merge of branch solver-preconditioner with trunk

AMDiS/AMDISConfig.cmake.in

@@ -68,6 +68,8 @@ set(AMDIS_NEED_ZOLTAN @ENABLE_ZOLTAN@)
 set(AMDIS_HAS_PARALLEL_DOMAIN @ENABLE_PARALLEL_DOMAIN@)
 set(AMDIS_OPENMP @ENABLE_OPENMP@)
 set(AMDIS_NEED_UMFPACK @ENABLE_UMFPACK@)
+set(AMDIS_NEED_HYPRE @ENABLE_HYPRE@)
+set(AMDIS_NEED_PETSC @ENABLE_PETSC@)
 set(AMDIS_NEED_PNG @ENABLE_PNG@)
 set(AMDIS_NEED_BDDCML @ENABLE_BDDCML@)
 set(AMDIS_NEED_MKL @ENABLE_MKL@)

AMDiS/AMDISUse.cmake

@@ -32,7 +32,42 @@ if(AMDIS_HAS_PARALLEL_DOMAIN)
 			message(FATAL_ERROR "could not find the metis libraries needed by amdis")
 		endif(METIS_LIB)
 	endif()
-endif(AMDIS_HAS_PARALLEL_DOMAIN)
+	
+elseif(AMDIS_NEED_PETSC)
+    find_package(MPI REQUIRED)
+    if(MPI_FOUND)
+	    list(APPEND AMDIS_LIBRARIES ${MPI_LIBRARIES})
+	    list(APPEND AMDIS_COMPILEFLAGS ${MPI_COMPILE_FLAGS})
+	    list(APPEND AMDIS_INCLUDE_DIRS ${MPI_INCLUDE_PATH})
+    endif(MPI_FOUND)
+	
+  set(CMAKE_MODULE_PATH ${AMDIS_DIR})
+    set(PETSC_EXECUTABLE_RUNS ON)
+    find_package(PETSc REQUIRED)
+    if(PETSC_FOUND)
+	    list(APPEND AMDIS_LIBRARIES ${PETSC_LIBRARY_SYS} ${PETSC_LIBRARIES})
+	    list(APPEND AMDIS_INCLUDE_DIRS ${PETSC_INCLUDES})
+    else()
+	    message(FATAL_ERROR "Could not find PETSc!")
+    endif(PETSC_FOUND)
+endif()
+
+if(AMDIS_NEED_HYPRE)
+  find_package(HYPRE REQUIRED)
+  if(HAVE_HYPRE)
+    if(NOT MPI_FOUND)
+      find_package(MPI REQUIRED)
+      if(MPI_FOUND)
+	    list(APPEND AMDIS_LIBRARIES ${MPI_LIBRARIES})
+	    list(APPEND AMDIS_COMPILEFLAGS ${MPI_COMPILE_FLAGS})
+	    list(APPEND AMDIS_INCLUDE_DIRS ${MPI_INCLUDE_PATH})
+      endif()
+    endif()
+    list(APPEND AMDIS_INCLUDE_DIRS ${HYPRE_INCLUDE_DIRECTORIES})
+    list(APPEND AMDIS_COMPILEFLAGS "-DMTL_HAS_HYPRE")
+    list(APPEND AMDIS_LIBRARIES ${HYPRE_LIBRARIES} )
+  endif()
+endif(AMDIS_NEED_HYPRE)
 
 #thats bad because it affects each target
 add_definitions(${AMDIS_COMPILEFLAGS})

AMDiS/CMakeLists.txt

@@ -40,12 +40,14 @@ endif()
 SET(ENABLE_PARALLEL_DOMAIN "OFF" CACHE STRING "use parallel domain decomposition. please set to one of: PMTL, PETSC, OFF" )
 option(USE_PETSC_DEV false)
 option(ENABLE_ZOLTAN false)
+option(ENABLE_PETSC "Use sequential PETSc solvers" false)
 option(ENABLE_UMFPACK "Use of UMFPACK solver" false)
+option(ENABLE_HYPRE "Use HYPRE AMG solver" false)
 option(ENABLE_PNG "use png reader/writer" false)
 option(ENABLE_BDDCML "Use of BDDCML library" false)
 option(ENABLE_EXTENSIONS "Use extensions" false)
 option(ENABLE_OPENMP "Use OpenMP" false)
-option(ENABLE_OUTPUT "AMDiS output priniting, disable only for debugging!" true)
+option(ENABLE_OUTPUT "AMDiS output printing, disable only for debugging!" true)
 
