diff --git a/AMDiS/CMakeLists.txt b/AMDiS/CMakeLists.txt
index a0a3f9e6b7d7b4a393c4be08df918373c49df94b..617a1946020f23cba35576ebd4362b6e39d5b42a 100644
--- a/AMDiS/CMakeLists.txt
+++ b/AMDiS/CMakeLists.txt
@@ -49,109 +49,114 @@ if(Boost_FOUND)
link_directories(${Boost_LIBRARY_DIRS})
endif(Boost_FOUND)
-SET(AMDIS_SRC ${SOURCE_DIR}/DOFIndexed.cc
- ${SOURCE_DIR}/io/GNUPlotWriter.cc
- ${SOURCE_DIR}/VertexVector.cc
- ${SOURCE_DIR}/PeriodicBC.cc
- ${SOURCE_DIR}/Recovery.cc
- ${SOURCE_DIR}/RecoveryEstimator.cc
- ${SOURCE_DIR}/ResidualEstimator.cc
- ${SOURCE_DIR}/Cholesky.cc
- ${SOURCE_DIR}/AdaptBase.cc
- ${SOURCE_DIR}/StandardProblemIteration.cc
- ${SOURCE_DIR}/ProblemScal.cc
- ${SOURCE_DIR}/ProblemVec.cc
- ${SOURCE_DIR}/ProblemImplicit.cc
- ${SOURCE_DIR}/ProblemVecDbg.cc
- ${SOURCE_DIR}/DualTraverse.cc
- ${SOURCE_DIR}/ElementData.cc
- ${SOURCE_DIR}/ComponentTraverseInfo.cc
- ${SOURCE_DIR}/CreatorMap.cc
- ${SOURCE_DIR}/ProblemInterpolScal.cc
- ${SOURCE_DIR}/ProblemInterpolVec.cc
- ${SOURCE_DIR}/io/MacroInfo.cc
- ${SOURCE_DIR}/io/MacroReader.cc
- ${SOURCE_DIR}/io/ValueReader.cc
- ${SOURCE_DIR}/Projection.cc
- ${SOURCE_DIR}/SubAssembler.cc
- ${SOURCE_DIR}/ZeroOrderAssembler.cc
- ${SOURCE_DIR}/FirstOrderAssembler.cc
- ${SOURCE_DIR}/SecondOrderAssembler.cc
- ${SOURCE_DIR}/Assembler.cc
- ${SOURCE_DIR}/AdaptInfo.cc
- ${SOURCE_DIR}/Marker.cc
- ${SOURCE_DIR}/SurfaceQuadrature.cc
- ${SOURCE_DIR}/LeafData.cc
- ${SOURCE_DIR}/BoundaryManager.cc
- ${SOURCE_DIR}/DirichletBC.cc
- ${SOURCE_DIR}/RobinBC.cc
- ${SOURCE_DIR}/io/FileWriter.cc
- ${SOURCE_DIR}/io/ElementFileWriter.cc
- ${SOURCE_DIR}/ElInfo.cc
- ${SOURCE_DIR}/ElInfoStack.cc
- ${SOURCE_DIR}/OperatorTerm.cc
- ${SOURCE_DIR}/ZeroOrderTerm.cc
- ${SOURCE_DIR}/FirstOrderTerm.cc
- ${SOURCE_DIR}/SecondOrderTerm.cc
- ${SOURCE_DIR}/Operator.cc
- ${SOURCE_DIR}/Mesh.cc
- ${SOURCE_DIR}/MeshStructure.cc
- ${SOURCE_DIR}/AdaptStationary.cc
+SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
+ ${SOURCE_DIR}/AdaptInfo.cc
${SOURCE_DIR}/AdaptInstationary.cc
- ${SOURCE_DIR}/DOFVector.cc
- ${SOURCE_DIR}/Estimator.cc
- ${SOURCE_DIR}/ProblemInstat.cc
- ${SOURCE_DIR}/ProblemNonLin.cc
- ${SOURCE_DIR}/NonLinUpdater.cc
- ${SOURCE_DIR}/QPsiPhi.cc
- ${SOURCE_DIR}/BasisFunction.cc
- ${SOURCE_DIR}/Boundary.cc
- ${SOURCE_DIR}/CoarseningManager.cc
- ${SOURCE_DIR}/CoarseningManager1d.cc
