AddInput(new ControlInput(VxEnum,TriaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+					}
+					break;
+				case VyEnum:
+					if (iomodel->Data(VyEnum)){
+						for(j=0;j<3;j++)nodeinputs[j]=iomodel->Data(VyEnum)[tria_vertex_ids[j]-1]/yts;
+						for(j=0;j<3;j++)cmmininputs[j]=iomodel->Data(InversionMinParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i]/yts;
+						for(j=0;j<3;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i]/yts;
+						this->inputs->AddInput(new ControlInput(VyEnum,TriaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+					}
+					break;
+				case FrictionCoefficientEnum:
+					if (iomodel->Data(FrictionCoefficientEnum)){
+						for(j=0;j<3;j++)nodeinputs[j]=iomodel->Data(FrictionCoefficientEnum)[tria_vertex_ids[j]-1];
+						for(j=0;j<3;j++)cmmininputs[j]=iomodel->Data(InversionMinParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i];
+						for(j=0;j<3;j++)cmmaxinputs[j]=iomodel->Data(InversionMaxParametersEnum)[(tria_vertex_ids[j]-1)*num_control_type+i];
+						this->inputs->AddInput(new ControlInput(FrictionCoefficientEnum,TriaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+					}
+					break;
+				case MaterialsRheologyBbarEnum:
+				case MaterialsRheologyZbarEnum:
+					/*Material will take care of it*/ break;
+				default:
+					_error_("Control " << EnumToStringx(reCast(iomodel->Data(InversionControlParametersEnum)[i])) << " not implemented yet");
+			}
+		}
+	}
+	#endif
+
+	/*DatasetInputs*/
+	if (control_analysis && iomodel->Data(InversionCostFunctionsCoefficientsEnum)){
+
+		/*Create inputs and add to DataSetInput*/
+		DatasetInput* datasetinput=new DatasetInput(InversionCostFunctionsCoefficientsEnum);
+		for(i=0;iData(InversionCostFunctionsCoefficientsEnum)[(tria_vertex_ids[j]-1)*num_cm_responses+i];
+			datasetinput->inputs->AddObject(new TriaP1Input(InversionCostFunctionsCoefficientsEnum,nodeinputs));
+		}
+
+		/*Add datasetinput to element inputs*/
+		this->inputs->AddInput(datasetinput);
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromSolution {{{*/
+void  Tria::InputUpdateFromSolution(IssmDouble* solution){
+
+	/*retrive parameters: */
+	int analysis_type;
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Just branch to the correct InputUpdateFromSolution generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+		#ifdef _HAVE_DIAGNOSTIC_
+		case DiagnosticHorizAnalysisEnum:
+			InputUpdateFromSolutionDiagnosticHoriz( solution);
+			break;
+		case DiagnosticHutterAnalysisEnum:
+			InputUpdateFromSolutionDiagnosticHoriz( solution);
+			break;
+		#endif
+		#ifdef _HAVE_CONTROL_
+		case AdjointHorizAnalysisEnum:
+			InputUpdateFromSolutionAdjointHoriz( solution);
+			break;
+		case AdjointBalancethicknessAnalysisEnum:
+			InputUpdateFromSolutionAdjointBalancethickness( solution);
+			break;
+		#endif
+		#ifdef _HAVE_HYDROLOGY_ 
+		case HydrologyAnalysisEnum:
+			InputUpdateFromSolutionHydrology(solution);
+			break ;
+		#endif
+	 	#ifdef _HAVE_BALANCED_
+		case BalancethicknessAnalysisEnum:
+			InputUpdateFromSolutionOneDof(solution,ThicknessEnum);
+			break;
+		#endif
+		case BedSlopeXAnalysisEnum:
+			InputUpdateFromSolutionOneDof(solution,BedSlopeXEnum);
+			break;
+		case BedSlopeYAnalysisEnum:
+			InputUpdateFromSolutionOneDof(solution,BedSlopeYEnum);
+			break;
+		case SurfaceSlopeXAnalysisEnum:
+			InputUpdateFromSolutionOneDof(solution,SurfaceSlopeXEnum);
+			break;
+		case SurfaceSlopeYAnalysisEnum:
+			InputUpdateFromSolutionOneDof(solution,SurfaceSlopeYEnum);
+			break;
+		case PrognosticAnalysisEnum:
+			InputUpdateFromSolutionPrognostic(solution);
+			break;
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromSolutionOneDof{{{*/
+void  Tria::InputUpdateFromSolutionOneDof(IssmDouble* solution,int enum_type){
+
+	const int numdof          = NDOF1*NUMVERTICES;
+
+	int*      doflist=NULL;
+	IssmDouble    values[numdof];
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(int i=0;i(values[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Add input to the element: */
+	this->inputs->AddInput(new TriaP1Input(enum_type,values));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromSolutionPrognostic{{{*/
+void  Tria::InputUpdateFromSolutionPrognostic(IssmDouble* solution){
+
+	/*Intermediaries*/
+	const int numdof = NDOF1*NUMVERTICES;
+
+	int       i,hydroadjustment;
+	int*      doflist=NULL;
+	IssmDouble    rho_ice,rho_water,minthickness;
+	IssmDouble    newthickness[numdof];
+	IssmDouble    newbed[numdof];
+	IssmDouble    newsurface[numdof];
+	IssmDouble    oldbed[NUMVERTICES];
+	IssmDouble    oldsurface[NUMVERTICES];
+	IssmDouble    oldthickness[NUMVERTICES];
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	this->parameters->FindParam(&minthickness,PrognosticMinThicknessEnum);
+	for(i=0;i(newthickness[i])) _error_("NaN found in solution vector");
+		/*Constrain thickness to be at least 1m*/
+		if(newthickness[i]parameters->FindParam(&hydroadjustment,PrognosticHydrostaticAdjustmentEnum);
+	rho_ice=matpar->GetRhoIce();
+	rho_water=matpar->GetRhoWater();
+
+	for(i=0;inodes[i]->IsGrounded()){
+			newsurface[i]=oldbed[i]+newthickness[i]; //surface = oldbed + newthickness
+			newbed[i]=oldbed[i];               //same bed: do nothing
+		}
+		else{ //this is an ice shelf
+
+			if(hydroadjustment==AbsoluteEnum){
+				newsurface[i]=newthickness[i]*(1-rho_ice/rho_water);
+				newbed[i]=newthickness[i]*(-rho_ice/rho_water);
+			}
+			else if(hydroadjustment==IncrementalEnum){
+				newsurface[i]=oldsurface[i]+(1.0-rho_ice/rho_water)*(newthickness[i]-oldthickness[i]); //surface = oldsurface + (1-di) * dH 
+				newbed[i]=oldbed[i]-rho_ice/rho_water*(newthickness[i]-oldthickness[i]); //bed = oldbed + di * dH
+			}
+			else _error_("Hydrostatic adjustment " << hydroadjustment << " (" << EnumToStringx(hydroadjustment) << ") not supported yet");
+		}
+	}
+
+	/*Add input to the element: */
+	this->inputs->AddInput(new TriaP1Input(ThicknessEnum,newthickness));
+	this->inputs->AddInput(new TriaP1Input(SurfaceEnum,newsurface));
+	this->inputs->AddInput(new TriaP1Input(BedEnum,newbed));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromVector(IssmDouble* vector, int name, int type);{{{*/
+void  Tria::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	switch(type){
+
+		case VertexEnum: {
+
+			/*New TriaP1Input*/
+			IssmDouble values[3];
+
+			/*Get values on the 3 vertices*/
+			for (int i=0;i<3;i++){
+				values[i]=vector[this->nodes[i]->GetVertexDof()];
+			}
+
+			/*update input*/
+			if (name==MaterialsRheologyBbarEnum || name==MaterialsRheologyBEnum || name==MaterialsRheologyZEnum || name==MaterialsRheologyZbarEnum){
+				material->inputs->AddInput(new TriaP1Input(name,values));
+			}
+			else{
+				this->inputs->AddInput(new TriaP1Input(name,values));
+			}
+			return;
+		}
+		default:
+			_error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromVector(int* vector, int name, int type);{{{*/
+void  Tria::InputUpdateFromVector(int* vector, int name, int type){
+	_error_("not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromVector(bool* vector, int name, int type);{{{*/
+void  Tria::InputUpdateFromVector(bool* vector, int name, int type){
+	_error_("not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Tria::InputCreate(IssmDouble scalar,int enum,int code);{{{*/
+void Tria::InputCreate(IssmDouble scalar,int name,int code){
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+	
+	if ((code==5) || (code==1)){ //boolean
+		this->inputs->AddInput(new BoolInput(name,reCast(scalar)));
+	}
+	else if ((code==6) || (code==2)){ //integer
+		this->inputs->AddInput(new IntInput(name,reCast(scalar)));
+	}
+	else if ((code==7) || (code==3)){ //IssmDouble
+		this->inputs->AddInput(new DoubleInput(name,reCast(scalar)));
+	}
+	else _error_("could not recognize nature of vector from code " << code);
+
+}
+/*}}}*/
+/*FUNCTION Tria::InputCreate(IssmDouble* vector,int index,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code){{{*/
+void Tria::InputCreate(IssmDouble* vector, int index,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code){//index into elements
+
+	/*Intermediaries*/
+	int    i,j,t;
+	int    tria_vertex_ids[3];
+	int    row;
+	IssmDouble nodeinputs[3];
+	IssmDouble time;
+	TransientInput* transientinput=NULL;
+	int    numberofvertices;
+	int    numberofelements;
+	IssmDouble yts;
+
+
+	/*Fetch parameters: */
+	iomodel->Constant(&numberofvertices,MeshNumberofverticesEnum);
+	iomodel->Constant(&numberofelements,MeshNumberofelementsEnum);
+	iomodel->Constant(&yts,ConstantsYtsEnum);
+
+	/*Branch on type of vector: nodal or elementary: */
+	if(vector_type==1){ //nodal vector
+
+		/*Recover vertices ids needed to initialize inputs*/
+		for(i=0;i<3;i++){ 
+			_assert_(iomodel->Data(MeshElementsEnum));
+			tria_vertex_ids[i]=reCast(iomodel->Data(MeshElementsEnum)[3*index+i]); //ids for vertices are in the elements array from Matlab
+		}
+
+		/*Are we in transient or static? */
+		if(M==numberofvertices){
+
+			/*create input values: */
+			for(i=0;i<3;i++)nodeinputs[i]=(IssmDouble)vector[tria_vertex_ids[i]-1];
+
+			/*process units: */
+			UnitConversion(&nodeinputs[0], 3 ,ExtToIuEnum, vector_enum);
+
+			/*create static input: */
+			this->inputs->AddInput(new TriaP1Input(vector_enum,nodeinputs));
+		}
+		else if(M==numberofvertices+1){
+			/*create transient input: */
+			for(t=0;tAddTimeInput(new TriaP1Input(vector_enum,nodeinputs),time);
+			}
+			this->inputs->AddInput(transientinput);
+		}
+		else _error_("nodal vector is either numberofnodes or numberofnodes+1 long. Field provided (" << EnumToStringx(vector_enum) << ") is " << M << " long");
+	}
+	else if(vector_type==2){ //element vector
+		/*Are we in transient or static? */
+		if(M==numberofelements){
+
+			/*static mode: create an input out of the element value: */
+
+			if (code==5){ //boolean
+				this->inputs->AddInput(new BoolInput(vector_enum,reCast(vector[index])));
+			}
+			else if (code==6){ //integer
+				this->inputs->AddInput(new IntInput(vector_enum,reCast(vector[index])));
+			}
+			else if (code==7){ //IssmDouble
+				this->inputs->AddInput(new DoubleInput(vector_enum,vector[index]));
+			}
+			else _error_("could not recognize nature of vector from code " << code);
+		}
+		else {
+			_error_("transient elementary inputs not supported yet!");
+		}
+	}
+	else{
+		_error_("Cannot add input for vector type " << vector_type << " (not supported)");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Tria::IsInput{{{*/
+bool Tria::IsInput(int name){
+	if (
+				name==ThicknessEnum ||
+				name==SurfaceEnum ||
+				name==BedEnum ||
+				name==SurfaceSlopeXEnum ||
+				name==SurfaceSlopeYEnum ||
+				name==BasalforcingsMeltingRateEnum ||
+				name==WatercolumnEnum || 
+				name==SurfaceforcingsMassBalanceEnum ||
+				name==SurfaceAreaEnum||
+				name==VxEnum ||
+				name==VyEnum ||
+				name==InversionVxObsEnum ||
+				name==InversionVyObsEnum ||
+				name==FrictionCoefficientEnum ||
+				name==MaterialsRheologyBbarEnum ||
+				name==MaterialsRheologyZbarEnum ||
+				name==GradientEnum ||
+				name==OldGradientEnum ||
+				name==QmuVxEnum ||
+				name==QmuVyEnum ||
+				name==QmuPressureEnum ||
+				name==QmuBedEnum ||
+				name==QmuThicknessEnum ||
+				name==QmuSurfaceEnum ||
+				name==QmuTemperatureEnum ||
+				name==QmuMeltingEnum
+		){
+		return true;
+	}
+	else return false;
+}
+/*}}}*/
+/*FUNCTION Tria::IsOnBed {{{*/
+bool Tria::IsOnBed(){
+	
+	bool onbed;
+	inputs->GetInputValue(&onbed,MeshElementonbedEnum);
+	return onbed;
+}
+/*}}}*/
+/*FUNCTION Tria::IsFloating {{{*/
+bool   Tria::IsFloating(){
+
+	bool shelf;
+	inputs->GetInputValue(&shelf,MaskElementonfloatingiceEnum);
+	return shelf;
+}
+/*}}}*/
+/*FUNCTION Tria::IsNodeOnShelf {{{*/
+bool   Tria::IsNodeOnShelf(){
+
+	int  i;
+	bool shelf=false;
+
+	for(i=0;i<3;i++){
+		if (nodes[i]->IsFloating()){
+			shelf=true;
+			break;
+		}
+	}
+	return shelf;
+}
+/*}}}*/
+/*FUNCTION Tria::IsNodeOnShelfFromFlags {{{*/
+bool   Tria::IsNodeOnShelfFromFlags(IssmDouble* flags){
+
+	int  i;
+	bool shelf=false;
+
+	for(i=0;i(flags[nodes[i]->Sid()])){
+			shelf=true;
+			break;
+		}
+	}
+	return shelf;
+}
+/*}}}*/
+/*FUNCTION Tria::IsOnWater {{{*/
+bool   Tria::IsOnWater(){
+
+	bool water;
+	inputs->GetInputValue(&water,MaskElementonwaterEnum);
+	return water;
+}
+/*}}}*/
+/*FUNCTION Tria::ListResultsInfo{{{*/
+void Tria::ListResultsInfo(int** in_resultsenums,int** in_resultssizes,IssmDouble** in_resultstimes,int** in_resultssteps,int* in_num_results){
+
+	/*Intermediaries*/
+	int     i;
+	int     numberofresults = 0;
+	int     *resultsenums   = NULL;
+	int     *resultssizes   = NULL;
+	IssmDouble  *resultstimes   = NULL;
+	int     *resultssteps   = NULL;
+
+	/*Checks*/
+	_assert_(in_num_results);
+
+	/*Count number of results*/
+	for(i=0;iresults->Size();i++){
+		ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+		numberofresults++;
+	}
+
+	if(numberofresults){
+
+		/*Allocate output*/
+		resultsenums=xNew(numberofresults);
+		resultssizes=xNew(numberofresults);
+		resultstimes=xNew(numberofresults);
+		resultssteps=xNew(numberofresults);
+
+		/*populate enums*/
+		for(i=0;iresults->Size();i++){
+			ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+			resultsenums[i]=elementresult->InstanceEnum();
+			resultstimes[i]=elementresult->GetTime();
+			resultssteps[i]=elementresult->GetStep();
+			if(elementresult->ObjectEnum()==TriaP1ElementResultEnum){
+				resultssizes[i]=P1Enum;
+			}
+			else{
+				resultssizes[i]=P0Enum;
+			}
+		}
+	}
+
+	/*Assign output pointers:*/
+	*in_num_results=numberofresults;
+	*in_resultsenums=resultsenums;
+	*in_resultssizes=resultssizes;
+	*in_resultstimes=resultstimes;
+	*in_resultssteps=resultssteps;
+
+}/*}}}*/
+/*FUNCTION Tria::MigrateGroundingLine{{{*/
+void  Tria::MigrateGroundingLine(IssmDouble* old_floating_ice,IssmDouble* sheet_ungrounding){
+
+	int     i,migration_style,unground;
+	bool    elementonshelf = false;
+	IssmDouble  bed_hydro,yts,gl_melting_rate;
+	IssmDouble  rho_water,rho_ice,density;
+	IssmDouble  melting[NUMVERTICES];
+	IssmDouble  h[NUMVERTICES],s[NUMVERTICES],b[NUMVERTICES],ba[NUMVERTICES];
+
+	/*Recover info at the vertices: */
+	parameters->FindParam(&migration_style,GroundinglineMigrationEnum);
+	parameters->FindParam(&yts,ConstantsYtsEnum);
+	GetInputListOnVertices(&h[0],ThicknessEnum);
+	GetInputListOnVertices(&s[0],SurfaceEnum);
+	GetInputListOnVertices(&b[0],BedEnum);
+	GetInputListOnVertices(&ba[0],BathymetryEnum);
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	density=rho_ice/rho_water;
+	
+	/*go through vertices, and update inputs, considering them to be TriaVertex type: */
+	for(i=0;i(old_floating_ice[nodes[i]->Sid()])){
+			if(b[i]<=ba[i]){ 
+				b[i]=ba[i];
+				s[i]=b[i]+h[i];
+				nodes[i]->inputs->AddInput(new BoolInput(MaskVertexonfloatingiceEnum,false));
+				nodes[i]->inputs->AddInput(new BoolInput(MaskVertexongroundediceEnum,true));
+			}
+		}
+		/*Ice sheet: if hydrostatic bed above bathymetry, ice sheet starts to unground, elso do nothing */
+		/*Change only if AgressiveMigration or if the ice sheet is in contact with the ocean*/
+		else{
+			bed_hydro=-density*h[i];
+			if (bed_hydro>ba[i]){
+				/*Unground only if the element is connected to the ice shelf*/
+				if(migration_style==AgressiveMigrationEnum){
+					s[i]=(1-density)*h[i];
+					b[i]=-density*h[i];
+					nodes[i]->inputs->AddInput(new BoolInput(MaskVertexonfloatingiceEnum,true));
+					nodes[i]->inputs->AddInput(new BoolInput(MaskVertexongroundediceEnum,false));
+				}
+				else if(migration_style==SoftMigrationEnum && reCast(sheet_ungrounding[nodes[i]->Sid()])){
+					s[i]=(1-density)*h[i];
+					b[i]=-density*h[i];
+					nodes[i]->inputs->AddInput(new BoolInput(MaskVertexonfloatingiceEnum,true));
+					nodes[i]->inputs->AddInput(new BoolInput(MaskVertexongroundediceEnum,false));
+				}
+			}
+		}
+	}
+
+	/*If at least one vertex is now floating, the element is now floating*/
+	for(i=0;iIsFloating()){
+			elementonshelf=true;
+			break;
+		}
+	}
+	
+   /*Add basal melting rate if element just ungrounded*/
+	if(!this->IsFloating() && elementonshelf==true){
+		for(i=0;iinputs->AddInput(new TriaP1Input(BasalforcingsMeltingRateEnum,&melting[0]));
+	} 
+
+	/*Update inputs*/
+   this->inputs->AddInput(new BoolInput(MaskElementonfloatingiceEnum,elementonshelf));
+
+	/*Update inputs*/    
+	this->inputs->AddInput(new TriaP1Input(SurfaceEnum,&s[0]));
+	this->inputs->AddInput(new TriaP1Input(BedEnum,&b[0]));
+}
+/*}}}*/
+/*FUNCTION Tria::MyRank {{{*/
+int    Tria::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Tria::NodalValue {{{*/
+int    Tria::NodalValue(IssmDouble* pvalue, int index, int natureofdataenum,bool process_units){
+
+	int         found = 0;
+	IssmDouble  value;
+	Input      *data  = NULL;
+	GaussTria  *gauss = NULL;
+
+	/*First, serarch the input: */
+	data=inputs->GetInput(natureofdataenum); 
+
+	/*figure out if we have the vertex id: */
+	found=0;
+	for(int i=0;iGetVertexId()){
+			/*Do we have natureofdataenum in our inputs? :*/
+			if(data){
+				/*ok, we are good. retrieve value of input at vertex :*/
+				gauss=new GaussTria(); gauss->GaussVertex(i);
+				data->GetInputValue(&value,gauss);
+				found=1;
+				break;
+			}
+		}
+	}
+
+	/*clean-up*/
+	delete gauss;
+
+	if(found)*pvalue=value;
+	return found;
+}
+/*}}}*/
+/*FUNCTION Tria::PatchFill{{{*/
+void  Tria::PatchFill(int* prow, Patch* patch){
+
+	int i,row;
+	int vertices_ids[3];
+
+	/*recover pointer: */
+	row=*prow;
+		
+	for(i=0;i<3;i++) vertices_ids[i]=nodes[i]->GetVertexId(); //vertices id start at column 3 of the patch.
+
+	for(i=0;iresults->Size();i++){
+		ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+
+		/*For this result,fill the information in the Patch object (element id + vertices ids), and then hand 
+		 *it to the result object, to fill the rest: */
+		patch->fillelementinfo(row,this->sid+1,vertices_ids,3);
+		elementresult->PatchFill(row,patch);
+
+		/*increment rower: */
+		row++;
+	}
+
+	/*Assign output pointers:*/
+	*prow=row;
+}
+/*}}}*/
+/*FUNCTION Tria::PatchSize{{{*/
+void  Tria::PatchSize(int* pnumrows, int* pnumvertices,int* pnumnodes){
+
+	int     i;
+	int     numrows       = 0;
+	int     numnodes      = 0;
+	int     temp_numnodes = 0;
+
+	/*Go through all the results objects, and update the counters: */
+	for (i=0;iresults->Size();i++){
+		ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+		/*first, we have one more result: */
+		numrows++;
+		/*now, how many vertices and how many nodal values for this result? :*/
+		temp_numnodes=elementresult->NumberOfNodalValues(); //ask result object.
+		if(temp_numnodes>numnodes)numnodes=temp_numnodes;
+	}
+
+	/*Assign output pointers:*/
+	*pnumrows=numrows;
+	*pnumvertices=NUMVERTICES;
+	*pnumnodes=numnodes;
+}
+/*}}}*/
+/*FUNCTION Tria::PotentialSheetUngrounding{{{*/
+void  Tria::PotentialSheetUngrounding(Vector* potential_sheet_ungrounding){
+
+	int     i;
+	IssmDouble  h[NUMVERTICES],ba[NUMVERTICES];
+	IssmDouble  bed_hydro;
+	IssmDouble  rho_water,rho_ice,density;
+	bool    elementonshelf = false;
+
+	/*material parameters: */
+	rho_water=matpar->GetRhoWater();
+	rho_ice=matpar->GetRhoIce();
+	density=rho_ice/rho_water;
+	GetInputListOnVertices(&h[0],ThicknessEnum);
+	GetInputListOnVertices(&ba[0],BathymetryEnum);
+
+	/*go through vertices, and figure out which ones are on the ice sheet, and want to unground: */
+	for(i=0;iIsFloating()){
+			bed_hydro=-density*h[i];
+			if (bed_hydro>ba[i]){
+				/*Vertex that could potentially unground, flag it*/
+				potential_sheet_ungrounding->SetValue(nodes[i]->Sid(),1,INS_VAL);
+			}
+		}
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::PositiveDegreeDay{{{*/
+void  Tria::PositiveDegreeDay(IssmDouble* pdds,IssmDouble* pds,IssmDouble signorm){
+
+   IssmDouble agd[NUMVERTICES];             // surface mass balance
+   IssmDouble monthlytemperatures[NUMVERTICES][12],monthlyprec[NUMVERTICES][12];
+   IssmDouble h[NUMVERTICES],s[NUMVERTICES];
+   IssmDouble rho_water,rho_ice;
+
+   /*Recover monthly temperatures and precipitation*/
+   Input*     input=inputs->GetInput(SurfaceforcingsMonthlytemperaturesEnum); _assert_(input);
+   Input*     input2=inputs->GetInput(SurfaceforcingsPrecipitationEnum); _assert_(input2);
+   GaussTria* gauss=new GaussTria();
+   IssmDouble time,yts;
+   this->parameters->FindParam(&time,TimeEnum);
+   this->parameters->FindParam(&yts,ConstantsYtsEnum);
+   for(int month=0;month<12;month++) {
+     for(int iv=0;ivGaussVertex(iv);
+       input->GetInputValue(&monthlytemperatures[iv][month],gauss,time+month/12.*yts);
+       monthlytemperatures[iv][month]=monthlytemperatures[iv][month]-273.15; // conversion from Kelvin to celcius
+       input2->GetInputValue(&monthlyprec[iv][month],gauss,time+month/12.*yts);
+       monthlyprec[iv][month]=monthlyprec[iv][month]*yts; // convertion in m/y
+     }
+   }
+
+  /*Recover info at the vertices: */
+  GetInputListOnVertices(&h[0],ThicknessEnum);
+  GetInputListOnVertices(&s[0],SurfaceEnum);
+
+  /*Get material parameters :*/
+  rho_ice=matpar->GetRhoIce();
+  rho_water=matpar->GetRhoFreshwater();
+
+   /*measure the surface mass balance*/
+   for (int iv = 0; ivinputs->AddInput(new TriaP1Input(SurfaceforcingsMassBalanceEnum,&agd[0]));
+   // this->inputs->AddInput(new TriaVertexInput(ThermalSpcTemperatureEnum,&Tsurf[0]));
+
+	/*clean-up*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::ProcessResultsUnits{{{*/
+void  Tria::ProcessResultsUnits(void){
+
+	int i;
+
+	for(i=0;iresults->Size();i++){
+		ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(i);
+		elementresult->ProcessUnits(this->parameters);
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::RequestedOutput{{{*/
+void Tria::RequestedOutput(int output_enum,int step,IssmDouble time){
+
+	if(IsInput(output_enum)){
+		/*just transfer this input to results, and we are done: */
+		InputToResult(output_enum,step,time);
+	}
+	else{
+		/*this input does not exist, compute it, and then transfer to results: */
+		switch(output_enum){
+			case StressTensorEnum: 
+				this->ComputeStressTensor();
+				InputToResult(StressTensorxxEnum,step,time);
+				InputToResult(StressTensorxyEnum,step,time);
+				InputToResult(StressTensorxzEnum,step,time);
+				InputToResult(StressTensoryyEnum,step,time);
+				InputToResult(StressTensoryzEnum,step,time);
+				InputToResult(StressTensorzzEnum,step,time);
+				break;
+
+			default:
+				/*do nothing, no need to derail the computation because one of the outputs requested cannot be found: */
+				break;
+		}
+	}
+
+}
+/*}}}*/
+/*FUNCTION Tria::SetClone {{{*/
+void  Tria::SetClone(int* minranks){
+
+	_error_("not implemented yet");
+}
+/*}}}*/
+/*FUNCTION Tria::SmearFunction {{{*/
+void  Tria::SmearFunction(Vector*  smearedvector,IssmDouble (*WeightFunction)(IssmDouble distance,IssmDouble radius),IssmDouble radius){
+	_error_("not implemented yet");
+
+}
+/*}}}*/
+/*FUNCTION Tria::SmbGradients{{{*/
+void Tria::SmbGradients(void){
+
+	int i;
+
+	// input
+   IssmDouble h[NUMVERTICES];					// ice thickness (m)		
+	IssmDouble s[NUMVERTICES];					// surface elevation (m)
+	IssmDouble a_pos[NUMVERTICES];				// Hs-SMB relation parameter 
+	IssmDouble b_pos[NUMVERTICES];				// Hs-SMB relation parameter
+	IssmDouble a_neg[NUMVERTICES];				// Hs-SMB relation parameter
+	IssmDouble b_neg[NUMVERTICES];				// Hs-SMB relation paremeter
+	IssmDouble Hc[NUMVERTICES];					// elevation of transition between accumulation regime and ablation regime
+	IssmDouble smb_pos_max[NUMVERTICES];		// maximum SMB value in the accumulation regime
+	IssmDouble smb_pos_min[NUMVERTICES];		// minimum SMB value in the accumulation regime
+   IssmDouble rho_water;                   // density of fresh water
+	IssmDouble rho_ice;                     // density of ice
+
+	// output
+	IssmDouble smb[NUMVERTICES];					// surface mass balance (m/yr ice)
+
+	/*Recover SmbGradients*/
+	GetInputListOnVertices(&Hc[0],SurfaceforcingsHcEnum);
+	GetInputListOnVertices(&smb_pos_max[0],SurfaceforcingsSmbPosMaxEnum);
+	GetInputListOnVertices(&smb_pos_min[0],SurfaceforcingsSmbPosMinEnum);
+	GetInputListOnVertices(&a_pos[0],SurfaceforcingsAPosEnum);
+	GetInputListOnVertices(&b_pos[0],SurfaceforcingsBPosEnum);
+	GetInputListOnVertices(&a_neg[0],SurfaceforcingsANegEnum);
+	GetInputListOnVertices(&b_neg[0],SurfaceforcingsBNegEnum);
+	
+   /*Recover surface elevatio at vertices: */
+	GetInputListOnVertices(&h[0],ThicknessEnum);
+	GetInputListOnVertices(&s[0],SurfaceEnum);
+
+   /*Get material parameters :*/
+   rho_ice=matpar->GetRhoIce();
+   rho_water=matpar->GetRhoFreshwater();
+			
+   // loop over all vertices
+   for(i=0;iHc[i]){
+	    smb[i]=a_pos[i]+b_pos[i]*s[i];
+		 if(smb[i]>smb_pos_max[i]){smb[i]=smb_pos_max[i];}
+		 if(smb[i]inputs->AddInput(new TriaP1Input(SurfaceforcingsMassBalanceEnum,&smb[0]));
+}
+/*}}}*/
+/*FUNCTION Tria::SetCurrentConfiguration {{{*/
+void  Tria::SetCurrentConfiguration(Elements* elementsin, Loads* loadsin, DataSet* nodesin, Materials* materialsin, Parameters* parametersin){
+	
+	/*go into parameters and get the analysis_counter: */
+	int analysis_counter;
+	parametersin->FindParam(&analysis_counter,AnalysisCounterEnum);
+
+	/*Get Element type*/
+	this->element_type=this->element_type_list[analysis_counter];
+
+	/*Pick up nodes*/
+	if(this->hnodes[analysis_counter]) this->nodes=(Node**)this->hnodes[analysis_counter]->deliverp();
+	else this->nodes=NULL;
+
+}
+/*}}}*/
+/*FUNCTION Tria::SurfaceArea {{{*/
+IssmDouble Tria::SurfaceArea(void){
+
+	IssmDouble S;
+	IssmDouble normal[3];
+	IssmDouble v13[3],v23[3];
+	IssmDouble xyz_list[NUMVERTICES][3];
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	for(int i=0;i<3;i++){
+		v13[i]=xyz_list[0][i]-xyz_list[2][i];
+		v23[i]=xyz_list[1][i]-xyz_list[2][i];
+	}
+
+	normal[0]=v13[1]*v23[2]-v13[2]*v23[1];
+	normal[1]=v13[2]*v23[0]-v13[0]*v23[2];
+	normal[2]=v13[0]*v23[1]-v13[1]*v23[0];
+
+	S = 0.5 * sqrt(normal[0]*normal[0] + normal[1]*normal[1] + normal[2]*normal[2]);
+
+	/*Return: */
+	return S;
+}
+/*}}}*/
+/*FUNCTION Tria::SurfaceNormal{{{*/
+void Tria::SurfaceNormal(IssmDouble* surface_normal, IssmDouble xyz_list[3][3]){
+
+	IssmDouble v13[3],v23[3];
+	IssmDouble normal[3];
+	IssmDouble normal_norm;
+
+	for(int i=0;i<3;i++){
+		v13[i]=xyz_list[0][i]-xyz_list[2][i];
+		v23[i]=xyz_list[1][i]-xyz_list[2][i];
+	}
+
+	normal[0]=v13[1]*v23[2]-v13[2]*v23[1];
+	normal[1]=v13[2]*v23[0]-v13[0]*v23[2];
+	normal[2]=v13[0]*v23[1]-v13[1]*v23[0];
+
+	normal_norm=sqrt( normal[0]*normal[0] + normal[1]*normal[1] + normal[2]*normal[2]);
+
+	*(surface_normal+0) = normal[0]/normal_norm;
+	*(surface_normal+1) = normal[1]/normal_norm;
+	*(surface_normal+2) = normal[2]/normal_norm;
+}
+/*}}}*/
+/*FUNCTION Tria::TimeAdapt{{{*/
+IssmDouble  Tria::TimeAdapt(void){
+
+	/*intermediary: */
+	int    i;
+	IssmDouble C,dt;
+	IssmDouble dx,dy;
+	IssmDouble maxx,minx;
+	IssmDouble maxy,miny;
+	IssmDouble maxabsvx,maxabsvy;
+	IssmDouble xyz_list[NUMVERTICES][3];
+
+	/*get CFL coefficient:*/
+	this->parameters->FindParam(&C,TimesteppingCflCoefficientEnum);
+
+	/*Get for Vx and Vy, the max of abs value: */
+	#ifdef _HAVE_RESPONSES_
+	this->MaxAbsVx(&maxabsvx,false);
+	this->MaxAbsVy(&maxabsvy,false);
+	#else
+		_error_("ISSM was not compiled with responses compiled in, exiting!");
+	#endif
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], this->nodes, NUMVERTICES);
+
+	minx=xyz_list[0][0];
+	maxx=xyz_list[0][0];
+	miny=xyz_list[0][1];
+	maxy=xyz_list[0][1];
+
+	for(i=1;imaxx)maxx=xyz_list[i][0];
+		if (xyz_list[i][1]maxy)maxy=xyz_list[i][1];
+	}
+	dx=maxx-minx;
+	dy=maxy-miny;
+
+	/*CFL criterion: */
+	dt=C/(maxabsvy/dx+maxabsvy/dy);
+
+	return dt;
+}
+/*}}}*/
+/*FUNCTION Tria::Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type){{{*/
+void Tria::Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type){ //i is the element index
+
+	/*Intermediaries*/
+	int    i,j;
+	int    tria_node_ids[3];
+	int    tria_vertex_ids[3];
+	int    tria_type;
+	IssmDouble nodeinputs[3];
+	IssmDouble yts;
+	int    progstabilization,balancestabilization;
+	bool   dakota_analysis;
+
+	/*Checks if debuging*/
+	/*{{{*/
+	_assert_(iomodel->Data(MeshElementsEnum));
+	/*}}}*/
+
+	/*Fetch parameters: */
+	iomodel->Constant(&yts,ConstantsYtsEnum);
+	iomodel->Constant(&progstabilization,PrognosticStabilizationEnum);
+	iomodel->Constant(&balancestabilization,BalancethicknessStabilizationEnum);
+	iomodel->Constant(&dakota_analysis,QmuIsdakotaEnum);
+
+	/*Recover element type*/
+	if ((analysis_type==PrognosticAnalysisEnum && progstabilization==3) || (analysis_type==BalancethicknessAnalysisEnum && balancestabilization==3)){
+		/*P1 Discontinuous Galerkin*/
+		tria_type=P1DGEnum;
+	}
+	else{
+		/*P1 Continuous Galerkin*/
+		tria_type=P1Enum;
+	}
+	this->SetElementType(tria_type,analysis_counter);
+
+	/*Recover vertices ids needed to initialize inputs*/
+	for(i=0;i<3;i++){ 
+		tria_vertex_ids[i]=reCast(iomodel->Data(MeshElementsEnum)[3*index+i]); //ids for vertices are in the elements array from Matlab
+	}
+
+	/*Recover nodes ids needed to initialize the node hook.*/
+	if (tria_type==P1DGEnum){
+		/*Discontinuous Galerkin*/
+		tria_node_ids[0]=iomodel->nodecounter+3*index+1;
+		tria_node_ids[1]=iomodel->nodecounter+3*index+2;
+		tria_node_ids[2]=iomodel->nodecounter+3*index+3;
+	}
+	else{
+		/*Continuous Galerkin*/
+		for(i=0;i<3;i++){ 
+			tria_node_ids[i]=iomodel->nodecounter+reCast(*(iomodel->Data(MeshElementsEnum)+3*index+i)); //ids for vertices are in the elements array from Matlab
+		}
+	}
+
+	/*hooks: */
+	this->SetHookNodes(tria_node_ids,analysis_counter); this->nodes=NULL; //set hook to nodes, for this analysis type
+
+	/*Fill with IoModel*/
+	this->InputUpdateFromIoModel(index,iomodel);
+
+	/*Defaults if not provided in iomodel*/
+	switch(analysis_type){
+
+		case DiagnosticHorizAnalysisEnum:
+
+			/*default vx,vy and vz: either observation or 0 */
+			if(!iomodel->Data(VxEnum)){
+				for(i=0;i<3;i++)nodeinputs[i]=0;
+				this->inputs->AddInput(new TriaP1Input(VxEnum,nodeinputs));
+				if(dakota_analysis) this->inputs->AddInput(new TriaP1Input(QmuVxEnum,nodeinputs));
+			}
+			if(!iomodel->Data(VyEnum)){
+				for(i=0;i<3;i++)nodeinputs[i]=0;
+				this->inputs->AddInput(new TriaP1Input(VyEnum,nodeinputs));
+				if(dakota_analysis) this->inputs->AddInput(new TriaP1Input(QmuVyEnum,nodeinputs));
+			}
+			if(!iomodel->Data(VzEnum)){
+				for(i=0;i<3;i++)nodeinputs[i]=0;
+				this->inputs->AddInput(new TriaP1Input(VzEnum,nodeinputs));
+				if(dakota_analysis) this->inputs->AddInput(new TriaP1Input(QmuVzEnum,nodeinputs));
+			}
+			if(!iomodel->Data(PressureEnum)){
+				for(i=0;i<3;i++)nodeinputs[i]=0;
+				if(dakota_analysis){
+					this->inputs->AddInput(new TriaP1Input(PressureEnum,nodeinputs));
+					this->inputs->AddInput(new TriaP1Input(QmuPressureEnum,nodeinputs));
+				}
+			}
+			break;
+
+		default:
+			/*No update for other solution types*/
+			break;
+
+	}
+
+	//this->parameters: we still can't point to it, it may not even exist. Configure will handle this.
+	this->parameters=NULL;
+}
+/*}}}*/
+/*FUNCTION Tria::UpdatePotentialSheetUngrounding{{{*/
+int Tria::UpdatePotentialSheetUngrounding(IssmDouble* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,IssmDouble* nodes_on_iceshelf){
+
+	int i;
+	int nflipped=0;
+
+	/*Go through nodes, and whoever is on the potential_sheet_ungrounding, ends up in nodes_on_iceshelf: */
+	for(i=0;i<3;i++){
+		if (reCast(vertices_potentially_ungrounding[nodes[i]->Sid()])){
+			vec_nodes_on_iceshelf->SetValue(nodes[i]->Sid(),1,INS_VAL);
+		
+			/*If node was not on ice shelf, we flipped*/
+			if(nodes_on_iceshelf[nodes[i]->Sid()]==0){
+				nflipped++;
+			}
+		}
+	}
+	return nflipped;
+}
+/*}}}*/
+
+#ifdef _HAVE_RESPONSES_
+/*FUNCTION Tria::IceVolume {{{*/
+IssmDouble Tria::IceVolume(void){
+
+	/*The volume of a troncated prism is base * 1/3 sum(length of edges)*/
+	IssmDouble base,surface,bed;
+	IssmDouble xyz_list[NUMVERTICES][3];
+
+	if(IsOnWater())return 0;
+
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*First calculate the area of the base (cross section triangle)
+	 * http://en.wikipedia.org/wiki/Triangle
+	 * base = 1/2 abs((xA-xC)(yB-yA)-(xA-xB)(yC-yA))*/
+	base = 1./2. * fabs((xyz_list[0][0]-xyz_list[2][0])*(xyz_list[1][1]-xyz_list[0][1]) - (xyz_list[0][0]-xyz_list[1][0])*(xyz_list[2][1]-xyz_list[0][1]));
+
+	/*Now get the average height*/
+	Input* surface_input = inputs->GetInput(SurfaceEnum); _assert_(surface_input);
+	Input* bed_input     = inputs->GetInput(BedEnum);     _assert_(bed_input);
+	surface_input->GetInputAverage(&surface);
+	bed_input->GetInputAverage(&bed);
+
+	/*Return: */
+	return base*(surface-bed);
+}
+/*}}}*/
+/*FUNCTION Tria::MassFlux {{{*/
+IssmDouble Tria::MassFlux( IssmDouble* segment,bool process_units){
+
+	const int    numdofs=2;
+
+	int        i,dim;
+	IssmDouble     mass_flux=0;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     normal[2];
+	IssmDouble     length,rho_ice;
+	IssmDouble     x1,y1,x2,y2,h1,h2;
+	IssmDouble     vx1,vx2,vy1,vy2;
+	GaussTria* gauss_1=NULL;
+	GaussTria* gauss_2=NULL;
+
+	/*Get material parameters :*/
+	rho_ice=matpar->GetRhoIce();
+
+	/*First off, check that this segment belongs to this element: */
+	if (reCast(*(segment+4))!=this->id)_error_("error message: segment with id " << reCast(*(segment+4)) << " does not belong to element with id:" << this->id);
+
+	/*Recover segment node locations: */
+	x1=*(segment+0); y1=*(segment+1); x2=*(segment+2); y2=*(segment+3);
+
+	/*Get xyz list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*get area coordinates of 0 and 1 locations: */
+	gauss_1=new GaussTria();
+	gauss_1->GaussFromCoords(x1,y1,&xyz_list[0][0]);
+	gauss_2=new GaussTria();
+	gauss_2->GaussFromCoords(x2,y2,&xyz_list[0][0]);
+
+	normal[0]=cos(atan2(x1-x2,y2-y1));
+	normal[1]=sin(atan2(x1-x2,y2-y1));
+
+	length=sqrt(pow(x2-x1,2)+pow(y2-y1,2));
+
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+	this->parameters->FindParam(&dim,MeshDimensionEnum);
+	Input* vx_input=NULL;
+	Input* vy_input=NULL;
+	if(dim==2){
+		vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+		vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+	}
+	else{
+		vx_input=inputs->GetInput(VxAverageEnum); _assert_(vx_input);
+		vy_input=inputs->GetInput(VyAverageEnum); _assert_(vy_input);
+	}
+
+	thickness_input->GetInputValue(&h1, gauss_1);
+	thickness_input->GetInputValue(&h2, gauss_2);
+	vx_input->GetInputValue(&vx1,gauss_1);
+	vx_input->GetInputValue(&vx2,gauss_2);
+	vy_input->GetInputValue(&vy1,gauss_1);
+	vy_input->GetInputValue(&vy2,gauss_2);
+
+	mass_flux= rho_ice*length*(  
+				(ONETHIRD*(h1-h2)*(vx1-vx2)+0.5*h2*(vx1-vx2)+0.5*(h1-h2)*vx2+h2*vx2)*normal[0]+
+				(ONETHIRD*(h1-h2)*(vy1-vy2)+0.5*h2*(vy1-vy2)+0.5*(h1-h2)*vy2+h2*vy2)*normal[1]
+				);
+
+	/*Process units: */
+	mass_flux=UnitConversion(mass_flux,IuToExtEnum,MassFluxEnum);
+
+	/*clean up and return:*/
+	delete gauss_1;
+	delete gauss_2;
+	return mass_flux;
+}
+/*}}}*/
+/*FUNCTION Tria::MaxAbsVx{{{*/
+void  Tria::MaxAbsVx(IssmDouble* pmaxabsvx, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxabsvx=this->inputs->MaxAbs(VxEnum);
+
+	/*process units if requested: */
+	if(process_units) maxabsvx=UnitConversion(maxabsvx,IuToExtEnum,VxEnum);
+
+	/*Assign output pointers:*/
+	*pmaxabsvx=maxabsvx;
+}
+/*}}}*/
+/*FUNCTION Tria::MaxAbsVy{{{*/
+void  Tria::MaxAbsVy(IssmDouble* pmaxabsvy, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxabsvy=this->inputs->MaxAbs(VyEnum);
+
+	/*process units if requested: */
+	if(process_units) maxabsvy=UnitConversion(maxabsvy,IuToExtEnum,VyEnum);
+
+	/*Assign output pointers:*/
+	*pmaxabsvy=maxabsvy;
+}
+/*}}}*/
+/*FUNCTION Tria::MaxAbsVz{{{*/
+void  Tria::MaxAbsVz(IssmDouble* pmaxabsvz, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxabsvz=this->inputs->MaxAbs(VzEnum);
+
+	/*process units if requested: */
+	if(process_units) maxabsvz=UnitConversion(maxabsvz,IuToExtEnum,VyEnum);
+
+	/*Assign output pointers:*/
+	*pmaxabsvz=maxabsvz;
+}
+/*}}}*/
+/*FUNCTION Tria::MaxVel{{{*/
+void  Tria::MaxVel(IssmDouble* pmaxvel, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxvel=this->inputs->Max(VelEnum);
+
+	/*process units if requested: */
+	if(process_units) maxvel=UnitConversion(maxvel,IuToExtEnum,VelEnum);
+
+	/*Assign output pointers:*/
+	*pmaxvel=maxvel;
+}
+/*}}}*/
+/*FUNCTION Tria::MaxVx{{{*/
+void  Tria::MaxVx(IssmDouble* pmaxvx, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxvx=this->inputs->Max(VxEnum);
+
+	/*process units if requested: */
+	if(process_units) maxvx=UnitConversion(maxvx,IuToExtEnum,VxEnum);
+
+	/*Assign output pointers:*/
+	*pmaxvx=maxvx;
+}
+/*}}}*/
+/*FUNCTION Tria::MaxVy{{{*/
+void  Tria::MaxVy(IssmDouble* pmaxvy, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxvy=this->inputs->Max(VyEnum);
+
+	/*process units if requested: */
+	if(process_units) maxvy=UnitConversion(maxvy,IuToExtEnum,VyEnum);
+
+	/*Assign output pointers:*/
+	*pmaxvy=maxvy;
+
+}
+/*}}}*/
+/*FUNCTION Tria::MaxVz{{{*/
+void  Tria::MaxVz(IssmDouble* pmaxvz, bool process_units){
+
+	/*Get maximum:*/
+	IssmDouble maxvz=this->inputs->Max(VzEnum);
+
+	/*process units if requested: */
+	if(process_units) maxvz=UnitConversion(maxvz,IuToExtEnum,VzEnum);
+
+	/*Assign output pointers:*/
+	*pmaxvz=maxvz;
+}
+/*}}}*/
+/*FUNCTION Tria::MinVel{{{*/
+void  Tria::MinVel(IssmDouble* pminvel, bool process_units){
+
+	/*Get minimum:*/
+	IssmDouble minvel=this->inputs->Min(VelEnum);
+
+	/*process units if requested: */
+	if(process_units) minvel=UnitConversion(minvel,IuToExtEnum,VelEnum);
+
+	/*Assign output pointers:*/
+	*pminvel=minvel;
+}
+/*}}}*/
+/*FUNCTION Tria::MinVx{{{*/
+void  Tria::MinVx(IssmDouble* pminvx, bool process_units){
+
+	/*Get minimum:*/
+	IssmDouble minvx=this->inputs->Min(VxEnum);
+
+	/*process units if requested: */
+	if(process_units) minvx=UnitConversion(minvx,IuToExtEnum,VxEnum);
+
+	/*Assign output pointers:*/
+	*pminvx=minvx;
+}
+/*}}}*/
+/*FUNCTION Tria::MinVy{{{*/
+void  Tria::MinVy(IssmDouble* pminvy, bool process_units){
+
+	/*Get minimum:*/
+	IssmDouble minvy=this->inputs->Min(VyEnum);
+
+	/*process units if requested: */
+	if(process_units) minvy=UnitConversion(minvy,IuToExtEnum,VyEnum);
+
+	/*Assign output pointers:*/
+	*pminvy=minvy;
+}
+/*}}}*/
+/*FUNCTION Tria::MinVz{{{*/
+void  Tria::MinVz(IssmDouble* pminvz, bool process_units){
+
+	/*Get minimum:*/
+	IssmDouble minvz=this->inputs->Min(VzEnum);
+
+	/*process units if requested: */
+	if(process_units) minvz=UnitConversion(minvz,IuToExtEnum,VzEnum);
+
+	/*Assign output pointers:*/
+	*pminvz=minvz;
+}
+/*}}}*/
+/*FUNCTION Tria::ElementResponse{{{*/
+void Tria::ElementResponse(IssmDouble* presponse,int response_enum,bool process_units){
+
+	switch(response_enum){
+		case MaterialsRheologyBbarEnum:
+			*presponse=this->material->GetBbar();
+			break;
+		case MaterialsRheologyZbarEnum:
+			*presponse=this->material->GetZbar();
+			break;
+		case VelEnum:{
+
+			/*Get input:*/
+			IssmDouble vel;
+			Input* vel_input;
+
+			vel_input=this->inputs->GetInput(VelEnum); _assert_(vel_input);
+			vel_input->GetInputAverage(&vel);
+
+			/*process units if requested: */
+			if(process_units) vel=UnitConversion(vel,IuToExtEnum,VelEnum);
+
+			/*Assign output pointers:*/
+			*presponse=vel;}
+			break;
+		default:  
+			_error_("Response type " << EnumToStringx(response_enum) << " not supported yet!");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Tria::TotalSmb {{{*/
+IssmDouble Tria::TotalSmb(void){
+
+	/*The smb[kg yr-1] of one element is area[m2] * smb [kg m^-2 yr^-1]*/
+	IssmDouble base,smb,rho_ice;
+	IssmDouble Total_Smb=0;
+	IssmDouble xyz_list[NUMVERTICES][3];
+
+	/*Get material parameters :*/
+	rho_ice=matpar->GetRhoIce();
+
+   if(IsOnWater())return 0;
+
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*First calculate the area of the base (cross section triangle)
+	 * http://en.wikipedia.org/wiki/Triangle
+	 * base = 1/2 abs((xA-xC)(yB-yA)-(xA-xB)(yC-yA))*/
+	base = 1./2. * fabs((xyz_list[0][0]-xyz_list[2][0])*(xyz_list[1][1]-xyz_list[0][1]) - (xyz_list[0][0]-xyz_list[1][0])*(xyz_list[2][1]-xyz_list[0][1]));	// area of element in m2
+
+	/*Now get the average SMB over the element*/
+	Input* smb_input = inputs->GetInput(SurfaceforcingsMassBalanceEnum); _assert_(smb_input);
+	smb_input->GetInputAverage(&smb);																								// average smb on element in m ice s-1
+   Total_Smb=rho_ice*base*smb;																											// smb on element in kg s-1
+	
+	/*Process units: */
+	Total_Smb=UnitConversion(Total_Smb,IuToExtEnum,TotalSmbEnum);																// smb on element in GigaTon yr-1
+	
+	/*Return: */
+	return Total_Smb;
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_DIAGNOSTIC_
+/*FUNCTION Tria::CreateKMatrixDiagnosticMacAyeal {{{*/
+ElementMatrix* Tria::CreateKMatrixDiagnosticMacAyeal(void){
+
+	/*compute all stiffness matrices for this element*/
+	ElementMatrix* Ke1=CreateKMatrixDiagnosticMacAyealViscous();
+	ElementMatrix* Ke2=CreateKMatrixDiagnosticMacAyealFriction();
+	ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+	
+	/*clean-up and return*/
+	delete Ke1;
+	delete Ke2;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixDiagnosticMacAyealViscous{{{*/
+ElementMatrix* Tria::CreateKMatrixDiagnosticMacAyealViscous(void){
+
+	/*Constants*/
+	const int  numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries*/
+	int        i,j,ig;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     viscosity,newviscosity,oldviscosity;
+	IssmDouble     viscosity_overshoot,thickness,Jdet;
+	IssmDouble     epsilon[3],oldepsilon[3];    /* epsilon=[exx,eyy,exy];    */
+	IssmDouble     B[3][numdof];
+	IssmDouble     Bprime[3][numdof];
+	IssmDouble     D[3][3]   = {0.0};
+	IssmDouble     D_scalar;
+	GaussTria *gauss = NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,MacAyealApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+	Input* vx_input=inputs->GetInput(VxEnum);               _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);               _assert_(vy_input);
+	Input* vxold_input=inputs->GetInput(VxPicardEnum);      _assert_(vxold_input);
+	Input* vyold_input=inputs->GetInput(VyPicardEnum);      _assert_(vyold_input);
+	this->parameters->FindParam(&viscosity_overshoot,DiagnosticViscosityOvershootEnum);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetBMacAyeal(&B[0][0], &xyz_list[0][0], gauss);
+		GetBprimeMacAyeal(&Bprime[0][0], &xyz_list[0][0], gauss);
+
+		this->GetStrainRate2d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		this->GetStrainRate2d(&oldepsilon[0],&xyz_list[0][0],gauss,vxold_input,vyold_input);
+		material->GetViscosity2d(&viscosity, &epsilon[0]);
+		material->GetViscosity2d(&oldviscosity, &oldepsilon[0]);
+		thickness_input->GetInputValue(&thickness, gauss);
+
+		newviscosity=viscosity+viscosity_overshoot*(viscosity-oldviscosity);
+		D_scalar=2*newviscosity*thickness*gauss->weight*Jdet;
+		for (i=0;i<3;i++) D[i][i]=D_scalar;
+
+		TripleMultiply(&B[0][0],3,numdof,1,
+					&D[0][0],3,3,0,
+					&Bprime[0][0],3,numdof,0,
+					&Ke->values[0],1);
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixDiagnosticMacAyealFriction {{{*/
+ElementMatrix* Tria::CreateKMatrixDiagnosticMacAyealFriction(void){
+
+	/*Constants*/
+	const int  numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries*/
+	int        i,j,ig;
+	int        analysis_type;
+	IssmDouble     MAXSLOPE  = .06; // 6 %
+	IssmDouble     MOUNTAINKEXPONENT = 10;
+	IssmDouble     slope_magnitude,alpha2;
+	IssmDouble     Jdet;
+	IssmDouble     L[2][numdof];
+	IssmDouble     DL[2][2]  = {{ 0,0 },{0,0}};
+	IssmDouble     DL_scalar;
+	IssmDouble     slope[2]  = {0.0,0.0};
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	Friction  *friction = NULL;
+	GaussTria *gauss    = NULL;
+
+	/*Initialize Element matrix and return if necessary*/
+	if(IsFloating()) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,MacAyealApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* surface_input=inputs->GetInput(SurfaceEnum); _assert_(surface_input);
+	Input* vx_input=inputs->GetInput(VxEnum);           _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);           _assert_(vy_input);
+	Input* vz_input=inputs->GetInput(VzEnum);           _assert_(vz_input);
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*build friction object, used later on: */
+	friction=new Friction("2d",inputs,matpar,analysis_type);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		// If we have a slope > 6% for this element,  it means  we are on a mountain. In this particular case, 
+		//velocity should be = 0. To achieve this result, we set alpha2_list to a very high value: */
+		surface_input->GetInputDerivativeValue(&slope[0],&xyz_list[0][0],gauss);
+		slope_magnitude=sqrt(slope[0]*slope[0]+slope[1]*slope[1]);
+		if(slope_magnitude>MAXSLOPE) alpha2=pow((IssmDouble)10,MOUNTAINKEXPONENT);
+		else friction->GetAlpha2(&alpha2, gauss,VxEnum,VyEnum,VzEnum);
+
+		GetL(&L[0][0], &xyz_list[0][0], gauss,NDOF2);
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		DL_scalar=alpha2*gauss->weight*Jdet;
+		for (i=0;i<2;i++) DL[i][i]=DL_scalar;
+		
+		TripleMultiply( &L[0][0],2,numdof,1,
+					&DL[0][0],2,2,0,
+					&L[0][0],2,numdof,0,
+					&Ke->values[0],1);
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixDiagnosticHutter{{{*/
+ElementMatrix* Tria::CreateKMatrixDiagnosticHutter(void){
+
+	/*Intermediaries*/
+	const int numdof=NUMVERTICES*NDOF2;
+	int    i,connectivity;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Create Element matrix*/
+	for(i=0;iGetConnectivity();
+		Ke->values[(2*i)*numdof  +(2*i)  ]=1/(IssmDouble)connectivity;
+		Ke->values[(2*i+1)*numdof+(2*i+1)]=1/(IssmDouble)connectivity;
+	}
+
+	/*Clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorDiagnosticMacAyeal {{{*/
+ElementVector* Tria::CreatePVectorDiagnosticMacAyeal(){
+
+	/*Constants*/
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries */
+	int            i,j,ig;
+	IssmDouble         driving_stress_baseline,thickness;
+	IssmDouble         Jdet;
+	IssmDouble         xyz_list[NUMVERTICES][3];
+	IssmDouble         slope[2];
+	IssmDouble         basis[3];
+	IssmDouble         pe_g_gaussian[numdof];
+	GaussTria*     gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,MacAyealApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input); 
+	Input* surface_input=inputs->GetInput(SurfaceEnum);     _assert_(surface_input);
+	Input* drag_input=inputs->GetInput(FrictionCoefficientEnum);_assert_(drag_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctions(basis, gauss);
+
+		thickness_input->GetInputValue(&thickness,gauss);
+		surface_input->GetInputDerivativeValue(&slope[0],&xyz_list[0][0],gauss);
+		driving_stress_baseline=matpar->GetRhoIce()*matpar->GetG()*thickness;
+
+		/*Build pe_g_gaussian vector: */
+		for (i=0;ivalues[i*NDOF2+j]+=-driving_stress_baseline*slope[j]*Jdet*gauss->weight*basis[i];
+			}
+		}
+	}
+
+	/*Transform coordinate system*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorDiagnosticHutter{{{*/
+ElementVector* Tria::CreatePVectorDiagnosticHutter(void){
+
+	/*Intermediaries */
+	int        i,connectivity;
+	IssmDouble     constant_part,ub,vb;
+	IssmDouble     rho_ice,gravity,n,B;
+	IssmDouble     slope2,thickness;
+	IssmDouble     slope[2];
+	GaussTria* gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	rho_ice=matpar->GetRhoIce();
+	gravity=matpar->GetG();
+	n=material->GetN();
+	B=material->GetBbar();
+	Input* slopex_input=inputs->GetInput(SurfaceSlopeXEnum); _assert_(slopex_input);
+	Input* slopey_input=inputs->GetInput(SurfaceSlopeYEnum); _assert_(slopey_input);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum);  _assert_(thickness_input);
+
+	/*Spawn 3 sing elements: */
+	gauss=new GaussTria();
+	for(i=0;iGaussVertex(i);
+
+		connectivity=nodes[i]->GetConnectivity();
+
+		thickness_input->GetInputValue(&thickness,gauss);
+		slopex_input->GetInputValue(&slope[0],gauss);
+		slopey_input->GetInputValue(&slope[1],gauss);
+		slope2=pow(slope[0],2)+pow(slope[1],2);
+
+		constant_part=-2*pow(rho_ice*gravity,n)*pow(slope2,((n-1)/2));
+
+		ub=-1.58*pow((IssmDouble)10.0,(IssmDouble)-10.0)*rho_ice*gravity*thickness*slope[0];
+		vb=-1.58*pow((IssmDouble)10.0,(IssmDouble)-10.0)*rho_ice*gravity*thickness*slope[1];
+
+		pe->values[2*i]  =(ub-2.0*pow(rho_ice*gravity,n)*pow(slope2,((n-1)/2.0))*pow(thickness,n)/(pow(B,n)*(n+1))*slope[0])/(IssmDouble)connectivity;
+		pe->values[2*i+1]=(vb-2.0*pow(rho_ice*gravity,n)*pow(slope2,((n-1)/2.0))*pow(thickness,n)/(pow(B,n)*(n+1))*slope[1])/(IssmDouble)connectivity;
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateJacobianDiagnosticMacayeal{{{*/
+ElementMatrix* Tria::CreateJacobianDiagnosticMacayeal(void){
+
+	/*Constants*/
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     Jdet,thickness;
+	IssmDouble     eps1dotdphii,eps1dotdphij;
+	IssmDouble     eps2dotdphii,eps2dotdphij;
+	IssmDouble     mu_prime;
+	IssmDouble     epsilon[3];/* epsilon=[exx,eyy,exy];*/
+	IssmDouble     eps1[2],eps2[2];
+	IssmDouble     phi[NUMVERTICES];
+	IssmDouble     dphi[2][NUMVERTICES];
+	GaussTria *gauss=NULL;
+
+	/*Initialize Jacobian with regular MacAyeal (first part of the Gateau derivative)*/
+	ElementMatrix* Ke=CreateKMatrixDiagnosticMacAyeal();
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsDerivatives(&dphi[0][0],&xyz_list[0][0],gauss);
+
+		thickness_input->GetInputValue(&thickness, gauss);
+		this->GetStrainRate2d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		material->GetViscosity2dDerivativeEpsSquare(&mu_prime,&epsilon[0]);
+		eps1[0]=2*epsilon[0]+epsilon[1];   eps2[0]=epsilon[2];
+		eps1[1]=epsilon[2];                eps2[1]=epsilon[0]+2*epsilon[1];
+
+		for(i=0;i<3;i++){
+			for(j=0;j<3;j++){
+				eps1dotdphii=eps1[0]*dphi[0][i]+eps1[1]*dphi[1][i];
+				eps1dotdphij=eps1[0]*dphi[0][j]+eps1[1]*dphi[1][j];
+				eps2dotdphii=eps2[0]*dphi[0][i]+eps2[1]*dphi[1][i];
+				eps2dotdphij=eps2[0]*dphi[0][j]+eps2[1]*dphi[1][j];
+
+				Ke->values[6*(2*i+0)+2*j+0]+=gauss->weight*Jdet*2*mu_prime*thickness*eps1dotdphij*eps1dotdphii;
+				Ke->values[6*(2*i+0)+2*j+1]+=gauss->weight*Jdet*2*mu_prime*thickness*eps2dotdphij*eps1dotdphii;
+				Ke->values[6*(2*i+1)+2*j+0]+=gauss->weight*Jdet*2*mu_prime*thickness*eps1dotdphij*eps2dotdphii;
+				Ke->values[6*(2*i+1)+2*j+1]+=gauss->weight*Jdet*2*mu_prime*thickness*eps2dotdphij*eps2dotdphii;
+			}
+		}
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::GetSolutionFromInputsDiagnosticHoriz{{{*/
+void  Tria::GetSolutionFromInputsDiagnosticHoriz(Vector* solution){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int          i;
+	int*         doflist=NULL;
+	IssmDouble       vx,vy;
+	IssmDouble       values[numdof];
+	GaussTria*   gauss=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Get inputs*/
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+
+	/*Ok, we have vx and vy in values, fill in vx and vy arrays: */
+	/*P1 element only for now*/
+	gauss=new GaussTria();
+	for(i=0;iGaussVertex(i);
+
+		/*Recover vx and vy*/
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		values[i*NDOF2+0]=vx;
+		values[i*NDOF2+1]=vy;
+	}
+
+	solution->SetValues(numdof,doflist,values,INS_VAL);
+
+	/*Free ressources:*/
+	delete gauss;
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Tria::GetSolutionFromInputsDiagnosticHutter{{{*/
+void  Tria::GetSolutionFromInputsDiagnosticHutter(Vector* solution){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int        i;
+	IssmDouble     vx,vy;
+	IssmDouble     values[numdof];
+	int       *doflist = NULL;
+	GaussTria *gauss   = NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Get inputs*/
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+
+	/*Ok, we have vx and vy in values, fill in vx and vy arrays: */
+	/*P1 element only for now*/
+	gauss=new GaussTria();
+	for(i=0;iGaussVertex(i);
+
+		/*Recover vx and vy*/
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		values[i*NDOF2+0]=vx;
+		values[i*NDOF2+1]=vy;
+	}
+
+	solution->SetValues(numdof,doflist,values,INS_VAL);
+
+	/*Free ressources:*/
+	delete gauss;
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromSolutionDiagnosticHoriz {{{*/
+void  Tria::InputUpdateFromSolutionDiagnosticHoriz(IssmDouble* solution){
+	
+	const int numdof=NDOF2*NUMVERTICES;
+
+	int       i;
+	int*      doflist=NULL;
+	IssmDouble    rho_ice,g;
+	IssmDouble    values[numdof];
+	IssmDouble    vx[NUMVERTICES];
+	IssmDouble    vy[NUMVERTICES];
+	IssmDouble    vz[NUMVERTICES];
+	IssmDouble    vel[NUMVERTICES];
+	IssmDouble    pressure[NUMVERTICES];
+	IssmDouble    thickness[NUMVERTICES];
+	
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(vx[i])) _error_("NaN found in solution vector");
+		if(xIsNan(vy[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Get Vz and compute vel*/
+	GetInputListOnVertices(&vz[0],VzEnum,0);
+	for(i=0;iGetRhoIce();
+	g=matpar->GetG();
+	GetInputListOnVertices(&thickness[0],ThicknessEnum);
+	for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+	this->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+	this->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new TriaP1Input(VxEnum,vx));
+	this->inputs->AddInput(new TriaP1Input(VyEnum,vy));
+	this->inputs->AddInput(new TriaP1Input(VelEnum,vel));
+	this->inputs->AddInput(new TriaP1Input(PressureEnum,pressure));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromSolutionDiagnosticHutter {{{*/
+void  Tria::InputUpdateFromSolutionDiagnosticHutter(IssmDouble* solution){
+	
+	const int numdof=NDOF2*NUMVERTICES;
+	
+	int       i;
+	int*      doflist=NULL;
+	IssmDouble    rho_ice,g;
+	IssmDouble    values[numdof];
+	IssmDouble    vx[NUMVERTICES];
+	IssmDouble    vy[NUMVERTICES];
+	IssmDouble    vz[NUMVERTICES];
+	IssmDouble    vel[NUMVERTICES];
+	IssmDouble    pressure[NUMVERTICES];
+	IssmDouble    thickness[NUMVERTICES];
+	
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(vx[i])) _error_("NaN found in solution vector");
+		if(xIsNan(vy[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Now Compute vel*/
+	GetInputListOnVertices(&vz[0],VzEnum,0.0); //default is 0
+	for(i=0;iGetRhoIce();
+	g=matpar->GetG();
+	GetInputListOnVertices(&thickness[0],ThicknessEnum);
+	for(i=0;iinputs->ChangeEnum(VxEnum,VxPicardEnum);
+	this->inputs->ChangeEnum(VyEnum,VyPicardEnum);
+	this->inputs->ChangeEnum(PressureEnum,PressurePicardEnum);
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new TriaP1Input(VxEnum,vx));
+	this->inputs->AddInput(new TriaP1Input(VyEnum,vy));
+	this->inputs->AddInput(new TriaP1Input(VelEnum,vel));
+	this->inputs->AddInput(new TriaP1Input(PressureEnum,pressure));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_CONTROL_
+/*FUNCTION Tria::InputControlUpdate{{{*/
+void  Tria::InputControlUpdate(IssmDouble scalar,bool save_parameter){
+
+	/*Intermediary*/
+	int    num_controls;
+	int*   control_type=NULL;
+	Input* input=NULL;
+
+	/*retrieve some parameters: */
+	this->parameters->FindParam(&num_controls,InversionNumControlParametersEnum);
+	this->parameters->FindParam(&control_type,NULL,InversionControlParametersEnum);
+
+	for(int i=0;iinputs->GetInput(control_type[i]); _assert_(input);
+		}
+		else{
+			input=(Input*)this->inputs->GetInput(control_type[i]);   _assert_(input);
+		}
+
+		if (input->ObjectEnum()!=ControlInputEnum){
+			_error_("input " << EnumToStringx(control_type[i]) << " is not a ControlInput");
+		}
+
+		((ControlInput*)input)->UpdateValue(scalar);
+		((ControlInput*)input)->Constrain();
+		if (save_parameter) ((ControlInput*)input)->SaveValue();
+
+	}
+
+	/*Clean up and return*/
+	xDelete(control_type);
+}
+/*}}}*/
+/*FUNCTION Tria::ControlInputGetGradient{{{*/
+void Tria::ControlInputGetGradient(Vector* gradient,int enum_type,int control_index){
+
+	int doflist1[NUMVERTICES];
+	Input* input=NULL;
+
+	if(enum_type==MaterialsRheologyBbarEnum || enum_type==MaterialsRheologyZbarEnum){
+		input=(Input*)material->inputs->GetInput(enum_type);
+	}
+	else{
+		input=inputs->GetInput(enum_type);
+	}
+	if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found");
+	if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
+
+	GradientIndexing(&doflist1[0],control_index);
+	((ControlInput*)input)->GetGradient(gradient,&doflist1[0]);
+
+}/*}}}*/
+/*FUNCTION Tria::ControlInputScaleGradient{{{*/
+void Tria::ControlInputScaleGradient(int enum_type,IssmDouble scale){
+
+	Input* input=NULL;
+
+	if(enum_type==MaterialsRheologyBbarEnum || enum_type==MaterialsRheologyZbarEnum){
+		input=(Input*)material->inputs->GetInput(enum_type);
+	}
+	else{
+		input=inputs->GetInput(enum_type);
+	}
+	if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found");
+	if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
+
+	((ControlInput*)input)->ScaleGradient(scale);
+}/*}}}*/
+/*FUNCTION Tria::ControlInputSetGradient{{{*/
+void Tria::ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index){
+
+	int    doflist1[NUMVERTICES];
+	IssmDouble grad_list[NUMVERTICES];
+	Input* grad_input=NULL;
+	Input* input=NULL;
+
+	if(enum_type==MaterialsRheologyBbarEnum || enum_type==MaterialsRheologyZbarEnum){
+		input=(Input*)material->inputs->GetInput(enum_type);
+	}
+	else{
+		input=inputs->GetInput(enum_type);
+	}
+	if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found");
+	if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
+
+	GradientIndexing(&doflist1[0],control_index);
+	for(int i=0;iSetGradient(grad_input);
+
+}/*}}}*/
+/*FUNCTION Tria::Gradj {{{*/
+void  Tria::Gradj(Vector* gradient,int control_type,int control_index){
+	/*dJ/dalpha = ∂L/∂alpha = ∂J/∂alpha + ∂/∂alpha(KU-F)*/
+
+	/*If on water, grad = 0: */
+	if(IsOnWater()) return;
+
+	/*First deal with ∂/∂alpha(KU-F)*/
+	switch(control_type){
+		case FrictionCoefficientEnum:
+			GradjDragMacAyeal(gradient,control_index);
+			break;
+		case MaterialsRheologyBbarEnum:
+			GradjBMacAyeal(gradient,control_index);
+			break;
+		case MaterialsRheologyZbarEnum:
+			GradjZMacAyeal(gradient,control_index);
+			break;
+		case BalancethicknessThickeningRateEnum:
+			GradjDhDtBalancedthickness(gradient,control_index);
+			break;
+		case VxEnum:
+			GradjVxBalancedthickness(gradient,control_index);
+			break;
+		case VyEnum:
+			GradjVyBalancedthickness(gradient,control_index);
+			break;
+		default:
+			_error_("control type not supported yet: " << control_type);
+	}
+
+	/*Now deal with ∂J/∂alpha*/
+	int        *responses = NULL;
+	int         num_responses,resp;
+	this->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum);
+	this->parameters->FindParam(&responses,NULL,NULL,StepResponsesEnum);
+
+	for(resp=0;resp(responses);
+}
+/*}}}*/
+/*FUNCTION Tria::GradjBGradient{{{*/
+void  Tria::GradjBGradient(Vector* gradient,int weight_index,int control_index){
+
+	int        i,ig;
+	int        doflist1[NUMVERTICES];
+	IssmDouble     Jdet,weight;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     dbasis[NDOF2][NUMVERTICES];
+	IssmDouble     dk[NDOF2]; 
+	IssmDouble     grade_g[NUMVERTICES]={0.0};
+	GaussTria  *gauss=NULL;
+
+	/*Retrieve all inputs we will be needing: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	GradientIndexing(&doflist1[0],control_index);
+	Input* rheologyb_input=material->inputs->GetInput(MaterialsRheologyBbarEnum); _assert_(rheologyb_input);
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);                _assert_(weights_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsDerivatives(&dbasis[0][0],&xyz_list[0][0],gauss);
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+
+		/*Build alpha_complement_list: */
+		rheologyb_input->GetInputDerivativeValue(&dk[0],&xyz_list[0][0],gauss);
+
+		/*Build gradje_g_gaussian vector (actually -dJ/ddrag): */
+		for (i=0;iweight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]);
+	}
+	gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+
+	/*Clean up and return*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::GradjZGradient{{{*/
+void  Tria::GradjZGradient(Vector* gradient,int weight_index,int control_index){
+
+	int        i,ig;
+	int        doflist1[NUMVERTICES];
+	IssmDouble     Jdet,weight;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     dbasis[NDOF2][NUMVERTICES];
+	IssmDouble     dk[NDOF2]; 
+	IssmDouble     grade_g[NUMVERTICES]={0.0};
+	GaussTria  *gauss=NULL;
+
+	/*Retrieve all inputs we will be needing: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	GradientIndexing(&doflist1[0],control_index);
+	Input* rheologyz_input=material->inputs->GetInput(MaterialsRheologyZbarEnum); _assert_(rheologyz_input);
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);                _assert_(weights_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsDerivatives(&dbasis[0][0],&xyz_list[0][0],gauss);
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+
+		/*Build alpha_complement_list: */
+		rheologyz_input->GetInputDerivativeValue(&dk[0],&xyz_list[0][0],gauss);
+
+		/*Build gradje_g_gaussian vector (actually -dJ/ddrag): */
+		for (i=0;iweight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]);
+	}
+	gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+
+	/*Clean up and return*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::GradjBMacAyeal{{{*/
+void  Tria::GradjBMacAyeal(Vector* gradient,int control_index){
+
+	/*Intermediaries*/
+	int        i,ig;
+	int        doflist[NUMVERTICES];
+	IssmDouble     vx,vy,lambda,mu,thickness,Jdet;
+	IssmDouble     viscosity_complement;
+	IssmDouble     dvx[NDOF2],dvy[NDOF2],dadjx[NDOF2],dadjy[NDOF2],dB[NDOF2]; 
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     basis[3],epsilon[3];
+	IssmDouble     grad[NUMVERTICES]={0.0};
+	GaussTria *gauss = NULL;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	GradientIndexing(&doflist[0],control_index);
+
+	/*Retrieve all inputs*/
+	Input* thickness_input=inputs->GetInput(ThicknessEnum);                     _assert_(thickness_input);
+	Input* vx_input=inputs->GetInput(VxEnum);                                   _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                                   _assert_(vy_input);
+	Input* adjointx_input=inputs->GetInput(AdjointxEnum);                       _assert_(adjointx_input);
+	Input* adjointy_input=inputs->GetInput(AdjointyEnum);                       _assert_(adjointy_input);
+	Input* rheologyb_input=material->inputs->GetInput(MaterialsRheologyBbarEnum); _assert_(rheologyb_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(4);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		thickness_input->GetInputValue(&thickness,gauss);
+		rheologyb_input->GetInputDerivativeValue(&dB[0],&xyz_list[0][0],gauss);
+		vx_input->GetInputDerivativeValue(&dvx[0],&xyz_list[0][0],gauss);
+		vy_input->GetInputDerivativeValue(&dvy[0],&xyz_list[0][0],gauss);
+		adjointx_input->GetInputDerivativeValue(&dadjx[0],&xyz_list[0][0],gauss);
+		adjointy_input->GetInputDerivativeValue(&dadjy[0],&xyz_list[0][0],gauss);
+
+		this->GetStrainRate2d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		material->GetViscosityComplement(&viscosity_complement,&epsilon[0]);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctions(basis,gauss);
+
+		/*standard gradient dJ/dki*/
+		for (i=0;iweight*basis[i];
+	}
+
+	gradient->SetValues(NUMVERTICES,doflist,grad,ADD_VAL);
+
+	/*clean-up*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::GradjZMacAyeal{{{*/
+void  Tria::GradjZMacAyeal(Vector* gradient,int control_index){
+
+	/*Intermediaries*/
+	int        i,ig;
+	int        doflist[NUMVERTICES];
+	IssmDouble     vx,vy,lambda,mu,thickness,Jdet;
+	IssmDouble     viscosity_complement;
+	IssmDouble     dvx[NDOF2],dvy[NDOF2],dadjx[NDOF2],dadjy[NDOF2],dZ[NDOF2]; 
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     basis[3],epsilon[3];
+	IssmDouble     grad[NUMVERTICES]={0.0};
+	GaussTria *gauss = NULL;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	GradientIndexing(&doflist[0],control_index);
+
+	/*Retrieve all inputs*/
+	Input* thickness_input=inputs->GetInput(ThicknessEnum);                     _assert_(thickness_input);
+	Input* vx_input=inputs->GetInput(VxEnum);                                   _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                                   _assert_(vy_input);
+	Input* adjointx_input=inputs->GetInput(AdjointxEnum);                       _assert_(adjointx_input);
+	Input* adjointy_input=inputs->GetInput(AdjointyEnum);                       _assert_(adjointy_input);
+	Input* rheologyz_input=material->inputs->GetInput(MaterialsRheologyZbarEnum); _assert_(rheologyz_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(4);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		thickness_input->GetInputValue(&thickness,gauss);
+		rheologyz_input->GetInputDerivativeValue(&dZ[0],&xyz_list[0][0],gauss);
+		vx_input->GetInputDerivativeValue(&dvx[0],&xyz_list[0][0],gauss);
+		vy_input->GetInputDerivativeValue(&dvy[0],&xyz_list[0][0],gauss);
+		adjointx_input->GetInputDerivativeValue(&dadjx[0],&xyz_list[0][0],gauss);
+		adjointy_input->GetInputDerivativeValue(&dadjy[0],&xyz_list[0][0],gauss);
+
+		this->GetStrainRate2d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		material->GetViscosityZComplement(&viscosity_complement,&epsilon[0]);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctions(basis,gauss);
+
+		/*standard gradient dJ/dki*/
+		for (i=0;iweight*basis[i];
+	}
+
+	gradient->SetValues(NUMVERTICES,doflist,grad,ADD_VAL);
+
+	/*clean-up*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::GradjDragMacAyeal {{{*/
+void  Tria::GradjDragMacAyeal(Vector* gradient,int control_index){
+
+	int        i,ig;
+	int        analysis_type;
+	int        doflist1[NUMVERTICES];
+	int        connectivity[NUMVERTICES];
+	IssmDouble     vx,vy,lambda,mu,alpha_complement,Jdet;
+	IssmDouble     bed,thickness,Neff,drag;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     dk[NDOF2]; 
+	IssmDouble     grade_g[NUMVERTICES]={0.0};
+	IssmDouble     grade_g_gaussian[NUMVERTICES];
+	IssmDouble     basis[3];
+	IssmDouble     epsilon[3]; /* epsilon=[exx,eyy,exy];*/
+	Friction*  friction=NULL;
+	GaussTria  *gauss=NULL;
+
+	if(IsFloating())return;
+
+	/*retrive parameters: */
+	parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	GradientIndexing(&doflist1[0],control_index);
+	this->GetConnectivityList(&connectivity[0]);
+
+	/*Build frictoin element, needed later: */
+	friction=new Friction("2d",inputs,matpar,analysis_type);
+
+	/*Retrieve all inputs we will be needing: */
+	Input* adjointx_input=inputs->GetInput(AdjointxEnum);                   _assert_(adjointx_input);
+	Input* adjointy_input=inputs->GetInput(AdjointyEnum);                   _assert_(adjointy_input);
+	Input* vx_input=inputs->GetInput(VxEnum);                               _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);                               _assert_(vy_input);
+	Input* dragcoefficient_input=inputs->GetInput(FrictionCoefficientEnum); _assert_(dragcoefficient_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(4);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctions(basis, gauss);
+
+		/*Build alpha_complement_list: */
+		friction->GetAlphaComplement(&alpha_complement, gauss,VxEnum,VyEnum,VzEnum);
+	
+		dragcoefficient_input->GetInputValue(&drag, gauss);
+		adjointx_input->GetInputValue(&lambda, gauss);
+		adjointy_input->GetInputValue(&mu, gauss);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		dragcoefficient_input->GetInputDerivativeValue(&dk[0],&xyz_list[0][0],gauss);
+
+		/*Build gradje_g_gaussian vector (actually -dJ/ddrag): */
+		for (i=0;iweight*basis[i];
+		}
+		
+		/*Add gradje_g_gaussian vector to gradje_g: */
+		for(i=0;i(grade_g[i]));
+			grade_g[i]+=grade_g_gaussian[i];
+		}
+	}
+	/*Analytical gradient*/
+	//delete gauss;
+	//gauss=new GaussTria();
+	//for (int iv=0;ivGaussVertex(iv);
+	//	friction->GetAlphaComplement(&alpha_complement, gauss,VxEnum,VyEnum,VzEnum);
+	//	dragcoefficient_input->GetInputValue(&drag, gauss);
+	//	adjointx_input->GetInputValue(&lambda, gauss);
+	//	adjointy_input->GetInputValue(&mu, gauss);
+	//	vx_input->GetInputValue(&vx,gauss);
+	//	vy_input->GetInputValue(&vy,gauss);
+	//	grade_g[iv] = -2*1.e+7*drag*alpha_complement*(lambda*vx+mu*vy)/((IssmDouble)connectivity[iv]);
+	//}
+	/*End Analytical gradient*/
+
+	gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+
+	/*Clean up and return*/
+	delete gauss;
+	delete friction;
+}
+/*}}}*/
+/*FUNCTION Tria::GradjDragGradient{{{*/
+void  Tria::GradjDragGradient(Vector* gradient, int weight_index,int control_index){
+
+	int        i,ig;
+	int        doflist1[NUMVERTICES];
+	IssmDouble     Jdet,weight;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     dbasis[NDOF2][NUMVERTICES];
+	IssmDouble     dk[NDOF2]; 
+	IssmDouble     grade_g[NUMVERTICES]={0.0};
+	GaussTria  *gauss=NULL;
+
+	/*Retrieve all inputs we will be needing: */
+	if(IsFloating())return;
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	GradientIndexing(&doflist1[0],control_index);
+	Input* dragcoefficient_input=inputs->GetInput(FrictionCoefficientEnum); _assert_(dragcoefficient_input);
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);                 _assert_(weights_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsDerivatives(&dbasis[0][0],&xyz_list[0][0],gauss);
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+
+		/*Build alpha_complement_list: */
+		dragcoefficient_input->GetInputDerivativeValue(&dk[0],&xyz_list[0][0],gauss);
+
+		/*Build gradje_g_gaussian vector (actually -dJ/ddrag): */
+		for (i=0;iweight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]);
+			_assert_(!xIsNan(grade_g[i]));
+		}
+	}
+	gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+
+	/*Clean up and return*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::GradjDhDtBalancedthickness{{{*/
+void  Tria::GradjDhDtBalancedthickness(Vector* gradient,int control_index){
+
+	/*Intermediaries*/
+	int    doflist1[NUMVERTICES];
+	IssmDouble lambda[NUMVERTICES];
+	IssmDouble gradient_g[NUMVERTICES];
+
+	/*Compute Gradient*/
+	GradientIndexing(&doflist1[0],control_index);
+	GetInputListOnVertices(&lambda[0],AdjointEnum);
+	for(int i=0;iSetValues(NUMVERTICES,doflist1,gradient_g,INS_VAL);
+}
+/*}}}*/
+/*FUNCTION Tria::GradjVxBalancedthickness{{{*/
+void  Tria::GradjVxBalancedthickness(Vector* gradient,int control_index){
+
+	/*Intermediaries*/
+	int        i,ig;
+	int        doflist1[NUMVERTICES];
+	IssmDouble     thickness,Jdet;
+	IssmDouble     basis[3];
+	IssmDouble     Dlambda[2],dp[2];
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     grade_g[NUMVERTICES] = {0.0};
+	GaussTria *gauss                = NULL;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	GradientIndexing(&doflist1[0],control_index);
+
+	/*Retrieve all inputs we will be needing: */
+	Input* adjoint_input=inputs->GetInput(AdjointEnum);     _assert_(adjoint_input);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctions(basis, gauss);
+		
+		adjoint_input->GetInputDerivativeValue(&Dlambda[0],&xyz_list[0][0],gauss);
+		thickness_input->GetInputValue(&thickness, gauss);
+		thickness_input->GetInputDerivativeValue(&dp[0],&xyz_list[0][0],gauss);
+
+		for(i=0;iweight*basis[i];
+	}
+
+	gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+
+	/*Clean up and return*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::GradjVyBalancedthickness{{{*/
+void  Tria::GradjVyBalancedthickness(Vector* gradient,int control_index){
+
+	/*Intermediaries*/
+	int        i,ig;
+	int        doflist1[NUMVERTICES];
+	IssmDouble     thickness,Jdet;
+	IssmDouble     basis[3];
+	IssmDouble     Dlambda[2],dp[2];
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     grade_g[NUMVERTICES] = {0.0};
+	GaussTria *gauss                = NULL;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	GradientIndexing(&doflist1[0],control_index);
+
+	/*Retrieve all inputs we will be needing: */
+	Input* adjoint_input=inputs->GetInput(AdjointEnum);     _assert_(adjoint_input);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctions(basis, gauss);
+
+		adjoint_input->GetInputDerivativeValue(&Dlambda[0],&xyz_list[0][0],gauss);
+		thickness_input->GetInputValue(&thickness, gauss);
+		thickness_input->GetInputDerivativeValue(&dp[0],&xyz_list[0][0],gauss);
+
+		for(i=0;iweight*basis[i];
+	}
+	gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+
+	/*Clean up and return*/
+	delete gauss;
+}
+/*}}}*/
+/*FUNCTION Tria::GradientIndexing{{{*/
+void  Tria::GradientIndexing(int* indexing,int control_index){
+
+	/*Get some parameters*/
+	int num_controls;
+	parameters->FindParam(&num_controls,InversionNumControlParametersEnum);
+
+	/*get gradient indices*/
+	for(int i=0;inodes[i]->GetVertexDof() + control_index;
+	}
+
+}
+/*}}}*/
+/*FUNCTION Tria::RheologyBbarAbsGradient{{{*/
+IssmDouble Tria::RheologyBbarAbsGradient(bool process_units,int weight_index){
+
+	/* Intermediaries */
+	int        ig;
+	IssmDouble     Jelem = 0;
+	IssmDouble     weight;
+	IssmDouble     Jdet;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     dp[NDOF2];
+	GaussTria *gauss = NULL;
+
+	/*retrieve parameters and inputs*/
+
+	/*If on water, return 0: */
+	if(IsOnWater()) return 0;
+
+	/*Retrieve all inputs we will be needing: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* weights_input  =inputs->GetInput(InversionCostFunctionsCoefficientsEnum);              _assert_(weights_input);
+	Input* rheologyb_input=material->inputs->GetInput(MaterialsRheologyBbarEnum); _assert_(rheologyb_input);
+
+	/* Start looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		rheologyb_input->GetInputDerivativeValue(&dp[0],&xyz_list[0][0],gauss);
+
+		/*Tikhonov regularization: J = 1/2 ((dp/dx)^2 + (dp/dy)^2) */ 
+		Jelem+=weight*1/2*(pow(dp[0],2.)+pow(dp[1],2.))*Jdet*gauss->weight;
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::SurfaceAverageVelMisfit {{{*/
+IssmDouble Tria::SurfaceAverageVelMisfit(bool process_units,int weight_index){
+
+	const int    numdof=2*NUMVERTICES;
+
+	int        i,ig;
+	IssmDouble     Jelem=0,S,Jdet;
+	IssmDouble     misfit;
+	IssmDouble     vx,vy,vxobs,vyobs,weight;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	GaussTria *gauss=NULL;
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Retrieve all inputs we will be needing: */
+	inputs->GetInputValue(&S,SurfaceAreaEnum);
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);   _assert_(weights_input);
+	Input* vx_input     =inputs->GetInput(VxEnum);        _assert_(vx_input);
+	Input* vy_input     =inputs->GetInput(VyEnum);        _assert_(vy_input);
+	Input* vxobs_input  =inputs->GetInput(InversionVxObsEnum);     _assert_(vxobs_input);
+	Input* vyobs_input  =inputs->GetInput(InversionVyObsEnum);     _assert_(vyobs_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(3);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vxobs_input->GetInputValue(&vxobs,gauss);
+		vyobs_input->GetInputValue(&vyobs,gauss);
+
+		/*Compute SurfaceAverageVelMisfitEnum:
+		 *
+		 *      1                    2              2
+		 * J = ---  sqrt(  (u - u   )  +  (v - v   )  )
+		 *      S                obs            obs
+		 */
+		misfit=1/S*sqrt( pow(vx-vxobs,2) + pow(vy-vyobs,2));
+
+		if(process_units)UnitConversion(misfit,IuToExtEnum,SurfaceAverageVelMisfitEnum);
+
+		/*Add to cost function*/
+		Jelem+=misfit*weight*Jdet*gauss->weight;
+	}
+
+	/*clean-up and Return: */
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::SurfaceLogVelMisfit {{{*/
+IssmDouble Tria::SurfaceLogVelMisfit(bool process_units,int weight_index){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int        i,ig;
+	IssmDouble     Jelem=0;
+	IssmDouble     misfit,Jdet;
+	IssmDouble     epsvel=2.220446049250313e-16;
+	IssmDouble     meanvel=3.170979198376458e-05; /*1000 m/yr*/
+	IssmDouble     velocity_mag,obs_velocity_mag;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     vx,vy,vxobs,vyobs,weight;
+	GaussTria *gauss=NULL;
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Retrieve all inputs we will be needing: */
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);   _assert_(weights_input);
+	Input* vx_input     =inputs->GetInput(VxEnum);        _assert_(vx_input);
+	Input* vy_input     =inputs->GetInput(VyEnum);        _assert_(vy_input);
+	Input* vxobs_input  =inputs->GetInput(InversionVxObsEnum);     _assert_(vxobs_input);
+	Input* vyobs_input  =inputs->GetInput(InversionVyObsEnum);     _assert_(vyobs_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(4);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vxobs_input->GetInputValue(&vxobs,gauss);
+		vyobs_input->GetInputValue(&vyobs,gauss);
+
+		/*Compute SurfaceLogVelMisfit:
+		 *                 [        vel + eps     ] 2
+		 * J = 4 \bar{v}^2 | log ( -----------  ) |  
+		 *                 [       vel   + eps    ]
+		 *                            obs
+		 */
+		velocity_mag    =sqrt(pow(vx,   2)+pow(vy,   2))+epsvel;
+		obs_velocity_mag=sqrt(pow(vxobs,2)+pow(vyobs,2))+epsvel;
+		misfit=4*pow(meanvel,2)*pow(log(velocity_mag/obs_velocity_mag),2);
+
+		if(process_units)UnitConversion(misfit,IuToExtEnum,SurfaceLogVelMisfitEnum);
+
+		/*Add to cost function*/
+		Jelem+=misfit*weight*Jdet*gauss->weight;
+	}
+
+	/*clean-up and Return: */
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::SurfaceLogVxVyMisfit {{{*/
+IssmDouble Tria::SurfaceLogVxVyMisfit(bool process_units,int weight_index){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int        i,ig;
+	int        fit=-1;
+	IssmDouble     Jelem=0, S=0;
+	IssmDouble     epsvel=2.220446049250313e-16;
+	IssmDouble     meanvel=3.170979198376458e-05; /*1000 m/yr*/
+	IssmDouble     misfit, Jdet;
+	IssmDouble     vx,vy,vxobs,vyobs,weight;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	GaussTria *gauss=NULL;
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Retrieve all inputs we will be needing: */
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);   _assert_(weights_input);
+	Input* vx_input     =inputs->GetInput(VxEnum);        _assert_(vx_input);
+	Input* vy_input     =inputs->GetInput(VyEnum);        _assert_(vy_input);
+	Input* vxobs_input  =inputs->GetInput(InversionVxObsEnum);     _assert_(vxobs_input);
+	Input* vyobs_input  =inputs->GetInput(InversionVyObsEnum);     _assert_(vyobs_input);
+	
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(4);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vxobs_input->GetInputValue(&vxobs,gauss);
+		vyobs_input->GetInputValue(&vyobs,gauss);
+
+		/*Compute SurfaceRelVelMisfit:
+		 *
+		 *      1            [        |u| + eps     2          |v| + eps     2  ]
+		 * J = --- \bar{v}^2 | log ( -----------  )   +  log ( -----------  )   |  
+		 *      2            [       |u    |+ eps              |v    |+ eps     ]
+		 *                              obs                       obs
+		 */
+		misfit=0.5*pow(meanvel,2)*(
+					pow(log((fabs(vx)+epsvel)/(fabs(vxobs)+epsvel)),2) +
+					pow(log((fabs(vy)+epsvel)/(fabs(vyobs)+epsvel)),2) );
+
+		if(process_units)UnitConversion(misfit,IuToExtEnum,SurfaceLogVxVyMisfitEnum);
+
+		/*Add to cost function*/
+		Jelem+=misfit*weight*Jdet*gauss->weight;
+	}
+
+	/*clean-up and Return: */
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::SurfaceAbsVelMisfit {{{*/
+IssmDouble Tria::SurfaceAbsVelMisfit(bool process_units,int weight_index){
+
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	int        i,ig;
+	IssmDouble     Jelem=0;
+	IssmDouble     misfit,Jdet;
+	IssmDouble     vx,vy,vxobs,vyobs,weight;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	GaussTria *gauss=NULL;
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Retrieve all inputs we will be needing: */
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);   _assert_(weights_input);
+	Input* vx_input     =inputs->GetInput(VxEnum);        _assert_(vx_input);
+	Input* vy_input     =inputs->GetInput(VyEnum);        _assert_(vy_input);
+	Input* vxobs_input  =inputs->GetInput(InversionVxObsEnum);     _assert_(vxobs_input);
+	Input* vyobs_input  =inputs->GetInput(InversionVyObsEnum);     _assert_(vyobs_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vxobs_input->GetInputValue(&vxobs,gauss);
+		vyobs_input->GetInputValue(&vyobs,gauss);
+
+		/*Compute SurfaceAbsVelMisfitEnum:
+		 *
+		 *      1  [           2              2 ]
+		 * J = --- | (u - u   )  +  (v - v   )  |
+		 *      2  [       obs            obs   ]
+		 *
+		 */
+		misfit=0.5*( pow(vx-vxobs,2) + pow(vy-vyobs,2) );
+
+		if(process_units)UnitConversion(misfit,IuToExtEnum,SurfaceAverageVelMisfitEnum);
+
+		/*Add to cost function*/
+		Jelem+=misfit*weight*Jdet*gauss->weight;
+	}
+
+	/*clean up and Return: */
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::SurfaceRelVelMisfit {{{*/
+IssmDouble Tria::SurfaceRelVelMisfit(bool process_units,int weight_index){
+	const int  numdof=2*NUMVERTICES;
+
+	int        i,ig;
+	IssmDouble     Jelem=0;
+	IssmDouble     scalex=1,scaley=1;
+	IssmDouble     misfit,Jdet;
+	IssmDouble     epsvel=2.220446049250313e-16;
+	IssmDouble     meanvel=3.170979198376458e-05; /*1000 m/yr*/
+	IssmDouble     vx,vy,vxobs,vyobs,weight;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	GaussTria *gauss=NULL;
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/* Get node coordinates and dof list: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+
+	/*Retrieve all inputs we will be needing: */
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);   _assert_(weights_input);
+	Input* vx_input     =inputs->GetInput(VxEnum);        _assert_(vx_input);
+	Input* vy_input     =inputs->GetInput(VyEnum);        _assert_(vy_input);
+	Input* vxobs_input  =inputs->GetInput(InversionVxObsEnum);     _assert_(vxobs_input);
+	Input* vyobs_input  =inputs->GetInput(InversionVyObsEnum);     _assert_(vyobs_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(4);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vxobs_input->GetInputValue(&vxobs,gauss);
+		vyobs_input->GetInputValue(&vyobs,gauss);
+
+		/*Compute SurfaceRelVelMisfit:
+		 *                        
+		 *      1  [     \bar{v}^2             2   \bar{v}^2              2 ]
+		 * J = --- | -------------  (u - u   ) + -------------  (v - v   )  |
+		 *      2  [  (u   + eps)^2       obs    (v   + eps)^2       obs    ]
+		 *              obs                        obs                      
+		 */
+		scalex=pow(meanvel/(vxobs+epsvel),2); if(vxobs==0)scalex=0;
+		scaley=pow(meanvel/(vyobs+epsvel),2); if(vyobs==0)scaley=0;
+		misfit=0.5*(scalex*pow((vx-vxobs),2)+scaley*pow((vy-vyobs),2));
+		if(process_units)UnitConversion(misfit,IuToExtEnum,SurfaceRelVelMisfitEnum);
+
+		/*Add to cost function*/
+		Jelem+=misfit*weight*Jdet*gauss->weight;
+	}
+
+	/*clean up and Return: */
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::ThicknessAbsGradient{{{*/
+IssmDouble Tria::ThicknessAbsGradient(bool process_units,int weight_index){
+
+	/* Intermediaries */
+	int        ig;
+	IssmDouble     Jelem = 0;
+	IssmDouble     weight;
+	IssmDouble     Jdet;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     dp[NDOF2];
+	GaussTria *gauss = NULL;
+
+	/*retrieve parameters and inputs*/
+
+	/*If on water, return 0: */
+	if(IsOnWater()) return 0;
+
+	/*Retrieve all inputs we will be needing: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* weights_input  =inputs->GetInput(InversionCostFunctionsCoefficientsEnum);   _assert_(weights_input);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+
+	/* Start looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		thickness_input->GetInputDerivativeValue(&dp[0],&xyz_list[0][0],gauss);
+
+		/*Tikhonov regularization: J = 1/2 ((dp/dx)^2 + (dp/dy)^2) */ 
+		Jelem+=weight*1/2*(dp[0]*dp[0]+dp[1]*dp[1])*Jdet*gauss->weight;
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::ThicknessAlongGradient{{{*/
+IssmDouble Tria::ThicknessAlongGradient(bool process_units,int weight_index){
+
+	/* Intermediaries */
+	int         ig;
+	IssmDouble  Jelem = 0;
+	IssmDouble  weight;
+	IssmDouble  Jdet;
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	IssmDouble  dp[NDOF2];
+	IssmDouble  vx,vy,vel;
+	GaussTria  *gauss                    = NULL;
+
+	/*retrieve parameters and inputs*/
+
+	/*If on water, return 0: */
+	if(IsOnWater()) return 0;
+
+	/*Retrieve all inputs we will be needing: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* weights_input  = inputs->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input);
+	Input* thickness_input= inputs->GetInput(ThicknessEnum);                          _assert_(thickness_input);
+	Input* vx_input       = inputs->GetInput(VxEnum);                                 _assert_(vx_input);
+	Input* vy_input       = inputs->GetInput(VyEnum);                                 _assert_(vy_input);
+
+	/* Start looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		thickness_input->GetInputDerivativeValue(&dp[0],&xyz_list[0][0],gauss);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vel = sqrt(vx*vx+vy*vy);
+		vx  = vx/(vel+1.e-9);
+		vy  = vy/(vel+1.e-9);
+
+		/*J = 1/2 ( vx*dH/dx + vy*dH/dy )^2 */
+		Jelem+=weight*1/2*(vx*dp[0] + vy*dp[1])*(vx*dp[0] + vy*dp[1])*Jdet*gauss->weight;
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::ThicknessAcrossGradient{{{*/
+IssmDouble Tria::ThicknessAcrossGradient(bool process_units,int weight_index){
+
+	/* Intermediaries */
+	int         ig;
+	IssmDouble  Jelem = 0;
+	IssmDouble  weight;
+	IssmDouble  Jdet;
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	IssmDouble  dp[NDOF2];
+	IssmDouble  vx,vy,vel;
+	GaussTria  *gauss                    = NULL;
+
+	/*retrieve parameters and inputs*/
+
+	/*If on water, return 0: */
+	if(IsOnWater()) return 0;
+
+	/*Retrieve all inputs we will be needing: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* weights_input  = inputs->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input);
+	Input* thickness_input= inputs->GetInput(ThicknessEnum);                          _assert_(thickness_input);
+	Input* vx_input       = inputs->GetInput(VxEnum);                                 _assert_(vx_input);
+	Input* vy_input       = inputs->GetInput(VyEnum);                                 _assert_(vy_input);
+
+	/* Start looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		thickness_input->GetInputDerivativeValue(&dp[0],&xyz_list[0][0],gauss);
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vel = sqrt(vx*vx+vy*vy);
+		vx  = vx/(vel+1.e-9);
+		vy  = vy/(vel+1.e-9);
+
+		/*J = 1/2 ( -vy*dH/dx + vx*dH/dy )^2 */
+		Jelem+=weight*1/2*(-vy*dp[0] + vx*dp[1])*(-vy*dp[0] + vx*dp[1])*Jdet*gauss->weight;
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::ThicknessAbsMisfit {{{*/
+IssmDouble Tria::ThicknessAbsMisfit(bool process_units,int weight_index){
+
+	/*Intermediaries*/
+	int        i,ig;
+	IssmDouble     thickness,thicknessobs,weight;
+	IssmDouble     Jdet;
+	IssmDouble     Jelem = 0;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	GaussTria *gauss = NULL;
+	IssmDouble     dH[2];
+
+	/*If on water, return 0: */
+	if(IsOnWater())return 0;
+
+	/*Retrieve all inputs we will be needing: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* thickness_input   =inputs->GetInput(ThicknessEnum);   _assert_(thickness_input);
+	Input* thicknessobs_input=inputs->GetInput(InversionThicknessObsEnum);_assert_(thicknessobs_input);
+	Input* weights_input     =inputs->GetInput(InversionCostFunctionsCoefficientsEnum);     _assert_(weights_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get parameters at gauss point*/
+		thickness_input->GetInputValue(&thickness,gauss);
+		thickness_input->GetInputDerivativeValue(&dH[0],&xyz_list[0][0],gauss);
+		thicknessobs_input->GetInputValue(&thicknessobs,gauss);
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+
+		/*compute ThicknessAbsMisfit*/
+		Jelem+=0.5*(thickness-thicknessobs)*(thickness-thicknessobs)*weight*Jdet*gauss->weight;
+	}
+
+	/* clean up and Return: */
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorAdjointBalancethickness{{{*/
+ElementVector* Tria::CreatePVectorAdjointBalancethickness(void){
+
+	/*Constants*/
+	const int    numdof=1*NUMVERTICES;
+
+	/*Intermediaries */
+	int         i,ig,resp;
+	IssmDouble  Jdet;
+	IssmDouble  thickness,thicknessobs,weight;
+	int         num_responses;
+	IssmDouble  xyz_list[NUMVERTICES][3];
+	IssmDouble  basis[3];
+	IssmDouble  dbasis[NDOF2][NUMVERTICES];
+	IssmDouble  dH[2];
+	IssmDouble  vx,vy,vel;
+	GaussTria *gauss     = NULL;
+	int       *responses = NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum);
+	this->parameters->FindParam(&responses,NULL,NULL,StepResponsesEnum);
+	Input* thickness_input    = inputs->GetInput(ThicknessEnum);                          _assert_(thickness_input);
+	Input* thicknessobs_input = inputs->GetInput(InversionThicknessObsEnum);              _assert_(thicknessobs_input);
+	Input* weights_input      = inputs->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input);
+	Input* vx_input           = inputs->GetInput(VxEnum);                                 _assert_(vx_input);
+	Input* vy_input           = inputs->GetInput(VyEnum);                                 _assert_(vy_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctions(basis, gauss);
+		GetNodalFunctionsDerivatives(&dbasis[0][0],&xyz_list[0][0],gauss);
+
+		thickness_input->GetInputValue(&thickness, gauss);
+		thickness_input->GetInputDerivativeValue(&dH[0],&xyz_list[0][0],gauss);
+		thicknessobs_input->GetInputValue(&thicknessobs, gauss);
+
+		/*Loop over all requested responses*/
+		for(resp=0;respGetInputValue(&weight, gauss,resp);
+				for(i=0;ivalues[i]+=(thicknessobs-thickness)*weight*Jdet*gauss->weight*basis[i];
+				break;
+			case ThicknessAbsGradientEnum:
+				weights_input->GetInputValue(&weight, gauss,resp);
+				for(i=0;ivalues[i]+= - weight*dH[0]*dbasis[0][i]*Jdet*gauss->weight;
+				for(i=0;ivalues[i]+= - weight*dH[1]*dbasis[1][i]*Jdet*gauss->weight;
+				break;
+			case ThicknessAlongGradientEnum:
+				weights_input->GetInputValue(&weight, gauss,resp);
+				vx_input->GetInputValue(&vx,gauss);
+				vy_input->GetInputValue(&vy,gauss);
+				vel = sqrt(vx*vx+vy*vy);
+				vx  = vx/(vel+1.e-9);
+				vy  = vy/(vel+1.e-9);
+				for(i=0;ivalues[i]+= - weight*(dH[0]*vx+dH[1]*vy)*(dbasis[0][i]*vx+dbasis[1][i]*vy)*Jdet*gauss->weight;
+				break;
+			case ThicknessAcrossGradientEnum:
+				weights_input->GetInputValue(&weight, gauss,resp);
+				vx_input->GetInputValue(&vx,gauss);
+				vy_input->GetInputValue(&vy,gauss);
+				vel = sqrt(vx*vx+vy*vy);
+				vx  = vx/(vel+1.e-9);
+				vy  = vy/(vel+1.e-9);
+				for(i=0;ivalues[i]+= - weight*(dH[0]*(-vy)+dH[1]*vx)*(dbasis[0][i]*(-vy)+dbasis[1][i]*vx)*Jdet*gauss->weight;
+				break;
+			default:
+				_error_("response " << EnumToStringx(responses[resp]) << " not supported yet");
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	xDelete(responses);
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorAdjointHoriz{{{*/
+ElementVector* Tria::CreatePVectorAdjointHoriz(void){
+
+	/*Constants*/
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,resp,ig;
+	int       *responses=NULL;
+	int        num_responses;
+	IssmDouble     Jdet;
+	IssmDouble     obs_velocity_mag,velocity_mag;
+	IssmDouble     dux,duy;
+	IssmDouble     epsvel=2.220446049250313e-16;
+	IssmDouble     meanvel=3.170979198376458e-05; /*1000 m/yr*/
+	IssmDouble     scalex=0,scaley=0,scale=0,S=0;
+	IssmDouble     vx,vy,vxobs,vyobs,weight;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     basis[3];
+	GaussTria* gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum);
+	this->parameters->FindParam(&responses,NULL,NULL,StepResponsesEnum);
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);   _assert_(weights_input);
+	Input* vx_input     =inputs->GetInput(VxEnum);        _assert_(vx_input);
+	Input* vy_input     =inputs->GetInput(VyEnum);        _assert_(vy_input);
+	Input* vxobs_input  =inputs->GetInput(InversionVxObsEnum);     _assert_(vxobs_input);
+	Input* vyobs_input  =inputs->GetInput(InversionVyObsEnum);     _assert_(vyobs_input);
+
+	/*Get Surface if required by one response*/
+	for(resp=0;respGetInputValue(&S,SurfaceAreaEnum); break;
+		}
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(4);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vxobs_input->GetInputValue(&vxobs,gauss);
+		vyobs_input->GetInputValue(&vyobs,gauss);
+		GetNodalFunctions(basis, gauss);
+
+		/*Loop over all requested responses*/
+		for(resp=0;respGetInputValue(&weight,gauss,resp);
+
+			switch(responses[resp]){
+				case SurfaceAbsVelMisfitEnum:
+					/*
+					 *      1  [           2              2 ]
+					 * J = --- | (u - u   )  +  (v - v   )  |
+					 *      2  [       obs            obs   ]
+					 *
+					 *        dJ
+					 * DU = - -- = (u   - u )
+					 *        du     obs
+					 */
+					for (i=0;ivalues[i*NDOF2+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF2+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case SurfaceRelVelMisfitEnum:
+					/*
+					 *      1  [     \bar{v}^2             2   \bar{v}^2              2 ]
+					 * J = --- | -------------  (u - u   ) + -------------  (v - v   )  |
+					 *      2  [  (u   + eps)^2       obs    (v   + eps)^2       obs    ]
+					 *              obs                        obs                      
+					 *
+					 *        dJ     \bar{v}^2
+					 * DU = - -- = ------------- (u   - u )
+					 *        du   (u   + eps)^2    obs
+					 *               obs
+					 */
+					for (i=0;ivalues[i*NDOF2+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF2+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case SurfaceLogVelMisfitEnum:
+					/*
+					 *                 [        vel + eps     ] 2
+					 * J = 4 \bar{v}^2 | log ( -----------  ) |  
+					 *                 [       vel   + eps    ]
+					 *                            obs
+					 *
+					 *        dJ                 2 * log(...)