 
 mark_as_advanced(ENABLE_OUTPUT)
@@ -80,7 +82,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/CoarseningManager2d.cc
 	      ${SOURCE_DIR}/CoarseningManager3d.cc
 	      ${SOURCE_DIR}/ComponentTraverseInfo.cc
-              ${SOURCE_DIR}/CouplingIterationInterface.cc
+	      ${SOURCE_DIR}/CouplingIterationInterface.cc
 	      ${SOURCE_DIR}/CreatorMap.cc
 	      ${SOURCE_DIR}/DOFAdmin.cc
 	      ${SOURCE_DIR}/DOFIndexed.cc
@@ -105,7 +107,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/Global.cc
 	      ${SOURCE_DIR}/GlobalDOFNumbering.cc
 	      ${SOURCE_DIR}/GlobalElementNumbering.cc
-              ${SOURCE_DIR}/Initfile.cc
+	      ${SOURCE_DIR}/Initfile.cc
 	      ${SOURCE_DIR}/Lagrange.cc
 	      ${SOURCE_DIR}/LeafData.cc
 	      ${SOURCE_DIR}/Line.cc
@@ -139,7 +141,6 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/SecondOrderTerm.cc
 	      ${SOURCE_DIR}/Serializer.cc
 	      ${SOURCE_DIR}/StandardProblemIteration.cc
-	      ${SOURCE_DIR}/SolverMatrix.cc
 	      ${SOURCE_DIR}/SubAssembler.cc
 	      ${SOURCE_DIR}/SubElInfo.cc
 	      ${SOURCE_DIR}/SubQuadrature.cc
@@ -175,6 +176,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/io/VtkWriter.cc
 	      ${SOURCE_DIR}/io/VtkVectorWriter.cc
 	      ${SOURCE_DIR}/nonlin/ProblemNonLin.cc
+	      ${SOURCE_DIR}/solver/SolverMatrix.cc
 	      ${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
 	      ${SOURCE_DIR}/time/RosenbrockMethod.cc
 	      ${SOURCE_DIR}/time/RosenbrockStationary.cc
@@ -230,11 +232,11 @@ if(ENABLE_PARALLEL_DOMAIN)
 
 	list(APPEND COMPILEFLAGS "-DHAVE_PARALLEL_DOMAIN_AMDIS=1")
 	SET(PARALLEL_DOMAIN_AMDIS_SRC
+		${SOURCE_DIR}/parallel/BddcMlSolver.cc
                	${SOURCE_DIR}/parallel/DofComm.cc
 		${SOURCE_DIR}/parallel/CheckerPartitioner.cc
 		${SOURCE_DIR}/parallel/ElementObjectDatabase.cc
 		${SOURCE_DIR}/parallel/InteriorBoundary.cc
-		${SOURCE_DIR}/parallel/MatrixNnzStructure.cc
 		${SOURCE_DIR}/parallel/MeshDistributor.cc 
 		${SOURCE_DIR}/parallel/MeshLevelData.cc 
 		${SOURCE_DIR}/parallel/MeshManipulation.cc
@@ -242,9 +244,10 @@ if(ENABLE_PARALLEL_DOMAIN)
 		${SOURCE_DIR}/parallel/MpiHelper.cc
 		${SOURCE_DIR}/parallel/ParallelDebug.cc
 		${SOURCE_DIR}/parallel/ParallelDofMapping.cc
-		${SOURCE_DIR}/parallel/ParallelProblemStatBase.cc
+		${SOURCE_DIR}/parallel/ParallelProblemStat.cc
+		${SOURCE_DIR}/parallel/ParallelSolver.cc
 		${SOURCE_DIR}/parallel/PeriodicMap.cc
-                ${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
+		${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
 		${SOURCE_DIR}/parallel/StdMpi.cc
 		${SOURCE_DIR}/parallel/ZoltanPartitioner.cc)
 		
