Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-ad.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-ad.sh (revision 11707) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour-ad.sh (revision 11708) @@ -8,15 +8,8 @@ --prefix=$ISSM_TIER \ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ - --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --without-blas-lapack-dir \ --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ --with-fortran-lib="/usr/local/lib/libgfortran.a" \ --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ @@ -41,4 +34,10 @@ #--without-prognostic \ - - +#--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +#--with-petsc-arch=$ISSM_ARCH \ +#--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +#--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +#--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +#--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +#--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +#--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ Index: /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour.sh =================================================================== --- /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour.sh (revision 11707) +++ /issm/branches/trunk-jpl-damage/configs/config-macosx64-larour.sh (revision 11708) @@ -9,15 +9,7 @@ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ - --with-petsc-arch=$ISSM_ARCH \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ - --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ - --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ - --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ - --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ --with-fortran-lib="/usr/local/lib/libgfortran.a" \ --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ @@ -25,3 +17,11 @@ --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-numthreads=8 \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ Index: /issm/branches/trunk-jpl-damage/cron/configs/macosx64_larour_validation =================================================================== --- /issm/branches/trunk-jpl-damage/cron/configs/macosx64_larour_validation (revision 11707) +++ /issm/branches/trunk-jpl-damage/cron/configs/macosx64_larour_validation (revision 11708) @@ -94,5 +94,5 @@ #ex: "'id',[101 102 103]" -NROPTIONS="'id',101:151" +NROPTIONS="'id',[101:136 138:151]" #------------------------# Index: /issm/branches/trunk-jpl-damage/m4/issm_options.m4 =================================================================== --- /issm/branches/trunk-jpl-damage/m4/issm_options.m4 (revision 11707) +++ /issm/branches/trunk-jpl-damage/m4/issm_options.m4 (revision 11708) @@ -19,4 +19,5 @@ AC_MSG_CHECKING(for serial compilation) AM_CONDITIONAL([NOSERIAL], [test $SERIAL_VALUE = no]) + AM_CONDITIONAL([SERIAL], [test $SERIAL_VALUE = yes]) AC_MSG_RESULT($SERIAL_VALUE) dnl }}} @@ -28,4 +29,5 @@ AC_MSG_CHECKING(for parallel compilation) AM_CONDITIONAL([NOPARALLEL], [test $PARALLEL_VALUE = no]) + AM_CONDITIONAL([PARALLEL], [test $PARALLEL_VALUE = yes]) AC_MSG_RESULT($PARALLEL_VALUE) ISSMEXT=".exe" @@ -505,12 +507,13 @@ [petsc root directory, necessary for parallel build]), [PETSC_ROOT=$withval],[PETSC_ROOT=""]) - - if test "$PARALLEL_VALUE" = "yes" ; then - if test "$PETSC_ROOT" = "" ; then - AC_MSG_ERROR([missing --with-petsc-dir argument for parallel compilation!]) - fi - fi - - dnl if test "$PARALLEL_VALUE" = "yes" ; then + + dnl Used to be necessary, not anymore. + dnl if test "$PARALLEL_VALUE" = "yes" ; then + dnl if test "$PETSC_ROOT" = "" ; then + dnl AC_MSG_ERROR([missing --with-petsc-dir argument for parallel compilation!]) + dnl fi + dnl fi + + if test -d "$PETSC_ROOT"; then AC_MSG_CHECKING(for petsc version) PETSC_MAJOR=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_MAJOR" | sed 's/#define PETSC_VERSION_MAJOR//' | sed 's/ //g'` @@ -519,7 +522,6 @@ AC_DEFINE_UNQUOTED([_PETSC_MINOR_],$PETSC_MINOR,[ Petsc version minor]) AC_MSG_RESULT($PETSC_MAJOR.$PETSC_MINOR) - dnl fi - - + fi + AC_ARG_WITH([petsc-arch], AS_HELP_STRING([--with-petsc-arch = DIR], @@ -527,9 +529,10 @@ [PETSC_ARCH=$withval],[PETSC_ARCH=""]) - if test "$PARALLEL_VALUE" = "yes" ; then - if test "$PETSC_ARCH" = "" ; then - AC_MSG_ERROR([missing --with-petsc-arch argument for parallel compilation!]) - fi - fi + dnl Used to be necessary, not anymore. + dnl if test "$PARALLEL_VALUE" = "yes" ; then + dnl if test "$PETSC_ARCH" = "" ; then + dnl AC_MSG_ERROR([missing --with-petsc-arch argument for parallel compilation!]) + dnl fi + dnl fi AC_MSG_CHECKING(for Petsc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH) @@ -573,9 +576,13 @@ fi - if test $HAVE_PETSC = no; then - AC_MSG_ERROR([could not find petsc. user should specify --with-petsc-dir and --with-petsc-arch options. Petsc is needed to run ISSM!]) - else - AC_MSG_RESULT($HAVE_PETSC) - fi + dnl used to e necessary, not anymore. + dnl if test $HAVE_PETSC = no; then + dnl AC_MSG_ERROR([could not find petsc. user should specify --with-petsc-dir and --with-petsc-arch options. Petsc is needed to run ISSM!]) + dnl else + dnl AC_MSG_RESULT($HAVE_PETSC) + dnl fi + + AM_CONDITIONAL([PETSC], [test x$HAVE_PETSC = xyes]) + AC_MSG_RESULT($HAVE_PETSC) dnl }}} dnl tao{{{1 Index: /issm/branches/trunk-jpl-damage/src/c/Container/Elements.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Elements.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Elements.cpp (revision 11708) @@ -175,5 +175,5 @@ double *resultstimes = NULL; double *vector_serial= NULL; - Vec vector = NULL; + Vector* vector = NULL; bool io_gather; bool results_as_patches; @@ -225,5 +225,5 @@ else if(resultssizes[i]==P0Enum) vectorsize=numberofelements; else _error_("Unkown result size: %s",EnumToStringx(resultssizes[i])); - vector=NewVec(vectorsize); + vector=new Vector(vectorsize); for(int j=0;jSize();j++){ @@ -231,9 +231,8 @@ element->GetVectorFromResults(vector,i,resultssizes[i]); } - VecAssemblyBegin(vector); - VecAssemblyEnd(vector); + vector->Assemble(); /*Serialize and add to results*/ - VecToMPISerial(&vector_serial,vector); + vector_serial=vector->ToMPISerial(); if(my_rank==0){ /*No need to add this vector for all cpus*/ @@ -242,5 +241,5 @@ /*clean up*/ - VecFree(&vector); + xdelete(&vector); xfree((void**)&vector_serial); } Index: /issm/branches/trunk-jpl-damage/src/c/Container/Parameters.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Parameters.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Parameters.cpp (revision 11708) @@ -227,6 +227,6 @@ } /*}}}*/ -/*FUNCTION Parameters::FindParam(Vec* pvec,int enum_type){{{1*/ -void Parameters::FindParam(Vec* pvec,int enum_type){ _assert_(this); +/*FUNCTION Parameters::FindParam(Vector** pvec,int enum_type){{{1*/ +void Parameters::FindParam(Vector** pvec,int enum_type){ _assert_(this); vector::iterator object; @@ -245,6 +245,6 @@ } /*}}}*/ -/*FUNCTION Parameters::FindParam(Mat* pmat,int enum_type){{{1*/ -void Parameters::FindParam(Mat* pmat,int enum_type){ _assert_(this); +/*FUNCTION Parameters::FindParam(Matrix** pmat,int enum_type){{{1*/ +void Parameters::FindParam(Matrix** pmat,int enum_type){ _assert_(this); vector::iterator object; @@ -389,6 +389,6 @@ } /*}}}*/ -/*FUNCTION Parameters::SetParam(Vec vector,int enum_type);{{{1*/ -void Parameters::SetParam(Vec vector,int enum_type){ +/*FUNCTION Parameters::SetParam(Vector* vector,int enum_type);{{{1*/ +void Parameters::SetParam(Vector* vector,int enum_type){ Param* param=NULL; @@ -398,9 +398,9 @@ if(param) param->SetValue(vector); //already exists, just set it. - else this->AddObject(new PetscVecParam(enum_type,vector)); //just add the new parameter. -} -/*}}}*/ -/*FUNCTION Parameters::SetParam(Mat matrix,int enum_type);{{{1*/ -void Parameters::SetParam(Mat matrix,int enum_type){ + else this->AddObject(new VectorParam(enum_type,vector)); //just add the new parameter. +} +/*}}}*/ +/*FUNCTION Parameters::SetParam(Matrix* matrix,int enum_type);{{{1*/ +void Parameters::SetParam(Matrix* matrix,int enum_type){ Param* param=NULL; @@ -410,5 +410,5 @@ if(param) param->SetValue(matrix); //already exists, just set it. - else this->AddObject(new PetscMatParam(enum_type,matrix)); //just add the new parameter. + else this->AddObject(new MatrixParam(enum_type,matrix)); //just add the new parameter. } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/Container/Parameters.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Container/Parameters.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/Container/Parameters.h (revision 11708) @@ -7,4 +7,6 @@ /*forward declarations */ +class Matrix; +class Vector; class Materials; class Parameters; @@ -37,6 +39,6 @@ void FindParam(double** pdoublearray,int* pM,int* pN,int enum_type); void FindParam(double*** parray,int* pM, int** pmdims_array,int** pndims_array,int enum_type); - void FindParam(Vec* pvec,int enum_type); - void FindParam(Mat* 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); @@ -50,6 +52,6 @@ void SetParam(int* intarray,int M,int enum_type); void SetParam(int* intarray,int M,int N,int enum_type); - void SetParam(Vec vec,int enum_type); - void SetParam(Mat 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); Index: /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/EnumDefinitions.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/EnumDefinitions.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/EnumDefinitions/EnumDefinitions.h (revision 11708) @@ -266,6 +266,6 @@ PentaEnum, PentaP1InputEnum, - PetscMatParamEnum, - PetscVecParamEnum, + MatrixParamEnum, + VectorParamEnum, RiftfrontEnum, SegmentEnum, Index: /issm/branches/trunk-jpl-damage/src/c/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/Makefile.am (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/Makefile.am (revision 11708) @@ -79,6 +79,4 @@ ./objects/ExternalResults/StringExternalResult.h\ ./objects/ExternalResults/StringExternalResult.cpp\ - ./objects/ExternalResults/PetscVecExternalResult.h\ - ./objects/ExternalResults/PetscVecExternalResult.cpp\ ./objects/Elements/Tria.h\ ./objects/Elements/Tria.cpp\ @@ -137,6 +135,4 @@ ./objects/Params/FileParam.cpp\ ./objects/Params/FileParam.h\ - ./objects/Params/PetscMatParam.cpp\ - ./objects/Params/PetscMatParam.h\ ./objects/Params/StringArrayParam.cpp\ ./objects/Params/StringArrayParam.h\ @@ -149,8 +145,10 @@ ./objects/Params/DoubleVecParam.cpp\ ./objects/Params/DoubleVecParam.h\ - ./objects/Params/PetscVecParam.cpp\ - ./objects/Params/PetscVecParam.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\ ./Container/Container.h\ ./Container/Constraints.h\ @@ -195,5 +193,5 @@ ./shared/Numerics/XZvectorsToCoordinateSystem.cpp\ ./shared/Numerics/UnitConversion.cpp\ - ./shared/Numerics/PetscOptionsFromAnalysis.cpp\ + ./shared/Numerics/OptionsFromAnalysis.cpp\ ./shared/Exceptions/exceptions.h\ ./shared/Exceptions/Exceptions.cpp\ @@ -209,37 +207,7 @@ ./shared/Elements/GetNumberOfDofs.cpp\ ./shared/String/sharedstring.h\ - ./toolkits/petsc\ - ./toolkits/petsc/patches\ - ./toolkits/petsc/patches/SolverEnum.h\ - ./toolkits/petsc/patches/petscpatches.h\ - ./toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp\ - ./toolkits/petsc/patches/MatlabVectorToPetscVector.cpp\ - ./toolkits/petsc/patches/PetscMatrixToMatlabMatrix.cpp\ - ./toolkits/petsc/patches/PetscVectorToMatlabVector.cpp\ - ./toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp\ - ./toolkits/petsc/patches/MatlabVectorToDoubleVector.cpp\ - ./toolkits/petsc/patches/PetscDetermineLocalSize.cpp\ - ./toolkits/petsc/patches/VecTranspose.cpp\ - ./toolkits/petsc/patches/VecToMPISerial.cpp\ - ./toolkits/petsc/patches/MatToSerial.cpp\ - ./toolkits/petsc/patches/VecMerge.cpp\ - ./toolkits/petsc/patches/NewVec.cpp\ - ./toolkits/petsc/patches/PetscOptionsDetermineSolverType.cpp\ - ./toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp\ - ./toolkits/petsc/patches/NewMat.cpp\ - ./toolkits/petsc/patches/SerialToVec.cpp\ - ./toolkits/petsc/patches/VecFree.cpp\ - ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ - ./toolkits/petsc/patches/KSPFree.cpp\ - ./toolkits/petsc/patches/ISFree.cpp\ - ./toolkits/petsc/patches/MatFree.cpp\ - ./toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp\ - ./toolkits/petsc/patches/VecPartition.cpp\ - ./toolkits/petsc/patches/MatPartition.cpp\ - ./toolkits/petsc/patches/MatInvert.cpp\ - ./toolkits/petsc/patches/MatMultPatch.cpp\ - ./toolkits/petsc/petscincludes.h\ ./toolkits/mpi/mpiincludes.h\ ./toolkits/mpi/patches/mpipatches.h\ + ./toolkits/mpi/patches/DetermineLocalSize.cpp\ ./toolkits/mpi/patches/MPI_Upperrow.cpp\ ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ @@ -249,4 +217,5 @@ ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp\ ./toolkits/triangle/triangleincludes.h\ + ./toolkitsenums.h\ ./toolkits.h\ ./io/io.h\ @@ -268,6 +237,4 @@ ./modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp\ ./modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp\ - ./modules/ParsePetscOptionsx/ParsePetscOptionsx.h\ - ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\ ./modules/NodesDofx/NodesDofx.h\ ./modules/NodesDofx/NodesDofx.cpp\ @@ -344,7 +311,5 @@ ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.cpp\ ./modules/Solverx/Solverx.cpp\ - ./modules/Solverx/SolverxPetsc.cpp\ ./modules/Solverx/Solverx.h\ - ./modules/Solverx/DofTypesToIndexSet.cpp\ ./modules/VecMergex/VecMergex.cpp\ ./modules/VecMergex/VecMergex.h\ @@ -731,8 +696,49 @@ ./toolkits/matlab/MatlabMatrixToMatrix.cpp\ ./toolkits/matlab/MatlabVectorToVector.cpp\ + ./toolkits/double/MatlabVectorToDoubleVector.cpp\ + ./toolkits/double/double.h\ + ./toolkits/double/MatlabMatrixToDoubleMatrix.cpp\ ./io/Matlab/matlabio.h\ ./io/Matlab/WriteMatlabData.cpp\ ./io/Matlab/FetchMatlabData.cpp\ ./io/Matlab/OptionParse.cpp +#}}} +#Petsc sources {{{1 +petsc_sources= ./toolkits/petsc\ + ./toolkits/petsc/patches\ + ./toolkits/petsc/patches/SolverEnum.h\ + ./toolkits/petsc/patches/petscpatches.h\ + ./toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp\ + ./toolkits/petsc/patches/MatlabVectorToPetscVector.cpp\ + ./toolkits/petsc/patches/PetscMatrixToMatlabMatrix.cpp\ + ./toolkits/petsc/patches/PetscVectorToMatlabVector.cpp\ + ./toolkits/petsc/patches/VecTranspose.cpp\ + ./toolkits/petsc/patches/VecToMPISerial.cpp\ + ./toolkits/petsc/patches/MatToSerial.cpp\ + ./toolkits/petsc/patches/VecMerge.cpp\ + ./toolkits/petsc/patches/NewVec.cpp\ + ./toolkits/petsc/patches/PetscOptionsDetermineSolverType.cpp\ + ./toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp\ + ./toolkits/petsc/patches/NewMat.cpp\ + ./toolkits/petsc/patches/SerialToVec.cpp\ + ./toolkits/petsc/patches/VecFree.cpp\ + ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ + ./toolkits/petsc/patches/KSPFree.cpp\ + ./toolkits/petsc/patches/ISFree.cpp\ + ./toolkits/petsc/patches/MatFree.cpp\ + ./toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp\ + ./toolkits/petsc/patches/VecPartition.cpp\ + ./toolkits/petsc/patches/MatPartition.cpp\ + ./toolkits/petsc/patches/MatInvert.cpp\ + ./toolkits/petsc/patches/MatMultPatch.cpp\ + ./toolkits/petsc/patches/ISSMToPetscInsertMode.cpp\ + ./toolkits/petsc/patches/ISSMToPetscNormMode.cpp\ + ./toolkits/petsc/petscincludes.h\ + ./shared/Numerics/PetscOptionsFromAnalysis.cpp\ + ./modules/ParsePetscOptionsx/ParsePetscOptionsx.h\ + ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\ + ./modules/Solverx/SolverxPetsc.cpp\ + ./modules/Solverx/DofTypesToIndexSet.cpp + #}}} #Serialsources {{{1 @@ -835,4 +841,9 @@ endif +if PETSC +issm_sources += $(petsc_sources) +issm_psources += $(petsc_psources) +endif + if TRANSIENT issm_sources += $(transient_sources) @@ -898,4 +909,5 @@ #ISSM serial library {{{1 +if SERIAL libISSM_a_SOURCES = $(issm_sources) libISSM_a_SOURCES += $(serial_sources) @@ -910,9 +922,12 @@ libISSM_a_CXXFLAGS += -DMX_COMPAT_32 endif +endif #}}} #ISSM parallel library {{{1 +if PARALLEL libpISSM_a_SOURCES = $(issm_sources) libpISSM_a_SOURCES += $(issm_psources) libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXFLAGS) $(CXXOPTFLAGS) +endif #}}} #Overload library, to overload any non-standard symbols. {{{1 Index: /issm/branches/trunk-jpl-damage/src/c/io/Matlab/FetchMatlabData.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/io/Matlab/FetchMatlabData.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/io/Matlab/FetchMatlabData.cpp (revision 11708) @@ -276,31 +276,4 @@ } /*}}}*/ -/*FUNCTION FetchMatlabData(Mat* pmatrix,const mxArray* dataref){{{1*/ -void FetchMatlabData(Mat* pmatrix,const mxArray* dataref){ - - Mat outmatrix=NULL; - int dummy=0; - - if (mxIsClass(dataref,"double") ){ - - /*Check dataref is not pointing to NaN: */ - if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ - outmatrix=NULL; - } - else{ - - /*Convert matlab matrix to petsc matrix: */ - MatlabMatrixToPetscMatrix(&outmatrix,&dummy,&dummy,dataref); - } - } - else{ - /*This is an error: we don't have the correct input!: */ - _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); - } - - /*Assign output pointers:*/ - *pmatrix=outmatrix; -} -/*}}}*/ /*FUNCTION FetchMatlabData(Matrix** pmatrix,const mxArray* dataref){{{1*/ void FetchMatlabData(Matrix** pmatrix,const mxArray* dataref){ @@ -451,28 +424,4 @@ *pvector=outvector; if (pM)*pM=outvector_rows; -} -/*}}}*/ -/*FUNCTION FetchMatlabData(Vec* pvector,const mxArray* dataref){{{1*/ -void FetchMatlabData(Vec* pvector,const mxArray* dataref){ - - Vec vector=NULL; - int dummy; - - if(mxIsEmpty(dataref)){ - /*Nothing to pick up. Just initialize matrix pointer to NULL: */ - vector=NULL; - } - else if (mxIsClass(dataref,"double") ){ - - /*Convert matlab vector to petsc vector: */ - MatlabVectorToPetscVector(&vector,&dummy,dataref); - } - else{ - /*This is an error: we don't have the correct input!: */ - _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); - } - - /*Assign output pointers:*/ - *pvector=vector; } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/io/Matlab/WriteMatlabData.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/io/Matlab/WriteMatlabData.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/io/Matlab/WriteMatlabData.cpp (revision 11708) @@ -41,21 +41,4 @@ } /*}}}*/ -/*FUNCTION WriteMatlabData(mxArray** pdataref,Mat matrix){{{1*/ -void WriteMatlabData(mxArray** pdataref,Mat matrix){ - - mxArray* dataref=NULL; - - if(matrix){ - - /*call toolkit routine: */ - PetscMatrixToMatlabMatrix(&dataref,matrix); - } - else{ - dataref = mxCreateDoubleMatrix(0,0,mxREAL); - } - - *pdataref=dataref; -} -/*}}}*/ /*FUNCTION WriteMatlabData(mxArray** pdataref,Matrix* matrix){{{1*/ void WriteMatlabData(mxArray** pdataref,Matrix* matrix){ @@ -123,21 +106,4 @@ } *pdataref=dataref; -} -/*}}}*/ -/*FUNCTION WriteMatlabData(mxArray** pdataref,Vec vector){{{1*/ -void WriteMatlabData(mxArray** pdataref,Vec vector){ - - mxArray* dataref=NULL; - - if(vector){ - - /*call toolkit routine: */ - PetscVectorToMatlabVector(&dataref,vector); - } - else{ - dataref = mxCreateDoubleMatrix(0,0,mxREAL); - } - *pdataref=dataref; - } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/io/Matlab/matlabio.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/io/Matlab/matlabio.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/io/Matlab/matlabio.h (revision 11708) @@ -16,9 +16,7 @@ #include void WriteMatlabData(mxArray** pdataref,DataSet* dataset); -void WriteMatlabData(mxArray** pdataref,Mat matrix); void WriteMatlabData(mxArray** pdataref,Matrix* matrix); void WriteMatlabData(mxArray** pdataref,double* matrix, int M,int N); void WriteMatlabData(mxArray** pdataref,int* matrix, int M,int N); -void WriteMatlabData(mxArray** pdataref,Vec vector); void WriteMatlabData(mxArray** pdataref,Vector* vector); void WriteMatlabData(mxArray** pdataref,double* vector, int M); @@ -35,5 +33,4 @@ void FetchMatlabData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref); void FetchMatlabData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); -void FetchMatlabData(Mat* pmatrix,const mxArray* dataref); void FetchMatlabData(Matrix** pmatrix,const mxArray* dataref); void FetchMatlabData(int** pvector,int* pM,const mxArray* dataref); @@ -41,5 +38,4 @@ void FetchMatlabData(double** pvector,int* pM,const mxArray* dataref); void FetchMatlabData(bool** pvector,int* pM,const mxArray* dataref); -void FetchMatlabData(Vec* pvector,const mxArray* dataref); void FetchMatlabData(Vector** pvector,const mxArray* dataref); void FetchMatlabData(char** pstring,const mxArray* dataref); Index: /issm/branches/trunk-jpl-damage/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp (revision 11708) @@ -29,7 +29,7 @@ /*output: */ - Vec partition_contributions=NULL; - Vec partition_areas=NULL; - Vec vec_average=NULL; + Vector* partition_contributions=NULL; + Vector* partition_areas=NULL; + Vector* vec_average=NULL; double* average=NULL; @@ -44,7 +44,7 @@ /*allocate: */ - partition_contributions=NewVec(npart); - partition_areas=NewVec(npart); - vec_average=NewVec(npart); + partition_contributions=new Vector(npart); + partition_areas=new Vector(npart); + vec_average=new Vector(npart); /*loop on each element, and add contribution of the element to the partition (surface weighted average): */ @@ -55,21 +55,18 @@ /*Assemble: */ - VecAssemblyBegin(partition_contributions); - VecAssemblyEnd(partition_contributions); - - VecAssemblyBegin(partition_areas); - VecAssemblyEnd(partition_areas); + partition_contributions->Assemble(); + partition_areas->Assemble(); /*We have the partition_areas and the partition_contributions for each partition -> compute the surfae weighted average: */ - VecPointwiseDivide(vec_average,partition_contributions,partition_areas); + vec_average->PointwiseDivide(partition_contributions,partition_areas); /*serialize:*/ - VecToMPISerial(&average,vec_average); + average=vec_average->ToMPISerial(); /*Free ressources:*/ xfree((void**)&qmu_part); - VecFree(&partition_contributions); - VecFree(&partition_areas); - VecFree(&vec_average); + xdelete(&partition_contributions); + xdelete(&partition_areas); + xdelete(&vec_average); /*Assign output pointers:*/ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp (revision 11708) @@ -10,5 +10,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void ComputeBasalStressx( Vec* psigma,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){ +void ComputeBasalStressx( Vector** psigma,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){ /*Intermediary*/ @@ -19,5 +19,5 @@ /*output: */ - Vec sigma=NULL; + Vector* sigma=NULL; /*Recover numberofelements: */ @@ -25,5 +25,5 @@ /*Allocate sigma on numberofelements: */ - sigma=NewVec((int)numberofelements); + sigma=new Vector((int)numberofelements); /*Compute basal stress for each element: */ @@ -34,6 +34,5 @@ /*Assemble vector: */ - VecAssemblyBegin(sigma); - VecAssemblyEnd(sigma); + sigma->Assemble(); /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.h (revision 11708) @@ -10,5 +10,5 @@ /* local prototypes: */ -void ComputeBasalStressx( Vec* pp_g,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); +void ComputeBasalStressx( Vector** pp_g,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); #endif /* _COMPUTEBASALSTRESSX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp (revision 11708) @@ -10,5 +10,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void ComputeStrainRatex( Vec* peps,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){ +void ComputeStrainRatex( Vector** peps,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){ /*Intermediary*/ @@ -19,5 +19,5 @@ /*output: */ - Vec eps=NULL; + Vector* eps=NULL; /*Recover numberofelements: */ @@ -25,5 +25,5 @@ /*Allocate eps on numberofelements (only 1 dof): */ - eps=NewVec(numberofelements); + eps=new Vector(numberofelements); /*Compute basal stress for each element: */ @@ -34,6 +34,5 @@ /*Assemble vector: */ - VecAssemblyBegin(eps); - VecAssemblyEnd(eps); + eps->Assemble(); /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.h (revision 11708) @@ -10,5 +10,5 @@ /* local prototypes: */ -void