+					 * DU = - -- = - 4 \bar{v}^2 -------------  u
+					 *        du                 vel^2 + eps
+					 *            
+					 */
+					for (i=0;ivalues[i*NDOF2+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF2+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case SurfaceAverageVelMisfitEnum:
+					/*
+					 *      1                    2              2
+					 * J = ---  sqrt(  (u - u   )  +  (v - v   )  )
+					 *      S                obs            obs
+					 *
+					 *        dJ      1       1 
+					 * DU = - -- = - --- ----------- * 2 (u - u   )
+					 *        du      S  2 sqrt(...)           obs
+					 */
+					for (i=0;ivalues[i*NDOF2+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF2+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case SurfaceLogVxVyMisfitEnum:
+					/*
+					 *      1            [        |u| + eps     2          |v| + eps     2  ]
+					 * J = --- \bar{v}^2 | log ( -----------  )   +  log ( -----------  )   |  
+					 *      2            [       |u    |+ eps              |v    |+ eps     ]
+					 *                              obs                       obs
+					 *        dJ                              1      u                             1
+					 * DU = - -- = - \bar{v}^2 log(u...) --------- ----  ~ - \bar{v}^2 log(u...) ------
+					 *        du                         |u| + eps  |u|                           u + eps
+					 */
+					for (i=0;ivalues[i*NDOF2+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF2+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case DragCoefficientAbsGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				case ThicknessAbsGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				case ThicknessAlongGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				case ThicknessAcrossGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				case RheologyBbarAbsGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				default:
+					_error_("response " << EnumToStringx(responses[resp]) << " not supported yet");
+			}
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	xDelete(responses);
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorAdjointStokes{{{*/
+ElementVector* Tria::CreatePVectorAdjointStokes(void){
+
+	/*Intermediaries */
+	int        i,resp,ig;
+	int       *responses=NULL;
+	int        num_responses;
+	IssmDouble     Jdet;
+	IssmDouble     obs_velocity_mag,velocity_mag;
+	IssmDouble     dux,duy;
+	IssmDouble     epsvel=2.220446049250313e-16;
+	IssmDouble     meanvel=3.170979198376458e-05; /*1000 m/yr*/
+	IssmDouble     scalex=0,scaley=0,scale=0,S=0;
+	IssmDouble     vx,vy,vxobs,vyobs,weight;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     basis[3];
+	GaussTria* gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum);
+	this->parameters->FindParam(&responses,NULL,NULL,StepResponsesEnum);
+	Input* weights_input = inputs->GetInput(InversionCostFunctionsCoefficientsEnum);   _assert_(weights_input);
+	Input* vx_input      = inputs->GetInput(VxEnum);        _assert_(vx_input);
+	Input* vy_input      = inputs->GetInput(VyEnum);        _assert_(vy_input);
+	Input* vxobs_input   = inputs->GetInput(InversionVxObsEnum);     _assert_(vxobs_input);
+	Input* vyobs_input   = inputs->GetInput(InversionVyObsEnum);     _assert_(vyobs_input);
+
+	/*Get Surface if required by one response*/
+	for(resp=0;respGetInputValue(&S,SurfaceAreaEnum); break;
+		}
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(4);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vxobs_input->GetInputValue(&vxobs,gauss);
+		vyobs_input->GetInputValue(&vyobs,gauss);
+		GetNodalFunctions(basis, gauss);
+
+		/*Loop over all requested responses*/
+		for(resp=0;respGetInputValue(&weight,gauss,resp);
+
+			switch(responses[resp]){
+
+				case SurfaceAbsVelMisfitEnum:
+					/*
+					 *      1  [           2              2 ]
+					 * J = --- | (u - u   )  +  (v - v   )  |
+					 *      2  [       obs            obs   ]
+					 *
+					 *        dJ
+					 * DU = - -- = (u   - u )
+					 *        du     obs
+					 */
+					for (i=0;ivalues[i*NDOF4+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF4+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case SurfaceRelVelMisfitEnum:
+					/*
+					 *      1  [     \bar{v}^2             2   \bar{v}^2              2 ]
+					 * J = --- | -------------  (u - u   ) + -------------  (v - v   )  |
+					 *      2  [  (u   + eps)^2       obs    (v   + eps)^2       obs    ]
+					 *              obs                        obs                      
+					 *
+					 *        dJ     \bar{v}^2
+					 * DU = - -- = ------------- (u   - u )
+					 *        du   (u   + eps)^2    obs
+					 *               obs
+					 */
+					for (i=0;ivalues[i*NDOF4+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF4+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case SurfaceLogVelMisfitEnum:
+					/*
+					 *                 [        vel + eps     ] 2
+					 * J = 4 \bar{v}^2 | log ( -----------  ) |  
+					 *                 [       vel   + eps    ]
+					 *                            obs
+					 *
+					 *        dJ                 2 * log(...)
+					 * DU = - -- = - 4 \bar{v}^2 -------------  u
+					 *        du                 vel^2 + eps
+					 *            
+					 */
+					for (i=0;ivalues[i*NDOF4+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF4+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case SurfaceAverageVelMisfitEnum:
+					/*
+					 *      1                    2              2
+					 * J = ---  sqrt(  (u - u   )  +  (v - v   )  )
+					 *      S                obs            obs
+					 *
+					 *        dJ      1       1 
+					 * DU = - -- = - --- ----------- * 2 (u - u   )
+					 *        du      S  2 sqrt(...)           obs
+					 */
+					for (i=0;ivalues[i*NDOF4+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF4+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case SurfaceLogVxVyMisfitEnum:
+					/*
+					 *      1            [        |u| + eps     2          |v| + eps     2  ]
+					 * J = --- \bar{v}^2 | log ( -----------  )   +  log ( -----------  )   |  
+					 *      2            [       |u    |+ eps              |v    |+ eps     ]
+					 *                              obs                       obs
+					 *        dJ                              1      u                             1
+					 * DU = - -- = - \bar{v}^2 log(u...) --------- ----  ~ - \bar{v}^2 log(u...) ------
+					 *        du                         |u| + eps  |u|                           u + eps
+					 */
+					for (i=0;ivalues[i*NDOF4+0]+=dux*weight*Jdet*gauss->weight*basis[i]; 
+						pe->values[i*NDOF4+1]+=duy*weight*Jdet*gauss->weight*basis[i]; 
+					}
+					break;
+				case DragCoefficientAbsGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				case ThicknessAbsGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				case ThicknessAcrossGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				case ThicknessAlongGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				case RheologyBbarAbsGradientEnum:
+					/*Nothing in P vector*/
+					break;
+				default:
+					_error_("response " << EnumToStringx(responses[resp]) << " not supported yet");
+			}
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	xDelete(responses);
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::DragCoefficientAbsGradient{{{*/
+IssmDouble Tria::DragCoefficientAbsGradient(bool process_units,int weight_index){
+
+	/* Intermediaries */
+	int        ig;
+	IssmDouble     Jelem = 0;
+	IssmDouble     weight;
+	IssmDouble     Jdet;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     dp[NDOF2];
+	GaussTria *gauss = NULL;
+
+	/*retrieve parameters and inputs*/
+
+	/*If on water, return 0: */
+	if(IsOnWater()) return 0;
+
+	/*Retrieve all inputs we will be needing: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);         _assert_(weights_input);
+	Input* drag_input   =inputs->GetInput(FrictionCoefficientEnum); _assert_(drag_input);
+
+	/* Start looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		/* Get Jacobian determinant: */
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+
+		/*Get all parameters at gaussian point*/
+		weights_input->GetInputValue(&weight,gauss,weight_index);
+		drag_input->GetInputDerivativeValue(&dp[0],&xyz_list[0][0],gauss);
+
+		/*Tikhonov regularization: J = 1/2 ((dp/dx)^2 + (dp/dy)^2) */ 
+		Jelem+=weight*1/2*(dp[0]*dp[0]+dp[1]*dp[1])*Jdet*gauss->weight;
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Jelem;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixAdjointBalancethickness {{{*/
+ElementMatrix* Tria::CreateKMatrixAdjointBalancethickness(void){
+
+	ElementMatrix* Ke=NULL;
+
+	/*Get Element Matrix of the forward model*/
+	switch(GetElementType()){
+		case P1Enum:
+			Ke=CreateKMatrixBalancethickness_CG();
+			break;
+		case P1DGEnum:
+			Ke=CreateKMatrixBalancethickness_DG();
+			break;
+		default:
+			_error_("Element type " << EnumToStringx(GetElementType()) << " not supported yet");
+	}
+
+	/*Transpose and return Ke*/
+	Ke->Transpose();
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixAdjointMacAyeal{{{*/
+ElementMatrix* Tria::CreateKMatrixAdjointMacAyeal(void){
+
+	/*Constants*/
+	const int    numdof=NDOF2*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	bool       incomplete_adjoint;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     Jdet,thickness;
+	IssmDouble     eps1dotdphii,eps1dotdphij;
+	IssmDouble     eps2dotdphii,eps2dotdphij;
+	IssmDouble     mu_prime;
+	IssmDouble     epsilon[3];/* epsilon=[exx,eyy,exy];*/
+	IssmDouble     eps1[2],eps2[2];
+	IssmDouble     phi[NUMVERTICES];
+	IssmDouble     dphi[2][NUMVERTICES];
+	GaussTria *gauss=NULL;
+
+	/*Initialize Jacobian with regular MacAyeal (first part of the Gateau derivative)*/
+	parameters->FindParam(&incomplete_adjoint,InversionIncompleteAdjointEnum);
+	ElementMatrix* Ke=CreateKMatrixDiagnosticMacAyeal();
+	if(incomplete_adjoint) return Ke;
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
+	Input* thickness_input=inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdet, &xyz_list[0][0],gauss);
+		GetNodalFunctionsDerivatives(&dphi[0][0],&xyz_list[0][0],gauss);
+
+		thickness_input->GetInputValue(&thickness, gauss);
+		this->GetStrainRate2d(&epsilon[0],&xyz_list[0][0],gauss,vx_input,vy_input);
+		material->GetViscosity2dDerivativeEpsSquare(&mu_prime,&epsilon[0]);
+		eps1[0]=2*epsilon[0]+epsilon[1];   eps2[0]=epsilon[2];
+		eps1[1]=epsilon[2];                eps2[1]=epsilon[0]+2*epsilon[1];
+
+		for(i=0;i<3;i++){
+			for(j=0;j<3;j++){
+				eps1dotdphii=eps1[0]*dphi[0][i]+eps1[1]*dphi[1][i];
+				eps1dotdphij=eps1[0]*dphi[0][j]+eps1[1]*dphi[1][j];
+				eps2dotdphii=eps2[0]*dphi[0][i]+eps2[1]*dphi[1][i];
+				eps2dotdphij=eps2[0]*dphi[0][j]+eps2[1]*dphi[1][j];
+
+				Ke->values[6*(2*i+0)+2*j+0]+=gauss->weight*Jdet*2*mu_prime*thickness*eps1dotdphij*eps1dotdphii;
+				Ke->values[6*(2*i+0)+2*j+1]+=gauss->weight*Jdet*2*mu_prime*thickness*eps2dotdphij*eps1dotdphii;
+				Ke->values[6*(2*i+1)+2*j+0]+=gauss->weight*Jdet*2*mu_prime*thickness*eps1dotdphij*eps2dotdphii;
+				Ke->values[6*(2*i+1)+2*j+1]+=gauss->weight*Jdet*2*mu_prime*thickness*eps2dotdphij*eps2dotdphii;
+			}
+		}
+	}
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,nodes,NUMVERTICES,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	//Ke->Transpose();
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromSolutionAdjointHoriz {{{*/
+void  Tria::InputUpdateFromSolutionAdjointHoriz(IssmDouble* solution){
+
+	const int numdof=NDOF2*NUMVERTICES;
+
+	int       i;
+	int*      doflist=NULL;
+	IssmDouble    values[numdof];
+	IssmDouble    lambdax[NUMVERTICES];
+	IssmDouble    lambday[NUMVERTICES];
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(lambdax[i])) _error_("NaN found in solution vector");
+		if(xIsNan(lambday[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new TriaP1Input(AdjointxEnum,lambdax));
+	this->inputs->AddInput(new TriaP1Input(AdjointyEnum,lambday));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromSolutionAdjointBalancethickness {{{*/
+void  Tria::InputUpdateFromSolutionAdjointBalancethickness(IssmDouble* solution){
+
+	const int numdof=NDOF1*NUMVERTICES;
+
+	int       i;
+	int*      doflist=NULL;
+	IssmDouble    values[numdof];
+	IssmDouble    lambda[NUMVERTICES];
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(i=0;i(lambda[i])) _error_("NaN found in solution vector");
+	}
+
+	/*Add vx and vy as inputs to the tria element: */
+	this->inputs->AddInput(new TriaP1Input(AdjointEnum,lambda));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Tria::GetVectorFromControlInputs{{{*/
+void  Tria::GetVectorFromControlInputs(Vector* vector,int control_enum,int control_index,const char* data){
+
+	int doflist1[NUMVERTICES];
+	Input *input=NULL;
+
+	/*Get out if this is not an element input*/
+	if(!IsInput(control_enum)) return;
+
+	/*Prepare index list*/
+	GradientIndexing(&doflist1[0],control_index);
+
+	/*Get input (either in element or material)*/
+	if(control_enum==MaterialsRheologyBbarEnum || control_enum==MaterialsRheologyZbarEnum){
+		input=(Input*)material->inputs->GetInput(control_enum); _assert_(input);
+	}
+	else{
+		input=(Input*)this->inputs->GetInput(control_enum);   _assert_(input);
+	}
+
+	/*Check that it is a ControlInput*/
+	if (input->ObjectEnum()!=ControlInputEnum){
+		_error_("input " << EnumToStringx(control_enum) << " is not a ControlInput");
+	}
+
+	((ControlInput*)input)->GetVectorFromInputs(vector,&doflist1[0],data);
+}
+/*}}}*/
+/*FUNCTION Tria::SetControlInputsFromVector{{{*/
+void  Tria::SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index){
+
+	IssmDouble  values[NUMVERTICES];
+	int     doflist1[NUMVERTICES];
+	Input  *input     = NULL;
+	Input  *new_input = NULL;
+
+	/*Get out if this is not an element input*/
+	if(!IsInput(control_enum)) return;
+
+	/*Prepare index list*/
+	GradientIndexing(&doflist1[0],control_index);
+
+	/*Get values on vertices*/
+	for (int i=0;iinputs->GetInput(control_enum); _assert_(input);
+	}
+	else{
+		input=(Input*)this->inputs->GetInput(control_enum);   _assert_(input);
+	}
+
+	if (input->ObjectEnum()!=ControlInputEnum){
+		_error_("input " << EnumToStringx(control_enum) << " is not a ControlInput");
+	}
+
+	((ControlInput*)input)->SetInput(new_input);
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_HYDROLOGY_
+/*FUNCTION Tria::CreateHydrologyWaterVelocityInput {{{*/
+void Tria::CreateHydrologyWaterVelocityInput(void){
+
+	/*material parameters: */
+	IssmDouble mu_water;
+	IssmDouble VelocityFactor;  // This factor represents the number 12 in laminar flow velocity which can vary by differnt hydrology.CR
+	IssmDouble n_man,CR;
+	IssmDouble w;
+	IssmDouble rho_ice, rho_water, g;
+	IssmDouble dsdx,dsdy,dbdx,dbdy;
+	IssmDouble vx[NUMVERTICES];
+	IssmDouble vy[NUMVERTICES];
+	GaussTria *gauss = NULL;
+
+	/*Retrieve all inputs and parameters*/
+	rho_ice=matpar->GetRhoIce();
+	rho_water=matpar->GetRhoWater();
+	g=matpar->GetG();
+	CR=matpar->GetHydrologyCR(); // To have Lebrocq equavalent equation: CR=0.01,n_man=0.02
+	n_man=matpar->GetHydrologyN(); 
+	mu_water=matpar->GetMuWater();
+	Input* surfaceslopex_input=inputs->GetInput(SurfaceSlopeXEnum); _assert_(surfaceslopex_input);
+	Input* surfaceslopey_input=inputs->GetInput(SurfaceSlopeYEnum); _assert_(surfaceslopey_input);
+	Input* bedslopex_input=inputs->GetInput(BedSlopeXEnum);         _assert_(bedslopex_input);
+	Input* bedslopey_input=inputs->GetInput(BedSlopeYEnum);         _assert_(bedslopey_input);
+	Input* watercolumn_input=inputs->GetInput(WatercolumnEnum);     _assert_(watercolumn_input);
+
+	/* compute VelocityFactor */
+	VelocityFactor= n_man*CR*CR*rho_water*g/mu_water;
+	
+	gauss=new GaussTria();
+	for (int iv=0;ivGaussVertex(iv);
+		surfaceslopex_input->GetInputValue(&dsdx,gauss);
+		surfaceslopey_input->GetInputValue(&dsdy,gauss);
+		bedslopex_input->GetInputValue(&dbdx,gauss);
+		bedslopey_input->GetInputValue(&dbdy,gauss);
+		watercolumn_input->GetInputValue(&w,gauss);
+
+		/* Water velocity x and y components */
+	//	vx[iv]= - w*w/(12 * mu_water)*(rho_ice*g*dsdx+(rho_water-rho_ice)*g*dbdx);
+	//	vy[iv]= - w*w/(12 * mu_water)*(rho_ice*g*dsdy+(rho_water-rho_ice)*g*dbdy);
+		vx[iv]= - w*w/(VelocityFactor* mu_water)*(rho_ice*g*dsdx+(rho_water-rho_ice)*g*dbdx);
+		vy[iv]= - w*w/(VelocityFactor* mu_water)*(rho_ice*g*dsdy+(rho_water-rho_ice)*g*dbdy);
+	}
+
+	/*clean-up*/
+	delete gauss;
+
+	/*Add to inputs*/
+	this->inputs->AddInput(new TriaP1Input(HydrologyWaterVxEnum,vx));
+	this->inputs->AddInput(new TriaP1Input(HydrologyWaterVyEnum,vy));
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixHydrology{{{*/
+ElementMatrix* Tria::CreateKMatrixHydrology(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	IssmDouble     diffusivity;
+	int        i,j,ig;
+	IssmDouble     Jdettria,DL_scalar,dt,h;
+	IssmDouble     vx,vy,vel,dvxdx,dvydy;
+	IssmDouble     dvx[2],dvy[2];
+	IssmDouble     v_gauss[2]={0.0};
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     L[NUMVERTICES];
+	IssmDouble     B[2][NUMVERTICES];
+	IssmDouble     Bprime[2][NUMVERTICES];
+	IssmDouble     K[2][2]                        ={0.0};
+	IssmDouble     KDL[2][2]                      ={0.0};
+	IssmDouble     DL[2][2]                        ={0.0};
+	IssmDouble     DLprime[2][2]                   ={0.0};
+	GaussTria *gauss=NULL;
+
+	/*Skip if water or ice shelf element*/
+	if(IsOnWater() | IsFloating()) return NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Create water velocity vx and vy from current inputs*/
+	CreateHydrologyWaterVelocityInput();
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	this->parameters->FindParam(&diffusivity,HydrologyStabilizationEnum);
+	Input* vx_input=inputs->GetInput(HydrologyWaterVxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(HydrologyWaterVyEnum); _assert_(vy_input);
+	h=sqrt(2*this->GetArea());
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		GetL(&L[0], &xyz_list[0][0], gauss,NDOF1);
+
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+		vx_input->GetInputDerivativeValue(&dvx[0],&xyz_list[0][0],gauss);
+		vy_input->GetInputDerivativeValue(&dvy[0],&xyz_list[0][0],gauss);
+
+		DL_scalar=gauss->weight*Jdettria;
+
+		TripleMultiply( &L[0],1,numdof,1,
+					&DL_scalar,1,1,0,
+					&L[0],1,numdof,0,
+					&Ke->values[0],1);
+
+		GetBPrognostic(&B[0][0], &xyz_list[0][0], gauss);
+		GetBprimePrognostic(&Bprime[0][0], &xyz_list[0][0], gauss);
+
+		dvxdx=dvx[0];
+		dvydy=dvy[1];
+		DL_scalar=dt*gauss->weight*Jdettria;
+
+		DL[0][0]=DL_scalar*dvxdx;
+		DL[1][1]=DL_scalar*dvydy;
+		DLprime[0][0]=DL_scalar*vx;
+		DLprime[1][1]=DL_scalar*vy;
+
+		TripleMultiply( &B[0][0],2,numdof,1,
+					&DL[0][0],2,2,0,
+					&B[0][0],2,numdof,0,
+					&Ke->values[0],1);
+
+		TripleMultiply( &B[0][0],2,numdof,1,
+					&DLprime[0][0],2,2,0,
+					&Bprime[0][0],2,numdof,0,
+					&Ke->values[0],1);
+
+		/*Artificial diffusivity*/
+		vel=sqrt(vx*vx+vy*vy);
+		K[0][0]=diffusivity*h/(2*vel)*vx*vx;
+		K[1][0]=diffusivity*h/(2*vel)*vy*vx;
+		K[0][1]=diffusivity*h/(2*vel)*vx*vy;
+		K[1][1]=diffusivity*h/(2*vel)*vy*vy;
+		KDL[0][0]=DL_scalar*K[0][0];
+		KDL[1][0]=DL_scalar*K[1][0];
+		KDL[0][1]=DL_scalar*K[0][1];
+		KDL[1][1]=DL_scalar*K[1][1];
+
+		TripleMultiply( &Bprime[0][0],2,numdof,1,
+					&KDL[0][0],2,2,0,
+					&Bprime[0][0],2,numdof,0,
+					&Ke->values[0],1);
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorHydrology {{{*/
+ElementVector* Tria::CreatePVectorHydrology(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     Jdettria,dt;
+	IssmDouble     basal_melting_g;
+	IssmDouble     old_watercolumn_g;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     basis[numdof];
+	GaussTria* gauss=NULL;
+
+	/*Skip if water or ice shelf element*/
+	if(IsOnWater() | IsFloating()) return NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	Input* basal_melting_input=inputs->GetInput(BasalforcingsMeltingRateEnum); _assert_(basal_melting_input);
+	Input* old_watercolumn_input=inputs->GetInput(WaterColumnOldEnum);         _assert_(old_watercolumn_input);
+
+	/*Initialize basal_melting_correction_g to 0, do not forget!:*/
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		GetNodalFunctions(basis, gauss);
+
+		basal_melting_input->GetInputValue(&basal_melting_g,gauss);
+		old_watercolumn_input->GetInputValue(&old_watercolumn_g,gauss);
+
+		if(reCast(dt))for(i=0;ivalues[i]+=Jdettria*gauss->weight*(old_watercolumn_g+dt*basal_melting_g)*basis[i];
+		else  for(i=0;ivalues[i]+=Jdettria*gauss->weight*basal_melting_g*basis[i];
+	}
+		
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::GetSolutionFromInputsHydrology{{{*/
+void  Tria::GetSolutionFromInputsHydrology(Vector* solution){
+
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	int i;
+	int*         doflist=NULL;
+	IssmDouble       watercolumn;
+	IssmDouble       values[numdof];
+	GaussTria*   gauss=NULL;
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Get inputs*/
+	Input* watercolumn_input=inputs->GetInput(WatercolumnEnum); _assert_(watercolumn_input);
+
+	/*Ok, we have watercolumn values, fill in watercolumn array: */
+	/*P1 element only for now*/
+	gauss=new GaussTria();
+	for(i=0;iGaussVertex(i);
+
+		/*Recover watercolumn*/
+		watercolumn_input->GetInputValue(&watercolumn,gauss);
+		values[i]=watercolumn;
+	}
+
+	solution->SetValues(numdof,doflist,values,INS_VAL);
+
+	/*Free ressources:*/
+	delete gauss;
+	xDelete(doflist);
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromSolutionHydrology{{{*/
+void  Tria::InputUpdateFromSolutionHydrology(IssmDouble* solution){
+
+	/*Intermediaries*/
+	const int   numdof         = NDOF1 *NUMVERTICES;
+	int        *doflist        = NULL;
+	IssmDouble  values[numdof];
+
+	/*Get dof list: */
+	GetDofList(&doflist,NoneApproximationEnum,GsetEnum);
+
+	/*Use the dof list to index into the solution vector: */
+	for(int i=0;i(values[i])) _error_("NaN found in solution vector");
+		if (values[i]<10e-10) values[i]=10e-10; //correcting the water column to positive values
+	}
+
+	/*Add input to the element: */
+	this->inputs->AddInput(new TriaP1Input(WatercolumnEnum,values));
+
+	/*Free ressources:*/
+	xDelete(doflist);
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_DAKOTA_
+/*FUNCTION Tria::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type);{{{*/
+void  Tria::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){
+	
+	int i,j;
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	switch(type){
+
+		case VertexEnum:
+
+			/*New TriaP1Input*/
+			IssmDouble values[3];
+
+			/*Get values on the 3 vertices*/
+			for (i=0;i<3;i++){
+				values[i]=vector[this->nodes[i]->GetSidList()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!)
+			}
+
+			/*Branch on the specified type of update: */
+			switch(name){
+				case ThicknessEnum:
+					IssmDouble  thickness[3];
+					IssmDouble  thickness_init[3];
+					IssmDouble  hydrostatic_ratio[3];
+					IssmDouble  surface[3];
+					IssmDouble  bed[3];
+					
+					/*retrieve inputs: */
+					GetInputListOnVertices(&thickness_init[0],ThicknessEnum);
+					GetInputListOnVertices(&hydrostatic_ratio[0],GeometryHydrostaticRatioEnum);
+					GetInputListOnVertices(&bed[0],BedEnum);
+					GetInputListOnVertices(&surface[0],SurfaceEnum);
+
+					/*build new bed and surface: */
+					if (this->IsFloating()){
+						/*hydrostatic equilibrium: */
+						IssmDouble rho_ice,rho_water,di;
+						rho_ice   = this->matpar->GetRhoIce();
+						rho_water = this->matpar->GetRhoWater();
+						di        = rho_ice/rho_water;
+
+						/*build new thickness: */
+						for (j=0; j<3; j++) {
+							/*  for observed/interpolated/hydrostatic thickness, remove scaling from any hydrostatic thickness  */
+							if (hydrostatic_ratio[j] >= 0.)
+								thickness[j]=values[j]-(values[j]/thickness_init[j]-1.)*hydrostatic_ratio[j]*surface[j]/(1.-di);
+							/*  for minimum thickness, don't scale  */
+							else
+								thickness[j]=thickness_init[j];
+
+							/*  check the computed thickness and update bed*/
+							if (thickness[j] < 0.) thickness[j]=1./(1.-di);
+							bed[j]=surface[j]-thickness[j];
+						}
+					}
+					else{
+						/*build new thickness: */
+						for (j=0; j<3; j++) {
+							/*  for observed thickness, use scaled value  */
+							if (hydrostatic_ratio[j] >= 0.)
+								thickness[j]=values[j];
+							/*  for minimum thickness, don't scale  */
+							else
+								thickness[j]=thickness_init[j];
+						}
+
+						/*update bed on grounded ice: */
+						for(j=0;j<3;j++)bed[j]=surface[j]-thickness[j];
+					}
+
+					/*Add new inputs: */
+					this->inputs->AddInput(new TriaP1Input(ThicknessEnum,thickness));
+					this->inputs->AddInput(new TriaP1Input(BedEnum,bed));
+					this->inputs->AddInput(new TriaP1Input(SurfaceEnum,surface));
+
+					break;
+				default:
+					this->inputs->AddInput(new TriaP1Input(name,values));
+			}
+			break;
+
+		default:
+			_error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromVectorDakota(int* vector, int name, int type);{{{*/
+void  Tria::InputUpdateFromVectorDakota(int* vector, int name, int type){
+	_error_("not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromVectorDakota(bool* vector, int name, int type);{{{*/
+void  Tria::InputUpdateFromVectorDakota(bool* vector, int name, int type){
+	_error_("not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Tria::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type);{{{*/
+void  Tria::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type){
+	
+	int i,j,t;
+	TransientInput* transientinput=NULL;
+	IssmDouble values[3];
+	IssmDouble time;
+	int row;
+	IssmDouble yts;
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	switch(type){
+
+		case VertexEnum:
+			
+			/*Create transient input: */
+						
+			parameters->FindParam(&yts,ConstantsYtsEnum);
+			for(t=0;tnodes[i]->GetSidList();
+					values[i]=(IssmDouble)matrix[ncols*row+t];
+				}
+
+				/*time? :*/
+				time=(IssmDouble)matrix[(nrows-1)*ncols+t]*yts;
+
+				if(t==0) transientinput=new TransientInput(name);
+				transientinput->AddTimeInput(new TriaP1Input(name,values),time);
+				transientinput->Configure(parameters);
+			}
+			this->inputs->AddInput(transientinput);
+			break;
+
+		default:
+			_error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_BALANCED_
+/*FUNCTION Tria::CreateKMatrixBalancethickness {{{*/
+ElementMatrix* Tria::CreateKMatrixBalancethickness(void){
+
+	switch(GetElementType()){
+		case P1Enum:
+			return CreateKMatrixBalancethickness_CG();
+		case P1DGEnum:
+			return CreateKMatrixBalancethickness_DG();
+		default:
+			_error_("Element type " << EnumToStringx(GetElementType()) << " not supported yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixBalancethickness_CG {{{*/
+ElementMatrix* Tria::CreateKMatrixBalancethickness_CG(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        stabilization;
+	int        i,j,ig,dim;
+	IssmDouble     Jdettria,vx,vy,dvxdx,dvydy,vel,h;
+	IssmDouble     dvx[2],dvy[2];
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     L[NUMVERTICES];
+	IssmDouble     B[2][NUMVERTICES];
+	IssmDouble     Bprime[2][NUMVERTICES];
+	IssmDouble     K[2][2]                          = {0.0};
+	IssmDouble     KDL[2][2]                        = {0.0};
+	IssmDouble     DL[2][2]                         = {0.0};
+	IssmDouble     DLprime[2][2]                    = {0.0};
+	IssmDouble     DL_scalar;
+	GaussTria *gauss                            = NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all Inputs and parameters: */
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&stabilization,BalancethicknessStabilizationEnum);
+	this->parameters->FindParam(&dim,MeshDimensionEnum);
+	Input* vxaverage_input=NULL;
+	Input* vyaverage_input=NULL;
+	if(dim==2){
+		vxaverage_input=inputs->GetInput(VxEnum); _assert_(vxaverage_input);
+		vyaverage_input=inputs->GetInput(VyEnum); _assert_(vyaverage_input);
+	}
+	else{
+		vxaverage_input=inputs->GetInput(VxAverageEnum); _assert_(vxaverage_input);
+		vyaverage_input=inputs->GetInput(VyAverageEnum); _assert_(vyaverage_input);
+	}
+	h=sqrt(2*this->GetArea());
+
+	/*Start looping on the number of gaussian points:*/
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		GetBPrognostic(&B[0][0], &xyz_list[0][0], gauss);
+		GetBprimePrognostic(&Bprime[0][0], &xyz_list[0][0], gauss);
+
+		vxaverage_input->GetInputValue(&vx,gauss);
+		vyaverage_input->GetInputValue(&vy,gauss);
+		vxaverage_input->GetInputDerivativeValue(&dvx[0],&xyz_list[0][0],gauss);
+		vyaverage_input->GetInputDerivativeValue(&dvy[0],&xyz_list[0][0],gauss);
+
+		dvxdx=dvx[0];
+		dvydy=dvy[1];
+		DL_scalar=gauss->weight*Jdettria;
+
+		DL[0][0]=DL_scalar*dvxdx;
+		DL[1][1]=DL_scalar*dvydy;
+
+		DLprime[0][0]=DL_scalar*vx;
+		DLprime[1][1]=DL_scalar*vy;
+
+		TripleMultiply( &B[0][0],2,numdof,1,
+					&DL[0][0],2,2,0,
+					&B[0][0],2,numdof,0,
+					&Ke->values[0],1);
+
+		TripleMultiply( &B[0][0],2,numdof,1,
+					&DLprime[0][0],2,2,0,
+					&Bprime[0][0],2,numdof,0,
+					&Ke->values[0],1);
+
+		if(stabilization==1){
+			/*Streamline upwinding*/
+			vel=sqrt(vx*vx+vy*vy);
+			K[0][0]=h/(2*vel)*vx*vx;
+			K[1][0]=h/(2*vel)*vy*vx;
+			K[0][1]=h/(2*vel)*vx*vy;
+			K[1][1]=h/(2*vel)*vy*vy;
+		}
+		else if(stabilization==2){
+			/*MacAyeal*/
+			vxaverage_input->GetInputAverage(&vx);
+			vyaverage_input->GetInputAverage(&vy);
+			K[0][0]=h/2.0*fabs(vx);
+			K[0][1]=0.;
+			K[1][0]=0.;
+			K[1][1]=h/2.0*fabs(vy);
+		}
+		if(stabilization==1 || stabilization==2){
+			KDL[0][0]=DL_scalar*K[0][0];
+			KDL[1][0]=DL_scalar*K[1][0];
+			KDL[0][1]=DL_scalar*K[0][1];
+			KDL[1][1]=DL_scalar*K[1][1];
+			TripleMultiply( &Bprime[0][0],2,numdof,1,
+						&KDL[0][0],2,2,0,
+						&Bprime[0][0],2,numdof,0,
+						&Ke->values[0],1);
+		}
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreateKMatrixBalancethickness_DG {{{*/
+ElementMatrix* Tria::CreateKMatrixBalancethickness_DG(void){
+
+	/*Constants*/
+	const int  numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries*/
+	int        i,j,ig,dim;
+	IssmDouble     vx,vy,Jdettria;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     B[2][NUMVERTICES];
+	IssmDouble     Bprime[2][NUMVERTICES];
+	IssmDouble     DL[2][2]={0.0};
+	IssmDouble     DL_scalar;
+	GaussTria  *gauss=NULL;
+
+	/*Initialize Element matrix*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters,NoneApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	this->parameters->FindParam(&dim,MeshDimensionEnum);
+	Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
+	Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
+
+	/*Start looping on the number of gaussian points:*/
+	gauss=new GaussTria(2);
+	for (ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		/*WARNING: B and Bprime are inverted compared to usual prognostic!!!!*/
+		GetBPrognostic(&Bprime[0][0], &xyz_list[0][0], gauss);
+		GetBprimePrognostic(&B[0][0], &xyz_list[0][0], gauss);
+
+		vx_input->GetInputValue(&vx,gauss);
+		vy_input->GetInputValue(&vy,gauss);
+
+		DL_scalar=-gauss->weight*Jdettria;
+		DL[0][0]=DL_scalar*vx;
+		DL[1][1]=DL_scalar*vy;
+
+		TripleMultiply( &B[0][0],2,numdof,1,
+					&DL[0][0],2,2,0,
+					&Bprime[0][0],2,numdof,0,
+					&Ke->values[0],1);
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorBalancethickness{{{*/
+ElementVector* Tria::CreatePVectorBalancethickness(void){
+
+	switch(GetElementType()){
+		case P1Enum:
+			return CreatePVectorBalancethickness_CG();
+			break;
+		case P1DGEnum:
+			return CreatePVectorBalancethickness_DG();
+		default:
+			_error_("Element type " << EnumToStringx(GetElementType()) << " not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorBalancethickness_CG{{{*/
+ElementVector* Tria::CreatePVectorBalancethickness_CG(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+	
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     dhdt_g,basal_melting_g,surface_mass_balance_g,Jdettria;
+	IssmDouble     L[NUMVERTICES];
+	GaussTria* gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* surface_mass_balance_input=inputs->GetInput(SurfaceforcingsMassBalanceEnum); _assert_(surface_mass_balance_input);
+	Input* basal_melting_input=inputs->GetInput(BasalforcingsMeltingRateEnum);          _assert_(basal_melting_input);
+	Input* dhdt_input=inputs->GetInput(BalancethicknessThickeningRateEnum);             _assert_(dhdt_input);
+	
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		surface_mass_balance_input->GetInputValue(&surface_mass_balance_g,gauss);
+		basal_melting_input->GetInputValue(&basal_melting_g,gauss);
+		dhdt_input->GetInputValue(&dhdt_g,gauss);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		GetL(&L[0], &xyz_list[0][0], gauss,NDOF1);
+
+		for(i=0;ivalues[i]+=Jdettria*gauss->weight*(surface_mass_balance_g-basal_melting_g-dhdt_g)*L[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Tria::CreatePVectorBalancethickness_DG {{{*/
+ElementVector* Tria::CreatePVectorBalancethickness_DG(void){
+
+	/*Constants*/
+	const int    numdof=NDOF1*NUMVERTICES;
+
+	/*Intermediaries */
+	int        i,j,ig;
+	IssmDouble     xyz_list[NUMVERTICES][3];
+	IssmDouble     basal_melting_g,surface_mass_balance_g,dhdt_g,Jdettria;
+	IssmDouble     L[NUMVERTICES];
+	GaussTria* gauss=NULL;
+
+	/*Initialize Element vector*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
+	Input* surface_mass_balance_input=inputs->GetInput(SurfaceforcingsMassBalanceEnum); _assert_(surface_mass_balance_input);
+	Input* basal_melting_input=inputs->GetInput(BasalforcingsMeltingRateEnum);          _assert_(basal_melting_input);
+	Input* dhdt_input=inputs->GetInput(BalancethicknessThickeningRateEnum);                                       _assert_(dhdt_input);
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		surface_mass_balance_input->GetInputValue(&surface_mass_balance_g,gauss);
+		basal_melting_input->GetInputValue(&basal_melting_g,gauss);
+		dhdt_input->GetInputValue(&dhdt_g,gauss);
+
+		GetJacobianDeterminant2d(&Jdettria, &xyz_list[0][0],gauss);
+		GetL(&L[0], &xyz_list[0][0], gauss,NDOF1);
+
+		for(i=0;ivalues[i]+=Jdettria*gauss->weight*(surface_mass_balance_g-basal_melting_g-dhdt_g)*L[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+#endif
Index: /issm/trunk/src/c/classes/objects/Elements/Tria.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/Tria.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/Tria.h	(revision 13395)
@@ -0,0 +1,243 @@
+/*! \file Tria.h 
+ *  \brief: header file for tria object
+ */
+
+#ifndef _TRIA_H_
+#define _TRIA_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Element.h"
+#include "./TriaHook.h"
+#include "./TriaRef.h"
+class Parameters;
+class Inputs;
+class IoModel;
+class Node;
+class Material;
+class Matpar;
+class ElementMatrix;
+class ElementVector;
+
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+/*}}}*/
+
+class Tria: public Element,public TriaHook,public TriaRef{
+
+	public:
+
+		int  id;
+		int  sid;
+
+		Node   **nodes;    // 3 nodes
+		Material  *material;   // 1 material ice
+		Matpar  *matpar;   // 1 material parameter
+		int      horizontalneighborsids[3];
+
+		Parameters *parameters;   //pointer to solution parameters
+		Inputs     *inputs;
+		Results    *results;
+
+		/*Tria constructors, destructors {{{*/
+		Tria();
+		Tria(int tria_id,int tria_sid,int i, IoModel* iomodel,int nummodels);
+		~Tria();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Update virtual functions resolution: {{{*/
+		void  InputUpdateFromSolution(IssmDouble* solutiong);
+		void  InputUpdateFromVector(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVector(int* vector, int name, int type);
+		void  InputUpdateFromVector(bool* vector, int name, int type);
+		#ifdef _HAVE_DAKOTA_
+		void  InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(int* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(bool* vector, int name, int type);
+		void  InputUpdateFromMatrixDakota(IssmDouble* matrix, int nows, int ncols, int name, int type);
+		#endif
+		void  InputUpdateFromConstant(IssmDouble constant, int name);
+		void  InputUpdateFromConstant(int constant, int name);
+		void  InputUpdateFromConstant(bool constant, int name);
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel);
+		/*}}}*/
+		/*Element virtual functions definitions: {{{*/
+		void   AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,IssmDouble* vertex_response,IssmDouble* qmu_part);
+		void   ComputeBasalStress(Vector* sigma_b);
+		void   ComputeStrainRate(Vector* eps);
+		void   ComputeStressTensor();
+		void   Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters);
+		void   SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters);
+		void   CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df);
+		void   CreatePVector(Vector* pf);
+		void   CreateJacobianMatrix(Matrix* Jff);
+		void   Delta18oParameterization(void);
+		int    GetNodeIndex(Node* node);
+		int    Sid();
+		bool   IsOnBed();
+		bool   IsFloating(); 
+		bool   IsNodeOnShelf(); 
+		bool   IsNodeOnShelfFromFlags(IssmDouble* flags);
+		bool   IsOnWater(); 
+		void   GetSolutionFromInputs(Vector* solution);
+		void   GetVectorFromInputs(Vector* vector, int name_enum);
+		void   GetVectorFromResults(Vector* vector,int offset,int enum_in,int interp);
+		void   InputArtificialNoise(int enum_type,IssmDouble min, IssmDouble max);
+		bool   InputConvergence(IssmDouble* eps, int* enums,int num_enums,int* criterionenums,IssmDouble* criterionvalues,int num_criterionenums);
+		void   InputCreate(IssmDouble scalar,int name,int code);
+		void   InputCreate(IssmDouble* vector, int index,IoModel* iomodel,int M,int N,int vector_type,int vector_enum,int code);
+		void   InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum=MeshElementsEnum);
+		void   InputDuplicate(int original_enum,int new_enum);
+		void   InputScale(int enum_type,IssmDouble scale_factor);
+		void   InputToResult(int enum_type,int step,IssmDouble time);
+		void   DeleteResults(void);
+		void   MaterialUpdateFromTemperature(void){_error_("not implemented yet");};
+		void   MigrateGroundingLine(IssmDouble* oldfloating,IssmDouble* sheet_ungrounding);
+		int    NodalValue(IssmDouble* pvalue, int index, int natureofdataenum,bool process_units);
+		void   PotentialSheetUngrounding(Vector* potential_sheet_ungrounding);
+		void   PositiveDegreeDay(IssmDouble* pdds,IssmDouble* pds,IssmDouble signorm);
+		void   RequestedOutput(int output_enum,int step,IssmDouble time);
+		void   ListResultsInfo(int** results_enums,int** results_size,IssmDouble** results_times,int** results_steps,int* num_results);
+		void   PatchFill(int* pcount, Patch* patch);
+		void   PatchSize(int* pnumrows, int* pnumvertices,int* pnumnodes);
+		void   ProcessResultsUnits(void);
+		void   ResetCoordinateSystem(void){_error_("not implemented yet");};
+		void	 SmbGradients();
+		IssmDouble SurfaceArea(void);
+		void   Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type);
+		int    UpdatePotentialSheetUngrounding(IssmDouble* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,IssmDouble* nodes_on_iceshelf);
+		IssmDouble TimeAdapt();
+		int*   GetHorizontalNeighboorSids(void);
+		void   SmearFunction(Vector* smearedvector,IssmDouble (*WeightFunction)(IssmDouble distance,IssmDouble radius),IssmDouble radius);
+
+		#ifdef _HAVE_RESPONSES_
+		IssmDouble IceVolume(void);
+		IssmDouble TotalSmb(void);
+		void   MinVel(IssmDouble* pminvel, bool process_units);
+		void   MinVx(IssmDouble* pminvx, bool process_units);
+		void   MinVy(IssmDouble* pminvy, bool process_units);
+		void   MinVz(IssmDouble* pminvz, bool process_units);
+		IssmDouble MassFlux(IssmDouble* segment,bool process_units);
+		void   MaxAbsVx(IssmDouble* pmaxabsvx, bool process_units);
+		void   MaxAbsVy(IssmDouble* pmaxabsvy, bool process_units);
+		void   MaxAbsVz(IssmDouble* pmaxabsvz, bool process_units);
+		void   ElementResponse(IssmDouble* presponse,int response_enum,bool process_units);
+		void   MaxVel(IssmDouble* pmaxvel, bool process_units);
+		void   MaxVx(IssmDouble* pmaxvx, bool process_units);
+		void   MaxVy(IssmDouble* pmaxvy, bool process_units);
+		void   MaxVz(IssmDouble* pmaxvz, bool process_units);
+		#endif
+
+
+		#ifdef _HAVE_CONTROL_
+		IssmDouble DragCoefficientAbsGradient(bool process_units,int weight_index);
+		void   GradientIndexing(int* indexing,int control_index);
+		void   Gradj(Vector* gradient,int control_type,int control_index);
+		void   GradjBGradient(Vector* gradient,int weight_index,int control_index);
+		void   GradjZGradient(Vector* gradient,int weight_index,int control_index);
+		void   GradjBMacAyeal(Vector* gradient,int control_index);
+		void   GradjZMacAyeal(Vector* gradient,int control_index);
+		void   GradjDragMacAyeal(Vector* gradient,int control_index);
+		void   GradjDragStokes(Vector* gradient,int control_index);
+		void   GradjDragGradient(Vector* gradient,int weight_index,int control_index);
+		void   GradjDhDtBalancedthickness(Vector* gradient,int control_index);
+		void   GradjVxBalancedthickness(Vector* gradient,int control_index);
+		void   GradjVyBalancedthickness(Vector* gradient,int control_index);
+		void   GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data);
+		void   SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index);
+		void   ControlInputGetGradient(Vector* gradient,int enum_type,int control_index);
+		void   ControlInputScaleGradient(int enum_type,IssmDouble scale);
+		void   ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index);
+		IssmDouble RheologyBbarAbsGradient(bool process_units,int weight_index);
+		IssmDouble ThicknessAbsMisfit(     bool process_units,int weight_index);
+		IssmDouble SurfaceAbsVelMisfit(    bool process_units,int weight_index);
+		IssmDouble ThicknessAbsGradient(   bool process_units,int weight_index);
+		IssmDouble ThicknessAlongGradient( bool process_units,int weight_index);
+		IssmDouble ThicknessAcrossGradient(bool process_units,int weight_index);
+		IssmDouble SurfaceRelVelMisfit(    bool process_units,int weight_index);
+		IssmDouble SurfaceLogVelMisfit(    bool process_units,int weight_index);
+		IssmDouble SurfaceLogVxVyMisfit(   bool process_units,int weight_index);
+		IssmDouble SurfaceAverageVelMisfit(bool process_units,int weight_index);
+		void   InputControlUpdate(IssmDouble scalar,bool save_parameter);
+		#endif
+
+		/*}}}*/
+		/*Tria specific routines:{{{*/
+		ElementMatrix* CreateKMatrixBalancethickness(void);
+		ElementMatrix* CreateKMatrixBalancethickness_DG(void);
+		ElementMatrix* CreateKMatrixBalancethickness_CG(void);
+		ElementMatrix* CreateKMatrixMelting(void);
+		ElementMatrix* CreateKMatrixPrognostic(void);
+		ElementMatrix* CreateKMatrixPrognostic_CG(void);
+		ElementMatrix* CreateKMatrixPrognostic_DG(void);
+		ElementMatrix* CreateMassMatrix(void);
+		ElementVector* CreatePVectorBalancethickness(void);
+		ElementVector* CreatePVectorBalancethickness_DG(void);
+		ElementVector* CreatePVectorBalancethickness_CG(void);
+		ElementVector* CreatePVectorPrognostic(void);
+		ElementVector* CreatePVectorPrognostic_CG(void);
+		ElementVector* CreatePVectorPrognostic_DG(void);
+		ElementVector* CreatePVectorSlope(void);
+		IssmDouble         GetArea(void);
+		int            GetElementType(void);
+		void	         GetDofList(int** pdoflist,int approximation_enum,int setenum);
+		void	         GetDofList1(int* doflist);
+		void           GetSidList(int* sidlist);
+		void           GetConnectivityList(int* connectivity);
+		void           GetInputListOnVertices(IssmDouble* pvalue,int enumtype);
+		void           GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue);
+		void           GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue,int index); //TO BE REMOVED
+		void           GetInputValue(IssmDouble* pvalue,Node* node,int enumtype);
+		void           GetStrainRate2d(IssmDouble* epsilon,IssmDouble* xyz_list, GaussTria* gauss, Input* vx_input, Input* vy_input);
+		void	         InputUpdateFromSolutionOneDof(IssmDouble* solution,int enum_type);
+		void	         InputUpdateFromSolutionPrognostic(IssmDouble* solution);
+		bool	         IsInput(int name);
+		void	         SetClone(int* minranks);
+		void	         SurfaceNormal(IssmDouble* surface_normal, IssmDouble xyz_list[3][3]);
+		
+		#ifdef _HAVE_DIAGNOSTIC_
+		ElementMatrix* CreateKMatrixDiagnosticMacAyeal(void);
+		ElementMatrix* CreateKMatrixDiagnosticMacAyealViscous(void);
+		ElementMatrix* CreateKMatrixDiagnosticMacAyealFriction(void);
+		ElementMatrix* CreateKMatrixDiagnosticHutter(void);
+		ElementVector* CreatePVectorDiagnosticMacAyeal(void);
+		ElementVector* CreatePVectorDiagnosticHutter(void);
+		ElementMatrix* CreateJacobianDiagnosticMacayeal(void);
+		void	  GetSolutionFromInputsDiagnosticHoriz(Vector* solution);
+		void	  GetSolutionFromInputsDiagnosticHutter(Vector* solution);
+		void	  InputUpdateFromSolutionDiagnosticHoriz( IssmDouble* solution);
+		void	  InputUpdateFromSolutionDiagnosticHutter( IssmDouble* solution);
+		#endif
+
+		#ifdef _HAVE_CONTROL_
+		ElementMatrix* CreateKMatrixAdjointBalancethickness(void);
+		ElementMatrix* CreateKMatrixAdjointMacAyeal(void);
+		ElementVector* CreatePVectorAdjointHoriz(void);
+		ElementVector* CreatePVectorAdjointStokes(void);
+		ElementVector* CreatePVectorAdjointBalancethickness(void);
+		void	  InputUpdateFromSolutionAdjointBalancethickness( IssmDouble* solution);
+		void	  InputUpdateFromSolutionAdjointHoriz( IssmDouble* solution);
+		#endif
+
+		#ifdef _HAVE_HYDROLOGY_
+		ElementMatrix* CreateKMatrixHydrology(void);
+		ElementVector* CreatePVectorHydrology(void);
+		void      CreateHydrologyWaterVelocityInput(void);
+		void	  GetSolutionFromInputsHydrology(Vector* solution);
+		void	  InputUpdateFromSolutionHydrology(IssmDouble* solution);
+		#endif
+		#ifdef _HAVE_BALANCED_
+		#endif
+
+		/*}}}*/
+
+};
+#endif  /* _TRIA_H */
Index: /issm/trunk/src/c/classes/objects/Elements/TriaHook.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/TriaHook.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/TriaHook.cpp	(revision 13395)
@@ -0,0 +1,72 @@
+/*!\file TriaHook.c
+ * \brief: implementation of the TriaHook object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Object constructors and destructor*/
+/*FUNCTION TriaHook::TriaHook(){{{*/
+TriaHook::TriaHook(){
+	numanalyses=UNDEF;
+	this->hnodes=NULL;
+	this->hmaterial=NULL;
+	this->hmatpar=NULL;
+}
+/*}}}*/
+/*FUNCTION TriaHook::~TriaHook(){{{*/
+TriaHook::~TriaHook(){
+	int i;
+
+	for(i=0;inumanalyses;i++){
+		if (this->hnodes[i]) delete this->hnodes[i];
+	}
+	delete [] this->hnodes;
+	delete hmaterial;
+	delete hmatpar;
+
+}
+/*}}}*/
+/*FUNCTION TriaHook::TriaHook(int in_numanalyses,int material_id, int matpar_id){{{*/
+TriaHook::TriaHook(int in_numanalyses,int material_id, IoModel* iomodel){
+
+	/*intermediary: */
+	int matpar_id;
+
+	/*retrieve parameters: */
+	iomodel->Constant(&matpar_id,MeshNumberofelementsEnum); matpar_id++;
+	
+	this->numanalyses=in_numanalyses;
+	this->hnodes= new Hook*[in_numanalyses];
+	this->hmaterial=new Hook(&material_id,1);
+	this->hmatpar=new Hook(&matpar_id,1);
+
+	//Initialize hnodes as NULL
+	for(int i=0;inumanalyses;i++){
+		this->hnodes[i]=NULL;
+	}
+
+}
+/*}}}*/
+
+/*FUNCTION TriaHook::SetHookNodes{{{*/
+void TriaHook::SetHookNodes(int* node_ids,int analysis_counter){
+
+	/*initialize hook*/
+	this->hnodes[analysis_counter]=new Hook(node_ids,3);
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Elements/TriaHook.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/TriaHook.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/TriaHook.h	(revision 13395)
@@ -0,0 +1,31 @@
+/*!\file: TriaHook.h
+ * \brief prototypes for TriaHook.h
+ */ 
+
+#ifndef _TRIAHOOK_H_
+#define  _TRIAHOOK_H_
+
+class Hook;
+class IoModel;
+
+class TriaHook{
+
+	public: 
+		int    numanalyses; //number of analysis types
+		Hook** hnodes; // 3 nodes for each analysis type
+		Hook*  hmaterial; // 1 ice material
+		Hook*  hmatpar; // 1 material parameter
+
+
+		/*FUNCTION constructors, destructors {{{*/
+		TriaHook();
+		TriaHook(int in_numanalyses,int material_id, IoModel* iomodel);
+		~TriaHook();
+		void SetHookNodes(int* node_ids,int analysis_counter);
+		/*}}}*/
+
+};
+
+
+#endif //ifndef _TRIAHOOK_H_
+
Index: /issm/trunk/src/c/classes/objects/Elements/TriaRef.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Elements/TriaRef.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Elements/TriaRef.cpp	(revision 13395)
@@ -0,0 +1,503 @@
+/*!\file TriaRef.c
+ * \brief: implementation of the TriaRef object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Element macros*/
+#define NUMNODES 3
+
+/*Object constructors and destructor*/
+/*FUNCTION TriaRef::TriaRef(){{{*/
+TriaRef::TriaRef(){
+	this->element_type_list=NULL;
+}
+/*}}}*/
+/*FUNCTION TriaRef::TriaRef(int* types,int nummodels){{{*/
+
+TriaRef::TriaRef(const int nummodels){
+
+	/*Only allocate pointer*/
+	element_type_list=xNew(nummodels);
+
+}
+/*}}}*/
+/*FUNCTION TriaRef::~TriaRef(){{{*/
+TriaRef::~TriaRef(){
+	xDelete(element_type_list);
+}
+/*}}}*/
+
+/*Management*/
+/*FUNCTION TriaRef::SetElementType{{{*/
+void TriaRef::SetElementType(int type,int type_counter){
+
+	_assert_(type==P1Enum || type==P1DGEnum);
+
+	/*initialize element type*/
+	this->element_type_list[type_counter]=type;
+}
+/*}}}*/
+
+/*Reference Element numerics*/
+/*FUNCTION TriaRef::GetBMacAyeal {{{*/
+void TriaRef::GetBMacAyeal(IssmDouble* B, IssmDouble* xyz_list, GaussTria* gauss){
+	/*Compute B  matrix. B=[B1 B2 B3] where Bi is of size 3*NDOF2. 
+	 * For node i, Bi can be expressed in the actual coordinate system
+	 * by: 
+	 *       Bi=[ dh/dx           0    ]
+	 *          [   0           dh/dy  ]
+	 *          [ 1/2*dh/dy  1/2*dh/dx ]
+	 * where h is the interpolation function for node i.