@@ -253,13 +256,13 @@ if(ENABLE_PARALLEL_DOMAIN)
 		set(PETSC_EXECUTABLE_RUNS ON)
 		find_package(PETSc REQUIRED)
 		include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
+		list(APPEND COMPILEFLAGS "-DHAVE_PARALLEL_PETSC")
 		list(APPEND AMDIS_INCLUDE_DIRS ${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
 		list(APPEND PARALLEL_DOMAIN_AMDIS_SRC 
-			${SOURCE_DIR}/parallel/BddcMlSolver.cc
+			${SOURCE_DIR}/parallel/MatrixNnzStructure.cc
 			${SOURCE_DIR}/parallel/ParallelCoarseSpaceSolver.cc
 			${SOURCE_DIR}/parallel/PetscHelper.cc
 			${SOURCE_DIR}/parallel/PetscSolver.cc
-			${SOURCE_DIR}/parallel/PetscProblemStat.cc
 			${SOURCE_DIR}/parallel/PetscSolverFeti.cc
 			${SOURCE_DIR}/parallel/PetscSolverFetiDebug.cc
 			${SOURCE_DIR}/parallel/PetscSolverFetiMonitor.cc
@@ -269,14 +272,17 @@ if(ENABLE_PARALLEL_DOMAIN)
 			${SOURCE_DIR}/parallel/PetscSolverGlobalBlockMatrix.cc
 			${SOURCE_DIR}/parallel/PetscSolverNavierStokes.cc
 			${SOURCE_DIR}/parallel/PetscSolverNSCH.cc
-                        ${SOURCE_DIR}/parallel/PetscSolverCahnHilliard2.cc
-                        ${SOURCE_DIR}/parallel/PetscSolverCahnHilliard.cc                        
-			${SOURCE_DIR}/parallel/PetscSolverSchur.cc)
+			${SOURCE_DIR}/parallel/PetscSolverCahnHilliard2.cc
+			${SOURCE_DIR}/parallel/PetscSolverCahnHilliard.cc                        
+			${SOURCE_DIR}/parallel/PetscSolverSchur.cc
+			${SOURCE_DIR}/solver/PetscTypes.cc)
 	elseif(ENABLE_PARALLEL_DOMAIN STREQUAL "PMTL")
 		set(MTL_INCLUDE_DIR "")
 		find_package(MTL REQUIRED)
 		list(APPEND COMPILEFLAGS "-DMTL_HAS_MPI" "-DHAVE_PARALLEL_MTL4")
-		list(APPEND PARALLEL_DOMAIN_AMDIS_SRC ${SOURCE_DIR}/parallel/Mtl4Solver.cc)
+# 		list(APPEND PARALLEL_DOMAIN_AMDIS_SRC 
+# 			${SOURCE_DIR}/parallel/PMTL_ProblemStat.cc
+# 			)
 		list(APPEND AMDIS_LIBS ${MTL_LIBRARIES})
 	else()
 		message(SEND_ERROR "Set the domain-decomposition version correctly.")
@@ -290,6 +296,24 @@ if(ENABLE_PARALLEL_DOMAIN)
 endif(ENABLE_PARALLEL_DOMAIN)
 
 
+if(ENABLE_PETSC)
+  find_package(MPI REQUIRED)
+  if(MPI_FOUND)
+    list(APPEND COMPILEFLAGS "${MPI_COMPILE_FLAGS}")
+    include_directories(${MPI_INCLUDE_PATH})
+  endif(MPI_FOUND)
+	
+  set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH};/usr/share/cmake-2.8/Modules/;${CMAKE_SOURCE_DIR}/")
+  set(PETSC_EXECUTABLE_RUNS ON)
+  find_package(PETSc REQUIRED)
+  include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
+  list(APPEND AMDIS_INCLUDE_DIRS ${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
+  list(APPEND COMPILEFLAGS "-DHAVE_PETSC" "-DPETSC_VERSION=${PETSC_VERSION}")
+  
+  list(APPEND AMDIS_SRC   
+	${SOURCE_DIR}/solver/PetscSolver.cc
+	${SOURCE_DIR}/solver/PetscTypes.cc)
+endif(ENABLE_PETSC)
 
 if(ENABLE_UMFPACK)
 	find_file(UMFPACK_H umfpack.h
@@ -306,6 +330,24 @@ if(ENABLE_UMFPACK)
 endif(ENABLE_UMFPACK)
 
