Index: /issm/trunk-jpl/m4/issm_options.m4 =================================================================== --- /issm/trunk-jpl/m4/issm_options.m4 (revision 18317) +++ /issm/trunk-jpl/m4/issm_options.m4 (revision 18318) @@ -1623,4 +1623,18 @@ dnl Capabilities + dnl with-bamg{{{ + AC_ARG_WITH([bamg], + AS_HELP_STRING([--with-bamg = YES],[compile with bamg capabilities (default is yes)]), + [BAMG=$withval],[BAMG=yes]) + AC_MSG_CHECKING(for bamg capability compilation) + + HAVE_BAMG=no + if test "x$BAMG" = "xyes"; then + HAVE_BAMG=yes + AC_DEFINE([_HAVE_BAMG_],[1],[with bamg meshing capability]) + fi + AM_CONDITIONAL([BAMG], [test x$HAVE_BAMG = xyes]) + AC_MSG_RESULT($HAVE_BAMG) + dnl }}} dnl with-kml{{{ AC_ARG_WITH([kml], Index: /issm/trunk-jpl/src/c/Makefile.am =================================================================== --- /issm/trunk-jpl/src/c/Makefile.am (revision 18317) +++ /issm/trunk-jpl/src/c/Makefile.am (revision 18318) @@ -459,176 +459,7 @@ endif #}}} -#Petsc sources {{{ -if PETSC -issm_sources += ./toolkits/petsc\ - ./toolkits/petsc/patches\ - ./toolkits/petsc/patches/SolverEnum.h\ - ./toolkits/petsc/patches/petscpatches.h\ - ./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/VecFree.cpp\ - ./toolkits/petsc/patches/KSPFree.cpp\ - ./toolkits/petsc/patches/MatFree.cpp\ - ./toolkits/petsc/patches/MatMultPatch.cpp\ - ./toolkits/petsc/patches/ISSMToPetscMatrixType.cpp\ - ./toolkits/petsc/patches/ISSMToPetscInsertMode.cpp\ - ./toolkits/petsc/patches/ISSMToPetscNormMode.cpp\ - ./toolkits/petsc/objects/petscobjects.h\ - ./toolkits/petsc/objects/PetscMat.h\ - ./toolkits/petsc/objects/PetscMat.cpp\ - ./toolkits/petsc/objects/PetscVec.h\ - ./toolkits/petsc/objects/PetscVec.cpp\ - ./toolkits/petsc/objects/PetscSolver.cpp\ - ./toolkits/petsc/objects/PetscSolver.h\ - ./toolkits/petsc/petscincludes.h -endif -#}}} -#Mumps sources {{{ -if MUMPS -issm_sources += ./toolkits/mumps\ - ./toolkits/mumps/mumpsincludes.h\ - ./toolkits/mumps/MumpsSolve.cpp -endif -#}}} -#Gsl sources {{{ -if GSL -issm_sources += ./toolkits/gsl\ - ./toolkits/gsl/gslincludes.h\ - ./toolkits/gsl/DenseGslSolve.cpp -endif -#}}} -#Analyses{{{ -if ADJOINTBALANCETHICKNESS -issm_sources += ./analyses/AdjointBalancethicknessAnalysis.cpp -endif -if ADJOINTBALANCETHICKNESS2 -issm_sources += ./analyses/AdjointBalancethickness2Analysis.cpp -endif -if ADJOINTHORIZ -issm_sources += ./analyses/AdjointHorizAnalysis.cpp -endif -if BALANCETHICKNESS -issm_sources += ./analyses/BalancethicknessAnalysis.cpp -endif -if BALANCETHICKNESS2 -issm_sources += ./analyses/Balancethickness2Analysis.cpp -endif -if BALANCETHICKNESSSOFT -issm_sources += ./analyses/BalancethicknessSoftAnalysis.cpp -endif -if BALANCEVELOCITY -issm_sources += ./analyses/BalancevelocityAnalysis.cpp -endif -if L2PROJECTIONBASE -issm_sources += ./analyses/L2ProjectionBaseAnalysis.cpp -endif -if DAMAGEEVOLUTION -issm_sources += ./analyses/DamageEvolutionAnalysis.cpp -endif -if STRESSBALANCE -issm_sources += ./analyses/StressbalanceAnalysis.cpp -endif -if UZAWAPRESSURE -issm_sources += ./analyses/UzawaPressureAnalysis.cpp -endif -if STRESSBALANCESIA -issm_sources += ./analyses/StressbalanceSIAAnalysis.cpp -endif -if STRESSBALANCEVERTICAL -issm_sources += ./analyses/StressbalanceVerticalAnalysis.cpp -endif -if ENTHALPY -issm_sources += ./analyses/EnthalpyAnalysis.cpp -endif -if HYDROLOGYSHREVE -issm_sources += ./analyses/HydrologyShreveAnalysis.cpp -endif -if HYDROLOGYDCINEFFICIENT -issm_sources += ./analyses/HydrologyDCInefficientAnalysis.cpp -endif -if HYDROLOGYDCEFFICIENT -issm_sources += ./analyses/HydrologyDCEfficientAnalysis.cpp -endif -if L2PROJECTIONEPL -issm_sources += ./analyses/L2ProjectionEPLAnalysis.cpp -endif -if MELTING -issm_sources += ./analyses/MeltingAnalysis.cpp -endif -if MASSTRANSPORT -issm_sources += ./analyses/MasstransportAnalysis.cpp -endif -if FREESURFACEBASE -issm_sources += ./analyses/FreeSurfaceBaseAnalysis.cpp -endif -if FREESURFACETOP -issm_sources += ./analyses/FreeSurfaceTopAnalysis.cpp -endif -if EXTRUDEFROMBASE -issm_sources += ./analyses/ExtrudeFromBaseAnalysis.cpp -endif -if EXTRUDEFROMTOP -issm_sources += ./analyses/ExtrudeFromTopAnalysis.cpp -endif -if DEPTHAVERAGE -issm_sources += ./analyses/DepthAverageAnalysis.cpp -endif -if THERMAL -issm_sources += ./analyses/ThermalAnalysis.cpp -endif -if SMOOTHEDSURFACESLOPEX -issm_sources += ./analyses/SmoothedSurfaceSlopeXAnalysis.cpp -endif -if SMOOTHEDSURFACESLOPEY -issm_sources += ./analyses/SmoothedSurfaceSlopeYAnalysis.cpp -endif -if MESHDEFORMATION -issm_sources += ./analyses/MeshdeformationAnalysis.cpp -endif -if LEVELSET -issm_sources += ./analyses/LevelsetAnalysis.cpp -endif -if EXTRAPOLATION -issm_sources += ./analyses/ExtrapolationAnalysis.cpp -endif -if LSFREINITIALIZATION -issm_sources += ./analyses/LsfReinitializationAnalysis.cpp -endif -#}}} -#Gia sources {{{ -if GIA -issm_sources += ./cores/gia_core.cpp\ - ./analyses/GiaAnalysis.cpp\ - ./modules/GiaDeflectionCorex/GiaDeflectionCorex.cpp\ - ./modules/GiaDeflectionCorex/distme.f\ - ./modules/GiaDeflectionCorex/freed.f\ - ./modules/GiaDeflectionCorex/ojrule.f\ - ./modules/GiaDeflectionCorex/pwise.f\ - ./modules/GiaDeflectionCorex/qwise.f\ - ./modules/GiaDeflectionCorex/stot.f\ - ./modules/GiaDeflectionCorex/what0.f -endif -#}}} -#Mpi sources {{{ -if MPI -issm_sources += ./toolkits/issm/IssmMpiDenseMat.h\ - ./toolkits/issm/IssmMpiVec.h -endif -#}}} -#Metis sources {{{ -if METIS -issm_sources += ./toolkits/metis/patches/metispatches.h\ - ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp -endif -#}}} - -#Wrapper sources -#Bamg sources {{{ -bamg_sources = ./bamg/bamgobjects.h\ +#BAMG sources {{{ +if BAMG +issm_sources += ./bamg/bamgobjects.h\ ./bamg/BamgGeom.h\ ./bamg/BamgGeom.cpp\ @@ -695,27 +526,178 @@ ./modules/BamgTriangulatex/BamgTriangulatex.cpp\ ./modules/BamgTriangulatex/BamgTriangulatex.h -#}}} -#Kriging sources {{{ -if KRIGING -kriging_sources = ./classes/kriging/Observations.h\ - ./classes/kriging/Observations.cpp\ - ./classes/kriging/Variogram.h \ - ./classes/kriging/GaussianVariogram.h\ - ./classes/kriging/GaussianVariogram.cpp\ - ./classes/kriging/ExponentialVariogram.h\ - ./classes/kriging/ExponentialVariogram.cpp\ - ./classes/kriging/SphericalVariogram.h\ - ./classes/kriging/SphericalVariogram.cpp\ - ./classes/kriging/PowerVariogram.h\ - ./classes/kriging/PowerVariogram.cpp\ - ./classes/kriging/Quadtree.h\ - ./classes/kriging/Quadtree.cpp\ - ./classes/kriging/Observation.h\ - ./classes/kriging/Observation.cpp\ - ./modules/Krigingx/Krigingx.cpp\ - ./modules/Krigingx/Krigingx.h\ - ./modules/Krigingx/pKrigingx.cpp -issm_sources +=$(kriging_sources) -endif +endif +#}}} +#Petsc sources {{{ +if PETSC +issm_sources += ./toolkits/petsc\ + ./toolkits/petsc/patches\ + ./toolkits/petsc/patches/SolverEnum.h\ + ./toolkits/petsc/patches/petscpatches.h\ + ./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/VecFree.cpp\ + ./toolkits/petsc/patches/KSPFree.cpp\ + ./toolkits/petsc/patches/MatFree.cpp\ + ./toolkits/petsc/patches/MatMultPatch.cpp\ + ./toolkits/petsc/patches/ISSMToPetscMatrixType.cpp\ + ./toolkits/petsc/patches/ISSMToPetscInsertMode.cpp\ + ./toolkits/petsc/patches/ISSMToPetscNormMode.cpp\ + ./toolkits/petsc/objects/petscobjects.h\ + ./toolkits/petsc/objects/PetscMat.h\ + ./toolkits/petsc/objects/PetscMat.cpp\ + ./toolkits/petsc/objects/PetscVec.h\ + ./toolkits/petsc/objects/PetscVec.cpp\ + ./toolkits/petsc/objects/PetscSolver.cpp\ + ./toolkits/petsc/objects/PetscSolver.h\ + ./toolkits/petsc/petscincludes.h +endif +#}}} +#Mumps sources {{{ +if MUMPS +issm_sources += ./toolkits/mumps\ + ./toolkits/mumps/mumpsincludes.h\ + ./toolkits/mumps/MumpsSolve.cpp +endif +#}}} +#Gsl sources {{{ +if GSL +issm_sources += ./toolkits/gsl\ + ./toolkits/gsl/gslincludes.h\ + ./toolkits/gsl/DenseGslSolve.cpp +endif +#}}} +#Analyses{{{ +if ADJOINTBALANCETHICKNESS +issm_sources += ./analyses/AdjointBalancethicknessAnalysis.cpp +endif +if ADJOINTBALANCETHICKNESS2 +issm_sources += ./analyses/AdjointBalancethickness2Analysis.cpp +endif +if ADJOINTHORIZ +issm_sources += ./analyses/AdjointHorizAnalysis.cpp +endif +if BALANCETHICKNESS +issm_sources += ./analyses/BalancethicknessAnalysis.cpp +endif +if BALANCETHICKNESS2 +issm_sources += ./analyses/Balancethickness2Analysis.cpp +endif +if BALANCETHICKNESSSOFT +issm_sources += ./analyses/BalancethicknessSoftAnalysis.cpp +endif +if BALANCEVELOCITY +issm_sources += ./analyses/BalancevelocityAnalysis.cpp +endif +if L2PROJECTIONBASE +issm_sources += ./analyses/L2ProjectionBaseAnalysis.cpp +endif +if DAMAGEEVOLUTION +issm_sources += ./analyses/DamageEvolutionAnalysis.cpp +endif +if STRESSBALANCE +issm_sources += ./analyses/StressbalanceAnalysis.cpp +endif +if UZAWAPRESSURE +issm_sources += ./analyses/UzawaPressureAnalysis.cpp +endif +if STRESSBALANCESIA +issm_sources += ./analyses/StressbalanceSIAAnalysis.cpp +endif +if STRESSBALANCEVERTICAL +issm_sources += ./analyses/StressbalanceVerticalAnalysis.cpp +endif +if ENTHALPY +issm_sources += ./analyses/EnthalpyAnalysis.cpp +endif +if HYDROLOGYSHREVE +issm_sources += ./analyses/HydrologyShreveAnalysis.cpp +endif +if HYDROLOGYDCINEFFICIENT +issm_sources += ./analyses/HydrologyDCInefficientAnalysis.cpp +endif +if HYDROLOGYDCEFFICIENT +issm_sources += ./analyses/HydrologyDCEfficientAnalysis.cpp +endif +if L2PROJECTIONEPL +issm_sources += ./analyses/L2ProjectionEPLAnalysis.cpp +endif +if MELTING +issm_sources += ./analyses/MeltingAnalysis.cpp +endif +if MASSTRANSPORT +issm_sources += ./analyses/MasstransportAnalysis.cpp +endif +if FREESURFACEBASE +issm_sources += ./analyses/FreeSurfaceBaseAnalysis.cpp +endif +if FREESURFACETOP +issm_sources += ./analyses/FreeSurfaceTopAnalysis.cpp +endif +if EXTRUDEFROMBASE +issm_sources += ./analyses/ExtrudeFromBaseAnalysis.cpp +endif +if EXTRUDEFROMTOP +issm_sources += ./analyses/ExtrudeFromTopAnalysis.cpp +endif +if DEPTHAVERAGE +issm_sources += ./analyses/DepthAverageAnalysis.cpp +endif +if THERMAL +issm_sources += ./analyses/ThermalAnalysis.cpp +endif +if SMOOTHEDSURFACESLOPEX +issm_sources += ./analyses/SmoothedSurfaceSlopeXAnalysis.cpp +endif +if SMOOTHEDSURFACESLOPEY +issm_sources += ./analyses/SmoothedSurfaceSlopeYAnalysis.cpp +endif +if MESHDEFORMATION +issm_sources += ./analyses/MeshdeformationAnalysis.cpp +endif +if LEVELSET +issm_sources += ./analyses/LevelsetAnalysis.cpp +endif +if EXTRAPOLATION +issm_sources += ./analyses/ExtrapolationAnalysis.cpp +endif +if LSFREINITIALIZATION +issm_sources += ./analyses/LsfReinitializationAnalysis.cpp +endif +#}}} +#Gia sources {{{ +if GIA +issm_sources += ./cores/gia_core.cpp\ + ./analyses/GiaAnalysis.cpp\ + ./modules/GiaDeflectionCorex/GiaDeflectionCorex.cpp\ + ./modules/GiaDeflectionCorex/distme.f\ + ./modules/GiaDeflectionCorex/freed.f\ + ./modules/GiaDeflectionCorex/ojrule.f\ + ./modules/GiaDeflectionCorex/pwise.f\ + ./modules/GiaDeflectionCorex/qwise.f\ + ./modules/GiaDeflectionCorex/stot.f\ + ./modules/GiaDeflectionCorex/what0.f +endif +#}}} +#Mpi sources {{{ +if MPI +issm_sources += ./toolkits/issm/IssmMpiDenseMat.h\ + ./toolkits/issm/IssmMpiVec.h +endif +#}}} +#Metis sources {{{ +if METIS +issm_sources += ./toolkits/metis/patches/metispatches.h\ + ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp +endif +#}}} + +#Wrapper sources +#Bamg sources {{{ + #}}} #Kml sources {{{ @@ -845,4 +827,30 @@ endif #}}} + +#kriging (WRAPPER and executable) +#Kriging sources {{{ +if KRIGING +issm_sources +=./classes/kriging/Observations.h\ + ./classes/kriging/Observations.cpp\ + ./classes/kriging/Variogram.h \ + ./classes/kriging/GaussianVariogram.h\ + ./classes/kriging/GaussianVariogram.cpp\ + ./classes/kriging/ExponentialVariogram.h\ + ./classes/kriging/ExponentialVariogram.cpp\ + ./classes/kriging/SphericalVariogram.h\ + ./classes/kriging/SphericalVariogram.cpp\ + ./classes/kriging/PowerVariogram.h\ + ./classes/kriging/PowerVariogram.cpp\ + ./classes/kriging/Quadtree.h\ + ./classes/kriging/Quadtree.cpp\ + ./classes/kriging/Observation.h\ + ./classes/kriging/Observation.cpp\ + ./modules/Krigingx/pKrigingx.cpp + +modules_sources +=./modules/Krigingx/Krigingx.cpp\ + ./modules/Krigingx/Krigingx.h\ + ./modules/Krigingx/pKrigingx.cpp +endif +#}}} #}}} #Library flags and sources {{{