- ${SOURCE_DIR}/CoarseningManager2d.cc
- ${SOURCE_DIR}/CoarseningManager3d.cc
- ${SOURCE_DIR}/DOFAdmin.cc
- ${SOURCE_DIR}/DOFMatrix.cc
- ${SOURCE_DIR}/Element.cc
- ${SOURCE_DIR}/ElInfo1d.cc
- ${SOURCE_DIR}/ElInfo2d.cc
- ${SOURCE_DIR}/ElInfo3d.cc
- ${SOURCE_DIR}/FiniteElemSpace.cc
- ${SOURCE_DIR}/FixVec.cc
- ${SOURCE_DIR}/Global.cc
- ${SOURCE_DIR}/Lagrange.cc
- ${SOURCE_DIR}/Line.cc
- ${SOURCE_DIR}/MacroElement.cc
- ${SOURCE_DIR}/io/MacroWriter.cc
- ${SOURCE_DIR}/Parameters.cc
- ${SOURCE_DIR}/Parametric.cc
- ${SOURCE_DIR}/Quadrature.cc
- ${SOURCE_DIR}/RCNeighbourList.cc
- ${SOURCE_DIR}/RefinementManager.cc
- ${SOURCE_DIR}/RefinementManager1d.cc
- ${SOURCE_DIR}/RefinementManager2d.cc
- ${SOURCE_DIR}/RefinementManager3d.cc
- ${SOURCE_DIR}/Tetrahedron.cc
- ${SOURCE_DIR}/Traverse.cc
- ${SOURCE_DIR}/TraverseParallel.cc
- ${SOURCE_DIR}/Triangle.cc
- ${SOURCE_DIR}/io/ValueWriter.cc
- ${SOURCE_DIR}/io/VtkWriter.cc
- ${SOURCE_DIR}/io/DofWriter.cc
- ${SOURCE_DIR}/io/PngWriter.cc
- ${SOURCE_DIR}/io/PovrayWriter.cc
- ${SOURCE_DIR}/io/DataCollector.cc
- ${SOURCE_DIR}/ScalableQuadrature.cc
- ${SOURCE_DIR}/SubElInfo.cc
- ${SOURCE_DIR}/parallel/InteriorBoundary.cc
- ${SOURCE_DIR}/ElementDofIterator.cc
+ ${SOURCE_DIR}/AdaptStationary.cc
+ ${SOURCE_DIR}/Assembler.cc
+ ${SOURCE_DIR}/BasisFunction.cc
+ ${SOURCE_DIR}/Boundary.cc
+ ${SOURCE_DIR}/BoundaryManager.cc
+ ${SOURCE_DIR}/Cholesky.cc
+ ${SOURCE_DIR}/CoarseningManager.cc
+ ${SOURCE_DIR}/CoarseningManager1d.cc
+ ${SOURCE_DIR}/CoarseningManager2d.cc
+ ${SOURCE_DIR}/CoarseningManager3d.cc
+ ${SOURCE_DIR}/ComponentTraverseInfo.cc
+ ${SOURCE_DIR}/CreatorMap.cc
+ ${SOURCE_DIR}/DOFAdmin.cc
+ ${SOURCE_DIR}/DOFIndexed.cc
+ ${SOURCE_DIR}/DOFMatrix.cc
+ ${SOURCE_DIR}/DOFVector.cc
${SOURCE_DIR}/Debug.cc
+ ${SOURCE_DIR}/DirichletBC.cc
+ ${SOURCE_DIR}/DualTraverse.cc
+ ${SOURCE_DIR}/ElInfo.cc
+ ${SOURCE_DIR}/ElInfo1d.cc
+ ${SOURCE_DIR}/ElInfo2d.cc
+ ${SOURCE_DIR}/ElInfo3d.cc
+ ${SOURCE_DIR}/ElInfoStack.cc
+ ${SOURCE_DIR}/Element.cc
+ ${SOURCE_DIR}/ElementData.cc
+ ${SOURCE_DIR}/ElementDofIterator.cc
+ ${SOURCE_DIR}/Estimator.cc
+ ${SOURCE_DIR}/FiniteElemSpace.cc
+ ${SOURCE_DIR}/FirstOrderAssembler.cc
+ ${SOURCE_DIR}/FirstOrderTerm.cc
+ ${SOURCE_DIR}/FixVec.cc
+ ${SOURCE_DIR}/Global.cc
+ ${SOURCE_DIR}/GlobalDOFNumbering.cc