ComputeStrainRatex(Vec* eps_g,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); +void ComputeStrainRatex(Vector** eps_g,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); #endif /* _COMPUTESTRAINRATEX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 11708) @@ -11,5 +11,5 @@ #include "./ContourToMeshx.h" -int ContourToMeshx( Vec* pin_nod,Vec* pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue) { +int ContourToMeshx( Vector** pin_nod,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue) { int noerr=1; @@ -30,9 +30,9 @@ /*output: */ - Vec in_nod=NULL; - Vec in_elem=NULL; + Vector* in_nod=NULL; + Vector* in_elem=NULL; - in_nod=NewVec(nods); - in_elem=NewVec(nel); + in_nod=new Vector(nods); + in_elem=new Vector(nel); /*initialize thread parameters: */ @@ -49,9 +49,8 @@ /*Assemble in_nod: */ - VecAssemblyBegin(in_nod); - VecAssemblyEnd(in_nod); + in_nod->Assemble(); /*Get in_nod serialised for next operation: */ - VecToMPISerial(&in_nod_serial,in_nod); + in_nod_serial=in_nod->ToMPISerial(); /*Take care of the case where an element interpolation has been requested: */ @@ -59,5 +58,5 @@ for (n=0;nSetValue(n,value,INS_VAL); } } @@ -65,6 +64,5 @@ /*Assemble vectors: */ - VecAssemblyBegin(in_elem); - VecAssemblyEnd(in_elem); + in_elem->Assemble(); /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 11708) @@ -17,5 +17,5 @@ int nods; int edgevalue; - Vec in_nod; + Vector* in_nod; double* x; double* y; @@ -25,5 +25,5 @@ /* local prototypes: */ -int ContourToMeshx( Vec* pin_nods,Vec* pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue); +int ContourToMeshx( Vector** pin_nods,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue); void* ContourToMeshxt(void* vContourToMeshxThreadStruct); Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 11708) @@ -39,5 +39,5 @@ double* x=NULL; double* y=NULL; - Vec in_nod=NULL; + Vector* in_nod=NULL; Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.cpp (revision 11708) @@ -4,5 +4,5 @@ #include "./ContourToNodesx.h" -int ContourToNodesx( Vec* pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue){ +int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue){ int i; @@ -17,7 +17,7 @@ /*output: */ - Vec flags=NULL; + Vector* flags=NULL; - flags=NewVec(nods); + flags=new Vector(nods); /*Loop through all contours: */ @@ -31,6 +31,5 @@ /*Assemble vector: */ - VecAssemblyBegin(flags); - VecAssemblyEnd(flags); + flags->Assemble(); /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ContourToNodesx/ContourToNodesx.h (revision 11708) @@ -11,5 +11,5 @@ /* local prototypes: */ -int ContourToNodesx( Vec* pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue); +int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue); #endif /* _CONTOURTONODESX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp (revision 11708) @@ -9,10 +9,10 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void ControlInputGetGradientx( Vec* pgradient, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){ +void ControlInputGetGradientx( Vector** pgradient, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){ /*Intermediaries*/ int num_controls; int *control_type = NULL; - Vec gradient=NULL; + Vector* gradient=NULL; /*Retrieve some parameters*/ @@ -21,5 +21,5 @@ /*Allocate and populate gradient*/ - gradient=NewVec(num_controls*vertices->NumberOfVertices()); + gradient=new Vector(num_controls*vertices->NumberOfVertices()); for(int i=0;iAssemble(); /*Clean up and return*/ Index: /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.h (revision 11708) @@ -8,5 +8,5 @@ #include "../../Container/Container.h" -void ControlInputGetGradientx( Vec* pgradient, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); +void ControlInputGetGradientx( Vector** pgradient, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); #endif Index: /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp (revision 11708) @@ -30,9 +30,9 @@ } -void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec gradient){ +void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* gradient){ /*Serialize gradient*/ double* serial_gradient=NULL; - VecToMPISerial(&serial_gradient,gradient); + serial_gradient=gradient->ToMPISerial(); ControlInputSetGradientx(elements,nodes,vertices, loads, materials, parameters,serial_gradient); Index: /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.h (revision 11708) @@ -9,5 +9,5 @@ void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,double* gradient); -void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec gradient); +void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* gradient); #endif Index: /issm/branches/trunk-jpl-damage/src/c/modules/EnumToStringx/EnumToStringx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 11708) @@ -262,6 +262,6 @@ case PentaEnum : return "Penta"; case PentaP1InputEnum : return "PentaP1Input"; - case PetscMatParamEnum : return "PetscMatParam"; - case PetscVecParamEnum : return "PetscVecParam"; + case MatrixParamEnum : return "MatrixParam"; + case VectorParamEnum : return "VectorParam"; case RiftfrontEnum : return "Riftfront"; case SegmentEnum : return "Segment"; Index: /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp (revision 11708) @@ -9,9 +9,9 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void GetVectorFromControlInputsx(Vec* pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){ +void GetVectorFromControlInputsx(Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){ int num_controls; int *control_type = NULL; - Vec vector=NULL; + Vector* vector=NULL; /*Retrieve some parameters*/ @@ -20,5 +20,5 @@ /*Allocate and populate gradient*/ - vector=NewVec(num_controls*vertices->NumberOfVertices()); + vector=new Vector(num_controls*vertices->NumberOfVertices()); for(int i=0;iAssemble(); /*Assign output pointers:*/ @@ -43,11 +42,11 @@ /*intermediary: */ - Vec vec_vector=NULL; + Vector* vec_vector=NULL; GetVectorFromControlInputsx( &vec_vector, elements,nodes, vertices, loads, materials, parameters,data); - VecToMPISerial(&vector,vec_vector); + vector=vec_vector->ToMPISerial(); /*Free ressources:*/ - VecFree(&vec_vector); + xdelete(&vec_vector); /*Assign output pointers:*/ Index: /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h (revision 11708) @@ -9,5 +9,5 @@ /* local prototypes: */ -void GetVectorFromControlInputsx( Vec* pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); +void GetVectorFromControlInputsx( Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); void GetVectorFromControlInputsx( double** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); Index: /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp (revision 11708) @@ -9,13 +9,13 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void GetVectorFromInputsx( Vec* pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, int name, int type){ +void GetVectorFromInputsx( Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, int name, int type){ int i; - Vec vector=NULL; + Vector* vector=NULL; if(type==VertexEnum){ /*Allocate vector*/ - vector=NewVec(vertices->NumberOfVertices()); + vector=new Vector(vertices->NumberOfVertices()); /*Look up in elements*/ @@ -35,6 +35,5 @@ } - VecAssemblyBegin(vector); - VecAssemblyEnd(vector); + vector->Assemble(); /*Assign output pointers:*/ @@ -48,11 +47,11 @@ /*intermediary: */ - Vec vec_vector=NULL; + Vector* vec_vector=NULL; GetVectorFromInputsx( &vec_vector, elements,nodes, vertices, loads, materials, parameters, name, type); - VecToMPISerial(&vector,vec_vector); + vector=vec_vector->ToMPISerial(); /*Free ressources:*/ - VecFree(&vec_vector); + xdelete(&vec_vector); /*Assign output pointers:*/ Index: /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h (revision 11708) @@ -9,5 +9,5 @@ /* local prototypes: */ -void GetVectorFromInputsx( Vec* pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int name,int type); +void GetVectorFromInputsx( Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int name,int type); void GetVectorFromInputsx( double** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int name,int type); Index: /issm/branches/trunk-jpl-damage/src/c/modules/Gradjx/Gradjx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Gradjx/Gradjx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Gradjx/Gradjx.cpp (revision 11708) @@ -10,5 +10,5 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void Gradjx(Vec* pgradient,double** pnorm_list, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){ +void Gradjx(Vector** pgradient,double** pnorm_list, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){ int i,j,numberofvertices; @@ -17,6 +17,6 @@ double *norm_list = NULL; int *control_type = NULL; - Vec gradient = NULL; - Vec *gradient_list = NULL; + Vector* gradient = NULL; + Vector* *gradient_list = NULL; /*retrieve some parameters: */ @@ -26,10 +26,10 @@ /*Allocate gradient_list */ - gradient_list = (Vec*)xmalloc(num_controls*sizeof(Vec)); + gradient_list = (Vector**)xmalloc(num_controls*sizeof(Vector*)); norm_list = (double*)xmalloc(num_controls*sizeof(double)); for(i=0;iAssemble(); - VecNorm(gradient_list[i],NORM_INFINITY,&norm_list[i]); + norm_list[i]=gradient_list[i]->Norm(NORM_INF); } /*Add all gradient_list together*/ for(i=0;iAXPY(gradient_list[i],1.0); + xdelete(&gradient_list[i]); } /*Check that gradient is clean*/ - VecNorm(gradient,NORM_INFINITY,&norm_inf); + norm_inf=gradient->Norm(NORM_INF); if(norm_inf<=0) _error_("||∂J/∂α||∞ = 0 gradient norm is zero"); if(isnan(norm_inf))_error_("||∂J/∂α||∞ = NaN gradient norm is NaN"); Index: /issm/branches/trunk-jpl-damage/src/c/modules/Gradjx/Gradjx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Gradjx/Gradjx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Gradjx/Gradjx.h (revision 11708) @@ -10,5 +10,5 @@ /* local prototypes: */ -void Gradjx(Vec* pgrad_g,double** pgrad_norm,Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters); +void Gradjx(Vector** pgrad_g,double** pgrad_norm,Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters); #endif /* _GRADJX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 11708) @@ -17,5 +17,5 @@ double* vertices_ungrounding = NULL; double* old_floatingice = NULL; - Vec vec_old_floatingice = NULL; + Vector* vec_old_floatingice = NULL; Element* element = NULL; @@ -39,5 +39,5 @@ /*Create vector with vertices initially floating and serialize*/ vec_old_floatingice=CreateNodesOnFloatingIce(nodes,analysis_type); - VecToMPISerial(&old_floatingice,vec_old_floatingice); + old_floatingice=vec_old_floatingice->ToMPISerial(); /*Migrate grounding line : */ @@ -48,5 +48,5 @@ /*free ressouces: */ - VecFree(&vec_old_floatingice); + xdelete(&vec_old_floatingice); xfree((void**)&vertices_potentially_ungrounding); xfree((void**)&vertices_ungrounding); @@ -55,13 +55,13 @@ /*FUNCTION CreateNodesOnFloatingIce {{{1*/ -Vec CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type){ +Vector* CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type){ int i,numnods; - Vec vec_nodes_on_floatingice = NULL; + Vector* vec_nodes_on_floatingice = NULL; Node *node = NULL; /*First, initialize nodes_on_floatingice, which will track which nodes have changed status: */ numnods=nodes->NumberOfNodes(configuration_type); - vec_nodes_on_floatingice=NewVec(numnods); + vec_nodes_on_floatingice=new Vector(numnods); /*Loop through nodes, and fill vec_nodes_on_floatingice: */ @@ -70,5 +70,5 @@ if(node->InAnalysis(configuration_type)){ if(node->IsFloating()){ - VecSetValue(vec_nodes_on_floatingice,node->Sid(),1.0,INSERT_VALUES); + vec_nodes_on_floatingice->SetValue(node->Sid(),1.0,INS_VAL); } } @@ -76,6 +76,5 @@ /*Assemble vector: */ - VecAssemblyBegin(vec_nodes_on_floatingice); - VecAssemblyEnd(vec_nodes_on_floatingice); + vec_nodes_on_floatingice->Assemble(); return vec_nodes_on_floatingice; @@ -87,10 +86,10 @@ int i,numberofvertices; double* vertices_potentially_ungrounding = NULL; - Vec vec_vertices_potentially_ungrounding = NULL; + Vector* vec_vertices_potentially_ungrounding = NULL; Element* element = NULL; /*Initialize vector with number of vertices*/ numberofvertices=vertices->NumberOfVertices(); - vec_vertices_potentially_ungrounding=NewVec(numberofvertices); //grounded vertex that could start floating + vec_vertices_potentially_ungrounding=new Vector(numberofvertices); //grounded vertex that could start floating /*Fill vector vertices_potentially_floating: */ @@ -101,10 +100,9 @@ /*Assemble vector and serialize */ - VecAssemblyBegin(vec_vertices_potentially_ungrounding); - VecAssemblyEnd(vec_vertices_potentially_ungrounding); - VecToMPISerial(&vertices_potentially_ungrounding,vec_vertices_potentially_ungrounding); + vec_vertices_potentially_ungrounding->Assemble(); + vertices_potentially_ungrounding=vec_vertices_potentially_ungrounding->ToMPISerial(); /*free ressouces and return: */ - VecFree(&vec_vertices_potentially_ungrounding); + xdelete(&vec_vertices_potentially_ungrounding); return vertices_potentially_ungrounding; } @@ -118,6 +116,6 @@ double* nodes_on_floatingice = NULL; double* elements_neighboring_floatingce = NULL; - Vec vec_elements_neighboring_floatingice = NULL; - Vec vec_nodes_on_floatingice = NULL; + Vector* vec_elements_neighboring_floatingice = NULL; + Vector* vec_nodes_on_floatingice = NULL; Node* node = NULL; Element* element = NULL; @@ -130,5 +128,5 @@ /*recover vec_nodes_on_floatingice*/ vec_nodes_on_floatingice=CreateNodesOnFloatingIce(nodes,analysis_type); - VecToMPISerial(&nodes_on_floatingice,vec_nodes_on_floatingice); + nodes_on_floatingice=vec_nodes_on_floatingice->ToMPISerial(); nflipped=1; //bootstrap @@ -136,16 +134,15 @@ /*Vector of size number of elements*/ - vec_elements_neighboring_floatingice=NewVec(elements->NumberOfElements(),true); + vec_elements_neighboring_floatingice=new Vector(elements->NumberOfElements(),true); /*Figure out if any of the nodes of the element will be floating -> elements neighbouting the floating ice*/ for(i=0;iSize();i++){ element=(Element*)elements->GetObjectByOffset(i); - VecSetValue(vec_elements_neighboring_floatingice,element->Sid(),element->IsNodeOnShelfFromFlags(nodes_on_floatingice)?1.0:0.0,INSERT_VALUES); + vec_elements_neighboring_floatingice->SetValue(element->Sid(),element->IsNodeOnShelfFromFlags(nodes_on_floatingice)?1.0:0.0,INS_VAL); } /*Assemble vector and serialize: */ - VecAssemblyBegin(vec_elements_neighboring_floatingice); - VecAssemblyEnd(vec_elements_neighboring_floatingice); - VecToMPISerial(&elements_neighboring_floatingce,vec_elements_neighboring_floatingice); + vec_elements_neighboring_floatingice->Assemble(); + elements_neighboring_floatingce=vec_elements_neighboring_floatingice->ToMPISerial(); /*Go through elements_neighboring_floatingce, and update vector of the nodes that will start floating*/ @@ -157,6 +154,5 @@ } } - VecAssemblyBegin(vec_nodes_on_floatingice); - VecAssemblyEnd(vec_nodes_on_floatingice); + vec_nodes_on_floatingice->Assemble(); MPI_Allreduce(&local_nflipped,&nflipped,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); @@ -168,10 +164,10 @@ /*Assemble and serialize:*/ - VecFree(&vec_elements_neighboring_floatingice); - VecToMPISerial(&nodes_on_floatingice,vec_nodes_on_floatingice); + xdelete(&vec_elements_neighboring_floatingice); + nodes_on_floatingice=vec_nodes_on_floatingice->ToMPISerial(); } /*Free ressources:*/ - VecFree(&vec_nodes_on_floatingice); + xdelete(&vec_nodes_on_floatingice); xfree((void**)&elements_neighboring_floatingce); Index: /issm/branches/trunk-jpl-damage/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.h (revision 11708) @@ -14,5 +14,5 @@ void GroundinglineMigrationx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters); -Vec CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type); +Vector* CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type); double* PotentialSheetUngrounding(Elements* elements,Vertices* vertices,Parameters* parameters); double* PropagateFloatingiceToGroundedNeighbors(Elements* elements,Nodes* nodes,Vertices* vertices,Parameters* parameters,double* vertices_potentially_ungrounding); Index: /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp (revision 11708) @@ -9,9 +9,9 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec vector, int name, int type){ +void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* vector, int name, int type){ double* serial_vector=NULL; - VecToMPISerial(&serial_vector,vector); + serial_vector=vector->ToMPISerial(); InputUpdateFromVectorDakotax( elements,nodes, vertices, loads, materials, parameters,serial_vector,name, type); Index: /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h (revision 11708) @@ -10,5 +10,5 @@ /* local prototypes: */ -void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec vector, int name,int type); +void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* vector, int name,int type); void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,double* vector, int name,int type); void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int* vector, int name,int type); Index: /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp (revision 11708) @@ -9,9 +9,9 @@ #include "../../EnumDefinitions/EnumDefinitions.h" -void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec vector, int name, int type){ +void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* vector, int name, int type){ double* serial_vector=NULL; - VecToMPISerial(&serial_vector,vector); + serial_vector=vector->ToMPISerial(); InputUpdateFromVectorx( elements,nodes, vertices, loads, materials, parameters,serial_vector,name, type); Index: /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h (revision 11708) @@ -10,5 +10,5 @@ /* local prototypes: */ -void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec vector, int name,int type); +void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* vector, int name,int type); void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,double* vector, int name,int type); void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int* vector, int name,int type); Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp (revision 11708) @@ -16,8 +16,8 @@ /*InterpFromGridToMeshx{{{*/ -int InterpFromGridToMeshx( Vec* pdata_mesh,double* x_in, int x_rows, double* y_in, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods,double default_value, int interpenum){ +int InterpFromGridToMeshx( Vector** pdata_mesh,double* x_in, int x_rows, double* y_in, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods,double default_value, int interpenum){ /*output: */ - Vec data_mesh=NULL; + Vector* data_mesh=NULL; /*Intermediary*/ @@ -46,5 +46,5 @@ /*Allocate output vector: */ - data_mesh=NewVec(nods); + data_mesh=new Vector(nods); /*Find out what kind of coordinates (x_in,y_in) have been given is input*/ @@ -124,5 +124,5 @@ double *y = gate->y; int nods = gate->nods; - Vec data_mesh = gate->data_mesh; + Vector* data_mesh = gate->data_mesh; double *data = gate->data; double default_value = gate->default_value; @@ -179,5 +179,5 @@ } - VecSetValue(data_mesh,i,data_value,INSERT_VALUES); + data_mesh->SetValue(i,data_value,INS_VAL); } }/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h (revision 11708) @@ -23,8 +23,8 @@ double* x_mesh; double* y_mesh; - Vec data_mesh; + Vector* data_mesh; } InterpFromGridToMeshxThreadStruct; -int InterpFromGridToMeshx( Vec* pdata_mesh,double* x, int x_rows, double* y, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods, double default_value, int interpenum=BilinearInterpEnum); +int InterpFromGridToMeshx( Vector** pdata_mesh,double* x, int x_rows, double* y, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods, double default_value, int interpenum=BilinearInterpEnum); void* InterpFromGridToMeshxt(void* vInterpFromGridToMeshxThreadStruct); bool findindices(int* pn,int* pm,double* x,int x_rows, double* y,int y_rows, double xgrid,double ygrid); Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp (revision 11708) @@ -10,10 +10,10 @@ #include "../modules.h" -int InterpFromMesh2dx( Vec* pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime, +int InterpFromMesh2dx( Vector** pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime, double* default_values,int num_default_values,Contour** contours,int numcontours){ /*Output*/ - Vec data_prime=NULL; + Vector* data_prime=NULL; /*Intermediary*/ @@ -28,5 +28,5 @@ /*contours: */ - Vec vec_incontour=NULL; + Vector* vec_incontour=NULL; double* incontour=NULL; @@ -72,8 +72,8 @@ /*Initialize output*/ - data_prime=NewVec(nods_prime); + data_prime=new Vector(nods_prime); if(num_default_values){ - if(num_default_values==1)for (i=0;iSetValue(i,default_values[0],INS_VAL); + else for (i=0;iSetValue(i,default_values[i],INS_VAL); } @@ -81,5 +81,5 @@ if(numcontours){ ContourToNodesx( &vec_incontour,x_prime,y_prime,nods_prime,contours,numcontours,1); - VecToMPISerial(&incontour,vec_incontour); + incontour=vec_incontour->ToMPISerial(); } else{ Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.h (revision 11708) @@ -23,5 +23,5 @@ double ymin,ymax; int nods_prime; - Vec data_prime; + Vector* data_prime; double* x_prime; double* y_prime; @@ -33,5 +33,5 @@ } InterpFromMesh2dxThreadStruct; -int InterpFromMesh2dx( Vec* pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime, +int InterpFromMesh2dx( Vector** pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime, double* default_values,int num_default_values,Contour** contours,int numcontours); Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp (revision 11708) @@ -24,5 +24,5 @@ double ymin,ymax; int nods_prime; - Vec data_prime=NULL; + Vector* data_prime=NULL; double* x_prime=NULL; double* y_prime=NULL; @@ -120,5 +120,5 @@ /*insert value and go to the next point*/ - VecSetValue(data_prime,j,data_value,INSERT_VALUES); + data_prime->SetValue(j,data_value,INS_VAL); } } Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 11708) @@ -32,5 +32,5 @@ /*default values: */ - Vec vec_incontour=NULL; + Vector* vec_incontour=NULL; double* incontour=NULL; bool skip_bamg=false; @@ -51,5 +51,5 @@ if(num_default_values){ ContourToNodesx( &vec_incontour,x_interp,y_interp,nods_interp,contours,numcontours,1); - VecToMPISerial(&incontour,vec_incontour); + incontour=vec_incontour->ToMPISerial(); } Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp (revision 11708) @@ -7,8 +7,8 @@ #include "../../include/include.h" -int InterpFromMeshToMesh3dx( Vec* pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value) { +int InterpFromMeshToMesh3dx( Vector** pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value) { /*Output*/ - Vec data_prime=NULL; + Vector* data_prime=NULL; /*Intermediary*/ @@ -54,6 +54,6 @@ /*Initialize output*/ - data_prime=NewVec(nods_prime); - for (i=0;iSetValue(i,default_value,INS_VAL); /*Loop over the elements*/ @@ -127,5 +127,5 @@ /*insert value and go to the next point*/ - VecSetValue(data_prime,j,data_value,INSERT_VALUES); + data_prime->SetValue(j,data_value,INS_VAL); } } Index: /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h (revision 11708) @@ -8,5 +8,5 @@ #include "../../toolkits/toolkits.h" -int InterpFromMeshToMesh3dx( Vec* pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value); +int InterpFromMeshToMesh3dx( Vector** pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value); #endif /* _INTERPFROMMESHTOMESH3DX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/Orthx/Orthx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Orthx/Orthx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Orthx/Orthx.cpp (revision 11708) @@ -5,8 +5,8 @@ #include "./Orthx.h" -void Orthx( Vec* pnewgradj, Vec gradj, Vec oldgradj){ +void Orthx( Vector** pnewgradj, Vector* gradj, Vector* oldgradj){ /*output: */ - Vec newgradj=NULL; + Vector* newgradj=NULL; /*intermediary:*/ @@ -14,15 +14,15 @@ /*Initialize output*/ - VecDuplicate(gradj,&newgradj); - VecCopy(gradj,newgradj); + newgradj=gradj->Duplicate(); + gradj->Copy(newgradj); /*rough orthagonalization gradient=gradient-(gradient'*oldgradient)*oldgradient /norm(oldgradient)^2; */ if(oldgradj){ - VecNorm(oldgradj,NORM_2,&norm_old); + norm_old=oldgradj->Norm(NORM_TWO); _assert_(norm_old!