+	 *
+	 * We assume B has been allocated already, of size: 3x(NDOF2*NUMNODES)
+	 */
+
+	int i;
+	IssmDouble dbasis[NDOF2][NUMNODES];
+
+	/*Get dh1dh2dh3 in actual coordinate system: */
+	GetNodalFunctionsDerivatives(&dbasis[0][0],xyz_list,gauss);
+
+	/*Build B: */
+	for (i=0;icoord1;
+	basis[1]=gauss->coord2;
+	basis[2]=gauss->coord3;
+
+}
+/*}}}*/
+/*FUNCTION TriaRef::GetSegmentNodalFunctions{{{*/
+void TriaRef::GetSegmentNodalFunctions(IssmDouble* basis,GaussTria* gauss,int index1,int index2){
+	/*This routine returns the values of the nodal functions  at the gaussian point.*/
+
+	IssmDouble BasisFunctions[3];
+
+	GetNodalFunctions(&BasisFunctions[0],gauss);
+
+	_assert_(index1>=0 && index1<3);
+	_assert_(index2>=0 && index2<3);
+	basis[0]=BasisFunctions[index1];
+	basis[1]=BasisFunctions[index2];
+}
+/*}}}*/
+/*FUNCTION TriaRef::GetNodalFunctionsDerivatives{{{*/
+void TriaRef::GetNodalFunctionsDerivatives(IssmDouble* dbasis,IssmDouble* xyz_list, GaussTria* gauss){
+
+	/*This routine returns the values of the nodal functions derivatives  (with respect to the 
+	 * actual coordinate system): */
+	int       i;
+	IssmDouble    dbasis_ref[NDOF2][NUMNODES];
+	IssmDouble    Jinv[NDOF2][NDOF2];
+
+	/*Get derivative values with respect to parametric coordinate system: */
+	GetNodalFunctionsDerivativesReference(&dbasis_ref[0][0], gauss); 
+
+	/*Get Jacobian invert: */
+	GetJacobianInvert(&Jinv[0][0], xyz_list, gauss);
+
+	/*Build dbasis: 
+	 *
+	 * [dhi/dx]= Jinv*[dhi/dr]
+	 * [dhi/dy]       [dhi/ds]
+	 */
+	for (i=0;i
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "../Object.h"
+#include "../Node.h"
+/*}}}*/
+
+class ExternalResult: public Object{
+
+	public: 
+		
+		virtual        ~ExternalResult(){};
+		/*Virtual functions:{{{*/
+		virtual int   InstanceEnum()=0;
+		virtual void  WriteData(FILE* fid,bool io_gather)=0;
+		virtual void  GetResultName(char**)=0;
+		virtual int   GetStep(void)=0;
+		/*}}}*/
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/ExternalResults/GenericExternalResult.h
===================================================================
--- /issm/trunk/src/c/classes/objects/ExternalResults/GenericExternalResult.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/ExternalResults/GenericExternalResult.h	(revision 13395)
@@ -0,0 +1,326 @@
+/*! \file GenericExternalResult.h 
+ *  \brief: header file for generic external result object
+ */
+
+#ifndef _GENERIC_EXTERNAL_RESULT_
+#define _GENERIC_EXTERNAL_RESULT_
+
+/*Headers:{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../shared/Numerics/recast.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "./ExternalResult.h"
+/*}}}*/
+
+template  
+class GenericExternalResult: public ExternalResult {
+
+	private: 
+		int id;
+		int enum_type;
+		ResultType value;
+		int M;
+		int N;
+		int step;
+		IssmDouble time;
+	
+	public:
+		/*Diverse: must be in front, as it is used in what follows*/
+		void GenericEcho(void){/*{{{*/
+			_printLine_("   id: " << this->id);
+			_printLine_("   enum:  " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+			_printLine_("   step: " << this->step);
+			_printLine_("   time: " << this->time);
+		}
+		/*}}}*/
+		void GenericWriteData(FILE* fid){/*{{{*/ 
+
+			int     length;
+			IssmPDouble  passiveDouble;
+			char*   name = NULL;
+
+			/*First write enum: */
+			EnumToStringx(&name,this->enum_type);
+			length=(strlen(name)+1)*sizeof(char);
+			fwrite(&length,sizeof(int),1,fid);
+			fwrite(name,length,1,fid);
+			xDelete(name);
+
+			/*Now write time and step: */
+			passiveDouble=reCast(time);
+			fwrite(&passiveDouble,sizeof(IssmPDouble),1,fid);
+			fwrite(&step,sizeof(int),1,fid);
+		} /*}}}*/
+
+		/*GenericExternalResult constructors and  destructors*/
+		GenericExternalResult(){ /*{{{*/
+			id  = 0;
+			enum_type = NoneEnum;
+			M=0;
+			N=0;
+			step=0;
+			time=0;
+		} /*}}}*/
+		GenericExternalResult(int in_id, int in_enum_type,ResultType in_values, int in_M,int in_N,int in_step,IssmDouble in_time){/*{{{*/
+			_error_("template GenericExternalResult(int in_id, int in_enum_type,double* in_values, int in_M,int in_N,int in_step,IssmDouble in_time) not implemented for this ResultType\n");
+		}
+/*}}}*/
+		GenericExternalResult(int in_id, int in_enum_type,ResultType in_value,int in_step, IssmDouble in_time){ /*{{{*/
+			id=in_id;
+			enum_type=in_enum_type;
+			value=in_value;
+			step=in_step;
+			time=in_time;
+		}
+		/*}}}*/
+		~GenericExternalResult(){ /*{{{*/
+		} /*}}}*/
+
+		/*Object virtual functions definitions:*/
+		void Echo(void){ /*{{{*/
+			this->DeepEcho();
+		}
+		/*}}}*/
+		void DeepEcho(void){ /*{{{*/
+			_error_("template DeepEcho not implemented for this ResultType\n");
+		}
+		/*}}}*/
+		int Id(void){ /*{{{*/ 
+			return -1; 
+		} /*}}}*/
+		int MyRank(void){ /*{{{*/
+			extern int my_rank;
+			return my_rank; 
+		} /*}}}*/
+		int ObjectEnum(void){ /*{{{*/
+			_error_("template ObjectEnum not implemented for this ResultType\n");
+		} /*}}}*/
+		Object* copy(void) { /*{{{*/
+			return new GenericExternalResult(this->id,this->enum_type,this->value,this->step,this->time);
+		} /*}}}*/
+
+		/*GenericExternalResult management: */
+void WriteData(FILE* fid,bool io_gather){ /*{{{*/
+			
+	extern  int my_rank;
+	int     type;
+	int     size;
+	IssmPDouble  passiveDouble;
+	
+	/*return if now on cpu 0: */
+	if(my_rank)return;
+
+	/*use generic part, same for all ResultTypes: */
+	this->GenericWriteData(fid);
+
+	/*writing a IssmPDouble for Matlab or Python to post-process, type is 1, size is 1: */
+	type=1;
+	size=1;
+	fwrite(&type,sizeof(int),1,fid);
+	fwrite(&size,sizeof(int),1,fid);
+
+	/*cast to a IssmPDouble: */
+	passiveDouble=reCast(value);
+	fwrite(&passiveDouble,size*sizeof(IssmPDouble),1,fid);
+
+} /*}}}*/
+void GetResultName(char** pname){ /*{{{*/
+	EnumToStringx(pname,this->enum_type);
+} /*}}}*/
+int GetStep(void){ /*{{{*/
+	return this->step;
+} /*}}}*/
+int InstanceEnum(void){ /*{{{*/
+	return this->enum_type;
+} /*}}}*/
+};
+
+/*Specific instantiations for bool: */
+template <> inline void GenericExternalResult::DeepEcho(void){ /*{{{*/
+
+	_printLine_("GenericExternalResult:");
+	this->GenericEcho();
+	_printLine_("   value: " <<(this->value?"true":"false"));
+
+} /*}}}*/
+template <> inline int GenericExternalResult::ObjectEnum(void){ /*{{{*/
+	return BoolExternalResultEnum;
+} /*}}}*/
+
+/*Specific instantiations for int: */
+template <> inline void GenericExternalResult::DeepEcho(void){ /*{{{*/
+
+	_printLine_("GenericExternalResult:");
+	this->GenericEcho();
+	_printLine_("   value: " << this->value);
+
+} /*}}}*/
+template <> inline int GenericExternalResult::ObjectEnum(void){ /*{{{*/
+	return IntExternalResultEnum;
+} /*}}}*/
+
+/*Specific instantiations for double: */
+template <> inline void GenericExternalResult::DeepEcho(void){ /*{{{*/
+
+	_printLine_("GenericExternalResult:");
+	this->GenericEcho();
+	_printLine_("   value: " << this->value);
+
+} /*}}}*/
+template <> inline int GenericExternalResult::ObjectEnum(void){ /*{{{*/
+	return DoubleExternalResultEnum;
+} /*}}}*/
+
+/*Specific instantiations for char*: */
+template <> inline GenericExternalResult::GenericExternalResult(int in_id, int in_enum_type,char* in_value,int in_step, IssmDouble in_time){ /*{{{*/
+
+	id=in_id;
+	enum_type=in_enum_type;
+	value=xNew(strlen(in_value)+1);
+	xMemCpy(value,in_value,(strlen(in_value)+1));
+	step=in_step;
+	time=in_time;
+
+} /*}}}*/
+template <> inline GenericExternalResult::~GenericExternalResult(){ /*{{{*/
+	xDelete(value);
+} /*}}}*/
+template <> inline void GenericExternalResult::DeepEcho(void){ /*{{{*/
+
+	_printLine_("GenericExternalResult:");
+	this->GenericEcho();
+	_printLine_("   value: " << this->value);
+
+} /*}}}*/
+template <> inline void GenericExternalResult::WriteData(FILE* fid,bool io_gather){ /*{{{*/
+
+	extern  int my_rank;
+	int     type;
+	int     length;
+
+	/*return if now on cpu 0: */
+	if(my_rank)return;
+
+	/*use generic part, same for all ResultTypes: */
+	this->GenericWriteData(fid);
+
+	/*writing a string, type is 2: */
+	type=2;
+	fwrite(&type,sizeof(int),1,fid);
+
+	length=(strlen(this->value)+1)*sizeof(char);
+	fwrite(&length,sizeof(int),1,fid);
+	fwrite(this->value,length,1,fid);
+}
+/*}}}*/
+template <> inline int GenericExternalResult::ObjectEnum(void){ /*{{{*/
+	return StringExternalResultEnum;
+} /*}}}*/
+
+/*Specific instantiations for IssmPDouble*: */
+template <> inline GenericExternalResult::GenericExternalResult(int in_id, int in_enum_type,IssmPDouble* in_values, int in_M,int in_N,int in_step,IssmDouble in_time){/*{{{*/
+
+	id=in_id;
+	enum_type=in_enum_type;
+	M=in_M;
+	N=in_N;
+	
+	step=in_step;
+	time=in_time;
+
+	/*Copy result in values*/
+	if(M*N){
+		value=xNew(M*N);
+		xMemCpy(value,in_values,M*N);
+	}
+	else value=NULL;
+}
+/*}}}*/
+template <> inline GenericExternalResult::GenericExternalResult(int in_id, int in_enum_type,IssmPDouble* in_value,int in_step, IssmDouble in_time){ /*{{{*/
+	_error_("you cannot initialize a GenericExternalResult without providing the dimensions of the matrix! Please use a more appropriate constructor!");
+} /*}}}*/
+template <> inline GenericExternalResult::~GenericExternalResult(){ /*{{{*/
+	xDelete(value);
+} /*}}}*/
+template <> inline void GenericExternalResult::Echo(void){ /*{{{*/
+	
+	int i,j;
+
+	_printLine_("GenericExternalResult:");
+	this->GenericEcho();
+	_printLine_("   matrix size: " << this->M << "-" << this->N);
+
+} /*}}}*/
+template <> inline void GenericExternalResult::DeepEcho(void){ /*{{{*/
+	
+	int i,j;
+
+	_printLine_("GenericExternalResult:");
+	this->GenericEcho();
+	
+	_printLine_("   matrix size: " << this->M << "-" << this->N);
+	for (i=0;iM;i++){  
+		_printString_("   [ ");
+		for (j=0;jN;j++){
+			_printString_( " " << setw(11) << setprecision (5) << this->value[i*this->N+j]);
+		}  
+		_printLine_(" ]");
+	}  
+
+} /*}}}*/
+template <> inline Object* GenericExternalResult::copy(void){ /*{{{*/
+	return new GenericExternalResult(this->id,this->enum_type,this->value,this->M,this->N,this->step,this->time);
+} /*}}}*/
+template <> inline void GenericExternalResult::WriteData(FILE* fid,bool io_gather){ /*{{{*/
+	
+	extern  int my_rank;
+	int     length;
+	int     type;
+	int     rows,cols;
+	char   *name    = NULL;
+	extern  int my_rank;
+	IssmPDouble passiveDouble;
+
+	if(io_gather){
+		/*we are gathering the data on cpu 0, don't write on other cpus: */
+		if(my_rank) return;
+	}
+
+	/*First write enum: */
+	EnumToStringx(&name,this->enum_type);
+	length=(strlen(name)+1)*sizeof(char);
+	fwrite(&length,sizeof(int),1,fid);
+	fwrite(name,length,1,fid);
+	xDelete(name);
+
+	/*Now write time and step: */
+	passiveDouble=reCast(time);
+	fwrite(&passiveDouble,sizeof(IssmPDouble),1,fid);
+	fwrite(&step,sizeof(int),1,fid);
+
+	/*writing a IssmDouble array, type is 3:*/
+	type=3;
+	fwrite(&type,sizeof(int),1,fid);
+	rows=this->M;
+	fwrite(&rows,sizeof(int),1,fid);
+	cols=this->N;
+	fwrite(&cols,sizeof(int),1,fid);
+	fwrite(value,cols*rows*sizeof(IssmPDouble),1,fid);
+
+}
+/*}}}*/
+template <> inline int GenericExternalResult::ObjectEnum(void){ /*{{{*/
+	return DoubleMatExternalResultEnum;
+} /*}}}*/
+
+#endif  /* _EXTERNAL_RESULTOBJECT_H */
Index: /issm/trunk/src/c/classes/objects/Inputs/BoolInput.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/BoolInput.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/BoolInput.cpp	(revision 13395)
@@ -0,0 +1,193 @@
+/*!\file BoolInput.c
+ * \brief: implementation of the BoolInput object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*BoolInput constructors and destructor*/
+/*FUNCTION BoolInput::BoolInput(){{{*/
+BoolInput::BoolInput(){
+	return;
+}
+/*}}}*/
+/*FUNCTION BoolInput::BoolInput(IssmDouble* values){{{*/
+BoolInput::BoolInput(int in_enum_type,IssmBool in_value){
+
+	enum_type=in_enum_type;
+	value=in_value;
+}
+/*}}}*/
+/*FUNCTION BoolInput::~BoolInput(){{{*/
+BoolInput::~BoolInput(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION BoolInput::Echo {{{*/
+void BoolInput::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION BoolInput::DeepEcho{{{*/
+void BoolInput::DeepEcho(void){
+
+	_printLine_("BoolInput:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: " <<(value?"true":"false"));
+}
+/*}}}*/
+/*FUNCTION BoolInput::Id{{{*/
+int    BoolInput::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION BoolInput::MyRank{{{*/
+int    BoolInput::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION BoolInput::ObjectEnum{{{*/
+int BoolInput::ObjectEnum(void){
+
+	return BoolInputEnum;
+
+}
+/*}}}*/
+/*FUNCTION BoolInput::copy{{{*/
+Object* BoolInput::copy() {
+	
+	return new BoolInput(this->enum_type,this->value);
+
+}
+/*}}}*/
+	
+/*BoolInput management*/
+/*FUNCTION BoolInput::InstanceEnum{{{*/
+int BoolInput::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION BoolInput::SpawnTriaInput{{{*/
+Input* BoolInput::SpawnTriaInput(int* indices){
+
+		/*output*/
+		BoolInput* outinput=new BoolInput();
+
+		/*only copy current value*/
+		outinput->enum_type=this->enum_type;
+		outinput->value=this->value;
+
+		/*Assign output*/
+		return outinput;
+
+}
+/*}}}*/
+/*FUNCTION BoolInput::SpawnResult{{{*/
+ElementResult* BoolInput::SpawnResult(int step, IssmDouble time){
+	
+	return new BoolElementResult(this->enum_type,this->value,step,time);
+
+}
+/*}}}*/
+
+/*Object functions*/
+/*FUNCTION BoolInput::GetInputValue(bool* pvalue) {{{*/
+void BoolInput::GetInputValue(bool* pvalue){
+	*pvalue=value;
+}
+/*}}}*/
+/*FUNCTION BoolInput::GetInputValue(int* pvalue){{{*/
+void BoolInput::GetInputValue(int* pvalue){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION BoolInput::GetInputValue(IssmDouble* pvalue){{{*/
+void BoolInput::GetInputValue(IssmDouble* pvalue){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION BoolInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){{{*/
+void BoolInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION BoolInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){{{*/
+void BoolInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION BoolInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){{{*/
+void BoolInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION BoolInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void BoolInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION BoolInput::ChangeEnum{{{*/
+void BoolInput::ChangeEnum(int newenumtype){
+	this->enum_type=newenumtype;
+}
+/*}}}*/
+/*FUNCTION BoolInput::SquareMin{{{*/
+void BoolInput::SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters){
+	/*square of a bool is the bool itself: */
+	*psquaremin=value;
+}
+/*}}}*/
+/*FUNCTION BoolInput::Scale{{{*/
+void BoolInput::Scale(IssmDouble scale_factor){
+	/*a bool cannot be scaled: */
+}
+/*}}}*/
+/*FUNCTION BoolInput::AXPY{{{*/
+void BoolInput::AXPY(Input* xinput,IssmDouble scalar){
+
+	BoolInput*  xboolinput=NULL;
+
+	/*xinput is of the same type, so cast it: */
+	xboolinput=(BoolInput*)xinput;
+
+	/*Carry out the AXPY operation depending on type:*/
+	switch(xinput->ObjectEnum()){
+
+		case BoolInputEnum:
+			this->value=reCast(this->value+scalar*xboolinput->value);
+			return;
+
+		default:
+			_error_("not implemented yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION BoolInput::Extrude{{{*/
+void BoolInput::Extrude(void){
+
+	/*do nothing*/
+	return;
+}
+/*}}}*/
+/*FUNCTION BoolInput::GetVectorFromInputs{{{*/
+void BoolInput::GetVectorFromInputs(Vector* vector,int* doflist){
+
+	_error_("not supporte yet!");
+
+}
+/*}}}*/
+/*FUNCTION BoolInput::GetValuesPtr{{{*/
+void BoolInput::GetValuesPtr(IssmDouble** pvalues,int* pnum_values){
+
+	_error_("not supported yet!");
+
+}
+/*}}}*/
+/*FUNCTION BoolInput::Configure{{{*/
+void BoolInput::Configure(Parameters* parameters){
+	/*do nothing: */
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Inputs/BoolInput.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/BoolInput.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/BoolInput.h	(revision 13395)
@@ -0,0 +1,85 @@
+/*! \file BoolInput.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _BOOLINPUT_H_
+#define _BOOLINPUT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Input.h"
+#include "../../../include/include.h"
+class GaussTria;
+/*}}}*/
+
+class BoolInput: public Input{
+
+	public:
+		/*just hold 3 values for 3 vertices: */
+		int    enum_type;
+		IssmBool value;
+
+		/*BoolInput constructors, destructors: {{{*/
+		BoolInput();
+		BoolInput(int enum_type,IssmBool value);
+		~BoolInput();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*BoolInput management: {{{*/
+		int   InstanceEnum();
+		Input* SpawnTriaInput(int* indices);
+		Input* PointwiseDivide(Input* inputB){_error_("not implemented yet");};
+		Input* PointwiseMin(Input* inputB){_error_("not implemented yet");};
+		Input* PointwiseMax(Input* inputB){_error_("not implemented yet");};
+		ElementResult* SpawnResult(int step, IssmDouble time);
+		void Configure(Parameters* parameters);
+		void AddTimeValues(IssmDouble* values,int step,IssmDouble time){_error_("not supported yet");};
+		/*}}}*/
+		/*numerics: {{{*/
+		void GetInputValue(bool* pvalue);
+		void GetInputValue(int* pvalue);
+		void GetInputValue(IssmDouble* pvalue);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss ,int index){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss ,int index){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss);
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetInputAverage(IssmDouble* pvalue){_error_("not implemented yet");};
+		void GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void ChangeEnum(int newenumtype);
+		void SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters);
+		void ConstrainMin(IssmDouble minimum){_error_("not implemented yet");};
+		IssmDouble InfinityNorm(void){_error_("InfinityNorm not implemented for booleans");};
+		IssmDouble Max(void){_error_("Max not implemented for booleans");};
+		IssmDouble MaxAbs(void){_error_("Max not implemented for booleans");};
+		IssmDouble Min(void){_error_("Min not implemented for booleans");};
+		IssmDouble MinAbs(void){_error_("Min not implemented for booleans");};
+		void Scale(IssmDouble scale_factor);
+		void ArtificialNoise(IssmDouble min,IssmDouble max){_error_("not implemented yet");};
+		void AXPY(Input* xinput,IssmDouble scalar);
+		void Constrain(IssmDouble cm_min, IssmDouble cm_max){_error_("Constrain not implemented for booleans");};
+		void Extrude(void);
+		void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");};
+		void GetVectorFromInputs(Vector* vector,int* doflist);
+		void GetValuesPtr(IssmDouble** pvalues,int* pnum_values);
+		/*}}}*/
+
+};
+#endif  /* _BOOLINPUT_H */
Index: /issm/trunk/src/c/classes/objects/Inputs/ControlInput.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/ControlInput.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/ControlInput.cpp	(revision 13395)
@@ -0,0 +1,282 @@
+/*!\file ControlInput.c
+ * \brief: implementation of the ControlInput object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*ControlInput constructors and destructor*/
+/*FUNCTION ControlInput::ControlInput(){{{*/
+ControlInput::ControlInput(){
+	control_id  = 0;
+	values      = NULL;
+	savedvalues = NULL;
+	minvalues   = NULL;
+	maxvalues   = NULL;
+	gradient    = NULL;
+}
+/*}}}*/
+/*FUNCTION ControlInput::ControlInput(int enum_type,int enum_input,IssmDouble* pvalues,IssmDouble* pmin,IssmDouble* pmax,int id){{{*/
+ControlInput::ControlInput(int in_enum_type,int enum_input,IssmDouble* pvalues,IssmDouble* pmin,IssmDouble* pmax,int id){
+
+	control_id=id;
+	enum_type=in_enum_type;
+
+	switch(enum_input){
+		case TriaP1InputEnum:
+			values     =new TriaP1Input(enum_type,pvalues);
+			savedvalues=new TriaP1Input(enum_type,pvalues);
+			minvalues  =new TriaP1Input(enum_type,pmin);
+			maxvalues  =new TriaP1Input(enum_type,pmax);
+			break;
+		case PentaP1InputEnum:
+			values     =new PentaP1Input(enum_type,pvalues);
+			savedvalues=new PentaP1Input(enum_type,pvalues);
+			minvalues  =new PentaP1Input(enum_type,pmin);
+			maxvalues  =new PentaP1Input(enum_type,pmax);
+			break;
+		default:
+			_error_("Input of Enum " << EnumToStringx(enum_input) << " not supported yet by ControlInput");
+	}
+	gradient   =NULL;
+}
+/*}}}*/
+/*FUNCTION ControlInput::~ControlInput(){{{*/
+ControlInput::~ControlInput(){
+	delete values;
+	delete savedvalues;
+	delete minvalues;
+	delete maxvalues;
+	delete gradient;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+		/*FUNCTION ControlInput::Echo {{{*/
+void ControlInput::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION ControlInput::DeepEcho{{{*/
+void ControlInput::DeepEcho(void){
+
+	_printLine_("ControlInput:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("---values: ");     if (values)      values->Echo();
+	_printLine_("---savedvalues: ");if (savedvalues) savedvalues->Echo();
+	_printLine_("---minvalues: ");  if (minvalues)   minvalues->Echo();
+	_printLine_("---maxvalues: ");  if (maxvalues)   maxvalues->Echo();
+	_printLine_("---gradient: ");   if (gradient)    gradient->Echo();
+}
+/*}}}*/
+/*FUNCTION ControlInput::Id{{{*/
+int    ControlInput::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION ControlInput::MyRank{{{*/
+int    ControlInput::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION ControlInput::ObjectEnum{{{*/
+int ControlInput::ObjectEnum(void){
+
+	return ControlInputEnum;
+
+}
+/*}}}*/
+/*FUNCTION ControlInput::copy{{{*/
+Object* ControlInput::copy() {
+	
+	ControlInput* output=NULL;
+
+	output = new ControlInput();
+	output->enum_type=this->enum_type;
+	output->control_id=this->control_id;
+
+	if(values)      output->values=(Input*)this->values->copy();
+	if(savedvalues) output->savedvalues=(Input*)this->savedvalues->copy();
+	if(minvalues)   output->minvalues=(Input*)this->minvalues->copy();
+	if(maxvalues)   output->maxvalues=(Input*)this->maxvalues->copy();
+	if(gradient)    output->gradient=(Input*)this->gradient->copy();
+
+	return output;
+}
+/*}}}*/
+	
+/*ControlInput management*/
+/*FUNCTION ControlInput::InstanceEnum{{{*/
+int ControlInput::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+
+/*Object functions*/
+/*FUNCTION ControlInput::Constrain(){{{*/
+void ControlInput::Constrain(void){
+
+	Input* newvalues=NULL;
+
+	newvalues=this->values->PointwiseMin(maxvalues);
+	delete values; this->values=newvalues;
+	newvalues=this->values->PointwiseMax(minvalues);
+	delete values; this->values=newvalues;
+}/*}}}*/
+/*FUNCTION ControlInput::Constrain(IssmDouble min, IssmDouble max){{{*/
+void ControlInput::Constrain(IssmDouble min, IssmDouble max){
+	   values->Constrain(min,max);
+}/*}}}*/
+/*FUNCTION ControlInput::Extrude{{{*/
+void ControlInput::Extrude(void){
+	values->Extrude();
+	savedvalues->Extrude();
+	//gradient->Extrude();
+}/*}}}*/
+/*FUNCTION ControlInput::GetGradient{{{*/
+void ControlInput::GetGradient(Vector* gradient_vec,int* doflist){
+	if(gradient) gradient->GetVectorFromInputs(gradient_vec,doflist);
+}/*}}}*/
+/*FUNCTION ControlInput::ScaleGradient{{{*/
+void ControlInput::ScaleGradient(IssmDouble scaling_factor){
+	if(!gradient) _error_("Gradient of ControlInput " << EnumToStringx(enum_type) << " not found");
+	gradient->Scale(scaling_factor);
+}/*}}}*/
+/*FUNCTION ControlInput::SetGradient{{{*/
+void ControlInput::SetGradient(Input* gradient_in){
+
+	/*Get enum for current gradient*/
+	switch(this->control_id){
+		case 1:
+			gradient_in->ChangeEnum(Gradient1Enum);
+			break;
+		case 2:
+			gradient_in->ChangeEnum(Gradient2Enum);
+			break;
+		case 3:
+			gradient_in->ChangeEnum(Gradient3Enum);
+			break;
+		default:
+			_error_("more than 3 controls not implemented yet (Gradient " << this->control_id << " was requested). EnumDefinitions.h needs to be updated.");
+	}
+
+	/*Delete old gradient and assign new gradient*/
+	if(gradient) delete gradient;
+	gradient=gradient_in;
+
+}/*}}}*/
+/*FUNCTION ControlInput::SetInput{{{*/
+void ControlInput::SetInput(Input* in_input){
+
+	delete values; this->values=in_input;
+	this->SaveValue(); //because this is what SpawnResult saves FIXME
+
+}/*}}}*/
+/*FUNCTION ControlInput::SpawnResult{{{*/
+ElementResult* ControlInput::SpawnResult(int step, IssmDouble time){
+	return savedvalues->SpawnResult(step,time);
+}/*}}}*/
+/*FUNCTION ControlInput::SpawnTriaInput{{{*/
+Input* ControlInput::SpawnTriaInput(int* indices){
+	return values->SpawnTriaInput(indices);
+}/*}}}*/
+/*FUNCTION ControlInput::SpawnGradient{{{*/
+ElementResult* ControlInput::SpawnGradient(int step, IssmDouble time){
+	_assert_(gradient);
+	return gradient->SpawnResult(step,time);
+}/*}}}*/
+/*FUNCTION ControlInput::GetVectorFromInputs(Vector* vector,int* doflist){{{*/
+void ControlInput::GetVectorFromInputs(Vector* vector,int* doflist){
+	values->GetVectorFromInputs(vector,doflist);
+}/*}}}*/
+/*FUNCTION ControlInput::GetVectorFromInputs(Vector* vector,int* doflist,const char* data){{{*/
+void ControlInput::GetVectorFromInputs(Vector* vector,int* doflist,const char* data){
+	 if(strcmp(data,"value")==0){
+		 _assert_(values);
+		 values->GetVectorFromInputs(vector,doflist);
+	 }
+	 else if (strcmp(data,"lowerbound")==0){
+		 _assert_(minvalues);
+		 minvalues->GetVectorFromInputs(vector,doflist);
+	 }
+	 else if (strcmp(data,"upperbound")==0){
+		 _assert_(maxvalues);
+		 maxvalues->GetVectorFromInputs(vector,doflist);
+	 }
+	 else if (strcmp(data,"gradient")==0){
+		 _assert_(gradient);
+		 gradient->GetVectorFromInputs(vector,doflist);
+	 }
+	 else{
+		 _error_("Data " << data << " not supported yet");
+	 }
+}/*}}}*/
+/*FUNCTION ControlInput::GetInputAverage(IssmDouble* pvalue){{{*/
+void ControlInput::GetInputAverage(IssmDouble* pvalue){
+	values->GetInputAverage(pvalue);
+}/*}}}*/
+/*FUNCTION ControlInput::GetInputValue(bool* pvalue){{{*/
+void ControlInput::GetInputValue(bool* pvalue){
+	values->GetInputValue(pvalue);
+}/*}}}*/
+/*FUNCTION ControlInput::GetInputValue(int* pvalue){{{*/
+void ControlInput::GetInputValue(int* pvalue){
+	values->GetInputValue(pvalue);
+}/*}}}*/
+/*FUNCTION ControlInput::GetInputValue(IssmDouble* pvalue){{{*/
+void ControlInput::GetInputValue(IssmDouble* pvalue){
+	values->GetInputValue(pvalue);
+}/*}}}*/
+/*FUNCTION ControlInput::GetInputValue(IssmDouble* pvalue){{{*/
+void ControlInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){
+	values->GetInputValue(pvalue,gauss);
+}/*}}}*/
+/*FUNCTION ControlInput::GetInputValue(IssmDouble* pvalue){{{*/
+void ControlInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){
+	values->GetInputValue(pvalue,gauss);
+}/*}}}*/
+/*FUNCTION ControlInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){{{*/
+void ControlInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){
+	values->GetInputDerivativeValue(derivativevalues,xyz_list,gauss);
+}/*}}}*/
+/*FUNCTION ControlInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void ControlInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){
+	values->GetInputDerivativeValue(derivativevalues,xyz_list,gauss);
+}/*}}}*/
+/*FUNCTION ControlInput::SaveValue{{{*/
+void ControlInput::SaveValue(void){
+	if(!values) _error_("Values of " << EnumToStringx(this->enum_type) << " not found");
+
+	if(savedvalues) delete this->savedvalues;
+	this->savedvalues=(Input*)this->values->copy();
+}/*}}}*/
+/*FUNCTION ControlInput::UpdateValue{{{*/
+void ControlInput::UpdateValue(IssmDouble scalar){
+	if(!gradient)    _error_("Gradient of " << EnumToStringx(this->enum_type) << " not found");
+	if(!savedvalues) _error_("Values of " << EnumToStringx(this->enum_type) << " not found");
+
+	if(values) delete this->values;
+	this->values=(Input*)this->savedvalues->copy();
+	this->values->AXPY(gradient,scalar);
+}/*}}}*/
+/*FUNCTION ControlInput::VerticallyIntegrate{{{*/
+void ControlInput::VerticallyIntegrate(Input* thickness_input){
+	values->VerticallyIntegrate(thickness_input);
+}/*}}}*/
+/*FUNCTION ControlInput::Configure{{{*/
+void ControlInput::Configure(Parameters* parameters){
+	/*do nothing: */
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Inputs/ControlInput.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/ControlInput.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/ControlInput.h	(revision 13395)
@@ -0,0 +1,98 @@
+/*! \file ControlInput.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _CONTROLINPUT_H_
+#define _CONTROLINPUT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Input.h"
+#include "../../../include/include.h"
+class GaussTria;
+/*}}}*/
+
+class ControlInput: public Input{
+
+	public:
+		int    enum_type;
+		int    control_id;
+		Input* values;
+		Input* savedvalues;
+		Input* minvalues;
+		Input* maxvalues;
+		Input* gradient;
+
+		/*ControlInput constructors, destructors: {{{*/
+		ControlInput();
+		ControlInput(int enum_type,int enum_input,IssmDouble* pvalues,IssmDouble* pmin,IssmDouble* pmax,int id);
+		~ControlInput();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*ControlInput management: {{{*/
+		int    InstanceEnum();
+		Input* SpawnTriaInput(int* indices);
+		Input* PointwiseDivide(Input* inputB){_error_("not implemented yet");};
+		Input* PointwiseMin(Input* inputB){_error_("not implemented yet");};
+		Input* PointwiseMax(Input* inputB){_error_("not implemented yet");};
+		ElementResult* SpawnResult(int step, IssmDouble time);
+		void AddTimeValues(IssmDouble* values,int step,IssmDouble time){_error_("not supported yet");};
+		void Configure(Parameters* parameters);
+		/*}}}*/
+		/*numerics: {{{*/
+		void SetInput(Input* in_input);
+		void GetInputValue(bool* pvalue);
+		void GetInputValue(int* pvalue);
+		void GetInputValue(IssmDouble* pvalue);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss ,int index){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss ,int index){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss);
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetInputAverage(IssmDouble* pvalue);
+		void GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void ChangeEnum(int newenumtype){_error_("not implemented yet");};
+		void SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters){_error_("not implemented yet");};
+		void ConstrainMin(IssmDouble minimum){_error_("not implemented yet");};
+		void Scale(IssmDouble scale_factor){_error_("not implemented yet");};
+		void ArtificialNoise(IssmDouble min,IssmDouble max){_error_("not implemented yet");};
+		void AXPY(Input* xinput,IssmDouble scalar){_error_("not implemented yet");};
+		void Constrain(void);
+		void Constrain(IssmDouble min,IssmDouble max);
+		IssmDouble InfinityNorm(void){_error_("not implemented yet");};
+		IssmDouble Max(void){_error_("not implemented yet");};
+		IssmDouble MaxAbs(void){_error_("not implemented yet");};
+		IssmDouble Min(void){_error_("not implemented yet");};
+		IssmDouble MinAbs(void){_error_("not implemented yet");};
+		void Extrude(void);
+		void VerticallyIntegrate(Input* thickness_input);
+		void GetVectorFromInputs(Vector* vector,int* doflist,const char* data);
+		void GetVectorFromInputs(Vector* vector,int* doflist);
+		void GetValuesPtr(IssmDouble** pvalues,int* pnum_values){_error_("not implemented yet");};
+		ElementResult* SpawnGradient(int step, IssmDouble time);
+		void GetGradient(Vector* gradient_vec,int* doflist);
+		void ScaleGradient(IssmDouble scale);
+		void SetGradient(Input* gradient_in);
+		void UpdateValue(IssmDouble scalar);
+		void SaveValue(void);
+		/*}}}*/
+
+};
+#endif  /* _CONTROLINPUT_H */
Index: /issm/trunk/src/c/classes/objects/Inputs/DatasetInput.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/DatasetInput.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/DatasetInput.cpp	(revision 13395)
@@ -0,0 +1,122 @@
+/*!\file DatasetInput.c
+ * \brief: implementation of the datasetinput object
+ */
+/*Headers{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*DatasetInput constructors and destructor*/
+/*FUNCTION DatasetInput::DatasetInput(){{{*/
+DatasetInput::DatasetInput(){
+	enum_type=UNDEF;
+	inputs=NULL;
+}
+/*}}}*/
+/*FUNCTION DatasetInput::DatasetInput(int in_enum_type) {{{*/
+DatasetInput::DatasetInput(int in_enum_type){
+
+	enum_type  = in_enum_type;
+	inputs     = new Inputs();
+}
+/*}}}*/
+/*FUNCTION DatasetInput::~DatasetInput(){{{*/
+DatasetInput::~DatasetInput(){
+	delete inputs;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+		/*FUNCTION DatasetInput::Echo {{{*/
+void DatasetInput::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION DatasetInput::DeepEcho{{{*/
+void DatasetInput::DeepEcho(void){
+
+	_printLine_("DatasetInput:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("---inputs: "); inputs->Echo();
+}
+/*}}}*/
+/*FUNCTION DatasetInput::Id{{{*/
+int    DatasetInput::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION DatasetInput::MyRank{{{*/
+int    DatasetInput::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION DatasetInput::ObjectEnum{{{*/
+int DatasetInput::ObjectEnum(void){
+
+	return DatasetInputEnum;
+
+}
+/*}}}*/
+/*FUNCTION DatasetInput::copy{{{*/
+Object* DatasetInput::copy() {
+	
+	DatasetInput* output=NULL;
+
+	output = new DatasetInput();
+	output->enum_type=this->enum_type;
+	output->inputs=(Inputs*)this->inputs->Copy();
+
+	return output;
+}
+/*}}}*/
+/*FUNCTION DatasetInput::SpawnTriaInput{{{*/
+Input* DatasetInput::SpawnTriaInput(int* indices){
+
+	/*output*/
+	DatasetInput* outinput=NULL;
+
+	/*Create new Datasetinput (copy of current input)*/
+	outinput=new DatasetInput();
+	outinput->enum_type=this->enum_type;
+	outinput->inputs=(Inputs*)this->inputs->SpawnTriaInputs(indices);
+
+	/*Assign output*/
+	return outinput;
+}
+/*}}}*/
+	
+/*DatasetInput management*/
+/*FUNCTION DatasetInput::InstanceEnum{{{*/
+int DatasetInput::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+
+/*Object functions*/
+/*FUNCTION DatasetInput::Configure{{{*/
+void DatasetInput::Configure(Parameters* parameters){
+	/*do nothing: */
+}
+/*}}}*/
+/*FUNCTION DatasetInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss,int index){{{*/
+void DatasetInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss,int index){
+
+	/*Get requested input within dataset*/
+	if(index<0 || index > inputs->Size()-1) _error_("index requested (" << index << ") exceeds dataset size (" << inputs->Size() << ")");
+	Input* input=(Input*)this->inputs->GetObjectByOffset(index);
+	
+	input->GetInputValue(pvalue,gauss);
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Inputs/DatasetInput.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/DatasetInput.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/DatasetInput.h	(revision 13395)
@@ -0,0 +1,92 @@
+/*! \file DatasetInput.h 
+ *  \brief: header file for datasetinput object
+ */
+
+
+#ifndef _DATASETINPUT_H_
+#define _DATASETINPUT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Input.h"
+#include "../../../include/include.h"
+class GaussTria;
+/*}}}*/
+
+class DatasetInput: public Input{
+
+	public:
+		int    enum_type;
+
+		Inputs*     inputs;
+
+		/*DatasetInput constructors, destructors: {{{*/
+		DatasetInput();
+		DatasetInput(int enum_type);
+		~DatasetInput();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id();
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*DatasetInput management: {{{*/
+		int    InstanceEnum();
+		Input* SpawnTriaInput(int* indices);
+		Input* PointwiseDivide(Input* inputB){_error_("not implemented yet");};
+		Input* PointwiseMin(Input* inputB){_error_("not implemented yet");};
+		Input* PointwiseMax(Input* inputB){_error_("not implemented yet");};
+		ElementResult* SpawnResult(int step, IssmDouble time){_error_("not implemented yet");};
+		void AddTimeValues(IssmDouble* values,int step,IssmDouble time){_error_("not supported yet");};
+		void Configure(Parameters* parameters);
+		/*}}}*/
+		/*numerics: {{{*/
+		void GetInputValue(bool* pvalue){_error_("not implemented yet");};
+		void GetInputValue(int* pvalue){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss ,int index);
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss ,int index){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetInputAverage(IssmDouble* pvalue){_error_("not implemented yet");};
+		void GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void ChangeEnum(int newenumtype){_error_("not implemented yet");};
+		void SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters){_error_("not implemented yet");};
+		void ConstrainMin(IssmDouble minimum){_error_("not implemented yet");};
+		void Scale(IssmDouble scale_factor){_error_("not implemented yet");};
+		void ArtificialNoise(IssmDouble min,IssmDouble max){_error_("not implemented yet");};
+		void AXPY(Input* xinput,IssmDouble scalar){_error_("not implemented yet");};
+		void Constrain(void){_error_("not implemented yet");};
+		void Constrain(IssmDouble min,IssmDouble max){_error_("not implemented yet");};
+		IssmDouble InfinityNorm(void){_error_("not implemented yet");};
+		IssmDouble Max(void){_error_("not implemented yet");};
+		IssmDouble MaxAbs(void){_error_("not implemented yet");};
+		IssmDouble Min(void){_error_("not implemented yet");};
+		IssmDouble MinAbs(void){_error_("not implemented yet");};
+		void Extrude(void){_error_("not implemented yet");};
+		void VerticallyIntegrate(Input* thickness_input){_error_("not implemented yet");};
+		void GetVectorFromInputs(Vector* vector,int* doflist){_error_("not implemented yet");};
+		void GetValuesPtr(IssmDouble** pvalues,int* pnum_values){_error_("not implemented yet");};
+		ElementResult* SpawnGradient(int step, IssmDouble time){_error_("not implemented yet");};
+		void GetGradient(Vector* gradient_vec,int* doflist){_error_("not implemented yet");};
+		void ScaleGradient(IssmDouble scale){_error_("not implemented yet");};
+		void SetGradient(Input* gradient_in){_error_("not implemented yet");};
+		void UpdateValue(IssmDouble scalar){_error_("not implemented yet");};
+		void SaveValue(void){_error_("not implemented yet");};
+		/*}}}*/
+
+};
+#endif  /* _DATASETINPUT_H */
Index: /issm/trunk/src/c/classes/objects/Inputs/DoubleInput.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/DoubleInput.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/DoubleInput.cpp	(revision 13395)
@@ -0,0 +1,359 @@
+/*!\file DoubleInput.c
+ * \brief: implementation of the DoubleInput object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*DoubleInput constructors and destructor*/
+/*FUNCTION DoubleInput::DoubleInput(){{{*/
+DoubleInput::DoubleInput(){
+	return;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::DoubleInput(IssmDouble value){{{*/
+DoubleInput::DoubleInput(int in_enum_type,IssmDouble in_value){
+
+	enum_type=in_enum_type;
+	value=in_value;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::~DoubleInput(){{{*/
+DoubleInput::~DoubleInput(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+		/*FUNCTION DoubleInput::Echo {{{*/
+void DoubleInput::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION DoubleInput::DeepEcho{{{*/
+void DoubleInput::DeepEcho(void){
+
+	_printLine_("DoubleInput:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: " << this->value);
+}
+/*}}}*/
+/*FUNCTION DoubleInput::Id{{{*/
+int    DoubleInput::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION DoubleInput::MyRank{{{*/
+int    DoubleInput::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION DoubleInput::ObjectEnum{{{*/
+int DoubleInput::ObjectEnum(void){
+
+	return DoubleInputEnum;
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::copy{{{*/
+Object* DoubleInput::copy() {
+	
+	return new DoubleInput(this->enum_type,this->value);
+
+}
+/*}}}*/
+	
+/*DoubleInput management*/
+/*FUNCTION DoubleInput::InstanceEnum{{{*/
+int DoubleInput::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::SpawnTriaInput{{{*/
+Input* DoubleInput::SpawnTriaInput(int* indices){
+
+	/*output*/
+	DoubleInput* outinput=new DoubleInput();
+
+	/*only copy current value*/
+	outinput->enum_type=this->enum_type;
+	outinput->value=this->value;
+
+	/*Assign output*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::SpawnResult{{{*/
+ElementResult* DoubleInput::SpawnResult(int step, IssmDouble time){
+
+	return new DoubleElementResult(this->enum_type,this->value,step,time);
+
+}
+/*}}}*/
+
+/*Object functions*/
+/*FUNCTION DoubleInput::GetInputValue(bool* pvalue) {{{*/
+void DoubleInput::GetInputValue(bool* pvalue){
+	_error_("Double input of enum " << EnumToStringx(enum_type) << " cannot return a boolean");
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetInputValue(int* pvalue){{{*/
+void DoubleInput::GetInputValue(int* pvalue){
+	_error_("Double input of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return an integer");
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetInputValue(IssmDouble* pvalue){{{*/
+void DoubleInput::GetInputValue(IssmDouble* pvalue){
+
+	/*return value*/
+	*pvalue=value;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){{{*/
+void DoubleInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){*pvalue=this->value;}
+/*}}}*/
+/*FUNCTION DoubleInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){{{*/
+void DoubleInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){*pvalue=this->value;}
+/*}}}*/
+/*FUNCTION DoubleInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){{{*/
+void DoubleInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION DoubleInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void DoubleInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION DoubleInput::GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss){{{*/
+void DoubleInput::GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss){
+	/*Epsilon is zero as vx is constant over the element*/
+	for(int i=0;i<3;i++) epsilonvx[i]=0;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss){{{*/
+void DoubleInput::GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss){
+	/*Epsilon is zero as vy is constant over the element*/
+	for(int i=0;i<3;i++) epsilonvy[i]=0;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void DoubleInput::GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){
+	/*Epsilon is zero as vx is constant over the element*/
+	for(int i=0;i<6;i++) epsilonvx[i]=0;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void DoubleInput::GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){
+	/*Epsilon is zero as vy is constant over the element*/
+	for(int i=0;i<6;i++) epsilonvy[i]=0;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void DoubleInput::GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss){
+	/*Epsilon is zero as vz is constant over the element*/
+	for(int i=0;i<6;i++) epsilonvz[i]=0;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void DoubleInput::GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){
+	/*Epsilon is zero as vx is constant over the element*/
+	for(int i=0;i<5;i++) epsilonvx[i]=0;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void DoubleInput::GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){
+	/*Epsilon is zero as vy is constant over the element*/
+	for(int i=0;i<5;i++) epsilonvy[i]=0;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::ChangeEnum{{{*/
+void DoubleInput::ChangeEnum(int newenumtype){
+	this->enum_type=newenumtype;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::SquareMin{{{*/
+void DoubleInput::SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters){
+
+	/*square min of a IssmDouble is the square of the IssmDouble itself: */
+	*psquaremin=pow(value,2);
+}
+/*}}}*/
+/*FUNCTION DoubleInput::Scale{{{*/
+void DoubleInput::Scale(IssmDouble scale_factor){
+	value=value*scale_factor;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::ConstrainMin{{{*/
+void DoubleInput::ConstrainMin(IssmDouble minimum){
+	if (valueObjectEnum()){
+
+		case DoubleInputEnum:
+			this->value=this->value+scalar*xIssmDoubleinput->value;
+			return;
+
+		default:
+			_error_("not implemented yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::Constrain{{{*/
+void DoubleInput::Constrain(IssmDouble cm_min, IssmDouble cm_max){
+
+	if(!xIsNan(cm_min)) if (this->valuevalue=cm_min;
+	if(!xIsNan(cm_max)) if (this->value>cm_max)this->value=cm_max;
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::Max{{{*/
+IssmDouble DoubleInput::Max(void){
+	return this->value;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::MaxAbs{{{*/
+IssmDouble DoubleInput::MaxAbs(void){
+	return fabs(this->value);
+}
+/*}}}*/
+/*FUNCTION DoubleInput::Min{{{*/
+IssmDouble DoubleInput::Min(void){
+	return this->value;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::MinAbs{{{*/
+IssmDouble DoubleInput::MinAbs(void){
+	return fabs(this->value);
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetVectorFromInputs{{{*/
+void DoubleInput::GetVectorFromInputs(Vector* vector,int* doflist){
+
+	_error_("not supporte yet!");
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetValuesPtr{{{*/
+void DoubleInput::GetValuesPtr(IssmDouble** pvalues,int* pnum_values){
+
+	_error_("not supported yet!");
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::GetInputAverage{{{*/
+void DoubleInput::GetInputAverage(IssmDouble* pvalue){
+	*pvalue=value;
+}
+/*}}}*/
+/*FUNCTION DoubleInput::VerticallyIntegrate{{{*/
+void DoubleInput::VerticallyIntegrate(Input* thickness_input){
+
+	/*Intermediaries*/
+	IssmDouble thickness_value;
+
+	/*Check that input provided is a thickness*/
+	if (thickness_input->InstanceEnum()!=ThicknessEnum) _error_("Input provided is not a Thickness (enum_type is " << EnumToStringx(thickness_input->InstanceEnum()) << ")");
+
+	/*vertically integrate depending on type:*/
+	switch(thickness_input->ObjectEnum()){
+
+		case PentaP1InputEnum:
+			thickness_input->GetInputAverage(&thickness_value);
+			this->value=this->value*thickness_value;
+			return;
+
+		default:
+			_error_("not implemented yet");
+	}
+}
+/*}}}*/
+/*FUNCTION DoubleInput::PointwiseDivide{{{*/
+Input* DoubleInput::PointwiseDivide(Input* inputB){
+
+	/*Ouput*/
+	DoubleInput* outinput=NULL;
+
+	/*Intermediaries*/
+	IssmDouble       Bvalue;
+
+	/*Check that inputB is of the same type*/
+	inputB->GetInputAverage(&Bvalue);
+
+	/*Create new DoubleInput*/
+	outinput=new DoubleInput(this->enum_type,this->value/Bvalue);
+
+	/*Return output pointer*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::PointwiseMin{{{*/
+Input* DoubleInput::PointwiseMin(Input* input){
+
+	/*Ouput*/
+	DoubleInput* outinput=NULL;
+
+	/*Intermediaries*/
+	IssmDouble       min;
+
+	/*Check that inputB is of the same type*/
+	if (input->Min() < this->Min()) min=input->Min();
+	else min=this->Min();
+
+	/*Create new DoubleInput*/
+	outinput=new DoubleInput(this->enum_type,min);
+
+	/*Return output pointer*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::PointwiseMax{{{*/
+Input* DoubleInput::PointwiseMax(Input* input){
+
+	/*Ouput*/
+	DoubleInput* outinput=NULL;
+
+	/*Intermediaries*/
+	IssmDouble       max;
+
+	/*Check that inputB is of the same type*/
+	if (input->Max() > this->Max()) max=input->Max();
+	else max=this->Max();
+
+	/*Create new DoubleInput*/
+	outinput=new DoubleInput(this->enum_type,max);
+
+	/*Return output pointer*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION DoubleInput::Configure{{{*/
+void DoubleInput::Configure(Parameters* parameters){
+	/*do nothing: */
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Inputs/DoubleInput.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/DoubleInput.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/DoubleInput.h	(revision 13395)
@@ -0,0 +1,84 @@
+/*! \file DoubleInput.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _DOUBLEINPUT_H_
+#define _DOUBLEINPUT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Input.h"
+#include "../../../include/include.h"
+class GaussTria;
+/*}}}*/
+
+class DoubleInput: public Input{
+
+	public:
+		int    enum_type;
+		IssmDouble value;
+
+		/*DoubleInput constructors, destructors: {{{*/
+		DoubleInput();
+		DoubleInput(int enum_type,IssmDouble value);
+		~DoubleInput();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*DoubleInput management: {{{*/
+		int   InstanceEnum();
+		Input* SpawnTriaInput(int* indices);
+		Input* PointwiseDivide(Input* inputB);
+		Input* PointwiseMin(Input* inputB);
+		Input* PointwiseMax(Input* inputB);
+		ElementResult* SpawnResult(int step, IssmDouble time);
+		void AddTimeValues(IssmDouble* values,int step,IssmDouble time){_error_("not supported yet");};
+		void Configure(Parameters* parameters);
+		/*}}}*/
+		/*numerics: {{{*/
+		void GetInputValue(bool* pvalue);
+		void GetInputValue(int* pvalue);
+		void GetInputValue(IssmDouble* pvalue);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss ,int index){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss ,int index){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss);
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetInputAverage(IssmDouble* pvalue);
+		void GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss);
+		void GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss);
+		void GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss);
+		void ChangeEnum(int newenumtype);
+		void SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters);
+		void ConstrainMin(IssmDouble minimum);
+		void Scale(IssmDouble scale_factor);
+		void ArtificialNoise(IssmDouble min,IssmDouble max){_error_("not implemented yet");};
+		void AXPY(Input* xinput,IssmDouble scalar);
+		void Constrain(IssmDouble cm_min, IssmDouble cm_max);
+		IssmDouble InfinityNorm(void){_error_("not implemented yet");};
+		IssmDouble Max(void);
+		IssmDouble MaxAbs(void);
+		IssmDouble Min(void);
+		IssmDouble MinAbs(void);
+		void Extrude(void){_error_("not supported yet");};
+		void VerticallyIntegrate(Input* thickness_input);
+		void GetVectorFromInputs(Vector* vector,int* doflist);
+		void GetValuesPtr(IssmDouble** pvalues,int* pnum_values);
+		/*}}}*/
+
+};
+#endif  /* _DOUBLEINPUT_H */
Index: /issm/trunk/src/c/classes/objects/Inputs/Input.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/Input.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/Input.h	(revision 13395)
@@ -0,0 +1,69 @@
+/*!\file:  Input.h
+ * \brief abstract class for Input object
+ */ 
+
+
+#ifndef _INPUT_H_
+#define _INPUT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../Object.h"
+class Node;
+class ElementResult;
+class GaussTria;
+class Parameters;
+/*}}}*/
+
+class Input: public Object{
+
+	public: 
+		
+		virtual        ~Input(){};
+
+		virtual int  InstanceEnum()=0; 
+		virtual void GetInputValue(bool* pvalue)=0;
+		virtual void GetInputValue(int* pvalue)=0;
+		virtual void GetInputValue(IssmDouble* pvalue)=0;
+		virtual void GetInputValue(IssmDouble* pvalue,GaussTria* gauss)=0;
+		virtual void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss)=0;
+		virtual void GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time)=0;
+		virtual void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time)=0;
+		virtual void GetInputValue(IssmDouble* pvalue,GaussTria* gauss ,int index)=0;
+		virtual void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,int index)=0;
+		virtual void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss)=0;
+		virtual void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss)=0;
+		virtual void GetInputAverage(IssmDouble* pvalue)=0;
+		virtual void GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss)=0;
+		virtual void GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss)=0;
+		virtual void GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss)=0;
+		virtual void GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss)=0;
+		virtual void GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss)=0;
+		virtual void GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss)=0;
+		virtual void GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss)=0;
+		virtual void ChangeEnum(int newenumtype)=0;
+		virtual void Configure(Parameters* parameters)=0;
+
+		virtual void   SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters)=0;
+		virtual void   ConstrainMin(IssmDouble minimum)=0;
+		virtual IssmDouble InfinityNorm(void)=0;
+		virtual IssmDouble MaxAbs(void)=0;
+		virtual IssmDouble MinAbs(void)=0;
+		virtual IssmDouble Max(void)=0;
+		virtual IssmDouble Min(void)=0;
+		virtual void   Scale(IssmDouble scale_factor)=0;
+		virtual void   ArtificialNoise(IssmDouble min,IssmDouble max)=0;
+		virtual void   AXPY(Input* xinput,IssmDouble scalar)=0;
+		virtual void   Constrain(IssmDouble cm_min, IssmDouble cm_max)=0;
+		virtual void   VerticallyIntegrate(Input* thickness_input)=0;
+		virtual void   Extrude()=0;
+		virtual void   GetVectorFromInputs(Vector* vector,int* doflist)=0;
+		virtual void   GetValuesPtr(IssmDouble** pvalues,int* pnum_values)=0;
+		
+		virtual Input* SpawnTriaInput(int* indices)=0;
+		virtual Input* PointwiseDivide(Input* inputB)=0;
+		virtual Input* PointwiseMax(Input* inputmax)=0;
+		virtual Input* PointwiseMin(Input* inputmin)=0;
+		virtual ElementResult* SpawnResult(int step, IssmDouble time)=0;
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/Inputs/IntInput.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/IntInput.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/IntInput.cpp	(revision 13395)
@@ -0,0 +1,199 @@
+/*!\file IntInput.c
+ * \brief: implementation of the IntInput object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*IntInput constructors and destructor*/
+/*FUNCTION IntInput::IntInput(){{{*/
+IntInput::IntInput(){
+	return;
+}
+/*}}}*/
+/*FUNCTION IntInput::IntInput(IssmDouble* values){{{*/
+IntInput::IntInput(int in_enum_type,IssmInt in_value){
+
+	enum_type=in_enum_type;
+	value=in_value;
+}
+/*}}}*/
+/*FUNCTION IntInput::~IntInput(){{{*/
+IntInput::~IntInput(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION IntInput::DeepEcho{{{*/
+void IntInput::DeepEcho(void){
+
+	_printLine_("IntInput:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: " << (int)this->value);
+}
+/*}}}*/
+/*FUNCTION IntInput::Id{{{*/
+int    IntInput::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION IntInput::MyRank{{{*/
+int    IntInput::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION IntInput::ObjectEnum{{{*/
+int IntInput::ObjectEnum(void){
+
+	return IntInputEnum;
+
+}
+/*}}}*/
+/*FUNCTION IntInput::copy{{{*/
+Object* IntInput::copy() {
+	
+	return new IntInput(this->enum_type,this->value);
+
+}
+/*}}}*/
+
+/*IntInput management*/
+/*FUNCTION IntInput::Echo {{{*/
+void IntInput::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION IntInput::InstanceEnum{{{*/
+int IntInput::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION IntInput::SpawnTriaInput{{{*/
+Input* IntInput::SpawnTriaInput(int* indices){
+
+	/*output*/
+	IntInput* outinput=new IntInput();
+
+	/*only copy current value*/
+	outinput->enum_type=this->enum_type;
+	outinput->value=this->value;
+
+	/*Assign output*/
+	return outinput;
+}
+/*}}}*/
+/*FUNCTION IntInput::SpawnResult{{{*/
+ElementResult* IntInput::SpawnResult(int step, IssmDouble time){
+	
+	_error_("not supported yet!");
+
+}
+/*}}}*/
+
+/*Object functions*/
+/*FUNCTION IntInput::GetInputValue(bool* pvalue) {{{*/
+void IntInput::GetInputValue(bool* pvalue){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION IntInput::GetInputValue(int* pvalue){{{*/
+void IntInput::GetInputValue(int* pvalue){
+	*pvalue=value;
+}
+/*}}}*/
+/*FUNCTION IntInput::GetInputValue(IssmDouble* pvalue){{{*/
+void IntInput::GetInputValue(IssmDouble* pvalue){
+	_error_("IntInput cannot return a IssmDouble in parallel");
+}
+/*}}}*/
+/*FUNCTION IntInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){{{*/
+void IntInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION IntInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){{{*/
+void IntInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION IntInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){{{*/
+void IntInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION IntInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void IntInput::GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){_error_("not supported yet!");}
+/*}}}*/
+/*FUNCTION IntInput::ChangeEnum{{{*/
+void IntInput::ChangeEnum(int newenumtype){
+	this->enum_type=newenumtype;
+}
+/*}}}*/
+/*FUNCTION IntInput::SquareMin{{{*/
+void IntInput::SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters){
+
+	/*square min of an integer is the square of the integer itself: */
+	*psquaremin=pow((IssmDouble)value,2);
+}
+/*}}}*/
+/*FUNCTION IntInput::Scale{{{*/
+void IntInput::Scale(IssmDouble scale_factor){
+	IssmDouble dvalue=(IssmDouble)value*scale_factor;
+	value=reCast(dvalue);
+}
+/*}}}*/
+/*FUNCTION IntInput::AXPY{{{*/
+void IntInput::AXPY(Input* xinput,IssmDouble scalar){
+
+	IssmDouble dvalue;
+	IntInput*  xintinput=NULL;
+
+	/*xinput is of the same type, so cast it: */
+	xintinput=(IntInput*)xinput;
+
+	/*Carry out the AXPY operation depending on type:*/
+	switch(xinput->ObjectEnum()){
+
+		case IntInputEnum:
+			dvalue=(IssmDouble)this->value+scalar*(IssmDouble)xintinput->value;
+			this->value=reCast(dvalue);
+			return;
+
+		default:
+			_error_("not implemented yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION IntInput::Constrain{{{*/
+void IntInput::Constrain(IssmDouble cm_min, IssmDouble cm_max){
+
+	if(!xIsNan(cm_min)) if (this->valuevalue=reCast(cm_min);
+	if(!xIsNan(cm_max)) if (this->value>cm_max)this->value=reCast(cm_max);
+
+}
+/*}}}*/
+/*FUNCTION IntInput::GetVectorFromInputs{{{*/
+void IntInput::GetVectorFromInputs(Vector* vector,int* doflist){
+
+	_error_("not supporte yet!");
+
+}
+/*}}}*/
+/*FUNCTION IntInput::GetValuesPtr{{{*/
+void IntInput::GetValuesPtr(IssmDouble** pvalues,int* pnum_values){
+
+	_error_("not supported yet!");
+
+}
+/*}}}*/
+/*FUNCTION IntInput::Configure{{{*/
+void IntInput::Configure(Parameters* parameters){
+	/*do nothing: */
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Inputs/IntInput.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/IntInput.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/IntInput.h	(revision 13395)
@@ -0,0 +1,85 @@
+/*! \file IntInput.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _INTINPUT_H_
+#define _INTINPUT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Input.h"
+#include "../../../include/include.h"
+class GaussTria;
+/*}}}*/
+
+class IntInput: public Input{
+
+	public:
+		/*just hold 3 values for 3 vertices: */
+		int    enum_type;
+		IssmInt value;
+
+		/*IntInput constructors, destructors: {{{*/
+		IntInput();
+		IntInput(int enum_type,IssmInt value);
+		~IntInput();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*IntInput management: {{{*/
+		int   InstanceEnum();
+		Input* SpawnTriaInput(int* indices);
+		Input* PointwiseDivide(Input* inputB){_error_("not implemented yet");};
+		Input* PointwiseMin(Input* inputB){_error_("not implemented yet");};
+		Input* PointwiseMax(Input* inputB){_error_("not implemented yet");};
+		ElementResult* SpawnResult(int step, IssmDouble time);
+		void AddTimeValues(IssmDouble* values,int step,IssmDouble time){_error_("not supported yet");};
+		void Configure(Parameters* parameters);
+		/*}}}*/
+		/*numerics: {{{*/
+		void GetInputValue(bool* pvalue);
+		void GetInputValue(int* pvalue);
+		void GetInputValue(IssmDouble* pvalue);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss ,int index){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss ,int index){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss);
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetInputAverage(IssmDouble* pvalue){_error_("not implemented yet");};
+		void GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void ChangeEnum(int newenumtype);
+		void SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters);
+		void ConstrainMin(IssmDouble minimum){_error_("not implemented yet");};
+		void Scale(IssmDouble scale_factor);
+		void ArtificialNoise(IssmDouble min,IssmDouble max){_error_("not implemented yet");};
+		void AXPY(Input* xinput,IssmDouble scalar);
+		void Constrain(IssmDouble cm_min, IssmDouble cm_max);
+		IssmDouble InfinityNorm(void){_error_("InfinityNorm not implemented for integers");};
+		IssmDouble Max(void){_error_("Max not implemented for integers");};
+		IssmDouble MaxAbs(void){_error_("Max not implemented for integers");};
+		IssmDouble Min(void){_error_("Min not implemented for integers");};
+		IssmDouble MinAbs(void){_error_("Min not implemented for integers");};
+		void Extrude(void){_error_("not supported yet");};
+		void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");};
+		void GetVectorFromInputs(Vector* vector,int* doflist);
+		void GetValuesPtr(IssmDouble** pvalues,int* pnum_values);
+		/*}}}*/
+
+};
+#endif  /* _INTINPUT_H */
Index: /issm/trunk/src/c/classes/objects/Inputs/PentaP1Input.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/PentaP1Input.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/PentaP1Input.cpp	(revision 13395)
@@ -0,0 +1,629 @@
+/*!\file PentaP1Input.c
+ * \brief: implementation of the PentaP1Input object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*PentaP1Input constructors and destructor*/
+/*FUNCTION PentaP1Input::PentaP1Input(){{{*/
+PentaP1Input::PentaP1Input(){
+	return;
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::PentaP1Input(int in_enum_type,IssmDouble* values){{{*/
+PentaP1Input::PentaP1Input(int in_enum_type,IssmDouble* in_values)
+		:PentaRef(1)
+{
+
+	/*Set PentaRef*/
+	this->SetElementType(P1Enum,0);
+	this->element_type=P1Enum;
+
+	enum_type=in_enum_type;
+	values[0]=in_values[0];
+	values[1]=in_values[1];
+	values[2]=in_values[2];
+	values[3]=in_values[3];
+	values[4]=in_values[4];
+	values[5]=in_values[5];
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::~PentaP1Input(){{{*/
+PentaP1Input::~PentaP1Input(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION PentaP1Input::Echo {{{*/
+void PentaP1Input::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::DeepEcho{{{*/
+void PentaP1Input::DeepEcho(void){
+
+	_printLine_("PentaP1Input:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   values: [" << this->values[0] << " " << this->values[1] << " " << this->values[2] << " " << this->values[3] << " " << this->values[4] << " " << this->values[5] << "]");
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::Id{{{*/
+int    PentaP1Input::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION PentaP1Input::MyRank{{{*/
+int    PentaP1Input::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::ObjectEnum{{{*/
+int PentaP1Input::ObjectEnum(void){
+
+	return PentaP1InputEnum;
+
+}
+/*}}}*/
+	
+/*PentaP1Input management*/
+/*FUNCTION PentaP1Input::copy{{{*/
+Object* PentaP1Input::copy() {
+	
+	return new PentaP1Input(this->enum_type,this->values);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::InstanceEnum{{{*/
+int PentaP1Input::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::SpawnTriaInput{{{*/
+Input* PentaP1Input::SpawnTriaInput(int* indices){
+
+	/*output*/
+	TriaP1Input* outinput=NULL;
+	IssmDouble newvalues[3];
+
+	/*Loop over the new indices*/
+	for(int i=0;i<3;i++){
+
+		/*Check index value*/
+		_assert_(indices[i]>=0 && indices[i]<6);
+
+		/*Assign value to new input*/
+		newvalues[i]=this->values[indices[i]];
+	}
+
+	/*Create new Tria input*/
+	outinput=new TriaP1Input(this->enum_type,&newvalues[0]);
+
+	/*Assign output*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::SpawnResult{{{*/
+ElementResult* PentaP1Input::SpawnResult(int step, IssmDouble time){
+
+	return new PentaP1ElementResult(this->enum_type,this->values,step,time);
+
+}
+/*}}}*/
+
+/*Object functions*/
+/*FUNCTION PentaP1Input::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){{{*/
+void PentaP1Input::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){
+
+	/*Call PentaRef function*/
+	PentaRef::GetInputValue(pvalue,&values[0],gauss);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::GetInputDerivativeValue(IssmDouble* p, IssmDouble* xyz_list, GaussPenta* gauss){{{*/
+void PentaP1Input::GetInputDerivativeValue(IssmDouble* p, IssmDouble* xyz_list, GaussPenta* gauss){
+
+	/*Call PentaRef function*/
+	PentaRef::GetInputDerivativeValue(p,&values[0],xyz_list,gauss);
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::GetVxStrainRate3d{{{*/
+void PentaP1Input::GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){
+	int i,j;
+
+	const int numnodes=6;
+	const int DOFVELOCITY=3;
+	IssmDouble B[8][27];
+	IssmDouble B_reduced[6][DOFVELOCITY*numnodes];
+	IssmDouble velocity[numnodes][DOFVELOCITY];
+
+	/*Get B matrix: */
+	GetBStokes(&B[0][0], xyz_list, gauss);
+	/*Create a reduced matrix of B to get rid of pressure */
+	for (i=0;i<6;i++){
+		for (j=0;j<3;j++){
+			B_reduced[i][j]=B[i][j];
+		}
+		for (j=4;j<7;j++){
+			B_reduced[i][j-1]=B[i][j];
+		}
+		for (j=8;j<11;j++){
+			B_reduced[i][j-2]=B[i][j];
+		}
+		for (j=12;j<15;j++){
+			B_reduced[i][j-3]=B[i][j];
+		}
+		for (j=16;j<19;j++){
+			B_reduced[i][j-4]=B[i][j];
+		}
+		for (j=20;j<23;j++){
+			B_reduced[i][j-5]=B[i][j];
+		}
+	}
+
+	/*Here, we are computing the strain rate of (vx,0,0)*/
+	for(i=0;ivalues[i];
+		velocity[i][1]=0.0;
+		velocity[i][2]=0.0;
+	}
+	/*Multiply B by velocity, to get strain rate: */
+	MatrixMultiply(&B_reduced[0][0],6,DOFVELOCITY*numnodes,0,&velocity[0][0],DOFVELOCITY*numnodes,1,0,epsilonvx,0);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::GetVyStrainRate3d{{{*/
+void PentaP1Input::GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){
+	int i,j;
+
+	const int numnodes=6;
+	const int DOFVELOCITY=3;
+	IssmDouble B[8][27];
+	IssmDouble B_reduced[6][DOFVELOCITY*numnodes];
+	IssmDouble velocity[numnodes][DOFVELOCITY];
+
+	/*Get B matrix: */
+	GetBStokes(&B[0][0], xyz_list, gauss);
+	/*Create a reduced matrix of B to get rid of pressure */
+	for (i=0;i<6;i++){
+		for (j=0;j<3;j++){
+			B_reduced[i][j]=B[i][j];
+		}
+		for (j=4;j<7;j++){
+			B_reduced[i][j-1]=B[i][j];
+		}
+		for (j=8;j<11;j++){
+			B_reduced[i][j-2]=B[i][j];
+		}
+		for (j=12;j<15;j++){
+			B_reduced[i][j-3]=B[i][j];
+		}
+		for (j=16;j<19;j++){
+			B_reduced[i][j-4]=B[i][j];
+		}
+		for (j=20;j<23;j++){
+			B_reduced[i][j-5]=B[i][j];
+		}
+	}
+
+	/*Here, we are computing the strain rate of (0,vy,0)*/
+	for(i=0;ivalues[i];
+		velocity[i][2]=0.0;
+	}
+	/*Multiply B by velocity, to get strain rate: */
+	MatrixMultiply(&B_reduced[0][0],6,DOFVELOCITY*numnodes,0,&velocity[0][0],DOFVELOCITY*numnodes,1,0,epsilonvy,0);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::GetVzStrainRate3d{{{*/
+void PentaP1Input::GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss){
+	int i,j;
+
+	const int numnodes=6;
+	const int DOFVELOCITY=3;
+	IssmDouble B[8][27];
+	IssmDouble B_reduced[6][DOFVELOCITY*numnodes];
+	IssmDouble velocity[numnodes][DOFVELOCITY];
+
+	/*Get B matrix: */
+	GetBStokes(&B[0][0], xyz_list, gauss);
+	/*Create a reduced matrix of B to get rid of pressure */
+	for (i=0;i<6;i++){
+		for (j=0;j<3;j++){
+			B_reduced[i][j]=B[i][j];
+		}
+		for (j=4;j<7;j++){
+			B_reduced[i][j-1]=B[i][j];
+		}
+		for (j=8;j<11;j++){
+			B_reduced[i][j-2]=B[i][j];
+		}
+		for (j=12;j<15;j++){
+			B_reduced[i][j-3]=B[i][j];
+		}
+		for (j=16;j<19;j++){
+			B_reduced[i][j-4]=B[i][j];
+		}
+		for (j=20;j<23;j++){
+			B_reduced[i][j-5]=B[i][j];
+		}
+	}
+
+	/*Here, we are computing the strain rate of (0,0,vz)*/
+	for(i=0;ivalues[i];
+	}
+
+	/*Multiply B by velocity, to get strain rate: */
+	MatrixMultiply(&B_reduced[0][0],6,DOFVELOCITY*numnodes,0,&velocity[0][0],DOFVELOCITY*numnodes,1,0,epsilonvz,0);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::GetVxStrainRate3dPattyn{{{*/
+void PentaP1Input::GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){
+
+	int i;
+	const int numnodes=6;
+	IssmDouble B[5][NDOF2*numnodes];
+	IssmDouble velocity[numnodes][NDOF2];
+
+	/*Get B matrix: */
+	GetBPattyn(&B[0][0], xyz_list, gauss);
+
+	/*Here, we are computing the strain rate of (vx,0)*/
+	for(i=0;ivalues[i];
+		velocity[i][1]=0.0;
+	}
+
+	/*Multiply B by velocity, to get strain rate: */
+	MatrixMultiply( &B[0][0],5,NDOF2*numnodes,0,
+				&velocity[0][0],NDOF2*numnodes,1,0,
+				epsilonvx,0);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::GetVyStrainRate3dPattyn{{{*/
+void PentaP1Input::GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){
+
+	int i;
+	const int numnodes=6;
+	IssmDouble B[5][NDOF2*numnodes];
+	IssmDouble velocity[numnodes][NDOF2];
+
+	/*Get B matrix: */
+	GetBPattyn(&B[0][0], xyz_list, gauss);
+
+	/*Here, we are computing the strain rate of (0,vy)*/
+	for(i=0;ivalues[i];
+	}
+
+	/*Multiply B by velocity, to get strain rate: */
+	MatrixMultiply( &B[0][0],5,NDOF2*numnodes,0,
+				&velocity[0][0],NDOF2*numnodes,1,0,
+				epsilonvy,0);
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::ChangeEnum{{{*/
+void PentaP1Input::ChangeEnum(int newenumtype){
+	this->enum_type=newenumtype;
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::GetInputAverage{{{*/
+void PentaP1Input::GetInputAverage(IssmDouble* pvalue){
+	*pvalue=1./6.*(values[0]+values[1]+values[2]+values[3]+values[4]+values[5]);
+}
+/*}}}*/
+
+/*Intermediary*/
+/*FUNCTION PentaP1Input::SquareMin{{{*/
+void PentaP1Input::SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters){
+
+	int i;
+	const int numnodes=6;
+	IssmDouble valuescopy[numnodes];
+	IssmDouble squaremin;
+
+	/*First,  copy values, to process units if requested: */
+	for(i=0;ivalues[i];
+
+	/*Process units if requested: */
+	if(process_units)UnitConversion(&valuescopy[0],numnodes,IuToExtEnum,enum_type);
+
+	/*Now, figure out minimum of valuescopy: */
+	squaremin=pow(valuescopy[0],2);
+	for(i=1;inorm) norm=fabs(values[i]);
+	return norm;
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::Max{{{*/
+IssmDouble PentaP1Input::Max(void){
+
+	const int numnodes=6;
+	IssmDouble    max=values[0];
+
+	for(int i=1;imax) max=values[i];
+	}
+	return max;
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::MaxAbs{{{*/
+IssmDouble PentaP1Input::MaxAbs(void){
+
+	const int numnodes=6;
+	IssmDouble    max=fabs(values[0]);
+
+	for(int i=1;imax) max=fabs(values[i]);
+	}
+	return max;
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::Min{{{*/
+IssmDouble PentaP1Input::Min(void){
+
+	const int numnodes=6;
+	IssmDouble    min=values[0];
+
+	for(int i=1;iObjectEnum()){
+
+		case PentaP1InputEnum:{
+			PentaP1Input* cast_input=(PentaP1Input*)xinput;
+			for(i=0;ivalues[i]=this->values[i]+scalar*(cast_input->values[i]);}
+			return;
+		case ControlInputEnum:{
+			ControlInput* cont_input=(ControlInput*)xinput;
+			if(cont_input->values->ObjectEnum()!=PentaP1InputEnum) _error_("not supported yet");
+			PentaP1Input* cast_input=(PentaP1Input*)cont_input->values;
+			for(i=0;ivalues[i]=this->values[i]+scalar*(cast_input->values[i]);}
+			return;
+		default:
+			_error_("not implemented yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::Constrain{{{*/
+void PentaP1Input::Constrain(IssmDouble cm_min, IssmDouble cm_max){
+
+	int i;
+	const int numnodes=6;
+		
+	if(!xIsNan(cm_min)) for(i=0;ivalues[i]values[i]=cm_min;
+	if(!xIsNan(cm_max)) for(i=0;ivalues[i]>cm_max)this->values[i]=cm_max;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::Extrude{{{*/
+void PentaP1Input::Extrude(void){
+
+	int i;
+
+	/*First 3 values copied on 3 last values*/
+	for(i=0;i<3;i++) this->values[3+i]=this->values[i];
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::VerticallyIntegrate{{{*/
+void PentaP1Input::VerticallyIntegrate(Input* thickness_input){
+
+	/*Intermediaries*/
+	int i;
+	const int  numnodes = 6;
+	int        num_thickness_values;
+	IssmDouble    *thickness_values = NULL;
+
+	/*Check that input provided is a thickness*/
+	if (thickness_input->InstanceEnum()!=ThicknessEnum) _error_("Input provided is not a Thickness (enum_type is " << EnumToStringx(thickness_input->InstanceEnum()) << ")");
+
+	/*Get Thickness value pointer*/
+	thickness_input->GetValuesPtr(&thickness_values,&num_thickness_values);
+
+	/*vertically integrate depending on type:*/
+	switch(thickness_input->ObjectEnum()){
+
+		case PentaP1InputEnum:
+			for(i=0;i<3;i++){
+				this->values[i]=0.5*(this->values[i]+this->values[i+3]) * thickness_values[i];
+				this->values[i+3]=this->values[i];
+			}
+			return;
+
+		default:
+			_error_("not implemented yet");
+	}
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::PointwiseDivide{{{*/
+Input* PentaP1Input::PointwiseDivide(Input* inputB){
+
+	/*Ouput*/
+	PentaP1Input* outinput=NULL;
+
+	/*Intermediaries*/
+	int               i;
+	PentaP1Input *xinputB     = NULL;
+	int               B_numvalues;
+	const int         numnodes    = 6;
+	IssmDouble            AdotBvalues[numnodes];
+
+	/*Check that inputB is of the same type*/
+	if (inputB->ObjectEnum()!=PentaP1InputEnum) _error_("Operation not permitted because inputB is of type " << EnumToStringx(inputB->ObjectEnum()));
+	xinputB=(PentaP1Input*)inputB;
+
+	/*Create point wise sum*/
+	for(i=0;ivalues[i]!=0);
+		AdotBvalues[i]=this->values[i]/xinputB->values[i];
+	}
+
+	/*Create new Penta vertex input (copy of current input)*/
+	outinput=new PentaP1Input(this->enum_type,&AdotBvalues[0]);
+
+	/*Return output pointer*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::PointwiseMin{{{*/
+Input* PentaP1Input::PointwiseMin(Input* inputB){
+
+	/*Ouput*/
+	PentaP1Input* outinput=NULL;
+
+	/*Intermediaries*/
+	int               i;
+	PentaP1Input *xinputB     = NULL;
+	int               B_numvalues;
+	const int         numnodes    = 6;
+	IssmDouble            minvalues[numnodes];
+
+	/*Check that inputB is of the same type*/
+	if (inputB->ObjectEnum()!=PentaP1InputEnum) _error_("Operation not permitted because inputB is of type " << EnumToStringx(inputB->ObjectEnum()));
+	xinputB=(PentaP1Input*)inputB;
+
+	/*Create point wise min*/
+	for(i=0;ivalues[i] > xinputB->values[i]) minvalues[i]=xinputB->values[i];
+		else minvalues[i]=this->values[i];
+	}
+
+	/*Create new Penta vertex input (copy of current input)*/
+	outinput=new PentaP1Input(this->enum_type,&minvalues[0]);
+
+	/*Return output pointer*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::PointwiseMax{{{*/
+Input* PentaP1Input::PointwiseMax(Input* inputB){
+
+	/*Ouput*/
+	PentaP1Input* outinput=NULL;
+
+	/*Intermediaries*/
+	int               i;
+	PentaP1Input *xinputB     = NULL;
+	int               B_numvalues;
+	const int         numnodes    = 6;
+	IssmDouble            maxvalues[numnodes];
+
+	/*Check that inputB is of the same type*/
+	if (inputB->ObjectEnum()!=PentaP1InputEnum) _error_("Operation not permitted because inputB is of type " << EnumToStringx(inputB->ObjectEnum()));
+	xinputB=(PentaP1Input*)inputB;
+
+	/*Create point wise max*/
+	for(i=0;ivalues[i] < xinputB->values[i]) maxvalues[i]=xinputB->values[i];
+		else maxvalues[i]=this->values[i];
+	}
+
+	/*Create new Penta vertex input (copy of current input)*/
+	outinput=new PentaP1Input(this->enum_type,&maxvalues[0]);
+
+	/*Return output pointer*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::GetVectorFromInputs{{{*/
+void PentaP1Input::GetVectorFromInputs(Vector* vector,int* doflist){
+
+	const int numvertices=6;
+	vector->SetValues(numvertices,doflist,this->values,INS_VAL);
+
+} /*}}}*/
+/*FUNCTION PentaP1Input::GetValuesPtr{{{*/
+void PentaP1Input::GetValuesPtr(IssmDouble** pvalues,int* pnum_values){
+
+	*pvalues=this->values;
+	*pnum_values=6;
+
+}
+/*}}}*/
+/*FUNCTION PentaP1Input::Configure{{{*/
+void PentaP1Input::Configure(Parameters* parameters){
+	/*do nothing: */
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Inputs/PentaP1Input.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/PentaP1Input.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/PentaP1Input.h	(revision 13395)
@@ -0,0 +1,86 @@
+/*! \file PentaP1Input.h 
+ *  \brief: header file for PentaP1Input object
+ */
+
+
+#ifndef _PENTAP1INPUT_H_
+#define _PENTAP1INPUT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Input.h"
+#include "../Elements/PentaRef.h"
+class GaussTria;
+/*}}}*/
+
+class PentaP1Input: public Input, public PentaRef{
+
+	public:
+		/*just hold 6 values for 6 vertices: */
+		int    enum_type;
+		IssmDouble values[6];
+
+		/*PentaP1Input constructors, destructors: {{{*/
+		PentaP1Input();
+		PentaP1Input(int enum_type,IssmDouble* values);
+		~PentaP1Input();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*PentaP1Input management: {{{*/
+		int   InstanceEnum();
+		Input* SpawnTriaInput(int* indices);
+		Input* PointwiseDivide(Input* inputB);
+		Input* PointwiseMin(Input* inputB);
+		Input* PointwiseMax(Input* inputB);
+		ElementResult* SpawnResult(int step, IssmDouble time);
+		void AddTimeValues(IssmDouble* values,int step,IssmDouble time){_error_("not supported yet");};
+		void Configure(Parameters* parameters);
+		/*}}}*/
+		/*numerics: {{{*/
+		void GetInputValue(bool* pvalue){_error_("not implemented yet");};
+		void GetInputValue(int* pvalue){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss ,int index){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss ,int index){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetInputAverage(IssmDouble* pvalue);
+		void GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss);
+		void GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss);
+		void ChangeEnum(int newenumtype);
+
+		void SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters);
+		void ConstrainMin(IssmDouble minimum);
+		void Scale(IssmDouble scale_factor);
+		void ArtificialNoise(IssmDouble min,IssmDouble max){_error_("not implemented yet");};
+		void AXPY(Input* xinput,IssmDouble scalar);
+		void Constrain(IssmDouble cm_min, IssmDouble cm_max);
+		IssmDouble InfinityNorm(void);
+		IssmDouble Max(void);
+		IssmDouble MaxAbs(void);
+		IssmDouble Min(void);
+		IssmDouble MinAbs(void);
+		void Extrude(void);
+		void VerticallyIntegrate(Input* thickness_input);
+		void GetVectorFromInputs(Vector* vector,int* doflist);
+		void GetValuesPtr(IssmDouble** pvalues,int* pnum_values);
+		/*}}}*/
+
+};
+#endif  /* _PENTAP1INPUT_H */
Index: /issm/trunk/src/c/classes/objects/Inputs/TransientInput.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/TransientInput.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/TransientInput.cpp	(revision 13395)
@@ -0,0 +1,494 @@
+/*!\file TransientInput.c
+ * \brief: implementation of the TransientInput object
+ */
+/*Headers{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*TransientInput constructors and destructor*/
+/*FUNCTION TransientInput::TransientInput(){{{*/
+TransientInput::TransientInput(){
+
+	enum_type=UNDEF;
+	inputs=NULL;
+	this->numtimesteps=0;
+	this->parameters=NULL;
+	this->timesteps=NULL;
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::TransientInput(int in_enum_type){{{*/
+TransientInput::TransientInput(int in_enum_type)
+{
+	/*Set Enum*/
+	enum_type=in_enum_type;
+
+	/*Allocate values and timesteps, and copy: */
+	this->numtimesteps=0;
+	this->timesteps=NULL;
+	inputs = new Inputs();
+	this->parameters=NULL;
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::~TransientInput{{{*/
+TransientInput::~TransientInput(){
+	xDelete(this->timesteps);
+	this->timesteps=NULL;
+	this->numtimesteps=0;
+	parameters=NULL;
+	delete this->inputs;
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION TransientInput::Echo {{{*/
+void TransientInput::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION TransientInput::DeepEcho{{{*/
+void TransientInput::DeepEcho(void){
+
+	int i;
+
+	_printLine_("TransientInput:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   numtimesteps: " << this->numtimesteps);
+	_printLine_("---inputs: "); 
+	for(i=0;inumtimesteps;i++){
+		_printLine_("   time: " << this->timesteps[i] << "  ");
+		((Input*)this->inputs->GetObjectByOffset(i))->Echo();
+	}
+}
+/*}}}*/
+/*FUNCTION TransientInput::Id{{{*/
+int    TransientInput::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION TransientInput::MyRank{{{*/
+int    TransientInput::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION TransientInput::ObjectEnum{{{*/
+int TransientInput::ObjectEnum(void){
+
+	return TransientInputEnum;
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::copy{{{*/
+Object* TransientInput::copy() {
+
+	TransientInput* output=NULL;
+
+	output = new TransientInput();
+	output->enum_type=this->enum_type;
+	output->numtimesteps=this->numtimesteps;
+	output->timesteps=xNew(this->numtimesteps);
+        xMemCpy(output->timesteps,this->timesteps,this->numtimesteps);
+	output->inputs=(Inputs*)this->inputs->Copy();
+	output->parameters=this->parameters;
+
+	return output;
+
+}
+/*}}}*/
+	
+/*TransientInput management*/
+/*FUNCTION TransientInput::InstanceEnum{{{*/
+int TransientInput::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::SpawnTriaInput{{{*/
+Input* TransientInput::SpawnTriaInput(int* indices){
+
+	/*output*/
+	TransientInput* outinput=NULL;
+
+	/*Create new Transientinput (copy of current input)*/
+	outinput=new TransientInput();
+	outinput->enum_type=this->enum_type;
+	outinput->numtimesteps=this->numtimesteps;
+	outinput->timesteps=xNew(this->numtimesteps);
+	xMemCpy(outinput->timesteps,this->timesteps,this->numtimesteps);
+	outinput->inputs=(Inputs*)this->inputs->SpawnTriaInputs(indices);
+	outinput->parameters=this->parameters;
+
+	/*Assign output*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::SpawnResult{{{*/
+ElementResult* TransientInput::SpawnResult(int step, IssmDouble time){
+
+	ElementResult* elementresult=NULL;
+
+	/*Ok, we want to spawn an ElementResult. We have the time, just get 
+	 *the correct values: */
+	Input* input=GetTimeInput(time);
+
+	elementresult=input->SpawnResult(step,time);
+
+   delete input;
+
+	return elementresult;
+}
+/*}}}*/
+
+/*Object functions*/
+/*FUNCTION TransientInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){{{*/
+void TransientInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){
+	IssmDouble time;
+
+	/*First, recover current time from parameters: */
+	this->parameters->FindParam(&time,TimeEnum);
+
+	/*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+
+	/*Call input function*/
+	input->GetInputValue(pvalue,gauss);
+
+	delete input;
+}
+/*}}}*/
+/*FUNCTION TransientInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){{{*/
+void TransientInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){
+	IssmDouble time;
+
+	/*First, recover current time from parameters: */
+	this->parameters->FindParam(&time,TimeEnum);
+
+	/*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+
+	/*Call input function*/
+	input->GetInputValue(pvalue,gauss);
+
+	delete input;
+}
+/*}}}*/
+/*FUNCTION TransientInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time){{{*/
+void TransientInput::GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time){
+
+	/*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+
+	/*Call input function*/
+	input->GetInputValue(pvalue,gauss);
+
+	delete input;
+}
+/*}}}*/
+/*FUNCTION TransientInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time){{{*/
+void TransientInput::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time){
+
+	/*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+
+	/*Call input function*/
+	input->GetInputValue(pvalue,gauss);
+
+	delete input;
+}
+/*}}}*/
+/*FUNCTION TransientInput::GetInputDerivativeValue(IssmDouble* p, IssmDouble* xyz_list, GaussTria* gauss){{{*/
+void TransientInput::GetInputDerivativeValue(IssmDouble* p, IssmDouble* xyz_list, GaussTria* gauss){
+
+	IssmDouble time;
+
+	/*First, recover current time from parameters: */
+	parameters->FindParam(&time,TimeEnum);
+
+	/*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+		   
+	/*Call input function*/
+	input->GetInputDerivativeValue(p,xyz_list,gauss);
+
+	delete input;
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::ChangeEnum{{{*/
+void TransientInput::ChangeEnum(int newenumtype){
+	this->enum_type=newenumtype;
+}
+/*}}}*/
+/*FUNCTION TransientInput::GetInputAverage{{{*/
+void TransientInput::GetInputAverage(IssmDouble* pvalue){
+	
+	IssmDouble time;
+
+	/*First, recover current time from parameters: */
+	parameters->FindParam(&time,TimeEnum);
+
+	/*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+
+	/*Call input function*/
+	input->GetInputAverage(pvalue);
+			   
+	delete input;
+
+}
+/*}}}*/
+
+/*Intermediary*/
+/*FUNCTION TransientInput::AddTimeInput{{{*/
+void TransientInput::AddTimeInput(Input* input,IssmDouble time){
+
+	/*insert values at time step: */
+	if (this->numtimesteps>0 && time<=this->timesteps[this->numtimesteps-1]) _assert_("timestep values must increase sequentially");
+
+	//copy timesteps, add the new time, delete previous timesteps, and add the new input: inputs->AddObject(input);
+	IssmDouble* old_timesteps=NULL;
+
+	if (this->numtimesteps > 0){
+		old_timesteps=xNew(this->numtimesteps);
+		xMemCpy(old_timesteps,this->timesteps,this->numtimesteps);
+		xDelete(this->timesteps);
+	}
+
+	this->numtimesteps=this->numtimesteps+1;
+	this->timesteps=xNew(this->numtimesteps);
+
+	if (this->numtimesteps > 1){
+		xMemCpy(this->timesteps,old_timesteps,this->numtimesteps-1);
+		xDelete(old_timesteps);
+	}
+
+	/*go ahead and plug: */
+	this->timesteps[this->numtimesteps-1]=time;
+	inputs->AddObject(input);
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::Extrude{{{*/
+void TransientInput::Extrude(void){
+
+	for(int i=0;inumtimesteps;i++){
+		((Input*)this->inputs->GetObjectByOffset(i))->Extrude();
+	}
+}
+/*}}}*/
+/*FUNCTION TransientInput::SquareMin{{{*/
+void TransientInput::SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters){
+
+	IssmDouble time;
+
+	/*First, recover current time from parameters: */
+	parameters->FindParam(&time,TimeEnum);
+
+   /*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+		   
+	/*Call input function*/
+	input->SquareMin(psquaremin,process_units,parameters);
+			   
+	delete input;
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::InfinityNorm{{{*/
+IssmDouble TransientInput::InfinityNorm(void){
+
+	IssmDouble time;
+	IssmDouble infnorm;
+
+	/*First, recover current time from parameters: */
+	parameters->FindParam(&time,TimeEnum);
+
+   /*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+
+	/*Call input function*/
+	infnorm=input->InfinityNorm();
+			   
+	/*Clean-up and return*/
+	delete input;
+	return infnorm;
+}
+/*}}}*/
+/*FUNCTION TransientInput::Max{{{*/
+IssmDouble TransientInput::Max(void){
+
+	IssmDouble time;
+	IssmDouble max;
+
+	/*First, recover current time from parameters: */
+	parameters->FindParam(&time,TimeEnum);
+
+   /*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+		   
+	/*Call input function*/
+	max=input->Max();
+			   
+	delete input;
+
+	return max;
+}
+/*}}}*/
+/*FUNCTION TransientInput::MaxAbs{{{*/
+IssmDouble TransientInput::MaxAbs(void){
+
+	IssmDouble time;
+	IssmDouble maxabs;
+
+	/*First, recover current time from parameters: */
+	parameters->FindParam(&time,TimeEnum);
+
+	/*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+
+	/*Call input function*/
+	maxabs=input->MaxAbs();
+
+	/*Clean-up and return*/
+	delete input;
+	return maxabs;
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::Min{{{*/
+IssmDouble TransientInput::Min(void){
+
+	IssmDouble time;
+	IssmDouble min;
+
+	/*First, recover current time from parameters: */
+	parameters->FindParam(&time,TimeEnum);
+
+   /*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+
+	/*Call input function*/
+	min=input->Min();
+
+	/*Clean-up and return*/
+	delete input;
+	return min;
+
+}
+/*}}}*/
+/*FUNCTION TransientInput::MinAbs{{{*/
+IssmDouble TransientInput::MinAbs(void){
+
+	IssmDouble time;
+	IssmDouble minabs;
+
+	/*First, recover current time from parameters: */
+	parameters->FindParam(&time,TimeEnum);
+
+	/*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+
+	/*Call input function*/
+	minabs=input->MinAbs();
+			   
+	/*Clean-up and return*/
+	delete input;
+	return minabs;
+}
+/*}}}*/
+/*FUNCTION TransientInput::GetVectorFromInputs{{{*/
+void TransientInput::GetVectorFromInputs(Vector* vector,int* doflist){
+
+	IssmDouble time;
+
+	/*First, recover current time from parameters: */
+	parameters->FindParam(&time,TimeEnum);
+
+	/*Retrieve interpolated values for this time step: */
+	Input* input=GetTimeInput(time);
+		   
+	/*Call input function*/
+	input->GetVectorFromInputs(vector,doflist);
+			   
+	delete input;
+
+} /*}}}*/
+/*FUNCTION TransientInput::GetTimeInput{{{*/
+Input* TransientInput::GetTimeInput(IssmDouble intime){
+
+	int     i,j;
+	IssmDouble  deltat;
+	IssmDouble  alpha1,alpha2;
+	bool    found=false;
+	Input*  input=NULL;
+	Input*  input1=NULL;
+	Input*  input2=NULL;
+
+	/*Ok, we have the time, go through the timesteps, and figure out which interval we 
+	 *fall within. Then interpolate the values on this interval: */
+	if(intimetimesteps[0]){
+		/*get values for the first time: */
+		input=(Input*)((Input*)this->inputs->GetObjectByOffset(0))->copy();
+		found=true;
+	}
+	else if(intime>this->timesteps[this->numtimesteps-1]){
+		/*get values for the last time: */
+		input=(Input*)((Input*)this->inputs->GetObjectByOffset(numtimesteps-1))->copy();
+		found=true;
+	}
+	else{
+		/*Find which interval we fall within: */
+		for(i=0;inumtimesteps;i++){
+			if(intime==this->timesteps[i]){
+				/*We are right on one step time: */
+				input=(Input*)((Input*)this->inputs->GetObjectByOffset(i))->copy();
+				found=true;
+				break; //we are done with the time interpolation.
+			}
+			else{
+				if(this->timesteps[i]timesteps[i+1]){
+					/*ok, we have the interval ]i:i+1[. Interpolate linearly for now: */
+					deltat=this->timesteps[i+1]-this->timesteps[i];
+					alpha2=(intime-this->timesteps[i])/deltat;
+					alpha1=(1.0-alpha2);
+
+					input1=(Input*)this->inputs->GetObjectByOffset(i); 
+					input2=(Input*)this->inputs->GetObjectByOffset(i+1);
+
+					input=(Input*)input1->copy();
+					input->Scale(alpha1);
+					input->AXPY(input2,alpha2);
+
+					found=true;
+					break;
+				}
+				else continue; //keep looking on the next interval
+			}
+		}
+	}
+	if(!found)_error_("did not find time interval on which to interpolate forcing values!");
+
+	/*Assign output pointer*/
+	return input;
+}
+/*}}}*/
+/*FUNCTION TransientInput::Configure{{{*/
+void TransientInput::Configure(Parameters* parameters){
+	this->parameters=parameters;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Inputs/TransientInput.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/TransientInput.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/TransientInput.h	(revision 13395)
@@ -0,0 +1,90 @@
+/*! \file TransientInput.h 
+ *  \brief: header file for transientinput object
+ */
+
+
+#ifndef _TRANSIENTINPUT_H_
+#define _TRANSIENTINPUT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Input.h"
+class GaussTria;
+class Parameters;
+/*}}}*/
+
+class TransientInput: public Input{
+
+	public:
+		int     enum_type;
+		int     numtimesteps;
+		Inputs* inputs;
+		IssmDouble* timesteps;
+		Parameters* parameters; //to find current time.
+
+		/*TransientInput constructors, destructors: {{{*/
+		TransientInput();
+		TransientInput(int enum_type);
+		~TransientInput();
+		void AddTimeInput(Input* input,IssmDouble time);
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		int   Id();
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*TransientInput management: {{{*/
+		int    InstanceEnum();
+		Input* SpawnTriaInput(int* indices);
+		Input* PointwiseDivide(Input* forcingB){_error_("not implemented yet");};
+		Input* PointwiseMin(Input* forcingB){_error_("not implemented yet");};
+		Input* PointwiseMax(Input* forcingB){_error_("not implemented yet");};
+		ElementResult* SpawnResult(int step, IssmDouble time);
+		void Configure(Parameters* parameters);
+		/*}}}*/
+		/*numerics: {{{*/
+		void GetInputValue(bool* pvalue){_error_("not implemented yet");};
+		void GetInputValue(int* pvalue){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time);
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time);
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss ,int index){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss ,int index){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss);
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetInputAverage(IssmDouble* pvalue);
+		void GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void ChangeEnum(int newenumtype);
+
+		void SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters);
+		void ConstrainMin(IssmDouble minimum){_error_("not implemented yet");};
+		void Scale(IssmDouble scale_factor){_error_("not implemented yet");};
+		void ArtificialNoise(IssmDouble min,IssmDouble max){_error_("not implemented yet");};
+		void AXPY(Input* xforcing,IssmDouble scalar){_error_("not implemented yet");};
+		void Constrain(IssmDouble cm_min, IssmDouble cm_max){_error_("not implemented yet");};
+		IssmDouble InfinityNorm(void);
+		IssmDouble Max(void);
+		IssmDouble MaxAbs(void);
+		IssmDouble Min(void);
+		IssmDouble MinAbs(void);
+		void Extrude(void);
+		void VerticallyIntegrate(Input* thickness_forcing){_error_("not supported yet");};
+		void GetVectorFromInputs(Vector* vector,int* doflist);
+		void GetValuesPtr(IssmDouble** pvalues,int* pnum_values){_error_("not supported yet");};
+      void GetTimeValues(IssmDouble* values,IssmDouble time){_error_("not implemented yet");};
+		Input* GetTimeInput(IssmDouble time);
+		/*}}}*/
+
+};
+#endif  /* _TRANSIENTINPUT_H */
Index: /issm/trunk/src/c/classes/objects/Inputs/TriaP1Input.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/TriaP1Input.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/TriaP1Input.cpp	(revision 13395)
@@ -0,0 +1,422 @@
+/*!\file TriaP1Input.c
+ * \brief: implementation of the TriaP1Input object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*TriaP1Input constructors and destructor*/
+/*FUNCTION TriaP1Input::TriaP1Input(){{{*/
+TriaP1Input::TriaP1Input(){
+	return;
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::TriaP1Input(int in_enum_type,IssmDouble* values){{{*/
+TriaP1Input::TriaP1Input(int in_enum_type,IssmDouble* in_values)
+	:TriaRef(1)
+{
+
+	/*Set TriaRef*/
+	this->SetElementType(P1Enum,0);
+	this->element_type=P1Enum;
+
+	/*Set Enum*/
+	enum_type=in_enum_type;
+
+	/*Set values*/
+	values[0]=in_values[0];
+	values[1]=in_values[1];
+	values[2]=in_values[2];
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::~TriaP1Input(){{{*/
+TriaP1Input::~TriaP1Input(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION TriaP1Input::Echo {{{*/
+void TriaP1Input::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::DeepEcho{{{*/
+void TriaP1Input::DeepEcho(void){
+
+	_printLine_("TriaP1Input:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   values: [" << this->values[0] << " " << this->values[1] << " " << this->values[2] << "]");
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::Id{{{*/
+int    TriaP1Input::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION TriaP1Input::MyRank{{{*/
+int    TriaP1Input::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::ObjectEnum{{{*/
+int TriaP1Input::ObjectEnum(void){
+
+	return TriaP1InputEnum;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::copy{{{*/
+Object* TriaP1Input::copy() {
+	
+	return new TriaP1Input(this->enum_type,this->values);
+
+}
+/*}}}*/
+	
+/*TriaP1Input management*/
+/*FUNCTION TriaP1Input::InstanceEnum{{{*/
+int TriaP1Input::InstanceEnum(void){
+
+	return this->enum_type;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::SpawnTriaInput{{{*/
+Input* TriaP1Input::SpawnTriaInput(int* indices){
+
+	/*output*/
+	TriaP1Input* outinput=NULL;
+
+	/*Create new Tria input (copy of current input)*/
+	outinput=new TriaP1Input(this->enum_type,&this->values[0]);
+
+	/*Assign output*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::SpawnResult{{{*/
+ElementResult* TriaP1Input::SpawnResult(int step, IssmDouble time){
+
+	return new TriaP1ElementResult(this->enum_type,this->values,step,time);
+
+}
+/*}}}*/
+
+/*Object functions*/
+/*FUNCTION TriaP1Input::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){{{*/
+void TriaP1Input::GetInputValue(IssmDouble* pvalue,GaussTria* gauss){
+
+	/*Call TriaRef function*/
+	TriaRef::GetInputValue(pvalue,&values[0],gauss);
+
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::GetInputDerivativeValue(IssmDouble* p, IssmDouble* xyz_list, GaussTria* gauss){{{*/
+void TriaP1Input::GetInputDerivativeValue(IssmDouble* p, IssmDouble* xyz_list, GaussTria* gauss){
+
+	/*Call TriaRef function*/
+	TriaRef::GetInputDerivativeValue(p,&values[0],xyz_list,gauss);
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::GetVxStrainRate2d{{{*/
+void TriaP1Input::GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss){
+
+	/*Intermediary*/
+	int       i;
+	const int numnodes=3;
+	IssmDouble B[3][NDOF2*numnodes];
+	IssmDouble velocity[3][NDOF2];
+
+	/*Get B matrix: */
+	GetBMacAyeal(&B[0][0], xyz_list, gauss);
+
+	/*Here, we are computing the strain rate of (vx,0)*/
+	for(i=0;i<3;i++){
+		velocity[i][0]=this->values[i];
+		velocity[i][1]=0.0;
+	}
+	/*Get epsilon(vx) = B*velocity*/
+	MatrixMultiply( &B[0][0],3,NDOF2*numnodes,0,
+				&velocity[0][0],NDOF2*numnodes,1,0,
+				epsilonvx,0);
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::GetVyStrainRate2d{{{*/
+void TriaP1Input::GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss){
+
+	/*Intermediary*/
+	int       i;
+	const int numnodes=3;
+	IssmDouble B[3][NDOF2*numnodes];
+	IssmDouble velocity[3][NDOF2];
+
+	/*Get B matrix: */
+	GetBMacAyeal(&B[0][0], xyz_list, gauss);
+
+	/*Here, we are computing the strain rate of (0,vy)*/
+	for(i=0;i<3;i++){
+		velocity[i][0]=0.0;
+		velocity[i][1]=this->values[i];
+	}
+	/*Get epsilon(vy) = B*velocity*/
+	MatrixMultiply( &B[0][0],3,NDOF2*numnodes,0,
+				&velocity[0][0],NDOF2*numnodes,1,0,
+				epsilonvy,0);
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::ChangeEnum{{{*/
+void TriaP1Input::ChangeEnum(int newenumtype){
+	this->enum_type=newenumtype;
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::GetInputAverage{{{*/
+void TriaP1Input::GetInputAverage(IssmDouble* pvalue){
+	*pvalue=1./3.*(values[0]+values[1]+values[2]);
+}
+/*}}}*/
+
+/*Intermediary*/
+/*FUNCTION TriaP1Input::SquareMin{{{*/
+void TriaP1Input::SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters){
+
+	int i;
+	const int numnodes=3;
+	IssmDouble valuescopy[numnodes];
+	IssmDouble squaremin;
+
+	/*First,  copy values, to process units if requested: */
+	for(i=0;ivalues[i];
+
+	/*Process units if requested: */
+	if(process_units)UnitConversion(&valuescopy[0],numnodes,IuToExtEnum,enum_type);
+
+	/*Now, figure out minimum of valuescopy: */
+	squaremin=pow(valuescopy[0],2);
+	for(i=1;inorm) norm=fabs(values[i]);
+	return norm;
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::Max{{{*/
+IssmDouble TriaP1Input::Max(void){
+
+	const int numnodes=3;
+	IssmDouble    max=values[0];
+
+	for(int i=1;imax) max=values[i];
+	}
+	return max;
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::MaxAbs{{{*/
+IssmDouble TriaP1Input::MaxAbs(void){
+
+	const int numnodes=3;
+	IssmDouble    max=fabs(values[0]);
+
+	for(int i=1;imax) max=fabs(values[i]);
+	}
+	return max;
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::Min{{{*/
+IssmDouble TriaP1Input::Min(void){
+
+	const int numnodes=3;
+	IssmDouble    min=values[0];
+
+	for(int i=1;iObjectEnum()){
+
+		case TriaP1InputEnum :
+			for(i=0;ivalues[i]=this->values[i]+scalar*xtriavertexinput->values[i];
+			return;
+
+		default :
+			_error_("not implemented yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::Constrain{{{*/
+void TriaP1Input::Constrain(IssmDouble cm_min, IssmDouble cm_max){
+
+	int i;
+	const int numnodes=3;
+		
+	if(!xIsNan(cm_min)) for(i=0;ivalues[i]values[i]=cm_min;
+	if(!xIsNan(cm_max)) for(i=0;ivalues[i]>cm_max)this->values[i]=cm_max;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::GetVectorFromInputs{{{*/
+void TriaP1Input::GetVectorFromInputs(Vector* vector,int* doflist){
+
+	const int numvertices=3;
+	vector->SetValues(numvertices,doflist,this->values,INS_VAL);
+
+} /*}}}*/
+/*FUNCTION TriaP1Input::GetValuesPtr{{{*/
+void TriaP1Input::GetValuesPtr(IssmDouble** pvalues,int* pnum_values){
+
+	*pvalues=this->values;
+	if(pnum_values)*pnum_values=3;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::PointwiseMin{{{*/
+Input* TriaP1Input::PointwiseMin(Input* inputB){
+
+	/*Ouput*/
+	TriaP1Input* outinput=NULL;
+
+	/*Intermediaries*/
+	int               i;
+	TriaP1Input *xinputB     = NULL;
+	int               B_numvalues;
+	const int         numnodes    = 3;
+	IssmDouble            minvalues[numnodes];
+
+	/*Check that inputB is of the same type*/
+	if (inputB->ObjectEnum()!=TriaP1InputEnum) _error_("Operation not permitted because inputB is of type " << EnumToStringx(inputB->ObjectEnum()));
+	xinputB=(TriaP1Input*)inputB;
+
+	/*Create point wise min*/
+	for(i=0;ivalues[i] > xinputB->values[i]) minvalues[i]=xinputB->values[i];
+		else minvalues[i]=this->values[i];
+	}
+
+	/*Create new Tria vertex input (copy of current input)*/
+	outinput=new TriaP1Input(this->enum_type,&minvalues[0]);
+
+	/*Return output pointer*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::PointwiseMax{{{*/
+Input* TriaP1Input::PointwiseMax(Input* inputB){
+
+	/*Ouput*/
+	TriaP1Input* outinput=NULL;
+
+	/*Intermediaries*/
+	int               i;
+	TriaP1Input *xinputB     = NULL;
+	int               B_numvalues;
+	const int         numnodes    = 3;
+	IssmDouble            maxvalues[numnodes];
+
+	/*Check that inputB is of the same type*/
+	if (inputB->ObjectEnum()!=TriaP1InputEnum) _error_("Operation not permitted because inputB is of type " << EnumToStringx(inputB->ObjectEnum()));
+	xinputB=(TriaP1Input*)inputB;
+
+	/*Create point wise max*/
+	for(i=0;ivalues[i] < xinputB->values[i]) maxvalues[i]=xinputB->values[i];
+		else maxvalues[i]=this->values[i];
+	}
+
+	/*Create new Tria vertex input (copy of current input)*/
+	outinput=new TriaP1Input(this->enum_type,&maxvalues[0]);
+
+	/*Return output pointer*/
+	return outinput;
+
+}
+/*}}}*/
+/*FUNCTION TriaP1Input::Configure{{{*/
+void TriaP1Input::Configure(Parameters* parameters){
+	/*do nothing: */
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Inputs/TriaP1Input.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Inputs/TriaP1Input.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Inputs/TriaP1Input.h	(revision 13395)
@@ -0,0 +1,86 @@
+/*! \file TriaP1Input.h 
+ *  \brief: header file for TriaP1Input object
+ */
+
+
+#ifndef _TRIAP1INPUT_H_
+#define _TRIAP1INPUT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Input.h"
+#include "../Elements/TriaRef.h"
+class GaussTria;
+/*}}}*/
+
+class TriaP1Input: public Input,public TriaRef{
+
+	public:
+		/*just hold 3 values for 3 vertices: */
+		int    enum_type;
+		IssmDouble values[3];
+
+		/*TriaP1Input constructors, destructors: {{{*/
+		TriaP1Input();
+		TriaP1Input(int enum_type,IssmDouble* values);
+		~TriaP1Input();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*TriaP1Input management: {{{*/
+		int   InstanceEnum();
+		Input* SpawnTriaInput(int* indices);
+		Input* PointwiseDivide(Input* inputB){_error_("not implemented yet");};
+		Input* PointwiseMin(Input* inputB);
+		Input* PointwiseMax(Input* inputB);
+		ElementResult* SpawnResult(int step, IssmDouble time);
+		void AddTimeValues(IssmDouble* values,int step,IssmDouble time){_error_("not supported yet");};
+		void Configure(Parameters* parameters);
+		/*}}}*/
+		/*numerics: {{{*/
+		void GetInputValue(bool* pvalue){_error_("not implemented yet");}
+		void GetInputValue(int* pvalue){_error_("not implemented yet");}
+		void GetInputValue(IssmDouble* pvalue){_error_("not implemented yet");}
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss);
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,IssmDouble time){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussTria* gauss ,int index){_error_("not implemented yet");};
+		void GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,int index){_error_("not implemented yet");};
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussTria* gauss);
+		void GetInputDerivativeValue(IssmDouble* derivativevalues, IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetInputAverage(IssmDouble* pvalue);
+		void GetVxStrainRate2d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussTria* gauss);
+		void GetVyStrainRate2d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussTria* gauss);
+		void GetVxStrainRate3d(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3d(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVzStrainRate3d(IssmDouble* epsilonvz,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVxStrainRate3dPattyn(IssmDouble* epsilonvx,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void GetVyStrainRate3dPattyn(IssmDouble* epsilonvy,IssmDouble* xyz_list, GaussPenta* gauss){_error_("not implemented yet");};
+		void ChangeEnum(int newenumtype);
+
+		void SquareMin(IssmDouble* psquaremin, bool process_units,Parameters* parameters);
+		void ConstrainMin(IssmDouble minimum);
+		void Scale(IssmDouble scale_factor);
+		void ArtificialNoise(IssmDouble min,IssmDouble max);
+		void AXPY(Input* xinput,IssmDouble scalar);
+		void Constrain(IssmDouble cm_min, IssmDouble cm_max);
+		IssmDouble InfinityNorm(void);
+		IssmDouble Max(void);
+		IssmDouble MaxAbs(void);
+		IssmDouble Min(void);
+		IssmDouble MinAbs(void);
+		void Extrude(void){_error_("not supported yet");};
+		void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");};
+		void GetVectorFromInputs(Vector* vector,int* doflist);
+		void GetValuesPtr(IssmDouble** pvalues,int* pnum_values);
+		/*}}}*/
+
+};
+#endif  /* _TRIAP1INPUT_H */
Index: /issm/trunk/src/c/classes/objects/KML/KMLFileReadUtils.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KMLFileReadUtils.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KMLFileReadUtils.cpp	(revision 13395)
@@ -0,0 +1,724 @@
+/*!\file KMLFileUtils.cpp
+ * \brief: utilities for kml file reading.