+ ${SOURCE_DIR}/GlobalElementNumbering.cc
+ ${SOURCE_DIR}/Lagrange.cc
+ ${SOURCE_DIR}/LeafData.cc
+ ${SOURCE_DIR}/Line.cc
+ ${SOURCE_DIR}/MacroElement.cc
+ ${SOURCE_DIR}/Marker.cc
+ ${SOURCE_DIR}/Mesh.cc
+ ${SOURCE_DIR}/MeshStructure.cc
+ ${SOURCE_DIR}/NonLinUpdater.cc
+ ${SOURCE_DIR}/Operator.cc
+ ${SOURCE_DIR}/OperatorTerm.cc
+ ${SOURCE_DIR}/Parameters.cc
+ ${SOURCE_DIR}/Parametric.cc
+ ${SOURCE_DIR}/PeriodicBC.cc
+ ${SOURCE_DIR}/ProblemImplicit.cc
+ ${SOURCE_DIR}/ProblemInstat.cc
+ ${SOURCE_DIR}/ProblemInterpolScal.cc
+ ${SOURCE_DIR}/ProblemInterpolVec.cc
+ ${SOURCE_DIR}/ProblemNonLin.cc
+ ${SOURCE_DIR}/ProblemScal.cc
+ ${SOURCE_DIR}/ProblemVec.cc
+ ${SOURCE_DIR}/ProblemVecDbg.cc
+ ${SOURCE_DIR}/Projection.cc
+ ${SOURCE_DIR}/QPInfo.cc
+ ${SOURCE_DIR}/QPsiPhi.cc
+ ${SOURCE_DIR}/Quadrature.cc
+ ${SOURCE_DIR}/RCNeighbourList.cc
+ ${SOURCE_DIR}/Recovery.cc
+ ${SOURCE_DIR}/RecoveryEstimator.cc
+ ${SOURCE_DIR}/RefinementManager.cc
+ ${SOURCE_DIR}/RefinementManager1d.cc
+ ${SOURCE_DIR}/RefinementManager2d.cc
+ ${SOURCE_DIR}/RefinementManager3d.cc
+ ${SOURCE_DIR}/ResidualEstimator.cc
+ ${SOURCE_DIR}/ResidualParallelEstimator.cc
+ ${SOURCE_DIR}/RobinBC.cc
+ ${SOURCE_DIR}/ScalableQuadrature.cc
+ ${SOURCE_DIR}/SecondOrderAssembler.cc
+ ${SOURCE_DIR}/SecondOrderTerm.cc
${SOURCE_DIR}/Serializer.cc
+ ${SOURCE_DIR}/StandardProblemIteration.cc
+ ${SOURCE_DIR}/SubAssembler.cc
+ ${SOURCE_DIR}/SubElInfo.cc
+ ${SOURCE_DIR}/SubQuadrature.cc
+ ${SOURCE_DIR}/SurfaceQuadrature.cc
+ ${SOURCE_DIR}/Tetrahedron.cc
+ ${SOURCE_DIR}/Traverse.cc
+ ${SOURCE_DIR}/TraverseParallel.cc
+ ${SOURCE_DIR}/Triangle.cc
+ ${SOURCE_DIR}/VertexVector.cc
+ ${SOURCE_DIR}/ZeroOrderAssembler.cc
+ ${SOURCE_DIR}/ZeroOrderTerm.cc
${SOURCE_DIR}/io/ArhReader.cc
${SOURCE_DIR}/io/ArhWriter.cc
- ${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
- ${SOURCE_DIR}/time/RosenbrockStationary.cc
+ ${SOURCE_DIR}/io/DataCollector.cc
+ ${SOURCE_DIR}/io/DofWriter.cc
+ ${SOURCE_DIR}/io/ElementFileWriter.cc
+ ${SOURCE_DIR}/io/FileWriter.cc
+ ${SOURCE_DIR}/io/GNUPlotWriter.cc
+ ${SOURCE_DIR}/io/MacroInfo.cc
+ ${SOURCE_DIR}/io/MacroReader.cc
+ ${SOURCE_DIR}/io/MacroWriter.cc
+ ${SOURCE_DIR}/io/PngWriter.cc
+ ${SOURCE_DIR}/io/PovrayWriter.cc
+ ${SOURCE_DIR}/io/ValueReader.cc
+ ${SOURCE_DIR}/io/ValueWriter.cc
+ ${SOURCE_DIR}/io/VtkWriter.cc