=0); - VecDot(newgradj,oldgradj,&dot_product); + dot_product=newgradj->Dot(oldgradj); _assert_(dot_product!=NAN); - VecAXPY(newgradj, -dot_product/pow(norm_old,2), oldgradj); + newgradj->AXPY(oldgradj,-dot_product/pow(norm_old,2)); } Index: /issm/branches/trunk-jpl-damage/src/c/modules/Orthx/Orthx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Orthx/Orthx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Orthx/Orthx.h (revision 11708) @@ -11,5 +11,5 @@ /* local prototypes: */ -void Orthx( Vec* pnewgradj, Vec gradj, Vec oldgradj); +void Orthx( Vector** pnewgradj, Vector* gradj, Vector* oldgradj); #endif /* _ORTHX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp (revision 11708) @@ -4,9 +4,9 @@ #include "./PointCloudFindNeighborsx.h" -int PointCloudFindNeighborsx( Vec* pflags,double* x, double* y, int nods, double mindistance,double multithread){ +int PointCloudFindNeighborsx( Vector** pflags,double* x, double* y, int nods, double mindistance,double multithread){ /*output: */ - Vec flags=NULL; - flags=NewVec(nods); + Vector* flags=NULL; + flags=new Vector(nods); /*threading: */ @@ -31,6 +31,5 @@ /*Assemble vector: */ - VecAssemblyBegin(flags); - VecAssemblyEnd(flags); + flags->Assemble(); /*Assign output pointers: */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h (revision 11708) @@ -11,5 +11,5 @@ /* local prototypes: */ -int PointCloudFindNeighborsx( Vec* pflags,double* x, double* y, int nods, double mindistance,double multithread); +int PointCloudFindNeighborsx( Vector** pflags,double* x, double* y, int nods, double mindistance,double multithread); /*threading: */ @@ -20,5 +20,5 @@ int nods; double mindistance; - Vec flags; + Vector* flags; Index: /issm/branches/trunk-jpl-damage/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp (revision 11708) @@ -17,5 +17,5 @@ int nods; double mindistance; - Vec flags; + Vector* flags; /*recover handle and gate: */ @@ -62,6 +62,6 @@ /*insert value and go to the next point*/ - if(!already[i]) VecSetValue(flags,i,1,INSERT_VALUES); - if(!already[j]) VecSetValue(flags,j,2,INSERT_VALUES); + if(!already[i]) flags->SetValue(i,1,INS_VAL); + if(!already[j]) flags->SetValue(j,2,INS_VAL); already[i]=true; already[j]=true; Index: /issm/branches/trunk-jpl-damage/src/c/modules/Reduceloadx/Reduceloadx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11708) @@ -46,11 +46,11 @@ } - pf->AXPY(Kfsy_s,-1); + pf->AXPY(Kfsy_s,-1.); } /*Free ressources and return*/ - delete y_s0; - delete Kfsy_s; + xdelete(&y_s0); + xdelete(&Kfsy_s); } Index: /issm/branches/trunk-jpl-damage/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 11708) @@ -28,9 +28,9 @@ } -void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec vector){ +void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* vector){ double* serial_vector=NULL; - VecToMPISerial(&serial_vector,vector); + serial_vector=vector->ToMPISerial(); SetControlInputsFromVectorx(elements,nodes, vertices, loads, materials, parameters,serial_vector); Index: /issm/branches/trunk-jpl-damage/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h (revision 11708) @@ -9,5 +9,5 @@ /* local prototypes: */ -void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec vector); +void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* vector); void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,double* vector); Index: /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.cpp (revision 11708) @@ -20,9 +20,20 @@ uf=new Vector(); + /*Intermediary: */ + int analysis_type; + #ifdef _HAVE_PETSC_ - Vec uf0_vector=NULL; - if (uf0)uf0_vector=uf0->vector; + Vec uf0_vector = NULL; + Vec df_vector = NULL; + if(uf0) uf0_vector=uf0->vector; + if(df) df_vector = df->vector; - SolverxPetsc(&uf->vector, Kff->matrix, pf->vector, uf0_vector, df->vector, parameters); + /*In serial mode, the Petsc Options database has not been initialized properly: */ + #ifdef _SERIAL_ + parameters->FindParam(&analysis_type,AnalysisTypeEnum); + PetscOptionsFromAnalysis(parameters,analysis_type); + #endif + + SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); VecGetSize(uf->vector,&uf->M); #else Index: /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/Solverx/Solverx.h (revision 11708) @@ -6,10 +6,20 @@ #define _SOLVERX_H +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + #include "../../objects/objects.h" /* local prototypes: */ void Solverx(Vector** puf, Matrix* Kff, Vector* pf, Vector* uf0,Vector* df, Parameters* parameters); + +#ifdef _HAVE_PETSC_ void SolverxPetsc(Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df, Parameters* parameters); void DofTypesToIndexSet(IS* pisv, IS* pisp, Vec df,int typeenum); +#endif + #endif /* _SOLVERX_H */ Index: /issm/branches/trunk-jpl-damage/src/c/modules/StringToEnumx/StringToEnumx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 11708) @@ -137,10 +137,10 @@ else if (strcmp(name,"PrognosticHydrostaticAdjustment")==0) return PrognosticHydrostaticAdjustmentEnum; else if (strcmp(name,"PrognosticMinThickness")==0) return PrognosticMinThicknessEnum; - else if (strcmp(name,"PrognosticPenaltyFactor")==0) return PrognosticPenaltyFactorEnum; - else if (strcmp(name,"PrognosticSpcthickness")==0) return PrognosticSpcthicknessEnum; else stage=2; } if(stage==2){ - if (strcmp(name,"PrognosticStabilization")==0) return PrognosticStabilizationEnum; + if (strcmp(name,"PrognosticPenaltyFactor")==0) return PrognosticPenaltyFactorEnum; + else if (strcmp(name,"PrognosticSpcthickness")==0) return PrognosticSpcthicknessEnum; + else if (strcmp(name,"PrognosticStabilization")==0) return PrognosticStabilizationEnum; else if (strcmp(name,"PrognosticVertexPairing")==0) return PrognosticVertexPairingEnum; else if (strcmp(name,"QmuIsdakota")==0) return QmuIsdakotaEnum; @@ -269,6 +269,6 @@ else if (strcmp(name,"Penta")==0) return PentaEnum; else if (strcmp(name,"PentaP1Input")==0) return PentaP1InputEnum; - else if (strcmp(name,"PetscMatParam")==0) return PetscMatParamEnum; - else if (strcmp(name,"PetscVecParam")==0) return PetscVecParamEnum; + else if (strcmp(name,"MatrixParam")==0) return MatrixParamEnum; + else if (strcmp(name,"VectorParam")==0) return VectorParamEnum; else if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; else if (strcmp(name,"Segment")==0) return SegmentEnum; Index: /issm/branches/trunk-jpl-damage/src/c/modules/SystemMatricesx/SystemMatricesx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11708) @@ -69,6 +69,4 @@ Kfs->Assemble(); df->Assemble(); - - } @@ -88,10 +86,9 @@ if (load->InAnalysis(configuration_type)) load->CreatePVector(pf); } - pf->Assemble(); } /*Now, figure out maximum value of K_gg, so that we can penalize it correctly: */ - kmax=Kff->Norm(NORM_INFINITY); + kmax=Kff->Norm(NORM_INF); /*Now, deal with penalties*/ @@ -119,16 +116,15 @@ pf->Assemble(); - pf->Assemble(); } /*Assign output pointers: */ if(pKff) *pKff=Kff; - else delete Kff; + else xdelete(&Kff); if(pKfs) *pKfs=Kfs; - else delete Kfs; + else xdelete(&Kfs); if(ppf) *ppf=pf; - else delete pf; + else xdelete(&pf); if(pdf) *pdf=df; - else delete df; + else xdelete(&df); if(pkmax) *pkmax=kmax; } Index: /issm/branches/trunk-jpl-damage/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp (revision 11708) @@ -13,5 +13,5 @@ int i; - Vec vz = NULL; + Vector* vz = NULL; Vertex *vertex = NULL; double *thickness = NULL; @@ -23,5 +23,5 @@ /*Allocate vector*/ - vz=NewVec(vertices->NumberOfVertices()); + vz=new Vector(vertices->NumberOfVertices()); /*Update verices new geometry: */ @@ -32,6 +32,5 @@ /*Assemble mesh velocity*/ - VecAssemblyBegin(vz); - VecAssemblyEnd(vz); + vz->Assemble(); /*Update element inputs*/ @@ -41,5 +40,5 @@ xfree((void**)&thickness); xfree((void**)&bed); - VecFree(&vz); + xdelete(&vz); return 1; } Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.cpp (revision 11708) @@ -185,11 +185,11 @@ /*}}}*/ /*FUNCTION BoolElementResult::GetVectorFromResults{{{1*/ -void BoolElementResult::GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs){ +void BoolElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){ _error_("cannot return vector on vertices"); } /*}}}*/ /*FUNCTION BoolElementResult::GetElementVectorFromResults{{{1*/ -void BoolElementResult::GetElementVectorFromResults(Vec vector,int dof){ +void BoolElementResult::GetElementVectorFromResults(Vector* vector,int dof){ - VecSetValue(vector,dof,(double)value,INSERT_VALUES); + vector->SetValue(dof,value,INS_VAL); } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/BoolElementResult.h (revision 11708) @@ -53,6 +53,6 @@ /*BoolElementResult management: {{{1*/ int InstanceEnum(); - void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs); - void GetElementVectorFromResults(Vec vector,int dof); + void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs); + void GetElementVectorFromResults(Vector* vector,int dof); /*}}}*/ }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/DoubleElementResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/DoubleElementResult.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/DoubleElementResult.h (revision 11708) @@ -53,6 +53,6 @@ /*DoubleElementResult management: {{{1*/ int InstanceEnum(); - void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs){_error_("not implemented");}; - void GetElementVectorFromResults(Vec vector,int dof){_error_("not implemented");}; + void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){_error_("not implemented");}; + void GetElementVectorFromResults(Vector* vector,int dof){_error_("not implemented");}; /*}}}*/ }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/ElementResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/ElementResult.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/ElementResult.h (revision 11708) @@ -25,6 +25,6 @@ virtual void PatchFill(int row, Patch* patch)=0; virtual int InstanceEnum()=0; - virtual void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdof)=0; - virtual void GetElementVectorFromResults(Vec vector,int dof)=0; + virtual void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdof)=0; + virtual void GetElementVectorFromResults(Vector* vector,int dof)=0; }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 11708) @@ -195,5 +195,5 @@ /*}}}*/ /*FUNCTION PentaP1ElementResult::GetVectorFromResults{{{1*/ -void PentaP1ElementResult::GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs){ +void PentaP1ElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){ double data[6]; @@ -201,9 +201,9 @@ if(numdofs!=6)_error_("Result %s is a PentaP1ElementResult and cannot write vector of %i dofs",numdofs); for(int i=0;i<6;i++) data[i]=this->values[i]/(double)connectivitylist[i]; - VecSetValues(vector,numdofs,doflist,(const double*)&data,ADD_VALUES); + vector->SetValues(numdofs,doflist,&data[0],ADD_VAL); } /*}}}*/ /*FUNCTION PentaP1ElementResult::GetElementVectorFromResults{{{1*/ -void PentaP1ElementResult::GetElementVectorFromResults(Vec vector,int dof){ +void PentaP1ElementResult::GetElementVectorFromResults(Vector* vector,int dof){ _error_("Result %s is a PentaP1ElementResult and should not write vector of size numberofelemenrs",EnumToStringx(enum_type)); Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 11708) @@ -52,6 +52,6 @@ /*PentaP1ElementResult management: {{{1*/ int InstanceEnum(); - void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs); - void GetElementVectorFromResults(Vec vector,int dof); + void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs); + void GetElementVectorFromResults(Vector* vector,int dof); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 11708) @@ -184,5 +184,5 @@ /*}}}*/ /*FUNCTION TriaP1ElementResult::GetVectorFromResults{{{1*/ -void TriaP1ElementResult::GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs){ +void TriaP1ElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){ double data[3]; @@ -190,10 +190,9 @@ if(numdofs!=3)_error_("Result %s is a TriaP1ElementResult and cannot write vector of %i dofs",numdofs); for(int i=0;i<3;i++) data[i]=this->values[i]/(double)connectivitylist[i]; - VecSetValues(vector,numdofs,doflist,(const double*)&data,ADD_VALUES); + vector->SetValues(numdofs,doflist,&data[0],ADD_VAL); } /*}}}*/ /*FUNCTION TriaP1ElementResult::GetElementVectorFromResults{{{1*/ -void TriaP1ElementResult::GetElementVectorFromResults(Vec vector,int dof){ - +void TriaP1ElementResult::GetElementVectorFromResults(Vector* vector,int dof){ _error_("Result %s is a TriaP1ElementResult and should not write vector of size numberofelemenrs",EnumToStringx(enum_type)); } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 11708) @@ -51,6 +51,6 @@ /*TriaP1ElementResult management: {{{1*/ int InstanceEnum(); - void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs); - void GetElementVectorFromResults(Vec vector,int dof); + void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs); + void GetElementVectorFromResults(Vector* vector,int dof); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Element.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Element.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Element.h (revision 11708) @@ -46,6 +46,6 @@ virtual double SurfaceArea(void)=0; virtual void InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum)=0; - virtual void ComputeBasalStress(Vec sigma_b)=0; - virtual void ComputeStrainRate(Vec eps)=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; @@ -62,17 +62,17 @@ virtual int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units)=0; virtual void InputScale(int enum_type,double scale_factor)=0; - virtual void GetVectorFromInputs(Vec vector, int name_enum)=0; - virtual void GetVectorFromResults(Vec vector,int id,int interp)=0; + virtual void GetVectorFromInputs(Vector* vector, int name_enum)=0; + virtual void GetVectorFromResults(Vector* vector,int id,int interp)=0; virtual void InputArtificialNoise(int enum_type,double min,double max)=0; virtual bool InputConvergence(double* eps, int* enums,int num_enums,int* criterionenums,double* criterionvalues,int num_criterionenums)=0; - virtual void AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part)=0; + virtual void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part)=0; virtual int* GetHorizontalNeighboorSids(void)=0; virtual double TimeAdapt()=0; virtual void MigrateGroundingLine(double* old_floating_ice,double* sheet_ungrounding)=0; - virtual void PotentialSheetUngrounding(Vec potential_sheet_ungrounding)=0; + virtual void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding)=0; virtual void PositiveDegreeDay(void)=0; - virtual int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf)=0; + virtual int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf)=0; virtual void ResetCoordinateSystem()=0; - virtual void SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius)=0; + virtual void SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius)=0; #ifdef _HAVE_RESPONSES_ @@ -94,5 +94,5 @@ #ifdef _HAVE_CONTROL_ - virtual void Gradj(Vec gradient,int control_type,int control_index)=0; + virtual void Gradj(Vector* gradient,int control_type,int control_index)=0; virtual double ThicknessAbsMisfit(bool process_units ,int weight_index)=0; virtual double SurfaceAbsVelMisfit(bool process_units ,int weight_index)=0; @@ -104,8 +104,8 @@ virtual double RheologyBbarAbsGradient(bool process_units,int weight_index)=0; virtual double DragCoefficientAbsGradient(bool process_units,int weight_index)=0; - virtual void ControlInputGetGradient(Vec gradient,int enum_type,int control_index)=0; + virtual void ControlInputGetGradient(Vector* gradient,int enum_type,int control_index)=0; virtual void ControlInputSetGradient(double* gradient,int enum_type,int control_index)=0; virtual void ControlInputScaleGradient(int enum_type, double scale)=0; - virtual void GetVectorFromControlInputs(Vec gradient,int control_enum,int control_index,const char* data)=0; + virtual void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data)=0; virtual void SetControlInputsFromVector(double* vector,int control_enum,int control_index)=0; virtual void InputControlUpdate(double scalar,bool save_parameter)=0; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.cpp (revision 11708) @@ -302,5 +302,5 @@ /*Other*/ /*FUNCTION Penta::AverageOntoPartition {{{1*/ -void Penta::AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part){ +void Penta::AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part){ _error_("Not supported yet!"); } @@ -383,5 +383,5 @@ /*}}}*/ /*FUNCTION Penta::ComputeBasalStress {{{1*/ -void Penta::ComputeBasalStress(Vec sigma_b){ +void Penta::ComputeBasalStress(Vector* sigma_b){ int i,j,ig; @@ -417,5 +417,5 @@ if(!IsOnBed()){ //put zero - VecSetValue(sigma_b,id-1,0.0,INSERT_VALUES); + sigma_b->SetValue(id-1,0.0,INS_VAL); return; } @@ -469,9 +469,9 @@ /*Add value to output*/ - VecSetValue(sigma_b,id-1,value,INSERT_VALUES); + sigma_b->SetValue(id-1,value,INS_VAL); } /*}}}*/ /*FUNCTION Penta::ComputeStrainRate {{{1*/ -void Penta::ComputeStrainRate(Vec eps){ +void Penta::ComputeStrainRate(Vector* eps){ _error_("Not implemented yet"); @@ -1218,5 +1218,5 @@ /*}}}*/ /*FUNCTION Penta::GetVectorFromInputs{{{1*/ -void Penta::GetVectorFromInputs(Vec vector,int input_enum){ +void Penta::GetVectorFromInputs(Vector* vector,int input_enum){ int doflist1[NUMVERTICES]; @@ -1237,5 +1237,5 @@ /*}}}*/ /*FUNCTION Penta::GetVectorFromResults{{{1*/ -void Penta::GetVectorFromResults(Vec vector,int offset,int interp){ +void Penta::GetVectorFromResults(Vector* vector,int offset,int interp){ /*Get result*/ @@ -2422,5 +2422,5 @@ /*}}}*/ /*FUNCTION Penta::PotentialSheetUngrounding{{{1*/ -void Penta::PotentialSheetUngrounding(Vec potential_sheet_ungrounding){ +void Penta::PotentialSheetUngrounding(Vector* potential_sheet_ungrounding){ int i; @@ -2444,5 +2444,5 @@ if (bed_hydro>ba[i]){ /*Vertex that could potentially unground, flag it*/ - VecSetValue(potential_sheet_ungrounding,nodes[i]->Sid(),1,INSERT_VALUES); + potential_sheet_ungrounding->SetValue(nodes[i]->Sid(),1,INS_VAL); } } @@ -2942,5 +2942,5 @@ /*}}}*/ /*FUNCTION Penta::UpdatePotentialSheetUngrounding{{{1*/ -int Penta::UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf){ +int Penta::UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf){ int i; @@ -2950,5 +2950,5 @@ for(i=0;iSid()]){ - VecSetValue(vec_nodes_on_iceshelf,nodes[i]->Sid(),1,INSERT_VALUES); + vec_nodes_on_iceshelf->SetValue(nodes[i]->Sid(),1,INS_VAL); /*If node was not on ice shelf, we flipped*/ @@ -3010,5 +3010,5 @@ /*}}}*/ /*FUNCTION Penta::SmearFunction {{{1*/ -void Penta::SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius){ +void Penta::SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius){ _error_("not implemented yet"); } @@ -4213,5 +4213,5 @@ /*Add value to global vector*/ - solution->SetValues(numdof,doflist,values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INS_VAL); /*Free ressources:*/ @@ -4244,5 +4244,5 @@ /*Add value to global vector*/ - solution->SetValues(numdof,doflist,values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INS_VAL); /*Free ressources:*/ @@ -4404,5 +4404,5 @@ #ifdef _HAVE_CONTROL_ /*FUNCTION Penta::ControlInputGetGradient{{{1*/ -void Penta::ControlInputGetGradient(Vec gradient,int enum_type,int control_index){ +void Penta::ControlInputGetGradient(Vector* gradient,int enum_type,int control_index){ int doflist1[NUMVERTICES]; @@ -4729,5 +4729,5 @@ /*}}}*/ /*FUNCTION Penta::Gradj {{{1*/ -void Penta::Gradj(Vec gradient,int control_type,int control_index){ +void Penta::Gradj(Vector* gradient,int control_type,int control_index){ /*dJ/dalpha = ∂L/∂alpha = ∂J/∂alpha + ∂/∂alpha(KU-F)*/ @@ -4820,5 +4820,5 @@ /*}}}*/ /*FUNCTION Penta::GradjDragMacAyeal {{{1*/ -void Penta::GradjDragMacAyeal(Vec gradient,int control_index){ +void Penta::GradjDragMacAyeal(Vector* gradient,int control_index){ /*Gradient is 0 if on shelf or not on bed*/ @@ -4832,5 +4832,5 @@ } /*}}}*/ /*FUNCTION Penta::GradjDragPattyn {{{1*/ -void Penta::GradjDragPattyn(Vec gradient,int control_index){ +void Penta::GradjDragPattyn(Vector* gradient,int control_index){ int i,j,ig; @@ -4895,5 +4895,5 @@ } } - VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); /*Clean up and return*/ @@ -4903,5 +4903,5 @@ /*}}}*/ /*FUNCTION Penta::GradjDragStokes {{{1*/ -void Penta::GradjDragStokes(Vec gradient,int control_index){ +void Penta::GradjDragStokes(Vector* gradient,int control_index){ int i,j,ig; @@ -4988,5 +4988,5 @@ } - VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); delete friction; @@ -4995,5 +4995,5 @@ /*}}}*/ /*FUNCTION Penta::GradjBbarMacAyeal {{{1*/ -void Penta::GradjBbarMacAyeal(Vec gradient,int control_index){ +void Penta::GradjBbarMacAyeal(Vector* gradient,int control_index){ /*This element should be collapsed into a tria element at its base*/ @@ -5013,5 +5013,5 @@ } /*}}}*/ /*FUNCTION Penta::GradjBbarPattyn {{{1*/ -void Penta::GradjBbarPattyn(Vec gradient,int control_index){ +void Penta::GradjBbarPattyn(Vector* gradient,int control_index){ /*Gradient is computed on bed only (Bbar)*/ @@ -5030,5 +5030,5 @@ } /*}}}*/ /*FUNCTION Penta::GradjBbarStokes {{{1*/ -void Penta::GradjBbarStokes(Vec gradient,int control_index){ +void Penta::GradjBbarStokes(Vector* gradient,int control_index){ /*Gradient is computed on bed only (Bbar)*/ @@ -5406,5 +5406,5 @@ /*}}}*/ /*FUNCTION Penta::GetVectorFromControlInputs{{{1*/ -void Penta::GetVectorFromControlInputs(Vec vector,int control_enum,int control_index,const char* data){ +void Penta::GetVectorFromControlInputs(Vector* vector,int control_enum,int control_index,const char* data){ int doflist1[NUMVERTICES]; @@ -7896,5 +7896,5 @@ /*Add value to global vector*/ - solution->SetValues(numdof,doflist,values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INS_VAL); /*Free ressources:*/ @@ -7932,5 +7932,5 @@ /*Add value to global vector*/ - solution->SetValues(numdof,doflist,values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INS_VAL); /*Free ressources:*/ @@ -7965,5 +7965,5 @@ /*Add value to global vector*/ - solution->SetValues(numdof,doflist,values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INS_VAL); /*Free ressources:*/ @@ -8010,5 +8010,5 @@ /*Add value to global vector*/ - solution->SetValues(numdof,doflist,values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INS_VAL); /*Free ressources:*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Penta.h (revision 11708) @@ -79,8 +79,8 @@ /*}}}*/ /*Element virtual functions definitions: {{{1*/ - void AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part); + void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part); void BasalFrictionCreateInput(void); - void ComputeBasalStress(Vec sigma_b); - void ComputeStrainRate(Vec eps); + void ComputeBasalStress(Vector* sigma_b); + void ComputeStrainRate(Vector* eps); void ComputeStressTensor(); void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); @@ -93,6 +93,6 @@ void GetSolutionFromInputs(Vector* solution); double GetZcoord(GaussPenta* gauss); - void GetVectorFromInputs(Vec vector,int name_enum); - void GetVectorFromResults(Vec vector,int offset,int interp); + void GetVectorFromInputs(Vector* vector,int name_enum); + void GetVectorFromResults(Vector* vector,int offset,int interp); int Sid(); @@ -107,5 +107,5 @@ void InputToResult(int enum_type,int step,double time); void MigrateGroundingLine(double* old_floating_ice,double* sheet_ungrounding); - void PotentialSheetUngrounding(Vec potential_sheet_ungrounding); + void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding); void RequestedOutput(int output_enum,int step,double time); void ListResultsInfo(int** results_enums,int** results_size,double** results_times,int** results_steps,int* num_results); @@ -117,10 +117,10 @@ double SurfaceArea(void); void Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type); - int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf); + int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf); int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); double