 
+if(ENABLE_HYPRE)
+  include(FindHYPRE.cmake)
+  message("have hypre: ${HAVE_HYPRE}")
+  if(HAVE_HYPRE)
+    if(NOT MPI_FOUND)
+      find_package(MPI REQUIRED)
+      if(MPI_FOUND)
+	list(APPEND COMPILEFLAGS "${MPI_COMPILE_FLAGS}")
+	include_directories(${MPI_INCLUDE_PATH})
+      endif()
+    endif()
+    include_directories(${HYPRE_INCLUDE_DIRECTORIES})
+    list(APPEND COMPILEFLAGS "-DMTL_HAS_HYPRE")
+    list(APPEND MYLIBS ${HYPRE_LIBRARIES} )
+  endif()
+endif(ENABLE_HYPRE)
+  
+  
 if(ENABLE_PNG)
 	find_file(PNG_H png.h
 			    HINTS ENV CPATH /usr/include
@@ -374,6 +416,13 @@ if(ENABLE_EXTENSIONS)
 	      ${EXTENSIONS_DIR}/POperators.cc
 	      ${EXTENSIONS_DIR}/time/ExtendedRosenbrockStationary.cc
 	      ${EXTENSIONS_DIR}/pugixml/src/pugixml.cpp)
+	      
+      if(ENABLE_PETSC)
+	list(APPEND EXTENSIONS_SRC
+	      ${EXTENSIONS_DIR}/preconditioner/PetscPreconPfc.cc
+	      ${EXTENSIONS_DIR}/preconditioner/PetscPreconCahnHilliard.cc)
+      endif(ENABLE_PETSC)
+      
       list(APPEND COMPILEFLAGS "-DHAVE_EXTENSIONS=1")
       list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR})
       list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/time)
@@ -401,6 +450,13 @@ if(ENABLE_EXTENSIONS)
       FILE(GLOB HEADERS "${EXTENSIONS_DIR}/time/*.hh")
       INSTALL(FILES ${HEADERS}
 	      DESTINATION include/amdis/extensions/time/)
+	      
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/preconditioner/*.h")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/preconditioner/)
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/preconditioner/*.hh")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/preconditioner/)
 
       list(APPEND deb_add_dirs "include/amdis/extensions/time")
 
@@ -438,7 +494,7 @@ if(ENABLE_EXTENSIONS)
 		  ${EXTENSIONS_DIR}/base_problems/NavierStokes_TH_MultiPhase_RB.cc
 		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Base.cc
     # 	      ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal.cc
-# 		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Phase.cc
+		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Phase.cc
 		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_RB.cc)
 	list(APPEND COMPILEFLAGS "-DHAVE_BASE_PROBLEMS=1")
 	list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/base_problems)
@@ -562,10 +618,20 @@ INSTALL(FILES ${HEADERS}
 	DESTINATION include/amdis/time/)
 list(APPEND deb_add_dirs "include/amdis/time")
 
-FILE(GLOB HEADERS "${SOURCE_DIR}/itl/*.hpp")
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/*.h")
+INSTALL(FILES ${HEADERS} 
+	DESTINATION include/amdis/solver)
+list(APPEND deb_add_dirs "include/amdis/solver")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/*.hh")
+INSTALL(FILES ${HEADERS} 
+	DESTINATION include/amdis/solver)
+list(APPEND deb_add_dirs "include/amdis/solver")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/itl/*.hpp")
 INSTALL(FILES ${HEADERS} 
-	DESTINATION include/amdis/itl)
-list(APPEND deb_add_dirs "include/amdis/itl")
+	DESTINATION include/amdis/solver/itl)
+list(APPEND deb_add_dirs "include/amdis/solver/itl")
 
 FILE(GLOB HEADERS "${SOURCE_DIR}/io/*.h")
 INSTALL(FILES ${HEADERS}
@@ -604,7 +670,10 @@ INSTALL(FILES ${AMDIS_BINARY_DIR}/AMDISConfig.cmake
 	DESTINATION share/amdis/)
 list(APPEND deb_add_dirs "share/amdis/")
 