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*FUNCTION  KMLFileToken(FILE* fid,int* pncom=NULL,char*** ppcom=NULL) {{{*/
+char* KMLFileToken(FILE* fid,
+				   int* pncom=NULL,char*** ppcom=NULL){
+
+/*  get the next token (tag or field) in the file  */
+
+	bool    inew=1,itag=0,ifield=0;
+	int     c;
+	int     ibuf=0,buflen=1024,bufblk=1024;
+	char    *buffer=NULL,*bufferc=NULL,**pcom2=NULL;
+
+	buffer=xNew(buflen);
+	buffer[0]='\0';
+
+/*  read kml file character-by-character  */
+
+//  note that fgets includes newline
+//	fgets(buffer,buflen,fid);
+
+	while ((c=getc(fid)) != EOF) {
+		/*  ignore leading blanks  */
+		if (inew && isspace(c))
+			continue;
+
+		/*  distinguish between tag or field  */
+		if (!itag && !ifield) {
+
+			/*  distinguish between tag or comment  */
+			if (c == '<') {
+				ungetc(c,fid);
+				if (!(bufferc=KMLFileTokenComment(fid))) {
+					c=getc(fid);
+					itag=1;
+				}
+				else {
+					if (pncom && ppcom) {
+						(*pncom)++;
+						pcom2=xNew(*pncom);
+						memcpy(pcom2,*ppcom,(*pncom-1)*sizeof(char*));
+						xDelete(*ppcom);
+						*ppcom=pcom2;
+						pcom2=NULL;
+//						*ppcom=(char **) xrealloc(*ppcom,*pncom*sizeof(char*));
+						(*ppcom)[*pncom-1]=bufferc;
+					}
+					else
+						xDelete(bufferc);
+					inew=1;
+					continue;
+				}
+			}
+			else
+				ifield=1;
+			inew=0;
+			KMLFileTokenBuffer(&buffer,&ibuf,&buflen,
+							   c,
+							   bufblk);
+		}
+
+		/*  accumulate tag, not including newlines  */
+		else if (itag) {
+			if (c != '\n') {
+				inew=0;
+				KMLFileTokenBuffer(&buffer,&ibuf,&buflen,
+								   c,
+								   bufblk);
+				if (c == '>')
+					break;
+			}
+			else
+				inew=1;
+		}
+
+		/*  accumulate field, including newlines  */
+		else if (ifield) {
+			/*  distinguish between another tag or comment  */
+			if (c == '<') {
+				ungetc(c,fid);
+				if (!(bufferc=KMLFileTokenComment(fid)))
+					break;
+				else
+					if (pncom && ppcom) {
+						(*pncom)++;
+						pcom2=xNew(*pncom);
+						memcpy(pcom2,*ppcom,(*pncom-1)*sizeof(char*));
+						xDelete(*ppcom);
+						*ppcom=pcom2;
+						pcom2=NULL;
+//						*ppcom=(char **) xrealloc(*ppcom,*pncom*sizeof(char*));
+						(*ppcom)[*pncom-1]=bufferc;
+					}
+					else
+						xDelete(bufferc);
+			}
+			else {
+				inew=0;
+				KMLFileTokenBuffer(&buffer,&ibuf,&buflen,
+								   c,
+								   bufblk);
+				if (c == '\n')
+					inew=1;
+			}
+		}
+
+	}
+
+/*  remove trailing blanks or newline  */
+
+	while (ibuf > 0)
+		if (isspace(buffer[ibuf-1]))
+			ibuf--;
+		else {
+			buffer[ibuf]='\0';
+			break;
+		}
+
+//	if      (itag)
+//		_pprintLine_("tag buffer (length=" << ibuf << "):");
+//	else if (ifield)
+//		_pprintLine_("field buffer (length=" << ibuf << "):");
+//	_pprintLine_(buffer);
+
+	if (!ibuf)
+		xDelete(buffer);
+
+	return(buffer);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenComment(FILE* fid) {{{*/
+char* KMLFileTokenComment(FILE* fid){
+
+/*  check for comment in the file and read it  */
+
+	bool    inew=1;
+	int     i;
+	int     c;
+	int     ibuf=0,buflen=1024,bufblk=1024;
+	char*   buffer=NULL;
+
+	buffer=xNew(buflen);
+	buffer[0]='\0';
+
+/*  read kml file character-by-character  */
+
+	while ((c=getc(fid)) != EOF) {
+		/*  ignore leading blanks  */
+		if (inew && isspace(c))
+			continue;
+
+		inew=0;
+		KMLFileTokenBuffer(&buffer,&ibuf,&buflen,
+						   c,
+						   bufblk);
+
+		/*  check for comment  */
+		if (ibuf <= 4) {
+			if ((ibuf == 1 && buffer[0] != '<') ||
+				(ibuf == 2 && buffer[1] != '!') ||
+				(ibuf == 3 && buffer[2] != '-') ||
+				(ibuf == 4 && buffer[3] != '-')) {
+				for (i=ibuf-1; i>=0; i--)
+					ungetc(buffer[i],fid);
+				xDelete(buffer);
+				return(buffer);
+			}
+		}
+
+		/*  accumulate comment, including newlines  */
+		else
+			if (buffer[ibuf-3]=='-' && buffer[ibuf-2]=='-' && buffer[ibuf-1]=='>')
+				break;
+	}
+
+/*  remove trailing blanks or newline  */
+
+	while (ibuf > 0)
+		if (isspace(buffer[ibuf-1]))
+			ibuf--;
+		else {
+			buffer[ibuf]='\0';
+			break;
+		}
+
+//	_pprintLine_("comment buffer (length=" << ibuf << "):");
+//	_pprintLine_(buffer);
+
+	if (!ibuf)
+		xDelete(buffer);
+
+	return(buffer);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenBuffer {{{*/
+void KMLFileTokenBuffer(char** pbuffer,int* pibuf,int* pbuflen,
+						int c,
+						int bufblk){
+
+/*  add the specified character to the token buffer  */
+
+	char*   buffer2=NULL;
+
+/*  check buffer length and realloc if necessary  */
+
+	if (*pibuf+2 > *pbuflen) {
+		*pbuflen+=bufblk;
+		buffer2=xNew(*pbuflen);
+		memcpy(buffer2,*pbuffer,(*pbuflen-bufblk)*sizeof(char));
+		xDelete(*pbuffer);
+		*pbuffer=buffer2;
+		buffer2=NULL;
+//		*pbuffer=(char *) xrealloc(*pbuffer,*pbuflen*sizeof(char));
+	}
+
+/*  add character and terminator  */
+
+	(*pbuffer)[(*pibuf)++]=c;
+	(*pbuffer)[ *pibuf   ]='\0';
+
+	return;
+}
+/*}}}*/
+/*FUNCTION  KMLFileTagName {{{*/
+char* KMLFileTagName(char* pname,
+					 char* ktag){
+
+	return(KMLFileTagName(pname,NULL,0,
+						  ktag));
+}
+/*}}}*/
+/*FUNCTION  KMLFileTagName {{{*/
+char* KMLFileTagName(char* pname,int *m,int maxlen,
+					 char* ktag){
+
+/*  for the given tag buffer, read and store the name  */
+
+	char*   ktagi;
+	char*   ktokn;
+
+	if (strncmp(&ktag[0],"<"        ,1) || strncmp(&ktag[strlen(ktag)-1],">",1))
+		_error_("KMLFileTagName -- Missing tag delimiters in " << ktag << ".\n");
+
+/*  strtok modifies ktag, so work on copy  */
+
+	ktagi=xNew(strlen(ktag)+1);
+	memcpy(ktagi,ktag,(strlen(ktag)+1)*sizeof(char));
+
+/*  skip opening delimeter and find subsequent blank or closing delimiter  */
+
+	ktokn=strtok(ktagi,"< >");
+//	_pprintLine_("KMLFileTagName -- initial token=\"" << ktokn << "\".");
+
+	if (!pname) {
+		if (maxlen)
+			pname=xNew(maxlen       +1);
+		else
+			pname=xNew(strlen(ktokn)+1);
+	}
+
+	if (maxlen && (maxlen < strlen(ktokn))) {
+		_pprintLine_("KMLFileTagName -- string field too short for " << ktag << ".");
+		_pprintLine_("KMLFileTagName -- \"" << ktokn << "\" truncated to " << maxlen << " characters.");
+		strncpy(pname,ktokn,maxlen);
+	}
+	else
+		memcpy(pname,ktokn,(strlen(ktokn)+1)*sizeof(char));
+
+	xDelete(ktagi);
+
+	if (m)
+		*m=strlen(pname);
+
+	return(pname);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTagAttrib {{{*/
+int KMLFileTagAttrib(KML_Object* kobj,
+					 char* ktag){
+
+/*  for the given tag buffer, read and store the attributes  */
+
+	char*   ktagi;
+	char*   ktokn;
+	char*   ktokv;
+	char    quote[]={'\"','\0'};
+	int     isolo=0;
+
+/*  strtok modifies ktag, so work on copy  */
+
+	ktagi=xNew(strlen(ktag)+1);
+	memcpy(ktagi,ktag,(strlen(ktag)+1)*sizeof(char));
+
+/*  loop through tag to find all attributes  */
+
+	/*  return first non blank and move past subsequent blank  */
+	ktokn=strtok(ktagi," ");
+//	_pprintLine_("KMLFileTagAttrib -- initial token=\"" << ktokn << "\".");
+
+	/*  return next non " =?/>" and move past subsequent " =?/>"  */
+	while (ktokn=strtok(NULL," =?/>")) {
+
+		/*  return next non quote and move past subsequent quote  */
+		ktokv=strtok(NULL,quote);
+//		_pprintLine_("KMLFileTagAttrib -- attribute " << ktokn << "=\"" << ktokv << "\".");
+
+/*  add the attribute to the dataset  */
+
+		if (kobj)
+			kobj->AddAttrib(ktokn,ktokv);
+	}
+
+	xDelete(ktagi);
+
+/*  check for xml declaration, dtd declaration, or solo tag  */
+
+	if ((!strncmp(&ktag[0],"",2)) ||
+		(!strncmp(&ktag[0],"",1)) ||
+		(!strncmp(&ktag[0],"<"        ,1) && !strncmp(&ktag[strlen(ktag)-2],"/>",2)))
+		isolo=1;
+//	_pprintLine_("KMLFileTagAttrib -- isolo=" << isolo << ".");
+
+	return(isolo);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenParse {{{*/
+int KMLFileTokenParse(int* pival,
+					  char* ktag,
+					  FILE* fid){
+
+	char*   kstr;
+
+/*  get next token and convert to appropriate format  */
+
+	if (!(kstr=KMLFileToken(fid,
+							NULL,NULL)) ||
+		(kstr[0] == '<'))
+		_error_("KMLFileTokenParse -- Missing integer field for " << ktag << ".\n");
+
+	sscanf(kstr,"%d",pival);
+	xDelete(kstr);
+
+/*  get additional token and compare to closing tag  */
+
+	if (ktag)
+		if (!(kstr=KMLFileToken(fid,
+								NULL,NULL)) ||
+			(kstr[0] != '<') ||
+			(kstr[1] != '/') ||
+			(strncmp(&(kstr[2]),&(ktag[1]),strlen(ktag)-1)))
+		  {_error_("KMLFileTokenParse -- Missing closing tag for " << ktag << ".\n");}
+		else
+			xDelete(kstr);
+
+//	_pprintLine_("KMLFileTokenParse -- " << ktag << "=" << *pival << ".");
+
+	return(0);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenParse {{{*/
+int KMLFileTokenParse(bool* pbval, char* ktag, FILE* fid){
+
+	int     ival;
+	char*   kstr;
+
+/*  get next token and convert to appropriate format  */
+
+	if (!(kstr=KMLFileToken(fid,
+							NULL,NULL)) ||
+		(kstr[0] == '<'))
+	  {_error_("KMLFileTokenParse -- Missing bool field for " << ktag << ".\n");}
+
+	sscanf(kstr,"%d",&ival);
+	*pbval=(bool)ival;
+	xDelete(kstr);
+
+/*  get additional token and compare to closing tag  */
+
+	if (ktag)
+		if (!(kstr=KMLFileToken(fid,
+								NULL,NULL)) ||
+			(kstr[0] != '<') ||
+			(kstr[1] != '/') ||
+			(strncmp(&(kstr[2]),&(ktag[1]),strlen(ktag)-1)))
+		  {_error_("KMLFileTokenParse -- Missing closing tag for " << ktag << ".\n");}
+		else
+			xDelete(kstr);
+
+//	_pprintLine_("KMLFileTokenParse -- " << ktag << "=" << (*pbval ? "true" : "false") << ".");
+
+	return(0);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenParse {{{*/
+char* KMLFileTokenParse(char* pstr,
+						char* ktag,
+						FILE* fid){
+
+	return(KMLFileTokenParse(pstr,NULL,0,
+							 ktag,
+							 fid));
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenParse {{{*/
+char* KMLFileTokenParse(char* pstr,int *m,int maxlen,
+						char* ktag,
+						FILE* fid){
+
+	char*   kstr;
+
+/*  get next token and allocate if necessary  */
+
+	if (!(kstr=KMLFileToken(fid,
+							NULL,NULL)) ||
+		(kstr[0] == '<'))
+		_error_("KMLFileTokenParse -- Missing string field for " << ktag << ".\n");
+
+	if (!pstr) {
+		if (maxlen)
+			pstr=xNew(maxlen      +1);
+		else
+			pstr=xNew(strlen(kstr)+1);
+	}
+
+	if (maxlen && (maxlen < strlen(kstr))) {
+		_pprintLine_("KMLFileTokenParse -- string field too short for " << ktag << ".");
+		_pprintLine_("KMLFileTokenParse -- \"" << kstr << "\" truncated to " << maxlen << " characters.");
+		strncpy(pstr,kstr,maxlen);
+	}
+	else
+		memcpy(pstr,kstr,(strlen(kstr)+1)*sizeof(char));
+
+	xDelete(kstr);
+
+	if (m)
+		*m=strlen(pstr);
+
+/*  get additional token and compare to closing tag  */
+
+	if (ktag)
+		if (!(kstr=KMLFileToken(fid,
+								NULL,NULL)) ||
+			(kstr[0] != '<') ||
+			(kstr[1] != '/') ||
+			(strncmp(&(kstr[2]),&(ktag[1]),strlen(ktag)-1)))
+		  {_error_("KMLFileTokenParse -- Missing closing tag for " << ktag << ".\n");}
+		else
+			xDelete(kstr);
+
+//	_pprintLine_("KMLFileTokenParse -- " << ktag << "=\"" << pstr << "\".");
+
+	return(pstr);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenParse {{{*/
+int KMLFileTokenParse(float* pfval,
+					  char* ktag,
+					  FILE* fid){
+
+	char*   kstr;
+
+/*  get next token and convert to appropriate format  */
+
+	if (!(kstr=KMLFileToken(fid,
+							NULL,NULL)) ||
+		(kstr[0] == '<'))
+	  {_error_("KMLFileTokenParse -- Missing integer field for " << ktag << ".\n");}
+
+	sscanf(kstr,"%g",pfval);
+	xDelete(kstr);
+
+/*  get additional token and compare to closing tag  */
+
+	if (ktag)
+		if (!(kstr=KMLFileToken(fid,
+								NULL,NULL)) ||
+			(kstr[0] != '<') ||
+			(kstr[1] != '/') ||
+			(strncmp(&(kstr[2]),&(ktag[1]),strlen(ktag)-1)))
+		  {_error_("KMLFileTokenParse -- Missing closing tag for " << ktag << ".\n");}
+		else
+			xDelete(kstr);
+
+//	_pprintLine_("KMLFileTokenParse -- " << ktag << "=" << *pfval << ".");
+
+	return(0);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenParse {{{*/
+int KMLFileTokenParse(double* pdval,
+					  char* ktag,
+					  FILE* fid){
+
+	char*   kstr;
+
+/*  get next token and convert to appropriate format  */
+
+	if (!(kstr=KMLFileToken(fid,
+							NULL,NULL)) ||
+		(kstr[0] == '<'))
+		_error_("KMLFileTokenParse -- Missing integer field for " << ktag << ".\n");
+
+	sscanf(kstr,"%lg",pdval);
+	xDelete(kstr);
+
+/*  get additional token and compare to closing tag  */
+
+	if (ktag)
+		if (!(kstr=KMLFileToken(fid,
+								NULL,NULL)) ||
+			(kstr[0] != '<') ||
+			(kstr[1] != '/') ||
+			(strncmp(&(kstr[2]),&(ktag[1]),strlen(ktag)-1)))
+		  {_error_("KMLFileTokenParse -- Missing closing tag for " << ktag << ".\n");}
+		else
+			xDelete(kstr);
+
+//	_pprintLine_("KMLFileTokenParse -- " << ktag << "=" << *pdval << ".");
+
+	return(0);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenParse {{{*/
+int KMLFileTokenParse(double **pdval,int* m,int maxlen,
+					  char* ktag,
+					  FILE* fid){
+
+	int     i=-1,j;
+	char*   kstr;
+	char*   ktok;
+	double* dval2=NULL;
+	char    delim[]={' ',',','\f','\n','\r','\t','\v','\0'};
+
+/*  get next token and allocate if necessary  */
+
+	if (!(kstr=KMLFileToken(fid,
+							NULL,NULL)) ||
+		(kstr[0] == '<'))
+		_error_("KMLFileTokenParse -- Missing double [m] field for " << ktag << ".\n");
+
+	if (!*pdval)
+		if (maxlen)
+			*pdval=xNew(maxlen            );
+		else
+			*pdval=xNew((strlen(kstr)+1)/2);
+
+/*  loop through string to get all values  */
+
+	ktok=strtok(kstr,delim);
+	while (ktok) {
+		i++;
+		if (maxlen && (maxlen < i+1))
+			_error_("KMLFileTokenParse -- Double [m] field too short for " << ktag << ".\n");
+		sscanf(ktok,"%lg",&((*pdval)[i]));
+		ktok=strtok(NULL,delim);
+	}
+	xDelete(kstr);
+
+	if (!maxlen)
+		dval2=xNew(i+1);
+		memcpy(dval2,*pdval,(i+1)*sizeof(double));
+		xDelete(*pdval);
+		*pdval=dval2;
+		dval2=NULL;
+//		*pdval=(double *) xrealloc(*pdval,(i+1)*sizeof(double));
+
+	if (m)
+		*m=i+1;
+
+/*  get additional token and compare to closing tag  */
+
+	if (ktag)
+		if (!(kstr=KMLFileToken(fid,
+								NULL,NULL)) ||
+			(kstr[0] != '<') ||
+			(kstr[1] != '/') ||
+			(strncmp(&(kstr[2]),&(ktag[1]),strlen(ktag)-1)))
+		  {_error_("KMLFileTokenParse -- Missing closing tag for " << ktag << ".\n");}
+		else
+			xDelete(kstr);
+
+//	_pprintLine_("KMLFileTokenParse -- " << ktag << "=...");
+//	for (j=0; j<=i; j++)
+//		_pprintLine_("   [" << j << "]: " << (*pdval)[j] << "g");
+
+	return(0);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTokenParse {{{*/
+int KMLFileTokenParse(double **pdval,int* m,int n,int maxlen,
+					  char* ktag,
+					  FILE* fid){
+
+	int     i=-1,j=-1;
+	char*   kstr;
+	char*   ktok;
+	double* dval2=NULL;
+	char    delim[]={' ',',','\f','\n','\r','\t','\v','\0'};
+
+/*  get next token and allocate if necessary  */
+
+	if (!(kstr=KMLFileToken(fid,
+							NULL,NULL)) ||
+		(kstr[0] == '<'))
+		_error_("KMLFileTokenParse -- Missing double [m x n] field for " << ktag << ".\n");
+
+	if (!*pdval)
+		if (maxlen)
+			*pdval=xNew(maxlen*n          );
+		else
+			*pdval=xNew((strlen(kstr)+1)/2);
+
+/*  loop through string to get all values  */
+
+	ktok=strtok(kstr,delim);
+	while (ktok) {
+		i++;
+		if (maxlen && (maxlen*n < i+1))
+			_error_("KMLFileTokenParse -- Double [m x n] field too short for " << ktag << ".\n");
+		j=(j+1) % n;
+		sscanf(ktok,"%lg",&((*pdval)[i]));
+		ktok=strtok(NULL,delim);
+	}
+	xDelete(kstr);
+
+	if (!maxlen)
+		dval2=xNew((i+1)*n);
+		memcpy(dval2,*pdval,((i+1)*n)*sizeof(double));
+		xDelete(*pdval);
+		*pdval=dval2;
+		dval2=NULL;
+//		*pdval=(double *) xrealloc(*pdval,((i+1)*n)*sizeof(double));
+
+	if (m)
+		*m=((i+1)+(n-1))/n;
+
+	if ((i+1) % n)
+		_pprintLine_("KMLFileTokenParse -- Double [m x n] field for " << ktag << " does not have multiple of n values.");
+
+/*  get additional token and compare to closing tag  */
+
+	if (ktag)
+		if (!(kstr=KMLFileToken(fid,
+								NULL,NULL)) ||
+			(kstr[0] != '<') ||
+			(kstr[1] != '/') ||
+			(strncmp(&(kstr[2]),&(ktag[1]),strlen(ktag)-1)))
+		  {_error_("KMLFileTokenParse -- Missing closing tag for " << ktag << ".\n");}
+		else
+			xDelete(kstr);
+
+//	_pprintLine_("KMLFileTokenParse -- " << ktag << "=...");
+//	for (j=0; j<=i; j++)
+//		_pprintLine_("   [" << j << "]: " << (*pdval)[j] << "g");
+
+	return(0);
+}
+/*}}}*/
+/*FUNCTION  KMLFileTagSkip {{{*/
+int KMLFileTagSkip(char* ktag,
+				   FILE* fid){
+
+	char*   kstr;
+
+/*  note that tags of the same type can be nested inside each other, so for each
+	opening tag, must find corresponding closing tag  */
+
+	_pprintLine_("KMLFileTagSkip -- input tag " << ktag << ".");
+
+/*  if next token is a closing tag, compare to input  */
+
+	while (kstr=KMLFileToken(fid,
+							 NULL,NULL)) {
+		if      ((kstr[0] == '<') &&
+				 (kstr[1] == '/') &&
+				 (!strncmp(&(kstr[2]),&(ktag[1]),(strcspn(ktag," >")-1)/sizeof(char)))) {
+			_pprintLine_("KMLFileTagSkip -- closing tag " << kstr << ".");
+			xDelete(kstr);
+			return(0);
+		}
+
+/*  if next token is an opening tag, call recursively  */
+
+		else if ((kstr[0] == '<') &&
+				 (kstr[1] != '/')) {
+			_pprintLine_("KMLFileTagSkip -- opening tag " << kstr << ".");
+			KMLFileTagSkip(kstr,
+						   fid);
+		}
+
+/*  if next token is a closing tag, error out  */
+
+		else if ((kstr[0] == '<') &&
+				 (kstr[1] == '/')) {
+			_error_("KMLFileTagSkip -- Unexpected closing tag " << kstr << ".\n");
+		}
+
+		xDelete(kstr);
+	}
+
+	_error_("KMLFileTokenParse -- Corresponding closing tag for " << ktag << " not found.\n");
+
+	return(0);
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KMLFileReadUtils.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KMLFileReadUtils.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KMLFileReadUtils.h	(revision 13395)
@@ -0,0 +1,57 @@
+/*!\file:  KMLFileReadUtils.h
+ * \brief: header file for kml file reading utilities.
+ */ 
+
+#ifndef _KMLFILEREADUTILS_H
+#define _KMLFILEREADUTILS_H
+
+/*Headers:{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "../Object.h"
+/*}}}*/
+
+/* local prototypes: */
+char* KMLFileToken(FILE* fid,
+				   int* pncom,char*** ppcom);
+char* KMLFileTokenComment(FILE* fid);
+void KMLFileTokenBuffer(char** pbuffer,int* pibuf,int* pbuflen,
+						int c,
+						int bufblk);
+char* KMLFileTagName(char* pname,
+					 char* ktag);
+char* KMLFileTagName(char* pname,int *m,int maxlen,
+					 char* ktag);
+int KMLFileTagAttrib(KML_Object* kobj,
+					 char* ktag);
+int KMLFileTokenParse(int* pival,
+					  char* ktag,
+					  FILE* fid);
+int KMLFileTokenParse(bool* pbval,
+					  char* ktag,
+					  FILE* fid);
+char* KMLFileTokenParse(char* pstr,
+						char* ktag,
+						FILE* fid);
+char* KMLFileTokenParse(char* pstr,int *m,int maxlen,
+						char* ktag,
+						FILE* fid);
+int KMLFileTokenParse(float* pfval,
+					  char* ktag,
+					  FILE* fid);
+int KMLFileTokenParse(double* pdval,
+					  char* ktag,
+					  FILE* fid);
+int KMLFileTokenParse(double **pdval,int* m,int maxlen,
+					  char* ktag,
+					  FILE* fid);
+int KMLFileTokenParse(double **pdval,int* m,int n,int maxlen,
+					  char* ktag,
+					  FILE* fid);
+int KMLFileTagSkip(char* ktag,
+				   FILE* fid);
+
+#endif  /* _KMLFILEREADUTILS_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Attribute.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Attribute.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Attribute.cpp	(revision 13395)
@@ -0,0 +1,133 @@
+/*!\file KML_Attribute.cpp
+ * \brief: implementation of the kml_attribute object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Attribute::KML_Attribute(){{{*/
+KML_Attribute::KML_Attribute(){
+
+	name      =NULL;
+	value     =NULL;
+
+}
+/*}}}*/
+/*FUNCTION KML_Attribute::~KML_Attribute(){{{*/
+KML_Attribute::~KML_Attribute(){
+
+	if (name      ) xDelete(name);
+	if (value     ) xDelete(value);
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Attribute::Echo {{{*/
+void  KML_Attribute::Echo(){
+
+	int   i;
+	bool  flag=true;
+
+	if(flag) _pprintString_("    ");
+	for (i=0;i<10-strlen(name);i++)
+		if(flag) _pprintString_(" ");
+	if(flag) _pprintLine_(name << ": \"" << value << "\"");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Attribute::DeepEcho {{{*/
+void  KML_Attribute::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Attribute::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Attribute::DeepEcho {{{*/
+void  KML_Attribute::DeepEcho(const char* indent){
+
+	int   i;
+	bool  flag=true;
+
+	if(flag) _pprintString_(indent << "    ");
+	for (i=0;i<10-strlen(name);i++)
+		if(flag) _pprintString_(" ");
+	if(flag) _pprintLine_(name << ": \"" << value << "\"");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Attribute::Write {{{*/
+void  KML_Attribute::Write(FILE* filout,const char* indent){
+
+//  attributes always written in keyword line of kml_object
+
+	fprintf(filout,"%s%s=\"%s\"",indent,name,value);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Attribute::Read {{{*/
+void  KML_Attribute::Read(FILE* fid,char* kstr){
+
+//  attributes always read in keyword line of kml_object
+
+	;
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Attribute::Alloc {{{*/
+void  KML_Attribute::Alloc(const char* namei,const char* valuei){
+
+	name =xNew(strlen(namei )+1);
+	memcpy(name,namei,(strlen(namei)+1)*sizeof(char));
+
+	value=xNew(strlen(valuei)+1);
+	memcpy(value,valuei,(strlen(valuei)+1)*sizeof(char));
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Attribute::Add {{{*/
+void  KML_Attribute::Add(DataSet* attrib){
+
+	attrib->AddObject((Object*)this);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Attribute::Get {{{*/
+void  KML_Attribute::Get(char** pvalueo,char* deflt){
+
+	if (!value || !strlen(value)) {
+		*pvalueo=xNew(strlen(deflt)+1);
+		memcpy(*pvalueo,deflt,(strlen(deflt)+1)*sizeof(char));
+	}
+	else {
+		*pvalueo=xNew(strlen(value)+1);
+		memcpy(*pvalueo,value,(strlen(value)+1)*sizeof(char));
+	}
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Attribute.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Attribute.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Attribute.h	(revision 13395)
@@ -0,0 +1,50 @@
+/*! \file KML_Attribute.h 
+ *  \brief: header file for kml_attribute object
+ */
+
+#ifndef _KML_ATTRIBUTE_H_
+#define _KML_ATTRIBUTE_H_
+
+/*Headers:{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "../Object.h"
+class DataSet;
+/*}}}*/
+
+class KML_Attribute: public Object {
+
+	public:
+
+		char* name;
+		char* value;
+
+		/*KML_Attribute constructors, destructors {{{*/
+		KML_Attribute();
+		~KML_Attribute();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		virtual void  Echo();
+		virtual void  DeepEcho();
+		virtual void  DeepEcho(const char* indent);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+		/*virtual functions: */
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		void  Alloc(const char* namei,const char* valuei);
+		void  Add(DataSet* attrib);
+		void  Get(char** pvalueo,char* deflt);
+
+};
+#endif  /* _KML_ATTRIBUTE_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_ColorStyle.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_ColorStyle.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_ColorStyle.cpp	(revision 13395)
@@ -0,0 +1,109 @@
+/*!\file KML_ColorStyle.cpp
+ * \brief: implementation of the kml_colorstyle abstract object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_ColorStyle::KML_ColorStyle(){{{*/
+KML_ColorStyle::KML_ColorStyle(){
+
+	strcpy(color     ,"ffffffff");
+	strcpy(colormode ,"normal");
+
+}
+/*}}}*/
+/*FUNCTION KML_ColorStyle::~KML_ColorStyle(){{{*/
+KML_ColorStyle::~KML_ColorStyle(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_ColorStyle::Echo {{{*/
+void  KML_ColorStyle::Echo(){
+
+	bool  flag=true;
+
+	KML_SubStyle::Echo();
+
+	if(flag) _pprintLine_("         color: " << color);
+	if(flag) _pprintLine_("     colormode: " << colormode);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_ColorStyle::DeepEcho {{{*/
+void  KML_ColorStyle::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_ColorStyle::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_ColorStyle::DeepEcho {{{*/
+void  KML_ColorStyle::DeepEcho(const char* indent){
+
+	bool  flag=true;
+
+	KML_SubStyle::DeepEcho(indent);
+
+	if(flag) _pprintLine_(indent << "         color: " << color);
+	if(flag) _pprintLine_(indent << "     colormode: " << colormode);
+}
+/*}}}*/
+/*FUNCTION KML_ColorStyle::Write {{{*/
+void  KML_ColorStyle::Write(FILE* filout,const char* indent){
+
+	KML_SubStyle::Write(filout,indent);
+
+	if (color     && strlen(color))
+		fprintf(filout,"%s  %s\n",indent,color);
+	if (colormode && strlen(colormode))
+		fprintf(filout,"%s  %s\n",indent,colormode);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_ColorStyle::Read {{{*/
+void  KML_ColorStyle::Read(FILE* fid,char* kstr){
+
+/*  process field within opening and closing tags  */
+
+	if      (!strncmp(kstr,""))
+		KMLFileTokenParse( color     ,NULL,KML_COLORSTYLE_COLOR_LENGTH, kstr, fid);
+	else if (!strcmp(kstr,""))
+		KMLFileTokenParse( colormode ,NULL,KML_COLORSTYLE_COLORMODE_LENGTH, kstr, fid);
+
+	else if (!strncmp(kstr,"<",1))
+		KML_SubStyle::Read(fid,kstr);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_ColorStyle.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_ColorStyle.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_ColorStyle.h	(revision 13395)
@@ -0,0 +1,48 @@
+/*! \file KML_ColorStyle.h 
+ *  \brief: header file for kml_colorstyle abstract object
+ */
+
+#ifndef _KML_COLORSTYLE_H_
+#define _KML_COLORSTYLE_H_
+
+#define KML_COLORSTYLE_COLOR_LENGTH      8
+#define KML_COLORSTYLE_COLORMODE_LENGTH  6
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_SubStyle.h"
+/*}}}*/
+
+class KML_ColorStyle: public KML_SubStyle {
+
+	public:
+
+		char  color[KML_COLORSTYLE_COLOR_LENGTH+1];
+		char  colormode[KML_COLORSTYLE_COLORMODE_LENGTH+1];
+
+		/*KML_ColorStyle constructors, destructors {{{*/
+		KML_ColorStyle();
+		~KML_ColorStyle();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_COLORSTYLE_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Comment.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Comment.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Comment.cpp	(revision 13395)
@@ -0,0 +1,118 @@
+/*!\file KML_Comment.cpp
+ * \brief: implementation of the kml_comment object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Comment::KML_Comment(){{{*/
+KML_Comment::KML_Comment(){
+
+	value     =NULL;
+
+}
+/*}}}*/
+/*FUNCTION KML_Comment::~KML_Comment(){{{*/
+KML_Comment::~KML_Comment(){
+
+	if (value     ) xDelete(value);
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Comment::Echo {{{*/
+void  KML_Comment::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintString_("    ");
+	if(flag) _pprintLine_(value);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Comment::DeepEcho {{{*/
+void  KML_Comment::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Comment::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Comment::DeepEcho {{{*/
+void  KML_Comment::DeepEcho(const char* indent){
+
+	bool  flag=true;
+
+	if(flag) _pprintString_(indent << "    ");
+	if(flag) _pprintLine_(value);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Comment::Write {{{*/
+void  KML_Comment::Write(FILE* filout,const char* indent){
+
+	if (strncmp(&value[0]              ,"" ,3))
+		fprintf(filout,"%s-->\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Comment::Read {{{*/
+void  KML_Comment::Read(FILE* fid,char* kstr){
+
+//  comments always read as part of KMLFileToken
+
+	;
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Comment::Alloc {{{*/
+void  KML_Comment::Alloc(const char* valuei){
+
+	value=xNew(strlen(valuei)+1);
+	memcpy(value,valuei,(strlen(valuei)+1)*sizeof(char));
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Comment::Add {{{*/
+void  KML_Comment::Add(DataSet* commnt){
+
+	commnt->AddObject((Object*)this);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Comment::Get {{{*/
+void  KML_Comment::Get(char** pvalueo){
+
+	*pvalueo=xNew(strlen(value)+1);
+	memcpy(*pvalueo,value,(strlen(value)+1)*sizeof(char));
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Comment.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Comment.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Comment.h	(revision 13395)
@@ -0,0 +1,50 @@
+/*! \file KML_Comment.h 
+ *  \brief: header file for kml_comment object
+ */
+
+#ifndef _KML_COMMENT_H_
+#define _KML_COMMENT_H_
+
+/*Headers:{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "../Object.h"
+class DataSet;
+/*}}}*/
+
+class KML_Comment: public Object {
+
+	public:
+
+		char* name;
+		char* value;
+
+		/*KML_Comment constructors, destructors {{{*/
+		KML_Comment();
+		~KML_Comment();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		virtual void  Echo();
+		virtual void  DeepEcho();
+		virtual void  DeepEcho(const char* indent);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+		/*virtual functions: */
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		void  Alloc(const char* valuei);
+		void  Add(DataSet* commnt);
+		void  Get(char** pvalueo);
+
+};
+#endif  /* _KML_COMMENT_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Container.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Container.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Container.cpp	(revision 13395)
@@ -0,0 +1,168 @@
+/*!\file KML_Container.cpp
+ * \brief: implementation of the kml_container abstract object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Container::KML_Container(){{{*/
+KML_Container::KML_Container(){
+
+	feature   =new DataSet;
+
+}
+/*}}}*/
+/*FUNCTION KML_Container::~KML_Container(){{{*/
+KML_Container::~KML_Container(){
+
+	if (feature) {
+		delete feature;
+		feature   =NULL;
+	}
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Container::Echo {{{*/
+void  KML_Container::Echo(){
+
+	bool  flag=true;
+
+	KML_Feature::Echo();
+
+	if(flag) _pprintLine_("       feature: (size=" << feature->Size() << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Container::DeepEcho {{{*/
+void  KML_Container::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Container::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Container::DeepEcho {{{*/
+void  KML_Container::DeepEcho(const char* indent){
+
+	int   i;
+	char  indent2[81];
+	bool  flag=true;
+
+	KML_Feature::DeepEcho(indent);
+
+/*  loop over the features for the container  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+	if (feature->Size())
+		for (i=0; iSize(); i++) {
+			if(flag) _pprintLine_(indent << "       feature: -------- begin [" << i << "] --------");
+			((KML_Feature *)feature->GetObjectByOffset(i))->DeepEcho(indent2);
+			if(flag) _pprintLine_(indent << "       feature: --------  end  [" << i << "] --------");
+		}
+	else
+		if(flag) _pprintLine_(indent << "       feature: [empty]");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Container::Write {{{*/
+void  KML_Container::Write(FILE* filout,const char* indent){
+
+	int   i;
+	char  indent2[81];
+
+	KML_Feature::Write(filout,indent);
+
+/*  loop over the features for the container  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+
+	strcat(indent2,"  ");
+
+	for (i=0; iSize(); i++)
+		((KML_Feature *)feature->GetObjectByOffset(i))->Write(filout,indent2);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Container::Read {{{*/
+void  KML_Container::Read(FILE* fid,char* kstr){
+
+	KML_Object*  kobj;
+
+/*  process field within opening and closing tags  */
+
+	if      (!strncmp(kstr,"(kstr);
+		return;
+	}
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		feature   ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		feature   ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		feature   ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		feature   ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"<",1))
+		KML_Feature::Read(fid,kstr);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Container::WriteExp {{{*/
+void  KML_Container::WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp){
+
+	int   i;
+
+/*  loop over the features for the container  */
+
+	for (i=0; iSize(); i++)
+		((KML_Object *)feature->GetObjectByOffset(i))->WriteExp(fid,nstr,sgn,cm,sp);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Container.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Container.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Container.h	(revision 13395)
@@ -0,0 +1,46 @@
+/*! \file KML_Container.h 
+ *  \brief: header file for kml_container abstract object
+ */
+
+#ifndef _KML_CONTAINER_H_
+#define _KML_CONTAINER_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Feature.h"
+class DataSet;
+/*}}}*/
+
+class KML_Container: public KML_Feature {
+
+	public:
+
+		DataSet* feature;
+
+		/*KML_Container constructors, destructors {{{*/
+		KML_Container();
+		~KML_Container();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		void  WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_CONTAINER_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Document.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Document.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Document.cpp	(revision 13395)
@@ -0,0 +1,127 @@
+/*!\file KML_Document.cpp
+ * \brief: implementation of the kml_document object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Document::KML_Document(){{{*/
+KML_Document::KML_Document(){
+
+	;
+
+}
+/*}}}*/
+/*FUNCTION KML_Document::~KML_Document(){{{*/
+KML_Document::~KML_Document(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Document::Echo {{{*/
+void  KML_Document::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_Document:");
+	KML_Container::Echo();
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Document::DeepEcho {{{*/
+void  KML_Document::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Document::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Document::DeepEcho {{{*/
+void  KML_Document::DeepEcho(const char* indent){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_Document:");
+	KML_Container::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Document::Write {{{*/
+void  KML_Document::Write(FILE* filout,const char* indent){
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Container::Write(filout,indent);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Document::Read {{{*/
+void  KML_Document::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,"(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Document.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Document.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Document.h	(revision 13395)
@@ -0,0 +1,43 @@
+/*! \file KML_Document.h 
+ *  \brief: header file for kml_document object
+ */
+
+#ifndef _KML_DOCUMENT_H_
+#define _KML_DOCUMENT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Container.h"
+class KML_Feature;
+/*}}}*/
+
+class KML_Document: public KML_Container {
+
+	public:
+
+		/*KML_Document constructors, destructors {{{*/
+		KML_Document();
+		~KML_Document();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_DOCUMENT_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Feature.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Feature.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Feature.cpp	(revision 13395)
@@ -0,0 +1,179 @@
+/*!\file KML_Feature.cpp
+ * \brief: implementation of the kml_feature abstract object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Feature::KML_Feature(){{{*/
+KML_Feature::KML_Feature(){
+
+	memcpy(name,"",(strlen("")+1)*sizeof(char));
+
+	visibility=true;
+	open      =false;
+	memcpy(snippet,"",(strlen("")+1)*sizeof(char));
+	memcpy(descript,"",(strlen("")+1)*sizeof(char));
+	memcpy(styleurl,"",(strlen("")+1)*sizeof(char));
+	style     =new DataSet;
+
+}
+/*}}}*/
+/*FUNCTION KML_Feature::~KML_Feature(){{{*/
+KML_Feature::~KML_Feature(){
+
+	if (style) {
+		delete style;
+		style     =NULL;
+	}
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Feature::Echo {{{*/
+void  KML_Feature::Echo(){
+
+	bool  flag=true;
+
+	KML_Object::Echo();
+
+	if(flag) _pprintLine_("          name: \"" << name << "\"");
+	if(flag) _pprintLine_("    visibility: " << (visibility ? "true" : "false"));
+	if(flag) _pprintLine_("          open: " << (open ? "true" : "false"));
+	if(flag) _pprintLine_("       snippet: \"" << snippet << "\"");
+	if(flag) _pprintLine_("      descript: \"" << descript << "\"");
+	if(flag) _pprintLine_("      styleurl: \"" << styleurl << "\"");
+	if(flag) _pprintLine_("         style: (size=" << style->Size() << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Feature::DeepEcho {{{*/
+void  KML_Feature::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Feature::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Feature::DeepEcho {{{*/
+void  KML_Feature::DeepEcho(const char* indent){
+
+	int   i;
+	char  indent2[81];
+	bool  flag=true;
+
+	KML_Object::DeepEcho(indent);
+
+	if(flag) _pprintLine_(indent << "          name: \"" << name << "\"");
+	if(flag) _pprintLine_(indent << "    visibility: " << (visibility ? "true" : "false"));
+	if(flag) _pprintLine_(indent << "          open: " << (open ? "true" : "false"));
+	if(flag) _pprintLine_(indent << "       snippet: \"" << snippet << "\"");
+	if(flag) _pprintLine_(indent << "      descript: \"" << descript << "\"");
+	if(flag) _pprintLine_(indent << "      styleurl: \"" << styleurl << "\"");
+
+/*  loop over any styles for the feature  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+	if (style->Size())
+		for (i=0; iSize(); i++) {
+			if(flag) _pprintLine_(indent << "         style: -------- begin [" << i << "] --------");
+			((KML_Style *)style->GetObjectByOffset(i))->DeepEcho(indent2);
+			if(flag) _pprintLine_(indent << "         style: --------  end  [" << i << "] --------");
+		}
+	else
+		if(flag) _pprintLine_(indent << "         style: [empty]");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Feature::Write {{{*/
+void  KML_Feature::Write(FILE* filout,const char* indent){
+
+	int   i;
+	char  indent2[81];
+
+	KML_Object::Write(filout,indent);
+
+	if (name     && strlen(name))
+		fprintf(filout,"%s  %s\n",indent,name);
+	fprintf(filout,"%s  %d\n",indent,(visibility ? 1 : 0));
+	fprintf(filout,"%s  %d\n",indent,(open ? 1 : 0));
+	if (snippet  && strlen(snippet))
+		fprintf(filout,"%s  %s\n",indent,snippet);
+	if (descript && strlen(descript))
+		fprintf(filout,"%s  %s\n",indent,descript);
+	if (styleurl && strlen(styleurl))
+		fprintf(filout,"%s  %s\n",indent,styleurl);
+
+/*  loop over any styles for the feature  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+
+	strcat(indent2,"  ");
+
+    for (i=0; iSize(); i++)
+        ((KML_Style *)style->GetObjectByOffset(i))->Write(filout,indent2);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Feature::Read {{{*/
+void  KML_Feature::Read(FILE* fid,char* kstr){
+
+	KML_Object*  kobj;
+
+/*  process field within opening and closing tags  */
+
+	if      (!strncmp(kstr,"Read(fid,kstr);
+		style     ->AddObject((Object*)kobj);
+	}
+
+	else if (!strcmp(kstr,""))
+		KMLFileTokenParse( name      ,NULL,KML_FEATURE_NAME_LENGTH, kstr, fid);
+	else if (!strcmp(kstr,""))
+		KMLFileTokenParse(&visibility, kstr, fid);
+	else if (!strcmp(kstr,""))
+		KMLFileTokenParse(&open      , kstr, fid);
+	else if (!strncmp(kstr,""))
+		KMLFileTokenParse( descript  ,NULL,KML_FEATURE_DESCRIPT_LENGTH, kstr, fid);
+	else if (!strcmp(kstr,""))
+		KMLFileTokenParse( styleurl  ,NULL,KML_FEATURE_STYLEURL_LENGTH, kstr, fid);
+
+	else if (!strncmp(kstr,"<",1))
+		KML_Object::Read(fid,kstr);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Feature.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Feature.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Feature.h	(revision 13395)
@@ -0,0 +1,57 @@
+/*! \file KML_Feature.h 
+ *  \brief: header file for kml_feature abstract object
+ */
+
+#ifndef _KML_FEATURE_H_
+#define _KML_FEATURE_H_
+
+#define KML_FEATURE_NAME_LENGTH         80
+#define KML_FEATURE_SNIPPET_LENGTH     160
+#define KML_FEATURE_DESCRIPT_LENGTH   3200
+#define KML_FEATURE_STYLEURL_LENGTH     80
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Object.h"
+class KML_Style;
+class DataSet;
+/*}}}*/
+
+class KML_Feature: public KML_Object {
+
+	public:
+
+		char  name[KML_FEATURE_NAME_LENGTH+1];
+		bool  visibility;
+		bool  open;
+		char  snippet[KML_FEATURE_SNIPPET_LENGTH+1];
+		char  descript[KML_FEATURE_DESCRIPT_LENGTH+1];
+		char  styleurl[KML_FEATURE_STYLEURL_LENGTH+1];
+		DataSet* style;
+
+		/*KML_Feature constructors, destructors {{{*/
+		KML_Feature();
+		~KML_Feature();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_FEATURE_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_File.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_File.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_File.cpp	(revision 13395)
@@ -0,0 +1,140 @@
+/*!\file KML_File.cpp
+ * \brief: implementation of the kml_file object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_File::KML_File(){{{*/
+KML_File::KML_File(){
+
+	;
+
+}
+/*}}}*/
+/*FUNCTION KML_File::~KML_File(){{{*/
+KML_File::~KML_File(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_File::Echo {{{*/
+void  KML_File::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_File:");
+	KML_Object::Echo();
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_File::DeepEcho {{{*/
+void  KML_File::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_File::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_File::DeepEcho {{{*/
+void  KML_File::DeepEcho(const char* indent){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_File:");
+	KML_Object::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_File::Write {{{*/
+void  KML_File::Write(FILE* filout,const char* indent){
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Object::Write(filout,indent);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_File::Read {{{*/
+void  KML_File::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+	KML_Object*  kobj;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,"(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_File::WriteExp {{{*/
+void  KML_File::WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp){
+
+	int   i;
+
+/*  loop over the kml objects for the file  */
+
+	for (i=0; iSize(); i++)
+		((KML_Object *)kmlobj->GetObjectByOffset(i))->WriteExp(fid,nstr,sgn,cm,sp);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_File.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_File.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_File.h	(revision 13395)
@@ -0,0 +1,44 @@
+/*! \file KML_File.h 
+ *  \brief: header file for kml_file object
+ */
+
+#ifndef _KML_FILE_H_
+#define _KML_FILE_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Feature.h"
+class DataSet;
+/*}}}*/
+
+class KML_File: public KML_Object {
+
+	public:
+
+		/*KML_File constructors, destructors {{{*/
+		KML_File();
+		~KML_File();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		void  WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_FILE_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Folder.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Folder.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Folder.cpp	(revision 13395)
@@ -0,0 +1,126 @@
+/*!\file KML_Folder.cpp
+ * \brief: implementation of the kml_folder object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Folder::KML_Folder(){{{*/
+KML_Folder::KML_Folder(){
+
+	;
+
+}
+/*}}}*/
+/*FUNCTION KML_Folder::~KML_Folder(){{{*/
+KML_Folder::~KML_Folder(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Folder::Echo {{{*/
+void  KML_Folder::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_Folder:");
+	KML_Container::Echo();
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Folder::DeepEcho {{{*/
+void  KML_Folder::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Folder::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Folder::DeepEcho {{{*/
+void  KML_Folder::DeepEcho(const char* indent){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_Folder:");
+	KML_Container::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Folder::Write {{{*/
+void  KML_Folder::Write(FILE* filout,const char* indent){
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Container::Write(filout,indent);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Folder::Read {{{*/
+void  KML_Folder::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,"(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Folder.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Folder.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Folder.h	(revision 13395)
@@ -0,0 +1,43 @@
+/*! \file KML_Folder.h 
+ *  \brief: header file for kml_folder object
+ */
+
+#ifndef _KML_FOLDER_H_
+#define _KML_FOLDER_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Container.h"
+class KML_Feature;
+/*}}}*/
+
+class KML_Folder: public KML_Container {
+
+	public:
+
+		/*KML_Folder constructors, destructors {{{*/
+		KML_Folder();
+		~KML_Folder();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_FOLDER_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Geometry.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Geometry.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Geometry.cpp	(revision 13395)
@@ -0,0 +1,90 @@
+/*!\file KML_Geometry.cpp
+ * \brief: implementation of the kml_geometry abstract object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Geometry::KML_Geometry(){{{*/
+KML_Geometry::KML_Geometry(){
+
+	;
+
+}
+/*}}}*/
+/*FUNCTION KML_Geometry::~KML_Geometry(){{{*/
+KML_Geometry::~KML_Geometry(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Geometry::Echo {{{*/
+void  KML_Geometry::Echo(){
+
+	this->KML_Object::Echo();
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Geometry::DeepEcho {{{*/
+void  KML_Geometry::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Geometry::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Geometry::DeepEcho {{{*/
+void  KML_Geometry::DeepEcho(const char* indent){
+
+	this->KML_Object::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Geometry::Write {{{*/
+void  KML_Geometry::Write(FILE* filout,const char* indent){
+
+	KML_Object::Write(filout,indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Geometry::Read {{{*/
+void  KML_Geometry::Read(FILE* fid,char* kstr){
+
+/*  process field within opening and closing tags  */
+
+	if      (!strncmp(kstr,"
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_GroundOverlay::KML_GroundOverlay(){{{*/
+KML_GroundOverlay::KML_GroundOverlay(){
+
+	altitude  = 0.;
+	memcpy(altmode,"clampToGround",(strlen("clampToGround")+1)*sizeof(char));
+
+	llbox     =NULL;
+
+}
+/*}}}*/
+/*FUNCTION KML_GroundOverlay::~KML_GroundOverlay(){{{*/
+KML_GroundOverlay::~KML_GroundOverlay(){
+
+	if (llbox) {
+		delete llbox;
+		llbox     =NULL;
+	}
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_GroundOverlay::Echo {{{*/
+void  KML_GroundOverlay::Echo(){
+
+	_printLine_("KML_GroundOverlay:");
+	KML_Overlay::Echo();
+
+	_printLine_("         altitude: " << altitude);
+	_printLine_("          altmode: " << altmode);
+	_printLine_("            llbox: " << llbox);
+}
+/*}}}*/
+/*FUNCTION KML_GroundOverlay::DeepEcho {{{*/
+void  KML_GroundOverlay::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_GroundOverlay::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_GroundOverlay::DeepEcho {{{*/
+void  KML_GroundOverlay::DeepEcho(const char* indent){
+
+	char  indent2[81];
+
+	_printLine_(indent << "KML_GroundOverlay:");
+	KML_Overlay::DeepEcho(indent);
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+	_printLine_(indent<<"      altitude: " << altitude);
+	_printLine_(indent<<"       altmode: " << altmode);
+	if (llbox)
+	 llbox->DeepEcho(indent2);
+	else
+	 _printLine_(indent<<"         llbox: " << llbox);
+}
+/*}}}*/
+/*FUNCTION KML_GroundOverlay::Write {{{*/
+void  KML_GroundOverlay::Write(FILE* filout,const char* indent){
+
+	char  indent2[81];
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Overlay::Write(filout,indent);
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+
+	strcat(indent2,"  ");
+
+	fprintf(filout,"%s  %0.16g\n",indent,altitude);
+	fprintf(filout,"%s  %s\n",indent,altmode);
+	if (llbox)
+		llbox->Write(filout,indent2);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_GroundOverlay::Read {{{*/
+void  KML_GroundOverlay::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,""))
+			KMLFileTokenParse(&altitude  ,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse( altmode   ,NULL,KML_GROUNDOVERLAY_ALTMODE_LENGTH,
+							  kstri,
+							  fid);
+		else if (!strncmp(kstri,"Read(fid,kstri);
+		}
+
+		else if (!strncmp(kstri,"<",1))
+			KML_Overlay::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_GroundOverlay.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_GroundOverlay.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_GroundOverlay.h	(revision 13395)
@@ -0,0 +1,49 @@
+/*! \file KML_GroundOverlay.h 
+ *  \brief: header file for kml_groundoverlay object
+ */
+
+#ifndef _KML_GROUNDOVERLAY_H_
+#define _KML_GROUNDOVERLAY_H_
+
+#define KML_GROUNDOVERLAY_ALTMODE_LENGTH    18
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Overlay.h"
+class KML_LatLonBox;
+/*}}}*/
+
+class KML_GroundOverlay: public KML_Overlay {
+
+	public:
+
+		double altitude;
+		char  altmode[KML_GROUNDOVERLAY_ALTMODE_LENGTH+1];
+		KML_LatLonBox* llbox;
+
+		/*KML_GroundOverlay constructors, destructors {{{*/
+		KML_GroundOverlay();
+		~KML_GroundOverlay();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_GROUNDOVERLAY_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Icon.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Icon.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Icon.cpp	(revision 13395)
@@ -0,0 +1,182 @@
+/*!\file KML_Icon.cpp
+ * \brief: implementation of the kml_feature abstract object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Icon::KML_Icon(){{{*/
+KML_Icon::KML_Icon(){
+
+	strcpy(href      ,"");
+	strcpy(refmode   ,"onChange");
+	refint    = 4.;
+	strcpy(vrefmode  ,"never");
+	vreftime  = 4.;
+	vboundsc  = 1.;
+	strcpy(vformat   ,"");
+	strcpy(hquery    ,"");
+
+}
+/*}}}*/
+/*FUNCTION KML_Icon::~KML_Icon(){{{*/
+KML_Icon::~KML_Icon(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Icon::Echo {{{*/
+void  KML_Icon::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_Icon:");
+	KML_Object::Echo();
+
+	if(flag) _pprintLine_("          href: \"" << href << "\"");
+	if(flag) _pprintLine_("       refmode: \"" << refmode << "\"");
+	if(flag) _pprintLine_("        refint: " << refint);
+	if(flag) _pprintLine_("      vrefmode: \"" << vrefmode << "\"");
+	if(flag) _pprintLine_("      vreftime: " << vreftime);
+	if(flag) _pprintLine_("      vboundsc: " << vboundsc);
+	if(flag) _pprintLine_("       vformat: \"" << vformat << "\"");
+	if(flag) _pprintLine_("        hquery: \"" << hquery << "\"");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Icon::DeepEcho {{{*/
+void  KML_Icon::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Icon::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Icon::DeepEcho {{{*/
+void  KML_Icon::DeepEcho(const char* indent){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_Icon:");
+	KML_Object::DeepEcho(indent);
+
+	if(flag) _pprintLine_(indent << "          href: \"" << href << "\"");
+	if(flag) _pprintLine_(indent << "       refmode: \"" << refmode << "\"");
+	if(flag) _pprintLine_(indent << "        refint: " << refint);
+	if(flag) _pprintLine_(indent << "      vrefmode: \"" << vrefmode << "\"");
+	if(flag) _pprintLine_(indent << "      vreftime: " << vreftime);
+	if(flag) _pprintLine_(indent << "      vboundsc: " << vboundsc);
+	if(flag) _pprintLine_(indent << "       vformat: \"" << vformat << "\"");
+	if(flag) _pprintLine_(indent << "        hquery: \"" << hquery << "\"");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Icon::Write {{{*/
+void  KML_Icon::Write(FILE* filout,const char* indent){
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Object::Write(filout,indent);
+
+	if (href     && strlen(href))
+		fprintf(filout,"%s  %s\n",indent,href);
+	if (refmode  && strlen(refmode))
+		fprintf(filout,"%s  %s\n",indent,refmode);
+	fprintf(filout,"%s  %g\n",indent,refint);
+	if (vrefmode && strlen(vrefmode))
+		fprintf(filout,"%s  %s\n",indent,vrefmode);
+	fprintf(filout,"%s  %g\n",indent,vreftime);
+	fprintf(filout,"%s  %g\n",indent,vboundsc);
+	if (vformat  && strlen(vformat))
+		fprintf(filout,"%s  %s\n",indent,vformat);
+	if (hquery   && strlen(hquery))
+		fprintf(filout,"%s  %s\n",indent,hquery);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Icon::Read {{{*/
+void  KML_Icon::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,""))
+			KMLFileTokenParse( href      ,NULL,KML_ICON_HREF_LENGTH, kstri, fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse( refmode   ,NULL,KML_ICON_REFMODE_LENGTH, kstri, fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&refint    , kstri, fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse( vrefmode  ,NULL,KML_ICON_VREFMODE_LENGTH, kstri, fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&vreftime  , kstri, fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&vboundsc  , kstri, fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse( vformat   ,NULL,KML_ICON_VFORMAT_LENGTH, kstri, fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse( hquery    ,NULL,KML_ICON_HQUERY_LENGTH, kstri, fid);
+
+		else if (!strncmp(kstri,"<",1))
+			KML_Object::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Icon.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Icon.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Icon.h	(revision 13395)
@@ -0,0 +1,57 @@
+/*! \file KML_Icon.h 
+ *  \brief: header file for kml_icon object
+ */
+
+#ifndef _KML_ICON_H_
+#define _KML_ICON_H_
+
+#define KML_ICON_HREF_LENGTH      800
+#define KML_ICON_REFMODE_LENGTH    10
+#define KML_ICON_VREFMODE_LENGTH    9
+#define KML_ICON_VFORMAT_LENGTH   800
+#define KML_ICON_HQUERY_LENGTH    800
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Object.h"
+/*}}}*/
+
+class KML_Icon: public KML_Object {
+
+	public:
+
+		char  href[KML_ICON_HREF_LENGTH+1];
+		char  refmode[KML_ICON_REFMODE_LENGTH+1];
+		float refint;
+		char  vrefmode[KML_ICON_VREFMODE_LENGTH+1];
+		float vreftime;
+		float vboundsc;
+		char  vformat[KML_ICON_VFORMAT_LENGTH+1];
+		char  hquery[KML_ICON_HQUERY_LENGTH+1];
+
+		/*KML_Icon constructors, destructors {{{*/
+		KML_Icon();
+		~KML_Icon();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_ICON_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_LatLonBox.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_LatLonBox.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_LatLonBox.cpp	(revision 13395)
@@ -0,0 +1,162 @@
+/*!\file KML_LatLonBox.cpp
+ * \brief: implementation of the kml_feature abstract object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_LatLonBox::KML_LatLonBox(){{{*/
+KML_LatLonBox::KML_LatLonBox(){
+
+	north     = 0.;
+	south     = 0.;
+	east      = 0.;
+	west      = 0.;
+	rotation  = 0.;
+
+}
+/*}}}*/
+/*FUNCTION KML_LatLonBox::~KML_LatLonBox(){{{*/
+KML_LatLonBox::~KML_LatLonBox(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_LatLonBox::Echo {{{*/
+void  KML_LatLonBox::Echo(){
+
+
+	_printLine_("KML_LatLonBox:");
+	KML_Object::Echo();
+
+	_printLine_("         north: " << north);
+	_printLine_("         south: " << south);
+	_printLine_("          east: " << east);
+	_printLine_("          west: " << west);
+	_printLine_("      rotation: " << rotation);
+}
+/*}}}*/
+/*FUNCTION KML_LatLonBox::DeepEcho {{{*/
+void  KML_LatLonBox::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_LatLonBox::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LatLonBox::DeepEcho {{{*/
+void  KML_LatLonBox::DeepEcho(const char* indent){
+
+	_printLine_(indent << "KML_LatLonBox:");
+	KML_Object::DeepEcho(indent);
+
+	_printLine_("         north: " << north);
+	_printLine_("         south: " << south);
+	_printLine_("          east: " << east);
+	_printLine_("          west: " << west);
+	_printLine_("      rotation: " << rotation);
+}
+/*}}}*/
+/*FUNCTION KML_LatLonBox::Write {{{*/
+void  KML_LatLonBox::Write(FILE* filout,const char* indent){
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Object::Write(filout,indent);
+
+	fprintf(filout,"%s  %0.16g\n",indent,north);
+	fprintf(filout,"%s  %0.16g\n",indent,south);
+	fprintf(filout,"%s  %0.16g\n",indent,east);
+	fprintf(filout,"%s  %0.16g\n",indent,west);
+	fprintf(filout,"%s  %0.16g\n",indent,rotation);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LatLonBox::Read {{{*/
+void  KML_LatLonBox::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,""))
+			KMLFileTokenParse(&north     ,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&south     ,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&east      ,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&west      ,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&rotation  ,
+							  kstri,
+							  fid);
+
+		else if (!strncmp(kstri,"<",1))
+			KML_Object::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_LatLonBox.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_LatLonBox.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_LatLonBox.h	(revision 13395)
@@ -0,0 +1,48 @@
+/*! \file KML_LatLonBox.h 
+ *  \brief: header file for kml_latlonbox object
+ */
+
+#ifndef _KML_LATLONBOX_H_
+#define _KML_LATLONBOX_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Object.h"
+/*}}}*/
+
+class KML_LatLonBox: public KML_Object {
+
+	public:
+
+		double north;
+		double south;
+		double east;
+		double west;
+		double rotation;
+
+		/*KML_LatLonBox constructors, destructors {{{*/
+		KML_LatLonBox();
+		~KML_LatLonBox();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_LATLONBOX_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_LineString.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_LineString.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_LineString.cpp	(revision 13395)
@@ -0,0 +1,230 @@
+/*!\file KML_LineString.cpp
+ * \brief: implementation of the kml_linestring object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+#include "../../../modules/Ll2xyx/Ll2xyx.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_LineString::KML_LineString(){{{*/
+KML_LineString::KML_LineString(){
+
+	extrude   =false;
+	tessellate=false;
+	memcpy(altmode,"clampToGround",(strlen("clampToGround")+1)*sizeof(char));
+
+	ncoord    =0;
+	coords    =NULL;
+
+}
+/*}}}*/
+/*FUNCTION KML_LineString::~KML_LineString(){{{*/
+KML_LineString::~KML_LineString(){
+
+	if (coords) xDelete(coords);
+
+	coords    =NULL;
+	ncoord    =0;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_LineString::Echo {{{*/
+void  KML_LineString::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_LineString:");
+	KML_Geometry::Echo();
+
+	if(flag) _pprintLine_("       extrude: " << (extrude ? "true" : "false"));
+	if(flag) _pprintLine_("    tessellate: " << (tessellate ? "true" : "false"));
+	if(flag) _pprintLine_("       altmode: \"" << altmode << "\"");
+	if(flag) _pprintLine_("        coords: (ncoord=" << ncoord << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LineString::DeepEcho {{{*/
+void  KML_LineString::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_LineString::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LineString::DeepEcho {{{*/
+void  KML_LineString::DeepEcho(const char* indent){
+
+	int   i;
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_LineString:");
+	KML_Geometry::DeepEcho(indent);
+
+	if(flag) _pprintLine_(indent << "       extrude: " << (extrude ? "true" : "false"));
+	if(flag) _pprintLine_(indent << "    tessellate: " << (tessellate ? "true" : "false"));
+	if(flag) _pprintLine_(indent << "       altmode: \"" << altmode << "\"");
+	if(flag) _pprintLine_(indent << "        coords: (ncoord=" << ncoord << ")");
+	for (i=0; i\n");
+	WriteCommnt(filout,indent);
+
+	KML_Geometry::Write(filout,indent);
+
+	fprintf(filout,"%s  %d\n",indent,(extrude ? 1 : 0));
+	fprintf(filout,"%s  %d\n",indent,(tessellate ? 1 : 0));
+	fprintf(filout,"%s  %s\n",indent,altmode);
+	fprintf(filout,"%s  \n",indent);
+
+/*  loop over the coordinates for the linestring  */
+
+	for (i=0; i\n",indent);
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LineString::Read {{{*/
+void  KML_LineString::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,""))
+			KMLFileTokenParse(&extrude   ,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&tessellate,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse( altmode   ,NULL,KML_LINESTRING_ALTMODE_LENGTH,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&coords    ,&ncoord    ,0,
+							  kstri,
+							  fid);
+
+		else if (!strncmp(kstri,"<",1))
+			KML_Geometry::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LineString::WriteExp {{{*/
+void  KML_LineString::WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp){
+
+	int     i;
+	double  *lat,*lon,*x,*y;
+	char    nstr2[81];
+
+/*  extract latitude and longitude into vectors  */
+
+	lat=xNew(ncoord);
+	lon=xNew(ncoord);
+	for (i=0; i(ncoord);
+	y  =xNew(ncoord);
+	Ll2xyx(x,y,lat,lon,ncoord,sgn,cm,sp);
+
+/*  write header  */
+
+	memcpy(nstr2,nstr,(strlen(nstr)+1)*sizeof(char));
+
+	for (i=0; i(y);
+	xDelete(x);
+	xDelete(lon);
+	xDelete(lat);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_LineString.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_LineString.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_LineString.h	(revision 13395)
@@ -0,0 +1,51 @@
+/*! \file KML_LineString.h 
+ *  \brief: header file for kml_linestring object
+ */
+
+#ifndef _KML_LINESTRING_H_
+#define _KML_LINESTRING_H_
+
+#define KML_LINESTRING_ALTMODE_LENGTH    18
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Geometry.h"
+/*}}}*/
+
+class KML_LineString: public KML_Geometry {
+
+	public:
+
+		bool    extrude;
+		bool    tessellate;
+		char    altmode[KML_LINESTRING_ALTMODE_LENGTH+1];
+		int     ncoord;
+		double *coords;
+
+		/*KML_LineString constructors, destructors {{{*/
+		KML_LineString();
+		~KML_LineString();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		void  WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_LINESTRING_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_LineStyle.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_LineStyle.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_LineStyle.cpp	(revision 13395)
@@ -0,0 +1,138 @@
+/*!\file KML_LineStyle.cpp
+ * \brief: implementation of the kml_linestyle object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_LineStyle::KML_LineStyle(){{{*/
+KML_LineStyle::KML_LineStyle(){
+
+	width     =1.;
+
+}
+/*}}}*/
+/*FUNCTION KML_LineStyle::~KML_LineStyle(){{{*/
+KML_LineStyle::~KML_LineStyle(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_LineStyle::Echo {{{*/
+void  KML_LineStyle::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_LineStyle:");
+	KML_ColorStyle::Echo();
+
+	if(flag) _pprintLine_("         width: " << width);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LineStyle::DeepEcho {{{*/
+void  KML_LineStyle::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_LineStyle::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LineStyle::DeepEcho {{{*/
+void  KML_LineStyle::DeepEcho(const char* indent){
+
+	int   i;
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_LineStyle:");
+	KML_ColorStyle::DeepEcho(indent);
+
+	if(flag) _pprintLine_(indent << "         width: " << width);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LineStyle::Write {{{*/
+void  KML_LineStyle::Write(FILE* filout,const char* indent){
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_ColorStyle::Write(filout,indent);
+
+	fprintf(filout,"%s  %g\n",indent,width);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LineStyle::Read {{{*/
+void  KML_LineStyle::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,""))
+			KMLFileTokenParse(&width     ,
+							  kstri,
+							  fid);
+
+		else if (!strncmp(kstri,"<",1))
+			KML_ColorStyle::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_LineStyle.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_LineStyle.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_LineStyle.h	(revision 13395)
@@ -0,0 +1,44 @@
+/*! \file KML_LineStyle.h 
+ *  \brief: header file for kml_linestyle object
+ */
+
+#ifndef _KML_LINESTYLE_H_
+#define _KML_LINESTYLE_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_ColorStyle.h"
+/*}}}*/
+
+class KML_LineStyle: public KML_ColorStyle {
+
+	public:
+
+		float width;
+
+		/*KML_LineStyle constructors, destructors {{{*/
+		KML_LineStyle();
+		~KML_LineStyle();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_LINESTYLE_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_LinearRing.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_LinearRing.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_LinearRing.cpp	(revision 13395)
@@ -0,0 +1,224 @@
+/*!\file KML_LinearRing.cpp
+ * \brief: implementation of the kml_linearring object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+#include "../../../modules/Ll2xyx/Ll2xyx.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_LinearRing::KML_LinearRing(){{{*/
+KML_LinearRing::KML_LinearRing(){
+
+	extrude   =false;
+	tessellate=false;
+	memcpy(altmode,"clampToGround",(strlen("clampToGround")+1)*sizeof(char));
+
+	ncoord    =0;
+	coords    =NULL;
+
+}
+/*}}}*/
+/*FUNCTION KML_LinearRing::~KML_LinearRing(){{{*/
+KML_LinearRing::~KML_LinearRing(){
+
+	if (coords) xDelete(coords);
+
+	coords    =NULL;
+	ncoord    =0;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_LinearRing::Echo {{{*/
+void  KML_LinearRing::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_LinearRing:");
+	KML_Geometry::Echo();
+
+	if(flag) _pprintLine_("       extrude: " << (extrude ? "true" : "false"));
+	if(flag) _pprintLine_("    tessellate: " << (tessellate ? "true" : "false"));
+	if(flag) _pprintLine_("       altmode: \"" << altmode << "\"");
+	if(flag) _pprintLine_("        coords: (ncoord=" << ncoord << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LinearRing::DeepEcho {{{*/
+void  KML_LinearRing::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_LinearRing::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LinearRing::DeepEcho {{{*/
+void  KML_LinearRing::DeepEcho(const char* indent){
+
+	int   i;
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_LinearRing:");
+	KML_Geometry::DeepEcho(indent);
+
+	if(flag) _pprintLine_(indent << "       extrude: " << (extrude ? "true" : "false"));
+	if(flag) _pprintLine_(indent << "    tessellate: " << (tessellate ? "true" : "false"));
+	if(flag) _pprintLine_(indent << "       altmode: \"" << altmode << "\"");
+	if(flag) _pprintLine_(indent << "        coords: (ncoord=" << ncoord << ")");
+	for (i=0; i\n");
+	WriteCommnt(filout,indent);
+
+	KML_Geometry::Write(filout,indent);
+
+	fprintf(filout,"%s  %d\n",indent,(extrude ? 1 : 0));
+	fprintf(filout,"%s  %d\n",indent,(tessellate ? 1 : 0));
+	fprintf(filout,"%s  %s\n",indent,altmode);
+	fprintf(filout,"%s  \n",indent);
+
+/*  loop over the coordinates for the linearring  */
+
+	for (i=0; i\n",indent);
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LinearRing::Read {{{*/
+void  KML_LinearRing::Read(FILE* fid,char* kstr){
+
+	char  *kstri = NULL;
+	int    ncom  = 0;
+	char **pcom  = NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,kstr)) return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,&ncom,&pcom)){
+		if (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,""))
+			KMLFileTokenParse(&extrude,kstri,fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&tessellate,kstri,fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(altmode,NULL,KML_LINEARRING_ALTMODE_LENGTH,kstri,fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&coords,&ncoord,3,0,kstri,fid);
+		else if (!strncmp(kstri,"<",1))
+			KML_Geometry::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for(ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_LinearRing::WriteExp {{{*/
+void  KML_LinearRing::WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp){
+
+	int     i;
+	double  *lat,*lon,*x,*y;
+	char    nstr2[81];
+
+/*  extract latitude and longitude into vectors  */
+
+	lat=xNew(ncoord);
+	lon=xNew(ncoord);
+	for (i=0; i(ncoord);
+	y  =xNew(ncoord);
+	Ll2xyx(x,y,lat,lon,ncoord,sgn,cm,sp);
+
+/*  write header  */
+
+	memcpy(nstr2,nstr,(strlen(nstr)+1)*sizeof(char));
+
+	for (i=0; i(y);
+	xDelete(x);
+	xDelete(lon);
+	xDelete(lat);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_LinearRing.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_LinearRing.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_LinearRing.h	(revision 13395)
@@ -0,0 +1,51 @@
+/*! \file KML_LinearRing.h 
+ *  \brief: header file for kml_linearring object
+ */
+
+#ifndef _KML_LINEARRING_H_
+#define _KML_LINEARRING_H_
+
+#define KML_LINEARRING_ALTMODE_LENGTH    18
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Geometry.h"
+/*}}}*/
+
+class KML_LinearRing: public KML_Geometry {
+
+	public:
+
+		bool     extrude;
+		bool     tessellate;
+		char     altmode[KML_LINEARRING_ALTMODE_LENGTH+1];
+		int      ncoord;
+		double  *coords;
+
+		/*KML_LinearRing constructors, destructors {{{*/
+		KML_LinearRing();
+		~KML_LinearRing();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		void  WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_LINEARRING_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_MultiGeometry.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_MultiGeometry.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_MultiGeometry.cpp	(revision 13395)
@@ -0,0 +1,203 @@
+/*!\file KML_MultiGeometry.cpp
+ * \brief: implementation of the kml_multigeometry object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_MultiGeometry::KML_MultiGeometry(){{{*/
+KML_MultiGeometry::KML_MultiGeometry(){
+
+	geometry  =new DataSet;
+
+}
+/*}}}*/
+/*FUNCTION KML_MultiGeometry::~KML_MultiGeometry(){{{*/
+KML_MultiGeometry::~KML_MultiGeometry(){
+
+	if (geometry) {
+		delete geometry;
+		geometry  =NULL;
+	}
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_MultiGeometry::Echo {{{*/
+void  KML_MultiGeometry::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_Multigeometry:");
+	KML_Geometry::Echo();
+
+	if(flag) _pprintLine_("      geometry: (size=" << geometry->Size() << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_MultiGeometry::DeepEcho {{{*/
+void  KML_MultiGeometry::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_MultiGeometry::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_MultiGeometry::DeepEcho {{{*/
+void  KML_MultiGeometry::DeepEcho(const char* indent){
+
+	int   i;
+	char  indent2[81];
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_Multigeometry:");
+	KML_Geometry::DeepEcho(indent);
+
+/*  loop over the geometry elements for the multigeometry  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+	if (geometry->Size())
+		for (i=0; iSize(); i++) {
+			if(flag) _pprintLine_(indent << "      geometry: -------- begin [" << i << "] --------");
+			((KML_Geometry *)geometry->GetObjectByOffset(i))->DeepEcho(indent2);
+			if(flag) _pprintLine_(indent << "      geometry: --------  end  [" << i << "] --------");
+		}
+	else
+		if(flag) _pprintLine_(indent << "      geometry: [empty]");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_MultiGeometry::Write {{{*/
+void  KML_MultiGeometry::Write(FILE* filout,const char* indent){
+
+	int   i;
+	char  indent2[81];
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Geometry::Write(filout,indent);
+
+/*  loop over the geometry elements for the multigeometry  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+
+	strcat(indent2,"  ");
+
+	for (i=0; iSize(); i++)
+		((KML_Geometry *)geometry->GetObjectByOffset(i))->Write(filout,indent2);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_MultiGeometry::Read {{{*/
+void  KML_MultiGeometry::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+	KML_Object*  kobj;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"<",1))
+			KML_Geometry::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_MultiGeometry::WriteExp {{{*/
+void  KML_MultiGeometry::WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp){
+
+	int   i;
+
+/*  loop over the geometry elements for the multigeometry  */
+
+	for (i=0; iSize(); i++)
+		((KML_Object *)geometry->GetObjectByOffset(i))->WriteExp(fid,nstr,sgn,cm,sp);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_MultiGeometry.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_MultiGeometry.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_MultiGeometry.h	(revision 13395)
@@ -0,0 +1,47 @@
+/*! \file KML_MultiGeometry.h 
+ *  \brief: header file for kml_multigeometry object
+ */
+
+#ifndef _KML_MULTIGEOMETRY_H_
+#define _KML_MULTIGEOMETRY_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Geometry.h"
+class KML_Geometry;
+class DataSet;
+/*}}}*/
+
+class KML_MultiGeometry: public KML_Geometry {
+
+	public:
+
+		DataSet* geometry;
+
+		/*KML_MultiGeometry constructors, destructors {{{*/
+		KML_MultiGeometry();
+		~KML_MultiGeometry();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		void  WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_MULTIGEOMETRY_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Object.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Object.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Object.cpp	(revision 13395)
@@ -0,0 +1,387 @@
+/*!\file KML_Object.cpp
+ * \brief: implementation of the kml_object abstract object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Object::KML_Object(){{{*/
+KML_Object::KML_Object(){
+
+	attrib    =new DataSet;
+	commnt    =new DataSet;
+	kmlobj    =new DataSet;
+
+}
+/*}}}*/
+/*FUNCTION KML_Object::~KML_Object(){{{*/
+KML_Object::~KML_Object(){
+
+	if (attrib) {
+		delete attrib;
+		attrib    =NULL;
+	}
+	if (commnt) {
+		delete commnt;
+		commnt    =NULL;
+	}
+	if (kmlobj) {
+		delete kmlobj;
+		kmlobj    =NULL;
+	}
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Object::Echo {{{*/
+void  KML_Object::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("        attrib: (size=" << attrib->Size() << ")");
+	if(flag) _pprintLine_("        commnt: (size=" << commnt->Size() << ")");
+	if(flag) _pprintLine_("        kmlobj: (size=" << kmlobj->Size() << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::DeepEcho {{{*/
+void  KML_Object::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Object::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::DeepEcho {{{*/
+void  KML_Object::DeepEcho(const char* indent){
+
+	int   i;
+	char  indent2[81];
+	bool  flag=true;
+
+/*  loop over the attributes for the object  */
+
+	if (attrib->Size())
+		for (i=0; iSize(); i++) {
+			((KML_Attribute *)attrib->GetObjectByOffset(i))->DeepEcho(indent);
+		}
+	else
+		if(flag) _pprintLine_(indent << "        attrib: [empty]");
+
+/*  loop over the comments for the object  */
+
+	if (commnt->Size())
+		for (i=0; iSize(); i++) {
+			((KML_Comment *)commnt->GetObjectByOffset(i))->DeepEcho(indent);
+		}
+	else
+		if(flag) _pprintLine_(indent << "        commnt: [empty]");
+
+/*  loop over the unknown objects for the object  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+	if (kmlobj->Size())
+		for (i=0; iSize(); i++) {
+            if(flag) _pprintLine_(indent << "        kmlobj: -------- begin [" << i << "] --------");
+			((KML_Unknown *)kmlobj->GetObjectByOffset(i))->DeepEcho(indent2);
+            if(flag) _pprintLine_(indent << "        kmlobj: --------  end  [" << i << "] --------");
+		}
+	else
+		if(flag) _pprintLine_(indent << "        kmlobj: [empty]");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::Write {{{*/
+void  KML_Object::Write(FILE* filout,const char* indent){
+
+	int   i;
+	char  indent2[81];
+
+//  attributes always written in keyword line of derived classes
+//  comments always written after keyword line of derived classes
+
+/*  loop over the unknown objects for the object  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+	if (kmlobj->Size())
+		for (i=0; iSize(); i++) {
+			((KML_Unknown *)kmlobj->GetObjectByOffset(i))->Write(filout,indent2);
+		}
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::Read {{{*/
+void  KML_Object::Read(FILE* fid,char* kstr){
+
+	KML_Object*  kobj;
+
+/*  process field within opening and closing tags  */
+
+	if      (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+//	else if (!strncmp(kstr,"Read(fid,kstr);
+//		kmlobj    ->AddObject((Object*)kobj);
+//	}
+
+//	else if (!strncmp(kstr,"Read(fid,kstr);
+//		kmlobj    ->AddObject((Object*)kobj);
+//	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+//	else if (!strncmp(kstr,"Read(fid,kstr);
+//		kmlobj    ->AddObject((Object*)kobj);
+//	}
+
+//	else if (!strncmp(kstr,"Read(fid,kstr);
+//		kmlobj    ->AddObject((Object*)kobj);
+//	}
+
+	else if (!strncmp(kstr,"<",1)) {
+		_pprintLine_("KML_Object::Read -- Unrecognized opening tag " << kstr << ".");
+//		KMLFileTagSkip(kstr,
+//					   fid);
+		kobj=(KML_Object*)new KML_Unknown();
+		kobj->Read(fid,kstr);
+		kmlobj    ->AddObject((Object*)kobj);
+	}
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::WriteExp {{{*/
+void  KML_Object::WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp){
+
+	;
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::AddAttrib {{{*/
+void  KML_Object::AddAttrib(const char* name,const char* value){
+
+	KML_Attribute* katt=NULL;
+
+	katt=new KML_Attribute();
+	katt->Alloc(name,value);
+	katt->Add(attrib);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::FindAttrib {{{*/
+void  KML_Object::FindAttrib(char** pvalue,char* name,char* deflt){
+
+	int   i;
+	KML_Attribute* katt=NULL;
+
+/*  loop over any attributes for the object  */
+
+	if (attrib->Size())
+		for (i=0; iSize(); i++)
+			if (!strcmp(((KML_Attribute *)attrib->GetObjectByOffset(i))->name,name)) {
+				katt=(KML_Attribute *)attrib->GetObjectByOffset(i);
+				break;
+			}
+
+/*  if found, get the value; otherwise use the default  */
+
+	if (katt)
+		katt->Get(pvalue,deflt);
+	else {
+		*pvalue=xNew(strlen(deflt)+1);
+		memcpy(*pvalue,deflt,(strlen(deflt)+1)*sizeof(char));
+	}
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::WriteAttrib {{{*/
+void  KML_Object::WriteAttrib(FILE* filout,const char* indent){
+
+//  attributes always written in keyword line of kml_object
+
+/*  loop over any attributes for the object  */
+
+	if (attrib->Size())
+		for (int i=0; iSize(); i++)
+			((KML_Attribute *)attrib->GetObjectByOffset(i))->Write(filout,indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::AddCommnt {{{*/
+void  KML_Object::AddCommnt(int ncom,char** pcom){
+
+	int   i;
+	KML_Comment* kcom=NULL;
+
+	for (i=0; iAlloc(pcom[i]);
+		kcom->Add(commnt);