TimeAdapt(); int* GetHorizontalNeighboorSids(void); void ViscousHeatingCreateInput(void); - void SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius); + void SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius); #ifdef _HAVE_RESPONSES_ @@ -144,14 +144,14 @@ double DragCoefficientAbsGradient(bool process_units,int weight_index); void GradientIndexing(int* indexing,int control_index); - void Gradj(Vec gradient,int control_type,int control_index); - void GradjDragMacAyeal(Vec gradient,int control_index); - void GradjDragPattyn(Vec gradient,int control_index); - void GradjDragStokes(Vec gradient,int control_index); - void GradjBbarMacAyeal(Vec gradient,int control_index); - void GradjBbarPattyn(Vec gradient,int control_index); - void GradjBbarStokes(Vec gradient,int control_index); - void GetVectorFromControlInputs(Vec gradient,int control_enum,int control_index,const char* data); + 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(double* vector,int control_enum,int control_index); - void ControlInputGetGradient(Vec gradient,int enum_type,int control_index); + void ControlInputGetGradient(Vector* gradient,int enum_type,int control_index); void ControlInputScaleGradient(int enum_type,double scale); void ControlInputSetGradient(double* gradient,int enum_type,int control_index); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.cpp (revision 11708) @@ -279,5 +279,5 @@ /*Other*/ /*FUNCTION Tria::AverageOntoPartition {{{1*/ -void Tria::AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part){ +void Tria::AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part){ bool already=false; @@ -312,6 +312,6 @@ } if(!already){ - VecSetValue(partition_contributions,partition[i],mean*area,ADD_VALUES); - VecSetValue(partition_areas,partition[i],area,ADD_VALUES); + partition_contributions->SetValue(partition[i],mean*area,ADD_VAL); + partition_areas->SetValue(partition[i],area,ADD_VAL); }; } @@ -925,10 +925,10 @@ /*}}}*/ /*FUNCTION Tria::ComputeBasalStress {{{1*/ -void Tria::ComputeBasalStress(Vec eps){ +void Tria::ComputeBasalStress(Vector* eps){ _error_("Not Implemented yet"); } /*}}}*/ /*FUNCTION Tria::ComputeStrainRate {{{1*/ -void Tria::ComputeStrainRate(Vec eps){ +void Tria::ComputeStrainRate(Vector* eps){ _error_("Not Implemented yet"); } @@ -1324,5 +1324,5 @@ /*}}}*/ /*FUNCTION Tria::GetVectorFromInputs{{{1*/ -void Tria::GetVectorFromInputs(Vec vector,int input_enum){ +void Tria::GetVectorFromInputs(Vector* vector,int input_enum){ int doflist1[NUMVERTICES]; @@ -1343,5 +1343,5 @@ /*}}}*/ /*FUNCTION Tria::GetVectorFromResults{{{1*/ -void Tria::GetVectorFromResults(Vec vector,int offset,int interp){ +void Tria::GetVectorFromResults(Vector* vector,int offset,int interp){ /*Get result*/ @@ -2207,5 +2207,5 @@ /*}}}*/ /*FUNCTION Tria::PotentialSheetUngrounding{{{1*/ -void Tria::PotentialSheetUngrounding(Vec potential_sheet_ungrounding){ +void Tria::PotentialSheetUngrounding(Vector* potential_sheet_ungrounding){ int i; @@ -2229,5 +2229,5 @@ if (bed_hydro>ba[i]){ /*Vertex that could potentially unground, flag it*/ - VecSetValue(potential_sheet_ungrounding,nodes[i]->Sid(),1,INSERT_VALUES); + potential_sheet_ungrounding->SetValue(nodes[i]->Sid(),1,INS_VAL); } } @@ -2287,5 +2287,5 @@ /*}}}1*/ /*FUNCTION Tria::SmearFunction {{{1*/ -void Tria::SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius){ +void Tria::SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius){ _error_("not implemented yet"); @@ -2508,5 +2508,5 @@ /*}}}*/ /*FUNCTION Tria::UpdatePotentialSheetUngrounding{{{1*/ -int Tria::UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf){ +int Tria::UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf){ int i; @@ -2516,5 +2516,5 @@ for(i=0;i<3;i++){ if (vertices_potentially_ungrounding[nodes[i]->Sid()]){ - VecSetValue(vec_nodes_on_iceshelf,nodes[i]->Sid(),1,INSERT_VALUES); + vec_nodes_on_iceshelf->SetValue(nodes[i]->Sid(),1,INS_VAL); /*If node was not on ice shelf, we flipped*/ @@ -3174,5 +3174,5 @@ } - solution->SetValues(numdof,doflist,values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INS_VAL); /*Free ressources:*/ @@ -3213,5 +3213,5 @@ } - solution->SetValues(numdof,doflist,values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INS_VAL); /*Free ressources:*/ @@ -3381,5 +3381,5 @@ /*}}}*/ /*FUNCTION Tria::ControlInputGetGradient{{{1*/ -void Tria::ControlInputGetGradient(Vec gradient,int enum_type,int control_index){ +void Tria::ControlInputGetGradient(Vector* gradient,int enum_type,int control_index){ int doflist1[NUMVERTICES]; @@ -3440,5 +3440,5 @@ }/*}}}*/ /*FUNCTION Tria::Gradj {{{1*/ -void Tria::Gradj(Vec gradient,int control_type,int control_index){ +void Tria::Gradj(Vector* gradient,int control_type,int control_index){ /*dJ/dalpha = ∂L/∂alpha = ∂J/∂alpha + ∂/∂alpha(KU-F)*/ @@ -3502,5 +3502,5 @@ /*}}}*/ /*FUNCTION Tria::GradjBGradient{{{1*/ -void Tria::GradjBGradient(Vec gradient,int weight_index,int control_index){ +void Tria::GradjBGradient(Vector* gradient,int weight_index,int control_index){ int i,ig; @@ -3535,5 +3535,5 @@ for (i=0;iweight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]); } - VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); /*Clean up and return*/ @@ -3542,5 +3542,5 @@ /*}}}*/ /*FUNCTION Tria::GradjZGradient{{{1*/ -void Tria::GradjZGradient(Vec gradient,int weight_index,int control_index){ +void Tria::GradjZGradient(Vector* gradient,int weight_index,int control_index){ int i,ig; @@ -3575,5 +3575,5 @@ for (i=0;iweight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]); } - VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); /*Clean up and return*/ @@ -3582,5 +3582,5 @@ /*}}}*/ /*FUNCTION Tria::GradjBMacAyeal{{{1*/ -void Tria::GradjBMacAyeal(Vec gradient,int control_index){ +void Tria::GradjBMacAyeal(Vector* gradient,int control_index){ /*Intermediaries*/ @@ -3632,5 +3632,5 @@ } - VecSetValues(gradient,NUMVERTICES,doflist,(const double*)grad,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist,grad,ADD_VAL); /*clean-up*/ @@ -3639,5 +3639,5 @@ /*}}}*/ /*FUNCTION Tria::GradjZMacAyeal{{{1*/ -void Tria::GradjZMacAyeal(Vec gradient,int control_index){ +void Tria::GradjZMacAyeal(Vector* gradient,int control_index){ /*Intermediaries*/ @@ -3689,5 +3689,5 @@ } - VecSetValues(gradient,NUMVERTICES,doflist,(const double*)grad,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist,grad,ADD_VAL); /*clean-up*/ @@ -3696,5 +3696,5 @@ /*}}}*/ /*FUNCTION Tria::GradjDragMacAyeal {{{1*/ -void Tria::GradjDragMacAyeal(Vec gradient,int control_index){ +void Tria::GradjDragMacAyeal(Vector* gradient,int control_index){ int i,ig; @@ -3776,5 +3776,5 @@ /*End Analytical gradient*/ - VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); /*Clean up and return*/ @@ -3784,5 +3784,5 @@ /*}}}*/ /*FUNCTION Tria::GradjDragGradient{{{1*/ -void Tria::GradjDragGradient(Vec gradient, int weight_index,int control_index){ +void Tria::GradjDragGradient(Vector* gradient, int weight_index,int control_index){ int i,ig; @@ -3821,5 +3821,5 @@ } } - VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); /*Clean up and return*/ @@ -3828,5 +3828,5 @@ /*}}}*/ /*FUNCTION Tria::GradjDhDtBalancedthickness{{{1*/ -void Tria::GradjDhDtBalancedthickness(Vec gradient,int control_index){ +void Tria::GradjDhDtBalancedthickness(Vector* gradient,int control_index){ /*Intermediaries*/ @@ -3840,9 +3840,9 @@ for(int i=0;iSetValues(NUMVERTICES,doflist1,gradient_g,INS_VAL); } /*}}}*/ /*FUNCTION Tria::GradjVxBalancedthickness{{{1*/ -void Tria::GradjVxBalancedthickness(Vec gradient,int control_index){ +void Tria::GradjVxBalancedthickness(Vector* gradient,int control_index){ /*Intermediaries*/ @@ -3880,5 +3880,5 @@ } - VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); /*Clean up and return*/ @@ -3887,5 +3887,5 @@ /*}}}*/ /*FUNCTION Tria::GradjVyBalancedthickness{{{1*/ -void Tria::GradjVyBalancedthickness(Vec gradient,int control_index){ +void Tria::GradjVyBalancedthickness(Vector* gradient,int control_index){ /*Intermediaries*/ @@ -3922,5 +3922,5 @@ for(i=0;iweight*basis[i]; } - VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); + gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); /*Clean up and return*/ @@ -5016,5 +5016,5 @@ /*}}}*/ /*FUNCTION Tria::GetVectorFromControlInputs{{{1*/ -void Tria::GetVectorFromControlInputs(Vec vector,int control_enum,int control_index,const char* data){ +void Tria::GetVectorFromControlInputs(Vector* vector,int control_enum,int control_index,const char* data){ int doflist1[NUMVERTICES]; @@ -5318,5 +5318,5 @@ } - solution->SetValues(numdof,doflist,values,INSERT_VALUES); + solution->SetValues(numdof,doflist,values,INS_VAL); /*Free ressources:*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Elements/Tria.h (revision 11708) @@ -76,7 +76,7 @@ /*}}}*/ /*Element virtual functions definitions: {{{1*/ - void AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part); - void ComputeBasalStress(Vec sigma_b); - void ComputeStrainRate(Vec eps); + void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* 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); @@ -93,6 +93,6 @@ bool IsOnWater(); void GetSolutionFromInputs(Vector* solution); - void GetVectorFromInputs(Vec vector, int name_enum); - void GetVectorFromResults(Vec vector,int offset,int interp); + void GetVectorFromInputs(Vector* vector, int name_enum); + void GetVectorFromResults(Vector* vector,int offset,int interp); void InputArtificialNoise(int enum_type,double min, double max); bool InputConvergence(double* eps, int* enums,int num_enums,int* criterionenums,double* criterionvalues,int num_criterionenums); @@ -107,5 +107,5 @@ void MigrateGroundingLine(double* oldfloating,double* sheet_ungrounding); int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); - void PotentialSheetUngrounding(Vec potential_sheet_ungrounding); + void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding); void PositiveDegreeDay(void); void RequestedOutput(int output_enum,int step,double time); @@ -117,8 +117,8 @@ double SurfaceArea(void); void Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type); - int UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf); + int UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf); double TimeAdapt(); int* GetHorizontalNeighboorSids(void); - void SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius); + void SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius); #ifdef _HAVE_RESPONSES_ @@ -143,18 +143,18 @@ double DragCoefficientAbsGradient(bool process_units,int weight_index); void GradientIndexing(int* indexing,int control_index); - void Gradj(Vec gradient,int control_type,int control_index); - void GradjBGradient(Vec gradient,int weight_index,int control_index); - void GradjZGradient(Vec gradient,int weight_index,int control_index); - void GradjBMacAyeal(Vec gradient,int control_index); - void GradjZMacAyeal(Vec gradient,int control_index); - void GradjDragMacAyeal(Vec gradient,int control_index); - void GradjDragStokes(Vec gradient,int control_index); - void GradjDragGradient(Vec gradient,int weight_index,int control_index); - void GradjDhDtBalancedthickness(Vec gradient,int control_index); - void GradjVxBalancedthickness(Vec gradient,int control_index); - void GradjVyBalancedthickness(Vec gradient,int control_index); - void GetVectorFromControlInputs(Vec gradient,int control_enum,int control_index,const char* data); + 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(double* vector,int control_enum,int control_index); - void ControlInputGetGradient(Vec gradient,int enum_type,int control_index); + void ControlInputGetGradient(Vector* gradient,int enum_type,int control_index); void ControlInputScaleGradient(int enum_type,double scale); void ControlInputSetGradient(double* gradient,int enum_type,int control_index); Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 11708) @@ -27,5 +27,5 @@ /*}}}*/ /*FUNCTION PetscVecExternalResult::PetscVecExternalResult(int enum_type,IssmPetscVec value){{{1*/ -PetscVecExternalResult::PetscVecExternalResult(int in_id, int in_enum_type,Vec in_value,int in_step, double in_time){ +PetscVecExternalResult::PetscVecExternalResult(int in_id, int in_enum_type,Vector* in_value,int in_step, double in_time){ id=in_id; @@ -35,6 +35,6 @@ if(in_value){ - VecDuplicate(in_value,&value); - VecCopy(in_value,value); + value=in_value->Duplicate(); + in_value->Copy(value); } else value=NULL; Index: /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 11708) @@ -33,5 +33,5 @@ int id; int enum_type; - Vec value; + Vector* value; int step; double time; @@ -40,5 +40,5 @@ /*PetscVecExternalResult constructors, destructors: {{{1*/ PetscVecExternalResult(); - PetscVecExternalResult(int id,int enum_type,Vec value, int step, double time); + PetscVecExternalResult(int id,int enum_type,Vector* value, int step, double time); ~PetscVecExternalResult(); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/FemModel.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/FemModel.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/FemModel.cpp (revision 11708) @@ -144,4 +144,5 @@ 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)){ @@ -149,4 +150,5 @@ _printf_(VerboseSolver()," petsc Options set for analysis type: %s\n",EnumToStringx(analysis_type)); } + #endif } Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.cpp (revision 11708) @@ -233,5 +233,5 @@ /*}}}*/ /*FUNCTION BoolInput::GetVectorFromInputs{{{1*/ -void BoolInput::GetVectorFromInputs(Vec vector,int* doflist){ +void BoolInput::GetVectorFromInputs(Vector* vector,int* doflist){ _error_(" not supporte yet!"); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/BoolInput.h (revision 11708) @@ -81,5 +81,5 @@ void Extrude(void); void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; - void GetVectorFromInputs(Vec vector,int* doflist); + void GetVectorFromInputs(Vector* vector,int* doflist); void GetValuesPtr(double** pvalues,int* pnum_values); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/ControlInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/ControlInput.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/ControlInput.cpp (revision 11708) @@ -355,5 +355,5 @@ }/*}}}*/ /*FUNCTION ControlInput::GetGradient{{{1*/ -void ControlInput::GetGradient(Vec gradient_vec,int* doflist){ +void ControlInput::GetGradient(Vector* gradient_vec,int* doflist){ if(gradient) gradient->GetVectorFromInputs(gradient_vec,doflist); }/*}}}*/ @@ -406,10 +406,10 @@ return gradient->SpawnResult(step,time); }/*}}}*/ -/*FUNCTION ControlInput::GetVectorFromInputs(Vec vector,int* doflist){{{1*/ -void ControlInput::GetVectorFromInputs(Vec vector,int* doflist){ +/*FUNCTION ControlInput::GetVectorFromInputs(Vector* vector,int* doflist){{{1*/ +void ControlInput::GetVectorFromInputs(Vector* vector,int* doflist){ values->GetVectorFromInputs(vector,doflist); }/*}}}*/ -/*FUNCTION ControlInput::GetVectorFromInputs(Vec vector,int* doflist,const char* data){{{1*/ -void ControlInput::GetVectorFromInputs(Vec vector,int* doflist,const char* data){ +/*FUNCTION ControlInput::GetVectorFromInputs(Vector* vector,int* doflist,const char* data){{{1*/ +void ControlInput::GetVectorFromInputs(Vector* vector,int* doflist,const char* data){ if(strcmp(data,"value")==0){ _assert_(values); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/ControlInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/ControlInput.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/ControlInput.h (revision 11708) @@ -87,9 +87,9 @@ void Extrude(void); void VerticallyIntegrate(Input* thickness_input); - void GetVectorFromInputs(Vec vector,int* doflist,const char* data); - void GetVectorFromInputs(Vec vector,int* doflist); + void GetVectorFromInputs(Vector* vector,int* doflist,const char* data); + void GetVectorFromInputs(Vector* vector,int* doflist); void GetValuesPtr(double** pvalues,int* pnum_values){_error_("not implemented yet");}; ElementResult* SpawnGradient(int step, double time); - void GetGradient(Vec gradient_vec,int* doflist); + void GetGradient(Vector* gradient_vec,int* doflist); void ScaleGradient(double scale); void SetGradient(Input* gradient_in); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DatasetInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DatasetInput.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DatasetInput.h (revision 11708) @@ -82,8 +82,8 @@ void Extrude(void){_error_("not implemented yet");}; void VerticallyIntegrate(Input* thickness_input){_error_("not implemented yet");}; - void GetVectorFromInputs(Vec vector,int* doflist){_error_("not implemented yet");}; + void GetVectorFromInputs(Vector* vector,int* doflist){_error_("not implemented yet");}; void GetValuesPtr(double** pvalues,int* pnum_values){_error_("not implemented yet");}; ElementResult* SpawnGradient(int step, double time){_error_("not implemented yet");}; - void GetGradient(Vec gradient_vec,int* doflist){_error_("not implemented yet");}; + void GetGradient(Vector* gradient_vec,int* doflist){_error_("not implemented yet");}; void ScaleGradient(double scale){_error_("not implemented yet");}; void SetGradient(Input* gradient_in){_error_("not implemented yet");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.cpp (revision 11708) @@ -310,5 +310,5 @@ /*}}}*/ /*FUNCTION DoubleInput::GetVectorFromInputs{{{1*/ -void DoubleInput::GetVectorFromInputs(Vec vector,int* doflist){ +void DoubleInput::GetVectorFromInputs(Vector* vector,int* doflist){ _error_(" not supporte yet!"); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/DoubleInput.h (revision 11708) @@ -80,5 +80,5 @@ void Extrude(void){_error_("not supported yet");}; void VerticallyIntegrate(Input* thickness_input); - void GetVectorFromInputs(Vec vector,int* doflist); + void GetVectorFromInputs(Vector* vector,int* doflist); void GetValuesPtr(double** pvalues,int* pnum_values); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/Input.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/Input.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/Input.h (revision 11708) @@ -56,5 +56,5 @@ virtual void VerticallyIntegrate(Input* thickness_input)=0; virtual void Extrude()=0; - virtual void GetVectorFromInputs(Vec vector,int* doflist)=0; + virtual void GetVectorFromInputs(Vector* vector,int* doflist)=0; virtual void GetValuesPtr(double** pvalues,int* pnum_values)=0; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.cpp (revision 11708) @@ -231,5 +231,5 @@ /*}}}*/ /*FUNCTION IntInput::GetVectorFromInputs{{{1*/ -void IntInput::GetVectorFromInputs(Vec vector,int* doflist){ +void IntInput::GetVectorFromInputs(Vector* vector,int* doflist){ _error_(" not supporte yet!"); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/IntInput.h (revision 11708) @@ -81,5 +81,5 @@ void Extrude(void){_error_("not supported yet");}; void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; - void GetVectorFromInputs(Vec vector,int* doflist); + void GetVectorFromInputs(Vector* vector,int* doflist); void GetValuesPtr(double** pvalues,int* pnum_values); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.cpp (revision 11708) @@ -660,8 +660,8 @@ /*}}}*/ /*FUNCTION PentaP1Input::GetVectorFromInputs{{{1*/ -void PentaP1Input::GetVectorFromInputs(Vec vector,int* doflist){ +void PentaP1Input::GetVectorFromInputs(Vector* vector,int* doflist){ const int numvertices=6; - VecSetValues(vector,numvertices,doflist,(const double*)this->values,INSERT_VALUES); + vector->SetValues(numvertices,doflist,this->values,INS_VAL); } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/PentaP1Input.h (revision 11708) @@ -82,5 +82,5 @@ void Extrude(void); void VerticallyIntegrate(Input* thickness_input); - void GetVectorFromInputs(Vec vector,int* doflist); + void GetVectorFromInputs(Vector* vector,int* doflist); void GetValuesPtr(double** pvalues,int* pnum_values); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.cpp (revision 11708) @@ -440,5 +440,5 @@ /*}}}*/ /*FUNCTION TransientInput::GetVectorFromInputs{{{1*/ -void TransientInput::GetVectorFromInputs(Vec vector,int* doflist){ +void TransientInput::GetVectorFromInputs(Vector* vector,int* doflist){ double time; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TransientInput.h (revision 11708) @@ -84,5 +84,5 @@ void Extrude(void){_error_("not supported yet");} void VerticallyIntegrate(Input* thickness_forcing){_error_("not supported yet");}; - void GetVectorFromInputs(Vec vector,int* doflist); + void GetVectorFromInputs(Vector* vector,int* doflist); void GetValuesPtr(double** pvalues,int* pnum_values){_error_("not supported yet");}; void GetTimeValues(double* values,double time){_error_("not implemented yet");}; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.cpp (revision 11708) @@ -391,8 +391,8 @@ /*}}}*/ /*FUNCTION TriaP1Input::GetVectorFromInputs{{{1*/ -void TriaP1Input::GetVectorFromInputs(Vec vector,int* doflist){ +void TriaP1Input::GetVectorFromInputs(Vector* vector,int* doflist){ const int numvertices=3; - VecSetValues(vector,numvertices,doflist,(const double*)this->values,INSERT_VALUES); + vector->SetValues(numvertices,doflist,this->values,INS_VAL); } /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Inputs/TriaP1Input.h (revision 11708) @@ -82,5 +82,5 @@ void Extrude(void){_error_("not supported yet");}; void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; - void GetVectorFromInputs(Vec vector,int* doflist); + void GetVectorFromInputs(Vector* vector,int* doflist); void GetValuesPtr(double** pvalues,int* pnum_values); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Material.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Material.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Material.h (revision 11708) @@ -22,5 +22,5 @@ virtual void InputDuplicate(int original_enum,int new_enum)=0; virtual void Configure(Elements* elements)=0; - virtual void GetVectorFromInputs(Vec vector,int input_enum)=0; + virtual void GetVectorFromInputs(Vector* vector,int input_enum)=0; }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.cpp (revision 11708) @@ -249,5 +249,5 @@ /*}}}*/ /*FUNCTION Matice::GetVectorFromInputs{{{1*/ -void Matice::GetVectorFromInputs(Vec vector,int input_enum){ +void Matice::GetVectorFromInputs(Vector* vector,int input_enum){ /*Intermediaries*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matice.h (revision 11708) @@ -60,5 +60,5 @@ void InputDuplicate(int original_enum,int new_enum); void Configure(Elements* elements); - void GetVectorFromInputs(Vec vector,int input_enum); + void GetVectorFromInputs(Vector* vector,int input_enum); /*}}}*/ /*Matice Numerics: {{{1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matpar.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matpar.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Materials/Matpar.h (revision 11708) @@ -71,5 +71,5 @@ void InputDuplicate(int original_enum,int new_enum){_error_("not implemented yet");}; void Configure(Elements* elements); - void GetVectorFromInputs(Vec vector,int input_enum){return;} + void GetVectorFromInputs(Vector* vector,int input_enum){return;} /*}}}*/ /*Numerics: {{{1*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Node.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Node.