-INSTALL(FILES ${AMDIS_SOURCE_DIR}/AMDISUse.cmake 
+# INSTALL(FILES ${AMDIS_SOURCE_DIR}/AMDISUse.cmake 
+# 	DESTINATION share/amdis/)
+FILE(GLOB CMAKE_FILES "${AMDIS_SOURCE_DIR}/*.cmake")
+INSTALL(FILES ${CMAKE_FILES}
 	DESTINATION share/amdis/)
 
 #install mtl

AMDiS/FindHYPRE.cmake

+find_file(HYPRE_H HYPRE.h)
+find_library(HYPRE_LIB HYPRE)
+if(HYPRE_H AND HYPRE_LIB)
+	set(HAVE_HYPRE ON)
+	find_package(MPI REQUIRED)
+	#append each library in the hypre_lib directory beginning with HYPRE to the list of hypre libraries
+	get_filename_component(HLIB_PATH ${HYPRE_LIB} PATH)
+	file(GLOB HYPRE_OTHER ${HLIB_PATH}/${CMAKE_SHARED_LIBRARY_PREFIX}HYPRE*${CMAKE_SHARED_LIBRARY_SUFFIX})
+	find_library(LAPACK_LIB lapack)
+	set(HYPRE_LIBRARIES ${MPI_LIBRARIES} ${HYPRE_LIB} ${HYPRE_OTHER} ${LAPACK_LIB})
+	message("hypre libraries: ${HYPRE_LIBRARIES}")
+	get_filename_component(HYPRE_INCLUDE_DIRECTORIES ${HYPRE_H} PATH)
+	list(APPEND HYPRE_INCLUDE_DIRECTORIES ${MPI_CXX_INCLUDE_PATH})
+else()
+	if(HAVE_HYPRE)
+		message("could not find hypre:")
+		message("library: ${HYPRE_LIB}")
+		message("header: ${HYPRE_H}")
+	endif()
+	set(HAVE_HYPRE FALSE)
+endif()

AMDiS/doc/Doxyfile

@@ -281,7 +281,7 @@ SUBGROUPING            = YES
 # be useful for C code in case the coding convention dictates that all compound 
 # types are typedef'ed and only the typedef is referenced, never the tag name.
 
-TYPEDEF_HIDES_STRUCT   = NO
+TYPEDEF_HIDES_STRUCT   = YES
 
 # The SYMBOL_CACHE_SIZE determines the size of the internal cache use to 
 # determine which symbols to keep in memory and which to flush to disk. 
@@ -591,12 +591,15 @@ WARN_LOGFILE           =
 # with spaces.
 
 INPUT                  = ../src/ \
-                         ../src/io \
                          ../src/compositeFEM \
+                         ../src/est \
+                         ../src/io \
+                         ../src/nonlin \
                          ../src/parallel \
                          ../src/reinit \
+                         ../src/solver \
+                         ../src/solver/itl \
                          ../src/time \
-                         ../src/nonlin
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
@@ -613,7 +616,7 @@ INPUT_ENCODING         = UTF-8
 # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
 # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
 
-FILE_PATTERNS          = *.h
+FILE_PATTERNS          = *.h *.hpp
 
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories 
 # should be searched for input files as well. Possible values are YES and NO. 
@@ -1374,7 +1377,7 @@ INCLUDE_FILE_PATTERNS  =
 # undefined via #undef or recursively expanded use the := operator 
 # instead of the = operator.
 
-PREDEFINED             = 
+PREDEFINED             = HAVE_PARALLEL_DOMAIN_AMDIS HAVE_PARALLEL_MTL4 HAVE_UMFPACK MTL_HAS_UMFPACK HAVE_PETSC
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
 # this tag can be used to specify a list of macro names that should be expanded. 

