Index: /issm/trunk-jpl/src/ad/Makefile.am =================================================================== --- /issm/trunk-jpl/src/ad/Makefile.am (revision 11657) +++ /issm/trunk-jpl/src/ad/Makefile.am (revision 11658) @@ -1,28 +1,25 @@ -INCLUDES = @DAKOTAINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ - -#This Makefile.am is for automatic differentiation of the parallel version of ISSM. -#We do not compile in serial mode -#If user requests no parallel compilation, we compile an empty ISSM. -#Compilation can still be blocked if user has not activated --with-adic compilation +INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ +EXEEXT=$(ISSMEXT) #Library declaration {{{1 - +#Compile serial library, and then try and compile parallel library +if NOSERIAL if NOPARALLEL lib_LIBRARIES = else -lib_LIBRARIES = libpISSM.a libOverload.a -endif - -if ADIC2 -lib_LIBRARIES += libAD.a libpISSMRose.a -endif - -#}}} -#Overload library, to overload any non-standard symbols. {{{1 -libOverload_a_SOURCES = ./shared/String/stricmp.c -libOverload_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) -#}}} -#ISSM library {{{1 -libpISSM_a_SOURCES = ./include/macros.h\ +lib_LIBRARIES = libpISSM.a libOverload.a +endif +else +if NOPARALLEL +lib_LIBRARIES = libISSM.a libOverload.a +else +lib_LIBRARIES = libISSM.a libpISSM.a libOverload.a +endif +endif +#}}} + +#sources +#Core sources{{{1 +core_sources = ./include/macros.h\ ./include/typedefs.h\ ./include/types.h\ @@ -38,4 +35,8 @@ ./objects/Material.h\ ./objects/Load.h\ + ./objects/Contour.h\ + ./objects/Contour.cpp\ + ./objects/OptArgs.h\ + ./objects/OptPars.h\ ./objects/Loads/Friction.h\ ./objects/Loads/Friction.cpp\ @@ -61,6 +62,6 @@ ./objects/ElementResults/DoubleElementResult.h\ ./objects/ElementResults/DoubleElementResult.cpp\ - ./objects/ElementResults/TriaVertexElementResult.h\ - ./objects/ElementResults/TriaVertexElementResult.cpp\ + ./objects/ElementResults/TriaP1ElementResult.h\ + ./objects/ElementResults/TriaP1ElementResult.cpp\ ./objects/ElementResults/BoolElementResult.h\ ./objects/ElementResults/BoolElementResult.cpp\ @@ -88,6 +89,6 @@ ./objects/Inputs/Input.h\ ./objects/Inputs/InputLocal.h\ - ./objects/Inputs/TriaVertexInput.h\ - ./objects/Inputs/TriaVertexInput.cpp\ + ./objects/Inputs/TriaP1Input.h\ + ./objects/Inputs/TriaP1Input.cpp\ ./objects/Inputs/BoolInput.h\ ./objects/Inputs/BoolInput.cpp\ @@ -138,4 +139,6 @@ ./objects/Params/DoubleMatParam.cpp\ ./objects/Params/DoubleMatParam.h\ + ./objects/Params/DoubleTransientMatParam.cpp\ + ./objects/Params/DoubleTransientMatParam.h\ ./objects/Params/DoubleMatArrayParam.cpp\ ./objects/Params/DoubleMatArrayParam.h\ @@ -161,4 +164,6 @@ ./Container/Nodes.h\ ./Container/Nodes.cpp\ + ./Container/Options.h\ + ./Container/Options.cpp\ ./Container/Parameters.h\ ./Container/Parameters.cpp\ @@ -181,5 +186,8 @@ ./shared/Numerics/GaussPoints.cpp\ ./shared/Numerics/cross.cpp\ + ./shared/Numerics/isnan.h\ + ./shared/Numerics/isnan.cpp\ ./shared/Numerics/extrema.cpp\ + ./shared/Numerics/XZvectorsToCoordinateSystem.cpp\ ./shared/Numerics/UnitConversion.cpp\ ./shared/Numerics/PetscOptionsFromAnalysis.cpp\ @@ -244,5 +252,4 @@ ./io/PrintfFunction.cpp\ ./EnumDefinitions/EnumDefinitions.h\ - ./EnumDefinitions/EnumToModelField.cpp\ ./modules/ModelProcessorx/ModelProcessorx.h\ ./modules/ModelProcessorx/ModelProcessorx.cpp\ @@ -261,4 +268,6 @@ ./modules/NodesDofx/NodesDofx.h\ ./modules/NodesDofx/NodesDofx.cpp\ + ./modules/NodalValuex/NodalValuex.h\ + ./modules/NodalValuex/NodalValuex.cpp\ ./modules/VerticesDofx/VerticesDofx.h\ ./modules/VerticesDofx/VerticesDofx.cpp\ @@ -269,4 +278,6 @@ ./modules/InputScalex/InputScalex.h\ ./modules/InputScalex/InputScalex.cpp\ + ./modules/SurfaceAreax/SurfaceAreax.h\ + ./modules/SurfaceAreax/SurfaceAreax.cpp\ ./modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h\ ./modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp\ @@ -299,4 +310,6 @@ ./modules/SpcNodesx/SpcNodesx.h\ ./modules/SpcNodesx/SpcNodesx.cpp\ + ./modules/PositiveDegreeDayx/PositiveDegreeDayx.h\ + ./modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp\ ./modules/UpdateConstraintsx/UpdateConstraintsx.h\ ./modules/UpdateConstraintsx/UpdateConstraintsx.cpp\ @@ -313,11 +326,17 @@ ./modules/SystemMatricesx/SystemMatricesx.cpp\ ./modules/SystemMatricesx/SystemMatricesx.h\ + ./modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp\ + ./modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h\ ./modules/ConstraintsStatex/ConstraintsStatex.cpp\ ./modules/ConstraintsStatex/ConstraintsStatex.h\ ./modules/ConstraintsStatex/ConstraintsStateLocal.h\ + ./modules/Responsex/Responsex.h\ + ./modules/Responsex/Responsex.cpp\ ./modules/RequestedOutputsx/RequestedOutputsx.h\ ./modules/RequestedOutputsx/RequestedOutputsx.cpp\ ./modules/ResetConstraintsx/ResetConstraintsx.h\ ./modules/ResetConstraintsx/ResetConstraintsx.cpp\ + ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.h\ + ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.cpp\ ./modules/Solverx/Solverx.cpp\ ./modules/Solverx/Solverx.h\ @@ -332,4 +351,5 @@ ./modules/InputConvergencex/InputConvergencex.h\ ./solutions/convergence.cpp\ + ./solutions/ProcessArguments.cpp\ ./solutions/WriteLockFile.cpp\ ./solutions/ResetBoundaryConditions.cpp\ @@ -337,12 +357,9 @@ ./solutions/CorePointerFromSolutionEnum.cpp\ ./solvers/solver_linear.cpp\ - ./solvers/solver_nonlinear.cpp - - -libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) + ./solvers/solver_nonlinear.cpp\ + ./solvers/solver_newton.cpp #}}} #DAKOTA sources {{{1 -if DAKOTA -libpISSM_a_SOURCES += ./objects/DakotaPlugin.h\ +dakota_sources = ./objects/DakotaPlugin.h\ ./objects/DakotaPlugin.cpp\ ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.h\ @@ -352,4 +369,6 @@ ./modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h\ ./modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp\ + ./modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.h\ + ./modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.cpp\ ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\ @@ -359,40 +378,27 @@ ./modules/Dakotax/DakotaFree.cpp\ ./modules/Dakotax/SpawnCore.cpp\ - ./modules/Dakotax/SpawnCoreParallel.cpp\ ./modules/Dakotax/DescriptorIndex.cpp\ ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ - ./modules/ModelProcessorx/Qmu/CreateParametersQmu.cpp\ + ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\ ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h -endif +dakota_psources= ./modules/Dakotax/SpawnCoreParallel.cpp #}}} #Transient sources {{{1 -if TRANSIENT -libpISSM_a_SOURCES += ./solutions/transient_core.cpp\ - ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp -endif +transient_sources = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp +transient_psources = ./solutions/transient_core.cpp #}}} #Steadystate sources {{{1 -if STEADYSTATE -libpISSM_a_SOURCES += ./solutions/steadystate_core.cpp\ - ./solutions/steadystateconvergence.cpp -endif +steadystate_psources = ./solutions/steadystate_core.cpp\ + ./solutions/steadystateconvergence.cpp #}}} #Prognostic sources {{{1 -if PROGNOSTIC -libpISSM_a_SOURCES += ./solutions/prognostic_core.cpp\ - ./modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp\ - ./modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp\ - ./modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp\ - ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp - -endif +prognostic_sources = ./modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp\ + ./modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp\ + ./modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp\ + ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp +prognostic_psources = ./solutions/prognostic_core.cpp #}}} #Thermal sources {{{1 -if THERMAL -libpISSM_a_SOURCES += ./solutions/thermal_core.cpp\ - ./solutions/thermal_core_step.cpp\ - ./solutions/enthalpy_core.cpp\ - ./solvers/solver_thermal_nonlinear.cpp\ - ./modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp\ +thermal_sources = ./modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp\ ./modules/ModelProcessorx/Thermal/CreateNodesThermal.cpp\ ./modules/ModelProcessorx/Thermal/CreateConstraintsThermal.cpp\ @@ -409,19 +415,13 @@ ./modules/ConstraintsStatex/ThermalIsPresent.cpp\ ./modules/ResetConstraintsx/ThermalConstraintsReset.cpp -endif + +thermal_psources = ./solutions/thermal_core.cpp\ + ./solutions/thermal_core_step.cpp\ + ./solutions/enthalpy_core.cpp\ + ./solutions/enthalpy_core_step.cpp\ + ./solvers/solver_thermal_nonlinear.cpp #}}} #Control sources {{{1 -if CONTROL -libpISSM_a_SOURCES += ./solutions/control_core.cpp\ - ./solutions/controltao_core.cpp\ - ./solutions/controlrestart.cpp\ - ./solutions/controlconvergence.cpp\ - ./solutions/objectivefunctionC.cpp\ - ./solutions/gradient_core.cpp\ - ./solutions/adjointdiagnostic_core.cpp\ - ./solutions/adjointbalancethickness_core.cpp\ - ./solutions/AdjointCorePointerFromSolutionEnum.cpp\ - ./solvers/solver_adjoint_linear.cpp\ - ./modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp\ +control_sources= ./modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp\ ./modules/ControlInputGetGradientx/ControlInputGetGradientx.h\ ./modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp\ @@ -429,4 +429,8 @@ ./modules/ControlInputScaleGradientx/ControlInputScaleGradientx.cpp\ ./modules/ControlInputScaleGradientx/ControlInputScaleGradientx.h\ + ./modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp\ + ./modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h\ + ./modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp\ + ./modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h\ ./modules/ModelProcessorx/Control/CreateParametersControl.cpp\ ./modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp\ @@ -461,86 +465,87 @@ ./shared/Numerics/BrentSearch.cpp\ ./shared/Numerics/OptimalSearch.cpp\ - ./shared/Numerics/OptFunc.cpp\ - ./objects/OptArgs.h\ - ./objects/OptPars.h - -endif + ./shared/Numerics/OptFunc.cpp + +control_psources=./solutions/control_core.cpp\ + ./solutions/controltao_core.cpp\ + ./solutions/controlrestart.cpp\ + ./solutions/controlconvergence.cpp\ + ./solutions/objectivefunctionC.cpp\ + ./solutions/gradient_core.cpp\ + ./solutions/adjointdiagnostic_core.cpp\ + ./solutions/adjointbalancethickness_core.cpp\ + ./solutions/AdjointCorePointerFromSolutionEnum.cpp\ + ./solvers/solver_adjoint_linear.cpp + #}}} #Hydrology sources {{{1 -if HYDROLOGY -libpISSM_a_SOURCES += ./modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp\ - ./modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp\ - ./modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp\ - ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp\ - ./solutions/hydrology_core.cpp\ - ./solutions/hydrology_core_step.cpp -endif +hydrology_sources = ./modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp\ + ./modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp\ + ./modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp\ + ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp + +hydrology_psources = ./solutions/hydrology_core.cpp\ + ./solutions/hydrology_core_step.cpp #}}} #Diagnostic sources {{{1 -if DIAGNOSTIC -libpISSM_a_SOURCES += ./modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp\ - ./modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp \ - ./modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp \ - ./modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp\ - ./modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp\ - ./modules/ModelProcessorx/DiagnosticVert/CreateNodesDiagnosticVert.cpp \ - ./modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp \ - ./modules/ModelProcessorx/DiagnosticVert/CreateLoadsDiagnosticVert.cpp\ - ./modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp\ - ./modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp \ - ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ - ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp\ - ./solutions/diagnostic_core.cpp\ - ./solvers/solver_stokescoupling_nonlinear.cpp -endif +diagnostic_sources = ./modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp\ + ./modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp \ + ./modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp \ + ./modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp\ + ./modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp\ + ./modules/ModelProcessorx/DiagnosticVert/CreateNodesDiagnosticVert.cpp \ + ./modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp \ + ./modules/ModelProcessorx/DiagnosticVert/CreateLoadsDiagnosticVert.cpp\ + ./modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp\ + ./modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp \ + ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ + ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \ + ./shared/Elements/CoordinateSystemTransform.cpp\ + ./shared/Elements/TransformLoadVectorCoord.cpp \ + ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ + ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \ + ./shared/Elements/TransformSolutionCoord.cpp +diagnostic_psources =./solutions/diagnostic_core.cpp\ + ./solvers/solver_stokescoupling_nonlinear.cpp #}}} #Balanced sources {{{1 -if BALANCED -libpISSM_a_SOURCES += ./modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp\ - ./modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp\ - ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\ - ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp\ - ./solutions/balancethickness_core.cpp -endif +balanced_sources = ./modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp\ + ./modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp\ + ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\ + ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp +balanced_psources = ./solutions/balancethickness_core.cpp #}}} #Responses sources {{{1 -if RESPONSES -libpISSM_a_SOURCES += ./modules/MinVelx/MinVelx.h\ - ./modules/MinVelx/MinVelx.cpp\ - ./modules/MaxVelx/MaxVelx.h\ - ./modules/MaxVelx/MaxVelx.cpp\ - ./modules/MaxAbsVxx/MaxAbsVxx.h\ - ./modules/MaxAbsVxx/MaxAbsVxx.cpp\ - ./modules/MaxAbsVyx/MaxAbsVyx.h\ - ./modules/MaxAbsVyx/MaxAbsVyx.cpp\ - ./modules/MaxAbsVzx/MaxAbsVzx.h\ - ./modules/MaxAbsVzx/MaxAbsVzx.cpp\ - ./modules/MaxVxx/MaxVxx.h\ - ./modules/MaxVxx/MaxVxx.cpp\ - ./modules/MaxVyx/MaxVyx.h\ - ./modules/MaxVyx/MaxVyx.cpp\ - ./modules/MaxVzx/MaxVzx.h\ - ./modules/MaxVzx/MaxVzx.cpp\ - ./modules/MinVxx/MinVxx.h\ - ./modules/MinVxx/MinVxx.cpp\ - ./modules/MinVyx/MinVyx.h\ - ./modules/MinVyx/MinVyx.cpp\ - ./modules/MinVzx/MinVzx.h\ - ./modules/MinVzx/MinVzx.cpp\ - ./modules/RheologyBbarx/RheologyBbarx.cpp\ - ./modules/RheologyBbarx/RheologyBbarx.h\ - ./modules/MassFluxx/MassFluxx.cpp\ - ./modules/MassFluxx/MassFluxx.h\ - ./modules/NodalValuex/NodalValuex.h\ - ./modules/NodalValuex/NodalValuex.cpp\ - ./modules/SurfaceAreax/SurfaceAreax.h\ - ./modules/SurfaceAreax/SurfaceAreax.cpp\ - ./modules/Responsex/Responsex.h\ - ./modules/Responsex/Responsex.cpp -endif +responses_sources = ./modules/MinVelx/MinVelx.h\ + ./modules/MinVelx/MinVelx.cpp\ + ./modules/MaxVelx/MaxVelx.h\ + ./modules/MaxVelx/MaxVelx.cpp\ + ./modules/MaxAbsVxx/MaxAbsVxx.h\ + ./modules/MaxAbsVxx/MaxAbsVxx.cpp\ + ./modules/MaxAbsVyx/MaxAbsVyx.h\ + ./modules/MaxAbsVyx/MaxAbsVyx.cpp\ + ./modules/MaxAbsVzx/MaxAbsVzx.h\ + ./modules/MaxAbsVzx/MaxAbsVzx.cpp\ + ./modules/MaxVxx/MaxVxx.h\ + ./modules/MaxVxx/MaxVxx.cpp\ + ./modules/MaxVyx/MaxVyx.h\ + ./modules/MaxVyx/MaxVyx.cpp\ + ./modules/MaxVzx/MaxVzx.h\ + ./modules/MaxVzx/MaxVzx.cpp\ + ./modules/MinVxx/MinVxx.h\ + ./modules/MinVxx/MinVxx.cpp\ + ./modules/MinVyx/MinVyx.h\ + ./modules/MinVyx/MinVyx.cpp\ + ./modules/MinVzx/MinVzx.h\ + ./modules/MinVzx/MinVzx.cpp\ + ./modules/IceVolumex/IceVolumex.h\ + ./modules/IceVolumex/IceVolumex.cpp\ + ./modules/ElementResponsex/ElementResponsex.h\ + ./modules/ElementResponsex/ElementResponsex.cpp\ + ./modules/MassFluxx/MassFluxx.cpp\ + ./modules/MassFluxx/MassFluxx.h #}}} #Slope sources {{{1 -if SLOPE -libpISSM_a_SOURCES += ./modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp\ +slope_sources = ./modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp\ ./modules/ModelProcessorx/BedSlope/CreateNodesBedSlope.cpp \ ./modules/ModelProcessorx/BedSlope/CreateConstraintsBedSlope.cpp\ @@ -549,82 +554,412 @@ ./modules/ModelProcessorx/SurfaceSlope/CreateNodesSurfaceSlope.cpp \ ./modules/ModelProcessorx/SurfaceSlope/CreateConstraintsSurfaceSlope.cpp\ - ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp\ - ./solutions/surfaceslope_core.cpp\ + ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp +slope_psources = ./solutions/surfaceslope_core.cpp\ ./solutions/bedslope_core.cpp -endif -#}}} -#GroundingLine sources {{{1 +#}}} +#Groundingline sources {{{1 +groundingline_sources= ./modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp\ + ./modules/GroundinglineMigrationx/GroundinglineMigrationx.h +#}}} +#Rifts sources {{{1 +rifts_sources = ./objects/Loads/Riftfront.cpp\ + ./objects/Loads/Riftfront.h\ + ./modules/ConstraintsStatex/RiftConstraintsState.cpp +#}}} +#3D sources {{{1 +threed_sources = ./objects/Gauss/GaussPenta.h\ + ./objects/Gauss/GaussPenta.cpp\ + ./objects/ElementResults/PentaP1ElementResult.h\ + ./objects/ElementResults/PentaP1ElementResult.cpp\ + ./objects/Inputs/PentaP1Input.h\ + ./objects/Inputs/PentaP1Input.cpp\ + ./objects/Elements/Penta.h\ + ./objects/Elements/Penta.cpp\ + ./objects/Elements/PentaHook.h\ + ./objects/Elements/PentaHook.cpp\ + ./objects/Elements/PentaRef.h\ + ./objects/Elements/PentaRef.cpp +#}}} +#Bamg sources {{{1 +bamg_sources = ./objects/Bamg/BamgGeom.h\ + ./objects/Bamg/BamgGeom.cpp\ + ./objects/Bamg/BamgMesh.h\ + ./objects/Bamg/BamgMesh.cpp\ + ./objects/Bamg/BamgOpts.h\ + ./objects/Bamg/BamgOpts.cpp\ + ./objects/Bamg/CrackedEdge.h\ + ./objects/Bamg/CrackedEdge.cpp\ + ./objects/Bamg/Curve.h\ + ./objects/Bamg/Curve.cpp\ + ./objects/Bamg/Direction.h\ + ./objects/Bamg/Direction.cpp\ + ./objects/Bamg/DoubleAndInt.h\ + ./objects/Bamg/Edge.h\ + ./objects/Bamg/Edge.cpp\ + ./objects/Bamg/GeomEdge.h\ + ./objects/Bamg/GeomEdge.cpp\ + ./objects/Bamg/GeomSubDomain.h\ + ./objects/Bamg/GeomSubDomain.cpp\ + ./objects/Bamg/GeomVertex.h\ + ./objects/Bamg/GeomVertex.cpp\ + ./objects/Bamg/Geometry.cpp\ + ./objects/Bamg/Geometry.h\ + ./objects/Bamg/ListofIntersectionTriangles.cpp\ + ./objects/Bamg/ListofIntersectionTriangles.h\ + ./objects/Bamg/EigenMetric.cpp\ + ./objects/Bamg/Metric.cpp\ + ./objects/Bamg/Metric.h\ + ./objects/Bamg/QuadTree.cpp\ + ./objects/Bamg/QuadTree.h\ + ./objects/Bamg/R2.h\ + ./objects/Bamg/SetOfE4.cpp\ + ./objects/Bamg/SetOfE4.h\ + ./objects/Bamg/SubDomain.h\ + ./objects/Bamg/SubDomain.cpp\ + ./objects/Bamg/AdjacentTriangle.h\ + ./objects/Bamg/AdjacentTriangle.cpp\ + ./objects/Bamg/Triangle.cpp\ + ./objects/Bamg/Triangle.h\ + ./objects/Bamg/BamgVertex.cpp\ + ./objects/Bamg/BamgVertex.h\ + ./objects/Bamg/VertexOnEdge.h\ + ./objects/Bamg/VertexOnEdge.cpp\ + ./objects/Bamg/VertexOnGeom.h\ + ./objects/Bamg/VertexOnGeom.cpp\ + ./objects/Bamg/VertexOnVertex.h\ + ./objects/Bamg/VertexOnVertex.cpp\ + ./objects/Bamg/Mesh.cpp\ + ./objects/Bamg/Mesh.h\ + ./shared/Bamg/Abs.h \ + ./shared/Bamg/BigPrimeNumber.h\ + ./shared/Bamg/BigPrimeNumber.cpp\ + ./shared/Bamg/BinaryRand.h \ + ./shared/Bamg/det.h \ + ./shared/Bamg/Exchange.h \ + ./shared/Bamg/extrema.h \ + ./shared/Bamg/HeapSort.h \ + ./shared/Bamg/OppositeAngle.h \ + ./modules/Bamgx/Bamgx.cpp\ + ./modules/Bamgx/Bamgx.h\ + ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\ + ./modules/BamgConvertMeshx/BamgConvertMeshx.h\ + ./modules/BamgTriangulatex/BamgTriangulatex.cpp\ + ./modules/BamgTriangulatex/BamgTriangulatex.h +#}}} +#Kml sources {{{1 +kml_sources = ./modules/Exp2Kmlx/Exp2Kmlx.h\ + ./modules/Exp2Kmlx/Exp2Kmlx.cpp\ + ./modules/Kml2Expx/Kml2Expx.h\ + ./modules/Kml2Expx/Kml2Expx.cpp\ + ./modules/Shp2Kmlx/Shp2Kmlx.h\ + ./modules/Shp2Kmlx/Shp2Kmlx.cpp\ + ./modules/KMLFileReadx/KMLFileReadx.h\ + ./modules/KMLFileReadx/KMLFileReadx.cpp\ + ./modules/KMLMeshWritex/KMLMeshWritex.h\ + ./modules/KMLMeshWritex/KMLMeshWritex.cpp\ + ./modules/KMLOverlayx/KMLOverlayx.h\ + ./modules/KMLOverlayx/KMLOverlayx.cpp\ + ./objects/KML/KML_Attribute.cpp\ + ./objects/KML/KML_Attribute.h\ + ./objects/KML/KML_Comment.cpp\ + ./objects/KML/KML_Comment.h\ + ./objects/KML/KML_ColorStyle.cpp\ + ./objects/KML/KML_ColorStyle.h\ + ./objects/KML/KML_Container.cpp\ + ./objects/KML/KML_Container.h\ + ./objects/KML/KML_Document.cpp\ + ./objects/KML/KML_Document.h\ + ./objects/KML/KML_Feature.cpp\ + ./objects/KML/KML_Feature.h\ + ./objects/KML/KML_File.cpp\ + ./objects/KML/KML_File.h\ + ./objects/KML/KML_Folder.cpp\ + ./objects/KML/KML_Folder.h\ + ./objects/KML/KML_Geometry.cpp\ + ./objects/KML/KML_Geometry.h\ + ./objects/KML/KML_GroundOverlay.cpp\ + ./objects/KML/KML_GroundOverlay.h\ + ./objects/KML/KML_Icon.cpp\ + ./objects/KML/KML_Icon.h\ + ./objects/KML/KML_LatLonBox.cpp\ + ./objects/KML/KML_LatLonBox.h\ + ./objects/KML/KML_LinearRing.cpp\ + ./objects/KML/KML_LinearRing.h\ + ./objects/KML/KML_LineString.cpp\ + ./objects/KML/KML_LineString.h\ + ./objects/KML/KML_LineStyle.cpp\ + ./objects/KML/KML_LineStyle.h\ + ./objects/KML/KML_MultiGeometry.cpp\ + ./objects/KML/KML_MultiGeometry.h\ + ./objects/KML/KML_Object.cpp\ + ./objects/KML/KML_Object.h\ + ./objects/KML/KML_Overlay.cpp\ + ./objects/KML/KML_Overlay.h\ + ./objects/KML/KML_Point.cpp\ + ./objects/KML/KML_Point.h\ + ./objects/KML/KML_Placemark.cpp\ + ./objects/KML/KML_Placemark.h\ + ./objects/KML/KML_Polygon.cpp\ + ./objects/KML/KML_Polygon.h\ + ./objects/KML/KML_PolyStyle.cpp\ + ./objects/KML/KML_PolyStyle.h\ + ./objects/KML/KML_Style.cpp\ + ./objects/KML/KML_Style.h\ + ./objects/KML/KML_StyleSelector.cpp\ + ./objects/KML/KML_StyleSelector.h\ + ./objects/KML/KML_SubStyle.cpp\ + ./objects/KML/KML_SubStyle.h\ + ./objects/KML/KML_Unknown.cpp\ + ./objects/KML/KML_Unknown.h\ + ./objects/KML/KMLFileReadUtils.cpp\ + ./objects/KML/KMLFileReadUtils.h +#}}} +#Matlab sources {{{1 +matlab_sources= ./shared/Matlab/matlabshared.h\ + ./shared/Matlab/ModuleBoot.cpp\ + ./shared/Matlab/ModuleEnd.cpp\ + ./shared/Matlab/mxGetAssignedField.cpp\ + ./shared/Matlab/mxGetField.cpp\ + ./shared/Matlab/CheckNumMatlabArguments.cpp\ + ./toolkits/matlab/matlabincludes.h\ + ./toolkits/matlab/MatlabNArrayToNArray.cpp\ + ./io/Matlab/matlabio.h\ + ./io/Matlab/WriteMatlabData.cpp\ + ./io/Matlab/FetchMatlabData.cpp\ + ./io/Matlab/OptionParse.cpp +#}}} +#Serialsources {{{1 +serial_sources= ./objects/Options/Option.cpp\ + ./objects/Options/Option.h\ + ./objects/Options/OptionDouble.cpp\ + ./objects/Options/OptionDouble.h\ + ./objects/Options/OptionLogical.cpp\ + ./objects/Options/OptionLogical.h\ + ./objects/Options/OptionChar.cpp\ + ./objects/Options/OptionChar.h\ + ./objects/Options/OptionStruct.cpp\ + ./objects/Options/OptionStruct.h\ + ./objects/Options/OptionCell.cpp\ + ./objects/Options/OptionCell.h\ + ./objects/Options/OptionUtilities.cpp\ + ./objects/Options/OptionUtilities.h\ + ./shared/Threads/issm_threads.h\ + ./shared/Threads/LaunchThread.cpp\ + ./shared/Threads/PartitionRange.cpp\ + ./shared/Exp/exp.h\ + ./shared/Exp/IsInPoly.cpp\ + ./shared/Exp/IsInPolySerial.cpp\ + ./shared/Exp/DomainOutlineRead.cpp\ + ./shared/Exp/DomainOutlineWrite.cpp\ + ./shared/TriMesh/trimesh.h\ + ./shared/TriMesh/AssociateSegmentToElement.cpp\ + ./shared/TriMesh/GridInsideHole.cpp\ + ./shared/TriMesh/OrderSegments.cpp\ + ./shared/TriMesh/SplitMeshForRifts.cpp\ + ./shared/TriMesh/TriMeshUtils.cpp\ + ./modules/AddExternalResultx/AddExternalResultx.h\ + ./modules/AddExternalResultx/AddExternalResultx.cpp\ + ./modules/Chacox/Chacox.h\ + ./modules/Chacox/Chacox.cpp\ + ./modules/Chacox/input_parse.cpp\ + ./modules/Chacox/chaco_seconds.cpp\ + ./modules/Chacox/user_params.cpp\ + ./modules/Dakotax/SpawnCoreSerial.cpp\ + ./modules/TriaSearchx/TriaSearchx.h\ + ./modules/TriaSearchx/TriaSearchx.cpp\ + ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h\ + ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp\ + ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp\ + ./modules/Xy2llx/Xy2llx.h\ + ./modules/Xy2llx/Xy2llx.cpp\ + ./modules/Ll2xyx/Ll2xyx.h\ + ./modules/Ll2xyx/Ll2xyx.cpp\ + ./modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp\ + ./modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h\ + ./modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp\ + ./modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp\ + ./modules/InterpFromMesh2dx/InterpFromMesh2dx.h\ + ./modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp\ + ./modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h\ + ./modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp\ + ./modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h\ + ./modules/InterpFromMeshToGridx/InterpFromMeshToGridx.cpp\ + ./modules/InterpFromMeshToGridx/InterpFromMeshToGridx.h\ + ./modules/HoleFillerx/HoleFillerx.cpp\ + ./modules/HoleFillerx/HoleFillerx.h\ + ./modules/AverageFilterx/AverageFilterx.cpp\ + ./modules/AverageFilterx/AverageFilterx.h\ + ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.cpp\ + ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.h\ + ./modules/MeshProfileIntersectionx/MeshSegmentsIntersection.cpp\ + ./modules/MeshProfileIntersectionx/ElementSegmentsIntersection.cpp\ + ./modules/MeshProfileIntersectionx/ElementSegment.cpp\ + ./modules/MeshProfileIntersectionx/SegmentIntersect.cpp\ + ./modules/MeshProfileIntersectionx/NodeInElement.cpp\ + ./modules/ContourToMeshx/ContourToMeshx.cpp\ + ./modules/ContourToMeshx/ContourToMeshxt.cpp\ + ./modules/ContourToMeshx/ContourToMeshx.h\ + ./modules/ContourToNodesx/ContourToNodesx.cpp\ + ./modules/ContourToNodesx/ContourToNodesx.h\ + ./modules/Reducevectorgtosx/Reducevectorgtosx.cpp\ + ./modules/Reducevectorgtosx/Reducevectorgtosx.h\ + ./modules/NodeConnectivityx/NodeConnectivityx.cpp\ + ./modules/NodeConnectivityx/NodeConnectivityx.h\ + ./modules/ElementConnectivityx/ElementConnectivityx.cpp\ + ./modules/ElementConnectivityx/ElementConnectivityx.h\ + ./modules/Scotchx/Scotchx.cpp\ + ./modules/Scotchx/Scotchx.h\ + ./modules/PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.cpp\ + ./modules/PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.h +#}}} + +#ISSM sources are a combination of core sources and sources related to specific capabilities (which can +#be activated by autotools conditionals +#{{{1 + +#First the core +issm_sources = $(core_sources) +issm_psources = + +#Now the optional source +if DAKOTA +issm_sources += $(dakota_sources) +issm_psources += $(dakota_psources) +endif + +if TRANSIENT +issm_sources += $(transient_sources) +issm_psources += $(transient_psources) +endif + +if STEADYSTATE +issm_sources += $(steadystate_sources) +issm_psources += $(steadystate_psources) +endif + +if PROGNOSTIC +issm_sources += $(prognostic_sources) +issm_psources += $(prognostic_psources) +endif + +if THERMAL +issm_sources += $(thermal_sources) +issm_psources += $(thermal_psources) +endif + +if CONTROL +issm_sources += $(control_sources) +issm_psources += $(control_psources) +endif + +if HYDROLOGY +issm_sources += $(hydrology_sources) +issm_psources += $(hydrology_psources) +endif + +if DIAGNOSTIC +issm_sources += $(diagnostic_sources) +issm_psources += $(diagnostic_psources) +endif + +if BALANCED +issm_sources += $(balanced_sources) +issm_psources += $(balanced_psources) +endif + +if RESPONSES +issm_sources += $(responses_sources) +endif + +if SLOPE +issm_sources += $(slope_sources) +issm_psources += $(slope_psources) +endif + if GROUNDINGLINE -libpISSM_a_SOURCES += ./modules/GroundingLineMigrationx/GroundingLineMigrationx.cpp\ - ./modules/GroundingLineMigrationx/GroundingLineMigrationx.h\ - ./modules/GroundingLineMigrationx/GroundingLineMigrationxLocal.h\ - ./modules/GroundingLineMigrationx/GroundingLineMigrationxUtils.cpp\ - ./solutions/groundinglinemigration2d_core.cpp -endif -#}}} -#Rifts sources {{{1 +issm_sources += $(groundingline_sources) +endif + if RIFTS -libpISSM_a_SOURCES += ./objects/Loads/Riftfront.cpp\ - ./objects/Loads/Riftfront.h\ - ./modules/ConstraintsStatex/RiftConstraintsState.cpp -endif -#}}} -#3D sources {{{1 +issm_sources += $(rifts_sources) +endif + if THREED -libpISSM_a_SOURCES += ./objects/Gauss/GaussPenta.h\ - ./objects/Gauss/GaussPenta.cpp\ - ./objects/ElementResults/PentaVertexElementResult.h\ - ./objects/ElementResults/PentaVertexElementResult.cpp\ - ./objects/Inputs/PentaVertexInput.h\ - ./objects/Inputs/PentaVertexInput.cpp\ - ./objects/Elements/Penta.h\ - ./objects/Elements/Penta.cpp\ - ./objects/Elements/PentaHook.h\ - ./objects/Elements/PentaHook.cpp\ - ./objects/Elements/PentaRef.h\ - ./objects/Elements/PentaRef.cpp -endif -#}}} - -#ADIC2 library, for automatic differentiation {{{1 -if ADIC2 +issm_sources += $(threed_sources) +endif +#}}} + +#ISSM serial library {{{1 +libISSM_a_SOURCES = $(issm_sources) +libISSM_a_SOURCES += $(serial_sources) +libISSM_a_SOURCES += $(bamg_sources) +libISSM_a_SOURCES += $(kml_sources) +libISSM_a_SOURCES += $(matlab_sources) + +libISSM_a_CXXFLAGS = -fPIC -DMATLAB -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) +if LARGEARRAYS +libISSM_a_CXXFLAGS += -D__GCC4BUILD__ +else +libISSM_a_CXXFLAGS += -DMX_COMPAT_32 +endif +#}}} +#ISSM parallel library {{{1 +libpISSM_a_SOURCES = $(issm_sources) +libpISSM_a_SOURCES += $(issm_psources) +libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXFLAGS) $(CXXOPTFLAGS) +#}}} +#Overload library, to overload any non-standard symbols. {{{1 +libOverload_a_SOURCES = ./shared/String/stricmp.c +libOverload_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) $(CFLAGS) +#}}} + +#Executable {{{1 +if NOPARALLEL +bin_PROGRAMS = +else +bin_PROGRAMS = issm +endif + +#Standard libraries +LDADD = ./libpISSM.a ./libOverload.a + +#External packages +LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) + +issm_SOURCES = solutions/issm.cpp +issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) +#}}} + +#Automatic differentiation: append this fold to the end of the src/c/Makefile.am to get this Makefile.am {{{ +if ADIC2 +lib_LIBRARIES += libAD.a libpISSMRose.a + +#ADIC2 library, for automatic differentiation #libAD_a_SOURCES = ./mini1.ad.c libAD_a_SOURCES = libAD_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) + + #test rose preprocessing %.r2cpp.cpp : %.cpp testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_PARALLEL_ -D_C_ -I. -I../.. $(INCLUDES) $< - libpISSMRose_a_SOURCES = $(libpISSM_a_SOURCES:.cpp=.r2cpp.cpp) libpISSMRose_a_CXXFLAGS= -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) + + + #Automatic differentiation rules: %.ad.c: %.c adic2 -mforward $< --nary -endif -#}}} -#Executable {{{1 - -if NOPARALLEL -bin_PROGRAMS = -else -bin_PROGRAMS = issm.exe issmRose.exe -endif - -#Standard libraries -LDADD = ./libOverload.a -issm_exe_LDADD = ./libpISSM.a $(LDADD) -if ADIC2 + + + +#Executable +bin_PROGRAMS += issmRose.exe issmRose_exe_LDADD = ./libpISSMRose.a $(LDADD) -endif - -#External packages -LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(ADIC2LIB) - - -issm_exe_SOURCES = solutions/issm.cpp -issm_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) issmRose_exe_SOURCES = solutions/issm.cpp issmRose_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) - -#}}} +LDADD += $(ADIC2LIB) + +endif #}}}