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Node.cpp (revision 11708) @@ -568,5 +568,5 @@ /*}}}*/ /*FUNCTION Node::CreateVecSets {{{1*/ -void Node::CreateVecSets(Vec pv_g,Vec pv_f,Vec pv_s){ +void Node::CreateVecSets(Vector* pv_g,Vector* pv_f,Vector* pv_s){ double gvalue=1.0; //all nodes are in the g set; @@ -578,13 +578,13 @@ /*g set: */ - VecSetValues(pv_g,1,&indexing.gdoflist[i],&gvalue,INSERT_VALUES); + pv_g->SetValue(indexing.gdoflist[i],gvalue,INS_VAL); /*f set: */ value=(double)this->indexing.f_set[i]; - VecSetValues(pv_f,1,&indexing.gdoflist[i],&value,INSERT_VALUES); + pv_f->SetValue(indexing.gdoflist[i],value,INS_VAL); /*s set: */ value=(double)this->indexing.s_set[i]; - VecSetValues(pv_s,1,&indexing.gdoflist[i],&value,INSERT_VALUES); + pv_s->SetValue(indexing.gdoflist[i],value,INS_VAL); } @@ -613,5 +613,5 @@ /*Add values into constraint vector: */ - ys->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); + ys->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INS_VAL); } @@ -897,5 +897,5 @@ /*Add values into ug: */ - ug->SetValues(this->indexing.fsize,indices,values,INSERT_VALUES); + ug->SetValues(this->indexing.fsize,indices,values,INS_VAL); } } @@ -915,5 +915,5 @@ /*Add values into ug: */ - ug->SetValues(this->indexing.ssize,indices,values,INSERT_VALUES); + ug->SetValues(this->indexing.ssize,indices,values,INS_VAL); } } @@ -945,5 +945,5 @@ /*Add values into ug: */ - vector->SetValues(this->indexing.fsize,this->indexing.fdoflist,values,INSERT_VALUES); + vector->SetValues(this->indexing.fsize,this->indexing.fdoflist,values,INS_VAL); } } @@ -961,5 +961,5 @@ /*Add values into ug: */ - vector->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); + vector->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INS_VAL); } } Index: /issm/branches/trunk-jpl-damage/src/c/objects/Node.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Node.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Node.h (revision 11708) @@ -87,5 +87,5 @@ void DofInFSet(int dof); int GetDof(int dofindex,int setenum); - void CreateVecSets(Vec pv_g,Vec pv_f,Vec pv_s); + void CreateVecSets(Vector* pv_g,Vector* pv_f,Vector* pv_s); int GetConnectivity(); void GetDofList(int* poutdoflist,int approximation_enum,int setenum); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.cpp (revision 11708) @@ -17,5 +17,7 @@ #include "../../Container/Container.h" #include "../../include/include.h" +#include "../../toolkits/toolkits.h" #include "./Matrix.h" + /*}}}*/ @@ -61,4 +63,37 @@ #ifdef _HAVE_PETSC_ this->matrix=NewMat(pM,pN,sparsity); + #else + this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); + #endif + #ifdef _HAVE_ADOLC_ + this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); + #endif +} +/*}}}*/ +/*FUNCTION Matrix::Matrix(double* serial_mat, int M,int N,double sparsity){{{1*/ +Matrix::Matrix(double* serial_mat, int pM,int pN,double sparsity){ + + this->M=pM; + this->N=pN; + + #ifdef _HAVE_PETSC_ + int i; + int* idxm=NULL; + int* idxn=NULL; + + this->matrix=NewMat(pM,pN,sparsity); + + idxm=(int*)xmalloc(M*sizeof(int)); + idxn=(int*)xmalloc(N*sizeof(int)); + for(i=0;imatrix,M,idxm,N,idxn,serial_mat,INSERT_VALUES); + + MatAssemblyBegin(this->matrix,MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(this->matrix,MAT_FINAL_ASSEMBLY); + + xfree((void**)&idxm); + xfree((void**)&idxn); #else this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); @@ -160,9 +195,9 @@ /*}}}*/ /*FUNCTION Matrix::Norm{{{1*/ -double Matrix::Norm(int norm_type){ +double Matrix::Norm(NormMode norm_type){ double norm=0; #ifdef _HAVE_PETSC_ - MatNorm(this->matrix,(NormType)norm_type,&norm); + MatNorm(this->matrix,ISSMToPetscNormMode(norm_type),&norm); #else _error_("not implemented yet!"); @@ -201,2 +236,29 @@ } /*}}}*/ +/*FUNCTION Matrix::Duplicate{{{1*/ +Matrix* Matrix::Duplicate(void){ + + Matrix* output=NULL; + + output=new Matrix(); + + #ifdef _HAVE_PETSC + MatDuplicate(this->matrix,MAT_COPY_VALUES,&output->matrix); + #else + _error_("not implemented yet!"); + #endif +} +/*}}}*/ +/*FUNCTION Matrix::ToSerial{{{1*/ +double* Matrix::ToSerial(void){ + + double* output=NULL; + + #ifdef _HAVE_PETSC + MatToSerial(&output,this->matrix); + #else + _error_("not implemented yet!"); + #endif + return output; +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Matrix.h (revision 11708) @@ -14,5 +14,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif -#include "../Object.h" #include "../../toolkits/toolkits.h" #include "../../EnumDefinitions/EnumDefinitions.h" @@ -48,4 +47,5 @@ Matrix(int M,int N); Matrix(int M,int N,double sparsity); + Matrix(double* serial_mat,int M,int N,double sparsity); Matrix(int M,int N,int connectivity,int numberofdofspernode); ~Matrix(); @@ -57,8 +57,10 @@ #endif void Assemble(void); - double Norm(int norm_type); + double Norm(NormMode norm_type); void GetSize(int* pM,int* pN); void GetLocalSize(int* pM,int* pN); void MatMult(Vector* X,Vector* AX); + Matrix* Duplicate(void); + double* ToSerial(void); /*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.cpp (revision 11708) @@ -17,4 +17,5 @@ #include "../../Container/Container.h" #include "../../include/include.h" +#include "../../toolkits/toolkits.h" #include "./Vector.h" /*}}}*/ @@ -49,5 +50,47 @@ } /*}}}*/ -/*FUNCTION Vector::~Vector(){{{1*/ +/*FUNCTION Vector::Vector(double* serial_vec,int M){{{1*/ +Vector::Vector(double* serial_vec,int pM){ + + int i,j; + + #ifdef _HAVE_PETSC_ + int* idxm=NULL; + + this->vector=NewVec(pM); + + idxm=(int*)xmalloc(M*sizeof(int)); + for(i=0;ivector,M,idxm,serial_vec,INSERT_VALUES); + + VecAssemblyBegin(this->vector); + VecAssemblyEnd(this->vector); + + xfree((void**)&idxm); + + #else + this->M=pM; + this->vector=(double*)xcalloc(pM,sizeof(double)); + #endif + #ifdef _HAVE_ADOLC_ + this->avector=(adouble*)xmalloc(pM*sizeof(adouble)); + #endif +} +/*}}}*/ +#ifdef _HAVE_PETSC_ +/*FUNCTION Vector::Vector(Vec petsc_vec){{{1*/ +Vector::Vector(Vec petsc_vec){ + + /*Get Vector size*/ + VecGetSize(petsc_vec,&this->M); + + /*copy vector*/ + VecDuplicate(petsc_vec,&this->vector); + VecCopy(petsc_vec,this->vector); + +} +/*}}}*/ +#endif + /*FUNCTION Vector::~Vector(){{{1*/ Vector::~Vector(){ @@ -116,15 +159,40 @@ /*}}}*/ /*FUNCTION Vector::SetValues{{{1*/ -void Vector::SetValues(int ssize, int* list, double* values, int mode){ - - - #ifdef _HAVE_PETSC_ - VecSetValues(this->vector,ssize,list,values,(InsertMode)mode); - #else - _error_("not implemented yet!"); - #endif - -} -/*}}}*/ +void Vector::SetValues(int ssize, int* list, double* values, InsMode mode){ + + + #ifdef _HAVE_PETSC_ + VecSetValues(this->vector,ssize,list,values,ISSMToPetscInsertMode(mode)); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION Vector::SetValue{{{1*/ +void Vector::SetValue(int dof, double value, InsMode mode){ + + + #ifdef _HAVE_PETSC_ + VecSetValues(this->vector,1,&dof,&value,ISSMToPetscInsertMode(mode)); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ +/*FUNCTION Vector::GetValue{{{1*/ +void Vector::GetValue(double* pvalue,int dof){ + + + #ifdef _HAVE_PETSC_ + VecGetValues(this->vector,1,&dof,pvalue); + #else + _error_("not implemented yet!"); + #endif + +} +/*}}}*/ + /*FUNCTION Vector::GetSize{{{1*/ void Vector::GetSize(int* pM){ @@ -170,5 +238,5 @@ #ifdef _HAVE_PETSC_ - this->Set(value); + VecSet(this->vector,value); #else _error_("not implemented yet!"); @@ -185,5 +253,4 @@ _error_("not implemented yet!"); #endif - } /*}}}*/ @@ -226,9 +293,9 @@ /*}}}*/ /*FUNCTION Vector::Norm{{{1*/ -double Vector::Norm(int norm_type){ +double Vector::Norm(NormMode norm_type){ double norm=0; #ifdef _HAVE_PETSC_ - VecNorm(this->vector,(NormType)norm_type,&norm); + VecNorm(this->vector,ISSMToPetscNormMode(norm_type),&norm); #else _error_("not implemented yet!"); @@ -247,2 +314,24 @@ } /*}}}*/ +/*FUNCTION Vector::Scale{{{1*/ +double Vector::Dot(Vector* vector){ + + double dot; + #ifdef _HAVE_PETSC_ + VecDot(this->vector,vector->vector,&dot); + #else + _error_("not implemented yet!"); + #endif + return dot; +} +/*}}}*/ +/*FUNCTION Vector::PointwiseDivide{{{1*/ +void Vector::PointwiseDivide(Vector* x,Vector* y){ + + #ifdef _HAVE_PETSC_ + VecPointwiseDivide(this->vector,x->vector,y->vector); + #else + _error_("not implemented yet!"); + #endif +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Numerics/Vector.h (revision 11708) @@ -14,5 +14,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif -#include "../Object.h" #include "../../toolkits/toolkits.h" #include "../../EnumDefinitions/EnumDefinitions.h" @@ -22,5 +21,4 @@ #endif - #ifdef _SERIAL_ #include "mex.h" @@ -47,4 +45,8 @@ Vector(); Vector(int M,bool fromlocalsize=false); + Vector(double* serial_vec,int pM); + #ifdef _HAVE_PETSC_ + Vector(Vec petsc_vec); + #endif ~Vector(); /*}}}*/ @@ -55,5 +57,7 @@ #endif void Assemble(void); - void SetValues(int ssize, int* list, double* values, int mode); + void SetValues(int ssize, int* list, double* values, InsMode mode); + void SetValue(int dof, double value, InsMode mode); + void GetValue(double* pvalue, int dof); void GetSize(int* pM); void GetLocalSize(int* pM); @@ -64,6 +68,8 @@ double* ToMPISerial(void); void Copy(Vector* to); - double Norm(int norm_type); + double Norm(NormMode norm_type); void Scale(double scale_factor); + void PointwiseDivide(Vector* x,Vector* y); + double Dot(Vector* vector); /*}}}*/ }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/BoolParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/BoolParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/BoolParam.h (revision 11708) @@ -61,6 +61,6 @@ void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("Bool param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Bool param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("Bool param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("Bool param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("Bool param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("Bool param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("Bool param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -74,6 +74,6 @@ void SetValue(int* intarray,int M){_error_("Bool param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} void SetValue(int* pintarray,int M,int N){_error_("Bool param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("Bool param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("Bool param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("Bool param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("Bool param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("Bool param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Bool param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatArrayParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatArrayParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatArrayParam.h (revision 11708) @@ -64,6 +64,6 @@ void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("DoubleMatArray param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims); - void GetParameterValue(Vec* pvec){_error_("DoubleMatArray param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("DoubleMatArray param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("DoubleMatArray param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("DoubleMatArray param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("DoubleMatArray param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -77,6 +77,6 @@ void SetValue(int* intarray,int M){_error_("DoubleMatArray param of enum %i (%s) cannot hold a int vec array",enum_type,EnumToStringx(enum_type));} void SetValue(int* intarray,int M,int N){_error_("DoubleMatArray param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("DoubleMatArray param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("DoubleMatArray param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("DoubleMatArray param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("DoubleMatArray param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("Bool param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array); Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleMatParam.h (revision 11708) @@ -63,6 +63,6 @@ void GetParameterValue(double** pdoublearray,int* pM,int* pN); void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("DoubleMat param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("DoubleMat param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("DoubleMat param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("DoubleMat param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("DoubleMat param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("DoubleMat param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -76,6 +76,6 @@ void SetValue(int* intarray,int M){_error_("DoubleMat param of enum %i (%s) cannot hold a int vec array",enum_type,EnumToStringx(enum_type));} void SetValue(int* intarray,int M,int N){_error_("DoubleMat param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));}; - void SetValue(Vec vec){_error_("DoubleMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("DoubleMat param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("DoubleMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("DoubleMat param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("DoubleMat param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("DoubleMat param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleParam.h (revision 11708) @@ -62,6 +62,6 @@ void GetParameterValue(double** pdoublearray,int* pM, int* pN); void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Double param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("Double param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("Double param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("Double param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("Double param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("Double param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -75,6 +75,6 @@ void SetValue(int* intarray,int M){_error_("Double param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} void SetValue(int* pintarray,int M,int N){_error_("Double param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("Double param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("Double param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("Double param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("Double param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("Double param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Double param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleVecParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleVecParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/DoubleVecParam.h (revision 11708) @@ -62,6 +62,6 @@ void GetParameterValue(double** pdoublearray,int* pM, int* pN); void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("DoubleVec param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("DoubleVec param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("DoubleVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("DoubleVec param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("DoubleVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("DoubleVec param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -75,6 +75,6 @@ void SetValue(int* intarray,int M){_error_("DoubleVec param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));}; void SetValue(int* pintarray,int M,int N){_error_("DoubleVec param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("DoubleVec param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("DoubleVec param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("DoubleVec param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("DoubleVec param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("DoubleVec param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("DoubleVec param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/FileParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/FileParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/FileParam.h (revision 11708) @@ -61,6 +61,6 @@ void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("FileParam of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("File param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("FileParam of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("FileParam of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("FileParam of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("FileParam of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){*pfid=value;}; @@ -74,6 +74,6 @@ void SetValue(int* intarray,int M){_error_("FileParam of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} void SetValue(int* pintarray,int M,int N){_error_("FileParam of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("FileParam of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("FileParam of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("FileParam of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("FileParam of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("File param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("File param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntMatParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntMatParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntMatParam.h (revision 11708) @@ -63,6 +63,6 @@ void GetParameterValue(double** pdoublearray,int* pM,int* pN){_error_("IntMat param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));}; void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("IntMat param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("IntMat param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("IntMat param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("IntMat param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("IntMat param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("IntMat param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -76,6 +76,6 @@ void SetValue(int* intarray,int M){_error_("IntMat param of enum %i (%s) cannot hold a int vec array",enum_type,EnumToStringx(enum_type));}; void SetValue(int* intarray,int M,int N); - void SetValue(Vec vec){_error_("IntMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("IntMat param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("IntMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("IntMat param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("IntMat param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("IntMat param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntParam.h (revision 11708) @@ -62,6 +62,6 @@ void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("Int param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Int param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("Int param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("Int param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("Int param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("Int param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("Int param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -75,6 +75,6 @@ void SetValue(double* doublearray,int M){_error_("Int param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} void SetValue(double* pdoublearray,int M,int N){_error_("Int param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("Int param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("Int param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("Int param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("Int param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("Int param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Int param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntVecParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntVecParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/IntVecParam.h (revision 11708) @@ -63,6 +63,6 @@ void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("IntVec param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("IntVec param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("IntVec param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("IntVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("IntVec param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("IntVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("IntVec param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -76,6 +76,6 @@ void SetValue(int* intarray,int M); void SetValue(int* pintarray,int M,int N){_error_("IntVec param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("IntVec param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("IntVec param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("IntVec param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("IntVec param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("IntVec param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("IntVec param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.cpp (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.cpp (revision 11708) @@ -0,0 +1,227 @@ +/*!\file MatrixParam.c + * \brief: implementation of the MatrixParam object + */ + +/*header files: */ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../Container/Container.h" +#include "../../include/include.h" +/*}}}*/ + +/*MatrixParam constructors and destructor*/ +/*FUNCTION MatrixParam::MatrixParam(){{{1*/ +MatrixParam::MatrixParam(){ + return; +} +/*}}}*/ +/*FUNCTION MatrixParam::MatrixParam(int enum_type,Matrix* value){{{1*/ +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(){{{1*/ +MatrixParam::~MatrixParam(){ + xdelete(&value); +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION MatrixParam::Echo {{{1*/ +void MatrixParam::Echo(void){ + + printf("MatrixParam:\n"); + printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); + +} +/*}}}*/ +/*FUNCTION MatrixParam::DeepEcho{{{1*/ +void MatrixParam::DeepEcho(void){ + + int i; + printf("MatrixParam:\n"); + printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); + this->value->Echo(); +} +/*}}}*/ +/*FUNCTION MatrixParam::Id{{{1*/ +int MatrixParam::Id(void){ return -1; } +/*}}}*/ +/*FUNCTION MatrixParam::MyRank{{{1*/ +int MatrixParam::MyRank(void){ + extern int my_rank; + return my_rank; +} +/*}}}*/ +#ifdef _SERIAL_ +/*FUNCTION MatrixParam::Marshall{{{1*/ +void MatrixParam::Marshall(char** pmarshalled_dataset){ + + char* marshalled_dataset=NULL; + int enum_value=0; + int M,N; + double* serial_mat=NULL; + + /*recover marshalled_dataset: */ + marshalled_dataset=*pmarshalled_dataset; + + /*get enum value of MatrixParam: */ + enum_value=MatrixParamEnum; + + /*marshall enum: */ + memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); + + /*marshall MatrixParam data: */ + memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); + if(value){ + value->GetSize(&M,&N); + serial_mat=value->ToSerial(); + memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); + memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); + memcpy(marshalled_dataset,serial_mat,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); + } + else{ + M=0; + N=0; + memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); + memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); + } + + /*Free ressources:*/ + xfree((void**)&serial_mat); + + /*return:*/ + *pmarshalled_dataset=marshalled_dataset; +} +/*}}}*/ +/*FUNCTION MatrixParam::MarshallSize{{{1*/ +int MatrixParam::MarshallSize(){ + + int M=0; + int N=0; + if(value)value->GetSize(&M,&N); + + return sizeof(M)+ + sizeof(N)+ + M*N*sizeof(double)+ + +sizeof(enum_type)+ + +sizeof(int); //sizeof(int) for enum value +} +/*}}}*/ +/*FUNCTION MatrixParam::Demarshall{{{1*/ +void MatrixParam::Demarshall(char** pmarshalled_dataset){ + + char* marshalled_dataset=NULL; + int M,N; + double* serial_mat=NULL; + + /*recover marshalled_dataset: */ + marshalled_dataset=*pmarshalled_dataset; + + /*this time, no need to get enum type, the pointer directly points to the beginning of the + *object data (thanks to DataSet::Demarshall):*/ + memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); + + /*data: */ + memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); + memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); + if(M!=0 && N!