AMDiS/src/AMDiS.cc

-//
-// Software License for AMDiS
-//
-// Copyright (c) 2010 Dresden University of Technology 
-// All rights reserved.
-// Authors: Simon Vey, Thomas Witkowski et al.
-//
-// This file is part of AMDiS
-//
-// See also license.opensource.txt in the distribution.
+/******************************************************************************
+ *
+ * AMDiS - Adaptive multidimensional simulations
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
+ *
+ * Authors: 
+ * Simon Vey, Thomas Witkowski, Andreas Naumann, Simon Praetorius, et al.
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * This file is part of AMDiS
+ *
+ * See also license.opensource.txt in the distribution.
+ * 
+ ******************************************************************************/
 
 
 #include "AMDiS.h"
@@ -21,24 +30,28 @@ namespace AMDiS {
 
   using namespace std;
 
-#if defined(HAVE_PARALLEL_DOMAIN_AMDIS) && defined(HAVE_PARALLEL_MTL4)
+#if defined(HAVE_PARALLEL_MTL4)
   mtl::par::environment* mtl_environment = NULL;
 #endif
 
   void init(int argc, char **argv, std::string initFileName)
   {
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-#ifdef HAVE_PARALLEL_MTL4
+#if defined(HAVE_PARALLEL_DOMAIN_AMDIS) || defined(HAVE_PETSC)
+  #ifdef HAVE_PARALLEL_MTL4
     mtl_environment = new mtl::par::environment(argc, argv);
-#else
+  #else
     PetscInitialize(&argc, &argv, NULL, NULL);
-    mpi::startRand();
-#endif
-
-#ifdef HAVE_ZOLTAN
+    #if defined(HAVE_PARALLEL_DOMAIN_AMDIS)
+    Parallel::mpi::startRand();
+    #else
+    srand(time(NULL));
+    #endif
+  #endif
+
+  #ifdef HAVE_ZOLTAN
     float zoltanVersion = 0.0;
     Zoltan_Initialize(argc, argv, &zoltanVersion);
-#endif
+  #endif
 #endif
     
     Parameters::clearData();
@@ -104,6 +117,7 @@ namespace AMDiS {
     if (vm.count("parameters") && !ignoreCommandline)
       Parameters::readArgv(vm["parameters"].as<std::string>(),0);
     
+    
     // initialize global strcutures using parameters
     Global::init();
   }
@@ -123,15 +137,20 @@ namespace AMDiS {
   void finalize()
   {
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-    MeshDistributor::globalMeshDistributor->exitParallelization();
-    delete MeshDistributor::globalMeshDistributor;
-#ifdef HAVE_PARALLEL_MTL4
+    Parallel::MeshDistributor::globalMeshDistributor->exitParallelization();
+    delete Parallel::MeshDistributor::globalMeshDistributor;
+  #ifdef HAVE_PARALLEL_MTL4
     if (mtl_environment)
       delete mtl_environment;
-#else
+  #else
     PetscFinalize();
+  #endif
 #endif
+    
+#ifdef HAVE_PETSC
+    PetscFinalize();
 #endif
+    
   }
 
 }

AMDiS/src/AMDiS.h

-// ============================================================================
-// ==                                                                        ==
-// == AMDiS - Adaptive multidimensional simulations                          ==
-// ==                                                                        ==
-// ==  http://www.amdis-fem.org                                              ==
-// ==                                                                        ==
-// ============================================================================
-//
-// Software License for AMDiS
-//
-// Copyright (c) 2010 Dresden University of Technology 
-// All rights reserved.
-// Authors: Simon Vey, Thomas Witkowski et al.
-//
-// This file is part of AMDiS
-//
-// See also license.opensource.txt in the distribution.
+/******************************************************************************
+ *
+ * AMDiS - Adaptive multidimensional simulations
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
+ *
+ * Authors: 
+ * Simon Vey, Thomas Witkowski, Andreas Naumann, Simon Praetorius, et al.
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * This file is part of AMDiS
+ *
+ * See also license.opensource.txt in the distribution.
+ * 
+ ******************************************************************************/
 
 
 
@@ -66,8 +68,6 @@
 #include "Functors.h"
 #include "Global.h"
 #include "Initfile.h"
-#include "ITL_Preconditioner.h"
-#include "ITL_Solver.h"
 #include "Lagrange.h"
 #include "LeafData.h"
 #include "Line.h"
@@ -78,7 +78,6 @@
 #include "Mesh.h"
 #include "MeshStructure.h"
 #include "ComponentTraverseInfo.h"
-#include "OEMSolver.h"
 #include "Operator.h"
 #include "OperatorTerm.h"
 #include "Parametric.h"
@@ -131,6 +130,10 @@
 #include "nonlin/ProblemNonLin.h"
 #include "nonlin/NonLinSolver.h"
 