+	}
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::AddCommnt {{{*/
+void  KML_Object::AddCommnt(char* value){
+
+	KML_Comment* kcom=NULL;
+
+	kcom=new KML_Comment();
+	kcom->Alloc(value);
+	kcom->Add(commnt);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::FindCommnt {{{*/
+void  KML_Object::FindCommnt(char** pvalue,int inum){
+
+	KML_Comment* kcom=NULL;
+
+/*  loop over any comments for the object  */
+
+	if (inum <= commnt->Size())
+		kcom=(KML_Comment *)commnt->GetObjectByOffset(inum-1);
+
+/*  if found, get the value; otherwise use the NULL  */
+
+	if (kcom)
+		kcom->Get(pvalue);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Object::WriteCommnt {{{*/
+void  KML_Object::WriteCommnt(FILE* filout,const char* indent){
+
+	int   i;
+
+//  comments always written after keyword line of kml_object
+
+/*  loop over any comments for the object  */
+
+	if (commnt->Size())
+		for (i=0; iSize(); i++)
+			((KML_Comment *)commnt->GetObjectByOffset(i))->Write(filout,indent);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Object.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Object.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Object.h	(revision 13395)
@@ -0,0 +1,56 @@
+/*! \file KML_Object.h 
+ *  \brief: header file for kml_object abstract object
+ */
+
+#ifndef _KML_OBJECT_H_
+#define _KML_OBJECT_H_
+
+/*Headers:{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "../Object.h"
+class DataSet;
+/*}}}*/
+
+class KML_Object: public Object {
+
+	public:
+
+		DataSet* attrib;
+		DataSet* commnt;
+		DataSet* kmlobj;
+
+		/*KML_Object constructors, destructors {{{*/
+		KML_Object();
+		~KML_Object();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		virtual void  Echo();
+		virtual void  DeepEcho();
+		virtual void  DeepEcho(const char* indent);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+		/*virtual functions: */
+		virtual void  Write(FILE* fid,const char* indent)=0;
+		virtual void  Read(FILE* fid,char* kstr)=0;
+		virtual void  WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp);
+		virtual void  AddAttrib(const char* name,const char* value);
+		virtual void  FindAttrib(char** pvalue,char* name,char* deflt);
+		virtual void  WriteAttrib(FILE* fid,const char* indent);
+		virtual void  AddCommnt(int ncom,char** pcom);
+		virtual void  AddCommnt(char* value);
+		virtual void  FindCommnt(char** pvalue,int inum);
+		virtual void  WriteCommnt(FILE* fid,const char* indent);
+
+};
+#endif  /* _KML_OBJECT_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Overlay.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Overlay.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Overlay.cpp	(revision 13395)
@@ -0,0 +1,135 @@
+/*!\file KML_Overlay.cpp
+ * \brief: implementation of the kml_overlay abstract object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Overlay::KML_Overlay(){{{*/
+KML_Overlay::KML_Overlay(){
+
+	strcpy(color     ,"ffffffff");
+	memcpy(color,"ffffffff",(strlen("ffffffff")+1)*sizeof(char));
+
+	draword   = 0;
+	icon      =NULL;
+
+}
+/*}}}*/
+/*FUNCTION KML_Overlay::~KML_Overlay(){{{*/
+KML_Overlay::~KML_Overlay(){
+
+	if (icon) {
+		delete icon;
+		icon      =NULL;
+	}
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Overlay::Echo {{{*/
+void  KML_Overlay::Echo(){
+
+	KML_Feature::Echo();
+	_pprintLine_("         color: \"" << color << "\"");
+	_pprintLine_("       draword: " << draword);
+	_pprintLine_("          icon: " << icon);
+}
+/*}}}*/
+/*FUNCTION KML_Overlay::DeepEcho {{{*/
+void  KML_Overlay::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Overlay::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Overlay::DeepEcho {{{*/
+void  KML_Overlay::DeepEcho(const char* indent){
+
+	char  indent2[81];
+	KML_Feature::DeepEcho(indent);
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+	_pprintLine_(indent << "         color: " << color);
+	_pprintLine_(indent << "       draword: " << draword);
+	if (icon)
+		icon->DeepEcho(indent2);
+	else
+		_pprintLine_(indent << "          icon: " << icon);
+}
+/*}}}*/
+/*FUNCTION KML_Overlay::Write {{{*/
+void  KML_Overlay::Write(FILE* filout,const char* indent){
+
+	char  indent2[81];
+
+	KML_Feature::Write(filout,indent);
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+
+	strcat(indent2,"  ");
+
+	if (color     && strlen(color))
+		fprintf(filout,"%s  %s\n",indent,color);
+	fprintf(filout,"%s  %d\n",indent,draword);
+	if (icon)
+		icon->Write(filout,indent2);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Overlay::Read {{{*/
+void  KML_Overlay::Read(FILE* fid,char* kstr){
+
+/*  process field within opening and closing tags  */
+
+	if      (!strncmp(kstr,"(kstr);
+		return;
+	}
+	else if (!strncmp(kstr,""))
+		KMLFileTokenParse( color     ,NULL,KML_OVERLAY_COLOR_LENGTH,
+						  kstr,
+						  fid);
+	else if (!strcmp(kstr,""))
+		KMLFileTokenParse(&draword   ,
+						  kstr,
+						  fid);
+
+	else if (!strncmp(kstr,"Read(fid,kstr);
+	}
+
+	else if (!strncmp(kstr,"<",1))
+		KML_Feature::Read(fid,kstr);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Overlay.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Overlay.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Overlay.h	(revision 13395)
@@ -0,0 +1,49 @@
+/*! \file KML_Overlay.h 
+ *  \brief: header file for kml_overlay abstract object
+ */
+
+#ifndef _KML_OVERLAY_H_
+#define _KML_OVERLAY_H_
+
+#define KML_OVERLAY_COLOR_LENGTH  8
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Feature.h"
+class KML_Icon;
+/*}}}*/
+
+class KML_Overlay: public KML_Feature {
+
+	public:
+
+		char  color[KML_OVERLAY_COLOR_LENGTH+1];
+		int   draword;
+		KML_Icon* icon;
+
+		/*KML_Overlay constructors, destructors {{{*/
+		KML_Overlay();
+		~KML_Overlay();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_OVERLAY_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Placemark.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Placemark.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Placemark.cpp	(revision 13395)
@@ -0,0 +1,210 @@
+/*!\file KML_Placemark.cpp
+ * \brief: implementation of the kml_placemark object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Placemark::KML_Placemark(){{{*/
+KML_Placemark::KML_Placemark(){
+
+	geometry  =new DataSet;
+
+}
+/*}}}*/
+/*FUNCTION KML_Placemark::~KML_Placemark(){{{*/
+KML_Placemark::~KML_Placemark(){
+
+	if (geometry) {
+		delete geometry;
+		geometry  =NULL;
+	}
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Placemark::Echo {{{*/
+void  KML_Placemark::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_Placemark:");
+	KML_Feature::Echo();
+
+	if(flag) _pprintLine_("      geometry: (size=" << geometry->Size() << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Placemark::DeepEcho {{{*/
+void  KML_Placemark::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Placemark::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Placemark::DeepEcho {{{*/
+void  KML_Placemark::DeepEcho(const char* indent){
+
+	int   i;
+	char  indent2[81];
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_Placemark:");
+	KML_Feature::DeepEcho(indent);
+
+/*  loop over the geometry elements for the placemark  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+	if (geometry->Size())
+		for (i=0; iSize(); i++) {
+			if(flag) _pprintLine_(indent << "      geometry: -------- begin [" << i << "] --------");
+			((KML_Geometry *)geometry->GetObjectByOffset(i))->DeepEcho(indent2);
+			if(flag) _pprintLine_(indent << "      geometry: --------  end  [" << i << "] --------");
+		}
+	else
+		if(flag) _pprintLine_(indent << "      geometry: [empty]");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Placemark::Write {{{*/
+void  KML_Placemark::Write(FILE* filout,const char* indent){
+
+	int   i;
+	char  indent2[81];
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Feature::Write(filout,indent);
+
+/*  loop over the geometry elements for the placemark  */
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+
+	strcat(indent2,"  ");
+
+	for (i=0; iSize(); i++)
+		((KML_Geometry *)geometry->GetObjectByOffset(i))->Write(filout,indent2);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Placemark::Read {{{*/
+void  KML_Placemark::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+	KML_Object*  kobj;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+			geometry  ->AddObject((Object*)kobj);
+		}
+
+		else if (!strncmp(kstri,"<",1))
+			KML_Feature::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Placemark::WriteExp {{{*/
+void  KML_Placemark::WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp){
+
+	int   i;
+	char  nstr2[81];
+
+/*  loop over the geometry elements for the placemark  */
+
+	for (i=0; iSize(); i++) {
+		if (strlen(nstr))
+			sprintf(nstr2,"%s %s",nstr,name);
+		else
+			sprintf(nstr2,"%s",name);
+
+		((KML_Object *)geometry->GetObjectByOffset(i))->WriteExp(fid,nstr2,sgn,cm,sp);
+	}
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Placemark.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Placemark.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Placemark.h	(revision 13395)
@@ -0,0 +1,47 @@
+/*! \file KML_Placemark.h 
+ *  \brief: header file for kml_placemark object
+ */
+
+#ifndef _KML_PLACEMARK_H_
+#define _KML_PLACEMARK_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Feature.h"
+class KML_Geometry;
+class DataSet;
+/*}}}*/
+
+class KML_Placemark: public KML_Feature {
+
+	public:
+
+		DataSet* geometry;
+
+		/*KML_Placemark constructors, destructors {{{*/
+		KML_Placemark();
+		~KML_Placemark();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		void  WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_PLACEMARK_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Point.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Point.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Point.cpp	(revision 13395)
@@ -0,0 +1,193 @@
+/*!\file KML_Point.cpp
+ * \brief: implementation of the kml_point object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+#include "../../../modules/Ll2xyx/Ll2xyx.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Point::KML_Point(){{{*/
+KML_Point::KML_Point(){
+
+	extrude   =false;
+	memcpy(altmode,"clampToGround",(strlen("clampToGround")+1)*sizeof(char));
+
+	coords[0] = 0.;
+	coords[1] = 0.;
+	coords[2] = 0.;
+
+}
+/*}}}*/
+/*FUNCTION KML_Point::~KML_Point(){{{*/
+KML_Point::~KML_Point(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Point::Echo {{{*/
+void  KML_Point::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_Point:");
+	KML_Geometry::Echo();
+
+	if(flag) _pprintLine_("       extrude: " << (extrude ? "true" : "false"));
+	if(flag) _pprintLine_("       altmode: \"" << altmode << "\"");
+	if(flag) _pprintLine_("        coords: (" << coords[0] << "," << coords[1] << "," << coords[2] << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Point::DeepEcho {{{*/
+void  KML_Point::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Point::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Point::DeepEcho {{{*/
+void  KML_Point::DeepEcho(const char* indent){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_Point:");
+	KML_Geometry::DeepEcho(indent);
+
+	if(flag) _pprintLine_(indent << "       extrude: " << (extrude ? "true" : "false"));
+	if(flag) _pprintLine_(indent << "       altmode: \"" << altmode << "\"");
+	if(flag) _pprintLine_(indent << "        coords: (" << coords[0] << "," << coords[1] << "," << coords[2] << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Point::Write {{{*/
+void  KML_Point::Write(FILE* filout,const char* indent){
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Geometry::Write(filout,indent);
+
+	fprintf(filout,"%s  %d\n",indent,(extrude ? 1 : 0));
+	fprintf(filout,"%s  %s\n",indent,altmode);
+	fprintf(filout,"%s  %0.16g,%0.16g,%0.16g\n",
+			indent,coords[0],coords[1],coords[2]);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Point::Read {{{*/
+void  KML_Point::Read(FILE* fid,char* kstr){
+
+	double*      pcoords=&coords[0];
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,""))
+			KMLFileTokenParse(&extrude   , kstri, fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse( altmode   ,NULL,KML_POINT_ALTMODE_LENGTH, kstri, fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&pcoords   ,NULL,3, kstri, fid);
+
+		else if (!strncmp(kstri,"<",1))
+			KML_Geometry::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Point::WriteExp {{{*/
+void  KML_Point::WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp){
+
+	int     i;
+	double  lat,lon,x,y;
+	char    nstr2[81];
+
+/*  extract latitude and longitude  */
+
+	lon=coords[0];
+	lat=coords[1];
+
+/*  convert latitude and longitude to x and y  */
+
+	Ll2xyx(&x,&y,&lat,&lon,1,sgn,cm,sp);
+
+/*  write header  */
+
+	memcpy(nstr2,nstr,(strlen(nstr)+1)*sizeof(char));
+
+	for (i=0; i
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_PolyStyle::KML_PolyStyle(){{{*/
+KML_PolyStyle::KML_PolyStyle(){
+
+	fill      =true;
+	outline   =true;
+
+}
+/*}}}*/
+/*FUNCTION KML_PolyStyle::~KML_PolyStyle(){{{*/
+KML_PolyStyle::~KML_PolyStyle(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_PolyStyle::Echo {{{*/
+void  KML_PolyStyle::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_PolyStyle:");
+	KML_ColorStyle::Echo();
+
+	if(flag) _pprintLine_("          fill: " << fill);
+	if(flag) _pprintLine_("       outline: " << outline);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_PolyStyle::DeepEcho {{{*/
+void  KML_PolyStyle::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_PolyStyle::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_PolyStyle::DeepEcho {{{*/
+void  KML_PolyStyle::DeepEcho(const char* indent){
+
+	int   i;
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_PolyStyle:");
+	KML_ColorStyle::DeepEcho(indent);
+
+	if(flag) _pprintLine_(indent << "          fill: " << fill);
+	if(flag) _pprintLine_(indent << "       outline: " << outline);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_PolyStyle::Write {{{*/
+void  KML_PolyStyle::Write(FILE* filout,const char* indent){
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_ColorStyle::Write(filout,indent);
+
+	fprintf(filout,"%s  %d\n",indent,fill);
+	fprintf(filout,"%s  %d\n",indent,outline);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_PolyStyle::Read {{{*/
+void  KML_PolyStyle::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,""))
+			KMLFileTokenParse(&fill      ,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&outline   ,
+							  kstri,
+							  fid);
+
+		else if (!strncmp(kstri,"<",1))
+			KML_ColorStyle::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_PolyStyle.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_PolyStyle.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_PolyStyle.h	(revision 13395)
@@ -0,0 +1,45 @@
+/*! \file KML_PolyStyle.h 
+ *  \brief: header file for kml_polystyle object
+ */
+
+#ifndef _KML_POLYSTYLE_H_
+#define _KML_POLYSTYLE_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_ColorStyle.h"
+/*}}}*/
+
+class KML_PolyStyle: public KML_ColorStyle {
+
+	public:
+
+		int   fill;
+		int   outline;
+
+		/*KML_PolyStyle constructors, destructors {{{*/
+		KML_PolyStyle();
+		~KML_PolyStyle();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_POLYSTYLE_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Polygon.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Polygon.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Polygon.cpp	(revision 13395)
@@ -0,0 +1,298 @@
+/*!\file KML_Polygon.cpp
+ * \brief: implementation of the kml_polygon object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Polygon::KML_Polygon(){{{*/
+KML_Polygon::KML_Polygon(){
+
+	extrude   =false;
+	tessellate=false;
+	memcpy(altmode,"clampToGround",(strlen("clampToGround")+1)*sizeof(char));
+
+	outer     =new DataSet;
+	inner     =new DataSet;
+
+}
+/*}}}*/
+/*FUNCTION KML_Polygon::~KML_Polygon(){{{*/
+KML_Polygon::~KML_Polygon(){
+
+	if (inner) {
+		delete inner;
+		inner     =NULL;
+	}
+
+	if (outer) {
+		delete outer;
+		outer     =NULL;
+	}
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Polygon::Echo {{{*/
+void  KML_Polygon::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_Polygon:");
+	KML_Geometry::Echo();
+
+	if(flag) _pprintLine_("       extrude: " << (extrude ? "true" : "false"));
+	if(flag) _pprintLine_("    tessellate: " << (tessellate ? "true" : "false"));
+	if(flag) _pprintLine_("       altmode: \"" << altmode << "\"");
+	if(flag) _pprintLine_("         outer: (size=" << outer->Size() << ")");
+	if(flag) _pprintLine_("         inner: (size=" << inner->Size() << ")");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Polygon::DeepEcho {{{*/
+void  KML_Polygon::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Polygon::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Polygon::DeepEcho {{{*/
+void  KML_Polygon::DeepEcho(const char* indent){
+
+	int   i;
+	char  indent2[81];
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_Polygon:");
+	KML_Geometry::DeepEcho(indent);
+
+	if(flag) _pprintLine_(indent << "       extrude: " << (extrude ? "true" : "false"));
+	if(flag) _pprintLine_(indent << "    tessellate: " << (tessellate ? "true" : "false"));
+	if(flag) _pprintLine_(indent << "       altmode: \"" << altmode << "\"");
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+	if (outer->Size())
+		for (i=0; iSize(); i++) {
+			if(flag) _pprintLine_(indent << "         outer: -------- begin [" << i << "] --------");
+			((KML_LinearRing *)outer->GetObjectByOffset(i))->DeepEcho(indent2);
+			if(flag) _pprintLine_(indent << "         outer: --------  end  [" << i << "] --------");
+		}
+	else
+		if(flag) _pprintLine_(indent << "         outer: [empty]");
+
+	if (inner->Size())
+		for (i=0; iSize(); i++) {
+			if(flag) _pprintLine_(indent << "         inner: -------- begin [" << i << "] --------");
+			((KML_LinearRing *)inner->GetObjectByOffset(i))->DeepEcho(indent2);
+			if(flag) _pprintLine_(indent << "         inner: --------  end  [" << i << "] --------");
+		}
+	else
+		if(flag) _pprintLine_(indent << "         inner: [empty]");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Polygon::Write {{{*/
+void  KML_Polygon::Write(FILE* filout,const char* indent){
+
+	int   i;
+	char  indent4[81];
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_Geometry::Write(filout,indent);
+
+	fprintf(filout,"%s  %d\n",indent,(extrude ? 1 : 0));
+	fprintf(filout,"%s  %d\n",indent,(tessellate ? 1 : 0));
+	fprintf(filout,"%s  %s\n",indent,altmode);
+
+	memcpy(indent4,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent4,"    ");
+
+/*  check outer boundary for the polygon  */
+
+	fprintf(filout,"%s  \n",indent);
+	if (outer->Size())
+		((KML_LinearRing *)outer->GetObjectByOffset(0))->Write(filout,indent4);
+	fprintf(filout,"%s  \n",indent);
+
+/*  loop over any inner boundaries for the polygon  */
+
+	for (i=0; iSize(); i++) {
+		fprintf(filout,"%s  \n",indent);
+		((KML_LinearRing *)inner->GetObjectByOffset(i))->Write(filout,indent4);
+		fprintf(filout,"%s  \n",indent);
+	}
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Polygon::Read {{{*/
+void  KML_Polygon::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	char*        kstrj;
+	int          ncom=0;
+	char**       pcom=NULL;
+	KML_Object*  kobj;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,""))
+			KMLFileTokenParse(&extrude   ,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse(&tessellate,
+							  kstri,
+							  fid);
+		else if (!strcmp(kstri,""))
+			KMLFileTokenParse( altmode   ,NULL,KML_POLYGON_ALTMODE_LENGTH,
+							  kstri,
+							  fid);
+
+		else if (!strcmp(kstri,""))
+
+/*  loop over and process fields within outer boundary  */
+
+			while (kstrj=KMLFileToken(fid,
+									  &ncom,&pcom)) {
+				if      (!strncmp(kstrj,"(kstrj);
+					break;
+				}
+				else if (!strncmp(kstrj,"Read(fid,kstrj);
+					outer     ->AddObject((Object*)kobj);
+				}
+
+				else if (!strncmp(kstrj,"<",1))
+					KML_Geometry::Read(fid,kstrj);
+
+				xDelete(kstrj);
+			}
+
+		else if (!strcmp(kstri,""))
+
+/*  loop over and process fields within inner boundaries  */
+
+			while (kstrj=KMLFileToken(fid,
+									  &ncom,&pcom)) {
+				if      (!strncmp(kstrj,"(kstrj);
+					break;
+				}
+				else if (!strncmp(kstrj,"Read(fid,kstrj);
+					inner     ->AddObject((Object*)kobj);
+				}
+
+				else if (!strncmp(kstrj,"<",1))
+					KML_Geometry::Read(fid,kstrj);
+
+				xDelete(kstrj);
+			}
+
+
+		else if (!strncmp(kstri,"<",1))
+			KML_Geometry::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Polygon::WriteExp {{{*/
+void  KML_Polygon::WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp){
+
+	int   i;
+	char  nstr2[81];
+
+/*  check outer boundary for the polygon  */
+
+	if (outer->Size()) {
+		if (strlen(nstr))
+			sprintf(nstr2,"%s (outer)",nstr);
+		else
+			sprintf(nstr2,"(outer)");
+
+		((KML_LinearRing *)outer->GetObjectByOffset(0))->WriteExp(fid,nstr2,sgn,cm,sp);
+	}
+
+/*  loop over any inner boundaries for the polygon  */
+
+	for (i=0; iSize(); i++) {
+		if (strlen(nstr))
+			sprintf(nstr2,"%s (inner %d of %d)",nstr,i+1,inner->Size());
+		else
+			sprintf(nstr2,"(inner %d of %d)",i+1,inner->Size());
+
+		((KML_LinearRing *)inner->GetObjectByOffset(i))->WriteExp(fid,nstr2,sgn,cm,sp);
+	}
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Polygon.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Polygon.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Polygon.h	(revision 13395)
@@ -0,0 +1,53 @@
+/*! \file KML_Polygon.h 
+ *  \brief: header file for kml_polygon object
+ */
+
+#ifndef _KML_POLYGON_H_
+#define _KML_POLYGON_H_
+
+#define KML_POLYGON_ALTMODE_LENGTH    18
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Geometry.h"
+class KML_LinearRing;
+class DataSet;
+/*}}}*/
+
+class KML_Polygon: public KML_Geometry {
+
+	public:
+
+		bool  extrude;
+		bool  tessellate;
+		char  altmode[KML_POLYGON_ALTMODE_LENGTH+1];
+		DataSet* outer;
+		DataSet* inner;
+
+		/*KML_Polygon constructors, destructors {{{*/
+		KML_Polygon();
+		~KML_Polygon();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		void  WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_POLYGON_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_Style.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Style.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Style.cpp	(revision 13395)
@@ -0,0 +1,239 @@
+/*!\file KML_Style.cpp
+ * \brief: implementation of the kml_style object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Style::KML_Style(){{{*/
+KML_Style::KML_Style(){
+
+	icon      =NULL;
+	label     =NULL;
+	line      =NULL;
+	poly      =NULL;
+	balloon   =NULL;
+	list      =NULL;
+
+}
+/*}}}*/
+/*FUNCTION KML_Style::~KML_Style(){{{*/
+KML_Style::~KML_Style(){
+
+	if (list) {
+//		delete list;
+		list      =NULL;
+	}
+	if (balloon) {
+//		delete balloon;
+		balloon   =NULL;
+	}
+	if (poly) {
+		delete poly;
+		poly      =NULL;
+	}
+	if (line) {
+		delete line;
+		line      =NULL;
+	}
+	if (label) {
+//		delete label;
+		label     =NULL;
+	}
+	if (icon) {
+//		delete icon;
+		icon      =NULL;
+	}
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Style::Echo {{{*/
+void  KML_Style::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_Style:");
+	KML_StyleSelector::Echo();
+
+	if(flag) _pprintLine_("          icon: " << icon);
+	if(flag) _pprintLine_("         label: " << label);
+	if(flag) _pprintLine_("          line: " << line);
+	if(flag) _pprintLine_("          poly: " << poly);
+	if(flag) _pprintLine_("       balloon: " << balloon);
+	if(flag) _pprintLine_("          list: " << list);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Style::DeepEcho {{{*/
+void  KML_Style::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Style::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Style::DeepEcho {{{*/
+void  KML_Style::DeepEcho(const char* indent){
+
+	char  indent2[81];
+	bool  flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_Style:");
+	KML_StyleSelector::DeepEcho(indent);
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+	strcat(indent2,"  ");
+
+//	if (icon)
+//		icon->DeepEcho(indent2);
+//	else
+		if(flag) _pprintLine_(indent << "          icon: " << icon);
+//	if (label)
+//		label->DeepEcho(indent2);
+//	else
+		if(flag) _pprintLine_(indent << "         label: " << label);
+	if (line)
+		line->DeepEcho(indent2);
+	else
+		if(flag) _pprintLine_(indent << "          line: " << line);
+	if (poly)
+		poly->DeepEcho(indent2);
+	else
+		if(flag) _pprintLine_(indent << "          poly: " << poly);
+//	if (balloon)
+//		balloon->DeepEcho(indent2);
+//	else
+		if(flag) _pprintLine_(indent << "       balloon: " << balloon);
+//	if (list)
+//		list->DeepEcho(indent2);
+//	else
+		if(flag) _pprintLine_(indent << "          list: " << list);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Style::Write {{{*/
+void  KML_Style::Write(FILE* filout,const char* indent){
+
+	char  indent2[81];
+
+	fprintf(filout,"%s\n");
+	WriteCommnt(filout,indent);
+
+	KML_StyleSelector::Write(filout,indent);
+
+	memcpy(indent2,indent,(strlen(indent)+1)*sizeof(char));
+
+	strcat(indent2,"  ");
+
+//	if (icon)
+//		icon->Write(filout,indent2);
+//	if (label)
+//		label->Write(filout,indent2);
+	if (line)
+		line->Write(filout,indent2);
+	if (poly)
+		poly->Write(filout,indent2);
+//	if (balloon)
+//		balloon->Write(filout,indent2);
+//	if (list)
+//		list->Write(filout,indent2);
+
+	fprintf(filout,"%s\n",indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Style::Read {{{*/
+void  KML_Style::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	int          ncom=0;
+	char**       pcom=NULL;
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+		if      (!strncmp(kstri,"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,"Read(fid,kstri);
+//		}
+
+//		else if (!strncmp(kstri,"Read(fid,kstri);
+//		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+		}
+
+		else if (!strncmp(kstri,"Read(fid,kstri);
+		}
+
+//		else if (!strncmp(kstri,"Read(fid,kstri);
+//		}
+
+//		else if (!strncmp(kstri,"Read(fid,kstri);
+//		}
+
+		else if (!strncmp(kstri,"<",1))
+			KML_StyleSelector::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Style.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Style.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Style.h	(revision 13395)
@@ -0,0 +1,51 @@
+/*! \file KML_Style.h 
+ *  \brief: header file for kml_style object
+ */
+
+#ifndef _KML_STYLE_H_
+#define _KML_STYLE_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_StyleSelector.h"
+class KML_LineStyle;
+class KML_PolyStyle;
+/*}}}*/
+
+class KML_Style: public KML_StyleSelector {
+
+	public:
+
+		void* icon;
+		void* label;
+		KML_LineStyle* line;
+		KML_PolyStyle* poly;
+		void* balloon;
+		void* list;
+
+		/*KML_Style constructors, destructors {{{*/
+		KML_Style();
+		~KML_Style();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_STYLE_H */
+
Index: /issm/trunk/src/c/classes/objects/KML/KML_StyleSelector.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_StyleSelector.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_StyleSelector.cpp	(revision 13395)
@@ -0,0 +1,95 @@
+/*!\file KML_StyleSelector.cpp
+ * \brief: implementation of the kml_styleselector abstract object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_StyleSelector::KML_StyleSelector(){{{*/
+KML_StyleSelector::KML_StyleSelector(){
+
+	;
+
+}
+/*}}}*/
+/*FUNCTION KML_StyleSelector::~KML_StyleSelector(){{{*/
+KML_StyleSelector::~KML_StyleSelector(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_StyleSelector::Echo {{{*/
+void  KML_StyleSelector::Echo(){
+
+	KML_Object::Echo();
+
+	return;
+}
+/*}}}*/
+
+/*FUNCTION KML_StyleSelector::DeepEcho {{{*/
+void  KML_StyleSelector::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_StyleSelector::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+
+/*FUNCTION KML_StyleSelector::DeepEcho {{{*/
+void  KML_StyleSelector::DeepEcho(const char* indent){
+
+	KML_Object::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+
+/*FUNCTION KML_StyleSelector::Write {{{*/
+void  KML_StyleSelector::Write(FILE* filout,const char* indent){
+
+	KML_Object::Write(filout,indent);
+
+	return;
+}
+/*}}}*/
+
+/*FUNCTION KML_StyleSelector::Read {{{*/
+void  KML_StyleSelector::Read(FILE* fid,char* kstr){
+
+/*  process field within opening and closing tags  */
+
+	if      (!strncmp(kstr,"
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_SubStyle::KML_SubStyle(){{{*/
+KML_SubStyle::KML_SubStyle(){
+
+	;
+
+}
+/*}}}*/
+/*FUNCTION KML_SubStyle::~KML_SubStyle(){{{*/
+KML_SubStyle::~KML_SubStyle(){
+
+	;
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_SubStyle::Echo {{{*/
+void  KML_SubStyle::Echo(){
+
+	KML_Object::Echo();
+
+	return;
+}
+/*}}}*/
+
+/*FUNCTION KML_SubStyle::DeepEcho {{{*/
+void  KML_SubStyle::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_SubStyle::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+
+/*FUNCTION KML_SubStyle::DeepEcho {{{*/
+void  KML_SubStyle::DeepEcho(const char* indent){
+
+	KML_Object::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+
+/*FUNCTION KML_SubStyle::Write {{{*/
+void  KML_SubStyle::Write(FILE* filout,const char* indent){
+
+	KML_Object::Write(filout,indent);
+
+	return;
+}
+/*}}}*/
+
+/*FUNCTION KML_SubStyle::Read {{{*/
+void  KML_SubStyle::Read(FILE* fid,char* kstr){
+
+/*  process field within opening and closing tags  */
+
+	if      (!strncmp(kstr,"
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../io/io.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*Constructors/destructor/copy*/
+/*FUNCTION KML_Unknown::KML_Unknown(){{{*/
+KML_Unknown::KML_Unknown(){
+
+	name      =NULL;
+	value     =NULL;
+
+}
+/*}}}*/
+/*FUNCTION KML_Unknown::~KML_Unknown(){{{*/
+KML_Unknown::~KML_Unknown(){
+
+	if (name      ) xDelete(name);
+	if (value     ) xDelete(value);
+
+}
+/*}}}*/
+
+/*Other*/
+/*FUNCTION KML_Unknown::Echo {{{*/
+void  KML_Unknown::Echo(){
+
+	bool  flag=true;
+
+	if(flag) _pprintLine_("KML_Unknown " << name << ":");
+	KML_Object::Echo();
+
+	if (value     )
+		if(flag) _pprintLine_("         value: \"" << value << "\"");
+    else
+        if(flag) _pprintLine_("         value: [none]");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Unknown::DeepEcho {{{*/
+void  KML_Unknown::DeepEcho(){
+
+	char  indent[81]="";
+
+	KML_Unknown::DeepEcho(indent);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Unknown::DeepEcho {{{*/
+void  KML_Unknown::DeepEcho(const char* indent){
+
+	char*        valuei;
+	char*        vtoken;
+	char         nl[]={'\n','\0'};
+	bool         flag=true;
+
+	if(flag) _pprintLine_(indent << "KML_Unknown " << name << ":");
+	KML_Object::DeepEcho(indent);
+
+	if (value     ) {
+		valuei=xNew(strlen(value)+1);
+		memcpy(valuei,value,(strlen(value)+1)*sizeof(char)); 
+        
+		vtoken=strtok(valuei,nl);
+		if(flag) _pprintString_(indent << "         value: \"" << vtoken);
+    
+		while (vtoken=strtok(NULL,nl))
+			if(flag) _pprintString_("\n" << indent << "                 " << vtoken);
+		if(flag) _pprintLine_("\"");
+
+		xDelete(valuei);
+	}
+    else
+        if(flag) _pprintLine_(indent << "         value: [none]");
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Unknown::Write {{{*/
+void  KML_Unknown::Write(FILE* filout,const char* indent){
+
+	char*        valuei;
+	char*        vtoken;
+	char         nl[]={'\n','\0'};
+
+	fprintf(filout,"%s<%s",indent,name);
+	WriteAttrib(filout," ");
+	fprintf(filout,">\n");
+	WriteCommnt(filout,indent);
+
+	if (value     ) {
+		valuei=xNew(strlen(value)+1);
+		memcpy(valuei,value,(strlen(value)+1)*sizeof(char)); 
+        
+		vtoken=strtok(valuei,nl);
+		fprintf(filout,"%s  %s\n",indent,vtoken);
+    
+		while (vtoken=strtok(NULL,nl))
+			fprintf(filout,"%s  %s\n",indent,vtoken);
+
+		xDelete(valuei);
+	}
+
+	KML_Object::Write(filout,indent);
+
+	fprintf(filout,"%s\n",indent,name);
+
+	return;
+}
+/*}}}*/
+/*FUNCTION KML_Unknown::Read {{{*/
+void  KML_Unknown::Read(FILE* fid,char* kstr){
+
+	char*        kstri;
+	char*        value2=NULL;
+	int          ncom=0;
+	char**       pcom=NULL;
+	char         nl[]={'\n','\0'};
+
+/*  get object name  */
+
+	name=KMLFileTagName(NULL,
+						kstr);
+//	_pprintLine_("KML_Unknown::Read -- opening name=" << name << ".");
+
+/*  get object attributes and check for solo tag  */
+
+	if (KMLFileTagAttrib(this,
+						 kstr))
+		return;
+
+/*  loop over and process fields within opening and closing tags  */
+
+	while (kstri=KMLFileToken(fid,
+							  &ncom,&pcom)) {
+//		_pprintLine_("KML_Unknown::Read -- kstri=" << kstri << ".");
+		if      (!strncmp(&kstri[0],"(kstri);
+			break;
+		}
+		else if (!strncmp(kstri,"(strlen(value)+1+strlen(kstri)+1);
+				memcpy(value2,value,(strlen(value)+1)*sizeof(char));
+				xDelete(value);
+				value=value2;
+				value2=NULL;
+//				value=(char *) xrealloc(value,(strlen(value)+1+strlen(kstri)+1)*sizeof(char));
+				strcat(value,nl);
+				strcat(value,kstri);
+			}
+			else {
+				value=xNew(strlen(kstri)+1);
+				memcpy(value,kstri,(strlen(kstri)+1)*sizeof(char));
+			}
+		}
+
+		else if (!strncmp(kstri,"<",1))
+			KML_Object::Read(fid,kstri);
+
+		xDelete(kstri);
+	}
+
+	this->AddCommnt(ncom,pcom);
+
+	for (ncom; ncom>0; ncom--)
+		xDelete(pcom[ncom-1]);
+	xDelete(pcom);
+
+	return;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/KML/KML_Unknown.h
===================================================================
--- /issm/trunk/src/c/classes/objects/KML/KML_Unknown.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/KML/KML_Unknown.h	(revision 13395)
@@ -0,0 +1,45 @@
+/*! \file KML_Unknown.h 
+ *  \brief: header file for kml_unknown object
+ */
+
+#ifndef _KML_UNKNOWN_H_
+#define _KML_UNKNOWN_H_
+
+/*Headers:*/
+/*{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "./KML_Object.h"
+/*}}}*/
+
+class KML_Unknown: public KML_Object {
+
+	public:
+
+		char* name;
+		char* value;
+
+		/*KML_Unknown constructors, destructors {{{*/
+		KML_Unknown();
+		~KML_Unknown();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		void  Echo();
+		void  DeepEcho();
+		void  DeepEcho(const char* indent);
+		void  Write(FILE* fid,const char* indent);
+		void  Read(FILE* fid,char* kstr);
+		int   Id(){_error_("Not implemented yet.");};
+		int   MyRank(){_error_("Not implemented yet.");};
+		void  Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   MarshallSize(){_error_("Not implemented yet.");};
+		void  Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");};
+		int   ObjectEnum(){_error_("Not implemented yet.");};
+		Object* copy(){_error_("Not implemented yet.");};
+		/*}}}*/
+
+};
+#endif  /* _KML_UNKNOWN_H */
+
Index: /issm/trunk/src/c/classes/objects/Loads/Friction.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Friction.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Friction.cpp	(revision 13395)
@@ -0,0 +1,334 @@
+/*!\file Friction.c
+ * \brief: implementation of the Friction object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../Container/Container.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../include/include.h"
+/*}}}*/	
+
+/*Constructors/destructors*/
+/*FUNCTION Friction::Friction() {{{*/
+Friction::Friction(){
+	this->element_type=NULL;
+	this->inputs=NULL;
+	this->matpar=NULL;
+}
+/*}}}*/
+/*FUNCTION Friction::Friction(const char* element_type, Inputs* inputs,Matpar* matpar,int analysis_type){{{*/
+Friction::Friction(const char* element_type_in,Inputs* inputs_in,Matpar* matpar_in, int in_analysis_type){
+
+	this->analysis_type=in_analysis_type;
+	this->inputs=inputs_in;
+	this->element_type=xNew(strlen(element_type_in)+1);
+	xMemCpy(this->element_type,element_type_in,(strlen(element_type_in)+1));
+
+	this->matpar=matpar_in;
+}
+/*}}}*/
+/*FUNCTION Friction::~Friction() {{{*/
+Friction::~Friction(){
+	xDelete(element_type);
+}
+/*}}}*/
+
+/*methods: */
+/*FUNCTION Friction::Echo {{{*/
+void Friction::Echo(void){
+	_printLine_("Friction:");
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	_printLine_("   element_type: " << this->element_type);
+	inputs->Echo();
+	matpar->Echo();
+}
+/*}}}*/
+/*FUNCTION Friction::GetAlpha2(IssmDouble* palpha2, GaussTria* gauss,int vxenum,int vyenum,int vzenum){{{*/
+void Friction::GetAlpha2(IssmDouble* palpha2, GaussTria* gauss,int vxenum,int vyenum,int vzenum){
+
+	/*This routine calculates the basal friction coefficient 
+	  alpha2= drag^2 * Neff ^r * vel ^s, with Neff=rho_ice*g*thickness+rho_ice*g*bed, r=q/p and s=1/p**/
+
+	/*diverse: */
+	IssmDouble  r,s;
+	IssmDouble  drag_p, drag_q;
+	IssmDouble  gravity,rho_ice,rho_water;
+	IssmDouble  Neff;
+	IssmDouble  thickness,bed;
+	IssmDouble  vx,vy,vz,vmag;
+	IssmDouble  drag_coefficient;
+	IssmDouble  alpha2;
+
+	/*Recover parameters: */
+	inputs->GetInputValue(&drag_p,FrictionPEnum);
+	inputs->GetInputValue(&drag_q,FrictionQEnum);
+	this->GetInputValue(&thickness, gauss,ThicknessEnum);
+	this->GetInputValue(&bed, gauss,BedEnum);
+	this->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum);
+
+	/*Get material parameters: */
+	gravity=matpar->GetG();
+	rho_ice=matpar->GetRhoIce();
+	rho_water=matpar->GetRhoWater();
+
+	//compute r and q coefficients: */
+	r=drag_q/drag_p;
+	s=1./drag_p;
+
+	//From bed and thickness, compute effective pressure when drag is viscous:
+	Neff=gravity*(rho_ice*thickness+rho_water*bed);
+
+	/*If effective pressure becomes negative, sliding becomes unstable (Paterson 4th edition p 148). This is because 
+	  the water pressure is so high, the ice sheet elevates over its ice bumps and slides. But the limit behaviour 
+	  for friction should be an ice shelf sliding (no basal drag). Therefore, for any effective pressure Neff < 0, we should 
+	  replace it by Neff=0 (ie, equival it to an ice shelf)*/
+	if (Neff<0)Neff=0;
+
+	if(strcmp(element_type,"2d")==0){
+		this->GetInputValue(&vx, gauss,vxenum);
+		this->GetInputValue(&vy, gauss,vyenum);
+		vmag=sqrt(pow(vx,2)+pow(vy,2));
+	}
+	else if (strcmp(element_type,"3d")==0){
+		this->GetInputValue(&vx, gauss,vxenum);
+		this->GetInputValue(&vy, gauss,vyenum);
+		this->GetInputValue(&vz, gauss,vzenum);
+		vmag=sqrt(pow(vx,2)+pow(vy,2)+pow(vz,2));
+	}
+	else _error_("element_type "<< element_type << " not supported yet");
+
+	/*Checks that s-1>0 if v=0*/
+        if(vmag==0 && (s-1)<0) _error_("velocity is 0 and (s-1)=" << (s-1) << "<0, alpha_complement is Inf");
+
+	alpha2=pow(drag_coefficient,2)*pow(Neff,r)*pow(vmag,(s-1));
+	_assert_(!xIsNan(alpha2));
+
+	/*Assign output pointers:*/
+	*palpha2=alpha2;
+}
+/*}}}*/
+/*FUNCTION Friction::GetAlpha2(IssmDouble* palpha2, GaussPenta* gauss,int vxenum,int vyenum,int vzenum){{{*/
+void Friction::GetAlpha2(IssmDouble* palpha2, GaussPenta* gauss,int vxenum,int vyenum,int vzenum){
+
+	/*This routine calculates the basal friction coefficient 
+	  alpha2= drag^2 * Neff ^r * vel ^s, with Neff=rho_ice*g*thickness+rho_ice*g*bed, r=q/p and s=1/p**/
+
+	/*diverse: */
+	IssmDouble  r,s;
+	IssmDouble  drag_p, drag_q;
+	IssmDouble  gravity,rho_ice,rho_water;
+	IssmDouble  Neff;
+	IssmDouble  thickness,bed;
+	IssmDouble  vx,vy,vz,vmag;
+	IssmDouble  drag_coefficient;
+	IssmDouble  alpha2;
+
+	/*Recover parameters: */
+	inputs->GetInputValue(&drag_p,FrictionPEnum);
+	inputs->GetInputValue(&drag_q,FrictionQEnum);
+	this->GetInputValue(&thickness, gauss,ThicknessEnum);
+	this->GetInputValue(&bed, gauss,BedEnum);
+	this->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum);
+
+	/*Get material parameters: */
+	gravity=matpar->GetG();
+	rho_ice=matpar->GetRhoIce();
+	rho_water=matpar->GetRhoWater();
+
+	//compute r and q coefficients: */
+	r=drag_q/drag_p;
+	s=1./drag_p;
+
+	//From bed and thickness, compute effective pressure when drag is viscous:
+	Neff=gravity*(rho_ice*thickness+rho_water*bed);
+
+	/*If effective pressure becomes negative, sliding becomes unstable (Paterson 4th edition p 148). This is because 
+	  the water pressure is so high, the ice sheet elevates over its ice bumps and slides. But the limit behaviour 
+	  for friction should be an ice shelf sliding (no basal drag). Therefore, for any effective pressure Neff < 0, we should 
+	  replace it by Neff=0 (ie, equival it to an ice shelf)*/
+	if (Neff<0)Neff=0;
+
+	if(strcmp(element_type,"2d")==0){
+		this->GetInputValue(&vx, gauss,vxenum);
+		this->GetInputValue(&vy, gauss,vyenum);
+		vmag=sqrt(pow(vx,2)+pow(vy,2));
+	}
+	else if (strcmp(element_type,"3d")==0){
+		this->GetInputValue(&vx, gauss,vxenum);
+		this->GetInputValue(&vy, gauss,vyenum);
+		this->GetInputValue(&vz, gauss,vzenum);
+		vmag=sqrt(pow(vx,2)+pow(vy,2)+pow(vz,2));
+	}
+	else _error_("element_type "<< element_type << " not supported yet");
+
+	/*Checks that s-1>0 if v=0*/
+	if(vmag==0 && (s-1)<0) _error_("velocity is 0 and (s-1)=" << (s-1) << "<0, alpha_complement is Inf");
+
+	alpha2=pow(drag_coefficient,2)*pow(Neff,r)*pow(vmag,(s-1));
+	_assert_(!xIsNan(alpha2));
+
+	/*Assign output pointers:*/
+	*palpha2=alpha2;
+}
+/*}}}*/
+/*FUNCTION Friction::GetAlphaComplement(IssmDouble* palpha_complement, GaussTria* gauss,int vxenum,int vyenum,int vzenum) {{{*/
+void Friction::GetAlphaComplement(IssmDouble* palpha_complement, GaussTria* gauss,int vxenum,int vyenum,int vzenum){
+
+	/* FrictionGetAlpha2 computes alpha2= drag^2 * Neff ^r * vel ^s, with Neff=rho_ice*g*thickness+rho_ice*g*bed, r=q/p and s=1/p. 
+	 * FrictionGetAlphaComplement is used in control methods on drag, and it computes: 
+	 * alpha_complement= Neff ^r * vel ^s*/
+
+	/*diverse: */
+	int     i;
+	IssmDouble  r,s;
+	IssmDouble  vx,vy,vz,vmag;
+	IssmDouble  drag_p,drag_q;
+	IssmDouble  Neff;
+	IssmDouble  drag_coefficient;
+	IssmDouble  bed,thickness;
+	IssmDouble  gravity,rho_ice,rho_water;
+	IssmDouble  alpha_complement;
+
+	/*Recover parameters: */
+	inputs->GetInputValue(&drag_p,FrictionPEnum);
+	inputs->GetInputValue(&drag_q,FrictionQEnum);
+	this->GetInputValue(&thickness, gauss,ThicknessEnum);
+	this->GetInputValue(&bed, gauss,BedEnum);
+	this->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum);
+
+	/*Get material parameters: */
+	gravity=matpar->GetG();
+	rho_ice=matpar->GetRhoIce();
+	rho_water=matpar->GetRhoWater();
+
+	//compute r and q coefficients: */
+	r=drag_q/drag_p;
+	s=1./drag_p;
+
+	//From bed and thickness, compute effective pressure when drag is viscous:
+	Neff=gravity*(rho_ice*thickness+rho_water*bed);
+
+	/*If effective pressure becomes negative, sliding becomes unstable (Paterson 4th edition p 148). This is because 
+	  the water pressure is so high, the ice sheet elevates over its ice bumps and slides. But the limit behaviour 
+	  for friction should be an ice shelf sliding (no basal drag). Therefore, for any effective pressure Neff < 0, we should 
+	  replace it by Neff=0 (ie, equival it to an ice shelf)*/
+	if (Neff<0)Neff=0;
+
+	//We need the velocity magnitude to evaluate the basal stress:
+	if(strcmp(element_type,"2d")==0){
+		this->GetInputValue(&vx, gauss,vxenum);
+		this->GetInputValue(&vy, gauss,vyenum);
+		vmag=sqrt(pow(vx,2)+pow(vy,2));
+	}
+	else if (strcmp(element_type,"3d")==0){
+		this->GetInputValue(&vx, gauss,vxenum);
+		this->GetInputValue(&vy, gauss,vyenum);
+		this->GetInputValue(&vz, gauss,vzenum);
+		vmag=sqrt(pow(vx,2)+pow(vy,2)+pow(vz,2));
+	}
+	else _error_("element_type "<< element_type << " not supported yet");
+
+	/*Checks that s-1>0 if v=0*/
+	if(vmag==0 && (s-1)<0) _error_("velocity is 0 and (s-1)=" << (s-1) << "<0, alpha_complement is Inf");
+
+	alpha_complement=pow(Neff,r)*pow(vmag,(s-1));            _assert_(!xIsNan(alpha_complement));
+
+	/*Assign output pointers:*/
+	*palpha_complement=alpha_complement;
+}
+/*}}}*/
+/*FUNCTION Friction::GetAlphaComplement(IssmDouble* palpha_complement, GaussPenta* gauss,int vxenum,int vyenum,int vzenum) {{{*/
+void Friction::GetAlphaComplement(IssmDouble* palpha_complement, GaussPenta* gauss,int vxenum,int vyenum,int vzenum){
+
+	/* FrictionGetAlpha2 computes alpha2= drag^2 * Neff ^r * vel ^s, with Neff=rho_ice*g*thickness+rho_ice*g*bed, r=q/p and s=1/p. 
+	 * FrictionGetAlphaComplement is used in control methods on drag, and it computes: 
+	 * alpha_complement= Neff ^r * vel ^s*/
+
+	/*diverse: */
+	int     i;
+	IssmDouble  r,s;
+	IssmDouble  vx,vy,vz,vmag;
+	IssmDouble  drag_p,drag_q;
+	IssmDouble  Neff;
+	IssmDouble  drag_coefficient;
+	IssmDouble  bed,thickness;
+	IssmDouble  gravity,rho_ice,rho_water;
+	IssmDouble  alpha_complement;
+
+	/*Recover parameters: */
+	inputs->GetInputValue(&drag_p,FrictionPEnum);
+	inputs->GetInputValue(&drag_q,FrictionQEnum);
+	this->GetInputValue(&thickness, gauss,ThicknessEnum);
+	this->GetInputValue(&bed, gauss,BedEnum);
+	this->GetInputValue(&drag_coefficient, gauss,FrictionCoefficientEnum);
+
+	/*Get material parameters: */
+	gravity=matpar->GetG();
+	rho_ice=matpar->GetRhoIce();
+	rho_water=matpar->GetRhoWater();
+
+	//compute r and q coefficients: */
+	r=drag_q/drag_p;
+	s=1./drag_p;
+
+	//From bed and thickness, compute effective pressure when drag is viscous:
+	Neff=gravity*(rho_ice*thickness+rho_water*bed);
+
+	/*If effective pressure becomes negative, sliding becomes unstable (Paterson 4th edition p 148). This is because 
+	  the water pressure is so high, the ice sheet elevates over its ice bumps and slides. But the limit behaviour 
+	  for friction should be an ice shelf sliding (no basal drag). Therefore, for any effective pressure Neff < 0, we should 
+	  replace it by Neff=0 (ie, equival it to an ice shelf)*/
+	if (Neff<0)Neff=0;
+
+	//We need the velocity magnitude to evaluate the basal stress:
+	if(strcmp(element_type,"2d")==0){
+		this->GetInputValue(&vx, gauss,vxenum);
+		this->GetInputValue(&vy, gauss,vyenum);
+		vmag=sqrt(pow(vx,2)+pow(vy,2));
+	}
+	else if (strcmp(element_type,"3d")==0){
+		this->GetInputValue(&vx, gauss,vxenum);
+		this->GetInputValue(&vy, gauss,vyenum);
+		this->GetInputValue(&vz, gauss,vzenum);
+		vmag=sqrt(pow(vx,2)+pow(vy,2)+pow(vz,2));
+	}
+	else _error_("element_type "<< element_type << " not supported yet");
+
+	/*Checks that s-1>0 if v=0*/
+	if(vmag==0 && (s-1)<0) _error_("velocity is 0 and (s-1)=" << (s-1) << "<0, alpha_complement is Inf");
+
+	alpha_complement=pow(Neff,r)*pow(vmag,(s-1));            _assert_(!xIsNan(alpha_complement));
+
+	/*Assign output pointers:*/
+	*palpha_complement=alpha_complement;
+}
+/*}}}*/
+/*FUNCTION Friction::GetInputValue{{{*/
+void Friction::GetInputValue(IssmDouble* pvalue,GaussTria* gauss,int enum_type){
+
+	Input* input=inputs->GetInput(enum_type);
+	if(!input) _error_("input " << EnumToStringx(enum_type) << " not found");
+	input->GetInputValue(pvalue,gauss);
+
+}
+/*}}}*/
+/*FUNCTION Friction::GetInputValue{{{*/
+void Friction::GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,int enum_type){
+
+	Input* input=inputs->GetInput(enum_type);
+	if(!input) _error_("input " << EnumToStringx(enum_type) << " not found");
+	input->GetInputValue(pvalue,gauss);
+
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Loads/Friction.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Friction.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Friction.h	(revision 13395)
@@ -0,0 +1,38 @@
+/*!\file Friction.h
+ * \brief: header file for friction object
+ */
+
+#ifndef _FRICTION_H_
+#define _FRICTION_H_
+
+/*Headers:*/
+/*{{{*/
+class Inputs;
+class Matpar;
+/*}}}*/
+
+class Friction{
+
+	public:
+		int analysis_type;
+
+		char* element_type;
+		Inputs* inputs;
+		Matpar* matpar;
+
+		/*methods: */
+		Friction();
+		Friction(const char* element_type, Inputs* inputs,Matpar* matpar, int analysis_type);
+		~Friction();
+	
+		void  Echo(void);
+		void  GetAlpha2(IssmDouble* palpha2, GaussTria* gauss,int vxenum,int vyenum,int vzenum);
+		void  GetAlpha2(IssmDouble* palpha2, GaussPenta* gauss,int vxenum,int vyenum,int vzenum);
+		void  GetAlphaComplement(IssmDouble* alpha_complement, GaussTria* gauss,int vxenum,int vyenum,int vzenum);
+		void  GetAlphaComplement(IssmDouble* alpha_complement, GaussPenta* gauss,int vxenum,int vyenum,int vzenum);
+		void  GetInputValue(IssmDouble* pvalue,GaussTria* gauss,int enum_type);
+		void  GetInputValue(IssmDouble* pvalue,GaussPenta* gauss,int enum_type);
+
+};
+
+#endif  /* _FRICTION_H_ */
Index: /issm/trunk/src/c/classes/objects/Loads/Icefront.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Icefront.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Icefront.cpp	(revision 13395)
@@ -0,0 +1,743 @@
+/*!\file Icefront.c
+ * \brief: implementation of the Icefront object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../include/include.h"
+/*}}}*/	
+
+/*Load macros*/
+#define NUMVERTICESSEG 2
+#define NUMVERTICESQUA 4
+
+/*Icefront constructors and destructor*/
+/*FUNCTION Icefront::Icefront() {{{*/
+Icefront::Icefront(){
+
+	this->inputs=NULL;
+	this->parameters=NULL;
+
+	this->hnodes=NULL;
+	this->nodes= NULL;
+	this->helement=NULL;
+	this->element= NULL;
+	this->hmatpar=NULL;
+	this->matpar= NULL;
+}
+/*}}}*/
+/*FUNCTION Icefront::Icefront(int id, int i, IoModel* iomodel,int analysis_type) {{{*/
+Icefront::Icefront(int icefront_id,int i, IoModel* iomodel,int in_icefront_type, int in_analysis_type){
+
+	int segment_width;
+	int element;
+	int num_nodes; 
+	int dim;
+	int numberofelements;
+
+	/*icefront constructor data: */
+	int  icefront_eid;
+	int  icefront_mparid;
+	int  icefront_node_ids[NUMVERTICESQUA]; //initialize with largest size
+	int  icefront_fill;
+	
+	/*find parameters: */
+	iomodel->Constant(&dim,MeshDimensionEnum);
+	iomodel->Constant(&numberofelements,MeshNumberofelementsEnum);
+
+	/*First, retrieve element index and element type: */
+	if (dim==2){
+		segment_width=4;
+	}
+	else{
+		segment_width=6;
+	}
+	_assert_(iomodel->Data(DiagnosticIcefrontEnum));
+	element=reCast(*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+segment_width-2)-1); //element is in the penultimate column (node1 node2 ... elem fill)
+
+	/*Build ids for hook constructors: */
+	icefront_eid=reCast( *(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+segment_width-2)); //matlab indexing
+	icefront_mparid=numberofelements+1; //matlab indexing
+
+	if (in_icefront_type==MacAyeal2dIceFrontEnum || in_icefront_type==MacAyeal3dIceFrontEnum){
+		icefront_node_ids[0]=iomodel->nodecounter+reCast(*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+0));
+		icefront_node_ids[1]=iomodel->nodecounter+reCast(*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+1));
+	}
+	else if (in_icefront_type==PattynIceFrontEnum || in_icefront_type==StokesIceFrontEnum){
+		icefront_node_ids[0]=iomodel->nodecounter+reCast(*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+0));
+		icefront_node_ids[1]=iomodel->nodecounter+reCast(*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+1));
+		icefront_node_ids[2]=iomodel->nodecounter+reCast(*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+2));
+		icefront_node_ids[3]=iomodel->nodecounter+reCast(*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+3));
+	}
+	else _error_("in_icefront_type " << EnumToStringx(in_icefront_type) << " not supported yet!");
+
+	if (in_icefront_type==PattynIceFrontEnum || in_icefront_type==StokesIceFrontEnum)
+	 num_nodes=4;
+	else 
+	 num_nodes=2;
+
+	/*Fill*/
+	icefront_fill=reCast(iomodel->Data(DiagnosticIcefrontEnum)[segment_width*i+segment_width-1]);
+	
+	/*Ok, we have everything to build the object: */
+	this->id=icefront_id;
+	this->analysis_type=in_analysis_type;
+
+	/*Hooks: */
+	this->hnodes=new Hook(icefront_node_ids,num_nodes);
+	this->helement=new Hook(&icefront_eid,1);
+	this->hmatpar=new Hook(&icefront_mparid,1);
+
+	//intialize  and add as many inputs per element as requested: 
+	this->inputs=new Inputs();
+	this->inputs->AddInput(new IntInput(FillEnum,icefront_fill));
+	this->inputs->AddInput(new IntInput(TypeEnum,in_icefront_type));
+	
+	//parameters and hooked fields: we still can't point to them, they may not even exist. Configure will handle this.
+	this->parameters=NULL;
+	this->nodes= NULL;
+	this->element= NULL;
+	this->matpar= NULL;
+}
+
+
+/*}}}*/
+/*FUNCTION Icefront::~Icefront() {{{*/
+Icefront::~Icefront(){
+	delete inputs;
+	this->parameters=NULL;
+	delete hnodes;
+	delete helement;
+	delete hmatpar;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION Icefront::Echo {{{*/
+void Icefront::Echo(void){
+	_printLine_("Icefront:");
+	_printLine_("   id: " << id);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	hnodes->Echo();
+	helement->Echo();
+	hmatpar->Echo();
+	_printLine_("   parameters: " << parameters);
+	if(parameters)parameters->Echo();
+	_printLine_("   inputs: " << inputs);
+	if(inputs)inputs->Echo();
+}
+/*}}}*/
+/*FUNCTION Icefront::DeepEcho{{{*/
+void Icefront::DeepEcho(void){
+
+	_printLine_("Icefront:");
+	_printLine_("   id: " << id);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	hnodes->DeepEcho();
+	helement->DeepEcho();
+	hmatpar->DeepEcho();
+	_printLine_("   parameters: " << parameters);
+	if(parameters)parameters->DeepEcho();
+	_printLine_("   inputs: " << inputs);
+	if(inputs)inputs->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION Icefront::Id {{{*/
+int    Icefront::Id(void){ return id; }
+/*}}}*/
+/*FUNCTION Icefront::MyRank {{{*/
+int    Icefront::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Icefront::ObjectEnum{{{*/
+int Icefront::ObjectEnum(void){
+
+	return IcefrontEnum;
+
+}
+/*}}}*/
+/*FUNCTION Icefront::copy {{{*/
+Object* Icefront::copy() {
+	
+	Icefront* icefront=NULL;
+
+	icefront=new Icefront();
+
+	/*copy fields: */
+	icefront->id=this->id;
+	icefront->analysis_type=this->analysis_type;
+	if(this->inputs){
+		icefront->inputs=(Inputs*)this->inputs->Copy();
+	}
+	else{
+		icefront->inputs=new Inputs();
+	}
+	/*point parameters: */
+	icefront->parameters=this->parameters;
+
+	/*now deal with hooks and objects: */
+	icefront->hnodes=(Hook*)this->hnodes->copy();
+	icefront->helement=(Hook*)this->helement->copy();
+	icefront->hmatpar=(Hook*)this->hmatpar->copy();
+
+	/*corresponding fields*/
+	icefront->nodes  =(Node**)icefront->hnodes->deliverp();
+	icefront->element=(Element*)icefront->helement->delivers();
+	icefront->matpar =(Matpar*)icefront->hmatpar->delivers();
+
+	return icefront;
+
+}
+/*}}}*/
+
+/*Load virtual functions definitions:*/
+/*FUNCTION Icefront::Configure {{{*/
+void  Icefront::Configure(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+	/*Take care of hooking up all objects for this element, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and offsets hidden in hooks: */
+	hnodes->configure(nodesin);
+	helement->configure(elementsin);
+	hmatpar->configure(materialsin);
+
+	/*Initialize hooked fields*/
+	this->nodes  =(Node**)hnodes->deliverp();
+	this->element=(Element*)helement->delivers();
+	this->matpar =(Matpar*)hmatpar->delivers();
+
+	/*point parameters to real dataset: */
+	this->parameters=parametersin;
+}
+/*}}}*/
+/*FUNCTION Icefront::SetCurrentConfiguration {{{*/
+void  Icefront::SetCurrentConfiguration(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+}
+/*}}}*/
+/*FUNCTION Icefront::CreateKMatrix {{{*/
+void  Icefront::CreateKMatrix(Matrix* Kff, Matrix* Kfs){
+
+	/*No stiffness loads applied, do nothing: */
+	return;
+
+}
+/*}}}*/
+/*FUNCTION Icefront::CreatePVector {{{*/
+void  Icefront::CreatePVector(Vector* pf){
+
+	/*Checks in debugging mode*/
+	/*{{{*/
+	_assert_(nodes);
+	_assert_(element);
+	_assert_(matpar);
+	/*}}}*/
+
+	/*Retrieve parameters: */
+	ElementVector* pe=NULL;
+	int analysis_type;
+	this->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Just branch to the correct element icefront vector generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+		#ifdef _HAVE_DIAGNOSTIC_
+		case DiagnosticHorizAnalysisEnum:
+			pe=CreatePVectorDiagnosticHoriz();
+			break;
+		#endif
+		#ifdef _HAVE_CONTROL_
+		case AdjointHorizAnalysisEnum:
+			pe=CreatePVectorAdjointHoriz();
+			break;
+		#endif
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global Vector*/
+	if(pe){
+		pe->AddToGlobal(pf);
+		delete pe;
+	}
+}
+/*}}}*/
+/*FUNCTION Icefront::CreateJacobianMatrix{{{*/
+void  Icefront::CreateJacobianMatrix(Matrix* Jff){
+	this->CreateKMatrix(Jff,NULL);
+}
+/*}}}*/
+/*FUNCTION Icefront::PenaltyCreateKMatrix {{{*/
+void  Icefront::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs, IssmDouble kmax){
+	/*do nothing: */
+	return;
+}
+/*}}}*/
+/*FUNCTION Icefront::PenaltyCreatePVector{{{*/
+void  Icefront::PenaltyCreatePVector(Vector* pf,IssmDouble kmax){
+	/*do nothing: */
+	return;
+}
+/*}}}*/
+/*FUNCTION Icefront::PenaltyCreateJacobianMatrix{{{*/
+void  Icefront::PenaltyCreateJacobianMatrix(Matrix* Jff,IssmDouble kmax){
+	this->PenaltyCreateKMatrix(Jff,NULL,kmax);
+}
+/*}}}*/
+/*FUNCTION Icefront::InAnalysis{{{*/
+bool Icefront::InAnalysis(int in_analysis_type){
+	if (in_analysis_type==this->analysis_type)return true;
+	else return false;
+}
+/*}}}*/
+
+/*Update virtual functions definitions:*/
+/*FUNCTION Icefront::InputUpdateFromVector(IssmDouble* vector, int name, int type) {{{*/
+void  Icefront::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromVector(int* vector, int name, int type) {{{*/
+void  Icefront::InputUpdateFromVector(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromVector(bool* vector, int name, int type) {{{*/
+void  Icefront::InputUpdateFromVector(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type) {{{*/
+void  Icefront::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type) {{{*/
+void  Icefront::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromVectorDakota(int* vector, int name, int type) {{{*/
+void  Icefront::InputUpdateFromVectorDakota(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromVectorDakota(bool* vector, int name, int type) {{{*/
+void  Icefront::InputUpdateFromVectorDakota(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromConstant(IssmDouble constant, int name) {{{*/
+void  Icefront::InputUpdateFromConstant(IssmDouble constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromConstant(int constant, int name) {{{*/
+void  Icefront::InputUpdateFromConstant(int constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromConstant(bool constant, int name) {{{*/
+void  Icefront::InputUpdateFromConstant(bool constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Icefront::InputUpdateFromSolution{{{*/
+void  Icefront::InputUpdateFromSolution(IssmDouble* solution){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+
+/*Icefront numerics: */
+#ifdef _HAVE_DIAGNOSTIC_
+/*FUNCTION Icefront::CreatePVectorDiagnosticHoriz {{{*/
+ElementVector* Icefront::CreatePVectorDiagnosticHoriz(void){
+
+	int type;
+	inputs->GetInputValue(&type,TypeEnum);
+
+	switch(type){
+		case MacAyeal2dIceFrontEnum:
+			return CreatePVectorDiagnosticMacAyeal2d();
+        #ifdef _HAVE_3D_
+		case MacAyeal3dIceFrontEnum:
+			return CreatePVectorDiagnosticMacAyeal3d();
+		case PattynIceFrontEnum:
+			return CreatePVectorDiagnosticPattyn();
+		case StokesIceFrontEnum:
+			return CreatePVectorDiagnosticStokes();
+	    #endif
+		default:
+			_error_("Icefront type " << EnumToStringx(type) << " not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Icefront::CreatePVectorDiagnosticMacAyeal2d{{{*/
+ElementVector* Icefront::CreatePVectorDiagnosticMacAyeal2d(void){
+
+	/*Constants*/
+	const int numnodes= NUMVERTICESSEG;
+	const int numdofs = numnodes *NDOF2;
+
+	/*Intermediary*/
+	int        ig,index1,index2,fill;
+	IssmDouble     Jdet;
+	IssmDouble     thickness,bed,pressure,ice_pressure,rho_water,rho_ice,gravity;
+	IssmDouble     water_pressure,air_pressure,surface_under_water,base_under_water;
+	IssmDouble     xyz_list[numnodes][3];
+	IssmDouble     normal[2];
+	IssmDouble     L[2];
+	GaussTria *gauss;
+
+	Tria* tria=((Tria*)element);
+
+	/*Initialize Element vector and return if necessary*/
+	if(tria->IsOnWater()) return NULL;
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICESSEG,this->parameters,MacAyealApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0],nodes,numnodes);
+	Input* thickness_input=tria->inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+	Input* bed_input      =tria->inputs->GetInput(BedEnum);       _assert_(bed_input);
+	inputs->GetInputValue(&fill,FillEnum);
+	rho_water=matpar->GetRhoWater();
+	rho_ice  =matpar->GetRhoIce();
+	gravity  =matpar->GetG();
+	GetSegmentNormal(&normal[0],xyz_list);
+
+	/*Start looping on Gaussian points*/
+	index1=tria->GetNodeIndex(nodes[0]);
+	index2=tria->GetNodeIndex(nodes[1]);
+	gauss=new GaussTria(index1,index2,3);
+
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		thickness_input->GetInputValue(&thickness,gauss);
+		bed_input->GetInputValue(&bed,gauss);
+
+		switch(fill){
+			case WaterEnum:
+				surface_under_water=min(0.,thickness+bed); // 0 if the top of the glacier is above water level
+				base_under_water=min(0.,bed);              // 0 if the bottom of the glacier is above water level
+				water_pressure=1.0/2.0*gravity*rho_water*(pow(surface_under_water,2) - pow(base_under_water,2));
+				break;
+			case AirEnum:
+				water_pressure=0;
+				break;
+			case IceEnum:
+				water_pressure=-1.0/2.0*gravity*rho_ice*pow(thickness,2); // we are facing a wall of ice. use water_pressure to cancel the lithostatic pressure.
+				break;
+			default:
+				_error_("fill type " << EnumToStringx(fill) << " not supported yet");
+		}
+		ice_pressure=1.0/2.0*gravity*rho_ice*pow(thickness,2);
+		air_pressure=0;
+		pressure = ice_pressure + water_pressure + air_pressure;
+
+		tria->GetSegmentJacobianDeterminant(&Jdet,&xyz_list[0][0],gauss);
+		tria->GetSegmentNodalFunctions(&L[0],gauss,index1,index2);
+
+		for (int i=0;ivalues[2*i+0]+= pressure*Jdet*gauss->weight*normal[0]*L[i];
+			pe->values[2*i+1]+= pressure*Jdet*gauss->weight*normal[1]*L[i];
+		}
+	}
+
+	/*Transform load vector*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICESSEG,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+#endif
+
+#ifdef _HAVE_CONTROL_
+/*FUNCTION Icefront::CreatePVectorAdjointHoriz {{{*/
+ElementVector* Icefront::CreatePVectorAdjointHoriz(void){
+
+	/*No load vector applied to the adjoint*/
+	return NULL;
+}
+/*}}}*/
+#endif
+#ifdef _HAVE_3D_
+/*FUNCTION Icefront::CreatePVectorDiagnosticMacAyeal3d{{{*/
+ElementVector* Icefront::CreatePVectorDiagnosticMacAyeal3d(void){
+
+	Icefront* icefront=NULL;
+	Penta*    penta=NULL;
+	Tria*     tria=NULL;
+	bool      onbed;
+
+	/*Cast element onto Penta*/
+	penta   =(Penta*)this->element;
+
+	/*Return if not on bed*/
+	if(!penta->IsOnBed() || penta->IsOnWater()) return NULL;
+
+	/*Spawn Tria and call MacAyeal2d*/
+	tria    =(Tria*)penta->SpawnTria(0,1,2);
+	icefront=(Icefront*)this->copy();
+	icefront->element=tria;
+	icefront->inputs->AddInput(new IntInput(TypeEnum,MacAyeal2dIceFrontEnum));
+	ElementVector* pe=icefront->CreatePVectorDiagnosticMacAyeal2d();
+
+	/*clean-up and return*/
+	delete tria->material;
+	delete tria;
+	delete icefront;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Icefront::CreatePVectorDiagnosticPattyn{{{*/
+ElementVector* Icefront::CreatePVectorDiagnosticPattyn(void){
+
+	/*Constants*/
+	const int numdofs = NUMVERTICESQUA *NDOF2;
+
+	/*Intermediaries*/
+	int         i,j,ig,index1,index2,index3,index4;
+	int         fill;
+	IssmDouble      surface,pressure,ice_pressure,rho_water,rho_ice,gravity;
+	IssmDouble      water_pressure,air_pressure;
+	IssmDouble      Jdet,z_g;
+	IssmDouble      xyz_list[NUMVERTICESQUA][3];
+	IssmDouble      normal[3];
+	IssmDouble      l1l4[4];
+	GaussPenta *gauss = NULL;
+
+	Penta* penta=(Penta*)element;
+
+	/*Initialize Element vector and return if necessary*/
+	if(penta->IsOnWater()) return NULL;
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICESQUA,this->parameters,PattynApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICESQUA);
+	Input* surface_input  =penta->inputs->GetInput(SurfaceEnum);   _assert_(surface_input);
+	inputs->GetInputValue(&fill,FillEnum);
+	rho_water=matpar->GetRhoWater();
+	rho_ice  =matpar->GetRhoIce();
+	gravity  =matpar->GetG();
+	GetQuadNormal(&normal[0],xyz_list);
+
+	/*Identify which nodes are in the quad: */
+	index1=element->GetNodeIndex(nodes[0]);
+	index2=element->GetNodeIndex(nodes[1]);
+	index3=element->GetNodeIndex(nodes[2]);
+	index4=element->GetNodeIndex(nodes[3]);
+
+	/* Start  looping on the number of gaussian points: */
+	IssmDouble zmax=xyz_list[0][2]; for(i=1;izmax) zmax=xyz_list[i][2];
+	IssmDouble zmin=xyz_list[0][2]; for(i=1;i0 && zmin<0) gauss=new GaussPenta(index1,index2,index3,index4,3,10); //refined in vertical because of the sea level discontinuity
+	else                 gauss=new GaussPenta(index1,index2,index3,index4,3,3);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		penta->GetQuadNodalFunctions(l1l4,gauss,index1,index2,index3,index4);
+		penta->GetQuadJacobianDeterminant(&Jdet,xyz_list,gauss);
+		z_g=penta->GetZcoord(gauss);
+		surface_input->GetInputValue(&surface,gauss);
+
+		switch(fill){
+			case WaterEnum:
+				water_pressure=rho_water*gravity*min(0.,z_g);//0 if the gaussian point is above water level
+				break;
+			case AirEnum:
+				water_pressure=0;
+				break;
+			default:
+				_error_("fill type " << EnumToStringx(fill) << " not supported yet");
+		}
+		ice_pressure=rho_ice*gravity*(surface-z_g);
+		air_pressure=0;
+		pressure = ice_pressure + water_pressure + air_pressure;
+
+		for(i=0;ivalues[i*NDOF2+j]+=Jdet*gauss->weight*pressure*l1l4[i]*normal[j];
+	}
+
+	/*Transform load vector*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICESQUA,XYEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Icefront::CreatePVectorDiagnosticStokes{{{*/
+ElementVector* Icefront::CreatePVectorDiagnosticStokes(void){
+
+	/*Constants*/
+	const int numdofs = NUMVERTICESQUA *NDOF4;
+
+	/*Intermediaries*/
+	int         i,j,ig,index1,index2,index3,index4;
+	int         fill;
+	IssmDouble      pressure,rho_water,gravity;
+	IssmDouble      water_pressure,air_pressure;
+	IssmDouble      Jdet,z_g;
+	IssmDouble      xyz_list[NUMVERTICESQUA][3];
+	IssmDouble      normal[3];
+	IssmDouble      l1l4[4];
+	GaussPenta *gauss = NULL;
+
+	Penta* penta=(Penta*)element;
+
+	/*Initialize Element vector and return if necessary*/
+	if(penta->IsOnWater()) return NULL;
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICESQUA,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICESQUA);
+	inputs->GetInputValue(&fill,FillEnum);
+	rho_water=matpar->GetRhoWater();
+	gravity  =matpar->GetG();
+	GetQuadNormal(&normal[0],xyz_list);
+
+	/*Identify which nodes are in the quad: */
+	index1=element->GetNodeIndex(nodes[0]);
+	index2=element->GetNodeIndex(nodes[1]);
+	index3=element->GetNodeIndex(nodes[2]);
+	index4=element->GetNodeIndex(nodes[3]);
+
+	/* Start  looping on the number of gaussian points: */
+	IssmDouble zmax=xyz_list[0][2]; for(i=1;izmax) zmax=xyz_list[i][2];
+	IssmDouble zmin=xyz_list[0][2]; for(i=1;i0 && zmin<0) gauss=new GaussPenta(index1,index2,index3,index4,3,30); //refined in vertical because of the sea level discontinuity
+	else                 gauss=new GaussPenta(index1,index2,index3,index4,3,3);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		penta->GetQuadNodalFunctions(l1l4,gauss,index1,index2,index3,index4);
+		penta->GetQuadJacobianDeterminant(&Jdet,xyz_list,gauss);
+		z_g=penta->GetZcoord(gauss);
+
+		switch(fill){
+			case WaterEnum:
+				water_pressure=rho_water*gravity*min(0.,z_g);//0 if the gaussian point is above water level
+				break;
+			case AirEnum:
+				water_pressure=0;
+				break;
+			default:
+				_error_("fill type " << EnumToStringx(fill) << " not supported yet");
+		}
+		air_pressure=0;
+		pressure = water_pressure + air_pressure; //no ice pressure fore Stokes
+
+		for(i=0;ivalues[i*NDOF4+j]+=Jdet*gauss->weight*pressure*l1l4[i]*normal[j];
+				else     pe->values[i*NDOF4+j]+=0; //pressure term
+			}
+		}
+	}
+
+	/*Transform load vector*/
+	TransformLoadVectorCoord(pe,nodes,NUMVERTICESQUA,XYZPEnum);
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+#endif
+/*FUNCTION Icefront::GetDofList {{{*/
+void  Icefront::GetDofList(int** pdoflist,int approximation_enum,int setenum){
+
+	int i,j;
+	int numberofdofs=0;
+	int count=0;
+	int type;
+	int numberofnodes=2;
+
+	/*output: */
+	int* doflist=NULL;
+
+	
+	/*recover type: */
+	inputs->GetInputValue(&type,TypeEnum);
+
+	/*Some checks for debugging*/
+	_assert_(nodes);
+		
+	/*How many nodes? :*/
+	if(type==MacAyeal2dIceFrontEnum || type==MacAyeal3dIceFrontEnum)
+	 numberofnodes=2;
+	else 
+	 numberofnodes=4;
+	
+	/*Figure out size of doflist: */
+	for(i=0;iGetNumberOfDofs(approximation_enum,setenum);
+	}
+
+	/*Allocate: */
+	doflist=xNew(numberofdofs);
+
+	/*Populate: */
+	count=0;
+	for(i=0;iGetDofList(doflist+count,approximation_enum,setenum);
+		count+=nodes[i]->GetNumberOfDofs(approximation_enum,setenum);
+	}
+
+	/*Assign output pointers:*/
+	*pdoflist=doflist;
+}
+/*}}}*/
+/*FUNCTION Icefront::GetSegmentNormal {{{*/
+void Icefront:: GetSegmentNormal(IssmDouble* normal,IssmDouble xyz_list[4][3]){
+
+	/*Build unit outward pointing vector*/
+	const int numnodes=NUMVERTICESSEG;
+	IssmDouble vector[2];
+	IssmDouble norm;
+
+	vector[0]=xyz_list[1][0] - xyz_list[0][0];
+	vector[1]=xyz_list[1][1] - xyz_list[0][1];
+
+	norm=sqrt(pow(vector[0],2.0)+pow(vector[1],2.0));
+
+	normal[0]= + vector[1]/norm;
+	normal[1]= - vector[0]/norm;
+}
+/*}}}*/
+/*FUNCTION Icefront::GetQuadNormal {{{*/
+void Icefront:: GetQuadNormal(IssmDouble* normal,IssmDouble xyz_list[4][3]){
+
+	/*Build unit outward pointing vector*/
+	IssmDouble AB[3];
+	IssmDouble AC[3];
+	IssmDouble norm;
+
+	AB[0]=xyz_list[1][0] - xyz_list[0][0];
+	AB[1]=xyz_list[1][1] - xyz_list[0][1];
+	AB[2]=xyz_list[1][2] - xyz_list[0][2];
+	AC[0]=xyz_list[2][0] - xyz_list[0][0];
+	AC[1]=xyz_list[2][1] - xyz_list[0][1];
+	AC[2]=xyz_list[2][2] - xyz_list[0][2];
+
+	cross(normal,AB,AC);
+	norm=sqrt(pow(normal[0],2.0)+pow(normal[1],2.0)+pow(normal[2],2.0));
+
+	for(int i=0;i<3;i++) normal[i]=normal[i]/norm;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Loads/Icefront.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Icefront.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Icefront.h	(revision 13395)
@@ -0,0 +1,98 @@
+/*!\file Icefront.h
+ * \brief: header file for icefront object
+ */
+
+#ifndef _ICEFRONT_H_
+#define _ICEFRONT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Load.h"
+class Hook;
+class Inputs;
+class Parameters;
+class Matpar;
+class Node;
+class Element;
+class IoModel;
+class ElementVector;
+/*}}}*/
+
+class Icefront: public Load {
+
+	public:
+		int id;
+		int analysis_type;
+
+		/*hooks: */
+		Hook* hnodes;
+		Hook* helement;
+		Hook* hmatpar;
+
+		/*Corresponding fields*/
+		Matpar   *matpar;
+		Node    **nodes;
+		Element  *element;
+
+		/*inputs and parameters: */
+		Inputs* inputs;
+		Parameters* parameters;
+
+		/*Icefront constructors, destructors: {{{*/
+		Icefront();
+		Icefront(int icefront_id,int i, IoModel* iomodel,int in_icefront_type, int analysis_type);
+		~Icefront();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Update virtual functions definitions: {{{*/
+		void  InputUpdateFromVector(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVector(int* vector, int name, int type);
+		void  InputUpdateFromVector(bool* vector, int name, int type);
+		void  InputUpdateFromMatrixDakota(IssmDouble* matrix,int ncols,int nrows, int name, int type);
+		void  InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(int* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(bool* vector, int name, int type);
+		void  InputUpdateFromConstant(IssmDouble constant, int name);
+		void  InputUpdateFromConstant(int constant, int name);
+		void  InputUpdateFromConstant(bool constant, int name);
+		void  InputUpdateFromSolution(IssmDouble* solution);
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel){_error_("not implemented yet");};
+		/*}}}*/
+		/*Load virtual functions definitions: {{{*/
+		void  Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  CreateKMatrix(Matrix* Kff, Matrix* Kfs);
+		void  CreatePVector(Vector* pf);
+		void  CreateJacobianMatrix(Matrix* Jff);
+		void  PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, IssmDouble kmax);
+		void  PenaltyCreatePVector(Vector*  pf, IssmDouble kmax);
+		void  PenaltyCreateJacobianMatrix(Matrix* Jff,IssmDouble kmax);
+		bool  InAnalysis(int analysis_type);
+		/*}}}*/
+		/*Load management: {{{*/
+		void GetDofList(int** pdoflist,int approximation_enum,int setenum);
+		void GetSegmentNormal(IssmDouble* normal,IssmDouble xyz_list[2][3]);
+		void GetQuadNormal(IssmDouble* normal,IssmDouble xyz_list[4][3]);
+		#ifdef _HAVE_CONTROL_
+		ElementVector* CreatePVectorAdjointHoriz(void);
+		#endif
+		#ifdef _HAVE_DIAGNOSTIC_
+		ElementVector* CreatePVectorDiagnosticHoriz(void);
+		ElementVector* CreatePVectorDiagnosticMacAyeal2d(void);
+		#endif
+        #ifdef _HAVE_3D_
+		ElementVector* CreatePVectorDiagnosticMacAyeal3d(void);
+		ElementVector* CreatePVectorDiagnosticPattyn(void);
+		ElementVector* CreatePVectorDiagnosticStokes(void);
+	    #endif
+		/*}}}*/
+};
+
+#endif  /* _ICEFRONT_H_ */
Index: /issm/trunk/src/c/classes/objects/Loads/Load.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Load.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Load.h	(revision 13395)
@@ -0,0 +1,40 @@
+/*!\file:  Load.h
+ * \brief abstract class for Load object
+ * This class is a place holder for the Icefront  and the Penpair loads.
+ * It is derived from Load, so DataSets can contain them.
+ */ 
+
+
+#ifndef _LOAD_H_
+#define _LOAD_H_
+
+/*Headers:*/
+/*{{{*/
+class Object;
+template  class Matrix;
+template  class Vector;
+
+#include "../Object.h"
+#include "../../../toolkits/toolkits.h"
+#include "../../../Container/Container.h"
+/*}}}*/
+
+class Load: public Object,public Update{
+
+	public: 
+
+		virtual       ~Load(){};
+		
+		/*Virtual functions: {{{*/
+		virtual void  Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters)=0;
+		virtual void  SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters)=0;
+		virtual void  CreateKMatrix(Matrix* Kff, Matrix* Kfs)=0;
+		virtual void  CreatePVector(Vector* pf)=0;
+		virtual void  CreateJacobianMatrix(Matrix* Jff)=0;
+		virtual void  PenaltyCreateJacobianMatrix(Matrix* Jff,IssmDouble kmax)=0;
+		virtual void  PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs, IssmDouble kmax)=0;
+		virtual void  PenaltyCreatePVector(Vector* pf, IssmDouble kmax)=0;
+		virtual bool  InAnalysis(int analysis_type)=0;
+		/*}}}*/
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/Loads/Numericalflux.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Numericalflux.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Numericalflux.cpp	(revision 13395)
@@ -0,0 +1,880 @@
+/*!\file Numericalflux.c
+ * \brief: implementation of the Numericalflux object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../include/include.h"
+#include "../../classes.h"
+/*}}}*/	
+
+/*Load macros*/
+#define NUMVERTICES_INTERNAL 4
+#define NUMVERTICES_BOUNDARY 2
+
+/*Numericalflux constructors and destructor*/
+/*FUNCTION Numericalflux::Numericalflux(){{{*/
+Numericalflux::Numericalflux(){
+	this->inputs=NULL;
+	this->parameters=NULL;
+	this->helement=NULL;
+	this->element=NULL;
+	this->hnodes=NULL;
+	this->nodes=NULL;
+}
+/*}}}*/
+/*}}}*//*FUNCTION Numericalflux::Numericalflux(int id, int i, IoModel* iomodel, int analysis_type) {{{*/
+Numericalflux::Numericalflux(int numericalflux_id,int i, IoModel* iomodel, int in_analysis_type){
+
+	/* Intermediary */
+	int  e1,e2;
+	int  i1,i2;
+	int  j;
+	int  pos1,pos2,pos3,pos4;
+	int  num_nodes;
+	int  num_elems;
+
+	/*numericalflux constructor data: */
+	int   numericalflux_elem_ids[2];
+	int   numericalflux_mparid;
+	int   numericalflux_node_ids[4];
+	int   numericalflux_type;
+
+	int    numberofelements;
+
+	/*Fetch parameters: */
+	iomodel->Constant(&numberofelements,MeshNumberofelementsEnum);
+
+	/* Get MatPar id */
+	numericalflux_mparid=numberofelements+1; //matlab indexing
+
+	/*First, see wether this is an internal or boundary edge (if e2=-1)*/
+	if (iomodel->Data(MeshEdgesEnum)[4*i+3]==-1.){ //edges are [node1 node2 elem1 elem2]
+		/* Boundary edge, only one element */
+		e1=reCast(iomodel->Data(MeshEdgesEnum)[4*i+2]);
+		e2=reCast(UNDEF);
+		num_elems=1;
+		num_nodes=2;
+		numericalflux_type=BoundaryEnum;
+		numericalflux_elem_ids[0]=e1;
+	}
+	else{
+		/* internal edge: connected to 2 elements */
+		e1=reCast(iomodel->Data(MeshEdgesEnum)[4*i+2]);
+		e2=reCast(iomodel->Data(MeshEdgesEnum)[4*i+3]);
+		num_elems=2;
+		num_nodes=4;
+		numericalflux_type=InternalEnum;
+		numericalflux_elem_ids[0]=e1;
+		numericalflux_elem_ids[1]=e2;
+	}
+
+	/*1: Get vertices ids*/
+	i1=reCast(iomodel->Data(MeshEdgesEnum)[4*i+0]);
+	i2=reCast(iomodel->Data(MeshEdgesEnum)[4*i+1]);
+
+	if (numericalflux_type==InternalEnum){
+
+		/*Now, we must get the nodes of the 4 nodes located on the edge*/
+
+		/*2: Get the column where these ids are located in the index*/
+		pos1=pos2=pos3=pos4=UNDEF;
+		for(j=0;j<3;j++){
+			if (iomodel->Data(MeshElementsEnum)[3*(e1-1)+j]==i1) pos1=j+1;
+			if (iomodel->Data(MeshElementsEnum)[3*(e1-1)+j]==i2) pos2=j+1;
+			if (iomodel->Data(MeshElementsEnum)[3*(e2-1)+j]==i1) pos3=j+1;
+			if (iomodel->Data(MeshElementsEnum)[3*(e2-1)+j]==i2) pos4=j+1;
+		}
+		_assert_(pos1!=UNDEF && pos2!=UNDEF && pos3!=UNDEF && pos4!=UNDEF);
+
+		/*3: We have the id of the elements and the position of the vertices in the index
+		 * we can compute their dofs!*/
+		numericalflux_node_ids[0]=iomodel->nodecounter+3*(e1-1)+pos1;
+		numericalflux_node_ids[1]=iomodel->nodecounter+3*(e1-1)+pos2;
+		numericalflux_node_ids[2]=iomodel->nodecounter+3*(e2-1)+pos3;
+		numericalflux_node_ids[3]=iomodel->nodecounter+3*(e2-1)+pos4;
+	}
+	else{
+
+		/*2: Get the column where these ids are located in the index*/
+		pos1=pos2=UNDEF;
+		for(j=0;j<3;j++){
+			if (iomodel->Data(MeshElementsEnum)[3*(e1-1)+j]==i1) pos1=j+1;
+			if (iomodel->Data(MeshElementsEnum)[3*(e1-1)+j]==i2) pos2=j+1;
+		}
+		_assert_(pos1!=UNDEF && pos2!=UNDEF);
+
+		/*3: We have the id of the elements and the position of the vertices in the index
+		 * we can compute their dofs!*/
+		numericalflux_node_ids[0]=iomodel->nodecounter+3*(e1-1)+pos1;
+		numericalflux_node_ids[1]=iomodel->nodecounter+3*(e1-1)+pos2;
+	}
+
+	/*Ok, we have everything to build the object: */
+	this->id=numericalflux_id;
+	this->analysis_type=in_analysis_type;
+
+	/*Hooks: */
+	this->hnodes  =new Hook(numericalflux_node_ids,num_nodes);
+	this->helement=new Hook(numericalflux_elem_ids,1); // take only the first element for now
+
+	//intialize  and add as many inputs per element as requested: 
+	this->inputs=new Inputs();
+	this->inputs->AddInput(new IntInput(TypeEnum,numericalflux_type));
+
+	//this->parameters: we still can't point to it, it may not even exist. Configure will handle this.