=0){ + serial_mat=(double*)xmalloc(M*N*sizeof(double)); + memcpy(serial_mat,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); + value=new Matrix(serial_mat,M,N,.001); + } + else{ + value=NULL; + } + + /*Free ressources:*/ + xfree((void**)&serial_mat); + + /*return: */ + *pmarshalled_dataset=marshalled_dataset; +} +/*}}}*/ +#endif +/*FUNCTION MatrixParam::ObjectEnum{{{1*/ +int MatrixParam::ObjectEnum(void){ + + return MatrixParamEnum; + +} +/*}}}*/ +/*FUNCTION MatrixParam::copy{{{1*/ +Object* MatrixParam::copy() { + + return new MatrixParam(this->enum_type,this->value); + +} +/*}}}*/ + +/*MatrixParam virtual functions definitions: */ +/*FUNCTION MatrixParam::GetParameterValue{{{1*/ +void MatrixParam::GetParameterValue(Matrix** poutput){ + Matrix* output=NULL; + + if(value){ + output=value->Duplicate(); + } + *poutput=output; +} +/*}}}*/ +/*FUNCTION MatrixParam::GetParameterName{{{1*/ +void MatrixParam::GetParameterName(char**pname){ + EnumToStringx(pname,this->enum_type); +} +/*}}}*/ +/*FUNCTION MatrixParam::SetMatlabField{{{1*/ +#ifdef _SERIAL_ +void MatrixParam::SetMatlabField(mxArray* dataref){ + + char* name=NULL; + int M,N; + double* doublemat=NULL; + mxArray* pfield=NULL; + + doublemat=value->ToSerial(); + value->GetSize(&M,&N); + this->GetParameterName(&name); + + pfield=mxCreateDoubleMatrix(0,0,mxREAL); + mxSetM(pfield,M); + mxSetN(pfield,N); + mxSetPr(pfield,doublemat); + mxSetField( dataref, 0, name, pfield); +} +#endif +/*}}}*/ +/*FUNCTION MatrixParam::SetValue{{{1*/ +void MatrixParam::SetValue(Matrix* matrix){ + + /*avoid leak: */ + xdelete(&value); + + /*copy: */ + value=matrix->Duplicate(); +} +/*}}}*/ +/*FUNCTION MatrixParam::UnitConversion{{{1*/ +void MatrixParam::UnitConversion(int direction_enum){ + /*do nothing, no unit conversion*/ +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.h (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/MatrixParam.h (revision 11708) @@ -0,0 +1,90 @@ +/*! \file MatrixParam.h + * \brief: header file for MatrixParam object + */ + + +#ifndef _MATRIXPARAM_H_ +#define _MATRIXPARAM_H_ + +/*Headers:*/ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#ifdef _SERIAL_ +#include +#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: {{{1*/ + MatrixParam(); + MatrixParam(int enum_type,Matrix* value); + ~MatrixParam(); + /*}}}*/ + /*Object virtual functions definitions:{{{1 */ + void Echo(); + void DeepEcho(); + int Id(); + int MyRank(); + #ifdef _SERIAL_ + void Marshall(char** pmarshalled_dataset); + int MarshallSize(); + void Demarshall(char** pmarshalled_dataset); + #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ + /*Param vritual function definitions: {{{1*/ + int InstanceEnum(){return enum_type;} + void GetParameterValue(bool* pbool){_error_("Matrix param of enum %i (%s) cannot return a bool",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(int* pinteger){_error_("Matrix param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(int** pintarray,int* pM){_error_("Matrix param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Matrix param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double* pdouble){_error_("Matrix param of enum %i (%s) cannot return a double",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(char** pstring){_error_("Matrix param of enum %i (%s) cannot return a string",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(char*** pstringarray,int* pM){_error_("Matrix param of enum %i (%s) cannot return a string array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM){_error_("Matrix param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("Matrix param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Matrix param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("Matrix param of enum %i (%s) cannot return a vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** poutput); + void GetParameterValue(FILE** pfid){_error_("Matrix param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){_error_("Matrix param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} + void SetValue(int integer){_error_("Matrix param of enum %i (%s) cannot hold an integer",enum_type,EnumToStringx(enum_type));} + void SetValue(double scalar){_error_("Matrix param of enum %i (%s) cannot hold a scalar",enum_type,EnumToStringx(enum_type));} + void SetValue(char* string){_error_("Matrix param of enum %i (%s) cannot hold a string",enum_type,EnumToStringx(enum_type));} + void SetValue(char** stringarray,int M){_error_("Matrix param of enum %i (%s) cannot hold a string array",enum_type,EnumToStringx(enum_type));} + void SetValue(double* doublearray,int M){_error_("Matrix param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(double* pdoublearray,int M,int N){_error_("Matrix param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M){_error_("Matrix param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* pintarray,int M,int N){_error_("Matrix param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("Matrix param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat); + void SetValue(FILE* fid){_error_("Matrix param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Matrix param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); + #ifdef _SERIAL_ + void SetMatlabField(mxArray* dataref); + #endif + + /*}}}*/ +}; +#endif /* _MATRIXPARAM_H */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/Param.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/Param.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/Param.h (revision 11708) @@ -41,6 +41,6 @@ virtual void GetParameterValue(double** pdoublearray,int* pM,int* pN)=0; virtual void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims)=0; - virtual void GetParameterValue(Vec* pvec)=0; - virtual void GetParameterValue(Mat* pmat)=0; + virtual void GetParameterValue(Vector** pvec)=0; + virtual void GetParameterValue(Matrix** pmat)=0; virtual void GetParameterValue(FILE** pfid)=0; @@ -54,6 +54,6 @@ virtual void SetValue(int* intarray,int M)=0; virtual void SetValue(int* pintarray,int M,int N)=0; - virtual void SetValue(Vec vec)=0; - virtual void SetValue(Mat mat)=0; + virtual void SetValue(Vector* vec)=0; + virtual void SetValue(Matrix* mat)=0; virtual void SetValue(FILE* fid)=0; virtual void SetValue(double** array, int M, int* mdim_array, int* ndim_array)=0; Index: sm/branches/trunk-jpl-damage/src/c/objects/Params/PetscMatParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/PetscMatParam.cpp (revision 11707) +++ (revision ) @@ -1,242 +1,0 @@ -/*!\file PetscMatParam.c - * \brief: implementation of the PetscMatParam object - */ - -/*header files: */ -/*{{{1*/ -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#include -#include -#include "../objects.h" -#include "../../EnumDefinitions/EnumDefinitions.h" -#include "../../shared/shared.h" -#include "../../Container/Container.h" -#include "../../include/include.h" -/*}}}*/ - -/*PetscMatParam constructors and destructor*/ -/*FUNCTION PetscMatParam::PetscMatParam(){{{1*/ -PetscMatParam::PetscMatParam(){ - return; -} -/*}}}*/ -/*FUNCTION PetscMatParam::PetscMatParam(int enum_type,IssmPetscMat value){{{1*/ -PetscMatParam::PetscMatParam(int in_enum_type,Mat in_value){ - - enum_type=in_enum_type; - - value=NULL; - - if(in_value){ - MatDuplicate(in_value,MAT_COPY_VALUES,&value); - } -} -/*}}}*/ -/*FUNCTION PetscMatParam::~PetscMatParam(){{{1*/ -PetscMatParam::~PetscMatParam(){ - MatFree(&value); -} -/*}}}*/ - -/*Object virtual functions definitions:*/ -/*FUNCTION PetscMatParam::Echo {{{1*/ -void PetscMatParam::Echo(void){ - - printf("PetscMatParam:\n"); - printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); - -} -/*}}}*/ -/*FUNCTION PetscMatParam::DeepEcho{{{1*/ -void PetscMatParam::DeepEcho(void){ - - int i; - printf("PetscMatParam:\n"); - printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); - MatView(value,PETSC_VIEWER_STDOUT_WORLD); -} -/*}}}*/ -/*FUNCTION PetscMatParam::Id{{{1*/ -int PetscMatParam::Id(void){ return -1; } -/*}}}*/ -/*FUNCTION PetscMatParam::MyRank{{{1*/ -int PetscMatParam::MyRank(void){ - extern int my_rank; - return my_rank; -} -/*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION PetscMatParam::Marshall{{{1*/ -void PetscMatParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int M,N; - double* serial_mat=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of PetscMatParam: */ - enum_value=PetscMatParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall PetscMatParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - if(value){ - MatGetSize(value,&M,&N); - MatToSerial(&serial_mat,value); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - memcpy(marshalled_dataset,serial_mat,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); - } - else{ - M=0; - N=0; - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - } - - /*Free ressources:*/ - xfree((void**)&serial_mat); - - /*return:*/ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION PetscMatParam::MarshallSize{{{1*/ -int PetscMatParam::MarshallSize(){ - - int M=0; - int N=0; - if(value)MatGetSize(value,&M,&N); - - return sizeof(M)+ - sizeof(N)+ - M*N*sizeof(double)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION PetscMatParam::Demarshall{{{1*/ -void PetscMatParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i,j; - int M,N; - double* serial_mat=NULL; - int* idxm=NULL; - int* idxn=NULL; - double sparsity=.001; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); - if(M!=0 && N!=0){ - serial_mat=(double*)xmalloc(M*N*sizeof(double)); - memcpy(serial_mat,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); - value=NewMat(M,N,sparsity); - idxm=(int*)xmalloc(M*sizeof(int)); - idxn=(int*)xmalloc(N*sizeof(int)); - for(i=0;ienum_type,this->value); - -} -/*}}}*/ - -/*PetscMatParam virtual functions definitions: */ -/*FUNCTION PetscMatParam::GetParameterValue{{{1*/ -void PetscMatParam::GetParameterValue(Mat* poutput){ - Mat output=NULL; - - if(value){ - MatDuplicate(value,MAT_COPY_VALUES,&output); - } - *poutput=output; -} -/*}}}*/ -/*FUNCTION PetscMatParam::GetParameterName{{{1*/ -void PetscMatParam::GetParameterName(char**pname){ - EnumToStringx(pname,this->enum_type); -} -/*}}}*/ -/*FUNCTION PetscMatParam::SetMatlabField{{{1*/ -#ifdef _SERIAL_ -void PetscMatParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - int M,N; - double* doublemat=NULL; - mxArray* pfield=NULL; - - MatToSerial(&doublemat,value); - MatGetSize(value,&M,&N); - this->GetParameterName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,N); - mxSetPr(pfield,doublemat); - mxSetField( dataref, 0, name, pfield); -} -#endif -/*}}}*/ -/*FUNCTION PetscMatParam::SetValue{{{1*/ -void PetscMatParam::SetValue(Mat matrix){ - - /*avoid leak: */ - MatFree(&value); - - /*copy: */ - MatDuplicate(matrix,MAT_COPY_VALUES,&value); -} -/*}}}*/ -/*FUNCTION PetscMatParam::UnitConversion{{{1*/ -void PetscMatParam::UnitConversion(int direction_enum){ - /*do nothing, no unit conversion*/ -} -/*}}}*/ Index: sm/branches/trunk-jpl-damage/src/c/objects/Params/PetscMatParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/PetscMatParam.h (revision 11707) +++ (revision ) @@ -1,90 +1,0 @@ -/*! \file PetscMatParam.h - * \brief: header file for triavertexinput object - */ - - -#ifndef _PETSCMATPARAM_H_ -#define _PETSCMATPARAM_H_ - -/*Headers:*/ -/*{{{1*/ -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#ifdef _SERIAL_ -#include -#endif - -#include "./Param.h" -#include "../../include/include.h" -#include "../../shared/shared.h" -/*}}}*/ - -class PetscMatParam: public Param{ - - private: - /*just hold 3 values for 3 vertices: */ - int enum_type; - Mat value; - - public: - /*PetscMatParam constructors, destructors: {{{1*/ - PetscMatParam(); - PetscMatParam(int enum_type,Mat value); - ~PetscMatParam(); - /*}}}*/ - /*Object virtual functions definitions:{{{1 */ - void Echo(); - void DeepEcho(); - int Id(); - int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif - int ObjectEnum(); - Object* copy(); - /*}}}*/ - /*Param vritual function definitions: {{{1*/ - int InstanceEnum(){return enum_type;} - void GetParameterValue(bool* pbool){_error_("PetscMat param of enum %i (%s) cannot return a bool",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(int* pinteger){_error_("PetscMat param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(int** pintarray,int* pM){_error_("PetscMat param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(int** pintarray,int* pM,int* pN){_error_("PetscMat param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(double* pdouble){_error_("PetscMat param of enum %i (%s) cannot return a double",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(char** pstring){_error_("PetscMat param of enum %i (%s) cannot return a string",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(char*** pstringarray,int* pM){_error_("PetscMat param of enum %i (%s) cannot return a string array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(double** pdoublearray,int* pM){_error_("PetscMat param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("PetscMat param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("PetscMat param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("PetscMat param of enum %i (%s) cannot return a vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* poutput); - void GetParameterValue(FILE** pfid){_error_("PetscMat param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} - - void SetValue(bool boolean){_error_("PetscMat param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} - void SetValue(int integer){_error_("PetscMat param of enum %i (%s) cannot hold an integer",enum_type,EnumToStringx(enum_type));} - void SetValue(double scalar){_error_("PetscMat param of enum %i (%s) cannot hold a scalar",enum_type,EnumToStringx(enum_type));} - void SetValue(char* string){_error_("PetscMat param of enum %i (%s) cannot hold a string",enum_type,EnumToStringx(enum_type));} - void SetValue(char** stringarray,int M){_error_("PetscMat param of enum %i (%s) cannot hold a string array",enum_type,EnumToStringx(enum_type));} - void SetValue(double* doublearray,int M){_error_("PetscMat param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} - void SetValue(double* pdoublearray,int M,int N){_error_("PetscMat param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} - void SetValue(int* intarray,int M){_error_("PetscMat param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} - void SetValue(int* pintarray,int M,int N){_error_("PetscMat param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("PetscMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat); - void SetValue(FILE* fid){_error_("PetscMat param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} - void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("PetscMat param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} - void UnitConversion(int direction_enum); - - void GetParameterName(char**pname); - #ifdef _SERIAL_ - void SetMatlabField(mxArray* dataref); - #endif - - /*}}}*/ -}; -#endif /* _PETSCMATPARAM_H */ Index: sm/branches/trunk-jpl-damage/src/c/objects/Params/PetscVecParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/PetscVecParam.cpp (revision 11707) +++ (revision ) @@ -1,237 +1,0 @@ -/*!\file PetscVecParam.c - * \brief: implementation of the PetscVecParam object - */ - -/*header files: */ -/*{{{1*/ -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#include -#include -#include "../objects.h" -#include "../../EnumDefinitions/EnumDefinitions.h" -#include "../../shared/shared.h" -#include "../../Container/Container.h" -#include "../../include/include.h" -/*}}}*/ - -/*PetscVecParam constructors and destructor*/ -/*FUNCTION PetscVecParam::PetscVecParam(){{{1*/ -PetscVecParam::PetscVecParam(){ - return; -} -/*}}}*/ -/*FUNCTION PetscVecParam::PetscVecParam(int enum_type,IssmPetscVec value){{{1*/ -PetscVecParam::PetscVecParam(int in_enum_type,Vec in_value){ - - enum_type=in_enum_type; - - value=NULL; - - if(in_value){ - VecDuplicate(in_value,&value); - VecCopy(in_value,value); - } -} -/*}}}*/ -/*FUNCTION PetscVecParam::~PetscVecParam(){{{1*/ -PetscVecParam::~PetscVecParam(){ - VecFree(&value); -} -/*}}}*/ - -/*Object virtual functions definitions:*/ -/*FUNCTION PetscVecParam::Echo {{{1*/ -void PetscVecParam::Echo(void){ - - printf("PetscVecParam:\n"); - printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); - -} -/*}}}*/ -/*FUNCTION PetscVecParam::DeepEcho{{{1*/ -void PetscVecParam::DeepEcho(void){ - - int i; - printf("PetscVecParam:\n"); - printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); - VecView(value,PETSC_VIEWER_STDOUT_WORLD); -} -/*}}}*/ -/*FUNCTION PetscVecParam::Id{{{1*/ -int PetscVecParam::Id(void){ return -1; } -/*}}}*/ -/*FUNCTION PetscVecParam::MyRank{{{1*/ -int PetscVecParam::MyRank(void){ - extern int my_rank; - return my_rank; -} -/*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION PetscVecParam::Marshall{{{1*/ -void PetscVecParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int M; - double* serial_value=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of PetscVecParam: */ - enum_value=PetscVecParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall PetscVecParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - if(value){ - VecGetSize(value,&M); - VecToMPISerial(&serial_value,value); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - } - else{ - M=0; - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - } - /*Free ressources:*/ - xfree((void**)&serial_value); - - /*return:*/ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION PetscVecParam::MarshallSize{{{1*/ -int PetscVecParam::MarshallSize(){ - - int M=0; - if(value)VecGetSize(value,&M); - - return sizeof(M)+M*sizeof(double) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION PetscVecParam::Demarshall{{{1*/ -void PetscVecParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int M; - double* serial_vec=NULL; - int* idxm=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - if(M){ - serial_vec=(double*)xmalloc(M*sizeof(double)); - memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - - value=NewVec(M); - idxm=(int*)xmalloc(M*sizeof(int)); - for(i=0;ienum_type,this->value); - -} -/*}}}*/ - -/*PetscVecParam virtual functions definitions: */ -/*FUNCTION PetscVecParam::GetParameterValue{{{1*/ -void PetscVecParam::GetParameterValue(Vec* poutput){ - Vec output=NULL; - - if(value){ - VecDuplicate(value,&output); - VecCopy(value,output); - } - *poutput=output; -} -/*}}}*/ -/*FUNCTION PetscVecParam::GetParameterName{{{1*/ -void PetscVecParam::GetParameterName(char**pname){ - EnumToStringx(pname,this->enum_type); -} -/*}}}*/ -/*FUNCTION PetscVecParam::SetMatlabField{{{1*/ -#ifdef _SERIAL_ -void PetscVecParam::SetMatlabField(mxArray* dataref){ - - mxArray* pfield=NULL; - char* name=NULL; - double* doublevec=NULL; - int M; - - VecToMPISerial(&doublevec,value); - VecGetSize(value,&M); - this->GetParameterName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,1); - mxSetPr(pfield,doublevec); - - mxSetField( dataref, 0, name, pfield); -} -#endif -/*}}}*/ -/*FUNCTION PetscVecParam::SetValue{{{1*/ -void PetscVecParam::SetValue(Vec vector){ - - /*avoid leak: */ - VecFree(&value); - - /*copy: */ - VecDuplicate(vector,&value); - VecCopy(vector,value); -} -/*}}}*/ -/*FUNCTION PetscVecParam::UnitConversion{{{1*/ -void PetscVecParam::UnitConversion(int direction_enum){ - /*do nothing, no unit conversion*/ -} -/*}}}*/ Index: sm/branches/trunk-jpl-damage/src/c/objects/Params/PetscVecParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/PetscVecParam.h (revision 11707) +++ (revision ) @@ -1,90 +1,0 @@ -/*! \file PetscVecParam.h - * \brief: header file for triavertexinput object - */ - - -#ifndef _PETSCVECPARAM_H_ -#define _PETSCVECPARAM_H_ - -/*Headers:*/ -/*{{{1*/ -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#ifdef _SERIAL_ -#include -#endif - -#include "./Param.h" -#include "../../include/include.h" -#include "../../shared/shared.h" -/*}}}*/ - -class PetscVecParam: public Param{ - - private: - /*just hold 3 values for 3 vertices: */ - int enum_type; - Vec value; - - public: - /*PetscVecParam constructors, destructors: {{{1*/ - PetscVecParam(); - PetscVecParam(int enum_type,Vec value); - ~PetscVecParam(); - /*}}}*/ - /*Object virtual functions definitions:{{{1 */ - void Echo(); - void DeepEcho(); - int Id(); - int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif - int ObjectEnum(); - Object* copy(); - /*}}}*/ - /*Param vritual function definitions: {{{1*/ - int InstanceEnum(){return enum_type;} - void GetParameterValue(bool* pbool){_error_("PetscVec param of enum %i (%s) cannot return a bool",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(int* pinteger){_error_("PetscVec param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(int** pintarray,int* pM){_error_("PetscVec param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(int** pintarray,int* pM,int* pN){_error_("PetscVec param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(double* pdouble){_error_("PetscVec param of enum %i (%s) cannot return a double",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(char** pstring){_error_("PetscVec param of enum %i (%s) cannot return a string",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(char*** pstringarray,int* pM){_error_("PetscVec param of enum %i (%s) cannot return a string array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(double** pdoublearray,int* pM){_error_("PetscVec param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("PetscVec param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("PetscVec param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("PetscVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* poutput); - void GetParameterValue(FILE** pfid){_error_("PetscVec of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} - - void SetValue(bool boolean){_error_("PetscVec of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} - void SetValue(int integer){_error_("PetscVec of enum %i (%s) cannot hold an integer",enum_type,EnumToStringx(enum_type));} - void SetValue(double scalar){_error_("PetscVec of enum %i (%s) cannot hold a scalar",enum_type,EnumToStringx(enum_type));} - void SetValue(char* string){_error_("PetscVec of enum %i (%s) cannot hold a string",enum_type,EnumToStringx(enum_type));} - void SetValue(char** stringarray,int M){_error_("PetscVec of enum %i (%s) cannot hold a string array",enum_type,EnumToStringx(enum_type));} - void SetValue(double* doublearray,int M){_error_("PetscVec of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} - void SetValue(double* pdoublearray,int M,int N){_error_("PetscVec of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} - void SetValue(int* intarray,int M){_error_("PetscVec of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} - void SetValue(int* pintarray,int M,int N){_error_("PetscVec of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec); - void SetValue(Mat mat){_error_("PetscVec of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} - void SetValue(FILE* fid){_error_("PetscVec of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} - void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("PetscVec param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} - void UnitConversion(int direction_enum); - - void GetParameterName(char**pname); - #ifdef _SERIAL_ - void SetMatlabField(mxArray* dataref); - #endif - - /*}}}*/ -}; -#endif /* _PETSCVECPARAM_H */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringArrayParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringArrayParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringArrayParam.h (revision 11708) @@ -64,6 +64,6 @@ void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("StringArray param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Vec param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("StringArray param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("StringArray param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("StringArray param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("StringArray param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("StringArray param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -77,6 +77,6 @@ void SetValue(int* intarray,int M){_error_("StringArray param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} void SetValue(int* pintarray,int M,int N){_error_("StringArray param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("StringArray param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("StringArray param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("StringArray param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("StringArray param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("StringArray param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("StringArray param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringParam.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/StringParam.h (revision 11708) @@ -62,6 +62,6 @@ void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("String param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("String param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Vec* pvec){_error_("String param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} - void GetParameterValue(Mat* pmat){_error_("String param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** pvec){_error_("String param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("String param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} void GetParameterValue(FILE** pfid){_error_("Bool param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} @@ -75,6 +75,6 @@ void SetValue(int* intarray,int M){_error_("String param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} void SetValue(int* pintarray,int M,int N){_error_("String param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} - void SetValue(Vec vec){_error_("String param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} - void SetValue(Mat mat){_error_("String param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec){_error_("String param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} + void SetValue(Matrix* mat){_error_("String param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} void SetValue(FILE* fid){_error_("String param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("String param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.cpp (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.cpp (revision 11708) @@ -0,0 +1,227 @@ +/*!\file VectorParam.c + * \brief: implementation of the VectorParam object + */ + +/*header files: */ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../Container/Container.h" +#include "../../include/include.h" +/*}}}*/ + +/*VectorParam constructors and destructor*/ +/*FUNCTION VectorParam::VectorParam(){{{1*/ +VectorParam::VectorParam(){ + return; +} +/*}}}*/ +/*FUNCTION VectorParam::VectorParam(int enum_type,IssmVector value){{{1*/ +VectorParam::VectorParam(int in_enum_type,Vector* in_value){ + + enum_type=in_enum_type; + + value=NULL; + + if(in_value){ + value=in_value->Duplicate(); + in_value->Copy(value); + } +} +/*}}}*/ +/*FUNCTION VectorParam::~VectorParam(){{{1*/ +VectorParam::~VectorParam(){ + xdelete(&value); +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION VectorParam::Echo {{{1*/ +void VectorParam::Echo(void){ + + printf("VectorParam:\n"); + printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); + +} +/*}}}*/ +/*FUNCTION VectorParam::DeepEcho{{{1*/ +void VectorParam::DeepEcho(void){ + + int i; + printf("VectorParam:\n"); + printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); + value->Echo(); +} +/*}}}*/ +/*FUNCTION VectorParam::Id{{{1*/ +int VectorParam::Id(void){ return -1; } +/*}}}*/ +/*FUNCTION VectorParam::MyRank{{{1*/ +int VectorParam::MyRank(void){ + extern int my_rank; + return my_rank; +} +/*}}}*/ +#ifdef _SERIAL_ +/*FUNCTION VectorParam::Marshall{{{1*/ +void VectorParam::Marshall(char** pmarshalled_dataset){ + + char* marshalled_dataset=NULL; + int enum_value=0; + int M; + double* serial_value=NULL; + + /*recover marshalled_dataset: */ + marshalled_dataset=*pmarshalled_dataset; + + /*get enum value of VectorParam: */ + enum_value=VectorParamEnum; + + /*marshall enum: */ + memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); + + /*marshall VectorParam data: */ + memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); + if(value){ + value->GetSize(&M); + serial_value=value->ToMPISerial(); + memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); + memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); + } + else{ + M=0; + memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); + } + /*Free ressources:*/ + xfree((void**)&serial_value); + + /*return:*/ + *pmarshalled_dataset=marshalled_dataset; +} +/*}}}*/ +/*FUNCTION VectorParam::MarshallSize{{{1*/ +int VectorParam::MarshallSize(){ + + int M=0; + if(value)value->GetSize(&M); + + return sizeof(M)+M*sizeof(double) + +sizeof(enum_type)+ + +sizeof(int); //sizeof(int) for enum value +} +/*}}}*/ +/*FUNCTION VectorParam::Demarshall{{{1*/ +void VectorParam::Demarshall(char** pmarshalled_dataset){ + + char* marshalled_dataset=NULL; + int i; + double* serial_vec=NULL; + int M; + + /*recover marshalled_dataset: */ + marshalled_dataset=*pmarshalled_dataset; + + /*this time, no need to get enum type, the pointer directly points to the beginning of the + *object data (thanks to DataSet::Demarshall):*/ + memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); + + /*data: */ + + memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); + if(M){ + serial_vec=(double*)xmalloc(M*sizeof(double)); + memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); + + value=new Vector(serial_vec,M); + } + else{ + value=NULL; + } + + /*Free ressources:*/ + xfree((void**)&serial_vec); + + /*return: */ + *pmarshalled_dataset=marshalled_dataset; +} +/*}}}*/ +#endif +/*FUNCTION VectorParam::ObjectEnum{{{1*/ +int VectorParam::ObjectEnum(void){ + + return VectorParamEnum; + +} +/*}}}*/ +/*FUNCTION VectorParam::copy{{{1*/ +Object* VectorParam::copy() { + + return new VectorParam(this->enum_type,this->value); + +} +/*}}}*/ + +/*VectorParam virtual functions definitions: */ +/*FUNCTION VectorParam::GetParameterValue{{{1*/ +void VectorParam::GetParameterValue(Vector** poutput){ + Vector* output=NULL; + + if(value){ + output=value->Duplicate(); + value->Copy(output); + } + *poutput=output; +} +/*}}}*/ +/*FUNCTION VectorParam::GetParameterName{{{1*/ +void VectorParam::GetParameterName(char**pname){ + EnumToStringx(pname,this->enum_type); +} +/*}}}*/ +/*FUNCTION VectorParam::SetMatlabField{{{1*/ +#ifdef _SERIAL_ +void VectorParam::SetMatlabField(mxArray* dataref){ + + mxArray* pfield=NULL; + char* name=NULL; + double* doublevec=NULL; + int M; + + doublevec=value->ToMPISerial(); + value->GetSize(&M); + this->GetParameterName(&name); + + pfield=mxCreateDoubleMatrix(0,0,mxREAL); + mxSetM(pfield,M); + mxSetN(pfield,1); + mxSetPr(pfield,doublevec); + + mxSetField( dataref, 0, name, pfield); +} +#endif +/*}}}*/ +/*FUNCTION VectorParam::SetValue{{{1*/ +void VectorParam::SetValue(Vector* vector){ + + /*avoid leak: */ + xdelete(&value); + + /*copy: */ + value=vector->Duplicate(); + vector->Copy(value); +} +/*}}}*/ +/*FUNCTION VectorParam::UnitConversion{{{1*/ +void VectorParam::UnitConversion(int direction_enum){ + /*do nothing, no unit conversion*/ +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.h (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Params/VectorParam.h (revision 11708) @@ -0,0 +1,90 @@ +/*! \file VectorParam.h + * \brief: header file for triavertexinput object + */ + + +#ifndef _VECTORPARAM_H_ +#define _VECTORPARAM_H_ + +/*Headers:*/ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#ifdef _SERIAL_ +#include +#endif + +#include "./Param.h" +#include "../../include/include.h" +#include "../../shared/shared.h" +/*}}}*/ + +class VectorParam: public Param{ + + private: + /*just hold 3 values for 3 vertices: */ + int enum_type; + Vector* value; + + public: + /*VectorParam constructors, destructors: {{{1*/ + VectorParam(); + VectorParam(int enum_type,Vector* value); + ~VectorParam(); + /*}}}*/ + /*Object virtual functions definitions:{{{1 */ + void Echo(); + void DeepEcho(); + int Id(); + int MyRank(); + #ifdef _SERIAL_ + void Marshall(char** pmarshalled_dataset); + int MarshallSize(); + void Demarshall(char** pmarshalled_dataset); + #endif + int ObjectEnum(); + Object* copy(); + /*}}}*/ + /*Param vritual function definitions: {{{1*/ + int InstanceEnum(){return enum_type;} + void GetParameterValue(bool* pbool){_error_("Vector param of enum %i (%s) cannot return a bool",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(int* pinteger){_error_("Vector param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(int** pintarray,int* pM){_error_("Vector param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Vector param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double* pdouble){_error_("Vector param of enum %i (%s) cannot return a double",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(char** pstring){_error_("Vector param of enum %i (%s) cannot return a string",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(char*** pstringarray,int* pM){_error_("Vector param of enum %i (%s) cannot return a string array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM){_error_("Vector param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("Vector param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Vector param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Matrix** pmat){_error_("Vector param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(Vector** poutput); + void GetParameterValue(FILE** pfid){_error_("Vector of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){_error_("Vector of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} + void SetValue(int integer){_error_("Vector of enum %i (%s) cannot hold an integer",enum_type,EnumToStringx(enum_type));} + void SetValue(double scalar){_error_("Vector of enum %i (%s) cannot hold a scalar",enum_type,EnumToStringx(enum_type));} + void SetValue(char* string){_error_("Vector of enum %i (%s) cannot hold a string",enum_type,EnumToStringx(enum_type));} + void SetValue(char** stringarray,int M){_error_("Vector of enum %i (%s) cannot hold a string array",enum_type,EnumToStringx(enum_type));} + void SetValue(double* doublearray,int M){_error_("Vector of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(double* pdoublearray,int M,int N){_error_("Vector of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M){_error_("Vector of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* pintarray,int M,int N){_error_("Vector of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} + void SetValue(Vector* vec); + void SetValue(Matrix* mat){_error_("Vector of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("Vector of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Vector param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); + + void GetParameterName(char**pname); + #ifdef _SERIAL_ + void SetMatlabField(mxArray* dataref); + #endif + + /*}}}*/ +}; +#endif /* _VECTORPARAM_H */ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.cpp (revision 11708) @@ -273,5 +273,5 @@ /*}}}*/ /*FUNCTION Vertex::UpdateVertexPosition {{{1*/ -void Vertex::UpdatePosition(Vec vz,Parameters* parameters,double* thickness,double* bed){ +void Vertex::UpdatePosition(Vector* vz,Parameters* parameters,double* thickness,double* bed){ double oldz,newz; @@ -288,5 +288,5 @@ /*put vz in vector*/ - VecSetValue(vz,this->dof,velz,INSERT_VALUES); -} -/*}}}*/ + vz->SetValue(this->dof,velz,INS_VAL); +} +/*}}}*/ Index: /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/Vertex.h (revision 11708) @@ -10,4 +10,6 @@ #include "./Object.h" class IoModel; +class Vector; +class Parameters; #include "../shared/Exceptions/exceptions.h" #include "../toolkits/toolkits.h" @@ -63,5 +65,5 @@ int Sid(void); int Connectivity(void); - void UpdatePosition(Vec vz,Parameters* parameters,double* thickness,double* bed); + void UpdatePosition(Vector* vz,Parameters* parameters,double* thickness,double* bed); /*}}}*/ }; Index: /issm/branches/trunk-jpl-damage/src/c/objects/objects.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/objects/objects.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/objects/objects.h (revision 11708) @@ -135,6 +135,6 @@ #include "./Params/FileParam.h" #include "./Params/Param.h" -#include "./Params/PetscMatParam.h" -#include "./Params/PetscVecParam.h" +#include "./Params/MatrixParam.h" +#include "./Params/VectorParam.h" #include "./Params/StringArrayParam.h" #include "./Params/StringParam.h" Index: /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Alloc/alloc.cpp (revision 11708) @@ -67,12 +67,11 @@ } -void xfree( void* *pv){ +void xfree(void* *pv){ - if (pv && *pv) { - + if (pv && *pv){ #ifdef _SERIAL_ - mxFree(*pv); + mxFree(*pv); #else - free(*pv); + free(*pv); #endif @@ -81,18 +80,34 @@ } -void xdelete( Matrix** pv){ - - if (pv && *pv) { - +void xdelete(Matrix** pv){ + + if (pv && *pv){ + #ifdef _PARALLEL_ + /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we + * don't actually free memory in Matlab, we let the memory manager do that. We only + * free in parallel: */ delete *pv; + #else + /*Actually, still get rid of internal Petsc matrix. Quick fix until Matlab handles C++ + * correctly: */ + MatFree(&(*pv)->matrix); + #endif *pv=NULL; } } -void xdelete( Vector** pv){ +void xdelete(Vector** pv){ - if (pv && *pv) { - + if (pv && *pv){ + #ifdef _PARALLEL_ + /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we + * don't actually free memory in Matlab, we let the memory manager do that. We only + * free in parallel: */ delete *pv; + #else + /*Actually, still get rid of internal Petsc vector. Quick fix until Matlab handles C++ + * correctly: */ + VecFree(&(*pv)->vector); + #endif *pv=NULL; } @@ -100,5 +115,5 @@ -void* xrealloc ( void* pv, int size){ +void* xrealloc( void* pv, int size){ register void* value=NULL; Index: /issm/branches/trunk-jpl-damage/src/c/shared/Exp/IsInPoly.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Exp/IsInPoly.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Exp/IsInPoly.cpp (revision 11708) @@ -15,5 +15,5 @@ /*IsInPoly {{{1*/ -int IsInPoly(Vec in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue){ +int IsInPoly(Vector* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue){ int i; @@ -37,5 +37,5 @@ //Get current value of value[i] -> do not change it if != 0 - VecGetValues(in,1,&i,&value); + in->GetValue(&value,i); if (value){ /*this vertex already is inside one of the contours, continue*/ @@ -51,10 +51,10 @@ value=pnpoly(numvertices,xc,yc,x0,y0,edgevalue); } - VecSetValues(in,1,&i,&value,INSERT_VALUES); + in->SetValue(i,value,INS_VAL); } return 1; }/*}}}*/ /*IsOutsidePoly {{{1*/ -int IsOutsidePoly(Vec in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue){ +int IsOutsidePoly(Vector* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue){ int i,j; @@ -78,5 +78,5 @@ //Get current value of value[i] -> do not change it if != 0 - VecGetValues(in,1,&i,&value); + in->GetValue(&value,i); if (value){ /*this vertex already is inside one of the contours, continue*/ @@ -92,5 +92,5 @@ value=1-pnpoly(numvertices,xc,yc,x0,y0,edgevalue); } - VecSetValues(in,1,&i,&value,INSERT_VALUES); + in->SetValue(i,value,INS_VAL); } return 1; Index: /issm/branches/trunk-jpl-damage/src/c/shared/Exp/exp.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Exp/exp.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Exp/exp.h (revision 11708) @@ -9,6 +9,6 @@ #include "../../toolkits/toolkits.h" -int IsInPoly(Vec in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue); -int IsOutsidePoly(Vec in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue); +int IsInPoly(Vector* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue); +int IsOutsidePoly(Vector* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue); int IsInPolySerial(double* in,double* xc,double* yc,int numvertices,double* x,double* y,int nods, int edgevalue); int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname,bool whole); Index: /issm/branches/trunk-jpl-damage/src/c/shared/Matlab/ModuleBoot.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Matlab/ModuleBoot.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Matlab/ModuleBoot.cpp (revision 11708) @@ -5,4 +5,11 @@ #include "../../toolkits/toolkits.h" + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + int my_rank; @@ -16,32 +23,34 @@ /*Some test for MPI_Init crash with mpich2 1.4 on larsen, just ignore*/ - #if _PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 1 - if(0){ - int mp_init = 0; - PetscErrorCode ierr; - extern PetscBool PetscBeganMPI; - MPI_Initialized(&mp_init); - if(mp_init!=1){ - MPI_Init(NULL,NULL); - PetscBeganMPI = PETSC_TRUE; + #ifdef _HAVE_PETSC_ + #if _PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 1 + if(0){ + int mp_init = 0; + PetscErrorCode ierr; + extern PetscBool PetscBeganMPI; + MPI_Initialized(&mp_init); + if(mp_init!=1){ + MPI_Init(NULL,NULL); + PetscBeganMPI = PETSC_TRUE; + ierr=PetscInitializeNoArguments();CHKERRQ(ierr); + } + } + else if (0){ + PetscErrorCode ierr; + PetscBool flg; + ierr=PetscInitialized(&flg);CHKERRQ(ierr); + if(flg){ + extern PetscBool PetscBeganMPI; + PetscBeganMPI = PETSC_FALSE; + ierr=PetscFinalize();CHKERRQ(ierr); + } ierr=PetscInitializeNoArguments();CHKERRQ(ierr); - } - } - else if (0){ - PetscErrorCode ierr; - PetscBool flg; - ierr=PetscInitialized(&flg);CHKERRQ(ierr); - if(flg){ - extern PetscBool PetscBeganMPI; - PetscBeganMPI = PETSC_FALSE; - ierr=PetscFinalize();CHKERRQ(ierr); + ierr=PetscPopSignalHandler();CHKERRQ(ierr); } - ierr=PetscInitializeNoArguments();CHKERRQ(ierr); - ierr=PetscPopSignalHandler();CHKERRQ(ierr); - } + #endif + + /*Initialize Petsc: */ + PetscInitializeNoArguments(); #endif - - /*Initialize Petsc: */ - PetscInitializeNoArguments(); return 1; Index: /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/OptionsFromAnalysis.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 11708) @@ -0,0 +1,80 @@ +/*!\file: OptionsFromAnalysis.cpp + * \brief: figure out ISSM options for current analysis, return a string. + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../../objects/objects.h" +#include "../../Container/Parameters.h" +#include "../../EnumDefinitions/EnumDefinitions.h" + +char* OptionsFromAnalysis(Parameters* parameters,int analysis_type){ + + /*output: */ + char* outstring=NULL; + + /*intermediary: */ + int dummy; + double* analyses=NULL; + char** strings=NULL; + char* string=NULL; + int numanalyses; + int found=-1; + int i; + + numanalyses=0; + parameters->FindParam(&strings,&numanalyses,PetscOptionsStringsEnum); + + #ifdef _SERIAL_ //do not take this away, because ISSM loads analyses as a Double Param instead of a DoubleVec Param when running with only 1 analysis + if(numanalyses==1){ analyses=(double*)xmalloc(1*sizeof(double)); parameters->FindParam(analyses,PetscOptionsAnalysesEnum); + } + else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); + #else + parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); + #endif + + if(numanalyses==0)return NULL; //we did not find petsc options, don't bother. + + /*ok, go through analyses and figure out if it corresponds to our analysis_type: */ + found=-1; + for(i=0;iFindParam(&strings,&numanalyses,PetscOptionsStringsEnum); - - #ifdef _SERIAL_ //do not take this away, because ISSM loads analyses as a Double Param instead of a DoubleVec Param when running with only 1 analysis - if(numanalyses==1){ analyses=(double*)xmalloc(1*sizeof(double)); parameters->FindParam(analyses,PetscOptionsAnalysesEnum); - } - else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); - #else - parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); - #endif - - if(numanalyses==0)return; //we did not find petsc options, don't bother. - - /*ok, go through analyses and figure out if it corresponds to our analysis_type: */ - found=-1; - for(i=0;i @@ -33,7 +33,7 @@ double *dummy = NULL; int *control_list = NULL; - Vec X = NULL; - Vec XL = NULL; - Vec XU = NULL; + Vector *X = NULL; + Vector *XL = NULL; + Vector *XU = NULL; /*Initialize TAO*/ @@ -68,8 +68,8 @@ GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); - TaoSetInitialVector(tao,X); - TaoSetVariableBounds(tao,XL,XU); - VecFree(&XL); - VecFree(&XU); + TaoSetInitialVector(tao,X->vector); + TaoSetVariableBounds(tao,XL->vector,XU->vector); + xdelete(&XL); + xdelete(&XU); user.femmodel=femmodel; @@ -80,5 +80,5 @@ TaoSolve(tao); TaoView(tao,PETSC_VIEWER_STDOUT_WORLD); - TaoGetSolutionVector(tao,&X); + TaoGetSolutionVector(tao,&X->vector); SetControlInputsFromVectorx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,X); for(int i=0;ielements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,X); + xdelete(&X); /*Recover some parameters*/ @@ -136,5 +141,5 @@ /*Compute gradient*/ Gradjx(&gradient,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); - VecCopy(gradient,G); VecFree(&gradient); + VecCopy(gradient->vector,G); xdelete(&gradient); VecScale(G,-1.); Index: /issm/branches/trunk-jpl-damage/src/c/solutions/convergence.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solutions/convergence.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/solutions/convergence.cpp (revision 11708) @@ -52,6 +52,6 @@ //compute norm(KUF), norm(F) and residue - nKUF=KUF->Norm(NORM_2); - nF=pf->Norm(NORM_2); + nKUF=KUF->Norm(NORM_TWO); + nF=pf->Norm(NORM_TWO); solver_residue=nKUF/nF; _printf_(true,"\n%s%g\n"," solver residue: norm(KU-F)/norm(F)=",solver_residue); @@ -67,6 +67,6 @@ KUold=uf->Duplicate(); Kff->MatMult(old_uf,KUold); KUoldF=KUold->Duplicate();KUold->Copy(KUoldF); KUoldF->AYPX(pf,-1.0); - nKUoldF=KUoldF->Norm(NORM_2); - nF=pf->Norm(NORM_2); + nKUoldF=KUoldF->Norm(NORM_TWO); + nF=pf->Norm(NORM_TWO); res=nKUoldF/nF; if (isnan(res)){ @@ -94,5 +94,5 @@ //compute norm(du)/norm(u) duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); - ndu=duf->Norm(NORM_2); nu=old_uf->Norm(NORM_2); + ndu=duf->Norm(NORM_TWO); nu=old_uf->Norm(NORM_TWO); if (isnan(ndu) || isnan(nu)) _error_("convergence criterion is NaN!"); @@ -120,5 +120,5 @@ //compute max(du) duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); - ndu=duf->Norm(NORM_2); nduinf=duf->Norm(NORM_INFINITY); + ndu=duf->Norm(NORM_TWO); nduinf=duf->Norm(NORM_INF); if (isnan(ndu) || isnan(nu)) _error_("convergence criterion is NaN!"); Index: /issm/branches/trunk-jpl-damage/src/c/solutions/gradient_core.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solutions/gradient_core.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/solutions/gradient_core.cpp (revision 11708) @@ -18,7 +18,7 @@ double norm_inf; double *norm_list = NULL; - Vec new_gradient = NULL; - Vec gradient = NULL; - Vec old_gradient = NULL; + Vector* new_gradient = NULL; + Vector* gradient = NULL; + Vector* old_gradient = NULL; /*Compute gradient*/ @@ -29,5 +29,5 @@ _printf_(VerboseControl()," orthogonalization\n"); ControlInputGetGradientx(&old_gradient,femmodel->elements,femmodel->nodes, femmodel->vertices,femmodel->loads, femmodel->materials,femmodel->parameters); - Orthx(&new_gradient,gradient,old_gradient); VecFree(&old_gradient); VecFree(&gradient); + Orthx(&new_gradient,gradient,old_gradient); xdelete(&old_gradient); xdelete(&gradient); } else{ @@ -36,5 +36,5 @@ /*Check that gradient is clean*/ - VecNorm(new_gradient,NORM_INFINITY,&norm_inf); + norm_inf=new_gradient->Norm(NORM_INF); if(norm_inf<=0) _error_("||∂J/∂α||∞ = 0 gradient norm is zero"); if(isnan(norm_inf))_error_("||∂J/∂α||∞ = NaN gradient norm is NaN"); @@ -42,5 +42,5 @@ /*plug back into inputs: */ ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,new_gradient); - VecFree(&new_gradient); + xdelete(&new_gradient); /*Scale Gradients*/ Index: /issm/branches/trunk-jpl-damage/src/c/solutions/issm.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/solutions/issm.