+#include "solver/ITL_Preconditioner.h"
+#include "solver/ITL_Solver.h"
+#include "solver/LinearSolver.h"
+
 #include "time/RosenbrockAdaptInstationary.h"
 #include "time/RosenbrockStationary.h"
 
@@ -140,17 +143,21 @@
 #include "parallel/MpiHelper.h"
 #include "parallel/ParallelDebug.h"
 #include "parallel/StdMpi.h"
+#include "parallel/ParallelProblemStat.h"
 
 #if HAVE_PARALLEL_MTL4
-#include "parallel/Mtl4Solver.h"
+#include "parallel/PMTL4Solver.h"
 #else
-#include "parallel/PetscProblemStat.h"
 #include "parallel/PetscSolver.h"
 #include "parallel/PetscSolverNavierStokes.h"
 #endif
 
 #endif
 
+#if HAVE_PETSC
+#include <petsc.h>
+#endif
+
 namespace AMDiS {
 
   void init(int argc, char **argv, std::string initFileName = "");

AMDiS/src/AMDiS_fwd.h

-// ============================================================================
-// ==                                                                        ==
-// == AMDiS - Adaptive multidimensional simulations                          ==
-// ==                                                                        ==
-// ==  http://www.amdis-fem.org                                              ==
-// ==                                                                        ==
-// ============================================================================
-//
-// Software License for AMDiS
-//
-// Copyright (c) 2010 Dresden University of Technology 
-// All rights reserved.
-// Authors: Simon Vey, Thomas Witkowski et al.
-//
-// This file is part of AMDiS
-//
-// See also license.opensource.txt in the distribution.
+/******************************************************************************
+ *
+ * AMDiS - Adaptive multidimensional simulations
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
+ *
+ * Authors: 
+ * Simon Vey, Thomas Witkowski, Andreas Naumann, Simon Praetorius, et al.
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * This file is part of AMDiS
+ *
+ * See also license.opensource.txt in the distribution.
+ * 
+ ******************************************************************************/
 
 
 
@@ -34,10 +36,10 @@ namespace AMDiS {
   class Assembler;
   class BasisFunction; 
   class BoundaryManager;
-  class CGSolver;
+//   class CGSolver;
   class CoarseningManager;
   class CouplingIterationInterface;
-  class DiagonalPreconditioner; 
+//   class DiagonalPreconditioner; 
   class DOFAdmin; 
   class DOFContainer;
   class DOFIndexedBase;
@@ -53,8 +55,8 @@ namespace AMDiS {
   class FileWriterInterface;
   class FiniteElemSpace; 
   class Flag;
-  class IdentityPreconditioner; 
-  class InteriorBoundary;
+//   class IdentityPreconditioner; 
+//  class Parallel::InteriorBoundary;
   class LeafDataPeriodic;
   class LevelAdmin;
   class Line;
@@ -63,7 +65,7 @@ namespace AMDiS {
   class Marker;
   class Mesh; 
   class MeshStructure;
-  class OEMSolver;
+  class LinearSolver;
   class Operator;
   class OperatorTerm;
   class Parametric;
@@ -99,13 +101,23 @@ namespace AMDiS {
   class VertexVector;
 
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-  class ElementObjectDatabase;
-  class FeSpaceDofMap;
-  class MatrixNnzStructure;
-  class MeshLevelData;
-  class PetscSolver;
-  class PetscSolverFeti;
-  class PetscSolverFetiDebug;
+  namespace Parallel {
+    class ElementObjectDatabase;
+    class FeSpaceDofMap;
+    class MatrixNnzStructure;
+    class MeshLevelData;
+    class PetscSolver;
+    class PetscSolverFeti;
+    class PetscSolverFetiDebug;
+    class PetscSolverSchur;
+    class PetscSolverGlobalMatrix;
+    class PetscSolverGlobalBlockMatrix;
+    class PetscSolverCahnHilliard;
+    class PetscSolverNavierStokes;
+    class ParallelDofMapping;
+    class ParallelProblemStat;