+	this->parameters=NULL;
+	this->element=NULL;
+	this->nodes=NULL;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::~Numericalflux(){{{*/
+Numericalflux::~Numericalflux(){
+	delete inputs;
+	this->parameters=NULL;
+	delete helement;
+	delete hnodes;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION Numericalflux::Echo {{{*/
+void Numericalflux::Echo(void){
+	_printLine_("Numericalflux:");
+	_printLine_("   id: " << id);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	hnodes->Echo();
+	helement->Echo();
+	_printLine_("   parameters: " << parameters);
+	_printLine_("   inputs: " << inputs);
+}
+/*}}}*/
+/*FUNCTION Numericalflux::DeepEcho {{{*/
+void Numericalflux::DeepEcho(void){
+
+	_printLine_("Numericalflux:");
+	_printLine_("   id: " << id);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	hnodes->DeepEcho();
+	helement->DeepEcho();
+	_printLine_("   parameters");
+	if(parameters)
+	 parameters->DeepEcho();
+	else
+	 _printLine_("      NULL");
+	_printLine_("   inputs");
+	inputs->DeepEcho();
+	
+}		
+/*}}}*/
+/*FUNCTION Numericalflux::Id {{{*/
+int    Numericalflux::Id(void){
+	return id;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::MyRank {{{*/
+int    Numericalflux::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Numericalflux::ObjectEnum{{{*/
+int Numericalflux::ObjectEnum(void){
+
+	return NumericalfluxEnum;
+
+}
+/*}}}*/
+/*FUNCTION Numericalflux::copy {{{*/
+Object* Numericalflux::copy() {
+	
+	Numericalflux* numericalflux=NULL;
+
+	numericalflux=new Numericalflux();
+
+	/*copy fields: */
+	numericalflux->id=this->id;
+	numericalflux->analysis_type=this->analysis_type;
+	if(this->inputs){
+		numericalflux->inputs=(Inputs*)this->inputs->Copy();
+	}
+	else{
+		numericalflux->inputs=new Inputs();
+	}
+	/*point parameters: */
+	numericalflux->parameters=this->parameters;
+
+	/*now deal with hooks and objects: */
+	numericalflux->hnodes=(Hook*)this->hnodes->copy();
+	numericalflux->helement=(Hook*)this->helement->copy();
+
+	/*corresponding fields*/
+	numericalflux->nodes  =(Node**)numericalflux->hnodes->deliverp();
+	numericalflux->element=(Element*)numericalflux->helement->delivers();
+
+	return numericalflux;
+}
+/*}}}*/
+
+/*Load virtual functions definitions:*/
+/*FUNCTION Numericalflux::Configure {{{*/
+void  Numericalflux::Configure(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+	/*Take care of hooking up all objects for this element, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and offsets hidden in hooks: */
+	hnodes->configure(nodesin);
+	helement->configure(elementsin);
+
+	/*Initialize hooked fields*/
+	this->nodes  =(Node**)hnodes->deliverp();
+	this->element=(Element*)helement->delivers();
+
+	/*point parameters to real dataset: */
+	this->parameters=parametersin;
+
+}
+/*}}}*/
+/*FUNCTION Numericalflux::SetCurrentConfiguration {{{*/
+void  Numericalflux::SetCurrentConfiguration(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreateKMatrix {{{*/
+void  Numericalflux::CreateKMatrix(Matrix* Kff, Matrix* Kfs){
+
+	/*recover some parameters*/
+	ElementMatrix* Ke=NULL;
+	int analysis_type;
+	this->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	/*Just branch to the correct element stiffness matrix generator, according to the type of analysis we are carrying out: */
+	switch(analysis_type){
+		case PrognosticAnalysisEnum:
+			Ke=CreateKMatrixPrognostic();
+			break;
+		case BalancethicknessAnalysisEnum:
+			Ke=CreateKMatrixBalancethickness();
+			break;
+		case AdjointBalancethicknessAnalysisEnum:
+			Ke=CreateKMatrixAdjointBalancethickness();
+			break;
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global matrix*/
+	if(Ke){
+		Ke->AddToGlobal(Kff,Kfs);
+		delete Ke;
+	}
+
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreatePVector {{{*/
+void  Numericalflux::CreatePVector(Vector* pf){
+
+	/*recover some parameters*/
+	ElementVector* pe=NULL;
+	int analysis_type;
+	this->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	switch(analysis_type){
+		case PrognosticAnalysisEnum:
+			pe=CreatePVectorPrognostic();
+			break;
+		case BalancethicknessAnalysisEnum:
+			pe=CreatePVectorBalancethickness();
+			break;
+		case AdjointBalancethicknessAnalysisEnum:
+			pe=CreatePVectorAdjointBalancethickness();
+			break;
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global matrix*/
+	if(pe){
+		pe->AddToGlobal(pf);
+		delete pe;
+	}
+
+}
+/*}}}*/
+/*FUNCTION Numericalflux::PenaltyCreateKMatrix {{{*/
+void  Numericalflux::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,IssmDouble kmax){
+
+	/*No stiffness loads applied, do nothing: */
+	return;
+
+}
+/*}}}*/
+/*FUNCTION Numericalflux::PenaltyCreatePVector{{{*/
+void  Numericalflux::PenaltyCreatePVector(Vector* pf,IssmDouble kmax){
+
+	/*No penalty loads applied, do nothing: */
+	return;
+
+}
+/*}}}*/
+/*FUNCTION Numericalflux::InAnalysis{{{*/
+bool Numericalflux::InAnalysis(int in_analysis_type){
+	if (in_analysis_type==this->analysis_type) return true;
+	else return false;
+}
+/*}}}*/
+
+/*Numericalflux management*/
+/*FUNCTION Numericalflux::CreateKMatrixPrognostic{{{*/
+ElementMatrix* Numericalflux::CreateKMatrixPrognostic(void){
+
+	int type;
+	inputs->GetInputValue(&type,TypeEnum);
+
+	switch(type){
+		case InternalEnum:
+			return CreateKMatrixPrognosticInternal();
+		case BoundaryEnum:
+			return CreateKMatrixPrognosticBoundary();
+		default:
+			_error_("type not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreateKMatrixPrognosticInternal {{{*/
+ElementMatrix* Numericalflux::CreateKMatrixPrognosticInternal(void){
+
+	/* constants*/
+	const int numdof=NDOF1*NUMVERTICES_INTERNAL;
+
+	/* Intermediaries*/
+	int        i,j,ig,index1,index2;
+	IssmDouble     DL1,DL2,Jdet,dt,vx,vy,UdotN;
+	IssmDouble     xyz_list[NUMVERTICES_INTERNAL][3];
+	IssmDouble     normal[2];
+	IssmDouble     B[numdof];
+	IssmDouble     Bprime[numdof];
+	IssmDouble     Ke_g1[numdof][numdof];
+	IssmDouble     Ke_g2[numdof][numdof];
+	GaussTria *gauss;
+
+	/*Initialize Element matrix and return if necessary*/
+	Tria*  tria=(Tria*)element;
+	if(tria->IsOnWater()) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES_INTERNAL,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes,NUMVERTICES_INTERNAL);
+	parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	Input* vxaverage_input=tria->inputs->GetInput(VxEnum);
+	Input* vyaverage_input=tria->inputs->GetInput(VyEnum);
+	GetNormal(&normal[0],xyz_list);
+
+	/* Start  looping on the number of gaussian points: */
+	index1=tria->GetNodeIndex(nodes[0]);
+	index2=tria->GetNodeIndex(nodes[1]);
+	gauss=new GaussTria(index1,index2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		tria->GetSegmentBFlux(&B[0],gauss,index1,index2);
+		tria->GetSegmentBprimeFlux(&Bprime[0],gauss,index1,index2);
+
+		vxaverage_input->GetInputValue(&vx,gauss);
+		vyaverage_input->GetInputValue(&vy,gauss);
+		UdotN=vx*normal[0]+vy*normal[1];
+		tria->GetSegmentJacobianDeterminant(&Jdet,&xyz_list[0][0],gauss);
+		DL1=gauss->weight*Jdet*dt*UdotN/2;
+		DL2=gauss->weight*Jdet*dt*fabs(UdotN)/2;
+
+		TripleMultiply(&B[0],1,numdof,1,
+					&DL1,1,1,0,
+					&Bprime[0],1,numdof,0,
+					&Ke_g1[0][0],0);
+		TripleMultiply(&B[0],1,numdof,1,
+					&DL2,1,1,0,
+					&B[0],1,numdof,0,
+					&Ke_g2[0][0],0);
+
+		for(i=0;ivalues[i*numdof+j]+=Ke_g1[i][j];
+		for(i=0;ivalues[i*numdof+j]+=Ke_g2[i][j];
+	}
+	
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreateKMatrixPrognosticBoundary {{{*/
+ElementMatrix* Numericalflux::CreateKMatrixPrognosticBoundary(void){
+
+	/* constants*/
+	const int numdof=NDOF1*NUMVERTICES_BOUNDARY;
+
+	/* Intermediaries*/
+	int        i,j,ig,index1,index2;
+	IssmDouble     DL,Jdet,dt,vx,vy,mean_vx,mean_vy,UdotN;
+	IssmDouble     xyz_list[NUMVERTICES_BOUNDARY][3];
+	IssmDouble     normal[2];
+	IssmDouble     L[numdof];
+	IssmDouble     Ke_g[numdof][numdof];
+	GaussTria *gauss;
+
+	/*Initialize Element matrix and return if necessary*/
+	ElementMatrix* Ke = NULL;
+	Tria*  tria=(Tria*)element;
+	if(tria->IsOnWater()) return NULL;
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0],nodes,NUMVERTICES_BOUNDARY);
+	parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	Input* vxaverage_input=tria->inputs->GetInput(VxEnum); _assert_(vxaverage_input);
+	Input* vyaverage_input=tria->inputs->GetInput(VyEnum); _assert_(vyaverage_input);
+	GetNormal(&normal[0],xyz_list);
+
+	/*Check wether it is an inflow or outflow BC (0 is the middle of the segment)*/
+	index1=tria->GetNodeIndex(nodes[0]);
+	index2=tria->GetNodeIndex(nodes[1]);
+
+	gauss=new GaussTria();
+	gauss->GaussEdgeCenter(index1,index2);
+	vxaverage_input->GetInputValue(&mean_vx,gauss);
+	vyaverage_input->GetInputValue(&mean_vy,gauss);
+	delete gauss;
+
+	UdotN=mean_vx*normal[0]+mean_vy*normal[1];
+	if (UdotN<=0){
+		return NULL; /*(u,n)<0 -> inflow, PenaltyCreatePVector will take care of it*/
+	}
+	else{
+		Ke=new ElementMatrix(nodes,NUMVERTICES_BOUNDARY,this->parameters);
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(index1,index2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		tria->GetSegmentNodalFunctions(&L[0],gauss,index1,index2);
+
+		vxaverage_input->GetInputValue(&vx,gauss);
+		vyaverage_input->GetInputValue(&vy,gauss);
+		UdotN=vx*normal[0]+vy*normal[1];
+		tria->GetSegmentJacobianDeterminant(&Jdet,&xyz_list[0][0],gauss);
+		DL=gauss->weight*Jdet*dt*UdotN;
+
+		TripleMultiply(&L[0],1,numdof,1,
+					&DL,1,1,0,
+					&L[0],1,numdof,0,
+					&Ke_g[0][0],0);
+
+		for(i=0;ivalues[i*numdof+j]+=Ke_g[i][j];
+	} 
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreateKMatrixBalancethickness{{{*/
+ElementMatrix* Numericalflux::CreateKMatrixBalancethickness(void){
+
+	int type;
+	inputs->GetInputValue(&type,TypeEnum);
+
+	switch(type){
+		case InternalEnum:
+			return CreateKMatrixBalancethicknessInternal();
+		case BoundaryEnum:
+			return CreateKMatrixBalancethicknessBoundary();
+		default:
+			_error_("type not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreateKMatrixBalancethicknessInternal {{{*/
+ElementMatrix* Numericalflux::CreateKMatrixBalancethicknessInternal(void){
+
+	/* constants*/
+	const int numdof=NDOF1*NUMVERTICES_INTERNAL;
+
+	/* Intermediaries*/
+	int        i,j,ig,index1,index2;
+	IssmDouble     DL1,DL2,Jdet,vx,vy,UdotN;
+	IssmDouble     xyz_list[NUMVERTICES_INTERNAL][3];
+	IssmDouble     normal[2];
+	IssmDouble     B[numdof];
+	IssmDouble     Bprime[numdof];
+	IssmDouble     Ke_g1[numdof][numdof];
+	IssmDouble     Ke_g2[numdof][numdof];
+	GaussTria *gauss;
+
+	/*Initialize Element matrix and return if necessary*/
+	Tria*  tria=(Tria*)element;
+	if(tria->IsOnWater()) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES_INTERNAL,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0], nodes,NUMVERTICES_INTERNAL);
+	Input* vxaverage_input=tria->inputs->GetInput(VxEnum);
+	Input* vyaverage_input=tria->inputs->GetInput(VyEnum);
+	GetNormal(&normal[0],xyz_list);
+
+	/* Start  looping on the number of gaussian points: */
+	index1=tria->GetNodeIndex(nodes[0]);
+	index2=tria->GetNodeIndex(nodes[1]);
+	gauss=new GaussTria(index1,index2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		tria->GetSegmentBFlux(&B[0],gauss,index1,index2);
+		tria->GetSegmentBprimeFlux(&Bprime[0],gauss,index1,index2);
+
+		vxaverage_input->GetInputValue(&vx,gauss);
+		vyaverage_input->GetInputValue(&vy,gauss);
+		UdotN=vx*normal[0]+vy*normal[1];
+		tria->GetSegmentJacobianDeterminant(&Jdet,&xyz_list[0][0],gauss);
+		DL1=gauss->weight*Jdet*UdotN/2;
+		DL2=gauss->weight*Jdet*fabs(UdotN)/2;
+
+		TripleMultiply(&B[0],1,numdof,1,
+					&DL1,1,1,0,
+					&Bprime[0],1,numdof,0,
+					&Ke_g1[0][0],0);
+		TripleMultiply(&B[0],1,numdof,1,
+					&DL2,1,1,0,
+					&B[0],1,numdof,0,
+					&Ke_g2[0][0],0);
+
+		for(i=0;ivalues[i*numdof+j]+=Ke_g1[i][j];
+		for(i=0;ivalues[i*numdof+j]+=Ke_g2[i][j];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreateKMatrixBalancethicknessBoundary {{{*/
+ElementMatrix* Numericalflux::CreateKMatrixBalancethicknessBoundary(void){
+
+	/* constants*/
+	const int numdof=NDOF1*NUMVERTICES_BOUNDARY;
+
+	/* Intermediaries*/
+	int        i,j,ig,index1,index2;
+	IssmDouble     DL,Jdet,vx,vy,mean_vx,mean_vy,UdotN;
+	IssmDouble     xyz_list[NUMVERTICES_BOUNDARY][3];
+	IssmDouble     normal[2];
+	IssmDouble     L[numdof];
+	IssmDouble     Ke_g[numdof][numdof];
+	GaussTria *gauss;
+
+	/*Initialize Element matrix and return if necessary*/
+	ElementMatrix* Ke = NULL;
+	Tria*  tria=(Tria*)element;
+	if(tria->IsOnWater()) return NULL;
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0],nodes,NUMVERTICES_BOUNDARY);
+	Input* vxaverage_input=tria->inputs->GetInput(VxEnum);
+	Input* vyaverage_input=tria->inputs->GetInput(VyEnum);
+	GetNormal(&normal[0],xyz_list);
+
+	/*Check wether it is an inflow or outflow BC (0 is the middle of the segment)*/
+	index1=tria->GetNodeIndex(nodes[0]);
+	index2=tria->GetNodeIndex(nodes[1]);
+
+	gauss=new GaussTria();
+	gauss->GaussEdgeCenter(index1,index2);
+	vxaverage_input->GetInputValue(&mean_vx,gauss);
+	vyaverage_input->GetInputValue(&mean_vy,gauss);
+	delete gauss;
+
+	UdotN=mean_vx*normal[0]+mean_vy*normal[1];
+	if (UdotN<=0){
+		return NULL; /*(u,n)<0 -> inflow, PenaltyCreatePVector will take care of it*/
+	}
+	else{
+		Ke=new ElementMatrix(nodes,NUMVERTICES_BOUNDARY,this->parameters);
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(index1,index2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		tria->GetSegmentNodalFunctions(&L[0],gauss,index1,index2);
+
+		vxaverage_input->GetInputValue(&vx,gauss);
+		vyaverage_input->GetInputValue(&vy,gauss);
+		UdotN=vx*normal[0]+vy*normal[1];
+		tria->GetSegmentJacobianDeterminant(&Jdet,&xyz_list[0][0],gauss);
+		DL=gauss->weight*Jdet*UdotN;
+
+		TripleMultiply(&L[0],1,numdof,1,
+					&DL,1,1,0,
+					&L[0],1,numdof,0,
+					&Ke_g[0][0],0);
+
+		for(i=0;ivalues[i*numdof+j]+=Ke_g[i][j];
+	} 
+
+	/*Clean up and return*/
+	delete gauss;
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreateKMatrixAdjointBalancethickness{{{*/
+ElementMatrix* Numericalflux::CreateKMatrixAdjointBalancethickness(void){
+
+	int type;
+	inputs->GetInputValue(&type,TypeEnum);
+
+	switch(type){
+		case InternalEnum:
+			return CreateKMatrixAdjointBalancethicknessInternal();
+		case BoundaryEnum:
+			return CreateKMatrixAdjointBalancethicknessBoundary();
+		default:
+			_error_("type not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreateKMatrixAdjointBalancethicknessInternal {{{*/
+ElementMatrix* Numericalflux::CreateKMatrixAdjointBalancethicknessInternal(void){
+
+	ElementMatrix* Ke=CreateKMatrixBalancethicknessInternal();
+	if (Ke) Ke->Transpose();
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreateKMatrixAdjointBalancethicknessBoundary {{{*/
+ElementMatrix* Numericalflux::CreateKMatrixAdjointBalancethicknessBoundary(void){
+
+	ElementMatrix* Ke=CreateKMatrixBalancethicknessBoundary();
+	if(Ke) Ke->Transpose();
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreatePVectorPrognostic{{{*/
+ElementVector* Numericalflux::CreatePVectorPrognostic(void){
+
+	int type;
+	inputs->GetInputValue(&type,TypeEnum);
+
+	switch(type){
+		case InternalEnum:
+			return CreatePVectorPrognosticInternal();
+		case BoundaryEnum:
+			return CreatePVectorPrognosticBoundary();
+		default:
+			_error_("type not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreatePVectorPrognosticInternal{{{*/
+ElementVector* Numericalflux::CreatePVectorPrognosticInternal(void){
+
+	/*Nothing added to PVector*/
+	return NULL;
+
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreatePVectorPrognosticBoundary{{{*/
+ElementVector* Numericalflux::CreatePVectorPrognosticBoundary(void){
+
+	/* constants*/
+	const int numdof=NDOF1*NUMVERTICES_BOUNDARY;
+
+	/* Intermediaries*/
+	int        i,j,ig,index1,index2;
+	IssmDouble     DL,Jdet,dt,vx,vy,mean_vx,mean_vy,UdotN,thickness;
+	IssmDouble     xyz_list[NUMVERTICES_BOUNDARY][3];
+	IssmDouble     normal[2];
+	IssmDouble     L[numdof];
+	GaussTria *gauss;
+
+	/*Initialize Load Vector and return if necessary*/
+	ElementVector* pe = NULL;
+	Tria*  tria=(Tria*)element;
+	if(tria->IsOnWater()) return NULL;
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0],nodes,NUMVERTICES_BOUNDARY);
+	parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	Input* vxaverage_input   =tria->inputs->GetInput(VxEnum);                     _assert_(vxaverage_input); 
+	Input* vyaverage_input   =tria->inputs->GetInput(VyEnum);                     _assert_(vyaverage_input);
+	Input* spcthickness_input=tria->inputs->GetInput(PrognosticSpcthicknessEnum); _assert_(spcthickness_input);
+	GetNormal(&normal[0],xyz_list);
+
+	/*Check wether it is an inflow or outflow BC (0 is the middle of the segment)*/
+	index1=tria->GetNodeIndex(nodes[0]);
+	index2=tria->GetNodeIndex(nodes[1]);
+
+	gauss=new GaussTria();
+	gauss->GaussEdgeCenter(index1,index2);
+	vxaverage_input->GetInputValue(&mean_vx,gauss);
+	vyaverage_input->GetInputValue(&mean_vy,gauss);
+	delete gauss;
+
+	UdotN=mean_vx*normal[0]+mean_vy*normal[1];
+	if (UdotN>0){
+		return NULL; /*(u,n)>0 -> outflow, PenaltyCreateKMatrix will take care of it*/
+	}
+	else{
+		pe=new ElementVector(nodes,NUMVERTICES_BOUNDARY,this->parameters);
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(index1,index2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		tria->GetSegmentNodalFunctions(&L[0],gauss,index1,index2);
+
+		vxaverage_input->GetInputValue(&vx,gauss);
+		vyaverage_input->GetInputValue(&vy,gauss);
+		spcthickness_input->GetInputValue(&thickness,gauss);
+		if(xIsNan(thickness)) _error_("Cannot weakly apply constraint because NaN was provided");
+
+		UdotN=vx*normal[0]+vy*normal[1];
+		tria->GetSegmentJacobianDeterminant(&Jdet,&xyz_list[0][0],gauss);
+		DL= - gauss->weight*Jdet*dt*UdotN*thickness;
+
+		for(i=0;ivalues[i] += DL*L[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreatePVectorBalancethickness{{{*/
+ElementVector* Numericalflux::CreatePVectorBalancethickness(void){
+
+	int type;
+	inputs->GetInputValue(&type,TypeEnum);
+
+	switch(type){
+		case InternalEnum:
+			return CreatePVectorBalancethicknessInternal();
+		case BoundaryEnum:
+			return CreatePVectorBalancethicknessBoundary();
+		default:
+			_error_("type not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreatePVectorBalancethicknessInternal{{{*/
+ElementVector* Numericalflux::CreatePVectorBalancethicknessInternal(void){
+
+	/*Nothing added to PVector*/
+	return NULL;
+
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreatePVectorBalancethicknessBoundary{{{*/
+ElementVector* Numericalflux::CreatePVectorBalancethicknessBoundary(void){
+
+	/* constants*/
+	const int numdof=NDOF1*NUMVERTICES_BOUNDARY;
+
+	/* Intermediaries*/
+	int        i,j,ig,index1,index2;
+	IssmDouble     DL,Jdet,vx,vy,mean_vx,mean_vy,UdotN,thickness;
+	IssmDouble     xyz_list[NUMVERTICES_BOUNDARY][3];
+	IssmDouble     normal[2];
+	IssmDouble     L[numdof];
+	GaussTria *gauss;
+
+	/*Initialize Load Vector and return if necessary*/
+	ElementVector* pe = NULL;
+	Tria*  tria=(Tria*)element;
+	if(tria->IsOnWater()) return NULL;
+
+	/*Retrieve all inputs and parameters*/
+	GetVerticesCoordinates(&xyz_list[0][0],nodes,NUMVERTICES_BOUNDARY);
+	Input* vxaverage_input=tria->inputs->GetInput(VxEnum); _assert_(vxaverage_input); 
+	Input* vyaverage_input=tria->inputs->GetInput(VyEnum); _assert_(vyaverage_input);
+	Input* thickness_input=tria->inputs->GetInput(ThicknessEnum); _assert_(thickness_input);
+	GetNormal(&normal[0],xyz_list);
+
+	/*Check wether it is an inflow or outflow BC (0 is the middle of the segment)*/
+	index1=tria->GetNodeIndex(nodes[0]);
+	index2=tria->GetNodeIndex(nodes[1]);
+
+	gauss=new GaussTria();
+	gauss->GaussEdgeCenter(index1,index2);
+	vxaverage_input->GetInputValue(&mean_vx,gauss);
+	vyaverage_input->GetInputValue(&mean_vy,gauss);
+	delete gauss;
+	UdotN=mean_vx*normal[0]+mean_vy*normal[1];
+	if (UdotN>0){
+		return NULL; /*(u,n)>0 -> outflow, PenaltyCreateKMatrix will take care of it*/
+	}
+	else{
+		pe=new ElementVector(nodes,NUMVERTICES_BOUNDARY,this->parameters);
+	}
+
+	/* Start  looping on the number of gaussian points: */
+	gauss=new GaussTria(index1,index2,2);
+	for(ig=gauss->begin();igend();ig++){
+
+		gauss->GaussPoint(ig);
+
+		tria->GetSegmentNodalFunctions(&L[0],gauss,index1,index2);
+
+		vxaverage_input->GetInputValue(&vx,gauss);
+		vyaverage_input->GetInputValue(&vy,gauss);
+		thickness_input->GetInputValue(&thickness,gauss);
+
+		UdotN=vx*normal[0]+vy*normal[1];
+		tria->GetSegmentJacobianDeterminant(&Jdet,&xyz_list[0][0],gauss);
+		DL= - gauss->weight*Jdet*UdotN*thickness;
+
+		for(i=0;ivalues[i] += DL*L[i];
+	}
+
+	/*Clean up and return*/
+	delete gauss;
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::CreatePVectorAdjointBalancethickness{{{*/
+ElementVector* Numericalflux::CreatePVectorAdjointBalancethickness(void){
+
+	/*No PVector for the Adjoint*/
+	return NULL;
+}
+/*}}}*/
+/*FUNCTION Numericalflux::GetNormal {{{*/
+void Numericalflux:: GetNormal(IssmDouble* normal,IssmDouble xyz_list[4][3]){
+
+	/*Build unit outward pointing vector*/
+	IssmDouble vector[2];
+	IssmDouble norm;
+
+	vector[0]=xyz_list[1][0] - xyz_list[0][0];
+	vector[1]=xyz_list[1][1] - xyz_list[0][1];
+
+	norm=sqrt(pow(vector[0],2.0)+pow(vector[1],2.0));
+
+	normal[0]= + vector[1]/norm;
+	normal[1]= - vector[0]/norm;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Loads/Numericalflux.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Numericalflux.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Numericalflux.h	(revision 13395)
@@ -0,0 +1,97 @@
+/*!\file Numericalflux.h
+ * \brief: header file for icefront object
+ */
+
+#ifndef _NUMERICALFLUX_H_
+#define _NUMERICALFLUX_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Load.h"
+class Hook;
+class Parameters;
+class Inputs;
+class IoModel;
+class ElementMatrix;
+class ElementVector;
+/*}}}*/
+
+class Numericalflux: public Load {
+
+	public: 
+		int         id;
+		int analysis_type;
+
+		/*Hooks*/
+		Hook*       helement;
+		Hook*       hnodes;
+
+		/*Corresponding fields*/
+		Element* element;
+		Node**   nodes;
+
+		Parameters *parameters;
+		Inputs     *inputs;
+
+
+		/*Numericalflux constructors,destructors {{{*/
+		Numericalflux();
+		Numericalflux(int numericalflux_id,int i, IoModel* iomodel,int analysis_type);
+		~Numericalflux();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Update virtual functions resolution: {{{*/
+		void    InputUpdateFromVector(IssmDouble* vector, int name, int type){/*Do nothing*/}
+		void    InputUpdateFromVector(int* vector, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromVector(bool* vector, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type){/*Do nothing*/}
+		void    InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){/*Do nothing*/}
+		void    InputUpdateFromVectorDakota(int* vector, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromVectorDakota(bool* vector, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromConstant(IssmDouble constant, int name){/*Do nothing*/};
+		void    InputUpdateFromConstant(int constant, int name){/*Do nothing*/};
+		void    InputUpdateFromConstant(bool constant, int name){_error_("Not implemented yet!");}
+		void    InputUpdateFromSolution(IssmDouble* solution){_error_("Not implemented yet!");}
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel){_error_("not implemented yet");};
+		/*}}}*/
+		/*Load virtual functions definitions: {{{*/
+		void  Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  CreateKMatrix(Matrix* Kff, Matrix* Kfs);
+		void  CreatePVector(Vector* pf);
+		void  CreateJacobianMatrix(Matrix* Jff){_error_("Not implemented yet");};
+		void  PenaltyCreateJacobianMatrix(Matrix* Jff,IssmDouble kmax){_error_("Not implemented yet");};
+		void  PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, IssmDouble kmax);
+		void  PenaltyCreatePVector(Vector* pf, IssmDouble kmax);
+		bool  InAnalysis(int analysis_type);
+		/*}}}*/
+		/*Numericalflux management:{{{*/
+		void  GetNormal(IssmDouble* normal,IssmDouble xyz_list[4][3]);
+		ElementMatrix* CreateKMatrixPrognostic(void);
+		ElementMatrix* CreateKMatrixPrognosticInternal(void);
+		ElementMatrix* CreateKMatrixPrognosticBoundary(void);
+		ElementMatrix* CreateKMatrixBalancethickness(void);
+		ElementMatrix* CreateKMatrixBalancethicknessInternal(void);
+		ElementMatrix* CreateKMatrixBalancethicknessBoundary(void);
+		ElementMatrix* CreateKMatrixAdjointBalancethickness(void);
+		ElementMatrix* CreateKMatrixAdjointBalancethicknessInternal(void);
+		ElementMatrix* CreateKMatrixAdjointBalancethicknessBoundary(void);
+		ElementVector* CreatePVectorPrognostic(void);
+		ElementVector* CreatePVectorPrognosticInternal(void);
+		ElementVector* CreatePVectorPrognosticBoundary(void);
+		ElementVector* CreatePVectorBalancethickness(void);
+		ElementVector* CreatePVectorBalancethicknessInternal(void);
+		ElementVector* CreatePVectorBalancethicknessBoundary(void);
+		ElementVector* CreatePVectorAdjointBalancethickness(void);
+		/*}}}*/
+
+};
+
+#endif  /* _NUMERICALFLUX_H_ */
Index: /issm/trunk/src/c/classes/objects/Loads/Pengrid.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Pengrid.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Pengrid.cpp	(revision 13395)
@@ -0,0 +1,620 @@
+/*!\file Pengrid.c
+ * \brief: implementation of the Pengrid object
+ */
+
+/*Headers*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+/*}}}*/
+	
+/*Element macros*/
+#define NUMVERTICES   1
+
+/*Pengrid constructors and destructor*/
+/*FUNCTION Pengrid::Pengrid(){{{*/
+Pengrid::Pengrid(){
+	this->inputs=NULL;
+	this->parameters=NULL;
+	this->hnode=NULL;
+	this->node=NULL;
+	this->helement=NULL;
+	this->element=NULL;
+	this->hmatpar=NULL;
+	this->matpar=NULL;
+	
+	/*not active, not zigzagging: */
+	active=0;
+	zigzag_counter=0;
+
+}
+/*}}}*/
+/*FUNCTION Pengrid::Pengrid(int index, int id, IoModel* iomodel,int analysis_type){{{*/
+Pengrid::Pengrid(int id, int index, IoModel* iomodel, int in_analysis_type){ //i is the element index
+
+	int i,j;
+	int pengrid_node_id;
+	int pengrid_matpar_id;
+	int pengrid_element_id;
+
+	int numberofvertices;
+	int numberofelements;
+
+	/*Fetch parameters: */
+	iomodel->Constant(&numberofvertices,MeshNumberofverticesEnum);
+	iomodel->Constant(&numberofelements,MeshNumberofelementsEnum);
+
+	/*Some checks if debugging activated*/
+	_assert_(iomodel->singlenodetoelementconnectivity);
+	_assert_(index>=0 && indexid=id;
+	this->analysis_type=in_analysis_type;
+	
+	/*hooks: */
+	pengrid_node_id=iomodel->nodecounter+index+1;
+	pengrid_element_id=iomodel->singlenodetoelementconnectivity[index];
+	_assert_(pengrid_element_id);
+	pengrid_matpar_id=numberofelements+1; //refers to the constant material parameters object
+
+	this->hnode=new Hook(&pengrid_node_id,1);
+	this->helement=new Hook(&pengrid_element_id,1);
+	this->hmatpar=new Hook(&pengrid_matpar_id,1);
+
+	//initialize inputs: none needed
+	this->inputs=new Inputs();
+
+	//this->parameters: we still can't point to it, it may not even exist. Configure will handle this.
+	this->parameters=NULL;
+	this->node=NULL;
+	this->element=NULL;
+	this->matpar=NULL;
+
+	//let's not forget internals
+	this->active=0;
+	this->zigzag_counter=0;
+
+}
+/*}}}*/
+/*FUNCTION Pengrid::~Pengrid(){{{*/
+Pengrid::~Pengrid(){
+	delete inputs;
+	delete hnode;
+	delete helement;
+	delete hmatpar;
+	return;
+}
+/*}}}*/
+			
+/*Object virtual functions definitions:*/
+/*FUNCTION Pengrid::Echo {{{*/
+void Pengrid::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION Pengrid::DeepEcho{{{*/
+void Pengrid::DeepEcho(void){
+
+	_printLine_("Pengrid:");
+	_printLine_("   id: " << id);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	hnode->DeepEcho();
+	helement->DeepEcho();
+	hmatpar->DeepEcho();
+	_printLine_("   active " << this->active);
+	_printLine_("   zigzag_counter " << this->zigzag_counter);
+	_printLine_("   parameters");
+	parameters->DeepEcho();
+	_printLine_("   inputs");
+	inputs->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION Pengrid::Id {{{*/
+int    Pengrid::Id(void){ return id; }
+/*}}}*/
+/*FUNCTION Pengrid::MyRank {{{*/
+int    Pengrid::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Pengrid::ObjectEnum{{{*/
+int Pengrid::ObjectEnum(void){
+
+	return PengridEnum;
+}
+/*}}}*/
+/*FUNCTION Icefront::copy {{{*/
+Object* Pengrid::copy() {
+	
+	Pengrid* pengrid=NULL;
+
+	pengrid=new Pengrid();
+
+	/*copy fields: */
+	pengrid->id=this->id;
+	pengrid->analysis_type=this->analysis_type;
+	if(this->inputs){
+		pengrid->inputs=(Inputs*)this->inputs->Copy();
+	}
+	else{
+		pengrid->inputs=new Inputs();
+	}
+	/*point parameters: */
+	pengrid->parameters=this->parameters;
+
+	/*now deal with hooks and objects: */
+	pengrid->hnode=(Hook*)this->hnode->copy();
+	pengrid->hmatpar=(Hook*)this->hmatpar->copy();
+	pengrid->helement=(Hook*)this->helement->copy();
+
+	/*corresponding fields*/
+	pengrid->node  =(Node*)pengrid->hnode->delivers();
+	pengrid->matpar =(Matpar*)pengrid->hmatpar->delivers();
+	pengrid->element=(Element*)pengrid->helement->delivers();
+
+	//let's not forget internals
+	pengrid->active=this->active=0;
+	pengrid->zigzag_counter=this->zigzag_counter=0;
+
+	return pengrid;
+
+}
+/*}}}*/
+
+/*Load virtual functions definitions:*/
+/*FUNCTION Pengrid::Configure {{{*/
+void  Pengrid::Configure(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+	/*Take care of hooking up all objects for this load, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and offsets hidden in hooks: */
+	hnode->configure(nodesin);
+	helement->configure(elementsin);
+	hmatpar->configure(materialsin);
+
+	/*Get corresponding fields*/
+	node=(Node*)hnode->delivers();
+	element=(Element*)helement->delivers();
+	matpar=(Matpar*)hmatpar->delivers();
+
+	/*point parameters to real dataset: */
+	this->parameters=parametersin;
+}
+/*}}}*/
+/*FUNCTION Pengrid::SetCurrentConfiguration {{{*/
+void  Pengrid::SetCurrentConfiguration(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+}
+/*}}}*/
+/*FUNCTION Pengrid::CreateKMatrix {{{*/
+void  Pengrid::CreateKMatrix(Matrix* Kff, Matrix* Kfs){
+
+	/*No loads applied, do nothing: */
+	return;
+
+}
+/*}}}*/
+/*FUNCTION Pengrid::CreatePVector {{{*/
+void  Pengrid::CreatePVector(Vector* pf){
+
+	/*No loads applied, do nothing: */
+	return;
+
+}
+/*}}}*/
+/*FUNCTION Pengrid::PenaltyCreateMatrix {{{*/
+void  Pengrid::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,IssmDouble kmax){
+
+	/*Retrieve parameters: */
+	ElementMatrix* Ke=NULL;
+	int analysis_type;
+	this->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	switch(analysis_type){
+		#ifdef _HAVE_DIAGNOSTIC_
+		case DiagnosticHorizAnalysisEnum: case AdjointHorizAnalysisEnum:
+			Ke=PenaltyCreateKMatrixDiagnosticStokes(kmax);
+			break;
+		#endif
+		#ifdef _HAVE_THERMAL_
+		case ThermalAnalysisEnum:
+			Ke=PenaltyCreateKMatrixThermal(kmax);
+			break;
+		case MeltingAnalysisEnum:
+			Ke=PenaltyCreateKMatrixMelting(kmax);
+			break;
+		#endif
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global matrix*/
+	if(Ke){
+		Ke->AddToGlobal(Kff,Kfs);
+		delete Ke;
+	}
+}
+/*}}}*/
+/*FUNCTION Pengrid::PenaltyCreatePVector {{{*/
+void  Pengrid::PenaltyCreatePVector(Vector* pf,IssmDouble kmax){
+
+	/*Retrieve parameters: */
+	ElementVector* pe=NULL;
+	int analysis_type;
+	this->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	switch(analysis_type){
+		#ifdef _HAVE_DIAGNOSTIC_
+		case ThermalAnalysisEnum:
+			pe=PenaltyCreatePVectorThermal(kmax);
+			break;
+		#endif
+		#ifdef _HAVE_THERMAL_
+		case MeltingAnalysisEnum:
+			pe=PenaltyCreatePVectorMelting(kmax);
+			break;
+		case DiagnosticHorizAnalysisEnum: case AdjointHorizAnalysisEnum:
+			break;
+		#endif
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global Vector*/
+	if(pe){
+		pe->AddToGlobal(pf);
+		delete pe;
+	}
+}
+/*}}}*/
+/*FUNCTION Pengrid::InAnalysis{{{*/
+bool Pengrid::InAnalysis(int in_analysis_type){
+	if (in_analysis_type==this->analysis_type)return true;
+	else return false;
+}
+/*}}}*/
+
+/*Update virtual functions definitions:*/
+/*FUNCTION Pengrid::InputUpdateFromVector(IssmDouble* vector, int name, int type) {{{*/
+void  Pengrid::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromVector(int* vector, int name, int type) {{{*/
+void  Pengrid::InputUpdateFromVector(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromVector(bool* vector, int name, int type) {{{*/
+void  Pengrid::InputUpdateFromVector(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromMatrixDakota(IssmDouble* vector, int nrows, int ncols, int name, int type) {{{*/
+void  Pengrid::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type) {{{*/
+void  Pengrid::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromVectorDakota(int* vector, int name, int type) {{{*/
+void  Pengrid::InputUpdateFromVectorDakota(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromVectorDakota(bool* vector, int name, int type) {{{*/
+void  Pengrid::InputUpdateFromVectorDakota(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromConstant(IssmDouble constant, int name) {{{*/
+void  Pengrid::InputUpdateFromConstant(IssmDouble constant, int name){
+	switch(name){
+
+		case MeltingOffsetEnum:
+			inputs->AddInput(new DoubleInput(name,constant));
+			return;
+
+	}
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromConstant(int constant, int name) {{{*/
+void  Pengrid::InputUpdateFromConstant(int constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromConstant(bool constant, int name) {{{*/
+void  Pengrid::InputUpdateFromConstant(bool constant, int name){
+
+	switch(name){
+
+		case ResetPenaltiesEnum:
+			if (constant) zigzag_counter=0;
+			return;
+
+	}
+}
+/*}}}*/
+/*FUNCTION Pengrid::InputUpdateFromSolution{{{*/
+void  Pengrid::InputUpdateFromSolution(IssmDouble* solution){
+	/*Nothing updated yet*/
+}
+/*}}}*/		
+
+/*Pengrid management:*/
+/*FUNCTION Pengrid::ConstraintActivate {{{*/
+void  Pengrid::ConstraintActivate(int* punstable){
+
+	int analysis_type;
+
+	/*Retrieve parameters: */
+	this->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	if (analysis_type==DiagnosticHorizAnalysisEnum){
+		/*No penalty to check*/
+		return;
+	}
+	else if (analysis_type==ThermalAnalysisEnum){
+		ConstraintActivateThermal(punstable);
+	}
+	else if (analysis_type==MeltingAnalysisEnum){
+		/*No penalty to check*/
+		return;
+	}
+	else{
+		_error_("analysis: " << EnumToStringx(analysis_type) << " not supported yet");
+	}
+
+}
+/*}}}*/
+/*FUNCTION Pengrid::ConstraintActivateThermal {{{*/
+void  Pengrid::ConstraintActivateThermal(int* punstable){
+
+	//   The penalty is stable if it doesn't change during to successive iterations.   
+
+	int    found=0;
+	const int numnodes=1;
+	IssmDouble pressure;
+	IssmDouble temperature;
+	IssmDouble t_pmp;
+	int    new_active;
+	int    unstable=0;
+	int    reset_penalties=0;
+	int    penalty_lock;
+
+	/*recover pointers: */
+	Penta* penta=(Penta*)element;
+	
+	/*check that pengrid is not a clone (penalty to be added only once)*/
+	if (node->IsClone()){
+		unstable=0;
+		*punstable=unstable;
+		return;
+	}
+
+	//First recover pressure and temperature values, using the element: */
+	penta->GetInputValue(&pressure,node,PressureEnum);
+	penta->GetInputValue(&temperature,node,TemperaturePicardEnum);
+
+	//Recover our data:
+	parameters->FindParam(&penalty_lock,ThermalPenaltyLockEnum);
+	
+	//Compute pressure melting point
+	t_pmp=matpar->TMeltingPoint(pressure);
+
+	//Figure out if temperature is over melting_point, in which case, this penalty needs to be activated.
+
+	if (temperature>t_pmp){
+		new_active=1;
+	}
+	else{
+		new_active=0;
+	}
+
+
+	//Figure out stability of this penalty
+	if (active==new_active){
+		unstable=0;
+	}
+	else{
+		unstable=1;
+		if(penalty_lock)zigzag_counter++;
+	}
+
+	/*If penalty keeps zigzagging more than 5 times: */
+	if(penalty_lock){
+		if(zigzag_counter>penalty_lock){
+			unstable=0;
+			active=1;
+		}
+	}
+
+	//Set penalty flag
+	active=new_active;
+
+	//*Assign output pointers:*/
+	*punstable=unstable;
+}
+/*}}}*/
+#ifdef _HAVE_DIAGNOSTIC_
+/*FUNCTION Pengrid::PenaltyCreateKMatrixDiagnosticStokes {{{*/
+ElementMatrix* Pengrid::PenaltyCreateKMatrixDiagnosticStokes(IssmDouble kmax){
+	
+	const int numdof = NUMVERTICES *NDOF4;
+	IssmDouble    slope[2];
+	IssmDouble    penalty_offset;
+	int       approximation;
+
+	Penta* penta=(Penta*)element;
+
+	/*Initialize Element vector and return if necessary*/
+	penta->inputs->GetInputValue(&approximation,ApproximationEnum);
+	if(approximation!=StokesApproximationEnum &&  approximation!=PattynStokesApproximationEnum) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(&node,1,this->parameters,StokesApproximationEnum);
+
+	/*Retrieve all inputs and parameters*/
+	parameters->FindParam(&penalty_offset,DiagnosticPenaltyFactorEnum);
+	penta->GetInputValue(&slope[0],node,BedSlopeXEnum);
+	penta->GetInputValue(&slope[1],node,BedSlopeYEnum);
+
+	/*Create elementary matrix: add penalty to constrain wb (wb=ub*db/dx+vb*db/dy)*/
+	Ke->values[2*NDOF4+0]=-slope[0]*kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[2*NDOF4+1]=-slope[1]*kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[2*NDOF4+2]= kmax*pow((IssmDouble)10,penalty_offset);
+
+	/*Transform Coordinate System*/
+	TransformStiffnessMatrixCoord(Ke,&node,NUMVERTICES,XYZPEnum);
+
+	/*Clean up and return*/
+	return Ke;
+}
+/*}}}*/
+#endif
+#ifdef _HAVE_THERMAL_
+/*FUNCTION Pengrid::PenaltyCreateKMatrixMelting {{{*/
+ElementMatrix* Pengrid::PenaltyCreateKMatrixMelting(IssmDouble kmax){
+
+	const int numdof=NUMVERTICES*NDOF1;
+	IssmDouble pressure,temperature,t_pmp;
+	IssmDouble penalty_factor;
+
+	Penta* penta=(Penta*)element;
+
+	/*check that pengrid is not a clone (penalty to be added only once)*/
+	if (node->IsClone()) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(&node,1,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	penta->GetInputValue(&pressure,node,PressureEnum);
+	penta->GetInputValue(&temperature,node,TemperatureEnum);
+	parameters->FindParam(&penalty_factor,ThermalPenaltyFactorEnum);
+	
+	/*Compute pressure melting point*/
+	t_pmp=matpar->GetMeltingPoint()-matpar->GetBeta()*pressure;
+
+	/*Add penalty load*/
+	if (temperaturevalues[0]=kmax*pow((IssmDouble)10,penalty_factor);
+	}
+
+	/*Clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Pengrid::PenaltyCreateKMatrixThermal {{{*/
+ElementMatrix* Pengrid::PenaltyCreateKMatrixThermal(IssmDouble kmax){
+
+	const int numdof=NUMVERTICES*NDOF1;
+	IssmDouble    penalty_factor;
+
+	/*Initialize Element matrix and return if necessary*/
+	if(!this->active) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(&node,NUMVERTICES,this->parameters);
+
+	/*recover parameters: */
+	parameters->FindParam(&penalty_factor,ThermalPenaltyFactorEnum);
+
+	Ke->values[0]=kmax*pow((IssmDouble)10,penalty_factor);
+
+	/*Clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Pengrid::PenaltyCreatePVectorMelting {{{*/
+ElementVector* Pengrid::PenaltyCreatePVectorMelting(IssmDouble kmax){
+	
+	const int numdof=NUMVERTICES*NDOF1;
+	IssmDouble pressure;
+	IssmDouble temperature;
+	IssmDouble melting_offset;
+	IssmDouble t_pmp;
+	IssmDouble dt,penalty_factor;
+
+	/*recover pointers: */
+	Penta* penta=(Penta*)element;
+
+	/*check that pengrid is not a clone (penalty to be added only once)*/
+	if (node->IsClone()) return NULL;
+	ElementVector* pe=new ElementVector(&node,NUMVERTICES,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	penta->GetInputValue(&pressure,node,PressureEnum);
+	penta->GetInputValue(&temperature,node,TemperatureEnum);
+	inputs->GetInputValue(&melting_offset,MeltingOffsetEnum);
+	parameters->FindParam(&dt,TimesteppingTimeStepEnum);
+	parameters->FindParam(&penalty_factor,ThermalPenaltyFactorEnum);
+
+	/*Compute pressure melting point*/
+	t_pmp=matpar->GetMeltingPoint()-matpar->GetBeta()*pressure;
+
+	/*Add penalty load
+	  This time, the penalty must have the same value as the one used for the thermal computation
+	  so that the corresponding melting can be computed correctly
+	  In the thermal computation, we used kmax=melting_offset, and the same penalty_factor*/
+	if (temperaturevalues[0]=0;
+	}
+	else{
+		if (reCast(dt)) pe->values[0]=melting_offset*pow((IssmDouble)10,penalty_factor)*(temperature-t_pmp)/dt;
+		else    pe->values[0]=melting_offset*pow((IssmDouble)10,penalty_factor)*(temperature-t_pmp);
+	}
+
+	/*Clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Pengrid::PenaltyCreatePVectorThermal {{{*/
+ElementVector* Pengrid::PenaltyCreatePVectorThermal(IssmDouble kmax){
+
+	const int numdof=NUMVERTICES*NDOF1;
+	IssmDouble pressure;
+	IssmDouble t_pmp;
+	IssmDouble penalty_factor;
+
+	Penta* penta=(Penta*)element;
+
+	/*Initialize Element matrix and return if necessary*/
+	if(!this->active) return NULL;
+	ElementVector* pe=new ElementVector(&node,1,this->parameters);
+
+	/*Retrieve all inputs and parameters*/
+	penta->GetInputValue(&pressure,node,PressureEnum);
+	parameters->FindParam(&penalty_factor,ThermalPenaltyFactorEnum);
+
+	/*Compute pressure melting point*/
+	t_pmp=matpar->GetMeltingPoint()-matpar->GetBeta()*pressure;
+
+	pe->values[0]=kmax*pow((IssmDouble)10,penalty_factor)*t_pmp;
+
+	/*Clean up and return*/
+	return pe;
+}
+/*}}}*/
+#endif
+/*FUNCTION Pengrid::ResetConstraint {{{*/
+void  Pengrid::ResetConstraint(void){
+	active=0;
+	zigzag_counter=0;
+}
+/*}}}*/
+/*FUNCTION Pengrid::UpdateInputs {{{*/
+void  Pengrid::UpdateInputs(IssmDouble* solution){
+	_error_("not supported yet!");
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Loads/Pengrid.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Pengrid.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Pengrid.h	(revision 13395)
@@ -0,0 +1,100 @@
+/*!\file Pengrid.h
+ * \brief: header file for pengrid object */
+
+#ifndef _PENGRID_H_
+#define _PENGRID_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Load.h"
+class Hook;
+class Inputs;
+class Parameters;
+class IoModel;
+/*}}}*/
+
+class Pengrid: public Load{
+
+	private: 
+
+		int		id;
+		int analysis_type;
+		
+		/*Hooks*/
+		Hook* hnode;  //hook to 1 node
+		Hook* helement;  //hook to 1 element
+		Hook* hmatpar; //hook to 1 matpar
+
+		/*Corresponding fields*/
+		Node    *node;
+		Element *element;
+		Matpar  *matpar;
+
+		Parameters* parameters; //pointer to solution parameters
+		Inputs*  inputs;
+	
+		/*internals: */
+		int active;
+		int zigzag_counter;
+
+	public:
+
+		/*Pengrid constructors, destructors {{{*/
+		Pengrid();
+		Pengrid(int index, int id, IoModel* iomodel,int analysis_type);
+		~Pengrid();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Update virtual functions resolution: {{{*/
+		void  InputUpdateFromVector(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVector(int* vector, int name, int type);
+		void  InputUpdateFromVector(bool* vector, int name, int type);
+		void  InputUpdateFromMatrixDakota(IssmDouble* matrix ,int nrows, int ncols, int name, int type);
+		void  InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(int* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(bool* vector, int name, int type);
+		void  InputUpdateFromConstant(IssmDouble constant, int name);
+		void  InputUpdateFromConstant(int constant, int name);
+		void  InputUpdateFromConstant(bool constant, int name);
+		void  InputUpdateFromSolution(IssmDouble* solution);
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel){_error_("not implemented yet");};
+		/*}}}*/
+		/*Load virtual functions definitions: {{{*/
+		void  Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  CreateKMatrix(Matrix* Kff, Matrix* Kfs);
+		void  CreatePVector(Vector* pf);
+		void  CreateJacobianMatrix(Matrix* Jff){_error_("Not implemented yet");};
+		void  PenaltyCreateJacobianMatrix(Matrix* Jff,IssmDouble kmax){_error_("Not implemented yet");};
+		void  PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, IssmDouble kmax);
+		void  PenaltyCreatePVector(Vector* pf, IssmDouble kmax);
+		bool  InAnalysis(int analysis_type);
+		/*}}}*/
+		/*Pengrid management {{{*/
+		#ifdef _HAVE_DIAGNOSTIC_
+		ElementMatrix* PenaltyCreateKMatrixDiagnosticStokes(IssmDouble kmax);
+		#endif
+		#ifdef _HAVE_THERMAL_
+		ElementMatrix* PenaltyCreateKMatrixThermal(IssmDouble kmax);
+		ElementMatrix* PenaltyCreateKMatrixMelting(IssmDouble kmax);
+		ElementVector* PenaltyCreatePVectorThermal(IssmDouble kmax);
+		ElementVector* PenaltyCreatePVectorMelting(IssmDouble kmax);
+		#endif
+		void  ConstraintActivate(int* punstable);
+		void  ConstraintActivateThermal(int* punstable);
+		void  UpdateInputs(IssmDouble* solution);
+		void  ResetConstraint(void);
+		/*}}}*/
+
+};
+
+#endif  /* _PENGRID_H_ */
+
+
Index: /issm/trunk/src/c/classes/objects/Loads/Penpair.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Penpair.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Penpair.cpp	(revision 13395)
@@ -0,0 +1,355 @@
+/*!\file Penpair.c
+ * \brief: implementation of the Penpair object
+ */
+
+/*Headers*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+/*Element macros*/
+#define NUMVERTICES 2
+
+/*Penpair constructors and destructor*/
+/*FUNCTION Penpair::constructor {{{*/
+Penpair::Penpair(){
+
+	this->hnodes=NULL;
+	this->nodes=NULL;
+	this->parameters=NULL;
+	return;
+}
+/*}}}*/
+/*FUNCTION Penpair::creation {{{*/
+Penpair::Penpair(int penpair_id, int* penpair_node_ids,int in_analysis_type){
+	
+	this->id=penpair_id;
+	this->analysis_type=in_analysis_type;
+	this->hnodes=new Hook(penpair_node_ids,2);
+	this->parameters=NULL;
+	this->nodes=NULL;
+	
+	return;
+}
+/*}}}*/
+/*FUNCTION Penpair::destructor {{{*/
+Penpair::~Penpair(){
+	delete hnodes;
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION Penpair::Echo {{{*/
+void Penpair::Echo(void){
+
+	int i;
+
+	_printLine_("Penpair:");
+	_printLine_("   id: " << id);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	hnodes->Echo();
+	
+	return;
+}
+/*}}}*/
+/*FUNCTION Penpair::DeepEcho {{{*/
+void Penpair::DeepEcho(void){
+
+	_printLine_("Penpair:");
+	_printLine_("   id: " << id);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	hnodes->DeepEcho();
+
+	return;
+}		
+/*}}}*/
+/*FUNCTION Penpair::Id {{{*/
+int    Penpair::Id(void){ return id; }
+/*}}}*/
+/*FUNCTION Penpair::MyRank {{{*/
+int    Penpair::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Penpair::ObjectEnum{{{*/
+int Penpair::ObjectEnum(void){
+
+	return PenpairEnum;
+}
+/*}}}*/
+/*FUNCTION Penpair::copy {{{*/
+Object* Penpair::copy() {
+	
+	Penpair* penpair=NULL;
+
+	penpair=new Penpair();
+
+	/*copy fields: */
+	penpair->id=this->id;
+	penpair->analysis_type=this->analysis_type;
+
+	/*now deal with hooks and objects: */
+	penpair->hnodes=(Hook*)this->hnodes->copy();
+	penpair->nodes =(Node**)penpair->hnodes->deliverp();
+
+	/*point parameters: */
+	penpair->parameters=this->parameters;
+
+	return penpair;
+
+}
+/*}}}*/
+		
+/*Load virtual functions definitions:*/
+/*FUNCTION Penpair::Configure {{{*/
+void  Penpair::Configure(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+	/*Take care of hooking up all objects for this element, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and offsets hidden in hooks: */
+	hnodes->configure(nodesin);
+
+	/*Initialize hooked fields*/
+	this->nodes  =(Node**)hnodes->deliverp();
+
+	/*point parameters to real dataset: */
+	this->parameters=parametersin;
+
+}
+/*}}}*/
+/*FUNCTION Penpair::SetCurrentConfiguration {{{*/
+void  Penpair::SetCurrentConfiguration(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+}
+/*}}}*/
+/*FUNCTION Penpair::CreateKMatrix {{{*/
+void  Penpair::CreateKMatrix(Matrix* Kff, Matrix* Kfs){
+	/*If you code this piece, don't forget that a penalty will be inactive if it is dealing with clone nodes*/
+	/*No loads applied, do nothing: */
+	return;
+
+}
+/*}}}*/
+/*FUNCTION Penpair::CreatePVector {{{*/
+void  Penpair::CreatePVector(Vector* pf){
+
+	/*No loads applied, do nothing: */
+	return;
+
+}
+/*}}}*/
+/*FUNCTION Penpair::CreateJacobianMatrix{{{*/
+void  Penpair::CreateJacobianMatrix(Matrix* Jff){
+	this->CreateKMatrix(Jff,NULL);
+}
+/*}}}*/
+/*FUNCTION Penpair::PenaltyCreateKMatrix {{{*/
+void  Penpair::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,IssmDouble kmax){
+
+	/*Retrieve parameters: */
+	ElementMatrix* Ke=NULL;
+	int analysis_type;
+	this->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	switch(analysis_type){
+		case DiagnosticHorizAnalysisEnum:
+			Ke=PenaltyCreateKMatrixDiagnosticHoriz(kmax);
+			break;
+		case PrognosticAnalysisEnum:
+			Ke=PenaltyCreateKMatrixPrognostic(kmax);
+			break;
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global Vector*/
+	if(Ke){
+		Ke->AddToGlobal(Kff,Kfs);
+		delete Ke;
+	}
+}
+/*}}}*/
+/*FUNCTION Penpair::PenaltyCreatePVector {{{*/
+void  Penpair::PenaltyCreatePVector(Vector* pf,IssmDouble kmax){
+	/*No loads applied, do nothing: */
+	return;
+}
+/*}}}*/
+/*FUNCTION Penpair::PenaltyCreateJacobianMatrix{{{*/
+void  Penpair::PenaltyCreateJacobianMatrix(Matrix* Jff,IssmDouble kmax){
+	this->PenaltyCreateKMatrix(Jff,NULL,kmax);
+}
+/*}}}*/
+/*FUNCTION Penpair::InAnalysis{{{*/
+bool Penpair::InAnalysis(int in_analysis_type){
+	if (in_analysis_type==this->analysis_type)return true;
+	else return false;
+}
+/*}}}*/
+
+/*Update virtual functions definitions:*/
+/*FUNCTION Penpair::InputUpdateFromConstant(IssmDouble constant, int name) {{{*/
+void  Penpair::InputUpdateFromConstant(IssmDouble constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Penpair::InputUpdateFromConstant(int constant, int name) {{{*/
+void  Penpair::InputUpdateFromConstant(int constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Penpair::InputUpdateFromConstant(bool constant, int name) {{{*/
+void  Penpair::InputUpdateFromConstant(bool constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Penpair::InputUpdateFromVector(IssmDouble* vector, int name, int type) {{{*/
+void  Penpair::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Penpair::InputUpdateFromVector(int* vector, int name, int type) {{{*/
+void  Penpair::InputUpdateFromVector(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Penpair::InputUpdateFromVector(bool* vector, int name, int type) {{{*/
+void  Penpair::InputUpdateFromVector(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+
+/*Penpair management:*/
+/*FUNCTION Penpair::PenaltyCreateKMatrixDiagnosticHoriz{{{*/
+ElementMatrix* Penpair::PenaltyCreateKMatrixDiagnosticHoriz(IssmDouble kmax){
+
+	int    approximation0=nodes[0]->GetApproximation();
+	int    approximation1=nodes[1]->GetApproximation();
+
+	switch(approximation0){
+		case MacAyealApproximationEnum:
+			switch(approximation1){
+				case MacAyealApproximationEnum: return PenaltyCreateKMatrixDiagnosticMacAyealPattyn(kmax); 
+				case PattynApproximationEnum:   return PenaltyCreateKMatrixDiagnosticMacAyealPattyn(kmax); 
+				default: _error_("not supported yet");
+			}
+		case PattynApproximationEnum:
+			switch(approximation1){
+				case MacAyealApproximationEnum: return PenaltyCreateKMatrixDiagnosticMacAyealPattyn(kmax); 
+				case PattynApproximationEnum:   return PenaltyCreateKMatrixDiagnosticMacAyealPattyn(kmax); 
+				default: _error_("not supported yet");
+			}
+		case StokesApproximationEnum:
+			switch(approximation1){
+				case StokesApproximationEnum: return PenaltyCreateKMatrixDiagnosticStokes(kmax); 
+				case NoneApproximationEnum: return   PenaltyCreateKMatrixDiagnosticStokes(kmax); 
+				default: _error_("not supported yet");
+			}
+		case NoneApproximationEnum:
+			switch(approximation1){
+				case StokesApproximationEnum: return PenaltyCreateKMatrixDiagnosticStokes(kmax); 
+				case NoneApproximationEnum: return   PenaltyCreateKMatrixDiagnosticStokes(kmax); 
+				default: _error_("not supported yet");
+			}
+		default: _error_("not supported yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Penpair::PenaltyCreateKMatrixDiagnosticMacAyealPattyn {{{*/
+ElementMatrix* Penpair::PenaltyCreateKMatrixDiagnosticMacAyealPattyn(IssmDouble kmax){
+	
+	const int numdof=NUMVERTICES*NDOF2;
+	IssmDouble penalty_offset;
+
+	/*Initialize Element vector and return if necessary*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters);
+
+	/*recover parameters: */
+	parameters->FindParam(&penalty_offset,DiagnosticPenaltyFactorEnum);
+
+	//Create elementary matrix: add penalty to 
+	Ke->values[0*numdof+0]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[0*numdof+2]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[2*numdof+0]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[2*numdof+2]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+
+	Ke->values[1*numdof+1]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[1*numdof+3]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[3*numdof+1]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[3*numdof+3]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+
+	/*Clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penpair::PenaltyCreateKMatrixDiagnosticStokes {{{*/
+ElementMatrix* Penpair::PenaltyCreateKMatrixDiagnosticStokes(IssmDouble kmax){
+	
+	const int numdof=NUMVERTICES*NDOF4;
+	IssmDouble penalty_offset;
+
+	/*Initialize Element vector and return if necessary*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters);
+
+	/*recover parameters: */
+	parameters->FindParam(&penalty_offset,DiagnosticPenaltyFactorEnum);
+
+	//Create elementary matrix: add penalty to 
+	Ke->values[0*numdof+0]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[0*numdof+4]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[4*numdof+0]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[4*numdof+4]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+
+	Ke->values[1*numdof+1]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[1*numdof+5]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[5*numdof+1]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[5*numdof+5]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+	
+	Ke->values[2*numdof+2]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[2*numdof+6]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[6*numdof+2]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[6*numdof+6]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+
+	Ke->values[3*numdof+3]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[3*numdof+7]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[7*numdof+3]=-kmax*pow((IssmDouble)10.0,penalty_offset);
+	Ke->values[7*numdof+7]=+kmax*pow((IssmDouble)10.0,penalty_offset);
+
+	/*Clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Penpair::PenaltyCreateKMatrixPrognostic {{{*/
+ElementMatrix* Penpair::PenaltyCreateKMatrixPrognostic(IssmDouble kmax){
+
+	const int numdof=NUMVERTICES*NDOF1;
+	IssmDouble penalty_factor;
+
+	/*Initialize Element vector and return if necessary*/
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters);
+
+	/*recover parameters: */
+	parameters->FindParam(&penalty_factor,PrognosticPenaltyFactorEnum);
+
+	//Create elementary matrix: add penalty to 
+	Ke->values[0*numdof+0]=+kmax*pow((IssmDouble)10.0,penalty_factor);
+	Ke->values[0*numdof+1]=-kmax*pow((IssmDouble)10.0,penalty_factor);
+	Ke->values[1*numdof+0]=-kmax*pow((IssmDouble)10.0,penalty_factor);
+	Ke->values[1*numdof+1]=+kmax*pow((IssmDouble)10.0,penalty_factor);
+
+	/*Clean up and return*/
+	return Ke;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Loads/Penpair.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Penpair.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Penpair.h	(revision 13395)
@@ -0,0 +1,77 @@
+/*!\file Penpair.h
+ * \brief: header file for penpair object */
+
+#ifndef _PENPAIR_H_
+#define _PENPAIR_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Load.h"
+#include "../Node.h"
+#include "../Elements/Element.h"
+
+class Element;
+/*}}}*/
+
+class Penpair: public Load{
+
+	private: 
+		int		id;
+		int analysis_type;
+		
+		Hook* hnodes;  //hook to 2 nodes
+		Node** nodes;
+
+		Parameters* parameters; //pointer to solution parameters
+
+	public:
+
+		/*Penpair constructors, destructors: {{{*/
+		Penpair();
+		Penpair(int penpair_id,int* penpair_node_ids,int analysis_type);
+		~Penpair();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Update virtual functions resolution: {{{*/
+		void  InputUpdateFromVector(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVector(int* vector, int name, int type);
+		void  InputUpdateFromVector(bool* vector, int name, int type);
+		void  InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrow, int ncols,int name, int type){_error_("Not implemented yet!");}
+		void  InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){_error_("Not implemented yet!");}
+		void  InputUpdateFromVectorDakota(int* vector, int name, int type){_error_("Not implemented yet!");}
+		void  InputUpdateFromVectorDakota(bool* vector, int name, int type){_error_("Not implemented yet!");}
+		void  InputUpdateFromConstant(IssmDouble constant, int name);
+		void  InputUpdateFromConstant(int constant, int name);
+		void  InputUpdateFromConstant(bool constant, int name);
+		void  InputUpdateFromSolution(IssmDouble* solution){_error_("Not implemented yet!");}
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel){_error_("not implemented yet");};
+		/*}}}*/
+			/*Load virtual functions definitions: {{{*/
+		void  Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  CreateKMatrix(Matrix* Kff, Matrix* Kfs);
+		void  CreatePVector(Vector* pf);
+		void  CreateJacobianMatrix(Matrix* Jff);
+		void  PenaltyCreateKMatrix(Matrix* Kff,Matrix* Kfs,IssmDouble kmax);
+		void  PenaltyCreatePVector(Vector* pf, IssmDouble kmax);
+		void  PenaltyCreateJacobianMatrix(Matrix* Jff,IssmDouble kmax);
+		bool  InAnalysis(int analysis_type);
+		/*}}}*/
+			/*Penpair management: {{{*/
+		ElementMatrix* PenaltyCreateKMatrixDiagnosticHoriz(IssmDouble kmax);
+		ElementMatrix* PenaltyCreateKMatrixDiagnosticMacAyealPattyn(IssmDouble kmax);
+		ElementMatrix* PenaltyCreateKMatrixDiagnosticStokes(IssmDouble kmax);
+		ElementMatrix* PenaltyCreateKMatrixPrognostic(IssmDouble kmax);
+		/*}}}*/
+};
+
+#endif  /* _PENPAIR_H_ */
+
+
Index: /issm/trunk/src/c/classes/objects/Loads/Riftfront.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Riftfront.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Riftfront.cpp	(revision 13395)
@@ -0,0 +1,916 @@
+/*!\file Riftfront.cpp
+ * \brief: implementation of the Riftfront object
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../include/include.h"
+#include "../../../modules/ModelProcessorx/ModelProcessorx.h"
+#include "../../classes.h"
+/*}}}*/
+
+/*Element macros*/
+#define NUMVERTICES 2
+
+/*Riftfront constructors and destructor*/
+/*FUNCTION Riftfront::Riftfront(){{{*/
+Riftfront::Riftfront(){
+	this->inputs=NULL;
+	this->parameters=NULL;
+	this->hnodes=NULL;
+	this->helements=NULL;
+	this->hmatpar=NULL;
+	this->nodes=NULL;
+	this->elements=NULL;
+	this->matpar=NULL;
+}
+/*}}}*/
+/*FUNCTION Riftfront::Riftfront(int id, int i, IoModel* iomodel,int analysis_type){{{*/
+Riftfront::Riftfront(int riftfront_id,int i, IoModel* iomodel,int riftfront_analysis_type){
+
+	/*data: */
+	int    riftfront_node_ids[2];
+	int    riftfront_elem_ids[2];
+	int    riftfront_matpar_id;
+	int    riftfront_type;
+	int    riftfront_fill;
+	IssmDouble riftfront_friction;
+	IssmDouble riftfront_fractionincrement;
+	bool   riftfront_shelf;
+	int    numberofelements;
+	int    penalty_lock;
+
+	/*intermediary: */
+	int el1    ,el2;
+	int node1  ,node2;
+
+	/*Fetch parameters: */
+	iomodel->Constant(&numberofelements,MeshNumberofelementsEnum);
+	iomodel->Constant(&penalty_lock,DiagnosticRiftPenaltyLockEnum);
+
+	/*Ok, retrieve all the data needed to add a penalty between the two nodes: */
+	el1=reCast(*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+2));
+	el2=reCast(*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+3)) ;
+
+	node1=reCast(*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+0));
+	node2=reCast(*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+1));
+
+	/*id: */
+	this->id=riftfront_id;
+	this->analysis_type=riftfront_analysis_type;
+
+	/*hooks: */
+	riftfront_node_ids[0]=iomodel->nodecounter+node1;
+	riftfront_node_ids[1]=iomodel->nodecounter+node2;
+	riftfront_elem_ids[0]=el1;
+	riftfront_elem_ids[1]=el2;
+	riftfront_matpar_id=numberofelements+1; //matlab indexing
+
+	/*Hooks: */
+	this->hnodes=new Hook(riftfront_node_ids,2);
+	this->helements=new Hook(riftfront_elem_ids,2);
+	this->hmatpar=new Hook(&riftfront_matpar_id,1);
+
+	/*computational parameters: */
+	this->active=0;
+	this->frozen=0;
+	this->counter=0;
+	this->prestable=0;
+	this->penalty_lock=penalty_lock;
+	this->material_converged=0;
+	this->normal[0]=*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+4);
+	this->normal[1]=*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+5);
+	this->length=*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+6);
+	this->fraction=*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+9);
+	this->state=reCast(*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+11));
+
+	//intialize inputs, and add as many inputs per element as requested: 
+	this->inputs=new Inputs();
+		
+	riftfront_type=SegmentRiftfrontEnum;
+	riftfront_fill = reCast(*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+7));
+	riftfront_friction=*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+8);
+	riftfront_fractionincrement=*(iomodel->Data(RiftsRiftstructEnum)+RIFTINFOSIZE*i+10);
+	riftfront_shelf=reCast(iomodel->Data(MaskVertexonfloatingiceEnum)[node1-1]);
+
+	this->inputs->AddInput(new IntInput(TypeEnum,riftfront_type));
+	this->inputs->AddInput(new IntInput(FillEnum,riftfront_fill));
+	this->inputs->AddInput(new DoubleInput(FrictionEnum,riftfront_friction));
+	this->inputs->AddInput(new DoubleInput(FractionIncrementEnum,riftfront_fractionincrement));
+	this->inputs->AddInput(new BoolInput(SegmentOnIceShelfEnum,riftfront_shelf));
+	
+	//parameters and hooked fields: we still can't point to them, they may not even exist. Configure will handle this.
+	this->parameters=NULL;
+	this->nodes= NULL;
+	this->elements= NULL;
+	this->matpar= NULL;
+		
+}
+/*}}}*/
+/*FUNCTION Riftfront::~Riftfront(){{{*/
+Riftfront::~Riftfront(){
+	delete inputs;
+	this->parameters=NULL;
+
+	delete hnodes;
+	delete helements;
+	delete hmatpar;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION Riftfront::Echo {{{*/
+void Riftfront::Echo(void){
+
+	Input* input=NULL;
+	int fill;
+	IssmDouble friction,fractionincrement;
+
+	
+	/*recover some inputs first: */
+	input=(Input*)this->inputs->GetInput(FillEnum); input->GetInputValue(&fill);
+	input=(Input*)this->inputs->GetInput(FrictionEnum); input->GetInputValue(&friction);
+	input=(Input*)this->inputs->GetInput(FractionIncrementEnum); input->GetInputValue(&fractionincrement);
+
+	_printLine_("Riftfront:");
+	_printLine_("   id: " << id);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	_printLine_("   hnodes: " << hnodes);
+	_printLine_("   helements: " << helements);
+	_printLine_("   hmatpar: " << hmatpar);
+	_printLine_("   parameters: " << parameters);
+	_printLine_("   inputs: " << inputs);
+	_printLine_("   internal parameters: ");
+	_printLine_("   normal: " << normal[0] << "|" << normal[1]);
+	_printLine_("   length: " << length);
+	_printLine_("   penalty_lock: " << penalty_lock);
+	_printLine_("   active: " <<(active ? "true":"false"));
+	_printLine_("   counter: " << counter);
+	_printLine_("   prestable: " << (prestable ? "true":"false"));
+	_printLine_("   material_converged: " << (material_converged ? "true":"false"));
+	_printLine_("   fill: " << fill);
+	_printLine_("   friction: " << friction);
+	_printLine_("   fraction: " << fraction);
+	_printLine_("   fractionincrement: " << fractionincrement);
+	_printLine_("   state: " << state);
+	_printLine_("   frozen: " << (frozen ? "true":"false"));
+		
+}
+/*}}}*/
+/*FUNCTION Riftfront::DeepEcho{{{*/
+void Riftfront::DeepEcho(void){
+
+	_printLine_("Riftfront:");
+	_printLine_("   id: " << id);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	hnodes->DeepEcho();
+	helements->DeepEcho();
+	hmatpar->DeepEcho();
+	_printLine_("   parameters");
+	if(parameters)parameters->DeepEcho();
+	_printLine_("   inputs");
+	if(inputs)inputs->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION Riftfront::Id {{{*/
+int    Riftfront::Id(void){ return id; }
+/*}}}*/
+/*FUNCTION Riftfront::MyRank {{{*/
+int    Riftfront::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Riftfront::ObjectEnum{{{*/
+int Riftfront::ObjectEnum(void){
+
+	return RiftfrontEnum;
+
+}
+/*}}}*/
+/*FUNCTION Riftfront::copy {{{*/
+Object* Riftfront::copy() {
+	
+	Riftfront* riftfront=NULL;
+
+	riftfront=new Riftfront();
+
+	/*copy fields: */
+	riftfront->id=this->id;
+	riftfront->analysis_type=this->analysis_type;
+	if(this->inputs){
+		riftfront->inputs=(Inputs*)this->inputs->Copy();
+	}
+	else{
+		riftfront->inputs=new Inputs();
+	}
+	/*point parameters: */
+	riftfront->parameters=this->parameters;
+
+	/*now deal with hooks and objects: */
+	riftfront->hnodes=(Hook*)this->hnodes->copy();
+	riftfront->helements=(Hook*)this->helements->copy();
+	riftfront->hmatpar=(Hook*)this->hmatpar->copy();
+
+	/*corresponding fields*/
+	riftfront->nodes   =(Node**)riftfront->hnodes->deliverp();
+	riftfront->elements=(Element**)riftfront->helements->deliverp();
+	riftfront->matpar  =(Matpar*)riftfront->hmatpar->delivers();
+
+	/*internal data: */
+	riftfront->penalty_lock=this->penalty_lock;
+	riftfront->active=this->active;
+	riftfront->frozen=this->frozen;
+	riftfront->state=this->state;
+	riftfront->counter=this->counter;
+	riftfront->prestable=this->prestable;
+	riftfront->material_converged=this->material_converged;
+	riftfront->normal[0]=this->normal[0];
+	riftfront->normal[1]=this->normal[1];
+	riftfront->length=this->length;
+	riftfront->fraction=this->fraction;
+	
+	return riftfront;
+
+}
+/*}}}*/
+		
+/*Update virtual functions definitions:*/
+/*FUNCTION Riftfront::InputUpdateFromConstant(bool constant,int name) {{{*/
+void  Riftfront::InputUpdateFromConstant(bool constant,int name){
+
+	/*Check that name is a Riftfront input*/
+	if (!IsInput(name)) return;
+
+	/*update input*/
+	this->inputs->AddInput(new BoolInput(name,constant));
+
+}
+/*}}}*/
+/*FUNCTION Riftfront::InputUpdateFromConstant(IssmDouble constant,int name) {{{*/
+void  Riftfront::InputUpdateFromConstant(IssmDouble constant,int name){
+
+	/*Check that name is a Riftfront input*/
+	if (!IsInput(name)) return;
+
+	/*update input*/
+	this->inputs->AddInput(new DoubleInput(name,constant));
+
+}
+/*}}}*/
+/*FUNCTION Riftfront::InputUpdateFromConstant(IssmDouble* constant,int name) {{{*/
+void    Riftfront::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+
+	/*Check that name is a Riftfront input*/
+	if (!IsInput(name)) return;
+
+	/*update input*/
+	_error_("not implemented yet");
+	//this->inputs->AddInput(new DoubleInput(name,constant));
+
+}
+/*}}}*/
+
+
+/*Load virtual functions definitions:*/
+/*FUNCTION Riftfront::Configure {{{*/
+void  Riftfront::Configure(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+	/*Take care of hooking up all objects for this element, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and offsets hidden in hooks: */
+	hnodes->configure(nodesin);
+	helements->configure(elementsin);
+	hmatpar->configure(materialsin);
+
+	/*Initialize hooked fields*/
+	this->nodes   =(Node**)hnodes->deliverp();
+	this->elements=(Element**)helements->deliverp();
+	this->matpar  =(Matpar*)hmatpar->delivers();
+
+	/*point parameters to real dataset: */
+	this->parameters=parametersin;
+
+}
+/*}}}*/
+/*FUNCTION Riftfront::SetCurrentConfiguration {{{*/
+void  Riftfront::SetCurrentConfiguration(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+}
+/*}}}*/
+/*FUNCTION Riftfront::PenaltyCreateKMatrix {{{*/
+void  Riftfront::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,IssmDouble kmax){
+
+	/*Retrieve parameters: */
+	ElementMatrix* Ke=NULL;
+	int analysis_type;
+	this->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	switch(analysis_type){
+		case DiagnosticHorizAnalysisEnum:
+			Ke=PenaltyCreateKMatrixDiagnosticHoriz(kmax);
+			break;
+		case AdjointHorizAnalysisEnum:
+			Ke=PenaltyCreateKMatrixDiagnosticHoriz(kmax);
+			break;
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global Vector*/
+	if(Ke){
+		Ke->AddToGlobal(Kff,Kfs);
+		delete Ke;
+	}
+}
+/*}}}*/
+/*FUNCTION Riftfront::PenaltyCreatePVector {{{*/
+void  Riftfront::PenaltyCreatePVector(Vector* pf,IssmDouble kmax){
+
+	/*Retrieve parameters: */
+	ElementVector* pe=NULL;
+	int analysis_type;
+	this->parameters->FindParam(&analysis_type,AnalysisTypeEnum);
+
+	switch(analysis_type){
+		case DiagnosticHorizAnalysisEnum:
+			pe=PenaltyCreatePVectorDiagnosticHoriz(kmax);
+			break;
+		case AdjointHorizAnalysisEnum:
+			/*No penalty applied on load vector*/
+			break;
+		default:
+			_error_("analysis " << analysis_type << " (" << EnumToStringx(analysis_type) << ") not supported yet");
+	}
+
+	/*Add to global Vector*/
+	if(pe){
+		pe->AddToGlobal(pf);
+		delete pe;
+	}
+}
+/*}}}*/
+/*FUNCTION Riftfront::CreateKMatrix {{{*/
+void  Riftfront::CreateKMatrix(Matrix* Kff, Matrix* Kfs){
+	/*do nothing: */
+	return;
+}
+/*}}}*/
+/*FUNCTION Riftfront::CreatePVector {{{*/
+void  Riftfront::CreatePVector(Vector* pf){
+	/*do nothing: */
+	return;
+}
+/*}}}*/
+/*FUNCTION Riftfront::InAnalysis{{{*/
+bool Riftfront::InAnalysis(int in_analysis_type){
+	if (in_analysis_type==this->analysis_type) return true;
+	else return false;
+}
+/*}}}*/
+
+/*Riftfront numerics*/
+/*FUNCTION Riftfront::PenaltyCreateKMatrixDiagnosticHoriz {{{*/
+ElementMatrix* Riftfront::PenaltyCreateKMatrixDiagnosticHoriz(IssmDouble kmax){
+
+	const int   numdof = NDOF2*NUMVERTICES;
+	int         i,j;
+	int         dofs[1]             = {0};
+	IssmDouble      Ke_gg[4][4];
+	IssmDouble      thickness;
+	IssmDouble      h[2];
+	IssmDouble      penalty_offset;
+	IssmDouble      friction;
+
+	/*Objects: */
+	Tria       *tria1               = NULL;
+	Tria       *tria2               = NULL;
+
+	/*enum of element? */
+	if(elements[0]->ObjectEnum()!=TriaEnum)_error_("only Tria element allowed for Riftfront load!");
+	tria1=(Tria*)elements[0];
+	tria2=(Tria*)elements[1];
+
+	/*Initialize Element Matrix*/
+	if(!this->active) return NULL;
+	ElementMatrix* Ke=new ElementMatrix(nodes,NUMVERTICES,this->parameters);
+
+	/*Get some parameters: */
+	this->parameters->FindParam(&penalty_offset,DiagnosticPenaltyFactorEnum);
+	this->inputs->GetInputValue(&friction,FrictionEnum);
+	tria1->GetInputValue(&h[0],nodes[0],ThicknessEnum);
+	tria2->GetInputValue(&h[1],nodes[1],ThicknessEnum);
+	if (h[0]!=h[1])_error_("different thicknesses not supported for rift fronts");
+	thickness=h[0];
+
+	/*There is contact, we need to constrain the normal velocities (zero penetration), and the 
+	 *contact slip friction. */
+
+	/*From Peter Wriggers book (Computational Contact Mechanics, p191): */
+	Ke->values[0*numdof+0]+= +pow(normal[0],2)*kmax*pow(10,penalty_offset);
+	Ke->values[0*numdof+1]+= +normal[0]*normal[1]*kmax*pow(10,penalty_offset);
+	Ke->values[0*numdof+2]+= -pow(normal[0],2)*kmax*pow(10,penalty_offset);
+	Ke->values[0*numdof+3]+= -normal[0]*normal[1]*kmax*pow(10,penalty_offset);
+
+	Ke->values[1*numdof+0]+= +normal[0]*normal[1]*kmax*pow(10,penalty_offset);
+	Ke->values[1*numdof+1]+= +pow(normal[1],2)*kmax*pow(10,penalty_offset);
+	Ke->values[1*numdof+2]+= -normal[0]*normal[1]*kmax*pow(10,penalty_offset);
+	Ke->values[1*numdof+3]+= -pow(normal[1],2)*kmax*pow(10,penalty_offset);
+
+	Ke->values[2*numdof+0]+= -pow(normal[0],2)*kmax*pow(10,penalty_offset);
+	Ke->values[2*numdof+1]+= -normal[0]*normal[1]*kmax*pow(10,penalty_offset);
+	Ke->values[2*numdof+2]+= +pow(normal[0],2)*kmax*pow(10,penalty_offset);
+	Ke->values[2*numdof+3]+= +normal[0]*normal[1]*kmax*pow(10,penalty_offset);
+
+	Ke->values[3*numdof+0]+= -normal[0]*normal[1]*kmax*pow(10,penalty_offset);
+	Ke->values[3*numdof+1]+= -pow(normal[1],2)*kmax*pow(10,penalty_offset);
+	Ke->values[3*numdof+2]+= +normal[0]*normal[1]*kmax*pow(10,penalty_offset);
+	Ke->values[3*numdof+3]+= +pow(normal[1],2)*kmax*pow(10,penalty_offset);
+
+	/*Now take care of the friction: of type sigma=frictiontangent_velocity2-tangent_velocity1)*/
+
+	Ke->values[0*numdof+0]+= +pow(normal[1],2)*thickness*length*friction;
+	Ke->values[0*numdof+1]+= -normal[0]*normal[1]*thickness*length*friction;
+	Ke->values[0*numdof+2]+= -pow(normal[1],2)*thickness*length*friction;
+	Ke->values[0*numdof+3]+= +normal[0]*normal[1]*thickness*length*friction;
+
+	Ke->values[1*numdof+0]+= -normal[0]*normal[1]*thickness*length*friction;
+	Ke->values[1*numdof+1]+= +pow(normal[0],2)*thickness*length*friction;
+	Ke->values[1*numdof+2]+= +normal[0]*normal[1]*thickness*length*friction;
+	Ke->values[1*numdof+3]+= -pow(normal[0],2)*thickness*length*friction;
+
+	Ke->values[2*numdof+0]+= -pow(normal[1],2)*thickness*length*friction;
+	Ke->values[2*numdof+1]+= +normal[0]*normal[1]*thickness*length*friction;
+	Ke->values[2*numdof+2]+= +pow(normal[1],2)*thickness*length*friction;
+	Ke->values[2*numdof+3]+= -normal[0]*normal[1]*thickness*length*friction;
+
+	Ke->values[3*numdof+0]+= +normal[0]*normal[1]*thickness*length*friction;
+	Ke->values[3*numdof+1]+= -pow(normal[0],2)*thickness*length*friction;
+	Ke->values[3*numdof+2]+= -normal[0]*normal[1]*thickness*length*friction;
+	Ke->values[3*numdof+3]+= +pow(normal[0],2)*thickness*length*friction;
+
+	/*Clean up and return*/
+	return Ke;
+}
+/*}}}*/
+/*FUNCTION Riftfront::PenaltyCreatePVectorDiagnosticHoriz {{{*/
+ElementVector* Riftfront::PenaltyCreatePVectorDiagnosticHoriz(IssmDouble kmax){
+
+	const int   numdof = NDOF2*NUMVERTICES;
+	int         i,j;
+	IssmDouble      rho_ice;
+	IssmDouble      rho_water;
+	IssmDouble      gravity;
+	IssmDouble      thickness;
+	IssmDouble      h[2];
+	IssmDouble      bed;
+	IssmDouble      b[2];
+	IssmDouble      pressure;
+	IssmDouble      pressure_litho;
+	IssmDouble      pressure_air;
+	IssmDouble      pressure_melange;
+	IssmDouble      pressure_water;
+	int         fill;
+	bool        shelf;
+
+	/*Objects: */
+	Tria       *tria1               = NULL;
+	Tria       *tria2               = NULL;
+
+	/*enum of element? */
+	if(elements[0]->ObjectEnum()!=TriaEnum)_error_("only Tria element allowed for Riftfront load!");
+	tria1=(Tria*)elements[0];
+	tria2=(Tria*)elements[1];
+
+	/*Initialize Element Matrix*/
+	if(this->active) return NULL; /*The penalty is active. No loads implied here.*/
+	ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters);
+
+	/*Get some inputs: */
+	this->inputs->GetInputValue(&fill,FillEnum);
+	this->inputs->GetInputValue(&shelf,SegmentOnIceShelfEnum);
+	rho_ice=matpar->GetRhoIce();
+	rho_water=matpar->GetRhoWater();
+	gravity=matpar->GetG();
+	tria1->GetInputValue(&h[0],nodes[0],ThicknessEnum);
+	tria2->GetInputValue(&h[1],nodes[1],ThicknessEnum);
+	if (h[0]!=h[1])_error_("different thicknesses not supported for rift fronts");
+	thickness=h[0];
+	tria1->GetInputValue(&b[0],nodes[0],BedEnum);
+	tria2->GetInputValue(&b[1],nodes[1],BedEnum);
+	if (b[0]!=b[1])_error_("different beds not supported for rift fronts");
+	bed=b[0];
+
+	/*Ok, this rift is opening. We should put loads on both sides of the rift flanks. Because we are dealing with contact mechanics, 
+	 * and we want to avoid zigzagging of the loads, we want lump the loads onto nodes, not onto surfaces between nodes.:*/
+
+	/*Ok, to compute the pressure, we are going to need material properties, thickness and bed for the two nodes. We assume those properties to 
+	 * be the same across the rift.: */
+
+	/*Ok, now compute the pressure (in norm) that is being applied to the flanks, depending on the type of fill: */
+	if(fill==WaterEnum){
+		if(shelf){
+			/*We are on an ice shelf, hydrostatic equilibrium is used to determine the pressure for water fill: */
+			pressure=rho_ice*gravity*pow(thickness,(IssmDouble)2)/(IssmDouble)2  - rho_water*gravity*pow(bed,(IssmDouble)2)/(IssmDouble)2; 
+		}
+		else{
+			//We are on an icesheet, we assume the water column fills the entire front: */
+			pressure=rho_ice*gravity*pow(thickness,(IssmDouble)2)/(IssmDouble)2  - rho_water*gravity*pow(thickness,(IssmDouble)2)/(IssmDouble)2; 
+		}
+	}
+	else if(fill==AirEnum){
+		pressure=rho_ice*gravity*pow(thickness,(IssmDouble)2)/(IssmDouble)2;   //icefront on an ice sheet, pressure imbalance ice vs air.
+	}
+	else if(fill==IceEnum){ //icefront finding itself against another icefront (pressure imbalance is fully compensated, ice vs ice)
+		pressure=0;
+	}
+	else if(fill==MelangeEnum){ //icefront finding itself against another icefront (pressure imbalance is fully compensated, ice vs ice)
+
+		if(!shelf) _error_("fill type " << fill << " not supported on ice sheets yet.");
+
+		pressure_litho=rho_ice*gravity*pow(thickness,(IssmDouble)2)/(IssmDouble)2;
+		pressure_air=0;
+		pressure_melange=rho_ice*gravity*pow(fraction*thickness,(IssmDouble)2)/(IssmDouble)2;
+		pressure_water=1.0/2.0*rho_water*gravity*  ( pow(bed,2.0)-pow(rho_ice/rho_water*fraction*thickness,2.0) );
+
+		pressure=pressure_litho-pressure_air-pressure_melange-pressure_water;
+	}
+	else{
+		_error_("fill type " << fill << " not supported yet.");
+	}
+
+	/*Ok, add contribution to first node, along the normal i==0: */
+	for (j=0;j<2;j++){
+		pe->values[j]+=pressure*normal[j]*length;
+	}
+
+	/*Add contribution to second node, along the opposite normal: i==1 */
+	for (j=0;j<2;j++){
+		pe->values[2+j]+= -pressure*normal[j]*length;
+	}	
+
+	/*Clean up and return*/
+	return pe;
+}
+/*}}}*/
+/*FUNCTION Riftfront::Constrain {{{*/
+#define _ZIGZAGCOUNTER_
+
+int Riftfront::Constrain(int* punstable){
+
+	const int   numnodes        = 2;
+	IssmDouble      max_penetration;
+	IssmDouble      penetration;
+	int         activate;
+	int         found;
+	int         unstable;
+	IssmDouble      vx1;
+	IssmDouble      vy1;
+	IssmDouble      vx2;
+	IssmDouble      vy2;
+	IssmDouble      fractionincrement;
+
+	/*Objects: */
+	Tria       *tria1           = NULL;
+	Tria       *tria2           = NULL;
+
+	/*enum of element? */
+	if(elements[0]->ObjectEnum()!=TriaEnum)_error_("only Tria element allowed for Riftfront load!");
+
+	/*recover elements on both side of rift: */
+	tria1=(Tria*)elements[0];
+	tria2=(Tria*)elements[1];
+
+	/*Is this constraint frozen? In which case we don't touch: */
+	if (this->frozen){
+		*punstable=0;
+		return 1;
+	}
+
+	/*Is this rift segment state specified by user input? :*/
+	if (this->state==OpenEnum || this->state==ClosedEnum){
+
+		if(this->state==OpenEnum)this->active=0;
+		if(this->state==ClosedEnum)this->active=1;
+		
+		/*this segment is like frozen, no instability here: */
+		*punstable=0;
+		return 1;
+	}
+
+
+	/*recover parameters: */
+	this->inputs->GetInputValue(&fractionincrement,FractionIncrementEnum);
+
+	/*First recover velocity: */
+	tria1->GetInputValue(&vx1,nodes[0],VxEnum);
+	tria2->GetInputValue(&vx2,nodes[1],VxEnum);
+	tria1->GetInputValue(&vy1,nodes[0],VyEnum);
+	tria2->GetInputValue(&vy2,nodes[1],VyEnum);
+
+	/*Node 1 faces node 2, compute penetration of 2 into 1 (V2-V1).N (with N normal vector, and V velocity vector: */
+	penetration=(vx2-vx1)*normal[0]+(vy2-vy1)*normal[1];
+
+	/*activation: */
+	if(penetration<0)activate=1;
+	else  activate=0;
+
+	/*Here, we try to avoid zigzaging. When a penalty activates and deactivates for more than penalty_lock times, 
+	 * we increase the fraction of melange:*/
+	if(this->counter>this->penalty_lock){
+		/*reset counter: */
+		this->counter=0;
+		/*increase melange fraction: */
+		this->fraction+=fractionincrement;
+		if (this->fraction>1)this->fraction=(IssmDouble)1.0;
+		//_printLine_("riftfront " << this->Id() << " fraction: " << this->fraction);
+	}
+
+	//Figure out stability of this penalty
+	if(this->active==activate){
+		unstable=0;
+	}
+	else{
+		unstable=1;
+		this->counter++;
+	}
+
+	//Set penalty flag
+	this->active=activate;
+
+	//if ((penetration>0) && (this->active==1))_printLine_("Riftfront " << Id() << " wants to be released");
+
+	/*assign output pointer: */
+	*punstable=unstable;
+	return 1;
+}
+/*}}}*/
+/*FUNCTION Riftfront::FreezeConstraints{{{*/
+void   Riftfront::FreezeConstraints(void){
+
+	/*Just set frozen flag to 1: */
+	this->frozen=1;
+
+}
+/*}}}*/
+/*FUNCTION Riftfront::IsFrozen{{{*/
+bool   Riftfront::IsFrozen(void){
+
+	/*Just set frozen flag to 1: */
+	if(this->frozen)return 1;
+	else return 0;
+}
+/*}}}*/
+/*FUNCTION Riftfront::IsMaterialStable {{{*/
+int   Riftfront::IsMaterialStable(void){
+
+	int found=0;
+	IssmDouble converged=0;
+
+	this->inputs->GetInputValue(&converged,ConvergedEnum);
+
+	if(reCast(converged)){
+		/*ok, material non-linearity has converged. If that was already the case, we keep 
+		 * constraining the rift front. If it was not, and this is the first time the material 
+		 * has converged, we start constraining now!: */
+		this->material_converged=1;
+	}
+
+	return this->material_converged;
+}
+/*}}}*/
+/*FUNCTION Riftfront::MaxPenetration {{{*/
+int   Riftfront::MaxPenetration(IssmDouble* ppenetration){
+
+	const int     numnodes=2;
+	IssmDouble        max_penetration;
+	IssmDouble        penetration=0;
+	int           found;
+	IssmDouble      vx1;
+	IssmDouble      vy1;
+	IssmDouble      vx2;
+	IssmDouble      vy2;
+
+	/*Objects: */
+	Tria       *tria1           = NULL;
+	Tria       *tria2           = NULL;
+
+	/*enum of element? */
+	if(elements[0]->ObjectEnum()!=TriaEnum)_error_("only Tria element allowed for Riftfront load!");
+
+	/*recover elements on both side of rift: */
+	tria1=(Tria*)elements[0];
+	tria2=(Tria*)elements[1];
+
+	//initialize: 
+	penetration=-1;
+
+	/*recover velocity: */
+	tria1->GetInputValue(&vx1,nodes[0],VxEnum);
+	tria2->GetInputValue(&vx2,nodes[1],VxEnum);
+	tria1->GetInputValue(&vy1,nodes[0],VyEnum);
+	tria2->GetInputValue(&vy2,nodes[1],VyEnum);
+
+	/*Node1 faces node2, compute penetration of 2 into 1 (V2-V1).N (with N normal vector, and V velocity vector: */
+	penetration=(vx2-vx1)*normal[0]+(vy2-vy1)*normal[1];
+
+	/*Now, we return penetration only if we are active!: */
+	if(this->active==0)penetration=-1;
+
+	/*If we are zigzag locked, same thing: */
+	if(this->counter>this->penalty_lock)penetration=-1;
+	
+	/*assign output pointer: */
+	*ppenetration=penetration;
+	return 1;
+}
+/*}}}*/
+/*FUNCTION Riftfront::Penetration {{{*/
+int   Riftfront::Penetration(IssmDouble* ppenetration){
+
+	IssmDouble    vx1;
+	IssmDouble    vy1;
+	IssmDouble    vx2;
+	IssmDouble    vy2;
+
+	IssmDouble    penetration;
+	int       found;
+
+	/*Objects: */
+	Tria     *tria1       = NULL;
+	Tria     *tria2       = NULL;
+
+	/*enum of element? */
+	if(elements[0]->ObjectEnum()!=TriaEnum)_error_("only Tria element allowed for Riftfront load!");
+
+	/*recover elements on both side of rift: */
+	tria1=(Tria*)elements[0];
+	tria2=(Tria*)elements[1];
+
+	/*First recover velocity: */
+	tria1->GetInputValue(&vx1,nodes[0],VxEnum);
+	tria2->GetInputValue(&vx2,nodes[1],VxEnum);
+	tria1->GetInputValue(&vy1,nodes[0],VyEnum);
+	tria2->GetInputValue(&vy2,nodes[1],VyEnum);
+
+	/*Node 1 faces node 2, compute penetration of 2 into 1 (V2-V1).N (with N normal vector, and V velocity vector: */
+	penetration=(vx2-vx1)*normal[0]+(vy2-vy1)*normal[1];
+
+	/*Now, we return penetration only if we are active!: */
+	if(this->active==0)penetration=0;
+	
+	/*assign output pointer: */
+	*ppenetration=penetration;
+	return 1;
+}
+/*}}}*/
+/*FUNCTION Riftfront::PotentialUnstableConstraint {{{*/
+int   Riftfront::PotentialUnstableConstraint(int* punstable){
+
+
+	const int   numnodes        = 2;
+	IssmDouble      max_penetration;
+	IssmDouble      penetration;
+	int         activate;
+	int         unstable;
+	int         found;
+	IssmDouble      vx1;
+	IssmDouble      vy1;
+	IssmDouble      vx2;
+	IssmDouble      vy2;
+
+	/*Objects: */
+	Tria       *tria1           = NULL;
+	Tria       *tria2           = NULL;
+
+	/*enum of element? */
+	if(elements[0]->ObjectEnum()!=TriaEnum)_error_("only Tria element allowed for Riftfront load!");
+
+	/*recover elements on both side of rift: */
+	tria1=(Tria*)elements[0];
+	tria2=(Tria*)elements[1];
+
+	/*First recover velocity: */
+	tria1->GetInputValue(&vx1,nodes[0],VxEnum);
+	tria2->GetInputValue(&vx2,nodes[1],VxEnum);
+	tria1->GetInputValue(&vy1,nodes[0],VyEnum);
+	tria2->GetInputValue(&vy2,nodes[1],VyEnum);
+
+	/*Node 1 faces node 2, compute penetration of 2 into 1 (V2-V1).N (with N normal vector, and V velocity vector: */
+	penetration=(vx2-vx1)*normal[0]+(vy2-vy1)*normal[1];
+
+	/*Ok, we are looking for positive penetration in an active constraint: */
+	if(this->active){
+		if (penetration>=0){
+			unstable=1;
+		}
+		else{
+			unstable=0;
+		}
+	}
+	else{
+		unstable=0;
+	}
+
+	/*assign output pointer: */
+	*punstable=unstable;
+	return 1;
+}
+/*}}}*/
+/*FUNCTION Riftfront::PreConstrain {{{*/
+int   Riftfront::PreConstrain(int* punstable){
+
+	const int   numnodes    = 2;
+	IssmDouble      penetration;
+	int         unstable;
+	int         found;
+	IssmDouble      vx1;
+	IssmDouble      vy1;
+	IssmDouble      vx2;
+	IssmDouble      vy2;
+
+	/*Objects: */
+	Tria       *tria1       = NULL;
+	Tria       *tria2       = NULL;
+
+	/*enum of element? */
+	if(elements[0]->ObjectEnum()!=TriaEnum)_error_("only Tria element allowed for Riftfront load!");
+
+	/*recover elements on both side of rift: */
+	tria1=(Tria*)elements[0];
+	tria2=(Tria*)elements[1];
+
+	/*First recover velocity: */
+	tria1->GetInputValue(&vx1,nodes[0],VxEnum);
+	tria2->GetInputValue(&vx2,nodes[1],VxEnum);
+	tria1->GetInputValue(&vy1,nodes[0],VyEnum);
+	tria2->GetInputValue(&vy2,nodes[1],VyEnum);
+
+	/*Node 1 faces node 2, compute penetration of 2 into 1 (V2-V1).N (with N normal vector, and V velocity vector: */
+	penetration=(vx2-vx1)*normal[0]+(vy2-vy1)*normal[1];
+
+	/*Ok, we are preconstraining here. Ie, anything that penetrates is constrained until stability of the entire set 
+	 * of constraints is reached.: */
+	if(penetration<0){
+		if (!this->active){
+			/*This is the first time penetration happens: */
+			this->active=1;
+			unstable=1;
+		}
+		else{
+			/*This constraint was already active: */
+			this->active=1;
+			unstable=0;
+		}
+	}
+	else{
+		/*No penetration happening. : */
+		if (!this->active){
+			/*This penalty was not active, and no penetration happening. Do nonthing: */
+			this->active=0;
+			unstable=0; 
+		}
+		else{
+			/*Ok, this penalty wants to get released. But not now, this is preconstraint, not constraint: */
+			this->active=1;
+			unstable=0;
+		}
+	}
+
+	/*assign output pointer: */
+	*punstable=unstable;
+	return 1;
+}
+/*}}}*/
+/*FUNCTION Riftfront::PreStable {{{*/
+bool  Riftfront::PreStable(){
+	return prestable;
+}
+/*}}}*/
+/*FUNCTION Riftfront::SetPreStable {{{*/
+void Riftfront::SetPreStable(){
+	prestable=1;
+}
+/*}}}*/
+/*FUNCTION Riftfront::IsInput{{{*/
+bool Riftfront::IsInput(int name){
+	if (
+				name==ConvergedEnum ||
+				name==ThicknessEnum ||
+				name==SurfaceEnum ||
+				name==BedEnum 
+		){
+		return true;
+	}
+	else return false;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Loads/Riftfront.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Loads/Riftfront.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Loads/Riftfront.h	(revision 13395)
@@ -0,0 +1,104 @@
+/*!\file Riftfront.h
+ * \brief: header file for riftfront object
+ */
+
+#ifndef _RIFTFRONT_H_
+#define _RIFTFRONT_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Load.h"
+class Hook;
+class Parameters;
+class Inputs;
+class IoModel;
+/*}}}*/
+
+class Riftfront: public Load {
+
+	public:
+		int		id;
+		int     analysis_type;
+
+		/*hooks: */
+		Hook* hnodes;
+		Hook* helements;
+		Hook* hmatpar;
+		
+		/*Corresponding fields*/
+		Matpar   *matpar;
+		Node    **nodes;
+		Element **elements;
+
+		/*computational: */
+		int      penalty_lock;
+		bool     active;
+		bool     frozen;
+		int      counter;
+		bool     prestable;
+		bool     material_converged;
+		IssmDouble   normal[2];
+		IssmDouble   length;
+		IssmDouble   fraction;
+		int      state;
+		
+		Parameters* parameters; //pointer to solution parameters
+		Inputs*  inputs;
+
+
+		/*Riftfrontconstructors,destructors: {{{*/
+		Riftfront();
+		Riftfront(int riftfront_id,int i, IoModel* iomodel,int analysis_type);
+		~Riftfront();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Update virtual functions resolution: {{{*/
+		void    InputUpdateFromVector(IssmDouble* vector, int name, int type);
+		void    InputUpdateFromVector(int* vector, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromVector(bool* vector, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows,int ncols, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromVectorDakota(int* vector, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromVectorDakota(bool* vector, int name, int type){_error_("Not implemented yet!");}
+		void    InputUpdateFromConstant(IssmDouble constant, int name);
+		void    InputUpdateFromConstant(int constant, int name){_error_("Not implemented yet!");}
+		void    InputUpdateFromConstant(bool constant, int name);
+		void    InputUpdateFromSolution(IssmDouble* solution){_error_("Not implemented yet!");}
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel){_error_("not implemented yet");};
+		/*}}}*/
+		/*Load virtual functions definitions: {{{*/
+		void  Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void  CreateKMatrix(Matrix* Kff, Matrix* Kfs);
+		void  CreatePVector(Vector* pf);
+		void  CreateJacobianMatrix(Matrix* Jff){_error_("Not implemented yet");};
+		void  PenaltyCreateJacobianMatrix(Matrix* Jff,IssmDouble kmax){_error_("Not implemented yet");};
+		void  PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, IssmDouble kmax);
+		void  PenaltyCreatePVector(Vector* pf, IssmDouble kmax);
+		bool  InAnalysis(int analysis_type);
+		/*}}}*/
+		/*Riftfront specific routines: {{{*/
+		bool  PreStable();
+		ElementMatrix* PenaltyCreateKMatrixDiagnosticHoriz(IssmDouble kmax);
+		ElementVector* PenaltyCreatePVectorDiagnosticHoriz(IssmDouble kmax);
+		void  SetPreStable();
+		int   PreConstrain(int* punstable);
+		int   Constrain(int* punstable);
+		void  FreezeConstraints(void);
+		bool  IsFrozen(void);
+		int   Penetration(IssmDouble* ppenetration);
+		int   MaxPenetration(IssmDouble* ppenetration);
+		int   PotentialUnstableConstraint(int* punstable);
+		int   IsMaterialStable(void);
+		bool  IsInput(int name);
+		/*}}}*/
+};
+
+#endif  /* _RIFTFRONT_H_ */
Index: /issm/trunk/src/c/classes/objects/Materials/Matdamageice.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Materials/Matdamageice.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Materials/Matdamageice.cpp	(revision 13395)
@@ -0,0 +1,896 @@
+/*!\file Matdamageice.c
+ * \brief: implementation of the Matdamageice object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../include/include.h"
+		
+/*Matdamageice constructors and destructor*/
+/*FUNCTION Matdamageice::Matdamageice(){{{*/
+Matdamageice::Matdamageice(){
+	this->inputs=NULL;
+	this->helement=NULL;
+	return;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::Matdamageice(int id, int index, IoModel* iomodel, int num_vertices){{{*/
+Matdamageice::Matdamageice(int matice_mid,int index, IoModel* iomodel){
+
+	/*Intermediaries:*/
+	int    i;
+	int    matice_eid;
+
+	/*Initialize id*/
+	this->mid=matice_mid;
+
+	/*Initialize inputs*/
+	this->inputs=new Inputs();
+
+	/*Initialize inputs from IoModel*/
+	this->InputUpdateFromIoModel(index,iomodel);
+
+	/*Hooks: */
+	matice_eid=index+1;
+	this->helement=new Hook(&matice_eid,1);
+
+	return;
+
+}
+/*}}}*/
+/*FUNCTION Matdamageice::~Matdamageice(){{{*/
+Matdamageice::~Matdamageice(){
+	delete helement;
+	delete inputs;
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION Matdamageice::Echo {{{*/
+void Matdamageice::Echo(void){
+
+	_printLine_("Matdamageice:");
+	_printLine_("   mid: " << mid);
+	_printLine_("   inputs:");
+	inputs->Echo();
+	_printLine_("   element:");
+	helement->Echo();
+}
+/*}}}*/
+/*FUNCTION Matdamageice::DeepEcho {{{*/
+void Matdamageice::DeepEcho(void){
+
+	_printLine_("Matdamageice:");
+	_printLine_("   mid: " << mid);
+	_printLine_("   inputs:");
+	inputs->DeepEcho();
+	_printLine_("   element:");
+	helement->Echo();
+}		
+/*}}}*/
+/*FUNCTION Matdamageice::Id {{{*/
+int    Matdamageice::Id(void){ return mid; }
+/*}}}*/
+/*FUNCTION Matdamageice::MyRank {{{*/
+int    Matdamageice::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Matdamageice::ObjectEnum{{{*/
+int Matdamageice::ObjectEnum(void){
+
+	return MatdamageiceEnum;
+
+}
+/*}}}*/
+/*FUNCTION Matdamageice::copy {{{*/
+Object* Matdamageice::copy() {
+
+	/*Output*/
+	Matdamageice* matice=NULL;
+
+	/*Initialize output*/
+	matice=new Matdamageice();
+
+	/*copy fields: */
+	matice->mid=this->mid;
+	matice->helement=(Hook*)this->helement->copy();
+	if(this->inputs) matice->inputs=(Inputs*)this->inputs->Copy();
+	else  matice->inputs=new Inputs();
+
+	return matice;
+}
+/*}}}*/
+
+/*Matdamageice management*/
+/*FUNCTION Matdamageice::Configure {{{*/
+void  Matdamageice::Configure(Elements* elementsin){
+
+	/*Take care of hooking up all objects for this element, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and offsets hidden in hooks: */
+	helement->configure(elementsin);
+}
+/*}}}*/
+/*FUNCTION Matdamageice::SetCurrentConfiguration {{{*/
+void  Matdamageice::SetCurrentConfiguration(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetA {{{*/
+IssmDouble Matdamageice::GetA(){
+	/*
+	 * A = 1/B^n
+	 */
+
+	IssmDouble B,n;
+
+	inputs->GetInputAverage(&B,MaterialsRheologyBEnum);
+	n=this->GetN();
+
+	return pow(B,-n);
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetB {{{*/
+IssmDouble Matdamageice::GetB(){
+
+	/*Output*/
+	IssmDouble B;
+
+	inputs->GetInputAverage(&B,MaterialsRheologyBEnum);
+	return B;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetBbar {{{*/
+IssmDouble Matdamageice::GetBbar(){
+
+	/*Output*/
+	IssmDouble Bbar;
+
+	inputs->GetInputAverage(&Bbar,MaterialsRheologyBbarEnum);
+	return Bbar;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetN {{{*/
+IssmDouble Matdamageice::GetN(){
+
+	/*Output*/
+	IssmDouble n;
+
+	inputs->GetInputAverage(&n,MaterialsRheologyNEnum);
+	return n;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetZ {{{*/
+IssmDouble Matdamageice::GetZ(){
+
+	/*Output*/
+	IssmDouble Z;
+
+	inputs->GetInputAverage(&Z,MaterialsRheologyZEnum);
+	return Z;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetZbar {{{*/
+IssmDouble Matdamageice::GetZbar(){
+
+	/*Output*/
+	IssmDouble Zbar;
+
+	inputs->GetInputAverage(&Zbar,MaterialsRheologyZbarEnum);
+	return Zbar;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetVectorFromInputs{{{*/
+void  Matdamageice::GetVectorFromInputs(Vector* vector,int input_enum){
+
+	/*Intermediaries*/
+	Element *element= NULL;
+
+	/*Recover element*/
+	element=(Element*)helement->delivers();
+
+	/*Check that input_enum is a material input*/
+	if (!IsInput(input_enum)) return;
+
+	switch(element->ObjectEnum()){
+
+		case TriaEnum:{
+
+			/*Prepare index list*/
+			int doflist1[3];
+			for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexDof();
+
+			/*Get input (either in element or material)*/
+			Input* input=inputs->GetInput(input_enum);
+			if(!input) _error_("Input " << EnumToStringx(input_enum) << " not found in material");
+
+			/*We found the enum.  Use its values to fill into the vector, using the vertices ids: */
+			input->GetVectorFromInputs(vector,&doflist1[0]);}
+			break;
+
+		default: _error_("element " << EnumToStringx(element->ObjectEnum()) << " not implemented yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetViscosity2d {{{*/
+void  Matdamageice::GetViscosity2d(IssmDouble* pviscosity, IssmDouble* epsilon){
+	/*From a string tensor and a material object, return viscosity, using Glen's flow law.