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/solutions/issm.cpp (revision 11708) @@ -37,4 +37,5 @@ double start_core, finish_core; double start_init, finish_init; + int ierr; MODULEBOOT(); @@ -44,7 +45,12 @@ #endif - /*Initialize Petsc and get start time*/ - int ierr=PetscInitialize(&argc,&argv,(char*)0,""); + /*Initialize environments: Petsc, MPI, etc...: */ + #ifdef _HAVE_PETSC_ + ierr=PetscInitialize(&argc,&argv,(char*)0,""); if(ierr) _error_("Could not initialize Petsc"); + #else + MPI_Init(&argc,&argv); + #endif + MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime(); @@ -130,6 +136,12 @@ _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",finish_core-start_core); _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600),int(int(finish-start)%3600/60),int(finish-start)%60); + + _printf_(true,"closing MPI and Petsc\n"); + #ifdef _HAVE_PETSC_ PetscFinalize(); + #else + MPI_Finalize(); + #endif /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/double/MatlabMatrixToDoubleMatrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/double/MatlabMatrixToDoubleMatrix.cpp (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/double/MatlabMatrixToDoubleMatrix.cpp (revision 11708) @@ -0,0 +1,97 @@ +/* \file MatlabMatrixToDoubleMatrix.cpp + * \brief: convert a sparse or dense matlab matrix to a double* pointer + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#ifdef _SERIAL_ + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ + + int i,j,count,rows,cols; + double *pmxdoublematrix = NULL; + float *pmxsinglematrix = NULL; + + /*output: */ + double* matrix=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + + /*Ok, first check if we are dealing with a sparse or full matrix: */ + if (mxIsSparse(mxmatrix)){ + + /*Dealing with sparse matrix: recover size first: */ + pmxdoublematrix=(double*)mxGetPr(mxmatrix); + rows=mxGetM(mxmatrix); + cols=mxGetN(mxmatrix); + matrix=(double*)xcalloc(rows*cols,sizeof(double)); + + /*Now, get ir,jc and pr: */ + ir=mxGetIr(mxmatrix); + jc=mxGetJc(mxmatrix); + + /*Now, start inserting data into double* matrix: */ + count=0; + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#ifdef _SERIAL_ + +#include + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){ + + int rows,cols; + double* mxvector_ptr=NULL; + int ierr; + int i,j; + + /*output: */ + double* vector=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + double* pr=NULL; + int count; + int nnz; + int nz; + + /*Ok, first check if we are dealing with a sparse or full vector: */ + if (mxIsSparse(mxvector)){ + + /*Dealing with sparse vector: recover size first: */ + mxvector_ptr=(double*)mxGetPr(mxvector); + rows=mxGetM(mxvector); + cols=mxGetN(mxvector); + nnz=mxGetNzmax(mxvector); + + /*Check that input is actualy a vector*/ + if (cols!=1) _error_("input vector of size %ix%i should have only one column",rows,cols); + + nz=(int)((double)nnz/(double)rows); + + vector=(double*)xcalloc(rows,sizeof(double)); + + /*Now, get ir,jc and pr: */ + pr=mxGetPr(mxvector); + ir=mxGetIr(mxvector); + jc=mxGetJc(mxvector); + + /*Now, start inserting data into sparse vector: */ + count=0; + for(i=0;i +#include + + +#include "../../../shared/shared.h" + +int DetermineLocalSize(int global_size){ + + /*output: */ + int local_size; + + /*intermediary: */ + int i; + int row_rest; + int* num_local_rows=NULL; + + /*from MPI: */ + extern int num_procs; + extern int my_rank; + + /*We are not bound by any library, just use what seems most logical*/ + num_local_rows=(int*)xmalloc(num_procs*sizeof(int)); + + for (i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +/*ISSM includes: */ +#include "../../toolkitsenums.h" +#include "../../../shared/shared.h" + + +InsertMode ISSMToPetscInsertMode(InsMode mode){ + + switch(mode){ + case ADD_VAL: + return ADD_VALUES; + break; + case INS_VAL: + return INSERT_VALUES; + break; + default: + _error_("unknown insert mode!"); + break; + } +} Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/ISSMToPetscNormMode.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/ISSMToPetscNormMode.cpp (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/ISSMToPetscNormMode.cpp (revision 11708) @@ -0,0 +1,35 @@ +/* \file ISSMToPetscNormMode.cpp + * \brief: convert NormMode from ISSM to Petsc + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +/*ISSM includes: */ +#include "../../toolkitsenums.h" +#include "../../../shared/shared.h" + + +NormType ISSMToPetscNormMode(NormMode mode){ + + switch(mode){ + case NORM_INF: + return NORM_INFINITY; + break; + case NORM_TWO: + return NORM_2; + break; + default: + _error_("unknown norm !"); + break; + } +} Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatPartition.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatPartition.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatPartition.cpp (revision 11708) @@ -15,4 +15,5 @@ #include "../../../shared/shared.h" +#include "../../mpi/patches/mpipatches.h" int MatPartition(Mat* poutmatrix,Mat matrixA,double* row_partition_vector,int row_partition_vector_size , @@ -97,5 +98,5 @@ /*Call MatGetSubMatrix*/ - csize=PetscDetermineLocalSize(col_partition_vector_size); + csize=DetermineLocalSize(col_partition_vector_size); if(col_partition_vector_size==row_partition_vector_size){ #if _PETSC_MAJOR_ >= 3 Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatToSerial.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatToSerial.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatToSerial.cpp (revision 11708) @@ -2,4 +2,11 @@ * \brief gather a Petsc Mat matrix onto cpu 0 */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + #include "../petscincludes.h" Index: sm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp (revision 11707) +++ (revision ) @@ -1,102 +1,0 @@ -/* \file MatlabMatrixToDoubleMatrix.cpp - * \brief: convert a sparse or dense matlab matrix to a double* pointer - */ - - -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#ifdef _SERIAL_ - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Matlab includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" - -int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ - - int i,j,count,rows,cols; - double *pmxdoublematrix = NULL; - float *pmxsinglematrix = NULL; - - /*output: */ - double* matrix=NULL; - - /*matlab indices: */ - mwIndex* ir=NULL; - mwIndex* jc=NULL; - - /*Ok, first check if we are dealing with a sparse or full matrix: */ - if (mxIsSparse(mxmatrix)){ - - /*Dealing with sparse matrix: recover size first: */ - pmxdoublematrix=(double*)mxGetPr(mxmatrix); - rows=mxGetM(mxmatrix); - cols=mxGetN(mxmatrix); - matrix=(double*)xcalloc(rows*cols,sizeof(double)); - - /*Now, get ir,jc and pr: */ - ir=mxGetIr(mxmatrix); - jc=mxGetJc(mxmatrix); - - /*Now, start inserting data into double* matrix: */ - count=0; - for(i=0;i -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#ifdef _SERIAL_ - -#include - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - - -/*Matlab includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" - -int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){ - - int rows,cols; - double* mxvector_ptr=NULL; - int ierr; - int i,j; - - /*output: */ - double* vector=NULL; - - /*matlab indices: */ - mwIndex* ir=NULL; - mwIndex* jc=NULL; - double* pr=NULL; - int count; - int nnz; - int nz; - - /*Ok, first check if we are dealing with a sparse or full vector: */ - if (mxIsSparse(mxvector)){ - - /*Dealing with sparse vector: recover size first: */ - mxvector_ptr=(double*)mxGetPr(mxvector); - rows=mxGetM(mxvector); - cols=mxGetN(mxvector); - nnz=mxGetNzmax(mxvector); - - /*Check that input is actualy a vector*/ - if (cols!=1) _error_("input vector of size %ix%i should have only one column",rows,cols); - - nz=(int)((double)nnz/(double)rows); - - vector=(double*)xcalloc(rows,sizeof(double)); - - /*Now, get ir,jc and pr: */ - pr=mxGetPr(mxvector); - ir=mxGetIr(mxvector); - jc=mxGetJc(mxvector); - - /*Now, start inserting data into sparse vector: */ - count=0; - for(i=0;i -#include - - -#include "../../../shared/shared.h" - -int PetscDetermineLocalSize(int global_size){ - - /*output: */ - int local_size; - - /*intermediary: */ - int i; - int row_rest; - int* num_local_rows=NULL; - - /*from MPI: */ - extern int num_procs; - extern int my_rank; - - /*We are not bound by any library, just use what seems most logical*/ - num_local_rows=(int*)xmalloc(num_procs*sizeof(int)); - - for (i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + #include "../petscincludes.h" Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/petscpatches.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/petscpatches.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/patches/petscpatches.h (revision 11708) @@ -12,4 +12,5 @@ #include "./SolverEnum.h" +#include "../../toolkitsenums.h" class Parameters; @@ -21,9 +22,6 @@ int PetscMatrixToMatlabMatrix(mxArray** pdataref,Mat matrix); int PetscVectorToMatlabVector(mxArray** pdataref,Vec vector); -int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix); -int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector); #endif -int PetscDetermineLocalSize(int global_size); Vec NewVec(int size,bool fromlocalsize=false); Mat NewMat(int M,int N); @@ -49,4 +47,6 @@ void VecDuplicatePatch(Vec* output, Vec input); Vec SerialToVec(double* vector,int vector_size); +InsertMode ISSMToPetscInsertMode(InsMode mode); +NormType ISSMToPetscNormMode(NormMode mode); #endif Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/petscincludes.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/petscincludes.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/petsc/petscincludes.h (revision 11708) @@ -5,4 +5,6 @@ #ifndef _PETSC_INCLUDES_H_ #define _PETSC_INCLUDES_H_ + +#ifdef _HAVE_PETSC_ /*Petsc includes: */ @@ -16,2 +18,3 @@ #endif +#endif Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/plapack/plapackincludes.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/plapack/plapackincludes.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/plapack/plapackincludes.h (revision 11708) @@ -6,4 +6,11 @@ #define _PLA_INCLUDES_H_ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + #include "PLA.h" @@ -12,5 +19,7 @@ /*our own patches: */ +#ifdef _HAVE_PETSC_ #include "patches/petscpatches.h" +#endif Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/toolkits.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/toolkits.h (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/toolkits.h (revision 11708) @@ -6,9 +6,20 @@ #define _TOOLKITS_H_ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#ifdef _HAVE_PETSC_ #include "./petsc/petscincludes.h" +#endif + #include "./mpi/mpiincludes.h" #include "./metis/metisincludes.h" #include "./triangle/triangleincludes.h" #include "./matlab/matlabincludes.h" +#include "./double/double.h" +#include "./toolkitsenums.h" #endif Index: /issm/branches/trunk-jpl-damage/src/c/toolkits/toolkitsenums.h =================================================================== --- /issm/branches/trunk-jpl-damage/src/c/toolkits/toolkitsenums.h (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/c/toolkits/toolkitsenums.h (revision 11708) @@ -0,0 +1,17 @@ +/* \file toolkitsenums.h + * \brief: enums that encompasse all of the toolkit APIs. This mainly maps into PETSC enums. + */ + +#ifndef _TOOLKITSENUMS_H_ +#define _TOOLKITSENUMS_H_ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +typedef enum {INS_VAL, ADD_VAL} InsMode; +typedef enum {NORM_INF,NORM_TWO} NormMode; + +#endif Index: /issm/branches/trunk-jpl-damage/src/m/classes/inversion.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/classes/inversion.m (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/m/classes/inversion.m (revision 11708) @@ -91,8 +91,7 @@ checkfield(md,'inversion.iscontrol','values',[0 1]); - checkfield(md,'inversion.control_parameters','cell',1,'values',{'BalancethicknessThickeningRate' 'FrictionCoefficient' 'MaterialsRheologyBbar' 'MaterialsRheologyZbar' 'Vx' 'Vy'}); checkfield(md,'inversion.tao','values',[0 1]); checkfield(md,'inversion.incomplete_adjoint','values',[0 1]); - checkfield(md,'inversion.control_parameters','cell',1,'values',{'BalancethicknessThickeningRate' 'FrictionCoefficient' 'MaterialsRheologyBbar' 'Vx' 'Vy'}); + checkfield(md,'inversion.control_parameters','cell',1,'values',{'BalancethicknessThickeningRate' 'FrictionCoefficient' 'MaterialsRheologyBbar' 'MaterialsRheologyZbar' 'Vx' 'Vy'}); checkfield(md,'inversion.nsteps','numel',1,'>=',1); checkfield(md,'inversion.maxiter_per_step','size',[md.inversion.nsteps 1],'>=',0); Index: /issm/branches/trunk-jpl-damage/src/m/enum/MatrixParamEnum.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/enum/MatrixParamEnum.m (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/m/enum/MatrixParamEnum.m (revision 11708) @@ -0,0 +1,11 @@ +function macro=MatrixParamEnum() +%MATRIXPARAMENUM - Enum of MatrixParam +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=MatrixParamEnum() + +macro=StringToEnum('MatrixParam'); Index: sm/branches/trunk-jpl-damage/src/m/enum/PetscMatParamEnum.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/enum/PetscMatParamEnum.m (revision 11707) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=PetscMatParamEnum() -%PETSCMATPARAMENUM - Enum of PetscMatParam -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=PetscMatParamEnum() - -macro=StringToEnum('PetscMatParam'); Index: sm/branches/trunk-jpl-damage/src/m/enum/PetscVecParamEnum.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/enum/PetscVecParamEnum.m (revision 11707) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=PetscVecParamEnum() -%PETSCVECPARAMENUM - Enum of PetscVecParam -% -% WARNING: DO NOT MODIFY THIS FILE -% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh -% Please read src/c/EnumDefinitions/README for more information -% -% Usage: -% macro=PetscVecParamEnum() - -macro=StringToEnum('PetscVecParam'); Index: /issm/branches/trunk-jpl-damage/src/m/enum/VectorParamEnum.m =================================================================== --- /issm/branches/trunk-jpl-damage/src/m/enum/VectorParamEnum.m (revision 11708) +++ /issm/branches/trunk-jpl-damage/src/m/enum/VectorParamEnum.m (revision 11708) @@ -0,0 +1,11 @@ +function macro=VectorParamEnum() +%VECTORPARAMENUM - Enum of VectorParam +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=VectorParamEnum() + +macro=StringToEnum('VectorParam'); Index: /issm/branches/trunk-jpl-damage/src/mex/ComputeBasalStress/ComputeBasalStress.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/ComputeBasalStress/ComputeBasalStress.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/ComputeBasalStress/ComputeBasalStress.cpp (revision 11708) @@ -17,5 +17,5 @@ /* output datasets: */ - Vec sigma_g=NULL; + Vector* sigma_g=NULL; /*Boot module: */ @@ -51,5 +51,5 @@ delete loads; delete parameters; - VecFree(&sigma_g); + xdelete(&sigma_g); /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/ContourToMesh/ContourToMesh.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/ContourToMesh/ContourToMesh.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/ContourToMesh/ContourToMesh.cpp (revision 11708) @@ -33,7 +33,7 @@ /* output: */ - Vec in_nod=NULL; + Vector* in_nod=NULL; int nods; - Vec in_elem=NULL; + Vector* in_elem=NULL; int nel; Index: /issm/branches/trunk-jpl-damage/src/mex/ContourToNodes/ContourToNodes.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/ContourToNodes/ContourToNodes.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/ContourToNodes/ContourToNodes.cpp (revision 11708) @@ -35,5 +35,5 @@ /* output: */ - Vec flags=NULL; + Vector* flags=NULL; int nods; Index: /issm/branches/trunk-jpl-damage/src/mex/ControlInputGetGradient/ControlInputGetGradient.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/ControlInputGetGradient/ControlInputGetGradient.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/ControlInputGetGradient/ControlInputGetGradient.cpp (revision 11708) @@ -14,5 +14,5 @@ Materials *materials = NULL; Parameters *parameters = NULL; - Vec gradient = NULL; + Vector* gradient = NULL; /* output datasets: elements and loads*/ Index: /issm/branches/trunk-jpl-damage/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp (revision 11708) @@ -32,5 +32,5 @@ /*Free ressources: */ delete nodes; - delete ys; + xdelete(&ys); /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/GetVectorFromInputs/GetVectorFromInputs.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/GetVectorFromInputs/GetVectorFromInputs.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/GetVectorFromInputs/GetVectorFromInputs.cpp (revision 11708) @@ -16,5 +16,5 @@ int name_enum; int type_enum; - Vec ug=NULL; + Vector* ug=NULL; /* output datasets: elements and loads*/ Index: /issm/branches/trunk-jpl-damage/src/mex/Gradj/Gradj.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Gradj/Gradj.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/Gradj/Gradj.cpp (revision 11708) @@ -18,5 +18,5 @@ /* output datasets: */ - Vec gradient = NULL; + Vector* gradient = NULL; /*Boot module: */ @@ -54,5 +54,5 @@ delete materials; delete parameters; - VecFree(&gradient); + xdelete(&gradient); /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp (revision 11708) @@ -8,11 +8,11 @@ /*input datasets: */ - Elements* elements=NULL; - Nodes* nodes=NULL; - Vertices* vertices=NULL; - Loads* loads=NULL; - Materials* materials=NULL; - Parameters* parameters=NULL; - Vector* solution=NULL; + Elements *elements = NULL; + Nodes *nodes = NULL; + Vertices *vertices = NULL; + Loads *loads = NULL; + Materials *materials = NULL; + Parameters *parameters = NULL; + Vector *solution = NULL; /*Boot module: */ @@ -50,5 +50,5 @@ delete materials; delete parameters; - delete solution; + xdelete(&solution); /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.cpp (revision 11708) @@ -37,5 +37,5 @@ /* output: */ - Vec data_mesh=NULL; + Vector* data_mesh=NULL; /*Boot module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/InterpFromMesh2d/InterpFromMesh2d.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/InterpFromMesh2d/InterpFromMesh2d.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/InterpFromMesh2d/InterpFromMesh2d.cpp (revision 11708) @@ -61,5 +61,5 @@ /* output: */ - Vec data_prime=NULL; + Vector* data_prime=NULL; /*Boot module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp (revision 11708) @@ -55,5 +55,5 @@ /* output: */ - Vec data_prime=NULL; + Vector* data_prime=NULL; /*Boot module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Makefile.am (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/Makefile.am (revision 11708) @@ -76,5 +76,4 @@ SurfaceArea\ SystemMatrices\ - Test\ TimeAdapt\ TriaSearch\ @@ -206,7 +205,4 @@ GroundinglineMigration/GroundinglineMigration.h -Test_SOURCES = Test/Test.cpp\ - Test/Test.h - HoleFiller_SOURCES = HoleFiller/HoleFiller.cpp\ HoleFiller/HoleFiller.h Index: /issm/branches/trunk-jpl-damage/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp (revision 11708) @@ -45,7 +45,7 @@ /*Free ressources: */ - delete uf; - delete ug; - delete ys; + xdelete(&uf); + xdelete(&ug); + xdelete(&ys); delete nodes; delete parameters; Index: /issm/branches/trunk-jpl-damage/src/mex/Orth/Orth.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Orth/Orth.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/Orth/Orth.cpp (revision 11708) @@ -8,9 +8,9 @@ /*input datasets: */ - Vec gradj=NULL; - Vec oldgradj=NULL; + Vector* gradj=NULL; + Vector* oldgradj=NULL; /* output datasets: */ - Vec newgradj=NULL; + Vector* newgradj=NULL; /*Boot module: */ @@ -31,7 +31,7 @@ /*Free ressources: */ - VecFree(&gradj); - VecFree(&oldgradj); - VecFree(&newgradj); + xdelete(&gradj); + xdelete(&oldgradj); + xdelete(&newgradj); /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp (revision 11708) @@ -17,5 +17,5 @@ /* output: */ - Vec flags=NULL; + Vector* flags=NULL; /*Boot module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/Reduceload/Reduceload.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Reduceload/Reduceload.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/Reduceload/Reduceload.cpp (revision 11708) @@ -40,7 +40,7 @@ /*Free ressources: */ - delete pf; - delete Kfs; - delete ys; + xdelete(&pf); + xdelete(&Kfs); + xdelete(&ys); MODULEEND(); Index: /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtof/Reducevectorgtof.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11708) @@ -8,10 +8,10 @@ /*input datasets: */ - Vector* ug=NULL; - Nodes* nodes=NULL; - Parameters* parameters=NULL; + Vector *ug = NULL; + Nodes *nodes = NULL; + Parameters *parameters = NULL; /* output datasets: */ - Vector* uf=NULL; + Vector *uf = NULL; /*Boot module: */ @@ -35,6 +35,6 @@ delete nodes; delete parameters; - delete ug; - delete uf; + xdelete(&ug); + xdelete(&uf); /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtos/Reducevectorgtos.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtos/Reducevectorgtos.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/Reducevectorgtos/Reducevectorgtos.cpp (revision 11708) @@ -35,6 +35,6 @@ delete nodes; delete parameters; - delete yg; - delete ys; + xdelete(&yg); + xdelete(&ys); /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/ResetCoordinateSystem/ResetCoordinateSystem.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/ResetCoordinateSystem/ResetCoordinateSystem.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/ResetCoordinateSystem/ResetCoordinateSystem.cpp (revision 11708) @@ -17,5 +17,5 @@ /* output datasets: */ - Vec sigma_g=NULL; + Vector* sigma_g=NULL; /*Boot module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/Solver/Solver.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/Solver/Solver.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/Solver/Solver.cpp (revision 11708) @@ -15,14 +15,12 @@ Parameters *parameters = NULL; int analysis_type; - char option[100]; - #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) - PetscTruth flag; - #else - PetscBool flag; - #endif - - /*Matlab solver: */ + char* options=NULL; + char* token=NULL; + char* option=NULL; + + /*For use of matlab solver: */ mxArray* array[2]; + /*Start module: */ MODULEBOOT(); @@ -34,14 +32,10 @@ /*In serial mode, we have not set any petsc options, do it now: */ - #ifdef _SERIAL_ - parameters->FindParam(&analysis_type,AnalysisTypeEnum); - PetscOptionsFromAnalysis(parameters,analysis_type); - #endif - /*Retrieve solver type: */ - PetscOptionsGetString(PETSC_NULL,"-ksp_type",&option[0],100,&flag); + options=OptionsFromAnalysis(parameters,analysis_type); + token=strstr(options,"--ksp_type"); /*Fetch rest of data only if not running the matlab solver: */ - if (strcmp(option,"matlab")!=0){ + if ((token==NULL) || (strncmp(token+10,"matlab",6)!=0)){ /*Input datasets: */ @@ -58,5 +52,5 @@ } else{ - /*Matlab solver: */ + /*Call Matlab solver: */ if (VerboseModule()) printf(" Solving\n"); array[0]=KFF; @@ -66,9 +60,9 @@ /*Free ressources: */ - delete Kff; - delete pf; - delete uf0; - delete uf; - delete df; + xdelete(&Kff); + xdelete(&pf); + xdelete(&uf0); + xdelete(&uf); + xdelete(&df); delete parameters; Index: /issm/branches/trunk-jpl-damage/src/mex/SystemMatrices/SystemMatrices.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/SystemMatrices/SystemMatrices.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/SystemMatrices/SystemMatrices.cpp (revision 11708) @@ -72,8 +72,8 @@ delete materials; delete parameters; - delete Kff; - delete Kfs; - delete pf; - delete df; + xdelete(&Kff); + xdelete(&Kfs); + xdelete(&pf); + xdelete(&df); /*end module: */ Index: /issm/branches/trunk-jpl-damage/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp =================================================================== --- /issm/branches/trunk-jpl-damage/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp (revision 11707) +++ /issm/branches/trunk-jpl-damage/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp (revision 11708) @@ -32,5 +32,5 @@ /*Free ressources: */ - delete yg; + xdelete(&yg); delete constraints; delete nodes;