+ ${SOURCE_DIR}/parallel/InteriorBoundary.cc
+ ${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
${SOURCE_DIR}/time/RosenbrockMethod.cc
+ ${SOURCE_DIR}/time/RosenbrockStationary.cc
)
if(ENABLE_PARALLEL_DOMAIN)
@@ -187,16 +192,17 @@ if(ENABLE_PARALLEL_DOMAIN)
find_package(PETSc REQUIRED)
include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
SET(PARALLEL_DOMAIN_AMDIS_SRC
- ${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
+ ${SOURCE_DIR}/parallel/ElementObjectData.cc
${SOURCE_DIR}/parallel/MeshDistributor.cc
- ${SOURCE_DIR}/parallel/MeshPartitioner.cc
${SOURCE_DIR}/parallel/MeshManipulation.cc
- ${SOURCE_DIR}/parallel/StdMpi.cc
- ${SOURCE_DIR}/parallel/ParallelDebug.cc
+ ${SOURCE_DIR}/parallel/MeshPartitioner.cc
${SOURCE_DIR}/parallel/MpiHelper.cc
- ${SOURCE_DIR}/parallel/ElementObjectData.cc
+ ${SOURCE_DIR}/parallel/ParallelDebug.cc
${SOURCE_DIR}/parallel/ParallelProblemStatBase.cc
+ ${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
+ $(SOURCE_DIR)/parallel/PetscProblemStat.cc
${SOURCE_DIR}/parallel/PetscSolver.cc
+ ${SOURCE_DIR}/parallel/StdMpi.cc
${SOURCE_DIR}/parallel/ZoltanPartitioner.cc)
SET(COMPILEFLAGS "${COMPILEFLAGS} -DHAVE_PARALLEL_DOMAIN_AMDIS=1")
INSTALL(FILES ResolveCompilerPaths.cmake FindPackageMultipass.cmake FindPETSc.cmake
@@ -263,11 +269,15 @@ if(ENABLE_MKL)
SET(COMPILEFLAGS "${COMPILEFLAGS} -DHAVE_MKL=1")
endif(ENABLE_MKL)
-SET(COMPOSITE_SOURCE_DIR compositeFEM/src)
-SET(COMPOSITE_FEM_SRC ${COMPOSITE_SOURCE_DIR}/CFE_Integration.cc ${COMPOSITE_SOURCE_DIR}/CFE_NormAndErrorFcts.cc
- ${COMPOSITE_SOURCE_DIR}/CompositeFEMMethods.cc ${COMPOSITE_SOURCE_DIR}/LevelSetAdaptMesh.cc
- ${COMPOSITE_SOURCE_DIR}/PenaltyOperator.cc ${COMPOSITE_SOURCE_DIR}/ElementLevelSet.cc
- ${COMPOSITE_SOURCE_DIR}/CompositeFEMOperator.cc ${COMPOSITE_SOURCE_DIR}/SubPolytope.cc
+SET(COMPOSITE_SOURCE_DIR ${SOURCE_DIR)/compositeFEM)
+SET(COMPOSITE_FEM_SRC ${COMPOSITE_SOURCE_DIR}/CFE_Integration.cc
+ ${COMPOSITE_SOURCE_DIR}/CFE_NormAndErrorFcts.cc
+ ${COMPOSITE_SOURCE_DIR}/CompositeFEMMethods.cc
+ ${COMPOSITE_SOURCE_DIR}/CompositeFEMOperator.cc
+ ${COMPOSITE_SOURCE_DIR}/LevelSetAdaptMesh.cc
+ ${COMPOSITE_SOURCE_DIR}/PenaltyOperator.cc
+ ${COMPOSITE_SOURCE_DIR}/ElementLevelSet.cc
+ ${COMPOSITE_SOURCE_DIR}/SubPolytope.cc
${COMPOSITE_SOURCE_DIR}/SubElementAssembler.cc )
#mtl4 includes