+												   Z * B
+	  viscosity= -------------------------------------------------------------------
+						  2[ exx^2+eyy^2+exx*eyy+exy^2+exz^2+eyz^2 ]^[(n-1)/2n]
+
+	  where viscosity is the viscotiy, B the flow law parameter , (u,v) the velocity 
+	  vector, and n the flow law exponent.
+
+	  If epsilon is NULL, it means this is the first time SystemMatrices is being run, and we 
+	  return 10^14, initial viscosity.
+	  */
+
+	/*output: */
+	IssmDouble viscosity;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy;
+
+	/*Intermediary: */
+	IssmDouble A,e;
+	IssmDouble Btmp,B,n,Z;
+
+	/*Get B and n*/
+	Btmp=GetBbar();
+	Z=GetZbar();
+	n=GetN();
+	B=Z*Btmp;
+
+	if (n==1){
+		/*Viscous behaviour! viscosity=B: */
+		viscosity=B/2;
+	}
+	else{
+		if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0)){
+			viscosity=0.5*pow((IssmDouble)10,(IssmDouble)14);
+		}
+		else{
+			/*Retrive strain rate components: */
+			exx=*(epsilon+0);
+			eyy=*(epsilon+1);
+			exy=*(epsilon+2);
+
+			/*Build viscosity: viscosity=B/(2*A^e) */
+			A=pow(exx,2)+pow(eyy,2)+pow(exy,2)+exx*eyy;
+			if(A==0){
+				/*Maxiviscositym viscosity for 0 shear areas: */
+				viscosity=2.5*pow(10.,17.);
+			}
+			else{
+				e=(n-1)/(2*n);
+				viscosity=B/(2*pow(A,e));
+			}
+		}
+	}
+
+	/*Checks in debugging mode*/
+	if(viscosity<=0) _error_("Negative viscosity");
+	_assert_(B>0);
+	_assert_(n>0);
+
+	/*Return: */
+	*pviscosity=viscosity;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetViscosity3d {{{*/
+void  Matdamageice::GetViscosity3d(IssmDouble* pviscosity3d, IssmDouble* epsilon){
+
+	/*Return viscosity accounting for steady state power law creep [Thomas and MacAyeal, 1982]: 
+	 *
+	 *                                               B
+	 * viscosity3d= -------------------------------------------------------------------
+	 *                      2[ exx^2+eyy^2+exx*eyy+exy^2+exz^2+eyz^2 ]^[(n-1)/2n]
+	 *
+	 *     where mu is the viscotiy, B the flow law parameter , (u,v) the velocity 
+	 *     vector, and n the flow law exponent.
+	 *
+	 * If epsilon is NULL, it means this is the first time Emg is being run, and we 
+	 * return g, initial viscosity.
+	 */
+	
+	/*output: */
+	IssmDouble viscosity3d;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy,exz,eyz;
+
+	/*Intermediaries: */
+	IssmDouble A,e;
+	IssmDouble B,n,Z;
+
+	/*Get B, Z and n*/
+	n=GetN();
+	Z=GetZ();
+	B=Z*GetB();
+
+	if (n==1){
+		/*Viscous behaviour! viscosity3d=B: */
+		viscosity3d=B/2;
+	}
+	else{
+		if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0) && 
+				(epsilon[3]==0) && (epsilon[4]==0)){
+			viscosity3d=0.5*pow((IssmDouble)10,(IssmDouble)14);
+		}
+		else{
+
+			/*Retrive strain rate components: */
+			exx=*(epsilon+0);
+			eyy=*(epsilon+1);
+			exy=*(epsilon+2);
+			exz=*(epsilon+3);
+			eyz=*(epsilon+4);
+
+			/*Build viscosity: viscosity3d=2*B/(2*A^e) */
+			A=pow(exx,2)+pow(eyy,2)+pow(exy,2)+pow(exz,2)+pow(eyz,2)+exx*eyy;
+			if(A==0){
+				/*Maxiviscosity3dm viscosity for 0 shear areas: */
+				viscosity3d=2.25*pow((IssmDouble)10,(IssmDouble)17);
+			}
+			else{
+				e=(n-1)/2/n;
+			
+				viscosity3d=B/(2*pow(A,e));
+			}
+		}
+	}
+
+	/*Checks in debugging mode*/
+	if(viscosity3d<=0) _error_("Negative viscosity");
+	_assert_(B>0);
+	_assert_(n>0);
+
+	/*Assign output pointers:*/
+	*pviscosity3d=viscosity3d;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetViscosity3dStokes {{{*/
+void  Matdamageice::GetViscosity3dStokes(IssmDouble* pviscosity3d, IssmDouble* epsilon){
+	/*Return viscosity accounting for steady state power law creep [Thomas and MacAyeal, 1982]: 
+	 *
+	 *                                          B
+	 * viscosity3d= -------------------------------------------------------------------
+	 *                   2[ exx^2+eyy^2+exx*eyy+exy^2+exz^2+eyz^2 ]^[(n-1)/2n]
+	 *
+	 *     where mu is the viscotiy, B the flow law parameter , (u,v) the velocity 
+	 *     vector, and n the flow law exponent.
+	 *
+	 * If epsilon is NULL, it means this is the first time Emg is being run, and we 
+	 * return g, initial viscosity.
+	 */
+	
+	/*output: */
+	IssmDouble viscosity3d;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy,exz,eyz,ezz;
+
+	/*Intermediaries: */
+	IssmDouble A,e;
+	IssmDouble B,n,Z;
+	IssmDouble eps0;
+
+	/*Get B and n*/
+	eps0=pow((IssmDouble)10,(IssmDouble)-27);
+	n=GetN();
+	Z=GetZ();
+	B=Z*GetB();
+	
+	if (n==1){
+		/*Viscous behaviour! viscosity3d=B: */
+		viscosity3d=B/2;
+	}
+	else{
+		if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0) && 
+				(epsilon[3]==0) && (epsilon[4]==0) && (epsilon[5]==0)){
+			viscosity3d=0.5*pow((IssmDouble)10,(IssmDouble)14);
+		}
+		else{
+
+			/*Retrive strain rate components: */
+			exx=*(epsilon+0);
+			eyy=*(epsilon+1);
+			ezz=*(epsilon+2); //not used
+			exy=*(epsilon+3);
+			exz=*(epsilon+4);
+			eyz=*(epsilon+5);
+
+			/*Build viscosity: viscosity3d=B/(2*A^e) */
+			A=pow(exx,2)+pow(eyy,2)+pow(exy,2)+pow(exz,2)+pow(eyz,2)+exx*eyy+pow(eps0,2);
+			if(A==0){
+				/*Maxiviscosity3dm viscosity for 0 shear areas: */
+				viscosity3d=2.25*pow((IssmDouble)10,(IssmDouble)17);
+			}
+			else{
+				e=(n-1)/2/n;
+				viscosity3d=B/(2*pow(A,e));
+			}
+		}
+	}
+
+	/*Checks in debugging mode*/
+	if(viscosity3d<=0) _error_("Negative viscosity");
+	_assert_(B>0);
+	_assert_(n>0);
+
+	/*Assign output pointers:*/
+	*pviscosity3d=viscosity3d;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetViscosityComplement {{{*/
+void  Matdamageice::GetViscosityComplement(IssmDouble* pviscosity_complement, IssmDouble* epsilon){
+	/*Return viscosity accounting for steady state power law creep [Thomas and MacAyeal, 1982]: 
+	 *
+	 *  										                1
+	 * viscosity= -------------------------------------------------------------------
+	 *  				  2[ exx^2+eyy^2+exx*eyy+exy^2+exz^2+eyz^2 ]^[(n-1)/2n]
+	 *
+	 * If epsilon is NULL, it means this is the first time Gradjb is being run, and we 
+	 * return mu20, initial viscosity.
+	 */
+	
+	/*output: */
+	IssmDouble viscosity_complement;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy;
+
+	/*Intermediary value A and exponent e: */
+	IssmDouble A,e;
+	IssmDouble B,n;
+
+	/*Get B and n*/
+	B=GetBbar();
+	n=GetN();
+
+	if(epsilon){
+		exx=*(epsilon+0);
+		eyy=*(epsilon+1);
+		exy=*(epsilon+2);
+
+		/*Build viscosity: mu2=B/(2*A^e) */
+		A=pow(exx,2)+pow(eyy,2)+pow(exy,2)+exx*eyy;
+		if(A==0){
+			/*Maximum viscosity_complement for 0 shear areas: */
+			viscosity_complement=2.25*pow((IssmDouble)10,(IssmDouble)17);
+		}
+		else{
+			e=(n-1)/(2*n);
+		
+			viscosity_complement=1/(2*pow(A,e));
+		}
+	}
+	else{
+		viscosity_complement=4.5*pow((IssmDouble)10,(IssmDouble)17);
+	}
+
+	/*Checks in debugging mode*/
+	_assert_(B>0);
+	_assert_(n>0);
+	_assert_(viscosity_complement>0);
+		
+	/*Return: */
+	*pviscosity_complement=viscosity_complement;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetViscosityZComplement {{{*/
+void  Matdamageice::GetViscosityZComplement(IssmDouble* pviscosity_complement, IssmDouble* epsilon){
+	/*Return viscosity derivative for control method d(mu)/dZ: 
+	 *
+	 *  										               B 
+	 * dviscosity= -------------------------------------------------------------------
+	 *  				  2[ exx^2+eyy^2+exx*eyy+exy^2+exz^2+eyz^2 ]^[(n-1)/2n]
+	 *
+	 * If epsilon is NULL, it means this is the first time Gradjb is being run, and we 
+	 * return mu20, initial viscosity.
+	 */
+	
+	/*output: */
+	IssmDouble viscosity_complement;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy;
+
+	/*Intermediary value A and exponent e: */
+	IssmDouble A,e;
+	IssmDouble B,n;
+
+	/*Get B and n*/
+	B=GetBbar();
+	n=GetN();
+
+	if(epsilon){
+		exx=*(epsilon+0);
+		eyy=*(epsilon+1);
+		exy=*(epsilon+2);
+
+		/*Build viscosity: mu2=B/(2*A^e) */
+		A=pow(exx,2)+pow(eyy,2)+pow(exy,2)+exx*eyy;
+		if(A==0){
+			/*Maximum viscosity_complement for 0 shear areas: */
+			viscosity_complement=2.25*pow((IssmDouble)10,(IssmDouble)17);
+		}
+		else{
+			e=(n-1)/(2*n);
+		
+			viscosity_complement=B/(2*pow(A,e));
+		}
+	}
+	else{
+		viscosity_complement=4.5*pow((IssmDouble)10,(IssmDouble)17);
+	}
+
+	/*Checks in debugging mode*/
+	_assert_(B>0);
+	_assert_(n>0);
+	_assert_(viscosity_complement>0);
+		
+	/*Return: */
+	*pviscosity_complement=viscosity_complement;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetViscosityDerivativeEpsSquare{{{*/
+void  Matdamageice::GetViscosityDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* epsilon){
+
+	/*output: */
+	IssmDouble mu_prime;
+	IssmDouble mu,n,eff2;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy,exz,eyz;
+
+	/*Get visocisty and n*/
+	GetViscosity3d(&mu,epsilon);
+	n=GetN();
+
+	if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0) && 
+				(epsilon[3]==0) && (epsilon[4]==0)){
+		mu_prime=0.5*pow((IssmDouble)10,(IssmDouble)14);
+	}
+	else{
+		/*Retrive strain rate components: */
+		exx=epsilon[0];
+		eyy=epsilon[1];
+		exy=epsilon[2];
+		exz=epsilon[3];
+		eyz=epsilon[4];
+		eff2 = exx*exx + eyy*eyy + exx*eyy + exy*exy + exz*exz + eyz*eyz;
+
+		mu_prime=(1-n)/(2*n) * mu/eff2;
+	}
+
+	/*Assign output pointers:*/
+	*pmu_prime=mu_prime;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::GetViscosity2dDerivativeEpsSquare{{{*/
+void  Matdamageice::GetViscosity2dDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* epsilon){
+
+	/*output: */
+	IssmDouble mu_prime;
+	IssmDouble mu,n,eff2;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy,exz;
+
+	/*Get visocisty and n*/
+	GetViscosity2d(&mu,epsilon);
+	n=GetN();
+
+	if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0)){
+		mu_prime=0.5*pow((IssmDouble)10,(IssmDouble)14);
+	}
+	else{
+		/*Retrive strain rate components: */
+		exx=epsilon[0];
+		eyy=epsilon[1];
+		exy=epsilon[2];
+		eff2 = exx*exx + eyy*eyy + exx*eyy + exy*exy ;
+
+		mu_prime=(1-n)/(2*n) * mu/eff2;
+	}
+
+	/*Assign output pointers:*/
+	*pmu_prime=mu_prime;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputDuplicate{{{*/
+void  Matdamageice::InputDuplicate(int original_enum,int new_enum){
+
+	/*Call inputs method*/
+	if (IsInput(original_enum)) inputs->DuplicateInput(original_enum,new_enum);
+
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromVector(IssmDouble* vector, int name, int type) {{{*/
+void  Matdamageice::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+
+	/*Intermediaries*/
+	Element *element      = NULL;
+
+	/*Recover element*/
+	element=(Element*)helement->delivers();
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	switch(type){
+
+		case VertexEnum:
+
+			switch(element->ObjectEnum()){
+
+				case TriaEnum: {
+					IssmDouble values[3];
+					for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexDof()];
+					this->inputs->AddInput(new TriaP1Input(name,values));
+					return;
+				}
+				default: _error_("element " << EnumToStringx(element->ObjectEnum()) << " not implemented yet");
+			}
+		default: _error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromVector(int* vector, int name, int type) {{{*/
+void  Matdamageice::InputUpdateFromVector(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromVector(bool* vector, int name, int type) {{{*/
+void  Matdamageice::InputUpdateFromVector(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type) {{{*/
+void  Matdamageice::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){
+
+	/*Intermediaries*/
+	Element *element      = NULL;
+	Parameters* parameters= NULL;
+	int         dim;
+
+	/*Recover element*/
+	element=(Element*)helement->delivers();
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	switch(type){
+
+		case VertexEnum:
+
+			switch(element->ObjectEnum()){
+
+				case TriaEnum: {
+					IssmDouble values[3];
+					for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetSidList()]; //use sid list, to index into serial oriented vector 
+					this->inputs->AddInput(new TriaP1Input(name,values));
+					/*Special case for rheology B in 2D: Pourave land for this solution{{{*/
+					if(name==MaterialsRheologyBEnum){
+						/*Are we in 2D?:*/
+						if(element->ObjectEnum()==TriaEnum){
+							parameters=((Tria*)(element))->parameters;
+						}
+						else{
+							parameters=((Penta*)(element))->parameters;
+						}
+						parameters->FindParam(&dim,MeshDimensionEnum);
+						if(dim==2){
+							/*Dupliacte rheology input: */
+							this->inputs->AddInput(new TriaP1Input(MaterialsRheologyBbarEnum,values));
+						}
+					}
+					/*}}}*/
+					return;
+				}
+				default: _error_("element " << EnumToStringx(element->ObjectEnum()) << " not implemented yet");
+			}
+		default: _error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+
+
+
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromMatrixDakota(int* vector, int name, int type) {{{*/
+void  Matdamageice::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols,int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromVectorDakota(int* vector, int name, int type) {{{*/
+void  Matdamageice::InputUpdateFromVectorDakota(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromVectorDakota(bool* vector, int name, int type) {{{*/
+void  Matdamageice::InputUpdateFromVectorDakota(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromConstant(IssmDouble constant, int name) {{{*/
+void  Matdamageice::InputUpdateFromConstant(IssmDouble constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromConstant(int constant, int name) {{{*/
+void  Matdamageice::InputUpdateFromConstant(int constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromConstant(bool constant, int name) {{{*/
+void  Matdamageice::InputUpdateFromConstant(bool constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromSolution{{{*/
+void  Matdamageice::InputUpdateFromSolution(IssmDouble* solution){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matdamageice::InputUpdateFromIoModel{{{*/
+void Matdamageice::InputUpdateFromIoModel(int index, IoModel* iomodel){
+
+	int i,j;
+
+	int    dim;
+	bool   control_analysis;
+	int    num_control_type;
+
+	/*Fetch parameters: */
+	iomodel->Constant(&dim,MeshDimensionEnum);
+	iomodel->Constant(&control_analysis,InversionIscontrolEnum);
+	if(control_analysis) iomodel->Constant(&num_control_type,InversionNumControlParametersEnum);
+
+	/*if 2d*/
+	if(dim==2){
+
+		/*Intermediaries*/
+		const int num_vertices = 3; //Tria has 3 vertices
+		IssmDouble    nodeinputs[num_vertices];
+		IssmDouble    cmmininputs[num_vertices];
+		IssmDouble    cmmaxinputs[num_vertices];
+
+		/*Get B*/
+		if (iomodel->Data(MaterialsRheologyBEnum)) {
+			for(i=0;iData(MaterialsRheologyBEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+i]-1)];
+			this->inputs->AddInput(new TriaP1Input(MaterialsRheologyBbarEnum,nodeinputs));
+		}
+
+		/*Get n*/
+		if (iomodel->Data(MaterialsRheologyNEnum)) {
+			for(i=0;iData(MaterialsRheologyNEnum)[index];
+			this->inputs->AddInput(new TriaP1Input(MaterialsRheologyNEnum,nodeinputs));
+		}
+
+		/*Get Z*/
+		if (iomodel->Data(MaterialsRheologyZEnum)) {
+			for(i=0;iData(MaterialsRheologyZEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+i]-1)];
+			this->inputs->AddInput(new TriaP1Input(MaterialsRheologyZbarEnum,nodeinputs));
+		}
+
+		/*Control Inputs*/
+		#ifdef _HAVE_CONTROL_
+		if (control_analysis && iomodel->Data(InversionControlParametersEnum)){
+			for(i=0;i(iomodel->Data(InversionControlParametersEnum)[i])){
+					case MaterialsRheologyBbarEnum:
+						if (iomodel->Data(MaterialsRheologyBEnum)){
+							_assert_(iomodel->Data(MaterialsRheologyBEnum));_assert_(iomodel->Data(InversionMinParametersEnum)); _assert_(iomodel->Data(InversionMaxParametersEnum)); 
+							for(j=0;jData(MaterialsRheologyBEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)];
+							for(j=0;jData(InversionMinParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							for(j=0;jData(InversionMaxParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							this->inputs->AddInput(new ControlInput(MaterialsRheologyBbarEnum,TriaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+						}
+						break;
+					case MaterialsRheologyZbarEnum:
+						if (iomodel->Data(MaterialsRheologyZEnum)){
+							_assert_(iomodel->Data(MaterialsRheologyZEnum));_assert_(iomodel->Data(InversionMinParametersEnum)); _assert_(iomodel->Data(InversionMaxParametersEnum)); 
+							for(j=0;jData(MaterialsRheologyZEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)];
+							for(j=0;jData(InversionMinParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							for(j=0;jData(InversionMaxParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							this->inputs->AddInput(new ControlInput(MaterialsRheologyZbarEnum,TriaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+						}
+						break;
+
+				}
+			}
+		}
+		#endif
+	}
+
+	/*if 3d*/
+	#ifdef _HAVE_3D_
+	else if(dim==3){
+
+		/*Intermediaries*/
+		const int num_vertices = 6; //Penta has 6 vertices
+		IssmDouble    nodeinputs[num_vertices];
+		IssmDouble    cmmininputs[num_vertices];
+		IssmDouble    cmmaxinputs[num_vertices];
+
+		/*Get B*/
+		if (iomodel->Data(MaterialsRheologyBEnum)) {
+			for(i=0;iData(MaterialsRheologyBEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+i]-1)];
+			this->inputs->AddInput(new PentaP1Input(MaterialsRheologyBEnum,nodeinputs));
+		}
+
+		/*Get n*/
+		if (iomodel->Data(MaterialsRheologyNEnum)) {
+			for(i=0;iData(MaterialsRheologyNEnum)[index];
+			this->inputs->AddInput(new PentaP1Input(MaterialsRheologyNEnum,nodeinputs));
+		}
+
+		/*Get Z*/
+		if (iomodel->Data(MaterialsRheologyZEnum)) {
+			for(i=0;iData(MaterialsRheologyZEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+i]-1)];
+			this->inputs->AddInput(new PentaP1Input(MaterialsRheologyZEnum,nodeinputs));
+		}
+
+		/*Control Inputs*/
+		#ifdef _HAVE_CONTROL_
+		if (control_analysis && iomodel->Data(InversionControlParametersEnum)){
+			for(i=0;i(iomodel->Data(InversionControlParametersEnum)[i])){
+					case MaterialsRheologyBbarEnum:
+						if (iomodel->Data(MaterialsRheologyBEnum)){
+							_assert_(iomodel->Data(MaterialsRheologyBEnum));_assert_(iomodel->Data(InversionMinParametersEnum)); _assert_(iomodel->Data(InversionMaxParametersEnum)); 
+							for(j=0;jData(MaterialsRheologyBEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)];
+							for(j=0;jData(InversionMinParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							for(j=0;jData(InversionMaxParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							this->inputs->AddInput(new ControlInput(MaterialsRheologyBEnum,PentaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+						}
+						break;
+					case MaterialsRheologyZbarEnum:
+						if (iomodel->Data(MaterialsRheologyZEnum)){
+							_assert_(iomodel->Data(MaterialsRheologyZEnum));_assert_(iomodel->Data(InversionMinParametersEnum)); _assert_(iomodel->Data(InversionMaxParametersEnum)); 
+							for(j=0;jData(MaterialsRheologyZEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)];
+							for(j=0;jData(InversionMinParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							for(j=0;jData(InversionMaxParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							this->inputs->AddInput(new ControlInput(MaterialsRheologyZEnum,PentaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+						}
+						break;
+				}
+			}
+		}
+		#endif
+	}
+	#endif
+	else{
+		_error_("Mesh type not supported yet!");
+	}
+
+	return;
+}
+/*}}}*/
+/*FUNCTION Matdamageice::IsInput{{{*/
+bool Matdamageice::IsInput(int name){
+	if (
+				name==MaterialsRheologyBEnum ||
+				name==MaterialsRheologyBbarEnum ||
+				name==MaterialsRheologyNEnum ||
+				name==MaterialsRheologyZEnum ||
+				name==MaterialsRheologyZbarEnum
+		){
+		return true;
+	}
+	else return false;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Materials/Matdamageice.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Materials/Matdamageice.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Materials/Matdamageice.h	(revision 13395)
@@ -0,0 +1,70 @@
+/*!\file Matdamageice.h
+ * \brief: header file for matice object
+ */
+
+#ifndef MATDAMAGEICE_H_
+#define MATDAMAGEICE_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Material.h"
+class IoModel;
+/*}}}*/
+
+class Matdamageice: public Material{
+
+	private: 
+		int	   mid;
+		Hook* helement;
+
+	public:
+		/*Matdamageice constructors, destructors: {{{*/
+		Matdamageice();
+		Matdamageice(int mid,int i, IoModel* iomodel);
+		~Matdamageice();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Update virtual functions definitions: {{{*/
+		void  InputUpdateFromVector(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVector(int* vector, int name, int type);
+		void  InputUpdateFromVector(bool* vector, int name, int type);
+		void  InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrow, int ncols, int name, int type);
+		void  InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(int* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(bool* vector, int name, int type);
+		void  InputUpdateFromConstant(IssmDouble constant, int name);
+		void  InputUpdateFromConstant(int constant, int name);
+		void  InputUpdateFromConstant(bool constant, int name);
+		void  InputUpdateFromSolution(IssmDouble* solution);
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel);
+		/*}}}*/
+		/*Material virtual functions resolution: {{{*/
+		void   InputDuplicate(int original_enum,int new_enum);
+		void   Configure(Elements* elements);
+		void   GetVectorFromInputs(Vector* vector,int input_enum);
+		void   SetCurrentConfiguration(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin);
+		void   GetViscosity2d(IssmDouble* pviscosity, IssmDouble* pepsilon);
+		void   GetViscosity3d(IssmDouble* pviscosity3d, IssmDouble* pepsilon);
+		void   GetViscosity3dStokes(IssmDouble* pviscosity3d, IssmDouble* epsilon);
+		void   GetViscosityComplement(IssmDouble* pviscosity_complement, IssmDouble* pepsilon);
+		void   GetViscosityZComplement(IssmDouble* pviscosity_complement, IssmDouble* pepsilon);
+		void   GetViscosityDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* pepsilon);
+		void   GetViscosity2dDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* pepsilon);
+		IssmDouble GetA();
+		IssmDouble GetB();
+		IssmDouble GetBbar();
+		IssmDouble GetN();
+		IssmDouble GetZ();
+		IssmDouble GetZbar();
+		bool   IsInput(int name);
+		/*}}}*/
+};
+
+#endif  /* _MATICE_H_ */
Index: /issm/trunk/src/c/classes/objects/Materials/Material.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Materials/Material.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Materials/Material.h	(revision 13395)
@@ -0,0 +1,42 @@
+/*!\file:  Material.h
+ * \brief abstract class for Material object
+ */ 
+
+
+#ifndef _MATERIAL_H_
+#define _MATERIAL_H_
+
+/*Headers:*/
+/*{{{*/
+class Object;
+#include "../Object.h"
+#include "../../../toolkits/toolkits.h"
+/*}}}*/
+
+class Material: public Object,public Update{
+
+	public: 
+		Inputs*  inputs;
+		virtual       ~Material(){};
+		/*WARNING: input should not be public but it is an easy way to update B from T (using UpdateFromSolution) from Pentas*/
+
+		/*Numerics*/
+		virtual void       InputDuplicate(int original_enum,int new_enum)=0;
+		virtual void       Configure(Elements* elements)=0;
+		virtual void       GetVectorFromInputs(Vector* vector,int input_enum)=0;
+		virtual void       GetViscosity2d(IssmDouble* pviscosity, IssmDouble* pepsilon)=0;
+		virtual void       GetViscosity3d(IssmDouble* pviscosity3d, IssmDouble* pepsilon)=0;
+		virtual void       GetViscosity3dStokes(IssmDouble* pviscosity3d, IssmDouble* epsilon)=0;
+		virtual void       GetViscosityComplement(IssmDouble* pviscosity_complement, IssmDouble* pepsilon)=0;
+		virtual void       GetViscosityZComplement(IssmDouble* pviscosity_complement, IssmDouble* pepsilon)=0;
+		virtual void       GetViscosityDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* pepsilon)=0;
+		virtual void       GetViscosity2dDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* pepsilon)=0;
+		virtual IssmDouble GetA()=0;
+		virtual IssmDouble GetB()=0;
+		virtual IssmDouble GetBbar()=0;
+		virtual IssmDouble GetN()=0;
+		virtual IssmDouble GetZ()=0;
+		virtual IssmDouble GetZbar()=0;
+
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/Materials/Matice.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Materials/Matice.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Materials/Matice.cpp	(revision 13395)
@@ -0,0 +1,783 @@
+/*!\file Matice.c
+ * \brief: implementation of the Matice object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../include/include.h"
+		
+/*Matice constructors and destructor*/
+/*FUNCTION Matice::Matice(){{{*/
+Matice::Matice(){
+	this->inputs=NULL;
+	this->helement=NULL;
+	return;
+}
+/*}}}*/
+/*FUNCTION Matice::Matice(int id, int index, IoModel* iomodel, int num_vertices){{{*/
+Matice::Matice(int matice_mid,int index, IoModel* iomodel){
+
+	/*Intermediaries:*/
+	int    i;
+	int    matice_eid;
+
+	/*Initialize id*/
+	this->mid=matice_mid;
+
+	/*Initialize inputs*/
+	this->inputs=new Inputs();
+
+	/*Initialize inputs from IoModel*/
+	this->InputUpdateFromIoModel(index,iomodel);
+
+	/*Hooks: */
+	matice_eid=index+1;
+	this->helement=new Hook(&matice_eid,1);
+
+	return;
+
+}
+/*}}}*/
+/*FUNCTION Matice::~Matice(){{{*/
+Matice::~Matice(){
+	delete helement;
+	delete inputs;
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION Matice::Echo {{{*/
+void Matice::Echo(void){
+
+	_printLine_("Matice:");
+	_printLine_("   mid: " << mid);
+	_printLine_("   inputs:");
+	inputs->Echo();
+	_printLine_("   element:");
+	helement->Echo();
+}
+/*}}}*/
+/*FUNCTION Matice::DeepEcho {{{*/
+void Matice::DeepEcho(void){
+
+	_printLine_("Matice:");
+	_printLine_("   mid: " << mid);
+	_printLine_("   inputs:");
+	inputs->DeepEcho();
+	_printLine_("   element:");
+	helement->Echo();
+}		
+/*}}}*/
+/*FUNCTION Matice::Id {{{*/
+int    Matice::Id(void){ return mid; }
+/*}}}*/
+/*FUNCTION Matice::MyRank {{{*/
+int    Matice::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Matice::ObjectEnum{{{*/
+int Matice::ObjectEnum(void){
+
+	return MaticeEnum;
+
+}
+/*}}}*/
+/*FUNCTION Matice::copy {{{*/
+Object* Matice::copy() {
+
+	/*Output*/
+	Matice* matice=NULL;
+
+	/*Initialize output*/
+	matice=new Matice();
+
+	/*copy fields: */
+	matice->mid=this->mid;
+	matice->helement=(Hook*)this->helement->copy();
+	if(this->inputs) matice->inputs=(Inputs*)this->inputs->Copy();
+	else  matice->inputs=new Inputs();
+
+	return matice;
+}
+/*}}}*/
+
+/*Matice management*/
+/*FUNCTION Matice::Configure {{{*/
+void  Matice::Configure(Elements* elementsin){
+
+	/*Take care of hooking up all objects for this element, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and offsets hidden in hooks: */
+	helement->configure(elementsin);
+}
+/*}}}*/
+/*FUNCTION Matice::SetCurrentConfiguration {{{*/
+void  Matice::SetCurrentConfiguration(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin){
+
+}
+/*}}}*/
+/*FUNCTION Matice::GetA {{{*/
+IssmDouble Matice::GetA(){
+	/*
+	 * A = 1/B^n
+	 */
+
+	IssmDouble B,n;
+
+	inputs->GetInputAverage(&B,MaterialsRheologyBEnum);
+	n=this->GetN();
+
+	return pow(B,-n);
+}
+/*}}}*/
+/*FUNCTION Matice::GetB {{{*/
+IssmDouble Matice::GetB(){
+
+	/*Output*/
+	IssmDouble B;
+
+	inputs->GetInputAverage(&B,MaterialsRheologyBEnum);
+	return B;
+}
+/*}}}*/
+/*FUNCTION Matice::GetBbar {{{*/
+IssmDouble Matice::GetBbar(){
+
+	/*Output*/
+	IssmDouble Bbar;
+
+	inputs->GetInputAverage(&Bbar,MaterialsRheologyBbarEnum);
+	return Bbar;
+}
+/*}}}*/
+/*FUNCTION Matice::GetN {{{*/
+IssmDouble Matice::GetN(){
+
+	/*Output*/
+	IssmDouble n;
+
+	inputs->GetInputAverage(&n,MaterialsRheologyNEnum);
+	return n;
+}
+/*}}}*/
+/*FUNCTION Matice::GetVectorFromInputs{{{*/
+void  Matice::GetVectorFromInputs(Vector* vector,int input_enum){
+
+	/*Intermediaries*/
+	Element *element= NULL;
+
+	/*Recover element*/
+	element=(Element*)helement->delivers();
+
+	/*Check that input_enum is a material input*/
+	if (!IsInput(input_enum)) return;
+
+	switch(element->ObjectEnum()){
+
+		case TriaEnum:{
+
+			/*Prepare index list*/
+			int doflist1[3];
+			for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexDof();
+
+			/*Get input (either in element or material)*/
+			Input* input=inputs->GetInput(input_enum);
+			if(!input) _error_("Input " << EnumToStringx(input_enum) << " not found in material");
+
+			/*We found the enum.  Use its values to fill into the vector, using the vertices ids: */
+			input->GetVectorFromInputs(vector,&doflist1[0]);}
+			break;
+
+		default: _error_("element " << EnumToStringx(element->ObjectEnum()) << " not implemented yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Matice::GetViscosity2d {{{*/
+void  Matice::GetViscosity2d(IssmDouble* pviscosity, IssmDouble* epsilon){
+	/*From a string tensor and a material object, return viscosity, using Glen's flow law.
+												    B
+	  viscosity= -------------------------------------------------------------------
+						  2[ exx^2+eyy^2+exx*eyy+exy^2+exz^2+eyz^2 ]^[(n-1)/2n]
+
+	  where viscosity is the viscotiy, B the flow law parameter , (u,v) the velocity 
+	  vector, and n the flow law exponent.
+
+	  If epsilon is NULL, it means this is the first time SystemMatrices is being run, and we 
+	  return 10^14, initial viscosity.
+	  */
+
+	/*output: */
+	IssmDouble viscosity;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy;
+
+	/*Intermediary: */
+	IssmDouble A,e;
+	IssmDouble B,n;
+
+	/*Get B and n*/
+	B=GetBbar();
+	n=GetN();
+
+	if (n==1){
+		/*Viscous behaviour! viscosity=B: */
+		viscosity=B/2;
+	}
+	else{
+		if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0)){
+			viscosity=0.5*pow((IssmDouble)10,(IssmDouble)14);
+		}
+		else{
+			/*Retrive strain rate components: */
+			exx=*(epsilon+0);
+			eyy=*(epsilon+1);
+			exy=*(epsilon+2);
+
+			/*Build viscosity: viscosity=B/(2*A^e) */
+			A=pow(exx,2)+pow(eyy,2)+pow(exy,2)+exx*eyy;
+			if(A==0){
+				/*Maxiviscositym viscosity for 0 shear areas: */
+				viscosity=2.5*pow(10.,17.);
+			}
+			else{
+				e=(n-1)/(2*n);
+				viscosity=B/(2*pow(A,e));
+			}
+		}
+	}
+
+	/*Checks in debugging mode*/
+	if(viscosity<=0) _error_("Negative viscosity");
+	_assert_(B>0);
+	_assert_(n>0);
+
+	/*Return: */
+	*pviscosity=viscosity;
+}
+/*}}}*/
+/*FUNCTION Matice::GetViscosity3d {{{*/
+void  Matice::GetViscosity3d(IssmDouble* pviscosity3d, IssmDouble* epsilon){
+
+	/*Return viscosity accounting for steady state power law creep [Thomas and MacAyeal, 1982]: 
+	 *
+	 *                                               B
+	 * viscosity3d= -------------------------------------------------------------------
+	 *                      2[ exx^2+eyy^2+exx*eyy+exy^2+exz^2+eyz^2 ]^[(n-1)/2n]
+	 *
+	 *     where mu is the viscotiy, B the flow law parameter , (u,v) the velocity 
+	 *     vector, and n the flow law exponent.
+	 *
+	 * If epsilon is NULL, it means this is the first time Emg is being run, and we 
+	 * return g, initial viscosity.
+	 */
+	
+	/*output: */
+	IssmDouble viscosity3d;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy,exz,eyz;
+
+	/*Intermediaries: */
+	IssmDouble A,e;
+	IssmDouble B,n;
+
+	/*Get B and n*/
+	B=GetB();
+	n=GetN();
+
+	if (n==1){
+		/*Viscous behaviour! viscosity3d=B: */
+		viscosity3d=B/2;
+	}
+	else{
+		if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0) && 
+				(epsilon[3]==0) && (epsilon[4]==0)){
+			viscosity3d=0.5*pow((IssmDouble)10,(IssmDouble)14);
+		}
+		else{
+
+			/*Retrive strain rate components: */
+			exx=*(epsilon+0);
+			eyy=*(epsilon+1);
+			exy=*(epsilon+2);
+			exz=*(epsilon+3);
+			eyz=*(epsilon+4);
+
+			/*Build viscosity: viscosity3d=2*B/(2*A^e) */
+			A=pow(exx,2)+pow(eyy,2)+pow(exy,2)+pow(exz,2)+pow(eyz,2)+exx*eyy;
+			if(A==0){
+				/*Maxiviscosity3dm viscosity for 0 shear areas: */
+				viscosity3d=2.25*pow((IssmDouble)10,(IssmDouble)17);
+			}
+			else{
+				e=(n-1)/2/n;
+			
+				viscosity3d=B/(2*pow(A,e));
+			}
+		}
+	}
+
+	/*Checks in debugging mode*/
+	if(viscosity3d<=0) _error_("Negative viscosity");
+	_assert_(B>0);
+	_assert_(n>0);
+
+	/*Assign output pointers:*/
+	*pviscosity3d=viscosity3d;
+}
+/*}}}*/
+/*FUNCTION Matice::GetViscosity3dStokes {{{*/
+void  Matice::GetViscosity3dStokes(IssmDouble* pviscosity3d, IssmDouble* epsilon){
+	/*Return viscosity accounting for steady state power law creep [Thomas and MacAyeal, 1982]: 
+	 *
+	 *                                          B
+	 * viscosity3d= -------------------------------------------------------------------
+	 *                   2[ exx^2+eyy^2+exx*eyy+exy^2+exz^2+eyz^2 ]^[(n-1)/2n]
+	 *
+	 *     where mu is the viscotiy, B the flow law parameter , (u,v) the velocity 
+	 *     vector, and n the flow law exponent.
+	 *
+	 * If epsilon is NULL, it means this is the first time Emg is being run, and we 
+	 * return g, initial viscosity.
+	 */
+	
+	/*output: */
+	IssmDouble viscosity3d;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy,exz,eyz,ezz;
+
+	/*Intermediaries: */
+	IssmDouble A,e;
+	IssmDouble B,n;
+	IssmDouble eps0;
+
+	/*Get B and n*/
+	eps0=pow((IssmDouble)10,(IssmDouble)-27);
+	B=GetB();
+	n=GetN();
+	
+	if (n==1){
+		/*Viscous behaviour! viscosity3d=B: */
+		viscosity3d=B/2;
+	}
+	else{
+		if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0) && 
+				(epsilon[3]==0) && (epsilon[4]==0) && (epsilon[5]==0)){
+			viscosity3d=0.5*pow((IssmDouble)10,(IssmDouble)14);
+		}
+		else{
+
+			/*Retrive strain rate components: */
+			exx=*(epsilon+0);
+			eyy=*(epsilon+1);
+			ezz=*(epsilon+2); //not used
+			exy=*(epsilon+3);
+			exz=*(epsilon+4);
+			eyz=*(epsilon+5);
+
+			/*Build viscosity: viscosity3d=B/(2*A^e) */
+			A=pow(exx,2)+pow(eyy,2)+pow(exy,2)+pow(exz,2)+pow(eyz,2)+exx*eyy+pow(eps0,2);
+			if(A==0){
+				/*Maxiviscosity3dm viscosity for 0 shear areas: */
+				viscosity3d=2.25*pow((IssmDouble)10,(IssmDouble)17);
+			}
+			else{
+				e=(n-1)/2/n;
+				viscosity3d=B/(2*pow(A,e));
+			}
+		}
+	}
+
+	/*Checks in debugging mode*/
+	if(viscosity3d<=0) _error_("Negative viscosity");
+	_assert_(B>0);
+	_assert_(n>0);
+
+	/*Assign output pointers:*/
+	*pviscosity3d=viscosity3d;
+}
+/*}}}*/
+/*FUNCTION Matice::GetViscosityComplement {{{*/
+void  Matice::GetViscosityComplement(IssmDouble* pviscosity_complement, IssmDouble* epsilon){
+	/*Return viscosity accounting for steady state power law creep [Thomas and MacAyeal, 1982]: 
+	 *
+	 *  										                1
+	 * viscosity= -------------------------------------------------------------------
+	 *  				  2[ exx^2+eyy^2+exx*eyy+exy^2+exz^2+eyz^2 ]^[(n-1)/2n]
+	 *
+	 * If epsilon is NULL, it means this is the first time Gradjb is being run, and we 
+	 * return mu20, initial viscosity.
+	 */
+	
+	/*output: */
+	IssmDouble viscosity_complement;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy;
+
+	/*Intermediary value A and exponent e: */
+	IssmDouble A,e;
+	IssmDouble B,n;
+
+	/*Get B and n*/
+	B=GetBbar();
+	n=GetN();
+
+	if(epsilon){
+		exx=*(epsilon+0);
+		eyy=*(epsilon+1);
+		exy=*(epsilon+2);
+
+		/*Build viscosity: mu2=B/(2*A^e) */
+		A=pow(exx,2)+pow(eyy,2)+pow(exy,2)+exx*eyy;
+		if(A==0){
+			/*Maximum viscosity_complement for 0 shear areas: */
+			viscosity_complement=2.25*pow((IssmDouble)10,(IssmDouble)17);
+		}
+		else{
+			e=(n-1)/(2*n);
+		
+			viscosity_complement=1/(2*pow(A,e));
+		}
+	}
+	else{
+		viscosity_complement=4.5*pow((IssmDouble)10,(IssmDouble)17);
+	}
+
+	/*Checks in debugging mode*/
+	_assert_(B>0);
+	_assert_(n>0);
+	_assert_(viscosity_complement>0);
+		
+	/*Return: */
+	*pviscosity_complement=viscosity_complement;
+}
+/*}}}*/
+/*FUNCTION Matice::GetViscosityDerivativeEpsSquare{{{*/
+void  Matice::GetViscosityDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* epsilon){
+
+	/*output: */
+	IssmDouble mu_prime;
+	IssmDouble mu,n,eff2;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy,exz,eyz;
+
+	/*Get visocisty and n*/
+	GetViscosity3d(&mu,epsilon);
+	n=GetN();
+
+	if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0) && 
+				(epsilon[3]==0) && (epsilon[4]==0)){
+		mu_prime=0.5*pow((IssmDouble)10,(IssmDouble)14);
+	}
+	else{
+		/*Retrive strain rate components: */
+		exx=epsilon[0];
+		eyy=epsilon[1];
+		exy=epsilon[2];
+		exz=epsilon[3];
+		eyz=epsilon[4];
+		eff2 = exx*exx + eyy*eyy + exx*eyy + exy*exy + exz*exz + eyz*eyz;
+
+		mu_prime=(1-n)/(2*n) * mu/eff2;
+	}
+
+	/*Assign output pointers:*/
+	*pmu_prime=mu_prime;
+}
+/*}}}*/
+/*FUNCTION Matice::GetViscosity2dDerivativeEpsSquare{{{*/
+void  Matice::GetViscosity2dDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* epsilon){
+
+	/*output: */
+	IssmDouble mu_prime;
+	IssmDouble mu,n,eff2;
+
+	/*input strain rate: */
+	IssmDouble exx,eyy,exy,exz;
+
+	/*Get visocisty and n*/
+	GetViscosity2d(&mu,epsilon);
+	n=GetN();
+
+	if((epsilon[0]==0) && (epsilon[1]==0) && (epsilon[2]==0)){
+		mu_prime=0.5*pow((IssmDouble)10,(IssmDouble)14);
+	}
+	else{
+		/*Retrive strain rate components: */
+		exx=epsilon[0];
+		eyy=epsilon[1];
+		exy=epsilon[2];
+		eff2 = exx*exx + eyy*eyy + exx*eyy + exy*exy ;
+
+		mu_prime=(1-n)/(2*n) * mu/eff2;
+	}
+
+	/*Assign output pointers:*/
+	*pmu_prime=mu_prime;
+}
+/*}}}*/
+/*FUNCTION Matice::InputDuplicate{{{*/
+void  Matice::InputDuplicate(int original_enum,int new_enum){
+
+	/*Call inputs method*/
+	if (IsInput(original_enum)) inputs->DuplicateInput(original_enum,new_enum);
+
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromVector(IssmDouble* vector, int name, int type) {{{*/
+void  Matice::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+
+	/*Intermediaries*/
+	Element *element      = NULL;
+
+	/*Recover element*/
+	element=(Element*)helement->delivers();
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	switch(type){
+
+		case VertexEnum:
+
+			switch(element->ObjectEnum()){
+
+				case TriaEnum: {
+					IssmDouble values[3];
+					for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexDof()];
+					this->inputs->AddInput(new TriaP1Input(name,values));
+					return;
+				}
+				default: _error_("element " << EnumToStringx(element->ObjectEnum()) << " not implemented yet");
+			}
+		default: _error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromVector(int* vector, int name, int type) {{{*/
+void  Matice::InputUpdateFromVector(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromVector(bool* vector, int name, int type) {{{*/
+void  Matice::InputUpdateFromVector(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type) {{{*/
+void  Matice::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){
+
+	/*Intermediaries*/
+	Element *element      = NULL;
+	Parameters* parameters= NULL;
+	int         dim;
+
+	/*Recover element*/
+	element=(Element*)helement->delivers();
+
+	/*Check that name is an element input*/
+	if (!IsInput(name)) return;
+
+	switch(type){
+
+		case VertexEnum:
+
+			switch(element->ObjectEnum()){
+
+				case TriaEnum: {
+					IssmDouble values[3];
+					for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetSidList()]; //use sid list, to index into serial oriented vector 
+					this->inputs->AddInput(new TriaP1Input(name,values));
+					/*Special case for rheology B in 2D: Pourave land for this solution{{{*/
+					if(name==MaterialsRheologyBEnum){
+						/*Are we in 2D?:*/
+						if(element->ObjectEnum()==TriaEnum){
+							parameters=((Tria*)(element))->parameters;
+						}
+						else{
+							parameters=((Penta*)(element))->parameters;
+						}
+						parameters->FindParam(&dim,MeshDimensionEnum);
+						if(dim==2){
+							/*Dupliacte rheology input: */
+							this->inputs->AddInput(new TriaP1Input(MaterialsRheologyBbarEnum,values));
+						}
+					}
+					/*}}}*/
+					return;
+				}
+				default: _error_("element " << EnumToStringx(element->ObjectEnum()) << " not implemented yet");
+			}
+		default: _error_("type " << type << " (" << EnumToStringx(type) << ") not implemented yet");
+	}
+
+
+
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromMatrixDakota(int* vector, int name, int type) {{{*/
+void  Matice::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols,int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromVectorDakota(int* vector, int name, int type) {{{*/
+void  Matice::InputUpdateFromVectorDakota(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromVectorDakota(bool* vector, int name, int type) {{{*/
+void  Matice::InputUpdateFromVectorDakota(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromConstant(IssmDouble constant, int name) {{{*/
+void  Matice::InputUpdateFromConstant(IssmDouble constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromConstant(int constant, int name) {{{*/
+void  Matice::InputUpdateFromConstant(int constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromConstant(bool constant, int name) {{{*/
+void  Matice::InputUpdateFromConstant(bool constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromSolution{{{*/
+void  Matice::InputUpdateFromSolution(IssmDouble* solution){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matice::InputUpdateFromIoModel{{{*/
+void Matice::InputUpdateFromIoModel(int index, IoModel* iomodel){
+
+	int i,j;
+
+	int    dim;
+	bool   control_analysis;
+	int    num_control_type;
+
+	/*Fetch parameters: */
+	iomodel->Constant(&dim,MeshDimensionEnum);
+	iomodel->Constant(&control_analysis,InversionIscontrolEnum);
+	if(control_analysis) iomodel->Constant(&num_control_type,InversionNumControlParametersEnum);
+
+	/*if 2d*/
+	if(dim==2){
+
+		/*Intermediaries*/
+		const int num_vertices = 3; //Tria has 3 vertices
+		IssmDouble    nodeinputs[num_vertices];
+		IssmDouble    cmmininputs[num_vertices];
+		IssmDouble    cmmaxinputs[num_vertices];
+
+		/*Get B*/
+		if (iomodel->Data(MaterialsRheologyBEnum)) {
+			for(i=0;iData(MaterialsRheologyBEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+i]-1)];
+			this->inputs->AddInput(new TriaP1Input(MaterialsRheologyBbarEnum,nodeinputs));
+		}
+
+		/*Get n*/
+		if (iomodel->Data(MaterialsRheologyNEnum)) {
+			for(i=0;iData(MaterialsRheologyNEnum)[index];
+			this->inputs->AddInput(new TriaP1Input(MaterialsRheologyNEnum,nodeinputs));
+		}
+
+		/*Control Inputs*/
+		#ifdef _HAVE_CONTROL_
+		if (control_analysis && iomodel->Data(InversionControlParametersEnum)){
+			for(i=0;i(iomodel->Data(InversionControlParametersEnum)[i])){
+					case MaterialsRheologyBbarEnum:
+						if (iomodel->Data(MaterialsRheologyBEnum)){
+							_assert_(iomodel->Data(MaterialsRheologyBEnum));_assert_(iomodel->Data(InversionMinParametersEnum)); _assert_(iomodel->Data(InversionMaxParametersEnum)); 
+							for(j=0;jData(MaterialsRheologyBEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)];
+							for(j=0;jData(InversionMinParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							for(j=0;jData(InversionMaxParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							this->inputs->AddInput(new ControlInput(MaterialsRheologyBbarEnum,TriaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+						}
+						break;
+				}
+			}
+		}
+		#endif
+	}
+
+	/*if 3d*/
+	#ifdef _HAVE_3D_
+	else if(dim==3){
+
+		/*Intermediaries*/
+		const int num_vertices = 6; //Penta has 6 vertices
+		IssmDouble    nodeinputs[num_vertices];
+		IssmDouble    cmmininputs[num_vertices];
+		IssmDouble    cmmaxinputs[num_vertices];
+
+		/*Get B*/
+		if (iomodel->Data(MaterialsRheologyBEnum)) {
+			for(i=0;iData(MaterialsRheologyBEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+i]-1)];
+			this->inputs->AddInput(new PentaP1Input(MaterialsRheologyBEnum,nodeinputs));
+		}
+
+		/*Get n*/
+		if (iomodel->Data(MaterialsRheologyNEnum)) {
+			for(i=0;iData(MaterialsRheologyNEnum)[index];
+			this->inputs->AddInput(new PentaP1Input(MaterialsRheologyNEnum,nodeinputs));
+		}
+
+		/*Control Inputs*/
+		#ifdef _HAVE_CONTROL_
+		if (control_analysis && iomodel->Data(InversionControlParametersEnum)){
+			for(i=0;i(iomodel->Data(InversionControlParametersEnum)[i])){
+					case MaterialsRheologyBbarEnum:
+						if (iomodel->Data(MaterialsRheologyBEnum)){
+							_assert_(iomodel->Data(MaterialsRheologyBEnum));_assert_(iomodel->Data(InversionMinParametersEnum)); _assert_(iomodel->Data(InversionMaxParametersEnum)); 
+							for(j=0;jData(MaterialsRheologyBEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)];
+							for(j=0;jData(InversionMinParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							for(j=0;jData(InversionMaxParametersEnum)[reCast(iomodel->Data(MeshElementsEnum)[num_vertices*index+j]-1)*num_control_type+i];
+							this->inputs->AddInput(new ControlInput(MaterialsRheologyBEnum,PentaP1InputEnum,nodeinputs,cmmininputs,cmmaxinputs,i+1));
+						}
+						break;
+				}
+			}
+		}
+		#endif
+	}
+	#endif
+	else{
+		_error_("Mesh type not supported yet!");
+	}
+
+	return;
+}
+/*}}}*/
+/*FUNCTION Matice::IsInput{{{*/
+bool Matice::IsInput(int name){
+	if (
+				name==MaterialsRheologyBEnum ||
+				name==MaterialsRheologyBbarEnum ||
+				name==MaterialsRheologyNEnum
+		){
+		return true;
+	}
+	else return false;
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Materials/Matice.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Materials/Matice.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Materials/Matice.h	(revision 13395)
@@ -0,0 +1,70 @@
+/*!\file Matice.h
+ * \brief: header file for matice object
+ */
+
+#ifndef MATICE_H_
+#define MATICE_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Material.h"
+class IoModel;
+/*}}}*/
+
+class Matice: public Material{
+
+	private: 
+		int	   mid;
+		Hook* helement;
+
+	public:
+		/*Matice constructors, destructors: {{{*/
+		Matice();
+		Matice(int mid,int i, IoModel* iomodel);
+		~Matice();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Update virtual functions definitions: {{{*/
+		void  InputUpdateFromVector(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVector(int* vector, int name, int type);
+		void  InputUpdateFromVector(bool* vector, int name, int type);
+		void  InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrow, int ncols, int name, int type);
+		void  InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(int* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(bool* vector, int name, int type);
+		void  InputUpdateFromConstant(IssmDouble constant, int name);
+		void  InputUpdateFromConstant(int constant, int name);
+		void  InputUpdateFromConstant(bool constant, int name);
+		void  InputUpdateFromSolution(IssmDouble* solution);
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel);
+		/*}}}*/
+		/*Material virtual functions resolution: {{{*/
+		void   InputDuplicate(int original_enum,int new_enum);
+		void   Configure(Elements* elements);
+		void   GetVectorFromInputs(Vector* vector,int input_enum);
+		void       SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters);
+		void       GetViscosity2d(IssmDouble* pviscosity, IssmDouble* pepsilon);
+		void       GetViscosity3d(IssmDouble* pviscosity3d, IssmDouble* pepsilon);
+		void       GetViscosity3dStokes(IssmDouble* pviscosity3d, IssmDouble* epsilon);
+		void       GetViscosityComplement(IssmDouble* pviscosity_complement, IssmDouble* pepsilon);
+		void GetViscosityZComplement(IssmDouble*, IssmDouble*){_error_("not supported");};
+		void       GetViscosityDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* pepsilon);
+		void       GetViscosity2dDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* pepsilon);
+		IssmDouble GetA();
+		IssmDouble GetB();
+		IssmDouble GetBbar();
+		IssmDouble GetZ(){_error_("not supported");};
+		IssmDouble GetZbar(){_error_("not supported");};
+		IssmDouble GetN();
+		bool       IsInput(int name);
+		/*}}}*/
+};
+
+#endif  /* _MATICE_H_ */
Index: /issm/trunk/src/c/classes/objects/Materials/Matpar.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Materials/Matpar.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Materials/Matpar.cpp	(revision 13395)
@@ -0,0 +1,362 @@
+/*!\file Matpar.c
+ * \brief: implementation of the Matpar object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../../classes.h"
+#include "../../../shared/shared.h"
+#include "../../../include/include.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+		
+/*Matpar constructors and destructor*/
+/*FUNCTION Matpar::Matpar() {{{*/
+Matpar::Matpar(){
+	return;
+}
+/*}}}*/
+/*FUNCTION Matpar::Matpar(int matpar_mid,IoModel* iomodel){{{*/
+Matpar::Matpar(int matpar_mid, IoModel* iomodel){
+
+	this->mid = matpar_mid;
+	iomodel->Constant(&this->rho_ice,MaterialsRhoIceEnum);
+	iomodel->Constant(&this->rho_water,MaterialsRhoWaterEnum);
+	iomodel->Constant(&this->rho_freshwater,MaterialsRhoFreshwaterEnum);
+	iomodel->Constant(&this->mu_water,MaterialsMuWaterEnum);
+	iomodel->Constant(&this->heatcapacity,MaterialsHeatcapacityEnum);
+	iomodel->Constant(&this->thermalconductivity,MaterialsThermalconductivityEnum);
+	iomodel->Constant(&this->latentheat,MaterialsLatentheatEnum);
+	iomodel->Constant(&this->beta,MaterialsBetaEnum);
+	iomodel->Constant(&this->meltingpoint,MaterialsMeltingpointEnum);
+	iomodel->Constant(&this->referencetemperature,ConstantsReferencetemperatureEnum);
+	iomodel->Constant(&this->mixed_layer_capacity,MaterialsMixedLayerCapacityEnum);
+	iomodel->Constant(&this->thermal_exchange_velocity,MaterialsThermalExchangeVelocityEnum);
+	iomodel->Constant(&this->g,ConstantsGEnum);
+	
+	iomodel->Constant(&this->hydro_CR,HydrologyCREnum);
+	iomodel->Constant(&this->kn,HydrologyKnEnum);
+	iomodel->Constant(&this->hydro_n,HydrologyNEnum);
+	iomodel->Constant(&this->hydro_p,HydrologyPEnum);
+	iomodel->Constant(&this->hydro_q,HydrologyQEnum);
+	this->inputs=NULL; /*not used here*/
+}
+/*}}}*/
+/*FUNCTION Matpar::~Matpar() {{{*/
+Matpar::~Matpar(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION Matpar::Echo {{{*/
+void Matpar::Echo(void){
+
+	_printLine_("Matpar:");
+	_printLine_("   mid: " << mid);
+	_printLine_("   rho_ice: " << rho_ice);
+	_printLine_("   rho_water: " << rho_water);
+	_printLine_("   rho_freshwater: " << rho_freshwater);
+	_printLine_("   mu_water: " << mu_water);
+	_printLine_("   heatcapacity: " << heatcapacity);
+	_printLine_("   thermalconductivity: " << thermalconductivity);
+	_printLine_("   latentheat: " << latentheat);
+	_printLine_("   beta: " << beta);
+	_printLine_("   meltingpoint: " << meltingpoint);
+	_printLine_("   referencetemperature: " << referencetemperature);
+	_printLine_("   mixed_layer_capacity: " << mixed_layer_capacity);
+	_printLine_("   thermal_exchange_velocity: " << thermal_exchange_velocity);
+	_printLine_("   g: " << g);
+	return;
+}
+/*}}}*/
+/*FUNCTION Matpar::DeepEcho {{{*/
+void Matpar::DeepEcho(void){
+
+	this->Echo();
+}		
+/*}}}*/
+/*FUNCTION Matpar::Id {{{*/
+int    Matpar::Id(void){ return mid; }
+/*}}}*/
+/*FUNCTION Matpar::MyRank {{{*/
+int    Matpar::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Matpar::ObjectEnum{{{*/
+int Matpar::ObjectEnum(void){
+
+	return MatparEnum;
+
+}
+/*}}}*/
+/*FUNCTION Matpar::copy {{{*/
+Object* Matpar::copy() {
+	return new Matpar(*this); 
+}
+/*}}}*/
+
+/*Update virtual functions definitions:*/
+/*FUNCTION Matpar::InputUpdateFromVector(IssmDouble* vector, int name, int type) {{{*/
+void   Matpar::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromVector(int* vector, int name, int type) {{{*/
+void   Matpar::InputUpdateFromVector(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromVector(bool* vector, int name, int type) {{{*/
+void   Matpar::InputUpdateFromVector(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type) {{{*/
+void   Matpar::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromVectorDakota(int* vector, int name, int type) {{{*/
+void   Matpar::InputUpdateFromVectorDakota(int* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromVectorDakota(bool* vector, int name, int type) {{{*/
+void   Matpar::InputUpdateFromVectorDakota(bool* vector, int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromMatrixDakota(int* vector, int name, int type) {{{*/
+void  Matpar::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols,int name, int type){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromConstant(IssmDouble constant, int name) {{{*/
+void   Matpar::InputUpdateFromConstant(IssmDouble constant, int name){
+
+	switch(name){
+		case MaterialsRhoIceEnum:
+			this->rho_ice=constant;
+			break;
+		case MaterialsRhoWaterEnum:
+			this->rho_water=constant;
+			break;
+		case MaterialsRhoFreshwaterEnum:
+			this->rho_freshwater=constant;
+			break;
+		case MaterialsMuWaterEnum:
+			this->mu_water=constant;
+			break;
+		case MaterialsHeatcapacityEnum:
+			this->heatcapacity=constant;
+			break;
+		case MaterialsThermalconductivityEnum:
+			this->thermalconductivity=constant;
+			break;
+		case  MaterialsLatentheatEnum:
+			this->latentheat=constant;
+			break;
+		case  MaterialsBetaEnum:
+			this->beta=constant;
+			break;
+		case  MaterialsMeltingpointEnum:
+			this->meltingpoint=constant;
+			break;
+		case  ConstantsReferencetemperatureEnum:
+			this->referencetemperature=constant;
+			break;
+		case  MaterialsMixedLayerCapacityEnum:
+			this->mixed_layer_capacity=constant;
+			break;
+		case  MaterialsThermalExchangeVelocityEnum:
+			this->thermalconductivity=constant;
+			break;
+		case  ConstantsGEnum:
+			this->g=constant;
+			break;
+		default: 
+			break;
+	}
+
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromConstant(int constant, int name) {{{*/
+void   Matpar::InputUpdateFromConstant(int constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromConstant(bool constant, int name) {{{*/
+void   Matpar::InputUpdateFromConstant(bool constant, int name){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Matpar::InputUpdateFromSolution{{{*/
+void   Matpar::InputUpdateFromSolution(IssmDouble* solution){
+	/*Nothing updated yet*/
+}
+/*}}}*/
+
+/*Matpar management: */
+/*FUNCTION Matpar::Configure {{{*/
+void  Matpar::Configure(Elements* elementsin){
+
+	/*nothing done yet!*/
+
+}
+/*}}}*/
+/*FUNCTION Matpar::GetBeta {{{*/
+IssmDouble Matpar::GetBeta(){
+	return beta;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetG {{{*/
+IssmDouble Matpar::GetG(){
+	return g;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetHeatCapacity {{{*/
+IssmDouble Matpar::GetHeatCapacity(){
+	return heatcapacity;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetLatentHeat {{{*/
+IssmDouble Matpar::GetLatentHeat(){
+	return latentheat;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetMeltingPoint {{{*/
+IssmDouble Matpar::GetMeltingPoint(){
+	return meltingpoint;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetReferenceTemperature {{{*/
+IssmDouble Matpar::GetReferenceTemperature(){
+	return referencetemperature;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetMixedLayerCapacity {{{*/
+IssmDouble Matpar::GetMixedLayerCapacity(){
+	return mixed_layer_capacity;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetRhoIce {{{*/
+IssmDouble Matpar::GetRhoIce(){
+	
+	return rho_ice;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetRhoWater {{{*/
+IssmDouble Matpar::GetRhoWater(){
+	return rho_water;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetRhoFreshwater {{{*/
+IssmDouble Matpar::GetRhoFreshwater(){
+	return rho_freshwater;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetMuWater {{{*/
+IssmDouble Matpar::GetMuWater(){
+	return mu_water;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetThermalConductivity {{{*/
+IssmDouble Matpar::GetThermalConductivity(){
+	return thermalconductivity;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetThermalExchangeVelocity {{{*/
+IssmDouble Matpar::GetThermalExchangeVelocity(){
+	return thermal_exchange_velocity;
+}
+/*}}}*/
+/*FUNCTION Matpar::GetKn {{{*/		 
+IssmDouble Matpar::GetKn(){			 
+	return kn;		 
+}		 
+/*}}}*/			 
+/*FUNCTION Matpar::GetHydrologyP {{{*/			 
+IssmDouble Matpar::GetHydrologyP(){		 
+	return hydro_p;			 
+}		 
+/*}}}*/			 
+/*FUNCTION Matqar::GetHydrologyQ {{{*/			 
+IssmDouble Matpar::GetHydrologyQ(){		 
+	return hydro_q;			 
+}		 
+/*}}}*/			 
+/*FUNCTION Matpar::GetHydrologyCR {{{*/		 
+IssmDouble Matpar::GetHydrologyCR(){		 
+	return hydro_CR;		 
+}		 
+/*}}}*/			 
+/*FUNCTION Matpar::GetHydrologyN {{{*/			 
+IssmDouble Matpar::GetHydrologyN(){		 
+	return hydro_n;			 
+}		 
+/*}}}*/ 
+/*FUNCTION Matpar::TMeltingPoint {{{*/
+IssmDouble Matpar::TMeltingPoint(IssmDouble pressure){
+	return meltingpoint-beta*pressure;
+}
+/*}}}*/
+/*FUNCTION Matpar::PureIceEnthalpy{{{*/
+IssmDouble Matpar::PureIceEnthalpy(IssmDouble pressure){
+	return heatcapacity*(TMeltingPoint(pressure)-referencetemperature);
+}
+/*}}}*/
+/*FUNCTION Matpar::GetEnthalpyDiffusionParameter{{{*/
+IssmDouble Matpar::GetEnthalpyDiffusionParameter(IssmDouble enthalpy,IssmDouble pressure){
+	if(enthalpy* vector,int input_enum){return;}
+		void       GetViscosity2d(IssmDouble* pviscosity, IssmDouble* pepsilon){_error_("not supported");};
+		void       GetViscosity3d(IssmDouble* pviscosity3d, IssmDouble* pepsilon){_error_("not supported");};
+		void       GetViscosity3dStokes(IssmDouble* pviscosity3d, IssmDouble* epsilon){_error_("not supported");};
+		void       GetViscosityComplement(IssmDouble* pviscosity_complement, IssmDouble* pepsilon){_error_("not supported");};
+		void       GetViscosityZComplement(IssmDouble* pviscosity_complement, IssmDouble* pepsilon){_error_("not supported");};
+		void       GetViscosityDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* pepsilon){_error_("not supported");};
+		void       GetViscosity2dDerivativeEpsSquare(IssmDouble* pmu_prime, IssmDouble* pepsilon){_error_("not supported");};
+		IssmDouble GetA(){_error_("not supported");};
+		IssmDouble GetB(){_error_("not supported");};
+		IssmDouble GetBbar(){_error_("not supported");};
+		IssmDouble GetN(){_error_("not supported");};
+		IssmDouble GetZ(){_error_("not supported");};
+		IssmDouble GetZbar(){_error_("not supported");};
+		/*}}}*/
+		/*Numerics: {{{*/
+		IssmDouble GetG();
+		IssmDouble GetRhoIce();
+		IssmDouble GetRhoWater();
+		IssmDouble GetRhoFreshwater();
+		IssmDouble GetMuWater();
+		IssmDouble GetMixedLayerCapacity();
+		IssmDouble GetThermalExchangeVelocity();
+		IssmDouble GetHeatCapacity();
+		IssmDouble GetThermalConductivity();
+		IssmDouble GetLatentHeat();
+		IssmDouble GetBeta();
+		IssmDouble GetMeltingPoint();
+		IssmDouble GetReferenceTemperature();
+		IssmDouble GetKn();
+		IssmDouble GetHydrologyP();
+		IssmDouble GetHydrologyQ();
+		IssmDouble GetHydrologyCR();
+		IssmDouble GetHydrologyN();
+		IssmDouble TMeltingPoint(IssmDouble pressure);
+		IssmDouble PureIceEnthalpy(IssmDouble pressure);
+		IssmDouble GetEnthalpyDiffusionParameter(IssmDouble enthalpy,IssmDouble pressure);
+		void   EnthalpyToThermal(IssmDouble* ptemperature,IssmDouble* pwaterfraction,IssmDouble enthalpy,IssmDouble pressure);
+		void   ThermalToEnthalpy(IssmDouble* penthalpy,IssmDouble temperature,IssmDouble waterfraction,IssmDouble pressure);
+		/*}}}*/
+
+};
+
+#endif  /* _MATPAR_H_ */
Index: /issm/trunk/src/c/classes/objects/Node.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Node.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Node.cpp	(revision 13395)
@@ -0,0 +1,1012 @@
+/*!\file Node.c
+ * \brief: implementation of the Node object
+ */
+
+/*Include files: {{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "./objects.h"
+#include "../../Container/Container.h"
+#include "../../EnumDefinitions/EnumDefinitions.h"
+#include "../../shared/shared.h"
+#include "../../include/include.h"
+#include "../../modules/modules.h"
+/*}}}*/
+
+/*Node constructors and destructors:*/
+/*FUNCTION Node::Node() default constructor {{{*/
+Node::Node(){
+		 this->inputs=NULL;
+		 this->hvertex=NULL;
+		 return;
+}
+/*}}}*/
+/*FUNCTION Node::Node(int node_id,int node_sid,int vertex_id,int io_index, IoModel* iomodel,int analysis_type) {{{*/
+Node::Node(int node_id,int node_sid,int vertex_id,int io_index, IoModel* iomodel,int analysis_type){
+
+	/*Intermediary*/
+	int k,l;
+	int gsize;
+	int dim;
+
+	/*Fetch parameters: */
+	iomodel->Constant(&dim,MeshDimensionEnum);
+
+	/*id: */
+	this->id=node_id; 
+	this->sid=node_sid; 
+	this->analysis_type=analysis_type;
+
+	/*Initialize coord_system: Identity matrix by default*/
+	for(k=0;k<3;k++) for(l=0;l<3;l++) this->coord_system[k][l]=0.0;
+	for(k=0;k<3;k++) this->coord_system[k][k]=1.0;
+
+	/*indexing:*/
+	DistributeNumDofs(&this->indexing,analysis_type,iomodel->Data(FlowequationVertexEquationEnum)+io_index); //number of dofs per node
+	gsize=this->indexing.gsize;
+
+	/*Hooks*/
+	this->hvertex=new Hook(&vertex_id,1); //node id is the same as the vertex id, continuous galerkin!
+
+	//intialize inputs, and add as many inputs per element as requested: 
+	this->inputs=new Inputs();
+	if (iomodel->Data(MeshVertexonbedEnum))
+	 this->inputs->AddInput(new BoolInput(MeshVertexonbedEnum,reCast(iomodel->Data(MeshVertexonbedEnum)[io_index])));
+	if (iomodel->Data(MeshVertexonsurfaceEnum))
+	 this->inputs->AddInput(new BoolInput(MeshVertexonsurfaceEnum,reCast(iomodel->Data(MeshVertexonsurfaceEnum)[io_index])));
+	if (iomodel->Data(MaskVertexonfloatingiceEnum))
+	 this->inputs->AddInput(new BoolInput(MaskVertexonfloatingiceEnum,reCast(iomodel->Data(MaskVertexonfloatingiceEnum)[io_index])));
+	if (iomodel->Data(MaskVertexongroundediceEnum))
+	  this->inputs->AddInput(new BoolInput(MaskVertexongroundediceEnum,reCast(iomodel->Data(MaskVertexongroundediceEnum)[io_index])));
+	if (analysis_type==DiagnosticHorizAnalysisEnum)
+	 this->inputs->AddInput(new IntInput(ApproximationEnum,reCast(iomodel->Data(FlowequationVertexEquationEnum)[io_index])));
+	/*set single point constraints: */
+
+	/*spc all nodes on water*/
+	if (!iomodel->Data(MaskVertexonwaterEnum)) _error_("iomodel->nodeonwater is NULL");
+	if (reCast(iomodel->Data(MaskVertexonwaterEnum)[io_index])){
+		for(k=1;k<=gsize;k++){
+			this->FreezeDof(k);
+		}
+	}
+
+	/*Diagnostic Horiz*/
+	#ifdef _HAVE_DIAGNOSTIC_
+	if (analysis_type==DiagnosticHorizAnalysisEnum){
+
+		/*Coordinate system provided, convert to coord_system matrix*/
+		_assert_(iomodel->Data(DiagnosticReferentialEnum)); 
+		XZvectorsToCoordinateSystem(&this->coord_system[0][0],iomodel->Data(DiagnosticReferentialEnum)+io_index*6);
+
+		if (dim==3){
+			/*We have a  3d mesh, we may have collapsed elements, hence dead nodes. Freeze them out: */
+			_assert_(iomodel->Data(MeshVertexonbedEnum)); 
+			_assert_(iomodel->Data(FlowequationVertexEquationEnum));
+			if (iomodel->Data(FlowequationVertexEquationEnum)[io_index]==MacAyealApproximationEnum && !reCast(iomodel->Data(MeshVertexonbedEnum)[io_index])){
+				for(k=1;k<=gsize;k++) this->FreezeDof(k);
+			}
+			if (iomodel->Data(FlowequationVertexEquationEnum)[io_index]==L1L2ApproximationEnum && !reCast(iomodel->Data(MeshVertexonbedEnum)[io_index])){
+				for(k=1;k<=gsize;k++) this->FreezeDof(k);
+			}
+			if (iomodel->Data(FlowequationVertexEquationEnum)[io_index]==MacAyealPattynApproximationEnum && reCast(iomodel->Data(FlowequationBordermacayealEnum)[io_index])){
+				if(!reCast(iomodel->Data(MeshVertexonbedEnum)[io_index])){
+					for(k=1;k<=gsize;k++) this->FreezeDof(k);
+				}
+			}
+			if (iomodel->Data(FlowequationVertexEquationEnum)[io_index]==MacAyealStokesApproximationEnum && reCast(iomodel->Data(FlowequationBordermacayealEnum)[io_index])){
+				if(!reCast(iomodel->Data(MeshVertexonbedEnum)[io_index])){
+					for(k=1;k<=2;k++) this->FreezeDof(k);
+				}
+			}
+		}
+		/*spc all nodes on hutter*/
+		if (iomodel->Data(FlowequationVertexEquationEnum)[io_index]==HutterApproximationEnum){
+			for(k=1;k<=gsize;k++){
+				this->FreezeDof(k);
+			}
+		}
+	}
+	#endif
+
+	/*Diagnostic Hutter*/
+	if (analysis_type==DiagnosticHutterAnalysisEnum){
+		_assert_(iomodel->Data(FlowequationVertexEquationEnum));
+		/*Constrain all nodes that are not Hutter*/
+		if (reCast(iomodel->Data(FlowequationVertexEquationEnum)[io_index])!=HutterApproximationEnum){
+			for(k=1;k<=gsize;k++){
+				this->FreezeDof(k);
+			}
+		}
+	}
+
+	/*Prognostic/ Melting/ Slopecompute/ Balancethickness*/
+	if (
+				analysis_type==PrognosticAnalysisEnum || 
+				analysis_type==MeltingAnalysisEnum || 
+				analysis_type==BedSlopeAnalysisEnum || 
+				analysis_type==SurfaceSlopeAnalysisEnum || 
+				analysis_type==BalancethicknessAnalysisEnum
+				){
+		if (dim==3){
+			/*On a 3d mesh, we may have collapsed elements, hence dead nodes. Freeze them out: */
+			_assert_(iomodel->Data(MeshVertexonbedEnum));
+			if (!(reCast(iomodel->Data(MeshVertexonbedEnum)[io_index]))){
+				for(k=1;k<=gsize;k++){
+					this->FreezeDof(k);
+				}
+			}
+		}
+	}
+
+}
+/*}}}*/
+/*FUNCTION Node::~Node(){{{*/
+Node::~Node(){
+	delete inputs;
+	delete hvertex;
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION Node::Echo{{{*/
+void Node::Echo(void){
+
+	_printLine_("Node:");
+	_printLine_("   id: " << id);
+	_printLine_("   sid: " << sid);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	indexing.Echo();
+	_printLine_("   hvertex:     not displayed");
+	_printLine_("   inputs:      " << inputs);
+
+
+}
+/*}}}*/
+/*FUNCTION Node::DeepEcho{{{*/
+void Node::DeepEcho(void){
+
+	_printLine_("Node:");
+	_printLine_("   id: " << id);
+	_printLine_("   sid: " << sid);
+	_printLine_("   analysis_type: " << EnumToStringx(analysis_type));
+	indexing.DeepEcho();
+	_printLine_("Vertex:");
+	hvertex->DeepEcho();
+	_printLine_("   inputs");
+
+
+}
+/*}}}*/
+/*FUNCTION Node::Id{{{*/
+int    Node::Id(void){ return id; }
+/*}}}*/
+/*FUNCTION Node::MyRank{{{*/
+int    Node::MyRank(void){ 
+	extern int my_rank;
+
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION Node::ObjectEnum{{{*/
+int Node::ObjectEnum(void){
+
+	return NodeEnum;
+
+}
+/*}}}*/
+
+/*Node management:*/
+/*FUNCTION Node::Configure {{{*/
+void  Node::Configure(DataSet* nodesin,Vertices* verticesin){
+
+	/*Take care of hooking up all objects for this element, ie links the objects in the hooks to their respective 
+	 * datasets, using internal ids and off_sets hidden in hooks: */
+	hvertex->configure(verticesin);
+
+}/*}}}*/
+/*FUNCTION Node::SetCurrentConfiguration {{{*/
+void  Node::SetCurrentConfiguration(DataSet* nodesin,Vertices* verticesin){
+
+}/*}}}*/
+/*FUNCTION Node::GetDof {{{*/
+int   Node::GetDof(int dofindex,int setenum){
+
+	if(setenum==GsetEnum){
+		_assert_(dofindex>=0 && dofindex=0 && dofindex=0 && dofindexhvertex->delivers();
+
+	return vertex->dof;
+}
+/*}}}*/
+/*FUNCTION Node::GetDofList{{{*/
+void  Node::GetDofList(int* outdoflist,int approximation_enum,int setenum){
+	int i;
+	int count=0;
+	int count2=0;
+		
+	if(approximation_enum==NoneApproximationEnum){
+		if(setenum==GsetEnum)for(i=0;iindexing.gsize;i++) outdoflist[i]=indexing.gdoflist[i];
+		if(setenum==FsetEnum)for(i=0;iindexing.fsize;i++) outdoflist[i]=indexing.fdoflist[i];
+		if(setenum==SsetEnum)for(i=0;iindexing.ssize;i++) outdoflist[i]=indexing.sdoflist[i];
+	}
+	else{
+
+		if(setenum==GsetEnum){
+			if(indexing.doftype){
+				count=0;
+				for(i=0;iindexing.gsize;i++){
+					if(indexing.doftype[i]==approximation_enum){
+						outdoflist[count]=indexing.gdoflist[i];
+						count++;
+					}
+				}
+				_assert_(count); //at least one dof should be the approximation requested
+			}
+			else for(i=0;iindexing.gsize;i++) outdoflist[i]=indexing.gdoflist[i];
+		}
+		else if(setenum==FsetEnum){
+			if(indexing.doftype){
+				count=0;
+				count2=0;
+				for(i=0;iindexing.gsize;i++){
+					if(indexing.f_set[i]){
+						if(indexing.doftype[i]==approximation_enum){
+							outdoflist[count]=indexing.fdoflist[count2];
+							count++;
+						}
+						count2++;
+					}
+				}
+			}
+			else for(i=0;iindexing.fsize;i++) outdoflist[i]=indexing.fdoflist[i];
+		}
+		else if(setenum==SsetEnum){
+			if(indexing.doftype){
+				count=0;
+				count2=0;
+				for(i=0;iindexing.gsize;i++){
+					if(indexing.s_set[i]){
+						if(indexing.doftype[i]==approximation_enum){
+							outdoflist[count]=indexing.sdoflist[count2];
+							count++;
+						}
+						count2++;
+					}
+				}
+			}
+			else for(i=0;iindexing.ssize;i++) outdoflist[i]=indexing.sdoflist[i];
+		}
+		else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+	}
+}
+/*}}}*/
+/*FUNCTION Node::GetSidList{{{*/
+int  Node::GetSidList(void){
+
+	Vertex* vertex=NULL;
+
+	vertex=(Vertex*)this->hvertex->delivers();
+
+	return vertex->sid;
+}
+/*}}}*/
+/*FUNCTION Node::GetLocalDofList{{{*/
+void  Node::GetLocalDofList(int* outdoflist,int approximation_enum,int setenum){
+	int i;
+	int count=0;
+	int count2=0;
+		
+	if(approximation_enum==NoneApproximationEnum){
+		if(setenum==GsetEnum)for(i=0;iindexing.gsize;i++) outdoflist[i]=i;
+		else if(setenum==FsetEnum){
+			count=0;
+			for(i=0;iindexing.gsize;i++){
+				if(indexing.f_set[i]){
+					outdoflist[count]=i;
+					count++;
+				}
+			}
+		}
+		else if(setenum==SsetEnum){
+			count=0;
+			for(i=0;iindexing.gsize;i++){
+				if(indexing.s_set[i]){
+					outdoflist[count]=i;
+					count++;
+				}
+			}
+		}
+		else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+	}
+	else{
+
+		if(setenum==GsetEnum){
+			if(indexing.doftype){
+				count=0;
+				for(i=0;iindexing.gsize;i++){
+					if(indexing.doftype[i]==approximation_enum){
+						outdoflist[count]=count;
+						count++;
+					}
+				}
+				_assert_(count);
+			}
+			else for(i=0;iindexing.gsize;i++) outdoflist[i]=i;
+		}
+		else if(setenum==FsetEnum){
+
+			if(indexing.doftype){
+				count=0;
+				count2=0;
+				for(i=0;iindexing.gsize;i++){
+					if(indexing.doftype[i]==approximation_enum){
+						if(indexing.f_set[i]){
+							outdoflist[count]=count2;
+							count++;
+						}
+						count2++;
+					}
+				}
+				_assert_(count2);
+			}
+			else{
+
+				count=0;
+				for(i=0;iindexing.gsize;i++){
+					if(indexing.f_set[i]){
+						outdoflist[count]=i;
+						count++;
+					}
+				}
+			}
+		}
+		else if(setenum==SsetEnum){
+			if(indexing.doftype){
+				count=0;
+				count2=0;
+				for(i=0;iindexing.gsize;i++){
+					if(indexing.doftype[i]==approximation_enum){
+						if(indexing.s_set[i]){
+							outdoflist[count]=count2;
+							count++;
+						}
+						count2++;
+					}
+				}
+				_assert_(count2);
+			}
+			else{
+				count=0;
+				for(i=0;iindexing.gsize;i++){
+					if(indexing.s_set[i]){
+						outdoflist[count]=i;
+						count++;
+					}
+				}
+			}
+		}
+		else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+	}
+}
+/*}}}*/
+/*FUNCTION Node::Sid{{{*/
+int    Node::Sid(void){ return sid; }
+/*}}}*/
+/*FUNCTION Node::GetVertexId {{{*/
+int   Node::GetVertexId(void){
+
+	Vertex*  vertex=NULL;
+
+	vertex=(Vertex*)hvertex->delivers();
+	return vertex->id;
+}
+/*}}}*/
+/*FUNCTION Node::GetVertexDof {{{*/
+int   Node::GetVertexDof(void){
+
+	Vertex*  vertex=NULL;
+
+	vertex=(Vertex*)hvertex->delivers();
+	return vertex->dof;
+}
+/*}}}*/
+#ifdef _HAVE_DIAGNOSTIC_
+/*FUNCTION Node::GetCoordinateSystem{{{*/
+void Node::GetCoordinateSystem(IssmDouble* coord_system_out){
+
+	/*Copy coord_system*/
+	for(int k=0;k<3;k++) for(int l=0;l<3;l++) coord_system_out[3*k+l]=this->coord_system[k][l];
+
+}
+/*}}}*/
+#endif
+/*FUNCTION Node::SetVertexDof {{{*/
+void   Node::SetVertexDof(int in_dof){
+
+	Vertex*  vertex=NULL;
+
+	vertex=(Vertex*)hvertex->delivers();
+	vertex->dof=in_dof;
+
+}
+/*}}}*/
+/*FUNCTION Node::InAnalysis{{{*/
+bool Node::InAnalysis(int in_analysis_type){
+	if (in_analysis_type==this->analysis_type) return true;
+	else return false;
+}
+/*}}}*/
+
+/*Node numerics:*/
+/*FUNCTION Node::ApplyConstraints{{{*/
+void  Node::ApplyConstraint(int dof,IssmDouble value){
+
+	int index;
+
+	/*Dof should be added in the s set, describing which 
+	 * dofs are constrained to a certain value (dirichlet boundary condition*/
+	DofInSSet(dof-1);
+	this->indexing.svalues[dof-1]=value;
+}
+/*}}}*/
+/*FUNCTION Node::RelaxConstraint{{{*/
+void  Node::RelaxConstraint(int dof){
+
+	/*Dof should be added to the f-set, and taken out of the s-set:*/
+	DofInFSet(dof-1);
+	this->indexing.svalues[dof-1]=NAN;
+}
+/*}}}*/
+/*FUNCTION Node::CreateVecSets {{{*/
+void  Node::CreateVecSets(Vector* pv_g,Vector* pv_f,Vector* pv_s){
+
+	IssmDouble gvalue=1.0; //all nodes are in the g set;
+	IssmDouble value;
+
+	int i;
+
+	for(i=0;iindexing.gsize;i++){
+
+		/*g set: */
+		pv_g->SetValue(indexing.gdoflist[i],gvalue,INS_VAL);
+		
+		/*f set: */
+		value=(IssmDouble)this->indexing.f_set[i];
+		pv_f->SetValue(indexing.gdoflist[i],value,INS_VAL);
+
+		/*s set: */
+		value=(IssmDouble)this->indexing.s_set[i];
+		pv_s->SetValue(indexing.gdoflist[i],value,INS_VAL);
+
+	}
+
+
+}
+/*}}}*/
+/*FUNCTION Node::CreateNodalConstraints{{{*/
+void  Node::CreateNodalConstraints(Vector* ys){
+
+	int i;
+	IssmDouble* values=NULL;
+	int count;
+
+	/*Recover values for s set and plug them in constraints vector: */
+	if(this->indexing.ssize){
+		values=xNew(this->indexing.ssize);
+		count=0;
+		for(i=0;iindexing.gsize;i++){
+			if(this->indexing.s_set[i]){
+				values[count]=this->indexing.svalues[i];
+				_assert_(!xIsNan(values[count]));
+				count++;
+			}
+		}
+		
+		/*Add values into constraint vector: */
+		ys->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INS_VAL);
+	}
+
+	/*Free ressources:*/
+	xDelete(values);
+
+
+}
+/*}}}*/
+/*FUNCTION Node::DofInSSet {{{*/
+void  Node::DofInSSet(int dof){
+
+	/*Put dof for this node into the s set (ie, this dof will be constrained 
+	 * to a fixed value during computations. */
+
+	this->indexing.f_set[dof]=0; //n splits into f (for which we solve) and s (single point constraints)
+	this->indexing.s_set[dof]=1;
+}
+/*}}}*/
+/*FUNCTION Node::DofInFSet {{{*/
+void  Node::DofInFSet(int dof){
+
+	/*Put dof for this node into the f set (ie, this dof will NOT be constrained 
+	 * to a fixed value during computations. */
+
+	this->indexing.f_set[dof]=1; 
+	this->indexing.s_set[dof]=0;
+}
+/*}}}*/
+/*FUNCTION Node::FreezeDof{{{*/
+void  Node::FreezeDof(int dof){
+	
+	DofInSSet(dof-1); //with 0 displacement for this dof.
+
+}
+/*}}}*/
+/*FUNCTION Node::GetApproximation {{{*/
+int   Node::GetApproximation(){
+
+	int approximation;
+
+	/*recover parameters: */
+	inputs->GetInputValue(&approximation,ApproximationEnum);
+
+	return approximation;
+}
+/*}}}*/
+/*FUNCTION Node::GetConnectivity {{{*/
+int Node::GetConnectivity(){
+
+	Vertex*  vertex=NULL;
+	vertex=(Vertex*)hvertex->delivers();
+	return vertex->connectivity;
+}
+/*}}}*/
+/*FUNCTION Node::GetNumberOfDofs{{{*/
+int   Node::GetNumberOfDofs(int approximation_enum,int setenum){
+
+	/*Get number of degrees of freedom in a node, for a certain set (g,f or s-set)
+	 *and for a certain approximation type: */
+	
+	int i;
+	int numdofs=0;
+
+	if(approximation_enum==NoneApproximationEnum){
+		if (setenum==GsetEnum) numdofs=this->indexing.gsize;
+		else if (setenum==FsetEnum) numdofs=this->indexing.fsize;
+		else if (setenum==SsetEnum) numdofs=this->indexing.ssize;
+		else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+	}
+	else{
+		if(setenum==GsetEnum){
+			if(this->indexing.doftype){
+				numdofs=0;
+				for(i=0;iindexing.gsize;i++){
+					if(this->indexing.doftype[i]==approximation_enum) numdofs++;
+				}
+			}
+			else numdofs=this->indexing.gsize;
+		}
+		else if (setenum==FsetEnum){
+			if(this->indexing.doftype){
+				numdofs=0;
+				for(i=0;iindexing.gsize;i++){
+					if((this->indexing.doftype[i]==approximation_enum) && (this->indexing.f_set[i])) numdofs++;
+				}
+			}
+			else numdofs=this->indexing.fsize;
+		}
+		else if (setenum==SsetEnum){
+			if(this->indexing.doftype){
+				numdofs=0;
+				for(i=0;iindexing.gsize;i++){
+					if((this->indexing.doftype[i]==approximation_enum) && (this->indexing.s_set[i])) numdofs++;
+				}
+			}
+			else numdofs=this->indexing.ssize;
+		}
+		else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+	}
+	return numdofs;
+}
+/*}}}*/
+/*FUNCTION Node::GetSigma {{{*/
+IssmDouble Node::GetSigma(){
+	Vertex* vertex=NULL;
+
+	vertex=(Vertex*)hvertex->delivers();
+	return vertex->sigma;
+}
+/*}}}*/
+/*FUNCTION Node::GetX {{{*/
+IssmDouble Node::GetX(){
+	Vertex* vertex=NULL;
+
+	vertex=(Vertex*)hvertex->delivers();
+	return vertex->x;
+}
+/*}}}*/
+/*FUNCTION Node::GetY {{{*/
+IssmDouble Node::GetY(){
+	Vertex* vertex=NULL;
+
+	vertex=(Vertex*)hvertex->delivers();
+	return vertex->y;
+}
+/*}}}*/
+/*FUNCTION Node::GetZ {{{*/
+IssmDouble Node::GetZ(){
+	Vertex* vertex=NULL;
+
+	vertex=(Vertex*)hvertex->delivers();
+	return vertex->z;
+}
+/*}}}*/
+/*FUNCTION Node::IsClone {{{*/
+int   Node::IsClone(){
+	
+	return indexing.clone;
+
+}
+/*}}}*/
+/*FUNCTION Node::IsOnBed {{{*/
+int   Node::IsOnBed(){
+
+	bool onbed;
+
+	/*recover parameters: */
+	inputs->GetInputValue(&onbed,MeshVertexonbedEnum);
+
+	return onbed;
+}
+/*}}}*/
+/*FUNCTION Node::IsGrounded {{{*/
+int   Node::IsGrounded(){
+
+	bool onsheet;
+
+	/*recover parameters: */
+	inputs->GetInputValue(&onsheet,MaskVertexongroundediceEnum);
+
+	return onsheet;
+}		
+/*}}}*/
+/*FUNCTION Node::IsFloating {{{*/
+int   Node::IsFloating(){
+	
+	bool onshelf;
+
+	/*recover parameters: */
+	inputs->GetInputValue(&onshelf,MaskVertexonfloatingiceEnum);
+
+	return onshelf;
+}
+/*}}}*/
+/*FUNCTION Node::IsOnSurface {{{*/
+int   Node::IsOnSurface(){
+
+	bool onsurface;
+
+	/*recover parameters: */
+	inputs->GetInputValue(&onsurface,MeshVertexonsurfaceEnum);
+
+	return onsurface;
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromVector(IssmDouble* vector, int name, int type){{{*/
+void  Node::InputUpdateFromVector(IssmDouble* vector, int name, int type){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromVector(int* vector, int name, int type){{{*/
+void  Node::InputUpdateFromVector(int* vector, int name, int type){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromVector(bool* vector, int name, int type){{{*/
+void  Node::InputUpdateFromVector(bool* vector, int name, int type){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){{{*/
+void  Node::InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type){{{*/
+void  Node::InputUpdateFromMatrixDakota(IssmDouble* matrix, int nrows, int ncols, int name, int type){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromVectorDakota(int* vector, int name, int type){{{*/
+void  Node::InputUpdateFromVectorDakota(int* vector, int name, int type){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromVectorDakota(bool* vector, int name, int type){{{*/
+void  Node::InputUpdateFromVectorDakota(bool* vector, int name, int type){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromConstant(IssmDouble constant, int name){{{*/
+void  Node::InputUpdateFromConstant(IssmDouble constant, int name){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromConstant(int constant, int name){{{*/
+void  Node::InputUpdateFromConstant(int constant, int name){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::InputUpdateFromConstant(bool constant, int name){{{*/
+void  Node::InputUpdateFromConstant(bool constant, int name){
+
+	/*Nothing updated yet*/
+}
+/*}}}*/
+/*FUNCTION Node::UpdateSpcs {{{*/
+void   Node::UpdateSpcs(IssmDouble* ys){
+
+	int     count=0;
+	int     i;
+
+	count=0;
+	for(i=0;iindexing.gsize;i++){
+		if(this->indexing.s_set[i]){
+			this->indexing.svalues[i]=ys[this->indexing.sdoflist[count]];
+			count++;
+		}
+	}
+}
+/*}}}*/
+/*FUNCTION Node::VecMerge {{{*/
+void   Node::VecMerge(Vector* ug, IssmDouble* vector_serial,int setenum){
+
+	IssmDouble* values=NULL;
+	int*    indices=NULL;
+	int     count=0;
+	int     i;
+
+	if(setenum==FsetEnum){
+		if(this->indexing.fsize){
+			indices=xNew(this->indexing.fsize);
+ 			values=xNew(this->indexing.fsize);
+
+			for(i=0;iindexing.gsize;i++){
+				if(this->indexing.f_set[i]){
+					_assert_(vector_serial);
+					values[count]=vector_serial[this->indexing.fdoflist[count]];
+					indices[count]=this->indexing.gdoflist[i];
+					count++;
+				}
+			}
+
+			/*Add values into ug: */
+			ug->SetValues(this->indexing.fsize,indices,values,INS_VAL);
+		}
+	}
+	else if(setenum==SsetEnum){
+		if(this->indexing.ssize){
+			indices=xNew(this->indexing.ssize);
+			values=xNew(this->indexing.ssize);
+
+			for(i=0;iindexing.gsize;i++){
+				if(this->indexing.s_set[i]){
+					_assert_(vector_serial);
+					values[count]=vector_serial[this->indexing.sdoflist[count]];
+					indices[count]=this->indexing.gdoflist[i];
+					count++;
+				}
+			}
+
+			/*Add values into ug: */
+			ug->SetValues(this->indexing.ssize,indices,values,INS_VAL);
+		}
+	}
+	else _error_("VecMerge can only merge from the s or f-set onto the g-set!");
+
+	/*Free ressources:*/
+	xDelete(values);
+	xDelete(indices);
+}
+/*}}}*/
+/*FUNCTION Node::VecReduce {{{*/
+void   Node::VecReduce(Vector* vector, IssmDouble* ug_serial,int setenum){
+
+	IssmDouble* values=NULL;
+	int     count=0;
+	int     i;
+
+	if(setenum==FsetEnum){
+		if(this->indexing.fsize){
+ 			values=xNew(this->indexing.fsize);
+
+			for(i=0;iindexing.gsize;i++){
+				if(this->indexing.f_set[i]){
+					_assert_(ug_serial);
+					values[count]=ug_serial[this->indexing.gdoflist[i]];
+					count++;
+				}
+			}
+
+			/*Add values into ug: */
+			vector->SetValues(this->indexing.fsize,this->indexing.fdoflist,values,INS_VAL);
+		}
+	}
+	else if(setenum==SsetEnum){
+		if(this->indexing.ssize){
+			values=xNew(this->indexing.ssize);
+
+			for(i=0;iindexing.gsize;i++){
+				if(this->indexing.s_set[i]){
+					_assert_(ug_serial);
+					values[count]=ug_serial[this->indexing.gdoflist[i]];
+					count++;
+				}
+			}
+
+			/*Add values into ug: */
+			vector->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INS_VAL);
+		}
+	}
+	else _error_("VecReduce can only merge from the s or f-set onto the g-set!");
+
+	/*Free ressources:*/
+	xDelete(values);
+}
+/*}}}*/
+
+/* DofObject routines:*/
+/*FUNCTION Node::DistributeDofs{{{*/
+void  Node::DistributeDofs(int* pdofcount,int setenum){
+
+	int i;
+	extern int my_rank;
+	int dofcount;
+
+	dofcount=*pdofcount;
+
+	/*Initialize: */
+	if(setenum==FsetEnum) this->indexing.InitSet(setenum);
+	if(setenum==SsetEnum) this->indexing.InitSet(setenum);
+	
+		
+	/*For clone nodfs, don't distribute dofs, we will get them from another cpu in UpdateCloneDofs!*/
+	if(indexing.clone){
+		return;
+	}
+
+	/*This node should distribute dofs for setenum set (eg, f_set or s_set), go ahead: */
+
+	if(setenum==GsetEnum){
+		for(i=0;iindexing.gsize;i++){
+			indexing.gdoflist[i]=dofcount+i;
+		}
+		dofcount+=this->indexing.gsize;
+	}
+	else if(setenum==FsetEnum){
+		for(i=0;iindexing.fsize;i++){
+			indexing.fdoflist[i]=dofcount+i;
+		}
+		dofcount+=this->indexing.fsize;
+	}
+	else if(setenum==SsetEnum){
+		for(i=0;iindexing.ssize;i++){
+			indexing.sdoflist[i]=dofcount+i;
+		}
+		dofcount+=this->indexing.ssize;
+	}
+	else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+
+
+	/*Assign output pointers: */
+	*pdofcount=dofcount;
+
+}
+/*}}}*/
+/*FUNCTION Node::Off_setDofs{{{*/
+void  Node::OffsetDofs(int dofcount,int setenum){
+	
+	int i;
+	extern int my_rank;
+	
+	if(indexing.clone){
+		/*This node is a clone, don't off_set the dofs!: */
+		return;
+	}
+
+	/*This node should off_set the dofs, go ahead: */
+	if(setenum==GsetEnum){
+		for(i=0;iindexing.gsize;i++) indexing.gdoflist[i]+=dofcount;
+	}
+	else if(setenum==FsetEnum){
+		for(i=0;iindexing.fsize;i++) indexing.fdoflist[i]+=dofcount;
+	}
+	else if(setenum==SsetEnum){
+		for(i=0;iindexing.ssize;i++) indexing.sdoflist[i]+=dofcount;
+	}
+	else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+}
+/*}}}*/
+/*FUNCTION Node::ShowTrueDofs{{{*/
+void  Node::ShowTrueDofs(int* truedofs, int ncols,int setenum){
+
+	int j;
+	extern int my_rank;
+	
+	/*Are we a clone? : */
+	if(indexing.clone)return;
+
+	/*Ok, we are not a clone, just plug our dofs into truedofs: */
+	if(setenum==GsetEnum)for(j=0;jindexing.gsize;j++)  *(truedofs+ncols*sid+j)=indexing.gdoflist[j];
+	else if(setenum==FsetEnum)for(j=0;jindexing.fsize;j++)  *(truedofs+ncols*sid+j)=indexing.fdoflist[j];
+	else if(setenum==SsetEnum)for(j=0;jindexing.ssize;j++)  *(truedofs+ncols*sid+j)=indexing.sdoflist[j];
+	else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+
+}
+/*}}}*/
+/*FUNCTION Node::UpdateCloneDofs{{{*/
+void  Node::UpdateCloneDofs(int* alltruedofs,int ncols,int setenum){
+
+	int j;
+	extern int my_rank;
+	
+	/*If we are not a clone, don't update, we already have dofs!: */
+	if(indexing.clone==0)return;
+
+
+	/*Ok, we are a clone node, but we did not create the dofs for this node.
+	 *      * Therefore, our doflist is garbage right now. Go pick it up in the alltruedofs: */
+	if(setenum==GsetEnum)for(j=0;jindexing.gsize;j++) indexing.gdoflist[j]=*(alltruedofs+ncols*sid+j);
+	else if(setenum==FsetEnum)for(j=0;jindexing.fsize;j++) indexing.fdoflist[j]=*(alltruedofs+ncols*sid+j);
+	else if(setenum==SsetEnum)for(j=0;jindexing.ssize;j++) indexing.sdoflist[j]=*(alltruedofs+ncols*sid+j);
+	else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
+
+}
+/*}}}*/
+/*FUNCTION Node::SetClone {{{*/
+void  Node::SetClone(int* minranks){
+
+	extern int my_rank;
+
+	if (minranks[sid]==my_rank){
+		indexing.clone=0;
+	}
+	else{
+		/*!there is a cpu with lower rank that has the same node, 
+		therefore, I am a clone*/
+		indexing.clone=1; 	
+	}
+
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Node.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Node.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Node.h	(revision 13395)
@@ -0,0 +1,113 @@
+/*!\file Node.h
+ * \brief: header file for node object
+ */
+
+#ifndef _NODE_H_
+#define _NODE_H_
+
+/*Headers:*/
+/*{{{*/
+#include "./Object.h"
+#include "../../shared/shared.h"
+#include "../DofIndexing.h"
+class  Inputs;
+class  Hook;
+class  IoModel;
+class  DataSet;
+class  Vertices;
+template  class  Vector;
+template  class  Matrix;
+#include "../Update.h"
+/*}}}*/
+
+class Node: public Object ,public Update{
+
+	public: 
+
+		int	    id;  //unique arbitrary id.
+		int     sid; //sid for "serial" id, ie the rank of this node in the nodes dataset, if the dataset was serial on 1 cpu.
+				
+		DofIndexing    indexing;
+		Hook*          hvertex;
+		Inputs*        inputs; //properties of this node
+		int            analysis_type;
+		IssmDouble         coord_system[3][3];
+
+		/*Node constructors, destructors {{{*/
+		Node();
+		Node(int node_id,int node_sid, int vertex_id,int io_index, IoModel* iomodel,int analysis_type);
+		~Node();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy(){_error_("Not implemented yet (similar to Elements)");};
+		/*}}}*/
+		/*Update virtual functions definitions: {{{*/
+		
+		void  InputUpdateFromVector(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVector(int* vector, int name, int type);
+		void  InputUpdateFromVector(bool* vector, int name, int type);
+		void  InputUpdateFromMatrixDakota(IssmDouble* matrix,int nrows, int ncols, int name, int type);
+		void  InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(int* vector, int name, int type);
+		void  InputUpdateFromVectorDakota(bool* vector, int name, int type);
+		void  InputUpdateFromConstant(IssmDouble constant, int name);
+		void  InputUpdateFromConstant(int constant, int name);
+		void  InputUpdateFromConstant(bool constant, int name);
+		void  InputUpdateFromSolution(IssmDouble* solution){_error_("Not implemented yet!");}
+		void  InputUpdateFromIoModel(int index, IoModel* iomodel){_error_("Not implemented yet!");}
+		/*}}}*/
+		/*Node numerical routines {{{*/
+		void   Configure(DataSet* nodes,Vertices* vertices);
+		void   CreateNodalConstraints(Vector* ys);
+		void   SetCurrentConfiguration(DataSet* nodes,Vertices* vertices);
+		int    Sid(void); 
+		int    GetVertexDof(void);
+		int    GetVertexId(void);
+#ifdef _HAVE_DIAGNOSTIC_
+		void   GetCoordinateSystem(IssmDouble* coord_system_out);
+#endif
+		void   SetVertexDof(int in_dof);
+		bool   InAnalysis(int analysis_type);
+		int    GetApproximation();
+		int    GetNumberOfDofs(int approximation_enum,int setenum);
+		int    IsClone();
+		void   ApplyConstraint(int dof,IssmDouble value);
+		void   RelaxConstraint(int dof);
+		void   DofInSSet(int dof);
+		void   DofInFSet(int dof);
+		int    GetDof(int dofindex,int setenum);
+		void   CreateVecSets(Vector* pv_g,Vector* pv_f,Vector* pv_s);
+		int    GetConnectivity();
+		void   GetDofList(int* poutdoflist,int approximation_enum,int setenum);
+		void   GetLocalDofList(int* poutdoflist,int approximation_enum,int setenum);
+		int    GetDofList1(void);
+		int    GetSidList(void);
+		IssmDouble GetX();
+		IssmDouble GetY();
+		IssmDouble GetZ();
+		IssmDouble GetSigma();
+		int    IsOnBed();
+		int    IsOnSurface();
+		void   FreezeDof(int dof);
+		int    IsFloating();
+		int    IsGrounded();
+		void   UpdateSpcs(IssmDouble* ys);
+		void   VecMerge(Vector* ug, IssmDouble* vector_serial,int setenum);
+		void   VecReduce(Vector* vector, IssmDouble* ug_serial,int setnum);
+		
+		/*}}}*/
+		/*Dof Object routines {{{*/
+		void  DistributeDofs(int* pdofcount,int setenum);
+		void  OffsetDofs(int dofcount,int setenum);
+		void  ShowTrueDofs(int* truerows,int ncols,int setenum);
+		void  UpdateCloneDofs(int* alltruerows,int ncols,int setenum);
+		void  SetClone(int* minranks);
+		/*}}}*/
+};
+
+#endif  /* _NODE_H_ */
Index: /issm/trunk/src/c/classes/objects/Object.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Object.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Object.h	(revision 13395)
@@ -0,0 +1,27 @@
+/*
+ * Object.h:
+ * \brief prototype for abstract Object class
+ * \file Object.h
+ * This prototype describes the Object class. This is an abstract class, parent 
+ * to any other objects (Quad, Tria, Node , etc ...), that can be included in a 
+ * DataSet.
+ */
+
+
+#ifndef _OBJECT_H_
+#define _OBJECT_H_
+
+class Object {
+
+	public: 
+
+		virtual       ~Object() {};
+		virtual void  Echo()=0;
+		virtual void  DeepEcho()=0;
+		virtual int   Id()=0;
+		virtual int   MyRank()=0;
+		virtual int   ObjectEnum()=0;
+		virtual Object* copy()=0;
+
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/Options/GenericOption.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Options/GenericOption.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Options/GenericOption.h	(revision 13395)
@@ -0,0 +1,128 @@
+/*! \file GenericOption.h 
+ *  \brief: header file for generic option object
+ */
+
+#ifndef _GENERIC_OPTION_
+#define _GENERIC_OPTION_
+
+/*Headers:{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../io/io.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "./OptionUtilities.h"
+
+#include "../Object.h"
+/*}}}*/
+
+template  
+class GenericOption: public Option {
+
+	public:
+
+		char* name;
+		OptionType value;
+
+		int   numel; //in case OptionType is an array
+		int   ndims; //in case OptionType is a multi-dimensional array: */
+		int*  size;
+
+		/*GenericOption constructors, destructors*/
+		GenericOption(){ /*{{{*/
+
+			name  =NULL;
+			numel =0;
+			ndims =0;
+			size  =NULL;
+
+
+		} /*}}}*/
+		~GenericOption(){ /*{{{*/
+
+			if(size) xDelete(size);
+			if(name) xDelete(name);
+
+		} /*}}}*/
+
+		/*Object virtual functions definitions:*/
+		void Echo(){ /*{{{*/
+
+			this->DeepEcho();
+
+		} /*}}}*/
+		void DeepEcho(){ /*{{{*/
+
+			char  indent[81]="";
+			this->DeepEcho(indent);
+
+		} /*}}}*/
+		void DeepEcho(char* indent){ /*{{{*/
+
+			char  cstr[81];
+			bool  flag=true;
+
+			if(flag) _pprintLine_(indent << "         name: \"" << name << "\"");
+			if(flag) _pprintLine_(indent << "         numel: " << numel);
+			if(flag) _pprintLine_(indent << "         ndims: " << ndims);
+			if(size){
+				StringFromSize(cstr,size,ndims);
+				if(flag) _pprintLine_(indent << "          size: " << cstr);
+			}
+			else if(flag) _pprintLine_(indent << "          size: [empty]");
+			_printLine_(indent << "         value: " << value);;
+		} /*}}}*/
+		int   Id(){_error_("Not implemented yet");};
+		int   MyRank(){_error_("Not implemented yet");};
+		int   ObjectEnum(){return GenericOptionEnum;};
+		Object* copy(){_error_("Not implemented yet");};
+		
+		/*GenericOption functions: */
+		char* Name(){return name;};
+		int   NumEl(){return numel;};
+		int   NDims(){return ndims;};
+		int*  Size(){return size;};
+		void  Get(OptionType* pvalue){ *pvalue=value; };
+};
+
+#ifdef _HAVE_ADOLC_ //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. 
+template <> inline void GenericOption::Get(IssmPDouble** pvalue){ /*{{{*/
+
+	/*Copy vector*/
+	IssmPDouble* outvalue=xNew(this->NumEl());
+	for(int i=0;iNumEl();i++) outvalue[i]=this->value[i];
+
+	/*Assign output pointer*/
+	*pvalue=outvalue;
+} /*}}}*/
+#endif
+template <> inline void GenericOption::Get(IssmDouble** pvalue){ /*{{{*/
+
+	/*Copy vector*/
+	IssmDouble* outvalue=xNew(this->NumEl());
+	for(int i=0;iNumEl();i++) outvalue[i]=this->value[i];
+
+	/*Assign output pointer*/
+	*pvalue=outvalue;
+} /*}}}*/
+template <> inline void GenericOption::Get(char** pvalue){ /*{{{*/
+
+	char* outstring=NULL;
+	int   stringsize;
+
+	stringsize=strlen(this->value)+1;
+	outstring=xNew(stringsize);
+	xMemCpy(outstring,this->value,stringsize);
+
+	*pvalue=outstring;
+} 
+/*}}}*/
+
+#endif  /* _OPTIONOBJECT_H */
Index: /issm/trunk/src/c/classes/objects/Options/Option.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Options/Option.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Options/Option.h	(revision 13395)
@@ -0,0 +1,43 @@
+/*! \file Option.h 
+ *  \brief: header file for option abstract object
+ */
+
+#ifndef _OPTIONOBJECT_H_
+#define _OPTIONOBJECT_H_
+
+/*Headers:{{{*/
+#include "../../../include/include.h"
+#include "../../../shared/Exceptions/exceptions.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+
+#include "../Object.h"
+/*}}}*/
+
+class Option: public Object {
+
+	public:
+
+		
+		/*Option constructors, destructors {{{*/
+		Option(){};
+		~Option(){};
+		/*}}}*/
+		/*Object virtual functions definitions:{{{*/
+		virtual void  Echo()= 0;
+		virtual void  DeepEcho()= 0;
+		virtual void  DeepEcho(char  *indent)=0;
+		int           Id(){_error_("Not implemented yet"); };
+		int           MyRank(){_error_("Not implemented yet"); };
+		int           ObjectEnum(){return OptionEnum;              };
+		Object       *copy(){_error_("Not implemented yet"); };
+		/*}}}*/
+
+		/*virtual functions: */
+		virtual char* Name()=0;
+		virtual int   NumEl()=0;
+		virtual int   NDims()=0;
+		virtual int*  Size()=0;
+
+};
+#endif  /* _OPTIONOBJECT_H */
+
Index: /issm/trunk/src/c/classes/objects/Options/OptionUtilities.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Options/OptionUtilities.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Options/OptionUtilities.cpp	(revision 13395)
@@ -0,0 +1,114 @@
+/*!\file OptionUtilities.cpp
+ * \brief: implementation of the options utilities
+ */
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*FUNCTION ColumnWiseDimsFromIndex{{{*/
+int ColumnWiseDimsFromIndex(int* dims,int index,int* size,int ndims){
+
+	int   i;
+	int   aprod=1;
+
+	/*check for index too large  */
+	for (i=0;i= aprod) _error_("Index " << index << " exceeds number of elements " << aprod << ".");
+
+	/*calculate the dimensions (being careful of integer division)  */
+	for (i=ndims-1; i>=0; i--) {
+		aprod=reCast(((IssmPDouble)aprod+0.5)/(IssmPDouble)size[i]);
+		dims[i]=(int)floor(((IssmPDouble)index+0.5)/(IssmPDouble)aprod);
+		index-=dims[i]*aprod;
+	}
+
+	return(0);
+}/*}}}*/
+/*FUNCTION IndexFromColumnWiseDims{{{*/
+int IndexFromColumnWiseDims(int* dims, int* size, int ndims) {
+
+	int   i;
+	int   index=0;
+
+	/*check for any dimension too large  */
+	for (i=0;i= size[i]) _error_("Dimension " << i << " of " << dims[i] << " exceeds size of " << size[i] << ".");
+	}
+
+	/*calculate the index  */
+	for (i=ndims-1; i>=0; i--){
+		index*=size[i];
+		index+=dims[i];
+	}
+
+	return(index);
+}/*}}}*/
+/*FUNCTION RowWiseDimsFromIndex{{{*/
+int RowWiseDimsFromIndex(int* dims, int index, int* size, int ndims) {
+
+	int   i;
+	int   aprod=1;
+
+	/*check for index too large  */
+	for (i=0; i= aprod) _error_("Index " << index << " exceeds number of elements " << aprod << ".");
+
+	/*calculate the dimensions (being careful of integer division)  */
+	for (i=0; i= size[i]) _error_("Dimension " << i << " of " << dims[i] << " exceeds size of " << size[i] << ".");
+	}
+
+	/*calculate the index  */
+	for (i=0; i
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*BoolParam constructors and destructor*/
+/*FUNCTION BoolParam::BoolParam(){{{*/
+BoolParam::BoolParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION BoolParam::BoolParam(int enum_type,IssmBool value){{{*/
+BoolParam::BoolParam(int in_enum_type,IssmBool in_value){
+
+	enum_type=in_enum_type;
+	value=in_value;
+}
+/*}}}*/
+/*FUNCTION BoolParam::~BoolParam(){{{*/
+BoolParam::~BoolParam(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION BoolParam::Echo {{{*/
+void BoolParam::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION BoolParam::DeepEcho{{{*/
+void BoolParam::DeepEcho(void){
+
+	_printLine_("BoolParam:");
+	_printLine_("   enum:  " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: " <<(this->value?"true":"false"));
+}
+/*}}}*/
+/*FUNCTION BoolParam::Id{{{*/
+int    BoolParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION BoolParam::MyRank{{{*/
+int    BoolParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION BoolParam::ObjectEnum{{{*/
+int BoolParam::ObjectEnum(void){
+
+	return BoolParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION BoolParam::copy{{{*/
+Object* BoolParam::copy() {
+	
+	return new BoolParam(this->enum_type,this->value);
+
+}
+/*}}}*/
+
+/*BoolParam virtual functions definitions: */
+/*FUNCTION BoolParam::GetParameterName{{{*/
+void BoolParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION BoolParam::UnitConversion{{{*/
+void  BoolParam::UnitConversion(int direction_enum){
+	/*do nothing, no unit conversion*/
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/BoolParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/BoolParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/BoolParam.h	(revision 13395)
@@ -0,0 +1,77 @@
+/*! \file BoolParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _BOOLPARAM_H_
+#define _BOOLPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class BoolParam: public Param{
+
+	public:
+		/*just hold 3 values for 3 vertices: */
+		int enum_type;
+		IssmBool value;
+
+		/*BoolParam constructors, destructors: {{{*/
+		BoolParam();
+		BoolParam(int enum_type,IssmBool value);
+		~BoolParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){*pbool=value;}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an integer");}
+		void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");}
+
+		void  SetValue(bool boolean){this->value=boolean;}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an int");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an IssmPDouble");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(int* pintarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+		
+		void GetParameterName(char**pname);
+		/*}}}*/
+};
+#endif  /* _BOOLPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/DoubleMatArrayParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleMatArrayParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleMatArrayParam.cpp	(revision 13395)
@@ -0,0 +1,252 @@
+/*!\file DoubleMatArrayParam.c
+ * \brief: implementation of the DoubleMatArrayParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*DoubleMatArrayParam constructors and destructor*/
+/*FUNCTION DoubleMatArrayParam::DoubleMatArrayParam(){{{*/
+DoubleMatArrayParam::DoubleMatArrayParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION DoubleMatArrayParam::DoubleMatArrayParam(int enum_type,IssmDouble** array, int M, int* mdim_array, int* ndim_array){{{*/
+DoubleMatArrayParam::DoubleMatArrayParam(int in_enum_type,IssmDouble** in_array, int in_M, int* in_mdim_array, int* in_ndim_array){
+
+	int i;
+	IssmDouble* matrix=NULL;
+	int     m,n;
+
+	enum_type=in_enum_type;
+	M=in_M;
+	if(M){
+		array=xNew(M);
+		mdim_array=xNew(M);
+		ndim_array=xNew(M);
+
+		for(i=0;i(m*n);
+				xMemCpy(matrix,in_array[i],m*n);
+			}
+			else{
+				matrix=NULL;
+			}
+			array[i]=matrix;
+		}
+	}
+	else{
+		array=NULL;
+		mdim_array=NULL;
+		ndim_array=NULL;
+	}
+}
+/*}}}*/
+/*FUNCTION DoubleMatArrayParam::~DoubleMatArrayParam(){{{*/
+DoubleMatArrayParam::~DoubleMatArrayParam(){
+
+	int i;
+	IssmDouble* matrix=NULL;
+
+	xDelete(mdim_array);
+	xDelete(ndim_array);
+
+	for(i=0;i(matrix);
+	}
+	
+	xDelete(array);
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION DoubleMatArrayParam::Echo {{{*/
+void DoubleMatArrayParam::Echo(void){
+
+	_printLine_("DoubleMatArrayParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   array size: " << this->M);
+	_printLine_("   array pointer: " << this->array);
+
+}
+/*}}}*/
+/*FUNCTION DoubleMatArrayParam::DeepEcho{{{*/
+void DoubleMatArrayParam::DeepEcho(void){
+
+	int i,j,k;
+	int m,n;
+	IssmDouble* matrix=NULL;
+	
+	_printLine_("DoubleMatArrayParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   array size: " << this->M);
+	for(i=0;ienum_type,this->array, this->M, this->mdim_array,this->ndim_array);
+
+}
+/*}}}*/
+
+/*DoubleMatArrayParam virtual functions definitions: */
+/*FUNCTION DoubleMatArrayParam::GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){{{*/
+void  DoubleMatArrayParam::GetParameterValue(IssmDouble*** pout_array, int* pout_M,int** pout_mdim_array, int** pout_ndim_array){
+
+	int i,m,n;
+	IssmDouble* matrix=NULL;
+	IssmDouble* out_matrix=NULL;
+
+	/*output: */
+	IssmDouble** out_array=NULL;
+	int      out_M;
+	int*     out_mdim_array=NULL;
+	int*     out_ndim_array=NULL;
+
+
+	out_M=this->M;
+	if(out_M){
+		out_array=xNew(M);
+		out_mdim_array=xNew(M);
+		out_ndim_array=xNew(M);
+
+		xMemCpy(out_mdim_array,this->mdim_array,M);
+		xMemCpy(out_ndim_array,this->ndim_array,M);
+
+		for(i=0;iM;i++){
+			matrix=this->array[i];
+			m=this->mdim_array[i];
+			n=this->ndim_array[i];
+
+			if(m*n){
+				out_matrix=xNew(m*n);
+				xMemCpy(out_matrix,matrix,m*n);
+			}
+			else{
+				out_matrix=NULL;
+			}
+			out_array[i]=out_matrix;
+		}
+	}
+	else{
+		out_array=NULL;
+		out_matrix=NULL;
+		out_ndim_array=NULL;
+	}
+
+
+	/*Assign output pointers:*/
+	if(pout_M) *pout_M=out_M;
+	if(pout_mdim_array) *pout_mdim_array=out_mdim_array;
+	if(pout_ndim_array) *pout_ndim_array=out_ndim_array;
+	*pout_array=out_array;
+
+}
+/*}}}*/
+/*FUNCTION DoubleMatArrayParam::GetParameterName{{{*/
+void DoubleMatArrayParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION DoubleMatArrayParam::SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){{{*/
+void  DoubleMatArrayParam::SetValue(IssmDouble** in_array, int in_M, int* in_mdim_array, int* in_ndim_array){
+
+	int i,m,n;
+	IssmDouble* in_matrix=NULL;
+	IssmDouble* matrix=NULL;
+
+	/*avoid leak: */
+	xDelete(mdim_array);
+	xDelete(ndim_array);
+	for(i=0;i(matrix);
+	}
+	xDelete(array);
+
+	/*copy data: */
+	this->M=in_M;
+	this->array=xNew(M);
+	this->mdim_array=xNew(M);
+	this->ndim_array=xNew(M);
+	
+	xMemCpy(this->mdim_array,in_mdim_array,M);
+	xMemCpy(this->ndim_array,in_ndim_array,M);
+
+	for(i=0;i(m*n);
+		xMemCpy(matrix,in_matrix,m*n);
+
+		this->array[i]=matrix;
+	}
+
+}
+/*}}}*/
+/*FUNCTION DoubleMatArrayParam::UnitConversion{{{*/
+void  DoubleMatArrayParam::UnitConversion(int direction_enum){
+	/*go through all matrices and convert: */
+	for (int i=0;iM;i++){
+		IssmDouble* matrix=this->array[i];
+		int     m=this->mdim_array[i];
+		int     n=this->ndim_array[i];
+		::UnitConversion(matrix,m*n,direction_enum,this->enum_type);
+	}
+
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/DoubleMatArrayParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleMatArrayParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleMatArrayParam.h	(revision 13395)
@@ -0,0 +1,81 @@
+/*! \file DoubleMatArrayParam.h 
+ *  \brief: header file for object holding an array of serial matrices
+ */
+
+
+#ifndef _DOUBLEMATARRAYPARAM_H_
+#define _DOUBLEMATARRAYPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class DoubleMatArrayParam: public Param{
+
+	private: 
+		int      enum_type;
+		IssmDouble** array; //array of matrices
+		int      M; //size of array
+		int*     mdim_array; //m-dimensions of matrices in the array
+		int*     ndim_array; //n-dimensions -f matrices in the array
+
+	public:
+		/*DoubleMatArrayParam constructors, destructors: {{{*/
+		DoubleMatArrayParam();
+		DoubleMatArrayParam(int enum_type,IssmDouble** array, int M, int* mdim_array, int* ndim_array);
+		~DoubleMatArrayParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a bool");}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << "cannot return an integer");}
+		void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << "cannot return an array of integers");}
+		void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << "cannot return an array of integers");}
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims);
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a FILE");}
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a boolean");}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold an integer");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a scalar");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a IssmDouble vec array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a IssmDouble mat array");}
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a int vec array");}
+		void  SetValue(int* intarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a int mat array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Bool param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array);
+		void  UnitConversion(int direction_enum);
+
+		void GetParameterName(char**pname);
+
+		/*}}}*/
+};
+#endif  /* _DOUBLEMATARRAYPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/DoubleMatParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleMatParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleMatParam.cpp	(revision 13395)
@@ -0,0 +1,136 @@
+/*!\file DoubleMatParam.c
+ * \brief: implementation of the DoubleMatParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*DoubleMatParam constructors and destructor*/
+/*FUNCTION DoubleMatParam::DoubleMatParam(){{{*/
+DoubleMatParam::DoubleMatParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::DoubleMatParam(int enum_type,IssmDoubleMat value){{{*/
+DoubleMatParam::DoubleMatParam(int in_enum_type,IssmDouble* in_value, int in_M,int in_N){
+
+	enum_type=in_enum_type;
+	M=in_M;
+	N=in_N;
+
+	value=xNew(M*N);
+	xMemCpy(value,in_value,M*N);
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::~DoubleMatParam(){{{*/
+DoubleMatParam::~DoubleMatParam(){
+	xDelete(value);
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION DoubleMatParam::Echo {{{*/
+void DoubleMatParam::Echo(void){
+
+	_printLine_("DoubleMatParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   matrix size: " << this->M << "x" << this->N);
+
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::DeepEcho{{{*/
+void DoubleMatParam::DeepEcho(void){
+
+	int i,j;
+	
+	_printLine_("DoubleMatParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   matrix size: " << this->M << "x" << this->N);
+	for(i=0;iM;i++){
+		for(i=0;iN;i++){
+			_printLine_(i << " " << j << " " << *(this->value+N*i+j));
+		}
+	}
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::Id{{{*/
+int    DoubleMatParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION DoubleMatParam::MyRank{{{*/
+int    DoubleMatParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::ObjectEnum{{{*/
+int DoubleMatParam::ObjectEnum(void){
+
+	return DoubleMatParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::copy{{{*/
+Object* DoubleMatParam::copy() {
+	
+	return new DoubleMatParam(this->enum_type,this->value,this->M,this->N);
+
+}
+/*}}}*/
+
+/*DoubleMatParam virtual functions definitions: */
+/*FUNCTION DoubleMatParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM,int* pN){{{*/
+void  DoubleMatParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM,int* pN){
+	IssmDouble* output=NULL;
+
+	output=xNew(M*N);
+	xMemCpy(output,value,M*N);
+
+	/*Assign output pointers:*/
+	if(pM) *pM=M;
+	if(pN) *pN=N;
+	*pIssmDoublearray=output;
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::GetParameterValue(int** pintarray,int* pM,int* pN){{{*/
+void  DoubleMatParam::GetParameterValue(int** pintarray,int* pM,int* pN){
+	_error_("DoubleMat of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return an array of int");
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::GetParameterName{{{*/
+void DoubleMatParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::SetValue{{{*/
+void  DoubleMatParam::SetValue(IssmDouble* IssmDoublearray,int in_M,int in_N){
+
+	/*avoid leak: */
+	xDelete(this->value);
+
+	this->value=xNew(in_M*in_N);
+	xMemCpy(this->value,IssmDoublearray,in_M*in_N);
+
+	this->M=in_M;
+	this->N=in_N;
+}
+/*}}}*/
+/*FUNCTION DoubleMatParam::UnitConversion{{{*/
+void  DoubleMatParam::UnitConversion(int direction_enum){
+	::UnitConversion(this->value,this->M*this->N,direction_enum,this->enum_type);
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/DoubleMatParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleMatParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleMatParam.h	(revision 13395)
@@ -0,0 +1,80 @@
+/*! \file DoubleMatParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _DOUBLEMATPARAM_H_
+#define _DOUBLEMATPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class DoubleMatParam: public Param{
+
+	protected: 
+		int enum_type;
+		IssmDouble* value;
+		int M;
+		int N;
+
+	public:
+		/*DoubleMatParam constructors, destructors: {{{*/
+		DoubleMatParam();
+		DoubleMatParam(int enum_type,IssmDouble* value,int M,int N);
+		~DoubleMatParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an integer");}
+		void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(int** pintarray,int* pM,int* pN);
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM,int* pN);
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");}
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a scalar");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble vec array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M,int N);
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int vec array");}
+		void  SetValue(int* intarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int mat array");};
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+
+		void GetParameterName(char**pname);
+
+		/*}}}*/
+};
+#endif  /* _DOUBLEMATPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/DoubleParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleParam.cpp	(revision 13395)
@@ -0,0 +1,116 @@
+/*!\file DoubleParam.c
+ * \brief: implementation of the DoubleParam object
+ */
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+
+/*DoubleParam constructors and destructor*/
+/*FUNCTION DoubleParam::DoubleParam(){{{*/
+DoubleParam::DoubleParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION DoubleParam::DoubleParam(int enum_type,IssmDouble value){{{*/
+DoubleParam::DoubleParam(int in_enum_type,IssmDouble in_value){
+
+	enum_type=in_enum_type;
+	value=in_value;
+}
+/*}}}*/
+/*FUNCTION DoubleParam::~DoubleParam(){{{*/
+DoubleParam::~DoubleParam(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION DoubleParam::Echo {{{*/
+void DoubleParam::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION DoubleParam::DeepEcho{{{*/
+void DoubleParam::DeepEcho(void){
+
+	_printLine_("DoubleParam:");
+	_printLine_("   enum:  " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: " << this->value);
+}
+/*}}}*/
+/*FUNCTION DoubleParam::Id{{{*/
+int    DoubleParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION DoubleParam::MyRank{{{*/
+int    DoubleParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION DoubleParam::ObjectEnum{{{*/
+int DoubleParam::ObjectEnum(void){
+
+	return DoubleParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION DoubleParam::copy{{{*/
+Object* DoubleParam::copy() {
+	
+	return new DoubleParam(this->enum_type,this->value);
+
+}
+/*}}}*/
+
+/*DoubleParam virtual functions definitions: */
+/*FUNCTION DoubleParam::GetParameterName{{{*/
+void DoubleParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION DoubleParam::GetParameterValue(int* pinteger){{{*/
+void DoubleParam::GetParameterValue(int* pinteger){
+	_error_("Double param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return an integer");
+}
+/*}}}*/
+/*FUNCTION DoubleParam::GetParameterValue(bool* pbool){{{*/
+void DoubleParam::GetParameterValue(bool* pbool){
+	_error_("Double param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return an bool");
+}
+/*}}}*/
+/*FUNCTION DoubleParam::GetParameterValue(int** pintarray,int* pM){{{*/
+void DoubleParam::GetParameterValue(int** pintarray,int* pM){
+	_error_("Double param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return an array of integers");
+}
+/*}}}*/
+/*FUNCTION DoubleParam::GetParameterValue(int** pintarray,int* pM,int* pN){{{*/
+void DoubleParam::GetParameterValue(int** pintarray,int* pM,int* pN){
+	_error_("Double param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return an array of integers");
+}
+/*}}}*/
+/*FUNCTION DoubleParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){{{*/
+void DoubleParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){
+	_error_("Double param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return an array of IssmDouble");
+}
+/*}}}*/
+/*FUNCTION DoubleParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM,int* pN){{{*/
+void DoubleParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM,int* pN){
+	_error_("Double param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return an array of IssmDouble");
+}
+/*}}}*/
+/*FUNCTION DoubleParam::UnitConversion{{{*/
+void  DoubleParam::UnitConversion(int direction_enum){
+	::UnitConversion(&this->value,1,direction_enum,this->enum_type);
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/DoubleParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleParam.h	(revision 13395)
@@ -0,0 +1,79 @@
+/*! \file DoubleParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _DOUBLEPARAM_H_
+#define _DOUBLEPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class DoubleParam: public Param{
+
+	private: 
+		/*just hold 3 values for 3 vertices: */
+		int enum_type;
+		IssmDouble value;
+
+	public:
+		/*DoubleParam constructors, destructors: {{{*/
+		DoubleParam();
+		DoubleParam(int enum_type,IssmDouble value);
+		~DoubleParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool);
+		void  GetParameterValue(int* pinteger);
+		void  GetParameterValue(int** pintarray,int* pM);
+		void  GetParameterValue(int** pintarray,int* pM,int* pN);
+		void  GetParameterValue(IssmDouble* pIssmDouble){*pIssmDouble=value;}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM);
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN);
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");}
+
+		void  SetValue(bool boolean){this->value=(IssmDouble)boolean;}
+		void  SetValue(int integer){this->value=(IssmDouble)integer;}
+		void  SetValue(IssmDouble scalar){this->value=(IssmDouble)scalar;}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(int* pintarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+
+		void GetParameterName(char**pname);
+
+		/*}}}*/
+};
+#endif  /* _DOUBLEPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/DoubleTransientMatParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleTransientMatParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleTransientMatParam.cpp	(revision 13395)
@@ -0,0 +1,30 @@
+/*!\file DoubleTransientMatParam.c
+ * \brief: implementation of the DoubleTransientMatParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*FUNCTION DoubleTransientMatParam::DoubleTransientMatParam(int enum_type,IssmDoubleMat value){{{*/
+DoubleTransientMatParam::DoubleTransientMatParam(int in_enum_type,IssmDouble* in_value, int in_M,int in_N):DoubleMatParam(in_enum_type,in_value,in_M,in_N){
+}
+/*}}}*/
+/*FUNCTION DoubleTransientMatParam::UnitConversion{{{*/
+void  DoubleTransientMatParam::UnitConversion(int direction_enum){
+	::UnitConversion(this->value,(this->M-1)*this->N,direction_enum,this->enum_type);
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/DoubleTransientMatParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleTransientMatParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleTransientMatParam.h	(revision 13395)
@@ -0,0 +1,32 @@
+/*! \file DoubleTransientMatParam.h 
+ *  \brief: header file for DoubleTransientMatParam object
+ */
+
+
+#ifndef _DOUBLETRANSIENTMATPARAM_H_
+#define _DOUBLETRANSIENTMATPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class DoubleTransientMatParam: public DoubleMatParam{
+
+	public:
+		/*DoubleTransientMatParam constructors, destructors: {{{*/
+		DoubleTransientMatParam(int enum_type,IssmDouble* value,int M,int N);
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		void  UnitConversion(int direction_enum);
+		/*}}}*/
+};
+#endif  /* _DOUBLETRANSIENTMATPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/DoubleVecParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleVecParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleVecParam.cpp	(revision 13395)
@@ -0,0 +1,150 @@
+/*!\file DoubleVecParam.c
+ * \brief: implementation of the DoubleVecParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*DoubleVecParam constructors and destructor*/
+/*FUNCTION DoubleVecParam::DoubleVecParam(){{{*/
+DoubleVecParam::DoubleVecParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::DoubleVecParam(int enum_type,IssmDoubleVec values,int M){{{*/
+DoubleVecParam::DoubleVecParam(int in_enum_type,IssmDouble* in_values, int in_M){
+
+	enum_type=in_enum_type;
+	M=in_M;
+
+	values=xNew(M);
+	xMemCpy(values,in_values,M);
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::~DoubleVecParam(){{{*/
+DoubleVecParam::~DoubleVecParam(){
+	xDelete(values);
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION DoubleVecParam::Echo {{{*/
+void DoubleVecParam::Echo(void){
+
+	_printLine_("DoubleVecParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   vector size: " << this->M);
+
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::DeepEcho{{{*/
+void DoubleVecParam::DeepEcho(void){
+
+	int i;
+	
+	_printLine_("DoubleVecParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   vector size: " << this->M);
+	for(i=0;iM;i++){
+		_printLine_(i << " " << this->values[i]);
+	}
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::Id{{{*/
+int    DoubleVecParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION DoubleVecParam::MyRank{{{*/
+int    DoubleVecParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::ObjectEnum{{{*/
+int DoubleVecParam::ObjectEnum(void){
+
+	return DoubleVecParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::copy{{{*/
+Object* DoubleVecParam::copy() {
+	
+	return new DoubleVecParam(this->enum_type,this->values,this->M);
+
+}
+/*}}}*/
+
+/*DoubleVecParam virtual functions definitions: */
+/*FUNCTION DoubleVecParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){{{*/
+void  DoubleVecParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){
+	IssmDouble* output=NULL;
+	int M;
+
+	M=this->M;
+	output=xNew(M);
+	xMemCpy(output,values,M);
+
+	/*Assign output pointers:*/
+	if(pM) *pM=M;
+	*pIssmDoublearray=output;
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){{{*/
+void  DoubleVecParam::GetParameterValue(IssmDouble** pIssmDoublearray,int* pM,int* pN){
+	IssmDouble* output=NULL;
+	int M;
+	int N;
+
+	N=1;
+	M=this->M;
+	output=xNew(M);
+	xMemCpy(output,values,M);
+
+	/*Assign output pointers:*/
+	if(pM) *pM=M;
+	if(pN) *pN=N;
+	*pIssmDoublearray=output;
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::GetParameterValue(int** pintarray,int* pM){{{*/
+void  DoubleVecParam::GetParameterValue(int** pintarray,int* pM){
+	_error_("DoubleVec param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return an array of int");
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::GetParameterName{{{*/
+void DoubleVecParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::SetValue{{{*/
+void  DoubleVecParam::SetValue(IssmDouble* IssmDoublearray,int in_M){
+
+	/*avoid leak: */
+	xDelete(this->values);
+
+	this->values=xNew(in_M);
+	xMemCpy(this->values,IssmDoublearray,in_M);
+
+	this->M=in_M;
+}
+/*}}}*/
+/*FUNCTION DoubleVecParam::UnitConversion{{{*/
+void  DoubleVecParam::UnitConversion(int direction_enum){
+	::UnitConversion(this->values,this->M,direction_enum,this->enum_type);
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/DoubleVecParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/DoubleVecParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/DoubleVecParam.h	(revision 13395)
@@ -0,0 +1,78 @@
+/*! \file DoubleVecParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _DOUBLEVECPARAM_H_
+#define _DOUBLEVECPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class DoubleVecParam: public Param{
+
+	private: 
+		int enum_type;
+		IssmDouble* values;
+		int M;
+
+	public:
+		/*DoubleVecParam constructors, destructors: {{{*/
+		DoubleVecParam();
+		DoubleVecParam(int enum_type,IssmDouble* values,int M);
+		~DoubleVecParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param virtual functions definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an integer");}
+		void  GetParameterValue(int** pintarray,int* pM);
+		void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");};
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM);
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN);
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");}
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a scalar");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M);
+		void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble mat array");}
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int mat array");};
+		void  SetValue(int* pintarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int mat array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+		
+		void GetParameterName(char**pname);
+		/*}}}*/
+};
+#endif  /* _DOUBLEVECPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/FileParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/FileParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/FileParam.cpp	(revision 13395)
@@ -0,0 +1,89 @@
+/*!\file FileParam.c
+ * \brief: implementation of the FileParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*FileParam constructors and destructor*/
+/*FUNCTION FileParam::FileParam(){{{*/
+FileParam::FileParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION FileParam::FileParam(int enum_type,FILE *value){{{*/
+FileParam::FileParam(int in_enum_type,FILE* in_value){
+
+	enum_type=in_enum_type;
+	value=in_value;
+}
+/*}}}*/
+/*FUNCTION FileParam::~FileParam(){{{*/
+FileParam::~FileParam(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION FileParam::Echo {{{*/
+void FileParam::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION FileParam::DeepEcho{{{*/
+void FileParam::DeepEcho(void){
+
+	_printLine_("FileParam:");
+	_printLine_("   enum:  " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: " << this->value);
+}
+/*}}}*/
+/*FUNCTION FileParam::Id{{{*/
+int    FileParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION FileParam::MyRank{{{*/
+int    FileParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION FileParam::ObjectEnum{{{*/
+int FileParam::ObjectEnum(void){
+
+	return FileParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION FileParam::copy{{{*/
+Object* FileParam::copy() {
+	
+	return new FileParam(this->enum_type,this->value);
+
+}
+/*}}}*/
+
+/*FileParam virtual functions definitions: */
+/*FUNCTION FileParam::GetParameterName{{{*/
+void FileParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION FileParam::UnitConversion{{{*/
+void  FileParam::UnitConversion(int direction_enum){
+	/*do nothing, no unit conversion*/
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/FileParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/FileParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/FileParam.h	(revision 13395)
@@ -0,0 +1,78 @@
+/*! \file FileParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _FILEPARAM_H_
+#define _FILEPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class FileParam: public Param{
+
+	private: 
+		int   enum_type;
+		FILE* value;
+
+	public:
+		/*FileParam constructors, destructors: {{{*/
+		FileParam();
+		FileParam(int enum_type,FILE* fid);
+		~FileParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){  _error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("File param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){*pfid=value;};
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(int* pintarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("File param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("File param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+
+		void GetParameterName(char**pname);
+
+		/*}}}*/
+};
+#endif  /* _INTPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/GenericParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/GenericParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/GenericParam.h	(revision 13395)
@@ -0,0 +1,102 @@
+/*
+ * GenericParam.h
+ *
+ *  Created on: Aug 29, 2012
+ *      Author: utke
+ */
+
+#ifndef GENERICPARAM_H_
+#define GENERICPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+        #include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+/**
+ * here we have a class that holds an instance of P
+ * but because it should live side by side with
+ * the other instances derived from Param it - unfortunately -
+ * inherits all the accessors that are useless in this context
+ */
+template  class GenericParam: public Param{
+
+        private:
+                P myP;
+                int myEnumVal;
+
+        public:
+                /*GenericParam constructors, destructors: {{{*/
+                GenericParam(int enumVal) : myEnumVal(enumVal){};
+                ~GenericParam(){};
+                /*}}}*/
+                /*Object virtual functions definitions:{{{ */
+                // unfortunately,  having to implement such a printer method implies
+                // that any structured P must provide the friend << operator
+                void  DeepEcho() {
+                  _printLine_("GenericParam:");
+                  _printLine_("   enum:  " << myEnumVal << " (" << EnumToStringx(myEnumVal) << ")");
+                  _printLine_("   value: " << myP);;
+                }
+                void  Echo() {DeepEcho();};
+                int   Id(){ return -1; };
+                int   MyRank() { extern int my_rank; return my_rank;} ;
+                int   ObjectEnum() {return AdolcParamEnum;};
+
+                // the "copy"  has to implement the base class abstract function
+                // but I would prefer to drop this not to hide a "new" in here because
+                // it does not clarify  ownership of the newed up instance...
+                // use the default copy constructor instead
+                Object* copy() { return new GenericParam
(*this); };
+                /*}}}*/
+                /*Param vritual function definitions: {{{*/
+                int   InstanceEnum(){return myEnumVal;}
+                void GetParameterName(char**pname) {EnumToStringx(pname,this->myEnumVal);}
+
+                P& GetParameterValue() { return myP;}
+                const P& GetParameterValue()const { return myP;};
+
+                // none of these apply ...
+                void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a bool");}
+                void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return an integer");}
+                void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return an array of integers");}
+                void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return an array of integers");}
+                void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a IssmDouble");}
+                void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a IssmDouble for a given time");}
+                void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a string");}
+                void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a string array");}
+                void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a IssmDouble array");}
+                void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a IssmDouble array");}
+                void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a matrix array");}
+                void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a Vec");}
+                void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a Mat");}
+                void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a FILE");}
+
+                void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold a bool");}
+                void  SetValue(int integer){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold an integer");}
+                void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold an int array");}
+                void  SetValue(int* intarray,int M,int N){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold an int array");}
+                void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold an IssmDouble");}
+                void  SetValue(char* string){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold a string");}
+                void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold a string array");}
+                void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold a IssmDouble array");}
+                void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold a IssmDouble array");}
+                void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold a Vec");}
+                void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold a Mat");}
+                void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold a FILE");}
+                void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold an array of matrices");}
+                void  UnitConversion(int direction_enum) {/* nothing useful here either */};
+
+                /*}}}*/
+};
+
+
+#endif /* GENERICPARAM_H_ */
Index: /issm/trunk/src/c/classes/objects/Params/IntMatParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/IntMatParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/IntMatParam.cpp	(revision 13395)
@@ -0,0 +1,131 @@
+/*!\file IntMatParam.c
+ * \brief: implementation of the IntMatParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*IntMatParam constructors and destructor*/
+/*FUNCTION IntMatParam::IntMatParam(){{{*/
+IntMatParam::IntMatParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION IntMatParam::IntMatParam(int enum_type,IssmIntMat value){{{*/
+IntMatParam::IntMatParam(int in_enum_type,int* in_value, int in_M,int in_N){
+
+	enum_type=in_enum_type;
+	M=in_M;
+	N=in_N;
+
+	value=xNew(M*N);
+	xMemCpy(value,in_value,M*N);
+}
+/*}}}*/
+/*FUNCTION IntMatParam::~IntMatParam(){{{*/
+IntMatParam::~IntMatParam(){
+	xDelete(value);
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION IntMatParam::Echo {{{*/
+void IntMatParam::Echo(void){
+
+	_printLine_("IntMatParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   matrix size: " << this->M << "x" << this->N);
+
+}
+/*}}}*/
+/*FUNCTION IntMatParam::DeepEcho{{{*/
+void IntMatParam::DeepEcho(void){
+
+	int i,j;
+	
+	_printLine_("IntMatParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   matrix size: " << this->M << "x" << this->N);
+	for(i=0;iM;i++){
+		for(i=0;iN;i++){
+			_printLine_("(" << i << "," << j << ") " << *(this->value+N*i+j));
+		}
+	}
+}
+/*}}}*/
+/*FUNCTION IntMatParam::Id{{{*/
+int    IntMatParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION IntMatParam::MyRank{{{*/
+int    IntMatParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION IntMatParam::ObjectEnum{{{*/
+int IntMatParam::ObjectEnum(void){
+
+	return IntMatParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION IntMatParam::copy{{{*/
+Object* IntMatParam::copy() {
+	
+	return new IntMatParam(this->enum_type,this->value,this->M,this->N);
+
+}
+/*}}}*/
+
+/*IntMatParam virtual functions definitions: */
+/*FUNCTION IntMatParam::GetParameterValue{{{*/
+void  IntMatParam::GetParameterValue(int** pintarray,int* pM,int* pN){
+	int* output=NULL;
+
+	output=xNew(M*N);
+	xMemCpy(output,value,M*N);
+
+	/*Assign output pointers:*/
+	if(pM) *pM=M;
+	if(pN) *pN=N;
+	*pintarray=output;
+}
+/*}}}*/
+/*FUNCTION IntMatParam::GetParameterName{{{*/
+void IntMatParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION IntMatParam::SetValue{{{*/
+void  IntMatParam::SetValue(int* intarray,int in_M,int in_N){
+
+	/*avoid leak: */
+	xDelete(this->value);
+
+	this->value=xNew(in_M*in_N);
+	xMemCpy(this->value,intarray,in_M*in_N);
+
+	this->M=in_M;
+	this->N=in_N;
+}
+/*}}}*/
+/*FUNCTION IntMatParam::UnitConversion{{{*/
+void  IntMatParam::UnitConversion(int direction_enum){
+	/*do nothing, no unit conversion*/
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/IntMatParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/IntMatParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/IntMatParam.h	(revision 13395)
@@ -0,0 +1,80 @@
+/*! \file IntMatParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _INTMATPARAM_H_
+#define _INTMATPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class IntMatParam: public Param{
+
+	private: 
+		int enum_type;
+		int* value;
+		int M;
+		int N;
+
+	public:
+		/*IntMatParam constructors, destructors: {{{*/
+		IntMatParam();
+		IntMatParam(int enum_type,int* value,int M,int N);
+		~IntMatParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an integer");}
+		void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(int** pintarray,int* pM,int* pN);
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");};
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");}
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a scalar");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble vec array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble vec array");};
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int vec array");};
+		void  SetValue(int* intarray,int M,int N);
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+
+		void GetParameterName(char**pname);
+
+		/*}}}*/
+};
+#endif  /* _INTMATPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/IntParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/IntParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/IntParam.cpp	(revision 13395)
@@ -0,0 +1,89 @@
+/*!\file IntParam.c
+ * \brief: implementation of the IntParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*IntParam constructors and destructor*/
+/*FUNCTION IntParam::IntParam(){{{*/
+IntParam::IntParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION IntParam::IntParam(int enum_type,IssmInt value){{{*/
+IntParam::IntParam(int in_enum_type,IssmInt in_value){
+
+	enum_type=in_enum_type;
+	value=in_value;
+}
+/*}}}*/
+/*FUNCTION IntParam::~IntParam(){{{*/
+IntParam::~IntParam(){
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION IntParam::Echo {{{*/
+void IntParam::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION IntParam::DeepEcho{{{*/
+void IntParam::DeepEcho(void){
+
+	_printLine_("IntParam:");
+	_printLine_("   enum:  " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: " << this->value);
+}
+/*}}}*/
+/*FUNCTION IntParam::Id{{{*/
+int    IntParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION IntParam::MyRank{{{*/
+int    IntParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION IntParam::ObjectEnum{{{*/
+int IntParam::ObjectEnum(void){
+
+	return IntParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION IntParam::copy{{{*/
+Object* IntParam::copy() {
+	
+	return new IntParam(this->enum_type,this->value);
+
+}
+/*}}}*/
+
+/*IntParam virtual functions definitions: */
+/*FUNCTION IntParam::GetParameterName{{{*/
+void IntParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION IntParam::UnitConversion{{{*/
+void  IntParam::UnitConversion(int direction_enum){
+	/*do nothing, no unit conversion*/
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/IntParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/IntParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/IntParam.h	(revision 13395)
@@ -0,0 +1,79 @@
+/*! \file IntParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _INTPARAM_H_
+#define _INTPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class IntParam: public Param{
+
+	private: 
+		/*just hold 3 values for 3 vertices: */
+		int enum_type;
+		IssmInt value;
+
+	public:
+		/*IntParam constructors, destructors: {{{*/
+		IntParam();
+		IntParam(int enum_type,IssmInt value);
+		~IntParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");}
+		void  GetParameterValue(int* pinteger){*pinteger=value;}
+		void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");}
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a bool");}
+		void  SetValue(int integer){this->value=integer;}
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an int array");}
+		void  SetValue(int* intarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an int array");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an IssmDouble");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+
+		void GetParameterName(char**pname);
+
+		/*}}}*/
+};
+#endif  /* _INTPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/IntVecParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/IntVecParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/IntVecParam.cpp	(revision 13395)
@@ -0,0 +1,147 @@
+/*!\file IntVecParam.c
+ * \brief: implementation of the IntVecParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*IntVecParam constructors and destructor*/
+/*FUNCTION IntVecParam::IntVecParam(){{{*/
+IntVecParam::IntVecParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION IntVecParam::IntVecParam(int enum_type,int* values,int M){{{*/
+IntVecParam::IntVecParam(int in_enum_type,int* in_values, int in_M){
+
+	enum_type=in_enum_type;
+	M=in_M;
+
+	if(M){
+		values=xNew(M);
+		xMemCpy(values,in_values,M);
+	}
+	else values=NULL;
+}
+/*}}}*/
+/*FUNCTION IntVecParam::IntVecParam(int enum_type,IssmDouble* values,int M){{{*/
+IntVecParam::IntVecParam(int in_enum_type,IssmDouble* in_values, int in_M){
+
+	enum_type=in_enum_type;
+	M=in_M;
+
+	if(M){
+		values=xNew(M);
+		for(int i=0;i(in_values[i]);
+	}
+	else values=NULL;
+}
+/*}}}*/
+/*FUNCTION IntVecParam::~IntVecParam(){{{*/
+IntVecParam::~IntVecParam(){
+	xDelete(values);
+	return;
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION IntVecParam::Echo {{{*/
+void IntVecParam::Echo(void){
+
+	_printLine_("IntVecParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   vector size: " << this->M);
+
+}
+/*}}}*/
+/*FUNCTION IntVecParam::DeepEcho{{{*/
+void IntVecParam::DeepEcho(void){
+
+	int i;
+	
+	_printLine_("IntVecParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   vector size: " << this->M);
+	for(i=0;iM;i++){
+		_printLine_(i << " " << this->values[i]);
+	}
+}
+/*}}}*/
+/*FUNCTION IntVecParam::Id{{{*/
+int    IntVecParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION IntVecParam::MyRank{{{*/
+int    IntVecParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION IntVecParam::ObjectEnum{{{*/
+int IntVecParam::ObjectEnum(void){
+
+	return IntVecParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION IntVecParam::copy{{{*/
+Object* IntVecParam::copy() {
+	
+	return new IntVecParam(this->enum_type,this->values,this->M);
+
+}
+/*}}}*/
+
+/*IntVecParam virtual functions definitions: */
+/*FUNCTION IntVecParam::GetParameterValue{{{*/
+void  IntVecParam::GetParameterValue(int** pintarray,int* pM){
+	int* output=NULL;
+
+	if(M){
+		output=xNew(M);
+		xMemCpy(output,values,M);
+	}
+
+	/*Assign output pointers:*/
+	if(pM) *pM=M;
+	*pintarray=output;
+}
+/*}}}*/
+/*FUNCTION IntVecParam::GetParameterName{{{*/
+void IntVecParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION IntVecParam::SetValue{{{*/
+void  IntVecParam::SetValue(int* intarray,int in_M){
+
+	/*avoid leak: */
+	xDelete(this->values);
+
+	if(in_M){
+		this->values=xNew(in_M);
+		xMemCpy(this->values,intarray,in_M);
+	}
+	else this->values=NULL;
+
+	this->M=in_M;
+}
+/*}}}*/
+/*FUNCTION IntVecParam::UnitConversion{{{*/
+void  IntVecParam::UnitConversion(int direction_enum){
+	/*do nothing, no unit conversion*/
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/IntVecParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/IntVecParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/IntVecParam.h	(revision 13395)
@@ -0,0 +1,79 @@
+/*! \file IntVecParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _INTVECPARAM_H_
+#define _INTVECPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class IntVecParam: public Param{
+
+	private: 
+		int enum_type;
+		int* values;
+		int M;
+
+	public:
+		/*IntVecParam constructors, destructors: {{{*/
+		IntVecParam();
+		IntVecParam(int enum_type,int* values,int M);
+		IntVecParam(int enum_type,IssmDouble* values,int M);
+		~IntVecParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param virtual functions definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an integer");}
+		void  GetParameterValue(int** pintarray,int* pM);
+		void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix");}
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array (maybe in serial?)");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");}
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a scalar");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble mat array");}
+		void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble mat array");}
+		void  SetValue(int* intarray,int M);
+		void  SetValue(int* pintarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int mat array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+		
+		void GetParameterName(char**pname);
+		/*}}}*/
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/Params/MatrixParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/MatrixParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/MatrixParam.cpp	(revision 13395)
@@ -0,0 +1,117 @@
+/*!\file MatrixParam.c
+ * \brief: implementation of the MatrixParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*MatrixParam constructors and destructor*/
+/*FUNCTION MatrixParam::MatrixParam(){{{*/
+MatrixParam::MatrixParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION MatrixParam::MatrixParam(int enum_type,Matrix* value){{{*/
+MatrixParam::MatrixParam(int in_enum_type,Matrix* in_value){
+
+	enum_type=in_enum_type;
+	value=NULL;
+
+	if(in_value){
+		value=in_value->Duplicate();
+	}
+}
+/*}}}*/
+/*FUNCTION MatrixParam::~MatrixParam(){{{*/
+MatrixParam::~MatrixParam(){
+	xdelete(&value);
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION MatrixParam::Echo {{{*/
+void MatrixParam::Echo(void){
+
+	_printLine_("MatrixParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+
+}
+/*}}}*/
+/*FUNCTION MatrixParam::DeepEcho{{{*/
+void MatrixParam::DeepEcho(void){
+
+	int i;
+	_printLine_("MatrixParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	this->value->Echo();
+}
+/*}}}*/
+/*FUNCTION MatrixParam::Id{{{*/
+int    MatrixParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION MatrixParam::MyRank{{{*/
+int    MatrixParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION MatrixParam::ObjectEnum{{{*/
+int MatrixParam::ObjectEnum(void){
+
+	return MatrixParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION MatrixParam::copy{{{*/
+Object* MatrixParam::copy() {
+	
+	return new MatrixParam(this->enum_type,this->value);
+
+}
+/*}}}*/
+
+/*MatrixParam virtual functions definitions: */
+/*FUNCTION MatrixParam::GetParameterValue{{{*/
+void  MatrixParam::GetParameterValue(Matrix** poutput){
+	Matrix* output=NULL;
+
+	if(value){
+		output=value->Duplicate();
+	}
+	*poutput=output;
+}
+/*}}}*/
+/*FUNCTION MatrixParam::GetParameterName{{{*/
+void MatrixParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION MatrixParam::SetValue{{{*/
+void  MatrixParam::SetValue(Matrix* matrix){
+	
+	/*avoid leak: */
+	xdelete(&value);
+	
+	/*copy: */
+	value=matrix->Duplicate();
+}
+/*}}}*/
+/*FUNCTION MatrixParam::UnitConversion{{{*/
+void  MatrixParam::UnitConversion(int direction_enum){
+	/*do nothing, no unit conversion*/
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/MatrixParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/MatrixParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/MatrixParam.h	(revision 13395)
@@ -0,0 +1,79 @@
+/*! \file MatrixParam.h 
+ *  \brief: header file for MatrixParam object
+ */
+
+
+#ifndef _MATRIXPARAM_H_
+#define _MATRIXPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class MatrixParam: public Param{
+
+	private: 
+		/*just hold 3 values for 3 vertices: */
+		int enum_type;
+		Matrix* value;
+
+	public:
+		/*MatrixParam constructors, destructors: {{{*/
+		MatrixParam();
+		MatrixParam(int enum_type,Matrix* value);
+		~MatrixParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an integer");}
+		void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a vec");}
+		void  GetParameterValue(Matrix** poutput);
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");}
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a scalar");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(int* pintarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat);
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+
+		void GetParameterName(char**pname);
+
+		/*}}}*/
+};
+#endif  /* _MATRIXPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/Param.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/Param.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/Param.h	(revision 13395)
@@ -0,0 +1,60 @@
+/*!\file:  Param.h
+ * \brief abstract class for Param object
+ */ 
+
+
+#ifndef _PARAM_H_
+#define _PARAM_H_
+
+/*Headers:*/
+/*{{{*/
+
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "../Object.h"
+#include "../Node.h"
+/*}}}*/
+
+class Param: public Object{
+
+	public: 
+		virtual        ~Param(){};
+
+		/*Virtual functions:*/
+		virtual int   InstanceEnum()=0;
+		virtual void  GetParameterValue(bool* pbool)=0;
+		virtual void  GetParameterValue(int* pinteger)=0;
+		virtual void  GetParameterValue(int** pintarray,int* pM)=0;
+		virtual void  GetParameterValue(int** pintarray,int* pM,int* pN)=0;
+		virtual void  GetParameterValue(IssmDouble* pIssmDouble)=0;
+		virtual void  GetParameterValue(IssmDouble* pdouble,IssmDouble time)=0;
+		virtual void  GetParameterValue(char** pstring)=0;
+		virtual void  GetParameterValue(char*** pstringarray,int* pM)=0;
+		virtual void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM)=0;
+		virtual void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM,int* pN)=0;
+		virtual void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims)=0;
+		virtual void  GetParameterValue(Vector** pvec)=0;
+		virtual void  GetParameterValue(Matrix** pmat)=0;
+		virtual void  GetParameterValue(FILE** pfid)=0;
+		
+		virtual void  SetValue(bool boolean)=0;
+		virtual void  SetValue(int integer)=0;
+		virtual void  SetValue(IssmDouble scalar)=0;
+		virtual void  SetValue(char* string)=0;
+		virtual void  SetValue(char** stringarray,int M)=0;
+		virtual void  SetValue(IssmDouble* IssmDoublearray,int M)=0;
+		virtual void  SetValue(IssmDouble* pIssmDoublearray,int M,int N)=0;
+		virtual void  SetValue(int* intarray,int M)=0;
+		virtual void  SetValue(int* pintarray,int M,int N)=0;
+		virtual void  SetValue(Vector* vec)=0;
+		virtual void  SetValue(Matrix* mat)=0;
+		virtual void  SetValue(FILE* fid)=0;
+		virtual void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array)=0;
+		virtual void  UnitConversion(int direction_enum)=0;
+		virtual void  GetParameterName(char**pname)=0;
+};
+#endif
Index: /issm/trunk/src/c/classes/objects/Params/StringArrayParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/StringArrayParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/StringArrayParam.cpp	(revision 13395)
@@ -0,0 +1,179 @@
+/*!\file StringArrayParam.c
+ * \brief: implementation of the StringArrayParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*StringArrayParam constructors and destructor*/
+/*FUNCTION StringArrayParam::StringArrayParam(){{{*/
+StringArrayParam::StringArrayParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION StringArrayParam::StringArrayParam(int enum_type,char** in_values,int in_numstrings){{{*/
+StringArrayParam::StringArrayParam(int in_enum_type,char** in_values, int in_numstrings){
+
+	int i;
+	int size;
+
+	enum_type=in_enum_type;
+	numstrings=in_numstrings;
+
+	if(numstrings){
+		value=xNew(numstrings);
+		for(i=0;i(size);
+			xMemCpy(string,in_values[i],size);
+			value[i]=string;
+		}
+	}
+	else value=NULL;
+	
+}
+/*}}}*/
+/*FUNCTION StringArrayParam::~StringArrayParam(){{{*/
+StringArrayParam::~StringArrayParam(){
+		
+	int i;
+	
+	char* string=NULL;
+	for(i=0;inumstrings;i++){
+		string=value[i];
+		xDelete(string);
+	}
+	xDelete(value);
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION StringArrayParam::Echo {{{*/
+void StringArrayParam::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION StringArrayParam::DeepEcho{{{*/
+void StringArrayParam::DeepEcho(void){
+
+	int i;
+	char* string=NULL;
+
+	_printLine_("StringArrayParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	for(i=0;inumstrings;i++){
+		string=this->value[i];
+		_printLine_("   " << i << ": " << string);
+	}
+}
+/*}}}*/
+/*FUNCTION StringArrayParam::Id{{{*/
+int    StringArrayParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION StringArrayParam::MyRank{{{*/
+int    StringArrayParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION StringArrayParam::ObjectEnum{{{*/
+int StringArrayParam::ObjectEnum(void){
+
+	return StringArrayParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION StringArrayParam::copy{{{*/
+Object* StringArrayParam::copy() {
+	
+	return new StringArrayParam(this->enum_type,this->value,this->numstrings);
+
+}
+/*}}}*/
+
+/*StringArrayParam virtual functions definitions: */
+/*FUNCTION StringArrayParam::GetParameterValue{{{*/
+void  StringArrayParam::GetParameterValue(char*** pstringarray,int* pM){
+	
+	int   i;
+	char** outstrings=NULL;
+	int   M;
+	char* string=NULL;
+	char* string2=NULL;
+	int   stringsize;
+
+	M=this->numstrings;
+	if(this->numstrings){
+		outstrings=xNew(this->numstrings);
+
+		for(i=0;inumstrings;i++){
+			string=this->value[i];
+			stringsize=strlen(string)+1;
+
+			string2=xNew(stringsize);
+			xMemCpy(string2,string,stringsize);
+
+			outstrings[i]=string2;
+		}
+	}
+	else outstrings=NULL;
+
+	/*Assign output pointers:*/
+	*pM=M;
+	*pstringarray=outstrings;
+}
+/*}}}*/
+/*FUNCTION StringArrayParam::GetParameterName{{{*/
+void StringArrayParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION StringArrayParam::SetValue{{{*/
+void  StringArrayParam::SetValue(char** stringarray,int M){
+	
+	int   i;
+	char *string     = NULL;
+	char *string2    = NULL;
+	int   stringsize;
+
+	/*first, avoid leak: */
+	for(i=0;inumstrings;i++){
+		string=this->value[i];
+		xDelete(string);
+	}
+	xDelete(this->value);
+
+	/*copy: */
+	this->numstrings=M;
+	this->value=xNew(this->numstrings);
+	for(i=0;inumstrings;i++){
+		string=stringarray[i];
+		stringsize=strlen(string)+1;
+
+		string2=xNew(stringsize);
+		xMemCpy(string2,string,stringsize);
+
+		this->value[i]=string2;
+	}
+}
+/*}}}*/
+/*FUNCTION StringArrayParam::UnitConversion{{{*/
+void  StringArrayParam::UnitConversion(int direction_enum){
+	/*do nothing, no unit conversion*/
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/StringArrayParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/StringArrayParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/StringArrayParam.h	(revision 13395)
@@ -0,0 +1,80 @@
+/*! \file StringArrayParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _STRINGARRAYPARAM_H_
+#define _STRINGARRAYPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class StringArrayParam: public Param{
+
+	private: 
+		/*just hold 3 values for 3 vertices: */
+		int      enum_type;
+		char**   value;
+		int      numstrings;
+
+
+	public:
+		/*StringArrayParam constructors, destructors: {{{*/
+		StringArrayParam();
+		StringArrayParam(int enum_type,char** values, int numstrings);
+		~StringArrayParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an integer");}
+		void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");}
+		void  GetParameterValue(char*** pstringarray,int* pM);
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Vec param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");}
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a scalar");}
+		void  SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");}
+		void  SetValue(char** stringarray,int M);
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(int* pintarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+
+		void GetParameterName(char**pname);
+		/*}}}*/
+};
+#endif  /* _STRINGARRAYPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/StringParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/StringParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/StringParam.cpp	(revision 13395)
@@ -0,0 +1,121 @@
+/*!\file StringParam.c
+ * \brief: implementation of the StringParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*StringParam constructors and destructor*/
+/*FUNCTION StringParam::StringParam(){{{*/
+StringParam::StringParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION StringParam::StringParam(int enum_type,IssmString value){{{*/
+StringParam::StringParam(int in_enum_type,char* in_value){
+
+	enum_type=in_enum_type;
+	value=xNew(strlen(in_value)+1);
+	xMemCpy(value,in_value,(strlen(in_value)+1));
+
+	
+}
+/*}}}*/
+/*FUNCTION StringParam::~StringParam(){{{*/
+StringParam::~StringParam(){
+	xDelete(value);
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION StringParam::Echo {{{*/
+void StringParam::Echo(void){
+	this->DeepEcho();
+}
+/*}}}*/
+/*FUNCTION StringParam::DeepEcho{{{*/
+void StringParam::DeepEcho(void){
+	_printLine_("StringParam:");
+	_printLine_("   enum:  " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   value: " << this->value);
+}
+/*}}}*/
+/*FUNCTION StringParam::Id{{{*/
+int    StringParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION StringParam::MyRank{{{*/
+int    StringParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION StringParam::ObjectEnum{{{*/
+int StringParam::ObjectEnum(void){
+
+	return StringParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION StringParam::copy{{{*/
+Object* StringParam::copy() {
+	
+	return new StringParam(this->enum_type,this->value);
+
+}
+/*}}}*/
+
+/*StringParam virtual functions definitions: */
+/*FUNCTION StringParam::GetParameterValue{{{*/
+void  StringParam::GetParameterValue(char** pstring){
+	
+	char* outstring=NULL;
+	int   stringsize;
+
+	stringsize=strlen(this->value)+1;
+
+	outstring=xNew(stringsize);
+	xMemCpy(outstring,this->value,stringsize);
+
+	*pstring=outstring;
+
+}
+/*}}}*/
+/*FUNCTION StringParam::GetParameterName{{{*/
+void StringParam::GetParameterName(char**pname){
+	EnumToStringx(pname,this->enum_type);
+}
+/*}}}*/
+/*FUNCTION StringParam::SetValue{{{*/
+void  StringParam::SetValue(char* string){
+	
+	int   stringsize;
+	
+	/*avoid leak: */
+	xDelete(this->value);
+
+	/*copy: */
+	stringsize=strlen(string)+1;
+	this->value=xNew(stringsize);
+	xMemCpy(this->value,string,stringsize);
+
+}
+/*}}}*/
+/*FUNCTION StringParam::UnitConversion{{{*/
+void  StringParam::UnitConversion(int direction_enum){
+	/*do nothing, no unit conversion*/
+}
+/*}}}*/
Index: /issm/trunk/src/c/classes/objects/Params/StringParam.h
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/StringParam.h	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/StringParam.h	(revision 13395)
@@ -0,0 +1,79 @@
+/*! \file StringParam.h 
+ *  \brief: header file for triavertexinput object
+ */
+
+
+#ifndef _STRINGPARAM_H_
+#define _STRINGPARAM_H_
+
+/*Headers:*/
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "./Param.h"
+#include "../../../include/include.h"
+#include "../../../shared/shared.h"
+/*}}}*/
+
+class StringParam: public Param{
+
+	private: 
+		/*just hold 3 values for 3 vertices: */
+		int enum_type;
+		char* value;
+
+	public:
+		/*StringParam constructors, destructors: {{{*/
+		StringParam();
+		StringParam(int enum_type,char* value);
+		~StringParam();
+		/*}}}*/
+		/*Object virtual functions definitions:{{{ */
+		void  Echo();
+		void  DeepEcho();
+		int   Id(); 
+		int   MyRank();
+		int   ObjectEnum();
+		Object* copy();
+		/*}}}*/
+		/*Param vritual function definitions: {{{*/
+		int   InstanceEnum(){return enum_type;}
+		void  GetParameterValue(bool* pbool){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");}
+		void  GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an integer");}
+		void  GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return an array of integers");}
+		void  GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");}
+		void  GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");}
+		void  GetParameterValue(char** pstring);
+		void  GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");}
+		void  GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a matrix array");}
+		void  GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");}
+		void  GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");}
+		void  GetParameterValue(FILE** pfid){_error_("Bool param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return a FILE");}
+
+		void  SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");}
+		void  SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");}
+		void  SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a scalar");}
+		void  SetValue(char* string);
+		void  SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");}
+		void  SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");}
+		void  SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(int* pintarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");}
+		void  SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");}
+		void  SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");}
+		void  SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a FILE");}
+		void  SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an array of matrices");}
+		void  UnitConversion(int direction_enum);
+
+		void GetParameterName(char**pname);
+
+		/*}}}*/
+};
+#endif  /* _STRINGPARAM_H */
Index: /issm/trunk/src/c/classes/objects/Params/TransientParam.cpp
===================================================================
--- /issm/trunk/src/c/classes/objects/Params/TransientParam.cpp	(revision 13395)
+++ /issm/trunk/src/c/classes/objects/Params/TransientParam.cpp	(revision 13395)
@@ -0,0 +1,151 @@
+/*!\file TransientParam.c
+ * \brief: implementation of the TransientParam object
+ */
+
+/*header files: */
+/*{{{*/
+#ifdef HAVE_CONFIG_H
+	#include 
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include 
+#include 
+#include "../objects.h"
+#include "../../../EnumDefinitions/EnumDefinitions.h"
+#include "../../../shared/shared.h"
+#include "../../../Container/Container.h"
+#include "../../../include/include.h"
+/*}}}*/
+
+/*TransientParam constructors and destructor*/
+/*FUNCTION TransientParam::TransientParam(){{{*/
+TransientParam::TransientParam(){
+	return;
+}
+/*}}}*/
+/*FUNCTION TransientParam::TransientParam(int enum_type,IssmDoubleMat value){{{*/
+TransientParam::TransientParam(int in_enum_type,IssmDouble* in_values,IssmDouble* in_time,int in_N){
+
+	_assert_(in_values && in_time);
+
+	enum_type=in_enum_type;
+	N=in_N;
+
+	values=xNew(N);
+	xMemCpy(values,in_values,N);
+
+	timesteps=xNew(N);
+	xMemCpy(timesteps,in_time,N);
+}
+/*}}}*/
+/*FUNCTION TransientParam::~TransientParam(){{{*/
+TransientParam::~TransientParam(){
+	xDelete(values);
+	xDelete(timesteps);
+}
+/*}}}*/
+
+/*Object virtual functions definitions:*/
+/*FUNCTION TransientParam::Echo {{{*/
+void TransientParam::Echo(void){
+
+	_printLine_("TransientParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   size: " << this->N);
+
+}
+/*}}}*/
+/*FUNCTION TransientParam::DeepEcho{{{*/
+void TransientParam::DeepEcho(void){
+
+	int i,j;
+	
+	_printLine_("TransientParam:");
+	_printLine_("   enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")");
+	_printLine_("   size: " << this->N);
+	for(i=0;iN;i++){
+		_printLine_(   "time: " << this->timesteps[i] << " value: " << this->values[i]);
+	}
+}
+/*}}}*/
+/*FUNCTION TransientParam::Id{{{*/
+int    TransientParam::Id(void){ return -1; }
+/*}}}*/
+/*FUNCTION TransientParam::MyRank{{{*/
+int    TransientParam::MyRank(void){ 
+	extern int my_rank;
+	return my_rank; 
+}
+/*}}}*/
+/*FUNCTION TransientParam::ObjectEnum{{{*/
+int TransientParam::ObjectEnum(void){
+
+	return TransientParamEnum;
+
+}
+/*}}}*/
+/*FUNCTION TransientParam::copy{{{*/
+Object* TransientParam::copy() {
+	
+	return new TransientParam(this->enum_type,this->values,this->timesteps,this->N);
+
+}
+/*}}}*/
+
+/*TransientParam virtual functions definitions: */
+/*FUNCTION TransientParam::GetParameterValue(IssmDouble* pdouble,IssmDouble time){{{*/
+void  TransientParam::GetParameterValue(IssmDouble* pdouble,IssmDouble time){
+
+	IssmDouble output;
+	bool   found;
+
+	/*Ok, we have the time, go through the timesteps, and figure out which interval we 
+	 *fall within. Then interpolate the values on this interval: */
+	if(timetimesteps[0]){
+		/*get values for the first time: */
+		output=this->values[0];
+		found=true;
+	}
+	else if(time>this->timesteps[this->N-1]){
+		/*get values for the last time: */
+		output=this->values[this->N-1];
+		found=true;
+	}
+	else{
+		/*Find which interval we fall within: */
+		for(int i=0;iN;i++){
+			if(time==this->timesteps[i]){
+				/*We are right on one step time: */
+				output=this->values[i];
+				found=true;
+				break; //we are done with the time interpolation.
+			}
+			else{
+				if(this->timesteps[i]